Starting phenix.real_space_refine on Mon Sep 14 15:33:11 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7pbt_13302/09_2026/7pbt_13302_neut_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/7pbt_13302/09_2026/7pbt_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/cci-nas-00/data/ceres_data/7pbt_13302/09_2026/7pbt_13302.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7pbt_13302/09_2026/7pbt_13302.map" model { file = "/net/cci-nas-00/data/ceres_data/7pbt_13302/09_2026/7pbt_13302_neut_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7pbt_13302/09_2026/7pbt_13302_neut_trim.cif" } 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 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. Time to flip 1 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2.1-6174/lib/python3.11/site-packages/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: 5.65, per 1000 atoms: 0.18 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 - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 3.23 Conformation dependent library (CDL) restraints added in 1.1 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... Secondary structure from input PDB file: 105 helices and 19 sheets defined 60.3% alpha, 11.3% beta 10 base pairs and 28 stacking pairs defined. Time for finding SS restraints: 6.10 Creating SS restraints... Processing helix chain 'A' and resid 31 through 49 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 64 through 77 removed outlier: 3.541A pdb=" N PHE A 70 " --> pdb=" O THR A 66 " (cutoff:3.500A) Processing helix chain 'A' and resid 86 through 88 No H-bonds generated for 'chain 'A' and resid 86 through 88' Processing helix chain 'A' and resid 90 through 100 removed outlier: 3.656A pdb=" N LEU A 94 " --> pdb=" O LYS A 90 " (cutoff:3.500A) 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 115 Processing helix chain 'A' and resid 116 through 130 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 160 through 164 Processing helix chain 'A' and resid 165 through 170 Processing helix chain 'A' and resid 182 through 197 removed outlier: 3.596A pdb=" N GLU A 188 " --> pdb=" O PRO A 184 " (cutoff:3.500A) Processing helix chain 'A' and resid 202 through 213 Processing helix chain 'A' and resid 216 through 234 Processing helix chain 'A' and resid 240 through 252 removed outlier: 4.159A pdb=" N ASP A 245 " --> pdb=" O ASP A 241 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N GLN A 246 " --> pdb=" O LYS A 242 " (cutoff:3.500A) Processing helix chain 'A' and resid 259 through 274 Processing helix chain 'A' and resid 279 through 288 Processing helix chain 'A' and resid 290 through 297 Processing helix chain 'A' and resid 298 through 305 removed outlier: 3.731A pdb=" N LEU A 302 " --> pdb=" O TYR A 298 " (cutoff:3.500A) Processing helix chain 'A' and resid 318 through 326 Processing helix chain 'B' and resid 31 through 48 Processing helix chain 'B' and resid 64 through 77 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 86 through 88 No H-bonds generated for 'chain 'B' and resid 86 through 88' Processing helix chain 'B' and resid 90 through 99 removed outlier: 3.535A pdb=" N LEU B 94 " --> pdb=" O LYS B 90 " (cutoff:3.500A) Processing helix chain 'B' and resid 112 through 115 Processing helix chain 'B' and resid 116 through 130 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 138 through 142 Processing helix chain 'B' and resid 160 through 164 Processing helix chain 'B' and resid 165 through 170 Processing helix chain 'B' and resid 182 through 197 Processing helix chain 'B' and resid 202 through 211 Processing helix chain 'B' and resid 216 through 234 Processing helix chain 'B' and resid 240 through 252 Processing helix chain 'B' and resid 259 through 273 Processing helix chain 'B' and resid 279 through 287 Processing helix chain 'B' and resid 290 through 297 Processing helix chain 'B' and resid 298 through 305 removed outlier: 3.513A pdb=" N LEU B 302 " --> pdb=" O TYR B 298 " (cutoff:3.500A) Processing helix chain 'B' and resid 318 through 326 Processing helix chain 'C' and resid 31 through 48 Processing helix chain 'C' and resid 64 through 77 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 86 through 88 No H-bonds generated for 'chain 'C' and resid 86 through 88' Processing helix chain 'C' and resid 90 through 99 removed outlier: 3.576A pdb=" N LEU C 94 " --> pdb=" O LYS C 90 " (cutoff:3.500A) Processing helix chain 'C' and resid 112 through 115 Processing helix chain 'C' and resid 116 through 129 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 160 through 164 Processing helix chain 'C' and resid 165 through 170 Processing helix chain 'C' and resid 182 through 197 Processing helix chain 'C' and resid 202 through 213 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 216 through 235 Processing helix chain 'C' and resid 240 through 252 removed outlier: 4.104A pdb=" N ASP C 245 " --> pdb=" O ASP C 241 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N GLN C 246 " --> pdb=" O LYS C 242 " (cutoff:3.500A) Processing helix chain 'C' and resid 259 through 274 Processing helix chain 'C' and resid 279 through 288 Processing helix chain 'C' and resid 290 through 297 Processing helix chain 'C' and resid 298 through 305 removed outlier: 3.908A pdb=" N LEU C 302 " --> pdb=" O TYR C 298 " (cutoff:3.500A) Processing helix chain 'C' and resid 318 through 326 Processing helix chain 'D' and resid 31 through 47 removed outlier: 3.648A pdb=" N ILE D 40 " --> pdb=" O ASP D 36 " (cutoff:3.500A) Processing helix chain 'D' and resid 64 through 77 removed outlier: 3.587A pdb=" N PHE D 70 " --> pdb=" O THR D 66 " (cutoff:3.500A) Processing helix chain 'D' and resid 86 through 88 No H-bonds generated for 'chain 'D' and resid 86 through 88' Processing helix chain 'D' and resid 90 through 101 removed outlier: 3.705A pdb=" N LEU D 94 " --> pdb=" O LYS D 90 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N LEU D 101 " --> pdb=" O ILE D 97 " (cutoff:3.500A) Processing helix chain 'D' and resid 112 through 115 Processing helix chain 'D' and resid 116 through 130 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 165 through 172 removed outlier: 3.518A pdb=" N ARG D 171 " --> pdb=" O PRO D 167 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N PHE D 172 " --> pdb=" O LEU D 168 " (cutoff:3.500A) Processing helix chain 'D' and resid 182 through 197 removed outlier: 3.581A pdb=" N ILE D 196 " --> pdb=" O ARG D 192 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N PHE D 197 " --> pdb=" O THR D 193 " (cutoff:3.500A) Processing helix chain 'D' and resid 202 through 212 Processing helix chain 'D' and resid 216 through 235 Processing helix chain 'D' and resid 240 through 251 Processing helix chain 'D' and resid 259 through 274 Processing helix chain 'D' and resid 279 through 288 Processing helix chain 'D' and resid 290 through 297 Processing helix chain 'D' and resid 298 through 305 removed outlier: 3.618A pdb=" N LEU D 302 " --> pdb=" O TYR D 298 " (cutoff:3.500A) Processing helix chain 'D' and resid 318 through 326 Processing helix chain 'E' and resid 31 through 49 Processing helix chain 'E' and resid 64 through 77 Processing helix chain 'E' and resid 90 through 100 removed outlier: 3.543A pdb=" N LEU E 94 " --> pdb=" O LYS E 90 " (cutoff:3.500A) Processing helix chain 'E' and resid 112 through 115 removed outlier: 3.853A pdb=" N MET E 115 " --> pdb=" O ILE E 112 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 112 through 115' Processing helix chain 'E' and resid 116 through 130 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 160 through 164 Processing helix chain 'E' and resid 165 through 170 Processing helix chain 'E' and resid 182 through 197 removed outlier: 3.802A pdb=" N GLU E 188 " --> pdb=" O PRO E 184 " (cutoff:3.500A) Processing helix chain 'E' and resid 202 through 212 Processing helix chain 'E' and resid 216 through 235 removed outlier: 3.769A pdb=" N ILE E 233 " --> pdb=" O ASP E 229 " (cutoff:3.500A) Processing helix chain 'E' and resid 240 through 251 Processing helix chain 'E' and resid 259 through 273 Processing helix chain 'E' and resid 279 through 287 Processing helix chain 'E' and resid 290 through 298 Processing helix chain 'E' and resid 298 through 305 removed outlier: 3.604A pdb=" N LEU E 302 " --> pdb=" O TYR E 298 " (cutoff:3.500A) Processing helix chain 'E' and resid 318 through 326 Processing helix chain 'F' and resid 31 through 48 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) removed outlier: 3.539A pdb=" N ARG F 48 " --> pdb=" O ALA F 44 " (cutoff:3.500A) Processing helix chain 'F' and resid 64 through 77 removed outlier: 3.518A pdb=" N PHE F 70 " --> pdb=" O THR F 66 " (cutoff:3.500A) Processing helix chain 'F' and resid 86 through 88 No H-bonds generated for 'chain 'F' and resid 86 through 88' Processing helix chain 'F' and resid 90 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 111 through 115 Processing helix chain 'F' and resid 116 through 130 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 138 through 142 Processing helix chain 'F' and resid 160 through 164 Processing helix chain 'F' and resid 165 through 170 Processing helix chain 'F' and resid 182 through 197 Processing helix chain 'F' and resid 202 through 212 Processing helix chain 'F' and resid 216 through 234 Processing helix chain 'F' and resid 240 through 251 Processing helix chain 'F' and resid 259 through 272 Processing helix chain 'F' and resid 279 through 288 Processing helix chain 'F' and resid 290 through 297 Processing helix chain 'F' and resid 297 through 305 removed outlier: 4.234A pdb=" N TYR F 301 " --> pdb=" O MET F 297 " (cutoff:3.500A) Processing helix chain 'F' and resid 318 through 326 Processing helix chain 'G' and resid 157 through 170 Processing helix chain 'G' and resid 173 through 183 Processing helix chain 'G' and resid 190 through 203 Processing sheet with id=AA1, first strand: chain 'A' and resid 80 through 84 removed outlier: 6.353A pdb=" N LEU A 107 " --> pdb=" O VAL A 155 " (cutoff:3.500A) removed outlier: 8.040A pdb=" N ALA A 157 " --> pdb=" O LEU A 107 " (cutoff:3.500A) removed outlier: 7.016A pdb=" N ILE A 109 " --> pdb=" O ALA A 157 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 131 through 137 Processing sheet with id=AA3, first strand: chain 'A' and resid 308 through 311 Processing sheet with id=AA4, first strand: chain 'B' and resid 80 through 84 removed outlier: 6.515A pdb=" N LYS B 81 " --> pdb=" O PHE B 108 " (cutoff:3.500A) removed outlier: 7.798A pdb=" N ASP B 110 " --> pdb=" O LYS B 81 " (cutoff:3.500A) removed outlier: 7.084A pdb=" N THR B 83 " --> pdb=" O ASP B 110 " (cutoff:3.500A) removed outlier: 6.354A pdb=" N LEU B 107 " --> pdb=" O VAL B 155 " (cutoff:3.500A) removed outlier: 8.058A pdb=" N ALA B 157 " --> pdb=" O LEU B 107 " (cutoff:3.500A) removed outlier: 6.963A pdb=" N ILE B 109 " --> pdb=" O ALA B 157 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 131 through 136 Processing sheet with id=AA6, first strand: chain 'B' and resid 308 through 311 Processing sheet with id=AA7, first strand: chain 'C' and resid 80 through 84 removed outlier: 6.444A pdb=" N LEU C 107 " --> pdb=" O VAL C 155 " (cutoff:3.500A) removed outlier: 8.097A pdb=" N ALA C 157 " --> pdb=" O LEU C 107 " (cutoff:3.500A) removed outlier: 7.058A pdb=" N ILE C 109 " --> pdb=" O ALA C 157 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 131 through 136 Processing sheet with id=AA9, first strand: chain 'C' and resid 308 through 311 Processing sheet with id=AB1, first strand: chain 'D' and resid 80 through 84 removed outlier: 6.429A pdb=" N LEU D 107 " --> pdb=" O VAL D 155 " (cutoff:3.500A) removed outlier: 7.759A pdb=" N ALA D 157 " --> pdb=" O LEU D 107 " (cutoff:3.500A) removed outlier: 6.817A pdb=" N ILE D 109 " --> pdb=" O ALA D 157 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'D' and resid 131 through 137 Processing sheet with id=AB3, first strand: chain 'D' and resid 308 through 311 Processing sheet with id=AB4, first strand: chain 'E' and resid 80 through 84 removed outlier: 6.197A pdb=" N LYS E 81 " --> pdb=" O PHE E 108 " (cutoff:3.500A) removed outlier: 7.713A pdb=" N ASP E 110 " --> pdb=" O LYS E 81 " (cutoff:3.500A) removed outlier: 7.076A pdb=" N THR E 83 " --> pdb=" O ASP E 110 " (cutoff:3.500A) removed outlier: 6.271A pdb=" N LEU E 107 " --> pdb=" O VAL E 155 " (cutoff:3.500A) removed outlier: 7.736A pdb=" N ALA E 157 " --> pdb=" O LEU E 107 " (cutoff:3.500A) removed outlier: 6.867A pdb=" N ILE E 109 " --> pdb=" O ALA E 157 " (cutoff:3.500A) removed outlier: 6.764A pdb=" N LEU E 56 " --> pdb=" O GLY E 176 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'E' and resid 131 through 136 Processing sheet with id=AB6, first strand: chain 'E' and resid 200 through 201 removed outlier: 7.414A pdb=" N THR E 200 " --> pdb=" O ILE E 239 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB6 Processing sheet with id=AB7, first strand: chain 'E' and resid 308 through 311 Processing sheet with id=AB8, first strand: chain 'F' and resid 80 through 84 removed outlier: 6.276A pdb=" N LEU F 107 " --> pdb=" O VAL F 155 " (cutoff:3.500A) removed outlier: 7.872A pdb=" N ALA F 157 " --> pdb=" O LEU F 107 " (cutoff:3.500A) removed outlier: 7.016A pdb=" N ILE F 109 " --> pdb=" O ALA F 157 " (cutoff:3.500A) removed outlier: 6.676A pdb=" N LEU F 56 " --> pdb=" O GLY F 176 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'F' and resid 131 through 136 Processing sheet with id=AC1, first strand: chain 'F' and resid 308 through 311 801 hydrogen bonds defined for protein. 2295 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: 8.95 Time building geometry restraints manager: 4.37 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: 0.00 - 2.10: 56701 2.10 - 4.21: 524 4.21 - 6.31: 52 6.31 - 8.42: 19 8.42 - 10.52: 11 Bond angle restraints: 57307 Sorted by residual: angle pdb=" O4' DA V 11 " pdb=" C1' DA V 11 " pdb=" N9 DA V 11 " ideal model delta sigma weight residual 108.00 111.05 -3.05 7.00e-01 2.04e+00 1.90e+01 angle pdb=" C4' DC V 8 " pdb=" O4' DC V 8 " pdb=" C1' DC V 8 " ideal model delta sigma weight residual 110.10 105.83 4.27 1.00e+00 1.00e+00 1.82e+01 angle pdb=" N3 DT V 3 " pdb=" C4 DT V 3 " pdb=" O4 DT V 3 " ideal model delta sigma weight residual 119.90 122.40 -2.50 6.00e-01 2.78e+00 1.74e+01 angle pdb=" N3 DT U 6 " pdb=" C4 DT U 6 " pdb=" O4 DT U 6 " ideal model delta sigma weight residual 119.90 122.35 -2.45 6.00e-01 2.78e+00 1.67e+01 angle pdb=" N3 DT V 4 " pdb=" C4 DT V 4 " pdb=" O4 DT V 4 " ideal model delta sigma weight residual 119.90 122.34 -2.44 6.00e-01 2.78e+00 1.66e+01 ... (remaining 57302 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 34.57: 14162 34.57 - 69.14: 543 69.14 - 103.72: 26 103.72 - 138.29: 1 138.29 - 172.86: 3 Dihedral angle restraints: 14735 sinusoidal: 8466 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 14732 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.079: 2251 0.079 - 0.158: 225 0.158 - 0.237: 8 0.237 - 0.316: 3 0.316 - 0.395: 1 Chirality restraints: 2488 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 2.34 -2.73 -0.40 2.00e-01 2.50e+01 3.91e+00 chirality pdb=" C3' AGS C 401 " pdb=" C2' AGS C 401 " pdb=" C4' AGS C 401 " pdb=" O3' AGS C 401 " both_signs ideal model delta sigma weight residual False -2.37 -2.62 0.25 2.00e-01 2.50e+01 1.59e+00 chirality pdb=" C3' AGS A 401 " pdb=" C2' AGS A 401 " pdb=" C4' AGS A 401 " pdb=" O3' AGS A 401 " both_signs ideal model delta sigma weight residual False -2.37 -2.62 0.25 2.00e-01 2.50e+01 1.57e+00 ... (remaining 2485 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: 784 2.14 - 2.75: 56728 2.75 - 3.37: 84420 3.37 - 3.98: 108764 3.98 - 4.60: 175045 Nonbonded interactions: 425741 Sorted by model distance: nonbonded pdb=" OE2 GLU C 299 " pdb="HH11 ARG C 315 " model vdw 1.524 2.450 nonbonded pdb=" HH TYR A 273 " pdb=" OD1 ASN A 286 " model vdw 1.526 2.450 nonbonded pdb=" O PHE D 172 " pdb="HH12 ARG E 222 " model vdw 1.545 2.450 nonbonded pdb=" OD1 ASP D 240 " pdb=" H ILE D 243 " model vdw 1.554 2.450 nonbonded pdb=" HG1 THR A 311 " pdb=" O GLY A 314 " model vdw 1.557 2.450 ... (remaining 425736 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' 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: 4.400 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.210 Extract box with map and model: 0.530 Check model and map are aligned: 0.100 Set scattering table: 0.100 Process input model: 38.380 Find NCS groups from input model: 0.630 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.010 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.370 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 45.780 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7872 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 0.097 16220 Z= 0.251 Angle : 0.768 10.523 22091 Z= 0.436 Chirality : 0.047 0.395 2488 Planarity : 0.010 0.136 2739 Dihedral : 15.637 172.861 6323 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. 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 ARG 0.025 0.003 ARG D 310 TYR 0.031 0.005 TYR D 273 PHE 0.017 0.003 PHE C 108 HIS 0.011 0.003 HIS B 54 Details of bonding type rmsd/Z covalent geometry : bond 0.00461 / 0.25 (16220) covalent geometry : angle 0.76761 / 0.44 (22091) hydrogen bonds : bond 0.23646 / 15.46 ( 822) hydrogen bonds : angle 8.53527 / 5.92 ( 2337) *********************** 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 to be fit. rotamer outliers: 2 poor density : 387 time to evaluate : 0.810 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 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: 0.7399 (t70) REVERT: A 286 ASN cc_start: 0.6816 (m110) cc_final: 0.5995 (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: 0.7852 (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: 0.8131 (tpt) REVERT: C 124 TYR cc_start: 0.7342 (m-10) cc_final: 0.6964 (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: 0.4054 (t-90) REVERT: D 245 ASP cc_start: 0.7275 (m-30) cc_final: 0.7040 (m-30) REVERT: D 264 LYS cc_start: 0.7952 (tttt) cc_final: 0.7599 (ttpt) REVERT: E 127 MET cc_start: 0.4807 (mtp) cc_final: 0.4534 (mtp) REVERT: E 131 TYR cc_start: 0.6725 (p90) cc_final: 0.6155 (p90) REVERT: E 171 ARG cc_start: 0.6673 (mmt-90) cc_final: 0.6305 (tpp-160) REVERT: E 177 HIS cc_start: 0.7023 (t-170) cc_final: 0.6798 (t-170) REVERT: E 303 ILE cc_start: 0.8696 (mt) cc_final: 0.8449 (mm) REVERT: F 81 LYS cc_start: 0.7396 (mttt) cc_final: 0.7158 (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: 0.7312 (p) outliers start: 2 outliers final: 1 residues processed: 388 average time/residue: 0.3313 time to fit residues: 182.4338 Evaluate side-chains 245 residues out of total 1603 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 244 time to evaluate : 0.802 ------------------------------------------------------------------------------- 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 98 optimal weight: 2.9990 chunk 107 optimal weight: 2.9990 chunk 10 optimal weight: 0.9990 chunk 66 optimal weight: 0.6980 chunk 130 optimal weight: 3.9990 chunk 124 optimal weight: 2.9990 chunk 103 optimal weight: 3.9990 chunk 77 optimal weight: 0.9980 chunk 122 optimal weight: 0.2980 chunk 91 optimal weight: 0.9990 chunk 149 optimal weight: 0.5980 overall best weight: 0.7182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 99 ASN D 74 ASN D 113 HIS D 221 ASN E 304 GLN F 82 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3402 r_free = 0.3402 target = 0.123301 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2994 r_free = 0.2994 target = 0.093900 restraints weight = 65008.828| |-----------------------------------------------------------------------------| r_work (start): 0.2933 rms_B_bonded: 1.90 r_work: 0.2811 rms_B_bonded: 2.12 restraints_weight: 0.5000 r_work: 0.2695 rms_B_bonded: 3.54 restraints_weight: 0.2500 r_work (final): 0.2695 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8288 moved from start: 0.2180 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 16220 Z= 0.172 Angle : 0.644 6.959 22091 Z= 0.346 Chirality : 0.043 0.156 2488 Planarity : 0.006 0.068 2739 Dihedral : 15.331 177.917 2600 Min Nonbonded Distance : 1.807 Molprobity Statistics. All-atom Clashscore : 1.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.42 % Favored : 99.58 % Rotamer: Outliers : 0.44 % Allowed : 5.36 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.94 (0.19), residues: 1902 helix: 0.71 (0.16), residues: 1044 sheet: 1.14 (0.31), residues: 281 loop : 0.49 (0.25), residues: 577 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG F 212 TYR 0.013 0.001 TYR C 131 PHE 0.009 0.001 PHE E 58 HIS 0.004 0.001 HIS C 146 Details of bonding type rmsd/Z covalent geometry : bond 0.00368 / 0.17 (16220) covalent geometry : angle 0.64360 / 0.35 (22091) hydrogen bonds : bond 0.07750 / 5.03 ( 822) hydrogen bonds : angle 6.22973 / 4.36 ( 2337) *********************** 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 251 residues out of total 1603 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 244 time to evaluate : 0.850 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 76 MET cc_start: 0.8987 (mmm) cc_final: 0.8355 (mmt) REVERT: A 144 SER cc_start: 0.8565 (p) cc_final: 0.8239 (t) REVERT: A 160 ARG cc_start: 0.7950 (ptp90) cc_final: 0.7668 (ptp-110) REVERT: A 252 ASP cc_start: 0.8058 (t0) cc_final: 0.7743 (t0) REVERT: B 117 MET cc_start: 0.8066 (tpp) cc_final: 0.7481 (tpp) REVERT: B 194 SER cc_start: 0.9143 (m) cc_final: 0.8926 (m) REVERT: B 291 ARG cc_start: 0.8213 (ttm170) cc_final: 0.7922 (ttm110) REVERT: C 115 MET cc_start: 0.8851 (mtm) cc_final: 0.8646 (mtm) REVERT: C 117 MET cc_start: 0.8490 (tpt) cc_final: 0.8193 (tpt) REVERT: C 125 SER cc_start: 0.8179 (m) cc_final: 0.7773 (t) REVERT: D 146 HIS cc_start: 0.4441 (t-90) cc_final: 0.4077 (t-90) REVERT: D 264 LYS cc_start: 0.8257 (tttt) cc_final: 0.7974 (ttpt) REVERT: D 311 THR cc_start: 0.8057 (m) cc_final: 0.7787 (p) REVERT: E 117 MET cc_start: 0.6063 (tpt) cc_final: 0.5504 (tpp) REVERT: E 121 GLU cc_start: 0.7249 (mt-10) cc_final: 0.6814 (mm-30) REVERT: E 127 MET cc_start: 0.5037 (mtp) cc_final: 0.4834 (mtp) REVERT: E 131 TYR cc_start: 0.6768 (p90) cc_final: 0.6136 (p90) REVERT: E 171 ARG cc_start: 0.6849 (mmt-90) cc_final: 0.6501 (tpp-160) REVERT: F 81 LYS cc_start: 0.7979 (mttt) cc_final: 0.7668 (tttt) REVERT: F 225 LYS cc_start: 0.8524 (mttt) cc_final: 0.8221 (mtpp) REVERT: F 249 THR cc_start: 0.7978 (m) cc_final: 0.7568 (p) outliers start: 7 outliers final: 3 residues processed: 250 average time/residue: 0.2991 time to fit residues: 109.0741 Evaluate side-chains 231 residues out of total 1603 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 228 time to evaluate : 0.826 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 53 ASP Chi-restraints excluded: chain E residue 95 VAL Chi-restraints excluded: chain F residue 147 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 191 random chunks: chunk 44 optimal weight: 0.8980 chunk 121 optimal weight: 0.4980 chunk 40 optimal weight: 0.3980 chunk 183 optimal weight: 5.9990 chunk 3 optimal weight: 1.9990 chunk 75 optimal weight: 0.9980 chunk 104 optimal weight: 0.6980 chunk 111 optimal weight: 0.8980 chunk 39 optimal weight: 0.0970 chunk 5 optimal weight: 0.5980 chunk 134 optimal weight: 2.9990 overall best weight: 0.4578 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 99 ASN B 286 ASN D 79 ASN ** D 286 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 304 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3429 r_free = 0.3429 target = 0.125485 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3041 r_free = 0.3041 target = 0.097134 restraints weight = 64630.719| |-----------------------------------------------------------------------------| r_work (start): 0.2978 rms_B_bonded: 1.80 r_work: 0.2834 rms_B_bonded: 2.15 restraints_weight: 0.5000 r_work: 0.2720 rms_B_bonded: 3.61 restraints_weight: 0.2500 r_work (final): 0.2720 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8277 moved from start: 0.2621 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 16220 Z= 0.123 Angle : 0.545 5.719 22091 Z= 0.288 Chirality : 0.040 0.229 2488 Planarity : 0.005 0.053 2739 Dihedral : 14.609 179.619 2597 Min Nonbonded Distance : 1.847 Molprobity Statistics. All-atom Clashscore : 1.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.00 % Favored : 99.00 % Rotamer: Outliers : 0.69 % Allowed : 5.68 % Favored : 93.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.98 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.27 (0.19), residues: 1902 helix: 1.05 (0.16), residues: 1049 sheet: 1.03 (0.31), residues: 280 loop : 0.63 (0.25), residues: 573 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 143 TYR 0.015 0.001 TYR A 322 PHE 0.014 0.001 PHE D 70 HIS 0.004 0.001 HIS D 113 Details of bonding type rmsd/Z covalent geometry : bond 0.00251 / 0.12 (16220) covalent geometry : angle 0.54476 / 0.29 (22091) hydrogen bonds : bond 0.05738 / 3.71 ( 822) hydrogen bonds : angle 5.44127 / 3.80 ( 2337) *********************** 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 247 residues out of total 1603 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 236 time to evaluate : 0.835 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 76 MET cc_start: 0.8901 (mmm) cc_final: 0.8258 (mmt) REVERT: A 144 SER cc_start: 0.8591 (p) cc_final: 0.8301 (t) REVERT: A 252 ASP cc_start: 0.7993 (t0) cc_final: 0.7686 (t0) REVERT: B 194 SER cc_start: 0.9199 (m) cc_final: 0.8979 (m) REVERT: B 291 ARG cc_start: 0.8252 (ttm170) cc_final: 0.7982 (ttm110) REVERT: C 125 SER cc_start: 0.8269 (m) cc_final: 0.7891 (t) REVERT: C 194 SER cc_start: 0.9237 (t) cc_final: 0.8892 (t) REVERT: D 146 HIS cc_start: 0.4397 (t-90) cc_final: 0.4097 (t-90) REVERT: D 264 LYS cc_start: 0.8362 (tttt) cc_final: 0.8080 (ttpt) REVERT: D 311 THR cc_start: 0.7967 (m) cc_final: 0.7752 (p) REVERT: E 117 MET cc_start: 0.5790 (tpt) cc_final: 0.5436 (mmt) REVERT: E 121 GLU cc_start: 0.7250 (OUTLIER) cc_final: 0.6905 (mm-30) REVERT: E 127 MET cc_start: 0.4982 (mtp) cc_final: 0.4767 (mtp) REVERT: E 131 TYR cc_start: 0.6772 (p90) cc_final: 0.6196 (p90) REVERT: E 171 ARG cc_start: 0.6878 (mmt-90) cc_final: 0.6486 (ttm-80) REVERT: F 81 LYS cc_start: 0.8010 (mttt) cc_final: 0.7742 (tttt) REVERT: F 225 LYS cc_start: 0.8427 (mttt) cc_final: 0.8158 (mtpp) REVERT: F 249 THR cc_start: 0.8116 (m) cc_final: 0.7716 (p) outliers start: 11 outliers final: 7 residues processed: 244 average time/residue: 0.2915 time to fit residues: 104.0914 Evaluate side-chains 231 residues out of total 1603 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 223 time to evaluate : 0.795 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 315 ARG 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 311 THR Chi-restraints excluded: chain E residue 95 VAL Chi-restraints excluded: chain E residue 121 GLU Chi-restraints excluded: chain F residue 147 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 191 random chunks: chunk 187 optimal weight: 3.9990 chunk 68 optimal weight: 0.9980 chunk 2 optimal weight: 0.9980 chunk 21 optimal weight: 1.9990 chunk 165 optimal weight: 2.9990 chunk 40 optimal weight: 0.2980 chunk 129 optimal weight: 0.6980 chunk 61 optimal weight: 0.9980 chunk 120 optimal weight: 0.0470 chunk 184 optimal weight: 3.9990 chunk 107 optimal weight: 1.9990 overall best weight: 0.6078 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 99 ASN B 232 GLN ** D 286 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 304 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3449 r_free = 0.3449 target = 0.126629 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3071 r_free = 0.3071 target = 0.098953 restraints weight = 64425.775| |-----------------------------------------------------------------------------| r_work (start): 0.3002 rms_B_bonded: 1.71 r_work: 0.2844 rms_B_bonded: 2.29 restraints_weight: 0.5000 r_work: 0.2733 rms_B_bonded: 3.82 restraints_weight: 0.2500 r_work (final): 0.2733 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8357 moved from start: 0.2829 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 16220 Z= 0.128 Angle : 0.532 7.223 22091 Z= 0.280 Chirality : 0.040 0.143 2488 Planarity : 0.005 0.056 2739 Dihedral : 14.338 173.934 2597 Min Nonbonded Distance : 1.836 Molprobity Statistics. All-atom Clashscore : 1.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.00 % Favored : 99.00 % Rotamer: Outliers : 0.56 % Allowed : 6.36 % Favored : 93.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.98 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.39 (0.19), residues: 1902 helix: 1.20 (0.16), residues: 1049 sheet: 1.00 (0.30), residues: 277 loop : 0.62 (0.25), residues: 576 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 312 TYR 0.014 0.001 TYR A 273 PHE 0.009 0.001 PHE D 70 HIS 0.004 0.001 HIS D 146 Details of bonding type rmsd/Z covalent geometry : bond 0.00275 / 0.13 (16220) covalent geometry : angle 0.53219 / 0.28 (22091) hydrogen bonds : bond 0.04972 / 3.22 ( 822) hydrogen bonds : angle 5.18515 / 3.62 ( 2337) *********************** 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 233 residues out of total 1603 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 224 time to evaluate : 0.634 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 76 MET cc_start: 0.8966 (mmm) cc_final: 0.8399 (mmt) REVERT: A 252 ASP cc_start: 0.8164 (t0) cc_final: 0.7901 (t0) REVERT: B 194 SER cc_start: 0.9190 (m) cc_final: 0.8987 (m) REVERT: B 291 ARG cc_start: 0.8297 (ttm170) cc_final: 0.8064 (ttm110) REVERT: C 125 SER cc_start: 0.8370 (m) cc_final: 0.8056 (t) REVERT: D 264 LYS cc_start: 0.8445 (tttt) cc_final: 0.8215 (ttpt) REVERT: E 117 MET cc_start: 0.5724 (tpt) cc_final: 0.5468 (mmt) REVERT: E 121 GLU cc_start: 0.7225 (mt-10) cc_final: 0.6983 (mm-30) REVERT: E 127 MET cc_start: 0.5228 (mtp) cc_final: 0.4755 (mtp) REVERT: E 131 TYR cc_start: 0.6722 (p90) cc_final: 0.6160 (p90) REVERT: F 81 LYS cc_start: 0.8080 (mttt) cc_final: 0.7862 (tttt) REVERT: F 225 LYS cc_start: 0.8513 (mttt) cc_final: 0.8257 (mtpp) REVERT: F 249 THR cc_start: 0.8093 (m) cc_final: 0.7714 (p) REVERT: G 192 GLU cc_start: 0.6053 (tt0) cc_final: 0.5703 (mp0) outliers start: 9 outliers final: 7 residues processed: 229 average time/residue: 0.3080 time to fit residues: 102.2713 Evaluate side-chains 220 residues out of total 1603 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 213 time to evaluate : 0.831 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 315 ARG 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 311 THR Chi-restraints excluded: chain E residue 95 VAL Chi-restraints excluded: chain F residue 147 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 191 random chunks: chunk 96 optimal weight: 1.9990 chunk 43 optimal weight: 0.9990 chunk 18 optimal weight: 1.9990 chunk 156 optimal weight: 0.9980 chunk 144 optimal weight: 0.8980 chunk 176 optimal weight: 2.9990 chunk 34 optimal weight: 0.9990 chunk 106 optimal weight: 1.9990 chunk 61 optimal weight: 1.9990 chunk 98 optimal weight: 0.8980 chunk 2 optimal weight: 0.9990 overall best weight: 0.9584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 54 HIS B 99 ASN B 324 HIS D 79 ASN ** D 286 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 304 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3423 r_free = 0.3423 target = 0.124378 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3035 r_free = 0.3035 target = 0.096264 restraints weight = 64872.778| |-----------------------------------------------------------------------------| r_work (start): 0.2977 rms_B_bonded: 1.74 r_work: 0.2821 rms_B_bonded: 2.26 restraints_weight: 0.5000 r_work: 0.2709 rms_B_bonded: 3.76 restraints_weight: 0.2500 r_work (final): 0.2709 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8367 moved from start: 0.3025 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= 0.161 Angle : 0.538 7.872 22091 Z= 0.283 Chirality : 0.041 0.153 2488 Planarity : 0.005 0.059 2739 Dihedral : 14.301 163.314 2597 Min Nonbonded Distance : 1.812 Molprobity Statistics. All-atom Clashscore : 1.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.26 % Favored : 98.74 % Rotamer: Outliers : 0.62 % Allowed : 7.30 % Favored : 92.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.98 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.29 (0.19), residues: 1902 helix: 1.21 (0.16), residues: 1049 sheet: 0.90 (0.30), residues: 276 loop : 0.41 (0.24), residues: 577 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG G 200 TYR 0.011 0.001 TYR C 131 PHE 0.010 0.001 PHE D 70 HIS 0.004 0.001 HIS A 255 Details of bonding type rmsd/Z covalent geometry : bond 0.00370 / 0.16 (16220) covalent geometry : angle 0.53799 / 0.28 (22091) hydrogen bonds : bond 0.05154 / 3.32 ( 822) hydrogen bonds : angle 5.05512 / 3.53 ( 2337) *********************** 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 233 residues out of total 1603 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 223 time to evaluate : 0.843 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 76 MET cc_start: 0.8951 (mmm) cc_final: 0.8314 (mmt) REVERT: A 90 LYS cc_start: 0.8887 (pttt) cc_final: 0.8669 (pttm) REVERT: A 252 ASP cc_start: 0.8189 (t0) cc_final: 0.7937 (t0) REVERT: A 312 ARG cc_start: 0.8187 (mmm160) cc_final: 0.7875 (mmm160) REVERT: B 194 SER cc_start: 0.9199 (m) cc_final: 0.8988 (m) REVERT: B 291 ARG cc_start: 0.8297 (ttm170) cc_final: 0.8062 (ttm110) REVERT: C 125 SER cc_start: 0.8377 (m) cc_final: 0.8079 (t) REVERT: D 264 LYS cc_start: 0.8421 (tttt) cc_final: 0.8146 (ttpt) REVERT: E 127 MET cc_start: 0.5161 (mtp) cc_final: 0.4763 (mtp) REVERT: E 131 TYR cc_start: 0.6742 (p90) cc_final: 0.6198 (p90) REVERT: F 33 LYS cc_start: 0.8318 (mttp) cc_final: 0.8045 (mmtm) REVERT: F 81 LYS cc_start: 0.8141 (mttt) cc_final: 0.7936 (tttt) REVERT: F 225 LYS cc_start: 0.8490 (mttt) cc_final: 0.8219 (mtpp) REVERT: F 249 THR cc_start: 0.8112 (m) cc_final: 0.7748 (p) REVERT: F 267 ARG cc_start: 0.4857 (mtm110) cc_final: 0.4653 (mtm-85) REVERT: G 192 GLU cc_start: 0.6121 (tt0) cc_final: 0.5756 (mp0) outliers start: 10 outliers final: 7 residues processed: 228 average time/residue: 0.3233 time to fit residues: 105.9230 Evaluate side-chains 219 residues out of total 1603 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 212 time to evaluate : 0.862 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 315 ARG 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 311 THR Chi-restraints excluded: chain E residue 95 VAL 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 135 optimal weight: 0.5980 chunk 123 optimal weight: 3.9990 chunk 35 optimal weight: 0.8980 chunk 132 optimal weight: 1.9990 chunk 42 optimal weight: 0.9990 chunk 119 optimal weight: 0.8980 chunk 163 optimal weight: 0.6980 chunk 27 optimal weight: 0.3980 chunk 74 optimal weight: 1.9990 chunk 40 optimal weight: 0.9980 chunk 124 optimal weight: 1.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 99 ASN D 286 ASN F 324 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3432 r_free = 0.3432 target = 0.125135 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3046 r_free = 0.3046 target = 0.096995 restraints weight = 64712.329| |-----------------------------------------------------------------------------| r_work (start): 0.2986 rms_B_bonded: 1.75 r_work: 0.2831 rms_B_bonded: 2.27 restraints_weight: 0.5000 r_work: 0.2719 rms_B_bonded: 3.78 restraints_weight: 0.2500 r_work (final): 0.2719 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8357 moved from start: 0.3159 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= 0.123 Angle : 0.514 7.207 22091 Z= 0.270 Chirality : 0.040 0.147 2488 Planarity : 0.005 0.059 2739 Dihedral : 14.180 152.602 2597 Min Nonbonded Distance : 1.844 Molprobity Statistics. All-atom Clashscore : 1.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.16 % Favored : 98.84 % Rotamer: Outliers : 0.75 % Allowed : 8.17 % Favored : 91.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.98 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.40 (0.19), residues: 1902 helix: 1.33 (0.16), residues: 1048 sheet: 0.84 (0.30), residues: 276 loop : 0.44 (0.24), residues: 578 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 143 TYR 0.016 0.001 TYR C 131 PHE 0.009 0.001 PHE D 70 HIS 0.003 0.001 HIS A 255 Details of bonding type rmsd/Z covalent geometry : bond 0.00271 / 0.12 (16220) covalent geometry : angle 0.51436 / 0.27 (22091) hydrogen bonds : bond 0.04553 / 2.94 ( 822) hydrogen bonds : angle 4.95607 / 3.46 ( 2337) *********************** 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 226 residues out of total 1603 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 214 time to evaluate : 0.798 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 76 MET cc_start: 0.8943 (mmm) cc_final: 0.8318 (mmt) REVERT: A 252 ASP cc_start: 0.8175 (t0) cc_final: 0.7905 (t0) REVERT: B 194 SER cc_start: 0.9195 (m) cc_final: 0.8981 (m) REVERT: B 291 ARG cc_start: 0.8316 (ttm170) cc_final: 0.8071 (ttm110) REVERT: C 125 SER cc_start: 0.8383 (m) cc_final: 0.8081 (t) REVERT: D 264 LYS cc_start: 0.8426 (tttt) cc_final: 0.8145 (ttpt) REVERT: E 68 MET cc_start: 0.8484 (tpt) cc_final: 0.7645 (tpt) REVERT: E 121 GLU cc_start: 0.7302 (mt-10) cc_final: 0.6927 (mm-30) REVERT: E 127 MET cc_start: 0.5324 (mtp) cc_final: 0.4950 (mtp) REVERT: E 131 TYR cc_start: 0.6809 (p90) cc_final: 0.6138 (p90) REVERT: F 33 LYS cc_start: 0.8346 (mttp) cc_final: 0.8049 (mmtm) REVERT: F 81 LYS cc_start: 0.8184 (mttt) cc_final: 0.7886 (tttt) REVERT: F 163 MET cc_start: 0.8675 (mtt) cc_final: 0.8332 (mtt) REVERT: F 225 LYS cc_start: 0.8495 (mttt) cc_final: 0.8232 (mtpp) REVERT: F 249 THR cc_start: 0.8114 (m) cc_final: 0.7746 (p) REVERT: G 192 GLU cc_start: 0.6021 (tt0) cc_final: 0.5686 (mp0) outliers start: 12 outliers final: 9 residues processed: 221 average time/residue: 0.3152 time to fit residues: 100.3416 Evaluate side-chains 219 residues out of total 1603 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 210 time to evaluate : 0.867 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 144 SER Chi-restraints excluded: chain A residue 315 ARG Chi-restraints excluded: chain B residue 163 MET 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 311 THR Chi-restraints excluded: chain E residue 95 VAL Chi-restraints excluded: chain F residue 147 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 191 random chunks: chunk 184 optimal weight: 2.9990 chunk 96 optimal weight: 0.8980 chunk 121 optimal weight: 0.5980 chunk 112 optimal weight: 0.9980 chunk 20 optimal weight: 0.9990 chunk 123 optimal weight: 2.9990 chunk 172 optimal weight: 1.9990 chunk 106 optimal weight: 0.9990 chunk 46 optimal weight: 1.9990 chunk 133 optimal weight: 0.6980 chunk 130 optimal weight: 0.8980 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 99 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3422 r_free = 0.3422 target = 0.124342 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3036 r_free = 0.3036 target = 0.096326 restraints weight = 65205.936| |-----------------------------------------------------------------------------| r_work (start): 0.3003 rms_B_bonded: 1.74 r_work: 0.2848 rms_B_bonded: 2.29 restraints_weight: 0.5000 r_work: 0.2736 rms_B_bonded: 3.82 restraints_weight: 0.2500 r_work (final): 0.2736 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8379 moved from start: 0.3255 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= 0.140 Angle : 0.518 7.379 22091 Z= 0.271 Chirality : 0.040 0.151 2488 Planarity : 0.005 0.058 2739 Dihedral : 14.079 153.356 2597 Min Nonbonded Distance : 1.830 Molprobity Statistics. All-atom Clashscore : 1.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.47 % Favored : 98.53 % Rotamer: Outliers : 0.56 % Allowed : 9.11 % Favored : 90.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.98 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.37 (0.19), residues: 1902 helix: 1.32 (0.16), residues: 1051 sheet: 0.75 (0.31), residues: 268 loop : 0.44 (0.24), residues: 583 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 143 TYR 0.012 0.001 TYR C 131 PHE 0.009 0.001 PHE A 108 HIS 0.004 0.001 HIS A 255 Details of bonding type rmsd/Z covalent geometry : bond 0.00320 / 0.14 (16220) covalent geometry : angle 0.51813 / 0.27 (22091) hydrogen bonds : bond 0.04598 / 2.97 ( 822) hydrogen bonds : angle 4.89840 / 3.41 ( 2337) *********************** 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 223 residues out of total 1603 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 214 time to evaluate : 0.751 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 76 MET cc_start: 0.8927 (mmm) cc_final: 0.8325 (mmt) REVERT: A 252 ASP cc_start: 0.8210 (t0) cc_final: 0.7943 (t0) REVERT: A 312 ARG cc_start: 0.8138 (mmm160) cc_final: 0.7850 (mmm160) REVERT: B 194 SER cc_start: 0.9204 (m) cc_final: 0.8993 (m) REVERT: B 291 ARG cc_start: 0.8336 (ttm170) cc_final: 0.8052 (ttm110) REVERT: C 125 SER cc_start: 0.8384 (m) cc_final: 0.8093 (t) REVERT: D 100 ASP cc_start: 0.7291 (t0) cc_final: 0.7089 (t0) REVERT: D 264 LYS cc_start: 0.8450 (tttt) cc_final: 0.8187 (ttpt) REVERT: E 76 MET cc_start: 0.7948 (mmm) cc_final: 0.7692 (tpt) REVERT: E 121 GLU cc_start: 0.7026 (mt-10) cc_final: 0.6593 (mm-30) REVERT: E 127 MET cc_start: 0.5311 (mtp) cc_final: 0.4909 (mtp) REVERT: E 131 TYR cc_start: 0.6769 (p90) cc_final: 0.6120 (p90) REVERT: F 33 LYS cc_start: 0.8422 (mttp) cc_final: 0.8144 (mmtm) REVERT: F 81 LYS cc_start: 0.8193 (mttt) cc_final: 0.7926 (tttt) REVERT: F 163 MET cc_start: 0.8750 (mtt) cc_final: 0.8429 (mtt) REVERT: F 225 LYS cc_start: 0.8544 (mttt) cc_final: 0.8267 (mtpp) REVERT: F 249 THR cc_start: 0.8121 (m) cc_final: 0.7761 (p) REVERT: F 267 ARG cc_start: 0.4997 (mtm110) cc_final: 0.4664 (mtm-85) REVERT: G 192 GLU cc_start: 0.6082 (tt0) cc_final: 0.5737 (mp0) outliers start: 9 outliers final: 8 residues processed: 218 average time/residue: 0.3062 time to fit residues: 96.3255 Evaluate side-chains 210 residues out of total 1603 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 202 time to evaluate : 0.747 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 144 SER Chi-restraints excluded: chain A residue 315 ARG Chi-restraints excluded: chain B residue 163 MET 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 311 THR Chi-restraints excluded: chain E residue 95 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 191 random chunks: chunk 174 optimal weight: 1.9990 chunk 104 optimal weight: 4.9990 chunk 34 optimal weight: 1.9990 chunk 13 optimal weight: 0.8980 chunk 33 optimal weight: 0.1980 chunk 140 optimal weight: 0.7980 chunk 166 optimal weight: 0.6980 chunk 116 optimal weight: 0.9980 chunk 177 optimal weight: 1.9990 chunk 67 optimal weight: 0.9990 chunk 189 optimal weight: 3.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 99 ASN D 74 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3426 r_free = 0.3426 target = 0.124655 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3042 r_free = 0.3042 target = 0.096713 restraints weight = 64890.564| |-----------------------------------------------------------------------------| r_work (start): 0.3007 rms_B_bonded: 1.73 r_work: 0.2852 rms_B_bonded: 2.29 restraints_weight: 0.5000 r_work: 0.2741 rms_B_bonded: 3.82 restraints_weight: 0.2500 r_work (final): 0.2741 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8383 moved from start: 0.3336 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 16220 Z= 0.125 Angle : 0.510 7.779 22091 Z= 0.266 Chirality : 0.040 0.144 2488 Planarity : 0.005 0.057 2739 Dihedral : 14.041 153.248 2597 Min Nonbonded Distance : 1.844 Molprobity Statistics. All-atom Clashscore : 1.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.16 % Favored : 98.84 % Rotamer: Outliers : 0.62 % Allowed : 9.23 % Favored : 90.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.98 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.44 (0.19), residues: 1902 helix: 1.39 (0.16), residues: 1051 sheet: 0.82 (0.30), residues: 276 loop : 0.40 (0.25), residues: 575 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 315 TYR 0.025 0.001 TYR F 298 PHE 0.008 0.001 PHE D 70 HIS 0.003 0.001 HIS A 255 Details of bonding type rmsd/Z covalent geometry : bond 0.00281 / 0.12 (16220) covalent geometry : angle 0.51023 / 0.27 (22091) hydrogen bonds : bond 0.04359 / 2.82 ( 822) hydrogen bonds : angle 4.85299 / 3.37 ( 2337) *********************** 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 215 residues out of total 1603 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 205 time to evaluate : 0.799 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 76 MET cc_start: 0.8919 (mmm) cc_final: 0.8327 (mmt) REVERT: A 312 ARG cc_start: 0.8149 (mmm160) cc_final: 0.7898 (mmm160) REVERT: B 117 MET cc_start: 0.8202 (tpp) cc_final: 0.7723 (tpp) REVERT: B 194 SER cc_start: 0.9201 (m) cc_final: 0.8992 (m) REVERT: B 291 ARG cc_start: 0.8356 (ttm170) cc_final: 0.8071 (ttm110) REVERT: C 125 SER cc_start: 0.8392 (m) cc_final: 0.8124 (t) REVERT: D 264 LYS cc_start: 0.8457 (tttt) cc_final: 0.8198 (ttpt) REVERT: E 68 MET cc_start: 0.8720 (tpt) cc_final: 0.7724 (tpt) REVERT: E 76 MET cc_start: 0.7938 (mmm) cc_final: 0.7679 (tpt) REVERT: E 121 GLU cc_start: 0.7078 (mt-10) cc_final: 0.6652 (mm-30) REVERT: E 131 TYR cc_start: 0.6750 (p90) cc_final: 0.6115 (p90) REVERT: F 33 LYS cc_start: 0.8416 (mttp) cc_final: 0.8149 (mmtm) REVERT: F 81 LYS cc_start: 0.8217 (mttt) cc_final: 0.7982 (tttt) REVERT: F 163 MET cc_start: 0.8742 (mtt) cc_final: 0.8435 (mtt) REVERT: F 225 LYS cc_start: 0.8540 (mttt) cc_final: 0.8268 (mtpp) REVERT: F 249 THR cc_start: 0.8112 (m) cc_final: 0.7757 (p) REVERT: F 267 ARG cc_start: 0.4996 (mtm110) cc_final: 0.4641 (mtm-85) REVERT: G 192 GLU cc_start: 0.6052 (tt0) cc_final: 0.5714 (mp0) outliers start: 10 outliers final: 10 residues processed: 212 average time/residue: 0.3286 time to fit residues: 100.5182 Evaluate side-chains 211 residues out of total 1603 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 201 time to evaluate : 1.120 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 144 SER Chi-restraints excluded: chain A residue 315 ARG Chi-restraints excluded: chain B residue 163 MET Chi-restraints excluded: chain B residue 204 GLU Chi-restraints excluded: chain C residue 53 ASP Chi-restraints excluded: chain C residue 199 MET 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 G residue 178 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 191 random chunks: chunk 103 optimal weight: 0.9990 chunk 122 optimal weight: 0.9980 chunk 181 optimal weight: 0.6980 chunk 32 optimal weight: 0.7980 chunk 61 optimal weight: 0.9990 chunk 19 optimal weight: 0.9980 chunk 91 optimal weight: 0.8980 chunk 49 optimal weight: 0.9980 chunk 23 optimal weight: 1.9990 chunk 81 optimal weight: 0.9990 chunk 4 optimal weight: 0.4980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 99 ASN D 74 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3425 r_free = 0.3425 target = 0.124572 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3041 r_free = 0.3041 target = 0.096523 restraints weight = 65303.383| |-----------------------------------------------------------------------------| r_work (start): 0.2951 rms_B_bonded: 1.74 r_work: 0.2801 rms_B_bonded: 2.23 restraints_weight: 0.5000 r_work: 0.2690 rms_B_bonded: 3.72 restraints_weight: 0.2500 r_work (final): 0.2690 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8352 moved from start: 0.3360 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.087 16220 Z= 0.135 Angle : 0.716 59.196 22091 Z= 0.403 Chirality : 0.040 0.196 2488 Planarity : 0.005 0.057 2739 Dihedral : 14.040 153.308 2597 Min Nonbonded Distance : 1.842 Molprobity Statistics. All-atom Clashscore : 2.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.21 % Favored : 98.79 % Rotamer: Outliers : 0.56 % Allowed : 9.36 % Favored : 90.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.98 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.43 (0.19), residues: 1902 helix: 1.38 (0.16), residues: 1053 sheet: 0.82 (0.30), residues: 276 loop : 0.40 (0.25), residues: 573 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 315 TYR 0.014 0.001 TYR C 131 PHE 0.018 0.001 PHE E 172 HIS 0.003 0.001 HIS C 146 Details of bonding type rmsd/Z covalent geometry : bond 0.00311 / 0.14 (16220) covalent geometry : angle 0.71563 / 0.40 (22091) hydrogen bonds : bond 0.04379 / 2.83 ( 822) hydrogen bonds : angle 4.85595 / 3.38 ( 2337) *********************** 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 211 residues out of total 1603 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 202 time to evaluate : 0.885 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 312 ARG cc_start: 0.8158 (mmm160) cc_final: 0.7859 (mmm160) REVERT: B 117 MET cc_start: 0.8159 (tpp) cc_final: 0.7665 (tpp) REVERT: B 194 SER cc_start: 0.9199 (m) cc_final: 0.8986 (m) REVERT: B 291 ARG cc_start: 0.8313 (ttm170) cc_final: 0.8014 (ttm110) REVERT: C 125 SER cc_start: 0.8399 (m) cc_final: 0.8107 (t) REVERT: D 264 LYS cc_start: 0.8433 (tttt) cc_final: 0.8154 (ttpt) REVERT: E 68 MET cc_start: 0.8722 (tpt) cc_final: 0.7751 (tpt) REVERT: E 76 MET cc_start: 0.7929 (mmm) cc_final: 0.7674 (tpt) REVERT: E 121 GLU cc_start: 0.7089 (mt-10) cc_final: 0.6637 (mm-30) REVERT: E 131 TYR cc_start: 0.6754 (p90) cc_final: 0.6117 (p90) REVERT: F 33 LYS cc_start: 0.8427 (mttp) cc_final: 0.8140 (mmtm) REVERT: F 81 LYS cc_start: 0.8206 (mttt) cc_final: 0.7915 (tttt) REVERT: F 163 MET cc_start: 0.8716 (mtt) cc_final: 0.8392 (mtt) REVERT: F 225 LYS cc_start: 0.8510 (mttt) cc_final: 0.8230 (mtpp) REVERT: F 249 THR cc_start: 0.8124 (m) cc_final: 0.7753 (p) REVERT: F 267 ARG cc_start: 0.4981 (mtm110) cc_final: 0.4625 (mtm-85) REVERT: G 192 GLU cc_start: 0.6060 (tt0) cc_final: 0.5712 (mp0) outliers start: 9 outliers final: 9 residues processed: 207 average time/residue: 0.3214 time to fit residues: 95.6677 Evaluate side-chains 211 residues out of total 1603 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 202 time to evaluate : 0.819 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 144 SER Chi-restraints excluded: chain A residue 315 ARG Chi-restraints excluded: chain B residue 163 MET Chi-restraints excluded: chain B residue 204 GLU Chi-restraints excluded: chain C residue 53 ASP Chi-restraints excluded: chain C residue 199 MET Chi-restraints excluded: chain C residue 311 THR Chi-restraints excluded: chain E residue 95 VAL 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 177 optimal weight: 2.9990 chunk 51 optimal weight: 0.9980 chunk 76 optimal weight: 0.9980 chunk 48 optimal weight: 0.9990 chunk 40 optimal weight: 0.5980 chunk 63 optimal weight: 0.9990 chunk 68 optimal weight: 0.7980 chunk 83 optimal weight: 0.0570 chunk 97 optimal weight: 50.0000 chunk 0 optimal weight: 0.9990 chunk 116 optimal weight: 0.9990 overall best weight: 0.6898 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 99 ASN D 74 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3425 r_free = 0.3425 target = 0.124599 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3041 r_free = 0.3041 target = 0.096581 restraints weight = 65097.219| |-----------------------------------------------------------------------------| r_work (start): 0.2939 rms_B_bonded: 1.74 r_work: 0.2788 rms_B_bonded: 2.22 restraints_weight: 0.5000 r_work: 0.2677 rms_B_bonded: 3.70 restraints_weight: 0.2500 r_work (final): 0.2677 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8344 moved from start: 0.3363 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.070 16220 Z= 0.132 Angle : 0.714 59.200 22091 Z= 0.400 Chirality : 0.040 0.151 2488 Planarity : 0.005 0.057 2739 Dihedral : 14.039 153.271 2597 Min Nonbonded Distance : 1.842 Molprobity Statistics. All-atom Clashscore : 2.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.21 % Favored : 98.79 % Rotamer: Outliers : 0.50 % Allowed : 9.48 % Favored : 90.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.98 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.43 (0.19), residues: 1902 helix: 1.39 (0.16), residues: 1053 sheet: 0.82 (0.30), residues: 276 loop : 0.40 (0.25), residues: 573 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 315 TYR 0.013 0.001 TYR C 131 PHE 0.007 0.001 PHE D 70 HIS 0.003 0.001 HIS C 146 Details of bonding type rmsd/Z covalent geometry : bond 0.00300 / 0.13 (16220) covalent geometry : angle 0.71447 / 0.40 (22091) hydrogen bonds : bond 0.04368 / 2.82 ( 822) hydrogen bonds : angle 4.85278 / 3.37 ( 2337) ********************** 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 210 residues out of total 1603 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 202 time to evaluate : 0.822 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 312 ARG cc_start: 0.8161 (mmm160) cc_final: 0.7869 (mmm160) REVERT: B 117 MET cc_start: 0.8144 (tpp) cc_final: 0.7648 (tpp) REVERT: B 194 SER cc_start: 0.9194 (m) cc_final: 0.8979 (m) REVERT: B 291 ARG cc_start: 0.8299 (ttm170) cc_final: 0.7999 (ttm110) REVERT: C 125 SER cc_start: 0.8400 (m) cc_final: 0.8103 (t) REVERT: D 264 LYS cc_start: 0.8430 (tttt) cc_final: 0.8145 (ttpt) REVERT: E 68 MET cc_start: 0.8716 (tpt) cc_final: 0.7752 (tpt) REVERT: E 76 MET cc_start: 0.7929 (mmm) cc_final: 0.7672 (tpt) REVERT: E 121 GLU cc_start: 0.7098 (mt-10) cc_final: 0.6634 (mm-30) REVERT: E 131 TYR cc_start: 0.6752 (p90) cc_final: 0.6114 (p90) REVERT: F 33 LYS cc_start: 0.8432 (mttp) cc_final: 0.8140 (mmtm) REVERT: F 81 LYS cc_start: 0.8203 (mttt) cc_final: 0.7901 (tttt) REVERT: F 163 MET cc_start: 0.8706 (mtt) cc_final: 0.8379 (mtt) REVERT: F 225 LYS cc_start: 0.8506 (mttt) cc_final: 0.8225 (mtpp) REVERT: F 249 THR cc_start: 0.8131 (m) cc_final: 0.7755 (p) REVERT: F 267 ARG cc_start: 0.4975 (mtm110) cc_final: 0.4621 (mtm-85) REVERT: G 192 GLU cc_start: 0.6068 (tt0) cc_final: 0.5719 (mp0) outliers start: 8 outliers final: 8 residues processed: 206 average time/residue: 0.3171 time to fit residues: 93.8888 Evaluate side-chains 210 residues out of total 1603 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 202 time to evaluate : 0.805 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 144 SER Chi-restraints excluded: chain A residue 315 ARG Chi-restraints excluded: chain B residue 163 MET Chi-restraints excluded: chain B residue 204 GLU Chi-restraints excluded: chain C residue 53 ASP Chi-restraints excluded: chain C residue 199 MET Chi-restraints excluded: chain C residue 311 THR Chi-restraints excluded: chain E residue 95 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 191 random chunks: chunk 128 optimal weight: 1.9990 chunk 92 optimal weight: 1.9990 chunk 112 optimal weight: 0.9980 chunk 138 optimal weight: 1.9990 chunk 61 optimal weight: 0.9990 chunk 150 optimal weight: 0.9990 chunk 20 optimal weight: 0.9990 chunk 183 optimal weight: 3.9990 chunk 179 optimal weight: 1.9990 chunk 136 optimal weight: 0.6980 chunk 98 optimal weight: 0.2980 overall best weight: 0.7984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 99 ASN D 74 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3426 r_free = 0.3426 target = 0.124661 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3041 r_free = 0.3041 target = 0.096605 restraints weight = 65181.574| |-----------------------------------------------------------------------------| r_work (start): 0.2940 rms_B_bonded: 1.74 r_work: 0.2794 rms_B_bonded: 2.15 restraints_weight: 0.5000 r_work: 0.2684 rms_B_bonded: 3.58 restraints_weight: 0.2500 r_work (final): 0.2684 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8282 moved from start: 0.3365 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.070 16220 Z= 0.132 Angle : 0.714 59.200 22091 Z= 0.400 Chirality : 0.040 0.151 2488 Planarity : 0.005 0.057 2739 Dihedral : 14.039 153.271 2597 Min Nonbonded Distance : 1.842 Molprobity Statistics. All-atom Clashscore : 2.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.21 % Favored : 98.79 % Rotamer: Outliers : 0.50 % Allowed : 9.48 % Favored : 90.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.98 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.43 (0.19), residues: 1902 helix: 1.39 (0.16), residues: 1053 sheet: 0.82 (0.30), residues: 276 loop : 0.40 (0.25), residues: 573 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 315 TYR 0.013 0.001 TYR C 131 PHE 0.007 0.001 PHE D 70 HIS 0.003 0.001 HIS C 146 Details of bonding type rmsd/Z covalent geometry : bond 0.00300 / 0.13 (16220) covalent geometry : angle 0.71447 / 0.40 (22091) hydrogen bonds : bond 0.04368 / 2.82 ( 822) hydrogen bonds : angle 4.85278 / 3.37 ( 2337) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7254.64 seconds wall clock time: 123 minutes 27.89 seconds (7407.89 seconds total)