Starting phenix.real_space_refine on Wed Mar 4 10:55:59 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7vly_32031/03_2026/7vly_32031.cif Found real_map, /net/cci-nas-00/data/ceres_data/7vly_32031/03_2026/7vly_32031.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.45 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7vly_32031/03_2026/7vly_32031.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7vly_32031/03_2026/7vly_32031.map" model { file = "/net/cci-nas-00/data/ceres_data/7vly_32031/03_2026/7vly_32031.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7vly_32031/03_2026/7vly_32031.cif" } resolution = 2.45 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= 0.003 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 87 5.16 5 C 8706 2.51 5 N 2217 2.21 5 O 2337 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 36 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 13347 Number of models: 1 Model: "" Number of chains: 18 Chain: "Y" Number of atoms: 1773 Number of conformers: 1 Conformer: "" Number of residues, atoms: 247, 1773 Classifications: {'peptide': 247} Link IDs: {'PTRANS': 9, 'TRANS': 237} Chain: "Z" Number of atoms: 2307 Number of conformers: 1 Conformer: "" Number of residues, atoms: 297, 2307 Classifications: {'peptide': 297} Link IDs: {'PTRANS': 11, 'TRANS': 285} Chain: "A" Number of atoms: 347 Number of conformers: 1 Conformer: "" Number of residues, atoms: 47, 347 Classifications: {'peptide': 47} Modifications used: {'COO': 1} Link IDs: {'TRANS': 46} Chain: "C" Number of atoms: 1773 Number of conformers: 1 Conformer: "" Number of residues, atoms: 247, 1773 Classifications: {'peptide': 247} Link IDs: {'PTRANS': 9, 'TRANS': 237} Chain: "D" Number of atoms: 2307 Number of conformers: 1 Conformer: "" Number of residues, atoms: 297, 2307 Classifications: {'peptide': 297} Link IDs: {'PTRANS': 11, 'TRANS': 285} Chain: "E" Number of atoms: 347 Number of conformers: 1 Conformer: "" Number of residues, atoms: 47, 347 Classifications: {'peptide': 47} Modifications used: {'COO': 1} Link IDs: {'TRANS': 46} Chain: "F" Number of atoms: 1773 Number of conformers: 1 Conformer: "" Number of residues, atoms: 247, 1773 Classifications: {'peptide': 247} Link IDs: {'PTRANS': 9, 'TRANS': 237} Chain: "G" Number of atoms: 2307 Number of conformers: 1 Conformer: "" Number of residues, atoms: 297, 2307 Classifications: {'peptide': 297} Link IDs: {'PTRANS': 11, 'TRANS': 285} Chain: "H" Number of atoms: 347 Number of conformers: 1 Conformer: "" Number of residues, atoms: 47, 347 Classifications: {'peptide': 47} Modifications used: {'COO': 1} Link IDs: {'TRANS': 46} Chain: "Z" Number of atoms: 12 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 12 Unusual residues: {'MAN': 1} Classifications: {'undetermined': 1} Chain: "D" Number of atoms: 12 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 12 Unusual residues: {'MAN': 1} Classifications: {'undetermined': 1} Chain: "G" Number of atoms: 12 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 12 Unusual residues: {'MAN': 1} Classifications: {'undetermined': 1} Chain: "Y" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} Chain: "A" Number of atoms: 8 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 8 Classifications: {'water': 8} Link IDs: {None: 7} Chain: "C" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} Chain: "E" Number of atoms: 8 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 8 Classifications: {'water': 8} Link IDs: {None: 7} Chain: "F" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} Chain: "H" Number of atoms: 8 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 8 Classifications: {'water': 8} Link IDs: {None: 7} Time building chain proxies: 3.04, per 1000 atoms: 0.23 Number of scatterers: 13347 At special positions: 0 Unit cell: (128.182, 120.592, 105.412, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 87 16.00 O 2337 8.00 N 2217 7.00 C 8706 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=6, symmetry=0 Simple disulfide: pdb=" SG CYS A 9 " - pdb=" SG CYS A 14 " distance=2.03 Simple disulfide: pdb=" SG CYS A 24 " - pdb=" SG CYS A 44 " distance=2.03 Simple disulfide: pdb=" SG CYS E 9 " - pdb=" SG CYS E 14 " distance=2.03 Simple disulfide: pdb=" SG CYS E 24 " - pdb=" SG CYS E 44 " distance=2.03 Simple disulfide: pdb=" SG CYS H 9 " - pdb=" SG CYS H 14 " distance=2.03 Simple disulfide: pdb=" SG CYS H 24 " - pdb=" SG CYS H 44 " 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 Time building additional restraints: 1.20 Conformation dependent library (CDL) restraints added in 645.6 milliseconds 3510 Ramachandran restraints generated. 1755 Oldfield, 0 Emsley, 1755 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3162 Finding SS restraints... Secondary structure from input PDB file: 82 helices and 3 sheets defined 74.9% alpha, 0.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.37 Creating SS restraints... Processing helix chain 'Y' and resid 2 through 23 removed outlier: 3.861A pdb=" N ILE Y 21 " --> pdb=" O GLY Y 17 " (cutoff:3.500A) Processing helix chain 'Y' and resid 29 through 40 removed outlier: 4.420A pdb=" N THR Y 35 " --> pdb=" O LEU Y 31 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N VAL Y 40 " --> pdb=" O LEU Y 36 " (cutoff:3.500A) Processing helix chain 'Y' and resid 43 through 58 Processing helix chain 'Y' and resid 71 through 85 removed outlier: 4.090A pdb=" N ALA Y 75 " --> pdb=" O ASP Y 71 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N ALA Y 80 " --> pdb=" O SER Y 76 " (cutoff:3.500A) Processing helix chain 'Y' and resid 92 through 131 removed outlier: 3.859A pdb=" N ILE Y 101 " --> pdb=" O ILE Y 97 " (cutoff:3.500A) Proline residue: Y 102 - end of helix removed outlier: 4.179A pdb=" N VAL Y 119 " --> pdb=" O ARG Y 115 " (cutoff:3.500A) Proline residue: Y 120 - end of helix Processing helix chain 'Y' and resid 133 through 161 removed outlier: 4.127A pdb=" N VAL Y 137 " --> pdb=" O ASN Y 133 " (cutoff:3.500A) removed outlier: 4.001A pdb=" N GLU Y 138 " --> pdb=" O ILE Y 134 " (cutoff:3.500A) removed outlier: 3.856A pdb=" N ILE Y 152 " --> pdb=" O GLN Y 148 " (cutoff:3.500A) Proline residue: Y 155 - end of helix removed outlier: 3.952A pdb=" N PHE Y 161 " --> pdb=" O ALA Y 157 " (cutoff:3.500A) Processing helix chain 'Y' and resid 166 through 173 Processing helix chain 'Y' and resid 175 through 187 removed outlier: 3.624A pdb=" N GLY Y 187 " --> pdb=" O ALA Y 183 " (cutoff:3.500A) Processing helix chain 'Y' and resid 188 through 201 removed outlier: 4.138A pdb=" N VAL Y 192 " --> pdb=" O MET Y 188 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N GLY Y 193 " --> pdb=" O VAL Y 189 " (cutoff:3.500A) removed outlier: 3.870A pdb=" N VAL Y 197 " --> pdb=" O GLY Y 193 " (cutoff:3.500A) Processing helix chain 'Y' and resid 206 through 217 Processing helix chain 'Y' and resid 223 through 246 removed outlier: 3.622A pdb=" N MET Y 244 " --> pdb=" O ASN Y 240 " (cutoff:3.500A) removed outlier: 4.312A pdb=" N GLY Y 245 " --> pdb=" O LEU Y 241 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N GLY Y 246 " --> pdb=" O SER Y 242 " (cutoff:3.500A) Processing helix chain 'Z' and resid 8 through 19 Processing helix chain 'Z' and resid 20 through 22 No H-bonds generated for 'chain 'Z' and resid 20 through 22' Processing helix chain 'Z' and resid 32 through 40 Processing helix chain 'Z' and resid 40 through 48 Processing helix chain 'Z' and resid 52 through 62 Processing helix chain 'Z' and resid 68 through 70 No H-bonds generated for 'chain 'Z' and resid 68 through 70' Processing helix chain 'Z' and resid 71 through 89 removed outlier: 4.473A pdb=" N ILE Z 75 " --> pdb=" O ILE Z 71 " (cutoff:3.500A) removed outlier: 3.873A pdb=" N GLU Z 85 " --> pdb=" O ALA Z 81 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N ARG Z 86 " --> pdb=" O LEU Z 82 " (cutoff:3.500A) Processing helix chain 'Z' and resid 96 through 117 removed outlier: 4.079A pdb=" N LYS Z 101 " --> pdb=" O ILE Z 97 " (cutoff:3.500A) removed outlier: 4.100A pdb=" N VAL Z 102 " --> pdb=" O GLN Z 98 " (cutoff:3.500A) removed outlier: 4.378A pdb=" N GLY Z 106 " --> pdb=" O VAL Z 102 " (cutoff:3.500A) Proline residue: Z 107 - end of helix Proline residue: Z 114 - end of helix Processing helix chain 'Z' and resid 119 through 133 removed outlier: 3.859A pdb=" N MET Z 123 " --> pdb=" O THR Z 119 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N LEU Z 131 " --> pdb=" O LEU Z 127 " (cutoff:3.500A) Processing helix chain 'Z' and resid 137 through 165 Processing helix chain 'Z' and resid 165 through 171 removed outlier: 3.564A pdb=" N ILE Z 169 " --> pdb=" O ALA Z 165 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N THR Z 170 " --> pdb=" O GLY Z 166 " (cutoff:3.500A) removed outlier: 3.948A pdb=" N ASP Z 171 " --> pdb=" O SER Z 167 " (cutoff:3.500A) No H-bonds generated for 'chain 'Z' and resid 165 through 171' Processing helix chain 'Z' and resid 175 through 201 removed outlier: 3.666A pdb=" N VAL Z 201 " --> pdb=" O VAL Z 197 " (cutoff:3.500A) Processing helix chain 'Z' and resid 230 through 241 Processing helix chain 'Z' and resid 253 through 261 removed outlier: 3.570A pdb=" N LEU Z 260 " --> pdb=" O ASN Z 256 " (cutoff:3.500A) Processing helix chain 'Z' and resid 263 through 279 Processing helix chain 'Z' and resid 282 through 300 Processing helix chain 'A' and resid 17 through 36 Processing helix chain 'C' and resid 2 through 23 removed outlier: 3.954A pdb=" N ILE C 21 " --> pdb=" O GLY C 17 " (cutoff:3.500A) Processing helix chain 'C' and resid 29 through 40 removed outlier: 4.421A pdb=" N THR C 35 " --> pdb=" O LEU C 31 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N VAL C 40 " --> pdb=" O LEU C 36 " (cutoff:3.500A) Processing helix chain 'C' and resid 43 through 58 Processing helix chain 'C' and resid 71 through 85 removed outlier: 4.069A pdb=" N ALA C 75 " --> pdb=" O ASP C 71 " (cutoff:3.500A) Processing helix chain 'C' and resid 92 through 130 removed outlier: 3.882A pdb=" N ILE C 101 " --> pdb=" O ILE C 97 " (cutoff:3.500A) Proline residue: C 102 - end of helix removed outlier: 4.091A pdb=" N VAL C 119 " --> pdb=" O ARG C 115 " (cutoff:3.500A) Proline residue: C 120 - end of helix Processing helix chain 'C' and resid 133 through 161 removed outlier: 4.174A pdb=" N VAL C 137 " --> pdb=" O ASN C 133 " (cutoff:3.500A) removed outlier: 3.951A pdb=" N GLU C 138 " --> pdb=" O ILE C 134 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N ILE C 152 " --> pdb=" O GLN C 148 " (cutoff:3.500A) Proline residue: C 155 - end of helix removed outlier: 3.948A pdb=" N PHE C 161 " --> pdb=" O ALA C 157 " (cutoff:3.500A) Processing helix chain 'C' and resid 166 through 173 Processing helix chain 'C' and resid 175 through 187 removed outlier: 3.663A pdb=" N GLY C 187 " --> pdb=" O ALA C 183 " (cutoff:3.500A) Processing helix chain 'C' and resid 188 through 201 removed outlier: 4.100A pdb=" N VAL C 192 " --> pdb=" O MET C 188 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N GLY C 193 " --> pdb=" O VAL C 189 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N VAL C 197 " --> pdb=" O GLY C 193 " (cutoff:3.500A) Processing helix chain 'C' and resid 206 through 217 Processing helix chain 'C' and resid 223 through 243 removed outlier: 3.512A pdb=" N LYS C 243 " --> pdb=" O LEU C 239 " (cutoff:3.500A) Processing helix chain 'D' and resid 8 through 19 Processing helix chain 'D' and resid 20 through 22 No H-bonds generated for 'chain 'D' and resid 20 through 22' Processing helix chain 'D' and resid 32 through 40 Processing helix chain 'D' and resid 40 through 48 Processing helix chain 'D' and resid 52 through 62 Processing helix chain 'D' and resid 71 through 89 removed outlier: 4.519A pdb=" N ILE D 75 " --> pdb=" O ILE D 71 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N GLU D 85 " --> pdb=" O ALA D 81 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N ARG D 86 " --> pdb=" O LEU D 82 " (cutoff:3.500A) Processing helix chain 'D' and resid 96 through 117 removed outlier: 4.098A pdb=" N LYS D 101 " --> pdb=" O ILE D 97 " (cutoff:3.500A) removed outlier: 4.314A pdb=" N GLY D 106 " --> pdb=" O VAL D 102 " (cutoff:3.500A) Proline residue: D 107 - end of helix Proline residue: D 114 - end of helix Processing helix chain 'D' and resid 119 through 133 removed outlier: 3.717A pdb=" N MET D 123 " --> pdb=" O THR D 119 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N LEU D 131 " --> pdb=" O LEU D 127 " (cutoff:3.500A) Processing helix chain 'D' and resid 137 through 165 Processing helix chain 'D' and resid 165 through 171 removed outlier: 3.667A pdb=" N ILE D 169 " --> pdb=" O ALA D 165 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N THR D 170 " --> pdb=" O GLY D 166 " (cutoff:3.500A) removed outlier: 3.919A pdb=" N ASP D 171 " --> pdb=" O SER D 167 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 165 through 171' Processing helix chain 'D' and resid 175 through 201 removed outlier: 3.644A pdb=" N VAL D 201 " --> pdb=" O VAL D 197 " (cutoff:3.500A) Processing helix chain 'D' and resid 230 through 241 Processing helix chain 'D' and resid 253 through 261 removed outlier: 3.556A pdb=" N LEU D 260 " --> pdb=" O ASN D 256 " (cutoff:3.500A) Processing helix chain 'D' and resid 263 through 279 Processing helix chain 'D' and resid 282 through 300 Processing helix chain 'E' and resid 17 through 36 Processing helix chain 'F' and resid 2 through 23 removed outlier: 3.940A pdb=" N ILE F 21 " --> pdb=" O GLY F 17 " (cutoff:3.500A) Processing helix chain 'F' and resid 29 through 40 removed outlier: 4.408A pdb=" N THR F 35 " --> pdb=" O LEU F 31 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N VAL F 40 " --> pdb=" O LEU F 36 " (cutoff:3.500A) Processing helix chain 'F' and resid 43 through 58 Processing helix chain 'F' and resid 71 through 85 removed outlier: 4.071A pdb=" N ALA F 75 " --> pdb=" O ASP F 71 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N ALA F 80 " --> pdb=" O SER F 76 " (cutoff:3.500A) Processing helix chain 'F' and resid 92 through 130 removed outlier: 3.873A pdb=" N ILE F 101 " --> pdb=" O ILE F 97 " (cutoff:3.500A) Proline residue: F 102 - end of helix removed outlier: 4.128A pdb=" N VAL F 119 " --> pdb=" O ARG F 115 " (cutoff:3.500A) Proline residue: F 120 - end of helix Processing helix chain 'F' and resid 133 through 161 removed outlier: 4.146A pdb=" N VAL F 137 " --> pdb=" O ASN F 133 " (cutoff:3.500A) removed outlier: 3.975A pdb=" N GLU F 138 " --> pdb=" O ILE F 134 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N ILE F 152 " --> pdb=" O GLN F 148 " (cutoff:3.500A) Proline residue: F 155 - end of helix removed outlier: 3.932A pdb=" N PHE F 161 " --> pdb=" O ALA F 157 " (cutoff:3.500A) Processing helix chain 'F' and resid 166 through 173 Processing helix chain 'F' and resid 175 through 187 removed outlier: 3.651A pdb=" N GLY F 187 " --> pdb=" O ALA F 183 " (cutoff:3.500A) Processing helix chain 'F' and resid 188 through 201 removed outlier: 4.134A pdb=" N VAL F 192 " --> pdb=" O MET F 188 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N GLY F 193 " --> pdb=" O VAL F 189 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N VAL F 197 " --> pdb=" O GLY F 193 " (cutoff:3.500A) Processing helix chain 'F' and resid 206 through 217 Processing helix chain 'F' and resid 223 through 243 Processing helix chain 'G' and resid 8 through 19 Processing helix chain 'G' and resid 20 through 22 No H-bonds generated for 'chain 'G' and resid 20 through 22' Processing helix chain 'G' and resid 32 through 40 Processing helix chain 'G' and resid 40 through 48 Processing helix chain 'G' and resid 52 through 62 Processing helix chain 'G' and resid 71 through 89 removed outlier: 4.511A pdb=" N ILE G 75 " --> pdb=" O ILE G 71 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N GLU G 85 " --> pdb=" O ALA G 81 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N ARG G 86 " --> pdb=" O LEU G 82 " (cutoff:3.500A) Processing helix chain 'G' and resid 98 through 117 removed outlier: 3.504A pdb=" N VAL G 102 " --> pdb=" O GLN G 98 " (cutoff:3.500A) removed outlier: 4.131A pdb=" N GLY G 106 " --> pdb=" O VAL G 102 " (cutoff:3.500A) Proline residue: G 107 - end of helix Proline residue: G 114 - end of helix Processing helix chain 'G' and resid 119 through 133 removed outlier: 3.918A pdb=" N MET G 123 " --> pdb=" O THR G 119 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N LEU G 131 " --> pdb=" O LEU G 127 " (cutoff:3.500A) Processing helix chain 'G' and resid 137 through 165 Processing helix chain 'G' and resid 165 through 171 removed outlier: 3.658A pdb=" N ILE G 169 " --> pdb=" O ALA G 165 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N THR G 170 " --> pdb=" O GLY G 166 " (cutoff:3.500A) removed outlier: 3.944A pdb=" N ASP G 171 " --> pdb=" O SER G 167 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 165 through 171' Processing helix chain 'G' and resid 175 through 201 removed outlier: 3.636A pdb=" N VAL G 201 " --> pdb=" O VAL G 197 " (cutoff:3.500A) Processing helix chain 'G' and resid 230 through 241 Processing helix chain 'G' and resid 253 through 261 removed outlier: 3.615A pdb=" N LEU G 260 " --> pdb=" O ASN G 256 " (cutoff:3.500A) Processing helix chain 'G' and resid 263 through 279 Processing helix chain 'G' and resid 282 through 300 Processing helix chain 'H' and resid 17 through 36 Processing sheet with id=AA1, first strand: chain 'Z' and resid 208 through 210 Processing sheet with id=AA2, first strand: chain 'D' and resid 208 through 210 Processing sheet with id=AA3, first strand: chain 'G' and resid 208 through 210 880 hydrogen bonds defined for protein. 2631 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: 2.15 Time building geometry restraints manager: 1.54 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 4182 1.34 - 1.46: 3071 1.46 - 1.58: 6196 1.58 - 1.70: 0 1.70 - 1.82: 150 Bond restraints: 13599 Sorted by residual: bond pdb=" C5 MAN G 401 " pdb=" O5 MAN G 401 " ideal model delta sigma weight residual 1.418 1.458 -0.040 2.00e-02 2.50e+03 3.99e+00 bond pdb=" C5 MAN Z 401 " pdb=" O5 MAN Z 401 " ideal model delta sigma weight residual 1.418 1.458 -0.040 2.00e-02 2.50e+03 3.99e+00 bond pdb=" C5 MAN D 401 " pdb=" O5 MAN D 401 " ideal model delta sigma weight residual 1.418 1.457 -0.039 2.00e-02 2.50e+03 3.86e+00 bond pdb=" C ALA D 206 " pdb=" N PRO D 207 " ideal model delta sigma weight residual 1.333 1.352 -0.019 1.20e-02 6.94e+03 2.63e+00 bond pdb=" C ALA G 206 " pdb=" N PRO G 207 " ideal model delta sigma weight residual 1.333 1.352 -0.019 1.20e-02 6.94e+03 2.54e+00 ... (remaining 13594 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.69: 18108 1.69 - 3.38: 286 3.38 - 5.08: 64 5.08 - 6.77: 22 6.77 - 8.46: 6 Bond angle restraints: 18486 Sorted by residual: angle pdb=" C LYS Z 49 " pdb=" N THR Z 50 " pdb=" CA THR Z 50 " ideal model delta sigma weight residual 121.71 115.21 6.50 1.39e+00 5.18e-01 2.18e+01 angle pdb=" C LYS G 49 " pdb=" N THR G 50 " pdb=" CA THR G 50 " ideal model delta sigma weight residual 121.71 115.28 6.43 1.39e+00 5.18e-01 2.14e+01 angle pdb=" C LYS D 49 " pdb=" N THR D 50 " pdb=" CA THR D 50 " ideal model delta sigma weight residual 121.71 115.36 6.35 1.39e+00 5.18e-01 2.09e+01 angle pdb=" CA LYS G 164 " pdb=" CB LYS G 164 " pdb=" CG LYS G 164 " ideal model delta sigma weight residual 114.10 122.14 -8.04 2.00e+00 2.50e-01 1.62e+01 angle pdb=" C PHE Z 205 " pdb=" N ALA Z 206 " pdb=" CA ALA Z 206 " ideal model delta sigma weight residual 122.28 118.79 3.49 1.02e+00 9.61e-01 1.17e+01 ... (remaining 18481 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 23.47: 7319 23.47 - 46.94: 553 46.94 - 70.41: 68 70.41 - 93.88: 28 93.88 - 117.34: 6 Dihedral angle restraints: 7974 sinusoidal: 3018 harmonic: 4956 Sorted by residual: dihedral pdb=" C2 MAN G 401 " pdb=" C1 MAN G 401 " pdb=" O5 MAN G 401 " pdb=" C5 MAN G 401 " ideal model delta sinusoidal sigma weight residual -57.62 59.72 -117.34 1 3.00e+01 1.11e-03 1.56e+01 dihedral pdb=" C2 MAN Z 401 " pdb=" C1 MAN Z 401 " pdb=" O5 MAN Z 401 " pdb=" C5 MAN Z 401 " ideal model delta sinusoidal sigma weight residual -57.62 59.64 -117.26 1 3.00e+01 1.11e-03 1.56e+01 dihedral pdb=" C2 MAN D 401 " pdb=" C1 MAN D 401 " pdb=" O5 MAN D 401 " pdb=" C5 MAN D 401 " ideal model delta sinusoidal sigma weight residual -57.62 59.57 -117.19 1 3.00e+01 1.11e-03 1.55e+01 ... (remaining 7971 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.025: 1237 0.025 - 0.051: 507 0.051 - 0.076: 310 0.076 - 0.102: 116 0.102 - 0.127: 35 Chirality restraints: 2205 Sorted by residual: chirality pdb=" CA ILE C 162 " pdb=" N ILE C 162 " pdb=" C ILE C 162 " pdb=" CB ILE C 162 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 4.06e-01 chirality pdb=" CA ILE Y 162 " pdb=" N ILE Y 162 " pdb=" C ILE Y 162 " pdb=" CB ILE Y 162 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.12 2.00e-01 2.50e+01 3.83e-01 chirality pdb=" CA ILE F 162 " pdb=" N ILE F 162 " pdb=" C ILE F 162 " pdb=" CB ILE F 162 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.12 2.00e-01 2.50e+01 3.77e-01 ... (remaining 2202 not shown) Planarity restraints: 2274 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ALA C 69 " -0.050 5.00e-02 4.00e+02 7.70e-02 9.48e+00 pdb=" N PRO C 70 " 0.133 5.00e-02 4.00e+02 pdb=" CA PRO C 70 " -0.041 5.00e-02 4.00e+02 pdb=" CD PRO C 70 " -0.042 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ALA Y 69 " 0.050 5.00e-02 4.00e+02 7.59e-02 9.21e+00 pdb=" N PRO Y 70 " -0.131 5.00e-02 4.00e+02 pdb=" CA PRO Y 70 " 0.040 5.00e-02 4.00e+02 pdb=" CD PRO Y 70 " 0.042 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ALA F 69 " 0.049 5.00e-02 4.00e+02 7.57e-02 9.17e+00 pdb=" N PRO F 70 " -0.131 5.00e-02 4.00e+02 pdb=" CA PRO F 70 " 0.040 5.00e-02 4.00e+02 pdb=" CD PRO F 70 " 0.041 5.00e-02 4.00e+02 ... (remaining 2271 not shown) Histogram of nonbonded interaction distances: 2.23 - 2.77: 2281 2.77 - 3.30: 13273 3.30 - 3.83: 23862 3.83 - 4.37: 26955 4.37 - 4.90: 45800 Nonbonded interactions: 112171 Sorted by model distance: nonbonded pdb=" OE2 GLU Y 205 " pdb=" NZ LYS Z 183 " model vdw 2.232 3.120 nonbonded pdb=" O ALA Y 72 " pdb=" OG SER Y 76 " model vdw 2.234 3.040 nonbonded pdb=" OD2 ASP G 113 " pdb=" O6 MAN G 401 " model vdw 2.241 3.040 nonbonded pdb=" OD2 ASP D 113 " pdb=" O6 MAN D 401 " model vdw 2.254 3.040 nonbonded pdb=" OD2 ASP Z 113 " pdb=" O6 MAN Z 401 " model vdw 2.255 3.040 ... (remaining 112166 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 'E' selection = chain 'H' } ncs_group { reference = chain 'C' selection = chain 'F' selection = chain 'Y' } ncs_group { reference = chain 'D' selection = chain 'G' selection = chain 'Z' } 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 individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.490 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.220 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 13.150 Find NCS groups from input model: 0.170 Set up NCS constraints: 0.020 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:6.540 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 21.640 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8183 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 : 0.002 0.040 13605 Z= 0.129 Angle : 0.612 8.460 18498 Z= 0.346 Chirality : 0.040 0.127 2205 Planarity : 0.005 0.077 2274 Dihedral : 17.023 117.345 4794 Min Nonbonded Distance : 2.232 Molprobity Statistics. All-atom Clashscore : 6.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.05 % Favored : 95.95 % Rotamer: Outliers : 2.49 % Allowed : 17.44 % Favored : 80.07 % 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 are not related in a simple way. whole: 1.19 (0.21), residues: 1755 helix: 1.66 (0.15), residues: 1245 sheet: None (None), residues: 0 loop : -1.44 (0.28), residues: 510 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG C 127 TYR 0.008 0.001 TYR Z 219 PHE 0.008 0.001 PHE Z 144 TRP 0.015 0.001 TRP D 26 HIS 0.003 0.001 HIS Z 298 Details of bonding type rmsd covalent geometry : bond 0.00247 (13599) covalent geometry : angle 0.61174 (18486) SS BOND : bond 0.00081 ( 6) SS BOND : angle 0.58776 ( 12) hydrogen bonds : bond 0.14745 ( 880) hydrogen bonds : angle 5.28426 ( 2631) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3510 Ramachandran restraints generated. 1755 Oldfield, 0 Emsley, 1755 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3510 Ramachandran restraints generated. 1755 Oldfield, 0 Emsley, 1755 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 279 residues out of total 1365 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 245 time to evaluate : 0.485 Fit side-chains REVERT: Y 23 ASP cc_start: 0.7718 (t0) cc_final: 0.7498 (t0) REVERT: Y 44 LEU cc_start: 0.8301 (tp) cc_final: 0.7943 (tm) REVERT: Y 124 LEU cc_start: 0.7909 (mt) cc_final: 0.7685 (mt) REVERT: Y 143 SER cc_start: 0.8221 (m) cc_final: 0.8014 (m) REVERT: Z 104 MET cc_start: 0.8300 (mtp) cc_final: 0.7657 (mtm) REVERT: Z 237 GLN cc_start: 0.7986 (mt0) cc_final: 0.7769 (mt0) REVERT: C 143 SER cc_start: 0.8067 (m) cc_final: 0.7859 (m) REVERT: D 60 ARG cc_start: 0.7352 (mtm-85) cc_final: 0.6905 (mtp180) REVERT: D 98 GLN cc_start: 0.7881 (tm-30) cc_final: 0.7539 (tm130) REVERT: G 237 GLN cc_start: 0.7956 (mt0) cc_final: 0.7678 (mm110) outliers start: 34 outliers final: 16 residues processed: 271 average time/residue: 0.5294 time to fit residues: 157.8292 Evaluate side-chains 249 residues out of total 1365 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 233 time to evaluate : 0.482 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Z residue 117 TRP Chi-restraints excluded: chain Z residue 293 VAL Chi-restraints excluded: chain A residue 44 CYS Chi-restraints excluded: chain C residue 95 SER Chi-restraints excluded: chain C residue 116 THR Chi-restraints excluded: chain C residue 197 VAL Chi-restraints excluded: chain D residue 7 LEU Chi-restraints excluded: chain D residue 39 SER Chi-restraints excluded: chain D residue 117 TRP Chi-restraints excluded: chain D residue 293 VAL Chi-restraints excluded: chain E residue 44 CYS Chi-restraints excluded: chain F residue 95 SER Chi-restraints excluded: chain F residue 116 THR Chi-restraints excluded: chain G residue 7 LEU Chi-restraints excluded: chain G residue 117 TRP Chi-restraints excluded: chain H residue 44 CYS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 171 random chunks: chunk 98 optimal weight: 0.9990 chunk 107 optimal weight: 2.9990 chunk 10 optimal weight: 3.9990 chunk 66 optimal weight: 6.9990 chunk 130 optimal weight: 0.0050 chunk 124 optimal weight: 7.9990 chunk 103 optimal weight: 0.0570 chunk 77 optimal weight: 0.6980 chunk 122 optimal weight: 0.0570 chunk 91 optimal weight: 1.9990 chunk 149 optimal weight: 0.9990 overall best weight: 0.3632 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Y 240 ASN Z 98 GLN Z 179 GLN ** Z 230 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 237 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 238 GLN D 148 ASN D 159 GLN D 179 GLN D 204 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4104 r_free = 0.4104 target = 0.179806 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3740 r_free = 0.3740 target = 0.146392 restraints weight = 13700.938| |-----------------------------------------------------------------------------| r_work (start): 0.3740 rms_B_bonded: 2.07 r_work: 0.3516 rms_B_bonded: 2.34 restraints_weight: 0.5000 r_work: 0.3409 rms_B_bonded: 3.83 restraints_weight: 0.2500 r_work (final): 0.3409 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8449 moved from start: 0.1001 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 13605 Z= 0.114 Angle : 0.546 7.055 18498 Z= 0.278 Chirality : 0.040 0.178 2205 Planarity : 0.005 0.071 2274 Dihedral : 6.025 59.512 1929 Min Nonbonded Distance : 2.594 Molprobity Statistics. All-atom Clashscore : 5.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.67 % Favored : 95.33 % Rotamer: Outliers : 3.44 % Allowed : 16.12 % Favored : 80.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.68 (0.20), residues: 1755 helix: 2.17 (0.15), residues: 1242 sheet: None (None), residues: 0 loop : -1.65 (0.26), residues: 513 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 127 TYR 0.007 0.001 TYR D 219 PHE 0.014 0.001 PHE Y 161 TRP 0.010 0.001 TRP D 222 HIS 0.003 0.001 HIS Z 298 Details of bonding type rmsd covalent geometry : bond 0.00229 (13599) covalent geometry : angle 0.54609 (18486) SS BOND : bond 0.00041 ( 6) SS BOND : angle 0.20231 ( 12) hydrogen bonds : bond 0.03894 ( 880) hydrogen bonds : angle 3.90781 ( 2631) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3510 Ramachandran restraints generated. 1755 Oldfield, 0 Emsley, 1755 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3510 Ramachandran restraints generated. 1755 Oldfield, 0 Emsley, 1755 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 292 residues out of total 1365 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 245 time to evaluate : 0.495 Fit side-chains revert: symmetry clash REVERT: Y 44 LEU cc_start: 0.8205 (tp) cc_final: 0.7819 (tm) REVERT: Z 104 MET cc_start: 0.8433 (mtp) cc_final: 0.7914 (mtm) REVERT: Z 247 GLU cc_start: 0.7714 (pt0) cc_final: 0.7434 (pm20) REVERT: C 126 ASP cc_start: 0.7358 (m-30) cc_final: 0.7051 (m-30) REVERT: D 14 ARG cc_start: 0.7910 (mtm-85) cc_final: 0.7691 (mtm180) REVERT: D 26 TRP cc_start: 0.7988 (OUTLIER) cc_final: 0.5476 (m100) REVERT: D 85 GLU cc_start: 0.6512 (OUTLIER) cc_final: 0.6248 (mt-10) REVERT: D 98 GLN cc_start: 0.7537 (tm-30) cc_final: 0.7051 (mm110) REVERT: D 104 MET cc_start: 0.8207 (mtp) cc_final: 0.7805 (mtm) REVERT: D 142 LEU cc_start: 0.8624 (OUTLIER) cc_final: 0.8388 (tp) REVERT: G 26 TRP cc_start: 0.8114 (OUTLIER) cc_final: 0.5624 (m100) outliers start: 47 outliers final: 15 residues processed: 272 average time/residue: 0.5324 time to fit residues: 159.1813 Evaluate side-chains 245 residues out of total 1365 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 226 time to evaluate : 0.459 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Y residue 95 SER Chi-restraints excluded: chain Y residue 130 GLU Chi-restraints excluded: chain Y residue 150 ILE Chi-restraints excluded: chain Y residue 216 VAL Chi-restraints excluded: chain Z residue 7 LEU Chi-restraints excluded: chain Z residue 73 SER Chi-restraints excluded: chain C residue 99 ILE Chi-restraints excluded: chain C residue 197 VAL Chi-restraints excluded: chain C residue 216 VAL Chi-restraints excluded: chain D residue 26 TRP Chi-restraints excluded: chain D residue 59 LYS Chi-restraints excluded: chain D residue 85 GLU Chi-restraints excluded: chain D residue 142 LEU Chi-restraints excluded: chain D residue 178 LEU Chi-restraints excluded: chain F residue 216 VAL Chi-restraints excluded: chain G residue 7 LEU Chi-restraints excluded: chain G residue 26 TRP Chi-restraints excluded: chain G residue 142 LEU Chi-restraints excluded: chain H residue 11 LYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 171 random chunks: chunk 17 optimal weight: 8.9990 chunk 150 optimal weight: 0.9980 chunk 15 optimal weight: 0.9980 chunk 95 optimal weight: 5.9990 chunk 120 optimal weight: 1.9990 chunk 74 optimal weight: 5.9990 chunk 56 optimal weight: 2.9990 chunk 26 optimal weight: 6.9990 chunk 115 optimal weight: 7.9990 chunk 139 optimal weight: 6.9990 chunk 43 optimal weight: 3.9990 overall best weight: 2.1986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Y 240 ASN Z 179 GLN Z 230 GLN Z 238 GLN D 204 GLN D 239 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4020 r_free = 0.4020 target = 0.171683 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3630 r_free = 0.3630 target = 0.136881 restraints weight = 13651.767| |-----------------------------------------------------------------------------| r_work (start): 0.3628 rms_B_bonded: 2.10 r_work: 0.3389 rms_B_bonded: 2.32 restraints_weight: 0.5000 r_work: 0.3279 rms_B_bonded: 3.80 restraints_weight: 0.2500 r_work (final): 0.3279 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8576 moved from start: 0.1473 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 13605 Z= 0.185 Angle : 0.616 9.702 18498 Z= 0.319 Chirality : 0.045 0.200 2205 Planarity : 0.006 0.092 2274 Dihedral : 4.660 25.529 1911 Min Nonbonded Distance : 2.466 Molprobity Statistics. All-atom Clashscore : 5.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.24 % Favored : 94.76 % Rotamer: Outliers : 3.74 % Allowed : 16.70 % Favored : 79.56 % 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 are not related in a simple way. whole: 1.44 (0.20), residues: 1755 helix: 1.98 (0.15), residues: 1248 sheet: None (None), residues: 0 loop : -1.78 (0.26), residues: 507 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG Z 199 TYR 0.008 0.002 TYR A 3 PHE 0.016 0.002 PHE Z 191 TRP 0.013 0.002 TRP Z 26 HIS 0.005 0.001 HIS Z 68 Details of bonding type rmsd covalent geometry : bond 0.00440 (13599) covalent geometry : angle 0.61581 (18486) SS BOND : bond 0.00305 ( 6) SS BOND : angle 0.52505 ( 12) hydrogen bonds : bond 0.05012 ( 880) hydrogen bonds : angle 4.06622 ( 2631) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3510 Ramachandran restraints generated. 1755 Oldfield, 0 Emsley, 1755 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3510 Ramachandran restraints generated. 1755 Oldfield, 0 Emsley, 1755 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 297 residues out of total 1365 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 246 time to evaluate : 0.421 Fit side-chains REVERT: Z 168 LYS cc_start: 0.5898 (tmmt) cc_final: 0.5380 (tmtt) REVERT: Z 247 GLU cc_start: 0.7827 (pt0) cc_final: 0.7487 (pm20) REVERT: C 117 LEU cc_start: 0.8524 (OUTLIER) cc_final: 0.8239 (tt) REVERT: D 10 ARG cc_start: 0.7542 (OUTLIER) cc_final: 0.7050 (tpt-90) REVERT: D 98 GLN cc_start: 0.7712 (tm-30) cc_final: 0.7119 (mm110) REVERT: D 168 LYS cc_start: 0.6059 (tmmt) cc_final: 0.5464 (tmtt) REVERT: G 237 GLN cc_start: 0.8185 (OUTLIER) cc_final: 0.7908 (mm-40) outliers start: 51 outliers final: 24 residues processed: 274 average time/residue: 0.5131 time to fit residues: 154.4998 Evaluate side-chains 260 residues out of total 1365 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 233 time to evaluate : 0.425 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Y residue 95 SER Chi-restraints excluded: chain Y residue 116 THR Chi-restraints excluded: chain Y residue 216 VAL Chi-restraints excluded: chain Z residue 7 LEU Chi-restraints excluded: chain Z residue 142 LEU Chi-restraints excluded: chain A residue 23 THR Chi-restraints excluded: chain C residue 11 LEU Chi-restraints excluded: chain C residue 116 THR Chi-restraints excluded: chain C residue 117 LEU Chi-restraints excluded: chain C residue 121 ILE Chi-restraints excluded: chain C residue 174 MET Chi-restraints excluded: chain C residue 197 VAL Chi-restraints excluded: chain C residue 216 VAL Chi-restraints excluded: chain D residue 10 ARG Chi-restraints excluded: chain D residue 59 LYS Chi-restraints excluded: chain D residue 142 LEU Chi-restraints excluded: chain D residue 237 GLN Chi-restraints excluded: chain F residue 116 THR Chi-restraints excluded: chain F residue 121 ILE Chi-restraints excluded: chain F residue 216 VAL Chi-restraints excluded: chain G residue 7 LEU Chi-restraints excluded: chain G residue 71 ILE Chi-restraints excluded: chain G residue 142 LEU Chi-restraints excluded: chain G residue 237 GLN Chi-restraints excluded: chain G residue 293 VAL Chi-restraints excluded: chain G residue 299 LEU Chi-restraints excluded: chain H residue 23 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 171 random chunks: chunk 67 optimal weight: 0.9980 chunk 39 optimal weight: 6.9990 chunk 13 optimal weight: 0.0020 chunk 100 optimal weight: 5.9990 chunk 2 optimal weight: 4.9990 chunk 7 optimal weight: 2.9990 chunk 4 optimal weight: 8.9990 chunk 98 optimal weight: 4.9990 chunk 122 optimal weight: 9.9990 chunk 131 optimal weight: 10.0000 chunk 128 optimal weight: 8.9990 overall best weight: 2.7994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Y 240 ASN Z 230 GLN Z 238 GLN C 168 GLN D 148 ASN D 179 GLN D 204 GLN D 230 GLN F 240 ASN G 159 GLN G 230 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3997 r_free = 0.3997 target = 0.169569 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3604 r_free = 0.3604 target = 0.134711 restraints weight = 13591.806| |-----------------------------------------------------------------------------| r_work (start): 0.3601 rms_B_bonded: 2.10 r_work: 0.3361 rms_B_bonded: 2.32 restraints_weight: 0.5000 r_work: 0.3252 rms_B_bonded: 3.76 restraints_weight: 0.2500 r_work (final): 0.3252 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8604 moved from start: 0.1803 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.054 13605 Z= 0.220 Angle : 0.654 9.363 18498 Z= 0.339 Chirality : 0.046 0.158 2205 Planarity : 0.006 0.088 2274 Dihedral : 4.947 33.798 1911 Min Nonbonded Distance : 2.484 Molprobity Statistics. All-atom Clashscore : 6.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.70 % Favored : 94.30 % Rotamer: Outliers : 4.18 % Allowed : 16.92 % Favored : 78.90 % 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 are not related in a simple way. whole: 1.11 (0.20), residues: 1755 helix: 1.74 (0.15), residues: 1242 sheet: None (None), residues: 0 loop : -1.87 (0.25), residues: 513 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG G 199 TYR 0.011 0.002 TYR A 3 PHE 0.018 0.002 PHE D 118 TRP 0.017 0.002 TRP Z 26 HIS 0.007 0.001 HIS Z 68 Details of bonding type rmsd covalent geometry : bond 0.00533 (13599) covalent geometry : angle 0.65353 (18486) SS BOND : bond 0.00466 ( 6) SS BOND : angle 0.69157 ( 12) hydrogen bonds : bond 0.05312 ( 880) hydrogen bonds : angle 4.16811 ( 2631) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3510 Ramachandran restraints generated. 1755 Oldfield, 0 Emsley, 1755 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3510 Ramachandran restraints generated. 1755 Oldfield, 0 Emsley, 1755 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 295 residues out of total 1365 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 238 time to evaluate : 0.504 Fit side-chains REVERT: Y 117 LEU cc_start: 0.8470 (OUTLIER) cc_final: 0.7913 (tt) REVERT: Z 168 LYS cc_start: 0.6055 (tmmt) cc_final: 0.5510 (tmtt) REVERT: Z 237 GLN cc_start: 0.8143 (mt0) cc_final: 0.7851 (mt0) REVERT: Z 247 GLU cc_start: 0.7865 (pt0) cc_final: 0.7517 (pm20) REVERT: C 24 GLU cc_start: 0.8878 (OUTLIER) cc_final: 0.8541 (mt-10) REVERT: C 117 LEU cc_start: 0.8507 (OUTLIER) cc_final: 0.8216 (tt) REVERT: D 10 ARG cc_start: 0.7462 (OUTLIER) cc_final: 0.6869 (tpt-90) REVERT: D 98 GLN cc_start: 0.7714 (tm-30) cc_final: 0.7078 (mm110) REVERT: D 168 LYS cc_start: 0.6187 (tmmt) cc_final: 0.5563 (tmtt) REVERT: D 247 GLU cc_start: 0.7973 (pt0) cc_final: 0.7589 (pm20) REVERT: F 159 LEU cc_start: 0.8206 (OUTLIER) cc_final: 0.7998 (mt) outliers start: 57 outliers final: 32 residues processed: 268 average time/residue: 0.5606 time to fit residues: 164.9250 Evaluate side-chains 272 residues out of total 1365 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 235 time to evaluate : 0.496 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Y residue 39 LEU Chi-restraints excluded: chain Y residue 95 SER Chi-restraints excluded: chain Y residue 116 THR Chi-restraints excluded: chain Y residue 117 LEU Chi-restraints excluded: chain Y residue 204 LYS Chi-restraints excluded: chain Y residue 216 VAL Chi-restraints excluded: chain Z residue 7 LEU Chi-restraints excluded: chain Z residue 138 LEU Chi-restraints excluded: chain Z residue 142 LEU Chi-restraints excluded: chain A residue 23 THR Chi-restraints excluded: chain C residue 11 LEU Chi-restraints excluded: chain C residue 24 GLU Chi-restraints excluded: chain C residue 35 THR Chi-restraints excluded: chain C residue 95 SER Chi-restraints excluded: chain C residue 116 THR Chi-restraints excluded: chain C residue 117 LEU Chi-restraints excluded: chain C residue 121 ILE Chi-restraints excluded: chain C residue 174 MET Chi-restraints excluded: chain C residue 197 VAL Chi-restraints excluded: chain C residue 216 VAL Chi-restraints excluded: chain D residue 10 ARG Chi-restraints excluded: chain D residue 59 LYS Chi-restraints excluded: chain D residue 71 ILE Chi-restraints excluded: chain D residue 142 LEU Chi-restraints excluded: chain D residue 178 LEU Chi-restraints excluded: chain D residue 246 SER Chi-restraints excluded: chain F residue 95 SER Chi-restraints excluded: chain F residue 116 THR Chi-restraints excluded: chain F residue 121 ILE Chi-restraints excluded: chain F residue 150 ILE Chi-restraints excluded: chain F residue 159 LEU Chi-restraints excluded: chain F residue 201 MET Chi-restraints excluded: chain F residue 216 VAL Chi-restraints excluded: chain G residue 7 LEU Chi-restraints excluded: chain G residue 71 ILE Chi-restraints excluded: chain G residue 142 LEU Chi-restraints excluded: chain H residue 23 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 171 random chunks: chunk 79 optimal weight: 1.9990 chunk 86 optimal weight: 5.9990 chunk 68 optimal weight: 2.9990 chunk 75 optimal weight: 3.9990 chunk 101 optimal weight: 10.0000 chunk 12 optimal weight: 5.9990 chunk 159 optimal weight: 20.0000 chunk 36 optimal weight: 2.9990 chunk 125 optimal weight: 0.7980 chunk 37 optimal weight: 3.9990 chunk 65 optimal weight: 1.9990 overall best weight: 2.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Y 240 ASN Z 98 GLN Z 230 GLN Z 238 GLN C 168 GLN D 148 ASN D 179 GLN D 204 GLN F 240 ASN G 230 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4000 r_free = 0.4000 target = 0.169849 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3625 r_free = 0.3625 target = 0.136174 restraints weight = 13594.017| |-----------------------------------------------------------------------------| r_work (start): 0.3621 rms_B_bonded: 1.90 r_work: 0.3373 rms_B_bonded: 2.32 restraints_weight: 0.5000 r_work: 0.3264 rms_B_bonded: 3.78 restraints_weight: 0.2500 r_work (final): 0.3264 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8590 moved from start: 0.1785 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 13605 Z= 0.182 Angle : 0.617 12.244 18498 Z= 0.318 Chirality : 0.044 0.153 2205 Planarity : 0.006 0.077 2274 Dihedral : 4.882 36.309 1911 Min Nonbonded Distance : 2.469 Molprobity Statistics. All-atom Clashscore : 5.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.75 % Favored : 94.25 % Rotamer: Outliers : 3.52 % Allowed : 17.95 % Favored : 78.53 % 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 are not related in a simple way. whole: 1.20 (0.20), residues: 1755 helix: 1.81 (0.15), residues: 1248 sheet: None (None), residues: 0 loop : -1.87 (0.26), residues: 507 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG G 199 TYR 0.010 0.002 TYR A 3 PHE 0.016 0.002 PHE G 191 TRP 0.016 0.002 TRP Z 26 HIS 0.005 0.001 HIS Z 68 Details of bonding type rmsd covalent geometry : bond 0.00436 (13599) covalent geometry : angle 0.61714 (18486) SS BOND : bond 0.00351 ( 6) SS BOND : angle 0.59732 ( 12) hydrogen bonds : bond 0.04897 ( 880) hydrogen bonds : angle 4.06595 ( 2631) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3510 Ramachandran restraints generated. 1755 Oldfield, 0 Emsley, 1755 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3510 Ramachandran restraints generated. 1755 Oldfield, 0 Emsley, 1755 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 286 residues out of total 1365 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 238 time to evaluate : 0.497 Fit side-chains REVERT: Y 44 LEU cc_start: 0.8238 (tp) cc_final: 0.7802 (tm) REVERT: Y 117 LEU cc_start: 0.8426 (OUTLIER) cc_final: 0.7852 (tt) REVERT: Y 243 LYS cc_start: 0.8286 (mtmm) cc_final: 0.8079 (mtmt) REVERT: Z 168 LYS cc_start: 0.6125 (tmmt) cc_final: 0.5564 (tmtt) REVERT: Z 237 GLN cc_start: 0.8127 (mt0) cc_final: 0.7832 (mt0) REVERT: Z 247 GLU cc_start: 0.7912 (pt0) cc_final: 0.7564 (pm20) REVERT: C 117 LEU cc_start: 0.8454 (OUTLIER) cc_final: 0.8190 (tt) REVERT: C 126 ASP cc_start: 0.7361 (OUTLIER) cc_final: 0.7045 (m-30) REVERT: D 10 ARG cc_start: 0.7397 (OUTLIER) cc_final: 0.6819 (tpt-90) REVERT: D 98 GLN cc_start: 0.7667 (tm-30) cc_final: 0.7050 (mm110) REVERT: D 168 LYS cc_start: 0.6172 (tmmt) cc_final: 0.5576 (tmtt) REVERT: D 247 GLU cc_start: 0.7972 (pt0) cc_final: 0.7565 (pm20) REVERT: F 117 LEU cc_start: 0.8628 (OUTLIER) cc_final: 0.8309 (tt) REVERT: F 127 ARG cc_start: 0.7134 (OUTLIER) cc_final: 0.6276 (mtt180) REVERT: F 159 LEU cc_start: 0.8186 (OUTLIER) cc_final: 0.7981 (mt) outliers start: 48 outliers final: 28 residues processed: 266 average time/residue: 0.5327 time to fit residues: 156.0502 Evaluate side-chains 267 residues out of total 1365 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 232 time to evaluate : 0.442 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Y residue 95 SER Chi-restraints excluded: chain Y residue 116 THR Chi-restraints excluded: chain Y residue 117 LEU Chi-restraints excluded: chain Y residue 216 VAL Chi-restraints excluded: chain Z residue 7 LEU Chi-restraints excluded: chain Z residue 142 LEU Chi-restraints excluded: chain Z residue 293 VAL Chi-restraints excluded: chain C residue 11 LEU Chi-restraints excluded: chain C residue 85 LEU Chi-restraints excluded: chain C residue 95 SER Chi-restraints excluded: chain C residue 116 THR Chi-restraints excluded: chain C residue 117 LEU Chi-restraints excluded: chain C residue 121 ILE Chi-restraints excluded: chain C residue 126 ASP Chi-restraints excluded: chain C residue 174 MET Chi-restraints excluded: chain C residue 197 VAL Chi-restraints excluded: chain C residue 216 VAL Chi-restraints excluded: chain D residue 7 LEU Chi-restraints excluded: chain D residue 10 ARG Chi-restraints excluded: chain D residue 59 LYS Chi-restraints excluded: chain D residue 142 LEU Chi-restraints excluded: chain D residue 178 LEU Chi-restraints excluded: chain D residue 237 GLN Chi-restraints excluded: chain F residue 95 SER Chi-restraints excluded: chain F residue 116 THR Chi-restraints excluded: chain F residue 117 LEU Chi-restraints excluded: chain F residue 121 ILE Chi-restraints excluded: chain F residue 127 ARG Chi-restraints excluded: chain F residue 159 LEU Chi-restraints excluded: chain F residue 201 MET Chi-restraints excluded: chain F residue 216 VAL Chi-restraints excluded: chain G residue 7 LEU Chi-restraints excluded: chain G residue 71 ILE Chi-restraints excluded: chain G residue 142 LEU Chi-restraints excluded: chain H residue 23 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 171 random chunks: chunk 29 optimal weight: 5.9990 chunk 9 optimal weight: 0.0470 chunk 49 optimal weight: 0.7980 chunk 158 optimal weight: 7.9990 chunk 89 optimal weight: 0.9990 chunk 146 optimal weight: 0.6980 chunk 166 optimal weight: 3.9990 chunk 136 optimal weight: 0.5980 chunk 45 optimal weight: 2.9990 chunk 65 optimal weight: 3.9990 chunk 164 optimal weight: 2.9990 overall best weight: 0.6280 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Y 240 ASN Z 98 GLN Z 230 GLN Z 238 GLN C 168 GLN D 148 ASN D 179 GLN D 204 GLN D 238 GLN F 240 ASN G 230 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4052 r_free = 0.4052 target = 0.174810 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3673 r_free = 0.3673 target = 0.140990 restraints weight = 13522.042| |-----------------------------------------------------------------------------| r_work (start): 0.3672 rms_B_bonded: 2.11 r_work: 0.3441 rms_B_bonded: 2.31 restraints_weight: 0.5000 r_work: 0.3333 rms_B_bonded: 3.79 restraints_weight: 0.2500 r_work (final): 0.3333 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8519 moved from start: 0.1628 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 13605 Z= 0.114 Angle : 0.539 11.749 18498 Z= 0.275 Chirality : 0.040 0.123 2205 Planarity : 0.005 0.074 2274 Dihedral : 4.537 32.380 1911 Min Nonbonded Distance : 2.508 Molprobity Statistics. All-atom Clashscore : 4.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.96 % Favored : 95.04 % Rotamer: Outliers : 2.12 % Allowed : 19.85 % Favored : 78.02 % 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 are not related in a simple way. whole: 1.68 (0.21), residues: 1755 helix: 2.22 (0.15), residues: 1245 sheet: None (None), residues: 0 loop : -1.84 (0.26), residues: 510 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 127 TYR 0.007 0.001 TYR A 3 PHE 0.012 0.001 PHE G 191 TRP 0.013 0.001 TRP D 26 HIS 0.002 0.000 HIS Z 298 Details of bonding type rmsd covalent geometry : bond 0.00241 (13599) covalent geometry : angle 0.53895 (18486) SS BOND : bond 0.00112 ( 6) SS BOND : angle 0.33138 ( 12) hydrogen bonds : bond 0.03823 ( 880) hydrogen bonds : angle 3.79136 ( 2631) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3510 Ramachandran restraints generated. 1755 Oldfield, 0 Emsley, 1755 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3510 Ramachandran restraints generated. 1755 Oldfield, 0 Emsley, 1755 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 263 residues out of total 1365 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 234 time to evaluate : 0.404 Fit side-chains REVERT: Y 44 LEU cc_start: 0.8244 (tp) cc_final: 0.7824 (tm) REVERT: Y 243 LYS cc_start: 0.8182 (mtmm) cc_final: 0.7942 (mtmt) REVERT: Z 168 LYS cc_start: 0.6111 (tmmt) cc_final: 0.5555 (tmtt) REVERT: Z 237 GLN cc_start: 0.8127 (mt0) cc_final: 0.7835 (mt0) REVERT: Z 247 GLU cc_start: 0.7864 (pt0) cc_final: 0.7519 (pm20) REVERT: C 85 LEU cc_start: 0.7941 (OUTLIER) cc_final: 0.7660 (pt) REVERT: C 112 MET cc_start: 0.8502 (mtm) cc_final: 0.8089 (mtp) REVERT: C 126 ASP cc_start: 0.7085 (OUTLIER) cc_final: 0.6798 (m-30) REVERT: D 98 GLN cc_start: 0.7550 (tm-30) cc_final: 0.7037 (mm110) REVERT: D 142 LEU cc_start: 0.8627 (OUTLIER) cc_final: 0.8420 (tp) REVERT: D 168 LYS cc_start: 0.6025 (tmmt) cc_final: 0.5441 (tmtt) REVERT: D 247 GLU cc_start: 0.7895 (pt0) cc_final: 0.7518 (pm20) REVERT: G 237 GLN cc_start: 0.8102 (OUTLIER) cc_final: 0.7847 (mm-40) outliers start: 29 outliers final: 15 residues processed: 250 average time/residue: 0.5194 time to fit residues: 142.4884 Evaluate side-chains 245 residues out of total 1365 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 226 time to evaluate : 0.413 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Y residue 154 ILE Chi-restraints excluded: chain Y residue 216 VAL Chi-restraints excluded: chain Z residue 7 LEU Chi-restraints excluded: chain Z residue 142 LEU Chi-restraints excluded: chain Z residue 284 ILE Chi-restraints excluded: chain C residue 85 LEU Chi-restraints excluded: chain C residue 126 ASP Chi-restraints excluded: chain C residue 197 VAL Chi-restraints excluded: chain C residue 216 VAL Chi-restraints excluded: chain D residue 7 LEU Chi-restraints excluded: chain D residue 59 LYS Chi-restraints excluded: chain D residue 142 LEU Chi-restraints excluded: chain D residue 246 SER Chi-restraints excluded: chain F residue 150 ILE Chi-restraints excluded: chain F residue 201 MET Chi-restraints excluded: chain F residue 216 VAL Chi-restraints excluded: chain G residue 7 LEU Chi-restraints excluded: chain G residue 142 LEU Chi-restraints excluded: chain G residue 237 GLN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 171 random chunks: chunk 27 optimal weight: 8.9990 chunk 153 optimal weight: 6.9990 chunk 118 optimal weight: 0.7980 chunk 70 optimal weight: 0.0270 chunk 49 optimal weight: 4.9990 chunk 103 optimal weight: 0.4980 chunk 46 optimal weight: 0.0170 chunk 114 optimal weight: 10.0000 chunk 164 optimal weight: 2.9990 chunk 86 optimal weight: 5.9990 chunk 161 optimal weight: 2.9990 overall best weight: 0.8678 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Y 240 ASN Z 98 GLN Z 179 GLN Z 230 GLN Z 238 GLN C 168 GLN D 148 ASN D 179 GLN D 204 GLN D 238 GLN F 240 ASN G 230 GLN G 238 GLN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4048 r_free = 0.4048 target = 0.174364 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3670 r_free = 0.3670 target = 0.140365 restraints weight = 13600.347| |-----------------------------------------------------------------------------| r_work (start): 0.3670 rms_B_bonded: 2.00 r_work: 0.3431 rms_B_bonded: 2.35 restraints_weight: 0.5000 r_work: 0.3321 rms_B_bonded: 3.87 restraints_weight: 0.2500 r_work (final): 0.3321 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8536 moved from start: 0.1662 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 13605 Z= 0.120 Angle : 0.552 11.839 18498 Z= 0.280 Chirality : 0.041 0.138 2205 Planarity : 0.005 0.073 2274 Dihedral : 4.475 30.622 1911 Min Nonbonded Distance : 2.475 Molprobity Statistics. All-atom Clashscore : 4.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.19 % Favored : 94.81 % Rotamer: Outliers : 2.20 % Allowed : 20.15 % Favored : 77.66 % 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 are not related in a simple way. whole: 1.74 (0.21), residues: 1755 helix: 2.25 (0.15), residues: 1251 sheet: None (None), residues: 0 loop : -1.80 (0.27), residues: 504 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 127 TYR 0.007 0.001 TYR A 3 PHE 0.014 0.001 PHE G 191 TRP 0.014 0.001 TRP D 26 HIS 0.003 0.001 HIS Z 68 Details of bonding type rmsd covalent geometry : bond 0.00264 (13599) covalent geometry : angle 0.55250 (18486) SS BOND : bond 0.00129 ( 6) SS BOND : angle 0.39824 ( 12) hydrogen bonds : bond 0.03927 ( 880) hydrogen bonds : angle 3.77346 ( 2631) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3510 Ramachandran restraints generated. 1755 Oldfield, 0 Emsley, 1755 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3510 Ramachandran restraints generated. 1755 Oldfield, 0 Emsley, 1755 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 258 residues out of total 1365 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 228 time to evaluate : 0.501 Fit side-chains REVERT: Y 44 LEU cc_start: 0.8249 (tp) cc_final: 0.7837 (tm) REVERT: Y 243 LYS cc_start: 0.8148 (mtmm) cc_final: 0.7937 (mtmt) REVERT: Z 168 LYS cc_start: 0.6079 (tmmt) cc_final: 0.5532 (tmtt) REVERT: Z 237 GLN cc_start: 0.8149 (mt0) cc_final: 0.7861 (mt0) REVERT: Z 247 GLU cc_start: 0.7883 (pt0) cc_final: 0.7529 (pm20) REVERT: C 85 LEU cc_start: 0.7914 (OUTLIER) cc_final: 0.7616 (pt) REVERT: C 112 MET cc_start: 0.8527 (mtm) cc_final: 0.8118 (mtp) REVERT: C 117 LEU cc_start: 0.8429 (OUTLIER) cc_final: 0.8174 (tt) REVERT: D 98 GLN cc_start: 0.7636 (tm-30) cc_final: 0.7034 (mm110) REVERT: D 168 LYS cc_start: 0.5947 (tmmt) cc_final: 0.5385 (tmtt) REVERT: D 247 GLU cc_start: 0.7920 (pt0) cc_final: 0.7514 (pm20) REVERT: G 237 GLN cc_start: 0.8112 (OUTLIER) cc_final: 0.7854 (mm-40) outliers start: 30 outliers final: 17 residues processed: 246 average time/residue: 0.5430 time to fit residues: 146.7428 Evaluate side-chains 250 residues out of total 1365 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 230 time to evaluate : 0.417 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Y residue 154 ILE Chi-restraints excluded: chain Y residue 216 VAL Chi-restraints excluded: chain Z residue 7 LEU Chi-restraints excluded: chain Z residue 142 LEU Chi-restraints excluded: chain Z residue 284 ILE Chi-restraints excluded: chain C residue 85 LEU Chi-restraints excluded: chain C residue 116 THR Chi-restraints excluded: chain C residue 117 LEU Chi-restraints excluded: chain C residue 197 VAL Chi-restraints excluded: chain C residue 216 VAL Chi-restraints excluded: chain D residue 7 LEU Chi-restraints excluded: chain D residue 59 LYS Chi-restraints excluded: chain D residue 178 LEU Chi-restraints excluded: chain D residue 246 SER Chi-restraints excluded: chain F residue 150 ILE Chi-restraints excluded: chain F residue 201 MET Chi-restraints excluded: chain F residue 216 VAL Chi-restraints excluded: chain G residue 142 LEU Chi-restraints excluded: chain G residue 237 GLN Chi-restraints excluded: chain G residue 293 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 171 random chunks: chunk 138 optimal weight: 2.9990 chunk 23 optimal weight: 0.5980 chunk 126 optimal weight: 0.9980 chunk 63 optimal weight: 2.9990 chunk 104 optimal weight: 9.9990 chunk 99 optimal weight: 7.9990 chunk 43 optimal weight: 4.9990 chunk 68 optimal weight: 4.9990 chunk 152 optimal weight: 4.9990 chunk 3 optimal weight: 3.9990 chunk 134 optimal weight: 0.6980 overall best weight: 1.6584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Y 240 ASN Z 98 GLN Z 179 GLN Z 230 GLN Z 238 GLN C 168 GLN F 240 ASN G 230 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4025 r_free = 0.4025 target = 0.172133 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3641 r_free = 0.3641 target = 0.137901 restraints weight = 13502.127| |-----------------------------------------------------------------------------| r_work (start): 0.3641 rms_B_bonded: 2.05 r_work: 0.3399 rms_B_bonded: 2.31 restraints_weight: 0.5000 r_work: 0.3289 rms_B_bonded: 3.78 restraints_weight: 0.2500 r_work (final): 0.3289 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8568 moved from start: 0.1795 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 13605 Z= 0.155 Angle : 0.596 12.462 18498 Z= 0.303 Chirality : 0.043 0.143 2205 Planarity : 0.006 0.075 2274 Dihedral : 4.589 32.498 1909 Min Nonbonded Distance : 2.462 Molprobity Statistics. All-atom Clashscore : 4.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.47 % Favored : 94.53 % Rotamer: Outliers : 2.20 % Allowed : 20.07 % Favored : 77.73 % 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 are not related in a simple way. whole: 1.60 (0.21), residues: 1755 helix: 2.11 (0.15), residues: 1254 sheet: None (None), residues: 0 loop : -1.78 (0.27), residues: 501 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG C 127 TYR 0.008 0.001 TYR A 3 PHE 0.015 0.002 PHE D 191 TRP 0.015 0.001 TRP Z 26 HIS 0.004 0.001 HIS Z 68 Details of bonding type rmsd covalent geometry : bond 0.00365 (13599) covalent geometry : angle 0.59576 (18486) SS BOND : bond 0.00277 ( 6) SS BOND : angle 0.51626 ( 12) hydrogen bonds : bond 0.04467 ( 880) hydrogen bonds : angle 3.89784 ( 2631) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3510 Ramachandran restraints generated. 1755 Oldfield, 0 Emsley, 1755 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3510 Ramachandran restraints generated. 1755 Oldfield, 0 Emsley, 1755 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 267 residues out of total 1365 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 237 time to evaluate : 0.506 Fit side-chains REVERT: Y 243 LYS cc_start: 0.8202 (mtmm) cc_final: 0.7963 (mtmt) REVERT: Z 168 LYS cc_start: 0.6121 (tmmt) cc_final: 0.5579 (tmtt) REVERT: Z 237 GLN cc_start: 0.8151 (mt0) cc_final: 0.7865 (mt0) REVERT: Z 247 GLU cc_start: 0.7861 (pt0) cc_final: 0.7521 (pm20) REVERT: C 85 LEU cc_start: 0.8031 (OUTLIER) cc_final: 0.7742 (pt) REVERT: C 112 MET cc_start: 0.8547 (mtm) cc_final: 0.8137 (mtp) REVERT: C 117 LEU cc_start: 0.8483 (OUTLIER) cc_final: 0.8214 (tt) REVERT: D 98 GLN cc_start: 0.7673 (tm-30) cc_final: 0.7044 (mm110) REVERT: D 168 LYS cc_start: 0.5973 (tmmt) cc_final: 0.5405 (tmtt) REVERT: D 247 GLU cc_start: 0.7935 (pt0) cc_final: 0.7530 (pm20) REVERT: G 237 GLN cc_start: 0.8116 (OUTLIER) cc_final: 0.7859 (mm-40) outliers start: 30 outliers final: 20 residues processed: 253 average time/residue: 0.5448 time to fit residues: 151.5234 Evaluate side-chains 256 residues out of total 1365 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 233 time to evaluate : 0.547 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Y residue 116 THR Chi-restraints excluded: chain Y residue 154 ILE Chi-restraints excluded: chain Y residue 204 LYS Chi-restraints excluded: chain Y residue 216 VAL Chi-restraints excluded: chain Z residue 7 LEU Chi-restraints excluded: chain Z residue 142 LEU Chi-restraints excluded: chain Z residue 293 VAL Chi-restraints excluded: chain C residue 11 LEU Chi-restraints excluded: chain C residue 85 LEU Chi-restraints excluded: chain C residue 95 SER Chi-restraints excluded: chain C residue 116 THR Chi-restraints excluded: chain C residue 117 LEU Chi-restraints excluded: chain C residue 197 VAL Chi-restraints excluded: chain C residue 216 VAL Chi-restraints excluded: chain D residue 7 LEU Chi-restraints excluded: chain D residue 59 LYS Chi-restraints excluded: chain D residue 246 SER Chi-restraints excluded: chain F residue 116 THR Chi-restraints excluded: chain F residue 150 ILE Chi-restraints excluded: chain F residue 201 MET Chi-restraints excluded: chain F residue 216 VAL Chi-restraints excluded: chain G residue 142 LEU Chi-restraints excluded: chain G residue 237 GLN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 171 random chunks: chunk 143 optimal weight: 0.8980 chunk 125 optimal weight: 3.9990 chunk 4 optimal weight: 3.9990 chunk 170 optimal weight: 4.9990 chunk 50 optimal weight: 3.9990 chunk 32 optimal weight: 7.9990 chunk 89 optimal weight: 4.9990 chunk 144 optimal weight: 0.7980 chunk 69 optimal weight: 0.5980 chunk 97 optimal weight: 8.9990 chunk 45 optimal weight: 5.9990 overall best weight: 2.0584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Y 240 ASN Z 98 GLN Z 159 GLN Z 230 GLN Z 238 GLN C 148 GLN C 168 GLN D 148 ASN D 238 GLN F 240 ASN G 230 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4013 r_free = 0.4013 target = 0.171023 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3623 r_free = 0.3623 target = 0.136198 restraints weight = 13676.702| |-----------------------------------------------------------------------------| r_work (start): 0.3619 rms_B_bonded: 2.07 r_work: 0.3383 rms_B_bonded: 2.29 restraints_weight: 0.5000 r_work: 0.3274 rms_B_bonded: 3.73 restraints_weight: 0.2500 r_work (final): 0.3274 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8574 moved from start: 0.1883 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 13605 Z= 0.177 Angle : 0.622 12.422 18498 Z= 0.318 Chirality : 0.044 0.149 2205 Planarity : 0.006 0.075 2274 Dihedral : 4.749 36.199 1909 Min Nonbonded Distance : 2.409 Molprobity Statistics. All-atom Clashscore : 5.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.47 % Favored : 94.53 % Rotamer: Outliers : 2.86 % Allowed : 19.71 % Favored : 77.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.45 (0.20), residues: 1755 helix: 2.01 (0.15), residues: 1248 sheet: None (None), residues: 0 loop : -1.82 (0.26), residues: 507 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG C 127 TYR 0.009 0.002 TYR A 3 PHE 0.015 0.002 PHE D 191 TRP 0.015 0.002 TRP Z 26 HIS 0.005 0.001 HIS Z 68 Details of bonding type rmsd covalent geometry : bond 0.00424 (13599) covalent geometry : angle 0.62179 (18486) SS BOND : bond 0.00342 ( 6) SS BOND : angle 0.58631 ( 12) hydrogen bonds : bond 0.04776 ( 880) hydrogen bonds : angle 3.99737 ( 2631) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3510 Ramachandran restraints generated. 1755 Oldfield, 0 Emsley, 1755 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3510 Ramachandran restraints generated. 1755 Oldfield, 0 Emsley, 1755 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 278 residues out of total 1365 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 239 time to evaluate : 0.487 Fit side-chains REVERT: Y 44 LEU cc_start: 0.8225 (tp) cc_final: 0.7793 (tm) REVERT: Y 117 LEU cc_start: 0.8425 (OUTLIER) cc_final: 0.7870 (tt) REVERT: Y 243 LYS cc_start: 0.8225 (mtmm) cc_final: 0.7986 (mtmt) REVERT: Z 168 LYS cc_start: 0.6275 (tmmt) cc_final: 0.5731 (tmtt) REVERT: Z 237 GLN cc_start: 0.8117 (mt0) cc_final: 0.7827 (mt0) REVERT: Z 247 GLU cc_start: 0.7894 (pt0) cc_final: 0.7554 (pm20) REVERT: C 85 LEU cc_start: 0.8055 (OUTLIER) cc_final: 0.7792 (pt) REVERT: C 112 MET cc_start: 0.8536 (mtm) cc_final: 0.8131 (mtp) REVERT: C 117 LEU cc_start: 0.8466 (OUTLIER) cc_final: 0.8187 (tt) REVERT: D 168 LYS cc_start: 0.6037 (tmmt) cc_final: 0.5472 (tmtt) REVERT: D 247 GLU cc_start: 0.7946 (pt0) cc_final: 0.7529 (pm20) REVERT: F 117 LEU cc_start: 0.8622 (OUTLIER) cc_final: 0.8296 (tt) REVERT: F 127 ARG cc_start: 0.7066 (OUTLIER) cc_final: 0.6248 (mtt180) REVERT: G 237 GLN cc_start: 0.8080 (OUTLIER) cc_final: 0.7841 (mm-40) outliers start: 39 outliers final: 26 residues processed: 264 average time/residue: 0.5559 time to fit residues: 160.8969 Evaluate side-chains 263 residues out of total 1365 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 231 time to evaluate : 0.546 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Y residue 116 THR Chi-restraints excluded: chain Y residue 117 LEU Chi-restraints excluded: chain Y residue 150 ILE Chi-restraints excluded: chain Y residue 154 ILE Chi-restraints excluded: chain Y residue 204 LYS Chi-restraints excluded: chain Y residue 216 VAL Chi-restraints excluded: chain Z residue 97 ILE Chi-restraints excluded: chain Z residue 142 LEU Chi-restraints excluded: chain Z residue 293 VAL Chi-restraints excluded: chain C residue 11 LEU Chi-restraints excluded: chain C residue 85 LEU Chi-restraints excluded: chain C residue 95 SER Chi-restraints excluded: chain C residue 116 THR Chi-restraints excluded: chain C residue 117 LEU Chi-restraints excluded: chain C residue 174 MET Chi-restraints excluded: chain C residue 197 VAL Chi-restraints excluded: chain C residue 216 VAL Chi-restraints excluded: chain D residue 7 LEU Chi-restraints excluded: chain D residue 59 LYS Chi-restraints excluded: chain D residue 142 LEU Chi-restraints excluded: chain D residue 246 SER Chi-restraints excluded: chain F residue 8 LEU Chi-restraints excluded: chain F residue 95 SER Chi-restraints excluded: chain F residue 116 THR Chi-restraints excluded: chain F residue 117 LEU Chi-restraints excluded: chain F residue 127 ARG Chi-restraints excluded: chain F residue 150 ILE Chi-restraints excluded: chain F residue 201 MET Chi-restraints excluded: chain F residue 216 VAL Chi-restraints excluded: chain G residue 7 LEU Chi-restraints excluded: chain G residue 142 LEU Chi-restraints excluded: chain G residue 237 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 171 random chunks: chunk 46 optimal weight: 0.7980 chunk 36 optimal weight: 1.9990 chunk 153 optimal weight: 6.9990 chunk 6 optimal weight: 2.9990 chunk 161 optimal weight: 5.9990 chunk 166 optimal weight: 1.9990 chunk 18 optimal weight: 9.9990 chunk 151 optimal weight: 0.8980 chunk 9 optimal weight: 1.9990 chunk 87 optimal weight: 0.8980 chunk 159 optimal weight: 0.9980 overall best weight: 1.1182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Y 240 ASN Z 98 GLN Z 179 GLN Z 230 GLN Z 238 GLN C 168 GLN D 148 ASN D 204 GLN D 238 GLN F 240 ASN G 230 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4035 r_free = 0.4035 target = 0.173134 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3651 r_free = 0.3651 target = 0.138836 restraints weight = 13523.454| |-----------------------------------------------------------------------------| r_work (start): 0.3652 rms_B_bonded: 2.05 r_work: 0.3414 rms_B_bonded: 2.35 restraints_weight: 0.5000 r_work: 0.3304 rms_B_bonded: 3.87 restraints_weight: 0.2500 r_work (final): 0.3304 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8554 moved from start: 0.1807 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 13605 Z= 0.133 Angle : 0.577 12.214 18498 Z= 0.293 Chirality : 0.042 0.135 2205 Planarity : 0.006 0.074 2274 Dihedral : 4.583 34.952 1909 Min Nonbonded Distance : 2.502 Molprobity Statistics. All-atom Clashscore : 5.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.07 % Favored : 94.93 % Rotamer: Outliers : 1.83 % Allowed : 20.95 % Favored : 77.22 % 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 are not related in a simple way. whole: 1.61 (0.21), residues: 1755 helix: 2.14 (0.15), residues: 1251 sheet: None (None), residues: 0 loop : -1.84 (0.27), residues: 504 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 127 TYR 0.008 0.001 TYR A 3 PHE 0.015 0.001 PHE G 191 TRP 0.016 0.001 TRP G 26 HIS 0.003 0.001 HIS Z 68 Details of bonding type rmsd covalent geometry : bond 0.00300 (13599) covalent geometry : angle 0.57699 (18486) SS BOND : bond 0.00190 ( 6) SS BOND : angle 0.47288 ( 12) hydrogen bonds : bond 0.04181 ( 880) hydrogen bonds : angle 3.88083 ( 2631) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3510 Ramachandran restraints generated. 1755 Oldfield, 0 Emsley, 1755 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3510 Ramachandran restraints generated. 1755 Oldfield, 0 Emsley, 1755 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 262 residues out of total 1365 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 237 time to evaluate : 0.522 Fit side-chains REVERT: Y 44 LEU cc_start: 0.8223 (tp) cc_final: 0.7778 (tm) REVERT: Y 243 LYS cc_start: 0.8162 (mtmm) cc_final: 0.7945 (mtmt) REVERT: Z 168 LYS cc_start: 0.6227 (tmmt) cc_final: 0.5689 (tmtt) REVERT: Z 237 GLN cc_start: 0.8145 (mt0) cc_final: 0.7865 (mt0) REVERT: Z 247 GLU cc_start: 0.7897 (pt0) cc_final: 0.7559 (pm20) REVERT: C 85 LEU cc_start: 0.7982 (OUTLIER) cc_final: 0.7681 (pt) REVERT: C 112 MET cc_start: 0.8519 (mtm) cc_final: 0.8104 (mtp) REVERT: C 117 LEU cc_start: 0.8445 (OUTLIER) cc_final: 0.8193 (tt) REVERT: D 168 LYS cc_start: 0.6027 (tmmt) cc_final: 0.5442 (tmtt) REVERT: D 247 GLU cc_start: 0.7952 (pt0) cc_final: 0.7540 (pm20) REVERT: G 237 GLN cc_start: 0.8099 (OUTLIER) cc_final: 0.7845 (mm-40) outliers start: 25 outliers final: 20 residues processed: 251 average time/residue: 0.5413 time to fit residues: 149.4853 Evaluate side-chains 257 residues out of total 1365 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 234 time to evaluate : 0.594 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Y residue 116 THR Chi-restraints excluded: chain Y residue 154 ILE Chi-restraints excluded: chain Y residue 204 LYS Chi-restraints excluded: chain Y residue 216 VAL Chi-restraints excluded: chain Z residue 7 LEU Chi-restraints excluded: chain Z residue 97 ILE Chi-restraints excluded: chain Z residue 142 LEU Chi-restraints excluded: chain C residue 11 LEU Chi-restraints excluded: chain C residue 85 LEU Chi-restraints excluded: chain C residue 116 THR Chi-restraints excluded: chain C residue 117 LEU Chi-restraints excluded: chain C residue 197 VAL Chi-restraints excluded: chain C residue 216 VAL Chi-restraints excluded: chain D residue 7 LEU Chi-restraints excluded: chain D residue 59 LYS Chi-restraints excluded: chain D residue 142 LEU Chi-restraints excluded: chain D residue 246 SER Chi-restraints excluded: chain F residue 150 ILE Chi-restraints excluded: chain F residue 201 MET Chi-restraints excluded: chain F residue 216 VAL Chi-restraints excluded: chain G residue 7 LEU Chi-restraints excluded: chain G residue 142 LEU Chi-restraints excluded: chain G residue 237 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 171 random chunks: chunk 5 optimal weight: 8.9990 chunk 143 optimal weight: 2.9990 chunk 77 optimal weight: 0.9990 chunk 110 optimal weight: 3.9990 chunk 32 optimal weight: 8.9990 chunk 86 optimal weight: 2.9990 chunk 112 optimal weight: 0.9990 chunk 147 optimal weight: 0.1980 chunk 115 optimal weight: 6.9990 chunk 137 optimal weight: 0.6980 chunk 25 optimal weight: 0.8980 overall best weight: 0.7584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Y 240 ASN Z 98 GLN Z 179 GLN Z 230 GLN Z 238 GLN C 168 GLN D 204 GLN F 240 ASN G 230 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4058 r_free = 0.4058 target = 0.175314 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3680 r_free = 0.3680 target = 0.141225 restraints weight = 13607.518| |-----------------------------------------------------------------------------| r_work (start): 0.3679 rms_B_bonded: 2.03 r_work: 0.3436 rms_B_bonded: 2.45 restraints_weight: 0.5000 r_work: 0.3325 rms_B_bonded: 4.03 restraints_weight: 0.2500 r_work (final): 0.3325 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8525 moved from start: 0.1730 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 13605 Z= 0.117 Angle : 0.554 11.713 18498 Z= 0.280 Chirality : 0.041 0.139 2205 Planarity : 0.005 0.073 2274 Dihedral : 4.384 30.788 1909 Min Nonbonded Distance : 2.447 Molprobity Statistics. All-atom Clashscore : 5.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.96 % Favored : 95.04 % Rotamer: Outliers : 1.47 % Allowed : 21.54 % Favored : 77.00 % 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 are not related in a simple way. whole: 1.84 (0.21), residues: 1755 helix: 2.32 (0.15), residues: 1251 sheet: None (None), residues: 0 loop : -1.78 (0.27), residues: 504 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 127 TYR 0.007 0.001 TYR D 219 PHE 0.013 0.001 PHE G 191 TRP 0.015 0.001 TRP D 26 HIS 0.002 0.001 HIS Z 68 Details of bonding type rmsd covalent geometry : bond 0.00256 (13599) covalent geometry : angle 0.55418 (18486) SS BOND : bond 0.00110 ( 6) SS BOND : angle 0.39455 ( 12) hydrogen bonds : bond 0.03771 ( 880) hydrogen bonds : angle 3.76800 ( 2631) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6019.66 seconds wall clock time: 102 minutes 46.80 seconds (6166.80 seconds total)