Starting phenix.real_space_refine on Thu Jul 31 03:14:36 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7vly_32031/07_2025/7vly_32031.cif Found real_map, /net/cci-nas-00/data/ceres_data/7vly_32031/07_2025/7vly_32031.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.45 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7vly_32031/07_2025/7vly_32031.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7vly_32031/07_2025/7vly_32031.map" model { file = "/net/cci-nas-00/data/ceres_data/7vly_32031/07_2025/7vly_32031.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7vly_32031/07_2025/7vly_32031.cif" } resolution = 2.45 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.003 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): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/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: 8.24, per 1000 atoms: 0.62 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: 3.68 Conformation dependent library (CDL) restraints added in 2.0 seconds 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: 1.34 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: 4.13 Time building geometry restraints manager: 4.40 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 4182 1.34 - 1.46: 3071 1.46 - 1.58: 6196 1.58 - 1.70: 0 1.70 - 1.82: 150 Bond restraints: 13599 Sorted by residual: bond pdb=" C5 MAN G 401 " pdb=" O5 MAN G 401 " ideal model delta sigma weight residual 1.418 1.458 -0.040 2.00e-02 2.50e+03 3.99e+00 bond pdb=" C5 MAN Z 401 " pdb=" O5 MAN Z 401 " ideal model delta sigma weight residual 1.418 1.458 -0.040 2.00e-02 2.50e+03 3.99e+00 bond pdb=" C5 MAN D 401 " pdb=" O5 MAN D 401 " ideal model delta sigma weight residual 1.418 1.457 -0.039 2.00e-02 2.50e+03 3.86e+00 bond pdb=" C ALA D 206 " pdb=" N PRO D 207 " ideal model delta sigma weight residual 1.333 1.352 -0.019 1.20e-02 6.94e+03 2.63e+00 bond pdb=" C ALA G 206 " pdb=" N PRO G 207 " ideal model delta sigma weight residual 1.333 1.352 -0.019 1.20e-02 6.94e+03 2.54e+00 ... (remaining 13594 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.69: 18108 1.69 - 3.38: 286 3.38 - 5.08: 64 5.08 - 6.77: 22 6.77 - 8.46: 6 Bond angle restraints: 18486 Sorted by residual: angle pdb=" C LYS Z 49 " pdb=" N THR Z 50 " pdb=" CA THR Z 50 " ideal model delta sigma weight residual 121.71 115.21 6.50 1.39e+00 5.18e-01 2.18e+01 angle pdb=" C LYS G 49 " pdb=" N THR G 50 " pdb=" CA THR G 50 " ideal model delta sigma weight residual 121.71 115.28 6.43 1.39e+00 5.18e-01 2.14e+01 angle pdb=" C LYS D 49 " pdb=" N THR D 50 " pdb=" CA THR D 50 " ideal model delta sigma weight residual 121.71 115.36 6.35 1.39e+00 5.18e-01 2.09e+01 angle pdb=" CA LYS G 164 " pdb=" CB LYS G 164 " pdb=" CG LYS G 164 " ideal model delta sigma weight residual 114.10 122.14 -8.04 2.00e+00 2.50e-01 1.62e+01 angle pdb=" C PHE Z 205 " pdb=" N ALA Z 206 " pdb=" CA ALA Z 206 " ideal model delta sigma weight residual 122.28 118.79 3.49 1.02e+00 9.61e-01 1.17e+01 ... (remaining 18481 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 23.47: 7319 23.47 - 46.94: 553 46.94 - 70.41: 68 70.41 - 93.88: 28 93.88 - 117.34: 6 Dihedral angle restraints: 7974 sinusoidal: 3018 harmonic: 4956 Sorted by residual: dihedral pdb=" C2 MAN G 401 " pdb=" C1 MAN G 401 " pdb=" O5 MAN G 401 " pdb=" C5 MAN G 401 " ideal model delta sinusoidal sigma weight residual -57.62 59.72 -117.34 1 3.00e+01 1.11e-03 1.56e+01 dihedral pdb=" C2 MAN Z 401 " pdb=" C1 MAN Z 401 " pdb=" O5 MAN Z 401 " pdb=" C5 MAN Z 401 " ideal model delta sinusoidal sigma weight residual -57.62 59.64 -117.26 1 3.00e+01 1.11e-03 1.56e+01 dihedral pdb=" C2 MAN D 401 " pdb=" C1 MAN D 401 " pdb=" O5 MAN D 401 " pdb=" C5 MAN D 401 " ideal model delta sinusoidal sigma weight residual -57.62 59.57 -117.19 1 3.00e+01 1.11e-03 1.55e+01 ... (remaining 7971 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.025: 1237 0.025 - 0.051: 507 0.051 - 0.076: 310 0.076 - 0.102: 116 0.102 - 0.127: 35 Chirality restraints: 2205 Sorted by residual: chirality pdb=" CA ILE C 162 " pdb=" N ILE C 162 " pdb=" C ILE C 162 " pdb=" CB ILE C 162 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 4.06e-01 chirality pdb=" CA ILE Y 162 " pdb=" N ILE Y 162 " pdb=" C ILE Y 162 " pdb=" CB ILE Y 162 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.12 2.00e-01 2.50e+01 3.83e-01 chirality pdb=" CA ILE F 162 " pdb=" N ILE F 162 " pdb=" C ILE F 162 " pdb=" CB ILE F 162 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.12 2.00e-01 2.50e+01 3.77e-01 ... (remaining 2202 not shown) Planarity restraints: 2274 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ALA C 69 " -0.050 5.00e-02 4.00e+02 7.70e-02 9.48e+00 pdb=" N PRO C 70 " 0.133 5.00e-02 4.00e+02 pdb=" CA PRO C 70 " -0.041 5.00e-02 4.00e+02 pdb=" CD PRO C 70 " -0.042 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ALA Y 69 " 0.050 5.00e-02 4.00e+02 7.59e-02 9.21e+00 pdb=" N PRO Y 70 " -0.131 5.00e-02 4.00e+02 pdb=" CA PRO Y 70 " 0.040 5.00e-02 4.00e+02 pdb=" CD PRO Y 70 " 0.042 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ALA F 69 " 0.049 5.00e-02 4.00e+02 7.57e-02 9.17e+00 pdb=" N PRO F 70 " -0.131 5.00e-02 4.00e+02 pdb=" CA PRO F 70 " 0.040 5.00e-02 4.00e+02 pdb=" CD PRO F 70 " 0.041 5.00e-02 4.00e+02 ... (remaining 2271 not shown) Histogram of nonbonded interaction distances: 2.23 - 2.77: 2281 2.77 - 3.30: 13273 3.30 - 3.83: 23862 3.83 - 4.37: 26955 4.37 - 4.90: 45800 Nonbonded interactions: 112171 Sorted by model distance: nonbonded pdb=" OE2 GLU Y 205 " pdb=" NZ LYS Z 183 " model vdw 2.232 3.120 nonbonded pdb=" O ALA Y 72 " pdb=" OG SER Y 76 " model vdw 2.234 3.040 nonbonded pdb=" OD2 ASP G 113 " pdb=" O6 MAN G 401 " model vdw 2.241 3.040 nonbonded pdb=" OD2 ASP D 113 " pdb=" O6 MAN D 401 " model vdw 2.254 3.040 nonbonded pdb=" OD2 ASP Z 113 " pdb=" O6 MAN Z 401 " model vdw 2.255 3.040 ... (remaining 112166 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'E' selection = chain 'H' } ncs_group { reference = chain 'C' selection = chain 'F' selection = chain 'Y' } ncs_group { reference = chain 'D' selection = chain 'G' selection = chain 'Z' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.350 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.570 Check model and map are aligned: 0.100 Set scattering table: 0.130 Process input model: 34.860 Find NCS groups from input model: 0.460 Set up NCS constraints: 0.080 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:14.580 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 52.140 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8183 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 13605 Z= 0.129 Angle : 0.612 8.460 18498 Z= 0.346 Chirality : 0.040 0.127 2205 Planarity : 0.005 0.077 2274 Dihedral : 17.023 117.345 4794 Min Nonbonded Distance : 2.232 Molprobity Statistics. All-atom Clashscore : 6.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.05 % Favored : 95.95 % Rotamer: Outliers : 2.49 % Allowed : 17.44 % Favored : 80.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 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 TRP 0.015 0.001 TRP D 26 HIS 0.003 0.001 HIS Z 298 PHE 0.008 0.001 PHE Z 144 TYR 0.008 0.001 TYR Z 219 ARG 0.008 0.000 ARG C 127 Details of bonding type rmsd hydrogen bonds : bond 0.14745 ( 880) hydrogen bonds : angle 5.28426 ( 2631) SS BOND : bond 0.00081 ( 6) SS BOND : angle 0.58776 ( 12) covalent geometry : bond 0.00247 (13599) covalent geometry : angle 0.61174 (18486) *********************** 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 : 1.458 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: 1.0933 time to fit residues: 326.3000 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 : 1.479 ------------------------------------------------------------------------------- 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 144 optimal weight: 0.6980 chunk 129 optimal weight: 6.9990 chunk 71 optimal weight: 0.9990 chunk 44 optimal weight: 6.9990 chunk 87 optimal weight: 2.9990 chunk 69 optimal weight: 0.0070 chunk 134 optimal weight: 3.9990 chunk 51 optimal weight: 0.5980 chunk 81 optimal weight: 2.9990 chunk 99 optimal weight: 6.9990 chunk 155 optimal weight: 0.8980 overall best weight: 0.6400 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Y 240 ASN Z 98 GLN Z 179 GLN ** Z 230 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 237 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 238 GLN D 148 ASN D 159 GLN D 179 GLN D 204 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4083 r_free = 0.4083 target = 0.177762 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3712 r_free = 0.3712 target = 0.143924 restraints weight = 13655.226| |-----------------------------------------------------------------------------| r_work (start): 0.3711 rms_B_bonded: 2.08 r_work: 0.3482 rms_B_bonded: 2.34 restraints_weight: 0.5000 r_work: 0.3374 rms_B_bonded: 3.85 restraints_weight: 0.2500 r_work (final): 0.3374 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8484 moved from start: 0.0936 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= 0.122 Angle : 0.560 7.405 18498 Z= 0.286 Chirality : 0.041 0.163 2205 Planarity : 0.005 0.072 2274 Dihedral : 6.458 62.649 1929 Min Nonbonded Distance : 2.588 Molprobity Statistics. All-atom Clashscore : 4.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.62 % Favored : 95.38 % Rotamer: Outliers : 3.52 % Allowed : 15.97 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.63 (0.20), residues: 1755 helix: 2.13 (0.15), residues: 1242 sheet: None (None), residues: 0 loop : -1.66 (0.26), residues: 513 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP D 222 HIS 0.003 0.001 HIS Z 298 PHE 0.013 0.001 PHE Y 161 TYR 0.006 0.001 TYR D 219 ARG 0.004 0.000 ARG C 127 Details of bonding type rmsd hydrogen bonds : bond 0.04297 ( 880) hydrogen bonds : angle 3.98306 ( 2631) SS BOND : bond 0.00064 ( 6) SS BOND : angle 0.15704 ( 12) covalent geometry : bond 0.00256 (13599) covalent geometry : angle 0.56052 (18486) *********************** 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 291 residues out of total 1365 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 243 time to evaluate : 1.828 Fit side-chains revert: symmetry clash REVERT: Y 44 LEU cc_start: 0.8199 (tp) cc_final: 0.7784 (tm) REVERT: Z 104 MET cc_start: 0.8486 (mtp) cc_final: 0.8072 (mtm) REVERT: Z 247 GLU cc_start: 0.7733 (pt0) cc_final: 0.7437 (pm20) REVERT: C 126 ASP cc_start: 0.7363 (m-30) cc_final: 0.7052 (m-30) REVERT: D 14 ARG cc_start: 0.7924 (mtm-85) cc_final: 0.7713 (mtm180) REVERT: D 26 TRP cc_start: 0.8307 (OUTLIER) cc_final: 0.5421 (m100) REVERT: D 85 GLU cc_start: 0.6501 (OUTLIER) cc_final: 0.6199 (mt-10) REVERT: D 98 GLN cc_start: 0.7697 (tm-30) cc_final: 0.7066 (mm110) REVERT: D 142 LEU cc_start: 0.8657 (OUTLIER) cc_final: 0.8440 (tp) REVERT: G 26 TRP cc_start: 0.8395 (OUTLIER) cc_final: 0.5662 (m100) outliers start: 48 outliers final: 15 residues processed: 275 average time/residue: 1.2354 time to fit residues: 374.2167 Evaluate side-chains 251 residues out of total 1365 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 232 time to evaluate : 1.345 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Y residue 95 SER Chi-restraints excluded: chain Y residue 130 GLU Chi-restraints excluded: chain Y residue 150 ILE Chi-restraints excluded: chain Y residue 216 VAL Chi-restraints excluded: chain Z residue 7 LEU Chi-restraints excluded: chain Z residue 73 SER Chi-restraints excluded: chain C residue 99 ILE Chi-restraints excluded: chain C residue 197 VAL Chi-restraints excluded: chain C residue 216 VAL Chi-restraints excluded: chain D residue 26 TRP Chi-restraints excluded: chain D residue 59 LYS Chi-restraints excluded: chain D residue 85 GLU Chi-restraints excluded: chain D residue 142 LEU Chi-restraints excluded: chain D residue 178 LEU Chi-restraints excluded: chain F residue 216 VAL Chi-restraints excluded: chain G residue 7 LEU Chi-restraints excluded: chain G residue 26 TRP Chi-restraints excluded: chain G residue 142 LEU Chi-restraints excluded: chain H residue 11 LYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 171 random chunks: chunk 35 optimal weight: 3.9990 chunk 28 optimal weight: 6.9990 chunk 136 optimal weight: 3.9990 chunk 102 optimal weight: 7.9990 chunk 124 optimal weight: 3.9990 chunk 84 optimal weight: 0.8980 chunk 53 optimal weight: 4.9990 chunk 164 optimal weight: 2.9990 chunk 40 optimal weight: 3.9990 chunk 114 optimal weight: 10.0000 chunk 54 optimal weight: 8.9990 overall best weight: 3.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Y 240 ASN Z 98 GLN Z 230 GLN Z 238 GLN D 159 GLN D 204 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3997 r_free = 0.3997 target = 0.169578 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3598 r_free = 0.3598 target = 0.134485 restraints weight = 13572.756| |-----------------------------------------------------------------------------| r_work (start): 0.3598 rms_B_bonded: 2.05 r_work: 0.3358 rms_B_bonded: 2.34 restraints_weight: 0.5000 r_work: 0.3249 rms_B_bonded: 3.80 restraints_weight: 0.2500 r_work (final): 0.3249 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8607 moved from start: 0.1635 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.058 13605 Z= 0.244 Angle : 0.684 10.072 18498 Z= 0.355 Chirality : 0.048 0.256 2205 Planarity : 0.006 0.077 2274 Dihedral : 4.877 29.781 1911 Min Nonbonded Distance : 2.464 Molprobity Statistics. All-atom Clashscore : 6.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.41 % Favored : 94.59 % Rotamer: Outliers : 4.69 % Allowed : 16.34 % Favored : 78.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.11 (0.20), residues: 1755 helix: 1.70 (0.14), residues: 1248 sheet: None (None), residues: 0 loop : -1.80 (0.26), residues: 507 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP Z 26 HIS 0.007 0.001 HIS Z 68 PHE 0.020 0.002 PHE D 118 TYR 0.010 0.002 TYR A 3 ARG 0.005 0.001 ARG Z 199 Details of bonding type rmsd hydrogen bonds : bond 0.05648 ( 880) hydrogen bonds : angle 4.25396 ( 2631) SS BOND : bond 0.00506 ( 6) SS BOND : angle 0.77137 ( 12) covalent geometry : bond 0.00597 (13599) covalent geometry : angle 0.68443 (18486) *********************** 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 304 residues out of total 1365 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 240 time to evaluate : 1.386 Fit side-chains REVERT: Z 168 LYS cc_start: 0.5922 (tmmt) cc_final: 0.5391 (tmtt) REVERT: C 117 LEU cc_start: 0.8548 (OUTLIER) cc_final: 0.8228 (tt) REVERT: D 10 ARG cc_start: 0.7480 (OUTLIER) cc_final: 0.6987 (tpt-90) REVERT: D 98 GLN cc_start: 0.7737 (tm-30) cc_final: 0.7122 (mm110) REVERT: D 168 LYS cc_start: 0.6093 (tmmt) cc_final: 0.5498 (tmtt) REVERT: D 247 GLU cc_start: 0.7913 (pt0) cc_final: 0.7540 (pm20) outliers start: 64 outliers final: 30 residues processed: 273 average time/residue: 1.3083 time to fit residues: 392.3960 Evaluate side-chains 264 residues out of total 1365 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 232 time to evaluate : 1.861 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Y residue 35 THR Chi-restraints excluded: chain Y residue 39 LEU Chi-restraints excluded: chain Y residue 95 SER Chi-restraints excluded: chain Y residue 103 LEU Chi-restraints excluded: chain Y residue 116 THR Chi-restraints excluded: chain Y residue 204 LYS Chi-restraints excluded: chain Y residue 216 VAL Chi-restraints excluded: chain Z residue 7 LEU Chi-restraints excluded: chain Z residue 73 SER 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 201 MET 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 F residue 35 THR 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 H residue 23 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 171 random chunks: chunk 9 optimal weight: 0.9980 chunk 129 optimal weight: 4.9990 chunk 81 optimal weight: 1.9990 chunk 147 optimal weight: 0.9980 chunk 77 optimal weight: 3.9990 chunk 150 optimal weight: 0.9990 chunk 5 optimal weight: 0.9980 chunk 95 optimal weight: 3.9990 chunk 154 optimal weight: 2.9990 chunk 93 optimal weight: 0.6980 chunk 79 optimal weight: 1.9990 overall best weight: 0.9382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Y 240 ASN Z 230 GLN Z 237 GLN Z 238 GLN C 168 GLN D 148 ASN D 179 GLN F 240 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4040 r_free = 0.4040 target = 0.173638 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3664 r_free = 0.3664 target = 0.139937 restraints weight = 13436.716| |-----------------------------------------------------------------------------| r_work (start): 0.3665 rms_B_bonded: 2.01 r_work: 0.3430 rms_B_bonded: 2.27 restraints_weight: 0.5000 r_work: 0.3322 rms_B_bonded: 3.72 restraints_weight: 0.2500 r_work (final): 0.3322 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8537 moved from start: 0.1504 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= 0.126 Angle : 0.551 7.766 18498 Z= 0.284 Chirality : 0.041 0.135 2205 Planarity : 0.005 0.075 2274 Dihedral : 4.583 28.262 1911 Min Nonbonded Distance : 2.490 Molprobity Statistics. All-atom Clashscore : 5.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.73 % Favored : 95.27 % Rotamer: Outliers : 2.56 % Allowed : 18.68 % Favored : 78.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.54 (0.20), residues: 1755 helix: 2.07 (0.15), residues: 1248 sheet: None (None), residues: 0 loop : -1.78 (0.26), residues: 507 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP Z 26 HIS 0.002 0.001 HIS Z 68 PHE 0.015 0.001 PHE G 191 TYR 0.007 0.001 TYR A 3 ARG 0.004 0.000 ARG C 127 Details of bonding type rmsd hydrogen bonds : bond 0.04126 ( 880) hydrogen bonds : angle 3.90214 ( 2631) SS BOND : bond 0.00142 ( 6) SS BOND : angle 0.36723 ( 12) covalent geometry : bond 0.00280 (13599) covalent geometry : angle 0.55134 (18486) *********************** 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 273 residues out of total 1365 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 238 time to evaluate : 1.404 Fit side-chains revert: symmetry clash REVERT: Y 117 LEU cc_start: 0.8341 (OUTLIER) cc_final: 0.7826 (tt) REVERT: Y 243 LYS cc_start: 0.8169 (mtmm) cc_final: 0.7948 (mtmt) REVERT: Z 168 LYS cc_start: 0.5935 (tmmt) cc_final: 0.5414 (tmtt) REVERT: C 117 LEU cc_start: 0.8405 (OUTLIER) cc_final: 0.8165 (tt) REVERT: D 98 GLN cc_start: 0.7590 (tm-30) cc_final: 0.7048 (mm110) REVERT: D 168 LYS cc_start: 0.6134 (tmmt) cc_final: 0.5541 (tmtt) REVERT: D 247 GLU cc_start: 0.7925 (pt0) cc_final: 0.7542 (pm20) outliers start: 35 outliers final: 21 residues processed: 259 average time/residue: 1.2210 time to fit residues: 347.7729 Evaluate side-chains 254 residues out of total 1365 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 231 time to evaluate : 1.524 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Y residue 95 SER Chi-restraints excluded: chain Y residue 116 THR Chi-restraints excluded: chain Y residue 117 LEU Chi-restraints excluded: chain Y residue 216 VAL Chi-restraints excluded: chain Z residue 7 LEU Chi-restraints excluded: chain C residue 11 LEU Chi-restraints excluded: chain C residue 116 THR Chi-restraints excluded: chain C residue 117 LEU Chi-restraints excluded: chain C residue 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 D residue 237 GLN 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 H residue 11 LYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 171 random chunks: chunk 8 optimal weight: 0.9990 chunk 163 optimal weight: 2.9990 chunk 27 optimal weight: 9.9990 chunk 166 optimal weight: 0.6980 chunk 140 optimal weight: 0.0060 chunk 80 optimal weight: 0.6980 chunk 16 optimal weight: 5.9990 chunk 111 optimal weight: 9.9990 chunk 51 optimal weight: 0.0370 chunk 144 optimal weight: 0.6980 chunk 126 optimal weight: 1.9990 overall best weight: 0.4274 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Y 240 ASN Z 98 GLN Z 230 GLN Z 238 GLN C 168 GLN D 148 ASN D 179 GLN D 230 GLN D 238 GLN F 240 ASN G 230 GLN G 237 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4076 r_free = 0.4076 target = 0.177266 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3713 r_free = 0.3713 target = 0.144075 restraints weight = 13700.163| |-----------------------------------------------------------------------------| r_work (start): 0.3714 rms_B_bonded: 2.09 r_work: 0.3481 rms_B_bonded: 2.31 restraints_weight: 0.5000 r_work: 0.3374 rms_B_bonded: 3.79 restraints_weight: 0.2500 r_work (final): 0.3374 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8484 moved from start: 0.1478 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= 0.105 Angle : 0.526 12.470 18498 Z= 0.266 Chirality : 0.040 0.132 2205 Planarity : 0.005 0.072 2274 Dihedral : 4.296 24.900 1911 Min Nonbonded Distance : 2.512 Molprobity Statistics. All-atom Clashscore : 4.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.50 % Favored : 95.50 % Rotamer: Outliers : 2.12 % Allowed : 19.71 % Favored : 78.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.89 (0.21), residues: 1755 helix: 2.38 (0.15), residues: 1245 sheet: None (None), residues: 0 loop : -1.76 (0.26), residues: 510 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP Z 26 HIS 0.002 0.000 HIS Z 298 PHE 0.010 0.001 PHE G 191 TYR 0.007 0.001 TYR D 219 ARG 0.007 0.000 ARG C 127 Details of bonding type rmsd hydrogen bonds : bond 0.03522 ( 880) hydrogen bonds : angle 3.68820 ( 2631) SS BOND : bond 0.00062 ( 6) SS BOND : angle 0.27027 ( 12) covalent geometry : bond 0.00220 (13599) covalent geometry : angle 0.52593 (18486) *********************** 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 277 residues out of total 1365 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 248 time to evaluate : 1.206 Fit side-chains REVERT: Y 44 LEU cc_start: 0.8193 (tp) cc_final: 0.7794 (tm) REVERT: Y 82 ILE cc_start: 0.8502 (mt) cc_final: 0.8253 (mt) REVERT: Z 168 LYS cc_start: 0.5950 (tmmt) cc_final: 0.5404 (tmtt) REVERT: Z 237 GLN cc_start: 0.8159 (OUTLIER) cc_final: 0.7787 (mt0) REVERT: Z 247 GLU cc_start: 0.7792 (pt0) cc_final: 0.7503 (pm20) REVERT: C 112 MET cc_start: 0.8474 (mtm) cc_final: 0.8010 (mtp) REVERT: C 189 VAL cc_start: 0.8141 (t) cc_final: 0.7859 (t) REVERT: D 98 GLN cc_start: 0.7533 (tm-30) cc_final: 0.7085 (mm110) REVERT: D 168 LYS cc_start: 0.6007 (tmmt) cc_final: 0.5432 (tmtt) REVERT: D 247 GLU cc_start: 0.7888 (pt0) cc_final: 0.7520 (pm20) outliers start: 29 outliers final: 11 residues processed: 264 average time/residue: 1.3403 time to fit residues: 389.0055 Evaluate side-chains 244 residues out of total 1365 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 232 time to evaluate : 2.472 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 237 GLN Chi-restraints excluded: chain C residue 216 VAL Chi-restraints excluded: chain D residue 7 LEU Chi-restraints excluded: chain D residue 59 LYS Chi-restraints excluded: chain D residue 178 LEU Chi-restraints excluded: chain F residue 150 ILE Chi-restraints excluded: chain F residue 216 VAL Chi-restraints excluded: chain G residue 7 LEU Chi-restraints excluded: chain G residue 142 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 171 random chunks: chunk 141 optimal weight: 0.7980 chunk 40 optimal weight: 2.9990 chunk 1 optimal weight: 2.9990 chunk 108 optimal weight: 2.9990 chunk 67 optimal weight: 5.9990 chunk 146 optimal weight: 0.0040 chunk 87 optimal weight: 1.9990 chunk 52 optimal weight: 2.9990 chunk 139 optimal weight: 0.9980 chunk 69 optimal weight: 1.9990 chunk 100 optimal weight: 5.9990 overall best weight: 1.1596 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Y 240 ASN Z 98 GLN Z 179 GLN Z 230 GLN Z 238 GLN D 179 GLN D 204 GLN D 230 GLN D 238 GLN D 239 GLN G 230 GLN G 237 GLN G 238 GLN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4045 r_free = 0.4045 target = 0.174241 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3661 r_free = 0.3661 target = 0.139723 restraints weight = 13689.034| |-----------------------------------------------------------------------------| r_work (start): 0.3660 rms_B_bonded: 2.07 r_work: 0.3419 rms_B_bonded: 2.41 restraints_weight: 0.5000 r_work: 0.3309 rms_B_bonded: 3.96 restraints_weight: 0.2500 r_work (final): 0.3309 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8544 moved from start: 0.1662 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 13605 Z= 0.131 Angle : 0.560 11.529 18498 Z= 0.284 Chirality : 0.041 0.184 2205 Planarity : 0.005 0.072 2274 Dihedral : 4.365 24.914 1910 Min Nonbonded Distance : 2.504 Molprobity Statistics. All-atom Clashscore : 5.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.36 % Favored : 94.64 % Rotamer: Outliers : 2.42 % Allowed : 20.00 % Favored : 77.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.84 (0.21), residues: 1755 helix: 2.33 (0.15), residues: 1245 sheet: None (None), residues: 0 loop : -1.74 (0.26), residues: 510 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP Z 26 HIS 0.004 0.001 HIS G 61 PHE 0.015 0.001 PHE G 191 TYR 0.007 0.001 TYR A 3 ARG 0.006 0.001 ARG C 127 Details of bonding type rmsd hydrogen bonds : bond 0.04081 ( 880) hydrogen bonds : angle 3.79660 ( 2631) SS BOND : bond 0.00189 ( 6) SS BOND : angle 0.38854 ( 12) covalent geometry : bond 0.00299 (13599) covalent geometry : angle 0.56057 (18486) *********************** 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 260 residues out of total 1365 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 227 time to evaluate : 1.375 Fit side-chains REVERT: Y 44 LEU cc_start: 0.8237 (tp) cc_final: 0.7798 (tm) REVERT: Z 168 LYS cc_start: 0.6009 (tmmt) cc_final: 0.5469 (tmtt) REVERT: Z 237 GLN cc_start: 0.8178 (OUTLIER) cc_final: 0.7808 (mt0) REVERT: Z 247 GLU cc_start: 0.7863 (pt0) cc_final: 0.7494 (pm20) REVERT: C 112 MET cc_start: 0.8522 (mtm) cc_final: 0.8079 (mtp) REVERT: C 117 LEU cc_start: 0.8466 (OUTLIER) cc_final: 0.8195 (tt) REVERT: D 98 GLN cc_start: 0.7653 (tm-30) cc_final: 0.7042 (mm110) REVERT: D 168 LYS cc_start: 0.6011 (tmmt) cc_final: 0.5442 (tmtt) REVERT: D 247 GLU cc_start: 0.7954 (pt0) cc_final: 0.7547 (pm20) outliers start: 33 outliers final: 21 residues processed: 247 average time/residue: 1.1083 time to fit residues: 301.3407 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 : 1.356 ------------------------------------------------------------------------------- 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 204 LYS Chi-restraints excluded: chain Y residue 216 VAL Chi-restraints excluded: chain Z residue 7 LEU Chi-restraints excluded: chain Z residue 142 LEU Chi-restraints excluded: chain Z residue 237 GLN Chi-restraints excluded: chain Z residue 293 VAL Chi-restraints excluded: chain C residue 85 LEU Chi-restraints excluded: chain C residue 95 SER Chi-restraints excluded: chain C residue 116 THR Chi-restraints excluded: chain C residue 117 LEU Chi-restraints excluded: chain C residue 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 116 THR Chi-restraints excluded: chain F residue 150 ILE 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 Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 171 random chunks: chunk 111 optimal weight: 20.0000 chunk 76 optimal weight: 0.9990 chunk 131 optimal weight: 2.9990 chunk 15 optimal weight: 0.2980 chunk 129 optimal weight: 0.6980 chunk 158 optimal weight: 0.0050 chunk 0 optimal weight: 10.0000 chunk 46 optimal weight: 0.9980 chunk 89 optimal weight: 0.0770 chunk 130 optimal weight: 0.1980 chunk 139 optimal weight: 3.9990 overall best weight: 0.2552 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Y 240 ASN Z 98 GLN Z 179 GLN Z 230 GLN Z 238 GLN D 179 GLN D 204 GLN D 230 GLN F 240 ASN G 230 GLN G 237 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4105 r_free = 0.4105 target = 0.179951 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3741 r_free = 0.3741 target = 0.146543 restraints weight = 13656.210| |-----------------------------------------------------------------------------| r_work (start): 0.3733 rms_B_bonded: 2.00 r_work: 0.3511 rms_B_bonded: 2.33 restraints_weight: 0.5000 r_work: 0.3402 rms_B_bonded: 3.85 restraints_weight: 0.2500 r_work (final): 0.3402 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8451 moved from start: 0.1629 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= 0.101 Angle : 0.522 11.141 18498 Z= 0.262 Chirality : 0.040 0.159 2205 Planarity : 0.005 0.070 2274 Dihedral : 4.150 25.404 1910 Min Nonbonded Distance : 2.481 Molprobity Statistics. All-atom Clashscore : 5.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.39 % Favored : 95.61 % Rotamer: Outliers : 1.68 % Allowed : 20.66 % Favored : 77.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.06 (0.21), residues: 1755 helix: 2.49 (0.15), residues: 1251 sheet: None (None), residues: 0 loop : -1.72 (0.27), residues: 504 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP Z 26 HIS 0.002 0.000 HIS Z 298 PHE 0.008 0.001 PHE Z 144 TYR 0.008 0.001 TYR D 219 ARG 0.007 0.000 ARG C 127 Details of bonding type rmsd hydrogen bonds : bond 0.03252 ( 880) hydrogen bonds : angle 3.62457 ( 2631) SS BOND : bond 0.00015 ( 6) SS BOND : angle 0.21161 ( 12) covalent geometry : bond 0.00207 (13599) covalent geometry : angle 0.52169 (18486) *********************** 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 269 residues out of total 1365 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 246 time to evaluate : 1.372 Fit side-chains revert: symmetry clash REVERT: Y 44 LEU cc_start: 0.8215 (tp) cc_final: 0.7819 (tm) REVERT: Y 82 ILE cc_start: 0.8449 (mt) cc_final: 0.8180 (mt) REVERT: Y 127 ARG cc_start: 0.6571 (OUTLIER) cc_final: 0.5990 (mtt180) REVERT: Z 168 LYS cc_start: 0.5887 (tmmt) cc_final: 0.5364 (tmtt) REVERT: Z 247 GLU cc_start: 0.7814 (pt0) cc_final: 0.7498 (pm20) REVERT: C 44 LEU cc_start: 0.8233 (tp) cc_final: 0.7875 (tm) REVERT: C 112 MET cc_start: 0.8484 (mtm) cc_final: 0.8036 (mtp) REVERT: C 189 VAL cc_start: 0.8059 (t) cc_final: 0.7815 (t) REVERT: D 60 ARG cc_start: 0.7250 (mtm-85) cc_final: 0.6896 (mtp180) REVERT: D 98 GLN cc_start: 0.7603 (tm-30) cc_final: 0.7052 (mm110) REVERT: D 168 LYS cc_start: 0.5949 (tmmt) cc_final: 0.5380 (tmtt) REVERT: D 247 GLU cc_start: 0.7960 (pt0) cc_final: 0.7532 (pm20) REVERT: F 127 ARG cc_start: 0.6944 (mtt180) cc_final: 0.6693 (mtt180) outliers start: 23 outliers final: 10 residues processed: 257 average time/residue: 1.3046 time to fit residues: 367.5765 Evaluate side-chains 247 residues out of total 1365 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 236 time to evaluate : 1.167 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Y residue 127 ARG 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 D residue 7 LEU Chi-restraints excluded: chain D residue 59 LYS Chi-restraints excluded: chain F residue 150 ILE Chi-restraints excluded: chain G residue 7 LEU Chi-restraints excluded: chain G residue 293 VAL Chi-restraints excluded: chain H residue 11 LYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 171 random chunks: chunk 64 optimal weight: 0.9980 chunk 67 optimal weight: 3.9990 chunk 93 optimal weight: 0.9980 chunk 68 optimal weight: 4.9990 chunk 90 optimal weight: 4.9990 chunk 121 optimal weight: 4.9990 chunk 103 optimal weight: 6.9990 chunk 113 optimal weight: 0.8980 chunk 162 optimal weight: 1.9990 chunk 95 optimal weight: 5.9990 chunk 128 optimal weight: 2.9990 overall best weight: 1.5784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Y 240 ASN Z 98 GLN Z 179 GLN Z 230 GLN Z 238 GLN D 159 GLN D 230 GLN D 238 GLN G 238 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4037 r_free = 0.4037 target = 0.173348 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3541 r_free = 0.3541 target = 0.130844 restraints weight = 13681.265| |-----------------------------------------------------------------------------| r_work (start): 0.3536 rms_B_bonded: 1.65 r_work: 0.3426 rms_B_bonded: 2.20 restraints_weight: 0.5000 r_work: 0.3322 rms_B_bonded: 3.59 restraints_weight: 0.2500 r_work (final): 0.3322 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8537 moved from start: 0.1772 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 13605 Z= 0.150 Angle : 0.586 12.192 18498 Z= 0.296 Chirality : 0.042 0.176 2205 Planarity : 0.005 0.072 2274 Dihedral : 4.402 25.344 1910 Min Nonbonded Distance : 2.456 Molprobity Statistics. All-atom Clashscore : 4.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.58 % Favored : 94.42 % Rotamer: Outliers : 1.98 % Allowed : 21.10 % Favored : 76.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.86 (0.21), residues: 1755 helix: 2.33 (0.15), residues: 1251 sheet: None (None), residues: 0 loop : -1.74 (0.27), residues: 504 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP Z 147 HIS 0.004 0.001 HIS Z 68 PHE 0.015 0.002 PHE D 191 TYR 0.007 0.001 TYR G 219 ARG 0.006 0.001 ARG C 127 Details of bonding type rmsd hydrogen bonds : bond 0.04283 ( 880) hydrogen bonds : angle 3.83013 ( 2631) SS BOND : bond 0.00238 ( 6) SS BOND : angle 0.46080 ( 12) covalent geometry : bond 0.00352 (13599) covalent geometry : angle 0.58571 (18486) *********************** 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 262 residues out of total 1365 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 235 time to evaluate : 2.055 Fit side-chains REVERT: Z 168 LYS cc_start: 0.5997 (tmmt) cc_final: 0.5468 (tmtt) REVERT: Z 237 GLN cc_start: 0.8185 (OUTLIER) cc_final: 0.7827 (mt0) REVERT: Z 247 GLU cc_start: 0.7832 (pt0) cc_final: 0.7501 (pm20) REVERT: C 112 MET cc_start: 0.8502 (mtm) cc_final: 0.8065 (mtp) REVERT: D 98 GLN cc_start: 0.7695 (tm-30) cc_final: 0.7068 (mm110) REVERT: D 168 LYS cc_start: 0.6050 (tmmt) cc_final: 0.5475 (tmtt) REVERT: D 247 GLU cc_start: 0.7947 (pt0) cc_final: 0.7556 (pm20) outliers start: 27 outliers final: 19 residues processed: 249 average time/residue: 1.3270 time to fit residues: 362.9886 Evaluate side-chains 249 residues out of total 1365 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 229 time to evaluate : 1.870 ------------------------------------------------------------------------------- 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 154 ILE Chi-restraints excluded: chain Z residue 7 LEU Chi-restraints excluded: chain Z residue 142 LEU Chi-restraints excluded: chain Z residue 237 GLN Chi-restraints excluded: chain Z residue 293 VAL Chi-restraints excluded: chain C residue 11 LEU Chi-restraints excluded: chain C residue 85 LEU Chi-restraints excluded: chain C residue 116 THR Chi-restraints excluded: chain C residue 174 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 237 GLN Chi-restraints excluded: chain D residue 246 SER Chi-restraints excluded: chain F residue 8 LEU Chi-restraints excluded: chain F residue 150 ILE Chi-restraints excluded: chain G residue 7 LEU 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 104 optimal weight: 9.9990 chunk 115 optimal weight: 5.9990 chunk 90 optimal weight: 0.7980 chunk 60 optimal weight: 3.9990 chunk 67 optimal weight: 6.9990 chunk 44 optimal weight: 6.9990 chunk 68 optimal weight: 0.7980 chunk 144 optimal weight: 0.7980 chunk 22 optimal weight: 0.8980 chunk 161 optimal weight: 0.7980 chunk 84 optimal weight: 8.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Y 240 ASN Z 98 GLN Z 148 ASN Z 179 GLN Z 230 GLN Z 238 GLN C 168 GLN D 230 GLN F 240 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4058 r_free = 0.4058 target = 0.175382 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3678 r_free = 0.3678 target = 0.141095 restraints weight = 13554.436| |-----------------------------------------------------------------------------| r_work (start): 0.3678 rms_B_bonded: 2.06 r_work: 0.3441 rms_B_bonded: 2.38 restraints_weight: 0.5000 r_work: 0.3330 rms_B_bonded: 3.92 restraints_weight: 0.2500 r_work (final): 0.3330 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8524 moved from start: 0.1720 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 13605 Z= 0.117 Angle : 0.553 11.638 18498 Z= 0.278 Chirality : 0.041 0.173 2205 Planarity : 0.005 0.071 2274 Dihedral : 4.319 26.019 1910 Min Nonbonded Distance : 2.421 Molprobity Statistics. All-atom Clashscore : 5.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.79 % Favored : 95.21 % Rotamer: Outliers : 1.61 % Allowed : 21.10 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.92 (0.21), residues: 1755 helix: 2.37 (0.15), residues: 1251 sheet: None (None), residues: 0 loop : -1.71 (0.27), residues: 504 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP E 18 HIS 0.002 0.001 HIS Z 61 PHE 0.013 0.001 PHE G 191 TYR 0.006 0.001 TYR D 219 ARG 0.007 0.000 ARG C 127 Details of bonding type rmsd hydrogen bonds : bond 0.03820 ( 880) hydrogen bonds : angle 3.75616 ( 2631) SS BOND : bond 0.00136 ( 6) SS BOND : angle 0.36835 ( 12) covalent geometry : bond 0.00256 (13599) covalent geometry : angle 0.55296 (18486) *********************** 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 249 residues out of total 1365 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 227 time to evaluate : 1.534 Fit side-chains REVERT: Y 44 LEU cc_start: 0.8203 (tp) cc_final: 0.7775 (tm) REVERT: Z 237 GLN cc_start: 0.8177 (OUTLIER) cc_final: 0.7819 (mt0) REVERT: Z 247 GLU cc_start: 0.7838 (pt0) cc_final: 0.7487 (pm20) REVERT: C 44 LEU cc_start: 0.8232 (tp) cc_final: 0.7868 (tm) REVERT: C 112 MET cc_start: 0.8509 (mtm) cc_final: 0.8078 (mtp) REVERT: D 98 GLN cc_start: 0.7698 (tm-30) cc_final: 0.7032 (mm110) REVERT: D 168 LYS cc_start: 0.6020 (tmmt) cc_final: 0.5448 (tmtt) REVERT: D 247 GLU cc_start: 0.7980 (pt0) cc_final: 0.7548 (pm20) REVERT: F 127 ARG cc_start: 0.6965 (mtt180) cc_final: 0.6725 (mtt180) REVERT: G 59 LYS cc_start: 0.8042 (mptp) cc_final: 0.7752 (mptp) outliers start: 22 outliers final: 17 residues processed: 239 average time/residue: 1.1507 time to fit residues: 302.3920 Evaluate side-chains 244 residues out of total 1365 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 226 time to evaluate : 1.394 ------------------------------------------------------------------------------- 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 237 GLN Chi-restraints excluded: chain C residue 85 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 150 ILE 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 Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 171 random chunks: chunk 2 optimal weight: 4.9990 chunk 133 optimal weight: 1.9990 chunk 82 optimal weight: 0.5980 chunk 44 optimal weight: 5.9990 chunk 19 optimal weight: 1.9990 chunk 107 optimal weight: 2.9990 chunk 99 optimal weight: 4.9990 chunk 32 optimal weight: 7.9990 chunk 102 optimal weight: 0.2980 chunk 17 optimal weight: 3.9990 chunk 115 optimal weight: 7.9990 overall best weight: 1.5786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Y 240 ASN Z 98 GLN Z 179 GLN Z 230 GLN Z 238 GLN D 159 GLN F 240 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4032 r_free = 0.4032 target = 0.172858 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3647 r_free = 0.3647 target = 0.138398 restraints weight = 13517.586| |-----------------------------------------------------------------------------| r_work (start): 0.3644 rms_B_bonded: 2.10 r_work: 0.3402 rms_B_bonded: 2.40 restraints_weight: 0.5000 r_work: 0.3294 rms_B_bonded: 3.88 restraints_weight: 0.2500 r_work (final): 0.3294 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8561 moved from start: 0.1818 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 13605 Z= 0.152 Angle : 0.597 12.127 18498 Z= 0.301 Chirality : 0.043 0.179 2205 Planarity : 0.005 0.072 2274 Dihedral : 4.511 28.739 1910 Min Nonbonded Distance : 2.453 Molprobity Statistics. All-atom Clashscore : 5.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.64 % Favored : 94.36 % Rotamer: Outliers : 1.61 % Allowed : 21.32 % Favored : 77.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.74 (0.21), residues: 1755 helix: 2.21 (0.15), residues: 1254 sheet: None (None), residues: 0 loop : -1.71 (0.27), residues: 501 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP Z 147 HIS 0.004 0.001 HIS Z 68 PHE 0.015 0.001 PHE D 191 TYR 0.007 0.001 TYR A 3 ARG 0.007 0.001 ARG C 127 Details of bonding type rmsd hydrogen bonds : bond 0.04363 ( 880) hydrogen bonds : angle 3.88374 ( 2631) SS BOND : bond 0.00284 ( 6) SS BOND : angle 0.52109 ( 12) covalent geometry : bond 0.00359 (13599) covalent geometry : angle 0.59689 (18486) ********************** 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 259 residues out of total 1365 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 237 time to evaluate : 2.250 Fit side-chains REVERT: Y 44 LEU cc_start: 0.8222 (tp) cc_final: 0.7779 (tm) REVERT: Z 168 LYS cc_start: 0.6035 (tmmt) cc_final: 0.5520 (tmtt) REVERT: Z 237 GLN cc_start: 0.8163 (OUTLIER) cc_final: 0.7800 (mt0) REVERT: Z 247 GLU cc_start: 0.7835 (pt0) cc_final: 0.7500 (pm20) REVERT: C 112 MET cc_start: 0.8514 (mtm) cc_final: 0.8080 (mtp) REVERT: D 168 LYS cc_start: 0.6077 (tmmt) cc_final: 0.5502 (tmtt) REVERT: D 237 GLN cc_start: 0.8232 (OUTLIER) cc_final: 0.7856 (mt0) REVERT: D 247 GLU cc_start: 0.7990 (pt0) cc_final: 0.7569 (pm20) outliers start: 22 outliers final: 15 residues processed: 251 average time/residue: 1.5968 time to fit residues: 439.4191 Evaluate side-chains 249 residues out of total 1365 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 232 time to evaluate : 1.523 ------------------------------------------------------------------------------- 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 Z residue 237 GLN Chi-restraints excluded: chain C residue 11 LEU Chi-restraints excluded: chain C residue 85 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 95 SER Chi-restraints excluded: chain F residue 116 THR Chi-restraints excluded: chain F residue 150 ILE Chi-restraints excluded: chain F residue 174 MET Chi-restraints excluded: chain F residue 216 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 171 random chunks: chunk 147 optimal weight: 0.4980 chunk 43 optimal weight: 4.9990 chunk 107 optimal weight: 3.9990 chunk 69 optimal weight: 0.6980 chunk 163 optimal weight: 1.9990 chunk 75 optimal weight: 9.9990 chunk 35 optimal weight: 0.7980 chunk 94 optimal weight: 1.9990 chunk 24 optimal weight: 1.9990 chunk 123 optimal weight: 0.5980 chunk 9 optimal weight: 0.8980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Y 240 ASN Z 98 GLN Z 179 GLN Z 230 GLN Z 238 GLN C 148 GLN C 168 GLN D 238 GLN F 240 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4062 r_free = 0.4062 target = 0.175731 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3683 r_free = 0.3683 target = 0.141481 restraints weight = 13596.205| |-----------------------------------------------------------------------------| r_work (start): 0.3683 rms_B_bonded: 2.03 r_work: 0.3437 rms_B_bonded: 2.49 restraints_weight: 0.5000 r_work: 0.3324 rms_B_bonded: 4.11 restraints_weight: 0.2500 r_work (final): 0.3324 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8526 moved from start: 0.1741 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= 0.114 Angle : 0.554 11.640 18498 Z= 0.278 Chirality : 0.041 0.173 2205 Planarity : 0.005 0.071 2274 Dihedral : 4.294 27.714 1908 Min Nonbonded Distance : 2.401 Molprobity Statistics. All-atom Clashscore : 5.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.67 % Favored : 95.33 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.91 (0.21), residues: 1755 helix: 2.36 (0.15), residues: 1251 sheet: None (None), residues: 0 loop : -1.70 (0.27), residues: 504 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP E 18 HIS 0.002 0.001 HIS G 298 PHE 0.013 0.001 PHE G 191 TYR 0.006 0.001 TYR Z 219 ARG 0.007 0.000 ARG C 127 Details of bonding type rmsd hydrogen bonds : bond 0.03760 ( 880) hydrogen bonds : angle 3.76746 ( 2631) SS BOND : bond 0.00121 ( 6) SS BOND : angle 0.37890 ( 12) covalent geometry : bond 0.00246 (13599) covalent geometry : angle 0.55380 (18486) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 14015.69 seconds wall clock time: 249 minutes 27.42 seconds (14967.42 seconds total)