Starting phenix.real_space_refine on Fri Jul 3 00:09:35 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7dtu_30854/07_2026/7dtu_30854.cif Found real_map, /net/cci-nas-00/data/ceres_data/7dtu_30854/07_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 { model { file = "/net/cci-nas-00/data/ceres_data/7dtu_30854/07_2026/7dtu_30854.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7dtu_30854/07_2026/7dtu_30854.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7dtu_30854/07_2026/7dtu_30854.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7dtu_30854/07_2026/7dtu_30854.map" restraint_files = "/net/cci-nas-00/data/ceres_data/7dtu_30854/07_2026/7dtu_30854.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7dtu_30854/07_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-6108/lib/python3.11/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 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 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 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 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 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 chiralities: 3 Time building chain proxies: 2.47, per 1000 atoms: 0.23 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: 0.86 Conformation dependent library (CDL) restraints added in 523.9 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: 0.24 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: 1.61 Time building geometry restraints manager: 1.15 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: 5836 17.94 - 35.88: 469 35.88 - 53.82: 75 53.82 - 71.76: 16 71.76 - 89.70: 16 Dihedral angle restraints: 6412 sinusoidal: 1898 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 6409 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: 0.01 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: 2.240 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.000 Extract box with map and model: 0.190 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 10.590 Find NCS groups from input model: 0.150 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:1.020 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 14.280 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7889 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 : 14.571 89.703 3430 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/Z covalent geometry : bond 0.00592 / 0.29 (11046) covalent geometry : angle 0.90289 / 0.51 (15102) SS BOND : bond 0.20540 / 8.58 ( 18) SS BOND : angle 4.47510 / 2.51 ( 36) hydrogen bonds : bond 0.13364 / 8.91 ( 492) hydrogen bonds : angle 5.78684 / 3.97 ( 1398) link_BETA1-4 : bond 0.00398 / 0.20 ( 4) link_BETA1-4 : angle 2.80826 / 1.64 ( 12) link_NAG-ASN : bond 0.01331 / 0.84 ( 10) link_NAG-ASN : angle 4.78932 / 2.71 ( 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 : 0.418 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: 0.0744 time to fit residues: 2.3772 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 : 0.395 ------------------------------------------------------------------------------- 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... 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 = 0.3128 r_free = 0.3128 target = 0.034654 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2806 r_free = 0.2806 target = 0.027329 restraints weight = 143103.106| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.2830 r_free = 0.2830 target = 0.027858 restraints weight = 97391.816| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.2848 r_free = 0.2848 target = 0.028244 restraints weight = 73831.300| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.2860 r_free = 0.2860 target = 0.028517 restraints weight = 60034.738| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.2867 r_free = 0.2867 target = 0.028649 restraints weight = 51569.483| |-----------------------------------------------------------------------------| r_work (final): 0.2840 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7971 moved from start: 0.1123 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 11078 Z= 0.147 Angle : 0.605 8.280 15180 Z= 0.321 Chirality : 0.046 0.295 1800 Planarity : 0.004 0.036 1984 Dihedral : 5.499 20.097 1630 Min Nonbonded Distance : 2.402 Molprobity Statistics. All-atom Clashscore : 7.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.88 % Favored : 93.12 % Rotamer: Outliers : 0.00 % Allowed : 5.27 % Favored : 94.73 % 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: -2.43 (0.21), residues: 1540 helix: -0.26 (0.19), residues: 608 sheet: -3.33 (0.32), residues: 210 loop : -2.24 (0.23), residues: 722 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 535 TYR 0.017 0.002 TYR B 573 PHE 0.011 0.001 PHE A 270 TRP 0.014 0.001 TRP A 352 HIS 0.003 0.001 HIS A 338 Details of bonding type rmsd/Z covalent geometry : bond 0.00304 / 0.15 (11046) covalent geometry : angle 0.58607 / 0.32 (15102) SS BOND : bond 0.00709 / 0.44 ( 18) SS BOND : angle 1.49637 / 0.80 ( 36) hydrogen bonds : bond 0.04153 / 2.75 ( 492) hydrogen bonds : angle 4.80181 / 3.31 ( 1398) link_BETA1-4 : bond 0.00314 / 0.17 ( 4) link_BETA1-4 : angle 1.49259 / 0.76 ( 12) link_NAG-ASN : bond 0.00635 / 0.40 ( 10) link_NAG-ASN : angle 2.92579 / 1.70 ( 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 : 0.427 Fit side-chains revert: symmetry clash REVERT: A 307 MET cc_start: 0.8420 (mmp) cc_final: 0.8096 (mmm) REVERT: A 464 LEU cc_start: 0.9401 (mt) cc_final: 0.9031 (mt) REVERT: A 473 MET cc_start: 0.7605 (ptp) cc_final: 0.6963 (mpp) REVERT: B 197 MET cc_start: 0.9010 (mtm) cc_final: 0.8526 (mtp) REVERT: B 464 LEU cc_start: 0.9437 (mt) cc_final: 0.9088 (mt) REVERT: B 473 MET cc_start: 0.7674 (ptp) cc_final: 0.6958 (mpp) outliers start: 0 outliers final: 0 residues processed: 18 average time/residue: 0.0693 time to fit residues: 2.5767 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 : 0.437 ------------------------------------------------------------------------------- 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: 1.9990 chunk 104 optimal weight: 4.9990 chunk 106 optimal weight: 0.7980 chunk 64 optimal weight: 50.0000 chunk 26 optimal weight: 0.7980 chunk 38 optimal weight: 20.0000 chunk 138 optimal weight: 20.0000 chunk 135 optimal weight: 6.9990 chunk 142 optimal weight: 7.9990 chunk 148 optimal weight: 50.0000 chunk 107 optimal weight: 6.9990 overall best weight: 3.1186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** 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 = 0.3114 r_free = 0.3114 target = 0.034273 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2801 r_free = 0.2801 target = 0.027194 restraints weight = 146756.302| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.2825 r_free = 0.2825 target = 0.027707 restraints weight = 100277.681| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.2842 r_free = 0.2842 target = 0.028081 restraints weight = 76068.322| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.2856 r_free = 0.2856 target = 0.028363 restraints weight = 61815.297| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.2864 r_free = 0.2864 target = 0.028543 restraints weight = 52931.978| |-----------------------------------------------------------------------------| r_work (final): 0.2838 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7977 moved from start: 0.1462 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= 0.159 Angle : 0.578 8.023 15180 Z= 0.306 Chirality : 0.045 0.283 1800 Planarity : 0.003 0.035 1984 Dihedral : 5.082 18.788 1630 Min Nonbonded Distance : 2.391 Molprobity Statistics. All-atom Clashscore : 7.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.82 % Favored : 93.18 % Rotamer: Outliers : 0.00 % Allowed : 5.85 % Favored : 94.15 % 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: -1.75 (0.22), residues: 1540 helix: 0.50 (0.20), residues: 614 sheet: -2.96 (0.35), residues: 198 loop : -2.12 (0.24), residues: 728 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 69 TYR 0.017 0.002 TYR B 573 PHE 0.014 0.001 PHE A 38 TRP 0.011 0.001 TRP A 458 HIS 0.002 0.001 HIS B 192 Details of bonding type rmsd/Z covalent geometry : bond 0.00333 / 0.16 (11046) covalent geometry : angle 0.56122 / 0.30 (15102) SS BOND : bond 0.00393 / 0.23 ( 18) SS BOND : angle 1.05642 / 0.60 ( 36) hydrogen bonds : bond 0.03808 / 2.51 ( 492) hydrogen bonds : angle 4.65377 / 3.23 ( 1398) link_BETA1-4 : bond 0.00205 / 0.11 ( 4) link_BETA1-4 : angle 1.65908 / 0.85 ( 12) link_NAG-ASN : bond 0.00705 / 0.45 ( 10) link_NAG-ASN : angle 2.83241 / 1.68 ( 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 16 residues out of total 1354 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 16 time to evaluate : 0.434 Fit side-chains REVERT: A 197 MET cc_start: 0.9077 (mtm) cc_final: 0.8504 (mtp) REVERT: A 464 LEU cc_start: 0.9430 (mt) cc_final: 0.9066 (mt) REVERT: B 197 MET cc_start: 0.9088 (mtm) cc_final: 0.8504 (mtp) REVERT: B 307 MET cc_start: 0.8642 (mmp) cc_final: 0.8247 (mmm) REVERT: B 464 LEU cc_start: 0.9447 (mt) cc_final: 0.9071 (mt) outliers start: 0 outliers final: 0 residues processed: 16 average time/residue: 0.0693 time to fit residues: 2.3732 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 : 0.310 ------------------------------------------------------------------------------- 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: 30.0000 chunk 97 optimal weight: 8.9990 chunk 40 optimal weight: 2.9990 chunk 48 optimal weight: 9.9990 chunk 68 optimal weight: 50.0000 chunk 70 optimal weight: 6.9990 chunk 42 optimal weight: 3.9990 chunk 71 optimal weight: 4.9990 chunk 58 optimal weight: 7.9990 chunk 84 optimal weight: 9.9990 overall best weight: 4.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** 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: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3093 r_free = 0.3093 target = 0.033565 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2784 r_free = 0.2784 target = 0.026612 restraints weight = 149857.255| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.2810 r_free = 0.2810 target = 0.027119 restraints weight = 103112.444| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.2827 r_free = 0.2827 target = 0.027493 restraints weight = 78554.424| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.2839 r_free = 0.2839 target = 0.027743 restraints weight = 64356.810| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.2848 r_free = 0.2848 target = 0.027935 restraints weight = 55792.321| |-----------------------------------------------------------------------------| r_work (final): 0.2822 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8020 moved from start: 0.1832 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.041 11078 Z= 0.229 Angle : 0.635 7.737 15180 Z= 0.338 Chirality : 0.045 0.270 1800 Planarity : 0.004 0.034 1984 Dihedral : 5.084 18.095 1630 Min Nonbonded Distance : 2.365 Molprobity Statistics. All-atom Clashscore : 9.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.27 % Favored : 92.73 % Rotamer: Outliers : 0.00 % Allowed : 3.40 % Favored : 96.60 % 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: -1.52 (0.22), residues: 1540 helix: 0.84 (0.20), residues: 618 sheet: -2.98 (0.35), residues: 198 loop : -2.11 (0.23), residues: 724 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 69 TYR 0.016 0.002 TYR B 573 PHE 0.016 0.002 PHE A 38 TRP 0.012 0.001 TRP A 458 HIS 0.004 0.001 HIS B 192 Details of bonding type rmsd/Z covalent geometry : bond 0.00477 / 0.23 (11046) covalent geometry : angle 0.61924 / 0.33 (15102) SS BOND : bond 0.00448 / 0.27 ( 18) SS BOND : angle 1.11959 / 0.60 ( 36) hydrogen bonds : bond 0.03933 / 2.58 ( 492) hydrogen bonds : angle 4.78352 / 3.33 ( 1398) link_BETA1-4 : bond 0.00235 / 0.13 ( 4) link_BETA1-4 : angle 1.92008 / 0.92 ( 12) link_NAG-ASN : bond 0.00715 / 0.46 ( 10) link_NAG-ASN : angle 2.80656 / 1.65 ( 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 16 residues out of total 1354 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 16 time to evaluate : 0.432 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 197 MET cc_start: 0.9058 (mtm) cc_final: 0.8490 (mtp) REVERT: B 197 MET cc_start: 0.9097 (mtm) cc_final: 0.8481 (mtp) REVERT: B 307 MET cc_start: 0.8727 (mmp) cc_final: 0.8475 (mmm) outliers start: 0 outliers final: 0 residues processed: 16 average time/residue: 0.0750 time to fit residues: 2.4126 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 : 0.418 ------------------------------------------------------------------------------- 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: 0.7980 chunk 60 optimal weight: 8.9990 chunk 31 optimal weight: 9.9990 chunk 133 optimal weight: 50.0000 chunk 4 optimal weight: 4.9990 chunk 41 optimal weight: 1.9990 chunk 152 optimal weight: 5.9990 chunk 153 optimal weight: 10.0000 chunk 71 optimal weight: 40.0000 chunk 32 optimal weight: 20.0000 chunk 120 optimal weight: 0.9990 overall best weight: 2.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 117 GLN ** 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: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3113 r_free = 0.3113 target = 0.034128 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2806 r_free = 0.2806 target = 0.027160 restraints weight = 146950.356| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.2830 r_free = 0.2830 target = 0.027676 restraints weight = 100827.757| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.2849 r_free = 0.2849 target = 0.028058 restraints weight = 76687.275| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.2861 r_free = 0.2861 target = 0.028330 restraints weight = 62459.761| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.2869 r_free = 0.2869 target = 0.028494 restraints weight = 53623.307| |-----------------------------------------------------------------------------| r_work (final): 0.2842 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7984 moved from start: 0.1997 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= 0.149 Angle : 0.568 7.633 15180 Z= 0.299 Chirality : 0.044 0.270 1800 Planarity : 0.003 0.034 1984 Dihedral : 4.842 18.508 1630 Min Nonbonded Distance : 2.399 Molprobity Statistics. All-atom Clashscore : 8.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.01 % Favored : 92.99 % Rotamer: Outliers : 0.00 % Allowed : 3.40 % Favored : 96.60 % 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: -1.25 (0.22), residues: 1540 helix: 1.20 (0.20), residues: 618 sheet: -3.04 (0.33), residues: 208 loop : -2.00 (0.24), residues: 714 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 69 TYR 0.016 0.002 TYR A 573 PHE 0.011 0.001 PHE B 589 TRP 0.009 0.001 TRP A 352 HIS 0.002 0.000 HIS A 312 Details of bonding type rmsd/Z covalent geometry : bond 0.00318 / 0.15 (11046) covalent geometry : angle 0.55080 / 0.29 (15102) SS BOND : bond 0.00407 / 0.24 ( 18) SS BOND : angle 1.45499 / 0.76 ( 36) hydrogen bonds : bond 0.03585 / 2.35 ( 492) hydrogen bonds : angle 4.58864 / 3.18 ( 1398) link_BETA1-4 : bond 0.00244 / 0.14 ( 4) link_BETA1-4 : angle 1.58291 / 0.79 ( 12) link_NAG-ASN : bond 0.00703 / 0.44 ( 10) link_NAG-ASN : angle 2.68248 / 1.59 ( 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 : 0.399 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 197 MET cc_start: 0.9154 (mtm) cc_final: 0.8556 (mtp) REVERT: B 197 MET cc_start: 0.9173 (mtm) cc_final: 0.8575 (mtp) outliers start: 0 outliers final: 0 residues processed: 16 average time/residue: 0.0691 time to fit residues: 2.2825 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 : 0.302 ------------------------------------------------------------------------------- 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: 3.9990 chunk 76 optimal weight: 20.0000 chunk 75 optimal weight: 5.9990 chunk 8 optimal weight: 5.9990 chunk 51 optimal weight: 9.9990 chunk 12 optimal weight: 0.0870 chunk 49 optimal weight: 9.9990 chunk 72 optimal weight: 30.0000 chunk 135 optimal weight: 6.9990 chunk 37 optimal weight: 10.0000 chunk 83 optimal weight: 9.9990 overall best weight: 4.6166 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** 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 = 0.3101 r_free = 0.3101 target = 0.033828 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2791 r_free = 0.2791 target = 0.026924 restraints weight = 149591.656| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.2816 r_free = 0.2816 target = 0.027431 restraints weight = 103013.605| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.2834 r_free = 0.2834 target = 0.027797 restraints weight = 78615.367| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.2845 r_free = 0.2845 target = 0.028031 restraints weight = 64428.670| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 44)----------------| | r_work = 0.2856 r_free = 0.2856 target = 0.028258 restraints weight = 55815.776| |-----------------------------------------------------------------------------| r_work (final): 0.2831 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8011 moved from start: 0.2155 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 11078 Z= 0.211 Angle : 0.610 7.680 15180 Z= 0.323 Chirality : 0.045 0.267 1800 Planarity : 0.004 0.034 1984 Dihedral : 4.901 18.884 1630 Min Nonbonded Distance : 2.370 Molprobity Statistics. All-atom Clashscore : 10.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.86 % Favored : 92.14 % Rotamer: Outliers : 0.00 % Allowed : 2.81 % Favored : 97.19 % 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: -1.17 (0.22), residues: 1540 helix: 1.21 (0.20), residues: 630 sheet: -2.69 (0.37), residues: 164 loop : -2.16 (0.23), residues: 746 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 0.002 PHE B 589 TRP 0.012 0.001 TRP A 352 HIS 0.003 0.001 HIS A 192 Details of bonding type rmsd/Z covalent geometry : bond 0.00442 / 0.21 (11046) covalent geometry : angle 0.59362 / 0.32 (15102) SS BOND : bond 0.00487 / 0.28 ( 18) SS BOND : angle 1.39646 / 0.85 ( 36) hydrogen bonds : bond 0.03720 / 2.43 ( 492) hydrogen bonds : angle 4.65798 / 3.24 ( 1398) link_BETA1-4 : bond 0.00235 / 0.13 ( 4) link_BETA1-4 : angle 1.81736 / 0.87 ( 12) link_NAG-ASN : bond 0.00715 / 0.46 ( 10) link_NAG-ASN : angle 2.73788 / 1.62 ( 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 : 0.446 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 197 MET cc_start: 0.9122 (mtm) cc_final: 0.8457 (mtp) REVERT: A 307 MET cc_start: 0.8482 (mmp) cc_final: 0.8071 (mmm) REVERT: B 197 MET cc_start: 0.9140 (mtm) cc_final: 0.8476 (mtp) REVERT: B 307 MET cc_start: 0.8702 (mmp) cc_final: 0.8501 (mmm) outliers start: 0 outliers final: 0 residues processed: 16 average time/residue: 0.0732 time to fit residues: 2.3459 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 : 0.406 ------------------------------------------------------------------------------- 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: 9.9990 chunk 37 optimal weight: 0.6980 chunk 144 optimal weight: 50.0000 chunk 118 optimal weight: 3.9990 chunk 6 optimal weight: 10.0000 chunk 93 optimal weight: 6.9990 chunk 14 optimal weight: 0.9990 chunk 3 optimal weight: 5.9990 chunk 134 optimal weight: 40.0000 chunk 47 optimal weight: 0.8980 chunk 51 optimal weight: 6.9990 overall best weight: 2.5186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** 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 = 0.3118 r_free = 0.3118 target = 0.034237 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2806 r_free = 0.2806 target = 0.027221 restraints weight = 146524.501| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.2832 r_free = 0.2832 target = 0.027750 restraints weight = 100781.678| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.2851 r_free = 0.2851 target = 0.028130 restraints weight = 76394.542| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.2863 r_free = 0.2863 target = 0.028388 restraints weight = 62304.003| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.2873 r_free = 0.2873 target = 0.028605 restraints weight = 53841.001| |-----------------------------------------------------------------------------| r_work (final): 0.2846 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7977 moved from start: 0.2277 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= 0.135 Angle : 0.549 7.695 15180 Z= 0.287 Chirality : 0.044 0.264 1800 Planarity : 0.003 0.034 1984 Dihedral : 4.673 17.268 1630 Min Nonbonded Distance : 2.406 Molprobity Statistics. All-atom Clashscore : 8.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.21 % Favored : 92.79 % Rotamer: Outliers : 0.00 % Allowed : 1.41 % Favored : 98.59 % 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: -0.97 (0.22), residues: 1540 helix: 1.41 (0.21), residues: 620 sheet: -2.57 (0.37), residues: 164 loop : -2.03 (0.23), residues: 756 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 69 TYR 0.016 0.001 TYR A 573 PHE 0.010 0.001 PHE A 589 TRP 0.009 0.001 TRP B 352 HIS 0.002 0.000 HIS B 192 Details of bonding type rmsd/Z covalent geometry : bond 0.00287 / 0.14 (11046) covalent geometry : angle 0.53363 / 0.28 (15102) SS BOND : bond 0.00324 / 0.20 ( 18) SS BOND : angle 0.99930 / 0.61 ( 36) hydrogen bonds : bond 0.03429 / 2.24 ( 492) hydrogen bonds : angle 4.44962 / 3.09 ( 1398) link_BETA1-4 : bond 0.00236 / 0.13 ( 4) link_BETA1-4 : angle 1.51625 / 0.75 ( 12) link_NAG-ASN : bond 0.00681 / 0.43 ( 10) link_NAG-ASN : angle 2.66313 / 1.59 ( 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 : 0.634 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 197 MET cc_start: 0.9146 (mtm) cc_final: 0.8538 (mtp) REVERT: A 307 MET cc_start: 0.8499 (mmp) cc_final: 0.8159 (mmm) REVERT: B 197 MET cc_start: 0.9153 (mtm) cc_final: 0.8525 (mtp) outliers start: 0 outliers final: 0 residues processed: 16 average time/residue: 0.0739 time to fit residues: 2.4711 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 : 0.501 ------------------------------------------------------------------------------- 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: 0.9990 chunk 61 optimal weight: 30.0000 chunk 79 optimal weight: 5.9990 chunk 147 optimal weight: 5.9990 chunk 136 optimal weight: 6.9990 chunk 36 optimal weight: 10.0000 chunk 141 optimal weight: 5.9990 chunk 89 optimal weight: 3.9990 chunk 8 optimal weight: 0.9980 chunk 140 optimal weight: 9.9990 overall best weight: 2.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** 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 = 0.3114 r_free = 0.3114 target = 0.034166 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2798 r_free = 0.2798 target = 0.027046 restraints weight = 146424.335| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.2823 r_free = 0.2823 target = 0.027563 restraints weight = 100493.623| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.2841 r_free = 0.2841 target = 0.027942 restraints weight = 76566.594| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.2854 r_free = 0.2854 target = 0.028223 restraints weight = 62440.783| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 21)----------------| | r_work = 0.2862 r_free = 0.2862 target = 0.028393 restraints weight = 53638.382| |-----------------------------------------------------------------------------| r_work (final): 0.2836 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7985 moved from start: 0.2417 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 11078 Z= 0.142 Angle : 0.552 7.689 15180 Z= 0.288 Chirality : 0.044 0.267 1800 Planarity : 0.003 0.034 1984 Dihedral : 4.553 17.098 1630 Min Nonbonded Distance : 2.404 Molprobity Statistics. All-atom Clashscore : 8.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.95 % Favored : 93.05 % Rotamer: Outliers : 0.00 % Allowed : 1.64 % Favored : 98.36 % 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: -0.81 (0.22), residues: 1540 helix: 1.54 (0.21), residues: 622 sheet: -2.54 (0.37), residues: 164 loop : -1.94 (0.23), residues: 754 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 69 TYR 0.015 0.001 TYR B 573 PHE 0.011 0.001 PHE A 589 TRP 0.011 0.001 TRP B 352 HIS 0.002 0.001 HIS B 192 Details of bonding type rmsd/Z covalent geometry : bond 0.00302 / 0.14 (11046) covalent geometry : angle 0.53738 / 0.29 (15102) SS BOND : bond 0.00300 / 0.18 ( 18) SS BOND : angle 0.99113 / 0.59 ( 36) hydrogen bonds : bond 0.03392 / 2.22 ( 492) hydrogen bonds : angle 4.36804 / 3.03 ( 1398) link_BETA1-4 : bond 0.00224 / 0.13 ( 4) link_BETA1-4 : angle 1.53583 / 0.74 ( 12) link_NAG-ASN : bond 0.00680 / 0.43 ( 10) link_NAG-ASN : angle 2.63465 / 1.58 ( 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 16 residues out of total 1354 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 16 time to evaluate : 0.441 Fit side-chains revert: symmetry clash REVERT: A 197 MET cc_start: 0.9143 (mtm) cc_final: 0.8550 (mtp) REVERT: A 307 MET cc_start: 0.8551 (mmp) cc_final: 0.8153 (mmm) REVERT: B 197 MET cc_start: 0.9150 (mtm) cc_final: 0.8524 (mtp) outliers start: 0 outliers final: 0 residues processed: 16 average time/residue: 0.0743 time to fit residues: 2.4803 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 : 0.421 ------------------------------------------------------------------------------- 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: 10.0000 chunk 115 optimal weight: 4.9990 chunk 107 optimal weight: 1.9990 chunk 25 optimal weight: 3.9990 chunk 73 optimal weight: 9.9990 chunk 10 optimal weight: 50.0000 chunk 90 optimal weight: 8.9990 chunk 62 optimal weight: 10.0000 chunk 121 optimal weight: 8.9990 chunk 108 optimal weight: 4.9990 chunk 78 optimal weight: 2.9990 overall best weight: 3.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** 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 = 0.3105 r_free = 0.3105 target = 0.033969 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.2795 r_free = 0.2795 target = 0.027021 restraints weight = 147150.628| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.2820 r_free = 0.2820 target = 0.027525 restraints weight = 101651.879| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.2838 r_free = 0.2838 target = 0.027889 restraints weight = 77911.020| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.2849 r_free = 0.2849 target = 0.028109 restraints weight = 63902.970| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.2859 r_free = 0.2859 target = 0.028346 restraints weight = 55543.121| |-----------------------------------------------------------------------------| r_work (final): 0.2832 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7999 moved from start: 0.2526 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 11078 Z= 0.178 Angle : 0.580 7.684 15180 Z= 0.305 Chirality : 0.045 0.265 1800 Planarity : 0.003 0.033 1984 Dihedral : 4.647 17.052 1630 Min Nonbonded Distance : 2.390 Molprobity Statistics. All-atom Clashscore : 9.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.66 % Favored : 92.34 % Rotamer: Outliers : 0.00 % Allowed : 1.41 % Favored : 98.59 % 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: -0.94 (0.22), residues: 1540 helix: 1.38 (0.21), residues: 634 sheet: -2.57 (0.37), residues: 164 loop : -2.02 (0.23), residues: 742 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 69 TYR 0.015 0.001 TYR A 573 PHE 0.014 0.001 PHE B 76 TRP 0.011 0.001 TRP A 352 HIS 0.004 0.001 HIS B 192 Details of bonding type rmsd/Z covalent geometry : bond 0.00375 / 0.18 (11046) covalent geometry : angle 0.56467 / 0.30 (15102) SS BOND : bond 0.00399 / 0.25 ( 18) SS BOND : angle 1.04659 / 0.62 ( 36) hydrogen bonds : bond 0.03495 / 2.28 ( 492) hydrogen bonds : angle 4.43628 / 3.08 ( 1398) link_BETA1-4 : bond 0.00166 / 0.10 ( 4) link_BETA1-4 : angle 1.65735 / 0.78 ( 12) link_NAG-ASN : bond 0.00673 / 0.42 ( 10) link_NAG-ASN : angle 2.67171 / 1.60 ( 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 14 residues out of total 1354 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 14 time to evaluate : 0.420 Fit side-chains REVERT: A 197 MET cc_start: 0.9143 (mtm) cc_final: 0.8481 (mtp) REVERT: A 307 MET cc_start: 0.8662 (mmp) cc_final: 0.8297 (mmm) REVERT: B 197 MET cc_start: 0.9019 (mtm) cc_final: 0.8420 (mtp) outliers start: 0 outliers final: 0 residues processed: 14 average time/residue: 0.0695 time to fit residues: 2.1815 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 : 0.405 ------------------------------------------------------------------------------- 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: 0.4980 chunk 83 optimal weight: 9.9990 chunk 133 optimal weight: 50.0000 chunk 12 optimal weight: 0.9980 chunk 135 optimal weight: 4.9990 chunk 28 optimal weight: 9.9990 chunk 4 optimal weight: 4.9990 chunk 113 optimal weight: 10.0000 chunk 141 optimal weight: 50.0000 chunk 37 optimal weight: 9.9990 chunk 104 optimal weight: 10.0000 overall best weight: 4.2986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 164 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 260 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 359 HIS ** 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: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3100 r_free = 0.3100 target = 0.033699 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2790 r_free = 0.2790 target = 0.026720 restraints weight = 145681.120| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.2814 r_free = 0.2814 target = 0.027216 restraints weight = 101466.246| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.2831 r_free = 0.2831 target = 0.027574 restraints weight = 78071.274| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.2843 r_free = 0.2843 target = 0.027834 restraints weight = 64363.351| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.2852 r_free = 0.2852 target = 0.028018 restraints weight = 55880.475| |-----------------------------------------------------------------------------| r_work (final): 0.2827 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8013 moved from start: 0.2684 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= 0.197 Angle : 0.606 7.833 15180 Z= 0.320 Chirality : 0.045 0.257 1800 Planarity : 0.004 0.037 1984 Dihedral : 4.758 17.863 1630 Min Nonbonded Distance : 2.384 Molprobity Statistics. All-atom Clashscore : 10.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.73 % Favored : 92.27 % Rotamer: Outliers : 0.00 % Allowed : 0.47 % Favored : 99.53 % 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: -0.97 (0.22), residues: 1540 helix: 1.39 (0.21), residues: 632 sheet: -2.57 (0.37), residues: 162 loop : -2.07 (0.23), residues: 746 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 69 TYR 0.018 0.002 TYR A 63 PHE 0.017 0.002 PHE B 76 TRP 0.010 0.001 TRP B 352 HIS 0.003 0.001 HIS A 192 Details of bonding type rmsd/Z covalent geometry : bond 0.00413 / 0.20 (11046) covalent geometry : angle 0.59024 / 0.32 (15102) SS BOND : bond 0.00374 / 0.23 ( 18) SS BOND : angle 1.30505 / 0.80 ( 36) hydrogen bonds : bond 0.03673 / 2.41 ( 492) hydrogen bonds : angle 4.49504 / 3.11 ( 1398) link_BETA1-4 : bond 0.00202 / 0.11 ( 4) link_BETA1-4 : angle 1.74990 / 0.81 ( 12) link_NAG-ASN : bond 0.00684 / 0.43 ( 10) link_NAG-ASN : angle 2.66940 / 1.60 ( 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 14 residues out of total 1354 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 14 time to evaluate : 0.377 Fit side-chains REVERT: A 197 MET cc_start: 0.9128 (mtm) cc_final: 0.8446 (mtp) REVERT: A 307 MET cc_start: 0.8712 (mmp) cc_final: 0.8458 (mmm) REVERT: B 197 MET cc_start: 0.8990 (mtm) cc_final: 0.8356 (mtp) outliers start: 0 outliers final: 0 residues processed: 14 average time/residue: 0.0697 time to fit residues: 2.1437 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 : 0.395 ------------------------------------------------------------------------------- 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: 9.9990 chunk 32 optimal weight: 20.0000 chunk 131 optimal weight: 9.9990 chunk 139 optimal weight: 6.9990 chunk 111 optimal weight: 0.0980 chunk 16 optimal weight: 0.8980 chunk 133 optimal weight: 50.0000 chunk 54 optimal weight: 9.9990 chunk 90 optimal weight: 0.6980 chunk 5 optimal weight: 0.9990 chunk 114 optimal weight: 0.9990 overall best weight: 0.7384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** 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 = 0.3129 r_free = 0.3129 target = 0.034619 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.2825 r_free = 0.2825 target = 0.027601 restraints weight = 145365.410| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.2849 r_free = 0.2849 target = 0.028106 restraints weight = 101245.837| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.2866 r_free = 0.2866 target = 0.028475 restraints weight = 77772.837| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.2879 r_free = 0.2879 target = 0.028752 restraints weight = 63758.567| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.2886 r_free = 0.2886 target = 0.028910 restraints weight = 54881.640| |-----------------------------------------------------------------------------| r_work (final): 0.2858 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7936 moved from start: 0.2809 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 11078 Z= 0.096 Angle : 0.541 7.767 15180 Z= 0.278 Chirality : 0.044 0.269 1800 Planarity : 0.003 0.033 1984 Dihedral : 4.383 16.685 1630 Min Nonbonded Distance : 2.439 Molprobity Statistics. All-atom Clashscore : 7.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.30 % Favored : 93.70 % Rotamer: Outliers : 0.00 % Allowed : 0.47 % Favored : 99.53 % 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: -0.67 (0.23), residues: 1540 helix: 1.62 (0.21), residues: 636 sheet: -2.56 (0.37), residues: 152 loop : -1.87 (0.24), residues: 752 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 69 TYR 0.015 0.001 TYR A 573 PHE 0.009 0.001 PHE B 351 TRP 0.011 0.001 TRP B 208 HIS 0.001 0.000 HIS B 192 Details of bonding type rmsd/Z covalent geometry : bond 0.00200 / 0.10 (11046) covalent geometry : angle 0.52718 / 0.28 (15102) SS BOND : bond 0.00307 / 0.19 ( 18) SS BOND : angle 0.79435 / 0.49 ( 36) hydrogen bonds : bond 0.03247 / 2.13 ( 492) hydrogen bonds : angle 4.17587 / 2.88 ( 1398) link_BETA1-4 : bond 0.00355 / 0.19 ( 4) link_BETA1-4 : angle 1.34444 / 0.70 ( 12) link_NAG-ASN : bond 0.00774 / 0.49 ( 10) link_NAG-ASN : angle 2.60143 / 1.58 ( 30) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1426.52 seconds wall clock time: 25 minutes 39.91 seconds (1539.91 seconds total)