Starting phenix.real_space_refine on Mon May 26 01:01:22 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9b39_44132/05_2025/9b39_44132.cif Found real_map, /net/cci-nas-00/data/ceres_data/9b39_44132/05_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/9b39_44132/05_2025/9b39_44132.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9b39_44132/05_2025/9b39_44132.map" model { file = "/net/cci-nas-00/data/ceres_data/9b39_44132/05_2025/9b39_44132.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9b39_44132/05_2025/9b39_44132.cif" } resolution = 3.84 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.002 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): 0.08s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/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: 27.58, per 1000 atoms: 1.00 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: 7.75 Conformation dependent library (CDL) restraints added in 6.3 seconds 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: 2.76 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: 8.68 Time building geometry restraints manager: 8.88 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 874 or resid 1001 or resid 1002 through 1005)) selection = (chain 'B' and (resid 33 through 470 or resid 472 through 534 or resid 536 throu \ gh 874 or resid 1001 or resid 1002 through 1005)) selection = (chain 'C' and (resid 33 through 470 or resid 472 through 534 or resid 536 throu \ gh 874 or resid 1001 or resid 1002 through 1005)) selection = (chain 'D' and (resid 33 through 470 or resid 472 through 534 or resid 536 throu \ gh 874 or resid 1001 or resid 1002 through 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: 0.680 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 1.090 Check model and map are aligned: 0.200 Set scattering table: 0.250 Process input model: 74.160 Find NCS groups from input model: 1.730 Set up NCS constraints: 0.190 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: 0.010 Load rotamer database and sin/cos tables:2.560 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 80.890 ------------------------------------------------------------------------------- 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -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 TRP 0.052 0.005 TRP B 589 HIS 0.038 0.004 HIS D 253 PHE 0.049 0.004 PHE A 167 TYR 0.051 0.004 TYR D 195 ARG 0.021 0.001 ARG B 583 Details of bonding type rmsd link_NAG-ASN : bond 0.01384 ( 30) link_NAG-ASN : angle 6.81165 ( 90) 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_ALPHA1-3 : bond 0.01145 ( 5) link_ALPHA1-3 : angle 2.98150 ( 15) hydrogen bonds : bond 0.30041 ( 945) hydrogen bonds : angle 9.86480 ( 2756) SS BOND : bond 0.00342 ( 8) SS BOND : angle 1.66973 ( 16) covalent geometry : bond 0.00868 (28123) covalent geometry : angle 1.53549 (38071) *********************** 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 : 2.998 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: 0.3925 time to fit residues: 283.6569 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 : 3.196 ------------------------------------------------------------------------------- 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 283 optimal weight: 1.9990 chunk 254 optimal weight: 0.9990 chunk 141 optimal weight: 8.9990 chunk 86 optimal weight: 4.9990 chunk 171 optimal weight: 5.9990 chunk 136 optimal weight: 0.9980 chunk 263 optimal weight: 0.6980 chunk 101 optimal weight: 5.9990 chunk 160 optimal weight: 6.9990 chunk 196 optimal weight: 5.9990 chunk 305 optimal weight: 0.9980 overall best weight: 1.1384 ------------------------------------------------------------------------------- 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 747 GLN A 754 GLN B 34 HIS B 123 ASN ** 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 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: 37 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4066 r_free = 0.4066 target = 0.105629 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3533 r_free = 0.3533 target = 0.076316 restraints weight = 138132.680| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3498 r_free = 0.3498 target = 0.075980 restraints weight = 79417.710| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3506 r_free = 0.3506 target = 0.076418 restraints weight = 54156.752| |-----------------------------------------------------------------------------| r_work (final): 0.3523 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3524 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3524 r_free = 0.3524 target_work(ls_wunit_k1) = 0.077 | | occupancies: max = 1.00 min = 0.38 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3524 r_free = 0.3524 target_work(ls_wunit_k1) = 0.077 | | occupancies: max = 1.00 min = 0.01 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| r_final: 0.3524 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7987 moved from start: 0.2420 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= 0.183 Angle : 1.046 17.600 38261 Z= 0.501 Chirality : 0.054 0.526 4412 Planarity : 0.007 0.137 4753 Dihedral : 18.872 110.424 4840 Min Nonbonded Distance : 2.372 Molprobity Statistics. All-atom Clashscore : 14.77 Ramachandran Plot: Outliers : 0.98 % Allowed : 14.14 % Favored : 84.88 % Rotamer: Outliers : 1.56 % Allowed : 11.32 % Favored : 87.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.52 % Cis-general : 0.00 % Twisted Proline : 6.06 % Twisted General : 0.74 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.33 (0.12), residues: 3365 helix: -1.90 (0.11), residues: 1464 sheet: -4.39 (0.22), residues: 329 loop : -3.50 (0.14), residues: 1572 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.041 0.003 TRP B 589 HIS 0.012 0.001 HIS D 253 PHE 0.037 0.002 PHE B 643 TYR 0.023 0.002 TYR C 254 ARG 0.013 0.001 ARG D 68 Details of bonding type rmsd link_NAG-ASN : bond 0.00856 ( 30) link_NAG-ASN : angle 4.95049 ( 90) link_ALPHA1-6 : bond 0.01002 ( 5) link_ALPHA1-6 : angle 2.81884 ( 15) link_BETA1-4 : bond 0.01135 ( 18) link_BETA1-4 : angle 4.48617 ( 54) link_ALPHA1-3 : bond 0.01463 ( 5) link_ALPHA1-3 : angle 2.93681 ( 15) hydrogen bonds : bond 0.05375 ( 945) hydrogen bonds : angle 5.74318 ( 2756) SS BOND : bond 0.00176 ( 8) SS BOND : angle 1.13712 ( 16) covalent geometry : bond 0.00394 (28123) covalent geometry : angle 1.00254 (38071) *********************** 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 342 residues out of total 2931 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 300 time to evaluate : 3.387 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: 0.9517 (OUTLIER) cc_final: 0.9174 (tm) REVERT: A 454 TYR cc_start: 0.8858 (m-80) cc_final: 0.8628 (m-80) REVERT: A 517 LEU cc_start: 0.8948 (mm) cc_final: 0.8723 (mm) REVERT: A 612 PHE cc_start: 0.8793 (OUTLIER) cc_final: 0.8129 (p90) REVERT: A 620 MET cc_start: 0.8805 (mmm) cc_final: 0.7958 (mmm) REVERT: A 709 MET cc_start: 0.9108 (mmm) cc_final: 0.8899 (mmm) REVERT: A 768 THR cc_start: 0.7682 (OUTLIER) cc_final: 0.7475 (p) REVERT: A 770 MET cc_start: 0.8537 (tpp) cc_final: 0.7883 (tpp) REVERT: A 824 PHE cc_start: 0.8431 (m-80) cc_final: 0.8022 (m-80) REVERT: B 247 MET cc_start: 0.8713 (mmm) cc_final: 0.8368 (mtp) REVERT: B 612 PHE cc_start: 0.8145 (m-10) cc_final: 0.7922 (m-80) REVERT: B 639 ILE cc_start: 0.8983 (mm) cc_final: 0.8671 (pt) REVERT: B 664 MET cc_start: 0.6025 (ptm) cc_final: 0.5367 (tpt) REVERT: B 719 LYS cc_start: 0.8886 (mttp) cc_final: 0.7721 (tppt) REVERT: B 762 LYS cc_start: 0.8294 (mppt) cc_final: 0.7665 (mmtt) REVERT: B 842 PHE cc_start: 0.7380 (t80) cc_final: 0.7045 (t80) REVERT: C 250 GLU cc_start: 0.7796 (OUTLIER) cc_final: 0.7247 (tp30) REVERT: C 448 LYS cc_start: 0.8243 (mtmm) cc_final: 0.7783 (tptp) REVERT: C 454 TYR cc_start: 0.8208 (m-80) cc_final: 0.7924 (m-80) REVERT: C 463 CYS cc_start: 0.9150 (m) cc_final: 0.8718 (m) REVERT: C 501 MET cc_start: 0.8760 (mpt) cc_final: 0.8316 (mmm) REVERT: C 556 LEU cc_start: 0.8967 (mp) cc_final: 0.8580 (tt) REVERT: C 619 LEU cc_start: 0.9486 (tp) cc_final: 0.9103 (tt) REVERT: C 651 TYR cc_start: 0.8872 (t80) cc_final: 0.8407 (t80) REVERT: C 679 LYS cc_start: 0.9342 (ptmm) cc_final: 0.9019 (pttm) REVERT: C 691 MET cc_start: 0.8513 (tmt) cc_final: 0.8281 (tmm) REVERT: D 114 SER cc_start: 0.9454 (m) cc_final: 0.9170 (t) REVERT: D 248 MET cc_start: 0.8934 (mmm) cc_final: 0.8637 (mmm) REVERT: D 316 MET cc_start: 0.8945 (mtt) cc_final: 0.8554 (mmm) REVERT: D 340 MET cc_start: 0.7711 (tpp) cc_final: 0.7268 (tmm) REVERT: D 360 MET cc_start: 0.8800 (tpp) cc_final: 0.8527 (tpp) REVERT: D 562 ASP cc_start: 0.8574 (t70) cc_final: 0.8237 (t0) REVERT: D 566 TYR cc_start: 0.7953 (m-10) cc_final: 0.7690 (m-80) REVERT: D 584 PHE cc_start: 0.8706 (t80) cc_final: 0.8290 (t80) REVERT: D 588 GLU cc_start: 0.8390 (tp30) cc_final: 0.8140 (mm-30) REVERT: D 662 GLU cc_start: 0.8898 (mm-30) cc_final: 0.8603 (tm-30) REVERT: D 691 MET cc_start: 0.8748 (tmm) cc_final: 0.8202 (tmm) REVERT: D 780 ILE cc_start: 0.8822 (OUTLIER) cc_final: 0.8555 (tp) REVERT: D 793 MET cc_start: 0.8800 (tpp) cc_final: 0.8516 (ttp) REVERT: D 861 MET cc_start: 0.6308 (mtt) cc_final: 0.5973 (mmm) outliers start: 42 outliers final: 19 residues processed: 326 average time/residue: 0.3945 time to fit residues: 210.3809 Evaluate side-chains 256 residues out of total 2931 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 232 time to evaluate : 2.984 ------------------------------------------------------------------------------- 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 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 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 83 optimal weight: 30.0000 chunk 290 optimal weight: 0.7980 chunk 234 optimal weight: 10.0000 chunk 160 optimal weight: 8.9990 chunk 306 optimal weight: 8.9990 chunk 15 optimal weight: 0.7980 chunk 259 optimal weight: 4.9990 chunk 203 optimal weight: 0.7980 chunk 32 optimal weight: 6.9990 chunk 127 optimal weight: 6.9990 chunk 325 optimal weight: 0.7980 overall best weight: 1.6382 ------------------------------------------------------------------------------- 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 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 C 621 GLN C 819 ASN D 593 HIS D 786 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4084 r_free = 0.4084 target = 0.105966 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3565 r_free = 0.3565 target = 0.077554 restraints weight = 168384.977| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3532 r_free = 0.3532 target = 0.077469 restraints weight = 73070.412| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3546 r_free = 0.3546 target = 0.078363 restraints weight = 53793.041| |-----------------------------------------------------------------------------| r_work (final): 0.3511 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3512 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3512 r_free = 0.3512 target_work(ls_wunit_k1) = 0.076 | | occupancies: max = 1.00 min = 0.01 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3512 r_free = 0.3512 target_work(ls_wunit_k1) = 0.076 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| r_final: 0.3512 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7994 moved from start: 0.3019 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 28189 Z= 0.176 Angle : 0.973 15.172 38261 Z= 0.462 Chirality : 0.052 0.533 4412 Planarity : 0.006 0.122 4753 Dihedral : 16.911 105.676 4838 Min Nonbonded Distance : 2.211 Molprobity Statistics. All-atom Clashscore : 14.68 Ramachandran Plot: Outliers : 0.77 % Allowed : 14.58 % Favored : 84.64 % Rotamer: Outliers : 2.24 % Allowed : 12.55 % Favored : 85.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.52 % Cis-general : 0.00 % Twisted Proline : 5.30 % Twisted General : 0.65 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.60 (0.13), residues: 3365 helix: -1.03 (0.12), residues: 1454 sheet: -4.24 (0.22), residues: 333 loop : -3.33 (0.15), residues: 1578 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.038 0.002 TRP B 589 HIS 0.011 0.001 HIS D 350 PHE 0.039 0.002 PHE B 643 TYR 0.021 0.002 TYR C 252 ARG 0.008 0.001 ARG D 68 Details of bonding type rmsd link_NAG-ASN : bond 0.00820 ( 30) link_NAG-ASN : angle 4.69645 ( 90) link_ALPHA1-6 : bond 0.01425 ( 5) link_ALPHA1-6 : angle 2.83607 ( 15) link_BETA1-4 : bond 0.01008 ( 18) link_BETA1-4 : angle 4.17988 ( 54) link_ALPHA1-3 : bond 0.01779 ( 5) link_ALPHA1-3 : angle 3.00974 ( 15) hydrogen bonds : bond 0.04483 ( 945) hydrogen bonds : angle 5.21464 ( 2756) SS BOND : bond 0.00204 ( 8) SS BOND : angle 1.20882 ( 16) covalent geometry : bond 0.00384 (28123) covalent geometry : angle 0.93129 (38071) *********************** 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 331 residues out of total 2931 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 269 time to evaluate : 3.005 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: 0.9508 (OUTLIER) cc_final: 0.9188 (tm) REVERT: A 298 MET cc_start: 0.7921 (tmm) cc_final: 0.7574 (tmm) REVERT: A 316 MET cc_start: 0.8355 (mmm) cc_final: 0.7668 (tpt) REVERT: A 454 TYR cc_start: 0.8785 (m-80) cc_final: 0.8518 (m-80) REVERT: A 517 LEU cc_start: 0.9084 (mm) cc_final: 0.8769 (mm) REVERT: A 578 LEU cc_start: 0.9392 (pp) cc_final: 0.9050 (tp) REVERT: A 606 PHE cc_start: 0.8467 (m-80) cc_final: 0.8135 (t80) REVERT: A 612 PHE cc_start: 0.8657 (OUTLIER) cc_final: 0.8001 (p90) REVERT: A 620 MET cc_start: 0.8879 (mmm) cc_final: 0.7491 (mmm) REVERT: A 627 MET cc_start: 0.8810 (mmp) cc_final: 0.8255 (tpt) REVERT: A 691 MET cc_start: 0.8780 (ttp) cc_final: 0.8463 (ptm) REVERT: A 709 MET cc_start: 0.9168 (mmm) cc_final: 0.8890 (mmm) REVERT: A 714 GLN cc_start: 0.7436 (tp-100) cc_final: 0.7157 (tp-100) REVERT: A 768 THR cc_start: 0.8051 (OUTLIER) cc_final: 0.7818 (p) REVERT: A 770 MET cc_start: 0.8546 (tpp) cc_final: 0.7928 (tpp) REVERT: A 815 LEU cc_start: 0.8232 (OUTLIER) cc_final: 0.7953 (pp) REVERT: A 824 PHE cc_start: 0.8473 (m-80) cc_final: 0.7879 (m-80) REVERT: B 248 MET cc_start: 0.8279 (mmm) cc_final: 0.7990 (mmm) REVERT: B 651 TYR cc_start: 0.8874 (t80) cc_final: 0.8466 (t80) REVERT: B 719 LYS cc_start: 0.8921 (mttp) cc_final: 0.7848 (tppt) REVERT: B 737 MET cc_start: 0.5747 (mmm) cc_final: 0.5365 (mmt) REVERT: B 762 LYS cc_start: 0.8253 (mppt) cc_final: 0.7646 (mmtt) REVERT: C 55 LEU cc_start: 0.9520 (OUTLIER) cc_final: 0.9297 (tp) REVERT: C 250 GLU cc_start: 0.7569 (OUTLIER) cc_final: 0.7155 (tp30) REVERT: C 360 MET cc_start: 0.9161 (mmm) cc_final: 0.8863 (mmm) REVERT: C 428 LEU cc_start: 0.7923 (tt) cc_final: 0.7609 (tp) REVERT: C 454 TYR cc_start: 0.8159 (m-80) cc_final: 0.7891 (m-80) REVERT: C 463 CYS cc_start: 0.9128 (m) cc_final: 0.8703 (m) REVERT: C 501 MET cc_start: 0.8695 (mpt) cc_final: 0.8312 (mmm) REVERT: C 556 LEU cc_start: 0.8896 (mp) cc_final: 0.8539 (tt) REVERT: C 620 MET cc_start: 0.9314 (mmm) cc_final: 0.9079 (mmp) REVERT: C 686 GLU cc_start: 0.8621 (tt0) cc_final: 0.8186 (pt0) REVERT: C 705 MET cc_start: 0.9044 (mtp) cc_final: 0.8442 (mtt) REVERT: C 723 GLU cc_start: 0.8206 (tt0) cc_final: 0.7760 (pt0) REVERT: C 764 TYR cc_start: 0.6285 (m-10) cc_final: 0.6067 (m-80) REVERT: C 794 MET cc_start: 0.8303 (ptm) cc_final: 0.8059 (ttm) REVERT: D 248 MET cc_start: 0.8971 (mmm) cc_final: 0.8658 (mmm) REVERT: D 316 MET cc_start: 0.9049 (mtt) cc_final: 0.8631 (mmm) REVERT: D 360 MET cc_start: 0.8863 (tpp) cc_final: 0.8608 (tpp) REVERT: D 584 PHE cc_start: 0.8721 (t80) cc_final: 0.7973 (t80) REVERT: D 588 GLU cc_start: 0.8281 (tp30) cc_final: 0.8005 (mm-30) REVERT: D 664 MET cc_start: 0.8874 (tpp) cc_final: 0.8604 (tmm) REVERT: D 691 MET cc_start: 0.8757 (tmm) cc_final: 0.8230 (tmm) REVERT: D 722 GLU cc_start: 0.9451 (mt-10) cc_final: 0.8980 (mp0) REVERT: D 737 MET cc_start: 0.8246 (tmm) cc_final: 0.8042 (tmm) REVERT: D 780 ILE cc_start: 0.8767 (OUTLIER) cc_final: 0.8525 (tp) REVERT: D 793 MET cc_start: 0.8782 (tpp) cc_final: 0.8544 (ptt) REVERT: D 824 PHE cc_start: 0.8449 (m-80) cc_final: 0.8173 (m-80) REVERT: D 861 MET cc_start: 0.6241 (mtt) cc_final: 0.5933 (mmm) outliers start: 62 outliers final: 34 residues processed: 316 average time/residue: 0.3575 time to fit residues: 186.9736 Evaluate side-chains 274 residues out of total 2931 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 233 time to evaluate : 3.379 ------------------------------------------------------------------------------- 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 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 140 ASP Chi-restraints excluded: chain B residue 149 LEU Chi-restraints excluded: chain B residue 183 ILE Chi-restraints excluded: chain B residue 201 ILE Chi-restraints excluded: chain B residue 226 VAL Chi-restraints excluded: chain B residue 391 VAL 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 55 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 701 THR Chi-restraints excluded: chain C residue 827 LEU Chi-restraints excluded: chain D residue 234 MET 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 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 239 optimal weight: 2.9990 chunk 192 optimal weight: 2.9990 chunk 286 optimal weight: 0.8980 chunk 20 optimal weight: 0.4980 chunk 321 optimal weight: 7.9990 chunk 78 optimal weight: 10.0000 chunk 30 optimal weight: 5.9990 chunk 5 optimal weight: 0.4980 chunk 1 optimal weight: 3.9990 chunk 297 optimal weight: 9.9990 chunk 109 optimal weight: 4.9990 overall best weight: 1.5784 ------------------------------------------------------------------------------- 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 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 Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4078 r_free = 0.4078 target = 0.105974 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3553 r_free = 0.3553 target = 0.076307 restraints weight = 174781.360| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3526 r_free = 0.3526 target = 0.077566 restraints weight = 74418.911| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3544 r_free = 0.3544 target = 0.078401 restraints weight = 49033.160| |-----------------------------------------------------------------------------| r_work (final): 0.3513 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3514 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3514 r_free = 0.3514 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 = 0.3514 r_free = 0.3514 target_work(ls_wunit_k1) = 0.076 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| r_final: 0.3514 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7999 moved from start: 0.3406 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 28189 Z= 0.166 Angle : 0.946 14.350 38261 Z= 0.445 Chirality : 0.051 0.507 4412 Planarity : 0.005 0.124 4753 Dihedral : 15.561 103.650 4838 Min Nonbonded Distance : 2.333 Molprobity Statistics. All-atom Clashscore : 13.98 Ramachandran Plot: Outliers : 0.68 % Allowed : 14.08 % Favored : 85.24 % Rotamer: Outliers : 2.21 % Allowed : 13.63 % Favored : 84.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.52 % Cis-general : 0.00 % Twisted Proline : 5.30 % Twisted General : 0.59 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.19 (0.14), residues: 3365 helix: -0.57 (0.13), residues: 1462 sheet: -4.08 (0.23), residues: 334 loop : -3.25 (0.15), residues: 1569 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.002 TRP B 589 HIS 0.009 0.001 HIS D 253 PHE 0.045 0.002 PHE C 262 TYR 0.020 0.002 TYR C 252 ARG 0.005 0.000 ARG D 713 Details of bonding type rmsd link_NAG-ASN : bond 0.00808 ( 30) link_NAG-ASN : angle 4.65002 ( 90) link_ALPHA1-6 : bond 0.01486 ( 5) link_ALPHA1-6 : angle 2.87268 ( 15) link_BETA1-4 : bond 0.01028 ( 18) link_BETA1-4 : angle 4.20046 ( 54) link_ALPHA1-3 : bond 0.01926 ( 5) link_ALPHA1-3 : angle 3.08179 ( 15) hydrogen bonds : bond 0.03933 ( 945) hydrogen bonds : angle 5.03019 ( 2756) SS BOND : bond 0.00159 ( 8) SS BOND : angle 1.11041 ( 16) covalent geometry : bond 0.00361 (28123) covalent geometry : angle 0.90308 (38071) *********************** 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 306 residues out of total 2931 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 245 time to evaluate : 3.204 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: A 85 LEU cc_start: 0.9453 (OUTLIER) cc_final: 0.9068 (tm) REVERT: A 298 MET cc_start: 0.7990 (tmm) cc_final: 0.7526 (tmm) REVERT: A 316 MET cc_start: 0.8332 (mmm) cc_final: 0.7663 (tpt) REVERT: A 454 TYR cc_start: 0.8717 (m-80) cc_final: 0.8438 (m-80) REVERT: A 501 MET cc_start: 0.8669 (mmp) cc_final: 0.8424 (mmt) REVERT: A 517 LEU cc_start: 0.9072 (mm) cc_final: 0.8739 (mm) REVERT: A 612 PHE cc_start: 0.8440 (OUTLIER) cc_final: 0.7857 (p90) REVERT: A 620 MET cc_start: 0.8810 (mmm) cc_final: 0.7857 (mmm) REVERT: A 691 MET cc_start: 0.8808 (ttp) cc_final: 0.8501 (ptm) REVERT: A 709 MET cc_start: 0.9154 (mmm) cc_final: 0.8846 (mmm) REVERT: A 714 GLN cc_start: 0.7583 (tp-100) cc_final: 0.7327 (tp-100) REVERT: A 738 GLU cc_start: 0.7617 (mp0) cc_final: 0.7256 (mp0) REVERT: A 768 THR cc_start: 0.7897 (OUTLIER) cc_final: 0.7683 (p) REVERT: A 770 MET cc_start: 0.8555 (tpp) cc_final: 0.7948 (tpp) REVERT: A 824 PHE cc_start: 0.8393 (m-80) cc_final: 0.7905 (m-80) REVERT: B 55 LEU cc_start: 0.9346 (OUTLIER) cc_final: 0.9037 (mm) REVERT: B 73 ASN cc_start: 0.7438 (OUTLIER) cc_final: 0.7211 (m110) REVERT: B 248 MET cc_start: 0.8270 (mmm) cc_final: 0.8040 (mmm) REVERT: B 651 TYR cc_start: 0.8773 (t80) cc_final: 0.8291 (t80) REVERT: B 719 LYS cc_start: 0.8959 (mttp) cc_final: 0.7888 (tppt) REVERT: B 793 MET cc_start: 0.8288 (mmp) cc_final: 0.8053 (mmt) REVERT: C 323 MET cc_start: 0.9196 (mmm) cc_final: 0.8985 (tpp) REVERT: C 360 MET cc_start: 0.9051 (mmm) cc_final: 0.8741 (mmm) REVERT: C 448 LYS cc_start: 0.8486 (mtmm) cc_final: 0.7853 (tptp) REVERT: C 454 TYR cc_start: 0.8123 (m-80) cc_final: 0.7852 (m-80) REVERT: C 463 CYS cc_start: 0.9072 (m) cc_final: 0.8720 (m) REVERT: C 501 MET cc_start: 0.8691 (mpt) cc_final: 0.8285 (mmm) REVERT: C 565 MET cc_start: 0.9187 (mtm) cc_final: 0.8861 (ptp) REVERT: C 619 LEU cc_start: 0.9560 (tp) cc_final: 0.9072 (tt) REVERT: C 647 ILE cc_start: 0.8841 (mm) cc_final: 0.8629 (pt) REVERT: C 679 LYS cc_start: 0.9335 (ptmm) cc_final: 0.8990 (pttm) REVERT: C 686 GLU cc_start: 0.8602 (tt0) cc_final: 0.8307 (pt0) REVERT: C 794 MET cc_start: 0.8207 (ptm) cc_final: 0.8002 (ttm) REVERT: D 248 MET cc_start: 0.8980 (mmm) cc_final: 0.8679 (mmm) REVERT: D 584 PHE cc_start: 0.8395 (t80) cc_final: 0.7914 (t80) REVERT: D 588 GLU cc_start: 0.8303 (tp30) cc_final: 0.7360 (mm-30) REVERT: D 590 TYR cc_start: 0.8298 (p90) cc_final: 0.8060 (p90) REVERT: D 606 PHE cc_start: 0.8601 (OUTLIER) cc_final: 0.8223 (t80) REVERT: D 691 MET cc_start: 0.8730 (tmm) cc_final: 0.8082 (tmm) REVERT: D 709 MET cc_start: 0.7504 (mmt) cc_final: 0.7283 (mpp) REVERT: D 722 GLU cc_start: 0.9500 (mt-10) cc_final: 0.9047 (mp0) REVERT: D 780 ILE cc_start: 0.8755 (OUTLIER) cc_final: 0.8508 (tp) REVERT: D 793 MET cc_start: 0.8799 (tpp) cc_final: 0.8555 (ttp) REVERT: D 861 MET cc_start: 0.6078 (mtt) cc_final: 0.5829 (mmm) outliers start: 61 outliers final: 36 residues processed: 291 average time/residue: 0.3463 time to fit residues: 167.8143 Evaluate side-chains 272 residues out of total 2931 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 229 time to evaluate : 3.065 ------------------------------------------------------------------------------- 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 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 736 LEU Chi-restraints excluded: chain A residue 768 THR 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 183 ILE Chi-restraints excluded: chain B residue 195 TYR Chi-restraints excluded: chain B residue 201 ILE Chi-restraints excluded: chain B residue 226 VAL 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 375 ILE Chi-restraints excluded: chain C residue 411 LEU Chi-restraints excluded: chain C residue 701 THR Chi-restraints excluded: chain C residue 758 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 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 336 random chunks: chunk 297 optimal weight: 8.9990 chunk 165 optimal weight: 6.9990 chunk 86 optimal weight: 0.7980 chunk 48 optimal weight: 9.9990 chunk 106 optimal weight: 2.9990 chunk 14 optimal weight: 0.8980 chunk 201 optimal weight: 4.9990 chunk 137 optimal weight: 5.9990 chunk 205 optimal weight: 5.9990 chunk 175 optimal weight: 5.9990 chunk 7 optimal weight: 0.9980 overall best weight: 2.1384 ------------------------------------------------------------------------------- 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** A 792 HIS ** 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 654 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 328 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3950 r_free = 0.3950 target = 0.102327 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3335 r_free = 0.3335 target = 0.071108 restraints weight = 200515.412| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3320 r_free = 0.3320 target = 0.071272 restraints weight = 88157.495| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3344 r_free = 0.3344 target = 0.072693 restraints weight = 63439.479| |-----------------------------------------------------------------------------| r_work (final): 0.3334 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3331 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3331 r_free = 0.3331 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 = 0.3331 r_free = 0.3331 target_work(ls_wunit_k1) = 0.071 | | occupancies: max = 1.00 min = 0.01 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| r_final: 0.3331 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8020 moved from start: 0.3685 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.071 28189 Z= 0.181 Angle : 0.927 13.585 38261 Z= 0.436 Chirality : 0.050 0.516 4412 Planarity : 0.005 0.129 4753 Dihedral : 14.346 100.684 4838 Min Nonbonded Distance : 2.341 Molprobity Statistics. All-atom Clashscore : 14.51 Ramachandran Plot: Outliers : 0.51 % Allowed : 14.49 % Favored : 85.00 % Rotamer: Outliers : 2.35 % Allowed : 13.91 % Favored : 83.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.52 % Cis-general : 0.00 % Twisted Proline : 5.30 % Twisted General : 0.59 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.87 (0.14), residues: 3365 helix: -0.23 (0.13), residues: 1458 sheet: -4.05 (0.24), residues: 324 loop : -3.13 (0.15), residues: 1583 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.002 TRP B 589 HIS 0.008 0.001 HIS D 253 PHE 0.043 0.002 PHE B 612 TYR 0.017 0.002 TYR A 443 ARG 0.005 0.001 ARG B 354 Details of bonding type rmsd link_NAG-ASN : bond 0.00786 ( 30) link_NAG-ASN : angle 4.44839 ( 90) link_ALPHA1-6 : bond 0.01455 ( 5) link_ALPHA1-6 : angle 2.76186 ( 15) link_BETA1-4 : bond 0.00950 ( 18) link_BETA1-4 : angle 4.33410 ( 54) link_ALPHA1-3 : bond 0.02110 ( 5) link_ALPHA1-3 : angle 3.24553 ( 15) hydrogen bonds : bond 0.03731 ( 945) hydrogen bonds : angle 4.91948 ( 2756) SS BOND : bond 0.00166 ( 8) SS BOND : angle 1.10080 ( 16) covalent geometry : bond 0.00397 (28123) covalent geometry : angle 0.88511 (38071) *********************** 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 306 residues out of total 2931 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 241 time to evaluate : 2.997 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: 0.9430 (OUTLIER) cc_final: 0.9053 (tm) REVERT: A 298 MET cc_start: 0.8029 (tmm) cc_final: 0.7569 (tmm) REVERT: A 316 MET cc_start: 0.8351 (mmm) cc_final: 0.7673 (tpt) REVERT: A 454 TYR cc_start: 0.8826 (m-80) cc_final: 0.8514 (m-80) REVERT: A 501 MET cc_start: 0.8536 (mmp) cc_final: 0.8252 (mmt) REVERT: A 517 LEU cc_start: 0.9110 (OUTLIER) cc_final: 0.8752 (mm) REVERT: A 612 PHE cc_start: 0.8427 (p90) cc_final: 0.7900 (p90) REVERT: A 620 MET cc_start: 0.8856 (mmm) cc_final: 0.8028 (mmm) REVERT: A 627 MET cc_start: 0.8751 (mmp) cc_final: 0.8062 (tpt) REVERT: A 691 MET cc_start: 0.8713 (ttp) cc_final: 0.8346 (ptm) REVERT: A 709 MET cc_start: 0.9098 (mmm) cc_final: 0.8781 (mmm) REVERT: A 714 GLN cc_start: 0.7729 (tp-100) cc_final: 0.7463 (tp-100) REVERT: A 738 GLU cc_start: 0.7957 (mp0) cc_final: 0.7496 (mp0) REVERT: A 770 MET cc_start: 0.8548 (tpp) cc_final: 0.7745 (tpp) REVERT: A 824 PHE cc_start: 0.8361 (m-80) cc_final: 0.7853 (m-80) REVERT: A 867 MET cc_start: 0.6065 (ttp) cc_final: 0.5865 (tpt) REVERT: B 55 LEU cc_start: 0.9368 (OUTLIER) cc_final: 0.9027 (mm) REVERT: B 73 ASN cc_start: 0.7389 (OUTLIER) cc_final: 0.7155 (m110) REVERT: B 651 TYR cc_start: 0.8759 (t80) cc_final: 0.8383 (t80) REVERT: B 680 ILE cc_start: 0.7755 (OUTLIER) cc_final: 0.7198 (tp) REVERT: B 719 LYS cc_start: 0.8990 (mttp) cc_final: 0.8689 (mmtt) REVERT: C 250 GLU cc_start: 0.7626 (OUTLIER) cc_final: 0.6831 (tp30) REVERT: C 323 MET cc_start: 0.9093 (mmm) cc_final: 0.8865 (tpp) REVERT: C 441 GLU cc_start: 0.8363 (tp30) cc_final: 0.8043 (mp0) REVERT: C 448 LYS cc_start: 0.8484 (mtmm) cc_final: 0.7952 (tptp) REVERT: C 454 TYR cc_start: 0.8079 (m-80) cc_final: 0.7851 (m-80) REVERT: C 463 CYS cc_start: 0.9112 (m) cc_final: 0.8769 (m) REVERT: C 501 MET cc_start: 0.8751 (mpt) cc_final: 0.8332 (mmm) REVERT: C 620 MET cc_start: 0.9318 (mmm) cc_final: 0.8985 (mmp) REVERT: C 627 MET cc_start: 0.7362 (mmp) cc_final: 0.7136 (mmp) REVERT: C 647 ILE cc_start: 0.8805 (mm) cc_final: 0.8578 (pt) REVERT: C 664 MET cc_start: 0.8710 (ptp) cc_final: 0.8492 (mpp) REVERT: C 679 LYS cc_start: 0.9332 (ptmm) cc_final: 0.8992 (pttm) REVERT: C 686 GLU cc_start: 0.8589 (tt0) cc_final: 0.8354 (pt0) REVERT: C 737 MET cc_start: 0.6928 (ppp) cc_final: 0.6389 (ppp) REVERT: C 764 TYR cc_start: 0.6724 (m-80) cc_final: 0.6521 (m-80) REVERT: D 248 MET cc_start: 0.8690 (mmm) cc_final: 0.8358 (mmm) REVERT: D 606 PHE cc_start: 0.8591 (OUTLIER) cc_final: 0.8221 (t80) REVERT: D 691 MET cc_start: 0.8722 (tmm) cc_final: 0.7980 (tmm) REVERT: D 722 GLU cc_start: 0.9527 (mt-10) cc_final: 0.9074 (mp0) REVERT: D 737 MET cc_start: 0.8012 (tmm) cc_final: 0.7634 (ppp) REVERT: D 780 ILE cc_start: 0.8788 (OUTLIER) cc_final: 0.8557 (tp) REVERT: D 793 MET cc_start: 0.8735 (tpp) cc_final: 0.8433 (ttp) REVERT: D 861 MET cc_start: 0.6085 (mtt) cc_final: 0.5839 (mmm) REVERT: D 867 MET cc_start: 0.7033 (OUTLIER) cc_final: 0.6635 (ppp) outliers start: 65 outliers final: 39 residues processed: 288 average time/residue: 0.3314 time to fit residues: 160.5151 Evaluate side-chains 271 residues out of total 2931 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 223 time to evaluate : 3.032 ------------------------------------------------------------------------------- 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 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 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 226 VAL 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 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 674 LEU Chi-restraints excluded: chain D residue 713 ARG Chi-restraints excluded: chain D residue 780 ILE Chi-restraints excluded: chain D residue 867 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 336 random chunks: chunk 331 optimal weight: 8.9990 chunk 160 optimal weight: 9.9990 chunk 88 optimal weight: 5.9990 chunk 229 optimal weight: 6.9990 chunk 9 optimal weight: 8.9990 chunk 138 optimal weight: 6.9990 chunk 218 optimal weight: 10.0000 chunk 330 optimal weight: 8.9990 chunk 306 optimal weight: 4.9990 chunk 33 optimal weight: 0.9990 chunk 58 optimal weight: 0.7980 overall best weight: 3.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 129 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 131 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 165 GLN ** A 253 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 677 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 802 ASN ** 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 286 ASN C 654 ASN D 136 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3915 r_free = 0.3915 target = 0.100439 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3319 r_free = 0.3319 target = 0.070173 restraints weight = 160275.528| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3259 r_free = 0.3259 target = 0.068807 restraints weight = 82698.958| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3280 r_free = 0.3280 target = 0.069788 restraints weight = 62022.609| |-----------------------------------------------------------------------------| r_work (final): 0.3268 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3268 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3268 r_free = 0.3268 target_work(ls_wunit_k1) = 0.068 | | occupancies: max = 1.00 min = 0.01 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3268 r_free = 0.3268 target_work(ls_wunit_k1) = 0.068 | | occupancies: max = 1.00 min = 0.01 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| r_final: 0.3268 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8098 moved from start: 0.3879 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.075 28189 Z= 0.269 Angle : 0.972 14.723 38261 Z= 0.461 Chirality : 0.052 0.552 4412 Planarity : 0.006 0.134 4753 Dihedral : 13.799 103.360 4838 Min Nonbonded Distance : 2.308 Molprobity Statistics. All-atom Clashscore : 16.25 Ramachandran Plot: Outliers : 0.57 % Allowed : 15.12 % Favored : 84.32 % Rotamer: Outliers : 2.38 % Allowed : 14.25 % Favored : 83.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.52 % Cis-general : 0.00 % Twisted Proline : 5.30 % Twisted General : 0.62 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.87 (0.14), residues: 3365 helix: -0.16 (0.13), residues: 1473 sheet: -4.14 (0.23), residues: 347 loop : -3.18 (0.15), residues: 1545 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.002 TRP B 589 HIS 0.009 0.002 HIS B 253 PHE 0.038 0.002 PHE B 643 TYR 0.018 0.002 TYR B 252 ARG 0.007 0.001 ARG D 280 Details of bonding type rmsd link_NAG-ASN : bond 0.00823 ( 30) link_NAG-ASN : angle 4.41016 ( 90) link_ALPHA1-6 : bond 0.01443 ( 5) link_ALPHA1-6 : angle 2.83036 ( 15) link_BETA1-4 : bond 0.00972 ( 18) link_BETA1-4 : angle 4.08547 ( 54) link_ALPHA1-3 : bond 0.02337 ( 5) link_ALPHA1-3 : angle 3.29149 ( 15) hydrogen bonds : bond 0.03839 ( 945) hydrogen bonds : angle 5.08254 ( 2756) SS BOND : bond 0.00255 ( 8) SS BOND : angle 1.05314 ( 16) covalent geometry : bond 0.00596 (28123) covalent geometry : angle 0.93363 (38071) *********************** 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 298 residues out of total 2931 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 232 time to evaluate : 3.266 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: 0.9455 (OUTLIER) cc_final: 0.9113 (tm) REVERT: A 298 MET cc_start: 0.8087 (tmm) cc_final: 0.7654 (tmm) REVERT: A 316 MET cc_start: 0.8473 (mmm) cc_final: 0.7849 (tpt) REVERT: A 454 TYR cc_start: 0.8633 (m-80) cc_final: 0.8376 (m-80) REVERT: A 517 LEU cc_start: 0.9099 (OUTLIER) cc_final: 0.8728 (mm) REVERT: A 565 MET cc_start: 0.8510 (ptt) cc_final: 0.8301 (ptt) REVERT: A 606 PHE cc_start: 0.8403 (m-80) cc_final: 0.8189 (t80) REVERT: A 612 PHE cc_start: 0.8408 (p90) cc_final: 0.7817 (p90) REVERT: A 627 MET cc_start: 0.8705 (mmp) cc_final: 0.8014 (tpt) REVERT: A 709 MET cc_start: 0.9112 (mmm) cc_final: 0.8792 (mmm) REVERT: A 714 GLN cc_start: 0.7813 (tp-100) cc_final: 0.7511 (tp-100) REVERT: A 738 GLU cc_start: 0.7985 (mp0) cc_final: 0.7744 (mp0) REVERT: A 770 MET cc_start: 0.8755 (tpp) cc_final: 0.7860 (tpp) REVERT: A 824 PHE cc_start: 0.8353 (m-80) cc_final: 0.7762 (m-80) REVERT: A 867 MET cc_start: 0.6080 (ttp) cc_final: 0.5853 (tpt) REVERT: B 55 LEU cc_start: 0.9392 (OUTLIER) cc_final: 0.9078 (mm) REVERT: B 73 ASN cc_start: 0.7419 (OUTLIER) cc_final: 0.7190 (m110) REVERT: B 651 TYR cc_start: 0.8856 (t80) cc_final: 0.8464 (t80) REVERT: B 680 ILE cc_start: 0.7768 (OUTLIER) cc_final: 0.7170 (tp) REVERT: B 719 LYS cc_start: 0.9002 (mttp) cc_final: 0.7964 (tppt) REVERT: B 794 MET cc_start: 0.7205 (mmt) cc_final: 0.6937 (mmt) REVERT: C 50 MET cc_start: 0.7805 (tmm) cc_final: 0.7526 (tmm) REVERT: C 250 GLU cc_start: 0.7734 (OUTLIER) cc_final: 0.6970 (tp30) REVERT: C 323 MET cc_start: 0.9070 (mmm) cc_final: 0.8839 (tpp) REVERT: C 413 MET cc_start: 0.7811 (ppp) cc_final: 0.6876 (ppp) REVERT: C 454 TYR cc_start: 0.8236 (m-80) cc_final: 0.8010 (m-80) REVERT: C 463 CYS cc_start: 0.9103 (m) cc_final: 0.8784 (m) REVERT: C 484 GLU cc_start: 0.8308 (mp0) cc_final: 0.7896 (tp30) REVERT: C 501 MET cc_start: 0.8755 (mpt) cc_final: 0.8508 (mmt) REVERT: C 556 LEU cc_start: 0.8544 (mm) cc_final: 0.8176 (mt) REVERT: C 619 LEU cc_start: 0.9589 (tp) cc_final: 0.9232 (tt) REVERT: C 679 LYS cc_start: 0.9391 (ptmm) cc_final: 0.8925 (ptpp) REVERT: C 737 MET cc_start: 0.7124 (ppp) cc_final: 0.6613 (ppp) REVERT: C 764 TYR cc_start: 0.7125 (m-80) cc_final: 0.6748 (m-80) REVERT: D 248 MET cc_start: 0.8648 (mmm) cc_final: 0.8279 (mmm) REVERT: D 606 PHE cc_start: 0.8583 (OUTLIER) cc_final: 0.8230 (t80) REVERT: D 691 MET cc_start: 0.8777 (tmm) cc_final: 0.8050 (tmm) REVERT: D 722 GLU cc_start: 0.9562 (mt-10) cc_final: 0.9129 (mp0) REVERT: D 780 ILE cc_start: 0.8856 (OUTLIER) cc_final: 0.8628 (tp) REVERT: D 793 MET cc_start: 0.8671 (tpp) cc_final: 0.8299 (ptt) REVERT: D 861 MET cc_start: 0.6074 (mtt) cc_final: 0.5769 (mmm) REVERT: D 867 MET cc_start: 0.7150 (OUTLIER) cc_final: 0.6715 (ppp) outliers start: 66 outliers final: 41 residues processed: 279 average time/residue: 0.3487 time to fit residues: 164.3302 Evaluate side-chains 266 residues out of total 2931 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 216 time to evaluate : 3.420 ------------------------------------------------------------------------------- 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 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 226 VAL 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 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 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 446 PHE Chi-restraints excluded: chain C residue 690 THR 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 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 Chi-restraints excluded: chain D residue 780 ILE Chi-restraints excluded: chain D residue 867 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 336 random chunks: chunk 36 optimal weight: 8.9990 chunk 82 optimal weight: 20.0000 chunk 247 optimal weight: 5.9990 chunk 271 optimal weight: 0.9980 chunk 238 optimal weight: 10.0000 chunk 152 optimal weight: 0.6980 chunk 109 optimal weight: 4.9990 chunk 26 optimal weight: 5.9990 chunk 296 optimal weight: 8.9990 chunk 207 optimal weight: 7.9990 chunk 65 optimal weight: 20.0000 overall best weight: 3.7386 ------------------------------------------------------------------------------- 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 610 ASN ** A 677 GLN ** 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 D 786 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3916 r_free = 0.3916 target = 0.100548 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3271 r_free = 0.3271 target = 0.068096 restraints weight = 172749.665| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3244 r_free = 0.3244 target = 0.068346 restraints weight = 81424.591| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3268 r_free = 0.3268 target = 0.069427 restraints weight = 59977.697| |-----------------------------------------------------------------------------| r_work (final): 0.3253 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3252 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3252 r_free = 0.3252 target_work(ls_wunit_k1) = 0.067 | | occupancies: max = 1.00 min = 0.01 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3252 r_free = 0.3252 target_work(ls_wunit_k1) = 0.067 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| r_final: 0.3252 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8144 moved from start: 0.4050 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.090 28189 Z= 0.249 Angle : 0.960 14.395 38261 Z= 0.453 Chirality : 0.052 0.566 4412 Planarity : 0.005 0.124 4753 Dihedral : 13.247 102.704 4838 Min Nonbonded Distance : 2.322 Molprobity Statistics. All-atom Clashscore : 16.32 Ramachandran Plot: Outliers : 0.57 % Allowed : 14.67 % Favored : 84.76 % Rotamer: Outliers : 2.52 % Allowed : 14.65 % Favored : 82.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.52 % Cis-general : 0.00 % Twisted Proline : 5.30 % Twisted General : 0.56 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.78 (0.14), residues: 3365 helix: -0.07 (0.13), residues: 1466 sheet: -4.06 (0.24), residues: 332 loop : -3.17 (0.15), residues: 1567 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.002 TRP B 589 HIS 0.008 0.002 HIS D 253 PHE 0.063 0.002 PHE B 643 TYR 0.024 0.002 TYR C 254 ARG 0.005 0.001 ARG D 280 Details of bonding type rmsd link_NAG-ASN : bond 0.00786 ( 30) link_NAG-ASN : angle 4.31989 ( 90) link_ALPHA1-6 : bond 0.01433 ( 5) link_ALPHA1-6 : angle 2.74160 ( 15) link_BETA1-4 : bond 0.00978 ( 18) link_BETA1-4 : angle 4.15747 ( 54) link_ALPHA1-3 : bond 0.02273 ( 5) link_ALPHA1-3 : angle 3.34516 ( 15) hydrogen bonds : bond 0.03815 ( 945) hydrogen bonds : angle 5.08754 ( 2756) SS BOND : bond 0.00264 ( 8) SS BOND : angle 1.16728 ( 16) covalent geometry : bond 0.00554 (28123) covalent geometry : angle 0.92187 (38071) *********************** 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 293 residues out of total 2931 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 223 time to evaluate : 3.488 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: 0.9369 (OUTLIER) cc_final: 0.9005 (tm) REVERT: A 298 MET cc_start: 0.8021 (tmm) cc_final: 0.7574 (tmm) REVERT: A 316 MET cc_start: 0.8398 (mmm) cc_final: 0.7743 (tpt) REVERT: A 454 TYR cc_start: 0.8587 (m-80) cc_final: 0.8326 (m-80) REVERT: A 517 LEU cc_start: 0.8916 (OUTLIER) cc_final: 0.8623 (mm) REVERT: A 606 PHE cc_start: 0.8430 (OUTLIER) cc_final: 0.8195 (t80) REVERT: A 612 PHE cc_start: 0.8324 (OUTLIER) cc_final: 0.7735 (p90) REVERT: A 709 MET cc_start: 0.9116 (mmm) cc_final: 0.8784 (mmm) REVERT: A 714 GLN cc_start: 0.7783 (tp-100) cc_final: 0.7483 (tp-100) REVERT: A 738 GLU cc_start: 0.8117 (mp0) cc_final: 0.7816 (mp0) REVERT: A 770 MET cc_start: 0.8473 (tpp) cc_final: 0.7699 (tpp) REVERT: B 55 LEU cc_start: 0.9336 (OUTLIER) cc_final: 0.9058 (mm) REVERT: B 73 ASN cc_start: 0.7369 (OUTLIER) cc_final: 0.7158 (m110) REVERT: B 589 TRP cc_start: 0.6484 (OUTLIER) cc_final: 0.6075 (m100) REVERT: B 651 TYR cc_start: 0.8860 (t80) cc_final: 0.8539 (t80) REVERT: B 680 ILE cc_start: 0.7817 (OUTLIER) cc_final: 0.7222 (tp) REVERT: B 719 LYS cc_start: 0.9010 (mttp) cc_final: 0.7971 (tppt) REVERT: B 794 MET cc_start: 0.7156 (mmt) cc_final: 0.6872 (mmt) REVERT: C 50 MET cc_start: 0.7664 (tmm) cc_final: 0.7409 (tmm) REVERT: C 323 MET cc_start: 0.8912 (mmm) cc_final: 0.8685 (tpp) REVERT: C 413 MET cc_start: 0.7619 (ppp) cc_final: 0.6711 (ppp) REVERT: C 454 TYR cc_start: 0.8213 (m-80) cc_final: 0.7987 (m-80) REVERT: C 463 CYS cc_start: 0.9078 (m) cc_final: 0.8596 (m) REVERT: C 501 MET cc_start: 0.8794 (mpt) cc_final: 0.8313 (mmm) REVERT: C 556 LEU cc_start: 0.8523 (mm) cc_final: 0.8196 (mt) REVERT: C 565 MET cc_start: 0.9120 (mtm) cc_final: 0.8751 (ptp) REVERT: C 619 LEU cc_start: 0.9572 (tp) cc_final: 0.9268 (tt) REVERT: C 679 LYS cc_start: 0.9403 (ptmm) cc_final: 0.8920 (ptpp) REVERT: C 737 MET cc_start: 0.7132 (ppp) cc_final: 0.6654 (ppp) REVERT: C 764 TYR cc_start: 0.6743 (m-80) cc_final: 0.6529 (m-80) REVERT: C 815 LEU cc_start: 0.8385 (mt) cc_final: 0.7815 (mt) REVERT: D 50 MET cc_start: 0.8002 (tmm) cc_final: 0.7786 (tmm) REVERT: D 248 MET cc_start: 0.8543 (mmm) cc_final: 0.8319 (mmm) REVERT: D 606 PHE cc_start: 0.8496 (OUTLIER) cc_final: 0.8195 (t80) REVERT: D 691 MET cc_start: 0.8719 (tmm) cc_final: 0.7981 (tmm) REVERT: D 722 GLU cc_start: 0.9552 (mt-10) cc_final: 0.9090 (mp0) REVERT: D 737 MET cc_start: 0.7810 (tmm) cc_final: 0.7447 (ppp) REVERT: D 861 MET cc_start: 0.6049 (mtt) cc_final: 0.5656 (mmm) REVERT: D 867 MET cc_start: 0.7186 (OUTLIER) cc_final: 0.6740 (ppp) outliers start: 70 outliers final: 47 residues processed: 273 average time/residue: 0.3467 time to fit residues: 157.7705 Evaluate side-chains 273 residues out of total 2931 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 216 time to evaluate : 2.981 ------------------------------------------------------------------------------- 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 249 THR 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 606 PHE Chi-restraints excluded: chain A residue 608 LEU Chi-restraints excluded: chain A residue 612 PHE 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 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 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 226 VAL Chi-restraints excluded: chain B residue 376 THR 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 544 LYS 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 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 260 ASP 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 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 674 LEU Chi-restraints excluded: chain D residue 713 ARG Chi-restraints excluded: chain D residue 867 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 336 random chunks: chunk 75 optimal weight: 6.9990 chunk 34 optimal weight: 2.9990 chunk 248 optimal weight: 9.9990 chunk 31 optimal weight: 10.0000 chunk 162 optimal weight: 10.0000 chunk 293 optimal weight: 4.9990 chunk 61 optimal weight: 0.6980 chunk 97 optimal weight: 3.9990 chunk 121 optimal weight: 1.9990 chunk 299 optimal weight: 5.9990 chunk 13 optimal weight: 0.9990 overall best weight: 2.1388 ------------------------------------------------------------------------------- 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 129 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 232 HIS ** C 621 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 786 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3936 r_free = 0.3936 target = 0.101741 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3321 r_free = 0.3321 target = 0.070657 restraints weight = 189005.512| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3315 r_free = 0.3315 target = 0.071188 restraints weight = 82360.121| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3329 r_free = 0.3329 target = 0.072107 restraints weight = 62082.426| |-----------------------------------------------------------------------------| r_work (final): 0.3323 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3323 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3323 r_free = 0.3323 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 = 0.3323 r_free = 0.3323 target_work(ls_wunit_k1) = 0.070 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| r_final: 0.3323 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8027 moved from start: 0.4234 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.060 28189 Z= 0.179 Angle : 0.927 14.643 38261 Z= 0.434 Chirality : 0.050 0.542 4412 Planarity : 0.005 0.118 4753 Dihedral : 12.669 100.391 4838 Min Nonbonded Distance : 2.341 Molprobity Statistics. All-atom Clashscore : 15.13 Ramachandran Plot: Outliers : 0.48 % Allowed : 14.52 % Favored : 85.00 % Rotamer: Outliers : 2.14 % Allowed : 15.20 % Favored : 82.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.52 % Cis-general : 0.00 % Twisted Proline : 5.30 % Twisted General : 0.43 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.59 (0.14), residues: 3365 helix: 0.08 (0.13), residues: 1466 sheet: -3.90 (0.24), residues: 326 loop : -3.08 (0.15), residues: 1573 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.002 TRP B 589 HIS 0.007 0.001 HIS D 253 PHE 0.052 0.002 PHE B 643 TYR 0.021 0.002 TYR C 254 ARG 0.006 0.000 ARG B 358 Details of bonding type rmsd link_NAG-ASN : bond 0.00784 ( 30) link_NAG-ASN : angle 4.20304 ( 90) link_ALPHA1-6 : bond 0.01471 ( 5) link_ALPHA1-6 : angle 2.44970 ( 15) link_BETA1-4 : bond 0.00985 ( 18) link_BETA1-4 : angle 4.11780 ( 54) link_ALPHA1-3 : bond 0.02364 ( 5) link_ALPHA1-3 : angle 3.40042 ( 15) hydrogen bonds : bond 0.03644 ( 945) hydrogen bonds : angle 4.95507 ( 2756) SS BOND : bond 0.00212 ( 8) SS BOND : angle 1.08930 ( 16) covalent geometry : bond 0.00398 (28123) covalent geometry : angle 0.88924 (38071) *********************** 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 294 residues out of total 2931 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 235 time to evaluate : 3.017 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: 0.9361 (OUTLIER) cc_final: 0.8939 (tm) REVERT: A 264 LEU cc_start: 0.8365 (tt) cc_final: 0.8077 (tt) REVERT: A 298 MET cc_start: 0.8133 (tmm) cc_final: 0.7655 (tmm) REVERT: A 316 MET cc_start: 0.8328 (mmm) cc_final: 0.7309 (tpt) REVERT: A 454 TYR cc_start: 0.8570 (m-80) cc_final: 0.8305 (m-80) REVERT: A 491 GLN cc_start: 0.7841 (OUTLIER) cc_final: 0.7621 (tp40) REVERT: A 517 LEU cc_start: 0.9143 (OUTLIER) cc_final: 0.8796 (mm) REVERT: A 606 PHE cc_start: 0.8459 (OUTLIER) cc_final: 0.8209 (t80) REVERT: A 612 PHE cc_start: 0.8372 (OUTLIER) cc_final: 0.7774 (p90) REVERT: A 709 MET cc_start: 0.9094 (mmm) cc_final: 0.8756 (mmm) REVERT: A 714 GLN cc_start: 0.7762 (tp-100) cc_final: 0.7524 (tp-100) REVERT: A 738 GLU cc_start: 0.8126 (mp0) cc_final: 0.7808 (mp0) REVERT: A 770 MET cc_start: 0.8435 (tpp) cc_final: 0.7551 (tpp) REVERT: B 55 LEU cc_start: 0.9380 (OUTLIER) cc_final: 0.9083 (mm) REVERT: B 73 ASN cc_start: 0.7530 (OUTLIER) cc_final: 0.7326 (m110) REVERT: B 544 LYS cc_start: 0.7458 (OUTLIER) cc_final: 0.7164 (ptpp) REVERT: B 589 TRP cc_start: 0.6344 (OUTLIER) cc_final: 0.5980 (m100) REVERT: B 651 TYR cc_start: 0.8836 (t80) cc_final: 0.8397 (t80) REVERT: B 680 ILE cc_start: 0.7786 (OUTLIER) cc_final: 0.7180 (tp) REVERT: B 719 LYS cc_start: 0.9007 (mttp) cc_final: 0.7960 (tppt) REVERT: B 794 MET cc_start: 0.7132 (mmt) cc_final: 0.6815 (mmt) REVERT: B 867 MET cc_start: 0.6242 (tmm) cc_final: 0.5201 (mmp) REVERT: C 50 MET cc_start: 0.7709 (tmm) cc_final: 0.6920 (tmm) REVERT: C 323 MET cc_start: 0.8967 (mmm) cc_final: 0.8760 (tpp) REVERT: C 360 MET cc_start: 0.9097 (mmm) cc_final: 0.8871 (mmm) REVERT: C 413 MET cc_start: 0.7747 (ppp) cc_final: 0.6792 (ppp) REVERT: C 428 LEU cc_start: 0.8388 (tt) cc_final: 0.8042 (tp) REVERT: C 454 TYR cc_start: 0.8214 (m-80) cc_final: 0.8000 (m-80) REVERT: C 463 CYS cc_start: 0.9097 (m) cc_final: 0.8659 (m) REVERT: C 501 MET cc_start: 0.8859 (mpt) cc_final: 0.8285 (mmm) REVERT: C 556 LEU cc_start: 0.8543 (mm) cc_final: 0.8234 (mt) REVERT: C 559 LEU cc_start: 0.9219 (mt) cc_final: 0.9015 (tp) REVERT: C 565 MET cc_start: 0.9130 (mtm) cc_final: 0.8753 (ptp) REVERT: C 619 LEU cc_start: 0.9557 (tp) cc_final: 0.9322 (tt) REVERT: C 679 LYS cc_start: 0.9386 (ptmm) cc_final: 0.8916 (ptpp) REVERT: C 737 MET cc_start: 0.7086 (ppp) cc_final: 0.6599 (ppp) REVERT: C 764 TYR cc_start: 0.6882 (m-80) cc_final: 0.6580 (m-80) REVERT: C 815 LEU cc_start: 0.8471 (mt) cc_final: 0.7866 (mt) REVERT: D 50 MET cc_start: 0.7990 (tmm) cc_final: 0.7714 (tmm) REVERT: D 248 MET cc_start: 0.8701 (mmm) cc_final: 0.8403 (mmm) REVERT: D 584 PHE cc_start: 0.8407 (t80) cc_final: 0.8102 (t80) REVERT: D 606 PHE cc_start: 0.8495 (OUTLIER) cc_final: 0.8282 (t80) REVERT: D 691 MET cc_start: 0.8744 (tmm) cc_final: 0.7989 (tmm) REVERT: D 722 GLU cc_start: 0.9551 (mt-10) cc_final: 0.9085 (mp0) REVERT: D 793 MET cc_start: 0.8577 (tpp) cc_final: 0.8259 (ppp) REVERT: D 794 MET cc_start: 0.6919 (tmm) cc_final: 0.5381 (ppp) REVERT: D 861 MET cc_start: 0.6089 (mtt) cc_final: 0.5705 (mmm) REVERT: D 867 MET cc_start: 0.7157 (OUTLIER) cc_final: 0.6695 (ppp) outliers start: 59 outliers final: 43 residues processed: 278 average time/residue: 0.3450 time to fit residues: 162.1218 Evaluate side-chains 282 residues out of total 2931 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 227 time to evaluate : 5.174 ------------------------------------------------------------------------------- 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 249 THR 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 491 GLN Chi-restraints excluded: chain A residue 517 LEU Chi-restraints excluded: chain A residue 606 PHE Chi-restraints excluded: chain A residue 612 PHE 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 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 195 TYR Chi-restraints excluded: chain B residue 201 ILE Chi-restraints excluded: chain B residue 226 VAL Chi-restraints excluded: chain B residue 376 THR 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 544 LYS 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 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 D residue 164 VAL 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 674 LEU Chi-restraints excluded: chain D residue 713 ARG Chi-restraints excluded: chain D residue 867 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 336 random chunks: chunk 102 optimal weight: 0.5980 chunk 105 optimal weight: 0.9980 chunk 178 optimal weight: 3.9990 chunk 318 optimal weight: 6.9990 chunk 53 optimal weight: 5.9990 chunk 197 optimal weight: 0.9980 chunk 328 optimal weight: 0.7980 chunk 303 optimal weight: 20.0000 chunk 108 optimal weight: 3.9990 chunk 317 optimal weight: 0.0040 chunk 123 optimal weight: 0.0370 overall best weight: 0.4870 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 129 HIS ** 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 B 610 ASN ** C 129 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 335 GLN ** D 196 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 491 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 622 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3949 r_free = 0.3949 target = 0.102878 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3325 r_free = 0.3325 target = 0.070587 restraints weight = 203188.140| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3308 r_free = 0.3308 target = 0.071664 restraints weight = 100132.777| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3335 r_free = 0.3335 target = 0.072766 restraints weight = 62814.068| |-----------------------------------------------------------------------------| r_work (final): 0.3303 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3306 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3306 r_free = 0.3306 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 = 0.3306 r_free = 0.3306 target_work(ls_wunit_k1) = 0.070 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| r_final: 0.3306 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7992 moved from start: 0.4552 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 28189 Z= 0.141 Angle : 0.911 14.192 38261 Z= 0.422 Chirality : 0.050 0.479 4412 Planarity : 0.005 0.114 4753 Dihedral : 11.906 104.982 4838 Min Nonbonded Distance : 2.404 Molprobity Statistics. All-atom Clashscore : 13.16 Ramachandran Plot: Outliers : 0.48 % Allowed : 12.83 % Favored : 86.70 % Rotamer: Outliers : 1.90 % Allowed : 15.88 % Favored : 82.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.52 % Cis-general : 0.00 % Twisted Proline : 3.79 % Twisted General : 0.43 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.42 (0.15), residues: 3365 helix: 0.19 (0.13), residues: 1480 sheet: -3.73 (0.25), residues: 334 loop : -2.98 (0.15), residues: 1551 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.002 TRP B 589 HIS 0.006 0.001 HIS A 111 PHE 0.051 0.002 PHE B 643 TYR 0.025 0.001 TYR C 254 ARG 0.013 0.000 ARG A 866 Details of bonding type rmsd link_NAG-ASN : bond 0.00805 ( 30) link_NAG-ASN : angle 4.05430 ( 90) link_ALPHA1-6 : bond 0.01446 ( 5) link_ALPHA1-6 : angle 2.36413 ( 15) link_BETA1-4 : bond 0.01034 ( 18) link_BETA1-4 : angle 4.03167 ( 54) link_ALPHA1-3 : bond 0.02500 ( 5) link_ALPHA1-3 : angle 3.64946 ( 15) hydrogen bonds : bond 0.03426 ( 945) hydrogen bonds : angle 4.76884 ( 2756) SS BOND : bond 0.00173 ( 8) SS BOND : angle 1.20014 ( 16) covalent geometry : bond 0.00297 (28123) covalent geometry : angle 0.87366 (38071) *********************** 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 301 residues out of total 2931 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 249 time to evaluate : 3.839 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: A 85 LEU cc_start: 0.9198 (OUTLIER) cc_final: 0.8777 (tm) REVERT: A 298 MET cc_start: 0.8075 (tmm) cc_final: 0.7596 (tmm) REVERT: A 316 MET cc_start: 0.8123 (mmm) cc_final: 0.7724 (tpt) REVERT: A 454 TYR cc_start: 0.8438 (m-80) cc_final: 0.8187 (m-80) REVERT: A 517 LEU cc_start: 0.8959 (mm) cc_final: 0.8689 (mm) REVERT: A 606 PHE cc_start: 0.8462 (OUTLIER) cc_final: 0.8131 (t80) REVERT: A 612 PHE cc_start: 0.8315 (OUTLIER) cc_final: 0.7716 (p90) REVERT: A 709 MET cc_start: 0.9097 (mmm) cc_final: 0.8759 (mmm) REVERT: A 714 GLN cc_start: 0.7915 (tp-100) cc_final: 0.7603 (tp-100) REVERT: A 718 VAL cc_start: 0.6963 (OUTLIER) cc_final: 0.6560 (m) REVERT: A 738 GLU cc_start: 0.8186 (mp0) cc_final: 0.7984 (mp0) REVERT: A 770 MET cc_start: 0.8179 (tpp) cc_final: 0.7331 (tpp) REVERT: A 867 MET cc_start: 0.8372 (mtp) cc_final: 0.6777 (tpt) REVERT: B 55 LEU cc_start: 0.9375 (OUTLIER) cc_final: 0.9161 (mm) REVERT: B 73 ASN cc_start: 0.7656 (OUTLIER) cc_final: 0.7385 (m110) REVERT: B 589 TRP cc_start: 0.6169 (OUTLIER) cc_final: 0.5826 (m100) REVERT: B 651 TYR cc_start: 0.8748 (t80) cc_final: 0.8181 (t80) REVERT: B 680 ILE cc_start: 0.7850 (OUTLIER) cc_final: 0.7287 (tp) REVERT: B 719 LYS cc_start: 0.9008 (mttp) cc_final: 0.7890 (tppt) REVERT: B 794 MET cc_start: 0.7180 (mmt) cc_final: 0.6866 (mmt) REVERT: B 867 MET cc_start: 0.6179 (tmm) cc_final: 0.5091 (mmp) REVERT: C 50 MET cc_start: 0.7641 (tmm) cc_final: 0.7077 (tmm) REVERT: C 323 MET cc_start: 0.8810 (mmm) cc_final: 0.8606 (tpp) REVERT: C 413 MET cc_start: 0.7675 (ppp) cc_final: 0.6752 (ppp) REVERT: C 428 LEU cc_start: 0.8180 (tt) cc_final: 0.7868 (tp) REVERT: C 454 TYR cc_start: 0.8149 (m-80) cc_final: 0.7945 (m-80) REVERT: C 463 CYS cc_start: 0.9063 (m) cc_final: 0.8608 (m) REVERT: C 484 GLU cc_start: 0.8239 (mp0) cc_final: 0.7896 (tp30) REVERT: C 501 MET cc_start: 0.8764 (mpt) cc_final: 0.8188 (mmm) REVERT: C 556 LEU cc_start: 0.8415 (mm) cc_final: 0.8094 (mp) REVERT: C 565 MET cc_start: 0.9094 (mtm) cc_final: 0.8763 (ptp) REVERT: C 619 LEU cc_start: 0.9514 (tp) cc_final: 0.9313 (tt) REVERT: C 679 LYS cc_start: 0.9310 (ptmm) cc_final: 0.8882 (ptpp) REVERT: C 737 MET cc_start: 0.7181 (ppp) cc_final: 0.6569 (ppp) REVERT: C 764 TYR cc_start: 0.6733 (m-80) cc_final: 0.6431 (m-80) REVERT: C 793 MET cc_start: 0.9003 (ppp) cc_final: 0.8777 (ppp) REVERT: C 815 LEU cc_start: 0.8441 (mt) cc_final: 0.7824 (mt) REVERT: D 50 MET cc_start: 0.8284 (tmm) cc_final: 0.8039 (tmm) REVERT: D 248 MET cc_start: 0.8467 (mmm) cc_final: 0.8222 (mmm) REVERT: D 691 MET cc_start: 0.8732 (tmm) cc_final: 0.7950 (tmm) REVERT: D 705 MET cc_start: 0.8108 (pmm) cc_final: 0.7787 (pmm) REVERT: D 722 GLU cc_start: 0.9475 (mt-10) cc_final: 0.9000 (mp0) REVERT: D 793 MET cc_start: 0.8711 (tpp) cc_final: 0.8239 (ppp) REVERT: D 794 MET cc_start: 0.6866 (tmm) cc_final: 0.5449 (ppp) REVERT: D 861 MET cc_start: 0.6280 (mtt) cc_final: 0.5907 (mmm) outliers start: 52 outliers final: 31 residues processed: 287 average time/residue: 0.3620 time to fit residues: 175.9307 Evaluate side-chains 270 residues out of total 2931 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 231 time to evaluate : 3.415 ------------------------------------------------------------------------------- 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 606 PHE Chi-restraints excluded: chain A residue 612 PHE Chi-restraints excluded: chain A residue 686 GLU Chi-restraints excluded: chain A residue 718 VAL 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 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 226 VAL 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 589 TRP Chi-restraints excluded: chain B residue 680 ILE Chi-restraints excluded: chain B residue 682 TYR 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 411 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 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 336 random chunks: chunk 96 optimal weight: 4.9990 chunk 305 optimal weight: 5.9990 chunk 245 optimal weight: 0.0020 chunk 0 optimal weight: 10.0000 chunk 179 optimal weight: 3.9990 chunk 295 optimal weight: 20.0000 chunk 224 optimal weight: 10.0000 chunk 290 optimal weight: 0.0770 chunk 80 optimal weight: 9.9990 chunk 246 optimal weight: 0.9980 chunk 10 optimal weight: 3.9990 overall best weight: 1.8150 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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** C 137 GLN ** D 491 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 = 0.3933 r_free = 0.3933 target = 0.101950 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3301 r_free = 0.3301 target = 0.069611 restraints weight = 198473.868| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3274 r_free = 0.3274 target = 0.069948 restraints weight = 106234.551| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3298 r_free = 0.3298 target = 0.071153 restraints weight = 70251.772| |-----------------------------------------------------------------------------| r_work (final): 0.3269 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3272 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3272 r_free = 0.3272 target_work(ls_wunit_k1) = 0.069 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3272 r_free = 0.3272 target_work(ls_wunit_k1) = 0.069 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| r_final: 0.3272 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8028 moved from start: 0.4621 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 28189 Z= 0.167 Angle : 0.912 14.063 38261 Z= 0.423 Chirality : 0.050 0.486 4412 Planarity : 0.005 0.111 4753 Dihedral : 11.577 106.301 4838 Min Nonbonded Distance : 2.385 Molprobity Statistics. All-atom Clashscore : 14.44 Ramachandran Plot: Outliers : 0.48 % Allowed : 13.36 % Favored : 86.16 % Rotamer: Outliers : 1.60 % Allowed : 16.32 % Favored : 82.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.52 % Cis-general : 0.00 % Twisted Proline : 3.79 % Twisted General : 0.46 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.34 (0.15), residues: 3365 helix: 0.27 (0.13), residues: 1483 sheet: -3.76 (0.25), residues: 332 loop : -2.95 (0.15), residues: 1550 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.002 TRP B 589 HIS 0.006 0.001 HIS A 111 PHE 0.055 0.002 PHE B 643 TYR 0.021 0.001 TYR C 254 ARG 0.004 0.000 ARG D 713 Details of bonding type rmsd link_NAG-ASN : bond 0.00751 ( 30) link_NAG-ASN : angle 4.03756 ( 90) link_ALPHA1-6 : bond 0.01325 ( 5) link_ALPHA1-6 : angle 2.40294 ( 15) link_BETA1-4 : bond 0.00995 ( 18) link_BETA1-4 : angle 4.03505 ( 54) link_ALPHA1-3 : bond 0.02493 ( 5) link_ALPHA1-3 : angle 3.65838 ( 15) hydrogen bonds : bond 0.03441 ( 945) hydrogen bonds : angle 4.78417 ( 2756) SS BOND : bond 0.00185 ( 8) SS BOND : angle 1.13297 ( 16) covalent geometry : bond 0.00370 (28123) covalent geometry : angle 0.87575 (38071) ********************** 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 277 residues out of total 2931 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 234 time to evaluate : 3.363 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: A 85 LEU cc_start: 0.9274 (OUTLIER) cc_final: 0.8836 (tm) REVERT: A 298 MET cc_start: 0.8088 (tmm) cc_final: 0.7602 (tmm) REVERT: A 316 MET cc_start: 0.8120 (mmm) cc_final: 0.7114 (tpt) REVERT: A 454 TYR cc_start: 0.8444 (m-80) cc_final: 0.8184 (m-80) REVERT: A 517 LEU cc_start: 0.8984 (mm) cc_final: 0.8671 (mm) REVERT: A 606 PHE cc_start: 0.8394 (OUTLIER) cc_final: 0.8117 (t80) REVERT: A 612 PHE cc_start: 0.8328 (OUTLIER) cc_final: 0.7745 (p90) REVERT: A 627 MET cc_start: 0.8544 (mmp) cc_final: 0.7865 (tpt) REVERT: A 709 MET cc_start: 0.9051 (mmm) cc_final: 0.8709 (mmm) REVERT: A 714 GLN cc_start: 0.7795 (tp-100) cc_final: 0.7445 (tp-100) REVERT: A 718 VAL cc_start: 0.6970 (OUTLIER) cc_final: 0.6760 (m) REVERT: A 770 MET cc_start: 0.8268 (tpp) cc_final: 0.7679 (tpp) REVERT: A 867 MET cc_start: 0.8235 (mtp) cc_final: 0.6877 (tpt) REVERT: B 55 LEU cc_start: 0.9270 (OUTLIER) cc_final: 0.8973 (mm) REVERT: B 73 ASN cc_start: 0.7643 (OUTLIER) cc_final: 0.7364 (m110) REVERT: B 589 TRP cc_start: 0.6243 (OUTLIER) cc_final: 0.5918 (m100) REVERT: B 608 LEU cc_start: 0.8878 (pt) cc_final: 0.8625 (mm) REVERT: B 651 TYR cc_start: 0.8713 (t80) cc_final: 0.8307 (t80) REVERT: B 680 ILE cc_start: 0.7860 (OUTLIER) cc_final: 0.7310 (tp) REVERT: B 719 LYS cc_start: 0.9026 (mttp) cc_final: 0.7914 (tppt) REVERT: B 794 MET cc_start: 0.7187 (mmt) cc_final: 0.6945 (mmt) REVERT: B 867 MET cc_start: 0.6278 (tmm) cc_final: 0.5098 (mmp) REVERT: C 50 MET cc_start: 0.7708 (tmm) cc_final: 0.7136 (tmm) REVERT: C 323 MET cc_start: 0.8857 (mmm) cc_final: 0.8643 (tpp) REVERT: C 413 MET cc_start: 0.7685 (ppp) cc_final: 0.6725 (ppp) REVERT: C 428 LEU cc_start: 0.8152 (tt) cc_final: 0.7845 (tp) REVERT: C 463 CYS cc_start: 0.9052 (m) cc_final: 0.8616 (m) REVERT: C 484 GLU cc_start: 0.8253 (mp0) cc_final: 0.7889 (tp30) REVERT: C 501 MET cc_start: 0.8786 (mpt) cc_final: 0.8260 (mmm) REVERT: C 556 LEU cc_start: 0.8402 (mm) cc_final: 0.8093 (mp) REVERT: C 679 LYS cc_start: 0.9317 (ptmm) cc_final: 0.8911 (ptpp) REVERT: C 737 MET cc_start: 0.7111 (ppp) cc_final: 0.6582 (ppp) REVERT: C 764 TYR cc_start: 0.6748 (m-80) cc_final: 0.6512 (m-80) REVERT: C 793 MET cc_start: 0.8927 (ppp) cc_final: 0.8636 (ppp) REVERT: C 815 LEU cc_start: 0.8516 (mt) cc_final: 0.7906 (mt) REVERT: D 248 MET cc_start: 0.8520 (mmm) cc_final: 0.8284 (mmm) REVERT: D 691 MET cc_start: 0.8694 (tmm) cc_final: 0.7902 (tmm) REVERT: D 705 MET cc_start: 0.8066 (pmm) cc_final: 0.7694 (pmm) REVERT: D 722 GLU cc_start: 0.9511 (mt-10) cc_final: 0.9058 (mp0) REVERT: D 793 MET cc_start: 0.8715 (tpp) cc_final: 0.8276 (ppp) REVERT: D 794 MET cc_start: 0.6863 (tmm) cc_final: 0.5591 (ppp) REVERT: D 861 MET cc_start: 0.6111 (mtt) cc_final: 0.5724 (mmm) outliers start: 43 outliers final: 32 residues processed: 265 average time/residue: 0.3507 time to fit residues: 157.5089 Evaluate side-chains 269 residues out of total 2931 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 229 time to evaluate : 4.168 ------------------------------------------------------------------------------- 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 606 PHE Chi-restraints excluded: chain A residue 612 PHE Chi-restraints excluded: chain A residue 646 ILE Chi-restraints excluded: chain A residue 718 VAL 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 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 226 VAL Chi-restraints excluded: chain B residue 376 THR 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 589 TRP 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 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 411 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 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 320 optimal weight: 20.0000 chunk 252 optimal weight: 8.9990 chunk 173 optimal weight: 0.8980 chunk 283 optimal weight: 0.0370 chunk 185 optimal weight: 0.2980 chunk 156 optimal weight: 4.9990 chunk 247 optimal weight: 9.9990 chunk 116 optimal weight: 1.9990 chunk 119 optimal weight: 0.9980 chunk 73 optimal weight: 0.9990 chunk 177 optimal weight: 5.9990 overall best weight: 0.6460 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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** ** C 129 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 137 GLN 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 = 0.3962 r_free = 0.3962 target = 0.103616 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3371 r_free = 0.3371 target = 0.073527 restraints weight = 190105.988| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3335 r_free = 0.3335 target = 0.072933 restraints weight = 95269.027| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3352 r_free = 0.3352 target = 0.073887 restraints weight = 73919.519| |-----------------------------------------------------------------------------| r_work (final): 0.3317 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3317 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3317 r_free = 0.3317 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 = 0.3317 r_free = 0.3317 target_work(ls_wunit_k1) = 0.071 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| r_final: 0.3317 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7966 moved from start: 0.4856 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 28189 Z= 0.141 Angle : 0.912 16.673 38261 Z= 0.422 Chirality : 0.049 0.465 4412 Planarity : 0.005 0.110 4753 Dihedral : 11.035 108.282 4838 Min Nonbonded Distance : 2.422 Molprobity Statistics. All-atom Clashscore : 12.93 Ramachandran Plot: Outliers : 0.45 % Allowed : 12.92 % Favored : 86.64 % Rotamer: Outliers : 1.50 % Allowed : 16.73 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.23 (0.15), residues: 3365 helix: 0.32 (0.13), residues: 1482 sheet: -3.58 (0.25), residues: 326 loop : -2.89 (0.16), residues: 1557 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP B 589 HIS 0.006 0.001 HIS D 253 PHE 0.063 0.002 PHE B 643 TYR 0.022 0.001 TYR C 254 ARG 0.005 0.000 ARG D 713 Details of bonding type rmsd link_NAG-ASN : bond 0.00783 ( 30) link_NAG-ASN : angle 3.96020 ( 90) link_ALPHA1-6 : bond 0.01302 ( 5) link_ALPHA1-6 : angle 2.35979 ( 15) link_BETA1-4 : bond 0.01060 ( 18) link_BETA1-4 : angle 3.99430 ( 54) link_ALPHA1-3 : bond 0.02451 ( 5) link_ALPHA1-3 : angle 3.78438 ( 15) hydrogen bonds : bond 0.03352 ( 945) hydrogen bonds : angle 4.71384 ( 2756) SS BOND : bond 0.00178 ( 8) SS BOND : angle 1.20605 ( 16) covalent geometry : bond 0.00301 (28123) covalent geometry : angle 0.87632 (38071) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 9244.97 seconds wall clock time: 163 minutes 10.31 seconds (9790.31 seconds total)