Starting phenix.real_space_refine on Tue Jul 29 05:56:26 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7dtu_30854/07_2025/7dtu_30854.cif Found real_map, /net/cci-nas-00/data/ceres_data/7dtu_30854/07_2025/7dtu_30854.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7dtu_30854/07_2025/7dtu_30854.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7dtu_30854/07_2025/7dtu_30854.map" model { file = "/net/cci-nas-00/data/ceres_data/7dtu_30854/07_2025/7dtu_30854.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7dtu_30854/07_2025/7dtu_30854.cif" } resolution = 4.4 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 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): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/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: {'GLN:plan1': 6, 'HIS:plan': 3, 'TYR:plan': 7, 'ASN:plan1': 10, 'TRP:plan': 3, 'ASP:plan': 11, 'PHE:plan': 36, 'GLU:plan': 22, 'ARG:plan': 8} 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: {'GLN:plan1': 6, 'HIS:plan': 3, 'TYR:plan': 7, 'ASN:plan1': 10, 'TRP:plan': 3, 'ASP:plan': 11, 'PHE:plan': 36, 'GLU:plan': 22, 'ARG:plan': 8} Unresolved non-hydrogen planarities: 522 Chain: "C" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "D" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "E" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "F" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 15 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 15 Classifications: {'peptide': 1} Modifications used: {'COO': 1} Chain: "A" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 42 Unusual residues: {'NAG': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "B" Number of atoms: 15 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 15 Classifications: {'peptide': 1} Modifications used: {'COO': 1} Chain: "B" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 42 Unusual residues: {'NAG': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Time building chain proxies: 6.99, per 1000 atoms: 0.64 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: 2.87 Conformation dependent library (CDL) restraints added in 1.6 seconds 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: 1.14 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: 3.17 Time building geometry restraints manager: 3.00 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 3605 1.34 - 1.46: 2471 1.46 - 1.58: 4916 1.58 - 1.70: 0 1.70 - 1.82: 54 Bond restraints: 11046 Sorted by residual: bond pdb=" C1 NAG B1103 " pdb=" O5 NAG B1103 " ideal model delta sigma weight residual 1.406 1.476 -0.070 2.00e-02 2.50e+03 1.22e+01 bond pdb=" C1 NAG A1103 " pdb=" O5 NAG A1103 " ideal model delta sigma weight residual 1.406 1.476 -0.070 2.00e-02 2.50e+03 1.21e+01 bond pdb=" C1 NAG A1102 " pdb=" O5 NAG A1102 " ideal model delta sigma weight residual 1.406 1.443 -0.037 2.00e-02 2.50e+03 3.40e+00 bond pdb=" C1 NAG B1102 " pdb=" O5 NAG B1102 " ideal model delta sigma weight residual 1.406 1.442 -0.036 2.00e-02 2.50e+03 3.29e+00 bond pdb=" C1 NAG B1104 " pdb=" O5 NAG B1104 " ideal model delta sigma weight residual 1.406 1.441 -0.035 2.00e-02 2.50e+03 3.07e+00 ... (remaining 11041 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.66: 14147 1.66 - 3.31: 822 3.31 - 4.97: 77 4.97 - 6.62: 43 6.62 - 8.28: 13 Bond angle restraints: 15102 Sorted by residual: angle pdb=" CA TYR A 573 " pdb=" CB TYR A 573 " pdb=" CG TYR A 573 " ideal model delta sigma weight residual 113.90 120.59 -6.69 1.80e+00 3.09e-01 1.38e+01 angle pdb=" CA TYR B 573 " pdb=" CB TYR B 573 " pdb=" CG TYR B 573 " ideal model delta sigma weight residual 113.90 120.51 -6.61 1.80e+00 3.09e-01 1.35e+01 angle pdb=" C GLU B 572 " pdb=" N TYR B 573 " pdb=" CA TYR B 573 " ideal model delta sigma weight residual 121.54 128.54 -7.00 1.91e+00 2.74e-01 1.34e+01 angle pdb=" C GLU A 572 " pdb=" N TYR A 573 " pdb=" CA TYR A 573 " ideal model delta sigma weight residual 121.54 128.49 -6.95 1.91e+00 2.74e-01 1.32e+01 angle pdb=" C CYS A 101 " pdb=" N ASN A 102 " pdb=" CA ASN A 102 " ideal model delta sigma weight residual 122.40 127.67 -5.27 1.45e+00 4.76e-01 1.32e+01 ... (remaining 15097 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.94: 6090 17.94 - 35.88: 485 35.88 - 53.82: 91 53.82 - 71.76: 24 71.76 - 89.70: 16 Dihedral angle restraints: 6706 sinusoidal: 2192 harmonic: 4514 Sorted by residual: dihedral pdb=" CB CYS B 677 " pdb=" SG CYS B 677 " pdb=" SG CYS B 765 " pdb=" CB CYS B 765 " ideal model delta sinusoidal sigma weight residual 93.00 164.95 -71.95 1 1.00e+01 1.00e-02 6.62e+01 dihedral pdb=" CB CYS A 677 " pdb=" SG CYS A 677 " pdb=" SG CYS A 765 " pdb=" CB CYS A 765 " ideal model delta sinusoidal sigma weight residual 93.00 164.94 -71.94 1 1.00e+01 1.00e-02 6.62e+01 dihedral pdb=" CB CYS A 568 " pdb=" SG CYS A 568 " pdb=" SG CYS A 582 " pdb=" CB CYS A 582 " ideal model delta sinusoidal sigma weight residual 93.00 160.35 -67.35 1 1.00e+01 1.00e-02 5.90e+01 ... (remaining 6703 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.051: 1249 0.051 - 0.102: 406 0.102 - 0.152: 121 0.152 - 0.203: 16 0.203 - 0.254: 8 Chirality restraints: 1800 Sorted by residual: chirality pdb=" CG LEU B 37 " pdb=" CB LEU B 37 " pdb=" CD1 LEU B 37 " pdb=" CD2 LEU B 37 " both_signs ideal model delta sigma weight residual False -2.59 -2.34 -0.25 2.00e-01 2.50e+01 1.61e+00 chirality pdb=" CG LEU A 37 " pdb=" CB LEU A 37 " pdb=" CD1 LEU A 37 " pdb=" CD2 LEU A 37 " both_signs ideal model delta sigma weight residual False -2.59 -2.34 -0.25 2.00e-01 2.50e+01 1.60e+00 chirality pdb=" C1 NAG A1104 " pdb=" ND2 ASN A 468 " pdb=" C2 NAG A1104 " pdb=" O5 NAG A1104 " both_signs ideal model delta sigma weight residual False -2.40 -2.18 -0.22 2.00e-01 2.50e+01 1.26e+00 ... (remaining 1797 not shown) Planarity restraints: 1994 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA THR B 445 " 0.011 2.00e-02 2.50e+03 2.28e-02 5.21e+00 pdb=" C THR B 445 " -0.039 2.00e-02 2.50e+03 pdb=" O THR B 445 " 0.015 2.00e-02 2.50e+03 pdb=" N ASN B 446 " 0.013 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA THR A 445 " -0.011 2.00e-02 2.50e+03 2.28e-02 5.20e+00 pdb=" C THR A 445 " 0.039 2.00e-02 2.50e+03 pdb=" O THR A 445 " -0.015 2.00e-02 2.50e+03 pdb=" N ASN A 446 " -0.013 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C CYS A 585 " 0.034 5.00e-02 4.00e+02 5.11e-02 4.18e+00 pdb=" N PRO A 586 " -0.088 5.00e-02 4.00e+02 pdb=" CA PRO A 586 " 0.027 5.00e-02 4.00e+02 pdb=" CD PRO A 586 " 0.028 5.00e-02 4.00e+02 ... (remaining 1991 not shown) Histogram of nonbonded interaction distances: 2.28 - 2.80: 3299 2.80 - 3.33: 10444 3.33 - 3.85: 19032 3.85 - 4.38: 20463 4.38 - 4.90: 33105 Nonbonded interactions: 86343 Sorted by model distance: nonbonded pdb=" O SER B 171 " pdb=" NH2 ARG B 185 " model vdw 2.277 3.120 nonbonded pdb=" O SER A 171 " pdb=" NH2 ARG A 185 " model vdw 2.277 3.120 nonbonded pdb=" O GLU A 525 " pdb=" NH2 ARG A 535 " model vdw 2.299 3.120 nonbonded pdb=" O GLU B 525 " pdb=" NH2 ARG B 535 " model vdw 2.299 3.120 nonbonded pdb=" OH TYR A 203 " pdb=" OE1 GLU A 525 " model vdw 2.315 3.040 ... (remaining 86338 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 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: 1.480 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.370 Check model and map are aligned: 0.070 Set scattering table: 0.080 Process input model: 26.400 Find NCS groups from input model: 0.380 Set up NCS constraints: 0.060 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:2.790 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 31.640 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7980 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.010 0.616 11078 Z= 0.508 Angle : 0.954 17.326 15180 Z= 0.528 Chirality : 0.056 0.254 1800 Planarity : 0.005 0.051 1984 Dihedral : 14.686 89.703 3724 Min Nonbonded Distance : 2.277 Molprobity Statistics. All-atom Clashscore : 6.85 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -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 TRP 0.015 0.002 TRP A 458 HIS 0.005 0.001 HIS B 429 PHE 0.024 0.002 PHE B 270 TYR 0.023 0.003 TYR B 573 ARG 0.007 0.001 ARG A 69 Details of bonding type rmsd link_NAG-ASN : bond 0.01331 ( 10) link_NAG-ASN : angle 4.78932 ( 30) link_BETA1-4 : bond 0.00398 ( 4) link_BETA1-4 : angle 2.80826 ( 12) hydrogen bonds : bond 0.13364 ( 492) hydrogen bonds : angle 5.78684 ( 1398) SS BOND : bond 0.20540 ( 18) SS BOND : angle 4.47510 ( 36) covalent geometry : bond 0.00592 (11046) covalent geometry : angle 0.90289 (15102) *********************** 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 : 1.276 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: 0.1825 time to fit residues: 6.3828 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 : 1.342 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 130 optimal weight: 0.5980 chunk 116 optimal weight: 7.9990 chunk 64 optimal weight: 50.0000 chunk 39 optimal weight: 6.9990 chunk 78 optimal weight: 1.9990 chunk 62 optimal weight: 0.0870 chunk 120 optimal weight: 6.9990 chunk 46 optimal weight: 7.9990 chunk 73 optimal weight: 7.9990 chunk 89 optimal weight: 2.9990 chunk 139 optimal weight: 10.0000 overall best weight: 2.5364 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 72 GLN ** A 164 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 193 GLN ** A 260 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 312 HIS A 361 GLN A 400 ASN A 419 ASN A 429 HIS A 432 GLN A 463 HIS B 72 GLN ** B 164 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 193 GLN ** B 260 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 312 HIS B 361 GLN B 400 ASN B 419 ASN B 429 HIS B 432 GLN B 463 HIS Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3126 r_free = 0.3126 target = 0.034537 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2817 r_free = 0.2817 target = 0.027458 restraints weight = 144273.123| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.2841 r_free = 0.2841 target = 0.027983 restraints weight = 99309.359| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.2859 r_free = 0.2859 target = 0.028358 restraints weight = 75174.007| |-----------------------------------------------------------------------------| r_work (final): 0.2828 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8070 moved from start: 0.1017 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= 0.152 Angle : 0.615 8.292 15180 Z= 0.328 Chirality : 0.045 0.284 1800 Planarity : 0.004 0.038 1984 Dihedral : 7.218 56.036 1924 Min Nonbonded Distance : 2.435 Molprobity Statistics. All-atom Clashscore : 7.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.40 % Favored : 92.60 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.53 (0.20), residues: 1540 helix: -0.36 (0.19), residues: 608 sheet: -3.36 (0.31), residues: 210 loop : -2.29 (0.23), residues: 722 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 208 HIS 0.003 0.001 HIS A 338 PHE 0.013 0.001 PHE A 38 TYR 0.019 0.002 TYR B 573 ARG 0.002 0.000 ARG B 205 Details of bonding type rmsd link_NAG-ASN : bond 0.00734 ( 10) link_NAG-ASN : angle 3.10472 ( 30) link_BETA1-4 : bond 0.00374 ( 4) link_BETA1-4 : angle 1.62070 ( 12) hydrogen bonds : bond 0.04306 ( 492) hydrogen bonds : angle 4.82845 ( 1398) SS BOND : bond 0.00328 ( 18) SS BOND : angle 1.54583 ( 36) covalent geometry : bond 0.00319 (11046) covalent geometry : angle 0.59452 (15102) *********************** 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 : 1.126 Fit side-chains REVERT: A 197 MET cc_start: 0.9002 (mtm) cc_final: 0.8522 (mtp) REVERT: A 307 MET cc_start: 0.8417 (mmp) cc_final: 0.8115 (mmm) REVERT: A 464 LEU cc_start: 0.9397 (mt) cc_final: 0.9023 (mt) REVERT: A 473 MET cc_start: 0.7671 (ptp) cc_final: 0.7051 (mpp) REVERT: B 197 MET cc_start: 0.8981 (mtm) cc_final: 0.8481 (mtp) REVERT: B 464 LEU cc_start: 0.9402 (mt) cc_final: 0.9025 (mt) REVERT: B 473 MET cc_start: 0.7777 (ptp) cc_final: 0.7010 (mpp) outliers start: 0 outliers final: 0 residues processed: 18 average time/residue: 0.1556 time to fit residues: 6.0448 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 : 1.299 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 129 optimal weight: 3.9990 chunk 45 optimal weight: 9.9990 chunk 152 optimal weight: 20.0000 chunk 20 optimal weight: 6.9990 chunk 44 optimal weight: 0.8980 chunk 18 optimal weight: 8.9990 chunk 16 optimal weight: 0.7980 chunk 78 optimal weight: 4.9990 chunk 88 optimal weight: 9.9990 chunk 27 optimal weight: 6.9990 chunk 105 optimal weight: 0.0970 overall best weight: 2.1582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 164 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 260 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 164 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 260 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3125 r_free = 0.3125 target = 0.034548 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2812 r_free = 0.2812 target = 0.027397 restraints weight = 146246.304| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.2837 r_free = 0.2837 target = 0.027929 restraints weight = 99783.382| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.2855 r_free = 0.2855 target = 0.028314 restraints weight = 75334.531| |-----------------------------------------------------------------------------| r_work (final): 0.2824 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8063 moved from start: 0.1426 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 11078 Z= 0.127 Angle : 0.557 7.910 15180 Z= 0.294 Chirality : 0.044 0.275 1800 Planarity : 0.003 0.035 1984 Dihedral : 6.300 52.665 1924 Min Nonbonded Distance : 2.477 Molprobity Statistics. All-atom Clashscore : 6.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.62 % Favored : 93.38 % Rotamer: Outliers : 0.00 % Allowed : 4.45 % Favored : 95.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.76 (0.22), residues: 1540 helix: 0.47 (0.20), residues: 614 sheet: -2.93 (0.35), residues: 198 loop : -2.11 (0.24), residues: 728 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 208 HIS 0.001 0.000 HIS A 338 PHE 0.011 0.001 PHE A 38 TYR 0.017 0.002 TYR B 573 ARG 0.003 0.000 ARG A 69 Details of bonding type rmsd link_NAG-ASN : bond 0.00696 ( 10) link_NAG-ASN : angle 2.74116 ( 30) link_BETA1-4 : bond 0.00254 ( 4) link_BETA1-4 : angle 1.45792 ( 12) hydrogen bonds : bond 0.03686 ( 492) hydrogen bonds : angle 4.60711 ( 1398) SS BOND : bond 0.00323 ( 18) SS BOND : angle 0.80520 ( 36) covalent geometry : bond 0.00265 (11046) covalent geometry : angle 0.54225 (15102) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3080 Ramachandran restraints generated. 1540 Oldfield, 0 Emsley, 1540 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3080 Ramachandran restraints generated. 1540 Oldfield, 0 Emsley, 1540 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 18 residues out of total 1354 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 18 time to evaluate : 1.120 Fit side-chains revert: symmetry clash REVERT: A 197 MET cc_start: 0.9086 (mtm) cc_final: 0.8555 (mtp) REVERT: A 464 LEU cc_start: 0.9441 (mt) cc_final: 0.9065 (mt) REVERT: B 197 MET cc_start: 0.9084 (mtm) cc_final: 0.8527 (mtp) REVERT: B 307 MET cc_start: 0.8602 (mmp) cc_final: 0.8293 (mmm) REVERT: B 464 LEU cc_start: 0.9446 (mt) cc_final: 0.9066 (mt) REVERT: B 473 MET cc_start: 0.7616 (ptp) cc_final: 0.6941 (mpp) outliers start: 0 outliers final: 0 residues processed: 18 average time/residue: 0.1670 time to fit residues: 6.6100 Evaluate side-chains 17 residues out of total 1354 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 17 time to evaluate : 1.298 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 43 optimal weight: 8.9990 chunk 118 optimal weight: 3.9990 chunk 106 optimal weight: 5.9990 chunk 48 optimal weight: 7.9990 chunk 35 optimal weight: 2.9990 chunk 91 optimal weight: 7.9990 chunk 123 optimal weight: 7.9990 chunk 70 optimal weight: 5.9990 chunk 89 optimal weight: 0.0770 chunk 86 optimal weight: 0.9980 chunk 15 optimal weight: 6.9990 overall best weight: 2.8144 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 164 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 260 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 466 HIS ** 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: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3115 r_free = 0.3115 target = 0.034189 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2811 r_free = 0.2811 target = 0.027262 restraints weight = 145967.688| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.2836 r_free = 0.2836 target = 0.027778 restraints weight = 102245.006| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.2851 r_free = 0.2851 target = 0.028123 restraints weight = 78274.805| |-----------------------------------------------------------------------------| r_work (final): 0.2822 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8073 moved from start: 0.1728 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 11078 Z= 0.145 Angle : 0.554 7.886 15180 Z= 0.293 Chirality : 0.044 0.274 1800 Planarity : 0.003 0.033 1984 Dihedral : 5.888 51.756 1924 Min Nonbonded Distance : 2.511 Molprobity Statistics. All-atom Clashscore : 7.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.62 % Favored : 93.38 % Rotamer: Outliers : 0.00 % Allowed : 3.98 % Favored : 96.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.40 (0.22), residues: 1540 helix: 0.96 (0.21), residues: 608 sheet: -2.95 (0.35), residues: 202 loop : -1.99 (0.24), residues: 730 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 352 HIS 0.002 0.001 HIS A 466 PHE 0.012 0.001 PHE A 38 TYR 0.016 0.002 TYR A 573 ARG 0.004 0.000 ARG A 69 Details of bonding type rmsd link_NAG-ASN : bond 0.00672 ( 10) link_NAG-ASN : angle 2.68651 ( 30) link_BETA1-4 : bond 0.00293 ( 4) link_BETA1-4 : angle 1.48472 ( 12) hydrogen bonds : bond 0.03529 ( 492) hydrogen bonds : angle 4.52789 ( 1398) SS BOND : bond 0.00372 ( 18) SS BOND : angle 1.19058 ( 36) covalent geometry : bond 0.00304 (11046) covalent geometry : angle 0.53801 (15102) *********************** 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 : 1.105 Fit side-chains revert: symmetry clash REVERT: A 197 MET cc_start: 0.9126 (mtm) cc_final: 0.8552 (mtp) REVERT: B 197 MET cc_start: 0.9127 (mtm) cc_final: 0.8550 (mtp) REVERT: B 464 LEU cc_start: 0.9471 (mt) cc_final: 0.9082 (mt) outliers start: 0 outliers final: 0 residues processed: 16 average time/residue: 0.1588 time to fit residues: 5.5937 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 : 1.128 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 76 optimal weight: 40.0000 chunk 46 optimal weight: 0.4980 chunk 9 optimal weight: 0.9990 chunk 100 optimal weight: 9.9990 chunk 66 optimal weight: 5.9990 chunk 35 optimal weight: 4.9990 chunk 18 optimal weight: 10.0000 chunk 84 optimal weight: 9.9990 chunk 63 optimal weight: 0.0000 chunk 140 optimal weight: 0.0070 chunk 119 optimal weight: 6.9990 overall best weight: 1.3006 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 117 GLN ** A 164 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 260 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 117 GLN ** B 260 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3132 r_free = 0.3132 target = 0.034772 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2823 r_free = 0.2823 target = 0.027513 restraints weight = 142638.276| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.2849 r_free = 0.2849 target = 0.028054 restraints weight = 96986.732| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 19)----------------| | r_work = 0.2864 r_free = 0.2864 target = 0.028392 restraints weight = 73207.899| |-----------------------------------------------------------------------------| r_work (final): 0.2830 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8047 moved from start: 0.1998 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 11078 Z= 0.098 Angle : 0.524 7.769 15180 Z= 0.272 Chirality : 0.044 0.276 1800 Planarity : 0.003 0.031 1984 Dihedral : 5.463 50.611 1924 Min Nonbonded Distance : 2.573 Molprobity Statistics. All-atom Clashscore : 6.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.10 % Favored : 93.90 % Rotamer: Outliers : 0.00 % Allowed : 2.93 % Favored : 97.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.08 (0.22), residues: 1540 helix: 1.29 (0.21), residues: 618 sheet: -2.98 (0.33), residues: 204 loop : -1.85 (0.24), residues: 718 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 208 HIS 0.001 0.000 HIS A 312 PHE 0.008 0.001 PHE B 356 TYR 0.016 0.001 TYR A 573 ARG 0.003 0.000 ARG A 69 Details of bonding type rmsd link_NAG-ASN : bond 0.00704 ( 10) link_NAG-ASN : angle 2.56701 ( 30) link_BETA1-4 : bond 0.00320 ( 4) link_BETA1-4 : angle 1.31772 ( 12) hydrogen bonds : bond 0.03244 ( 492) hydrogen bonds : angle 4.33399 ( 1398) SS BOND : bond 0.00263 ( 18) SS BOND : angle 0.94630 ( 36) covalent geometry : bond 0.00208 (11046) covalent geometry : angle 0.50943 (15102) *********************** 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 21 residues out of total 1354 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 21 time to evaluate : 1.244 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 197 MET cc_start: 0.9121 (mtm) cc_final: 0.8552 (mtp) REVERT: A 307 MET cc_start: 0.8364 (mmm) cc_final: 0.8029 (mmm) REVERT: B 197 MET cc_start: 0.9117 (mtm) cc_final: 0.8513 (mtp) REVERT: B 307 MET cc_start: 0.8378 (mmm) cc_final: 0.7975 (mmm) REVERT: B 464 LEU cc_start: 0.9483 (mt) cc_final: 0.9089 (mt) outliers start: 0 outliers final: 0 residues processed: 21 average time/residue: 0.1676 time to fit residues: 7.2916 Evaluate side-chains 17 residues out of total 1354 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 17 time to evaluate : 1.251 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 54 optimal weight: 10.0000 chunk 56 optimal weight: 50.0000 chunk 75 optimal weight: 30.0000 chunk 37 optimal weight: 1.9990 chunk 48 optimal weight: 0.5980 chunk 112 optimal weight: 8.9990 chunk 103 optimal weight: 0.8980 chunk 97 optimal weight: 7.9990 chunk 73 optimal weight: 8.9990 chunk 1 optimal weight: 1.9990 chunk 146 optimal weight: 30.0000 overall best weight: 2.6986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 164 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 260 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 164 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 260 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3122 r_free = 0.3122 target = 0.034332 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2819 r_free = 0.2819 target = 0.027354 restraints weight = 147017.402| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.2844 r_free = 0.2844 target = 0.027869 restraints weight = 101515.225| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.2862 r_free = 0.2862 target = 0.028251 restraints weight = 77282.233| |-----------------------------------------------------------------------------| r_work (final): 0.2831 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8066 moved from start: 0.2107 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= 0.139 Angle : 0.537 7.939 15180 Z= 0.281 Chirality : 0.044 0.274 1800 Planarity : 0.003 0.031 1984 Dihedral : 5.419 51.459 1924 Min Nonbonded Distance : 2.574 Molprobity Statistics. All-atom Clashscore : 7.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.30 % Favored : 93.70 % Rotamer: Outliers : 0.00 % Allowed : 2.22 % Favored : 97.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.91 (0.22), residues: 1540 helix: 1.38 (0.21), residues: 630 sheet: -2.42 (0.37), residues: 184 loop : -1.97 (0.24), residues: 726 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 352 HIS 0.003 0.001 HIS A 495 PHE 0.009 0.001 PHE A 589 TYR 0.016 0.001 TYR B 573 ARG 0.003 0.000 ARG A 69 Details of bonding type rmsd link_NAG-ASN : bond 0.00667 ( 10) link_NAG-ASN : angle 2.63222 ( 30) link_BETA1-4 : bond 0.00247 ( 4) link_BETA1-4 : angle 1.41008 ( 12) hydrogen bonds : bond 0.03303 ( 492) hydrogen bonds : angle 4.32041 ( 1398) SS BOND : bond 0.00336 ( 18) SS BOND : angle 0.93737 ( 36) covalent geometry : bond 0.00295 (11046) covalent geometry : angle 0.52214 (15102) *********************** 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 18 residues out of total 1354 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 18 time to evaluate : 1.151 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 197 MET cc_start: 0.9116 (mtm) cc_final: 0.8572 (mtp) REVERT: A 307 MET cc_start: 0.8426 (mmm) cc_final: 0.8100 (mmm) REVERT: B 197 MET cc_start: 0.9154 (mtm) cc_final: 0.8571 (mtp) REVERT: B 307 MET cc_start: 0.8488 (mmm) cc_final: 0.8076 (mmm) outliers start: 0 outliers final: 0 residues processed: 18 average time/residue: 0.1642 time to fit residues: 6.2637 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 : 1.158 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 149 optimal weight: 40.0000 chunk 133 optimal weight: 50.0000 chunk 142 optimal weight: 10.0000 chunk 3 optimal weight: 3.9990 chunk 33 optimal weight: 5.9990 chunk 30 optimal weight: 9.9990 chunk 132 optimal weight: 50.0000 chunk 145 optimal weight: 1.9990 chunk 131 optimal weight: 6.9990 chunk 67 optimal weight: 0.8980 chunk 119 optimal weight: 9.9990 overall best weight: 3.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 164 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 260 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 164 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 260 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3113 r_free = 0.3113 target = 0.034133 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2805 r_free = 0.2805 target = 0.027146 restraints weight = 149605.570| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.2831 r_free = 0.2831 target = 0.027668 restraints weight = 102697.140| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.2849 r_free = 0.2849 target = 0.028050 restraints weight = 77790.126| |-----------------------------------------------------------------------------| r_work (final): 0.2819 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8093 moved from start: 0.2195 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 11078 Z= 0.187 Angle : 0.570 7.638 15180 Z= 0.301 Chirality : 0.044 0.261 1800 Planarity : 0.003 0.032 1984 Dihedral : 5.544 50.628 1924 Min Nonbonded Distance : 2.545 Molprobity Statistics. All-atom Clashscore : 9.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.14 % Favored : 92.86 % Rotamer: Outliers : 0.00 % Allowed : 1.29 % Favored : 98.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.82 (0.22), residues: 1540 helix: 1.57 (0.21), residues: 618 sheet: -2.48 (0.36), residues: 184 loop : -1.95 (0.24), residues: 738 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 458 HIS 0.003 0.001 HIS B 192 PHE 0.012 0.001 PHE B 589 TYR 0.016 0.002 TYR A 573 ARG 0.004 0.000 ARG A 69 Details of bonding type rmsd link_NAG-ASN : bond 0.00675 ( 10) link_NAG-ASN : angle 2.58710 ( 30) link_BETA1-4 : bond 0.00257 ( 4) link_BETA1-4 : angle 1.60510 ( 12) hydrogen bonds : bond 0.03466 ( 492) hydrogen bonds : angle 4.40680 ( 1398) SS BOND : bond 0.00389 ( 18) SS BOND : angle 1.01233 ( 36) covalent geometry : bond 0.00395 (11046) covalent geometry : angle 0.55554 (15102) *********************** 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 18 residues out of total 1354 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 18 time to evaluate : 1.225 Fit side-chains revert: symmetry clash REVERT: A 197 MET cc_start: 0.9149 (mtm) cc_final: 0.8547 (mtp) REVERT: A 307 MET cc_start: 0.8492 (mmm) cc_final: 0.8140 (mmm) REVERT: B 197 MET cc_start: 0.9164 (mtm) cc_final: 0.8562 (mtp) REVERT: B 307 MET cc_start: 0.8556 (mmm) cc_final: 0.8151 (mmm) outliers start: 0 outliers final: 0 residues processed: 18 average time/residue: 0.1612 time to fit residues: 6.2502 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 : 1.121 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 153 optimal weight: 30.0000 chunk 67 optimal weight: 50.0000 chunk 139 optimal weight: 8.9990 chunk 47 optimal weight: 6.9990 chunk 114 optimal weight: 2.9990 chunk 61 optimal weight: 8.9990 chunk 26 optimal weight: 0.5980 chunk 74 optimal weight: 20.0000 chunk 151 optimal weight: 20.0000 chunk 11 optimal weight: 20.0000 chunk 34 optimal weight: 0.0070 overall best weight: 3.9204 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 164 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 260 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 164 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 260 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3103 r_free = 0.3103 target = 0.033697 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2797 r_free = 0.2797 target = 0.026751 restraints weight = 143500.830| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.2821 r_free = 0.2821 target = 0.027243 restraints weight = 100993.357| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.2838 r_free = 0.2838 target = 0.027602 restraints weight = 78126.776| |-----------------------------------------------------------------------------| r_work (final): 0.2816 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8095 moved from start: 0.2346 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 11078 Z= 0.183 Angle : 0.577 7.559 15180 Z= 0.306 Chirality : 0.044 0.255 1800 Planarity : 0.003 0.033 1984 Dihedral : 5.595 49.231 1924 Min Nonbonded Distance : 2.540 Molprobity Statistics. All-atom Clashscore : 9.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.21 % Favored : 92.79 % Rotamer: Outliers : 0.00 % Allowed : 0.82 % Favored : 99.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.85 (0.22), residues: 1540 helix: 1.51 (0.21), residues: 628 sheet: -2.55 (0.38), residues: 164 loop : -1.99 (0.23), residues: 748 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 352 HIS 0.003 0.001 HIS B 192 PHE 0.013 0.001 PHE B 76 TYR 0.015 0.002 TYR B 573 ARG 0.005 0.000 ARG A 69 Details of bonding type rmsd link_NAG-ASN : bond 0.00681 ( 10) link_NAG-ASN : angle 2.59212 ( 30) link_BETA1-4 : bond 0.00270 ( 4) link_BETA1-4 : angle 1.58960 ( 12) hydrogen bonds : bond 0.03478 ( 492) hydrogen bonds : angle 4.44394 ( 1398) SS BOND : bond 0.00337 ( 18) SS BOND : angle 1.15417 ( 36) covalent geometry : bond 0.00385 (11046) covalent geometry : angle 0.56251 (15102) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3080 Ramachandran restraints generated. 1540 Oldfield, 0 Emsley, 1540 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3080 Ramachandran restraints generated. 1540 Oldfield, 0 Emsley, 1540 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 17 residues out of total 1354 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 17 time to evaluate : 1.298 Fit side-chains revert: symmetry clash REVERT: A 197 MET cc_start: 0.9030 (mtm) cc_final: 0.8485 (mtp) REVERT: A 307 MET cc_start: 0.8470 (mmm) cc_final: 0.8142 (mmm) REVERT: B 307 MET cc_start: 0.8512 (mmm) cc_final: 0.8129 (mmm) outliers start: 0 outliers final: 0 residues processed: 17 average time/residue: 0.1610 time to fit residues: 6.1457 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 : 1.194 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 34 optimal weight: 4.9990 chunk 140 optimal weight: 8.9990 chunk 55 optimal weight: 30.0000 chunk 126 optimal weight: 8.9990 chunk 125 optimal weight: 0.7980 chunk 123 optimal weight: 9.9990 chunk 18 optimal weight: 8.9990 chunk 74 optimal weight: 20.0000 chunk 111 optimal weight: 0.9990 chunk 23 optimal weight: 9.9990 chunk 95 optimal weight: 3.9990 overall best weight: 3.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 164 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 260 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 472 ASN ** 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 = 0.3106 r_free = 0.3106 target = 0.034004 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2795 r_free = 0.2795 target = 0.027040 restraints weight = 149093.024| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.2820 r_free = 0.2820 target = 0.027560 restraints weight = 102566.904| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.2838 r_free = 0.2838 target = 0.027929 restraints weight = 78061.670| |-----------------------------------------------------------------------------| r_work (final): 0.2809 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8103 moved from start: 0.2464 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 11078 Z= 0.184 Angle : 0.578 7.580 15180 Z= 0.306 Chirality : 0.044 0.256 1800 Planarity : 0.003 0.033 1984 Dihedral : 5.634 48.611 1924 Min Nonbonded Distance : 2.535 Molprobity Statistics. All-atom Clashscore : 9.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.79 % Favored : 92.21 % Rotamer: Outliers : 0.12 % Allowed : 1.41 % Favored : 98.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.81 (0.22), residues: 1540 helix: 1.55 (0.20), residues: 628 sheet: -2.55 (0.38), residues: 164 loop : -1.97 (0.24), residues: 748 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 352 HIS 0.002 0.001 HIS B 192 PHE 0.013 0.001 PHE A 589 TYR 0.016 0.001 TYR A 573 ARG 0.005 0.000 ARG A 69 Details of bonding type rmsd link_NAG-ASN : bond 0.00688 ( 10) link_NAG-ASN : angle 2.58758 ( 30) link_BETA1-4 : bond 0.00256 ( 4) link_BETA1-4 : angle 1.58725 ( 12) hydrogen bonds : bond 0.03513 ( 492) hydrogen bonds : angle 4.45154 ( 1398) SS BOND : bond 0.00427 ( 18) SS BOND : angle 1.00224 ( 36) covalent geometry : bond 0.00388 (11046) covalent geometry : angle 0.56420 (15102) *********************** 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 17 residues out of total 1354 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 16 time to evaluate : 1.324 Fit side-chains REVERT: A 197 MET cc_start: 0.9026 (mtm) cc_final: 0.8428 (mtp) REVERT: A 307 MET cc_start: 0.8549 (mmm) cc_final: 0.8131 (mmm) REVERT: B 197 MET cc_start: 0.9081 (mtm) cc_final: 0.8542 (mtp) REVERT: B 307 MET cc_start: 0.8555 (mmm) cc_final: 0.8110 (mmm) outliers start: 1 outliers final: 0 residues processed: 17 average time/residue: 0.1589 time to fit residues: 6.2009 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 : 1.217 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 29 optimal weight: 10.0000 chunk 66 optimal weight: 2.9990 chunk 135 optimal weight: 6.9990 chunk 45 optimal weight: 8.9990 chunk 140 optimal weight: 6.9990 chunk 125 optimal weight: 7.9990 chunk 121 optimal weight: 8.9990 chunk 63 optimal weight: 2.9990 chunk 3 optimal weight: 0.0670 chunk 8 optimal weight: 4.9990 chunk 115 optimal weight: 7.9990 overall best weight: 3.6126 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 164 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 260 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 164 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 260 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3108 r_free = 0.3108 target = 0.034067 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2797 r_free = 0.2797 target = 0.027095 restraints weight = 147884.521| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.2822 r_free = 0.2822 target = 0.027605 restraints weight = 102164.156| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.2839 r_free = 0.2839 target = 0.027972 restraints weight = 77896.351| |-----------------------------------------------------------------------------| r_work (final): 0.2810 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8098 moved from start: 0.2568 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 11078 Z= 0.172 Angle : 0.569 7.629 15180 Z= 0.300 Chirality : 0.044 0.252 1800 Planarity : 0.003 0.034 1984 Dihedral : 5.586 48.043 1924 Min Nonbonded Distance : 2.545 Molprobity Statistics. All-atom Clashscore : 9.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.95 % Favored : 93.05 % Rotamer: Outliers : 0.00 % Allowed : 0.35 % Favored : 99.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.85 (0.22), residues: 1540 helix: 1.48 (0.20), residues: 646 sheet: -2.53 (0.38), residues: 164 loop : -2.04 (0.23), residues: 730 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 352 HIS 0.002 0.001 HIS A 192 PHE 0.012 0.001 PHE B 589 TYR 0.015 0.001 TYR B 573 ARG 0.005 0.000 ARG A 69 Details of bonding type rmsd link_NAG-ASN : bond 0.00678 ( 10) link_NAG-ASN : angle 2.59236 ( 30) link_BETA1-4 : bond 0.00268 ( 4) link_BETA1-4 : angle 1.50643 ( 12) hydrogen bonds : bond 0.03465 ( 492) hydrogen bonds : angle 4.40405 ( 1398) SS BOND : bond 0.00334 ( 18) SS BOND : angle 1.12291 ( 36) covalent geometry : bond 0.00363 (11046) covalent geometry : angle 0.55441 (15102) ********************** 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 16 residues out of total 1354 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 16 time to evaluate : 1.012 Fit side-chains REVERT: A 197 MET cc_start: 0.9041 (mtm) cc_final: 0.8503 (mtp) REVERT: A 307 MET cc_start: 0.8596 (mmm) cc_final: 0.8203 (mmm) REVERT: B 197 MET cc_start: 0.9072 (mtm) cc_final: 0.8494 (mtp) REVERT: B 307 MET cc_start: 0.8532 (mmm) cc_final: 0.8094 (mmm) outliers start: 0 outliers final: 0 residues processed: 16 average time/residue: 0.1622 time to fit residues: 5.6729 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 : 1.208 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 143 optimal weight: 30.0000 chunk 96 optimal weight: 0.9980 chunk 68 optimal weight: 40.0000 chunk 79 optimal weight: 3.9990 chunk 62 optimal weight: 2.9990 chunk 136 optimal weight: 9.9990 chunk 137 optimal weight: 6.9990 chunk 67 optimal weight: 20.0000 chunk 47 optimal weight: 6.9990 chunk 69 optimal weight: 8.9990 chunk 56 optimal weight: 50.0000 overall best weight: 4.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 164 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 260 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 359 HIS ** 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 = 0.3103 r_free = 0.3103 target = 0.034113 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2799 r_free = 0.2799 target = 0.027070 restraints weight = 147140.386| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.2825 r_free = 0.2825 target = 0.027600 restraints weight = 100833.704| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.2842 r_free = 0.2842 target = 0.027973 restraints weight = 76698.089| |-----------------------------------------------------------------------------| r_work (final): 0.2814 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8114 moved from start: 0.2680 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 11078 Z= 0.204 Angle : 0.597 7.520 15180 Z= 0.317 Chirality : 0.045 0.250 1800 Planarity : 0.004 0.035 1984 Dihedral : 5.736 47.717 1924 Min Nonbonded Distance : 2.516 Molprobity Statistics. All-atom Clashscore : 10.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.05 % Favored : 91.95 % Rotamer: Outliers : 0.00 % Allowed : 1.05 % Favored : 98.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.89 (0.22), residues: 1540 helix: 1.47 (0.20), residues: 646 sheet: -2.54 (0.38), residues: 162 loop : -2.10 (0.23), residues: 732 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 352 HIS 0.003 0.001 HIS A 192 PHE 0.016 0.002 PHE B 76 TYR 0.015 0.002 TYR B 573 ARG 0.005 0.000 ARG A 69 Details of bonding type rmsd link_NAG-ASN : bond 0.00700 ( 10) link_NAG-ASN : angle 2.61003 ( 30) link_BETA1-4 : bond 0.00305 ( 4) link_BETA1-4 : angle 1.67377 ( 12) hydrogen bonds : bond 0.03617 ( 492) hydrogen bonds : angle 4.48509 ( 1398) SS BOND : bond 0.00419 ( 18) SS BOND : angle 1.09119 ( 36) covalent geometry : bond 0.00429 (11046) covalent geometry : angle 0.58321 (15102) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2722.32 seconds wall clock time: 48 minutes 18.98 seconds (2898.98 seconds total)