Starting phenix.real_space_refine on Fri Jul 3 10:58:37 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7aip_11801/07_2026/7aip_11801.cif Found real_map, /net/cci-nas-00/data/ceres_data/7aip_11801/07_2026/7aip_11801.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.12 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/cci-nas-00/data/ceres_data/7aip_11801/07_2026/7aip_11801.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7aip_11801/07_2026/7aip_11801.cif" model { file = "/net/cci-nas-00/data/ceres_data/7aip_11801/07_2026/7aip_11801.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7aip_11801/07_2026/7aip_11801.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7aip_11801/07_2026/7aip_11801.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7aip_11801/07_2026/7aip_11801.map" } resolution = 3.12 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= 0.005 sd= 0.070 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: 6 Type Number sf(0) Gaussians P 10 5.49 5 Mg 2 5.21 5 S 96 5.16 5 C 8769 2.51 5 N 2216 2.21 5 O 2442 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 6 residue(s): 0.02s 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: 13535 Number of models: 1 Model: "" Number of chains: 10 Chain: "A" Number of atoms: 6670 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 867, 6663 Classifications: {'peptide': 867} Incomplete info: {'truncation_to_alanine': 19} Link IDs: {'PTRANS': 37, 'TRANS': 829} Chain breaks: 3 Unresolved non-hydrogen bonds: 75 Unresolved non-hydrogen angles: 88 Unresolved non-hydrogen dihedrals: 66 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 1, 'ASN:plan1': 2, 'PHE:plan': 1, 'HIS:plan': 1, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 35 Conformer: "B" Number of residues, atoms: 867, 6663 Classifications: {'peptide': 867} Incomplete info: {'truncation_to_alanine': 19} Link IDs: {'PTRANS': 37, 'TRANS': 829} Chain breaks: 3 Unresolved non-hydrogen bonds: 75 Unresolved non-hydrogen angles: 88 Unresolved non-hydrogen dihedrals: 66 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 1, 'ASN:plan1': 2, 'PHE:plan': 1, 'HIS:plan': 1, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 35 bond proxies already assigned to first conformer: 6811 Chain: "B" Number of atoms: 6663 Number of conformers: 1 Conformer: "" Number of residues, atoms: 867, 6663 Classifications: {'peptide': 867} Incomplete info: {'truncation_to_alanine': 19} Link IDs: {'PTRANS': 37, 'TRANS': 829} Chain breaks: 3 Unresolved non-hydrogen bonds: 75 Unresolved non-hydrogen angles: 88 Unresolved non-hydrogen dihedrals: 66 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 1, 'ASN:plan1': 2, 'PHE:plan': 1, 'HIS:plan': 1, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 35 Chain: "C" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen chiralities: 3 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: "J" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen chiralities: 3 Chain: "M" 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: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "A" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} Time building chain proxies: 4.52, per 1000 atoms: 0.33 Number of scatterers: 13535 At special positions: 0 Unit cell: (109.65, 109.65, 150.45, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 96 16.00 P 10 15.00 Mg 2 11.99 O 2442 8.00 N 2216 7.00 C 8769 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=6, symmetry=0 Simple disulfide: pdb=" SG CYS A 163 " - pdb=" SG CYS A 626 " distance=2.04 Simple disulfide: pdb=" SG CYS A 308 " - pdb=" SG CYS A 323 " distance=2.03 Simple disulfide: pdb=" SG CYS A 343 " - pdb=" SG CYS A 353 " distance=2.03 Simple disulfide: pdb=" SG CYS B 163 " - pdb=" SG CYS B 626 " distance=2.04 Simple disulfide: pdb=" SG CYS B 308 " - pdb=" SG CYS B 323 " distance=2.03 Simple disulfide: pdb=" SG CYS B 343 " - pdb=" SG CYS B 353 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied BETA1-4 " NAG C 1 " - " NAG C 2 " " NAG C 2 " - " BMA C 3 " " NAG F 1 " - " NAG F 2 " " NAG J 1 " - " NAG J 2 " " NAG J 2 " - " BMA J 3 " " NAG M 1 " - " NAG M 2 " NAG-ASN " NAG C 1 " - " ASN A 312 " " NAG F 1 " - " ASN A 361 " " NAG J 1 " - " ASN B 312 " " NAG M 1 " - " ASN B 361 " Time building additional restraints: 1.23 Conformation dependent library (CDL) restraints added in 762.8 milliseconds 3414 Ramachandran restraints generated. 1707 Oldfield, 0 Emsley, 1707 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3190 Finding SS restraints... Secondary structure from input PDB file: 64 helices and 8 sheets defined 60.9% alpha, 6.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.50 Creating SS restraints... Processing helix chain 'A' and resid 120 through 133 removed outlier: 5.812A pdb=" N LEU A 126 " --> pdb=" O MET A 122 " (cutoff:3.500A) Proline residue: A 127 - end of helix Processing helix chain 'A' and resid 134 through 177 removed outlier: 4.708A pdb=" N PHE A 138 " --> pdb=" O GLY A 134 " (cutoff:3.500A) removed outlier: 5.188A pdb=" N THR A 142 " --> pdb=" O PHE A 138 " (cutoff:3.500A) removed outlier: 5.476A pdb=" N TRP A 143 " --> pdb=" O LEU A 139 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N MET A 144 " --> pdb=" O ARG A 140 " (cutoff:3.500A) removed outlier: 6.671A pdb=" N VAL A 150 " --> pdb=" O GLY A 146 " (cutoff:3.500A) removed outlier: 9.270A pdb=" N LEU A 151 " --> pdb=" O THR A 147 " (cutoff:3.500A) removed outlier: 4.032A pdb=" N GLN A 152 " --> pdb=" O ALA A 148 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N CYS A 163 " --> pdb=" O ILE A 159 " (cutoff:3.500A) removed outlier: 4.024A pdb=" N THR A 164 " --> pdb=" O CYS A 160 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N ASN A 177 " --> pdb=" O ALA A 173 " (cutoff:3.500A) Processing helix chain 'A' and resid 185 through 227 removed outlier: 4.101A pdb=" N ILE A 189 " --> pdb=" O SER A 185 " (cutoff:3.500A) Proline residue: A 195 - end of helix removed outlier: 3.544A pdb=" N CYS A 204 " --> pdb=" O ALA A 200 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N TYR A 227 " --> pdb=" O ILE A 223 " (cutoff:3.500A) Processing helix chain 'A' and resid 245 through 269 Processing helix chain 'A' and resid 269 through 301 removed outlier: 5.487A pdb=" N SER A 278 " --> pdb=" O ASN A 274 " (cutoff:3.500A) removed outlier: 5.711A pdb=" N LEU A 279 " --> pdb=" O LYS A 275 " (cutoff:3.500A) removed outlier: 4.015A pdb=" N PHE A 280 " --> pdb=" O PHE A 276 " (cutoff:3.500A) removed outlier: 3.916A pdb=" N LEU A 281 " --> pdb=" O ALA A 277 " (cutoff:3.500A) removed outlier: 4.240A pdb=" N PHE A 300 " --> pdb=" O ILE A 296 " (cutoff:3.500A) Processing helix chain 'A' and resid 336 through 343 Processing helix chain 'A' and resid 354 through 360 removed outlier: 3.917A pdb=" N MET A 358 " --> pdb=" O ASP A 354 " (cutoff:3.500A) Processing helix chain 'A' and resid 374 through 379 Processing helix chain 'A' and resid 407 through 411 Processing helix chain 'A' and resid 419 through 428 removed outlier: 3.878A pdb=" N LEU A 423 " --> pdb=" O SER A 419 " (cutoff:3.500A) Processing helix chain 'A' and resid 429 through 431 No H-bonds generated for 'chain 'A' and resid 429 through 431' Processing helix chain 'A' and resid 446 through 477 Proline residue: A 452 - end of helix Processing helix chain 'A' and resid 494 through 498 Processing helix chain 'A' and resid 504 through 536 removed outlier: 3.842A pdb=" N VAL A 508 " --> pdb=" O PRO A 504 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N ILE A 509 " --> pdb=" O TRP A 505 " (cutoff:3.500A) Proline residue: A 527 - end of helix Processing helix chain 'A' and resid 543 through 547 Processing helix chain 'A' and resid 557 through 570 Processing helix chain 'A' and resid 573 through 602 Proline residue: A 579 - end of helix Processing helix chain 'A' and resid 615 through 634 removed outlier: 3.582A pdb=" N SER A 619 " --> pdb=" O HIS A 615 " (cutoff:3.500A) removed outlier: 4.087A pdb=" N SER A 634 " --> pdb=" O MET A 630 " (cutoff:3.500A) Processing helix chain 'A' and resid 634 through 661 Processing helix chain 'A' and resid 664 through 682 removed outlier: 4.121A pdb=" N GLU A 682 " --> pdb=" O LEU A 678 " (cutoff:3.500A) Processing helix chain 'A' and resid 709 through 720 removed outlier: 3.800A pdb=" N THR A 713 " --> pdb=" O PRO A 709 " (cutoff:3.500A) Processing helix chain 'A' and resid 734 through 738 Processing helix chain 'A' and resid 739 through 756 Processing helix chain 'A' and resid 769 through 780 Processing helix chain 'A' and resid 805 through 820 removed outlier: 3.800A pdb=" N LYS A 809 " --> pdb=" O PRO A 805 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N THR A 810 " --> pdb=" O ARG A 806 " (cutoff:3.500A) removed outlier: 4.215A pdb=" N PHE A 811 " --> pdb=" O ALA A 807 " (cutoff:3.500A) Processing helix chain 'A' and resid 830 through 834 removed outlier: 3.622A pdb=" N TYR A 834 " --> pdb=" O ILE A 831 " (cutoff:3.500A) Processing helix chain 'A' and resid 854 through 867 Proline residue: A 862 - end of helix Processing helix chain 'A' and resid 868 through 872 Processing helix chain 'A' and resid 888 through 903 removed outlier: 3.797A pdb=" N HIS A 901 " --> pdb=" O VAL A 897 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N LEU A 902 " --> pdb=" O PHE A 898 " (cutoff:3.500A) Processing helix chain 'A' and resid 918 through 926 Processing helix chain 'A' and resid 1015 through 1033 Processing helix chain 'A' and resid 1052 through 1064 removed outlier: 3.810A pdb=" N THR A1064 " --> pdb=" O LEU A1060 " (cutoff:3.500A) Processing helix chain 'B' and resid 120 through 133 removed outlier: 5.812A pdb=" N LEU B 126 " --> pdb=" O MET B 122 " (cutoff:3.500A) Proline residue: B 127 - end of helix Processing helix chain 'B' and resid 134 through 177 removed outlier: 4.708A pdb=" N PHE B 138 " --> pdb=" O GLY B 134 " (cutoff:3.500A) removed outlier: 5.188A pdb=" N THR B 142 " --> pdb=" O PHE B 138 " (cutoff:3.500A) removed outlier: 5.477A pdb=" N TRP B 143 " --> pdb=" O LEU B 139 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N MET B 144 " --> pdb=" O ARG B 140 " (cutoff:3.500A) removed outlier: 6.671A pdb=" N VAL B 150 " --> pdb=" O GLY B 146 " (cutoff:3.500A) removed outlier: 9.270A pdb=" N LEU B 151 " --> pdb=" O THR B 147 " (cutoff:3.500A) removed outlier: 4.033A pdb=" N GLN B 152 " --> pdb=" O ALA B 148 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N CYS B 163 " --> pdb=" O ILE B 159 " (cutoff:3.500A) removed outlier: 4.024A pdb=" N THR B 164 " --> pdb=" O CYS B 160 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N ASN B 177 " --> pdb=" O ALA B 173 " (cutoff:3.500A) Processing helix chain 'B' and resid 185 through 227 removed outlier: 4.101A pdb=" N ILE B 189 " --> pdb=" O SER B 185 " (cutoff:3.500A) Proline residue: B 195 - end of helix removed outlier: 3.545A pdb=" N CYS B 204 " --> pdb=" O ALA B 200 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N TYR B 227 " --> pdb=" O ILE B 223 " (cutoff:3.500A) Processing helix chain 'B' and resid 245 through 269 Processing helix chain 'B' and resid 269 through 301 removed outlier: 5.486A pdb=" N SER B 278 " --> pdb=" O ASN B 274 " (cutoff:3.500A) removed outlier: 5.711A pdb=" N LEU B 279 " --> pdb=" O LYS B 275 " (cutoff:3.500A) removed outlier: 4.016A pdb=" N PHE B 280 " --> pdb=" O PHE B 276 " (cutoff:3.500A) removed outlier: 3.916A pdb=" N LEU B 281 " --> pdb=" O ALA B 277 " (cutoff:3.500A) removed outlier: 4.240A pdb=" N PHE B 300 " --> pdb=" O ILE B 296 " (cutoff:3.500A) Processing helix chain 'B' and resid 336 through 343 Processing helix chain 'B' and resid 354 through 360 removed outlier: 3.918A pdb=" N MET B 358 " --> pdb=" O ASP B 354 " (cutoff:3.500A) Processing helix chain 'B' and resid 374 through 379 Processing helix chain 'B' and resid 407 through 411 Processing helix chain 'B' and resid 419 through 428 removed outlier: 3.877A pdb=" N LEU B 423 " --> pdb=" O SER B 419 " (cutoff:3.500A) Processing helix chain 'B' and resid 429 through 431 No H-bonds generated for 'chain 'B' and resid 429 through 431' Processing helix chain 'B' and resid 446 through 477 Proline residue: B 452 - end of helix Processing helix chain 'B' and resid 494 through 498 Processing helix chain 'B' and resid 504 through 536 removed outlier: 3.841A pdb=" N VAL B 508 " --> pdb=" O PRO B 504 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N ILE B 509 " --> pdb=" O TRP B 505 " (cutoff:3.500A) Proline residue: B 527 - end of helix Processing helix chain 'B' and resid 543 through 547 Processing helix chain 'B' and resid 557 through 570 Processing helix chain 'B' and resid 573 through 602 Proline residue: B 579 - end of helix Processing helix chain 'B' and resid 615 through 634 removed outlier: 3.582A pdb=" N SER B 619 " --> pdb=" O HIS B 615 " (cutoff:3.500A) removed outlier: 4.088A pdb=" N SER B 634 " --> pdb=" O MET B 630 " (cutoff:3.500A) Processing helix chain 'B' and resid 634 through 661 Processing helix chain 'B' and resid 664 through 682 removed outlier: 4.122A pdb=" N GLU B 682 " --> pdb=" O LEU B 678 " (cutoff:3.500A) Processing helix chain 'B' and resid 709 through 720 removed outlier: 3.800A pdb=" N THR B 713 " --> pdb=" O PRO B 709 " (cutoff:3.500A) Processing helix chain 'B' and resid 734 through 738 Processing helix chain 'B' and resid 739 through 756 Processing helix chain 'B' and resid 769 through 780 Processing helix chain 'B' and resid 805 through 820 removed outlier: 3.800A pdb=" N LYS B 809 " --> pdb=" O PRO B 805 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N THR B 810 " --> pdb=" O ARG B 806 " (cutoff:3.500A) removed outlier: 4.216A pdb=" N PHE B 811 " --> pdb=" O ALA B 807 " (cutoff:3.500A) Processing helix chain 'B' and resid 830 through 834 removed outlier: 3.622A pdb=" N TYR B 834 " --> pdb=" O ILE B 831 " (cutoff:3.500A) Processing helix chain 'B' and resid 854 through 867 Proline residue: B 862 - end of helix Processing helix chain 'B' and resid 868 through 872 Processing helix chain 'B' and resid 888 through 903 removed outlier: 3.797A pdb=" N HIS B 901 " --> pdb=" O VAL B 897 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N LEU B 902 " --> pdb=" O PHE B 898 " (cutoff:3.500A) Processing helix chain 'B' and resid 918 through 926 Processing helix chain 'B' and resid 1015 through 1033 Processing helix chain 'B' and resid 1052 through 1064 removed outlier: 3.811A pdb=" N THR B1064 " --> pdb=" O LEU B1060 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 313 through 314 Processing sheet with id=AA2, first strand: chain 'A' and resid 326 through 329 Processing sheet with id=AA3, first strand: chain 'A' and resid 761 through 767 removed outlier: 6.331A pdb=" N LEU A 695 " --> pdb=" O VAL A 792 " (cutoff:3.500A) removed outlier: 6.621A pdb=" N VAL A 791 " --> pdb=" O LEU A 826 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N LEU A1072 " --> pdb=" O VAL A 827 " (cutoff:3.500A) removed outlier: 4.112A pdb=" N VAL A1070 " --> pdb=" O LYS A 829 " (cutoff:3.500A) removed outlier: 6.364A pdb=" N VAL A1039 " --> pdb=" O LEU A1071 " (cutoff:3.500A) removed outlier: 7.673A pdb=" N VAL A1073 " --> pdb=" O VAL A1039 " (cutoff:3.500A) removed outlier: 6.621A pdb=" N LEU A1041 " --> pdb=" O VAL A1073 " (cutoff:3.500A) removed outlier: 8.502A pdb=" N LEU A1040 " --> pdb=" O HIS A 845 " (cutoff:3.500A) removed outlier: 6.926A pdb=" N ASP A 847 " --> pdb=" O LEU A1040 " (cutoff:3.500A) removed outlier: 8.873A pdb=" N ASN A1042 " --> pdb=" O ASP A 847 " (cutoff:3.500A) removed outlier: 6.818A pdb=" N ILE A 846 " --> pdb=" O ARG A 877 " (cutoff:3.500A) removed outlier: 7.534A pdb=" N PHE A 879 " --> pdb=" O ILE A 846 " (cutoff:3.500A) removed outlier: 6.057A pdb=" N VAL A 848 " --> pdb=" O PHE A 879 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N GLU A 907 " --> pdb=" O MET A 876 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 782 through 783 removed outlier: 3.639A pdb=" N LEU A 783 " --> pdb=" O MET A 786 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 313 through 314 Processing sheet with id=AA6, first strand: chain 'B' and resid 326 through 329 Processing sheet with id=AA7, first strand: chain 'B' and resid 761 through 767 removed outlier: 6.331A pdb=" N LEU B 695 " --> pdb=" O VAL B 792 " (cutoff:3.500A) removed outlier: 6.621A pdb=" N VAL B 791 " --> pdb=" O LEU B 826 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N LEU B1072 " --> pdb=" O VAL B 827 " (cutoff:3.500A) removed outlier: 4.112A pdb=" N VAL B1070 " --> pdb=" O LYS B 829 " (cutoff:3.500A) removed outlier: 6.364A pdb=" N VAL B1039 " --> pdb=" O LEU B1071 " (cutoff:3.500A) removed outlier: 7.673A pdb=" N VAL B1073 " --> pdb=" O VAL B1039 " (cutoff:3.500A) removed outlier: 6.622A pdb=" N LEU B1041 " --> pdb=" O VAL B1073 " (cutoff:3.500A) removed outlier: 8.502A pdb=" N LEU B1040 " --> pdb=" O HIS B 845 " (cutoff:3.500A) removed outlier: 6.926A pdb=" N ASP B 847 " --> pdb=" O LEU B1040 " (cutoff:3.500A) removed outlier: 8.873A pdb=" N ASN B1042 " --> pdb=" O ASP B 847 " (cutoff:3.500A) removed outlier: 6.818A pdb=" N ILE B 846 " --> pdb=" O ARG B 877 " (cutoff:3.500A) removed outlier: 7.535A pdb=" N PHE B 879 " --> pdb=" O ILE B 846 " (cutoff:3.500A) removed outlier: 6.058A pdb=" N VAL B 848 " --> pdb=" O PHE B 879 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N GLU B 907 " --> pdb=" O MET B 876 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 782 through 783 removed outlier: 3.639A pdb=" N LEU B 783 " --> pdb=" O MET B 786 " (cutoff:3.500A) 766 hydrogen bonds defined for protein. 2201 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: 2.25 Time building geometry restraints manager: 1.59 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: 4213 1.34 - 1.47: 3483 1.47 - 1.59: 5975 1.59 - 1.72: 26 1.72 - 1.84: 152 Bond restraints: 13849 Sorted by residual: bond pdb=" C4 ATP B1201 " pdb=" C5 ATP B1201 " ideal model delta sigma weight residual 1.388 1.465 -0.077 1.00e-02 1.00e+04 5.91e+01 bond pdb=" C4 ATP A1201 " pdb=" C5 ATP A1201 " ideal model delta sigma weight residual 1.388 1.464 -0.076 1.00e-02 1.00e+04 5.81e+01 bond pdb=" C5 ATP A1201 " pdb=" C6 ATP A1201 " ideal model delta sigma weight residual 1.409 1.479 -0.070 1.00e-02 1.00e+04 4.89e+01 bond pdb=" C5 ATP B1201 " pdb=" C6 ATP B1201 " ideal model delta sigma weight residual 1.409 1.478 -0.069 1.00e-02 1.00e+04 4.75e+01 bond pdb=" C8 ATP A1201 " pdb=" N7 ATP A1201 " ideal model delta sigma weight residual 1.310 1.355 -0.045 1.00e-02 1.00e+04 1.99e+01 ... (remaining 13844 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.97: 18627 2.97 - 5.94: 207 5.94 - 8.91: 36 8.91 - 11.89: 4 11.89 - 14.86: 4 Bond angle restraints: 18878 Sorted by residual: angle pdb=" PB ATP A1201 " pdb=" O3B ATP A1201 " pdb=" PG ATP A1201 " ideal model delta sigma weight residual 139.87 125.01 14.86 1.00e+00 1.00e+00 2.21e+02 angle pdb=" PB ATP B1201 " pdb=" O3B ATP B1201 " pdb=" PG ATP B1201 " ideal model delta sigma weight residual 139.87 125.02 14.85 1.00e+00 1.00e+00 2.21e+02 angle pdb=" PA ATP B1201 " pdb=" O3A ATP B1201 " pdb=" PB ATP B1201 " ideal model delta sigma weight residual 136.83 123.66 13.17 1.00e+00 1.00e+00 1.73e+02 angle pdb=" PA ATP A1201 " pdb=" O3A ATP A1201 " pdb=" PB ATP A1201 " ideal model delta sigma weight residual 136.83 123.69 13.14 1.00e+00 1.00e+00 1.73e+02 angle pdb=" C5 ATP B1201 " pdb=" C4 ATP B1201 " pdb=" N3 ATP B1201 " ideal model delta sigma weight residual 126.80 118.62 8.18 1.00e+00 1.00e+00 6.69e+01 ... (remaining 18873 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.89: 6992 17.89 - 35.78: 793 35.78 - 53.67: 192 53.67 - 71.57: 25 71.57 - 89.46: 14 Dihedral angle restraints: 8016 sinusoidal: 3034 harmonic: 4982 Sorted by residual: dihedral pdb=" CB CYS B 343 " pdb=" SG CYS B 343 " pdb=" SG CYS B 353 " pdb=" CB CYS B 353 " ideal model delta sinusoidal sigma weight residual 93.00 141.07 -48.07 1 1.00e+01 1.00e-02 3.18e+01 dihedral pdb=" CB CYS A 343 " pdb=" SG CYS A 343 " pdb=" SG CYS A 353 " pdb=" CB CYS A 353 " ideal model delta sinusoidal sigma weight residual 93.00 141.04 -48.04 1 1.00e+01 1.00e-02 3.18e+01 dihedral pdb=" CA GLN A 693 " pdb=" C GLN A 693 " pdb=" N LEU A 694 " pdb=" CA LEU A 694 " ideal model delta harmonic sigma weight residual -180.00 -161.72 -18.28 0 5.00e+00 4.00e-02 1.34e+01 ... (remaining 8013 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.068: 1910 0.068 - 0.136: 296 0.136 - 0.203: 15 0.203 - 0.271: 8 0.271 - 0.339: 2 Chirality restraints: 2231 Sorted by residual: chirality pdb=" C1 NAG F 1 " pdb=" ND2 ASN A 361 " pdb=" C2 NAG F 1 " pdb=" O5 NAG F 1 " both_signs ideal model delta sigma weight residual False -2.40 -2.74 0.34 2.00e-01 2.50e+01 2.87e+00 chirality pdb=" C1 NAG M 1 " pdb=" ND2 ASN B 361 " pdb=" C2 NAG M 1 " pdb=" O5 NAG M 1 " both_signs ideal model delta sigma weight residual False -2.40 -2.74 0.34 2.00e-01 2.50e+01 2.83e+00 chirality pdb=" C4 NAG M 1 " pdb=" C3 NAG M 1 " pdb=" C5 NAG M 1 " pdb=" O4 NAG M 1 " both_signs ideal model delta sigma weight residual False -2.53 -2.27 -0.26 2.00e-01 2.50e+01 1.73e+00 ... (remaining 2228 not shown) Planarity restraints: 2324 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA TRP B 808 " -0.014 2.00e-02 2.50e+03 2.75e-02 7.59e+00 pdb=" C TRP B 808 " 0.048 2.00e-02 2.50e+03 pdb=" O TRP B 808 " -0.018 2.00e-02 2.50e+03 pdb=" N LYS B 809 " -0.016 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA TRP A 808 " -0.014 2.00e-02 2.50e+03 2.75e-02 7.58e+00 pdb=" C TRP A 808 " 0.048 2.00e-02 2.50e+03 pdb=" O TRP A 808 " -0.018 2.00e-02 2.50e+03 pdb=" N LYS A 809 " -0.016 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LEU A 137 " 0.012 2.00e-02 2.50e+03 2.44e-02 5.96e+00 pdb=" C LEU A 137 " -0.042 2.00e-02 2.50e+03 pdb=" O LEU A 137 " 0.016 2.00e-02 2.50e+03 pdb=" N PHE A 138 " 0.014 2.00e-02 2.50e+03 ... (remaining 2321 not shown) Histogram of nonbonded interaction distances: 2.21 - 2.75: 2065 2.75 - 3.29: 12937 3.29 - 3.83: 21296 3.83 - 4.36: 23646 4.36 - 4.90: 43608 Nonbonded interactions: 103552 Sorted by model distance: nonbonded pdb=" NZ LYS B 809 " pdb=" OD2 ASP B 813 " model vdw 2.215 3.120 nonbonded pdb=" NZ LYS A 809 " pdb=" OD2 ASP A 813 " model vdw 2.215 3.120 nonbonded pdb=" OG1 THR B 713 " pdb=" OE1 GLU B 756 " model vdw 2.254 3.040 nonbonded pdb=" OG1 THR A 713 " pdb=" OE1 GLU A 756 " model vdw 2.254 3.040 nonbonded pdb=" O ARG B 806 " pdb="MG MG B1202 " model vdw 2.256 2.170 ... (remaining 103547 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' and (resid 116 through 775 or resid 777 through 1202)) selection = (chain 'B' and (resid 116 through 775 or resid 777 through 1202)) } ncs_group { reference = chain 'C' selection = chain 'J' } ncs_group { reference = chain 'F' selection = chain 'M' } 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=0.50 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic 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: 2.820 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.260 Check model and map are aligned: 0.020 Set scattering table: 0.050 Process input model: 15.200 Find NCS groups from input model: 0.270 Set up NCS constraints: 0.040 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:1.360 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 20.040 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8372 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 : 0.007 0.077 13865 Z= 0.323 Angle : 0.868 14.857 18920 Z= 0.490 Chirality : 0.050 0.339 2231 Planarity : 0.005 0.046 2320 Dihedral : 15.924 89.457 4808 Min Nonbonded Distance : 2.215 Molprobity Statistics. All-atom Clashscore : 7.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.52 % Favored : 96.48 % Rotamer: Outliers : 0.71 % Allowed : 21.40 % Favored : 77.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.49 (0.19), residues: 1707 helix: 0.28 (0.16), residues: 943 sheet: -2.10 (0.40), residues: 136 loop : -2.72 (0.22), residues: 628 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 866 TYR 0.011 0.001 TYR A 739 PHE 0.020 0.002 PHE B 541 TRP 0.029 0.002 TRP A 143 HIS 0.008 0.001 HIS A 853 Details of bonding type rmsd/Z covalent geometry : bond 0.00685 / 0.32 (13849) covalent geometry : angle 0.83431 / 0.48 (18878) SS BOND : bond 0.00561 / 0.34 ( 6) SS BOND : angle 3.83462 / 1.92 ( 12) hydrogen bonds : bond 0.15333 / 10.52 ( 766) hydrogen bonds : angle 5.41242 / 3.86 ( 2201) link_BETA1-4 : bond 0.00503 / 0.32 ( 6) link_BETA1-4 : angle 4.01190 / 2.50 ( 18) link_NAG-ASN : bond 0.00328 / 0.19 ( 4) link_NAG-ASN : angle 7.27737 / 4.08 ( 12) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3414 Ramachandran restraints generated. 1707 Oldfield, 0 Emsley, 1707 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3414 Ramachandran restraints generated. 1707 Oldfield, 0 Emsley, 1707 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 210 residues out of total 1447 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 200 time to evaluate : 0.511 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 443 ASP cc_start: 0.7243 (m-30) cc_final: 0.6872 (t0) REVERT: A 583 MET cc_start: 0.8014 (mmp) cc_final: 0.7741 (mmp) REVERT: A 903 ARG cc_start: 0.6998 (OUTLIER) cc_final: 0.5280 (pmt170) REVERT: B 443 ASP cc_start: 0.7219 (m-30) cc_final: 0.6844 (t0) REVERT: B 903 ARG cc_start: 0.6982 (OUTLIER) cc_final: 0.5205 (pmt170) outliers start: 10 outliers final: 6 residues processed: 210 average time/residue: 0.1189 time to fit residues: 34.6759 Evaluate side-chains 167 residues out of total 1447 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 159 time to evaluate : 0.499 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 320 PHE Chi-restraints excluded: chain A residue 353 CYS Chi-restraints excluded: chain A residue 879 PHE Chi-restraints excluded: chain A residue 903 ARG Chi-restraints excluded: chain B residue 320 PHE Chi-restraints excluded: chain B residue 353 CYS Chi-restraints excluded: chain B residue 879 PHE Chi-restraints excluded: chain B residue 903 ARG Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 172 random chunks: chunk 98 optimal weight: 4.9990 chunk 107 optimal weight: 1.9990 chunk 10 optimal weight: 0.5980 chunk 66 optimal weight: 1.9990 chunk 130 optimal weight: 0.6980 chunk 124 optimal weight: 0.6980 chunk 103 optimal weight: 3.9990 chunk 77 optimal weight: 0.0070 chunk 122 optimal weight: 0.8980 chunk 91 optimal weight: 0.7980 chunk 149 optimal weight: 3.9990 overall best weight: 0.5598 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 152 GLN A 344 HIS A 547 HIS A 593 ASN A 599 GLN A 655 GLN A 717 GLN A 747 GLN A 751 ASN A 776 HIS B ** A 853 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1026 ASN B 152 GLN B 344 HIS B 547 HIS B 593 ASN B 599 GLN B 655 GLN B 717 GLN B 747 GLN B 751 ASN B 853 HIS B1026 ASN Total number of N/Q/H flips: 22 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4008 r_free = 0.4008 target = 0.170566 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3513 r_free = 0.3513 target = 0.124947 restraints weight = 20570.124| |-----------------------------------------------------------------------------| r_work (start): 0.3466 rms_B_bonded: 2.78 r_work: 0.3308 rms_B_bonded: 3.29 restraints_weight: 0.5000 r_work (final): 0.3308 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3309 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3309 r_free = 0.3309 target_work(ls_wunit_k1) = 0.107 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3308 r_free = 0.3308 target_work(ls_wunit_k1) = 0.107 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 5 (7 function evaluations) r_final: 0.3308 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8491 moved from start: 0.1270 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 13865 Z= 0.124 Angle : 0.617 9.332 18920 Z= 0.299 Chirality : 0.042 0.256 2231 Planarity : 0.004 0.037 2320 Dihedral : 6.242 87.668 1902 Min Nonbonded Distance : 2.279 Molprobity Statistics. All-atom Clashscore : 4.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.17 % Favored : 97.83 % Rotamer: Outliers : 2.34 % Allowed : 22.47 % Favored : 75.19 % 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: 0.01 (0.20), residues: 1707 helix: 1.56 (0.17), residues: 947 sheet: -1.32 (0.40), residues: 136 loop : -2.24 (0.22), residues: 624 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 317 TYR 0.010 0.001 TYR A1056 PHE 0.014 0.001 PHE A 320 TRP 0.015 0.001 TRP A 143 HIS 0.012 0.001 HIS A 853 Details of bonding type rmsd/Z covalent geometry : bond 0.00269 / 0.12 (13849) covalent geometry : angle 0.60530 / 0.30 (18878) SS BOND : bond 0.00441 / 0.28 ( 6) SS BOND : angle 1.71122 / 0.91 ( 12) hydrogen bonds : bond 0.04800 / 3.25 ( 766) hydrogen bonds : angle 4.03995 / 2.90 ( 2201) link_BETA1-4 : bond 0.00459 / 0.27 ( 6) link_BETA1-4 : angle 2.80020 / 1.74 ( 18) link_NAG-ASN : bond 0.00200 / 0.12 ( 4) link_NAG-ASN : angle 3.12649 / 1.91 ( 12) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3414 Ramachandran restraints generated. 1707 Oldfield, 0 Emsley, 1707 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3414 Ramachandran restraints generated. 1707 Oldfield, 0 Emsley, 1707 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 210 residues out of total 1447 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 177 time to evaluate : 0.593 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 443 ASP cc_start: 0.7867 (m-30) cc_final: 0.6712 (t0) REVERT: A 543 ARG cc_start: 0.7734 (OUTLIER) cc_final: 0.7031 (ttp80) REVERT: A 1061 GLU cc_start: 0.7972 (tp30) cc_final: 0.7696 (tp30) REVERT: B 443 ASP cc_start: 0.7830 (m-30) cc_final: 0.6706 (t0) REVERT: B 543 ARG cc_start: 0.7665 (OUTLIER) cc_final: 0.7005 (ttp80) REVERT: B 591 PHE cc_start: 0.8437 (OUTLIER) cc_final: 0.7789 (m-80) REVERT: B 1061 GLU cc_start: 0.7998 (tp30) cc_final: 0.7727 (tp30) outliers start: 33 outliers final: 19 residues processed: 197 average time/residue: 0.1121 time to fit residues: 32.6534 Evaluate side-chains 178 residues out of total 1447 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 156 time to evaluate : 0.486 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 120 THR Chi-restraints excluded: chain A residue 159 ILE Chi-restraints excluded: chain A residue 299 ILE Chi-restraints excluded: chain A residue 320 PHE Chi-restraints excluded: chain A residue 322 ILE Chi-restraints excluded: chain A residue 413 VAL Chi-restraints excluded: chain A residue 543 ARG Chi-restraints excluded: chain A residue 879 PHE Chi-restraints excluded: chain A residue 1073 VAL Chi-restraints excluded: chain A residue 1081 ILE Chi-restraints excluded: chain B residue 159 ILE Chi-restraints excluded: chain B residue 248 LEU Chi-restraints excluded: chain B residue 299 ILE Chi-restraints excluded: chain B residue 320 PHE Chi-restraints excluded: chain B residue 322 ILE Chi-restraints excluded: chain B residue 363 THR Chi-restraints excluded: chain B residue 413 VAL Chi-restraints excluded: chain B residue 543 ARG Chi-restraints excluded: chain B residue 569 ILE Chi-restraints excluded: chain B residue 591 PHE Chi-restraints excluded: chain B residue 879 PHE Chi-restraints excluded: chain B residue 1073 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 172 random chunks: chunk 161 optimal weight: 10.0000 chunk 2 optimal weight: 2.9990 chunk 78 optimal weight: 10.0000 chunk 48 optimal weight: 5.9990 chunk 129 optimal weight: 1.9990 chunk 165 optimal weight: 7.9990 chunk 23 optimal weight: 0.0270 chunk 152 optimal weight: 0.0060 chunk 62 optimal weight: 0.7980 chunk 89 optimal weight: 1.9990 chunk 59 optimal weight: 0.7980 overall best weight: 0.7256 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 547 HIS A 853 HIS A 868 HIS B 547 HIS B 853 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4016 r_free = 0.4016 target = 0.171167 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3516 r_free = 0.3516 target = 0.125124 restraints weight = 23743.410| |-----------------------------------------------------------------------------| r_work (start): 0.3455 rms_B_bonded: 2.95 r_work: 0.3295 rms_B_bonded: 3.42 restraints_weight: 0.5000 r_work (final): 0.3295 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3298 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3298 r_free = 0.3298 target_work(ls_wunit_k1) = 0.107 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3298 r_free = 0.3298 target_work(ls_wunit_k1) = 0.107 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (8 function evaluations) r_final: 0.3298 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8494 moved from start: 0.1583 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 13865 Z= 0.115 Angle : 0.579 9.582 18920 Z= 0.277 Chirality : 0.041 0.273 2231 Planarity : 0.004 0.034 2320 Dihedral : 5.975 89.487 1892 Min Nonbonded Distance : 2.208 Molprobity Statistics. All-atom Clashscore : 3.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.58 % Favored : 97.42 % Rotamer: Outliers : 2.48 % Allowed : 22.89 % Favored : 74.63 % 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 (0.21), residues: 1707 helix: 2.01 (0.17), residues: 951 sheet: -0.56 (0.44), residues: 132 loop : -1.93 (0.22), residues: 624 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 317 TYR 0.008 0.001 TYR A1056 PHE 0.022 0.001 PHE B1059 TRP 0.015 0.001 TRP A 850 HIS 0.010 0.001 HIS A 853 Details of bonding type rmsd/Z covalent geometry : bond 0.00258 / 0.12 (13849) covalent geometry : angle 0.56746 / 0.27 (18878) SS BOND : bond 0.00336 / 0.22 ( 6) SS BOND : angle 1.40407 / 0.68 ( 12) hydrogen bonds : bond 0.04356 / 2.96 ( 766) hydrogen bonds : angle 3.71678 / 2.67 ( 2201) link_BETA1-4 : bond 0.00486 / 0.30 ( 6) link_BETA1-4 : angle 2.52516 / 1.59 ( 18) link_NAG-ASN : bond 0.00169 / 0.09 ( 4) link_NAG-ASN : angle 3.27698 / 2.04 ( 12) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3414 Ramachandran restraints generated. 1707 Oldfield, 0 Emsley, 1707 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3414 Ramachandran restraints generated. 1707 Oldfield, 0 Emsley, 1707 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 205 residues out of total 1447 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 170 time to evaluate : 0.320 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 171 MET cc_start: 0.7848 (mmm) cc_final: 0.7506 (tpt) REVERT: A 443 ASP cc_start: 0.7853 (m-30) cc_final: 0.6694 (t0) REVERT: A 543 ARG cc_start: 0.7772 (OUTLIER) cc_final: 0.7074 (ttp80) REVERT: A 1061 GLU cc_start: 0.8015 (tp30) cc_final: 0.7726 (tp30) REVERT: B 380 LEU cc_start: 0.9142 (OUTLIER) cc_final: 0.8902 (tt) REVERT: B 443 ASP cc_start: 0.7830 (m-30) cc_final: 0.6691 (t0) REVERT: B 543 ARG cc_start: 0.7730 (OUTLIER) cc_final: 0.7041 (ttp80) REVERT: B 590 LEU cc_start: 0.8895 (OUTLIER) cc_final: 0.8692 (tp) REVERT: B 1061 GLU cc_start: 0.8069 (tp30) cc_final: 0.7806 (tp30) outliers start: 35 outliers final: 22 residues processed: 191 average time/residue: 0.1079 time to fit residues: 30.4738 Evaluate side-chains 183 residues out of total 1447 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 157 time to evaluate : 0.490 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 159 ILE Chi-restraints excluded: chain A residue 299 ILE Chi-restraints excluded: chain A residue 320 PHE Chi-restraints excluded: chain A residue 322 ILE Chi-restraints excluded: chain A residue 413 VAL Chi-restraints excluded: chain A residue 543 ARG Chi-restraints excluded: chain A residue 591 PHE Chi-restraints excluded: chain A residue 879 PHE Chi-restraints excluded: chain A residue 1081 ILE Chi-restraints excluded: chain B residue 159 ILE Chi-restraints excluded: chain B residue 221 ILE Chi-restraints excluded: chain B residue 299 ILE Chi-restraints excluded: chain B residue 320 PHE Chi-restraints excluded: chain B residue 322 ILE Chi-restraints excluded: chain B residue 380 LEU Chi-restraints excluded: chain B residue 413 VAL Chi-restraints excluded: chain B residue 495 VAL Chi-restraints excluded: chain B residue 543 ARG Chi-restraints excluded: chain B residue 590 LEU Chi-restraints excluded: chain B residue 591 PHE Chi-restraints excluded: chain B residue 630 MET Chi-restraints excluded: chain B residue 792 VAL Chi-restraints excluded: chain B residue 879 PHE Chi-restraints excluded: chain B residue 1073 VAL Chi-restraints excluded: chain B residue 1080 VAL Chi-restraints excluded: chain B residue 1081 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 172 random chunks: chunk 160 optimal weight: 3.9990 chunk 134 optimal weight: 2.9990 chunk 127 optimal weight: 1.9990 chunk 126 optimal weight: 1.9990 chunk 116 optimal weight: 0.5980 chunk 10 optimal weight: 0.8980 chunk 115 optimal weight: 1.9990 chunk 167 optimal weight: 6.9990 chunk 119 optimal weight: 0.8980 chunk 108 optimal weight: 3.9990 chunk 149 optimal weight: 2.9990 overall best weight: 1.2784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 547 HIS B 177 ASN B 547 HIS B 853 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4000 r_free = 0.4000 target = 0.169649 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3515 r_free = 0.3515 target = 0.125011 restraints weight = 18122.829| |-----------------------------------------------------------------------------| r_work (start): 0.3456 rms_B_bonded: 2.57 r_work: 0.3295 rms_B_bonded: 3.13 restraints_weight: 0.5000 r_work (final): 0.3295 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3301 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3301 r_free = 0.3301 target_work(ls_wunit_k1) = 0.107 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3301 r_free = 0.3301 target_work(ls_wunit_k1) = 0.107 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3301 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8484 moved from start: 0.1663 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 13865 Z= 0.141 Angle : 0.585 9.593 18920 Z= 0.279 Chirality : 0.042 0.276 2231 Planarity : 0.003 0.037 2320 Dihedral : 5.893 88.478 1892 Min Nonbonded Distance : 2.167 Molprobity Statistics. All-atom Clashscore : 4.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.75 % Favored : 97.25 % Rotamer: Outliers : 3.19 % Allowed : 21.97 % Favored : 74.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.84 (0.21), residues: 1707 helix: 2.14 (0.17), residues: 951 sheet: -0.44 (0.43), residues: 136 loop : -1.85 (0.22), residues: 620 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 317 TYR 0.008 0.001 TYR A1056 PHE 0.019 0.001 PHE B1059 TRP 0.020 0.001 TRP A 850 HIS 0.005 0.001 HIS B 853 Details of bonding type rmsd/Z covalent geometry : bond 0.00339 / 0.14 (13849) covalent geometry : angle 0.57336 / 0.28 (18878) SS BOND : bond 0.00479 / 0.31 ( 6) SS BOND : angle 1.53686 / 0.74 ( 12) hydrogen bonds : bond 0.04613 / 3.13 ( 766) hydrogen bonds : angle 3.66122 / 2.63 ( 2201) link_BETA1-4 : bond 0.00479 / 0.28 ( 6) link_BETA1-4 : angle 2.47883 / 1.55 ( 18) link_NAG-ASN : bond 0.00146 / 0.09 ( 4) link_NAG-ASN : angle 3.15837 / 1.96 ( 12) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3414 Ramachandran restraints generated. 1707 Oldfield, 0 Emsley, 1707 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3414 Ramachandran restraints generated. 1707 Oldfield, 0 Emsley, 1707 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 211 residues out of total 1447 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 166 time to evaluate : 0.436 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 443 ASP cc_start: 0.7866 (m-30) cc_final: 0.6696 (t0) REVERT: A 543 ARG cc_start: 0.7789 (OUTLIER) cc_final: 0.7132 (ttp80) REVERT: A 623 MET cc_start: 0.8342 (ttp) cc_final: 0.8135 (ttt) REVERT: A 1061 GLU cc_start: 0.7991 (tp30) cc_final: 0.7693 (tp30) REVERT: B 380 LEU cc_start: 0.9149 (OUTLIER) cc_final: 0.8898 (tt) REVERT: B 443 ASP cc_start: 0.7845 (m-30) cc_final: 0.6681 (t0) REVERT: B 543 ARG cc_start: 0.7718 (OUTLIER) cc_final: 0.7042 (ttp80) REVERT: B 591 PHE cc_start: 0.8410 (OUTLIER) cc_final: 0.7710 (m-10) REVERT: B 1061 GLU cc_start: 0.8037 (tp30) cc_final: 0.7789 (tp30) outliers start: 45 outliers final: 31 residues processed: 196 average time/residue: 0.1044 time to fit residues: 30.7478 Evaluate side-chains 194 residues out of total 1447 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 159 time to evaluate : 0.500 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 159 ILE Chi-restraints excluded: chain A residue 221 ILE Chi-restraints excluded: chain A residue 299 ILE Chi-restraints excluded: chain A residue 320 PHE Chi-restraints excluded: chain A residue 322 ILE Chi-restraints excluded: chain A residue 363 THR Chi-restraints excluded: chain A residue 413 VAL Chi-restraints excluded: chain A residue 495 VAL Chi-restraints excluded: chain A residue 543 ARG Chi-restraints excluded: chain A residue 569 ILE Chi-restraints excluded: chain A residue 591 PHE Chi-restraints excluded: chain A residue 772 GLU Chi-restraints excluded: chain A residue 879 PHE Chi-restraints excluded: chain A residue 1073 VAL Chi-restraints excluded: chain A residue 1081 ILE Chi-restraints excluded: chain B residue 159 ILE Chi-restraints excluded: chain B residue 179 VAL Chi-restraints excluded: chain B residue 221 ILE Chi-restraints excluded: chain B residue 299 ILE Chi-restraints excluded: chain B residue 320 PHE Chi-restraints excluded: chain B residue 322 ILE Chi-restraints excluded: chain B residue 380 LEU Chi-restraints excluded: chain B residue 413 VAL Chi-restraints excluded: chain B residue 418 THR Chi-restraints excluded: chain B residue 462 THR Chi-restraints excluded: chain B residue 495 VAL Chi-restraints excluded: chain B residue 543 ARG Chi-restraints excluded: chain B residue 591 PHE Chi-restraints excluded: chain B residue 630 MET Chi-restraints excluded: chain B residue 772 GLU Chi-restraints excluded: chain B residue 792 VAL Chi-restraints excluded: chain B residue 879 PHE Chi-restraints excluded: chain B residue 1073 VAL Chi-restraints excluded: chain B residue 1080 VAL Chi-restraints excluded: chain B residue 1081 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 172 random chunks: chunk 144 optimal weight: 0.9980 chunk 26 optimal weight: 0.0570 chunk 37 optimal weight: 0.0060 chunk 49 optimal weight: 4.9990 chunk 38 optimal weight: 0.5980 chunk 95 optimal weight: 0.6980 chunk 147 optimal weight: 5.9990 chunk 138 optimal weight: 3.9990 chunk 74 optimal weight: 0.6980 chunk 118 optimal weight: 5.9990 chunk 146 optimal weight: 2.9990 overall best weight: 0.4114 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 547 HIS B 547 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4036 r_free = 0.4036 target = 0.172627 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3553 r_free = 0.3553 target = 0.127354 restraints weight = 23675.012| |-----------------------------------------------------------------------------| r_work (start): 0.3473 rms_B_bonded: 2.88 r_work: 0.3312 rms_B_bonded: 3.40 restraints_weight: 0.5000 r_work (final): 0.3312 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3319 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3319 r_free = 0.3319 target_work(ls_wunit_k1) = 0.108 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3319 r_free = 0.3319 target_work(ls_wunit_k1) = 0.108 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3319 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8486 moved from start: 0.1889 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.023 13865 Z= 0.102 Angle : 0.551 9.527 18920 Z= 0.262 Chirality : 0.040 0.273 2231 Planarity : 0.003 0.039 2320 Dihedral : 5.778 87.519 1892 Min Nonbonded Distance : 2.162 Molprobity Statistics. All-atom Clashscore : 3.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.40 % Favored : 97.60 % Rotamer: Outliers : 2.91 % Allowed : 21.97 % Favored : 75.12 % 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: 1.19 (0.21), residues: 1707 helix: 2.39 (0.17), residues: 951 sheet: -0.14 (0.45), residues: 132 loop : -1.66 (0.22), residues: 624 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 317 TYR 0.008 0.001 TYR A1056 PHE 0.017 0.001 PHE B1059 TRP 0.019 0.001 TRP B 850 HIS 0.004 0.001 HIS A 394 Details of bonding type rmsd/Z covalent geometry : bond 0.00217 / 0.10 (13849) covalent geometry : angle 0.53984 / 0.26 (18878) SS BOND : bond 0.00373 / 0.23 ( 6) SS BOND : angle 1.34692 / 0.67 ( 12) hydrogen bonds : bond 0.03985 / 2.70 ( 766) hydrogen bonds : angle 3.52242 / 2.53 ( 2201) link_BETA1-4 : bond 0.00486 / 0.29 ( 6) link_BETA1-4 : angle 2.35603 / 1.49 ( 18) link_NAG-ASN : bond 0.00248 / 0.14 ( 4) link_NAG-ASN : angle 3.22067 / 1.99 ( 12) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3414 Ramachandran restraints generated. 1707 Oldfield, 0 Emsley, 1707 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3414 Ramachandran restraints generated. 1707 Oldfield, 0 Emsley, 1707 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 207 residues out of total 1447 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 166 time to evaluate : 0.493 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 443 ASP cc_start: 0.7833 (m-30) cc_final: 0.6721 (t0) REVERT: A 543 ARG cc_start: 0.7792 (OUTLIER) cc_final: 0.7236 (ttp80) REVERT: A 737 GLU cc_start: 0.7525 (pm20) cc_final: 0.6989 (pm20) REVERT: A 1061 GLU cc_start: 0.8023 (tp30) cc_final: 0.7733 (tp30) REVERT: B 152 GLN cc_start: 0.7981 (OUTLIER) cc_final: 0.7692 (mt0) REVERT: B 264 LEU cc_start: 0.7710 (tp) cc_final: 0.7119 (mm) REVERT: B 380 LEU cc_start: 0.9167 (OUTLIER) cc_final: 0.8886 (tt) REVERT: B 443 ASP cc_start: 0.7813 (m-30) cc_final: 0.6694 (t0) REVERT: B 543 ARG cc_start: 0.7786 (OUTLIER) cc_final: 0.7151 (ttp80) REVERT: B 1061 GLU cc_start: 0.8014 (tp30) cc_final: 0.7779 (tp30) outliers start: 41 outliers final: 27 residues processed: 196 average time/residue: 0.1086 time to fit residues: 31.9881 Evaluate side-chains 192 residues out of total 1447 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 161 time to evaluate : 0.371 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 299 ILE Chi-restraints excluded: chain A residue 320 PHE Chi-restraints excluded: chain A residue 322 ILE Chi-restraints excluded: chain A residue 363 THR Chi-restraints excluded: chain A residue 413 VAL Chi-restraints excluded: chain A residue 543 ARG Chi-restraints excluded: chain A residue 569 ILE Chi-restraints excluded: chain A residue 591 PHE Chi-restraints excluded: chain A residue 772 GLU Chi-restraints excluded: chain A residue 879 PHE Chi-restraints excluded: chain A residue 1073 VAL Chi-restraints excluded: chain B residue 152 GLN Chi-restraints excluded: chain B residue 159 ILE Chi-restraints excluded: chain B residue 221 ILE Chi-restraints excluded: chain B residue 299 ILE Chi-restraints excluded: chain B residue 320 PHE Chi-restraints excluded: chain B residue 322 ILE Chi-restraints excluded: chain B residue 363 THR Chi-restraints excluded: chain B residue 380 LEU Chi-restraints excluded: chain B residue 413 VAL Chi-restraints excluded: chain B residue 462 THR Chi-restraints excluded: chain B residue 495 VAL Chi-restraints excluded: chain B residue 543 ARG Chi-restraints excluded: chain B residue 569 ILE Chi-restraints excluded: chain B residue 591 PHE Chi-restraints excluded: chain B residue 772 GLU Chi-restraints excluded: chain B residue 792 VAL Chi-restraints excluded: chain B residue 879 PHE Chi-restraints excluded: chain B residue 1073 VAL Chi-restraints excluded: chain B residue 1080 VAL Chi-restraints excluded: chain B residue 1081 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 172 random chunks: chunk 9 optimal weight: 0.7980 chunk 121 optimal weight: 3.9990 chunk 135 optimal weight: 5.9990 chunk 32 optimal weight: 4.9990 chunk 48 optimal weight: 0.9980 chunk 60 optimal weight: 4.9990 chunk 53 optimal weight: 0.9980 chunk 51 optimal weight: 4.9990 chunk 101 optimal weight: 5.9990 chunk 62 optimal weight: 1.9990 chunk 163 optimal weight: 6.9990 overall best weight: 1.7584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 547 HIS B 547 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3978 r_free = 0.3978 target = 0.167768 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3477 r_free = 0.3477 target = 0.122069 restraints weight = 23838.639| |-----------------------------------------------------------------------------| r_work (start): 0.3420 rms_B_bonded: 3.10 r_work: 0.3256 rms_B_bonded: 3.38 restraints_weight: 0.5000 r_work (final): 0.3256 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3265 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3265 r_free = 0.3265 target_work(ls_wunit_k1) = 0.105 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3265 r_free = 0.3265 target_work(ls_wunit_k1) = 0.105 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3265 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8529 moved from start: 0.1838 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 13865 Z= 0.170 Angle : 0.600 9.714 18920 Z= 0.289 Chirality : 0.043 0.278 2231 Planarity : 0.004 0.040 2320 Dihedral : 5.959 86.909 1892 Min Nonbonded Distance : 2.120 Molprobity Statistics. All-atom Clashscore : 3.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.52 % Favored : 96.48 % Rotamer: Outliers : 3.26 % Allowed : 22.11 % Favored : 74.63 % 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: 1.05 (0.21), residues: 1707 helix: 2.28 (0.17), residues: 945 sheet: -0.39 (0.42), residues: 136 loop : -1.66 (0.22), residues: 626 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 140 TYR 0.011 0.001 TYR B 654 PHE 0.022 0.002 PHE A1059 TRP 0.021 0.001 TRP B 850 HIS 0.003 0.001 HIS B 845 Details of bonding type rmsd/Z covalent geometry : bond 0.00418 / 0.17 (13849) covalent geometry : angle 0.58987 / 0.29 (18878) SS BOND : bond 0.00496 / 0.31 ( 6) SS BOND : angle 1.62464 / 0.78 ( 12) hydrogen bonds : bond 0.05015 / 3.40 ( 766) hydrogen bonds : angle 3.65147 / 2.61 ( 2201) link_BETA1-4 : bond 0.00453 / 0.28 ( 6) link_BETA1-4 : angle 2.43562 / 1.52 ( 18) link_NAG-ASN : bond 0.00068 / 0.04 ( 4) link_NAG-ASN : angle 3.00522 / 1.86 ( 12) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3414 Ramachandran restraints generated. 1707 Oldfield, 0 Emsley, 1707 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3414 Ramachandran restraints generated. 1707 Oldfield, 0 Emsley, 1707 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 216 residues out of total 1447 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 170 time to evaluate : 0.517 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 443 ASP cc_start: 0.7921 (m-30) cc_final: 0.6727 (t0) REVERT: A 543 ARG cc_start: 0.7762 (OUTLIER) cc_final: 0.7267 (ttp80) REVERT: A 591 PHE cc_start: 0.8426 (OUTLIER) cc_final: 0.7933 (m-10) REVERT: A 737 GLU cc_start: 0.7525 (pm20) cc_final: 0.6961 (pm20) REVERT: A 809 LYS cc_start: 0.7830 (tptp) cc_final: 0.7435 (tptt) REVERT: A 879 PHE cc_start: 0.6483 (OUTLIER) cc_final: 0.5870 (m-80) REVERT: A 1061 GLU cc_start: 0.8011 (tp30) cc_final: 0.7728 (tp30) REVERT: B 332 GLU cc_start: 0.8399 (OUTLIER) cc_final: 0.7943 (pm20) REVERT: B 380 LEU cc_start: 0.9182 (OUTLIER) cc_final: 0.8912 (tt) REVERT: B 443 ASP cc_start: 0.7909 (m-30) cc_final: 0.6726 (t0) REVERT: B 543 ARG cc_start: 0.7783 (OUTLIER) cc_final: 0.7256 (ttp80) REVERT: B 591 PHE cc_start: 0.8434 (OUTLIER) cc_final: 0.7953 (m-10) REVERT: B 859 MET cc_start: 0.7959 (mpp) cc_final: 0.7702 (mmt) REVERT: B 1061 GLU cc_start: 0.8004 (tp30) cc_final: 0.7762 (tp30) outliers start: 46 outliers final: 30 residues processed: 202 average time/residue: 0.1101 time to fit residues: 33.1739 Evaluate side-chains 205 residues out of total 1447 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 168 time to evaluate : 0.543 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 159 ILE Chi-restraints excluded: chain A residue 221 ILE Chi-restraints excluded: chain A residue 299 ILE Chi-restraints excluded: chain A residue 320 PHE Chi-restraints excluded: chain A residue 363 THR Chi-restraints excluded: chain A residue 413 VAL Chi-restraints excluded: chain A residue 495 VAL Chi-restraints excluded: chain A residue 543 ARG Chi-restraints excluded: chain A residue 591 PHE Chi-restraints excluded: chain A residue 630 MET Chi-restraints excluded: chain A residue 772 GLU Chi-restraints excluded: chain A residue 792 VAL Chi-restraints excluded: chain A residue 879 PHE Chi-restraints excluded: chain A residue 1062 VAL Chi-restraints excluded: chain A residue 1073 VAL Chi-restraints excluded: chain A residue 1081 ILE Chi-restraints excluded: chain B residue 159 ILE Chi-restraints excluded: chain B residue 179 VAL Chi-restraints excluded: chain B residue 221 ILE Chi-restraints excluded: chain B residue 299 ILE Chi-restraints excluded: chain B residue 320 PHE Chi-restraints excluded: chain B residue 322 ILE Chi-restraints excluded: chain B residue 332 GLU Chi-restraints excluded: chain B residue 363 THR Chi-restraints excluded: chain B residue 380 LEU Chi-restraints excluded: chain B residue 413 VAL Chi-restraints excluded: chain B residue 462 THR Chi-restraints excluded: chain B residue 495 VAL Chi-restraints excluded: chain B residue 543 ARG Chi-restraints excluded: chain B residue 591 PHE Chi-restraints excluded: chain B residue 630 MET Chi-restraints excluded: chain B residue 632 VAL Chi-restraints excluded: chain B residue 772 GLU Chi-restraints excluded: chain B residue 792 VAL Chi-restraints excluded: chain B residue 879 PHE Chi-restraints excluded: chain B residue 1080 VAL Chi-restraints excluded: chain B residue 1081 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 172 random chunks: chunk 121 optimal weight: 1.9990 chunk 31 optimal weight: 0.9980 chunk 69 optimal weight: 0.5980 chunk 85 optimal weight: 1.9990 chunk 86 optimal weight: 7.9990 chunk 118 optimal weight: 1.9990 chunk 33 optimal weight: 1.9990 chunk 48 optimal weight: 2.9990 chunk 74 optimal weight: 0.7980 chunk 127 optimal weight: 0.9990 chunk 10 optimal weight: 1.9990 overall best weight: 1.0784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 547 HIS B 547 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3996 r_free = 0.3996 target = 0.169448 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3525 r_free = 0.3525 target = 0.126079 restraints weight = 16149.735| |-----------------------------------------------------------------------------| r_work (start): 0.3464 rms_B_bonded: 2.39 r_work: 0.3307 rms_B_bonded: 2.97 restraints_weight: 0.5000 r_work: 0.3157 rms_B_bonded: 4.75 restraints_weight: 0.2500 r_work (final): 0.3157 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3166 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3166 r_free = 0.3166 target_work(ls_wunit_k1) = 0.098 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3166 r_free = 0.3166 target_work(ls_wunit_k1) = 0.098 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3166 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8568 moved from start: 0.1952 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 13865 Z= 0.128 Angle : 0.564 9.590 18920 Z= 0.269 Chirality : 0.041 0.270 2231 Planarity : 0.003 0.039 2320 Dihedral : 5.927 86.168 1892 Min Nonbonded Distance : 2.115 Molprobity Statistics. All-atom Clashscore : 3.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.75 % Favored : 97.25 % Rotamer: Outliers : 3.12 % Allowed : 22.54 % Favored : 74.34 % 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: 1.22 (0.21), residues: 1707 helix: 2.31 (0.17), residues: 959 sheet: -0.40 (0.42), residues: 140 loop : -1.43 (0.23), residues: 608 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 317 TYR 0.008 0.001 TYR A1056 PHE 0.022 0.001 PHE A1059 TRP 0.024 0.001 TRP A 850 HIS 0.003 0.001 HIS A 394 Details of bonding type rmsd/Z covalent geometry : bond 0.00302 / 0.13 (13849) covalent geometry : angle 0.55323 / 0.27 (18878) SS BOND : bond 0.00392 / 0.24 ( 6) SS BOND : angle 1.51599 / 0.73 ( 12) hydrogen bonds : bond 0.04492 / 3.05 ( 766) hydrogen bonds : angle 3.57441 / 2.56 ( 2201) link_BETA1-4 : bond 0.00455 / 0.28 ( 6) link_BETA1-4 : angle 2.35463 / 1.48 ( 18) link_NAG-ASN : bond 0.00131 / 0.08 ( 4) link_NAG-ASN : angle 3.05261 / 1.88 ( 12) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3414 Ramachandran restraints generated. 1707 Oldfield, 0 Emsley, 1707 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3414 Ramachandran restraints generated. 1707 Oldfield, 0 Emsley, 1707 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 217 residues out of total 1447 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 173 time to evaluate : 0.370 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 443 ASP cc_start: 0.7988 (m-30) cc_final: 0.6713 (t0) REVERT: A 543 ARG cc_start: 0.7809 (OUTLIER) cc_final: 0.7324 (ttp80) REVERT: A 591 PHE cc_start: 0.8490 (OUTLIER) cc_final: 0.7902 (m-10) REVERT: A 737 GLU cc_start: 0.7520 (pm20) cc_final: 0.6982 (pm20) REVERT: A 859 MET cc_start: 0.7966 (mpp) cc_final: 0.7712 (mmt) REVERT: A 879 PHE cc_start: 0.6670 (OUTLIER) cc_final: 0.6048 (m-80) REVERT: A 1061 GLU cc_start: 0.8066 (tp30) cc_final: 0.7756 (tp30) REVERT: B 332 GLU cc_start: 0.8368 (OUTLIER) cc_final: 0.8006 (pp20) REVERT: B 380 LEU cc_start: 0.9170 (OUTLIER) cc_final: 0.8894 (tt) REVERT: B 443 ASP cc_start: 0.7938 (m-30) cc_final: 0.6697 (t0) REVERT: B 543 ARG cc_start: 0.7844 (OUTLIER) cc_final: 0.7255 (ttp80) REVERT: B 591 PHE cc_start: 0.8500 (OUTLIER) cc_final: 0.7922 (m-10) REVERT: B 859 MET cc_start: 0.7993 (mpp) cc_final: 0.7747 (mmt) REVERT: B 1061 GLU cc_start: 0.8095 (tp30) cc_final: 0.7833 (tp30) outliers start: 44 outliers final: 33 residues processed: 203 average time/residue: 0.0919 time to fit residues: 28.0951 Evaluate side-chains 207 residues out of total 1447 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 167 time to evaluate : 0.464 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 159 ILE Chi-restraints excluded: chain A residue 221 ILE Chi-restraints excluded: chain A residue 299 ILE Chi-restraints excluded: chain A residue 320 PHE Chi-restraints excluded: chain A residue 363 THR Chi-restraints excluded: chain A residue 413 VAL Chi-restraints excluded: chain A residue 495 VAL Chi-restraints excluded: chain A residue 543 ARG Chi-restraints excluded: chain A residue 569 ILE Chi-restraints excluded: chain A residue 591 PHE Chi-restraints excluded: chain A residue 739 TYR Chi-restraints excluded: chain A residue 772 GLU Chi-restraints excluded: chain A residue 792 VAL Chi-restraints excluded: chain A residue 879 PHE Chi-restraints excluded: chain A residue 1062 VAL Chi-restraints excluded: chain A residue 1073 VAL Chi-restraints excluded: chain A residue 1080 VAL Chi-restraints excluded: chain A residue 1081 ILE Chi-restraints excluded: chain B residue 159 ILE Chi-restraints excluded: chain B residue 179 VAL Chi-restraints excluded: chain B residue 221 ILE Chi-restraints excluded: chain B residue 299 ILE Chi-restraints excluded: chain B residue 320 PHE Chi-restraints excluded: chain B residue 322 ILE Chi-restraints excluded: chain B residue 332 GLU Chi-restraints excluded: chain B residue 363 THR Chi-restraints excluded: chain B residue 380 LEU Chi-restraints excluded: chain B residue 413 VAL Chi-restraints excluded: chain B residue 462 THR Chi-restraints excluded: chain B residue 495 VAL Chi-restraints excluded: chain B residue 543 ARG Chi-restraints excluded: chain B residue 591 PHE Chi-restraints excluded: chain B residue 630 MET Chi-restraints excluded: chain B residue 632 VAL Chi-restraints excluded: chain B residue 739 TYR Chi-restraints excluded: chain B residue 772 GLU Chi-restraints excluded: chain B residue 792 VAL Chi-restraints excluded: chain B residue 879 PHE Chi-restraints excluded: chain B residue 1080 VAL Chi-restraints excluded: chain B residue 1081 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 172 random chunks: chunk 16 optimal weight: 0.6980 chunk 123 optimal weight: 2.9990 chunk 39 optimal weight: 0.9980 chunk 70 optimal weight: 0.9990 chunk 161 optimal weight: 10.0000 chunk 101 optimal weight: 6.9990 chunk 145 optimal weight: 0.9980 chunk 93 optimal weight: 0.8980 chunk 120 optimal weight: 0.9980 chunk 86 optimal weight: 7.9990 chunk 150 optimal weight: 3.9990 overall best weight: 0.9180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 547 HIS B 547 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4013 r_free = 0.4013 target = 0.170567 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3538 r_free = 0.3538 target = 0.126386 restraints weight = 20102.476| |-----------------------------------------------------------------------------| r_work (start): 0.3453 rms_B_bonded: 2.64 r_work: 0.3296 rms_B_bonded: 3.15 restraints_weight: 0.5000 r_work (final): 0.3296 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3309 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3309 r_free = 0.3309 target_work(ls_wunit_k1) = 0.108 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3309 r_free = 0.3309 target_work(ls_wunit_k1) = 0.108 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3309 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8463 moved from start: 0.2068 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 13865 Z= 0.119 Angle : 0.559 9.606 18920 Z= 0.267 Chirality : 0.041 0.272 2231 Planarity : 0.003 0.040 2320 Dihedral : 5.871 85.311 1892 Min Nonbonded Distance : 2.112 Molprobity Statistics. All-atom Clashscore : 3.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.28 % Favored : 96.72 % Rotamer: Outliers : 3.19 % Allowed : 22.47 % Favored : 74.34 % 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: 1.36 (0.21), residues: 1707 helix: 2.36 (0.17), residues: 971 sheet: -0.22 (0.43), residues: 140 loop : -1.36 (0.23), residues: 596 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 317 TYR 0.008 0.001 TYR A1056 PHE 0.024 0.001 PHE B1059 TRP 0.020 0.001 TRP A 850 HIS 0.003 0.001 HIS A 394 Details of bonding type rmsd/Z covalent geometry : bond 0.00279 / 0.12 (13849) covalent geometry : angle 0.54876 / 0.26 (18878) SS BOND : bond 0.00362 / 0.23 ( 6) SS BOND : angle 1.43284 / 0.69 ( 12) hydrogen bonds : bond 0.04267 / 2.90 ( 766) hydrogen bonds : angle 3.51848 / 2.52 ( 2201) link_BETA1-4 : bond 0.00437 / 0.27 ( 6) link_BETA1-4 : angle 2.30712 / 1.45 ( 18) link_NAG-ASN : bond 0.00146 / 0.08 ( 4) link_NAG-ASN : angle 3.03691 / 1.86 ( 12) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3414 Ramachandran restraints generated. 1707 Oldfield, 0 Emsley, 1707 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3414 Ramachandran restraints generated. 1707 Oldfield, 0 Emsley, 1707 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 213 residues out of total 1447 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 168 time to evaluate : 0.344 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 152 GLN cc_start: 0.7999 (OUTLIER) cc_final: 0.7744 (mt0) REVERT: A 443 ASP cc_start: 0.7879 (m-30) cc_final: 0.6741 (t0) REVERT: A 543 ARG cc_start: 0.7658 (OUTLIER) cc_final: 0.7174 (ttp80) REVERT: A 591 PHE cc_start: 0.8341 (OUTLIER) cc_final: 0.7989 (m-80) REVERT: A 737 GLU cc_start: 0.7529 (pm20) cc_final: 0.7006 (pm20) REVERT: A 859 MET cc_start: 0.7837 (mpp) cc_final: 0.7579 (mmt) REVERT: A 879 PHE cc_start: 0.6466 (OUTLIER) cc_final: 0.5780 (m-80) REVERT: A 1061 GLU cc_start: 0.7996 (tp30) cc_final: 0.7735 (tp30) REVERT: B 332 GLU cc_start: 0.8323 (OUTLIER) cc_final: 0.8015 (pp20) REVERT: B 380 LEU cc_start: 0.9155 (OUTLIER) cc_final: 0.8874 (tt) REVERT: B 443 ASP cc_start: 0.7871 (m-30) cc_final: 0.6728 (t0) REVERT: B 543 ARG cc_start: 0.7701 (OUTLIER) cc_final: 0.7194 (ttp80) REVERT: B 859 MET cc_start: 0.7914 (mpp) cc_final: 0.7649 (mmt) REVERT: B 879 PHE cc_start: 0.6338 (OUTLIER) cc_final: 0.5722 (m-80) REVERT: B 1061 GLU cc_start: 0.8031 (tp30) cc_final: 0.7818 (tp30) outliers start: 45 outliers final: 35 residues processed: 198 average time/residue: 0.1024 time to fit residues: 30.1382 Evaluate side-chains 209 residues out of total 1447 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 166 time to evaluate : 0.392 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 152 GLN Chi-restraints excluded: chain A residue 159 ILE Chi-restraints excluded: chain A residue 221 ILE Chi-restraints excluded: chain A residue 299 ILE Chi-restraints excluded: chain A residue 320 PHE Chi-restraints excluded: chain A residue 363 THR Chi-restraints excluded: chain A residue 413 VAL Chi-restraints excluded: chain A residue 495 VAL Chi-restraints excluded: chain A residue 543 ARG Chi-restraints excluded: chain A residue 569 ILE Chi-restraints excluded: chain A residue 591 PHE Chi-restraints excluded: chain A residue 630 MET Chi-restraints excluded: chain A residue 739 TYR Chi-restraints excluded: chain A residue 772 GLU Chi-restraints excluded: chain A residue 792 VAL Chi-restraints excluded: chain A residue 879 PHE Chi-restraints excluded: chain A residue 1062 VAL Chi-restraints excluded: chain A residue 1073 VAL Chi-restraints excluded: chain A residue 1080 VAL Chi-restraints excluded: chain A residue 1081 ILE Chi-restraints excluded: chain B residue 159 ILE Chi-restraints excluded: chain B residue 179 VAL Chi-restraints excluded: chain B residue 221 ILE Chi-restraints excluded: chain B residue 299 ILE Chi-restraints excluded: chain B residue 320 PHE Chi-restraints excluded: chain B residue 332 GLU Chi-restraints excluded: chain B residue 363 THR Chi-restraints excluded: chain B residue 380 LEU Chi-restraints excluded: chain B residue 413 VAL Chi-restraints excluded: chain B residue 462 THR Chi-restraints excluded: chain B residue 495 VAL Chi-restraints excluded: chain B residue 543 ARG Chi-restraints excluded: chain B residue 569 ILE Chi-restraints excluded: chain B residue 591 PHE Chi-restraints excluded: chain B residue 630 MET Chi-restraints excluded: chain B residue 632 VAL Chi-restraints excluded: chain B residue 739 TYR Chi-restraints excluded: chain B residue 772 GLU Chi-restraints excluded: chain B residue 792 VAL Chi-restraints excluded: chain B residue 860 LEU Chi-restraints excluded: chain B residue 879 PHE Chi-restraints excluded: chain B residue 1080 VAL Chi-restraints excluded: chain B residue 1081 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 172 random chunks: chunk 13 optimal weight: 4.9990 chunk 145 optimal weight: 0.5980 chunk 67 optimal weight: 0.0010 chunk 47 optimal weight: 3.9990 chunk 32 optimal weight: 8.9990 chunk 96 optimal weight: 1.9990 chunk 126 optimal weight: 0.7980 chunk 27 optimal weight: 0.0170 chunk 146 optimal weight: 4.9990 chunk 90 optimal weight: 0.9990 chunk 114 optimal weight: 0.9980 overall best weight: 0.4824 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 547 HIS B 547 HIS B 868 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4045 r_free = 0.4045 target = 0.173526 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3598 r_free = 0.3598 target = 0.131187 restraints weight = 16108.175| |-----------------------------------------------------------------------------| r_work (start): 0.3512 rms_B_bonded: 2.33 r_work: 0.3366 rms_B_bonded: 2.87 restraints_weight: 0.5000 r_work: 0.3215 rms_B_bonded: 4.65 restraints_weight: 0.2500 r_work (final): 0.3215 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3231 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3231 r_free = 0.3231 target_work(ls_wunit_k1) = 0.102 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3231 r_free = 0.3231 target_work(ls_wunit_k1) = 0.102 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (7 function evaluations) r_final: 0.3231 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8506 moved from start: 0.2298 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 13865 Z= 0.099 Angle : 0.534 9.536 18920 Z= 0.254 Chirality : 0.040 0.272 2231 Planarity : 0.003 0.040 2320 Dihedral : 5.690 84.028 1892 Min Nonbonded Distance : 2.126 Molprobity Statistics. All-atom Clashscore : 3.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.64 % Favored : 97.36 % Rotamer: Outliers : 2.48 % Allowed : 23.39 % Favored : 74.13 % 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: 1.63 (0.21), residues: 1707 helix: 2.53 (0.17), residues: 971 sheet: 0.07 (0.44), residues: 140 loop : -1.21 (0.23), residues: 596 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 317 TYR 0.009 0.001 TYR A1056 PHE 0.023 0.001 PHE B1059 TRP 0.018 0.001 TRP A 850 HIS 0.004 0.001 HIS A 394 Details of bonding type rmsd/Z covalent geometry : bond 0.00217 / 0.10 (13849) covalent geometry : angle 0.52356 / 0.25 (18878) SS BOND : bond 0.00298 / 0.19 ( 6) SS BOND : angle 1.26326 / 0.61 ( 12) hydrogen bonds : bond 0.03639 / 2.47 ( 766) hydrogen bonds : angle 3.39722 / 2.43 ( 2201) link_BETA1-4 : bond 0.00469 / 0.29 ( 6) link_BETA1-4 : angle 2.20198 / 1.39 ( 18) link_NAG-ASN : bond 0.00190 / 0.11 ( 4) link_NAG-ASN : angle 3.06059 / 1.87 ( 12) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3414 Ramachandran restraints generated. 1707 Oldfield, 0 Emsley, 1707 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3414 Ramachandran restraints generated. 1707 Oldfield, 0 Emsley, 1707 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 203 residues out of total 1447 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 168 time to evaluate : 0.533 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 152 GLN cc_start: 0.7942 (OUTLIER) cc_final: 0.7641 (mt0) REVERT: A 320 PHE cc_start: 0.8292 (OUTLIER) cc_final: 0.7703 (p90) REVERT: A 443 ASP cc_start: 0.7927 (m-30) cc_final: 0.6673 (t0) REVERT: A 543 ARG cc_start: 0.7734 (OUTLIER) cc_final: 0.7279 (ttp80) REVERT: A 587 MET cc_start: 0.8305 (tpt) cc_final: 0.7834 (tpt) REVERT: A 591 PHE cc_start: 0.8453 (OUTLIER) cc_final: 0.7986 (m-80) REVERT: A 737 GLU cc_start: 0.7647 (pm20) cc_final: 0.7115 (pm20) REVERT: A 879 PHE cc_start: 0.6681 (OUTLIER) cc_final: 0.5966 (m-80) REVERT: A 1061 GLU cc_start: 0.8050 (tp30) cc_final: 0.7767 (tp30) REVERT: B 320 PHE cc_start: 0.8326 (OUTLIER) cc_final: 0.7850 (p90) REVERT: B 380 LEU cc_start: 0.9154 (OUTLIER) cc_final: 0.8860 (tt) REVERT: B 443 ASP cc_start: 0.7917 (m-30) cc_final: 0.6711 (t0) REVERT: B 543 ARG cc_start: 0.7720 (OUTLIER) cc_final: 0.7155 (ttp80) REVERT: B 591 PHE cc_start: 0.8400 (OUTLIER) cc_final: 0.8022 (m-10) REVERT: B 859 MET cc_start: 0.7986 (mpp) cc_final: 0.7731 (mmt) REVERT: B 879 PHE cc_start: 0.6555 (OUTLIER) cc_final: 0.5885 (m-80) REVERT: B 1025 LEU cc_start: 0.7793 (OUTLIER) cc_final: 0.7487 (tt) REVERT: B 1061 GLU cc_start: 0.8119 (tp30) cc_final: 0.7883 (tp30) outliers start: 35 outliers final: 23 residues processed: 194 average time/residue: 0.1030 time to fit residues: 30.1476 Evaluate side-chains 198 residues out of total 1447 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 164 time to evaluate : 0.510 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 152 GLN Chi-restraints excluded: chain A residue 299 ILE Chi-restraints excluded: chain A residue 320 PHE Chi-restraints excluded: chain A residue 363 THR Chi-restraints excluded: chain A residue 495 VAL Chi-restraints excluded: chain A residue 543 ARG Chi-restraints excluded: chain A residue 569 ILE Chi-restraints excluded: chain A residue 591 PHE Chi-restraints excluded: chain A residue 739 TYR Chi-restraints excluded: chain A residue 772 GLU Chi-restraints excluded: chain A residue 792 VAL Chi-restraints excluded: chain A residue 879 PHE Chi-restraints excluded: chain A residue 1073 VAL Chi-restraints excluded: chain A residue 1080 VAL Chi-restraints excluded: chain B residue 179 VAL Chi-restraints excluded: chain B residue 221 ILE Chi-restraints excluded: chain B residue 299 ILE Chi-restraints excluded: chain B residue 320 PHE Chi-restraints excluded: chain B residue 363 THR Chi-restraints excluded: chain B residue 380 LEU Chi-restraints excluded: chain B residue 462 THR Chi-restraints excluded: chain B residue 495 VAL Chi-restraints excluded: chain B residue 543 ARG Chi-restraints excluded: chain B residue 591 PHE Chi-restraints excluded: chain B residue 630 MET Chi-restraints excluded: chain B residue 739 TYR Chi-restraints excluded: chain B residue 772 GLU Chi-restraints excluded: chain B residue 792 VAL Chi-restraints excluded: chain B residue 860 LEU Chi-restraints excluded: chain B residue 879 PHE Chi-restraints excluded: chain B residue 1025 LEU Chi-restraints excluded: chain B residue 1073 VAL Chi-restraints excluded: chain B residue 1080 VAL Chi-restraints excluded: chain B residue 1081 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 172 random chunks: chunk 87 optimal weight: 0.9990 chunk 103 optimal weight: 3.9990 chunk 156 optimal weight: 0.9990 chunk 148 optimal weight: 0.9990 chunk 52 optimal weight: 2.9990 chunk 64 optimal weight: 7.9990 chunk 59 optimal weight: 0.6980 chunk 60 optimal weight: 2.9990 chunk 62 optimal weight: 2.9990 chunk 39 optimal weight: 0.0470 chunk 35 optimal weight: 1.9990 overall best weight: 0.7484 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4028 r_free = 0.4028 target = 0.172565 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3536 r_free = 0.3536 target = 0.126604 restraints weight = 23884.148| |-----------------------------------------------------------------------------| r_work (start): 0.3468 rms_B_bonded: 2.97 r_work: 0.3303 rms_B_bonded: 3.48 restraints_weight: 0.5000 r_work (final): 0.3303 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3305 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3305 r_free = 0.3305 target_work(ls_wunit_k1) = 0.108 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3305 r_free = 0.3305 target_work(ls_wunit_k1) = 0.108 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3305 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8470 moved from start: 0.2316 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 13865 Z= 0.110 Angle : 0.547 9.636 18920 Z= 0.260 Chirality : 0.040 0.274 2231 Planarity : 0.003 0.040 2320 Dihedral : 5.648 83.585 1892 Min Nonbonded Distance : 2.113 Molprobity Statistics. All-atom Clashscore : 3.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.93 % Favored : 97.07 % Rotamer: Outliers : 2.55 % Allowed : 23.67 % Favored : 73.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.67 (0.21), residues: 1707 helix: 2.55 (0.17), residues: 971 sheet: 0.09 (0.44), residues: 140 loop : -1.17 (0.23), residues: 596 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B1078 TYR 0.007 0.001 TYR B 636 PHE 0.024 0.001 PHE A1059 TRP 0.009 0.001 TRP B 850 HIS 0.003 0.001 HIS A 394 Details of bonding type rmsd/Z covalent geometry : bond 0.00254 / 0.11 (13849) covalent geometry : angle 0.53708 / 0.26 (18878) SS BOND : bond 0.00304 / 0.19 ( 6) SS BOND : angle 1.29664 / 0.62 ( 12) hydrogen bonds : bond 0.03885 / 2.64 ( 766) hydrogen bonds : angle 3.40093 / 2.43 ( 2201) link_BETA1-4 : bond 0.00470 / 0.29 ( 6) link_BETA1-4 : angle 2.21668 / 1.40 ( 18) link_NAG-ASN : bond 0.00153 / 0.09 ( 4) link_NAG-ASN : angle 2.95641 / 1.81 ( 12) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3414 Ramachandran restraints generated. 1707 Oldfield, 0 Emsley, 1707 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3414 Ramachandran restraints generated. 1707 Oldfield, 0 Emsley, 1707 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 198 residues out of total 1447 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 162 time to evaluate : 0.503 Fit side-chains revert: symmetry clash REVERT: A 152 GLN cc_start: 0.7980 (OUTLIER) cc_final: 0.7670 (mt0) REVERT: A 320 PHE cc_start: 0.8363 (OUTLIER) cc_final: 0.7830 (p90) REVERT: A 443 ASP cc_start: 0.7851 (m-30) cc_final: 0.6720 (t0) REVERT: A 543 ARG cc_start: 0.7684 (OUTLIER) cc_final: 0.7222 (ttp80) REVERT: A 587 MET cc_start: 0.8144 (tpt) cc_final: 0.7678 (tpt) REVERT: A 591 PHE cc_start: 0.8386 (OUTLIER) cc_final: 0.7928 (m-80) REVERT: A 737 GLU cc_start: 0.7633 (pm20) cc_final: 0.7104 (pm20) REVERT: A 809 LYS cc_start: 0.7941 (tptp) cc_final: 0.7540 (tptt) REVERT: A 879 PHE cc_start: 0.6576 (OUTLIER) cc_final: 0.5795 (m-80) REVERT: A 1061 GLU cc_start: 0.8007 (tp30) cc_final: 0.7746 (tp30) REVERT: B 320 PHE cc_start: 0.8360 (OUTLIER) cc_final: 0.7922 (p90) REVERT: B 380 LEU cc_start: 0.9166 (OUTLIER) cc_final: 0.8867 (tt) REVERT: B 443 ASP cc_start: 0.7910 (m-30) cc_final: 0.6765 (t0) REVERT: B 543 ARG cc_start: 0.7710 (OUTLIER) cc_final: 0.7223 (ttp80) REVERT: B 591 PHE cc_start: 0.8337 (OUTLIER) cc_final: 0.7971 (m-10) REVERT: B 859 MET cc_start: 0.7997 (mpp) cc_final: 0.7741 (mpp) REVERT: B 879 PHE cc_start: 0.6554 (OUTLIER) cc_final: 0.5864 (m-80) REVERT: B 1025 LEU cc_start: 0.7782 (OUTLIER) cc_final: 0.7489 (tt) REVERT: B 1061 GLU cc_start: 0.8071 (tp30) cc_final: 0.7853 (tp30) outliers start: 36 outliers final: 24 residues processed: 190 average time/residue: 0.1120 time to fit residues: 31.6900 Evaluate side-chains 195 residues out of total 1447 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 160 time to evaluate : 0.488 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 152 GLN Chi-restraints excluded: chain A residue 299 ILE Chi-restraints excluded: chain A residue 320 PHE Chi-restraints excluded: chain A residue 363 THR Chi-restraints excluded: chain A residue 495 VAL Chi-restraints excluded: chain A residue 543 ARG Chi-restraints excluded: chain A residue 569 ILE Chi-restraints excluded: chain A residue 591 PHE Chi-restraints excluded: chain A residue 739 TYR Chi-restraints excluded: chain A residue 772 GLU Chi-restraints excluded: chain A residue 792 VAL Chi-restraints excluded: chain A residue 879 PHE Chi-restraints excluded: chain A residue 1062 VAL Chi-restraints excluded: chain A residue 1073 VAL Chi-restraints excluded: chain A residue 1080 VAL Chi-restraints excluded: chain A residue 1081 ILE Chi-restraints excluded: chain B residue 179 VAL Chi-restraints excluded: chain B residue 221 ILE Chi-restraints excluded: chain B residue 299 ILE Chi-restraints excluded: chain B residue 320 PHE Chi-restraints excluded: chain B residue 363 THR Chi-restraints excluded: chain B residue 380 LEU Chi-restraints excluded: chain B residue 462 THR Chi-restraints excluded: chain B residue 495 VAL Chi-restraints excluded: chain B residue 543 ARG Chi-restraints excluded: chain B residue 569 ILE Chi-restraints excluded: chain B residue 591 PHE Chi-restraints excluded: chain B residue 739 TYR Chi-restraints excluded: chain B residue 772 GLU Chi-restraints excluded: chain B residue 792 VAL Chi-restraints excluded: chain B residue 879 PHE Chi-restraints excluded: chain B residue 1025 LEU Chi-restraints excluded: chain B residue 1073 VAL Chi-restraints excluded: chain B residue 1080 VAL Chi-restraints excluded: chain B residue 1081 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 172 random chunks: chunk 93 optimal weight: 0.7980 chunk 107 optimal weight: 7.9990 chunk 15 optimal weight: 7.9990 chunk 49 optimal weight: 4.9990 chunk 119 optimal weight: 0.9980 chunk 135 optimal weight: 5.9990 chunk 111 optimal weight: 4.9990 chunk 168 optimal weight: 9.9990 chunk 4 optimal weight: 1.9990 chunk 70 optimal weight: 0.9980 chunk 143 optimal weight: 1.9990 overall best weight: 1.3584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3966 r_free = 0.3966 target = 0.165560 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3486 r_free = 0.3486 target = 0.121766 restraints weight = 20086.141| |-----------------------------------------------------------------------------| r_work (start): 0.3451 rms_B_bonded: 2.54 r_work: 0.3293 rms_B_bonded: 3.11 restraints_weight: 0.5000 r_work: 0.3141 rms_B_bonded: 4.99 restraints_weight: 0.2500 r_work (final): 0.3141 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3157 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3157 r_free = 0.3157 target_work(ls_wunit_k1) = 0.097 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3157 r_free = 0.3157 target_work(ls_wunit_k1) = 0.097 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3157 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8636 moved from start: 0.2193 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 13865 Z= 0.145 Angle : 0.578 9.704 18920 Z= 0.277 Chirality : 0.042 0.273 2231 Planarity : 0.003 0.041 2320 Dihedral : 5.694 83.196 1892 Min Nonbonded Distance : 2.109 Molprobity Statistics. All-atom Clashscore : 3.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.17 % Favored : 96.83 % Rotamer: Outliers : 2.55 % Allowed : 23.81 % Favored : 73.64 % 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: 1.54 (0.21), residues: 1707 helix: 2.44 (0.17), residues: 971 sheet: -0.04 (0.43), residues: 140 loop : -1.20 (0.23), residues: 596 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A1078 TYR 0.009 0.001 TYR A 654 PHE 0.025 0.001 PHE A1059 TRP 0.013 0.001 TRP A 850 HIS 0.003 0.001 HIS A 394 Details of bonding type rmsd/Z covalent geometry : bond 0.00353 / 0.14 (13849) covalent geometry : angle 0.56847 / 0.27 (18878) SS BOND : bond 0.00386 / 0.24 ( 6) SS BOND : angle 1.55347 / 0.74 ( 12) hydrogen bonds : bond 0.04622 / 3.13 ( 766) hydrogen bonds : angle 3.51634 / 2.51 ( 2201) link_BETA1-4 : bond 0.00444 / 0.27 ( 6) link_BETA1-4 : angle 2.28551 / 1.43 ( 18) link_NAG-ASN : bond 0.00068 / 0.04 ( 4) link_NAG-ASN : angle 2.85195 / 1.74 ( 12) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3663.61 seconds wall clock time: 63 minutes 18.00 seconds (3798.00 seconds total)