Starting phenix.real_space_refine on Sun Jun 30 14:19:00 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9axf_43966/06_2024/9axf_43966.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9axf_43966/06_2024/9axf_43966.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9axf_43966/06_2024/9axf_43966.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9axf_43966/06_2024/9axf_43966.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9axf_43966/06_2024/9axf_43966.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9axf_43966/06_2024/9axf_43966.pdb" } resolution = 3.5 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.002 sd= 0.043 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 7 9.91 5 P 2 5.49 5 S 123 5.16 5 Cl 2 4.86 5 C 13769 2.51 5 N 3464 2.21 5 O 3975 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "R GLU 56": "OE1" <-> "OE2" Residue "R GLU 59": "OE1" <-> "OE2" Residue "R GLU 202": "OE1" <-> "OE2" Residue "R TYR 203": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R GLU 231": "OE1" <-> "OE2" Residue "R GLU 250": "OE1" <-> "OE2" Residue "R PHE 270": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R GLU 350": "OE1" <-> "OE2" Residue "R GLU 354": "OE1" <-> "OE2" Residue "R GLU 481": "OE1" <-> "OE2" Residue "R GLU 519": "OE1" <-> "OE2" Residue "R GLU 525": "OE1" <-> "OE2" Residue "R GLU 536": "OE1" <-> "OE2" Residue "R GLU 556": "OE1" <-> "OE2" Residue "R GLU 567": "OE1" <-> "OE2" Residue "R GLU 572": "OE1" <-> "OE2" Residue "R GLU 593": "OE1" <-> "OE2" Residue "R GLU 602": "OE1" <-> "OE2" Residue "R GLU 755": "OE1" <-> "OE2" Residue "R GLU 803": "OE1" <-> "OE2" Residue "R GLU 837": "OE1" <-> "OE2" Residue "Q GLU 231": "OE1" <-> "OE2" Residue "Q GLU 354": "OE1" <-> "OE2" Residue "Q GLU 456": "OE1" <-> "OE2" Residue "Q GLU 519": "OE1" <-> "OE2" Residue "Q GLU 525": "OE1" <-> "OE2" Residue "Q GLU 536": "OE1" <-> "OE2" Residue "Q GLU 564": "OE1" <-> "OE2" Residue "Q TYR 744": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q GLU 755": "OE1" <-> "OE2" Residue "A GLU 14": "OE1" <-> "OE2" Residue "A GLU 20": "OE1" <-> "OE2" Residue "A GLU 71": "OE1" <-> "OE2" Residue "A GLU 92": "OE1" <-> "OE2" Residue "A GLU 166": "OE1" <-> "OE2" Residue "B PHE 253": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 260": "OE1" <-> "OE2" Residue "H GLU 26": "OE1" <-> "OE2" Time to flip residues: 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5370/modules/chem_data/mon_lib" Total number of atoms: 21342 Number of models: 1 Model: "" Number of chains: 15 Chain: "R" Number of atoms: 6632 Number of conformers: 1 Conformer: "" Number of residues, atoms: 832, 6632 Classifications: {'peptide': 832} Link IDs: {'CIS': 1, 'PTRANS': 32, 'TRANS': 798} Chain breaks: 1 Chain: "Q" Number of atoms: 6293 Number of conformers: 1 Conformer: "" Number of residues, atoms: 791, 6293 Classifications: {'peptide': 791} Link IDs: {'CIS': 1, 'PTRANS': 30, 'TRANS': 759} Chain breaks: 2 Chain: "A" Number of atoms: 1879 Number of conformers: 1 Conformer: "" Number of residues, atoms: 228, 1879 Classifications: {'peptide': 228} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 221} Chain breaks: 1 Chain: "B" Number of atoms: 2601 Number of conformers: 1 Conformer: "" Number of residues, atoms: 338, 2601 Classifications: {'peptide': 338} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 332} Chain: "G" Number of atoms: 433 Number of conformers: 1 Conformer: "" Number of residues, atoms: 56, 433 Classifications: {'peptide': 56} Link IDs: {'PTRANS': 4, 'TRANS': 51} Chain: "H" Number of atoms: 1795 Number of conformers: 1 Conformer: "" Number of residues, atoms: 234, 1795 Classifications: {'peptide': 234} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 223} Chain breaks: 1 Chain: "N" Number of atoms: 961 Number of conformers: 1 Conformer: "" Number of residues, atoms: 126, 961 Classifications: {'peptide': 126} Link IDs: {'PTRANS': 5, 'TRANS': 120} 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: "R" Number of atoms: 72 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 72 Unusual residues: {'NAG': 4, 'TCR': 1} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "R" Number of atoms: 287 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 287 Unusual residues: {' CA': 3, '9IG': 1, 'AV0': 1, 'CLR': 3, 'PO4': 1, 'Y01': 3} Classifications: {'undetermined': 12} Link IDs: {None: 11} Chain: "Q" Number of atoms: 72 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 72 Unusual residues: {'NAG': 4, 'TCR': 1} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "Q" Number of atoms: 205 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 205 Unusual residues: {' CA': 4, '9IG': 1, 'CLR': 5, 'PO4': 1, 'Y01': 1} Classifications: {'undetermined': 12} Link IDs: {None: 11} Time building chain proxies: 14.19, per 1000 atoms: 0.66 Number of scatterers: 21342 At special positions: 0 Unit cell: (108.876, 132.508, 245.604, 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 7 19.99 Cl 2 17.00 S 123 16.00 P 2 15.00 O 3975 8.00 N 3464 7.00 C 13769 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=22, symmetry=0 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 Q 60 " - pdb=" SG CYS Q 101 " distance=2.04 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 568 " - pdb=" SG CYS Q 582 " distance=2.03 Simple disulfide: pdb=" SG CYS Q 585 " - pdb=" SG CYS Q 598 " distance=2.03 Simple disulfide: pdb=" SG CYS Q 677 " - pdb=" SG CYS Q 765 " distance=2.03 Simple disulfide: pdb=" SG CYS H 42 " - pdb=" SG CYS H 116 " distance=2.04 Simple disulfide: pdb=" SG CYS H 179 " - pdb=" SG CYS H 249 " distance=2.03 Simple disulfide: pdb=" SG CYS N 22 " - pdb=" SG CYS N 96 " distance=2.03 Simple disulfide: pdb=" SG CYS N 99 " - pdb=" SG CYS N 107 " distance=2.03 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 R 488 " " NAG D 1 " - " ASN R 541 " " NAG E 1 " - " ASN Q 488 " " NAG F 1 " - " ASN Q 541 " " NAG Q1001 " - " ASN Q 261 " " NAG Q1002 " - " ASN Q 287 " " NAG Q1003 " - " ASN Q 468 " " NAG Q1004 " - " ASN Q 594 " " NAG R1001 " - " ASN R 261 " " NAG R1002 " - " ASN R 287 " " NAG R1003 " - " ASN R 468 " " NAG R1004 " - " ASN R 594 " Time building additional restraints: 8.48 Conformation dependent library (CDL) restraints added in 4.1 seconds 5162 Ramachandran restraints generated. 2581 Oldfield, 0 Emsley, 2581 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4878 Finding SS restraints... Secondary structure from input PDB file: 80 helices and 31 sheets defined 39.9% alpha, 19.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.40 Creating SS restraints... Processing helix chain 'R' and resid 64 through 84 Processing helix chain 'R' and resid 103 through 116 removed outlier: 3.533A pdb=" N ALA R 107 " --> pdb=" O THR R 103 " (cutoff:3.500A) Processing helix chain 'R' and resid 117 through 122 removed outlier: 3.549A pdb=" N ILE R 120 " --> pdb=" O GLN R 117 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N ASP R 121 " --> pdb=" O ASN R 118 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N SER R 122 " --> pdb=" O LYS R 119 " (cutoff:3.500A) No H-bonds generated for 'chain 'R' and resid 117 through 122' Processing helix chain 'R' and resid 146 through 160 removed outlier: 3.838A pdb=" N LEU R 156 " --> pdb=" O ALA R 152 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N PHE R 160 " --> pdb=" O LEU R 156 " (cutoff:3.500A) Processing helix chain 'R' and resid 171 through 176 removed outlier: 3.516A pdb=" N ASN R 176 " --> pdb=" O LEU R 173 " (cutoff:3.500A) Processing helix chain 'R' and resid 190 through 204 Processing helix chain 'R' and resid 218 through 233 removed outlier: 3.740A pdb=" N GLY R 222 " --> pdb=" O TYR R 218 " (cutoff:3.500A) Processing helix chain 'R' and resid 248 through 262 Processing helix chain 'R' and resid 272 through 287 Proline residue: R 278 - end of helix Processing helix chain 'R' and resid 307 through 309 No H-bonds generated for 'chain 'R' and resid 307 through 309' Processing helix chain 'R' and resid 310 through 315 Processing helix chain 'R' and resid 329 through 336 Processing helix chain 'R' and resid 347 through 357 Processing helix chain 'R' and resid 400 through 404 Processing helix chain 'R' and resid 415 through 436 Processing helix chain 'R' and resid 444 through 448 Processing helix chain 'R' and resid 451 through 455 removed outlier: 3.849A pdb=" N VAL R 455 " --> pdb=" O ILE R 452 " (cutoff:3.500A) Processing helix chain 'R' and resid 456 through 466 Processing helix chain 'R' and resid 529 through 533 Processing helix chain 'R' and resid 610 through 637 Processing helix chain 'R' and resid 640 through 646 removed outlier: 3.532A pdb=" N THR R 646 " --> pdb=" O ILE R 642 " (cutoff:3.500A) Processing helix chain 'R' and resid 647 through 666 Processing helix chain 'R' and resid 673 through 707 removed outlier: 4.828A pdb=" N GLN R 681 " --> pdb=" O CYS R 677 " (cutoff:3.500A) Proline residue: R 682 - end of helix removed outlier: 3.643A pdb=" N VAL R 689 " --> pdb=" O GLY R 685 " (cutoff:3.500A) Processing helix chain 'R' and resid 716 through 746 removed outlier: 3.603A pdb=" N PHE R 725 " --> pdb=" O LEU R 721 " (cutoff:3.500A) Processing helix chain 'R' and resid 769 through 794 removed outlier: 3.761A pdb=" N LEU R 773 " --> pdb=" O SER R 769 " (cutoff:3.500A) Processing helix chain 'R' and resid 804 through 814 removed outlier: 3.961A pdb=" N THR R 808 " --> pdb=" O ALA R 804 " (cutoff:3.500A) Processing helix chain 'R' and resid 816 through 821 removed outlier: 3.567A pdb=" N PHE R 821 " --> pdb=" O VAL R 817 " (cutoff:3.500A) Processing helix chain 'R' and resid 821 through 827 Processing helix chain 'R' and resid 830 through 862 removed outlier: 3.984A pdb=" N SER R 834 " --> pdb=" O GLY R 830 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N PHE R 853 " --> pdb=" O LEU R 849 " (cutoff:3.500A) removed outlier: 6.330A pdb=" N ASN R 855 " --> pdb=" O CYS R 851 " (cutoff:3.500A) removed outlier: 5.442A pdb=" N LYS R 856 " --> pdb=" O ILE R 852 " (cutoff:3.500A) Processing helix chain 'R' and resid 863 through 867 Processing helix chain 'R' and resid 868 through 882 Processing helix chain 'Q' and resid 21 through 25 removed outlier: 4.015A pdb=" N ARG Q 25 " --> pdb=" O PRO Q 22 " (cutoff:3.500A) Processing helix chain 'Q' and resid 64 through 84 Processing helix chain 'Q' and resid 103 through 115 removed outlier: 3.560A pdb=" N ALA Q 107 " --> pdb=" O THR Q 103 " (cutoff:3.500A) Processing helix chain 'Q' and resid 115 through 121 Processing helix chain 'Q' and resid 146 through 159 Processing helix chain 'Q' and resid 171 through 176 removed outlier: 3.828A pdb=" N ASN Q 176 " --> pdb=" O LEU Q 173 " (cutoff:3.500A) Processing helix chain 'Q' and resid 190 through 204 Processing helix chain 'Q' and resid 218 through 233 removed outlier: 3.675A pdb=" N GLY Q 222 " --> pdb=" O TYR Q 218 " (cutoff:3.500A) Processing helix chain 'Q' and resid 248 through 262 Processing helix chain 'Q' and resid 272 through 287 Proline residue: Q 278 - end of helix Processing helix chain 'Q' and resid 307 through 309 No H-bonds generated for 'chain 'Q' and resid 307 through 309' Processing helix chain 'Q' and resid 310 through 315 Processing helix chain 'Q' and resid 329 through 336 Processing helix chain 'Q' and resid 347 through 357 Processing helix chain 'Q' and resid 400 through 404 Processing helix chain 'Q' and resid 415 through 436 Processing helix chain 'Q' and resid 444 through 448 Processing helix chain 'Q' and resid 456 through 466 Processing helix chain 'Q' and resid 525 through 528 Processing helix chain 'Q' and resid 529 through 533 Processing helix chain 'Q' and resid 610 through 637 Processing helix chain 'Q' and resid 640 through 645 Processing helix chain 'Q' and resid 647 through 665 removed outlier: 3.712A pdb=" N SER Q 665 " --> pdb=" O CYS Q 661 " (cutoff:3.500A) Processing helix chain 'Q' and resid 666 through 669 removed outlier: 3.949A pdb=" N ILE Q 669 " --> pdb=" O LEU Q 666 " (cutoff:3.500A) No H-bonds generated for 'chain 'Q' and resid 666 through 669' Processing helix chain 'Q' and resid 673 through 699 removed outlier: 4.916A pdb=" N GLN Q 681 " --> pdb=" O CYS Q 677 " (cutoff:3.500A) Proline residue: Q 682 - end of helix Processing helix chain 'Q' and resid 723 through 746 removed outlier: 3.842A pdb=" N MET Q 734 " --> pdb=" O LEU Q 730 " (cutoff:3.500A) removed outlier: 4.218A pdb=" N GLN Q 735 " --> pdb=" O CYS Q 731 " (cutoff:3.500A) Processing helix chain 'Q' and resid 769 through 794 removed outlier: 3.719A pdb=" N LEU Q 773 " --> pdb=" O SER Q 769 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N SER Q 794 " --> pdb=" O PHE Q 790 " (cutoff:3.500A) Processing helix chain 'Q' and resid 798 through 828 removed outlier: 6.062A pdb=" N ALA Q 804 " --> pdb=" O ASN Q 800 " (cutoff:3.500A) removed outlier: 6.969A pdb=" N LYS Q 805 " --> pdb=" O PHE Q 801 " (cutoff:3.500A) removed outlier: 4.220A pdb=" N PHE Q 806 " --> pdb=" O ASN Q 802 " (cutoff:3.500A) Proline residue: Q 823 - end of helix Processing helix chain 'Q' and resid 832 through 853 removed outlier: 3.612A pdb=" N VAL Q 836 " --> pdb=" O PHE Q 832 " (cutoff:3.500A) removed outlier: 4.311A pdb=" N GLU Q 837 " --> pdb=" O VAL Q 833 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N SER Q 845 " --> pdb=" O ILE Q 841 " (cutoff:3.500A) Processing helix chain 'Q' and resid 853 through 862 Processing helix chain 'A' and resid 6 through 33 removed outlier: 3.661A pdb=" N THR A 33 " --> pdb=" O VAL A 29 " (cutoff:3.500A) Processing helix chain 'A' and resid 95 through 100 Processing helix chain 'A' and resid 117 through 130 Processing helix chain 'A' and resid 131 through 135 removed outlier: 3.644A pdb=" N ARG A 135 " --> pdb=" O ARG A 132 " (cutoff:3.500A) Processing helix chain 'A' and resid 145 through 156 Processing helix chain 'A' and resid 159 through 164 removed outlier: 4.244A pdb=" N TYR A 163 " --> pdb=" O LYS A 159 " (cutoff:3.500A) Processing helix chain 'A' and resid 165 through 168 Processing helix chain 'A' and resid 183 through 202 removed outlier: 3.700A pdb=" N PHE A 197 " --> pdb=" O ILE A 193 " (cutoff:3.500A) Processing helix chain 'A' and resid 222 through 243 Processing helix chain 'B' and resid 4 through 24 Processing helix chain 'B' and resid 29 through 34 Processing helix chain 'G' and resid 9 through 24 removed outlier: 3.555A pdb=" N ASN G 24 " --> pdb=" O LYS G 20 " (cutoff:3.500A) Processing helix chain 'G' and resid 29 through 44 removed outlier: 3.504A pdb=" N ALA G 33 " --> pdb=" O LYS G 29 " (cutoff:3.500A) Processing helix chain 'H' and resid 48 through 52 Processing helix chain 'H' and resid 82 through 85 removed outlier: 3.636A pdb=" N LYS H 85 " --> pdb=" O ASP H 82 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 82 through 85' Processing helix chain 'H' and resid 107 through 111 Processing helix chain 'H' and resid 240 through 244 Processing helix chain 'N' and resid 28 through 32 Processing helix chain 'N' and resid 87 through 91 removed outlier: 3.775A pdb=" N THR N 91 " --> pdb=" O PRO N 88 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'R' and resid 26 through 28 removed outlier: 6.022A pdb=" N ILE R 32 " --> pdb=" O GLY R 94 " (cutoff:3.500A) removed outlier: 7.601A pdb=" N ARG R 96 " --> pdb=" O ILE R 32 " (cutoff:3.500A) removed outlier: 6.376A pdb=" N LEU R 34 " --> pdb=" O ARG R 96 " (cutoff:3.500A) removed outlier: 7.899A pdb=" N PHE R 98 " --> pdb=" O LEU R 34 " (cutoff:3.500A) removed outlier: 6.371A pdb=" N GLY R 36 " --> pdb=" O PHE R 98 " (cutoff:3.500A) removed outlier: 6.909A pdb=" N ILE R 33 " --> pdb=" O THR R 138 " (cutoff:3.500A) removed outlier: 4.065A pdb=" N ALA R 140 " --> pdb=" O ILE R 33 " (cutoff:3.500A) removed outlier: 8.522A pdb=" N VAL R 165 " --> pdb=" O ILE R 139 " (cutoff:3.500A) removed outlier: 6.327A pdb=" N VAL R 141 " --> pdb=" O VAL R 165 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'R' and resid 130 through 131 Processing sheet with id=AA3, first strand: chain 'R' and resid 236 through 243 removed outlier: 8.028A pdb=" N VAL R 209 " --> pdb=" O ASP R 238 " (cutoff:3.500A) removed outlier: 7.006A pdb=" N SER R 240 " --> pdb=" O VAL R 209 " (cutoff:3.500A) removed outlier: 6.960A pdb=" N THR R 211 " --> pdb=" O SER R 240 " (cutoff:3.500A) removed outlier: 6.005A pdb=" N LEU R 242 " --> pdb=" O THR R 211 " (cutoff:3.500A) removed outlier: 6.571A pdb=" N ALA R 213 " --> pdb=" O LEU R 242 " (cutoff:3.500A) removed outlier: 4.707A pdb=" N VAL R 266 " --> pdb=" O TRP R 208 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'R' and resid 318 through 322 removed outlier: 6.843A pdb=" N TYR R 489 " --> pdb=" O TYR R 510 " (cutoff:3.500A) removed outlier: 4.738A pdb=" N TYR R 510 " --> pdb=" O TYR R 489 " (cutoff:3.500A) removed outlier: 6.597A pdb=" N ILE R 491 " --> pdb=" O VAL R 508 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'R' and resid 469 through 470 removed outlier: 3.529A pdb=" N PHE R 469 " --> pdb=" O VAL R 477 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'R' and resid 550 through 551 Processing sheet with id=AA7, first strand: chain 'R' and resid 572 through 573 Processing sheet with id=AA8, first strand: chain 'R' and resid 589 through 591 Processing sheet with id=AA9, first strand: chain 'R' and resid 602 through 604 removed outlier: 3.607A pdb=" N ILE R 763 " --> pdb=" O GLU R 604 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'Q' and resid 26 through 28 removed outlier: 6.468A pdb=" N ILE Q 32 " --> pdb=" O GLY Q 94 " (cutoff:3.500A) removed outlier: 7.749A pdb=" N ARG Q 96 " --> pdb=" O ILE Q 32 " (cutoff:3.500A) removed outlier: 6.550A pdb=" N LEU Q 34 " --> pdb=" O ARG Q 96 " (cutoff:3.500A) removed outlier: 7.879A pdb=" N PHE Q 98 " --> pdb=" O LEU Q 34 " (cutoff:3.500A) removed outlier: 6.377A pdb=" N GLY Q 36 " --> pdb=" O PHE Q 98 " (cutoff:3.500A) removed outlier: 6.903A pdb=" N ILE Q 33 " --> pdb=" O THR Q 138 " (cutoff:3.500A) removed outlier: 4.058A pdb=" N ALA Q 140 " --> pdb=" O ILE Q 33 " (cutoff:3.500A) removed outlier: 8.428A pdb=" N VAL Q 165 " --> pdb=" O ILE Q 139 " (cutoff:3.500A) removed outlier: 6.325A pdb=" N VAL Q 141 " --> pdb=" O VAL Q 165 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'Q' and resid 236 through 243 removed outlier: 8.068A pdb=" N VAL Q 209 " --> pdb=" O ASP Q 238 " (cutoff:3.500A) removed outlier: 6.967A pdb=" N SER Q 240 " --> pdb=" O VAL Q 209 " (cutoff:3.500A) removed outlier: 6.825A pdb=" N THR Q 211 " --> pdb=" O SER Q 240 " (cutoff:3.500A) removed outlier: 5.975A pdb=" N LEU Q 242 " --> pdb=" O THR Q 211 " (cutoff:3.500A) removed outlier: 6.439A pdb=" N ALA Q 213 " --> pdb=" O LEU Q 242 " (cutoff:3.500A) removed outlier: 4.760A pdb=" N VAL Q 266 " --> pdb=" O TRP Q 208 " (cutoff:3.500A) removed outlier: 6.866A pdb=" N TYR Q 489 " --> pdb=" O TYR Q 510 " (cutoff:3.500A) removed outlier: 4.800A pdb=" N TYR Q 510 " --> pdb=" O TYR Q 489 " (cutoff:3.500A) removed outlier: 6.316A pdb=" N ILE Q 491 " --> pdb=" O VAL Q 508 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'Q' and resid 469 through 470 Processing sheet with id=AB4, first strand: chain 'Q' and resid 550 through 554 Processing sheet with id=AB5, first strand: chain 'Q' and resid 589 through 591 Processing sheet with id=AB6, first strand: chain 'Q' and resid 602 through 604 removed outlier: 3.662A pdb=" N ILE Q 763 " --> pdb=" O GLU Q 604 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'A' and resid 71 through 75 removed outlier: 3.818A pdb=" N ALA A 105 " --> pdb=" O ARG A 35 " (cutoff:3.500A) removed outlier: 6.356A pdb=" N ILE A 106 " --> pdb=" O ILE A 140 " (cutoff:3.500A) removed outlier: 7.334A pdb=" N PHE A 142 " --> pdb=" O ILE A 106 " (cutoff:3.500A) removed outlier: 6.526A pdb=" N PHE A 108 " --> pdb=" O PHE A 142 " (cutoff:3.500A) removed outlier: 6.900A pdb=" N ASN A 144 " --> pdb=" O PHE A 108 " (cutoff:3.500A) removed outlier: 6.346A pdb=" N VAL A 110 " --> pdb=" O ASN A 144 " (cutoff:3.500A) removed outlier: 7.126A pdb=" N VAL A 139 " --> pdb=" O TYR A 212 " (cutoff:3.500A) removed outlier: 7.948A pdb=" N HIS A 214 " --> pdb=" O VAL A 139 " (cutoff:3.500A) removed outlier: 6.557A pdb=" N LEU A 141 " --> pdb=" O HIS A 214 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'B' and resid 46 through 51 removed outlier: 5.337A pdb=" N THR B 47 " --> pdb=" O ASN B 340 " (cutoff:3.500A) removed outlier: 6.654A pdb=" N ASN B 340 " --> pdb=" O THR B 47 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N ARG B 49 " --> pdb=" O ILE B 338 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 58 through 63 removed outlier: 3.800A pdb=" N ALA B 60 " --> pdb=" O ALA B 73 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 6.516A pdb=" N LEU B 79 " --> pdb=" O ALA B 92 " (cutoff:3.500A) removed outlier: 4.447A pdb=" N ALA B 92 " --> pdb=" O LEU B 79 " (cutoff:3.500A) removed outlier: 6.601A pdb=" N ILE B 81 " --> pdb=" O VAL B 90 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 100 through 105 removed outlier: 6.987A pdb=" N GLY B 115 " --> pdb=" O MET B 101 " (cutoff:3.500A) removed outlier: 4.364A pdb=" N CYS B 103 " --> pdb=" O ALA B 113 " (cutoff:3.500A) removed outlier: 6.566A pdb=" N ALA B 113 " --> pdb=" O CYS B 103 " (cutoff:3.500A) removed outlier: 5.230A pdb=" N TYR B 105 " --> pdb=" O TYR B 111 " (cutoff:3.500A) removed outlier: 7.334A pdb=" N TYR B 111 " --> pdb=" O TYR B 105 " (cutoff:3.500A) removed outlier: 4.101A pdb=" N GLY B 116 " --> pdb=" O ILE B 120 " (cutoff:3.500A) removed outlier: 4.790A pdb=" N ILE B 120 " --> pdb=" O GLY B 116 " (cutoff:3.500A) removed outlier: 6.063A pdb=" N CYS B 121 " --> pdb=" O GLU B 138 " (cutoff:3.500A) removed outlier: 4.428A pdb=" N GLU B 138 " --> pdb=" O CYS B 121 " (cutoff:3.500A) removed outlier: 6.574A pdb=" N ILE B 123 " --> pdb=" O SER B 136 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N ARG B 134 " --> pdb=" O ASN B 125 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 146 through 153 removed outlier: 3.520A pdb=" N CYS B 148 " --> pdb=" O SER B 160 " (cutoff:3.500A) removed outlier: 6.644A pdb=" N GLN B 156 " --> pdb=" O LEU B 152 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N ILE B 157 " --> pdb=" O TRP B 169 " (cutoff:3.500A) removed outlier: 3.949A pdb=" N THR B 165 " --> pdb=" O SER B 161 " (cutoff:3.500A) removed outlier: 6.263A pdb=" N ASP B 170 " --> pdb=" O GLN B 176 " (cutoff:3.500A) removed outlier: 5.855A pdb=" N GLN B 176 " --> pdb=" O ASP B 170 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 187 through 192 removed outlier: 7.029A pdb=" N GLY B 202 " --> pdb=" O MET B 188 " (cutoff:3.500A) removed outlier: 4.388A pdb=" N LEU B 190 " --> pdb=" O VAL B 200 " (cutoff:3.500A) removed outlier: 6.632A pdb=" N VAL B 200 " --> pdb=" O LEU B 190 " (cutoff:3.500A) removed outlier: 5.068A pdb=" N LEU B 192 " --> pdb=" O LEU B 198 " (cutoff:3.500A) removed outlier: 7.173A pdb=" N LEU B 198 " --> pdb=" O LEU B 192 " (cutoff:3.500A) removed outlier: 4.042A pdb=" N SER B 207 " --> pdb=" O ALA B 203 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N GLN B 220 " --> pdb=" O LEU B 210 " (cutoff:3.500A) removed outlier: 7.051A pdb=" N ASP B 212 " --> pdb=" O CYS B 218 " (cutoff:3.500A) removed outlier: 6.455A pdb=" N CYS B 218 " --> pdb=" O ASP B 212 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 229 through 234 removed outlier: 6.527A pdb=" N CYS B 250 " --> pdb=" O THR B 263 " (cutoff:3.500A) removed outlier: 4.479A pdb=" N THR B 263 " --> pdb=" O CYS B 250 " (cutoff:3.500A) removed outlier: 6.679A pdb=" N LEU B 252 " --> pdb=" O LEU B 261 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N GLN B 259 " --> pdb=" O ASP B 254 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 273 through 278 removed outlier: 3.635A pdb=" N SER B 275 " --> pdb=" O GLY B 288 " (cutoff:3.500A) removed outlier: 6.536A pdb=" N CYS B 294 " --> pdb=" O VAL B 307 " (cutoff:3.500A) removed outlier: 4.456A pdb=" N VAL B 307 " --> pdb=" O CYS B 294 " (cutoff:3.500A) removed outlier: 6.579A pdb=" N VAL B 296 " --> pdb=" O ALA B 305 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'H' and resid 23 through 27 Processing sheet with id=AC7, first strand: chain 'H' and resid 30 through 32 removed outlier: 6.085A pdb=" N GLY H 30 " --> pdb=" O THR H 138 " (cutoff:3.500A) removed outlier: 6.752A pdb=" N MET H 54 " --> pdb=" O TYR H 70 " (cutoff:3.500A) removed outlier: 4.416A pdb=" N TYR H 70 " --> pdb=" O MET H 54 " (cutoff:3.500A) removed outlier: 6.494A pdb=" N TRP H 56 " --> pdb=" O VAL H 68 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'H' and resid 30 through 32 removed outlier: 6.085A pdb=" N GLY H 30 " --> pdb=" O THR H 138 " (cutoff:3.500A) removed outlier: 4.386A pdb=" N PHE H 130 " --> pdb=" O ARG H 118 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'H' and resid 160 through 162 removed outlier: 3.545A pdb=" N ALA H 231 " --> pdb=" O SER H 228 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'H' and resid 214 through 215 removed outlier: 6.437A pdb=" N TRP H 196 " --> pdb=" O LEU H 208 " (cutoff:3.500A) removed outlier: 4.575A pdb=" N TYR H 210 " --> pdb=" O LEU H 194 " (cutoff:3.500A) removed outlier: 6.462A pdb=" N LEU H 194 " --> pdb=" O TYR H 210 " (cutoff:3.500A) removed outlier: 4.017A pdb=" N THR H 258 " --> pdb=" O GLN H 251 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'H' and resid 214 through 215 removed outlier: 6.437A pdb=" N TRP H 196 " --> pdb=" O LEU H 208 " (cutoff:3.500A) removed outlier: 4.575A pdb=" N TYR H 210 " --> pdb=" O LEU H 194 " (cutoff:3.500A) removed outlier: 6.462A pdb=" N LEU H 194 " --> pdb=" O TYR H 210 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'N' and resid 3 through 7 Processing sheet with id=AD4, first strand: chain 'N' and resid 58 through 60 removed outlier: 5.370A pdb=" N TRP N 47 " --> pdb=" O ARG N 38 " (cutoff:3.500A) removed outlier: 6.153A pdb=" N ARG N 38 " --> pdb=" O TRP N 47 " (cutoff:3.500A) 965 hydrogen bonds defined for protein. 2691 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 8.34 Time building geometry restraints manager: 9.33 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 6686 1.34 - 1.46: 5204 1.46 - 1.58: 9814 1.58 - 1.70: 2 1.70 - 1.82: 159 Bond restraints: 21865 Sorted by residual: bond pdb=" CAI Y01 R1013 " pdb=" CAK Y01 R1013 " ideal model delta sigma weight residual 1.492 1.404 0.088 2.00e-02 2.50e+03 1.92e+01 bond pdb=" CAI Y01 R1014 " pdb=" CAK Y01 R1014 " ideal model delta sigma weight residual 1.492 1.406 0.086 2.00e-02 2.50e+03 1.84e+01 bond pdb=" CAI Y01 Q1012 " pdb=" CAK Y01 Q1012 " ideal model delta sigma weight residual 1.492 1.407 0.085 2.00e-02 2.50e+03 1.79e+01 bond pdb=" CAI Y01 R1012 " pdb=" CAK Y01 R1012 " ideal model delta sigma weight residual 1.492 1.408 0.084 2.00e-02 2.50e+03 1.76e+01 bond pdb=" O4 PO4 Q1006 " pdb=" P PO4 Q1006 " ideal model delta sigma weight residual 1.568 1.506 0.062 2.00e-02 2.50e+03 9.70e+00 ... (remaining 21860 not shown) Histogram of bond angle deviations from ideal: 98.11 - 105.36: 411 105.36 - 112.61: 11395 112.61 - 119.85: 7361 119.85 - 127.10: 10315 127.10 - 134.35: 228 Bond angle restraints: 29710 Sorted by residual: angle pdb=" CAM Y01 Q1012 " pdb=" CAY Y01 Q1012 " pdb=" OAW Y01 Q1012 " ideal model delta sigma weight residual 111.19 123.02 -11.83 3.00e+00 1.11e-01 1.55e+01 angle pdb=" N ILE Q 305 " pdb=" CA ILE Q 305 " pdb=" C ILE Q 305 " ideal model delta sigma weight residual 111.90 108.71 3.19 8.10e-01 1.52e+00 1.55e+01 angle pdb=" OAG Y01 R1013 " pdb=" CAY Y01 R1013 " pdb=" OAW Y01 R1013 " ideal model delta sigma weight residual 123.38 111.76 11.62 3.00e+00 1.11e-01 1.50e+01 angle pdb=" OAG Y01 R1014 " pdb=" CAY Y01 R1014 " pdb=" OAW Y01 R1014 " ideal model delta sigma weight residual 123.38 111.78 11.60 3.00e+00 1.11e-01 1.49e+01 angle pdb=" OAG Y01 Q1012 " pdb=" CAY Y01 Q1012 " pdb=" OAW Y01 Q1012 " ideal model delta sigma weight residual 123.38 111.85 11.53 3.00e+00 1.11e-01 1.48e+01 ... (remaining 29705 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 32.72: 13486 32.72 - 65.43: 283 65.43 - 98.15: 21 98.15 - 130.86: 1 130.86 - 163.58: 2 Dihedral angle restraints: 13793 sinusoidal: 6230 harmonic: 7563 Sorted by residual: 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 93.00 179.09 -86.09 1 1.00e+01 1.00e-02 8.94e+01 dihedral pdb=" CB CYS Q 60 " pdb=" SG CYS Q 60 " pdb=" SG CYS Q 101 " pdb=" CB CYS Q 101 " ideal model delta sinusoidal sigma weight residual -86.00 -21.45 -64.55 1 1.00e+01 1.00e-02 5.47e+01 dihedral pdb=" CB CYS Q 585 " pdb=" SG CYS Q 585 " pdb=" SG CYS Q 598 " pdb=" CB CYS Q 598 " ideal model delta sinusoidal sigma weight residual -86.00 -137.64 51.64 1 1.00e+01 1.00e-02 3.64e+01 ... (remaining 13790 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.079: 2988 0.079 - 0.159: 315 0.159 - 0.238: 23 0.238 - 0.317: 27 0.317 - 0.397: 11 Chirality restraints: 3364 Sorted by residual: chirality pdb=" C17 CLR Q1013 " pdb=" C13 CLR Q1013 " pdb=" C16 CLR Q1013 " pdb=" C20 CLR Q1013 " both_signs ideal model delta sigma weight residual False 2.55 2.95 -0.40 2.00e-01 2.50e+01 3.94e+00 chirality pdb=" C17 CLR R1015 " pdb=" C13 CLR R1015 " pdb=" C16 CLR R1015 " pdb=" C20 CLR R1015 " both_signs ideal model delta sigma weight residual False 2.55 2.94 -0.38 2.00e-01 2.50e+01 3.68e+00 chirality pdb=" C17 CLR Q1017 " pdb=" C13 CLR Q1017 " pdb=" C16 CLR Q1017 " pdb=" C20 CLR Q1017 " both_signs ideal model delta sigma weight residual False 2.55 2.93 -0.38 2.00e-01 2.50e+01 3.62e+00 ... (remaining 3361 not shown) Planarity restraints: 3702 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LEU Q 88 " -0.045 5.00e-02 4.00e+02 6.80e-02 7.40e+00 pdb=" N PRO Q 89 " 0.118 5.00e-02 4.00e+02 pdb=" CA PRO Q 89 " -0.035 5.00e-02 4.00e+02 pdb=" CD PRO Q 89 " -0.038 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR A 172 " -0.044 5.00e-02 4.00e+02 6.75e-02 7.29e+00 pdb=" N PRO A 173 " 0.117 5.00e-02 4.00e+02 pdb=" CA PRO A 173 " -0.036 5.00e-02 4.00e+02 pdb=" CD PRO A 173 " -0.037 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB TYR Q 425 " 0.015 2.00e-02 2.50e+03 1.78e-02 6.32e+00 pdb=" CG TYR Q 425 " -0.042 2.00e-02 2.50e+03 pdb=" CD1 TYR Q 425 " 0.018 2.00e-02 2.50e+03 pdb=" CD2 TYR Q 425 " 0.002 2.00e-02 2.50e+03 pdb=" CE1 TYR Q 425 " -0.003 2.00e-02 2.50e+03 pdb=" CE2 TYR Q 425 " 0.013 2.00e-02 2.50e+03 pdb=" CZ TYR Q 425 " 0.002 2.00e-02 2.50e+03 pdb=" OH TYR Q 425 " -0.004 2.00e-02 2.50e+03 ... (remaining 3699 not shown) Histogram of nonbonded interaction distances: 2.16 - 2.71: 612 2.71 - 3.26: 20715 3.26 - 3.80: 33396 3.80 - 4.35: 44273 4.35 - 4.90: 74668 Nonbonded interactions: 173664 Sorted by model distance: nonbonded pdb=" NH1 ARG A 15 " pdb=" O VAL B 90 " model vdw 2.162 2.520 nonbonded pdb=" O ILE Q 741 " pdb=" OG1 THR Q 745 " model vdw 2.210 2.440 nonbonded pdb=" OG SER N 17 " pdb=" OD1 ASN N 84 " model vdw 2.243 2.440 nonbonded pdb=" OE1 GLU B 215 " pdb=" NH2 ARG B 219 " model vdw 2.254 2.520 nonbonded pdb=" NH2 ARG B 256 " pdb=" OD2 ASP G 36 " model vdw 2.261 2.520 ... (remaining 173659 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 20 through 863 or resid 1001 through 1005 or resid 1006 th \ rough 1009 or resid 1012 or resid 1015 through 1017)) selection = (chain 'R' and (resid 20 through 700 or resid 723 through 863 or resid 1001 thro \ ugh 1005 or resid 1006 through 1009 or resid 1012 or resid 1015 through 1017)) } 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: 19.750 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 25.290 Check model and map are aligned: 0.150 Set scattering table: 0.220 Process input model: 60.880 Find NCS groups from input model: 1.080 Set up NCS constraints: 0.150 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:2.860 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 110.390 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7671 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 : 0.005 0.088 21865 Z= 0.335 Angle : 0.779 11.829 29710 Z= 0.382 Chirality : 0.057 0.397 3364 Planarity : 0.005 0.068 3690 Dihedral : 13.153 163.577 8849 Min Nonbonded Distance : 2.162 Molprobity Statistics. All-atom Clashscore : 5.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.40 % Favored : 97.60 % Rotamer: Outliers : 0.00 % Allowed : 0.22 % Favored : 99.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.09 % Cis-general : 0.08 % 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: 0.13 (0.16), residues: 2581 helix: 1.30 (0.17), residues: 897 sheet: -0.15 (0.22), residues: 560 loop : -0.72 (0.18), residues: 1124 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP B 211 HIS 0.004 0.001 HIS A 209 PHE 0.020 0.001 PHE B 234 TYR 0.042 0.002 TYR Q 425 ARG 0.010 0.001 ARG Q 286 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5162 Ramachandran restraints generated. 2581 Oldfield, 0 Emsley, 2581 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5162 Ramachandran restraints generated. 2581 Oldfield, 0 Emsley, 2581 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 423 residues out of total 2246 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 423 time to evaluate : 2.169 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 679 LEU cc_start: 0.8119 (tp) cc_final: 0.7899 (tp) REVERT: R 865 SER cc_start: 0.8938 (m) cc_final: 0.8526 (t) REVERT: Q 31 ASP cc_start: 0.7743 (m-30) cc_final: 0.7510 (m-30) REVERT: Q 96 ARG cc_start: 0.8230 (mtp85) cc_final: 0.7810 (mtp-110) REVERT: Q 354 GLU cc_start: 0.7527 (mm-30) cc_final: 0.7256 (mp0) REVERT: Q 476 GLN cc_start: 0.7896 (mm110) cc_final: 0.7627 (mp10) REVERT: Q 760 ILE cc_start: 0.8569 (mt) cc_final: 0.8318 (mt) REVERT: A 110 VAL cc_start: 0.8477 (t) cc_final: 0.8203 (p) REVERT: A 242 GLU cc_start: 0.7477 (tp30) cc_final: 0.7013 (tp30) REVERT: B 76 ASP cc_start: 0.7488 (p0) cc_final: 0.7150 (p0) REVERT: B 270 ILE cc_start: 0.8419 (pt) cc_final: 0.8182 (pt) REVERT: H 230 THR cc_start: 0.8161 (p) cc_final: 0.7948 (p) outliers start: 0 outliers final: 0 residues processed: 423 average time/residue: 0.3538 time to fit residues: 222.9602 Evaluate side-chains 360 residues out of total 2246 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 360 time to evaluate : 1.850 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 257 random chunks: chunk 217 optimal weight: 0.7980 chunk 194 optimal weight: 0.6980 chunk 108 optimal weight: 2.9990 chunk 66 optimal weight: 0.0870 chunk 131 optimal weight: 1.9990 chunk 104 optimal weight: 1.9990 chunk 201 optimal weight: 0.9990 chunk 77 optimal weight: 0.6980 chunk 122 optimal weight: 0.6980 chunk 149 optimal weight: 0.7980 chunk 233 optimal weight: 1.9990 overall best weight: 0.5958 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 260 GLN Q 24 GLN ** A 82 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 130 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7696 moved from start: 0.0774 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 21865 Z= 0.244 Angle : 0.539 7.177 29710 Z= 0.287 Chirality : 0.043 0.203 3364 Planarity : 0.004 0.053 3690 Dihedral : 8.665 137.602 4110 Min Nonbonded Distance : 2.134 Molprobity Statistics. All-atom Clashscore : 5.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.63 % Favored : 97.37 % Rotamer: Outliers : 1.25 % Allowed : 6.46 % Favored : 92.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.09 % Cis-general : 0.08 % 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 (0.16), residues: 2581 helix: 1.82 (0.17), residues: 883 sheet: 0.03 (0.22), residues: 558 loop : -0.64 (0.18), residues: 1140 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP Q 818 HIS 0.004 0.001 HIS B 183 PHE 0.020 0.001 PHE A 74 TYR 0.015 0.001 TYR H 210 ARG 0.006 0.001 ARG Q 185 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5162 Ramachandran restraints generated. 2581 Oldfield, 0 Emsley, 2581 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5162 Ramachandran restraints generated. 2581 Oldfield, 0 Emsley, 2581 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 393 residues out of total 2246 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 365 time to evaluate : 2.508 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 700 ASN cc_start: 0.8476 (t0) cc_final: 0.8179 (t0) REVERT: R 865 SER cc_start: 0.8864 (m) cc_final: 0.8590 (t) REVERT: Q 31 ASP cc_start: 0.7775 (m-30) cc_final: 0.7555 (m-30) REVERT: Q 96 ARG cc_start: 0.8156 (mtp85) cc_final: 0.7774 (mtp180) REVERT: Q 270 PHE cc_start: 0.8194 (OUTLIER) cc_final: 0.7641 (t80) REVERT: A 242 GLU cc_start: 0.7620 (tp30) cc_final: 0.7113 (tp30) REVERT: B 270 ILE cc_start: 0.8400 (pt) cc_final: 0.8188 (pt) REVERT: H 230 THR cc_start: 0.8163 (p) cc_final: 0.7956 (p) outliers start: 28 outliers final: 21 residues processed: 375 average time/residue: 0.3550 time to fit residues: 198.2043 Evaluate side-chains 376 residues out of total 2246 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 354 time to evaluate : 2.285 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 228 GLU Chi-restraints excluded: chain R residue 531 SER Chi-restraints excluded: chain R residue 566 VAL Chi-restraints excluded: chain R residue 609 THR Chi-restraints excluded: chain R residue 639 ASN Chi-restraints excluded: chain Q residue 223 ILE Chi-restraints excluded: chain Q residue 270 PHE Chi-restraints excluded: chain Q residue 412 THR Chi-restraints excluded: chain Q residue 587 ASP Chi-restraints excluded: chain Q residue 697 VAL Chi-restraints excluded: chain Q residue 744 TYR Chi-restraints excluded: chain A residue 114 ASP Chi-restraints excluded: chain A residue 177 THR Chi-restraints excluded: chain A residue 201 SER Chi-restraints excluded: chain A residue 244 ASN Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 177 THR Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain G residue 25 ILE Chi-restraints excluded: chain H residue 25 VAL Chi-restraints excluded: chain H residue 136 THR Chi-restraints excluded: chain H residue 161 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 257 random chunks: chunk 129 optimal weight: 2.9990 chunk 72 optimal weight: 2.9990 chunk 194 optimal weight: 0.9990 chunk 158 optimal weight: 0.6980 chunk 64 optimal weight: 0.9990 chunk 233 optimal weight: 0.9980 chunk 252 optimal weight: 2.9990 chunk 208 optimal weight: 1.9990 chunk 231 optimal weight: 0.6980 chunk 79 optimal weight: 0.9990 chunk 187 optimal weight: 0.9990 overall best weight: 0.8784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 493 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 855 ASN Q 429 HIS Q 493 ASN Q 495 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7723 moved from start: 0.1040 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.046 21865 Z= 0.330 Angle : 0.568 8.019 29710 Z= 0.300 Chirality : 0.044 0.213 3364 Planarity : 0.004 0.051 3690 Dihedral : 8.080 106.409 4110 Min Nonbonded Distance : 2.123 Molprobity Statistics. All-atom Clashscore : 4.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.98 % Favored : 97.02 % Rotamer: Outliers : 2.00 % Allowed : 8.41 % Favored : 89.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.09 % Cis-general : 0.08 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.49 (0.16), residues: 2581 helix: 1.81 (0.17), residues: 884 sheet: 0.02 (0.22), residues: 554 loop : -0.68 (0.18), residues: 1143 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP Q 818 HIS 0.005 0.001 HIS B 183 PHE 0.018 0.002 PHE A 74 TYR 0.017 0.002 TYR B 59 ARG 0.007 0.001 ARG Q 25 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5162 Ramachandran restraints generated. 2581 Oldfield, 0 Emsley, 2581 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5162 Ramachandran restraints generated. 2581 Oldfield, 0 Emsley, 2581 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 411 residues out of total 2246 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 366 time to evaluate : 2.253 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 453 LYS cc_start: 0.8058 (mttt) cc_final: 0.7719 (mtpp) REVERT: R 700 ASN cc_start: 0.8460 (t0) cc_final: 0.8180 (t0) REVERT: R 730 LEU cc_start: 0.6354 (OUTLIER) cc_final: 0.6059 (mp) REVERT: R 865 SER cc_start: 0.8946 (m) cc_final: 0.8625 (t) REVERT: Q 31 ASP cc_start: 0.7830 (m-30) cc_final: 0.7598 (m-30) REVERT: Q 270 PHE cc_start: 0.8238 (OUTLIER) cc_final: 0.7756 (t80) REVERT: Q 340 ARG cc_start: 0.7764 (mtt-85) cc_final: 0.7490 (mmt90) REVERT: Q 576 GLU cc_start: 0.7765 (pm20) cc_final: 0.7395 (pm20) REVERT: A 238 MET cc_start: 0.8349 (OUTLIER) cc_final: 0.8111 (ttp) REVERT: A 242 GLU cc_start: 0.7588 (tp30) cc_final: 0.7046 (tp30) REVERT: B 76 ASP cc_start: 0.7686 (p0) cc_final: 0.7403 (p0) REVERT: B 270 ILE cc_start: 0.8407 (pt) cc_final: 0.8183 (pt) REVERT: H 226 SER cc_start: 0.8569 (m) cc_final: 0.8185 (p) REVERT: H 230 THR cc_start: 0.8197 (p) cc_final: 0.7975 (p) outliers start: 45 outliers final: 33 residues processed: 382 average time/residue: 0.3577 time to fit residues: 205.0049 Evaluate side-chains 395 residues out of total 2246 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 359 time to evaluate : 1.833 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 228 GLU Chi-restraints excluded: chain R residue 531 SER Chi-restraints excluded: chain R residue 566 VAL Chi-restraints excluded: chain R residue 598 CYS Chi-restraints excluded: chain R residue 609 THR Chi-restraints excluded: chain R residue 730 LEU Chi-restraints excluded: chain Q residue 223 ILE Chi-restraints excluded: chain Q residue 258 VAL Chi-restraints excluded: chain Q residue 270 PHE Chi-restraints excluded: chain Q residue 355 THR Chi-restraints excluded: chain Q residue 412 THR Chi-restraints excluded: chain Q residue 566 VAL Chi-restraints excluded: chain Q residue 587 ASP Chi-restraints excluded: chain Q residue 697 VAL Chi-restraints excluded: chain Q residue 744 TYR Chi-restraints excluded: chain Q residue 833 VAL Chi-restraints excluded: chain A residue 83 MET Chi-restraints excluded: chain A residue 177 THR Chi-restraints excluded: chain A residue 201 SER Chi-restraints excluded: chain A residue 221 THR Chi-restraints excluded: chain A residue 238 MET Chi-restraints excluded: chain A residue 244 ASN Chi-restraints excluded: chain B residue 143 THR Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 177 THR Chi-restraints excluded: chain B residue 195 ASP Chi-restraints excluded: chain B residue 213 VAL Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain G residue 25 ILE Chi-restraints excluded: chain H residue 25 VAL Chi-restraints excluded: chain H residue 98 THR Chi-restraints excluded: chain H residue 119 SER Chi-restraints excluded: chain H residue 136 THR Chi-restraints excluded: chain H residue 161 THR Chi-restraints excluded: chain N residue 63 SER Chi-restraints excluded: chain N residue 110 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 257 random chunks: chunk 231 optimal weight: 1.9990 chunk 175 optimal weight: 1.9990 chunk 121 optimal weight: 2.9990 chunk 25 optimal weight: 0.3980 chunk 111 optimal weight: 0.0970 chunk 156 optimal weight: 0.1980 chunk 234 optimal weight: 3.9990 chunk 248 optimal weight: 0.8980 chunk 122 optimal weight: 0.9980 chunk 222 optimal weight: 0.6980 chunk 66 optimal weight: 0.9980 overall best weight: 0.4578 ------------------------------------------------------------------------------- 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** ** R 493 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 855 ASN Q 495 HIS ** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7699 moved from start: 0.1124 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 21865 Z= 0.198 Angle : 0.496 6.758 29710 Z= 0.264 Chirality : 0.041 0.169 3364 Planarity : 0.004 0.049 3690 Dihedral : 7.291 74.881 4110 Min Nonbonded Distance : 2.160 Molprobity Statistics. All-atom Clashscore : 4.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.83 % Favored : 97.17 % Rotamer: Outliers : 2.00 % Allowed : 10.15 % Favored : 87.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.09 % Cis-general : 0.08 % 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: 0.67 (0.16), residues: 2581 helix: 2.03 (0.17), residues: 879 sheet: 0.05 (0.22), residues: 554 loop : -0.57 (0.18), residues: 1148 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP Q 818 HIS 0.004 0.001 HIS A 209 PHE 0.020 0.001 PHE A 74 TYR 0.014 0.001 TYR H 210 ARG 0.005 0.000 ARG Q 54 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5162 Ramachandran restraints generated. 2581 Oldfield, 0 Emsley, 2581 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5162 Ramachandran restraints generated. 2581 Oldfield, 0 Emsley, 2581 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 410 residues out of total 2246 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 365 time to evaluate : 2.514 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 700 ASN cc_start: 0.8492 (t0) cc_final: 0.8211 (t0) REVERT: R 865 SER cc_start: 0.8924 (m) cc_final: 0.8569 (t) REVERT: Q 31 ASP cc_start: 0.7812 (m-30) cc_final: 0.7567 (m-30) REVERT: Q 270 PHE cc_start: 0.8237 (OUTLIER) cc_final: 0.7758 (t80) REVERT: Q 340 ARG cc_start: 0.7756 (mtt-85) cc_final: 0.7489 (mmt90) REVERT: Q 576 GLU cc_start: 0.7801 (pm20) cc_final: 0.7389 (pm20) REVERT: A 242 GLU cc_start: 0.7530 (tp30) cc_final: 0.7050 (tp30) REVERT: B 76 ASP cc_start: 0.7645 (p0) cc_final: 0.7346 (p0) REVERT: B 270 ILE cc_start: 0.8401 (pt) cc_final: 0.8176 (pt) REVERT: H 230 THR cc_start: 0.8200 (p) cc_final: 0.7966 (p) outliers start: 45 outliers final: 38 residues processed: 383 average time/residue: 0.3599 time to fit residues: 207.0999 Evaluate side-chains 393 residues out of total 2246 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 354 time to evaluate : 2.360 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 228 GLU Chi-restraints excluded: chain R residue 412 THR Chi-restraints excluded: chain R residue 566 VAL Chi-restraints excluded: chain R residue 592 ASN Chi-restraints excluded: chain R residue 598 CYS Chi-restraints excluded: chain R residue 599 ILE Chi-restraints excluded: chain R residue 609 THR Chi-restraints excluded: chain R residue 639 ASN Chi-restraints excluded: chain R residue 869 ILE Chi-restraints excluded: chain Q residue 44 VAL Chi-restraints excluded: chain Q residue 60 CYS Chi-restraints excluded: chain Q residue 223 ILE Chi-restraints excluded: chain Q residue 250 GLU Chi-restraints excluded: chain Q residue 270 PHE Chi-restraints excluded: chain Q residue 412 THR Chi-restraints excluded: chain Q residue 497 SER Chi-restraints excluded: chain Q residue 587 ASP Chi-restraints excluded: chain Q residue 697 VAL Chi-restraints excluded: chain Q residue 744 TYR Chi-restraints excluded: chain Q residue 764 THR Chi-restraints excluded: chain A residue 83 MET Chi-restraints excluded: chain A residue 114 ASP Chi-restraints excluded: chain A residue 177 THR Chi-restraints excluded: chain A residue 201 SER Chi-restraints excluded: chain A residue 221 THR Chi-restraints excluded: chain A residue 244 ASN Chi-restraints excluded: chain B residue 119 ASN Chi-restraints excluded: chain B residue 143 THR Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 172 GLU Chi-restraints excluded: chain B residue 177 THR Chi-restraints excluded: chain B residue 195 ASP Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain G residue 25 ILE Chi-restraints excluded: chain H residue 25 VAL Chi-restraints excluded: chain H residue 98 THR Chi-restraints excluded: chain H residue 136 THR Chi-restraints excluded: chain H residue 161 THR Chi-restraints excluded: chain N residue 110 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 257 random chunks: chunk 206 optimal weight: 2.9990 chunk 141 optimal weight: 0.9980 chunk 3 optimal weight: 0.4980 chunk 184 optimal weight: 7.9990 chunk 102 optimal weight: 1.9990 chunk 211 optimal weight: 0.4980 chunk 171 optimal weight: 0.0980 chunk 0 optimal weight: 2.9990 chunk 126 optimal weight: 0.9980 chunk 222 optimal weight: 2.9990 chunk 62 optimal weight: 0.9980 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 27 GLN ** R 338 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 493 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 512 ASN R 855 ASN Q 495 HIS ** A 82 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 16 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7709 moved from start: 0.1232 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.073 21865 Z= 0.246 Angle : 0.512 6.825 29710 Z= 0.272 Chirality : 0.042 0.164 3364 Planarity : 0.004 0.049 3690 Dihedral : 7.005 58.452 4110 Min Nonbonded Distance : 2.137 Molprobity Statistics. All-atom Clashscore : 4.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.14 % Favored : 96.86 % Rotamer: Outliers : 2.27 % Allowed : 10.82 % Favored : 86.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.09 % Cis-general : 0.08 % 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: 0.65 (0.16), residues: 2581 helix: 2.01 (0.17), residues: 885 sheet: 0.01 (0.22), residues: 560 loop : -0.57 (0.18), residues: 1136 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP Q 818 HIS 0.004 0.001 HIS H 55 PHE 0.020 0.001 PHE A 74 TYR 0.014 0.001 TYR H 210 ARG 0.006 0.000 ARG Q 54 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5162 Ramachandran restraints generated. 2581 Oldfield, 0 Emsley, 2581 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5162 Ramachandran restraints generated. 2581 Oldfield, 0 Emsley, 2581 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 421 residues out of total 2246 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 370 time to evaluate : 2.231 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 270 PHE cc_start: 0.8406 (OUTLIER) cc_final: 0.7930 (m-80) REVERT: R 700 ASN cc_start: 0.8501 (t0) cc_final: 0.8235 (t0) REVERT: R 730 LEU cc_start: 0.6340 (OUTLIER) cc_final: 0.6080 (mp) REVERT: R 865 SER cc_start: 0.8932 (m) cc_final: 0.8603 (t) REVERT: Q 31 ASP cc_start: 0.7823 (m-30) cc_final: 0.7565 (m-30) REVERT: Q 190 ASP cc_start: 0.8002 (m-30) cc_final: 0.7658 (m-30) REVERT: Q 270 PHE cc_start: 0.8238 (OUTLIER) cc_final: 0.7784 (t80) REVERT: Q 340 ARG cc_start: 0.7769 (mtt-85) cc_final: 0.7515 (mmt90) REVERT: Q 576 GLU cc_start: 0.7859 (pm20) cc_final: 0.7424 (pm20) REVERT: A 242 GLU cc_start: 0.7520 (tp30) cc_final: 0.7027 (tp30) REVERT: B 76 ASP cc_start: 0.7636 (p0) cc_final: 0.7331 (p0) REVERT: B 270 ILE cc_start: 0.8396 (pt) cc_final: 0.8172 (pt) REVERT: H 230 THR cc_start: 0.8208 (p) cc_final: 0.7963 (p) outliers start: 51 outliers final: 39 residues processed: 393 average time/residue: 0.3490 time to fit residues: 207.9154 Evaluate side-chains 407 residues out of total 2246 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 365 time to evaluate : 2.546 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 223 ILE Chi-restraints excluded: chain R residue 228 GLU Chi-restraints excluded: chain R residue 270 PHE Chi-restraints excluded: chain R residue 531 SER Chi-restraints excluded: chain R residue 566 VAL Chi-restraints excluded: chain R residue 609 THR Chi-restraints excluded: chain R residue 639 ASN Chi-restraints excluded: chain R residue 730 LEU Chi-restraints excluded: chain R residue 869 ILE Chi-restraints excluded: chain Q residue 44 VAL Chi-restraints excluded: chain Q residue 60 CYS Chi-restraints excluded: chain Q residue 223 ILE Chi-restraints excluded: chain Q residue 270 PHE Chi-restraints excluded: chain Q residue 412 THR Chi-restraints excluded: chain Q residue 497 SER Chi-restraints excluded: chain Q residue 587 ASP Chi-restraints excluded: chain Q residue 697 VAL Chi-restraints excluded: chain Q residue 744 TYR Chi-restraints excluded: chain Q residue 764 THR Chi-restraints excluded: chain Q residue 842 LEU Chi-restraints excluded: chain A residue 49 ILE Chi-restraints excluded: chain A residue 83 MET Chi-restraints excluded: chain A residue 177 THR Chi-restraints excluded: chain A residue 201 SER Chi-restraints excluded: chain A residue 216 THR Chi-restraints excluded: chain A residue 221 THR Chi-restraints excluded: chain A residue 244 ASN Chi-restraints excluded: chain B residue 119 ASN Chi-restraints excluded: chain B residue 143 THR Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 172 GLU Chi-restraints excluded: chain B residue 177 THR Chi-restraints excluded: chain B residue 195 ASP Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain G residue 25 ILE Chi-restraints excluded: chain H residue 25 VAL Chi-restraints excluded: chain H residue 98 THR Chi-restraints excluded: chain H residue 136 THR Chi-restraints excluded: chain H residue 161 THR Chi-restraints excluded: chain N residue 63 SER Chi-restraints excluded: chain N residue 91 THR Chi-restraints excluded: chain N residue 110 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 257 random chunks: chunk 83 optimal weight: 1.9990 chunk 223 optimal weight: 5.9990 chunk 49 optimal weight: 2.9990 chunk 145 optimal weight: 0.8980 chunk 61 optimal weight: 1.9990 chunk 248 optimal weight: 0.9990 chunk 206 optimal weight: 3.9990 chunk 115 optimal weight: 0.8980 chunk 20 optimal weight: 1.9990 chunk 82 optimal weight: 1.9990 chunk 130 optimal weight: 0.9990 overall best weight: 1.1586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 493 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 855 ASN ** Q 524 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 82 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 155 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7745 moved from start: 0.1408 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.066 21865 Z= 0.420 Angle : 0.610 8.404 29710 Z= 0.320 Chirality : 0.046 0.173 3364 Planarity : 0.005 0.055 3690 Dihedral : 7.203 60.445 4110 Min Nonbonded Distance : 2.099 Molprobity Statistics. All-atom Clashscore : 5.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.33 % Favored : 96.67 % Rotamer: Outliers : 2.89 % Allowed : 10.86 % Favored : 86.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.09 % Cis-general : 0.08 % Twisted Proline : 1.09 % 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: 0.42 (0.16), residues: 2581 helix: 1.75 (0.17), residues: 886 sheet: -0.06 (0.22), residues: 555 loop : -0.68 (0.18), residues: 1140 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP Q 818 HIS 0.005 0.001 HIS B 183 PHE 0.020 0.002 PHE A 74 TYR 0.025 0.002 TYR N 95 ARG 0.007 0.001 ARG Q 54 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5162 Ramachandran restraints generated. 2581 Oldfield, 0 Emsley, 2581 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5162 Ramachandran restraints generated. 2581 Oldfield, 0 Emsley, 2581 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 436 residues out of total 2246 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 65 poor density : 371 time to evaluate : 2.364 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 25 ARG cc_start: 0.7324 (ptt-90) cc_final: 0.7010 (ptt-90) REVERT: R 270 PHE cc_start: 0.8421 (OUTLIER) cc_final: 0.7953 (m-80) REVERT: R 512 ASN cc_start: 0.8552 (t0) cc_final: 0.8239 (t0) REVERT: R 700 ASN cc_start: 0.8475 (t0) cc_final: 0.8213 (t0) REVERT: R 730 LEU cc_start: 0.6521 (OUTLIER) cc_final: 0.6182 (mp) REVERT: R 776 LEU cc_start: 0.7201 (OUTLIER) cc_final: 0.6899 (mp) REVERT: Q 31 ASP cc_start: 0.7868 (m-30) cc_final: 0.7640 (m-30) REVERT: Q 190 ASP cc_start: 0.8103 (m-30) cc_final: 0.7731 (m-30) REVERT: Q 270 PHE cc_start: 0.8240 (OUTLIER) cc_final: 0.7784 (t80) REVERT: Q 340 ARG cc_start: 0.7824 (mtt-85) cc_final: 0.7577 (mmt90) REVERT: Q 576 GLU cc_start: 0.7915 (pm20) cc_final: 0.7450 (pm20) REVERT: Q 808 THR cc_start: 0.8376 (m) cc_final: 0.8057 (p) REVERT: A 242 GLU cc_start: 0.7494 (tp30) cc_final: 0.6947 (tp30) REVERT: B 76 ASP cc_start: 0.7744 (p0) cc_final: 0.7396 (p0) REVERT: B 101 MET cc_start: 0.8346 (mtt) cc_final: 0.8079 (mtt) REVERT: B 270 ILE cc_start: 0.8412 (pt) cc_final: 0.8189 (pt) REVERT: H 226 SER cc_start: 0.8594 (m) cc_final: 0.8287 (p) REVERT: H 230 THR cc_start: 0.8216 (p) cc_final: 0.8011 (p) outliers start: 65 outliers final: 50 residues processed: 400 average time/residue: 0.3539 time to fit residues: 212.7595 Evaluate side-chains 416 residues out of total 2246 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 362 time to evaluate : 2.537 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 223 ILE Chi-restraints excluded: chain R residue 228 GLU Chi-restraints excluded: chain R residue 270 PHE Chi-restraints excluded: chain R residue 531 SER Chi-restraints excluded: chain R residue 566 VAL Chi-restraints excluded: chain R residue 592 ASN Chi-restraints excluded: chain R residue 609 THR Chi-restraints excluded: chain R residue 730 LEU Chi-restraints excluded: chain R residue 776 LEU Chi-restraints excluded: chain R residue 869 ILE Chi-restraints excluded: chain Q residue 44 VAL Chi-restraints excluded: chain Q residue 60 CYS Chi-restraints excluded: chain Q residue 223 ILE Chi-restraints excluded: chain Q residue 258 VAL Chi-restraints excluded: chain Q residue 270 PHE Chi-restraints excluded: chain Q residue 355 THR Chi-restraints excluded: chain Q residue 412 THR Chi-restraints excluded: chain Q residue 437 CYS Chi-restraints excluded: chain Q residue 470 THR Chi-restraints excluded: chain Q residue 478 THR Chi-restraints excluded: chain Q residue 497 SER Chi-restraints excluded: chain Q residue 566 VAL Chi-restraints excluded: chain Q residue 587 ASP Chi-restraints excluded: chain Q residue 599 ILE Chi-restraints excluded: chain Q residue 697 VAL Chi-restraints excluded: chain Q residue 744 TYR Chi-restraints excluded: chain Q residue 833 VAL Chi-restraints excluded: chain Q residue 842 LEU Chi-restraints excluded: chain Q residue 848 LEU Chi-restraints excluded: chain A residue 49 ILE Chi-restraints excluded: chain A residue 177 THR Chi-restraints excluded: chain A residue 201 SER Chi-restraints excluded: chain A residue 216 THR Chi-restraints excluded: chain A residue 221 THR Chi-restraints excluded: chain A residue 244 ASN Chi-restraints excluded: chain B residue 119 ASN Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 143 THR Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 172 GLU Chi-restraints excluded: chain B residue 177 THR Chi-restraints excluded: chain B residue 195 ASP Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain G residue 25 ILE Chi-restraints excluded: chain H residue 25 VAL Chi-restraints excluded: chain H residue 89 THR Chi-restraints excluded: chain H residue 98 THR Chi-restraints excluded: chain H residue 113 MET Chi-restraints excluded: chain H residue 119 SER Chi-restraints excluded: chain H residue 136 THR Chi-restraints excluded: chain H residue 161 THR Chi-restraints excluded: chain N residue 63 SER Chi-restraints excluded: chain N residue 91 THR Chi-restraints excluded: chain N residue 110 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 257 random chunks: chunk 239 optimal weight: 0.1980 chunk 28 optimal weight: 0.9990 chunk 141 optimal weight: 0.9980 chunk 181 optimal weight: 0.9980 chunk 140 optimal weight: 0.7980 chunk 209 optimal weight: 0.9990 chunk 138 optimal weight: 0.8980 chunk 247 optimal weight: 0.5980 chunk 155 optimal weight: 1.9990 chunk 151 optimal weight: 0.9980 chunk 114 optimal weight: 0.7980 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 493 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 27 GLN Q 524 ASN A 75 GLN ** A 82 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7721 moved from start: 0.1401 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 21865 Z= 0.257 Angle : 0.526 6.862 29710 Z= 0.279 Chirality : 0.042 0.165 3364 Planarity : 0.004 0.053 3690 Dihedral : 6.792 56.915 4110 Min Nonbonded Distance : 2.150 Molprobity Statistics. All-atom Clashscore : 5.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.02 % Favored : 96.98 % Rotamer: Outliers : 2.89 % Allowed : 11.49 % Favored : 85.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.09 % Cis-general : 0.08 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.56 (0.16), residues: 2581 helix: 1.94 (0.17), residues: 880 sheet: -0.07 (0.22), residues: 561 loop : -0.61 (0.18), residues: 1140 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP Q 818 HIS 0.004 0.001 HIS A 209 PHE 0.022 0.001 PHE A 74 TYR 0.014 0.001 TYR H 210 ARG 0.007 0.000 ARG Q 54 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5162 Ramachandran restraints generated. 2581 Oldfield, 0 Emsley, 2581 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5162 Ramachandran restraints generated. 2581 Oldfield, 0 Emsley, 2581 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 430 residues out of total 2246 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 65 poor density : 365 time to evaluate : 2.724 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 270 PHE cc_start: 0.8404 (OUTLIER) cc_final: 0.7964 (m-80) REVERT: R 512 ASN cc_start: 0.8517 (t0) cc_final: 0.8200 (t0) REVERT: R 700 ASN cc_start: 0.8513 (t0) cc_final: 0.8230 (t0) REVERT: R 730 LEU cc_start: 0.6379 (OUTLIER) cc_final: 0.6087 (mp) REVERT: R 776 LEU cc_start: 0.7140 (OUTLIER) cc_final: 0.6849 (mp) REVERT: Q 31 ASP cc_start: 0.7854 (m-30) cc_final: 0.7621 (m-30) REVERT: Q 96 ARG cc_start: 0.8275 (mtp85) cc_final: 0.7759 (mtp180) REVERT: Q 190 ASP cc_start: 0.8012 (m-30) cc_final: 0.7655 (m-30) REVERT: Q 270 PHE cc_start: 0.8253 (OUTLIER) cc_final: 0.7749 (t80) REVERT: Q 340 ARG cc_start: 0.7813 (mtt-85) cc_final: 0.7571 (mmt90) REVERT: A 73 LYS cc_start: 0.8346 (mmtt) cc_final: 0.7969 (mmtt) REVERT: A 242 GLU cc_start: 0.7449 (tp30) cc_final: 0.6933 (tp30) REVERT: B 76 ASP cc_start: 0.7689 (p0) cc_final: 0.7309 (p0) REVERT: B 270 ILE cc_start: 0.8422 (pt) cc_final: 0.8199 (pt) REVERT: H 226 SER cc_start: 0.8585 (m) cc_final: 0.8228 (p) REVERT: H 230 THR cc_start: 0.8183 (p) cc_final: 0.7942 (p) outliers start: 65 outliers final: 51 residues processed: 395 average time/residue: 0.3563 time to fit residues: 212.5139 Evaluate side-chains 416 residues out of total 2246 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 55 poor density : 361 time to evaluate : 2.361 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 58 VAL Chi-restraints excluded: chain R residue 223 ILE Chi-restraints excluded: chain R residue 228 GLU Chi-restraints excluded: chain R residue 270 PHE Chi-restraints excluded: chain R residue 412 THR Chi-restraints excluded: chain R residue 531 SER Chi-restraints excluded: chain R residue 566 VAL Chi-restraints excluded: chain R residue 592 ASN Chi-restraints excluded: chain R residue 609 THR Chi-restraints excluded: chain R residue 654 LEU Chi-restraints excluded: chain R residue 730 LEU Chi-restraints excluded: chain R residue 776 LEU Chi-restraints excluded: chain R residue 869 ILE Chi-restraints excluded: chain Q residue 44 VAL Chi-restraints excluded: chain Q residue 60 CYS Chi-restraints excluded: chain Q residue 223 ILE Chi-restraints excluded: chain Q residue 250 GLU Chi-restraints excluded: chain Q residue 270 PHE Chi-restraints excluded: chain Q residue 412 THR Chi-restraints excluded: chain Q residue 437 CYS Chi-restraints excluded: chain Q residue 478 THR Chi-restraints excluded: chain Q residue 497 SER Chi-restraints excluded: chain Q residue 566 VAL Chi-restraints excluded: chain Q residue 587 ASP Chi-restraints excluded: chain Q residue 599 ILE Chi-restraints excluded: chain Q residue 697 VAL Chi-restraints excluded: chain Q residue 744 TYR Chi-restraints excluded: chain Q residue 833 VAL Chi-restraints excluded: chain Q residue 842 LEU Chi-restraints excluded: chain Q residue 848 LEU Chi-restraints excluded: chain A residue 49 ILE Chi-restraints excluded: chain A residue 177 THR Chi-restraints excluded: chain A residue 201 SER Chi-restraints excluded: chain A residue 216 THR Chi-restraints excluded: chain A residue 221 THR Chi-restraints excluded: chain A residue 244 ASN Chi-restraints excluded: chain B residue 119 ASN Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 143 THR Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 172 GLU Chi-restraints excluded: chain B residue 177 THR Chi-restraints excluded: chain B residue 186 ASP Chi-restraints excluded: chain B residue 195 ASP Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain G residue 25 ILE Chi-restraints excluded: chain H residue 25 VAL Chi-restraints excluded: chain H residue 89 THR Chi-restraints excluded: chain H residue 98 THR Chi-restraints excluded: chain H residue 136 THR Chi-restraints excluded: chain H residue 161 THR Chi-restraints excluded: chain N residue 63 SER Chi-restraints excluded: chain N residue 69 THR Chi-restraints excluded: chain N residue 91 THR Chi-restraints excluded: chain N residue 110 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 257 random chunks: chunk 153 optimal weight: 1.9990 chunk 98 optimal weight: 0.9980 chunk 147 optimal weight: 0.9980 chunk 74 optimal weight: 0.9990 chunk 48 optimal weight: 0.9990 chunk 47 optimal weight: 0.2980 chunk 157 optimal weight: 0.9980 chunk 168 optimal weight: 0.7980 chunk 122 optimal weight: 2.9990 chunk 23 optimal weight: 0.8980 chunk 194 optimal weight: 0.9980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 493 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 524 ASN ** A 82 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 155 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7728 moved from start: 0.1458 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.049 21865 Z= 0.303 Angle : 0.546 7.568 29710 Z= 0.289 Chirality : 0.043 0.178 3364 Planarity : 0.004 0.054 3690 Dihedral : 6.749 57.096 4110 Min Nonbonded Distance : 2.129 Molprobity Statistics. All-atom Clashscore : 5.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.22 % Favored : 96.78 % Rotamer: Outliers : 3.12 % Allowed : 11.22 % Favored : 85.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.09 % Cis-general : 0.08 % 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: 0.50 (0.16), residues: 2581 helix: 1.88 (0.17), residues: 886 sheet: -0.11 (0.22), residues: 561 loop : -0.64 (0.18), residues: 1134 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP Q 818 HIS 0.004 0.001 HIS B 183 PHE 0.022 0.002 PHE A 74 TYR 0.014 0.002 TYR A 30 ARG 0.007 0.000 ARG Q 54 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5162 Ramachandran restraints generated. 2581 Oldfield, 0 Emsley, 2581 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5162 Ramachandran restraints generated. 2581 Oldfield, 0 Emsley, 2581 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 426 residues out of total 2246 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 70 poor density : 356 time to evaluate : 2.266 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 25 ARG cc_start: 0.7254 (ptt-90) cc_final: 0.7037 (ptt-90) REVERT: R 270 PHE cc_start: 0.8408 (OUTLIER) cc_final: 0.7974 (m-80) REVERT: R 512 ASN cc_start: 0.8519 (t0) cc_final: 0.8202 (t0) REVERT: R 700 ASN cc_start: 0.8498 (t0) cc_final: 0.8223 (t0) REVERT: R 730 LEU cc_start: 0.6415 (OUTLIER) cc_final: 0.6111 (mp) REVERT: R 776 LEU cc_start: 0.7150 (OUTLIER) cc_final: 0.6854 (mp) REVERT: Q 31 ASP cc_start: 0.7861 (m-30) cc_final: 0.7605 (m-30) REVERT: Q 270 PHE cc_start: 0.8267 (OUTLIER) cc_final: 0.7795 (t80) REVERT: Q 340 ARG cc_start: 0.7821 (mtt-85) cc_final: 0.7582 (mmt90) REVERT: A 242 GLU cc_start: 0.7441 (tp30) cc_final: 0.6914 (tp30) REVERT: B 76 ASP cc_start: 0.7703 (p0) cc_final: 0.7340 (p0) REVERT: B 270 ILE cc_start: 0.8424 (pt) cc_final: 0.8198 (pt) REVERT: H 226 SER cc_start: 0.8593 (m) cc_final: 0.8235 (p) REVERT: H 230 THR cc_start: 0.8201 (p) cc_final: 0.7972 (p) outliers start: 70 outliers final: 55 residues processed: 390 average time/residue: 0.3584 time to fit residues: 211.1537 Evaluate side-chains 416 residues out of total 2246 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 59 poor density : 357 time to evaluate : 2.406 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 58 VAL Chi-restraints excluded: chain R residue 223 ILE Chi-restraints excluded: chain R residue 228 GLU Chi-restraints excluded: chain R residue 270 PHE Chi-restraints excluded: chain R residue 531 SER Chi-restraints excluded: chain R residue 566 VAL Chi-restraints excluded: chain R residue 592 ASN Chi-restraints excluded: chain R residue 609 THR Chi-restraints excluded: chain R residue 639 ASN Chi-restraints excluded: chain R residue 730 LEU Chi-restraints excluded: chain R residue 776 LEU Chi-restraints excluded: chain R residue 833 VAL Chi-restraints excluded: chain R residue 865 SER Chi-restraints excluded: chain R residue 869 ILE Chi-restraints excluded: chain Q residue 44 VAL Chi-restraints excluded: chain Q residue 60 CYS Chi-restraints excluded: chain Q residue 223 ILE Chi-restraints excluded: chain Q residue 270 PHE Chi-restraints excluded: chain Q residue 355 THR Chi-restraints excluded: chain Q residue 412 THR Chi-restraints excluded: chain Q residue 437 CYS Chi-restraints excluded: chain Q residue 470 THR Chi-restraints excluded: chain Q residue 478 THR Chi-restraints excluded: chain Q residue 497 SER Chi-restraints excluded: chain Q residue 566 VAL Chi-restraints excluded: chain Q residue 587 ASP Chi-restraints excluded: chain Q residue 599 ILE Chi-restraints excluded: chain Q residue 697 VAL Chi-restraints excluded: chain Q residue 744 TYR Chi-restraints excluded: chain Q residue 833 VAL Chi-restraints excluded: chain Q residue 842 LEU Chi-restraints excluded: chain Q residue 848 LEU Chi-restraints excluded: chain A residue 49 ILE Chi-restraints excluded: chain A residue 177 THR Chi-restraints excluded: chain A residue 201 SER Chi-restraints excluded: chain A residue 216 THR Chi-restraints excluded: chain A residue 221 THR Chi-restraints excluded: chain A residue 244 ASN Chi-restraints excluded: chain B residue 119 ASN Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 143 THR Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 172 GLU Chi-restraints excluded: chain B residue 177 THR Chi-restraints excluded: chain B residue 186 ASP Chi-restraints excluded: chain B residue 195 ASP Chi-restraints excluded: chain B residue 317 CYS Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain G residue 25 ILE Chi-restraints excluded: chain H residue 25 VAL Chi-restraints excluded: chain H residue 98 THR Chi-restraints excluded: chain H residue 119 SER Chi-restraints excluded: chain H residue 136 THR Chi-restraints excluded: chain H residue 161 THR Chi-restraints excluded: chain N residue 63 SER Chi-restraints excluded: chain N residue 69 THR Chi-restraints excluded: chain N residue 83 MET Chi-restraints excluded: chain N residue 91 THR Chi-restraints excluded: chain N residue 110 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 257 random chunks: chunk 225 optimal weight: 1.9990 chunk 237 optimal weight: 1.9990 chunk 216 optimal weight: 1.9990 chunk 230 optimal weight: 0.5980 chunk 138 optimal weight: 0.9980 chunk 100 optimal weight: 0.7980 chunk 181 optimal weight: 0.8980 chunk 70 optimal weight: 0.3980 chunk 208 optimal weight: 0.5980 chunk 218 optimal weight: 3.9990 chunk 151 optimal weight: 0.2980 overall best weight: 0.5380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 493 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 524 ASN A 75 GLN ** A 82 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7710 moved from start: 0.1470 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 21865 Z= 0.220 Angle : 0.503 6.643 29710 Z= 0.267 Chirality : 0.042 0.173 3364 Planarity : 0.004 0.052 3690 Dihedral : 6.449 53.857 4110 Min Nonbonded Distance : 2.179 Molprobity Statistics. All-atom Clashscore : 5.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.18 % Favored : 96.82 % Rotamer: Outliers : 2.72 % Allowed : 11.93 % Favored : 85.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.09 % Cis-general : 0.08 % 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: 0.63 (0.17), residues: 2581 helix: 2.02 (0.17), residues: 885 sheet: -0.07 (0.22), residues: 555 loop : -0.58 (0.18), residues: 1141 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP Q 818 HIS 0.006 0.001 HIS A 82 PHE 0.019 0.001 PHE A 228 TYR 0.014 0.001 TYR H 210 ARG 0.007 0.000 ARG Q 54 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5162 Ramachandran restraints generated. 2581 Oldfield, 0 Emsley, 2581 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5162 Ramachandran restraints generated. 2581 Oldfield, 0 Emsley, 2581 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 426 residues out of total 2246 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 61 poor density : 365 time to evaluate : 2.283 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 25 ARG cc_start: 0.7210 (ptt-90) cc_final: 0.6958 (ptt-90) REVERT: R 270 PHE cc_start: 0.8416 (OUTLIER) cc_final: 0.7967 (m-80) REVERT: R 512 ASN cc_start: 0.8495 (t0) cc_final: 0.8193 (t0) REVERT: R 700 ASN cc_start: 0.8509 (t0) cc_final: 0.8210 (t0) REVERT: R 730 LEU cc_start: 0.6277 (OUTLIER) cc_final: 0.6008 (mp) REVERT: R 776 LEU cc_start: 0.7100 (OUTLIER) cc_final: 0.6810 (mp) REVERT: Q 31 ASP cc_start: 0.7844 (m-30) cc_final: 0.7598 (m-30) REVERT: Q 96 ARG cc_start: 0.8086 (mtp85) cc_final: 0.7696 (mtp180) REVERT: Q 190 ASP cc_start: 0.8010 (m-30) cc_final: 0.7666 (m-30) REVERT: Q 270 PHE cc_start: 0.8231 (OUTLIER) cc_final: 0.7754 (t80) REVERT: Q 340 ARG cc_start: 0.7812 (mtt-85) cc_final: 0.7584 (mmt90) REVERT: Q 808 THR cc_start: 0.8331 (m) cc_final: 0.8103 (p) REVERT: A 242 GLU cc_start: 0.7436 (tp30) cc_final: 0.6944 (tp30) REVERT: B 270 ILE cc_start: 0.8420 (pt) cc_final: 0.8196 (pt) REVERT: H 226 SER cc_start: 0.8598 (m) cc_final: 0.8351 (p) REVERT: H 230 THR cc_start: 0.8179 (p) cc_final: 0.7935 (p) REVERT: N 60 TYR cc_start: 0.8122 (m-80) cc_final: 0.7865 (m-80) outliers start: 61 outliers final: 52 residues processed: 393 average time/residue: 0.3459 time to fit residues: 205.5666 Evaluate side-chains 415 residues out of total 2246 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 56 poor density : 359 time to evaluate : 2.463 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 58 VAL Chi-restraints excluded: chain R residue 223 ILE Chi-restraints excluded: chain R residue 228 GLU Chi-restraints excluded: chain R residue 270 PHE Chi-restraints excluded: chain R residue 531 SER Chi-restraints excluded: chain R residue 598 CYS Chi-restraints excluded: chain R residue 609 THR Chi-restraints excluded: chain R residue 639 ASN Chi-restraints excluded: chain R residue 730 LEU Chi-restraints excluded: chain R residue 776 LEU Chi-restraints excluded: chain R residue 833 VAL Chi-restraints excluded: chain R residue 869 ILE Chi-restraints excluded: chain Q residue 44 VAL Chi-restraints excluded: chain Q residue 60 CYS Chi-restraints excluded: chain Q residue 223 ILE Chi-restraints excluded: chain Q residue 250 GLU Chi-restraints excluded: chain Q residue 270 PHE Chi-restraints excluded: chain Q residue 355 THR Chi-restraints excluded: chain Q residue 412 THR Chi-restraints excluded: chain Q residue 437 CYS Chi-restraints excluded: chain Q residue 470 THR Chi-restraints excluded: chain Q residue 478 THR Chi-restraints excluded: chain Q residue 497 SER Chi-restraints excluded: chain Q residue 566 VAL Chi-restraints excluded: chain Q residue 587 ASP Chi-restraints excluded: chain Q residue 599 ILE Chi-restraints excluded: chain Q residue 697 VAL Chi-restraints excluded: chain Q residue 744 TYR Chi-restraints excluded: chain Q residue 842 LEU Chi-restraints excluded: chain Q residue 848 LEU Chi-restraints excluded: chain A residue 49 ILE Chi-restraints excluded: chain A residue 177 THR Chi-restraints excluded: chain A residue 201 SER Chi-restraints excluded: chain A residue 216 THR Chi-restraints excluded: chain A residue 221 THR Chi-restraints excluded: chain A residue 238 MET Chi-restraints excluded: chain A residue 244 ASN Chi-restraints excluded: chain B residue 119 ASN Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 143 THR Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 172 GLU Chi-restraints excluded: chain B residue 177 THR Chi-restraints excluded: chain B residue 186 ASP Chi-restraints excluded: chain B residue 195 ASP Chi-restraints excluded: chain B residue 317 CYS Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain G residue 25 ILE Chi-restraints excluded: chain H residue 25 VAL Chi-restraints excluded: chain H residue 98 THR Chi-restraints excluded: chain H residue 136 THR Chi-restraints excluded: chain H residue 161 THR Chi-restraints excluded: chain N residue 63 SER Chi-restraints excluded: chain N residue 69 THR Chi-restraints excluded: chain N residue 91 THR Chi-restraints excluded: chain N residue 110 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 257 random chunks: chunk 244 optimal weight: 0.0270 chunk 148 optimal weight: 0.9980 chunk 115 optimal weight: 1.9990 chunk 169 optimal weight: 0.7980 chunk 256 optimal weight: 0.7980 chunk 235 optimal weight: 0.0670 chunk 203 optimal weight: 0.9980 chunk 21 optimal weight: 0.6980 chunk 157 optimal weight: 0.9990 chunk 125 optimal weight: 0.6980 chunk 161 optimal weight: 0.6980 overall best weight: 0.4376 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 493 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 855 ASN Q 24 GLN Q 524 ASN ** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7701 moved from start: 0.1521 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 21865 Z= 0.194 Angle : 0.492 7.075 29710 Z= 0.262 Chirality : 0.041 0.176 3364 Planarity : 0.004 0.049 3690 Dihedral : 6.260 52.658 4110 Min Nonbonded Distance : 2.187 Molprobity Statistics. All-atom Clashscore : 5.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.22 % Favored : 96.78 % Rotamer: Outliers : 2.54 % Allowed : 12.56 % Favored : 84.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.09 % Cis-general : 0.08 % 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: 0.72 (0.17), residues: 2581 helix: 2.11 (0.17), residues: 885 sheet: -0.03 (0.22), residues: 560 loop : -0.53 (0.18), residues: 1136 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP Q 818 HIS 0.005 0.001 HIS Q 41 PHE 0.019 0.001 PHE A 74 TYR 0.014 0.001 TYR H 210 ARG 0.007 0.000 ARG Q 54 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5162 Ramachandran restraints generated. 2581 Oldfield, 0 Emsley, 2581 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5162 Ramachandran restraints generated. 2581 Oldfield, 0 Emsley, 2581 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 419 residues out of total 2246 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 57 poor density : 362 time to evaluate : 2.267 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 270 PHE cc_start: 0.8397 (OUTLIER) cc_final: 0.7939 (m-80) REVERT: R 512 ASN cc_start: 0.8483 (t0) cc_final: 0.8210 (t0) REVERT: R 700 ASN cc_start: 0.8493 (t0) cc_final: 0.8207 (t0) REVERT: R 707 GLU cc_start: 0.7238 (mt-10) cc_final: 0.7028 (mt-10) REVERT: R 729 PHE cc_start: 0.7137 (t80) cc_final: 0.6762 (t80) REVERT: R 730 LEU cc_start: 0.6262 (OUTLIER) cc_final: 0.6019 (mp) REVERT: R 776 LEU cc_start: 0.7070 (OUTLIER) cc_final: 0.6775 (mp) REVERT: Q 31 ASP cc_start: 0.7845 (m-30) cc_final: 0.7597 (m-30) REVERT: Q 96 ARG cc_start: 0.8067 (mtp85) cc_final: 0.7701 (mtp180) REVERT: Q 190 ASP cc_start: 0.7955 (m-30) cc_final: 0.7618 (m-30) REVERT: Q 270 PHE cc_start: 0.8218 (OUTLIER) cc_final: 0.7715 (t80) REVERT: Q 340 ARG cc_start: 0.7784 (mtt-85) cc_final: 0.7428 (mmt90) REVERT: Q 794 SER cc_start: 0.8408 (m) cc_final: 0.8088 (p) REVERT: A 73 LYS cc_start: 0.8197 (mmtt) cc_final: 0.7519 (mmmt) REVERT: A 242 GLU cc_start: 0.7444 (tp30) cc_final: 0.6957 (tp30) REVERT: B 270 ILE cc_start: 0.8403 (pt) cc_final: 0.8186 (pt) REVERT: H 230 THR cc_start: 0.8204 (p) cc_final: 0.7952 (p) REVERT: N 60 TYR cc_start: 0.8099 (m-80) cc_final: 0.7839 (m-80) outliers start: 57 outliers final: 47 residues processed: 391 average time/residue: 0.3483 time to fit residues: 204.9376 Evaluate side-chains 408 residues out of total 2246 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 357 time to evaluate : 2.382 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 58 VAL Chi-restraints excluded: chain R residue 223 ILE Chi-restraints excluded: chain R residue 228 GLU Chi-restraints excluded: chain R residue 270 PHE Chi-restraints excluded: chain R residue 531 SER Chi-restraints excluded: chain R residue 609 THR Chi-restraints excluded: chain R residue 639 ASN Chi-restraints excluded: chain R residue 730 LEU Chi-restraints excluded: chain R residue 776 LEU Chi-restraints excluded: chain R residue 833 VAL Chi-restraints excluded: chain R residue 869 ILE Chi-restraints excluded: chain Q residue 44 VAL Chi-restraints excluded: chain Q residue 60 CYS Chi-restraints excluded: chain Q residue 223 ILE Chi-restraints excluded: chain Q residue 250 GLU Chi-restraints excluded: chain Q residue 270 PHE Chi-restraints excluded: chain Q residue 355 THR Chi-restraints excluded: chain Q residue 412 THR Chi-restraints excluded: chain Q residue 437 CYS Chi-restraints excluded: chain Q residue 470 THR Chi-restraints excluded: chain Q residue 497 SER Chi-restraints excluded: chain Q residue 566 VAL Chi-restraints excluded: chain Q residue 587 ASP Chi-restraints excluded: chain Q residue 697 VAL Chi-restraints excluded: chain Q residue 744 TYR Chi-restraints excluded: chain Q residue 842 LEU Chi-restraints excluded: chain A residue 49 ILE Chi-restraints excluded: chain A residue 177 THR Chi-restraints excluded: chain A residue 201 SER Chi-restraints excluded: chain A residue 216 THR Chi-restraints excluded: chain A residue 221 THR Chi-restraints excluded: chain A residue 238 MET Chi-restraints excluded: chain A residue 244 ASN Chi-restraints excluded: chain B residue 119 ASN Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 143 THR Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 177 THR Chi-restraints excluded: chain B residue 186 ASP Chi-restraints excluded: chain B residue 195 ASP Chi-restraints excluded: chain B residue 317 CYS Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain G residue 25 ILE Chi-restraints excluded: chain H residue 25 VAL Chi-restraints excluded: chain H residue 98 THR Chi-restraints excluded: chain H residue 136 THR Chi-restraints excluded: chain H residue 161 THR Chi-restraints excluded: chain N residue 63 SER Chi-restraints excluded: chain N residue 69 THR Chi-restraints excluded: chain N residue 91 THR Chi-restraints excluded: chain N residue 110 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 257 random chunks: chunk 217 optimal weight: 0.7980 chunk 62 optimal weight: 1.9990 chunk 187 optimal weight: 1.9990 chunk 30 optimal weight: 0.5980 chunk 56 optimal weight: 0.9990 chunk 204 optimal weight: 0.9980 chunk 85 optimal weight: 0.9990 chunk 209 optimal weight: 0.9980 chunk 25 optimal weight: 0.6980 chunk 37 optimal weight: 0.9980 chunk 179 optimal weight: 0.9980 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 493 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 24 GLN Q 524 ASN A 75 GLN ** A 82 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3203 r_free = 0.3203 target = 0.100601 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2914 r_free = 0.2914 target = 0.084458 restraints weight = 34509.633| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.2943 r_free = 0.2943 target = 0.086119 restraints weight = 24562.151| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.2974 r_free = 0.2974 target = 0.087781 restraints weight = 18536.242| |-----------------------------------------------------------------------------| r_work (final): 0.2950 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7699 moved from start: 0.1544 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.040 21865 Z= 0.305 Angle : 0.548 7.583 29710 Z= 0.289 Chirality : 0.043 0.182 3364 Planarity : 0.004 0.053 3690 Dihedral : 6.466 56.968 4110 Min Nonbonded Distance : 2.126 Molprobity Statistics. All-atom Clashscore : 5.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.37 % Favored : 96.63 % Rotamer: Outliers : 2.58 % Allowed : 12.60 % Favored : 84.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.09 % Cis-general : 0.08 % 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: 0.58 (0.16), residues: 2581 helix: 1.96 (0.17), residues: 886 sheet: -0.09 (0.22), residues: 561 loop : -0.59 (0.18), residues: 1134 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP Q 818 HIS 0.010 0.001 HIS A 82 PHE 0.023 0.002 PHE A 74 TYR 0.014 0.002 TYR A 30 ARG 0.008 0.000 ARG Q 54 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5070.30 seconds wall clock time: 91 minutes 15.88 seconds (5475.88 seconds total)