Starting phenix.real_space_refine on Wed Aug 7 10:44:12 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9ayf_43990/08_2024/9ayf_43990.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9ayf_43990/08_2024/9ayf_43990.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9ayf_43990/08_2024/9ayf_43990.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9ayf_43990/08_2024/9ayf_43990.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9ayf_43990/08_2024/9ayf_43990.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9ayf_43990/08_2024/9ayf_43990.cif" } resolution = 3.6 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= 0.002 sd= 0.040 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 7 Type Number sf(0) Gaussians Ca 8 9.91 5 P 2 5.49 5 S 118 5.16 5 Cl 2 4.86 5 C 12592 2.51 5 N 3218 2.21 5 O 3690 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "Q GLU 109": "OE1" <-> "OE2" Residue "Q GLU 249": "OE1" <-> "OE2" Residue "Q GLU 282": "OE1" <-> "OE2" Residue "Q GLU 399": "OE1" <-> "OE2" Residue "Q GLU 475": "OE1" <-> "OE2" Residue "Q GLU 536": "OE1" <-> "OE2" Residue "Q GLU 564": "OE1" <-> "OE2" Residue "Q GLU 567": "OE1" <-> "OE2" Residue "R GLU 79": "OE1" <-> "OE2" Residue "R GLU 191": "OE1" <-> "OE2" Residue "R GLU 228": "OE1" <-> "OE2" Residue "R GLU 249": "OE1" <-> "OE2" Residue "R GLU 251": "OE1" <-> "OE2" Residue "R GLU 332": "OE1" <-> "OE2" Residue "R GLU 564": "OE1" <-> "OE2" Residue "R GLU 649": "OE1" <-> "OE2" Residue "R GLU 757": "OE1" <-> "OE2" Residue "R GLU 767": "OE1" <-> "OE2" Residue "H TYR 121": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 183": "OE1" <-> "OE2" Residue "B GLU 130": "OE1" <-> "OE2" Time to flip residues: 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/chem_data/mon_lib" Total number of atoms: 19630 Number of models: 1 Model: "" Number of chains: 14 Chain: "Q" Number of atoms: 6202 Number of conformers: 1 Conformer: "" Number of residues, atoms: 780, 6202 Classifications: {'peptide': 780} Link IDs: {'CIS': 1, 'PTRANS': 30, 'TRANS': 748} Chain breaks: 3 Chain: "R" Number of atoms: 6499 Number of conformers: 1 Conformer: "" Number of residues, atoms: 816, 6499 Classifications: {'peptide': 816} Link IDs: {'CIS': 1, 'PTRANS': 32, 'TRANS': 782} Chain breaks: 2 Chain: "H" Number of atoms: 1785 Number of conformers: 1 Conformer: "" Number of residues, atoms: 232, 1785 Classifications: {'peptide': 232} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 221} Chain breaks: 1 Chain: "A" Number of atoms: 1733 Number of conformers: 1 Conformer: "" Number of residues, atoms: 214, 1733 Classifications: {'peptide': 214} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 212} Chain breaks: 1 Chain: "B" Number of atoms: 2607 Number of conformers: 1 Conformer: "" Number of residues, atoms: 339, 2607 Classifications: {'peptide': 339} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 333} Chain: "G" Number of atoms: 447 Number of conformers: 1 Conformer: "" Number of residues, atoms: 58, 447 Classifications: {'peptide': 58} Link IDs: {'PTRANS': 4, 'TRANS': 53} Chain: "C" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "D" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "E" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "F" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "Q" Number of atoms: 58 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 58 Unusual residues: {'NAG': 3, 'TCR': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "Q" Number of atoms: 30 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 30 Unusual residues: {' CA': 4, '9IG': 1, 'PO4': 1} Classifications: {'undetermined': 6} Link IDs: {None: 5} Chain: "R" Number of atoms: 58 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 58 Unusual residues: {'NAG': 3, 'TCR': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "R" Number of atoms: 99 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 99 Unusual residues: {' CA': 4, '9IG': 1, 'AV0': 1, 'PO4': 1} Classifications: {'undetermined': 7} Link IDs: {None: 6} Time building chain proxies: 13.65, per 1000 atoms: 0.70 Number of scatterers: 19630 At special positions: 0 Unit cell: (118.16, 132.508, 248.136, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Ca 8 19.99 Cl 2 17.00 S 118 16.00 P 2 15.00 O 3690 8.00 N 3218 7.00 C 12592 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=18, symmetry=0 Simple disulfide: pdb=" SG CYS Q 60 " - pdb=" SG CYS Q 101 " distance=2.03 Simple disulfide: pdb=" SG CYS Q 236 " - pdb=" SG CYS Q 561 " distance=2.03 Simple disulfide: pdb=" SG CYS Q 358 " - pdb=" SG CYS Q 395 " distance=2.03 Simple disulfide: pdb=" SG CYS Q 437 " - pdb=" SG CYS Q 449 " distance=2.03 Simple disulfide: pdb=" SG CYS Q 542 " - pdb=" SG CYS Q 562 " distance=2.03 Simple disulfide: pdb=" SG CYS Q 546 " - pdb=" SG CYS Q 565 " distance=2.03 Simple disulfide: pdb=" SG CYS Q 677 " - pdb=" SG CYS Q 765 " distance=2.03 Simple disulfide: pdb=" SG CYS R 60 " - pdb=" SG CYS R 101 " distance=2.03 Simple disulfide: pdb=" SG CYS R 236 " - pdb=" SG CYS R 561 " distance=2.03 Simple disulfide: pdb=" SG CYS R 358 " - pdb=" SG CYS R 395 " distance=2.03 Simple disulfide: pdb=" SG CYS R 437 " - pdb=" SG CYS R 449 " distance=2.03 Simple disulfide: pdb=" SG CYS R 542 " - pdb=" SG CYS R 562 " distance=2.03 Simple disulfide: pdb=" SG CYS R 546 " - pdb=" SG CYS R 565 " distance=2.03 Simple disulfide: pdb=" SG CYS R 568 " - pdb=" SG CYS R 582 " distance=2.03 Simple disulfide: pdb=" SG CYS R 585 " - pdb=" SG CYS R 598 " distance=2.03 Simple disulfide: pdb=" SG CYS R 677 " - pdb=" SG CYS R 765 " distance=2.03 Simple disulfide: pdb=" SG CYS H 42 " - pdb=" SG CYS H 116 " distance=2.03 Simple disulfide: pdb=" SG CYS H 179 " - pdb=" SG CYS H 249 " distance=2.04 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 Links applied BETA1-4 " NAG C 1 " - " NAG C 2 " " NAG D 1 " - " NAG D 2 " " NAG E 1 " - " NAG E 2 " " NAG F 1 " - " NAG F 2 " NAG-ASN " NAG C 1 " - " ASN Q 488 " " NAG D 1 " - " ASN Q 541 " " NAG E 1 " - " ASN R 488 " " NAG F 1 " - " ASN R 541 " " NAG Q1001 " - " ASN Q 261 " " NAG Q1002 " - " ASN Q 287 " " NAG Q1003 " - " ASN Q 468 " " NAG R1001 " - " ASN R 261 " " NAG R1002 " - " ASN R 287 " " NAG R1003 " - " ASN R 468 " Time building additional restraints: 7.90 Conformation dependent library (CDL) restraints added in 3.2 seconds 4826 Ramachandran restraints generated. 2413 Oldfield, 0 Emsley, 2413 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4576 Finding SS restraints... Secondary structure from input PDB file: 72 helices and 26 sheets defined 41.1% alpha, 17.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.31 Creating SS restraints... Processing helix chain 'Q' and resid 64 through 84 removed outlier: 3.664A pdb=" N PHE Q 68 " --> pdb=" O ASN Q 64 " (cutoff:3.500A) Processing helix chain 'Q' and resid 103 through 115 removed outlier: 3.547A pdb=" N ALA Q 107 " --> pdb=" O THR Q 103 " (cutoff:3.500A) Processing helix chain 'Q' and resid 115 through 124 Processing helix chain 'Q' and resid 146 through 159 Processing helix chain 'Q' and resid 171 through 176 removed outlier: 3.738A pdb=" N ASN Q 176 " --> pdb=" O LEU Q 173 " (cutoff:3.500A) Processing helix chain 'Q' and resid 190 through 204 Processing helix chain 'Q' and resid 218 through 233 removed outlier: 3.858A pdb=" N GLY Q 222 " --> pdb=" O TYR Q 218 " (cutoff:3.500A) Processing helix chain 'Q' and resid 248 through 261 Processing helix chain 'Q' and resid 272 through 287 Proline residue: Q 278 - end of helix Processing helix chain 'Q' and resid 307 through 309 No H-bonds generated for 'chain 'Q' and resid 307 through 309' Processing helix chain 'Q' and resid 310 through 315 Processing helix chain 'Q' and resid 329 through 336 Processing helix chain 'Q' and resid 347 through 357 Processing helix chain 'Q' and resid 416 through 436 Processing helix chain 'Q' and resid 444 through 448 Processing helix chain 'Q' and resid 456 through 466 removed outlier: 3.500A pdb=" N VAL Q 460 " --> pdb=" O GLU Q 456 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N HIS Q 466 " --> pdb=" O LYS Q 462 " (cutoff:3.500A) Processing helix chain 'Q' and resid 525 through 528 Processing helix chain 'Q' and resid 529 through 533 Processing helix chain 'Q' and resid 610 through 637 Processing helix chain 'Q' and resid 640 through 646 Processing helix chain 'Q' and resid 647 through 664 Processing helix chain 'Q' and resid 665 through 669 removed outlier: 3.717A pdb=" N PHE Q 668 " --> pdb=" O SER Q 665 " (cutoff:3.500A) removed outlier: 3.820A pdb=" N ILE Q 669 " --> pdb=" O LEU Q 666 " (cutoff:3.500A) No H-bonds generated for 'chain 'Q' and resid 665 through 669' Processing helix chain 'Q' and resid 673 through 698 removed outlier: 5.128A pdb=" N GLN Q 681 " --> pdb=" O CYS Q 677 " (cutoff:3.500A) Proline residue: Q 682 - end of helix Processing helix chain 'Q' and resid 723 through 746 removed outlier: 3.769A pdb=" N LEU Q 730 " --> pdb=" O LEU Q 726 " (cutoff:3.500A) removed outlier: 4.475A pdb=" N CYS Q 731 " --> pdb=" O LEU Q 727 " (cutoff:3.500A) removed outlier: 3.932A pdb=" N THR Q 732 " --> pdb=" O VAL Q 728 " (cutoff:3.500A) Processing helix chain 'Q' and resid 769 through 794 removed outlier: 3.618A pdb=" N LEU Q 773 " --> pdb=" O SER Q 769 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N SER Q 794 " --> pdb=" O PHE Q 790 " (cutoff:3.500A) Processing helix chain 'Q' and resid 798 through 828 removed outlier: 3.730A pdb=" N GLU Q 803 " --> pdb=" O GLU Q 799 " (cutoff:3.500A) removed outlier: 6.188A pdb=" N ALA Q 804 " --> pdb=" O ASN Q 800 " (cutoff:3.500A) removed outlier: 6.844A pdb=" N LYS Q 805 " --> pdb=" O PHE Q 801 " (cutoff:3.500A) removed outlier: 4.170A pdb=" N PHE Q 806 " --> pdb=" O ASN Q 802 " (cutoff:3.500A) Proline residue: Q 823 - end of helix Processing helix chain 'Q' and resid 832 through 854 removed outlier: 3.664A pdb=" N GLU Q 837 " --> pdb=" O VAL Q 833 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N LEU Q 842 " --> pdb=" O VAL Q 838 " (cutoff:3.500A) Processing helix chain 'Q' and resid 854 through 861 Processing helix chain 'R' and resid 64 through 83 removed outlier: 3.508A pdb=" N PHE R 68 " --> pdb=" O ASN R 64 " (cutoff:3.500A) Processing helix chain 'R' and resid 103 through 115 removed outlier: 3.651A pdb=" N ALA R 107 " --> pdb=" O THR R 103 " (cutoff:3.500A) Processing helix chain 'R' and resid 115 through 124 Processing helix chain 'R' and resid 146 through 159 removed outlier: 3.746A pdb=" N LEU R 156 " --> pdb=" O ALA R 152 " (cutoff:3.500A) Processing helix chain 'R' and resid 172 through 176 removed outlier: 3.561A pdb=" N ASN R 176 " --> pdb=" O LEU R 173 " (cutoff:3.500A) Processing helix chain 'R' and resid 190 through 204 Processing helix chain 'R' and resid 218 through 233 removed outlier: 4.048A pdb=" N GLY R 222 " --> pdb=" O TYR R 218 " (cutoff:3.500A) Processing helix chain 'R' and resid 248 through 262 removed outlier: 3.557A pdb=" N ILE R 252 " --> pdb=" O ASP R 248 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N SER R 262 " --> pdb=" O VAL R 258 " (cutoff:3.500A) Processing helix chain 'R' and resid 272 through 287 Proline residue: R 278 - end of helix Processing helix chain 'R' and resid 307 through 309 No H-bonds generated for 'chain 'R' and resid 307 through 309' Processing helix chain 'R' and resid 310 through 315 Processing helix chain 'R' and resid 329 through 336 removed outlier: 3.535A pdb=" N PHE R 333 " --> pdb=" O GLY R 329 " (cutoff:3.500A) Processing helix chain 'R' and resid 347 through 357 Processing helix chain 'R' and resid 415 through 436 removed outlier: 3.600A pdb=" N ASN R 419 " --> pdb=" O ARG R 415 " (cutoff:3.500A) Processing helix chain 'R' and resid 444 through 448 Processing helix chain 'R' and resid 456 through 466 removed outlier: 3.516A pdb=" N HIS R 466 " --> pdb=" O LYS R 462 " (cutoff:3.500A) Processing helix chain 'R' and resid 525 through 528 Processing helix chain 'R' and resid 610 through 637 Processing helix chain 'R' and resid 640 through 646 removed outlier: 3.584A pdb=" N THR R 646 " --> pdb=" O ILE R 642 " (cutoff:3.500A) Processing helix chain 'R' and resid 647 through 665 removed outlier: 3.773A pdb=" N SER R 665 " --> pdb=" O CYS R 661 " (cutoff:3.500A) Processing helix chain 'R' and resid 666 through 669 Processing helix chain 'R' and resid 673 through 708 removed outlier: 4.764A pdb=" N GLN R 681 " --> pdb=" O CYS R 677 " (cutoff:3.500A) Proline residue: R 682 - end of helix removed outlier: 3.747A pdb=" N GLY R 685 " --> pdb=" O GLN R 681 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N ALA R 708 " --> pdb=" O LEU R 704 " (cutoff:3.500A) Processing helix chain 'R' and resid 722 through 746 removed outlier: 3.660A pdb=" N LEU R 726 " --> pdb=" O ASN R 722 " (cutoff:3.500A) removed outlier: 4.212A pdb=" N MET R 734 " --> pdb=" O LEU R 730 " (cutoff:3.500A) removed outlier: 4.656A pdb=" N GLN R 735 " --> pdb=" O CYS R 731 " (cutoff:3.500A) Processing helix chain 'R' and resid 769 through 794 removed outlier: 3.832A pdb=" N LEU R 773 " --> pdb=" O SER R 769 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N SER R 794 " --> pdb=" O PHE R 790 " (cutoff:3.500A) Processing helix chain 'R' and resid 798 through 802 Processing helix chain 'R' and resid 803 through 827 Proline residue: R 823 - end of helix Processing helix chain 'R' and resid 830 through 862 removed outlier: 4.273A pdb=" N SER R 834 " --> pdb=" O GLY R 830 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N PHE R 854 " --> pdb=" O ALA R 850 " (cutoff:3.500A) removed outlier: 5.583A pdb=" N ASN R 855 " --> pdb=" O CYS R 851 " (cutoff:3.500A) removed outlier: 5.247A pdb=" N LYS R 856 " --> pdb=" O ILE R 852 " (cutoff:3.500A) Processing helix chain 'R' and resid 863 through 867 removed outlier: 4.098A pdb=" N ARG R 866 " --> pdb=" O LYS R 863 " (cutoff:3.500A) Processing helix chain 'R' and resid 868 through 877 removed outlier: 3.803A pdb=" N VAL R 872 " --> pdb=" O THR R 868 " (cutoff:3.500A) Processing helix chain 'H' and resid 48 through 52 removed outlier: 3.530A pdb=" N PHE H 52 " --> pdb=" O PHE H 49 " (cutoff:3.500A) Processing helix chain 'H' and resid 94 through 96 No H-bonds generated for 'chain 'H' and resid 94 through 96' Processing helix chain 'H' and resid 107 through 111 removed outlier: 3.541A pdb=" N THR H 111 " --> pdb=" O SER H 108 " (cutoff:3.500A) Processing helix chain 'A' and resid 6 through 32 removed outlier: 3.712A pdb=" N ARG A 32 " --> pdb=" O GLU A 28 " (cutoff:3.500A) Processing helix chain 'A' and resid 45 through 49 Processing helix chain 'A' and resid 92 through 101 removed outlier: 4.286A pdb=" N ILE A 97 " --> pdb=" O LYS A 94 " (cutoff:3.500A) removed outlier: 5.897A pdb=" N HIS A 98 " --> pdb=" O LYS A 95 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N CYS A 99 " --> pdb=" O TRP A 96 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N GLU A 101 " --> pdb=" O HIS A 98 " (cutoff:3.500A) Processing helix chain 'A' and resid 114 through 130 Processing helix chain 'A' and resid 145 through 156 Processing helix chain 'A' and resid 157 through 161 removed outlier: 3.829A pdb=" N ILE A 160 " --> pdb=" O PRO A 157 " (cutoff:3.500A) Processing helix chain 'A' and resid 170 through 185 removed outlier: 3.716A pdb=" N ALA A 174 " --> pdb=" O THR A 170 " (cutoff:3.500A) Processing helix chain 'A' and resid 205 through 226 Processing helix chain 'B' and resid 3 through 26 Processing helix chain 'B' and resid 29 through 35 Processing helix chain 'G' and resid 8 through 24 Processing helix chain 'G' and resid 29 through 44 removed outlier: 3.738A pdb=" N ALA G 33 " --> pdb=" O LYS G 29 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'Q' and resid 26 through 28 removed outlier: 6.411A pdb=" N ILE Q 32 " --> pdb=" O GLY Q 94 " (cutoff:3.500A) removed outlier: 7.864A pdb=" N ARG Q 96 " --> pdb=" O ILE Q 32 " (cutoff:3.500A) removed outlier: 6.412A pdb=" N LEU Q 34 " --> pdb=" O ARG Q 96 " (cutoff:3.500A) removed outlier: 7.940A pdb=" N PHE Q 98 " --> pdb=" O LEU Q 34 " (cutoff:3.500A) removed outlier: 6.718A pdb=" N GLY Q 36 " --> pdb=" O PHE Q 98 " (cutoff:3.500A) removed outlier: 6.903A pdb=" N ILE Q 33 " --> pdb=" O THR Q 138 " (cutoff:3.500A) removed outlier: 3.994A pdb=" N ALA Q 140 " --> pdb=" O ILE Q 33 " (cutoff:3.500A) removed outlier: 8.522A pdb=" N VAL Q 165 " --> pdb=" O ILE Q 139 " (cutoff:3.500A) removed outlier: 6.396A pdb=" N VAL Q 141 " --> pdb=" O VAL Q 165 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'Q' and resid 236 through 243 removed outlier: 8.063A pdb=" N VAL Q 209 " --> pdb=" O ASP Q 238 " (cutoff:3.500A) removed outlier: 7.073A pdb=" N SER Q 240 " --> pdb=" O VAL Q 209 " (cutoff:3.500A) removed outlier: 7.075A pdb=" N THR Q 211 " --> pdb=" O SER Q 240 " (cutoff:3.500A) removed outlier: 6.067A pdb=" N LEU Q 242 " --> pdb=" O THR Q 211 " (cutoff:3.500A) removed outlier: 6.471A pdb=" N ALA Q 213 " --> pdb=" O LEU Q 242 " (cutoff:3.500A) removed outlier: 7.082A pdb=" N TRP Q 208 " --> pdb=" O VAL Q 266 " (cutoff:3.500A) removed outlier: 8.540A pdb=" N VAL Q 268 " --> pdb=" O TRP Q 208 " (cutoff:3.500A) removed outlier: 6.659A pdb=" N GLY Q 210 " --> pdb=" O VAL Q 268 " (cutoff:3.500A) removed outlier: 8.128A pdb=" N PHE Q 270 " --> pdb=" O GLY Q 210 " (cutoff:3.500A) removed outlier: 7.018A pdb=" N ILE Q 212 " --> pdb=" O PHE Q 270 " (cutoff:3.500A) removed outlier: 6.132A pdb=" N TRP Q 293 " --> pdb=" O ILE Q 318 " (cutoff:3.500A) removed outlier: 8.032A pdb=" N PHE Q 320 " --> pdb=" O TRP Q 293 " (cutoff:3.500A) removed outlier: 7.313A pdb=" N ALA Q 295 " --> pdb=" O PHE Q 320 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N GLY Q 509 " --> pdb=" O ILE Q 491 " (cutoff:3.500A) removed outlier: 6.030A pdb=" N ASN Q 493 " --> pdb=" O GLU Q 507 " (cutoff:3.500A) removed outlier: 5.604A pdb=" N GLU Q 507 " --> pdb=" O ASN Q 493 " (cutoff:3.500A) removed outlier: 7.082A pdb=" N HIS Q 495 " --> pdb=" O PHE Q 505 " (cutoff:3.500A) removed outlier: 5.928A pdb=" N PHE Q 505 " --> pdb=" O HIS Q 495 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'Q' and resid 468 through 470 Processing sheet with id=AA4, first strand: chain 'Q' and resid 550 through 552 Processing sheet with id=AA5, first strand: chain 'Q' and resid 572 through 573 Processing sheet with id=AA6, first strand: chain 'Q' and resid 589 through 591 Processing sheet with id=AA7, first strand: chain 'Q' and resid 602 through 604 removed outlier: 6.228A pdb=" N GLU Q 602 " --> pdb=" O ILE Q 761 " (cutoff:3.500A) removed outlier: 7.132A pdb=" N ILE Q 763 " --> pdb=" O GLU Q 602 " (cutoff:3.500A) removed outlier: 6.699A pdb=" N GLU Q 604 " --> pdb=" O ILE Q 763 " (cutoff:3.500A) removed outlier: 8.935A pdb=" N CYS Q 765 " --> pdb=" O GLU Q 604 " (cutoff:3.500A) removed outlier: 8.511A pdb=" N ILE Q 760 " --> pdb=" O GLU Q 755 " (cutoff:3.500A) removed outlier: 5.543A pdb=" N GLU Q 755 " --> pdb=" O ILE Q 760 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'R' and resid 26 through 28 removed outlier: 6.147A pdb=" N ILE R 32 " --> pdb=" O GLY R 94 " (cutoff:3.500A) removed outlier: 7.695A pdb=" N ARG R 96 " --> pdb=" O ILE R 32 " (cutoff:3.500A) removed outlier: 6.587A pdb=" N LEU R 34 " --> pdb=" O ARG R 96 " (cutoff:3.500A) removed outlier: 7.859A pdb=" N PHE R 98 " --> pdb=" O LEU R 34 " (cutoff:3.500A) removed outlier: 6.460A pdb=" N GLY R 36 " --> pdb=" O PHE R 98 " (cutoff:3.500A) removed outlier: 6.706A pdb=" N ILE R 33 " --> pdb=" O THR R 138 " (cutoff:3.500A) removed outlier: 4.053A pdb=" N ALA R 140 " --> pdb=" O ILE R 33 " (cutoff:3.500A) removed outlier: 8.625A pdb=" N VAL R 165 " --> pdb=" O ILE R 139 " (cutoff:3.500A) removed outlier: 6.457A pdb=" N VAL R 141 " --> pdb=" O VAL R 165 " (cutoff:3.500A) removed outlier: 6.076A pdb=" N GLN R 164 " --> pdb=" O LEU R 184 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'R' and resid 236 through 243 removed outlier: 8.205A pdb=" N VAL R 209 " --> pdb=" O ASP R 238 " (cutoff:3.500A) removed outlier: 7.064A pdb=" N SER R 240 " --> pdb=" O VAL R 209 " (cutoff:3.500A) removed outlier: 6.927A pdb=" N THR R 211 " --> pdb=" O SER R 240 " (cutoff:3.500A) removed outlier: 6.031A pdb=" N LEU R 242 " --> pdb=" O THR R 211 " (cutoff:3.500A) removed outlier: 6.572A pdb=" N ALA R 213 " --> pdb=" O LEU R 242 " (cutoff:3.500A) removed outlier: 7.146A pdb=" N TRP R 208 " --> pdb=" O VAL R 266 " (cutoff:3.500A) removed outlier: 8.483A pdb=" N VAL R 268 " --> pdb=" O TRP R 208 " (cutoff:3.500A) removed outlier: 6.600A pdb=" N GLY R 210 " --> pdb=" O VAL R 268 " (cutoff:3.500A) removed outlier: 8.088A pdb=" N PHE R 270 " --> pdb=" O GLY R 210 " (cutoff:3.500A) removed outlier: 6.897A pdb=" N ILE R 212 " --> pdb=" O PHE R 270 " (cutoff:3.500A) removed outlier: 6.407A pdb=" N TRP R 293 " --> pdb=" O ILE R 318 " (cutoff:3.500A) removed outlier: 8.328A pdb=" N PHE R 320 " --> pdb=" O TRP R 293 " (cutoff:3.500A) removed outlier: 7.424A pdb=" N ALA R 295 " --> pdb=" O PHE R 320 " (cutoff:3.500A) removed outlier: 6.845A pdb=" N TYR R 489 " --> pdb=" O TYR R 510 " (cutoff:3.500A) removed outlier: 4.770A pdb=" N TYR R 510 " --> pdb=" O TYR R 489 " (cutoff:3.500A) removed outlier: 6.655A pdb=" N ILE R 491 " --> pdb=" O VAL R 508 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'R' and resid 469 through 470 removed outlier: 3.782A pdb=" N PHE R 469 " --> pdb=" O VAL R 477 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'R' and resid 550 through 554 Processing sheet with id=AB3, first strand: chain 'R' and resid 572 through 573 Processing sheet with id=AB4, first strand: chain 'R' and resid 589 through 591 Processing sheet with id=AB5, first strand: chain 'R' and resid 602 through 604 removed outlier: 6.037A pdb=" N GLU R 602 " --> pdb=" O ILE R 761 " (cutoff:3.500A) removed outlier: 7.323A pdb=" N ILE R 763 " --> pdb=" O GLU R 602 " (cutoff:3.500A) removed outlier: 6.657A pdb=" N GLU R 604 " --> pdb=" O ILE R 763 " (cutoff:3.500A) removed outlier: 8.804A pdb=" N CYS R 765 " --> pdb=" O GLU R 604 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'H' and resid 23 through 27 Processing sheet with id=AB7, first strand: chain 'H' and resid 30 through 32 removed outlier: 6.367A pdb=" N GLY H 30 " --> pdb=" O THR H 138 " (cutoff:3.500A) removed outlier: 6.772A pdb=" N MET H 54 " --> pdb=" O TYR H 70 " (cutoff:3.500A) removed outlier: 4.372A pdb=" N TYR H 70 " --> pdb=" O MET H 54 " (cutoff:3.500A) removed outlier: 6.512A pdb=" N TRP H 56 " --> pdb=" O VAL H 68 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'H' and resid 166 through 168 removed outlier: 5.778A pdb=" N VAL H 167 " --> pdb=" O GLU H 266 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N ILE H 209 " --> pdb=" O TRP H 196 " (cutoff:3.500A) removed outlier: 6.106A pdb=" N LEU H 198 " --> pdb=" O LEU H 207 " (cutoff:3.500A) removed outlier: 5.538A pdb=" N LEU H 207 " --> pdb=" O LEU H 198 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'H' and resid 175 through 180 Processing sheet with id=AC1, first strand: chain 'A' and resid 70 through 75 removed outlier: 3.707A pdb=" N ALA A 105 " --> pdb=" O LYS A 35 " (cutoff:3.500A) removed outlier: 6.721A pdb=" N ILE A 139 " --> pdb=" O TYR A 195 " (cutoff:3.500A) removed outlier: 7.701A pdb=" N HIS A 197 " --> pdb=" O ILE A 139 " (cutoff:3.500A) removed outlier: 6.410A pdb=" N LEU A 141 " --> pdb=" O HIS A 197 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 58 through 63 removed outlier: 7.035A pdb=" N ALA B 73 " --> pdb=" O TYR B 59 " (cutoff:3.500A) removed outlier: 4.506A pdb=" N MET B 61 " --> pdb=" O VAL B 71 " (cutoff:3.500A) removed outlier: 6.878A pdb=" N VAL B 71 " --> pdb=" O MET B 61 " (cutoff:3.500A) removed outlier: 5.386A pdb=" N TRP B 63 " --> pdb=" O LEU B 69 " (cutoff:3.500A) removed outlier: 7.368A pdb=" N LEU B 69 " --> pdb=" O TRP B 63 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N SER B 74 " --> pdb=" O LYS B 78 " (cutoff:3.500A) removed outlier: 4.004A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 6.394A pdb=" N LEU B 79 " --> pdb=" O ALA B 92 " (cutoff:3.500A) removed outlier: 4.283A pdb=" N ALA B 92 " --> pdb=" O LEU B 79 " (cutoff:3.500A) removed outlier: 6.672A pdb=" N ILE B 81 " --> pdb=" O VAL B 90 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 100 through 105 removed outlier: 6.975A pdb=" N GLY B 115 " --> pdb=" O MET B 101 " (cutoff:3.500A) removed outlier: 4.353A pdb=" N CYS B 103 " --> pdb=" O ALA B 113 " (cutoff:3.500A) removed outlier: 6.456A pdb=" N ALA B 113 " --> pdb=" O CYS B 103 " (cutoff:3.500A) removed outlier: 5.044A pdb=" N TYR B 105 " --> pdb=" O TYR B 111 " (cutoff:3.500A) removed outlier: 7.179A pdb=" N TYR B 111 " --> pdb=" O TYR B 105 " (cutoff:3.500A) removed outlier: 4.219A pdb=" N GLY B 116 " --> pdb=" O ILE B 120 " (cutoff:3.500A) removed outlier: 4.916A pdb=" N ILE B 120 " --> pdb=" O GLY B 116 " (cutoff:3.500A) removed outlier: 6.001A pdb=" N ASN B 125 " --> pdb=" O VAL B 135 " (cutoff:3.500A) removed outlier: 6.136A pdb=" N VAL B 135 " --> pdb=" O ASN B 125 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 146 through 151 removed outlier: 6.772A pdb=" N SER B 160 " --> pdb=" O SER B 147 " (cutoff:3.500A) removed outlier: 4.296A pdb=" N CYS B 149 " --> pdb=" O VAL B 158 " (cutoff:3.500A) removed outlier: 6.762A pdb=" N VAL B 158 " --> pdb=" O CYS B 149 " (cutoff:3.500A) removed outlier: 5.220A pdb=" N PHE B 151 " --> pdb=" O GLN B 156 " (cutoff:3.500A) removed outlier: 7.781A pdb=" N GLN B 156 " --> pdb=" O PHE B 151 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N THR B 165 " --> pdb=" O SER B 161 " (cutoff:3.500A) removed outlier: 6.657A pdb=" N ASP B 170 " --> pdb=" O GLN B 176 " (cutoff:3.500A) removed outlier: 5.889A pdb=" N GLN B 176 " --> pdb=" O ASP B 170 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 187 through 192 removed outlier: 6.952A pdb=" N GLY B 202 " --> pdb=" O MET B 188 " (cutoff:3.500A) removed outlier: 4.341A pdb=" N LEU B 190 " --> pdb=" O VAL B 200 " (cutoff:3.500A) removed outlier: 6.707A pdb=" N VAL B 200 " --> pdb=" O LEU B 190 " (cutoff:3.500A) removed outlier: 5.281A pdb=" N LEU B 192 " --> pdb=" O LEU B 198 " (cutoff:3.500A) removed outlier: 7.449A pdb=" N LEU B 198 " --> pdb=" O LEU B 192 " (cutoff:3.500A) removed outlier: 3.876A pdb=" N SER B 207 " --> pdb=" O ALA B 203 " (cutoff:3.500A) removed outlier: 3.939A pdb=" N GLN B 220 " --> pdb=" O LEU B 210 " (cutoff:3.500A) removed outlier: 6.835A pdb=" N ASP B 212 " --> pdb=" O CYS B 218 " (cutoff:3.500A) removed outlier: 6.642A pdb=" N CYS B 218 " --> pdb=" O ASP B 212 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 229 through 234 removed outlier: 3.650A pdb=" N ALA B 231 " --> pdb=" O GLY B 244 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N ALA B 242 " --> pdb=" O CYS B 233 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N ARG B 251 " --> pdb=" O THR B 243 " (cutoff:3.500A) removed outlier: 6.625A pdb=" N CYS B 250 " --> pdb=" O THR B 263 " (cutoff:3.500A) removed outlier: 4.521A pdb=" N THR B 263 " --> pdb=" O CYS B 250 " (cutoff:3.500A) removed outlier: 6.747A pdb=" N LEU B 252 " --> pdb=" O LEU B 261 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N GLN B 259 " --> pdb=" O ASP B 254 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'B' and resid 273 through 278 removed outlier: 4.328A pdb=" N SER B 275 " --> pdb=" O GLY B 288 " (cutoff:3.500A) removed outlier: 6.725A pdb=" N CYS B 294 " --> pdb=" O VAL B 307 " (cutoff:3.500A) removed outlier: 4.619A pdb=" N VAL B 307 " --> pdb=" O CYS B 294 " (cutoff:3.500A) removed outlier: 6.706A pdb=" N VAL B 296 " --> pdb=" O ALA B 305 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'B' and resid 315 through 320 869 hydrogen bonds defined for protein. 2478 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: 8.77 Time building geometry restraints manager: 8.50 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 6208 1.34 - 1.46: 5080 1.46 - 1.58: 8636 1.58 - 1.70: 2 1.70 - 1.82: 154 Bond restraints: 20080 Sorted by residual: bond pdb=" CB PRO R 308 " pdb=" CG PRO R 308 " ideal model delta sigma weight residual 1.492 1.683 -0.191 5.00e-02 4.00e+02 1.46e+01 bond pdb=" C05 9IG Q1010 " pdb=" O09 9IG Q1010 " ideal model delta sigma weight residual 1.348 1.410 -0.062 2.00e-02 2.50e+03 9.48e+00 bond pdb=" O3 PO4 R1005 " pdb=" P PO4 R1005 " ideal model delta sigma weight residual 1.569 1.508 0.061 2.00e-02 2.50e+03 9.43e+00 bond pdb=" C05 9IG R1011 " pdb=" O09 9IG R1011 " ideal model delta sigma weight residual 1.348 1.409 -0.061 2.00e-02 2.50e+03 9.28e+00 bond pdb=" O4 PO4 Q1005 " pdb=" P PO4 Q1005 " ideal model delta sigma weight residual 1.568 1.508 0.060 2.00e-02 2.50e+03 9.14e+00 ... (remaining 20075 not shown) Histogram of bond angle deviations from ideal: 94.52 - 102.54: 62 102.54 - 110.56: 5589 110.56 - 118.59: 10223 118.59 - 126.61: 11035 126.61 - 134.63: 300 Bond angle restraints: 27209 Sorted by residual: angle pdb=" CA PRO R 308 " pdb=" N PRO R 308 " pdb=" CD PRO R 308 " ideal model delta sigma weight residual 112.00 95.64 16.36 1.40e+00 5.10e-01 1.37e+02 angle pdb=" CA PRO R 89 " pdb=" N PRO R 89 " pdb=" CD PRO R 89 " ideal model delta sigma weight residual 112.00 96.02 15.98 1.40e+00 5.10e-01 1.30e+02 angle pdb=" N PRO R 308 " pdb=" CD PRO R 308 " pdb=" CG PRO R 308 " ideal model delta sigma weight residual 103.20 94.52 8.68 1.50e+00 4.44e-01 3.35e+01 angle pdb=" N PRO R 89 " pdb=" CD PRO R 89 " pdb=" CG PRO R 89 " ideal model delta sigma weight residual 103.20 95.00 8.20 1.50e+00 4.44e-01 2.99e+01 angle pdb=" N PRO R 308 " pdb=" CA PRO R 308 " pdb=" CB PRO R 308 " ideal model delta sigma weight residual 103.25 98.68 4.57 1.05e+00 9.07e-01 1.89e+01 ... (remaining 27204 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 21.89: 11187 21.89 - 43.77: 808 43.77 - 65.66: 114 65.66 - 87.54: 25 87.54 - 109.43: 6 Dihedral angle restraints: 12140 sinusoidal: 5057 harmonic: 7083 Sorted by residual: dihedral pdb=" CB CYS H 42 " pdb=" SG CYS H 42 " pdb=" SG CYS H 116 " pdb=" CB CYS H 116 " ideal model delta sinusoidal sigma weight residual 93.00 135.58 -42.58 1 1.00e+01 1.00e-02 2.53e+01 dihedral pdb=" CB CYS Q 546 " pdb=" SG CYS Q 546 " pdb=" SG CYS Q 565 " pdb=" CB CYS Q 565 " ideal model delta sinusoidal sigma weight residual -86.00 -126.25 40.25 1 1.00e+01 1.00e-02 2.27e+01 dihedral pdb=" CA GLN R 260 " pdb=" C GLN R 260 " pdb=" N ASN R 261 " pdb=" CA ASN R 261 " ideal model delta harmonic sigma weight residual -180.00 -157.54 -22.46 0 5.00e+00 4.00e-02 2.02e+01 ... (remaining 12137 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.094: 2910 0.094 - 0.189: 146 0.189 - 0.283: 8 0.283 - 0.377: 4 0.377 - 0.471: 1 Chirality restraints: 3069 Sorted by residual: chirality pdb=" C1 NAG R1001 " pdb=" ND2 ASN R 261 " pdb=" C2 NAG R1001 " pdb=" O5 NAG R1001 " both_signs ideal model delta sigma weight residual False -2.40 -1.93 -0.47 2.00e-01 2.50e+01 5.56e+00 chirality pdb=" CCV AV0 R1010 " pdb=" CCR AV0 R1010 " pdb=" CCT AV0 R1010 " pdb=" OAU AV0 R1010 " both_signs ideal model delta sigma weight residual False -2.30 -2.66 0.37 2.00e-01 2.50e+01 3.34e+00 chirality pdb=" CCW AV0 R1010 " pdb=" CCS AV0 R1010 " pdb=" CCU AV0 R1010 " pdb=" OAV AV0 R1010 " both_signs ideal model delta sigma weight residual False -2.29 -2.61 0.32 2.00e-01 2.50e+01 2.53e+00 ... (remaining 3066 not shown) Planarity restraints: 3438 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LEU R 88 " -0.106 5.00e-02 4.00e+02 1.47e-01 3.44e+01 pdb=" N PRO R 89 " 0.253 5.00e-02 4.00e+02 pdb=" CA PRO R 89 " -0.071 5.00e-02 4.00e+02 pdb=" CD PRO R 89 " -0.076 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C MET R 307 " 0.103 5.00e-02 4.00e+02 1.43e-01 3.25e+01 pdb=" N PRO R 308 " -0.246 5.00e-02 4.00e+02 pdb=" CA PRO R 308 " 0.069 5.00e-02 4.00e+02 pdb=" CD PRO R 308 " 0.074 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LYS R 863 " 0.056 5.00e-02 4.00e+02 8.46e-02 1.15e+01 pdb=" N PRO R 864 " -0.146 5.00e-02 4.00e+02 pdb=" CA PRO R 864 " 0.045 5.00e-02 4.00e+02 pdb=" CD PRO R 864 " 0.046 5.00e-02 4.00e+02 ... (remaining 3435 not shown) Histogram of nonbonded interaction distances: 2.19 - 2.73: 1194 2.73 - 3.27: 18960 3.27 - 3.82: 31475 3.82 - 4.36: 38623 4.36 - 4.90: 66552 Nonbonded interactions: 156804 Sorted by model distance: nonbonded pdb=" O ARG R 795 " pdb=" OAS AV0 R1010 " model vdw 2.191 3.040 nonbonded pdb=" O PHE Q 351 " pdb=" OG1 THR Q 355 " model vdw 2.228 3.040 nonbonded pdb=" NE2 GLN R 117 " pdb=" O ILE R 135 " model vdw 2.229 3.120 nonbonded pdb=" O SER R 171 " pdb=" NH2 ARG R 185 " model vdw 2.302 3.120 nonbonded pdb=" ND2 ASN B 340 " pdb=" OD1 ASN G 59 " model vdw 2.323 3.120 ... (remaining 156799 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' } ncs_group { reference = (chain 'Q' and (resid 22 through 865 or resid 1001 through 1002 or resid 1006 th \ rough 1008 or resid 1010)) selection = (chain 'R' and (resid 22 through 698 or resid 722 through 865 or resid 1002 thro \ ugh 1003 or resid 1007 through 1009 or resid 1011)) } 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: 0.010 Normalize map: mean=0, sd=1: 23.740 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.000 Check model and map are aligned: 0.000 Set scattering table: 0.000 Process input model: 57.080 Find NCS groups from input model: 0.580 Set up NCS constraints: 0.070 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.010 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.590 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 84.080 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7430 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 : 0.004 0.191 20080 Z= 0.270 Angle : 0.674 16.364 27209 Z= 0.371 Chirality : 0.045 0.471 3069 Planarity : 0.006 0.147 3428 Dihedral : 14.714 109.431 7510 Min Nonbonded Distance : 2.191 Molprobity Statistics. All-atom Clashscore : 5.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.49 % Favored : 97.51 % Rotamer: Outliers : 0.00 % Allowed : 15.11 % Favored : 84.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.22 % Cis-general : 0.09 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.19 (0.17), residues: 2413 helix: 1.44 (0.17), residues: 909 sheet: -0.23 (0.23), residues: 505 loop : -0.86 (0.19), residues: 999 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP A 96 HIS 0.006 0.001 HIS Q 312 PHE 0.013 0.001 PHE Q 854 TYR 0.014 0.001 TYR Q 435 ARG 0.007 0.000 ARG Q 678 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4826 Ramachandran restraints generated. 2413 Oldfield, 0 Emsley, 2413 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4826 Ramachandran restraints generated. 2413 Oldfield, 0 Emsley, 2413 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 367 residues out of total 2105 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 367 time to evaluate : 2.072 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: Q 117 GLN cc_start: 0.6293 (tp-100) cc_final: 0.5861 (tm-30) REVERT: Q 728 VAL cc_start: 0.7627 (p) cc_final: 0.7267 (p) REVERT: R 248 ASP cc_start: 0.7464 (p0) cc_final: 0.7234 (p0) REVERT: R 284 VAL cc_start: 0.8341 (p) cc_final: 0.8082 (p) REVERT: R 285 ARG cc_start: 0.6947 (ttt180) cc_final: 0.6730 (ttt180) REVERT: R 481 GLU cc_start: 0.6783 (pm20) cc_final: 0.6530 (pm20) REVERT: R 486 VAL cc_start: 0.8109 (m) cc_final: 0.7898 (p) REVERT: A 20 ASP cc_start: 0.7815 (m-30) cc_final: 0.7422 (m-30) REVERT: A 53 MET cc_start: 0.5196 (tpp) cc_final: 0.4936 (tpt) REVERT: A 222 ASN cc_start: 0.8104 (m-40) cc_final: 0.7684 (m-40) REVERT: B 86 THR cc_start: 0.8551 (p) cc_final: 0.8338 (m) REVERT: B 130 GLU cc_start: 0.7834 (mp0) cc_final: 0.7572 (mp0) outliers start: 0 outliers final: 0 residues processed: 367 average time/residue: 0.3447 time to fit residues: 186.8445 Evaluate side-chains 342 residues out of total 2105 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 342 time to evaluate : 2.239 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 241 random chunks: chunk 203 optimal weight: 0.6980 chunk 182 optimal weight: 1.9990 chunk 101 optimal weight: 0.1980 chunk 62 optimal weight: 0.5980 chunk 123 optimal weight: 1.9990 chunk 97 optimal weight: 0.7980 chunk 188 optimal weight: 0.8980 chunk 73 optimal weight: 0.8980 chunk 114 optimal weight: 0.7980 chunk 140 optimal weight: 0.6980 chunk 218 optimal weight: 0.7980 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** Q 312 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Q 647 ASN R 253 GLN ** R 338 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** R 495 HIS R 583 ASN H 59 GLN H 214 ASN A 73 HIS A 131 ASN B 155 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7500 moved from start: 0.1025 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 20080 Z= 0.249 Angle : 0.564 9.168 27209 Z= 0.299 Chirality : 0.043 0.208 3069 Planarity : 0.005 0.072 3428 Dihedral : 7.034 98.179 3069 Min Nonbonded Distance : 2.216 Molprobity Statistics. All-atom Clashscore : 4.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.07 % Favored : 96.93 % Rotamer: Outliers : 2.76 % Allowed : 14.20 % Favored : 83.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.22 % Cis-general : 0.09 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.35 (0.17), residues: 2413 helix: 1.67 (0.17), residues: 902 sheet: -0.18 (0.23), residues: 509 loop : -0.84 (0.19), residues: 1002 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP R 719 HIS 0.012 0.001 HIS A 80 PHE 0.023 0.002 PHE R 637 TYR 0.019 0.002 TYR Q 652 ARG 0.007 0.000 ARG B 96 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4826 Ramachandran restraints generated. 2413 Oldfield, 0 Emsley, 2413 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4826 Ramachandran restraints generated. 2413 Oldfield, 0 Emsley, 2413 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 408 residues out of total 2105 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 58 poor density : 350 time to evaluate : 1.987 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: Q 25 ARG cc_start: 0.7923 (ptp-170) cc_final: 0.7651 (ptp90) REVERT: Q 199 ASP cc_start: 0.7179 (m-30) cc_final: 0.6978 (m-30) REVERT: Q 624 ILE cc_start: 0.8363 (OUTLIER) cc_final: 0.8135 (mp) REVERT: Q 728 VAL cc_start: 0.7668 (p) cc_final: 0.7390 (p) REVERT: R 118 ASN cc_start: 0.5893 (m110) cc_final: 0.5490 (m-40) REVERT: R 481 GLU cc_start: 0.6790 (pm20) cc_final: 0.6583 (pm20) REVERT: R 637 PHE cc_start: 0.7763 (m-80) cc_final: 0.7425 (m-80) REVERT: A 112 LEU cc_start: 0.5872 (mt) cc_final: 0.5605 (tp) REVERT: A 120 GLU cc_start: 0.5644 (OUTLIER) cc_final: 0.5326 (pm20) REVERT: A 131 ASN cc_start: 0.7614 (m110) cc_final: 0.7228 (m110) REVERT: B 303 ASP cc_start: 0.7717 (OUTLIER) cc_final: 0.7444 (t0) outliers start: 58 outliers final: 36 residues processed: 385 average time/residue: 0.3312 time to fit residues: 190.7128 Evaluate side-chains 379 residues out of total 2105 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 340 time to evaluate : 2.009 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Q residue 32 ILE Chi-restraints excluded: chain Q residue 223 ILE Chi-restraints excluded: chain Q residue 360 LEU Chi-restraints excluded: chain Q residue 443 LEU Chi-restraints excluded: chain Q residue 486 VAL Chi-restraints excluded: chain Q residue 560 THR Chi-restraints excluded: chain Q residue 624 ILE Chi-restraints excluded: chain Q residue 634 PHE Chi-restraints excluded: chain Q residue 650 LEU Chi-restraints excluded: chain Q residue 698 LYS Chi-restraints excluded: chain Q residue 723 LEU Chi-restraints excluded: chain Q residue 737 VAL Chi-restraints excluded: chain Q residue 743 LEU Chi-restraints excluded: chain Q residue 836 VAL Chi-restraints excluded: chain R residue 139 ILE Chi-restraints excluded: chain R residue 184 LEU Chi-restraints excluded: chain R residue 284 VAL Chi-restraints excluded: chain R residue 470 THR Chi-restraints excluded: chain R residue 485 LEU Chi-restraints excluded: chain R residue 592 ASN Chi-restraints excluded: chain R residue 761 ILE Chi-restraints excluded: chain R residue 812 LEU Chi-restraints excluded: chain R residue 833 VAL Chi-restraints excluded: chain R residue 861 LEU Chi-restraints excluded: chain H residue 117 VAL Chi-restraints excluded: chain H residue 209 ILE Chi-restraints excluded: chain A residue 28 GLU Chi-restraints excluded: chain A residue 91 SER Chi-restraints excluded: chain A residue 120 GLU Chi-restraints excluded: chain A residue 225 ASP Chi-restraints excluded: chain B residue 97 SER Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 181 THR Chi-restraints excluded: chain B residue 247 ASP Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 303 ASP Chi-restraints excluded: chain G residue 9 ILE Chi-restraints excluded: chain G residue 28 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 241 random chunks: chunk 121 optimal weight: 1.9990 chunk 67 optimal weight: 0.3980 chunk 182 optimal weight: 1.9990 chunk 149 optimal weight: 0.9980 chunk 60 optimal weight: 0.7980 chunk 219 optimal weight: 0.8980 chunk 236 optimal weight: 10.0000 chunk 195 optimal weight: 0.8980 chunk 217 optimal weight: 0.4980 chunk 74 optimal weight: 0.5980 chunk 175 optimal weight: 0.6980 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Q 312 HIS Q 647 ASN R 495 HIS R 753 ASN H 59 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7513 moved from start: 0.1307 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 20080 Z= 0.238 Angle : 0.539 7.819 27209 Z= 0.287 Chirality : 0.042 0.184 3069 Planarity : 0.004 0.055 3428 Dihedral : 6.714 97.378 3069 Min Nonbonded Distance : 2.264 Molprobity Statistics. All-atom Clashscore : 4.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.74 % Favored : 97.26 % Rotamer: Outliers : 2.99 % Allowed : 15.20 % Favored : 81.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.22 % Cis-general : 0.09 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.37 (0.17), residues: 2413 helix: 1.70 (0.17), residues: 907 sheet: -0.14 (0.23), residues: 508 loop : -0.88 (0.19), residues: 998 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP R 719 HIS 0.008 0.001 HIS R 338 PHE 0.021 0.002 PHE R 637 TYR 0.017 0.001 TYR H 210 ARG 0.005 0.000 ARG B 96 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4826 Ramachandran restraints generated. 2413 Oldfield, 0 Emsley, 2413 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4826 Ramachandran restraints generated. 2413 Oldfield, 0 Emsley, 2413 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 408 residues out of total 2105 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 63 poor density : 345 time to evaluate : 2.094 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: Q 624 ILE cc_start: 0.8388 (OUTLIER) cc_final: 0.8138 (mp) REVERT: Q 728 VAL cc_start: 0.7686 (p) cc_final: 0.7369 (p) REVERT: Q 735 GLN cc_start: 0.7772 (tp40) cc_final: 0.7375 (tp40) REVERT: Q 849 LEU cc_start: 0.8565 (OUTLIER) cc_final: 0.8097 (tp) REVERT: R 185 ARG cc_start: 0.8328 (OUTLIER) cc_final: 0.7483 (ptp-170) REVERT: R 481 GLU cc_start: 0.6770 (pm20) cc_final: 0.6553 (pm20) REVERT: R 637 PHE cc_start: 0.7719 (m-80) cc_final: 0.7447 (m-80) REVERT: A 120 GLU cc_start: 0.5665 (OUTLIER) cc_final: 0.5362 (pm20) REVERT: B 234 PHE cc_start: 0.8089 (OUTLIER) cc_final: 0.7345 (t80) REVERT: B 303 ASP cc_start: 0.7735 (OUTLIER) cc_final: 0.7474 (t0) outliers start: 63 outliers final: 46 residues processed: 383 average time/residue: 0.3510 time to fit residues: 200.9991 Evaluate side-chains 392 residues out of total 2105 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 340 time to evaluate : 2.217 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Q residue 24 GLN Chi-restraints excluded: chain Q residue 32 ILE Chi-restraints excluded: chain Q residue 139 ILE Chi-restraints excluded: chain Q residue 223 ILE Chi-restraints excluded: chain Q residue 232 GLU Chi-restraints excluded: chain Q residue 360 LEU Chi-restraints excluded: chain Q residue 412 THR Chi-restraints excluded: chain Q residue 443 LEU Chi-restraints excluded: chain Q residue 486 VAL Chi-restraints excluded: chain Q residue 560 THR Chi-restraints excluded: chain Q residue 578 ASP Chi-restraints excluded: chain Q residue 624 ILE Chi-restraints excluded: chain Q residue 634 PHE Chi-restraints excluded: chain Q residue 650 LEU Chi-restraints excluded: chain Q residue 698 LYS Chi-restraints excluded: chain Q residue 723 LEU Chi-restraints excluded: chain Q residue 737 VAL Chi-restraints excluded: chain Q residue 738 ILE Chi-restraints excluded: chain Q residue 834 SER Chi-restraints excluded: chain Q residue 836 VAL Chi-restraints excluded: chain Q residue 849 LEU Chi-restraints excluded: chain R residue 139 ILE Chi-restraints excluded: chain R residue 184 LEU Chi-restraints excluded: chain R residue 185 ARG Chi-restraints excluded: chain R residue 284 VAL Chi-restraints excluded: chain R residue 412 THR Chi-restraints excluded: chain R residue 470 THR Chi-restraints excluded: chain R residue 485 LEU Chi-restraints excluded: chain R residue 554 ILE Chi-restraints excluded: chain R residue 592 ASN Chi-restraints excluded: chain R residue 646 THR Chi-restraints excluded: chain R residue 689 VAL Chi-restraints excluded: chain R residue 761 ILE Chi-restraints excluded: chain R residue 812 LEU Chi-restraints excluded: chain R residue 861 LEU Chi-restraints excluded: chain H residue 117 VAL Chi-restraints excluded: chain H residue 161 THR Chi-restraints excluded: chain A residue 28 GLU Chi-restraints excluded: chain A residue 91 SER Chi-restraints excluded: chain A residue 120 GLU Chi-restraints excluded: chain A residue 225 ASP Chi-restraints excluded: chain B residue 79 LEU Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 181 THR Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 247 ASP Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 303 ASP Chi-restraints excluded: chain B residue 317 CYS Chi-restraints excluded: chain G residue 9 ILE Chi-restraints excluded: chain G residue 28 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 241 random chunks: chunk 216 optimal weight: 1.9990 chunk 164 optimal weight: 0.7980 chunk 113 optimal weight: 0.9990 chunk 24 optimal weight: 0.9980 chunk 104 optimal weight: 1.9990 chunk 147 optimal weight: 2.9990 chunk 220 optimal weight: 0.9980 chunk 232 optimal weight: 0.9990 chunk 114 optimal weight: 0.5980 chunk 208 optimal weight: 1.9990 chunk 62 optimal weight: 0.9990 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 312 HIS R 495 HIS H 59 GLN A 131 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7547 moved from start: 0.1666 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.039 20080 Z= 0.331 Angle : 0.584 8.161 27209 Z= 0.309 Chirality : 0.044 0.186 3069 Planarity : 0.004 0.053 3428 Dihedral : 6.578 96.890 3069 Min Nonbonded Distance : 2.251 Molprobity Statistics. All-atom Clashscore : 4.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.61 % Favored : 96.39 % Rotamer: Outliers : 3.99 % Allowed : 15.58 % Favored : 80.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.22 % Cis-general : 0.09 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.22 (0.17), residues: 2413 helix: 1.59 (0.17), residues: 904 sheet: -0.17 (0.23), residues: 504 loop : -1.01 (0.19), residues: 1005 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP R 719 HIS 0.010 0.001 HIS R 338 PHE 0.026 0.002 PHE R 814 TYR 0.017 0.002 TYR H 210 ARG 0.005 0.000 ARG R 185 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4826 Ramachandran restraints generated. 2413 Oldfield, 0 Emsley, 2413 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4826 Ramachandran restraints generated. 2413 Oldfield, 0 Emsley, 2413 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 431 residues out of total 2105 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 84 poor density : 347 time to evaluate : 2.089 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: Q 624 ILE cc_start: 0.8410 (OUTLIER) cc_final: 0.8156 (mp) REVERT: Q 728 VAL cc_start: 0.7707 (p) cc_final: 0.7409 (p) REVERT: Q 849 LEU cc_start: 0.8598 (OUTLIER) cc_final: 0.8170 (tp) REVERT: R 185 ARG cc_start: 0.8329 (OUTLIER) cc_final: 0.7551 (ptp-170) REVERT: R 637 PHE cc_start: 0.7828 (m-80) cc_final: 0.7610 (m-80) REVERT: A 33 GLU cc_start: 0.7160 (mm-30) cc_final: 0.6823 (mm-30) REVERT: A 118 MET cc_start: 0.6202 (tmm) cc_final: 0.5917 (tmm) REVERT: A 120 GLU cc_start: 0.5713 (OUTLIER) cc_final: 0.5418 (pm20) REVERT: A 136 ASP cc_start: 0.7480 (t0) cc_final: 0.7105 (t0) REVERT: B 156 GLN cc_start: 0.8212 (OUTLIER) cc_final: 0.7703 (mt0) REVERT: B 234 PHE cc_start: 0.8239 (OUTLIER) cc_final: 0.7462 (t80) REVERT: B 303 ASP cc_start: 0.7812 (OUTLIER) cc_final: 0.7579 (t0) outliers start: 84 outliers final: 64 residues processed: 398 average time/residue: 0.3277 time to fit residues: 195.1362 Evaluate side-chains 416 residues out of total 2105 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 71 poor density : 345 time to evaluate : 2.079 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Q residue 24 GLN Chi-restraints excluded: chain Q residue 32 ILE Chi-restraints excluded: chain Q residue 139 ILE Chi-restraints excluded: chain Q residue 223 ILE Chi-restraints excluded: chain Q residue 232 GLU Chi-restraints excluded: chain Q residue 263 THR Chi-restraints excluded: chain Q residue 360 LEU Chi-restraints excluded: chain Q residue 412 THR Chi-restraints excluded: chain Q residue 443 LEU Chi-restraints excluded: chain Q residue 486 VAL Chi-restraints excluded: chain Q residue 560 THR Chi-restraints excluded: chain Q residue 578 ASP Chi-restraints excluded: chain Q residue 624 ILE Chi-restraints excluded: chain Q residue 634 PHE Chi-restraints excluded: chain Q residue 650 LEU Chi-restraints excluded: chain Q residue 698 LYS Chi-restraints excluded: chain Q residue 723 LEU Chi-restraints excluded: chain Q residue 737 VAL Chi-restraints excluded: chain Q residue 738 ILE Chi-restraints excluded: chain Q residue 834 SER Chi-restraints excluded: chain Q residue 836 VAL Chi-restraints excluded: chain Q residue 849 LEU Chi-restraints excluded: chain R residue 139 ILE Chi-restraints excluded: chain R residue 184 LEU Chi-restraints excluded: chain R residue 185 ARG Chi-restraints excluded: chain R residue 244 SER Chi-restraints excluded: chain R residue 284 VAL Chi-restraints excluded: chain R residue 412 THR Chi-restraints excluded: chain R residue 455 VAL Chi-restraints excluded: chain R residue 470 THR Chi-restraints excluded: chain R residue 485 LEU Chi-restraints excluded: chain R residue 503 ILE Chi-restraints excluded: chain R residue 577 THR Chi-restraints excluded: chain R residue 583 ASN Chi-restraints excluded: chain R residue 592 ASN Chi-restraints excluded: chain R residue 599 ILE Chi-restraints excluded: chain R residue 619 PHE Chi-restraints excluded: chain R residue 646 THR Chi-restraints excluded: chain R residue 705 VAL Chi-restraints excluded: chain R residue 715 HIS Chi-restraints excluded: chain R residue 761 ILE Chi-restraints excluded: chain R residue 788 PHE Chi-restraints excluded: chain R residue 812 LEU Chi-restraints excluded: chain R residue 833 VAL Chi-restraints excluded: chain R residue 861 LEU Chi-restraints excluded: chain H residue 117 VAL Chi-restraints excluded: chain H residue 136 THR Chi-restraints excluded: chain H residue 161 THR Chi-restraints excluded: chain H residue 175 VAL Chi-restraints excluded: chain H residue 179 CYS Chi-restraints excluded: chain H residue 198 LEU Chi-restraints excluded: chain H residue 209 ILE Chi-restraints excluded: chain H residue 212 MET Chi-restraints excluded: chain A residue 28 GLU Chi-restraints excluded: chain A residue 91 SER Chi-restraints excluded: chain A residue 120 GLU Chi-restraints excluded: chain A residue 218 ILE Chi-restraints excluded: chain A residue 225 ASP Chi-restraints excluded: chain B residue 79 LEU Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 156 GLN Chi-restraints excluded: chain B residue 181 THR Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 247 ASP Chi-restraints excluded: chain B residue 303 ASP Chi-restraints excluded: chain B residue 317 CYS Chi-restraints excluded: chain G residue 9 ILE Chi-restraints excluded: chain G residue 28 ILE Chi-restraints excluded: chain G residue 38 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 241 random chunks: chunk 194 optimal weight: 0.5980 chunk 132 optimal weight: 0.0370 chunk 3 optimal weight: 2.9990 chunk 173 optimal weight: 2.9990 chunk 96 optimal weight: 0.0870 chunk 198 optimal weight: 2.9990 chunk 161 optimal weight: 1.9990 chunk 0 optimal weight: 1.9990 chunk 118 optimal weight: 0.2980 chunk 209 optimal weight: 0.3980 chunk 58 optimal weight: 0.2980 overall best weight: 0.2236 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Q 400 ASN R 495 HIS H 133 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7488 moved from start: 0.1707 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 20080 Z= 0.141 Angle : 0.479 7.354 27209 Z= 0.257 Chirality : 0.041 0.165 3069 Planarity : 0.004 0.051 3428 Dihedral : 6.169 95.623 3069 Min Nonbonded Distance : 2.334 Molprobity Statistics. All-atom Clashscore : 4.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.32 % Favored : 97.68 % Rotamer: Outliers : 2.61 % Allowed : 17.34 % Favored : 80.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.22 % Cis-general : 0.09 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.55 (0.17), residues: 2413 helix: 1.85 (0.17), residues: 908 sheet: -0.01 (0.23), residues: 511 loop : -0.81 (0.19), residues: 994 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.001 TRP R 719 HIS 0.009 0.001 HIS R 338 PHE 0.014 0.001 PHE Q 854 TYR 0.012 0.001 TYR H 210 ARG 0.005 0.000 ARG R 465 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4826 Ramachandran restraints generated. 2413 Oldfield, 0 Emsley, 2413 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4826 Ramachandran restraints generated. 2413 Oldfield, 0 Emsley, 2413 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 401 residues out of total 2105 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 55 poor density : 346 time to evaluate : 2.274 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: Q 595 HIS cc_start: 0.7078 (m170) cc_final: 0.6861 (m170) REVERT: Q 624 ILE cc_start: 0.8335 (OUTLIER) cc_final: 0.8038 (mp) REVERT: Q 637 PHE cc_start: 0.7592 (m-80) cc_final: 0.7335 (m-80) REVERT: Q 728 VAL cc_start: 0.7689 (p) cc_final: 0.7374 (p) REVERT: Q 849 LEU cc_start: 0.8606 (OUTLIER) cc_final: 0.8263 (tp) REVERT: R 637 PHE cc_start: 0.7721 (m-80) cc_final: 0.7497 (m-80) REVERT: R 730 LEU cc_start: 0.7467 (OUTLIER) cc_final: 0.6962 (mp) REVERT: A 33 GLU cc_start: 0.7110 (mm-30) cc_final: 0.6790 (mm-30) REVERT: A 76 PHE cc_start: 0.7175 (t80) cc_final: 0.6904 (t80) REVERT: A 118 MET cc_start: 0.6109 (tmm) cc_final: 0.5888 (tmm) REVERT: A 120 GLU cc_start: 0.5619 (OUTLIER) cc_final: 0.5330 (pm20) REVERT: A 131 ASN cc_start: 0.7719 (OUTLIER) cc_final: 0.7375 (m-40) REVERT: A 136 ASP cc_start: 0.7449 (t0) cc_final: 0.7060 (t0) REVERT: B 76 ASP cc_start: 0.7416 (p0) cc_final: 0.7211 (p0) REVERT: B 234 PHE cc_start: 0.8206 (OUTLIER) cc_final: 0.7370 (t80) REVERT: B 303 ASP cc_start: 0.7729 (OUTLIER) cc_final: 0.7483 (t0) outliers start: 55 outliers final: 35 residues processed: 378 average time/residue: 0.3175 time to fit residues: 180.6351 Evaluate side-chains 375 residues out of total 2105 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 333 time to evaluate : 2.070 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Q residue 32 ILE Chi-restraints excluded: chain Q residue 223 ILE Chi-restraints excluded: chain Q residue 232 GLU Chi-restraints excluded: chain Q residue 360 LEU Chi-restraints excluded: chain Q residue 412 THR Chi-restraints excluded: chain Q residue 443 LEU Chi-restraints excluded: chain Q residue 578 ASP Chi-restraints excluded: chain Q residue 624 ILE Chi-restraints excluded: chain Q residue 634 PHE Chi-restraints excluded: chain Q residue 650 LEU Chi-restraints excluded: chain Q residue 723 LEU Chi-restraints excluded: chain Q residue 737 VAL Chi-restraints excluded: chain Q residue 743 LEU Chi-restraints excluded: chain Q residue 849 LEU Chi-restraints excluded: chain R residue 139 ILE Chi-restraints excluded: chain R residue 284 VAL Chi-restraints excluded: chain R residue 470 THR Chi-restraints excluded: chain R residue 582 CYS Chi-restraints excluded: chain R residue 592 ASN Chi-restraints excluded: chain R residue 618 LEU Chi-restraints excluded: chain R residue 619 PHE Chi-restraints excluded: chain R residue 715 HIS Chi-restraints excluded: chain R residue 730 LEU Chi-restraints excluded: chain R residue 761 ILE Chi-restraints excluded: chain R residue 812 LEU Chi-restraints excluded: chain H residue 117 VAL Chi-restraints excluded: chain H residue 136 THR Chi-restraints excluded: chain H residue 161 THR Chi-restraints excluded: chain H residue 212 MET Chi-restraints excluded: chain A residue 91 SER Chi-restraints excluded: chain A residue 120 GLU Chi-restraints excluded: chain A residue 131 ASN Chi-restraints excluded: chain A residue 225 ASP Chi-restraints excluded: chain B residue 40 VAL Chi-restraints excluded: chain B residue 79 LEU Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 247 ASP Chi-restraints excluded: chain B residue 303 ASP Chi-restraints excluded: chain B residue 317 CYS Chi-restraints excluded: chain G residue 9 ILE Chi-restraints excluded: chain G residue 38 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 241 random chunks: chunk 78 optimal weight: 1.9990 chunk 209 optimal weight: 0.0980 chunk 46 optimal weight: 0.7980 chunk 136 optimal weight: 1.9990 chunk 57 optimal weight: 0.5980 chunk 233 optimal weight: 1.9990 chunk 193 optimal weight: 2.9990 chunk 107 optimal weight: 0.4980 chunk 19 optimal weight: 0.9980 chunk 77 optimal weight: 0.7980 chunk 122 optimal weight: 1.9990 overall best weight: 0.5580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 338 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7520 moved from start: 0.1807 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.029 20080 Z= 0.229 Angle : 0.520 7.419 27209 Z= 0.276 Chirality : 0.042 0.165 3069 Planarity : 0.004 0.050 3428 Dihedral : 6.141 94.648 3069 Min Nonbonded Distance : 2.267 Molprobity Statistics. All-atom Clashscore : 4.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.19 % Favored : 96.81 % Rotamer: Outliers : 3.61 % Allowed : 17.24 % Favored : 79.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.22 % Cis-general : 0.09 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.52 (0.17), residues: 2413 helix: 1.86 (0.17), residues: 906 sheet: -0.01 (0.23), residues: 512 loop : -0.87 (0.19), residues: 995 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP R 719 HIS 0.005 0.001 HIS H 55 PHE 0.022 0.001 PHE R 814 TYR 0.016 0.001 TYR H 210 ARG 0.006 0.000 ARG Q 205 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4826 Ramachandran restraints generated. 2413 Oldfield, 0 Emsley, 2413 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4826 Ramachandran restraints generated. 2413 Oldfield, 0 Emsley, 2413 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 418 residues out of total 2105 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 76 poor density : 342 time to evaluate : 2.231 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: Q 624 ILE cc_start: 0.8372 (OUTLIER) cc_final: 0.8054 (mp) REVERT: Q 637 PHE cc_start: 0.7653 (m-80) cc_final: 0.7398 (m-80) REVERT: Q 728 VAL cc_start: 0.7743 (OUTLIER) cc_final: 0.7439 (p) REVERT: Q 849 LEU cc_start: 0.8635 (OUTLIER) cc_final: 0.8250 (tp) REVERT: R 637 PHE cc_start: 0.7777 (m-80) cc_final: 0.7547 (m-80) REVERT: R 730 LEU cc_start: 0.7514 (OUTLIER) cc_final: 0.6982 (mp) REVERT: A 33 GLU cc_start: 0.7146 (mm-30) cc_final: 0.6856 (mm-30) REVERT: A 120 GLU cc_start: 0.5645 (OUTLIER) cc_final: 0.5353 (pm20) REVERT: A 131 ASN cc_start: 0.7737 (OUTLIER) cc_final: 0.7493 (m-40) REVERT: A 136 ASP cc_start: 0.7493 (t0) cc_final: 0.7063 (t0) REVERT: B 86 THR cc_start: 0.8629 (p) cc_final: 0.8407 (m) REVERT: B 155 ASN cc_start: 0.7683 (t0) cc_final: 0.7401 (t0) REVERT: B 234 PHE cc_start: 0.8245 (OUTLIER) cc_final: 0.7441 (t80) REVERT: B 303 ASP cc_start: 0.7721 (OUTLIER) cc_final: 0.7479 (t0) outliers start: 76 outliers final: 59 residues processed: 389 average time/residue: 0.3543 time to fit residues: 211.1919 Evaluate side-chains 410 residues out of total 2105 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 67 poor density : 343 time to evaluate : 2.226 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Q residue 32 ILE Chi-restraints excluded: chain Q residue 139 ILE Chi-restraints excluded: chain Q residue 223 ILE Chi-restraints excluded: chain Q residue 232 GLU Chi-restraints excluded: chain Q residue 263 THR Chi-restraints excluded: chain Q residue 360 LEU Chi-restraints excluded: chain Q residue 395 CYS Chi-restraints excluded: chain Q residue 412 THR Chi-restraints excluded: chain Q residue 443 LEU Chi-restraints excluded: chain Q residue 578 ASP Chi-restraints excluded: chain Q residue 624 ILE Chi-restraints excluded: chain Q residue 634 PHE Chi-restraints excluded: chain Q residue 650 LEU Chi-restraints excluded: chain Q residue 698 LYS Chi-restraints excluded: chain Q residue 723 LEU Chi-restraints excluded: chain Q residue 728 VAL Chi-restraints excluded: chain Q residue 737 VAL Chi-restraints excluded: chain Q residue 738 ILE Chi-restraints excluded: chain Q residue 834 SER Chi-restraints excluded: chain Q residue 849 LEU Chi-restraints excluded: chain R residue 139 ILE Chi-restraints excluded: chain R residue 184 LEU Chi-restraints excluded: chain R residue 284 VAL Chi-restraints excluded: chain R residue 404 VAL Chi-restraints excluded: chain R residue 412 THR Chi-restraints excluded: chain R residue 470 THR Chi-restraints excluded: chain R residue 485 LEU Chi-restraints excluded: chain R residue 503 ILE Chi-restraints excluded: chain R residue 583 ASN Chi-restraints excluded: chain R residue 592 ASN Chi-restraints excluded: chain R residue 599 ILE Chi-restraints excluded: chain R residue 618 LEU Chi-restraints excluded: chain R residue 619 PHE Chi-restraints excluded: chain R residue 646 THR Chi-restraints excluded: chain R residue 704 LEU Chi-restraints excluded: chain R residue 715 HIS Chi-restraints excluded: chain R residue 730 LEU Chi-restraints excluded: chain R residue 761 ILE Chi-restraints excluded: chain R residue 812 LEU Chi-restraints excluded: chain R residue 861 LEU Chi-restraints excluded: chain H residue 117 VAL Chi-restraints excluded: chain H residue 136 THR Chi-restraints excluded: chain H residue 161 THR Chi-restraints excluded: chain H residue 175 VAL Chi-restraints excluded: chain H residue 179 CYS Chi-restraints excluded: chain H residue 212 MET Chi-restraints excluded: chain H residue 239 LEU Chi-restraints excluded: chain A residue 91 SER Chi-restraints excluded: chain A residue 120 GLU Chi-restraints excluded: chain A residue 131 ASN Chi-restraints excluded: chain A residue 135 THR Chi-restraints excluded: chain A residue 216 ASP Chi-restraints excluded: chain A residue 218 ILE Chi-restraints excluded: chain A residue 225 ASP Chi-restraints excluded: chain B residue 40 VAL Chi-restraints excluded: chain B residue 79 LEU Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 181 THR Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 247 ASP Chi-restraints excluded: chain B residue 270 ILE Chi-restraints excluded: chain B residue 303 ASP Chi-restraints excluded: chain B residue 317 CYS Chi-restraints excluded: chain G residue 9 ILE Chi-restraints excluded: chain G residue 28 ILE Chi-restraints excluded: chain G residue 38 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 241 random chunks: chunk 224 optimal weight: 0.0370 chunk 26 optimal weight: 1.9990 chunk 132 optimal weight: 0.8980 chunk 170 optimal weight: 1.9990 chunk 131 optimal weight: 0.7980 chunk 196 optimal weight: 0.0470 chunk 130 optimal weight: 0.5980 chunk 232 optimal weight: 0.9990 chunk 145 optimal weight: 2.9990 chunk 141 optimal weight: 0.9990 chunk 107 optimal weight: 0.8980 overall best weight: 0.4756 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 253 GLN ** R 338 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** R 754 GLN A 131 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7513 moved from start: 0.1876 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 20080 Z= 0.199 Angle : 0.507 7.286 27209 Z= 0.270 Chirality : 0.041 0.166 3069 Planarity : 0.004 0.051 3428 Dihedral : 6.067 94.019 3069 Min Nonbonded Distance : 2.292 Molprobity Statistics. All-atom Clashscore : 4.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.78 % Favored : 97.22 % Rotamer: Outliers : 3.47 % Allowed : 17.34 % Favored : 79.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.22 % Cis-general : 0.09 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.56 (0.17), residues: 2413 helix: 1.89 (0.17), residues: 905 sheet: 0.02 (0.23), residues: 511 loop : -0.84 (0.19), residues: 997 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.001 TRP R 719 HIS 0.004 0.001 HIS H 55 PHE 0.019 0.001 PHE R 814 TYR 0.014 0.001 TYR H 210 ARG 0.007 0.000 ARG R 465 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4826 Ramachandran restraints generated. 2413 Oldfield, 0 Emsley, 2413 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4826 Ramachandran restraints generated. 2413 Oldfield, 0 Emsley, 2413 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 417 residues out of total 2105 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 73 poor density : 344 time to evaluate : 2.145 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: Q 624 ILE cc_start: 0.8348 (OUTLIER) cc_final: 0.8030 (mp) REVERT: Q 637 PHE cc_start: 0.7619 (m-80) cc_final: 0.7378 (m-80) REVERT: Q 728 VAL cc_start: 0.7680 (OUTLIER) cc_final: 0.7367 (p) REVERT: Q 849 LEU cc_start: 0.8622 (OUTLIER) cc_final: 0.8282 (tp) REVERT: R 637 PHE cc_start: 0.7757 (m-80) cc_final: 0.7536 (m-80) REVERT: R 659 LEU cc_start: 0.8101 (mt) cc_final: 0.7874 (mt) REVERT: R 730 LEU cc_start: 0.7499 (OUTLIER) cc_final: 0.6986 (mp) REVERT: R 870 GLU cc_start: 0.7370 (OUTLIER) cc_final: 0.6951 (mt-10) REVERT: A 120 GLU cc_start: 0.5595 (OUTLIER) cc_final: 0.5317 (pm20) REVERT: A 131 ASN cc_start: 0.7744 (OUTLIER) cc_final: 0.7440 (m-40) REVERT: A 136 ASP cc_start: 0.7484 (t0) cc_final: 0.7055 (t0) REVERT: B 155 ASN cc_start: 0.7735 (t0) cc_final: 0.6912 (t0) REVERT: B 172 GLU cc_start: 0.6273 (mm-30) cc_final: 0.6016 (mm-30) REVERT: B 234 PHE cc_start: 0.8237 (OUTLIER) cc_final: 0.7437 (t80) REVERT: B 303 ASP cc_start: 0.7707 (OUTLIER) cc_final: 0.7486 (t0) outliers start: 73 outliers final: 55 residues processed: 393 average time/residue: 0.3172 time to fit residues: 188.0479 Evaluate side-chains 403 residues out of total 2105 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 64 poor density : 339 time to evaluate : 2.099 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Q residue 24 GLN Chi-restraints excluded: chain Q residue 32 ILE Chi-restraints excluded: chain Q residue 223 ILE Chi-restraints excluded: chain Q residue 232 GLU Chi-restraints excluded: chain Q residue 263 THR Chi-restraints excluded: chain Q residue 360 LEU Chi-restraints excluded: chain Q residue 395 CYS Chi-restraints excluded: chain Q residue 443 LEU Chi-restraints excluded: chain Q residue 578 ASP Chi-restraints excluded: chain Q residue 624 ILE Chi-restraints excluded: chain Q residue 634 PHE Chi-restraints excluded: chain Q residue 650 LEU Chi-restraints excluded: chain Q residue 676 THR Chi-restraints excluded: chain Q residue 698 LYS Chi-restraints excluded: chain Q residue 723 LEU Chi-restraints excluded: chain Q residue 728 VAL Chi-restraints excluded: chain Q residue 737 VAL Chi-restraints excluded: chain Q residue 743 LEU Chi-restraints excluded: chain Q residue 834 SER Chi-restraints excluded: chain Q residue 849 LEU Chi-restraints excluded: chain R residue 80 GLU Chi-restraints excluded: chain R residue 139 ILE Chi-restraints excluded: chain R residue 184 LEU Chi-restraints excluded: chain R residue 284 VAL Chi-restraints excluded: chain R residue 412 THR Chi-restraints excluded: chain R residue 470 THR Chi-restraints excluded: chain R residue 485 LEU Chi-restraints excluded: chain R residue 503 ILE Chi-restraints excluded: chain R residue 583 ASN Chi-restraints excluded: chain R residue 592 ASN Chi-restraints excluded: chain R residue 599 ILE Chi-restraints excluded: chain R residue 618 LEU Chi-restraints excluded: chain R residue 619 PHE Chi-restraints excluded: chain R residue 646 THR Chi-restraints excluded: chain R residue 715 HIS Chi-restraints excluded: chain R residue 730 LEU Chi-restraints excluded: chain R residue 761 ILE Chi-restraints excluded: chain R residue 812 LEU Chi-restraints excluded: chain R residue 833 VAL Chi-restraints excluded: chain R residue 870 GLU Chi-restraints excluded: chain H residue 117 VAL Chi-restraints excluded: chain H residue 136 THR Chi-restraints excluded: chain H residue 161 THR Chi-restraints excluded: chain H residue 175 VAL Chi-restraints excluded: chain H residue 179 CYS Chi-restraints excluded: chain H residue 212 MET Chi-restraints excluded: chain H residue 239 LEU Chi-restraints excluded: chain A residue 91 SER Chi-restraints excluded: chain A residue 120 GLU Chi-restraints excluded: chain A residue 131 ASN Chi-restraints excluded: chain A residue 135 THR Chi-restraints excluded: chain A residue 216 ASP Chi-restraints excluded: chain A residue 218 ILE Chi-restraints excluded: chain A residue 225 ASP Chi-restraints excluded: chain B residue 40 VAL Chi-restraints excluded: chain B residue 79 LEU Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 247 ASP Chi-restraints excluded: chain B residue 303 ASP Chi-restraints excluded: chain B residue 317 CYS Chi-restraints excluded: chain G residue 9 ILE Chi-restraints excluded: chain G residue 28 ILE Chi-restraints excluded: chain G residue 38 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 241 random chunks: chunk 143 optimal weight: 0.7980 chunk 92 optimal weight: 1.9990 chunk 138 optimal weight: 0.9980 chunk 69 optimal weight: 1.9990 chunk 45 optimal weight: 1.9990 chunk 147 optimal weight: 0.7980 chunk 158 optimal weight: 1.9990 chunk 114 optimal weight: 0.9990 chunk 21 optimal weight: 0.7980 chunk 182 optimal weight: 1.9990 chunk 211 optimal weight: 0.0870 overall best weight: 0.6958 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 27 GLN ** R 338 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7532 moved from start: 0.1966 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 20080 Z= 0.268 Angle : 0.547 7.451 27209 Z= 0.289 Chirality : 0.043 0.166 3069 Planarity : 0.004 0.053 3428 Dihedral : 6.116 94.000 3069 Min Nonbonded Distance : 2.270 Molprobity Statistics. All-atom Clashscore : 4.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.36 % Favored : 96.64 % Rotamer: Outliers : 3.85 % Allowed : 17.29 % Favored : 78.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.22 % Cis-general : 0.09 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.49 (0.17), residues: 2413 helix: 1.84 (0.17), residues: 903 sheet: -0.03 (0.23), residues: 512 loop : -0.88 (0.19), residues: 998 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP R 719 HIS 0.005 0.001 HIS H 55 PHE 0.024 0.002 PHE R 814 TYR 0.015 0.002 TYR H 210 ARG 0.005 0.000 ARG Q 205 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4826 Ramachandran restraints generated. 2413 Oldfield, 0 Emsley, 2413 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4826 Ramachandran restraints generated. 2413 Oldfield, 0 Emsley, 2413 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 418 residues out of total 2105 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 81 poor density : 337 time to evaluate : 2.111 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: Q 624 ILE cc_start: 0.8360 (OUTLIER) cc_final: 0.8044 (mp) REVERT: Q 637 PHE cc_start: 0.7626 (m-80) cc_final: 0.7368 (m-80) REVERT: Q 728 VAL cc_start: 0.7688 (OUTLIER) cc_final: 0.7383 (p) REVERT: Q 849 LEU cc_start: 0.8616 (OUTLIER) cc_final: 0.8237 (tp) REVERT: R 730 LEU cc_start: 0.7539 (OUTLIER) cc_final: 0.7024 (mp) REVERT: R 870 GLU cc_start: 0.7368 (OUTLIER) cc_final: 0.6952 (mt-10) REVERT: A 120 GLU cc_start: 0.5647 (OUTLIER) cc_final: 0.5366 (pm20) REVERT: A 136 ASP cc_start: 0.7498 (t0) cc_final: 0.7082 (t0) REVERT: B 86 THR cc_start: 0.8648 (p) cc_final: 0.8425 (m) REVERT: B 234 PHE cc_start: 0.8264 (OUTLIER) cc_final: 0.7425 (t80) REVERT: B 303 ASP cc_start: 0.7686 (OUTLIER) cc_final: 0.7484 (t0) outliers start: 81 outliers final: 68 residues processed: 387 average time/residue: 0.3234 time to fit residues: 189.7923 Evaluate side-chains 412 residues out of total 2105 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 76 poor density : 336 time to evaluate : 2.100 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Q residue 24 GLN Chi-restraints excluded: chain Q residue 32 ILE Chi-restraints excluded: chain Q residue 139 ILE Chi-restraints excluded: chain Q residue 223 ILE Chi-restraints excluded: chain Q residue 232 GLU Chi-restraints excluded: chain Q residue 263 THR Chi-restraints excluded: chain Q residue 360 LEU Chi-restraints excluded: chain Q residue 395 CYS Chi-restraints excluded: chain Q residue 401 ILE Chi-restraints excluded: chain Q residue 443 LEU Chi-restraints excluded: chain Q residue 486 VAL Chi-restraints excluded: chain Q residue 560 THR Chi-restraints excluded: chain Q residue 578 ASP Chi-restraints excluded: chain Q residue 624 ILE Chi-restraints excluded: chain Q residue 634 PHE Chi-restraints excluded: chain Q residue 650 LEU Chi-restraints excluded: chain Q residue 676 THR Chi-restraints excluded: chain Q residue 698 LYS Chi-restraints excluded: chain Q residue 723 LEU Chi-restraints excluded: chain Q residue 728 VAL Chi-restraints excluded: chain Q residue 737 VAL Chi-restraints excluded: chain Q residue 738 ILE Chi-restraints excluded: chain Q residue 743 LEU Chi-restraints excluded: chain Q residue 834 SER Chi-restraints excluded: chain Q residue 849 LEU Chi-restraints excluded: chain R residue 27 GLN Chi-restraints excluded: chain R residue 139 ILE Chi-restraints excluded: chain R residue 184 LEU Chi-restraints excluded: chain R residue 284 VAL Chi-restraints excluded: chain R residue 409 ILE Chi-restraints excluded: chain R residue 412 THR Chi-restraints excluded: chain R residue 470 THR Chi-restraints excluded: chain R residue 485 LEU Chi-restraints excluded: chain R residue 503 ILE Chi-restraints excluded: chain R residue 583 ASN Chi-restraints excluded: chain R residue 592 ASN Chi-restraints excluded: chain R residue 599 ILE Chi-restraints excluded: chain R residue 618 LEU Chi-restraints excluded: chain R residue 619 PHE Chi-restraints excluded: chain R residue 646 THR Chi-restraints excluded: chain R residue 690 LEU Chi-restraints excluded: chain R residue 715 HIS Chi-restraints excluded: chain R residue 730 LEU Chi-restraints excluded: chain R residue 761 ILE Chi-restraints excluded: chain R residue 812 LEU Chi-restraints excluded: chain R residue 833 VAL Chi-restraints excluded: chain R residue 861 LEU Chi-restraints excluded: chain R residue 870 GLU Chi-restraints excluded: chain H residue 117 VAL Chi-restraints excluded: chain H residue 136 THR Chi-restraints excluded: chain H residue 161 THR Chi-restraints excluded: chain H residue 175 VAL Chi-restraints excluded: chain H residue 179 CYS Chi-restraints excluded: chain H residue 212 MET Chi-restraints excluded: chain H residue 233 THR Chi-restraints excluded: chain H residue 239 LEU Chi-restraints excluded: chain A residue 28 GLU Chi-restraints excluded: chain A residue 91 SER Chi-restraints excluded: chain A residue 120 GLU Chi-restraints excluded: chain A residue 135 THR Chi-restraints excluded: chain A residue 216 ASP Chi-restraints excluded: chain A residue 218 ILE Chi-restraints excluded: chain A residue 225 ASP Chi-restraints excluded: chain B residue 40 VAL Chi-restraints excluded: chain B residue 79 LEU Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 181 THR Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 247 ASP Chi-restraints excluded: chain B residue 270 ILE Chi-restraints excluded: chain B residue 303 ASP Chi-restraints excluded: chain B residue 317 CYS Chi-restraints excluded: chain G residue 9 ILE Chi-restraints excluded: chain G residue 28 ILE Chi-restraints excluded: chain G residue 38 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 241 random chunks: chunk 222 optimal weight: 0.0980 chunk 203 optimal weight: 9.9990 chunk 216 optimal weight: 0.9980 chunk 130 optimal weight: 0.8980 chunk 94 optimal weight: 0.9980 chunk 169 optimal weight: 0.5980 chunk 66 optimal weight: 0.0670 chunk 195 optimal weight: 0.6980 chunk 204 optimal weight: 5.9990 chunk 215 optimal weight: 0.4980 chunk 142 optimal weight: 0.0370 overall best weight: 0.2596 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 27 GLN ** R 338 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** R 495 HIS A 131 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7495 moved from start: 0.1994 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 20080 Z= 0.153 Angle : 0.490 7.095 27209 Z= 0.262 Chirality : 0.041 0.157 3069 Planarity : 0.004 0.050 3428 Dihedral : 5.961 93.049 3069 Min Nonbonded Distance : 2.312 Molprobity Statistics. All-atom Clashscore : 4.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.49 % Favored : 97.51 % Rotamer: Outliers : 3.04 % Allowed : 18.15 % Favored : 78.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.22 % Cis-general : 0.09 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.69 (0.17), residues: 2413 helix: 2.02 (0.17), residues: 901 sheet: 0.07 (0.23), residues: 511 loop : -0.77 (0.19), residues: 1001 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.001 TRP R 719 HIS 0.003 0.001 HIS H 55 PHE 0.015 0.001 PHE A 76 TYR 0.013 0.001 TYR H 210 ARG 0.006 0.000 ARG Q 205 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4826 Ramachandran restraints generated. 2413 Oldfield, 0 Emsley, 2413 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4826 Ramachandran restraints generated. 2413 Oldfield, 0 Emsley, 2413 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 398 residues out of total 2105 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 64 poor density : 334 time to evaluate : 2.370 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: Q 624 ILE cc_start: 0.8312 (OUTLIER) cc_final: 0.7988 (mp) REVERT: Q 637 PHE cc_start: 0.7526 (m-80) cc_final: 0.7065 (m-80) REVERT: Q 728 VAL cc_start: 0.7696 (OUTLIER) cc_final: 0.7378 (p) REVERT: Q 834 SER cc_start: 0.8021 (OUTLIER) cc_final: 0.7346 (p) REVERT: Q 849 LEU cc_start: 0.8648 (OUTLIER) cc_final: 0.8375 (tp) REVERT: R 592 ASN cc_start: 0.7757 (OUTLIER) cc_final: 0.6978 (m110) REVERT: R 637 PHE cc_start: 0.7729 (m-80) cc_final: 0.7515 (m-80) REVERT: R 659 LEU cc_start: 0.8096 (mt) cc_final: 0.7853 (mt) REVERT: R 870 GLU cc_start: 0.7364 (OUTLIER) cc_final: 0.6937 (mt-10) REVERT: A 120 GLU cc_start: 0.5516 (OUTLIER) cc_final: 0.5225 (pm20) REVERT: A 131 ASN cc_start: 0.7662 (OUTLIER) cc_final: 0.7357 (m-40) REVERT: A 136 ASP cc_start: 0.7466 (t0) cc_final: 0.7037 (t0) REVERT: B 87 THR cc_start: 0.8804 (OUTLIER) cc_final: 0.8500 (m) REVERT: B 234 PHE cc_start: 0.8240 (OUTLIER) cc_final: 0.7354 (t80) outliers start: 64 outliers final: 45 residues processed: 375 average time/residue: 0.3204 time to fit residues: 180.8404 Evaluate side-chains 384 residues out of total 2105 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 55 poor density : 329 time to evaluate : 2.218 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Q residue 139 ILE Chi-restraints excluded: chain Q residue 223 ILE Chi-restraints excluded: chain Q residue 232 GLU Chi-restraints excluded: chain Q residue 360 LEU Chi-restraints excluded: chain Q residue 395 CYS Chi-restraints excluded: chain Q residue 443 LEU Chi-restraints excluded: chain Q residue 486 VAL Chi-restraints excluded: chain Q residue 624 ILE Chi-restraints excluded: chain Q residue 634 PHE Chi-restraints excluded: chain Q residue 650 LEU Chi-restraints excluded: chain Q residue 723 LEU Chi-restraints excluded: chain Q residue 728 VAL Chi-restraints excluded: chain Q residue 737 VAL Chi-restraints excluded: chain Q residue 743 LEU Chi-restraints excluded: chain Q residue 834 SER Chi-restraints excluded: chain Q residue 849 LEU Chi-restraints excluded: chain R residue 80 GLU Chi-restraints excluded: chain R residue 139 ILE Chi-restraints excluded: chain R residue 284 VAL Chi-restraints excluded: chain R residue 470 THR Chi-restraints excluded: chain R residue 485 LEU Chi-restraints excluded: chain R residue 503 ILE Chi-restraints excluded: chain R residue 583 ASN Chi-restraints excluded: chain R residue 592 ASN Chi-restraints excluded: chain R residue 618 LEU Chi-restraints excluded: chain R residue 619 PHE Chi-restraints excluded: chain R residue 689 VAL Chi-restraints excluded: chain R residue 715 HIS Chi-restraints excluded: chain R residue 761 ILE Chi-restraints excluded: chain R residue 812 LEU Chi-restraints excluded: chain R residue 870 GLU Chi-restraints excluded: chain H residue 117 VAL Chi-restraints excluded: chain H residue 136 THR Chi-restraints excluded: chain H residue 161 THR Chi-restraints excluded: chain H residue 175 VAL Chi-restraints excluded: chain H residue 179 CYS Chi-restraints excluded: chain H residue 212 MET Chi-restraints excluded: chain H residue 233 THR Chi-restraints excluded: chain A residue 28 GLU Chi-restraints excluded: chain A residue 91 SER Chi-restraints excluded: chain A residue 120 GLU Chi-restraints excluded: chain A residue 131 ASN Chi-restraints excluded: chain A residue 135 THR Chi-restraints excluded: chain A residue 218 ILE Chi-restraints excluded: chain A residue 225 ASP Chi-restraints excluded: chain B residue 40 VAL Chi-restraints excluded: chain B residue 79 LEU Chi-restraints excluded: chain B residue 87 THR Chi-restraints excluded: chain B residue 181 THR Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 247 ASP Chi-restraints excluded: chain B residue 317 CYS Chi-restraints excluded: chain G residue 9 ILE Chi-restraints excluded: chain G residue 38 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 241 random chunks: chunk 228 optimal weight: 0.8980 chunk 139 optimal weight: 0.8980 chunk 108 optimal weight: 0.0020 chunk 159 optimal weight: 3.9990 chunk 240 optimal weight: 0.9980 chunk 220 optimal weight: 1.9990 chunk 191 optimal weight: 2.9990 chunk 19 optimal weight: 0.8980 chunk 147 optimal weight: 1.9990 chunk 117 optimal weight: 1.9990 chunk 151 optimal weight: 0.4980 overall best weight: 0.6388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 27 GLN R 495 HIS A 131 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7524 moved from start: 0.2051 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 20080 Z= 0.253 Angle : 0.547 11.972 27209 Z= 0.288 Chirality : 0.042 0.162 3069 Planarity : 0.004 0.053 3428 Dihedral : 6.026 93.463 3069 Min Nonbonded Distance : 2.271 Molprobity Statistics. All-atom Clashscore : 4.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.32 % Favored : 96.68 % Rotamer: Outliers : 2.99 % Allowed : 18.43 % Favored : 78.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.22 % Cis-general : 0.09 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.56 (0.17), residues: 2413 helix: 1.89 (0.17), residues: 905 sheet: 0.03 (0.23), residues: 512 loop : -0.85 (0.19), residues: 996 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.002 TRP R 719 HIS 0.010 0.001 HIS R 338 PHE 0.024 0.002 PHE R 814 TYR 0.015 0.001 TYR H 210 ARG 0.009 0.000 ARG B 214 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4826 Ramachandran restraints generated. 2413 Oldfield, 0 Emsley, 2413 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4826 Ramachandran restraints generated. 2413 Oldfield, 0 Emsley, 2413 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 393 residues out of total 2105 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 63 poor density : 330 time to evaluate : 2.086 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: Q 624 ILE cc_start: 0.8339 (OUTLIER) cc_final: 0.8032 (mp) REVERT: Q 637 PHE cc_start: 0.7584 (m-80) cc_final: 0.7194 (m-80) REVERT: Q 728 VAL cc_start: 0.7707 (OUTLIER) cc_final: 0.7406 (p) REVERT: Q 849 LEU cc_start: 0.8644 (OUTLIER) cc_final: 0.8307 (tp) REVERT: R 592 ASN cc_start: 0.7758 (OUTLIER) cc_final: 0.6969 (m110) REVERT: R 659 LEU cc_start: 0.8129 (mt) cc_final: 0.7882 (mt) REVERT: R 870 GLU cc_start: 0.7359 (OUTLIER) cc_final: 0.6935 (mt-10) REVERT: A 120 GLU cc_start: 0.5583 (OUTLIER) cc_final: 0.5285 (pm20) REVERT: A 131 ASN cc_start: 0.7626 (OUTLIER) cc_final: 0.7340 (m110) REVERT: A 136 ASP cc_start: 0.7484 (t0) cc_final: 0.7035 (t0) REVERT: B 87 THR cc_start: 0.8833 (OUTLIER) cc_final: 0.8541 (m) REVERT: B 234 PHE cc_start: 0.8266 (OUTLIER) cc_final: 0.7416 (t80) outliers start: 63 outliers final: 51 residues processed: 370 average time/residue: 0.3435 time to fit residues: 192.0429 Evaluate side-chains 389 residues out of total 2105 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 60 poor density : 329 time to evaluate : 2.012 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Q residue 139 ILE Chi-restraints excluded: chain Q residue 223 ILE Chi-restraints excluded: chain Q residue 232 GLU Chi-restraints excluded: chain Q residue 360 LEU Chi-restraints excluded: chain Q residue 395 CYS Chi-restraints excluded: chain Q residue 401 ILE Chi-restraints excluded: chain Q residue 443 LEU Chi-restraints excluded: chain Q residue 486 VAL Chi-restraints excluded: chain Q residue 560 THR Chi-restraints excluded: chain Q residue 624 ILE Chi-restraints excluded: chain Q residue 634 PHE Chi-restraints excluded: chain Q residue 650 LEU Chi-restraints excluded: chain Q residue 676 THR Chi-restraints excluded: chain Q residue 698 LYS Chi-restraints excluded: chain Q residue 723 LEU Chi-restraints excluded: chain Q residue 728 VAL Chi-restraints excluded: chain Q residue 737 VAL Chi-restraints excluded: chain Q residue 834 SER Chi-restraints excluded: chain Q residue 849 LEU Chi-restraints excluded: chain R residue 139 ILE Chi-restraints excluded: chain R residue 284 VAL Chi-restraints excluded: chain R residue 470 THR Chi-restraints excluded: chain R residue 485 LEU Chi-restraints excluded: chain R residue 503 ILE Chi-restraints excluded: chain R residue 583 ASN Chi-restraints excluded: chain R residue 592 ASN Chi-restraints excluded: chain R residue 618 LEU Chi-restraints excluded: chain R residue 619 PHE Chi-restraints excluded: chain R residue 646 THR Chi-restraints excluded: chain R residue 715 HIS Chi-restraints excluded: chain R residue 761 ILE Chi-restraints excluded: chain R residue 812 LEU Chi-restraints excluded: chain R residue 870 GLU Chi-restraints excluded: chain H residue 117 VAL Chi-restraints excluded: chain H residue 136 THR Chi-restraints excluded: chain H residue 161 THR Chi-restraints excluded: chain H residue 175 VAL Chi-restraints excluded: chain H residue 179 CYS Chi-restraints excluded: chain H residue 212 MET Chi-restraints excluded: chain H residue 233 THR Chi-restraints excluded: chain A residue 28 GLU Chi-restraints excluded: chain A residue 91 SER Chi-restraints excluded: chain A residue 120 GLU Chi-restraints excluded: chain A residue 131 ASN Chi-restraints excluded: chain A residue 135 THR Chi-restraints excluded: chain A residue 218 ILE Chi-restraints excluded: chain A residue 225 ASP Chi-restraints excluded: chain B residue 40 VAL Chi-restraints excluded: chain B residue 79 LEU Chi-restraints excluded: chain B residue 87 THR Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 181 THR Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 247 ASP Chi-restraints excluded: chain B residue 270 ILE Chi-restraints excluded: chain B residue 317 CYS Chi-restraints excluded: chain G residue 9 ILE Chi-restraints excluded: chain G residue 28 ILE Chi-restraints excluded: chain G residue 38 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 241 random chunks: chunk 203 optimal weight: 0.0050 chunk 58 optimal weight: 3.9990 chunk 176 optimal weight: 0.1980 chunk 28 optimal weight: 0.5980 chunk 53 optimal weight: 0.3980 chunk 191 optimal weight: 2.9990 chunk 80 optimal weight: 2.9990 chunk 196 optimal weight: 0.1980 chunk 24 optimal weight: 0.7980 chunk 35 optimal weight: 0.5980 chunk 168 optimal weight: 1.9990 overall best weight: 0.2794 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 27 GLN A 131 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3365 r_free = 0.3365 target = 0.108523 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3016 r_free = 0.3016 target = 0.088379 restraints weight = 33097.516| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3044 r_free = 0.3044 target = 0.089919 restraints weight = 24055.697| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3066 r_free = 0.3066 target = 0.091144 restraints weight = 19681.749| |-----------------------------------------------------------------------------| r_work (final): 0.3059 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7485 moved from start: 0.2048 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 20080 Z= 0.161 Angle : 0.505 11.340 27209 Z= 0.268 Chirality : 0.041 0.157 3069 Planarity : 0.004 0.051 3428 Dihedral : 5.952 92.815 3069 Min Nonbonded Distance : 2.303 Molprobity Statistics. All-atom Clashscore : 4.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.74 % Favored : 97.26 % Rotamer: Outliers : 2.76 % Allowed : 18.76 % Favored : 78.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.22 % Cis-general : 0.09 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.69 (0.17), residues: 2413 helix: 2.03 (0.17), residues: 899 sheet: 0.12 (0.23), residues: 509 loop : -0.79 (0.19), residues: 1005 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.001 TRP R 719 HIS 0.009 0.001 HIS R 338 PHE 0.017 0.001 PHE R 814 TYR 0.014 0.001 TYR H 210 ARG 0.008 0.000 ARG B 96 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4707.65 seconds wall clock time: 92 minutes 46.72 seconds (5566.72 seconds total)