Starting phenix.real_space_refine on Mon Jun 16 03:32:45 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9avl_43908/06_2025/9avl_43908.cif Found real_map, /net/cci-nas-00/data/ceres_data/9avl_43908/06_2025/9avl_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_43908/06_2025/9avl_43908.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9avl_43908/06_2025/9avl_43908.map" model { file = "/net/cci-nas-00/data/ceres_data/9avl_43908/06_2025/9avl_43908.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9avl_43908/06_2025/9avl_43908.cif" } resolution = 3.8 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.002 sd= 0.041 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): 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/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, 64 Unusual residues: {' CA': 3, '9IG': 1, 'PO4': 1, 'Y01': 1} Classifications: {'undetermined': 6} Link IDs: {None: 5} Chain: "R" Number of atoms: 58 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 58 Unusual residues: {'NAG': 3, 'TCR': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "R" Number of atoms: 80 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 80 Unusual residues: {' CA': 3, '9IG': 1, 'A1AF7': 1, 'PO4': 1} Classifications: {'undetermined': 6} Link IDs: {None: 5} Time building chain proxies: 10.87, per 1000 atoms: 0.60 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: 4.95 Conformation dependent library (CDL) restraints added in 2.4 seconds 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: 2.14 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: 7.84 Time building geometry restraints manager: 5.81 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 873 or resid 1001 through 1002 or resid 1003 th \ rough 1007)) selection = (chain 'R' and (resid 22 through 360 or resid 393 through 710 or resid 722 throu \ gh 873 or resid 1003 through 1004 or resid 1005 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: 26.540 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: 0.790 Check model and map are aligned: 0.140 Set scattering table: 0.180 Process input model: 47.490 Find NCS groups from input model: 0.780 Set up NCS constraints: 0.100 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:3.080 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 79.130 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7184 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 : 6.25 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.08 (0.17), residues: 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 TRP 0.019 0.002 TRP R 719 HIS 0.005 0.001 HIS B 183 PHE 0.023 0.002 PHE Q 634 TYR 0.025 0.002 TYR B 59 ARG 0.007 0.000 ARG A 24 Details of bonding type rmsd link_NAG-ASN : bond 0.00279 ( 8) link_NAG-ASN : angle 2.00264 ( 24) link_BETA1-4 : bond 0.00436 ( 4) link_BETA1-4 : angle 1.61571 ( 12) hydrogen bonds : bond 0.13417 ( 875) hydrogen bonds : angle 5.77387 ( 2505) SS BOND : bond 0.00174 ( 17) SS BOND : angle 1.05482 ( 34) covalent geometry : bond 0.00467 (18558) covalent geometry : angle 0.66684 (25136) *********************** 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 : 1.951 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: 0.7672 (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: 0.6796 (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: 0.4857 (mt) REVERT: A 277 LYS cc_start: 0.7643 (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: 0.3362 time to fit residues: 190.7701 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 : 2.153 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 222 random chunks: chunk 187 optimal weight: 0.0770 chunk 168 optimal weight: 0.9990 chunk 93 optimal weight: 0.4980 chunk 57 optimal weight: 0.9990 chunk 113 optimal weight: 0.9990 chunk 89 optimal weight: 0.5980 chunk 174 optimal weight: 1.9990 chunk 67 optimal weight: 0.1980 chunk 105 optimal weight: 0.9990 chunk 129 optimal weight: 1.9990 chunk 201 optimal weight: 0.9990 overall best weight: 0.4740 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3280 r_free = 0.3280 target = 0.103299 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3011 r_free = 0.3011 target = 0.087783 restraints weight = 29494.368| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3008 r_free = 0.3008 target = 0.087617 restraints weight = 30410.756| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3009 r_free = 0.3009 target = 0.087720 restraints weight = 27317.577| |-----------------------------------------------------------------------------| r_work (final): 0.2965 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7246 moved from start: 0.1115 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 18587 Z= 0.155 Angle : 0.541 9.334 25206 Z= 0.286 Chirality : 0.044 0.264 2826 Planarity : 0.004 0.047 3170 Dihedral : 7.619 87.246 2816 Min Nonbonded Distance : 2.368 Molprobity Statistics. All-atom Clashscore : 5.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.97 % Favored : 97.03 % Rotamer: Outliers : 0.82 % Allowed : 6.70 % Favored : 92.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.09 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.17 (0.17), residues: 2223 helix: 1.36 (0.17), residues: 940 sheet: -0.48 (0.26), residues: 369 loop : -0.90 (0.19), residues: 914 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP Q 818 HIS 0.004 0.001 HIS B 183 PHE 0.017 0.002 PHE Q 612 TYR 0.016 0.002 TYR B 59 ARG 0.004 0.000 ARG Q 638 Details of bonding type rmsd link_NAG-ASN : bond 0.00354 ( 8) link_NAG-ASN : angle 1.53400 ( 24) link_BETA1-4 : bond 0.00295 ( 4) link_BETA1-4 : angle 1.39476 ( 12) hydrogen bonds : bond 0.05424 ( 875) hydrogen bonds : angle 4.51005 ( 2505) SS BOND : bond 0.00152 ( 17) SS BOND : angle 1.14409 ( 34) covalent geometry : bond 0.00357 (18558) covalent geometry : angle 0.53714 (25136) *********************** 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 359 residues out of total 1941 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 343 time to evaluate : 2.106 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: Q 286 ARG cc_start: 0.7821 (mtp85) cc_final: 0.7616 (mtp85) REVERT: Q 287 ASN cc_start: 0.7899 (t0) cc_final: 0.7666 (t0) REVERT: Q 762 PHE cc_start: 0.7088 (m-80) cc_final: 0.6703 (m-80) REVERT: Q 811 MET cc_start: 0.7868 (mmp) cc_final: 0.7553 (mmp) REVERT: R 88 LEU cc_start: 0.7519 (mm) cc_final: 0.7291 (mm) REVERT: R 117 GLN cc_start: 0.7195 (tt0) cc_final: 0.6886 (tm-30) REVERT: R 253 GLN cc_start: 0.6460 (mp-120) cc_final: 0.6137 (mm-40) REVERT: R 736 ILE cc_start: 0.7641 (pt) cc_final: 0.7432 (pt) REVERT: R 795 ARG cc_start: 0.7444 (ptt-90) cc_final: 0.7116 (ptt-90) REVERT: A 273 LEU cc_start: 0.6454 (mp) cc_final: 0.5899 (mt) REVERT: B 37 LEU cc_start: 0.7039 (tt) cc_final: 0.6761 (tt) REVERT: B 237 ASN cc_start: 0.8487 (t0) cc_final: 0.8251 (t0) REVERT: G 21 MET cc_start: 0.6574 (mmm) cc_final: 0.6330 (tmm) outliers start: 16 outliers final: 12 residues processed: 353 average time/residue: 0.3598 time to fit residues: 183.1850 Evaluate side-chains 329 residues out of total 1941 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 317 time to evaluate : 1.852 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Q residue 92 THR Chi-restraints excluded: chain Q residue 560 THR 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 322 LEU Chi-restraints excluded: chain R residue 409 ILE Chi-restraints excluded: chain R residue 640 THR Chi-restraints excluded: chain A residue 50 VAL 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 4 optimal weight: 0.9990 chunk 177 optimal weight: 0.7980 chunk 91 optimal weight: 0.9980 chunk 72 optimal weight: 0.0050 chunk 141 optimal weight: 0.0970 chunk 200 optimal weight: 0.3980 chunk 80 optimal weight: 1.9990 chunk 194 optimal weight: 1.9990 chunk 49 optimal weight: 2.9990 chunk 53 optimal weight: 0.9990 chunk 216 optimal weight: 0.8980 overall best weight: 0.4392 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3278 r_free = 0.3278 target = 0.103346 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3003 r_free = 0.3003 target = 0.087598 restraints weight = 29445.240| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3001 r_free = 0.3001 target = 0.087614 restraints weight = 28781.735| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3004 r_free = 0.3004 target = 0.087749 restraints weight = 27911.759| |-----------------------------------------------------------------------------| r_work (final): 0.2983 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7258 moved from start: 0.1416 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 18587 Z= 0.140 Angle : 0.510 9.318 25206 Z= 0.270 Chirality : 0.043 0.269 2826 Planarity : 0.004 0.044 3170 Dihedral : 7.215 86.300 2816 Min Nonbonded Distance : 2.364 Molprobity Statistics. All-atom Clashscore : 4.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.79 % Favored : 97.21 % Rotamer: Outliers : 0.93 % Allowed : 9.38 % Favored : 89.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.09 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.31 (0.17), residues: 2223 helix: 1.53 (0.17), residues: 940 sheet: -0.44 (0.26), residues: 362 loop : -0.88 (0.19), residues: 921 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP R 719 HIS 0.006 0.001 HIS R 463 PHE 0.014 0.001 PHE Q 634 TYR 0.015 0.001 TYR B 145 ARG 0.003 0.000 ARG Q 638 Details of bonding type rmsd link_NAG-ASN : bond 0.00192 ( 8) link_NAG-ASN : angle 1.57961 ( 24) link_BETA1-4 : bond 0.00296 ( 4) link_BETA1-4 : angle 1.35137 ( 12) hydrogen bonds : bond 0.05096 ( 875) hydrogen bonds : angle 4.33876 ( 2505) SS BOND : bond 0.00205 ( 17) SS BOND : angle 1.11531 ( 34) covalent geometry : bond 0.00324 (18558) covalent geometry : angle 0.50538 (25136) *********************** 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 346 residues out of total 1941 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 328 time to evaluate : 1.889 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: Q 287 ASN cc_start: 0.7894 (t0) cc_final: 0.7671 (t0) REVERT: Q 354 GLU cc_start: 0.6619 (mm-30) cc_final: 0.6187 (mm-30) REVERT: Q 355 THR cc_start: 0.7955 (m) cc_final: 0.7691 (m) REVERT: Q 762 PHE cc_start: 0.7003 (m-80) cc_final: 0.6606 (m-80) REVERT: R 88 LEU cc_start: 0.7570 (mm) cc_final: 0.7348 (mm) REVERT: R 117 GLN cc_start: 0.7177 (tt0) cc_final: 0.6892 (tm-30) REVERT: R 253 GLN cc_start: 0.6540 (mp-120) cc_final: 0.6157 (mp10) REVERT: R 589 PHE cc_start: 0.7288 (m-80) cc_final: 0.6894 (m-80) REVERT: R 736 ILE cc_start: 0.7609 (pt) cc_final: 0.7399 (pt) REVERT: R 795 ARG cc_start: 0.7449 (ptt-90) cc_final: 0.7094 (ptt-90) REVERT: A 273 LEU cc_start: 0.6496 (mp) cc_final: 0.6055 (tp) REVERT: B 37 LEU cc_start: 0.7056 (tt) cc_final: 0.6729 (tt) REVERT: B 237 ASN cc_start: 0.8484 (t0) cc_final: 0.8239 (t0) REVERT: B 301 LYS cc_start: 0.7354 (mmtt) cc_final: 0.7053 (mmtp) outliers start: 18 outliers final: 15 residues processed: 339 average time/residue: 0.3525 time to fit residues: 172.9137 Evaluate side-chains 328 residues out of total 1941 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 313 time to evaluate : 1.821 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Q residue 422 LEU Chi-restraints excluded: chain Q residue 516 LYS 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 289 THR Chi-restraints excluded: chain R residue 322 LEU Chi-restraints excluded: chain R residue 409 ILE Chi-restraints excluded: chain R residue 625 PHE Chi-restraints excluded: chain R residue 640 THR Chi-restraints excluded: chain A residue 263 SER 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 193 optimal weight: 0.0170 chunk 17 optimal weight: 1.9990 chunk 5 optimal weight: 1.9990 chunk 72 optimal weight: 0.6980 chunk 124 optimal weight: 0.5980 chunk 195 optimal weight: 0.9990 chunk 219 optimal weight: 1.9990 chunk 144 optimal weight: 0.9990 chunk 34 optimal weight: 0.9980 chunk 104 optimal weight: 1.9990 chunk 91 optimal weight: 0.9980 overall best weight: 0.6618 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3252 r_free = 0.3252 target = 0.101238 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2991 r_free = 0.2991 target = 0.086581 restraints weight = 29813.931| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.2987 r_free = 0.2987 target = 0.086339 restraints weight = 30731.984| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.2987 r_free = 0.2987 target = 0.086399 restraints weight = 28744.623| |-----------------------------------------------------------------------------| r_work (final): 0.2995 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7266 moved from start: 0.1717 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 18587 Z= 0.181 Angle : 0.546 9.606 25206 Z= 0.287 Chirality : 0.044 0.259 2826 Planarity : 0.004 0.045 3170 Dihedral : 6.921 74.923 2816 Min Nonbonded Distance : 2.328 Molprobity Statistics. All-atom Clashscore : 5.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.24 % Favored : 96.76 % Rotamer: Outliers : 1.75 % Allowed : 10.15 % Favored : 88.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.09 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.25 (0.17), residues: 2223 helix: 1.47 (0.17), residues: 941 sheet: -0.51 (0.26), residues: 362 loop : -0.89 (0.19), residues: 920 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP R 719 HIS 0.004 0.001 HIS R 463 PHE 0.019 0.002 PHE Q 634 TYR 0.017 0.002 TYR B 145 ARG 0.003 0.000 ARG Q 227 Details of bonding type rmsd link_NAG-ASN : bond 0.00164 ( 8) link_NAG-ASN : angle 1.79250 ( 24) link_BETA1-4 : bond 0.00338 ( 4) link_BETA1-4 : angle 1.46618 ( 12) hydrogen bonds : bond 0.05451 ( 875) hydrogen bonds : angle 4.37984 ( 2505) SS BOND : bond 0.00191 ( 17) SS BOND : angle 1.02234 ( 34) covalent geometry : bond 0.00432 (18558) covalent geometry : angle 0.54198 (25136) *********************** 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 358 residues out of total 1941 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 324 time to evaluate : 2.036 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: Q 270 PHE cc_start: 0.7318 (OUTLIER) cc_final: 0.6915 (m-80) REVERT: Q 286 ARG cc_start: 0.7808 (mtp85) cc_final: 0.7608 (mtp85) REVERT: Q 287 ASN cc_start: 0.7932 (t0) cc_final: 0.7713 (t0) REVERT: Q 292 ILE cc_start: 0.7811 (mm) cc_final: 0.7426 (mp) REVERT: Q 354 GLU cc_start: 0.6588 (mm-30) cc_final: 0.6194 (mm-30) REVERT: Q 762 PHE cc_start: 0.7026 (m-80) cc_final: 0.6652 (m-80) REVERT: R 117 GLN cc_start: 0.7213 (tt0) cc_final: 0.6895 (tm-30) REVERT: R 253 GLN cc_start: 0.6506 (OUTLIER) cc_final: 0.6137 (mp10) REVERT: R 795 ARG cc_start: 0.7431 (ptt-90) cc_final: 0.7032 (ptt-90) REVERT: A 273 LEU cc_start: 0.6569 (mp) cc_final: 0.6048 (tp) REVERT: B 37 LEU cc_start: 0.7149 (OUTLIER) cc_final: 0.6868 (tt) REVERT: B 237 ASN cc_start: 0.8463 (t0) cc_final: 0.8227 (t0) outliers start: 34 outliers final: 24 residues processed: 342 average time/residue: 0.3628 time to fit residues: 178.7531 Evaluate side-chains 342 residues out of total 1941 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 315 time to evaluate : 2.026 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Q residue 159 LEU 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 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 289 THR Chi-restraints excluded: chain R residue 322 LEU Chi-restraints excluded: chain R residue 409 ILE Chi-restraints excluded: chain R residue 410 ASP 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 A residue 198 MET Chi-restraints excluded: chain A residue 263 SER 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 Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 222 random chunks: chunk 164 optimal weight: 0.9990 chunk 124 optimal weight: 0.9980 chunk 24 optimal weight: 0.9980 chunk 88 optimal weight: 1.9990 chunk 193 optimal weight: 0.8980 chunk 79 optimal weight: 0.7980 chunk 196 optimal weight: 1.9990 chunk 163 optimal weight: 0.9990 chunk 76 optimal weight: 0.6980 chunk 16 optimal weight: 0.9990 chunk 98 optimal weight: 0.9980 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3249 r_free = 0.3249 target = 0.101195 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2960 r_free = 0.2960 target = 0.084969 restraints weight = 29837.561| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.2960 r_free = 0.2960 target = 0.085045 restraints weight = 29049.316| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.2962 r_free = 0.2962 target = 0.085187 restraints weight = 26718.354| |-----------------------------------------------------------------------------| r_work (final): 0.2940 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7314 moved from start: 0.1952 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.047 18587 Z= 0.227 Angle : 0.585 9.560 25206 Z= 0.306 Chirality : 0.046 0.269 2826 Planarity : 0.004 0.047 3170 Dihedral : 6.831 63.323 2816 Min Nonbonded Distance : 2.312 Molprobity Statistics. All-atom Clashscore : 5.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.55 % Favored : 96.45 % Rotamer: Outliers : 2.42 % Allowed : 11.18 % Favored : 86.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.09 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.13 (0.17), residues: 2223 helix: 1.34 (0.17), residues: 940 sheet: -0.59 (0.26), residues: 362 loop : -0.89 (0.20), residues: 921 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP R 719 HIS 0.005 0.001 HIS A 213 PHE 0.020 0.002 PHE Q 634 TYR 0.018 0.002 TYR B 145 ARG 0.006 0.001 ARG Q 233 Details of bonding type rmsd link_NAG-ASN : bond 0.00182 ( 8) link_NAG-ASN : angle 1.99312 ( 24) link_BETA1-4 : bond 0.00386 ( 4) link_BETA1-4 : angle 1.57805 ( 12) hydrogen bonds : bond 0.05904 ( 875) hydrogen bonds : angle 4.48112 ( 2505) SS BOND : bond 0.00299 ( 17) SS BOND : angle 1.26327 ( 34) covalent geometry : bond 0.00549 (18558) covalent geometry : angle 0.57925 (25136) *********************** 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 379 residues out of total 1941 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 332 time to evaluate : 1.915 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: Q 227 ARG cc_start: 0.7401 (ttp80) cc_final: 0.7136 (ttp80) REVERT: Q 270 PHE cc_start: 0.7301 (OUTLIER) cc_final: 0.6857 (m-80) REVERT: Q 292 ILE cc_start: 0.7865 (mm) cc_final: 0.7471 (mp) REVERT: Q 354 GLU cc_start: 0.6597 (mm-30) cc_final: 0.6221 (mm-30) REVERT: Q 454 LYS cc_start: 0.8060 (mttt) cc_final: 0.7652 (mmmm) REVERT: R 253 GLN cc_start: 0.6578 (OUTLIER) cc_final: 0.6161 (mp10) REVERT: R 584 LYS cc_start: 0.7587 (tppt) cc_final: 0.7337 (mmmt) REVERT: R 795 ARG cc_start: 0.7454 (ptt-90) cc_final: 0.6972 (ptt-90) REVERT: A 13 VAL cc_start: 0.7767 (t) cc_final: 0.7511 (m) REVERT: B 195 ASP cc_start: 0.7828 (p0) cc_final: 0.7531 (p0) REVERT: B 234 PHE cc_start: 0.8308 (OUTLIER) cc_final: 0.7480 (t80) outliers start: 47 outliers final: 33 residues processed: 357 average time/residue: 0.3565 time to fit residues: 184.5491 Evaluate side-chains 356 residues out of total 1941 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 320 time to evaluate : 1.876 ------------------------------------------------------------------------------- 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 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 398 ASP 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 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 737 VAL Chi-restraints excluded: chain A residue 50 VAL Chi-restraints excluded: chain A residue 198 MET Chi-restraints excluded: chain A residue 263 SER 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 234 PHE Chi-restraints excluded: chain G residue 25 ILE Chi-restraints excluded: chain G residue 42 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 222 random chunks: chunk 217 optimal weight: 8.9990 chunk 82 optimal weight: 0.6980 chunk 164 optimal weight: 0.7980 chunk 135 optimal weight: 1.9990 chunk 110 optimal weight: 0.9990 chunk 61 optimal weight: 1.9990 chunk 94 optimal weight: 0.6980 chunk 21 optimal weight: 0.9990 chunk 72 optimal weight: 0.6980 chunk 73 optimal weight: 0.5980 chunk 216 optimal weight: 0.9980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3257 r_free = 0.3257 target = 0.101504 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2989 r_free = 0.2989 target = 0.086520 restraints weight = 29671.101| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.2986 r_free = 0.2986 target = 0.086315 restraints weight = 24452.513| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.2985 r_free = 0.2985 target = 0.086278 restraints weight = 23495.370| |-----------------------------------------------------------------------------| r_work (final): 0.2977 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7291 moved from start: 0.2040 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= 0.187 Angle : 0.554 9.181 25206 Z= 0.291 Chirality : 0.044 0.281 2826 Planarity : 0.004 0.047 3170 Dihedral : 6.617 60.514 2816 Min Nonbonded Distance : 2.328 Molprobity Statistics. All-atom Clashscore : 5.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.46 % Favored : 96.54 % Rotamer: Outliers : 2.58 % Allowed : 11.75 % Favored : 85.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.09 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.19 (0.17), residues: 2223 helix: 1.40 (0.17), residues: 939 sheet: -0.58 (0.26), residues: 362 loop : -0.86 (0.20), residues: 922 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP R 719 HIS 0.004 0.001 HIS B 183 PHE 0.017 0.002 PHE Q 806 TYR 0.019 0.002 TYR B 145 ARG 0.007 0.000 ARG G 27 Details of bonding type rmsd link_NAG-ASN : bond 0.00272 ( 8) link_NAG-ASN : angle 1.98267 ( 24) link_BETA1-4 : bond 0.00390 ( 4) link_BETA1-4 : angle 1.54047 ( 12) hydrogen bonds : bond 0.05531 ( 875) hydrogen bonds : angle 4.42764 ( 2505) SS BOND : bond 0.00200 ( 17) SS BOND : angle 0.98675 ( 34) covalent geometry : bond 0.00448 (18558) covalent geometry : angle 0.54902 (25136) *********************** 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 388 residues out of total 1941 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 338 time to evaluate : 2.025 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: Q 227 ARG cc_start: 0.7392 (ttp80) cc_final: 0.7161 (ttp80) REVERT: Q 270 PHE cc_start: 0.7303 (OUTLIER) cc_final: 0.6875 (m-80) REVERT: Q 286 ARG cc_start: 0.7908 (mtp85) cc_final: 0.7617 (mtp85) REVERT: Q 292 ILE cc_start: 0.7860 (mm) cc_final: 0.7464 (mp) REVERT: Q 354 GLU cc_start: 0.6596 (mm-30) cc_final: 0.6216 (mm-30) REVERT: Q 454 LYS cc_start: 0.8042 (mttt) cc_final: 0.7570 (mmmm) REVERT: R 117 GLN cc_start: 0.7217 (tt0) cc_final: 0.6917 (tm-30) REVERT: R 253 GLN cc_start: 0.6588 (OUTLIER) cc_final: 0.6174 (mp10) REVERT: R 341 LYS cc_start: 0.7394 (mttt) cc_final: 0.7166 (mmtp) REVERT: R 577 THR cc_start: 0.7802 (OUTLIER) cc_final: 0.7450 (t) REVERT: R 776 LEU cc_start: 0.7268 (OUTLIER) cc_final: 0.6852 (mp) REVERT: R 795 ARG cc_start: 0.7442 (ptt-90) cc_final: 0.6973 (ptt-90) REVERT: R 825 TYR cc_start: 0.7439 (t80) cc_final: 0.7239 (t80) REVERT: B 37 LEU cc_start: 0.7103 (tt) cc_final: 0.6841 (tt) REVERT: B 234 PHE cc_start: 0.8311 (OUTLIER) cc_final: 0.7569 (t80) outliers start: 50 outliers final: 35 residues processed: 370 average time/residue: 0.3412 time to fit residues: 183.0968 Evaluate side-chains 356 residues out of total 1941 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 316 time to evaluate : 1.976 ------------------------------------------------------------------------------- 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 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 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 410 ASP Chi-restraints excluded: chain R residue 434 ILE 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 587 ASP Chi-restraints excluded: chain R residue 625 PHE Chi-restraints excluded: chain R residue 640 THR Chi-restraints excluded: chain R residue 737 VAL Chi-restraints excluded: chain R residue 776 LEU 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 B residue 46 ARG Chi-restraints excluded: chain B residue 86 THR 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 318 LEU Chi-restraints excluded: chain G residue 25 ILE Chi-restraints excluded: chain G residue 42 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 222 random chunks: chunk 189 optimal weight: 0.9990 chunk 2 optimal weight: 1.9990 chunk 126 optimal weight: 2.9990 chunk 142 optimal weight: 0.5980 chunk 188 optimal weight: 0.9980 chunk 21 optimal weight: 2.9990 chunk 167 optimal weight: 1.9990 chunk 212 optimal weight: 0.8980 chunk 127 optimal weight: 0.9980 chunk 190 optimal weight: 0.5980 chunk 86 optimal weight: 0.9980 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3248 r_free = 0.3248 target = 0.101016 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.2973 r_free = 0.2973 target = 0.085618 restraints weight = 29675.779| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.2969 r_free = 0.2969 target = 0.085390 restraints weight = 26992.673| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.2968 r_free = 0.2968 target = 0.085387 restraints weight = 26391.903| |-----------------------------------------------------------------------------| r_work (final): 0.2957 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7304 moved from start: 0.2131 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.055 18587 Z= 0.214 Angle : 0.575 9.228 25206 Z= 0.301 Chirality : 0.045 0.328 2826 Planarity : 0.004 0.047 3170 Dihedral : 6.628 63.587 2816 Min Nonbonded Distance : 2.321 Molprobity Statistics. All-atom Clashscore : 5.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.51 % Favored : 96.49 % Rotamer: Outliers : 2.78 % Allowed : 12.26 % Favored : 84.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.09 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.14 (0.17), residues: 2223 helix: 1.34 (0.17), residues: 940 sheet: -0.65 (0.26), residues: 362 loop : -0.86 (0.20), residues: 921 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP R 719 HIS 0.004 0.001 HIS A 213 PHE 0.018 0.002 PHE Q 806 TYR 0.022 0.002 TYR A 290 ARG 0.006 0.000 ARG G 27 Details of bonding type rmsd link_NAG-ASN : bond 0.00179 ( 8) link_NAG-ASN : angle 2.08489 ( 24) link_BETA1-4 : bond 0.00299 ( 4) link_BETA1-4 : angle 1.58279 ( 12) hydrogen bonds : bond 0.05740 ( 875) hydrogen bonds : angle 4.45464 ( 2505) SS BOND : bond 0.00231 ( 17) SS BOND : angle 1.00167 ( 34) covalent geometry : bond 0.00518 (18558) covalent geometry : angle 0.56964 (25136) *********************** 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 386 residues out of total 1941 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 332 time to evaluate : 1.866 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: Q 249 GLU cc_start: 0.7233 (mp0) cc_final: 0.7024 (mp0) REVERT: Q 270 PHE cc_start: 0.7287 (OUTLIER) cc_final: 0.6873 (m-80) REVERT: Q 286 ARG cc_start: 0.7908 (mtp85) cc_final: 0.7626 (mtp85) REVERT: Q 292 ILE cc_start: 0.7860 (mm) cc_final: 0.7454 (mp) REVERT: Q 354 GLU cc_start: 0.6593 (mm-30) cc_final: 0.6204 (mm-30) REVERT: Q 454 LYS cc_start: 0.8049 (mttt) cc_final: 0.7839 (mmtp) REVERT: R 253 GLN cc_start: 0.6583 (OUTLIER) cc_final: 0.6164 (mp10) REVERT: R 577 THR cc_start: 0.7812 (OUTLIER) cc_final: 0.7488 (t) REVERT: R 776 LEU cc_start: 0.7284 (OUTLIER) cc_final: 0.6856 (mp) REVERT: R 795 ARG cc_start: 0.7458 (ptt-90) cc_final: 0.7007 (ptt-90) REVERT: B 37 LEU cc_start: 0.7145 (tt) cc_final: 0.6895 (tt) REVERT: B 195 ASP cc_start: 0.7912 (p0) cc_final: 0.7654 (p0) REVERT: B 234 PHE cc_start: 0.8319 (OUTLIER) cc_final: 0.7562 (t80) outliers start: 54 outliers final: 45 residues processed: 366 average time/residue: 0.3422 time to fit residues: 183.0748 Evaluate side-chains 373 residues out of total 1941 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 323 time to evaluate : 1.855 ------------------------------------------------------------------------------- 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 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 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 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 587 ASP 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 316 THR Chi-restraints excluded: chain B residue 31 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 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 Chi-restraints excluded: chain G residue 42 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 222 random chunks: chunk 36 optimal weight: 0.9990 chunk 181 optimal weight: 0.8980 chunk 21 optimal weight: 1.9990 chunk 38 optimal weight: 0.5980 chunk 15 optimal weight: 0.6980 chunk 0 optimal weight: 1.9990 chunk 97 optimal weight: 0.9990 chunk 202 optimal weight: 0.5980 chunk 121 optimal weight: 0.9980 chunk 99 optimal weight: 0.4980 chunk 49 optimal weight: 0.6980 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3256 r_free = 0.3256 target = 0.101383 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2984 r_free = 0.2984 target = 0.086170 restraints weight = 29623.135| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.2980 r_free = 0.2980 target = 0.085954 restraints weight = 24979.154| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.2980 r_free = 0.2980 target = 0.085947 restraints weight = 23892.510| |-----------------------------------------------------------------------------| r_work (final): 0.2976 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7294 moved from start: 0.2196 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 18587 Z= 0.173 Angle : 0.548 9.209 25206 Z= 0.290 Chirality : 0.044 0.311 2826 Planarity : 0.004 0.047 3170 Dihedral : 6.497 62.304 2816 Min Nonbonded Distance : 2.334 Molprobity Statistics. All-atom Clashscore : 5.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.28 % Favored : 96.72 % Rotamer: Outliers : 2.73 % Allowed : 12.67 % Favored : 84.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.09 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.25 (0.18), residues: 2223 helix: 1.44 (0.17), residues: 940 sheet: -0.61 (0.26), residues: 374 loop : -0.80 (0.20), residues: 909 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP R 719 HIS 0.004 0.001 HIS B 183 PHE 0.016 0.002 PHE Q 806 TYR 0.018 0.001 TYR B 145 ARG 0.006 0.000 ARG G 27 Details of bonding type rmsd link_NAG-ASN : bond 0.00188 ( 8) link_NAG-ASN : angle 1.99724 ( 24) link_BETA1-4 : bond 0.00314 ( 4) link_BETA1-4 : angle 1.52325 ( 12) hydrogen bonds : bond 0.05400 ( 875) hydrogen bonds : angle 4.40171 ( 2505) SS BOND : bond 0.00183 ( 17) SS BOND : angle 0.88809 ( 34) covalent geometry : bond 0.00412 (18558) covalent geometry : angle 0.54366 (25136) *********************** 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 374 residues out of total 1941 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 321 time to evaluate : 2.021 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: Q 270 PHE cc_start: 0.7300 (OUTLIER) cc_final: 0.6841 (m-80) REVERT: Q 292 ILE cc_start: 0.7855 (mm) cc_final: 0.7457 (mp) REVERT: Q 354 GLU cc_start: 0.6582 (mm-30) cc_final: 0.6215 (mm-30) REVERT: Q 422 LEU cc_start: 0.7694 (OUTLIER) cc_final: 0.7470 (mt) REVERT: Q 454 LYS cc_start: 0.8051 (mttt) cc_final: 0.7841 (mmtp) REVERT: Q 727 LEU cc_start: 0.7407 (OUTLIER) cc_final: 0.7144 (tt) REVERT: R 253 GLN cc_start: 0.6584 (OUTLIER) cc_final: 0.6178 (mp10) REVERT: R 577 THR cc_start: 0.7846 (OUTLIER) cc_final: 0.7520 (t) REVERT: R 776 LEU cc_start: 0.7262 (OUTLIER) cc_final: 0.6841 (mp) REVERT: R 795 ARG cc_start: 0.7488 (ptt-90) cc_final: 0.7019 (ptt-90) REVERT: B 37 LEU cc_start: 0.7169 (tt) cc_final: 0.6896 (tt) REVERT: B 195 ASP cc_start: 0.7972 (p0) cc_final: 0.7676 (p0) REVERT: B 205 ASP cc_start: 0.7744 (p0) cc_final: 0.6990 (p0) REVERT: B 207 SER cc_start: 0.8505 (t) cc_final: 0.8043 (p) REVERT: B 234 PHE cc_start: 0.8283 (OUTLIER) cc_final: 0.7529 (t80) REVERT: B 273 ILE cc_start: 0.8171 (OUTLIER) cc_final: 0.7970 (mp) outliers start: 53 outliers final: 43 residues processed: 352 average time/residue: 0.3496 time to fit residues: 179.7579 Evaluate side-chains 365 residues out of total 1941 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 314 time to evaluate : 2.030 ------------------------------------------------------------------------------- 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 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 727 LEU 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 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 587 ASP 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 240 MET 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 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 273 ILE Chi-restraints excluded: chain B residue 274 THR Chi-restraints excluded: chain B residue 318 LEU Chi-restraints excluded: chain G residue 21 MET Chi-restraints excluded: chain G residue 25 ILE Chi-restraints excluded: chain G residue 42 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 222 random chunks: chunk 37 optimal weight: 1.9990 chunk 108 optimal weight: 1.9990 chunk 162 optimal weight: 5.9990 chunk 219 optimal weight: 0.9990 chunk 182 optimal weight: 0.9980 chunk 5 optimal weight: 0.9980 chunk 11 optimal weight: 0.9980 chunk 195 optimal weight: 0.9990 chunk 73 optimal weight: 0.6980 chunk 10 optimal weight: 0.0050 chunk 206 optimal weight: 0.6980 overall best weight: 0.6794 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3250 r_free = 0.3250 target = 0.100955 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.2973 r_free = 0.2973 target = 0.085372 restraints weight = 29902.175| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.2971 r_free = 0.2971 target = 0.085282 restraints weight = 31282.760| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.2971 r_free = 0.2971 target = 0.085316 restraints weight = 28360.133| |-----------------------------------------------------------------------------| r_work (final): 0.2971 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7295 moved from start: 0.2249 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 18587 Z= 0.186 Angle : 0.561 9.005 25206 Z= 0.295 Chirality : 0.045 0.355 2826 Planarity : 0.004 0.047 3170 Dihedral : 6.503 62.324 2816 Min Nonbonded Distance : 2.329 Molprobity Statistics. All-atom Clashscore : 5.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.46 % Favored : 96.54 % Rotamer: Outliers : 2.73 % Allowed : 12.88 % Favored : 84.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.09 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.23 (0.18), residues: 2223 helix: 1.41 (0.17), residues: 940 sheet: -0.61 (0.26), residues: 374 loop : -0.79 (0.20), residues: 909 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP R 719 HIS 0.004 0.001 HIS A 213 PHE 0.017 0.002 PHE Q 806 TYR 0.019 0.001 TYR B 145 ARG 0.007 0.000 ARG G 27 Details of bonding type rmsd link_NAG-ASN : bond 0.00180 ( 8) link_NAG-ASN : angle 2.17532 ( 24) link_BETA1-4 : bond 0.00305 ( 4) link_BETA1-4 : angle 1.54650 ( 12) hydrogen bonds : bond 0.05493 ( 875) hydrogen bonds : angle 4.39520 ( 2505) SS BOND : bond 0.00216 ( 17) SS BOND : angle 0.97988 ( 34) covalent geometry : bond 0.00445 (18558) covalent geometry : angle 0.55507 (25136) *********************** 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 379 residues out of total 1941 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 326 time to evaluate : 1.809 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: Q 270 PHE cc_start: 0.7294 (OUTLIER) cc_final: 0.6835 (m-80) REVERT: Q 286 ARG cc_start: 0.7864 (mtp85) cc_final: 0.7637 (mtp85) REVERT: Q 292 ILE cc_start: 0.7856 (mm) cc_final: 0.7466 (mp) REVERT: Q 354 GLU cc_start: 0.6564 (mm-30) cc_final: 0.6222 (mm-30) REVERT: Q 727 LEU cc_start: 0.7435 (OUTLIER) cc_final: 0.7167 (tt) REVERT: R 253 GLN cc_start: 0.6582 (OUTLIER) cc_final: 0.6201 (mp10) REVERT: R 577 THR cc_start: 0.7812 (OUTLIER) cc_final: 0.7512 (t) REVERT: R 776 LEU cc_start: 0.7280 (OUTLIER) cc_final: 0.6853 (mp) REVERT: R 795 ARG cc_start: 0.7486 (ptt-90) cc_final: 0.7032 (ptt-90) REVERT: B 37 LEU cc_start: 0.7146 (tt) cc_final: 0.6865 (tt) REVERT: B 195 ASP cc_start: 0.8024 (p0) cc_final: 0.7713 (p0) REVERT: B 205 ASP cc_start: 0.7744 (p0) cc_final: 0.6943 (p0) REVERT: B 207 SER cc_start: 0.8496 (t) cc_final: 0.8041 (p) REVERT: B 234 PHE cc_start: 0.8279 (OUTLIER) cc_final: 0.7522 (t80) REVERT: B 273 ILE cc_start: 0.8178 (OUTLIER) cc_final: 0.7976 (mp) outliers start: 53 outliers final: 45 residues processed: 358 average time/residue: 0.3912 time to fit residues: 208.9543 Evaluate side-chains 372 residues out of total 1941 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 320 time to evaluate : 1.961 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Q residue 61 ILE 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 609 THR 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 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 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 587 ASP 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 240 MET 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 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 273 ILE Chi-restraints excluded: chain B residue 274 THR Chi-restraints excluded: chain B residue 318 LEU Chi-restraints excluded: chain G residue 25 ILE Chi-restraints excluded: chain G residue 42 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 222 random chunks: chunk 95 optimal weight: 0.4980 chunk 76 optimal weight: 0.7980 chunk 34 optimal weight: 0.0000 chunk 58 optimal weight: 0.9980 chunk 32 optimal weight: 0.9990 chunk 123 optimal weight: 0.2980 chunk 144 optimal weight: 0.7980 chunk 143 optimal weight: 0.5980 chunk 203 optimal weight: 0.9990 chunk 39 optimal weight: 1.9990 chunk 128 optimal weight: 0.9980 overall best weight: 0.4384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3266 r_free = 0.3266 target = 0.102180 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2999 r_free = 0.2999 target = 0.086979 restraints weight = 29659.406| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.2996 r_free = 0.2996 target = 0.086853 restraints weight = 26623.622| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.2997 r_free = 0.2997 target = 0.086914 restraints weight = 24987.866| |-----------------------------------------------------------------------------| r_work (final): 0.2973 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7270 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 : 0.003 0.039 18587 Z= 0.140 Angle : 0.525 8.778 25206 Z= 0.278 Chirality : 0.043 0.321 2826 Planarity : 0.004 0.047 3170 Dihedral : 6.313 64.453 2816 Min Nonbonded Distance : 2.359 Molprobity Statistics. All-atom Clashscore : 5.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.24 % Favored : 96.76 % Rotamer: Outliers : 2.27 % Allowed : 13.45 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.40 (0.18), residues: 2223 helix: 1.58 (0.17), residues: 934 sheet: -0.49 (0.26), residues: 372 loop : -0.73 (0.20), residues: 917 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP R 719 HIS 0.003 0.001 HIS B 183 PHE 0.015 0.001 PHE Q 806 TYR 0.018 0.001 TYR B 145 ARG 0.007 0.000 ARG G 27 Details of bonding type rmsd link_NAG-ASN : bond 0.00216 ( 8) link_NAG-ASN : angle 1.87477 ( 24) link_BETA1-4 : bond 0.00268 ( 4) link_BETA1-4 : angle 1.44439 ( 12) hydrogen bonds : bond 0.04983 ( 875) hydrogen bonds : angle 4.27536 ( 2505) SS BOND : bond 0.00142 ( 17) SS BOND : angle 0.81740 ( 34) covalent geometry : bond 0.00325 (18558) covalent geometry : angle 0.52053 (25136) ********************** 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 366 residues out of total 1941 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 322 time to evaluate : 2.093 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: Q 270 PHE cc_start: 0.7325 (OUTLIER) cc_final: 0.6877 (m-80) REVERT: Q 292 ILE cc_start: 0.7847 (mm) cc_final: 0.7473 (mp) REVERT: Q 354 GLU cc_start: 0.6557 (mm-30) cc_final: 0.6239 (mm-30) REVERT: Q 572 GLU cc_start: 0.6453 (mt-10) cc_final: 0.5878 (mt-10) REVERT: Q 727 LEU cc_start: 0.7408 (OUTLIER) cc_final: 0.7148 (tt) REVERT: R 253 GLN cc_start: 0.6583 (OUTLIER) cc_final: 0.6211 (mp10) REVERT: R 577 THR cc_start: 0.7845 (OUTLIER) cc_final: 0.7526 (t) REVERT: R 679 LEU cc_start: 0.8031 (mt) cc_final: 0.7661 (mt) REVERT: R 771 MET cc_start: 0.6443 (mmt) cc_final: 0.5780 (mmt) REVERT: R 776 LEU cc_start: 0.7217 (OUTLIER) cc_final: 0.6796 (mp) REVERT: R 795 ARG cc_start: 0.7469 (ptt-90) cc_final: 0.7031 (ptt-90) REVERT: B 37 LEU cc_start: 0.7156 (tt) cc_final: 0.6862 (tt) REVERT: B 195 ASP cc_start: 0.8063 (p0) cc_final: 0.7776 (p0) REVERT: B 205 ASP cc_start: 0.7713 (p0) cc_final: 0.6907 (p0) REVERT: B 207 SER cc_start: 0.8493 (t) cc_final: 0.8029 (p) REVERT: B 234 PHE cc_start: 0.8289 (OUTLIER) cc_final: 0.7575 (t80) REVERT: B 273 ILE cc_start: 0.8137 (OUTLIER) cc_final: 0.7813 (mp) outliers start: 44 outliers final: 33 residues processed: 349 average time/residue: 0.3477 time to fit residues: 175.8880 Evaluate side-chains 354 residues out of total 1941 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 314 time to evaluate : 2.010 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Q residue 61 ILE 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 609 THR Chi-restraints excluded: chain Q residue 727 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 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 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 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 46 ARG Chi-restraints excluded: chain B residue 86 THR Chi-restraints excluded: chain B residue 135 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 206 optimal weight: 0.6980 chunk 104 optimal weight: 1.9990 chunk 16 optimal weight: 0.9990 chunk 27 optimal weight: 0.3980 chunk 32 optimal weight: 0.9990 chunk 4 optimal weight: 0.9990 chunk 0 optimal weight: 1.9990 chunk 57 optimal weight: 1.9990 chunk 120 optimal weight: 0.8980 chunk 188 optimal weight: 0.9990 chunk 58 optimal weight: 0.8980 overall best weight: 0.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3244 r_free = 0.3244 target = 0.100874 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.2972 r_free = 0.2972 target = 0.085562 restraints weight = 29854.295| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.2967 r_free = 0.2967 target = 0.085333 restraints weight = 30315.059| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.2967 r_free = 0.2967 target = 0.085375 restraints weight = 28337.658| |-----------------------------------------------------------------------------| r_work (final): 0.2938 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7297 moved from start: 0.2324 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.052 18587 Z= 0.206 Angle : 0.572 8.921 25206 Z= 0.300 Chirality : 0.045 0.300 2826 Planarity : 0.004 0.047 3170 Dihedral : 6.473 65.812 2816 Min Nonbonded Distance : 2.329 Molprobity Statistics. All-atom Clashscore : 5.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.51 % Favored : 96.49 % Rotamer: Outliers : 2.32 % Allowed : 13.40 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.28 (0.18), residues: 2223 helix: 1.44 (0.17), residues: 934 sheet: -0.56 (0.26), residues: 374 loop : -0.76 (0.20), residues: 915 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP R 719 HIS 0.004 0.001 HIS A 213 PHE 0.017 0.002 PHE Q 806 TYR 0.019 0.002 TYR B 145 ARG 0.007 0.001 ARG G 27 Details of bonding type rmsd link_NAG-ASN : bond 0.00210 ( 8) link_NAG-ASN : angle 1.98003 ( 24) link_BETA1-4 : bond 0.00340 ( 4) link_BETA1-4 : angle 1.57085 ( 12) hydrogen bonds : bond 0.05590 ( 875) hydrogen bonds : angle 4.39624 ( 2505) SS BOND : bond 0.00218 ( 17) SS BOND : angle 0.98346 ( 34) covalent geometry : bond 0.00500 (18558) covalent geometry : angle 0.56685 (25136) Origin is already at (0, 0, 0), no shifts will be applied Model does not fit in PDB format. =============================================================================== Job complete usr+sys time: 5928.38 seconds wall clock time: 103 minutes 2.29 seconds (6182.29 seconds total)