Starting phenix.real_space_refine on Sat Apr 13 07:56:20 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6w6i_21556/04_2024/6w6i_21556_neut_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6w6i_21556/04_2024/6w6i_21556.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6w6i_21556/04_2024/6w6i_21556.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6w6i_21556/04_2024/6w6i_21556.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6w6i_21556/04_2024/6w6i_21556_neut_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6w6i_21556/04_2024/6w6i_21556_neut_updated.pdb" } resolution = 3.5 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.003 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 34 5.49 5 S 68 5.16 5 C 17468 2.51 5 N 5138 2.21 5 O 5460 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 197": "NH1" <-> "NH2" Residue "A GLU 217": "OE1" <-> "OE2" Residue "A GLU 230": "OE1" <-> "OE2" Residue "A ASP 241": "OD1" <-> "OD2" Residue "A TYR 251": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 254": "OE1" <-> "OE2" Residue "A GLU 308": "OE1" <-> "OE2" Residue "A ASP 318": "OD1" <-> "OD2" Residue "A ARG 357": "NH1" <-> "NH2" Residue "A ASP 379": "OD1" <-> "OD2" Residue "A ARG 403": "NH1" <-> "NH2" Residue "A GLU 427": "OE1" <-> "OE2" Residue "A GLU 440": "OE1" <-> "OE2" Residue "A ASP 540": "OD1" <-> "OD2" Residue "A ARG 552": "NH1" <-> "NH2" Residue "A GLU 557": "OE1" <-> "OE2" Residue "A PHE 603": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 627": "OD1" <-> "OD2" Residue "A GLU 628": "OE1" <-> "OE2" Residue "A TYR 639": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 659": "OE1" <-> "OE2" Residue "A ARG 669": "NH1" <-> "NH2" Residue "A ARG 796": "NH1" <-> "NH2" Residue "A ASP 817": "OD1" <-> "OD2" Residue "A ASP 832": "OD1" <-> "OD2" Residue "B ASP 178": "OD1" <-> "OD2" Residue "B ARG 197": "NH1" <-> "NH2" Residue "B GLU 319": "OE1" <-> "OE2" Residue "B ARG 333": "NH1" <-> "NH2" Residue "B ARG 357": "NH1" <-> "NH2" Residue "B ASP 393": "OD1" <-> "OD2" Residue "B ARG 403": "NH1" <-> "NH2" Residue "B GLU 415": "OE1" <-> "OE2" Residue "B ASP 435": "OD1" <-> "OD2" Residue "B GLU 436": "OE1" <-> "OE2" Residue "B GLU 448": "OE1" <-> "OE2" Residue "B GLU 466": "OE1" <-> "OE2" Residue "B GLU 531": "OE1" <-> "OE2" Residue "B ASP 537": "OD1" <-> "OD2" Residue "B ARG 552": "NH1" <-> "NH2" Residue "B ASP 595": "OD1" <-> "OD2" Residue "B PHE 603": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 605": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 623": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 655": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 669": "NH1" <-> "NH2" Residue "B PHE 678": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 680": "OE1" <-> "OE2" Residue "B ASP 697": "OD1" <-> "OD2" Residue "B PHE 739": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 743": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 780": "NH1" <-> "NH2" Residue "C ARG 197": "NH1" <-> "NH2" Residue "C GLU 256": "OE1" <-> "OE2" Residue "C ASP 278": "OD1" <-> "OD2" Residue "C GLU 345": "OE1" <-> "OE2" Residue "C ARG 357": "NH1" <-> "NH2" Residue "C ASP 368": "OD1" <-> "OD2" Residue "C ASP 379": "OD1" <-> "OD2" Residue "C ARG 403": "NH1" <-> "NH2" Residue "C GLU 436": "OE1" <-> "OE2" Residue "C ASP 540": "OD1" <-> "OD2" Residue "C ASP 584": "OD1" <-> "OD2" Residue "C PHE 605": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 622": "OD1" <-> "OD2" Residue "C ASP 627": "OD1" <-> "OD2" Residue "C TYR 639": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 655": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 669": "NH1" <-> "NH2" Residue "C PHE 678": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 710": "OD1" <-> "OD2" Residue "C GLU 729": "OE1" <-> "OE2" Residue "C ASP 766": "OD1" <-> "OD2" Residue "C ASP 817": "OD1" <-> "OD2" Residue "D ARG 188": "NH1" <-> "NH2" Residue "D ARG 197": "NH1" <-> "NH2" Residue "D GLU 254": "OE1" <-> "OE2" Residue "D GLU 279": "OE1" <-> "OE2" Residue "D ARG 333": "NH1" <-> "NH2" Residue "D TYR 338": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 357": "NH1" <-> "NH2" Residue "D ASP 368": "OD1" <-> "OD2" Residue "D ARG 403": "NH1" <-> "NH2" Residue "D ARG 552": "NH1" <-> "NH2" Residue "D PHE 605": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 627": "OD1" <-> "OD2" Residue "D ASP 635": "OD1" <-> "OD2" Residue "D TYR 655": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 669": "NH1" <-> "NH2" Residue "D PHE 678": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 711": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 739": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 766": "OD1" <-> "OD2" Residue "D ARG 780": "NH1" <-> "NH2" Residue "D PHE 798": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 817": "OD1" <-> "OD2" Residue "D ASP 841": "OD1" <-> "OD2" Residue "D ASP 843": "OD1" <-> "OD2" Residue "E ARG 173": "NH1" <-> "NH2" Residue "E GLU 174": "OE1" <-> "OE2" Residue "E ARG 197": "NH1" <-> "NH2" Residue "E ASP 241": "OD1" <-> "OD2" Residue "E ARG 252": "NH1" <-> "NH2" Residue "E ASP 278": "OD1" <-> "OD2" Residue "E GLU 279": "OE1" <-> "OE2" Residue "E GLU 319": "OE1" <-> "OE2" Residue "E ARG 321": "NH1" <-> "NH2" Residue "E ASP 327": "OD1" <-> "OD2" Residue "E GLU 345": "OE1" <-> "OE2" Residue "E ASP 356": "OD1" <-> "OD2" Residue "E ARG 357": "NH1" <-> "NH2" Residue "E ASP 393": "OD1" <-> "OD2" Residue "E ARG 403": "NH1" <-> "NH2" Residue "E ASP 407": "OD1" <-> "OD2" Residue "E ASP 536": "OD1" <-> "OD2" Residue "E ARG 552": "NH1" <-> "NH2" Residue "E ASP 566": "OD1" <-> "OD2" Residue "E ARG 588": "NH1" <-> "NH2" Residue "E PHE 603": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 605": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ASP 622": "OD1" <-> "OD2" Residue "E ASP 635": "OD1" <-> "OD2" Residue "E TYR 639": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ARG 669": "NH1" <-> "NH2" Residue "E PHE 678": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ASP 679": "OD1" <-> "OD2" Residue "E ASP 697": "OD1" <-> "OD2" Residue "E ASP 749": "OD1" <-> "OD2" Residue "E ASP 766": "OD1" <-> "OD2" Residue "E ARG 775": "NH1" <-> "NH2" Residue "E ASP 799": "OD1" <-> "OD2" Residue "E ARG 808": "NH1" <-> "NH2" Residue "E ASP 832": "OD1" <-> "OD2" Residue "F ARG 173": "NH1" <-> "NH2" Residue "F ARG 197": "NH1" <-> "NH2" Residue "F GLU 217": "OE1" <-> "OE2" Residue "F ASP 227": "OD1" <-> "OD2" Residue "F ASP 278": "OD1" <-> "OD2" Residue "F ARG 321": "NH1" <-> "NH2" Residue "F ARG 357": "NH1" <-> "NH2" Residue "F TYR 381": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 386": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ARG 403": "NH1" <-> "NH2" Residue "F GLU 405": "OE1" <-> "OE2" Residue "F GLU 415": "OE1" <-> "OE2" Residue "F GLU 424": "OE1" <-> "OE2" Residue "F GLU 434": "OE1" <-> "OE2" Residue "F ASP 451": "OD1" <-> "OD2" Residue "F GLU 454": "OE1" <-> "OE2" Residue "F GLU 531": "OE1" <-> "OE2" Residue "F ASP 536": "OD1" <-> "OD2" Residue "F ARG 552": "NH1" <-> "NH2" Residue "F GLU 555": "OE1" <-> "OE2" Residue "F PHE 605": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ASP 622": "OD1" <-> "OD2" Residue "F PHE 623": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ASP 627": "OD1" <-> "OD2" Residue "F GLU 628": "OE1" <-> "OE2" Residue "F GLU 641": "OE1" <-> "OE2" Residue "F ARG 669": "NH1" <-> "NH2" Residue "F GLU 680": "OE1" <-> "OE2" Residue "F ASP 687": "OD1" <-> "OD2" Residue "F ASP 703": "OD1" <-> "OD2" Residue "F PHE 739": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 743": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 759": "OE1" <-> "OE2" Residue "F ASP 766": "OD1" <-> "OD2" Residue "F ARG 796": "NH1" <-> "NH2" Residue "F ASP 817": "OD1" <-> "OD2" Time to flip residues: 0.12s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5288/modules/chem_data/mon_lib" Total number of atoms: 28168 Number of models: 1 Model: "" Number of chains: 13 Chain: "A" Number of atoms: 4796 Number of conformers: 1 Conformer: "" Number of residues, atoms: 620, 4796 Classifications: {'peptide': 620} Link IDs: {'PTRANS': 24, 'TRANS': 595} Chain breaks: 2 Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 24 Unresolved non-hydrogen chiralities: 12 Chain: "B" Number of atoms: 4804 Number of conformers: 1 Conformer: "" Number of residues, atoms: 621, 4804 Classifications: {'peptide': 621} Link IDs: {'PTRANS': 24, 'TRANS': 596} Chain breaks: 2 Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 24 Unresolved non-hydrogen chiralities: 12 Chain: "C" Number of atoms: 4821 Number of conformers: 1 Conformer: "" Number of residues, atoms: 624, 4821 Classifications: {'peptide': 624} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 24, 'TRANS': 599} Chain breaks: 2 Unresolved non-hydrogen bonds: 15 Unresolved non-hydrogen angles: 27 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 12 Chain: "D" Number of atoms: 4321 Number of conformers: 1 Conformer: "" Number of residues, atoms: 562, 4321 Classifications: {'peptide': 562} Link IDs: {'PTRANS': 24, 'TRANS': 537} Chain breaks: 2 Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen chiralities: 10 Chain: "E" Number of atoms: 4230 Number of conformers: 1 Conformer: "" Number of residues, atoms: 548, 4230 Classifications: {'peptide': 548} Link IDs: {'PTRANS': 23, 'TRANS': 524} Chain breaks: 3 Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen chiralities: 10 Chain: "F" Number of atoms: 4702 Number of conformers: 1 Conformer: "" Number of residues, atoms: 605, 4702 Classifications: {'peptide': 605} Link IDs: {'PTRANS': 24, 'TRANS': 580} Chain breaks: 3 Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 24 Unresolved non-hydrogen chiralities: 12 Chain: "N" 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: "A" 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: "C" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'AGS': 1} Classifications: {'undetermined': 1} Chain: "D" Number of atoms: 93 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 93 Unusual residues: {'AGS': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "E" Number of atoms: 58 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 58 Unusual residues: {'ADP': 1, 'AGS': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "F" 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: 15.36, per 1000 atoms: 0.55 Number of scatterers: 28168 At special positions: 0 Unit cell: (137.472, 147.138, 134.25, 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 68 16.00 P 34 15.00 O 5460 8.00 N 5138 7.00 C 17468 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=4, symmetry=0 Number of additional bonds: simple=4, symmetry=0 Coordination: Other bonds: Time building additional restraints: 11.57 Conformation dependent library (CDL) restraints added in 5.3 seconds 7080 Ramachandran restraints generated. 3540 Oldfield, 0 Emsley, 3540 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6628 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 170 helices and 21 sheets defined 45.8% alpha, 5.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 6.27 Creating SS restraints... Processing helix chain 'A' and resid 160 through 163 No H-bonds generated for 'chain 'A' and resid 160 through 163' Processing helix chain 'A' and resid 169 through 174 removed outlier: 3.669A pdb=" N GLU A 174 " --> pdb=" O ALA A 170 " (cutoff:3.500A) Processing helix chain 'A' and resid 184 through 194 Processing helix chain 'A' and resid 213 through 225 Processing helix chain 'A' and resid 230 through 232 No H-bonds generated for 'chain 'A' and resid 230 through 232' Processing helix chain 'A' and resid 242 through 245 No H-bonds generated for 'chain 'A' and resid 242 through 245' Processing helix chain 'A' and resid 255 through 268 Processing helix chain 'A' and resid 280 through 283 Processing helix chain 'A' and resid 301 through 306 Processing helix chain 'A' and resid 317 through 323 removed outlier: 4.274A pdb=" N ARG A 321 " --> pdb=" O LEU A 317 " (cutoff:3.500A) Processing helix chain 'A' and resid 325 through 333 removed outlier: 3.885A pdb=" N ALA A 328 " --> pdb=" O GLU A 325 " (cutoff:3.500A) removed outlier: 6.472A pdb=" N ALA A 329 " --> pdb=" O LYS A 326 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N GLU A 331 " --> pdb=" O ALA A 328 " (cutoff:3.500A) removed outlier: 4.179A pdb=" N ARG A 332 " --> pdb=" O ALA A 329 " (cutoff:3.500A) Processing helix chain 'A' and resid 344 through 361 removed outlier: 5.648A pdb=" N ASP A 356 " --> pdb=" O ARG A 352 " (cutoff:3.500A) removed outlier: 5.533A pdb=" N ARG A 357 " --> pdb=" O GLY A 353 " (cutoff:3.500A) removed outlier: 3.933A pdb=" N TYR A 358 " --> pdb=" O LEU A 354 " (cutoff:3.500A) Processing helix chain 'A' and resid 368 through 376 removed outlier: 4.159A pdb=" N ALA A 375 " --> pdb=" O LEU A 371 " (cutoff:3.500A) Processing helix chain 'A' and resid 387 through 390 No H-bonds generated for 'chain 'A' and resid 387 through 390' Processing helix chain 'A' and resid 392 through 406 removed outlier: 3.940A pdb=" N SER A 400 " --> pdb=" O ASP A 396 " (cutoff:3.500A) Processing helix chain 'A' and resid 416 through 430 removed outlier: 3.512A pdb=" N ARG A 422 " --> pdb=" O ARG A 418 " (cutoff:3.500A) removed outlier: 3.880A pdb=" N ALA A 429 " --> pdb=" O ILE A 425 " (cutoff:3.500A) Processing helix chain 'A' and resid 439 through 468 removed outlier: 3.587A pdb=" N ALA A 443 " --> pdb=" O ALA A 439 " (cutoff:3.500A) removed outlier: 4.185A pdb=" N LYS A 444 " --> pdb=" O GLU A 440 " (cutoff:3.500A) removed outlier: 3.927A pdb=" N LEU A 445 " --> pdb=" O ARG A 441 " (cutoff:3.500A) removed outlier: 4.865A pdb=" N SER A 447 " --> pdb=" O ALA A 443 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N LYS A 455 " --> pdb=" O ASP A 451 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N GLN A 464 " --> pdb=" O THR A 460 " (cutoff:3.500A) Processing helix chain 'A' and resid 536 through 544 Processing helix chain 'A' and resid 557 through 560 No H-bonds generated for 'chain 'A' and resid 557 through 560' Processing helix chain 'A' and resid 564 through 570 removed outlier: 3.878A pdb=" N LYS A 570 " --> pdb=" O ASP A 566 " (cutoff:3.500A) Processing helix chain 'A' and resid 576 through 590 removed outlier: 3.955A pdb=" N ALA A 581 " --> pdb=" O ALA A 577 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N ALA A 585 " --> pdb=" O ALA A 581 " (cutoff:3.500A) removed outlier: 4.170A pdb=" N VAL A 586 " --> pdb=" O VAL A 582 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N ARG A 587 " --> pdb=" O SER A 583 " (cutoff:3.500A) removed outlier: 4.143A pdb=" N SER A 589 " --> pdb=" O ALA A 585 " (cutoff:3.500A) Processing helix chain 'A' and resid 615 through 625 removed outlier: 3.539A pdb=" N LEU A 624 " --> pdb=" O LEU A 620 " (cutoff:3.500A) removed outlier: 3.867A pdb=" N PHE A 625 " --> pdb=" O ALA A 621 " (cutoff:3.500A) Processing helix chain 'A' and resid 642 through 645 Processing helix chain 'A' and resid 665 through 668 No H-bonds generated for 'chain 'A' and resid 665 through 668' Processing helix chain 'A' and resid 681 through 683 No H-bonds generated for 'chain 'A' and resid 681 through 683' Processing helix chain 'A' and resid 688 through 690 No H-bonds generated for 'chain 'A' and resid 688 through 690' Processing helix chain 'A' and resid 692 through 695 No H-bonds generated for 'chain 'A' and resid 692 through 695' Processing helix chain 'A' and resid 729 through 738 Processing helix chain 'A' and resid 741 through 744 No H-bonds generated for 'chain 'A' and resid 741 through 744' Processing helix chain 'A' and resid 758 through 777 removed outlier: 3.572A pdb=" N LEU A 761 " --> pdb=" O PRO A 758 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N VAL A 762 " --> pdb=" O GLU A 759 " (cutoff:3.500A) removed outlier: 4.461A pdb=" N ARG A 763 " --> pdb=" O GLU A 760 " (cutoff:3.500A) removed outlier: 4.515A pdb=" N ASP A 766 " --> pdb=" O ARG A 763 " (cutoff:3.500A) Processing helix chain 'A' and resid 787 through 796 Processing helix chain 'A' and resid 805 through 823 removed outlier: 4.438A pdb=" N ASP A 817 " --> pdb=" O GLN A 813 " (cutoff:3.500A) removed outlier: 4.275A pdb=" N GLN A 818 " --> pdb=" O ALA A 814 " (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 225 Processing helix chain 'B' and resid 242 through 245 Processing helix chain 'B' and resid 254 through 268 Processing helix chain 'B' and resid 280 through 283 Processing helix chain 'B' and resid 300 through 306 removed outlier: 3.628A pdb=" N ALA B 305 " --> pdb=" O LYS B 301 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N ARG B 306 " --> pdb=" O PRO B 302 " (cutoff:3.500A) Processing helix chain 'B' and resid 317 through 323 removed outlier: 4.124A pdb=" N ARG B 321 " --> pdb=" O LEU B 317 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N LYS B 322 " --> pdb=" O ASP B 318 " (cutoff:3.500A) Processing helix chain 'B' and resid 331 through 333 No H-bonds generated for 'chain 'B' and resid 331 through 333' Processing helix chain 'B' and resid 344 through 361 removed outlier: 3.531A pdb=" N GLY B 349 " --> pdb=" O GLU B 345 " (cutoff:3.500A) removed outlier: 5.244A pdb=" N ASP B 356 " --> pdb=" O ARG B 352 " (cutoff:3.500A) removed outlier: 5.407A pdb=" N ARG B 357 " --> pdb=" O GLY B 353 " (cutoff:3.500A) removed outlier: 3.888A pdb=" N TYR B 358 " --> pdb=" O LEU B 354 " (cutoff:3.500A) removed outlier: 4.166A pdb=" N VAL B 360 " --> pdb=" O ASP B 356 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N HIS B 361 " --> pdb=" O ARG B 357 " (cutoff:3.500A) Processing helix chain 'B' and resid 368 through 379 removed outlier: 3.528A pdb=" N ALA B 373 " --> pdb=" O SER B 369 " (cutoff:3.500A) removed outlier: 3.860A pdb=" N ALA B 375 " --> pdb=" O LEU B 371 " (cutoff:3.500A) removed outlier: 4.039A pdb=" N SER B 378 " --> pdb=" O ALA B 374 " (cutoff:3.500A) removed outlier: 3.832A pdb=" N ASP B 379 " --> pdb=" O ALA B 375 " (cutoff:3.500A) Processing helix chain 'B' and resid 388 through 407 removed outlier: 5.015A pdb=" N ASP B 393 " --> pdb=" O LYS B 390 " (cutoff:3.500A) removed outlier: 4.266A pdb=" N LEU B 394 " --> pdb=" O ALA B 391 " (cutoff:3.500A) Processing helix chain 'B' and resid 415 through 430 removed outlier: 3.507A pdb=" N ARG B 422 " --> pdb=" O ARG B 418 " (cutoff:3.500A) removed outlier: 4.588A pdb=" N ILE B 425 " --> pdb=" O ARG B 421 " (cutoff:3.500A) Processing helix chain 'B' and resid 437 through 468 removed outlier: 3.667A pdb=" N GLU B 440 " --> pdb=" O ALA B 437 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N ARG B 441 " --> pdb=" O SER B 438 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N LEU B 442 " --> pdb=" O ALA B 439 " (cutoff:3.500A) removed outlier: 3.971A pdb=" N ALA B 443 " --> pdb=" O GLU B 440 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N LEU B 445 " --> pdb=" O LEU B 442 " (cutoff:3.500A) removed outlier: 4.597A pdb=" N ARG B 446 " --> pdb=" O ALA B 443 " (cutoff:3.500A) removed outlier: 4.278A pdb=" N LEU B 449 " --> pdb=" O ARG B 446 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N LYS B 453 " --> pdb=" O ALA B 450 " (cutoff:3.500A) removed outlier: 4.467A pdb=" N LEU B 456 " --> pdb=" O LYS B 453 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N THR B 460 " --> pdb=" O ALA B 457 " (cutoff:3.500A) removed outlier: 3.862A pdb=" N TRP B 463 " --> pdb=" O THR B 460 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N ASN B 465 " --> pdb=" O ARG B 462 " (cutoff:3.500A) removed outlier: 4.528A pdb=" N ASN B 468 " --> pdb=" O ASN B 465 " (cutoff:3.500A) Processing helix chain 'B' and resid 537 through 544 Processing helix chain 'B' and resid 557 through 562 Processing helix chain 'B' and resid 576 through 582 removed outlier: 3.937A pdb=" N ALA B 581 " --> pdb=" O ALA B 577 " (cutoff:3.500A) Processing helix chain 'B' and resid 584 through 590 removed outlier: 3.746A pdb=" N ARG B 588 " --> pdb=" O ASP B 584 " (cutoff:3.500A) removed outlier: 4.230A pdb=" N SER B 589 " --> pdb=" O ALA B 585 " (cutoff:3.500A) Processing helix chain 'B' and resid 616 through 625 removed outlier: 3.956A pdb=" N ALA B 621 " --> pdb=" O ALA B 617 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N PHE B 625 " --> pdb=" O ALA B 621 " (cutoff:3.500A) Processing helix chain 'B' and resid 642 through 645 Processing helix chain 'B' and resid 665 through 668 No H-bonds generated for 'chain 'B' and resid 665 through 668' Processing helix chain 'B' and resid 681 through 683 No H-bonds generated for 'chain 'B' and resid 681 through 683' Processing helix chain 'B' and resid 688 through 695 removed outlier: 4.740A pdb=" N GLN B 694 " --> pdb=" O ASP B 690 " (cutoff:3.500A) removed outlier: 4.322A pdb=" N VAL B 695 " --> pdb=" O VAL B 691 " (cutoff:3.500A) Processing helix chain 'B' and resid 732 through 735 No H-bonds generated for 'chain 'B' and resid 732 through 735' Processing helix chain 'B' and resid 741 through 744 No H-bonds generated for 'chain 'B' and resid 741 through 744' Processing helix chain 'B' and resid 759 through 779 removed outlier: 4.741A pdb=" N ARG B 763 " --> pdb=" O GLU B 760 " (cutoff:3.500A) removed outlier: 3.999A pdb=" N VAL B 765 " --> pdb=" O VAL B 762 " (cutoff:3.500A) removed outlier: 3.997A pdb=" N GLN B 778 " --> pdb=" O ARG B 775 " (cutoff:3.500A) Processing helix chain 'B' and resid 787 through 796 removed outlier: 3.730A pdb=" N ALA B 794 " --> pdb=" O LYS B 790 " (cutoff:3.500A) Processing helix chain 'B' and resid 806 through 823 removed outlier: 3.669A pdb=" N GLN B 812 " --> pdb=" O ARG B 808 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N GLY B 816 " --> pdb=" O GLN B 812 " (cutoff:3.500A) removed outlier: 4.518A pdb=" N ASP B 817 " --> pdb=" O GLN B 813 " (cutoff:3.500A) removed outlier: 4.314A pdb=" N GLN B 818 " --> pdb=" O ALA B 814 " (cutoff:3.500A) Processing helix chain 'C' and resid 160 through 164 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 225 Processing helix chain 'C' and resid 230 through 232 No H-bonds generated for 'chain 'C' and resid 230 through 232' Processing helix chain 'C' and resid 254 through 268 removed outlier: 3.662A pdb=" N ARG C 258 " --> pdb=" O GLU C 254 " (cutoff:3.500A) Processing helix chain 'C' and resid 280 through 282 No H-bonds generated for 'chain 'C' and resid 280 through 282' Processing helix chain 'C' and resid 301 through 305 removed outlier: 3.932A pdb=" N ALA C 305 " --> pdb=" O LYS C 301 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 301 through 305' Processing helix chain 'C' and resid 328 through 333 removed outlier: 3.715A pdb=" N ARG C 332 " --> pdb=" O ALA C 328 " (cutoff:3.500A) removed outlier: 4.697A pdb=" N ARG C 333 " --> pdb=" O ALA C 329 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 328 through 333' Processing helix chain 'C' and resid 344 through 354 removed outlier: 3.561A pdb=" N GLY C 349 " --> pdb=" O GLU C 345 " (cutoff:3.500A) Processing helix chain 'C' and resid 357 through 361 Processing helix chain 'C' and resid 368 through 380 removed outlier: 4.087A pdb=" N ASP C 379 " --> pdb=" O ALA C 375 " (cutoff:3.500A) Processing helix chain 'C' and resid 387 through 390 No H-bonds generated for 'chain 'C' and resid 387 through 390' Processing helix chain 'C' and resid 392 through 406 Processing helix chain 'C' and resid 414 through 430 removed outlier: 3.800A pdb=" N ALA C 429 " --> pdb=" O ILE C 425 " (cutoff:3.500A) Processing helix chain 'C' and resid 437 through 468 removed outlier: 3.574A pdb=" N ARG C 441 " --> pdb=" O ALA C 437 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N LYS C 444 " --> pdb=" O GLU C 440 " (cutoff:3.500A) removed outlier: 4.642A pdb=" N LEU C 445 " --> pdb=" O ARG C 441 " (cutoff:3.500A) removed outlier: 4.145A pdb=" N SER C 447 " --> pdb=" O ALA C 443 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N LYS C 455 " --> pdb=" O ASP C 451 " (cutoff:3.500A) Processing helix chain 'C' and resid 537 through 544 Processing helix chain 'C' and resid 558 through 570 removed outlier: 5.668A pdb=" N GLU C 565 " --> pdb=" O LEU C 561 " (cutoff:3.500A) removed outlier: 5.921A pdb=" N ASP C 566 " --> pdb=" O LEU C 562 " (cutoff:3.500A) removed outlier: 4.011A pdb=" N LYS C 570 " --> pdb=" O ASP C 566 " (cutoff:3.500A) Processing helix chain 'C' and resid 576 through 590 removed outlier: 4.055A pdb=" N ALA C 581 " --> pdb=" O ALA C 577 " (cutoff:3.500A) removed outlier: 3.884A pdb=" N SER C 589 " --> pdb=" O ALA C 585 " (cutoff:3.500A) removed outlier: 3.881A pdb=" N ARG C 590 " --> pdb=" O VAL C 586 " (cutoff:3.500A) Processing helix chain 'C' and resid 613 through 625 Processing helix chain 'C' and resid 628 through 630 No H-bonds generated for 'chain 'C' and resid 628 through 630' Processing helix chain 'C' and resid 642 through 648 removed outlier: 3.517A pdb=" N ALA C 646 " --> pdb=" O HIS C 643 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N ARG C 647 " --> pdb=" O THR C 644 " (cutoff:3.500A) Processing helix chain 'C' and resid 664 through 668 Processing helix chain 'C' and resid 681 through 683 No H-bonds generated for 'chain 'C' and resid 681 through 683' Processing helix chain 'C' and resid 693 through 697 Processing helix chain 'C' and resid 730 through 738 removed outlier: 3.841A pdb=" N ARG C 736 " --> pdb=" O LEU C 732 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N ALA C 737 " --> pdb=" O ALA C 733 " (cutoff:3.500A) Processing helix chain 'C' and resid 741 through 746 removed outlier: 4.108A pdb=" N ARG C 746 " --> pdb=" O GLU C 742 " (cutoff:3.500A) Processing helix chain 'C' and resid 761 through 778 removed outlier: 4.301A pdb=" N GLN C 778 " --> pdb=" O LYS C 774 " (cutoff:3.500A) Processing helix chain 'C' and resid 787 through 796 removed outlier: 3.820A pdb=" N ALA C 794 " --> pdb=" O LYS C 790 " (cutoff:3.500A) Processing helix chain 'C' and resid 806 through 823 removed outlier: 5.269A pdb=" N ASP C 817 " --> pdb=" O GLN C 813 " (cutoff:3.500A) removed outlier: 5.132A pdb=" N GLN C 818 " --> pdb=" O ALA C 814 " (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: 4.211A pdb=" N VAL D 216 " --> pdb=" O LYS D 212 " (cutoff:3.500A) Processing helix chain 'D' and resid 230 through 232 No H-bonds generated for 'chain 'D' and resid 230 through 232' Processing helix chain 'D' and resid 255 through 268 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 301 through 306 removed outlier: 4.211A pdb=" N ARG D 306 " --> pdb=" O PRO D 302 " (cutoff:3.500A) Processing helix chain 'D' and resid 317 through 323 Processing helix chain 'D' and resid 328 through 333 removed outlier: 4.854A pdb=" N ARG D 333 " --> pdb=" O ALA D 329 " (cutoff:3.500A) Processing helix chain 'D' and resid 344 through 361 removed outlier: 5.343A pdb=" N ASP D 356 " --> pdb=" O ARG D 352 " (cutoff:3.500A) removed outlier: 5.626A pdb=" N ARG D 357 " --> pdb=" O GLY D 353 " (cutoff:3.500A) removed outlier: 3.846A pdb=" N TYR D 358 " --> pdb=" O LEU D 354 " (cutoff:3.500A) Processing helix chain 'D' and resid 368 through 380 removed outlier: 4.236A pdb=" N ASP D 379 " --> pdb=" O ALA D 375 " (cutoff:3.500A) Processing helix chain 'D' and resid 387 through 406 removed outlier: 3.871A pdb=" N ILE D 392 " --> pdb=" O PRO D 388 " (cutoff:3.500A) removed outlier: 4.146A pdb=" N LEU D 394 " --> pdb=" O LYS D 390 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N VAL D 395 " --> pdb=" O ALA D 391 " (cutoff:3.500A) Processing helix chain 'D' and resid 537 through 544 Processing helix chain 'D' and resid 557 through 562 Processing helix chain 'D' and resid 569 through 571 No H-bonds generated for 'chain 'D' and resid 569 through 571' Processing helix chain 'D' and resid 576 through 591 removed outlier: 3.840A pdb=" N THR D 580 " --> pdb=" O LYS D 576 " (cutoff:3.500A) removed outlier: 4.451A pdb=" N ALA D 581 " --> pdb=" O ALA D 577 " (cutoff:3.500A) Processing helix chain 'D' and resid 613 through 625 Processing helix chain 'D' and resid 636 through 638 No H-bonds generated for 'chain 'D' and resid 636 through 638' Processing helix chain 'D' and resid 642 through 648 removed outlier: 3.569A pdb=" N VAL D 645 " --> pdb=" O LYS D 642 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N ARG D 647 " --> pdb=" O THR D 644 " (cutoff:3.500A) Processing helix chain 'D' and resid 663 through 669 Processing helix chain 'D' and resid 689 through 695 removed outlier: 4.793A pdb=" N GLN D 694 " --> pdb=" O ASP D 690 " (cutoff:3.500A) Processing helix chain 'D' and resid 728 through 738 removed outlier: 3.529A pdb=" N LEU D 732 " --> pdb=" O ALA D 728 " (cutoff:3.500A) removed outlier: 3.845A pdb=" N ALA D 733 " --> pdb=" O GLU D 729 " (cutoff:3.500A) removed outlier: 4.380A pdb=" N ALA D 734 " --> pdb=" O GLN D 730 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N ARG D 736 " --> pdb=" O LEU D 732 " (cutoff:3.500A) Processing helix chain 'D' and resid 741 through 744 No H-bonds generated for 'chain 'D' and resid 741 through 744' Processing helix chain 'D' and resid 761 through 775 Processing helix chain 'D' and resid 787 through 795 Processing helix chain 'D' and resid 805 through 824 removed outlier: 4.293A pdb=" N ARG D 808 " --> pdb=" O ARG D 805 " (cutoff:3.500A) removed outlier: 5.208A pdb=" N ARG D 809 " --> pdb=" O PRO D 806 " (cutoff:3.500A) removed outlier: 5.474A pdb=" N GLY D 816 " --> pdb=" O GLN D 813 " (cutoff:3.500A) removed outlier: 6.040A pdb=" N ASP D 817 " --> pdb=" O ALA D 814 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N LYS D 821 " --> pdb=" O GLN D 818 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N LEU D 823 " --> pdb=" O ALA D 820 " (cutoff:3.500A) removed outlier: 4.315A pdb=" N LEU D 824 " --> pdb=" O LYS D 821 " (cutoff:3.500A) Processing helix chain 'E' and resid 171 through 173 No H-bonds generated for 'chain 'E' and resid 171 through 173' Processing helix chain 'E' and resid 185 through 195 removed outlier: 3.790A pdb=" N SER E 195 " --> pdb=" O VAL E 191 " (cutoff:3.500A) Processing helix chain 'E' and resid 212 through 225 Processing helix chain 'E' and resid 242 through 244 No H-bonds generated for 'chain 'E' and resid 242 through 244' Processing helix chain 'E' and resid 255 through 268 Processing helix chain 'E' and resid 280 through 282 No H-bonds generated for 'chain 'E' and resid 280 through 282' Processing helix chain 'E' and resid 301 through 306 removed outlier: 4.037A pdb=" N ARG E 306 " --> pdb=" O PRO E 302 " (cutoff:3.500A) Processing helix chain 'E' and resid 317 through 323 Processing helix chain 'E' and resid 331 through 333 No H-bonds generated for 'chain 'E' and resid 331 through 333' Processing helix chain 'E' and resid 344 through 353 removed outlier: 3.779A pdb=" N GLY E 349 " --> pdb=" O GLU E 345 " (cutoff:3.500A) Processing helix chain 'E' and resid 356 through 361 Processing helix chain 'E' and resid 368 through 381 Processing helix chain 'E' and resid 387 through 406 removed outlier: 3.934A pdb=" N ILE E 392 " --> pdb=" O PRO E 388 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N LEU E 394 " --> pdb=" O LYS E 390 " (cutoff:3.500A) removed outlier: 4.124A pdb=" N ILE E 406 " --> pdb=" O LEU E 402 " (cutoff:3.500A) Processing helix chain 'E' and resid 536 through 546 removed outlier: 4.588A pdb=" N VAL E 541 " --> pdb=" O ASP E 537 " (cutoff:3.500A) Processing helix chain 'E' and resid 558 through 563 removed outlier: 4.340A pdb=" N ARG E 563 " --> pdb=" O ALA E 559 " (cutoff:3.500A) Processing helix chain 'E' and resid 576 through 589 Processing helix chain 'E' and resid 613 through 624 removed outlier: 4.236A pdb=" N ALA E 617 " --> pdb=" O LYS E 613 " (cutoff:3.500A) removed outlier: 3.917A pdb=" N ASP E 622 " --> pdb=" O LYS E 618 " (cutoff:3.500A) Processing helix chain 'E' and resid 643 through 648 removed outlier: 3.771A pdb=" N LEU E 648 " --> pdb=" O VAL E 645 " (cutoff:3.500A) Processing helix chain 'E' and resid 681 through 683 No H-bonds generated for 'chain 'E' and resid 681 through 683' Processing helix chain 'E' and resid 688 through 697 Processing helix chain 'E' and resid 730 through 738 Processing helix chain 'E' and resid 762 through 777 removed outlier: 4.017A pdb=" N LYS E 774 " --> pdb=" O ALA E 770 " (cutoff:3.500A) removed outlier: 4.062A pdb=" N ARG E 775 " --> pdb=" O GLN E 771 " (cutoff:3.500A) removed outlier: 4.308A pdb=" N LEU E 776 " --> pdb=" O LEU E 772 " (cutoff:3.500A) removed outlier: 4.612A pdb=" N ALA E 777 " --> pdb=" O GLY E 773 " (cutoff:3.500A) Processing helix chain 'E' and resid 787 through 797 removed outlier: 4.138A pdb=" N ALA E 794 " --> pdb=" O LYS E 790 " (cutoff:3.500A) removed outlier: 3.922A pdb=" N GLN E 795 " --> pdb=" O ARG E 791 " (cutoff:3.500A) removed outlier: 4.071A pdb=" N ARG E 796 " --> pdb=" O TRP E 792 " (cutoff:3.500A) Processing helix chain 'E' and resid 805 through 807 No H-bonds generated for 'chain 'E' and resid 805 through 807' Processing helix chain 'E' and resid 809 through 819 removed outlier: 3.605A pdb=" N ALA E 814 " --> pdb=" O LEU E 810 " (cutoff:3.500A) Processing helix chain 'E' and resid 822 through 825 No H-bonds generated for 'chain 'E' and resid 822 through 825' Processing helix chain 'F' and resid 170 through 174 Processing helix chain 'F' and resid 184 through 194 Processing helix chain 'F' and resid 212 through 225 Processing helix chain 'F' and resid 256 through 268 removed outlier: 4.162A pdb=" N LYS F 260 " --> pdb=" O GLU F 256 " (cutoff:3.500A) removed outlier: 4.192A pdb=" N ALA F 261 " --> pdb=" O GLU F 257 " (cutoff:3.500A) removed outlier: 4.195A pdb=" N ASP F 265 " --> pdb=" O ALA F 261 " (cutoff:3.500A) removed outlier: 4.100A pdb=" N ILE F 266 " --> pdb=" O VAL F 262 " (cutoff:3.500A) Processing helix chain 'F' and resid 280 through 282 No H-bonds generated for 'chain 'F' and resid 280 through 282' Processing helix chain 'F' and resid 302 through 305 No H-bonds generated for 'chain 'F' and resid 302 through 305' Processing helix chain 'F' and resid 317 through 323 Processing helix chain 'F' and resid 331 through 333 No H-bonds generated for 'chain 'F' and resid 331 through 333' Processing helix chain 'F' and resid 344 through 358 removed outlier: 4.010A pdb=" N GLY F 349 " --> pdb=" O GLU F 345 " (cutoff:3.500A) removed outlier: 3.862A pdb=" N ASP F 356 " --> pdb=" O ARG F 352 " (cutoff:3.500A) removed outlier: 5.530A pdb=" N ARG F 357 " --> pdb=" O GLY F 353 " (cutoff:3.500A) Processing helix chain 'F' and resid 368 through 381 removed outlier: 3.872A pdb=" N SER F 378 " --> pdb=" O ALA F 374 " (cutoff:3.500A) removed outlier: 5.540A pdb=" N ASP F 379 " --> pdb=" O ALA F 375 " (cutoff:3.500A) removed outlier: 5.359A pdb=" N ARG F 380 " --> pdb=" O THR F 376 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N TYR F 381 " --> pdb=" O LEU F 377 " (cutoff:3.500A) Processing helix chain 'F' and resid 387 through 406 removed outlier: 4.957A pdb=" N ILE F 392 " --> pdb=" O PRO F 388 " (cutoff:3.500A) removed outlier: 3.851A pdb=" N VAL F 395 " --> pdb=" O ALA F 391 " (cutoff:3.500A) Processing helix chain 'F' and resid 416 through 427 Processing helix chain 'F' and resid 439 through 468 removed outlier: 3.674A pdb=" N LYS F 444 " --> pdb=" O GLU F 440 " (cutoff:3.500A) removed outlier: 4.475A pdb=" N SER F 447 " --> pdb=" O ALA F 443 " (cutoff:3.500A) removed outlier: 4.091A pdb=" N GLU F 454 " --> pdb=" O ALA F 450 " (cutoff:3.500A) removed outlier: 3.919A pdb=" N LYS F 455 " --> pdb=" O ASP F 451 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N GLN F 464 " --> pdb=" O THR F 460 " (cutoff:3.500A) removed outlier: 3.879A pdb=" N ASN F 465 " --> pdb=" O THR F 461 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N GLU F 466 " --> pdb=" O ARG F 462 " (cutoff:3.500A) Processing helix chain 'F' and resid 536 through 543 Processing helix chain 'F' and resid 558 through 570 removed outlier: 4.083A pdb=" N LEU F 562 " --> pdb=" O THR F 558 " (cutoff:3.500A) removed outlier: 5.196A pdb=" N GLU F 565 " --> pdb=" O LEU F 561 " (cutoff:3.500A) removed outlier: 5.758A pdb=" N ASP F 566 " --> pdb=" O LEU F 562 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N GLY F 569 " --> pdb=" O GLU F 565 " (cutoff:3.500A) removed outlier: 3.905A pdb=" N LYS F 570 " --> pdb=" O ASP F 566 " (cutoff:3.500A) Processing helix chain 'F' and resid 576 through 583 Processing helix chain 'F' and resid 587 through 590 No H-bonds generated for 'chain 'F' and resid 587 through 590' Processing helix chain 'F' and resid 615 through 625 removed outlier: 3.636A pdb=" N LEU F 624 " --> pdb=" O LEU F 620 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N PHE F 625 " --> pdb=" O ALA F 621 " (cutoff:3.500A) Processing helix chain 'F' and resid 628 through 630 No H-bonds generated for 'chain 'F' and resid 628 through 630' Processing helix chain 'F' and resid 642 through 647 removed outlier: 4.040A pdb=" N ALA F 646 " --> pdb=" O HIS F 643 " (cutoff:3.500A) Processing helix chain 'F' and resid 665 through 668 No H-bonds generated for 'chain 'F' and resid 665 through 668' Processing helix chain 'F' and resid 681 through 683 No H-bonds generated for 'chain 'F' and resid 681 through 683' Processing helix chain 'F' and resid 688 through 698 removed outlier: 3.972A pdb=" N LEU F 693 " --> pdb=" O ASP F 690 " (cutoff:3.500A) removed outlier: 3.873A pdb=" N LEU F 696 " --> pdb=" O LEU F 693 " (cutoff:3.500A) removed outlier: 4.612A pdb=" N ASP F 697 " --> pdb=" O GLN F 694 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N GLU F 698 " --> pdb=" O VAL F 695 " (cutoff:3.500A) Processing helix chain 'F' and resid 729 through 738 Processing helix chain 'F' and resid 758 through 760 No H-bonds generated for 'chain 'F' and resid 758 through 760' Processing helix chain 'F' and resid 762 through 777 Processing helix chain 'F' and resid 787 through 796 Processing helix chain 'F' and resid 805 through 823 removed outlier: 4.542A pdb=" N ASP F 817 " --> pdb=" O GLN F 813 " (cutoff:3.500A) removed outlier: 4.952A pdb=" N GLN F 818 " --> pdb=" O ALA F 814 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'A' and resid 335 through 338 removed outlier: 7.095A pdb=" N GLY A 313 " --> pdb=" O LEU A 204 " (cutoff:3.500A) removed outlier: 8.795A pdb=" N GLY A 206 " --> pdb=" O GLY A 313 " (cutoff:3.500A) removed outlier: 6.619A pdb=" N THR A 315 " --> pdb=" O GLY A 206 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 602 through 604 removed outlier: 6.524A pdb=" N LEU A 716 " --> pdb=" O PHE A 603 " (cutoff:3.500A) removed outlier: 7.152A pdb=" N VAL A 632 " --> pdb=" O LEU A 677 " (cutoff:3.500A) removed outlier: 8.182A pdb=" N ASP A 679 " --> pdb=" O VAL A 632 " (cutoff:3.500A) removed outlier: 7.341A pdb=" N ILE A 634 " --> pdb=" O ASP A 679 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'A' and resid 700 through 702 Processing sheet with id= D, first strand: chain 'B' and resid 165 through 167 removed outlier: 3.676A pdb=" N THR B 166 " --> pdb=" O ALA B 239 " (cutoff:3.500A) removed outlier: 4.863A pdb=" N ASP B 278 " --> pdb=" O LEU B 240 " (cutoff:3.500A) removed outlier: 5.891A pdb=" N VAL B 312 " --> pdb=" O ILE B 277 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N THR B 315 " --> pdb=" O LEU B 204 " (cutoff:3.500A) removed outlier: 6.169A pdb=" N GLN B 335 " --> pdb=" O VAL B 203 " (cutoff:3.500A) removed outlier: 7.350A pdb=" N ILE B 205 " --> pdb=" O GLN B 335 " (cutoff:3.500A) removed outlier: 6.127A pdb=" N VAL B 337 " --> pdb=" O ILE B 205 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'B' and resid 601 through 604 removed outlier: 3.611A pdb=" N LEU B 718 " --> pdb=" O PHE B 603 " (cutoff:3.500A) removed outlier: 6.867A pdb=" N VAL B 632 " --> pdb=" O LEU B 677 " (cutoff:3.500A) removed outlier: 7.525A pdb=" N ASP B 679 " --> pdb=" O VAL B 632 " (cutoff:3.500A) removed outlier: 6.976A pdb=" N ILE B 634 " --> pdb=" O ASP B 679 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'B' and resid 700 through 702 Processing sheet with id= G, first strand: chain 'B' and resid 782 through 784 removed outlier: 3.559A pdb=" N VAL B 834 " --> pdb=" O GLN B 782 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'C' and resid 335 through 338 removed outlier: 6.796A pdb=" N GLY C 313 " --> pdb=" O LEU C 204 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N ALA C 314 " --> pdb=" O ILE C 277 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'C' and resid 601 through 603 removed outlier: 3.508A pdb=" N PHE C 603 " --> pdb=" O LEU C 716 " (cutoff:3.500A) removed outlier: 7.116A pdb=" N VAL C 632 " --> pdb=" O LEU C 677 " (cutoff:3.500A) removed outlier: 7.942A pdb=" N ASP C 679 " --> pdb=" O VAL C 632 " (cutoff:3.500A) removed outlier: 7.476A pdb=" N ILE C 634 " --> pdb=" O ASP C 679 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'C' and resid 700 through 702 removed outlier: 3.510A pdb=" N LEU C 701 " --> pdb=" O VAL C 709 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'C' and resid 783 through 785 removed outlier: 7.444A pdb=" N VAL C 834 " --> pdb=" O GLN C 784 " (cutoff:3.500A) No H-bonds generated for sheet with id= K Processing sheet with id= L, first strand: chain 'D' and resid 335 through 338 removed outlier: 6.855A pdb=" N GLY D 313 " --> pdb=" O LEU D 204 " (cutoff:3.500A) removed outlier: 3.907A pdb=" N ALA D 314 " --> pdb=" O ILE D 277 " (cutoff:3.500A) Processing sheet with id= M, first strand: chain 'D' and resid 604 through 606 Processing sheet with id= N, first strand: chain 'D' and resid 632 through 635 removed outlier: 6.032A pdb=" N ILE D 715 " --> pdb=" O VAL D 676 " (cutoff:3.500A) removed outlier: 7.639A pdb=" N PHE D 678 " --> pdb=" O ILE D 715 " (cutoff:3.500A) removed outlier: 7.058A pdb=" N ILE D 717 " --> pdb=" O PHE D 678 " (cutoff:3.500A) Processing sheet with id= O, first strand: chain 'D' and resid 782 through 784 Processing sheet with id= P, first strand: chain 'E' and resid 313 through 315 Processing sheet with id= Q, first strand: chain 'E' and resid 237 through 240 removed outlier: 6.958A pdb=" N ILE E 274 " --> pdb=" O VAL E 238 " (cutoff:3.500A) removed outlier: 8.386A pdb=" N LEU E 240 " --> pdb=" O ILE E 274 " (cutoff:3.500A) removed outlier: 7.091A pdb=" N PHE E 276 " --> pdb=" O LEU E 240 " (cutoff:3.500A) No H-bonds generated for sheet with id= Q Processing sheet with id= R, first strand: chain 'E' and resid 601 through 604 removed outlier: 3.958A pdb=" N PHE E 603 " --> pdb=" O LEU E 716 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N LEU E 718 " --> pdb=" O PHE E 603 " (cutoff:3.500A) Processing sheet with id= S, first strand: chain 'F' and resid 336 through 338 removed outlier: 6.302A pdb=" N VAL F 203 " --> pdb=" O VAL F 337 " (cutoff:3.500A) removed outlier: 6.817A pdb=" N GLY F 313 " --> pdb=" O LEU F 204 " (cutoff:3.500A) removed outlier: 8.643A pdb=" N GLY F 206 " --> pdb=" O GLY F 313 " (cutoff:3.500A) removed outlier: 7.006A pdb=" N THR F 315 " --> pdb=" O GLY F 206 " (cutoff:3.500A) removed outlier: 4.317A pdb=" N ALA F 314 " --> pdb=" O ILE F 277 " (cutoff:3.500A) Processing sheet with id= T, first strand: chain 'F' and resid 601 through 606 removed outlier: 3.540A pdb=" N LEU F 718 " --> pdb=" O PHE F 603 " (cutoff:3.500A) removed outlier: 3.885A pdb=" N SER F 720 " --> pdb=" O PHE F 605 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N THR F 719 " --> pdb=" O PHE F 678 " (cutoff:3.500A) removed outlier: 6.857A pdb=" N VAL F 632 " --> pdb=" O LEU F 677 " (cutoff:3.500A) removed outlier: 7.417A pdb=" N ASP F 679 " --> pdb=" O VAL F 632 " (cutoff:3.500A) removed outlier: 7.134A pdb=" N ILE F 634 " --> pdb=" O ASP F 679 " (cutoff:3.500A) Processing sheet with id= U, first strand: chain 'F' and resid 700 through 702 885 hydrogen bonds defined for protein. 2382 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: 9.28 Time building geometry restraints manager: 12.50 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.37: 10113 1.37 - 1.51: 9129 1.51 - 1.66: 9180 1.66 - 1.80: 113 1.80 - 1.95: 13 Bond restraints: 28548 Sorted by residual: bond pdb=" C4 ADP F 902 " pdb=" C5 ADP F 902 " ideal model delta sigma weight residual 1.490 1.381 0.109 2.00e-02 2.50e+03 2.96e+01 bond pdb=" C4 ADP E 902 " pdb=" C5 ADP E 902 " ideal model delta sigma weight residual 1.490 1.382 0.108 2.00e-02 2.50e+03 2.94e+01 bond pdb=" C5 ADP E 902 " pdb=" C6 ADP E 902 " ideal model delta sigma weight residual 1.490 1.408 0.082 2.00e-02 2.50e+03 1.69e+01 bond pdb=" CA GLU C 760 " pdb=" C GLU C 760 " ideal model delta sigma weight residual 1.523 1.465 0.058 1.41e-02 5.03e+03 1.69e+01 bond pdb=" C5 ADP F 902 " pdb=" C6 ADP F 902 " ideal model delta sigma weight residual 1.490 1.408 0.082 2.00e-02 2.50e+03 1.67e+01 ... (remaining 28543 not shown) Histogram of bond angle deviations from ideal: 99.24 - 106.19: 718 106.19 - 113.14: 15863 113.14 - 120.09: 10511 120.09 - 127.05: 11242 127.05 - 134.00: 276 Bond angle restraints: 38610 Sorted by residual: angle pdb=" N ILE F 413 " pdb=" CA ILE F 413 " pdb=" C ILE F 413 " ideal model delta sigma weight residual 113.53 105.06 8.47 9.80e-01 1.04e+00 7.47e+01 angle pdb=" N VAL E 801 " pdb=" CA VAL E 801 " pdb=" C VAL E 801 " ideal model delta sigma weight residual 113.53 106.16 7.37 9.80e-01 1.04e+00 5.66e+01 angle pdb=" N VAL B 801 " pdb=" CA VAL B 801 " pdb=" C VAL B 801 " ideal model delta sigma weight residual 113.71 107.37 6.34 9.50e-01 1.11e+00 4.46e+01 angle pdb=" N ILE C 413 " pdb=" CA ILE C 413 " pdb=" C ILE C 413 " ideal model delta sigma weight residual 112.12 106.87 5.25 8.40e-01 1.42e+00 3.91e+01 angle pdb=" N VAL C 246 " pdb=" CA VAL C 246 " pdb=" C VAL C 246 " ideal model delta sigma weight residual 111.91 107.35 4.56 8.90e-01 1.26e+00 2.62e+01 ... (remaining 38605 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 34.41: 17137 34.41 - 68.81: 479 68.81 - 103.22: 22 103.22 - 137.63: 4 137.63 - 172.03: 2 Dihedral angle restraints: 17644 sinusoidal: 7367 harmonic: 10277 Sorted by residual: dihedral pdb=" CA LEU B 387 " pdb=" C LEU B 387 " pdb=" N PRO B 388 " pdb=" CA PRO B 388 " ideal model delta harmonic sigma weight residual -180.00 -117.79 -62.21 0 5.00e+00 4.00e-02 1.55e+02 dihedral pdb=" CA PHE C 386 " pdb=" C PHE C 386 " pdb=" N LEU C 387 " pdb=" CA LEU C 387 " ideal model delta harmonic sigma weight residual 180.00 -141.17 -38.83 0 5.00e+00 4.00e-02 6.03e+01 dihedral pdb=" O1B ADP F 902 " pdb=" O3A ADP F 902 " pdb=" PB ADP F 902 " pdb=" PA ADP F 902 " ideal model delta sinusoidal sigma weight residual -60.00 112.03 -172.03 1 2.00e+01 2.50e-03 4.78e+01 ... (remaining 17641 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.040: 2714 0.040 - 0.081: 1261 0.081 - 0.121: 364 0.121 - 0.162: 68 0.162 - 0.202: 5 Chirality restraints: 4412 Sorted by residual: chirality pdb=" CB ILE E 548 " pdb=" CA ILE E 548 " pdb=" CG1 ILE E 548 " pdb=" CG2 ILE E 548 " both_signs ideal model delta sigma weight residual False 2.64 2.44 0.20 2.00e-01 2.50e+01 1.02e+00 chirality pdb=" CA ASP B 799 " pdb=" N ASP B 799 " pdb=" C ASP B 799 " pdb=" CB ASP B 799 " both_signs ideal model delta sigma weight residual False 2.51 2.32 0.19 2.00e-01 2.50e+01 8.75e-01 chirality pdb=" CA ASP C 799 " pdb=" N ASP C 799 " pdb=" C ASP C 799 " pdb=" CB ASP C 799 " both_signs ideal model delta sigma weight residual False 2.51 2.33 0.18 2.00e-01 2.50e+01 8.36e-01 ... (remaining 4409 not shown) Planarity restraints: 5056 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LEU B 387 " 0.063 5.00e-02 4.00e+02 9.54e-02 1.46e+01 pdb=" N PRO B 388 " -0.165 5.00e-02 4.00e+02 pdb=" CA PRO B 388 " 0.052 5.00e-02 4.00e+02 pdb=" CD PRO B 388 " 0.051 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LYS C 301 " 0.036 5.00e-02 4.00e+02 5.39e-02 4.65e+00 pdb=" N PRO C 302 " -0.093 5.00e-02 4.00e+02 pdb=" CA PRO C 302 " 0.027 5.00e-02 4.00e+02 pdb=" CD PRO C 302 " 0.030 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB PHE B 798 " 0.016 2.00e-02 2.50e+03 1.55e-02 4.22e+00 pdb=" CG PHE B 798 " -0.036 2.00e-02 2.50e+03 pdb=" CD1 PHE B 798 " 0.010 2.00e-02 2.50e+03 pdb=" CD2 PHE B 798 " 0.006 2.00e-02 2.50e+03 pdb=" CE1 PHE B 798 " -0.001 2.00e-02 2.50e+03 pdb=" CE2 PHE B 798 " 0.004 2.00e-02 2.50e+03 pdb=" CZ PHE B 798 " 0.002 2.00e-02 2.50e+03 ... (remaining 5053 not shown) Histogram of nonbonded interaction distances: 1.81 - 2.43: 172 2.43 - 3.05: 19091 3.05 - 3.67: 39765 3.67 - 4.28: 58727 4.28 - 4.90: 97996 Nonbonded interactions: 215751 Sorted by model distance: nonbonded pdb=" OG1 THR E 614 " pdb=" O1A ADP E 902 " model vdw 1.813 2.440 nonbonded pdb=" CG2 ILE F 350 " pdb=" C2 ADP F 902 " model vdw 1.870 3.760 nonbonded pdb=" OG1 THR F 213 " pdb=" O1A ADP F 902 " model vdw 1.985 2.440 nonbonded pdb=" O1A ADP F 902 " pdb=" O3' ADP F 902 " model vdw 2.054 2.440 nonbonded pdb=" OG1 THR F 236 " pdb=" O GLN F 272 " model vdw 2.088 2.440 ... (remaining 215746 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 159 through 245 or resid 255 through 284 or resid 298 thro \ ugh 407 or resid 530 through 845 or resid 901)) selection = (chain 'B' and (resid 159 through 245 or resid 255 through 284 or resid 298 thro \ ugh 407 or resid 530 through 845 or resid 901)) selection = (chain 'C' and (resid 159 through 245 or resid 255 through 284 or resid 298 thro \ ugh 407 or resid 530 through 845 or resid 901)) selection = (chain 'D' and (resid 159 through 245 or resid 255 through 284 or resid 298 thro \ ugh 407 or resid 530 through 845 or resid 901)) selection = (chain 'E' and (resid 159 through 245 or resid 255 through 284 or resid 298 thro \ ugh 845 or resid 901)) selection = (chain 'F' and (resid 159 through 407 or resid 530 through 845 or resid 901)) } 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 group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.220 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.040 Extract box with map and model: 11.790 Check model and map are aligned: 0.450 Set scattering table: 0.280 Process input model: 76.240 Find NCS groups from input model: 2.570 Set up NCS constraints: 0.160 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:3.200 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 96.970 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8414 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 : 0.007 0.109 28548 Z= 0.466 Angle : 0.858 13.958 38610 Z= 0.484 Chirality : 0.048 0.202 4412 Planarity : 0.005 0.095 5056 Dihedral : 15.805 172.032 11016 Min Nonbonded Distance : 1.813 Molprobity Statistics. All-atom Clashscore : 12.00 Ramachandran Plot: Outliers : 0.17 % Allowed : 13.16 % Favored : 86.67 % Rotamer: Outliers : 0.85 % Allowed : 9.06 % Favored : 90.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.70 % Twisted General : 0.12 % 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: -4.61 (0.12), residues: 3540 helix: -2.44 (0.10), residues: 1740 sheet: -3.11 (0.24), residues: 365 loop : -3.73 (0.13), residues: 1435 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.002 TRP D 545 HIS 0.007 0.002 HIS B 643 PHE 0.036 0.002 PHE B 798 TYR 0.012 0.002 TYR D 639 ARG 0.005 0.001 ARG A 418 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7080 Ramachandran restraints generated. 3540 Oldfield, 0 Emsley, 3540 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7080 Ramachandran restraints generated. 3540 Oldfield, 0 Emsley, 3540 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 272 residues out of total 2925 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 247 time to evaluate : 3.291 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 564 MET cc_start: 0.8305 (ttp) cc_final: 0.8080 (ttp) REVERT: D 685 HIS cc_start: 0.8569 (OUTLIER) cc_final: 0.7602 (p90) REVERT: E 647 ARG cc_start: 0.8121 (ttp80) cc_final: 0.7837 (ttm110) REVERT: F 310 ARG cc_start: 0.6792 (mmp-170) cc_final: 0.6305 (mmp80) REVERT: F 628 GLU cc_start: 0.8178 (tp30) cc_final: 0.7699 (tp30) outliers start: 25 outliers final: 23 residues processed: 272 average time/residue: 0.5366 time to fit residues: 212.5428 Evaluate side-chains 178 residues out of total 2925 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 154 time to evaluate : 3.204 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 166 THR Chi-restraints excluded: chain A residue 461 THR Chi-restraints excluded: chain A residue 558 THR Chi-restraints excluded: chain B residue 166 THR Chi-restraints excluded: chain B residue 460 THR Chi-restraints excluded: chain B residue 461 THR Chi-restraints excluded: chain B residue 533 VAL Chi-restraints excluded: chain B residue 580 THR Chi-restraints excluded: chain B residue 644 THR Chi-restraints excluded: chain B residue 738 THR Chi-restraints excluded: chain C residue 558 THR Chi-restraints excluded: chain D residue 236 THR Chi-restraints excluded: chain D residue 558 THR Chi-restraints excluded: chain D residue 600 THR Chi-restraints excluded: chain D residue 644 THR Chi-restraints excluded: chain D residue 685 HIS Chi-restraints excluded: chain D residue 738 THR Chi-restraints excluded: chain E residue 236 THR Chi-restraints excluded: chain E residue 275 THR Chi-restraints excluded: chain E residue 600 THR Chi-restraints excluded: chain E residue 674 THR Chi-restraints excluded: chain F residue 275 THR Chi-restraints excluded: chain F residue 833 THR Chi-restraints excluded: chain F residue 836 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 358 random chunks: chunk 302 optimal weight: 9.9990 chunk 271 optimal weight: 10.0000 chunk 150 optimal weight: 2.9990 chunk 92 optimal weight: 1.9990 chunk 183 optimal weight: 1.9990 chunk 144 optimal weight: 0.1980 chunk 280 optimal weight: 4.9990 chunk 108 optimal weight: 0.8980 chunk 170 optimal weight: 0.7980 chunk 208 optimal weight: 0.9980 chunk 325 optimal weight: 10.0000 overall best weight: 0.9782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 201 ASN A 268 ASN A 281 HIS A 323 HIS B 323 HIS B 335 GLN B 361 HIS B 643 HIS B 685 HIS B 812 GLN B 813 GLN C 335 GLN C 361 HIS C 575 GLN C 663 GLN C 778 GLN D 361 HIS D 643 HIS D 705 HIS D 827 GLN E 201 ASN E 685 HIS F 298 ASN F 685 HIS F 705 HIS Total number of N/Q/H flips: 25 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8357 moved from start: 0.1294 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 28548 Z= 0.179 Angle : 0.629 10.467 38610 Z= 0.312 Chirality : 0.043 0.193 4412 Planarity : 0.005 0.089 5056 Dihedral : 11.269 165.688 4224 Min Nonbonded Distance : 2.112 Molprobity Statistics. All-atom Clashscore : 9.39 Ramachandran Plot: Outliers : 0.11 % Allowed : 9.83 % Favored : 90.06 % Rotamer: Outliers : 1.57 % Allowed : 14.23 % Favored : 84.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.70 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.20 (0.13), residues: 3540 helix: -1.27 (0.12), residues: 1743 sheet: -2.62 (0.24), residues: 385 loop : -3.01 (0.15), residues: 1412 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP D 545 HIS 0.013 0.001 HIS E 281 PHE 0.040 0.002 PHE D 798 TYR 0.013 0.001 TYR E 164 ARG 0.006 0.000 ARG F 808 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7080 Ramachandran restraints generated. 3540 Oldfield, 0 Emsley, 3540 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7080 Ramachandran restraints generated. 3540 Oldfield, 0 Emsley, 3540 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 242 residues out of total 2925 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 196 time to evaluate : 3.506 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 564 MET cc_start: 0.7900 (ttp) cc_final: 0.7489 (ttp) REVERT: C 468 ASN cc_start: 0.7599 (p0) cc_final: 0.7373 (p0) REVERT: D 685 HIS cc_start: 0.8376 (OUTLIER) cc_final: 0.7516 (p90) REVERT: E 564 MET cc_start: 0.7588 (mmm) cc_final: 0.7310 (mmm) REVERT: E 647 ARG cc_start: 0.7977 (ttp80) cc_final: 0.7754 (ttm110) REVERT: F 310 ARG cc_start: 0.6784 (mmp-170) cc_final: 0.6427 (mmp80) REVERT: F 393 ASP cc_start: 0.7313 (OUTLIER) cc_final: 0.7064 (t0) REVERT: F 412 GLU cc_start: 0.8011 (OUTLIER) cc_final: 0.7588 (pm20) REVERT: F 628 GLU cc_start: 0.8143 (tp30) cc_final: 0.7898 (tp30) outliers start: 46 outliers final: 27 residues processed: 235 average time/residue: 0.4468 time to fit residues: 162.9255 Evaluate side-chains 192 residues out of total 2925 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 162 time to evaluate : 3.787 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 299 MET Chi-restraints excluded: chain A residue 317 LEU Chi-restraints excluded: chain A residue 346 ASP Chi-restraints excluded: chain A residue 670 ARG Chi-restraints excluded: chain B residue 280 LEU Chi-restraints excluded: chain B residue 316 THR Chi-restraints excluded: chain B residue 461 THR Chi-restraints excluded: chain B residue 533 VAL Chi-restraints excluded: chain B residue 644 THR Chi-restraints excluded: chain B residue 675 VAL Chi-restraints excluded: chain B residue 838 VAL Chi-restraints excluded: chain C residue 649 ILE Chi-restraints excluded: chain C residue 659 GLU Chi-restraints excluded: chain D residue 234 ASP Chi-restraints excluded: chain D residue 299 MET Chi-restraints excluded: chain D residue 318 ASP Chi-restraints excluded: chain D residue 593 VAL Chi-restraints excluded: chain D residue 685 HIS Chi-restraints excluded: chain D residue 838 VAL Chi-restraints excluded: chain E residue 275 THR Chi-restraints excluded: chain E residue 316 THR Chi-restraints excluded: chain E residue 600 THR Chi-restraints excluded: chain F residue 236 THR Chi-restraints excluded: chain F residue 275 THR Chi-restraints excluded: chain F residue 284 VAL Chi-restraints excluded: chain F residue 318 ASP Chi-restraints excluded: chain F residue 378 SER Chi-restraints excluded: chain F residue 393 ASP Chi-restraints excluded: chain F residue 412 GLU Chi-restraints excluded: chain F residue 836 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 358 random chunks: chunk 180 optimal weight: 3.9990 chunk 100 optimal weight: 0.9990 chunk 270 optimal weight: 6.9990 chunk 221 optimal weight: 2.9990 chunk 89 optimal weight: 0.9990 chunk 325 optimal weight: 0.0270 chunk 351 optimal weight: 0.7980 chunk 290 optimal weight: 20.0000 chunk 322 optimal weight: 10.0000 chunk 111 optimal weight: 2.9990 chunk 261 optimal weight: 9.9990 overall best weight: 1.1644 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 575 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 201 ASN E 818 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8352 moved from start: 0.1603 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 28548 Z= 0.179 Angle : 0.589 9.427 38610 Z= 0.290 Chirality : 0.042 0.189 4412 Planarity : 0.004 0.085 5056 Dihedral : 10.843 161.499 4208 Min Nonbonded Distance : 2.109 Molprobity Statistics. All-atom Clashscore : 8.89 Ramachandran Plot: Outliers : 0.14 % Allowed : 10.03 % Favored : 89.83 % Rotamer: Outliers : 2.39 % Allowed : 16.28 % Favored : 81.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.70 % 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: -2.65 (0.14), residues: 3540 helix: -0.82 (0.13), residues: 1731 sheet: -2.30 (0.25), residues: 385 loop : -2.71 (0.15), residues: 1424 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.001 TRP F 545 HIS 0.004 0.001 HIS C 643 PHE 0.040 0.001 PHE D 798 TYR 0.009 0.001 TYR E 164 ARG 0.003 0.000 ARG F 563 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7080 Ramachandran restraints generated. 3540 Oldfield, 0 Emsley, 3540 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7080 Ramachandran restraints generated. 3540 Oldfield, 0 Emsley, 3540 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 254 residues out of total 2925 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 70 poor density : 184 time to evaluate : 3.144 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 564 MET cc_start: 0.7934 (ttp) cc_final: 0.7453 (ttp) REVERT: B 603 PHE cc_start: 0.8990 (OUTLIER) cc_final: 0.7396 (p90) REVERT: D 685 HIS cc_start: 0.8346 (OUTLIER) cc_final: 0.7733 (p90) REVERT: D 713 ASN cc_start: 0.8772 (OUTLIER) cc_final: 0.8550 (p0) REVERT: E 201 ASN cc_start: 0.8651 (OUTLIER) cc_final: 0.8384 (p0) REVERT: E 245 MET cc_start: 0.1625 (mmt) cc_final: 0.1362 (mmt) REVERT: E 299 MET cc_start: 0.8207 (tmm) cc_final: 0.7830 (tmm) REVERT: E 545 TRP cc_start: 0.8073 (m100) cc_final: 0.7809 (m100) REVERT: E 564 MET cc_start: 0.7518 (mmm) cc_final: 0.7272 (mmm) REVERT: E 647 ARG cc_start: 0.7958 (ttp80) cc_final: 0.7747 (ttm110) REVERT: E 829 HIS cc_start: 0.6931 (t70) cc_final: 0.6543 (m90) REVERT: F 299 MET cc_start: 0.5548 (pmm) cc_final: 0.5176 (tpt) REVERT: F 310 ARG cc_start: 0.6760 (mmp-170) cc_final: 0.6463 (mmp80) REVERT: F 324 ILE cc_start: 0.8398 (OUTLIER) cc_final: 0.8042 (tp) REVERT: F 412 GLU cc_start: 0.7855 (OUTLIER) cc_final: 0.7605 (pm20) REVERT: F 754 GLU cc_start: 0.6887 (OUTLIER) cc_final: 0.6602 (pt0) outliers start: 70 outliers final: 39 residues processed: 243 average time/residue: 0.4383 time to fit residues: 166.3820 Evaluate side-chains 196 residues out of total 2925 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 150 time to evaluate : 3.307 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 246 VAL Chi-restraints excluded: chain A residue 299 MET Chi-restraints excluded: chain A residue 317 LEU Chi-restraints excluded: chain A residue 367 THR Chi-restraints excluded: chain A residue 419 LEU Chi-restraints excluded: chain A residue 600 THR Chi-restraints excluded: chain A residue 670 ARG Chi-restraints excluded: chain A residue 702 THR Chi-restraints excluded: chain A residue 776 LEU Chi-restraints excluded: chain B residue 280 LEU Chi-restraints excluded: chain B residue 316 THR Chi-restraints excluded: chain B residue 393 ASP Chi-restraints excluded: chain B residue 603 PHE Chi-restraints excluded: chain B residue 675 VAL Chi-restraints excluded: chain B residue 838 VAL Chi-restraints excluded: chain C residue 166 THR Chi-restraints excluded: chain C residue 649 ILE Chi-restraints excluded: chain C residue 713 ASN Chi-restraints excluded: chain D residue 234 ASP Chi-restraints excluded: chain D residue 237 ILE Chi-restraints excluded: chain D residue 299 MET Chi-restraints excluded: chain D residue 318 ASP Chi-restraints excluded: chain D residue 383 THR Chi-restraints excluded: chain D residue 685 HIS Chi-restraints excluded: chain D residue 713 ASN Chi-restraints excluded: chain D residue 838 VAL Chi-restraints excluded: chain E residue 201 ASN Chi-restraints excluded: chain E residue 275 THR Chi-restraints excluded: chain E residue 309 LEU Chi-restraints excluded: chain E residue 316 THR Chi-restraints excluded: chain E residue 600 THR Chi-restraints excluded: chain E residue 632 VAL Chi-restraints excluded: chain E residue 757 ASN Chi-restraints excluded: chain E residue 801 VAL Chi-restraints excluded: chain F residue 224 VAL Chi-restraints excluded: chain F residue 236 THR Chi-restraints excluded: chain F residue 275 THR Chi-restraints excluded: chain F residue 284 VAL Chi-restraints excluded: chain F residue 318 ASP Chi-restraints excluded: chain F residue 324 ILE Chi-restraints excluded: chain F residue 361 HIS Chi-restraints excluded: chain F residue 378 SER Chi-restraints excluded: chain F residue 412 GLU Chi-restraints excluded: chain F residue 754 GLU Chi-restraints excluded: chain F residue 834 VAL Chi-restraints excluded: chain F residue 836 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 358 random chunks: chunk 321 optimal weight: 0.7980 chunk 244 optimal weight: 0.8980 chunk 169 optimal weight: 2.9990 chunk 36 optimal weight: 6.9990 chunk 155 optimal weight: 5.9990 chunk 218 optimal weight: 5.9990 chunk 326 optimal weight: 6.9990 chunk 346 optimal weight: 0.9990 chunk 170 optimal weight: 4.9990 chunk 309 optimal weight: 1.9990 chunk 93 optimal weight: 2.9990 overall best weight: 1.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 452 GLN B 795 GLN ** C 575 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 818 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8360 moved from start: 0.1765 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 28548 Z= 0.205 Angle : 0.592 10.318 38610 Z= 0.291 Chirality : 0.042 0.245 4412 Planarity : 0.004 0.087 5056 Dihedral : 10.690 158.401 4205 Min Nonbonded Distance : 2.114 Molprobity Statistics. All-atom Clashscore : 8.98 Ramachandran Plot: Outliers : 0.14 % Allowed : 9.97 % Favored : 89.89 % Rotamer: Outliers : 2.98 % Allowed : 17.10 % Favored : 79.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.70 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.40 (0.14), residues: 3540 helix: -0.65 (0.13), residues: 1734 sheet: -2.10 (0.25), residues: 373 loop : -2.57 (0.16), residues: 1433 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.039 0.001 TRP F 545 HIS 0.004 0.001 HIS C 643 PHE 0.040 0.001 PHE D 798 TYR 0.018 0.001 TYR E 164 ARG 0.008 0.000 ARG D 780 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7080 Ramachandran restraints generated. 3540 Oldfield, 0 Emsley, 3540 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7080 Ramachandran restraints generated. 3540 Oldfield, 0 Emsley, 3540 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 241 residues out of total 2925 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 87 poor density : 154 time to evaluate : 3.493 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 603 PHE cc_start: 0.8642 (OUTLIER) cc_final: 0.7506 (p90) REVERT: B 564 MET cc_start: 0.7973 (ttp) cc_final: 0.7444 (ttp) REVERT: B 603 PHE cc_start: 0.9004 (OUTLIER) cc_final: 0.7422 (p90) REVERT: C 722 LEU cc_start: 0.8547 (OUTLIER) cc_final: 0.8297 (mp) REVERT: D 217 GLU cc_start: 0.7779 (OUTLIER) cc_final: 0.7411 (mp0) REVERT: D 685 HIS cc_start: 0.8320 (OUTLIER) cc_final: 0.7916 (p90) REVERT: D 713 ASN cc_start: 0.8757 (OUTLIER) cc_final: 0.8532 (p0) REVERT: D 827 GLN cc_start: 0.8168 (OUTLIER) cc_final: 0.7908 (pm20) REVERT: E 245 MET cc_start: 0.1555 (mmt) cc_final: 0.1288 (mmt) REVERT: E 545 TRP cc_start: 0.8064 (m100) cc_final: 0.7797 (m100) REVERT: E 564 MET cc_start: 0.7527 (mmm) cc_final: 0.7288 (mmm) REVERT: E 647 ARG cc_start: 0.8022 (ttp80) cc_final: 0.7736 (ttm110) REVERT: E 829 HIS cc_start: 0.7048 (t70) cc_final: 0.6628 (m90) REVERT: F 299 MET cc_start: 0.5682 (pmm) cc_final: 0.5202 (tpt) REVERT: F 306 ARG cc_start: 0.7957 (mtt90) cc_final: 0.6896 (tpp-160) REVERT: F 310 ARG cc_start: 0.6744 (mmp-170) cc_final: 0.6444 (mmp80) REVERT: F 324 ILE cc_start: 0.8384 (OUTLIER) cc_final: 0.8160 (tp) REVERT: F 412 GLU cc_start: 0.7822 (OUTLIER) cc_final: 0.7611 (pm20) REVERT: F 605 PHE cc_start: 0.7966 (OUTLIER) cc_final: 0.6787 (p90) outliers start: 87 outliers final: 55 residues processed: 231 average time/residue: 0.4191 time to fit residues: 155.0103 Evaluate side-chains 210 residues out of total 2925 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 65 poor density : 145 time to evaluate : 3.438 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 246 VAL Chi-restraints excluded: chain A residue 299 MET Chi-restraints excluded: chain A residue 317 LEU Chi-restraints excluded: chain A residue 346 ASP Chi-restraints excluded: chain A residue 367 THR Chi-restraints excluded: chain A residue 419 LEU Chi-restraints excluded: chain A residue 600 THR Chi-restraints excluded: chain A residue 603 PHE Chi-restraints excluded: chain A residue 670 ARG Chi-restraints excluded: chain A residue 702 THR Chi-restraints excluded: chain A residue 776 LEU Chi-restraints excluded: chain B residue 280 LEU Chi-restraints excluded: chain B residue 316 THR Chi-restraints excluded: chain B residue 387 LEU Chi-restraints excluded: chain B residue 393 ASP Chi-restraints excluded: chain B residue 533 VAL Chi-restraints excluded: chain B residue 603 PHE Chi-restraints excluded: chain B residue 675 VAL Chi-restraints excluded: chain B residue 783 LEU Chi-restraints excluded: chain B residue 828 VAL Chi-restraints excluded: chain B residue 838 VAL Chi-restraints excluded: chain C residue 166 THR Chi-restraints excluded: chain C residue 606 LEU Chi-restraints excluded: chain C residue 609 THR Chi-restraints excluded: chain C residue 649 ILE Chi-restraints excluded: chain C residue 659 GLU Chi-restraints excluded: chain C residue 713 ASN Chi-restraints excluded: chain C residue 722 LEU Chi-restraints excluded: chain D residue 161 LEU Chi-restraints excluded: chain D residue 217 GLU Chi-restraints excluded: chain D residue 234 ASP Chi-restraints excluded: chain D residue 237 ILE Chi-restraints excluded: chain D residue 284 VAL Chi-restraints excluded: chain D residue 299 MET Chi-restraints excluded: chain D residue 318 ASP Chi-restraints excluded: chain D residue 383 THR Chi-restraints excluded: chain D residue 593 VAL Chi-restraints excluded: chain D residue 605 PHE Chi-restraints excluded: chain D residue 685 HIS Chi-restraints excluded: chain D residue 713 ASN Chi-restraints excluded: chain D residue 718 LEU Chi-restraints excluded: chain D residue 827 GLN Chi-restraints excluded: chain D residue 838 VAL Chi-restraints excluded: chain E residue 200 ASN Chi-restraints excluded: chain E residue 275 THR Chi-restraints excluded: chain E residue 304 LEU Chi-restraints excluded: chain E residue 309 LEU Chi-restraints excluded: chain E residue 316 THR Chi-restraints excluded: chain E residue 632 VAL Chi-restraints excluded: chain E residue 801 VAL Chi-restraints excluded: chain F residue 224 VAL Chi-restraints excluded: chain F residue 236 THR Chi-restraints excluded: chain F residue 275 THR Chi-restraints excluded: chain F residue 284 VAL Chi-restraints excluded: chain F residue 318 ASP Chi-restraints excluded: chain F residue 324 ILE Chi-restraints excluded: chain F residue 350 ILE Chi-restraints excluded: chain F residue 361 HIS Chi-restraints excluded: chain F residue 378 SER Chi-restraints excluded: chain F residue 393 ASP Chi-restraints excluded: chain F residue 412 GLU Chi-restraints excluded: chain F residue 605 PHE Chi-restraints excluded: chain F residue 675 VAL Chi-restraints excluded: chain F residue 834 VAL Chi-restraints excluded: chain F residue 836 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 358 random chunks: chunk 288 optimal weight: 0.9990 chunk 196 optimal weight: 3.9990 chunk 5 optimal weight: 2.9990 chunk 257 optimal weight: 3.9990 chunk 142 optimal weight: 0.9990 chunk 295 optimal weight: 8.9990 chunk 239 optimal weight: 1.9990 chunk 0 optimal weight: 9.9990 chunk 176 optimal weight: 5.9990 chunk 310 optimal weight: 0.6980 chunk 87 optimal weight: 1.9990 overall best weight: 1.3388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 575 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 685 HIS E 201 ASN E 818 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8351 moved from start: 0.1956 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.067 28548 Z= 0.190 Angle : 0.575 9.881 38610 Z= 0.282 Chirality : 0.042 0.187 4412 Planarity : 0.004 0.086 5056 Dihedral : 10.457 154.461 4204 Min Nonbonded Distance : 2.128 Molprobity Statistics. All-atom Clashscore : 8.71 Ramachandran Plot: Outliers : 0.08 % Allowed : 9.77 % Favored : 90.14 % Rotamer: Outliers : 3.21 % Allowed : 17.99 % Favored : 78.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.70 % 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: -2.14 (0.14), residues: 3540 helix: -0.47 (0.13), residues: 1736 sheet: -2.05 (0.26), residues: 360 loop : -2.37 (0.16), residues: 1444 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.056 0.002 TRP F 545 HIS 0.003 0.001 HIS C 643 PHE 0.043 0.001 PHE D 798 TYR 0.015 0.001 TYR F 658 ARG 0.002 0.000 ARG F 563 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7080 Ramachandran restraints generated. 3540 Oldfield, 0 Emsley, 3540 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7080 Ramachandran restraints generated. 3540 Oldfield, 0 Emsley, 3540 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 257 residues out of total 2925 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 94 poor density : 163 time to evaluate : 3.594 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 603 PHE cc_start: 0.8665 (OUTLIER) cc_final: 0.7490 (p90) REVERT: B 564 MET cc_start: 0.7945 (ttp) cc_final: 0.7385 (ttp) REVERT: B 603 PHE cc_start: 0.9006 (OUTLIER) cc_final: 0.7417 (p90) REVERT: B 791 ARG cc_start: 0.7222 (ttm110) cc_final: 0.6986 (tpp80) REVERT: D 217 GLU cc_start: 0.7766 (OUTLIER) cc_final: 0.7411 (mp0) REVERT: D 564 MET cc_start: 0.8568 (tpp) cc_final: 0.8210 (ttt) REVERT: D 685 HIS cc_start: 0.8317 (OUTLIER) cc_final: 0.8043 (p90) REVERT: D 827 GLN cc_start: 0.8345 (OUTLIER) cc_final: 0.8003 (pm20) REVERT: E 201 ASN cc_start: 0.8684 (OUTLIER) cc_final: 0.8290 (p0) REVERT: E 245 MET cc_start: 0.1588 (mmt) cc_final: 0.1340 (mmt) REVERT: E 299 MET cc_start: 0.8239 (tmm) cc_final: 0.7909 (tmm) REVERT: E 564 MET cc_start: 0.7527 (mmm) cc_final: 0.7294 (mmm) REVERT: E 636 MET cc_start: 0.8977 (mmm) cc_final: 0.8744 (mmm) REVERT: E 647 ARG cc_start: 0.8000 (ttp80) cc_final: 0.7719 (ttm110) REVERT: E 829 HIS cc_start: 0.6946 (t70) cc_final: 0.6612 (m90) REVERT: F 310 ARG cc_start: 0.6735 (mmp-170) cc_final: 0.6456 (mmp80) REVERT: F 324 ILE cc_start: 0.8348 (OUTLIER) cc_final: 0.8113 (tp) REVERT: F 338 TYR cc_start: 0.7910 (OUTLIER) cc_final: 0.7542 (m-80) REVERT: F 412 GLU cc_start: 0.7812 (OUTLIER) cc_final: 0.7509 (pm20) REVERT: F 605 PHE cc_start: 0.7978 (OUTLIER) cc_final: 0.6813 (p90) outliers start: 94 outliers final: 62 residues processed: 246 average time/residue: 0.4155 time to fit residues: 164.2749 Evaluate side-chains 222 residues out of total 2925 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 72 poor density : 150 time to evaluate : 3.546 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 246 VAL Chi-restraints excluded: chain A residue 299 MET Chi-restraints excluded: chain A residue 346 ASP Chi-restraints excluded: chain A residue 367 THR Chi-restraints excluded: chain A residue 600 THR Chi-restraints excluded: chain A residue 603 PHE Chi-restraints excluded: chain A residue 632 VAL Chi-restraints excluded: chain A residue 670 ARG Chi-restraints excluded: chain A residue 702 THR Chi-restraints excluded: chain A residue 731 VAL Chi-restraints excluded: chain A residue 776 LEU Chi-restraints excluded: chain A residue 828 VAL Chi-restraints excluded: chain A residue 836 VAL Chi-restraints excluded: chain B residue 280 LEU Chi-restraints excluded: chain B residue 316 THR Chi-restraints excluded: chain B residue 347 THR Chi-restraints excluded: chain B residue 387 LEU Chi-restraints excluded: chain B residue 393 ASP Chi-restraints excluded: chain B residue 411 VAL Chi-restraints excluded: chain B residue 533 VAL Chi-restraints excluded: chain B residue 603 PHE Chi-restraints excluded: chain B residue 675 VAL Chi-restraints excluded: chain B residue 783 LEU Chi-restraints excluded: chain B residue 828 VAL Chi-restraints excluded: chain B residue 838 VAL Chi-restraints excluded: chain C residue 166 THR Chi-restraints excluded: chain C residue 606 LEU Chi-restraints excluded: chain C residue 609 THR Chi-restraints excluded: chain C residue 649 ILE Chi-restraints excluded: chain C residue 659 GLU Chi-restraints excluded: chain C residue 713 ASN Chi-restraints excluded: chain D residue 217 GLU Chi-restraints excluded: chain D residue 234 ASP Chi-restraints excluded: chain D residue 237 ILE Chi-restraints excluded: chain D residue 284 VAL Chi-restraints excluded: chain D residue 299 MET Chi-restraints excluded: chain D residue 318 ASP Chi-restraints excluded: chain D residue 383 THR Chi-restraints excluded: chain D residue 593 VAL Chi-restraints excluded: chain D residue 605 PHE Chi-restraints excluded: chain D residue 685 HIS Chi-restraints excluded: chain D residue 718 LEU Chi-restraints excluded: chain D residue 827 GLN Chi-restraints excluded: chain D residue 838 VAL Chi-restraints excluded: chain E residue 200 ASN Chi-restraints excluded: chain E residue 201 ASN Chi-restraints excluded: chain E residue 262 VAL Chi-restraints excluded: chain E residue 304 LEU Chi-restraints excluded: chain E residue 309 LEU Chi-restraints excluded: chain E residue 316 THR Chi-restraints excluded: chain E residue 632 VAL Chi-restraints excluded: chain E residue 634 ILE Chi-restraints excluded: chain E residue 679 ASP Chi-restraints excluded: chain E residue 690 ASP Chi-restraints excluded: chain E residue 757 ASN Chi-restraints excluded: chain F residue 224 VAL Chi-restraints excluded: chain F residue 236 THR Chi-restraints excluded: chain F residue 275 THR Chi-restraints excluded: chain F residue 284 VAL Chi-restraints excluded: chain F residue 303 MET Chi-restraints excluded: chain F residue 318 ASP Chi-restraints excluded: chain F residue 324 ILE Chi-restraints excluded: chain F residue 338 TYR Chi-restraints excluded: chain F residue 350 ILE Chi-restraints excluded: chain F residue 361 HIS Chi-restraints excluded: chain F residue 378 SER Chi-restraints excluded: chain F residue 412 GLU Chi-restraints excluded: chain F residue 605 PHE Chi-restraints excluded: chain F residue 675 VAL Chi-restraints excluded: chain F residue 824 LEU Chi-restraints excluded: chain F residue 834 VAL Chi-restraints excluded: chain F residue 836 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 358 random chunks: chunk 116 optimal weight: 0.9990 chunk 311 optimal weight: 7.9990 chunk 68 optimal weight: 0.6980 chunk 203 optimal weight: 0.9980 chunk 85 optimal weight: 0.4980 chunk 346 optimal weight: 10.0000 chunk 287 optimal weight: 1.9990 chunk 160 optimal weight: 0.9990 chunk 28 optimal weight: 3.9990 chunk 114 optimal weight: 2.9990 chunk 181 optimal weight: 1.9990 overall best weight: 0.8384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 452 GLN ** C 575 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 281 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8332 moved from start: 0.2143 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.053 28548 Z= 0.152 Angle : 0.559 10.076 38610 Z= 0.274 Chirality : 0.041 0.188 4412 Planarity : 0.004 0.085 5056 Dihedral : 10.222 153.619 4203 Min Nonbonded Distance : 2.108 Molprobity Statistics. All-atom Clashscore : 8.45 Ramachandran Plot: Outliers : 0.06 % Allowed : 9.41 % Favored : 90.54 % Rotamer: Outliers : 2.67 % Allowed : 19.19 % Favored : 78.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.70 % 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: -1.93 (0.14), residues: 3540 helix: -0.31 (0.13), residues: 1735 sheet: -1.98 (0.26), residues: 364 loop : -2.26 (0.16), residues: 1441 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.060 0.002 TRP F 545 HIS 0.007 0.001 HIS E 281 PHE 0.041 0.001 PHE D 798 TYR 0.009 0.001 TYR E 164 ARG 0.003 0.000 ARG D 401 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7080 Ramachandran restraints generated. 3540 Oldfield, 0 Emsley, 3540 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7080 Ramachandran restraints generated. 3540 Oldfield, 0 Emsley, 3540 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 247 residues out of total 2925 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 78 poor density : 169 time to evaluate : 3.310 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 603 PHE cc_start: 0.8653 (OUTLIER) cc_final: 0.7435 (p90) REVERT: B 564 MET cc_start: 0.7910 (ttp) cc_final: 0.7307 (ttp) REVERT: B 603 PHE cc_start: 0.8986 (OUTLIER) cc_final: 0.7356 (p90) REVERT: C 327 ASP cc_start: 0.8352 (t0) cc_final: 0.7893 (t70) REVERT: C 722 LEU cc_start: 0.8546 (OUTLIER) cc_final: 0.8316 (mp) REVERT: D 217 GLU cc_start: 0.7748 (OUTLIER) cc_final: 0.7405 (mp0) REVERT: D 685 HIS cc_start: 0.8296 (OUTLIER) cc_final: 0.7992 (p90) REVERT: D 827 GLN cc_start: 0.8336 (OUTLIER) cc_final: 0.7958 (pm20) REVERT: E 245 MET cc_start: 0.1573 (mmt) cc_final: 0.1325 (mmt) REVERT: E 281 HIS cc_start: 0.5216 (p-80) cc_final: 0.4451 (p90) REVERT: E 299 MET cc_start: 0.8225 (tmm) cc_final: 0.7900 (tmm) REVERT: E 404 MET cc_start: 0.8487 (ptt) cc_final: 0.7995 (mmt) REVERT: E 564 MET cc_start: 0.7532 (mmm) cc_final: 0.7323 (mmm) REVERT: E 647 ARG cc_start: 0.7986 (ttp80) cc_final: 0.7715 (ttm110) REVERT: E 829 HIS cc_start: 0.6816 (t70) cc_final: 0.6590 (m90) REVERT: F 310 ARG cc_start: 0.6661 (mmp-170) cc_final: 0.6420 (mmp80) REVERT: F 324 ILE cc_start: 0.8346 (OUTLIER) cc_final: 0.8123 (tp) REVERT: F 338 TYR cc_start: 0.7888 (OUTLIER) cc_final: 0.7528 (m-80) REVERT: F 412 GLU cc_start: 0.7770 (OUTLIER) cc_final: 0.7465 (pm20) REVERT: F 605 PHE cc_start: 0.7975 (OUTLIER) cc_final: 0.7037 (p90) outliers start: 78 outliers final: 57 residues processed: 238 average time/residue: 0.4127 time to fit residues: 157.5849 Evaluate side-chains 219 residues out of total 2925 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 67 poor density : 152 time to evaluate : 3.447 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 246 VAL Chi-restraints excluded: chain A residue 299 MET Chi-restraints excluded: chain A residue 317 LEU Chi-restraints excluded: chain A residue 346 ASP Chi-restraints excluded: chain A residue 367 THR Chi-restraints excluded: chain A residue 600 THR Chi-restraints excluded: chain A residue 603 PHE Chi-restraints excluded: chain A residue 632 VAL Chi-restraints excluded: chain A residue 670 ARG Chi-restraints excluded: chain A residue 702 THR Chi-restraints excluded: chain A residue 731 VAL Chi-restraints excluded: chain A residue 776 LEU Chi-restraints excluded: chain A residue 828 VAL Chi-restraints excluded: chain A residue 836 VAL Chi-restraints excluded: chain B residue 201 ASN Chi-restraints excluded: chain B residue 280 LEU Chi-restraints excluded: chain B residue 316 THR Chi-restraints excluded: chain B residue 347 THR Chi-restraints excluded: chain B residue 387 LEU Chi-restraints excluded: chain B residue 393 ASP Chi-restraints excluded: chain B residue 533 VAL Chi-restraints excluded: chain B residue 603 PHE Chi-restraints excluded: chain B residue 675 VAL Chi-restraints excluded: chain B residue 783 LEU Chi-restraints excluded: chain B residue 828 VAL Chi-restraints excluded: chain B residue 838 VAL Chi-restraints excluded: chain C residue 166 THR Chi-restraints excluded: chain C residue 606 LEU Chi-restraints excluded: chain C residue 609 THR Chi-restraints excluded: chain C residue 649 ILE Chi-restraints excluded: chain C residue 659 GLU Chi-restraints excluded: chain C residue 713 ASN Chi-restraints excluded: chain C residue 722 LEU Chi-restraints excluded: chain D residue 161 LEU Chi-restraints excluded: chain D residue 217 GLU Chi-restraints excluded: chain D residue 234 ASP Chi-restraints excluded: chain D residue 237 ILE Chi-restraints excluded: chain D residue 284 VAL Chi-restraints excluded: chain D residue 299 MET Chi-restraints excluded: chain D residue 318 ASP Chi-restraints excluded: chain D residue 593 VAL Chi-restraints excluded: chain D residue 605 PHE Chi-restraints excluded: chain D residue 685 HIS Chi-restraints excluded: chain D residue 713 ASN Chi-restraints excluded: chain D residue 827 GLN Chi-restraints excluded: chain D residue 838 VAL Chi-restraints excluded: chain E residue 200 ASN Chi-restraints excluded: chain E residue 262 VAL Chi-restraints excluded: chain E residue 316 THR Chi-restraints excluded: chain E residue 632 VAL Chi-restraints excluded: chain E residue 674 THR Chi-restraints excluded: chain E residue 776 LEU Chi-restraints excluded: chain F residue 224 VAL Chi-restraints excluded: chain F residue 236 THR Chi-restraints excluded: chain F residue 318 ASP Chi-restraints excluded: chain F residue 324 ILE Chi-restraints excluded: chain F residue 338 TYR Chi-restraints excluded: chain F residue 350 ILE Chi-restraints excluded: chain F residue 361 HIS Chi-restraints excluded: chain F residue 378 SER Chi-restraints excluded: chain F residue 393 ASP Chi-restraints excluded: chain F residue 412 GLU Chi-restraints excluded: chain F residue 605 PHE Chi-restraints excluded: chain F residue 675 VAL Chi-restraints excluded: chain F residue 824 LEU Chi-restraints excluded: chain F residue 834 VAL Chi-restraints excluded: chain F residue 836 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 358 random chunks: chunk 333 optimal weight: 1.9990 chunk 39 optimal weight: 3.9990 chunk 197 optimal weight: 0.0980 chunk 252 optimal weight: 10.0000 chunk 195 optimal weight: 4.9990 chunk 291 optimal weight: 5.9990 chunk 193 optimal weight: 0.9980 chunk 345 optimal weight: 2.9990 chunk 215 optimal weight: 8.9990 chunk 210 optimal weight: 0.5980 chunk 159 optimal weight: 5.9990 overall best weight: 1.3384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 575 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 818 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8345 moved from start: 0.2230 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 28548 Z= 0.185 Angle : 0.567 10.480 38610 Z= 0.277 Chirality : 0.042 0.182 4412 Planarity : 0.004 0.087 5056 Dihedral : 10.094 152.335 4202 Min Nonbonded Distance : 2.111 Molprobity Statistics. All-atom Clashscore : 8.62 Ramachandran Plot: Outliers : 0.08 % Allowed : 9.75 % Favored : 90.17 % Rotamer: Outliers : 3.04 % Allowed : 19.63 % Favored : 77.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.70 % 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: -1.81 (0.14), residues: 3540 helix: -0.20 (0.13), residues: 1736 sheet: -1.96 (0.26), residues: 360 loop : -2.19 (0.16), residues: 1444 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.054 0.001 TRP F 545 HIS 0.013 0.001 HIS E 281 PHE 0.041 0.001 PHE D 798 TYR 0.014 0.001 TYR F 658 ARG 0.004 0.000 ARG E 563 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7080 Ramachandran restraints generated. 3540 Oldfield, 0 Emsley, 3540 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7080 Ramachandran restraints generated. 3540 Oldfield, 0 Emsley, 3540 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 251 residues out of total 2925 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 89 poor density : 162 time to evaluate : 3.482 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 603 PHE cc_start: 0.8670 (OUTLIER) cc_final: 0.7427 (p90) REVERT: B 564 MET cc_start: 0.7966 (ttp) cc_final: 0.7316 (ttp) REVERT: B 603 PHE cc_start: 0.9004 (OUTLIER) cc_final: 0.7323 (p90) REVERT: B 605 PHE cc_start: 0.8963 (OUTLIER) cc_final: 0.8563 (p90) REVERT: C 327 ASP cc_start: 0.8371 (t0) cc_final: 0.7922 (t70) REVERT: C 465 ASN cc_start: 0.7850 (m-40) cc_final: 0.7467 (t0) REVERT: C 722 LEU cc_start: 0.8593 (OUTLIER) cc_final: 0.8362 (mp) REVERT: D 217 GLU cc_start: 0.7739 (OUTLIER) cc_final: 0.7368 (mp0) REVERT: E 245 MET cc_start: 0.1588 (mmt) cc_final: 0.1343 (mmt) REVERT: E 299 MET cc_start: 0.8246 (tmm) cc_final: 0.7912 (tmm) REVERT: E 404 MET cc_start: 0.8507 (ptt) cc_final: 0.7976 (mmt) REVERT: E 564 MET cc_start: 0.7593 (mmm) cc_final: 0.7392 (mmm) REVERT: E 647 ARG cc_start: 0.8030 (ttp80) cc_final: 0.7732 (ttm110) REVERT: E 829 HIS cc_start: 0.6834 (t70) cc_final: 0.6628 (m90) REVERT: F 310 ARG cc_start: 0.6696 (mmp-170) cc_final: 0.6448 (mmp80) REVERT: F 324 ILE cc_start: 0.8358 (OUTLIER) cc_final: 0.8116 (tp) REVERT: F 338 TYR cc_start: 0.7924 (OUTLIER) cc_final: 0.7539 (m-80) REVERT: F 412 GLU cc_start: 0.7785 (OUTLIER) cc_final: 0.7477 (pm20) outliers start: 89 outliers final: 70 residues processed: 239 average time/residue: 0.4086 time to fit residues: 158.1947 Evaluate side-chains 231 residues out of total 2925 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 78 poor density : 153 time to evaluate : 3.591 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 246 VAL Chi-restraints excluded: chain A residue 299 MET Chi-restraints excluded: chain A residue 317 LEU Chi-restraints excluded: chain A residue 346 ASP Chi-restraints excluded: chain A residue 367 THR Chi-restraints excluded: chain A residue 412 GLU Chi-restraints excluded: chain A residue 420 VAL Chi-restraints excluded: chain A residue 600 THR Chi-restraints excluded: chain A residue 603 PHE Chi-restraints excluded: chain A residue 632 VAL Chi-restraints excluded: chain A residue 670 ARG Chi-restraints excluded: chain A residue 702 THR Chi-restraints excluded: chain A residue 731 VAL Chi-restraints excluded: chain A residue 776 LEU Chi-restraints excluded: chain A residue 828 VAL Chi-restraints excluded: chain A residue 834 VAL Chi-restraints excluded: chain B residue 201 ASN Chi-restraints excluded: chain B residue 205 ILE Chi-restraints excluded: chain B residue 280 LEU Chi-restraints excluded: chain B residue 316 THR Chi-restraints excluded: chain B residue 347 THR Chi-restraints excluded: chain B residue 387 LEU Chi-restraints excluded: chain B residue 393 ASP Chi-restraints excluded: chain B residue 533 VAL Chi-restraints excluded: chain B residue 603 PHE Chi-restraints excluded: chain B residue 605 PHE Chi-restraints excluded: chain B residue 609 THR Chi-restraints excluded: chain B residue 675 VAL Chi-restraints excluded: chain B residue 783 LEU Chi-restraints excluded: chain B residue 828 VAL Chi-restraints excluded: chain B residue 838 VAL Chi-restraints excluded: chain C residue 166 THR Chi-restraints excluded: chain C residue 548 ILE Chi-restraints excluded: chain C residue 606 LEU Chi-restraints excluded: chain C residue 609 THR Chi-restraints excluded: chain C residue 649 ILE Chi-restraints excluded: chain C residue 659 GLU Chi-restraints excluded: chain C residue 713 ASN Chi-restraints excluded: chain C residue 722 LEU Chi-restraints excluded: chain D residue 161 LEU Chi-restraints excluded: chain D residue 217 GLU Chi-restraints excluded: chain D residue 234 ASP Chi-restraints excluded: chain D residue 237 ILE Chi-restraints excluded: chain D residue 299 MET Chi-restraints excluded: chain D residue 318 ASP Chi-restraints excluded: chain D residue 593 VAL Chi-restraints excluded: chain D residue 605 PHE Chi-restraints excluded: chain D residue 685 HIS Chi-restraints excluded: chain D residue 713 ASN Chi-restraints excluded: chain D residue 718 LEU Chi-restraints excluded: chain D residue 838 VAL Chi-restraints excluded: chain E residue 200 ASN Chi-restraints excluded: chain E residue 262 VAL Chi-restraints excluded: chain E residue 309 LEU Chi-restraints excluded: chain E residue 316 THR Chi-restraints excluded: chain E residue 632 VAL Chi-restraints excluded: chain E residue 634 ILE Chi-restraints excluded: chain E residue 674 THR Chi-restraints excluded: chain E residue 690 ASP Chi-restraints excluded: chain E residue 766 ASP Chi-restraints excluded: chain E residue 776 LEU Chi-restraints excluded: chain F residue 224 VAL Chi-restraints excluded: chain F residue 236 THR Chi-restraints excluded: chain F residue 284 VAL Chi-restraints excluded: chain F residue 318 ASP Chi-restraints excluded: chain F residue 324 ILE Chi-restraints excluded: chain F residue 338 TYR Chi-restraints excluded: chain F residue 350 ILE Chi-restraints excluded: chain F residue 361 HIS Chi-restraints excluded: chain F residue 378 SER Chi-restraints excluded: chain F residue 412 GLU Chi-restraints excluded: chain F residue 675 VAL Chi-restraints excluded: chain F residue 690 ASP Chi-restraints excluded: chain F residue 716 LEU Chi-restraints excluded: chain F residue 719 THR Chi-restraints excluded: chain F residue 824 LEU Chi-restraints excluded: chain F residue 834 VAL Chi-restraints excluded: chain F residue 836 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 358 random chunks: chunk 213 optimal weight: 7.9990 chunk 137 optimal weight: 7.9990 chunk 206 optimal weight: 5.9990 chunk 103 optimal weight: 0.9990 chunk 67 optimal weight: 0.8980 chunk 66 optimal weight: 0.7980 chunk 219 optimal weight: 0.9990 chunk 235 optimal weight: 7.9990 chunk 170 optimal weight: 3.9990 chunk 32 optimal weight: 0.9990 chunk 271 optimal weight: 10.0000 overall best weight: 0.9386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 705 HIS ** B 468 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 575 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8325 moved from start: 0.2387 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.053 28548 Z= 0.153 Angle : 0.555 10.136 38610 Z= 0.269 Chirality : 0.041 0.186 4412 Planarity : 0.004 0.086 5056 Dihedral : 9.864 153.040 4202 Min Nonbonded Distance : 2.116 Molprobity Statistics. All-atom Clashscore : 8.48 Ramachandran Plot: Outliers : 0.08 % Allowed : 9.07 % Favored : 90.85 % Rotamer: Outliers : 3.11 % Allowed : 19.94 % Favored : 76.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.70 % 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: -1.62 (0.14), residues: 3540 helix: -0.06 (0.13), residues: 1728 sheet: -1.82 (0.26), residues: 362 loop : -2.10 (0.16), residues: 1450 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.046 0.001 TRP F 545 HIS 0.004 0.001 HIS C 643 PHE 0.041 0.001 PHE D 798 TYR 0.008 0.001 TYR B 655 ARG 0.004 0.000 ARG B 791 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7080 Ramachandran restraints generated. 3540 Oldfield, 0 Emsley, 3540 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7080 Ramachandran restraints generated. 3540 Oldfield, 0 Emsley, 3540 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 260 residues out of total 2925 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 91 poor density : 169 time to evaluate : 3.495 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 603 PHE cc_start: 0.8648 (OUTLIER) cc_final: 0.7393 (p90) REVERT: B 564 MET cc_start: 0.7987 (ttp) cc_final: 0.7368 (ttp) REVERT: B 603 PHE cc_start: 0.8967 (OUTLIER) cc_final: 0.7290 (p90) REVERT: C 327 ASP cc_start: 0.8341 (t0) cc_final: 0.7877 (t70) REVERT: C 465 ASN cc_start: 0.7879 (m-40) cc_final: 0.7487 (t0) REVERT: C 722 LEU cc_start: 0.8559 (OUTLIER) cc_final: 0.8341 (mt) REVERT: D 217 GLU cc_start: 0.7749 (OUTLIER) cc_final: 0.7407 (mp0) REVERT: D 552 ARG cc_start: 0.7697 (OUTLIER) cc_final: 0.7480 (tmm-80) REVERT: D 827 GLN cc_start: 0.8340 (OUTLIER) cc_final: 0.7900 (pm20) REVERT: E 245 MET cc_start: 0.1562 (mmt) cc_final: 0.1328 (mmt) REVERT: E 299 MET cc_start: 0.8251 (tmm) cc_final: 0.7903 (tmm) REVERT: E 404 MET cc_start: 0.8487 (ptt) cc_final: 0.7970 (mmt) REVERT: E 564 MET cc_start: 0.7591 (mmm) cc_final: 0.7271 (mmm) REVERT: E 647 ARG cc_start: 0.8015 (ttp80) cc_final: 0.7723 (ttm110) REVERT: F 310 ARG cc_start: 0.6651 (mmp-170) cc_final: 0.6429 (mmp80) REVERT: F 324 ILE cc_start: 0.8325 (OUTLIER) cc_final: 0.8081 (tp) REVERT: F 338 TYR cc_start: 0.7907 (OUTLIER) cc_final: 0.7517 (m-80) REVERT: F 405 GLU cc_start: 0.7589 (OUTLIER) cc_final: 0.7386 (pp20) REVERT: F 412 GLU cc_start: 0.7780 (OUTLIER) cc_final: 0.7466 (pm20) outliers start: 91 outliers final: 70 residues processed: 248 average time/residue: 0.4081 time to fit residues: 163.8142 Evaluate side-chains 237 residues out of total 2925 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 80 poor density : 157 time to evaluate : 3.651 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 246 VAL Chi-restraints excluded: chain A residue 299 MET Chi-restraints excluded: chain A residue 317 LEU Chi-restraints excluded: chain A residue 346 ASP Chi-restraints excluded: chain A residue 412 GLU Chi-restraints excluded: chain A residue 420 VAL Chi-restraints excluded: chain A residue 600 THR Chi-restraints excluded: chain A residue 603 PHE Chi-restraints excluded: chain A residue 632 VAL Chi-restraints excluded: chain A residue 670 ARG Chi-restraints excluded: chain A residue 702 THR Chi-restraints excluded: chain A residue 731 VAL Chi-restraints excluded: chain A residue 776 LEU Chi-restraints excluded: chain A residue 828 VAL Chi-restraints excluded: chain A residue 834 VAL Chi-restraints excluded: chain B residue 201 ASN Chi-restraints excluded: chain B residue 205 ILE Chi-restraints excluded: chain B residue 280 LEU Chi-restraints excluded: chain B residue 316 THR Chi-restraints excluded: chain B residue 347 THR Chi-restraints excluded: chain B residue 387 LEU Chi-restraints excluded: chain B residue 393 ASP Chi-restraints excluded: chain B residue 533 VAL Chi-restraints excluded: chain B residue 603 PHE Chi-restraints excluded: chain B residue 675 VAL Chi-restraints excluded: chain B residue 828 VAL Chi-restraints excluded: chain B residue 838 VAL Chi-restraints excluded: chain C residue 166 THR Chi-restraints excluded: chain C residue 207 GLU Chi-restraints excluded: chain C residue 280 LEU Chi-restraints excluded: chain C residue 606 LEU Chi-restraints excluded: chain C residue 609 THR Chi-restraints excluded: chain C residue 649 ILE Chi-restraints excluded: chain C residue 713 ASN Chi-restraints excluded: chain C residue 722 LEU Chi-restraints excluded: chain D residue 161 LEU Chi-restraints excluded: chain D residue 217 GLU Chi-restraints excluded: chain D residue 234 ASP Chi-restraints excluded: chain D residue 237 ILE Chi-restraints excluded: chain D residue 284 VAL Chi-restraints excluded: chain D residue 299 MET Chi-restraints excluded: chain D residue 318 ASP Chi-restraints excluded: chain D residue 383 THR Chi-restraints excluded: chain D residue 552 ARG Chi-restraints excluded: chain D residue 593 VAL Chi-restraints excluded: chain D residue 605 PHE Chi-restraints excluded: chain D residue 685 HIS Chi-restraints excluded: chain D residue 718 LEU Chi-restraints excluded: chain D residue 827 GLN Chi-restraints excluded: chain D residue 838 VAL Chi-restraints excluded: chain E residue 200 ASN Chi-restraints excluded: chain E residue 262 VAL Chi-restraints excluded: chain E residue 275 THR Chi-restraints excluded: chain E residue 309 LEU Chi-restraints excluded: chain E residue 316 THR Chi-restraints excluded: chain E residue 632 VAL Chi-restraints excluded: chain E residue 634 ILE Chi-restraints excluded: chain E residue 674 THR Chi-restraints excluded: chain E residue 679 ASP Chi-restraints excluded: chain E residue 690 ASP Chi-restraints excluded: chain E residue 766 ASP Chi-restraints excluded: chain E residue 776 LEU Chi-restraints excluded: chain F residue 224 VAL Chi-restraints excluded: chain F residue 236 THR Chi-restraints excluded: chain F residue 284 VAL Chi-restraints excluded: chain F residue 303 MET Chi-restraints excluded: chain F residue 318 ASP Chi-restraints excluded: chain F residue 324 ILE Chi-restraints excluded: chain F residue 338 TYR Chi-restraints excluded: chain F residue 350 ILE Chi-restraints excluded: chain F residue 361 HIS Chi-restraints excluded: chain F residue 378 SER Chi-restraints excluded: chain F residue 405 GLU Chi-restraints excluded: chain F residue 412 GLU Chi-restraints excluded: chain F residue 675 VAL Chi-restraints excluded: chain F residue 690 ASP Chi-restraints excluded: chain F residue 716 LEU Chi-restraints excluded: chain F residue 824 LEU Chi-restraints excluded: chain F residue 834 VAL Chi-restraints excluded: chain F residue 836 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 358 random chunks: chunk 313 optimal weight: 6.9990 chunk 330 optimal weight: 0.9980 chunk 301 optimal weight: 20.0000 chunk 321 optimal weight: 0.0020 chunk 193 optimal weight: 0.9980 chunk 140 optimal weight: 2.9990 chunk 252 optimal weight: 9.9990 chunk 98 optimal weight: 4.9990 chunk 290 optimal weight: 8.9990 chunk 304 optimal weight: 0.0030 chunk 320 optimal weight: 6.9990 overall best weight: 1.0000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 468 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 575 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 281 HIS E 829 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8325 moved from start: 0.2471 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.091 28548 Z= 0.160 Angle : 0.568 11.771 38610 Z= 0.275 Chirality : 0.041 0.264 4412 Planarity : 0.004 0.086 5056 Dihedral : 9.772 153.758 4202 Min Nonbonded Distance : 2.117 Molprobity Statistics. All-atom Clashscore : 8.68 Ramachandran Plot: Outliers : 0.06 % Allowed : 9.27 % Favored : 90.68 % Rotamer: Outliers : 3.15 % Allowed : 20.04 % Favored : 76.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.70 % 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: -1.52 (0.15), residues: 3540 helix: 0.01 (0.13), residues: 1729 sheet: -1.77 (0.26), residues: 362 loop : -2.02 (0.16), residues: 1449 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.041 0.002 TRP F 545 HIS 0.024 0.001 HIS E 829 PHE 0.038 0.001 PHE D 798 TYR 0.014 0.001 TYR F 658 ARG 0.009 0.000 ARG B 563 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7080 Ramachandran restraints generated. 3540 Oldfield, 0 Emsley, 3540 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7080 Ramachandran restraints generated. 3540 Oldfield, 0 Emsley, 3540 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 253 residues out of total 2925 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 92 poor density : 161 time to evaluate : 3.479 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 603 PHE cc_start: 0.8641 (OUTLIER) cc_final: 0.7365 (p90) REVERT: B 563 ARG cc_start: 0.7852 (OUTLIER) cc_final: 0.7407 (ptt-90) REVERT: B 564 MET cc_start: 0.7980 (ttp) cc_final: 0.7356 (ttp) REVERT: B 603 PHE cc_start: 0.8983 (OUTLIER) cc_final: 0.7313 (p90) REVERT: C 327 ASP cc_start: 0.8358 (t0) cc_final: 0.7922 (t70) REVERT: C 465 ASN cc_start: 0.7868 (m-40) cc_final: 0.7581 (t0) REVERT: C 722 LEU cc_start: 0.8566 (OUTLIER) cc_final: 0.8340 (mt) REVERT: D 217 GLU cc_start: 0.7761 (OUTLIER) cc_final: 0.7405 (mp0) REVERT: D 827 GLN cc_start: 0.8348 (OUTLIER) cc_final: 0.7898 (pm20) REVERT: E 245 MET cc_start: 0.1591 (mmt) cc_final: 0.1355 (mmt) REVERT: E 299 MET cc_start: 0.8249 (tmm) cc_final: 0.7901 (tmm) REVERT: E 404 MET cc_start: 0.8504 (ptt) cc_final: 0.7964 (mmt) REVERT: E 564 MET cc_start: 0.7554 (mmm) cc_final: 0.7230 (mmm) REVERT: E 647 ARG cc_start: 0.8027 (ttp80) cc_final: 0.7741 (ttm110) REVERT: F 310 ARG cc_start: 0.6726 (mmp-170) cc_final: 0.6456 (mmp80) REVERT: F 324 ILE cc_start: 0.8326 (OUTLIER) cc_final: 0.8059 (tp) REVERT: F 338 TYR cc_start: 0.7898 (OUTLIER) cc_final: 0.7517 (m-80) REVERT: F 412 GLU cc_start: 0.7792 (OUTLIER) cc_final: 0.7476 (pm20) outliers start: 92 outliers final: 73 residues processed: 239 average time/residue: 0.4172 time to fit residues: 160.8088 Evaluate side-chains 240 residues out of total 2925 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 82 poor density : 158 time to evaluate : 3.380 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 246 VAL Chi-restraints excluded: chain A residue 299 MET Chi-restraints excluded: chain A residue 317 LEU Chi-restraints excluded: chain A residue 346 ASP Chi-restraints excluded: chain A residue 412 GLU Chi-restraints excluded: chain A residue 420 VAL Chi-restraints excluded: chain A residue 600 THR Chi-restraints excluded: chain A residue 603 PHE Chi-restraints excluded: chain A residue 632 VAL Chi-restraints excluded: chain A residue 670 ARG Chi-restraints excluded: chain A residue 674 THR Chi-restraints excluded: chain A residue 702 THR Chi-restraints excluded: chain A residue 731 VAL Chi-restraints excluded: chain A residue 776 LEU Chi-restraints excluded: chain A residue 828 VAL Chi-restraints excluded: chain A residue 834 VAL Chi-restraints excluded: chain A residue 836 VAL Chi-restraints excluded: chain B residue 201 ASN Chi-restraints excluded: chain B residue 205 ILE Chi-restraints excluded: chain B residue 280 LEU Chi-restraints excluded: chain B residue 316 THR Chi-restraints excluded: chain B residue 347 THR Chi-restraints excluded: chain B residue 387 LEU Chi-restraints excluded: chain B residue 393 ASP Chi-restraints excluded: chain B residue 445 LEU Chi-restraints excluded: chain B residue 533 VAL Chi-restraints excluded: chain B residue 563 ARG Chi-restraints excluded: chain B residue 603 PHE Chi-restraints excluded: chain B residue 675 VAL Chi-restraints excluded: chain B residue 701 LEU Chi-restraints excluded: chain B residue 828 VAL Chi-restraints excluded: chain B residue 838 VAL Chi-restraints excluded: chain C residue 166 THR Chi-restraints excluded: chain C residue 207 GLU Chi-restraints excluded: chain C residue 548 ILE Chi-restraints excluded: chain C residue 606 LEU Chi-restraints excluded: chain C residue 609 THR Chi-restraints excluded: chain C residue 649 ILE Chi-restraints excluded: chain C residue 713 ASN Chi-restraints excluded: chain C residue 722 LEU Chi-restraints excluded: chain D residue 161 LEU Chi-restraints excluded: chain D residue 217 GLU Chi-restraints excluded: chain D residue 234 ASP Chi-restraints excluded: chain D residue 237 ILE Chi-restraints excluded: chain D residue 284 VAL Chi-restraints excluded: chain D residue 383 THR Chi-restraints excluded: chain D residue 593 VAL Chi-restraints excluded: chain D residue 605 PHE Chi-restraints excluded: chain D residue 685 HIS Chi-restraints excluded: chain D residue 713 ASN Chi-restraints excluded: chain D residue 718 LEU Chi-restraints excluded: chain D residue 827 GLN Chi-restraints excluded: chain D residue 838 VAL Chi-restraints excluded: chain E residue 200 ASN Chi-restraints excluded: chain E residue 262 VAL Chi-restraints excluded: chain E residue 275 THR Chi-restraints excluded: chain E residue 309 LEU Chi-restraints excluded: chain E residue 316 THR Chi-restraints excluded: chain E residue 632 VAL Chi-restraints excluded: chain E residue 634 ILE Chi-restraints excluded: chain E residue 674 THR Chi-restraints excluded: chain E residue 679 ASP Chi-restraints excluded: chain E residue 690 ASP Chi-restraints excluded: chain E residue 766 ASP Chi-restraints excluded: chain E residue 776 LEU Chi-restraints excluded: chain F residue 224 VAL Chi-restraints excluded: chain F residue 236 THR Chi-restraints excluded: chain F residue 284 VAL Chi-restraints excluded: chain F residue 303 MET Chi-restraints excluded: chain F residue 318 ASP Chi-restraints excluded: chain F residue 324 ILE Chi-restraints excluded: chain F residue 338 TYR Chi-restraints excluded: chain F residue 350 ILE Chi-restraints excluded: chain F residue 361 HIS Chi-restraints excluded: chain F residue 378 SER Chi-restraints excluded: chain F residue 379 ASP Chi-restraints excluded: chain F residue 412 GLU Chi-restraints excluded: chain F residue 675 VAL Chi-restraints excluded: chain F residue 690 ASP Chi-restraints excluded: chain F residue 824 LEU Chi-restraints excluded: chain F residue 834 VAL Chi-restraints excluded: chain F residue 836 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 358 random chunks: chunk 211 optimal weight: 0.0770 chunk 340 optimal weight: 4.9990 chunk 207 optimal weight: 2.9990 chunk 161 optimal weight: 4.9990 chunk 236 optimal weight: 0.9990 chunk 356 optimal weight: 10.0000 chunk 328 optimal weight: 1.9990 chunk 284 optimal weight: 9.9990 chunk 29 optimal weight: 9.9990 chunk 219 optimal weight: 5.9990 chunk 174 optimal weight: 2.9990 overall best weight: 1.8146 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 336 GLN ** B 468 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 705 HIS C 323 HIS ** C 575 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 281 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8358 moved from start: 0.2409 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.081 28548 Z= 0.225 Angle : 0.603 12.224 38610 Z= 0.291 Chirality : 0.043 0.245 4412 Planarity : 0.004 0.090 5056 Dihedral : 9.865 153.178 4202 Min Nonbonded Distance : 2.113 Molprobity Statistics. All-atom Clashscore : 9.23 Ramachandran Plot: Outliers : 0.06 % Allowed : 9.94 % Favored : 90.00 % Rotamer: Outliers : 3.11 % Allowed : 20.08 % Favored : 76.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.70 % 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: -1.47 (0.15), residues: 3540 helix: 0.07 (0.13), residues: 1721 sheet: -1.79 (0.26), residues: 369 loop : -1.99 (0.16), residues: 1450 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.036 0.001 TRP F 545 HIS 0.005 0.001 HIS D 685 PHE 0.041 0.001 PHE D 798 TYR 0.008 0.001 TYR D 251 ARG 0.004 0.000 ARG F 401 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7080 Ramachandran restraints generated. 3540 Oldfield, 0 Emsley, 3540 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7080 Ramachandran restraints generated. 3540 Oldfield, 0 Emsley, 3540 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 247 residues out of total 2925 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 91 poor density : 156 time to evaluate : 4.258 Fit side-chains revert: symmetry clash REVERT: A 603 PHE cc_start: 0.8690 (OUTLIER) cc_final: 0.7368 (p90) REVERT: B 564 MET cc_start: 0.8024 (ttp) cc_final: 0.7407 (ttp) REVERT: B 603 PHE cc_start: 0.9004 (OUTLIER) cc_final: 0.7337 (p90) REVERT: C 327 ASP cc_start: 0.8342 (t0) cc_final: 0.7889 (t70) REVERT: C 465 ASN cc_start: 0.7973 (m-40) cc_final: 0.7405 (t0) REVERT: C 468 ASN cc_start: 0.7619 (p0) cc_final: 0.7381 (p0) REVERT: C 722 LEU cc_start: 0.8665 (OUTLIER) cc_final: 0.8436 (mp) REVERT: D 217 GLU cc_start: 0.7719 (OUTLIER) cc_final: 0.7326 (mp0) REVERT: D 827 GLN cc_start: 0.8352 (OUTLIER) cc_final: 0.7895 (pm20) REVERT: E 245 MET cc_start: 0.1628 (mmt) cc_final: 0.1377 (mmt) REVERT: E 299 MET cc_start: 0.8277 (tmm) cc_final: 0.7911 (tmm) REVERT: E 404 MET cc_start: 0.8542 (ptt) cc_final: 0.7956 (mmt) REVERT: E 564 MET cc_start: 0.7681 (mmm) cc_final: 0.7335 (mmm) REVERT: E 647 ARG cc_start: 0.8086 (ttp80) cc_final: 0.7765 (ttm110) REVERT: F 245 MET cc_start: 0.5613 (tpp) cc_final: 0.5388 (tpp) REVERT: F 310 ARG cc_start: 0.6786 (mmp-170) cc_final: 0.6535 (mmp80) REVERT: F 324 ILE cc_start: 0.8367 (OUTLIER) cc_final: 0.8098 (tp) REVERT: F 338 TYR cc_start: 0.7889 (OUTLIER) cc_final: 0.7507 (m-80) REVERT: F 412 GLU cc_start: 0.7804 (OUTLIER) cc_final: 0.7490 (pm20) REVERT: F 605 PHE cc_start: 0.7903 (OUTLIER) cc_final: 0.6968 (p90) outliers start: 91 outliers final: 75 residues processed: 239 average time/residue: 0.4025 time to fit residues: 155.7865 Evaluate side-chains 235 residues out of total 2925 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 84 poor density : 151 time to evaluate : 3.420 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 246 VAL Chi-restraints excluded: chain A residue 299 MET Chi-restraints excluded: chain A residue 317 LEU Chi-restraints excluded: chain A residue 346 ASP Chi-restraints excluded: chain A residue 367 THR Chi-restraints excluded: chain A residue 412 GLU Chi-restraints excluded: chain A residue 420 VAL Chi-restraints excluded: chain A residue 600 THR Chi-restraints excluded: chain A residue 603 PHE Chi-restraints excluded: chain A residue 632 VAL Chi-restraints excluded: chain A residue 670 ARG Chi-restraints excluded: chain A residue 674 THR Chi-restraints excluded: chain A residue 702 THR Chi-restraints excluded: chain A residue 731 VAL Chi-restraints excluded: chain A residue 776 LEU Chi-restraints excluded: chain A residue 828 VAL Chi-restraints excluded: chain A residue 834 VAL Chi-restraints excluded: chain A residue 836 VAL Chi-restraints excluded: chain B residue 205 ILE Chi-restraints excluded: chain B residue 280 LEU Chi-restraints excluded: chain B residue 316 THR Chi-restraints excluded: chain B residue 347 THR Chi-restraints excluded: chain B residue 387 LEU Chi-restraints excluded: chain B residue 393 ASP Chi-restraints excluded: chain B residue 445 LEU Chi-restraints excluded: chain B residue 533 VAL Chi-restraints excluded: chain B residue 603 PHE Chi-restraints excluded: chain B residue 609 THR Chi-restraints excluded: chain B residue 675 VAL Chi-restraints excluded: chain B residue 701 LEU Chi-restraints excluded: chain B residue 783 LEU Chi-restraints excluded: chain B residue 828 VAL Chi-restraints excluded: chain B residue 838 VAL Chi-restraints excluded: chain C residue 166 THR Chi-restraints excluded: chain C residue 207 GLU Chi-restraints excluded: chain C residue 548 ILE Chi-restraints excluded: chain C residue 606 LEU Chi-restraints excluded: chain C residue 609 THR Chi-restraints excluded: chain C residue 649 ILE Chi-restraints excluded: chain C residue 659 GLU Chi-restraints excluded: chain C residue 713 ASN Chi-restraints excluded: chain C residue 722 LEU Chi-restraints excluded: chain D residue 217 GLU Chi-restraints excluded: chain D residue 234 ASP Chi-restraints excluded: chain D residue 237 ILE Chi-restraints excluded: chain D residue 284 VAL Chi-restraints excluded: chain D residue 383 THR Chi-restraints excluded: chain D residue 593 VAL Chi-restraints excluded: chain D residue 605 PHE Chi-restraints excluded: chain D residue 685 HIS Chi-restraints excluded: chain D residue 713 ASN Chi-restraints excluded: chain D residue 718 LEU Chi-restraints excluded: chain D residue 827 GLN Chi-restraints excluded: chain D residue 838 VAL Chi-restraints excluded: chain E residue 200 ASN Chi-restraints excluded: chain E residue 262 VAL Chi-restraints excluded: chain E residue 275 THR Chi-restraints excluded: chain E residue 309 LEU Chi-restraints excluded: chain E residue 316 THR Chi-restraints excluded: chain E residue 632 VAL Chi-restraints excluded: chain E residue 674 THR Chi-restraints excluded: chain E residue 679 ASP Chi-restraints excluded: chain E residue 690 ASP Chi-restraints excluded: chain E residue 766 ASP Chi-restraints excluded: chain E residue 776 LEU Chi-restraints excluded: chain F residue 224 VAL Chi-restraints excluded: chain F residue 236 THR Chi-restraints excluded: chain F residue 284 VAL Chi-restraints excluded: chain F residue 303 MET Chi-restraints excluded: chain F residue 318 ASP Chi-restraints excluded: chain F residue 324 ILE Chi-restraints excluded: chain F residue 338 TYR Chi-restraints excluded: chain F residue 350 ILE Chi-restraints excluded: chain F residue 361 HIS Chi-restraints excluded: chain F residue 378 SER Chi-restraints excluded: chain F residue 379 ASP Chi-restraints excluded: chain F residue 412 GLU Chi-restraints excluded: chain F residue 605 PHE Chi-restraints excluded: chain F residue 675 VAL Chi-restraints excluded: chain F residue 690 ASP Chi-restraints excluded: chain F residue 719 THR Chi-restraints excluded: chain F residue 824 LEU Chi-restraints excluded: chain F residue 834 VAL Chi-restraints excluded: chain F residue 836 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 358 random chunks: chunk 225 optimal weight: 0.7980 chunk 302 optimal weight: 2.9990 chunk 87 optimal weight: 1.9990 chunk 261 optimal weight: 7.9990 chunk 41 optimal weight: 1.9990 chunk 78 optimal weight: 4.9990 chunk 284 optimal weight: 7.9990 chunk 119 optimal weight: 4.9990 chunk 292 optimal weight: 10.0000 chunk 36 optimal weight: 6.9990 chunk 52 optimal weight: 0.9980 overall best weight: 1.7586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 201 ASN ** C 575 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 281 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3634 r_free = 0.3634 target = 0.100555 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3203 r_free = 0.3203 target = 0.077263 restraints weight = 70554.566| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3243 r_free = 0.3243 target = 0.079269 restraints weight = 38124.471| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 49)----------------| | r_work = 0.3269 r_free = 0.3269 target = 0.080590 restraints weight = 25246.564| |-----------------------------------------------------------------------------| r_work (final): 0.3271 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8371 moved from start: 0.2447 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.074 28548 Z= 0.220 Angle : 0.601 11.744 38610 Z= 0.289 Chirality : 0.043 0.227 4412 Planarity : 0.004 0.090 5056 Dihedral : 9.859 153.737 4202 Min Nonbonded Distance : 2.113 Molprobity Statistics. All-atom Clashscore : 9.19 Ramachandran Plot: Outliers : 0.06 % Allowed : 9.69 % Favored : 90.25 % Rotamer: Outliers : 3.04 % Allowed : 20.21 % Favored : 76.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.70 % 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: -1.42 (0.15), residues: 3540 helix: 0.12 (0.13), residues: 1715 sheet: -1.75 (0.26), residues: 377 loop : -1.98 (0.16), residues: 1448 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.035 0.002 TRP F 545 HIS 0.008 0.001 HIS B 281 PHE 0.039 0.001 PHE D 798 TYR 0.014 0.001 TYR F 658 ARG 0.006 0.000 ARG B 563 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4888.04 seconds wall clock time: 90 minutes 37.64 seconds (5437.64 seconds total)