Starting phenix.real_space_refine on Wed Mar 4 05:04:32 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7dtu_30854/03_2026/7dtu_30854.cif Found real_map, /net/cci-nas-00/data/ceres_data/7dtu_30854/03_2026/7dtu_30854.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7dtu_30854/03_2026/7dtu_30854.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7dtu_30854/03_2026/7dtu_30854.map" model { file = "/net/cci-nas-00/data/ceres_data/7dtu_30854/03_2026/7dtu_30854.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7dtu_30854/03_2026/7dtu_30854.cif" } resolution = 4.4 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.002 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: 4 Type Number sf(0) Gaussians S 46 5.16 5 C 6808 2.51 5 N 1894 2.21 5 O 2098 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 20 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 10846 Number of models: 1 Model: "" Number of chains: 10 Chain: "A" Number of atoms: 5310 Number of conformers: 1 Conformer: "" Number of residues, atoms: 778, 5310 Classifications: {'peptide': 778} Incomplete info: {'truncation_to_alanine': 250} Link IDs: {'PTRANS': 29, 'TRANS': 748} Chain breaks: 3 Unresolved chain link angles: 7 Unresolved non-hydrogen bonds: 938 Unresolved non-hydrogen angles: 1205 Unresolved non-hydrogen dihedrals: 798 Unresolved non-hydrogen chiralities: 89 Planarities with less than four sites: {'HIS:plan': 3, 'PHE:plan': 36, 'GLU:plan': 22, 'ARG:plan': 8, 'ASP:plan': 11, 'ASN:plan1': 10, 'GLN:plan1': 6, 'TRP:plan': 3, 'TYR:plan': 7} Unresolved non-hydrogen planarities: 522 Chain: "B" Number of atoms: 5310 Number of conformers: 1 Conformer: "" Number of residues, atoms: 778, 5310 Classifications: {'peptide': 778} Incomplete info: {'truncation_to_alanine': 250} Link IDs: {'PTRANS': 29, 'TRANS': 748} Chain breaks: 3 Unresolved chain link angles: 7 Unresolved non-hydrogen bonds: 938 Unresolved non-hydrogen angles: 1205 Unresolved non-hydrogen dihedrals: 798 Unresolved non-hydrogen chiralities: 89 Planarities with less than four sites: {'HIS:plan': 3, 'PHE:plan': 36, 'GLU:plan': 22, 'ARG:plan': 8, 'ASP:plan': 11, 'ASN:plan1': 10, 'GLN:plan1': 6, 'TRP:plan': 3, 'TYR:plan': 7} Unresolved non-hydrogen planarities: 522 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: "A" Number of atoms: 15 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 15 Classifications: {'peptide': 1} Modifications used: {'COO': 1} Chain: "A" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 42 Unusual residues: {'NAG': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "B" Number of atoms: 15 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 15 Classifications: {'peptide': 1} Modifications used: {'COO': 1} Chain: "B" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 42 Unusual residues: {'NAG': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Time building chain proxies: 2.77, per 1000 atoms: 0.26 Number of scatterers: 10846 At special positions: 0 Unit cell: (95.95, 102.01, 181.8, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 46 16.00 O 2098 8.00 N 1894 7.00 C 6808 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=18, symmetry=0 Simple disulfide: pdb=" SG CYS A 60 " - pdb=" SG CYS A 101 " distance=2.04 Simple disulfide: pdb=" SG CYS A 236 " - pdb=" SG CYS A 561 " distance=1.41 Simple disulfide: pdb=" SG CYS A 358 " - pdb=" SG CYS A 395 " distance=2.02 Simple disulfide: pdb=" SG CYS A 437 " - pdb=" SG CYS A 449 " distance=2.04 Simple disulfide: pdb=" SG CYS A 542 " - pdb=" SG CYS A 562 " distance=2.03 Simple disulfide: pdb=" SG CYS A 546 " - pdb=" SG CYS A 565 " distance=2.03 Simple disulfide: pdb=" SG CYS A 568 " - pdb=" SG CYS A 582 " distance=2.03 Simple disulfide: pdb=" SG CYS A 585 " - pdb=" SG CYS A 598 " distance=2.03 Simple disulfide: pdb=" SG CYS A 677 " - pdb=" SG CYS A 765 " distance=2.02 Simple disulfide: pdb=" SG CYS B 60 " - pdb=" SG CYS B 101 " distance=2.04 Simple disulfide: pdb=" SG CYS B 236 " - pdb=" SG CYS B 561 " distance=1.42 Simple disulfide: pdb=" SG CYS B 358 " - pdb=" SG CYS B 395 " distance=2.02 Simple disulfide: pdb=" SG CYS B 437 " - pdb=" SG CYS B 449 " distance=2.04 Simple disulfide: pdb=" SG CYS B 542 " - pdb=" SG CYS B 562 " distance=2.03 Simple disulfide: pdb=" SG CYS B 546 " - pdb=" SG CYS B 565 " distance=2.03 Simple disulfide: pdb=" SG CYS B 568 " - pdb=" SG CYS B 582 " distance=2.03 Simple disulfide: pdb=" SG CYS B 585 " - pdb=" SG CYS B 598 " distance=2.03 Simple disulfide: pdb=" SG CYS B 677 " - pdb=" SG CYS B 765 " distance=2.02 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 A1102 " - " ASN A 287 " " NAG A1103 " - " ASN A 446 " " NAG A1104 " - " ASN A 468 " " NAG B1102 " - " ASN B 287 " " NAG B1103 " - " ASN B 446 " " NAG B1104 " - " ASN B 468 " " NAG C 1 " - " ASN A 488 " " NAG D 1 " - " ASN A 541 " " NAG E 1 " - " ASN B 488 " " NAG F 1 " - " ASN B 541 " Time building additional restraints: 0.87 Conformation dependent library (CDL) restraints added in 554.4 milliseconds 3080 Ramachandran restraints generated. 1540 Oldfield, 0 Emsley, 1540 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2928 Finding SS restraints... Secondary structure from input PDB file: 60 helices and 12 sheets defined 48.1% alpha, 8.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.39 Creating SS restraints... Processing helix chain 'A' and resid 64 through 84 removed outlier: 3.727A pdb=" N ALA A 77 " --> pdb=" O ALA A 73 " (cutoff:3.500A) Processing helix chain 'A' and resid 103 through 115 removed outlier: 4.429A pdb=" N SER A 113 " --> pdb=" O GLU A 109 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N PHE A 114 " --> pdb=" O ALA A 110 " (cutoff:3.500A) Processing helix chain 'A' and resid 116 through 122 removed outlier: 3.895A pdb=" N ASP A 121 " --> pdb=" O ASN A 118 " (cutoff:3.500A) Processing helix chain 'A' and resid 126 through 130 removed outlier: 3.655A pdb=" N ASN A 130 " --> pdb=" O GLU A 127 " (cutoff:3.500A) Processing helix chain 'A' and resid 146 through 161 removed outlier: 3.989A pdb=" N ASN A 155 " --> pdb=" O THR A 151 " (cutoff:3.500A) removed outlier: 4.508A pdb=" N LEU A 156 " --> pdb=" O ALA A 152 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N LEU A 157 " --> pdb=" O VAL A 153 " (cutoff:3.500A) removed outlier: 3.960A pdb=" N LEU A 159 " --> pdb=" O ASN A 155 " (cutoff:3.500A) removed outlier: 3.945A pdb=" N PHE A 160 " --> pdb=" O LEU A 156 " (cutoff:3.500A) Processing helix chain 'A' and resid 171 through 176 Processing helix chain 'A' and resid 190 through 204 removed outlier: 3.960A pdb=" N ILE A 201 " --> pdb=" O MET A 197 " (cutoff:3.500A) Processing helix chain 'A' and resid 218 through 233 removed outlier: 4.094A pdb=" N GLY A 222 " --> pdb=" O TYR A 218 " (cutoff:3.500A) Processing helix chain 'A' and resid 248 through 261 Processing helix chain 'A' and resid 276 through 287 Processing helix chain 'A' and resid 329 through 335 Processing helix chain 'A' and resid 338 through 342 removed outlier: 3.504A pdb=" N SER A 342 " --> pdb=" O PRO A 339 " (cutoff:3.500A) Processing helix chain 'A' and resid 346 through 357 removed outlier: 4.467A pdb=" N GLU A 350 " --> pdb=" O GLY A 346 " (cutoff:3.500A) Processing helix chain 'A' and resid 400 through 404 removed outlier: 3.790A pdb=" N SER A 403 " --> pdb=" O ASN A 400 " (cutoff:3.500A) removed outlier: 4.296A pdb=" N VAL A 404 " --> pdb=" O ILE A 401 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 400 through 404' Processing helix chain 'A' and resid 415 through 436 removed outlier: 3.786A pdb=" N TYR A 425 " --> pdb=" O TYR A 421 " (cutoff:3.500A) Processing helix chain 'A' and resid 444 through 448 Processing helix chain 'A' and resid 456 through 466 removed outlier: 3.749A pdb=" N HIS A 466 " --> pdb=" O LYS A 462 " (cutoff:3.500A) Processing helix chain 'A' and resid 524 through 528 removed outlier: 4.151A pdb=" N LYS A 527 " --> pdb=" O ASN A 524 " (cutoff:3.500A) Processing helix chain 'A' and resid 529 through 533 Processing helix chain 'A' and resid 610 through 637 removed outlier: 3.902A pdb=" N ALA A 615 " --> pdb=" O PRO A 611 " (cutoff:3.500A) removed outlier: 4.269A pdb=" N LEU A 616 " --> pdb=" O PHE A 612 " (cutoff:3.500A) Processing helix chain 'A' and resid 652 through 665 removed outlier: 4.564A pdb=" N SER A 665 " --> pdb=" O CYS A 661 " (cutoff:3.500A) Processing helix chain 'A' and resid 666 through 669 removed outlier: 3.875A pdb=" N ILE A 669 " --> pdb=" O LEU A 666 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 666 through 669' Processing helix chain 'A' and resid 673 through 679 Processing helix chain 'A' and resid 681 through 691 removed outlier: 4.019A pdb=" N SER A 687 " --> pdb=" O ALA A 683 " (cutoff:3.500A) Processing helix chain 'A' and resid 692 through 697 Processing helix chain 'A' and resid 728 through 746 removed outlier: 4.309A pdb=" N MET A 734 " --> pdb=" O LEU A 730 " (cutoff:3.500A) removed outlier: 3.901A pdb=" N TYR A 744 " --> pdb=" O VAL A 740 " (cutoff:3.500A) Processing helix chain 'A' and resid 770 through 792 removed outlier: 4.442A pdb=" N CYS A 781 " --> pdb=" O ILE A 777 " (cutoff:3.500A) removed outlier: 4.860A pdb=" N LEU A 782 " --> pdb=" O GLY A 778 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N ALA A 785 " --> pdb=" O CYS A 781 " (cutoff:3.500A) Processing helix chain 'A' and resid 793 through 797 removed outlier: 3.791A pdb=" N LYS A 796 " --> pdb=" O LYS A 793 " (cutoff:3.500A) Processing helix chain 'A' and resid 802 through 827 removed outlier: 4.110A pdb=" N ILE A 822 " --> pdb=" O TRP A 818 " (cutoff:3.500A) Proline residue: A 823 - end of helix Processing helix chain 'A' and resid 829 through 858 removed outlier: 4.056A pdb=" N SER A 834 " --> pdb=" O GLY A 830 " (cutoff:3.500A) removed outlier: 4.505A pdb=" N ALA A 835 " --> pdb=" O LYS A 831 " (cutoff:3.500A) removed outlier: 4.560A pdb=" N VAL A 836 " --> pdb=" O PHE A 832 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N GLU A 837 " --> pdb=" O VAL A 833 " (cutoff:3.500A) removed outlier: 4.740A pdb=" N ASN A 855 " --> pdb=" O CYS A 851 " (cutoff:3.500A) Processing helix chain 'B' and resid 64 through 84 removed outlier: 3.726A pdb=" N ALA B 77 " --> pdb=" O ALA B 73 " (cutoff:3.500A) Processing helix chain 'B' and resid 103 through 115 removed outlier: 4.428A pdb=" N SER B 113 " --> pdb=" O GLU B 109 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N PHE B 114 " --> pdb=" O ALA B 110 " (cutoff:3.500A) Processing helix chain 'B' and resid 116 through 122 removed outlier: 3.895A pdb=" N ASP B 121 " --> pdb=" O ASN B 118 " (cutoff:3.500A) Processing helix chain 'B' and resid 126 through 130 removed outlier: 3.655A pdb=" N ASN B 130 " --> pdb=" O GLU B 127 " (cutoff:3.500A) Processing helix chain 'B' and resid 146 through 161 removed outlier: 3.989A pdb=" N ASN B 155 " --> pdb=" O THR B 151 " (cutoff:3.500A) removed outlier: 4.509A pdb=" N LEU B 156 " --> pdb=" O ALA B 152 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N LEU B 157 " --> pdb=" O VAL B 153 " (cutoff:3.500A) removed outlier: 3.960A pdb=" N LEU B 159 " --> pdb=" O ASN B 155 " (cutoff:3.500A) removed outlier: 3.945A pdb=" N PHE B 160 " --> pdb=" O LEU B 156 " (cutoff:3.500A) Processing helix chain 'B' and resid 171 through 176 Processing helix chain 'B' and resid 190 through 204 removed outlier: 3.960A pdb=" N ILE B 201 " --> pdb=" O MET B 197 " (cutoff:3.500A) Processing helix chain 'B' and resid 218 through 233 removed outlier: 4.095A pdb=" N GLY B 222 " --> pdb=" O TYR B 218 " (cutoff:3.500A) Processing helix chain 'B' and resid 248 through 261 Processing helix chain 'B' and resid 276 through 287 Processing helix chain 'B' and resid 329 through 335 Processing helix chain 'B' and resid 338 through 342 removed outlier: 3.504A pdb=" N SER B 342 " --> pdb=" O PRO B 339 " (cutoff:3.500A) Processing helix chain 'B' and resid 346 through 357 removed outlier: 4.467A pdb=" N GLU B 350 " --> pdb=" O GLY B 346 " (cutoff:3.500A) Processing helix chain 'B' and resid 400 through 404 removed outlier: 3.789A pdb=" N SER B 403 " --> pdb=" O ASN B 400 " (cutoff:3.500A) removed outlier: 4.297A pdb=" N VAL B 404 " --> pdb=" O ILE B 401 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 400 through 404' Processing helix chain 'B' and resid 415 through 436 removed outlier: 3.785A pdb=" N TYR B 425 " --> pdb=" O TYR B 421 " (cutoff:3.500A) Processing helix chain 'B' and resid 444 through 448 Processing helix chain 'B' and resid 456 through 466 removed outlier: 3.748A pdb=" N HIS B 466 " --> pdb=" O LYS B 462 " (cutoff:3.500A) Processing helix chain 'B' and resid 524 through 528 removed outlier: 4.151A pdb=" N LYS B 527 " --> pdb=" O ASN B 524 " (cutoff:3.500A) Processing helix chain 'B' and resid 529 through 533 Processing helix chain 'B' and resid 610 through 637 removed outlier: 3.902A pdb=" N ALA B 615 " --> pdb=" O PRO B 611 " (cutoff:3.500A) removed outlier: 4.269A pdb=" N LEU B 616 " --> pdb=" O PHE B 612 " (cutoff:3.500A) Processing helix chain 'B' and resid 652 through 665 removed outlier: 4.564A pdb=" N SER B 665 " --> pdb=" O CYS B 661 " (cutoff:3.500A) Processing helix chain 'B' and resid 666 through 669 removed outlier: 3.874A pdb=" N ILE B 669 " --> pdb=" O LEU B 666 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 666 through 669' Processing helix chain 'B' and resid 673 through 679 Processing helix chain 'B' and resid 681 through 691 removed outlier: 4.020A pdb=" N SER B 687 " --> pdb=" O ALA B 683 " (cutoff:3.500A) Processing helix chain 'B' and resid 692 through 697 Processing helix chain 'B' and resid 728 through 746 removed outlier: 4.310A pdb=" N MET B 734 " --> pdb=" O LEU B 730 " (cutoff:3.500A) removed outlier: 3.901A pdb=" N TYR B 744 " --> pdb=" O VAL B 740 " (cutoff:3.500A) Processing helix chain 'B' and resid 770 through 792 removed outlier: 4.442A pdb=" N CYS B 781 " --> pdb=" O ILE B 777 " (cutoff:3.500A) removed outlier: 4.861A pdb=" N LEU B 782 " --> pdb=" O GLY B 778 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N ALA B 785 " --> pdb=" O CYS B 781 " (cutoff:3.500A) Processing helix chain 'B' and resid 793 through 797 removed outlier: 3.791A pdb=" N LYS B 796 " --> pdb=" O LYS B 793 " (cutoff:3.500A) Processing helix chain 'B' and resid 802 through 827 removed outlier: 4.111A pdb=" N ILE B 822 " --> pdb=" O TRP B 818 " (cutoff:3.500A) Proline residue: B 823 - end of helix Processing helix chain 'B' and resid 829 through 858 removed outlier: 4.057A pdb=" N SER B 834 " --> pdb=" O GLY B 830 " (cutoff:3.500A) removed outlier: 4.506A pdb=" N ALA B 835 " --> pdb=" O LYS B 831 " (cutoff:3.500A) removed outlier: 4.561A pdb=" N VAL B 836 " --> pdb=" O PHE B 832 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N GLU B 837 " --> pdb=" O VAL B 833 " (cutoff:3.500A) removed outlier: 4.740A pdb=" N ASN B 855 " --> pdb=" O CYS B 851 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 26 through 28 removed outlier: 5.647A pdb=" N ILE A 32 " --> pdb=" O GLY A 94 " (cutoff:3.500A) removed outlier: 7.335A pdb=" N ARG A 96 " --> pdb=" O ILE A 32 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 26 through 28 Processing sheet with id=AA3, first strand: chain 'A' and resid 141 through 142 removed outlier: 6.705A pdb=" N VAL A 141 " --> pdb=" O VAL A 165 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 236 through 243 removed outlier: 7.516A pdb=" N VAL A 209 " --> pdb=" O ASP A 238 " (cutoff:3.500A) removed outlier: 6.870A pdb=" N SER A 240 " --> pdb=" O VAL A 209 " (cutoff:3.500A) removed outlier: 6.932A pdb=" N THR A 211 " --> pdb=" O SER A 240 " (cutoff:3.500A) removed outlier: 6.069A pdb=" N LEU A 242 " --> pdb=" O THR A 211 " (cutoff:3.500A) removed outlier: 6.726A pdb=" N ALA A 213 " --> pdb=" O LEU A 242 " (cutoff:3.500A) removed outlier: 5.580A pdb=" N VAL A 266 " --> pdb=" O TRP A 208 " (cutoff:3.500A) removed outlier: 3.857A pdb=" N GLY A 210 " --> pdb=" O VAL A 266 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N VAL A 268 " --> pdb=" O GLY A 210 " (cutoff:3.500A) removed outlier: 3.861A pdb=" N ALA A 214 " --> pdb=" O PHE A 270 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 318 through 321 removed outlier: 3.716A pdb=" N GLY A 319 " --> pdb=" O ILE A 492 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N ALA A 321 " --> pdb=" O SER A 490 " (cutoff:3.500A) removed outlier: 6.137A pdb=" N ASN A 493 " --> pdb=" O GLU A 507 " (cutoff:3.500A) removed outlier: 5.497A pdb=" N GLU A 507 " --> pdb=" O ASN A 493 " (cutoff:3.500A) removed outlier: 6.493A pdb=" N HIS A 495 " --> pdb=" O PHE A 505 " (cutoff:3.500A) removed outlier: 5.045A pdb=" N PHE A 505 " --> pdb=" O HIS A 495 " (cutoff:3.500A) removed outlier: 3.887A pdb=" N PHE A 522 " --> pdb=" O TYR A 510 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 468 through 470 removed outlier: 3.652A pdb=" N PHE A 469 " --> pdb=" O VAL A 477 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 26 through 28 removed outlier: 5.648A pdb=" N ILE B 32 " --> pdb=" O GLY B 94 " (cutoff:3.500A) removed outlier: 7.334A pdb=" N ARG B 96 " --> pdb=" O ILE B 32 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 26 through 28 Processing sheet with id=AA9, first strand: chain 'B' and resid 141 through 142 removed outlier: 6.705A pdb=" N VAL B 141 " --> pdb=" O VAL B 165 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 236 through 243 removed outlier: 7.517A pdb=" N VAL B 209 " --> pdb=" O ASP B 238 " (cutoff:3.500A) removed outlier: 6.870A pdb=" N SER B 240 " --> pdb=" O VAL B 209 " (cutoff:3.500A) removed outlier: 6.933A pdb=" N THR B 211 " --> pdb=" O SER B 240 " (cutoff:3.500A) removed outlier: 6.068A pdb=" N LEU B 242 " --> pdb=" O THR B 211 " (cutoff:3.500A) removed outlier: 6.726A pdb=" N ALA B 213 " --> pdb=" O LEU B 242 " (cutoff:3.500A) removed outlier: 5.580A pdb=" N VAL B 266 " --> pdb=" O TRP B 208 " (cutoff:3.500A) removed outlier: 3.857A pdb=" N GLY B 210 " --> pdb=" O VAL B 266 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N VAL B 268 " --> pdb=" O GLY B 210 " (cutoff:3.500A) removed outlier: 3.861A pdb=" N ALA B 214 " --> pdb=" O PHE B 270 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 318 through 321 removed outlier: 3.716A pdb=" N GLY B 319 " --> pdb=" O ILE B 492 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N ALA B 321 " --> pdb=" O SER B 490 " (cutoff:3.500A) removed outlier: 6.137A pdb=" N ASN B 493 " --> pdb=" O GLU B 507 " (cutoff:3.500A) removed outlier: 5.498A pdb=" N GLU B 507 " --> pdb=" O ASN B 493 " (cutoff:3.500A) removed outlier: 6.494A pdb=" N HIS B 495 " --> pdb=" O PHE B 505 " (cutoff:3.500A) removed outlier: 5.046A pdb=" N PHE B 505 " --> pdb=" O HIS B 495 " (cutoff:3.500A) removed outlier: 3.888A pdb=" N PHE B 522 " --> pdb=" O TYR B 510 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 468 through 470 removed outlier: 3.652A pdb=" N PHE B 469 " --> pdb=" O VAL B 477 " (cutoff:3.500A) 500 hydrogen bonds defined for protein. 1398 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: 1.80 Time building geometry restraints manager: 1.14 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: 3605 1.34 - 1.46: 2471 1.46 - 1.58: 4916 1.58 - 1.70: 0 1.70 - 1.82: 54 Bond restraints: 11046 Sorted by residual: bond pdb=" C1 NAG B1103 " pdb=" O5 NAG B1103 " ideal model delta sigma weight residual 1.406 1.476 -0.070 2.00e-02 2.50e+03 1.22e+01 bond pdb=" C1 NAG A1103 " pdb=" O5 NAG A1103 " ideal model delta sigma weight residual 1.406 1.476 -0.070 2.00e-02 2.50e+03 1.21e+01 bond pdb=" C1 NAG A1102 " pdb=" O5 NAG A1102 " ideal model delta sigma weight residual 1.406 1.443 -0.037 2.00e-02 2.50e+03 3.40e+00 bond pdb=" C1 NAG B1102 " pdb=" O5 NAG B1102 " ideal model delta sigma weight residual 1.406 1.442 -0.036 2.00e-02 2.50e+03 3.29e+00 bond pdb=" C1 NAG B1104 " pdb=" O5 NAG B1104 " ideal model delta sigma weight residual 1.406 1.441 -0.035 2.00e-02 2.50e+03 3.07e+00 ... (remaining 11041 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.66: 14147 1.66 - 3.31: 822 3.31 - 4.97: 77 4.97 - 6.62: 43 6.62 - 8.28: 13 Bond angle restraints: 15102 Sorted by residual: angle pdb=" CA TYR A 573 " pdb=" CB TYR A 573 " pdb=" CG TYR A 573 " ideal model delta sigma weight residual 113.90 120.59 -6.69 1.80e+00 3.09e-01 1.38e+01 angle pdb=" CA TYR B 573 " pdb=" CB TYR B 573 " pdb=" CG TYR B 573 " ideal model delta sigma weight residual 113.90 120.51 -6.61 1.80e+00 3.09e-01 1.35e+01 angle pdb=" C GLU B 572 " pdb=" N TYR B 573 " pdb=" CA TYR B 573 " ideal model delta sigma weight residual 121.54 128.54 -7.00 1.91e+00 2.74e-01 1.34e+01 angle pdb=" C GLU A 572 " pdb=" N TYR A 573 " pdb=" CA TYR A 573 " ideal model delta sigma weight residual 121.54 128.49 -6.95 1.91e+00 2.74e-01 1.32e+01 angle pdb=" C CYS A 101 " pdb=" N ASN A 102 " pdb=" CA ASN A 102 " ideal model delta sigma weight residual 122.40 127.67 -5.27 1.45e+00 4.76e-01 1.32e+01 ... (remaining 15097 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.94: 6090 17.94 - 35.88: 485 35.88 - 53.82: 91 53.82 - 71.76: 24 71.76 - 89.70: 16 Dihedral angle restraints: 6706 sinusoidal: 2192 harmonic: 4514 Sorted by residual: dihedral pdb=" CB CYS B 677 " pdb=" SG CYS B 677 " pdb=" SG CYS B 765 " pdb=" CB CYS B 765 " ideal model delta sinusoidal sigma weight residual 93.00 164.95 -71.95 1 1.00e+01 1.00e-02 6.62e+01 dihedral pdb=" CB CYS A 677 " pdb=" SG CYS A 677 " pdb=" SG CYS A 765 " pdb=" CB CYS A 765 " ideal model delta sinusoidal sigma weight residual 93.00 164.94 -71.94 1 1.00e+01 1.00e-02 6.62e+01 dihedral pdb=" CB CYS A 568 " pdb=" SG CYS A 568 " pdb=" SG CYS A 582 " pdb=" CB CYS A 582 " ideal model delta sinusoidal sigma weight residual 93.00 160.35 -67.35 1 1.00e+01 1.00e-02 5.90e+01 ... (remaining 6703 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.051: 1249 0.051 - 0.102: 406 0.102 - 0.152: 121 0.152 - 0.203: 16 0.203 - 0.254: 8 Chirality restraints: 1800 Sorted by residual: chirality pdb=" CG LEU B 37 " pdb=" CB LEU B 37 " pdb=" CD1 LEU B 37 " pdb=" CD2 LEU B 37 " both_signs ideal model delta sigma weight residual False -2.59 -2.34 -0.25 2.00e-01 2.50e+01 1.61e+00 chirality pdb=" CG LEU A 37 " pdb=" CB LEU A 37 " pdb=" CD1 LEU A 37 " pdb=" CD2 LEU A 37 " both_signs ideal model delta sigma weight residual False -2.59 -2.34 -0.25 2.00e-01 2.50e+01 1.60e+00 chirality pdb=" C1 NAG A1104 " pdb=" ND2 ASN A 468 " pdb=" C2 NAG A1104 " pdb=" O5 NAG A1104 " both_signs ideal model delta sigma weight residual False -2.40 -2.18 -0.22 2.00e-01 2.50e+01 1.26e+00 ... (remaining 1797 not shown) Planarity restraints: 1994 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA THR B 445 " 0.011 2.00e-02 2.50e+03 2.28e-02 5.21e+00 pdb=" C THR B 445 " -0.039 2.00e-02 2.50e+03 pdb=" O THR B 445 " 0.015 2.00e-02 2.50e+03 pdb=" N ASN B 446 " 0.013 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA THR A 445 " -0.011 2.00e-02 2.50e+03 2.28e-02 5.20e+00 pdb=" C THR A 445 " 0.039 2.00e-02 2.50e+03 pdb=" O THR A 445 " -0.015 2.00e-02 2.50e+03 pdb=" N ASN A 446 " -0.013 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C CYS A 585 " 0.034 5.00e-02 4.00e+02 5.11e-02 4.18e+00 pdb=" N PRO A 586 " -0.088 5.00e-02 4.00e+02 pdb=" CA PRO A 586 " 0.027 5.00e-02 4.00e+02 pdb=" CD PRO A 586 " 0.028 5.00e-02 4.00e+02 ... (remaining 1991 not shown) Histogram of nonbonded interaction distances: 2.28 - 2.80: 3299 2.80 - 3.33: 10444 3.33 - 3.85: 19032 3.85 - 4.38: 20463 4.38 - 4.90: 33105 Nonbonded interactions: 86343 Sorted by model distance: nonbonded pdb=" O SER B 171 " pdb=" NH2 ARG B 185 " model vdw 2.277 3.120 nonbonded pdb=" O SER A 171 " pdb=" NH2 ARG A 185 " model vdw 2.277 3.120 nonbonded pdb=" O GLU A 525 " pdb=" NH2 ARG A 535 " model vdw 2.299 3.120 nonbonded pdb=" O GLU B 525 " pdb=" NH2 ARG B 535 " model vdw 2.299 3.120 nonbonded pdb=" OH TYR A 203 " pdb=" OE1 GLU A 525 " model vdw 2.315 3.040 ... (remaining 86338 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: 0.02 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' } ncs_group { reference = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.210 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: 0.180 Check model and map are aligned: 0.030 Set scattering table: 0.040 Process input model: 11.510 Find NCS groups from input model: 0.180 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.110 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 15.280 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7980 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 : 0.010 0.616 11078 Z= 0.508 Angle : 0.954 17.326 15180 Z= 0.528 Chirality : 0.056 0.254 1800 Planarity : 0.005 0.051 1984 Dihedral : 14.686 89.703 3724 Min Nonbonded Distance : 2.277 Molprobity Statistics. All-atom Clashscore : 6.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.42 % Favored : 90.58 % Rotamer: Outliers : 0.00 % Allowed : 11.94 % Favored : 88.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.95 (0.18), residues: 1540 helix: -2.02 (0.15), residues: 606 sheet: -3.70 (0.29), residues: 210 loop : -2.74 (0.21), residues: 724 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 69 TYR 0.023 0.003 TYR B 573 PHE 0.024 0.002 PHE B 270 TRP 0.015 0.002 TRP A 458 HIS 0.005 0.001 HIS B 429 Details of bonding type rmsd covalent geometry : bond 0.00592 (11046) covalent geometry : angle 0.90289 (15102) SS BOND : bond 0.20540 ( 18) SS BOND : angle 4.47510 ( 36) hydrogen bonds : bond 0.13364 ( 492) hydrogen bonds : angle 5.78684 ( 1398) link_BETA1-4 : bond 0.00398 ( 4) link_BETA1-4 : angle 2.80826 ( 12) link_NAG-ASN : bond 0.01331 ( 10) link_NAG-ASN : angle 4.78932 ( 30) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3080 Ramachandran restraints generated. 1540 Oldfield, 0 Emsley, 1540 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3080 Ramachandran restraints generated. 1540 Oldfield, 0 Emsley, 1540 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 16 residues out of total 1354 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 16 time to evaluate : 0.397 Fit side-chains REVERT: A 473 MET cc_start: 0.7651 (ptp) cc_final: 0.6859 (mpp) REVERT: B 473 MET cc_start: 0.7586 (ptp) cc_final: 0.6812 (mpp) outliers start: 0 outliers final: 0 residues processed: 16 average time/residue: 0.0643 time to fit residues: 2.2035 Evaluate side-chains 14 residues out of total 1354 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 14 time to evaluate : 0.381 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 98 optimal weight: 5.9990 chunk 107 optimal weight: 9.9990 chunk 10 optimal weight: 20.0000 chunk 66 optimal weight: 50.0000 chunk 130 optimal weight: 0.5980 chunk 124 optimal weight: 2.9990 chunk 103 optimal weight: 2.9990 chunk 77 optimal weight: 8.9990 chunk 122 optimal weight: 0.9990 chunk 91 optimal weight: 4.9990 chunk 149 optimal weight: 20.0000 overall best weight: 2.5188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 72 GLN ** A 164 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 193 GLN ** A 260 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 312 HIS A 361 GLN A 400 ASN A 419 ASN A 429 HIS A 432 GLN A 463 HIS B 72 GLN ** B 164 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 193 GLN ** B 260 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 312 HIS B 361 GLN B 400 ASN B 419 ASN B 429 HIS B 432 GLN B 463 HIS Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3127 r_free = 0.3127 target = 0.034551 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2817 r_free = 0.2817 target = 0.027450 restraints weight = 145385.172| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 23)----------------| | r_work = 0.2841 r_free = 0.2841 target = 0.027967 restraints weight = 99812.429| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.2859 r_free = 0.2859 target = 0.028350 restraints weight = 75661.487| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.2871 r_free = 0.2871 target = 0.028628 restraints weight = 61689.512| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.2878 r_free = 0.2878 target = 0.028780 restraints weight = 52801.911| |-----------------------------------------------------------------------------| r_work (final): 0.2850 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8047 moved from start: 0.1039 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 11078 Z= 0.149 Angle : 0.609 8.410 15180 Z= 0.324 Chirality : 0.045 0.282 1800 Planarity : 0.004 0.038 1984 Dihedral : 7.193 55.760 1924 Min Nonbonded Distance : 2.437 Molprobity Statistics. All-atom Clashscore : 7.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.53 % Favored : 92.47 % Rotamer: Outliers : 0.00 % Allowed : 5.04 % Favored : 94.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.50 (0.21), residues: 1540 helix: -0.33 (0.19), residues: 608 sheet: -3.34 (0.32), residues: 210 loop : -2.28 (0.23), residues: 722 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 535 TYR 0.018 0.002 TYR B 573 PHE 0.011 0.001 PHE A 270 TRP 0.013 0.001 TRP A 208 HIS 0.003 0.001 HIS A 338 Details of bonding type rmsd covalent geometry : bond 0.00307 (11046) covalent geometry : angle 0.58961 (15102) SS BOND : bond 0.00697 ( 18) SS BOND : angle 1.46350 ( 36) hydrogen bonds : bond 0.04185 ( 492) hydrogen bonds : angle 4.81955 ( 1398) link_BETA1-4 : bond 0.00198 ( 4) link_BETA1-4 : angle 1.55147 ( 12) link_NAG-ASN : bond 0.00717 ( 10) link_NAG-ASN : angle 3.03246 ( 30) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3080 Ramachandran restraints generated. 1540 Oldfield, 0 Emsley, 1540 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3080 Ramachandran restraints generated. 1540 Oldfield, 0 Emsley, 1540 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 18 residues out of total 1354 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 18 time to evaluate : 0.415 Fit side-chains REVERT: A 197 MET cc_start: 0.9003 (mtm) cc_final: 0.8529 (mtp) REVERT: A 307 MET cc_start: 0.8379 (mmp) cc_final: 0.8059 (mmm) REVERT: A 464 LEU cc_start: 0.9384 (mt) cc_final: 0.9011 (mt) REVERT: A 473 MET cc_start: 0.7657 (ptp) cc_final: 0.7036 (mpp) REVERT: B 197 MET cc_start: 0.8977 (mtm) cc_final: 0.8493 (mtp) REVERT: B 464 LEU cc_start: 0.9402 (mt) cc_final: 0.9030 (mt) REVERT: B 473 MET cc_start: 0.7763 (ptp) cc_final: 0.6995 (mpp) outliers start: 0 outliers final: 0 residues processed: 18 average time/residue: 0.0685 time to fit residues: 2.5586 Evaluate side-chains 16 residues out of total 1354 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 16 time to evaluate : 0.396 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 114 optimal weight: 0.9980 chunk 104 optimal weight: 6.9990 chunk 106 optimal weight: 9.9990 chunk 64 optimal weight: 0.0370 chunk 26 optimal weight: 0.9990 chunk 38 optimal weight: 20.0000 chunk 138 optimal weight: 30.0000 chunk 135 optimal weight: 1.9990 chunk 142 optimal weight: 6.9990 chunk 148 optimal weight: 50.0000 chunk 107 optimal weight: 9.9990 overall best weight: 2.2064 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 164 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 260 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 164 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 260 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3123 r_free = 0.3123 target = 0.034524 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2811 r_free = 0.2811 target = 0.027383 restraints weight = 145947.487| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.2835 r_free = 0.2835 target = 0.027898 restraints weight = 99683.301| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.2853 r_free = 0.2853 target = 0.028289 restraints weight = 75505.903| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.2866 r_free = 0.2866 target = 0.028573 restraints weight = 61407.667| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.2874 r_free = 0.2874 target = 0.028746 restraints weight = 52314.120| |-----------------------------------------------------------------------------| r_work (final): 0.2846 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8042 moved from start: 0.1427 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 11078 Z= 0.129 Angle : 0.558 7.939 15180 Z= 0.294 Chirality : 0.044 0.272 1800 Planarity : 0.003 0.035 1984 Dihedral : 6.295 52.615 1924 Min Nonbonded Distance : 2.479 Molprobity Statistics. All-atom Clashscore : 6.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.69 % Favored : 93.31 % Rotamer: Outliers : 0.00 % Allowed : 4.22 % Favored : 95.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.78 (0.22), residues: 1540 helix: 0.44 (0.20), residues: 614 sheet: -2.92 (0.35), residues: 198 loop : -2.11 (0.24), residues: 728 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 69 TYR 0.017 0.001 TYR B 573 PHE 0.012 0.001 PHE A 38 TRP 0.011 0.001 TRP A 208 HIS 0.001 0.000 HIS A 338 Details of bonding type rmsd covalent geometry : bond 0.00272 (11046) covalent geometry : angle 0.54226 (15102) SS BOND : bond 0.00311 ( 18) SS BOND : angle 0.87881 ( 36) hydrogen bonds : bond 0.03701 ( 492) hydrogen bonds : angle 4.61143 ( 1398) link_BETA1-4 : bond 0.00246 ( 4) link_BETA1-4 : angle 1.44384 ( 12) link_NAG-ASN : bond 0.00696 ( 10) link_NAG-ASN : angle 2.74796 ( 30) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3080 Ramachandran restraints generated. 1540 Oldfield, 0 Emsley, 1540 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3080 Ramachandran restraints generated. 1540 Oldfield, 0 Emsley, 1540 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 18 residues out of total 1354 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 18 time to evaluate : 0.317 Fit side-chains revert: symmetry clash REVERT: A 197 MET cc_start: 0.9075 (mtm) cc_final: 0.8535 (mtp) REVERT: A 464 LEU cc_start: 0.9433 (mt) cc_final: 0.9058 (mt) REVERT: A 473 MET cc_start: 0.7563 (ptp) cc_final: 0.6845 (mpp) REVERT: B 197 MET cc_start: 0.9050 (mtm) cc_final: 0.8504 (mtp) REVERT: B 307 MET cc_start: 0.8582 (mmp) cc_final: 0.8276 (mmm) REVERT: B 464 LEU cc_start: 0.9440 (mt) cc_final: 0.9063 (mt) REVERT: B 473 MET cc_start: 0.7613 (ptp) cc_final: 0.6932 (mpp) outliers start: 0 outliers final: 0 residues processed: 18 average time/residue: 0.0614 time to fit residues: 2.2738 Evaluate side-chains 17 residues out of total 1354 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 17 time to evaluate : 0.412 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 147 optimal weight: 5.9990 chunk 52 optimal weight: 10.0000 chunk 97 optimal weight: 9.9990 chunk 40 optimal weight: 4.9990 chunk 48 optimal weight: 10.0000 chunk 68 optimal weight: 10.0000 chunk 70 optimal weight: 6.9990 chunk 42 optimal weight: 2.9990 chunk 71 optimal weight: 6.9990 chunk 58 optimal weight: 7.9990 chunk 84 optimal weight: 9.9990 overall best weight: 5.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 117 GLN ** A 164 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 260 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 466 HIS B 117 GLN ** B 164 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 260 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 466 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3092 r_free = 0.3092 target = 0.033513 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2782 r_free = 0.2782 target = 0.026623 restraints weight = 150988.774| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.2807 r_free = 0.2807 target = 0.027127 restraints weight = 103942.859| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.2824 r_free = 0.2824 target = 0.027495 restraints weight = 79304.590| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.2837 r_free = 0.2837 target = 0.027757 restraints weight = 65008.733| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.2844 r_free = 0.2844 target = 0.027912 restraints weight = 56090.304| |-----------------------------------------------------------------------------| r_work (final): 0.2820 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8115 moved from start: 0.1787 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.046 11078 Z= 0.256 Angle : 0.665 7.661 15180 Z= 0.355 Chirality : 0.046 0.265 1800 Planarity : 0.004 0.037 1984 Dihedral : 6.521 51.718 1924 Min Nonbonded Distance : 2.436 Molprobity Statistics. All-atom Clashscore : 11.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.53 % Favored : 92.47 % Rotamer: Outliers : 0.00 % Allowed : 5.50 % Favored : 94.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.65 (0.21), residues: 1540 helix: 0.71 (0.20), residues: 618 sheet: -3.09 (0.34), residues: 202 loop : -2.13 (0.23), residues: 720 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 69 TYR 0.016 0.002 TYR B 421 PHE 0.018 0.002 PHE A 38 TRP 0.013 0.002 TRP A 458 HIS 0.004 0.001 HIS A 192 Details of bonding type rmsd covalent geometry : bond 0.00533 (11046) covalent geometry : angle 0.64853 (15102) SS BOND : bond 0.00510 ( 18) SS BOND : angle 1.46352 ( 36) hydrogen bonds : bond 0.04095 ( 492) hydrogen bonds : angle 4.86635 ( 1398) link_BETA1-4 : bond 0.00351 ( 4) link_BETA1-4 : angle 2.02797 ( 12) link_NAG-ASN : bond 0.00758 ( 10) link_NAG-ASN : angle 2.81496 ( 30) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3080 Ramachandran restraints generated. 1540 Oldfield, 0 Emsley, 1540 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3080 Ramachandran restraints generated. 1540 Oldfield, 0 Emsley, 1540 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 15 residues out of total 1354 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 15 time to evaluate : 0.402 Fit side-chains revert: symmetry clash REVERT: A 197 MET cc_start: 0.9048 (mtm) cc_final: 0.8471 (mtp) REVERT: A 307 MET cc_start: 0.8572 (mmp) cc_final: 0.8366 (mmm) REVERT: B 197 MET cc_start: 0.9060 (mtm) cc_final: 0.8468 (mtp) outliers start: 0 outliers final: 0 residues processed: 15 average time/residue: 0.0723 time to fit residues: 2.3234 Evaluate side-chains 15 residues out of total 1354 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 15 time to evaluate : 0.417 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 16 optimal weight: 6.9990 chunk 60 optimal weight: 7.9990 chunk 31 optimal weight: 0.9990 chunk 133 optimal weight: 50.0000 chunk 4 optimal weight: 6.9990 chunk 41 optimal weight: 3.9990 chunk 152 optimal weight: 2.9990 chunk 153 optimal weight: 9.9990 chunk 71 optimal weight: 50.0000 chunk 32 optimal weight: 7.9990 chunk 120 optimal weight: 0.9980 overall best weight: 3.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 164 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 260 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 260 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3113 r_free = 0.3113 target = 0.034191 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2805 r_free = 0.2805 target = 0.027195 restraints weight = 146283.248| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.2830 r_free = 0.2830 target = 0.027719 restraints weight = 100347.630| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 22)----------------| | r_work = 0.2844 r_free = 0.2844 target = 0.028039 restraints weight = 76119.630| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.2859 r_free = 0.2859 target = 0.028337 restraints weight = 63730.777| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.2867 r_free = 0.2867 target = 0.028510 restraints weight = 54401.110| |-----------------------------------------------------------------------------| r_work (final): 0.2839 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8069 moved from start: 0.1992 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 11078 Z= 0.153 Angle : 0.568 7.416 15180 Z= 0.300 Chirality : 0.045 0.264 1800 Planarity : 0.003 0.034 1984 Dihedral : 6.043 48.798 1924 Min Nonbonded Distance : 2.516 Molprobity Statistics. All-atom Clashscore : 7.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.69 % Favored : 93.31 % Rotamer: Outliers : 0.00 % Allowed : 3.04 % Favored : 96.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.26 (0.22), residues: 1540 helix: 1.20 (0.21), residues: 608 sheet: -2.94 (0.34), residues: 204 loop : -2.03 (0.23), residues: 728 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 69 TYR 0.016 0.002 TYR A 573 PHE 0.011 0.001 PHE A 589 TRP 0.009 0.001 TRP A 208 HIS 0.002 0.001 HIS A 429 Details of bonding type rmsd covalent geometry : bond 0.00321 (11046) covalent geometry : angle 0.55300 (15102) SS BOND : bond 0.00380 ( 18) SS BOND : angle 1.16128 ( 36) hydrogen bonds : bond 0.03630 ( 492) hydrogen bonds : angle 4.64986 ( 1398) link_BETA1-4 : bond 0.00254 ( 4) link_BETA1-4 : angle 1.44940 ( 12) link_NAG-ASN : bond 0.00710 ( 10) link_NAG-ASN : angle 2.62441 ( 30) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3080 Ramachandran restraints generated. 1540 Oldfield, 0 Emsley, 1540 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3080 Ramachandran restraints generated. 1540 Oldfield, 0 Emsley, 1540 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 16 residues out of total 1354 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 16 time to evaluate : 0.423 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 197 MET cc_start: 0.9145 (mtm) cc_final: 0.8555 (mtp) REVERT: A 307 MET cc_start: 0.8720 (mmp) cc_final: 0.8509 (mmm) REVERT: B 197 MET cc_start: 0.9162 (mtm) cc_final: 0.8566 (mtp) REVERT: B 307 MET cc_start: 0.8562 (mmp) cc_final: 0.8270 (mmm) outliers start: 0 outliers final: 0 residues processed: 16 average time/residue: 0.0732 time to fit residues: 2.4310 Evaluate side-chains 16 residues out of total 1354 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 16 time to evaluate : 0.268 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 97 optimal weight: 5.9990 chunk 76 optimal weight: 20.0000 chunk 75 optimal weight: 6.9990 chunk 8 optimal weight: 0.0870 chunk 51 optimal weight: 9.9990 chunk 12 optimal weight: 5.9990 chunk 49 optimal weight: 10.0000 chunk 72 optimal weight: 30.0000 chunk 135 optimal weight: 6.9990 chunk 37 optimal weight: 0.9990 chunk 83 optimal weight: 9.9990 overall best weight: 4.0166 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 164 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 260 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 164 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 260 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3106 r_free = 0.3106 target = 0.033951 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2796 r_free = 0.2796 target = 0.027023 restraints weight = 149020.208| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.2821 r_free = 0.2821 target = 0.027528 restraints weight = 102233.607| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.2838 r_free = 0.2838 target = 0.027899 restraints weight = 77924.084| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.2852 r_free = 0.2852 target = 0.028170 restraints weight = 63749.422| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.2860 r_free = 0.2860 target = 0.028358 restraints weight = 54908.003| |-----------------------------------------------------------------------------| r_work (final): 0.2834 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8085 moved from start: 0.2158 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 11078 Z= 0.191 Angle : 0.598 7.974 15180 Z= 0.316 Chirality : 0.045 0.258 1800 Planarity : 0.004 0.034 1984 Dihedral : 6.067 49.338 1924 Min Nonbonded Distance : 2.507 Molprobity Statistics. All-atom Clashscore : 9.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.86 % Favored : 92.14 % Rotamer: Outliers : 0.00 % Allowed : 2.11 % Favored : 97.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.15 (0.22), residues: 1540 helix: 1.25 (0.20), residues: 620 sheet: -2.56 (0.38), residues: 164 loop : -2.15 (0.22), residues: 756 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 69 TYR 0.016 0.002 TYR A 573 PHE 0.014 0.001 PHE A 589 TRP 0.012 0.001 TRP A 352 HIS 0.003 0.001 HIS B 192 Details of bonding type rmsd covalent geometry : bond 0.00403 (11046) covalent geometry : angle 0.58274 (15102) SS BOND : bond 0.00501 ( 18) SS BOND : angle 1.14719 ( 36) hydrogen bonds : bond 0.03664 ( 492) hydrogen bonds : angle 4.63270 ( 1398) link_BETA1-4 : bond 0.00283 ( 4) link_BETA1-4 : angle 1.65520 ( 12) link_NAG-ASN : bond 0.00705 ( 10) link_NAG-ASN : angle 2.69215 ( 30) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3080 Ramachandran restraints generated. 1540 Oldfield, 0 Emsley, 1540 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3080 Ramachandran restraints generated. 1540 Oldfield, 0 Emsley, 1540 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 16 residues out of total 1354 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 16 time to evaluate : 0.393 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 197 MET cc_start: 0.9149 (mtm) cc_final: 0.8482 (mtp) REVERT: B 197 MET cc_start: 0.9167 (mtm) cc_final: 0.8496 (mtp) REVERT: B 307 MET cc_start: 0.8562 (mmp) cc_final: 0.8311 (mmm) outliers start: 0 outliers final: 0 residues processed: 16 average time/residue: 0.0709 time to fit residues: 2.4274 Evaluate side-chains 16 residues out of total 1354 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 16 time to evaluate : 0.445 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 106 optimal weight: 10.0000 chunk 37 optimal weight: 0.9990 chunk 144 optimal weight: 2.9990 chunk 118 optimal weight: 2.9990 chunk 6 optimal weight: 3.9990 chunk 93 optimal weight: 6.9990 chunk 14 optimal weight: 4.9990 chunk 3 optimal weight: 8.9990 chunk 134 optimal weight: 40.0000 chunk 47 optimal weight: 0.5980 chunk 51 optimal weight: 9.9990 overall best weight: 2.3188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 164 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 260 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 164 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 260 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3117 r_free = 0.3117 target = 0.034047 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2810 r_free = 0.2810 target = 0.027021 restraints weight = 144181.899| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.2835 r_free = 0.2835 target = 0.027539 restraints weight = 100767.880| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.2852 r_free = 0.2852 target = 0.027899 restraints weight = 77207.962| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.2864 r_free = 0.2864 target = 0.028165 restraints weight = 63741.367| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.2870 r_free = 0.2870 target = 0.028289 restraints weight = 55199.542| |-----------------------------------------------------------------------------| r_work (final): 0.2846 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8056 moved from start: 0.2296 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 11078 Z= 0.125 Angle : 0.541 7.775 15180 Z= 0.282 Chirality : 0.044 0.259 1800 Planarity : 0.003 0.034 1984 Dihedral : 5.694 48.058 1924 Min Nonbonded Distance : 2.569 Molprobity Statistics. All-atom Clashscore : 8.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.43 % Favored : 93.57 % Rotamer: Outliers : 0.00 % Allowed : 2.58 % Favored : 97.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.92 (0.22), residues: 1540 helix: 1.46 (0.21), residues: 622 sheet: -2.48 (0.35), residues: 184 loop : -2.00 (0.24), residues: 734 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 69 TYR 0.016 0.001 TYR A 573 PHE 0.009 0.001 PHE A 589 TRP 0.009 0.001 TRP B 352 HIS 0.001 0.000 HIS A 312 Details of bonding type rmsd covalent geometry : bond 0.00265 (11046) covalent geometry : angle 0.52645 (15102) SS BOND : bond 0.00314 ( 18) SS BOND : angle 1.01044 ( 36) hydrogen bonds : bond 0.03360 ( 492) hydrogen bonds : angle 4.41555 ( 1398) link_BETA1-4 : bond 0.00285 ( 4) link_BETA1-4 : angle 1.35015 ( 12) link_NAG-ASN : bond 0.00695 ( 10) link_NAG-ASN : angle 2.60553 ( 30) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3080 Ramachandran restraints generated. 1540 Oldfield, 0 Emsley, 1540 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3080 Ramachandran restraints generated. 1540 Oldfield, 0 Emsley, 1540 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 16 residues out of total 1354 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 16 time to evaluate : 0.327 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 197 MET cc_start: 0.9141 (mtm) cc_final: 0.8483 (mtp) REVERT: B 197 MET cc_start: 0.9159 (mtm) cc_final: 0.8521 (mtp) REVERT: B 307 MET cc_start: 0.8504 (mmp) cc_final: 0.8275 (mmm) outliers start: 0 outliers final: 0 residues processed: 16 average time/residue: 0.0859 time to fit residues: 2.5410 Evaluate side-chains 15 residues out of total 1354 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 15 time to evaluate : 0.426 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 1 optimal weight: 1.9990 chunk 80 optimal weight: 0.7980 chunk 61 optimal weight: 9.9990 chunk 79 optimal weight: 6.9990 chunk 147 optimal weight: 6.9990 chunk 136 optimal weight: 6.9990 chunk 36 optimal weight: 9.9990 chunk 141 optimal weight: 40.0000 chunk 89 optimal weight: 3.9990 chunk 8 optimal weight: 6.9990 chunk 140 optimal weight: 9.9990 overall best weight: 4.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 164 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 260 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 359 HIS A 472 ASN ** B 164 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 260 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 472 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3105 r_free = 0.3105 target = 0.033926 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2796 r_free = 0.2796 target = 0.026995 restraints weight = 147914.342| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.2821 r_free = 0.2821 target = 0.027503 restraints weight = 101892.123| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.2838 r_free = 0.2838 target = 0.027872 restraints weight = 77554.962| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 41)----------------| | r_work = 0.2851 r_free = 0.2851 target = 0.028141 restraints weight = 63391.020| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.2860 r_free = 0.2860 target = 0.028324 restraints weight = 54630.363| |-----------------------------------------------------------------------------| r_work (final): 0.2832 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8086 moved from start: 0.2406 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 11078 Z= 0.195 Angle : 0.592 8.399 15180 Z= 0.313 Chirality : 0.045 0.259 1800 Planarity : 0.004 0.034 1984 Dihedral : 5.854 49.029 1924 Min Nonbonded Distance : 2.530 Molprobity Statistics. All-atom Clashscore : 10.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.47 % Favored : 92.53 % Rotamer: Outliers : 0.23 % Allowed : 1.87 % Favored : 97.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.91 (0.22), residues: 1540 helix: 1.47 (0.21), residues: 620 sheet: -2.49 (0.37), residues: 164 loop : -2.02 (0.23), residues: 756 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 69 TYR 0.015 0.002 TYR A 573 PHE 0.013 0.002 PHE A 589 TRP 0.012 0.001 TRP B 352 HIS 0.003 0.001 HIS B 192 Details of bonding type rmsd covalent geometry : bond 0.00409 (11046) covalent geometry : angle 0.57718 (15102) SS BOND : bond 0.00366 ( 18) SS BOND : angle 1.07140 ( 36) hydrogen bonds : bond 0.03583 ( 492) hydrogen bonds : angle 4.52701 ( 1398) link_BETA1-4 : bond 0.00222 ( 4) link_BETA1-4 : angle 1.61668 ( 12) link_NAG-ASN : bond 0.00681 ( 10) link_NAG-ASN : angle 2.67105 ( 30) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3080 Ramachandran restraints generated. 1540 Oldfield, 0 Emsley, 1540 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3080 Ramachandran restraints generated. 1540 Oldfield, 0 Emsley, 1540 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 17 residues out of total 1354 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 15 time to evaluate : 0.425 Fit side-chains revert: symmetry clash REVERT: A 197 MET cc_start: 0.9038 (mtm) cc_final: 0.8440 (mtp) REVERT: B 197 MET cc_start: 0.9140 (mtm) cc_final: 0.8465 (mtp) REVERT: B 307 MET cc_start: 0.8624 (mmp) cc_final: 0.8419 (mmm) outliers start: 2 outliers final: 0 residues processed: 17 average time/residue: 0.0699 time to fit residues: 2.6096 Evaluate side-chains 15 residues out of total 1354 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 15 time to evaluate : 0.372 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 112 optimal weight: 4.9990 chunk 115 optimal weight: 7.9990 chunk 107 optimal weight: 5.9990 chunk 25 optimal weight: 6.9990 chunk 73 optimal weight: 6.9990 chunk 10 optimal weight: 50.0000 chunk 90 optimal weight: 2.9990 chunk 62 optimal weight: 1.9990 chunk 121 optimal weight: 2.9990 chunk 108 optimal weight: 5.9990 chunk 78 optimal weight: 3.9990 overall best weight: 3.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 164 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 260 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 164 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 260 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 359 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3110 r_free = 0.3110 target = 0.034074 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2799 r_free = 0.2799 target = 0.027091 restraints weight = 146387.029| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.2824 r_free = 0.2824 target = 0.027611 restraints weight = 101320.377| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.2842 r_free = 0.2842 target = 0.027977 restraints weight = 77150.240| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.2854 r_free = 0.2854 target = 0.028245 restraints weight = 63040.233| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.2864 r_free = 0.2864 target = 0.028443 restraints weight = 54279.800| |-----------------------------------------------------------------------------| r_work (final): 0.2836 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8071 moved from start: 0.2507 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 11078 Z= 0.161 Angle : 0.570 8.301 15180 Z= 0.298 Chirality : 0.045 0.257 1800 Planarity : 0.003 0.034 1984 Dihedral : 5.797 47.905 1924 Min Nonbonded Distance : 2.549 Molprobity Statistics. All-atom Clashscore : 9.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.14 % Favored : 92.86 % Rotamer: Outliers : 0.00 % Allowed : 0.82 % Favored : 99.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.84 (0.22), residues: 1540 helix: 1.50 (0.21), residues: 622 sheet: -2.45 (0.37), residues: 164 loop : -1.96 (0.23), residues: 754 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 69 TYR 0.016 0.001 TYR B 573 PHE 0.012 0.001 PHE A 589 TRP 0.010 0.001 TRP B 352 HIS 0.002 0.001 HIS B 192 Details of bonding type rmsd covalent geometry : bond 0.00341 (11046) covalent geometry : angle 0.55537 (15102) SS BOND : bond 0.00338 ( 18) SS BOND : angle 1.00470 ( 36) hydrogen bonds : bond 0.03477 ( 492) hydrogen bonds : angle 4.44545 ( 1398) link_BETA1-4 : bond 0.00244 ( 4) link_BETA1-4 : angle 1.46511 ( 12) link_NAG-ASN : bond 0.00686 ( 10) link_NAG-ASN : angle 2.63205 ( 30) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3080 Ramachandran restraints generated. 1540 Oldfield, 0 Emsley, 1540 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3080 Ramachandran restraints generated. 1540 Oldfield, 0 Emsley, 1540 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 15 residues out of total 1354 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 15 time to evaluate : 0.409 Fit side-chains revert: symmetry clash REVERT: A 197 MET cc_start: 0.9008 (mtm) cc_final: 0.8399 (mtp) REVERT: A 473 MET cc_start: 0.7679 (mtt) cc_final: 0.6765 (mpp) REVERT: B 197 MET cc_start: 0.9144 (mtm) cc_final: 0.8514 (mtp) REVERT: B 307 MET cc_start: 0.8595 (mmp) cc_final: 0.8382 (mmm) REVERT: B 473 MET cc_start: 0.7685 (mtt) cc_final: 0.6772 (mpp) outliers start: 0 outliers final: 0 residues processed: 15 average time/residue: 0.0736 time to fit residues: 2.3043 Evaluate side-chains 15 residues out of total 1354 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 15 time to evaluate : 0.405 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 9 optimal weight: 3.9990 chunk 83 optimal weight: 10.0000 chunk 133 optimal weight: 50.0000 chunk 12 optimal weight: 10.0000 chunk 135 optimal weight: 3.9990 chunk 28 optimal weight: 9.9990 chunk 4 optimal weight: 3.9990 chunk 113 optimal weight: 10.0000 chunk 141 optimal weight: 0.0870 chunk 37 optimal weight: 8.9990 chunk 104 optimal weight: 1.9990 overall best weight: 2.8166 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 164 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 260 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 164 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 260 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3113 r_free = 0.3113 target = 0.034179 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2803 r_free = 0.2803 target = 0.027198 restraints weight = 145608.066| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.2829 r_free = 0.2829 target = 0.027721 restraints weight = 101100.621| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.2846 r_free = 0.2846 target = 0.028096 restraints weight = 76748.149| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.2859 r_free = 0.2859 target = 0.028369 restraints weight = 62627.370| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.2867 r_free = 0.2867 target = 0.028535 restraints weight = 53714.290| |-----------------------------------------------------------------------------| r_work (final): 0.2839 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8063 moved from start: 0.2615 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 11078 Z= 0.142 Angle : 0.562 9.461 15180 Z= 0.293 Chirality : 0.044 0.259 1800 Planarity : 0.003 0.034 1984 Dihedral : 5.652 48.125 1924 Min Nonbonded Distance : 2.552 Molprobity Statistics. All-atom Clashscore : 9.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.27 % Favored : 92.73 % Rotamer: Outliers : 0.00 % Allowed : 0.35 % Favored : 99.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.71 (0.22), residues: 1540 helix: 1.61 (0.21), residues: 622 sheet: -2.42 (0.37), residues: 162 loop : -1.88 (0.24), residues: 756 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 69 TYR 0.015 0.002 TYR A 573 PHE 0.011 0.001 PHE A 589 TRP 0.009 0.001 TRP B 352 HIS 0.002 0.001 HIS A 192 Details of bonding type rmsd covalent geometry : bond 0.00300 (11046) covalent geometry : angle 0.54788 (15102) SS BOND : bond 0.00372 ( 18) SS BOND : angle 1.01263 ( 36) hydrogen bonds : bond 0.03394 ( 492) hydrogen bonds : angle 4.33721 ( 1398) link_BETA1-4 : bond 0.00311 ( 4) link_BETA1-4 : angle 1.35532 ( 12) link_NAG-ASN : bond 0.00685 ( 10) link_NAG-ASN : angle 2.64305 ( 30) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3080 Ramachandran restraints generated. 1540 Oldfield, 0 Emsley, 1540 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3080 Ramachandran restraints generated. 1540 Oldfield, 0 Emsley, 1540 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 15 residues out of total 1354 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 15 time to evaluate : 0.400 Fit side-chains REVERT: A 197 MET cc_start: 0.9040 (mtm) cc_final: 0.8439 (mtp) REVERT: A 473 MET cc_start: 0.7649 (mtt) cc_final: 0.6743 (mpp) REVERT: B 197 MET cc_start: 0.9139 (mtm) cc_final: 0.8494 (mtp) REVERT: B 473 MET cc_start: 0.7674 (mtt) cc_final: 0.6708 (mpp) outliers start: 0 outliers final: 0 residues processed: 15 average time/residue: 0.0614 time to fit residues: 1.9766 Evaluate side-chains 14 residues out of total 1354 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 14 time to evaluate : 0.487 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 41 optimal weight: 7.9990 chunk 32 optimal weight: 20.0000 chunk 131 optimal weight: 7.9990 chunk 139 optimal weight: 8.9990 chunk 111 optimal weight: 8.9990 chunk 16 optimal weight: 0.5980 chunk 133 optimal weight: 50.0000 chunk 54 optimal weight: 3.9990 chunk 90 optimal weight: 0.0970 chunk 5 optimal weight: 4.9990 chunk 114 optimal weight: 0.9980 overall best weight: 2.1382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 164 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 260 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 164 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 260 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3121 r_free = 0.3121 target = 0.034365 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2811 r_free = 0.2811 target = 0.027332 restraints weight = 146709.087| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.2836 r_free = 0.2836 target = 0.027853 restraints weight = 100369.622| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.2854 r_free = 0.2854 target = 0.028236 restraints weight = 76310.651| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.2865 r_free = 0.2865 target = 0.028464 restraints weight = 62050.516| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.2876 r_free = 0.2876 target = 0.028705 restraints weight = 53866.022| |-----------------------------------------------------------------------------| r_work (final): 0.2848 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8047 moved from start: 0.2729 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 11078 Z= 0.120 Angle : 0.540 7.767 15180 Z= 0.282 Chirality : 0.044 0.261 1800 Planarity : 0.003 0.033 1984 Dihedral : 5.465 48.422 1924 Min Nonbonded Distance : 2.572 Molprobity Statistics. All-atom Clashscore : 8.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.08 % Favored : 92.92 % Rotamer: Outliers : 0.00 % Allowed : 0.35 % Favored : 99.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.65 (0.23), residues: 1540 helix: 1.61 (0.21), residues: 636 sheet: -2.50 (0.38), residues: 150 loop : -1.87 (0.24), residues: 754 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 69 TYR 0.015 0.001 TYR B 573 PHE 0.009 0.001 PHE B 589 TRP 0.009 0.001 TRP B 352 HIS 0.005 0.000 HIS B 192 Details of bonding type rmsd covalent geometry : bond 0.00256 (11046) covalent geometry : angle 0.52586 (15102) SS BOND : bond 0.00316 ( 18) SS BOND : angle 0.91400 ( 36) hydrogen bonds : bond 0.03250 ( 492) hydrogen bonds : angle 4.23305 ( 1398) link_BETA1-4 : bond 0.00338 ( 4) link_BETA1-4 : angle 1.29652 ( 12) link_NAG-ASN : bond 0.00692 ( 10) link_NAG-ASN : angle 2.61851 ( 30) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1388.78 seconds wall clock time: 24 minutes 51.30 seconds (1491.30 seconds total)