Starting phenix.real_space_refine on Sat Oct 11 11:24:31 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8un7_42394/10_2025/8un7_42394.cif Found real_map, /net/cci-nas-00/data/ceres_data/8un7_42394/10_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_42394/10_2025/8un7_42394.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8un7_42394/10_2025/8un7_42394.map" model { file = "/net/cci-nas-00/data/ceres_data/8un7_42394/10_2025/8un7_42394.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8un7_42394/10_2025/8un7_42394.cif" } resolution = 3.55 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 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): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5842/lib/python3.9/site-packages/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: 3.59, per 1000 atoms: 0.25 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: 1.08 Conformation dependent library (CDL) restraints added in 698.7 milliseconds Enol-peptide restraints added in 1.2 microseconds 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: 0.57 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: 2.13 Time building geometry restraints manager: 1.43 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: 0.01 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.120 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.000 Extract box with map and model: 0.220 Check model and map are aligned: 0.040 Set scattering table: 0.040 Process input model: 13.790 Find NCS groups from input model: 0.310 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.400 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 17.960 ------------------------------------------------------------------------------- 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 : 6.42 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -4.64 (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 ARG 0.003 0.000 ARG D 190 TYR 0.011 0.001 TYR E 45 PHE 0.018 0.001 PHE A 82 TRP 0.010 0.001 TRP E 235 HIS 0.003 0.001 HIS B 118 Details of bonding type rmsd covalent geometry : bond 0.00372 (14720) covalent geometry : angle 0.74695 (19920) SS BOND : bond 0.00130 ( 16) SS BOND : angle 0.71513 ( 32) hydrogen bonds : bond 0.22994 ( 320) hydrogen bonds : angle 8.51268 ( 888) link_NAG-ASN : bond 0.00711 ( 16) link_NAG-ASN : angle 1.86385 ( 48) *********************** 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 : 0.622 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: 0.1439 time to fit residues: 52.0072 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 : 0.550 ------------------------------------------------------------------------------- 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 98 optimal weight: 7.9990 chunk 107 optimal weight: 4.9990 chunk 10 optimal weight: 10.0000 chunk 66 optimal weight: 10.0000 chunk 130 optimal weight: 7.9990 chunk 124 optimal weight: 7.9990 chunk 103 optimal weight: 10.0000 chunk 77 optimal weight: 8.9990 chunk 122 optimal weight: 0.9990 chunk 91 optimal weight: 3.9990 chunk 149 optimal weight: 0.0370 overall best weight: 3.6066 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 198 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 198 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 198 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 198 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 = 0.3741 r_free = 0.3741 target = 0.155430 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3494 r_free = 0.3494 target = 0.135416 restraints weight = 18056.827| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3514 r_free = 0.3514 target = 0.137069 restraints weight = 14678.938| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3528 r_free = 0.3528 target = 0.138202 restraints weight = 12666.722| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3540 r_free = 0.3540 target = 0.139160 restraints weight = 11388.665| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3544 r_free = 0.3544 target = 0.139494 restraints weight = 10497.026| |-----------------------------------------------------------------------------| r_work (final): 0.3549 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8130 moved from start: 0.1132 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= 0.251 Angle : 0.702 5.231 20000 Z= 0.379 Chirality : 0.050 0.231 1976 Planarity : 0.005 0.059 2592 Dihedral : 9.163 57.762 2364 Min Nonbonded Distance : 2.252 Molprobity Statistics. All-atom Clashscore : 5.32 Ramachandran Plot: Outliers : 0.69 % Allowed : 15.44 % Favored : 83.87 % Rotamer: Outliers : 8.33 % Allowed : 23.26 % Favored : 68.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -4.64 (0.15), residues: 1736 helix: -1.87 (0.26), residues: 296 sheet: -1.34 (0.28), residues: 320 loop : -4.29 (0.11), residues: 1120 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG E 94 TYR 0.020 0.002 TYR E 110 PHE 0.028 0.002 PHE G 82 TRP 0.017 0.002 TRP D 235 HIS 0.005 0.002 HIS B 180 Details of bonding type rmsd covalent geometry : bond 0.00595 (14720) covalent geometry : angle 0.69482 (19920) SS BOND : bond 0.00350 ( 16) SS BOND : angle 0.65719 ( 32) hydrogen bonds : bond 0.05274 ( 320) hydrogen bonds : angle 6.31027 ( 888) link_NAG-ASN : bond 0.00569 ( 16) link_NAG-ASN : angle 2.20034 ( 48) *********************** 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 316 residues out of total 1440 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 120 poor density : 196 time to evaluate : 0.575 Fit side-chains REVERT: A 83 GLN cc_start: 0.9221 (OUTLIER) cc_final: 0.8444 (tp40) REVERT: A 197 GLN cc_start: 0.8020 (OUTLIER) cc_final: 0.7464 (mp10) REVERT: D 72 MET cc_start: 0.7508 (mmt) cc_final: 0.7189 (mmt) REVERT: D 157 GLU cc_start: 0.8023 (OUTLIER) cc_final: 0.7807 (tt0) REVERT: D 247 ARG cc_start: 0.7899 (OUTLIER) cc_final: 0.7496 (mtm180) REVERT: B 83 GLN cc_start: 0.9226 (OUTLIER) cc_final: 0.8435 (tp40) REVERT: B 197 GLN cc_start: 0.8019 (OUTLIER) cc_final: 0.7465 (mp10) REVERT: E 72 MET cc_start: 0.7503 (mmt) cc_final: 0.7194 (mmt) REVERT: E 157 GLU cc_start: 0.8047 (OUTLIER) cc_final: 0.7826 (tt0) REVERT: E 247 ARG cc_start: 0.7904 (OUTLIER) cc_final: 0.7498 (mtm180) REVERT: C 83 GLN cc_start: 0.9220 (OUTLIER) cc_final: 0.8440 (tp40) REVERT: C 197 GLN cc_start: 0.8017 (OUTLIER) cc_final: 0.7465 (mp10) REVERT: F 72 MET cc_start: 0.7513 (mmt) cc_final: 0.7199 (mmt) REVERT: F 157 GLU cc_start: 0.8038 (OUTLIER) cc_final: 0.7821 (tt0) REVERT: F 247 ARG cc_start: 0.7892 (OUTLIER) cc_final: 0.7493 (mtm180) REVERT: G 83 GLN cc_start: 0.9222 (OUTLIER) cc_final: 0.8431 (tp40) REVERT: G 197 GLN cc_start: 0.8020 (OUTLIER) cc_final: 0.7463 (mp10) REVERT: H 72 MET cc_start: 0.7518 (mmt) cc_final: 0.7202 (mmt) REVERT: H 157 GLU cc_start: 0.8029 (OUTLIER) cc_final: 0.7808 (tt0) REVERT: H 247 ARG cc_start: 0.7898 (OUTLIER) cc_final: 0.7495 (mtm180) outliers start: 120 outliers final: 48 residues processed: 288 average time/residue: 0.1529 time to fit residues: 61.3222 Evaluate side-chains 252 residues out of total 1440 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 188 time to evaluate : 0.511 ------------------------------------------------------------------------------- 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 165 VAL Chi-restraints excluded: chain A residue 197 GLN Chi-restraints excluded: chain A residue 199 CYS Chi-restraints excluded: chain A residue 207 PHE Chi-restraints excluded: chain A residue 248 THR 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 228 SER 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 165 VAL Chi-restraints excluded: chain B residue 197 GLN Chi-restraints excluded: chain B residue 199 CYS Chi-restraints excluded: chain B residue 207 PHE Chi-restraints excluded: chain B residue 248 THR 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 228 SER 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 165 VAL Chi-restraints excluded: chain C residue 197 GLN Chi-restraints excluded: chain C residue 199 CYS Chi-restraints excluded: chain C residue 207 PHE Chi-restraints excluded: chain C residue 248 THR 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 228 SER 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 165 VAL Chi-restraints excluded: chain G residue 197 GLN Chi-restraints excluded: chain G residue 199 CYS Chi-restraints excluded: chain G residue 207 PHE Chi-restraints excluded: chain G residue 248 THR 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 228 SER 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=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 45 optimal weight: 0.9980 chunk 29 optimal weight: 0.7980 chunk 136 optimal weight: 4.9990 chunk 129 optimal weight: 0.9980 chunk 64 optimal weight: 10.0000 chunk 112 optimal weight: 0.7980 chunk 132 optimal weight: 4.9990 chunk 108 optimal weight: 0.9980 chunk 158 optimal weight: 4.9990 chunk 77 optimal weight: 6.9990 chunk 35 optimal weight: 6.9990 overall best weight: 0.9180 ------------------------------------------------------------------------------- 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 = 0.3815 r_free = 0.3815 target = 0.161999 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3573 r_free = 0.3573 target = 0.142109 restraints weight = 17987.158| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3594 r_free = 0.3594 target = 0.143918 restraints weight = 14402.435| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3609 r_free = 0.3609 target = 0.145161 restraints weight = 12241.383| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3622 r_free = 0.3622 target = 0.146214 restraints weight = 10910.030| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 38)----------------| | r_work = 0.3632 r_free = 0.3632 target = 0.146953 restraints weight = 9955.364| |-----------------------------------------------------------------------------| r_work (final): 0.3637 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8028 moved from start: 0.1213 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.018 14752 Z= 0.098 Angle : 0.539 5.295 20000 Z= 0.287 Chirality : 0.044 0.229 1976 Planarity : 0.003 0.026 2592 Dihedral : 7.238 57.932 2320 Min Nonbonded Distance : 2.314 Molprobity Statistics. All-atom Clashscore : 3.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 13.36 % Favored : 86.64 % Rotamer: Outliers : 5.97 % Allowed : 24.03 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -4.30 (0.16), residues: 1736 helix: -1.07 (0.28), residues: 296 sheet: -1.24 (0.27), residues: 320 loop : -4.18 (0.12), residues: 1120 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B 94 TYR 0.007 0.001 TYR C 99 PHE 0.018 0.001 PHE C 82 TRP 0.010 0.001 TRP F 235 HIS 0.002 0.001 HIS C 118 Details of bonding type rmsd covalent geometry : bond 0.00202 (14720) covalent geometry : angle 0.53053 (19920) SS BOND : bond 0.00117 ( 16) SS BOND : angle 0.53251 ( 32) hydrogen bonds : bond 0.03334 ( 320) hydrogen bonds : angle 5.71481 ( 888) link_NAG-ASN : bond 0.00530 ( 16) link_NAG-ASN : angle 2.00875 ( 48) *********************** 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 314 residues out of total 1440 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 86 poor density : 228 time to evaluate : 0.623 Fit side-chains REVERT: A 50 GLN cc_start: 0.6241 (OUTLIER) cc_final: 0.5989 (mt0) REVERT: A 193 ASP cc_start: 0.6896 (m-30) cc_final: 0.6363 (m-30) REVERT: A 197 GLN cc_start: 0.7960 (OUTLIER) cc_final: 0.7482 (mp10) REVERT: D 72 MET cc_start: 0.7295 (OUTLIER) cc_final: 0.6947 (mmt) REVERT: B 50 GLN cc_start: 0.6243 (OUTLIER) cc_final: 0.5991 (mt0) REVERT: B 193 ASP cc_start: 0.6887 (m-30) cc_final: 0.6353 (m-30) REVERT: B 197 GLN cc_start: 0.7958 (OUTLIER) cc_final: 0.7482 (mp10) REVERT: E 72 MET cc_start: 0.7288 (OUTLIER) cc_final: 0.6941 (mmt) REVERT: C 50 GLN cc_start: 0.6244 (OUTLIER) cc_final: 0.6001 (mt0) REVERT: C 193 ASP cc_start: 0.6886 (m-30) cc_final: 0.6348 (m-30) REVERT: C 197 GLN cc_start: 0.7956 (OUTLIER) cc_final: 0.7484 (mp10) REVERT: F 72 MET cc_start: 0.7300 (OUTLIER) cc_final: 0.6948 (mmt) REVERT: G 50 GLN cc_start: 0.6247 (OUTLIER) cc_final: 0.5999 (mt0) REVERT: G 193 ASP cc_start: 0.6891 (m-30) cc_final: 0.6354 (m-30) REVERT: G 197 GLN cc_start: 0.7963 (OUTLIER) cc_final: 0.7489 (mp10) REVERT: H 72 MET cc_start: 0.7300 (OUTLIER) cc_final: 0.6952 (mmt) outliers start: 86 outliers final: 50 residues processed: 294 average time/residue: 0.1468 time to fit residues: 60.6727 Evaluate side-chains 260 residues out of total 1440 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 198 time to evaluate : 0.502 ------------------------------------------------------------------------------- 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 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 159 ASP Chi-restraints excluded: chain D residue 165 VAL Chi-restraints excluded: chain D residue 177 LEU Chi-restraints excluded: chain D residue 198 ASN 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 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 159 ASP Chi-restraints excluded: chain E residue 165 VAL Chi-restraints excluded: chain E residue 177 LEU Chi-restraints excluded: chain E residue 198 ASN 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 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 159 ASP Chi-restraints excluded: chain F residue 165 VAL Chi-restraints excluded: chain F residue 177 LEU Chi-restraints excluded: chain F residue 198 ASN 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 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 159 ASP Chi-restraints excluded: chain H residue 165 VAL Chi-restraints excluded: chain H residue 177 LEU Chi-restraints excluded: chain H residue 198 ASN Chi-restraints excluded: chain H residue 248 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 117 optimal weight: 4.9990 chunk 25 optimal weight: 8.9990 chunk 61 optimal weight: 4.9990 chunk 43 optimal weight: 7.9990 chunk 109 optimal weight: 8.9990 chunk 112 optimal weight: 0.9990 chunk 160 optimal weight: 10.0000 chunk 20 optimal weight: 9.9990 chunk 14 optimal weight: 9.9990 chunk 12 optimal weight: 6.9990 chunk 93 optimal weight: 3.9990 overall best weight: 4.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 198 ASN F 198 ASN H 198 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3730 r_free = 0.3730 target = 0.154352 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3473 r_free = 0.3473 target = 0.133522 restraints weight = 18251.189| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3493 r_free = 0.3493 target = 0.135255 restraints weight = 14769.115| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3510 r_free = 0.3510 target = 0.136614 restraints weight = 12619.794| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3522 r_free = 0.3522 target = 0.137562 restraints weight = 11236.761| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3530 r_free = 0.3530 target = 0.138269 restraints weight = 10309.022| |-----------------------------------------------------------------------------| r_work (final): 0.3536 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8143 moved from start: 0.1482 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.036 14752 Z= 0.294 Angle : 0.738 5.170 20000 Z= 0.395 Chirality : 0.052 0.219 1976 Planarity : 0.006 0.068 2592 Dihedral : 8.100 54.194 2316 Min Nonbonded Distance : 2.264 Molprobity Statistics. All-atom Clashscore : 4.78 Ramachandran Plot: Outliers : 0.46 % Allowed : 15.44 % Favored : 84.10 % Rotamer: Outliers : 6.94 % Allowed : 23.33 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -4.55 (0.16), residues: 1736 helix: -1.25 (0.29), residues: 296 sheet: -1.78 (0.28), residues: 344 loop : -4.26 (0.12), residues: 1096 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG D 94 TYR 0.023 0.002 TYR H 110 PHE 0.029 0.002 PHE H 82 TRP 0.018 0.002 TRP E 235 HIS 0.006 0.002 HIS F 180 Details of bonding type rmsd covalent geometry : bond 0.00698 (14720) covalent geometry : angle 0.73047 (19920) SS BOND : bond 0.00393 ( 16) SS BOND : angle 0.63939 ( 32) hydrogen bonds : bond 0.05207 ( 320) hydrogen bonds : angle 6.08134 ( 888) link_NAG-ASN : bond 0.00575 ( 16) link_NAG-ASN : angle 2.34227 ( 48) *********************** 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 300 residues out of total 1440 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 100 poor density : 200 time to evaluate : 0.550 Fit side-chains REVERT: A 83 GLN cc_start: 0.9243 (OUTLIER) cc_final: 0.8428 (tp40) REVERT: A 159 ASP cc_start: 0.6594 (OUTLIER) cc_final: 0.5762 (m-30) REVERT: A 197 GLN cc_start: 0.7958 (OUTLIER) cc_final: 0.7493 (mp10) REVERT: D 72 MET cc_start: 0.7527 (mmt) cc_final: 0.7168 (mmt) REVERT: D 157 GLU cc_start: 0.8043 (OUTLIER) cc_final: 0.7838 (tt0) REVERT: D 247 ARG cc_start: 0.7891 (OUTLIER) cc_final: 0.7492 (mtm180) REVERT: B 83 GLN cc_start: 0.9249 (OUTLIER) cc_final: 0.8422 (tp40) REVERT: B 159 ASP cc_start: 0.6568 (OUTLIER) cc_final: 0.5747 (m-30) REVERT: B 197 GLN cc_start: 0.7963 (OUTLIER) cc_final: 0.7497 (mp10) REVERT: E 72 MET cc_start: 0.7521 (mmt) cc_final: 0.7171 (mmt) REVERT: E 157 GLU cc_start: 0.8061 (OUTLIER) cc_final: 0.7858 (tt0) REVERT: E 247 ARG cc_start: 0.7897 (OUTLIER) cc_final: 0.7495 (mtm180) REVERT: C 83 GLN cc_start: 0.9241 (OUTLIER) cc_final: 0.8424 (tp40) REVERT: C 159 ASP cc_start: 0.6599 (OUTLIER) cc_final: 0.5755 (m-30) REVERT: C 197 GLN cc_start: 0.7963 (OUTLIER) cc_final: 0.7500 (mp10) REVERT: F 72 MET cc_start: 0.7533 (mmt) cc_final: 0.7178 (mmt) REVERT: F 157 GLU cc_start: 0.8052 (OUTLIER) cc_final: 0.7847 (tt0) REVERT: F 247 ARG cc_start: 0.7895 (OUTLIER) cc_final: 0.7494 (mtm180) REVERT: G 83 GLN cc_start: 0.9243 (OUTLIER) cc_final: 0.8423 (tp40) REVERT: G 159 ASP cc_start: 0.6580 (OUTLIER) cc_final: 0.5755 (m-30) REVERT: G 197 GLN cc_start: 0.7968 (OUTLIER) cc_final: 0.7503 (mp10) REVERT: H 72 MET cc_start: 0.7535 (mmt) cc_final: 0.7169 (mmt) REVERT: H 157 GLU cc_start: 0.8042 (OUTLIER) cc_final: 0.7839 (tt0) REVERT: H 247 ARG cc_start: 0.7900 (OUTLIER) cc_final: 0.7501 (mtm180) outliers start: 100 outliers final: 56 residues processed: 271 average time/residue: 0.1489 time to fit residues: 56.3088 Evaluate side-chains 272 residues out of total 1440 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 196 time to evaluate : 0.608 ------------------------------------------------------------------------------- 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 248 THR Chi-restraints excluded: chain D residue 89 SER Chi-restraints excluded: chain D residue 157 GLU 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 83 GLN Chi-restraints excluded: chain B residue 93 PHE Chi-restraints excluded: chain B residue 132 LEU Chi-restraints excluded: chain B residue 135 PHE Chi-restraints excluded: chain B residue 159 ASP Chi-restraints excluded: chain B residue 165 VAL Chi-restraints excluded: chain B residue 194 LEU Chi-restraints excluded: chain B residue 197 GLN Chi-restraints excluded: chain B residue 199 CYS Chi-restraints excluded: chain B residue 248 THR Chi-restraints excluded: chain B residue 250 MET Chi-restraints excluded: chain E residue 89 SER Chi-restraints excluded: chain E residue 157 GLU Chi-restraints excluded: chain E residue 165 VAL Chi-restraints excluded: chain E residue 177 LEU Chi-restraints excluded: chain E residue 198 ASN 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 248 THR Chi-restraints excluded: chain F residue 89 SER Chi-restraints excluded: chain F residue 157 GLU Chi-restraints excluded: chain F residue 165 VAL Chi-restraints excluded: chain F residue 177 LEU Chi-restraints excluded: chain F residue 198 ASN 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 248 THR Chi-restraints excluded: chain H residue 89 SER Chi-restraints excluded: chain H residue 157 GLU Chi-restraints excluded: chain H residue 165 VAL Chi-restraints excluded: chain H residue 177 LEU Chi-restraints excluded: chain H residue 198 ASN Chi-restraints excluded: chain H residue 227 LEU Chi-restraints excluded: chain H residue 244 SER Chi-restraints excluded: chain H residue 247 ARG Chi-restraints excluded: chain H residue 248 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 87 optimal weight: 0.0370 chunk 102 optimal weight: 7.9990 chunk 9 optimal weight: 0.9990 chunk 0 optimal weight: 10.0000 chunk 85 optimal weight: 1.9990 chunk 41 optimal weight: 8.9990 chunk 167 optimal weight: 8.9990 chunk 96 optimal weight: 4.9990 chunk 144 optimal weight: 7.9990 chunk 61 optimal weight: 5.9990 chunk 6 optimal weight: 0.9980 overall best weight: 1.8064 ------------------------------------------------------------------------------- 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 = 0.3774 r_free = 0.3774 target = 0.158158 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3525 r_free = 0.3525 target = 0.137705 restraints weight = 18090.725| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3547 r_free = 0.3547 target = 0.139589 restraints weight = 14370.383| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3564 r_free = 0.3564 target = 0.140970 restraints weight = 12146.512| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3575 r_free = 0.3575 target = 0.141903 restraints weight = 10757.297| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.3584 r_free = 0.3584 target = 0.142672 restraints weight = 9859.670| |-----------------------------------------------------------------------------| r_work (final): 0.3589 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8086 moved from start: 0.1371 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 14752 Z= 0.143 Angle : 0.606 7.082 20000 Z= 0.323 Chirality : 0.046 0.229 1976 Planarity : 0.004 0.038 2592 Dihedral : 6.966 51.347 2304 Min Nonbonded Distance : 2.277 Molprobity Statistics. All-atom Clashscore : 4.27 Ramachandran Plot: Outliers : 0.46 % Allowed : 14.75 % Favored : 84.79 % Rotamer: Outliers : 6.04 % Allowed : 23.96 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -4.40 (0.16), residues: 1736 helix: -0.93 (0.30), residues: 296 sheet: -1.70 (0.28), residues: 344 loop : -4.21 (0.12), residues: 1096 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG F 94 TYR 0.011 0.001 TYR H 110 PHE 0.022 0.001 PHE B 82 TRP 0.014 0.001 TRP H 235 HIS 0.002 0.001 HIS F 226 Details of bonding type rmsd covalent geometry : bond 0.00322 (14720) covalent geometry : angle 0.59697 (19920) SS BOND : bond 0.00290 ( 16) SS BOND : angle 0.59510 ( 32) hydrogen bonds : bond 0.03826 ( 320) hydrogen bonds : angle 5.67951 ( 888) link_NAG-ASN : bond 0.00548 ( 16) link_NAG-ASN : angle 2.22050 ( 48) *********************** 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 281 residues out of total 1440 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 87 poor density : 194 time to evaluate : 0.486 Fit side-chains REVERT: A 50 GLN cc_start: 0.6416 (OUTLIER) cc_final: 0.6167 (mt0) REVERT: A 72 MET cc_start: 0.6664 (OUTLIER) cc_final: 0.6164 (mmt) REVERT: A 78 LYS cc_start: 0.7693 (mptt) cc_final: 0.7178 (mptt) REVERT: A 83 GLN cc_start: 0.9183 (OUTLIER) cc_final: 0.8377 (tp40) REVERT: A 159 ASP cc_start: 0.6576 (OUTLIER) cc_final: 0.5786 (m-30) REVERT: A 197 GLN cc_start: 0.7893 (OUTLIER) cc_final: 0.7462 (mp10) REVERT: D 72 MET cc_start: 0.7437 (mmt) cc_final: 0.6936 (mmt) REVERT: B 50 GLN cc_start: 0.6415 (OUTLIER) cc_final: 0.6163 (mt0) REVERT: B 72 MET cc_start: 0.6663 (OUTLIER) cc_final: 0.6163 (mmt) REVERT: B 78 LYS cc_start: 0.7692 (mptt) cc_final: 0.7172 (mptt) REVERT: B 83 GLN cc_start: 0.9188 (OUTLIER) cc_final: 0.8368 (tp40) REVERT: B 159 ASP cc_start: 0.6549 (OUTLIER) cc_final: 0.5770 (m-30) REVERT: B 197 GLN cc_start: 0.7899 (OUTLIER) cc_final: 0.7461 (mp10) REVERT: E 72 MET cc_start: 0.7430 (mmt) cc_final: 0.6932 (mmt) REVERT: C 50 GLN cc_start: 0.6424 (OUTLIER) cc_final: 0.6175 (mt0) REVERT: C 72 MET cc_start: 0.6656 (OUTLIER) cc_final: 0.6167 (mmt) REVERT: C 78 LYS cc_start: 0.7686 (mptt) cc_final: 0.7173 (mptt) REVERT: C 83 GLN cc_start: 0.9181 (OUTLIER) cc_final: 0.8373 (tp40) REVERT: C 159 ASP cc_start: 0.6573 (OUTLIER) cc_final: 0.5784 (m-30) REVERT: C 197 GLN cc_start: 0.7893 (OUTLIER) cc_final: 0.7459 (mp10) REVERT: F 72 MET cc_start: 0.7441 (mmt) cc_final: 0.6939 (mmt) REVERT: G 50 GLN cc_start: 0.6421 (OUTLIER) cc_final: 0.6170 (mt0) REVERT: G 72 MET cc_start: 0.6652 (OUTLIER) cc_final: 0.6163 (mmt) REVERT: G 78 LYS cc_start: 0.7678 (mptt) cc_final: 0.7166 (mptt) REVERT: G 83 GLN cc_start: 0.9184 (OUTLIER) cc_final: 0.8371 (tp40) REVERT: G 159 ASP cc_start: 0.6557 (OUTLIER) cc_final: 0.5781 (m-30) REVERT: G 197 GLN cc_start: 0.7897 (OUTLIER) cc_final: 0.7467 (mp10) REVERT: H 72 MET cc_start: 0.7446 (mmt) cc_final: 0.6941 (mmt) outliers start: 87 outliers final: 55 residues processed: 269 average time/residue: 0.1518 time to fit residues: 57.0799 Evaluate side-chains 258 residues out of total 1440 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 183 time to evaluate : 0.554 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 50 GLN Chi-restraints excluded: chain A residue 72 MET Chi-restraints excluded: chain A residue 83 GLN Chi-restraints excluded: chain A residue 93 PHE Chi-restraints excluded: chain A residue 132 LEU Chi-restraints excluded: chain A residue 135 PHE Chi-restraints excluded: chain A residue 159 ASP Chi-restraints excluded: chain A residue 165 VAL Chi-restraints excluded: chain A residue 194 LEU Chi-restraints excluded: chain A residue 197 GLN Chi-restraints excluded: chain A residue 199 CYS Chi-restraints excluded: chain A residue 248 THR Chi-restraints excluded: chain D residue 68 VAL Chi-restraints excluded: chain D residue 89 SER Chi-restraints excluded: chain D residue 165 VAL Chi-restraints excluded: chain D residue 177 LEU Chi-restraints excluded: chain D residue 244 SER Chi-restraints excluded: chain D residue 248 THR Chi-restraints excluded: chain B residue 50 GLN Chi-restraints excluded: chain B residue 72 MET Chi-restraints excluded: chain B residue 83 GLN Chi-restraints excluded: chain B residue 93 PHE Chi-restraints excluded: chain B residue 132 LEU Chi-restraints excluded: chain B residue 135 PHE Chi-restraints excluded: chain B residue 159 ASP Chi-restraints excluded: chain B residue 165 VAL Chi-restraints excluded: chain B residue 194 LEU Chi-restraints excluded: chain B residue 197 GLN Chi-restraints excluded: chain B residue 199 CYS Chi-restraints excluded: chain B residue 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 198 ASN Chi-restraints excluded: chain E residue 244 SER Chi-restraints excluded: chain E residue 248 THR Chi-restraints excluded: chain C residue 50 GLN Chi-restraints excluded: chain C residue 72 MET Chi-restraints excluded: chain C residue 83 GLN Chi-restraints excluded: chain C residue 93 PHE Chi-restraints excluded: chain C residue 132 LEU Chi-restraints excluded: chain C residue 135 PHE Chi-restraints excluded: chain C residue 159 ASP Chi-restraints excluded: chain C residue 165 VAL Chi-restraints excluded: chain C residue 194 LEU Chi-restraints excluded: chain C residue 197 GLN Chi-restraints excluded: chain C residue 199 CYS Chi-restraints excluded: chain C residue 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 198 ASN Chi-restraints excluded: chain F residue 244 SER Chi-restraints excluded: chain F residue 248 THR Chi-restraints excluded: chain G residue 50 GLN Chi-restraints excluded: chain G residue 72 MET Chi-restraints excluded: chain G residue 83 GLN Chi-restraints excluded: chain G residue 93 PHE Chi-restraints excluded: chain G residue 132 LEU Chi-restraints excluded: chain G residue 135 PHE Chi-restraints excluded: chain G residue 159 ASP Chi-restraints excluded: chain G residue 165 VAL Chi-restraints excluded: chain G residue 194 LEU Chi-restraints excluded: chain G residue 197 GLN Chi-restraints excluded: chain G residue 199 CYS Chi-restraints excluded: chain G residue 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 198 ASN Chi-restraints excluded: chain H residue 244 SER 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 34 optimal weight: 9.9990 chunk 88 optimal weight: 5.9990 chunk 126 optimal weight: 10.0000 chunk 116 optimal weight: 0.0570 chunk 139 optimal weight: 9.9990 chunk 145 optimal weight: 7.9990 chunk 97 optimal weight: 9.9990 chunk 143 optimal weight: 5.9990 chunk 16 optimal weight: 2.9990 chunk 83 optimal weight: 8.9990 chunk 100 optimal weight: 0.0980 overall best weight: 3.0304 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 198 ASN F 198 ASN H 198 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3748 r_free = 0.3748 target = 0.156005 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3503 r_free = 0.3503 target = 0.135978 restraints weight = 18057.628| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3522 r_free = 0.3522 target = 0.137637 restraints weight = 14728.427| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3538 r_free = 0.3538 target = 0.138871 restraints weight = 12701.028| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3546 r_free = 0.3546 target = 0.139613 restraints weight = 11419.468| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3554 r_free = 0.3554 target = 0.140316 restraints weight = 10583.571| |-----------------------------------------------------------------------------| r_work (final): 0.3560 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8123 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 : 0.005 0.026 14752 Z= 0.210 Angle : 0.657 5.857 20000 Z= 0.351 Chirality : 0.048 0.225 1976 Planarity : 0.005 0.052 2592 Dihedral : 7.252 52.036 2304 Min Nonbonded Distance : 2.271 Molprobity Statistics. All-atom Clashscore : 4.74 Ramachandran Plot: Outliers : 0.46 % Allowed : 16.13 % Favored : 83.41 % Rotamer: Outliers : 7.99 % Allowed : 22.64 % Favored : 69.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -4.46 (0.16), residues: 1736 helix: -0.97 (0.30), residues: 296 sheet: -1.76 (0.28), residues: 344 loop : -4.25 (0.12), residues: 1096 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG E 94 TYR 0.017 0.002 TYR H 110 PHE 0.025 0.002 PHE A 82 TRP 0.016 0.001 TRP D 235 HIS 0.004 0.002 HIS H 180 Details of bonding type rmsd covalent geometry : bond 0.00494 (14720) covalent geometry : angle 0.64758 (19920) SS BOND : bond 0.00291 ( 16) SS BOND : angle 0.61645 ( 32) hydrogen bonds : bond 0.04437 ( 320) hydrogen bonds : angle 5.74456 ( 888) link_NAG-ASN : bond 0.00569 ( 16) link_NAG-ASN : angle 2.31355 ( 48) *********************** 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 308 residues out of total 1440 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 115 poor density : 193 time to evaluate : 0.563 Fit side-chains REVERT: A 50 GLN cc_start: 0.6401 (OUTLIER) cc_final: 0.6159 (mt0) REVERT: A 72 MET cc_start: 0.6554 (OUTLIER) cc_final: 0.5964 (mmt) REVERT: A 83 GLN cc_start: 0.9230 (OUTLIER) cc_final: 0.8433 (tp40) REVERT: A 159 ASP cc_start: 0.6589 (OUTLIER) cc_final: 0.5766 (m-30) REVERT: A 197 GLN cc_start: 0.7906 (OUTLIER) cc_final: 0.7522 (mp10) REVERT: D 72 MET cc_start: 0.7423 (mmt) cc_final: 0.7048 (mmt) REVERT: D 247 ARG cc_start: 0.7834 (OUTLIER) cc_final: 0.7442 (mtm180) REVERT: B 50 GLN cc_start: 0.6397 (OUTLIER) cc_final: 0.6157 (mt0) REVERT: B 72 MET cc_start: 0.6542 (OUTLIER) cc_final: 0.5962 (mmt) REVERT: B 83 GLN cc_start: 0.9233 (OUTLIER) cc_final: 0.8429 (tp40) REVERT: B 159 ASP cc_start: 0.6559 (OUTLIER) cc_final: 0.5752 (m-30) REVERT: B 197 GLN cc_start: 0.7910 (OUTLIER) cc_final: 0.7524 (mp10) REVERT: E 72 MET cc_start: 0.7408 (mmt) cc_final: 0.7046 (mmt) REVERT: E 247 ARG cc_start: 0.7841 (OUTLIER) cc_final: 0.7444 (mtm180) REVERT: C 50 GLN cc_start: 0.6404 (OUTLIER) cc_final: 0.6164 (mt0) REVERT: C 72 MET cc_start: 0.6540 (OUTLIER) cc_final: 0.5969 (mmt) REVERT: C 83 GLN cc_start: 0.9229 (OUTLIER) cc_final: 0.8433 (tp40) REVERT: C 159 ASP cc_start: 0.6594 (OUTLIER) cc_final: 0.5766 (m-30) REVERT: C 197 GLN cc_start: 0.7902 (OUTLIER) cc_final: 0.7518 (mp10) REVERT: F 72 MET cc_start: 0.7420 (mmt) cc_final: 0.7047 (mmt) REVERT: F 247 ARG cc_start: 0.7832 (OUTLIER) cc_final: 0.7440 (mtm180) REVERT: G 50 GLN cc_start: 0.6404 (OUTLIER) cc_final: 0.6160 (mt0) REVERT: G 72 MET cc_start: 0.6540 (OUTLIER) cc_final: 0.5963 (mmt) REVERT: G 83 GLN cc_start: 0.9227 (OUTLIER) cc_final: 0.8428 (tp40) REVERT: G 159 ASP cc_start: 0.6569 (OUTLIER) cc_final: 0.5764 (m-30) REVERT: G 197 GLN cc_start: 0.7914 (OUTLIER) cc_final: 0.7529 (mp10) REVERT: H 72 MET cc_start: 0.7426 (mmt) cc_final: 0.7048 (mmt) REVERT: H 247 ARG cc_start: 0.7840 (OUTLIER) cc_final: 0.7446 (mtm180) outliers start: 115 outliers final: 67 residues processed: 288 average time/residue: 0.1620 time to fit residues: 64.0720 Evaluate side-chains 275 residues out of total 1440 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 91 poor density : 184 time to evaluate : 0.599 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 50 GLN Chi-restraints excluded: chain A residue 72 MET Chi-restraints excluded: chain A residue 83 GLN Chi-restraints excluded: chain A residue 93 PHE Chi-restraints excluded: chain A residue 132 LEU Chi-restraints excluded: chain A residue 135 PHE Chi-restraints excluded: chain A residue 159 ASP Chi-restraints excluded: chain A residue 165 VAL Chi-restraints excluded: chain A residue 187 THR Chi-restraints excluded: chain A residue 194 LEU Chi-restraints excluded: chain A residue 197 GLN Chi-restraints excluded: chain A residue 199 CYS Chi-restraints excluded: chain A residue 248 THR Chi-restraints excluded: chain D residue 68 VAL Chi-restraints excluded: chain D residue 89 SER Chi-restraints excluded: chain D residue 139 THR 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 72 MET Chi-restraints excluded: chain B residue 83 GLN Chi-restraints excluded: chain B residue 93 PHE Chi-restraints excluded: chain B residue 132 LEU Chi-restraints excluded: chain B residue 135 PHE Chi-restraints excluded: chain B residue 159 ASP Chi-restraints excluded: chain B residue 165 VAL Chi-restraints excluded: chain B residue 187 THR Chi-restraints excluded: chain B residue 194 LEU Chi-restraints excluded: chain B residue 197 GLN Chi-restraints excluded: chain B residue 199 CYS Chi-restraints excluded: chain B residue 248 THR Chi-restraints excluded: chain E residue 68 VAL Chi-restraints excluded: chain E residue 89 SER Chi-restraints excluded: chain E residue 139 THR Chi-restraints excluded: chain E residue 165 VAL Chi-restraints excluded: chain E residue 177 LEU Chi-restraints excluded: chain E residue 198 ASN 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 72 MET Chi-restraints excluded: chain C residue 83 GLN Chi-restraints excluded: chain C residue 93 PHE Chi-restraints excluded: chain C residue 132 LEU Chi-restraints excluded: chain C residue 135 PHE Chi-restraints excluded: chain C residue 159 ASP Chi-restraints excluded: chain C residue 165 VAL Chi-restraints excluded: chain C residue 187 THR Chi-restraints excluded: chain C residue 194 LEU Chi-restraints excluded: chain C residue 197 GLN Chi-restraints excluded: chain C residue 199 CYS Chi-restraints excluded: chain C residue 248 THR Chi-restraints excluded: chain F residue 68 VAL Chi-restraints excluded: chain F residue 89 SER Chi-restraints excluded: chain F residue 139 THR Chi-restraints excluded: chain F residue 165 VAL Chi-restraints excluded: chain F residue 177 LEU Chi-restraints excluded: chain F residue 198 ASN 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 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 187 THR Chi-restraints excluded: chain G residue 194 LEU Chi-restraints excluded: chain G residue 197 GLN Chi-restraints excluded: chain G residue 199 CYS Chi-restraints excluded: chain G residue 248 THR Chi-restraints excluded: chain H residue 68 VAL Chi-restraints excluded: chain H residue 89 SER Chi-restraints excluded: chain H residue 139 THR Chi-restraints excluded: chain H residue 165 VAL Chi-restraints excluded: chain H residue 177 LEU Chi-restraints excluded: chain H residue 198 ASN 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 101 optimal weight: 2.9990 chunk 62 optimal weight: 7.9990 chunk 22 optimal weight: 9.9990 chunk 97 optimal weight: 9.9990 chunk 138 optimal weight: 3.9990 chunk 30 optimal weight: 7.9990 chunk 114 optimal weight: 7.9990 chunk 125 optimal weight: 7.9990 chunk 162 optimal weight: 0.3980 chunk 34 optimal weight: 9.9990 chunk 17 optimal weight: 6.9990 overall best weight: 4.4788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 198 ASN F 198 ASN H 198 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3725 r_free = 0.3725 target = 0.154064 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3477 r_free = 0.3477 target = 0.133900 restraints weight = 18086.313| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3492 r_free = 0.3492 target = 0.135268 restraints weight = 14973.752| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3509 r_free = 0.3509 target = 0.136586 restraints weight = 13048.285| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3519 r_free = 0.3519 target = 0.137393 restraints weight = 11732.356| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3521 r_free = 0.3521 target = 0.137637 restraints weight = 10866.047| |-----------------------------------------------------------------------------| r_work (final): 0.3527 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8157 moved from start: 0.1677 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.036 14752 Z= 0.300 Angle : 0.751 6.403 20000 Z= 0.401 Chirality : 0.052 0.224 1976 Planarity : 0.006 0.069 2592 Dihedral : 7.824 52.077 2304 Min Nonbonded Distance : 2.250 Molprobity Statistics. All-atom Clashscore : 5.14 Ramachandran Plot: Outliers : 0.69 % Allowed : 16.13 % Favored : 83.18 % Rotamer: Outliers : 7.50 % Allowed : 23.82 % Favored : 68.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -4.61 (0.16), residues: 1736 helix: -1.39 (0.28), residues: 312 sheet: -1.93 (0.27), residues: 344 loop : -4.26 (0.12), residues: 1080 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG F 94 TYR 0.023 0.002 TYR E 110 PHE 0.029 0.002 PHE F 82 TRP 0.020 0.002 TRP D 235 HIS 0.006 0.002 HIS D 180 Details of bonding type rmsd covalent geometry : bond 0.00713 (14720) covalent geometry : angle 0.74210 (19920) SS BOND : bond 0.00409 ( 16) SS BOND : angle 0.75750 ( 32) hydrogen bonds : bond 0.05145 ( 320) hydrogen bonds : angle 5.95705 ( 888) link_NAG-ASN : bond 0.00599 ( 16) link_NAG-ASN : angle 2.40857 ( 48) *********************** 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 312 residues out of total 1440 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 108 poor density : 204 time to evaluate : 0.592 Fit side-chains REVERT: A 83 GLN cc_start: 0.9243 (OUTLIER) cc_final: 0.8423 (tp40) REVERT: A 159 ASP cc_start: 0.6630 (OUTLIER) cc_final: 0.5781 (m-30) REVERT: A 197 GLN cc_start: 0.7948 (OUTLIER) cc_final: 0.7514 (mp10) REVERT: D 72 MET cc_start: 0.7505 (mmt) cc_final: 0.7217 (mmt) REVERT: D 157 GLU cc_start: 0.8090 (OUTLIER) cc_final: 0.7869 (tt0) REVERT: D 247 ARG cc_start: 0.7902 (OUTLIER) cc_final: 0.7521 (mtm180) REVERT: B 83 GLN cc_start: 0.9244 (OUTLIER) cc_final: 0.8416 (tp40) REVERT: B 159 ASP cc_start: 0.6603 (OUTLIER) cc_final: 0.5773 (m-30) REVERT: B 197 GLN cc_start: 0.7947 (OUTLIER) cc_final: 0.7513 (mp10) REVERT: E 72 MET cc_start: 0.7491 (mmt) cc_final: 0.7217 (mmt) REVERT: E 157 GLU cc_start: 0.8115 (OUTLIER) cc_final: 0.7895 (tt0) REVERT: E 247 ARG cc_start: 0.7909 (OUTLIER) cc_final: 0.7527 (mtm180) REVERT: C 83 GLN cc_start: 0.9243 (OUTLIER) cc_final: 0.8424 (tp40) REVERT: C 159 ASP cc_start: 0.6630 (OUTLIER) cc_final: 0.5783 (m-30) REVERT: C 197 GLN cc_start: 0.7940 (OUTLIER) cc_final: 0.7510 (mp10) REVERT: F 72 MET cc_start: 0.7499 (mmt) cc_final: 0.7211 (mmt) REVERT: F 157 GLU cc_start: 0.8107 (OUTLIER) cc_final: 0.7888 (tt0) REVERT: F 247 ARG cc_start: 0.7896 (OUTLIER) cc_final: 0.7511 (mtm180) REVERT: G 83 GLN cc_start: 0.9239 (OUTLIER) cc_final: 0.8420 (tp40) REVERT: G 159 ASP cc_start: 0.6608 (OUTLIER) cc_final: 0.5780 (m-30) REVERT: G 197 GLN cc_start: 0.7954 (OUTLIER) cc_final: 0.7521 (mp10) REVERT: H 72 MET cc_start: 0.7510 (mmt) cc_final: 0.7220 (mmt) REVERT: H 157 GLU cc_start: 0.8092 (OUTLIER) cc_final: 0.7870 (tt0) REVERT: H 247 ARG cc_start: 0.7902 (OUTLIER) cc_final: 0.7520 (mtm180) outliers start: 108 outliers final: 66 residues processed: 282 average time/residue: 0.1462 time to fit residues: 57.5510 Evaluate side-chains 282 residues out of total 1440 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 86 poor density : 196 time to evaluate : 0.501 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 83 GLN Chi-restraints excluded: chain A residue 93 PHE Chi-restraints excluded: chain A residue 132 LEU Chi-restraints excluded: chain A residue 135 PHE Chi-restraints excluded: chain A residue 159 ASP Chi-restraints excluded: chain A residue 165 VAL Chi-restraints excluded: chain A residue 194 LEU Chi-restraints excluded: chain A residue 197 GLN Chi-restraints excluded: chain A residue 199 CYS Chi-restraints excluded: chain A residue 207 PHE Chi-restraints excluded: chain A residue 248 THR Chi-restraints excluded: chain D residue 68 VAL Chi-restraints excluded: chain D residue 89 SER Chi-restraints excluded: chain D residue 139 THR Chi-restraints excluded: chain D residue 157 GLU 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 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 187 THR Chi-restraints excluded: chain B residue 194 LEU Chi-restraints excluded: chain B residue 197 GLN Chi-restraints excluded: chain B residue 199 CYS Chi-restraints excluded: chain B residue 207 PHE 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 139 THR Chi-restraints excluded: chain E residue 157 GLU Chi-restraints excluded: chain E residue 165 VAL Chi-restraints excluded: chain E residue 198 ASN 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 187 THR Chi-restraints excluded: chain C residue 194 LEU Chi-restraints excluded: chain C residue 197 GLN Chi-restraints excluded: chain C residue 199 CYS Chi-restraints excluded: chain C residue 207 PHE 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 139 THR Chi-restraints excluded: chain F residue 157 GLU Chi-restraints excluded: chain F residue 165 VAL Chi-restraints excluded: chain F residue 198 ASN 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 187 THR Chi-restraints excluded: chain G residue 194 LEU Chi-restraints excluded: chain G residue 197 GLN Chi-restraints excluded: chain G residue 199 CYS Chi-restraints excluded: chain G residue 207 PHE 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 139 THR Chi-restraints excluded: chain H residue 157 GLU Chi-restraints excluded: chain H residue 165 VAL Chi-restraints excluded: chain H residue 198 ASN 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 147 optimal weight: 8.9990 chunk 25 optimal weight: 0.6980 chunk 111 optimal weight: 3.9990 chunk 43 optimal weight: 5.9990 chunk 17 optimal weight: 0.9990 chunk 8 optimal weight: 0.9980 chunk 121 optimal weight: 0.7980 chunk 51 optimal weight: 1.9990 chunk 117 optimal weight: 0.7980 chunk 144 optimal weight: 7.9990 chunk 49 optimal weight: 1.9990 overall best weight: 0.8582 ------------------------------------------------------------------------------- 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 = 0.3798 r_free = 0.3798 target = 0.160634 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3548 r_free = 0.3548 target = 0.140106 restraints weight = 17887.380| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3570 r_free = 0.3570 target = 0.141980 restraints weight = 14149.010| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3587 r_free = 0.3587 target = 0.143369 restraints weight = 11988.830| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3597 r_free = 0.3597 target = 0.144211 restraints weight = 10609.856| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3603 r_free = 0.3603 target = 0.144745 restraints weight = 9757.201| |-----------------------------------------------------------------------------| r_work (final): 0.3609 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8061 moved from start: 0.1609 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 14752 Z= 0.107 Angle : 0.579 8.072 20000 Z= 0.305 Chirality : 0.045 0.236 1976 Planarity : 0.003 0.025 2592 Dihedral : 6.574 45.525 2304 Min Nonbonded Distance : 2.315 Molprobity Statistics. All-atom Clashscore : 4.12 Ramachandran Plot: Outliers : 0.46 % Allowed : 14.80 % Favored : 84.74 % Rotamer: Outliers : 5.07 % Allowed : 26.18 % Favored : 68.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -4.35 (0.16), residues: 1736 helix: -0.99 (0.29), residues: 312 sheet: -1.78 (0.28), residues: 344 loop : -4.14 (0.12), residues: 1080 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG H 129 TYR 0.008 0.001 TYR C 99 PHE 0.019 0.001 PHE A 82 TRP 0.014 0.001 TRP H 235 HIS 0.002 0.001 HIS B 118 Details of bonding type rmsd covalent geometry : bond 0.00228 (14720) covalent geometry : angle 0.56999 (19920) SS BOND : bond 0.00135 ( 16) SS BOND : angle 0.58735 ( 32) hydrogen bonds : bond 0.03210 ( 320) hydrogen bonds : angle 5.44333 ( 888) link_NAG-ASN : bond 0.00561 ( 16) link_NAG-ASN : angle 2.18601 ( 48) *********************** 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 269 residues out of total 1440 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 196 time to evaluate : 0.552 Fit side-chains REVERT: A 72 MET cc_start: 0.6629 (OUTLIER) cc_final: 0.6135 (mmt) REVERT: A 159 ASP cc_start: 0.6739 (OUTLIER) cc_final: 0.5969 (m-30) REVERT: A 197 GLN cc_start: 0.7878 (OUTLIER) cc_final: 0.7523 (mp10) REVERT: D 72 MET cc_start: 0.7375 (mmt) cc_final: 0.7053 (mmt) REVERT: B 72 MET cc_start: 0.6628 (OUTLIER) cc_final: 0.6136 (mmt) REVERT: B 159 ASP cc_start: 0.6704 (OUTLIER) cc_final: 0.5958 (m-30) REVERT: B 197 GLN cc_start: 0.7882 (OUTLIER) cc_final: 0.7520 (mp10) REVERT: E 72 MET cc_start: 0.7354 (mmt) cc_final: 0.7045 (mmt) REVERT: C 72 MET cc_start: 0.6637 (OUTLIER) cc_final: 0.6152 (mmt) REVERT: C 159 ASP cc_start: 0.6738 (OUTLIER) cc_final: 0.5968 (m-30) REVERT: C 197 GLN cc_start: 0.7895 (OUTLIER) cc_final: 0.7533 (mp10) REVERT: F 72 MET cc_start: 0.7369 (mmt) cc_final: 0.7047 (mmt) REVERT: G 72 MET cc_start: 0.6624 (OUTLIER) cc_final: 0.6139 (mmt) REVERT: G 159 ASP cc_start: 0.6712 (OUTLIER) cc_final: 0.5959 (m-30) REVERT: G 197 GLN cc_start: 0.7906 (OUTLIER) cc_final: 0.7543 (mp10) REVERT: H 72 MET cc_start: 0.7378 (mmt) cc_final: 0.7051 (mmt) outliers start: 73 outliers final: 56 residues processed: 253 average time/residue: 0.1583 time to fit residues: 54.9634 Evaluate side-chains 252 residues out of total 1440 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 184 time to evaluate : 0.698 ------------------------------------------------------------------------------- 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 187 THR Chi-restraints excluded: chain A residue 194 LEU Chi-restraints excluded: chain A residue 197 GLN Chi-restraints excluded: chain A residue 199 CYS Chi-restraints excluded: chain A residue 248 THR Chi-restraints excluded: chain D residue 49 TYR Chi-restraints excluded: chain D residue 68 VAL Chi-restraints excluded: chain D residue 89 SER Chi-restraints excluded: chain D residue 139 THR Chi-restraints excluded: chain D residue 165 VAL Chi-restraints excluded: chain D residue 248 THR 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 159 ASP Chi-restraints excluded: chain B residue 165 VAL Chi-restraints excluded: chain B residue 187 THR Chi-restraints excluded: chain B residue 194 LEU Chi-restraints excluded: chain B residue 197 GLN Chi-restraints excluded: chain B residue 199 CYS Chi-restraints excluded: chain B residue 248 THR Chi-restraints excluded: chain E residue 49 TYR Chi-restraints excluded: chain E residue 68 VAL Chi-restraints excluded: chain E residue 89 SER Chi-restraints excluded: chain E residue 139 THR Chi-restraints excluded: chain E residue 165 VAL Chi-restraints excluded: chain E residue 248 THR 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 187 THR Chi-restraints excluded: chain C residue 194 LEU Chi-restraints excluded: chain C residue 197 GLN Chi-restraints excluded: chain C residue 199 CYS Chi-restraints excluded: chain C residue 248 THR Chi-restraints excluded: chain F residue 49 TYR Chi-restraints excluded: chain F residue 68 VAL Chi-restraints excluded: chain F residue 89 SER Chi-restraints excluded: chain F residue 139 THR Chi-restraints excluded: chain F residue 165 VAL Chi-restraints excluded: chain F residue 248 THR 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 187 THR Chi-restraints excluded: chain G residue 194 LEU Chi-restraints excluded: chain G residue 197 GLN Chi-restraints excluded: chain G residue 199 CYS Chi-restraints excluded: chain G residue 248 THR Chi-restraints excluded: chain H residue 49 TYR Chi-restraints excluded: chain H residue 68 VAL Chi-restraints excluded: chain H residue 89 SER Chi-restraints excluded: chain H residue 139 THR Chi-restraints excluded: chain H residue 165 VAL 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 64 optimal weight: 8.9990 chunk 152 optimal weight: 5.9990 chunk 81 optimal weight: 10.0000 chunk 82 optimal weight: 0.9980 chunk 108 optimal weight: 0.9980 chunk 3 optimal weight: 0.9990 chunk 159 optimal weight: 4.9990 chunk 48 optimal weight: 4.9990 chunk 78 optimal weight: 3.9990 chunk 31 optimal weight: 2.9990 chunk 110 optimal weight: 0.9990 overall best weight: 1.3986 ------------------------------------------------------------------------------- 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 = 0.3787 r_free = 0.3787 target = 0.159777 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3546 r_free = 0.3546 target = 0.139989 restraints weight = 17880.139| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3565 r_free = 0.3565 target = 0.141632 restraints weight = 14516.654| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3578 r_free = 0.3578 target = 0.142690 restraints weight = 12494.231| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.3591 r_free = 0.3591 target = 0.143695 restraints weight = 11256.559| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.3596 r_free = 0.3596 target = 0.144077 restraints weight = 10402.873| |-----------------------------------------------------------------------------| r_work (final): 0.3601 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8071 moved from start: 0.1592 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.019 14752 Z= 0.121 Angle : 0.577 7.835 20000 Z= 0.304 Chirality : 0.045 0.226 1976 Planarity : 0.003 0.027 2592 Dihedral : 6.382 45.390 2304 Min Nonbonded Distance : 2.293 Molprobity Statistics. All-atom Clashscore : 4.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 15.38 % Favored : 84.62 % Rotamer: Outliers : 5.00 % Allowed : 26.25 % Favored : 68.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -4.27 (0.16), residues: 1736 helix: -0.88 (0.29), residues: 312 sheet: -1.72 (0.28), residues: 344 loop : -4.12 (0.12), residues: 1080 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG F 129 TYR 0.009 0.001 TYR B 99 PHE 0.021 0.001 PHE A 82 TRP 0.013 0.001 TRP H 235 HIS 0.002 0.001 HIS G 118 Details of bonding type rmsd covalent geometry : bond 0.00270 (14720) covalent geometry : angle 0.56799 (19920) SS BOND : bond 0.00154 ( 16) SS BOND : angle 0.46751 ( 32) hydrogen bonds : bond 0.03408 ( 320) hydrogen bonds : angle 5.44560 ( 888) link_NAG-ASN : bond 0.00553 ( 16) link_NAG-ASN : angle 2.13678 ( 48) *********************** 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 256 residues out of total 1440 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 184 time to evaluate : 0.581 Fit side-chains REVERT: A 72 MET cc_start: 0.6571 (OUTLIER) cc_final: 0.6150 (mmt) REVERT: A 159 ASP cc_start: 0.6708 (OUTLIER) cc_final: 0.5941 (m-30) REVERT: A 197 GLN cc_start: 0.7879 (OUTLIER) cc_final: 0.7550 (mp10) REVERT: D 72 MET cc_start: 0.7383 (mmt) cc_final: 0.7053 (mmt) REVERT: B 72 MET cc_start: 0.6568 (OUTLIER) cc_final: 0.6149 (mmt) REVERT: B 159 ASP cc_start: 0.6679 (OUTLIER) cc_final: 0.5936 (m-30) REVERT: B 197 GLN cc_start: 0.7882 (OUTLIER) cc_final: 0.7551 (mp10) REVERT: E 72 MET cc_start: 0.7367 (mmt) cc_final: 0.7045 (mmt) REVERT: C 72 MET cc_start: 0.6566 (OUTLIER) cc_final: 0.6156 (mmt) REVERT: C 159 ASP cc_start: 0.6714 (OUTLIER) cc_final: 0.5947 (m-30) REVERT: C 197 GLN cc_start: 0.7873 (OUTLIER) cc_final: 0.7541 (mp10) REVERT: F 72 MET cc_start: 0.7377 (mmt) cc_final: 0.7049 (mmt) REVERT: G 72 MET cc_start: 0.6560 (OUTLIER) cc_final: 0.6146 (mmt) REVERT: G 159 ASP cc_start: 0.6684 (OUTLIER) cc_final: 0.5937 (m-30) REVERT: G 197 GLN cc_start: 0.7876 (OUTLIER) cc_final: 0.7546 (mp10) REVERT: H 72 MET cc_start: 0.7387 (mmt) cc_final: 0.7052 (mmt) outliers start: 72 outliers final: 56 residues processed: 247 average time/residue: 0.1530 time to fit residues: 52.3632 Evaluate side-chains 252 residues out of total 1440 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 184 time to evaluate : 0.562 ------------------------------------------------------------------------------- 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 187 THR Chi-restraints excluded: chain A residue 194 LEU Chi-restraints excluded: chain A residue 197 GLN Chi-restraints excluded: chain A residue 199 CYS Chi-restraints excluded: chain A residue 248 THR Chi-restraints excluded: chain D residue 49 TYR Chi-restraints excluded: chain D residue 68 VAL Chi-restraints excluded: chain D residue 89 SER Chi-restraints excluded: chain D residue 105 ARG Chi-restraints excluded: chain D residue 165 VAL Chi-restraints excluded: chain D residue 248 THR 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 159 ASP Chi-restraints excluded: chain B residue 165 VAL Chi-restraints excluded: chain B residue 187 THR Chi-restraints excluded: chain B residue 194 LEU Chi-restraints excluded: chain B residue 197 GLN Chi-restraints excluded: chain B residue 199 CYS Chi-restraints excluded: chain B residue 248 THR Chi-restraints excluded: chain E residue 49 TYR Chi-restraints excluded: chain E residue 68 VAL Chi-restraints excluded: chain E residue 89 SER Chi-restraints excluded: chain E residue 105 ARG Chi-restraints excluded: chain E residue 165 VAL Chi-restraints excluded: chain E residue 248 THR 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 187 THR Chi-restraints excluded: chain C residue 194 LEU Chi-restraints excluded: chain C residue 197 GLN Chi-restraints excluded: chain C residue 199 CYS Chi-restraints excluded: chain C residue 248 THR Chi-restraints excluded: chain F residue 49 TYR Chi-restraints excluded: chain F residue 68 VAL Chi-restraints excluded: chain F residue 89 SER Chi-restraints excluded: chain F residue 105 ARG Chi-restraints excluded: chain F residue 165 VAL Chi-restraints excluded: chain F residue 248 THR 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 187 THR Chi-restraints excluded: chain G residue 194 LEU Chi-restraints excluded: chain G residue 197 GLN Chi-restraints excluded: chain G residue 199 CYS Chi-restraints excluded: chain G residue 248 THR Chi-restraints excluded: chain H residue 49 TYR Chi-restraints excluded: chain H residue 68 VAL Chi-restraints excluded: chain H residue 89 SER Chi-restraints excluded: chain H residue 105 ARG Chi-restraints excluded: chain H residue 165 VAL 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 53 optimal weight: 5.9990 chunk 114 optimal weight: 8.9990 chunk 106 optimal weight: 7.9990 chunk 83 optimal weight: 5.9990 chunk 141 optimal weight: 6.9990 chunk 138 optimal weight: 4.9990 chunk 127 optimal weight: 4.9990 chunk 160 optimal weight: 9.9990 chunk 71 optimal weight: 6.9990 chunk 166 optimal weight: 7.9990 chunk 148 optimal weight: 7.9990 overall best weight: 5.7990 ------------------------------------------------------------------------------- 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** E 198 ASN ** C 216 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 198 ASN H 198 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3708 r_free = 0.3708 target = 0.152478 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3449 r_free = 0.3449 target = 0.131816 restraints weight = 18359.932| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3469 r_free = 0.3469 target = 0.133480 restraints weight = 14939.823| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3482 r_free = 0.3482 target = 0.134535 restraints weight = 12858.671| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3495 r_free = 0.3495 target = 0.135639 restraints weight = 11603.134| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.3505 r_free = 0.3505 target = 0.136275 restraints weight = 10583.318| |-----------------------------------------------------------------------------| r_work (final): 0.3509 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8176 moved from start: 0.1829 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.046 14752 Z= 0.383 Angle : 0.838 8.062 20000 Z= 0.445 Chirality : 0.056 0.216 1976 Planarity : 0.007 0.088 2592 Dihedral : 8.390 52.157 2304 Min Nonbonded Distance : 2.239 Molprobity Statistics. All-atom Clashscore : 5.69 Ramachandran Plot: Outliers : 0.69 % Allowed : 17.28 % Favored : 82.03 % Rotamer: Outliers : 5.28 % Allowed : 26.25 % Favored : 68.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -4.70 (0.16), residues: 1736 helix: -1.48 (0.28), residues: 312 sheet: -2.03 (0.27), residues: 344 loop : -4.30 (0.12), residues: 1080 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG D 94 TYR 0.026 0.003 TYR E 110 PHE 0.033 0.002 PHE D 82 TRP 0.018 0.002 TRP H 235 HIS 0.007 0.002 HIS D 180 Details of bonding type rmsd covalent geometry : bond 0.00912 (14720) covalent geometry : angle 0.82965 (19920) SS BOND : bond 0.00520 ( 16) SS BOND : angle 0.85983 ( 32) hydrogen bonds : bond 0.05784 ( 320) hydrogen bonds : angle 6.13868 ( 888) link_NAG-ASN : bond 0.00690 ( 16) link_NAG-ASN : angle 2.48472 ( 48) ********************** 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 277 residues out of total 1440 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 201 time to evaluate : 0.550 Fit side-chains REVERT: A 159 ASP cc_start: 0.6639 (OUTLIER) cc_final: 0.5768 (m-30) REVERT: A 197 GLN cc_start: 0.7938 (OUTLIER) cc_final: 0.7465 (mp10) REVERT: D 72 MET cc_start: 0.7491 (mmt) cc_final: 0.7255 (mmt) REVERT: D 210 ARG cc_start: 0.7619 (tpt-90) cc_final: 0.7410 (tpt-90) REVERT: D 247 ARG cc_start: 0.7954 (OUTLIER) cc_final: 0.7602 (mtm180) REVERT: B 159 ASP cc_start: 0.6619 (OUTLIER) cc_final: 0.5772 (m-30) REVERT: B 197 GLN cc_start: 0.7938 (OUTLIER) cc_final: 0.7467 (mp10) REVERT: E 72 MET cc_start: 0.7488 (mmt) cc_final: 0.7254 (mmt) REVERT: E 247 ARG cc_start: 0.7958 (OUTLIER) cc_final: 0.7603 (mtm180) REVERT: C 159 ASP cc_start: 0.6635 (OUTLIER) cc_final: 0.5762 (m-30) REVERT: C 197 GLN cc_start: 0.7932 (OUTLIER) cc_final: 0.7464 (mp10) REVERT: F 72 MET cc_start: 0.7486 (mmt) cc_final: 0.7249 (mmt) REVERT: F 247 ARG cc_start: 0.7925 (OUTLIER) cc_final: 0.7575 (mtm180) REVERT: G 159 ASP cc_start: 0.6624 (OUTLIER) cc_final: 0.5772 (m-30) REVERT: G 197 GLN cc_start: 0.7931 (OUTLIER) cc_final: 0.7465 (mp10) REVERT: H 72 MET cc_start: 0.7486 (mmt) cc_final: 0.7250 (mmt) REVERT: H 247 ARG cc_start: 0.7929 (OUTLIER) cc_final: 0.7580 (mtm180) outliers start: 76 outliers final: 61 residues processed: 258 average time/residue: 0.1549 time to fit residues: 55.0645 Evaluate side-chains 270 residues out of total 1440 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 197 time to evaluate : 0.608 ------------------------------------------------------------------------------- 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 248 THR Chi-restraints excluded: chain D residue 49 TYR Chi-restraints excluded: chain D residue 68 VAL Chi-restraints excluded: chain D residue 89 SER Chi-restraints excluded: chain D residue 105 ARG 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 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 248 THR Chi-restraints excluded: chain E residue 49 TYR Chi-restraints excluded: chain E residue 68 VAL Chi-restraints excluded: chain E residue 89 SER Chi-restraints excluded: chain E residue 105 ARG Chi-restraints excluded: chain E residue 165 VAL Chi-restraints excluded: chain E residue 177 LEU Chi-restraints excluded: chain E residue 198 ASN 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 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 248 THR Chi-restraints excluded: chain F residue 49 TYR Chi-restraints excluded: chain F residue 68 VAL Chi-restraints excluded: chain F residue 89 SER Chi-restraints excluded: chain F residue 105 ARG 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 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 248 THR Chi-restraints excluded: chain H residue 49 TYR Chi-restraints excluded: chain H residue 68 VAL Chi-restraints excluded: chain H residue 89 SER Chi-restraints excluded: chain H residue 105 ARG 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 84 optimal weight: 10.0000 chunk 134 optimal weight: 0.9980 chunk 164 optimal weight: 4.9990 chunk 75 optimal weight: 0.8980 chunk 5 optimal weight: 2.9990 chunk 73 optimal weight: 4.9990 chunk 2 optimal weight: 0.9980 chunk 86 optimal weight: 1.9990 chunk 82 optimal weight: 1.9990 chunk 22 optimal weight: 3.9990 chunk 7 optimal weight: 0.9990 overall best weight: 1.1784 ------------------------------------------------------------------------------- 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 = 0.3784 r_free = 0.3784 target = 0.159425 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3541 r_free = 0.3541 target = 0.139563 restraints weight = 17923.485| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3561 r_free = 0.3561 target = 0.141231 restraints weight = 14462.072| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3576 r_free = 0.3576 target = 0.142497 restraints weight = 12426.949| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3585 r_free = 0.3585 target = 0.143239 restraints weight = 11105.621| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 41)----------------| | r_work = 0.3595 r_free = 0.3595 target = 0.144017 restraints weight = 10291.939| |-----------------------------------------------------------------------------| r_work (final): 0.3600 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8074 moved from start: 0.1631 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 14752 Z= 0.118 Angle : 0.600 9.555 20000 Z= 0.314 Chirality : 0.045 0.234 1976 Planarity : 0.003 0.026 2592 Dihedral : 6.846 48.100 2304 Min Nonbonded Distance : 2.305 Molprobity Statistics. All-atom Clashscore : 4.78 Ramachandran Plot: Outliers : 0.46 % Allowed : 14.52 % Favored : 85.02 % Rotamer: Outliers : 3.68 % Allowed : 27.57 % Favored : 68.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -4.42 (0.16), residues: 1736 helix: -1.10 (0.28), residues: 312 sheet: -1.92 (0.28), residues: 344 loop : -4.14 (0.13), residues: 1080 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG H 129 TYR 0.009 0.001 TYR G 99 PHE 0.020 0.001 PHE C 82 TRP 0.015 0.001 TRP D 235 HIS 0.003 0.001 HIS G 213 Details of bonding type rmsd covalent geometry : bond 0.00259 (14720) covalent geometry : angle 0.59029 (19920) SS BOND : bond 0.00158 ( 16) SS BOND : angle 1.04572 ( 32) hydrogen bonds : bond 0.03452 ( 320) hydrogen bonds : angle 5.48277 ( 888) link_NAG-ASN : bond 0.00603 ( 16) link_NAG-ASN : angle 2.12875 ( 48) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2249.88 seconds wall clock time: 39 minutes 39.79 seconds (2379.79 seconds total)