Starting phenix.real_space_refine on Thu Sep 26 11:53:53 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vly_32031/09_2024/7vly_32031.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vly_32031/09_2024/7vly_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/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vly_32031/09_2024/7vly_32031.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vly_32031/09_2024/7vly_32031.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vly_32031/09_2024/7vly_32031.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vly_32031/09_2024/7vly_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): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/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: 8.20, per 1000 atoms: 0.61 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: 3.17 Conformation dependent library (CDL) restraints added in 1.7 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: 1.19 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: 3.95 Time building geometry restraints manager: 3.70 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: 1.010 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: 0.460 Check model and map are aligned: 0.090 Set scattering table: 0.110 Process input model: 31.020 Find NCS groups from input model: 0.670 Set up NCS constraints: 0.100 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:12.510 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 45.990 ------------------------------------------------------------------------------- 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 13599 Z= 0.164 Angle : 0.612 8.460 18486 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 *********************** 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 fitting. rotamer outliers: 34 poor density : 245 time to evaluate : 2.037 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: 1.0646 time to fit residues: 319.1652 Evaluate side-chains 249 residues out of total 1365 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 233 time to evaluate : 1.346 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8223 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 13599 Z= 0.168 Angle : 0.560 7.406 18486 Z= 0.286 Chirality : 0.041 0.163 2205 Planarity : 0.005 0.072 2274 Dihedral : 6.457 62.648 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 *********************** 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 fitting. rotamer outliers: 48 poor density : 243 time to evaluate : 1.602 Fit side-chains revert: symmetry clash REVERT: Y 44 LEU cc_start: 0.8232 (tp) cc_final: 0.7871 (tm) REVERT: Z 104 MET cc_start: 0.8388 (mtp) cc_final: 0.7897 (mtm) REVERT: C 126 ASP cc_start: 0.7356 (m-30) cc_final: 0.7113 (m-30) REVERT: D 14 ARG cc_start: 0.7405 (mtm-85) cc_final: 0.7166 (mtm180) REVERT: D 26 TRP cc_start: 0.8071 (OUTLIER) cc_final: 0.5354 (m100) REVERT: D 85 GLU cc_start: 0.6302 (OUTLIER) cc_final: 0.6029 (mt-10) REVERT: D 98 GLN cc_start: 0.7580 (tm-30) cc_final: 0.7128 (mm110) REVERT: G 26 TRP cc_start: 0.8176 (OUTLIER) cc_final: 0.5624 (m100) outliers start: 48 outliers final: 15 residues processed: 275 average time/residue: 1.1152 time to fit residues: 337.9492 Evaluate side-chains 250 residues out of total 1365 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 232 time to evaluate : 1.511 ------------------------------------------------------------------------------- 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 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 86 optimal weight: 5.9990 chunk 48 optimal weight: 0.0870 chunk 129 optimal weight: 0.9990 chunk 105 optimal weight: 0.5980 chunk 42 optimal weight: 4.9990 chunk 155 optimal weight: 0.9980 chunk 168 optimal weight: 7.9990 chunk 138 optimal weight: 1.9990 chunk 154 optimal weight: 2.9990 chunk 53 optimal weight: 7.9990 chunk 124 optimal weight: 6.9990 overall best weight: 0.9362 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8253 moved from start: 0.1213 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 13599 Z= 0.178 Angle : 0.547 9.240 18486 Z= 0.280 Chirality : 0.041 0.128 2205 Planarity : 0.005 0.071 2274 Dihedral : 4.437 27.614 1911 Min Nonbonded Distance : 2.512 Molprobity Statistics. All-atom Clashscore : 5.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.56 % Favored : 95.44 % Rotamer: Outliers : 2.86 % Allowed : 17.95 % Favored : 79.19 % 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: 1.75 (0.20), residues: 1755 helix: 2.26 (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 0.010 0.001 TRP Z 26 HIS 0.003 0.001 HIS Z 68 PHE 0.013 0.001 PHE G 191 TYR 0.006 0.001 TYR G 219 ARG 0.006 0.000 ARG C 127 *********************** 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 278 residues out of total 1365 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 239 time to evaluate : 1.257 Fit side-chains REVERT: C 117 LEU cc_start: 0.8328 (OUTLIER) cc_final: 0.8093 (tt) REVERT: D 14 ARG cc_start: 0.7396 (mtm-85) cc_final: 0.7179 (mtm180) REVERT: D 98 GLN cc_start: 0.7465 (tm-30) cc_final: 0.7072 (mm110) REVERT: G 59 LYS cc_start: 0.8251 (OUTLIER) cc_final: 0.8025 (mptp) REVERT: G 237 GLN cc_start: 0.7984 (OUTLIER) cc_final: 0.7705 (mm-40) outliers start: 39 outliers final: 19 residues processed: 263 average time/residue: 1.0871 time to fit residues: 314.8665 Evaluate side-chains 259 residues out of total 1365 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 237 time to evaluate : 1.284 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Y residue 116 THR Chi-restraints excluded: chain Y residue 130 GLU Chi-restraints excluded: chain Y residue 216 VAL Chi-restraints excluded: chain Z residue 7 LEU Chi-restraints excluded: chain C residue 116 THR Chi-restraints excluded: chain C residue 117 LEU Chi-restraints excluded: chain C residue 121 ILE Chi-restraints excluded: chain C residue 197 VAL Chi-restraints excluded: chain C residue 201 MET Chi-restraints excluded: chain C residue 216 VAL Chi-restraints excluded: chain D residue 7 LEU Chi-restraints excluded: chain D residue 59 LYS Chi-restraints excluded: chain D residue 142 LEU Chi-restraints excluded: chain D residue 178 LEU Chi-restraints excluded: chain F residue 116 THR 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 59 LYS Chi-restraints excluded: chain G residue 142 LEU Chi-restraints excluded: chain G residue 237 GLN Chi-restraints excluded: chain G residue 293 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 171 random chunks: chunk 153 optimal weight: 2.9990 chunk 116 optimal weight: 5.9990 chunk 80 optimal weight: 0.8980 chunk 17 optimal weight: 7.9990 chunk 74 optimal weight: 4.9990 chunk 104 optimal weight: 10.0000 chunk 156 optimal weight: 5.9990 chunk 165 optimal weight: 0.9990 chunk 81 optimal weight: 2.9990 chunk 147 optimal weight: 0.9980 chunk 44 optimal weight: 7.9990 overall best weight: 1.7786 ------------------------------------------------------------------------------- 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 179 GLN D 204 GLN D 230 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8309 moved from start: 0.1544 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 13599 Z= 0.257 Angle : 0.590 8.544 18486 Z= 0.305 Chirality : 0.043 0.145 2205 Planarity : 0.006 0.074 2274 Dihedral : 4.560 25.803 1911 Min Nonbonded Distance : 2.492 Molprobity Statistics. All-atom Clashscore : 5.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.64 % Favored : 94.36 % Rotamer: Outliers : 3.44 % Allowed : 17.88 % Favored : 78.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 1.56 (0.20), residues: 1755 helix: 2.09 (0.15), residues: 1248 sheet: None (None), residues: 0 loop : -1.79 (0.26), residues: 507 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP Z 26 HIS 0.004 0.001 HIS Z 68 PHE 0.015 0.002 PHE G 191 TYR 0.009 0.001 TYR A 3 ARG 0.004 0.001 ARG Z 199 *********************** 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 293 residues out of total 1365 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 246 time to evaluate : 1.724 Fit side-chains REVERT: Y 44 LEU cc_start: 0.8274 (tp) cc_final: 0.7887 (tm) REVERT: Z 168 LYS cc_start: 0.5950 (tmmt) cc_final: 0.5507 (tmtt) REVERT: Z 237 GLN cc_start: 0.7925 (mt0) cc_final: 0.7671 (mt0) REVERT: C 117 LEU cc_start: 0.8399 (OUTLIER) cc_final: 0.8132 (tt) REVERT: D 98 GLN cc_start: 0.7517 (tm-30) cc_final: 0.7091 (mm110) REVERT: D 168 LYS cc_start: 0.6112 (tmmt) cc_final: 0.5607 (tmtt) REVERT: G 237 GLN cc_start: 0.7978 (OUTLIER) cc_final: 0.7704 (mm-40) outliers start: 47 outliers final: 23 residues processed: 270 average time/residue: 1.1212 time to fit residues: 332.3615 Evaluate side-chains 262 residues out of total 1365 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 237 time to evaluate : 1.463 ------------------------------------------------------------------------------- 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 A residue 23 THR Chi-restraints excluded: chain C residue 11 LEU Chi-restraints excluded: chain C residue 116 THR Chi-restraints excluded: chain C residue 117 LEU Chi-restraints excluded: chain C residue 121 ILE Chi-restraints excluded: chain C residue 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 121 ILE 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 237 GLN Chi-restraints excluded: chain H residue 23 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 171 random chunks: chunk 137 optimal weight: 0.9980 chunk 93 optimal weight: 0.6980 chunk 2 optimal weight: 4.9990 chunk 123 optimal weight: 3.9990 chunk 68 optimal weight: 0.9990 chunk 141 optimal weight: 0.7980 chunk 114 optimal weight: 10.0000 chunk 0 optimal weight: 10.0000 chunk 84 optimal weight: 6.9990 chunk 148 optimal weight: 0.9990 chunk 41 optimal weight: 2.9990 overall best weight: 0.8984 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 237 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 238 GLN C 168 GLN D 148 ASN D 179 GLN D 204 GLN F 240 ASN G 230 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8271 moved from start: 0.1517 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 13599 Z= 0.175 Angle : 0.546 12.017 18486 Z= 0.279 Chirality : 0.041 0.124 2205 Planarity : 0.005 0.072 2274 Dihedral : 4.422 24.914 1911 Min Nonbonded Distance : 2.499 Molprobity Statistics. All-atom Clashscore : 5.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.73 % Favored : 95.27 % Rotamer: Outliers : 2.64 % Allowed : 18.97 % Favored : 78.39 % 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: 1.77 (0.21), residues: 1755 helix: 2.27 (0.15), residues: 1245 sheet: None (None), residues: 0 loop : -1.77 (0.26), residues: 510 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 0.013 0.001 PHE G 191 TYR 0.007 0.001 TYR A 3 ARG 0.006 0.000 ARG C 127 *********************** 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 273 residues out of total 1365 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 237 time to evaluate : 1.285 Fit side-chains REVERT: Y 44 LEU cc_start: 0.8277 (tp) cc_final: 0.7895 (tm) REVERT: Z 60 ARG cc_start: 0.7334 (mtm-85) cc_final: 0.7098 (mtp180) REVERT: C 85 LEU cc_start: 0.7736 (OUTLIER) cc_final: 0.7438 (pt) REVERT: C 117 LEU cc_start: 0.8344 (OUTLIER) cc_final: 0.8114 (tt) REVERT: D 60 ARG cc_start: 0.7448 (mtm-85) cc_final: 0.7173 (mtp180) REVERT: D 98 GLN cc_start: 0.7438 (tm-30) cc_final: 0.7098 (mm110) REVERT: D 168 LYS cc_start: 0.6133 (tmmt) cc_final: 0.5626 (tmtt) REVERT: G 237 GLN cc_start: 0.7971 (OUTLIER) cc_final: 0.7731 (mm-40) outliers start: 36 outliers final: 20 residues processed: 257 average time/residue: 1.1251 time to fit residues: 318.3193 Evaluate side-chains 254 residues out of total 1365 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 231 time to evaluate : 1.316 ------------------------------------------------------------------------------- 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 150 ILE Chi-restraints excluded: chain Y residue 216 VAL Chi-restraints excluded: chain Z residue 7 LEU Chi-restraints excluded: chain Z residue 142 LEU Chi-restraints excluded: chain C residue 85 LEU Chi-restraints excluded: chain C residue 116 THR Chi-restraints excluded: chain C residue 117 LEU Chi-restraints excluded: chain C residue 197 VAL Chi-restraints excluded: chain C residue 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 237 GLN Chi-restraints excluded: chain F residue 116 THR Chi-restraints excluded: chain F residue 201 MET Chi-restraints excluded: chain F residue 216 VAL Chi-restraints excluded: chain G residue 7 LEU Chi-restraints excluded: chain G residue 142 LEU Chi-restraints excluded: chain G residue 237 GLN Chi-restraints excluded: chain G residue 293 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 171 random chunks: chunk 55 optimal weight: 0.0000 chunk 148 optimal weight: 0.8980 chunk 32 optimal weight: 0.9980 chunk 97 optimal weight: 9.9990 chunk 40 optimal weight: 0.8980 chunk 165 optimal weight: 2.9990 chunk 137 optimal weight: 3.9990 chunk 76 optimal weight: 0.6980 chunk 13 optimal weight: 0.8980 chunk 54 optimal weight: 4.9990 chunk 86 optimal weight: 6.9990 overall best weight: 0.6784 ------------------------------------------------------------------------------- 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 240 ASN D 179 GLN D 204 GLN D 238 GLN D 239 GLN F 240 ASN G 230 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8251 moved from start: 0.1562 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 13599 Z= 0.160 Angle : 0.537 12.145 18486 Z= 0.272 Chirality : 0.040 0.131 2205 Planarity : 0.005 0.071 2274 Dihedral : 4.310 24.442 1911 Min Nonbonded Distance : 2.511 Molprobity Statistics. All-atom Clashscore : 5.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.84 % Favored : 95.16 % Rotamer: Outliers : 2.27 % Allowed : 19.56 % 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: 1.92 (0.21), residues: 1755 helix: 2.40 (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 0.012 0.001 TRP Z 26 HIS 0.002 0.001 HIS D 68 PHE 0.012 0.001 PHE G 191 TYR 0.007 0.001 TYR D 219 ARG 0.007 0.000 ARG C 127 *********************** 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 270 residues out of total 1365 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 239 time to evaluate : 1.327 Fit side-chains REVERT: Y 243 LYS cc_start: 0.7737 (mtmm) cc_final: 0.7406 (mtmt) REVERT: Z 237 GLN cc_start: 0.8005 (OUTLIER) cc_final: 0.7644 (mt0) REVERT: C 85 LEU cc_start: 0.7756 (OUTLIER) cc_final: 0.7450 (pt) REVERT: C 117 LEU cc_start: 0.8330 (OUTLIER) cc_final: 0.8089 (tt) REVERT: D 98 GLN cc_start: 0.7432 (tm-30) cc_final: 0.7110 (mm110) REVERT: D 168 LYS cc_start: 0.6118 (tmmt) cc_final: 0.5612 (tmtt) REVERT: D 247 GLU cc_start: 0.7389 (pm20) cc_final: 0.7075 (tm-30) REVERT: G 237 GLN cc_start: 0.7934 (OUTLIER) cc_final: 0.7713 (mm-40) outliers start: 31 outliers final: 15 residues processed: 256 average time/residue: 1.1060 time to fit residues: 311.7588 Evaluate side-chains 252 residues out of total 1365 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 233 time to evaluate : 1.398 ------------------------------------------------------------------------------- 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 150 ILE Chi-restraints excluded: chain Y residue 216 VAL Chi-restraints excluded: chain Z residue 7 LEU Chi-restraints excluded: chain Z residue 142 LEU Chi-restraints excluded: chain Z residue 237 GLN Chi-restraints excluded: chain C residue 85 LEU Chi-restraints excluded: chain C residue 116 THR Chi-restraints excluded: chain C residue 117 LEU Chi-restraints excluded: chain C residue 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 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 237 GLN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 171 random chunks: chunk 159 optimal weight: 30.0000 chunk 18 optimal weight: 8.9990 chunk 94 optimal weight: 0.9980 chunk 120 optimal weight: 2.9990 chunk 93 optimal weight: 0.6980 chunk 139 optimal weight: 3.9990 chunk 92 optimal weight: 0.6980 chunk 164 optimal weight: 2.9990 chunk 103 optimal weight: 0.1980 chunk 100 optimal weight: 2.9990 chunk 76 optimal weight: 0.9990 overall best weight: 0.7182 ------------------------------------------------------------------------------- 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 238 GLN F 240 ASN G 230 GLN G 238 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8250 moved from start: 0.1616 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 13599 Z= 0.162 Angle : 0.540 11.916 18486 Z= 0.273 Chirality : 0.040 0.132 2205 Planarity : 0.005 0.071 2274 Dihedral : 4.257 24.574 1910 Min Nonbonded Distance : 2.454 Molprobity Statistics. All-atom Clashscore : 4.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.67 % Favored : 95.33 % Rotamer: Outliers : 2.71 % Allowed : 19.41 % Favored : 77.88 % 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: 1.94 (0.21), residues: 1755 helix: 2.40 (0.15), residues: 1251 sheet: None (None), residues: 0 loop : -1.75 (0.27), residues: 504 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 0.014 0.001 PHE F 161 TYR 0.007 0.001 TYR Z 219 ARG 0.007 0.000 ARG C 127 *********************** 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 fitting. rotamer outliers: 37 poor density : 232 time to evaluate : 1.478 Fit side-chains revert: symmetry clash REVERT: Y 44 LEU cc_start: 0.8244 (tp) cc_final: 0.7880 (tm) REVERT: Y 243 LYS cc_start: 0.7692 (mtmm) cc_final: 0.7489 (mtmt) REVERT: Z 237 GLN cc_start: 0.8006 (OUTLIER) cc_final: 0.7650 (mt0) REVERT: C 85 LEU cc_start: 0.7706 (OUTLIER) cc_final: 0.7391 (pt) REVERT: C 112 MET cc_start: 0.8110 (mtm) cc_final: 0.7707 (mtp) REVERT: C 117 LEU cc_start: 0.8333 (OUTLIER) cc_final: 0.8094 (tt) REVERT: D 98 GLN cc_start: 0.7492 (tm-30) cc_final: 0.7128 (mm110) REVERT: D 168 LYS cc_start: 0.6145 (tmmt) cc_final: 0.5635 (tmtt) outliers start: 37 outliers final: 22 residues processed: 253 average time/residue: 1.1081 time to fit residues: 308.8878 Evaluate side-chains 257 residues out of total 1365 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 232 time to evaluate : 1.441 ------------------------------------------------------------------------------- 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 150 ILE 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 116 THR Chi-restraints excluded: chain C residue 117 LEU Chi-restraints excluded: chain C residue 174 MET 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 178 LEU 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 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 101 optimal weight: 8.9990 chunk 65 optimal weight: 3.9990 chunk 98 optimal weight: 1.9990 chunk 49 optimal weight: 4.9990 chunk 32 optimal weight: 5.9990 chunk 31 optimal weight: 0.9980 chunk 104 optimal weight: 0.9980 chunk 112 optimal weight: 0.8980 chunk 81 optimal weight: 2.9990 chunk 15 optimal weight: 0.5980 chunk 129 optimal weight: 0.8980 overall best weight: 0.8780 ------------------------------------------------------------------------------- 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 204 GLN F 240 ASN G 230 GLN G 237 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8257 moved from start: 0.1675 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 13599 Z= 0.173 Angle : 0.553 12.368 18486 Z= 0.278 Chirality : 0.041 0.129 2205 Planarity : 0.005 0.071 2274 Dihedral : 4.273 24.954 1910 Min Nonbonded Distance : 2.472 Molprobity Statistics. All-atom Clashscore : 4.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.84 % Favored : 95.16 % Rotamer: Outliers : 2.49 % Allowed : 19.78 % Favored : 77.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 1.93 (0.21), residues: 1755 helix: 2.39 (0.15), residues: 1251 sheet: None (None), residues: 0 loop : -1.75 (0.27), residues: 504 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 0.013 0.001 PHE G 191 TYR 0.009 0.001 TYR Z 219 ARG 0.007 0.000 ARG C 127 *********************** 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 263 residues out of total 1365 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 229 time to evaluate : 1.562 Fit side-chains revert: symmetry clash REVERT: Y 44 LEU cc_start: 0.8252 (tp) cc_final: 0.7886 (tm) REVERT: Z 237 GLN cc_start: 0.8015 (OUTLIER) cc_final: 0.7653 (mt0) REVERT: C 85 LEU cc_start: 0.7756 (OUTLIER) cc_final: 0.7477 (pt) REVERT: C 112 MET cc_start: 0.8122 (mtm) cc_final: 0.7722 (mtp) REVERT: C 117 LEU cc_start: 0.8341 (OUTLIER) cc_final: 0.8105 (tt) REVERT: D 98 GLN cc_start: 0.7504 (tm-30) cc_final: 0.7113 (mm110) REVERT: D 168 LYS cc_start: 0.6162 (tmmt) cc_final: 0.5655 (tmtt) REVERT: F 201 MET cc_start: 0.7144 (OUTLIER) cc_final: 0.6157 (ptt) outliers start: 34 outliers final: 25 residues processed: 248 average time/residue: 1.2049 time to fit residues: 328.1896 Evaluate side-chains 256 residues out of total 1365 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 227 time to evaluate : 1.509 ------------------------------------------------------------------------------- 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 150 ILE Chi-restraints excluded: chain Y residue 154 ILE Chi-restraints excluded: chain Y residue 204 LYS Chi-restraints excluded: chain Y residue 216 VAL Chi-restraints excluded: chain Z residue 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 116 THR Chi-restraints excluded: chain C residue 117 LEU Chi-restraints excluded: chain C residue 174 MET 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 148 ASN Chi-restraints excluded: chain D residue 178 LEU Chi-restraints excluded: chain D residue 237 GLN Chi-restraints excluded: chain F residue 95 SER Chi-restraints excluded: chain F residue 116 THR Chi-restraints excluded: chain F residue 150 ILE Chi-restraints excluded: chain F residue 201 MET Chi-restraints excluded: chain F residue 216 VAL Chi-restraints excluded: chain G residue 7 LEU Chi-restraints excluded: chain G residue 142 LEU Chi-restraints excluded: chain G residue 293 VAL Chi-restraints excluded: chain H residue 11 LYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 171 random chunks: chunk 149 optimal weight: 1.9990 chunk 157 optimal weight: 2.9990 chunk 144 optimal weight: 0.6980 chunk 153 optimal weight: 2.9990 chunk 92 optimal weight: 1.9990 chunk 66 optimal weight: 0.6980 chunk 120 optimal weight: 0.9980 chunk 47 optimal weight: 9.9990 chunk 138 optimal weight: 2.9990 chunk 145 optimal weight: 3.9990 chunk 100 optimal weight: 5.9990 overall best weight: 1.2784 ------------------------------------------------------------------------------- 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 204 GLN F 240 ASN G 230 GLN G 237 GLN G 238 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8283 moved from start: 0.1744 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 13599 Z= 0.205 Angle : 0.573 12.202 18486 Z= 0.290 Chirality : 0.042 0.140 2205 Planarity : 0.005 0.072 2274 Dihedral : 4.379 25.289 1910 Min Nonbonded Distance : 2.404 Molprobity Statistics. All-atom Clashscore : 5.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.01 % Favored : 94.99 % Rotamer: Outliers : 2.56 % Allowed : 19.78 % 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: 1.81 (0.21), residues: 1755 helix: 2.30 (0.15), residues: 1251 sheet: None (None), residues: 0 loop : -1.78 (0.27), residues: 504 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP Z 26 HIS 0.003 0.001 HIS Z 68 PHE 0.016 0.001 PHE F 161 TYR 0.008 0.001 TYR Z 219 ARG 0.007 0.001 ARG C 127 *********************** 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 266 residues out of total 1365 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 231 time to evaluate : 1.468 Fit side-chains REVERT: Y 44 LEU cc_start: 0.8260 (tp) cc_final: 0.7870 (tm) REVERT: Z 237 GLN cc_start: 0.8003 (OUTLIER) cc_final: 0.7634 (mt0) REVERT: C 44 LEU cc_start: 0.8229 (tp) cc_final: 0.7901 (tm) REVERT: C 85 LEU cc_start: 0.7780 (OUTLIER) cc_final: 0.7491 (pt) REVERT: C 112 MET cc_start: 0.8137 (mtm) cc_final: 0.7744 (mtp) REVERT: C 117 LEU cc_start: 0.8368 (OUTLIER) cc_final: 0.8113 (tt) REVERT: D 98 GLN cc_start: 0.7533 (tm-30) cc_final: 0.7120 (mm110) REVERT: D 168 LYS cc_start: 0.6140 (tmmt) cc_final: 0.5633 (tmtt) REVERT: F 201 MET cc_start: 0.7283 (OUTLIER) cc_final: 0.6377 (ptt) outliers start: 35 outliers final: 25 residues processed: 248 average time/residue: 1.1668 time to fit residues: 318.2095 Evaluate side-chains 260 residues out of total 1365 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 231 time to evaluate : 1.490 ------------------------------------------------------------------------------- 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 150 ILE Chi-restraints excluded: chain Y residue 154 ILE Chi-restraints excluded: chain Y residue 204 LYS Chi-restraints excluded: chain Y residue 216 VAL Chi-restraints excluded: chain Z residue 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 116 THR Chi-restraints excluded: chain C residue 117 LEU Chi-restraints excluded: chain C residue 174 MET 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 148 ASN Chi-restraints excluded: chain D residue 178 LEU Chi-restraints excluded: chain D residue 237 GLN Chi-restraints excluded: chain F residue 95 SER Chi-restraints excluded: chain F residue 116 THR Chi-restraints excluded: chain F residue 150 ILE Chi-restraints excluded: chain F residue 201 MET Chi-restraints excluded: chain F residue 216 VAL Chi-restraints excluded: chain G residue 7 LEU Chi-restraints excluded: chain G residue 142 LEU Chi-restraints excluded: chain G residue 293 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 171 random chunks: chunk 162 optimal weight: 3.9990 chunk 99 optimal weight: 4.9990 chunk 77 optimal weight: 1.9990 chunk 112 optimal weight: 0.8980 chunk 170 optimal weight: 6.9990 chunk 156 optimal weight: 0.8980 chunk 135 optimal weight: 2.9990 chunk 14 optimal weight: 0.8980 chunk 104 optimal weight: 8.9990 chunk 83 optimal weight: 4.9990 chunk 107 optimal weight: 1.9990 overall best weight: 1.3384 ------------------------------------------------------------------------------- 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 204 GLN F 148 GLN F 240 ASN G 230 GLN G 237 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8286 moved from start: 0.1782 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 13599 Z= 0.212 Angle : 0.582 12.683 18486 Z= 0.293 Chirality : 0.042 0.145 2205 Planarity : 0.005 0.072 2274 Dihedral : 4.438 26.992 1910 Min Nonbonded Distance : 2.419 Molprobity Statistics. All-atom Clashscore : 5.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.41 % Favored : 94.59 % Rotamer: Outliers : 2.27 % Allowed : 20.07 % 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: 1.77 (0.21), residues: 1755 helix: 2.26 (0.15), residues: 1251 sheet: None (None), residues: 0 loop : -1.78 (0.27), residues: 504 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP Z 26 HIS 0.003 0.001 HIS Z 68 PHE 0.014 0.001 PHE G 191 TYR 0.009 0.001 TYR Z 219 ARG 0.007 0.001 ARG C 127 ********************** 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 266 residues out of total 1365 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 235 time to evaluate : 1.469 Fit side-chains REVERT: Y 44 LEU cc_start: 0.8266 (tp) cc_final: 0.7874 (tm) REVERT: Z 168 LYS cc_start: 0.6057 (tmmt) cc_final: 0.5594 (tmtt) REVERT: Z 237 GLN cc_start: 0.8008 (OUTLIER) cc_final: 0.7645 (mt0) REVERT: C 85 LEU cc_start: 0.7830 (OUTLIER) cc_final: 0.7561 (pt) REVERT: C 112 MET cc_start: 0.8131 (mtm) cc_final: 0.7742 (mtp) REVERT: C 117 LEU cc_start: 0.8383 (OUTLIER) cc_final: 0.8145 (tt) REVERT: D 168 LYS cc_start: 0.6154 (tmmt) cc_final: 0.5650 (tmtt) REVERT: F 201 MET cc_start: 0.7238 (OUTLIER) cc_final: 0.6312 (ptt) outliers start: 31 outliers final: 22 residues processed: 250 average time/residue: 1.1009 time to fit residues: 303.0043 Evaluate side-chains 258 residues out of total 1365 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 232 time to evaluate : 1.437 ------------------------------------------------------------------------------- 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 150 ILE 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 116 THR Chi-restraints excluded: chain C residue 117 LEU Chi-restraints excluded: chain C residue 174 MET 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 148 ASN Chi-restraints excluded: chain D residue 237 GLN Chi-restraints excluded: chain F residue 95 SER Chi-restraints excluded: chain F residue 116 THR Chi-restraints excluded: chain F residue 150 ILE Chi-restraints excluded: chain F residue 201 MET Chi-restraints excluded: chain F residue 216 VAL Chi-restraints excluded: chain G residue 142 LEU Chi-restraints excluded: chain G residue 293 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 171 random chunks: chunk 144 optimal weight: 0.6980 chunk 41 optimal weight: 0.8980 chunk 125 optimal weight: 3.9990 chunk 20 optimal weight: 0.8980 chunk 37 optimal weight: 0.9990 chunk 135 optimal weight: 2.9990 chunk 56 optimal weight: 5.9990 chunk 139 optimal weight: 2.9990 chunk 17 optimal weight: 6.9990 chunk 25 optimal weight: 0.9990 chunk 119 optimal weight: 7.9990 overall best weight: 0.8984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Y 240 ASN Z 98 GLN Z 179 GLN Z 230 GLN Z 238 GLN C 168 GLN D 204 GLN F 148 GLN F 240 ASN G 230 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4055 r_free = 0.4055 target = 0.175141 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3679 r_free = 0.3679 target = 0.141127 restraints weight = 13517.601| |-----------------------------------------------------------------------------| r_work (start): 0.3674 rms_B_bonded: 2.00 r_work: 0.3438 rms_B_bonded: 2.32 restraints_weight: 0.5000 r_work: 0.3329 rms_B_bonded: 3.82 restraints_weight: 0.2500 r_work (final): 0.3329 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8524 moved from start: 0.1742 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 13599 Z= 0.176 Angle : 0.561 12.044 18486 Z= 0.282 Chirality : 0.041 0.153 2205 Planarity : 0.005 0.071 2274 Dihedral : 4.296 26.217 1908 Min Nonbonded Distance : 2.405 Molprobity Statistics. All-atom Clashscore : 5.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.96 % Favored : 95.04 % Rotamer: Outliers : 1.98 % Allowed : 20.44 % 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: 1.88 (0.21), residues: 1755 helix: 2.34 (0.15), residues: 1251 sheet: None (None), residues: 0 loop : -1.74 (0.27), residues: 504 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP Z 26 HIS 0.002 0.001 HIS Z 68 PHE 0.013 0.001 PHE G 191 TYR 0.008 0.001 TYR Z 219 ARG 0.007 0.000 ARG C 127 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5383.91 seconds wall clock time: 94 minutes 27.20 seconds (5667.20 seconds total)