Starting phenix.real_space_refine on Thu Jun 12 18:45:11 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8un7_42394/06_2025/8un7_42394.cif Found real_map, /net/cci-nas-00/data/ceres_data/8un7_42394/06_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_42394/06_2025/8un7_42394.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8un7_42394/06_2025/8un7_42394.map" model { file = "/net/cci-nas-00/data/ceres_data/8un7_42394/06_2025/8un7_42394.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8un7_42394/06_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): 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/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: 9.86, per 1000 atoms: 0.69 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: 3.98 Conformation dependent library (CDL) restraints added in 1.9 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: 1.76 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: 4.30 Time building geometry restraints manager: 4.62 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: 0.06 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: 3.210 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: 0.640 Check model and map are aligned: 0.110 Set scattering table: 0.160 Process input model: 38.570 Find NCS groups from input model: 0.720 Set up NCS constraints: 0.070 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:3.470 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 46.970 ------------------------------------------------------------------------------- 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 : 1.599 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: 0.3129 time to fit residues: 112.9799 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 : 1.635 ------------------------------------------------------------------------------- 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 = 0.159334 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3542 r_free = 0.3542 target = 0.139340 restraints weight = 17964.061| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3560 r_free = 0.3560 target = 0.141013 restraints weight = 14629.967| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3576 r_free = 0.3576 target = 0.142276 restraints weight = 12559.049| |-----------------------------------------------------------------------------| r_work (final): 0.3580 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8090 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 5.646 20000 Z= 0.321 Chirality : 0.046 0.236 1976 Planarity : 0.004 0.037 2592 Dihedral : 8.213 54.454 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 1.96636 ( 48) hydrogen bonds : bond 0.04228 ( 320) hydrogen bonds : angle 6.02889 ( 888) SS BOND : bond 0.00150 ( 16) SS BOND : angle 0.52671 ( 32) covalent geometry : bond 0.00335 (14720) covalent geometry : angle 0.58916 (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 : 1.568 Fit side-chains REVERT: A 197 GLN cc_start: 0.7982 (OUTLIER) cc_final: 0.7452 (mp10) REVERT: D 72 MET cc_start: 0.7459 (OUTLIER) cc_final: 0.7036 (mmt) REVERT: D 157 GLU cc_start: 0.8006 (OUTLIER) cc_final: 0.7776 (tt0) REVERT: D 190 ARG cc_start: 0.8153 (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: 0.7984 (OUTLIER) cc_final: 0.7460 (mp10) REVERT: E 72 MET cc_start: 0.7457 (OUTLIER) cc_final: 0.7047 (mmt) REVERT: E 157 GLU cc_start: 0.8021 (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: 0.7982 (OUTLIER) cc_final: 0.7462 (mp10) REVERT: F 72 MET cc_start: 0.7468 (OUTLIER) cc_final: 0.7053 (mmt) REVERT: F 157 GLU cc_start: 0.8016 (OUTLIER) cc_final: 0.7789 (tt0) REVERT: F 247 ARG cc_start: 0.7790 (OUTLIER) cc_final: 0.7169 (mtt180) REVERT: G 197 GLN cc_start: 0.7986 (OUTLIER) cc_final: 0.7459 (mp10) REVERT: H 72 MET cc_start: 0.7473 (OUTLIER) cc_final: 0.7057 (mmt) REVERT: H 157 GLU cc_start: 0.8011 (OUTLIER) cc_final: 0.7778 (tt0) REVERT: H 247 ARG cc_start: 0.7792 (OUTLIER) cc_final: 0.7173 (mtt180) outliers start: 106 outliers final: 44 residues processed: 288 average time/residue: 0.3696 time to fit residues: 147.4597 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 : 1.570 ------------------------------------------------------------------------------- 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: 6.9990 chunk 7 optimal weight: 2.9990 chunk 115 optimal weight: 3.9990 chunk 40 optimal weight: 8.9990 chunk 17 optimal weight: 1.9990 chunk 134 optimal weight: 1.9990 chunk 125 optimal weight: 8.9990 chunk 91 optimal weight: 1.9990 chunk 79 optimal weight: 5.9990 chunk 65 optimal weight: 0.0770 chunk 24 optimal weight: 0.6980 overall best weight: 1.3544 ------------------------------------------------------------------------------- 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 = 0.3798 r_free = 0.3798 target = 0.160538 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3552 r_free = 0.3552 target = 0.140428 restraints weight = 17951.751| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3573 r_free = 0.3573 target = 0.142174 restraints weight = 14491.767| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 23)----------------| | r_work = 0.3583 r_free = 0.3583 target = 0.143105 restraints weight = 12351.655| |-----------------------------------------------------------------------------| r_work (final): 0.3586 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8076 moved from start: 0.1111 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= 0.120 Angle : 0.567 6.283 20000 Z= 0.303 Chirality : 0.045 0.219 1976 Planarity : 0.003 0.028 2592 Dihedral : 7.076 55.132 2316 Min Nonbonded Distance : 2.290 Molprobity Statistics. All-atom Clashscore : 3.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 14.52 % Favored : 85.48 % Rotamer: Outliers : 6.11 % Allowed : 23.89 % Favored : 70.00 % 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: -4.25 (0.16), residues: 1736 helix: -1.07 (0.28), residues: 296 sheet: -1.13 (0.28), residues: 320 loop : -4.16 (0.12), residues: 1120 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP H 235 HIS 0.002 0.001 HIS B 118 PHE 0.019 0.001 PHE G 82 TYR 0.008 0.001 TYR E 110 ARG 0.002 0.000 ARG D 94 Details of bonding type rmsd link_NAG-ASN : bond 0.00478 ( 16) link_NAG-ASN : angle 1.93579 ( 48) hydrogen bonds : bond 0.03727 ( 320) hydrogen bonds : angle 5.79140 ( 888) SS BOND : bond 0.00124 ( 16) SS BOND : angle 0.49442 ( 32) covalent geometry : bond 0.00263 (14720) covalent geometry : angle 0.56029 (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 308 residues out of total 1440 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 88 poor density : 220 time to evaluate : 1.852 Fit side-chains REVERT: A 50 GLN cc_start: 0.6298 (OUTLIER) cc_final: 0.5997 (mt0) REVERT: A 72 MET cc_start: 0.6722 (OUTLIER) cc_final: 0.6183 (mmt) REVERT: A 83 GLN cc_start: 0.9123 (OUTLIER) cc_final: 0.8349 (tp40) REVERT: A 197 GLN cc_start: 0.7983 (OUTLIER) cc_final: 0.7490 (mp10) REVERT: D 72 MET cc_start: 0.7460 (OUTLIER) cc_final: 0.7030 (mmt) REVERT: B 50 GLN cc_start: 0.6303 (OUTLIER) cc_final: 0.5999 (mt0) REVERT: B 72 MET cc_start: 0.6730 (OUTLIER) cc_final: 0.6190 (mmt) REVERT: B 83 GLN cc_start: 0.9136 (OUTLIER) cc_final: 0.8349 (tp40) REVERT: B 197 GLN cc_start: 0.7983 (OUTLIER) cc_final: 0.7493 (mp10) REVERT: E 72 MET cc_start: 0.7464 (OUTLIER) cc_final: 0.7046 (mmt) REVERT: C 50 GLN cc_start: 0.6301 (OUTLIER) cc_final: 0.6007 (mt0) REVERT: C 72 MET cc_start: 0.6727 (OUTLIER) cc_final: 0.6199 (mmt) REVERT: C 83 GLN cc_start: 0.9124 (OUTLIER) cc_final: 0.8348 (tp40) REVERT: C 197 GLN cc_start: 0.7978 (OUTLIER) cc_final: 0.7494 (mp10) REVERT: F 72 MET cc_start: 0.7474 (OUTLIER) cc_final: 0.7054 (mmt) REVERT: G 50 GLN cc_start: 0.6302 (OUTLIER) cc_final: 0.6002 (mt0) REVERT: G 72 MET cc_start: 0.6716 (OUTLIER) cc_final: 0.6184 (mmt) REVERT: G 83 GLN cc_start: 0.9129 (OUTLIER) cc_final: 0.8348 (tp40) REVERT: G 197 GLN cc_start: 0.7984 (OUTLIER) cc_final: 0.7497 (mp10) REVERT: H 72 MET cc_start: 0.7477 (OUTLIER) cc_final: 0.7056 (mmt) outliers start: 88 outliers final: 40 residues processed: 288 average time/residue: 0.3954 time to fit residues: 159.1134 Evaluate side-chains 260 residues out of total 1440 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 200 time to evaluate : 1.801 ------------------------------------------------------------------------------- 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 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 72 MET Chi-restraints excluded: chain D residue 177 LEU Chi-restraints excluded: chain D residue 199 CYS Chi-restraints excluded: chain D residue 244 SER 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 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 72 MET Chi-restraints excluded: chain E residue 177 LEU Chi-restraints excluded: chain E residue 199 CYS 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 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 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 244 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 38 optimal weight: 0.4980 chunk 107 optimal weight: 0.9980 chunk 120 optimal weight: 6.9990 chunk 46 optimal weight: 0.0050 chunk 61 optimal weight: 6.9990 chunk 126 optimal weight: 10.0000 chunk 24 optimal weight: 0.6980 chunk 147 optimal weight: 10.0000 chunk 84 optimal weight: 10.0000 chunk 125 optimal weight: 8.9990 chunk 11 optimal weight: 0.7980 overall best weight: 0.5994 ------------------------------------------------------------------------------- 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 = 0.3839 r_free = 0.3839 target = 0.164434 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3597 r_free = 0.3597 target = 0.144161 restraints weight = 17686.159| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3619 r_free = 0.3619 target = 0.146117 restraints weight = 13940.476| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3634 r_free = 0.3634 target = 0.147362 restraints weight = 11748.269| |-----------------------------------------------------------------------------| r_work (final): 0.3639 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8020 moved from start: 0.1463 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 14752 Z= 0.089 Angle : 0.520 5.599 20000 Z= 0.275 Chirality : 0.043 0.217 1976 Planarity : 0.002 0.023 2592 Dihedral : 6.286 57.359 2312 Min Nonbonded Distance : 2.348 Molprobity Statistics. All-atom Clashscore : 3.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 13.82 % Favored : 86.18 % Rotamer: Outliers : 5.28 % Allowed : 25.28 % Favored : 69.44 % 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: -4.06 (0.16), residues: 1736 helix: -0.64 (0.30), residues: 296 sheet: -1.06 (0.28), residues: 320 loop : -4.11 (0.12), residues: 1120 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP H 79 HIS 0.002 0.001 HIS G 118 PHE 0.016 0.001 PHE B 82 TYR 0.005 0.000 TYR F 99 ARG 0.001 0.000 ARG B 94 Details of bonding type rmsd link_NAG-ASN : bond 0.00496 ( 16) link_NAG-ASN : angle 1.94525 ( 48) hydrogen bonds : bond 0.02905 ( 320) hydrogen bonds : angle 5.44511 ( 888) SS BOND : bond 0.00093 ( 16) SS BOND : angle 0.46990 ( 32) covalent geometry : bond 0.00184 (14720) covalent geometry : angle 0.51170 (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 293 residues out of total 1440 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 217 time to evaluate : 1.553 Fit side-chains REVERT: A 72 MET cc_start: 0.6717 (OUTLIER) cc_final: 0.6319 (mmt) REVERT: A 78 LYS cc_start: 0.7663 (mptt) cc_final: 0.6704 (mmtt) REVERT: A 194 LEU cc_start: 0.7778 (OUTLIER) cc_final: 0.7407 (pt) REVERT: A 197 GLN cc_start: 0.7937 (OUTLIER) cc_final: 0.7543 (mp10) REVERT: D 72 MET cc_start: 0.7429 (OUTLIER) cc_final: 0.6975 (mmt) REVERT: D 129 ARG cc_start: 0.7795 (OUTLIER) cc_final: 0.7529 (ttt180) REVERT: B 72 MET cc_start: 0.6722 (OUTLIER) cc_final: 0.6321 (mmt) REVERT: B 78 LYS cc_start: 0.7672 (mptt) cc_final: 0.6710 (mmtt) REVERT: B 194 LEU cc_start: 0.7798 (OUTLIER) cc_final: 0.7420 (pt) REVERT: B 197 GLN cc_start: 0.7934 (OUTLIER) cc_final: 0.7541 (mp10) REVERT: E 72 MET cc_start: 0.7441 (OUTLIER) cc_final: 0.6991 (mmt) REVERT: E 129 ARG cc_start: 0.7786 (OUTLIER) cc_final: 0.7527 (ttt180) REVERT: C 72 MET cc_start: 0.6708 (OUTLIER) cc_final: 0.6275 (mmt) REVERT: C 78 LYS cc_start: 0.7663 (mptt) cc_final: 0.6710 (mmtt) REVERT: C 194 LEU cc_start: 0.7804 (OUTLIER) cc_final: 0.7413 (pt) REVERT: C 197 GLN cc_start: 0.7940 (OUTLIER) cc_final: 0.7545 (mp10) REVERT: F 72 MET cc_start: 0.7446 (OUTLIER) cc_final: 0.6993 (mmt) REVERT: F 129 ARG cc_start: 0.7796 (OUTLIER) cc_final: 0.7533 (ttt180) REVERT: G 72 MET cc_start: 0.6703 (OUTLIER) cc_final: 0.6265 (mmt) REVERT: G 78 LYS cc_start: 0.7656 (mptt) cc_final: 0.6704 (mmtt) REVERT: G 194 LEU cc_start: 0.7787 (OUTLIER) cc_final: 0.7414 (pt) REVERT: G 197 GLN cc_start: 0.7941 (OUTLIER) cc_final: 0.7547 (mp10) REVERT: H 72 MET cc_start: 0.7449 (OUTLIER) cc_final: 0.6995 (mmt) REVERT: H 129 ARG cc_start: 0.7796 (OUTLIER) cc_final: 0.7532 (ttt180) outliers start: 76 outliers final: 47 residues processed: 277 average time/residue: 0.3572 time to fit residues: 134.7371 Evaluate side-chains 267 residues out of total 1440 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 200 time to evaluate : 1.701 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 72 MET 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 248 THR Chi-restraints excluded: chain D residue 72 MET Chi-restraints excluded: chain D residue 89 SER Chi-restraints excluded: chain D residue 129 ARG Chi-restraints excluded: chain D residue 159 ASP 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 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 E residue 72 MET Chi-restraints excluded: chain E residue 89 SER Chi-restraints excluded: chain E residue 129 ARG Chi-restraints excluded: chain E residue 159 ASP 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 72 MET 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 248 THR Chi-restraints excluded: chain F residue 72 MET Chi-restraints excluded: chain F residue 89 SER Chi-restraints excluded: chain F residue 129 ARG Chi-restraints excluded: chain F residue 159 ASP 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 72 MET 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 89 SER Chi-restraints excluded: chain H residue 129 ARG Chi-restraints excluded: chain H residue 159 ASP 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 97 optimal weight: 9.9990 chunk 127 optimal weight: 0.2980 chunk 7 optimal weight: 4.9990 chunk 31 optimal weight: 7.9990 chunk 39 optimal weight: 10.0000 chunk 81 optimal weight: 9.9990 chunk 25 optimal weight: 7.9990 chunk 5 optimal weight: 2.9990 chunk 118 optimal weight: 9.9990 chunk 92 optimal weight: 6.9990 chunk 80 optimal weight: 5.9990 overall best weight: 4.2588 ------------------------------------------------------------------------------- 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 = 0.3738 r_free = 0.3738 target = 0.155143 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3488 r_free = 0.3488 target = 0.135000 restraints weight = 18258.512| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3506 r_free = 0.3506 target = 0.136498 restraints weight = 15129.414| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3518 r_free = 0.3518 target = 0.137556 restraints weight = 13143.822| |-----------------------------------------------------------------------------| r_work (final): 0.3523 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8158 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 : 0.007 0.035 14752 Z= 0.287 Angle : 0.718 5.319 20000 Z= 0.386 Chirality : 0.052 0.215 1976 Planarity : 0.006 0.066 2592 Dihedral : 7.284 56.920 2299 Min Nonbonded Distance : 2.274 Molprobity Statistics. All-atom Clashscore : 4.81 Ramachandran Plot: Outliers : 0.23 % Allowed : 16.36 % Favored : 83.41 % Rotamer: Outliers : 6.11 % Allowed : 24.72 % Favored : 69.17 % 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: -4.34 (0.16), residues: 1736 helix: -1.04 (0.29), residues: 296 sheet: -1.24 (0.28), residues: 320 loop : -4.24 (0.12), residues: 1120 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP F 235 HIS 0.006 0.002 HIS F 180 PHE 0.028 0.002 PHE F 82 TYR 0.022 0.002 TYR F 110 ARG 0.006 0.001 ARG H 94 Details of bonding type rmsd link_NAG-ASN : bond 0.00588 ( 16) link_NAG-ASN : angle 2.22197 ( 48) hydrogen bonds : bond 0.05162 ( 320) hydrogen bonds : angle 5.97580 ( 888) SS BOND : bond 0.00338 ( 16) SS BOND : angle 0.62975 ( 32) covalent geometry : bond 0.00684 (14720) covalent geometry : angle 0.71092 (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 290 residues out of total 1440 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 88 poor density : 202 time to evaluate : 4.184 Fit side-chains REVERT: A 83 GLN cc_start: 0.9200 (OUTLIER) cc_final: 0.8394 (tp40) REVERT: A 159 ASP cc_start: 0.6598 (OUTLIER) cc_final: 0.5779 (m-30) REVERT: A 197 GLN cc_start: 0.8010 (OUTLIER) cc_final: 0.7484 (mp10) REVERT: D 71 ASP cc_start: 0.7469 (t0) cc_final: 0.7243 (t0) REVERT: D 72 MET cc_start: 0.7495 (mmt) cc_final: 0.7170 (mmt) REVERT: D 157 GLU cc_start: 0.8067 (OUTLIER) cc_final: 0.7855 (tt0) REVERT: D 247 ARG cc_start: 0.7912 (OUTLIER) cc_final: 0.7526 (mtm180) REVERT: B 83 GLN cc_start: 0.9203 (OUTLIER) cc_final: 0.8384 (tp40) REVERT: B 159 ASP cc_start: 0.6569 (OUTLIER) cc_final: 0.5764 (m-30) REVERT: B 197 GLN cc_start: 0.8014 (OUTLIER) cc_final: 0.7491 (mp10) REVERT: E 71 ASP cc_start: 0.7469 (t0) cc_final: 0.7242 (t0) REVERT: E 72 MET cc_start: 0.7494 (mmt) cc_final: 0.7175 (mmt) REVERT: E 157 GLU cc_start: 0.8088 (OUTLIER) cc_final: 0.7878 (tt0) REVERT: E 247 ARG cc_start: 0.7923 (OUTLIER) cc_final: 0.7532 (mtm180) REVERT: C 83 GLN cc_start: 0.9200 (OUTLIER) cc_final: 0.8395 (tp40) REVERT: C 159 ASP cc_start: 0.6594 (OUTLIER) cc_final: 0.5766 (m-30) REVERT: C 197 GLN cc_start: 0.8008 (OUTLIER) cc_final: 0.7487 (mp10) REVERT: F 71 ASP cc_start: 0.7468 (t0) cc_final: 0.7235 (t0) REVERT: F 72 MET cc_start: 0.7498 (mmt) cc_final: 0.7176 (mmt) REVERT: F 157 GLU cc_start: 0.8083 (OUTLIER) cc_final: 0.7872 (tt0) REVERT: F 247 ARG cc_start: 0.7909 (OUTLIER) cc_final: 0.7523 (mtm180) REVERT: G 83 GLN cc_start: 0.9200 (OUTLIER) cc_final: 0.8390 (tp40) REVERT: G 159 ASP cc_start: 0.6580 (OUTLIER) cc_final: 0.5771 (m-30) REVERT: G 197 GLN cc_start: 0.8016 (OUTLIER) cc_final: 0.7491 (mp10) REVERT: H 71 ASP cc_start: 0.7474 (t0) cc_final: 0.7242 (t0) REVERT: H 72 MET cc_start: 0.7506 (mmt) cc_final: 0.7177 (mmt) REVERT: H 157 GLU cc_start: 0.8068 (OUTLIER) cc_final: 0.7855 (tt0) REVERT: H 247 ARG cc_start: 0.7913 (OUTLIER) cc_final: 0.7527 (mtm180) outliers start: 88 outliers final: 56 residues processed: 274 average time/residue: 0.3626 time to fit residues: 143.9296 Evaluate side-chains 275 residues out of total 1440 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 199 time to evaluate : 1.658 ------------------------------------------------------------------------------- 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 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 157 GLU 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 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 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 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 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 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 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: 0.0030 chunk 117 optimal weight: 3.9990 chunk 57 optimal weight: 8.9990 chunk 44 optimal weight: 0.0050 chunk 93 optimal weight: 1.9990 chunk 12 optimal weight: 4.9990 chunk 100 optimal weight: 6.9990 chunk 78 optimal weight: 0.5980 chunk 75 optimal weight: 3.9990 chunk 166 optimal weight: 8.9990 chunk 73 optimal weight: 4.9990 overall best weight: 1.3208 ------------------------------------------------------------------------------- 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 = 0.3793 r_free = 0.3793 target = 0.160056 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3547 r_free = 0.3547 target = 0.139858 restraints weight = 18128.735| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3567 r_free = 0.3567 target = 0.141556 restraints weight = 14661.932| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3578 r_free = 0.3578 target = 0.142516 restraints weight = 12562.179| |-----------------------------------------------------------------------------| r_work (final): 0.3584 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8089 moved from start: 0.1418 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= 0.116 Angle : 0.568 6.611 20000 Z= 0.302 Chirality : 0.045 0.227 1976 Planarity : 0.003 0.029 2592 Dihedral : 6.511 51.900 2299 Min Nonbonded Distance : 2.290 Molprobity Statistics. All-atom Clashscore : 3.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 14.06 % Favored : 85.94 % Rotamer: Outliers : 4.93 % Allowed : 26.46 % Favored : 68.61 % 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: -4.20 (0.16), residues: 1736 helix: -1.02 (0.29), residues: 312 sheet: -1.18 (0.28), residues: 320 loop : -4.14 (0.12), residues: 1104 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP E 235 HIS 0.002 0.001 HIS B 118 PHE 0.018 0.001 PHE G 82 TYR 0.009 0.001 TYR A 99 ARG 0.002 0.000 ARG E 94 Details of bonding type rmsd link_NAG-ASN : bond 0.00526 ( 16) link_NAG-ASN : angle 2.05661 ( 48) hydrogen bonds : bond 0.03510 ( 320) hydrogen bonds : angle 5.54591 ( 888) SS BOND : bond 0.00243 ( 16) SS BOND : angle 0.65877 ( 32) covalent geometry : bond 0.00252 (14720) covalent geometry : angle 0.55983 (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 271 residues out of total 1440 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 200 time to evaluate : 2.155 Fit side-chains REVERT: A 159 ASP cc_start: 0.6737 (OUTLIER) cc_final: 0.5993 (m-30) REVERT: A 194 LEU cc_start: 0.7793 (OUTLIER) cc_final: 0.7442 (pt) REVERT: A 197 GLN cc_start: 0.7972 (OUTLIER) cc_final: 0.7496 (mp10) REVERT: D 71 ASP cc_start: 0.7326 (t0) cc_final: 0.7118 (t0) REVERT: D 72 MET cc_start: 0.7426 (mmt) cc_final: 0.7125 (mmt) REVERT: B 83 GLN cc_start: 0.9116 (OUTLIER) cc_final: 0.8312 (tp40) REVERT: B 159 ASP cc_start: 0.6708 (OUTLIER) cc_final: 0.5972 (m-30) REVERT: B 194 LEU cc_start: 0.7807 (OUTLIER) cc_final: 0.7438 (pt) REVERT: B 197 GLN cc_start: 0.7981 (OUTLIER) cc_final: 0.7504 (mp10) REVERT: E 71 ASP cc_start: 0.7323 (t0) cc_final: 0.7114 (t0) REVERT: E 72 MET cc_start: 0.7424 (mmt) cc_final: 0.7123 (mmt) REVERT: C 83 GLN cc_start: 0.9111 (OUTLIER) cc_final: 0.8327 (tp40) REVERT: C 159 ASP cc_start: 0.6737 (OUTLIER) cc_final: 0.5984 (m-30) REVERT: C 194 LEU cc_start: 0.7804 (OUTLIER) cc_final: 0.7435 (pt) REVERT: C 197 GLN cc_start: 0.7977 (OUTLIER) cc_final: 0.7500 (mp10) REVERT: F 71 ASP cc_start: 0.7343 (t0) cc_final: 0.7125 (t0) REVERT: F 72 MET cc_start: 0.7425 (mmt) cc_final: 0.7127 (mmt) REVERT: G 83 GLN cc_start: 0.9119 (OUTLIER) cc_final: 0.8321 (tp40) REVERT: G 159 ASP cc_start: 0.6720 (OUTLIER) cc_final: 0.5981 (m-30) REVERT: G 194 LEU cc_start: 0.7802 (OUTLIER) cc_final: 0.7443 (pt) REVERT: G 197 GLN cc_start: 0.7980 (OUTLIER) cc_final: 0.7507 (mp10) REVERT: H 71 ASP cc_start: 0.7335 (t0) cc_final: 0.7123 (t0) REVERT: H 72 MET cc_start: 0.7442 (mmt) cc_final: 0.7136 (mmt) outliers start: 71 outliers final: 47 residues processed: 263 average time/residue: 0.4359 time to fit residues: 161.3227 Evaluate side-chains 254 residues out of total 1440 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 192 time to evaluate : 2.387 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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 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 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 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 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 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 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 35 optimal weight: 7.9990 chunk 96 optimal weight: 6.9990 chunk 101 optimal weight: 0.2980 chunk 11 optimal weight: 0.3980 chunk 30 optimal weight: 9.9990 chunk 38 optimal weight: 0.8980 chunk 117 optimal weight: 5.9990 chunk 68 optimal weight: 0.0980 chunk 125 optimal weight: 7.9990 chunk 75 optimal weight: 5.9990 chunk 56 optimal weight: 0.4980 overall best weight: 0.4380 ------------------------------------------------------------------------------- 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 = 0.3849 r_free = 0.3849 target = 0.165177 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3601 r_free = 0.3601 target = 0.144561 restraints weight = 17985.616| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3623 r_free = 0.3623 target = 0.146485 restraints weight = 14210.651| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3641 r_free = 0.3641 target = 0.147956 restraints weight = 11999.138| |-----------------------------------------------------------------------------| r_work (final): 0.3647 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8012 moved from start: 0.1734 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.020 14752 Z= 0.084 Angle : 0.509 7.001 20000 Z= 0.266 Chirality : 0.042 0.217 1976 Planarity : 0.002 0.020 2592 Dihedral : 5.778 47.855 2299 Min Nonbonded Distance : 2.363 Molprobity Statistics. All-atom Clashscore : 3.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 14.06 % Favored : 85.94 % Rotamer: Outliers : 4.72 % Allowed : 27.22 % Favored : 68.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.05 (0.16), residues: 1736 helix: -0.42 (0.31), residues: 296 sheet: -1.15 (0.28), residues: 320 loop : -4.13 (0.12), residues: 1120 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP E 235 HIS 0.002 0.001 HIS A 118 PHE 0.015 0.001 PHE A 82 TYR 0.005 0.000 TYR G 99 ARG 0.002 0.000 ARG C 94 Details of bonding type rmsd link_NAG-ASN : bond 0.00480 ( 16) link_NAG-ASN : angle 1.95793 ( 48) hydrogen bonds : bond 0.02655 ( 320) hydrogen bonds : angle 5.22046 ( 888) SS BOND : bond 0.00091 ( 16) SS BOND : angle 0.48409 ( 32) covalent geometry : bond 0.00168 (14720) covalent geometry : angle 0.50026 (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 296 residues out of total 1440 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 228 time to evaluate : 1.984 Fit side-chains REVERT: A 72 MET cc_start: 0.6637 (OUTLIER) cc_final: 0.6226 (mmt) REVERT: A 78 LYS cc_start: 0.7651 (mptt) cc_final: 0.6765 (mmtt) REVERT: A 159 ASP cc_start: 0.6804 (OUTLIER) cc_final: 0.6114 (m-30) REVERT: A 197 GLN cc_start: 0.7912 (OUTLIER) cc_final: 0.7503 (mp10) REVERT: D 72 MET cc_start: 0.7365 (mmt) cc_final: 0.7059 (mmt) REVERT: B 78 LYS cc_start: 0.7650 (mptt) cc_final: 0.7171 (mmtt) REVERT: B 159 ASP cc_start: 0.6784 (OUTLIER) cc_final: 0.6099 (m-30) REVERT: B 194 LEU cc_start: 0.7727 (OUTLIER) cc_final: 0.7520 (pt) REVERT: B 197 GLN cc_start: 0.7916 (OUTLIER) cc_final: 0.7505 (mp10) REVERT: E 72 MET cc_start: 0.7365 (mmt) cc_final: 0.7063 (mmt) REVERT: C 78 LYS cc_start: 0.7637 (mptt) cc_final: 0.7160 (mmtt) REVERT: C 159 ASP cc_start: 0.6809 (OUTLIER) cc_final: 0.6115 (m-30) REVERT: C 194 LEU cc_start: 0.7722 (OUTLIER) cc_final: 0.7516 (pt) REVERT: C 197 GLN cc_start: 0.7916 (OUTLIER) cc_final: 0.7507 (mp10) REVERT: F 72 MET cc_start: 0.7388 (mmt) cc_final: 0.7043 (mmt) REVERT: G 78 LYS cc_start: 0.7628 (mptt) cc_final: 0.7153 (mmtt) REVERT: G 159 ASP cc_start: 0.6793 (OUTLIER) cc_final: 0.6113 (m-30) REVERT: G 194 LEU cc_start: 0.7721 (OUTLIER) cc_final: 0.7516 (pt) REVERT: G 197 GLN cc_start: 0.7918 (OUTLIER) cc_final: 0.7508 (mp10) REVERT: H 72 MET cc_start: 0.7378 (mmt) cc_final: 0.7069 (mmt) outliers start: 68 outliers final: 39 residues processed: 283 average time/residue: 0.3217 time to fit residues: 127.0576 Evaluate side-chains 267 residues out of total 1440 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 216 time to evaluate : 2.379 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 72 MET 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 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 89 SER Chi-restraints excluded: chain D residue 165 VAL Chi-restraints excluded: chain D residue 244 SER 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 E residue 89 SER Chi-restraints excluded: chain E residue 165 VAL Chi-restraints excluded: chain E residue 244 SER 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 89 SER Chi-restraints excluded: chain F residue 165 VAL Chi-restraints excluded: chain F residue 244 SER 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 165 VAL Chi-restraints excluded: chain H residue 244 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 122 optimal weight: 8.9990 chunk 63 optimal weight: 10.0000 chunk 126 optimal weight: 10.0000 chunk 111 optimal weight: 6.9990 chunk 158 optimal weight: 3.9990 chunk 68 optimal weight: 1.9990 chunk 131 optimal weight: 1.9990 chunk 85 optimal weight: 6.9990 chunk 55 optimal weight: 9.9990 chunk 113 optimal weight: 6.9990 chunk 49 optimal weight: 4.9990 overall best weight: 3.9990 ------------------------------------------------------------------------------- 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 = 0.3742 r_free = 0.3742 target = 0.155554 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3483 r_free = 0.3483 target = 0.134673 restraints weight = 18145.156| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.3505 r_free = 0.3505 target = 0.136467 restraints weight = 14580.371| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3518 r_free = 0.3518 target = 0.137604 restraints weight = 12506.252| |-----------------------------------------------------------------------------| r_work (final): 0.3524 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8153 moved from start: 0.1605 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.033 14752 Z= 0.271 Angle : 0.713 7.018 20000 Z= 0.382 Chirality : 0.051 0.209 1976 Planarity : 0.006 0.064 2592 Dihedral : 7.213 53.726 2299 Min Nonbonded Distance : 2.278 Molprobity Statistics. All-atom Clashscore : 4.78 Ramachandran Plot: Outliers : 0.23 % Allowed : 16.13 % Favored : 83.64 % Rotamer: Outliers : 6.04 % Allowed : 25.90 % Favored : 68.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.36 (0.16), residues: 1736 helix: -1.14 (0.28), residues: 312 sheet: -1.73 (0.28), residues: 344 loop : -4.12 (0.12), residues: 1080 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP E 235 HIS 0.005 0.002 HIS H 180 PHE 0.027 0.002 PHE F 82 TYR 0.022 0.002 TYR E 110 ARG 0.005 0.001 ARG H 94 Details of bonding type rmsd link_NAG-ASN : bond 0.00561 ( 16) link_NAG-ASN : angle 2.17026 ( 48) hydrogen bonds : bond 0.04961 ( 320) hydrogen bonds : angle 5.83458 ( 888) SS BOND : bond 0.00318 ( 16) SS BOND : angle 0.68937 ( 32) covalent geometry : bond 0.00644 (14720) covalent geometry : angle 0.70594 (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 285 residues out of total 1440 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 87 poor density : 198 time to evaluate : 1.542 Fit side-chains REVERT: A 50 GLN cc_start: 0.6467 (OUTLIER) cc_final: 0.5997 (mt0) REVERT: A 83 GLN cc_start: 0.9199 (OUTLIER) cc_final: 0.8358 (tp40) REVERT: A 159 ASP cc_start: 0.6621 (OUTLIER) cc_final: 0.5802 (m-30) REVERT: A 197 GLN cc_start: 0.7975 (OUTLIER) cc_final: 0.7486 (mp10) REVERT: D 72 MET cc_start: 0.7454 (mmt) cc_final: 0.7031 (mmt) REVERT: D 247 ARG cc_start: 0.7904 (OUTLIER) cc_final: 0.7511 (mtm180) REVERT: B 50 GLN cc_start: 0.6467 (OUTLIER) cc_final: 0.5998 (mt0) REVERT: B 83 GLN cc_start: 0.9190 (OUTLIER) cc_final: 0.8339 (tp40) REVERT: B 159 ASP cc_start: 0.6603 (OUTLIER) cc_final: 0.5799 (m-30) REVERT: B 197 GLN cc_start: 0.7973 (OUTLIER) cc_final: 0.7482 (mp10) REVERT: E 72 MET cc_start: 0.7459 (mmt) cc_final: 0.7037 (mmt) REVERT: E 247 ARG cc_start: 0.7915 (OUTLIER) cc_final: 0.7517 (mtm180) REVERT: C 50 GLN cc_start: 0.6458 (OUTLIER) cc_final: 0.5991 (mt0) REVERT: C 83 GLN cc_start: 0.9200 (OUTLIER) cc_final: 0.8359 (tp40) REVERT: C 159 ASP cc_start: 0.6623 (OUTLIER) cc_final: 0.5796 (m-30) REVERT: C 197 GLN cc_start: 0.7966 (OUTLIER) cc_final: 0.7476 (mp10) REVERT: F 72 MET cc_start: 0.7478 (mmt) cc_final: 0.7077 (mmt) REVERT: F 247 ARG cc_start: 0.7899 (OUTLIER) cc_final: 0.7506 (mtm180) REVERT: G 50 GLN cc_start: 0.6458 (OUTLIER) cc_final: 0.5993 (mt0) REVERT: G 83 GLN cc_start: 0.9202 (OUTLIER) cc_final: 0.8353 (tp40) REVERT: G 159 ASP cc_start: 0.6608 (OUTLIER) cc_final: 0.5800 (m-30) REVERT: G 197 GLN cc_start: 0.7974 (OUTLIER) cc_final: 0.7481 (mp10) REVERT: H 72 MET cc_start: 0.7465 (mmt) cc_final: 0.7035 (mmt) REVERT: H 247 ARG cc_start: 0.7903 (OUTLIER) cc_final: 0.7511 (mtm180) outliers start: 87 outliers final: 59 residues processed: 273 average time/residue: 0.3208 time to fit residues: 122.0098 Evaluate side-chains 273 residues out of total 1440 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 79 poor density : 194 time to evaluate : 2.197 ------------------------------------------------------------------------------- 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 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 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 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 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 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 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 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 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 21 optimal weight: 10.0000 chunk 61 optimal weight: 5.9990 chunk 55 optimal weight: 9.9990 chunk 145 optimal weight: 8.9990 chunk 106 optimal weight: 10.0000 chunk 17 optimal weight: 0.8980 chunk 4 optimal weight: 3.9990 chunk 46 optimal weight: 0.7980 chunk 51 optimal weight: 4.9990 chunk 42 optimal weight: 10.0000 chunk 95 optimal weight: 0.7980 overall best weight: 2.2984 ------------------------------------------------------------------------------- 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 = 0.3767 r_free = 0.3767 target = 0.157968 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3524 r_free = 0.3524 target = 0.138110 restraints weight = 17913.116| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3542 r_free = 0.3542 target = 0.139673 restraints weight = 14612.152| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3554 r_free = 0.3554 target = 0.140708 restraints weight = 12663.173| |-----------------------------------------------------------------------------| r_work (final): 0.3558 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8118 moved from start: 0.1553 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.022 14752 Z= 0.167 Angle : 0.627 8.761 20000 Z= 0.333 Chirality : 0.047 0.223 1976 Planarity : 0.004 0.048 2592 Dihedral : 6.678 51.002 2299 Min Nonbonded Distance : 2.292 Molprobity Statistics. All-atom Clashscore : 4.63 Ramachandran Plot: Outliers : 0.23 % Allowed : 15.21 % Favored : 84.56 % Rotamer: Outliers : 5.00 % Allowed : 26.94 % Favored : 68.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.33 (0.16), residues: 1736 helix: -1.06 (0.29), residues: 312 sheet: -1.78 (0.28), residues: 344 loop : -4.09 (0.12), residues: 1080 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP D 235 HIS 0.003 0.001 HIS E 180 PHE 0.021 0.002 PHE B 82 TYR 0.013 0.001 TYR D 110 ARG 0.003 0.000 ARG H 94 Details of bonding type rmsd link_NAG-ASN : bond 0.00546 ( 16) link_NAG-ASN : angle 2.08057 ( 48) hydrogen bonds : bond 0.03969 ( 320) hydrogen bonds : angle 5.60694 ( 888) SS BOND : bond 0.00227 ( 16) SS BOND : angle 0.66688 ( 32) covalent geometry : bond 0.00388 (14720) covalent geometry : angle 0.61883 (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 267 residues out of total 1440 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 195 time to evaluate : 1.490 Fit side-chains REVERT: A 50 GLN cc_start: 0.6453 (OUTLIER) cc_final: 0.5970 (mt0) REVERT: A 83 GLN cc_start: 0.9172 (OUTLIER) cc_final: 0.8368 (tp40) REVERT: A 159 ASP cc_start: 0.6596 (OUTLIER) cc_final: 0.5794 (m-30) REVERT: A 197 GLN cc_start: 0.7951 (OUTLIER) cc_final: 0.7475 (mp10) REVERT: D 72 MET cc_start: 0.7493 (mmt) cc_final: 0.7131 (mmt) REVERT: D 247 ARG cc_start: 0.7806 (OUTLIER) cc_final: 0.7421 (mtm180) REVERT: B 50 GLN cc_start: 0.6454 (OUTLIER) cc_final: 0.5970 (mt0) REVERT: B 159 ASP cc_start: 0.6577 (OUTLIER) cc_final: 0.5795 (m-30) REVERT: B 197 GLN cc_start: 0.7917 (OUTLIER) cc_final: 0.7394 (mp10) REVERT: E 72 MET cc_start: 0.7492 (mmt) cc_final: 0.7132 (mmt) REVERT: E 247 ARG cc_start: 0.7813 (OUTLIER) cc_final: 0.7420 (mtm180) REVERT: C 50 GLN cc_start: 0.6459 (OUTLIER) cc_final: 0.5880 (mt0) REVERT: C 72 MET cc_start: 0.6573 (OUTLIER) cc_final: 0.6019 (mmt) REVERT: C 159 ASP cc_start: 0.6605 (OUTLIER) cc_final: 0.5793 (m-30) REVERT: C 197 GLN cc_start: 0.7910 (OUTLIER) cc_final: 0.7388 (mp10) REVERT: F 72 MET cc_start: 0.7510 (mmt) cc_final: 0.7156 (mmt) REVERT: F 247 ARG cc_start: 0.7797 (OUTLIER) cc_final: 0.7413 (mtm180) REVERT: G 50 GLN cc_start: 0.6462 (OUTLIER) cc_final: 0.5879 (mt0) REVERT: G 72 MET cc_start: 0.6562 (OUTLIER) cc_final: 0.6003 (mmt) REVERT: G 159 ASP cc_start: 0.6589 (OUTLIER) cc_final: 0.5798 (m-30) REVERT: G 197 GLN cc_start: 0.7919 (OUTLIER) cc_final: 0.7396 (mp10) REVERT: H 72 MET cc_start: 0.7503 (mmt) cc_final: 0.7129 (mmt) REVERT: H 247 ARG cc_start: 0.7804 (OUTLIER) cc_final: 0.7419 (mtm180) outliers start: 72 outliers final: 53 residues processed: 257 average time/residue: 0.3386 time to fit residues: 121.5078 Evaluate side-chains 267 residues out of total 1440 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 195 time to evaluate : 1.602 ------------------------------------------------------------------------------- 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 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 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 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 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 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 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 247 ARG Chi-restraints excluded: chain G residue 50 GLN Chi-restraints excluded: chain G residue 72 MET 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 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: 1.9990 chunk 32 optimal weight: 2.9990 chunk 44 optimal weight: 0.5980 chunk 111 optimal weight: 5.9990 chunk 165 optimal weight: 7.9990 chunk 92 optimal weight: 7.9990 chunk 7 optimal weight: 2.9990 chunk 148 optimal weight: 8.9990 chunk 69 optimal weight: 3.9990 chunk 47 optimal weight: 0.9990 chunk 104 optimal weight: 7.9990 overall best weight: 1.9188 ------------------------------------------------------------------------------- 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 = 0.3775 r_free = 0.3775 target = 0.158701 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3533 r_free = 0.3533 target = 0.138928 restraints weight = 17910.889| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3550 r_free = 0.3550 target = 0.140461 restraints weight = 14536.395| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3567 r_free = 0.3567 target = 0.141755 restraints weight = 12603.471| |-----------------------------------------------------------------------------| r_work (final): 0.3574 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8101 moved from start: 0.1579 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= 0.147 Angle : 0.601 8.521 20000 Z= 0.318 Chirality : 0.046 0.224 1976 Planarity : 0.004 0.040 2592 Dihedral : 6.443 51.533 2299 Min Nonbonded Distance : 2.293 Molprobity Statistics. All-atom Clashscore : 4.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 15.73 % Favored : 84.27 % Rotamer: Outliers : 5.56 % Allowed : 26.88 % 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: -4.29 (0.16), residues: 1736 helix: -1.00 (0.29), residues: 312 sheet: -1.75 (0.28), residues: 344 loop : -4.08 (0.12), residues: 1080 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP D 235 HIS 0.003 0.001 HIS F 180 PHE 0.021 0.001 PHE A 82 TYR 0.012 0.001 TYR F 110 ARG 0.003 0.000 ARG E 94 Details of bonding type rmsd link_NAG-ASN : bond 0.00530 ( 16) link_NAG-ASN : angle 2.05435 ( 48) hydrogen bonds : bond 0.03720 ( 320) hydrogen bonds : angle 5.51945 ( 888) SS BOND : bond 0.00190 ( 16) SS BOND : angle 0.59592 ( 32) covalent geometry : bond 0.00338 (14720) covalent geometry : angle 0.59285 (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 276 residues out of total 1440 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 80 poor density : 196 time to evaluate : 1.562 Fit side-chains REVERT: A 50 GLN cc_start: 0.6403 (OUTLIER) cc_final: 0.5921 (mt0) REVERT: A 83 GLN cc_start: 0.9153 (OUTLIER) cc_final: 0.8359 (tp40) REVERT: A 159 ASP cc_start: 0.6580 (OUTLIER) cc_final: 0.5808 (m-30) REVERT: A 197 GLN cc_start: 0.7921 (OUTLIER) cc_final: 0.7426 (mp10) REVERT: D 72 MET cc_start: 0.7482 (mmt) cc_final: 0.7157 (mmt) REVERT: D 247 ARG cc_start: 0.7781 (OUTLIER) cc_final: 0.7403 (mtm180) REVERT: B 50 GLN cc_start: 0.6407 (OUTLIER) cc_final: 0.5919 (mt0) REVERT: B 159 ASP cc_start: 0.6566 (OUTLIER) cc_final: 0.5815 (m-30) REVERT: B 197 GLN cc_start: 0.7894 (OUTLIER) cc_final: 0.7405 (mp10) REVERT: E 72 MET cc_start: 0.7466 (mmt) cc_final: 0.7148 (mmt) REVERT: E 247 ARG cc_start: 0.7782 (OUTLIER) cc_final: 0.7397 (mtm180) REVERT: C 50 GLN cc_start: 0.6426 (OUTLIER) cc_final: 0.5859 (mt0) REVERT: C 72 MET cc_start: 0.6561 (OUTLIER) cc_final: 0.6051 (mmt) REVERT: C 159 ASP cc_start: 0.6594 (OUTLIER) cc_final: 0.5812 (m-30) REVERT: C 197 GLN cc_start: 0.7883 (OUTLIER) cc_final: 0.7399 (mp10) REVERT: F 72 MET cc_start: 0.7458 (mmt) cc_final: 0.7134 (mmt) REVERT: F 247 ARG cc_start: 0.7770 (OUTLIER) cc_final: 0.7391 (mtm180) REVERT: G 50 GLN cc_start: 0.6426 (OUTLIER) cc_final: 0.5852 (mt0) REVERT: G 72 MET cc_start: 0.6549 (OUTLIER) cc_final: 0.6034 (mmt) REVERT: G 159 ASP cc_start: 0.6575 (OUTLIER) cc_final: 0.5813 (m-30) REVERT: G 197 GLN cc_start: 0.7892 (OUTLIER) cc_final: 0.7405 (mp10) REVERT: H 72 MET cc_start: 0.7485 (mmt) cc_final: 0.7149 (mmt) REVERT: H 247 ARG cc_start: 0.7778 (OUTLIER) cc_final: 0.7398 (mtm180) outliers start: 80 outliers final: 53 residues processed: 262 average time/residue: 0.3123 time to fit residues: 114.2785 Evaluate side-chains 272 residues out of total 1440 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 200 time to evaluate : 1.629 ------------------------------------------------------------------------------- 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 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 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 50 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 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 227 LEU Chi-restraints excluded: chain E residue 244 SER Chi-restraints excluded: chain E residue 247 ARG Chi-restraints excluded: chain C residue 50 GLN Chi-restraints excluded: chain C residue 72 MET 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 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 72 MET 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 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 74 optimal weight: 1.9990 chunk 62 optimal weight: 8.9990 chunk 22 optimal weight: 8.9990 chunk 0 optimal weight: 10.0000 chunk 120 optimal weight: 0.8980 chunk 165 optimal weight: 6.9990 chunk 126 optimal weight: 10.0000 chunk 141 optimal weight: 5.9990 chunk 21 optimal weight: 7.9990 chunk 160 optimal weight: 9.9990 chunk 114 optimal weight: 8.9990 overall best weight: 4.7788 ------------------------------------------------------------------------------- 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** ** C 216 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3725 r_free = 0.3725 target = 0.154135 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3467 r_free = 0.3467 target = 0.133414 restraints weight = 18301.165| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3489 r_free = 0.3489 target = 0.135182 restraints weight = 14698.152| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3506 r_free = 0.3506 target = 0.136497 restraints weight = 12598.554| |-----------------------------------------------------------------------------| r_work (final): 0.3510 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8170 moved from start: 0.1731 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.040 14752 Z= 0.320 Angle : 0.779 9.933 20000 Z= 0.413 Chirality : 0.053 0.219 1976 Planarity : 0.006 0.072 2592 Dihedral : 7.639 55.922 2299 Min Nonbonded Distance : 2.255 Molprobity Statistics. All-atom Clashscore : 4.78 Ramachandran Plot: Outliers : 0.23 % Allowed : 17.28 % Favored : 82.49 % Rotamer: Outliers : 5.21 % Allowed : 27.29 % 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: -4.61 (0.16), residues: 1736 helix: -1.28 (0.28), residues: 304 sheet: -1.94 (0.28), residues: 344 loop : -4.28 (0.12), residues: 1088 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP D 235 HIS 0.006 0.002 HIS E 180 PHE 0.031 0.002 PHE D 82 TYR 0.024 0.003 TYR D 110 ARG 0.007 0.001 ARG H 94 Details of bonding type rmsd link_NAG-ASN : bond 0.00629 ( 16) link_NAG-ASN : angle 2.26580 ( 48) hydrogen bonds : bond 0.05343 ( 320) hydrogen bonds : angle 6.00182 ( 888) SS BOND : bond 0.00447 ( 16) SS BOND : angle 0.82922 ( 32) covalent geometry : bond 0.00765 (14720) covalent geometry : angle 0.77214 (19920) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4838.13 seconds wall clock time: 88 minutes 36.88 seconds (5316.88 seconds total)