Starting phenix.real_space_refine on Fri Mar 6 13:52:33 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7pbt_13302/03_2026/7pbt_13302_neut_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/7pbt_13302/03_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 { model { file = "/net/cci-nas-00/data/ceres_data/7pbt_13302/03_2026/7pbt_13302_neut_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7pbt_13302/03_2026/7pbt_13302_neut_trim.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7pbt_13302/03_2026/7pbt_13302.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7pbt_13302/03_2026/7pbt_13302.map" } 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-dev-5986/lib/python3.9/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: 5.68, 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: 2.91 Conformation dependent library (CDL) restraints added in 928.0 milliseconds 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: 5.16 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: 7.62 Time building geometry restraints manager: 3.96 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 - 2.05: 56735 2.05 - 4.09: 517 4.09 - 6.14: 46 6.14 - 8.19: 4 8.19 - 10.24: 5 Bond angle restraints: 57307 Sorted by residual: angle pdb=" OP1 DT V 4 " pdb=" P DT V 4 " pdb=" OP2 DT V 4 " ideal model delta sigma weight residual 120.00 109.76 10.24 3.00e+00 1.11e-01 1.16e+01 angle pdb=" C2' ADP D 600 " pdb=" C3' ADP D 600 " pdb=" C4' ADP D 600 " ideal model delta sigma weight residual 111.00 101.58 9.42 3.00e+00 1.11e-01 9.85e+00 angle pdb=" O3' DT V 3 " pdb=" P DT V 4 " pdb=" OP1 DT V 4 " ideal model delta sigma weight residual 108.00 116.95 -8.95 3.00e+00 1.11e-01 8.91e+00 angle pdb=" C2' ADP F 600 " pdb=" C3' ADP F 600 " pdb=" C4' ADP F 600 " ideal model delta sigma weight residual 111.00 102.64 8.36 3.00e+00 1.11e-01 7.77e+00 angle pdb=" C1' ADP D 600 " pdb=" C2' ADP D 600 " pdb=" C3' ADP D 600 " ideal model delta sigma weight residual 111.00 102.66 8.34 3.00e+00 1.11e-01 7.74e+00 ... (remaining 57302 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 34.57: 14145 34.57 - 69.14: 513 69.14 - 103.72: 16 103.72 - 138.29: 4 138.29 - 172.86: 3 Dihedral angle restraints: 14681 sinusoidal: 8412 harmonic: 6269 Sorted by residual: dihedral pdb=" O2A ADP D 600 " pdb=" O3A ADP D 600 " pdb=" PA ADP D 600 " pdb=" PB ADP D 600 " ideal model delta sinusoidal sigma weight residual 300.00 127.14 172.86 1 2.00e+01 2.50e-03 4.78e+01 dihedral pdb=" O2A ADP E 600 " pdb=" O3A ADP E 600 " pdb=" PA ADP E 600 " pdb=" PB ADP E 600 " ideal model delta sinusoidal sigma weight residual -60.00 99.73 -159.73 1 2.00e+01 2.50e-03 4.65e+01 dihedral pdb=" O2A ADP F 600 " pdb=" O3A ADP F 600 " pdb=" PA ADP F 600 " pdb=" PB ADP F 600 " ideal model delta sinusoidal sigma weight residual -60.00 97.13 -157.12 1 2.00e+01 2.50e-03 4.61e+01 ... (remaining 14678 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.077: 2262 0.077 - 0.154: 229 0.154 - 0.231: 2 0.231 - 0.308: 0 0.308 - 0.385: 1 Chirality restraints: 2494 Sorted by residual: chirality pdb=" P DT V 4 " pdb=" OP1 DT V 4 " pdb=" OP2 DT V 4 " pdb=" O5' DT V 4 " both_signs ideal model delta sigma weight residual True 2.35 -2.73 -0.39 2.00e-01 2.50e+01 3.71e+00 chirality pdb=" CA PRO C 300 " pdb=" N PRO C 300 " pdb=" C PRO C 300 " pdb=" CB PRO C 300 " both_signs ideal model delta sigma weight residual False 2.72 2.55 0.17 2.00e-01 2.50e+01 6.91e-01 chirality pdb=" C3' ADP D 600 " pdb=" C2' ADP D 600 " pdb=" C4' ADP D 600 " pdb=" O3' ADP D 600 " both_signs ideal model delta sigma weight residual False -2.51 -2.67 0.16 2.00e-01 2.50e+01 6.11e-01 ... (remaining 2491 not shown) Planarity restraints: 4586 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG E 312 " -0.061 9.50e-02 1.11e+02 6.10e-02 7.47e+01 pdb=" NE ARG E 312 " -0.049 2.00e-02 2.50e+03 pdb=" CZ ARG E 312 " 0.046 2.00e-02 2.50e+03 pdb=" NH1 ARG E 312 " 0.109 2.00e-02 2.50e+03 pdb=" NH2 ARG E 312 " -0.020 2.00e-02 2.50e+03 pdb="HH11 ARG E 312 " 0.008 2.00e-02 2.50e+03 pdb="HH12 ARG E 312 " -0.111 2.00e-02 2.50e+03 pdb="HH21 ARG E 312 " 0.000 2.00e-02 2.50e+03 pdb="HH22 ARG E 312 " 0.020 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG C 192 " -0.140 9.50e-02 1.11e+02 6.52e-02 4.86e+01 pdb=" NE ARG C 192 " 0.005 2.00e-02 2.50e+03 pdb=" CZ ARG C 192 " -0.009 2.00e-02 2.50e+03 pdb=" NH1 ARG C 192 " -0.053 2.00e-02 2.50e+03 pdb=" NH2 ARG C 192 " 0.077 2.00e-02 2.50e+03 pdb="HH11 ARG C 192 " -0.001 2.00e-02 2.50e+03 pdb="HH12 ARG C 192 " 0.061 2.00e-02 2.50e+03 pdb="HH21 ARG C 192 " 0.003 2.00e-02 2.50e+03 pdb="HH22 ARG C 192 " -0.078 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG B 192 " -0.182 9.50e-02 1.11e+02 7.39e-02 4.40e+01 pdb=" NE ARG B 192 " -0.009 2.00e-02 2.50e+03 pdb=" CZ ARG B 192 " 0.007 2.00e-02 2.50e+03 pdb=" NH1 ARG B 192 " -0.031 2.00e-02 2.50e+03 pdb=" NH2 ARG B 192 " 0.081 2.00e-02 2.50e+03 pdb="HH11 ARG B 192 " -0.001 2.00e-02 2.50e+03 pdb="HH12 ARG B 192 " 0.040 2.00e-02 2.50e+03 pdb="HH21 ARG B 192 " 0.003 2.00e-02 2.50e+03 pdb="HH22 ARG B 192 " -0.083 2.00e-02 2.50e+03 ... (remaining 4583 not shown) Histogram of nonbonded interaction distances: 1.52 - 2.14: 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: 3.200 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.190 Extract box with map and model: 0.440 Check model and map are aligned: 0.090 Set scattering table: 0.080 Process input model: 33.780 Find NCS groups from input model: 0.580 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.160 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 39.570 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7773 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 16220 Z= 0.160 Angle : 0.693 10.235 22091 Z= 0.389 Chirality : 0.044 0.385 2494 Planarity : 0.010 0.136 2739 Dihedral : 14.997 172.861 6269 Min Nonbonded Distance : 1.830 Molprobity Statistics. All-atom Clashscore : 1.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.10 % Favored : 98.90 % Rotamer: Outliers : 0.12 % Allowed : 1.06 % Favored : 98.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.98 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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 covalent geometry : bond 0.00367 (16220) covalent geometry : angle 0.69341 (22091) hydrogen bonds : bond 0.23646 ( 822) hydrogen bonds : angle 8.53527 ( 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 : 0.825 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: 0.3526 time to fit residues: 190.1275 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 : 0.844 ------------------------------------------------------------------------------- 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: 0.9990 chunk 130 optimal weight: 3.9990 chunk 124 optimal weight: 2.9990 chunk 103 optimal weight: 3.9990 chunk 77 optimal weight: 0.9990 chunk 122 optimal weight: 0.2980 chunk 91 optimal weight: 0.9990 chunk 149 optimal weight: 0.5980 overall best weight: 0.7786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.3410 r_free = 0.3410 target = 0.123788 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3006 r_free = 0.3006 target = 0.094719 restraints weight = 64751.978| |-----------------------------------------------------------------------------| r_work (start): 0.2943 rms_B_bonded: 1.77 r_work: 0.2823 rms_B_bonded: 2.05 restraints_weight: 0.5000 r_work: 0.2710 rms_B_bonded: 3.42 restraints_weight: 0.2500 r_work (final): 0.2710 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8221 moved from start: 0.2247 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 16220 Z= 0.168 Angle : 0.618 6.963 22091 Z= 0.331 Chirality : 0.041 0.146 2494 Planarity : 0.005 0.058 2739 Dihedral : 15.085 178.794 2546 Min Nonbonded Distance : 1.794 Molprobity Statistics. All-atom Clashscore : 1.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.53 % Favored : 99.47 % Rotamer: Outliers : 0.56 % Allowed : 5.49 % Favored : 93.95 % 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: 0.96 (0.19), residues: 1902 helix: 0.72 (0.16), residues: 1050 sheet: 1.15 (0.31), residues: 281 loop : 0.51 (0.25), residues: 571 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 143 TYR 0.016 0.001 TYR A 329 PHE 0.009 0.001 PHE A 108 HIS 0.004 0.001 HIS C 146 Details of bonding type rmsd covalent geometry : bond 0.00363 (16220) covalent geometry : angle 0.61761 (22091) hydrogen bonds : bond 0.07003 ( 822) hydrogen bonds : angle 6.06373 ( 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 252 residues out of total 1603 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 243 time to evaluate : 0.715 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 76 MET cc_start: 0.8974 (mmm) cc_final: 0.8364 (mmt) REVERT: A 144 SER cc_start: 0.8563 (p) cc_final: 0.8257 (t) REVERT: A 160 ARG cc_start: 0.7924 (ptp90) cc_final: 0.7656 (ptp-110) REVERT: A 252 ASP cc_start: 0.8067 (t0) cc_final: 0.7762 (t0) REVERT: B 117 MET cc_start: 0.8052 (tpp) cc_final: 0.7717 (tpt) REVERT: B 194 SER cc_start: 0.9154 (m) cc_final: 0.8944 (m) REVERT: B 291 ARG cc_start: 0.8234 (ttm170) cc_final: 0.7953 (ttm110) REVERT: C 125 SER cc_start: 0.8220 (m) cc_final: 0.7819 (t) REVERT: D 146 HIS cc_start: 0.4471 (t-90) cc_final: 0.4119 (t-90) REVERT: D 264 LYS cc_start: 0.8272 (tttt) cc_final: 0.7990 (ttpt) REVERT: D 311 THR cc_start: 0.8063 (m) cc_final: 0.7783 (p) REVERT: E 117 MET cc_start: 0.6021 (tpt) cc_final: 0.5462 (tpp) REVERT: E 121 GLU cc_start: 0.7247 (mt-10) cc_final: 0.6841 (mm-30) REVERT: E 131 TYR cc_start: 0.6745 (p90) cc_final: 0.6118 (p90) REVERT: E 171 ARG cc_start: 0.6824 (mmt-90) cc_final: 0.6466 (tpp-160) REVERT: F 81 LYS cc_start: 0.7965 (mttt) cc_final: 0.7717 (tttt) REVERT: F 135 MET cc_start: 0.8386 (mmm) cc_final: 0.7235 (mmt) REVERT: F 225 LYS cc_start: 0.8507 (mttt) cc_final: 0.8200 (mtpp) REVERT: F 249 THR cc_start: 0.7999 (m) cc_final: 0.7602 (p) outliers start: 9 outliers final: 4 residues processed: 251 average time/residue: 0.3089 time to fit residues: 111.1670 Evaluate side-chains 231 residues out of total 1603 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 227 time to evaluate : 0.665 ------------------------------------------------------------------------------- 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 Chi-restraints excluded: chain G residue 178 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 191 random chunks: chunk 44 optimal weight: 0.9980 chunk 121 optimal weight: 0.7980 chunk 40 optimal weight: 0.9990 chunk 183 optimal weight: 0.9980 chunk 3 optimal weight: 0.9990 chunk 75 optimal weight: 1.9990 chunk 104 optimal weight: 0.8980 chunk 111 optimal weight: 0.7980 chunk 39 optimal weight: 0.5980 chunk 5 optimal weight: 0.8980 chunk 134 optimal weight: 2.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 54 HIS B 99 ASN B 286 ASN B 324 HIS D 79 ASN E 304 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3408 r_free = 0.3408 target = 0.123743 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3001 r_free = 0.3001 target = 0.094457 restraints weight = 64732.937| |-----------------------------------------------------------------------------| r_work (start): 0.2947 rms_B_bonded: 1.80 r_work: 0.2820 rms_B_bonded: 2.16 restraints_weight: 0.5000 r_work: 0.2706 rms_B_bonded: 3.60 restraints_weight: 0.2500 r_work (final): 0.2706 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8236 moved from start: 0.2766 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 16220 Z= 0.147 Angle : 0.544 5.701 22091 Z= 0.288 Chirality : 0.041 0.137 2494 Planarity : 0.005 0.055 2739 Dihedral : 15.101 176.699 2543 Min Nonbonded Distance : 1.798 Molprobity Statistics. All-atom Clashscore : 1.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.21 % Favored : 98.79 % Rotamer: Outliers : 0.81 % Allowed : 5.93 % Favored : 93.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.98 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 1.22 (0.19), residues: 1902 helix: 1.04 (0.16), residues: 1049 sheet: 1.02 (0.31), residues: 276 loop : 0.52 (0.25), residues: 577 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 143 TYR 0.020 0.001 TYR A 322 PHE 0.013 0.001 PHE D 70 HIS 0.004 0.001 HIS C 146 Details of bonding type rmsd covalent geometry : bond 0.00334 (16220) covalent geometry : angle 0.54362 (22091) hydrogen bonds : bond 0.05465 ( 822) hydrogen bonds : angle 5.31133 ( 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 241 residues out of total 1603 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 228 time to evaluate : 0.806 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 76 MET cc_start: 0.8888 (mmm) cc_final: 0.8183 (mmt) REVERT: A 144 SER cc_start: 0.8563 (p) cc_final: 0.8304 (t) REVERT: A 160 ARG cc_start: 0.7851 (ptp90) cc_final: 0.7551 (ptp-110) REVERT: A 252 ASP cc_start: 0.8045 (t0) cc_final: 0.7728 (t0) REVERT: A 312 ARG cc_start: 0.8124 (mmm160) cc_final: 0.7777 (mmm160) REVERT: B 194 SER cc_start: 0.9163 (m) cc_final: 0.8940 (m) REVERT: B 291 ARG cc_start: 0.8235 (ttm170) cc_final: 0.7954 (ttm110) REVERT: C 125 SER cc_start: 0.8366 (m) cc_final: 0.7983 (t) REVERT: D 146 HIS cc_start: 0.4458 (t-90) cc_final: 0.4040 (t-90) REVERT: D 264 LYS cc_start: 0.8340 (tttt) cc_final: 0.8048 (ttpt) REVERT: D 311 THR cc_start: 0.8077 (m) cc_final: 0.7801 (p) REVERT: E 117 MET cc_start: 0.5746 (tpt) cc_final: 0.5310 (mmm) REVERT: E 121 GLU cc_start: 0.7220 (OUTLIER) cc_final: 0.6842 (mm-30) REVERT: E 131 TYR cc_start: 0.6793 (p90) cc_final: 0.6224 (p90) REVERT: E 171 ARG cc_start: 0.6857 (mmt-90) cc_final: 0.6436 (ttm-80) REVERT: F 81 LYS cc_start: 0.8047 (mttt) cc_final: 0.7720 (tttt) REVERT: F 225 LYS cc_start: 0.8463 (mttt) cc_final: 0.8187 (mtpp) REVERT: F 249 THR cc_start: 0.8157 (m) cc_final: 0.7763 (p) REVERT: G 192 GLU cc_start: 0.6110 (tt0) cc_final: 0.5707 (mp0) outliers start: 13 outliers final: 9 residues processed: 235 average time/residue: 0.3275 time to fit residues: 108.7533 Evaluate side-chains 231 residues out of total 1603 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 221 time to evaluate : 0.594 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 315 ARG Chi-restraints excluded: chain B residue 163 MET Chi-restraints excluded: chain C residue 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 E residue 121 GLU Chi-restraints excluded: chain F residue 83 THR Chi-restraints excluded: chain F residue 147 LEU Chi-restraints excluded: chain G residue 178 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 191 random chunks: chunk 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: 0.9980 chunk 129 optimal weight: 0.5980 chunk 61 optimal weight: 1.9990 chunk 120 optimal weight: 0.9980 chunk 184 optimal weight: 3.9990 chunk 107 optimal weight: 1.9990 overall best weight: 0.9180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 99 ASN B 232 GLN D 79 ASN F 324 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3417 r_free = 0.3417 target = 0.123906 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3022 r_free = 0.3022 target = 0.095402 restraints weight = 64602.687| |-----------------------------------------------------------------------------| r_work (start): 0.2916 rms_B_bonded: 1.73 r_work: 0.2787 rms_B_bonded: 2.09 restraints_weight: 0.5000 r_work: 0.2676 rms_B_bonded: 3.49 restraints_weight: 0.2500 r_work (final): 0.2676 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8266 moved from start: 0.3001 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.029 16220 Z= 0.156 Angle : 0.539 6.943 22091 Z= 0.284 Chirality : 0.040 0.142 2494 Planarity : 0.005 0.059 2739 Dihedral : 15.016 163.662 2543 Min Nonbonded Distance : 1.783 Molprobity Statistics. All-atom Clashscore : 1.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.84 % Favored : 99.16 % Rotamer: Outliers : 0.62 % Allowed : 7.55 % Favored : 91.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.98 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 1.23 (0.19), residues: 1902 helix: 1.15 (0.16), residues: 1050 sheet: 0.94 (0.30), residues: 276 loop : 0.36 (0.24), residues: 576 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG G 200 TYR 0.013 0.001 TYR A 273 PHE 0.009 0.001 PHE A 108 HIS 0.004 0.001 HIS A 255 Details of bonding type rmsd covalent geometry : bond 0.00361 (16220) covalent geometry : angle 0.53930 (22091) hydrogen bonds : bond 0.04985 ( 822) hydrogen bonds : angle 5.10853 ( 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 231 residues out of total 1603 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 221 time to evaluate : 0.739 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 76 MET cc_start: 0.8939 (mmm) cc_final: 0.8303 (mmt) REVERT: A 144 SER cc_start: 0.8521 (p) cc_final: 0.8297 (t) REVERT: A 252 ASP cc_start: 0.8152 (t0) cc_final: 0.7894 (t0) REVERT: A 312 ARG cc_start: 0.8218 (mmm160) cc_final: 0.7842 (mmm160) REVERT: B 194 SER cc_start: 0.9200 (m) cc_final: 0.8986 (m) REVERT: B 291 ARG cc_start: 0.8268 (ttm170) cc_final: 0.7983 (ttm110) REVERT: C 125 SER cc_start: 0.8372 (m) cc_final: 0.8053 (t) REVERT: D 264 LYS cc_start: 0.8373 (tttt) cc_final: 0.8085 (ttpt) REVERT: D 311 THR cc_start: 0.8096 (m) cc_final: 0.7851 (p) REVERT: E 131 TYR cc_start: 0.6765 (p90) cc_final: 0.6204 (p90) REVERT: E 171 ARG cc_start: 0.6933 (mmt-90) cc_final: 0.6512 (ttm-80) REVERT: F 33 LYS cc_start: 0.8337 (mttp) cc_final: 0.8056 (mmtm) REVERT: F 81 LYS cc_start: 0.8101 (mttt) cc_final: 0.7810 (tttt) REVERT: F 225 LYS cc_start: 0.8513 (mttt) cc_final: 0.8222 (mtpp) REVERT: F 249 THR cc_start: 0.8107 (m) cc_final: 0.7726 (p) REVERT: G 192 GLU cc_start: 0.6099 (tt0) cc_final: 0.5717 (mp0) outliers start: 10 outliers final: 8 residues processed: 226 average time/residue: 0.3525 time to fit residues: 112.1091 Evaluate side-chains 217 residues out of total 1603 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 209 time to evaluate : 0.758 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 315 ARG Chi-restraints excluded: chain B residue 163 MET Chi-restraints excluded: chain C residue 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 191 random chunks: chunk 96 optimal weight: 0.9980 chunk 43 optimal weight: 2.9990 chunk 18 optimal weight: 0.9990 chunk 156 optimal weight: 0.9990 chunk 144 optimal weight: 1.9990 chunk 176 optimal weight: 1.9990 chunk 34 optimal weight: 1.9990 chunk 106 optimal weight: 0.0570 chunk 61 optimal weight: 0.9990 chunk 98 optimal weight: 1.9990 chunk 2 optimal weight: 0.9980 overall best weight: 0.8102 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 99 ASN ** D 286 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3418 r_free = 0.3418 target = 0.123996 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3028 r_free = 0.3028 target = 0.095830 restraints weight = 64460.107| |-----------------------------------------------------------------------------| r_work (start): 0.2918 rms_B_bonded: 1.79 r_work: 0.2790 rms_B_bonded: 2.06 restraints_weight: 0.5000 r_work: 0.2679 rms_B_bonded: 3.44 restraints_weight: 0.2500 r_work (final): 0.2679 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8266 moved from start: 0.3154 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= 0.139 Angle : 0.522 7.093 22091 Z= 0.273 Chirality : 0.040 0.137 2494 Planarity : 0.005 0.060 2739 Dihedral : 14.886 155.471 2543 Min Nonbonded Distance : 1.789 Molprobity Statistics. All-atom Clashscore : 1.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.21 % Favored : 98.79 % Rotamer: Outliers : 0.62 % Allowed : 8.42 % Favored : 90.95 % 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: 1.33 (0.19), residues: 1902 helix: 1.27 (0.16), residues: 1050 sheet: 0.79 (0.31), residues: 268 loop : 0.42 (0.24), residues: 584 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 143 TYR 0.016 0.001 TYR F 260 PHE 0.009 0.001 PHE D 70 HIS 0.004 0.001 HIS F 324 Details of bonding type rmsd covalent geometry : bond 0.00321 (16220) covalent geometry : angle 0.52182 (22091) hydrogen bonds : bond 0.04694 ( 822) hydrogen bonds : angle 4.98588 ( 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 223 residues out of total 1603 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 213 time to evaluate : 0.858 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 144 SER cc_start: 0.8515 (p) cc_final: 0.8287 (t) REVERT: A 312 ARG cc_start: 0.8171 (mmm160) cc_final: 0.7823 (mmm160) REVERT: B 194 SER cc_start: 0.9195 (m) cc_final: 0.8986 (m) REVERT: B 291 ARG cc_start: 0.8276 (ttm170) cc_final: 0.7977 (ttm110) REVERT: C 105 ASP cc_start: 0.8210 (OUTLIER) cc_final: 0.7924 (m-30) REVERT: C 125 SER cc_start: 0.8379 (m) cc_final: 0.8060 (t) REVERT: D 264 LYS cc_start: 0.8403 (tttt) cc_final: 0.8113 (ttpt) REVERT: D 311 THR cc_start: 0.8013 (m) cc_final: 0.7800 (p) REVERT: E 68 MET cc_start: 0.8286 (tpt) cc_final: 0.7494 (tpt) REVERT: E 76 MET cc_start: 0.7920 (mmm) cc_final: 0.7662 (tpt) REVERT: E 131 TYR cc_start: 0.6830 (p90) cc_final: 0.6157 (p90) REVERT: E 171 ARG cc_start: 0.6937 (mmt-90) cc_final: 0.6662 (ttm170) REVERT: F 33 LYS cc_start: 0.8419 (mttp) cc_final: 0.8080 (mmtm) REVERT: F 81 LYS cc_start: 0.8135 (mttt) cc_final: 0.7793 (tttt) REVERT: F 163 MET cc_start: 0.8684 (mtt) cc_final: 0.8336 (mtt) REVERT: F 225 LYS cc_start: 0.8508 (mttt) cc_final: 0.8215 (mtpp) REVERT: F 249 THR cc_start: 0.8117 (m) cc_final: 0.7731 (p) REVERT: F 267 ARG cc_start: 0.4734 (mtm110) cc_final: 0.4441 (mtm-85) REVERT: G 192 GLU cc_start: 0.6043 (tt0) cc_final: 0.5695 (mp0) outliers start: 10 outliers final: 8 residues processed: 219 average time/residue: 0.3712 time to fit residues: 113.4003 Evaluate side-chains 217 residues out of total 1603 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 208 time to evaluate : 0.799 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 315 ARG Chi-restraints excluded: chain B residue 163 MET Chi-restraints excluded: chain C residue 53 ASP Chi-restraints excluded: chain C residue 105 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 191 random chunks: chunk 135 optimal weight: 0.6980 chunk 123 optimal weight: 2.9990 chunk 35 optimal weight: 0.8980 chunk 132 optimal weight: 0.8980 chunk 42 optimal weight: 0.9980 chunk 119 optimal weight: 0.9980 chunk 163 optimal weight: 0.9980 chunk 27 optimal weight: 1.9990 chunk 74 optimal weight: 0.5980 chunk 40 optimal weight: 0.0980 chunk 124 optimal weight: 1.9990 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 99 ASN D 74 ASN D 286 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3428 r_free = 0.3428 target = 0.124758 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3037 r_free = 0.3037 target = 0.096409 restraints weight = 64753.226| |-----------------------------------------------------------------------------| r_work (start): 0.2947 rms_B_bonded: 1.77 r_work: 0.2824 rms_B_bonded: 2.02 restraints_weight: 0.5000 r_work: 0.2714 rms_B_bonded: 3.39 restraints_weight: 0.2500 r_work (final): 0.2714 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8272 moved from start: 0.3290 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 16220 Z= 0.122 Angle : 0.507 7.045 22091 Z= 0.263 Chirality : 0.039 0.133 2494 Planarity : 0.005 0.059 2739 Dihedral : 14.751 153.888 2543 Min Nonbonded Distance : 1.809 Molprobity Statistics. All-atom Clashscore : 1.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.05 % Favored : 98.95 % Rotamer: Outliers : 0.75 % Allowed : 8.55 % Favored : 90.70 % 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: 1.41 (0.19), residues: 1902 helix: 1.38 (0.16), residues: 1052 sheet: 0.81 (0.30), residues: 276 loop : 0.37 (0.24), residues: 574 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 315 TYR 0.016 0.001 TYR F 298 PHE 0.008 0.001 PHE D 70 HIS 0.003 0.001 HIS B 54 Details of bonding type rmsd covalent geometry : bond 0.00278 (16220) covalent geometry : angle 0.50729 (22091) hydrogen bonds : bond 0.04252 ( 822) hydrogen bonds : angle 4.84482 ( 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 224 residues out of total 1603 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 212 time to evaluate : 0.860 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 252 ASP cc_start: 0.8153 (t0) cc_final: 0.7883 (t0) REVERT: A 312 ARG cc_start: 0.8151 (mmm160) cc_final: 0.7825 (mmm160) REVERT: B 194 SER cc_start: 0.9192 (m) cc_final: 0.8979 (m) REVERT: B 291 ARG cc_start: 0.8300 (ttm170) cc_final: 0.8010 (ttm110) REVERT: C 125 SER cc_start: 0.8386 (m) cc_final: 0.8098 (t) REVERT: D 264 LYS cc_start: 0.8423 (tttt) cc_final: 0.8157 (ttpt) REVERT: E 68 MET cc_start: 0.8399 (tpt) cc_final: 0.7670 (tpt) REVERT: E 76 MET cc_start: 0.7912 (mmm) cc_final: 0.7649 (tpt) REVERT: E 121 GLU cc_start: 0.7114 (OUTLIER) cc_final: 0.6820 (mm-30) REVERT: E 131 TYR cc_start: 0.6777 (p90) cc_final: 0.6138 (p90) REVERT: E 171 ARG cc_start: 0.6866 (mmt-90) cc_final: 0.6448 (ttm-80) REVERT: F 33 LYS cc_start: 0.8403 (mttp) cc_final: 0.8117 (mmtm) REVERT: F 81 LYS cc_start: 0.8176 (mttt) cc_final: 0.7914 (tttt) REVERT: F 163 MET cc_start: 0.8702 (mtt) cc_final: 0.8376 (mtt) REVERT: F 225 LYS cc_start: 0.8495 (mttt) cc_final: 0.8211 (mtpp) REVERT: F 249 THR cc_start: 0.8105 (m) cc_final: 0.7732 (p) REVERT: G 192 GLU cc_start: 0.5953 (tt0) cc_final: 0.5657 (mp0) outliers start: 12 outliers final: 7 residues processed: 219 average time/residue: 0.3489 time to fit residues: 107.6222 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 : 0.800 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 163 MET 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 E residue 121 GLU 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: 1.9990 chunk 96 optimal weight: 0.8980 chunk 121 optimal weight: 0.6980 chunk 112 optimal weight: 0.9990 chunk 20 optimal weight: 0.9980 chunk 123 optimal weight: 2.9990 chunk 172 optimal weight: 2.9990 chunk 106 optimal weight: 1.9990 chunk 46 optimal weight: 1.9990 chunk 133 optimal weight: 3.9990 chunk 130 optimal weight: 0.9990 overall best weight: 0.9184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 99 ASN B 286 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3421 r_free = 0.3421 target = 0.124564 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3048 r_free = 0.3048 target = 0.097435 restraints weight = 65091.885| |-----------------------------------------------------------------------------| r_work (start): 0.2944 rms_B_bonded: 1.67 r_work: 0.2795 rms_B_bonded: 2.14 restraints_weight: 0.5000 r_work: 0.2686 rms_B_bonded: 3.58 restraints_weight: 0.2500 r_work (final): 0.2686 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8291 moved from start: 0.3361 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.026 16220 Z= 0.152 Angle : 0.520 7.259 22091 Z= 0.271 Chirality : 0.040 0.133 2494 Planarity : 0.005 0.059 2739 Dihedral : 14.756 154.733 2543 Min Nonbonded Distance : 1.780 Molprobity Statistics. All-atom Clashscore : 1.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.37 % Favored : 98.63 % Rotamer: Outliers : 0.69 % Allowed : 9.30 % 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: 1.33 (0.19), residues: 1902 helix: 1.31 (0.16), residues: 1054 sheet: 0.82 (0.30), residues: 276 loop : 0.31 (0.24), residues: 572 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 315 TYR 0.016 0.001 TYR F 260 PHE 0.008 0.001 PHE A 108 HIS 0.004 0.001 HIS B 54 Details of bonding type rmsd covalent geometry : bond 0.00354 (16220) covalent geometry : angle 0.52004 (22091) hydrogen bonds : bond 0.04529 ( 822) hydrogen bonds : angle 4.86557 ( 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 222 residues out of total 1603 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 211 time to evaluate : 0.821 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 312 ARG cc_start: 0.8169 (mmm160) cc_final: 0.7908 (mmm160) REVERT: B 194 SER cc_start: 0.9188 (m) cc_final: 0.8984 (m) REVERT: B 291 ARG cc_start: 0.8312 (ttm170) cc_final: 0.8005 (ttm110) REVERT: C 125 SER cc_start: 0.8417 (m) cc_final: 0.8121 (t) REVERT: D 264 LYS cc_start: 0.8456 (tttt) cc_final: 0.8187 (ttpt) REVERT: E 76 MET cc_start: 0.7975 (mmm) cc_final: 0.7719 (tpt) REVERT: E 121 GLU cc_start: 0.7138 (OUTLIER) cc_final: 0.6884 (mm-30) REVERT: E 131 TYR cc_start: 0.6803 (p90) cc_final: 0.6157 (p90) REVERT: E 171 ARG cc_start: 0.6881 (mmt-90) cc_final: 0.6443 (ttm-80) REVERT: F 33 LYS cc_start: 0.8426 (mttp) cc_final: 0.8133 (mmtm) REVERT: F 81 LYS cc_start: 0.8173 (mttt) cc_final: 0.7888 (tttt) REVERT: F 163 MET cc_start: 0.8486 (mtt) cc_final: 0.8180 (mtt) REVERT: F 225 LYS cc_start: 0.8524 (mttt) cc_final: 0.8236 (mtpp) REVERT: F 249 THR cc_start: 0.8196 (m) cc_final: 0.7825 (p) REVERT: G 192 GLU cc_start: 0.6002 (tt0) cc_final: 0.5754 (mp0) outliers start: 11 outliers final: 8 residues processed: 217 average time/residue: 0.3474 time to fit residues: 106.4840 Evaluate side-chains 214 residues out of total 1603 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 205 time to evaluate : 0.839 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 249 THR Chi-restraints excluded: chain B residue 163 MET Chi-restraints excluded: chain B residue 286 ASN 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 E residue 121 GLU Chi-restraints excluded: chain G residue 178 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 191 random chunks: chunk 174 optimal weight: 1.9990 chunk 104 optimal weight: 4.9990 chunk 34 optimal weight: 0.9990 chunk 13 optimal weight: 0.8980 chunk 33 optimal weight: 0.3980 chunk 140 optimal weight: 0.9990 chunk 166 optimal weight: 2.9990 chunk 116 optimal weight: 1.9990 chunk 177 optimal weight: 0.9980 chunk 67 optimal weight: 0.9980 chunk 189 optimal weight: 1.9990 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 74 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3416 r_free = 0.3416 target = 0.123709 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3020 r_free = 0.3020 target = 0.095255 restraints weight = 65175.948| |-----------------------------------------------------------------------------| r_work (start): 0.3000 rms_B_bonded: 1.77 r_work: 0.2875 rms_B_bonded: 2.10 restraints_weight: 0.5000 r_work: 0.2765 rms_B_bonded: 3.51 restraints_weight: 0.2500 r_work (final): 0.2765 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8319 moved from start: 0.3443 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= 0.144 Angle : 0.519 7.425 22091 Z= 0.270 Chirality : 0.040 0.130 2494 Planarity : 0.005 0.060 2739 Dihedral : 14.740 154.691 2543 Min Nonbonded Distance : 1.786 Molprobity Statistics. All-atom Clashscore : 1.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.42 % Favored : 98.58 % Rotamer: Outliers : 0.62 % Allowed : 9.42 % Favored : 89.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.98 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 1.38 (0.19), residues: 1902 helix: 1.33 (0.16), residues: 1053 sheet: 0.77 (0.31), residues: 268 loop : 0.44 (0.25), residues: 581 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 315 TYR 0.014 0.001 TYR C 131 PHE 0.008 0.001 PHE A 108 HIS 0.004 0.001 HIS B 54 Details of bonding type rmsd covalent geometry : bond 0.00335 (16220) covalent geometry : angle 0.51933 (22091) hydrogen bonds : bond 0.04462 ( 822) hydrogen bonds : angle 4.83186 ( 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 218 residues out of total 1603 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 208 time to evaluate : 0.853 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 312 ARG cc_start: 0.8140 (mmm160) cc_final: 0.7885 (mmm160) REVERT: B 291 ARG cc_start: 0.8328 (ttm170) cc_final: 0.8038 (ttm110) REVERT: C 105 ASP cc_start: 0.8182 (OUTLIER) cc_final: 0.7895 (m-30) REVERT: C 125 SER cc_start: 0.8408 (m) cc_final: 0.8132 (t) REVERT: D 264 LYS cc_start: 0.8460 (tttt) cc_final: 0.8214 (ttpt) REVERT: E 68 MET cc_start: 0.8763 (tpt) cc_final: 0.7922 (tpt) REVERT: E 76 MET cc_start: 0.7983 (mmm) cc_final: 0.7724 (tpt) REVERT: E 121 GLU cc_start: 0.7119 (OUTLIER) cc_final: 0.6882 (mm-30) REVERT: E 131 TYR cc_start: 0.6789 (p90) cc_final: 0.6161 (p90) REVERT: E 171 ARG cc_start: 0.6823 (mmt-90) cc_final: 0.6420 (ttm-80) REVERT: F 33 LYS cc_start: 0.8431 (mttp) cc_final: 0.8152 (mmtm) REVERT: F 81 LYS cc_start: 0.8190 (mttt) cc_final: 0.7950 (tttt) REVERT: F 163 MET cc_start: 0.8575 (mtt) cc_final: 0.8293 (mtt) REVERT: F 225 LYS cc_start: 0.8538 (mttt) cc_final: 0.8298 (mtpp) REVERT: F 249 THR cc_start: 0.8164 (m) cc_final: 0.7799 (p) REVERT: G 192 GLU cc_start: 0.5934 (tt0) cc_final: 0.5669 (mp0) outliers start: 10 outliers final: 6 residues processed: 214 average time/residue: 0.3518 time to fit residues: 104.7119 Evaluate side-chains 214 residues out of total 1603 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 206 time to evaluate : 0.798 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 249 THR Chi-restraints excluded: chain B residue 163 MET 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 121 GLU 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: 2.9990 chunk 122 optimal weight: 0.9980 chunk 181 optimal weight: 3.9990 chunk 32 optimal weight: 0.7980 chunk 61 optimal weight: 0.9980 chunk 19 optimal weight: 1.9990 chunk 91 optimal weight: 0.9980 chunk 49 optimal weight: 0.6980 chunk 23 optimal weight: 0.9980 chunk 81 optimal weight: 0.5980 chunk 4 optimal weight: 0.1980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3426 r_free = 0.3426 target = 0.124453 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3032 r_free = 0.3032 target = 0.096083 restraints weight = 65221.015| |-----------------------------------------------------------------------------| r_work (start): 0.2926 rms_B_bonded: 1.76 r_work: 0.2798 rms_B_bonded: 2.08 restraints_weight: 0.5000 r_work: 0.2687 rms_B_bonded: 3.49 restraints_weight: 0.2500 r_work (final): 0.2687 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8270 moved from start: 0.3547 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 16220 Z= 0.123 Angle : 0.502 7.594 22091 Z= 0.260 Chirality : 0.039 0.138 2494 Planarity : 0.005 0.059 2739 Dihedral : 14.664 153.086 2543 Min Nonbonded Distance : 1.810 Molprobity Statistics. All-atom Clashscore : 1.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.37 % Favored : 98.63 % Rotamer: Outliers : 0.56 % Allowed : 9.54 % Favored : 89.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.98 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 1.53 (0.19), residues: 1902 helix: 1.45 (0.16), residues: 1053 sheet: 0.80 (0.31), residues: 268 loop : 0.52 (0.25), residues: 581 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 169 TYR 0.016 0.001 TYR C 131 PHE 0.014 0.001 PHE D 70 HIS 0.003 0.001 HIS B 54 Details of bonding type rmsd covalent geometry : bond 0.00281 (16220) covalent geometry : angle 0.50242 (22091) hydrogen bonds : bond 0.04084 ( 822) hydrogen bonds : angle 4.73151 ( 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 223 residues out of total 1603 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 214 time to evaluate : 0.889 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 312 ARG cc_start: 0.8150 (mmm160) cc_final: 0.7911 (mmm160) REVERT: B 291 ARG cc_start: 0.8298 (ttm170) cc_final: 0.8070 (ttm110) REVERT: C 105 ASP cc_start: 0.8137 (OUTLIER) cc_final: 0.7840 (m-30) REVERT: C 125 SER cc_start: 0.8405 (m) cc_final: 0.8106 (t) REVERT: D 264 LYS cc_start: 0.8436 (tttt) cc_final: 0.8165 (ttpt) REVERT: E 68 MET cc_start: 0.8734 (tpt) cc_final: 0.7886 (tpt) REVERT: E 76 MET cc_start: 0.7995 (mmm) cc_final: 0.7743 (tpt) REVERT: E 121 GLU cc_start: 0.7105 (mt-10) cc_final: 0.6750 (mm-30) REVERT: E 131 TYR cc_start: 0.6904 (p90) cc_final: 0.6310 (p90) REVERT: E 163 MET cc_start: 0.7330 (ttt) cc_final: 0.6903 (ttm) REVERT: E 171 ARG cc_start: 0.6849 (mmt-90) cc_final: 0.6414 (ttm-80) REVERT: F 33 LYS cc_start: 0.8462 (mttp) cc_final: 0.8163 (mmtm) REVERT: F 81 LYS cc_start: 0.8138 (mttt) cc_final: 0.7802 (tttt) REVERT: F 225 LYS cc_start: 0.8455 (mttt) cc_final: 0.8224 (mtpp) REVERT: F 249 THR cc_start: 0.8187 (m) cc_final: 0.7806 (p) REVERT: G 192 GLU cc_start: 0.6111 (tt0) cc_final: 0.5834 (mp0) outliers start: 9 outliers final: 7 residues processed: 220 average time/residue: 0.3288 time to fit residues: 101.9101 Evaluate side-chains 216 residues out of total 1603 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 208 time to evaluate : 0.818 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 249 THR Chi-restraints excluded: chain B residue 163 MET 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 D residue 286 ASN 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: 0.9980 chunk 51 optimal weight: 0.9990 chunk 76 optimal weight: 0.6980 chunk 48 optimal weight: 0.9980 chunk 40 optimal weight: 0.6980 chunk 63 optimal weight: 0.9990 chunk 68 optimal weight: 0.9990 chunk 83 optimal weight: 1.9990 chunk 97 optimal weight: 1.9990 chunk 0 optimal weight: 1.9990 chunk 116 optimal weight: 0.8980 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 82 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3415 r_free = 0.3415 target = 0.123641 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3031 r_free = 0.3031 target = 0.095921 restraints weight = 65170.465| |-----------------------------------------------------------------------------| r_work (start): 0.2989 rms_B_bonded: 1.70 r_work: 0.2838 rms_B_bonded: 2.23 restraints_weight: 0.5000 r_work: 0.2727 rms_B_bonded: 3.72 restraints_weight: 0.2500 r_work (final): 0.2727 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8317 moved from start: 0.3594 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= 0.145 Angle : 0.519 8.579 22091 Z= 0.269 Chirality : 0.040 0.133 2494 Planarity : 0.005 0.058 2739 Dihedral : 14.661 153.790 2543 Min Nonbonded Distance : 1.787 Molprobity Statistics. All-atom Clashscore : 1.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.42 % Favored : 98.58 % Rotamer: Outliers : 0.56 % Allowed : 9.73 % Favored : 89.71 % 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: 1.45 (0.19), residues: 1902 helix: 1.40 (0.16), residues: 1053 sheet: 0.78 (0.31), residues: 268 loop : 0.44 (0.25), residues: 581 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 315 TYR 0.018 0.001 TYR F 260 PHE 0.008 0.001 PHE D 70 HIS 0.004 0.001 HIS B 54 Details of bonding type rmsd covalent geometry : bond 0.00339 (16220) covalent geometry : angle 0.51911 (22091) hydrogen bonds : bond 0.04320 ( 822) hydrogen bonds : angle 4.75249 ( 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 217 residues out of total 1603 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 208 time to evaluate : 0.681 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 312 ARG cc_start: 0.8134 (mmm160) cc_final: 0.7904 (mmm160) REVERT: B 291 ARG cc_start: 0.8363 (ttm170) cc_final: 0.8139 (ttm110) REVERT: C 105 ASP cc_start: 0.8181 (OUTLIER) cc_final: 0.7906 (m-30) REVERT: C 125 SER cc_start: 0.8460 (m) cc_final: 0.8144 (t) REVERT: D 264 LYS cc_start: 0.8470 (tttt) cc_final: 0.8217 (ttpt) REVERT: E 68 MET cc_start: 0.8752 (tpt) cc_final: 0.7929 (tpt) REVERT: E 76 MET cc_start: 0.8021 (mmm) cc_final: 0.7755 (tpt) REVERT: E 121 GLU cc_start: 0.7165 (OUTLIER) cc_final: 0.6828 (mm-30) REVERT: E 131 TYR cc_start: 0.6862 (p90) cc_final: 0.6287 (p90) REVERT: E 163 MET cc_start: 0.7354 (ttt) cc_final: 0.6917 (ttm) REVERT: E 171 ARG cc_start: 0.6857 (mmt-90) cc_final: 0.6434 (ttm-80) REVERT: F 33 LYS cc_start: 0.8480 (mttp) cc_final: 0.8195 (mmtm) REVERT: F 225 LYS cc_start: 0.8498 (mttt) cc_final: 0.8270 (mtpp) REVERT: F 249 THR cc_start: 0.8184 (m) cc_final: 0.7814 (p) REVERT: F 267 ARG cc_start: 0.4810 (mtm110) cc_final: 0.4530 (mtm-85) REVERT: G 192 GLU cc_start: 0.6125 (tt0) cc_final: 0.5852 (mp0) outliers start: 9 outliers final: 6 residues processed: 213 average time/residue: 0.3426 time to fit residues: 102.8400 Evaluate side-chains 216 residues out of total 1603 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 208 time to evaluate : 0.646 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 249 THR Chi-restraints excluded: chain B residue 163 MET 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 D residue 286 ASN Chi-restraints excluded: chain E residue 121 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 191 random chunks: chunk 128 optimal weight: 2.9990 chunk 92 optimal weight: 2.9990 chunk 112 optimal weight: 0.9990 chunk 138 optimal weight: 2.9990 chunk 61 optimal weight: 0.9980 chunk 150 optimal weight: 0.9990 chunk 20 optimal weight: 0.9990 chunk 183 optimal weight: 2.9990 chunk 179 optimal weight: 0.5980 chunk 136 optimal weight: 0.9990 chunk 98 optimal weight: 2.9990 overall best weight: 0.9186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3412 r_free = 0.3412 target = 0.123356 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3027 r_free = 0.3027 target = 0.095635 restraints weight = 65387.565| |-----------------------------------------------------------------------------| r_work (start): 0.2922 rms_B_bonded: 1.71 r_work: 0.2773 rms_B_bonded: 2.17 restraints_weight: 0.5000 r_work: 0.2661 rms_B_bonded: 3.62 restraints_weight: 0.2500 r_work (final): 0.2661 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8286 moved from start: 0.3662 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 16220 Z= 0.148 Angle : 0.522 8.226 22091 Z= 0.270 Chirality : 0.040 0.133 2494 Planarity : 0.005 0.058 2739 Dihedral : 14.682 155.114 2543 Min Nonbonded Distance : 1.792 Molprobity Statistics. All-atom Clashscore : 1.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.63 % Favored : 98.37 % Rotamer: Outliers : 0.69 % Allowed : 9.54 % Favored : 89.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.98 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 1.41 (0.19), residues: 1902 helix: 1.38 (0.16), residues: 1053 sheet: 0.73 (0.31), residues: 268 loop : 0.42 (0.25), residues: 581 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 315 TYR 0.016 0.001 TYR C 131 PHE 0.015 0.001 PHE D 70 HIS 0.004 0.001 HIS B 54 Details of bonding type rmsd covalent geometry : bond 0.00349 (16220) covalent geometry : angle 0.52202 (22091) hydrogen bonds : bond 0.04416 ( 822) hydrogen bonds : angle 4.76917 ( 2337) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7706.32 seconds wall clock time: 131 minutes 2.31 seconds (7862.31 seconds total)