Starting phenix.real_space_refine on Wed Aug 7 00:44:50 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9asb_43811/08_2024/9asb_43811.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9asb_43811/08_2024/9asb_43811.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9asb_43811/08_2024/9asb_43811.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9asb_43811/08_2024/9asb_43811.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9asb_43811/08_2024/9asb_43811.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9asb_43811/08_2024/9asb_43811.cif" } resolution = 3.4 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= 0.042 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 6 9.91 5 P 3 5.49 5 S 103 5.16 5 Cl 2 4.86 5 C 11689 2.51 5 N 3002 2.21 5 O 3380 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "Q ASP 50": "OD1" <-> "OD2" Residue "Q GLU 232": "OE1" <-> "OE2" Residue "Q GLU 250": "OE1" <-> "OE2" Residue "Q GLU 257": "OE1" <-> "OE2" Residue "Q GLU 353": "OE1" <-> "OE2" Residue "Q GLU 354": "OE1" <-> "OE2" Residue "Q PHE 356": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q GLU 399": "OE1" <-> "OE2" Residue "Q GLU 475": "OE1" <-> "OE2" Residue "Q GLU 481": "OE1" <-> "OE2" Residue "Q PHE 522": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q GLU 536": "OE1" <-> "OE2" Residue "Q PHE 539": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q ASP 575": "OD1" <-> "OD2" Residue "Q PHE 612": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q PHE 706": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q PHE 762": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q GLU 803": "OE1" <-> "OE2" Residue "Q PHE 814": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q GLU 837": "OE1" <-> "OE2" Residue "R ASP 31": "OD1" <-> "OD2" Residue "R TYR 161": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R ASP 190": "OD1" <-> "OD2" Residue "R GLU 228": "OE1" <-> "OE2" Residue "R GLU 249": "OE1" <-> "OE2" Residue "R GLU 257": "OE1" <-> "OE2" Residue "R GLU 282": "OE1" <-> "OE2" Residue "R PHE 356": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R TYR 425": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R GLU 475": "OE1" <-> "OE2" Residue "R GLU 507": "OE1" <-> "OE2" Residue "R GLU 526": "OE1" <-> "OE2" Residue "R GLU 536": "OE1" <-> "OE2" Residue "R PHE 667": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R PHE 706": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R TYR 744": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R GLU 755": "OE1" <-> "OE2" Residue "R GLU 799": "OE1" <-> "OE2" Residue "R GLU 803": "OE1" <-> "OE2" Residue "R PHE 809": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R PHE 832": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 77": "OD1" <-> "OD2" Residue "A ASP 114": "OD1" <-> "OD2" Residue "A ASP 147": "OD1" <-> "OD2" Residue "A TYR 163": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 164": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 174": "OE1" <-> "OE2" Residue "A TYR 191": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 195": "OD1" <-> "OD2" Residue "A ASP 220": "OD1" <-> "OD2" Residue "A PHE 228": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 38": "OD1" <-> "OD2" Residue "B ASP 76": "OD1" <-> "OD2" Residue "B TYR 105": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 124": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 130": "OE1" <-> "OE2" Residue "B PHE 199": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 241": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 267": "OD1" <-> "OD2" Residue "B PHE 278": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 323": "OD1" <-> "OD2" Time to flip residues: 1.76s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/chem_data/mon_lib" Total number of atoms: 18185 Number of models: 1 Model: "" Number of chains: 13 Chain: "Q" Number of atoms: 6402 Number of conformers: 1 Conformer: "" Number of residues, atoms: 804, 6402 Classifications: {'peptide': 804} Link IDs: {'CIS': 1, 'PTRANS': 31, 'TRANS': 771} Chain breaks: 3 Chain: "R" Number of atoms: 6449 Number of conformers: 1 Conformer: "" Number of residues, atoms: 809, 6449 Classifications: {'peptide': 809} Link IDs: {'CIS': 1, 'PTRANS': 32, 'TRANS': 775} Chain breaks: 2 Chain: "A" Number of atoms: 1928 Number of conformers: 1 Conformer: "" Number of residues, atoms: 234, 1928 Classifications: {'peptide': 234} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 227} 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: "C" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "D" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "E" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "F" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "Q" Number of atoms: 58 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 58 Unusual residues: {'NAG': 3, 'TCR': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "Q" Number of atoms: 65 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 65 Unusual residues: {' CA': 4, '9IG': 1, 'PO4': 1, 'Y01': 1} Classifications: {'undetermined': 7} Link IDs: {None: 6} Chain: "R" Number of atoms: 58 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 58 Unusual residues: {'NAG': 3, 'TCR': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "R" Number of atoms: 79 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 79 Unusual residues: {' CA': 2, '9IG': 1, 'A1AF7': 1, 'PO4': 1} Classifications: {'undetermined': 5} Link IDs: {None: 4} Time building chain proxies: 11.76, per 1000 atoms: 0.65 Number of scatterers: 18185 At special positions: 0 Unit cell: (93.225, 121.275, 246.675, 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 6 19.99 Cl 2 17.00 S 103 16.00 P 3 15.00 O 3380 8.00 N 3002 7.00 C 11689 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=16, symmetry=0 Simple disulfide: pdb=" SG CYS Q 60 " - pdb=" SG CYS Q 101 " distance=2.03 Simple disulfide: pdb=" SG CYS Q 236 " - pdb=" SG CYS Q 561 " distance=2.03 Simple disulfide: pdb=" SG CYS Q 358 " - pdb=" SG CYS Q 395 " distance=2.03 Simple disulfide: pdb=" SG CYS Q 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 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 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 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied BETA1-4 " NAG C 1 " - " NAG C 2 " " NAG D 1 " - " NAG D 2 " " NAG E 1 " - " NAG E 2 " " NAG F 1 " - " NAG F 2 " NAG-ASN " NAG C 1 " - " ASN Q 488 " " NAG D 1 " - " ASN Q 541 " " NAG E 1 " - " ASN R 488 " " NAG F 1 " - " ASN R 541 " " NAG Q1001 " - " ASN Q 261 " " NAG Q1002 " - " ASN Q 287 " " NAG Q1003 " - " ASN Q 468 " " NAG R1001 " - " ASN R 261 " " NAG R1002 " - " ASN R 287 " " NAG R1003 " - " ASN R 468 " Time building additional restraints: 6.81 Conformation dependent library (CDL) restraints added in 3.3 seconds 4438 Ramachandran restraints generated. 2219 Oldfield, 0 Emsley, 2219 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4222 Finding SS restraints... Secondary structure from input PDB file: 78 helices and 23 sheets defined 46.2% alpha, 15.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.51 Creating SS restraints... Processing helix chain 'Q' and resid 64 through 84 Processing helix chain 'Q' and resid 103 through 115 Processing helix chain 'Q' and resid 115 through 123 Processing helix chain 'Q' and resid 146 through 158 Processing helix chain 'Q' and resid 171 through 176 removed outlier: 3.507A 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: 3.569A 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 356 Processing helix chain 'Q' and resid 400 through 404 removed outlier: 3.733A pdb=" N VAL Q 404 " --> pdb=" O ILE Q 401 " (cutoff:3.500A) Processing helix chain 'Q' and resid 415 through 436 Processing helix chain 'Q' and resid 444 through 448 Processing helix chain 'Q' and resid 451 through 455 removed outlier: 3.991A pdb=" N VAL Q 455 " --> pdb=" O ILE Q 452 " (cutoff:3.500A) 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 646 Processing helix chain 'Q' and resid 647 through 665 removed outlier: 3.703A pdb=" N SER Q 665 " --> pdb=" O CYS Q 661 " (cutoff:3.500A) Processing helix chain 'Q' and resid 666 through 668 No H-bonds generated for 'chain 'Q' and resid 666 through 668' Processing helix chain 'Q' and resid 673 through 699 removed outlier: 4.609A 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 702 through 708 Processing helix chain 'Q' and resid 722 through 746 removed outlier: 3.770A pdb=" N GLN Q 735 " --> pdb=" O CYS Q 731 " (cutoff:3.500A) Processing helix chain 'Q' and resid 769 through 793 Processing helix chain 'Q' and resid 798 through 827 removed outlier: 6.045A pdb=" N ALA Q 804 " --> pdb=" O ASN Q 800 " (cutoff:3.500A) removed outlier: 6.555A pdb=" N LYS Q 805 " --> pdb=" O PHE Q 801 " (cutoff:3.500A) Proline residue: Q 823 - end of helix Processing helix chain 'Q' and resid 831 through 862 removed outlier: 3.965A pdb=" N ALA Q 835 " --> pdb=" O LYS Q 831 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N GLU Q 837 " --> pdb=" O VAL Q 833 " (cutoff:3.500A) removed outlier: 6.578A pdb=" N ASN Q 855 " --> pdb=" O CYS Q 851 " (cutoff:3.500A) removed outlier: 5.326A pdb=" N LYS Q 856 " --> pdb=" O ILE Q 852 " (cutoff:3.500A) Processing helix chain 'Q' and resid 863 through 867 removed outlier: 4.012A pdb=" N ARG Q 866 " --> pdb=" O LYS Q 863 " (cutoff:3.500A) Processing helix chain 'Q' and resid 868 through 873 Processing helix chain 'R' and resid 64 through 84 Processing helix chain 'R' and resid 103 through 115 Processing helix chain 'R' and resid 115 through 124 Processing helix chain 'R' and resid 146 through 160 removed outlier: 3.842A pdb=" N PHE R 160 " --> pdb=" O LEU R 156 " (cutoff:3.500A) Processing helix chain 'R' and resid 171 through 176 removed outlier: 3.510A pdb=" N ASN R 176 " --> pdb=" O LEU R 173 " (cutoff:3.500A) Processing helix chain 'R' and resid 190 through 204 removed outlier: 3.665A pdb=" N ALA R 194 " --> pdb=" O ASP R 190 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N THR R 195 " --> pdb=" O GLU R 191 " (cutoff:3.500A) Processing helix chain 'R' and resid 218 through 233 removed outlier: 3.577A pdb=" N GLY R 222 " --> pdb=" O TYR R 218 " (cutoff:3.500A) Processing helix chain 'R' and resid 248 through 261 Processing helix chain 'R' and resid 272 through 286 Proline residue: R 278 - end of helix Processing helix chain 'R' and resid 296 through 301 removed outlier: 4.531A pdb=" N SER R 301 " --> pdb=" O GLU R 297 " (cutoff:3.500A) 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 removed outlier: 3.615A pdb=" N VAL R 404 " --> pdb=" O ILE R 401 " (cutoff:3.500A) 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: 3.879A 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 525 through 528 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 Processing helix chain 'R' and resid 647 through 665 Processing helix chain 'R' and resid 666 through 669 removed outlier: 3.716A pdb=" N ILE R 669 " --> pdb=" O LEU R 666 " (cutoff:3.500A) No H-bonds generated for 'chain 'R' and resid 666 through 669' Processing helix chain 'R' and resid 673 through 707 removed outlier: 4.413A pdb=" N GLN R 681 " --> pdb=" O CYS R 677 " (cutoff:3.500A) Proline residue: R 682 - end of helix Processing helix chain 'R' and resid 718 through 746 Processing helix chain 'R' and resid 769 through 794 Processing helix chain 'R' and resid 798 through 802 Processing helix chain 'R' and resid 803 through 821 Processing helix chain 'R' and resid 821 through 826 Processing helix chain 'R' and resid 830 through 862 removed outlier: 3.813A pdb=" N SER R 834 " --> pdb=" O GLY R 830 " (cutoff:3.500A) removed outlier: 5.270A pdb=" N ASN R 855 " --> pdb=" O CYS R 851 " (cutoff:3.500A) removed outlier: 5.451A pdb=" N LYS R 856 " --> pdb=" O ILE R 852 " (cutoff:3.500A) Processing helix chain 'R' and resid 863 through 867 removed outlier: 4.003A pdb=" N ARG R 866 " --> pdb=" O LYS R 863 " (cutoff:3.500A) Processing helix chain 'A' and resid 6 through 33 removed outlier: 3.754A pdb=" N ALA A 11 " --> pdb=" O ALA A 7 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N GLN A 28 " --> pdb=" O GLN A 24 " (cutoff:3.500A) removed outlier: 3.932A pdb=" N VAL A 29 " --> pdb=" O LYS A 25 " (cutoff:3.500A) Processing helix chain 'A' and resid 41 through 44 Processing helix chain 'A' and resid 45 through 56 Processing helix chain 'A' and resid 117 through 131 Processing helix chain 'A' and resid 132 through 135 removed outlier: 3.549A pdb=" N ARG A 135 " --> pdb=" O ARG A 132 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 132 through 135' Processing helix chain 'A' and resid 145 through 155 removed outlier: 3.628A pdb=" N LEU A 149 " --> pdb=" O LYS A 145 " (cutoff:3.500A) Processing helix chain 'A' and resid 159 through 163 Processing helix chain 'A' and resid 183 through 203 removed outlier: 3.775A pdb=" N ILE A 200 " --> pdb=" O GLU A 196 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N ALA A 203 " --> pdb=" O ARG A 199 " (cutoff:3.500A) Processing helix chain 'A' and resid 222 through 243 Processing helix chain 'B' and resid 4 through 26 Processing helix chain 'B' and resid 29 through 34 Processing helix chain 'G' and resid 9 through 24 Processing helix chain 'G' and resid 29 through 44 removed outlier: 3.518A pdb=" N ALA G 33 " --> pdb=" O LYS G 29 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'Q' and resid 26 through 28 removed outlier: 6.078A pdb=" N ILE Q 32 " --> pdb=" O GLY Q 94 " (cutoff:3.500A) removed outlier: 7.410A pdb=" N ARG Q 96 " --> pdb=" O ILE Q 32 " (cutoff:3.500A) removed outlier: 6.407A pdb=" N LEU Q 34 " --> pdb=" O ARG Q 96 " (cutoff:3.500A) removed outlier: 7.670A pdb=" N PHE Q 98 " --> pdb=" O LEU Q 34 " (cutoff:3.500A) removed outlier: 6.324A pdb=" N GLY Q 36 " --> pdb=" O PHE Q 98 " (cutoff:3.500A) removed outlier: 6.866A pdb=" N ILE Q 33 " --> pdb=" O THR Q 138 " (cutoff:3.500A) removed outlier: 4.007A pdb=" N ALA Q 140 " --> pdb=" O ILE Q 33 " (cutoff:3.500A) removed outlier: 8.529A pdb=" N VAL Q 165 " --> pdb=" O ILE Q 139 " (cutoff:3.500A) removed outlier: 6.481A pdb=" N VAL Q 141 " --> pdb=" O VAL Q 165 " (cutoff:3.500A) removed outlier: 5.974A pdb=" N GLN Q 164 " --> pdb=" O LEU Q 184 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'Q' and resid 41 through 44 removed outlier: 7.144A pdb=" N ARG Q 62 " --> pdb=" O PHE Q 42 " (cutoff:3.500A) removed outlier: 6.431A pdb=" N VAL Q 44 " --> pdb=" O CYS Q 60 " (cutoff:3.500A) removed outlier: 6.292A pdb=" N CYS Q 60 " --> pdb=" O VAL Q 44 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'Q' and resid 236 through 243 removed outlier: 6.438A pdb=" N VAL Q 209 " --> pdb=" O ILE Q 237 " (cutoff:3.500A) removed outlier: 4.295A pdb=" N PHE Q 239 " --> pdb=" O VAL Q 209 " (cutoff:3.500A) removed outlier: 7.030A pdb=" N TRP Q 208 " --> pdb=" O VAL Q 266 " (cutoff:3.500A) removed outlier: 8.252A pdb=" N VAL Q 268 " --> pdb=" O TRP Q 208 " (cutoff:3.500A) removed outlier: 6.470A pdb=" N GLY Q 210 " --> pdb=" O VAL Q 268 " (cutoff:3.500A) removed outlier: 7.719A pdb=" N PHE Q 270 " --> pdb=" O GLY Q 210 " (cutoff:3.500A) removed outlier: 6.784A pdb=" N ILE Q 212 " --> pdb=" O PHE Q 270 " (cutoff:3.500A) removed outlier: 6.696A pdb=" N TYR Q 489 " --> pdb=" O TYR Q 510 " (cutoff:3.500A) removed outlier: 4.650A pdb=" N TYR Q 510 " --> pdb=" O TYR Q 489 " (cutoff:3.500A) removed outlier: 6.470A pdb=" N ILE Q 491 " --> pdb=" O VAL Q 508 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'Q' and resid 468 through 470 Processing sheet with id=AA5, first strand: chain 'Q' and resid 550 through 554 Processing sheet with id=AA6, first strand: chain 'Q' and resid 572 through 573 Processing sheet with id=AA7, first strand: chain 'Q' and resid 589 through 591 Processing sheet with id=AA8, first strand: chain 'Q' and resid 602 through 604 removed outlier: 6.394A pdb=" N GLU Q 602 " --> pdb=" O ILE Q 761 " (cutoff:3.500A) removed outlier: 7.391A pdb=" N ILE Q 763 " --> pdb=" O GLU Q 602 " (cutoff:3.500A) removed outlier: 7.109A pdb=" N GLU Q 604 " --> pdb=" O ILE Q 763 " (cutoff:3.500A) removed outlier: 9.053A pdb=" N CYS Q 765 " --> pdb=" O GLU Q 604 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'R' and resid 25 through 28 removed outlier: 6.066A pdb=" N ILE R 32 " --> pdb=" O GLY R 94 " (cutoff:3.500A) removed outlier: 7.497A pdb=" N ARG R 96 " --> pdb=" O ILE R 32 " (cutoff:3.500A) removed outlier: 6.358A pdb=" N LEU R 34 " --> pdb=" O ARG R 96 " (cutoff:3.500A) removed outlier: 7.705A pdb=" N PHE R 98 " --> pdb=" O LEU R 34 " (cutoff:3.500A) removed outlier: 6.298A pdb=" N GLY R 36 " --> pdb=" O PHE R 98 " (cutoff:3.500A) removed outlier: 6.780A pdb=" N ILE R 33 " --> pdb=" O THR R 138 " (cutoff:3.500A) removed outlier: 4.018A pdb=" N ALA R 140 " --> pdb=" O ILE R 33 " (cutoff:3.500A) removed outlier: 8.524A pdb=" N VAL R 165 " --> pdb=" O ILE R 139 " (cutoff:3.500A) removed outlier: 6.413A pdb=" N VAL R 141 " --> pdb=" O VAL R 165 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'R' and resid 236 through 243 removed outlier: 7.912A pdb=" N VAL R 209 " --> pdb=" O ASP R 238 " (cutoff:3.500A) removed outlier: 6.845A pdb=" N SER R 240 " --> pdb=" O VAL R 209 " (cutoff:3.500A) removed outlier: 6.772A pdb=" N THR R 211 " --> pdb=" O SER R 240 " (cutoff:3.500A) removed outlier: 5.713A pdb=" N LEU R 242 " --> pdb=" O THR R 211 " (cutoff:3.500A) removed outlier: 6.328A pdb=" N ALA R 213 " --> pdb=" O LEU R 242 " (cutoff:3.500A) removed outlier: 4.731A pdb=" N VAL R 266 " --> pdb=" O TRP R 208 " (cutoff:3.500A) removed outlier: 6.577A pdb=" N ILE R 267 " --> pdb=" O LEU R 294 " (cutoff:3.500A) removed outlier: 6.758A pdb=" N TYR R 489 " --> pdb=" O TYR R 510 " (cutoff:3.500A) removed outlier: 4.786A pdb=" N TYR R 510 " --> pdb=" O TYR R 489 " (cutoff:3.500A) removed outlier: 6.373A pdb=" N ILE R 491 " --> pdb=" O VAL R 508 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'R' and resid 468 through 470 Processing sheet with id=AB3, first strand: chain 'R' and resid 550 through 554 Processing sheet with id=AB4, first strand: chain 'R' and resid 572 through 573 Processing sheet with id=AB5, first strand: chain 'R' and resid 589 through 591 Processing sheet with id=AB6, first strand: chain 'R' and resid 602 through 604 Processing sheet with id=AB7, first strand: chain 'A' and resid 73 through 76 removed outlier: 6.430A pdb=" N ARG A 35 " --> pdb=" O ALA A 105 " (cutoff:3.500A) removed outlier: 7.433A pdb=" N ILE A 107 " --> pdb=" O ARG A 35 " (cutoff:3.500A) removed outlier: 6.224A pdb=" N LEU A 37 " --> pdb=" O ILE A 107 " (cutoff:3.500A) removed outlier: 7.210A pdb=" N VAL A 109 " --> pdb=" O LEU A 37 " (cutoff:3.500A) removed outlier: 6.898A pdb=" N LEU A 39 " --> pdb=" O VAL A 109 " (cutoff:3.500A) removed outlier: 9.030A pdb=" N ASP A 111 " --> pdb=" O LEU A 39 " (cutoff:3.500A) removed outlier: 6.234A pdb=" N ILE A 106 " --> pdb=" O ILE A 140 " (cutoff:3.500A) removed outlier: 6.691A pdb=" N PHE A 142 " --> pdb=" O ILE A 106 " (cutoff:3.500A) removed outlier: 6.183A pdb=" N PHE A 108 " --> pdb=" O PHE A 142 " (cutoff:3.500A) removed outlier: 6.427A pdb=" N ASN A 144 " --> pdb=" O PHE A 108 " (cutoff:3.500A) removed outlier: 5.819A pdb=" N VAL A 110 " --> pdb=" O ASN A 144 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'B' and resid 46 through 51 removed outlier: 6.180A pdb=" N THR B 47 " --> pdb=" O ASN B 340 " (cutoff:3.500A) removed outlier: 6.996A pdb=" N ASN B 340 " --> pdb=" O THR B 47 " (cutoff:3.500A) removed outlier: 3.636A 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: 7.006A pdb=" N ALA B 73 " --> pdb=" O TYR B 59 " (cutoff:3.500A) removed outlier: 4.337A pdb=" N MET B 61 " --> pdb=" O VAL B 71 " (cutoff:3.500A) removed outlier: 6.520A pdb=" N VAL B 71 " --> pdb=" O MET B 61 " (cutoff:3.500A) removed outlier: 5.154A pdb=" N TRP B 63 " --> pdb=" O LEU B 69 " (cutoff:3.500A) removed outlier: 7.058A pdb=" N LEU B 69 " --> pdb=" O TRP B 63 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N HIS B 91 " --> pdb=" O ILE B 81 " (cutoff:3.500A) removed outlier: 5.672A pdb=" N ASP B 83 " --> pdb=" O LYS B 89 " (cutoff:3.500A) removed outlier: 5.714A pdb=" N LYS B 89 " --> pdb=" O ASP B 83 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 102 through 105 removed outlier: 5.975A pdb=" N CYS B 121 " --> pdb=" O GLU B 138 " (cutoff:3.500A) removed outlier: 4.834A pdb=" N GLU B 138 " --> pdb=" O CYS B 121 " (cutoff:3.500A) removed outlier: 6.698A pdb=" N ILE B 123 " --> pdb=" O SER B 136 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 146 through 151 removed outlier: 4.071A pdb=" N THR B 165 " --> pdb=" O SER B 161 " (cutoff:3.500A) removed outlier: 4.608A pdb=" N THR B 178 " --> pdb=" O LEU B 168 " (cutoff:3.500A) removed outlier: 6.879A pdb=" N ASP B 170 " --> pdb=" O GLN B 176 " (cutoff:3.500A) removed outlier: 6.451A 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: 3.691A pdb=" N GLN B 220 " --> pdb=" O LEU B 210 " (cutoff:3.500A) removed outlier: 7.201A pdb=" N ASP B 212 " --> pdb=" O CYS B 218 " (cutoff:3.500A) removed outlier: 6.624A 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 232 removed outlier: 3.971A pdb=" N MET B 262 " --> pdb=" O LEU B 252 " (cutoff:3.500A) removed outlier: 5.990A pdb=" N ASP B 254 " --> pdb=" O GLU B 260 " (cutoff:3.500A) removed outlier: 5.876A pdb=" N GLU B 260 " --> pdb=" O ASP B 254 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 273 through 278 removed outlier: 4.315A pdb=" N SER B 275 " --> pdb=" O GLY B 288 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N ALA B 287 " --> pdb=" O ASN B 295 " (cutoff:3.500A) removed outlier: 6.185A pdb=" N ASP B 298 " --> pdb=" O ARG B 304 " (cutoff:3.500A) removed outlier: 6.261A pdb=" N ARG B 304 " --> pdb=" O ASP B 298 " (cutoff:3.500A) 868 hydrogen bonds defined for protein. 2487 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: 6.47 Time building geometry restraints manager: 7.54 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.34: 5710 1.34 - 1.46: 4353 1.46 - 1.58: 8407 1.58 - 1.71: 3 1.71 - 1.83: 132 Bond restraints: 18605 Sorted by residual: bond pdb=" CAI Y01 Q1011 " pdb=" CAK Y01 Q1011 " ideal model delta sigma weight residual 1.492 1.405 0.087 2.00e-02 2.50e+03 1.90e+01 bond pdb=" O3 PO4 Q1005 " pdb=" P PO4 Q1005 " ideal model delta sigma weight residual 1.569 1.505 0.064 2.00e-02 2.50e+03 1.03e+01 bond pdb=" O3 PO4 R1005 " pdb=" P PO4 R1005 " ideal model delta sigma weight residual 1.569 1.506 0.063 2.00e-02 2.50e+03 1.01e+01 bond pdb=" O4 PO4 R1005 " pdb=" P PO4 R1005 " ideal model delta sigma weight residual 1.568 1.505 0.063 2.00e-02 2.50e+03 9.78e+00 bond pdb=" O4 PO4 Q1005 " pdb=" P PO4 Q1005 " ideal model delta sigma weight residual 1.568 1.506 0.062 2.00e-02 2.50e+03 9.73e+00 ... (remaining 18600 not shown) Histogram of bond angle deviations from ideal: 97.48 - 104.84: 239 104.84 - 112.20: 9305 112.20 - 119.57: 6242 119.57 - 126.93: 9189 126.93 - 134.30: 237 Bond angle restraints: 25212 Sorted by residual: angle pdb=" OAG Y01 Q1011 " pdb=" CAY Y01 Q1011 " pdb=" OAW Y01 Q1011 " ideal model delta sigma weight residual 123.38 111.54 11.84 3.00e+00 1.11e-01 1.56e+01 angle pdb=" CAM Y01 Q1011 " pdb=" CAY Y01 Q1011 " pdb=" OAW Y01 Q1011 " ideal model delta sigma weight residual 111.19 122.58 -11.39 3.00e+00 1.11e-01 1.44e+01 angle pdb=" N ILE Q 305 " pdb=" CA ILE Q 305 " pdb=" C ILE Q 305 " ideal model delta sigma weight residual 112.12 108.98 3.14 8.40e-01 1.42e+00 1.39e+01 angle pdb=" N VAL R 508 " pdb=" CA VAL R 508 " pdb=" C VAL R 508 " ideal model delta sigma weight residual 112.43 109.47 2.96 9.20e-01 1.18e+00 1.04e+01 angle pdb=" CAV Y01 Q1011 " pdb=" CAZ Y01 Q1011 " pdb=" CBH Y01 Q1011 " ideal model delta sigma weight residual 116.96 126.10 -9.14 3.00e+00 1.11e-01 9.28e+00 ... (remaining 25207 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.88: 10275 17.88 - 35.76: 800 35.76 - 53.64: 145 53.64 - 71.52: 32 71.52 - 89.40: 15 Dihedral angle restraints: 11267 sinusoidal: 4746 harmonic: 6521 Sorted by residual: dihedral pdb=" CA ALA A 176 " pdb=" C ALA A 176 " pdb=" N THR A 177 " pdb=" CA THR A 177 " ideal model delta harmonic sigma weight residual 180.00 -160.06 -19.94 0 5.00e+00 4.00e-02 1.59e+01 dihedral pdb=" CB CYS Q 546 " pdb=" SG CYS Q 546 " pdb=" SG CYS Q 565 " pdb=" CB CYS Q 565 " ideal model delta sinusoidal sigma weight residual -86.00 -113.79 27.79 1 1.00e+01 1.00e-02 1.11e+01 dihedral pdb=" CA PRO A 178 " pdb=" C PRO A 178 " pdb=" N GLU A 179 " pdb=" CA GLU A 179 " ideal model delta harmonic sigma weight residual 180.00 163.39 16.61 0 5.00e+00 4.00e-02 1.10e+01 ... (remaining 11264 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.053: 2269 0.053 - 0.105: 482 0.105 - 0.158: 72 0.158 - 0.211: 7 0.211 - 0.264: 1 Chirality restraints: 2831 Sorted by residual: chirality pdb=" C02 A1AF7 R1009 " pdb=" C01 A1AF7 R1009 " pdb=" C03 A1AF7 R1009 " pdb=" O01 A1AF7 R1009 " both_signs ideal model delta sigma weight residual False 2.54 2.80 -0.26 2.00e-01 2.50e+01 1.74e+00 chirality pdb=" CBF Y01 Q1011 " pdb=" CAS Y01 Q1011 " pdb=" CBD Y01 Q1011 " pdb=" CBH Y01 Q1011 " both_signs ideal model delta sigma weight residual False -2.45 -2.64 0.20 2.00e-01 2.50e+01 9.56e-01 chirality pdb=" C05 A1AF7 R1009 " pdb=" C04 A1AF7 R1009 " pdb=" CAD A1AF7 R1009 " pdb=" OAF A1AF7 R1009 " both_signs ideal model delta sigma weight residual False -2.53 -2.71 0.19 2.00e-01 2.50e+01 8.72e-01 ... (remaining 2828 not shown) Planarity restraints: 3197 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LEU Q 438 " -0.055 5.00e-02 4.00e+02 8.30e-02 1.10e+01 pdb=" N PRO Q 439 " 0.144 5.00e-02 4.00e+02 pdb=" CA PRO Q 439 " -0.044 5.00e-02 4.00e+02 pdb=" CD PRO Q 439 " -0.045 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR A 177 " -0.051 5.00e-02 4.00e+02 7.82e-02 9.80e+00 pdb=" N PRO A 178 " 0.135 5.00e-02 4.00e+02 pdb=" CA PRO A 178 " -0.041 5.00e-02 4.00e+02 pdb=" CD PRO A 178 " -0.043 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C VAL G 54 " -0.035 5.00e-02 4.00e+02 5.32e-02 4.54e+00 pdb=" N PRO G 55 " 0.092 5.00e-02 4.00e+02 pdb=" CA PRO G 55 " -0.028 5.00e-02 4.00e+02 pdb=" CD PRO G 55 " -0.030 5.00e-02 4.00e+02 ... (remaining 3194 not shown) Histogram of nonbonded interaction distances: 2.17 - 2.71: 645 2.71 - 3.26: 18567 3.26 - 3.81: 30977 3.81 - 4.35: 39593 4.35 - 4.90: 65467 Nonbonded interactions: 155249 Sorted by model distance: nonbonded pdb=" OH TYR B 59 " pdb=" OE1 GLN B 75 " model vdw 2.168 3.040 nonbonded pdb=" NE2 GLN R 253 " pdb=" OE2 GLU R 257 " model vdw 2.176 3.120 nonbonded pdb=" OD1 ASN Q 468 " pdb=" NE2 GLN Q 476 " model vdw 2.180 3.120 nonbonded pdb=" OG SER R 175 " pdb=" NH2 ARG R 185 " model vdw 2.231 3.120 nonbonded pdb=" OD1 ASP R 588 " pdb=" NH2 ARG R 752 " model vdw 2.239 3.120 ... (remaining 155244 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' } ncs_group { reference = (chain 'Q' and (resid 21 through 867 or resid 1003 or resid 1008 through 1010)) selection = (chain 'R' and (resid 21 through 124 or resid 133 through 708 or resid 719 throu \ gh 867 or resid 1001 or resid 1006 through 1008)) } 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 individual isotropic 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: 14.870 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: 0.010 Extract box with map and model: 0.770 Check model and map are aligned: 0.140 Set scattering table: 0.260 Process input model: 53.220 Find NCS groups from input model: 0.730 Set up NCS constraints: 0.080 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: 0.000 Load rotamer database and sin/cos tables:2.690 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 72.770 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7529 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 0.087 18605 Z= 0.308 Angle : 0.666 11.841 25212 Z= 0.357 Chirality : 0.044 0.264 2831 Planarity : 0.005 0.083 3187 Dihedral : 13.475 89.404 6997 Min Nonbonded Distance : 2.168 Molprobity Statistics. All-atom Clashscore : 9.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.42 % Favored : 96.58 % Rotamer: Outliers : 0.00 % Allowed : 0.26 % Favored : 99.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.09 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.23 (0.18), residues: 2219 helix: 1.07 (0.17), residues: 905 sheet: -1.44 (0.27), residues: 358 loop : -0.72 (0.20), residues: 956 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP B 99 HIS 0.004 0.001 HIS A 209 PHE 0.021 0.002 PHE A 74 TYR 0.028 0.001 TYR B 85 ARG 0.005 0.000 ARG B 49 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4438 Ramachandran restraints generated. 2219 Oldfield, 0 Emsley, 2219 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4438 Ramachandran restraints generated. 2219 Oldfield, 0 Emsley, 2219 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 388 residues out of total 1940 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 388 time to evaluate : 2.085 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 27 GLN cc_start: 0.7704 (tt0) cc_final: 0.7501 (tt0) REVERT: R 52 LYS cc_start: 0.8111 (mttt) cc_final: 0.7880 (mtpt) REVERT: R 263 THR cc_start: 0.8087 (p) cc_final: 0.7846 (p) REVERT: R 636 LYS cc_start: 0.7308 (mtmt) cc_final: 0.6775 (mmtm) REVERT: R 756 LEU cc_start: 0.7907 (mt) cc_final: 0.7705 (mt) REVERT: A 130 ASN cc_start: 0.7383 (m110) cc_final: 0.7140 (m110) REVERT: A 160 ILE cc_start: 0.8539 (mp) cc_final: 0.8009 (mp) REVERT: A 195 ASP cc_start: 0.6566 (t70) cc_final: 0.6317 (t0) REVERT: B 291 ASP cc_start: 0.7286 (m-30) cc_final: 0.7035 (m-30) outliers start: 0 outliers final: 0 residues processed: 388 average time/residue: 0.3003 time to fit residues: 175.7871 Evaluate side-chains 357 residues out of total 1940 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 357 time to evaluate : 2.289 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 221 random chunks: chunk 186 optimal weight: 0.0670 chunk 167 optimal weight: 4.9990 chunk 92 optimal weight: 1.9990 chunk 57 optimal weight: 0.9980 chunk 112 optimal weight: 0.9990 chunk 89 optimal weight: 0.9990 chunk 173 optimal weight: 0.9980 chunk 67 optimal weight: 0.9990 chunk 105 optimal weight: 1.9990 chunk 128 optimal weight: 0.7980 chunk 200 optimal weight: 0.9980 overall best weight: 0.7718 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7581 moved from start: 0.0968 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.066 18605 Z= 0.357 Angle : 0.596 9.291 25212 Z= 0.314 Chirality : 0.045 0.224 2831 Planarity : 0.005 0.065 3187 Dihedral : 7.319 73.364 2862 Min Nonbonded Distance : 2.211 Molprobity Statistics. All-atom Clashscore : 7.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.24 % Favored : 96.76 % Rotamer: Outliers : 1.24 % Allowed : 7.94 % Favored : 90.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.09 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.17 (0.18), residues: 2219 helix: 1.17 (0.17), residues: 903 sheet: -1.42 (0.26), residues: 367 loop : -0.73 (0.20), residues: 949 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP Q 818 HIS 0.005 0.001 HIS A 209 PHE 0.019 0.002 PHE A 70 TYR 0.018 0.002 TYR R 421 ARG 0.007 0.001 ARG R 185 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4438 Ramachandran restraints generated. 2219 Oldfield, 0 Emsley, 2219 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4438 Ramachandran restraints generated. 2219 Oldfield, 0 Emsley, 2219 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 411 residues out of total 1940 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 387 time to evaluate : 1.997 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: Q 576 GLU cc_start: 0.7376 (pp20) cc_final: 0.6810 (pp20) REVERT: Q 769 SER cc_start: 0.8430 (t) cc_final: 0.8122 (m) REVERT: R 52 LYS cc_start: 0.8165 (mttt) cc_final: 0.7855 (mtpt) REVERT: R 191 GLU cc_start: 0.7697 (mm-30) cc_final: 0.7402 (mm-30) REVERT: R 598 CYS cc_start: 0.4678 (m) cc_final: 0.4468 (m) REVERT: R 636 LYS cc_start: 0.7452 (mtmt) cc_final: 0.6867 (mmtm) REVERT: R 756 LEU cc_start: 0.7974 (mt) cc_final: 0.7730 (mt) REVERT: A 43 ASN cc_start: 0.7502 (t0) cc_final: 0.6946 (t0) REVERT: A 110 VAL cc_start: 0.8708 (OUTLIER) cc_final: 0.8468 (p) REVERT: A 114 ASP cc_start: 0.8072 (m-30) cc_final: 0.7804 (m-30) REVERT: A 195 ASP cc_start: 0.6692 (t70) cc_final: 0.6350 (t0) REVERT: A 226 ARG cc_start: 0.7238 (mtt180) cc_final: 0.6886 (mtt180) REVERT: B 291 ASP cc_start: 0.7407 (m-30) cc_final: 0.7086 (m-30) outliers start: 24 outliers final: 16 residues processed: 394 average time/residue: 0.3203 time to fit residues: 190.1719 Evaluate side-chains 384 residues out of total 1940 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 367 time to evaluate : 1.944 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Q residue 247 SER Chi-restraints excluded: chain Q residue 565 CYS Chi-restraints excluded: chain Q residue 583 ASN Chi-restraints excluded: chain Q residue 588 ASP Chi-restraints excluded: chain Q residue 618 LEU Chi-restraints excluded: chain Q residue 697 VAL Chi-restraints excluded: chain R residue 61 ILE Chi-restraints excluded: chain R residue 240 SER Chi-restraints excluded: chain R residue 554 ILE Chi-restraints excluded: chain R residue 664 SER Chi-restraints excluded: chain R residue 676 THR Chi-restraints excluded: chain R residue 828 THR Chi-restraints excluded: chain A residue 29 VAL Chi-restraints excluded: chain A residue 92 GLU Chi-restraints excluded: chain A residue 110 VAL Chi-restraints excluded: chain B residue 103 CYS Chi-restraints excluded: chain B residue 228 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 221 random chunks: chunk 111 optimal weight: 2.9990 chunk 62 optimal weight: 0.9990 chunk 167 optimal weight: 6.9990 chunk 136 optimal weight: 0.9980 chunk 55 optimal weight: 0.6980 chunk 201 optimal weight: 1.9990 chunk 217 optimal weight: 3.9990 chunk 179 optimal weight: 0.0770 chunk 199 optimal weight: 0.7980 chunk 68 optimal weight: 2.9990 chunk 161 optimal weight: 0.7980 overall best weight: 0.6738 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7583 moved from start: 0.1237 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.064 18605 Z= 0.315 Angle : 0.563 8.032 25212 Z= 0.298 Chirality : 0.044 0.206 2831 Planarity : 0.004 0.058 3187 Dihedral : 6.756 65.183 2862 Min Nonbonded Distance : 2.266 Molprobity Statistics. All-atom Clashscore : 6.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.20 % Favored : 96.80 % Rotamer: Outliers : 1.80 % Allowed : 9.74 % Favored : 88.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.09 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.20 (0.18), residues: 2219 helix: 1.20 (0.17), residues: 909 sheet: -1.48 (0.25), residues: 375 loop : -0.80 (0.20), residues: 935 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP Q 818 HIS 0.004 0.001 HIS A 209 PHE 0.019 0.002 PHE A 70 TYR 0.015 0.002 TYR R 421 ARG 0.005 0.000 ARG B 256 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4438 Ramachandran restraints generated. 2219 Oldfield, 0 Emsley, 2219 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4438 Ramachandran restraints generated. 2219 Oldfield, 0 Emsley, 2219 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 418 residues out of total 1940 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 383 time to evaluate : 2.184 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: Q 576 GLU cc_start: 0.7361 (pp20) cc_final: 0.6795 (pp20) REVERT: R 52 LYS cc_start: 0.8162 (mttt) cc_final: 0.7839 (mtpt) REVERT: R 191 GLU cc_start: 0.7683 (mm-30) cc_final: 0.7446 (mm-30) REVERT: R 636 LYS cc_start: 0.7443 (mtmt) cc_final: 0.6853 (mmtm) REVERT: R 756 LEU cc_start: 0.8040 (mt) cc_final: 0.7775 (mt) REVERT: A 43 ASN cc_start: 0.7558 (t0) cc_final: 0.6801 (t0) REVERT: A 82 HIS cc_start: 0.6967 (t70) cc_final: 0.6599 (t70) REVERT: A 110 VAL cc_start: 0.8628 (OUTLIER) cc_final: 0.8426 (p) REVERT: A 111 ASP cc_start: 0.7222 (t0) cc_final: 0.6429 (t0) REVERT: A 114 ASP cc_start: 0.8061 (m-30) cc_final: 0.7780 (m-30) REVERT: A 130 ASN cc_start: 0.7454 (m110) cc_final: 0.7200 (m110) REVERT: A 195 ASP cc_start: 0.6726 (t70) cc_final: 0.6380 (t0) REVERT: B 165 THR cc_start: 0.7909 (OUTLIER) cc_final: 0.7493 (m) REVERT: B 291 ASP cc_start: 0.7438 (m-30) cc_final: 0.7069 (m-30) outliers start: 35 outliers final: 23 residues processed: 398 average time/residue: 0.2945 time to fit residues: 179.5335 Evaluate side-chains 384 residues out of total 1940 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 359 time to evaluate : 1.990 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Q residue 247 SER Chi-restraints excluded: chain Q residue 566 VAL Chi-restraints excluded: chain Q residue 588 ASP Chi-restraints excluded: chain Q residue 599 ILE Chi-restraints excluded: chain Q residue 618 LEU Chi-restraints excluded: chain Q residue 697 VAL Chi-restraints excluded: chain Q residue 848 LEU Chi-restraints excluded: chain R residue 61 ILE Chi-restraints excluded: chain R residue 232 GLU Chi-restraints excluded: chain R residue 240 SER Chi-restraints excluded: chain R residue 263 THR Chi-restraints excluded: chain R residue 554 ILE Chi-restraints excluded: chain R residue 583 ASN Chi-restraints excluded: chain R residue 676 THR Chi-restraints excluded: chain R residue 828 THR Chi-restraints excluded: chain A residue 29 VAL Chi-restraints excluded: chain A residue 110 VAL Chi-restraints excluded: chain B residue 103 CYS Chi-restraints excluded: chain B residue 161 SER Chi-restraints excluded: chain B residue 165 THR Chi-restraints excluded: chain B residue 223 THR Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain B residue 261 LEU Chi-restraints excluded: chain B residue 274 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 221 random chunks: chunk 198 optimal weight: 0.9980 chunk 151 optimal weight: 0.9980 chunk 104 optimal weight: 0.6980 chunk 22 optimal weight: 1.9990 chunk 95 optimal weight: 0.0570 chunk 135 optimal weight: 0.9990 chunk 201 optimal weight: 0.8980 chunk 213 optimal weight: 5.9990 chunk 105 optimal weight: 0.9980 chunk 191 optimal weight: 0.7980 chunk 57 optimal weight: 0.8980 overall best weight: 0.6698 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7587 moved from start: 0.1431 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.074 18605 Z= 0.315 Angle : 0.568 12.180 25212 Z= 0.300 Chirality : 0.044 0.210 2831 Planarity : 0.004 0.053 3187 Dihedral : 6.497 58.914 2862 Min Nonbonded Distance : 2.244 Molprobity Statistics. All-atom Clashscore : 6.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.47 % Favored : 96.53 % Rotamer: Outliers : 2.42 % Allowed : 11.80 % Favored : 85.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.09 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.21 (0.17), residues: 2219 helix: 1.20 (0.16), residues: 917 sheet: -1.53 (0.25), residues: 375 loop : -0.80 (0.20), residues: 927 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP Q 818 HIS 0.004 0.001 HIS A 209 PHE 0.018 0.002 PHE A 70 TYR 0.015 0.002 TYR R 421 ARG 0.004 0.000 ARG R 185 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4438 Ramachandran restraints generated. 2219 Oldfield, 0 Emsley, 2219 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4438 Ramachandran restraints generated. 2219 Oldfield, 0 Emsley, 2219 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 414 residues out of total 1940 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 367 time to evaluate : 1.988 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: Q 288 ILE cc_start: 0.8172 (OUTLIER) cc_final: 0.7971 (mp) REVERT: Q 576 GLU cc_start: 0.7368 (pp20) cc_final: 0.6798 (pp20) REVERT: R 52 LYS cc_start: 0.8177 (mttt) cc_final: 0.7845 (mtpt) REVERT: R 636 LYS cc_start: 0.7433 (mtmt) cc_final: 0.6826 (mmtm) REVERT: R 756 LEU cc_start: 0.8052 (mt) cc_final: 0.7781 (mt) REVERT: A 38 LEU cc_start: 0.7852 (tt) cc_final: 0.7639 (tt) REVERT: A 43 ASN cc_start: 0.7604 (t0) cc_final: 0.6807 (t0) REVERT: A 111 ASP cc_start: 0.7252 (t0) cc_final: 0.6516 (t0) REVERT: A 114 ASP cc_start: 0.8040 (m-30) cc_final: 0.7723 (m-30) REVERT: A 131 ASN cc_start: 0.7925 (t0) cc_final: 0.7663 (t0) REVERT: A 195 ASP cc_start: 0.6734 (t70) cc_final: 0.6408 (t0) REVERT: B 291 ASP cc_start: 0.7466 (m-30) cc_final: 0.7133 (m-30) outliers start: 47 outliers final: 26 residues processed: 394 average time/residue: 0.3230 time to fit residues: 196.6871 Evaluate side-chains 384 residues out of total 1940 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 357 time to evaluate : 2.132 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Q residue 247 SER Chi-restraints excluded: chain Q residue 288 ILE Chi-restraints excluded: chain Q residue 449 CYS Chi-restraints excluded: chain Q residue 566 VAL Chi-restraints excluded: chain Q residue 588 ASP Chi-restraints excluded: chain Q residue 618 LEU Chi-restraints excluded: chain Q residue 697 VAL Chi-restraints excluded: chain Q residue 848 LEU Chi-restraints excluded: chain R residue 61 ILE Chi-restraints excluded: chain R residue 139 ILE Chi-restraints excluded: chain R residue 232 GLU Chi-restraints excluded: chain R residue 240 SER Chi-restraints excluded: chain R residue 263 THR Chi-restraints excluded: chain R residue 403 SER Chi-restraints excluded: chain R residue 503 ILE Chi-restraints excluded: chain R residue 554 ILE Chi-restraints excluded: chain R residue 577 THR Chi-restraints excluded: chain R residue 609 THR Chi-restraints excluded: chain R residue 676 THR Chi-restraints excluded: chain R residue 828 THR Chi-restraints excluded: chain A residue 29 VAL Chi-restraints excluded: chain A residue 86 VAL Chi-restraints excluded: chain B residue 103 CYS Chi-restraints excluded: chain B residue 161 SER Chi-restraints excluded: chain B residue 223 THR Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 243 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 221 random chunks: chunk 177 optimal weight: 0.7980 chunk 121 optimal weight: 0.5980 chunk 3 optimal weight: 4.9990 chunk 159 optimal weight: 0.9980 chunk 88 optimal weight: 0.8980 chunk 182 optimal weight: 0.9990 chunk 147 optimal weight: 0.7980 chunk 0 optimal weight: 1.9990 chunk 109 optimal weight: 1.9990 chunk 191 optimal weight: 0.9980 chunk 53 optimal weight: 0.8980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7599 moved from start: 0.1556 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.046 18605 Z= 0.359 Angle : 0.580 13.142 25212 Z= 0.306 Chirality : 0.045 0.208 2831 Planarity : 0.004 0.052 3187 Dihedral : 6.423 58.013 2862 Min Nonbonded Distance : 2.230 Molprobity Statistics. All-atom Clashscore : 7.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.47 % Favored : 96.53 % Rotamer: Outliers : 2.42 % Allowed : 12.58 % Favored : 85.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.09 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.27 (0.17), residues: 2219 helix: 1.14 (0.16), residues: 918 sheet: -1.59 (0.25), residues: 375 loop : -0.82 (0.20), residues: 926 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP Q 818 HIS 0.005 0.001 HIS R 495 PHE 0.028 0.002 PHE A 74 TYR 0.016 0.002 TYR R 421 ARG 0.004 0.000 ARG Q 54 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4438 Ramachandran restraints generated. 2219 Oldfield, 0 Emsley, 2219 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4438 Ramachandran restraints generated. 2219 Oldfield, 0 Emsley, 2219 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 424 residues out of total 1940 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 377 time to evaluate : 2.160 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: Q 576 GLU cc_start: 0.7369 (pp20) cc_final: 0.6814 (pp20) REVERT: R 52 LYS cc_start: 0.8184 (mttt) cc_final: 0.7850 (mtpt) REVERT: R 636 LYS cc_start: 0.7452 (mtmt) cc_final: 0.6828 (mmtm) REVERT: R 756 LEU cc_start: 0.8083 (mt) cc_final: 0.7807 (mt) REVERT: A 38 LEU cc_start: 0.7873 (tt) cc_final: 0.7657 (tt) REVERT: A 43 ASN cc_start: 0.7606 (t0) cc_final: 0.6805 (t0) REVERT: A 111 ASP cc_start: 0.7254 (t0) cc_final: 0.6583 (t0) REVERT: A 114 ASP cc_start: 0.8055 (m-30) cc_final: 0.7732 (m-30) REVERT: A 131 ASN cc_start: 0.7900 (t0) cc_final: 0.7622 (t0) REVERT: A 195 ASP cc_start: 0.6773 (t70) cc_final: 0.6462 (t0) REVERT: B 93 ILE cc_start: 0.8770 (OUTLIER) cc_final: 0.8537 (mm) REVERT: B 291 ASP cc_start: 0.7469 (m-30) cc_final: 0.7155 (m-30) outliers start: 47 outliers final: 33 residues processed: 401 average time/residue: 0.3055 time to fit residues: 183.8131 Evaluate side-chains 396 residues out of total 1940 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 362 time to evaluate : 2.029 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Q residue 247 SER Chi-restraints excluded: chain Q residue 449 CYS Chi-restraints excluded: chain Q residue 566 VAL Chi-restraints excluded: chain Q residue 588 ASP Chi-restraints excluded: chain Q residue 618 LEU Chi-restraints excluded: chain Q residue 697 VAL Chi-restraints excluded: chain Q residue 848 LEU Chi-restraints excluded: chain Q residue 862 PHE Chi-restraints excluded: chain R residue 61 ILE Chi-restraints excluded: chain R residue 139 ILE Chi-restraints excluded: chain R residue 232 GLU Chi-restraints excluded: chain R residue 240 SER Chi-restraints excluded: chain R residue 263 THR Chi-restraints excluded: chain R residue 270 PHE Chi-restraints excluded: chain R residue 403 SER Chi-restraints excluded: chain R residue 503 ILE Chi-restraints excluded: chain R residue 537 VAL Chi-restraints excluded: chain R residue 554 ILE Chi-restraints excluded: chain R residue 577 THR Chi-restraints excluded: chain R residue 609 THR Chi-restraints excluded: chain R residue 664 SER Chi-restraints excluded: chain R residue 676 THR Chi-restraints excluded: chain R residue 828 THR Chi-restraints excluded: chain A residue 29 VAL Chi-restraints excluded: chain A residue 86 VAL Chi-restraints excluded: chain B residue 88 ASN Chi-restraints excluded: chain B residue 93 ILE Chi-restraints excluded: chain B residue 103 CYS Chi-restraints excluded: chain B residue 198 LEU Chi-restraints excluded: chain B residue 223 THR Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain B residue 266 HIS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 221 random chunks: chunk 71 optimal weight: 0.9980 chunk 192 optimal weight: 1.9990 chunk 42 optimal weight: 0.7980 chunk 125 optimal weight: 1.9990 chunk 52 optimal weight: 0.2980 chunk 213 optimal weight: 5.9990 chunk 177 optimal weight: 0.7980 chunk 99 optimal weight: 0.9980 chunk 17 optimal weight: 0.9990 chunk 70 optimal weight: 1.9990 chunk 112 optimal weight: 0.5980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7594 moved from start: 0.1669 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.049 18605 Z= 0.324 Angle : 0.568 9.025 25212 Z= 0.299 Chirality : 0.044 0.207 2831 Planarity : 0.005 0.087 3187 Dihedral : 6.318 56.481 2862 Min Nonbonded Distance : 2.247 Molprobity Statistics. All-atom Clashscore : 7.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.38 % Favored : 96.62 % Rotamer: Outliers : 2.27 % Allowed : 13.35 % Favored : 84.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.09 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.25 (0.18), residues: 2219 helix: 1.17 (0.16), residues: 922 sheet: -1.62 (0.25), residues: 375 loop : -0.80 (0.20), residues: 922 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP Q 818 HIS 0.004 0.001 HIS R 495 PHE 0.015 0.002 PHE B 199 TYR 0.015 0.002 TYR R 573 ARG 0.004 0.000 ARG Q 54 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4438 Ramachandran restraints generated. 2219 Oldfield, 0 Emsley, 2219 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4438 Ramachandran restraints generated. 2219 Oldfield, 0 Emsley, 2219 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 409 residues out of total 1940 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 365 time to evaluate : 1.982 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: Q 576 GLU cc_start: 0.7362 (pp20) cc_final: 0.6808 (pp20) REVERT: R 52 LYS cc_start: 0.8188 (mttt) cc_final: 0.7853 (mtpt) REVERT: R 636 LYS cc_start: 0.7439 (mtmt) cc_final: 0.6818 (mmtm) REVERT: R 756 LEU cc_start: 0.8103 (mt) cc_final: 0.7849 (mt) REVERT: A 38 LEU cc_start: 0.7932 (tt) cc_final: 0.7681 (tt) REVERT: A 43 ASN cc_start: 0.7582 (t0) cc_final: 0.6784 (t0) REVERT: A 111 ASP cc_start: 0.7252 (t0) cc_final: 0.6529 (t0) REVERT: A 114 ASP cc_start: 0.8065 (m-30) cc_final: 0.7726 (m-30) REVERT: A 131 ASN cc_start: 0.7897 (t0) cc_final: 0.7617 (t0) REVERT: A 195 ASP cc_start: 0.6760 (t70) cc_final: 0.6457 (t0) REVERT: B 59 TYR cc_start: 0.7938 (m-10) cc_final: 0.7622 (m-10) REVERT: B 93 ILE cc_start: 0.8757 (OUTLIER) cc_final: 0.8553 (mm) REVERT: B 291 ASP cc_start: 0.7461 (m-30) cc_final: 0.7122 (m-30) outliers start: 44 outliers final: 35 residues processed: 387 average time/residue: 0.2993 time to fit residues: 174.5616 Evaluate side-chains 397 residues out of total 1940 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 361 time to evaluate : 1.953 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Q residue 247 SER Chi-restraints excluded: chain Q residue 449 CYS Chi-restraints excluded: chain Q residue 556 GLU Chi-restraints excluded: chain Q residue 588 ASP Chi-restraints excluded: chain Q residue 618 LEU Chi-restraints excluded: chain Q residue 697 VAL Chi-restraints excluded: chain Q residue 848 LEU Chi-restraints excluded: chain R residue 61 ILE Chi-restraints excluded: chain R residue 139 ILE Chi-restraints excluded: chain R residue 232 GLU Chi-restraints excluded: chain R residue 240 SER Chi-restraints excluded: chain R residue 263 THR Chi-restraints excluded: chain R residue 270 PHE Chi-restraints excluded: chain R residue 403 SER Chi-restraints excluded: chain R residue 503 ILE Chi-restraints excluded: chain R residue 537 VAL Chi-restraints excluded: chain R residue 554 ILE Chi-restraints excluded: chain R residue 577 THR Chi-restraints excluded: chain R residue 609 THR Chi-restraints excluded: chain R residue 664 SER Chi-restraints excluded: chain R residue 676 THR Chi-restraints excluded: chain R residue 776 LEU Chi-restraints excluded: chain R residue 783 LEU Chi-restraints excluded: chain R residue 828 THR Chi-restraints excluded: chain A residue 29 VAL Chi-restraints excluded: chain A residue 86 VAL Chi-restraints excluded: chain B residue 88 ASN Chi-restraints excluded: chain B residue 93 ILE Chi-restraints excluded: chain B residue 99 TRP Chi-restraints excluded: chain B residue 103 CYS Chi-restraints excluded: chain B residue 198 LEU Chi-restraints excluded: chain B residue 217 MET Chi-restraints excluded: chain B residue 223 THR Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain B residue 266 HIS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 221 random chunks: chunk 206 optimal weight: 0.7980 chunk 24 optimal weight: 0.9980 chunk 121 optimal weight: 0.2980 chunk 156 optimal weight: 0.9980 chunk 120 optimal weight: 0.9990 chunk 179 optimal weight: 0.5980 chunk 119 optimal weight: 0.8980 chunk 213 optimal weight: 2.9990 chunk 133 optimal weight: 1.9990 chunk 129 optimal weight: 0.9980 chunk 98 optimal weight: 0.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7596 moved from start: 0.1748 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.045 18605 Z= 0.331 Angle : 0.572 8.037 25212 Z= 0.300 Chirality : 0.044 0.207 2831 Planarity : 0.004 0.051 3187 Dihedral : 6.289 55.839 2862 Min Nonbonded Distance : 2.237 Molprobity Statistics. All-atom Clashscore : 7.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.65 % Favored : 96.35 % Rotamer: Outliers : 2.37 % Allowed : 14.12 % Favored : 83.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.09 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.27 (0.18), residues: 2219 helix: 1.18 (0.16), residues: 922 sheet: -1.69 (0.25), residues: 380 loop : -0.81 (0.20), residues: 917 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP Q 818 HIS 0.005 0.001 HIS A 82 PHE 0.027 0.002 PHE A 74 TYR 0.015 0.002 TYR R 421 ARG 0.008 0.000 ARG A 132 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4438 Ramachandran restraints generated. 2219 Oldfield, 0 Emsley, 2219 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4438 Ramachandran restraints generated. 2219 Oldfield, 0 Emsley, 2219 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 415 residues out of total 1940 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 369 time to evaluate : 2.091 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: Q 262 SER cc_start: 0.8782 (t) cc_final: 0.8446 (t) REVERT: Q 576 GLU cc_start: 0.7377 (pp20) cc_final: 0.6838 (pp20) REVERT: R 52 LYS cc_start: 0.8192 (mttt) cc_final: 0.7852 (mtpt) REVERT: R 636 LYS cc_start: 0.7438 (mtmt) cc_final: 0.6830 (mmtm) REVERT: R 756 LEU cc_start: 0.8138 (mt) cc_final: 0.7889 (mt) REVERT: A 38 LEU cc_start: 0.7938 (tt) cc_final: 0.7682 (tt) REVERT: A 43 ASN cc_start: 0.7568 (t0) cc_final: 0.6847 (t0) REVERT: A 83 MET cc_start: 0.7619 (mtt) cc_final: 0.7415 (mtt) REVERT: A 131 ASN cc_start: 0.7858 (t0) cc_final: 0.7607 (t0) REVERT: A 195 ASP cc_start: 0.6754 (t70) cc_final: 0.6438 (t0) REVERT: A 242 GLU cc_start: 0.7223 (tm-30) cc_final: 0.6997 (tm-30) REVERT: B 59 TYR cc_start: 0.7926 (m-10) cc_final: 0.7602 (m-10) REVERT: B 267 ASP cc_start: 0.7550 (p0) cc_final: 0.7157 (p0) REVERT: B 291 ASP cc_start: 0.7458 (m-30) cc_final: 0.7120 (m-30) outliers start: 46 outliers final: 37 residues processed: 392 average time/residue: 0.3109 time to fit residues: 184.6207 Evaluate side-chains 399 residues out of total 1940 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 362 time to evaluate : 2.014 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Q residue 247 SER Chi-restraints excluded: chain Q residue 409 ILE Chi-restraints excluded: chain Q residue 449 CYS Chi-restraints excluded: chain Q residue 588 ASP Chi-restraints excluded: chain Q residue 599 ILE Chi-restraints excluded: chain Q residue 618 LEU Chi-restraints excluded: chain Q residue 848 LEU Chi-restraints excluded: chain R residue 61 ILE Chi-restraints excluded: chain R residue 139 ILE Chi-restraints excluded: chain R residue 232 GLU Chi-restraints excluded: chain R residue 240 SER Chi-restraints excluded: chain R residue 263 THR Chi-restraints excluded: chain R residue 270 PHE Chi-restraints excluded: chain R residue 403 SER Chi-restraints excluded: chain R residue 503 ILE Chi-restraints excluded: chain R residue 537 VAL Chi-restraints excluded: chain R residue 554 ILE Chi-restraints excluded: chain R residue 577 THR Chi-restraints excluded: chain R residue 609 THR Chi-restraints excluded: chain R residue 664 SER Chi-restraints excluded: chain R residue 676 THR Chi-restraints excluded: chain R residue 776 LEU Chi-restraints excluded: chain R residue 783 LEU Chi-restraints excluded: chain R residue 828 THR Chi-restraints excluded: chain A residue 29 VAL Chi-restraints excluded: chain A residue 86 VAL Chi-restraints excluded: chain A residue 92 GLU Chi-restraints excluded: chain B residue 88 ASN Chi-restraints excluded: chain B residue 99 TRP Chi-restraints excluded: chain B residue 103 CYS Chi-restraints excluded: chain B residue 198 LEU Chi-restraints excluded: chain B residue 217 MET Chi-restraints excluded: chain B residue 221 THR Chi-restraints excluded: chain B residue 223 THR Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain B residue 266 HIS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 221 random chunks: chunk 131 optimal weight: 0.0040 chunk 85 optimal weight: 0.7980 chunk 127 optimal weight: 0.7980 chunk 64 optimal weight: 0.0570 chunk 41 optimal weight: 0.9990 chunk 135 optimal weight: 0.9980 chunk 145 optimal weight: 0.0270 chunk 105 optimal weight: 0.7980 chunk 19 optimal weight: 0.9980 chunk 167 optimal weight: 0.8980 chunk 193 optimal weight: 1.9990 overall best weight: 0.3368 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7561 moved from start: 0.1825 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 18605 Z= 0.199 Angle : 0.532 10.596 25212 Z= 0.279 Chirality : 0.043 0.227 2831 Planarity : 0.004 0.047 3187 Dihedral : 5.984 55.182 2862 Min Nonbonded Distance : 2.325 Molprobity Statistics. All-atom Clashscore : 6.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.97 % Favored : 97.03 % Rotamer: Outliers : 1.65 % Allowed : 15.10 % Favored : 83.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.09 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.06 (0.18), residues: 2219 helix: 1.35 (0.17), residues: 922 sheet: -1.54 (0.25), residues: 380 loop : -0.73 (0.21), residues: 917 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP Q 818 HIS 0.003 0.001 HIS A 82 PHE 0.014 0.001 PHE Q 854 TYR 0.020 0.001 TYR R 573 ARG 0.006 0.000 ARG B 49 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4438 Ramachandran restraints generated. 2219 Oldfield, 0 Emsley, 2219 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4438 Ramachandran restraints generated. 2219 Oldfield, 0 Emsley, 2219 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 398 residues out of total 1940 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 366 time to evaluate : 2.189 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: Q 576 GLU cc_start: 0.7367 (pp20) cc_final: 0.6845 (pp20) REVERT: Q 773 LEU cc_start: 0.8499 (tt) cc_final: 0.8276 (tp) REVERT: R 52 LYS cc_start: 0.8198 (mttt) cc_final: 0.7876 (mtpt) REVERT: R 481 GLU cc_start: 0.6713 (mp0) cc_final: 0.6462 (mp0) REVERT: R 636 LYS cc_start: 0.7383 (mtmt) cc_final: 0.6782 (mmtm) REVERT: R 756 LEU cc_start: 0.8112 (mt) cc_final: 0.7875 (mt) REVERT: A 38 LEU cc_start: 0.7963 (tt) cc_final: 0.7740 (tt) REVERT: A 83 MET cc_start: 0.7446 (mtt) cc_final: 0.7238 (mtt) REVERT: A 111 ASP cc_start: 0.7117 (t0) cc_final: 0.6849 (t0) REVERT: A 114 ASP cc_start: 0.7879 (m-30) cc_final: 0.7622 (m-30) REVERT: A 195 ASP cc_start: 0.6716 (t70) cc_final: 0.6401 (t0) REVERT: B 59 TYR cc_start: 0.7896 (m-10) cc_final: 0.7565 (m-80) REVERT: B 267 ASP cc_start: 0.7460 (p0) cc_final: 0.7067 (p0) outliers start: 32 outliers final: 26 residues processed: 381 average time/residue: 0.3183 time to fit residues: 183.3821 Evaluate side-chains 375 residues out of total 1940 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 349 time to evaluate : 1.837 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Q residue 449 CYS Chi-restraints excluded: chain Q residue 618 LEU Chi-restraints excluded: chain Q residue 697 VAL Chi-restraints excluded: chain Q residue 848 LEU Chi-restraints excluded: chain R residue 61 ILE Chi-restraints excluded: chain R residue 232 GLU Chi-restraints excluded: chain R residue 263 THR Chi-restraints excluded: chain R residue 270 PHE Chi-restraints excluded: chain R residue 537 VAL Chi-restraints excluded: chain R residue 554 ILE Chi-restraints excluded: chain R residue 577 THR Chi-restraints excluded: chain R residue 609 THR Chi-restraints excluded: chain R residue 676 THR Chi-restraints excluded: chain R residue 776 LEU Chi-restraints excluded: chain R residue 783 LEU Chi-restraints excluded: chain R residue 828 THR Chi-restraints excluded: chain A residue 86 VAL Chi-restraints excluded: chain A residue 92 GLU Chi-restraints excluded: chain B residue 88 ASN Chi-restraints excluded: chain B residue 99 TRP Chi-restraints excluded: chain B residue 122 SER Chi-restraints excluded: chain B residue 198 LEU Chi-restraints excluded: chain B residue 223 THR Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain B residue 266 HIS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 221 random chunks: chunk 204 optimal weight: 1.9990 chunk 186 optimal weight: 0.7980 chunk 198 optimal weight: 1.9990 chunk 119 optimal weight: 0.9980 chunk 86 optimal weight: 0.9980 chunk 155 optimal weight: 0.9980 chunk 60 optimal weight: 0.7980 chunk 179 optimal weight: 1.9990 chunk 187 optimal weight: 2.9990 chunk 197 optimal weight: 0.9980 chunk 130 optimal weight: 0.6980 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7601 moved from start: 0.1886 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.051 18605 Z= 0.379 Angle : 0.597 10.742 25212 Z= 0.311 Chirality : 0.046 0.228 2831 Planarity : 0.004 0.051 3187 Dihedral : 6.266 57.007 2862 Min Nonbonded Distance : 2.212 Molprobity Statistics. All-atom Clashscore : 7.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.65 % Favored : 96.35 % Rotamer: Outliers : 1.80 % Allowed : 15.62 % Favored : 82.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.09 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.23 (0.18), residues: 2219 helix: 1.16 (0.16), residues: 927 sheet: -1.58 (0.25), residues: 366 loop : -0.80 (0.20), residues: 926 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP Q 818 HIS 0.005 0.001 HIS A 82 PHE 0.031 0.002 PHE A 74 TYR 0.017 0.002 TYR R 573 ARG 0.005 0.001 ARG B 49 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4438 Ramachandran restraints generated. 2219 Oldfield, 0 Emsley, 2219 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4438 Ramachandran restraints generated. 2219 Oldfield, 0 Emsley, 2219 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 403 residues out of total 1940 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 368 time to evaluate : 2.055 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: Q 576 GLU cc_start: 0.7384 (pp20) cc_final: 0.6813 (pp20) REVERT: R 52 LYS cc_start: 0.8196 (mttt) cc_final: 0.7838 (mtpt) REVERT: R 636 LYS cc_start: 0.7437 (mtmt) cc_final: 0.6815 (mmtm) REVERT: R 756 LEU cc_start: 0.8124 (mt) cc_final: 0.7895 (mt) REVERT: A 38 LEU cc_start: 0.7947 (tt) cc_final: 0.7683 (tt) REVERT: A 43 ASN cc_start: 0.7535 (t0) cc_final: 0.6989 (t0) REVERT: A 83 MET cc_start: 0.7531 (mtt) cc_final: 0.7329 (mtt) REVERT: A 111 ASP cc_start: 0.7156 (t0) cc_final: 0.6535 (t0) REVERT: A 114 ASP cc_start: 0.7859 (m-30) cc_final: 0.7598 (m-30) REVERT: A 131 ASN cc_start: 0.7894 (t0) cc_final: 0.7657 (t0) REVERT: A 195 ASP cc_start: 0.6724 (t70) cc_final: 0.6422 (t0) REVERT: B 59 TYR cc_start: 0.7947 (m-10) cc_final: 0.7577 (m-80) outliers start: 35 outliers final: 30 residues processed: 386 average time/residue: 0.3032 time to fit residues: 176.7797 Evaluate side-chains 388 residues out of total 1940 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 358 time to evaluate : 1.933 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Q residue 223 ILE Chi-restraints excluded: chain Q residue 247 SER Chi-restraints excluded: chain Q residue 409 ILE Chi-restraints excluded: chain Q residue 449 CYS Chi-restraints excluded: chain Q residue 618 LEU Chi-restraints excluded: chain Q residue 697 VAL Chi-restraints excluded: chain Q residue 848 LEU Chi-restraints excluded: chain R residue 61 ILE Chi-restraints excluded: chain R residue 232 GLU Chi-restraints excluded: chain R residue 263 THR Chi-restraints excluded: chain R residue 270 PHE Chi-restraints excluded: chain R residue 537 VAL Chi-restraints excluded: chain R residue 554 ILE Chi-restraints excluded: chain R residue 577 THR Chi-restraints excluded: chain R residue 609 THR Chi-restraints excluded: chain R residue 676 THR Chi-restraints excluded: chain R residue 783 LEU Chi-restraints excluded: chain R residue 828 THR Chi-restraints excluded: chain A residue 86 VAL Chi-restraints excluded: chain A residue 92 GLU Chi-restraints excluded: chain B residue 88 ASN Chi-restraints excluded: chain B residue 99 TRP Chi-restraints excluded: chain B residue 103 CYS Chi-restraints excluded: chain B residue 122 SER Chi-restraints excluded: chain B residue 198 LEU Chi-restraints excluded: chain B residue 221 THR Chi-restraints excluded: chain B residue 223 THR Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain B residue 266 HIS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 221 random chunks: chunk 209 optimal weight: 0.9980 chunk 128 optimal weight: 0.7980 chunk 99 optimal weight: 0.9990 chunk 145 optimal weight: 0.5980 chunk 220 optimal weight: 0.6980 chunk 202 optimal weight: 0.5980 chunk 175 optimal weight: 0.1980 chunk 18 optimal weight: 0.8980 chunk 135 optimal weight: 0.9980 chunk 107 optimal weight: 0.7980 chunk 139 optimal weight: 0.5980 overall best weight: 0.5380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7582 moved from start: 0.1928 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 18605 Z= 0.271 Angle : 0.571 10.468 25212 Z= 0.298 Chirality : 0.044 0.210 2831 Planarity : 0.004 0.049 3187 Dihedral : 6.136 59.889 2862 Min Nonbonded Distance : 2.273 Molprobity Statistics. All-atom Clashscore : 7.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.33 % Favored : 96.67 % Rotamer: Outliers : 1.60 % Allowed : 16.03 % Favored : 82.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.09 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.16 (0.18), residues: 2219 helix: 1.25 (0.16), residues: 926 sheet: -1.57 (0.25), residues: 380 loop : -0.77 (0.21), residues: 913 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP Q 818 HIS 0.004 0.001 HIS A 82 PHE 0.023 0.002 PHE A 228 TYR 0.016 0.001 TYR R 573 ARG 0.005 0.000 ARG B 49 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4438 Ramachandran restraints generated. 2219 Oldfield, 0 Emsley, 2219 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4438 Ramachandran restraints generated. 2219 Oldfield, 0 Emsley, 2219 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 390 residues out of total 1940 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 359 time to evaluate : 2.001 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 52 LYS cc_start: 0.8191 (mttt) cc_final: 0.7834 (mtpt) REVERT: R 636 LYS cc_start: 0.7416 (mtmt) cc_final: 0.6887 (mmtt) REVERT: A 38 LEU cc_start: 0.7963 (tt) cc_final: 0.7696 (tt) REVERT: A 43 ASN cc_start: 0.7514 (t0) cc_final: 0.6946 (t0) REVERT: A 111 ASP cc_start: 0.7128 (t0) cc_final: 0.6442 (t0) REVERT: A 114 ASP cc_start: 0.7854 (m-30) cc_final: 0.7582 (m-30) REVERT: A 131 ASN cc_start: 0.7907 (t0) cc_final: 0.7680 (t0) REVERT: A 195 ASP cc_start: 0.6723 (t70) cc_final: 0.6515 (t0) REVERT: B 59 TYR cc_start: 0.7926 (m-10) cc_final: 0.7597 (m-80) REVERT: B 99 TRP cc_start: 0.5159 (OUTLIER) cc_final: 0.4724 (p90) outliers start: 31 outliers final: 27 residues processed: 375 average time/residue: 0.2962 time to fit residues: 168.9615 Evaluate side-chains 383 residues out of total 1940 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 355 time to evaluate : 1.997 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Q residue 247 SER Chi-restraints excluded: chain Q residue 409 ILE Chi-restraints excluded: chain Q residue 449 CYS Chi-restraints excluded: chain Q residue 618 LEU Chi-restraints excluded: chain Q residue 697 VAL Chi-restraints excluded: chain Q residue 848 LEU Chi-restraints excluded: chain R residue 61 ILE Chi-restraints excluded: chain R residue 232 GLU Chi-restraints excluded: chain R residue 263 THR Chi-restraints excluded: chain R residue 270 PHE Chi-restraints excluded: chain R residue 537 VAL Chi-restraints excluded: chain R residue 554 ILE Chi-restraints excluded: chain R residue 577 THR Chi-restraints excluded: chain R residue 609 THR Chi-restraints excluded: chain R residue 676 THR Chi-restraints excluded: chain R residue 783 LEU Chi-restraints excluded: chain R residue 828 THR Chi-restraints excluded: chain A residue 86 VAL Chi-restraints excluded: chain A residue 92 GLU Chi-restraints excluded: chain B residue 88 ASN Chi-restraints excluded: chain B residue 99 TRP Chi-restraints excluded: chain B residue 122 SER Chi-restraints excluded: chain B residue 198 LEU Chi-restraints excluded: chain B residue 221 THR Chi-restraints excluded: chain B residue 223 THR Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain B residue 266 HIS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 221 random chunks: chunk 186 optimal weight: 0.8980 chunk 53 optimal weight: 0.0470 chunk 161 optimal weight: 0.8980 chunk 25 optimal weight: 0.0980 chunk 48 optimal weight: 0.7980 chunk 175 optimal weight: 0.6980 chunk 73 optimal weight: 0.4980 chunk 180 optimal weight: 1.9990 chunk 22 optimal weight: 0.6980 chunk 32 optimal weight: 0.9980 chunk 154 optimal weight: 0.6980 overall best weight: 0.4078 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3448 r_free = 0.3448 target = 0.114598 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3127 r_free = 0.3127 target = 0.095286 restraints weight = 28760.979| |-----------------------------------------------------------------------------| r_work (start): 0.3114 rms_B_bonded: 1.67 r_work: 0.2995 rms_B_bonded: 2.23 restraints_weight: 0.5000 r_work: 0.2843 rms_B_bonded: 3.77 restraints_weight: 0.2500 r_work (final): 0.2843 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7893 moved from start: 0.1982 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 18605 Z= 0.227 Angle : 0.554 10.169 25212 Z= 0.289 Chirality : 0.044 0.277 2831 Planarity : 0.004 0.048 3187 Dihedral : 5.963 56.817 2862 Min Nonbonded Distance : 2.289 Molprobity Statistics. All-atom Clashscore : 7.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.42 % Favored : 96.58 % Rotamer: Outliers : 1.70 % Allowed : 16.34 % Favored : 81.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.09 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.07 (0.18), residues: 2219 helix: 1.32 (0.16), residues: 926 sheet: -1.48 (0.25), residues: 380 loop : -0.73 (0.21), residues: 913 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP Q 818 HIS 0.004 0.001 HIS B 266 PHE 0.018 0.001 PHE Q 788 TYR 0.026 0.001 TYR R 573 ARG 0.005 0.000 ARG B 49 Origin is already at (0, 0, 0), no shifts will be applied Model does not fit in PDB format. =============================================================================== Job complete usr+sys time: 4658.00 seconds wall clock time: 82 minutes 54.05 seconds (4974.05 seconds total)