Starting phenix.real_space_refine on Sat Sep 12 02:12:56 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7vly_32031/09_2026/7vly_32031.cif Found real_map, /net/cci-nas-00/data/ceres_data/7vly_32031/09_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 { model { file = "/net/cci-nas-00/data/ceres_data/7vly_32031/09_2026/7vly_32031.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7vly_32031/09_2026/7vly_32031.cif" restraint_files = "/net/cci-nas-00/data/ceres_data/7vly_32031/09_2026/7vly_32031.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7vly_32031/09_2026/7vly_32031.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7vly_32031/09_2026/7vly_32031.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7vly_32031/09_2026/7vly_32031.map" } 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-2.2.1-6174/lib/python3.11/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: 2.33, per 1000 atoms: 0.17 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: 1.06 Conformation dependent library (CDL) restraints added in 466.1 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: 0.23 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: 1.62 Time building geometry restraints manager: 1.44 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 - 17.97: 6988 17.97 - 35.94: 701 35.94 - 53.91: 173 53.91 - 71.88: 28 71.88 - 89.85: 18 Dihedral angle restraints: 7908 sinusoidal: 2952 harmonic: 4956 Sorted by residual: dihedral pdb=" CA LYS D 51 " pdb=" C LYS D 51 " pdb=" N GLU D 52 " pdb=" CA GLU D 52 " ideal model delta harmonic sigma weight residual 180.00 -161.76 -18.24 0 5.00e+00 4.00e-02 1.33e+01 dihedral pdb=" CA LYS G 51 " pdb=" C LYS G 51 " pdb=" N GLU G 52 " pdb=" CA GLU G 52 " ideal model delta harmonic sigma weight residual -180.00 -162.06 -17.94 0 5.00e+00 4.00e-02 1.29e+01 dihedral pdb=" CA LYS Z 51 " pdb=" C LYS Z 51 " pdb=" N GLU Z 52 " pdb=" CA GLU Z 52 " ideal model delta harmonic sigma weight residual -180.00 -162.14 -17.86 0 5.00e+00 4.00e-02 1.28e+01 ... (remaining 7905 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: 0.980 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.000 Extract box with map and model: 0.250 Check model and map are aligned: 0.040 Set scattering table: 0.030 Process input model: 10.340 Find NCS groups from input model: 0.210 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: 0.010 Load rotamer database and sin/cos tables:6.350 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 18.240 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8481 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 : 15.828 89.848 4728 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/Z covalent geometry : bond 0.00247 / 0.13 (13599) covalent geometry : angle 0.61174 / 0.35 (18486) SS BOND : bond 0.00081 / 0.04 ( 6) SS BOND : angle 0.58776 / 0.32 ( 12) hydrogen bonds : bond 0.14745 / 10.35 ( 880) hydrogen bonds : angle 5.28426 / 3.79 ( 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 : 0.370 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: 0.4873 time to fit residues: 145.9733 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 : 0.580 ------------------------------------------------------------------------------- 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... 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 = 0.4101 r_free = 0.4101 target = 0.179546 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3734 r_free = 0.3734 target = 0.145898 restraints weight = 13715.970| |-----------------------------------------------------------------------------| r_work (start): 0.3734 rms_B_bonded: 2.03 r_work: 0.3504 rms_B_bonded: 2.44 restraints_weight: 0.5000 r_work: 0.3395 rms_B_bonded: 4.03 restraints_weight: 0.2500 r_work (final): 0.3395 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8706 moved from start: 0.0929 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= 0.112 Angle : 0.535 7.159 18498 Z= 0.275 Chirality : 0.040 0.120 2205 Planarity : 0.005 0.071 2274 Dihedral : 4.990 60.658 1863 Min Nonbonded Distance : 2.592 Molprobity Statistics. All-atom Clashscore : 5.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.67 % Favored : 95.33 % Rotamer: Outliers : 3.44 % Allowed : 16.04 % Favored : 80.51 % 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 0.004 0.000 ARG C 127 TYR 0.006 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/Z covalent geometry : bond 0.00227 / 0.11 (13599) covalent geometry : angle 0.53549 / 0.28 (18486) SS BOND : bond 0.00018 / 0.01 ( 6) SS BOND : angle 0.18813 / 0.10 ( 12) hydrogen bonds : bond 0.04063 / 2.83 ( 880) hydrogen bonds : angle 3.94466 / 2.79 ( 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 294 residues out of total 1365 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 247 time to evaluate : 0.494 Fit side-chains revert: symmetry clash REVERT: Y 44 LEU cc_start: 0.8195 (tp) cc_final: 0.7806 (tm) REVERT: Z 104 MET cc_start: 0.8430 (mtp) cc_final: 0.7904 (mtm) REVERT: Z 247 GLU cc_start: 0.7734 (pt0) cc_final: 0.7425 (pm20) REVERT: C 126 ASP cc_start: 0.7337 (m-30) cc_final: 0.7034 (m-30) REVERT: D 14 ARG cc_start: 0.7912 (mtm-85) cc_final: 0.7696 (mtm180) REVERT: D 26 TRP cc_start: 0.8210 (OUTLIER) cc_final: 0.5444 (m100) REVERT: D 60 ARG cc_start: 0.7285 (mtm-85) cc_final: 0.7028 (mtp180) REVERT: D 85 GLU cc_start: 0.6544 (OUTLIER) cc_final: 0.6289 (mt-10) REVERT: D 98 GLN cc_start: 0.7575 (tm-30) cc_final: 0.7055 (mm110) REVERT: D 142 LEU cc_start: 0.8637 (OUTLIER) cc_final: 0.8407 (tp) REVERT: G 26 TRP cc_start: 0.8318 (OUTLIER) cc_final: 0.5379 (m100) REVERT: G 237 GLN cc_start: 0.8095 (mt0) cc_final: 0.7796 (mm110) outliers start: 47 outliers final: 15 residues processed: 276 average time/residue: 0.4833 time to fit residues: 147.2808 Evaluate side-chains 250 residues out of total 1365 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 231 time to evaluate : 0.379 ------------------------------------------------------------------------------- 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 Z residue 181 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: 6.9990 chunk 150 optimal weight: 0.8980 chunk 15 optimal weight: 0.0020 chunk 95 optimal weight: 5.9990 chunk 120 optimal weight: 2.9990 chunk 74 optimal weight: 7.9990 chunk 56 optimal weight: 3.9990 chunk 26 optimal weight: 4.9990 chunk 115 optimal weight: 8.9990 chunk 139 optimal weight: 6.9990 chunk 43 optimal weight: 4.9990 overall best weight: 2.5794 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Y 240 ASN Z 98 GLN Z 230 GLN Z 238 GLN D 204 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4007 r_free = 0.4007 target = 0.170475 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3613 r_free = 0.3613 target = 0.135498 restraints weight = 13660.190| |-----------------------------------------------------------------------------| r_work (start): 0.3612 rms_B_bonded: 2.10 r_work: 0.3372 rms_B_bonded: 2.31 restraints_weight: 0.5000 r_work: 0.3263 rms_B_bonded: 3.78 restraints_weight: 0.2500 r_work (final): 0.3263 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8834 moved from start: 0.1550 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.050 13605 Z= 0.209 Angle : 0.648 10.320 18498 Z= 0.336 Chirality : 0.047 0.228 2205 Planarity : 0.006 0.091 2274 Dihedral : 4.679 26.988 1845 Min Nonbonded Distance : 2.475 Molprobity Statistics. All-atom Clashscore : 5.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.19 % Favored : 94.81 % Rotamer: Outliers : 4.10 % Allowed : 16.78 % Favored : 79.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 1.28 (0.20), residues: 1755 helix: 1.86 (0.15), residues: 1248 sheet: None (None), residues: 0 loop : -1.81 (0.26), residues: 507 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG D 199 TYR 0.010 0.002 TYR A 3 PHE 0.018 0.002 PHE D 118 TRP 0.017 0.002 TRP Z 26 HIS 0.006 0.001 HIS Z 68 Details of bonding type rmsd/Z covalent geometry : bond 0.00502 / 0.21 (13599) covalent geometry : angle 0.64828 / 0.34 (18486) SS BOND : bond 0.00422 / 0.25 ( 6) SS BOND : angle 0.65062 / 0.35 ( 12) hydrogen bonds : bond 0.05339 / 3.74 ( 880) hydrogen bonds : angle 4.15278 / 2.96 ( 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 300 residues out of total 1365 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 244 time to evaluate : 0.457 Fit side-chains REVERT: Z 168 LYS cc_start: 0.5930 (tmmt) cc_final: 0.5409 (tmtt) REVERT: C 117 LEU cc_start: 0.8532 (OUTLIER) cc_final: 0.8232 (tt) REVERT: D 10 ARG cc_start: 0.7528 (OUTLIER) cc_final: 0.7023 (tpt-90) REVERT: D 98 GLN cc_start: 0.7745 (tm-30) cc_final: 0.7140 (mm110) REVERT: D 168 LYS cc_start: 0.6087 (tmmt) cc_final: 0.5489 (tmtt) REVERT: D 247 GLU cc_start: 0.7911 (pt0) cc_final: 0.7540 (pm20) outliers start: 56 outliers final: 28 residues processed: 272 average time/residue: 0.4708 time to fit residues: 141.6663 Evaluate side-chains 265 residues out of total 1365 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 235 time to evaluate : 0.422 ------------------------------------------------------------------------------- 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 99 ILE 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 35 THR 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 237 GLN Chi-restraints excluded: chain F residue 116 THR Chi-restraints excluded: chain F residue 121 ILE Chi-restraints excluded: chain F residue 159 LEU 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 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: 0.7980 chunk 39 optimal weight: 6.9990 chunk 13 optimal weight: 0.0980 chunk 100 optimal weight: 1.9990 chunk 2 skipped: trial refinement blew up (Bond distance > max_reasonable_bond_distance: 56.3662 > 50:) chunk 7 optimal weight: 1.9990 chunk 4 optimal weight: 3.9990 chunk 98 optimal weight: 2.9990 chunk 122 optimal weight: 0.7980 chunk 131 optimal weight: 9.9990 chunk 128 optimal weight: 0.9990 overall best weight: 0.9384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Y 240 ASN Z 230 GLN Z 237 GLN Z 238 GLN C 168 GLN D 148 ASN D 179 GLN D 204 GLN D 230 GLN F 168 GLN F 240 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4042 r_free = 0.4042 target = 0.174003 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3664 r_free = 0.3664 target = 0.139785 restraints weight = 13628.502| |-----------------------------------------------------------------------------| r_work (start): 0.3664 rms_B_bonded: 2.07 r_work: 0.3430 rms_B_bonded: 2.30 restraints_weight: 0.5000 r_work: 0.3321 rms_B_bonded: 3.77 restraints_weight: 0.2500 r_work (final): 0.3321 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8783 moved from start: 0.1495 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= 0.124 Angle : 0.543 7.942 18498 Z= 0.281 Chirality : 0.041 0.129 2205 Planarity : 0.005 0.082 2274 Dihedral : 4.478 26.129 1845 Min Nonbonded Distance : 2.490 Molprobity Statistics. All-atom Clashscore : 5.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.79 % Favored : 95.21 % Rotamer: Outliers : 2.86 % Allowed : 18.53 % Favored : 78.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 1.63 (0.20), residues: 1755 helix: 2.14 (0.15), residues: 1248 sheet: None (None), residues: 0 loop : -1.75 (0.26), residues: 507 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 127 TYR 0.007 0.001 TYR A 3 PHE 0.013 0.001 PHE G 191 TRP 0.014 0.001 TRP Z 26 HIS 0.003 0.001 HIS Z 68 Details of bonding type rmsd/Z covalent geometry : bond 0.00270 / 0.12 (13599) covalent geometry : angle 0.54356 / 0.28 (18486) SS BOND : bond 0.00155 / 0.09 ( 6) SS BOND : angle 0.34065 / 0.18 ( 12) hydrogen bonds : bond 0.04125 / 2.88 ( 880) hydrogen bonds : angle 3.87165 / 2.75 ( 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 274 residues out of total 1365 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 235 time to evaluate : 0.432 Fit side-chains revert: symmetry clash REVERT: Y 44 LEU cc_start: 0.8222 (tp) cc_final: 0.7793 (tm) REVERT: Z 168 LYS cc_start: 0.5884 (tmmt) cc_final: 0.5378 (tmtt) REVERT: C 117 LEU cc_start: 0.8447 (OUTLIER) cc_final: 0.8195 (tt) REVERT: D 98 GLN cc_start: 0.7619 (tm-30) cc_final: 0.7057 (mm110) REVERT: D 142 LEU cc_start: 0.8669 (OUTLIER) cc_final: 0.8461 (tp) REVERT: D 168 LYS cc_start: 0.6087 (tmmt) cc_final: 0.5508 (tmtt) REVERT: D 247 GLU cc_start: 0.7901 (pt0) cc_final: 0.7531 (pm20) outliers start: 39 outliers final: 23 residues processed: 257 average time/residue: 0.4948 time to fit residues: 140.1788 Evaluate side-chains 256 residues out of total 1365 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 231 time to evaluate : 0.485 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 C residue 11 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 142 LEU Chi-restraints excluded: chain D residue 178 LEU Chi-restraints excluded: chain F residue 95 SER Chi-restraints excluded: chain F residue 116 THR Chi-restraints excluded: chain F residue 147 MET 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 142 LEU Chi-restraints excluded: chain G residue 293 VAL Chi-restraints excluded: chain H residue 11 LYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 171 random chunks: chunk 79 optimal weight: 0.5980 chunk 86 optimal weight: 6.9990 chunk 68 optimal weight: 0.9980 chunk 75 optimal weight: 10.0000 chunk 101 optimal weight: 6.9990 chunk 12 optimal weight: 0.8980 chunk 159 optimal weight: 1.9990 chunk 36 optimal weight: 1.9990 chunk 125 optimal weight: 4.9990 chunk 37 optimal weight: 4.9990 chunk 65 optimal weight: 5.9990 overall best weight: 1.2984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Y 240 ASN Z 98 GLN Z 230 GLN Z 238 GLN C 168 GLN D 179 GLN D 204 GLN D 230 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 = 0.4031 r_free = 0.4031 target = 0.172916 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3649 r_free = 0.3649 target = 0.138458 restraints weight = 13646.402| |-----------------------------------------------------------------------------| r_work (start): 0.3647 rms_B_bonded: 2.09 r_work: 0.3410 rms_B_bonded: 2.32 restraints_weight: 0.5000 r_work: 0.3302 rms_B_bonded: 3.79 restraints_weight: 0.2500 r_work (final): 0.3302 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8798 moved from start: 0.1573 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 13605 Z= 0.138 Angle : 0.569 12.416 18498 Z= 0.290 Chirality : 0.042 0.136 2205 Planarity : 0.005 0.073 2274 Dihedral : 4.483 26.963 1845 Min Nonbonded Distance : 2.493 Molprobity Statistics. All-atom Clashscore : 4.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.19 % Favored : 94.81 % Rotamer: Outliers : 3.15 % Allowed : 18.32 % 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: 1.64 (0.20), residues: 1755 helix: 2.16 (0.15), residues: 1248 sheet: None (None), residues: 0 loop : -1.77 (0.26), residues: 507 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 127 TYR 0.008 0.001 TYR A 3 PHE 0.014 0.001 PHE G 191 TRP 0.016 0.001 TRP Z 26 HIS 0.003 0.001 HIS Z 68 Details of bonding type rmsd/Z covalent geometry : bond 0.00317 / 0.14 (13599) covalent geometry : angle 0.56865 / 0.29 (18486) SS BOND : bond 0.00228 / 0.14 ( 6) SS BOND : angle 0.42443 / 0.23 ( 12) hydrogen bonds : bond 0.04285 / 3.00 ( 880) hydrogen bonds : angle 3.86657 / 2.75 ( 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 281 residues out of total 1365 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 238 time to evaluate : 0.472 Fit side-chains revert: symmetry clash REVERT: Z 168 LYS cc_start: 0.5942 (tmmt) cc_final: 0.5417 (tmtt) REVERT: C 117 LEU cc_start: 0.8463 (OUTLIER) cc_final: 0.8206 (tt) REVERT: D 98 GLN cc_start: 0.7630 (tm-30) cc_final: 0.7064 (mm110) REVERT: D 142 LEU cc_start: 0.8664 (OUTLIER) cc_final: 0.8457 (tp) REVERT: D 168 LYS cc_start: 0.6090 (tmmt) cc_final: 0.5494 (tmtt) REVERT: D 247 GLU cc_start: 0.7931 (pt0) cc_final: 0.7545 (pm20) REVERT: G 237 GLN cc_start: 0.8172 (OUTLIER) cc_final: 0.7896 (mm-40) outliers start: 43 outliers final: 25 residues processed: 260 average time/residue: 0.4857 time to fit residues: 139.6167 Evaluate side-chains 264 residues out of total 1365 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 236 time to evaluate : 0.414 ------------------------------------------------------------------------------- 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 C residue 15 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 201 MET 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 178 LEU Chi-restraints excluded: chain F residue 95 SER Chi-restraints excluded: chain F residue 116 THR 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 142 LEU Chi-restraints excluded: chain G residue 237 GLN Chi-restraints excluded: chain G residue 293 VAL Chi-restraints excluded: chain H residue 11 LYS 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: 4.9990 chunk 49 optimal weight: 4.9990 chunk 158 optimal weight: 0.0270 chunk 89 optimal weight: 0.6980 chunk 146 optimal weight: 0.7980 chunk 166 optimal weight: 2.9990 chunk 136 optimal weight: 0.9980 chunk 45 optimal weight: 4.9990 chunk 65 optimal weight: 3.9990 chunk 164 optimal weight: 1.9990 overall best weight: 0.9040 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Y 240 ASN Z 98 GLN Z 179 GLN Z 230 GLN Z 238 GLN C 168 GLN C 240 ASN D 148 ASN D 179 GLN D 204 GLN D 230 GLN D 238 GLN F 240 ASN G 230 GLN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4044 r_free = 0.4044 target = 0.173951 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3671 r_free = 0.3671 target = 0.139827 restraints weight = 13513.631| |-----------------------------------------------------------------------------| r_work (start): 0.3670 rms_B_bonded: 2.06 r_work: 0.3434 rms_B_bonded: 2.30 restraints_weight: 0.5000 r_work: 0.3325 rms_B_bonded: 3.78 restraints_weight: 0.2500 r_work (final): 0.3325 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8778 moved from start: 0.1578 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= 0.121 Angle : 0.552 11.566 18498 Z= 0.280 Chirality : 0.041 0.205 2205 Planarity : 0.005 0.072 2274 Dihedral : 4.405 26.181 1845 Min Nonbonded Distance : 2.482 Molprobity Statistics. All-atom Clashscore : 4.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.13 % Favored : 94.87 % Rotamer: Outliers : 2.78 % Allowed : 19.12 % Favored : 78.10 % 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: 2.24 (0.15), residues: 1251 sheet: None (None), residues: 0 loop : -1.79 (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 0.013 0.001 PHE G 191 TRP 0.014 0.001 TRP Z 26 HIS 0.003 0.001 HIS Z 68 Details of bonding type rmsd/Z covalent geometry : bond 0.00267 / 0.12 (13599) covalent geometry : angle 0.55224 / 0.28 (18486) SS BOND : bond 0.00148 / 0.09 ( 6) SS BOND : angle 0.36101 / 0.20 ( 12) hydrogen bonds : bond 0.03971 / 2.78 ( 880) hydrogen bonds : angle 3.79607 / 2.70 ( 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 273 residues out of total 1365 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 235 time to evaluate : 0.462 Fit side-chains revert: symmetry clash REVERT: Y 44 LEU cc_start: 0.8221 (tp) cc_final: 0.7802 (tm) REVERT: Y 243 LYS cc_start: 0.8333 (mtmm) cc_final: 0.8006 (mtmt) REVERT: Z 237 GLN cc_start: 0.8050 (mt0) cc_final: 0.7703 (mt0) REVERT: C 112 MET cc_start: 0.8502 (mtm) cc_final: 0.8056 (mtp) REVERT: C 117 LEU cc_start: 0.8435 (OUTLIER) cc_final: 0.8176 (tt) REVERT: D 98 GLN cc_start: 0.7583 (tm-30) cc_final: 0.7061 (mm110) REVERT: D 168 LYS cc_start: 0.6081 (tmmt) cc_final: 0.5490 (tmtt) REVERT: D 247 GLU cc_start: 0.7958 (pt0) cc_final: 0.7556 (pm20) REVERT: G 237 GLN cc_start: 0.8127 (OUTLIER) cc_final: 0.7877 (mm-40) outliers start: 38 outliers final: 22 residues processed: 257 average time/residue: 0.4812 time to fit residues: 136.4868 Evaluate side-chains 253 residues out of total 1365 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 229 time to evaluate : 0.489 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Y residue 116 THR 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 142 LEU Chi-restraints excluded: chain C residue 15 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 147 MET 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 Chi-restraints excluded: chain G residue 293 VAL Chi-restraints excluded: chain H residue 11 LYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 171 random chunks: chunk 27 optimal weight: 7.9990 chunk 153 optimal weight: 0.9980 chunk 118 optimal weight: 2.9990 chunk 70 optimal weight: 7.9990 chunk 49 optimal weight: 4.9990 chunk 103 optimal weight: 6.9990 chunk 46 optimal weight: 0.0980 chunk 114 optimal weight: 9.9990 chunk 164 optimal weight: 2.9990 chunk 86 optimal weight: 0.9990 chunk 161 optimal weight: 1.9990 overall best weight: 1.4186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Y 240 ASN Z 98 GLN Z 179 GLN Z 230 GLN Z 238 GLN C 168 GLN D 179 GLN D 204 GLN D 230 GLN D 238 GLN F 240 ASN G 230 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4028 r_free = 0.4028 target = 0.172589 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3644 r_free = 0.3644 target = 0.138128 restraints weight = 13569.549| |-----------------------------------------------------------------------------| r_work (start): 0.3645 rms_B_bonded: 2.09 r_work: 0.3409 rms_B_bonded: 2.31 restraints_weight: 0.5000 r_work: 0.3301 rms_B_bonded: 3.77 restraints_weight: 0.2500 r_work (final): 0.3301 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8800 moved from start: 0.1674 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 13605 Z= 0.143 Angle : 0.579 11.915 18498 Z= 0.294 Chirality : 0.042 0.138 2205 Planarity : 0.005 0.073 2274 Dihedral : 4.496 27.932 1845 Min Nonbonded Distance : 2.457 Molprobity Statistics. All-atom Clashscore : 5.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.30 % Favored : 94.70 % Rotamer: Outliers : 2.71 % Allowed : 19.49 % Favored : 77.80 % 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: 1.65 (0.21), residues: 1755 helix: 2.16 (0.15), residues: 1254 sheet: None (None), residues: 0 loop : -1.79 (0.26), residues: 501 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 127 TYR 0.008 0.001 TYR A 3 PHE 0.014 0.001 PHE G 191 TRP 0.016 0.001 TRP Z 26 HIS 0.004 0.001 HIS Z 68 Details of bonding type rmsd/Z covalent geometry : bond 0.00332 / 0.14 (13599) covalent geometry : angle 0.57892 / 0.29 (18486) SS BOND : bond 0.00244 / 0.15 ( 6) SS BOND : angle 0.45279 / 0.25 ( 12) hydrogen bonds : bond 0.04299 / 3.01 ( 880) hydrogen bonds : angle 3.86281 / 2.75 ( 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 270 residues out of total 1365 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 233 time to evaluate : 0.420 Fit side-chains REVERT: Y 243 LYS cc_start: 0.8300 (mtmm) cc_final: 0.8059 (mtmt) REVERT: Z 237 GLN cc_start: 0.8085 (mt0) cc_final: 0.7823 (mt0) REVERT: Z 247 GLU cc_start: 0.7907 (pt0) cc_final: 0.7554 (pm20) REVERT: C 112 MET cc_start: 0.8532 (mtm) cc_final: 0.8116 (mtp) REVERT: C 117 LEU cc_start: 0.8486 (OUTLIER) cc_final: 0.8212 (tt) REVERT: D 98 GLN cc_start: 0.7638 (tm-30) cc_final: 0.7043 (mm110) REVERT: D 168 LYS cc_start: 0.6126 (tmmt) cc_final: 0.5536 (tmtt) REVERT: D 247 GLU cc_start: 0.7960 (pt0) cc_final: 0.7568 (pm20) REVERT: G 237 GLN cc_start: 0.8124 (OUTLIER) cc_final: 0.7860 (mm-40) outliers start: 37 outliers final: 25 residues processed: 256 average time/residue: 0.4786 time to fit residues: 135.5367 Evaluate side-chains 257 residues out of total 1365 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 230 time to evaluate : 0.516 ------------------------------------------------------------------------------- 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 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 15 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 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 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 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: 1.9990 chunk 23 optimal weight: 0.5980 chunk 126 optimal weight: 0.8980 chunk 63 optimal weight: 1.9990 chunk 104 optimal weight: 8.9990 chunk 99 optimal weight: 6.9990 chunk 43 optimal weight: 0.7980 chunk 68 optimal weight: 3.9990 chunk 152 optimal weight: 3.9990 chunk 3 optimal weight: 0.7980 chunk 134 optimal weight: 0.9980 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Y 240 ASN Z 98 GLN Z 179 GLN Z 230 GLN Z 238 GLN C 148 GLN C 168 GLN D 179 GLN D 204 GLN F 240 ASN G 230 GLN G 238 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4052 r_free = 0.4052 target = 0.174774 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3675 r_free = 0.3675 target = 0.140766 restraints weight = 13565.143| |-----------------------------------------------------------------------------| r_work (start): 0.3676 rms_B_bonded: 1.99 r_work: 0.3432 rms_B_bonded: 2.43 restraints_weight: 0.5000 r_work: 0.3322 rms_B_bonded: 3.99 restraints_weight: 0.2500 r_work (final): 0.3322 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8778 moved from start: 0.1644 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= 0.118 Angle : 0.550 11.713 18498 Z= 0.278 Chirality : 0.041 0.176 2205 Planarity : 0.005 0.072 2274 Dihedral : 4.383 27.024 1845 Min Nonbonded Distance : 2.463 Molprobity Statistics. All-atom Clashscore : 5.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.79 % Favored : 95.21 % 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: 1.81 (0.21), residues: 1755 helix: 2.29 (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 Z 219 PHE 0.013 0.001 PHE G 191 TRP 0.015 0.001 TRP Z 26 HIS 0.002 0.001 HIS Z 68 Details of bonding type rmsd/Z covalent geometry : bond 0.00259 / 0.12 (13599) covalent geometry : angle 0.55045 / 0.28 (18486) SS BOND : bond 0.00130 / 0.08 ( 6) SS BOND : angle 0.35866 / 0.20 ( 12) hydrogen bonds : bond 0.03871 / 2.71 ( 880) hydrogen bonds : angle 3.77745 / 2.69 ( 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 260 residues out of total 1365 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 230 time to evaluate : 0.539 Fit side-chains REVERT: Y 44 LEU cc_start: 0.8206 (tp) cc_final: 0.7766 (tm) REVERT: Z 237 GLN cc_start: 0.8081 (mt0) cc_final: 0.7733 (mt0) REVERT: Z 247 GLU cc_start: 0.7853 (pt0) cc_final: 0.7486 (pm20) REVERT: C 112 MET cc_start: 0.8520 (mtm) cc_final: 0.8108 (mtp) REVERT: C 117 LEU cc_start: 0.8439 (OUTLIER) cc_final: 0.8187 (tt) REVERT: D 98 GLN cc_start: 0.7668 (tm-30) cc_final: 0.7054 (mm110) REVERT: D 168 LYS cc_start: 0.6036 (tmmt) cc_final: 0.5457 (tmtt) REVERT: D 247 GLU cc_start: 0.7913 (pt0) cc_final: 0.7512 (pm20) REVERT: F 127 ARG cc_start: 0.7038 (OUTLIER) cc_final: 0.6280 (mtt180) REVERT: G 237 GLN cc_start: 0.8117 (OUTLIER) cc_final: 0.7878 (mm-40) outliers start: 30 outliers final: 21 residues processed: 245 average time/residue: 0.5655 time to fit residues: 152.3930 Evaluate side-chains 250 residues out of total 1365 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 226 time to evaluate : 0.523 ------------------------------------------------------------------------------- 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 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 15 LEU Chi-restraints excluded: chain C residue 116 THR Chi-restraints excluded: chain C residue 117 LEU 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 148 ASN Chi-restraints excluded: chain D residue 237 GLN Chi-restraints excluded: chain F residue 116 THR 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 Chi-restraints excluded: chain G residue 293 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 171 random chunks: chunk 143 optimal weight: 1.9990 chunk 125 optimal weight: 4.9990 chunk 4 optimal weight: 5.9990 chunk 170 optimal weight: 0.8980 chunk 50 optimal weight: 0.5980 chunk 32 optimal weight: 8.9990 chunk 89 optimal weight: 3.9990 chunk 144 optimal weight: 0.6980 chunk 69 optimal weight: 5.9990 chunk 97 optimal weight: 0.7980 chunk 45 optimal weight: 2.9990 overall best weight: 0.9982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Y 240 ASN Z 98 GLN Z 179 GLN Z 230 GLN Z 238 GLN C 168 GLN D 179 GLN D 204 GLN D 230 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 = 0.4047 r_free = 0.4047 target = 0.174446 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3666 r_free = 0.3666 target = 0.140028 restraints weight = 13715.788| |-----------------------------------------------------------------------------| r_work (start): 0.3665 rms_B_bonded: 2.05 r_work: 0.3426 rms_B_bonded: 2.40 restraints_weight: 0.5000 r_work: 0.3317 rms_B_bonded: 3.93 restraints_weight: 0.2500 r_work (final): 0.3317 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8781 moved from start: 0.1681 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= 0.125 Angle : 0.562 11.594 18498 Z= 0.284 Chirality : 0.041 0.141 2205 Planarity : 0.005 0.072 2274 Dihedral : 4.360 26.989 1844 Min Nonbonded Distance : 2.428 Molprobity Statistics. All-atom Clashscore : 5.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.13 % Favored : 94.87 % Rotamer: Outliers : 2.12 % Allowed : 20.59 % Favored : 77.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 1.82 (0.21), residues: 1755 helix: 2.30 (0.15), residues: 1251 sheet: None (None), residues: 0 loop : -1.77 (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 F 161 TRP 0.015 0.001 TRP Z 26 HIS 0.003 0.001 HIS Z 68 Details of bonding type rmsd/Z covalent geometry : bond 0.00280 / 0.12 (13599) covalent geometry : angle 0.56198 / 0.28 (18486) SS BOND : bond 0.00176 / 0.11 ( 6) SS BOND : angle 0.44238 / 0.25 ( 12) hydrogen bonds : bond 0.03957 / 2.77 ( 880) hydrogen bonds : angle 3.77985 / 2.69 ( 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 257 residues out of total 1365 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 228 time to evaluate : 0.650 Fit side-chains REVERT: Y 44 LEU cc_start: 0.8214 (tp) cc_final: 0.7778 (tm) REVERT: Z 237 GLN cc_start: 0.8066 (mt0) cc_final: 0.7719 (mt0) REVERT: Z 247 GLU cc_start: 0.7868 (pt0) cc_final: 0.7505 (pm20) REVERT: C 85 LEU cc_start: 0.7879 (OUTLIER) cc_final: 0.7614 (pt) REVERT: C 112 MET cc_start: 0.8531 (mtm) cc_final: 0.8093 (mtp) REVERT: C 117 LEU cc_start: 0.8458 (OUTLIER) cc_final: 0.8210 (tt) REVERT: D 98 GLN cc_start: 0.7677 (tm-30) cc_final: 0.7050 (mm110) REVERT: D 168 LYS cc_start: 0.6030 (tmmt) cc_final: 0.5458 (tmtt) REVERT: D 247 GLU cc_start: 0.7914 (pt0) cc_final: 0.7511 (pm20) REVERT: F 127 ARG cc_start: 0.7013 (OUTLIER) cc_final: 0.6264 (mtt180) REVERT: G 138 LEU cc_start: 0.8183 (tp) cc_final: 0.7982 (tm) REVERT: G 237 GLN cc_start: 0.8122 (OUTLIER) cc_final: 0.7860 (mm-40) outliers start: 29 outliers final: 19 residues processed: 244 average time/residue: 0.5440 time to fit residues: 146.6400 Evaluate side-chains 249 residues out of total 1365 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 226 time to evaluate : 0.510 ------------------------------------------------------------------------------- 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 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 85 LEU Chi-restraints excluded: chain C residue 116 THR Chi-restraints excluded: chain C residue 117 LEU 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 237 GLN Chi-restraints excluded: chain D residue 246 SER Chi-restraints excluded: chain F residue 116 THR 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 Chi-restraints excluded: chain G residue 293 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 171 random chunks: chunk 46 optimal weight: 0.1980 chunk 36 optimal weight: 0.0970 chunk 153 optimal weight: 3.9990 chunk 6 optimal weight: 3.9990 chunk 161 optimal weight: 3.9990 chunk 166 optimal weight: 3.9990 chunk 18 optimal weight: 8.9990 chunk 151 optimal weight: 0.9980 chunk 9 optimal weight: 0.7980 chunk 87 optimal weight: 0.6980 chunk 159 optimal weight: 0.0030 overall best weight: 0.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Y 240 ASN Z 98 GLN Z 179 GLN Z 230 GLN Z 238 GLN C 168 GLN D 179 GLN D 230 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 = 0.4092 r_free = 0.4092 target = 0.178707 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3723 r_free = 0.3723 target = 0.144933 restraints weight = 13656.843| |-----------------------------------------------------------------------------| r_work (start): 0.3714 rms_B_bonded: 1.96 r_work: 0.3492 rms_B_bonded: 2.31 restraints_weight: 0.5000 r_work: 0.3383 rms_B_bonded: 3.83 restraints_weight: 0.2500 r_work (final): 0.3383 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8715 moved from start: 0.1658 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 13605 Z= 0.103 Angle : 0.533 12.122 18498 Z= 0.267 Chirality : 0.040 0.136 2205 Planarity : 0.005 0.071 2274 Dihedral : 4.160 26.063 1844 Min Nonbonded Distance : 2.438 Molprobity Statistics. All-atom Clashscore : 5.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.62 % Favored : 95.38 % Rotamer: Outliers : 1.47 % Allowed : 21.32 % 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: 2.01 (0.21), residues: 1755 helix: 2.45 (0.15), residues: 1251 sheet: None (None), residues: 0 loop : -1.72 (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 0.009 0.001 PHE Z 191 TRP 0.013 0.001 TRP Z 26 HIS 0.002 0.000 HIS Z 298 Details of bonding type rmsd/Z covalent geometry : bond 0.00215 / 0.10 (13599) covalent geometry : angle 0.53310 / 0.27 (18486) SS BOND : bond 0.00025 / 0.01 ( 6) SS BOND : angle 0.32613 / 0.19 ( 12) hydrogen bonds : bond 0.03359 / 2.34 ( 880) hydrogen bonds : angle 3.65355 / 2.59 ( 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 256 residues out of total 1365 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 236 time to evaluate : 0.526 Fit side-chains revert: symmetry clash REVERT: Y 44 LEU cc_start: 0.8182 (tp) cc_final: 0.7765 (tm) REVERT: Z 168 LYS cc_start: 0.5949 (tmmt) cc_final: 0.5428 (tmtt) REVERT: Z 237 GLN cc_start: 0.8044 (mt0) cc_final: 0.7710 (mt0) REVERT: Z 247 GLU cc_start: 0.7833 (pt0) cc_final: 0.7498 (pm20) REVERT: C 85 LEU cc_start: 0.7780 (OUTLIER) cc_final: 0.7455 (pt) REVERT: C 112 MET cc_start: 0.8504 (mtm) cc_final: 0.8087 (mtp) REVERT: C 189 VAL cc_start: 0.8092 (t) cc_final: 0.7850 (t) REVERT: C 204 LYS cc_start: 0.8707 (ptpp) cc_final: 0.8234 (pptt) REVERT: D 98 GLN cc_start: 0.7632 (tm-30) cc_final: 0.7007 (mm110) REVERT: D 168 LYS cc_start: 0.5889 (tmmt) cc_final: 0.5326 (tmtt) REVERT: D 247 GLU cc_start: 0.7897 (pt0) cc_final: 0.7498 (pm20) REVERT: E 13 SER cc_start: 0.8795 (m) cc_final: 0.8432 (p) REVERT: F 127 ARG cc_start: 0.6951 (mtt180) cc_final: 0.6704 (mtt180) REVERT: G 168 LYS cc_start: 0.6038 (tmmt) cc_final: 0.5397 (tmtt) REVERT: G 237 GLN cc_start: 0.8082 (OUTLIER) cc_final: 0.7843 (mm-40) REVERT: G 247 GLU cc_start: 0.7832 (pt0) cc_final: 0.6821 (tp30) outliers start: 20 outliers final: 13 residues processed: 247 average time/residue: 0.5521 time to fit residues: 150.4677 Evaluate side-chains 241 residues out of total 1365 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 226 time to evaluate : 0.500 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Y residue 154 ILE Chi-restraints excluded: chain Z residue 7 LEU Chi-restraints excluded: chain Z residue 142 LEU Chi-restraints excluded: chain C residue 85 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 123 MET Chi-restraints excluded: chain D residue 246 SER Chi-restraints excluded: chain F residue 95 SER Chi-restraints excluded: chain F residue 150 ILE Chi-restraints excluded: chain G residue 7 LEU Chi-restraints excluded: chain G residue 237 GLN Chi-restraints excluded: chain G residue 293 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 171 random chunks: chunk 5 optimal weight: 7.9990 chunk 143 optimal weight: 1.9990 chunk 77 optimal weight: 1.9990 chunk 110 optimal weight: 4.9990 chunk 32 optimal weight: 7.9990 chunk 86 optimal weight: 0.9990 chunk 112 optimal weight: 1.9990 chunk 147 optimal weight: 2.9990 chunk 115 optimal weight: 6.9990 chunk 137 optimal weight: 0.9980 chunk 25 optimal weight: 0.9990 overall best weight: 1.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Y 240 ASN Z 179 GLN Z 230 GLN Z 238 GLN F 240 ASN G 230 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4044 r_free = 0.4044 target = 0.173959 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3659 r_free = 0.3659 target = 0.139433 restraints weight = 13622.707| |-----------------------------------------------------------------------------| r_work (start): 0.3660 rms_B_bonded: 2.09 r_work: 0.3424 rms_B_bonded: 2.36 restraints_weight: 0.5000 r_work: 0.3317 rms_B_bonded: 3.87 restraints_weight: 0.2500 r_work (final): 0.3317 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8789 moved from start: 0.1768 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 13605 Z= 0.143 Angle : 0.586 11.695 18498 Z= 0.296 Chirality : 0.042 0.149 2205 Planarity : 0.005 0.072 2274 Dihedral : 4.339 25.617 1844 Min Nonbonded Distance : 2.412 Molprobity Statistics. All-atom Clashscore : 5.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.30 % Favored : 94.70 % Rotamer: Outliers : 1.54 % Allowed : 21.83 % Favored : 76.63 % 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: 1.88 (0.21), residues: 1755 helix: 2.34 (0.15), residues: 1251 sheet: None (None), residues: 0 loop : -1.74 (0.27), residues: 504 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG C 127 TYR 0.007 0.001 TYR G 219 PHE 0.016 0.002 PHE F 161 TRP 0.015 0.001 TRP Z 26 HIS 0.003 0.001 HIS Z 68 Details of bonding type rmsd/Z covalent geometry : bond 0.00333 / 0.14 (13599) covalent geometry : angle 0.58586 / 0.30 (18486) SS BOND : bond 0.00245 / 0.15 ( 6) SS BOND : angle 0.50956 / 0.29 ( 12) hydrogen bonds : bond 0.04135 / 2.90 ( 880) hydrogen bonds : angle 3.80084 / 2.70 ( 2631) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5642.92 seconds wall clock time: 96 minutes 40.81 seconds (5800.81 seconds total)