Starting phenix.real_space_refine on Mon Aug 25 11:19:25 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9b39_44132/08_2025/9b39_44132.cif Found real_map, /net/cci-nas-00/data/ceres_data/9b39_44132/08_2025/9b39_44132.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.84 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9b39_44132/08_2025/9b39_44132.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9b39_44132/08_2025/9b39_44132.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9b39_44132/08_2025/9b39_44132.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9b39_44132/08_2025/9b39_44132.map" } resolution = 3.84 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= 0.002 sd= 0.019 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 160 5.16 5 C 17571 2.51 5 N 4512 2.21 5 O 5279 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 64 residue(s): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 27522 Number of models: 1 Model: "" Number of chains: 22 Chain: "A" Number of atoms: 6684 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 842, 6677 Classifications: {'peptide': 842} Link IDs: {'PCIS': 1, 'PTRANS': 32, 'TRANS': 808} Conformer: "B" Number of residues, atoms: 842, 6677 Classifications: {'peptide': 842} Link IDs: {'PCIS': 1, 'PTRANS': 32, 'TRANS': 808} bond proxies already assigned to first conformer: 6818 Chain: "B" Number of atoms: 6680 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 842, 6677 Classifications: {'peptide': 842} Link IDs: {'PCIS': 1, 'PTRANS': 32, 'TRANS': 808} Conformer: "B" Number of residues, atoms: 842, 6677 Classifications: {'peptide': 842} Link IDs: {'PCIS': 1, 'PTRANS': 32, 'TRANS': 808} bond proxies already assigned to first conformer: 6823 Chain: "C" Number of atoms: 6680 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 842, 6677 Classifications: {'peptide': 842} Link IDs: {'PTRANS': 33, 'TRANS': 808} Conformer: "B" Number of residues, atoms: 842, 6677 Classifications: {'peptide': 842} Link IDs: {'PTRANS': 33, 'TRANS': 808} bond proxies already assigned to first conformer: 6823 Chain: "D" Number of atoms: 6680 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 842, 6677 Classifications: {'peptide': 842} Link IDs: {'PCIS': 1, 'PTRANS': 32, 'TRANS': 808} Conformer: "B" Number of residues, atoms: 842, 6677 Classifications: {'peptide': 842} Link IDs: {'PCIS': 1, 'PTRANS': 32, 'TRANS': 808} bond proxies already assigned to first conformer: 6823 Chain: "E" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "F" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "G" 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 dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "H" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "I" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "J" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "K" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "L" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "M" 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 dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "N" 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 dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "A" Number of atoms: 10 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 10 Classifications: {'peptide': 1} Modifications used: {'COO': 1} Chain: "A" Number of atoms: 56 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 56 Unusual residues: {'NAG': 4} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "B" Number of atoms: 10 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 10 Classifications: {'peptide': 1} Modifications used: {'COO': 1} Chain: "B" Number of atoms: 70 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 70 Unusual residues: {'NAG': 5} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "C" Number of atoms: 10 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 10 Classifications: {'peptide': 1} Modifications used: {'COO': 1} Chain: "C" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 84 Unusual residues: {'NAG': 6} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 6 Chain: "D" Number of atoms: 10 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 10 Classifications: {'peptide': 1} Modifications used: {'COO': 1} Chain: "D" Number of atoms: 70 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 70 Unusual residues: {'NAG': 5} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Time building chain proxies: 11.74, per 1000 atoms: 0.43 Number of scatterers: 27522 At special positions: 0 Unit cell: (157.798, 126.778, 205.002, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 160 16.00 O 5279 8.00 N 4512 7.00 C 17571 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=8, symmetry=0 Simple disulfide: pdb=" SG CYS A 96 " - pdb=" SG CYS A 347 " distance=2.03 Simple disulfide: pdb=" SG CYS A 750 " - pdb=" SG CYS A 804 " distance=2.03 Simple disulfide: pdb=" SG CYS B 96 " - pdb=" SG CYS B 347 " distance=2.03 Simple disulfide: pdb=" SG CYS B 750 " - pdb=" SG CYS B 804 " distance=2.03 Simple disulfide: pdb=" SG CYS C 96 " - pdb=" SG CYS C 347 " distance=2.03 Simple disulfide: pdb=" SG CYS C 750 " - pdb=" SG CYS C 804 " distance=2.03 Simple disulfide: pdb=" SG CYS D 96 " - pdb=" SG CYS D 347 " distance=2.03 Simple disulfide: pdb=" SG CYS D 750 " - pdb=" SG CYS D 804 " 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 ALPHA1-3 " BMA E 3 " - " MAN E 4 " " BMA F 3 " - " MAN F 4 " " BMA J 3 " - " MAN J 4 " " BMA K 3 " - " MAN K 4 " " BMA L 3 " - " MAN L 4 " ALPHA1-6 " BMA E 3 " - " MAN E 5 " " BMA F 3 " - " MAN F 5 " " BMA J 3 " - " MAN J 5 " " BMA K 3 " - " MAN K 5 " " BMA L 3 " - " MAN L 5 " BETA1-4 " NAG E 1 " - " NAG E 2 " " NAG E 2 " - " BMA E 3 " " NAG F 1 " - " NAG F 2 " " NAG F 2 " - " BMA F 3 " " NAG G 1 " - " NAG G 2 " " NAG G 2 " - " BMA G 3 " " NAG H 1 " - " NAG H 2 " " NAG I 1 " - " NAG I 2 " " NAG J 1 " - " NAG J 2 " " NAG J 2 " - " BMA J 3 " " NAG K 1 " - " NAG K 2 " " NAG K 2 " - " BMA K 3 " " NAG L 1 " - " NAG L 2 " " NAG L 2 " - " BMA L 3 " " NAG M 1 " - " NAG M 2 " " NAG M 2 " - " BMA M 3 " " NAG N 1 " - " NAG N 2 " " NAG N 2 " - " BMA N 3 " NAG-ASN " NAG A1002 " - " ASN A 67 " " NAG A1003 " - " ASN A 73 " " NAG A1004 " - " ASN A 423 " " NAG A1005 " - " ASN A 751 " " NAG B1002 " - " ASN B 67 " " NAG B1003 " - " ASN B 73 " " NAG B1004 " - " ASN B 378 " " NAG B1005 " - " ASN B 412 " " NAG B1006 " - " ASN B 546 " " NAG C1002 " - " ASN C 67 " " NAG C1003 " - " ASN C 73 " " NAG C1004 " - " ASN C 412 " " NAG C1005 " - " ASN C 423 " " NAG C1006 " - " ASN C 546 " " NAG C1007 " - " ASN C 751 " " NAG D1002 " - " ASN D 67 " " NAG D1003 " - " ASN D 73 " " NAG D1004 " - " ASN D 430 " " NAG D1005 " - " ASN D 546 " " NAG D1006 " - " ASN D 751 " " NAG E 1 " - " ASN A 275 " " NAG F 1 " - " ASN A 378 " " NAG G 1 " - " ASN A 412 " " NAG H 1 " - " ASN A 430 " " NAG I 1 " - " ASN B 275 " " NAG J 1 " - " ASN C 275 " " NAG K 1 " - " ASN C 378 " " NAG L 1 " - " ASN C 430 " " NAG M 1 " - " ASN D 378 " " NAG N 1 " - " ASN D 412 " Time building additional restraints: 2.33 Conformation dependent library (CDL) restraints added in 2.2 seconds Enol-peptide restraints added in 953.7 nanoseconds 6730 Ramachandran restraints generated. 3365 Oldfield, 0 Emsley, 3365 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6306 Finding SS restraints... Secondary structure from input PDB file: 116 helices and 32 sheets defined 45.7% alpha, 4.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.83 Creating SS restraints... Processing helix chain 'A' and resid 51 through 66 removed outlier: 3.514A pdb=" N LEU A 55 " --> pdb=" O GLY A 51 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N VAL A 61 " --> pdb=" O PHE A 57 " (cutoff:3.500A) Processing helix chain 'A' and resid 87 through 100 removed outlier: 3.554A pdb=" N GLN A 98 " --> pdb=" O LYS A 94 " (cutoff:3.500A) Processing helix chain 'A' and resid 112 through 126 removed outlier: 3.583A pdb=" N VAL A 118 " --> pdb=" O SER A 114 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N ALA A 124 " --> pdb=" O SER A 120 " (cutoff:3.500A) Processing helix chain 'A' and resid 152 through 168 removed outlier: 3.527A pdb=" N SER A 157 " --> pdb=" O PHE A 153 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N ARG A 158 " --> pdb=" O SER A 154 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N LEU A 161 " --> pdb=" O SER A 157 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N PHE A 167 " --> pdb=" O LEU A 163 " (cutoff:3.500A) Processing helix chain 'A' and resid 179 through 184 removed outlier: 3.995A pdb=" N ILE A 183 " --> pdb=" O SER A 179 " (cutoff:3.500A) Processing helix chain 'A' and resid 185 through 190 Processing helix chain 'A' and resid 190 through 195 removed outlier: 4.122A pdb=" N ARG A 194 " --> pdb=" O LYS A 190 " (cutoff:3.500A) Processing helix chain 'A' and resid 211 through 221 removed outlier: 3.735A pdb=" N ARG A 220 " --> pdb=" O LYS A 216 " (cutoff:3.500A) Processing helix chain 'A' and resid 231 through 245 removed outlier: 4.016A pdb=" N GLY A 237 " --> pdb=" O GLU A 233 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N ILE A 238 " --> pdb=" O MET A 234 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N LEU A 239 " --> pdb=" O ALA A 235 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N ALA A 244 " --> pdb=" O LYS A 240 " (cutoff:3.500A) Processing helix chain 'A' and resid 286 through 301 Processing helix chain 'A' and resid 317 through 337 removed outlier: 3.579A pdb=" N MET A 323 " --> pdb=" O ASP A 319 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N VAL A 327 " --> pdb=" O MET A 323 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N HIS A 328 " --> pdb=" O TYR A 324 " (cutoff:3.500A) Processing helix chain 'A' and resid 355 through 364 removed outlier: 3.685A pdb=" N LEU A 362 " --> pdb=" O ARG A 358 " (cutoff:3.500A) Processing helix chain 'A' and resid 461 through 475 Processing helix chain 'A' and resid 500 through 507 removed outlier: 4.001A pdb=" N GLU A 504 " --> pdb=" O GLY A 500 " (cutoff:3.500A) Processing helix chain 'A' and resid 520 through 527 removed outlier: 3.670A pdb=" N LYS A 525 " --> pdb=" O TYR A 521 " (cutoff:3.500A) removed outlier: 4.094A pdb=" N VAL A 526 " --> pdb=" O VAL A 522 " (cutoff:3.500A) Processing helix chain 'A' and resid 560 through 584 removed outlier: 3.550A pdb=" N LEU A 572 " --> pdb=" O LEU A 568 " (cutoff:3.500A) removed outlier: 3.932A pdb=" N VAL A 580 " --> pdb=" O CYS A 576 " (cutoff:3.500A) Processing helix chain 'A' and resid 607 through 620 removed outlier: 4.032A pdb=" N PHE A 612 " --> pdb=" O LEU A 608 " (cutoff:3.500A) removed outlier: 4.005A pdb=" N TRP A 613 " --> pdb=" O LEU A 609 " (cutoff:3.500A) Processing helix chain 'A' and resid 630 through 664 removed outlier: 3.686A pdb=" N VAL A 636 " --> pdb=" O SER A 632 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N ILE A 639 " --> pdb=" O ILE A 635 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N ILE A 646 " --> pdb=" O PHE A 642 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N ILE A 647 " --> pdb=" O PHE A 643 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N SER A 649 " --> pdb=" O LEU A 645 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N LEU A 659 " --> pdb=" O LEU A 655 " (cutoff:3.500A) removed outlier: 4.458A pdb=" N GLU A 662 " --> pdb=" O PHE A 658 " (cutoff:3.500A) Processing helix chain 'A' and resid 670 through 677 removed outlier: 3.525A pdb=" N LYS A 676 " --> pdb=" O ASP A 672 " (cutoff:3.500A) Processing helix chain 'A' and resid 688 through 696 removed outlier: 3.634A pdb=" N THR A 692 " --> pdb=" O GLY A 688 " (cutoff:3.500A) Processing helix chain 'A' and resid 699 through 712 Processing helix chain 'A' and resid 713 through 718 removed outlier: 3.584A pdb=" N VAL A 718 " --> pdb=" O GLN A 714 " (cutoff:3.500A) Processing helix chain 'A' and resid 721 through 731 removed outlier: 3.658A pdb=" N GLN A 726 " --> pdb=" O GLU A 722 " (cutoff:3.500A) removed outlier: 3.957A pdb=" N ARG A 727 " --> pdb=" O GLU A 723 " (cutoff:3.500A) Processing helix chain 'A' and resid 739 through 748 removed outlier: 3.718A pdb=" N ARG A 748 " --> pdb=" O PHE A 744 " (cutoff:3.500A) Processing helix chain 'A' and resid 774 through 788 Processing helix chain 'A' and resid 789 through 798 removed outlier: 4.280A pdb=" N GLU A 796 " --> pdb=" O HIS A 792 " (cutoff:3.500A) removed outlier: 3.855A pdb=" N LYS A 797 " --> pdb=" O MET A 793 " (cutoff:3.500A) Processing helix chain 'A' and resid 822 through 851 removed outlier: 3.664A pdb=" N GLY A 830 " --> pdb=" O VAL A 826 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N PHE A 836 " --> pdb=" O VAL A 832 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N GLY A 840 " --> pdb=" O PHE A 836 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N LYS A 845 " --> pdb=" O GLU A 841 " (cutoff:3.500A) Processing helix chain 'A' and resid 859 through 864 removed outlier: 3.781A pdb=" N GLU A 863 " --> pdb=" O SER A 859 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N GLU A 864 " --> pdb=" O ALA A 860 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 859 through 864' Processing helix chain 'B' and resid 51 through 67 removed outlier: 3.605A pdb=" N ALA B 56 " --> pdb=" O ALA B 52 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N ILE B 64 " --> pdb=" O ALA B 60 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N ASN B 65 " --> pdb=" O VAL B 61 " (cutoff:3.500A) Processing helix chain 'B' and resid 87 through 102 removed outlier: 3.500A pdb=" N CYS B 96 " --> pdb=" O SER B 92 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N GLN B 98 " --> pdb=" O LYS B 94 " (cutoff:3.500A) Processing helix chain 'B' and resid 111 through 126 removed outlier: 3.536A pdb=" N ASN B 116 " --> pdb=" O SER B 112 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N ALA B 117 " --> pdb=" O SER B 113 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N VAL B 118 " --> pdb=" O SER B 114 " (cutoff:3.500A) Processing helix chain 'B' and resid 152 through 167 removed outlier: 4.179A pdb=" N ARG B 158 " --> pdb=" O SER B 154 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N VAL B 164 " --> pdb=" O ILE B 160 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N GLN B 165 " --> pdb=" O LEU B 161 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N PHE B 166 " --> pdb=" O ASP B 162 " (cutoff:3.500A) Processing helix chain 'B' and resid 180 through 185 removed outlier: 3.537A pdb=" N ARG B 184 " --> pdb=" O THR B 180 " (cutoff:3.500A) Processing helix chain 'B' and resid 185 through 190 Processing helix chain 'B' and resid 211 through 221 removed outlier: 3.663A pdb=" N GLU B 217 " --> pdb=" O PRO B 213 " (cutoff:3.500A) Processing helix chain 'B' and resid 231 through 245 removed outlier: 3.835A pdb=" N LEU B 239 " --> pdb=" O ALA B 235 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N GLN B 241 " --> pdb=" O GLY B 237 " (cutoff:3.500A) removed outlier: 3.932A pdb=" N ALA B 244 " --> pdb=" O LYS B 240 " (cutoff:3.500A) Processing helix chain 'B' and resid 266 through 270 Processing helix chain 'B' and resid 286 through 300 removed outlier: 3.615A pdb=" N ILE B 292 " --> pdb=" O GLN B 288 " (cutoff:3.500A) Processing helix chain 'B' and resid 306 through 310 removed outlier: 3.687A pdb=" N SER B 309 " --> pdb=" O LYS B 306 " (cutoff:3.500A) removed outlier: 3.966A pdb=" N GLY B 310 " --> pdb=" O PRO B 307 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 306 through 310' Processing helix chain 'B' and resid 317 through 337 removed outlier: 3.564A pdb=" N VAL B 327 " --> pdb=" O MET B 323 " (cutoff:3.500A) removed outlier: 3.929A pdb=" N HIS B 328 " --> pdb=" O TYR B 324 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N VAL B 329 " --> pdb=" O ASP B 325 " (cutoff:3.500A) Processing helix chain 'B' and resid 355 through 365 removed outlier: 4.343A pdb=" N SER B 361 " --> pdb=" O THR B 357 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N GLU B 365 " --> pdb=" O SER B 361 " (cutoff:3.500A) Processing helix chain 'B' and resid 455 through 459 removed outlier: 3.858A pdb=" N ARG B 458 " --> pdb=" O GLY B 455 " (cutoff:3.500A) removed outlier: 3.971A pdb=" N PHE B 459 " --> pdb=" O ASN B 456 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 455 through 459' Processing helix chain 'B' and resid 461 through 475 removed outlier: 3.591A pdb=" N ILE B 473 " --> pdb=" O GLU B 469 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N LEU B 474 " --> pdb=" O LEU B 470 " (cutoff:3.500A) Processing helix chain 'B' and resid 499 through 507 Processing helix chain 'B' and resid 520 through 527 removed outlier: 3.511A pdb=" N VAL B 526 " --> pdb=" O VAL B 522 " (cutoff:3.500A) Processing helix chain 'B' and resid 560 through 583 Processing helix chain 'B' and resid 607 through 620 removed outlier: 3.950A pdb=" N VAL B 616 " --> pdb=" O PHE B 612 " (cutoff:3.500A) Processing helix chain 'B' and resid 630 through 661 removed outlier: 3.526A pdb=" N TRP B 640 " --> pdb=" O VAL B 636 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N SER B 649 " --> pdb=" O LEU B 645 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N ALA B 657 " --> pdb=" O ALA B 653 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N LEU B 659 " --> pdb=" O LEU B 655 " (cutoff:3.500A) Processing helix chain 'B' and resid 670 through 675 removed outlier: 3.689A pdb=" N LEU B 674 " --> pdb=" O SER B 670 " (cutoff:3.500A) Processing helix chain 'B' and resid 688 through 696 Processing helix chain 'B' and resid 699 through 710 removed outlier: 3.933A pdb=" N TRP B 706 " --> pdb=" O TYR B 702 " (cutoff:3.500A) removed outlier: 3.886A pdb=" N ALA B 707 " --> pdb=" O ASP B 703 " (cutoff:3.500A) removed outlier: 4.100A pdb=" N PHE B 708 " --> pdb=" O LYS B 704 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N SER B 710 " --> pdb=" O TRP B 706 " (cutoff:3.500A) Processing helix chain 'B' and resid 720 through 731 removed outlier: 3.534A pdb=" N ARG B 727 " --> pdb=" O GLU B 723 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N VAL B 728 " --> pdb=" O GLY B 724 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N LEU B 729 " --> pdb=" O ILE B 725 " (cutoff:3.500A) Processing helix chain 'B' and resid 738 through 749 removed outlier: 3.632A pdb=" N PHE B 744 " --> pdb=" O THR B 740 " (cutoff:3.500A) Processing helix chain 'B' and resid 774 through 789 removed outlier: 3.551A pdb=" N ILE B 778 " --> pdb=" O TYR B 774 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N ALA B 781 " --> pdb=" O LYS B 777 " (cutoff:3.500A) removed outlier: 4.180A pdb=" N GLU B 788 " --> pdb=" O GLN B 784 " (cutoff:3.500A) Processing helix chain 'B' and resid 789 through 799 removed outlier: 4.036A pdb=" N LYS B 797 " --> pdb=" O MET B 793 " (cutoff:3.500A) Processing helix chain 'B' and resid 821 through 853 removed outlier: 3.680A pdb=" N ILE B 825 " --> pdb=" O GLY B 821 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N LEU B 831 " --> pdb=" O LEU B 827 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N VAL B 835 " --> pdb=" O LEU B 831 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N PHE B 836 " --> pdb=" O VAL B 832 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N TYR B 844 " --> pdb=" O GLY B 840 " (cutoff:3.500A) removed outlier: 3.958A pdb=" N LEU B 852 " --> pdb=" O LYS B 848 " (cutoff:3.500A) Processing helix chain 'B' and resid 860 through 868 removed outlier: 3.952A pdb=" N GLU B 864 " --> pdb=" O ALA B 860 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N LEU B 865 " --> pdb=" O MET B 861 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N ARG B 866 " --> pdb=" O VAL B 862 " (cutoff:3.500A) Processing helix chain 'C' and resid 51 through 65 removed outlier: 3.720A pdb=" N ASN C 65 " --> pdb=" O VAL C 61 " (cutoff:3.500A) Processing helix chain 'C' and resid 87 through 102 Processing helix chain 'C' and resid 113 through 126 removed outlier: 3.841A pdb=" N ALA C 117 " --> pdb=" O SER C 113 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N SER C 120 " --> pdb=" O ASN C 116 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N ALA C 124 " --> pdb=" O SER C 120 " (cutoff:3.500A) Processing helix chain 'C' and resid 152 through 167 removed outlier: 3.609A pdb=" N SER C 157 " --> pdb=" O PHE C 153 " (cutoff:3.500A) Processing helix chain 'C' and resid 178 through 183 removed outlier: 3.739A pdb=" N LEU C 182 " --> pdb=" O SER C 179 " (cutoff:3.500A) Processing helix chain 'C' and resid 185 through 190 Processing helix chain 'C' and resid 211 through 221 removed outlier: 3.560A pdb=" N ARG C 220 " --> pdb=" O LYS C 216 " (cutoff:3.500A) Processing helix chain 'C' and resid 231 through 245 removed outlier: 3.719A pdb=" N GLY C 237 " --> pdb=" O GLU C 233 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N LEU C 243 " --> pdb=" O LEU C 239 " (cutoff:3.500A) removed outlier: 3.925A pdb=" N ALA C 244 " --> pdb=" O LYS C 240 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N MET C 245 " --> pdb=" O GLN C 241 " (cutoff:3.500A) Processing helix chain 'C' and resid 286 through 300 Processing helix chain 'C' and resid 317 through 337 removed outlier: 4.033A pdb=" N MET C 323 " --> pdb=" O ASP C 319 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N HIS C 328 " --> pdb=" O TYR C 324 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N GLN C 335 " --> pdb=" O SER C 331 " (cutoff:3.500A) removed outlier: 3.847A pdb=" N GLN C 336 " --> pdb=" O VAL C 332 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N PHE C 337 " --> pdb=" O ALA C 333 " (cutoff:3.500A) Processing helix chain 'C' and resid 355 through 365 removed outlier: 4.412A pdb=" N SER C 361 " --> pdb=" O THR C 357 " (cutoff:3.500A) Processing helix chain 'C' and resid 461 through 475 Processing helix chain 'C' and resid 500 through 507 Processing helix chain 'C' and resid 520 through 525 Processing helix chain 'C' and resid 560 through 582 removed outlier: 3.505A pdb=" N VAL C 574 " --> pdb=" O ALA C 570 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N VAL C 577 " --> pdb=" O GLY C 573 " (cutoff:3.500A) removed outlier: 4.240A pdb=" N PHE C 579 " --> pdb=" O SER C 575 " (cutoff:3.500A) Processing helix chain 'C' and resid 609 through 620 removed outlier: 3.603A pdb=" N TRP C 613 " --> pdb=" O LEU C 609 " (cutoff:3.500A) Processing helix chain 'C' and resid 630 through 665 removed outlier: 3.817A pdb=" N VAL C 636 " --> pdb=" O SER C 632 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N GLY C 638 " --> pdb=" O ARG C 634 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N ILE C 646 " --> pdb=" O PHE C 642 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N SER C 649 " --> pdb=" O LEU C 645 " (cutoff:3.500A) removed outlier: 3.834A pdb=" N ARG C 663 " --> pdb=" O LEU C 659 " (cutoff:3.500A) Processing helix chain 'C' and resid 670 through 675 Processing helix chain 'C' and resid 688 through 694 Processing helix chain 'C' and resid 699 through 712 Processing helix chain 'C' and resid 720 through 729 removed outlier: 3.508A pdb=" N GLY C 724 " --> pdb=" O SER C 720 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N VAL C 728 " --> pdb=" O GLY C 724 " (cutoff:3.500A) Processing helix chain 'C' and resid 738 through 749 removed outlier: 3.639A pdb=" N PHE C 744 " --> pdb=" O THR C 740 " (cutoff:3.500A) removed outlier: 4.505A pdb=" N GLN C 747 " --> pdb=" O GLU C 743 " (cutoff:3.500A) Processing helix chain 'C' and resid 773 through 788 removed outlier: 3.953A pdb=" N LYS C 777 " --> pdb=" O PRO C 773 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N ILE C 778 " --> pdb=" O TYR C 774 " (cutoff:3.500A) removed outlier: 4.650A pdb=" N THR C 779 " --> pdb=" O ARG C 775 " (cutoff:3.500A) Processing helix chain 'C' and resid 789 through 798 removed outlier: 3.746A pdb=" N MET C 793 " --> pdb=" O GLY C 789 " (cutoff:3.500A) Processing helix chain 'C' and resid 816 through 821 Processing helix chain 'C' and resid 822 through 853 removed outlier: 4.134A pdb=" N VAL C 835 " --> pdb=" O LEU C 831 " (cutoff:3.500A) removed outlier: 3.997A pdb=" N PHE C 836 " --> pdb=" O VAL C 832 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N VAL C 837 " --> pdb=" O LEU C 833 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N GLU C 853 " --> pdb=" O ASN C 849 " (cutoff:3.500A) Processing helix chain 'C' and resid 857 through 870 removed outlier: 4.006A pdb=" N VAL C 862 " --> pdb=" O CYS C 858 " (cutoff:3.500A) removed outlier: 3.951A pdb=" N GLU C 863 " --> pdb=" O SER C 859 " (cutoff:3.500A) removed outlier: 4.197A pdb=" N GLU C 864 " --> pdb=" O ALA C 860 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N ARG C 866 " --> pdb=" O VAL C 862 " (cutoff:3.500A) Processing helix chain 'D' and resid 51 through 67 Processing helix chain 'D' and resid 87 through 102 Processing helix chain 'D' and resid 111 through 126 removed outlier: 3.852A pdb=" N ASN D 116 " --> pdb=" O SER D 112 " (cutoff:3.500A) removed outlier: 4.180A pdb=" N SER D 120 " --> pdb=" O ASN D 116 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N ILE D 121 " --> pdb=" O ALA D 117 " (cutoff:3.500A) Processing helix chain 'D' and resid 154 through 168 removed outlier: 3.561A pdb=" N GLN D 165 " --> pdb=" O LEU D 161 " (cutoff:3.500A) Processing helix chain 'D' and resid 178 through 184 removed outlier: 3.616A pdb=" N LEU D 182 " --> pdb=" O SER D 179 " (cutoff:3.500A) Processing helix chain 'D' and resid 185 through 190 Processing helix chain 'D' and resid 191 through 194 Processing helix chain 'D' and resid 211 through 221 removed outlier: 3.622A pdb=" N LYS D 216 " --> pdb=" O LYS D 212 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N GLU D 217 " --> pdb=" O PRO D 213 " (cutoff:3.500A) Processing helix chain 'D' and resid 231 through 244 removed outlier: 3.501A pdb=" N ALA D 236 " --> pdb=" O HIS D 232 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N GLN D 241 " --> pdb=" O GLY D 237 " (cutoff:3.500A) Processing helix chain 'D' and resid 286 through 301 removed outlier: 3.618A pdb=" N ILE D 292 " --> pdb=" O GLN D 288 " (cutoff:3.500A) removed outlier: 4.142A pdb=" N GLU D 294 " --> pdb=" O SER D 290 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N GLU D 299 " --> pdb=" O LYS D 295 " (cutoff:3.500A) removed outlier: 3.929A pdb=" N LEU D 301 " --> pdb=" O SER D 297 " (cutoff:3.500A) Processing helix chain 'D' and resid 317 through 337 removed outlier: 3.812A pdb=" N MET D 323 " --> pdb=" O ASP D 319 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N VAL D 327 " --> pdb=" O MET D 323 " (cutoff:3.500A) removed outlier: 3.976A pdb=" N HIS D 328 " --> pdb=" O TYR D 324 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N ALA D 333 " --> pdb=" O VAL D 329 " (cutoff:3.500A) Processing helix chain 'D' and resid 355 through 364 removed outlier: 3.714A pdb=" N LEU D 362 " --> pdb=" O ARG D 358 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N LYS D 364 " --> pdb=" O MET D 360 " (cutoff:3.500A) Processing helix chain 'D' and resid 413 through 418 removed outlier: 3.868A pdb=" N GLN D 417 " --> pdb=" O MET D 413 " (cutoff:3.500A) Processing helix chain 'D' and resid 461 through 471 Processing helix chain 'D' and resid 491 through 495 removed outlier: 3.679A pdb=" N ASN D 495 " --> pdb=" O ASP D 492 " (cutoff:3.500A) Processing helix chain 'D' and resid 500 through 507 removed outlier: 3.705A pdb=" N GLU D 504 " --> pdb=" O GLY D 500 " (cutoff:3.500A) Processing helix chain 'D' and resid 520 through 527 removed outlier: 4.135A pdb=" N VAL D 526 " --> pdb=" O VAL D 522 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N ILE D 527 " --> pdb=" O ARG D 523 " (cutoff:3.500A) Processing helix chain 'D' and resid 560 through 585 removed outlier: 3.585A pdb=" N MET D 565 " --> pdb=" O PRO D 561 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N LEU D 568 " --> pdb=" O TRP D 564 " (cutoff:3.500A) removed outlier: 4.090A pdb=" N CYS D 576 " --> pdb=" O LEU D 572 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N VAL D 577 " --> pdb=" O GLY D 573 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N PHE D 579 " --> pdb=" O SER D 575 " (cutoff:3.500A) Processing helix chain 'D' and resid 607 through 620 removed outlier: 3.536A pdb=" N PHE D 612 " --> pdb=" O LEU D 608 " (cutoff:3.500A) removed outlier: 3.877A pdb=" N TRP D 613 " --> pdb=" O LEU D 609 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N GLY D 615 " --> pdb=" O SER D 611 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N GLY D 617 " --> pdb=" O TRP D 613 " (cutoff:3.500A) Processing helix chain 'D' and resid 630 through 665 removed outlier: 3.502A pdb=" N ARG D 634 " --> pdb=" O ALA D 630 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N VAL D 636 " --> pdb=" O SER D 632 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N GLY D 637 " --> pdb=" O THR D 633 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N ILE D 646 " --> pdb=" O PHE D 642 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N ILE D 648 " --> pdb=" O THR D 644 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N ARG D 663 " --> pdb=" O LEU D 659 " (cutoff:3.500A) Processing helix chain 'D' and resid 672 through 676 removed outlier: 3.519A pdb=" N LYS D 676 " --> pdb=" O ASP D 673 " (cutoff:3.500A) Processing helix chain 'D' and resid 688 through 696 Processing helix chain 'D' and resid 699 through 713 removed outlier: 3.564A pdb=" N LYS D 704 " --> pdb=" O SER D 700 " (cutoff:3.500A) removed outlier: 3.970A pdb=" N PHE D 708 " --> pdb=" O LYS D 704 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N MET D 709 " --> pdb=" O MET D 705 " (cutoff:3.500A) removed outlier: 4.010A pdb=" N SER D 710 " --> pdb=" O TRP D 706 " (cutoff:3.500A) removed outlier: 4.155A pdb=" N SER D 711 " --> pdb=" O ALA D 707 " (cutoff:3.500A) removed outlier: 4.151A pdb=" N ARG D 713 " --> pdb=" O MET D 709 " (cutoff:3.500A) Processing helix chain 'D' and resid 721 through 730 removed outlier: 3.747A pdb=" N LEU D 729 " --> pdb=" O ILE D 725 " (cutoff:3.500A) Processing helix chain 'D' and resid 738 through 749 removed outlier: 3.559A pdb=" N PHE D 744 " --> pdb=" O THR D 740 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N VAL D 745 " --> pdb=" O THR D 741 " (cutoff:3.500A) Processing helix chain 'D' and resid 774 through 789 removed outlier: 3.560A pdb=" N ALA D 781 " --> pdb=" O LYS D 777 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N GLU D 787 " --> pdb=" O LEU D 783 " (cutoff:3.500A) Processing helix chain 'D' and resid 789 through 799 removed outlier: 3.561A pdb=" N MET D 793 " --> pdb=" O GLY D 789 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N TRP D 798 " --> pdb=" O MET D 794 " (cutoff:3.500A) Processing helix chain 'D' and resid 816 through 821 removed outlier: 3.841A pdb=" N ILE D 820 " --> pdb=" O GLY D 816 " (cutoff:3.500A) Processing helix chain 'D' and resid 821 through 839 removed outlier: 3.631A pdb=" N VAL D 839 " --> pdb=" O VAL D 835 " (cutoff:3.500A) Processing helix chain 'D' and resid 839 through 853 Processing helix chain 'D' and resid 857 through 868 removed outlier: 4.121A pdb=" N VAL D 862 " --> pdb=" O CYS D 858 " (cutoff:3.500A) removed outlier: 4.183A pdb=" N GLU D 863 " --> pdb=" O SER D 859 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N LEU D 865 " --> pdb=" O MET D 861 " (cutoff:3.500A) Processing helix chain 'D' and resid 869 through 874 Processing sheet with id=AA1, first strand: chain 'A' and resid 129 through 131 Processing sheet with id=AA2, first strand: chain 'A' and resid 202 through 203 removed outlier: 3.783A pdb=" N TYR A 176 " --> pdb=" O ARG A 202 " (cutoff:3.500A) removed outlier: 6.637A pdb=" N VAL A 175 " --> pdb=" O ASP A 229 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA2 Processing sheet with id=AA3, first strand: chain 'A' and resid 253 through 255 removed outlier: 6.731A pdb=" N TYR A 254 " --> pdb=" O THR A 277 " (cutoff:3.500A) removed outlier: 8.713A pdb=" N PHE A 279 " --> pdb=" O TYR A 254 " (cutoff:3.500A) removed outlier: 6.463A pdb=" N VAL A 391 " --> pdb=" O ILE A 402 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N GLY A 410 " --> pdb=" O ASP A 406 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 435 through 437 removed outlier: 5.769A pdb=" N VAL A 435 " --> pdb=" O ARG A 481 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'A' and resid 528 through 529 Processing sheet with id=AA6, first strand: chain 'A' and resid 534 through 535 removed outlier: 3.560A pdb=" N MET A 534 " --> pdb=" O TYR A 764 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 538 through 539 Processing sheet with id=AA8, first strand: chain 'A' and resid 541 through 543 removed outlier: 3.601A pdb=" N TYR A 542 " --> pdb=" O THR A 753 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 78 through 83 removed outlier: 7.296A pdb=" N PHE B 38 " --> pdb=" O ASP B 79 " (cutoff:3.500A) removed outlier: 8.476A pdb=" N GLN B 81 " --> pdb=" O PHE B 38 " (cutoff:3.500A) removed outlier: 6.384A pdb=" N GLY B 40 " --> pdb=" O GLN B 81 " (cutoff:3.500A) removed outlier: 7.517A pdb=" N ILE B 83 " --> pdb=" O GLY B 40 " (cutoff:3.500A) removed outlier: 6.314A pdb=" N PHE B 42 " --> pdb=" O ILE B 83 " (cutoff:3.500A) removed outlier: 4.033A pdb=" N GLY B 39 " --> pdb=" O ALA B 105 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA9 Processing sheet with id=AB1, first strand: chain 'B' and resid 130 through 131 Processing sheet with id=AB2, first strand: chain 'B' and resid 202 through 203 removed outlier: 3.532A pdb=" N TYR B 176 " --> pdb=" O ARG B 202 " (cutoff:3.500A) removed outlier: 6.595A pdb=" N VAL B 175 " --> pdb=" O ASP B 229 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB2 Processing sheet with id=AB3, first strand: chain 'B' and resid 369 through 370 Processing sheet with id=AB4, first strand: chain 'B' and resid 389 through 395 removed outlier: 4.005A pdb=" N GLY B 403 " --> pdb=" O VAL B 391 " (cutoff:3.500A) removed outlier: 6.294A pdb=" N SER B 393 " --> pdb=" O LYS B 401 " (cutoff:3.500A) removed outlier: 5.739A pdb=" N LYS B 401 " --> pdb=" O SER B 393 " (cutoff:3.500A) removed outlier: 6.442A pdb=" N LYS B 395 " --> pdb=" O LEU B 399 " (cutoff:3.500A) removed outlier: 4.886A pdb=" N LEU B 399 " --> pdb=" O LYS B 395 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'B' and resid 434 through 437 Processing sheet with id=AB6, first strand: chain 'B' and resid 535 through 536 removed outlier: 3.505A pdb=" N LYS B 762 " --> pdb=" O LEU B 536 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'B' and resid 682 through 683 removed outlier: 3.835A pdb=" N PHE B 735 " --> pdb=" O LEU B 541 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N ILE B 540 " --> pdb=" O ILE B 755 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'C' and resid 41 through 43 Processing sheet with id=AB9, first strand: chain 'C' and resid 129 through 131 removed outlier: 7.035A pdb=" N HIS C 129 " --> pdb=" O VAL C 147 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB9 Processing sheet with id=AC1, first strand: chain 'C' and resid 202 through 203 removed outlier: 6.466A pdb=" N VAL C 174 " --> pdb=" O ARG C 202 " (cutoff:3.500A) removed outlier: 7.164A pdb=" N THR C 173 " --> pdb=" O ILE C 227 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC1 Processing sheet with id=AC2, first strand: chain 'C' and resid 277 through 280 removed outlier: 6.815A pdb=" N VAL C 391 " --> pdb=" O ILE C 402 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'C' and resid 432 through 435 Processing sheet with id=AC4, first strand: chain 'C' and resid 513 through 517 removed outlier: 7.902A pdb=" N ALA C 515 " --> pdb=" O GLY C 767 " (cutoff:3.500A) removed outlier: 5.909A pdb=" N GLY C 767 " --> pdb=" O ALA C 515 " (cutoff:3.500A) removed outlier: 4.118A pdb=" N LEU C 517 " --> pdb=" O GLY C 765 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'C' and resid 536 through 537 Processing sheet with id=AC6, first strand: chain 'D' and resid 34 through 35 removed outlier: 5.756A pdb=" N HIS D 34 " --> pdb=" O THR D 75 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC6 Processing sheet with id=AC7, first strand: chain 'D' and resid 38 through 39 removed outlier: 6.709A pdb=" N PHE D 38 " --> pdb=" O ASP D 79 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC7 Processing sheet with id=AC8, first strand: chain 'D' and resid 129 through 131 removed outlier: 4.033A pdb=" N GLY D 382 " --> pdb=" O TYR D 146 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'D' and resid 175 through 176 removed outlier: 3.658A pdb=" N TYR D 176 " --> pdb=" O ARG D 202 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC9 Processing sheet with id=AD1, first strand: chain 'D' and resid 225 through 226 Processing sheet with id=AD2, first strand: chain 'D' and resid 392 through 395 removed outlier: 3.720A pdb=" N GLU D 400 " --> pdb=" O SER D 393 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'D' and resid 445 through 446 Processing sheet with id=AD4, first strand: chain 'D' and resid 517 through 518 removed outlier: 4.566A pdb=" N LEU D 517 " --> pdb=" O GLY D 765 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N TYR D 764 " --> pdb=" O MET D 534 " (cutoff:3.500A) removed outlier: 4.225A pdb=" N MET D 534 " --> pdb=" O TYR D 764 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'D' and resid 540 through 542 removed outlier: 4.100A pdb=" N ILE D 540 " --> pdb=" O ILE D 755 " (cutoff:3.500A) 945 hydrogen bonds defined for protein. 2756 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: 5.27 Time building geometry restraints manager: 2.97 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.34: 8225 1.34 - 1.46: 6884 1.46 - 1.58: 12738 1.58 - 1.71: 4 1.71 - 1.83: 272 Bond restraints: 28123 Sorted by residual: bond pdb=" C ALA D 191 " pdb=" N PRO D 192 " ideal model delta sigma weight residual 1.336 1.405 -0.069 1.08e-02 8.57e+03 4.10e+01 bond pdb=" C ALA B 191 " pdb=" N PRO B 192 " ideal model delta sigma weight residual 1.336 1.401 -0.065 1.08e-02 8.57e+03 3.65e+01 bond pdb=" C1 NAG C1002 " pdb=" O5 NAG C1002 " ideal model delta sigma weight residual 1.406 1.511 -0.105 2.00e-02 2.50e+03 2.78e+01 bond pdb=" CA HIS A 136 " pdb=" CB HIS A 136 " ideal model delta sigma weight residual 1.527 1.461 0.067 1.30e-02 5.92e+03 2.62e+01 bond pdb=" C1 NAG G 2 " pdb=" O5 NAG G 2 " ideal model delta sigma weight residual 1.406 1.508 -0.102 2.00e-02 2.50e+03 2.60e+01 ... (remaining 28118 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.66: 37342 4.66 - 9.31: 674 9.31 - 13.97: 47 13.97 - 18.62: 5 18.62 - 23.28: 3 Bond angle restraints: 38071 Sorted by residual: angle pdb=" C GLU C 441 " pdb=" N PRO C 442 " pdb=" CA PRO C 442 " ideal model delta sigma weight residual 119.84 131.79 -11.95 1.25e+00 6.40e-01 9.14e+01 angle pdb=" C VAL C 274 " pdb=" N ASN C 275 " pdb=" CA ASN C 275 " ideal model delta sigma weight residual 122.41 111.14 11.27 1.41e+00 5.03e-01 6.38e+01 angle pdb=" C ARG A 374 " pdb=" N ILE A 375 " pdb=" CA ILE A 375 " ideal model delta sigma weight residual 121.97 136.29 -14.32 1.80e+00 3.09e-01 6.33e+01 angle pdb=" N VAL C 274 " pdb=" CA VAL C 274 " pdb=" C VAL C 274 " ideal model delta sigma weight residual 108.06 98.95 9.11 1.28e+00 6.10e-01 5.06e+01 angle pdb=" N ILE D 281 " pdb=" CA ILE D 281 " pdb=" C ILE D 281 " ideal model delta sigma weight residual 113.10 106.20 6.90 9.70e-01 1.06e+00 5.05e+01 ... (remaining 38066 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 25.61: 16704 25.61 - 51.23: 611 51.23 - 76.84: 108 76.84 - 102.46: 90 102.46 - 128.07: 82 Dihedral angle restraints: 17595 sinusoidal: 7795 harmonic: 9800 Sorted by residual: dihedral pdb=" CA GLU C 441 " pdb=" C GLU C 441 " pdb=" N PRO C 442 " pdb=" CA PRO C 442 " ideal model delta harmonic sigma weight residual -180.00 -111.51 -68.49 0 5.00e+00 4.00e-02 1.88e+02 dihedral pdb=" CA CYS D 804 " pdb=" C CYS D 804 " pdb=" N PRO D 805 " pdb=" CA PRO D 805 " ideal model delta harmonic sigma weight residual 180.00 119.70 60.30 0 5.00e+00 4.00e-02 1.45e+02 dihedral pdb=" CA PRO B 72 " pdb=" C PRO B 72 " pdb=" N ASN B 73 " pdb=" CA ASN B 73 " ideal model delta harmonic sigma weight residual -180.00 -123.31 -56.69 0 5.00e+00 4.00e-02 1.29e+02 ... (remaining 17592 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.197: 4338 0.197 - 0.394: 64 0.394 - 0.591: 8 0.591 - 0.788: 1 0.788 - 0.985: 1 Chirality restraints: 4412 Sorted by residual: chirality pdb=" C1 NAG H 1 " pdb=" ND2 ASN A 430 " pdb=" C2 NAG H 1 " pdb=" O5 NAG H 1 " both_signs ideal model delta sigma weight residual False -2.40 -1.42 -0.98 2.00e-01 2.50e+01 2.42e+01 chirality pdb=" C1 NAG D1004 " pdb=" ND2 ASN D 430 " pdb=" C2 NAG D1004 " pdb=" O5 NAG D1004 " both_signs ideal model delta sigma weight residual False -2.40 -1.79 -0.61 2.00e-01 2.50e+01 9.23e+00 chirality pdb=" C1 NAG B1006 " pdb=" ND2 ASN B 546 " pdb=" C2 NAG B1006 " pdb=" O5 NAG B1006 " both_signs ideal model delta sigma weight residual False -2.40 -1.82 -0.58 2.00e-01 2.50e+01 8.54e+00 ... (remaining 4409 not shown) Planarity restraints: 4783 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 NAG A1002 " -0.292 2.00e-02 2.50e+03 2.47e-01 7.66e+02 pdb=" C7 NAG A1002 " 0.076 2.00e-02 2.50e+03 pdb=" C8 NAG A1002 " -0.180 2.00e-02 2.50e+03 pdb=" N2 NAG A1002 " 0.426 2.00e-02 2.50e+03 pdb=" O7 NAG A1002 " -0.030 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG B1004 " 0.123 2.00e-02 2.50e+03 1.00e-01 1.26e+02 pdb=" C7 NAG B1004 " -0.039 2.00e-02 2.50e+03 pdb=" C8 NAG B1004 " 0.094 2.00e-02 2.50e+03 pdb=" N2 NAG B1004 " -0.157 2.00e-02 2.50e+03 pdb=" O7 NAG B1004 " -0.020 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C CYS D 804 " 0.078 5.00e-02 4.00e+02 1.18e-01 2.24e+01 pdb=" N PRO D 805 " -0.205 5.00e-02 4.00e+02 pdb=" CA PRO D 805 " 0.064 5.00e-02 4.00e+02 pdb=" CD PRO D 805 " 0.063 5.00e-02 4.00e+02 ... (remaining 4780 not shown) Histogram of nonbonded interaction distances: 2.18 - 2.73: 2456 2.73 - 3.27: 27886 3.27 - 3.81: 46112 3.81 - 4.36: 55049 4.36 - 4.90: 88381 Nonbonded interactions: 219884 Sorted by model distance: nonbonded pdb=" O ASP D 528 " pdb=" OG1 THR D 768 " model vdw 2.184 3.040 nonbonded pdb=" OE2 GLU A 250 " pdb=" OH TYR A 774 " model vdw 2.236 3.040 nonbonded pdb=" OE1 GLU D 738 " pdb=" OH TYR D 764 " model vdw 2.237 3.040 nonbonded pdb=" O LYS D 629 " pdb=" OG1 THR D 633 " model vdw 2.262 3.040 nonbonded pdb=" O PHE D 693 " pdb=" OG SER D 697 " model vdw 2.262 3.040 ... (remaining 219879 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 33 through 470 or resid 472 through 534 or resid 536 throu \ gh 1005)) selection = (chain 'B' and (resid 33 through 470 or resid 472 through 534 or resid 536 throu \ gh 1005)) selection = (chain 'C' and (resid 33 through 470 or resid 472 through 534 or resid 536 throu \ gh 1005)) selection = (chain 'D' and (resid 33 through 470 or resid 472 through 534 or resid 536 throu \ gh 1005)) } ncs_group { reference = chain 'E' selection = chain 'F' selection = chain 'J' selection = chain 'K' selection = chain 'L' } ncs_group { reference = chain 'G' selection = chain 'M' selection = chain 'N' } ncs_group { reference = chain 'H' selection = chain 'I' } 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=0.38 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.460 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.010 Extract box with map and model: 0.400 Check model and map are aligned: 0.080 Set scattering table: 0.080 Process input model: 31.340 Find NCS groups from input model: 0.910 Set up NCS constraints: 0.120 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:1.680 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 36.090 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7950 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 : 0.009 0.105 28189 Z= 0.416 Angle : 1.584 23.276 38261 Z= 0.868 Chirality : 0.073 0.985 4412 Planarity : 0.009 0.247 4753 Dihedral : 17.939 128.074 11265 Min Nonbonded Distance : 2.184 Molprobity Statistics. All-atom Clashscore : 7.62 Ramachandran Plot: Outliers : 1.46 % Allowed : 15.30 % Favored : 83.24 % Rotamer: Outliers : 0.44 % Allowed : 5.47 % Favored : 94.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.52 % Cis-general : 0.00 % Twisted Proline : 8.33 % Twisted General : 1.33 % 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 aren not related in a simple way. whole: -5.60 (0.11), residues: 3365 helix: -3.43 (0.09), residues: 1382 sheet: -4.66 (0.20), residues: 330 loop : -3.77 (0.13), residues: 1653 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.021 0.001 ARG B 583 TYR 0.051 0.004 TYR D 195 PHE 0.049 0.004 PHE A 167 TRP 0.052 0.005 TRP B 589 HIS 0.038 0.004 HIS D 253 Details of bonding type rmsd covalent geometry : bond 0.00868 (28123) covalent geometry : angle 1.53549 (38071) SS BOND : bond 0.00342 ( 8) SS BOND : angle 1.66973 ( 16) hydrogen bonds : bond 0.30041 ( 945) hydrogen bonds : angle 9.86480 ( 2756) link_ALPHA1-3 : bond 0.01145 ( 5) link_ALPHA1-3 : angle 2.98150 ( 15) link_ALPHA1-6 : bond 0.01448 ( 5) link_ALPHA1-6 : angle 2.66999 ( 15) link_BETA1-4 : bond 0.01490 ( 18) link_BETA1-4 : angle 5.80729 ( 54) link_NAG-ASN : bond 0.01384 ( 30) link_NAG-ASN : angle 6.81165 ( 90) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6730 Ramachandran restraints generated. 3365 Oldfield, 0 Emsley, 3365 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6730 Ramachandran restraints generated. 3365 Oldfield, 0 Emsley, 3365 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 466 residues out of total 2931 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 457 time to evaluate : 1.033 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 433 LEU cc_start: 0.9210 (mp) cc_final: 0.8862 (mt) REVERT: A 454 TYR cc_start: 0.8767 (m-80) cc_final: 0.8296 (m-80) REVERT: A 517 LEU cc_start: 0.9088 (mm) cc_final: 0.8624 (mm) REVERT: A 578 LEU cc_start: 0.9356 (tt) cc_final: 0.9125 (pp) REVERT: A 665 GLU cc_start: 0.7879 (mm-30) cc_final: 0.7550 (pp20) REVERT: A 824 PHE cc_start: 0.8673 (m-80) cc_final: 0.8097 (m-80) REVERT: A 867 MET cc_start: 0.7130 (tpt) cc_final: 0.6881 (tpp) REVERT: B 248 MET cc_start: 0.8212 (mmm) cc_final: 0.8005 (mmm) REVERT: B 608 LEU cc_start: 0.8909 (mp) cc_final: 0.8407 (mm) REVERT: B 612 PHE cc_start: 0.8305 (m-10) cc_final: 0.8066 (m-80) REVERT: B 639 ILE cc_start: 0.8987 (mm) cc_final: 0.8712 (pt) REVERT: B 694 PHE cc_start: 0.8360 (m-80) cc_final: 0.7721 (m-80) REVERT: B 719 LYS cc_start: 0.8853 (mttp) cc_final: 0.7771 (tppt) REVERT: B 784 GLN cc_start: 0.8905 (tt0) cc_final: 0.8568 (mt0) REVERT: B 810 LYS cc_start: 0.7423 (mttp) cc_final: 0.6495 (pttt) REVERT: B 815 LEU cc_start: 0.8638 (tp) cc_final: 0.8424 (tp) REVERT: B 842 PHE cc_start: 0.7530 (t80) cc_final: 0.6550 (t80) REVERT: C 360 MET cc_start: 0.9383 (tpt) cc_final: 0.8757 (tpt) REVERT: C 448 LYS cc_start: 0.8152 (mtmm) cc_final: 0.7750 (tptp) REVERT: C 454 TYR cc_start: 0.8302 (m-80) cc_final: 0.8005 (m-80) REVERT: C 501 MET cc_start: 0.8502 (mpt) cc_final: 0.8231 (mmm) REVERT: C 503 ARG cc_start: 0.9078 (ttt180) cc_final: 0.8838 (mmm-85) REVERT: C 556 LEU cc_start: 0.9014 (mp) cc_final: 0.8771 (tt) REVERT: C 584 PHE cc_start: 0.7537 (m-10) cc_final: 0.7207 (m-80) REVERT: C 627 MET cc_start: 0.7406 (mmp) cc_final: 0.6961 (mmp) REVERT: C 651 TYR cc_start: 0.9149 (t80) cc_final: 0.8768 (t80) REVERT: C 673 ASP cc_start: 0.8820 (m-30) cc_final: 0.8548 (m-30) REVERT: C 686 GLU cc_start: 0.8778 (tt0) cc_final: 0.8428 (tp30) REVERT: C 691 MET cc_start: 0.8542 (tmt) cc_final: 0.8172 (tmm) REVERT: C 705 MET cc_start: 0.9190 (mtp) cc_final: 0.8908 (mtp) REVERT: C 723 GLU cc_start: 0.8333 (mm-30) cc_final: 0.8047 (tp30) REVERT: C 764 TYR cc_start: 0.6979 (m-10) cc_final: 0.6631 (m-80) REVERT: C 815 LEU cc_start: 0.8704 (mt) cc_final: 0.8433 (mt) REVERT: D 114 SER cc_start: 0.9411 (m) cc_final: 0.9201 (t) REVERT: D 248 MET cc_start: 0.8773 (mmm) cc_final: 0.8558 (mmm) REVERT: D 566 TYR cc_start: 0.8474 (m-10) cc_final: 0.8107 (t80) REVERT: D 571 CYS cc_start: 0.8299 (t) cc_final: 0.8075 (p) REVERT: D 584 PHE cc_start: 0.8488 (t80) cc_final: 0.7997 (t80) REVERT: D 590 TYR cc_start: 0.8390 (p90) cc_final: 0.8151 (p90) REVERT: D 626 LEU cc_start: 0.8537 (OUTLIER) cc_final: 0.7914 (tt) REVERT: D 662 GLU cc_start: 0.9111 (mm-30) cc_final: 0.8812 (mm-30) REVERT: D 861 MET cc_start: 0.6402 (mtt) cc_final: 0.5872 (mmm) outliers start: 9 outliers final: 1 residues processed: 462 average time/residue: 0.1742 time to fit residues: 127.2067 Evaluate side-chains 256 residues out of total 2931 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 254 time to evaluate : 1.056 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 411 LEU Chi-restraints excluded: chain D residue 626 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 336 random chunks: chunk 197 optimal weight: 0.9980 chunk 215 optimal weight: 3.9990 chunk 20 optimal weight: 0.5980 chunk 132 optimal weight: 0.0980 chunk 261 optimal weight: 0.0570 chunk 248 optimal weight: 10.0000 chunk 207 optimal weight: 3.9990 chunk 155 optimal weight: 8.9990 chunk 244 optimal weight: 3.9990 chunk 183 optimal weight: 0.9990 chunk 298 optimal weight: 10.0000 overall best weight: 0.5500 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 84 ASN A 123 ASN ** A 129 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 131 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 136 HIS A 165 GLN A 186 GLN ** A 253 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 456 ASN A 491 GLN A 508 HIS A 604 ASN A 605 ASN A 622 GLN A 754 GLN B 34 HIS ** B 131 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 136 HIS ** B 286 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 549 ASN B 593 HIS B 654 ASN B 792 HIS C 123 ASN C 136 HIS C 165 GLN C 283 ASN C 491 GLN C 557 ASN C 622 GLN C 747 GLN D 65 ASN D 232 HIS D 286 ASN D 456 ASN D 491 GLN D 593 HIS D 604 ASN D 622 GLN ** D 714 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 747 GLN D 784 GLN Total number of N/Q/H flips: 36 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4110 r_free = 0.4110 target = 0.107362 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3589 r_free = 0.3589 target = 0.078140 restraints weight = 197020.955| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3570 r_free = 0.3570 target = 0.079260 restraints weight = 77351.868| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3589 r_free = 0.3589 target = 0.080316 restraints weight = 51138.390| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3592 r_free = 0.3592 target = 0.080195 restraints weight = 43502.391| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3603 r_free = 0.3603 target = 0.080856 restraints weight = 38461.872| |-----------------------------------------------------------------------------| r_work (final): 0.3579 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3578 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3578 r_free = 0.3578 target_work(ls_wunit_k1) = 0.080 | | occupancies: max = 1.00 min = 0.38 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3578 r_free = 0.3578 target_work(ls_wunit_k1) = 0.080 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| r_final: 0.3578 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7938 moved from start: 0.2491 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.073 28189 Z= 0.177 Angle : 1.044 17.701 38261 Z= 0.499 Chirality : 0.054 0.515 4412 Planarity : 0.007 0.136 4753 Dihedral : 18.701 110.151 4840 Min Nonbonded Distance : 2.379 Molprobity Statistics. All-atom Clashscore : 14.79 Ramachandran Plot: Outliers : 0.95 % Allowed : 13.93 % Favored : 85.12 % Rotamer: Outliers : 1.53 % Allowed : 11.42 % Favored : 87.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.52 % Cis-general : 0.00 % Twisted Proline : 6.06 % Twisted General : 0.71 % 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 aren not related in a simple way. whole: -4.33 (0.12), residues: 3365 helix: -1.91 (0.11), residues: 1463 sheet: -4.36 (0.22), residues: 322 loop : -3.50 (0.14), residues: 1580 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG D 68 TYR 0.024 0.002 TYR C 254 PHE 0.036 0.002 PHE B 643 TRP 0.042 0.003 TRP B 589 HIS 0.012 0.001 HIS D 253 Details of bonding type rmsd covalent geometry : bond 0.00374 (28123) covalent geometry : angle 1.00141 (38071) SS BOND : bond 0.00189 ( 8) SS BOND : angle 1.17037 ( 16) hydrogen bonds : bond 0.05298 ( 945) hydrogen bonds : angle 5.71425 ( 2756) link_ALPHA1-3 : bond 0.01370 ( 5) link_ALPHA1-3 : angle 2.88598 ( 15) link_ALPHA1-6 : bond 0.01383 ( 5) link_ALPHA1-6 : angle 2.75816 ( 15) link_BETA1-4 : bond 0.01102 ( 18) link_BETA1-4 : angle 4.48085 ( 54) link_NAG-ASN : bond 0.00881 ( 30) link_NAG-ASN : angle 4.92886 ( 90) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6730 Ramachandran restraints generated. 3365 Oldfield, 0 Emsley, 3365 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6730 Ramachandran restraints generated. 3365 Oldfield, 0 Emsley, 3365 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 354 residues out of total 2931 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 313 time to evaluate : 1.067 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 85 LEU cc_start: 0.9496 (OUTLIER) cc_final: 0.9157 (tm) REVERT: A 454 TYR cc_start: 0.8868 (m-80) cc_final: 0.8644 (m-80) REVERT: A 517 LEU cc_start: 0.8974 (mm) cc_final: 0.8765 (mm) REVERT: A 612 PHE cc_start: 0.8841 (OUTLIER) cc_final: 0.8170 (p90) REVERT: A 620 MET cc_start: 0.8782 (mmm) cc_final: 0.7883 (mmm) REVERT: A 768 THR cc_start: 0.7667 (OUTLIER) cc_final: 0.7450 (p) REVERT: A 770 MET cc_start: 0.8505 (tpp) cc_final: 0.7881 (tpp) REVERT: A 824 PHE cc_start: 0.8449 (m-80) cc_final: 0.8038 (m-80) REVERT: B 612 PHE cc_start: 0.8162 (m-10) cc_final: 0.7932 (m-80) REVERT: B 639 ILE cc_start: 0.8983 (mm) cc_final: 0.8666 (pt) REVERT: B 664 MET cc_start: 0.6024 (ptm) cc_final: 0.5373 (tpt) REVERT: B 719 LYS cc_start: 0.8839 (mttp) cc_final: 0.7702 (tppt) REVERT: B 762 LYS cc_start: 0.8300 (mppt) cc_final: 0.7701 (mmtt) REVERT: B 842 PHE cc_start: 0.7389 (t80) cc_final: 0.7051 (t80) REVERT: C 184 ARG cc_start: 0.8779 (mtm180) cc_final: 0.8537 (mtm-85) REVERT: C 250 GLU cc_start: 0.7720 (OUTLIER) cc_final: 0.7159 (tp30) REVERT: C 448 LYS cc_start: 0.8234 (mtmm) cc_final: 0.7796 (tptp) REVERT: C 454 TYR cc_start: 0.8225 (m-80) cc_final: 0.7944 (m-80) REVERT: C 463 CYS cc_start: 0.9137 (m) cc_final: 0.8707 (m) REVERT: C 501 MET cc_start: 0.8795 (mpt) cc_final: 0.8548 (mmt) REVERT: C 534 MET cc_start: 0.7196 (mtp) cc_final: 0.6971 (mtp) REVERT: C 556 LEU cc_start: 0.8960 (mp) cc_final: 0.8570 (tt) REVERT: C 619 LEU cc_start: 0.9470 (tp) cc_final: 0.9089 (tt) REVERT: C 691 MET cc_start: 0.8518 (tmt) cc_final: 0.8265 (tmm) REVERT: D 114 SER cc_start: 0.9448 (m) cc_final: 0.9125 (t) REVERT: D 245 MET cc_start: 0.8029 (ttm) cc_final: 0.7798 (ttm) REVERT: D 248 MET cc_start: 0.8896 (mmm) cc_final: 0.8634 (mmm) REVERT: D 316 MET cc_start: 0.8886 (mtt) cc_final: 0.8518 (mmm) REVERT: D 360 MET cc_start: 0.8849 (tpp) cc_final: 0.8545 (tpp) REVERT: D 562 ASP cc_start: 0.8428 (t70) cc_final: 0.8151 (t0) REVERT: D 566 TYR cc_start: 0.7909 (m-10) cc_final: 0.7675 (m-80) REVERT: D 584 PHE cc_start: 0.8690 (t80) cc_final: 0.8292 (t80) REVERT: D 588 GLU cc_start: 0.8445 (tp30) cc_final: 0.8202 (mm-30) REVERT: D 662 GLU cc_start: 0.8937 (mm-30) cc_final: 0.8634 (tm-30) REVERT: D 691 MET cc_start: 0.8755 (tmm) cc_final: 0.8210 (tmm) REVERT: D 780 ILE cc_start: 0.8810 (OUTLIER) cc_final: 0.8535 (tp) REVERT: D 793 MET cc_start: 0.8807 (tpp) cc_final: 0.8522 (ttp) REVERT: D 824 PHE cc_start: 0.8414 (m-80) cc_final: 0.8169 (m-80) REVERT: D 861 MET cc_start: 0.6301 (mtt) cc_final: 0.5952 (mmm) outliers start: 41 outliers final: 17 residues processed: 339 average time/residue: 0.1616 time to fit residues: 89.3653 Evaluate side-chains 263 residues out of total 2931 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 241 time to evaluate : 0.805 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 85 LEU Chi-restraints excluded: chain A residue 446 PHE Chi-restraints excluded: chain A residue 480 ILE Chi-restraints excluded: chain A residue 612 PHE Chi-restraints excluded: chain A residue 736 LEU Chi-restraints excluded: chain A residue 768 THR Chi-restraints excluded: chain B residue 160 ILE Chi-restraints excluded: chain B residue 183 ILE Chi-restraints excluded: chain B residue 201 ILE Chi-restraints excluded: chain B residue 477 THR Chi-restraints excluded: chain B residue 693 PHE Chi-restraints excluded: chain B residue 827 LEU Chi-restraints excluded: chain C residue 195 TYR Chi-restraints excluded: chain C residue 250 GLU Chi-restraints excluded: chain C residue 293 ILE Chi-restraints excluded: chain C residue 411 LEU Chi-restraints excluded: chain C residue 827 LEU Chi-restraints excluded: chain D residue 68 ARG Chi-restraints excluded: chain D residue 327 VAL Chi-restraints excluded: chain D residue 569 LEU Chi-restraints excluded: chain D residue 647 ILE Chi-restraints excluded: chain D residue 780 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 336 random chunks: chunk 204 optimal weight: 4.9990 chunk 233 optimal weight: 2.9990 chunk 258 optimal weight: 6.9990 chunk 284 optimal weight: 3.9990 chunk 23 optimal weight: 0.8980 chunk 302 optimal weight: 10.0000 chunk 71 optimal weight: 6.9990 chunk 35 optimal weight: 0.9980 chunk 115 optimal weight: 7.9990 chunk 109 optimal weight: 4.9990 chunk 197 optimal weight: 1.9990 overall best weight: 2.1786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 84 ASN ** A 129 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 131 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 253 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 621 GLN A 747 GLN ** B 131 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 253 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 286 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 137 GLN C 621 GLN D 786 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4070 r_free = 0.4070 target = 0.105338 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3535 r_free = 0.3535 target = 0.075674 restraints weight = 171238.517| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3503 r_free = 0.3503 target = 0.076223 restraints weight = 70800.949| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3523 r_free = 0.3523 target = 0.077356 restraints weight = 51375.391| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3526 r_free = 0.3526 target = 0.077217 restraints weight = 43305.936| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3551 r_free = 0.3551 target = 0.078571 restraints weight = 39828.741| |-----------------------------------------------------------------------------| r_work (final): 0.3550 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3525 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3525 r_free = 0.3525 target_work(ls_wunit_k1) = 0.076 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3525 r_free = 0.3525 target_work(ls_wunit_k1) = 0.076 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| r_final: 0.3525 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7965 moved from start: 0.3016 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 28189 Z= 0.196 Angle : 0.984 16.752 38261 Z= 0.466 Chirality : 0.052 0.539 4412 Planarity : 0.006 0.122 4753 Dihedral : 16.861 104.824 4838 Min Nonbonded Distance : 2.207 Molprobity Statistics. All-atom Clashscore : 15.11 Ramachandran Plot: Outliers : 0.77 % Allowed : 14.67 % Favored : 84.55 % Rotamer: Outliers : 2.28 % Allowed : 12.85 % Favored : 84.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.52 % Cis-general : 0.00 % Twisted Proline : 5.30 % Twisted General : 0.68 % 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 aren not related in a simple way. whole: -3.53 (0.13), residues: 3365 helix: -0.96 (0.12), residues: 1446 sheet: -4.23 (0.23), residues: 330 loop : -3.29 (0.15), residues: 1589 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG D 68 TYR 0.021 0.002 TYR C 252 PHE 0.039 0.002 PHE B 643 TRP 0.038 0.002 TRP B 589 HIS 0.016 0.002 HIS D 350 Details of bonding type rmsd covalent geometry : bond 0.00429 (28123) covalent geometry : angle 0.94274 (38071) SS BOND : bond 0.00188 ( 8) SS BOND : angle 1.15594 ( 16) hydrogen bonds : bond 0.04503 ( 945) hydrogen bonds : angle 5.23383 ( 2756) link_ALPHA1-3 : bond 0.01807 ( 5) link_ALPHA1-3 : angle 3.00527 ( 15) link_ALPHA1-6 : bond 0.01480 ( 5) link_ALPHA1-6 : angle 2.89161 ( 15) link_BETA1-4 : bond 0.00986 ( 18) link_BETA1-4 : angle 4.14491 ( 54) link_NAG-ASN : bond 0.00815 ( 30) link_NAG-ASN : angle 4.71205 ( 90) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6730 Ramachandran restraints generated. 3365 Oldfield, 0 Emsley, 3365 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6730 Ramachandran restraints generated. 3365 Oldfield, 0 Emsley, 3365 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 324 residues out of total 2931 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 261 time to evaluate : 1.053 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 85 LEU cc_start: 0.9550 (OUTLIER) cc_final: 0.9250 (tm) REVERT: A 298 MET cc_start: 0.7926 (tmm) cc_final: 0.7590 (tmm) REVERT: A 316 MET cc_start: 0.8427 (mmm) cc_final: 0.7776 (tpt) REVERT: A 454 TYR cc_start: 0.8824 (m-80) cc_final: 0.8566 (m-80) REVERT: A 501 MET cc_start: 0.8604 (mmp) cc_final: 0.8385 (mmt) REVERT: A 517 LEU cc_start: 0.9135 (mm) cc_final: 0.8787 (mm) REVERT: A 578 LEU cc_start: 0.9406 (pp) cc_final: 0.9068 (tp) REVERT: A 606 PHE cc_start: 0.8503 (m-80) cc_final: 0.8085 (t80) REVERT: A 612 PHE cc_start: 0.8796 (OUTLIER) cc_final: 0.8144 (p90) REVERT: A 620 MET cc_start: 0.9044 (mmm) cc_final: 0.7610 (mmm) REVERT: A 627 MET cc_start: 0.8823 (mmp) cc_final: 0.8200 (tpt) REVERT: A 691 MET cc_start: 0.8823 (ttp) cc_final: 0.8501 (ptm) REVERT: A 714 GLN cc_start: 0.7396 (tp-100) cc_final: 0.7112 (tp-100) REVERT: A 768 THR cc_start: 0.8004 (OUTLIER) cc_final: 0.7738 (p) REVERT: A 770 MET cc_start: 0.8630 (tpp) cc_final: 0.7822 (tpp) REVERT: A 824 PHE cc_start: 0.8482 (m-80) cc_final: 0.7867 (m-80) REVERT: B 612 PHE cc_start: 0.8205 (m-10) cc_final: 0.7994 (m-80) REVERT: B 651 TYR cc_start: 0.8995 (t80) cc_final: 0.8572 (t80) REVERT: B 719 LYS cc_start: 0.8873 (mttp) cc_final: 0.7842 (tppt) REVERT: B 737 MET cc_start: 0.5757 (mmm) cc_final: 0.5382 (mmt) REVERT: B 762 LYS cc_start: 0.8286 (mppt) cc_final: 0.7685 (mmtt) REVERT: C 250 GLU cc_start: 0.7751 (OUTLIER) cc_final: 0.6971 (tp30) REVERT: C 428 LEU cc_start: 0.8062 (tt) cc_final: 0.7775 (tp) REVERT: C 454 TYR cc_start: 0.8213 (m-80) cc_final: 0.7942 (m-80) REVERT: C 463 CYS cc_start: 0.9152 (m) cc_final: 0.8744 (m) REVERT: C 501 MET cc_start: 0.8757 (mpt) cc_final: 0.8351 (mmm) REVERT: C 534 MET cc_start: 0.6904 (mtp) cc_final: 0.6643 (mtm) REVERT: C 556 LEU cc_start: 0.9004 (mp) cc_final: 0.8635 (tt) REVERT: C 620 MET cc_start: 0.9360 (mmm) cc_final: 0.9134 (mmp) REVERT: C 686 GLU cc_start: 0.8729 (tt0) cc_final: 0.8435 (pt0) REVERT: C 705 MET cc_start: 0.9085 (mtp) cc_final: 0.8580 (mtt) REVERT: C 764 TYR cc_start: 0.6495 (m-10) cc_final: 0.6273 (m-80) REVERT: C 793 MET cc_start: 0.9180 (ppp) cc_final: 0.8962 (ppp) REVERT: D 114 SER cc_start: 0.9465 (m) cc_final: 0.9255 (t) REVERT: D 248 MET cc_start: 0.8959 (mmm) cc_final: 0.8599 (mmm) REVERT: D 316 MET cc_start: 0.9030 (mtt) cc_final: 0.8555 (mmm) REVERT: D 360 MET cc_start: 0.8921 (tpp) cc_final: 0.8670 (tpp) REVERT: D 584 PHE cc_start: 0.8769 (t80) cc_final: 0.8311 (t80) REVERT: D 588 GLU cc_start: 0.8337 (tp30) cc_final: 0.8060 (mm-30) REVERT: D 606 PHE cc_start: 0.8681 (OUTLIER) cc_final: 0.8108 (t80) REVERT: D 691 MET cc_start: 0.8793 (tmm) cc_final: 0.8274 (tmm) REVERT: D 722 GLU cc_start: 0.9467 (mt-10) cc_final: 0.8999 (mp0) REVERT: D 780 ILE cc_start: 0.8752 (OUTLIER) cc_final: 0.8517 (tp) REVERT: D 793 MET cc_start: 0.8830 (tpp) cc_final: 0.8523 (ptt) REVERT: D 824 PHE cc_start: 0.8478 (m-80) cc_final: 0.8179 (m-80) REVERT: D 861 MET cc_start: 0.6218 (mtt) cc_final: 0.5910 (mmm) outliers start: 63 outliers final: 34 residues processed: 308 average time/residue: 0.1553 time to fit residues: 78.8596 Evaluate side-chains 274 residues out of total 2931 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 234 time to evaluate : 1.035 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 85 LEU Chi-restraints excluded: chain A residue 172 VAL Chi-restraints excluded: chain A residue 375 ILE Chi-restraints excluded: chain A residue 446 PHE Chi-restraints excluded: chain A residue 480 ILE Chi-restraints excluded: chain A residue 612 PHE Chi-restraints excluded: chain A residue 736 LEU Chi-restraints excluded: chain A residue 768 THR Chi-restraints excluded: chain A residue 815 LEU Chi-restraints excluded: chain A residue 827 LEU Chi-restraints excluded: chain A residue 843 LEU Chi-restraints excluded: chain B residue 45 VAL Chi-restraints excluded: chain B residue 132 THR Chi-restraints excluded: chain B residue 140 ASP Chi-restraints excluded: chain B residue 149 LEU Chi-restraints excluded: chain B residue 160 ILE Chi-restraints excluded: chain B residue 183 ILE Chi-restraints excluded: chain B residue 201 ILE Chi-restraints excluded: chain B residue 391 VAL Chi-restraints excluded: chain B residue 445 LEU Chi-restraints excluded: chain B residue 477 THR Chi-restraints excluded: chain B residue 693 PHE Chi-restraints excluded: chain B residue 784 GLN Chi-restraints excluded: chain B residue 811 GLU Chi-restraints excluded: chain B residue 827 LEU Chi-restraints excluded: chain C residue 156 LEU Chi-restraints excluded: chain C residue 195 TYR Chi-restraints excluded: chain C residue 250 GLU Chi-restraints excluded: chain C residue 293 ILE Chi-restraints excluded: chain C residue 375 ILE Chi-restraints excluded: chain C residue 411 LEU Chi-restraints excluded: chain C residue 827 LEU Chi-restraints excluded: chain D residue 327 VAL Chi-restraints excluded: chain D residue 391 VAL Chi-restraints excluded: chain D residue 569 LEU Chi-restraints excluded: chain D residue 606 PHE Chi-restraints excluded: chain D residue 647 ILE Chi-restraints excluded: chain D residue 659 LEU Chi-restraints excluded: chain D residue 713 ARG Chi-restraints excluded: chain D residue 780 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 336 random chunks: chunk 39 optimal weight: 1.9990 chunk 311 optimal weight: 20.0000 chunk 10 optimal weight: 3.9990 chunk 215 optimal weight: 9.9990 chunk 75 optimal weight: 2.9990 chunk 234 optimal weight: 0.7980 chunk 35 optimal weight: 0.8980 chunk 248 optimal weight: 7.9990 chunk 222 optimal weight: 9.9990 chunk 176 optimal weight: 5.9990 chunk 160 optimal weight: 3.9990 overall best weight: 2.1386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 129 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 131 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 253 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 677 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 131 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 253 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 286 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 802 ASN C 819 ASN D 328 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4066 r_free = 0.4066 target = 0.105370 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3525 r_free = 0.3525 target = 0.075343 restraints weight = 169755.909| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3496 r_free = 0.3496 target = 0.075987 restraints weight = 74377.228| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3517 r_free = 0.3517 target = 0.077139 restraints weight = 51574.895| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3515 r_free = 0.3515 target = 0.076858 restraints weight = 45295.696| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3529 r_free = 0.3529 target = 0.077577 restraints weight = 39649.620| |-----------------------------------------------------------------------------| r_work (final): 0.3517 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3517 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3517 r_free = 0.3517 target_work(ls_wunit_k1) = 0.077 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3517 r_free = 0.3517 target_work(ls_wunit_k1) = 0.077 | | occupancies: max = 1.00 min = 0.01 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| r_final: 0.3517 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8006 moved from start: 0.3421 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 28189 Z= 0.183 Angle : 0.951 14.227 38261 Z= 0.449 Chirality : 0.051 0.518 4412 Planarity : 0.005 0.121 4753 Dihedral : 15.448 102.917 4838 Min Nonbonded Distance : 2.333 Molprobity Statistics. All-atom Clashscore : 14.84 Ramachandran Plot: Outliers : 0.65 % Allowed : 14.49 % Favored : 84.85 % Rotamer: Outliers : 2.14 % Allowed : 13.97 % Favored : 83.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.52 % Cis-general : 0.00 % Twisted Proline : 5.30 % Twisted General : 0.59 % 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 aren not related in a simple way. whole: -3.16 (0.14), residues: 3365 helix: -0.51 (0.13), residues: 1459 sheet: -4.14 (0.23), residues: 336 loop : -3.23 (0.15), residues: 1570 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG D 748 TYR 0.020 0.002 TYR C 252 PHE 0.041 0.002 PHE C 262 TRP 0.034 0.002 TRP B 589 HIS 0.009 0.001 HIS D 253 Details of bonding type rmsd covalent geometry : bond 0.00402 (28123) covalent geometry : angle 0.90782 (38071) SS BOND : bond 0.00163 ( 8) SS BOND : angle 1.05318 ( 16) hydrogen bonds : bond 0.03928 ( 945) hydrogen bonds : angle 5.04055 ( 2756) link_ALPHA1-3 : bond 0.01900 ( 5) link_ALPHA1-3 : angle 3.09119 ( 15) link_ALPHA1-6 : bond 0.01610 ( 5) link_ALPHA1-6 : angle 2.86191 ( 15) link_BETA1-4 : bond 0.00998 ( 18) link_BETA1-4 : angle 4.20341 ( 54) link_NAG-ASN : bond 0.00819 ( 30) link_NAG-ASN : angle 4.67710 ( 90) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6730 Ramachandran restraints generated. 3365 Oldfield, 0 Emsley, 3365 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6730 Ramachandran restraints generated. 3365 Oldfield, 0 Emsley, 3365 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 300 residues out of total 2931 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 241 time to evaluate : 1.069 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 85 LEU cc_start: 0.9510 (OUTLIER) cc_final: 0.9162 (tm) REVERT: A 298 MET cc_start: 0.7966 (tmm) cc_final: 0.7473 (tmm) REVERT: A 316 MET cc_start: 0.8392 (mmm) cc_final: 0.7756 (tpt) REVERT: A 454 TYR cc_start: 0.8786 (m-80) cc_final: 0.8511 (m-80) REVERT: A 517 LEU cc_start: 0.9151 (mm) cc_final: 0.8795 (mm) REVERT: A 612 PHE cc_start: 0.8623 (OUTLIER) cc_final: 0.8004 (p90) REVERT: A 620 MET cc_start: 0.8967 (mmm) cc_final: 0.7911 (mmm) REVERT: A 677 GLN cc_start: 0.8619 (OUTLIER) cc_final: 0.8235 (pp30) REVERT: A 691 MET cc_start: 0.8868 (ttp) cc_final: 0.8554 (ptm) REVERT: A 714 GLN cc_start: 0.7462 (tp-100) cc_final: 0.7250 (tp-100) REVERT: A 738 GLU cc_start: 0.7862 (mp0) cc_final: 0.7480 (mp0) REVERT: A 768 THR cc_start: 0.8035 (OUTLIER) cc_final: 0.7760 (p) REVERT: A 770 MET cc_start: 0.8590 (tpp) cc_final: 0.7847 (tpp) REVERT: A 824 PHE cc_start: 0.8447 (m-80) cc_final: 0.7944 (m-80) REVERT: B 55 LEU cc_start: 0.9374 (OUTLIER) cc_final: 0.8833 (mm) REVERT: B 73 ASN cc_start: 0.7439 (OUTLIER) cc_final: 0.7202 (m110) REVERT: B 651 TYR cc_start: 0.8823 (t80) cc_final: 0.8428 (t80) REVERT: B 719 LYS cc_start: 0.8931 (mttp) cc_final: 0.7889 (tppt) REVERT: C 448 LYS cc_start: 0.8534 (mtmm) cc_final: 0.7902 (tptp) REVERT: C 454 TYR cc_start: 0.8198 (m-80) cc_final: 0.7927 (m-80) REVERT: C 463 CYS cc_start: 0.9110 (m) cc_final: 0.8741 (p) REVERT: C 501 MET cc_start: 0.8773 (mpt) cc_final: 0.8338 (mmm) REVERT: C 534 MET cc_start: 0.6880 (mtp) cc_final: 0.6515 (mtp) REVERT: C 619 LEU cc_start: 0.9545 (tp) cc_final: 0.9096 (tt) REVERT: C 647 ILE cc_start: 0.8848 (mm) cc_final: 0.8612 (pt) REVERT: C 743 GLU cc_start: 0.8567 (mt-10) cc_final: 0.8361 (mt-10) REVERT: C 764 TYR cc_start: 0.6372 (m-10) cc_final: 0.6131 (m-80) REVERT: C 770 MET cc_start: 0.8964 (tpp) cc_final: 0.8723 (tpp) REVERT: C 793 MET cc_start: 0.9261 (ppp) cc_final: 0.9055 (ppp) REVERT: D 114 SER cc_start: 0.9429 (m) cc_final: 0.9205 (t) REVERT: D 194 ARG cc_start: 0.8063 (OUTLIER) cc_final: 0.7801 (pmt100) REVERT: D 248 MET cc_start: 0.8962 (mmm) cc_final: 0.8597 (mmm) REVERT: D 316 MET cc_start: 0.8971 (mtt) cc_final: 0.8764 (mmm) REVERT: D 584 PHE cc_start: 0.8760 (t80) cc_final: 0.8299 (t80) REVERT: D 588 GLU cc_start: 0.8409 (tp30) cc_final: 0.7388 (mm-30) REVERT: D 590 TYR cc_start: 0.8307 (p90) cc_final: 0.8022 (p90) REVERT: D 620 MET cc_start: 0.8569 (ttm) cc_final: 0.8336 (ttm) REVERT: D 691 MET cc_start: 0.8773 (tmm) cc_final: 0.8139 (tmm) REVERT: D 709 MET cc_start: 0.7923 (mmt) cc_final: 0.7626 (mpp) REVERT: D 722 GLU cc_start: 0.9518 (mt-10) cc_final: 0.9065 (mp0) REVERT: D 780 ILE cc_start: 0.8744 (OUTLIER) cc_final: 0.8505 (tp) REVERT: D 793 MET cc_start: 0.8712 (tpp) cc_final: 0.8329 (ptm) REVERT: D 861 MET cc_start: 0.6059 (mtt) cc_final: 0.5797 (mmm) outliers start: 59 outliers final: 38 residues processed: 283 average time/residue: 0.1441 time to fit residues: 68.7324 Evaluate side-chains 272 residues out of total 2931 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 226 time to evaluate : 0.851 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 50 MET Chi-restraints excluded: chain A residue 85 LEU Chi-restraints excluded: chain A residue 172 VAL Chi-restraints excluded: chain A residue 375 ILE Chi-restraints excluded: chain A residue 391 VAL Chi-restraints excluded: chain A residue 446 PHE Chi-restraints excluded: chain A residue 480 ILE Chi-restraints excluded: chain A residue 612 PHE Chi-restraints excluded: chain A residue 677 GLN Chi-restraints excluded: chain A residue 736 LEU Chi-restraints excluded: chain A residue 768 THR Chi-restraints excluded: chain A residue 815 LEU Chi-restraints excluded: chain A residue 827 LEU Chi-restraints excluded: chain A residue 843 LEU Chi-restraints excluded: chain B residue 45 VAL Chi-restraints excluded: chain B residue 55 LEU Chi-restraints excluded: chain B residue 73 ASN Chi-restraints excluded: chain B residue 140 ASP Chi-restraints excluded: chain B residue 156 LEU Chi-restraints excluded: chain B residue 160 ILE Chi-restraints excluded: chain B residue 183 ILE Chi-restraints excluded: chain B residue 195 TYR Chi-restraints excluded: chain B residue 201 ILE Chi-restraints excluded: chain B residue 391 VAL Chi-restraints excluded: chain B residue 477 THR Chi-restraints excluded: chain B residue 682 TYR Chi-restraints excluded: chain B residue 784 GLN Chi-restraints excluded: chain B residue 811 GLU Chi-restraints excluded: chain B residue 827 LEU Chi-restraints excluded: chain C residue 156 LEU Chi-restraints excluded: chain C residue 195 TYR Chi-restraints excluded: chain C residue 293 ILE Chi-restraints excluded: chain C residue 301 LEU Chi-restraints excluded: chain C residue 375 ILE Chi-restraints excluded: chain C residue 411 LEU Chi-restraints excluded: chain C residue 701 THR Chi-restraints excluded: chain C residue 827 LEU Chi-restraints excluded: chain D residue 194 ARG Chi-restraints excluded: chain D residue 327 VAL Chi-restraints excluded: chain D residue 391 VAL Chi-restraints excluded: chain D residue 453 LEU Chi-restraints excluded: chain D residue 647 ILE Chi-restraints excluded: chain D residue 659 LEU Chi-restraints excluded: chain D residue 674 LEU Chi-restraints excluded: chain D residue 713 ARG Chi-restraints excluded: chain D residue 780 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 336 random chunks: chunk 214 optimal weight: 10.0000 chunk 69 optimal weight: 6.9990 chunk 330 optimal weight: 7.9990 chunk 76 optimal weight: 3.9990 chunk 194 optimal weight: 3.9990 chunk 15 optimal weight: 0.4980 chunk 272 optimal weight: 0.7980 chunk 256 optimal weight: 9.9990 chunk 25 optimal weight: 9.9990 chunk 236 optimal weight: 6.9990 chunk 104 optimal weight: 0.9990 overall best weight: 2.0586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 129 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 131 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 253 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 677 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 131 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 253 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 286 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 286 ASN C 654 ASN ** D 622 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3948 r_free = 0.3948 target = 0.102260 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3281 r_free = 0.3281 target = 0.069121 restraints weight = 154983.242| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3280 r_free = 0.3280 target = 0.069602 restraints weight = 77567.054| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3303 r_free = 0.3303 target = 0.070792 restraints weight = 51843.897| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3310 r_free = 0.3310 target = 0.070951 restraints weight = 43114.992| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3316 r_free = 0.3316 target = 0.071218 restraints weight = 38627.966| |-----------------------------------------------------------------------------| r_work (final): 0.3307 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3302 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3302 r_free = 0.3302 target_work(ls_wunit_k1) = 0.069 | | occupancies: max = 1.00 min = 0.01 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3302 r_free = 0.3302 target_work(ls_wunit_k1) = 0.069 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| r_final: 0.3302 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8075 moved from start: 0.3710 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.068 28189 Z= 0.179 Angle : 0.927 14.850 38261 Z= 0.436 Chirality : 0.050 0.520 4412 Planarity : 0.005 0.134 4753 Dihedral : 14.264 100.607 4838 Min Nonbonded Distance : 2.345 Molprobity Statistics. All-atom Clashscore : 14.59 Ramachandran Plot: Outliers : 0.54 % Allowed : 14.37 % Favored : 85.09 % Rotamer: Outliers : 2.24 % Allowed : 14.62 % Favored : 83.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.52 % Cis-general : 0.00 % Twisted Proline : 5.30 % Twisted General : 0.59 % 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 aren not related in a simple way. whole: -2.89 (0.14), residues: 3365 helix: -0.25 (0.13), residues: 1461 sheet: -4.08 (0.24), residues: 314 loop : -3.15 (0.15), residues: 1590 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG D 713 TYR 0.025 0.002 TYR C 254 PHE 0.040 0.002 PHE B 612 TRP 0.032 0.002 TRP B 589 HIS 0.009 0.001 HIS D 253 Details of bonding type rmsd covalent geometry : bond 0.00395 (28123) covalent geometry : angle 0.88512 (38071) SS BOND : bond 0.00187 ( 8) SS BOND : angle 1.11376 ( 16) hydrogen bonds : bond 0.03729 ( 945) hydrogen bonds : angle 4.93236 ( 2756) link_ALPHA1-3 : bond 0.02110 ( 5) link_ALPHA1-3 : angle 3.20496 ( 15) link_ALPHA1-6 : bond 0.01433 ( 5) link_ALPHA1-6 : angle 2.72591 ( 15) link_BETA1-4 : bond 0.00984 ( 18) link_BETA1-4 : angle 4.32236 ( 54) link_NAG-ASN : bond 0.00784 ( 30) link_NAG-ASN : angle 4.45861 ( 90) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6730 Ramachandran restraints generated. 3365 Oldfield, 0 Emsley, 3365 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6730 Ramachandran restraints generated. 3365 Oldfield, 0 Emsley, 3365 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 304 residues out of total 2931 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 242 time to evaluate : 0.962 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 85 LEU cc_start: 0.9444 (OUTLIER) cc_final: 0.9084 (tm) REVERT: A 298 MET cc_start: 0.8001 (tmm) cc_final: 0.7539 (tmm) REVERT: A 316 MET cc_start: 0.8339 (mmm) cc_final: 0.7727 (tpt) REVERT: A 437 THR cc_start: 0.8109 (t) cc_final: 0.7837 (m) REVERT: A 454 TYR cc_start: 0.8688 (m-80) cc_final: 0.8408 (m-80) REVERT: A 517 LEU cc_start: 0.9090 (OUTLIER) cc_final: 0.8779 (mm) REVERT: A 612 PHE cc_start: 0.8564 (p90) cc_final: 0.7998 (p90) REVERT: A 620 MET cc_start: 0.8915 (mmm) cc_final: 0.8025 (mmm) REVERT: A 691 MET cc_start: 0.8796 (ttp) cc_final: 0.8409 (ptm) REVERT: A 714 GLN cc_start: 0.7642 (tp-100) cc_final: 0.7369 (tp-100) REVERT: A 738 GLU cc_start: 0.8068 (mp0) cc_final: 0.7600 (mp0) REVERT: A 770 MET cc_start: 0.8559 (tpp) cc_final: 0.7870 (tpp) REVERT: A 824 PHE cc_start: 0.8357 (m-80) cc_final: 0.7817 (m-80) REVERT: B 55 LEU cc_start: 0.9357 (OUTLIER) cc_final: 0.9155 (mm) REVERT: B 73 ASN cc_start: 0.7293 (OUTLIER) cc_final: 0.7067 (m110) REVERT: B 651 TYR cc_start: 0.8791 (t80) cc_final: 0.8381 (t80) REVERT: B 680 ILE cc_start: 0.7813 (OUTLIER) cc_final: 0.7229 (tp) REVERT: B 719 LYS cc_start: 0.8950 (mttp) cc_final: 0.8655 (mmtt) REVERT: B 793 MET cc_start: 0.8435 (mmp) cc_final: 0.8200 (mmt) REVERT: C 360 MET cc_start: 0.9040 (mmm) cc_final: 0.8828 (mmm) REVERT: C 413 MET cc_start: 0.7643 (ppp) cc_final: 0.6828 (ppp) REVERT: C 428 LEU cc_start: 0.8213 (tt) cc_final: 0.7917 (tp) REVERT: C 448 LYS cc_start: 0.8548 (mtmm) cc_final: 0.7900 (tptp) REVERT: C 454 TYR cc_start: 0.8090 (m-80) cc_final: 0.7838 (m-80) REVERT: C 463 CYS cc_start: 0.9069 (m) cc_final: 0.8578 (m) REVERT: C 501 MET cc_start: 0.8792 (mpt) cc_final: 0.8345 (mmm) REVERT: C 534 MET cc_start: 0.6913 (mtp) cc_final: 0.6598 (mtp) REVERT: C 620 MET cc_start: 0.9329 (mmm) cc_final: 0.9000 (mmp) REVERT: C 647 ILE cc_start: 0.8828 (mm) cc_final: 0.8596 (pt) REVERT: C 679 LYS cc_start: 0.9359 (ptmm) cc_final: 0.8961 (pttm) REVERT: C 737 MET cc_start: 0.6908 (ppp) cc_final: 0.6386 (ppp) REVERT: C 764 TYR cc_start: 0.6393 (m-10) cc_final: 0.6183 (m-80) REVERT: C 770 MET cc_start: 0.8909 (tpp) cc_final: 0.8640 (tpp) REVERT: D 114 SER cc_start: 0.9320 (m) cc_final: 0.9116 (t) REVERT: D 584 PHE cc_start: 0.8670 (t80) cc_final: 0.8232 (t80) REVERT: D 606 PHE cc_start: 0.8618 (OUTLIER) cc_final: 0.8201 (t80) REVERT: D 691 MET cc_start: 0.8773 (tmm) cc_final: 0.8042 (tmm) REVERT: D 722 GLU cc_start: 0.9520 (mt-10) cc_final: 0.9057 (mp0) REVERT: D 780 ILE cc_start: 0.8778 (OUTLIER) cc_final: 0.8559 (tp) REVERT: D 793 MET cc_start: 0.8771 (tpp) cc_final: 0.8421 (ppp) REVERT: D 794 MET cc_start: 0.6664 (tmm) cc_final: 0.5833 (ppp) REVERT: D 861 MET cc_start: 0.6063 (mtt) cc_final: 0.5815 (mmm) outliers start: 62 outliers final: 37 residues processed: 289 average time/residue: 0.1382 time to fit residues: 67.3661 Evaluate side-chains 268 residues out of total 2931 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 224 time to evaluate : 0.676 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 50 MET Chi-restraints excluded: chain A residue 85 LEU Chi-restraints excluded: chain A residue 172 VAL Chi-restraints excluded: chain A residue 375 ILE Chi-restraints excluded: chain A residue 391 VAL Chi-restraints excluded: chain A residue 446 PHE Chi-restraints excluded: chain A residue 480 ILE Chi-restraints excluded: chain A residue 517 LEU Chi-restraints excluded: chain A residue 736 LEU Chi-restraints excluded: chain A residue 794 MET Chi-restraints excluded: chain A residue 815 LEU Chi-restraints excluded: chain A residue 827 LEU Chi-restraints excluded: chain A residue 843 LEU Chi-restraints excluded: chain B residue 45 VAL Chi-restraints excluded: chain B residue 55 LEU Chi-restraints excluded: chain B residue 73 ASN Chi-restraints excluded: chain B residue 140 ASP Chi-restraints excluded: chain B residue 156 LEU Chi-restraints excluded: chain B residue 160 ILE Chi-restraints excluded: chain B residue 183 ILE Chi-restraints excluded: chain B residue 189 ILE Chi-restraints excluded: chain B residue 195 TYR Chi-restraints excluded: chain B residue 201 ILE Chi-restraints excluded: chain B residue 391 VAL Chi-restraints excluded: chain B residue 477 THR Chi-restraints excluded: chain B residue 680 ILE Chi-restraints excluded: chain B residue 682 TYR Chi-restraints excluded: chain B residue 811 GLU Chi-restraints excluded: chain B residue 827 LEU Chi-restraints excluded: chain C residue 156 LEU Chi-restraints excluded: chain C residue 195 TYR Chi-restraints excluded: chain C residue 301 LEU Chi-restraints excluded: chain C residue 375 ILE Chi-restraints excluded: chain C residue 411 LEU Chi-restraints excluded: chain C residue 701 THR Chi-restraints excluded: chain D residue 327 VAL Chi-restraints excluded: chain D residue 391 VAL Chi-restraints excluded: chain D residue 453 LEU Chi-restraints excluded: chain D residue 606 PHE Chi-restraints excluded: chain D residue 647 ILE Chi-restraints excluded: chain D residue 659 LEU Chi-restraints excluded: chain D residue 674 LEU Chi-restraints excluded: chain D residue 713 ARG Chi-restraints excluded: chain D residue 780 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 336 random chunks: chunk 121 optimal weight: 1.9990 chunk 298 optimal weight: 8.9990 chunk 226 optimal weight: 10.0000 chunk 54 optimal weight: 7.9990 chunk 167 optimal weight: 9.9990 chunk 145 optimal weight: 4.9990 chunk 202 optimal weight: 5.9990 chunk 110 optimal weight: 2.9990 chunk 235 optimal weight: 4.9990 chunk 299 optimal weight: 7.9990 chunk 292 optimal weight: 5.9990 overall best weight: 4.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 129 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 131 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 165 GLN ** A 677 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 131 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 253 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 286 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 137 GLN D 508 HIS ** D 622 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3913 r_free = 0.3913 target = 0.100278 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3279 r_free = 0.3279 target = 0.068165 restraints weight = 200824.331| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3255 r_free = 0.3255 target = 0.068808 restraints weight = 94655.123| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3274 r_free = 0.3274 target = 0.069613 restraints weight = 65646.107| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3275 r_free = 0.3275 target = 0.069547 restraints weight = 53931.093| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3291 r_free = 0.3291 target = 0.070276 restraints weight = 49816.784| |-----------------------------------------------------------------------------| r_work (final): 0.3264 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3264 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3264 r_free = 0.3264 target_work(ls_wunit_k1) = 0.068 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3264 r_free = 0.3264 target_work(ls_wunit_k1) = 0.068 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| r_final: 0.3264 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8111 moved from start: 0.3893 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.076 28189 Z= 0.275 Angle : 0.979 14.999 38261 Z= 0.464 Chirality : 0.052 0.554 4412 Planarity : 0.006 0.137 4753 Dihedral : 13.835 103.496 4838 Min Nonbonded Distance : 2.304 Molprobity Statistics. All-atom Clashscore : 16.87 Ramachandran Plot: Outliers : 0.57 % Allowed : 15.21 % Favored : 84.23 % Rotamer: Outliers : 2.41 % Allowed : 14.72 % Favored : 82.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.52 % Cis-general : 0.00 % Twisted Proline : 5.30 % Twisted General : 0.59 % 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 aren not related in a simple way. whole: -2.89 (0.14), residues: 3365 helix: -0.17 (0.13), residues: 1473 sheet: -4.20 (0.22), residues: 359 loop : -3.17 (0.15), residues: 1533 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG D 280 TYR 0.023 0.002 TYR B 254 PHE 0.043 0.002 PHE B 643 TRP 0.030 0.002 TRP B 589 HIS 0.009 0.002 HIS D 253 Details of bonding type rmsd covalent geometry : bond 0.00613 (28123) covalent geometry : angle 0.94095 (38071) SS BOND : bond 0.00226 ( 8) SS BOND : angle 1.03713 ( 16) hydrogen bonds : bond 0.03858 ( 945) hydrogen bonds : angle 5.11529 ( 2756) link_ALPHA1-3 : bond 0.02140 ( 5) link_ALPHA1-3 : angle 3.23557 ( 15) link_ALPHA1-6 : bond 0.01412 ( 5) link_ALPHA1-6 : angle 2.84312 ( 15) link_BETA1-4 : bond 0.00981 ( 18) link_BETA1-4 : angle 4.13823 ( 54) link_NAG-ASN : bond 0.00836 ( 30) link_NAG-ASN : angle 4.42838 ( 90) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6730 Ramachandran restraints generated. 3365 Oldfield, 0 Emsley, 3365 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6730 Ramachandran restraints generated. 3365 Oldfield, 0 Emsley, 3365 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 294 residues out of total 2931 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 227 time to evaluate : 0.851 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 85 LEU cc_start: 0.9410 (OUTLIER) cc_final: 0.9100 (tm) REVERT: A 298 MET cc_start: 0.7943 (tmm) cc_final: 0.7530 (tmm) REVERT: A 316 MET cc_start: 0.8385 (mmm) cc_final: 0.7815 (tpt) REVERT: A 454 TYR cc_start: 0.8576 (m-80) cc_final: 0.8323 (m-80) REVERT: A 517 LEU cc_start: 0.8917 (OUTLIER) cc_final: 0.8609 (mm) REVERT: A 565 MET cc_start: 0.8568 (ptt) cc_final: 0.8359 (ptt) REVERT: A 612 PHE cc_start: 0.8331 (p90) cc_final: 0.7775 (p90) REVERT: A 691 MET cc_start: 0.8696 (ttp) cc_final: 0.8359 (ptm) REVERT: A 714 GLN cc_start: 0.7795 (tp-100) cc_final: 0.7503 (tp-100) REVERT: A 738 GLU cc_start: 0.7878 (mp0) cc_final: 0.7400 (mp0) REVERT: A 770 MET cc_start: 0.8709 (tpp) cc_final: 0.7921 (tpp) REVERT: A 824 PHE cc_start: 0.8306 (m-80) cc_final: 0.7729 (m-80) REVERT: B 55 LEU cc_start: 0.9281 (OUTLIER) cc_final: 0.9014 (mm) REVERT: B 73 ASN cc_start: 0.7301 (OUTLIER) cc_final: 0.7082 (m110) REVERT: B 247 MET cc_start: 0.8540 (mmm) cc_final: 0.8235 (mtt) REVERT: B 651 TYR cc_start: 0.8743 (t80) cc_final: 0.8343 (t80) REVERT: B 680 ILE cc_start: 0.7775 (OUTLIER) cc_final: 0.7196 (tp) REVERT: B 719 LYS cc_start: 0.9009 (mttp) cc_final: 0.7862 (tppt) REVERT: B 793 MET cc_start: 0.8178 (mmp) cc_final: 0.7977 (mmt) REVERT: B 794 MET cc_start: 0.7209 (mmt) cc_final: 0.6955 (mmt) REVERT: C 248 MET cc_start: 0.8172 (mmm) cc_final: 0.7939 (mmm) REVERT: C 250 GLU cc_start: 0.7678 (OUTLIER) cc_final: 0.6929 (tp30) REVERT: C 413 MET cc_start: 0.7771 (ppp) cc_final: 0.6850 (ppp) REVERT: C 454 TYR cc_start: 0.8211 (m-80) cc_final: 0.7987 (m-80) REVERT: C 463 CYS cc_start: 0.9020 (m) cc_final: 0.8612 (p) REVERT: C 484 GLU cc_start: 0.8192 (mp0) cc_final: 0.7823 (tp30) REVERT: C 501 MET cc_start: 0.8699 (mpt) cc_final: 0.8487 (mmt) REVERT: C 534 MET cc_start: 0.6907 (mtp) cc_final: 0.6635 (mtp) REVERT: C 556 LEU cc_start: 0.8491 (mm) cc_final: 0.8111 (mt) REVERT: C 619 LEU cc_start: 0.9580 (tp) cc_final: 0.9243 (tt) REVERT: C 679 LYS cc_start: 0.9391 (ptmm) cc_final: 0.8952 (ptpp) REVERT: C 737 MET cc_start: 0.7106 (ppp) cc_final: 0.6654 (ppp) REVERT: C 764 TYR cc_start: 0.6425 (m-10) cc_final: 0.6221 (m-80) REVERT: D 606 PHE cc_start: 0.8494 (OUTLIER) cc_final: 0.8210 (t80) REVERT: D 620 MET cc_start: 0.8648 (ttm) cc_final: 0.8417 (ttm) REVERT: D 691 MET cc_start: 0.8748 (tmm) cc_final: 0.8005 (tmm) REVERT: D 722 GLU cc_start: 0.9554 (mt-10) cc_final: 0.9133 (mp0) REVERT: D 737 MET cc_start: 0.8188 (ppp) cc_final: 0.7913 (ppp) REVERT: D 793 MET cc_start: 0.8753 (tpp) cc_final: 0.8362 (ppp) REVERT: D 794 MET cc_start: 0.6741 (tmm) cc_final: 0.5934 (ppp) REVERT: D 861 MET cc_start: 0.6092 (mtt) cc_final: 0.5776 (mmm) outliers start: 67 outliers final: 39 residues processed: 279 average time/residue: 0.1362 time to fit residues: 64.5407 Evaluate side-chains 261 residues out of total 2931 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 215 time to evaluate : 1.003 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 85 LEU Chi-restraints excluded: chain A residue 172 VAL Chi-restraints excluded: chain A residue 391 VAL Chi-restraints excluded: chain A residue 446 PHE Chi-restraints excluded: chain A residue 480 ILE Chi-restraints excluded: chain A residue 517 LEU Chi-restraints excluded: chain A residue 646 ILE Chi-restraints excluded: chain A residue 736 LEU Chi-restraints excluded: chain A residue 815 LEU Chi-restraints excluded: chain A residue 827 LEU Chi-restraints excluded: chain A residue 843 LEU Chi-restraints excluded: chain B residue 45 VAL Chi-restraints excluded: chain B residue 50 MET Chi-restraints excluded: chain B residue 55 LEU Chi-restraints excluded: chain B residue 73 ASN Chi-restraints excluded: chain B residue 140 ASP Chi-restraints excluded: chain B residue 149 LEU Chi-restraints excluded: chain B residue 156 LEU Chi-restraints excluded: chain B residue 160 ILE Chi-restraints excluded: chain B residue 183 ILE Chi-restraints excluded: chain B residue 189 ILE Chi-restraints excluded: chain B residue 195 TYR Chi-restraints excluded: chain B residue 201 ILE Chi-restraints excluded: chain B residue 376 THR Chi-restraints excluded: chain B residue 391 VAL Chi-restraints excluded: chain B residue 477 THR Chi-restraints excluded: chain B residue 680 ILE Chi-restraints excluded: chain B residue 682 TYR Chi-restraints excluded: chain B residue 811 GLU Chi-restraints excluded: chain B residue 827 LEU Chi-restraints excluded: chain C residue 156 LEU Chi-restraints excluded: chain C residue 195 TYR Chi-restraints excluded: chain C residue 250 GLU Chi-restraints excluded: chain C residue 301 LEU Chi-restraints excluded: chain C residue 375 ILE Chi-restraints excluded: chain C residue 411 LEU Chi-restraints excluded: chain C residue 701 THR Chi-restraints excluded: chain D residue 327 VAL Chi-restraints excluded: chain D residue 391 VAL Chi-restraints excluded: chain D residue 453 LEU Chi-restraints excluded: chain D residue 569 LEU Chi-restraints excluded: chain D residue 606 PHE Chi-restraints excluded: chain D residue 647 ILE Chi-restraints excluded: chain D residue 659 LEU Chi-restraints excluded: chain D residue 674 LEU Chi-restraints excluded: chain D residue 713 ARG Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 336 random chunks: chunk 283 optimal weight: 9.9990 chunk 164 optimal weight: 5.9990 chunk 145 optimal weight: 2.9990 chunk 138 optimal weight: 6.9990 chunk 17 optimal weight: 1.9990 chunk 250 optimal weight: 30.0000 chunk 275 optimal weight: 0.9980 chunk 150 optimal weight: 10.0000 chunk 87 optimal weight: 0.9980 chunk 328 optimal weight: 4.9990 chunk 144 optimal weight: 2.9990 overall best weight: 1.9986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 84 ASN ** A 129 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 131 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 253 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 81 GLN ** B 131 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 253 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 286 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 137 GLN C 232 HIS ** D 622 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3942 r_free = 0.3942 target = 0.101945 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3325 r_free = 0.3325 target = 0.070858 restraints weight = 222181.372| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3314 r_free = 0.3314 target = 0.071308 restraints weight = 92835.832| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3332 r_free = 0.3332 target = 0.072349 restraints weight = 66591.323| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3338 r_free = 0.3338 target = 0.072363 restraints weight = 53855.454| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3350 r_free = 0.3350 target = 0.073004 restraints weight = 47768.415| |-----------------------------------------------------------------------------| r_work (final): 0.3343 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3340 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3340 r_free = 0.3340 target_work(ls_wunit_k1) = 0.071 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3340 r_free = 0.3340 target_work(ls_wunit_k1) = 0.071 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| r_final: 0.3340 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8021 moved from start: 0.4098 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 28189 Z= 0.173 Angle : 0.921 14.469 38261 Z= 0.432 Chirality : 0.050 0.531 4412 Planarity : 0.005 0.134 4753 Dihedral : 13.094 99.139 4838 Min Nonbonded Distance : 2.359 Molprobity Statistics. All-atom Clashscore : 14.86 Ramachandran Plot: Outliers : 0.48 % Allowed : 14.40 % Favored : 85.12 % Rotamer: Outliers : 2.21 % Allowed : 15.06 % Favored : 82.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.52 % Cis-general : 0.00 % Twisted Proline : 5.30 % Twisted General : 0.49 % 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 aren not related in a simple way. whole: -2.70 (0.14), residues: 3365 helix: -0.03 (0.13), residues: 1480 sheet: -4.01 (0.24), residues: 325 loop : -3.13 (0.15), residues: 1560 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D 713 TYR 0.015 0.002 TYR A 462 PHE 0.057 0.002 PHE B 643 TRP 0.028 0.002 TRP B 589 HIS 0.008 0.001 HIS D 253 Details of bonding type rmsd covalent geometry : bond 0.00383 (28123) covalent geometry : angle 0.88283 (38071) SS BOND : bond 0.00493 ( 8) SS BOND : angle 1.13159 ( 16) hydrogen bonds : bond 0.03608 ( 945) hydrogen bonds : angle 4.95211 ( 2756) link_ALPHA1-3 : bond 0.02094 ( 5) link_ALPHA1-3 : angle 3.23195 ( 15) link_ALPHA1-6 : bond 0.01537 ( 5) link_ALPHA1-6 : angle 2.64915 ( 15) link_BETA1-4 : bond 0.01041 ( 18) link_BETA1-4 : angle 4.11711 ( 54) link_NAG-ASN : bond 0.00775 ( 30) link_NAG-ASN : angle 4.23820 ( 90) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6730 Ramachandran restraints generated. 3365 Oldfield, 0 Emsley, 3365 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6730 Ramachandran restraints generated. 3365 Oldfield, 0 Emsley, 3365 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 294 residues out of total 2931 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 233 time to evaluate : 0.749 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 85 LEU cc_start: 0.9429 (OUTLIER) cc_final: 0.9043 (tm) REVERT: A 264 LEU cc_start: 0.8350 (tt) cc_final: 0.8058 (tt) REVERT: A 298 MET cc_start: 0.8078 (tmm) cc_final: 0.7620 (tmm) REVERT: A 316 MET cc_start: 0.8384 (mmm) cc_final: 0.7701 (tpt) REVERT: A 437 THR cc_start: 0.8197 (t) cc_final: 0.7942 (m) REVERT: A 454 TYR cc_start: 0.8642 (m-80) cc_final: 0.8354 (m-80) REVERT: A 517 LEU cc_start: 0.9024 (OUTLIER) cc_final: 0.8726 (mm) REVERT: A 612 PHE cc_start: 0.8494 (OUTLIER) cc_final: 0.7959 (p90) REVERT: A 714 GLN cc_start: 0.7708 (tp-100) cc_final: 0.7488 (tp-100) REVERT: A 738 GLU cc_start: 0.8149 (mp0) cc_final: 0.7834 (mp0) REVERT: A 770 MET cc_start: 0.8662 (tpp) cc_final: 0.7697 (tpp) REVERT: A 824 PHE cc_start: 0.8339 (m-80) cc_final: 0.7787 (m-80) REVERT: B 55 LEU cc_start: 0.9308 (OUTLIER) cc_final: 0.9009 (mm) REVERT: B 73 ASN cc_start: 0.7445 (OUTLIER) cc_final: 0.7238 (m110) REVERT: B 247 MET cc_start: 0.8652 (mmm) cc_final: 0.8396 (mtt) REVERT: B 360 MET cc_start: 0.8113 (tpt) cc_final: 0.7570 (tpt) REVERT: B 589 TRP cc_start: 0.6375 (OUTLIER) cc_final: 0.5969 (m100) REVERT: B 651 TYR cc_start: 0.8784 (t80) cc_final: 0.8379 (t80) REVERT: B 680 ILE cc_start: 0.7813 (OUTLIER) cc_final: 0.7199 (tp) REVERT: B 719 LYS cc_start: 0.8974 (mttp) cc_final: 0.7835 (tppt) REVERT: B 794 MET cc_start: 0.7210 (mmt) cc_final: 0.6932 (mmt) REVERT: C 413 MET cc_start: 0.7923 (ppp) cc_final: 0.6973 (ppp) REVERT: C 428 LEU cc_start: 0.8351 (tt) cc_final: 0.8070 (tp) REVERT: C 441 GLU cc_start: 0.8344 (tp30) cc_final: 0.8027 (mp0) REVERT: C 454 TYR cc_start: 0.8254 (m-80) cc_final: 0.8030 (m-80) REVERT: C 463 CYS cc_start: 0.9120 (m) cc_final: 0.8563 (p) REVERT: C 484 GLU cc_start: 0.8210 (mp0) cc_final: 0.7802 (tp30) REVERT: C 501 MET cc_start: 0.8811 (mpt) cc_final: 0.8274 (mmm) REVERT: C 534 MET cc_start: 0.6737 (mtp) cc_final: 0.6459 (mtp) REVERT: C 556 LEU cc_start: 0.8530 (mm) cc_final: 0.8176 (mp) REVERT: C 559 LEU cc_start: 0.9246 (mt) cc_final: 0.9029 (tp) REVERT: C 619 LEU cc_start: 0.9572 (tp) cc_final: 0.9324 (tt) REVERT: C 627 MET cc_start: 0.6997 (mmt) cc_final: 0.6018 (mmm) REVERT: C 679 LYS cc_start: 0.9378 (ptmm) cc_final: 0.8906 (ptpp) REVERT: C 743 GLU cc_start: 0.8616 (mt-10) cc_final: 0.8396 (mt-10) REVERT: C 764 TYR cc_start: 0.6404 (m-10) cc_final: 0.6185 (m-80) REVERT: C 815 LEU cc_start: 0.8485 (mt) cc_final: 0.7930 (mt) REVERT: D 584 PHE cc_start: 0.8443 (t80) cc_final: 0.7661 (t80) REVERT: D 606 PHE cc_start: 0.8605 (OUTLIER) cc_final: 0.8310 (t80) REVERT: D 625 GLU cc_start: 0.7977 (mm-30) cc_final: 0.7743 (mp0) REVERT: D 691 MET cc_start: 0.8769 (tmm) cc_final: 0.8033 (tmm) REVERT: D 722 GLU cc_start: 0.9568 (mt-10) cc_final: 0.9093 (mp0) REVERT: D 737 MET cc_start: 0.8413 (ppp) cc_final: 0.8128 (ppp) REVERT: D 793 MET cc_start: 0.8838 (tpp) cc_final: 0.8394 (ppp) REVERT: D 794 MET cc_start: 0.6766 (tmm) cc_final: 0.6088 (ppp) REVERT: D 861 MET cc_start: 0.5927 (mtt) cc_final: 0.5716 (mmm) outliers start: 61 outliers final: 39 residues processed: 280 average time/residue: 0.1304 time to fit residues: 62.2923 Evaluate side-chains 269 residues out of total 2931 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 222 time to evaluate : 0.868 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 50 MET Chi-restraints excluded: chain A residue 85 LEU Chi-restraints excluded: chain A residue 179 SER Chi-restraints excluded: chain A residue 375 ILE Chi-restraints excluded: chain A residue 391 VAL Chi-restraints excluded: chain A residue 446 PHE Chi-restraints excluded: chain A residue 480 ILE Chi-restraints excluded: chain A residue 517 LEU Chi-restraints excluded: chain A residue 612 PHE Chi-restraints excluded: chain A residue 815 LEU Chi-restraints excluded: chain A residue 843 LEU Chi-restraints excluded: chain B residue 45 VAL Chi-restraints excluded: chain B residue 50 MET Chi-restraints excluded: chain B residue 55 LEU Chi-restraints excluded: chain B residue 73 ASN Chi-restraints excluded: chain B residue 140 ASP Chi-restraints excluded: chain B residue 156 LEU Chi-restraints excluded: chain B residue 160 ILE Chi-restraints excluded: chain B residue 183 ILE Chi-restraints excluded: chain B residue 195 TYR Chi-restraints excluded: chain B residue 201 ILE Chi-restraints excluded: chain B residue 376 THR Chi-restraints excluded: chain B residue 391 VAL Chi-restraints excluded: chain B residue 477 THR Chi-restraints excluded: chain B residue 589 TRP Chi-restraints excluded: chain B residue 680 ILE Chi-restraints excluded: chain B residue 682 TYR Chi-restraints excluded: chain B residue 694 PHE Chi-restraints excluded: chain B residue 811 GLU Chi-restraints excluded: chain B residue 827 LEU Chi-restraints excluded: chain B residue 861 MET Chi-restraints excluded: chain C residue 156 LEU Chi-restraints excluded: chain C residue 195 TYR Chi-restraints excluded: chain C residue 301 LEU Chi-restraints excluded: chain C residue 375 ILE Chi-restraints excluded: chain C residue 411 LEU Chi-restraints excluded: chain C residue 446 PHE Chi-restraints excluded: chain C residue 701 THR Chi-restraints excluded: chain C residue 758 LEU Chi-restraints excluded: chain D residue 327 VAL Chi-restraints excluded: chain D residue 391 VAL Chi-restraints excluded: chain D residue 453 LEU Chi-restraints excluded: chain D residue 606 PHE Chi-restraints excluded: chain D residue 647 ILE Chi-restraints excluded: chain D residue 659 LEU Chi-restraints excluded: chain D residue 674 LEU Chi-restraints excluded: chain D residue 713 ARG Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 336 random chunks: chunk 158 optimal weight: 6.9990 chunk 213 optimal weight: 0.0370 chunk 107 optimal weight: 0.9990 chunk 211 optimal weight: 7.9990 chunk 102 optimal weight: 1.9990 chunk 251 optimal weight: 20.0000 chunk 284 optimal weight: 0.9990 chunk 215 optimal weight: 0.0770 chunk 254 optimal weight: 0.9990 chunk 283 optimal weight: 10.0000 chunk 123 optimal weight: 1.9990 overall best weight: 0.6222 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 129 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 131 GLN ** A 253 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 131 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 253 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 286 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 654 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 784 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 622 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3946 r_free = 0.3946 target = 0.102590 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3358 r_free = 0.3358 target = 0.072762 restraints weight = 192177.336| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3305 r_free = 0.3305 target = 0.071401 restraints weight = 101759.132| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3335 r_free = 0.3335 target = 0.072963 restraints weight = 76691.887| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3334 r_free = 0.3334 target = 0.072769 restraints weight = 63059.089| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3342 r_free = 0.3342 target = 0.073173 restraints weight = 54168.328| |-----------------------------------------------------------------------------| r_work (final): 0.3312 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3316 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3316 r_free = 0.3316 target_work(ls_wunit_k1) = 0.071 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3316 r_free = 0.3316 target_work(ls_wunit_k1) = 0.071 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| r_final: 0.3316 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7975 moved from start: 0.4389 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 28189 Z= 0.143 Angle : 0.917 14.508 38261 Z= 0.427 Chirality : 0.049 0.482 4412 Planarity : 0.005 0.133 4753 Dihedral : 12.340 103.049 4838 Min Nonbonded Distance : 2.390 Molprobity Statistics. All-atom Clashscore : 13.64 Ramachandran Plot: Outliers : 0.42 % Allowed : 13.36 % Favored : 86.22 % Rotamer: Outliers : 1.90 % Allowed : 15.37 % Favored : 82.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.52 % Cis-general : 0.00 % Twisted Proline : 5.30 % Twisted General : 0.43 % 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 aren not related in a simple way. whole: -2.50 (0.14), residues: 3365 helix: 0.11 (0.13), residues: 1474 sheet: -3.75 (0.24), residues: 337 loop : -3.01 (0.15), residues: 1554 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 358 TYR 0.016 0.001 TYR C 252 PHE 0.050 0.002 PHE B 643 TRP 0.031 0.002 TRP C 706 HIS 0.007 0.001 HIS D 253 Details of bonding type rmsd covalent geometry : bond 0.00302 (28123) covalent geometry : angle 0.87998 (38071) SS BOND : bond 0.00199 ( 8) SS BOND : angle 1.20597 ( 16) hydrogen bonds : bond 0.03479 ( 945) hydrogen bonds : angle 4.80363 ( 2756) link_ALPHA1-3 : bond 0.02362 ( 5) link_ALPHA1-3 : angle 3.44094 ( 15) link_ALPHA1-6 : bond 0.01544 ( 5) link_ALPHA1-6 : angle 2.36397 ( 15) link_BETA1-4 : bond 0.01025 ( 18) link_BETA1-4 : angle 4.06674 ( 54) link_NAG-ASN : bond 0.00805 ( 30) link_NAG-ASN : angle 4.07760 ( 90) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6730 Ramachandran restraints generated. 3365 Oldfield, 0 Emsley, 3365 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6730 Ramachandran restraints generated. 3365 Oldfield, 0 Emsley, 3365 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 308 residues out of total 2931 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 256 time to evaluate : 1.047 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 85 LEU cc_start: 0.9304 (OUTLIER) cc_final: 0.8946 (tm) REVERT: A 298 MET cc_start: 0.8034 (tmm) cc_final: 0.7558 (tmm) REVERT: A 316 MET cc_start: 0.8339 (mmm) cc_final: 0.7468 (tpt) REVERT: A 454 TYR cc_start: 0.8461 (m-80) cc_final: 0.8218 (m-80) REVERT: A 517 LEU cc_start: 0.9002 (mm) cc_final: 0.8703 (mm) REVERT: A 612 PHE cc_start: 0.8411 (OUTLIER) cc_final: 0.7927 (p90) REVERT: A 625 GLU cc_start: 0.8594 (pt0) cc_final: 0.7908 (pm20) REVERT: A 714 GLN cc_start: 0.7768 (tp-100) cc_final: 0.7457 (tp-100) REVERT: A 718 VAL cc_start: 0.7085 (OUTLIER) cc_final: 0.6718 (m) REVERT: A 738 GLU cc_start: 0.8057 (mp0) cc_final: 0.7797 (mp0) REVERT: A 770 MET cc_start: 0.8449 (tpp) cc_final: 0.7483 (tpp) REVERT: A 867 MET cc_start: 0.5499 (ttp) cc_final: 0.5127 (tpt) REVERT: B 55 LEU cc_start: 0.9301 (OUTLIER) cc_final: 0.9009 (mm) REVERT: B 73 ASN cc_start: 0.7467 (OUTLIER) cc_final: 0.7256 (m110) REVERT: B 245 MET cc_start: 0.8850 (tpp) cc_final: 0.8610 (mmt) REVERT: B 254 TYR cc_start: 0.8623 (m-80) cc_final: 0.8386 (m-80) REVERT: B 360 MET cc_start: 0.7936 (tpt) cc_final: 0.7668 (tpt) REVERT: B 589 TRP cc_start: 0.6302 (OUTLIER) cc_final: 0.5900 (m100) REVERT: B 651 TYR cc_start: 0.8646 (t80) cc_final: 0.8196 (t80) REVERT: B 680 ILE cc_start: 0.7815 (OUTLIER) cc_final: 0.7238 (tp) REVERT: B 694 PHE cc_start: 0.7711 (OUTLIER) cc_final: 0.5932 (m-80) REVERT: B 702 TYR cc_start: 0.8054 (OUTLIER) cc_final: 0.7811 (t80) REVERT: B 719 LYS cc_start: 0.8990 (mttp) cc_final: 0.8704 (mmtt) REVERT: B 793 MET cc_start: 0.8002 (mmp) cc_final: 0.7775 (mmt) REVERT: B 794 MET cc_start: 0.7103 (mmt) cc_final: 0.6796 (mmt) REVERT: B 867 MET cc_start: 0.6116 (tmm) cc_final: 0.5092 (mmp) REVERT: C 250 GLU cc_start: 0.7595 (OUTLIER) cc_final: 0.7087 (tp30) REVERT: C 323 MET cc_start: 0.9018 (mmm) cc_final: 0.8811 (tpp) REVERT: C 413 MET cc_start: 0.7912 (ppp) cc_final: 0.6952 (ppp) REVERT: C 428 LEU cc_start: 0.8090 (tt) cc_final: 0.7771 (tp) REVERT: C 454 TYR cc_start: 0.8175 (m-80) cc_final: 0.7970 (m-80) REVERT: C 463 CYS cc_start: 0.9061 (m) cc_final: 0.8542 (m) REVERT: C 484 GLU cc_start: 0.8115 (mp0) cc_final: 0.7747 (tp30) REVERT: C 501 MET cc_start: 0.8820 (mpt) cc_final: 0.8319 (mmm) REVERT: C 534 MET cc_start: 0.6918 (mtp) cc_final: 0.6717 (mtp) REVERT: C 556 LEU cc_start: 0.8426 (mm) cc_final: 0.8074 (mp) REVERT: C 619 LEU cc_start: 0.9537 (tp) cc_final: 0.9304 (tt) REVERT: C 679 LYS cc_start: 0.9305 (ptmm) cc_final: 0.8886 (ptpp) REVERT: C 737 MET cc_start: 0.7053 (ppp) cc_final: 0.6820 (ppp) REVERT: C 743 GLU cc_start: 0.8609 (mt-10) cc_final: 0.8400 (mt-10) REVERT: C 815 LEU cc_start: 0.8428 (mt) cc_final: 0.7802 (mt) REVERT: D 625 GLU cc_start: 0.7996 (mm-30) cc_final: 0.7739 (mp0) REVERT: D 669 ASP cc_start: 0.7689 (p0) cc_final: 0.7235 (t0) REVERT: D 691 MET cc_start: 0.8742 (tmm) cc_final: 0.7962 (tmm) REVERT: D 705 MET cc_start: 0.8138 (pmm) cc_final: 0.7806 (pmm) REVERT: D 722 GLU cc_start: 0.9498 (mt-10) cc_final: 0.9028 (mp0) REVERT: D 793 MET cc_start: 0.8728 (tpp) cc_final: 0.8285 (ppp) REVERT: D 794 MET cc_start: 0.6687 (tmm) cc_final: 0.6006 (ppp) REVERT: D 861 MET cc_start: 0.6090 (mtt) cc_final: 0.5685 (mmm) outliers start: 52 outliers final: 32 residues processed: 294 average time/residue: 0.1393 time to fit residues: 69.7341 Evaluate side-chains 278 residues out of total 2931 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 236 time to evaluate : 0.750 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 50 MET Chi-restraints excluded: chain A residue 85 LEU Chi-restraints excluded: chain A residue 172 VAL Chi-restraints excluded: chain A residue 179 SER Chi-restraints excluded: chain A residue 375 ILE Chi-restraints excluded: chain A residue 391 VAL Chi-restraints excluded: chain A residue 446 PHE Chi-restraints excluded: chain A residue 480 ILE Chi-restraints excluded: chain A residue 606 PHE Chi-restraints excluded: chain A residue 612 PHE Chi-restraints excluded: chain A residue 677 GLN Chi-restraints excluded: chain A residue 718 VAL Chi-restraints excluded: chain A residue 736 LEU Chi-restraints excluded: chain A residue 827 LEU Chi-restraints excluded: chain A residue 843 LEU Chi-restraints excluded: chain B residue 45 VAL Chi-restraints excluded: chain B residue 50 MET Chi-restraints excluded: chain B residue 55 LEU Chi-restraints excluded: chain B residue 73 ASN Chi-restraints excluded: chain B residue 140 ASP Chi-restraints excluded: chain B residue 183 ILE Chi-restraints excluded: chain B residue 195 TYR Chi-restraints excluded: chain B residue 201 ILE Chi-restraints excluded: chain B residue 477 THR Chi-restraints excluded: chain B residue 589 TRP Chi-restraints excluded: chain B residue 680 ILE Chi-restraints excluded: chain B residue 682 TYR Chi-restraints excluded: chain B residue 694 PHE Chi-restraints excluded: chain B residue 702 TYR Chi-restraints excluded: chain B residue 811 GLU Chi-restraints excluded: chain C residue 156 LEU Chi-restraints excluded: chain C residue 195 TYR Chi-restraints excluded: chain C residue 250 GLU Chi-restraints excluded: chain C residue 301 LEU Chi-restraints excluded: chain C residue 411 LEU Chi-restraints excluded: chain C residue 758 LEU Chi-restraints excluded: chain D residue 327 VAL Chi-restraints excluded: chain D residue 391 VAL Chi-restraints excluded: chain D residue 453 LEU Chi-restraints excluded: chain D residue 659 LEU Chi-restraints excluded: chain D residue 674 LEU Chi-restraints excluded: chain D residue 713 ARG Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 336 random chunks: chunk 271 optimal weight: 1.9990 chunk 242 optimal weight: 0.7980 chunk 257 optimal weight: 0.2980 chunk 98 optimal weight: 5.9990 chunk 255 optimal weight: 5.9990 chunk 65 optimal weight: 30.0000 chunk 121 optimal weight: 0.0470 chunk 181 optimal weight: 3.9990 chunk 320 optimal weight: 9.9990 chunk 177 optimal weight: 0.5980 chunk 202 optimal weight: 0.5980 overall best weight: 0.4678 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 84 ASN ** A 129 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 253 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 131 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 253 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 286 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 784 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 129 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 196 ASN D 491 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3964 r_free = 0.3964 target = 0.103532 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3340 r_free = 0.3340 target = 0.071300 restraints weight = 206608.626| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3323 r_free = 0.3323 target = 0.072222 restraints weight = 103415.199| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3348 r_free = 0.3348 target = 0.073305 restraints weight = 64863.508| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3344 r_free = 0.3344 target = 0.072991 restraints weight = 58185.883| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3362 r_free = 0.3362 target = 0.073865 restraints weight = 50993.627| |-----------------------------------------------------------------------------| r_work (final): 0.3330 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3332 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3332 r_free = 0.3332 target_work(ls_wunit_k1) = 0.072 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3332 r_free = 0.3332 target_work(ls_wunit_k1) = 0.072 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| r_final: 0.3332 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7959 moved from start: 0.4654 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 28189 Z= 0.139 Angle : 0.905 14.102 38261 Z= 0.419 Chirality : 0.049 0.469 4412 Planarity : 0.005 0.125 4753 Dihedral : 11.758 106.780 4838 Min Nonbonded Distance : 2.377 Molprobity Statistics. All-atom Clashscore : 13.11 Ramachandran Plot: Outliers : 0.45 % Allowed : 13.12 % Favored : 86.43 % Rotamer: Outliers : 2.11 % Allowed : 15.40 % Favored : 82.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.52 % Cis-general : 0.00 % Twisted Proline : 4.55 % Twisted General : 0.43 % 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 aren not related in a simple way. whole: -2.37 (0.14), residues: 3365 helix: 0.19 (0.13), residues: 1482 sheet: -3.57 (0.25), residues: 334 loop : -2.96 (0.15), residues: 1549 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D 713 TYR 0.019 0.001 TYR D 764 PHE 0.065 0.002 PHE B 612 TRP 0.027 0.002 TRP B 589 HIS 0.007 0.001 HIS D 253 Details of bonding type rmsd covalent geometry : bond 0.00291 (28123) covalent geometry : angle 0.86818 (38071) SS BOND : bond 0.00176 ( 8) SS BOND : angle 1.19462 ( 16) hydrogen bonds : bond 0.03477 ( 945) hydrogen bonds : angle 4.73599 ( 2756) link_ALPHA1-3 : bond 0.02454 ( 5) link_ALPHA1-3 : angle 3.62457 ( 15) link_ALPHA1-6 : bond 0.01428 ( 5) link_ALPHA1-6 : angle 2.36544 ( 15) link_BETA1-4 : bond 0.01032 ( 18) link_BETA1-4 : angle 3.99928 ( 54) link_NAG-ASN : bond 0.00788 ( 30) link_NAG-ASN : angle 4.00126 ( 90) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6730 Ramachandran restraints generated. 3365 Oldfield, 0 Emsley, 3365 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6730 Ramachandran restraints generated. 3365 Oldfield, 0 Emsley, 3365 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 315 residues out of total 2931 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 257 time to evaluate : 0.916 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 85 LEU cc_start: 0.9308 (OUTLIER) cc_final: 0.8872 (tm) REVERT: A 171 THR cc_start: 0.8083 (m) cc_final: 0.7838 (t) REVERT: A 298 MET cc_start: 0.8030 (tmm) cc_final: 0.7561 (tmm) REVERT: A 316 MET cc_start: 0.8116 (mmm) cc_final: 0.7712 (tpt) REVERT: A 454 TYR cc_start: 0.8484 (m-80) cc_final: 0.8229 (m-80) REVERT: A 517 LEU cc_start: 0.8867 (mm) cc_final: 0.8580 (mm) REVERT: A 612 PHE cc_start: 0.8447 (OUTLIER) cc_final: 0.7992 (p90) REVERT: A 625 GLU cc_start: 0.8443 (pt0) cc_final: 0.7945 (pm20) REVERT: A 627 MET cc_start: 0.8678 (mmp) cc_final: 0.7799 (tpt) REVERT: A 714 GLN cc_start: 0.7826 (tp-100) cc_final: 0.7603 (tp-100) REVERT: A 770 MET cc_start: 0.8165 (tpp) cc_final: 0.7663 (tpp) REVERT: A 867 MET cc_start: 0.5737 (ttp) cc_final: 0.5232 (tpt) REVERT: B 55 LEU cc_start: 0.9338 (OUTLIER) cc_final: 0.9040 (mm) REVERT: B 73 ASN cc_start: 0.7522 (OUTLIER) cc_final: 0.7248 (m110) REVERT: B 245 MET cc_start: 0.8865 (tpp) cc_final: 0.8617 (mmt) REVERT: B 254 TYR cc_start: 0.8670 (m-80) cc_final: 0.8400 (m-80) REVERT: B 340 MET cc_start: 0.5595 (mmm) cc_final: 0.5086 (mmm) REVERT: B 589 TRP cc_start: 0.6196 (OUTLIER) cc_final: 0.5846 (m100) REVERT: B 608 LEU cc_start: 0.9007 (pt) cc_final: 0.8720 (mm) REVERT: B 651 TYR cc_start: 0.8658 (t80) cc_final: 0.8139 (t80) REVERT: B 680 ILE cc_start: 0.7835 (OUTLIER) cc_final: 0.7274 (tp) REVERT: B 694 PHE cc_start: 0.7832 (OUTLIER) cc_final: 0.5711 (m-80) REVERT: B 719 LYS cc_start: 0.8996 (mttp) cc_final: 0.7876 (tppt) REVERT: B 793 MET cc_start: 0.8098 (mmp) cc_final: 0.7870 (mmt) REVERT: B 794 MET cc_start: 0.7218 (mmt) cc_final: 0.6882 (mmt) REVERT: B 867 MET cc_start: 0.6107 (tmm) cc_final: 0.5184 (mmp) REVERT: C 171 THR cc_start: 0.8086 (p) cc_final: 0.7846 (p) REVERT: C 248 MET cc_start: 0.7957 (mmm) cc_final: 0.7755 (tpp) REVERT: C 413 MET cc_start: 0.7592 (ppp) cc_final: 0.6701 (ppp) REVERT: C 428 LEU cc_start: 0.7894 (tt) cc_final: 0.7566 (tp) REVERT: C 463 CYS cc_start: 0.9074 (m) cc_final: 0.8664 (m) REVERT: C 484 GLU cc_start: 0.8113 (mp0) cc_final: 0.7771 (tp30) REVERT: C 501 MET cc_start: 0.8812 (mpt) cc_final: 0.8300 (mmm) REVERT: C 534 MET cc_start: 0.6965 (mtp) cc_final: 0.6691 (mtp) REVERT: C 556 LEU cc_start: 0.8338 (mm) cc_final: 0.8086 (mp) REVERT: C 619 LEU cc_start: 0.9558 (tp) cc_final: 0.9303 (tt) REVERT: C 679 LYS cc_start: 0.9282 (ptmm) cc_final: 0.9069 (pttp) REVERT: C 737 MET cc_start: 0.7155 (ppp) cc_final: 0.6643 (ppp) REVERT: C 743 GLU cc_start: 0.8647 (mt-10) cc_final: 0.8424 (mt-10) REVERT: C 815 LEU cc_start: 0.8422 (mt) cc_final: 0.7802 (mt) REVERT: D 272 SER cc_start: 0.9378 (m) cc_final: 0.9115 (p) REVERT: D 277 THR cc_start: 0.9743 (m) cc_final: 0.9328 (p) REVERT: D 609 LEU cc_start: 0.8240 (tp) cc_final: 0.7854 (mp) REVERT: D 669 ASP cc_start: 0.7725 (p0) cc_final: 0.7448 (t0) REVERT: D 691 MET cc_start: 0.8728 (tmm) cc_final: 0.7947 (tmm) REVERT: D 705 MET cc_start: 0.8094 (pmm) cc_final: 0.7836 (pmm) REVERT: D 722 GLU cc_start: 0.9493 (mt-10) cc_final: 0.9023 (mp0) REVERT: D 737 MET cc_start: 0.8302 (ppp) cc_final: 0.7571 (ppp) REVERT: D 793 MET cc_start: 0.8693 (tpp) cc_final: 0.8264 (ppp) REVERT: D 794 MET cc_start: 0.6662 (tmm) cc_final: 0.5898 (ppp) REVERT: D 861 MET cc_start: 0.6087 (mtt) cc_final: 0.5665 (mmm) outliers start: 58 outliers final: 36 residues processed: 298 average time/residue: 0.1337 time to fit residues: 68.3084 Evaluate side-chains 283 residues out of total 2931 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 240 time to evaluate : 0.717 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 50 MET Chi-restraints excluded: chain A residue 85 LEU Chi-restraints excluded: chain A residue 172 VAL Chi-restraints excluded: chain A residue 179 SER Chi-restraints excluded: chain A residue 375 ILE Chi-restraints excluded: chain A residue 391 VAL Chi-restraints excluded: chain A residue 446 PHE Chi-restraints excluded: chain A residue 480 ILE Chi-restraints excluded: chain A residue 612 PHE Chi-restraints excluded: chain A residue 677 GLN Chi-restraints excluded: chain A residue 686 GLU Chi-restraints excluded: chain A residue 736 LEU Chi-restraints excluded: chain A residue 794 MET Chi-restraints excluded: chain A residue 827 LEU Chi-restraints excluded: chain A residue 843 LEU Chi-restraints excluded: chain B residue 45 VAL Chi-restraints excluded: chain B residue 50 MET Chi-restraints excluded: chain B residue 55 LEU Chi-restraints excluded: chain B residue 73 ASN Chi-restraints excluded: chain B residue 140 ASP Chi-restraints excluded: chain B residue 183 ILE Chi-restraints excluded: chain B residue 195 TYR Chi-restraints excluded: chain B residue 201 ILE Chi-restraints excluded: chain B residue 376 THR Chi-restraints excluded: chain B residue 477 THR Chi-restraints excluded: chain B residue 589 TRP Chi-restraints excluded: chain B residue 639 ILE Chi-restraints excluded: chain B residue 680 ILE Chi-restraints excluded: chain B residue 682 TYR Chi-restraints excluded: chain B residue 694 PHE Chi-restraints excluded: chain B residue 811 GLU Chi-restraints excluded: chain C residue 195 TYR Chi-restraints excluded: chain C residue 260 ASP Chi-restraints excluded: chain C residue 301 LEU Chi-restraints excluded: chain C residue 411 LEU Chi-restraints excluded: chain C residue 690 THR Chi-restraints excluded: chain C residue 758 LEU Chi-restraints excluded: chain D residue 327 VAL Chi-restraints excluded: chain D residue 391 VAL Chi-restraints excluded: chain D residue 453 LEU Chi-restraints excluded: chain D residue 659 LEU Chi-restraints excluded: chain D residue 674 LEU Chi-restraints excluded: chain D residue 713 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 336 random chunks: chunk 191 optimal weight: 0.9980 chunk 156 optimal weight: 0.0470 chunk 243 optimal weight: 6.9990 chunk 71 optimal weight: 2.9990 chunk 40 optimal weight: 6.9990 chunk 165 optimal weight: 4.9990 chunk 14 optimal weight: 4.9990 chunk 276 optimal weight: 2.9990 chunk 309 optimal weight: 1.9990 chunk 105 optimal weight: 0.6980 chunk 60 optimal weight: 0.9980 overall best weight: 0.9480 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 84 ASN ** A 129 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 253 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 131 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 253 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 286 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 137 GLN C 196 ASN D 491 GLN ** D 621 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3961 r_free = 0.3961 target = 0.103390 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3337 r_free = 0.3337 target = 0.071943 restraints weight = 158304.596| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3325 r_free = 0.3325 target = 0.072047 restraints weight = 85680.476| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3334 r_free = 0.3334 target = 0.072573 restraints weight = 61227.426| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3348 r_free = 0.3348 target = 0.073133 restraints weight = 52730.069| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3350 r_free = 0.3350 target = 0.073293 restraints weight = 45925.053| |-----------------------------------------------------------------------------| r_work (final): 0.3323 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3319 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3319 r_free = 0.3319 target_work(ls_wunit_k1) = 0.071 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3319 r_free = 0.3319 target_work(ls_wunit_k1) = 0.071 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| r_final: 0.3319 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7969 moved from start: 0.4792 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.062 28189 Z= 0.146 Angle : 0.920 13.924 38261 Z= 0.425 Chirality : 0.049 0.453 4412 Planarity : 0.005 0.124 4753 Dihedral : 11.392 107.475 4838 Min Nonbonded Distance : 2.371 Molprobity Statistics. All-atom Clashscore : 13.57 Ramachandran Plot: Outliers : 0.39 % Allowed : 13.12 % Favored : 86.49 % Rotamer: Outliers : 1.73 % Allowed : 16.18 % Favored : 82.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.52 % Cis-general : 0.00 % Twisted Proline : 3.03 % Twisted General : 0.43 % 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 aren not related in a simple way. whole: -2.28 (0.15), residues: 3365 helix: 0.27 (0.13), residues: 1485 sheet: -3.58 (0.26), residues: 331 loop : -2.90 (0.15), residues: 1549 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D 713 TYR 0.024 0.001 TYR C 521 PHE 0.062 0.002 PHE B 643 TRP 0.027 0.002 TRP B 589 HIS 0.006 0.001 HIS D 253 Details of bonding type rmsd covalent geometry : bond 0.00320 (28123) covalent geometry : angle 0.88510 (38071) SS BOND : bond 0.00186 ( 8) SS BOND : angle 1.19211 ( 16) hydrogen bonds : bond 0.03387 ( 945) hydrogen bonds : angle 4.72304 ( 2756) link_ALPHA1-3 : bond 0.02510 ( 5) link_ALPHA1-3 : angle 3.69038 ( 15) link_ALPHA1-6 : bond 0.01367 ( 5) link_ALPHA1-6 : angle 2.35624 ( 15) link_BETA1-4 : bond 0.01028 ( 18) link_BETA1-4 : angle 4.00492 ( 54) link_NAG-ASN : bond 0.00763 ( 30) link_NAG-ASN : angle 3.96162 ( 90) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6730 Ramachandran restraints generated. 3365 Oldfield, 0 Emsley, 3365 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6730 Ramachandran restraints generated. 3365 Oldfield, 0 Emsley, 3365 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 291 residues out of total 2931 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 244 time to evaluate : 0.720 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 85 LEU cc_start: 0.9303 (OUTLIER) cc_final: 0.8886 (tm) REVERT: A 171 THR cc_start: 0.8213 (m) cc_final: 0.7964 (t) REVERT: A 247 MET cc_start: 0.7875 (ptp) cc_final: 0.7639 (ptp) REVERT: A 298 MET cc_start: 0.8083 (tmm) cc_final: 0.7591 (tmm) REVERT: A 316 MET cc_start: 0.8074 (mmm) cc_final: 0.7324 (tpt) REVERT: A 454 TYR cc_start: 0.8420 (m-80) cc_final: 0.8159 (m-80) REVERT: A 501 MET cc_start: 0.8612 (mmp) cc_final: 0.8402 (mmt) REVERT: A 517 LEU cc_start: 0.8933 (OUTLIER) cc_final: 0.8629 (mm) REVERT: A 612 PHE cc_start: 0.8459 (OUTLIER) cc_final: 0.7994 (p90) REVERT: A 770 MET cc_start: 0.8253 (tpp) cc_final: 0.7712 (tpp) REVERT: A 867 MET cc_start: 0.5568 (ttp) cc_final: 0.5233 (tpt) REVERT: B 55 LEU cc_start: 0.9314 (OUTLIER) cc_final: 0.9014 (mm) REVERT: B 73 ASN cc_start: 0.7473 (OUTLIER) cc_final: 0.7197 (m110) REVERT: B 589 TRP cc_start: 0.6228 (OUTLIER) cc_final: 0.5891 (m100) REVERT: B 608 LEU cc_start: 0.8910 (pt) cc_final: 0.8601 (mm) REVERT: B 651 TYR cc_start: 0.8669 (t80) cc_final: 0.8159 (t80) REVERT: B 680 ILE cc_start: 0.7831 (OUTLIER) cc_final: 0.7284 (tp) REVERT: B 694 PHE cc_start: 0.7879 (OUTLIER) cc_final: 0.6738 (m-80) REVERT: B 702 TYR cc_start: 0.7907 (OUTLIER) cc_final: 0.7571 (t80) REVERT: B 719 LYS cc_start: 0.8999 (mttp) cc_final: 0.7883 (tppt) REVERT: B 793 MET cc_start: 0.8120 (mmp) cc_final: 0.7873 (mmt) REVERT: B 867 MET cc_start: 0.6116 (tmm) cc_final: 0.5053 (mmp) REVERT: C 171 THR cc_start: 0.8209 (p) cc_final: 0.7993 (p) REVERT: C 413 MET cc_start: 0.7626 (ppp) cc_final: 0.6727 (ppp) REVERT: C 428 LEU cc_start: 0.7895 (tt) cc_final: 0.7562 (tp) REVERT: C 448 LYS cc_start: 0.8448 (mtmm) cc_final: 0.7796 (tptp) REVERT: C 463 CYS cc_start: 0.9017 (m) cc_final: 0.8431 (m) REVERT: C 484 GLU cc_start: 0.8161 (mp0) cc_final: 0.7823 (tp30) REVERT: C 501 MET cc_start: 0.8768 (mpt) cc_final: 0.8201 (mmm) REVERT: C 556 LEU cc_start: 0.8289 (mm) cc_final: 0.8087 (mp) REVERT: C 627 MET cc_start: 0.6439 (mmt) cc_final: 0.6223 (mmt) REVERT: C 679 LYS cc_start: 0.9293 (ptmm) cc_final: 0.9062 (ptpp) REVERT: C 737 MET cc_start: 0.7070 (ppp) cc_final: 0.6613 (ppp) REVERT: C 743 GLU cc_start: 0.8656 (mt-10) cc_final: 0.8441 (mt-10) REVERT: C 793 MET cc_start: 0.8921 (ppp) cc_final: 0.8641 (ppp) REVERT: C 815 LEU cc_start: 0.8429 (mt) cc_final: 0.7811 (mt) REVERT: D 272 SER cc_start: 0.9419 (m) cc_final: 0.9119 (p) REVERT: D 340 MET cc_start: 0.7332 (tpp) cc_final: 0.6949 (tmm) REVERT: D 669 ASP cc_start: 0.7689 (p0) cc_final: 0.7455 (t0) REVERT: D 691 MET cc_start: 0.8707 (tmm) cc_final: 0.7923 (tmm) REVERT: D 722 GLU cc_start: 0.9492 (mt-10) cc_final: 0.9008 (mp0) REVERT: D 726 GLN cc_start: 0.9282 (mt0) cc_final: 0.8919 (tm-30) REVERT: D 737 MET cc_start: 0.8345 (ppp) cc_final: 0.7676 (ppp) REVERT: D 793 MET cc_start: 0.8685 (tpp) cc_final: 0.8256 (ppp) REVERT: D 794 MET cc_start: 0.6708 (tmm) cc_final: 0.5949 (ppp) REVERT: D 861 MET cc_start: 0.6286 (mtt) cc_final: 0.5827 (mmm) outliers start: 47 outliers final: 36 residues processed: 277 average time/residue: 0.1333 time to fit residues: 63.0186 Evaluate side-chains 284 residues out of total 2931 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 239 time to evaluate : 0.868 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 50 MET Chi-restraints excluded: chain A residue 85 LEU Chi-restraints excluded: chain A residue 172 VAL Chi-restraints excluded: chain A residue 179 SER Chi-restraints excluded: chain A residue 375 ILE Chi-restraints excluded: chain A residue 391 VAL Chi-restraints excluded: chain A residue 446 PHE Chi-restraints excluded: chain A residue 480 ILE Chi-restraints excluded: chain A residue 517 LEU Chi-restraints excluded: chain A residue 612 PHE Chi-restraints excluded: chain A residue 686 GLU Chi-restraints excluded: chain A residue 736 LEU Chi-restraints excluded: chain A residue 794 MET Chi-restraints excluded: chain A residue 827 LEU Chi-restraints excluded: chain A residue 843 LEU Chi-restraints excluded: chain B residue 45 VAL Chi-restraints excluded: chain B residue 50 MET Chi-restraints excluded: chain B residue 55 LEU Chi-restraints excluded: chain B residue 73 ASN Chi-restraints excluded: chain B residue 140 ASP Chi-restraints excluded: chain B residue 149 LEU Chi-restraints excluded: chain B residue 183 ILE Chi-restraints excluded: chain B residue 195 TYR Chi-restraints excluded: chain B residue 201 ILE Chi-restraints excluded: chain B residue 376 THR Chi-restraints excluded: chain B residue 477 THR Chi-restraints excluded: chain B residue 589 TRP Chi-restraints excluded: chain B residue 680 ILE Chi-restraints excluded: chain B residue 682 TYR Chi-restraints excluded: chain B residue 694 PHE Chi-restraints excluded: chain B residue 702 TYR Chi-restraints excluded: chain B residue 811 GLU Chi-restraints excluded: chain B residue 861 MET Chi-restraints excluded: chain C residue 195 TYR Chi-restraints excluded: chain C residue 260 ASP Chi-restraints excluded: chain C residue 301 LEU Chi-restraints excluded: chain C residue 411 LEU Chi-restraints excluded: chain C residue 690 THR Chi-restraints excluded: chain C residue 758 LEU Chi-restraints excluded: chain D residue 327 VAL Chi-restraints excluded: chain D residue 391 VAL Chi-restraints excluded: chain D residue 453 LEU Chi-restraints excluded: chain D residue 659 LEU Chi-restraints excluded: chain D residue 674 LEU Chi-restraints excluded: chain D residue 713 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 336 random chunks: chunk 211 optimal weight: 5.9990 chunk 146 optimal weight: 4.9990 chunk 113 optimal weight: 2.9990 chunk 296 optimal weight: 7.9990 chunk 56 optimal weight: 6.9990 chunk 261 optimal weight: 0.3980 chunk 137 optimal weight: 6.9990 chunk 86 optimal weight: 2.9990 chunk 236 optimal weight: 2.9990 chunk 265 optimal weight: 0.7980 chunk 105 optimal weight: 2.9990 overall best weight: 2.0386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 84 ASN ** A 129 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 131 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 253 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 286 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 137 GLN D 196 ASN D 491 GLN ** D 622 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 786 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3941 r_free = 0.3941 target = 0.102247 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3310 r_free = 0.3310 target = 0.070732 restraints weight = 157031.517| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3288 r_free = 0.3288 target = 0.070450 restraints weight = 84680.944| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3300 r_free = 0.3300 target = 0.071114 restraints weight = 64025.765| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3313 r_free = 0.3313 target = 0.071652 restraints weight = 52809.386| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3318 r_free = 0.3318 target = 0.071882 restraints weight = 46141.332| |-----------------------------------------------------------------------------| r_work (final): 0.3296 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3292 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3292 r_free = 0.3292 target_work(ls_wunit_k1) = 0.070 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3292 r_free = 0.3292 target_work(ls_wunit_k1) = 0.070 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| r_final: 0.3292 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7999 moved from start: 0.4855 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.077 28189 Z= 0.176 Angle : 0.922 13.738 38261 Z= 0.429 Chirality : 0.049 0.467 4412 Planarity : 0.005 0.124 4753 Dihedral : 11.148 107.311 4838 Min Nonbonded Distance : 2.359 Molprobity Statistics. All-atom Clashscore : 14.08 Ramachandran Plot: Outliers : 0.36 % Allowed : 13.66 % Favored : 85.98 % Rotamer: Outliers : 2.01 % Allowed : 16.22 % Favored : 81.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.52 % Cis-general : 0.00 % Twisted Proline : 3.79 % Twisted General : 0.43 % 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 aren not related in a simple way. whole: -2.22 (0.15), residues: 3365 helix: 0.31 (0.13), residues: 1474 sheet: -3.58 (0.25), residues: 335 loop : -2.84 (0.16), residues: 1556 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D 713 TYR 0.021 0.001 TYR D 764 PHE 0.059 0.002 PHE B 643 TRP 0.027 0.002 TRP C 706 HIS 0.007 0.001 HIS D 253 Details of bonding type rmsd covalent geometry : bond 0.00397 (28123) covalent geometry : angle 0.88604 (38071) SS BOND : bond 0.00201 ( 8) SS BOND : angle 1.15556 ( 16) hydrogen bonds : bond 0.03434 ( 945) hydrogen bonds : angle 4.78701 ( 2756) link_ALPHA1-3 : bond 0.02447 ( 5) link_ALPHA1-3 : angle 3.71491 ( 15) link_ALPHA1-6 : bond 0.01366 ( 5) link_ALPHA1-6 : angle 2.38045 ( 15) link_BETA1-4 : bond 0.00986 ( 18) link_BETA1-4 : angle 4.01370 ( 54) link_NAG-ASN : bond 0.00728 ( 30) link_NAG-ASN : angle 3.97299 ( 90) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4477.54 seconds wall clock time: 78 minutes 27.69 seconds (4707.69 seconds total)