Starting phenix.real_space_refine on Sat May 11 18:38:26 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9ayf_43990/05_2024/9ayf_43990_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9ayf_43990/05_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_43990/05_2024/9ayf_43990.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9ayf_43990/05_2024/9ayf_43990.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9ayf_43990/05_2024/9ayf_43990_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9ayf_43990/05_2024/9ayf_43990_updated.pdb" } 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: 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5322/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: 10.38, per 1000 atoms: 0.53 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: 7.58 Conformation dependent library (CDL) restraints added in 3.6 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... running ksdssp... Secondary structure from input PDB file: 69 helices and 25 sheets defined 36.0% alpha, 16.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 4.43 Creating SS restraints... Processing helix chain 'Q' and resid 65 through 83 Processing helix chain 'Q' and resid 104 through 114 Processing helix chain 'Q' and resid 116 through 123 Processing helix chain 'Q' and resid 147 through 158 Processing helix chain 'Q' and resid 172 through 175 Processing helix chain 'Q' and resid 191 through 203 Processing helix chain 'Q' and resid 219 through 232 Processing helix chain 'Q' and resid 249 through 260 Processing helix chain 'Q' and resid 273 through 286 Proline residue: Q 278 - end of helix Processing helix chain 'Q' and resid 308 through 314 removed outlier: 4.575A pdb=" N HIS Q 312 " --> pdb=" O GLN Q 309 " (cutoff:3.500A) Processing helix chain 'Q' and resid 330 through 336 Processing helix chain 'Q' and resid 348 through 356 Processing helix chain 'Q' and resid 417 through 435 Processing helix chain 'Q' and resid 445 through 447 No H-bonds generated for 'chain 'Q' and resid 445 through 447' Processing helix chain 'Q' and resid 457 through 465 Processing helix chain 'Q' and resid 525 through 527 No H-bonds generated for 'chain 'Q' and resid 525 through 527' Processing helix chain 'Q' and resid 530 through 532 No H-bonds generated for 'chain 'Q' and resid 530 through 532' Processing helix chain 'Q' and resid 611 through 636 Processing helix chain 'Q' and resid 641 through 645 Processing helix chain 'Q' and resid 648 through 668 removed outlier: 3.904A pdb=" N SER Q 665 " --> pdb=" O CYS Q 661 " (cutoff:3.500A) removed outlier: 4.740A pdb=" N LEU Q 666 " --> pdb=" O PHE Q 662 " (cutoff:3.500A) removed outlier: 4.788A pdb=" N PHE Q 667 " --> pdb=" O SER Q 663 " (cutoff:3.500A) removed outlier: 5.018A pdb=" N PHE Q 668 " --> pdb=" O SER Q 664 " (cutoff:3.500A) Processing helix chain 'Q' and resid 674 through 697 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 745 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 770 through 793 Processing helix chain 'Q' and resid 799 through 827 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 831 through 853 removed outlier: 4.506A pdb=" N ILE Q 841 " --> pdb=" O VAL Q 838 " (cutoff:3.500A) Processing helix chain 'Q' and resid 855 through 860 Processing helix chain 'R' and resid 65 through 83 Processing helix chain 'R' and resid 104 through 114 Processing helix chain 'R' and resid 116 through 123 Processing helix chain 'R' and resid 147 through 158 removed outlier: 3.746A pdb=" N LEU R 156 " --> pdb=" O ALA R 152 " (cutoff:3.500A) Processing helix chain 'R' and resid 173 through 175 No H-bonds generated for 'chain 'R' and resid 173 through 175' Processing helix chain 'R' and resid 191 through 203 Processing helix chain 'R' and resid 219 through 232 Processing helix chain 'R' and resid 249 through 261 Processing helix chain 'R' and resid 273 through 286 Proline residue: R 278 - end of helix Processing helix chain 'R' and resid 308 through 314 removed outlier: 5.627A pdb=" N HIS R 312 " --> pdb=" O GLN R 309 " (cutoff:3.500A) Processing helix chain 'R' and resid 330 through 336 Processing helix chain 'R' and resid 348 through 356 Processing helix chain 'R' and resid 416 through 435 Processing helix chain 'R' and resid 445 through 447 No H-bonds generated for 'chain 'R' and resid 445 through 447' Processing helix chain 'R' and resid 457 through 465 Processing helix chain 'R' and resid 525 through 527 No H-bonds generated for 'chain 'R' and resid 525 through 527' Processing helix chain 'R' and resid 611 through 636 Processing helix chain 'R' and resid 641 through 645 Processing helix chain 'R' and resid 648 through 668 removed outlier: 3.773A pdb=" N SER R 665 " --> pdb=" O CYS R 661 " (cutoff:3.500A) removed outlier: 4.310A pdb=" N LEU R 666 " --> pdb=" O PHE R 662 " (cutoff:3.500A) removed outlier: 4.369A pdb=" N PHE R 667 " --> pdb=" O SER R 663 " (cutoff:3.500A) removed outlier: 4.658A pdb=" N PHE R 668 " --> pdb=" O SER R 664 " (cutoff:3.500A) Processing helix chain 'R' and resid 674 through 707 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) Processing helix chain 'R' and resid 723 through 745 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 770 through 794 removed outlier: 3.597A pdb=" N SER R 794 " --> pdb=" O PHE R 790 " (cutoff:3.500A) Processing helix chain 'R' and resid 799 through 801 No H-bonds generated for 'chain 'R' and resid 799 through 801' Processing helix chain 'R' and resid 804 through 826 Proline residue: R 823 - end of helix Processing helix chain 'R' and resid 831 through 861 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 864 through 866 No H-bonds generated for 'chain 'R' and resid 864 through 866' Processing helix chain 'R' and resid 869 through 876 Processing helix chain 'H' and resid 49 through 51 No H-bonds generated for 'chain 'H' and resid 49 through 51' 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 108 through 110 No H-bonds generated for 'chain 'H' and resid 108 through 110' Processing helix chain 'A' and resid 7 through 31 Processing helix chain 'A' and resid 46 through 48 No H-bonds generated for 'chain 'A' and resid 46 through 48' Processing helix chain 'A' and resid 93 through 95 No H-bonds generated for 'chain 'A' and resid 93 through 95' Processing helix chain 'A' and resid 97 through 100 Processing helix chain 'A' and resid 115 through 129 Processing helix chain 'A' and resid 146 through 155 Processing helix chain 'A' and resid 158 through 160 No H-bonds generated for 'chain 'A' and resid 158 through 160' Processing helix chain 'A' and resid 171 through 184 Processing helix chain 'A' and resid 206 through 226 Processing helix chain 'B' and resid 4 through 24 Processing helix chain 'B' and resid 30 through 36 removed outlier: 5.123A pdb=" N ASN B 36 " --> pdb=" O GLN B 32 " (cutoff:3.500A) Processing helix chain 'G' and resid 9 through 23 Processing helix chain 'G' and resid 30 through 43 Processing sheet with id= A, 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: 7.137A pdb=" N GLY Q 35 " --> pdb=" O ILE Q 139 " (cutoff:3.500A) removed outlier: 4.826A pdb=" N VAL Q 141 " --> pdb=" O GLY Q 35 " (cutoff:3.500A) removed outlier: 7.263A pdb=" N LEU Q 37 " --> pdb=" O VAL Q 141 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'Q' and resid 240 through 243 removed outlier: 9.551A pdb=" N GLU Q 241 " --> pdb=" O VAL Q 209 " (cutoff:3.500A) removed outlier: 6.987A pdb=" N THR Q 211 " --> pdb=" O GLU Q 241 " (cutoff:3.500A) removed outlier: 8.385A pdb=" N ILE Q 243 " --> pdb=" O THR Q 211 " (cutoff:3.500A) removed outlier: 6.740A pdb=" N ALA Q 213 " --> pdb=" O ILE Q 243 " (cutoff:3.500A) removed outlier: 6.558A pdb=" N VAL Q 266 " --> pdb=" O GLY Q 210 " (cutoff:3.500A) removed outlier: 7.975A pdb=" N ILE Q 212 " --> pdb=" O VAL Q 266 " (cutoff:3.500A) removed outlier: 6.061A pdb=" N VAL Q 268 " --> pdb=" O ILE Q 212 " (cutoff:3.500A) removed outlier: 8.096A pdb=" N ALA Q 214 " --> pdb=" O VAL Q 268 " (cutoff:3.500A) removed outlier: 7.887A pdb=" N PHE Q 270 " --> pdb=" O ALA Q 214 " (cutoff:3.500A) removed outlier: 6.276A pdb=" N ILE Q 292 " --> pdb=" O ILE Q 267 " (cutoff:3.500A) removed outlier: 7.318A pdb=" N VAL Q 269 " --> pdb=" O ILE Q 292 " (cutoff:3.500A) removed outlier: 6.315A pdb=" N LEU Q 294 " --> pdb=" O VAL Q 269 " (cutoff:3.500A) No H-bonds generated for sheet with id= B Processing sheet with id= C, first strand: chain 'Q' and resid 318 through 321 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= D, first strand: chain 'Q' and resid 468 through 470 Processing sheet with id= E, first strand: chain 'Q' and resid 550 through 552 Processing sheet with id= F, first strand: chain 'Q' and resid 589 through 591 Processing sheet with id= G, first strand: chain 'Q' and resid 602 through 604 Processing sheet with id= H, 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: 7.429A pdb=" N GLY R 35 " --> pdb=" O ILE R 139 " (cutoff:3.500A) removed outlier: 4.547A pdb=" N VAL R 141 " --> pdb=" O GLY R 35 " (cutoff:3.500A) removed outlier: 7.238A pdb=" N LEU R 37 " --> pdb=" O VAL R 141 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'R' and resid 240 through 243 removed outlier: 9.482A pdb=" N GLU R 241 " --> pdb=" O VAL R 209 " (cutoff:3.500A) removed outlier: 6.879A pdb=" N THR R 211 " --> pdb=" O GLU R 241 " (cutoff:3.500A) removed outlier: 8.028A pdb=" N ILE R 243 " --> pdb=" O THR R 211 " (cutoff:3.500A) removed outlier: 6.231A pdb=" N ALA R 213 " --> pdb=" O ILE R 243 " (cutoff:3.500A) removed outlier: 6.545A pdb=" N VAL R 266 " --> pdb=" O GLY R 210 " (cutoff:3.500A) removed outlier: 7.894A pdb=" N ILE R 212 " --> pdb=" O VAL R 266 " (cutoff:3.500A) removed outlier: 6.104A pdb=" N VAL R 268 " --> pdb=" O ILE R 212 " (cutoff:3.500A) removed outlier: 8.130A pdb=" N ALA R 214 " --> pdb=" O VAL R 268 " (cutoff:3.500A) removed outlier: 7.708A pdb=" N PHE R 270 " --> pdb=" O ALA R 214 " (cutoff:3.500A) removed outlier: 6.351A pdb=" N ILE R 292 " --> pdb=" O ILE R 267 " (cutoff:3.500A) removed outlier: 7.469A pdb=" N VAL R 269 " --> pdb=" O ILE R 292 " (cutoff:3.500A) removed outlier: 6.475A pdb=" N LEU R 294 " --> pdb=" O VAL R 269 " (cutoff:3.500A) No H-bonds generated for sheet with id= I Processing sheet with id= J, first strand: chain 'R' and resid 318 through 321 removed outlier: 5.962A pdb=" N ASN R 493 " --> pdb=" O GLU R 507 " (cutoff:3.500A) removed outlier: 5.392A pdb=" N GLU R 507 " --> pdb=" O ASN R 493 " (cutoff:3.500A) removed outlier: 7.033A pdb=" N HIS R 495 " --> pdb=" O PHE R 505 " (cutoff:3.500A) removed outlier: 5.611A pdb=" N PHE R 505 " --> pdb=" O HIS R 495 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'R' and resid 550 through 554 Processing sheet with id= L, first strand: chain 'R' and resid 589 through 591 Processing sheet with id= M, first strand: chain 'R' and resid 602 through 604 Processing sheet with id= N, first strand: chain 'H' and resid 23 through 27 Processing sheet with id= O, first strand: chain 'H' and resid 30 through 32 removed outlier: 3.595A pdb=" N VAL H 32 " --> pdb=" O THR H 138 " (cutoff:3.500A) removed outlier: 5.653A pdb=" N ARG H 58 " --> pdb=" O TRP H 67 " (cutoff:3.500A) removed outlier: 4.986A pdb=" N TRP H 67 " --> pdb=" O ARG H 58 " (cutoff:3.500A) removed outlier: 7.111A pdb=" N ALA H 60 " --> pdb=" O LEU H 65 " (cutoff:3.500A) removed outlier: 7.029A pdb=" N LEU H 65 " --> pdb=" O ALA H 60 " (cutoff:3.500A) Processing sheet with id= P, first strand: chain 'H' and resid 166 through 168 removed outlier: 6.870A pdb=" N LYS H 264 " --> pdb=" O VAL H 167 " (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= Q, first strand: chain 'H' and resid 175 through 180 Processing sheet with id= R, first strand: chain 'A' and resid 195 through 198 removed outlier: 3.707A pdb=" N ALA A 105 " --> pdb=" O LYS A 35 " (cutoff:3.500A) Processing sheet with id= S, 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: 3.595A pdb=" N HIS B 91 " --> pdb=" O ILE B 81 " (cutoff:3.500A) removed outlier: 6.559A pdb=" N ASP B 83 " --> pdb=" O LYS B 89 " (cutoff:3.500A) removed outlier: 5.977A pdb=" N LYS B 89 " --> pdb=" O ASP B 83 " (cutoff:3.500A) Processing sheet with id= T, 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= U, 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= V, 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= W, first strand: chain 'B' and resid 229 through 234 removed outlier: 6.985A pdb=" N GLY B 244 " --> pdb=" O ASN B 230 " (cutoff:3.500A) removed outlier: 4.688A pdb=" N ILE B 232 " --> pdb=" O ALA B 242 " (cutoff:3.500A) removed outlier: 6.905A pdb=" N ALA B 242 " --> pdb=" O ILE B 232 " (cutoff:3.500A) removed outlier: 5.202A pdb=" N PHE B 234 " --> pdb=" O ALA B 240 " (cutoff:3.500A) removed outlier: 7.276A pdb=" N ALA B 240 " --> pdb=" O PHE B 234 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N ARG B 251 " --> pdb=" O THR B 243 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N MET B 262 " --> pdb=" O LEU B 252 " (cutoff:3.500A) removed outlier: 6.046A pdb=" N ASP B 254 " --> pdb=" O GLU B 260 " (cutoff:3.500A) removed outlier: 5.855A pdb=" N GLU B 260 " --> pdb=" O ASP B 254 " (cutoff:3.500A) Processing sheet with id= X, first strand: chain 'B' and resid 276 through 278 removed outlier: 3.583A pdb=" N CYS B 294 " --> pdb=" O LEU B 308 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N GLY B 306 " --> pdb=" O VAL B 296 " (cutoff:3.500A) removed outlier: 6.640A pdb=" N ASP B 298 " --> pdb=" O ARG B 304 " (cutoff:3.500A) removed outlier: 6.751A pdb=" N ARG B 304 " --> pdb=" O ASP B 298 " (cutoff:3.500A) Processing sheet with id= Y, first strand: chain 'B' and resid 47 through 51 removed outlier: 6.755A pdb=" N ILE B 338 " --> pdb=" O ARG B 48 " (cutoff:3.500A) removed outlier: 4.656A pdb=" N THR B 50 " --> pdb=" O LEU B 336 " (cutoff:3.500A) removed outlier: 6.832A pdb=" N LEU B 336 " --> pdb=" O THR B 50 " (cutoff:3.500A) removed outlier: 3.872A pdb=" N PHE B 335 " --> pdb=" O SER B 331 " (cutoff:3.500A) 783 hydrogen bonds defined for protein. 2208 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: 7.05 Time building geometry restraints manager: 8.32 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: 1202 2.73 - 3.27: 19008 3.27 - 3.82: 31528 3.82 - 4.36: 38822 4.36 - 4.90: 66588 Nonbonded interactions: 157148 Sorted by model distance: nonbonded pdb=" O ARG R 795 " pdb=" OAS AV0 R1010 " model vdw 2.191 2.440 nonbonded pdb=" O PHE Q 351 " pdb=" OG1 THR Q 355 " model vdw 2.228 2.440 nonbonded pdb=" NE2 GLN R 117 " pdb=" O ILE R 135 " model vdw 2.229 2.520 nonbonded pdb=" O SER R 171 " pdb=" NH2 ARG R 185 " model vdw 2.302 2.520 nonbonded pdb=" ND2 ASN B 340 " pdb=" OD1 ASN G 59 " model vdw 2.323 2.520 ... (remaining 157143 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain '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: 0.000 Normalize map: mean=0, sd=1: 7.760 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.010 Extract box with map and model: 28.000 Check model and map are aligned: 0.150 Set scattering table: 0.160 Process input model: 53.230 Find NCS groups from input model: 1.060 Set up NCS constraints: 0.130 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:3.020 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 93.540 ------------------------------------------------------------------------------- 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= 0.273 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 : 2.022 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: 0.3508 time to fit residues: 190.1171 Evaluate side-chains 342 residues out of total 2105 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 342 time to evaluate : 2.139 ------------------------------------------------------------------------------- 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: 7.9990 chunk 182 optimal weight: 1.9990 chunk 101 optimal weight: 0.6980 chunk 62 optimal weight: 0.5980 chunk 123 optimal weight: 1.9990 chunk 97 optimal weight: 0.9990 chunk 188 optimal weight: 0.0470 chunk 73 optimal weight: 0.8980 chunk 114 optimal weight: 0.6980 chunk 140 optimal weight: 0.6980 chunk 218 optimal weight: 0.6980 overall best weight: 0.5478 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Q 647 ASN Q 724 GLN R 253 GLN ** R 338 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** R 493 ASN R 583 ASN H 59 GLN A 73 HIS A 131 ASN ** B 155 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7497 moved from start: 0.0899 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 20080 Z= 0.228 Angle : 0.538 9.008 27209 Z= 0.283 Chirality : 0.042 0.202 3069 Planarity : 0.004 0.073 3428 Dihedral : 6.937 96.601 3069 Min Nonbonded Distance : 2.151 Molprobity Statistics. All-atom Clashscore : 5.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.44 % Favored : 96.56 % Rotamer: Outliers : 3.33 % Allowed : 14.25 % Favored : 82.42 % 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: 0.31 (0.17), residues: 2413 helix: 1.53 (0.17), residues: 900 sheet: -0.23 (0.23), residues: 509 loop : -0.74 (0.20), residues: 1004 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP R 719 HIS 0.005 0.001 HIS Q 312 PHE 0.027 0.002 PHE R 637 TYR 0.016 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 421 residues out of total 2105 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 70 poor density : 351 time to evaluate : 2.251 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: Q 624 ILE cc_start: 0.8394 (OUTLIER) cc_final: 0.8152 (mp) REVERT: Q 728 VAL cc_start: 0.7659 (p) cc_final: 0.7383 (p) REVERT: R 185 ARG cc_start: 0.8324 (OUTLIER) cc_final: 0.7843 (ptp-170) REVERT: R 284 VAL cc_start: 0.8339 (OUTLIER) cc_final: 0.8101 (p) REVERT: R 398 ASP cc_start: 0.7540 (OUTLIER) cc_final: 0.7190 (p0) REVERT: R 481 GLU cc_start: 0.6765 (pm20) cc_final: 0.6515 (pm20) REVERT: R 637 PHE cc_start: 0.7722 (m-80) cc_final: 0.7382 (m-80) REVERT: A 20 ASP cc_start: 0.7754 (m-30) cc_final: 0.7432 (m-30) REVERT: A 120 GLU cc_start: 0.5691 (OUTLIER) cc_final: 0.5370 (pm20) REVERT: B 303 ASP cc_start: 0.7719 (OUTLIER) cc_final: 0.7454 (t0) outliers start: 70 outliers final: 44 residues processed: 396 average time/residue: 0.3519 time to fit residues: 209.6527 Evaluate side-chains 398 residues out of total 2105 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 348 time to evaluate : 2.033 ------------------------------------------------------------------------------- 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 436 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 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 764 THR Chi-restraints excluded: chain Q residue 834 SER Chi-restraints excluded: chain Q residue 836 VAL Chi-restraints excluded: chain Q residue 857 ILE 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 398 ASP Chi-restraints excluded: chain R residue 485 LEU Chi-restraints excluded: chain R residue 577 THR Chi-restraints excluded: chain R residue 588 ASP Chi-restraints excluded: chain R residue 592 ASN Chi-restraints excluded: chain R residue 761 ILE Chi-restraints excluded: chain R residue 800 ASN 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 26 GLU Chi-restraints excluded: chain H residue 41 SER Chi-restraints excluded: chain H residue 117 VAL Chi-restraints excluded: chain H residue 129 ASP Chi-restraints excluded: chain H residue 243 ASP 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 100 VAL 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 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=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 241 random chunks: chunk 121 optimal weight: 0.6980 chunk 67 optimal weight: 2.9990 chunk 182 optimal weight: 1.9990 chunk 149 optimal weight: 1.9990 chunk 60 optimal weight: 0.9990 chunk 219 optimal weight: 1.9990 chunk 236 optimal weight: 10.0000 chunk 195 optimal weight: 4.9990 chunk 217 optimal weight: 1.9990 chunk 74 optimal weight: 0.6980 chunk 175 optimal weight: 0.9980 overall best weight: 1.0784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Q 647 ASN Q 724 GLN H 59 GLN H 133 GLN A 131 ASN B 155 ASN B 259 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7558 moved from start: 0.1473 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.053 20080 Z= 0.392 Angle : 0.624 8.613 27209 Z= 0.327 Chirality : 0.045 0.175 3069 Planarity : 0.005 0.055 3428 Dihedral : 6.930 96.578 3069 Min Nonbonded Distance : 2.119 Molprobity Statistics. All-atom Clashscore : 6.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.81 % Favored : 96.19 % Rotamer: Outliers : 4.37 % Allowed : 15.30 % Favored : 80.33 % 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: 0.01 (0.17), residues: 2413 helix: 1.27 (0.17), residues: 894 sheet: -0.29 (0.23), residues: 503 loop : -0.92 (0.19), residues: 1016 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP R 719 HIS 0.009 0.002 HIS R 338 PHE 0.029 0.002 PHE R 814 TYR 0.017 0.002 TYR Q 63 ARG 0.006 0.001 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 442 residues out of total 2105 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 92 poor density : 350 time to evaluate : 2.092 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: Q 624 ILE cc_start: 0.8327 (OUTLIER) cc_final: 0.8082 (mp) REVERT: Q 728 VAL cc_start: 0.7718 (p) cc_final: 0.7428 (p) REVERT: R 185 ARG cc_start: 0.8342 (OUTLIER) cc_final: 0.7072 (ptp90) REVERT: R 398 ASP cc_start: 0.7567 (OUTLIER) cc_final: 0.7130 (p0) REVERT: R 637 PHE cc_start: 0.7811 (m-80) cc_final: 0.7596 (m-80) REVERT: A 118 MET cc_start: 0.6174 (tmm) cc_final: 0.5929 (tmm) REVERT: A 120 GLU cc_start: 0.5750 (OUTLIER) cc_final: 0.5453 (pm20) REVERT: A 136 ASP cc_start: 0.7521 (t0) cc_final: 0.7128 (t0) REVERT: B 87 THR cc_start: 0.8974 (OUTLIER) cc_final: 0.8658 (m) REVERT: B 234 PHE cc_start: 0.8183 (OUTLIER) cc_final: 0.7414 (t80) REVERT: B 303 ASP cc_start: 0.7860 (OUTLIER) cc_final: 0.7587 (t0) outliers start: 92 outliers final: 65 residues processed: 403 average time/residue: 0.3561 time to fit residues: 214.0729 Evaluate side-chains 412 residues out of total 2105 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 72 poor density : 340 time to evaluate : 2.274 ------------------------------------------------------------------------------- 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 412 THR Chi-restraints excluded: chain Q residue 436 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 676 THR 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 764 THR Chi-restraints excluded: chain Q residue 834 SER 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 185 ARG Chi-restraints excluded: chain R residue 284 VAL Chi-restraints excluded: chain R residue 398 ASP 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 577 THR Chi-restraints excluded: chain R residue 588 ASP Chi-restraints excluded: chain R residue 592 ASN Chi-restraints excluded: chain R residue 639 ASN Chi-restraints excluded: chain R residue 646 THR Chi-restraints excluded: chain R residue 690 LEU 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 800 ASN 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 26 GLU Chi-restraints excluded: chain H residue 117 VAL Chi-restraints excluded: chain H residue 129 ASP Chi-restraints excluded: chain H residue 161 THR Chi-restraints excluded: chain H residue 175 VAL Chi-restraints excluded: chain H residue 198 LEU Chi-restraints excluded: chain H residue 212 MET Chi-restraints excluded: chain H residue 243 ASP 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 87 THR 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 161 SER 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 292 PHE 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=4.00 ------------------------------------------------------------------------------- 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: 0.6980 chunk 24 optimal weight: 0.9990 chunk 104 optimal weight: 0.5980 chunk 147 optimal weight: 1.9990 chunk 220 optimal weight: 1.9990 chunk 232 optimal weight: 1.9990 chunk 114 optimal weight: 0.5980 chunk 208 optimal weight: 1.9990 chunk 62 optimal weight: 0.9990 overall best weight: 0.7382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Q 400 ASN Q 594 ASN B 155 ASN B 259 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7542 moved from start: 0.1560 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 20080 Z= 0.272 Angle : 0.551 8.397 27209 Z= 0.291 Chirality : 0.043 0.161 3069 Planarity : 0.004 0.051 3428 Dihedral : 6.625 95.669 3069 Min Nonbonded Distance : 2.132 Molprobity Statistics. All-atom Clashscore : 6.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.52 % Favored : 96.48 % Rotamer: Outliers : 4.51 % Allowed : 16.72 % Favored : 78.76 % 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: 0.08 (0.17), residues: 2413 helix: 1.32 (0.17), residues: 900 sheet: -0.26 (0.23), residues: 507 loop : -0.90 (0.19), residues: 1006 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP R 719 HIS 0.010 0.001 HIS R 338 PHE 0.022 0.002 PHE R 814 TYR 0.017 0.002 TYR R 435 ARG 0.004 0.000 ARG B 96 *********************** 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 438 residues out of total 2105 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 95 poor density : 343 time to evaluate : 2.156 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: Q 624 ILE cc_start: 0.8386 (OUTLIER) cc_final: 0.8127 (mp) REVERT: Q 728 VAL cc_start: 0.7689 (p) cc_final: 0.7394 (p) REVERT: R 185 ARG cc_start: 0.8341 (OUTLIER) cc_final: 0.7960 (ptp-170) REVERT: R 398 ASP cc_start: 0.7569 (OUTLIER) cc_final: 0.7112 (p0) REVERT: R 637 PHE cc_start: 0.7784 (m-80) cc_final: 0.7528 (m-80) REVERT: R 730 LEU cc_start: 0.7548 (OUTLIER) cc_final: 0.7005 (mp) REVERT: R 745 THR cc_start: 0.8569 (t) cc_final: 0.8344 (t) REVERT: A 120 GLU cc_start: 0.5699 (OUTLIER) cc_final: 0.5398 (pm20) REVERT: A 136 ASP cc_start: 0.7502 (t0) cc_final: 0.7128 (t0) REVERT: B 234 PHE cc_start: 0.8200 (OUTLIER) cc_final: 0.7432 (t80) REVERT: B 303 ASP cc_start: 0.7848 (OUTLIER) cc_final: 0.7628 (t0) outliers start: 95 outliers final: 73 residues processed: 404 average time/residue: 0.3490 time to fit residues: 210.7194 Evaluate side-chains 421 residues out of total 2105 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 80 poor density : 341 time to evaluate : 2.309 ------------------------------------------------------------------------------- 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 263 THR Chi-restraints excluded: chain Q residue 360 LEU Chi-restraints excluded: chain Q residue 436 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 617 THR Chi-restraints excluded: chain Q residue 624 ILE Chi-restraints excluded: chain Q residue 629 PHE 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 743 LEU Chi-restraints excluded: chain Q residue 764 THR Chi-restraints excluded: chain Q residue 834 SER Chi-restraints excluded: chain Q residue 836 VAL Chi-restraints excluded: chain Q residue 857 ILE 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 262 SER Chi-restraints excluded: chain R residue 284 VAL Chi-restraints excluded: chain R residue 398 ASP 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 570 ASP Chi-restraints excluded: chain R residue 577 THR Chi-restraints excluded: chain R residue 588 ASP 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 639 ASN 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 730 LEU Chi-restraints excluded: chain R residue 761 ILE Chi-restraints excluded: chain R residue 800 ASN Chi-restraints excluded: chain R residue 812 LEU Chi-restraints excluded: chain R residue 861 LEU Chi-restraints excluded: chain H residue 41 SER Chi-restraints excluded: chain H residue 117 VAL Chi-restraints excluded: chain H residue 129 ASP 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 212 MET Chi-restraints excluded: chain H residue 232 PHE Chi-restraints excluded: chain H residue 239 LEU Chi-restraints excluded: chain H residue 243 ASP 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 97 SER 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 270 ILE Chi-restraints excluded: chain B residue 292 PHE 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 241 random chunks: chunk 194 optimal weight: 0.6980 chunk 132 optimal weight: 0.3980 chunk 3 optimal weight: 1.9990 chunk 173 optimal weight: 0.9990 chunk 96 optimal weight: 1.9990 chunk 198 optimal weight: 0.4980 chunk 161 optimal weight: 0.8980 chunk 0 optimal weight: 1.9990 chunk 118 optimal weight: 0.9990 chunk 209 optimal weight: 0.6980 chunk 58 optimal weight: 1.9990 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Q 594 ASN ** R 338 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 259 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7538 moved from start: 0.1640 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= 0.247 Angle : 0.534 8.276 27209 Z= 0.282 Chirality : 0.042 0.226 3069 Planarity : 0.004 0.052 3428 Dihedral : 6.433 95.213 3069 Min Nonbonded Distance : 2.143 Molprobity Statistics. All-atom Clashscore : 5.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.36 % Favored : 96.64 % Rotamer: Outliers : 4.70 % Allowed : 17.29 % Favored : 78.00 % 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: 0.15 (0.17), residues: 2413 helix: 1.40 (0.17), residues: 900 sheet: -0.25 (0.23), residues: 509 loop : -0.86 (0.19), residues: 1004 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP R 719 HIS 0.004 0.001 HIS H 55 PHE 0.021 0.002 PHE R 814 TYR 0.017 0.001 TYR R 435 ARG 0.007 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 437 residues out of total 2105 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 99 poor density : 338 time to evaluate : 2.051 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: Q 624 ILE cc_start: 0.8370 (OUTLIER) cc_final: 0.8093 (mp) REVERT: Q 728 VAL cc_start: 0.7701 (p) cc_final: 0.7393 (p) REVERT: R 185 ARG cc_start: 0.8349 (OUTLIER) cc_final: 0.7912 (ptp-170) REVERT: R 398 ASP cc_start: 0.7566 (OUTLIER) cc_final: 0.7120 (p0) REVERT: R 730 LEU cc_start: 0.7524 (OUTLIER) cc_final: 0.6987 (mp) REVERT: A 120 GLU cc_start: 0.5714 (OUTLIER) cc_final: 0.5432 (pm20) REVERT: A 136 ASP cc_start: 0.7516 (t0) cc_final: 0.7151 (t0) REVERT: B 87 THR cc_start: 0.8892 (OUTLIER) cc_final: 0.8574 (m) REVERT: B 234 PHE cc_start: 0.8191 (OUTLIER) cc_final: 0.7441 (t80) REVERT: B 303 ASP cc_start: 0.7782 (OUTLIER) cc_final: 0.7547 (t0) outliers start: 99 outliers final: 76 residues processed: 404 average time/residue: 0.3514 time to fit residues: 212.7638 Evaluate side-chains 417 residues out of total 2105 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 84 poor density : 333 time to evaluate : 2.170 ------------------------------------------------------------------------------- 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 401 ILE Chi-restraints excluded: chain Q residue 412 THR Chi-restraints excluded: chain Q residue 436 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 617 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 738 ILE Chi-restraints excluded: chain Q residue 743 LEU Chi-restraints excluded: chain Q residue 764 THR Chi-restraints excluded: chain Q residue 834 SER Chi-restraints excluded: chain Q residue 836 VAL Chi-restraints excluded: chain Q residue 857 ILE 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 262 SER Chi-restraints excluded: chain R residue 284 VAL Chi-restraints excluded: chain R residue 398 ASP 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 570 ASP Chi-restraints excluded: chain R residue 577 THR Chi-restraints excluded: chain R residue 588 ASP 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 639 ASN 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 730 LEU Chi-restraints excluded: chain R residue 761 ILE Chi-restraints excluded: chain R residue 800 ASN 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 82 ASP Chi-restraints excluded: chain H residue 117 VAL Chi-restraints excluded: chain H residue 129 ASP 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 212 MET Chi-restraints excluded: chain H residue 230 THR Chi-restraints excluded: chain H residue 243 ASP 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 40 VAL Chi-restraints excluded: chain B residue 79 LEU Chi-restraints excluded: chain B residue 87 THR 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 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 Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 241 random chunks: chunk 78 optimal weight: 0.6980 chunk 209 optimal weight: 0.1980 chunk 46 optimal weight: 0.0000 chunk 136 optimal weight: 0.5980 chunk 57 optimal weight: 0.8980 chunk 233 optimal weight: 1.9990 chunk 193 optimal weight: 2.9990 chunk 107 optimal weight: 1.9990 chunk 19 optimal weight: 0.9990 chunk 77 optimal weight: 0.8980 chunk 122 optimal weight: 2.9990 overall best weight: 0.4784 ------------------------------------------------------------------------------- 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** B 259 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7525 moved from start: 0.1703 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 20080 Z= 0.198 Angle : 0.506 7.986 27209 Z= 0.269 Chirality : 0.041 0.187 3069 Planarity : 0.004 0.050 3428 Dihedral : 6.261 94.342 3069 Min Nonbonded Distance : 2.162 Molprobity Statistics. All-atom Clashscore : 6.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.48 % Favored : 96.52 % Rotamer: Outliers : 4.47 % Allowed : 17.67 % Favored : 77.86 % 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: 0.27 (0.17), residues: 2413 helix: 1.50 (0.17), residues: 904 sheet: -0.19 (0.23), residues: 508 loop : -0.79 (0.19), residues: 1001 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.001 TRP R 719 HIS 0.004 0.001 HIS Q 312 PHE 0.018 0.001 PHE R 814 TYR 0.016 0.001 TYR R 435 ARG 0.005 0.000 ARG B 96 *********************** 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 440 residues out of total 2105 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 94 poor density : 346 time to evaluate : 2.266 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: 0.8336 (OUTLIER) cc_final: 0.8036 (mp) REVERT: Q 728 VAL cc_start: 0.7720 (p) cc_final: 0.7413 (p) REVERT: Q 834 SER cc_start: 0.8502 (OUTLIER) cc_final: 0.8267 (p) REVERT: R 185 ARG cc_start: 0.8337 (OUTLIER) cc_final: 0.7888 (ptp-170) REVERT: R 398 ASP cc_start: 0.7536 (OUTLIER) cc_final: 0.7111 (p0) REVERT: R 730 LEU cc_start: 0.7488 (OUTLIER) cc_final: 0.6960 (mp) REVERT: A 76 PHE cc_start: 0.7166 (t80) cc_final: 0.6745 (t80) REVERT: A 120 GLU cc_start: 0.5662 (OUTLIER) cc_final: 0.5366 (pm20) REVERT: A 136 ASP cc_start: 0.7512 (t0) cc_final: 0.7147 (t0) REVERT: B 87 THR cc_start: 0.8880 (OUTLIER) cc_final: 0.8547 (m) REVERT: B 234 PHE cc_start: 0.8173 (OUTLIER) cc_final: 0.7395 (t80) REVERT: B 303 ASP cc_start: 0.7750 (OUTLIER) cc_final: 0.7542 (t0) outliers start: 94 outliers final: 73 residues processed: 407 average time/residue: 0.3461 time to fit residues: 210.4078 Evaluate side-chains 420 residues out of total 2105 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 82 poor density : 338 time to evaluate : 2.088 ------------------------------------------------------------------------------- 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 263 THR Chi-restraints excluded: chain Q residue 360 LEU Chi-restraints excluded: chain Q residue 401 ILE Chi-restraints excluded: chain Q residue 412 THR Chi-restraints excluded: chain Q residue 436 THR Chi-restraints excluded: chain Q residue 443 LEU Chi-restraints excluded: chain Q residue 560 THR Chi-restraints excluded: chain Q residue 578 ASP Chi-restraints excluded: chain Q residue 617 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 758 ASP Chi-restraints excluded: chain Q residue 764 THR Chi-restraints excluded: chain Q residue 834 SER Chi-restraints excluded: chain Q residue 836 VAL Chi-restraints excluded: chain Q residue 857 ILE 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 262 SER Chi-restraints excluded: chain R residue 284 VAL Chi-restraints excluded: chain R residue 398 ASP 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 554 ILE Chi-restraints excluded: chain R residue 570 ASP Chi-restraints excluded: chain R residue 577 THR Chi-restraints excluded: chain R residue 588 ASP 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 639 ASN 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 800 ASN Chi-restraints excluded: chain R residue 812 LEU Chi-restraints excluded: chain R residue 833 VAL Chi-restraints excluded: chain H residue 117 VAL Chi-restraints excluded: chain H residue 129 ASP 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 230 THR Chi-restraints excluded: chain H residue 239 LEU Chi-restraints excluded: chain H residue 243 ASP 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 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 87 THR Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 181 THR Chi-restraints excluded: chain B residue 198 LEU Chi-restraints excluded: chain B residue 200 VAL 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 241 random chunks: chunk 224 optimal weight: 0.9980 chunk 26 optimal weight: 0.5980 chunk 132 optimal weight: 0.4980 chunk 170 optimal weight: 2.9990 chunk 131 optimal weight: 0.7980 chunk 196 optimal weight: 7.9990 chunk 130 optimal weight: 0.7980 chunk 232 optimal weight: 0.8980 chunk 145 optimal weight: 1.9990 chunk 141 optimal weight: 0.6980 chunk 107 optimal weight: 0.6980 overall best weight: 0.6580 ------------------------------------------------------------------------------- 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** H 133 GLN B 176 GLN B 259 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7539 moved from start: 0.1787 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= 0.254 Angle : 0.535 8.036 27209 Z= 0.282 Chirality : 0.042 0.161 3069 Planarity : 0.004 0.052 3428 Dihedral : 6.258 94.194 3069 Min Nonbonded Distance : 2.155 Molprobity Statistics. All-atom Clashscore : 6.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.56 % Favored : 96.44 % Rotamer: Outliers : 4.66 % Allowed : 17.86 % Favored : 77.48 % 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: 0.23 (0.17), residues: 2413 helix: 1.50 (0.17), residues: 894 sheet: -0.19 (0.23), residues: 508 loop : -0.85 (0.19), residues: 1011 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP R 719 HIS 0.004 0.001 HIS H 55 PHE 0.023 0.002 PHE R 814 TYR 0.015 0.001 TYR R 435 ARG 0.005 0.000 ARG B 96 *********************** 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 439 residues out of total 2105 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 98 poor density : 341 time to evaluate : 1.975 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: Q 624 ILE cc_start: 0.8352 (OUTLIER) cc_final: 0.8040 (mp) REVERT: Q 728 VAL cc_start: 0.7676 (OUTLIER) cc_final: 0.7371 (p) REVERT: R 185 ARG cc_start: 0.8340 (OUTLIER) cc_final: 0.7917 (ptp-170) REVERT: R 398 ASP cc_start: 0.7559 (OUTLIER) cc_final: 0.7101 (p0) REVERT: R 730 LEU cc_start: 0.7512 (OUTLIER) cc_final: 0.6980 (mp) REVERT: R 795 ARG cc_start: 0.6557 (ptt90) cc_final: 0.6265 (ptt-90) REVERT: A 76 PHE cc_start: 0.7198 (t80) cc_final: 0.6755 (t80) REVERT: A 120 GLU cc_start: 0.5705 (OUTLIER) cc_final: 0.5421 (pm20) REVERT: A 136 ASP cc_start: 0.7516 (t0) cc_final: 0.7169 (t0) REVERT: B 87 THR cc_start: 0.8883 (OUTLIER) cc_final: 0.8558 (m) REVERT: B 234 PHE cc_start: 0.8192 (OUTLIER) cc_final: 0.7373 (t80) outliers start: 98 outliers final: 81 residues processed: 402 average time/residue: 0.3500 time to fit residues: 209.4798 Evaluate side-chains 426 residues out of total 2105 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 89 poor density : 337 time to evaluate : 2.084 ------------------------------------------------------------------------------- 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 401 ILE Chi-restraints excluded: chain Q residue 412 THR Chi-restraints excluded: chain Q residue 436 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 617 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 728 VAL Chi-restraints excluded: chain Q residue 737 VAL Chi-restraints excluded: chain Q residue 738 ILE Chi-restraints excluded: chain Q residue 758 ASP Chi-restraints excluded: chain Q residue 764 THR Chi-restraints excluded: chain Q residue 834 SER 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 185 ARG Chi-restraints excluded: chain R residue 244 SER Chi-restraints excluded: chain R residue 262 SER Chi-restraints excluded: chain R residue 284 VAL Chi-restraints excluded: chain R residue 398 ASP 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 570 ASP Chi-restraints excluded: chain R residue 577 THR Chi-restraints excluded: chain R residue 588 ASP 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 639 ASN 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 800 ASN 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 129 ASP 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 230 THR Chi-restraints excluded: chain H residue 239 LEU Chi-restraints excluded: chain H residue 243 ASP 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 128 ILE 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 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 198 LEU Chi-restraints excluded: chain B residue 200 VAL 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 241 random chunks: chunk 143 optimal weight: 2.9990 chunk 92 optimal weight: 1.9990 chunk 138 optimal weight: 0.8980 chunk 69 optimal weight: 1.9990 chunk 45 optimal weight: 0.9980 chunk 147 optimal weight: 0.8980 chunk 158 optimal weight: 0.6980 chunk 114 optimal weight: 0.9980 chunk 21 optimal weight: 0.9990 chunk 182 optimal weight: 0.2980 chunk 211 optimal weight: 0.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- 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** H 133 GLN B 259 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7547 moved from start: 0.1867 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 20080 Z= 0.283 Angle : 0.550 8.114 27209 Z= 0.290 Chirality : 0.043 0.166 3069 Planarity : 0.004 0.054 3428 Dihedral : 6.274 94.272 3069 Min Nonbonded Distance : 2.149 Molprobity Statistics. All-atom Clashscore : 5.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.69 % Favored : 96.31 % Rotamer: Outliers : 4.80 % Allowed : 17.77 % Favored : 77.43 % 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: 0.18 (0.17), residues: 2413 helix: 1.49 (0.17), residues: 886 sheet: -0.20 (0.23), residues: 508 loop : -0.89 (0.19), residues: 1019 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.002 TRP R 719 HIS 0.005 0.001 HIS H 55 PHE 0.025 0.002 PHE R 814 TYR 0.015 0.002 TYR H 115 ARG 0.004 0.000 ARG B 96 *********************** 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 442 residues out of total 2105 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 101 poor density : 341 time to evaluate : 3.112 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: Q 270 PHE cc_start: 0.8048 (OUTLIER) cc_final: 0.7773 (t80) REVERT: Q 624 ILE cc_start: 0.8345 (OUTLIER) cc_final: 0.8049 (mp) REVERT: Q 728 VAL cc_start: 0.7703 (OUTLIER) cc_final: 0.7385 (p) REVERT: R 185 ARG cc_start: 0.8347 (OUTLIER) cc_final: 0.7949 (ptp-170) REVERT: R 398 ASP cc_start: 0.7560 (OUTLIER) cc_final: 0.7117 (p0) REVERT: R 592 ASN cc_start: 0.7518 (OUTLIER) cc_final: 0.6772 (m110) REVERT: R 730 LEU cc_start: 0.7532 (OUTLIER) cc_final: 0.7011 (mp) REVERT: R 795 ARG cc_start: 0.6578 (ptt90) cc_final: 0.6272 (ptt-90) REVERT: A 120 GLU cc_start: 0.5703 (OUTLIER) cc_final: 0.5417 (pm20) REVERT: A 136 ASP cc_start: 0.7531 (t0) cc_final: 0.7117 (t0) REVERT: B 87 THR cc_start: 0.8934 (OUTLIER) cc_final: 0.8586 (m) REVERT: B 156 GLN cc_start: 0.8245 (mt0) cc_final: 0.7912 (mt0) REVERT: B 234 PHE cc_start: 0.8205 (OUTLIER) cc_final: 0.7395 (t80) outliers start: 101 outliers final: 86 residues processed: 404 average time/residue: 0.3585 time to fit residues: 217.9458 Evaluate side-chains 432 residues out of total 2105 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 96 poor density : 336 time to evaluate : 2.193 ------------------------------------------------------------------------------- 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 270 PHE 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 412 THR Chi-restraints excluded: chain Q residue 436 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 617 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 738 ILE Chi-restraints excluded: chain Q residue 743 LEU Chi-restraints excluded: chain Q residue 758 ASP Chi-restraints excluded: chain Q residue 764 THR Chi-restraints excluded: chain Q residue 834 SER 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 185 ARG Chi-restraints excluded: chain R residue 244 SER Chi-restraints excluded: chain R residue 262 SER Chi-restraints excluded: chain R residue 284 VAL Chi-restraints excluded: chain R residue 398 ASP Chi-restraints excluded: chain R residue 404 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 570 ASP Chi-restraints excluded: chain R residue 577 THR Chi-restraints excluded: chain R residue 588 ASP 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 639 ASN 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 800 ASN 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 41 SER Chi-restraints excluded: chain H residue 82 ASP Chi-restraints excluded: chain H residue 117 VAL Chi-restraints excluded: chain H residue 129 ASP 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 212 MET Chi-restraints excluded: chain H residue 230 THR Chi-restraints excluded: chain H residue 239 LEU Chi-restraints excluded: chain H residue 243 ASP 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 128 ILE Chi-restraints excluded: chain A residue 218 ILE Chi-restraints excluded: chain A residue 225 ASP Chi-restraints excluded: chain B residue 29 THR 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 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 198 LEU Chi-restraints excluded: chain B residue 200 VAL 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 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: 0.0970 chunk 203 optimal weight: 0.0060 chunk 216 optimal weight: 1.9990 chunk 130 optimal weight: 0.9980 chunk 94 optimal weight: 0.5980 chunk 169 optimal weight: 0.0980 chunk 66 optimal weight: 1.9990 chunk 195 optimal weight: 0.0770 chunk 204 optimal weight: 0.8980 chunk 215 optimal weight: 0.4980 chunk 142 optimal weight: 0.2980 overall best weight: 0.1152 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 476 GLN R 493 ASN H 133 GLN B 155 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7478 moved from start: 0.1877 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 20080 Z= 0.127 Angle : 0.462 7.045 27209 Z= 0.247 Chirality : 0.040 0.167 3069 Planarity : 0.004 0.052 3428 Dihedral : 5.931 93.065 3069 Min Nonbonded Distance : 2.201 Molprobity Statistics. All-atom Clashscore : 5.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.36 % Favored : 97.64 % Rotamer: Outliers : 2.95 % Allowed : 19.71 % Favored : 77.34 % 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: 0.51 (0.17), residues: 2413 helix: 1.75 (0.17), residues: 891 sheet: -0.01 (0.23), residues: 505 loop : -0.71 (0.19), residues: 1017 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.001 TRP R 719 HIS 0.009 0.001 HIS R 338 PHE 0.015 0.001 PHE R 522 TYR 0.013 0.001 TYR R 435 ARG 0.006 0.000 ARG B 96 *********************** 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 411 residues out of total 2105 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 62 poor density : 349 time to evaluate : 2.139 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: Q 624 ILE cc_start: 0.8275 (OUTLIER) cc_final: 0.7938 (mp) REVERT: Q 637 PHE cc_start: 0.7524 (m-80) cc_final: 0.7293 (m-80) REVERT: Q 728 VAL cc_start: 0.7648 (OUTLIER) cc_final: 0.7314 (p) REVERT: Q 735 GLN cc_start: 0.7778 (tp40) cc_final: 0.7545 (tp-100) REVERT: R 185 ARG cc_start: 0.8340 (OUTLIER) cc_final: 0.7694 (ptp-170) REVERT: R 260 GLN cc_start: 0.7075 (tt0) cc_final: 0.6861 (mt0) REVERT: R 398 ASP cc_start: 0.7575 (OUTLIER) cc_final: 0.7151 (p0) REVERT: R 592 ASN cc_start: 0.7519 (OUTLIER) cc_final: 0.6683 (m110) REVERT: R 596 THR cc_start: 0.7237 (p) cc_final: 0.7020 (p) REVERT: R 659 LEU cc_start: 0.8054 (mt) cc_final: 0.7811 (mt) REVERT: A 20 ASP cc_start: 0.7764 (m-30) cc_final: 0.7427 (m-30) REVERT: A 76 PHE cc_start: 0.7158 (t80) cc_final: 0.6752 (t80) REVERT: A 120 GLU cc_start: 0.5585 (OUTLIER) cc_final: 0.5311 (pm20) REVERT: A 136 ASP cc_start: 0.7487 (t0) cc_final: 0.7055 (t0) REVERT: B 87 THR cc_start: 0.8705 (OUTLIER) cc_final: 0.8175 (p) REVERT: B 156 GLN cc_start: 0.8180 (mt0) cc_final: 0.7850 (mt0) REVERT: B 234 PHE cc_start: 0.8121 (OUTLIER) cc_final: 0.7274 (t80) outliers start: 62 outliers final: 41 residues processed: 386 average time/residue: 0.3560 time to fit residues: 205.4030 Evaluate side-chains 392 residues out of total 2105 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 343 time to evaluate : 2.298 ------------------------------------------------------------------------------- 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 436 THR 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 723 LEU Chi-restraints excluded: chain Q residue 728 VAL Chi-restraints excluded: chain Q residue 758 ASP Chi-restraints excluded: chain Q residue 836 VAL Chi-restraints excluded: chain R residue 139 ILE Chi-restraints excluded: chain R residue 185 ARG Chi-restraints excluded: chain R residue 262 SER Chi-restraints excluded: chain R residue 284 VAL Chi-restraints excluded: chain R residue 398 ASP Chi-restraints excluded: chain R residue 404 VAL Chi-restraints excluded: chain R residue 455 VAL Chi-restraints excluded: chain R residue 470 THR Chi-restraints excluded: chain R residue 503 ILE Chi-restraints excluded: chain R residue 577 THR Chi-restraints excluded: chain R residue 582 CYS Chi-restraints excluded: chain R residue 588 ASP Chi-restraints excluded: chain R residue 592 ASN Chi-restraints excluded: chain R residue 619 PHE 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 833 VAL Chi-restraints excluded: chain H residue 83 THR Chi-restraints excluded: chain H residue 136 THR Chi-restraints excluded: chain H residue 175 VAL Chi-restraints excluded: chain H residue 179 CYS 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 218 ILE Chi-restraints excluded: chain A residue 225 ASP Chi-restraints excluded: chain B residue 40 VAL Chi-restraints excluded: chain B residue 87 THR Chi-restraints excluded: chain B residue 97 SER 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 Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 241 random chunks: chunk 228 optimal weight: 0.4980 chunk 139 optimal weight: 1.9990 chunk 108 optimal weight: 0.9980 chunk 159 optimal weight: 3.9990 chunk 240 optimal weight: 0.1980 chunk 220 optimal weight: 1.9990 chunk 191 optimal weight: 2.9990 chunk 19 optimal weight: 0.6980 chunk 147 optimal weight: 2.9990 chunk 117 optimal weight: 0.6980 chunk 151 optimal weight: 1.9990 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Q 594 ASN R 64 ASN R 493 ASN H 133 GLN B 259 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7529 moved from start: 0.1956 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 20080 Z= 0.241 Angle : 0.528 7.436 27209 Z= 0.278 Chirality : 0.042 0.170 3069 Planarity : 0.004 0.063 3428 Dihedral : 6.031 93.339 3069 Min Nonbonded Distance : 2.166 Molprobity Statistics. All-atom Clashscore : 6.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.36 % Favored : 96.64 % Rotamer: Outliers : 2.42 % Allowed : 20.62 % Favored : 76.96 % 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: 0.43 (0.17), residues: 2413 helix: 1.67 (0.17), residues: 890 sheet: -0.08 (0.23), residues: 507 loop : -0.73 (0.19), residues: 1016 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.002 TRP R 719 HIS 0.010 0.001 HIS R 338 PHE 0.024 0.001 PHE R 814 TYR 0.015 0.001 TYR R 435 ARG 0.005 0.000 ARG B 96 ********************** 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 397 residues out of total 2105 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 346 time to evaluate : 2.446 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: Q 270 PHE cc_start: 0.8021 (OUTLIER) cc_final: 0.7678 (t80) REVERT: Q 624 ILE cc_start: 0.8329 (OUTLIER) cc_final: 0.8013 (mp) REVERT: Q 728 VAL cc_start: 0.7724 (OUTLIER) cc_final: 0.7402 (p) REVERT: R 185 ARG cc_start: 0.8331 (OUTLIER) cc_final: 0.7890 (ptp-170) REVERT: R 398 ASP cc_start: 0.7597 (OUTLIER) cc_final: 0.7140 (p0) REVERT: R 592 ASN cc_start: 0.7559 (OUTLIER) cc_final: 0.6748 (m110) REVERT: A 20 ASP cc_start: 0.7793 (m-30) cc_final: 0.7468 (m-30) REVERT: A 120 GLU cc_start: 0.5666 (OUTLIER) cc_final: 0.5385 (pm20) REVERT: A 136 ASP cc_start: 0.7472 (t0) cc_final: 0.7059 (t0) REVERT: B 87 THR cc_start: 0.8916 (OUTLIER) cc_final: 0.8565 (m) REVERT: B 156 GLN cc_start: 0.8187 (mt0) cc_final: 0.7848 (mt0) REVERT: B 234 PHE cc_start: 0.8188 (OUTLIER) cc_final: 0.7404 (t80) outliers start: 51 outliers final: 40 residues processed: 379 average time/residue: 0.4016 time to fit residues: 227.0956 Evaluate side-chains 387 residues out of total 2105 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 338 time to evaluate : 2.277 ------------------------------------------------------------------------------- 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 270 PHE Chi-restraints excluded: chain Q residue 360 LEU Chi-restraints excluded: chain Q residue 436 THR 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 676 THR Chi-restraints excluded: chain Q residue 723 LEU Chi-restraints excluded: chain Q residue 728 VAL Chi-restraints excluded: chain Q residue 758 ASP Chi-restraints excluded: chain Q residue 836 VAL Chi-restraints excluded: chain R residue 139 ILE Chi-restraints excluded: chain R residue 185 ARG Chi-restraints excluded: chain R residue 284 VAL Chi-restraints excluded: chain R residue 398 ASP Chi-restraints excluded: chain R residue 404 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 503 ILE Chi-restraints excluded: chain R residue 577 THR Chi-restraints excluded: chain R residue 588 ASP Chi-restraints excluded: chain R residue 592 ASN Chi-restraints excluded: chain R residue 619 PHE 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 833 VAL Chi-restraints excluded: chain H residue 136 THR Chi-restraints excluded: chain H residue 175 VAL Chi-restraints excluded: chain H residue 179 CYS 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 218 ILE Chi-restraints excluded: chain A residue 225 ASP Chi-restraints excluded: chain B residue 40 VAL Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 87 THR Chi-restraints excluded: chain B residue 97 SER 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 Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 241 random chunks: chunk 203 optimal weight: 0.4980 chunk 58 optimal weight: 4.9990 chunk 176 optimal weight: 0.8980 chunk 28 optimal weight: 1.9990 chunk 53 optimal weight: 2.9990 chunk 191 optimal weight: 1.9990 chunk 80 optimal weight: 1.9990 chunk 196 optimal weight: 0.0670 chunk 24 optimal weight: 0.2980 chunk 35 optimal weight: 0.9980 chunk 168 optimal weight: 0.9990 overall best weight: 0.5518 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 133 GLN B 259 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3340 r_free = 0.3340 target = 0.106675 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3021 r_free = 0.3021 target = 0.088268 restraints weight = 33332.617| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3013 r_free = 0.3013 target = 0.087926 restraints weight = 32346.845| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3018 r_free = 0.3018 target = 0.088225 restraints weight = 29200.555| |-----------------------------------------------------------------------------| r_work (final): 0.3014 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7540 moved from start: 0.1976 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 20080 Z= 0.222 Angle : 0.519 7.442 27209 Z= 0.274 Chirality : 0.042 0.169 3069 Planarity : 0.004 0.059 3428 Dihedral : 6.027 93.173 3069 Min Nonbonded Distance : 2.168 Molprobity Statistics. All-atom Clashscore : 6.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.19 % Favored : 96.81 % Rotamer: Outliers : 2.76 % Allowed : 20.38 % Favored : 76.86 % 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: 0.40 (0.17), residues: 2413 helix: 1.63 (0.17), residues: 890 sheet: -0.10 (0.23), residues: 506 loop : -0.73 (0.19), residues: 1017 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.001 TRP R 719 HIS 0.010 0.001 HIS R 338 PHE 0.020 0.001 PHE R 814 TYR 0.015 0.001 TYR R 435 ARG 0.006 0.000 ARG B 96 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4866.07 seconds wall clock time: 90 minutes 43.51 seconds (5443.51 seconds total)