Starting phenix.real_space_refine on Wed Jan 22 07:28:39 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9asb_43811/01_2025/9asb_43811.cif Found real_map, /net/cci-nas-00/data/ceres_data/9asb_43811/01_2025/9asb_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/cci-nas-00/data/ceres_data/9asb_43811/01_2025/9asb_43811.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9asb_43811/01_2025/9asb_43811.map" model { file = "/net/cci-nas-00/data/ceres_data/9asb_43811/01_2025/9asb_43811.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9asb_43811/01_2025/9asb_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. Time to flip 61 residue(s): 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/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: 10.78, per 1000 atoms: 0.59 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 - 3.00 Amino acid : True - 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: 5.17 Conformation dependent library (CDL) restraints added in 2.6 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: 2.09 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: 7.46 Time building geometry restraints manager: 5.87 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: 0.00 - 2.37: 24890 2.37 - 4.74: 282 4.74 - 7.10: 30 7.10 - 9.47: 7 9.47 - 11.84: 3 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: 18.180 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.000 Check model and map are aligned: 0.000 Set scattering table: 0.000 Process input model: 46.630 Find NCS groups from input model: 0.740 Set up NCS constraints: 0.100 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.820 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 68.480 ------------------------------------------------------------------------------- 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 to be fit. rotamer outliers: 0 poor density : 388 time to evaluate : 1.993 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: 0.3215 time to fit residues: 187.6625 Evaluate side-chains 357 residues out of total 1940 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 357 time to evaluate : 1.953 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3427 r_free = 0.3427 target = 0.112682 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3106 r_free = 0.3106 target = 0.093475 restraints weight = 28683.934| |-----------------------------------------------------------------------------| r_work (start): 0.3099 rms_B_bonded: 1.64 r_work: 0.2985 rms_B_bonded: 2.17 restraints_weight: 0.5000 r_work: 0.2832 rms_B_bonded: 3.68 restraints_weight: 0.2500 r_work (final): 0.2832 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7897 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 to be fit. rotamer outliers: 24 poor density : 387 time to evaluate : 2.124 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: Q 576 GLU cc_start: 0.7480 (pp20) cc_final: 0.6834 (pp20) REVERT: Q 769 SER cc_start: 0.8501 (t) cc_final: 0.8205 (m) REVERT: R 52 LYS cc_start: 0.8191 (mttt) cc_final: 0.7781 (mtpt) REVERT: R 191 GLU cc_start: 0.8014 (mm-30) cc_final: 0.7735 (mm-30) REVERT: R 598 CYS cc_start: 0.5877 (m) cc_final: 0.5653 (m) REVERT: R 636 LYS cc_start: 0.7815 (mtmt) cc_final: 0.7139 (mmtm) REVERT: R 756 LEU cc_start: 0.8285 (mt) cc_final: 0.8003 (mt) REVERT: A 43 ASN cc_start: 0.7721 (t0) cc_final: 0.7076 (t0) REVERT: A 83 MET cc_start: 0.8122 (mtt) cc_final: 0.7917 (mtt) REVERT: A 110 VAL cc_start: 0.8883 (OUTLIER) cc_final: 0.8640 (p) REVERT: A 114 ASP cc_start: 0.8374 (m-30) cc_final: 0.8079 (m-30) REVERT: A 131 ASN cc_start: 0.8037 (t0) cc_final: 0.7829 (t0) REVERT: A 195 ASP cc_start: 0.7366 (t70) cc_final: 0.7002 (t0) REVERT: A 226 ARG cc_start: 0.7613 (mtt180) cc_final: 0.7298 (mtt180) REVERT: B 291 ASP cc_start: 0.7719 (m-30) cc_final: 0.7357 (m-30) outliers start: 24 outliers final: 16 residues processed: 394 average time/residue: 0.3144 time to fit residues: 186.9232 Evaluate side-chains 384 residues out of total 1940 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 367 time to evaluate : 2.119 ------------------------------------------------------------------------------- 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 40 optimal weight: 0.8980 chunk 25 optimal weight: 0.1980 chunk 212 optimal weight: 2.9990 chunk 110 optimal weight: 0.7980 chunk 79 optimal weight: 0.0070 chunk 150 optimal weight: 0.9980 chunk 199 optimal weight: 0.9990 chunk 44 optimal weight: 0.8980 chunk 209 optimal weight: 0.7980 chunk 86 optimal weight: 0.6980 chunk 213 optimal weight: 0.0470 overall best weight: 0.3496 ------------------------------------------------------------------------------- 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 = 0.3453 r_free = 0.3453 target = 0.114735 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3133 r_free = 0.3133 target = 0.095497 restraints weight = 28541.909| |-----------------------------------------------------------------------------| r_work (start): 0.3127 rms_B_bonded: 1.65 r_work: 0.3011 rms_B_bonded: 2.21 restraints_weight: 0.5000 r_work: 0.2859 rms_B_bonded: 3.73 restraints_weight: 0.2500 r_work (final): 0.2859 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7878 moved from start: 0.1195 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.060 18605 Z= 0.206 Angle : 0.526 8.094 25212 Z= 0.280 Chirality : 0.042 0.207 2831 Planarity : 0.004 0.057 3187 Dihedral : 6.588 62.386 2862 Min Nonbonded Distance : 2.324 Molprobity Statistics. All-atom Clashscore : 6.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.48 % Favored : 97.52 % Rotamer: Outliers : 1.60 % Allowed : 9.64 % Favored : 88.76 % 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: -0.04 (0.18), residues: 2219 helix: 1.29 (0.17), residues: 917 sheet: -1.37 (0.26), residues: 363 loop : -0.69 (0.20), residues: 939 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP Q 818 HIS 0.004 0.001 HIS A 209 PHE 0.019 0.001 PHE A 70 TYR 0.013 0.001 TYR R 421 ARG 0.004 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 424 residues out of total 1940 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 393 time to evaluate : 2.050 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: Q 572 GLU cc_start: 0.7275 (mt-10) cc_final: 0.6970 (mt-10) REVERT: Q 576 GLU cc_start: 0.7456 (pp20) cc_final: 0.6805 (pp20) REVERT: Q 773 LEU cc_start: 0.8697 (tt) cc_final: 0.8487 (tp) REVERT: R 52 LYS cc_start: 0.8184 (mttt) cc_final: 0.7772 (mtpt) REVERT: R 191 GLU cc_start: 0.7937 (mm-30) cc_final: 0.7683 (mm-30) REVERT: R 636 LYS cc_start: 0.7757 (mtmt) cc_final: 0.7111 (mmtm) REVERT: R 756 LEU cc_start: 0.8285 (mt) cc_final: 0.7972 (mt) REVERT: A 43 ASN cc_start: 0.7754 (t0) cc_final: 0.6906 (t0) REVERT: A 82 HIS cc_start: 0.7320 (t70) cc_final: 0.6889 (t70) REVERT: A 110 VAL cc_start: 0.8799 (OUTLIER) cc_final: 0.8593 (p) REVERT: A 111 ASP cc_start: 0.7758 (t0) cc_final: 0.6945 (t0) REVERT: A 114 ASP cc_start: 0.8368 (m-30) cc_final: 0.8037 (m-30) REVERT: A 190 LYS cc_start: 0.8615 (tttt) cc_final: 0.8394 (tttt) REVERT: A 195 ASP cc_start: 0.7392 (t70) cc_final: 0.7036 (t0) REVERT: A 238 MET cc_start: 0.7964 (ttm) cc_final: 0.7750 (ttt) REVERT: B 85 TYR cc_start: 0.8414 (m-80) cc_final: 0.8077 (m-80) REVERT: B 165 THR cc_start: 0.8049 (OUTLIER) cc_final: 0.7653 (m) REVERT: B 291 ASP cc_start: 0.7712 (m-30) cc_final: 0.7419 (m-30) outliers start: 31 outliers final: 21 residues processed: 406 average time/residue: 0.3000 time to fit residues: 186.1740 Evaluate side-chains 393 residues out of total 1940 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 370 time to evaluate : 2.006 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Q residue 565 CYS 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 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 110 VAL Chi-restraints excluded: chain B residue 88 ASN 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 274 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 221 random chunks: chunk 57 optimal weight: 0.9980 chunk 19 optimal weight: 0.8980 chunk 111 optimal weight: 0.0870 chunk 154 optimal weight: 0.5980 chunk 220 optimal weight: 2.9990 chunk 185 optimal weight: 2.9990 chunk 118 optimal weight: 1.9990 chunk 67 optimal weight: 0.9990 chunk 72 optimal weight: 0.5980 chunk 167 optimal weight: 5.9990 chunk 172 optimal weight: 1.9990 overall best weight: 0.6358 ------------------------------------------------------------------------------- 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 = 0.3435 r_free = 0.3435 target = 0.113628 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3114 r_free = 0.3114 target = 0.094449 restraints weight = 28825.892| |-----------------------------------------------------------------------------| r_work (start): 0.3101 rms_B_bonded: 1.63 r_work: 0.2985 rms_B_bonded: 2.17 restraints_weight: 0.5000 r_work: 0.2834 rms_B_bonded: 3.67 restraints_weight: 0.2500 r_work (final): 0.2834 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7897 moved from start: 0.1368 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.070 18605 Z= 0.305 Angle : 0.554 10.877 25212 Z= 0.292 Chirality : 0.044 0.205 2831 Planarity : 0.004 0.054 3187 Dihedral : 6.415 59.803 2862 Min Nonbonded Distance : 2.237 Molprobity Statistics. All-atom Clashscore : 6.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.06 % Favored : 96.94 % Rotamer: Outliers : 2.01 % Allowed : 11.24 % Favored : 86.75 % 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: -0.10 (0.18), residues: 2219 helix: 1.28 (0.16), residues: 916 sheet: -1.47 (0.25), residues: 375 loop : -0.73 (0.20), residues: 928 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 0.029 0.002 PHE A 74 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 412 residues out of total 1940 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 373 time to evaluate : 2.252 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: Q 576 GLU cc_start: 0.7469 (pp20) cc_final: 0.6813 (pp20) REVERT: Q 765 CYS cc_start: 0.7737 (m) cc_final: 0.7322 (m) REVERT: Q 773 LEU cc_start: 0.8700 (tt) cc_final: 0.8498 (tp) REVERT: R 52 LYS cc_start: 0.8197 (mttt) cc_final: 0.7783 (mtpt) REVERT: R 598 CYS cc_start: 0.5988 (m) cc_final: 0.5757 (m) REVERT: R 636 LYS cc_start: 0.7766 (mtmt) cc_final: 0.7107 (mmtm) REVERT: R 756 LEU cc_start: 0.8311 (mt) cc_final: 0.7995 (mt) REVERT: A 38 LEU cc_start: 0.8014 (tt) cc_final: 0.7792 (tt) REVERT: A 43 ASN cc_start: 0.7837 (t0) cc_final: 0.6965 (t0) REVERT: A 82 HIS cc_start: 0.7279 (t70) cc_final: 0.6903 (t70) REVERT: A 110 VAL cc_start: 0.8825 (OUTLIER) cc_final: 0.8614 (p) REVERT: A 111 ASP cc_start: 0.7800 (t0) cc_final: 0.7042 (t0) REVERT: A 114 ASP cc_start: 0.8364 (m-30) cc_final: 0.8064 (m-30) REVERT: A 130 ASN cc_start: 0.7681 (m110) cc_final: 0.7392 (m110) REVERT: A 131 ASN cc_start: 0.8095 (t0) cc_final: 0.7879 (t0) REVERT: A 195 ASP cc_start: 0.7402 (t70) cc_final: 0.7048 (t0) REVERT: B 266 HIS cc_start: 0.8110 (OUTLIER) cc_final: 0.7775 (m-70) REVERT: B 291 ASP cc_start: 0.7779 (m-30) cc_final: 0.7416 (m-30) outliers start: 39 outliers final: 27 residues processed: 394 average time/residue: 0.3111 time to fit residues: 187.6179 Evaluate side-chains 387 residues out of total 1940 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 358 time to evaluate : 2.027 ------------------------------------------------------------------------------- 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 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 776 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 240 SER Chi-restraints excluded: chain R residue 263 THR Chi-restraints excluded: chain R residue 403 SER 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 86 VAL Chi-restraints excluded: chain A residue 110 VAL Chi-restraints excluded: chain A residue 134 LEU Chi-restraints excluded: chain A residue 219 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 Chi-restraints excluded: chain B residue 266 HIS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 221 random chunks: chunk 144 optimal weight: 0.2980 chunk 204 optimal weight: 1.9990 chunk 17 optimal weight: 0.9980 chunk 102 optimal weight: 0.2980 chunk 77 optimal weight: 0.8980 chunk 96 optimal weight: 0.9980 chunk 182 optimal weight: 0.5980 chunk 214 optimal weight: 1.9990 chunk 113 optimal weight: 1.9990 chunk 138 optimal weight: 0.8980 chunk 146 optimal weight: 0.9980 overall best weight: 0.5980 ------------------------------------------------------------------------------- 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 = 0.3441 r_free = 0.3441 target = 0.114005 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3123 r_free = 0.3123 target = 0.095027 restraints weight = 28833.618| |-----------------------------------------------------------------------------| r_work (start): 0.3103 rms_B_bonded: 1.71 r_work: 0.2974 rms_B_bonded: 2.29 restraints_weight: 0.5000 r_work: 0.2819 rms_B_bonded: 3.87 restraints_weight: 0.2500 r_work (final): 0.2819 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7913 moved from start: 0.1521 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 18605 Z= 0.284 Angle : 0.546 9.431 25212 Z= 0.289 Chirality : 0.043 0.206 2831 Planarity : 0.004 0.051 3187 Dihedral : 6.217 56.995 2862 Min Nonbonded Distance : 2.263 Molprobity Statistics. All-atom Clashscore : 6.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.88 % Favored : 97.12 % Rotamer: Outliers : 2.16 % Allowed : 12.42 % Favored : 85.41 % 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: -0.12 (0.18), residues: 2219 helix: 1.29 (0.17), residues: 918 sheet: -1.50 (0.25), residues: 375 loop : -0.77 (0.20), residues: 926 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 0.015 0.002 PHE R 809 TYR 0.014 0.001 TYR R 421 ARG 0.004 0.000 ARG Q 185 *********************** 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 402 residues out of total 1940 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 360 time to evaluate : 2.317 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: Q 576 GLU cc_start: 0.7457 (pp20) cc_final: 0.6796 (pp20) REVERT: Q 765 CYS cc_start: 0.7734 (m) cc_final: 0.7469 (m) REVERT: Q 773 LEU cc_start: 0.8708 (tt) cc_final: 0.8501 (tp) REVERT: R 52 LYS cc_start: 0.8209 (mttt) cc_final: 0.7784 (mtpt) REVERT: R 454 LYS cc_start: 0.7778 (mtmt) cc_final: 0.7545 (tptp) REVERT: R 636 LYS cc_start: 0.7793 (mtmt) cc_final: 0.7102 (mmtm) REVERT: R 756 LEU cc_start: 0.8400 (mt) cc_final: 0.8069 (mt) REVERT: A 38 LEU cc_start: 0.8106 (tt) cc_final: 0.7864 (tt) REVERT: A 43 ASN cc_start: 0.7807 (t0) cc_final: 0.6928 (t0) REVERT: A 82 HIS cc_start: 0.7321 (t70) cc_final: 0.6980 (t70) REVERT: A 110 VAL cc_start: 0.8833 (OUTLIER) cc_final: 0.8627 (p) REVERT: A 111 ASP cc_start: 0.7789 (t0) cc_final: 0.7043 (t0) REVERT: A 114 ASP cc_start: 0.8363 (m-30) cc_final: 0.8039 (m-30) REVERT: A 131 ASN cc_start: 0.8114 (t0) cc_final: 0.7860 (t0) REVERT: A 195 ASP cc_start: 0.7410 (t70) cc_final: 0.7059 (t0) REVERT: A 238 MET cc_start: 0.8095 (ttm) cc_final: 0.7824 (ttt) REVERT: B 176 GLN cc_start: 0.8075 (mt0) cc_final: 0.7815 (mt0) REVERT: B 266 HIS cc_start: 0.8107 (OUTLIER) cc_final: 0.7773 (m-70) REVERT: B 291 ASP cc_start: 0.7797 (m-30) cc_final: 0.7443 (m-30) outliers start: 42 outliers final: 30 residues processed: 380 average time/residue: 0.3323 time to fit residues: 192.1465 Evaluate side-chains 383 residues out of total 1940 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 351 time to evaluate : 1.899 ------------------------------------------------------------------------------- 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 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 609 THR Chi-restraints excluded: chain R residue 676 THR Chi-restraints excluded: chain R residue 776 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 110 VAL Chi-restraints excluded: chain A residue 134 LEU Chi-restraints excluded: chain A residue 219 VAL Chi-restraints excluded: chain B residue 103 CYS Chi-restraints excluded: chain B residue 161 SER 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 133 optimal weight: 0.5980 chunk 196 optimal weight: 2.9990 chunk 168 optimal weight: 4.9990 chunk 80 optimal weight: 2.9990 chunk 142 optimal weight: 0.5980 chunk 145 optimal weight: 0.9990 chunk 212 optimal weight: 1.9990 chunk 106 optimal weight: 0.9980 chunk 15 optimal weight: 0.9990 chunk 46 optimal weight: 0.9980 chunk 216 optimal weight: 8.9990 overall best weight: 0.8382 ------------------------------------------------------------------------------- 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 = 0.3421 r_free = 0.3421 target = 0.112045 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3096 r_free = 0.3096 target = 0.092635 restraints weight = 28876.611| |-----------------------------------------------------------------------------| r_work (start): 0.3087 rms_B_bonded: 1.66 r_work: 0.2969 rms_B_bonded: 2.20 restraints_weight: 0.5000 r_work: 0.2817 rms_B_bonded: 3.71 restraints_weight: 0.2500 r_work (final): 0.2817 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7920 moved from start: 0.1633 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.050 18605 Z= 0.374 Angle : 0.584 12.812 25212 Z= 0.306 Chirality : 0.045 0.205 2831 Planarity : 0.004 0.052 3187 Dihedral : 6.322 58.901 2862 Min Nonbonded Distance : 2.219 Molprobity Statistics. All-atom Clashscore : 7.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.65 % Favored : 96.35 % Rotamer: Outliers : 2.11 % Allowed : 13.14 % Favored : 84.74 % 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: -0.25 (0.17), residues: 2219 helix: 1.19 (0.16), residues: 923 sheet: -1.63 (0.25), residues: 380 loop : -0.81 (0.20), residues: 916 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 0.033 0.002 PHE A 74 TYR 0.016 0.002 TYR R 421 ARG 0.005 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 400 residues out of total 1940 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 359 time to evaluate : 1.970 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: Q 576 GLU cc_start: 0.7456 (pp20) cc_final: 0.6802 (pp20) REVERT: R 52 LYS cc_start: 0.8229 (mttt) cc_final: 0.7817 (mtpt) REVERT: R 636 LYS cc_start: 0.7800 (mtmt) cc_final: 0.7107 (mmtm) REVERT: R 756 LEU cc_start: 0.8421 (mt) cc_final: 0.8092 (mt) REVERT: A 38 LEU cc_start: 0.8088 (tt) cc_final: 0.7828 (tt) REVERT: A 82 HIS cc_start: 0.7292 (t70) cc_final: 0.6952 (t70) REVERT: A 110 VAL cc_start: 0.8856 (OUTLIER) cc_final: 0.8606 (p) REVERT: A 111 ASP cc_start: 0.7780 (t0) cc_final: 0.7412 (t0) REVERT: A 114 ASP cc_start: 0.8375 (m-30) cc_final: 0.8055 (m-30) REVERT: A 119 GLN cc_start: 0.7328 (tp40) cc_final: 0.7040 (tp-100) REVERT: A 195 ASP cc_start: 0.7430 (t70) cc_final: 0.7069 (t0) REVERT: B 93 ILE cc_start: 0.8871 (OUTLIER) cc_final: 0.8663 (mm) REVERT: B 176 GLN cc_start: 0.8172 (mt0) cc_final: 0.7851 (mt0) REVERT: B 266 HIS cc_start: 0.8095 (OUTLIER) cc_final: 0.7751 (m-70) REVERT: B 291 ASP cc_start: 0.7808 (m-30) cc_final: 0.7433 (m-30) REVERT: B 340 ASN cc_start: 0.7986 (t0) cc_final: 0.7713 (t0) outliers start: 41 outliers final: 30 residues processed: 379 average time/residue: 0.3085 time to fit residues: 176.5277 Evaluate side-chains 381 residues out of total 1940 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 348 time to evaluate : 2.015 ------------------------------------------------------------------------------- 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 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 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 A residue 110 VAL 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 136 optimal weight: 0.7980 chunk 86 optimal weight: 0.2980 chunk 178 optimal weight: 0.1980 chunk 192 optimal weight: 1.9990 chunk 158 optimal weight: 0.5980 chunk 25 optimal weight: 0.5980 chunk 19 optimal weight: 0.9980 chunk 161 optimal weight: 0.8980 chunk 81 optimal weight: 0.4980 chunk 145 optimal weight: 0.9990 chunk 64 optimal weight: 1.9990 overall best weight: 0.4380 ------------------------------------------------------------------------------- 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 = 0.3444 r_free = 0.3444 target = 0.113838 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3127 r_free = 0.3127 target = 0.094707 restraints weight = 28601.912| |-----------------------------------------------------------------------------| r_work (start): 0.3117 rms_B_bonded: 1.63 r_work: 0.3002 rms_B_bonded: 2.17 restraints_weight: 0.5000 r_work: 0.2851 rms_B_bonded: 3.66 restraints_weight: 0.2500 r_work (final): 0.2851 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7889 moved from start: 0.1699 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 18605 Z= 0.230 Angle : 0.533 12.144 25212 Z= 0.282 Chirality : 0.043 0.207 2831 Planarity : 0.004 0.048 3187 Dihedral : 6.058 55.882 2862 Min Nonbonded Distance : 2.298 Molprobity Statistics. All-atom Clashscore : 7.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.93 % Favored : 97.07 % Rotamer: Outliers : 1.70 % Allowed : 14.54 % Favored : 83.76 % 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: -0.08 (0.18), residues: 2219 helix: 1.34 (0.17), residues: 922 sheet: -1.55 (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 209 PHE 0.016 0.001 PHE A 70 TYR 0.012 0.001 TYR R 421 ARG 0.004 0.000 ARG Q 54 *********************** 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 389 residues out of total 1940 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 356 time to evaluate : 2.082 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: Q 576 GLU cc_start: 0.7445 (pp20) cc_final: 0.6810 (pp20) REVERT: Q 773 LEU cc_start: 0.8719 (tt) cc_final: 0.8510 (tp) REVERT: R 52 LYS cc_start: 0.8213 (mttt) cc_final: 0.7792 (mtpt) REVERT: R 636 LYS cc_start: 0.7754 (mtmt) cc_final: 0.7139 (mmtt) REVERT: R 756 LEU cc_start: 0.8384 (mt) cc_final: 0.8075 (mt) REVERT: A 38 LEU cc_start: 0.8077 (tt) cc_final: 0.7837 (tt) REVERT: A 74 PHE cc_start: 0.7970 (p90) cc_final: 0.7553 (p90) REVERT: A 82 HIS cc_start: 0.7242 (t70) cc_final: 0.7006 (t70) REVERT: A 110 VAL cc_start: 0.8828 (OUTLIER) cc_final: 0.8566 (p) REVERT: A 111 ASP cc_start: 0.7735 (t0) cc_final: 0.7486 (t0) REVERT: A 195 ASP cc_start: 0.7371 (t70) cc_final: 0.7025 (t0) REVERT: B 176 GLN cc_start: 0.8098 (mt0) cc_final: 0.7759 (mt0) REVERT: B 266 HIS cc_start: 0.8110 (OUTLIER) cc_final: 0.7829 (m-70) REVERT: B 291 ASP cc_start: 0.7805 (m-30) cc_final: 0.7574 (m-30) outliers start: 33 outliers final: 25 residues processed: 373 average time/residue: 0.3347 time to fit residues: 190.2543 Evaluate side-chains 373 residues out of total 1940 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 346 time to evaluate : 2.157 ------------------------------------------------------------------------------- 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 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 537 VAL Chi-restraints excluded: chain R residue 554 ILE 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 828 THR Chi-restraints excluded: chain A residue 86 VAL Chi-restraints excluded: chain A residue 110 VAL 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 221 random chunks: chunk 162 optimal weight: 2.9990 chunk 43 optimal weight: 1.9990 chunk 121 optimal weight: 0.0170 chunk 49 optimal weight: 1.9990 chunk 118 optimal weight: 1.9990 chunk 1 optimal weight: 0.9990 chunk 89 optimal weight: 0.8980 chunk 127 optimal weight: 0.7980 chunk 11 optimal weight: 0.9980 chunk 6 optimal weight: 0.9990 chunk 65 optimal weight: 0.6980 overall best weight: 0.6818 ------------------------------------------------------------------------------- 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 = 0.3433 r_free = 0.3433 target = 0.113496 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3110 r_free = 0.3110 target = 0.094180 restraints weight = 28606.759| |-----------------------------------------------------------------------------| r_work (start): 0.3099 rms_B_bonded: 1.65 r_work: 0.2981 rms_B_bonded: 2.20 restraints_weight: 0.5000 r_work: 0.2828 rms_B_bonded: 3.72 restraints_weight: 0.2500 r_work (final): 0.2828 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7913 moved from start: 0.1773 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.043 18605 Z= 0.315 Angle : 0.566 11.844 25212 Z= 0.297 Chirality : 0.044 0.207 2831 Planarity : 0.004 0.051 3187 Dihedral : 6.140 56.743 2862 Min Nonbonded Distance : 2.231 Molprobity Statistics. All-atom Clashscore : 7.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.56 % Favored : 96.44 % Rotamer: Outliers : 2.16 % Allowed : 14.54 % Favored : 83.30 % 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: -0.14 (0.18), residues: 2219 helix: 1.28 (0.16), residues: 923 sheet: -1.59 (0.25), residues: 380 loop : -0.75 (0.21), residues: 916 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 421 ARG 0.004 0.000 ARG Q 54 *********************** 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 401 residues out of total 1940 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 359 time to evaluate : 2.274 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: Q 576 GLU cc_start: 0.7472 (pp20) cc_final: 0.6832 (pp20) REVERT: Q 773 LEU cc_start: 0.8717 (tt) cc_final: 0.8508 (tp) REVERT: R 52 LYS cc_start: 0.8221 (mttt) cc_final: 0.7800 (mtpt) REVERT: R 454 LYS cc_start: 0.7814 (mtmt) cc_final: 0.7596 (tptp) REVERT: R 636 LYS cc_start: 0.7766 (mtmt) cc_final: 0.7079 (mmtm) REVERT: R 756 LEU cc_start: 0.8434 (mt) cc_final: 0.8143 (mt) REVERT: A 38 LEU cc_start: 0.8087 (tt) cc_final: 0.7822 (tt) REVERT: A 73 LYS cc_start: 0.8411 (tppt) cc_final: 0.8093 (tppt) REVERT: A 82 HIS cc_start: 0.7337 (t70) cc_final: 0.7022 (t70) REVERT: A 110 VAL cc_start: 0.8841 (OUTLIER) cc_final: 0.8569 (p) REVERT: A 195 ASP cc_start: 0.7392 (t70) cc_final: 0.7048 (t0) REVERT: B 59 TYR cc_start: 0.8423 (m-10) cc_final: 0.8058 (m-80) REVERT: B 176 GLN cc_start: 0.8184 (mt0) cc_final: 0.7882 (mt0) REVERT: B 266 HIS cc_start: 0.8115 (OUTLIER) cc_final: 0.7847 (m-70) REVERT: B 291 ASP cc_start: 0.7795 (m-30) cc_final: 0.7555 (m-30) REVERT: B 340 ASN cc_start: 0.8105 (t0) cc_final: 0.7782 (t0) REVERT: G 51 LEU cc_start: 0.8505 (tp) cc_final: 0.8202 (mp) outliers start: 42 outliers final: 33 residues processed: 381 average time/residue: 0.3245 time to fit residues: 186.3334 Evaluate side-chains 387 residues out of total 1940 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 352 time to evaluate : 2.347 ------------------------------------------------------------------------------- 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 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 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 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 29 VAL Chi-restraints excluded: chain A residue 86 VAL Chi-restraints excluded: chain A residue 110 VAL 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 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 221 random chunks: chunk 61 optimal weight: 0.7980 chunk 128 optimal weight: 0.9980 chunk 108 optimal weight: 0.6980 chunk 13 optimal weight: 0.3980 chunk 163 optimal weight: 0.9990 chunk 124 optimal weight: 0.7980 chunk 57 optimal weight: 0.0670 chunk 53 optimal weight: 0.7980 chunk 88 optimal weight: 0.9990 chunk 180 optimal weight: 0.9980 chunk 76 optimal weight: 0.1980 overall best weight: 0.4318 ------------------------------------------------------------------------------- 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 = 0.3442 r_free = 0.3442 target = 0.113865 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3121 r_free = 0.3121 target = 0.094531 restraints weight = 28957.221| |-----------------------------------------------------------------------------| r_work (start): 0.3106 rms_B_bonded: 1.66 r_work: 0.2990 rms_B_bonded: 2.21 restraints_weight: 0.5000 r_work: 0.2838 rms_B_bonded: 3.73 restraints_weight: 0.2500 r_work (final): 0.2838 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7891 moved from start: 0.1821 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 18605 Z= 0.230 Angle : 0.546 10.871 25212 Z= 0.286 Chirality : 0.043 0.214 2831 Planarity : 0.004 0.048 3187 Dihedral : 5.977 56.042 2862 Min Nonbonded Distance : 2.298 Molprobity Statistics. All-atom Clashscore : 6.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.20 % Favored : 96.80 % Rotamer: Outliers : 1.91 % Allowed : 14.69 % Favored : 83.40 % 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: -0.03 (0.18), residues: 2219 helix: 1.37 (0.16), residues: 925 sheet: -1.52 (0.25), residues: 380 loop : -0.71 (0.21), residues: 914 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP Q 818 HIS 0.003 0.001 HIS A 209 PHE 0.015 0.001 PHE A 70 TYR 0.017 0.001 TYR R 573 ARG 0.008 0.000 ARG B 256 *********************** 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 399 residues out of total 1940 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 362 time to evaluate : 2.849 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: Q 773 LEU cc_start: 0.8730 (tt) cc_final: 0.8511 (tp) REVERT: R 52 LYS cc_start: 0.8228 (mttt) cc_final: 0.7823 (mtpt) REVERT: R 454 LYS cc_start: 0.7820 (mtmt) cc_final: 0.7607 (tptp) REVERT: R 636 LYS cc_start: 0.7744 (mtmt) cc_final: 0.7133 (mmtt) REVERT: R 756 LEU cc_start: 0.8405 (mt) cc_final: 0.8107 (mt) REVERT: A 38 LEU cc_start: 0.8093 (tt) cc_final: 0.7835 (tt) REVERT: A 43 ASN cc_start: 0.7800 (t0) cc_final: 0.7086 (t0) REVERT: A 82 HIS cc_start: 0.7334 (t70) cc_final: 0.7074 (t70) REVERT: A 110 VAL cc_start: 0.8779 (OUTLIER) cc_final: 0.8500 (p) REVERT: A 111 ASP cc_start: 0.7630 (t0) cc_final: 0.7050 (t0) REVERT: A 131 ASN cc_start: 0.8136 (t0) cc_final: 0.7889 (t0) REVERT: A 195 ASP cc_start: 0.7382 (t70) cc_final: 0.7026 (t0) REVERT: B 59 TYR cc_start: 0.8397 (m-10) cc_final: 0.8028 (m-80) REVERT: B 176 GLN cc_start: 0.8133 (mt0) cc_final: 0.7829 (mt0) REVERT: B 266 HIS cc_start: 0.8112 (OUTLIER) cc_final: 0.7904 (m-70) REVERT: B 291 ASP cc_start: 0.7759 (m-30) cc_final: 0.7512 (m-30) REVERT: B 340 ASN cc_start: 0.8189 (t0) cc_final: 0.7923 (t0) outliers start: 37 outliers final: 31 residues processed: 383 average time/residue: 0.3261 time to fit residues: 189.7815 Evaluate side-chains 382 residues out of total 1940 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 349 time to evaluate : 2.044 ------------------------------------------------------------------------------- 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 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 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 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 18 MET Chi-restraints excluded: chain A residue 86 VAL Chi-restraints excluded: chain A residue 110 VAL 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 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 221 random chunks: chunk 19 optimal weight: 0.9980 chunk 60 optimal weight: 0.7980 chunk 130 optimal weight: 0.6980 chunk 54 optimal weight: 0.7980 chunk 160 optimal weight: 0.3980 chunk 185 optimal weight: 1.9990 chunk 157 optimal weight: 1.9990 chunk 58 optimal weight: 1.9990 chunk 127 optimal weight: 0.8980 chunk 68 optimal weight: 0.0070 chunk 181 optimal weight: 0.9980 overall best weight: 0.5398 ------------------------------------------------------------------------------- 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 = 0.3439 r_free = 0.3439 target = 0.113633 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3118 r_free = 0.3118 target = 0.094358 restraints weight = 28672.765| |-----------------------------------------------------------------------------| r_work (start): 0.3109 rms_B_bonded: 1.64 r_work: 0.2994 rms_B_bonded: 2.18 restraints_weight: 0.5000 r_work: 0.2842 rms_B_bonded: 3.68 restraints_weight: 0.2500 r_work (final): 0.2842 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7896 moved from start: 0.1866 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 18605 Z= 0.270 Angle : 0.564 10.902 25212 Z= 0.295 Chirality : 0.044 0.212 2831 Planarity : 0.004 0.049 3187 Dihedral : 6.014 56.985 2862 Min Nonbonded Distance : 2.255 Molprobity Statistics. All-atom Clashscore : 7.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.47 % Favored : 96.53 % Rotamer: Outliers : 1.80 % Allowed : 15.15 % Favored : 83.04 % 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: 1.34 (0.16), residues: 926 sheet: -1.49 (0.25), residues: 380 loop : -0.74 (0.21), residues: 913 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP Q 818 HIS 0.003 0.001 HIS A 209 PHE 0.015 0.002 PHE A 70 TYR 0.022 0.002 TYR R 573 ARG 0.007 0.000 ARG B 256 ********************** 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 381 residues out of total 1940 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 346 time to evaluate : 2.007 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: Q 62 ARG cc_start: 0.8320 (mtp85) cc_final: 0.7860 (mtp180) REVERT: Q 576 GLU cc_start: 0.7497 (pp20) cc_final: 0.6913 (pp20) REVERT: Q 773 LEU cc_start: 0.8726 (tt) cc_final: 0.8510 (tp) REVERT: R 52 LYS cc_start: 0.8228 (mttt) cc_final: 0.7794 (mtpt) REVERT: R 454 LYS cc_start: 0.7821 (mtmt) cc_final: 0.7620 (tptp) REVERT: R 636 LYS cc_start: 0.7744 (mtmt) cc_final: 0.7157 (mmtt) REVERT: R 756 LEU cc_start: 0.8422 (mt) cc_final: 0.8150 (mt) REVERT: A 38 LEU cc_start: 0.8096 (tt) cc_final: 0.7832 (tt) REVERT: A 73 LYS cc_start: 0.8416 (OUTLIER) cc_final: 0.8137 (tppt) REVERT: A 82 HIS cc_start: 0.7342 (t70) cc_final: 0.7087 (t70) REVERT: A 110 VAL cc_start: 0.8771 (OUTLIER) cc_final: 0.8524 (p) REVERT: A 195 ASP cc_start: 0.7307 (t70) cc_final: 0.7099 (t0) REVERT: B 59 TYR cc_start: 0.8377 (m-10) cc_final: 0.7985 (m-80) REVERT: B 176 GLN cc_start: 0.8143 (mt0) cc_final: 0.7835 (mt0) REVERT: B 291 ASP cc_start: 0.7739 (m-30) cc_final: 0.7500 (m-30) REVERT: B 340 ASN cc_start: 0.8203 (t0) cc_final: 0.7971 (t0) outliers start: 35 outliers final: 31 residues processed: 364 average time/residue: 0.3220 time to fit residues: 178.1337 Evaluate side-chains 376 residues out of total 1940 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 343 time to evaluate : 2.147 ------------------------------------------------------------------------------- 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 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 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 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 73 LYS Chi-restraints excluded: chain A residue 86 VAL Chi-restraints excluded: chain A residue 110 VAL 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 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 Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 221 random chunks: chunk 38 optimal weight: 0.4980 chunk 213 optimal weight: 4.9990 chunk 57 optimal weight: 0.3980 chunk 176 optimal weight: 0.8980 chunk 207 optimal weight: 3.9990 chunk 63 optimal weight: 0.0980 chunk 75 optimal weight: 0.7980 chunk 107 optimal weight: 0.5980 chunk 53 optimal weight: 0.7980 chunk 112 optimal weight: 0.5980 chunk 74 optimal weight: 0.4980 overall best weight: 0.4180 ------------------------------------------------------------------------------- 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 = 0.3446 r_free = 0.3446 target = 0.114099 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3128 r_free = 0.3128 target = 0.094890 restraints weight = 28749.507| |-----------------------------------------------------------------------------| r_work (start): 0.3120 rms_B_bonded: 1.64 r_work: 0.3005 rms_B_bonded: 2.19 restraints_weight: 0.5000 r_work: 0.2853 rms_B_bonded: 3.70 restraints_weight: 0.2500 r_work (final): 0.2853 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7886 moved from start: 0.1913 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 18605 Z= 0.229 Angle : 0.549 10.914 25212 Z= 0.287 Chirality : 0.043 0.240 2831 Planarity : 0.004 0.048 3187 Dihedral : 5.918 58.814 2862 Min Nonbonded Distance : 2.290 Molprobity Statistics. All-atom Clashscore : 7.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.24 % Favored : 96.76 % Rotamer: Outliers : 1.86 % Allowed : 15.21 % Favored : 82.94 % 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: 0.00 (0.18), residues: 2219 helix: 1.40 (0.16), residues: 925 sheet: -1.45 (0.25), residues: 380 loop : -0.71 (0.21), residues: 914 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP Q 818 HIS 0.005 0.001 HIS B 266 PHE 0.015 0.001 PHE A 70 TYR 0.019 0.001 TYR R 573 ARG 0.007 0.000 ARG B 256 Origin is already at (0, 0, 0), no shifts will be applied Model does not fit in PDB format. =============================================================================== Job complete usr+sys time: 9173.69 seconds wall clock time: 166 minutes 27.53 seconds (9987.53 seconds total)