Starting phenix.real_space_refine on Sat Jul 4 03:45:48 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9avl_43908/07_2026/9avl_43908.cif Found real_map, /net/cci-nas-00/data/ceres_data/9avl_43908/07_2026/9avl_43908.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9avl_43908/07_2026/9avl_43908.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9avl_43908/07_2026/9avl_43908.map" model { file = "/net/cci-nas-00/data/ceres_data/9avl_43908/07_2026/9avl_43908.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9avl_43908/07_2026/9avl_43908.cif" } resolution = 3.8 write_initial_geo_file = False refinement { macro_cycles = 10 } 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= 0.041 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 110 5.16 5 Cl 2 4.86 5 C 11671 2.51 5 N 2973 2.21 5 O 3378 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 67 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 18143 Number of models: 1 Model: "" Number of chains: 13 Chain: "Q" Number of atoms: 6390 Number of conformers: 1 Conformer: "" Number of residues, atoms: 803, 6390 Classifications: {'peptide': 803} Link IDs: {'CIS': 1, 'PTRANS': 30, 'TRANS': 771} Chain breaks: 3 Chain: "R" Number of atoms: 6561 Number of conformers: 1 Conformer: "" Number of residues, atoms: 824, 6561 Classifications: {'peptide': 824} Link IDs: {'CIS': 1, 'PTRANS': 32, 'TRANS': 790} Chain breaks: 2 Chain: "A" Number of atoms: 1822 Number of conformers: 1 Conformer: "" Number of residues, atoms: 225, 1822 Classifications: {'peptide': 225} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 222} Chain breaks: 1 Chain: "B" Number of atoms: 2599 Number of conformers: 1 Conformer: "" Number of residues, atoms: 338, 2599 Classifications: {'peptide': 338} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 331} Chain: "G" Number of atoms: 427 Number of conformers: 1 Conformer: "" Number of residues, atoms: 55, 427 Classifications: {'peptide': 55} Link IDs: {'PTRANS': 4, 'TRANS': 50} 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: 30 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 30 Unusual residues: {'NAG': 1, 'TCR': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "Q" Number of atoms: 64 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 61 Ad-hoc single atom residues: {' CA': 3} Unusual residues: {'9IG': 1, 'PO4': 1, 'Y01': 1} Classifications: {'undetermined': 3} Link IDs: {None: 1} Chain breaks: 3 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: 80 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 77 Ad-hoc single atom residues: {' CA': 3} Unusual residues: {'9IG': 1, 'A1AF7': 1, 'PO4': 1} Classifications: {'undetermined': 3} Link IDs: {None: 1} Chain breaks: 3 Time building chain proxies: 4.42, per 1000 atoms: 0.24 Number of scatterers: 18143 At special positions: 0 Unit cell: (91.996, 124.068, 252.356, 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 110 16.00 P 3 15.00 O 3378 8.00 N 2973 7.00 C 11671 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=17, 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 546 " - pdb=" SG CYS R 565 " distance=2.03 Simple disulfide: pdb=" SG CYS R 568 " - pdb=" SG CYS R 582 " distance=2.03 Simple disulfide: pdb=" SG CYS R 585 " - pdb=" SG CYS R 598 " distance=2.03 Simple disulfide: pdb=" SG CYS R 677 " - pdb=" SG CYS R 765 " distance=2.03 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 468 " " NAG R1001 " - " ASN R 261 " " NAG R1002 " - " ASN R 287 " " NAG R1003 " - " ASN R 468 " Time building additional restraints: 1.82 Conformation dependent library (CDL) restraints added in 812.8 milliseconds 4446 Ramachandran restraints generated. 2223 Oldfield, 0 Emsley, 2223 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4226 Finding SS restraints... Secondary structure from input PDB file: 77 helices and 23 sheets defined 46.4% alpha, 15.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.63 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 124 Processing helix chain 'Q' and resid 146 through 160 removed outlier: 4.067A pdb=" N PHE Q 160 " --> pdb=" O LEU Q 156 " (cutoff:3.500A) Processing helix chain 'Q' and resid 171 through 176 removed outlier: 3.617A pdb=" N LEU Q 174 " --> pdb=" O SER Q 171 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N ASN Q 176 " --> pdb=" O LEU Q 173 " (cutoff:3.500A) Processing helix chain 'Q' and resid 190 through 205 Processing helix chain 'Q' and resid 218 through 233 removed outlier: 3.915A 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 removed outlier: 3.610A pdb=" N PHE Q 333 " --> pdb=" O GLY Q 329 " (cutoff:3.500A) Processing helix chain 'Q' and resid 347 through 357 Processing helix chain 'Q' and resid 400 through 404 Processing helix chain 'Q' and resid 415 through 436 Processing helix chain 'Q' and resid 444 through 448 Processing helix chain 'Q' and resid 451 through 455 removed outlier: 3.693A 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 Processing helix chain 'Q' and resid 673 through 699 removed outlier: 4.572A 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 701 through 710 Processing helix chain 'Q' and resid 723 through 746 Processing helix chain 'Q' and resid 769 through 794 removed outlier: 3.660A pdb=" N LEU Q 773 " --> pdb=" O SER Q 769 " (cutoff:3.500A) Processing helix chain 'Q' and resid 802 through 828 removed outlier: 3.634A pdb=" N PHE Q 806 " --> pdb=" O ASN Q 802 " (cutoff:3.500A) removed outlier: 4.360A pdb=" N ILE Q 822 " --> pdb=" O TRP Q 818 " (cutoff:3.500A) Proline residue: Q 823 - end of helix Processing helix chain 'Q' and resid 831 through 861 removed outlier: 4.065A pdb=" N ALA Q 835 " --> pdb=" O LYS Q 831 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N GLU Q 837 " --> pdb=" O VAL Q 833 " (cutoff:3.500A) removed outlier: 6.267A pdb=" N ASN Q 855 " --> pdb=" O CYS Q 851 " (cutoff:3.500A) removed outlier: 5.455A pdb=" N LYS Q 856 " --> pdb=" O ILE Q 852 " (cutoff:3.500A) Processing helix chain 'Q' and resid 863 through 867 removed outlier: 4.238A pdb=" N ARG Q 866 " --> pdb=" O LYS Q 863 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N ASN Q 867 " --> pdb=" O PRO Q 864 " (cutoff:3.500A) No H-bonds generated for 'chain 'Q' and resid 863 through 867' Processing helix chain 'Q' and resid 868 through 873 removed outlier: 3.518A pdb=" N VAL Q 872 " --> pdb=" O THR Q 868 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N ARG Q 873 " --> pdb=" O ILE Q 869 " (cutoff:3.500A) No H-bonds generated for 'chain 'Q' and resid 868 through 873' Processing helix chain 'R' and resid 64 through 83 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: 4.021A pdb=" N PHE R 160 " --> pdb=" O LEU R 156 " (cutoff:3.500A) Processing helix chain 'R' and resid 171 through 176 removed outlier: 3.625A pdb=" N ASN R 176 " --> pdb=" O LEU R 173 " (cutoff:3.500A) Processing helix chain 'R' and resid 190 through 204 Processing helix chain 'R' and resid 218 through 233 removed outlier: 3.706A pdb=" N GLY R 222 " --> pdb=" O TYR R 218 " (cutoff:3.500A) Processing helix chain 'R' and resid 248 through 262 Processing helix chain 'R' and resid 272 through 287 Proline residue: R 278 - end of helix Processing helix chain 'R' and resid 307 through 311 removed outlier: 3.758A pdb=" N PHE R 311 " --> pdb=" O PRO R 308 " (cutoff:3.500A) Processing helix chain 'R' and resid 329 through 335 Processing helix chain 'R' and resid 347 through 357 Processing helix chain 'R' and resid 400 through 404 Processing helix chain 'R' and resid 415 through 436 Processing helix chain 'R' and resid 444 through 448 Processing helix chain 'R' and resid 456 through 466 Processing helix chain 'R' and resid 529 through 533 Processing helix chain 'R' and resid 610 through 637 Processing helix chain 'R' and resid 640 through 646 removed outlier: 3.616A pdb=" N THR R 646 " --> pdb=" O ILE R 642 " (cutoff:3.500A) Processing helix chain 'R' and resid 647 through 665 removed outlier: 3.709A pdb=" N SER R 665 " --> pdb=" O CYS R 661 " (cutoff:3.500A) Processing helix chain 'R' and resid 666 through 668 No H-bonds generated for 'chain 'R' and resid 666 through 668' Processing helix chain 'R' and resid 673 through 708 removed outlier: 4.774A pdb=" N GLN R 681 " --> pdb=" O CYS R 677 " (cutoff:3.500A) Proline residue: R 682 - end of helix removed outlier: 3.537A pdb=" N ALA R 708 " --> pdb=" O LEU R 704 " (cutoff:3.500A) Processing helix chain 'R' and resid 714 through 719 Processing helix chain 'R' and resid 720 through 746 Processing helix chain 'R' and resid 769 through 794 removed outlier: 3.686A pdb=" N LEU R 773 " --> pdb=" O SER R 769 " (cutoff:3.500A) Processing helix chain 'R' and resid 798 through 802 removed outlier: 3.557A pdb=" N ASN R 802 " --> pdb=" O GLU R 799 " (cutoff:3.500A) Processing helix chain 'R' and resid 803 through 821 removed outlier: 3.619A pdb=" N PHE R 821 " --> pdb=" O VAL R 817 " (cutoff:3.500A) Processing helix chain 'R' and resid 821 through 827 Processing helix chain 'R' and resid 830 through 853 removed outlier: 3.691A pdb=" N SER R 834 " --> pdb=" O GLY R 830 " (cutoff:3.500A) Processing helix chain 'R' and resid 853 through 862 Processing helix chain 'R' and resid 863 through 867 removed outlier: 3.779A pdb=" N ARG R 866 " --> pdb=" O LYS R 863 " (cutoff:3.500A) Processing helix chain 'R' and resid 868 through 880 removed outlier: 3.570A pdb=" N VAL R 872 " --> pdb=" O THR R 868 " (cutoff:3.500A) removed outlier: 4.270A pdb=" N ALA R 880 " --> pdb=" O THR R 876 " (cutoff:3.500A) Processing helix chain 'A' and resid 6 through 32 removed outlier: 3.961A pdb=" N LYS A 32 " --> pdb=" O GLU A 28 " (cutoff:3.500A) Processing helix chain 'A' and resid 45 through 54 Processing helix chain 'A' and resid 207 through 216 removed outlier: 3.865A pdb=" N LYS A 210 " --> pdb=" O GLU A 207 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N TRP A 211 " --> pdb=" O ARG A 208 " (cutoff:3.500A) removed outlier: 5.672A pdb=" N ILE A 212 " --> pdb=" O LYS A 209 " (cutoff:3.500A) removed outlier: 5.673A pdb=" N HIS A 213 " --> pdb=" O LYS A 210 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N GLU A 216 " --> pdb=" O HIS A 213 " (cutoff:3.500A) Processing helix chain 'A' and resid 228 through 230 No H-bonds generated for 'chain 'A' and resid 228 through 230' Processing helix chain 'A' and resid 241 through 255 Processing helix chain 'A' and resid 270 through 281 removed outlier: 3.674A pdb=" N LYS A 279 " --> pdb=" O GLU A 275 " (cutoff:3.500A) Processing helix chain 'A' and resid 282 through 286 removed outlier: 3.545A pdb=" N ILE A 285 " --> pdb=" O PRO A 282 " (cutoff:3.500A) Processing helix chain 'A' and resid 295 through 309 removed outlier: 3.616A pdb=" N ALA A 299 " --> pdb=" O THR A 295 " (cutoff:3.500A) Processing helix chain 'A' and resid 329 through 352 removed outlier: 3.569A pdb=" N GLN A 333 " --> pdb=" O THR A 329 " (cutoff:3.500A) Processing helix chain 'B' and resid 4 through 26 Processing helix chain 'B' and resid 29 through 35 Processing helix chain 'G' and resid 10 through 24 Processing helix chain 'G' and resid 29 through 44 removed outlier: 3.575A pdb=" N ALA G 33 " --> pdb=" O LYS G 29 " (cutoff:3.500A) Processing helix chain 'G' and resid 55 through 59 Processing sheet with id=AA1, first strand: chain 'Q' and resid 26 through 28 removed outlier: 6.226A pdb=" N ILE Q 32 " --> pdb=" O GLY Q 94 " (cutoff:3.500A) removed outlier: 7.730A pdb=" N ARG Q 96 " --> pdb=" O ILE Q 32 " (cutoff:3.500A) removed outlier: 6.533A pdb=" N LEU Q 34 " --> pdb=" O ARG Q 96 " (cutoff:3.500A) removed outlier: 7.746A pdb=" N PHE Q 98 " --> pdb=" O LEU Q 34 " (cutoff:3.500A) removed outlier: 6.543A pdb=" N GLY Q 36 " --> pdb=" O PHE Q 98 " (cutoff:3.500A) removed outlier: 6.844A pdb=" N ILE Q 33 " --> pdb=" O THR Q 138 " (cutoff:3.500A) removed outlier: 3.987A pdb=" N ALA Q 140 " --> pdb=" O ILE Q 33 " (cutoff:3.500A) removed outlier: 8.313A pdb=" N VAL Q 165 " --> pdb=" O ILE Q 139 " (cutoff:3.500A) removed outlier: 6.278A pdb=" N VAL Q 141 " --> pdb=" O VAL Q 165 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'Q' and resid 236 through 243 removed outlier: 6.433A pdb=" N VAL Q 209 " --> pdb=" O ILE Q 237 " (cutoff:3.500A) removed outlier: 4.420A pdb=" N PHE Q 239 " --> pdb=" O VAL Q 209 " (cutoff:3.500A) removed outlier: 7.035A pdb=" N TRP Q 208 " --> pdb=" O VAL Q 266 " (cutoff:3.500A) removed outlier: 8.464A pdb=" N VAL Q 268 " --> pdb=" O TRP Q 208 " (cutoff:3.500A) removed outlier: 6.558A pdb=" N GLY Q 210 " --> pdb=" O VAL Q 268 " (cutoff:3.500A) removed outlier: 8.041A pdb=" N PHE Q 270 " --> pdb=" O GLY Q 210 " (cutoff:3.500A) removed outlier: 6.835A pdb=" N ILE Q 212 " --> pdb=" O PHE Q 270 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N PHE Q 320 " --> pdb=" O ALA Q 295 " (cutoff:3.500A) removed outlier: 6.810A pdb=" N TYR Q 489 " --> pdb=" O TYR Q 510 " (cutoff:3.500A) removed outlier: 4.798A pdb=" N TYR Q 510 " --> pdb=" O TYR Q 489 " (cutoff:3.500A) removed outlier: 6.339A pdb=" N ILE Q 491 " --> pdb=" O VAL Q 508 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'Q' and resid 468 through 470 Processing sheet with id=AA4, first strand: chain 'Q' and resid 550 through 554 Processing sheet with id=AA5, first strand: chain 'Q' and resid 572 through 573 Processing sheet with id=AA6, first strand: chain 'Q' and resid 589 through 591 Processing sheet with id=AA7, first strand: chain 'Q' and resid 602 through 604 removed outlier: 6.616A pdb=" N GLU Q 602 " --> pdb=" O ILE Q 761 " (cutoff:3.500A) removed outlier: 7.784A pdb=" N ILE Q 763 " --> pdb=" O GLU Q 602 " (cutoff:3.500A) removed outlier: 7.701A pdb=" N GLU Q 604 " --> pdb=" O ILE Q 763 " (cutoff:3.500A) removed outlier: 9.741A pdb=" N CYS Q 765 " --> pdb=" O GLU Q 604 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'R' and resid 26 through 28 removed outlier: 6.257A pdb=" N ILE R 32 " --> pdb=" O GLY R 94 " (cutoff:3.500A) removed outlier: 7.580A pdb=" N ARG R 96 " --> pdb=" O ILE R 32 " (cutoff:3.500A) removed outlier: 6.551A pdb=" N LEU R 34 " --> pdb=" O ARG R 96 " (cutoff:3.500A) removed outlier: 7.804A pdb=" N PHE R 98 " --> pdb=" O LEU R 34 " (cutoff:3.500A) removed outlier: 6.329A pdb=" N GLY R 36 " --> pdb=" O PHE R 98 " (cutoff:3.500A) removed outlier: 6.916A pdb=" N ILE R 33 " --> pdb=" O THR R 138 " (cutoff:3.500A) removed outlier: 4.112A pdb=" N ALA R 140 " --> pdb=" O ILE R 33 " (cutoff:3.500A) removed outlier: 8.669A pdb=" N VAL R 165 " --> pdb=" O ILE R 139 " (cutoff:3.500A) removed outlier: 6.441A pdb=" N VAL R 141 " --> pdb=" O VAL R 165 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'R' and resid 236 through 243 removed outlier: 8.175A pdb=" N VAL R 209 " --> pdb=" O ASP R 238 " (cutoff:3.500A) removed outlier: 7.190A pdb=" N SER R 240 " --> pdb=" O VAL R 209 " (cutoff:3.500A) removed outlier: 7.137A pdb=" N THR R 211 " --> pdb=" O SER R 240 " (cutoff:3.500A) removed outlier: 6.018A pdb=" N LEU R 242 " --> pdb=" O THR R 211 " (cutoff:3.500A) removed outlier: 6.499A pdb=" N ALA R 213 " --> pdb=" O LEU R 242 " (cutoff:3.500A) removed outlier: 4.875A pdb=" N VAL R 266 " --> pdb=" O TRP R 208 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'R' and resid 318 through 321 removed outlier: 6.621A pdb=" N TYR R 489 " --> pdb=" O TYR R 510 " (cutoff:3.500A) removed outlier: 4.638A pdb=" N TYR R 510 " --> pdb=" O TYR R 489 " (cutoff:3.500A) removed outlier: 6.542A 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 removed outlier: 3.573A pdb=" N ILE R 763 " --> pdb=" O GLU R 604 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'A' and resid 185 through 190 removed outlier: 3.852A pdb=" N ALA A 220 " --> pdb=" O LYS A 35 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'B' and resid 47 through 51 removed outlier: 3.640A pdb=" N ARG B 49 " --> pdb=" O ILE B 338 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 58 through 63 removed outlier: 3.612A pdb=" N SER B 74 " --> pdb=" O LYS B 78 " (cutoff:3.500A) removed outlier: 4.021A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 6.022A pdb=" N LEU B 79 " --> pdb=" O ALA B 92 " (cutoff:3.500A) removed outlier: 4.337A pdb=" N ALA B 92 " --> pdb=" O LEU B 79 " (cutoff:3.500A) removed outlier: 6.636A pdb=" N ILE B 81 " --> pdb=" O VAL B 90 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 100 through 105 removed outlier: 6.867A pdb=" N GLY B 115 " --> pdb=" O MET B 101 " (cutoff:3.500A) removed outlier: 4.357A pdb=" N CYS B 103 " --> pdb=" O ALA B 113 " (cutoff:3.500A) removed outlier: 6.451A pdb=" N ALA B 113 " --> pdb=" O CYS B 103 " (cutoff:3.500A) removed outlier: 5.021A pdb=" N TYR B 105 " --> pdb=" O PHE B 111 " (cutoff:3.500A) removed outlier: 7.030A pdb=" N PHE B 111 " --> pdb=" O TYR B 105 " (cutoff:3.500A) removed outlier: 6.664A pdb=" N CYS B 121 " --> pdb=" O GLU B 138 " (cutoff:3.500A) removed outlier: 4.481A pdb=" N GLU B 138 " --> pdb=" O CYS B 121 " (cutoff:3.500A) removed outlier: 6.595A 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 153 removed outlier: 3.817A pdb=" N CYS B 148 " --> pdb=" O SER B 160 " (cutoff:3.500A) removed outlier: 6.594A pdb=" N GLN B 156 " --> pdb=" O LEU B 152 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N ILE B 157 " --> pdb=" O TRP B 169 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N SER B 161 " --> pdb=" O THR B 165 " (cutoff:3.500A) removed outlier: 4.328A pdb=" N THR B 165 " --> pdb=" O SER B 161 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N VAL B 178 " --> pdb=" O LEU B 168 " (cutoff:3.500A) removed outlier: 6.218A pdb=" N ASP B 170 " --> pdb=" O GLN B 176 " (cutoff:3.500A) removed outlier: 6.006A 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: 6.998A pdb=" N GLY B 202 " --> pdb=" O MET B 188 " (cutoff:3.500A) removed outlier: 4.444A pdb=" N LEU B 190 " --> pdb=" O VAL B 200 " (cutoff:3.500A) removed outlier: 6.736A pdb=" N VAL B 200 " --> pdb=" O LEU B 190 " (cutoff:3.500A) removed outlier: 5.312A pdb=" N LEU B 192 " --> pdb=" O THR B 198 " (cutoff:3.500A) removed outlier: 7.609A pdb=" N THR B 198 " --> pdb=" O LEU B 192 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N GLN B 220 " --> pdb=" O LEU B 210 " (cutoff:3.500A) removed outlier: 7.207A pdb=" N ASP B 212 " --> pdb=" O CYS B 218 " (cutoff:3.500A) removed outlier: 6.913A pdb=" N CYS B 218 " --> pdb=" O ASP B 212 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 229 through 234 removed outlier: 3.650A pdb=" N ALA B 231 " --> pdb=" O GLY B 244 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N LEU B 262 " --> pdb=" O LEU B 252 " (cutoff:3.500A) removed outlier: 5.404A pdb=" N ASP B 254 " --> pdb=" O GLU B 260 " (cutoff:3.500A) removed outlier: 5.874A 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: 3.668A pdb=" N SER B 275 " --> pdb=" O GLY B 288 " (cutoff:3.500A) removed outlier: 4.417A pdb=" N ASN B 293 " --> pdb=" O TYR B 289 " (cutoff:3.500A) removed outlier: 6.502A pdb=" N CYS B 294 " --> pdb=" O VAL B 307 " (cutoff:3.500A) removed outlier: 4.570A pdb=" N VAL B 307 " --> pdb=" O CYS B 294 " (cutoff:3.500A) removed outlier: 6.137A pdb=" N ILE B 296 " --> pdb=" O ALA B 305 " (cutoff:3.500A) 875 hydrogen bonds defined for protein. 2505 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: 3.72 Time building geometry restraints manager: 2.40 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 5604 1.34 - 1.46: 3495 1.46 - 1.58: 9314 1.58 - 1.70: 3 1.70 - 1.82: 142 Bond restraints: 18558 Sorted by residual: bond pdb=" CAI Y01 Q1008 " pdb=" CAK Y01 Q1008 " ideal model delta sigma weight residual 1.492 1.408 0.084 2.00e-02 2.50e+03 1.78e+01 bond pdb=" O3 PO4 R1005 " pdb=" P PO4 R1005 " ideal model delta sigma weight residual 1.569 1.505 0.064 2.00e-02 2.50e+03 1.03e+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 1.00e+01 bond pdb=" O2 PO4 R1005 " pdb=" P PO4 R1005 " ideal model delta sigma weight residual 1.567 1.504 0.063 2.00e-02 2.50e+03 9.79e+00 bond pdb=" O2 PO4 Q1003 " pdb=" P PO4 Q1003 " ideal model delta sigma weight residual 1.567 1.505 0.062 2.00e-02 2.50e+03 9.68e+00 ... (remaining 18553 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.37: 24792 2.37 - 4.74: 299 4.74 - 7.11: 35 7.11 - 9.47: 6 9.47 - 11.84: 4 Bond angle restraints: 25136 Sorted by residual: angle pdb=" OAG Y01 Q1008 " pdb=" CAY Y01 Q1008 " pdb=" OAW Y01 Q1008 " 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 Q1008 " pdb=" CAY Y01 Q1008 " pdb=" OAW Y01 Q1008 " ideal model delta sigma weight residual 111.19 122.96 -11.77 3.00e+00 1.11e-01 1.54e+01 angle pdb=" CAV Y01 Q1008 " pdb=" CAZ Y01 Q1008 " pdb=" CBH Y01 Q1008 " ideal model delta sigma weight residual 116.96 127.70 -10.74 3.00e+00 1.11e-01 1.28e+01 angle pdb=" N GLY R 847 " pdb=" CA GLY R 847 " pdb=" C GLY R 847 " ideal model delta sigma weight residual 112.64 108.55 4.09 1.21e+00 6.83e-01 1.14e+01 angle pdb=" N ARG Q 680 " pdb=" CA ARG Q 680 " pdb=" C ARG Q 680 " ideal model delta sigma weight residual 111.02 115.06 -4.04 1.22e+00 6.72e-01 1.10e+01 ... (remaining 25131 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.70: 10214 17.70 - 35.39: 826 35.39 - 53.09: 133 53.09 - 70.78: 34 70.78 - 88.48: 11 Dihedral angle restraints: 11218 sinusoidal: 4689 harmonic: 6529 Sorted by residual: dihedral pdb=" CB CYS Q 585 " pdb=" SG CYS Q 585 " pdb=" SG CYS Q 598 " pdb=" CB CYS Q 598 " ideal model delta sinusoidal sigma weight residual 93.00 169.56 -76.56 1 1.00e+01 1.00e-02 7.37e+01 dihedral pdb=" CA ARG B 214 " pdb=" C ARG B 214 " pdb=" N ASP B 215 " pdb=" CA ASP B 215 " ideal model delta harmonic sigma weight residual -180.00 -158.97 -21.03 0 5.00e+00 4.00e-02 1.77e+01 dihedral pdb=" CB CYS R 546 " pdb=" SG CYS R 546 " pdb=" SG CYS R 565 " pdb=" CB CYS R 565 " ideal model delta sinusoidal sigma weight residual -86.00 -119.80 33.80 1 1.00e+01 1.00e-02 1.62e+01 ... (remaining 11215 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.051: 2220 0.051 - 0.103: 502 0.103 - 0.154: 95 0.154 - 0.206: 4 0.206 - 0.257: 5 Chirality restraints: 2826 Sorted by residual: chirality pdb=" CB ILE R 763 " pdb=" CA ILE R 763 " pdb=" CG1 ILE R 763 " pdb=" CG2 ILE R 763 " both_signs ideal model delta sigma weight residual False 2.64 2.39 0.26 2.00e-01 2.50e+01 1.65e+00 chirality pdb=" C1 NAG R1002 " pdb=" ND2 ASN R 287 " pdb=" C2 NAG R1002 " pdb=" O5 NAG R1002 " both_signs ideal model delta sigma weight residual False -2.40 -2.15 -0.25 2.00e-01 2.50e+01 1.56e+00 chirality pdb=" C02 A1AF7 R1010 " pdb=" C01 A1AF7 R1010 " pdb=" C03 A1AF7 R1010 " pdb=" O01 A1AF7 R1010 " both_signs ideal model delta sigma weight residual False 2.54 2.78 -0.25 2.00e-01 2.50e+01 1.52e+00 ... (remaining 2823 not shown) Planarity restraints: 3178 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ALA Q 843 " 0.011 2.00e-02 2.50e+03 2.13e-02 4.54e+00 pdb=" C ALA Q 843 " -0.037 2.00e-02 2.50e+03 pdb=" O ALA Q 843 " 0.014 2.00e-02 2.50e+03 pdb=" N ALA Q 844 " 0.012 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ALA R 843 " -0.010 2.00e-02 2.50e+03 2.03e-02 4.14e+00 pdb=" C ALA R 843 " 0.035 2.00e-02 2.50e+03 pdb=" O ALA R 843 " -0.013 2.00e-02 2.50e+03 pdb=" N ALA R 844 " -0.012 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C GLY R 273 " 0.033 5.00e-02 4.00e+02 4.98e-02 3.98e+00 pdb=" N PRO R 274 " -0.086 5.00e-02 4.00e+02 pdb=" CA PRO R 274 " 0.025 5.00e-02 4.00e+02 pdb=" CD PRO R 274 " 0.028 5.00e-02 4.00e+02 ... (remaining 3175 not shown) Histogram of nonbonded interaction distances: 2.17 - 2.71: 618 2.71 - 3.26: 18049 3.26 - 3.81: 29084 3.81 - 4.35: 37267 4.35 - 4.90: 63230 Nonbonded interactions: 148248 Sorted by model distance: nonbonded pdb=" O PHE Q 351 " pdb=" OG1 THR Q 355 " model vdw 2.168 3.040 nonbonded pdb=" OD2 ASP Q 238 " pdb=" OG SER Q 262 " model vdw 2.210 3.040 nonbonded pdb=" OH TYR A 320 " pdb=" OD2 ASP A 341 " model vdw 2.211 3.040 nonbonded pdb=" O GLU R 249 " pdb=" NE2 GLN R 253 " model vdw 2.217 3.120 nonbonded pdb=" ND2 ASN B 230 " pdb=" OD1 ASP B 246 " model vdw 2.231 3.120 ... (remaining 148243 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' } ncs_group { reference = (chain 'Q' and resid 22 through 1007) selection = (chain 'R' and (resid 22 through 360 or resid 393 through 710 or resid 722 throu \ gh 873 or resid 1003 through 1009)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 12.670 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: 0.020 Extract box with map and model: 0.440 Check model and map are aligned: 0.060 Set scattering table: 0.040 Process input model: 18.920 Find NCS groups from input model: 0.320 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.250 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 33.760 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7482 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 0.084 18587 Z= 0.219 Angle : 0.671 11.842 25206 Z= 0.357 Chirality : 0.045 0.257 2826 Planarity : 0.004 0.050 3170 Dihedral : 13.115 88.479 6941 Min Nonbonded Distance : 2.168 Molprobity Statistics. All-atom Clashscore : 6.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.83 % Favored : 97.17 % Rotamer: Outliers : 0.00 % Allowed : 0.21 % Favored : 99.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.09 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.08 (0.17), residues: 2223 helix: 1.09 (0.17), residues: 926 sheet: -0.50 (0.27), residues: 356 loop : -0.98 (0.19), residues: 941 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 24 TYR 0.025 0.002 TYR B 59 PHE 0.023 0.002 PHE Q 634 TRP 0.019 0.002 TRP R 719 HIS 0.005 0.001 HIS B 183 Details of bonding type rmsd/Z covalent geometry : bond 0.00467 / 0.22 (18558) covalent geometry : angle 0.66684 / 0.36 (25136) SS BOND : bond 0.00174 / 0.10 ( 17) SS BOND : angle 1.05482 / 0.75 ( 34) hydrogen bonds : bond 0.13417 / 9.13 ( 875) hydrogen bonds : angle 5.77387 / 4.07 ( 2505) link_BETA1-4 : bond 0.00436 / 0.29 ( 4) link_BETA1-4 : angle 1.61571 / 1.06 ( 12) link_NAG-ASN : bond 0.00279 / 0.16 ( 8) link_NAG-ASN : angle 2.00264 / 1.16 ( 24) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4446 Ramachandran restraints generated. 2223 Oldfield, 0 Emsley, 2223 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4446 Ramachandran restraints generated. 2223 Oldfield, 0 Emsley, 2223 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 387 residues out of total 1941 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 387 time to evaluate : 0.471 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: Q 176 ASN cc_start: 0.7735 (t0) cc_final: 0.7365 (t0) REVERT: Q 205 ARG cc_start: 0.7413 (mtm180) cc_final: 0.7195 (mtm110) REVERT: Q 207 ASN cc_start: 0.7147 (p0) cc_final: 0.6903 (p0) REVERT: Q 286 ARG cc_start: 0.7671 (mtp85) cc_final: 0.7465 (mtp85) REVERT: Q 287 ASN cc_start: 0.7796 (t0) cc_final: 0.7503 (t0) REVERT: Q 755 GLU cc_start: 0.6950 (pm20) cc_final: 0.6492 (pm20) REVERT: Q 762 PHE cc_start: 0.7115 (m-80) cc_final: 0.6634 (m-80) REVERT: Q 775 PHE cc_start: 0.7537 (m-10) cc_final: 0.7298 (m-80) REVERT: Q 811 MET cc_start: 0.7909 (mmp) cc_final: 0.7655 (mmp) REVERT: R 52 LYS cc_start: 0.7007 (mtmt) cc_final: 0.6705 (mttp) REVERT: R 88 LEU cc_start: 0.7422 (mm) cc_final: 0.7174 (mm) REVERT: R 252 ILE cc_start: 0.7078 (mm) cc_final: 0.6797 (mm) REVERT: R 253 GLN cc_start: 0.6486 (mp-120) cc_final: 0.6121 (mm-40) REVERT: R 341 LYS cc_start: 0.7276 (mttt) cc_final: 0.6902 (mttp) REVERT: R 736 ILE cc_start: 0.7260 (pt) cc_final: 0.7050 (pt) REVERT: A 33 GLU cc_start: 0.6995 (mp0) cc_final: 0.6762 (mp0) REVERT: A 207 GLU cc_start: 0.6745 (tt0) cc_final: 0.6430 (tt0) REVERT: A 273 LEU cc_start: 0.6671 (mp) cc_final: 0.4856 (mt) REVERT: A 277 LYS cc_start: 0.7642 (mtpt) cc_final: 0.7302 (mtmt) REVERT: A 298 GLU cc_start: 0.7202 (mt-10) cc_final: 0.6967 (mt-10) REVERT: B 37 LEU cc_start: 0.7259 (tt) cc_final: 0.6837 (tt) REVERT: B 237 ASN cc_start: 0.8487 (t0) cc_final: 0.8286 (t0) outliers start: 0 outliers final: 0 residues processed: 387 average time/residue: 0.1630 time to fit residues: 92.6914 Evaluate side-chains 346 residues out of total 1941 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 346 time to evaluate : 0.718 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 222 random chunks: chunk 216 optimal weight: 0.6980 chunk 98 optimal weight: 1.9990 chunk 194 optimal weight: 1.9990 chunk 107 optimal weight: 0.9980 chunk 10 optimal weight: 0.0020 chunk 66 optimal weight: 0.9980 chunk 130 optimal weight: 1.9990 chunk 124 optimal weight: 0.0870 chunk 103 optimal weight: 0.8980 chunk 200 optimal weight: 0.7980 chunk 212 optimal weight: 0.0980 overall best weight: 0.3366 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3288 r_free = 0.3288 target = 0.103857 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3010 r_free = 0.3010 target = 0.087883 restraints weight = 29494.092| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3021 r_free = 0.3021 target = 0.088489 restraints weight = 25984.189| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3023 r_free = 0.3023 target = 0.088611 restraints weight = 24229.336| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3027 r_free = 0.3027 target = 0.088834 restraints weight = 22897.302| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.3027 r_free = 0.3027 target = 0.088834 restraints weight = 22031.286| |-----------------------------------------------------------------------------| r_work (final): 0.3022 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7495 moved from start: 0.1015 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 18587 Z= 0.133 Angle : 0.521 8.851 25206 Z= 0.277 Chirality : 0.043 0.257 2826 Planarity : 0.004 0.046 3170 Dihedral : 7.635 84.568 2816 Min Nonbonded Distance : 2.461 Molprobity Statistics. All-atom Clashscore : 5.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.83 % Favored : 97.17 % Rotamer: Outliers : 0.67 % Allowed : 6.54 % Favored : 92.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.09 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.24 (0.17), residues: 2223 helix: 1.43 (0.17), residues: 940 sheet: -0.42 (0.26), residues: 367 loop : -0.89 (0.19), residues: 916 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG Q 638 TYR 0.014 0.001 TYR A 354 PHE 0.016 0.001 PHE Q 612 TRP 0.016 0.001 TRP Q 818 HIS 0.003 0.001 HIS B 183 Details of bonding type rmsd/Z covalent geometry : bond 0.00295 / 0.13 (18558) covalent geometry : angle 0.51698 / 0.28 (25136) SS BOND : bond 0.00189 / 0.11 ( 17) SS BOND : angle 1.06315 / 0.78 ( 34) hydrogen bonds : bond 0.05305 / 3.57 ( 875) hydrogen bonds : angle 4.49413 / 3.21 ( 2505) link_BETA1-4 : bond 0.00296 / 0.18 ( 4) link_BETA1-4 : angle 1.33467 / 0.84 ( 12) link_NAG-ASN : bond 0.00443 / 0.26 ( 8) link_NAG-ASN : angle 1.52609 / 1.05 ( 24) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4446 Ramachandran restraints generated. 2223 Oldfield, 0 Emsley, 2223 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4446 Ramachandran restraints generated. 2223 Oldfield, 0 Emsley, 2223 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 353 residues out of total 1941 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 340 time to evaluate : 0.716 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: Q 176 ASN cc_start: 0.7928 (t0) cc_final: 0.7593 (t0) REVERT: Q 287 ASN cc_start: 0.7908 (t0) cc_final: 0.7685 (t0) REVERT: Q 762 PHE cc_start: 0.7038 (m-80) cc_final: 0.6668 (m-80) REVERT: Q 811 MET cc_start: 0.7897 (mmp) cc_final: 0.7585 (mmp) REVERT: R 88 LEU cc_start: 0.7483 (mm) cc_final: 0.7263 (mm) REVERT: R 117 GLN cc_start: 0.7185 (tt0) cc_final: 0.6879 (tm-30) REVERT: R 253 GLN cc_start: 0.6461 (mp-120) cc_final: 0.6142 (mm-40) REVERT: R 736 ILE cc_start: 0.7616 (pt) cc_final: 0.7380 (pt) REVERT: R 795 ARG cc_start: 0.7449 (ptt-90) cc_final: 0.7147 (ptt-90) REVERT: R 811 MET cc_start: 0.8222 (mmt) cc_final: 0.7697 (mmt) REVERT: B 37 LEU cc_start: 0.7005 (tt) cc_final: 0.6753 (tt) REVERT: B 237 ASN cc_start: 0.8474 (t0) cc_final: 0.8250 (t0) REVERT: G 21 MET cc_start: 0.6724 (mmm) cc_final: 0.6517 (tmm) outliers start: 13 outliers final: 9 residues processed: 348 average time/residue: 0.1676 time to fit residues: 84.9426 Evaluate side-chains 324 residues out of total 1941 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 315 time to evaluate : 0.708 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Q residue 422 LEU Chi-restraints excluded: chain R residue 113 SER Chi-restraints excluded: chain R residue 118 ASN Chi-restraints excluded: chain R residue 289 THR Chi-restraints excluded: chain R residue 409 ILE Chi-restraints excluded: chain R residue 640 THR Chi-restraints excluded: chain A residue 263 SER Chi-restraints excluded: chain B residue 74 SER Chi-restraints excluded: chain B residue 135 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 222 random chunks: chunk 72 optimal weight: 1.9990 chunk 23 optimal weight: 0.9990 chunk 139 optimal weight: 0.9990 chunk 27 optimal weight: 1.9990 chunk 217 optimal weight: 6.9990 chunk 160 optimal weight: 0.5980 chunk 91 optimal weight: 0.9990 chunk 190 optimal weight: 0.9980 chunk 45 optimal weight: 0.7980 chunk 137 optimal weight: 0.9990 chunk 186 optimal weight: 0.8980 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3255 r_free = 0.3255 target = 0.102008 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.2981 r_free = 0.2981 target = 0.086556 restraints weight = 29880.342| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.2978 r_free = 0.2978 target = 0.086444 restraints weight = 28660.599| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.2977 r_free = 0.2977 target = 0.086408 restraints weight = 27770.126| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.2981 r_free = 0.2981 target = 0.086650 restraints weight = 26414.096| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.2982 r_free = 0.2982 target = 0.086702 restraints weight = 24934.087| |-----------------------------------------------------------------------------| r_work (final): 0.2981 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7548 moved from start: 0.1525 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.048 18587 Z= 0.224 Angle : 0.591 10.096 25206 Z= 0.309 Chirality : 0.046 0.313 2826 Planarity : 0.004 0.047 3170 Dihedral : 7.488 83.577 2816 Min Nonbonded Distance : 2.444 Molprobity Statistics. All-atom Clashscore : 5.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.51 % Favored : 96.49 % Rotamer: Outliers : 1.80 % Allowed : 8.91 % Favored : 89.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.09 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.09 (0.17), residues: 2223 helix: 1.32 (0.17), residues: 940 sheet: -0.58 (0.26), residues: 362 loop : -0.95 (0.19), residues: 921 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG Q 415 TYR 0.017 0.002 TYR B 59 PHE 0.022 0.002 PHE Q 634 TRP 0.019 0.002 TRP R 719 HIS 0.005 0.001 HIS A 213 Details of bonding type rmsd/Z covalent geometry : bond 0.00540 / 0.22 (18558) covalent geometry : angle 0.58611 / 0.31 (25136) SS BOND : bond 0.00413 / 0.24 ( 17) SS BOND : angle 1.33971 / 0.96 ( 34) hydrogen bonds : bond 0.05958 / 4.01 ( 875) hydrogen bonds : angle 4.54130 / 3.26 ( 2505) link_BETA1-4 : bond 0.00312 / 0.21 ( 4) link_BETA1-4 : angle 1.54646 / 1.01 ( 12) link_NAG-ASN : bond 0.00364 / 0.18 ( 8) link_NAG-ASN : angle 1.84464 / 1.30 ( 24) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4446 Ramachandran restraints generated. 2223 Oldfield, 0 Emsley, 2223 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4446 Ramachandran restraints generated. 2223 Oldfield, 0 Emsley, 2223 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 363 residues out of total 1941 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 328 time to evaluate : 0.741 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: Q 286 ARG cc_start: 0.7849 (mtp85) cc_final: 0.7592 (mtp85) REVERT: Q 287 ASN cc_start: 0.7895 (t0) cc_final: 0.7659 (t0) REVERT: R 117 GLN cc_start: 0.7179 (tt0) cc_final: 0.6881 (tm-30) REVERT: R 253 GLN cc_start: 0.6530 (mp-120) cc_final: 0.6224 (mp10) REVERT: R 589 PHE cc_start: 0.7309 (m-80) cc_final: 0.6916 (m-80) REVERT: R 795 ARG cc_start: 0.7471 (ptt-90) cc_final: 0.7062 (ptt-90) REVERT: R 811 MET cc_start: 0.8225 (mmt) cc_final: 0.7772 (mmt) REVERT: A 10 LYS cc_start: 0.7775 (mmtt) cc_final: 0.7485 (mmtt) REVERT: A 13 VAL cc_start: 0.7742 (t) cc_final: 0.7486 (m) REVERT: A 207 GLU cc_start: 0.6623 (tt0) cc_final: 0.6319 (tt0) REVERT: B 237 ASN cc_start: 0.8499 (t0) cc_final: 0.8255 (t0) outliers start: 35 outliers final: 25 residues processed: 346 average time/residue: 0.1672 time to fit residues: 84.3255 Evaluate side-chains 335 residues out of total 1941 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 310 time to evaluate : 0.714 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Q residue 92 THR Chi-restraints excluded: chain Q residue 422 LEU Chi-restraints excluded: chain Q residue 516 LYS Chi-restraints excluded: chain Q residue 529 LEU Chi-restraints excluded: chain Q residue 554 ILE Chi-restraints excluded: chain Q residue 560 THR Chi-restraints excluded: chain Q residue 793 LYS Chi-restraints excluded: chain R residue 113 SER Chi-restraints excluded: chain R residue 118 ASN Chi-restraints excluded: chain R residue 247 SER Chi-restraints excluded: chain R residue 289 THR Chi-restraints excluded: chain R residue 322 LEU Chi-restraints excluded: chain R residue 398 ASP Chi-restraints excluded: chain R residue 404 VAL Chi-restraints excluded: chain R residue 409 ILE Chi-restraints excluded: chain R residue 410 ASP Chi-restraints excluded: chain R residue 506 LYS Chi-restraints excluded: chain R residue 640 THR Chi-restraints excluded: chain R residue 676 THR Chi-restraints excluded: chain A residue 50 VAL Chi-restraints excluded: chain A residue 263 SER Chi-restraints excluded: chain A residue 273 LEU Chi-restraints excluded: chain B residue 46 ARG Chi-restraints excluded: chain B residue 74 SER Chi-restraints excluded: chain B residue 135 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 222 random chunks: chunk 161 optimal weight: 0.9980 chunk 69 optimal weight: 2.9990 chunk 158 optimal weight: 0.9990 chunk 48 optimal weight: 0.8980 chunk 189 optimal weight: 0.9980 chunk 163 optimal weight: 1.9990 chunk 178 optimal weight: 2.9990 chunk 122 optimal weight: 0.5980 chunk 103 optimal weight: 1.9990 chunk 156 optimal weight: 0.6980 chunk 21 optimal weight: 0.6980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3260 r_free = 0.3260 target = 0.102492 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2977 r_free = 0.2977 target = 0.086420 restraints weight = 29718.107| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.2971 r_free = 0.2971 target = 0.086170 restraints weight = 31581.476| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.2975 r_free = 0.2975 target = 0.086440 restraints weight = 28854.565| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.2982 r_free = 0.2982 target = 0.086852 restraints weight = 26489.842| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.2984 r_free = 0.2984 target = 0.086949 restraints weight = 25022.582| |-----------------------------------------------------------------------------| r_work (final): 0.2957 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7555 moved from start: 0.1800 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.045 18587 Z= 0.204 Angle : 0.565 9.694 25206 Z= 0.297 Chirality : 0.045 0.252 2826 Planarity : 0.004 0.047 3170 Dihedral : 7.132 73.534 2816 Min Nonbonded Distance : 2.442 Molprobity Statistics. All-atom Clashscore : 5.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.19 % Favored : 96.81 % Rotamer: Outliers : 2.16 % Allowed : 10.56 % Favored : 87.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.09 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.07 (0.17), residues: 2223 helix: 1.32 (0.17), residues: 940 sheet: -0.62 (0.26), residues: 362 loop : -0.96 (0.19), residues: 921 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG Q 233 TYR 0.017 0.002 TYR B 145 PHE 0.019 0.002 PHE Q 634 TRP 0.019 0.002 TRP R 719 HIS 0.006 0.001 HIS R 463 Details of bonding type rmsd/Z covalent geometry : bond 0.00492 / 0.20 (18558) covalent geometry : angle 0.55998 / 0.30 (25136) SS BOND : bond 0.00267 / 0.15 ( 17) SS BOND : angle 1.33805 / 1.04 ( 34) hydrogen bonds : bond 0.05684 / 3.83 ( 875) hydrogen bonds : angle 4.49610 / 3.23 ( 2505) link_BETA1-4 : bond 0.00361 / 0.25 ( 4) link_BETA1-4 : angle 1.50072 / 0.98 ( 12) link_NAG-ASN : bond 0.00277 / 0.15 ( 8) link_NAG-ASN : angle 1.73953 / 1.13 ( 24) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4446 Ramachandran restraints generated. 2223 Oldfield, 0 Emsley, 2223 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4446 Ramachandran restraints generated. 2223 Oldfield, 0 Emsley, 2223 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 367 residues out of total 1941 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 325 time to evaluate : 0.710 Fit side-chains revert: symmetry clash REVERT: Q 227 ARG cc_start: 0.7456 (ttp80) cc_final: 0.7212 (ttp80) REVERT: Q 270 PHE cc_start: 0.7306 (OUTLIER) cc_final: 0.6875 (m-80) REVERT: Q 286 ARG cc_start: 0.7822 (mtp85) cc_final: 0.7553 (mtp85) REVERT: Q 287 ASN cc_start: 0.7910 (t0) cc_final: 0.7650 (t0) REVERT: Q 354 GLU cc_start: 0.6629 (mm-30) cc_final: 0.6179 (mm-30) REVERT: R 117 GLN cc_start: 0.7203 (tt0) cc_final: 0.6884 (tm-30) REVERT: R 253 GLN cc_start: 0.6551 (OUTLIER) cc_final: 0.6148 (mp10) REVERT: R 795 ARG cc_start: 0.7437 (ptt-90) cc_final: 0.6991 (ptt-90) REVERT: A 10 LYS cc_start: 0.7572 (mmtt) cc_final: 0.7304 (mmtt) REVERT: A 13 VAL cc_start: 0.7733 (t) cc_final: 0.7489 (m) REVERT: A 207 GLU cc_start: 0.6656 (tt0) cc_final: 0.6407 (tt0) REVERT: B 37 LEU cc_start: 0.7059 (tt) cc_final: 0.6749 (tt) REVERT: B 234 PHE cc_start: 0.8252 (OUTLIER) cc_final: 0.7467 (t80) REVERT: B 237 ASN cc_start: 0.8467 (t0) cc_final: 0.8223 (t0) outliers start: 42 outliers final: 31 residues processed: 347 average time/residue: 0.1704 time to fit residues: 86.0473 Evaluate side-chains 351 residues out of total 1941 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 317 time to evaluate : 0.718 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Q residue 92 THR Chi-restraints excluded: chain Q residue 159 LEU Chi-restraints excluded: chain Q residue 263 THR Chi-restraints excluded: chain Q residue 270 PHE Chi-restraints excluded: chain Q residue 422 LEU Chi-restraints excluded: chain Q residue 452 ILE Chi-restraints excluded: chain Q residue 516 LYS Chi-restraints excluded: chain Q residue 529 LEU Chi-restraints excluded: chain Q residue 554 ILE Chi-restraints excluded: chain Q residue 560 THR Chi-restraints excluded: chain Q residue 609 THR Chi-restraints excluded: chain Q residue 793 LYS Chi-restraints excluded: chain R residue 113 SER Chi-restraints excluded: chain R residue 118 ASN Chi-restraints excluded: chain R residue 247 SER Chi-restraints excluded: chain R residue 253 GLN Chi-restraints excluded: chain R residue 270 PHE Chi-restraints excluded: chain R residue 289 THR Chi-restraints excluded: chain R residue 322 LEU Chi-restraints excluded: chain R residue 404 VAL Chi-restraints excluded: chain R residue 409 ILE Chi-restraints excluded: chain R residue 504 VAL Chi-restraints excluded: chain R residue 625 PHE Chi-restraints excluded: chain R residue 640 THR Chi-restraints excluded: chain R residue 676 THR Chi-restraints excluded: chain R residue 737 VAL Chi-restraints excluded: chain A residue 50 VAL Chi-restraints excluded: chain A residue 263 SER Chi-restraints excluded: chain A residue 273 LEU Chi-restraints excluded: chain B residue 46 ARG Chi-restraints excluded: chain B residue 74 SER Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 213 VAL Chi-restraints excluded: chain B residue 234 PHE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 222 random chunks: chunk 183 optimal weight: 0.9990 chunk 147 optimal weight: 0.9980 chunk 82 optimal weight: 0.9990 chunk 213 optimal weight: 0.5980 chunk 0 optimal weight: 1.9990 chunk 123 optimal weight: 1.9990 chunk 2 optimal weight: 0.0070 chunk 143 optimal weight: 0.6980 chunk 217 optimal weight: 7.9990 chunk 23 optimal weight: 0.9990 chunk 78 optimal weight: 0.9980 overall best weight: 0.6598 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3259 r_free = 0.3259 target = 0.101942 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.2973 r_free = 0.2973 target = 0.085688 restraints weight = 29582.514| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.2970 r_free = 0.2970 target = 0.085608 restraints weight = 32514.168| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.2974 r_free = 0.2974 target = 0.085854 restraints weight = 29430.882| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.2979 r_free = 0.2979 target = 0.086167 restraints weight = 27090.210| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.2981 r_free = 0.2981 target = 0.086293 restraints weight = 26440.255| |-----------------------------------------------------------------------------| r_work (final): 0.2972 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7553 moved from start: 0.1935 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 18587 Z= 0.181 Angle : 0.547 9.431 25206 Z= 0.288 Chirality : 0.044 0.252 2826 Planarity : 0.004 0.047 3170 Dihedral : 6.831 64.874 2816 Min Nonbonded Distance : 2.414 Molprobity Statistics. All-atom Clashscore : 5.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.10 % Favored : 96.90 % Rotamer: Outliers : 2.06 % Allowed : 11.80 % Favored : 86.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.09 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.15 (0.17), residues: 2223 helix: 1.39 (0.17), residues: 940 sheet: -0.58 (0.26), residues: 362 loop : -0.93 (0.19), residues: 921 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG G 27 TYR 0.017 0.002 TYR B 145 PHE 0.016 0.002 PHE Q 806 TRP 0.018 0.002 TRP R 719 HIS 0.004 0.001 HIS B 183 Details of bonding type rmsd/Z covalent geometry : bond 0.00432 / 0.18 (18558) covalent geometry : angle 0.54264 / 0.29 (25136) SS BOND : bond 0.00214 / 0.13 ( 17) SS BOND : angle 1.17389 / 0.92 ( 34) hydrogen bonds : bond 0.05481 / 3.70 ( 875) hydrogen bonds : angle 4.42607 / 3.19 ( 2505) link_BETA1-4 : bond 0.00292 / 0.20 ( 4) link_BETA1-4 : angle 1.51183 / 0.99 ( 12) link_NAG-ASN : bond 0.00222 / 0.12 ( 8) link_NAG-ASN : angle 1.78972 / 1.21 ( 24) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4446 Ramachandran restraints generated. 2223 Oldfield, 0 Emsley, 2223 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4446 Ramachandran restraints generated. 2223 Oldfield, 0 Emsley, 2223 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 369 residues out of total 1941 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 329 time to evaluate : 0.855 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: Q 270 PHE cc_start: 0.7302 (OUTLIER) cc_final: 0.6876 (m-80) REVERT: Q 286 ARG cc_start: 0.7811 (mtp85) cc_final: 0.7563 (mtp85) REVERT: Q 354 GLU cc_start: 0.6618 (mm-30) cc_final: 0.6183 (mm-30) REVERT: R 253 GLN cc_start: 0.6564 (OUTLIER) cc_final: 0.6170 (mp10) REVERT: R 577 THR cc_start: 0.7790 (m) cc_final: 0.7446 (t) REVERT: R 584 LYS cc_start: 0.7652 (tppt) cc_final: 0.7368 (mmmt) REVERT: R 776 LEU cc_start: 0.7272 (OUTLIER) cc_final: 0.6835 (mp) REVERT: R 795 ARG cc_start: 0.7446 (ptt-90) cc_final: 0.7007 (ptt-90) REVERT: A 10 LYS cc_start: 0.7688 (mmtt) cc_final: 0.7101 (mmtt) REVERT: A 13 VAL cc_start: 0.7741 (t) cc_final: 0.7461 (m) REVERT: A 207 GLU cc_start: 0.6634 (tt0) cc_final: 0.6376 (tt0) REVERT: B 37 LEU cc_start: 0.7094 (tt) cc_final: 0.6816 (tt) REVERT: B 195 ASP cc_start: 0.7833 (p0) cc_final: 0.7571 (p0) REVERT: B 234 PHE cc_start: 0.8275 (OUTLIER) cc_final: 0.7491 (t80) REVERT: B 237 ASN cc_start: 0.8451 (t0) cc_final: 0.8213 (t0) outliers start: 40 outliers final: 30 residues processed: 353 average time/residue: 0.1671 time to fit residues: 85.9838 Evaluate side-chains 353 residues out of total 1941 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 319 time to evaluate : 0.739 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Q residue 159 LEU Chi-restraints excluded: chain Q residue 263 THR Chi-restraints excluded: chain Q residue 270 PHE Chi-restraints excluded: chain Q residue 452 ILE Chi-restraints excluded: chain Q residue 516 LYS Chi-restraints excluded: chain Q residue 529 LEU Chi-restraints excluded: chain Q residue 554 ILE Chi-restraints excluded: chain Q residue 734 MET Chi-restraints excluded: chain Q residue 793 LYS Chi-restraints excluded: chain R residue 113 SER Chi-restraints excluded: chain R residue 118 ASN Chi-restraints excluded: chain R residue 247 SER Chi-restraints excluded: chain R residue 253 GLN Chi-restraints excluded: chain R residue 270 PHE Chi-restraints excluded: chain R residue 289 THR Chi-restraints excluded: chain R residue 322 LEU Chi-restraints excluded: chain R residue 404 VAL Chi-restraints excluded: chain R residue 409 ILE Chi-restraints excluded: chain R residue 504 VAL Chi-restraints excluded: chain R residue 506 LYS Chi-restraints excluded: chain R residue 625 PHE Chi-restraints excluded: chain R residue 640 THR Chi-restraints excluded: chain R residue 776 LEU Chi-restraints excluded: chain A residue 50 VAL Chi-restraints excluded: chain A residue 263 SER Chi-restraints excluded: chain A residue 273 LEU Chi-restraints excluded: chain A residue 316 THR Chi-restraints excluded: chain B residue 46 ARG Chi-restraints excluded: chain B residue 74 SER Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 213 VAL Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 318 LEU Chi-restraints excluded: chain G residue 25 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 222 random chunks: chunk 188 optimal weight: 0.9990 chunk 10 optimal weight: 0.0970 chunk 137 optimal weight: 0.5980 chunk 43 optimal weight: 0.6980 chunk 118 optimal weight: 0.8980 chunk 71 optimal weight: 0.9980 chunk 189 optimal weight: 0.9990 chunk 199 optimal weight: 0.9980 chunk 17 optimal weight: 1.9990 chunk 36 optimal weight: 0.9990 chunk 128 optimal weight: 0.3980 overall best weight: 0.5378 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3263 r_free = 0.3263 target = 0.101815 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.2972 r_free = 0.2972 target = 0.085418 restraints weight = 29439.957| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.2974 r_free = 0.2974 target = 0.085557 restraints weight = 27706.728| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.2978 r_free = 0.2978 target = 0.085793 restraints weight = 26176.889| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.2979 r_free = 0.2979 target = 0.085913 restraints weight = 26583.945| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.2985 r_free = 0.2985 target = 0.086206 restraints weight = 24601.777| |-----------------------------------------------------------------------------| r_work (final): 0.2980 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7553 moved from start: 0.2022 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 18587 Z= 0.157 Angle : 0.526 9.223 25206 Z= 0.277 Chirality : 0.043 0.231 2826 Planarity : 0.004 0.046 3170 Dihedral : 6.559 59.853 2816 Min Nonbonded Distance : 2.438 Molprobity Statistics. All-atom Clashscore : 5.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.06 % Favored : 96.94 % Rotamer: Outliers : 2.11 % Allowed : 12.52 % Favored : 85.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.09 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.26 (0.17), residues: 2223 helix: 1.49 (0.17), residues: 940 sheet: -0.54 (0.26), residues: 360 loop : -0.87 (0.20), residues: 923 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG G 27 TYR 0.016 0.001 TYR B 145 PHE 0.015 0.001 PHE Q 806 TRP 0.018 0.002 TRP R 719 HIS 0.004 0.001 HIS R 463 Details of bonding type rmsd/Z covalent geometry : bond 0.00370 / 0.16 (18558) covalent geometry : angle 0.52167 / 0.28 (25136) SS BOND : bond 0.00172 / 0.11 ( 17) SS BOND : angle 1.11910 / 0.92 ( 34) hydrogen bonds : bond 0.05227 / 3.52 ( 875) hydrogen bonds : angle 4.33735 / 3.12 ( 2505) link_BETA1-4 : bond 0.00306 / 0.20 ( 4) link_BETA1-4 : angle 1.48405 / 0.97 ( 12) link_NAG-ASN : bond 0.00254 / 0.14 ( 8) link_NAG-ASN : angle 1.64000 / 1.07 ( 24) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4446 Ramachandran restraints generated. 2223 Oldfield, 0 Emsley, 2223 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4446 Ramachandran restraints generated. 2223 Oldfield, 0 Emsley, 2223 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 367 residues out of total 1941 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 326 time to evaluate : 0.737 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: Q 270 PHE cc_start: 0.7310 (OUTLIER) cc_final: 0.6905 (m-80) REVERT: Q 354 GLU cc_start: 0.6593 (mm-30) cc_final: 0.6176 (mm-30) REVERT: Q 454 LYS cc_start: 0.8045 (mttt) cc_final: 0.7680 (mmmm) REVERT: Q 762 PHE cc_start: 0.7121 (m-80) cc_final: 0.6865 (m-80) REVERT: R 253 GLN cc_start: 0.6547 (OUTLIER) cc_final: 0.6160 (mp10) REVERT: R 776 LEU cc_start: 0.7256 (OUTLIER) cc_final: 0.6834 (mp) REVERT: R 795 ARG cc_start: 0.7427 (ptt-90) cc_final: 0.7016 (ptt-90) REVERT: R 811 MET cc_start: 0.8170 (mmt) cc_final: 0.7873 (mmt) REVERT: A 10 LYS cc_start: 0.8039 (mmtt) cc_final: 0.7370 (mmtt) REVERT: B 37 LEU cc_start: 0.7083 (tt) cc_final: 0.6783 (tt) REVERT: B 234 PHE cc_start: 0.8257 (OUTLIER) cc_final: 0.7550 (t80) REVERT: B 237 ASN cc_start: 0.8450 (t0) cc_final: 0.8216 (t0) outliers start: 41 outliers final: 32 residues processed: 353 average time/residue: 0.1672 time to fit residues: 86.3830 Evaluate side-chains 350 residues out of total 1941 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 314 time to evaluate : 0.690 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Q residue 263 THR Chi-restraints excluded: chain Q residue 270 PHE Chi-restraints excluded: chain Q residue 422 LEU Chi-restraints excluded: chain Q residue 452 ILE Chi-restraints excluded: chain Q residue 516 LYS Chi-restraints excluded: chain Q residue 529 LEU Chi-restraints excluded: chain Q residue 554 ILE Chi-restraints excluded: chain Q residue 609 THR Chi-restraints excluded: chain Q residue 734 MET Chi-restraints excluded: chain Q residue 737 VAL Chi-restraints excluded: chain Q residue 793 LYS Chi-restraints excluded: chain R residue 113 SER Chi-restraints excluded: chain R residue 118 ASN Chi-restraints excluded: chain R residue 247 SER Chi-restraints excluded: chain R residue 253 GLN Chi-restraints excluded: chain R residue 270 PHE Chi-restraints excluded: chain R residue 289 THR Chi-restraints excluded: chain R residue 322 LEU Chi-restraints excluded: chain R residue 404 VAL Chi-restraints excluded: chain R residue 409 ILE Chi-restraints excluded: chain R residue 504 VAL Chi-restraints excluded: chain R residue 506 LYS Chi-restraints excluded: chain R residue 585 CYS Chi-restraints excluded: chain R residue 625 PHE Chi-restraints excluded: chain R residue 640 THR Chi-restraints excluded: chain R residue 776 LEU Chi-restraints excluded: chain A residue 50 VAL Chi-restraints excluded: chain A residue 263 SER Chi-restraints excluded: chain A residue 273 LEU Chi-restraints excluded: chain A residue 316 THR Chi-restraints excluded: chain B residue 46 ARG Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 213 VAL Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 318 LEU Chi-restraints excluded: chain G residue 25 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 222 random chunks: chunk 96 optimal weight: 1.9990 chunk 21 optimal weight: 0.6980 chunk 204 optimal weight: 0.5980 chunk 104 optimal weight: 0.9980 chunk 98 optimal weight: 0.9980 chunk 203 optimal weight: 0.9980 chunk 149 optimal weight: 0.8980 chunk 166 optimal weight: 0.6980 chunk 114 optimal weight: 0.9980 chunk 131 optimal weight: 1.9990 chunk 30 optimal weight: 0.6980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3250 r_free = 0.3250 target = 0.101073 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2968 r_free = 0.2968 target = 0.085108 restraints weight = 29711.183| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.2964 r_free = 0.2964 target = 0.084977 restraints weight = 33577.565| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.2967 r_free = 0.2967 target = 0.085153 restraints weight = 30469.968| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.2973 r_free = 0.2973 target = 0.085513 restraints weight = 28108.999| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.2975 r_free = 0.2975 target = 0.085606 restraints weight = 26916.647| |-----------------------------------------------------------------------------| r_work (final): 0.2960 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7550 moved from start: 0.2100 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.049 18587 Z= 0.192 Angle : 0.555 9.300 25206 Z= 0.291 Chirality : 0.045 0.272 2826 Planarity : 0.004 0.047 3170 Dihedral : 6.526 58.680 2816 Min Nonbonded Distance : 2.418 Molprobity Statistics. All-atom Clashscore : 5.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.42 % Favored : 96.58 % Rotamer: Outliers : 2.68 % Allowed : 12.52 % Favored : 84.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.09 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.19 (0.17), residues: 2223 helix: 1.40 (0.17), residues: 940 sheet: -0.60 (0.26), residues: 362 loop : -0.85 (0.20), residues: 921 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG G 27 TYR 0.018 0.001 TYR B 145 PHE 0.017 0.002 PHE Q 806 TRP 0.019 0.002 TRP R 719 HIS 0.004 0.001 HIS A 213 Details of bonding type rmsd/Z covalent geometry : bond 0.00464 / 0.19 (18558) covalent geometry : angle 0.55008 / 0.29 (25136) SS BOND : bond 0.00202 / 0.12 ( 17) SS BOND : angle 1.08180 / 0.86 ( 34) hydrogen bonds : bond 0.05486 / 3.70 ( 875) hydrogen bonds : angle 4.39898 / 3.17 ( 2505) link_BETA1-4 : bond 0.00321 / 0.22 ( 4) link_BETA1-4 : angle 1.53689 / 1.02 ( 12) link_NAG-ASN : bond 0.00323 / 0.17 ( 8) link_NAG-ASN : angle 1.96718 / 1.41 ( 24) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4446 Ramachandran restraints generated. 2223 Oldfield, 0 Emsley, 2223 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4446 Ramachandran restraints generated. 2223 Oldfield, 0 Emsley, 2223 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 376 residues out of total 1941 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 324 time to evaluate : 0.721 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: Q 270 PHE cc_start: 0.7299 (OUTLIER) cc_final: 0.6884 (m-80) REVERT: Q 286 ARG cc_start: 0.7882 (mtp85) cc_final: 0.7662 (mtp85) REVERT: Q 354 GLU cc_start: 0.6608 (mm-30) cc_final: 0.6200 (mm-30) REVERT: Q 454 LYS cc_start: 0.8030 (mttt) cc_final: 0.7690 (mmmm) REVERT: Q 762 PHE cc_start: 0.7171 (m-80) cc_final: 0.6902 (m-80) REVERT: Q 767 GLU cc_start: 0.6592 (mm-30) cc_final: 0.6343 (mm-30) REVERT: R 117 GLN cc_start: 0.7217 (tt0) cc_final: 0.6854 (tm-30) REVERT: R 253 GLN cc_start: 0.6594 (OUTLIER) cc_final: 0.6214 (mp10) REVERT: R 577 THR cc_start: 0.7806 (OUTLIER) cc_final: 0.7469 (t) REVERT: R 776 LEU cc_start: 0.7296 (OUTLIER) cc_final: 0.6860 (mp) REVERT: R 795 ARG cc_start: 0.7462 (ptt-90) cc_final: 0.7011 (ptt-90) REVERT: A 13 VAL cc_start: 0.7900 (t) cc_final: 0.7510 (m) REVERT: B 37 LEU cc_start: 0.7136 (OUTLIER) cc_final: 0.6820 (tt) REVERT: B 195 ASP cc_start: 0.7866 (p0) cc_final: 0.7604 (p0) REVERT: B 234 PHE cc_start: 0.8294 (OUTLIER) cc_final: 0.7516 (t80) REVERT: B 237 ASN cc_start: 0.8441 (t0) cc_final: 0.8181 (t0) outliers start: 52 outliers final: 42 residues processed: 355 average time/residue: 0.1635 time to fit residues: 85.2960 Evaluate side-chains 361 residues out of total 1941 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 313 time to evaluate : 0.712 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Q residue 263 THR Chi-restraints excluded: chain Q residue 270 PHE Chi-restraints excluded: chain Q residue 422 LEU Chi-restraints excluded: chain Q residue 452 ILE Chi-restraints excluded: chain Q residue 516 LYS Chi-restraints excluded: chain Q residue 529 LEU Chi-restraints excluded: chain Q residue 554 ILE Chi-restraints excluded: chain Q residue 609 THR Chi-restraints excluded: chain Q residue 734 MET Chi-restraints excluded: chain Q residue 737 VAL Chi-restraints excluded: chain Q residue 793 LYS Chi-restraints excluded: chain R residue 113 SER Chi-restraints excluded: chain R residue 118 ASN Chi-restraints excluded: chain R residue 247 SER Chi-restraints excluded: chain R residue 253 GLN Chi-restraints excluded: chain R residue 270 PHE Chi-restraints excluded: chain R residue 289 THR Chi-restraints excluded: chain R residue 322 LEU Chi-restraints excluded: chain R residue 404 VAL Chi-restraints excluded: chain R residue 409 ILE Chi-restraints excluded: chain R residue 410 ASP Chi-restraints excluded: chain R residue 434 ILE Chi-restraints excluded: chain R residue 504 VAL Chi-restraints excluded: chain R residue 506 LYS Chi-restraints excluded: chain R residue 577 THR Chi-restraints excluded: chain R residue 585 CYS Chi-restraints excluded: chain R residue 625 PHE Chi-restraints excluded: chain R residue 640 THR Chi-restraints excluded: chain R residue 730 LEU Chi-restraints excluded: chain R residue 737 VAL Chi-restraints excluded: chain R residue 776 LEU Chi-restraints excluded: chain R residue 869 ILE Chi-restraints excluded: chain A residue 50 VAL Chi-restraints excluded: chain A residue 240 MET Chi-restraints excluded: chain A residue 263 SER Chi-restraints excluded: chain A residue 273 LEU Chi-restraints excluded: chain A residue 316 THR Chi-restraints excluded: chain B residue 31 THR Chi-restraints excluded: chain B residue 37 LEU Chi-restraints excluded: chain B residue 46 ARG Chi-restraints excluded: chain B residue 74 SER Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 200 VAL Chi-restraints excluded: chain B residue 213 VAL Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 274 THR Chi-restraints excluded: chain B residue 318 LEU Chi-restraints excluded: chain G residue 25 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 222 random chunks: chunk 73 optimal weight: 0.5980 chunk 69 optimal weight: 2.9990 chunk 28 optimal weight: 0.6980 chunk 173 optimal weight: 2.9990 chunk 127 optimal weight: 0.4980 chunk 155 optimal weight: 0.7980 chunk 176 optimal weight: 0.7980 chunk 5 optimal weight: 0.9990 chunk 98 optimal weight: 1.9990 chunk 138 optimal weight: 0.8980 chunk 129 optimal weight: 0.8980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3250 r_free = 0.3250 target = 0.101031 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2969 r_free = 0.2969 target = 0.085083 restraints weight = 29689.060| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.2965 r_free = 0.2965 target = 0.084984 restraints weight = 33577.586| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.2968 r_free = 0.2968 target = 0.085159 restraints weight = 30609.481| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.2973 r_free = 0.2973 target = 0.085434 restraints weight = 28924.624| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.2975 r_free = 0.2975 target = 0.085531 restraints weight = 26628.287| |-----------------------------------------------------------------------------| r_work (final): 0.2938 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7549 moved from start: 0.2169 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 18587 Z= 0.183 Angle : 0.551 9.120 25206 Z= 0.290 Chirality : 0.044 0.282 2826 Planarity : 0.004 0.047 3170 Dihedral : 6.480 62.139 2816 Min Nonbonded Distance : 2.434 Molprobity Statistics. All-atom Clashscore : 5.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.33 % Favored : 96.67 % Rotamer: Outliers : 2.99 % Allowed : 12.52 % Favored : 84.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.09 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.21 (0.18), residues: 2223 helix: 1.42 (0.17), residues: 940 sheet: -0.61 (0.26), residues: 362 loop : -0.83 (0.20), residues: 921 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG G 27 TYR 0.018 0.001 TYR B 145 PHE 0.017 0.002 PHE Q 806 TRP 0.019 0.002 TRP R 719 HIS 0.004 0.001 HIS A 213 Details of bonding type rmsd/Z covalent geometry : bond 0.00440 / 0.18 (18558) covalent geometry : angle 0.54659 / 0.29 (25136) SS BOND : bond 0.00200 / 0.12 ( 17) SS BOND : angle 0.99811 / 0.77 ( 34) hydrogen bonds : bond 0.05442 / 3.67 ( 875) hydrogen bonds : angle 4.39308 / 3.16 ( 2505) link_BETA1-4 : bond 0.00328 / 0.22 ( 4) link_BETA1-4 : angle 1.53208 / 1.01 ( 12) link_NAG-ASN : bond 0.00189 / 0.11 ( 8) link_NAG-ASN : angle 1.94256 / 1.38 ( 24) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4446 Ramachandran restraints generated. 2223 Oldfield, 0 Emsley, 2223 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4446 Ramachandran restraints generated. 2223 Oldfield, 0 Emsley, 2223 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 376 residues out of total 1941 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 318 time to evaluate : 0.888 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: Q 270 PHE cc_start: 0.7300 (OUTLIER) cc_final: 0.6847 (m-80) REVERT: Q 286 ARG cc_start: 0.7893 (mtp85) cc_final: 0.7628 (mtp85) REVERT: Q 354 GLU cc_start: 0.6599 (mm-30) cc_final: 0.6191 (mm-30) REVERT: Q 422 LEU cc_start: 0.7698 (OUTLIER) cc_final: 0.7488 (mt) REVERT: Q 454 LYS cc_start: 0.8027 (mttt) cc_final: 0.7569 (mmmm) REVERT: Q 476 GLN cc_start: 0.7855 (mm-40) cc_final: 0.7245 (mm-40) REVERT: Q 654 LEU cc_start: 0.8154 (OUTLIER) cc_final: 0.7954 (tt) REVERT: Q 727 LEU cc_start: 0.7446 (OUTLIER) cc_final: 0.7159 (tt) REVERT: Q 762 PHE cc_start: 0.7177 (m-80) cc_final: 0.6902 (m-80) REVERT: Q 767 GLU cc_start: 0.6587 (OUTLIER) cc_final: 0.6349 (mm-30) REVERT: R 253 GLN cc_start: 0.6600 (OUTLIER) cc_final: 0.6214 (mp10) REVERT: R 577 THR cc_start: 0.7839 (OUTLIER) cc_final: 0.7511 (t) REVERT: R 776 LEU cc_start: 0.7281 (OUTLIER) cc_final: 0.6850 (mp) REVERT: R 795 ARG cc_start: 0.7466 (ptt-90) cc_final: 0.7007 (ptt-90) REVERT: A 10 LYS cc_start: 0.8075 (mmtt) cc_final: 0.7509 (mmtt) REVERT: A 13 VAL cc_start: 0.7912 (t) cc_final: 0.7529 (m) REVERT: A 273 LEU cc_start: 0.6605 (OUTLIER) cc_final: 0.6331 (tp) REVERT: B 37 LEU cc_start: 0.7171 (OUTLIER) cc_final: 0.6847 (tt) REVERT: B 195 ASP cc_start: 0.7991 (p0) cc_final: 0.7696 (p0) REVERT: B 234 PHE cc_start: 0.8298 (OUTLIER) cc_final: 0.7523 (t80) REVERT: B 237 ASN cc_start: 0.8426 (t0) cc_final: 0.8177 (t0) outliers start: 58 outliers final: 45 residues processed: 353 average time/residue: 0.1640 time to fit residues: 84.8678 Evaluate side-chains 368 residues out of total 1941 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 312 time to evaluate : 0.695 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Q residue 61 ILE Chi-restraints excluded: chain Q residue 263 THR Chi-restraints excluded: chain Q residue 270 PHE Chi-restraints excluded: chain Q residue 422 LEU Chi-restraints excluded: chain Q residue 452 ILE Chi-restraints excluded: chain Q residue 516 LYS Chi-restraints excluded: chain Q residue 529 LEU Chi-restraints excluded: chain Q residue 554 ILE Chi-restraints excluded: chain Q residue 609 THR Chi-restraints excluded: chain Q residue 654 LEU Chi-restraints excluded: chain Q residue 727 LEU Chi-restraints excluded: chain Q residue 734 MET Chi-restraints excluded: chain Q residue 737 VAL Chi-restraints excluded: chain Q residue 767 GLU Chi-restraints excluded: chain Q residue 776 LEU Chi-restraints excluded: chain Q residue 793 LYS Chi-restraints excluded: chain R residue 113 SER Chi-restraints excluded: chain R residue 118 ASN Chi-restraints excluded: chain R residue 247 SER Chi-restraints excluded: chain R residue 253 GLN Chi-restraints excluded: chain R residue 270 PHE Chi-restraints excluded: chain R residue 289 THR Chi-restraints excluded: chain R residue 312 HIS Chi-restraints excluded: chain R residue 322 LEU Chi-restraints excluded: chain R residue 404 VAL Chi-restraints excluded: chain R residue 409 ILE Chi-restraints excluded: chain R residue 410 ASP Chi-restraints excluded: chain R residue 434 ILE Chi-restraints excluded: chain R residue 504 VAL Chi-restraints excluded: chain R residue 506 LYS Chi-restraints excluded: chain R residue 577 THR Chi-restraints excluded: chain R residue 585 CYS Chi-restraints excluded: chain R residue 625 PHE Chi-restraints excluded: chain R residue 640 THR Chi-restraints excluded: chain R residue 676 THR Chi-restraints excluded: chain R residue 730 LEU Chi-restraints excluded: chain R residue 737 VAL Chi-restraints excluded: chain R residue 776 LEU Chi-restraints excluded: chain R residue 811 MET Chi-restraints excluded: chain R residue 869 ILE Chi-restraints excluded: chain A residue 50 VAL Chi-restraints excluded: chain A residue 240 MET Chi-restraints excluded: chain A residue 263 SER Chi-restraints excluded: chain A residue 273 LEU Chi-restraints excluded: chain A residue 316 THR Chi-restraints excluded: chain B residue 31 THR Chi-restraints excluded: chain B residue 37 LEU Chi-restraints excluded: chain B residue 46 ARG Chi-restraints excluded: chain B residue 74 SER Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 200 VAL Chi-restraints excluded: chain B residue 213 VAL Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 274 THR Chi-restraints excluded: chain B residue 318 LEU Chi-restraints excluded: chain G residue 25 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 222 random chunks: chunk 208 optimal weight: 0.9990 chunk 184 optimal weight: 8.9990 chunk 13 optimal weight: 0.6980 chunk 120 optimal weight: 1.9990 chunk 125 optimal weight: 1.9990 chunk 22 optimal weight: 0.7980 chunk 106 optimal weight: 0.5980 chunk 175 optimal weight: 0.2980 chunk 103 optimal weight: 1.9990 chunk 139 optimal weight: 0.9990 chunk 170 optimal weight: 0.0970 overall best weight: 0.4978 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3264 r_free = 0.3264 target = 0.101722 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2977 r_free = 0.2977 target = 0.085418 restraints weight = 29590.618| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.2974 r_free = 0.2974 target = 0.085363 restraints weight = 33632.639| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.2979 r_free = 0.2979 target = 0.085664 restraints weight = 30169.788| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.2985 r_free = 0.2985 target = 0.086003 restraints weight = 27362.684| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.2988 r_free = 0.2988 target = 0.086164 restraints weight = 25882.814| |-----------------------------------------------------------------------------| r_work (final): 0.2985 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7540 moved from start: 0.2214 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 18587 Z= 0.150 Angle : 0.533 10.058 25206 Z= 0.281 Chirality : 0.044 0.322 2826 Planarity : 0.004 0.047 3170 Dihedral : 6.366 60.907 2816 Min Nonbonded Distance : 2.330 Molprobity Statistics. All-atom Clashscore : 5.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.33 % Favored : 96.67 % Rotamer: Outliers : 2.52 % Allowed : 13.14 % Favored : 84.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.09 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.32 (0.18), residues: 2223 helix: 1.50 (0.17), residues: 940 sheet: -0.52 (0.26), residues: 374 loop : -0.79 (0.20), residues: 909 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG G 27 TYR 0.018 0.001 TYR B 145 PHE 0.015 0.001 PHE Q 806 TRP 0.019 0.002 TRP R 719 HIS 0.003 0.001 HIS B 183 Details of bonding type rmsd/Z covalent geometry : bond 0.00352 / 0.15 (18558) covalent geometry : angle 0.52824 / 0.28 (25136) SS BOND : bond 0.00152 / 0.09 ( 17) SS BOND : angle 0.87103 / 0.65 ( 34) hydrogen bonds : bond 0.05136 / 3.47 ( 875) hydrogen bonds : angle 4.32647 / 3.11 ( 2505) link_BETA1-4 : bond 0.00266 / 0.17 ( 4) link_BETA1-4 : angle 1.46923 / 0.96 ( 12) link_NAG-ASN : bond 0.00185 / 0.10 ( 8) link_NAG-ASN : angle 1.97365 / 1.47 ( 24) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4446 Ramachandran restraints generated. 2223 Oldfield, 0 Emsley, 2223 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4446 Ramachandran restraints generated. 2223 Oldfield, 0 Emsley, 2223 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 362 residues out of total 1941 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 313 time to evaluate : 0.725 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: Q 270 PHE cc_start: 0.7310 (OUTLIER) cc_final: 0.6852 (m-80) REVERT: Q 286 ARG cc_start: 0.7875 (mtp85) cc_final: 0.7673 (mtp85) REVERT: Q 354 GLU cc_start: 0.6586 (mm-30) cc_final: 0.6203 (mm-30) REVERT: Q 454 LYS cc_start: 0.8010 (mttt) cc_final: 0.7807 (mmtp) REVERT: Q 476 GLN cc_start: 0.7869 (mm-40) cc_final: 0.7257 (mm-40) REVERT: Q 654 LEU cc_start: 0.8162 (OUTLIER) cc_final: 0.7954 (tt) REVERT: Q 727 LEU cc_start: 0.7410 (OUTLIER) cc_final: 0.7147 (tt) REVERT: Q 762 PHE cc_start: 0.7184 (m-80) cc_final: 0.6917 (m-80) REVERT: Q 767 GLU cc_start: 0.6575 (OUTLIER) cc_final: 0.6347 (mm-30) REVERT: R 253 GLN cc_start: 0.6568 (OUTLIER) cc_final: 0.6200 (mp10) REVERT: R 341 LYS cc_start: 0.7347 (mmtp) cc_final: 0.7147 (mppt) REVERT: R 577 THR cc_start: 0.7844 (OUTLIER) cc_final: 0.7523 (t) REVERT: R 679 LEU cc_start: 0.8050 (mt) cc_final: 0.7684 (mt) REVERT: R 771 MET cc_start: 0.6440 (mmt) cc_final: 0.5974 (mmt) REVERT: R 776 LEU cc_start: 0.7258 (OUTLIER) cc_final: 0.6844 (mp) REVERT: R 795 ARG cc_start: 0.7461 (ptt-90) cc_final: 0.7022 (ptt-90) REVERT: A 10 LYS cc_start: 0.8047 (mmtt) cc_final: 0.7834 (mmtt) REVERT: B 37 LEU cc_start: 0.7149 (OUTLIER) cc_final: 0.6828 (tt) REVERT: B 195 ASP cc_start: 0.7979 (p0) cc_final: 0.7670 (p0) REVERT: B 234 PHE cc_start: 0.8262 (OUTLIER) cc_final: 0.7554 (t80) REVERT: B 237 ASN cc_start: 0.8412 (t0) cc_final: 0.8170 (t0) outliers start: 49 outliers final: 38 residues processed: 342 average time/residue: 0.1689 time to fit residues: 84.3516 Evaluate side-chains 358 residues out of total 1941 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 311 time to evaluate : 0.708 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Q residue 263 THR Chi-restraints excluded: chain Q residue 270 PHE Chi-restraints excluded: chain Q residue 452 ILE Chi-restraints excluded: chain Q residue 516 LYS Chi-restraints excluded: chain Q residue 529 LEU Chi-restraints excluded: chain Q residue 554 ILE Chi-restraints excluded: chain Q residue 609 THR Chi-restraints excluded: chain Q residue 654 LEU Chi-restraints excluded: chain Q residue 727 LEU Chi-restraints excluded: chain Q residue 734 MET Chi-restraints excluded: chain Q residue 737 VAL Chi-restraints excluded: chain Q residue 760 ILE Chi-restraints excluded: chain Q residue 767 GLU Chi-restraints excluded: chain Q residue 793 LYS Chi-restraints excluded: chain R residue 113 SER Chi-restraints excluded: chain R residue 118 ASN Chi-restraints excluded: chain R residue 247 SER Chi-restraints excluded: chain R residue 253 GLN Chi-restraints excluded: chain R residue 270 PHE Chi-restraints excluded: chain R residue 289 THR Chi-restraints excluded: chain R residue 322 LEU Chi-restraints excluded: chain R residue 409 ILE Chi-restraints excluded: chain R residue 434 ILE Chi-restraints excluded: chain R residue 504 VAL Chi-restraints excluded: chain R residue 506 LYS Chi-restraints excluded: chain R residue 577 THR Chi-restraints excluded: chain R residue 585 CYS Chi-restraints excluded: chain R residue 625 PHE Chi-restraints excluded: chain R residue 640 THR Chi-restraints excluded: chain R residue 730 LEU Chi-restraints excluded: chain R residue 776 LEU Chi-restraints excluded: chain R residue 811 MET Chi-restraints excluded: chain R residue 869 ILE Chi-restraints excluded: chain A residue 50 VAL Chi-restraints excluded: chain A residue 240 MET Chi-restraints excluded: chain A residue 316 THR Chi-restraints excluded: chain B residue 31 THR Chi-restraints excluded: chain B residue 37 LEU Chi-restraints excluded: chain B residue 46 ARG Chi-restraints excluded: chain B residue 74 SER Chi-restraints excluded: chain B residue 86 THR Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 213 VAL Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 274 THR Chi-restraints excluded: chain B residue 318 LEU Chi-restraints excluded: chain G residue 25 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 222 random chunks: chunk 29 optimal weight: 1.9990 chunk 173 optimal weight: 2.9990 chunk 139 optimal weight: 0.9990 chunk 114 optimal weight: 2.9990 chunk 47 optimal weight: 0.0000 chunk 91 optimal weight: 0.9990 chunk 16 optimal weight: 0.9990 chunk 5 optimal weight: 1.9990 chunk 62 optimal weight: 0.9990 chunk 18 optimal weight: 1.9990 chunk 98 optimal weight: 0.9980 overall best weight: 0.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3246 r_free = 0.3246 target = 0.100820 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2961 r_free = 0.2961 target = 0.084955 restraints weight = 29716.855| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.2958 r_free = 0.2958 target = 0.084801 restraints weight = 33427.714| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.2959 r_free = 0.2959 target = 0.084852 restraints weight = 28710.786| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.2960 r_free = 0.2960 target = 0.084928 restraints weight = 28437.003| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.2961 r_free = 0.2961 target = 0.085008 restraints weight = 26983.123| |-----------------------------------------------------------------------------| r_work (final): 0.2945 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7565 moved from start: 0.2263 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.051 18587 Z= 0.209 Angle : 0.576 9.131 25206 Z= 0.301 Chirality : 0.046 0.392 2826 Planarity : 0.004 0.047 3170 Dihedral : 6.522 62.771 2816 Min Nonbonded Distance : 2.433 Molprobity Statistics. All-atom Clashscore : 5.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.73 % Favored : 96.27 % Rotamer: Outliers : 2.99 % Allowed : 12.73 % Favored : 84.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.09 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.18 (0.18), residues: 2223 helix: 1.37 (0.17), residues: 940 sheet: -0.62 (0.26), residues: 376 loop : -0.82 (0.20), residues: 907 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG G 27 TYR 0.020 0.002 TYR B 145 PHE 0.018 0.002 PHE Q 806 TRP 0.018 0.002 TRP R 719 HIS 0.006 0.001 HIS R 338 Details of bonding type rmsd/Z covalent geometry : bond 0.00504 / 0.21 (18558) covalent geometry : angle 0.56976 / 0.30 (25136) SS BOND : bond 0.00245 / 0.14 ( 17) SS BOND : angle 1.23495 / 1.03 ( 34) hydrogen bonds : bond 0.05638 / 3.79 ( 875) hydrogen bonds : angle 4.43023 / 3.19 ( 2505) link_BETA1-4 : bond 0.00311 / 0.21 ( 4) link_BETA1-4 : angle 1.57755 / 1.06 ( 12) link_NAG-ASN : bond 0.00175 / 0.10 ( 8) link_NAG-ASN : angle 2.26891 / 1.73 ( 24) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4446 Ramachandran restraints generated. 2223 Oldfield, 0 Emsley, 2223 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4446 Ramachandran restraints generated. 2223 Oldfield, 0 Emsley, 2223 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 379 residues out of total 1941 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 321 time to evaluate : 0.632 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: Q 270 PHE cc_start: 0.7299 (OUTLIER) cc_final: 0.6890 (m-80) REVERT: Q 354 GLU cc_start: 0.6577 (mm-30) cc_final: 0.6181 (mm-30) REVERT: Q 476 GLN cc_start: 0.7850 (mm-40) cc_final: 0.7270 (mm-40) REVERT: Q 654 LEU cc_start: 0.8154 (OUTLIER) cc_final: 0.7951 (tt) REVERT: Q 727 LEU cc_start: 0.7467 (OUTLIER) cc_final: 0.7157 (tt) REVERT: Q 762 PHE cc_start: 0.7218 (m-80) cc_final: 0.6930 (m-80) REVERT: Q 767 GLU cc_start: 0.6596 (OUTLIER) cc_final: 0.6338 (mm-30) REVERT: R 253 GLN cc_start: 0.6585 (OUTLIER) cc_final: 0.6190 (mp10) REVERT: R 577 THR cc_start: 0.7859 (OUTLIER) cc_final: 0.7551 (t) REVERT: R 776 LEU cc_start: 0.7303 (OUTLIER) cc_final: 0.6870 (mp) REVERT: R 795 ARG cc_start: 0.7478 (ptt-90) cc_final: 0.7007 (ptt-90) REVERT: A 10 LYS cc_start: 0.8030 (mmtt) cc_final: 0.7589 (mmtt) REVERT: A 13 VAL cc_start: 0.7889 (t) cc_final: 0.7482 (m) REVERT: B 37 LEU cc_start: 0.7166 (OUTLIER) cc_final: 0.6837 (tt) REVERT: B 195 ASP cc_start: 0.8046 (p0) cc_final: 0.7728 (p0) REVERT: B 234 PHE cc_start: 0.8277 (OUTLIER) cc_final: 0.7513 (t80) REVERT: B 237 ASN cc_start: 0.8434 (t0) cc_final: 0.8182 (t0) REVERT: B 273 ILE cc_start: 0.8178 (OUTLIER) cc_final: 0.7976 (mp) outliers start: 58 outliers final: 44 residues processed: 357 average time/residue: 0.1636 time to fit residues: 86.1530 Evaluate side-chains 369 residues out of total 1941 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 315 time to evaluate : 0.717 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Q residue 61 ILE Chi-restraints excluded: chain Q residue 263 THR Chi-restraints excluded: chain Q residue 270 PHE Chi-restraints excluded: chain Q residue 422 LEU Chi-restraints excluded: chain Q residue 452 ILE Chi-restraints excluded: chain Q residue 516 LYS Chi-restraints excluded: chain Q residue 529 LEU Chi-restraints excluded: chain Q residue 554 ILE Chi-restraints excluded: chain Q residue 609 THR Chi-restraints excluded: chain Q residue 654 LEU Chi-restraints excluded: chain Q residue 695 ILE Chi-restraints excluded: chain Q residue 727 LEU Chi-restraints excluded: chain Q residue 737 VAL Chi-restraints excluded: chain Q residue 760 ILE Chi-restraints excluded: chain Q residue 767 GLU Chi-restraints excluded: chain Q residue 776 LEU Chi-restraints excluded: chain Q residue 793 LYS Chi-restraints excluded: chain R residue 113 SER Chi-restraints excluded: chain R residue 118 ASN Chi-restraints excluded: chain R residue 247 SER Chi-restraints excluded: chain R residue 253 GLN Chi-restraints excluded: chain R residue 270 PHE Chi-restraints excluded: chain R residue 289 THR Chi-restraints excluded: chain R residue 312 HIS Chi-restraints excluded: chain R residue 322 LEU Chi-restraints excluded: chain R residue 404 VAL Chi-restraints excluded: chain R residue 409 ILE Chi-restraints excluded: chain R residue 434 ILE Chi-restraints excluded: chain R residue 504 VAL Chi-restraints excluded: chain R residue 506 LYS Chi-restraints excluded: chain R residue 577 THR Chi-restraints excluded: chain R residue 585 CYS Chi-restraints excluded: chain R residue 609 THR Chi-restraints excluded: chain R residue 625 PHE Chi-restraints excluded: chain R residue 640 THR Chi-restraints excluded: chain R residue 730 LEU Chi-restraints excluded: chain R residue 737 VAL Chi-restraints excluded: chain R residue 776 LEU Chi-restraints excluded: chain R residue 811 MET Chi-restraints excluded: chain R residue 869 ILE Chi-restraints excluded: chain A residue 50 VAL Chi-restraints excluded: chain A residue 263 SER Chi-restraints excluded: chain A residue 316 THR Chi-restraints excluded: chain B residue 31 THR Chi-restraints excluded: chain B residue 37 LEU Chi-restraints excluded: chain B residue 46 ARG Chi-restraints excluded: chain B residue 74 SER Chi-restraints excluded: chain B residue 86 THR Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 213 VAL Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 273 ILE Chi-restraints excluded: chain B residue 274 THR Chi-restraints excluded: chain B residue 318 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 222 random chunks: chunk 220 optimal weight: 0.0070 chunk 192 optimal weight: 0.6980 chunk 212 optimal weight: 0.5980 chunk 64 optimal weight: 0.5980 chunk 93 optimal weight: 0.9990 chunk 41 optimal weight: 0.6980 chunk 177 optimal weight: 1.9990 chunk 4 optimal weight: 0.9990 chunk 45 optimal weight: 2.9990 chunk 221 optimal weight: 0.7980 chunk 40 optimal weight: 0.9980 overall best weight: 0.5198 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3262 r_free = 0.3262 target = 0.102724 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.2977 r_free = 0.2977 target = 0.086583 restraints weight = 29766.439| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.2976 r_free = 0.2976 target = 0.086660 restraints weight = 29562.663| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.2976 r_free = 0.2976 target = 0.086708 restraints weight = 27680.107| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.2978 r_free = 0.2978 target = 0.086803 restraints weight = 26882.034| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.2980 r_free = 0.2980 target = 0.086916 restraints weight = 25705.861| |-----------------------------------------------------------------------------| r_work (final): 0.2957 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7555 moved from start: 0.2288 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 18587 Z= 0.156 Angle : 0.543 10.152 25206 Z= 0.287 Chirality : 0.044 0.348 2826 Planarity : 0.004 0.047 3170 Dihedral : 6.394 65.300 2816 Min Nonbonded Distance : 2.443 Molprobity Statistics. All-atom Clashscore : 5.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.37 % Favored : 96.63 % Rotamer: Outliers : 2.78 % Allowed : 13.29 % Favored : 83.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.09 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.30 (0.18), residues: 2223 helix: 1.49 (0.17), residues: 939 sheet: -0.55 (0.26), residues: 374 loop : -0.79 (0.20), residues: 910 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG G 27 TYR 0.018 0.001 TYR B 145 PHE 0.016 0.001 PHE Q 806 TRP 0.020 0.002 TRP R 719 HIS 0.009 0.001 HIS R 338 Details of bonding type rmsd/Z covalent geometry : bond 0.00369 / 0.16 (18558) covalent geometry : angle 0.53777 / 0.29 (25136) SS BOND : bond 0.00169 / 0.10 ( 17) SS BOND : angle 0.99934 / 0.82 ( 34) hydrogen bonds : bond 0.05182 / 3.49 ( 875) hydrogen bonds : angle 4.34961 / 3.13 ( 2505) link_BETA1-4 : bond 0.00277 / 0.18 ( 4) link_BETA1-4 : angle 1.48435 / 0.97 ( 12) link_NAG-ASN : bond 0.00241 / 0.13 ( 8) link_NAG-ASN : angle 2.02875 / 1.52 ( 24) Origin is already at (0, 0, 0), no shifts will be applied Model does not fit in PDB format. =============================================================================== Job complete usr+sys time: 3027.89 seconds wall clock time: 52 minutes 59.48 seconds (3179.48 seconds total)