Starting phenix.real_space_refine on Tue Feb 20 14:56:50 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6djv_7943/02_2024/6djv_7943_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6djv_7943/02_2024/6djv_7943.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6djv_7943/02_2024/6djv_7943.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6djv_7943/02_2024/6djv_7943.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6djv_7943/02_2024/6djv_7943_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6djv_7943/02_2024/6djv_7943_updated.pdb" } resolution = 3.9 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.007 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 891 atoms to isotropic. 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 64 5.16 5 C 16985 2.51 5 N 4966 2.21 5 O 5269 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 ARG 357": "NH1" <-> "NH2" Residue "A ARG 403": "NH1" <-> "NH2" Residue "A ARG 552": "NH1" <-> "NH2" Residue "A PHE 603": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 605": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 669": "NH1" <-> "NH2" Residue "B ARG 197": "NH1" <-> "NH2" Residue "B ARG 357": "NH1" <-> "NH2" Residue "B ARG 403": "NH1" <-> "NH2" Residue "B ARG 409": "NH1" <-> "NH2" Residue "B ARG 552": "NH1" <-> "NH2" Residue "B PHE 603": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 605": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 669": "NH1" <-> "NH2" Residue "B ARG 780": "NH1" <-> "NH2" Residue "B ARG 796": "NH1" <-> "NH2" Residue "C ARG 197": "NH1" <-> "NH2" Residue "C ARG 357": "NH1" <-> "NH2" Residue "C ARG 403": "NH1" <-> "NH2" Residue "C PHE 603": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 605": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 669": "NH1" <-> "NH2" Residue "C ARG 796": "NH1" <-> "NH2" Residue "D ARG 188": "NH1" <-> "NH2" Residue "D ARG 197": "NH1" <-> "NH2" Residue "D ARG 357": "NH1" <-> "NH2" Residue "D ARG 403": "NH1" <-> "NH2" Residue "D ARG 552": "NH1" <-> "NH2" Residue "D PHE 603": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 605": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 669": "NH1" <-> "NH2" Residue "D ARG 780": "NH1" <-> "NH2" Residue "E ARG 173": "NH1" <-> "NH2" Residue "E ARG 252": "NH1" <-> "NH2" Residue "E ARG 258": "NH1" <-> "NH2" Residue "E ARG 321": "NH1" <-> "NH2" Residue "E ARG 385": "NH1" <-> "NH2" Residue "E ARG 403": "NH1" <-> "NH2" Residue "E ARG 588": "NH1" <-> "NH2" Residue "E PHE 603": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 605": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ARG 669": "NH1" <-> "NH2" Residue "E ARG 808": "NH1" <-> "NH2" Residue "F ARG 183": "NH1" <-> "NH2" Residue "F ARG 357": "NH1" <-> "NH2" Residue "F ARG 403": "NH1" <-> "NH2" Residue "F ARG 552": "NH1" <-> "NH2" Residue "F PHE 603": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 605": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ARG 669": "NH1" <-> "NH2" Time to flip residues: 0.10s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 27318 Number of models: 1 Model: "" Number of chains: 13 Chain: "A" Number of atoms: 4649 Number of conformers: 1 Conformer: "" Number of residues, atoms: 610, 4649 Classifications: {'peptide': 610} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 24, 'TRANS': 585} Chain breaks: 3 Unresolved non-hydrogen bonds: 79 Unresolved non-hydrogen angles: 110 Unresolved non-hydrogen dihedrals: 48 Unresolved non-hydrogen chiralities: 18 Planarities with less than four sites: {'GLN:plan1': 2, 'GLU:plan': 5, 'ARG:plan': 4, 'ASN:plan1': 2} Unresolved non-hydrogen planarities: 47 Chain: "B" Number of atoms: 4657 Number of conformers: 1 Conformer: "" Number of residues, atoms: 611, 4657 Classifications: {'peptide': 611} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 24, 'TRANS': 586} Chain breaks: 3 Unresolved non-hydrogen bonds: 79 Unresolved non-hydrogen angles: 110 Unresolved non-hydrogen dihedrals: 49 Unresolved non-hydrogen chiralities: 18 Planarities with less than four sites: {'GLN:plan1': 2, 'GLU:plan': 5, 'ARG:plan': 4, 'ASN:plan1': 2} Unresolved non-hydrogen planarities: 47 Chain: "C" Number of atoms: 4678 Number of conformers: 1 Conformer: "" Number of residues, atoms: 615, 4678 Classifications: {'peptide': 615} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 24, 'TRANS': 590} Chain breaks: 3 Unresolved non-hydrogen bonds: 82 Unresolved non-hydrogen angles: 113 Unresolved non-hydrogen dihedrals: 51 Unresolved non-hydrogen chiralities: 18 Planarities with less than four sites: {'GLN:plan1': 2, 'GLU:plan': 5, 'ARG:plan': 4, 'ASN:plan1': 2} Unresolved non-hydrogen planarities: 47 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: "N" Number of atoms: 130 Number of conformers: 1 Conformer: "" Number of residues, atoms: 26, 130 Classifications: {'peptide': 26} Link IDs: {'TRANS': 25} 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: 4289 Number of conformers: 1 Conformer: "" Number of residues, atoms: 558, 4289 Classifications: {'peptide': 558} Link IDs: {'PTRANS': 23, 'TRANS': 534} Chain breaks: 2 Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen chiralities: 10 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: 62 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 62 Unusual residues: {'AGS': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "D" Number of atoms: 62 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 62 Unusual residues: {'AGS': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "E" Number of atoms: 54 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 54 Unusual residues: {'ADP': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "F" 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} Time building chain proxies: 14.75, per 1000 atoms: 0.54 Number of scatterers: 27318 At special positions: 0 Unit cell: (138.546, 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 64 16.00 P 34 15.00 O 5269 8.00 N 4966 7.00 C 16985 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 9.72 Conformation dependent library (CDL) restraints added in 4.9 seconds 6968 Ramachandran restraints generated. 3484 Oldfield, 0 Emsley, 3484 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6464 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 168 helices and 22 sheets defined 40.3% alpha, 5.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 5.55 Creating SS restraints... Processing helix chain 'A' and resid 160 through 164 removed outlier: 3.824A pdb=" N TYR A 164 " --> pdb=" O ALA A 160 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 160 through 164' Processing helix chain 'A' and resid 168 through 173 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 254 through 267 Processing helix chain 'A' and resid 301 through 306 removed outlier: 3.839A pdb=" N ARG A 306 " --> pdb=" O PRO A 302 " (cutoff:3.500A) Processing helix chain 'A' and resid 318 through 323 removed outlier: 3.579A pdb=" N HIS A 323 " --> pdb=" O GLU A 319 " (cutoff:3.500A) Processing helix chain 'A' and resid 330 through 332 No H-bonds generated for 'chain 'A' and resid 330 through 332' Processing helix chain 'A' and resid 344 through 351 Processing helix chain 'A' and resid 355 through 361 Processing helix chain 'A' and resid 368 through 380 removed outlier: 3.609A pdb=" N ALA A 375 " --> pdb=" O LEU A 371 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N SER A 378 " --> pdb=" O ALA A 374 " (cutoff:3.500A) removed outlier: 4.134A pdb=" N ASP A 379 " --> pdb=" O ALA A 375 " (cutoff:3.500A) removed outlier: 4.161A pdb=" N ARG A 380 " --> pdb=" O THR A 376 " (cutoff:3.500A) Processing helix chain 'A' and resid 392 through 406 removed outlier: 3.723A pdb=" N SER A 400 " --> pdb=" O ASP A 396 " (cutoff:3.500A) Processing helix chain 'A' and resid 412 through 430 Processing helix chain 'A' and resid 444 through 468 removed outlier: 3.566A pdb=" N LEU A 449 " --> pdb=" O ARG A 446 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N ASP A 451 " --> pdb=" O GLU A 448 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N LYS A 455 " --> pdb=" O GLN A 452 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N LEU A 456 " --> pdb=" O LYS A 453 " (cutoff:3.500A) removed outlier: 3.910A pdb=" N LEU A 459 " --> pdb=" O LEU A 456 " (cutoff:3.500A) Processing helix chain 'A' and resid 535 through 544 removed outlier: 4.095A pdb=" N ALA A 539 " --> pdb=" O PRO A 535 " (cutoff:3.500A) Processing helix chain 'A' and resid 558 through 561 No H-bonds generated for 'chain 'A' and resid 558 through 561' Processing helix chain 'A' and resid 564 through 570 removed outlier: 4.233A pdb=" N GLY A 569 " --> pdb=" O GLU A 565 " (cutoff:3.500A) removed outlier: 3.862A pdb=" N LYS A 570 " --> pdb=" O ASP A 566 " (cutoff:3.500A) Processing helix chain 'A' and resid 576 through 591 removed outlier: 3.822A pdb=" N ASP A 584 " --> pdb=" O THR A 580 " (cutoff:3.500A) removed outlier: 3.894A pdb=" N ALA A 585 " --> pdb=" O ALA A 581 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N VAL A 586 " --> pdb=" O VAL A 582 " (cutoff:3.500A) removed outlier: 3.950A pdb=" N ARG A 588 " --> pdb=" O ASP A 584 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N SER A 589 " --> pdb=" O ALA A 585 " (cutoff:3.500A) removed outlier: 3.897A pdb=" N ALA A 591 " --> pdb=" O ARG A 587 " (cutoff:3.500A) Processing helix chain 'A' and resid 615 through 620 Processing helix chain 'A' and resid 628 through 630 No H-bonds generated for 'chain 'A' and resid 628 through 630' Processing helix chain 'A' and resid 643 through 648 removed outlier: 3.539A pdb=" N ALA A 646 " --> pdb=" O HIS A 643 " (cutoff:3.500A) 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 688 through 690 No H-bonds generated for 'chain 'A' and resid 688 through 690' Processing helix chain 'A' and resid 729 through 738 removed outlier: 3.840A pdb=" N ARG A 736 " --> pdb=" O LEU A 732 " (cutoff:3.500A) 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 759 through 775 removed outlier: 4.462A pdb=" N ARG A 763 " --> pdb=" O GLU A 759 " (cutoff:3.500A) removed outlier: 4.526A pdb=" N ILE A 764 " --> pdb=" O GLU A 760 " (cutoff:3.500A) removed outlier: 4.017A pdb=" N ASP A 766 " --> pdb=" O VAL A 762 " (cutoff:3.500A) removed outlier: 4.749A pdb=" N ILE A 767 " --> pdb=" O ARG A 763 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N GLN A 768 " --> pdb=" O ILE A 764 " (cutoff:3.500A) Processing helix chain 'A' and resid 787 through 795 removed outlier: 3.884A pdb=" N ALA A 794 " --> pdb=" O LYS A 790 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N GLN A 795 " --> pdb=" O ARG A 791 " (cutoff:3.500A) Processing helix chain 'A' and resid 805 through 823 removed outlier: 3.676A pdb=" N ARG A 809 " --> pdb=" O ARG A 805 " (cutoff:3.500A) removed outlier: 4.064A pdb=" N GLN A 812 " --> pdb=" O ARG A 808 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N GLY A 816 " --> pdb=" O GLN A 812 " (cutoff:3.500A) removed outlier: 4.310A pdb=" N ASP A 817 " --> pdb=" O GLN A 813 " (cutoff:3.500A) removed outlier: 4.380A pdb=" N GLN A 818 " --> pdb=" O ALA A 814 " (cutoff:3.500A) Processing helix chain 'B' and resid 169 through 172 No H-bonds generated for 'chain 'B' and resid 169 through 172' Processing helix chain 'B' and resid 184 through 195 removed outlier: 3.595A pdb=" N SER B 195 " --> pdb=" O VAL B 191 " (cutoff:3.500A) Processing helix chain 'B' and resid 213 through 225 Processing helix chain 'B' and resid 230 through 232 No H-bonds generated for 'chain 'B' and resid 230 through 232' Processing helix chain 'B' and resid 244 through 246 No H-bonds generated for 'chain 'B' and resid 244 through 246' Processing helix chain 'B' and resid 255 through 268 Processing helix chain 'B' and resid 280 through 282 No H-bonds generated for 'chain 'B' and resid 280 through 282' Processing helix chain 'B' and resid 301 through 306 removed outlier: 4.196A pdb=" N ALA B 305 " --> pdb=" O LYS B 301 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N ARG B 306 " --> pdb=" O PRO B 302 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 301 through 306' Processing helix chain 'B' and resid 317 through 323 removed outlier: 3.888A pdb=" N ARG B 321 " --> pdb=" O LEU B 317 " (cutoff:3.500A) removed outlier: 3.945A pdb=" N LYS B 322 " --> pdb=" O ASP B 318 " (cutoff:3.500A) Processing helix chain 'B' and resid 325 through 327 No H-bonds generated for 'chain 'B' and resid 325 through 327' Processing helix chain 'B' and resid 330 through 333 No H-bonds generated for 'chain 'B' and resid 330 through 333' Processing helix chain 'B' and resid 344 through 353 removed outlier: 3.984A pdb=" N GLY B 349 " --> pdb=" O GLU B 345 " (cutoff:3.500A) Processing helix chain 'B' and resid 355 through 361 removed outlier: 4.429A pdb=" N VAL B 360 " --> pdb=" O ASP B 356 " (cutoff:3.500A) Processing helix chain 'B' and resid 369 through 377 removed outlier: 3.692A pdb=" N ALA B 374 " --> pdb=" O ALA B 370 " (cutoff:3.500A) removed outlier: 4.175A pdb=" N ALA B 375 " --> pdb=" O LEU B 371 " (cutoff:3.500A) Processing helix chain 'B' and resid 392 through 406 Processing helix chain 'B' and resid 412 through 430 Processing helix chain 'B' and resid 444 through 468 removed outlier: 3.566A pdb=" N LEU B 449 " --> pdb=" O ARG B 446 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N ASP B 451 " --> pdb=" O GLU B 448 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N LYS B 455 " --> pdb=" O GLN B 452 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N LEU B 456 " --> pdb=" O LYS B 453 " (cutoff:3.500A) removed outlier: 3.909A pdb=" N LEU B 459 " --> pdb=" O LEU B 456 " (cutoff:3.500A) Processing helix chain 'B' and resid 535 through 544 removed outlier: 3.604A pdb=" N ALA B 539 " --> pdb=" O PRO B 535 " (cutoff:3.500A) Processing helix chain 'B' and resid 558 through 562 Processing helix chain 'B' and resid 568 through 570 No H-bonds generated for 'chain 'B' and resid 568 through 570' Processing helix chain 'B' and resid 576 through 590 removed outlier: 3.693A pdb=" N VAL B 582 " --> pdb=" O ALA B 578 " (cutoff:3.500A) removed outlier: 4.138A pdb=" N ALA B 585 " --> pdb=" O ALA B 581 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N ARG B 587 " --> pdb=" O SER B 583 " (cutoff:3.500A) removed outlier: 4.282A pdb=" N ARG B 588 " --> pdb=" O ASP B 584 " (cutoff:3.500A) removed outlier: 4.102A pdb=" N SER B 589 " --> pdb=" O ALA B 585 " (cutoff:3.500A) Processing helix chain 'B' and resid 645 through 647 No H-bonds generated for 'chain 'B' and resid 645 through 647' 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 689 through 695 removed outlier: 4.436A pdb=" N GLN B 694 " --> pdb=" O ASP B 690 " (cutoff:3.500A) removed outlier: 3.995A pdb=" N VAL B 695 " --> pdb=" O VAL B 691 " (cutoff:3.500A) Processing helix chain 'B' and resid 729 through 733 Processing helix chain 'B' and resid 758 through 775 removed outlier: 3.803A pdb=" N VAL B 762 " --> pdb=" O PRO B 758 " (cutoff:3.500A) removed outlier: 4.423A pdb=" N ARG B 763 " --> pdb=" O GLU B 759 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N ILE B 764 " --> pdb=" O GLU B 760 " (cutoff:3.500A) removed outlier: 3.864A pdb=" N VAL B 765 " --> pdb=" O LEU B 761 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N ASP B 766 " --> pdb=" O VAL B 762 " (cutoff:3.500A) Processing helix chain 'B' and resid 787 through 796 removed outlier: 3.779A pdb=" N LEU B 793 " --> pdb=" O ALA B 789 " (cutoff:3.500A) removed outlier: 4.374A pdb=" N ALA B 794 " --> pdb=" O LYS B 790 " (cutoff:3.500A) removed outlier: 3.897A pdb=" N GLN B 795 " --> pdb=" O ARG B 791 " (cutoff:3.500A) Processing helix chain 'B' and resid 805 through 814 removed outlier: 4.914A pdb=" N VAL B 811 " --> pdb=" O ARG B 808 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N ALA B 814 " --> pdb=" O VAL B 811 " (cutoff:3.500A) Processing helix chain 'B' and resid 816 through 824 removed outlier: 3.877A pdb=" N LYS B 821 " --> pdb=" O ASP B 817 " (cutoff:3.500A) removed outlier: 3.967A pdb=" N LEU B 824 " --> pdb=" O ALA B 820 " (cutoff:3.500A) Processing helix chain 'C' and resid 160 through 164 removed outlier: 4.096A pdb=" N TYR C 164 " --> pdb=" O LEU C 161 " (cutoff:3.500A) Processing helix chain 'C' and resid 170 through 173 No H-bonds generated for 'chain 'C' and resid 170 through 173' Processing helix chain 'C' and resid 184 through 195 removed outlier: 3.659A pdb=" N SER C 195 " --> pdb=" O VAL C 191 " (cutoff:3.500A) 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 267 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 304 No H-bonds generated for 'chain 'C' and resid 301 through 304' Processing helix chain 'C' and resid 320 through 323 No H-bonds generated for 'chain 'C' and resid 320 through 323' Processing helix chain 'C' and resid 325 through 327 No H-bonds generated for 'chain 'C' and resid 325 through 327' Processing helix chain 'C' and resid 344 through 351 removed outlier: 3.537A pdb=" N GLY C 349 " --> pdb=" O GLU C 345 " (cutoff:3.500A) Processing helix chain 'C' and resid 358 through 361 No H-bonds generated for 'chain 'C' and resid 358 through 361' Processing helix chain 'C' and resid 368 through 379 removed outlier: 4.267A pdb=" N THR C 376 " --> pdb=" O VAL C 372 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N SER C 378 " --> pdb=" O ALA C 374 " (cutoff:3.500A) removed outlier: 4.891A pdb=" N ASP C 379 " --> pdb=" O ALA C 375 " (cutoff:3.500A) Processing helix chain 'C' and resid 392 through 406 removed outlier: 3.700A pdb=" N GLU C 405 " --> pdb=" O ARG C 401 " (cutoff:3.500A) Processing helix chain 'C' and resid 412 through 430 Processing helix chain 'C' and resid 444 through 468 removed outlier: 3.566A pdb=" N LEU C 449 " --> pdb=" O ARG C 446 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N ASP C 451 " --> pdb=" O GLU C 448 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N LYS C 455 " --> pdb=" O GLN C 452 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N LEU C 456 " --> pdb=" O LYS C 453 " (cutoff:3.500A) removed outlier: 3.910A pdb=" N LEU C 459 " --> pdb=" O LEU C 456 " (cutoff:3.500A) Processing helix chain 'C' and resid 535 through 543 removed outlier: 3.738A pdb=" N ALA C 539 " --> pdb=" O PRO C 535 " (cutoff:3.500A) Processing helix chain 'C' and resid 558 through 562 Processing helix chain 'C' and resid 568 through 570 No H-bonds generated for 'chain 'C' and resid 568 through 570' Processing helix chain 'C' and resid 576 through 591 removed outlier: 3.568A pdb=" N ALA C 581 " --> pdb=" O ALA C 577 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N ALA C 585 " --> pdb=" O ALA C 581 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N SER C 589 " --> pdb=" O ALA C 585 " (cutoff:3.500A) Processing helix chain 'C' and resid 613 through 619 removed outlier: 3.863A pdb=" N ALA C 617 " --> pdb=" O LYS C 613 " (cutoff:3.500A) Processing helix chain 'C' and resid 643 through 647 removed outlier: 3.682A pdb=" N ALA C 646 " --> pdb=" O HIS C 643 " (cutoff:3.500A) Processing helix chain 'C' and resid 665 through 668 No H-bonds generated for 'chain 'C' and resid 665 through 668' Processing helix chain 'C' and resid 732 through 738 removed outlier: 3.934A pdb=" N ARG C 736 " --> pdb=" O LEU C 732 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N ALA C 737 " --> pdb=" O ALA C 733 " (cutoff:3.500A) removed outlier: 3.900A pdb=" N THR C 738 " --> pdb=" O ALA C 734 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 732 through 738' Processing helix chain 'C' and resid 741 through 744 No H-bonds generated for 'chain 'C' and resid 741 through 744' Processing helix chain 'C' and resid 758 through 777 removed outlier: 3.867A pdb=" N VAL C 762 " --> pdb=" O PRO C 758 " (cutoff:3.500A) removed outlier: 3.882A pdb=" N ARG C 763 " --> pdb=" O GLU C 759 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N ILE C 764 " --> pdb=" O GLU C 760 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N ASP C 766 " --> pdb=" O VAL C 762 " (cutoff:3.500A) removed outlier: 3.934A pdb=" N ILE C 767 " --> pdb=" O ARG C 763 " (cutoff:3.500A) removed outlier: 4.169A pdb=" N GLY C 773 " --> pdb=" O LEU C 769 " (cutoff:3.500A) removed outlier: 4.027A pdb=" N ALA C 777 " --> pdb=" O GLY C 773 " (cutoff:3.500A) Processing helix chain 'C' and resid 787 through 795 removed outlier: 3.830A pdb=" N ALA C 794 " --> pdb=" O LYS C 790 " (cutoff:3.500A) Processing helix chain 'C' and resid 803 through 814 Proline residue: C 806 - end of helix removed outlier: 4.456A pdb=" N VAL C 811 " --> pdb=" O ARG C 808 " (cutoff:3.500A) Processing helix chain 'C' and resid 816 through 823 Processing helix chain 'D' and resid 168 through 172 Processing helix chain 'D' and resid 184 through 194 removed outlier: 4.540A pdb=" N GLN D 192 " --> pdb=" O ARG D 188 " (cutoff:3.500A) Processing helix chain 'D' and resid 214 through 224 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 242 through 244 No H-bonds generated for 'chain 'D' and resid 242 through 244' Processing helix chain 'D' and resid 255 through 268 removed outlier: 3.908A pdb=" N VAL D 262 " --> pdb=" O ARG D 258 " (cutoff:3.500A) Processing helix chain 'D' and resid 280 through 283 Processing helix chain 'D' and resid 301 through 306 removed outlier: 3.822A pdb=" N ALA D 305 " --> pdb=" O LYS D 301 " (cutoff:3.500A) removed outlier: 4.256A pdb=" N ARG D 306 " --> pdb=" O PRO D 302 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 301 through 306' Processing helix chain 'D' and resid 317 through 320 No H-bonds generated for 'chain 'D' and resid 317 through 320' Processing helix chain 'D' and resid 344 through 353 Processing helix chain 'D' and resid 358 through 361 No H-bonds generated for 'chain 'D' and resid 358 through 361' Processing helix chain 'D' and resid 368 through 377 Processing helix chain 'D' and resid 392 through 406 Processing helix chain 'D' and resid 537 through 544 Processing helix chain 'D' and resid 558 through 562 Processing helix chain 'D' and resid 565 through 570 removed outlier: 4.030A pdb=" N LYS D 570 " --> pdb=" O ASP D 566 " (cutoff:3.500A) Processing helix chain 'D' and resid 580 through 589 removed outlier: 3.591A pdb=" N ALA D 585 " --> pdb=" O ALA D 581 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N VAL D 586 " --> pdb=" O VAL D 582 " (cutoff:3.500A) removed outlier: 4.286A pdb=" N ARG D 588 " --> pdb=" O ASP D 584 " (cutoff:3.500A) Processing helix chain 'D' and resid 613 through 623 Processing helix chain 'D' and resid 642 through 647 removed outlier: 3.898A pdb=" N VAL D 645 " --> pdb=" O LYS D 642 " (cutoff:3.500A) removed outlier: 4.239A pdb=" N ALA D 646 " --> pdb=" O HIS D 643 " (cutoff:3.500A) removed outlier: 4.229A pdb=" N ARG D 647 " --> pdb=" O THR D 644 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 642 through 647' Processing helix chain 'D' and resid 663 through 669 removed outlier: 4.156A pdb=" N VAL D 668 " --> pdb=" O LEU D 664 " (cutoff:3.500A) Processing helix chain 'D' and resid 688 through 690 No H-bonds generated for 'chain 'D' and resid 688 through 690' Processing helix chain 'D' and resid 692 through 695 No H-bonds generated for 'chain 'D' and resid 692 through 695' Processing helix chain 'D' and resid 732 through 738 Processing helix chain 'D' and resid 760 through 775 removed outlier: 4.135A pdb=" N ILE D 764 " --> pdb=" O LEU D 761 " (cutoff:3.500A) Processing helix chain 'D' and resid 787 through 795 Processing helix chain 'D' and resid 803 through 805 No H-bonds generated for 'chain 'D' and resid 803 through 805' Processing helix chain 'D' and resid 807 through 824 removed outlier: 4.303A pdb=" N ASP D 817 " --> pdb=" O GLN D 813 " (cutoff:3.500A) removed outlier: 6.006A pdb=" N GLN D 818 " --> pdb=" O ALA D 814 " (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 186 through 194 Processing helix chain 'E' and resid 212 through 225 removed outlier: 3.782A pdb=" N ALA E 225 " --> pdb=" O GLN E 221 " (cutoff:3.500A) Processing helix chain 'E' and resid 230 through 232 No H-bonds generated for 'chain 'E' and resid 230 through 232' Processing helix chain 'E' and resid 257 through 267 removed outlier: 3.777A pdb=" N ALA E 261 " --> pdb=" O GLU E 257 " (cutoff:3.500A) 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 304 No H-bonds generated for 'chain 'E' and resid 301 through 304' Processing helix chain 'E' and resid 317 through 321 removed outlier: 3.652A pdb=" N ARG E 321 " --> pdb=" O LEU E 317 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 317 through 321' 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 Processing helix chain 'E' and resid 368 through 381 removed outlier: 4.363A pdb=" N VAL E 372 " --> pdb=" O ASP E 368 " (cutoff:3.500A) removed outlier: 3.996A pdb=" N ARG E 380 " --> pdb=" O THR E 376 " (cutoff:3.500A) removed outlier: 4.337A pdb=" N TYR E 381 " --> pdb=" O LEU E 377 " (cutoff:3.500A) Processing helix chain 'E' and resid 387 through 393 removed outlier: 3.825A pdb=" N ALA E 391 " --> pdb=" O LEU E 387 " (cutoff:3.500A) removed outlier: 4.294A pdb=" N ILE E 392 " --> pdb=" O PRO E 388 " (cutoff:3.500A) Processing helix chain 'E' and resid 401 through 406 removed outlier: 3.625A pdb=" N MET E 404 " --> pdb=" O ARG E 401 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N GLU E 405 " --> pdb=" O LEU E 402 " (cutoff:3.500A) Processing helix chain 'E' and resid 535 through 546 removed outlier: 4.094A pdb=" N VAL E 541 " --> pdb=" O ASP E 537 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N ALA E 544 " --> pdb=" O ASP E 540 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N THR E 546 " --> pdb=" O VAL E 542 " (cutoff:3.500A) Processing helix chain 'E' and resid 576 through 585 Processing helix chain 'E' and resid 589 through 591 No H-bonds generated for 'chain 'E' and resid 589 through 591' Processing helix chain 'E' and resid 615 through 624 removed outlier: 3.564A pdb=" N ASP E 622 " --> pdb=" O LYS E 618 " (cutoff:3.500A) removed outlier: 4.159A pdb=" N PHE E 623 " --> pdb=" O ALA E 619 " (cutoff:3.500A) Processing helix chain 'E' and resid 645 through 648 Processing helix chain 'E' and resid 665 through 667 No H-bonds generated for 'chain 'E' and resid 665 through 667' 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 689 through 695 removed outlier: 3.682A pdb=" N GLN E 694 " --> pdb=" O ASP E 690 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N VAL E 695 " --> pdb=" O VAL E 691 " (cutoff:3.500A) Processing helix chain 'E' and resid 729 through 738 Processing helix chain 'E' and resid 742 through 745 No H-bonds generated for 'chain 'E' and resid 742 through 745' Processing helix chain 'E' and resid 760 through 773 removed outlier: 3.624A pdb=" N ILE E 764 " --> pdb=" O LEU E 761 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N GLY E 773 " --> pdb=" O ALA E 770 " (cutoff:3.500A) Processing helix chain 'E' and resid 775 through 777 No H-bonds generated for 'chain 'E' and resid 775 through 777' Processing helix chain 'E' and resid 787 through 797 removed outlier: 4.122A pdb=" N ALA E 794 " --> pdb=" O LYS E 790 " (cutoff:3.500A) removed outlier: 3.863A pdb=" N GLN E 795 " --> pdb=" O ARG E 791 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N ARG E 796 " --> pdb=" O TRP E 792 " (cutoff:3.500A) Processing helix chain 'E' and resid 807 through 825 removed outlier: 4.154A pdb=" N GLN E 812 " --> pdb=" O ARG E 808 " (cutoff:3.500A) removed outlier: 3.971A pdb=" N ALA E 814 " --> pdb=" O LEU E 810 " (cutoff:3.500A) removed outlier: 4.289A pdb=" N ILE E 815 " --> pdb=" O VAL E 811 " (cutoff:3.500A) Processing helix chain 'F' and resid 169 through 173 Processing helix chain 'F' and resid 185 through 194 Processing helix chain 'F' and resid 213 through 225 Processing helix chain 'F' and resid 230 through 232 No H-bonds generated for 'chain 'F' and resid 230 through 232' Processing helix chain 'F' and resid 254 through 266 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 301 through 306 removed outlier: 4.380A pdb=" N ALA F 305 " --> pdb=" O LYS F 301 " (cutoff:3.500A) removed outlier: 4.516A pdb=" N ARG F 306 " --> pdb=" O PRO F 302 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 301 through 306' Processing helix chain 'F' and resid 319 through 321 No H-bonds generated for 'chain 'F' and resid 319 through 321' Processing helix chain 'F' and resid 324 through 326 No H-bonds generated for 'chain 'F' and resid 324 through 326' Processing helix chain 'F' and resid 328 through 333 removed outlier: 4.343A pdb=" N ARG F 332 " --> pdb=" O ALA F 329 " (cutoff:3.500A) Processing helix chain 'F' and resid 344 through 353 Processing helix chain 'F' and resid 357 through 361 Processing helix chain 'F' and resid 368 through 377 removed outlier: 3.975A pdb=" N ALA F 374 " --> pdb=" O ALA F 370 " (cutoff:3.500A) removed outlier: 4.602A pdb=" N ALA F 375 " --> pdb=" O LEU F 371 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N THR F 376 " --> pdb=" O VAL F 372 " (cutoff:3.500A) Processing helix chain 'F' and resid 390 through 405 removed outlier: 4.145A pdb=" N LEU F 394 " --> pdb=" O LYS F 390 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N VAL F 395 " --> pdb=" O ALA F 391 " (cutoff:3.500A) Processing helix chain 'F' and resid 535 through 542 Processing helix chain 'F' and resid 558 through 562 Processing helix chain 'F' and resid 568 through 570 No H-bonds generated for 'chain 'F' and resid 568 through 570' Processing helix chain 'F' and resid 576 through 591 removed outlier: 3.551A pdb=" N ALA F 581 " --> pdb=" O ALA F 577 " (cutoff:3.500A) removed outlier: 4.022A pdb=" N SER F 589 " --> pdb=" O ALA F 585 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N ARG F 590 " --> pdb=" O VAL F 586 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N ALA F 591 " --> pdb=" O ARG F 587 " (cutoff:3.500A) Processing helix chain 'F' and resid 617 through 624 removed outlier: 3.824A pdb=" N ALA F 621 " --> pdb=" O ALA F 617 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N ASP F 622 " --> pdb=" O LYS F 618 " (cutoff:3.500A) removed outlier: 4.015A pdb=" N PHE F 623 " --> pdb=" O ALA F 619 " (cutoff:3.500A) Processing helix chain 'F' and resid 642 through 647 removed outlier: 4.204A pdb=" N VAL F 645 " --> pdb=" O LYS F 642 " (cutoff:3.500A) removed outlier: 4.367A pdb=" N ALA F 646 " --> pdb=" O HIS F 643 " (cutoff:3.500A) Processing helix chain 'F' and resid 664 through 670 removed outlier: 3.875A pdb=" N VAL F 668 " --> pdb=" O LEU F 664 " (cutoff:3.500A) removed outlier: 4.121A pdb=" N ARG F 670 " --> pdb=" O GLU F 666 " (cutoff:3.500A) Processing helix chain 'F' and resid 688 through 695 removed outlier: 4.446A pdb=" N GLN F 694 " --> pdb=" O ASP F 690 " (cutoff:3.500A) removed outlier: 3.964A pdb=" N VAL F 695 " --> pdb=" O VAL F 691 " (cutoff:3.500A) Processing helix chain 'F' and resid 729 through 736 Processing helix chain 'F' and resid 761 through 777 removed outlier: 3.538A pdb=" N LEU F 776 " --> pdb=" O LEU F 772 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N ALA F 777 " --> pdb=" O GLY F 773 " (cutoff:3.500A) Processing helix chain 'F' and resid 787 through 795 removed outlier: 3.858A pdb=" N ALA F 794 " --> pdb=" O LYS F 790 " (cutoff:3.500A) Processing helix chain 'F' and resid 805 through 814 removed outlier: 3.659A pdb=" N ARG F 809 " --> pdb=" O ARG F 805 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N GLN F 812 " --> pdb=" O ARG F 808 " (cutoff:3.500A) Processing helix chain 'F' and resid 816 through 825 removed outlier: 3.857A pdb=" N LEU F 824 " --> pdb=" O ALA F 820 " (cutoff:3.500A) removed outlier: 3.851A pdb=" N ALA F 825 " --> pdb=" O LYS F 821 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'A' and resid 203 through 205 removed outlier: 6.926A pdb=" N GLY A 313 " --> pdb=" O LEU A 204 " (cutoff:3.500A) No H-bonds generated for sheet with id= A Processing sheet with id= B, first strand: chain 'A' and resid 601 through 605 removed outlier: 3.756A pdb=" N LEU A 718 " --> pdb=" O PHE A 603 " (cutoff:3.500A) removed outlier: 4.014A pdb=" N ILE A 634 " --> pdb=" O LEU A 677 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N ASP A 679 " --> pdb=" O ILE A 634 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'A' and resid 783 through 785 removed outlier: 6.839A pdb=" N VAL A 834 " --> pdb=" O GLN A 784 " (cutoff:3.500A) No H-bonds generated for sheet with id= C Processing sheet with id= D, first strand: chain 'B' and resid 335 through 338 removed outlier: 6.092A pdb=" N LEU B 311 " --> pdb=" O PRO B 202 " (cutoff:3.500A) removed outlier: 7.334A pdb=" N LEU B 204 " --> pdb=" O LEU B 311 " (cutoff:3.500A) removed outlier: 6.649A pdb=" N GLY B 313 " --> pdb=" O LEU B 204 " (cutoff:3.500A) removed outlier: 8.352A pdb=" N GLY B 206 " --> pdb=" O GLY B 313 " (cutoff:3.500A) removed outlier: 6.421A pdb=" N THR B 315 " --> pdb=" O GLY B 206 " (cutoff:3.500A) removed outlier: 4.773A pdb=" N ARG B 310 " --> pdb=" O ILE B 273 " (cutoff:3.500A) removed outlier: 4.066A pdb=" N ALA B 314 " --> pdb=" O ILE B 277 " (cutoff:3.500A) removed outlier: 6.307A pdb=" N THR B 236 " --> pdb=" O ILE B 274 " (cutoff:3.500A) removed outlier: 7.563A pdb=" N PHE B 276 " --> pdb=" O THR B 236 " (cutoff:3.500A) removed outlier: 6.559A pdb=" N VAL B 238 " --> pdb=" O PHE B 276 " (cutoff:3.500A) removed outlier: 8.247A pdb=" N ASP B 278 " --> pdb=" O VAL B 238 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'B' and resid 601 through 604 removed outlier: 6.848A pdb=" N VAL B 632 " --> pdb=" O LEU B 677 " (cutoff:3.500A) removed outlier: 7.822A pdb=" N ASP B 679 " --> pdb=" O VAL B 632 " (cutoff:3.500A) removed outlier: 8.286A pdb=" N ILE B 634 " --> pdb=" O ASP B 679 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'B' and resid 782 through 785 Processing sheet with id= G, first strand: chain 'C' and resid 335 through 338 removed outlier: 7.021A pdb=" N GLY C 313 " --> pdb=" O LEU C 204 " (cutoff:3.500A) removed outlier: 8.754A pdb=" N GLY C 206 " --> pdb=" O GLY C 313 " (cutoff:3.500A) removed outlier: 6.738A pdb=" N THR C 315 " --> pdb=" O GLY C 206 " (cutoff:3.500A) removed outlier: 4.157A pdb=" N ALA C 314 " --> pdb=" O ILE C 277 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'C' and resid 601 through 605 removed outlier: 6.871A pdb=" N VAL C 632 " --> pdb=" O LEU C 677 " (cutoff:3.500A) removed outlier: 7.793A pdb=" N ASP C 679 " --> pdb=" O VAL C 632 " (cutoff:3.500A) removed outlier: 7.688A pdb=" N ILE C 634 " --> pdb=" O ASP C 679 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'C' and resid 700 through 702 Processing sheet with id= J, first strand: chain 'C' and resid 783 through 785 removed outlier: 7.269A pdb=" N VAL C 834 " --> pdb=" O GLN C 784 " (cutoff:3.500A) No H-bonds generated for sheet with id= J Processing sheet with id= K, first strand: chain 'C' and resid 837 through 839 Processing sheet with id= L, first strand: chain 'D' and resid 204 through 206 removed outlier: 6.317A pdb=" N VAL D 337 " --> pdb=" O ILE D 205 " (cutoff:3.500A) No H-bonds generated for sheet with id= L Processing sheet with id= M, first strand: chain 'D' and resid 276 through 278 removed outlier: 6.160A pdb=" N VAL D 312 " --> pdb=" O ILE D 277 " (cutoff:3.500A) No H-bonds generated for sheet with id= M Processing sheet with id= N, first strand: chain 'D' and resid 632 through 635 removed outlier: 3.573A pdb=" N ASP D 679 " --> pdb=" O ILE D 634 " (cutoff:3.500A) removed outlier: 6.643A pdb=" N ILE D 715 " --> pdb=" O VAL D 676 " (cutoff:3.500A) removed outlier: 8.205A pdb=" N PHE D 678 " --> pdb=" O ILE D 715 " (cutoff:3.500A) removed outlier: 7.446A pdb=" N ILE D 717 " --> pdb=" O PHE D 678 " (cutoff:3.500A) Processing sheet with id= O, first strand: chain 'E' and resid 335 through 338 removed outlier: 6.355A pdb=" N LEU E 311 " --> pdb=" O PRO E 202 " (cutoff:3.500A) removed outlier: 7.619A pdb=" N LEU E 204 " --> pdb=" O LEU E 311 " (cutoff:3.500A) removed outlier: 7.045A pdb=" N GLY E 313 " --> pdb=" O LEU E 204 " (cutoff:3.500A) removed outlier: 8.402A pdb=" N GLY E 206 " --> pdb=" O GLY E 313 " (cutoff:3.500A) removed outlier: 6.300A pdb=" N THR E 315 " --> pdb=" O GLY E 206 " (cutoff:3.500A) removed outlier: 6.206A pdb=" N THR E 275 " --> pdb=" O VAL E 312 " (cutoff:3.500A) removed outlier: 8.481A pdb=" N ALA E 314 " --> pdb=" O THR E 275 " (cutoff:3.500A) removed outlier: 7.161A pdb=" N ILE E 277 " --> pdb=" O ALA E 314 " (cutoff:3.500A) removed outlier: 9.200A pdb=" N THR E 316 " --> pdb=" O ILE E 277 " (cutoff:3.500A) Processing sheet with id= P, first strand: chain 'E' and resid 631 through 635 removed outlier: 7.108A pdb=" N VAL E 675 " --> pdb=" O VAL E 632 " (cutoff:3.500A) removed outlier: 8.133A pdb=" N ILE E 634 " --> pdb=" O VAL E 675 " (cutoff:3.500A) removed outlier: 6.466A pdb=" N LEU E 677 " --> pdb=" O ILE E 634 " (cutoff:3.500A) removed outlier: 5.896A pdb=" N ILE E 715 " --> pdb=" O VAL E 676 " (cutoff:3.500A) removed outlier: 7.469A pdb=" N PHE E 678 " --> pdb=" O ILE E 715 " (cutoff:3.500A) removed outlier: 6.830A pdb=" N ILE E 717 " --> pdb=" O PHE E 678 " (cutoff:3.500A) No H-bonds generated for sheet with id= P Processing sheet with id= Q, first strand: chain 'E' and resid 700 through 702 Processing sheet with id= R, first strand: chain 'F' and resid 335 through 338 removed outlier: 6.766A pdb=" N GLY F 313 " --> pdb=" O LEU F 204 " (cutoff:3.500A) removed outlier: 8.512A pdb=" N GLY F 206 " --> pdb=" O GLY F 313 " (cutoff:3.500A) removed outlier: 6.572A pdb=" N THR F 315 " --> pdb=" O GLY F 206 " (cutoff:3.500A) removed outlier: 4.218A pdb=" N ALA F 314 " --> pdb=" O ILE F 277 " (cutoff:3.500A) Processing sheet with id= S, first strand: chain 'F' and resid 236 through 238 Processing sheet with id= T, first strand: chain 'F' and resid 601 through 605 removed outlier: 6.907A pdb=" N VAL F 632 " --> pdb=" O LEU F 677 " (cutoff:3.500A) removed outlier: 7.753A pdb=" N ASP F 679 " --> pdb=" O VAL F 632 " (cutoff:3.500A) removed outlier: 7.632A 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 Processing sheet with id= V, first strand: chain 'F' and resid 837 through 839 removed outlier: 3.911A pdb=" N SER F 839 " --> pdb=" O ALA F 842 " (cutoff:3.500A) 697 hydrogen bonds defined for protein. 1800 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 8.71 Time building geometry restraints manager: 10.50 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.39: 10804 1.39 - 1.56: 16734 1.56 - 1.73: 38 1.73 - 1.90: 108 1.90 - 2.08: 10 Bond restraints: 27694 Sorted by residual: bond pdb=" C4 AGS F 901 " pdb=" C5 AGS F 901 " ideal model delta sigma weight residual 1.386 1.471 -0.085 1.00e-02 1.00e+04 7.27e+01 bond pdb=" C4 AGS D 901 " pdb=" C5 AGS D 901 " ideal model delta sigma weight residual 1.386 1.471 -0.085 1.00e-02 1.00e+04 7.15e+01 bond pdb=" C5 AGS D 901 " pdb=" C6 AGS D 901 " ideal model delta sigma weight residual 1.409 1.482 -0.073 1.00e-02 1.00e+04 5.39e+01 bond pdb=" C5 AGS F 901 " pdb=" C6 AGS F 901 " ideal model delta sigma weight residual 1.409 1.481 -0.072 1.00e-02 1.00e+04 5.20e+01 bond pdb=" PG AGS F 901 " pdb=" S1G AGS F 901 " ideal model delta sigma weight residual 1.949 2.075 -0.126 2.00e-02 2.50e+03 4.00e+01 ... (remaining 27689 not shown) Histogram of bond angle deviations from ideal: 97.89 - 105.98: 661 105.98 - 114.07: 16016 114.07 - 122.15: 15590 122.15 - 130.24: 5106 130.24 - 138.33: 104 Bond angle restraints: 37477 Sorted by residual: angle pdb=" C5 AGS F 901 " pdb=" C4 AGS F 901 " pdb=" N3 AGS F 901 " ideal model delta sigma weight residual 126.80 118.65 8.15 7.41e-01 1.82e+00 1.21e+02 angle pdb=" C5 AGS D 901 " pdb=" C4 AGS D 901 " pdb=" N3 AGS D 901 " ideal model delta sigma weight residual 126.80 118.71 8.09 7.41e-01 1.82e+00 1.19e+02 angle pdb=" C4 AGS F 901 " pdb=" C5 AGS F 901 " pdb=" N7 AGS F 901 " ideal model delta sigma weight residual 110.73 106.56 4.17 4.52e-01 4.89e+00 8.50e+01 angle pdb=" C SER C 594 " pdb=" N ASP C 595 " pdb=" CA ASP C 595 " ideal model delta sigma weight residual 120.94 138.33 -17.39 1.90e+00 2.77e-01 8.38e+01 angle pdb=" C4 AGS D 901 " pdb=" C5 AGS D 901 " pdb=" N7 AGS D 901 " ideal model delta sigma weight residual 110.73 106.60 4.13 4.52e-01 4.89e+00 8.33e+01 ... (remaining 37472 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 32.67: 16647 32.67 - 65.33: 372 65.33 - 98.00: 27 98.00 - 130.67: 3 130.67 - 163.34: 3 Dihedral angle restraints: 17052 sinusoidal: 7016 harmonic: 10036 Sorted by residual: dihedral pdb=" CA SER C 839 " pdb=" C SER C 839 " pdb=" N PRO C 840 " pdb=" CA PRO C 840 " ideal model delta harmonic sigma weight residual 180.00 -134.77 -45.23 0 5.00e+00 4.00e-02 8.18e+01 dihedral pdb=" CA SER E 839 " pdb=" C SER E 839 " pdb=" N PRO E 840 " pdb=" CA PRO E 840 " ideal model delta harmonic sigma weight residual -180.00 -135.46 -44.54 0 5.00e+00 4.00e-02 7.93e+01 dihedral pdb=" CA LEU C 387 " pdb=" C LEU C 387 " pdb=" N PRO C 388 " pdb=" CA PRO C 388 " ideal model delta harmonic sigma weight residual 180.00 135.83 44.17 0 5.00e+00 4.00e-02 7.80e+01 ... (remaining 17049 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.082: 3696 0.082 - 0.164: 572 0.164 - 0.245: 27 0.245 - 0.327: 3 0.327 - 0.409: 2 Chirality restraints: 4300 Sorted by residual: chirality pdb=" CB ILE D 681 " pdb=" CA ILE D 681 " pdb=" CG1 ILE D 681 " pdb=" CG2 ILE D 681 " both_signs ideal model delta sigma weight residual False 2.64 2.24 0.41 2.00e-01 2.50e+01 4.19e+00 chirality pdb=" CA ARG E 805 " pdb=" N ARG E 805 " pdb=" C ARG E 805 " pdb=" CB ARG E 805 " both_signs ideal model delta sigma weight residual False 2.51 2.15 0.36 2.00e-01 2.50e+01 3.20e+00 chirality pdb=" CB VAL F 180 " pdb=" CA VAL F 180 " pdb=" CG1 VAL F 180 " pdb=" CG2 VAL F 180 " both_signs ideal model delta sigma weight residual False -2.63 -2.33 -0.30 2.00e-01 2.50e+01 2.27e+00 ... (remaining 4297 not shown) Planarity restraints: 4894 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ARG B 409 " 0.094 5.00e-02 4.00e+02 1.46e-01 3.41e+01 pdb=" N PRO B 410 " -0.252 5.00e-02 4.00e+02 pdb=" CA PRO B 410 " 0.086 5.00e-02 4.00e+02 pdb=" CD PRO B 410 " 0.073 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU C 387 " -0.081 5.00e-02 4.00e+02 1.22e-01 2.39e+01 pdb=" N PRO C 388 " 0.211 5.00e-02 4.00e+02 pdb=" CA PRO C 388 " -0.065 5.00e-02 4.00e+02 pdb=" CD PRO C 388 " -0.066 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU D 387 " -0.080 5.00e-02 4.00e+02 1.20e-01 2.32e+01 pdb=" N PRO D 388 " 0.208 5.00e-02 4.00e+02 pdb=" CA PRO D 388 " -0.063 5.00e-02 4.00e+02 pdb=" CD PRO D 388 " -0.066 5.00e-02 4.00e+02 ... (remaining 4891 not shown) Histogram of nonbonded interaction distances: 1.91 - 2.51: 138 2.51 - 3.11: 18861 3.11 - 3.71: 39545 3.71 - 4.30: 52840 4.30 - 4.90: 87354 Nonbonded interactions: 198738 Sorted by model distance: nonbonded pdb=" O TRP F 545 " pdb=" N GLY F 547 " model vdw 1.913 2.520 nonbonded pdb=" NH1 ARG B 418 " pdb=" OD1 ASP C 184 " model vdw 1.981 2.520 nonbonded pdb=" O LYS B 301 " pdb=" NH1 ARG B 333 " model vdw 1.986 2.520 nonbonded pdb=" NZ LYS E 199 " pdb=" O ARG E 332 " model vdw 2.082 2.520 nonbonded pdb=" O GLU B 412 " pdb=" N GLU B 415 " model vdw 2.148 2.520 ... (remaining 198733 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 246 or resid 252 through 285 or resid 298 thro \ ugh 407 or resid 530 through 845)) selection = (chain 'B' and (resid 159 through 246 or resid 252 through 285 or resid 298 thro \ ugh 407 or resid 530 through 845)) selection = (chain 'C' and (resid 159 through 246 or resid 252 through 285 or resid 298 thro \ ugh 407 or resid 530 through 845)) selection = (chain 'D' and (resid 159 through 246 or resid 252 through 285 or resid 298 thro \ ugh 407 or resid 530 through 845)) selection = (chain 'E' and resid 159 through 845) selection = (chain 'F' and (resid 159 through 246 or resid 252 through 285 or resid 298 thro \ ugh 845)) } 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: 1.300 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.160 Construct map_model_manager: 0.040 Extract box with map and model: 7.100 Check model and map are aligned: 0.390 Set scattering table: 0.240 Process input model: 68.080 Find NCS groups from input model: 2.330 Set up NCS constraints: 0.120 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:3.380 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 83.150 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7907 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 : 0.006 0.126 27694 Z= 0.414 Angle : 1.110 17.391 37477 Z= 0.617 Chirality : 0.056 0.409 4300 Planarity : 0.009 0.146 4894 Dihedral : 13.453 163.336 10588 Min Nonbonded Distance : 1.913 Molprobity Statistics. All-atom Clashscore : 6.34 Ramachandran Plot: Outliers : 0.43 % Allowed : 12.49 % Favored : 87.08 % Rotamer: Outliers : 0.72 % Allowed : 5.77 % Favored : 93.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 6.34 % 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: -4.95 (0.11), residues: 3484 helix: -3.40 (0.09), residues: 1474 sheet: -2.81 (0.24), residues: 352 loop : -3.23 (0.13), residues: 1658 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.043 0.004 TRP B 545 HIS 0.011 0.002 HIS D 685 PHE 0.030 0.003 PHE B 753 TYR 0.026 0.003 TYR E 655 ARG 0.011 0.001 ARG A 670 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6968 Ramachandran restraints generated. 3484 Oldfield, 0 Emsley, 3484 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6968 Ramachandran restraints generated. 3484 Oldfield, 0 Emsley, 3484 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 782 residues out of total 2852 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 762 time to evaluate : 2.823 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 265 ASP cc_start: 0.7271 (t0) cc_final: 0.7021 (t0) REVERT: A 554 LEU cc_start: 0.7984 (mt) cc_final: 0.7655 (mp) REVERT: A 597 ASN cc_start: 0.8019 (p0) cc_final: 0.7777 (p0) REVERT: B 277 ILE cc_start: 0.9268 (mt) cc_final: 0.8966 (tt) REVERT: B 318 ASP cc_start: 0.8293 (p0) cc_final: 0.8059 (p0) REVERT: B 426 GLU cc_start: 0.5858 (OUTLIER) cc_final: 0.5602 (mm-30) REVERT: B 697 ASP cc_start: 0.7642 (t70) cc_final: 0.7395 (t0) REVERT: C 442 LEU cc_start: 0.1934 (OUTLIER) cc_final: 0.1685 (mt) REVERT: C 732 LEU cc_start: 0.8906 (tm) cc_final: 0.8668 (tp) REVERT: D 257 GLU cc_start: 0.7434 (tm-30) cc_final: 0.7169 (tp30) REVERT: D 584 ASP cc_start: 0.7163 (m-30) cc_final: 0.6773 (t0) REVERT: D 631 MET cc_start: 0.7014 (pp-130) cc_final: 0.6618 (pp-130) REVERT: E 205 ILE cc_start: 0.9023 (mt) cc_final: 0.8816 (mt) REVERT: E 319 GLU cc_start: 0.7592 (mp0) cc_final: 0.7134 (mp0) REVERT: E 389 ASP cc_start: 0.8363 (p0) cc_final: 0.7972 (t70) REVERT: F 171 ARG cc_start: 0.7068 (mtp85) cc_final: 0.6509 (mtm180) REVERT: F 213 THR cc_start: 0.7418 (m) cc_final: 0.7156 (m) REVERT: F 244 SER cc_start: 0.7751 (p) cc_final: 0.7402 (t) REVERT: F 756 LEU cc_start: 0.8594 (mt) cc_final: 0.8373 (mt) outliers start: 20 outliers final: 10 residues processed: 781 average time/residue: 0.4999 time to fit residues: 557.9466 Evaluate side-chains 355 residues out of total 2852 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 343 time to evaluate : 2.821 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 416 VAL Chi-restraints excluded: chain A residue 461 THR Chi-restraints excluded: chain A residue 746 ARG Chi-restraints excluded: chain B residue 411 VAL Chi-restraints excluded: chain B residue 416 VAL Chi-restraints excluded: chain B residue 426 GLU Chi-restraints excluded: chain B residue 461 THR Chi-restraints excluded: chain C residue 411 VAL Chi-restraints excluded: chain C residue 416 VAL Chi-restraints excluded: chain C residue 442 LEU Chi-restraints excluded: chain C residue 461 THR Chi-restraints excluded: chain F residue 545 TRP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 350 random chunks: chunk 295 optimal weight: 30.0000 chunk 265 optimal weight: 0.9990 chunk 147 optimal weight: 9.9990 chunk 90 optimal weight: 4.9990 chunk 178 optimal weight: 0.2980 chunk 141 optimal weight: 7.9990 chunk 274 optimal weight: 2.9990 chunk 106 optimal weight: 0.9980 chunk 166 optimal weight: 5.9990 chunk 204 optimal weight: 3.9990 chunk 317 optimal weight: 0.9990 overall best weight: 1.2586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 272 GLN A 335 GLN A 336 GLN A 361 HIS A 643 HIS B 643 HIS B 685 HIS ** B 745 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 757 ASN C 361 HIS C 575 GLN C 784 GLN D 361 HIS E 362 HIS F 200 ASN F 361 HIS F 643 HIS ** F 663 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 705 HIS F 745 ASN F 784 GLN ** F 827 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 19 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8021 moved from start: 0.2797 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 27694 Z= 0.198 Angle : 0.708 15.113 37477 Z= 0.353 Chirality : 0.044 0.324 4300 Planarity : 0.006 0.097 4894 Dihedral : 11.690 153.938 4120 Min Nonbonded Distance : 2.084 Molprobity Statistics. All-atom Clashscore : 9.56 Ramachandran Plot: Outliers : 0.14 % Allowed : 10.39 % Favored : 89.47 % Rotamer: Outliers : 3.08 % Allowed : 12.58 % Favored : 84.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 4.93 % 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: -3.71 (0.13), residues: 3484 helix: -2.11 (0.12), residues: 1470 sheet: -2.29 (0.29), residues: 296 loop : -2.81 (0.14), residues: 1718 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.002 TRP D 792 HIS 0.007 0.001 HIS C 829 PHE 0.023 0.002 PHE D 625 TYR 0.026 0.002 TYR F 338 ARG 0.008 0.001 ARG E 352 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6968 Ramachandran restraints generated. 3484 Oldfield, 0 Emsley, 3484 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6968 Ramachandran restraints generated. 3484 Oldfield, 0 Emsley, 3484 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 492 residues out of total 2852 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 86 poor density : 406 time to evaluate : 3.110 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 597 ASN cc_start: 0.8461 (p0) cc_final: 0.8148 (p0) REVERT: B 217 GLU cc_start: 0.8031 (OUTLIER) cc_final: 0.7360 (mp0) REVERT: B 703 ASP cc_start: 0.8614 (p0) cc_final: 0.8112 (p0) REVERT: B 780 ARG cc_start: 0.7293 (mtm-85) cc_final: 0.7025 (mtm110) REVERT: C 623 PHE cc_start: 0.6987 (p90) cc_final: 0.6729 (p90) REVERT: C 732 LEU cc_start: 0.9002 (OUTLIER) cc_final: 0.8749 (tp) REVERT: D 257 GLU cc_start: 0.7392 (tm-30) cc_final: 0.7097 (tp30) REVERT: D 564 MET cc_start: 0.8139 (ptm) cc_final: 0.7788 (ptm) REVERT: D 584 ASP cc_start: 0.7237 (m-30) cc_final: 0.6776 (t0) REVERT: D 679 ASP cc_start: 0.7220 (m-30) cc_final: 0.6928 (m-30) REVERT: D 732 LEU cc_start: 0.8196 (OUTLIER) cc_final: 0.7959 (mm) REVERT: E 200 ASN cc_start: 0.8695 (p0) cc_final: 0.8112 (p0) REVERT: E 311 LEU cc_start: 0.8535 (OUTLIER) cc_final: 0.8128 (tm) REVERT: E 389 ASP cc_start: 0.8323 (p0) cc_final: 0.8059 (t70) REVERT: E 390 LYS cc_start: 0.7909 (mtpt) cc_final: 0.7520 (mtpp) REVERT: E 635 ASP cc_start: 0.7534 (t0) cc_final: 0.7322 (t0) REVERT: F 171 ARG cc_start: 0.7011 (mtp85) cc_final: 0.6489 (mtm180) REVERT: F 244 SER cc_start: 0.7687 (p) cc_final: 0.7423 (t) REVERT: F 692 LEU cc_start: 0.8834 (OUTLIER) cc_final: 0.8606 (tt) REVERT: F 732 LEU cc_start: 0.9156 (OUTLIER) cc_final: 0.8908 (tm) outliers start: 86 outliers final: 40 residues processed: 463 average time/residue: 0.3808 time to fit residues: 279.2573 Evaluate side-chains 361 residues out of total 2852 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 315 time to evaluate : 3.050 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 242 LEU Chi-restraints excluded: chain A residue 278 ASP Chi-restraints excluded: chain A residue 319 GLU Chi-restraints excluded: chain A residue 371 LEU Chi-restraints excluded: chain A residue 645 VAL Chi-restraints excluded: chain A residue 664 LEU Chi-restraints excluded: chain A residue 702 THR Chi-restraints excluded: chain A residue 705 HIS Chi-restraints excluded: chain A residue 748 ASP Chi-restraints excluded: chain A residue 772 LEU Chi-restraints excluded: chain B residue 217 GLU Chi-restraints excluded: chain B residue 242 LEU Chi-restraints excluded: chain B residue 404 MET Chi-restraints excluded: chain B residue 411 VAL Chi-restraints excluded: chain B residue 416 VAL Chi-restraints excluded: chain B residue 537 ASP Chi-restraints excluded: chain B residue 645 VAL Chi-restraints excluded: chain C residue 201 ASN Chi-restraints excluded: chain C residue 242 LEU Chi-restraints excluded: chain C residue 346 ASP Chi-restraints excluded: chain C residue 350 ILE Chi-restraints excluded: chain C residue 354 LEU Chi-restraints excluded: chain C residue 636 MET Chi-restraints excluded: chain C residue 692 LEU Chi-restraints excluded: chain C residue 708 THR Chi-restraints excluded: chain C residue 710 ASP Chi-restraints excluded: chain C residue 732 LEU Chi-restraints excluded: chain C residue 757 ASN Chi-restraints excluded: chain C residue 829 HIS Chi-restraints excluded: chain D residue 241 ASP Chi-restraints excluded: chain D residue 369 SER Chi-restraints excluded: chain D residue 626 ASP Chi-restraints excluded: chain D residue 732 LEU Chi-restraints excluded: chain D residue 747 LEU Chi-restraints excluded: chain E residue 241 ASP Chi-restraints excluded: chain E residue 311 LEU Chi-restraints excluded: chain E residue 536 ASP Chi-restraints excluded: chain E residue 572 VAL Chi-restraints excluded: chain F residue 311 LEU Chi-restraints excluded: chain F residue 545 TRP Chi-restraints excluded: chain F residue 586 VAL Chi-restraints excluded: chain F residue 692 LEU Chi-restraints excluded: chain F residue 710 ASP Chi-restraints excluded: chain F residue 732 LEU Chi-restraints excluded: chain F residue 830 ASP Chi-restraints excluded: chain F residue 838 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 350 random chunks: chunk 176 optimal weight: 8.9990 chunk 98 optimal weight: 0.4980 chunk 264 optimal weight: 5.9990 chunk 216 optimal weight: 10.0000 chunk 87 optimal weight: 20.0000 chunk 318 optimal weight: 5.9990 chunk 343 optimal weight: 1.9990 chunk 283 optimal weight: 0.9990 chunk 315 optimal weight: 0.9990 chunk 108 optimal weight: 8.9990 chunk 255 optimal weight: 9.9990 overall best weight: 2.0988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 185 ASN A 336 GLN B 597 ASN C 643 HIS D 768 GLN ** F 663 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 705 HIS F 771 GLN ** F 827 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8065 moved from start: 0.3265 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 27694 Z= 0.226 Angle : 0.686 13.099 37477 Z= 0.337 Chirality : 0.043 0.221 4300 Planarity : 0.005 0.108 4894 Dihedral : 11.171 165.055 4105 Min Nonbonded Distance : 2.117 Molprobity Statistics. All-atom Clashscore : 9.74 Ramachandran Plot: Outliers : 0.14 % Allowed : 10.62 % Favored : 89.24 % Rotamer: Outliers : 4.01 % Allowed : 14.59 % Favored : 81.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 4.23 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.15 (0.13), residues: 3484 helix: -1.46 (0.13), residues: 1476 sheet: -2.21 (0.26), residues: 334 loop : -2.64 (0.14), residues: 1674 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 545 HIS 0.004 0.001 HIS A 829 PHE 0.019 0.002 PHE C 605 TYR 0.018 0.001 TYR F 338 ARG 0.005 0.000 ARG C 332 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6968 Ramachandran restraints generated. 3484 Oldfield, 0 Emsley, 3484 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6968 Ramachandran restraints generated. 3484 Oldfield, 0 Emsley, 3484 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 425 residues out of total 2852 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 112 poor density : 313 time to evaluate : 3.115 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 597 ASN cc_start: 0.8391 (p0) cc_final: 0.8123 (p0) REVERT: B 217 GLU cc_start: 0.8109 (OUTLIER) cc_final: 0.7070 (mp0) REVERT: B 254 GLU cc_start: 0.7255 (mt-10) cc_final: 0.7044 (mt-10) REVERT: B 780 ARG cc_start: 0.7432 (mtm-85) cc_final: 0.7180 (mtm110) REVERT: C 631 MET cc_start: 0.9299 (ptm) cc_final: 0.8784 (ptm) REVERT: C 636 MET cc_start: 0.8647 (OUTLIER) cc_final: 0.8235 (mpp) REVERT: C 732 LEU cc_start: 0.9029 (OUTLIER) cc_final: 0.8727 (tp) REVERT: C 769 LEU cc_start: 0.8402 (OUTLIER) cc_final: 0.8134 (mm) REVERT: C 822 MET cc_start: 0.7940 (ppp) cc_final: 0.7737 (ppp) REVERT: D 257 GLU cc_start: 0.7582 (tm-30) cc_final: 0.7247 (tp30) REVERT: D 584 ASP cc_start: 0.7307 (m-30) cc_final: 0.6919 (t0) REVERT: D 718 LEU cc_start: 0.9189 (OUTLIER) cc_final: 0.8974 (pp) REVERT: D 732 LEU cc_start: 0.8262 (OUTLIER) cc_final: 0.7997 (mm) REVERT: E 311 LEU cc_start: 0.8570 (OUTLIER) cc_final: 0.8173 (tm) REVERT: E 390 LYS cc_start: 0.7888 (mtpt) cc_final: 0.7625 (mtpt) REVERT: E 635 ASP cc_start: 0.7584 (t0) cc_final: 0.7328 (t0) REVERT: F 171 ARG cc_start: 0.6983 (mtp85) cc_final: 0.6547 (mtm180) REVERT: F 371 LEU cc_start: 0.8452 (OUTLIER) cc_final: 0.8062 (mt) REVERT: F 692 LEU cc_start: 0.8820 (OUTLIER) cc_final: 0.8601 (tt) outliers start: 112 outliers final: 66 residues processed: 403 average time/residue: 0.3722 time to fit residues: 240.1890 Evaluate side-chains 359 residues out of total 2852 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 75 poor density : 284 time to evaluate : 3.232 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 180 VAL Chi-restraints excluded: chain A residue 201 ASN Chi-restraints excluded: chain A residue 224 VAL Chi-restraints excluded: chain A residue 278 ASP Chi-restraints excluded: chain A residue 319 GLU Chi-restraints excluded: chain A residue 371 LEU Chi-restraints excluded: chain A residue 404 MET Chi-restraints excluded: chain A residue 645 VAL Chi-restraints excluded: chain A residue 649 ILE Chi-restraints excluded: chain A residue 664 LEU Chi-restraints excluded: chain A residue 702 THR Chi-restraints excluded: chain A residue 705 HIS Chi-restraints excluded: chain A residue 748 ASP Chi-restraints excluded: chain A residue 772 LEU Chi-restraints excluded: chain A residue 841 ASP Chi-restraints excluded: chain B residue 217 GLU Chi-restraints excluded: chain B residue 242 LEU Chi-restraints excluded: chain B residue 404 MET Chi-restraints excluded: chain B residue 537 ASP Chi-restraints excluded: chain B residue 604 MET Chi-restraints excluded: chain B residue 634 ILE Chi-restraints excluded: chain B residue 645 VAL Chi-restraints excluded: chain B residue 690 ASP Chi-restraints excluded: chain C residue 201 ASN Chi-restraints excluded: chain C residue 242 LEU Chi-restraints excluded: chain C residue 346 ASP Chi-restraints excluded: chain C residue 350 ILE Chi-restraints excluded: chain C residue 354 LEU Chi-restraints excluded: chain C residue 383 THR Chi-restraints excluded: chain C residue 620 LEU Chi-restraints excluded: chain C residue 636 MET Chi-restraints excluded: chain C residue 671 ARG Chi-restraints excluded: chain C residue 692 LEU Chi-restraints excluded: chain C residue 708 THR Chi-restraints excluded: chain C residue 710 ASP Chi-restraints excluded: chain C residue 732 LEU Chi-restraints excluded: chain C residue 757 ASN Chi-restraints excluded: chain C residue 769 LEU Chi-restraints excluded: chain C residue 829 HIS Chi-restraints excluded: chain D residue 165 SER Chi-restraints excluded: chain D residue 193 VAL Chi-restraints excluded: chain D residue 201 ASN Chi-restraints excluded: chain D residue 237 ILE Chi-restraints excluded: chain D residue 241 ASP Chi-restraints excluded: chain D residue 311 LEU Chi-restraints excluded: chain D residue 626 ASP Chi-restraints excluded: chain D residue 718 LEU Chi-restraints excluded: chain D residue 732 LEU Chi-restraints excluded: chain D residue 747 LEU Chi-restraints excluded: chain D residue 808 ARG Chi-restraints excluded: chain D residue 834 VAL Chi-restraints excluded: chain E residue 241 ASP Chi-restraints excluded: chain E residue 311 LEU Chi-restraints excluded: chain E residue 315 THR Chi-restraints excluded: chain E residue 350 ILE Chi-restraints excluded: chain E residue 536 ASP Chi-restraints excluded: chain E residue 541 VAL Chi-restraints excluded: chain E residue 572 VAL Chi-restraints excluded: chain E residue 627 ASP Chi-restraints excluded: chain E residue 631 MET Chi-restraints excluded: chain E residue 696 LEU Chi-restraints excluded: chain E residue 787 LEU Chi-restraints excluded: chain E residue 807 LEU Chi-restraints excluded: chain E residue 837 ASN Chi-restraints excluded: chain F residue 371 LEU Chi-restraints excluded: chain F residue 545 TRP Chi-restraints excluded: chain F residue 648 LEU Chi-restraints excluded: chain F residue 659 GLU Chi-restraints excluded: chain F residue 691 VAL Chi-restraints excluded: chain F residue 692 LEU Chi-restraints excluded: chain F residue 772 LEU Chi-restraints excluded: chain F residue 817 ASP Chi-restraints excluded: chain F residue 828 VAL Chi-restraints excluded: chain F residue 830 ASP Chi-restraints excluded: chain F residue 838 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 350 random chunks: chunk 314 optimal weight: 0.4980 chunk 239 optimal weight: 40.0000 chunk 165 optimal weight: 8.9990 chunk 35 optimal weight: 7.9990 chunk 151 optimal weight: 30.0000 chunk 213 optimal weight: 2.9990 chunk 319 optimal weight: 7.9990 chunk 338 optimal weight: 8.9990 chunk 166 optimal weight: 5.9990 chunk 302 optimal weight: 6.9990 chunk 91 optimal weight: 1.9990 overall best weight: 3.6988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 336 GLN B 192 GLN B 361 HIS C 721 ASN E 575 GLN E 685 HIS F 200 ASN ** F 663 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 827 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8145 moved from start: 0.3701 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.049 27694 Z= 0.332 Angle : 0.732 11.937 37477 Z= 0.359 Chirality : 0.045 0.229 4300 Planarity : 0.006 0.113 4894 Dihedral : 11.201 180.000 4103 Min Nonbonded Distance : 2.100 Molprobity Statistics. All-atom Clashscore : 10.92 Ramachandran Plot: Outliers : 0.20 % Allowed : 11.54 % Favored : 88.26 % Rotamer: Outliers : 4.98 % Allowed : 15.77 % Favored : 79.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 3.52 % 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: -2.89 (0.14), residues: 3484 helix: -1.14 (0.13), residues: 1502 sheet: -2.23 (0.26), residues: 355 loop : -2.60 (0.15), residues: 1627 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP C 545 HIS 0.006 0.001 HIS D 643 PHE 0.027 0.002 PHE B 605 TYR 0.018 0.002 TYR F 338 ARG 0.006 0.001 ARG E 171 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6968 Ramachandran restraints generated. 3484 Oldfield, 0 Emsley, 3484 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6968 Ramachandran restraints generated. 3484 Oldfield, 0 Emsley, 3484 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 421 residues out of total 2852 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 139 poor density : 282 time to evaluate : 3.535 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 217 GLU cc_start: 0.8322 (OUTLIER) cc_final: 0.6984 (mp0) REVERT: C 561 LEU cc_start: 0.9171 (OUTLIER) cc_final: 0.8879 (mm) REVERT: C 636 MET cc_start: 0.8700 (OUTLIER) cc_final: 0.8425 (mpp) REVERT: C 713 ASN cc_start: 0.9441 (OUTLIER) cc_final: 0.8979 (p0) REVERT: C 769 LEU cc_start: 0.8278 (OUTLIER) cc_final: 0.7996 (mm) REVERT: C 822 MET cc_start: 0.8051 (ppp) cc_final: 0.7586 (ppp) REVERT: D 257 GLU cc_start: 0.7887 (tm-30) cc_final: 0.7381 (tp30) REVERT: D 584 ASP cc_start: 0.7407 (m-30) cc_final: 0.7038 (t0) REVERT: D 718 LEU cc_start: 0.9249 (OUTLIER) cc_final: 0.9040 (pp) REVERT: D 732 LEU cc_start: 0.8375 (OUTLIER) cc_final: 0.8059 (mm) REVERT: E 181 ILE cc_start: 0.8469 (OUTLIER) cc_final: 0.8253 (pt) REVERT: E 311 LEU cc_start: 0.8639 (OUTLIER) cc_final: 0.8256 (tm) REVERT: E 390 LYS cc_start: 0.7863 (mtpt) cc_final: 0.7561 (mtpt) REVERT: E 635 ASP cc_start: 0.7763 (t0) cc_final: 0.7493 (t0) REVERT: F 171 ARG cc_start: 0.6702 (mtp85) cc_final: 0.6288 (mtm180) REVERT: F 371 LEU cc_start: 0.8500 (OUTLIER) cc_final: 0.8090 (mt) REVERT: F 664 LEU cc_start: 0.9295 (tt) cc_final: 0.9066 (tp) REVERT: F 692 LEU cc_start: 0.8871 (OUTLIER) cc_final: 0.8563 (tt) REVERT: F 824 LEU cc_start: 0.9149 (OUTLIER) cc_final: 0.8849 (pp) outliers start: 139 outliers final: 89 residues processed: 394 average time/residue: 0.3712 time to fit residues: 235.8149 Evaluate side-chains 348 residues out of total 2852 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 101 poor density : 247 time to evaluate : 2.928 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 201 ASN Chi-restraints excluded: chain A residue 224 VAL Chi-restraints excluded: chain A residue 278 ASP Chi-restraints excluded: chain A residue 280 LEU Chi-restraints excluded: chain A residue 319 GLU Chi-restraints excluded: chain A residue 371 LEU Chi-restraints excluded: chain A residue 389 ASP Chi-restraints excluded: chain A residue 396 ASP Chi-restraints excluded: chain A residue 645 VAL Chi-restraints excluded: chain A residue 649 ILE Chi-restraints excluded: chain A residue 664 LEU Chi-restraints excluded: chain A residue 702 THR Chi-restraints excluded: chain A residue 772 LEU Chi-restraints excluded: chain A residue 841 ASP Chi-restraints excluded: chain B residue 163 LYS Chi-restraints excluded: chain B residue 201 ASN Chi-restraints excluded: chain B residue 217 GLU Chi-restraints excluded: chain B residue 242 LEU Chi-restraints excluded: chain B residue 300 ILE Chi-restraints excluded: chain B residue 324 ILE Chi-restraints excluded: chain B residue 371 LEU Chi-restraints excluded: chain B residue 404 MET Chi-restraints excluded: chain B residue 537 ASP Chi-restraints excluded: chain B residue 604 MET Chi-restraints excluded: chain B residue 645 VAL Chi-restraints excluded: chain B residue 675 VAL Chi-restraints excluded: chain B residue 681 ILE Chi-restraints excluded: chain B residue 702 THR Chi-restraints excluded: chain B residue 830 ASP Chi-restraints excluded: chain C residue 201 ASN Chi-restraints excluded: chain C residue 242 LEU Chi-restraints excluded: chain C residue 262 VAL Chi-restraints excluded: chain C residue 346 ASP Chi-restraints excluded: chain C residue 350 ILE Chi-restraints excluded: chain C residue 354 LEU Chi-restraints excluded: chain C residue 383 THR Chi-restraints excluded: chain C residue 561 LEU Chi-restraints excluded: chain C residue 636 MET Chi-restraints excluded: chain C residue 671 ARG Chi-restraints excluded: chain C residue 692 LEU Chi-restraints excluded: chain C residue 708 THR Chi-restraints excluded: chain C residue 710 ASP Chi-restraints excluded: chain C residue 713 ASN Chi-restraints excluded: chain C residue 732 LEU Chi-restraints excluded: chain C residue 757 ASN Chi-restraints excluded: chain C residue 769 LEU Chi-restraints excluded: chain C residue 829 HIS Chi-restraints excluded: chain C residue 834 VAL Chi-restraints excluded: chain D residue 165 SER Chi-restraints excluded: chain D residue 180 VAL Chi-restraints excluded: chain D residue 193 VAL Chi-restraints excluded: chain D residue 201 ASN Chi-restraints excluded: chain D residue 205 ILE Chi-restraints excluded: chain D residue 237 ILE Chi-restraints excluded: chain D residue 241 ASP Chi-restraints excluded: chain D residue 383 THR Chi-restraints excluded: chain D residue 572 VAL Chi-restraints excluded: chain D residue 595 ASP Chi-restraints excluded: chain D residue 626 ASP Chi-restraints excluded: chain D residue 648 LEU Chi-restraints excluded: chain D residue 718 LEU Chi-restraints excluded: chain D residue 720 SER Chi-restraints excluded: chain D residue 732 LEU Chi-restraints excluded: chain D residue 747 LEU Chi-restraints excluded: chain D residue 808 ARG Chi-restraints excluded: chain D residue 834 VAL Chi-restraints excluded: chain E residue 181 ILE Chi-restraints excluded: chain E residue 219 LEU Chi-restraints excluded: chain E residue 241 ASP Chi-restraints excluded: chain E residue 275 THR Chi-restraints excluded: chain E residue 311 LEU Chi-restraints excluded: chain E residue 315 THR Chi-restraints excluded: chain E residue 350 ILE Chi-restraints excluded: chain E residue 364 VAL Chi-restraints excluded: chain E residue 541 VAL Chi-restraints excluded: chain E residue 572 VAL Chi-restraints excluded: chain E residue 627 ASP Chi-restraints excluded: chain E residue 629 ARG Chi-restraints excluded: chain E residue 631 MET Chi-restraints excluded: chain E residue 696 LEU Chi-restraints excluded: chain E residue 787 LEU Chi-restraints excluded: chain E residue 807 LEU Chi-restraints excluded: chain E residue 837 ASN Chi-restraints excluded: chain F residue 187 ILE Chi-restraints excluded: chain F residue 371 LEU Chi-restraints excluded: chain F residue 545 TRP Chi-restraints excluded: chain F residue 586 VAL Chi-restraints excluded: chain F residue 648 LEU Chi-restraints excluded: chain F residue 659 GLU Chi-restraints excluded: chain F residue 668 VAL Chi-restraints excluded: chain F residue 675 VAL Chi-restraints excluded: chain F residue 691 VAL Chi-restraints excluded: chain F residue 692 LEU Chi-restraints excluded: chain F residue 695 VAL Chi-restraints excluded: chain F residue 710 ASP Chi-restraints excluded: chain F residue 772 LEU Chi-restraints excluded: chain F residue 817 ASP Chi-restraints excluded: chain F residue 824 LEU Chi-restraints excluded: chain F residue 828 VAL Chi-restraints excluded: chain F residue 830 ASP Chi-restraints excluded: chain F residue 838 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 350 random chunks: chunk 281 optimal weight: 10.0000 chunk 192 optimal weight: 4.9990 chunk 4 optimal weight: 4.9990 chunk 251 optimal weight: 3.9990 chunk 139 optimal weight: 3.9990 chunk 288 optimal weight: 0.2980 chunk 233 optimal weight: 0.9990 chunk 0 optimal weight: 10.0000 chunk 172 optimal weight: 6.9990 chunk 303 optimal weight: 0.0870 chunk 85 optimal weight: 9.9990 overall best weight: 1.8764 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 336 GLN D 643 HIS D 768 GLN F 323 HIS F 663 GLN F 705 HIS ** F 827 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8107 moved from start: 0.3894 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 27694 Z= 0.203 Angle : 0.659 17.896 37477 Z= 0.319 Chirality : 0.043 0.222 4300 Planarity : 0.005 0.108 4894 Dihedral : 10.841 178.026 4103 Min Nonbonded Distance : 2.130 Molprobity Statistics. All-atom Clashscore : 9.51 Ramachandran Plot: Outliers : 0.14 % Allowed : 9.96 % Favored : 89.90 % Rotamer: Outliers : 4.55 % Allowed : 17.13 % Favored : 78.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.11 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.49 (0.14), residues: 3484 helix: -0.82 (0.14), residues: 1489 sheet: -1.94 (0.27), residues: 326 loop : -2.38 (0.15), residues: 1669 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP E 545 HIS 0.005 0.001 HIS E 685 PHE 0.018 0.002 PHE B 386 TYR 0.016 0.001 TYR F 338 ARG 0.008 0.000 ARG A 333 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6968 Ramachandran restraints generated. 3484 Oldfield, 0 Emsley, 3484 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6968 Ramachandran restraints generated. 3484 Oldfield, 0 Emsley, 3484 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 419 residues out of total 2852 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 127 poor density : 292 time to evaluate : 3.045 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 597 ASN cc_start: 0.8448 (p0) cc_final: 0.8087 (p0) REVERT: B 217 GLU cc_start: 0.8264 (OUTLIER) cc_final: 0.6849 (mp0) REVERT: C 564 MET cc_start: 0.7919 (tpp) cc_final: 0.7362 (tpt) REVERT: C 636 MET cc_start: 0.8577 (OUTLIER) cc_final: 0.8287 (mpp) REVERT: C 732 LEU cc_start: 0.8892 (OUTLIER) cc_final: 0.8538 (tp) REVERT: C 769 LEU cc_start: 0.8190 (OUTLIER) cc_final: 0.7924 (mm) REVERT: D 257 GLU cc_start: 0.7820 (tm-30) cc_final: 0.7322 (tp30) REVERT: D 584 ASP cc_start: 0.7354 (m-30) cc_final: 0.6917 (t0) REVERT: D 718 LEU cc_start: 0.9204 (OUTLIER) cc_final: 0.8981 (pp) REVERT: D 732 LEU cc_start: 0.8257 (OUTLIER) cc_final: 0.7980 (mm) REVERT: E 311 LEU cc_start: 0.8626 (OUTLIER) cc_final: 0.8250 (tm) REVERT: E 390 LYS cc_start: 0.7845 (mtpt) cc_final: 0.7547 (mtpt) REVERT: E 635 ASP cc_start: 0.7765 (t0) cc_final: 0.7477 (t0) REVERT: F 171 ARG cc_start: 0.6621 (mtp85) cc_final: 0.6227 (mtm180) REVERT: F 371 LEU cc_start: 0.8496 (OUTLIER) cc_final: 0.8082 (mt) REVERT: F 664 LEU cc_start: 0.9264 (tt) cc_final: 0.8949 (tp) REVERT: F 692 LEU cc_start: 0.8840 (OUTLIER) cc_final: 0.8594 (tt) REVERT: F 817 ASP cc_start: 0.7745 (OUTLIER) cc_final: 0.7491 (p0) REVERT: F 824 LEU cc_start: 0.9058 (OUTLIER) cc_final: 0.8791 (pp) outliers start: 127 outliers final: 83 residues processed: 398 average time/residue: 0.3472 time to fit residues: 226.8082 Evaluate side-chains 361 residues out of total 2852 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 94 poor density : 267 time to evaluate : 3.151 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 201 ASN Chi-restraints excluded: chain A residue 224 VAL Chi-restraints excluded: chain A residue 278 ASP Chi-restraints excluded: chain A residue 280 LEU Chi-restraints excluded: chain A residue 315 THR Chi-restraints excluded: chain A residue 350 ILE Chi-restraints excluded: chain A residue 371 LEU Chi-restraints excluded: chain A residue 396 ASP Chi-restraints excluded: chain A residue 404 MET Chi-restraints excluded: chain A residue 635 ASP Chi-restraints excluded: chain A residue 645 VAL Chi-restraints excluded: chain A residue 649 ILE Chi-restraints excluded: chain A residue 664 LEU Chi-restraints excluded: chain A residue 702 THR Chi-restraints excluded: chain A residue 748 ASP Chi-restraints excluded: chain A residue 772 LEU Chi-restraints excluded: chain A residue 841 ASP Chi-restraints excluded: chain B residue 163 LYS Chi-restraints excluded: chain B residue 201 ASN Chi-restraints excluded: chain B residue 217 GLU Chi-restraints excluded: chain B residue 242 LEU Chi-restraints excluded: chain B residue 300 ILE Chi-restraints excluded: chain B residue 324 ILE Chi-restraints excluded: chain B residue 326 LYS Chi-restraints excluded: chain B residue 371 LEU Chi-restraints excluded: chain B residue 404 MET Chi-restraints excluded: chain B residue 537 ASP Chi-restraints excluded: chain B residue 645 VAL Chi-restraints excluded: chain B residue 702 THR Chi-restraints excluded: chain B residue 713 ASN Chi-restraints excluded: chain B residue 765 VAL Chi-restraints excluded: chain B residue 783 LEU Chi-restraints excluded: chain C residue 201 ASN Chi-restraints excluded: chain C residue 242 LEU Chi-restraints excluded: chain C residue 346 ASP Chi-restraints excluded: chain C residue 350 ILE Chi-restraints excluded: chain C residue 354 LEU Chi-restraints excluded: chain C residue 383 THR Chi-restraints excluded: chain C residue 606 LEU Chi-restraints excluded: chain C residue 636 MET Chi-restraints excluded: chain C residue 671 ARG Chi-restraints excluded: chain C residue 692 LEU Chi-restraints excluded: chain C residue 708 THR Chi-restraints excluded: chain C residue 710 ASP Chi-restraints excluded: chain C residue 732 LEU Chi-restraints excluded: chain C residue 757 ASN Chi-restraints excluded: chain C residue 769 LEU Chi-restraints excluded: chain C residue 834 VAL Chi-restraints excluded: chain D residue 165 SER Chi-restraints excluded: chain D residue 193 VAL Chi-restraints excluded: chain D residue 201 ASN Chi-restraints excluded: chain D residue 237 ILE Chi-restraints excluded: chain D residue 241 ASP Chi-restraints excluded: chain D residue 277 ILE Chi-restraints excluded: chain D residue 572 VAL Chi-restraints excluded: chain D residue 595 ASP Chi-restraints excluded: chain D residue 626 ASP Chi-restraints excluded: chain D residue 718 LEU Chi-restraints excluded: chain D residue 720 SER Chi-restraints excluded: chain D residue 732 LEU Chi-restraints excluded: chain D residue 747 LEU Chi-restraints excluded: chain D residue 808 ARG Chi-restraints excluded: chain D residue 834 VAL Chi-restraints excluded: chain E residue 219 LEU Chi-restraints excluded: chain E residue 240 LEU Chi-restraints excluded: chain E residue 241 ASP Chi-restraints excluded: chain E residue 275 THR Chi-restraints excluded: chain E residue 304 LEU Chi-restraints excluded: chain E residue 311 LEU Chi-restraints excluded: chain E residue 315 THR Chi-restraints excluded: chain E residue 350 ILE Chi-restraints excluded: chain E residue 364 VAL Chi-restraints excluded: chain E residue 536 ASP Chi-restraints excluded: chain E residue 541 VAL Chi-restraints excluded: chain E residue 572 VAL Chi-restraints excluded: chain E residue 631 MET Chi-restraints excluded: chain E residue 648 LEU Chi-restraints excluded: chain E residue 696 LEU Chi-restraints excluded: chain E residue 757 ASN Chi-restraints excluded: chain E residue 787 LEU Chi-restraints excluded: chain E residue 807 LEU Chi-restraints excluded: chain E residue 837 ASN Chi-restraints excluded: chain F residue 371 LEU Chi-restraints excluded: chain F residue 545 TRP Chi-restraints excluded: chain F residue 648 LEU Chi-restraints excluded: chain F residue 668 VAL Chi-restraints excluded: chain F residue 691 VAL Chi-restraints excluded: chain F residue 692 LEU Chi-restraints excluded: chain F residue 695 VAL Chi-restraints excluded: chain F residue 772 LEU Chi-restraints excluded: chain F residue 817 ASP Chi-restraints excluded: chain F residue 824 LEU Chi-restraints excluded: chain F residue 830 ASP Chi-restraints excluded: chain F residue 838 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 350 random chunks: chunk 113 optimal weight: 7.9990 chunk 304 optimal weight: 2.9990 chunk 66 optimal weight: 2.9990 chunk 198 optimal weight: 0.0030 chunk 83 optimal weight: 0.9980 chunk 338 optimal weight: 8.9990 chunk 281 optimal weight: 9.9990 chunk 156 optimal weight: 1.9990 chunk 28 optimal weight: 8.9990 chunk 112 optimal weight: 5.9990 chunk 177 optimal weight: 2.9990 overall best weight: 1.7996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 336 GLN A 795 GLN B 281 HIS C 575 GLN F 705 HIS F 827 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8107 moved from start: 0.4101 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 27694 Z= 0.198 Angle : 0.639 13.224 37477 Z= 0.310 Chirality : 0.043 0.217 4300 Planarity : 0.005 0.116 4894 Dihedral : 10.461 177.794 4103 Min Nonbonded Distance : 2.141 Molprobity Statistics. All-atom Clashscore : 9.32 Ramachandran Plot: Outliers : 0.14 % Allowed : 9.90 % Favored : 89.95 % Rotamer: Outliers : 4.62 % Allowed : 17.49 % Favored : 77.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.11 % 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: -2.24 (0.14), residues: 3484 helix: -0.54 (0.14), residues: 1484 sheet: -1.97 (0.27), residues: 328 loop : -2.28 (0.15), residues: 1672 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP E 545 HIS 0.004 0.001 HIS E 685 PHE 0.018 0.002 PHE A 605 TYR 0.014 0.001 TYR F 338 ARG 0.007 0.000 ARG A 629 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6968 Ramachandran restraints generated. 3484 Oldfield, 0 Emsley, 3484 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6968 Ramachandran restraints generated. 3484 Oldfield, 0 Emsley, 3484 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 422 residues out of total 2852 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 129 poor density : 293 time to evaluate : 3.176 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 597 ASN cc_start: 0.8466 (p0) cc_final: 0.8152 (p0) REVERT: B 217 GLU cc_start: 0.8244 (OUTLIER) cc_final: 0.6789 (mp0) REVERT: B 605 PHE cc_start: 0.9273 (OUTLIER) cc_final: 0.8723 (p90) REVERT: C 561 LEU cc_start: 0.9167 (OUTLIER) cc_final: 0.8880 (mm) REVERT: C 564 MET cc_start: 0.7873 (tpp) cc_final: 0.7350 (tpt) REVERT: C 636 MET cc_start: 0.8575 (OUTLIER) cc_final: 0.8180 (mpp) REVERT: C 732 LEU cc_start: 0.8897 (OUTLIER) cc_final: 0.8532 (tp) REVERT: C 769 LEU cc_start: 0.8223 (OUTLIER) cc_final: 0.7940 (mm) REVERT: D 257 GLU cc_start: 0.7877 (tm-30) cc_final: 0.7348 (tp30) REVERT: D 564 MET cc_start: 0.8115 (ptm) cc_final: 0.7899 (ptp) REVERT: D 584 ASP cc_start: 0.7411 (m-30) cc_final: 0.6933 (t0) REVERT: D 718 LEU cc_start: 0.9191 (OUTLIER) cc_final: 0.8953 (pp) REVERT: D 732 LEU cc_start: 0.8256 (OUTLIER) cc_final: 0.7981 (mm) REVERT: E 311 LEU cc_start: 0.8603 (OUTLIER) cc_final: 0.8234 (tm) REVERT: E 635 ASP cc_start: 0.7685 (t0) cc_final: 0.7474 (t0) REVERT: E 636 MET cc_start: 0.7598 (mpt) cc_final: 0.7326 (mpt) REVERT: F 171 ARG cc_start: 0.6620 (mtp85) cc_final: 0.6238 (mtm180) REVERT: F 371 LEU cc_start: 0.8538 (OUTLIER) cc_final: 0.8143 (mt) REVERT: F 664 LEU cc_start: 0.9235 (tt) cc_final: 0.8919 (tp) REVERT: F 692 LEU cc_start: 0.8836 (OUTLIER) cc_final: 0.8540 (tt) REVERT: F 817 ASP cc_start: 0.7766 (OUTLIER) cc_final: 0.7528 (p0) REVERT: F 824 LEU cc_start: 0.9058 (OUTLIER) cc_final: 0.8824 (pp) outliers start: 129 outliers final: 87 residues processed: 404 average time/residue: 0.3491 time to fit residues: 232.9386 Evaluate side-chains 369 residues out of total 2852 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 100 poor density : 269 time to evaluate : 3.072 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 201 ASN Chi-restraints excluded: chain A residue 224 VAL Chi-restraints excluded: chain A residue 246 VAL Chi-restraints excluded: chain A residue 278 ASP Chi-restraints excluded: chain A residue 315 THR Chi-restraints excluded: chain A residue 371 LEU Chi-restraints excluded: chain A residue 396 ASP Chi-restraints excluded: chain A residue 404 MET Chi-restraints excluded: chain A residue 620 LEU Chi-restraints excluded: chain A residue 645 VAL Chi-restraints excluded: chain A residue 649 ILE Chi-restraints excluded: chain A residue 664 LEU Chi-restraints excluded: chain A residue 692 LEU Chi-restraints excluded: chain A residue 748 ASP Chi-restraints excluded: chain A residue 772 LEU Chi-restraints excluded: chain A residue 841 ASP Chi-restraints excluded: chain B residue 163 LYS Chi-restraints excluded: chain B residue 201 ASN Chi-restraints excluded: chain B residue 217 GLU Chi-restraints excluded: chain B residue 242 LEU Chi-restraints excluded: chain B residue 275 THR Chi-restraints excluded: chain B residue 300 ILE Chi-restraints excluded: chain B residue 324 ILE Chi-restraints excluded: chain B residue 371 LEU Chi-restraints excluded: chain B residue 404 MET Chi-restraints excluded: chain B residue 416 VAL Chi-restraints excluded: chain B residue 537 ASP Chi-restraints excluded: chain B residue 605 PHE Chi-restraints excluded: chain B residue 606 LEU Chi-restraints excluded: chain B residue 645 VAL Chi-restraints excluded: chain B residue 702 THR Chi-restraints excluded: chain B residue 783 LEU Chi-restraints excluded: chain B residue 830 ASP Chi-restraints excluded: chain C residue 201 ASN Chi-restraints excluded: chain C residue 242 LEU Chi-restraints excluded: chain C residue 262 VAL Chi-restraints excluded: chain C residue 346 ASP Chi-restraints excluded: chain C residue 350 ILE Chi-restraints excluded: chain C residue 354 LEU Chi-restraints excluded: chain C residue 383 THR Chi-restraints excluded: chain C residue 561 LEU Chi-restraints excluded: chain C residue 606 LEU Chi-restraints excluded: chain C residue 636 MET Chi-restraints excluded: chain C residue 671 ARG Chi-restraints excluded: chain C residue 708 THR Chi-restraints excluded: chain C residue 710 ASP Chi-restraints excluded: chain C residue 732 LEU Chi-restraints excluded: chain C residue 757 ASN Chi-restraints excluded: chain C residue 769 LEU Chi-restraints excluded: chain C residue 834 VAL Chi-restraints excluded: chain D residue 165 SER Chi-restraints excluded: chain D residue 193 VAL Chi-restraints excluded: chain D residue 201 ASN Chi-restraints excluded: chain D residue 237 ILE Chi-restraints excluded: chain D residue 241 ASP Chi-restraints excluded: chain D residue 309 LEU Chi-restraints excluded: chain D residue 383 THR Chi-restraints excluded: chain D residue 572 VAL Chi-restraints excluded: chain D residue 595 ASP Chi-restraints excluded: chain D residue 626 ASP Chi-restraints excluded: chain D residue 714 THR Chi-restraints excluded: chain D residue 718 LEU Chi-restraints excluded: chain D residue 720 SER Chi-restraints excluded: chain D residue 732 LEU Chi-restraints excluded: chain D residue 747 LEU Chi-restraints excluded: chain D residue 808 ARG Chi-restraints excluded: chain D residue 834 VAL Chi-restraints excluded: chain E residue 240 LEU Chi-restraints excluded: chain E residue 241 ASP Chi-restraints excluded: chain E residue 304 LEU Chi-restraints excluded: chain E residue 311 LEU Chi-restraints excluded: chain E residue 315 THR Chi-restraints excluded: chain E residue 364 VAL Chi-restraints excluded: chain E residue 536 ASP Chi-restraints excluded: chain E residue 541 VAL Chi-restraints excluded: chain E residue 558 THR Chi-restraints excluded: chain E residue 572 VAL Chi-restraints excluded: chain E residue 605 PHE Chi-restraints excluded: chain E residue 631 MET Chi-restraints excluded: chain E residue 648 LEU Chi-restraints excluded: chain E residue 696 LEU Chi-restraints excluded: chain E residue 757 ASN Chi-restraints excluded: chain E residue 787 LEU Chi-restraints excluded: chain E residue 807 LEU Chi-restraints excluded: chain E residue 837 ASN Chi-restraints excluded: chain F residue 371 LEU Chi-restraints excluded: chain F residue 615 GLU Chi-restraints excluded: chain F residue 648 LEU Chi-restraints excluded: chain F residue 668 VAL Chi-restraints excluded: chain F residue 675 VAL Chi-restraints excluded: chain F residue 691 VAL Chi-restraints excluded: chain F residue 692 LEU Chi-restraints excluded: chain F residue 702 THR Chi-restraints excluded: chain F residue 722 LEU Chi-restraints excluded: chain F residue 772 LEU Chi-restraints excluded: chain F residue 817 ASP Chi-restraints excluded: chain F residue 824 LEU Chi-restraints excluded: chain F residue 828 VAL Chi-restraints excluded: chain F residue 830 ASP Chi-restraints excluded: chain F residue 838 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 350 random chunks: chunk 326 optimal weight: 0.0870 chunk 38 optimal weight: 0.0000 chunk 192 optimal weight: 5.9990 chunk 247 optimal weight: 10.0000 chunk 191 optimal weight: 0.5980 chunk 285 optimal weight: 6.9990 chunk 189 optimal weight: 0.3980 chunk 337 optimal weight: 6.9990 chunk 211 optimal weight: 2.9990 chunk 205 optimal weight: 6.9990 chunk 155 optimal weight: 5.9990 overall best weight: 0.8164 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 336 GLN F 200 ASN ** F 663 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 705 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8071 moved from start: 0.4259 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.054 27694 Z= 0.151 Angle : 0.629 14.053 37477 Z= 0.302 Chirality : 0.042 0.254 4300 Planarity : 0.005 0.116 4894 Dihedral : 10.051 177.324 4101 Min Nonbonded Distance : 2.163 Molprobity Statistics. All-atom Clashscore : 9.03 Ramachandran Plot: Outliers : 0.14 % Allowed : 8.93 % Favored : 90.93 % Rotamer: Outliers : 3.69 % Allowed : 18.42 % Favored : 77.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.41 % 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: -1.97 (0.14), residues: 3484 helix: -0.33 (0.14), residues: 1478 sheet: -1.70 (0.28), residues: 314 loop : -2.14 (0.15), residues: 1692 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 545 HIS 0.004 0.001 HIS E 705 PHE 0.018 0.001 PHE C 623 TYR 0.013 0.001 TYR F 338 ARG 0.007 0.000 ARG A 629 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6968 Ramachandran restraints generated. 3484 Oldfield, 0 Emsley, 3484 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6968 Ramachandran restraints generated. 3484 Oldfield, 0 Emsley, 3484 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 420 residues out of total 2852 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 103 poor density : 317 time to evaluate : 3.357 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 234 ASP cc_start: 0.8205 (m-30) cc_final: 0.7711 (p0) REVERT: A 597 ASN cc_start: 0.8452 (p0) cc_final: 0.8161 (p0) REVERT: B 605 PHE cc_start: 0.9247 (OUTLIER) cc_final: 0.8789 (p90) REVERT: C 561 LEU cc_start: 0.9155 (OUTLIER) cc_final: 0.8889 (mm) REVERT: C 636 MET cc_start: 0.8491 (OUTLIER) cc_final: 0.8088 (mpp) REVERT: C 732 LEU cc_start: 0.8883 (OUTLIER) cc_final: 0.8524 (tp) REVERT: C 769 LEU cc_start: 0.8140 (OUTLIER) cc_final: 0.7872 (mm) REVERT: C 822 MET cc_start: 0.7792 (ppp) cc_final: 0.7104 (ppp) REVERT: D 192 GLN cc_start: 0.8320 (pt0) cc_final: 0.7839 (pp30) REVERT: D 257 GLU cc_start: 0.7783 (tm-30) cc_final: 0.7246 (tp30) REVERT: D 564 MET cc_start: 0.8053 (ptm) cc_final: 0.7847 (ptp) REVERT: D 584 ASP cc_start: 0.7353 (m-30) cc_final: 0.6929 (t0) REVERT: D 718 LEU cc_start: 0.9168 (OUTLIER) cc_final: 0.8905 (pp) REVERT: D 732 LEU cc_start: 0.8176 (OUTLIER) cc_final: 0.7935 (mp) REVERT: E 311 LEU cc_start: 0.8640 (OUTLIER) cc_final: 0.8276 (tm) REVERT: E 636 MET cc_start: 0.7594 (mpt) cc_final: 0.7367 (mpt) REVERT: F 171 ARG cc_start: 0.6600 (mtp85) cc_final: 0.6182 (mtm180) REVERT: F 371 LEU cc_start: 0.8540 (OUTLIER) cc_final: 0.8135 (mt) REVERT: F 664 LEU cc_start: 0.9170 (tt) cc_final: 0.8901 (tp) REVERT: F 692 LEU cc_start: 0.8815 (OUTLIER) cc_final: 0.8527 (tt) REVERT: F 756 LEU cc_start: 0.8354 (mt) cc_final: 0.8021 (mp) REVERT: F 817 ASP cc_start: 0.7740 (OUTLIER) cc_final: 0.7515 (p0) outliers start: 103 outliers final: 70 residues processed: 403 average time/residue: 0.3488 time to fit residues: 231.5915 Evaluate side-chains 364 residues out of total 2852 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 81 poor density : 283 time to evaluate : 3.372 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 201 ASN Chi-restraints excluded: chain A residue 224 VAL Chi-restraints excluded: chain A residue 246 VAL Chi-restraints excluded: chain A residue 278 ASP Chi-restraints excluded: chain A residue 315 THR Chi-restraints excluded: chain A residue 371 LEU Chi-restraints excluded: chain A residue 396 ASP Chi-restraints excluded: chain A residue 404 MET Chi-restraints excluded: chain A residue 605 PHE Chi-restraints excluded: chain A residue 645 VAL Chi-restraints excluded: chain A residue 649 ILE Chi-restraints excluded: chain A residue 664 LEU Chi-restraints excluded: chain A residue 692 LEU Chi-restraints excluded: chain A residue 748 ASP Chi-restraints excluded: chain A residue 841 ASP Chi-restraints excluded: chain B residue 201 ASN Chi-restraints excluded: chain B residue 217 GLU Chi-restraints excluded: chain B residue 242 LEU Chi-restraints excluded: chain B residue 275 THR Chi-restraints excluded: chain B residue 300 ILE Chi-restraints excluded: chain B residue 404 MET Chi-restraints excluded: chain B residue 416 VAL Chi-restraints excluded: chain B residue 537 ASP Chi-restraints excluded: chain B residue 605 PHE Chi-restraints excluded: chain B residue 606 LEU Chi-restraints excluded: chain B residue 645 VAL Chi-restraints excluded: chain B residue 702 THR Chi-restraints excluded: chain B residue 713 ASN Chi-restraints excluded: chain B residue 830 ASP Chi-restraints excluded: chain C residue 201 ASN Chi-restraints excluded: chain C residue 242 LEU Chi-restraints excluded: chain C residue 346 ASP Chi-restraints excluded: chain C residue 350 ILE Chi-restraints excluded: chain C residue 383 THR Chi-restraints excluded: chain C residue 561 LEU Chi-restraints excluded: chain C residue 606 LEU Chi-restraints excluded: chain C residue 636 MET Chi-restraints excluded: chain C residue 671 ARG Chi-restraints excluded: chain C residue 708 THR Chi-restraints excluded: chain C residue 710 ASP Chi-restraints excluded: chain C residue 732 LEU Chi-restraints excluded: chain C residue 757 ASN Chi-restraints excluded: chain C residue 769 LEU Chi-restraints excluded: chain C residue 834 VAL Chi-restraints excluded: chain D residue 165 SER Chi-restraints excluded: chain D residue 193 VAL Chi-restraints excluded: chain D residue 201 ASN Chi-restraints excluded: chain D residue 237 ILE Chi-restraints excluded: chain D residue 241 ASP Chi-restraints excluded: chain D residue 383 THR Chi-restraints excluded: chain D residue 572 VAL Chi-restraints excluded: chain D residue 595 ASP Chi-restraints excluded: chain D residue 626 ASP Chi-restraints excluded: chain D residue 718 LEU Chi-restraints excluded: chain D residue 720 SER Chi-restraints excluded: chain D residue 732 LEU Chi-restraints excluded: chain D residue 747 LEU Chi-restraints excluded: chain D residue 808 ARG Chi-restraints excluded: chain E residue 241 ASP Chi-restraints excluded: chain E residue 275 THR Chi-restraints excluded: chain E residue 311 LEU Chi-restraints excluded: chain E residue 315 THR Chi-restraints excluded: chain E residue 364 VAL Chi-restraints excluded: chain E residue 536 ASP Chi-restraints excluded: chain E residue 541 VAL Chi-restraints excluded: chain E residue 558 THR Chi-restraints excluded: chain E residue 572 VAL Chi-restraints excluded: chain E residue 631 MET Chi-restraints excluded: chain E residue 696 LEU Chi-restraints excluded: chain E residue 757 ASN Chi-restraints excluded: chain E residue 787 LEU Chi-restraints excluded: chain E residue 807 LEU Chi-restraints excluded: chain F residue 371 LEU Chi-restraints excluded: chain F residue 615 GLU Chi-restraints excluded: chain F residue 692 LEU Chi-restraints excluded: chain F residue 702 THR Chi-restraints excluded: chain F residue 722 LEU Chi-restraints excluded: chain F residue 772 LEU Chi-restraints excluded: chain F residue 817 ASP Chi-restraints excluded: chain F residue 828 VAL Chi-restraints excluded: chain F residue 830 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 350 random chunks: chunk 208 optimal weight: 0.9980 chunk 134 optimal weight: 7.9990 chunk 201 optimal weight: 0.9990 chunk 101 optimal weight: 6.9990 chunk 66 optimal weight: 0.7980 chunk 65 optimal weight: 0.9980 chunk 214 optimal weight: 1.9990 chunk 229 optimal weight: 8.9990 chunk 166 optimal weight: 0.9980 chunk 31 optimal weight: 4.9990 chunk 265 optimal weight: 0.9980 overall best weight: 0.9580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 323 HIS A 336 GLN E 336 GLN ** F 663 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 705 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8068 moved from start: 0.4409 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.053 27694 Z= 0.160 Angle : 0.644 14.390 37477 Z= 0.305 Chirality : 0.042 0.193 4300 Planarity : 0.005 0.119 4894 Dihedral : 9.796 172.099 4101 Min Nonbonded Distance : 2.174 Molprobity Statistics. All-atom Clashscore : 9.07 Ramachandran Plot: Outliers : 0.14 % Allowed : 8.98 % Favored : 90.87 % Rotamer: Outliers : 3.76 % Allowed : 18.78 % Favored : 77.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.41 % 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: -1.83 (0.15), residues: 3484 helix: -0.20 (0.14), residues: 1485 sheet: -1.74 (0.28), residues: 327 loop : -2.06 (0.16), residues: 1672 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP D 545 HIS 0.004 0.001 HIS E 705 PHE 0.017 0.001 PHE B 386 TYR 0.021 0.001 TYR E 658 ARG 0.006 0.000 ARG D 629 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6968 Ramachandran restraints generated. 3484 Oldfield, 0 Emsley, 3484 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6968 Ramachandran restraints generated. 3484 Oldfield, 0 Emsley, 3484 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 409 residues out of total 2852 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 105 poor density : 304 time to evaluate : 3.101 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 234 ASP cc_start: 0.8196 (m-30) cc_final: 0.7740 (p0) REVERT: A 319 GLU cc_start: 0.7526 (tt0) cc_final: 0.7186 (tt0) REVERT: A 597 ASN cc_start: 0.8463 (p0) cc_final: 0.8179 (p0) REVERT: B 327 ASP cc_start: 0.7441 (t0) cc_final: 0.6532 (m-30) REVERT: B 605 PHE cc_start: 0.9276 (OUTLIER) cc_final: 0.8735 (p90) REVERT: C 636 MET cc_start: 0.8527 (OUTLIER) cc_final: 0.8160 (mpp) REVERT: C 732 LEU cc_start: 0.8872 (OUTLIER) cc_final: 0.8516 (tp) REVERT: C 769 LEU cc_start: 0.8135 (OUTLIER) cc_final: 0.7848 (mm) REVERT: C 822 MET cc_start: 0.7814 (ppp) cc_final: 0.7189 (ppp) REVERT: D 192 GLN cc_start: 0.8321 (pt0) cc_final: 0.7934 (pp30) REVERT: D 584 ASP cc_start: 0.7330 (m-30) cc_final: 0.7006 (t0) REVERT: D 629 ARG cc_start: 0.6508 (mtm-85) cc_final: 0.5827 (mtt-85) REVERT: D 718 LEU cc_start: 0.9171 (OUTLIER) cc_final: 0.8919 (pp) REVERT: D 732 LEU cc_start: 0.8171 (OUTLIER) cc_final: 0.7933 (mp) REVERT: E 311 LEU cc_start: 0.8636 (OUTLIER) cc_final: 0.8255 (tm) REVERT: F 171 ARG cc_start: 0.6552 (mtp85) cc_final: 0.6156 (mtm180) REVERT: F 371 LEU cc_start: 0.8537 (OUTLIER) cc_final: 0.8132 (mt) REVERT: F 664 LEU cc_start: 0.9182 (tt) cc_final: 0.8892 (tp) REVERT: F 692 LEU cc_start: 0.8750 (OUTLIER) cc_final: 0.8517 (tt) REVERT: F 756 LEU cc_start: 0.8413 (mt) cc_final: 0.8070 (mp) REVERT: F 817 ASP cc_start: 0.7740 (OUTLIER) cc_final: 0.7526 (p0) outliers start: 105 outliers final: 76 residues processed: 394 average time/residue: 0.3401 time to fit residues: 220.1809 Evaluate side-chains 366 residues out of total 2852 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 86 poor density : 280 time to evaluate : 3.000 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 201 ASN Chi-restraints excluded: chain A residue 224 VAL Chi-restraints excluded: chain A residue 246 VAL Chi-restraints excluded: chain A residue 278 ASP Chi-restraints excluded: chain A residue 315 THR Chi-restraints excluded: chain A residue 371 LEU Chi-restraints excluded: chain A residue 396 ASP Chi-restraints excluded: chain A residue 404 MET Chi-restraints excluded: chain A residue 605 PHE Chi-restraints excluded: chain A residue 645 VAL Chi-restraints excluded: chain A residue 664 LEU Chi-restraints excluded: chain A residue 692 LEU Chi-restraints excluded: chain A residue 748 ASP Chi-restraints excluded: chain A residue 841 ASP Chi-restraints excluded: chain B residue 201 ASN Chi-restraints excluded: chain B residue 217 GLU Chi-restraints excluded: chain B residue 242 LEU Chi-restraints excluded: chain B residue 275 THR Chi-restraints excluded: chain B residue 300 ILE Chi-restraints excluded: chain B residue 404 MET Chi-restraints excluded: chain B residue 416 VAL Chi-restraints excluded: chain B residue 537 ASP Chi-restraints excluded: chain B residue 583 SER Chi-restraints excluded: chain B residue 605 PHE Chi-restraints excluded: chain B residue 606 LEU Chi-restraints excluded: chain B residue 645 VAL Chi-restraints excluded: chain B residue 675 VAL Chi-restraints excluded: chain B residue 702 THR Chi-restraints excluded: chain B residue 713 ASN Chi-restraints excluded: chain B residue 783 LEU Chi-restraints excluded: chain B residue 830 ASP Chi-restraints excluded: chain C residue 201 ASN Chi-restraints excluded: chain C residue 242 LEU Chi-restraints excluded: chain C residue 346 ASP Chi-restraints excluded: chain C residue 350 ILE Chi-restraints excluded: chain C residue 383 THR Chi-restraints excluded: chain C residue 606 LEU Chi-restraints excluded: chain C residue 636 MET Chi-restraints excluded: chain C residue 671 ARG Chi-restraints excluded: chain C residue 708 THR Chi-restraints excluded: chain C residue 710 ASP Chi-restraints excluded: chain C residue 732 LEU Chi-restraints excluded: chain C residue 757 ASN Chi-restraints excluded: chain C residue 769 LEU Chi-restraints excluded: chain C residue 834 VAL Chi-restraints excluded: chain D residue 165 SER Chi-restraints excluded: chain D residue 193 VAL Chi-restraints excluded: chain D residue 201 ASN Chi-restraints excluded: chain D residue 237 ILE Chi-restraints excluded: chain D residue 241 ASP Chi-restraints excluded: chain D residue 309 LEU Chi-restraints excluded: chain D residue 383 THR Chi-restraints excluded: chain D residue 572 VAL Chi-restraints excluded: chain D residue 595 ASP Chi-restraints excluded: chain D residue 626 ASP Chi-restraints excluded: chain D residue 648 LEU Chi-restraints excluded: chain D residue 718 LEU Chi-restraints excluded: chain D residue 732 LEU Chi-restraints excluded: chain D residue 747 LEU Chi-restraints excluded: chain D residue 808 ARG Chi-restraints excluded: chain D residue 834 VAL Chi-restraints excluded: chain E residue 240 LEU Chi-restraints excluded: chain E residue 241 ASP Chi-restraints excluded: chain E residue 275 THR Chi-restraints excluded: chain E residue 311 LEU Chi-restraints excluded: chain E residue 315 THR Chi-restraints excluded: chain E residue 364 VAL Chi-restraints excluded: chain E residue 536 ASP Chi-restraints excluded: chain E residue 541 VAL Chi-restraints excluded: chain E residue 558 THR Chi-restraints excluded: chain E residue 572 VAL Chi-restraints excluded: chain E residue 631 MET Chi-restraints excluded: chain E residue 696 LEU Chi-restraints excluded: chain E residue 757 ASN Chi-restraints excluded: chain E residue 787 LEU Chi-restraints excluded: chain E residue 807 LEU Chi-restraints excluded: chain F residue 371 LEU Chi-restraints excluded: chain F residue 615 GLU Chi-restraints excluded: chain F residue 648 LEU Chi-restraints excluded: chain F residue 675 VAL Chi-restraints excluded: chain F residue 692 LEU Chi-restraints excluded: chain F residue 702 THR Chi-restraints excluded: chain F residue 722 LEU Chi-restraints excluded: chain F residue 772 LEU Chi-restraints excluded: chain F residue 817 ASP Chi-restraints excluded: chain F residue 830 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 350 random chunks: chunk 306 optimal weight: 30.0000 chunk 323 optimal weight: 10.0000 chunk 294 optimal weight: 0.0870 chunk 314 optimal weight: 8.9990 chunk 189 optimal weight: 6.9990 chunk 136 optimal weight: 3.9990 chunk 246 optimal weight: 2.9990 chunk 96 optimal weight: 7.9990 chunk 284 optimal weight: 4.9990 chunk 297 optimal weight: 0.9990 chunk 313 optimal weight: 5.9990 overall best weight: 2.6166 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 336 GLN D 336 GLN E 336 GLN ** F 663 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 705 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8127 moved from start: 0.4497 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 27694 Z= 0.255 Angle : 0.695 16.482 37477 Z= 0.330 Chirality : 0.044 0.178 4300 Planarity : 0.005 0.118 4894 Dihedral : 9.830 164.934 4101 Min Nonbonded Distance : 2.136 Molprobity Statistics. All-atom Clashscore : 10.09 Ramachandran Plot: Outliers : 0.14 % Allowed : 10.13 % Favored : 89.72 % Rotamer: Outliers : 3.84 % Allowed : 19.03 % Favored : 77.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.41 % 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: -1.88 (0.15), residues: 3484 helix: -0.17 (0.14), residues: 1503 sheet: -1.69 (0.28), residues: 346 loop : -2.20 (0.15), residues: 1635 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP C 545 HIS 0.004 0.001 HIS C 829 PHE 0.030 0.002 PHE C 623 TYR 0.012 0.001 TYR F 338 ARG 0.006 0.000 ARG D 629 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6968 Ramachandran restraints generated. 3484 Oldfield, 0 Emsley, 3484 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6968 Ramachandran restraints generated. 3484 Oldfield, 0 Emsley, 3484 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 379 residues out of total 2852 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 107 poor density : 272 time to evaluate : 3.105 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 597 ASN cc_start: 0.8530 (p0) cc_final: 0.8206 (p0) REVERT: B 217 GLU cc_start: 0.8284 (OUTLIER) cc_final: 0.6770 (mp0) REVERT: B 327 ASP cc_start: 0.7404 (t0) cc_final: 0.6790 (m-30) REVERT: B 605 PHE cc_start: 0.9330 (OUTLIER) cc_final: 0.8689 (p90) REVERT: C 636 MET cc_start: 0.8578 (OUTLIER) cc_final: 0.8249 (mpp) REVERT: C 732 LEU cc_start: 0.8915 (OUTLIER) cc_final: 0.8556 (tp) REVERT: C 769 LEU cc_start: 0.8151 (OUTLIER) cc_final: 0.7909 (mm) REVERT: C 822 MET cc_start: 0.7793 (ppp) cc_final: 0.7200 (ppp) REVERT: C 827 GLN cc_start: 0.6947 (OUTLIER) cc_final: 0.6643 (pt0) REVERT: D 192 GLN cc_start: 0.8474 (pt0) cc_final: 0.7938 (pp30) REVERT: D 584 ASP cc_start: 0.7387 (m-30) cc_final: 0.7031 (t0) REVERT: D 629 ARG cc_start: 0.6605 (mtm-85) cc_final: 0.5881 (mtt-85) REVERT: D 718 LEU cc_start: 0.9191 (OUTLIER) cc_final: 0.8977 (pp) REVERT: D 732 LEU cc_start: 0.8243 (OUTLIER) cc_final: 0.7963 (mp) REVERT: E 201 ASN cc_start: 0.9142 (OUTLIER) cc_final: 0.8552 (p0) REVERT: E 311 LEU cc_start: 0.8637 (OUTLIER) cc_final: 0.8302 (tm) REVERT: E 802 TYR cc_start: 0.6974 (m-80) cc_final: 0.6762 (m-80) REVERT: F 171 ARG cc_start: 0.6556 (mtp85) cc_final: 0.6151 (mtm180) REVERT: F 371 LEU cc_start: 0.8558 (OUTLIER) cc_final: 0.8142 (mt) REVERT: F 664 LEU cc_start: 0.9226 (tt) cc_final: 0.8930 (tp) REVERT: F 692 LEU cc_start: 0.8805 (OUTLIER) cc_final: 0.8541 (tt) REVERT: F 817 ASP cc_start: 0.7916 (OUTLIER) cc_final: 0.7555 (p0) outliers start: 107 outliers final: 78 residues processed: 369 average time/residue: 0.3420 time to fit residues: 208.3804 Evaluate side-chains 357 residues out of total 2852 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 91 poor density : 266 time to evaluate : 3.090 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 201 ASN Chi-restraints excluded: chain A residue 224 VAL Chi-restraints excluded: chain A residue 246 VAL Chi-restraints excluded: chain A residue 280 LEU Chi-restraints excluded: chain A residue 315 THR Chi-restraints excluded: chain A residue 371 LEU Chi-restraints excluded: chain A residue 396 ASP Chi-restraints excluded: chain A residue 620 LEU Chi-restraints excluded: chain A residue 645 VAL Chi-restraints excluded: chain A residue 664 LEU Chi-restraints excluded: chain A residue 693 LEU Chi-restraints excluded: chain A residue 841 ASP Chi-restraints excluded: chain B residue 201 ASN Chi-restraints excluded: chain B residue 217 GLU Chi-restraints excluded: chain B residue 242 LEU Chi-restraints excluded: chain B residue 275 THR Chi-restraints excluded: chain B residue 300 ILE Chi-restraints excluded: chain B residue 416 VAL Chi-restraints excluded: chain B residue 537 ASP Chi-restraints excluded: chain B residue 583 SER Chi-restraints excluded: chain B residue 605 PHE Chi-restraints excluded: chain B residue 606 LEU Chi-restraints excluded: chain B residue 645 VAL Chi-restraints excluded: chain B residue 675 VAL Chi-restraints excluded: chain B residue 702 THR Chi-restraints excluded: chain B residue 713 ASN Chi-restraints excluded: chain B residue 767 ILE Chi-restraints excluded: chain B residue 769 LEU Chi-restraints excluded: chain B residue 783 LEU Chi-restraints excluded: chain B residue 830 ASP Chi-restraints excluded: chain C residue 201 ASN Chi-restraints excluded: chain C residue 232 LEU Chi-restraints excluded: chain C residue 242 LEU Chi-restraints excluded: chain C residue 346 ASP Chi-restraints excluded: chain C residue 350 ILE Chi-restraints excluded: chain C residue 354 LEU Chi-restraints excluded: chain C residue 383 THR Chi-restraints excluded: chain C residue 606 LEU Chi-restraints excluded: chain C residue 636 MET Chi-restraints excluded: chain C residue 671 ARG Chi-restraints excluded: chain C residue 692 LEU Chi-restraints excluded: chain C residue 708 THR Chi-restraints excluded: chain C residue 710 ASP Chi-restraints excluded: chain C residue 732 LEU Chi-restraints excluded: chain C residue 757 ASN Chi-restraints excluded: chain C residue 769 LEU Chi-restraints excluded: chain C residue 827 GLN Chi-restraints excluded: chain C residue 834 VAL Chi-restraints excluded: chain D residue 165 SER Chi-restraints excluded: chain D residue 193 VAL Chi-restraints excluded: chain D residue 201 ASN Chi-restraints excluded: chain D residue 237 ILE Chi-restraints excluded: chain D residue 241 ASP Chi-restraints excluded: chain D residue 383 THR Chi-restraints excluded: chain D residue 566 ASP Chi-restraints excluded: chain D residue 572 VAL Chi-restraints excluded: chain D residue 595 ASP Chi-restraints excluded: chain D residue 626 ASP Chi-restraints excluded: chain D residue 718 LEU Chi-restraints excluded: chain D residue 720 SER Chi-restraints excluded: chain D residue 732 LEU Chi-restraints excluded: chain D residue 747 LEU Chi-restraints excluded: chain D residue 808 ARG Chi-restraints excluded: chain D residue 834 VAL Chi-restraints excluded: chain E residue 201 ASN Chi-restraints excluded: chain E residue 240 LEU Chi-restraints excluded: chain E residue 241 ASP Chi-restraints excluded: chain E residue 275 THR Chi-restraints excluded: chain E residue 311 LEU Chi-restraints excluded: chain E residue 315 THR Chi-restraints excluded: chain E residue 364 VAL Chi-restraints excluded: chain E residue 541 VAL Chi-restraints excluded: chain E residue 558 THR Chi-restraints excluded: chain E residue 572 VAL Chi-restraints excluded: chain E residue 605 PHE Chi-restraints excluded: chain E residue 631 MET Chi-restraints excluded: chain E residue 696 LEU Chi-restraints excluded: chain E residue 757 ASN Chi-restraints excluded: chain E residue 787 LEU Chi-restraints excluded: chain E residue 807 LEU Chi-restraints excluded: chain F residue 371 LEU Chi-restraints excluded: chain F residue 615 GLU Chi-restraints excluded: chain F residue 675 VAL Chi-restraints excluded: chain F residue 691 VAL Chi-restraints excluded: chain F residue 692 LEU Chi-restraints excluded: chain F residue 702 THR Chi-restraints excluded: chain F residue 722 LEU Chi-restraints excluded: chain F residue 772 LEU Chi-restraints excluded: chain F residue 817 ASP Chi-restraints excluded: chain F residue 828 VAL Chi-restraints excluded: chain F residue 830 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 350 random chunks: chunk 206 optimal weight: 1.9990 chunk 332 optimal weight: 0.0030 chunk 202 optimal weight: 0.0870 chunk 157 optimal weight: 0.8980 chunk 231 optimal weight: 1.9990 chunk 348 optimal weight: 0.5980 chunk 320 optimal weight: 2.9990 chunk 277 optimal weight: 8.9990 chunk 28 optimal weight: 5.9990 chunk 214 optimal weight: 1.9990 chunk 170 optimal weight: 2.9990 overall best weight: 0.7170 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 336 GLN ** B 335 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 663 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 705 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8069 moved from start: 0.4623 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.058 27694 Z= 0.160 Angle : 0.660 16.269 37477 Z= 0.310 Chirality : 0.042 0.182 4300 Planarity : 0.005 0.115 4894 Dihedral : 9.556 156.689 4101 Min Nonbonded Distance : 2.163 Molprobity Statistics. All-atom Clashscore : 9.19 Ramachandran Plot: Outliers : 0.14 % Allowed : 8.87 % Favored : 90.99 % Rotamer: Outliers : 2.94 % Allowed : 20.07 % Favored : 76.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.41 % 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: -1.67 (0.15), residues: 3484 helix: -0.02 (0.14), residues: 1484 sheet: -1.58 (0.29), residues: 314 loop : -2.04 (0.16), residues: 1686 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP D 545 HIS 0.004 0.000 HIS E 705 PHE 0.021 0.001 PHE C 623 TYR 0.025 0.001 TYR E 658 ARG 0.007 0.000 ARG D 629 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6968 Ramachandran restraints generated. 3484 Oldfield, 0 Emsley, 3484 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6968 Ramachandran restraints generated. 3484 Oldfield, 0 Emsley, 3484 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 384 residues out of total 2852 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 82 poor density : 302 time to evaluate : 3.035 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 234 ASP cc_start: 0.8168 (m-30) cc_final: 0.7740 (p0) REVERT: A 371 LEU cc_start: 0.9160 (OUTLIER) cc_final: 0.8937 (mt) REVERT: A 597 ASN cc_start: 0.8512 (p0) cc_final: 0.8228 (p0) REVERT: B 327 ASP cc_start: 0.7386 (t0) cc_final: 0.6522 (m-30) REVERT: B 605 PHE cc_start: 0.9259 (OUTLIER) cc_final: 0.8768 (p90) REVERT: C 636 MET cc_start: 0.8708 (mtm) cc_final: 0.8258 (mpp) REVERT: C 732 LEU cc_start: 0.8922 (OUTLIER) cc_final: 0.8592 (tp) REVERT: C 769 LEU cc_start: 0.8132 (OUTLIER) cc_final: 0.7871 (mm) REVERT: C 822 MET cc_start: 0.7788 (ppp) cc_final: 0.7251 (ppp) REVERT: C 827 GLN cc_start: 0.6887 (OUTLIER) cc_final: 0.6595 (pt0) REVERT: D 192 GLN cc_start: 0.8349 (pt0) cc_final: 0.7973 (pp30) REVERT: D 584 ASP cc_start: 0.7216 (m-30) cc_final: 0.7005 (t0) REVERT: D 629 ARG cc_start: 0.6558 (mtm-85) cc_final: 0.5719 (mtt-85) REVERT: D 718 LEU cc_start: 0.9145 (OUTLIER) cc_final: 0.8906 (pp) REVERT: D 732 LEU cc_start: 0.8208 (OUTLIER) cc_final: 0.7976 (mm) REVERT: E 311 LEU cc_start: 0.8642 (OUTLIER) cc_final: 0.8268 (tm) REVERT: E 325 GLU cc_start: 0.7001 (mm-30) cc_final: 0.6178 (mt-10) REVERT: E 748 ASP cc_start: 0.7396 (m-30) cc_final: 0.6747 (m-30) REVERT: F 171 ARG cc_start: 0.6637 (mtp85) cc_final: 0.6284 (mtm180) REVERT: F 371 LEU cc_start: 0.8564 (OUTLIER) cc_final: 0.8164 (mt) REVERT: F 664 LEU cc_start: 0.9154 (tt) cc_final: 0.8882 (tp) REVERT: F 692 LEU cc_start: 0.8810 (OUTLIER) cc_final: 0.8534 (tt) REVERT: F 756 LEU cc_start: 0.8381 (mt) cc_final: 0.8051 (mp) outliers start: 82 outliers final: 67 residues processed: 373 average time/residue: 0.3479 time to fit residues: 213.6179 Evaluate side-chains 361 residues out of total 2852 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 77 poor density : 284 time to evaluate : 3.049 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 201 ASN Chi-restraints excluded: chain A residue 224 VAL Chi-restraints excluded: chain A residue 246 VAL Chi-restraints excluded: chain A residue 280 LEU Chi-restraints excluded: chain A residue 315 THR Chi-restraints excluded: chain A residue 371 LEU Chi-restraints excluded: chain A residue 396 ASP Chi-restraints excluded: chain A residue 605 PHE Chi-restraints excluded: chain A residue 620 LEU Chi-restraints excluded: chain A residue 635 ASP Chi-restraints excluded: chain A residue 649 ILE Chi-restraints excluded: chain A residue 664 LEU Chi-restraints excluded: chain A residue 841 ASP Chi-restraints excluded: chain B residue 201 ASN Chi-restraints excluded: chain B residue 217 GLU Chi-restraints excluded: chain B residue 242 LEU Chi-restraints excluded: chain B residue 275 THR Chi-restraints excluded: chain B residue 300 ILE Chi-restraints excluded: chain B residue 416 VAL Chi-restraints excluded: chain B residue 537 ASP Chi-restraints excluded: chain B residue 583 SER Chi-restraints excluded: chain B residue 605 PHE Chi-restraints excluded: chain B residue 606 LEU Chi-restraints excluded: chain B residue 675 VAL Chi-restraints excluded: chain B residue 702 THR Chi-restraints excluded: chain B residue 713 ASN Chi-restraints excluded: chain B residue 767 ILE Chi-restraints excluded: chain B residue 769 LEU Chi-restraints excluded: chain B residue 783 LEU Chi-restraints excluded: chain B residue 830 ASP Chi-restraints excluded: chain C residue 201 ASN Chi-restraints excluded: chain C residue 242 LEU Chi-restraints excluded: chain C residue 346 ASP Chi-restraints excluded: chain C residue 350 ILE Chi-restraints excluded: chain C residue 354 LEU Chi-restraints excluded: chain C residue 383 THR Chi-restraints excluded: chain C residue 606 LEU Chi-restraints excluded: chain C residue 692 LEU Chi-restraints excluded: chain C residue 708 THR Chi-restraints excluded: chain C residue 732 LEU Chi-restraints excluded: chain C residue 757 ASN Chi-restraints excluded: chain C residue 769 LEU Chi-restraints excluded: chain C residue 827 GLN Chi-restraints excluded: chain C residue 834 VAL Chi-restraints excluded: chain D residue 193 VAL Chi-restraints excluded: chain D residue 201 ASN Chi-restraints excluded: chain D residue 241 ASP Chi-restraints excluded: chain D residue 383 THR Chi-restraints excluded: chain D residue 572 VAL Chi-restraints excluded: chain D residue 626 ASP Chi-restraints excluded: chain D residue 718 LEU Chi-restraints excluded: chain D residue 732 LEU Chi-restraints excluded: chain D residue 747 LEU Chi-restraints excluded: chain D residue 808 ARG Chi-restraints excluded: chain D residue 834 VAL Chi-restraints excluded: chain E residue 241 ASP Chi-restraints excluded: chain E residue 275 THR Chi-restraints excluded: chain E residue 311 LEU Chi-restraints excluded: chain E residue 315 THR Chi-restraints excluded: chain E residue 364 VAL Chi-restraints excluded: chain E residue 541 VAL Chi-restraints excluded: chain E residue 558 THR Chi-restraints excluded: chain E residue 572 VAL Chi-restraints excluded: chain E residue 605 PHE Chi-restraints excluded: chain E residue 696 LEU Chi-restraints excluded: chain E residue 757 ASN Chi-restraints excluded: chain E residue 787 LEU Chi-restraints excluded: chain E residue 807 LEU Chi-restraints excluded: chain F residue 311 LEU Chi-restraints excluded: chain F residue 371 LEU Chi-restraints excluded: chain F residue 615 GLU Chi-restraints excluded: chain F residue 675 VAL Chi-restraints excluded: chain F residue 691 VAL Chi-restraints excluded: chain F residue 692 LEU Chi-restraints excluded: chain F residue 722 LEU Chi-restraints excluded: chain F residue 772 LEU Chi-restraints excluded: chain F residue 830 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 350 random chunks: chunk 220 optimal weight: 3.9990 chunk 295 optimal weight: 30.0000 chunk 85 optimal weight: 1.9990 chunk 256 optimal weight: 4.9990 chunk 40 optimal weight: 6.9990 chunk 77 optimal weight: 7.9990 chunk 278 optimal weight: 3.9990 chunk 116 optimal weight: 4.9990 chunk 285 optimal weight: 0.4980 chunk 35 optimal weight: 3.9990 chunk 51 optimal weight: 0.6980 overall best weight: 2.2386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 336 GLN D 336 GLN D 827 GLN E 705 HIS ** F 663 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 705 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3544 r_free = 0.3544 target = 0.118662 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3170 r_free = 0.3170 target = 0.094952 restraints weight = 57843.491| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3192 r_free = 0.3192 target = 0.096370 restraints weight = 37392.483| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3221 r_free = 0.3221 target = 0.098223 restraints weight = 26401.089| |-----------------------------------------------------------------------------| r_work (final): 0.3217 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8121 moved from start: 0.4693 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 27694 Z= 0.229 Angle : 0.687 15.990 37477 Z= 0.324 Chirality : 0.043 0.180 4300 Planarity : 0.005 0.115 4894 Dihedral : 9.565 151.368 4101 Min Nonbonded Distance : 2.153 Molprobity Statistics. All-atom Clashscore : 10.04 Ramachandran Plot: Outliers : 0.14 % Allowed : 9.79 % Favored : 90.07 % Rotamer: Outliers : 3.19 % Allowed : 20.25 % Favored : 76.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.41 % 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: -1.68 (0.15), residues: 3484 helix: -0.03 (0.14), residues: 1488 sheet: -1.68 (0.28), residues: 339 loop : -2.03 (0.16), residues: 1657 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C 545 HIS 0.004 0.001 HIS E 705 PHE 0.021 0.002 PHE C 623 TYR 0.023 0.001 TYR E 658 ARG 0.010 0.000 ARG E 380 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5452.43 seconds wall clock time: 99 minutes 30.73 seconds (5970.73 seconds total)