Starting phenix.real_space_refine on Wed Jan 22 07:00:33 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9avl_43908/01_2025/9avl_43908.cif Found real_map, /net/cci-nas-00/data/ceres_data/9avl_43908/01_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_43908/01_2025/9avl_43908.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9avl_43908/01_2025/9avl_43908.map" model { file = "/net/cci-nas-00/data/ceres_data/9avl_43908/01_2025/9avl_43908.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9avl_43908/01_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-5571/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: 10.21, per 1000 atoms: 0.56 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: 5.23 Conformation dependent library (CDL) restraints added in 2.6 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: 1.96 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: 6.66 Time building geometry restraints manager: 5.90 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: 0.010 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 21.920 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.000 Check model and map are aligned: 0.000 Set scattering table: 0.000 Process input model: 43.430 Find NCS groups from input model: 0.730 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:3.010 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 69.210 ------------------------------------------------------------------------------- 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 18558 Z= 0.308 Angle : 0.667 11.842 25136 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 *********************** 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 : 2.151 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: 0.3608 time to fit residues: 202.3507 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 : 2.001 ------------------------------------------------------------------------------- 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: 1.9990 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: 0.5980 chunk 201 optimal weight: 0.9990 overall best weight: 0.3938 ------------------------------------------------------------------------------- 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 = 0.3290 r_free = 0.3290 target = 0.104326 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3007 r_free = 0.3007 target = 0.088138 restraints weight = 29428.223| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3015 r_free = 0.3015 target = 0.088684 restraints weight = 26789.252| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3021 r_free = 0.3021 target = 0.088955 restraints weight = 25155.951| |-----------------------------------------------------------------------------| r_work (final): 0.3010 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7245 moved from start: 0.1094 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 18558 Z= 0.209 Angle : 0.526 9.245 25136 Z= 0.280 Chirality : 0.043 0.263 2826 Planarity : 0.004 0.046 3170 Dihedral : 7.589 85.997 2816 Min Nonbonded Distance : 2.371 Molprobity Statistics. All-atom Clashscore : 4.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.79 % Favored : 97.21 % Rotamer: Outliers : 0.67 % Allowed : 6.65 % Favored : 92.68 % 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: 0.22 (0.17), residues: 2223 helix: 1.41 (0.17), residues: 940 sheet: -0.45 (0.26), residues: 369 loop : -0.89 (0.20), residues: 914 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP Q 818 HIS 0.003 0.001 HIS B 183 PHE 0.017 0.001 PHE Q 612 TYR 0.016 0.001 TYR B 59 ARG 0.004 0.000 ARG Q 638 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4446 Ramachandran restraints generated. 2223 Oldfield, 0 Emsley, 2223 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4446 Ramachandran restraints generated. 2223 Oldfield, 0 Emsley, 2223 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 353 residues out of total 1941 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 340 time to evaluate : 2.223 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: Q 176 ASN cc_start: 0.7957 (t0) cc_final: 0.7599 (t0) REVERT: Q 287 ASN cc_start: 0.7903 (t0) cc_final: 0.7664 (t0) REVERT: Q 697 VAL cc_start: 0.8031 (t) cc_final: 0.7681 (t) REVERT: Q 762 PHE cc_start: 0.7078 (m-80) cc_final: 0.6702 (m-80) REVERT: Q 811 MET cc_start: 0.7901 (mmp) cc_final: 0.7592 (mmp) REVERT: R 88 LEU cc_start: 0.7493 (mm) cc_final: 0.7266 (mm) REVERT: R 117 GLN cc_start: 0.7200 (tt0) cc_final: 0.6891 (tm-30) REVERT: R 253 GLN cc_start: 0.6503 (mp-120) cc_final: 0.6188 (mm-40) REVERT: R 736 ILE cc_start: 0.7620 (pt) cc_final: 0.7404 (pt) REVERT: R 795 ARG cc_start: 0.7437 (ptt-90) cc_final: 0.7117 (ptt-90) REVERT: A 277 LYS cc_start: 0.8084 (mtpt) cc_final: 0.7772 (mtpt) REVERT: B 37 LEU cc_start: 0.7023 (tt) cc_final: 0.6764 (tt) REVERT: B 237 ASN cc_start: 0.8489 (t0) cc_final: 0.8261 (t0) REVERT: G 21 MET cc_start: 0.6771 (mmm) cc_final: 0.6488 (tmm) outliers start: 13 outliers final: 9 residues processed: 349 average time/residue: 0.3694 time to fit residues: 185.0865 Evaluate side-chains 323 residues out of total 1941 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 314 time to evaluate : 1.965 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Q residue 422 LEU Chi-restraints excluded: chain R residue 113 SER Chi-restraints excluded: chain R residue 118 ASN Chi-restraints excluded: chain R residue 289 THR Chi-restraints excluded: chain R residue 409 ILE Chi-restraints excluded: chain R residue 640 THR Chi-restraints excluded: chain A residue 263 SER Chi-restraints excluded: chain B residue 74 SER Chi-restraints excluded: chain B residue 135 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 222 random chunks: chunk 4 optimal weight: 0.9980 chunk 177 optimal weight: 0.6980 chunk 91 optimal weight: 0.9990 chunk 72 optimal weight: 0.8980 chunk 141 optimal weight: 0.8980 chunk 200 optimal weight: 0.7980 chunk 80 optimal weight: 1.9990 chunk 194 optimal weight: 0.0980 chunk 49 optimal weight: 2.9990 chunk 53 optimal weight: 1.9990 chunk 216 optimal weight: 0.8980 overall best weight: 0.6780 ------------------------------------------------------------------------------- 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 = 0.3262 r_free = 0.3262 target = 0.102221 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2973 r_free = 0.2973 target = 0.086037 restraints weight = 29470.626| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.2977 r_free = 0.2977 target = 0.086269 restraints weight = 26877.432| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.2982 r_free = 0.2982 target = 0.086539 restraints weight = 26174.284| |-----------------------------------------------------------------------------| r_work (final): 0.2978 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7287 moved from start: 0.1532 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 18558 Z= 0.290 Angle : 0.551 9.641 25136 Z= 0.290 Chirality : 0.045 0.243 2826 Planarity : 0.004 0.046 3170 Dihedral : 7.295 82.844 2816 Min Nonbonded Distance : 2.329 Molprobity Statistics. All-atom Clashscore : 5.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.10 % Favored : 96.90 % Rotamer: Outliers : 1.44 % Allowed : 9.17 % Favored : 89.39 % 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: 0.20 (0.17), residues: 2223 helix: 1.42 (0.17), residues: 940 sheet: -0.53 (0.26), residues: 362 loop : -0.91 (0.19), residues: 921 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP R 719 HIS 0.006 0.001 HIS R 463 PHE 0.021 0.002 PHE Q 634 TYR 0.016 0.002 TYR A 354 ARG 0.003 0.000 ARG Q 415 *********************** 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 365 residues out of total 1941 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 337 time to evaluate : 2.066 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: Q 287 ASN cc_start: 0.7870 (t0) cc_final: 0.7652 (t0) REVERT: Q 762 PHE cc_start: 0.7023 (m-80) cc_final: 0.6647 (m-80) REVERT: R 88 LEU cc_start: 0.7622 (mm) cc_final: 0.7419 (mm) REVERT: R 117 GLN cc_start: 0.7185 (tt0) cc_final: 0.6892 (tm-30) REVERT: R 253 GLN cc_start: 0.6551 (mp-120) cc_final: 0.6247 (mp10) REVERT: R 589 PHE cc_start: 0.7294 (m-80) cc_final: 0.6929 (m-80) REVERT: R 795 ARG cc_start: 0.7446 (ptt-90) cc_final: 0.7043 (ptt-90) REVERT: A 207 GLU cc_start: 0.6624 (tt0) cc_final: 0.6308 (tt0) REVERT: B 37 LEU cc_start: 0.7104 (tt) cc_final: 0.6810 (tt) REVERT: B 237 ASN cc_start: 0.8501 (t0) cc_final: 0.8238 (t0) outliers start: 28 outliers final: 21 residues processed: 349 average time/residue: 0.3802 time to fit residues: 193.0395 Evaluate side-chains 337 residues out of total 1941 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 316 time to evaluate : 1.975 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Q residue 92 THR Chi-restraints excluded: chain Q residue 159 LEU Chi-restraints excluded: chain Q residue 516 LYS Chi-restraints excluded: chain Q residue 529 LEU Chi-restraints excluded: chain Q residue 554 ILE Chi-restraints excluded: chain Q residue 560 THR Chi-restraints excluded: chain Q residue 793 LYS Chi-restraints excluded: chain R residue 113 SER Chi-restraints excluded: chain R residue 118 ASN Chi-restraints excluded: chain R residue 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 625 PHE 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 A residue 273 LEU Chi-restraints excluded: chain B residue 46 ARG Chi-restraints excluded: chain B residue 74 SER Chi-restraints excluded: chain B residue 135 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 222 random chunks: chunk 193 optimal weight: 0.9990 chunk 17 optimal weight: 0.9980 chunk 5 optimal weight: 1.9990 chunk 72 optimal weight: 0.9990 chunk 124 optimal weight: 0.0470 chunk 195 optimal weight: 0.5980 chunk 219 optimal weight: 0.2980 chunk 144 optimal weight: 0.8980 chunk 34 optimal weight: 0.5980 chunk 104 optimal weight: 0.9990 chunk 91 optimal weight: 0.8980 overall best weight: 0.4878 ------------------------------------------------------------------------------- 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 = 0.3265 r_free = 0.3265 target = 0.102151 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3009 r_free = 0.3009 target = 0.087552 restraints weight = 29742.890| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3003 r_free = 0.3003 target = 0.087280 restraints weight = 33408.566| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3005 r_free = 0.3005 target = 0.087407 restraints weight = 30858.527| |-----------------------------------------------------------------------------| r_work (final): 0.2973 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7248 moved from start: 0.1721 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 18558 Z= 0.223 Angle : 0.507 9.405 25136 Z= 0.268 Chirality : 0.043 0.263 2826 Planarity : 0.004 0.045 3170 Dihedral : 6.836 75.007 2816 Min Nonbonded Distance : 2.351 Molprobity Statistics. All-atom Clashscore : 5.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.06 % Favored : 96.94 % Rotamer: Outliers : 1.70 % Allowed : 10.51 % Favored : 87.79 % 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: 0.30 (0.17), residues: 2223 helix: 1.54 (0.17), residues: 940 sheet: -0.48 (0.26), residues: 362 loop : -0.90 (0.19), residues: 921 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP R 719 HIS 0.004 0.001 HIS R 463 PHE 0.014 0.001 PHE Q 806 TYR 0.016 0.001 TYR B 145 ARG 0.003 0.000 ARG Q 227 *********************** 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 361 residues out of total 1941 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 328 time to evaluate : 2.033 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: Q 270 PHE cc_start: 0.7328 (OUTLIER) cc_final: 0.6935 (m-80) REVERT: Q 286 ARG cc_start: 0.7826 (mtp85) cc_final: 0.7624 (mtp85) REVERT: Q 354 GLU cc_start: 0.6563 (mm-30) cc_final: 0.6134 (mm-30) REVERT: Q 762 PHE cc_start: 0.7007 (m-80) cc_final: 0.6619 (m-80) REVERT: Q 767 GLU cc_start: 0.6593 (mm-30) cc_final: 0.6314 (mm-30) REVERT: R 117 GLN cc_start: 0.7211 (tt0) cc_final: 0.6902 (tm-30) REVERT: R 253 GLN cc_start: 0.6542 (OUTLIER) cc_final: 0.6179 (mp10) REVERT: R 795 ARG cc_start: 0.7424 (ptt-90) cc_final: 0.7023 (ptt-90) REVERT: A 207 GLU cc_start: 0.6595 (tt0) cc_final: 0.6347 (tt0) REVERT: B 37 LEU cc_start: 0.7079 (OUTLIER) cc_final: 0.6780 (tt) REVERT: B 195 ASP cc_start: 0.7828 (p0) cc_final: 0.7609 (p0) REVERT: B 234 PHE cc_start: 0.8199 (OUTLIER) cc_final: 0.7424 (t80) REVERT: B 237 ASN cc_start: 0.8437 (t0) cc_final: 0.8192 (t0) outliers start: 33 outliers final: 21 residues processed: 348 average time/residue: 0.3790 time to fit residues: 188.4419 Evaluate side-chains 348 residues out of total 1941 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 323 time to evaluate : 2.028 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Q residue 92 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 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 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 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 263 SER Chi-restraints excluded: chain A residue 273 LEU Chi-restraints excluded: chain B residue 37 LEU Chi-restraints excluded: chain B residue 46 ARG Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 234 PHE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 222 random chunks: chunk 164 optimal weight: 0.8980 chunk 124 optimal weight: 0.2980 chunk 24 optimal weight: 0.5980 chunk 88 optimal weight: 1.9990 chunk 193 optimal weight: 0.9980 chunk 79 optimal weight: 0.4980 chunk 196 optimal weight: 1.9990 chunk 163 optimal weight: 0.6980 chunk 76 optimal weight: 0.9990 chunk 16 optimal weight: 0.9980 chunk 98 optimal weight: 0.9990 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3265 r_free = 0.3265 target = 0.102105 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2981 r_free = 0.2981 target = 0.085998 restraints weight = 29793.610| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.2983 r_free = 0.2983 target = 0.086165 restraints weight = 29343.106| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.2985 r_free = 0.2985 target = 0.086320 restraints weight = 27026.264| |-----------------------------------------------------------------------------| r_work (final): 0.2943 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7284 moved from start: 0.1885 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 18558 Z= 0.261 Angle : 0.526 9.318 25136 Z= 0.277 Chirality : 0.044 0.246 2826 Planarity : 0.004 0.045 3170 Dihedral : 6.618 64.929 2816 Min Nonbonded Distance : 2.337 Molprobity Statistics. All-atom Clashscore : 5.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.10 % Favored : 96.90 % Rotamer: Outliers : 2.11 % Allowed : 11.49 % 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: 0.31 (0.17), residues: 2223 helix: 1.53 (0.17), residues: 941 sheet: -0.50 (0.26), residues: 362 loop : -0.85 (0.20), residues: 920 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 0.016 0.002 PHE Q 634 TYR 0.020 0.002 TYR A 290 ARG 0.007 0.000 ARG G 27 *********************** 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 376 residues out of total 1941 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 335 time to evaluate : 2.133 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: Q 270 PHE cc_start: 0.7327 (OUTLIER) cc_final: 0.6910 (m-80) REVERT: Q 286 ARG cc_start: 0.7822 (mtp85) cc_final: 0.7600 (mtp85) REVERT: Q 354 GLU cc_start: 0.6576 (mm-30) cc_final: 0.6181 (mm-30) REVERT: Q 454 LYS cc_start: 0.8027 (mttt) cc_final: 0.7682 (mmmm) REVERT: Q 762 PHE cc_start: 0.7088 (m-80) cc_final: 0.6675 (m-80) REVERT: Q 767 GLU cc_start: 0.6619 (mm-30) cc_final: 0.6340 (mm-30) REVERT: R 117 GLN cc_start: 0.7183 (tt0) cc_final: 0.6868 (tm-30) REVERT: R 253 GLN cc_start: 0.6547 (OUTLIER) cc_final: 0.6182 (mp10) REVERT: R 577 THR cc_start: 0.7768 (m) cc_final: 0.7407 (t) REVERT: R 776 LEU cc_start: 0.7277 (OUTLIER) cc_final: 0.6834 (mp) REVERT: R 795 ARG cc_start: 0.7429 (ptt-90) cc_final: 0.7014 (ptt-90) REVERT: A 207 GLU cc_start: 0.6630 (tt0) cc_final: 0.6384 (tt0) REVERT: B 37 LEU cc_start: 0.7126 (OUTLIER) cc_final: 0.6860 (tt) REVERT: B 195 ASP cc_start: 0.7890 (p0) cc_final: 0.7685 (p0) REVERT: B 234 PHE cc_start: 0.8245 (OUTLIER) cc_final: 0.7512 (t80) REVERT: B 237 ASN cc_start: 0.8465 (t0) cc_final: 0.8216 (t0) outliers start: 41 outliers final: 30 residues processed: 359 average time/residue: 0.3734 time to fit residues: 195.6237 Evaluate side-chains 352 residues out of total 1941 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 317 time to evaluate : 2.147 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Q residue 263 THR Chi-restraints excluded: chain Q residue 270 PHE Chi-restraints excluded: chain Q residue 307 MET Chi-restraints excluded: chain Q residue 452 ILE Chi-restraints excluded: chain Q residue 516 LYS Chi-restraints excluded: chain Q residue 529 LEU Chi-restraints excluded: chain Q residue 554 ILE Chi-restraints excluded: chain Q residue 560 THR Chi-restraints excluded: chain Q residue 609 THR Chi-restraints excluded: chain Q residue 734 MET Chi-restraints excluded: chain Q residue 793 LYS Chi-restraints excluded: chain R residue 113 SER Chi-restraints excluded: chain R residue 118 ASN Chi-restraints excluded: chain R residue 253 GLN Chi-restraints excluded: chain R residue 270 PHE Chi-restraints excluded: chain R residue 289 THR Chi-restraints excluded: chain R residue 322 LEU Chi-restraints excluded: chain R residue 404 VAL Chi-restraints excluded: chain R residue 409 ILE Chi-restraints excluded: chain R residue 504 VAL Chi-restraints excluded: chain R residue 506 LYS Chi-restraints excluded: chain R residue 625 PHE Chi-restraints excluded: chain R residue 640 THR Chi-restraints excluded: chain R residue 737 VAL Chi-restraints excluded: chain R residue 776 LEU Chi-restraints excluded: chain A residue 50 VAL Chi-restraints excluded: chain A residue 263 SER Chi-restraints excluded: chain A residue 273 LEU Chi-restraints excluded: chain A residue 276 GLU Chi-restraints excluded: chain B residue 37 LEU Chi-restraints excluded: chain B residue 46 ARG Chi-restraints excluded: chain B residue 74 SER Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain G residue 25 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 222 random chunks: chunk 217 optimal weight: 7.9990 chunk 82 optimal weight: 0.8980 chunk 164 optimal weight: 0.0980 chunk 135 optimal weight: 1.9990 chunk 110 optimal weight: 0.8980 chunk 61 optimal weight: 1.9990 chunk 94 optimal weight: 0.9990 chunk 21 optimal weight: 0.2980 chunk 72 optimal weight: 0.5980 chunk 73 optimal weight: 0.9990 chunk 216 optimal weight: 2.9990 overall best weight: 0.5580 ------------------------------------------------------------------------------- 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 = 0.3264 r_free = 0.3264 target = 0.102002 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2981 r_free = 0.2981 target = 0.085843 restraints weight = 29698.220| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.2980 r_free = 0.2980 target = 0.085870 restraints weight = 31612.297| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.2983 r_free = 0.2983 target = 0.086066 restraints weight = 28501.785| |-----------------------------------------------------------------------------| r_work (final): 0.2975 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7283 moved from start: 0.1993 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 18558 Z= 0.245 Angle : 0.516 9.234 25136 Z= 0.272 Chirality : 0.043 0.271 2826 Planarity : 0.004 0.046 3170 Dihedral : 6.436 57.281 2816 Min Nonbonded Distance : 2.344 Molprobity Statistics. All-atom Clashscore : 4.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.06 % Favored : 96.94 % Rotamer: Outliers : 2.32 % Allowed : 11.80 % Favored : 85.88 % 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: 0.37 (0.18), residues: 2223 helix: 1.57 (0.17), residues: 940 sheet: -0.47 (0.26), residues: 376 loop : -0.79 (0.20), residues: 907 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP R 719 HIS 0.004 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 *********************** 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 369 residues out of total 1941 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 324 time to evaluate : 1.945 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: Q 270 PHE cc_start: 0.7323 (OUTLIER) cc_final: 0.6881 (m-80) REVERT: Q 292 ILE cc_start: 0.7838 (mm) cc_final: 0.7418 (mp) REVERT: Q 354 GLU cc_start: 0.6582 (mm-30) cc_final: 0.6174 (mm-30) REVERT: Q 762 PHE cc_start: 0.7074 (m-80) cc_final: 0.6671 (m-80) REVERT: Q 767 GLU cc_start: 0.6607 (mm-30) cc_final: 0.6323 (mm-30) REVERT: R 117 GLN cc_start: 0.7190 (tt0) cc_final: 0.6851 (tm-30) REVERT: R 253 GLN cc_start: 0.6556 (OUTLIER) cc_final: 0.6180 (mp10) REVERT: R 795 ARG cc_start: 0.7435 (ptt-90) cc_final: 0.7009 (ptt-90) REVERT: A 207 GLU cc_start: 0.6632 (tt0) cc_final: 0.6395 (tt0) REVERT: B 37 LEU cc_start: 0.7130 (OUTLIER) cc_final: 0.6868 (tt) REVERT: B 234 PHE cc_start: 0.8254 (OUTLIER) cc_final: 0.7528 (t80) REVERT: B 237 ASN cc_start: 0.8438 (t0) cc_final: 0.8200 (t0) outliers start: 45 outliers final: 33 residues processed: 351 average time/residue: 0.3665 time to fit residues: 185.6377 Evaluate side-chains 358 residues out of total 1941 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 321 time to evaluate : 1.940 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Q residue 263 THR Chi-restraints excluded: chain Q residue 270 PHE Chi-restraints excluded: chain Q residue 307 MET 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 793 LYS Chi-restraints excluded: chain R residue 113 SER Chi-restraints excluded: chain R residue 118 ASN 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 504 VAL Chi-restraints excluded: chain R residue 506 LYS Chi-restraints excluded: chain R residue 625 PHE Chi-restraints excluded: chain R residue 640 THR Chi-restraints excluded: chain R residue 737 VAL Chi-restraints excluded: chain A residue 240 MET Chi-restraints excluded: chain A residue 263 SER Chi-restraints excluded: chain A residue 273 LEU Chi-restraints excluded: chain A residue 276 GLU Chi-restraints excluded: chain A residue 316 THR Chi-restraints excluded: chain B residue 37 LEU Chi-restraints excluded: chain B residue 46 ARG Chi-restraints excluded: chain B residue 74 SER Chi-restraints excluded: chain B residue 86 THR Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 274 THR Chi-restraints excluded: chain B residue 318 LEU Chi-restraints excluded: chain G residue 25 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 222 random chunks: chunk 189 optimal weight: 0.9980 chunk 2 optimal weight: 1.9990 chunk 126 optimal weight: 0.8980 chunk 142 optimal weight: 0.5980 chunk 188 optimal weight: 0.8980 chunk 21 optimal weight: 0.7980 chunk 167 optimal weight: 0.2980 chunk 212 optimal weight: 0.9990 chunk 127 optimal weight: 0.6980 chunk 190 optimal weight: 0.5980 chunk 86 optimal weight: 0.5980 overall best weight: 0.5580 ------------------------------------------------------------------------------- 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 = 0.3260 r_free = 0.3260 target = 0.101855 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2992 r_free = 0.2992 target = 0.086629 restraints weight = 29685.596| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.2989 r_free = 0.2989 target = 0.086472 restraints weight = 25934.898| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.2989 r_free = 0.2989 target = 0.086515 restraints weight = 24744.136| |-----------------------------------------------------------------------------| r_work (final): 0.2956 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7275 moved from start: 0.2099 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 18558 Z= 0.247 Angle : 0.520 9.058 25136 Z= 0.275 Chirality : 0.044 0.301 2826 Planarity : 0.004 0.046 3170 Dihedral : 6.366 59.640 2816 Min Nonbonded Distance : 2.338 Molprobity Statistics. All-atom Clashscore : 5.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.06 % Favored : 96.94 % Rotamer: Outliers : 2.52 % Allowed : 12.21 % Favored : 85.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.09 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 0.41 (0.18), residues: 2223 helix: 1.56 (0.17), residues: 941 sheet: -0.48 (0.26), residues: 376 loop : -0.71 (0.20), residues: 906 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP R 719 HIS 0.003 0.001 HIS B 183 PHE 0.014 0.001 PHE Q 806 TYR 0.018 0.001 TYR B 145 ARG 0.005 0.000 ARG G 27 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4446 Ramachandran restraints generated. 2223 Oldfield, 0 Emsley, 2223 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4446 Ramachandran restraints generated. 2223 Oldfield, 0 Emsley, 2223 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 376 residues out of total 1941 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 327 time to evaluate : 2.108 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: Q 270 PHE cc_start: 0.7319 (OUTLIER) cc_final: 0.6901 (m-80) REVERT: Q 292 ILE cc_start: 0.7871 (mm) cc_final: 0.7460 (mp) REVERT: Q 354 GLU cc_start: 0.6609 (mm-30) cc_final: 0.6210 (mm-30) REVERT: Q 476 GLN cc_start: 0.7871 (mm-40) cc_final: 0.7263 (mm-40) REVERT: Q 762 PHE cc_start: 0.7084 (m-80) cc_final: 0.6675 (m-80) REVERT: Q 767 GLU cc_start: 0.6596 (mm-30) cc_final: 0.6323 (mm-30) REVERT: R 117 GLN cc_start: 0.7168 (tt0) cc_final: 0.6846 (tm-30) REVERT: R 253 GLN cc_start: 0.6557 (OUTLIER) cc_final: 0.6210 (mp10) REVERT: R 577 THR cc_start: 0.7813 (OUTLIER) cc_final: 0.7475 (t) REVERT: R 679 LEU cc_start: 0.8055 (mt) cc_final: 0.7660 (mt) REVERT: R 776 LEU cc_start: 0.7254 (OUTLIER) cc_final: 0.6801 (mp) REVERT: R 795 ARG cc_start: 0.7421 (ptt-90) cc_final: 0.6993 (ptt-90) REVERT: R 825 TYR cc_start: 0.7456 (t80) cc_final: 0.7253 (t80) REVERT: B 37 LEU cc_start: 0.7120 (OUTLIER) cc_final: 0.6864 (tt) REVERT: B 195 ASP cc_start: 0.7824 (p0) cc_final: 0.7521 (p0) REVERT: B 234 PHE cc_start: 0.8273 (OUTLIER) cc_final: 0.7539 (t80) REVERT: B 237 ASN cc_start: 0.8426 (t0) cc_final: 0.8190 (t0) outliers start: 49 outliers final: 37 residues processed: 356 average time/residue: 0.3558 time to fit residues: 183.7571 Evaluate side-chains 357 residues out of total 1941 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 314 time to evaluate : 2.216 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Q residue 263 THR Chi-restraints excluded: chain Q residue 270 PHE Chi-restraints excluded: chain Q residue 307 MET 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 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 504 VAL Chi-restraints excluded: chain R residue 506 LYS Chi-restraints excluded: chain R residue 577 THR Chi-restraints excluded: chain R residue 625 PHE Chi-restraints excluded: chain R residue 640 THR Chi-restraints excluded: chain R residue 730 LEU Chi-restraints excluded: chain R residue 737 VAL Chi-restraints excluded: chain R residue 776 LEU Chi-restraints excluded: chain R residue 869 ILE Chi-restraints excluded: chain A residue 50 VAL Chi-restraints excluded: chain A residue 240 MET Chi-restraints excluded: chain A residue 263 SER Chi-restraints excluded: chain A residue 273 LEU Chi-restraints excluded: chain A residue 276 GLU Chi-restraints excluded: chain A residue 316 THR Chi-restraints excluded: chain B residue 31 THR Chi-restraints excluded: chain B residue 37 LEU Chi-restraints excluded: chain B residue 46 ARG Chi-restraints excluded: chain B residue 74 SER Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 222 random chunks: chunk 36 optimal weight: 0.9980 chunk 181 optimal weight: 1.9990 chunk 21 optimal weight: 1.9990 chunk 38 optimal weight: 0.7980 chunk 15 optimal weight: 0.9990 chunk 0 optimal weight: 1.9990 chunk 97 optimal weight: 0.8980 chunk 202 optimal weight: 1.9990 chunk 121 optimal weight: 0.0010 chunk 99 optimal weight: 0.6980 chunk 49 optimal weight: 1.9990 overall best weight: 0.6786 ------------------------------------------------------------------------------- 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 = 0.101926 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2975 r_free = 0.2975 target = 0.085962 restraints weight = 29632.945| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.2972 r_free = 0.2972 target = 0.085842 restraints weight = 29390.263| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.2972 r_free = 0.2972 target = 0.085862 restraints weight = 28202.119| |-----------------------------------------------------------------------------| r_work (final): 0.2968 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7298 moved from start: 0.2167 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 18558 Z= 0.289 Angle : 0.540 9.284 25136 Z= 0.284 Chirality : 0.044 0.346 2826 Planarity : 0.004 0.046 3170 Dihedral : 6.411 58.873 2816 Min Nonbonded Distance : 2.331 Molprobity Statistics. All-atom Clashscore : 5.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.15 % Favored : 96.85 % Rotamer: Outliers : 2.63 % Allowed : 12.06 % Favored : 85.32 % 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: 0.35 (0.18), residues: 2223 helix: 1.49 (0.17), residues: 941 sheet: -0.53 (0.26), residues: 376 loop : -0.70 (0.20), residues: 906 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP R 719 HIS 0.004 0.001 HIS A 213 PHE 0.016 0.002 PHE Q 806 TYR 0.018 0.001 TYR B 145 ARG 0.005 0.000 ARG Q 233 *********************** 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 377 residues out of total 1941 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 326 time to evaluate : 2.015 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: Q 270 PHE cc_start: 0.7306 (OUTLIER) cc_final: 0.6884 (m-80) REVERT: Q 292 ILE cc_start: 0.7864 (mm) cc_final: 0.7447 (mp) REVERT: Q 354 GLU cc_start: 0.6599 (mm-30) cc_final: 0.6202 (mm-30) REVERT: Q 476 GLN cc_start: 0.7864 (mm-40) cc_final: 0.7256 (mm-40) REVERT: Q 767 GLU cc_start: 0.6619 (mm-30) cc_final: 0.6356 (mm-30) REVERT: R 253 GLN cc_start: 0.6616 (OUTLIER) cc_final: 0.6224 (mp10) REVERT: R 577 THR cc_start: 0.7831 (OUTLIER) cc_final: 0.7506 (t) REVERT: R 776 LEU cc_start: 0.7262 (OUTLIER) cc_final: 0.6824 (mp) REVERT: R 795 ARG cc_start: 0.7438 (ptt-90) cc_final: 0.6982 (ptt-90) REVERT: R 825 TYR cc_start: 0.7466 (t80) cc_final: 0.7261 (t80) REVERT: B 37 LEU cc_start: 0.7159 (OUTLIER) cc_final: 0.6888 (tt) REVERT: B 195 ASP cc_start: 0.7932 (p0) cc_final: 0.7593 (p0) REVERT: B 234 PHE cc_start: 0.8289 (OUTLIER) cc_final: 0.7577 (t80) REVERT: B 237 ASN cc_start: 0.8434 (t0) cc_final: 0.8168 (t0) outliers start: 51 outliers final: 41 residues processed: 355 average time/residue: 0.3513 time to fit residues: 180.9455 Evaluate side-chains 368 residues out of total 1941 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 321 time to evaluate : 1.978 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Q residue 61 ILE Chi-restraints excluded: chain Q residue 263 THR Chi-restraints excluded: chain Q residue 270 PHE Chi-restraints excluded: chain Q residue 307 MET 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 697 VAL 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 253 GLN Chi-restraints excluded: chain R residue 270 PHE Chi-restraints excluded: chain R residue 289 THR Chi-restraints excluded: chain R residue 322 LEU Chi-restraints excluded: chain R residue 404 VAL Chi-restraints excluded: chain R residue 409 ILE Chi-restraints excluded: chain R residue 410 ASP Chi-restraints excluded: chain R residue 434 ILE Chi-restraints excluded: chain R residue 504 VAL Chi-restraints excluded: chain R residue 506 LYS Chi-restraints excluded: chain R residue 577 THR Chi-restraints excluded: chain R residue 585 CYS Chi-restraints excluded: chain R residue 625 PHE Chi-restraints excluded: chain R residue 640 THR Chi-restraints excluded: chain R residue 730 LEU Chi-restraints excluded: chain R residue 737 VAL Chi-restraints excluded: chain R residue 776 LEU Chi-restraints excluded: chain A residue 50 VAL Chi-restraints excluded: chain A residue 240 MET Chi-restraints excluded: chain A residue 263 SER Chi-restraints excluded: chain A residue 273 LEU Chi-restraints excluded: chain A residue 276 GLU Chi-restraints excluded: chain A residue 316 THR Chi-restraints excluded: chain B residue 37 LEU Chi-restraints excluded: chain B residue 46 ARG Chi-restraints excluded: chain B residue 74 SER Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 222 random chunks: chunk 37 optimal weight: 0.7980 chunk 108 optimal weight: 0.3980 chunk 162 optimal weight: 5.9990 chunk 219 optimal weight: 0.5980 chunk 182 optimal weight: 0.6980 chunk 5 optimal weight: 0.9980 chunk 11 optimal weight: 0.9990 chunk 195 optimal weight: 0.9990 chunk 73 optimal weight: 0.6980 chunk 10 optimal weight: 0.0060 chunk 206 optimal weight: 0.8980 overall best weight: 0.4796 ------------------------------------------------------------------------------- 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 = 0.101494 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2994 r_free = 0.2994 target = 0.086511 restraints weight = 29878.371| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.2986 r_free = 0.2986 target = 0.086134 restraints weight = 35106.459| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.2988 r_free = 0.2988 target = 0.086325 restraints weight = 35266.888| |-----------------------------------------------------------------------------| r_work (final): 0.2957 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7266 moved from start: 0.2229 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 18558 Z= 0.225 Angle : 0.516 8.864 25136 Z= 0.273 Chirality : 0.043 0.343 2826 Planarity : 0.004 0.046 3170 Dihedral : 6.301 59.885 2816 Min Nonbonded Distance : 2.346 Molprobity Statistics. All-atom Clashscore : 5.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.24 % Favored : 96.76 % Rotamer: Outliers : 2.58 % Allowed : 12.52 % Favored : 84.90 % 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: 0.45 (0.18), residues: 2223 helix: 1.56 (0.17), residues: 941 sheet: -0.46 (0.26), residues: 371 loop : -0.65 (0.20), residues: 911 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP R 719 HIS 0.007 0.001 HIS R 338 PHE 0.014 0.001 PHE Q 806 TYR 0.018 0.001 TYR B 145 ARG 0.005 0.000 ARG G 27 *********************** 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 374 residues out of total 1941 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 324 time to evaluate : 2.006 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: 0.6919 (m-80) REVERT: Q 292 ILE cc_start: 0.7862 (mm) cc_final: 0.7461 (mp) REVERT: Q 354 GLU cc_start: 0.6557 (mm-30) cc_final: 0.6169 (mm-30) REVERT: Q 762 PHE cc_start: 0.6931 (m-80) cc_final: 0.6623 (m-80) REVERT: Q 767 GLU cc_start: 0.6604 (mm-30) cc_final: 0.6350 (mm-30) REVERT: R 117 GLN cc_start: 0.7156 (tt0) cc_final: 0.6848 (tm-30) REVERT: R 253 GLN cc_start: 0.6628 (OUTLIER) cc_final: 0.6280 (mp10) REVERT: R 577 THR cc_start: 0.7784 (OUTLIER) cc_final: 0.7483 (t) REVERT: R 679 LEU cc_start: 0.8070 (mt) cc_final: 0.7674 (mt) REVERT: R 776 LEU cc_start: 0.7249 (OUTLIER) cc_final: 0.6788 (mp) REVERT: R 795 ARG cc_start: 0.7421 (ptt-90) cc_final: 0.7003 (ptt-90) REVERT: R 825 TYR cc_start: 0.7437 (t80) cc_final: 0.7233 (t80) REVERT: A 192 LYS cc_start: 0.7753 (mtmt) cc_final: 0.7365 (mtmt) REVERT: A 277 LYS cc_start: 0.7946 (mtpt) cc_final: 0.7735 (mtmt) REVERT: B 37 LEU cc_start: 0.7125 (OUTLIER) cc_final: 0.6850 (tt) REVERT: B 195 ASP cc_start: 0.7932 (p0) cc_final: 0.7599 (p0) REVERT: B 234 PHE cc_start: 0.8274 (OUTLIER) cc_final: 0.7563 (t80) REVERT: B 237 ASN cc_start: 0.8405 (t0) cc_final: 0.8158 (t0) outliers start: 50 outliers final: 38 residues processed: 352 average time/residue: 0.3488 time to fit residues: 177.7641 Evaluate side-chains 364 residues out of total 1941 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 320 time to evaluate : 2.030 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Q residue 123 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 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 253 GLN Chi-restraints excluded: chain R residue 270 PHE Chi-restraints excluded: chain R residue 289 THR Chi-restraints excluded: chain R residue 322 LEU Chi-restraints excluded: chain R residue 404 VAL Chi-restraints excluded: chain R residue 409 ILE Chi-restraints excluded: chain R residue 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 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 273 LEU Chi-restraints excluded: chain A residue 276 GLU Chi-restraints excluded: chain A residue 316 THR Chi-restraints excluded: chain B residue 31 THR Chi-restraints excluded: chain B residue 37 LEU Chi-restraints excluded: chain B residue 46 ARG Chi-restraints excluded: chain B residue 74 SER Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 213 VAL Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 274 THR Chi-restraints excluded: chain B residue 318 LEU Chi-restraints excluded: chain G residue 25 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 222 random chunks: chunk 95 optimal weight: 0.9980 chunk 76 optimal weight: 0.7980 chunk 34 optimal weight: 0.9980 chunk 58 optimal weight: 0.3980 chunk 32 optimal weight: 0.5980 chunk 123 optimal weight: 1.9990 chunk 144 optimal weight: 0.9980 chunk 143 optimal weight: 0.5980 chunk 203 optimal weight: 0.7980 chunk 39 optimal weight: 2.9990 chunk 128 optimal weight: 0.2980 overall best weight: 0.5380 ------------------------------------------------------------------------------- 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 = 0.3247 r_free = 0.3247 target = 0.100518 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2990 r_free = 0.2990 target = 0.085992 restraints weight = 29808.923| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.2987 r_free = 0.2987 target = 0.085842 restraints weight = 30196.952| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.2986 r_free = 0.2986 target = 0.085806 restraints weight = 29509.525| |-----------------------------------------------------------------------------| r_work (final): 0.2959 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7262 moved from start: 0.2274 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 18558 Z= 0.244 Angle : 0.524 8.881 25136 Z= 0.277 Chirality : 0.044 0.316 2826 Planarity : 0.004 0.046 3170 Dihedral : 6.282 60.619 2816 Min Nonbonded Distance : 2.345 Molprobity Statistics. All-atom Clashscore : 5.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.06 % Favored : 96.94 % Rotamer: Outliers : 2.47 % Allowed : 12.78 % Favored : 84.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.09 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.44 (0.18), residues: 2223 helix: 1.54 (0.17), residues: 941 sheet: -0.46 (0.26), residues: 371 loop : -0.65 (0.21), residues: 911 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP R 719 HIS 0.007 0.001 HIS R 338 PHE 0.014 0.001 PHE Q 806 TYR 0.018 0.001 TYR B 145 ARG 0.005 0.000 ARG Q 227 ********************** 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 369 residues out of total 1941 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 321 time to evaluate : 1.966 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: Q 270 PHE cc_start: 0.7324 (OUTLIER) cc_final: 0.6919 (m-80) REVERT: Q 292 ILE cc_start: 0.7864 (mm) cc_final: 0.7439 (mp) REVERT: Q 354 GLU cc_start: 0.6562 (mm-30) cc_final: 0.6180 (mm-30) REVERT: Q 454 LYS cc_start: 0.8056 (mmtp) cc_final: 0.7539 (mmmm) REVERT: Q 762 PHE cc_start: 0.6951 (m-80) cc_final: 0.6659 (m-80) REVERT: R 117 GLN cc_start: 0.7169 (tt0) cc_final: 0.6831 (tm-30) REVERT: R 253 GLN cc_start: 0.6631 (OUTLIER) cc_final: 0.6239 (mp10) REVERT: R 577 THR cc_start: 0.7779 (OUTLIER) cc_final: 0.7481 (t) REVERT: R 679 LEU cc_start: 0.8067 (mt) cc_final: 0.7667 (mt) REVERT: R 776 LEU cc_start: 0.7260 (OUTLIER) cc_final: 0.6801 (mp) REVERT: R 795 ARG cc_start: 0.7431 (ptt-90) cc_final: 0.7000 (ptt-90) REVERT: A 192 LYS cc_start: 0.7741 (mtmt) cc_final: 0.7463 (mtmt) REVERT: B 37 LEU cc_start: 0.7129 (OUTLIER) cc_final: 0.6851 (tt) REVERT: B 195 ASP cc_start: 0.8015 (p0) cc_final: 0.7696 (p0) REVERT: B 234 PHE cc_start: 0.8285 (OUTLIER) cc_final: 0.7569 (t80) REVERT: B 237 ASN cc_start: 0.8420 (t0) cc_final: 0.8156 (t0) REVERT: B 273 ILE cc_start: 0.8140 (OUTLIER) cc_final: 0.7807 (mp) outliers start: 48 outliers final: 40 residues processed: 349 average time/residue: 0.3558 time to fit residues: 179.2796 Evaluate side-chains 363 residues out of total 1941 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 316 time to evaluate : 2.059 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Q residue 61 ILE Chi-restraints excluded: chain Q residue 263 THR Chi-restraints excluded: chain Q residue 270 PHE Chi-restraints excluded: chain Q residue 307 MET 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 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 253 GLN Chi-restraints excluded: chain R residue 270 PHE Chi-restraints excluded: chain R residue 289 THR Chi-restraints excluded: chain R residue 322 LEU Chi-restraints excluded: chain R residue 404 VAL Chi-restraints excluded: chain R residue 409 ILE Chi-restraints excluded: chain R residue 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 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 273 LEU Chi-restraints excluded: chain A residue 276 GLU Chi-restraints excluded: chain A residue 298 GLU Chi-restraints excluded: chain A residue 316 THR Chi-restraints excluded: chain B residue 31 THR Chi-restraints excluded: chain B residue 37 LEU Chi-restraints excluded: chain B residue 46 ARG Chi-restraints excluded: chain B residue 74 SER Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 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 42 GLU 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: 0.0670 chunk 32 optimal weight: 1.9990 chunk 4 optimal weight: 0.7980 chunk 0 optimal weight: 1.9990 chunk 57 optimal weight: 0.9980 chunk 120 optimal weight: 1.9990 chunk 188 optimal weight: 0.9980 chunk 58 optimal weight: 0.3980 overall best weight: 0.5918 ------------------------------------------------------------------------------- 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 = 0.3255 r_free = 0.3255 target = 0.101357 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.2981 r_free = 0.2981 target = 0.085785 restraints weight = 29792.175| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.2975 r_free = 0.2975 target = 0.085512 restraints weight = 32768.432| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.2976 r_free = 0.2976 target = 0.085635 restraints weight = 30298.778| |-----------------------------------------------------------------------------| r_work (final): 0.2945 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7286 moved from start: 0.2302 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 18558 Z= 0.262 Angle : 0.530 8.881 25136 Z= 0.280 Chirality : 0.044 0.299 2826 Planarity : 0.004 0.046 3170 Dihedral : 6.297 60.760 2816 Min Nonbonded Distance : 2.342 Molprobity Statistics. All-atom Clashscore : 5.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.15 % Favored : 96.85 % Rotamer: Outliers : 2.68 % Allowed : 12.52 % Favored : 84.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.09 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.42 (0.18), residues: 2223 helix: 1.51 (0.17), residues: 940 sheet: -0.47 (0.26), residues: 371 loop : -0.63 (0.21), residues: 912 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP R 719 HIS 0.008 0.001 HIS R 338 PHE 0.015 0.001 PHE Q 806 TYR 0.019 0.001 TYR B 145 ARG 0.006 0.000 ARG Q 227 Origin is already at (0, 0, 0), no shifts will be applied Model does not fit in PDB format. =============================================================================== Job complete usr+sys time: 5498.41 seconds wall clock time: 99 minutes 37.08 seconds (5977.08 seconds total)