Starting phenix.real_space_refine on Fri May 16 08:21:50 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8un7_42394/05_2025/8un7_42394.cif Found real_map, /net/cci-nas-00/data/ceres_data/8un7_42394/05_2025/8un7_42394.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.55 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8un7_42394/05_2025/8un7_42394.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8un7_42394/05_2025/8un7_42394.map" model { file = "/net/cci-nas-00/data/ceres_data/8un7_42394/05_2025/8un7_42394.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8un7_42394/05_2025/8un7_42394.cif" } resolution = 3.55 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.002 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians Ca 8 9.91 5 S 56 5.16 5 C 9160 2.51 5 N 2344 2.21 5 O 2728 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 120 residue(s): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/chem_data/mon_lib" Total number of atoms: 14296 Number of models: 1 Model: "" Number of chains: 16 Chain: "A" Number of atoms: 1758 Number of conformers: 1 Conformer: "" Number of residues, atoms: 219, 1758 Classifications: {'peptide': 219} Link IDs: {'PTRANS': 6, 'TRANS': 212} Chain: "D" Number of atoms: 1758 Number of conformers: 1 Conformer: "" Number of residues, atoms: 219, 1758 Classifications: {'peptide': 219} Link IDs: {'PTRANS': 6, 'TRANS': 212} Chain: "B" Number of atoms: 1758 Number of conformers: 1 Conformer: "" Number of residues, atoms: 219, 1758 Classifications: {'peptide': 219} Link IDs: {'PTRANS': 6, 'TRANS': 212} Chain: "E" Number of atoms: 1758 Number of conformers: 1 Conformer: "" Number of residues, atoms: 219, 1758 Classifications: {'peptide': 219} Link IDs: {'PTRANS': 6, 'TRANS': 212} Chain: "C" Number of atoms: 1758 Number of conformers: 1 Conformer: "" Number of residues, atoms: 219, 1758 Classifications: {'peptide': 219} Link IDs: {'PTRANS': 6, 'TRANS': 212} Chain: "F" Number of atoms: 1758 Number of conformers: 1 Conformer: "" Number of residues, atoms: 219, 1758 Classifications: {'peptide': 219} Link IDs: {'PTRANS': 6, 'TRANS': 212} Chain: "G" Number of atoms: 1758 Number of conformers: 1 Conformer: "" Number of residues, atoms: 219, 1758 Classifications: {'peptide': 219} Link IDs: {'PTRANS': 6, 'TRANS': 212} Chain: "H" Number of atoms: 1758 Number of conformers: 1 Conformer: "" Number of residues, atoms: 219, 1758 Classifications: {'peptide': 219} Link IDs: {'PTRANS': 6, 'TRANS': 212} Chain: "A" Number of atoms: 29 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 29 Unusual residues: {' CA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "D" Number of atoms: 29 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 29 Unusual residues: {' CA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "B" Number of atoms: 29 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 29 Unusual residues: {' CA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "E" Number of atoms: 29 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 29 Unusual residues: {' CA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "C" Number of atoms: 29 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 29 Unusual residues: {' CA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "F" Number of atoms: 29 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 29 Unusual residues: {' CA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "G" Number of atoms: 29 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 29 Unusual residues: {' CA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "H" Number of atoms: 29 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 29 Unusual residues: {' CA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Time building chain proxies: 8.45, per 1000 atoms: 0.59 Number of scatterers: 14296 At special positions: 0 Unit cell: (110.295, 110.295, 108.585, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) Ca 8 19.99 S 56 16.00 O 2728 8.00 N 2344 7.00 C 9160 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=16, symmetry=0 Simple disulfide: pdb=" SG CYS A 41 " - pdb=" SG CYS A 70 " distance=2.03 Simple disulfide: pdb=" SG CYS A 199 " - pdb=" SG CYS A 212 " distance=2.03 Simple disulfide: pdb=" SG CYS D 41 " - pdb=" SG CYS D 70 " distance=2.03 Simple disulfide: pdb=" SG CYS D 199 " - pdb=" SG CYS D 212 " distance=2.03 Simple disulfide: pdb=" SG CYS B 41 " - pdb=" SG CYS B 70 " distance=2.03 Simple disulfide: pdb=" SG CYS B 199 " - pdb=" SG CYS B 212 " distance=2.03 Simple disulfide: pdb=" SG CYS E 41 " - pdb=" SG CYS E 70 " distance=2.03 Simple disulfide: pdb=" SG CYS E 199 " - pdb=" SG CYS E 212 " distance=2.03 Simple disulfide: pdb=" SG CYS C 41 " - pdb=" SG CYS C 70 " distance=2.03 Simple disulfide: pdb=" SG CYS C 199 " - pdb=" SG CYS C 212 " distance=2.03 Simple disulfide: pdb=" SG CYS F 41 " - pdb=" SG CYS F 70 " distance=2.03 Simple disulfide: pdb=" SG CYS F 199 " - pdb=" SG CYS F 212 " distance=2.03 Simple disulfide: pdb=" SG CYS G 41 " - pdb=" SG CYS G 70 " distance=2.03 Simple disulfide: pdb=" SG CYS G 199 " - pdb=" SG CYS G 212 " distance=2.03 Simple disulfide: pdb=" SG CYS H 41 " - pdb=" SG CYS H 70 " distance=2.03 Simple disulfide: pdb=" SG CYS H 199 " - pdb=" SG CYS H 212 " 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 NAG-ASN " NAG A 301 " - " ASN A 87 " " NAG A 302 " - " ASN A 137 " " NAG B 301 " - " ASN B 87 " " NAG B 302 " - " ASN B 137 " " NAG C 301 " - " ASN C 87 " " NAG C 302 " - " ASN C 137 " " NAG D 301 " - " ASN D 87 " " NAG D 302 " - " ASN D 137 " " NAG E 301 " - " ASN E 87 " " NAG E 302 " - " ASN E 137 " " NAG F 301 " - " ASN F 87 " " NAG F 302 " - " ASN F 137 " " NAG G 301 " - " ASN G 87 " " NAG G 302 " - " ASN G 137 " " NAG H 301 " - " ASN H 87 " " NAG H 302 " - " ASN H 137 " Time building additional restraints: 3.27 Conformation dependent library (CDL) restraints added in 1.7 seconds 3472 Ramachandran restraints generated. 1736 Oldfield, 0 Emsley, 1736 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3136 Finding SS restraints... Secondary structure from input PDB file: 40 helices and 20 sheets defined 18.0% alpha, 23.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.47 Creating SS restraints... Processing helix chain 'A' and resid 40 through 46 removed outlier: 3.547A pdb=" N ILE A 44 " --> pdb=" O ASP A 40 " (cutoff:3.500A) Processing helix chain 'A' and resid 95 through 102 Processing helix chain 'A' and resid 113 through 124 removed outlier: 3.980A pdb=" N LYS A 123 " --> pdb=" O LEU A 119 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N GLN A 124 " --> pdb=" O LEU A 120 " (cutoff:3.500A) Processing helix chain 'A' and resid 155 through 160 Processing helix chain 'A' and resid 193 through 199 removed outlier: 3.555A pdb=" N GLN A 197 " --> pdb=" O ASP A 193 " (cutoff:3.500A) Processing helix chain 'D' and resid 40 through 46 removed outlier: 3.827A pdb=" N ALA D 46 " --> pdb=" O ASP D 42 " (cutoff:3.500A) Processing helix chain 'D' and resid 95 through 102 Processing helix chain 'D' and resid 113 through 124 removed outlier: 3.806A pdb=" N LYS D 123 " --> pdb=" O LEU D 119 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N GLN D 124 " --> pdb=" O LEU D 120 " (cutoff:3.500A) Processing helix chain 'D' and resid 155 through 160 Processing helix chain 'D' and resid 194 through 199 removed outlier: 3.603A pdb=" N ASN D 198 " --> pdb=" O LEU D 194 " (cutoff:3.500A) Processing helix chain 'B' and resid 40 through 46 removed outlier: 3.547A pdb=" N ILE B 44 " --> pdb=" O ASP B 40 " (cutoff:3.500A) Processing helix chain 'B' and resid 95 through 102 Processing helix chain 'B' and resid 113 through 124 removed outlier: 3.980A pdb=" N LYS B 123 " --> pdb=" O LEU B 119 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N GLN B 124 " --> pdb=" O LEU B 120 " (cutoff:3.500A) Processing helix chain 'B' and resid 155 through 160 Processing helix chain 'B' and resid 193 through 199 removed outlier: 3.555A pdb=" N GLN B 197 " --> pdb=" O ASP B 193 " (cutoff:3.500A) Processing helix chain 'E' and resid 40 through 46 removed outlier: 3.827A pdb=" N ALA E 46 " --> pdb=" O ASP E 42 " (cutoff:3.500A) Processing helix chain 'E' and resid 95 through 102 Processing helix chain 'E' and resid 113 through 124 removed outlier: 3.806A pdb=" N LYS E 123 " --> pdb=" O LEU E 119 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N GLN E 124 " --> pdb=" O LEU E 120 " (cutoff:3.500A) Processing helix chain 'E' and resid 155 through 160 Processing helix chain 'E' and resid 194 through 199 removed outlier: 3.603A pdb=" N ASN E 198 " --> pdb=" O LEU E 194 " (cutoff:3.500A) Processing helix chain 'C' and resid 40 through 46 removed outlier: 3.547A pdb=" N ILE C 44 " --> pdb=" O ASP C 40 " (cutoff:3.500A) Processing helix chain 'C' and resid 95 through 102 Processing helix chain 'C' and resid 113 through 124 removed outlier: 3.980A pdb=" N LYS C 123 " --> pdb=" O LEU C 119 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N GLN C 124 " --> pdb=" O LEU C 120 " (cutoff:3.500A) Processing helix chain 'C' and resid 155 through 160 Processing helix chain 'C' and resid 193 through 199 removed outlier: 3.555A pdb=" N GLN C 197 " --> pdb=" O ASP C 193 " (cutoff:3.500A) Processing helix chain 'F' and resid 40 through 46 removed outlier: 3.827A pdb=" N ALA F 46 " --> pdb=" O ASP F 42 " (cutoff:3.500A) Processing helix chain 'F' and resid 95 through 102 Processing helix chain 'F' and resid 113 through 124 removed outlier: 3.806A pdb=" N LYS F 123 " --> pdb=" O LEU F 119 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N GLN F 124 " --> pdb=" O LEU F 120 " (cutoff:3.500A) Processing helix chain 'F' and resid 155 through 160 Processing helix chain 'F' and resid 194 through 199 removed outlier: 3.603A pdb=" N ASN F 198 " --> pdb=" O LEU F 194 " (cutoff:3.500A) Processing helix chain 'G' and resid 40 through 46 removed outlier: 3.547A pdb=" N ILE G 44 " --> pdb=" O ASP G 40 " (cutoff:3.500A) Processing helix chain 'G' and resid 95 through 102 Processing helix chain 'G' and resid 113 through 124 removed outlier: 3.980A pdb=" N LYS G 123 " --> pdb=" O LEU G 119 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N GLN G 124 " --> pdb=" O LEU G 120 " (cutoff:3.500A) Processing helix chain 'G' and resid 155 through 160 Processing helix chain 'G' and resid 193 through 199 removed outlier: 3.555A pdb=" N GLN G 197 " --> pdb=" O ASP G 193 " (cutoff:3.500A) Processing helix chain 'H' and resid 40 through 46 removed outlier: 3.827A pdb=" N ALA H 46 " --> pdb=" O ASP H 42 " (cutoff:3.500A) Processing helix chain 'H' and resid 95 through 102 Processing helix chain 'H' and resid 113 through 124 removed outlier: 3.806A pdb=" N LYS H 123 " --> pdb=" O LEU H 119 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N GLN H 124 " --> pdb=" O LEU H 120 " (cutoff:3.500A) Processing helix chain 'H' and resid 155 through 160 Processing helix chain 'H' and resid 194 through 199 removed outlier: 3.603A pdb=" N ASN H 198 " --> pdb=" O LEU H 194 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 53 through 57 removed outlier: 3.926A pdb=" N GLY A 53 " --> pdb=" O CYS A 70 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N CYS A 70 " --> pdb=" O GLY A 53 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 103 through 104 removed outlier: 3.754A pdb=" N TYR A 110 " --> pdb=" O LYS A 84 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N LYS A 84 " --> pdb=" O TYR A 110 " (cutoff:3.500A) removed outlier: 6.275A pdb=" N MET A 250 " --> pdb=" O PHE A 82 " (cutoff:3.500A) removed outlier: 4.349A pdb=" N LYS A 84 " --> pdb=" O THR A 248 " (cutoff:3.500A) removed outlier: 6.534A pdb=" N THR A 248 " --> pdb=" O LYS A 84 " (cutoff:3.500A) removed outlier: 6.859A pdb=" N GLY A 167 " --> pdb=" O ALA A 145 " (cutoff:3.500A) removed outlier: 7.013A pdb=" N PHE A 147 " --> pdb=" O VAL A 165 " (cutoff:3.500A) removed outlier: 7.129A pdb=" N VAL A 165 " --> pdb=" O PHE A 147 " (cutoff:3.500A) removed outlier: 6.857A pdb=" N ILE A 149 " --> pdb=" O LEU A 163 " (cutoff:3.500A) removed outlier: 7.176A pdb=" N LEU A 163 " --> pdb=" O ILE A 149 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'D' and resid 53 through 57 removed outlier: 3.789A pdb=" N GLY D 53 " --> pdb=" O CYS D 70 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N CYS D 70 " --> pdb=" O GLY D 53 " (cutoff:3.500A) removed outlier: 10.103A pdb=" N GLN D 83 " --> pdb=" O PRO D 67 " (cutoff:3.500A) removed outlier: 4.926A pdb=" N PHE D 69 " --> pdb=" O VAL D 81 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N VAL D 81 " --> pdb=" O PHE D 69 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N LYS D 84 " --> pdb=" O TYR D 110 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N TYR D 110 " --> pdb=" O LYS D 84 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'D' and resid 53 through 57 removed outlier: 3.789A pdb=" N GLY D 53 " --> pdb=" O CYS D 70 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N CYS D 70 " --> pdb=" O GLY D 53 " (cutoff:3.500A) removed outlier: 10.103A pdb=" N GLN D 83 " --> pdb=" O PRO D 67 " (cutoff:3.500A) removed outlier: 4.926A pdb=" N PHE D 69 " --> pdb=" O VAL D 81 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N VAL D 81 " --> pdb=" O PHE D 69 " (cutoff:3.500A) removed outlier: 6.305A pdb=" N MET D 250 " --> pdb=" O PHE D 82 " (cutoff:3.500A) removed outlier: 4.445A pdb=" N LYS D 84 " --> pdb=" O THR D 248 " (cutoff:3.500A) removed outlier: 6.541A pdb=" N THR D 248 " --> pdb=" O LYS D 84 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N ARG D 247 " --> pdb=" O GLU D 133 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N GLU D 133 " --> pdb=" O ARG D 247 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N GLU D 249 " --> pdb=" O ASP D 131 " (cutoff:3.500A) removed outlier: 6.808A pdb=" N GLY D 167 " --> pdb=" O ALA D 145 " (cutoff:3.500A) removed outlier: 7.265A pdb=" N PHE D 147 " --> pdb=" O VAL D 165 " (cutoff:3.500A) removed outlier: 7.293A pdb=" N VAL D 165 " --> pdb=" O PHE D 147 " (cutoff:3.500A) removed outlier: 6.908A pdb=" N ILE D 149 " --> pdb=" O LEU D 163 " (cutoff:3.500A) removed outlier: 7.068A pdb=" N LEU D 163 " --> pdb=" O ILE D 149 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'D' and resid 185 through 186 removed outlier: 3.621A pdb=" N SER D 186 " --> pdb=" O PHE D 207 " (cutoff:3.500A) removed outlier: 3.898A pdb=" N PHE D 207 " --> pdb=" O SER D 186 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA5 Processing sheet with id=AA6, first strand: chain 'B' and resid 53 through 57 removed outlier: 3.926A pdb=" N GLY B 53 " --> pdb=" O CYS B 70 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N CYS B 70 " --> pdb=" O GLY B 53 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 103 through 104 removed outlier: 3.754A pdb=" N TYR B 110 " --> pdb=" O LYS B 84 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N LYS B 84 " --> pdb=" O TYR B 110 " (cutoff:3.500A) removed outlier: 6.275A pdb=" N MET B 250 " --> pdb=" O PHE B 82 " (cutoff:3.500A) removed outlier: 4.349A pdb=" N LYS B 84 " --> pdb=" O THR B 248 " (cutoff:3.500A) removed outlier: 6.534A pdb=" N THR B 248 " --> pdb=" O LYS B 84 " (cutoff:3.500A) removed outlier: 6.859A pdb=" N GLY B 167 " --> pdb=" O ALA B 145 " (cutoff:3.500A) removed outlier: 7.013A pdb=" N PHE B 147 " --> pdb=" O VAL B 165 " (cutoff:3.500A) removed outlier: 7.129A pdb=" N VAL B 165 " --> pdb=" O PHE B 147 " (cutoff:3.500A) removed outlier: 6.857A pdb=" N ILE B 149 " --> pdb=" O LEU B 163 " (cutoff:3.500A) removed outlier: 7.176A pdb=" N LEU B 163 " --> pdb=" O ILE B 149 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'E' and resid 53 through 57 removed outlier: 3.789A pdb=" N GLY E 53 " --> pdb=" O CYS E 70 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N CYS E 70 " --> pdb=" O GLY E 53 " (cutoff:3.500A) removed outlier: 10.103A pdb=" N GLN E 83 " --> pdb=" O PRO E 67 " (cutoff:3.500A) removed outlier: 4.926A pdb=" N PHE E 69 " --> pdb=" O VAL E 81 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N VAL E 81 " --> pdb=" O PHE E 69 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N LYS E 84 " --> pdb=" O TYR E 110 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N TYR E 110 " --> pdb=" O LYS E 84 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'E' and resid 53 through 57 removed outlier: 3.789A pdb=" N GLY E 53 " --> pdb=" O CYS E 70 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N CYS E 70 " --> pdb=" O GLY E 53 " (cutoff:3.500A) removed outlier: 10.103A pdb=" N GLN E 83 " --> pdb=" O PRO E 67 " (cutoff:3.500A) removed outlier: 4.926A pdb=" N PHE E 69 " --> pdb=" O VAL E 81 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N VAL E 81 " --> pdb=" O PHE E 69 " (cutoff:3.500A) removed outlier: 6.305A pdb=" N MET E 250 " --> pdb=" O PHE E 82 " (cutoff:3.500A) removed outlier: 4.445A pdb=" N LYS E 84 " --> pdb=" O THR E 248 " (cutoff:3.500A) removed outlier: 6.541A pdb=" N THR E 248 " --> pdb=" O LYS E 84 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N ARG E 247 " --> pdb=" O GLU E 133 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N GLU E 133 " --> pdb=" O ARG E 247 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N GLU E 249 " --> pdb=" O ASP E 131 " (cutoff:3.500A) removed outlier: 6.808A pdb=" N GLY E 167 " --> pdb=" O ALA E 145 " (cutoff:3.500A) removed outlier: 7.265A pdb=" N PHE E 147 " --> pdb=" O VAL E 165 " (cutoff:3.500A) removed outlier: 7.293A pdb=" N VAL E 165 " --> pdb=" O PHE E 147 " (cutoff:3.500A) removed outlier: 6.908A pdb=" N ILE E 149 " --> pdb=" O LEU E 163 " (cutoff:3.500A) removed outlier: 7.068A pdb=" N LEU E 163 " --> pdb=" O ILE E 149 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'E' and resid 185 through 186 removed outlier: 3.621A pdb=" N SER E 186 " --> pdb=" O PHE E 207 " (cutoff:3.500A) removed outlier: 3.898A pdb=" N PHE E 207 " --> pdb=" O SER E 186 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB1 Processing sheet with id=AB2, first strand: chain 'C' and resid 53 through 57 removed outlier: 3.926A pdb=" N GLY C 53 " --> pdb=" O CYS C 70 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N CYS C 70 " --> pdb=" O GLY C 53 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 103 through 104 removed outlier: 3.754A pdb=" N TYR C 110 " --> pdb=" O LYS C 84 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N LYS C 84 " --> pdb=" O TYR C 110 " (cutoff:3.500A) removed outlier: 6.275A pdb=" N MET C 250 " --> pdb=" O PHE C 82 " (cutoff:3.500A) removed outlier: 4.349A pdb=" N LYS C 84 " --> pdb=" O THR C 248 " (cutoff:3.500A) removed outlier: 6.534A pdb=" N THR C 248 " --> pdb=" O LYS C 84 " (cutoff:3.500A) removed outlier: 6.859A pdb=" N GLY C 167 " --> pdb=" O ALA C 145 " (cutoff:3.500A) removed outlier: 7.013A pdb=" N PHE C 147 " --> pdb=" O VAL C 165 " (cutoff:3.500A) removed outlier: 7.129A pdb=" N VAL C 165 " --> pdb=" O PHE C 147 " (cutoff:3.500A) removed outlier: 6.857A pdb=" N ILE C 149 " --> pdb=" O LEU C 163 " (cutoff:3.500A) removed outlier: 7.176A pdb=" N LEU C 163 " --> pdb=" O ILE C 149 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'F' and resid 53 through 57 removed outlier: 3.789A pdb=" N GLY F 53 " --> pdb=" O CYS F 70 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N CYS F 70 " --> pdb=" O GLY F 53 " (cutoff:3.500A) removed outlier: 10.103A pdb=" N GLN F 83 " --> pdb=" O PRO F 67 " (cutoff:3.500A) removed outlier: 4.926A pdb=" N PHE F 69 " --> pdb=" O VAL F 81 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N VAL F 81 " --> pdb=" O PHE F 69 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N LYS F 84 " --> pdb=" O TYR F 110 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N TYR F 110 " --> pdb=" O LYS F 84 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'F' and resid 53 through 57 removed outlier: 3.789A pdb=" N GLY F 53 " --> pdb=" O CYS F 70 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N CYS F 70 " --> pdb=" O GLY F 53 " (cutoff:3.500A) removed outlier: 10.103A pdb=" N GLN F 83 " --> pdb=" O PRO F 67 " (cutoff:3.500A) removed outlier: 4.926A pdb=" N PHE F 69 " --> pdb=" O VAL F 81 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N VAL F 81 " --> pdb=" O PHE F 69 " (cutoff:3.500A) removed outlier: 6.305A pdb=" N MET F 250 " --> pdb=" O PHE F 82 " (cutoff:3.500A) removed outlier: 4.445A pdb=" N LYS F 84 " --> pdb=" O THR F 248 " (cutoff:3.500A) removed outlier: 6.541A pdb=" N THR F 248 " --> pdb=" O LYS F 84 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N ARG F 247 " --> pdb=" O GLU F 133 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N GLU F 133 " --> pdb=" O ARG F 247 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N GLU F 249 " --> pdb=" O ASP F 131 " (cutoff:3.500A) removed outlier: 6.808A pdb=" N GLY F 167 " --> pdb=" O ALA F 145 " (cutoff:3.500A) removed outlier: 7.265A pdb=" N PHE F 147 " --> pdb=" O VAL F 165 " (cutoff:3.500A) removed outlier: 7.293A pdb=" N VAL F 165 " --> pdb=" O PHE F 147 " (cutoff:3.500A) removed outlier: 6.908A pdb=" N ILE F 149 " --> pdb=" O LEU F 163 " (cutoff:3.500A) removed outlier: 7.068A pdb=" N LEU F 163 " --> pdb=" O ILE F 149 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'F' and resid 185 through 186 removed outlier: 3.621A pdb=" N SER F 186 " --> pdb=" O PHE F 207 " (cutoff:3.500A) removed outlier: 3.898A pdb=" N PHE F 207 " --> pdb=" O SER F 186 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB6 Processing sheet with id=AB7, first strand: chain 'G' and resid 53 through 57 removed outlier: 3.926A pdb=" N GLY G 53 " --> pdb=" O CYS G 70 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N CYS G 70 " --> pdb=" O GLY G 53 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'G' and resid 103 through 104 removed outlier: 3.754A pdb=" N TYR G 110 " --> pdb=" O LYS G 84 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N LYS G 84 " --> pdb=" O TYR G 110 " (cutoff:3.500A) removed outlier: 6.275A pdb=" N MET G 250 " --> pdb=" O PHE G 82 " (cutoff:3.500A) removed outlier: 4.349A pdb=" N LYS G 84 " --> pdb=" O THR G 248 " (cutoff:3.500A) removed outlier: 6.534A pdb=" N THR G 248 " --> pdb=" O LYS G 84 " (cutoff:3.500A) removed outlier: 6.859A pdb=" N GLY G 167 " --> pdb=" O ALA G 145 " (cutoff:3.500A) removed outlier: 7.013A pdb=" N PHE G 147 " --> pdb=" O VAL G 165 " (cutoff:3.500A) removed outlier: 7.129A pdb=" N VAL G 165 " --> pdb=" O PHE G 147 " (cutoff:3.500A) removed outlier: 6.857A pdb=" N ILE G 149 " --> pdb=" O LEU G 163 " (cutoff:3.500A) removed outlier: 7.176A pdb=" N LEU G 163 " --> pdb=" O ILE G 149 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'H' and resid 53 through 57 removed outlier: 3.789A pdb=" N GLY H 53 " --> pdb=" O CYS H 70 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N CYS H 70 " --> pdb=" O GLY H 53 " (cutoff:3.500A) removed outlier: 10.103A pdb=" N GLN H 83 " --> pdb=" O PRO H 67 " (cutoff:3.500A) removed outlier: 4.926A pdb=" N PHE H 69 " --> pdb=" O VAL H 81 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N VAL H 81 " --> pdb=" O PHE H 69 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N LYS H 84 " --> pdb=" O TYR H 110 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N TYR H 110 " --> pdb=" O LYS H 84 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'H' and resid 53 through 57 removed outlier: 3.789A pdb=" N GLY H 53 " --> pdb=" O CYS H 70 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N CYS H 70 " --> pdb=" O GLY H 53 " (cutoff:3.500A) removed outlier: 10.103A pdb=" N GLN H 83 " --> pdb=" O PRO H 67 " (cutoff:3.500A) removed outlier: 4.926A pdb=" N PHE H 69 " --> pdb=" O VAL H 81 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N VAL H 81 " --> pdb=" O PHE H 69 " (cutoff:3.500A) removed outlier: 6.305A pdb=" N MET H 250 " --> pdb=" O PHE H 82 " (cutoff:3.500A) removed outlier: 4.445A pdb=" N LYS H 84 " --> pdb=" O THR H 248 " (cutoff:3.500A) removed outlier: 6.541A pdb=" N THR H 248 " --> pdb=" O LYS H 84 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N ARG H 247 " --> pdb=" O GLU H 133 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N GLU H 133 " --> pdb=" O ARG H 247 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N GLU H 249 " --> pdb=" O ASP H 131 " (cutoff:3.500A) removed outlier: 6.808A pdb=" N GLY H 167 " --> pdb=" O ALA H 145 " (cutoff:3.500A) removed outlier: 7.265A pdb=" N PHE H 147 " --> pdb=" O VAL H 165 " (cutoff:3.500A) removed outlier: 7.293A pdb=" N VAL H 165 " --> pdb=" O PHE H 147 " (cutoff:3.500A) removed outlier: 6.908A pdb=" N ILE H 149 " --> pdb=" O LEU H 163 " (cutoff:3.500A) removed outlier: 7.068A pdb=" N LEU H 163 " --> pdb=" O ILE H 149 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'H' and resid 185 through 186 removed outlier: 3.621A pdb=" N SER H 186 " --> pdb=" O PHE H 207 " (cutoff:3.500A) removed outlier: 3.898A pdb=" N PHE H 207 " --> pdb=" O SER H 186 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC2 336 hydrogen bonds defined for protein. 888 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 3.45 Time building geometry restraints manager: 3.84 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 4360 1.33 - 1.46: 3252 1.46 - 1.58: 7028 1.58 - 1.70: 0 1.70 - 1.82: 80 Bond restraints: 14720 Sorted by residual: bond pdb=" C1 NAG B 302 " pdb=" O5 NAG B 302 " ideal model delta sigma weight residual 1.406 1.441 -0.035 2.00e-02 2.50e+03 3.15e+00 bond pdb=" C1 NAG G 302 " pdb=" O5 NAG G 302 " ideal model delta sigma weight residual 1.406 1.441 -0.035 2.00e-02 2.50e+03 3.15e+00 bond pdb=" C1 NAG A 302 " pdb=" O5 NAG A 302 " ideal model delta sigma weight residual 1.406 1.441 -0.035 2.00e-02 2.50e+03 3.15e+00 bond pdb=" C1 NAG C 302 " pdb=" O5 NAG C 302 " ideal model delta sigma weight residual 1.406 1.441 -0.035 2.00e-02 2.50e+03 3.15e+00 bond pdb=" CD GLU C 136 " pdb=" OE1 GLU C 136 " ideal model delta sigma weight residual 1.249 1.220 0.029 1.90e-02 2.77e+03 2.27e+00 ... (remaining 14715 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.46: 19592 2.46 - 4.91: 276 4.91 - 7.37: 40 7.37 - 9.82: 4 9.82 - 12.28: 8 Bond angle restraints: 19920 Sorted by residual: angle pdb=" CA GLU B 136 " pdb=" CB GLU B 136 " pdb=" CG GLU B 136 " ideal model delta sigma weight residual 114.10 126.38 -12.28 2.00e+00 2.50e-01 3.77e+01 angle pdb=" CA GLU C 136 " pdb=" CB GLU C 136 " pdb=" CG GLU C 136 " ideal model delta sigma weight residual 114.10 126.38 -12.28 2.00e+00 2.50e-01 3.77e+01 angle pdb=" CA GLU A 136 " pdb=" CB GLU A 136 " pdb=" CG GLU A 136 " ideal model delta sigma weight residual 114.10 126.38 -12.28 2.00e+00 2.50e-01 3.77e+01 angle pdb=" CA GLU G 136 " pdb=" CB GLU G 136 " pdb=" CG GLU G 136 " ideal model delta sigma weight residual 114.10 126.38 -12.28 2.00e+00 2.50e-01 3.77e+01 angle pdb=" C GLU G 136 " pdb=" CA GLU G 136 " pdb=" CB GLU G 136 " ideal model delta sigma weight residual 110.42 100.19 10.23 1.99e+00 2.53e-01 2.65e+01 ... (remaining 19915 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.13: 7180 17.13 - 34.26: 944 34.26 - 51.39: 340 51.39 - 68.52: 56 68.52 - 85.65: 24 Dihedral angle restraints: 8544 sinusoidal: 3544 harmonic: 5000 Sorted by residual: dihedral pdb=" CA ARG B 190 " pdb=" C ARG B 190 " pdb=" N ASP B 191 " pdb=" CA ASP B 191 " ideal model delta harmonic sigma weight residual -180.00 -150.25 -29.75 0 5.00e+00 4.00e-02 3.54e+01 dihedral pdb=" CA ARG A 190 " pdb=" C ARG A 190 " pdb=" N ASP A 191 " pdb=" CA ASP A 191 " ideal model delta harmonic sigma weight residual -180.00 -150.25 -29.75 0 5.00e+00 4.00e-02 3.54e+01 dihedral pdb=" CA ARG C 190 " pdb=" C ARG C 190 " pdb=" N ASP C 191 " pdb=" CA ASP C 191 " ideal model delta harmonic sigma weight residual 180.00 -150.25 -29.75 0 5.00e+00 4.00e-02 3.54e+01 ... (remaining 8541 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.039: 1332 0.039 - 0.077: 432 0.077 - 0.115: 152 0.115 - 0.154: 48 0.154 - 0.192: 12 Chirality restraints: 1976 Sorted by residual: chirality pdb=" C1 NAG G 302 " pdb=" ND2 ASN G 137 " pdb=" C2 NAG G 302 " pdb=" O5 NAG G 302 " both_signs ideal model delta sigma weight residual False -2.40 -2.21 -0.19 2.00e-01 2.50e+01 9.24e-01 chirality pdb=" C1 NAG B 302 " pdb=" ND2 ASN B 137 " pdb=" C2 NAG B 302 " pdb=" O5 NAG B 302 " both_signs ideal model delta sigma weight residual False -2.40 -2.21 -0.19 2.00e-01 2.50e+01 9.24e-01 chirality pdb=" C1 NAG C 302 " pdb=" ND2 ASN C 137 " pdb=" C2 NAG C 302 " pdb=" O5 NAG C 302 " both_signs ideal model delta sigma weight residual False -2.40 -2.21 -0.19 2.00e-01 2.50e+01 9.24e-01 ... (remaining 1973 not shown) Planarity restraints: 2608 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CG GLU B 136 " 0.011 2.00e-02 2.50e+03 2.23e-02 4.99e+00 pdb=" CD GLU B 136 " -0.039 2.00e-02 2.50e+03 pdb=" OE1 GLU B 136 " 0.014 2.00e-02 2.50e+03 pdb=" OE2 GLU B 136 " 0.014 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CG GLU C 136 " 0.011 2.00e-02 2.50e+03 2.23e-02 4.99e+00 pdb=" CD GLU C 136 " -0.039 2.00e-02 2.50e+03 pdb=" OE1 GLU C 136 " 0.014 2.00e-02 2.50e+03 pdb=" OE2 GLU C 136 " 0.014 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CG GLU G 136 " -0.011 2.00e-02 2.50e+03 2.23e-02 4.99e+00 pdb=" CD GLU G 136 " 0.039 2.00e-02 2.50e+03 pdb=" OE1 GLU G 136 " -0.014 2.00e-02 2.50e+03 pdb=" OE2 GLU G 136 " -0.014 2.00e-02 2.50e+03 ... (remaining 2605 not shown) Histogram of nonbonded interaction distances: 1.63 - 2.28: 16 2.28 - 2.94: 6524 2.94 - 3.59: 17416 3.59 - 4.25: 31200 4.25 - 4.90: 55740 Nonbonded interactions: 110896 Sorted by model distance: nonbonded pdb=" NE2 GLN D 192 " pdb="CA CA D 303 " model vdw 1.628 2.590 nonbonded pdb=" NE2 GLN H 192 " pdb="CA CA H 303 " model vdw 1.628 2.590 nonbonded pdb=" NE2 GLN F 192 " pdb="CA CA F 303 " model vdw 1.628 2.590 nonbonded pdb=" NE2 GLN E 192 " pdb="CA CA E 303 " model vdw 1.628 2.590 nonbonded pdb=" CB ASP A 191 " pdb="CA CA A 303 " model vdw 1.905 2.910 ... (remaining 110891 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: 0.05 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.030 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.550 Check model and map are aligned: 0.100 Set scattering table: 0.130 Process input model: 30.340 Find NCS groups from input model: 0.560 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.630 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 36.410 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8164 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 : 0.004 0.037 14752 Z= 0.184 Angle : 0.752 12.278 20000 Z= 0.417 Chirality : 0.047 0.192 1976 Planarity : 0.004 0.033 2592 Dihedral : 18.144 85.653 5360 Min Nonbonded Distance : 1.628 Molprobity Statistics. All-atom Clashscore : 6.45 Ramachandran Plot: Outliers : 0.92 % Allowed : 12.67 % Favored : 86.41 % Rotamer: Outliers : 4.72 % Allowed : 29.44 % Favored : 65.83 % Cbeta Deviations : 0.26 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.64 (0.15), residues: 1736 helix: -2.11 (0.28), residues: 240 sheet: -1.45 (0.28), residues: 320 loop : -4.10 (0.11), residues: 1176 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP E 235 HIS 0.003 0.001 HIS B 118 PHE 0.018 0.001 PHE A 82 TYR 0.011 0.001 TYR E 45 ARG 0.003 0.000 ARG D 190 Details of bonding type rmsd link_NAG-ASN : bond 0.00711 ( 16) link_NAG-ASN : angle 1.86385 ( 48) hydrogen bonds : bond 0.22994 ( 320) hydrogen bonds : angle 8.51268 ( 888) SS BOND : bond 0.00130 ( 16) SS BOND : angle 0.71513 ( 32) covalent geometry : bond 0.00372 (14720) covalent geometry : angle 0.74695 (19920) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3472 Ramachandran restraints generated. 1736 Oldfield, 0 Emsley, 1736 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3472 Ramachandran restraints generated. 1736 Oldfield, 0 Emsley, 1736 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 268 residues out of total 1440 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 200 time to evaluate : 1.428 Fit side-chains REVERT: A 50 GLN cc_start: 0.6416 (OUTLIER) cc_final: 0.5976 (mp-120) REVERT: A 193 ASP cc_start: 0.6914 (m-30) cc_final: 0.6449 (m-30) REVERT: A 197 GLN cc_start: 0.8053 (OUTLIER) cc_final: 0.7318 (mp10) REVERT: D 135 PHE cc_start: 0.6946 (OUTLIER) cc_final: 0.6329 (t80) REVERT: D 213 HIS cc_start: 0.6549 (OUTLIER) cc_final: 0.6326 (m-70) REVERT: B 50 GLN cc_start: 0.6411 (OUTLIER) cc_final: 0.5973 (mp-120) REVERT: B 193 ASP cc_start: 0.6922 (m-30) cc_final: 0.6452 (m-30) REVERT: B 197 GLN cc_start: 0.8059 (OUTLIER) cc_final: 0.7324 (mp10) REVERT: E 135 PHE cc_start: 0.6946 (OUTLIER) cc_final: 0.6330 (t80) REVERT: E 213 HIS cc_start: 0.6556 (OUTLIER) cc_final: 0.6332 (m-70) REVERT: C 50 GLN cc_start: 0.6416 (OUTLIER) cc_final: 0.5979 (mp-120) REVERT: C 193 ASP cc_start: 0.6924 (m-30) cc_final: 0.6457 (m-30) REVERT: C 197 GLN cc_start: 0.8056 (OUTLIER) cc_final: 0.7322 (mp10) REVERT: F 135 PHE cc_start: 0.6948 (OUTLIER) cc_final: 0.6334 (t80) REVERT: F 213 HIS cc_start: 0.6511 (OUTLIER) cc_final: 0.6288 (m-70) REVERT: G 50 GLN cc_start: 0.6413 (OUTLIER) cc_final: 0.5977 (mp-120) REVERT: G 193 ASP cc_start: 0.6919 (m-30) cc_final: 0.6453 (m-30) REVERT: G 197 GLN cc_start: 0.8052 (OUTLIER) cc_final: 0.7315 (mp10) REVERT: H 135 PHE cc_start: 0.6946 (OUTLIER) cc_final: 0.6333 (t80) REVERT: H 213 HIS cc_start: 0.6517 (OUTLIER) cc_final: 0.6290 (m-70) outliers start: 68 outliers final: 36 residues processed: 256 average time/residue: 0.3080 time to fit residues: 110.6938 Evaluate side-chains 248 residues out of total 1440 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 196 time to evaluate : 1.526 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 50 GLN Chi-restraints excluded: chain A residue 132 LEU Chi-restraints excluded: chain A residue 165 VAL Chi-restraints excluded: chain A residue 197 GLN Chi-restraints excluded: chain A residue 248 THR Chi-restraints excluded: chain D residue 68 VAL Chi-restraints excluded: chain D residue 80 THR Chi-restraints excluded: chain D residue 105 ARG Chi-restraints excluded: chain D residue 135 PHE Chi-restraints excluded: chain D residue 165 VAL Chi-restraints excluded: chain D residue 213 HIS Chi-restraints excluded: chain D residue 228 SER Chi-restraints excluded: chain D residue 248 THR Chi-restraints excluded: chain B residue 50 GLN Chi-restraints excluded: chain B residue 132 LEU Chi-restraints excluded: chain B residue 165 VAL Chi-restraints excluded: chain B residue 197 GLN Chi-restraints excluded: chain B residue 248 THR Chi-restraints excluded: chain E residue 68 VAL Chi-restraints excluded: chain E residue 80 THR Chi-restraints excluded: chain E residue 105 ARG Chi-restraints excluded: chain E residue 135 PHE Chi-restraints excluded: chain E residue 165 VAL Chi-restraints excluded: chain E residue 213 HIS Chi-restraints excluded: chain E residue 228 SER Chi-restraints excluded: chain E residue 248 THR Chi-restraints excluded: chain C residue 50 GLN Chi-restraints excluded: chain C residue 132 LEU Chi-restraints excluded: chain C residue 165 VAL Chi-restraints excluded: chain C residue 197 GLN Chi-restraints excluded: chain C residue 248 THR Chi-restraints excluded: chain F residue 68 VAL Chi-restraints excluded: chain F residue 80 THR Chi-restraints excluded: chain F residue 105 ARG Chi-restraints excluded: chain F residue 135 PHE Chi-restraints excluded: chain F residue 165 VAL Chi-restraints excluded: chain F residue 213 HIS Chi-restraints excluded: chain F residue 228 SER Chi-restraints excluded: chain F residue 248 THR Chi-restraints excluded: chain G residue 50 GLN Chi-restraints excluded: chain G residue 132 LEU Chi-restraints excluded: chain G residue 165 VAL Chi-restraints excluded: chain G residue 197 GLN Chi-restraints excluded: chain G residue 248 THR Chi-restraints excluded: chain H residue 68 VAL Chi-restraints excluded: chain H residue 80 THR Chi-restraints excluded: chain H residue 105 ARG Chi-restraints excluded: chain H residue 135 PHE Chi-restraints excluded: chain H residue 165 VAL Chi-restraints excluded: chain H residue 213 HIS Chi-restraints excluded: chain H residue 228 SER Chi-restraints excluded: chain H residue 248 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 141 optimal weight: 4.9990 chunk 127 optimal weight: 0.0060 chunk 70 optimal weight: 3.9990 chunk 43 optimal weight: 10.0000 chunk 85 optimal weight: 9.9990 chunk 68 optimal weight: 5.9990 chunk 131 optimal weight: 0.6980 chunk 50 optimal weight: 4.9990 chunk 80 optimal weight: 3.9990 chunk 98 optimal weight: 7.9990 chunk 152 optimal weight: 0.6980 overall best weight: 1.8800 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 198 ASN E 198 ASN F 198 ASN H 198 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3783 r_free = 0.3783 target = 0.159333 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3542 r_free = 0.3542 target = 0.139338 restraints weight = 17963.885| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3560 r_free = 0.3560 target = 0.140981 restraints weight = 14634.504| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3575 r_free = 0.3575 target = 0.142233 restraints weight = 12571.073| |-----------------------------------------------------------------------------| r_work (final): 0.3579 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8091 moved from start: 0.0965 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 14752 Z= 0.149 Angle : 0.596 5.649 20000 Z= 0.321 Chirality : 0.046 0.236 1976 Planarity : 0.004 0.037 2592 Dihedral : 8.213 54.449 2364 Min Nonbonded Distance : 2.238 Molprobity Statistics. All-atom Clashscore : 4.49 Ramachandran Plot: Outliers : 0.23 % Allowed : 14.75 % Favored : 85.02 % Rotamer: Outliers : 7.36 % Allowed : 22.92 % Favored : 69.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.49 (0.15), residues: 1736 helix: -1.61 (0.26), residues: 296 sheet: -1.33 (0.27), residues: 320 loop : -4.19 (0.12), residues: 1120 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP F 235 HIS 0.003 0.001 HIS F 180 PHE 0.022 0.001 PHE B 82 TYR 0.012 0.001 TYR D 110 ARG 0.003 0.000 ARG D 94 Details of bonding type rmsd link_NAG-ASN : bond 0.00420 ( 16) link_NAG-ASN : angle 1.96623 ( 48) hydrogen bonds : bond 0.04227 ( 320) hydrogen bonds : angle 6.02888 ( 888) SS BOND : bond 0.00149 ( 16) SS BOND : angle 0.52630 ( 32) covalent geometry : bond 0.00335 (14720) covalent geometry : angle 0.58915 (19920) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3472 Ramachandran restraints generated. 1736 Oldfield, 0 Emsley, 1736 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3472 Ramachandran restraints generated. 1736 Oldfield, 0 Emsley, 1736 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 318 residues out of total 1440 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 106 poor density : 212 time to evaluate : 1.441 Fit side-chains REVERT: A 197 GLN cc_start: 0.7983 (OUTLIER) cc_final: 0.7454 (mp10) REVERT: D 72 MET cc_start: 0.7459 (OUTLIER) cc_final: 0.7034 (mmt) REVERT: D 157 GLU cc_start: 0.8006 (OUTLIER) cc_final: 0.7776 (tt0) REVERT: D 190 ARG cc_start: 0.8152 (OUTLIER) cc_final: 0.7941 (mmp-170) REVERT: D 247 ARG cc_start: 0.7795 (OUTLIER) cc_final: 0.7175 (mtt180) REVERT: B 197 GLN cc_start: 0.7985 (OUTLIER) cc_final: 0.7460 (mp10) REVERT: E 72 MET cc_start: 0.7458 (OUTLIER) cc_final: 0.7045 (mmt) REVERT: E 157 GLU cc_start: 0.8022 (OUTLIER) cc_final: 0.7789 (tt0) REVERT: E 247 ARG cc_start: 0.7800 (OUTLIER) cc_final: 0.7177 (mtt180) REVERT: C 197 GLN cc_start: 0.7983 (OUTLIER) cc_final: 0.7462 (mp10) REVERT: F 72 MET cc_start: 0.7468 (OUTLIER) cc_final: 0.7052 (mmt) REVERT: F 157 GLU cc_start: 0.8016 (OUTLIER) cc_final: 0.7789 (tt0) REVERT: F 247 ARG cc_start: 0.7789 (OUTLIER) cc_final: 0.7168 (mtt180) REVERT: G 197 GLN cc_start: 0.7985 (OUTLIER) cc_final: 0.7459 (mp10) REVERT: H 72 MET cc_start: 0.7471 (OUTLIER) cc_final: 0.7055 (mmt) REVERT: H 157 GLU cc_start: 0.8010 (OUTLIER) cc_final: 0.7778 (tt0) REVERT: H 247 ARG cc_start: 0.7792 (OUTLIER) cc_final: 0.7172 (mtt180) outliers start: 106 outliers final: 44 residues processed: 288 average time/residue: 0.3016 time to fit residues: 119.6090 Evaluate side-chains 261 residues out of total 1440 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 200 time to evaluate : 1.421 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 50 GLN Chi-restraints excluded: chain A residue 93 PHE Chi-restraints excluded: chain A residue 132 LEU Chi-restraints excluded: chain A residue 165 VAL Chi-restraints excluded: chain A residue 197 GLN Chi-restraints excluded: chain A residue 199 CYS Chi-restraints excluded: chain A residue 248 THR Chi-restraints excluded: chain D residue 72 MET Chi-restraints excluded: chain D residue 157 GLU Chi-restraints excluded: chain D residue 177 LEU Chi-restraints excluded: chain D residue 190 ARG Chi-restraints excluded: chain D residue 198 ASN Chi-restraints excluded: chain D residue 199 CYS Chi-restraints excluded: chain D residue 227 LEU Chi-restraints excluded: chain D residue 247 ARG Chi-restraints excluded: chain D residue 248 THR Chi-restraints excluded: chain B residue 50 GLN Chi-restraints excluded: chain B residue 93 PHE Chi-restraints excluded: chain B residue 132 LEU Chi-restraints excluded: chain B residue 165 VAL Chi-restraints excluded: chain B residue 197 GLN Chi-restraints excluded: chain B residue 199 CYS Chi-restraints excluded: chain B residue 248 THR Chi-restraints excluded: chain E residue 72 MET Chi-restraints excluded: chain E residue 157 GLU Chi-restraints excluded: chain E residue 177 LEU Chi-restraints excluded: chain E residue 198 ASN Chi-restraints excluded: chain E residue 199 CYS Chi-restraints excluded: chain E residue 227 LEU Chi-restraints excluded: chain E residue 247 ARG Chi-restraints excluded: chain E residue 248 THR Chi-restraints excluded: chain C residue 50 GLN Chi-restraints excluded: chain C residue 93 PHE Chi-restraints excluded: chain C residue 132 LEU Chi-restraints excluded: chain C residue 165 VAL Chi-restraints excluded: chain C residue 197 GLN Chi-restraints excluded: chain C residue 199 CYS Chi-restraints excluded: chain C residue 248 THR Chi-restraints excluded: chain F residue 72 MET Chi-restraints excluded: chain F residue 157 GLU Chi-restraints excluded: chain F residue 177 LEU Chi-restraints excluded: chain F residue 198 ASN Chi-restraints excluded: chain F residue 199 CYS Chi-restraints excluded: chain F residue 227 LEU Chi-restraints excluded: chain F residue 247 ARG Chi-restraints excluded: chain F residue 248 THR Chi-restraints excluded: chain G residue 50 GLN Chi-restraints excluded: chain G residue 93 PHE Chi-restraints excluded: chain G residue 132 LEU Chi-restraints excluded: chain G residue 165 VAL Chi-restraints excluded: chain G residue 197 GLN Chi-restraints excluded: chain G residue 199 CYS Chi-restraints excluded: chain G residue 248 THR Chi-restraints excluded: chain H residue 72 MET Chi-restraints excluded: chain H residue 157 GLU Chi-restraints excluded: chain H residue 177 LEU Chi-restraints excluded: chain H residue 198 ASN Chi-restraints excluded: chain H residue 199 CYS Chi-restraints excluded: chain H residue 227 LEU Chi-restraints excluded: chain H residue 247 ARG Chi-restraints excluded: chain H residue 248 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 119 optimal weight: 7.9990 chunk 7 optimal weight: 2.9990 chunk 115 optimal weight: 3.9990 chunk 40 optimal weight: 8.9990 chunk 17 optimal weight: 2.9990 chunk 134 optimal weight: 1.9990 chunk 125 optimal weight: 8.9990 chunk 91 optimal weight: 2.9990 chunk 79 optimal weight: 1.9990 chunk 65 optimal weight: 0.0670 chunk 24 optimal weight: 0.9990 overall best weight: 1.6126 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 198 ASN E 198 ASN F 198 ASN H 198 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3789 r_free = 0.3789 target = 0.159748 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3544 r_free = 0.3544 target = 0.139708 restraints weight = 17974.699| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3564 r_free = 0.3564 target = 0.141415 restraints weight = 14495.147| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3580 r_free = 0.3580 target = 0.142723 restraints weight = 12418.019| |-----------------------------------------------------------------------------| r_work (final): 0.3587 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8081 moved from start: 0.1101 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 14752 Z= 0.131 Angle : 0.579 5.985 20000 Z= 0.310 Chirality : 0.045 0.220 1976 Planarity : 0.003 0.033 2592 Dihedral : 7.181 55.537 2316 Min Nonbonded Distance : 2.280 Molprobity Statistics. All-atom Clashscore : 4.05 Ramachandran Plot: Outliers : 0.23 % Allowed : 14.29 % Favored : 85.48 % Rotamer: Outliers : 6.32 % Allowed : 23.96 % Favored : 69.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.28 (0.16), residues: 1736 helix: -1.12 (0.28), residues: 296 sheet: -1.13 (0.28), residues: 320 loop : -4.18 (0.12), residues: 1120 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP D 235 HIS 0.002 0.001 HIS A 118 PHE 0.020 0.001 PHE G 82 TYR 0.010 0.001 TYR D 110 ARG 0.002 0.000 ARG D 94 Details of bonding type rmsd link_NAG-ASN : bond 0.00471 ( 16) link_NAG-ASN : angle 1.95270 ( 48) hydrogen bonds : bond 0.03885 ( 320) hydrogen bonds : angle 5.83422 ( 888) SS BOND : bond 0.00141 ( 16) SS BOND : angle 0.50781 ( 32) covalent geometry : bond 0.00294 (14720) covalent geometry : angle 0.57203 (19920) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3472 Ramachandran restraints generated. 1736 Oldfield, 0 Emsley, 1736 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3472 Ramachandran restraints generated. 1736 Oldfield, 0 Emsley, 1736 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 303 residues out of total 1440 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 91 poor density : 212 time to evaluate : 1.442 Fit side-chains REVERT: A 72 MET cc_start: 0.6689 (OUTLIER) cc_final: 0.6148 (mmt) REVERT: A 83 GLN cc_start: 0.9134 (OUTLIER) cc_final: 0.8360 (tp40) REVERT: A 197 GLN cc_start: 0.7988 (OUTLIER) cc_final: 0.7521 (mp10) REVERT: D 72 MET cc_start: 0.7476 (OUTLIER) cc_final: 0.7114 (mmt) REVERT: B 72 MET cc_start: 0.6691 (OUTLIER) cc_final: 0.6153 (mmt) REVERT: B 83 GLN cc_start: 0.9144 (OUTLIER) cc_final: 0.8361 (tp40) REVERT: B 197 GLN cc_start: 0.7991 (OUTLIER) cc_final: 0.7526 (mp10) REVERT: E 72 MET cc_start: 0.7467 (OUTLIER) cc_final: 0.7120 (mmt) REVERT: C 50 GLN cc_start: 0.6327 (OUTLIER) cc_final: 0.6061 (mt0) REVERT: C 72 MET cc_start: 0.6690 (OUTLIER) cc_final: 0.6160 (mmt) REVERT: C 83 GLN cc_start: 0.9132 (OUTLIER) cc_final: 0.8358 (tp40) REVERT: C 197 GLN cc_start: 0.7984 (OUTLIER) cc_final: 0.7522 (mp10) REVERT: F 72 MET cc_start: 0.7479 (OUTLIER) cc_final: 0.7126 (mmt) REVERT: G 50 GLN cc_start: 0.6329 (OUTLIER) cc_final: 0.6060 (mt0) REVERT: G 72 MET cc_start: 0.6677 (OUTLIER) cc_final: 0.6140 (mmt) REVERT: G 83 GLN cc_start: 0.9139 (OUTLIER) cc_final: 0.8360 (tp40) REVERT: G 197 GLN cc_start: 0.7991 (OUTLIER) cc_final: 0.7524 (mp10) REVERT: H 72 MET cc_start: 0.7484 (OUTLIER) cc_final: 0.7131 (mmt) outliers start: 91 outliers final: 47 residues processed: 287 average time/residue: 0.3012 time to fit residues: 120.8014 Evaluate side-chains 253 residues out of total 1440 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 188 time to evaluate : 1.490 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 72 MET Chi-restraints excluded: chain A residue 83 GLN Chi-restraints excluded: chain A residue 93 PHE Chi-restraints excluded: chain A residue 132 LEU Chi-restraints excluded: chain A residue 135 PHE Chi-restraints excluded: chain A residue 165 VAL Chi-restraints excluded: chain A residue 194 LEU Chi-restraints excluded: chain A residue 197 GLN Chi-restraints excluded: chain A residue 199 CYS Chi-restraints excluded: chain A residue 225 SER Chi-restraints excluded: chain A residue 248 THR Chi-restraints excluded: chain D residue 72 MET Chi-restraints excluded: chain D residue 177 LEU Chi-restraints excluded: chain D residue 199 CYS Chi-restraints excluded: chain D residue 227 LEU Chi-restraints excluded: chain D residue 244 SER Chi-restraints excluded: chain B residue 72 MET Chi-restraints excluded: chain B residue 83 GLN Chi-restraints excluded: chain B residue 93 PHE Chi-restraints excluded: chain B residue 132 LEU Chi-restraints excluded: chain B residue 135 PHE Chi-restraints excluded: chain B residue 165 VAL Chi-restraints excluded: chain B residue 194 LEU Chi-restraints excluded: chain B residue 197 GLN Chi-restraints excluded: chain B residue 199 CYS Chi-restraints excluded: chain B residue 225 SER Chi-restraints excluded: chain B residue 248 THR Chi-restraints excluded: chain E residue 72 MET Chi-restraints excluded: chain E residue 177 LEU Chi-restraints excluded: chain E residue 199 CYS Chi-restraints excluded: chain E residue 227 LEU Chi-restraints excluded: chain E residue 244 SER Chi-restraints excluded: chain C residue 50 GLN Chi-restraints excluded: chain C residue 72 MET Chi-restraints excluded: chain C residue 83 GLN Chi-restraints excluded: chain C residue 93 PHE Chi-restraints excluded: chain C residue 132 LEU Chi-restraints excluded: chain C residue 135 PHE Chi-restraints excluded: chain C residue 165 VAL Chi-restraints excluded: chain C residue 194 LEU Chi-restraints excluded: chain C residue 197 GLN Chi-restraints excluded: chain C residue 199 CYS Chi-restraints excluded: chain C residue 225 SER Chi-restraints excluded: chain C residue 248 THR Chi-restraints excluded: chain F residue 72 MET Chi-restraints excluded: chain F residue 177 LEU Chi-restraints excluded: chain F residue 199 CYS Chi-restraints excluded: chain F residue 227 LEU Chi-restraints excluded: chain F residue 244 SER Chi-restraints excluded: chain G residue 50 GLN Chi-restraints excluded: chain G residue 72 MET Chi-restraints excluded: chain G residue 83 GLN Chi-restraints excluded: chain G residue 93 PHE Chi-restraints excluded: chain G residue 132 LEU Chi-restraints excluded: chain G residue 135 PHE Chi-restraints excluded: chain G residue 165 VAL Chi-restraints excluded: chain G residue 194 LEU Chi-restraints excluded: chain G residue 197 GLN Chi-restraints excluded: chain G residue 199 CYS Chi-restraints excluded: chain G residue 248 THR Chi-restraints excluded: chain H residue 72 MET Chi-restraints excluded: chain H residue 177 LEU Chi-restraints excluded: chain H residue 199 CYS Chi-restraints excluded: chain H residue 227 LEU Chi-restraints excluded: chain H residue 244 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 38 optimal weight: 0.9990 chunk 107 optimal weight: 0.7980 chunk 120 optimal weight: 6.9990 chunk 46 optimal weight: 7.9990 chunk 61 optimal weight: 4.9990 chunk 126 optimal weight: 10.0000 chunk 24 optimal weight: 1.9990 chunk 147 optimal weight: 10.0000 chunk 84 optimal weight: 10.0000 chunk 125 optimal weight: 8.9990 chunk 11 optimal weight: 0.9990 overall best weight: 1.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3777 r_free = 0.3777 target = 0.158709 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3527 r_free = 0.3527 target = 0.138133 restraints weight = 17827.590| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3548 r_free = 0.3548 target = 0.139956 restraints weight = 14150.932| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3564 r_free = 0.3564 target = 0.141305 restraints weight = 11994.865| |-----------------------------------------------------------------------------| r_work (final): 0.3571 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8098 moved from start: 0.1240 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 14752 Z= 0.148 Angle : 0.589 5.305 20000 Z= 0.316 Chirality : 0.046 0.221 1976 Planarity : 0.004 0.038 2592 Dihedral : 6.972 59.456 2306 Min Nonbonded Distance : 2.269 Molprobity Statistics. All-atom Clashscore : 3.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 15.21 % Favored : 84.79 % Rotamer: Outliers : 6.25 % Allowed : 24.38 % Favored : 69.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.23 (0.16), residues: 1736 helix: -0.94 (0.29), residues: 296 sheet: -1.11 (0.28), residues: 320 loop : -4.19 (0.12), residues: 1120 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP D 235 HIS 0.002 0.001 HIS F 180 PHE 0.021 0.001 PHE C 82 TYR 0.012 0.001 TYR E 110 ARG 0.003 0.000 ARG E 94 Details of bonding type rmsd link_NAG-ASN : bond 0.00522 ( 16) link_NAG-ASN : angle 2.08473 ( 48) hydrogen bonds : bond 0.03913 ( 320) hydrogen bonds : angle 5.72082 ( 888) SS BOND : bond 0.00201 ( 16) SS BOND : angle 0.53999 ( 32) covalent geometry : bond 0.00340 (14720) covalent geometry : angle 0.58101 (19920) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3472 Ramachandran restraints generated. 1736 Oldfield, 0 Emsley, 1736 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3472 Ramachandran restraints generated. 1736 Oldfield, 0 Emsley, 1736 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 291 residues out of total 1440 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 90 poor density : 201 time to evaluate : 1.525 Fit side-chains REVERT: A 72 MET cc_start: 0.6673 (OUTLIER) cc_final: 0.6159 (mmt) REVERT: A 83 GLN cc_start: 0.9168 (OUTLIER) cc_final: 0.8396 (tp40) REVERT: A 159 ASP cc_start: 0.6718 (OUTLIER) cc_final: 0.5973 (m-30) REVERT: A 193 ASP cc_start: 0.6935 (m-30) cc_final: 0.6483 (m-30) REVERT: A 197 GLN cc_start: 0.7983 (OUTLIER) cc_final: 0.7478 (mp10) REVERT: D 45 TYR cc_start: 0.7641 (t80) cc_final: 0.7385 (t80) REVERT: D 72 MET cc_start: 0.7449 (mmt) cc_final: 0.7113 (mmt) REVERT: D 247 ARG cc_start: 0.7788 (OUTLIER) cc_final: 0.7356 (mtm180) REVERT: B 72 MET cc_start: 0.6642 (OUTLIER) cc_final: 0.6114 (mmt) REVERT: B 83 GLN cc_start: 0.9175 (OUTLIER) cc_final: 0.8396 (tp40) REVERT: B 159 ASP cc_start: 0.6689 (OUTLIER) cc_final: 0.5953 (m-30) REVERT: B 193 ASP cc_start: 0.6924 (m-30) cc_final: 0.6475 (m-30) REVERT: B 197 GLN cc_start: 0.7985 (OUTLIER) cc_final: 0.7481 (mp10) REVERT: E 45 TYR cc_start: 0.7641 (t80) cc_final: 0.7388 (t80) REVERT: E 72 MET cc_start: 0.7453 (mmt) cc_final: 0.7124 (mmt) REVERT: E 247 ARG cc_start: 0.7792 (OUTLIER) cc_final: 0.7354 (mtm180) REVERT: C 72 MET cc_start: 0.6687 (OUTLIER) cc_final: 0.6141 (mmt) REVERT: C 83 GLN cc_start: 0.9167 (OUTLIER) cc_final: 0.8398 (tp40) REVERT: C 159 ASP cc_start: 0.6715 (OUTLIER) cc_final: 0.5962 (m-30) REVERT: C 193 ASP cc_start: 0.6919 (m-30) cc_final: 0.6468 (m-30) REVERT: C 197 GLN cc_start: 0.7982 (OUTLIER) cc_final: 0.7478 (mp10) REVERT: F 72 MET cc_start: 0.7458 (mmt) cc_final: 0.7099 (mmt) REVERT: F 247 ARG cc_start: 0.7779 (OUTLIER) cc_final: 0.7346 (mtm180) REVERT: G 72 MET cc_start: 0.6670 (OUTLIER) cc_final: 0.6122 (mmt) REVERT: G 83 GLN cc_start: 0.9173 (OUTLIER) cc_final: 0.8390 (tp40) REVERT: G 159 ASP cc_start: 0.6705 (OUTLIER) cc_final: 0.5966 (m-30) REVERT: G 193 ASP cc_start: 0.6925 (m-30) cc_final: 0.6471 (m-30) REVERT: G 197 GLN cc_start: 0.7990 (OUTLIER) cc_final: 0.7483 (mp10) REVERT: H 72 MET cc_start: 0.7463 (mmt) cc_final: 0.7100 (mmt) REVERT: H 247 ARG cc_start: 0.7786 (OUTLIER) cc_final: 0.7350 (mtm180) outliers start: 90 outliers final: 54 residues processed: 275 average time/residue: 0.2972 time to fit residues: 113.7485 Evaluate side-chains 269 residues out of total 1440 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 195 time to evaluate : 1.431 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 72 MET Chi-restraints excluded: chain A residue 83 GLN Chi-restraints excluded: chain A residue 93 PHE Chi-restraints excluded: chain A residue 132 LEU Chi-restraints excluded: chain A residue 135 PHE Chi-restraints excluded: chain A residue 159 ASP Chi-restraints excluded: chain A residue 165 VAL Chi-restraints excluded: chain A residue 194 LEU Chi-restraints excluded: chain A residue 197 GLN Chi-restraints excluded: chain A residue 199 CYS Chi-restraints excluded: chain A residue 248 THR Chi-restraints excluded: chain D residue 89 SER Chi-restraints excluded: chain D residue 159 ASP Chi-restraints excluded: chain D residue 177 LEU Chi-restraints excluded: chain D residue 190 ARG Chi-restraints excluded: chain D residue 227 LEU Chi-restraints excluded: chain D residue 244 SER Chi-restraints excluded: chain D residue 247 ARG Chi-restraints excluded: chain D residue 248 THR Chi-restraints excluded: chain B residue 72 MET Chi-restraints excluded: chain B residue 83 GLN Chi-restraints excluded: chain B residue 93 PHE Chi-restraints excluded: chain B residue 132 LEU Chi-restraints excluded: chain B residue 135 PHE Chi-restraints excluded: chain B residue 159 ASP Chi-restraints excluded: chain B residue 165 VAL Chi-restraints excluded: chain B residue 194 LEU Chi-restraints excluded: chain B residue 197 GLN Chi-restraints excluded: chain B residue 199 CYS Chi-restraints excluded: chain B residue 248 THR Chi-restraints excluded: chain E residue 89 SER Chi-restraints excluded: chain E residue 159 ASP Chi-restraints excluded: chain E residue 177 LEU Chi-restraints excluded: chain E residue 227 LEU Chi-restraints excluded: chain E residue 244 SER Chi-restraints excluded: chain E residue 247 ARG Chi-restraints excluded: chain E residue 248 THR Chi-restraints excluded: chain C residue 72 MET Chi-restraints excluded: chain C residue 83 GLN Chi-restraints excluded: chain C residue 93 PHE Chi-restraints excluded: chain C residue 132 LEU Chi-restraints excluded: chain C residue 135 PHE Chi-restraints excluded: chain C residue 159 ASP Chi-restraints excluded: chain C residue 165 VAL Chi-restraints excluded: chain C residue 194 LEU Chi-restraints excluded: chain C residue 197 GLN Chi-restraints excluded: chain C residue 199 CYS Chi-restraints excluded: chain C residue 248 THR Chi-restraints excluded: chain F residue 89 SER Chi-restraints excluded: chain F residue 159 ASP Chi-restraints excluded: chain F residue 177 LEU Chi-restraints excluded: chain F residue 227 LEU Chi-restraints excluded: chain F residue 244 SER Chi-restraints excluded: chain F residue 247 ARG Chi-restraints excluded: chain F residue 248 THR Chi-restraints excluded: chain G residue 72 MET Chi-restraints excluded: chain G residue 83 GLN Chi-restraints excluded: chain G residue 93 PHE Chi-restraints excluded: chain G residue 132 LEU Chi-restraints excluded: chain G residue 135 PHE Chi-restraints excluded: chain G residue 159 ASP Chi-restraints excluded: chain G residue 165 VAL Chi-restraints excluded: chain G residue 194 LEU Chi-restraints excluded: chain G residue 197 GLN Chi-restraints excluded: chain G residue 199 CYS Chi-restraints excluded: chain G residue 225 SER Chi-restraints excluded: chain G residue 248 THR Chi-restraints excluded: chain H residue 89 SER Chi-restraints excluded: chain H residue 159 ASP Chi-restraints excluded: chain H residue 177 LEU Chi-restraints excluded: chain H residue 227 LEU Chi-restraints excluded: chain H residue 244 SER Chi-restraints excluded: chain H residue 247 ARG Chi-restraints excluded: chain H residue 248 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 97 optimal weight: 10.0000 chunk 127 optimal weight: 0.9980 chunk 7 optimal weight: 4.9990 chunk 31 optimal weight: 1.9990 chunk 39 optimal weight: 10.0000 chunk 81 optimal weight: 9.9990 chunk 25 optimal weight: 6.9990 chunk 5 optimal weight: 1.9990 chunk 118 optimal weight: 10.0000 chunk 92 optimal weight: 7.9990 chunk 80 optimal weight: 7.9990 overall best weight: 3.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3747 r_free = 0.3747 target = 0.155725 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3495 r_free = 0.3495 target = 0.135414 restraints weight = 18174.098| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3515 r_free = 0.3515 target = 0.137096 restraints weight = 14838.689| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3530 r_free = 0.3530 target = 0.138354 restraints weight = 12782.381| |-----------------------------------------------------------------------------| r_work (final): 0.3536 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8143 moved from start: 0.1387 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.029 14752 Z= 0.235 Angle : 0.676 5.182 20000 Z= 0.364 Chirality : 0.050 0.224 1976 Planarity : 0.005 0.056 2592 Dihedral : 7.380 55.925 2300 Min Nonbonded Distance : 2.273 Molprobity Statistics. All-atom Clashscore : 4.45 Ramachandran Plot: Outliers : 0.46 % Allowed : 16.01 % Favored : 83.53 % Rotamer: Outliers : 6.46 % Allowed : 24.51 % Favored : 69.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.35 (0.16), residues: 1736 helix: -1.05 (0.29), residues: 296 sheet: -1.21 (0.28), residues: 320 loop : -4.26 (0.12), residues: 1120 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP E 235 HIS 0.004 0.002 HIS E 180 PHE 0.026 0.002 PHE D 82 TYR 0.019 0.002 TYR F 110 ARG 0.005 0.001 ARG H 94 Details of bonding type rmsd link_NAG-ASN : bond 0.00576 ( 16) link_NAG-ASN : angle 2.26513 ( 48) hydrogen bonds : bond 0.04735 ( 320) hydrogen bonds : angle 5.89540 ( 888) SS BOND : bond 0.00305 ( 16) SS BOND : angle 0.62193 ( 32) covalent geometry : bond 0.00556 (14720) covalent geometry : angle 0.66808 (19920) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3472 Ramachandran restraints generated. 1736 Oldfield, 0 Emsley, 1736 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3472 Ramachandran restraints generated. 1736 Oldfield, 0 Emsley, 1736 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 295 residues out of total 1440 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 93 poor density : 202 time to evaluate : 1.473 Fit side-chains REVERT: A 83 GLN cc_start: 0.9218 (OUTLIER) cc_final: 0.8414 (tp40) REVERT: A 159 ASP cc_start: 0.6586 (OUTLIER) cc_final: 0.5777 (m-30) REVERT: A 197 GLN cc_start: 0.8011 (OUTLIER) cc_final: 0.7495 (mp10) REVERT: D 72 MET cc_start: 0.7546 (mmt) cc_final: 0.6963 (mmt) REVERT: D 247 ARG cc_start: 0.7876 (OUTLIER) cc_final: 0.7497 (mtm180) REVERT: B 83 GLN cc_start: 0.9226 (OUTLIER) cc_final: 0.8410 (tp40) REVERT: B 159 ASP cc_start: 0.6560 (OUTLIER) cc_final: 0.5766 (m-30) REVERT: B 197 GLN cc_start: 0.8015 (OUTLIER) cc_final: 0.7501 (mp10) REVERT: E 72 MET cc_start: 0.7546 (mmt) cc_final: 0.6970 (mmt) REVERT: E 157 GLU cc_start: 0.8084 (OUTLIER) cc_final: 0.7883 (tt0) REVERT: E 247 ARG cc_start: 0.7886 (OUTLIER) cc_final: 0.7499 (mtm180) REVERT: C 50 GLN cc_start: 0.6565 (OUTLIER) cc_final: 0.5994 (mt0) REVERT: C 83 GLN cc_start: 0.9216 (OUTLIER) cc_final: 0.8413 (tp40) REVERT: C 159 ASP cc_start: 0.6584 (OUTLIER) cc_final: 0.5766 (m-30) REVERT: C 197 GLN cc_start: 0.8013 (OUTLIER) cc_final: 0.7500 (mp10) REVERT: F 72 MET cc_start: 0.7543 (mmt) cc_final: 0.6958 (mmt) REVERT: F 157 GLU cc_start: 0.8074 (OUTLIER) cc_final: 0.7873 (tt0) REVERT: F 247 ARG cc_start: 0.7872 (OUTLIER) cc_final: 0.7487 (mtm180) REVERT: G 50 GLN cc_start: 0.6567 (OUTLIER) cc_final: 0.5995 (mt0) REVERT: G 83 GLN cc_start: 0.9218 (OUTLIER) cc_final: 0.8410 (tp40) REVERT: G 159 ASP cc_start: 0.6569 (OUTLIER) cc_final: 0.5772 (m-30) REVERT: G 197 GLN cc_start: 0.8020 (OUTLIER) cc_final: 0.7500 (mp10) REVERT: H 72 MET cc_start: 0.7553 (mmt) cc_final: 0.6954 (mmt) REVERT: H 157 GLU cc_start: 0.8063 (OUTLIER) cc_final: 0.7861 (tt0) REVERT: H 247 ARG cc_start: 0.7878 (OUTLIER) cc_final: 0.7492 (mtm180) outliers start: 93 outliers final: 56 residues processed: 279 average time/residue: 0.3038 time to fit residues: 117.2774 Evaluate side-chains 271 residues out of total 1440 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 194 time to evaluate : 1.455 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 83 GLN Chi-restraints excluded: chain A residue 93 PHE Chi-restraints excluded: chain A residue 132 LEU Chi-restraints excluded: chain A residue 135 PHE Chi-restraints excluded: chain A residue 159 ASP Chi-restraints excluded: chain A residue 165 VAL Chi-restraints excluded: chain A residue 194 LEU Chi-restraints excluded: chain A residue 197 GLN Chi-restraints excluded: chain A residue 199 CYS Chi-restraints excluded: chain A residue 207 PHE Chi-restraints excluded: chain A residue 225 SER Chi-restraints excluded: chain A residue 248 THR Chi-restraints excluded: chain D residue 89 SER Chi-restraints excluded: chain D residue 177 LEU Chi-restraints excluded: chain D residue 227 LEU Chi-restraints excluded: chain D residue 244 SER Chi-restraints excluded: chain D residue 247 ARG Chi-restraints excluded: chain D residue 248 THR Chi-restraints excluded: chain B residue 83 GLN Chi-restraints excluded: chain B residue 93 PHE Chi-restraints excluded: chain B residue 132 LEU Chi-restraints excluded: chain B residue 135 PHE Chi-restraints excluded: chain B residue 159 ASP Chi-restraints excluded: chain B residue 165 VAL Chi-restraints excluded: chain B residue 194 LEU Chi-restraints excluded: chain B residue 197 GLN Chi-restraints excluded: chain B residue 199 CYS Chi-restraints excluded: chain B residue 207 PHE Chi-restraints excluded: chain B residue 225 SER Chi-restraints excluded: chain B residue 248 THR Chi-restraints excluded: chain E residue 89 SER Chi-restraints excluded: chain E residue 157 GLU Chi-restraints excluded: chain E residue 177 LEU Chi-restraints excluded: chain E residue 227 LEU Chi-restraints excluded: chain E residue 244 SER Chi-restraints excluded: chain E residue 247 ARG Chi-restraints excluded: chain E residue 248 THR Chi-restraints excluded: chain C residue 50 GLN Chi-restraints excluded: chain C residue 83 GLN Chi-restraints excluded: chain C residue 93 PHE Chi-restraints excluded: chain C residue 132 LEU Chi-restraints excluded: chain C residue 135 PHE Chi-restraints excluded: chain C residue 159 ASP Chi-restraints excluded: chain C residue 165 VAL Chi-restraints excluded: chain C residue 194 LEU Chi-restraints excluded: chain C residue 197 GLN Chi-restraints excluded: chain C residue 199 CYS Chi-restraints excluded: chain C residue 207 PHE Chi-restraints excluded: chain C residue 225 SER Chi-restraints excluded: chain C residue 248 THR Chi-restraints excluded: chain F residue 89 SER Chi-restraints excluded: chain F residue 157 GLU Chi-restraints excluded: chain F residue 177 LEU Chi-restraints excluded: chain F residue 227 LEU Chi-restraints excluded: chain F residue 244 SER Chi-restraints excluded: chain F residue 247 ARG Chi-restraints excluded: chain F residue 248 THR Chi-restraints excluded: chain G residue 50 GLN Chi-restraints excluded: chain G residue 83 GLN Chi-restraints excluded: chain G residue 93 PHE Chi-restraints excluded: chain G residue 132 LEU Chi-restraints excluded: chain G residue 135 PHE Chi-restraints excluded: chain G residue 159 ASP Chi-restraints excluded: chain G residue 165 VAL Chi-restraints excluded: chain G residue 194 LEU Chi-restraints excluded: chain G residue 197 GLN Chi-restraints excluded: chain G residue 199 CYS Chi-restraints excluded: chain G residue 207 PHE Chi-restraints excluded: chain G residue 225 SER Chi-restraints excluded: chain G residue 248 THR Chi-restraints excluded: chain H residue 89 SER Chi-restraints excluded: chain H residue 157 GLU Chi-restraints excluded: chain H residue 177 LEU Chi-restraints excluded: chain H residue 227 LEU Chi-restraints excluded: chain H residue 244 SER Chi-restraints excluded: chain H residue 247 ARG Chi-restraints excluded: chain H residue 248 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 131 optimal weight: 0.6980 chunk 117 optimal weight: 4.9990 chunk 57 optimal weight: 6.9990 chunk 44 optimal weight: 0.0020 chunk 93 optimal weight: 0.9980 chunk 12 optimal weight: 5.9990 chunk 100 optimal weight: 1.9990 chunk 78 optimal weight: 5.9990 chunk 75 optimal weight: 4.9990 chunk 166 optimal weight: 6.9990 chunk 73 optimal weight: 1.9990 overall best weight: 1.1392 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3803 r_free = 0.3803 target = 0.160856 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3553 r_free = 0.3553 target = 0.140260 restraints weight = 18087.325| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3575 r_free = 0.3575 target = 0.142139 restraints weight = 14359.039| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3592 r_free = 0.3592 target = 0.143541 restraints weight = 12182.372| |-----------------------------------------------------------------------------| r_work (final): 0.3598 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8075 moved from start: 0.1401 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.018 14752 Z= 0.108 Angle : 0.553 6.288 20000 Z= 0.294 Chirality : 0.044 0.231 1976 Planarity : 0.003 0.027 2592 Dihedral : 6.419 47.821 2300 Min Nonbonded Distance : 2.305 Molprobity Statistics. All-atom Clashscore : 3.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 14.52 % Favored : 85.48 % Rotamer: Outliers : 6.74 % Allowed : 25.14 % Favored : 68.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -4.21 (0.16), residues: 1736 helix: -0.97 (0.29), residues: 312 sheet: -1.19 (0.28), residues: 320 loop : -4.16 (0.12), residues: 1104 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP D 235 HIS 0.003 0.001 HIS C 118 PHE 0.019 0.001 PHE A 82 TYR 0.008 0.001 TYR G 99 ARG 0.001 0.000 ARG F 94 Details of bonding type rmsd link_NAG-ASN : bond 0.00535 ( 16) link_NAG-ASN : angle 2.09274 ( 48) hydrogen bonds : bond 0.03323 ( 320) hydrogen bonds : angle 5.51709 ( 888) SS BOND : bond 0.00140 ( 16) SS BOND : angle 0.71237 ( 32) covalent geometry : bond 0.00234 (14720) covalent geometry : angle 0.54353 (19920) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3472 Ramachandran restraints generated. 1736 Oldfield, 0 Emsley, 1736 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3472 Ramachandran restraints generated. 1736 Oldfield, 0 Emsley, 1736 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 314 residues out of total 1440 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 97 poor density : 217 time to evaluate : 1.601 Fit side-chains REVERT: A 72 MET cc_start: 0.6622 (OUTLIER) cc_final: 0.6155 (mmt) REVERT: A 83 GLN cc_start: 0.9117 (OUTLIER) cc_final: 0.8346 (tp40) REVERT: A 197 GLN cc_start: 0.7943 (OUTLIER) cc_final: 0.7485 (mp10) REVERT: D 72 MET cc_start: 0.7208 (OUTLIER) cc_final: 0.6822 (mmt) REVERT: D 247 ARG cc_start: 0.7736 (OUTLIER) cc_final: 0.7321 (mtm180) REVERT: B 72 MET cc_start: 0.6621 (OUTLIER) cc_final: 0.6155 (mmt) REVERT: B 83 GLN cc_start: 0.9134 (OUTLIER) cc_final: 0.8347 (tp40) REVERT: B 197 GLN cc_start: 0.7949 (OUTLIER) cc_final: 0.7460 (mp10) REVERT: E 72 MET cc_start: 0.7201 (OUTLIER) cc_final: 0.6820 (mmt) REVERT: E 247 ARG cc_start: 0.7741 (OUTLIER) cc_final: 0.7320 (mtm180) REVERT: C 50 GLN cc_start: 0.6295 (OUTLIER) cc_final: 0.5678 (mt0) REVERT: C 72 MET cc_start: 0.6619 (OUTLIER) cc_final: 0.6125 (mmt) REVERT: C 83 GLN cc_start: 0.9120 (OUTLIER) cc_final: 0.8346 (tp40) REVERT: C 197 GLN cc_start: 0.7942 (OUTLIER) cc_final: 0.7459 (mp10) REVERT: F 72 MET cc_start: 0.7260 (OUTLIER) cc_final: 0.6859 (mmt) REVERT: F 247 ARG cc_start: 0.7725 (OUTLIER) cc_final: 0.7310 (mtm180) REVERT: G 50 GLN cc_start: 0.6294 (OUTLIER) cc_final: 0.5674 (mt0) REVERT: G 72 MET cc_start: 0.6614 (OUTLIER) cc_final: 0.6112 (mmt) REVERT: G 83 GLN cc_start: 0.9126 (OUTLIER) cc_final: 0.8347 (tp40) REVERT: G 197 GLN cc_start: 0.7952 (OUTLIER) cc_final: 0.7459 (mp10) REVERT: H 72 MET cc_start: 0.7261 (OUTLIER) cc_final: 0.6864 (mmt) REVERT: H 247 ARG cc_start: 0.7732 (OUTLIER) cc_final: 0.7315 (mtm180) outliers start: 97 outliers final: 59 residues processed: 294 average time/residue: 0.3016 time to fit residues: 124.5694 Evaluate side-chains 286 residues out of total 1440 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 81 poor density : 205 time to evaluate : 1.640 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 50 GLN Chi-restraints excluded: chain A residue 72 MET Chi-restraints excluded: chain A residue 83 GLN Chi-restraints excluded: chain A residue 93 PHE Chi-restraints excluded: chain A residue 132 LEU Chi-restraints excluded: chain A residue 135 PHE Chi-restraints excluded: chain A residue 165 VAL Chi-restraints excluded: chain A residue 187 THR Chi-restraints excluded: chain A residue 194 LEU Chi-restraints excluded: chain A residue 197 GLN Chi-restraints excluded: chain A residue 199 CYS Chi-restraints excluded: chain A residue 248 THR Chi-restraints excluded: chain D residue 68 VAL Chi-restraints excluded: chain D residue 72 MET Chi-restraints excluded: chain D residue 89 SER Chi-restraints excluded: chain D residue 165 VAL Chi-restraints excluded: chain D residue 177 LEU Chi-restraints excluded: chain D residue 244 SER Chi-restraints excluded: chain D residue 247 ARG Chi-restraints excluded: chain D residue 248 THR Chi-restraints excluded: chain B residue 50 GLN Chi-restraints excluded: chain B residue 72 MET Chi-restraints excluded: chain B residue 83 GLN Chi-restraints excluded: chain B residue 93 PHE Chi-restraints excluded: chain B residue 132 LEU Chi-restraints excluded: chain B residue 135 PHE Chi-restraints excluded: chain B residue 165 VAL Chi-restraints excluded: chain B residue 187 THR Chi-restraints excluded: chain B residue 194 LEU Chi-restraints excluded: chain B residue 197 GLN Chi-restraints excluded: chain B residue 199 CYS Chi-restraints excluded: chain B residue 248 THR Chi-restraints excluded: chain E residue 68 VAL Chi-restraints excluded: chain E residue 72 MET Chi-restraints excluded: chain E residue 89 SER Chi-restraints excluded: chain E residue 165 VAL Chi-restraints excluded: chain E residue 177 LEU Chi-restraints excluded: chain E residue 244 SER Chi-restraints excluded: chain E residue 247 ARG Chi-restraints excluded: chain E residue 248 THR Chi-restraints excluded: chain C residue 50 GLN Chi-restraints excluded: chain C residue 72 MET Chi-restraints excluded: chain C residue 83 GLN Chi-restraints excluded: chain C residue 93 PHE Chi-restraints excluded: chain C residue 132 LEU Chi-restraints excluded: chain C residue 135 PHE Chi-restraints excluded: chain C residue 165 VAL Chi-restraints excluded: chain C residue 187 THR Chi-restraints excluded: chain C residue 194 LEU Chi-restraints excluded: chain C residue 197 GLN Chi-restraints excluded: chain C residue 199 CYS Chi-restraints excluded: chain C residue 248 THR Chi-restraints excluded: chain F residue 68 VAL Chi-restraints excluded: chain F residue 72 MET Chi-restraints excluded: chain F residue 89 SER Chi-restraints excluded: chain F residue 165 VAL Chi-restraints excluded: chain F residue 177 LEU Chi-restraints excluded: chain F residue 244 SER Chi-restraints excluded: chain F residue 247 ARG Chi-restraints excluded: chain F residue 248 THR Chi-restraints excluded: chain G residue 50 GLN Chi-restraints excluded: chain G residue 72 MET Chi-restraints excluded: chain G residue 83 GLN Chi-restraints excluded: chain G residue 93 PHE Chi-restraints excluded: chain G residue 132 LEU Chi-restraints excluded: chain G residue 135 PHE Chi-restraints excluded: chain G residue 165 VAL Chi-restraints excluded: chain G residue 187 THR Chi-restraints excluded: chain G residue 194 LEU Chi-restraints excluded: chain G residue 197 GLN Chi-restraints excluded: chain G residue 199 CYS Chi-restraints excluded: chain G residue 225 SER Chi-restraints excluded: chain G residue 248 THR Chi-restraints excluded: chain H residue 68 VAL Chi-restraints excluded: chain H residue 72 MET Chi-restraints excluded: chain H residue 89 SER Chi-restraints excluded: chain H residue 165 VAL Chi-restraints excluded: chain H residue 177 LEU Chi-restraints excluded: chain H residue 244 SER Chi-restraints excluded: chain H residue 247 ARG Chi-restraints excluded: chain H residue 248 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 35 optimal weight: 0.0040 chunk 96 optimal weight: 6.9990 chunk 101 optimal weight: 0.7980 chunk 11 optimal weight: 3.9990 chunk 30 optimal weight: 9.9990 chunk 38 optimal weight: 4.9990 chunk 117 optimal weight: 5.9990 chunk 68 optimal weight: 0.0870 chunk 125 optimal weight: 7.9990 chunk 75 optimal weight: 5.9990 chunk 56 optimal weight: 0.9980 overall best weight: 1.1772 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3803 r_free = 0.3803 target = 0.161108 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3563 r_free = 0.3563 target = 0.141239 restraints weight = 18040.818| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3581 r_free = 0.3581 target = 0.142861 restraints weight = 14624.243| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3598 r_free = 0.3598 target = 0.144171 restraints weight = 12567.525| |-----------------------------------------------------------------------------| r_work (final): 0.3604 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8069 moved from start: 0.1489 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.018 14752 Z= 0.109 Angle : 0.549 7.016 20000 Z= 0.291 Chirality : 0.045 0.225 1976 Planarity : 0.003 0.026 2592 Dihedral : 6.168 45.349 2300 Min Nonbonded Distance : 2.309 Molprobity Statistics. All-atom Clashscore : 3.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 14.29 % Favored : 85.71 % Rotamer: Outliers : 5.83 % Allowed : 26.88 % Favored : 67.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.13 (0.16), residues: 1736 helix: -0.86 (0.30), residues: 312 sheet: -1.14 (0.28), residues: 320 loop : -4.13 (0.12), residues: 1104 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP D 235 HIS 0.002 0.001 HIS G 118 PHE 0.019 0.001 PHE G 82 TYR 0.008 0.001 TYR C 99 ARG 0.002 0.000 ARG E 94 Details of bonding type rmsd link_NAG-ASN : bond 0.00518 ( 16) link_NAG-ASN : angle 2.06722 ( 48) hydrogen bonds : bond 0.03329 ( 320) hydrogen bonds : angle 5.43489 ( 888) SS BOND : bond 0.00094 ( 16) SS BOND : angle 0.54586 ( 32) covalent geometry : bond 0.00237 (14720) covalent geometry : angle 0.53995 (19920) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3472 Ramachandran restraints generated. 1736 Oldfield, 0 Emsley, 1736 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3472 Ramachandran restraints generated. 1736 Oldfield, 0 Emsley, 1736 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 286 residues out of total 1440 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 84 poor density : 202 time to evaluate : 1.436 Fit side-chains REVERT: A 72 MET cc_start: 0.6640 (OUTLIER) cc_final: 0.6151 (mmt) REVERT: A 83 GLN cc_start: 0.9138 (OUTLIER) cc_final: 0.8369 (tp40) REVERT: A 159 ASP cc_start: 0.6809 (OUTLIER) cc_final: 0.6112 (m-30) REVERT: A 193 ASP cc_start: 0.6923 (m-30) cc_final: 0.6355 (m-30) REVERT: A 197 GLN cc_start: 0.7911 (OUTLIER) cc_final: 0.7469 (mp10) REVERT: D 72 MET cc_start: 0.7225 (mmt) cc_final: 0.6872 (mmt) REVERT: B 72 MET cc_start: 0.6640 (OUTLIER) cc_final: 0.6129 (mmt) REVERT: B 83 GLN cc_start: 0.9156 (OUTLIER) cc_final: 0.8375 (tp40) REVERT: B 159 ASP cc_start: 0.6786 (OUTLIER) cc_final: 0.6099 (m-30) REVERT: B 193 ASP cc_start: 0.6922 (m-30) cc_final: 0.6361 (m-30) REVERT: B 197 GLN cc_start: 0.7914 (OUTLIER) cc_final: 0.7472 (mp10) REVERT: E 72 MET cc_start: 0.7217 (mmt) cc_final: 0.6870 (mmt) REVERT: C 50 GLN cc_start: 0.6253 (OUTLIER) cc_final: 0.5622 (mt0) REVERT: C 72 MET cc_start: 0.6665 (OUTLIER) cc_final: 0.6129 (mmt) REVERT: C 83 GLN cc_start: 0.9142 (OUTLIER) cc_final: 0.8371 (tp40) REVERT: C 159 ASP cc_start: 0.6813 (OUTLIER) cc_final: 0.6111 (m-30) REVERT: C 193 ASP cc_start: 0.6919 (m-30) cc_final: 0.6358 (m-30) REVERT: C 197 GLN cc_start: 0.7908 (OUTLIER) cc_final: 0.7471 (mp10) REVERT: F 72 MET cc_start: 0.7284 (mmt) cc_final: 0.6900 (mmt) REVERT: G 50 GLN cc_start: 0.6256 (OUTLIER) cc_final: 0.5623 (mt0) REVERT: G 72 MET cc_start: 0.6603 (OUTLIER) cc_final: 0.6067 (mmt) REVERT: G 83 GLN cc_start: 0.9146 (OUTLIER) cc_final: 0.8375 (tp40) REVERT: G 159 ASP cc_start: 0.6835 (OUTLIER) cc_final: 0.6150 (m-30) REVERT: G 193 ASP cc_start: 0.6919 (m-30) cc_final: 0.6353 (m-30) REVERT: G 197 GLN cc_start: 0.7915 (OUTLIER) cc_final: 0.7474 (mp10) REVERT: H 72 MET cc_start: 0.7291 (mmt) cc_final: 0.6904 (mmt) outliers start: 84 outliers final: 58 residues processed: 274 average time/residue: 0.2986 time to fit residues: 113.8614 Evaluate side-chains 279 residues out of total 1440 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 203 time to evaluate : 1.619 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 50 GLN Chi-restraints excluded: chain A residue 72 MET Chi-restraints excluded: chain A residue 83 GLN Chi-restraints excluded: chain A residue 93 PHE Chi-restraints excluded: chain A residue 132 LEU Chi-restraints excluded: chain A residue 135 PHE Chi-restraints excluded: chain A residue 159 ASP Chi-restraints excluded: chain A residue 165 VAL Chi-restraints excluded: chain A residue 194 LEU Chi-restraints excluded: chain A residue 197 GLN Chi-restraints excluded: chain A residue 199 CYS Chi-restraints excluded: chain A residue 225 SER Chi-restraints excluded: chain A residue 248 THR Chi-restraints excluded: chain D residue 68 VAL Chi-restraints excluded: chain D residue 89 SER Chi-restraints excluded: chain D residue 165 VAL Chi-restraints excluded: chain D residue 177 LEU Chi-restraints excluded: chain D residue 244 SER Chi-restraints excluded: chain D residue 248 THR Chi-restraints excluded: chain B residue 50 GLN Chi-restraints excluded: chain B residue 72 MET Chi-restraints excluded: chain B residue 83 GLN Chi-restraints excluded: chain B residue 93 PHE Chi-restraints excluded: chain B residue 132 LEU Chi-restraints excluded: chain B residue 135 PHE Chi-restraints excluded: chain B residue 159 ASP Chi-restraints excluded: chain B residue 165 VAL Chi-restraints excluded: chain B residue 194 LEU Chi-restraints excluded: chain B residue 197 GLN Chi-restraints excluded: chain B residue 199 CYS Chi-restraints excluded: chain B residue 225 SER Chi-restraints excluded: chain B residue 248 THR Chi-restraints excluded: chain E residue 68 VAL Chi-restraints excluded: chain E residue 89 SER Chi-restraints excluded: chain E residue 165 VAL Chi-restraints excluded: chain E residue 177 LEU Chi-restraints excluded: chain E residue 244 SER Chi-restraints excluded: chain E residue 248 THR Chi-restraints excluded: chain C residue 50 GLN Chi-restraints excluded: chain C residue 72 MET Chi-restraints excluded: chain C residue 83 GLN Chi-restraints excluded: chain C residue 93 PHE Chi-restraints excluded: chain C residue 132 LEU Chi-restraints excluded: chain C residue 135 PHE Chi-restraints excluded: chain C residue 159 ASP Chi-restraints excluded: chain C residue 165 VAL Chi-restraints excluded: chain C residue 194 LEU Chi-restraints excluded: chain C residue 197 GLN Chi-restraints excluded: chain C residue 199 CYS Chi-restraints excluded: chain C residue 225 SER Chi-restraints excluded: chain C residue 248 THR Chi-restraints excluded: chain F residue 68 VAL Chi-restraints excluded: chain F residue 89 SER Chi-restraints excluded: chain F residue 165 VAL Chi-restraints excluded: chain F residue 177 LEU Chi-restraints excluded: chain F residue 244 SER Chi-restraints excluded: chain F residue 248 THR Chi-restraints excluded: chain G residue 50 GLN Chi-restraints excluded: chain G residue 72 MET Chi-restraints excluded: chain G residue 83 GLN Chi-restraints excluded: chain G residue 93 PHE Chi-restraints excluded: chain G residue 132 LEU Chi-restraints excluded: chain G residue 135 PHE Chi-restraints excluded: chain G residue 159 ASP Chi-restraints excluded: chain G residue 165 VAL Chi-restraints excluded: chain G residue 194 LEU Chi-restraints excluded: chain G residue 197 GLN Chi-restraints excluded: chain G residue 199 CYS Chi-restraints excluded: chain G residue 225 SER Chi-restraints excluded: chain G residue 248 THR Chi-restraints excluded: chain H residue 68 VAL Chi-restraints excluded: chain H residue 89 SER Chi-restraints excluded: chain H residue 165 VAL Chi-restraints excluded: chain H residue 177 LEU Chi-restraints excluded: chain H residue 244 SER Chi-restraints excluded: chain H residue 248 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 122 optimal weight: 3.9990 chunk 63 optimal weight: 10.0000 chunk 126 optimal weight: 10.0000 chunk 111 optimal weight: 5.9990 chunk 158 optimal weight: 3.9990 chunk 68 optimal weight: 0.0980 chunk 131 optimal weight: 0.9980 chunk 85 optimal weight: 0.9980 chunk 55 optimal weight: 10.0000 chunk 113 optimal weight: 6.9990 chunk 49 optimal weight: 6.9990 overall best weight: 2.0184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3779 r_free = 0.3779 target = 0.158977 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3529 r_free = 0.3529 target = 0.138299 restraints weight = 17925.982| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3551 r_free = 0.3551 target = 0.140158 restraints weight = 14268.395| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3566 r_free = 0.3566 target = 0.141452 restraints weight = 12139.839| |-----------------------------------------------------------------------------| r_work (final): 0.3572 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8102 moved from start: 0.1499 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.020 14752 Z= 0.150 Angle : 0.585 7.375 20000 Z= 0.312 Chirality : 0.046 0.221 1976 Planarity : 0.004 0.039 2592 Dihedral : 6.415 48.181 2300 Min Nonbonded Distance : 2.305 Molprobity Statistics. All-atom Clashscore : 4.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 15.09 % Favored : 84.91 % Rotamer: Outliers : 6.67 % Allowed : 25.76 % Favored : 67.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.27 (0.16), residues: 1736 helix: -0.71 (0.30), residues: 296 sheet: -1.70 (0.28), residues: 344 loop : -4.14 (0.12), residues: 1096 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP D 235 HIS 0.003 0.001 HIS D 180 PHE 0.021 0.001 PHE G 82 TYR 0.012 0.001 TYR D 110 ARG 0.003 0.000 ARG F 94 Details of bonding type rmsd link_NAG-ASN : bond 0.00526 ( 16) link_NAG-ASN : angle 2.10159 ( 48) hydrogen bonds : bond 0.03826 ( 320) hydrogen bonds : angle 5.53423 ( 888) SS BOND : bond 0.00165 ( 16) SS BOND : angle 0.56157 ( 32) covalent geometry : bond 0.00344 (14720) covalent geometry : angle 0.57693 (19920) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3472 Ramachandran restraints generated. 1736 Oldfield, 0 Emsley, 1736 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3472 Ramachandran restraints generated. 1736 Oldfield, 0 Emsley, 1736 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 293 residues out of total 1440 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 96 poor density : 197 time to evaluate : 1.777 Fit side-chains REVERT: A 72 MET cc_start: 0.6667 (OUTLIER) cc_final: 0.6111 (mmt) REVERT: A 83 GLN cc_start: 0.9169 (OUTLIER) cc_final: 0.8394 (tp40) REVERT: A 159 ASP cc_start: 0.6701 (OUTLIER) cc_final: 0.5951 (m-30) REVERT: A 197 GLN cc_start: 0.7937 (OUTLIER) cc_final: 0.7468 (mp10) REVERT: D 72 MET cc_start: 0.7392 (OUTLIER) cc_final: 0.7073 (mmt) REVERT: D 247 ARG cc_start: 0.7779 (OUTLIER) cc_final: 0.7368 (mtm180) REVERT: B 72 MET cc_start: 0.6661 (OUTLIER) cc_final: 0.6106 (mmt) REVERT: B 83 GLN cc_start: 0.9180 (OUTLIER) cc_final: 0.8394 (tp40) REVERT: B 159 ASP cc_start: 0.6672 (OUTLIER) cc_final: 0.5933 (m-30) REVERT: B 197 GLN cc_start: 0.7942 (OUTLIER) cc_final: 0.7479 (mp10) REVERT: E 72 MET cc_start: 0.7386 (OUTLIER) cc_final: 0.7072 (mmt) REVERT: E 247 ARG cc_start: 0.7781 (OUTLIER) cc_final: 0.7361 (mtm180) REVERT: C 50 GLN cc_start: 0.6388 (OUTLIER) cc_final: 0.5723 (mt0) REVERT: C 72 MET cc_start: 0.6642 (OUTLIER) cc_final: 0.6080 (mmt) REVERT: C 83 GLN cc_start: 0.9169 (OUTLIER) cc_final: 0.8388 (tp40) REVERT: C 159 ASP cc_start: 0.6701 (OUTLIER) cc_final: 0.5943 (m-30) REVERT: C 197 GLN cc_start: 0.7938 (OUTLIER) cc_final: 0.7475 (mp10) REVERT: F 72 MET cc_start: 0.7412 (OUTLIER) cc_final: 0.7131 (mmt) REVERT: F 247 ARG cc_start: 0.7770 (OUTLIER) cc_final: 0.7355 (mtm180) REVERT: G 50 GLN cc_start: 0.6392 (OUTLIER) cc_final: 0.5725 (mt0) REVERT: G 72 MET cc_start: 0.6632 (OUTLIER) cc_final: 0.6067 (mmt) REVERT: G 83 GLN cc_start: 0.9170 (OUTLIER) cc_final: 0.8390 (tp40) REVERT: G 159 ASP cc_start: 0.6685 (OUTLIER) cc_final: 0.5947 (m-30) REVERT: G 197 GLN cc_start: 0.7941 (OUTLIER) cc_final: 0.7478 (mp10) REVERT: H 72 MET cc_start: 0.7417 (OUTLIER) cc_final: 0.7140 (mmt) REVERT: H 247 ARG cc_start: 0.7777 (OUTLIER) cc_final: 0.7364 (mtm180) outliers start: 96 outliers final: 58 residues processed: 273 average time/residue: 0.2987 time to fit residues: 113.7885 Evaluate side-chains 283 residues out of total 1440 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 84 poor density : 199 time to evaluate : 1.515 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 50 GLN Chi-restraints excluded: chain A residue 72 MET Chi-restraints excluded: chain A residue 83 GLN Chi-restraints excluded: chain A residue 93 PHE Chi-restraints excluded: chain A residue 132 LEU Chi-restraints excluded: chain A residue 135 PHE Chi-restraints excluded: chain A residue 159 ASP Chi-restraints excluded: chain A residue 165 VAL Chi-restraints excluded: chain A residue 194 LEU Chi-restraints excluded: chain A residue 197 GLN Chi-restraints excluded: chain A residue 199 CYS Chi-restraints excluded: chain A residue 225 SER Chi-restraints excluded: chain A residue 248 THR Chi-restraints excluded: chain D residue 68 VAL Chi-restraints excluded: chain D residue 72 MET Chi-restraints excluded: chain D residue 89 SER Chi-restraints excluded: chain D residue 165 VAL Chi-restraints excluded: chain D residue 177 LEU Chi-restraints excluded: chain D residue 244 SER Chi-restraints excluded: chain D residue 247 ARG Chi-restraints excluded: chain D residue 248 THR Chi-restraints excluded: chain B residue 50 GLN Chi-restraints excluded: chain B residue 72 MET Chi-restraints excluded: chain B residue 83 GLN Chi-restraints excluded: chain B residue 93 PHE Chi-restraints excluded: chain B residue 132 LEU Chi-restraints excluded: chain B residue 135 PHE Chi-restraints excluded: chain B residue 159 ASP Chi-restraints excluded: chain B residue 165 VAL Chi-restraints excluded: chain B residue 194 LEU Chi-restraints excluded: chain B residue 197 GLN Chi-restraints excluded: chain B residue 199 CYS Chi-restraints excluded: chain B residue 225 SER Chi-restraints excluded: chain B residue 248 THR Chi-restraints excluded: chain E residue 68 VAL Chi-restraints excluded: chain E residue 72 MET Chi-restraints excluded: chain E residue 89 SER Chi-restraints excluded: chain E residue 165 VAL Chi-restraints excluded: chain E residue 177 LEU Chi-restraints excluded: chain E residue 244 SER Chi-restraints excluded: chain E residue 247 ARG Chi-restraints excluded: chain E residue 248 THR Chi-restraints excluded: chain C residue 50 GLN Chi-restraints excluded: chain C residue 72 MET Chi-restraints excluded: chain C residue 83 GLN Chi-restraints excluded: chain C residue 93 PHE Chi-restraints excluded: chain C residue 132 LEU Chi-restraints excluded: chain C residue 135 PHE Chi-restraints excluded: chain C residue 159 ASP Chi-restraints excluded: chain C residue 165 VAL Chi-restraints excluded: chain C residue 194 LEU Chi-restraints excluded: chain C residue 197 GLN Chi-restraints excluded: chain C residue 199 CYS Chi-restraints excluded: chain C residue 225 SER Chi-restraints excluded: chain C residue 248 THR Chi-restraints excluded: chain F residue 68 VAL Chi-restraints excluded: chain F residue 72 MET Chi-restraints excluded: chain F residue 89 SER Chi-restraints excluded: chain F residue 165 VAL Chi-restraints excluded: chain F residue 177 LEU Chi-restraints excluded: chain F residue 244 SER Chi-restraints excluded: chain F residue 247 ARG Chi-restraints excluded: chain F residue 248 THR Chi-restraints excluded: chain G residue 50 GLN Chi-restraints excluded: chain G residue 72 MET Chi-restraints excluded: chain G residue 83 GLN Chi-restraints excluded: chain G residue 93 PHE Chi-restraints excluded: chain G residue 132 LEU Chi-restraints excluded: chain G residue 135 PHE Chi-restraints excluded: chain G residue 159 ASP Chi-restraints excluded: chain G residue 165 VAL Chi-restraints excluded: chain G residue 194 LEU Chi-restraints excluded: chain G residue 197 GLN Chi-restraints excluded: chain G residue 199 CYS Chi-restraints excluded: chain G residue 225 SER Chi-restraints excluded: chain G residue 248 THR Chi-restraints excluded: chain H residue 68 VAL Chi-restraints excluded: chain H residue 72 MET Chi-restraints excluded: chain H residue 89 SER Chi-restraints excluded: chain H residue 165 VAL Chi-restraints excluded: chain H residue 177 LEU Chi-restraints excluded: chain H residue 244 SER Chi-restraints excluded: chain H residue 247 ARG Chi-restraints excluded: chain H residue 248 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 21 optimal weight: 10.0000 chunk 61 optimal weight: 2.9990 chunk 55 optimal weight: 9.9990 chunk 145 optimal weight: 9.9990 chunk 106 optimal weight: 10.0000 chunk 17 optimal weight: 6.9990 chunk 4 optimal weight: 5.9990 chunk 46 optimal weight: 5.9990 chunk 51 optimal weight: 1.9990 chunk 42 optimal weight: 8.9990 chunk 95 optimal weight: 4.9990 overall best weight: 4.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 237 GLN B 237 GLN C 237 GLN G 237 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3732 r_free = 0.3732 target = 0.154609 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3474 r_free = 0.3474 target = 0.133764 restraints weight = 18082.743| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3495 r_free = 0.3495 target = 0.135547 restraints weight = 14634.102| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3512 r_free = 0.3512 target = 0.136904 restraints weight = 12515.159| |-----------------------------------------------------------------------------| r_work (final): 0.3516 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8163 moved from start: 0.1621 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.037 14752 Z= 0.295 Angle : 0.738 8.301 20000 Z= 0.394 Chirality : 0.052 0.219 1976 Planarity : 0.006 0.066 2592 Dihedral : 7.488 53.227 2300 Min Nonbonded Distance : 2.261 Molprobity Statistics. All-atom Clashscore : 5.00 Ramachandran Plot: Outliers : 0.23 % Allowed : 16.82 % Favored : 82.95 % Rotamer: Outliers : 5.35 % Allowed : 27.15 % Favored : 67.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.52 (0.16), residues: 1736 helix: -1.27 (0.28), residues: 312 sheet: -1.87 (0.28), residues: 344 loop : -4.22 (0.12), residues: 1080 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP D 235 HIS 0.005 0.002 HIS H 180 PHE 0.030 0.002 PHE D 82 TYR 0.022 0.002 TYR H 110 ARG 0.006 0.001 ARG E 94 Details of bonding type rmsd link_NAG-ASN : bond 0.00610 ( 16) link_NAG-ASN : angle 2.27098 ( 48) hydrogen bonds : bond 0.05168 ( 320) hydrogen bonds : angle 5.93823 ( 888) SS BOND : bond 0.00378 ( 16) SS BOND : angle 0.78249 ( 32) covalent geometry : bond 0.00702 (14720) covalent geometry : angle 0.73077 (19920) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3472 Ramachandran restraints generated. 1736 Oldfield, 0 Emsley, 1736 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3472 Ramachandran restraints generated. 1736 Oldfield, 0 Emsley, 1736 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 274 residues out of total 1440 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 197 time to evaluate : 1.509 Fit side-chains REVERT: A 83 GLN cc_start: 0.9226 (OUTLIER) cc_final: 0.8414 (tp40) REVERT: A 159 ASP cc_start: 0.6639 (OUTLIER) cc_final: 0.5810 (m-30) REVERT: A 197 GLN cc_start: 0.7974 (OUTLIER) cc_final: 0.7451 (mp10) REVERT: D 72 MET cc_start: 0.7497 (mmt) cc_final: 0.7245 (mmt) REVERT: D 247 ARG cc_start: 0.7911 (OUTLIER) cc_final: 0.7530 (mtm180) REVERT: B 83 GLN cc_start: 0.9236 (OUTLIER) cc_final: 0.8413 (tp40) REVERT: B 159 ASP cc_start: 0.6616 (OUTLIER) cc_final: 0.5799 (m-30) REVERT: B 197 GLN cc_start: 0.7980 (OUTLIER) cc_final: 0.7461 (mp10) REVERT: E 72 MET cc_start: 0.7500 (mmt) cc_final: 0.7249 (mmt) REVERT: E 247 ARG cc_start: 0.7920 (OUTLIER) cc_final: 0.7530 (mtm180) REVERT: C 50 GLN cc_start: 0.6499 (OUTLIER) cc_final: 0.5902 (mt0) REVERT: C 83 GLN cc_start: 0.9229 (OUTLIER) cc_final: 0.8419 (tp40) REVERT: C 159 ASP cc_start: 0.6639 (OUTLIER) cc_final: 0.5808 (m-30) REVERT: C 197 GLN cc_start: 0.7976 (OUTLIER) cc_final: 0.7461 (mp10) REVERT: F 72 MET cc_start: 0.7493 (mmt) cc_final: 0.7240 (mmt) REVERT: F 247 ARG cc_start: 0.7909 (OUTLIER) cc_final: 0.7524 (mtm180) REVERT: G 50 GLN cc_start: 0.6497 (OUTLIER) cc_final: 0.5900 (mt0) REVERT: G 83 GLN cc_start: 0.9228 (OUTLIER) cc_final: 0.8417 (tp40) REVERT: G 159 ASP cc_start: 0.6626 (OUTLIER) cc_final: 0.5808 (m-30) REVERT: G 197 GLN cc_start: 0.7980 (OUTLIER) cc_final: 0.7457 (mp10) REVERT: H 72 MET cc_start: 0.7505 (mmt) cc_final: 0.7249 (mmt) REVERT: H 247 ARG cc_start: 0.7914 (OUTLIER) cc_final: 0.7529 (mtm180) outliers start: 77 outliers final: 54 residues processed: 265 average time/residue: 0.2993 time to fit residues: 109.9104 Evaluate side-chains 268 residues out of total 1440 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 196 time to evaluate : 1.420 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 50 GLN Chi-restraints excluded: chain A residue 83 GLN Chi-restraints excluded: chain A residue 93 PHE Chi-restraints excluded: chain A residue 132 LEU Chi-restraints excluded: chain A residue 135 PHE Chi-restraints excluded: chain A residue 159 ASP Chi-restraints excluded: chain A residue 165 VAL Chi-restraints excluded: chain A residue 194 LEU Chi-restraints excluded: chain A residue 197 GLN Chi-restraints excluded: chain A residue 199 CYS Chi-restraints excluded: chain A residue 225 SER Chi-restraints excluded: chain A residue 248 THR Chi-restraints excluded: chain D residue 68 VAL Chi-restraints excluded: chain D residue 89 SER Chi-restraints excluded: chain D residue 165 VAL Chi-restraints excluded: chain D residue 244 SER Chi-restraints excluded: chain D residue 247 ARG Chi-restraints excluded: chain D residue 248 THR Chi-restraints excluded: chain B residue 50 GLN Chi-restraints excluded: chain B residue 83 GLN Chi-restraints excluded: chain B residue 93 PHE Chi-restraints excluded: chain B residue 132 LEU Chi-restraints excluded: chain B residue 135 PHE Chi-restraints excluded: chain B residue 159 ASP Chi-restraints excluded: chain B residue 165 VAL Chi-restraints excluded: chain B residue 194 LEU Chi-restraints excluded: chain B residue 197 GLN Chi-restraints excluded: chain B residue 199 CYS Chi-restraints excluded: chain B residue 225 SER Chi-restraints excluded: chain B residue 248 THR Chi-restraints excluded: chain E residue 68 VAL Chi-restraints excluded: chain E residue 89 SER Chi-restraints excluded: chain E residue 165 VAL Chi-restraints excluded: chain E residue 244 SER Chi-restraints excluded: chain E residue 247 ARG Chi-restraints excluded: chain E residue 248 THR Chi-restraints excluded: chain C residue 50 GLN Chi-restraints excluded: chain C residue 83 GLN Chi-restraints excluded: chain C residue 93 PHE Chi-restraints excluded: chain C residue 132 LEU Chi-restraints excluded: chain C residue 135 PHE Chi-restraints excluded: chain C residue 159 ASP Chi-restraints excluded: chain C residue 165 VAL Chi-restraints excluded: chain C residue 194 LEU Chi-restraints excluded: chain C residue 197 GLN Chi-restraints excluded: chain C residue 199 CYS Chi-restraints excluded: chain C residue 225 SER Chi-restraints excluded: chain C residue 248 THR Chi-restraints excluded: chain F residue 68 VAL Chi-restraints excluded: chain F residue 89 SER Chi-restraints excluded: chain F residue 165 VAL Chi-restraints excluded: chain F residue 244 SER Chi-restraints excluded: chain F residue 247 ARG Chi-restraints excluded: chain F residue 248 THR Chi-restraints excluded: chain G residue 50 GLN Chi-restraints excluded: chain G residue 83 GLN Chi-restraints excluded: chain G residue 93 PHE Chi-restraints excluded: chain G residue 132 LEU Chi-restraints excluded: chain G residue 135 PHE Chi-restraints excluded: chain G residue 159 ASP Chi-restraints excluded: chain G residue 165 VAL Chi-restraints excluded: chain G residue 194 LEU Chi-restraints excluded: chain G residue 197 GLN Chi-restraints excluded: chain G residue 199 CYS Chi-restraints excluded: chain G residue 225 SER Chi-restraints excluded: chain G residue 248 THR Chi-restraints excluded: chain H residue 68 VAL Chi-restraints excluded: chain H residue 89 SER Chi-restraints excluded: chain H residue 165 VAL Chi-restraints excluded: chain H residue 244 SER Chi-restraints excluded: chain H residue 247 ARG Chi-restraints excluded: chain H residue 248 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 158 optimal weight: 2.9990 chunk 32 optimal weight: 4.9990 chunk 44 optimal weight: 0.0370 chunk 111 optimal weight: 2.9990 chunk 165 optimal weight: 4.9990 chunk 92 optimal weight: 4.9990 chunk 7 optimal weight: 0.7980 chunk 148 optimal weight: 6.9990 chunk 69 optimal weight: 0.6980 chunk 47 optimal weight: 2.9990 chunk 104 optimal weight: 8.9990 overall best weight: 1.5062 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3785 r_free = 0.3785 target = 0.159345 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3541 r_free = 0.3541 target = 0.139386 restraints weight = 17904.532| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3558 r_free = 0.3558 target = 0.140851 restraints weight = 14496.280| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3575 r_free = 0.3575 target = 0.142257 restraints weight = 12555.847| |-----------------------------------------------------------------------------| r_work (final): 0.3582 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8095 moved from start: 0.1541 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 14752 Z= 0.127 Angle : 0.594 9.897 20000 Z= 0.313 Chirality : 0.046 0.230 1976 Planarity : 0.004 0.036 2592 Dihedral : 6.495 49.792 2300 Min Nonbonded Distance : 2.288 Molprobity Statistics. All-atom Clashscore : 4.19 Ramachandran Plot: Outliers : 0.06 % Allowed : 14.00 % Favored : 85.94 % Rotamer: Outliers : 5.07 % Allowed : 27.57 % Favored : 67.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -4.37 (0.16), residues: 1736 helix: -1.00 (0.29), residues: 312 sheet: -1.82 (0.28), residues: 344 loop : -4.15 (0.12), residues: 1080 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP D 235 HIS 0.002 0.001 HIS C 118 PHE 0.020 0.001 PHE B 82 TYR 0.010 0.001 TYR G 99 ARG 0.002 0.000 ARG D 94 Details of bonding type rmsd link_NAG-ASN : bond 0.00553 ( 16) link_NAG-ASN : angle 2.03212 ( 48) hydrogen bonds : bond 0.03536 ( 320) hydrogen bonds : angle 5.50523 ( 888) SS BOND : bond 0.00269 ( 16) SS BOND : angle 1.07176 ( 32) covalent geometry : bond 0.00288 (14720) covalent geometry : angle 0.58567 (19920) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3472 Ramachandran restraints generated. 1736 Oldfield, 0 Emsley, 1736 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3472 Ramachandran restraints generated. 1736 Oldfield, 0 Emsley, 1736 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 264 residues out of total 1440 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 191 time to evaluate : 1.437 Fit side-chains REVERT: A 83 GLN cc_start: 0.9143 (OUTLIER) cc_final: 0.8370 (tp40) REVERT: A 159 ASP cc_start: 0.6727 (OUTLIER) cc_final: 0.5946 (m-30) REVERT: A 197 GLN cc_start: 0.7943 (OUTLIER) cc_final: 0.7372 (mp10) REVERT: D 72 MET cc_start: 0.7315 (mmt) cc_final: 0.6986 (mmt) REVERT: D 247 ARG cc_start: 0.7752 (OUTLIER) cc_final: 0.7301 (mtm180) REVERT: B 83 GLN cc_start: 0.9159 (OUTLIER) cc_final: 0.8375 (tp40) REVERT: B 159 ASP cc_start: 0.6696 (OUTLIER) cc_final: 0.5934 (m-30) REVERT: B 197 GLN cc_start: 0.7945 (OUTLIER) cc_final: 0.7380 (mp10) REVERT: E 72 MET cc_start: 0.7355 (mmt) cc_final: 0.7016 (mmt) REVERT: E 247 ARG cc_start: 0.7758 (OUTLIER) cc_final: 0.7298 (mtm180) REVERT: C 50 GLN cc_start: 0.6338 (OUTLIER) cc_final: 0.5696 (mt0) REVERT: C 72 MET cc_start: 0.6595 (OUTLIER) cc_final: 0.6089 (mmt) REVERT: C 83 GLN cc_start: 0.9147 (OUTLIER) cc_final: 0.8368 (tp40) REVERT: C 159 ASP cc_start: 0.6724 (OUTLIER) cc_final: 0.5970 (m-30) REVERT: C 197 GLN cc_start: 0.7946 (OUTLIER) cc_final: 0.7378 (mp10) REVERT: F 72 MET cc_start: 0.7366 (mmt) cc_final: 0.7035 (mmt) REVERT: F 247 ARG cc_start: 0.7748 (OUTLIER) cc_final: 0.7295 (mtm180) REVERT: G 50 GLN cc_start: 0.6346 (OUTLIER) cc_final: 0.5797 (mt0) REVERT: G 83 GLN cc_start: 0.9154 (OUTLIER) cc_final: 0.8375 (tp40) REVERT: G 159 ASP cc_start: 0.6708 (OUTLIER) cc_final: 0.5970 (m-30) REVERT: G 197 GLN cc_start: 0.7951 (OUTLIER) cc_final: 0.7377 (mp10) REVERT: H 72 MET cc_start: 0.7356 (mmt) cc_final: 0.7039 (mmt) REVERT: H 247 ARG cc_start: 0.7754 (OUTLIER) cc_final: 0.7297 (mtm180) outliers start: 73 outliers final: 50 residues processed: 251 average time/residue: 0.3093 time to fit residues: 106.9906 Evaluate side-chains 263 residues out of total 1440 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 194 time to evaluate : 1.554 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 50 GLN Chi-restraints excluded: chain A residue 83 GLN Chi-restraints excluded: chain A residue 93 PHE Chi-restraints excluded: chain A residue 132 LEU Chi-restraints excluded: chain A residue 135 PHE Chi-restraints excluded: chain A residue 159 ASP Chi-restraints excluded: chain A residue 165 VAL Chi-restraints excluded: chain A residue 194 LEU Chi-restraints excluded: chain A residue 197 GLN Chi-restraints excluded: chain A residue 225 SER Chi-restraints excluded: chain A residue 248 THR Chi-restraints excluded: chain D residue 68 VAL Chi-restraints excluded: chain D residue 89 SER Chi-restraints excluded: chain D residue 165 VAL Chi-restraints excluded: chain D residue 244 SER Chi-restraints excluded: chain D residue 247 ARG Chi-restraints excluded: chain D residue 248 THR Chi-restraints excluded: chain B residue 50 GLN Chi-restraints excluded: chain B residue 83 GLN Chi-restraints excluded: chain B residue 93 PHE Chi-restraints excluded: chain B residue 132 LEU Chi-restraints excluded: chain B residue 135 PHE Chi-restraints excluded: chain B residue 159 ASP Chi-restraints excluded: chain B residue 165 VAL Chi-restraints excluded: chain B residue 194 LEU Chi-restraints excluded: chain B residue 197 GLN Chi-restraints excluded: chain B residue 225 SER Chi-restraints excluded: chain B residue 248 THR Chi-restraints excluded: chain E residue 68 VAL Chi-restraints excluded: chain E residue 89 SER Chi-restraints excluded: chain E residue 165 VAL Chi-restraints excluded: chain E residue 244 SER Chi-restraints excluded: chain E residue 247 ARG Chi-restraints excluded: chain E residue 248 THR Chi-restraints excluded: chain C residue 50 GLN Chi-restraints excluded: chain C residue 72 MET Chi-restraints excluded: chain C residue 83 GLN Chi-restraints excluded: chain C residue 93 PHE Chi-restraints excluded: chain C residue 132 LEU Chi-restraints excluded: chain C residue 135 PHE Chi-restraints excluded: chain C residue 159 ASP Chi-restraints excluded: chain C residue 165 VAL Chi-restraints excluded: chain C residue 194 LEU Chi-restraints excluded: chain C residue 197 GLN Chi-restraints excluded: chain C residue 225 SER Chi-restraints excluded: chain C residue 248 THR Chi-restraints excluded: chain F residue 68 VAL Chi-restraints excluded: chain F residue 89 SER Chi-restraints excluded: chain F residue 165 VAL Chi-restraints excluded: chain F residue 244 SER Chi-restraints excluded: chain F residue 247 ARG Chi-restraints excluded: chain F residue 248 THR Chi-restraints excluded: chain G residue 50 GLN Chi-restraints excluded: chain G residue 83 GLN Chi-restraints excluded: chain G residue 93 PHE Chi-restraints excluded: chain G residue 132 LEU Chi-restraints excluded: chain G residue 135 PHE Chi-restraints excluded: chain G residue 159 ASP Chi-restraints excluded: chain G residue 165 VAL Chi-restraints excluded: chain G residue 194 LEU Chi-restraints excluded: chain G residue 197 GLN Chi-restraints excluded: chain G residue 225 SER Chi-restraints excluded: chain G residue 248 THR Chi-restraints excluded: chain H residue 68 VAL Chi-restraints excluded: chain H residue 89 SER Chi-restraints excluded: chain H residue 165 VAL Chi-restraints excluded: chain H residue 244 SER Chi-restraints excluded: chain H residue 247 ARG Chi-restraints excluded: chain H residue 248 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 74 optimal weight: 3.9990 chunk 62 optimal weight: 9.9990 chunk 22 optimal weight: 10.0000 chunk 0 optimal weight: 10.0000 chunk 120 optimal weight: 3.9990 chunk 165 optimal weight: 7.9990 chunk 126 optimal weight: 10.0000 chunk 141 optimal weight: 6.9990 chunk 21 optimal weight: 7.9990 chunk 160 optimal weight: 10.0000 chunk 114 optimal weight: 8.9990 overall best weight: 6.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 216 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 198 ASN ** C 216 ASN ** 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 = 0.3705 r_free = 0.3705 target = 0.152182 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3452 r_free = 0.3452 target = 0.132032 restraints weight = 18476.714| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3471 r_free = 0.3471 target = 0.133568 restraints weight = 15228.924| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3485 r_free = 0.3485 target = 0.134733 restraints weight = 13291.358| |-----------------------------------------------------------------------------| r_work (final): 0.3489 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8195 moved from start: 0.1842 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.010 0.049 14752 Z= 0.411 Angle : 0.862 9.952 20000 Z= 0.458 Chirality : 0.057 0.217 1976 Planarity : 0.007 0.084 2592 Dihedral : 8.337 55.649 2300 Min Nonbonded Distance : 2.237 Molprobity Statistics. All-atom Clashscore : 4.96 Ramachandran Plot: Outliers : 0.23 % Allowed : 17.97 % Favored : 81.80 % Rotamer: Outliers : 5.35 % Allowed : 28.06 % Favored : 66.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -4.78 (0.16), residues: 1736 helix: -1.60 (0.28), residues: 312 sheet: -2.04 (0.27), residues: 344 loop : -4.35 (0.12), residues: 1080 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP D 235 HIS 0.007 0.003 HIS H 180 PHE 0.035 0.003 PHE H 82 TYR 0.027 0.003 TYR E 110 ARG 0.008 0.001 ARG H 94 Details of bonding type rmsd link_NAG-ASN : bond 0.00678 ( 16) link_NAG-ASN : angle 2.42398 ( 48) hydrogen bonds : bond 0.06047 ( 320) hydrogen bonds : angle 6.18668 ( 888) SS BOND : bond 0.00548 ( 16) SS BOND : angle 1.32667 ( 32) covalent geometry : bond 0.00982 (14720) covalent geometry : angle 0.85405 (19920) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4132.35 seconds wall clock time: 73 minutes 22.27 seconds (4402.27 seconds total)