Starting phenix.real_space_refine on Thu Mar 21 22:19:17 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7pbs_13301/03_2024/7pbs_13301_neut_trim_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7pbs_13301/03_2024/7pbs_13301.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7pbs_13301/03_2024/7pbs_13301.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7pbs_13301/03_2024/7pbs_13301.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7pbs_13301/03_2024/7pbs_13301_neut_trim_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7pbs_13301/03_2024/7pbs_13301_neut_trim_updated.pdb" } resolution = 3.3 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: 7 Type Number sf(0) Gaussians P 47 5.49 5 Mg 5 5.21 5 S 102 5.16 5 C 9900 2.51 5 N 2683 2.21 5 O 3152 1.98 5 H 15439 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped None Time to flip residues: 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 31328 Number of models: 1 Model: "" Number of chains: 15 Chain: "A" Number of atoms: 4910 Number of conformers: 1 Conformer: "" Number of residues, atoms: 312, 4910 Classifications: {'peptide': 312} Modifications used: {'NH1NOTPRO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 13, 'TRANS': 297} Chain: "B" Number of atoms: 4910 Number of conformers: 1 Conformer: "" Number of residues, atoms: 312, 4910 Classifications: {'peptide': 312} Modifications used: {'NH1NOTPRO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 13, 'TRANS': 297} Chain: "C" Number of atoms: 4895 Number of conformers: 1 Conformer: "" Number of residues, atoms: 309, 4895 Classifications: {'peptide': 309} Modifications used: {'NH1NOTPRO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 13, 'TRANS': 294} Chain breaks: 1 Chain: "D" Number of atoms: 4934 Number of conformers: 1 Conformer: "" Number of residues, atoms: 313, 4934 Classifications: {'peptide': 313} Modifications used: {'NH1NOTPRO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 13, 'TRANS': 298} Chain: "E" Number of atoms: 4910 Number of conformers: 1 Conformer: "" Number of residues, atoms: 312, 4910 Classifications: {'peptide': 312} Modifications used: {'NH1NOTPRO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 13, 'TRANS': 297} Chain: "F" Number of atoms: 4910 Number of conformers: 1 Conformer: "" Number of residues, atoms: 312, 4910 Classifications: {'peptide': 312} Modifications used: {'NH1NOTPRO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 13, 'TRANS': 297} Chain: "G" Number of atoms: 719 Number of conformers: 1 Conformer: "" Number of residues, atoms: 48, 719 Classifications: {'peptide': 48} Modifications used: {'COO': 1, 'NH1NOTPRO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 45} Chain: "U" Number of atoms: 479 Number of conformers: 1 Conformer: "" Number of residues, atoms: 15, 479 Classifications: {'DNA': 15} Link IDs: {'rna3p': 14} Chain: "V" Number of atoms: 474 Number of conformers: 1 Conformer: "" Number of residues, atoms: 15, 474 Classifications: {'DNA': 15} Modifications used: {'3*END': 1} Link IDs: {'rna3p': 14} Chain: "A" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'AGS': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'AGS': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "C" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'AGS': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "D" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'AGS': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "E" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Chain: "F" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'AGS': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 13.24, per 1000 atoms: 0.42 Number of scatterers: 31328 At special positions: 0 Unit cell: (123.2, 137.5, 107.8, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) S 102 16.00 P 47 15.00 Mg 5 11.99 O 3152 8.00 N 2683 7.00 C 9900 6.00 H 15439 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 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: 25.26 Conformation dependent library (CDL) restraints added in 3.4 seconds 3804 Ramachandran restraints generated. 1902 Oldfield, 0 Emsley, 1902 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3526 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 104 helices and 18 sheets defined 50.9% alpha, 11.2% beta 12 base pairs and 28 stacking pairs defined. Time for finding SS restraints: 15.86 Creating SS restraints... Processing helix chain 'A' and resid 32 through 48 removed outlier: 3.617A pdb=" N ILE A 40 " --> pdb=" O ASP A 36 " (cutoff:3.500A) Processing helix chain 'A' and resid 65 through 76 removed outlier: 3.559A pdb=" N PHE A 70 " --> pdb=" O THR A 66 " (cutoff:3.500A) Processing helix chain 'A' and resid 85 through 87 No H-bonds generated for 'chain 'A' and resid 85 through 87' Processing helix chain 'A' and resid 91 through 100 removed outlier: 3.556A pdb=" N ASP A 100 " --> pdb=" O ALA A 96 " (cutoff:3.500A) Processing helix chain 'A' and resid 112 through 114 No H-bonds generated for 'chain 'A' and resid 112 through 114' Processing helix chain 'A' and resid 117 through 129 removed outlier: 4.413A pdb=" N VAL A 122 " --> pdb=" O ALA A 118 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N LEU A 123 " --> pdb=" O VAL A 119 " (cutoff:3.500A) removed outlier: 3.895A pdb=" N TYR A 124 " --> pdb=" O GLU A 120 " (cutoff:3.500A) removed outlier: 4.898A pdb=" N SER A 125 " --> pdb=" O GLU A 121 " (cutoff:3.500A) removed outlier: 3.861A pdb=" N ALA A 126 " --> pdb=" O VAL A 122 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N GLU A 128 " --> pdb=" O TYR A 124 " (cutoff:3.500A) Processing helix chain 'A' and resid 161 through 163 No H-bonds generated for 'chain 'A' and resid 161 through 163' Processing helix chain 'A' and resid 166 through 171 removed outlier: 3.733A pdb=" N ARG A 171 " --> pdb=" O PRO A 167 " (cutoff:3.500A) Processing helix chain 'A' and resid 183 through 197 removed outlier: 3.590A pdb=" N GLU A 188 " --> pdb=" O PRO A 184 " (cutoff:3.500A) Processing helix chain 'A' and resid 203 through 211 Processing helix chain 'A' and resid 217 through 233 Processing helix chain 'A' and resid 241 through 250 removed outlier: 3.612A pdb=" N ASP A 245 " --> pdb=" O ASP A 241 " (cutoff:3.500A) Processing helix chain 'A' and resid 260 through 273 Processing helix chain 'A' and resid 280 through 286 Processing helix chain 'A' and resid 291 through 297 Processing helix chain 'A' and resid 299 through 305 Processing helix chain 'A' and resid 319 through 325 Processing helix chain 'B' and resid 32 through 48 removed outlier: 3.585A pdb=" N ILE B 40 " --> pdb=" O ASP B 36 " (cutoff:3.500A) Processing helix chain 'B' and resid 65 through 76 removed outlier: 3.522A pdb=" N PHE B 70 " --> pdb=" O THR B 66 " (cutoff:3.500A) Processing helix chain 'B' and resid 85 through 87 No H-bonds generated for 'chain 'B' and resid 85 through 87' Processing helix chain 'B' and resid 91 through 100 Processing helix chain 'B' and resid 112 through 114 No H-bonds generated for 'chain 'B' and resid 112 through 114' Processing helix chain 'B' and resid 117 through 129 removed outlier: 3.524A pdb=" N GLU B 121 " --> pdb=" O MET B 117 " (cutoff:3.500A) removed outlier: 4.554A pdb=" N VAL B 122 " --> pdb=" O ALA B 118 " (cutoff:3.500A) removed outlier: 3.972A pdb=" N LEU B 123 " --> pdb=" O VAL B 119 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N TYR B 124 " --> pdb=" O GLU B 120 " (cutoff:3.500A) removed outlier: 4.885A pdb=" N SER B 125 " --> pdb=" O GLU B 121 " (cutoff:3.500A) removed outlier: 3.900A pdb=" N ALA B 126 " --> pdb=" O VAL B 122 " (cutoff:3.500A) Processing helix chain 'B' and resid 139 through 141 No H-bonds generated for 'chain 'B' and resid 139 through 141' Processing helix chain 'B' and resid 161 through 163 No H-bonds generated for 'chain 'B' and resid 161 through 163' Processing helix chain 'B' and resid 166 through 171 removed outlier: 3.793A pdb=" N ARG B 171 " --> pdb=" O PRO B 167 " (cutoff:3.500A) Processing helix chain 'B' and resid 183 through 196 Processing helix chain 'B' and resid 203 through 212 removed outlier: 3.852A pdb=" N ARG B 212 " --> pdb=" O GLU B 208 " (cutoff:3.500A) Processing helix chain 'B' and resid 217 through 233 Processing helix chain 'B' and resid 241 through 251 Processing helix chain 'B' and resid 260 through 272 Processing helix chain 'B' and resid 280 through 286 removed outlier: 3.505A pdb=" N ASN B 286 " --> pdb=" O THR B 282 " (cutoff:3.500A) Processing helix chain 'B' and resid 291 through 296 Processing helix chain 'B' and resid 299 through 304 Processing helix chain 'B' and resid 319 through 325 Processing helix chain 'C' and resid 32 through 47 Processing helix chain 'C' and resid 65 through 76 Processing helix chain 'C' and resid 91 through 100 removed outlier: 3.534A pdb=" N ASP C 100 " --> pdb=" O ALA C 96 " (cutoff:3.500A) Processing helix chain 'C' and resid 112 through 114 No H-bonds generated for 'chain 'C' and resid 112 through 114' Processing helix chain 'C' and resid 117 through 128 removed outlier: 4.137A pdb=" N VAL C 122 " --> pdb=" O ALA C 118 " (cutoff:3.500A) removed outlier: 4.408A pdb=" N SER C 125 " --> pdb=" O GLU C 121 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N ALA C 126 " --> pdb=" O VAL C 122 " (cutoff:3.500A) Processing helix chain 'C' and resid 161 through 163 No H-bonds generated for 'chain 'C' and resid 161 through 163' Processing helix chain 'C' and resid 166 through 171 removed outlier: 3.519A pdb=" N ALA C 170 " --> pdb=" O ASN C 166 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N ARG C 171 " --> pdb=" O PRO C 167 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 166 through 171' Processing helix chain 'C' and resid 183 through 196 Processing helix chain 'C' and resid 203 through 211 Processing helix chain 'C' and resid 217 through 234 Processing helix chain 'C' and resid 241 through 251 removed outlier: 3.691A pdb=" N ASP C 245 " --> pdb=" O ASP C 241 " (cutoff:3.500A) Processing helix chain 'C' and resid 260 through 272 Processing helix chain 'C' and resid 280 through 287 Processing helix chain 'C' and resid 291 through 297 Processing helix chain 'C' and resid 299 through 304 Processing helix chain 'C' and resid 319 through 325 Processing helix chain 'D' and resid 32 through 46 Processing helix chain 'D' and resid 65 through 76 Processing helix chain 'D' and resid 85 through 87 No H-bonds generated for 'chain 'D' and resid 85 through 87' Processing helix chain 'D' and resid 91 through 100 Processing helix chain 'D' and resid 112 through 114 No H-bonds generated for 'chain 'D' and resid 112 through 114' Processing helix chain 'D' and resid 117 through 129 removed outlier: 4.435A pdb=" N VAL D 122 " --> pdb=" O ALA D 118 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N TYR D 124 " --> pdb=" O GLU D 120 " (cutoff:3.500A) removed outlier: 4.900A pdb=" N SER D 125 " --> pdb=" O GLU D 121 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N ALA D 126 " --> pdb=" O VAL D 122 " (cutoff:3.500A) Processing helix chain 'D' and resid 166 through 171 removed outlier: 3.593A pdb=" N ARG D 171 " --> pdb=" O PRO D 167 " (cutoff:3.500A) Processing helix chain 'D' and resid 183 through 196 removed outlier: 3.667A pdb=" N GLU D 188 " --> pdb=" O PRO D 184 " (cutoff:3.500A) Processing helix chain 'D' and resid 203 through 212 removed outlier: 3.578A pdb=" N ARG D 212 " --> pdb=" O GLU D 208 " (cutoff:3.500A) Processing helix chain 'D' and resid 217 through 231 Processing helix chain 'D' and resid 241 through 250 Processing helix chain 'D' and resid 260 through 273 Processing helix chain 'D' and resid 280 through 287 removed outlier: 3.512A pdb=" N ASN D 286 " --> pdb=" O THR D 282 " (cutoff:3.500A) Processing helix chain 'D' and resid 291 through 296 Processing helix chain 'D' and resid 299 through 304 Processing helix chain 'D' and resid 319 through 325 Processing helix chain 'E' and resid 32 through 47 removed outlier: 3.532A pdb=" N ILE E 40 " --> pdb=" O ASP E 36 " (cutoff:3.500A) Processing helix chain 'E' and resid 65 through 76 Processing helix chain 'E' and resid 85 through 87 No H-bonds generated for 'chain 'E' and resid 85 through 87' Processing helix chain 'E' and resid 91 through 99 Processing helix chain 'E' and resid 112 through 114 No H-bonds generated for 'chain 'E' and resid 112 through 114' Processing helix chain 'E' and resid 117 through 129 removed outlier: 3.743A pdb=" N GLU E 121 " --> pdb=" O MET E 117 " (cutoff:3.500A) removed outlier: 4.576A pdb=" N VAL E 122 " --> pdb=" O ALA E 118 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N LEU E 123 " --> pdb=" O VAL E 119 " (cutoff:3.500A) removed outlier: 4.044A pdb=" N SER E 125 " --> pdb=" O GLU E 121 " (cutoff:3.500A) Processing helix chain 'E' and resid 166 through 171 removed outlier: 4.021A pdb=" N ARG E 171 " --> pdb=" O PRO E 167 " (cutoff:3.500A) Processing helix chain 'E' and resid 183 through 196 removed outlier: 3.816A pdb=" N GLU E 188 " --> pdb=" O PRO E 184 " (cutoff:3.500A) Processing helix chain 'E' and resid 203 through 212 Processing helix chain 'E' and resid 217 through 234 removed outlier: 3.736A pdb=" N ASP E 229 " --> pdb=" O LYS E 225 " (cutoff:3.500A) removed outlier: 3.932A pdb=" N ILE E 233 " --> pdb=" O ASP E 229 " (cutoff:3.500A) Processing helix chain 'E' and resid 241 through 250 Processing helix chain 'E' and resid 260 through 273 Processing helix chain 'E' and resid 280 through 286 removed outlier: 3.746A pdb=" N ASN E 286 " --> pdb=" O THR E 282 " (cutoff:3.500A) Processing helix chain 'E' and resid 291 through 297 Processing helix chain 'E' and resid 299 through 304 Processing helix chain 'E' and resid 319 through 325 Processing helix chain 'F' and resid 32 through 47 removed outlier: 3.712A pdb=" N GLN F 37 " --> pdb=" O LYS F 33 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N ILE F 40 " --> pdb=" O ASP F 36 " (cutoff:3.500A) Processing helix chain 'F' and resid 65 through 76 Processing helix chain 'F' and resid 85 through 87 No H-bonds generated for 'chain 'F' and resid 85 through 87' Processing helix chain 'F' and resid 91 through 100 removed outlier: 3.527A pdb=" N ASP F 100 " --> pdb=" O ALA F 96 " (cutoff:3.500A) Processing helix chain 'F' and resid 112 through 114 No H-bonds generated for 'chain 'F' and resid 112 through 114' Processing helix chain 'F' and resid 117 through 129 removed outlier: 4.483A pdb=" N VAL F 122 " --> pdb=" O ALA F 118 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N LEU F 123 " --> pdb=" O VAL F 119 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N TYR F 124 " --> pdb=" O GLU F 120 " (cutoff:3.500A) removed outlier: 4.840A pdb=" N SER F 125 " --> pdb=" O GLU F 121 " (cutoff:3.500A) removed outlier: 3.842A pdb=" N ALA F 126 " --> pdb=" O VAL F 122 " (cutoff:3.500A) Processing helix chain 'F' and resid 139 through 141 No H-bonds generated for 'chain 'F' and resid 139 through 141' Processing helix chain 'F' and resid 161 through 163 No H-bonds generated for 'chain 'F' and resid 161 through 163' Processing helix chain 'F' and resid 166 through 171 removed outlier: 4.041A pdb=" N ARG F 171 " --> pdb=" O PRO F 167 " (cutoff:3.500A) Processing helix chain 'F' and resid 183 through 196 Processing helix chain 'F' and resid 203 through 211 Processing helix chain 'F' and resid 217 through 233 Processing helix chain 'F' and resid 241 through 250 Processing helix chain 'F' and resid 260 through 272 Processing helix chain 'F' and resid 280 through 287 removed outlier: 3.669A pdb=" N VAL F 285 " --> pdb=" O GLY F 281 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N ASN F 286 " --> pdb=" O THR F 282 " (cutoff:3.500A) Processing helix chain 'F' and resid 291 through 296 Processing helix chain 'F' and resid 299 through 304 Processing helix chain 'F' and resid 319 through 325 Processing helix chain 'G' and resid 157 through 170 Processing helix chain 'G' and resid 174 through 182 Processing helix chain 'G' and resid 191 through 201 Processing sheet with id= A, first strand: chain 'A' and resid 174 through 177 Processing sheet with id= B, first strand: chain 'A' and resid 131 through 137 Processing sheet with id= C, first strand: chain 'A' and resid 308 through 311 Processing sheet with id= D, first strand: chain 'B' and resid 174 through 177 Processing sheet with id= E, first strand: chain 'B' and resid 131 through 136 Processing sheet with id= F, first strand: chain 'B' and resid 308 through 311 Processing sheet with id= G, first strand: chain 'C' and resid 174 through 177 Processing sheet with id= H, first strand: chain 'C' and resid 131 through 136 Processing sheet with id= I, first strand: chain 'C' and resid 308 through 311 Processing sheet with id= J, first strand: chain 'D' and resid 174 through 177 Processing sheet with id= K, first strand: chain 'D' and resid 131 through 136 Processing sheet with id= L, first strand: chain 'D' and resid 308 through 311 Processing sheet with id= M, first strand: chain 'E' and resid 174 through 177 Processing sheet with id= N, first strand: chain 'E' and resid 131 through 136 Processing sheet with id= O, first strand: chain 'E' and resid 308 through 311 Processing sheet with id= P, first strand: chain 'F' and resid 174 through 178 Processing sheet with id= Q, first strand: chain 'F' and resid 131 through 136 Processing sheet with id= R, first strand: chain 'F' and resid 308 through 311 670 hydrogen bonds defined for protein. 1959 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 25 hydrogen bonds 50 hydrogen bond angles 0 basepair planarities 12 basepair parallelities 28 stacking parallelities Total time for adding SS restraints: 11.34 Time building geometry restraints manager: 26.14 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.83 - 1.05: 15439 1.05 - 1.28: 2655 1.28 - 1.50: 6782 1.50 - 1.72: 6592 1.72 - 1.94: 199 Bond restraints: 31667 Sorted by residual: bond pdb=" N THR D 19 " pdb=" H1 THR D 19 " ideal model delta sigma weight residual 0.960 0.859 0.101 2.00e-02 2.50e+03 2.53e+01 bond pdb=" N THR E 19 " pdb=" H1 THR E 19 " ideal model delta sigma weight residual 0.960 0.860 0.100 2.00e-02 2.50e+03 2.52e+01 bond pdb=" N THR C 19 " pdb=" H1 THR C 19 " ideal model delta sigma weight residual 0.960 0.860 0.100 2.00e-02 2.50e+03 2.52e+01 bond pdb=" N THR B 19 " pdb=" H1 THR B 19 " ideal model delta sigma weight residual 0.960 0.860 0.100 2.00e-02 2.50e+03 2.52e+01 bond pdb=" N THR F 19 " pdb=" H1 THR F 19 " ideal model delta sigma weight residual 0.960 0.860 0.100 2.00e-02 2.50e+03 2.50e+01 ... (remaining 31662 not shown) Histogram of bond angle deviations from ideal: 99.81 - 107.07: 940 107.07 - 114.32: 38556 114.32 - 121.57: 12164 121.57 - 128.83: 5569 128.83 - 136.08: 92 Bond angle restraints: 57321 Sorted by residual: angle pdb=" N PHE B 197 " pdb=" CA PHE B 197 " pdb=" C PHE B 197 " ideal model delta sigma weight residual 110.48 104.85 5.63 1.48e+00 4.57e-01 1.45e+01 angle pdb=" N ILE E 233 " pdb=" CA ILE E 233 " pdb=" C ILE E 233 " ideal model delta sigma weight residual 111.62 108.75 2.87 7.90e-01 1.60e+00 1.32e+01 angle pdb=" OP1 DT V 4 " pdb=" P DT V 4 " pdb=" OP2 DT V 4 " ideal model delta sigma weight residual 120.00 109.22 10.78 3.00e+00 1.11e-01 1.29e+01 angle pdb=" O3' DT V 3 " pdb=" P DT V 4 " pdb=" OP1 DT V 4 " ideal model delta sigma weight residual 108.00 118.12 -10.12 3.00e+00 1.11e-01 1.14e+01 angle pdb=" N LEU D 251 " pdb=" CA LEU D 251 " pdb=" C LEU D 251 " ideal model delta sigma weight residual 110.20 105.10 5.10 1.58e+00 4.01e-01 1.04e+01 ... (remaining 57316 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 34.75: 14162 34.75 - 69.50: 515 69.50 - 104.25: 16 104.25 - 139.00: 3 139.00 - 173.75: 3 Dihedral angle restraints: 14699 sinusoidal: 8430 harmonic: 6269 Sorted by residual: dihedral pdb=" O2A ADP E 600 " pdb=" O3A ADP E 600 " pdb=" PA ADP E 600 " pdb=" PB ADP E 600 " ideal model delta sinusoidal sigma weight residual -60.00 97.10 -157.10 1 2.00e+01 2.50e-03 4.61e+01 dihedral pdb=" O1A AGS F 401 " pdb=" O3A AGS F 401 " pdb=" PA AGS F 401 " pdb=" PB AGS F 401 " ideal model delta sinusoidal sigma weight residual -67.73 106.02 -173.75 1 3.00e+01 1.11e-03 2.13e+01 dihedral pdb=" O1A AGS D 401 " pdb=" O3A AGS D 401 " pdb=" PA AGS D 401 " pdb=" PB AGS D 401 " ideal model delta sinusoidal sigma weight residual -67.73 76.82 -144.55 1 3.00e+01 1.11e-03 1.94e+01 ... (remaining 14696 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.083: 2269 0.083 - 0.166: 228 0.166 - 0.248: 0 0.248 - 0.331: 0 0.331 - 0.414: 1 Chirality restraints: 2498 Sorted by residual: chirality pdb=" P DT V 4 " pdb=" OP1 DT V 4 " pdb=" OP2 DT V 4 " pdb=" O5' DT V 4 " both_signs ideal model delta sigma weight residual True 2.35 -2.76 -0.41 2.00e-01 2.50e+01 4.28e+00 chirality pdb=" CA PRO C 300 " pdb=" N PRO C 300 " pdb=" C PRO C 300 " pdb=" CB PRO C 300 " both_signs ideal model delta sigma weight residual False 2.72 2.56 0.16 2.00e-01 2.50e+01 6.23e-01 chirality pdb=" C3' DA U 10 " pdb=" C4' DA U 10 " pdb=" O3' DA U 10 " pdb=" C2' DA U 10 " both_signs ideal model delta sigma weight residual False -2.66 -2.51 -0.15 2.00e-01 2.50e+01 5.88e-01 ... (remaining 2495 not shown) Planarity restraints: 4586 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG E 218 " 0.145 9.50e-02 1.11e+02 6.91e-02 5.71e+01 pdb=" NE ARG E 218 " 0.037 2.00e-02 2.50e+03 pdb=" CZ ARG E 218 " -0.029 2.00e-02 2.50e+03 pdb=" NH1 ARG E 218 " 0.005 2.00e-02 2.50e+03 pdb=" NH2 ARG E 218 " -0.099 2.00e-02 2.50e+03 pdb="HH11 ARG E 218 " -0.000 2.00e-02 2.50e+03 pdb="HH12 ARG E 218 " -0.013 2.00e-02 2.50e+03 pdb="HH21 ARG E 218 " -0.006 2.00e-02 2.50e+03 pdb="HH22 ARG E 218 " 0.099 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG E 160 " 0.312 9.50e-02 1.11e+02 1.13e-01 5.48e+01 pdb=" NE ARG E 160 " 0.023 2.00e-02 2.50e+03 pdb=" CZ ARG E 160 " -0.018 2.00e-02 2.50e+03 pdb=" NH1 ARG E 160 " -0.011 2.00e-02 2.50e+03 pdb=" NH2 ARG E 160 " -0.091 2.00e-02 2.50e+03 pdb="HH11 ARG E 160 " -0.000 2.00e-02 2.50e+03 pdb="HH12 ARG E 160 " -0.004 2.00e-02 2.50e+03 pdb="HH21 ARG E 160 " -0.004 2.00e-02 2.50e+03 pdb="HH22 ARG E 160 " 0.091 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG C 192 " -0.168 9.50e-02 1.11e+02 7.21e-02 4.99e+01 pdb=" NE ARG C 192 " -0.001 2.00e-02 2.50e+03 pdb=" CZ ARG C 192 " -0.003 2.00e-02 2.50e+03 pdb=" NH1 ARG C 192 " -0.043 2.00e-02 2.50e+03 pdb=" NH2 ARG C 192 " 0.083 2.00e-02 2.50e+03 pdb="HH11 ARG C 192 " -0.001 2.00e-02 2.50e+03 pdb="HH12 ARG C 192 " 0.053 2.00e-02 2.50e+03 pdb="HH21 ARG C 192 " 0.004 2.00e-02 2.50e+03 pdb="HH22 ARG C 192 " -0.084 2.00e-02 2.50e+03 ... (remaining 4583 not shown) Histogram of nonbonded interaction distances: 1.52 - 2.13: 774 2.13 - 2.75: 56601 2.75 - 3.37: 84113 3.37 - 3.98: 108720 3.98 - 4.60: 176001 Nonbonded interactions: 426209 Sorted by model distance: nonbonded pdb=" OE2 GLU D 120 " pdb=" HG SER D 165 " model vdw 1.516 1.850 nonbonded pdb=" HZ3 LYS E 81 " pdb=" O ASP E 100 " model vdw 1.525 1.850 nonbonded pdb=" O ALA B 138 " pdb=" HG1 THR B 141 " model vdw 1.534 1.850 nonbonded pdb=" HZ3 LYS D 46 " pdb=" O GLU D 75 " model vdw 1.538 1.850 nonbonded pdb=" HG1 THR A 311 " pdb=" O GLY A 314 " model vdw 1.568 1.850 ... (remaining 426204 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'A' and (resid 19 through 136 or resid 141 through 330)) selection = (chain 'B' and (resid 19 through 136 or resid 141 through 330)) selection = (chain 'C' and resid 19 through 330) selection = (chain 'D' and (resid 19 through 136 or resid 141 through 330)) selection = (chain 'E' and (resid 19 through 136 or resid 141 through 330)) selection = (chain 'F' and (resid 19 through 136 or resid 141 through 330)) } 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: 2.700 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: 0.470 Extract box with map and model: 11.160 Check model and map are aligned: 0.470 Set scattering table: 0.280 Process input model: 106.990 Find NCS groups from input model: 1.680 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: 0.010 Load rotamer database and sin/cos tables:3.040 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 126.880 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7624 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 : 0.005 0.041 16228 Z= 0.336 Angle : 0.715 10.783 22105 Z= 0.415 Chirality : 0.046 0.414 2498 Planarity : 0.011 0.137 2739 Dihedral : 14.970 173.751 6287 Min Nonbonded Distance : 1.778 Molprobity Statistics. All-atom Clashscore : 1.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.74 % Favored : 99.26 % Rotamer: Outliers : 0.25 % Allowed : 1.37 % Favored : 98.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.98 % 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: -0.18 (0.18), residues: 1902 helix: -0.48 (0.15), residues: 1018 sheet: 0.80 (0.30), residues: 309 loop : 0.47 (0.26), residues: 575 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.012 0.003 HIS B 113 PHE 0.020 0.003 PHE A 25 TYR 0.025 0.005 TYR E 273 ARG 0.025 0.003 ARG C 114 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3804 Ramachandran restraints generated. 1902 Oldfield, 0 Emsley, 1902 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3804 Ramachandran restraints generated. 1902 Oldfield, 0 Emsley, 1902 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 424 residues out of total 1603 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 420 time to evaluate : 2.636 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 33 LYS cc_start: 0.7757 (mtpt) cc_final: 0.7429 (mttt) REVERT: A 43 GLU cc_start: 0.7729 (mt-10) cc_final: 0.7475 (mt-10) REVERT: A 131 TYR cc_start: 0.8742 (p90) cc_final: 0.7984 (p90) REVERT: A 160 ARG cc_start: 0.8019 (ptp90) cc_final: 0.7770 (ptp-170) REVERT: A 234 MET cc_start: 0.7411 (ptp) cc_final: 0.7067 (ptp) REVERT: A 252 ASP cc_start: 0.7867 (t0) cc_final: 0.7416 (t0) REVERT: A 282 THR cc_start: 0.8514 (m) cc_final: 0.8032 (p) REVERT: A 292 GLU cc_start: 0.7277 (mt-10) cc_final: 0.6968 (tt0) REVERT: A 309 MET cc_start: 0.7326 (ttm) cc_final: 0.7123 (ttt) REVERT: A 325 MET cc_start: 0.7672 (mmm) cc_final: 0.7248 (mmt) REVERT: B 49 ASP cc_start: 0.7720 (t0) cc_final: 0.7440 (t0) REVERT: B 102 GLU cc_start: 0.7541 (mm-30) cc_final: 0.6945 (mt-10) REVERT: B 178 MET cc_start: 0.8658 (mmm) cc_final: 0.7603 (mmt) REVERT: B 199 MET cc_start: 0.7852 (mmp) cc_final: 0.7277 (tpt) REVERT: B 234 MET cc_start: 0.8342 (mmp) cc_final: 0.8123 (mmm) REVERT: C 47 LEU cc_start: 0.8037 (tp) cc_final: 0.7701 (mt) REVERT: C 260 TYR cc_start: 0.7683 (t80) cc_final: 0.7360 (t80) REVERT: D 78 VAL cc_start: 0.7517 (t) cc_final: 0.7270 (p) REVERT: D 264 LYS cc_start: 0.7838 (tttt) cc_final: 0.7482 (ttpt) REVERT: D 292 GLU cc_start: 0.7447 (mm-30) cc_final: 0.7162 (mp0) REVERT: D 309 MET cc_start: 0.7813 (mtp) cc_final: 0.7580 (mtp) REVERT: D 330 THR cc_start: 0.6052 (m) cc_final: 0.5665 (p) REVERT: E 76 MET cc_start: 0.8489 (mmm) cc_final: 0.7796 (mmt) REVERT: E 89 GLU cc_start: 0.7131 (mt-10) cc_final: 0.6159 (mm-30) REVERT: E 98 LEU cc_start: 0.8658 (mt) cc_final: 0.8372 (mm) REVERT: E 111 GLU cc_start: 0.7970 (mm-30) cc_final: 0.7733 (mt-10) REVERT: E 125 SER cc_start: 0.7697 (m) cc_final: 0.7490 (t) REVERT: E 143 ARG cc_start: 0.6340 (mtm180) cc_final: 0.6011 (mtm110) REVERT: E 179 GLU cc_start: 0.7682 (pt0) cc_final: 0.7456 (pt0) REVERT: E 242 LYS cc_start: 0.7315 (pttm) cc_final: 0.6655 (tppt) REVERT: E 267 ARG cc_start: 0.7120 (ttm-80) cc_final: 0.6663 (ttp-110) REVERT: E 299 GLU cc_start: 0.7020 (mt-10) cc_final: 0.6126 (mt-10) REVERT: E 301 TYR cc_start: 0.7101 (t80) cc_final: 0.6825 (t80) REVERT: F 102 GLU cc_start: 0.7187 (mt-10) cc_final: 0.6766 (mp0) REVERT: F 125 SER cc_start: 0.8456 (m) cc_final: 0.8213 (p) REVERT: F 143 ARG cc_start: 0.7562 (ptt90) cc_final: 0.7229 (ptt-90) REVERT: F 144 SER cc_start: 0.8630 (p) cc_final: 0.8349 (t) REVERT: F 199 MET cc_start: 0.7222 (tpp) cc_final: 0.6662 (tpp) REVERT: F 267 ARG cc_start: 0.6547 (ttm170) cc_final: 0.5891 (ttp80) REVERT: F 286 ASN cc_start: 0.7162 (m-40) cc_final: 0.6901 (m110) outliers start: 4 outliers final: 1 residues processed: 421 average time/residue: 0.7329 time to fit residues: 429.3928 Evaluate side-chains 277 residues out of total 1603 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 276 time to evaluate : 2.751 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 280 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 191 random chunks: chunk 161 optimal weight: 0.9980 chunk 144 optimal weight: 2.9990 chunk 80 optimal weight: 1.9990 chunk 49 optimal weight: 0.9980 chunk 97 optimal weight: 2.9990 chunk 77 optimal weight: 0.9980 chunk 149 optimal weight: 0.6980 chunk 57 optimal weight: 1.9990 chunk 91 optimal weight: 0.9980 chunk 111 optimal weight: 0.9990 chunk 173 optimal weight: 3.9990 overall best weight: 0.9380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 246 GLN D 232 GLN D 286 ASN E 74 ASN E 166 ASN F 23 GLN F 232 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7638 moved from start: 0.2240 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 16228 Z= 0.249 Angle : 0.588 8.107 22105 Z= 0.320 Chirality : 0.041 0.158 2498 Planarity : 0.005 0.062 2739 Dihedral : 15.209 171.609 2563 Min Nonbonded Distance : 1.747 Molprobity Statistics. All-atom Clashscore : 2.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.89 % Favored : 99.11 % Rotamer: Outliers : 0.94 % Allowed : 5.80 % Favored : 93.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.98 % 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: 0.79 (0.19), residues: 1902 helix: 0.61 (0.16), residues: 1028 sheet: 0.89 (0.29), residues: 317 loop : 0.46 (0.26), residues: 557 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS D 324 PHE 0.010 0.001 PHE E 58 TYR 0.011 0.001 TYR C 260 ARG 0.005 0.001 ARG A 218 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3804 Ramachandran restraints generated. 1902 Oldfield, 0 Emsley, 1902 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3804 Ramachandran restraints generated. 1902 Oldfield, 0 Emsley, 1902 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 282 residues out of total 1603 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 267 time to evaluate : 2.464 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 131 TYR cc_start: 0.8782 (p90) cc_final: 0.8244 (p90) REVERT: A 160 ARG cc_start: 0.8096 (ptp90) cc_final: 0.7807 (ptp-170) REVERT: A 234 MET cc_start: 0.7603 (ptp) cc_final: 0.7063 (ptp) REVERT: A 309 MET cc_start: 0.7304 (ttm) cc_final: 0.7080 (ttt) REVERT: A 325 MET cc_start: 0.7617 (mmm) cc_final: 0.7254 (mmt) REVERT: B 49 ASP cc_start: 0.7896 (t0) cc_final: 0.7685 (t0) REVERT: B 102 GLU cc_start: 0.7581 (mm-30) cc_final: 0.6976 (mt-10) REVERT: B 199 MET cc_start: 0.8055 (mmp) cc_final: 0.7313 (tpt) REVERT: B 234 MET cc_start: 0.8141 (mmp) cc_final: 0.7861 (mmm) REVERT: B 296 ASP cc_start: 0.7643 (OUTLIER) cc_final: 0.7417 (t0) REVERT: C 178 MET cc_start: 0.8728 (mmt) cc_final: 0.8171 (mmt) REVERT: C 260 TYR cc_start: 0.7364 (t80) cc_final: 0.7058 (t80) REVERT: D 78 VAL cc_start: 0.7591 (t) cc_final: 0.7337 (p) REVERT: D 117 MET cc_start: 0.6917 (ttm) cc_final: 0.6657 (mtp) REVERT: D 292 GLU cc_start: 0.7448 (mm-30) cc_final: 0.7023 (mp0) REVERT: D 309 MET cc_start: 0.7711 (mtp) cc_final: 0.7489 (mtp) REVERT: D 330 THR cc_start: 0.6069 (m) cc_final: 0.5698 (p) REVERT: E 35 LYS cc_start: 0.8062 (ttpt) cc_final: 0.7817 (mtmt) REVERT: E 89 GLU cc_start: 0.6816 (mt-10) cc_final: 0.6132 (mm-30) REVERT: E 98 LEU cc_start: 0.8485 (mt) cc_final: 0.8278 (mm) REVERT: E 143 ARG cc_start: 0.6297 (mtm180) cc_final: 0.5974 (mtm110) REVERT: E 179 GLU cc_start: 0.7547 (pt0) cc_final: 0.7284 (pt0) REVERT: E 255 HIS cc_start: 0.6783 (p-80) cc_final: 0.6185 (m90) REVERT: E 267 ARG cc_start: 0.7238 (ttm-80) cc_final: 0.6690 (ttp-110) REVERT: F 102 GLU cc_start: 0.7290 (mt-10) cc_final: 0.6766 (mp0) REVERT: F 125 SER cc_start: 0.8390 (m) cc_final: 0.8177 (p) REVERT: F 144 SER cc_start: 0.8691 (p) cc_final: 0.8419 (t) REVERT: F 267 ARG cc_start: 0.6543 (ttm170) cc_final: 0.5889 (ttp80) REVERT: F 286 ASN cc_start: 0.6896 (m-40) cc_final: 0.6678 (m110) REVERT: F 309 MET cc_start: 0.7157 (tpp) cc_final: 0.6602 (ttm) outliers start: 15 outliers final: 13 residues processed: 276 average time/residue: 0.6943 time to fit residues: 273.5240 Evaluate side-chains 263 residues out of total 1603 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 249 time to evaluate : 2.545 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 284 SER Chi-restraints excluded: chain B residue 142 SER Chi-restraints excluded: chain B residue 236 ASP Chi-restraints excluded: chain B residue 296 ASP Chi-restraints excluded: chain C residue 38 LEU Chi-restraints excluded: chain C residue 125 SER Chi-restraints excluded: chain C residue 132 ILE Chi-restraints excluded: chain C residue 183 LEU Chi-restraints excluded: chain D residue 106 ILE Chi-restraints excluded: chain D residue 328 ASP Chi-restraints excluded: chain E residue 297 MET Chi-restraints excluded: chain F residue 245 ASP Chi-restraints excluded: chain F residue 265 ILE Chi-restraints excluded: chain F residue 280 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 191 random chunks: chunk 96 optimal weight: 0.6980 chunk 53 optimal weight: 0.6980 chunk 144 optimal weight: 3.9990 chunk 118 optimal weight: 0.9990 chunk 47 optimal weight: 0.5980 chunk 173 optimal weight: 1.9990 chunk 187 optimal weight: 1.9990 chunk 154 optimal weight: 1.9990 chunk 172 optimal weight: 1.9990 chunk 59 optimal weight: 0.9980 chunk 139 optimal weight: 0.8980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 246 GLN ** E 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7635 moved from start: 0.2628 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 16228 Z= 0.208 Angle : 0.511 5.809 22105 Z= 0.275 Chirality : 0.039 0.146 2498 Planarity : 0.004 0.053 2739 Dihedral : 15.186 169.629 2563 Min Nonbonded Distance : 1.756 Molprobity Statistics. All-atom Clashscore : 2.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.10 % Favored : 98.90 % Rotamer: Outliers : 0.87 % Allowed : 6.36 % Favored : 92.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.98 % 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: 1.10 (0.19), residues: 1902 helix: 0.99 (0.17), residues: 1028 sheet: 0.73 (0.29), residues: 292 loop : 0.52 (0.26), residues: 582 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS D 177 PHE 0.007 0.001 PHE B 58 TYR 0.010 0.001 TYR C 260 ARG 0.005 0.000 ARG A 312 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3804 Ramachandran restraints generated. 1902 Oldfield, 0 Emsley, 1902 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3804 Ramachandran restraints generated. 1902 Oldfield, 0 Emsley, 1902 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 276 residues out of total 1603 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 262 time to evaluate : 2.408 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 131 TYR cc_start: 0.8713 (p90) cc_final: 0.8298 (p90) REVERT: A 160 ARG cc_start: 0.8131 (ptp90) cc_final: 0.7801 (ptp-170) REVERT: A 234 MET cc_start: 0.7612 (ptp) cc_final: 0.7016 (ptp) REVERT: A 325 MET cc_start: 0.7624 (mmm) cc_final: 0.7254 (mmt) REVERT: B 102 GLU cc_start: 0.7663 (mm-30) cc_final: 0.7020 (mt-10) REVERT: B 128 GLU cc_start: 0.7317 (OUTLIER) cc_final: 0.6932 (tt0) REVERT: B 199 MET cc_start: 0.8097 (mmp) cc_final: 0.7345 (tpt) REVERT: C 125 SER cc_start: 0.7674 (OUTLIER) cc_final: 0.7235 (p) REVERT: C 178 MET cc_start: 0.8719 (mmt) cc_final: 0.8090 (mmt) REVERT: D 78 VAL cc_start: 0.7633 (t) cc_final: 0.7375 (p) REVERT: D 272 MET cc_start: 0.8345 (mmm) cc_final: 0.8079 (mmm) REVERT: D 292 GLU cc_start: 0.7475 (mm-30) cc_final: 0.7068 (mp0) REVERT: D 330 THR cc_start: 0.6401 (m) cc_final: 0.6022 (p) REVERT: E 35 LYS cc_start: 0.7995 (ttpt) cc_final: 0.7741 (mtmt) REVERT: E 89 GLU cc_start: 0.6661 (mt-10) cc_final: 0.5969 (mm-30) REVERT: E 98 LEU cc_start: 0.8454 (mt) cc_final: 0.8226 (mm) REVERT: E 143 ARG cc_start: 0.6319 (mtm180) cc_final: 0.5971 (mtm110) REVERT: E 179 GLU cc_start: 0.7598 (pt0) cc_final: 0.7303 (pt0) REVERT: E 255 HIS cc_start: 0.6816 (p-80) cc_final: 0.6211 (m90) REVERT: E 267 ARG cc_start: 0.7153 (ttm-80) cc_final: 0.6588 (ttp-110) REVERT: E 309 MET cc_start: 0.4216 (ptt) cc_final: 0.3937 (ptt) REVERT: F 102 GLU cc_start: 0.7306 (mt-10) cc_final: 0.6785 (mp0) REVERT: F 125 SER cc_start: 0.8449 (m) cc_final: 0.8222 (p) REVERT: F 178 MET cc_start: 0.8336 (mtp) cc_final: 0.8083 (mmt) REVERT: F 195 GLU cc_start: 0.6928 (tp30) cc_final: 0.6693 (tp30) REVERT: F 286 ASN cc_start: 0.6933 (m-40) cc_final: 0.6609 (m110) outliers start: 14 outliers final: 8 residues processed: 268 average time/residue: 0.7205 time to fit residues: 279.3403 Evaluate side-chains 262 residues out of total 1603 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 252 time to evaluate : 2.523 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 284 SER Chi-restraints excluded: chain B residue 128 GLU Chi-restraints excluded: chain B residue 142 SER Chi-restraints excluded: chain B residue 236 ASP Chi-restraints excluded: chain C residue 125 SER Chi-restraints excluded: chain C residue 183 LEU Chi-restraints excluded: chain E residue 297 MET Chi-restraints excluded: chain F residue 245 ASP Chi-restraints excluded: chain F residue 265 ILE Chi-restraints excluded: chain F residue 280 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 191 random chunks: chunk 171 optimal weight: 1.9990 chunk 130 optimal weight: 3.9990 chunk 90 optimal weight: 0.3980 chunk 19 optimal weight: 1.9990 chunk 82 optimal weight: 0.9980 chunk 116 optimal weight: 0.9980 chunk 174 optimal weight: 0.9980 chunk 184 optimal weight: 2.9990 chunk 91 optimal weight: 0.7980 chunk 165 optimal weight: 2.9990 chunk 49 optimal weight: 0.8980 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7640 moved from start: 0.2852 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 16228 Z= 0.208 Angle : 0.498 5.803 22105 Z= 0.268 Chirality : 0.039 0.158 2498 Planarity : 0.004 0.046 2739 Dihedral : 15.185 169.990 2563 Min Nonbonded Distance : 1.754 Molprobity Statistics. All-atom Clashscore : 2.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.26 % Favored : 98.74 % Rotamer: Outliers : 0.94 % Allowed : 6.74 % Favored : 92.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.98 % 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: 1.14 (0.19), residues: 1902 helix: 1.09 (0.17), residues: 1027 sheet: 0.67 (0.29), residues: 292 loop : 0.44 (0.25), residues: 583 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS A 146 PHE 0.007 0.001 PHE B 58 TYR 0.014 0.001 TYR D 124 ARG 0.003 0.000 ARG A 291 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3804 Ramachandran restraints generated. 1902 Oldfield, 0 Emsley, 1902 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3804 Ramachandran restraints generated. 1902 Oldfield, 0 Emsley, 1902 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 265 residues out of total 1603 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 250 time to evaluate : 2.998 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 100 ASP cc_start: 0.7809 (m-30) cc_final: 0.7538 (t70) REVERT: A 131 TYR cc_start: 0.8702 (p90) cc_final: 0.8339 (p90) REVERT: A 144 SER cc_start: 0.8093 (p) cc_final: 0.7843 (t) REVERT: A 160 ARG cc_start: 0.8131 (ptp90) cc_final: 0.7797 (ptp-170) REVERT: A 199 MET cc_start: 0.8110 (mmt) cc_final: 0.7880 (mmt) REVERT: A 234 MET cc_start: 0.7609 (ptp) cc_final: 0.7197 (ptp) REVERT: A 325 MET cc_start: 0.7740 (mmm) cc_final: 0.7283 (mmt) REVERT: B 102 GLU cc_start: 0.7778 (mm-30) cc_final: 0.7148 (mt-10) REVERT: B 128 GLU cc_start: 0.7302 (OUTLIER) cc_final: 0.6965 (tt0) REVERT: B 199 MET cc_start: 0.8191 (mmp) cc_final: 0.7430 (tpt) REVERT: B 242 LYS cc_start: 0.7735 (tppt) cc_final: 0.7206 (tppt) REVERT: C 125 SER cc_start: 0.7626 (OUTLIER) cc_final: 0.7211 (p) REVERT: C 178 MET cc_start: 0.8720 (mmt) cc_final: 0.8186 (mmt) REVERT: D 78 VAL cc_start: 0.7643 (t) cc_final: 0.7406 (p) REVERT: D 272 MET cc_start: 0.8352 (mmm) cc_final: 0.8032 (mmm) REVERT: D 292 GLU cc_start: 0.7486 (mm-30) cc_final: 0.7104 (mp0) REVERT: E 89 GLU cc_start: 0.6681 (mt-10) cc_final: 0.5948 (mm-30) REVERT: E 143 ARG cc_start: 0.6391 (mtm180) cc_final: 0.6032 (mtm110) REVERT: E 179 GLU cc_start: 0.7635 (pt0) cc_final: 0.7332 (pt0) REVERT: E 255 HIS cc_start: 0.6734 (p-80) cc_final: 0.6253 (m90) REVERT: E 267 ARG cc_start: 0.7147 (ttm-80) cc_final: 0.6581 (ttp-110) REVERT: E 309 MET cc_start: 0.4258 (ptt) cc_final: 0.3982 (ptt) REVERT: F 102 GLU cc_start: 0.7316 (mt-10) cc_final: 0.6805 (mp0) REVERT: F 121 GLU cc_start: 0.8606 (mt-10) cc_final: 0.8403 (mm-30) REVERT: F 125 SER cc_start: 0.8441 (m) cc_final: 0.8216 (p) REVERT: F 286 ASN cc_start: 0.6979 (m-40) cc_final: 0.6617 (m110) outliers start: 15 outliers final: 12 residues processed: 259 average time/residue: 0.7128 time to fit residues: 265.7125 Evaluate side-chains 257 residues out of total 1603 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 243 time to evaluate : 2.508 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 284 SER Chi-restraints excluded: chain B residue 128 GLU Chi-restraints excluded: chain B residue 142 SER Chi-restraints excluded: chain B residue 144 SER Chi-restraints excluded: chain B residue 236 ASP Chi-restraints excluded: chain C residue 100 ASP Chi-restraints excluded: chain C residue 125 SER Chi-restraints excluded: chain C residue 183 LEU Chi-restraints excluded: chain C residue 292 GLU Chi-restraints excluded: chain D residue 153 THR Chi-restraints excluded: chain E residue 297 MET Chi-restraints excluded: chain F residue 245 ASP Chi-restraints excluded: chain F residue 265 ILE Chi-restraints excluded: chain F residue 280 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 191 random chunks: chunk 153 optimal weight: 1.9990 chunk 104 optimal weight: 4.9990 chunk 2 optimal weight: 0.9990 chunk 137 optimal weight: 1.9990 chunk 76 optimal weight: 0.5980 chunk 157 optimal weight: 1.9990 chunk 127 optimal weight: 0.7980 chunk 0 optimal weight: 0.9990 chunk 94 optimal weight: 2.9990 chunk 165 optimal weight: 1.9990 chunk 46 optimal weight: 0.9990 overall best weight: 0.8786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7644 moved from start: 0.3053 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 16228 Z= 0.216 Angle : 0.497 5.849 22105 Z= 0.266 Chirality : 0.039 0.160 2498 Planarity : 0.005 0.053 2739 Dihedral : 15.216 171.123 2563 Min Nonbonded Distance : 1.750 Molprobity Statistics. All-atom Clashscore : 2.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.58 % Favored : 98.42 % Rotamer: Outliers : 1.00 % Allowed : 7.11 % Favored : 91.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.98 % 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: 1.20 (0.19), residues: 1902 helix: 1.20 (0.17), residues: 1023 sheet: 0.59 (0.29), residues: 288 loop : 0.41 (0.25), residues: 591 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS A 146 PHE 0.007 0.001 PHE B 58 TYR 0.026 0.001 TYR A 322 ARG 0.007 0.000 ARG A 291 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3804 Ramachandran restraints generated. 1902 Oldfield, 0 Emsley, 1902 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3804 Ramachandran restraints generated. 1902 Oldfield, 0 Emsley, 1902 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 265 residues out of total 1603 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 249 time to evaluate : 2.520 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 100 ASP cc_start: 0.7807 (m-30) cc_final: 0.7550 (t70) REVERT: A 131 TYR cc_start: 0.8695 (p90) cc_final: 0.8332 (p90) REVERT: A 144 SER cc_start: 0.8034 (p) cc_final: 0.7748 (t) REVERT: A 160 ARG cc_start: 0.8108 (ptp90) cc_final: 0.7755 (ptp-170) REVERT: A 199 MET cc_start: 0.8210 (mmt) cc_final: 0.7996 (mmt) REVERT: A 234 MET cc_start: 0.7606 (ptp) cc_final: 0.7184 (ptp) REVERT: A 325 MET cc_start: 0.7634 (mmm) cc_final: 0.7227 (mmt) REVERT: B 102 GLU cc_start: 0.7863 (mm-30) cc_final: 0.7192 (mt-10) REVERT: B 128 GLU cc_start: 0.7256 (OUTLIER) cc_final: 0.6925 (tt0) REVERT: B 199 MET cc_start: 0.8222 (mmp) cc_final: 0.7422 (tpt) REVERT: B 242 LYS cc_start: 0.7768 (tppt) cc_final: 0.7195 (tppt) REVERT: C 125 SER cc_start: 0.7616 (OUTLIER) cc_final: 0.7204 (p) REVERT: C 178 MET cc_start: 0.8718 (mmt) cc_final: 0.8246 (mmt) REVERT: D 78 VAL cc_start: 0.7717 (t) cc_final: 0.7488 (p) REVERT: D 272 MET cc_start: 0.8357 (mmm) cc_final: 0.8048 (mmm) REVERT: D 292 GLU cc_start: 0.7448 (mm-30) cc_final: 0.7078 (mp0) REVERT: E 89 GLU cc_start: 0.6671 (mt-10) cc_final: 0.5934 (mm-30) REVERT: E 143 ARG cc_start: 0.6358 (mtm180) cc_final: 0.6053 (mtm110) REVERT: E 179 GLU cc_start: 0.7619 (pt0) cc_final: 0.7330 (pt0) REVERT: E 255 HIS cc_start: 0.6743 (p-80) cc_final: 0.6277 (m90) REVERT: E 267 ARG cc_start: 0.7180 (ttm-80) cc_final: 0.6568 (ttp-110) REVERT: E 309 MET cc_start: 0.4196 (ptt) cc_final: 0.3946 (ptt) REVERT: F 102 GLU cc_start: 0.7320 (mt-10) cc_final: 0.6816 (mp0) REVERT: F 125 SER cc_start: 0.8426 (m) cc_final: 0.8185 (p) REVERT: F 309 MET cc_start: 0.7081 (tpp) cc_final: 0.6693 (ttm) outliers start: 16 outliers final: 10 residues processed: 258 average time/residue: 0.6901 time to fit residues: 256.1346 Evaluate side-chains 256 residues out of total 1603 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 244 time to evaluate : 2.389 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 284 SER Chi-restraints excluded: chain B residue 128 GLU Chi-restraints excluded: chain B residue 142 SER Chi-restraints excluded: chain B residue 236 ASP Chi-restraints excluded: chain C residue 125 SER Chi-restraints excluded: chain C residue 183 LEU Chi-restraints excluded: chain C residue 292 GLU Chi-restraints excluded: chain D residue 153 THR Chi-restraints excluded: chain E residue 297 MET Chi-restraints excluded: chain F residue 245 ASP Chi-restraints excluded: chain F residue 280 LEU Chi-restraints excluded: chain F residue 313 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 191 random chunks: chunk 62 optimal weight: 0.7980 chunk 166 optimal weight: 1.9990 chunk 36 optimal weight: 0.9990 chunk 108 optimal weight: 1.9990 chunk 45 optimal weight: 0.9980 chunk 184 optimal weight: 2.9990 chunk 153 optimal weight: 1.9990 chunk 85 optimal weight: 0.8980 chunk 15 optimal weight: 1.9990 chunk 61 optimal weight: 0.9980 chunk 97 optimal weight: 0.9990 overall best weight: 0.9382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 146 HIS B 146 HIS ** E 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7649 moved from start: 0.3207 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 16228 Z= 0.227 Angle : 0.501 5.877 22105 Z= 0.268 Chirality : 0.040 0.148 2498 Planarity : 0.004 0.041 2739 Dihedral : 15.233 172.462 2563 Min Nonbonded Distance : 1.744 Molprobity Statistics. All-atom Clashscore : 2.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.52 % Favored : 98.48 % Rotamer: Outliers : 1.06 % Allowed : 8.05 % Favored : 90.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.98 % 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: 1.20 (0.19), residues: 1902 helix: 1.25 (0.17), residues: 1024 sheet: 0.78 (0.30), residues: 280 loop : 0.20 (0.25), residues: 598 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.008 0.001 HIS B 146 PHE 0.012 0.001 PHE C 108 TYR 0.012 0.001 TYR A 329 ARG 0.003 0.000 ARG A 312 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3804 Ramachandran restraints generated. 1902 Oldfield, 0 Emsley, 1902 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3804 Ramachandran restraints generated. 1902 Oldfield, 0 Emsley, 1902 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 272 residues out of total 1603 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 255 time to evaluate : 2.070 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 100 ASP cc_start: 0.7815 (m-30) cc_final: 0.7589 (t70) REVERT: A 131 TYR cc_start: 0.8686 (p90) cc_final: 0.8309 (p90) REVERT: A 144 SER cc_start: 0.7988 (p) cc_final: 0.7523 (t) REVERT: A 234 MET cc_start: 0.7670 (ptp) cc_final: 0.7277 (ptp) REVERT: A 325 MET cc_start: 0.7616 (mmm) cc_final: 0.7214 (mmt) REVERT: B 102 GLU cc_start: 0.7809 (mm-30) cc_final: 0.7155 (mt-10) REVERT: B 128 GLU cc_start: 0.7254 (OUTLIER) cc_final: 0.6938 (tt0) REVERT: B 199 MET cc_start: 0.8091 (mmp) cc_final: 0.7262 (tpt) REVERT: B 242 LYS cc_start: 0.7688 (tppt) cc_final: 0.7216 (tppt) REVERT: C 110 ASP cc_start: 0.8550 (t0) cc_final: 0.8254 (m-30) REVERT: C 125 SER cc_start: 0.7610 (OUTLIER) cc_final: 0.7210 (p) REVERT: C 178 MET cc_start: 0.8699 (mmt) cc_final: 0.8203 (mmt) REVERT: D 272 MET cc_start: 0.8366 (mmm) cc_final: 0.8051 (mmm) REVERT: D 292 GLU cc_start: 0.7432 (mm-30) cc_final: 0.7107 (mp0) REVERT: E 89 GLU cc_start: 0.6819 (mt-10) cc_final: 0.6106 (mm-30) REVERT: E 143 ARG cc_start: 0.6388 (mtm180) cc_final: 0.6070 (mtm110) REVERT: E 179 GLU cc_start: 0.7657 (pt0) cc_final: 0.7378 (pt0) REVERT: E 240 ASP cc_start: 0.6706 (m-30) cc_final: 0.5974 (t70) REVERT: E 255 HIS cc_start: 0.6912 (p-80) cc_final: 0.6338 (m90) REVERT: E 260 TYR cc_start: 0.7110 (t80) cc_final: 0.6745 (t80) REVERT: E 267 ARG cc_start: 0.7144 (ttm-80) cc_final: 0.6548 (ttp-110) REVERT: E 309 MET cc_start: 0.4224 (ptt) cc_final: 0.3971 (ptt) REVERT: F 102 GLU cc_start: 0.7309 (mt-10) cc_final: 0.6827 (mp0) REVERT: F 125 SER cc_start: 0.8416 (m) cc_final: 0.8180 (p) REVERT: F 309 MET cc_start: 0.7099 (tpp) cc_final: 0.6703 (ttm) outliers start: 17 outliers final: 12 residues processed: 264 average time/residue: 0.6962 time to fit residues: 265.1246 Evaluate side-chains 260 residues out of total 1603 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 246 time to evaluate : 2.578 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 284 SER Chi-restraints excluded: chain B residue 128 GLU Chi-restraints excluded: chain B residue 142 SER Chi-restraints excluded: chain B residue 144 SER Chi-restraints excluded: chain B residue 236 ASP Chi-restraints excluded: chain C residue 100 ASP Chi-restraints excluded: chain C residue 125 SER Chi-restraints excluded: chain C residue 183 LEU Chi-restraints excluded: chain D residue 153 THR Chi-restraints excluded: chain D residue 330 THR Chi-restraints excluded: chain E residue 297 MET Chi-restraints excluded: chain F residue 245 ASP Chi-restraints excluded: chain F residue 280 LEU Chi-restraints excluded: chain F residue 313 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 191 random chunks: chunk 178 optimal weight: 2.9990 chunk 20 optimal weight: 0.9980 chunk 105 optimal weight: 0.0060 chunk 134 optimal weight: 3.9990 chunk 104 optimal weight: 3.9990 chunk 155 optimal weight: 1.9990 chunk 103 optimal weight: 2.9990 chunk 184 optimal weight: 0.5980 chunk 115 optimal weight: 0.9990 chunk 112 optimal weight: 0.9980 chunk 84 optimal weight: 0.8980 overall best weight: 0.6996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7641 moved from start: 0.3311 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 16228 Z= 0.182 Angle : 0.483 6.386 22105 Z= 0.257 Chirality : 0.039 0.178 2498 Planarity : 0.004 0.040 2739 Dihedral : 15.206 172.522 2563 Min Nonbonded Distance : 1.782 Molprobity Statistics. All-atom Clashscore : 2.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.58 % Favored : 98.42 % Rotamer: Outliers : 0.94 % Allowed : 8.42 % Favored : 90.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.98 % 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: 1.33 (0.19), residues: 1902 helix: 1.40 (0.17), residues: 1023 sheet: 0.62 (0.29), residues: 290 loop : 0.29 (0.25), residues: 589 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS B 146 PHE 0.007 0.001 PHE E 58 TYR 0.012 0.001 TYR D 131 ARG 0.003 0.000 ARG A 291 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3804 Ramachandran restraints generated. 1902 Oldfield, 0 Emsley, 1902 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3804 Ramachandran restraints generated. 1902 Oldfield, 0 Emsley, 1902 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 266 residues out of total 1603 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 251 time to evaluate : 2.505 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 100 ASP cc_start: 0.7802 (m-30) cc_final: 0.7601 (t70) REVERT: A 131 TYR cc_start: 0.8668 (p90) cc_final: 0.8348 (p90) REVERT: A 144 SER cc_start: 0.7958 (p) cc_final: 0.7487 (t) REVERT: A 234 MET cc_start: 0.7661 (ptp) cc_final: 0.7264 (ptp) REVERT: A 325 MET cc_start: 0.7620 (mmm) cc_final: 0.7225 (mmt) REVERT: B 102 GLU cc_start: 0.7889 (mm-30) cc_final: 0.7158 (mt-10) REVERT: B 128 GLU cc_start: 0.7204 (OUTLIER) cc_final: 0.6905 (tt0) REVERT: B 199 MET cc_start: 0.8149 (mmp) cc_final: 0.7405 (tpt) REVERT: B 242 LYS cc_start: 0.7733 (tppt) cc_final: 0.7271 (tppt) REVERT: C 110 ASP cc_start: 0.8531 (t0) cc_final: 0.8274 (m-30) REVERT: C 125 SER cc_start: 0.7600 (OUTLIER) cc_final: 0.7194 (p) REVERT: D 272 MET cc_start: 0.8361 (mmm) cc_final: 0.8046 (mmm) REVERT: D 292 GLU cc_start: 0.7416 (mm-30) cc_final: 0.7105 (mp0) REVERT: E 89 GLU cc_start: 0.6839 (mt-10) cc_final: 0.6130 (mm-30) REVERT: E 143 ARG cc_start: 0.6393 (mtm180) cc_final: 0.6075 (mtm110) REVERT: E 179 GLU cc_start: 0.7675 (pt0) cc_final: 0.7399 (pt0) REVERT: E 240 ASP cc_start: 0.6680 (m-30) cc_final: 0.5875 (t70) REVERT: E 255 HIS cc_start: 0.6901 (p-80) cc_final: 0.6336 (m90) REVERT: E 260 TYR cc_start: 0.7098 (t80) cc_final: 0.6752 (t80) REVERT: E 267 ARG cc_start: 0.7185 (ttm-80) cc_final: 0.6616 (ttp-110) REVERT: E 309 MET cc_start: 0.4233 (ptt) cc_final: 0.3966 (ptt) REVERT: F 102 GLU cc_start: 0.7397 (mt-10) cc_final: 0.6891 (mp0) REVERT: F 202 THR cc_start: 0.8622 (t) cc_final: 0.8335 (p) REVERT: F 309 MET cc_start: 0.7094 (tpp) cc_final: 0.6710 (ttm) outliers start: 15 outliers final: 11 residues processed: 258 average time/residue: 0.6728 time to fit residues: 249.9415 Evaluate side-chains 259 residues out of total 1603 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 246 time to evaluate : 2.635 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 284 SER Chi-restraints excluded: chain B residue 128 GLU Chi-restraints excluded: chain B residue 142 SER Chi-restraints excluded: chain B residue 144 SER Chi-restraints excluded: chain B residue 236 ASP Chi-restraints excluded: chain C residue 125 SER Chi-restraints excluded: chain D residue 153 THR Chi-restraints excluded: chain D residue 286 ASN Chi-restraints excluded: chain D residue 330 THR Chi-restraints excluded: chain E residue 297 MET Chi-restraints excluded: chain F residue 245 ASP Chi-restraints excluded: chain F residue 280 LEU Chi-restraints excluded: chain F residue 313 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 191 random chunks: chunk 113 optimal weight: 1.9990 chunk 73 optimal weight: 2.9990 chunk 109 optimal weight: 0.9980 chunk 55 optimal weight: 0.9980 chunk 36 optimal weight: 0.9980 chunk 35 optimal weight: 0.8980 chunk 117 optimal weight: 1.9990 chunk 125 optimal weight: 1.9990 chunk 91 optimal weight: 1.9990 chunk 17 optimal weight: 0.9980 chunk 144 optimal weight: 1.9990 overall best weight: 0.9780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 54 HIS ** E 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7653 moved from start: 0.3392 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 16228 Z= 0.238 Angle : 0.508 6.793 22105 Z= 0.271 Chirality : 0.040 0.145 2498 Planarity : 0.005 0.040 2739 Dihedral : 15.246 174.779 2563 Min Nonbonded Distance : 1.742 Molprobity Statistics. All-atom Clashscore : 2.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.89 % Favored : 98.11 % Rotamer: Outliers : 0.94 % Allowed : 8.86 % Favored : 90.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.98 % 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: 1.18 (0.19), residues: 1902 helix: 1.34 (0.17), residues: 1021 sheet: 0.42 (0.29), residues: 302 loop : 0.17 (0.25), residues: 579 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.001 HIS B 146 PHE 0.009 0.001 PHE C 108 TYR 0.014 0.001 TYR A 322 ARG 0.003 0.000 ARG E 315 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3804 Ramachandran restraints generated. 1902 Oldfield, 0 Emsley, 1902 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3804 Ramachandran restraints generated. 1902 Oldfield, 0 Emsley, 1902 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 261 residues out of total 1603 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 246 time to evaluate : 2.387 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 100 ASP cc_start: 0.7829 (m-30) cc_final: 0.7624 (t70) REVERT: A 131 TYR cc_start: 0.8698 (p90) cc_final: 0.8357 (p90) REVERT: A 144 SER cc_start: 0.7945 (p) cc_final: 0.7482 (t) REVERT: A 234 MET cc_start: 0.7691 (ptp) cc_final: 0.7319 (ptp) REVERT: A 325 MET cc_start: 0.7641 (mmm) cc_final: 0.7240 (mmt) REVERT: B 102 GLU cc_start: 0.7867 (mm-30) cc_final: 0.7222 (mt-10) REVERT: B 128 GLU cc_start: 0.7213 (OUTLIER) cc_final: 0.6924 (tt0) REVERT: B 199 MET cc_start: 0.8173 (mmp) cc_final: 0.7432 (tpt) REVERT: B 242 LYS cc_start: 0.7738 (tppt) cc_final: 0.7276 (tppt) REVERT: C 78 VAL cc_start: 0.8624 (t) cc_final: 0.8392 (p) REVERT: C 110 ASP cc_start: 0.8617 (t0) cc_final: 0.8284 (m-30) REVERT: C 125 SER cc_start: 0.7562 (OUTLIER) cc_final: 0.7166 (p) REVERT: D 272 MET cc_start: 0.8356 (mmm) cc_final: 0.8021 (mmm) REVERT: D 292 GLU cc_start: 0.7410 (mm-30) cc_final: 0.7110 (mp0) REVERT: E 89 GLU cc_start: 0.6882 (mt-10) cc_final: 0.6175 (mm-30) REVERT: E 143 ARG cc_start: 0.6467 (mtm180) cc_final: 0.6151 (mtm110) REVERT: E 179 GLU cc_start: 0.7725 (pt0) cc_final: 0.7365 (pt0) REVERT: E 240 ASP cc_start: 0.6700 (m-30) cc_final: 0.5911 (t70) REVERT: E 255 HIS cc_start: 0.6933 (p-80) cc_final: 0.6280 (m90) REVERT: E 260 TYR cc_start: 0.7118 (t80) cc_final: 0.6747 (t80) REVERT: E 267 ARG cc_start: 0.7171 (ttm-80) cc_final: 0.6588 (ttp-110) REVERT: E 309 MET cc_start: 0.4403 (ptt) cc_final: 0.4185 (ptt) REVERT: F 102 GLU cc_start: 0.7485 (mt-10) cc_final: 0.6956 (mp0) REVERT: F 309 MET cc_start: 0.7103 (tpp) cc_final: 0.6716 (ttm) outliers start: 15 outliers final: 13 residues processed: 254 average time/residue: 0.7112 time to fit residues: 258.3509 Evaluate side-chains 260 residues out of total 1603 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 245 time to evaluate : 2.593 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 284 SER Chi-restraints excluded: chain B residue 128 GLU Chi-restraints excluded: chain B residue 142 SER Chi-restraints excluded: chain B residue 144 SER Chi-restraints excluded: chain B residue 236 ASP Chi-restraints excluded: chain C residue 100 ASP Chi-restraints excluded: chain C residue 125 SER Chi-restraints excluded: chain D residue 153 THR Chi-restraints excluded: chain D residue 286 ASN Chi-restraints excluded: chain D residue 330 THR Chi-restraints excluded: chain E residue 149 LEU Chi-restraints excluded: chain E residue 297 MET Chi-restraints excluded: chain F residue 245 ASP Chi-restraints excluded: chain F residue 280 LEU Chi-restraints excluded: chain F residue 313 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 191 random chunks: chunk 167 optimal weight: 0.5980 chunk 176 optimal weight: 1.9990 chunk 160 optimal weight: 1.9990 chunk 171 optimal weight: 1.9990 chunk 103 optimal weight: 0.4980 chunk 74 optimal weight: 0.2980 chunk 134 optimal weight: 0.8980 chunk 52 optimal weight: 1.9990 chunk 155 optimal weight: 0.8980 chunk 162 optimal weight: 0.0980 chunk 170 optimal weight: 0.6980 overall best weight: 0.4380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7628 moved from start: 0.3470 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 16228 Z= 0.145 Angle : 0.465 9.087 22105 Z= 0.245 Chirality : 0.038 0.134 2498 Planarity : 0.004 0.036 2739 Dihedral : 15.160 172.289 2563 Min Nonbonded Distance : 1.823 Molprobity Statistics. All-atom Clashscore : 2.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.10 % Favored : 98.90 % Rotamer: Outliers : 0.62 % Allowed : 9.23 % Favored : 90.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.98 % 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: 1.50 (0.19), residues: 1902 helix: 1.58 (0.17), residues: 1025 sheet: 0.65 (0.29), residues: 294 loop : 0.30 (0.25), residues: 583 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS B 146 PHE 0.007 0.001 PHE E 58 TYR 0.012 0.001 TYR A 322 ARG 0.005 0.000 ARG D 312 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3804 Ramachandran restraints generated. 1902 Oldfield, 0 Emsley, 1902 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3804 Ramachandran restraints generated. 1902 Oldfield, 0 Emsley, 1902 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 267 residues out of total 1603 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 257 time to evaluate : 2.737 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 131 TYR cc_start: 0.8645 (p90) cc_final: 0.8384 (p90) REVERT: A 144 SER cc_start: 0.7973 (p) cc_final: 0.7515 (t) REVERT: A 234 MET cc_start: 0.7621 (ptp) cc_final: 0.7234 (ptp) REVERT: A 252 ASP cc_start: 0.7717 (t0) cc_final: 0.7007 (t70) REVERT: A 283 LEU cc_start: 0.8113 (tp) cc_final: 0.7908 (tt) REVERT: A 325 MET cc_start: 0.7739 (mmm) cc_final: 0.7269 (mmt) REVERT: B 102 GLU cc_start: 0.8006 (mm-30) cc_final: 0.7257 (mt-10) REVERT: B 128 GLU cc_start: 0.7097 (OUTLIER) cc_final: 0.6844 (tt0) REVERT: B 199 MET cc_start: 0.8137 (mmp) cc_final: 0.7452 (tpt) REVERT: B 242 LYS cc_start: 0.7689 (tppt) cc_final: 0.7229 (tppt) REVERT: C 110 ASP cc_start: 0.8470 (t0) cc_final: 0.8254 (m-30) REVERT: C 125 SER cc_start: 0.7556 (m) cc_final: 0.7149 (p) REVERT: C 260 TYR cc_start: 0.7212 (t80) cc_final: 0.6808 (t80) REVERT: D 272 MET cc_start: 0.8322 (mmm) cc_final: 0.7985 (mmm) REVERT: D 292 GLU cc_start: 0.7405 (mm-30) cc_final: 0.7109 (mp0) REVERT: E 89 GLU cc_start: 0.6876 (mt-10) cc_final: 0.6160 (mm-30) REVERT: E 143 ARG cc_start: 0.6402 (mtm180) cc_final: 0.6082 (mtm110) REVERT: E 179 GLU cc_start: 0.7724 (pt0) cc_final: 0.7433 (pt0) REVERT: E 240 ASP cc_start: 0.6621 (m-30) cc_final: 0.5839 (t70) REVERT: E 255 HIS cc_start: 0.6939 (p-80) cc_final: 0.6381 (m90) REVERT: E 260 TYR cc_start: 0.7096 (t80) cc_final: 0.6749 (t80) REVERT: E 267 ARG cc_start: 0.7155 (ttm-80) cc_final: 0.6621 (ttp-110) REVERT: E 309 MET cc_start: 0.4239 (ptt) cc_final: 0.3969 (ptt) REVERT: F 102 GLU cc_start: 0.7390 (mt-10) cc_final: 0.6900 (mp0) REVERT: F 202 THR cc_start: 0.8546 (t) cc_final: 0.8291 (p) REVERT: F 309 MET cc_start: 0.7093 (tpp) cc_final: 0.6729 (ttm) outliers start: 10 outliers final: 8 residues processed: 261 average time/residue: 0.6978 time to fit residues: 258.6683 Evaluate side-chains 256 residues out of total 1603 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 247 time to evaluate : 2.622 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 128 GLU Chi-restraints excluded: chain B residue 144 SER Chi-restraints excluded: chain B residue 236 ASP Chi-restraints excluded: chain D residue 286 ASN Chi-restraints excluded: chain D residue 330 THR Chi-restraints excluded: chain E residue 297 MET Chi-restraints excluded: chain F residue 245 ASP Chi-restraints excluded: chain F residue 280 LEU Chi-restraints excluded: chain F residue 313 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 191 random chunks: chunk 112 optimal weight: 0.0770 chunk 181 optimal weight: 1.9990 chunk 110 optimal weight: 0.5980 chunk 86 optimal weight: 0.9980 chunk 126 optimal weight: 2.9990 chunk 190 optimal weight: 2.9990 chunk 175 optimal weight: 1.9990 chunk 151 optimal weight: 3.9990 chunk 15 optimal weight: 1.9990 chunk 117 optimal weight: 1.9990 chunk 92 optimal weight: 2.9990 overall best weight: 1.1342 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7656 moved from start: 0.3508 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 16228 Z= 0.268 Angle : 0.512 8.351 22105 Z= 0.273 Chirality : 0.040 0.143 2498 Planarity : 0.005 0.042 2739 Dihedral : 15.230 174.805 2563 Min Nonbonded Distance : 1.739 Molprobity Statistics. All-atom Clashscore : 2.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.89 % Favored : 98.11 % Rotamer: Outliers : 0.69 % Allowed : 9.36 % Favored : 89.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.98 % 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: 1.24 (0.19), residues: 1902 helix: 1.42 (0.17), residues: 1021 sheet: 0.35 (0.29), residues: 301 loop : 0.18 (0.25), residues: 580 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS B 146 PHE 0.009 0.001 PHE C 108 TYR 0.014 0.001 TYR A 322 ARG 0.004 0.000 ARG D 312 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3804 Ramachandran restraints generated. 1902 Oldfield, 0 Emsley, 1902 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3804 Ramachandran restraints generated. 1902 Oldfield, 0 Emsley, 1902 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 255 residues out of total 1603 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 244 time to evaluate : 2.628 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 131 TYR cc_start: 0.8689 (p90) cc_final: 0.8358 (p90) REVERT: A 144 SER cc_start: 0.7915 (p) cc_final: 0.7448 (t) REVERT: A 234 MET cc_start: 0.7675 (ptp) cc_final: 0.7246 (ptp) REVERT: A 325 MET cc_start: 0.7669 (mmm) cc_final: 0.7266 (mmt) REVERT: B 102 GLU cc_start: 0.7951 (mm-30) cc_final: 0.7236 (mt-10) REVERT: B 128 GLU cc_start: 0.7152 (OUTLIER) cc_final: 0.6852 (tt0) REVERT: B 199 MET cc_start: 0.8146 (mmp) cc_final: 0.7464 (tpt) REVERT: B 242 LYS cc_start: 0.7725 (tppt) cc_final: 0.7254 (tppt) REVERT: C 110 ASP cc_start: 0.8597 (t0) cc_final: 0.8234 (m-30) REVERT: C 125 SER cc_start: 0.7532 (m) cc_final: 0.7139 (p) REVERT: D 79 ASN cc_start: 0.7837 (m-40) cc_final: 0.7558 (m-40) REVERT: D 272 MET cc_start: 0.8341 (mmm) cc_final: 0.8003 (mmm) REVERT: D 292 GLU cc_start: 0.7409 (mm-30) cc_final: 0.7128 (mp0) REVERT: E 89 GLU cc_start: 0.6877 (mt-10) cc_final: 0.6168 (mm-30) REVERT: E 143 ARG cc_start: 0.6478 (mtm180) cc_final: 0.6158 (mtm110) REVERT: E 179 GLU cc_start: 0.7694 (pt0) cc_final: 0.7357 (pt0) REVERT: E 240 ASP cc_start: 0.6797 (m-30) cc_final: 0.5761 (t70) REVERT: E 255 HIS cc_start: 0.6988 (p-80) cc_final: 0.6334 (m90) REVERT: E 260 TYR cc_start: 0.7133 (t80) cc_final: 0.6764 (t80) REVERT: E 267 ARG cc_start: 0.7152 (ttm-80) cc_final: 0.6613 (ttp-110) REVERT: E 309 MET cc_start: 0.4483 (ptt) cc_final: 0.4275 (ptt) REVERT: F 102 GLU cc_start: 0.7403 (mt-10) cc_final: 0.6882 (mp0) REVERT: F 202 THR cc_start: 0.8614 (t) cc_final: 0.8340 (p) REVERT: F 309 MET cc_start: 0.7108 (tpp) cc_final: 0.6726 (ttm) outliers start: 11 outliers final: 8 residues processed: 249 average time/residue: 0.6816 time to fit residues: 246.9843 Evaluate side-chains 250 residues out of total 1603 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 241 time to evaluate : 2.509 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 128 GLU Chi-restraints excluded: chain B residue 144 SER Chi-restraints excluded: chain D residue 286 ASN Chi-restraints excluded: chain D residue 330 THR Chi-restraints excluded: chain E residue 149 LEU Chi-restraints excluded: chain E residue 297 MET Chi-restraints excluded: chain F residue 245 ASP Chi-restraints excluded: chain F residue 280 LEU Chi-restraints excluded: chain F residue 313 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 191 random chunks: chunk 120 optimal weight: 0.9980 chunk 161 optimal weight: 1.9990 chunk 46 optimal weight: 0.9980 chunk 139 optimal weight: 0.9990 chunk 22 optimal weight: 0.2980 chunk 42 optimal weight: 1.9990 chunk 151 optimal weight: 0.6980 chunk 63 optimal weight: 0.9990 chunk 155 optimal weight: 1.9990 chunk 19 optimal weight: 0.9990 chunk 27 optimal weight: 1.9990 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3435 r_free = 0.3435 target = 0.123309 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.2993 r_free = 0.2993 target = 0.092482 restraints weight = 65586.995| |-----------------------------------------------------------------------------| r_work (start): 0.2979 rms_B_bonded: 2.00 r_work: 0.2871 rms_B_bonded: 2.32 restraints_weight: 0.5000 r_work: 0.2754 rms_B_bonded: 3.87 restraints_weight: 0.2500 r_work (final): 0.2754 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8146 moved from start: 0.3558 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 16228 Z= 0.199 Angle : 0.487 10.210 22105 Z= 0.258 Chirality : 0.039 0.136 2498 Planarity : 0.004 0.038 2739 Dihedral : 15.224 174.446 2563 Min Nonbonded Distance : 1.764 Molprobity Statistics. All-atom Clashscore : 2.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.95 % Favored : 98.05 % Rotamer: Outliers : 0.69 % Allowed : 9.42 % Favored : 89.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.98 % 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: 1.30 (0.19), residues: 1902 helix: 1.46 (0.17), residues: 1021 sheet: 0.49 (0.29), residues: 296 loop : 0.18 (0.25), residues: 585 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS B 146 PHE 0.007 0.001 PHE E 58 TYR 0.013 0.001 TYR A 322 ARG 0.004 0.000 ARG D 312 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7471.65 seconds wall clock time: 131 minutes 32.60 seconds (7892.60 seconds total)