Starting phenix.real_space_refine on Tue Feb 20 12:12:19 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6oax_20004/02_2024/6oax_20004_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6oax_20004/02_2024/6oax_20004.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6oax_20004/02_2024/6oax_20004.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6oax_20004/02_2024/6oax_20004.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6oax_20004/02_2024/6oax_20004_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6oax_20004/02_2024/6oax_20004_updated.pdb" } resolution = 2.9 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= 0.003 sd= 0.189 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 33 5.49 5 S 104 5.16 5 C 17381 2.51 5 N 5047 2.21 5 O 5306 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "C ASP 184": "OD1" <-> "OD2" Residue "C ASP 241": "OD1" <-> "OD2" Residue "C TYR 357": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 596": "NH1" <-> "NH2" Residue "C GLU 658": "OE1" <-> "OE2" Residue "C ARG 667": "NH1" <-> "NH2" Residue "C ASP 701": "OD1" <-> "OD2" Residue "C PHE 709": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 731": "OE1" <-> "OE2" Residue "C TYR 734": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 749": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 756": "NH1" <-> "NH2" Residue "C ASP 797": "OD1" <-> "OD2" Residue "C GLU 826": "OE1" <-> "OE2" Residue "C GLU 837": "OE1" <-> "OE2" Residue "C ASP 851": "OD1" <-> "OD2" Residue "F TYR 164": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 170": "OE1" <-> "OE2" Residue "F GLU 173": "OE1" <-> "OE2" Residue "F GLU 254": "OE1" <-> "OE2" Residue "F GLU 270": "OE1" <-> "OE2" Residue "F GLU 307": "OE1" <-> "OE2" Residue "F ASP 326": "OD1" <-> "OD2" Residue "F ARG 331": "NH1" <-> "NH2" Residue "F GLU 358": "OE1" <-> "OE2" Residue "F ASP 367": "OD1" <-> "OD2" Residue "F TYR 380": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ASP 383": "OD1" <-> "OD2" Residue "F ASP 388": "OD1" <-> "OD2" Residue "F GLU 396": "OE1" <-> "OE2" Residue "F ASP 406": "OD1" <-> "OD2" Residue "F ASP 533": "OD1" <-> "OD2" Residue "F GLU 565": "OE1" <-> "OE2" Residue "F PHE 603": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 637": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 639": "OE1" <-> "OE2" Residue "F GLU 657": "OE1" <-> "OE2" Residue "F ASP 677": "OD1" <-> "OD2" Residue "F GLU 680": "OE1" <-> "OE2" Residue "F ASP 696": "OD1" <-> "OD2" Residue "F ASP 701": "OD1" <-> "OD2" Residue "F PHE 709": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ASP 733": "OD1" <-> "OD2" Residue "F GLU 739": "OE1" <-> "OE2" Residue "F GLU 752": "OE1" <-> "OE2" Residue "F ASP 797": "OD1" <-> "OD2" Residue "F TYR 808": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ARG 819": "NH1" <-> "NH2" Residue "F ASP 851": "OD1" <-> "OD2" Residue "E ASP 167": "OD1" <-> "OD2" Residue "E GLU 185": "OE1" <-> "OE2" Residue "E GLU 227": "OE1" <-> "OE2" Residue "E GLU 254": "OE1" <-> "OE2" Residue "E PHE 276": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ASP 317": "OD1" <-> "OD2" Residue "E GLU 324": "OE1" <-> "OE2" Residue "E PHE 333": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 344": "OE1" <-> "OE2" Residue "E GLU 410": "OE1" <-> "OE2" Residue "E ASP 578": "OD1" <-> "OD2" Residue "E ASP 624": "OD1" <-> "OD2" Residue "E GLU 627": "OE1" <-> "OE2" Residue "E ASP 695": "OD1" <-> "OD2" Residue "E ASP 696": "OD1" <-> "OD2" Residue "E PHE 729": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ARG 756": "NH1" <-> "NH2" Residue "E GLU 768": "OE1" <-> "OE2" Residue "E GLU 787": "OE1" <-> "OE2" Residue "E GLU 805": "OE1" <-> "OE2" Residue "E GLU 837": "OE1" <-> "OE2" Residue "E GLU 847": "OE1" <-> "OE2" Residue "D GLU 170": "OE1" <-> "OE2" Residue "D GLU 185": "OE1" <-> "OE2" Residue "D GLU 227": "OE1" <-> "OE2" Residue "D ASP 241": "OD1" <-> "OD2" Residue "D ASP 317": "OD1" <-> "OD2" Residue "D GLU 330": "OE1" <-> "OE2" Residue "D ASP 345": "OD1" <-> "OD2" Residue "D TYR 357": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 388": "OD1" <-> "OD2" Residue "D ASP 392": "OD1" <-> "OD2" Residue "D GLU 396": "OE1" <-> "OE2" Residue "D GLU 575": "OE1" <-> "OE2" Residue "D GLU 658": "OE1" <-> "OE2" Residue "D ASP 695": "OD1" <-> "OD2" Residue "D GLU 727": "OE1" <-> "OE2" Residue "D GLU 731": "OE1" <-> "OE2" Residue "D TYR 791": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 792": "OE1" <-> "OE2" Residue "D GLU 798": "OE1" <-> "OE2" Residue "B GLU 173": "OE1" <-> "OE2" Residue "B ASP 326": "OD1" <-> "OD2" Residue "B TYR 357": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 367": "OD1" <-> "OD2" Residue "B ARG 596": "NH1" <-> "NH2" Residue "B TYR 653": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 680": "OE1" <-> "OE2" Residue "B GLU 787": "OE1" <-> "OE2" Residue "B GLU 792": "OE1" <-> "OE2" Residue "B GLU 798": "OE1" <-> "OE2" Residue "A ASP 167": "OD1" <-> "OD2" Residue "A GLU 173": "OE1" <-> "OE2" Residue "A ASP 178": "OD1" <-> "OD2" Residue "A GLU 227": "OE1" <-> "OE2" Residue "A ASP 265": "OD1" <-> "OD2" Residue "A ASP 290": "OD1" <-> "OD2" Residue "A GLU 318": "OE1" <-> "OE2" Residue "A TYR 319": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 388": "OD1" <-> "OD2" Residue "A ASP 533": "OD1" <-> "OD2" Residue "A ARG 596": "NH1" <-> "NH2" Residue "A GLU 613": "OE1" <-> "OE2" Residue "A ASP 633": "OD1" <-> "OD2" Residue "A GLU 639": "OE1" <-> "OE2" Residue "A TYR 653": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 667": "NH1" <-> "NH2" Residue "A TYR 671": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 678": "OE1" <-> "OE2" Residue "A ASP 708": "OD1" <-> "OD2" Residue "A PHE 709": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 731": "OE1" <-> "OE2" Residue "A ASP 733": "OD1" <-> "OD2" Residue "A TYR 734": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 752": "OE1" <-> "OE2" Residue "A ARG 756": "NH1" <-> "NH2" Residue "A ASP 809": "OD1" <-> "OD2" Residue "A GLU 837": "OE1" <-> "OE2" Residue "A ASP 851": "OD1" <-> "OD2" Time to flip residues: 0.10s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 27871 Number of models: 1 Model: "" Number of chains: 13 Chain: "C" Number of atoms: 4577 Number of conformers: 1 Conformer: "" Number of residues, atoms: 581, 4577 Classifications: {'peptide': 581} Link IDs: {'PTRANS': 22, 'TRANS': 558} Chain breaks: 1 Chain: "F" Number of atoms: 4518 Number of conformers: 1 Conformer: "" Number of residues, atoms: 571, 4518 Classifications: {'peptide': 571} Link IDs: {'PTRANS': 22, 'TRANS': 548} Chain breaks: 2 Chain: "E" Number of atoms: 4555 Number of conformers: 1 Conformer: "" Number of residues, atoms: 579, 4555 Classifications: {'peptide': 579} Link IDs: {'PTRANS': 23, 'TRANS': 555} Chain breaks: 1 Chain: "D" Number of atoms: 4577 Number of conformers: 1 Conformer: "" Number of residues, atoms: 581, 4577 Classifications: {'peptide': 581} Link IDs: {'PTRANS': 22, 'TRANS': 558} Chain breaks: 1 Chain: "B" Number of atoms: 4577 Number of conformers: 1 Conformer: "" Number of residues, atoms: 581, 4577 Classifications: {'peptide': 581} Link IDs: {'PTRANS': 22, 'TRANS': 558} Chain breaks: 1 Chain: "A" Number of atoms: 4577 Number of conformers: 1 Conformer: "" Number of residues, atoms: 581, 4577 Classifications: {'peptide': 581} Link IDs: {'PTRANS': 22, 'TRANS': 558} Chain breaks: 1 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: 54 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 54 Unusual residues: {'ADP': 2} Classifications: {'undetermined': 2} Link IDs: {None: 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: 62 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 62 Unusual residues: {'AGS': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "A" 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} Time building chain proxies: 14.06, per 1000 atoms: 0.50 Number of scatterers: 27871 At special positions: 0 Unit cell: (119.712, 143.448, 144.48, 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 104 16.00 P 33 15.00 O 5306 8.00 N 5047 7.00 C 17381 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: 9.68 Conformation dependent library (CDL) restraints added in 5.3 seconds 6896 Ramachandran restraints generated. 3448 Oldfield, 0 Emsley, 3448 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6466 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 167 helices and 25 sheets defined 40.4% alpha, 6.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 6.60 Creating SS restraints... Processing helix chain 'C' and resid 168 through 173 Processing helix chain 'C' and resid 184 through 194 Processing helix chain 'C' and resid 213 through 219 Processing helix chain 'C' and resid 222 through 225 No H-bonds generated for 'chain 'C' and resid 222 through 225' Processing helix chain 'C' and resid 254 through 267 Processing helix chain 'C' and resid 280 through 283 Processing helix chain 'C' and resid 300 through 305 Processing helix chain 'C' and resid 316 through 322 removed outlier: 3.765A pdb=" N GLN C 321 " --> pdb=" O ASP C 317 " (cutoff:3.500A) 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 351 removed outlier: 3.662A pdb=" N ALA C 348 " --> pdb=" O GLU C 344 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N ILE C 349 " --> pdb=" O ASP C 345 " (cutoff:3.500A) Processing helix chain 'C' and resid 354 through 361 Processing helix chain 'C' and resid 367 through 380 Processing helix chain 'C' and resid 387 through 406 removed outlier: 3.909A pdb=" N LEU C 393 " --> pdb=" O LYS C 389 " (cutoff:3.500A) Processing helix chain 'C' and resid 533 through 543 removed outlier: 3.615A pdb=" N ARG C 542 " --> pdb=" O GLU C 538 " (cutoff:3.500A) Processing helix chain 'C' and resid 554 through 560 removed outlier: 3.515A pdb=" N LYS C 558 " --> pdb=" O SER C 554 " (cutoff:3.500A) Processing helix chain 'C' and resid 562 through 566 Processing helix chain 'C' and resid 574 through 588 removed outlier: 4.085A pdb=" N ALA C 579 " --> pdb=" O GLU C 575 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N ALA C 583 " --> pdb=" O ALA C 579 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N ILE C 584 " --> pdb=" O VAL C 580 " (cutoff:3.500A) Processing helix chain 'C' and resid 611 through 622 Processing helix chain 'C' and resid 634 through 636 No H-bonds generated for 'chain 'C' and resid 634 through 636' Processing helix chain 'C' and resid 640 through 645 removed outlier: 3.588A pdb=" N SER C 644 " --> pdb=" O HIS C 641 " (cutoff:3.500A) Processing helix chain 'C' and resid 661 through 668 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 691 through 695 Processing helix chain 'C' and resid 722 through 728 removed outlier: 3.588A pdb=" N GLU C 727 " --> pdb=" O ASP C 723 " (cutoff:3.500A) Processing helix chain 'C' and resid 734 through 737 No H-bonds generated for 'chain 'C' and resid 734 through 737' Processing helix chain 'C' and resid 768 through 787 removed outlier: 3.851A pdb=" N SER C 773 " --> pdb=" O GLN C 769 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N GLN C 776 " --> pdb=" O ALA C 772 " (cutoff:3.500A) Processing helix chain 'C' and resid 797 through 806 Processing helix chain 'C' and resid 815 through 824 Processing helix chain 'C' and resid 826 through 834 removed outlier: 3.522A pdb=" N GLN C 831 " --> pdb=" O ASN C 827 " (cutoff:3.500A) Processing helix chain 'F' and resid 170 through 172 No H-bonds generated for 'chain 'F' and resid 170 through 172' Processing helix chain 'F' and resid 189 through 192 No H-bonds generated for 'chain 'F' and resid 189 through 192' Processing helix chain 'F' and resid 214 through 220 removed outlier: 3.958A pdb=" N LEU F 219 " --> pdb=" O ILE F 215 " (cutoff:3.500A) removed outlier: 4.211A pdb=" N ALA F 220 " --> pdb=" O VAL F 216 " (cutoff:3.500A) Processing helix chain 'F' and resid 256 through 264 removed outlier: 3.815A pdb=" N LEU F 263 " --> pdb=" O LEU F 259 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N ASN F 264 " --> pdb=" O LYS F 260 " (cutoff:3.500A) Processing helix chain 'F' and resid 300 through 304 Processing helix chain 'F' and resid 319 through 322 No H-bonds generated for 'chain 'F' and resid 319 through 322' Processing helix chain 'F' and resid 349 through 357 removed outlier: 3.600A pdb=" N LEU F 353 " --> pdb=" O ILE F 349 " (cutoff:3.500A) removed outlier: 4.681A pdb=" N LYS F 354 " --> pdb=" O LEU F 350 " (cutoff:3.500A) removed outlier: 5.682A pdb=" N GLU F 355 " --> pdb=" O ARG F 351 " (cutoff:3.500A) removed outlier: 5.176A pdb=" N ARG F 356 " --> pdb=" O GLY F 352 " (cutoff:3.500A) Processing helix chain 'F' and resid 367 through 370 No H-bonds generated for 'chain 'F' and resid 367 through 370' Processing helix chain 'F' and resid 388 through 395 removed outlier: 3.990A pdb=" N ASP F 392 " --> pdb=" O ASP F 388 " (cutoff:3.500A) removed outlier: 4.290A pdb=" N LEU F 393 " --> pdb=" O LYS F 389 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N ASP F 395 " --> pdb=" O ILE F 391 " (cutoff:3.500A) Processing helix chain 'F' and resid 398 through 406 removed outlier: 4.548A pdb=" N ILE F 401 " --> pdb=" O ALA F 398 " (cutoff:3.500A) removed outlier: 4.638A pdb=" N ARG F 402 " --> pdb=" O SER F 399 " (cutoff:3.500A) removed outlier: 3.942A pdb=" N MET F 403 " --> pdb=" O SER F 400 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N GLN F 404 " --> pdb=" O ILE F 401 " (cutoff:3.500A) removed outlier: 4.556A pdb=" N ILE F 405 " --> pdb=" O ARG F 402 " (cutoff:3.500A) Processing helix chain 'F' and resid 534 through 542 removed outlier: 3.745A pdb=" N VAL F 539 " --> pdb=" O GLU F 535 " (cutoff:3.500A) removed outlier: 4.286A pdb=" N ARG F 542 " --> pdb=" O GLU F 538 " (cutoff:3.500A) Processing helix chain 'F' and resid 548 through 550 No H-bonds generated for 'chain 'F' and resid 548 through 550' Processing helix chain 'F' and resid 557 through 562 removed outlier: 4.448A pdb=" N ARG F 561 " --> pdb=" O LYS F 558 " (cutoff:3.500A) removed outlier: 3.979A pdb=" N MET F 562 " --> pdb=" O LEU F 559 " (cutoff:3.500A) Processing helix chain 'F' and resid 566 through 569 No H-bonds generated for 'chain 'F' and resid 566 through 569' Processing helix chain 'F' and resid 576 through 580 removed outlier: 3.628A pdb=" N ALA F 579 " --> pdb=" O ALA F 576 " (cutoff:3.500A) Processing helix chain 'F' and resid 611 through 623 removed outlier: 3.747A pdb=" N ALA F 619 " --> pdb=" O CYS F 615 " (cutoff:3.500A) Processing helix chain 'F' and resid 640 through 643 removed outlier: 4.133A pdb=" N VAL F 643 " --> pdb=" O LYS F 640 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 640 through 643' Processing helix chain 'F' and resid 684 through 690 removed outlier: 3.688A pdb=" N PHE F 687 " --> pdb=" O PRO F 684 " (cutoff:3.500A) removed outlier: 5.226A pdb=" N ASN F 688 " --> pdb=" O ASP F 685 " (cutoff:3.500A) removed outlier: 4.173A pdb=" N ILE F 689 " --> pdb=" O VAL F 686 " (cutoff:3.500A) removed outlier: 3.955A pdb=" N LEU F 690 " --> pdb=" O PHE F 687 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 684 through 690' Processing helix chain 'F' and resid 737 through 740 No H-bonds generated for 'chain 'F' and resid 737 through 740' Processing helix chain 'F' and resid 769 through 783 removed outlier: 3.730A pdb=" N ILE F 774 " --> pdb=" O HIS F 770 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N LEU F 779 " --> pdb=" O ALA F 775 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N LEU F 782 " --> pdb=" O GLN F 778 " (cutoff:3.500A) Processing helix chain 'F' and resid 797 through 801 removed outlier: 3.818A pdb=" N LYS F 801 " --> pdb=" O ASP F 797 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 797 through 801' Processing helix chain 'F' and resid 804 through 806 No H-bonds generated for 'chain 'F' and resid 804 through 806' Processing helix chain 'F' and resid 815 through 824 removed outlier: 3.741A pdb=" N LYS F 818 " --> pdb=" O ARG F 815 " (cutoff:3.500A) removed outlier: 4.256A pdb=" N ARG F 819 " --> pdb=" O PRO F 816 " (cutoff:3.500A) removed outlier: 4.017A pdb=" N GLN F 823 " --> pdb=" O ALA F 820 " (cutoff:3.500A) removed outlier: 3.932A pdb=" N GLN F 824 " --> pdb=" O ILE F 821 " (cutoff:3.500A) Processing helix chain 'F' and resid 826 through 835 Processing helix chain 'E' and resid 170 through 173 No H-bonds generated for 'chain 'E' and resid 170 through 173' Processing helix chain 'E' and resid 184 through 194 Processing helix chain 'E' and resid 213 through 225 removed outlier: 4.218A pdb=" N GLY E 218 " --> pdb=" O ALA E 214 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N GLN E 221 " --> pdb=" O GLU E 217 " (cutoff:3.500A) removed outlier: 4.177A pdb=" N ILE E 224 " --> pdb=" O ALA E 220 " (cutoff:3.500A) Processing helix chain 'E' and resid 256 through 263 Processing helix chain 'E' and resid 280 through 283 No H-bonds generated for 'chain 'E' and resid 280 through 283' Processing helix chain 'E' and resid 295 through 302 removed outlier: 3.924A pdb=" N LEU E 299 " --> pdb=" O ALA E 295 " (cutoff:3.500A) Proline residue: E 301 - end of helix Processing helix chain 'E' and resid 316 through 321 Processing helix chain 'E' and resid 343 through 360 removed outlier: 3.687A pdb=" N ALA E 348 " --> pdb=" O GLU E 344 " (cutoff:3.500A) removed outlier: 5.284A pdb=" N GLU E 355 " --> pdb=" O ARG E 351 " (cutoff:3.500A) removed outlier: 5.218A pdb=" N ARG E 356 " --> pdb=" O GLY E 352 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N TYR E 357 " --> pdb=" O LEU E 353 " (cutoff:3.500A) Processing helix chain 'E' and resid 367 through 380 removed outlier: 3.667A pdb=" N SER E 377 " --> pdb=" O ALA E 373 " (cutoff:3.500A) Processing helix chain 'E' and resid 386 through 406 removed outlier: 3.978A pdb=" N ILE E 391 " --> pdb=" O PRO E 387 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N LEU E 393 " --> pdb=" O LYS E 389 " (cutoff:3.500A) Processing helix chain 'E' and resid 533 through 543 removed outlier: 3.503A pdb=" N ARG E 542 " --> pdb=" O GLU E 538 " (cutoff:3.500A) Processing helix chain 'E' and resid 562 through 566 Processing helix chain 'E' and resid 574 through 588 removed outlier: 3.873A pdb=" N ALA E 579 " --> pdb=" O GLU E 575 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N ASN E 582 " --> pdb=" O ASP E 578 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N ALA E 583 " --> pdb=" O ALA E 579 " (cutoff:3.500A) removed outlier: 3.880A pdb=" N ARG E 586 " --> pdb=" O ASN E 582 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N SER E 587 " --> pdb=" O ALA E 583 " (cutoff:3.500A) Processing helix chain 'E' and resid 611 through 622 removed outlier: 3.739A pdb=" N CYS E 615 " --> pdb=" O LYS E 611 " (cutoff:3.500A) Processing helix chain 'E' and resid 634 through 636 No H-bonds generated for 'chain 'E' and resid 634 through 636' Processing helix chain 'E' and resid 640 through 645 removed outlier: 3.557A pdb=" N VAL E 643 " --> pdb=" O LYS E 640 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N SER E 644 " --> pdb=" O HIS E 641 " (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 removed outlier: 3.842A pdb=" N ALA E 665 " --> pdb=" O TYR E 661 " (cutoff:3.500A) 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 696 removed outlier: 3.825A pdb=" N ASN E 688 " --> pdb=" O PRO E 684 " (cutoff:3.500A) removed outlier: 3.921A pdb=" N ILE E 689 " --> pdb=" O ASP E 685 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N GLN E 692 " --> pdb=" O ASN E 688 " (cutoff:3.500A) removed outlier: 3.850A pdb=" N VAL E 693 " --> pdb=" O ILE E 689 " (cutoff:3.500A) Processing helix chain 'E' and resid 736 through 746 removed outlier: 3.520A pdb=" N SER E 746 " --> pdb=" O LEU E 742 " (cutoff:3.500A) Processing helix chain 'E' and resid 751 through 756 removed outlier: 3.502A pdb=" N ASN E 755 " --> pdb=" O PRO E 751 " (cutoff:3.500A) removed outlier: 3.869A pdb=" N ARG E 756 " --> pdb=" O GLU E 752 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 751 through 756' Processing helix chain 'E' and resid 768 through 786 removed outlier: 3.594A pdb=" N SER E 773 " --> pdb=" O GLN E 769 " (cutoff:3.500A) removed outlier: 4.080A pdb=" N GLN E 776 " --> pdb=" O ALA E 772 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N LEU E 782 " --> pdb=" O GLN E 778 " (cutoff:3.500A) Processing helix chain 'E' and resid 797 through 806 removed outlier: 3.745A pdb=" N LEU E 802 " --> pdb=" O GLU E 798 " (cutoff:3.500A) Processing helix chain 'E' and resid 815 through 824 Processing helix chain 'E' and resid 826 through 834 removed outlier: 3.540A pdb=" N ALA E 830 " --> pdb=" O GLU E 826 " (cutoff:3.500A) removed outlier: 3.543A 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 184 through 194 Processing helix chain 'D' and resid 212 through 225 removed outlier: 3.836A pdb=" N VAL D 216 " --> pdb=" O LYS D 212 " (cutoff:3.500A) removed outlier: 3.911A pdb=" N GLN D 221 " --> pdb=" O GLU D 217 " (cutoff:3.500A) removed outlier: 3.893A pdb=" N ILE D 224 " --> pdb=" O ALA D 220 " (cutoff:3.500A) Processing helix chain 'D' and resid 242 through 246 Processing helix chain 'D' and resid 254 through 267 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 295 through 305 removed outlier: 3.540A pdb=" N LEU D 299 " --> pdb=" O ALA D 295 " (cutoff:3.500A) Proline residue: D 301 - end of helix removed outlier: 3.646A pdb=" N ALA D 304 " --> pdb=" O LYS D 300 " (cutoff:3.500A) Processing helix chain 'D' and resid 316 through 322 removed outlier: 3.501A pdb=" N ARG D 320 " --> pdb=" O LEU D 316 " (cutoff:3.500A) Processing helix chain 'D' and resid 327 through 332 removed outlier: 4.210A pdb=" N ARG D 332 " --> pdb=" O ALA D 328 " (cutoff:3.500A) Processing helix chain 'D' and resid 343 through 352 Processing helix chain 'D' and resid 354 through 361 removed outlier: 3.828A pdb=" N HIS D 360 " --> pdb=" O ARG D 356 " (cutoff:3.500A) Processing helix chain 'D' and resid 367 through 380 removed outlier: 3.695A pdb=" N LEU D 376 " --> pdb=" O ALA D 372 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N HIS D 378 " --> pdb=" O ALA D 374 " (cutoff:3.500A) Processing helix chain 'D' and resid 386 through 406 removed outlier: 3.541A pdb=" N LEU D 393 " --> pdb=" O LYS D 389 " (cutoff:3.500A) Processing helix chain 'D' and resid 533 through 543 removed outlier: 3.635A pdb=" N ALA D 537 " --> pdb=" O ASP D 533 " (cutoff:3.500A) removed outlier: 4.000A pdb=" N GLU D 538 " --> pdb=" O ALA D 534 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N VAL D 539 " --> pdb=" O GLU D 535 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N ARG D 542 " --> pdb=" O GLU D 538 " (cutoff:3.500A) Processing helix chain 'D' and resid 556 through 560 Processing helix chain 'D' and resid 562 through 566 Processing helix chain 'D' and resid 574 through 588 removed outlier: 3.546A pdb=" N ALA D 579 " --> pdb=" O GLU D 575 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N ASN D 582 " --> pdb=" O ASP D 578 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N ALA D 583 " --> pdb=" O ALA D 579 " (cutoff:3.500A) Processing helix chain 'D' and resid 613 through 623 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 640 through 646 removed outlier: 3.971A pdb=" N VAL D 643 " --> pdb=" O LYS D 640 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N SER D 644 " --> pdb=" O HIS D 641 " (cutoff:3.500A) Processing helix chain 'D' and resid 662 through 668 removed outlier: 3.599A pdb=" N ARG D 668 " --> pdb=" O GLU D 664 " (cutoff:3.500A) Processing helix chain 'D' and resid 679 through 681 No H-bonds generated for 'chain 'D' and resid 679 through 681' Processing helix chain 'D' and resid 689 through 694 removed outlier: 3.871A pdb=" N VAL D 693 " --> pdb=" O ILE D 689 " (cutoff:3.500A) Processing helix chain 'D' and resid 722 through 728 removed outlier: 3.665A pdb=" N GLN D 726 " --> pdb=" O SER D 722 " (cutoff:3.500A) removed outlier: 3.902A pdb=" N GLU D 727 " --> pdb=" O ASP D 723 " (cutoff:3.500A) Processing helix chain 'D' and resid 734 through 748 removed outlier: 3.640A pdb=" N GLY D 743 " --> pdb=" O GLU D 739 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N VAL D 744 " --> pdb=" O LEU D 740 " (cutoff:3.500A) removed outlier: 4.050A pdb=" N HIS D 747 " --> pdb=" O GLY D 743 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N ASN D 748 " --> pdb=" O VAL D 744 " (cutoff:3.500A) Processing helix chain 'D' and resid 751 through 756 Processing helix chain 'D' and resid 768 through 787 removed outlier: 3.797A pdb=" N SER D 773 " --> pdb=" O GLN D 769 " (cutoff:3.500A) removed outlier: 3.967A pdb=" N GLN D 776 " --> pdb=" O ALA D 772 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N LEU D 782 " --> pdb=" O GLN D 778 " (cutoff:3.500A) Processing helix chain 'D' and resid 797 through 806 removed outlier: 3.897A pdb=" N GLU D 805 " --> pdb=" O LYS D 801 " (cutoff:3.500A) Processing helix chain 'D' and resid 815 through 824 Processing helix chain 'D' and resid 826 through 835 removed outlier: 3.625A pdb=" N GLN D 831 " --> pdb=" O ASN D 827 " (cutoff:3.500A) Processing helix chain 'B' and resid 168 through 173 Processing helix chain 'B' and resid 184 through 194 Processing helix chain 'B' and resid 213 through 222 removed outlier: 4.304A pdb=" N GLY B 218 " --> pdb=" O ALA B 214 " (cutoff:3.500A) removed outlier: 3.968A pdb=" N GLN B 221 " --> pdb=" O GLU B 217 " (cutoff:3.500A) Processing helix chain 'B' and resid 242 through 245 No H-bonds generated for 'chain 'B' and resid 242 through 245' Processing helix chain 'B' and resid 254 through 267 Processing helix chain 'B' and resid 280 through 282 No H-bonds generated for 'chain 'B' and resid 280 through 282' Processing helix chain 'B' and resid 295 through 304 Proline residue: B 301 - end of helix Processing helix chain 'B' and resid 316 through 321 removed outlier: 3.610A pdb=" N GLN B 321 " --> pdb=" O ASP B 317 " (cutoff:3.500A) Processing helix chain 'B' and resid 327 through 332 removed outlier: 3.537A pdb=" N ARG B 331 " --> pdb=" O ALA B 327 " (cutoff:3.500A) removed outlier: 4.048A pdb=" N ARG B 332 " --> pdb=" O ALA B 328 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 327 through 332' Processing helix chain 'B' and resid 343 through 361 removed outlier: 3.828A pdb=" N ALA B 348 " --> pdb=" O GLU B 344 " (cutoff:3.500A) removed outlier: 4.695A pdb=" N GLU B 355 " --> pdb=" O ARG B 351 " (cutoff:3.500A) removed outlier: 5.032A pdb=" N ARG B 356 " --> pdb=" O GLY B 352 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N LEU B 359 " --> pdb=" O GLU B 355 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N HIS B 360 " --> pdb=" O ARG B 356 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N HIS B 361 " --> pdb=" O TYR B 357 " (cutoff:3.500A) Processing helix chain 'B' and resid 367 through 380 removed outlier: 3.589A pdb=" N SER B 377 " --> pdb=" O ALA B 373 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N HIS B 378 " --> pdb=" O ALA B 374 " (cutoff:3.500A) Processing helix chain 'B' and resid 386 through 389 No H-bonds generated for 'chain 'B' and resid 386 through 389' Processing helix chain 'B' and resid 391 through 406 removed outlier: 3.511A pdb=" N ALA B 398 " --> pdb=" O ILE B 394 " (cutoff:3.500A) Processing helix chain 'B' and resid 533 through 544 Processing helix chain 'B' and resid 556 through 560 removed outlier: 3.532A pdb=" N LEU B 560 " --> pdb=" O ARG B 556 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 556 through 560' Processing helix chain 'B' and resid 562 through 566 Processing helix chain 'B' and resid 574 through 588 Processing helix chain 'B' and resid 611 through 622 Processing helix chain 'B' and resid 640 through 647 removed outlier: 3.691A pdb=" N VAL B 643 " --> pdb=" O LYS B 640 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N SER B 644 " --> pdb=" O HIS B 641 " (cutoff:3.500A) removed outlier: 4.052A pdb=" N VAL B 647 " --> pdb=" O SER B 644 " (cutoff:3.500A) Processing helix chain 'B' and resid 661 through 666 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 689 through 694 removed outlier: 3.960A pdb=" N VAL B 693 " --> pdb=" O ILE B 689 " (cutoff:3.500A) Processing helix chain 'B' and resid 734 through 745 removed outlier: 3.602A pdb=" N GLU B 739 " --> pdb=" O ALA B 735 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N GLY B 743 " --> pdb=" O GLU B 739 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N VAL B 744 " --> pdb=" O LEU B 740 " (cutoff:3.500A) Processing helix chain 'B' and resid 751 through 755 Processing helix chain 'B' and resid 768 through 784 removed outlier: 3.578A pdb=" N SER B 773 " --> pdb=" O GLN B 769 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N GLN B 776 " --> pdb=" O ALA B 772 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N LYS B 784 " --> pdb=" O LYS B 780 " (cutoff:3.500A) Processing helix chain 'B' and resid 797 through 799 No H-bonds generated for 'chain 'B' and resid 797 through 799' Processing helix chain 'B' and resid 801 through 806 removed outlier: 4.069A pdb=" N ASN B 806 " --> pdb=" O LEU B 803 " (cutoff:3.500A) Processing helix chain 'B' and resid 815 through 822 Processing helix chain 'B' and resid 826 through 833 removed outlier: 3.951A pdb=" N GLN B 831 " --> pdb=" O ASN B 827 " (cutoff:3.500A) Processing helix chain 'A' and resid 170 through 173 No H-bonds generated for 'chain 'A' and resid 170 through 173' Processing helix chain 'A' and resid 184 through 194 Processing helix chain 'A' and resid 213 through 225 removed outlier: 4.047A pdb=" N GLY A 218 " --> pdb=" O ALA A 214 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N GLN A 221 " --> pdb=" O GLU A 217 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N ARG A 222 " --> pdb=" O GLY A 218 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N ILE A 224 " --> pdb=" O ALA A 220 " (cutoff:3.500A) Processing helix chain 'A' and resid 256 through 268 removed outlier: 3.572A pdb=" N ASN A 264 " --> pdb=" O LYS A 260 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N LYS A 268 " --> pdb=" O ASN A 264 " (cutoff:3.500A) Processing helix chain 'A' and resid 280 through 282 No H-bonds generated for 'chain 'A' and resid 280 through 282' Processing helix chain 'A' and resid 300 through 304 Processing helix chain 'A' and resid 316 through 321 Processing helix chain 'A' and resid 327 through 332 removed outlier: 3.805A pdb=" N ARG A 331 " --> pdb=" O ALA A 327 " (cutoff:3.500A) removed outlier: 4.701A pdb=" N ARG A 332 " --> pdb=" O ALA A 328 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 327 through 332' Processing helix chain 'A' and resid 345 through 352 removed outlier: 3.879A pdb=" N ILE A 349 " --> pdb=" O ASP A 345 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N GLY A 352 " --> pdb=" O ALA A 348 " (cutoff:3.500A) Processing helix chain 'A' and resid 354 through 361 removed outlier: 3.951A pdb=" N HIS A 360 " --> pdb=" O ARG A 356 " (cutoff:3.500A) Processing helix chain 'A' and resid 368 through 380 removed outlier: 3.605A pdb=" N ALA A 373 " --> pdb=" O ALA A 369 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N ALA A 374 " --> pdb=" O ILE A 370 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N THR A 375 " --> pdb=" O VAL A 371 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N LEU A 376 " --> pdb=" O ALA A 372 " (cutoff:3.500A) removed outlier: 3.852A pdb=" N SER A 377 " --> pdb=" O ALA A 373 " (cutoff:3.500A) Processing helix chain 'A' and resid 386 through 401 removed outlier: 5.247A pdb=" N ILE A 391 " --> pdb=" O PRO A 387 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N ILE A 394 " --> pdb=" O ALA A 390 " (cutoff:3.500A) Processing helix chain 'A' and resid 533 through 543 Processing helix chain 'A' and resid 556 through 559 No H-bonds generated for 'chain 'A' and resid 556 through 559' Processing helix chain 'A' and resid 562 through 567 removed outlier: 4.017A pdb=" N LEU A 566 " --> pdb=" O MET A 562 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N HIS A 567 " --> pdb=" O GLU A 563 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 562 through 567' Processing helix chain 'A' and resid 574 through 580 Processing helix chain 'A' and resid 585 through 588 No H-bonds generated for 'chain 'A' and resid 585 through 588' Processing helix chain 'A' and resid 611 through 622 removed outlier: 3.815A pdb=" N CYS A 615 " --> pdb=" O LYS A 611 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N LYS A 616 " --> pdb=" O THR A 612 " (cutoff:3.500A) Processing helix chain 'A' and resid 640 through 643 removed outlier: 3.605A pdb=" N VAL A 643 " --> pdb=" O LYS A 640 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 640 through 643' Processing helix chain 'A' and resid 663 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 684 through 687 No H-bonds generated for 'chain 'A' and resid 684 through 687' Processing helix chain 'A' and resid 689 through 695 removed outlier: 4.009A pdb=" N GLN A 692 " --> pdb=" O ILE A 689 " (cutoff:3.500A) removed outlier: 4.812A pdb=" N VAL A 693 " --> pdb=" O LEU A 690 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N LEU A 694 " --> pdb=" O LEU A 691 " (cutoff:3.500A) removed outlier: 3.782A pdb=" N ASP A 695 " --> pdb=" O GLN A 692 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 689 through 695' Processing helix chain 'A' and resid 722 through 727 removed outlier: 3.863A pdb=" N GLU A 727 " --> pdb=" O ASP A 723 " (cutoff:3.500A) Processing helix chain 'A' and resid 768 through 774 removed outlier: 4.136A pdb=" N SER A 773 " --> pdb=" O GLN A 769 " (cutoff:3.500A) Processing helix chain 'A' and resid 782 through 784 No H-bonds generated for 'chain 'A' and resid 782 through 784' Processing helix chain 'A' and resid 800 through 806 removed outlier: 4.327A pdb=" N ASN A 806 " --> pdb=" O LEU A 802 " (cutoff:3.500A) Processing helix chain 'A' and resid 815 through 822 removed outlier: 3.712A pdb=" N ILE A 821 " --> pdb=" O LYS A 818 " (cutoff:3.500A) Processing helix chain 'A' and resid 827 through 830 No H-bonds generated for 'chain 'A' and resid 827 through 830' Processing sheet with id= A, first strand: chain 'C' and resid 165 through 167 removed outlier: 4.702A pdb=" N ASP C 278 " --> pdb=" O LEU C 240 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'C' and resid 202 through 206 removed outlier: 5.949A pdb=" N GLN C 334 " --> pdb=" O VAL C 203 " (cutoff:3.500A) removed outlier: 6.532A pdb=" N ILE C 205 " --> pdb=" O GLN C 334 " (cutoff:3.500A) removed outlier: 6.050A pdb=" N VAL C 336 " --> pdb=" O ILE C 205 " (cutoff:3.500A) No H-bonds generated for sheet with id= B Processing sheet with id= C, first strand: chain 'C' and resid 759 through 762 removed outlier: 6.271A pdb=" N VAL C 630 " --> pdb=" O LEU C 675 " (cutoff:3.500A) removed outlier: 7.104A pdb=" N ASP C 677 " --> pdb=" O VAL C 630 " (cutoff:3.500A) removed outlier: 6.830A 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 792 through 795 Processing sheet with id= F, first strand: chain 'F' and resid 333 through 337 removed outlier: 6.901A pdb=" N ASN F 201 " --> pdb=" O GLN F 334 " (cutoff:3.500A) removed outlier: 6.941A pdb=" N VAL F 336 " --> pdb=" O ASN F 201 " (cutoff:3.500A) removed outlier: 6.127A pdb=" N VAL F 203 " --> pdb=" O VAL F 336 " (cutoff:3.500A) removed outlier: 6.895A pdb=" N GLY F 312 " --> pdb=" O LEU F 204 " (cutoff:3.500A) No H-bonds generated for sheet with id= F Processing sheet with id= G, first strand: chain 'F' and resid 675 through 677 removed outlier: 7.028A pdb=" N ILE F 715 " --> pdb=" O LEU F 676 " (cutoff:3.500A) No H-bonds generated for sheet with id= G Processing sheet with id= H, first strand: chain 'E' and resid 759 through 762 removed outlier: 6.321A pdb=" N VAL E 630 " --> pdb=" O LEU E 675 " (cutoff:3.500A) removed outlier: 6.868A pdb=" N ASP E 677 " --> pdb=" O VAL E 630 " (cutoff:3.500A) removed outlier: 6.409A pdb=" N ILE E 632 " --> pdb=" O ASP E 677 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'E' and resid 698 through 700 Processing sheet with id= J, first strand: chain 'E' and resid 792 through 795 Processing sheet with id= K, first strand: chain 'D' and resid 165 through 167 removed outlier: 6.184A pdb=" N HIS D 309 " --> pdb=" O LEU D 275 " (cutoff:3.500A) removed outlier: 6.944A pdb=" N ILE D 277 " --> pdb=" O HIS D 309 " (cutoff:3.500A) removed outlier: 5.728A pdb=" N VAL D 311 " --> pdb=" O ILE D 277 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'D' and resid 202 through 206 removed outlier: 7.066A pdb=" N GLN D 334 " --> pdb=" O VAL D 203 " (cutoff:3.500A) removed outlier: 7.246A pdb=" N ILE D 205 " --> pdb=" O GLN D 334 " (cutoff:3.500A) removed outlier: 6.367A pdb=" N VAL D 336 " --> pdb=" O ILE D 205 " (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 762 removed outlier: 6.335A pdb=" N VAL D 630 " --> pdb=" O LEU D 675 " (cutoff:3.500A) removed outlier: 7.143A pdb=" N ASP D 677 " --> pdb=" O VAL D 630 " (cutoff:3.500A) removed outlier: 6.854A pdb=" N ILE D 632 " --> pdb=" O ASP D 677 " (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 165 through 167 removed outlier: 4.556A pdb=" N ASP B 278 " --> pdb=" O LEU B 240 " (cutoff:3.500A) removed outlier: 6.261A pdb=" N VAL B 311 " --> pdb=" O ILE B 277 " (cutoff:3.500A) Processing sheet with id= Q, first strand: chain 'B' and resid 202 through 205 removed outlier: 6.677A pdb=" N GLN B 334 " --> pdb=" O VAL B 203 " (cutoff:3.500A) removed outlier: 6.720A pdb=" N ILE B 205 " --> pdb=" O GLN B 334 " (cutoff:3.500A) removed outlier: 5.998A pdb=" N VAL B 336 " --> pdb=" O ILE B 205 " (cutoff:3.500A) No H-bonds generated for sheet with id= Q Processing sheet with id= R, first strand: chain 'B' and resid 601 through 605 removed outlier: 6.724A pdb=" N GLU B 759 " --> pdb=" O LEU B 602 " (cutoff:3.500A) removed outlier: 7.167A pdb=" N LEU B 604 " --> pdb=" O GLU B 759 " (cutoff:3.500A) removed outlier: 6.346A 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 630 through 633 removed outlier: 6.036A pdb=" N VAL B 713 " --> pdb=" O ILE B 674 " (cutoff:3.500A) removed outlier: 7.100A pdb=" N LEU B 676 " --> pdb=" O VAL B 713 " (cutoff:3.500A) removed outlier: 7.102A pdb=" N ILE B 715 " --> pdb=" O LEU B 676 " (cutoff:3.500A) 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 792 through 795 removed outlier: 3.847A pdb=" N LEU B 846 " --> pdb=" O HIS B 794 " (cutoff:3.500A) Processing sheet with id= V, first strand: chain 'A' and resid 202 through 205 removed outlier: 5.990A pdb=" N GLN A 334 " --> pdb=" O VAL A 203 " (cutoff:3.500A) removed outlier: 6.379A pdb=" N ILE A 205 " --> pdb=" O GLN A 334 " (cutoff:3.500A) removed outlier: 6.035A pdb=" N VAL A 336 " --> pdb=" O ILE A 205 " (cutoff:3.500A) No H-bonds generated for sheet with id= V Processing sheet with id= W, first strand: chain 'A' and resid 236 through 238 Processing sheet with id= X, first strand: chain 'A' and resid 599 through 604 Processing sheet with id= Y, first strand: chain 'A' and resid 698 through 700 697 hydrogen bonds defined for protein. 2004 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: 9.31 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: 1.21 - 1.36: 9899 1.36 - 1.51: 8397 1.51 - 1.66: 9813 1.66 - 1.81: 173 1.81 - 1.96: 14 Bond restraints: 28296 Sorted by residual: bond pdb=" C ARG A 815 " pdb=" N PRO A 816 " ideal model delta sigma weight residual 1.337 1.397 -0.060 9.80e-03 1.04e+04 3.78e+01 bond pdb=" C GLY C 648 " pdb=" N ALA C 649 " ideal model delta sigma weight residual 1.329 1.246 0.083 1.86e-02 2.89e+03 1.97e+01 bond pdb=" CA SER B 600 " pdb=" CB SER B 600 " ideal model delta sigma weight residual 1.527 1.451 0.076 1.75e-02 3.27e+03 1.89e+01 bond pdb=" CA LEU B 676 " pdb=" CB LEU B 676 " ideal model delta sigma weight residual 1.526 1.452 0.074 1.76e-02 3.23e+03 1.75e+01 bond pdb=" CB THR B 314 " pdb=" CG2 THR B 314 " ideal model delta sigma weight residual 1.521 1.414 0.107 3.30e-02 9.18e+02 1.04e+01 ... (remaining 28291 not shown) Histogram of bond angle deviations from ideal: 95.78 - 103.85: 410 103.85 - 111.92: 12810 111.92 - 119.98: 13235 119.98 - 128.05: 11611 128.05 - 136.12: 193 Bond angle restraints: 38259 Sorted by residual: angle pdb=" N PHE E 337 " pdb=" CA PHE E 337 " pdb=" C PHE E 337 " ideal model delta sigma weight residual 110.23 121.97 -11.74 1.45e+00 4.76e-01 6.55e+01 angle pdb=" N GLU C 850 " pdb=" CA GLU C 850 " pdb=" C GLU C 850 " ideal model delta sigma weight residual 109.95 100.71 9.24 1.44e+00 4.82e-01 4.12e+01 angle pdb=" N VAL F 343 " pdb=" CA VAL F 343 " pdb=" C VAL F 343 " ideal model delta sigma weight residual 113.22 105.80 7.42 1.23e+00 6.61e-01 3.64e+01 angle pdb=" N ILE A 215 " pdb=" CA ILE A 215 " pdb=" C ILE A 215 " ideal model delta sigma weight residual 111.81 106.63 5.18 8.60e-01 1.35e+00 3.63e+01 angle pdb=" N VAL B 548 " pdb=" CA VAL B 548 " pdb=" C VAL B 548 " ideal model delta sigma weight residual 112.29 106.81 5.48 9.40e-01 1.13e+00 3.40e+01 ... (remaining 38254 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 33.14: 16774 33.14 - 66.27: 610 66.27 - 99.41: 39 99.41 - 132.54: 5 132.54 - 165.68: 3 Dihedral angle restraints: 17431 sinusoidal: 7389 harmonic: 10042 Sorted by residual: dihedral pdb=" O1B ADP F 901 " pdb=" O3A ADP F 901 " pdb=" PB ADP F 901 " pdb=" PA ADP F 901 " ideal model delta sinusoidal sigma weight residual -60.00 55.90 -115.91 1 2.00e+01 2.50e-03 3.45e+01 dihedral pdb=" O1B ADP A 902 " pdb=" O3A ADP A 902 " pdb=" PB ADP A 902 " pdb=" PA ADP A 902 " ideal model delta sinusoidal sigma weight residual -60.00 53.29 -113.30 1 2.00e+01 2.50e-03 3.35e+01 dihedral pdb=" CA GLN A 385 " pdb=" C GLN A 385 " pdb=" N LEU A 386 " pdb=" CA LEU A 386 " ideal model delta harmonic sigma weight residual 180.00 -151.36 -28.64 0 5.00e+00 4.00e-02 3.28e+01 ... (remaining 17428 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.073: 3301 0.073 - 0.145: 908 0.145 - 0.218: 96 0.218 - 0.290: 19 0.290 - 0.363: 4 Chirality restraints: 4328 Sorted by residual: 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 -2.27 -0.36 2.00e-01 2.50e+01 3.29e+00 chirality pdb=" CB VAL D 609 " pdb=" CA VAL D 609 " pdb=" CG1 VAL D 609 " pdb=" CG2 VAL D 609 " both_signs ideal model delta sigma weight residual False -2.63 -2.27 -0.36 2.00e-01 2.50e+01 3.22e+00 chirality pdb=" CB ILE F 571 " pdb=" CA ILE F 571 " pdb=" CG1 ILE F 571 " pdb=" CG2 ILE F 571 " both_signs ideal model delta sigma weight residual False 2.64 2.32 0.33 2.00e-01 2.50e+01 2.68e+00 ... (remaining 4325 not shown) Planarity restraints: 4991 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LYS E 300 " 0.057 5.00e-02 4.00e+02 8.49e-02 1.15e+01 pdb=" N PRO E 301 " -0.147 5.00e-02 4.00e+02 pdb=" CA PRO E 301 " 0.042 5.00e-02 4.00e+02 pdb=" CD PRO E 301 " 0.048 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASP A 367 " 0.054 5.00e-02 4.00e+02 8.03e-02 1.03e+01 pdb=" N PRO A 368 " -0.139 5.00e-02 4.00e+02 pdb=" CA PRO A 368 " 0.040 5.00e-02 4.00e+02 pdb=" CD PRO A 368 " 0.045 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASP E 367 " 0.050 5.00e-02 4.00e+02 7.51e-02 9.03e+00 pdb=" N PRO E 368 " -0.130 5.00e-02 4.00e+02 pdb=" CA PRO E 368 " 0.037 5.00e-02 4.00e+02 pdb=" CD PRO E 368 " 0.042 5.00e-02 4.00e+02 ... (remaining 4988 not shown) Histogram of nonbonded interaction distances: 1.81 - 2.43: 123 2.43 - 3.04: 14979 3.04 - 3.66: 43686 3.66 - 4.28: 68189 4.28 - 4.90: 110802 Nonbonded interactions: 237779 Sorted by model distance: nonbonded pdb=" O ALA E 339 " pdb=" O GLU E 340 " model vdw 1.807 3.040 nonbonded pdb=" O MET E 298 " pdb=" CG PRO E 301 " model vdw 2.214 3.440 nonbonded pdb=" CD2 LEU D 204 " pdb=" O LYS D 212 " model vdw 2.217 3.460 nonbonded pdb=" O2A AGS D 901 " pdb=" O2B AGS D 901 " model vdw 2.223 2.440 nonbonded pdb=" O PRO C 651 " pdb=" OG SER D 644 " model vdw 2.227 2.440 ... (remaining 237774 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 283 or resid 294 through 408 or resid 529 thro \ ugh 857)) selection = (chain 'B' and (resid 161 through 283 or resid 294 through 408 or resid 529 thro \ ugh 857)) selection = (chain 'C' and (resid 161 through 283 or resid 294 through 408 or resid 529 thro \ ugh 857)) selection = (chain 'D' and (resid 161 through 283 or resid 294 through 408 or resid 529 thro \ ugh 857)) selection = (chain 'E' and (resid 161 through 283 or resid 294 through 408 or resid 529 thro \ ugh 857)) selection = (chain 'F' and (resid 161 through 408 or resid 529 through 857)) } 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: 0.730 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: 5.230 Check model and map are aligned: 0.410 Set scattering table: 0.230 Process input model: 71.850 Find NCS groups from input model: 2.220 Set up NCS constraints: 0.110 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:12.010 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 92.820 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7393 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 0.124 28296 Z= 0.764 Angle : 1.184 13.611 38259 Z= 0.667 Chirality : 0.066 0.363 4328 Planarity : 0.008 0.085 4991 Dihedral : 16.589 165.676 10965 Min Nonbonded Distance : 1.807 Molprobity Statistics. All-atom Clashscore : 12.66 Ramachandran Plot: Outliers : 0.35 % Allowed : 7.74 % Favored : 91.91 % Rotamer: Outliers : 0.93 % Allowed : 9.09 % Favored : 89.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -5.39 (0.10), residues: 3448 helix: -4.58 (0.06), residues: 1524 sheet: -3.40 (0.25), residues: 260 loop : -2.45 (0.13), residues: 1664 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP E 543 HIS 0.016 0.002 HIS A 747 PHE 0.024 0.004 PHE E 276 TYR 0.020 0.003 TYR B 653 ARG 0.012 0.001 ARG F 585 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6896 Ramachandran restraints generated. 3448 Oldfield, 0 Emsley, 3448 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6896 Ramachandran restraints generated. 3448 Oldfield, 0 Emsley, 3448 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 620 residues out of total 2916 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 593 time to evaluate : 3.138 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 221 GLN cc_start: 0.8654 (mt0) cc_final: 0.8409 (mt0) REVERT: F 251 TYR cc_start: 0.5641 (m-80) cc_final: 0.5348 (m-80) REVERT: F 275 LEU cc_start: 0.6701 (tp) cc_final: 0.6149 (tm) REVERT: F 276 PHE cc_start: 0.6791 (m-10) cc_final: 0.6191 (m-80) REVERT: F 314 THR cc_start: 0.7200 (p) cc_final: 0.6989 (p) REVERT: F 331 ARG cc_start: 0.6814 (tpp-160) cc_final: 0.5226 (ttm-80) REVERT: F 333 PHE cc_start: 0.6663 (m-80) cc_final: 0.6323 (m-80) REVERT: F 356 ARG cc_start: 0.3801 (tpt170) cc_final: 0.2794 (tmt-80) REVERT: F 569 ARG cc_start: 0.5713 (ttp80) cc_final: 0.5236 (ptp-170) REVERT: F 585 ARG cc_start: 0.4975 (mtp85) cc_final: 0.4448 (tpm-80) REVERT: F 629 MET cc_start: 0.5200 (ttt) cc_final: 0.4929 (mmt) REVERT: F 634 MET cc_start: 0.4233 (mmp) cc_final: 0.4017 (mmt) REVERT: F 638 MET cc_start: 0.0537 (mmp) cc_final: 0.0143 (mpt) REVERT: E 217 GLU cc_start: 0.7122 (mt-10) cc_final: 0.6644 (mp0) REVERT: E 252 ARG cc_start: 0.6710 (mpp-170) cc_final: 0.5693 (tpt170) REVERT: E 298 MET cc_start: 0.6019 (mtp) cc_final: 0.5534 (mtt) REVERT: E 317 ASP cc_start: 0.7654 (m-30) cc_final: 0.7137 (m-30) REVERT: E 322 TYR cc_start: 0.7720 (m-80) cc_final: 0.7450 (m-80) REVERT: E 638 MET cc_start: 0.8553 (mtm) cc_final: 0.8308 (mtm) REVERT: E 705 ARG cc_start: 0.6639 (mtt180) cc_final: 0.6260 (mtt180) REVERT: E 751 PRO cc_start: 0.8616 (Cg_exo) cc_final: 0.8367 (Cg_endo) REVERT: E 752 GLU cc_start: 0.7273 (pm20) cc_final: 0.7068 (pm20) REVERT: E 822 GLN cc_start: 0.7999 (mt0) cc_final: 0.7400 (tt0) REVERT: D 163 LYS cc_start: 0.8642 (mtmt) cc_final: 0.8053 (mptt) REVERT: D 260 LYS cc_start: 0.7629 (mttt) cc_final: 0.7276 (mttm) REVERT: D 300 LYS cc_start: 0.8957 (mtpt) cc_final: 0.8588 (mtmm) REVERT: D 695 ASP cc_start: 0.7698 (t0) cc_final: 0.7229 (t70) REVERT: D 769 GLN cc_start: 0.8040 (pm20) cc_final: 0.7664 (pm20) REVERT: D 847 GLU cc_start: 0.7446 (mp0) cc_final: 0.7176 (mm-30) REVERT: D 857 GLN cc_start: 0.6715 (mm-40) cc_final: 0.6513 (tp40) REVERT: B 251 TYR cc_start: 0.8344 (m-80) cc_final: 0.7878 (m-10) REVERT: B 264 ASN cc_start: 0.7936 (m-40) cc_final: 0.7696 (m-40) REVERT: B 376 LEU cc_start: 0.8412 (mt) cc_final: 0.8200 (mp) REVERT: B 558 LYS cc_start: 0.8133 (tttm) cc_final: 0.7925 (ttpt) REVERT: B 831 GLN cc_start: 0.7274 (pp30) cc_final: 0.7016 (pp30) REVERT: B 832 GLN cc_start: 0.7760 (tt0) cc_final: 0.7557 (tm-30) REVERT: A 288 LYS cc_start: 0.6721 (OUTLIER) cc_final: 0.6476 (tttt) REVERT: A 551 MET cc_start: 0.1061 (mpp) cc_final: 0.0819 (mmm) outliers start: 27 outliers final: 7 residues processed: 610 average time/residue: 1.7189 time to fit residues: 1187.1730 Evaluate side-chains 412 residues out of total 2916 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 404 time to evaluate : 3.204 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 386 LEU Chi-restraints excluded: chain F residue 632 ILE Chi-restraints excluded: chain E residue 293 MET Chi-restraints excluded: chain D residue 359 LEU Chi-restraints excluded: chain B residue 290 ASP Chi-restraints excluded: chain B residue 294 ASP Chi-restraints excluded: chain A residue 246 VAL Chi-restraints excluded: chain A residue 288 LYS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 348 random chunks: chunk 293 optimal weight: 1.9990 chunk 263 optimal weight: 0.9980 chunk 146 optimal weight: 0.8980 chunk 90 optimal weight: 9.9990 chunk 177 optimal weight: 0.9980 chunk 140 optimal weight: 2.9990 chunk 272 optimal weight: 1.9990 chunk 105 optimal weight: 8.9990 chunk 165 optimal weight: 0.9990 chunk 203 optimal weight: 0.8980 chunk 316 optimal weight: 2.9990 overall best weight: 0.9582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 225 ASN ** C 297 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 692 GLN C 719 ASN C 748 ASN C 778 GLN ** C 824 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 404 GLN F 776 GLN F 778 GLN E 195 GLN ** E 281 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 360 HIS E 564 GLN ** E 769 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 776 GLN E 778 GLN E 823 GLN E 824 GLN D 297 ASN D 309 HIS D 334 GLN D 360 HIS D 385 GLN D 688 ASN D 806 ASN D 824 GLN B 225 ASN B 364 GLN ** B 755 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 823 GLN B 832 GLN A 174 GLN A 272 ASN A 564 GLN A 582 ASN A 692 GLN A 794 HIS A 831 GLN Total number of N/Q/H flips: 34 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7364 moved from start: 0.1800 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 28296 Z= 0.231 Angle : 0.666 8.354 38259 Z= 0.340 Chirality : 0.046 0.200 4328 Planarity : 0.006 0.068 4991 Dihedral : 12.314 173.576 4099 Min Nonbonded Distance : 2.183 Molprobity Statistics. All-atom Clashscore : 13.97 Ramachandran Plot: Outliers : 0.03 % Allowed : 5.66 % Favored : 94.32 % Rotamer: Outliers : 3.50 % Allowed : 16.50 % Favored : 80.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.16 (0.12), residues: 3448 helix: -3.25 (0.10), residues: 1532 sheet: -2.88 (0.25), residues: 312 loop : -2.05 (0.14), residues: 1604 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP D 543 HIS 0.007 0.001 HIS E 281 PHE 0.013 0.001 PHE E 276 TYR 0.016 0.001 TYR E 164 ARG 0.009 0.000 ARG C 561 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6896 Ramachandran restraints generated. 3448 Oldfield, 0 Emsley, 3448 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6896 Ramachandran restraints generated. 3448 Oldfield, 0 Emsley, 3448 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 546 residues out of total 2916 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 102 poor density : 444 time to evaluate : 3.628 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 221 GLN cc_start: 0.8587 (mt0) cc_final: 0.8339 (mt0) REVERT: C 305 ARG cc_start: 0.6101 (mtt-85) cc_final: 0.5599 (mtm-85) REVERT: C 307 GLU cc_start: 0.8438 (mt-10) cc_final: 0.8135 (mt-10) REVERT: C 710 ARG cc_start: 0.7952 (mtt90) cc_final: 0.7660 (mtt-85) REVERT: F 251 TYR cc_start: 0.5580 (m-80) cc_final: 0.5232 (m-80) REVERT: F 276 PHE cc_start: 0.6589 (m-10) cc_final: 0.6292 (m-80) REVERT: F 300 LYS cc_start: 0.3811 (OUTLIER) cc_final: 0.3006 (mmtt) REVERT: F 331 ARG cc_start: 0.6671 (tpp-160) cc_final: 0.5025 (ttm-80) REVERT: F 356 ARG cc_start: 0.3757 (tpt170) cc_final: 0.2842 (tmt-80) REVERT: F 585 ARG cc_start: 0.4854 (mtp85) cc_final: 0.4479 (tpm-80) REVERT: F 629 MET cc_start: 0.5289 (ttt) cc_final: 0.5009 (mmt) REVERT: F 638 MET cc_start: 0.0069 (mmp) cc_final: -0.0276 (mpt) REVERT: F 720 LEU cc_start: 0.5760 (OUTLIER) cc_final: 0.5389 (tp) REVERT: F 752 GLU cc_start: 0.2444 (tm-30) cc_final: 0.2102 (pm20) REVERT: E 164 TYR cc_start: 0.8150 (m-10) cc_final: 0.7593 (m-10) REVERT: E 217 GLU cc_start: 0.6962 (mt-10) cc_final: 0.6564 (mp0) REVERT: E 252 ARG cc_start: 0.6629 (mpp-170) cc_final: 0.5754 (tpt170) REVERT: E 561 ARG cc_start: 0.7229 (mtm110) cc_final: 0.7023 (mtm110) REVERT: E 629 MET cc_start: 0.8921 (ptt) cc_final: 0.8599 (ptp) REVERT: E 638 MET cc_start: 0.8503 (mtm) cc_final: 0.8244 (mtm) REVERT: E 656 TYR cc_start: 0.7839 (p90) cc_final: 0.7235 (p90) REVERT: E 696 ASP cc_start: 0.6242 (OUTLIER) cc_final: 0.5828 (t0) REVERT: E 705 ARG cc_start: 0.6552 (mtt180) cc_final: 0.6253 (mtt180) REVERT: E 737 MET cc_start: 0.7913 (tpp) cc_final: 0.7306 (tpt) REVERT: E 752 GLU cc_start: 0.7270 (pm20) cc_final: 0.6960 (pm20) REVERT: E 780 LYS cc_start: 0.7829 (mtmt) cc_final: 0.7480 (mmtp) REVERT: E 798 GLU cc_start: 0.7840 (OUTLIER) cc_final: 0.7407 (pt0) REVERT: E 822 GLN cc_start: 0.7885 (mt0) cc_final: 0.7283 (tt0) REVERT: D 163 LYS cc_start: 0.8582 (mtmt) cc_final: 0.8024 (mptt) REVERT: D 184 ASP cc_start: 0.7560 (t0) cc_final: 0.7357 (m-30) REVERT: D 300 LYS cc_start: 0.8760 (mtpt) cc_final: 0.8486 (mtmm) REVERT: D 529 ASN cc_start: 0.7351 (p0) cc_final: 0.7066 (p0) REVERT: D 552 MET cc_start: 0.4138 (mmt) cc_final: 0.3858 (mmm) REVERT: D 695 ASP cc_start: 0.7626 (t0) cc_final: 0.7141 (t70) REVERT: D 750 ARG cc_start: 0.7541 (mtp85) cc_final: 0.6950 (mmp80) REVERT: D 769 GLN cc_start: 0.8014 (pm20) cc_final: 0.7670 (pm20) REVERT: B 268 LYS cc_start: 0.8081 (mmpt) cc_final: 0.7807 (mttp) REVERT: B 555 GLU cc_start: 0.7314 (tt0) cc_final: 0.7107 (tm-30) REVERT: B 558 LYS cc_start: 0.8120 (tttm) cc_final: 0.7878 (ttpt) REVERT: B 831 GLN cc_start: 0.7201 (pp30) cc_final: 0.6966 (pp30) REVERT: B 832 GLN cc_start: 0.7875 (tt0) cc_final: 0.7518 (tm-30) REVERT: A 396 GLU cc_start: 0.7223 (mt-10) cc_final: 0.7000 (mt-10) REVERT: A 551 MET cc_start: 0.1054 (mpp) cc_final: 0.0843 (mmm) REVERT: A 564 GLN cc_start: 0.7619 (OUTLIER) cc_final: 0.7116 (tm-30) outliers start: 102 outliers final: 28 residues processed: 510 average time/residue: 1.4864 time to fit residues: 876.1172 Evaluate side-chains 426 residues out of total 2916 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 393 time to evaluate : 3.460 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 228 VAL Chi-restraints excluded: chain C residue 314 THR Chi-restraints excluded: chain C residue 317 ASP Chi-restraints excluded: chain C residue 386 LEU Chi-restraints excluded: chain F residue 300 LYS Chi-restraints excluded: chain F residue 570 VAL Chi-restraints excluded: chain F residue 643 VAL Chi-restraints excluded: chain F residue 720 LEU Chi-restraints excluded: chain E residue 191 ILE Chi-restraints excluded: chain E residue 246 VAL Chi-restraints excluded: chain E residue 367 ASP Chi-restraints excluded: chain E residue 532 THR Chi-restraints excluded: chain E residue 540 LEU Chi-restraints excluded: chain E residue 549 SER Chi-restraints excluded: chain E residue 696 ASP Chi-restraints excluded: chain E residue 758 ASP Chi-restraints excluded: chain E residue 798 GLU Chi-restraints excluded: chain E residue 802 LEU Chi-restraints excluded: chain E residue 843 VAL Chi-restraints excluded: chain D residue 293 MET Chi-restraints excluded: chain D residue 535 GLU Chi-restraints excluded: chain B residue 307 GLU Chi-restraints excluded: chain B residue 383 ASP Chi-restraints excluded: chain B residue 548 VAL Chi-restraints excluded: chain B residue 554 SER Chi-restraints excluded: chain B residue 679 VAL Chi-restraints excluded: chain B residue 757 ILE Chi-restraints excluded: chain B residue 780 LYS Chi-restraints excluded: chain A residue 246 VAL Chi-restraints excluded: chain A residue 330 GLU Chi-restraints excluded: chain A residue 392 ASP Chi-restraints excluded: chain A residue 564 GLN Chi-restraints excluded: chain A residue 626 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 348 random chunks: chunk 175 optimal weight: 0.9990 chunk 98 optimal weight: 30.0000 chunk 263 optimal weight: 0.8980 chunk 215 optimal weight: 3.9990 chunk 87 optimal weight: 0.0170 chunk 316 optimal weight: 6.9990 chunk 342 optimal weight: 0.9980 chunk 281 optimal weight: 9.9990 chunk 313 optimal weight: 10.0000 chunk 107 optimal weight: 0.8980 chunk 253 optimal weight: 4.9990 overall best weight: 0.7620 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 297 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 719 ASN ** C 824 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 281 HIS E 195 GLN ** E 281 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 641 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 776 GLN E 778 GLN D 174 GLN D 334 GLN D 831 GLN B 195 GLN B 755 ASN B 770 HIS A 281 HIS ** A 297 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7343 moved from start: 0.2237 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 28296 Z= 0.196 Angle : 0.587 7.331 38259 Z= 0.296 Chirality : 0.044 0.224 4328 Planarity : 0.005 0.071 4991 Dihedral : 11.681 178.399 4084 Min Nonbonded Distance : 2.060 Molprobity Statistics. All-atom Clashscore : 12.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.63 % Favored : 94.37 % Rotamer: Outliers : 3.77 % Allowed : 18.59 % Favored : 77.64 % 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: -3.23 (0.13), residues: 3448 helix: -2.27 (0.11), residues: 1541 sheet: -2.81 (0.25), residues: 311 loop : -1.70 (0.15), residues: 1596 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP D 543 HIS 0.009 0.001 HIS E 281 PHE 0.013 0.001 PHE E 276 TYR 0.011 0.001 TYR B 783 ARG 0.009 0.000 ARG D 332 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6896 Ramachandran restraints generated. 3448 Oldfield, 0 Emsley, 3448 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6896 Ramachandran restraints generated. 3448 Oldfield, 0 Emsley, 3448 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 542 residues out of total 2916 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 110 poor density : 432 time to evaluate : 4.106 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 305 ARG cc_start: 0.6135 (mtt-85) cc_final: 0.5548 (mtm-85) REVERT: C 307 GLU cc_start: 0.8412 (mt-10) cc_final: 0.8127 (mt-10) REVERT: C 561 ARG cc_start: 0.7499 (mtm110) cc_final: 0.7109 (ptt180) REVERT: C 710 ARG cc_start: 0.7916 (mtt90) cc_final: 0.7655 (mtt-85) REVERT: F 251 TYR cc_start: 0.5458 (m-80) cc_final: 0.5139 (m-80) REVERT: F 275 LEU cc_start: 0.6929 (tp) cc_final: 0.6544 (tm) REVERT: F 300 LYS cc_start: 0.3936 (OUTLIER) cc_final: 0.3103 (mmtt) REVERT: F 331 ARG cc_start: 0.6723 (tpp-160) cc_final: 0.5078 (ttm-80) REVERT: F 356 ARG cc_start: 0.3599 (tpt170) cc_final: 0.2700 (tmt-80) REVERT: F 585 ARG cc_start: 0.4872 (mtp85) cc_final: 0.4421 (tpm-80) REVERT: F 629 MET cc_start: 0.5334 (ttt) cc_final: 0.5106 (mmt) REVERT: F 638 MET cc_start: -0.0390 (mmp) cc_final: -0.0804 (mpt) REVERT: F 720 LEU cc_start: 0.5548 (OUTLIER) cc_final: 0.5221 (tp) REVERT: F 793 ILE cc_start: 0.7250 (OUTLIER) cc_final: 0.6951 (tp) REVERT: E 164 TYR cc_start: 0.8139 (m-10) cc_final: 0.7502 (m-10) REVERT: E 217 GLU cc_start: 0.7000 (mt-10) cc_final: 0.6643 (mp0) REVERT: E 252 ARG cc_start: 0.6703 (mpp-170) cc_final: 0.5719 (tpt90) REVERT: E 317 ASP cc_start: 0.7440 (m-30) cc_final: 0.7023 (m-30) REVERT: E 629 MET cc_start: 0.9020 (ptt) cc_final: 0.8587 (ptp) REVERT: E 638 MET cc_start: 0.8509 (mtm) cc_final: 0.8239 (mtm) REVERT: E 656 TYR cc_start: 0.7726 (p90) cc_final: 0.7210 (p90) REVERT: E 696 ASP cc_start: 0.6090 (OUTLIER) cc_final: 0.5775 (t0) REVERT: E 705 ARG cc_start: 0.6515 (mtt180) cc_final: 0.6216 (mtt180) REVERT: E 752 GLU cc_start: 0.7258 (pm20) cc_final: 0.7014 (pm20) REVERT: E 780 LYS cc_start: 0.7878 (mtmt) cc_final: 0.7637 (mptm) REVERT: E 822 GLN cc_start: 0.7813 (mt0) cc_final: 0.7390 (tt0) REVERT: D 163 LYS cc_start: 0.8622 (mtmt) cc_final: 0.8060 (mptt) REVERT: D 535 GLU cc_start: 0.7308 (OUTLIER) cc_final: 0.7076 (pp20) REVERT: D 552 MET cc_start: 0.4591 (mmt) cc_final: 0.4213 (mmm) REVERT: D 695 ASP cc_start: 0.7473 (t0) cc_final: 0.7197 (t0) REVERT: D 750 ARG cc_start: 0.7597 (mtp85) cc_final: 0.7019 (mmp80) REVERT: D 769 GLN cc_start: 0.7979 (pm20) cc_final: 0.7606 (pm20) REVERT: B 268 LYS cc_start: 0.8067 (mmpt) cc_final: 0.7812 (mttp) REVERT: B 558 LYS cc_start: 0.8127 (tttm) cc_final: 0.7848 (ttpt) REVERT: B 705 ARG cc_start: 0.7676 (tpp-160) cc_final: 0.7114 (ttp-110) REVERT: B 776 GLN cc_start: 0.8258 (mm-40) cc_final: 0.7822 (mt0) REVERT: B 784 LYS cc_start: 0.7260 (mmtm) cc_final: 0.6767 (mmtp) REVERT: B 832 GLN cc_start: 0.7790 (tt0) cc_final: 0.7510 (tm-30) REVERT: A 396 GLU cc_start: 0.7212 (mt-10) cc_final: 0.6987 (mt-10) REVERT: A 551 MET cc_start: 0.1199 (mpp) cc_final: 0.0954 (mmm) outliers start: 110 outliers final: 42 residues processed: 499 average time/residue: 1.5649 time to fit residues: 904.6359 Evaluate side-chains 426 residues out of total 2916 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 379 time to evaluate : 3.161 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 228 VAL Chi-restraints excluded: chain C residue 314 THR Chi-restraints excluded: chain C residue 317 ASP Chi-restraints excluded: chain C residue 342 SER Chi-restraints excluded: chain C residue 386 LEU Chi-restraints excluded: chain C residue 533 ASP Chi-restraints excluded: chain C residue 580 VAL Chi-restraints excluded: chain C residue 741 VAL Chi-restraints excluded: chain F residue 300 LYS Chi-restraints excluded: chain F residue 551 MET Chi-restraints excluded: chain F residue 632 ILE Chi-restraints excluded: chain F residue 720 LEU Chi-restraints excluded: chain F residue 768 GLU Chi-restraints excluded: chain F residue 779 LEU Chi-restraints excluded: chain F residue 793 ILE Chi-restraints excluded: chain E residue 161 LEU Chi-restraints excluded: chain E residue 190 THR Chi-restraints excluded: chain E residue 262 VAL Chi-restraints excluded: chain E residue 367 ASP Chi-restraints excluded: chain E residue 532 THR Chi-restraints excluded: chain E residue 540 LEU Chi-restraints excluded: chain E residue 549 SER Chi-restraints excluded: chain E residue 696 ASP Chi-restraints excluded: chain E residue 758 ASP Chi-restraints excluded: chain E residue 843 VAL Chi-restraints excluded: chain D residue 293 MET Chi-restraints excluded: chain D residue 298 MET Chi-restraints excluded: chain D residue 314 THR Chi-restraints excluded: chain D residue 532 THR Chi-restraints excluded: chain D residue 535 GLU Chi-restraints excluded: chain D residue 752 GLU Chi-restraints excluded: chain B residue 283 MET Chi-restraints excluded: chain B residue 294 ASP Chi-restraints excluded: chain B residue 317 ASP Chi-restraints excluded: chain B residue 383 ASP Chi-restraints excluded: chain B residue 548 VAL Chi-restraints excluded: chain B residue 604 LEU Chi-restraints excluded: chain B residue 679 VAL Chi-restraints excluded: chain B residue 732 LEU Chi-restraints excluded: chain A residue 232 LEU Chi-restraints excluded: chain A residue 317 ASP Chi-restraints excluded: chain A residue 330 GLU Chi-restraints excluded: chain A residue 392 ASP Chi-restraints excluded: chain A residue 532 THR Chi-restraints excluded: chain A residue 686 VAL Chi-restraints excluded: chain A residue 693 VAL Chi-restraints excluded: chain A residue 716 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 348 random chunks: chunk 312 optimal weight: 8.9990 chunk 238 optimal weight: 4.9990 chunk 164 optimal weight: 0.9980 chunk 35 optimal weight: 6.9990 chunk 151 optimal weight: 0.2980 chunk 212 optimal weight: 1.9990 chunk 317 optimal weight: 20.0000 chunk 336 optimal weight: 6.9990 chunk 165 optimal weight: 0.1980 chunk 301 optimal weight: 9.9990 chunk 90 optimal weight: 7.9990 overall best weight: 1.6984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 297 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 719 ASN ** C 824 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 195 GLN ** E 281 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 769 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 776 GLN D 334 GLN D 703 GLN D 831 GLN B 195 GLN B 719 ASN ** A 297 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 385 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7384 moved from start: 0.2423 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 28296 Z= 0.279 Angle : 0.606 8.140 38259 Z= 0.302 Chirality : 0.046 0.253 4328 Planarity : 0.004 0.050 4991 Dihedral : 11.592 176.660 4083 Min Nonbonded Distance : 2.078 Molprobity Statistics. All-atom Clashscore : 13.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.00 % Favored : 94.00 % Rotamer: Outliers : 3.81 % Allowed : 20.27 % Favored : 75.93 % 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: -2.82 (0.13), residues: 3448 helix: -1.87 (0.12), residues: 1547 sheet: -2.75 (0.25), residues: 321 loop : -1.51 (0.15), residues: 1580 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP D 543 HIS 0.008 0.001 HIS E 281 PHE 0.017 0.001 PHE E 276 TYR 0.018 0.001 TYR B 783 ARG 0.009 0.000 ARG F 569 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6896 Ramachandran restraints generated. 3448 Oldfield, 0 Emsley, 3448 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6896 Ramachandran restraints generated. 3448 Oldfield, 0 Emsley, 3448 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 515 residues out of total 2916 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 111 poor density : 404 time to evaluate : 3.278 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 305 ARG cc_start: 0.6199 (mtt-85) cc_final: 0.5563 (mtm-85) REVERT: C 307 GLU cc_start: 0.8480 (mt-10) cc_final: 0.8161 (mt-10) REVERT: C 335 LYS cc_start: 0.8732 (mtmm) cc_final: 0.8526 (mttm) REVERT: C 561 ARG cc_start: 0.7529 (mtm110) cc_final: 0.7174 (ptt180) REVERT: C 613 GLU cc_start: 0.8126 (tp30) cc_final: 0.7911 (tp30) REVERT: C 710 ARG cc_start: 0.7954 (mtt90) cc_final: 0.7693 (mtt-85) REVERT: F 251 TYR cc_start: 0.5476 (m-80) cc_final: 0.5108 (m-80) REVERT: F 275 LEU cc_start: 0.6631 (tp) cc_final: 0.6268 (tm) REVERT: F 300 LYS cc_start: 0.3884 (OUTLIER) cc_final: 0.3034 (mmtt) REVERT: F 320 ARG cc_start: 0.6049 (mtm110) cc_final: 0.5821 (mtt-85) REVERT: F 331 ARG cc_start: 0.6669 (tpp-160) cc_final: 0.5036 (ttm-80) REVERT: F 356 ARG cc_start: 0.3665 (tpt170) cc_final: 0.2753 (tmt-80) REVERT: F 585 ARG cc_start: 0.4856 (mtp85) cc_final: 0.4359 (tpm-80) REVERT: F 629 MET cc_start: 0.5435 (ttt) cc_final: 0.5144 (mmt) REVERT: F 638 MET cc_start: -0.0399 (mmp) cc_final: -0.0874 (mpt) REVERT: F 752 GLU cc_start: 0.2401 (tm-30) cc_final: 0.1994 (pm20) REVERT: F 793 ILE cc_start: 0.7262 (OUTLIER) cc_final: 0.6966 (tp) REVERT: F 800 LEU cc_start: 0.6947 (OUTLIER) cc_final: 0.6612 (pp) REVERT: E 164 TYR cc_start: 0.8175 (m-10) cc_final: 0.7815 (m-10) REVERT: E 217 GLU cc_start: 0.7032 (mt-10) cc_final: 0.6703 (mp0) REVERT: E 252 ARG cc_start: 0.6683 (mpp-170) cc_final: 0.5526 (tpt90) REVERT: E 264 ASN cc_start: 0.8093 (m-40) cc_final: 0.7770 (t0) REVERT: E 317 ASP cc_start: 0.7476 (m-30) cc_final: 0.7077 (m-30) REVERT: E 629 MET cc_start: 0.9059 (ptt) cc_final: 0.8567 (ptp) REVERT: E 638 MET cc_start: 0.8527 (mtm) cc_final: 0.8263 (mtm) REVERT: E 656 TYR cc_start: 0.7752 (p90) cc_final: 0.7218 (p90) REVERT: E 696 ASP cc_start: 0.6079 (OUTLIER) cc_final: 0.5785 (t0) REVERT: E 705 ARG cc_start: 0.6615 (mtt180) cc_final: 0.6302 (mtt180) REVERT: E 737 MET cc_start: 0.7923 (tpp) cc_final: 0.7393 (tpt) REVERT: E 752 GLU cc_start: 0.7240 (pm20) cc_final: 0.6936 (pm20) REVERT: E 780 LYS cc_start: 0.7889 (mtmt) cc_final: 0.7639 (mptm) REVERT: E 822 GLN cc_start: 0.7808 (mt0) cc_final: 0.7437 (tt0) REVERT: D 163 LYS cc_start: 0.8637 (mtmt) cc_final: 0.8061 (mptt) REVERT: D 527 LEU cc_start: 0.4661 (OUTLIER) cc_final: 0.4328 (pp) REVERT: D 552 MET cc_start: 0.4619 (mmt) cc_final: 0.4286 (mmm) REVERT: D 695 ASP cc_start: 0.7479 (t0) cc_final: 0.7187 (t0) REVERT: D 750 ARG cc_start: 0.7641 (mtp85) cc_final: 0.7041 (mmp80) REVERT: D 769 GLN cc_start: 0.8004 (pm20) cc_final: 0.7678 (pm20) REVERT: B 162 LYS cc_start: 0.6517 (OUTLIER) cc_final: 0.5845 (mtmm) REVERT: B 268 LYS cc_start: 0.8104 (mmtt) cc_final: 0.7889 (mttt) REVERT: B 555 GLU cc_start: 0.7326 (tt0) cc_final: 0.7029 (tt0) REVERT: B 558 LYS cc_start: 0.8159 (tttm) cc_final: 0.7835 (ttpp) REVERT: B 560 LEU cc_start: 0.8998 (OUTLIER) cc_final: 0.8738 (mt) REVERT: B 632 ILE cc_start: 0.8897 (OUTLIER) cc_final: 0.8417 (mp) REVERT: B 705 ARG cc_start: 0.7739 (tpp-160) cc_final: 0.7146 (ttp-110) REVERT: B 776 GLN cc_start: 0.8264 (mm-40) cc_final: 0.7899 (mt0) REVERT: B 832 GLN cc_start: 0.7856 (tt0) cc_final: 0.7561 (tm-30) REVERT: A 396 GLU cc_start: 0.7219 (mt-10) cc_final: 0.6964 (mt-10) REVERT: A 551 MET cc_start: 0.1223 (mpp) cc_final: 0.1018 (mmm) outliers start: 111 outliers final: 50 residues processed: 474 average time/residue: 1.4757 time to fit residues: 809.2429 Evaluate side-chains 435 residues out of total 2916 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 58 poor density : 377 time to evaluate : 2.971 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 190 THR Chi-restraints excluded: chain C residue 228 VAL Chi-restraints excluded: chain C residue 314 THR Chi-restraints excluded: chain C residue 386 LEU Chi-restraints excluded: chain C residue 533 ASP Chi-restraints excluded: chain C residue 580 VAL Chi-restraints excluded: chain F residue 300 LYS Chi-restraints excluded: chain F residue 551 MET Chi-restraints excluded: chain F residue 603 PHE Chi-restraints excluded: chain F residue 662 LEU Chi-restraints excluded: chain F residue 779 LEU Chi-restraints excluded: chain F residue 793 ILE Chi-restraints excluded: chain F residue 800 LEU Chi-restraints excluded: chain E residue 161 LEU Chi-restraints excluded: chain E residue 190 THR Chi-restraints excluded: chain E residue 262 VAL Chi-restraints excluded: chain E residue 367 ASP Chi-restraints excluded: chain E residue 532 THR Chi-restraints excluded: chain E residue 540 LEU Chi-restraints excluded: chain E residue 549 SER Chi-restraints excluded: chain E residue 696 ASP Chi-restraints excluded: chain E residue 758 ASP Chi-restraints excluded: chain E residue 843 VAL Chi-restraints excluded: chain D residue 200 ASN Chi-restraints excluded: chain D residue 242 MET Chi-restraints excluded: chain D residue 293 MET Chi-restraints excluded: chain D residue 298 MET Chi-restraints excluded: chain D residue 314 THR Chi-restraints excluded: chain D residue 527 LEU Chi-restraints excluded: chain D residue 532 THR Chi-restraints excluded: chain D residue 535 GLU Chi-restraints excluded: chain D residue 752 GLU Chi-restraints excluded: chain B residue 162 LYS Chi-restraints excluded: chain B residue 294 ASP Chi-restraints excluded: chain B residue 314 THR Chi-restraints excluded: chain B residue 317 ASP Chi-restraints excluded: chain B residue 383 ASP Chi-restraints excluded: chain B residue 548 VAL Chi-restraints excluded: chain B residue 560 LEU Chi-restraints excluded: chain B residue 604 LEU Chi-restraints excluded: chain B residue 629 MET Chi-restraints excluded: chain B residue 632 ILE Chi-restraints excluded: chain B residue 679 VAL Chi-restraints excluded: chain B residue 689 ILE Chi-restraints excluded: chain B residue 732 LEU Chi-restraints excluded: chain B residue 744 VAL Chi-restraints excluded: chain B residue 757 ILE Chi-restraints excluded: chain B residue 780 LYS Chi-restraints excluded: chain A residue 232 LEU Chi-restraints excluded: chain A residue 317 ASP Chi-restraints excluded: chain A residue 330 GLU Chi-restraints excluded: chain A residue 392 ASP Chi-restraints excluded: chain A residue 532 THR Chi-restraints excluded: chain A residue 641 HIS Chi-restraints excluded: chain A residue 642 SER Chi-restraints excluded: chain A residue 686 VAL Chi-restraints excluded: chain A residue 693 VAL Chi-restraints excluded: chain A residue 716 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 348 random chunks: chunk 280 optimal weight: 0.0970 chunk 190 optimal weight: 0.9980 chunk 4 optimal weight: 0.3980 chunk 250 optimal weight: 3.9990 chunk 138 optimal weight: 0.9980 chunk 287 optimal weight: 8.9990 chunk 232 optimal weight: 0.8980 chunk 0 optimal weight: 4.9990 chunk 171 optimal weight: 10.0000 chunk 301 optimal weight: 5.9990 chunk 84 optimal weight: 0.2980 overall best weight: 0.5378 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 297 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 824 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 192 GLN ** E 281 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 776 GLN ** D 334 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 703 GLN D 794 HIS B 195 GLN B 719 ASN ** A 297 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 360 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7320 moved from start: 0.2748 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 28296 Z= 0.163 Angle : 0.560 9.202 38259 Z= 0.276 Chirality : 0.043 0.202 4328 Planarity : 0.004 0.074 4991 Dihedral : 11.073 172.352 4083 Min Nonbonded Distance : 2.109 Molprobity Statistics. All-atom Clashscore : 12.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.22 % Favored : 94.78 % Rotamer: Outliers : 3.43 % Allowed : 22.22 % Favored : 74.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.30 (0.14), residues: 3448 helix: -1.38 (0.13), residues: 1574 sheet: -2.54 (0.26), residues: 318 loop : -1.29 (0.16), residues: 1556 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP D 543 HIS 0.013 0.001 HIS E 281 PHE 0.020 0.001 PHE F 276 TYR 0.022 0.001 TYR F 322 ARG 0.008 0.000 ARG F 631 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6896 Ramachandran restraints generated. 3448 Oldfield, 0 Emsley, 3448 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6896 Ramachandran restraints generated. 3448 Oldfield, 0 Emsley, 3448 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 510 residues out of total 2916 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 100 poor density : 410 time to evaluate : 3.353 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 305 ARG cc_start: 0.6157 (mtt-85) cc_final: 0.5542 (mtm-85) REVERT: C 307 GLU cc_start: 0.8428 (mt-10) cc_final: 0.8131 (mt-10) REVERT: C 561 ARG cc_start: 0.7291 (mtm110) cc_final: 0.7071 (ptt180) REVERT: C 613 GLU cc_start: 0.8100 (tp30) cc_final: 0.7893 (tp30) REVERT: C 710 ARG cc_start: 0.7827 (mtt90) cc_final: 0.7529 (mtt-85) REVERT: F 251 TYR cc_start: 0.5481 (m-80) cc_final: 0.5133 (m-80) REVERT: F 275 LEU cc_start: 0.6396 (tp) cc_final: 0.5946 (tm) REVERT: F 276 PHE cc_start: 0.6623 (m-10) cc_final: 0.6190 (m-80) REVERT: F 300 LYS cc_start: 0.3862 (tptp) cc_final: 0.3045 (mmtt) REVERT: F 320 ARG cc_start: 0.6102 (mtm110) cc_final: 0.5900 (mtt-85) REVERT: F 331 ARG cc_start: 0.6860 (tpp-160) cc_final: 0.5295 (ttm-80) REVERT: F 356 ARG cc_start: 0.3444 (tpt170) cc_final: 0.2609 (tmt-80) REVERT: F 585 ARG cc_start: 0.4938 (mtp85) cc_final: 0.4560 (tpm-80) REVERT: F 629 MET cc_start: 0.5399 (ttt) cc_final: 0.5074 (mmt) REVERT: F 638 MET cc_start: -0.0415 (mmp) cc_final: -0.0959 (mpt) REVERT: F 716 MET cc_start: 0.5736 (mtt) cc_final: 0.5418 (mmm) REVERT: F 800 LEU cc_start: 0.6906 (OUTLIER) cc_final: 0.6529 (pp) REVERT: E 164 TYR cc_start: 0.8119 (m-10) cc_final: 0.7769 (m-10) REVERT: E 217 GLU cc_start: 0.7071 (mt-10) cc_final: 0.6728 (mp0) REVERT: E 252 ARG cc_start: 0.6696 (mpp-170) cc_final: 0.5524 (tpt90) REVERT: E 317 ASP cc_start: 0.7247 (m-30) cc_final: 0.6896 (m-30) REVERT: E 532 THR cc_start: 0.7994 (OUTLIER) cc_final: 0.7740 (p) REVERT: E 561 ARG cc_start: 0.7186 (mtm110) cc_final: 0.6514 (ptp90) REVERT: E 629 MET cc_start: 0.9015 (ptt) cc_final: 0.8598 (ptp) REVERT: E 638 MET cc_start: 0.8445 (mtm) cc_final: 0.8105 (mtm) REVERT: E 656 TYR cc_start: 0.7775 (p90) cc_final: 0.7252 (p90) REVERT: E 696 ASP cc_start: 0.5911 (OUTLIER) cc_final: 0.5689 (t0) REVERT: E 752 GLU cc_start: 0.7220 (pm20) cc_final: 0.6986 (pm20) REVERT: E 780 LYS cc_start: 0.7810 (mtmt) cc_final: 0.7584 (mptm) REVERT: E 822 GLN cc_start: 0.7623 (mt0) cc_final: 0.7344 (tt0) REVERT: D 163 LYS cc_start: 0.8655 (mtmt) cc_final: 0.8095 (mptt) REVERT: D 527 LEU cc_start: 0.4483 (OUTLIER) cc_final: 0.4143 (pp) REVERT: D 535 GLU cc_start: 0.7228 (OUTLIER) cc_final: 0.6999 (pp20) REVERT: D 552 MET cc_start: 0.4671 (mmt) cc_final: 0.4240 (mmm) REVERT: D 695 ASP cc_start: 0.7225 (t0) cc_final: 0.6983 (t0) REVERT: D 750 ARG cc_start: 0.7622 (mtp85) cc_final: 0.7059 (mmp80) REVERT: B 162 LYS cc_start: 0.6474 (OUTLIER) cc_final: 0.5815 (mtmm) REVERT: B 268 LYS cc_start: 0.8067 (mmtt) cc_final: 0.7818 (mttt) REVERT: B 558 LYS cc_start: 0.8103 (tttm) cc_final: 0.7775 (ttpt) REVERT: B 560 LEU cc_start: 0.8961 (OUTLIER) cc_final: 0.8716 (mt) REVERT: B 634 MET cc_start: 0.8392 (mmm) cc_final: 0.8139 (mmm) REVERT: B 776 GLN cc_start: 0.8246 (mm-40) cc_final: 0.7856 (mt0) REVERT: B 832 GLN cc_start: 0.7833 (tt0) cc_final: 0.7582 (tm-30) REVERT: A 242 MET cc_start: 0.8277 (mmt) cc_final: 0.7969 (mmt) REVERT: A 551 MET cc_start: 0.1236 (mpp) cc_final: 0.1033 (mmm) REVERT: A 834 LEU cc_start: 0.1586 (OUTLIER) cc_final: 0.1000 (tm) outliers start: 100 outliers final: 32 residues processed: 470 average time/residue: 1.4671 time to fit residues: 798.7587 Evaluate side-chains 414 residues out of total 2916 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 374 time to evaluate : 2.928 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 228 VAL Chi-restraints excluded: chain C residue 314 THR Chi-restraints excluded: chain C residue 386 LEU Chi-restraints excluded: chain C residue 533 ASP Chi-restraints excluded: chain C residue 552 MET Chi-restraints excluded: chain F residue 662 LEU Chi-restraints excluded: chain F residue 800 LEU Chi-restraints excluded: chain E residue 190 THR Chi-restraints excluded: chain E residue 203 VAL Chi-restraints excluded: chain E residue 262 VAL Chi-restraints excluded: chain E residue 367 ASP Chi-restraints excluded: chain E residue 532 THR Chi-restraints excluded: chain E residue 540 LEU Chi-restraints excluded: chain E residue 696 ASP Chi-restraints excluded: chain E residue 758 ASP Chi-restraints excluded: chain E residue 843 VAL Chi-restraints excluded: chain D residue 232 LEU Chi-restraints excluded: chain D residue 242 MET Chi-restraints excluded: chain D residue 293 MET Chi-restraints excluded: chain D residue 298 MET Chi-restraints excluded: chain D residue 314 THR Chi-restraints excluded: chain D residue 527 LEU Chi-restraints excluded: chain D residue 532 THR Chi-restraints excluded: chain D residue 535 GLU Chi-restraints excluded: chain D residue 752 GLU Chi-restraints excluded: chain B residue 162 LYS Chi-restraints excluded: chain B residue 294 ASP Chi-restraints excluded: chain B residue 317 ASP Chi-restraints excluded: chain B residue 548 VAL Chi-restraints excluded: chain B residue 560 LEU Chi-restraints excluded: chain B residue 604 LEU Chi-restraints excluded: chain B residue 679 VAL Chi-restraints excluded: chain B residue 732 LEU Chi-restraints excluded: chain A residue 316 LEU Chi-restraints excluded: chain A residue 330 GLU Chi-restraints excluded: chain A residue 392 ASP Chi-restraints excluded: chain A residue 532 THR Chi-restraints excluded: chain A residue 693 VAL Chi-restraints excluded: chain A residue 716 MET Chi-restraints excluded: chain A residue 834 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 348 random chunks: chunk 113 optimal weight: 3.9990 chunk 302 optimal weight: 0.3980 chunk 66 optimal weight: 2.9990 chunk 197 optimal weight: 0.0870 chunk 83 optimal weight: 1.9990 chunk 336 optimal weight: 7.9990 chunk 279 optimal weight: 4.9990 chunk 155 optimal weight: 6.9990 chunk 27 optimal weight: 2.9990 chunk 111 optimal weight: 0.0470 chunk 176 optimal weight: 1.9990 overall best weight: 0.9060 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 297 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 719 ASN ** C 824 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 192 GLN E 595 ASN ** E 769 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 776 GLN D 334 GLN D 703 GLN D 776 GLN D 794 HIS B 174 GLN B 195 GLN B 719 ASN B 755 ASN B 822 GLN ** A 297 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 360 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 641 HIS Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7339 moved from start: 0.2872 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 28296 Z= 0.196 Angle : 0.566 9.446 38259 Z= 0.278 Chirality : 0.044 0.258 4328 Planarity : 0.004 0.070 4991 Dihedral : 10.953 171.878 4083 Min Nonbonded Distance : 2.120 Molprobity Statistics. All-atom Clashscore : 13.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.66 % Favored : 94.34 % Rotamer: Outliers : 3.70 % Allowed : 23.08 % Favored : 73.22 % 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: -2.06 (0.14), residues: 3448 helix: -1.11 (0.13), residues: 1569 sheet: -2.52 (0.25), residues: 343 loop : -1.18 (0.16), residues: 1536 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP D 543 HIS 0.012 0.001 HIS E 281 PHE 0.013 0.001 PHE F 276 TYR 0.023 0.001 TYR B 783 ARG 0.008 0.000 ARG F 631 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6896 Ramachandran restraints generated. 3448 Oldfield, 0 Emsley, 3448 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6896 Ramachandran restraints generated. 3448 Oldfield, 0 Emsley, 3448 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 499 residues out of total 2916 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 108 poor density : 391 time to evaluate : 3.369 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 305 ARG cc_start: 0.6172 (mtt-85) cc_final: 0.5741 (mtm-85) REVERT: C 307 GLU cc_start: 0.8442 (mt-10) cc_final: 0.8201 (mt-10) REVERT: C 561 ARG cc_start: 0.7367 (mtm110) cc_final: 0.7131 (ptt180) REVERT: C 613 GLU cc_start: 0.8110 (tp30) cc_final: 0.7887 (tp30) REVERT: C 710 ARG cc_start: 0.7857 (mtt90) cc_final: 0.7544 (mtt-85) REVERT: F 251 TYR cc_start: 0.5439 (m-80) cc_final: 0.5089 (m-80) REVERT: F 264 ASN cc_start: 0.5902 (OUTLIER) cc_final: 0.5499 (t0) REVERT: F 275 LEU cc_start: 0.6234 (tp) cc_final: 0.5786 (tm) REVERT: F 276 PHE cc_start: 0.6654 (m-10) cc_final: 0.6196 (m-80) REVERT: F 300 LYS cc_start: 0.3869 (tptp) cc_final: 0.3021 (mmtt) REVERT: F 331 ARG cc_start: 0.6966 (tpp-160) cc_final: 0.5407 (ttm-80) REVERT: F 356 ARG cc_start: 0.3365 (tpt170) cc_final: 0.2610 (tmt-80) REVERT: F 585 ARG cc_start: 0.4929 (mtp85) cc_final: 0.4520 (tpm-80) REVERT: F 629 MET cc_start: 0.5409 (ttt) cc_final: 0.5092 (mmt) REVERT: F 638 MET cc_start: -0.0400 (mmp) cc_final: -0.1037 (mpt) REVERT: F 793 ILE cc_start: 0.7190 (OUTLIER) cc_final: 0.6859 (tp) REVERT: F 800 LEU cc_start: 0.6860 (OUTLIER) cc_final: 0.6468 (pp) REVERT: E 164 TYR cc_start: 0.8156 (m-10) cc_final: 0.7887 (m-80) REVERT: E 217 GLU cc_start: 0.7077 (mt-10) cc_final: 0.6724 (mp0) REVERT: E 252 ARG cc_start: 0.6707 (mpp-170) cc_final: 0.5529 (tpt170) REVERT: E 277 ILE cc_start: 0.0155 (OUTLIER) cc_final: -0.0118 (tp) REVERT: E 317 ASP cc_start: 0.7242 (m-30) cc_final: 0.6907 (m-30) REVERT: E 532 THR cc_start: 0.8024 (OUTLIER) cc_final: 0.7771 (p) REVERT: E 561 ARG cc_start: 0.7050 (mtm110) cc_final: 0.6707 (ptt90) REVERT: E 629 MET cc_start: 0.9033 (ptt) cc_final: 0.8596 (ptp) REVERT: E 638 MET cc_start: 0.8443 (mtm) cc_final: 0.8052 (mtm) REVERT: E 656 TYR cc_start: 0.7822 (p90) cc_final: 0.7248 (p90) REVERT: E 698 ARG cc_start: 0.8034 (OUTLIER) cc_final: 0.6982 (mmm160) REVERT: E 737 MET cc_start: 0.7948 (tpp) cc_final: 0.7437 (tpt) REVERT: E 752 GLU cc_start: 0.7233 (pm20) cc_final: 0.7006 (pm20) REVERT: E 780 LYS cc_start: 0.7838 (mtmt) cc_final: 0.7604 (mptm) REVERT: E 822 GLN cc_start: 0.7666 (mt0) cc_final: 0.7417 (tt0) REVERT: D 163 LYS cc_start: 0.8640 (mtmt) cc_final: 0.8079 (mptt) REVERT: D 527 LEU cc_start: 0.4518 (OUTLIER) cc_final: 0.4204 (pp) REVERT: D 535 GLU cc_start: 0.7353 (OUTLIER) cc_final: 0.7084 (pp20) REVERT: D 552 MET cc_start: 0.4679 (mmt) cc_final: 0.4271 (mmm) REVERT: D 695 ASP cc_start: 0.7267 (t0) cc_final: 0.7028 (t0) REVERT: D 750 ARG cc_start: 0.7634 (mtp85) cc_final: 0.7070 (mmp80) REVERT: D 823 GLN cc_start: 0.7646 (mt0) cc_final: 0.7254 (mt0) REVERT: B 162 LYS cc_start: 0.6495 (OUTLIER) cc_final: 0.5819 (mtmm) REVERT: B 268 LYS cc_start: 0.8058 (mmtt) cc_final: 0.7834 (mttt) REVERT: B 558 LYS cc_start: 0.8110 (tttm) cc_final: 0.7809 (ttpp) REVERT: B 560 LEU cc_start: 0.8944 (OUTLIER) cc_final: 0.8664 (mt) REVERT: B 634 MET cc_start: 0.8398 (mmm) cc_final: 0.8122 (mmm) REVERT: B 776 GLN cc_start: 0.8268 (mm-40) cc_final: 0.7877 (mt0) REVERT: B 832 GLN cc_start: 0.7822 (tt0) cc_final: 0.7578 (tm-30) REVERT: A 242 MET cc_start: 0.8246 (mmt) cc_final: 0.7865 (mmt) REVERT: A 392 ASP cc_start: 0.7395 (OUTLIER) cc_final: 0.7126 (m-30) REVERT: A 551 MET cc_start: 0.1283 (mpp) cc_final: 0.1068 (mmm) REVERT: A 834 LEU cc_start: 0.1647 (OUTLIER) cc_final: 0.1055 (tm) outliers start: 108 outliers final: 45 residues processed: 461 average time/residue: 1.5182 time to fit residues: 821.7105 Evaluate side-chains 425 residues out of total 2916 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 57 poor density : 368 time to evaluate : 3.392 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 228 VAL Chi-restraints excluded: chain C residue 314 THR Chi-restraints excluded: chain C residue 386 LEU Chi-restraints excluded: chain C residue 393 LEU Chi-restraints excluded: chain C residue 533 ASP Chi-restraints excluded: chain C residue 716 MET Chi-restraints excluded: chain F residue 264 ASN Chi-restraints excluded: chain F residue 647 VAL Chi-restraints excluded: chain F residue 662 LEU Chi-restraints excluded: chain F residue 793 ILE Chi-restraints excluded: chain F residue 800 LEU Chi-restraints excluded: chain F residue 806 ASN Chi-restraints excluded: chain E residue 190 THR Chi-restraints excluded: chain E residue 203 VAL Chi-restraints excluded: chain E residue 277 ILE Chi-restraints excluded: chain E residue 316 LEU Chi-restraints excluded: chain E residue 367 ASP Chi-restraints excluded: chain E residue 532 THR Chi-restraints excluded: chain E residue 540 LEU Chi-restraints excluded: chain E residue 698 ARG Chi-restraints excluded: chain E residue 758 ASP Chi-restraints excluded: chain D residue 232 LEU Chi-restraints excluded: chain D residue 242 MET Chi-restraints excluded: chain D residue 293 MET Chi-restraints excluded: chain D residue 298 MET Chi-restraints excluded: chain D residue 314 THR Chi-restraints excluded: chain D residue 527 LEU Chi-restraints excluded: chain D residue 532 THR Chi-restraints excluded: chain D residue 535 GLU Chi-restraints excluded: chain D residue 752 GLU Chi-restraints excluded: chain D residue 771 ILE Chi-restraints excluded: chain D residue 837 GLU Chi-restraints excluded: chain B residue 162 LYS Chi-restraints excluded: chain B residue 294 ASP Chi-restraints excluded: chain B residue 314 THR Chi-restraints excluded: chain B residue 317 ASP Chi-restraints excluded: chain B residue 548 VAL Chi-restraints excluded: chain B residue 560 LEU Chi-restraints excluded: chain B residue 604 LEU Chi-restraints excluded: chain B residue 629 MET Chi-restraints excluded: chain B residue 638 MET Chi-restraints excluded: chain B residue 679 VAL Chi-restraints excluded: chain B residue 685 ASP Chi-restraints excluded: chain B residue 689 ILE Chi-restraints excluded: chain B residue 732 LEU Chi-restraints excluded: chain B residue 744 VAL Chi-restraints excluded: chain B residue 757 ILE Chi-restraints excluded: chain B residue 780 LYS Chi-restraints excluded: chain A residue 232 LEU Chi-restraints excluded: chain A residue 316 LEU Chi-restraints excluded: chain A residue 330 GLU Chi-restraints excluded: chain A residue 392 ASP Chi-restraints excluded: chain A residue 532 THR Chi-restraints excluded: chain A residue 693 VAL Chi-restraints excluded: chain A residue 716 MET Chi-restraints excluded: chain A residue 724 LEU Chi-restraints excluded: chain A residue 834 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 348 random chunks: chunk 324 optimal weight: 0.0870 chunk 37 optimal weight: 0.0970 chunk 191 optimal weight: 3.9990 chunk 245 optimal weight: 0.9980 chunk 190 optimal weight: 0.9990 chunk 283 optimal weight: 10.0000 chunk 188 optimal weight: 3.9990 chunk 335 optimal weight: 0.9990 chunk 209 optimal weight: 0.2980 chunk 204 optimal weight: 0.5980 chunk 154 optimal weight: 0.5980 overall best weight: 0.3356 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 297 ASN ** C 824 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 703 GLN E 192 GLN E 726 GLN ** E 769 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 334 GLN D 703 GLN D 794 HIS B 174 GLN B 195 GLN B 719 ASN ** A 297 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 360 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 641 HIS Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7295 moved from start: 0.3120 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 28296 Z= 0.155 Angle : 0.556 9.207 38259 Z= 0.272 Chirality : 0.043 0.221 4328 Planarity : 0.004 0.058 4991 Dihedral : 10.613 173.046 4083 Min Nonbonded Distance : 2.139 Molprobity Statistics. All-atom Clashscore : 12.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.99 % Favored : 95.01 % Rotamer: Outliers : 3.19 % Allowed : 23.70 % Favored : 73.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.74 (0.14), residues: 3448 helix: -0.81 (0.13), residues: 1567 sheet: -2.36 (0.27), residues: 312 loop : -1.09 (0.16), residues: 1569 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 543 HIS 0.009 0.001 HIS E 281 PHE 0.019 0.001 PHE F 603 TYR 0.020 0.001 TYR B 783 ARG 0.008 0.000 ARG B 819 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6896 Ramachandran restraints generated. 3448 Oldfield, 0 Emsley, 3448 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6896 Ramachandran restraints generated. 3448 Oldfield, 0 Emsley, 3448 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 489 residues out of total 2916 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 93 poor density : 396 time to evaluate : 3.252 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 305 ARG cc_start: 0.6120 (mtt-85) cc_final: 0.5725 (mtm-85) REVERT: C 307 GLU cc_start: 0.8416 (mt-10) cc_final: 0.8156 (mt-10) REVERT: C 561 ARG cc_start: 0.7256 (mtm110) cc_final: 0.7052 (ptt180) REVERT: C 613 GLU cc_start: 0.8085 (tp30) cc_final: 0.7878 (tp30) REVERT: C 838 LEU cc_start: 0.8324 (mp) cc_final: 0.8123 (mt) REVERT: F 251 TYR cc_start: 0.5355 (m-80) cc_final: 0.4827 (m-80) REVERT: F 264 ASN cc_start: 0.5901 (m-40) cc_final: 0.5499 (t0) REVERT: F 275 LEU cc_start: 0.6189 (tp) cc_final: 0.5712 (tm) REVERT: F 276 PHE cc_start: 0.6605 (m-10) cc_final: 0.6075 (m-80) REVERT: F 300 LYS cc_start: 0.3897 (tptp) cc_final: 0.3009 (mmtt) REVERT: F 331 ARG cc_start: 0.6995 (tpp-160) cc_final: 0.5362 (ttm-80) REVERT: F 356 ARG cc_start: 0.3218 (tpt170) cc_final: 0.2555 (tmt-80) REVERT: F 585 ARG cc_start: 0.4812 (mtp85) cc_final: 0.4426 (tpm-80) REVERT: F 629 MET cc_start: 0.5347 (ttt) cc_final: 0.5037 (mmt) REVERT: F 638 MET cc_start: -0.0575 (mmp) cc_final: -0.1162 (mpt) REVERT: F 716 MET cc_start: 0.5680 (mtt) cc_final: 0.3381 (tpp) REVERT: F 800 LEU cc_start: 0.6736 (OUTLIER) cc_final: 0.6349 (pp) REVERT: E 164 TYR cc_start: 0.8122 (m-10) cc_final: 0.7207 (m-10) REVERT: E 217 GLU cc_start: 0.7081 (mt-10) cc_final: 0.6732 (mp0) REVERT: E 252 ARG cc_start: 0.6610 (mpp-170) cc_final: 0.5446 (tpt170) REVERT: E 277 ILE cc_start: 0.0022 (OUTLIER) cc_final: -0.0296 (tp) REVERT: E 317 ASP cc_start: 0.7013 (m-30) cc_final: 0.6694 (m-30) REVERT: E 561 ARG cc_start: 0.7008 (mtm110) cc_final: 0.6684 (ptt90) REVERT: E 629 MET cc_start: 0.9033 (ptt) cc_final: 0.8564 (ptp) REVERT: E 638 MET cc_start: 0.8352 (mtm) cc_final: 0.7945 (mtm) REVERT: E 656 TYR cc_start: 0.7787 (p90) cc_final: 0.7273 (p90) REVERT: E 698 ARG cc_start: 0.8120 (OUTLIER) cc_final: 0.7211 (mmm160) REVERT: E 737 MET cc_start: 0.7913 (tpp) cc_final: 0.7396 (tpt) REVERT: E 752 GLU cc_start: 0.7247 (pm20) cc_final: 0.7043 (pm20) REVERT: E 780 LYS cc_start: 0.7825 (mtmt) cc_final: 0.7501 (mmtp) REVERT: D 163 LYS cc_start: 0.8628 (mtmt) cc_final: 0.8079 (mptt) REVERT: D 527 LEU cc_start: 0.4466 (OUTLIER) cc_final: 0.4159 (pp) REVERT: D 535 GLU cc_start: 0.7081 (OUTLIER) cc_final: 0.6876 (pp20) REVERT: D 552 MET cc_start: 0.4644 (mmt) cc_final: 0.4242 (mmm) REVERT: D 750 ARG cc_start: 0.7627 (mtp85) cc_final: 0.7067 (mmp80) REVERT: D 857 GLN cc_start: 0.6262 (OUTLIER) cc_final: 0.6018 (mp10) REVERT: B 162 LYS cc_start: 0.6456 (OUTLIER) cc_final: 0.5802 (mtmm) REVERT: B 198 THR cc_start: 0.8222 (t) cc_final: 0.7963 (p) REVERT: B 242 MET cc_start: 0.8032 (mmt) cc_final: 0.7686 (mmt) REVERT: B 268 LYS cc_start: 0.8037 (mmtt) cc_final: 0.7816 (mttt) REVERT: B 558 LYS cc_start: 0.8116 (tttm) cc_final: 0.7825 (ttpt) REVERT: B 560 LEU cc_start: 0.8872 (OUTLIER) cc_final: 0.8587 (mt) REVERT: B 634 MET cc_start: 0.8424 (mmm) cc_final: 0.8198 (mmm) REVERT: B 705 ARG cc_start: 0.7662 (tpp-160) cc_final: 0.7221 (ttp-110) REVERT: B 776 GLN cc_start: 0.8226 (mm-40) cc_final: 0.7875 (mt0) REVERT: B 784 LYS cc_start: 0.7216 (mmtm) cc_final: 0.7000 (mmtm) REVERT: B 832 GLN cc_start: 0.7948 (tt0) cc_final: 0.7568 (tm-30) REVERT: A 834 LEU cc_start: 0.1688 (OUTLIER) cc_final: 0.1110 (tm) outliers start: 93 outliers final: 44 residues processed: 456 average time/residue: 1.4338 time to fit residues: 759.1322 Evaluate side-chains 427 residues out of total 2916 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 374 time to evaluate : 3.104 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 228 VAL Chi-restraints excluded: chain C residue 314 THR Chi-restraints excluded: chain C residue 386 LEU Chi-restraints excluded: chain C residue 393 LEU Chi-restraints excluded: chain C residue 533 ASP Chi-restraints excluded: chain C residue 580 VAL Chi-restraints excluded: chain C residue 716 MET Chi-restraints excluded: chain F residue 314 THR Chi-restraints excluded: chain F residue 338 VAL Chi-restraints excluded: chain F residue 647 VAL Chi-restraints excluded: chain F residue 662 LEU Chi-restraints excluded: chain F residue 800 LEU Chi-restraints excluded: chain F residue 806 ASN Chi-restraints excluded: chain E residue 190 THR Chi-restraints excluded: chain E residue 277 ILE Chi-restraints excluded: chain E residue 316 LEU Chi-restraints excluded: chain E residue 367 ASP Chi-restraints excluded: chain E residue 540 LEU Chi-restraints excluded: chain E residue 698 ARG Chi-restraints excluded: chain E residue 758 ASP Chi-restraints excluded: chain E residue 843 VAL Chi-restraints excluded: chain D residue 232 LEU Chi-restraints excluded: chain D residue 242 MET Chi-restraints excluded: chain D residue 293 MET Chi-restraints excluded: chain D residue 298 MET Chi-restraints excluded: chain D residue 314 THR Chi-restraints excluded: chain D residue 527 LEU Chi-restraints excluded: chain D residue 532 THR Chi-restraints excluded: chain D residue 535 GLU Chi-restraints excluded: chain D residue 752 GLU Chi-restraints excluded: chain D residue 771 ILE Chi-restraints excluded: chain D residue 837 GLU Chi-restraints excluded: chain D residue 857 GLN Chi-restraints excluded: chain B residue 162 LYS Chi-restraints excluded: chain B residue 294 ASP Chi-restraints excluded: chain B residue 314 THR Chi-restraints excluded: chain B residue 317 ASP Chi-restraints excluded: chain B residue 548 VAL Chi-restraints excluded: chain B residue 560 LEU Chi-restraints excluded: chain B residue 604 LEU Chi-restraints excluded: chain B residue 629 MET Chi-restraints excluded: chain B residue 638 MET Chi-restraints excluded: chain B residue 679 VAL Chi-restraints excluded: chain B residue 689 ILE Chi-restraints excluded: chain B residue 732 LEU Chi-restraints excluded: chain B residue 780 LYS Chi-restraints excluded: chain A residue 232 LEU Chi-restraints excluded: chain A residue 330 GLU Chi-restraints excluded: chain A residue 532 THR Chi-restraints excluded: chain A residue 642 SER Chi-restraints excluded: chain A residue 693 VAL Chi-restraints excluded: chain A residue 716 MET Chi-restraints excluded: chain A residue 834 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 348 random chunks: chunk 207 optimal weight: 3.9990 chunk 133 optimal weight: 0.9980 chunk 200 optimal weight: 5.9990 chunk 101 optimal weight: 9.9990 chunk 65 optimal weight: 0.5980 chunk 64 optimal weight: 8.9990 chunk 213 optimal weight: 0.9990 chunk 228 optimal weight: 0.2980 chunk 165 optimal weight: 6.9990 chunk 31 optimal weight: 2.9990 chunk 263 optimal weight: 0.8980 overall best weight: 0.7582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 824 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 703 GLN E 192 GLN ** E 769 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 776 GLN D 334 GLN D 703 GLN D 794 HIS ** D 822 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 195 GLN B 719 ASN B 822 GLN ** A 297 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 360 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7315 moved from start: 0.3217 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 28296 Z= 0.183 Angle : 0.565 9.658 38259 Z= 0.276 Chirality : 0.044 0.262 4328 Planarity : 0.004 0.070 4991 Dihedral : 10.501 172.918 4083 Min Nonbonded Distance : 2.145 Molprobity Statistics. All-atom Clashscore : 13.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.08 % Favored : 94.92 % Rotamer: Outliers : 2.98 % Allowed : 24.21 % Favored : 72.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.56 (0.14), residues: 3448 helix: -0.63 (0.13), residues: 1562 sheet: -2.29 (0.26), residues: 329 loop : -1.02 (0.16), residues: 1557 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 543 HIS 0.008 0.001 HIS A 641 PHE 0.011 0.001 PHE E 276 TYR 0.011 0.001 TYR C 357 ARG 0.009 0.000 ARG C 705 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6896 Ramachandran restraints generated. 3448 Oldfield, 0 Emsley, 3448 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6896 Ramachandran restraints generated. 3448 Oldfield, 0 Emsley, 3448 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 471 residues out of total 2916 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 87 poor density : 384 time to evaluate : 3.347 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 305 ARG cc_start: 0.6214 (mtt-85) cc_final: 0.5811 (mtm-85) REVERT: C 307 GLU cc_start: 0.8445 (mt-10) cc_final: 0.8204 (mt-10) REVERT: C 613 GLU cc_start: 0.8112 (tp30) cc_final: 0.7859 (tp30) REVERT: F 251 TYR cc_start: 0.5610 (m-80) cc_final: 0.5097 (m-80) REVERT: F 264 ASN cc_start: 0.5997 (OUTLIER) cc_final: 0.5620 (t0) REVERT: F 275 LEU cc_start: 0.6166 (tp) cc_final: 0.5678 (tm) REVERT: F 276 PHE cc_start: 0.6685 (m-10) cc_final: 0.6164 (m-80) REVERT: F 300 LYS cc_start: 0.4023 (tptp) cc_final: 0.3101 (mmtt) REVERT: F 331 ARG cc_start: 0.6969 (tpp-160) cc_final: 0.5398 (ttm-80) REVERT: F 356 ARG cc_start: 0.3296 (tpt170) cc_final: 0.2614 (tmt-80) REVERT: F 585 ARG cc_start: 0.4843 (mtp85) cc_final: 0.4426 (tpm-80) REVERT: F 629 MET cc_start: 0.5416 (ttt) cc_final: 0.5048 (mmt) REVERT: F 638 MET cc_start: -0.0846 (mmp) cc_final: -0.1502 (mpt) REVERT: F 716 MET cc_start: 0.5434 (mtt) cc_final: 0.3342 (tpt) REVERT: F 781 ARG cc_start: 0.7669 (ptp-110) cc_final: 0.7465 (ttp-110) REVERT: F 793 ILE cc_start: 0.7172 (OUTLIER) cc_final: 0.6782 (tp) REVERT: F 800 LEU cc_start: 0.6830 (OUTLIER) cc_final: 0.6426 (pp) REVERT: E 164 TYR cc_start: 0.8129 (m-10) cc_final: 0.7371 (m-10) REVERT: E 217 GLU cc_start: 0.6998 (mt-10) cc_final: 0.6629 (mp0) REVERT: E 277 ILE cc_start: 0.0227 (OUTLIER) cc_final: -0.0140 (tp) REVERT: E 561 ARG cc_start: 0.7040 (mtm110) cc_final: 0.6690 (ptt90) REVERT: E 629 MET cc_start: 0.9084 (ptt) cc_final: 0.8596 (ptp) REVERT: E 638 MET cc_start: 0.8378 (mtm) cc_final: 0.8013 (mtm) REVERT: E 656 TYR cc_start: 0.7728 (p90) cc_final: 0.7221 (p90) REVERT: E 698 ARG cc_start: 0.8124 (OUTLIER) cc_final: 0.7138 (mmm160) REVERT: E 750 ARG cc_start: 0.7210 (mtm-85) cc_final: 0.6893 (mtm-85) REVERT: E 780 LYS cc_start: 0.7833 (mtmt) cc_final: 0.7512 (mmtp) REVERT: D 163 LYS cc_start: 0.8612 (mtmt) cc_final: 0.8063 (mptt) REVERT: D 527 LEU cc_start: 0.4496 (OUTLIER) cc_final: 0.4223 (pp) REVERT: D 552 MET cc_start: 0.4651 (mmt) cc_final: 0.4299 (mmm) REVERT: D 750 ARG cc_start: 0.7636 (mtp85) cc_final: 0.7071 (mmp80) REVERT: B 162 LYS cc_start: 0.6449 (OUTLIER) cc_final: 0.5768 (mtmm) REVERT: B 198 THR cc_start: 0.8313 (t) cc_final: 0.8056 (p) REVERT: B 242 MET cc_start: 0.8024 (mmt) cc_final: 0.7676 (mmt) REVERT: B 268 LYS cc_start: 0.8047 (mmtt) cc_final: 0.7828 (mttt) REVERT: B 552 MET cc_start: 0.4832 (OUTLIER) cc_final: 0.4324 (mpp) REVERT: B 558 LYS cc_start: 0.8109 (tttm) cc_final: 0.7854 (ttpt) REVERT: B 560 LEU cc_start: 0.8869 (OUTLIER) cc_final: 0.8606 (mt) REVERT: B 634 MET cc_start: 0.8411 (mmm) cc_final: 0.8174 (mmm) REVERT: B 776 GLN cc_start: 0.8246 (mm-40) cc_final: 0.7898 (mt0) REVERT: B 832 GLN cc_start: 0.7953 (tt0) cc_final: 0.7538 (tm-30) REVERT: A 551 MET cc_start: 0.1350 (mmm) cc_final: 0.0571 (mpp) REVERT: A 834 LEU cc_start: 0.1759 (OUTLIER) cc_final: 0.1196 (tm) outliers start: 87 outliers final: 45 residues processed: 434 average time/residue: 1.4710 time to fit residues: 742.3064 Evaluate side-chains 431 residues out of total 2916 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 55 poor density : 376 time to evaluate : 3.243 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 162 LYS Chi-restraints excluded: chain C residue 228 VAL Chi-restraints excluded: chain C residue 314 THR Chi-restraints excluded: chain C residue 386 LEU Chi-restraints excluded: chain C residue 393 LEU Chi-restraints excluded: chain C residue 533 ASP Chi-restraints excluded: chain C residue 580 VAL Chi-restraints excluded: chain C residue 716 MET Chi-restraints excluded: chain C residue 761 VAL Chi-restraints excluded: chain F residue 264 ASN Chi-restraints excluded: chain F residue 338 VAL Chi-restraints excluded: chain F residue 371 VAL Chi-restraints excluded: chain F residue 574 ASN Chi-restraints excluded: chain F residue 647 VAL Chi-restraints excluded: chain F residue 793 ILE Chi-restraints excluded: chain F residue 800 LEU Chi-restraints excluded: chain F residue 806 ASN Chi-restraints excluded: chain E residue 190 THR Chi-restraints excluded: chain E residue 277 ILE Chi-restraints excluded: chain E residue 316 LEU Chi-restraints excluded: chain E residue 367 ASP Chi-restraints excluded: chain E residue 540 LEU Chi-restraints excluded: chain E residue 698 ARG Chi-restraints excluded: chain E residue 758 ASP Chi-restraints excluded: chain E residue 793 ILE Chi-restraints excluded: chain E residue 843 VAL Chi-restraints excluded: chain D residue 242 MET Chi-restraints excluded: chain D residue 293 MET Chi-restraints excluded: chain D residue 298 MET Chi-restraints excluded: chain D residue 314 THR Chi-restraints excluded: chain D residue 527 LEU Chi-restraints excluded: chain D residue 532 THR Chi-restraints excluded: chain D residue 771 ILE Chi-restraints excluded: chain D residue 837 GLU Chi-restraints excluded: chain B residue 162 LYS Chi-restraints excluded: chain B residue 294 ASP Chi-restraints excluded: chain B residue 314 THR Chi-restraints excluded: chain B residue 548 VAL Chi-restraints excluded: chain B residue 552 MET Chi-restraints excluded: chain B residue 560 LEU Chi-restraints excluded: chain B residue 604 LEU Chi-restraints excluded: chain B residue 629 MET Chi-restraints excluded: chain B residue 638 MET Chi-restraints excluded: chain B residue 679 VAL Chi-restraints excluded: chain B residue 689 ILE Chi-restraints excluded: chain B residue 732 LEU Chi-restraints excluded: chain B residue 744 VAL Chi-restraints excluded: chain B residue 780 LYS Chi-restraints excluded: chain A residue 232 LEU Chi-restraints excluded: chain A residue 330 GLU Chi-restraints excluded: chain A residue 532 THR Chi-restraints excluded: chain A residue 642 SER Chi-restraints excluded: chain A residue 693 VAL Chi-restraints excluded: chain A residue 716 MET Chi-restraints excluded: chain A residue 834 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 348 random chunks: chunk 305 optimal weight: 0.0970 chunk 321 optimal weight: 2.9990 chunk 293 optimal weight: 0.7980 chunk 312 optimal weight: 20.0000 chunk 188 optimal weight: 0.5980 chunk 136 optimal weight: 0.9980 chunk 245 optimal weight: 0.4980 chunk 95 optimal weight: 30.0000 chunk 282 optimal weight: 6.9990 chunk 295 optimal weight: 10.0000 chunk 311 optimal weight: 6.9990 overall best weight: 0.5978 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 719 ASN ** C 806 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 824 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 703 GLN E 192 GLN ** E 769 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 334 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 703 GLN D 794 HIS B 195 GLN B 719 ASN B 822 GLN ** A 360 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 641 HIS Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7298 moved from start: 0.3350 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 28296 Z= 0.170 Angle : 0.566 10.126 38259 Z= 0.277 Chirality : 0.044 0.245 4328 Planarity : 0.004 0.073 4991 Dihedral : 10.338 173.730 4083 Min Nonbonded Distance : 2.043 Molprobity Statistics. All-atom Clashscore : 13.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.93 % Favored : 95.07 % Rotamer: Outliers : 2.64 % Allowed : 25.03 % Favored : 72.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.39 (0.14), residues: 3448 helix: -0.48 (0.14), residues: 1549 sheet: -2.22 (0.27), residues: 327 loop : -0.93 (0.16), residues: 1572 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 543 HIS 0.005 0.001 HIS A 281 PHE 0.010 0.001 PHE D 729 TYR 0.011 0.001 TYR C 357 ARG 0.008 0.000 ARG C 705 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6896 Ramachandran restraints generated. 3448 Oldfield, 0 Emsley, 3448 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6896 Ramachandran restraints generated. 3448 Oldfield, 0 Emsley, 3448 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 469 residues out of total 2916 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 77 poor density : 392 time to evaluate : 3.309 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 305 ARG cc_start: 0.6179 (mtt-85) cc_final: 0.5781 (mtm-85) REVERT: C 307 GLU cc_start: 0.8429 (mt-10) cc_final: 0.8183 (mt-10) REVERT: C 613 GLU cc_start: 0.8108 (tp30) cc_final: 0.7850 (tp30) REVERT: F 264 ASN cc_start: 0.6007 (m-40) cc_final: 0.5630 (t0) REVERT: F 275 LEU cc_start: 0.6169 (tp) cc_final: 0.5678 (tm) REVERT: F 276 PHE cc_start: 0.6673 (m-10) cc_final: 0.6175 (m-80) REVERT: F 300 LYS cc_start: 0.3949 (OUTLIER) cc_final: 0.3037 (mmtt) REVERT: F 331 ARG cc_start: 0.6959 (tpp-160) cc_final: 0.5379 (ttm-80) REVERT: F 585 ARG cc_start: 0.4761 (mtp85) cc_final: 0.4376 (tpm-80) REVERT: F 629 MET cc_start: 0.5457 (ttt) cc_final: 0.5067 (mmt) REVERT: F 638 MET cc_start: -0.0894 (mmp) cc_final: -0.1583 (mpt) REVERT: F 716 MET cc_start: 0.5409 (mtt) cc_final: 0.3383 (tpp) REVERT: F 793 ILE cc_start: 0.7148 (OUTLIER) cc_final: 0.6744 (tp) REVERT: F 800 LEU cc_start: 0.6802 (OUTLIER) cc_final: 0.6403 (pp) REVERT: E 164 TYR cc_start: 0.8125 (m-10) cc_final: 0.7436 (m-10) REVERT: E 217 GLU cc_start: 0.6966 (mt-10) cc_final: 0.6609 (mp0) REVERT: E 277 ILE cc_start: 0.0331 (OUTLIER) cc_final: -0.0072 (tp) REVERT: E 561 ARG cc_start: 0.7030 (mtm110) cc_final: 0.6710 (ptt90) REVERT: E 629 MET cc_start: 0.9082 (ptt) cc_final: 0.8588 (ptp) REVERT: E 638 MET cc_start: 0.8370 (mtm) cc_final: 0.7924 (mtm) REVERT: E 656 TYR cc_start: 0.7730 (p90) cc_final: 0.7208 (p90) REVERT: E 698 ARG cc_start: 0.8098 (OUTLIER) cc_final: 0.7157 (mmm160) REVERT: E 734 TYR cc_start: 0.7639 (t80) cc_final: 0.7395 (t80) REVERT: E 780 LYS cc_start: 0.7837 (mtmt) cc_final: 0.7604 (mptm) REVERT: D 163 LYS cc_start: 0.8612 (mtmt) cc_final: 0.8072 (mptt) REVERT: D 527 LEU cc_start: 0.4438 (OUTLIER) cc_final: 0.4186 (pp) REVERT: D 552 MET cc_start: 0.4627 (mmt) cc_final: 0.4249 (mmm) REVERT: D 750 ARG cc_start: 0.7634 (mtp85) cc_final: 0.7068 (mmp80) REVERT: B 162 LYS cc_start: 0.6420 (OUTLIER) cc_final: 0.5752 (mtmm) REVERT: B 198 THR cc_start: 0.8345 (t) cc_final: 0.8117 (p) REVERT: B 242 MET cc_start: 0.8010 (mmt) cc_final: 0.7650 (mmt) REVERT: B 268 LYS cc_start: 0.8040 (mmtt) cc_final: 0.7827 (mttt) REVERT: B 552 MET cc_start: 0.5062 (OUTLIER) cc_final: 0.4525 (mpp) REVERT: B 558 LYS cc_start: 0.8117 (tttm) cc_final: 0.7870 (ttpt) REVERT: B 634 MET cc_start: 0.8419 (mmm) cc_final: 0.8120 (mmm) REVERT: B 705 ARG cc_start: 0.7670 (tpp-160) cc_final: 0.7225 (ttp-110) REVERT: B 776 GLN cc_start: 0.8250 (mm-40) cc_final: 0.7911 (mt0) REVERT: B 819 ARG cc_start: 0.7910 (ttm-80) cc_final: 0.7661 (ttm-80) REVERT: B 832 GLN cc_start: 0.7889 (tt0) cc_final: 0.7505 (tm-30) REVERT: A 551 MET cc_start: 0.1160 (mmm) cc_final: 0.0126 (mpp) REVERT: A 598 ILE cc_start: 0.8736 (OUTLIER) cc_final: 0.8510 (mp) REVERT: A 633 ASP cc_start: 0.6513 (t70) cc_final: 0.6081 (p0) REVERT: A 716 MET cc_start: 0.8206 (OUTLIER) cc_final: 0.7995 (mtm) REVERT: A 834 LEU cc_start: 0.1805 (OUTLIER) cc_final: 0.1258 (tm) outliers start: 77 outliers final: 39 residues processed: 440 average time/residue: 1.4950 time to fit residues: 761.9424 Evaluate side-chains 417 residues out of total 2916 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 367 time to evaluate : 3.222 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 228 VAL Chi-restraints excluded: chain C residue 314 THR Chi-restraints excluded: chain C residue 386 LEU Chi-restraints excluded: chain C residue 393 LEU Chi-restraints excluded: chain C residue 533 ASP Chi-restraints excluded: chain C residue 580 VAL Chi-restraints excluded: chain C residue 716 MET Chi-restraints excluded: chain F residue 300 LYS Chi-restraints excluded: chain F residue 338 VAL Chi-restraints excluded: chain F residue 371 VAL Chi-restraints excluded: chain F residue 632 ILE Chi-restraints excluded: chain F residue 793 ILE Chi-restraints excluded: chain F residue 800 LEU Chi-restraints excluded: chain F residue 806 ASN Chi-restraints excluded: chain E residue 190 THR Chi-restraints excluded: chain E residue 277 ILE Chi-restraints excluded: chain E residue 316 LEU Chi-restraints excluded: chain E residue 367 ASP Chi-restraints excluded: chain E residue 540 LEU Chi-restraints excluded: chain E residue 698 ARG Chi-restraints excluded: chain E residue 758 ASP Chi-restraints excluded: chain E residue 843 VAL Chi-restraints excluded: chain D residue 242 MET Chi-restraints excluded: chain D residue 293 MET Chi-restraints excluded: chain D residue 298 MET Chi-restraints excluded: chain D residue 314 THR Chi-restraints excluded: chain D residue 527 LEU Chi-restraints excluded: chain D residue 532 THR Chi-restraints excluded: chain D residue 609 VAL Chi-restraints excluded: chain D residue 771 ILE Chi-restraints excluded: chain D residue 837 GLU Chi-restraints excluded: chain B residue 162 LYS Chi-restraints excluded: chain B residue 294 ASP Chi-restraints excluded: chain B residue 314 THR Chi-restraints excluded: chain B residue 548 VAL Chi-restraints excluded: chain B residue 552 MET Chi-restraints excluded: chain B residue 604 LEU Chi-restraints excluded: chain B residue 638 MET Chi-restraints excluded: chain B residue 679 VAL Chi-restraints excluded: chain B residue 719 ASN Chi-restraints excluded: chain B residue 732 LEU Chi-restraints excluded: chain B residue 744 VAL Chi-restraints excluded: chain A residue 232 LEU Chi-restraints excluded: chain A residue 330 GLU Chi-restraints excluded: chain A residue 532 THR Chi-restraints excluded: chain A residue 598 ILE Chi-restraints excluded: chain A residue 693 VAL Chi-restraints excluded: chain A residue 716 MET Chi-restraints excluded: chain A residue 724 LEU Chi-restraints excluded: chain A residue 834 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 348 random chunks: chunk 205 optimal weight: 0.0070 chunk 330 optimal weight: 7.9990 chunk 201 optimal weight: 0.8980 chunk 156 optimal weight: 0.6980 chunk 229 optimal weight: 3.9990 chunk 346 optimal weight: 20.0000 chunk 319 optimal weight: 5.9990 chunk 276 optimal weight: 0.6980 chunk 28 optimal weight: 0.9980 chunk 213 optimal weight: 0.9980 chunk 169 optimal weight: 0.8980 overall best weight: 0.6398 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 806 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 824 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 703 GLN E 192 GLN ** E 769 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 776 GLN ** D 334 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 703 GLN D 794 HIS D 806 ASN D 822 GLN B 195 GLN ** B 719 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 360 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7298 moved from start: 0.3417 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 28296 Z= 0.176 Angle : 0.573 10.156 38259 Z= 0.279 Chirality : 0.044 0.258 4328 Planarity : 0.004 0.071 4991 Dihedral : 10.254 173.555 4083 Min Nonbonded Distance : 2.155 Molprobity Statistics. All-atom Clashscore : 12.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.87 % Favored : 95.13 % Rotamer: Outliers : 2.26 % Allowed : 25.86 % Favored : 71.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.31 (0.15), residues: 3448 helix: -0.39 (0.14), residues: 1554 sheet: -2.24 (0.26), residues: 342 loop : -0.87 (0.16), residues: 1552 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 543 HIS 0.010 0.001 HIS E 281 PHE 0.009 0.001 PHE F 276 TYR 0.011 0.001 TYR C 357 ARG 0.009 0.000 ARG C 705 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6896 Ramachandran restraints generated. 3448 Oldfield, 0 Emsley, 3448 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6896 Ramachandran restraints generated. 3448 Oldfield, 0 Emsley, 3448 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 443 residues out of total 2916 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 66 poor density : 377 time to evaluate : 3.700 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 257 GLU cc_start: 0.8083 (tt0) cc_final: 0.7873 (tt0) REVERT: C 305 ARG cc_start: 0.6180 (mtt-85) cc_final: 0.5789 (mtm-85) REVERT: C 307 GLU cc_start: 0.8434 (mt-10) cc_final: 0.8181 (mt-10) REVERT: C 613 GLU cc_start: 0.8130 (tp30) cc_final: 0.7871 (tp30) REVERT: F 264 ASN cc_start: 0.6105 (OUTLIER) cc_final: 0.5678 (t0) REVERT: F 275 LEU cc_start: 0.6240 (tp) cc_final: 0.5743 (tm) REVERT: F 276 PHE cc_start: 0.6656 (m-10) cc_final: 0.6178 (m-80) REVERT: F 300 LYS cc_start: 0.3940 (OUTLIER) cc_final: 0.3017 (mmtt) REVERT: F 331 ARG cc_start: 0.6937 (tpp-160) cc_final: 0.5384 (ttm-80) REVERT: F 356 ARG cc_start: 0.3284 (tpt170) cc_final: 0.2625 (tmt-80) REVERT: F 585 ARG cc_start: 0.4756 (mtp85) cc_final: 0.4367 (tpm-80) REVERT: F 629 MET cc_start: 0.5384 (ttt) cc_final: 0.5041 (mmt) REVERT: F 638 MET cc_start: -0.0962 (mmp) cc_final: -0.1621 (mpt) REVERT: F 716 MET cc_start: 0.5432 (mtt) cc_final: 0.3483 (tpp) REVERT: F 793 ILE cc_start: 0.7126 (OUTLIER) cc_final: 0.6711 (tp) REVERT: F 800 LEU cc_start: 0.6842 (OUTLIER) cc_final: 0.6436 (pp) REVERT: E 164 TYR cc_start: 0.8112 (m-10) cc_final: 0.7520 (m-10) REVERT: E 217 GLU cc_start: 0.7016 (mt-10) cc_final: 0.6666 (mp0) REVERT: E 277 ILE cc_start: 0.0512 (OUTLIER) cc_final: 0.0092 (tp) REVERT: E 318 GLU cc_start: 0.7050 (tm-30) cc_final: 0.6450 (tm-30) REVERT: E 561 ARG cc_start: 0.7036 (mtm110) cc_final: 0.6716 (ptt90) REVERT: E 629 MET cc_start: 0.9098 (ptt) cc_final: 0.8601 (ptp) REVERT: E 638 MET cc_start: 0.8371 (mtm) cc_final: 0.7917 (mtm) REVERT: E 656 TYR cc_start: 0.7836 (p90) cc_final: 0.7356 (p90) REVERT: E 698 ARG cc_start: 0.8066 (OUTLIER) cc_final: 0.7106 (mmm160) REVERT: E 706 THR cc_start: 0.8590 (m) cc_final: 0.7857 (t) REVERT: E 734 TYR cc_start: 0.7686 (t80) cc_final: 0.7438 (t80) REVERT: E 737 MET cc_start: 0.8128 (tpp) cc_final: 0.7684 (tpt) REVERT: E 780 LYS cc_start: 0.7843 (mtmt) cc_final: 0.7608 (mptm) REVERT: D 163 LYS cc_start: 0.8629 (mtmt) cc_final: 0.8081 (mptt) REVERT: D 552 MET cc_start: 0.4703 (mmt) cc_final: 0.4328 (mmm) REVERT: D 750 ARG cc_start: 0.7635 (mtp85) cc_final: 0.7070 (mmp80) REVERT: B 162 LYS cc_start: 0.6379 (OUTLIER) cc_final: 0.5698 (mtmm) REVERT: B 242 MET cc_start: 0.7999 (mmt) cc_final: 0.7662 (mmt) REVERT: B 250 LYS cc_start: 0.8516 (ttpm) cc_final: 0.8315 (ttmt) REVERT: B 268 LYS cc_start: 0.8035 (mmtt) cc_final: 0.7818 (mttt) REVERT: B 552 MET cc_start: 0.5063 (OUTLIER) cc_final: 0.4506 (mpp) REVERT: B 558 LYS cc_start: 0.8090 (tttm) cc_final: 0.7863 (ttpt) REVERT: B 634 MET cc_start: 0.8411 (mmm) cc_final: 0.8106 (mmm) REVERT: B 705 ARG cc_start: 0.7658 (tpp-160) cc_final: 0.7224 (ttp-110) REVERT: B 776 GLN cc_start: 0.8245 (mm-40) cc_final: 0.7905 (mt0) REVERT: B 832 GLN cc_start: 0.7884 (tt0) cc_final: 0.7475 (tm-30) REVERT: A 551 MET cc_start: 0.1114 (mmm) cc_final: -0.0282 (mpt) REVERT: A 598 ILE cc_start: 0.8750 (OUTLIER) cc_final: 0.8524 (mp) REVERT: A 633 ASP cc_start: 0.6499 (t70) cc_final: 0.6087 (p0) REVERT: A 716 MET cc_start: 0.8226 (OUTLIER) cc_final: 0.7975 (mtm) REVERT: A 737 MET cc_start: 0.5767 (mpp) cc_final: 0.5251 (mpp) REVERT: A 834 LEU cc_start: 0.1822 (OUTLIER) cc_final: 0.1299 (tm) outliers start: 66 outliers final: 41 residues processed: 418 average time/residue: 1.4538 time to fit residues: 708.2440 Evaluate side-chains 416 residues out of total 2916 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 364 time to evaluate : 3.122 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 228 VAL Chi-restraints excluded: chain C residue 314 THR Chi-restraints excluded: chain C residue 386 LEU Chi-restraints excluded: chain C residue 393 LEU Chi-restraints excluded: chain C residue 533 ASP Chi-restraints excluded: chain C residue 580 VAL Chi-restraints excluded: chain C residue 716 MET Chi-restraints excluded: chain C residue 761 VAL Chi-restraints excluded: chain F residue 264 ASN Chi-restraints excluded: chain F residue 300 LYS Chi-restraints excluded: chain F residue 338 VAL Chi-restraints excluded: chain F residue 371 VAL Chi-restraints excluded: chain F residue 632 ILE Chi-restraints excluded: chain F residue 793 ILE Chi-restraints excluded: chain F residue 800 LEU Chi-restraints excluded: chain F residue 806 ASN Chi-restraints excluded: chain E residue 190 THR Chi-restraints excluded: chain E residue 277 ILE Chi-restraints excluded: chain E residue 367 ASP Chi-restraints excluded: chain E residue 540 LEU Chi-restraints excluded: chain E residue 549 SER Chi-restraints excluded: chain E residue 689 ILE Chi-restraints excluded: chain E residue 698 ARG Chi-restraints excluded: chain E residue 758 ASP Chi-restraints excluded: chain E residue 843 VAL Chi-restraints excluded: chain D residue 242 MET Chi-restraints excluded: chain D residue 293 MET Chi-restraints excluded: chain D residue 298 MET Chi-restraints excluded: chain D residue 314 THR Chi-restraints excluded: chain D residue 532 THR Chi-restraints excluded: chain D residue 752 GLU Chi-restraints excluded: chain D residue 837 GLU Chi-restraints excluded: chain B residue 162 LYS Chi-restraints excluded: chain B residue 294 ASP Chi-restraints excluded: chain B residue 314 THR Chi-restraints excluded: chain B residue 548 VAL Chi-restraints excluded: chain B residue 552 MET Chi-restraints excluded: chain B residue 604 LEU Chi-restraints excluded: chain B residue 638 MET Chi-restraints excluded: chain B residue 679 VAL Chi-restraints excluded: chain B residue 732 LEU Chi-restraints excluded: chain B residue 744 VAL Chi-restraints excluded: chain B residue 757 ILE Chi-restraints excluded: chain A residue 232 LEU Chi-restraints excluded: chain A residue 316 LEU Chi-restraints excluded: chain A residue 330 GLU Chi-restraints excluded: chain A residue 532 THR Chi-restraints excluded: chain A residue 598 ILE Chi-restraints excluded: chain A residue 693 VAL Chi-restraints excluded: chain A residue 716 MET Chi-restraints excluded: chain A residue 724 LEU Chi-restraints excluded: chain A residue 834 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 348 random chunks: chunk 219 optimal weight: 4.9990 chunk 294 optimal weight: 5.9990 chunk 84 optimal weight: 9.9990 chunk 254 optimal weight: 9.9990 chunk 40 optimal weight: 0.0010 chunk 76 optimal weight: 0.7980 chunk 276 optimal weight: 2.9990 chunk 115 optimal weight: 10.0000 chunk 283 optimal weight: 0.8980 chunk 35 optimal weight: 0.9980 chunk 50 optimal weight: 0.0470 overall best weight: 0.5484 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 719 ASN C 755 ASN ** C 806 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 824 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 703 GLN E 192 GLN ** E 769 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 824 GLN ** D 334 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 692 GLN D 794 HIS D 806 ASN D 822 GLN B 719 ASN ** A 360 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4384 r_free = 0.4384 target = 0.214627 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3745 r_free = 0.3745 target = 0.147846 restraints weight = 28114.231| |-----------------------------------------------------------------------------| r_work (start): 0.3702 rms_B_bonded: 1.98 r_work: 0.3586 rms_B_bonded: 2.47 restraints_weight: 0.5000 r_work: 0.3446 rms_B_bonded: 4.02 restraints_weight: 0.2500 r_work (final): 0.3446 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7228 moved from start: 0.3529 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 28296 Z= 0.169 Angle : 0.567 10.075 38259 Z= 0.276 Chirality : 0.044 0.242 4328 Planarity : 0.004 0.061 4991 Dihedral : 10.097 173.752 4083 Min Nonbonded Distance : 2.055 Molprobity Statistics. All-atom Clashscore : 13.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.81 % Favored : 95.19 % Rotamer: Outliers : 2.16 % Allowed : 26.23 % Favored : 71.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.23 (0.15), residues: 3448 helix: -0.33 (0.14), residues: 1556 sheet: -2.24 (0.25), residues: 357 loop : -0.80 (0.16), residues: 1535 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 543 HIS 0.008 0.001 HIS E 281 PHE 0.033 0.001 PHE A 621 TYR 0.010 0.001 TYR C 357 ARG 0.012 0.000 ARG C 852 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 12414.81 seconds wall clock time: 220 minutes 7.95 seconds (13207.95 seconds total)