Starting phenix.real_space_refine (version: dev) on Tue Feb 28 00:37:25 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7pbs_13301/02_2023/7pbs_13301_neut_trim_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7pbs_13301/02_2023/7pbs_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_13301/02_2023/7pbs_13301.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7pbs_13301/02_2023/7pbs_13301.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7pbs_13301/02_2023/7pbs_13301_neut_trim_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7pbs_13301/02_2023/7pbs_13301_neut_trim_updated.pdb" } resolution = 3.3 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- 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 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-4877/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: 14.52, per 1000 atoms: 0.46 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: 25.51 Conformation dependent library (CDL) restraints added in 2.5 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: 13.89 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: 12.42 Time building geometry restraints manager: 26.31 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: 12175 34.75 - 69.50: 293 69.50 - 104.25: 16 104.25 - 139.00: 3 139.00 - 173.75: 3 Dihedral angle restraints: 12490 sinusoidal: 6221 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 12487 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 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. 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: 1.910 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: 0.450 Extract box with map and model: 12.860 Check model and map are aligned: 0.460 Process input model: 106.990 Find NCS groups from input model: 1.580 Set up NCS constraints: 0.090 Set refine NCS operators: 0.000 Set scattering table: 0.280 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.870 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 127.490 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7711 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 : 14.694 173.751 6204 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 % 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 *********************** 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 : 2.244 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 outliers start: 4 outliers final: 1 residues processed: 421 average time/residue: 0.7625 time to fit residues: 446.0289 Evaluate side-chains 259 residues out of total 1603 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 258 time to evaluate : 2.691 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.3452 time to fit residues: 3.8774 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 1.9990 chunk 97 optimal weight: 2.9990 chunk 77 optimal weight: 0.9990 chunk 149 optimal weight: 1.9990 chunk 57 optimal weight: 0.9990 chunk 91 optimal weight: 0.9980 chunk 111 optimal weight: 0.7980 chunk 173 optimal weight: 0.8980 overall best weight: 0.9382 ------------------------------------------------------------------------------- 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: 0.7725 moved from start: 0.2441 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= 0.248 Angle : 0.593 5.961 22105 Z= 0.322 Chirality : 0.041 0.158 2498 Planarity : 0.005 0.064 2739 Dihedral : 14.739 178.917 2478 Min Nonbonded Distance : 1.757 Molprobity Statistics. All-atom Clashscore : 2.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.00 % Favored : 99.00 % Rotamer Outliers : 1.06 % 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: 0.77 (0.19), residues: 1902 helix: 0.56 (0.16), residues: 1028 sheet: 0.94 (0.29), residues: 315 loop : 0.49 (0.26), residues: 559 *********************** 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 271 residues out of total 1603 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 254 time to evaluate : 2.494 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 outliers start: 17 outliers final: 15 residues processed: 266 average time/residue: 0.6983 time to fit residues: 265.6703 Evaluate side-chains 259 residues out of total 1603 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 244 time to evaluate : 2.449 Switching outliers to nearest non-outliers outliers start: 15 outliers final: 0 residues processed: 15 average time/residue: 0.3225 time to fit residues: 12.1453 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 191 random chunks: chunk 96 optimal weight: 0.7980 chunk 53 optimal weight: 2.9990 chunk 144 optimal weight: 3.9990 chunk 118 optimal weight: 0.9980 chunk 47 optimal weight: 0.9990 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: 0.9990 chunk 139 optimal weight: 2.9990 overall best weight: 1.1586 ------------------------------------------------------------------------------- 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: 0.7737 moved from start: 0.2851 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= 0.279 Angle : 0.552 5.812 22105 Z= 0.296 Chirality : 0.041 0.148 2498 Planarity : 0.005 0.055 2739 Dihedral : 14.958 179.823 2478 Min Nonbonded Distance : 1.721 Molprobity Statistics. All-atom Clashscore : 2.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.37 % Favored : 98.63 % Rotamer Outliers : 0.37 % 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: 0.89 (0.19), residues: 1902 helix: 0.76 (0.16), residues: 1029 sheet: 0.73 (0.29), residues: 296 loop : 0.50 (0.26), residues: 577 *********************** 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 253 residues out of total 1603 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 247 time to evaluate : 2.507 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 outliers start: 6 outliers final: 1 residues processed: 249 average time/residue: 0.6986 time to fit residues: 249.9841 Evaluate side-chains 235 residues out of total 1603 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 234 time to evaluate : 2.856 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.3293 time to fit residues: 3.5804 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 2.9990 chunk 90 optimal weight: 0.3980 chunk 19 optimal weight: 1.9990 chunk 82 optimal weight: 0.9980 chunk 116 optimal weight: 0.9990 chunk 174 optimal weight: 0.9990 chunk 184 optimal weight: 0.9990 chunk 91 optimal weight: 0.0370 chunk 165 optimal weight: 1.9990 chunk 49 optimal weight: 0.9990 overall best weight: 0.6862 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7724 moved from start: 0.3062 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.033 16228 Z= 0.189 Angle : 0.505 5.786 22105 Z= 0.269 Chirality : 0.039 0.144 2498 Planarity : 0.004 0.043 2739 Dihedral : 14.980 178.454 2478 Min Nonbonded Distance : 1.758 Molprobity Statistics. All-atom Clashscore : 2.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.10 % Favored : 98.90 % Rotamer Outliers : 0.50 % 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: 1.05 (0.19), residues: 1902 helix: 1.01 (0.17), residues: 1029 sheet: 0.65 (0.29), residues: 294 loop : 0.41 (0.26), residues: 579 *********************** 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 249 residues out of total 1603 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 241 time to evaluate : 2.462 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 8 outliers final: 6 residues processed: 245 average time/residue: 0.7539 time to fit residues: 266.2109 Evaluate side-chains 240 residues out of total 1603 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 234 time to evaluate : 2.491 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 0 residues processed: 6 average time/residue: 0.3486 time to fit residues: 7.0350 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 191 random chunks: chunk 153 optimal weight: 3.9990 chunk 104 optimal weight: 3.9990 chunk 2 optimal weight: 0.9990 chunk 137 optimal weight: 2.9990 chunk 76 optimal weight: 0.0770 chunk 157 optimal weight: 1.9990 chunk 127 optimal weight: 0.7980 chunk 0 optimal weight: 1.9990 chunk 94 optimal weight: 1.9990 chunk 165 optimal weight: 2.9990 chunk 46 optimal weight: 1.9990 overall best weight: 1.1744 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 146 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7744 moved from start: 0.3266 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= 0.277 Angle : 0.540 5.948 22105 Z= 0.289 Chirality : 0.041 0.146 2498 Planarity : 0.005 0.052 2739 Dihedral : 15.094 179.815 2478 Min Nonbonded Distance : 1.698 Molprobity Statistics. All-atom Clashscore : 2.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.95 % Favored : 98.05 % Rotamer Outliers : 0.50 % 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: 0.92 (0.19), residues: 1902 helix: 0.97 (0.17), residues: 1025 sheet: 0.54 (0.29), residues: 290 loop : 0.25 (0.25), residues: 587 *********************** 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 245 residues out of total 1603 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 237 time to evaluate : 2.464 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 8 outliers final: 6 residues processed: 239 average time/residue: 0.6960 time to fit residues: 239.1704 Evaluate side-chains 237 residues out of total 1603 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 231 time to evaluate : 2.554 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 0 residues processed: 6 average time/residue: 0.3450 time to fit residues: 6.9720 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 191 random chunks: chunk 62 optimal weight: 0.5980 chunk 166 optimal weight: 0.8980 chunk 36 optimal weight: 0.9990 chunk 108 optimal weight: 1.9990 chunk 45 optimal weight: 0.9990 chunk 184 optimal weight: 0.6980 chunk 153 optimal weight: 3.9990 chunk 85 optimal weight: 0.0970 chunk 15 optimal weight: 0.9980 chunk 61 optimal weight: 0.0670 chunk 97 optimal weight: 1.9990 overall best weight: 0.4716 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 146 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7719 moved from start: 0.3415 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.028 16228 Z= 0.152 Angle : 0.485 6.182 22105 Z= 0.256 Chirality : 0.038 0.154 2498 Planarity : 0.004 0.037 2739 Dihedral : 14.992 176.827 2478 Min Nonbonded Distance : 1.791 Molprobity Statistics. All-atom Clashscore : 2.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.00 % Favored : 99.00 % Rotamer Outliers : 0.12 % 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: 1.28 (0.19), residues: 1902 helix: 1.30 (0.17), residues: 1026 sheet: 0.66 (0.30), residues: 280 loop : 0.36 (0.25), residues: 596 *********************** 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 240 residues out of total 1603 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 238 time to evaluate : 2.669 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 2 outliers final: 0 residues processed: 239 average time/residue: 0.6857 time to fit residues: 233.2552 Evaluate side-chains 230 residues out of total 1603 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 230 time to evaluate : 2.668 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 3.2309 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 0.9980 chunk 134 optimal weight: 2.9990 chunk 104 optimal weight: 1.9990 chunk 155 optimal weight: 1.9990 chunk 103 optimal weight: 5.9990 chunk 184 optimal weight: 0.5980 chunk 115 optimal weight: 1.9990 chunk 112 optimal weight: 0.2980 chunk 84 optimal weight: 0.6980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 146 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7726 moved from start: 0.3485 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.029 16228 Z= 0.189 Angle : 0.487 5.769 22105 Z= 0.258 Chirality : 0.039 0.142 2498 Planarity : 0.004 0.037 2739 Dihedral : 14.939 175.812 2478 Min Nonbonded Distance : 1.750 Molprobity Statistics. All-atom Clashscore : 2.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.63 % Favored : 98.37 % Rotamer Outliers : 0.44 % 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: 1.31 (0.19), residues: 1902 helix: 1.36 (0.17), residues: 1025 sheet: 0.71 (0.29), residues: 285 loop : 0.27 (0.25), residues: 592 *********************** 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 237 residues out of total 1603 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 230 time to evaluate : 2.720 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 7 outliers final: 4 residues processed: 231 average time/residue: 0.6973 time to fit residues: 231.0165 Evaluate side-chains 232 residues out of total 1603 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 228 time to evaluate : 2.245 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.3448 time to fit residues: 5.3794 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 0.9990 chunk 55 optimal weight: 0.4980 chunk 36 optimal weight: 1.9990 chunk 35 optimal weight: 0.3980 chunk 117 optimal weight: 0.6980 chunk 125 optimal weight: 1.9990 chunk 91 optimal weight: 1.9990 chunk 17 optimal weight: 0.9980 chunk 144 optimal weight: 3.9990 overall best weight: 0.7182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 146 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7724 moved from start: 0.3572 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.029 16228 Z= 0.181 Angle : 0.486 6.321 22105 Z= 0.256 Chirality : 0.039 0.144 2498 Planarity : 0.004 0.036 2739 Dihedral : 14.892 174.901 2478 Min Nonbonded Distance : 1.759 Molprobity Statistics. All-atom Clashscore : 2.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.84 % Favored : 98.16 % Rotamer Outliers : 0.37 % 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: 1.35 (0.19), residues: 1902 helix: 1.43 (0.17), residues: 1024 sheet: 0.55 (0.29), residues: 295 loop : 0.31 (0.25), residues: 583 *********************** 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 238 residues out of total 1603 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 232 time to evaluate : 2.592 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 6 outliers final: 1 residues processed: 233 average time/residue: 0.6850 time to fit residues: 230.0559 Evaluate side-chains 228 residues out of total 1603 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 227 time to evaluate : 2.551 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.3158 time to fit residues: 3.7835 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 191 random chunks: chunk 167 optimal weight: 0.9990 chunk 176 optimal weight: 1.9990 chunk 160 optimal weight: 0.7980 chunk 171 optimal weight: 1.9990 chunk 103 optimal weight: 0.0570 chunk 74 optimal weight: 0.9980 chunk 134 optimal weight: 2.9990 chunk 52 optimal weight: 1.9990 chunk 155 optimal weight: 0.9980 chunk 162 optimal weight: 0.4980 chunk 170 optimal weight: 0.5980 overall best weight: 0.5898 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7719 moved from start: 0.3647 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.029 16228 Z= 0.163 Angle : 0.473 6.900 22105 Z= 0.249 Chirality : 0.038 0.136 2498 Planarity : 0.004 0.036 2739 Dihedral : 14.832 173.641 2478 Min Nonbonded Distance : 1.781 Molprobity Statistics. All-atom Clashscore : 2.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.58 % Favored : 98.42 % Rotamer Outliers : 0.12 % 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: 1.49 (0.20), residues: 1902 helix: 1.55 (0.17), residues: 1023 sheet: 0.55 (0.29), residues: 295 loop : 0.40 (0.26), residues: 584 *********************** 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 240 residues out of total 1603 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 238 time to evaluate : 2.687 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 2 outliers final: 1 residues processed: 238 average time/residue: 0.7812 time to fit residues: 272.4963 Evaluate side-chains 231 residues out of total 1603 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 230 time to evaluate : 2.606 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.3652 time to fit residues: 3.8539 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 191 random chunks: chunk 112 optimal weight: 0.9990 chunk 181 optimal weight: 0.8980 chunk 110 optimal weight: 0.7980 chunk 86 optimal weight: 0.9990 chunk 126 optimal weight: 2.9990 chunk 190 optimal weight: 2.9990 chunk 175 optimal weight: 1.9990 chunk 151 optimal weight: 0.0060 chunk 15 optimal weight: 1.9990 chunk 117 optimal weight: 0.0570 chunk 92 optimal weight: 2.9990 overall best weight: 0.5516 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7716 moved from start: 0.3704 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.029 16228 Z= 0.156 Angle : 0.468 6.993 22105 Z= 0.246 Chirality : 0.038 0.135 2498 Planarity : 0.004 0.035 2739 Dihedral : 14.792 172.989 2478 Min Nonbonded Distance : 1.796 Molprobity Statistics. All-atom Clashscore : 2.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.63 % Favored : 98.37 % Rotamer Outliers : 0.06 % 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: 1.54 (0.20), residues: 1902 helix: 1.62 (0.17), residues: 1022 sheet: 0.46 (0.28), residues: 305 loop : 0.44 (0.26), residues: 575 ********************** 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 237 residues out of total 1603 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 236 time to evaluate : 3.134 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 1 outliers final: 1 residues processed: 236 average time/residue: 0.7122 time to fit residues: 241.1259 Evaluate side-chains 232 residues out of total 1603 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 231 time to evaluate : 2.537 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.3329 time to fit residues: 3.7707 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 0.1980 chunk 46 optimal weight: 0.9980 chunk 139 optimal weight: 0.7980 chunk 22 optimal weight: 0.9980 chunk 42 optimal weight: 0.9980 chunk 151 optimal weight: 2.9990 chunk 63 optimal weight: 0.9990 chunk 155 optimal weight: 1.9990 chunk 19 optimal weight: 0.5980 chunk 27 optimal weight: 1.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3433 r_free = 0.3433 target = 0.123241 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3033 r_free = 0.3033 target = 0.094706 restraints weight = 65737.830| |-----------------------------------------------------------------------------| r_work (start): 0.3017 rms_B_bonded: 1.86 r_work: 0.2878 rms_B_bonded: 2.30 restraints_weight: 0.5000 r_work: 0.2760 rms_B_bonded: 3.85 restraints_weight: 0.2500 r_work (final): 0.2760 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8202 moved from start: 0.3747 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.029 16228 Z= 0.188 Angle : 0.480 6.507 22105 Z= 0.253 Chirality : 0.039 0.144 2498 Planarity : 0.004 0.036 2739 Dihedral : 14.794 174.309 2478 Min Nonbonded Distance : 1.779 Molprobity Statistics. All-atom Clashscore : 2.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.84 % Favored : 98.16 % Rotamer Outliers : 0.12 % 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: 1.48 (0.20), residues: 1902 helix: 1.58 (0.17), residues: 1022 sheet: 0.43 (0.28), residues: 305 loop : 0.39 (0.26), residues: 575 =============================================================================== Job complete usr+sys time: 7264.66 seconds wall clock time: 129 minutes 38.47 seconds (7778.47 seconds total)