Starting phenix.real_space_refine on Thu Mar 21 22:01:05 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7pbt_13302/03_2024/7pbt_13302_neut_trim_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7pbt_13302/03_2024/7pbt_13302.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/7pbt_13302/03_2024/7pbt_13302.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7pbt_13302/03_2024/7pbt_13302.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7pbt_13302/03_2024/7pbt_13302_neut_trim_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7pbt_13302/03_2024/7pbt_13302_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 45 5.49 5 Mg 3 5.21 5 S 100 5.16 5 C 9900 2.51 5 N 2683 2.21 5 O 3148 1.98 5 H 15439 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "D TYR 327": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Time to flip residues: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 31318 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: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 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: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Time building chain proxies: 14.38, per 1000 atoms: 0.46 Number of scatterers: 31318 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 100 16.00 P 45 15.00 Mg 3 11.99 O 3148 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: 25.52 Conformation dependent library (CDL) restraints added in 3.1 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 50.8% alpha, 11.1% beta 10 base pairs and 28 stacking pairs defined. Time for finding SS restraints: 15.13 Creating SS restraints... Processing helix chain 'A' and resid 32 through 48 removed outlier: 3.572A pdb=" N GLN A 37 " --> pdb=" O LYS A 33 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N ILE A 40 " --> pdb=" O ASP A 36 " (cutoff:3.500A) Processing helix chain 'A' and resid 65 through 76 removed outlier: 3.541A 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: 3.578A 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: 4.577A pdb=" N VAL A 122 " --> pdb=" O ALA A 118 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N LEU A 123 " --> pdb=" O VAL A 119 " (cutoff:3.500A) removed outlier: 3.888A pdb=" N TYR A 124 " --> pdb=" O GLU A 120 " (cutoff:3.500A) removed outlier: 4.776A pdb=" N SER A 125 " --> pdb=" O GLU A 121 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N ALA A 126 " --> pdb=" O VAL A 122 " (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: 3.849A pdb=" N ARG A 171 " --> pdb=" O PRO A 167 " (cutoff:3.500A) Processing helix chain 'A' and resid 183 through 196 removed outlier: 3.596A pdb=" N GLU A 188 " --> pdb=" O PRO A 184 " (cutoff:3.500A) Processing helix chain 'A' and resid 203 through 212 Processing helix chain 'A' and resid 217 through 231 Processing helix chain 'A' and resid 243 through 251 Processing helix chain 'A' and resid 260 through 273 Processing helix chain 'A' and resid 280 through 287 Processing helix chain 'A' and resid 291 through 296 Processing helix chain 'A' and resid 299 through 304 Processing helix chain 'A' and resid 319 through 325 Processing helix chain 'B' and resid 32 through 47 Processing helix chain 'B' and resid 65 through 76 removed outlier: 3.610A pdb=" N PHE B 70 " --> pdb=" O THR B 66 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N ALA B 73 " --> pdb=" O ALA B 69 " (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 removed outlier: 3.671A pdb=" N ASP B 100 " --> pdb=" O ALA B 96 " (cutoff:3.500A) 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: 4.382A pdb=" N VAL B 122 " --> pdb=" O ALA B 118 " (cutoff:3.500A) removed outlier: 3.902A pdb=" N LEU B 123 " --> pdb=" O VAL B 119 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N TYR B 124 " --> pdb=" O GLU B 120 " (cutoff:3.500A) removed outlier: 4.912A pdb=" N SER B 125 " --> pdb=" O GLU B 121 " (cutoff:3.500A) removed outlier: 3.847A 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: 3.757A 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: 3.785A 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 Processing helix chain 'B' and resid 291 through 297 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 removed outlier: 3.551A pdb=" N PHE C 70 " --> pdb=" O THR C 66 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N ALA C 73 " --> pdb=" O ALA C 69 " (cutoff:3.500A) Processing helix chain 'C' and resid 85 through 87 No H-bonds generated for 'chain 'C' and resid 85 through 87' Processing helix chain 'C' and resid 91 through 100 removed outlier: 3.611A 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: 4.045A pdb=" N VAL C 122 " --> pdb=" O ALA C 118 " (cutoff:3.500A) removed outlier: 4.336A pdb=" N SER C 125 " --> pdb=" O GLU C 121 " (cutoff:3.500A) removed outlier: 3.572A 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: 3.964A pdb=" N ARG C 171 " --> pdb=" O PRO C 167 " (cutoff:3.500A) Processing helix chain 'C' and resid 183 through 196 Processing helix chain 'C' and resid 203 through 212 removed outlier: 3.647A pdb=" N LEU C 209 " --> pdb=" O ALA C 205 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N ARG C 212 " --> pdb=" O GLU C 208 " (cutoff:3.500A) Processing helix chain 'C' and resid 217 through 234 Processing helix chain 'C' and resid 243 through 251 Processing helix chain 'C' and resid 260 through 273 Processing helix chain 'C' and resid 280 through 286 Processing helix chain 'C' and resid 291 through 296 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 removed outlier: 3.648A pdb=" N ILE D 40 " --> pdb=" O ASP D 36 " (cutoff:3.500A) Processing helix chain 'D' and resid 65 through 76 removed outlier: 3.587A pdb=" N PHE D 70 " --> pdb=" O THR D 66 " (cutoff:3.500A) 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: 4.549A pdb=" N VAL D 122 " --> pdb=" O ALA D 118 " (cutoff:3.500A) removed outlier: 4.520A pdb=" N SER D 125 " --> pdb=" O GLU D 121 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N ALA D 126 " --> pdb=" O VAL D 122 " (cutoff:3.500A) Processing helix chain 'D' and resid 166 through 171 removed outlier: 3.518A pdb=" N ARG D 171 " --> pdb=" O PRO D 167 " (cutoff:3.500A) Processing helix chain 'D' and resid 183 through 196 removed outlier: 3.581A pdb=" N ILE D 196 " --> pdb=" O ARG D 192 " (cutoff:3.500A) Processing helix chain 'D' and resid 203 through 211 Processing helix chain 'D' and resid 217 through 234 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 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 48 Processing helix chain 'E' and resid 65 through 76 Processing helix chain 'E' and resid 91 through 100 Processing helix chain 'E' and resid 117 through 129 removed outlier: 4.402A pdb=" N VAL E 122 " --> pdb=" O ALA E 118 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N LEU E 123 " --> pdb=" O VAL E 119 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N SER E 125 " --> pdb=" O GLU E 121 " (cutoff:3.500A) Processing helix chain 'E' and resid 161 through 163 No H-bonds generated for 'chain 'E' and resid 161 through 163' Processing helix chain 'E' and resid 166 through 171 removed outlier: 3.863A pdb=" N ARG E 171 " --> pdb=" O PRO E 167 " (cutoff:3.500A) Processing helix chain 'E' and resid 183 through 196 removed outlier: 3.802A pdb=" N GLU E 188 " --> pdb=" O PRO E 184 " (cutoff:3.500A) Processing helix chain 'E' and resid 203 through 213 Processing helix chain 'E' and resid 217 through 234 removed outlier: 3.769A 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 272 Processing helix chain 'E' and resid 280 through 286 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: 3.878A pdb=" N GLN F 37 " --> pdb=" O LYS F 33 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N ILE F 40 " --> pdb=" O ASP F 36 " (cutoff:3.500A) Processing helix chain 'F' and resid 65 through 76 removed outlier: 3.518A pdb=" N PHE F 70 " --> pdb=" O THR F 66 " (cutoff:3.500A) 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: 3.565A 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: 4.512A pdb=" N VAL F 122 " --> pdb=" O ALA F 118 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N LEU F 123 " --> pdb=" O VAL F 119 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N TYR F 124 " --> pdb=" O GLU F 120 " (cutoff:3.500A) removed outlier: 4.809A pdb=" N SER F 125 " --> pdb=" O GLU F 121 " (cutoff:3.500A) removed outlier: 3.729A 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: 4.168A 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 271 Processing helix chain 'F' and resid 280 through 287 Processing helix chain 'F' and resid 291 through 296 Processing helix chain 'F' and resid 298 through 304 Processing helix chain 'F' and resid 319 through 325 Processing helix chain 'G' and resid 157 through 169 Processing helix chain 'G' and resid 174 through 182 Processing helix chain 'G' and resid 191 through 202 Processing sheet with id= A, first strand: chain 'A' and resid 174 through 177 removed outlier: 3.566A pdb=" N ALA A 157 " --> pdb=" O ILE A 109 " (cutoff:3.500A) 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 removed outlier: 3.644A pdb=" N ALA C 157 " --> pdb=" O ILE C 109 " (cutoff:3.500A) 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 137 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 177 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 311 669 hydrogen bonds defined for protein. 1959 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 21 hydrogen bonds 42 hydrogen bond angles 0 basepair planarities 10 basepair parallelities 28 stacking parallelities Total time for adding SS restraints: 12.01 Time building geometry restraints manager: 26.46 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: 6668 1.50 - 1.72: 6700 1.72 - 1.94: 197 Bond restraints: 31659 Sorted by residual: bond pdb=" N THR E 19 " pdb=" H1 THR E 19 " ideal model delta sigma weight residual 0.960 0.859 0.101 2.00e-02 2.50e+03 2.55e+01 bond pdb=" N SER G 156 " pdb=" H1 SER G 156 " 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 2.50e+01 bond pdb=" N THR D 19 " pdb=" H1 THR D 19 " ideal model delta sigma weight residual 0.960 0.860 0.100 2.00e-02 2.50e+03 2.50e+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 2.48e+01 ... (remaining 31654 not shown) Histogram of bond angle deviations from ideal: 99.51 - 106.94: 798 106.94 - 114.36: 38865 114.36 - 121.79: 12341 121.79 - 129.21: 5238 129.21 - 136.64: 65 Bond angle restraints: 57307 Sorted by residual: angle pdb=" OP1 DT V 4 " pdb=" P DT V 4 " pdb=" OP2 DT V 4 " ideal model delta sigma weight residual 120.00 109.76 10.24 3.00e+00 1.11e-01 1.16e+01 angle pdb=" C2' ADP D 600 " pdb=" C3' ADP D 600 " pdb=" C4' ADP D 600 " ideal model delta sigma weight residual 111.00 101.58 9.42 3.00e+00 1.11e-01 9.85e+00 angle pdb=" O3' DT V 3 " pdb=" P DT V 4 " pdb=" OP1 DT V 4 " ideal model delta sigma weight residual 108.00 116.95 -8.95 3.00e+00 1.11e-01 8.91e+00 angle pdb=" C2' ADP F 600 " pdb=" C3' ADP F 600 " pdb=" C4' ADP F 600 " ideal model delta sigma weight residual 111.00 102.64 8.36 3.00e+00 1.11e-01 7.77e+00 angle pdb=" C1' ADP D 600 " pdb=" C2' ADP D 600 " pdb=" C3' ADP D 600 " ideal model delta sigma weight residual 111.00 102.66 8.34 3.00e+00 1.11e-01 7.74e+00 ... (remaining 57302 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 34.57: 14145 34.57 - 69.14: 513 69.14 - 103.72: 16 103.72 - 138.29: 4 138.29 - 172.86: 3 Dihedral angle restraints: 14681 sinusoidal: 8412 harmonic: 6269 Sorted by residual: dihedral pdb=" O2A ADP D 600 " pdb=" O3A ADP D 600 " pdb=" PA ADP D 600 " pdb=" PB ADP D 600 " ideal model delta sinusoidal sigma weight residual 300.00 127.14 172.86 1 2.00e+01 2.50e-03 4.78e+01 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 99.73 -159.73 1 2.00e+01 2.50e-03 4.65e+01 dihedral pdb=" O2A ADP F 600 " pdb=" O3A ADP F 600 " pdb=" PA ADP F 600 " pdb=" PB ADP F 600 " ideal model delta sinusoidal sigma weight residual -60.00 97.13 -157.12 1 2.00e+01 2.50e-03 4.61e+01 ... (remaining 14678 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.077: 2262 0.077 - 0.154: 229 0.154 - 0.231: 2 0.231 - 0.308: 0 0.308 - 0.385: 1 Chirality restraints: 2494 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 -2.73 -0.39 2.00e-01 2.50e+01 3.71e+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 2.55 0.17 2.00e-01 2.50e+01 6.91e-01 chirality pdb=" C3' ADP D 600 " pdb=" C2' ADP D 600 " pdb=" C4' ADP D 600 " pdb=" O3' ADP D 600 " both_signs ideal model delta sigma weight residual False -2.51 -2.67 0.16 2.00e-01 2.50e+01 6.11e-01 ... (remaining 2491 not shown) Planarity restraints: 4586 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG E 312 " -0.061 9.50e-02 1.11e+02 6.10e-02 7.47e+01 pdb=" NE ARG E 312 " -0.049 2.00e-02 2.50e+03 pdb=" CZ ARG E 312 " 0.046 2.00e-02 2.50e+03 pdb=" NH1 ARG E 312 " 0.109 2.00e-02 2.50e+03 pdb=" NH2 ARG E 312 " -0.020 2.00e-02 2.50e+03 pdb="HH11 ARG E 312 " 0.008 2.00e-02 2.50e+03 pdb="HH12 ARG E 312 " -0.111 2.00e-02 2.50e+03 pdb="HH21 ARG E 312 " 0.000 2.00e-02 2.50e+03 pdb="HH22 ARG E 312 " 0.020 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG C 192 " -0.140 9.50e-02 1.11e+02 6.52e-02 4.86e+01 pdb=" NE ARG C 192 " 0.005 2.00e-02 2.50e+03 pdb=" CZ ARG C 192 " -0.009 2.00e-02 2.50e+03 pdb=" NH1 ARG C 192 " -0.053 2.00e-02 2.50e+03 pdb=" NH2 ARG C 192 " 0.077 2.00e-02 2.50e+03 pdb="HH11 ARG C 192 " -0.001 2.00e-02 2.50e+03 pdb="HH12 ARG C 192 " 0.061 2.00e-02 2.50e+03 pdb="HH21 ARG C 192 " 0.003 2.00e-02 2.50e+03 pdb="HH22 ARG C 192 " -0.078 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG B 192 " -0.182 9.50e-02 1.11e+02 7.39e-02 4.40e+01 pdb=" NE ARG B 192 " -0.009 2.00e-02 2.50e+03 pdb=" CZ ARG B 192 " 0.007 2.00e-02 2.50e+03 pdb=" NH1 ARG B 192 " -0.031 2.00e-02 2.50e+03 pdb=" NH2 ARG B 192 " 0.081 2.00e-02 2.50e+03 pdb="HH11 ARG B 192 " -0.001 2.00e-02 2.50e+03 pdb="HH12 ARG B 192 " 0.040 2.00e-02 2.50e+03 pdb="HH21 ARG B 192 " 0.003 2.00e-02 2.50e+03 pdb="HH22 ARG B 192 " -0.083 2.00e-02 2.50e+03 ... (remaining 4583 not shown) Histogram of nonbonded interaction distances: 1.52 - 2.14: 810 2.14 - 2.75: 56845 2.75 - 3.37: 84544 3.37 - 3.98: 108974 3.98 - 4.60: 175225 Nonbonded interactions: 426398 Sorted by model distance: nonbonded pdb=" OE2 GLU C 299 " pdb="HH11 ARG C 315 " model vdw 1.524 1.850 nonbonded pdb=" HH TYR A 273 " pdb=" OD1 ASN A 286 " model vdw 1.526 1.850 nonbonded pdb=" O PHE D 172 " pdb="HH12 ARG E 222 " model vdw 1.545 1.850 nonbonded pdb=" OD1 ASP D 240 " pdb=" H ILE D 243 " model vdw 1.554 1.850 nonbonded pdb=" HG1 THR A 311 " pdb=" O GLY A 314 " model vdw 1.557 1.850 ... (remaining 426393 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: 2.890 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: 0.460 Extract box with map and model: 11.160 Check model and map are aligned: 0.470 Set scattering table: 0.300 Process input model: 110.680 Find NCS groups from input model: 1.680 Set up NCS constraints: 0.090 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:2.910 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 130.650 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7773 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 : 0.004 0.032 16220 Z= 0.235 Angle : 0.693 10.235 22091 Z= 0.389 Chirality : 0.044 0.385 2494 Planarity : 0.010 0.136 2739 Dihedral : 14.997 172.861 6269 Min Nonbonded Distance : 1.830 Molprobity Statistics. All-atom Clashscore : 1.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.10 % Favored : 98.90 % Rotamer: Outliers : 0.12 % Allowed : 1.06 % Favored : 98.81 % 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: -0.27 (0.18), residues: 1902 helix: -0.47 (0.15), residues: 1018 sheet: 0.56 (0.29), residues: 335 loop : 0.39 (0.26), residues: 549 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.011 0.003 HIS B 54 PHE 0.017 0.003 PHE C 108 TYR 0.031 0.005 TYR D 273 ARG 0.025 0.003 ARG D 310 *********************** 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 389 residues out of total 1603 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 387 time to evaluate : 2.468 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: A 76 MET cc_start: 0.8835 (mmm) cc_final: 0.8233 (mmt) REVERT: A 160 ARG cc_start: 0.7552 (ptp90) cc_final: 0.7217 (ptp-110) REVERT: A 252 ASP cc_start: 0.7618 (t0) cc_final: 0.7398 (t70) REVERT: A 286 ASN cc_start: 0.6816 (m110) cc_final: 0.5994 (m110) REVERT: A 312 ARG cc_start: 0.7991 (tpt170) cc_final: 0.7748 (mmm160) REVERT: B 76 MET cc_start: 0.8936 (mmm) cc_final: 0.8362 (mmt) REVERT: B 267 ARG cc_start: 0.8244 (ttm110) cc_final: 0.7853 (ttm110) REVERT: B 291 ARG cc_start: 0.7924 (ttm170) cc_final: 0.7620 (ttm110) REVERT: C 117 MET cc_start: 0.8447 (tpt) cc_final: 0.8130 (tpt) REVERT: C 124 TYR cc_start: 0.7342 (m-10) cc_final: 0.6963 (m-80) REVERT: C 125 SER cc_start: 0.7820 (m) cc_final: 0.7263 (t) REVERT: D 146 HIS cc_start: 0.4506 (t-90) cc_final: 0.4041 (t-90) REVERT: D 245 ASP cc_start: 0.7275 (m-30) cc_final: 0.7039 (m-30) REVERT: D 264 LYS cc_start: 0.7952 (tttt) cc_final: 0.7616 (ttpt) REVERT: E 24 TYR cc_start: 0.7000 (m-80) cc_final: 0.6262 (m-80) REVERT: E 127 MET cc_start: 0.4807 (mtp) cc_final: 0.4531 (mtp) REVERT: E 131 TYR cc_start: 0.6725 (p90) cc_final: 0.6152 (p90) REVERT: E 171 ARG cc_start: 0.6673 (mmt-90) cc_final: 0.6307 (tpp-160) REVERT: E 177 HIS cc_start: 0.7023 (t-170) cc_final: 0.6799 (t-170) REVERT: E 303 ILE cc_start: 0.8696 (mt) cc_final: 0.8466 (mt) REVERT: F 81 LYS cc_start: 0.7396 (mttt) cc_final: 0.7159 (tttt) REVERT: F 125 SER cc_start: 0.8879 (m) cc_final: 0.8678 (t) REVERT: F 225 LYS cc_start: 0.8141 (mttt) cc_final: 0.7815 (mtpp) REVERT: F 249 THR cc_start: 0.7706 (m) cc_final: 0.7311 (p) outliers start: 2 outliers final: 1 residues processed: 388 average time/residue: 0.7324 time to fit residues: 396.5541 Evaluate side-chains 247 residues out of total 1603 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 246 time to evaluate : 2.577 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 199 MET Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 191 random chunks: chunk 161 optimal weight: 0.6980 chunk 144 optimal weight: 2.9990 chunk 80 optimal weight: 0.9980 chunk 49 optimal weight: 0.9990 chunk 97 optimal weight: 1.9990 chunk 77 optimal weight: 0.0970 chunk 149 optimal weight: 0.8980 chunk 57 optimal weight: 0.9980 chunk 91 optimal weight: 0.9990 chunk 111 optimal weight: 0.7980 chunk 173 optimal weight: 0.9980 overall best weight: 0.6978 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 99 ASN C 82 GLN D 74 ASN D 113 HIS D 221 ASN E 304 GLN F 82 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7789 moved from start: 0.2122 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 16220 Z= 0.209 Angle : 0.576 6.002 22091 Z= 0.308 Chirality : 0.040 0.148 2494 Planarity : 0.005 0.052 2739 Dihedral : 15.185 178.226 2546 Min Nonbonded Distance : 1.797 Molprobity Statistics. All-atom Clashscore : 2.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.37 % Favored : 99.63 % Rotamer: Outliers : 0.62 % Allowed : 5.18 % Favored : 94.20 % 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: 0.95 (0.19), residues: 1902 helix: 0.77 (0.16), residues: 1027 sheet: 0.68 (0.28), residues: 330 loop : 0.67 (0.27), residues: 545 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS A 255 PHE 0.008 0.001 PHE A 108 TYR 0.014 0.001 TYR A 329 ARG 0.006 0.001 ARG B 143 *********************** 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 262 residues out of total 1603 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 252 time to evaluate : 2.742 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 76 MET cc_start: 0.8791 (mmm) cc_final: 0.8129 (mmt) REVERT: A 144 SER cc_start: 0.8479 (p) cc_final: 0.8142 (t) REVERT: A 252 ASP cc_start: 0.7594 (t0) cc_final: 0.7301 (t0) REVERT: B 291 ARG cc_start: 0.7809 (ttm170) cc_final: 0.7525 (ttm110) REVERT: C 125 SER cc_start: 0.7760 (m) cc_final: 0.7265 (t) REVERT: D 146 HIS cc_start: 0.4490 (t-90) cc_final: 0.4196 (t-90) REVERT: D 264 LYS cc_start: 0.7795 (tttt) cc_final: 0.7495 (ttpt) REVERT: D 311 THR cc_start: 0.7475 (m) cc_final: 0.7150 (p) REVERT: E 24 TYR cc_start: 0.6843 (m-80) cc_final: 0.6180 (m-80) REVERT: E 121 GLU cc_start: 0.7221 (mt-10) cc_final: 0.7016 (mt-10) REVERT: E 127 MET cc_start: 0.4706 (mtp) cc_final: 0.4203 (mtp) REVERT: E 131 TYR cc_start: 0.6725 (p90) cc_final: 0.6114 (p90) REVERT: E 171 ARG cc_start: 0.6703 (mmt-90) cc_final: 0.6413 (tpp-160) REVERT: E 289 GLU cc_start: 0.6602 (mm-30) cc_final: 0.6220 (mm-30) REVERT: F 81 LYS cc_start: 0.7443 (mttt) cc_final: 0.7151 (tttt) REVERT: F 135 MET cc_start: 0.8168 (mmm) cc_final: 0.6898 (mmt) REVERT: F 225 LYS cc_start: 0.8049 (mttt) cc_final: 0.7717 (mtpp) REVERT: F 249 THR cc_start: 0.7788 (m) cc_final: 0.7413 (p) outliers start: 10 outliers final: 5 residues processed: 261 average time/residue: 0.7160 time to fit residues: 272.0788 Evaluate side-chains 239 residues out of total 1603 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 234 time to evaluate : 2.562 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 53 ASP Chi-restraints excluded: chain E residue 95 VAL Chi-restraints excluded: chain E residue 194 SER Chi-restraints excluded: chain F residue 147 LEU Chi-restraints excluded: chain G residue 178 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 191 random chunks: chunk 96 optimal weight: 0.0980 chunk 53 optimal weight: 1.9990 chunk 144 optimal weight: 1.9990 chunk 118 optimal weight: 0.9980 chunk 47 optimal weight: 0.9990 chunk 173 optimal weight: 0.3980 chunk 187 optimal weight: 2.9990 chunk 154 optimal weight: 1.9990 chunk 172 optimal weight: 0.3980 chunk 59 optimal weight: 0.9980 chunk 139 optimal weight: 1.9990 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 99 ASN B 286 ASN C 82 GLN D 79 ASN D 286 ASN E 304 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7788 moved from start: 0.2536 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 16220 Z= 0.171 Angle : 0.507 5.596 22091 Z= 0.266 Chirality : 0.039 0.136 2494 Planarity : 0.004 0.052 2739 Dihedral : 15.112 175.153 2543 Min Nonbonded Distance : 1.824 Molprobity Statistics. All-atom Clashscore : 2.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.84 % Favored : 99.16 % Rotamer: Outliers : 0.75 % Allowed : 5.80 % Favored : 93.45 % 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: 1.42 (0.20), residues: 1902 helix: 1.21 (0.17), residues: 1026 sheet: 0.78 (0.29), residues: 319 loop : 0.81 (0.27), residues: 557 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS A 255 PHE 0.012 0.001 PHE D 70 TYR 0.010 0.001 TYR E 260 ARG 0.004 0.000 ARG B 143 *********************** 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 246 residues out of total 1603 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 234 time to evaluate : 2.579 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 76 MET cc_start: 0.8765 (mmm) cc_final: 0.8335 (mmt) REVERT: A 144 SER cc_start: 0.8513 (p) cc_final: 0.8182 (t) REVERT: A 312 ARG cc_start: 0.7995 (mmm160) cc_final: 0.7577 (mmm160) REVERT: B 291 ARG cc_start: 0.7717 (ttm170) cc_final: 0.7485 (ttm110) REVERT: C 115 MET cc_start: 0.8860 (mtm) cc_final: 0.8511 (mtm) REVERT: C 125 SER cc_start: 0.7793 (m) cc_final: 0.7289 (t) REVERT: D 146 HIS cc_start: 0.4469 (t-90) cc_final: 0.3998 (t-90) REVERT: D 264 LYS cc_start: 0.7936 (tttt) cc_final: 0.7633 (ttpt) REVERT: D 311 THR cc_start: 0.7502 (m) cc_final: 0.7195 (p) REVERT: E 127 MET cc_start: 0.4609 (mtp) cc_final: 0.4398 (mtp) REVERT: E 131 TYR cc_start: 0.6740 (p90) cc_final: 0.6163 (p90) REVERT: E 171 ARG cc_start: 0.6710 (mmt-90) cc_final: 0.6330 (ttm-80) REVERT: F 81 LYS cc_start: 0.7450 (mttt) cc_final: 0.7135 (tttt) REVERT: F 225 LYS cc_start: 0.7996 (mttt) cc_final: 0.7707 (mtpp) REVERT: F 249 THR cc_start: 0.7958 (m) cc_final: 0.7573 (p) REVERT: G 192 GLU cc_start: 0.6119 (tt0) cc_final: 0.5791 (mp0) outliers start: 12 outliers final: 10 residues processed: 242 average time/residue: 0.6963 time to fit residues: 241.7490 Evaluate side-chains 234 residues out of total 1603 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 224 time to evaluate : 2.742 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 110 ASP Chi-restraints excluded: chain C residue 53 ASP Chi-restraints excluded: chain C residue 199 MET Chi-restraints excluded: chain C residue 284 SER Chi-restraints excluded: chain C residue 311 THR Chi-restraints excluded: chain E residue 95 VAL Chi-restraints excluded: chain E residue 194 SER Chi-restraints excluded: chain F residue 83 THR Chi-restraints excluded: chain F residue 147 LEU Chi-restraints excluded: chain G residue 178 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 191 random chunks: chunk 171 optimal weight: 0.6980 chunk 130 optimal weight: 0.7980 chunk 90 optimal weight: 0.9990 chunk 19 optimal weight: 0.9990 chunk 82 optimal weight: 0.9990 chunk 116 optimal weight: 0.9980 chunk 174 optimal weight: 1.9990 chunk 184 optimal weight: 2.9990 chunk 91 optimal weight: 0.5980 chunk 165 optimal weight: 1.9990 chunk 49 optimal weight: 0.9990 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 54 HIS B 99 ASN B 232 GLN D 79 ASN E 304 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7805 moved from start: 0.2811 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 16220 Z= 0.210 Angle : 0.515 6.180 22091 Z= 0.269 Chirality : 0.040 0.149 2494 Planarity : 0.005 0.055 2739 Dihedral : 15.060 166.632 2543 Min Nonbonded Distance : 1.783 Molprobity Statistics. All-atom Clashscore : 2.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.79 % Favored : 99.21 % Rotamer: Outliers : 1.00 % Allowed : 6.55 % Favored : 92.45 % 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: 1.46 (0.19), residues: 1902 helix: 1.33 (0.17), residues: 1025 sheet: 0.70 (0.29), residues: 314 loop : 0.71 (0.26), residues: 563 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.001 HIS A 255 PHE 0.009 0.001 PHE F 307 TYR 0.013 0.001 TYR C 131 ARG 0.005 0.000 ARG B 143 *********************** 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 238 residues out of total 1603 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 222 time to evaluate : 2.697 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 144 SER cc_start: 0.8468 (p) cc_final: 0.8199 (t) REVERT: A 312 ARG cc_start: 0.8085 (mmm160) cc_final: 0.7648 (mmm160) REVERT: B 291 ARG cc_start: 0.7707 (ttm170) cc_final: 0.7457 (ttm110) REVERT: C 125 SER cc_start: 0.7854 (m) cc_final: 0.7344 (t) REVERT: D 146 HIS cc_start: 0.4410 (t-90) cc_final: 0.4207 (t-90) REVERT: D 264 LYS cc_start: 0.7890 (tttt) cc_final: 0.7523 (ttpt) REVERT: D 311 THR cc_start: 0.7450 (m) cc_final: 0.7168 (p) REVERT: E 127 MET cc_start: 0.4643 (mtp) cc_final: 0.4211 (mtp) REVERT: E 131 TYR cc_start: 0.6928 (p90) cc_final: 0.6220 (p90) REVERT: E 171 ARG cc_start: 0.6770 (mmt-90) cc_final: 0.6474 (tpp-160) REVERT: F 33 LYS cc_start: 0.8319 (mttp) cc_final: 0.7885 (mmtm) REVERT: F 81 LYS cc_start: 0.7509 (mttt) cc_final: 0.7125 (tttt) REVERT: F 225 LYS cc_start: 0.7972 (mttt) cc_final: 0.7673 (mtpp) REVERT: F 249 THR cc_start: 0.7977 (m) cc_final: 0.7582 (p) REVERT: G 192 GLU cc_start: 0.6110 (tt0) cc_final: 0.5832 (mp0) outliers start: 16 outliers final: 13 residues processed: 231 average time/residue: 0.7037 time to fit residues: 232.2926 Evaluate side-chains 228 residues out of total 1603 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 215 time to evaluate : 2.460 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 49 ASP Chi-restraints excluded: chain C residue 53 ASP Chi-restraints excluded: chain C residue 132 ILE Chi-restraints excluded: chain C residue 199 MET Chi-restraints excluded: chain C residue 284 SER Chi-restraints excluded: chain C residue 311 THR Chi-restraints excluded: chain E residue 95 VAL Chi-restraints excluded: chain E residue 121 GLU Chi-restraints excluded: chain E residue 194 SER Chi-restraints excluded: chain E residue 296 ASP Chi-restraints excluded: chain F residue 83 THR Chi-restraints excluded: chain F residue 147 LEU Chi-restraints excluded: chain G residue 178 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 191 random chunks: chunk 153 optimal weight: 0.7980 chunk 104 optimal weight: 6.9990 chunk 2 optimal weight: 0.9990 chunk 137 optimal weight: 3.9990 chunk 76 optimal weight: 0.9980 chunk 157 optimal weight: 1.9990 chunk 127 optimal weight: 0.0470 chunk 0 optimal weight: 0.9990 chunk 94 optimal weight: 1.9990 chunk 165 optimal weight: 2.9990 chunk 46 optimal weight: 1.9990 overall best weight: 0.7682 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 232 GLN B 99 ASN C 82 GLN D 79 ASN E 304 GLN F 232 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7806 moved from start: 0.2974 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 16220 Z= 0.192 Angle : 0.498 7.821 22091 Z= 0.259 Chirality : 0.039 0.133 2494 Planarity : 0.004 0.056 2739 Dihedral : 14.934 167.257 2543 Min Nonbonded Distance : 1.806 Molprobity Statistics. All-atom Clashscore : 2.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.74 % Favored : 99.26 % Rotamer: Outliers : 1.06 % Allowed : 7.11 % Favored : 91.83 % 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: 1.57 (0.19), residues: 1902 helix: 1.47 (0.17), residues: 1022 sheet: 0.66 (0.29), residues: 311 loop : 0.73 (0.26), residues: 569 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS A 255 PHE 0.009 0.001 PHE D 70 TYR 0.013 0.001 TYR F 298 ARG 0.005 0.000 ARG G 200 *********************** 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 240 residues out of total 1603 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 223 time to evaluate : 2.635 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 144 SER cc_start: 0.8517 (p) cc_final: 0.8209 (t) REVERT: A 312 ARG cc_start: 0.8053 (mmm160) cc_final: 0.7647 (mmm160) REVERT: B 259 ASP cc_start: 0.7362 (t0) cc_final: 0.6781 (m-30) REVERT: B 291 ARG cc_start: 0.7710 (ttm170) cc_final: 0.7434 (ttm110) REVERT: C 105 ASP cc_start: 0.7737 (OUTLIER) cc_final: 0.7387 (m-30) REVERT: C 125 SER cc_start: 0.7865 (m) cc_final: 0.7353 (t) REVERT: D 264 LYS cc_start: 0.7874 (tttt) cc_final: 0.7509 (ttpt) REVERT: D 311 THR cc_start: 0.7446 (m) cc_final: 0.7174 (p) REVERT: E 121 GLU cc_start: 0.7116 (OUTLIER) cc_final: 0.6913 (mt-10) REVERT: E 127 MET cc_start: 0.4715 (mtp) cc_final: 0.4311 (mtp) REVERT: E 131 TYR cc_start: 0.6933 (p90) cc_final: 0.6256 (p90) REVERT: F 33 LYS cc_start: 0.8335 (mttp) cc_final: 0.7896 (mmtm) REVERT: F 81 LYS cc_start: 0.7509 (mttt) cc_final: 0.7099 (tttt) REVERT: F 225 LYS cc_start: 0.7982 (mttt) cc_final: 0.7673 (mtpp) REVERT: F 249 THR cc_start: 0.8068 (m) cc_final: 0.7675 (p) REVERT: G 192 GLU cc_start: 0.6096 (tt0) cc_final: 0.5779 (mp0) outliers start: 17 outliers final: 13 residues processed: 233 average time/residue: 0.6919 time to fit residues: 231.1053 Evaluate side-chains 230 residues out of total 1603 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 215 time to evaluate : 2.600 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 315 ARG Chi-restraints excluded: chain B residue 110 ASP Chi-restraints excluded: chain B residue 163 MET Chi-restraints excluded: chain C residue 49 ASP Chi-restraints excluded: chain C residue 53 ASP Chi-restraints excluded: chain C residue 105 ASP Chi-restraints excluded: chain C residue 199 MET Chi-restraints excluded: chain C residue 284 SER Chi-restraints excluded: chain C residue 311 THR Chi-restraints excluded: chain E residue 95 VAL Chi-restraints excluded: chain E residue 121 GLU Chi-restraints excluded: chain E residue 194 SER Chi-restraints excluded: chain E residue 296 ASP Chi-restraints excluded: chain F residue 83 THR Chi-restraints excluded: chain G residue 178 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 191 random chunks: chunk 62 optimal weight: 0.9990 chunk 166 optimal weight: 2.9990 chunk 36 optimal weight: 0.9990 chunk 108 optimal weight: 0.8980 chunk 45 optimal weight: 0.9980 chunk 184 optimal weight: 4.9990 chunk 153 optimal weight: 3.9990 chunk 85 optimal weight: 0.7980 chunk 15 optimal weight: 0.9980 chunk 61 optimal weight: 1.9990 chunk 97 optimal weight: 1.9990 overall best weight: 0.9382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 99 ASN C 82 GLN E 304 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7818 moved from start: 0.3110 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 16220 Z= 0.232 Angle : 0.512 6.959 22091 Z= 0.265 Chirality : 0.040 0.140 2494 Planarity : 0.005 0.057 2739 Dihedral : 14.881 169.196 2543 Min Nonbonded Distance : 1.772 Molprobity Statistics. All-atom Clashscore : 2.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.00 % Favored : 99.00 % Rotamer: Outliers : 1.00 % Allowed : 8.36 % 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: 1.46 (0.20), residues: 1902 helix: 1.41 (0.17), residues: 1026 sheet: 0.60 (0.30), residues: 302 loop : 0.59 (0.26), residues: 574 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.001 HIS A 255 PHE 0.008 0.001 PHE A 108 TYR 0.027 0.001 TYR A 322 ARG 0.003 0.000 ARG B 143 *********************** 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 235 residues out of total 1603 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 219 time to evaluate : 2.481 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 144 SER cc_start: 0.8495 (p) cc_final: 0.8176 (t) REVERT: A 269 MET cc_start: 0.6912 (mtp) cc_final: 0.6544 (mtp) REVERT: A 312 ARG cc_start: 0.8076 (mmm160) cc_final: 0.7701 (mmm160) REVERT: B 259 ASP cc_start: 0.7421 (t0) cc_final: 0.6836 (m-30) REVERT: B 284 SER cc_start: 0.8704 (m) cc_final: 0.8475 (p) REVERT: B 291 ARG cc_start: 0.7745 (ttm170) cc_final: 0.7539 (ttm110) REVERT: C 125 SER cc_start: 0.7937 (m) cc_final: 0.7439 (t) REVERT: D 264 LYS cc_start: 0.7894 (tttt) cc_final: 0.7518 (ttpt) REVERT: D 311 THR cc_start: 0.7421 (m) cc_final: 0.7144 (p) REVERT: E 121 GLU cc_start: 0.7127 (OUTLIER) cc_final: 0.6910 (mt-10) REVERT: E 127 MET cc_start: 0.4763 (mtp) cc_final: 0.4339 (mtp) REVERT: E 131 TYR cc_start: 0.6847 (p90) cc_final: 0.6181 (p90) REVERT: F 33 LYS cc_start: 0.8398 (mttp) cc_final: 0.8010 (mmtm) REVERT: F 81 LYS cc_start: 0.7637 (mttt) cc_final: 0.7185 (tttt) REVERT: F 163 MET cc_start: 0.8242 (mtt) cc_final: 0.7773 (mtt) REVERT: F 225 LYS cc_start: 0.8037 (mttt) cc_final: 0.7744 (mtpp) REVERT: F 249 THR cc_start: 0.8112 (m) cc_final: 0.7699 (p) REVERT: G 192 GLU cc_start: 0.6185 (tt0) cc_final: 0.5864 (mp0) outliers start: 16 outliers final: 13 residues processed: 230 average time/residue: 0.7341 time to fit residues: 241.7984 Evaluate side-chains 227 residues out of total 1603 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 213 time to evaluate : 2.568 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 315 ARG Chi-restraints excluded: chain B residue 163 MET Chi-restraints excluded: chain C residue 49 ASP Chi-restraints excluded: chain C residue 53 ASP Chi-restraints excluded: chain C residue 199 MET Chi-restraints excluded: chain C residue 284 SER Chi-restraints excluded: chain C residue 311 THR Chi-restraints excluded: chain E residue 95 VAL Chi-restraints excluded: chain E residue 121 GLU Chi-restraints excluded: chain E residue 194 SER Chi-restraints excluded: chain E residue 213 SER Chi-restraints excluded: chain E residue 296 ASP Chi-restraints excluded: chain F residue 284 SER Chi-restraints excluded: chain G residue 178 SER 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: 0.0270 chunk 134 optimal weight: 3.9990 chunk 104 optimal weight: 0.8980 chunk 155 optimal weight: 0.7980 chunk 103 optimal weight: 0.7980 chunk 184 optimal weight: 0.6980 chunk 115 optimal weight: 1.9990 chunk 112 optimal weight: 0.9980 chunk 84 optimal weight: 0.8980 overall best weight: 0.6438 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 99 ASN C 82 GLN D 74 ASN E 304 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7805 moved from start: 0.3239 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 16220 Z= 0.170 Angle : 0.488 7.363 22091 Z= 0.251 Chirality : 0.039 0.130 2494 Planarity : 0.004 0.056 2739 Dihedral : 14.793 166.997 2543 Min Nonbonded Distance : 1.832 Molprobity Statistics. All-atom Clashscore : 2.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.63 % Favored : 99.37 % Rotamer: Outliers : 0.81 % Allowed : 8.80 % Favored : 90.39 % 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: 1.63 (0.20), residues: 1902 helix: 1.58 (0.17), residues: 1023 sheet: 0.57 (0.29), residues: 302 loop : 0.67 (0.26), residues: 577 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS A 255 PHE 0.008 0.001 PHE D 70 TYR 0.015 0.001 TYR C 131 ARG 0.004 0.000 ARG B 143 *********************** 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 232 residues out of total 1603 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 219 time to evaluate : 2.516 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 144 SER cc_start: 0.8484 (p) cc_final: 0.8194 (t) REVERT: A 269 MET cc_start: 0.6665 (mtp) cc_final: 0.6248 (mtp) REVERT: A 312 ARG cc_start: 0.8096 (mmm160) cc_final: 0.7747 (mmm160) REVERT: B 259 ASP cc_start: 0.7326 (t0) cc_final: 0.6770 (m-30) REVERT: B 284 SER cc_start: 0.8686 (m) cc_final: 0.8465 (p) REVERT: B 291 ARG cc_start: 0.7734 (ttm170) cc_final: 0.7529 (ttm110) REVERT: B 323 GLU cc_start: 0.7671 (tp30) cc_final: 0.7412 (tp30) REVERT: C 125 SER cc_start: 0.7924 (m) cc_final: 0.7427 (t) REVERT: D 100 ASP cc_start: 0.7044 (t0) cc_final: 0.6830 (t0) REVERT: D 264 LYS cc_start: 0.7773 (tttt) cc_final: 0.7406 (ttpt) REVERT: D 311 THR cc_start: 0.7422 (m) cc_final: 0.7187 (p) REVERT: E 121 GLU cc_start: 0.7079 (OUTLIER) cc_final: 0.6860 (mt-10) REVERT: E 127 MET cc_start: 0.4710 (mtp) cc_final: 0.4375 (mtp) REVERT: E 131 TYR cc_start: 0.6918 (p90) cc_final: 0.6274 (p90) REVERT: F 33 LYS cc_start: 0.8386 (mttp) cc_final: 0.8004 (mmtm) REVERT: F 81 LYS cc_start: 0.7678 (mttt) cc_final: 0.7271 (tttt) REVERT: F 163 MET cc_start: 0.8253 (mtt) cc_final: 0.7799 (mtt) REVERT: F 225 LYS cc_start: 0.8016 (mttt) cc_final: 0.7690 (mtpp) REVERT: F 249 THR cc_start: 0.8115 (m) cc_final: 0.7701 (p) REVERT: G 192 GLU cc_start: 0.6030 (tt0) cc_final: 0.5801 (mp0) outliers start: 13 outliers final: 11 residues processed: 228 average time/residue: 0.7131 time to fit residues: 234.1466 Evaluate side-chains 225 residues out of total 1603 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 213 time to evaluate : 2.714 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 315 ARG Chi-restraints excluded: chain B residue 163 MET Chi-restraints excluded: chain C residue 49 ASP Chi-restraints excluded: chain C residue 53 ASP Chi-restraints excluded: chain C residue 199 MET Chi-restraints excluded: chain C residue 284 SER Chi-restraints excluded: chain C residue 311 THR Chi-restraints excluded: chain D residue 74 ASN Chi-restraints excluded: chain E residue 95 VAL Chi-restraints excluded: chain E residue 121 GLU Chi-restraints excluded: chain E residue 194 SER Chi-restraints excluded: chain G residue 178 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 191 random chunks: chunk 113 optimal weight: 0.9990 chunk 73 optimal weight: 2.9990 chunk 109 optimal weight: 0.3980 chunk 55 optimal weight: 0.9980 chunk 36 optimal weight: 0.9980 chunk 35 optimal weight: 0.5980 chunk 117 optimal weight: 0.7980 chunk 125 optimal weight: 1.9990 chunk 91 optimal weight: 0.9990 chunk 17 optimal weight: 0.8980 chunk 144 optimal weight: 1.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 99 ASN C 82 GLN E 304 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7810 moved from start: 0.3289 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 16220 Z= 0.191 Angle : 0.493 7.361 22091 Z= 0.254 Chirality : 0.039 0.126 2494 Planarity : 0.004 0.056 2739 Dihedral : 14.770 167.103 2543 Min Nonbonded Distance : 1.797 Molprobity Statistics. All-atom Clashscore : 2.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.68 % Favored : 99.32 % Rotamer: Outliers : 1.00 % Allowed : 8.86 % 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: 1.59 (0.20), residues: 1902 helix: 1.56 (0.17), residues: 1022 sheet: 0.53 (0.29), residues: 302 loop : 0.66 (0.26), residues: 578 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS A 255 PHE 0.007 0.001 PHE D 70 TYR 0.015 0.001 TYR C 131 ARG 0.004 0.000 ARG B 143 *********************** 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 230 residues out of total 1603 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 214 time to evaluate : 2.282 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 144 SER cc_start: 0.8483 (p) cc_final: 0.8193 (t) REVERT: A 269 MET cc_start: 0.6711 (mtp) cc_final: 0.6315 (mtp) REVERT: A 312 ARG cc_start: 0.8093 (mmm160) cc_final: 0.7793 (mmm160) REVERT: B 259 ASP cc_start: 0.7348 (t0) cc_final: 0.6778 (m-30) REVERT: B 284 SER cc_start: 0.8705 (m) cc_final: 0.8477 (p) REVERT: B 291 ARG cc_start: 0.7740 (ttm170) cc_final: 0.7529 (ttm110) REVERT: B 323 GLU cc_start: 0.7675 (tp30) cc_final: 0.7416 (tp30) REVERT: C 125 SER cc_start: 0.7932 (m) cc_final: 0.7435 (t) REVERT: D 100 ASP cc_start: 0.7072 (t0) cc_final: 0.6851 (t0) REVERT: D 264 LYS cc_start: 0.7783 (tttt) cc_final: 0.7413 (ttpt) REVERT: D 311 THR cc_start: 0.7437 (m) cc_final: 0.7203 (p) REVERT: E 121 GLU cc_start: 0.7082 (OUTLIER) cc_final: 0.6865 (mt-10) REVERT: E 127 MET cc_start: 0.4694 (mtp) cc_final: 0.4386 (mtp) REVERT: E 131 TYR cc_start: 0.6977 (p90) cc_final: 0.6353 (p90) REVERT: F 33 LYS cc_start: 0.8400 (mttp) cc_final: 0.8014 (mmtm) REVERT: F 81 LYS cc_start: 0.7692 (mttt) cc_final: 0.7287 (tttt) REVERT: F 163 MET cc_start: 0.8265 (mtt) cc_final: 0.7778 (mtt) REVERT: F 225 LYS cc_start: 0.8004 (mttt) cc_final: 0.7714 (mtpp) REVERT: F 249 THR cc_start: 0.8121 (m) cc_final: 0.7708 (p) REVERT: G 192 GLU cc_start: 0.6033 (tt0) cc_final: 0.5806 (mp0) outliers start: 16 outliers final: 13 residues processed: 226 average time/residue: 0.6601 time to fit residues: 214.3489 Evaluate side-chains 227 residues out of total 1603 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 213 time to evaluate : 2.340 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 315 ARG Chi-restraints excluded: chain B residue 163 MET Chi-restraints excluded: chain C residue 49 ASP Chi-restraints excluded: chain C residue 53 ASP Chi-restraints excluded: chain C residue 199 MET Chi-restraints excluded: chain C residue 284 SER Chi-restraints excluded: chain C residue 311 THR Chi-restraints excluded: chain E residue 95 VAL Chi-restraints excluded: chain E residue 121 GLU Chi-restraints excluded: chain E residue 194 SER Chi-restraints excluded: chain E residue 213 SER Chi-restraints excluded: chain F residue 284 SER Chi-restraints excluded: chain F residue 328 ASP Chi-restraints excluded: chain G residue 178 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 191 random chunks: chunk 167 optimal weight: 1.9990 chunk 176 optimal weight: 1.9990 chunk 160 optimal weight: 1.9990 chunk 171 optimal weight: 1.9990 chunk 103 optimal weight: 1.9990 chunk 74 optimal weight: 0.8980 chunk 134 optimal weight: 0.5980 chunk 52 optimal weight: 1.9990 chunk 155 optimal weight: 0.4980 chunk 162 optimal weight: 0.0670 chunk 170 optimal weight: 0.9990 overall best weight: 0.6120 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 99 ASN C 82 GLN D 74 ASN E 304 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7803 moved from start: 0.3380 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 16220 Z= 0.166 Angle : 0.482 7.654 22091 Z= 0.247 Chirality : 0.039 0.126 2494 Planarity : 0.004 0.056 2739 Dihedral : 14.682 164.964 2543 Min Nonbonded Distance : 1.827 Molprobity Statistics. All-atom Clashscore : 2.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.00 % Favored : 99.00 % Rotamer: Outliers : 0.87 % Allowed : 9.17 % 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: 1.73 (0.20), residues: 1902 helix: 1.66 (0.17), residues: 1024 sheet: 0.75 (0.30), residues: 282 loop : 0.64 (0.25), residues: 596 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS A 255 PHE 0.006 0.001 PHE A 108 TYR 0.017 0.001 TYR C 131 ARG 0.002 0.000 ARG G 179 *********************** 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 235 residues out of total 1603 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 221 time to evaluate : 2.656 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 144 SER cc_start: 0.8479 (p) cc_final: 0.8204 (t) REVERT: A 269 MET cc_start: 0.6703 (mtp) cc_final: 0.6269 (mtp) REVERT: A 312 ARG cc_start: 0.8083 (mmm160) cc_final: 0.7808 (mmm160) REVERT: B 259 ASP cc_start: 0.7272 (t0) cc_final: 0.6719 (m-30) REVERT: B 284 SER cc_start: 0.8705 (m) cc_final: 0.8481 (p) REVERT: B 291 ARG cc_start: 0.7734 (ttm170) cc_final: 0.7533 (ttm110) REVERT: B 323 GLU cc_start: 0.7680 (tp30) cc_final: 0.7420 (tp30) REVERT: C 125 SER cc_start: 0.7927 (m) cc_final: 0.7434 (t) REVERT: D 100 ASP cc_start: 0.7075 (t0) cc_final: 0.6857 (t0) REVERT: D 264 LYS cc_start: 0.7777 (tttt) cc_final: 0.7400 (ttpt) REVERT: D 311 THR cc_start: 0.7441 (m) cc_final: 0.7232 (p) REVERT: E 121 GLU cc_start: 0.7084 (OUTLIER) cc_final: 0.6828 (mt-10) REVERT: E 131 TYR cc_start: 0.7061 (p90) cc_final: 0.6458 (p90) REVERT: F 33 LYS cc_start: 0.8405 (mttp) cc_final: 0.8021 (mmtm) REVERT: F 81 LYS cc_start: 0.7662 (mttt) cc_final: 0.7280 (tttt) REVERT: F 163 MET cc_start: 0.8301 (mtt) cc_final: 0.7826 (mtt) REVERT: F 225 LYS cc_start: 0.7971 (mttt) cc_final: 0.7708 (mtpp) REVERT: F 249 THR cc_start: 0.8120 (m) cc_final: 0.7720 (p) outliers start: 14 outliers final: 12 residues processed: 232 average time/residue: 0.6723 time to fit residues: 225.0417 Evaluate side-chains 230 residues out of total 1603 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 217 time to evaluate : 2.237 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 315 ARG Chi-restraints excluded: chain B residue 163 MET Chi-restraints excluded: chain B residue 286 ASN Chi-restraints excluded: chain C residue 49 ASP Chi-restraints excluded: chain C residue 53 ASP Chi-restraints excluded: chain C residue 199 MET Chi-restraints excluded: chain C residue 284 SER Chi-restraints excluded: chain C residue 311 THR Chi-restraints excluded: chain D residue 286 ASN Chi-restraints excluded: chain E residue 121 GLU Chi-restraints excluded: chain E residue 194 SER Chi-restraints excluded: chain F residue 284 SER Chi-restraints excluded: chain G residue 178 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 191 random chunks: chunk 112 optimal weight: 0.9980 chunk 181 optimal weight: 1.9990 chunk 110 optimal weight: 1.9990 chunk 86 optimal weight: 0.9990 chunk 126 optimal weight: 1.9990 chunk 190 optimal weight: 2.9990 chunk 175 optimal weight: 1.9990 chunk 151 optimal weight: 2.9990 chunk 15 optimal weight: 0.9980 chunk 117 optimal weight: 0.6980 chunk 92 optimal weight: 2.9990 overall best weight: 1.1384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 99 ASN D 82 GLN E 304 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7830 moved from start: 0.3445 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 16220 Z= 0.272 Angle : 0.530 9.957 22091 Z= 0.274 Chirality : 0.041 0.159 2494 Planarity : 0.005 0.056 2739 Dihedral : 14.763 168.702 2543 Min Nonbonded Distance : 1.765 Molprobity Statistics. All-atom Clashscore : 2.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.31 % Favored : 98.69 % Rotamer: Outliers : 0.94 % Allowed : 9.30 % Favored : 89.77 % 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: 1.45 (0.20), residues: 1902 helix: 1.45 (0.17), residues: 1023 sheet: 0.40 (0.30), residues: 296 loop : 0.60 (0.25), residues: 583 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.001 HIS A 255 PHE 0.009 0.001 PHE A 108 TYR 0.017 0.001 TYR C 131 ARG 0.003 0.000 ARG C 315 ********************** 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 229 residues out of total 1603 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 214 time to evaluate : 2.725 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 144 SER cc_start: 0.8464 (p) cc_final: 0.8111 (t) REVERT: A 269 MET cc_start: 0.6733 (mtp) cc_final: 0.6288 (mtp) REVERT: A 312 ARG cc_start: 0.8092 (mmm160) cc_final: 0.7811 (mmm160) REVERT: B 259 ASP cc_start: 0.7489 (t0) cc_final: 0.6908 (m-30) REVERT: B 291 ARG cc_start: 0.7777 (ttm170) cc_final: 0.7519 (ttm110) REVERT: B 323 GLU cc_start: 0.7640 (tp30) cc_final: 0.7402 (tp30) REVERT: C 125 SER cc_start: 0.7976 (m) cc_final: 0.7480 (t) REVERT: D 311 THR cc_start: 0.7461 (m) cc_final: 0.7216 (p) REVERT: E 24 TYR cc_start: 0.6536 (m-80) cc_final: 0.5611 (m-80) REVERT: E 81 LYS cc_start: 0.6830 (mttp) cc_final: 0.5622 (mtpt) REVERT: E 121 GLU cc_start: 0.7055 (OUTLIER) cc_final: 0.6782 (mt-10) REVERT: E 127 MET cc_start: 0.4611 (mtp) cc_final: 0.4307 (mtp) REVERT: E 131 TYR cc_start: 0.6891 (p90) cc_final: 0.6452 (p90) REVERT: F 33 LYS cc_start: 0.8470 (mttp) cc_final: 0.8070 (mmtm) REVERT: F 81 LYS cc_start: 0.7652 (mttt) cc_final: 0.7240 (tttt) REVERT: F 163 MET cc_start: 0.8318 (mtt) cc_final: 0.7798 (mtt) REVERT: F 225 LYS cc_start: 0.8022 (mttt) cc_final: 0.7724 (mtpp) REVERT: F 249 THR cc_start: 0.8114 (m) cc_final: 0.7730 (p) outliers start: 15 outliers final: 14 residues processed: 225 average time/residue: 0.7186 time to fit residues: 232.0747 Evaluate side-chains 227 residues out of total 1603 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 212 time to evaluate : 2.488 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 315 ARG Chi-restraints excluded: chain B residue 163 MET Chi-restraints excluded: chain C residue 49 ASP Chi-restraints excluded: chain C residue 53 ASP Chi-restraints excluded: chain C residue 199 MET Chi-restraints excluded: chain C residue 284 SER Chi-restraints excluded: chain C residue 311 THR Chi-restraints excluded: chain D residue 286 ASN Chi-restraints excluded: chain E residue 121 GLU Chi-restraints excluded: chain E residue 194 SER Chi-restraints excluded: chain E residue 213 SER Chi-restraints excluded: chain E residue 296 ASP Chi-restraints excluded: chain F residue 284 SER Chi-restraints excluded: chain F residue 328 ASP Chi-restraints excluded: chain G residue 178 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 191 random chunks: chunk 120 optimal weight: 0.9990 chunk 161 optimal weight: 0.5980 chunk 46 optimal weight: 0.9980 chunk 139 optimal weight: 1.9990 chunk 22 optimal weight: 0.8980 chunk 42 optimal weight: 0.6980 chunk 151 optimal weight: 0.8980 chunk 63 optimal weight: 0.9990 chunk 155 optimal weight: 0.9990 chunk 19 optimal weight: 0.9990 chunk 27 optimal weight: 2.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 99 ASN C 82 GLN E 304 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3397 r_free = 0.3397 target = 0.122271 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3005 r_free = 0.3005 target = 0.094286 restraints weight = 65076.294| |-----------------------------------------------------------------------------| r_work (start): 0.2944 rms_B_bonded: 1.69 r_work: 0.2797 rms_B_bonded: 2.18 restraints_weight: 0.5000 r_work: 0.2687 rms_B_bonded: 3.60 restraints_weight: 0.2500 r_work (final): 0.2687 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8308 moved from start: 0.3495 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 16220 Z= 0.201 Angle : 0.502 7.661 22091 Z= 0.257 Chirality : 0.039 0.128 2494 Planarity : 0.004 0.056 2739 Dihedral : 14.752 167.982 2543 Min Nonbonded Distance : 1.802 Molprobity Statistics. All-atom Clashscore : 2.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.21 % Favored : 98.79 % Rotamer: Outliers : 0.94 % Allowed : 9.54 % Favored : 89.52 % 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: 1.53 (0.17), residues: 1023 sheet: 0.46 (0.30), residues: 302 loop : 0.48 (0.25), residues: 577 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS A 255 PHE 0.008 0.001 PHE A 108 TYR 0.017 0.001 TYR C 131 ARG 0.002 0.000 ARG A 169 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7151.22 seconds wall clock time: 125 minutes 56.58 seconds (7556.58 seconds total)