Starting phenix.real_space_refine on Mon Jul 6 00:33:16 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7pbt_13302/07_2026/7pbt_13302_neut_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/7pbt_13302/07_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_13302/07_2026/7pbt_13302_neut_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7pbt_13302/07_2026/7pbt_13302_neut_trim.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7pbt_13302/07_2026/7pbt_13302.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7pbt_13302/07_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): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 31318 Number of models: 1 Model: "" Number of chains: 15 Chain: "A" Number of atoms: 4910 Number of conformers: 1 Conformer: "" Number of residues, atoms: 312, 4910 Classifications: {'peptide': 312} Modifications used: {'NH1NOTPRO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 13, 'TRANS': 297} Chain: "B" Number of atoms: 4910 Number of conformers: 1 Conformer: "" Number of residues, atoms: 312, 4910 Classifications: {'peptide': 312} Modifications used: {'NH1NOTPRO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 13, 'TRANS': 297} Chain: "C" Number of atoms: 4895 Number of conformers: 1 Conformer: "" Number of residues, atoms: 309, 4895 Classifications: {'peptide': 309} Modifications used: {'NH1NOTPRO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 13, 'TRANS': 294} Chain breaks: 1 Chain: "D" Number of atoms: 4934 Number of conformers: 1 Conformer: "" Number of residues, atoms: 313, 4934 Classifications: {'peptide': 313} Modifications used: {'NH1NOTPRO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 13, 'TRANS': 298} Chain: "E" Number of atoms: 4910 Number of conformers: 1 Conformer: "" Number of residues, atoms: 312, 4910 Classifications: {'peptide': 312} Modifications used: {'NH1NOTPRO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 13, 'TRANS': 297} Chain: "F" Number of atoms: 4910 Number of conformers: 1 Conformer: "" Number of residues, atoms: 312, 4910 Classifications: {'peptide': 312} Modifications used: {'NH1NOTPRO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 13, 'TRANS': 297} Chain: "G" Number of atoms: 719 Number of conformers: 1 Conformer: "" Number of residues, atoms: 48, 719 Classifications: {'peptide': 48} Modifications used: {'COO': 1, 'NH1NOTPRO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 45} Chain: "U" Number of atoms: 479 Number of conformers: 1 Conformer: "" Number of residues, atoms: 15, 479 Classifications: {'DNA': 15} Link IDs: {'rna3p': 14} Chain: "V" Number of atoms: 474 Number of conformers: 1 Conformer: "" Number of residues, atoms: 15, 474 Classifications: {'DNA': 15} Modifications used: {'3*END': 1} Link IDs: {'rna3p': 14} Chain: "A" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'AGS': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'AGS': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "C" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'AGS': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "D" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Chain: "E" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Chain: "F" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Time building chain proxies: 5.18, per 1000 atoms: 0.17 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: 2.36 Conformation dependent library (CDL) restraints added in 872.5 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: 4.96 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: 7.16 Time building geometry restraints manager: 3.28 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.83 - 1.05: 15439 1.05 - 1.28: 2655 1.28 - 1.50: 6668 1.50 - 1.72: 6700 1.72 - 1.94: 197 Bond restraints: 31659 Sorted by residual: bond pdb=" N THR E 19 " pdb=" H1 THR E 19 " ideal model delta sigma weight residual 0.960 0.859 0.101 2.00e-02 2.50e+03 2.55e+01 bond pdb=" N SER G 156 " pdb=" H1 SER G 156 " ideal model delta sigma weight residual 0.960 0.860 0.100 2.00e-02 2.50e+03 2.52e+01 bond pdb=" N THR B 19 " pdb=" H1 THR B 19 " ideal model delta sigma weight residual 0.960 0.860 0.100 2.00e-02 2.50e+03 2.50e+01 bond pdb=" N THR D 19 " pdb=" H1 THR D 19 " ideal model delta sigma weight residual 0.960 0.860 0.100 2.00e-02 2.50e+03 2.50e+01 bond pdb=" N THR F 19 " pdb=" H1 THR F 19 " ideal model delta sigma weight residual 0.960 0.860 0.100 2.00e-02 2.50e+03 2.48e+01 ... (remaining 31654 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.10: 56702 2.10 - 4.21: 523 4.21 - 6.31: 52 6.31 - 8.42: 19 8.42 - 10.52: 11 Bond angle restraints: 57307 Sorted by residual: angle pdb=" O4' DA V 11 " pdb=" C1' DA V 11 " pdb=" N9 DA V 11 " ideal model delta sigma weight residual 108.00 111.05 -3.05 7.00e-01 2.04e+00 1.90e+01 angle pdb=" C4' DC V 8 " pdb=" O4' DC V 8 " pdb=" C1' DC V 8 " ideal model delta sigma weight residual 110.10 105.83 4.27 1.00e+00 1.00e+00 1.82e+01 angle pdb=" N3 DT V 3 " pdb=" C4 DT V 3 " pdb=" O4 DT V 3 " ideal model delta sigma weight residual 119.90 122.40 -2.50 6.00e-01 2.78e+00 1.74e+01 angle pdb=" N3 DT U 6 " pdb=" C4 DT U 6 " pdb=" O4 DT U 6 " ideal model delta sigma weight residual 119.90 122.35 -2.45 6.00e-01 2.78e+00 1.67e+01 angle pdb=" N3 DT V 4 " pdb=" C4 DT V 4 " pdb=" O4 DT V 4 " ideal model delta sigma weight residual 119.90 122.34 -2.44 6.00e-01 2.78e+00 1.66e+01 ... (remaining 57302 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 34.57: 14162 34.57 - 69.14: 543 69.14 - 103.72: 26 103.72 - 138.29: 1 138.29 - 172.86: 3 Dihedral angle restraints: 14735 sinusoidal: 8466 harmonic: 6269 Sorted by residual: dihedral pdb=" O2A ADP D 600 " pdb=" O3A ADP D 600 " pdb=" PA ADP D 600 " pdb=" PB ADP D 600 " ideal model delta sinusoidal sigma weight residual 300.00 127.14 172.86 1 2.00e+01 2.50e-03 4.78e+01 dihedral pdb=" O2A ADP E 600 " pdb=" O3A ADP E 600 " pdb=" PA ADP E 600 " pdb=" PB ADP E 600 " ideal model delta sinusoidal sigma weight residual -60.00 99.73 -159.73 1 2.00e+01 2.50e-03 4.65e+01 dihedral pdb=" O2A ADP F 600 " pdb=" O3A ADP F 600 " pdb=" PA ADP F 600 " pdb=" PB ADP F 600 " ideal model delta sinusoidal sigma weight residual -60.00 97.13 -157.12 1 2.00e+01 2.50e-03 4.61e+01 ... (remaining 14732 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.079: 2251 0.079 - 0.158: 225 0.158 - 0.237: 8 0.237 - 0.316: 3 0.316 - 0.395: 1 Chirality restraints: 2488 Sorted by residual: chirality pdb=" P DT V 4 " pdb=" OP1 DT V 4 " pdb=" OP2 DT V 4 " pdb=" O5' DT V 4 " both_signs ideal model delta sigma weight residual True 2.34 -2.73 -0.40 2.00e-01 2.50e+01 3.91e+00 chirality pdb=" C3' AGS C 401 " pdb=" C2' AGS C 401 " pdb=" C4' AGS C 401 " pdb=" O3' AGS C 401 " both_signs ideal model delta sigma weight residual False -2.37 -2.62 0.25 2.00e-01 2.50e+01 1.59e+00 chirality pdb=" C3' AGS A 401 " pdb=" C2' AGS A 401 " pdb=" C4' AGS A 401 " pdb=" O3' AGS A 401 " both_signs ideal model delta sigma weight residual False -2.37 -2.62 0.25 2.00e-01 2.50e+01 1.57e+00 ... (remaining 2485 not shown) Planarity restraints: 4586 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG E 312 " -0.061 9.50e-02 1.11e+02 6.10e-02 7.47e+01 pdb=" NE ARG E 312 " -0.049 2.00e-02 2.50e+03 pdb=" CZ ARG E 312 " 0.046 2.00e-02 2.50e+03 pdb=" NH1 ARG E 312 " 0.109 2.00e-02 2.50e+03 pdb=" NH2 ARG E 312 " -0.020 2.00e-02 2.50e+03 pdb="HH11 ARG E 312 " 0.008 2.00e-02 2.50e+03 pdb="HH12 ARG E 312 " -0.111 2.00e-02 2.50e+03 pdb="HH21 ARG E 312 " 0.000 2.00e-02 2.50e+03 pdb="HH22 ARG E 312 " 0.020 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG C 192 " -0.140 9.50e-02 1.11e+02 6.52e-02 4.86e+01 pdb=" NE ARG C 192 " 0.005 2.00e-02 2.50e+03 pdb=" CZ ARG C 192 " -0.009 2.00e-02 2.50e+03 pdb=" NH1 ARG C 192 " -0.053 2.00e-02 2.50e+03 pdb=" NH2 ARG C 192 " 0.077 2.00e-02 2.50e+03 pdb="HH11 ARG C 192 " -0.001 2.00e-02 2.50e+03 pdb="HH12 ARG C 192 " 0.061 2.00e-02 2.50e+03 pdb="HH21 ARG C 192 " 0.003 2.00e-02 2.50e+03 pdb="HH22 ARG C 192 " -0.078 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG B 192 " -0.182 9.50e-02 1.11e+02 7.39e-02 4.40e+01 pdb=" NE ARG B 192 " -0.009 2.00e-02 2.50e+03 pdb=" CZ ARG B 192 " 0.007 2.00e-02 2.50e+03 pdb=" NH1 ARG B 192 " -0.031 2.00e-02 2.50e+03 pdb=" NH2 ARG B 192 " 0.081 2.00e-02 2.50e+03 pdb="HH11 ARG B 192 " -0.001 2.00e-02 2.50e+03 pdb="HH12 ARG B 192 " 0.040 2.00e-02 2.50e+03 pdb="HH21 ARG B 192 " 0.003 2.00e-02 2.50e+03 pdb="HH22 ARG B 192 " -0.083 2.00e-02 2.50e+03 ... (remaining 4583 not shown) Histogram of nonbonded interaction distances: 1.52 - 2.14: 784 2.14 - 2.75: 56728 2.75 - 3.37: 84420 3.37 - 3.98: 108764 3.98 - 4.60: 175045 Nonbonded interactions: 425741 Sorted by model distance: nonbonded pdb=" OE2 GLU C 299 " pdb="HH11 ARG C 315 " model vdw 1.524 2.450 nonbonded pdb=" HH TYR A 273 " pdb=" OD1 ASN A 286 " model vdw 1.526 2.450 nonbonded pdb=" O PHE D 172 " pdb="HH12 ARG E 222 " model vdw 1.545 2.450 nonbonded pdb=" OD1 ASP D 240 " pdb=" H ILE D 243 " model vdw 1.554 2.450 nonbonded pdb=" HG1 THR A 311 " pdb=" O GLY A 314 " model vdw 1.557 2.450 ... (remaining 425736 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 19 through 136 or resid 141 through 330)) selection = (chain 'B' and (resid 19 through 136 or resid 141 through 330)) selection = (chain 'C' and resid 19 through 330) selection = (chain 'D' and (resid 19 through 136 or resid 141 through 330)) selection = (chain 'E' and (resid 19 through 136 or resid 141 through 330)) selection = (chain 'F' and (resid 19 through 136 or resid 141 through 330)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.210 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: 0.180 Extract box with map and model: 0.450 Check model and map are aligned: 0.080 Set scattering table: 0.080 Process input model: 31.600 Find NCS groups from input model: 0.680 Set up NCS constraints: 0.060 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: 0.000 Load rotamer database and sin/cos tables:1.120 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 37.460 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7872 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.097 16220 Z= 0.251 Angle : 0.767 10.523 22091 Z= 0.435 Chirality : 0.047 0.395 2488 Planarity : 0.010 0.136 2739 Dihedral : 15.637 172.861 6323 Min Nonbonded Distance : 1.830 Molprobity Statistics. All-atom Clashscore : 1.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.10 % Favored : 98.90 % Rotamer: Outliers : 0.12 % Allowed : 1.06 % Favored : 98.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.98 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.27 (0.18), residues: 1902 helix: -0.47 (0.15), residues: 1018 sheet: 0.56 (0.29), residues: 335 loop : 0.39 (0.26), residues: 549 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.025 0.003 ARG D 310 TYR 0.031 0.005 TYR D 273 PHE 0.017 0.003 PHE C 108 HIS 0.011 0.003 HIS B 54 Details of bonding type rmsd/Z covalent geometry : bond 0.00461 / 0.25 (16220) covalent geometry : angle 0.76669 / 0.43 (22091) hydrogen bonds : bond 0.23646 / 15.46 ( 822) hydrogen bonds : angle 8.53527 / 5.92 ( 2337) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3804 Ramachandran restraints generated. 1902 Oldfield, 0 Emsley, 1902 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3804 Ramachandran restraints generated. 1902 Oldfield, 0 Emsley, 1902 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 389 residues out of total 1603 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 387 time to evaluate : 0.820 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: 0.3169 time to fit residues: 173.6826 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 : 0.528 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 199 MET Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 191 random chunks: chunk 98 optimal weight: 2.9990 chunk 107 optimal weight: 2.9990 chunk 10 optimal weight: 0.9990 chunk 66 optimal weight: 0.6980 chunk 130 optimal weight: 3.9990 chunk 124 optimal weight: 2.9990 chunk 103 optimal weight: 3.9990 chunk 77 optimal weight: 0.9980 chunk 122 optimal weight: 0.2980 chunk 91 optimal weight: 0.9990 chunk 149 optimal weight: 0.5980 overall best weight: 0.7182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 99 ASN D 74 ASN D 113 HIS D 221 ASN E 304 GLN F 82 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3405 r_free = 0.3405 target = 0.123449 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3000 r_free = 0.3000 target = 0.094221 restraints weight = 64783.744| |-----------------------------------------------------------------------------| r_work (start): 0.2923 rms_B_bonded: 1.88 r_work: 0.2802 rms_B_bonded: 2.08 restraints_weight: 0.5000 r_work: 0.2688 rms_B_bonded: 3.47 restraints_weight: 0.2500 r_work (final): 0.2688 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8242 moved from start: 0.2130 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 16220 Z= 0.170 Angle : 0.637 6.629 22091 Z= 0.346 Chirality : 0.042 0.154 2488 Planarity : 0.006 0.069 2739 Dihedral : 15.395 177.967 2600 Min Nonbonded Distance : 1.809 Molprobity Statistics. All-atom Clashscore : 1.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.42 % Favored : 99.58 % Rotamer: Outliers : 0.44 % Allowed : 5.30 % Favored : 94.26 % 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: 0.90 (0.19), residues: 1902 helix: 0.66 (0.16), residues: 1045 sheet: 1.16 (0.31), residues: 281 loop : 0.47 (0.25), residues: 576 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 48 TYR 0.014 0.001 TYR C 131 PHE 0.008 0.001 PHE E 58 HIS 0.004 0.001 HIS C 146 Details of bonding type rmsd/Z covalent geometry : bond 0.00357 / 0.17 (16220) covalent geometry : angle 0.63728 / 0.35 (22091) hydrogen bonds : bond 0.07875 / 5.12 ( 822) hydrogen bonds : angle 6.32408 / 4.43 ( 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: 7 poor density : 245 time to evaluate : 0.627 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 76 MET cc_start: 0.8966 (mmm) cc_final: 0.8408 (mmt) REVERT: A 144 SER cc_start: 0.8555 (p) cc_final: 0.8223 (t) REVERT: A 160 ARG cc_start: 0.7910 (ptp90) cc_final: 0.7596 (ptp-110) REVERT: A 252 ASP cc_start: 0.8045 (t0) cc_final: 0.7739 (t0) REVERT: B 117 MET cc_start: 0.8044 (tpp) cc_final: 0.7444 (tpp) REVERT: B 194 SER cc_start: 0.9115 (m) cc_final: 0.8888 (m) REVERT: B 291 ARG cc_start: 0.8163 (ttm170) cc_final: 0.7860 (ttm110) REVERT: C 115 MET cc_start: 0.8852 (mtm) cc_final: 0.8642 (mtm) REVERT: C 117 MET cc_start: 0.8470 (tpt) cc_final: 0.8179 (tpt) REVERT: C 125 SER cc_start: 0.8167 (m) cc_final: 0.7738 (t) REVERT: D 79 ASN cc_start: 0.8104 (m-40) cc_final: 0.7758 (m-40) REVERT: D 146 HIS cc_start: 0.4423 (t-90) cc_final: 0.4112 (t-90) REVERT: D 264 LYS cc_start: 0.8169 (tttt) cc_final: 0.7883 (ttpt) REVERT: D 311 THR cc_start: 0.7966 (m) cc_final: 0.7676 (p) REVERT: E 117 MET cc_start: 0.6051 (tpt) cc_final: 0.5748 (tpp) REVERT: E 121 GLU cc_start: 0.7212 (mt-10) cc_final: 0.6804 (mm-30) REVERT: E 127 MET cc_start: 0.5022 (mtp) cc_final: 0.4815 (mtp) REVERT: E 131 TYR cc_start: 0.6778 (p90) cc_final: 0.6147 (p90) REVERT: E 171 ARG cc_start: 0.6864 (mmt-90) cc_final: 0.6500 (tpp-160) REVERT: F 81 LYS cc_start: 0.7953 (mttt) cc_final: 0.7601 (tttt) REVERT: F 225 LYS cc_start: 0.8471 (mttt) cc_final: 0.8166 (mtpp) REVERT: F 249 THR cc_start: 0.7987 (m) cc_final: 0.7574 (p) outliers start: 7 outliers final: 4 residues processed: 251 average time/residue: 0.2854 time to fit residues: 104.0376 Evaluate side-chains 234 residues out of total 1603 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 230 time to evaluate : 0.737 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 53 ASP Chi-restraints excluded: chain C residue 105 ASP Chi-restraints excluded: chain E residue 95 VAL Chi-restraints excluded: chain F residue 147 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 191 random chunks: chunk 44 optimal weight: 0.0270 chunk 121 optimal weight: 0.5980 chunk 40 optimal weight: 0.7980 chunk 183 optimal weight: 3.9990 chunk 3 optimal weight: 1.9990 chunk 75 optimal weight: 1.9990 chunk 104 optimal weight: 0.9990 chunk 111 optimal weight: 0.6980 chunk 39 optimal weight: 0.7980 chunk 5 optimal weight: 0.5980 chunk 134 optimal weight: 2.9990 overall best weight: 0.5438 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 99 ASN B 286 ASN D 286 ASN E 304 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3422 r_free = 0.3422 target = 0.124900 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3034 r_free = 0.3034 target = 0.096648 restraints weight = 64495.805| |-----------------------------------------------------------------------------| r_work (start): 0.2971 rms_B_bonded: 1.79 r_work: 0.2828 rms_B_bonded: 2.13 restraints_weight: 0.5000 r_work: 0.2713 rms_B_bonded: 3.55 restraints_weight: 0.2500 r_work (final): 0.2713 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8245 moved from start: 0.2621 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 16220 Z= 0.128 Angle : 0.552 5.958 22091 Z= 0.293 Chirality : 0.041 0.234 2488 Planarity : 0.005 0.053 2739 Dihedral : 14.645 179.368 2597 Min Nonbonded Distance : 1.839 Molprobity Statistics. All-atom Clashscore : 1.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.10 % Favored : 98.90 % Rotamer: Outliers : 0.62 % Allowed : 6.05 % Favored : 93.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.98 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.22 (0.19), residues: 1902 helix: 1.01 (0.16), residues: 1049 sheet: 1.05 (0.31), residues: 280 loop : 0.58 (0.25), residues: 573 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 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 D 113 Details of bonding type rmsd/Z covalent geometry : bond 0.00268 / 0.13 (16220) covalent geometry : angle 0.55217 / 0.29 (22091) hydrogen bonds : bond 0.05748 / 3.71 ( 822) hydrogen bonds : angle 5.45950 / 3.82 ( 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 246 residues out of total 1603 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 236 time to evaluate : 0.642 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 76 MET cc_start: 0.8894 (mmm) cc_final: 0.8251 (mmt) REVERT: A 144 SER cc_start: 0.8596 (p) cc_final: 0.8301 (t) REVERT: A 160 ARG cc_start: 0.7767 (ptp90) cc_final: 0.7428 (ptp-110) REVERT: A 252 ASP cc_start: 0.8082 (t0) cc_final: 0.7771 (t0) REVERT: B 194 SER cc_start: 0.9116 (m) cc_final: 0.8895 (m) REVERT: B 291 ARG cc_start: 0.8220 (ttm170) cc_final: 0.7926 (ttm110) REVERT: C 125 SER cc_start: 0.8300 (m) cc_final: 0.7912 (t) REVERT: D 146 HIS cc_start: 0.4452 (t-90) cc_final: 0.4102 (t-90) REVERT: D 264 LYS cc_start: 0.8318 (tttt) cc_final: 0.8018 (ttpt) REVERT: D 311 THR cc_start: 0.7984 (m) cc_final: 0.7720 (p) REVERT: E 117 MET cc_start: 0.5698 (tpt) cc_final: 0.5346 (mmt) REVERT: E 121 GLU cc_start: 0.7241 (OUTLIER) cc_final: 0.6874 (mm-30) REVERT: E 127 MET cc_start: 0.4915 (mtp) cc_final: 0.4707 (mtp) REVERT: E 131 TYR cc_start: 0.6793 (p90) cc_final: 0.6209 (p90) REVERT: E 171 ARG cc_start: 0.6886 (mmt-90) cc_final: 0.6476 (ttm-80) REVERT: F 81 LYS cc_start: 0.7982 (mttt) cc_final: 0.7673 (tttt) REVERT: F 135 MET cc_start: 0.8386 (tpp) cc_final: 0.7596 (mmt) REVERT: F 225 LYS cc_start: 0.8412 (mttt) cc_final: 0.8134 (mtpp) REVERT: F 249 THR cc_start: 0.8124 (m) cc_final: 0.7714 (p) outliers start: 10 outliers final: 6 residues processed: 243 average time/residue: 0.3068 time to fit residues: 107.9086 Evaluate side-chains 229 residues out of total 1603 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 222 time to evaluate : 0.864 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 315 ARG Chi-restraints excluded: chain C residue 53 ASP Chi-restraints excluded: chain C residue 199 MET Chi-restraints excluded: chain C residue 311 THR Chi-restraints excluded: chain E residue 95 VAL Chi-restraints excluded: chain E residue 121 GLU Chi-restraints excluded: chain F residue 147 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 191 random chunks: chunk 187 optimal weight: 3.9990 chunk 68 optimal weight: 0.9980 chunk 2 optimal weight: 0.9980 chunk 21 optimal weight: 1.9990 chunk 165 optimal weight: 2.9990 chunk 40 optimal weight: 0.8980 chunk 129 optimal weight: 0.9980 chunk 61 optimal weight: 0.8980 chunk 120 optimal weight: 0.7980 chunk 184 optimal weight: 0.3980 chunk 107 optimal weight: 1.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 54 HIS B 99 ASN B 232 GLN D 79 ASN E 304 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3419 r_free = 0.3419 target = 0.124110 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3018 r_free = 0.3018 target = 0.095191 restraints weight = 64503.321| |-----------------------------------------------------------------------------| r_work (start): 0.2945 rms_B_bonded: 1.73 r_work: 0.2816 rms_B_bonded: 2.14 restraints_weight: 0.5000 r_work: 0.2705 rms_B_bonded: 3.57 restraints_weight: 0.2500 r_work (final): 0.2705 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8338 moved from start: 0.2865 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 16220 Z= 0.148 Angle : 0.544 8.181 22091 Z= 0.287 Chirality : 0.040 0.159 2488 Planarity : 0.005 0.057 2739 Dihedral : 14.391 172.703 2597 Min Nonbonded Distance : 1.815 Molprobity Statistics. All-atom Clashscore : 1.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.95 % Favored : 99.05 % Rotamer: Outliers : 0.62 % Allowed : 6.61 % Favored : 92.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.98 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 1.30 (0.19), residues: 1902 helix: 1.16 (0.16), residues: 1049 sheet: 0.97 (0.30), residues: 276 loop : 0.50 (0.24), residues: 577 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 312 TYR 0.020 0.001 TYR A 322 PHE 0.009 0.001 PHE D 70 HIS 0.004 0.001 HIS D 146 Details of bonding type rmsd/Z covalent geometry : bond 0.00332 / 0.15 (16220) covalent geometry : angle 0.54391 / 0.29 (22091) hydrogen bonds : bond 0.05192 / 3.36 ( 822) hydrogen bonds : angle 5.16738 / 3.61 ( 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 234 residues out of total 1603 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 224 time to evaluate : 0.643 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 76 MET cc_start: 0.8966 (mmm) cc_final: 0.8337 (mmt) REVERT: A 252 ASP cc_start: 0.8158 (t0) cc_final: 0.7889 (t0) REVERT: B 194 SER cc_start: 0.9191 (m) cc_final: 0.8973 (m) REVERT: B 291 ARG cc_start: 0.8241 (ttm170) cc_final: 0.7994 (ttm110) REVERT: C 125 SER cc_start: 0.8344 (m) cc_final: 0.8035 (t) REVERT: D 146 HIS cc_start: 0.4381 (t-90) cc_final: 0.4177 (t-90) REVERT: D 264 LYS cc_start: 0.8338 (tttt) cc_final: 0.8058 (ttpt) REVERT: D 311 THR cc_start: 0.8132 (m) cc_final: 0.7900 (p) REVERT: E 117 MET cc_start: 0.5746 (tpt) cc_final: 0.5474 (mmt) REVERT: E 121 GLU cc_start: 0.7326 (mt-10) cc_final: 0.6966 (mm-30) REVERT: E 127 MET cc_start: 0.5175 (mtp) cc_final: 0.4735 (mtp) REVERT: E 131 TYR cc_start: 0.6754 (p90) cc_final: 0.6202 (p90) REVERT: F 81 LYS cc_start: 0.8039 (mttt) cc_final: 0.7772 (tttt) REVERT: F 225 LYS cc_start: 0.8513 (mttt) cc_final: 0.8246 (mtpp) REVERT: F 249 THR cc_start: 0.8112 (m) cc_final: 0.7722 (p) REVERT: G 192 GLU cc_start: 0.6056 (tt0) cc_final: 0.5690 (mp0) outliers start: 10 outliers final: 9 residues processed: 230 average time/residue: 0.3093 time to fit residues: 101.9634 Evaluate side-chains 225 residues out of total 1603 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 216 time to evaluate : 0.638 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 315 ARG Chi-restraints excluded: chain B residue 204 GLU Chi-restraints excluded: chain C residue 53 ASP Chi-restraints excluded: chain C residue 132 ILE Chi-restraints excluded: chain C residue 199 MET Chi-restraints excluded: chain C residue 311 THR Chi-restraints excluded: chain E residue 95 VAL Chi-restraints excluded: chain F residue 147 LEU 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: 1.9990 chunk 43 optimal weight: 0.9990 chunk 18 optimal weight: 1.9990 chunk 156 optimal weight: 0.9990 chunk 144 optimal weight: 0.7980 chunk 176 optimal weight: 0.3980 chunk 34 optimal weight: 0.9980 chunk 106 optimal weight: 0.6980 chunk 61 optimal weight: 1.9990 chunk 98 optimal weight: 0.2980 chunk 2 optimal weight: 0.9990 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 99 ASN D 79 ASN E 304 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3439 r_free = 0.3439 target = 0.125641 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3053 r_free = 0.3053 target = 0.097443 restraints weight = 64722.358| |-----------------------------------------------------------------------------| r_work (start): 0.3002 rms_B_bonded: 1.75 r_work: 0.2847 rms_B_bonded: 2.30 restraints_weight: 0.5000 r_work: 0.2733 rms_B_bonded: 3.84 restraints_weight: 0.2500 r_work (final): 0.2733 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8367 moved from start: 0.3049 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= 0.118 Angle : 0.509 7.492 22091 Z= 0.268 Chirality : 0.040 0.145 2488 Planarity : 0.005 0.058 2739 Dihedral : 14.257 162.815 2597 Min Nonbonded Distance : 1.853 Molprobity Statistics. All-atom Clashscore : 1.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.21 % Favored : 98.79 % Rotamer: Outliers : 0.56 % Allowed : 7.67 % Favored : 91.77 % 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: 1.43 (0.19), residues: 1902 helix: 1.31 (0.16), residues: 1050 sheet: 0.92 (0.30), residues: 276 loop : 0.51 (0.24), residues: 576 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG G 200 TYR 0.012 0.001 TYR C 131 PHE 0.010 0.001 PHE D 70 HIS 0.003 0.001 HIS A 255 Details of bonding type rmsd/Z covalent geometry : bond 0.00257 / 0.12 (16220) covalent geometry : angle 0.50927 / 0.27 (22091) hydrogen bonds : bond 0.04611 / 2.98 ( 822) hydrogen bonds : angle 4.97300 / 3.47 ( 2337) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3804 Ramachandran restraints generated. 1902 Oldfield, 0 Emsley, 1902 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3804 Ramachandran restraints generated. 1902 Oldfield, 0 Emsley, 1902 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 233 residues out of total 1603 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 224 time to evaluate : 0.961 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 76 MET cc_start: 0.8953 (mmm) cc_final: 0.8343 (mmt) REVERT: A 90 LYS cc_start: 0.8901 (pttt) cc_final: 0.8694 (pttm) REVERT: A 252 ASP cc_start: 0.8165 (t0) cc_final: 0.7909 (t0) REVERT: A 312 ARG cc_start: 0.8090 (mmm160) cc_final: 0.7819 (mmm160) REVERT: B 194 SER cc_start: 0.9202 (m) cc_final: 0.8995 (m) REVERT: B 291 ARG cc_start: 0.8298 (ttm170) cc_final: 0.8077 (ttm110) REVERT: C 105 ASP cc_start: 0.8257 (OUTLIER) cc_final: 0.7987 (m-30) REVERT: C 125 SER cc_start: 0.8371 (m) cc_final: 0.8084 (t) REVERT: D 264 LYS cc_start: 0.8430 (tttt) cc_final: 0.8170 (ttpt) REVERT: E 127 MET cc_start: 0.5279 (mtp) cc_final: 0.4851 (mtp) REVERT: E 131 TYR cc_start: 0.6707 (p90) cc_final: 0.6170 (p90) REVERT: F 33 LYS cc_start: 0.8299 (mttp) cc_final: 0.8014 (mmtm) REVERT: F 163 MET cc_start: 0.8663 (mtt) cc_final: 0.8330 (mtt) REVERT: F 225 LYS cc_start: 0.8512 (mttt) cc_final: 0.8256 (mtpp) REVERT: F 249 THR cc_start: 0.8111 (m) cc_final: 0.7734 (p) REVERT: F 267 ARG cc_start: 0.4911 (mtm110) cc_final: 0.4637 (mtm-85) REVERT: G 192 GLU cc_start: 0.6108 (tt0) cc_final: 0.5772 (mp0) outliers start: 9 outliers final: 7 residues processed: 229 average time/residue: 0.3277 time to fit residues: 106.9037 Evaluate side-chains 221 residues out of total 1603 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 213 time to evaluate : 0.850 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 315 ARG Chi-restraints excluded: chain B residue 204 GLU Chi-restraints excluded: chain C residue 53 ASP Chi-restraints excluded: chain C residue 105 ASP Chi-restraints excluded: chain C residue 199 MET Chi-restraints excluded: chain C residue 311 THR Chi-restraints excluded: chain E residue 95 VAL Chi-restraints excluded: chain 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: 3.9990 chunk 123 optimal weight: 2.9990 chunk 35 optimal weight: 0.9980 chunk 132 optimal weight: 2.9990 chunk 42 optimal weight: 0.8980 chunk 119 optimal weight: 0.8980 chunk 163 optimal weight: 0.9990 chunk 27 optimal weight: 1.9990 chunk 74 optimal weight: 1.9990 chunk 40 optimal weight: 0.9980 chunk 124 optimal weight: 1.9990 overall best weight: 0.9582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 99 ASN D 79 ASN F 324 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3427 r_free = 0.3427 target = 0.125002 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3049 r_free = 0.3049 target = 0.097371 restraints weight = 64433.198| |-----------------------------------------------------------------------------| r_work (start): 0.2935 rms_B_bonded: 1.70 r_work: 0.2782 rms_B_bonded: 2.19 restraints_weight: 0.5000 r_work: 0.2670 rms_B_bonded: 3.65 restraints_weight: 0.2500 r_work (final): 0.2670 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8342 moved from start: 0.3169 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 16220 Z= 0.160 Angle : 0.530 7.441 22091 Z= 0.278 Chirality : 0.040 0.150 2488 Planarity : 0.005 0.059 2739 Dihedral : 14.188 152.764 2597 Min Nonbonded Distance : 1.823 Molprobity Statistics. All-atom Clashscore : 1.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.10 % Favored : 98.90 % Rotamer: Outliers : 0.75 % Allowed : 8.42 % Favored : 90.83 % 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: 1.35 (0.19), residues: 1902 helix: 1.28 (0.16), residues: 1050 sheet: 0.76 (0.31), residues: 268 loop : 0.48 (0.24), residues: 584 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 315 TYR 0.015 0.001 TYR F 260 PHE 0.009 0.001 PHE A 108 HIS 0.004 0.001 HIS A 255 Details of bonding type rmsd/Z covalent geometry : bond 0.00371 / 0.16 (16220) covalent geometry : angle 0.53037 / 0.28 (22091) hydrogen bonds : bond 0.04836 / 3.12 ( 822) hydrogen bonds : angle 4.97319 / 3.47 ( 2337) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3804 Ramachandran restraints generated. 1902 Oldfield, 0 Emsley, 1902 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3804 Ramachandran restraints generated. 1902 Oldfield, 0 Emsley, 1902 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 226 residues out of total 1603 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 214 time to evaluate : 0.784 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 76 MET cc_start: 0.8932 (mmm) cc_final: 0.8315 (mmt) REVERT: A 252 ASP cc_start: 0.8197 (t0) cc_final: 0.7929 (t0) REVERT: A 312 ARG cc_start: 0.8195 (mmm160) cc_final: 0.7910 (mmm160) REVERT: B 194 SER cc_start: 0.9200 (m) cc_final: 0.8985 (m) REVERT: B 291 ARG cc_start: 0.8277 (ttm170) cc_final: 0.8024 (ttm110) REVERT: C 105 ASP cc_start: 0.8209 (OUTLIER) cc_final: 0.7908 (m-30) REVERT: C 125 SER cc_start: 0.8379 (m) cc_final: 0.8063 (t) REVERT: D 264 LYS cc_start: 0.8422 (tttt) cc_final: 0.8134 (ttpt) REVERT: E 68 MET cc_start: 0.8324 (tpt) cc_final: 0.7563 (tpt) REVERT: E 76 MET cc_start: 0.7929 (mmm) cc_final: 0.7682 (tpt) REVERT: E 121 GLU cc_start: 0.7407 (OUTLIER) cc_final: 0.7019 (mm-30) REVERT: E 127 MET cc_start: 0.5306 (mtp) cc_final: 0.4937 (mtp) REVERT: E 131 TYR cc_start: 0.6832 (p90) cc_final: 0.6165 (p90) REVERT: F 33 LYS cc_start: 0.8349 (mttp) cc_final: 0.8040 (mmtm) REVERT: F 163 MET cc_start: 0.8630 (mtt) cc_final: 0.8276 (mtt) REVERT: F 225 LYS cc_start: 0.8501 (mttt) cc_final: 0.8209 (mtpp) REVERT: F 249 THR cc_start: 0.8124 (m) cc_final: 0.7747 (p) REVERT: F 267 ARG cc_start: 0.4747 (mtm110) cc_final: 0.4456 (mtm-85) REVERT: G 192 GLU cc_start: 0.6023 (tt0) cc_final: 0.5689 (mp0) outliers start: 12 outliers final: 10 residues processed: 220 average time/residue: 0.3100 time to fit residues: 97.5332 Evaluate side-chains 222 residues out of total 1603 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 210 time to evaluate : 0.885 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 315 ARG Chi-restraints excluded: chain B residue 163 MET Chi-restraints excluded: chain B residue 204 GLU 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 E residue 121 GLU Chi-restraints excluded: chain F residue 147 LEU Chi-restraints excluded: chain G residue 178 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 191 random chunks: chunk 184 optimal weight: 3.9990 chunk 96 optimal weight: 0.9990 chunk 121 optimal weight: 0.3980 chunk 112 optimal weight: 0.9990 chunk 20 optimal weight: 0.9990 chunk 123 optimal weight: 2.9990 chunk 172 optimal weight: 0.0670 chunk 106 optimal weight: 0.9990 chunk 46 optimal weight: 1.9990 chunk 133 optimal weight: 0.9980 chunk 130 optimal weight: 0.6980 overall best weight: 0.6320 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 99 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3432 r_free = 0.3432 target = 0.125088 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3048 r_free = 0.3048 target = 0.097042 restraints weight = 65218.919| |-----------------------------------------------------------------------------| r_work (start): 0.2946 rms_B_bonded: 1.75 r_work: 0.2792 rms_B_bonded: 2.24 restraints_weight: 0.5000 r_work: 0.2680 rms_B_bonded: 3.73 restraints_weight: 0.2500 r_work (final): 0.2680 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8345 moved from start: 0.3262 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 16220 Z= 0.116 Angle : 0.503 7.178 22091 Z= 0.262 Chirality : 0.039 0.147 2488 Planarity : 0.005 0.058 2739 Dihedral : 14.076 152.757 2597 Min Nonbonded Distance : 1.845 Molprobity Statistics. All-atom Clashscore : 1.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.37 % Favored : 98.63 % Rotamer: Outliers : 0.56 % Allowed : 9.11 % Favored : 90.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.98 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.44 (0.19), residues: 1902 helix: 1.40 (0.16), residues: 1050 sheet: 0.82 (0.30), residues: 276 loop : 0.39 (0.24), residues: 576 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 315 TYR 0.015 0.001 TYR C 131 PHE 0.009 0.001 PHE D 70 HIS 0.003 0.001 HIS F 324 Details of bonding type rmsd/Z covalent geometry : bond 0.00255 / 0.12 (16220) covalent geometry : angle 0.50260 / 0.26 (22091) hydrogen bonds : bond 0.04362 / 2.82 ( 822) hydrogen bonds : angle 4.85815 / 3.39 ( 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 220 residues out of total 1603 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 211 time to evaluate : 0.886 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 76 MET cc_start: 0.8917 (mmm) cc_final: 0.8319 (mmt) REVERT: A 90 LYS cc_start: 0.8884 (pttt) cc_final: 0.8672 (pttm) REVERT: A 252 ASP cc_start: 0.8178 (t0) cc_final: 0.7902 (t0) REVERT: A 312 ARG cc_start: 0.8212 (mmm160) cc_final: 0.7978 (mmm160) REVERT: B 194 SER cc_start: 0.9198 (m) cc_final: 0.8979 (m) REVERT: B 291 ARG cc_start: 0.8294 (ttm170) cc_final: 0.8043 (ttm110) REVERT: C 125 SER cc_start: 0.8383 (m) cc_final: 0.8072 (t) REVERT: D 264 LYS cc_start: 0.8425 (tttt) cc_final: 0.8132 (ttpt) REVERT: E 68 MET cc_start: 0.8412 (tpt) cc_final: 0.7737 (tpt) REVERT: E 76 MET cc_start: 0.7923 (mmm) cc_final: 0.7663 (tpt) REVERT: E 121 GLU cc_start: 0.7217 (mt-10) cc_final: 0.6909 (mm-30) REVERT: E 127 MET cc_start: 0.5185 (mtp) cc_final: 0.4768 (mtp) REVERT: E 131 TYR cc_start: 0.6786 (p90) cc_final: 0.6120 (p90) REVERT: F 163 MET cc_start: 0.8688 (mtt) cc_final: 0.8358 (mtt) REVERT: F 225 LYS cc_start: 0.8477 (mttt) cc_final: 0.8214 (mtpp) REVERT: F 249 THR cc_start: 0.8128 (m) cc_final: 0.7755 (p) REVERT: F 267 ARG cc_start: 0.4749 (mtm110) cc_final: 0.4460 (mtm-85) REVERT: G 192 GLU cc_start: 0.6010 (tt0) cc_final: 0.5686 (mp0) outliers start: 9 outliers final: 7 residues processed: 217 average time/residue: 0.3322 time to fit residues: 103.1697 Evaluate side-chains 209 residues out of total 1603 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 202 time to evaluate : 0.758 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 144 SER Chi-restraints excluded: chain A residue 315 ARG Chi-restraints excluded: chain B residue 204 GLU Chi-restraints excluded: chain C residue 53 ASP Chi-restraints excluded: chain C residue 199 MET Chi-restraints excluded: chain C residue 311 THR Chi-restraints excluded: chain E residue 95 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 191 random chunks: chunk 174 optimal weight: 0.9980 chunk 104 optimal weight: 0.2980 chunk 34 optimal weight: 1.9990 chunk 13 optimal weight: 0.0370 chunk 33 optimal weight: 0.6980 chunk 140 optimal weight: 1.9990 chunk 166 optimal weight: 0.7980 chunk 116 optimal weight: 0.9980 chunk 177 optimal weight: 1.9990 chunk 67 optimal weight: 0.9980 chunk 189 optimal weight: 3.9990 overall best weight: 0.5658 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 99 ASN D 74 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3435 r_free = 0.3435 target = 0.125368 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3054 r_free = 0.3054 target = 0.097387 restraints weight = 64852.923| |-----------------------------------------------------------------------------| r_work (start): 0.2950 rms_B_bonded: 1.75 r_work: 0.2797 rms_B_bonded: 2.23 restraints_weight: 0.5000 r_work: 0.2685 rms_B_bonded: 3.72 restraints_weight: 0.2500 r_work (final): 0.2685 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8340 moved from start: 0.3332 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 16220 Z= 0.114 Angle : 0.499 7.567 22091 Z= 0.260 Chirality : 0.039 0.143 2488 Planarity : 0.005 0.057 2739 Dihedral : 14.015 151.164 2597 Min Nonbonded Distance : 1.847 Molprobity Statistics. All-atom Clashscore : 1.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.21 % Favored : 98.79 % 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: 1.51 (0.19), residues: 1902 helix: 1.45 (0.16), residues: 1051 sheet: 0.84 (0.30), residues: 276 loop : 0.43 (0.24), residues: 575 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 143 TYR 0.020 0.001 TYR F 298 PHE 0.008 0.001 PHE D 70 HIS 0.003 0.001 HIS A 255 Details of bonding type rmsd/Z covalent geometry : bond 0.00250 / 0.11 (16220) covalent geometry : angle 0.49941 / 0.26 (22091) hydrogen bonds : bond 0.04200 / 2.72 ( 822) hydrogen bonds : angle 4.80618 / 3.34 ( 2337) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3804 Ramachandran restraints generated. 1902 Oldfield, 0 Emsley, 1902 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3804 Ramachandran restraints generated. 1902 Oldfield, 0 Emsley, 1902 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 215 residues out of total 1603 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 206 time to evaluate : 0.871 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 76 MET cc_start: 0.8897 (mmm) cc_final: 0.8329 (mmt) REVERT: A 90 LYS cc_start: 0.8872 (pttt) cc_final: 0.8663 (pttm) REVERT: A 312 ARG cc_start: 0.8185 (mmm160) cc_final: 0.7949 (mmm160) REVERT: B 117 MET cc_start: 0.8121 (tpp) cc_final: 0.7633 (tpp) REVERT: B 194 SER cc_start: 0.9201 (m) cc_final: 0.8982 (m) REVERT: B 291 ARG cc_start: 0.8289 (ttm170) cc_final: 0.8029 (ttm110) REVERT: C 125 SER cc_start: 0.8409 (m) cc_final: 0.8110 (t) REVERT: D 264 LYS cc_start: 0.8336 (tttt) cc_final: 0.8054 (ttpt) REVERT: E 68 MET cc_start: 0.8447 (tpt) cc_final: 0.7821 (tpt) REVERT: E 76 MET cc_start: 0.7912 (mmm) cc_final: 0.7655 (tpt) REVERT: E 121 GLU cc_start: 0.7246 (mt-10) cc_final: 0.6947 (mm-30) REVERT: E 131 TYR cc_start: 0.6783 (p90) cc_final: 0.6141 (p90) REVERT: F 33 LYS cc_start: 0.8327 (mttp) cc_final: 0.8066 (mmtm) REVERT: F 163 MET cc_start: 0.8691 (mtt) cc_final: 0.8366 (mtt) REVERT: F 225 LYS cc_start: 0.8469 (mttt) cc_final: 0.8204 (mtpp) REVERT: F 249 THR cc_start: 0.8125 (m) cc_final: 0.7752 (p) REVERT: G 192 GLU cc_start: 0.6064 (tt0) cc_final: 0.5726 (mp0) outliers start: 9 outliers final: 8 residues processed: 212 average time/residue: 0.3294 time to fit residues: 100.1647 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 : 0.837 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 144 SER Chi-restraints excluded: chain B residue 163 MET Chi-restraints excluded: chain B residue 204 GLU Chi-restraints excluded: chain C residue 53 ASP Chi-restraints excluded: chain C residue 199 MET Chi-restraints excluded: chain C residue 311 THR Chi-restraints excluded: chain D residue 74 ASN Chi-restraints excluded: chain E residue 95 VAL 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: 0.9990 chunk 181 optimal weight: 2.9990 chunk 32 optimal weight: 0.8980 chunk 61 optimal weight: 0.9980 chunk 19 optimal weight: 0.9980 chunk 91 optimal weight: 0.8980 chunk 49 optimal weight: 0.6980 chunk 23 optimal weight: 1.9990 chunk 81 optimal weight: 0.9980 chunk 4 optimal weight: 0.4980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 99 ASN D 74 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3432 r_free = 0.3432 target = 0.125080 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3049 r_free = 0.3049 target = 0.097044 restraints weight = 65220.733| |-----------------------------------------------------------------------------| r_work (start): 0.3013 rms_B_bonded: 1.76 r_work: 0.2859 rms_B_bonded: 2.29 restraints_weight: 0.5000 r_work: 0.2747 rms_B_bonded: 3.82 restraints_weight: 0.2500 r_work (final): 0.2747 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8370 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 : 0.003 0.075 16220 Z= 0.136 Angle : 0.711 59.200 22091 Z= 0.402 Chirality : 0.040 0.175 2488 Planarity : 0.005 0.057 2739 Dihedral : 14.013 151.445 2597 Min Nonbonded Distance : 1.842 Molprobity Statistics. All-atom Clashscore : 2.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.21 % Favored : 98.79 % Rotamer: Outliers : 0.50 % Allowed : 9.67 % Favored : 89.83 % 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: 1.50 (0.19), residues: 1902 helix: 1.45 (0.16), residues: 1051 sheet: 0.84 (0.30), residues: 276 loop : 0.43 (0.24), residues: 575 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 143 TYR 0.013 0.001 TYR C 131 PHE 0.013 0.001 PHE E 172 HIS 0.003 0.001 HIS C 146 Details of bonding type rmsd/Z covalent geometry : bond 0.00304 / 0.14 (16220) covalent geometry : angle 0.71062 / 0.40 (22091) hydrogen bonds : bond 0.04253 / 2.75 ( 822) hydrogen bonds : angle 4.81322 / 3.34 ( 2337) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3804 Ramachandran restraints generated. 1902 Oldfield, 0 Emsley, 1902 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3804 Ramachandran restraints generated. 1902 Oldfield, 0 Emsley, 1902 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 211 residues out of total 1603 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 203 time to evaluate : 0.904 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 76 MET cc_start: 0.8915 (mmm) cc_final: 0.8345 (mmt) REVERT: A 312 ARG cc_start: 0.8163 (mmm160) cc_final: 0.7941 (mmm160) REVERT: B 117 MET cc_start: 0.8167 (tpp) cc_final: 0.7692 (tpp) REVERT: B 194 SER cc_start: 0.9205 (m) cc_final: 0.8987 (m) REVERT: B 291 ARG cc_start: 0.8322 (ttm170) cc_final: 0.8073 (ttm110) REVERT: C 125 SER cc_start: 0.8412 (m) cc_final: 0.8134 (t) REVERT: D 264 LYS cc_start: 0.8360 (tttt) cc_final: 0.8094 (ttpt) REVERT: E 68 MET cc_start: 0.8477 (tpt) cc_final: 0.7882 (tpt) REVERT: E 76 MET cc_start: 0.7922 (mmm) cc_final: 0.7672 (tpt) REVERT: E 121 GLU cc_start: 0.7215 (mt-10) cc_final: 0.6965 (mm-30) REVERT: E 131 TYR cc_start: 0.6753 (p90) cc_final: 0.6121 (p90) REVERT: F 33 LYS cc_start: 0.8319 (mttp) cc_final: 0.8074 (mmtm) REVERT: F 163 MET cc_start: 0.8729 (mtt) cc_final: 0.8420 (mtt) REVERT: F 225 LYS cc_start: 0.8503 (mttt) cc_final: 0.8247 (mtpp) REVERT: F 249 THR cc_start: 0.8120 (m) cc_final: 0.7760 (p) REVERT: G 192 GLU cc_start: 0.6063 (tt0) cc_final: 0.5727 (mp0) outliers start: 8 outliers final: 8 residues processed: 207 average time/residue: 0.3071 time to fit residues: 91.2370 Evaluate side-chains 211 residues out of total 1603 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 203 time to evaluate : 0.847 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 144 SER Chi-restraints excluded: chain B residue 163 MET Chi-restraints excluded: chain B residue 204 GLU Chi-restraints excluded: chain C residue 53 ASP Chi-restraints excluded: chain C residue 199 MET Chi-restraints excluded: chain C residue 311 THR Chi-restraints excluded: chain E residue 95 VAL Chi-restraints excluded: chain F residue 147 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 191 random chunks: chunk 177 optimal weight: 2.9990 chunk 51 optimal weight: 0.9980 chunk 76 optimal weight: 0.9990 chunk 48 optimal weight: 0.9990 chunk 40 optimal weight: 0.0980 chunk 63 optimal weight: 0.9990 chunk 68 optimal weight: 1.9990 chunk 83 optimal weight: 1.9990 chunk 97 optimal weight: 9.9990 chunk 0 optimal weight: 1.9990 chunk 116 optimal weight: 0.9980 overall best weight: 0.8184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 99 ASN D 74 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3431 r_free = 0.3431 target = 0.124958 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3050 r_free = 0.3050 target = 0.097084 restraints weight = 64924.057| |-----------------------------------------------------------------------------| r_work (start): 0.2944 rms_B_bonded: 1.75 r_work: 0.2791 rms_B_bonded: 2.22 restraints_weight: 0.5000 r_work: 0.2681 rms_B_bonded: 3.67 restraints_weight: 0.2500 r_work (final): 0.2681 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8332 moved from start: 0.3367 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.075 16220 Z= 0.136 Angle : 0.711 59.200 22091 Z= 0.402 Chirality : 0.040 0.175 2488 Planarity : 0.005 0.057 2739 Dihedral : 14.013 151.445 2597 Min Nonbonded Distance : 1.842 Molprobity Statistics. All-atom Clashscore : 2.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.21 % Favored : 98.79 % Rotamer: Outliers : 0.50 % Allowed : 9.73 % 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: 1.50 (0.19), residues: 1902 helix: 1.45 (0.16), residues: 1051 sheet: 0.84 (0.30), residues: 276 loop : 0.43 (0.24), residues: 575 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 143 TYR 0.013 0.001 TYR C 131 PHE 0.013 0.001 PHE E 172 HIS 0.003 0.001 HIS C 146 Details of bonding type rmsd/Z covalent geometry : bond 0.00304 / 0.14 (16220) covalent geometry : angle 0.71062 / 0.40 (22091) hydrogen bonds : bond 0.04253 / 2.75 ( 822) hydrogen bonds : angle 4.81322 / 3.34 ( 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 211 residues out of total 1603 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 203 time to evaluate : 0.868 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 76 MET cc_start: 0.8898 (mmm) cc_final: 0.8334 (mmt) REVERT: A 312 ARG cc_start: 0.8171 (mmm160) cc_final: 0.7946 (mmm160) REVERT: B 117 MET cc_start: 0.8107 (tpp) cc_final: 0.7617 (tpp) REVERT: B 194 SER cc_start: 0.9199 (m) cc_final: 0.8977 (m) REVERT: B 291 ARG cc_start: 0.8277 (ttm170) cc_final: 0.8008 (ttm110) REVERT: C 125 SER cc_start: 0.8415 (m) cc_final: 0.8108 (t) REVERT: D 264 LYS cc_start: 0.8329 (tttt) cc_final: 0.8036 (ttpt) REVERT: E 68 MET cc_start: 0.8441 (tpt) cc_final: 0.7826 (tpt) REVERT: E 76 MET cc_start: 0.7904 (mmm) cc_final: 0.7654 (tpt) REVERT: E 121 GLU cc_start: 0.7238 (mt-10) cc_final: 0.6949 (mm-30) REVERT: E 131 TYR cc_start: 0.6777 (p90) cc_final: 0.6138 (p90) REVERT: F 33 LYS cc_start: 0.8339 (mttp) cc_final: 0.8070 (mmtm) REVERT: F 163 MET cc_start: 0.8685 (mtt) cc_final: 0.8355 (mtt) REVERT: F 225 LYS cc_start: 0.8465 (mttt) cc_final: 0.8200 (mtpp) REVERT: F 249 THR cc_start: 0.8130 (m) cc_final: 0.7751 (p) REVERT: G 192 GLU cc_start: 0.6082 (tt0) cc_final: 0.5743 (mp0) outliers start: 8 outliers final: 8 residues processed: 207 average time/residue: 0.3386 time to fit residues: 100.3853 Evaluate side-chains 211 residues out of total 1603 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 203 time to evaluate : 0.900 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 144 SER Chi-restraints excluded: chain B residue 163 MET Chi-restraints excluded: chain B residue 204 GLU Chi-restraints excluded: chain C residue 53 ASP Chi-restraints excluded: chain C residue 199 MET Chi-restraints excluded: chain C residue 311 THR Chi-restraints excluded: chain E residue 95 VAL Chi-restraints excluded: chain F residue 147 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 191 random chunks: chunk 128 optimal weight: 1.9990 chunk 92 optimal weight: 1.9990 chunk 112 optimal weight: 0.9990 chunk 138 optimal weight: 1.9990 chunk 61 optimal weight: 0.9990 chunk 150 optimal weight: 1.9990 chunk 20 optimal weight: 0.9980 chunk 183 optimal weight: 6.9990 chunk 179 optimal weight: 1.9990 chunk 136 optimal weight: 0.9990 chunk 98 optimal weight: 0.9980 overall best weight: 0.9986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 99 ASN D 74 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3430 r_free = 0.3430 target = 0.124919 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3049 r_free = 0.3049 target = 0.097024 restraints weight = 65056.624| |-----------------------------------------------------------------------------| r_work (start): 0.2998 rms_B_bonded: 1.75 r_work: 0.2841 rms_B_bonded: 2.30 restraints_weight: 0.5000 r_work: 0.2730 rms_B_bonded: 3.83 restraints_weight: 0.2500 r_work (final): 0.2730 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8371 moved from start: 0.3366 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.075 16220 Z= 0.136 Angle : 0.711 59.200 22091 Z= 0.402 Chirality : 0.040 0.175 2488 Planarity : 0.005 0.057 2739 Dihedral : 14.013 151.445 2597 Min Nonbonded Distance : 1.842 Molprobity Statistics. All-atom Clashscore : 2.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.21 % Favored : 98.79 % Rotamer: Outliers : 0.50 % Allowed : 9.73 % 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: 1.50 (0.19), residues: 1902 helix: 1.45 (0.16), residues: 1051 sheet: 0.84 (0.30), residues: 276 loop : 0.43 (0.24), residues: 575 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 143 TYR 0.013 0.001 TYR C 131 PHE 0.013 0.001 PHE E 172 HIS 0.003 0.001 HIS C 146 Details of bonding type rmsd/Z covalent geometry : bond 0.00304 / 0.14 (16220) covalent geometry : angle 0.71062 / 0.40 (22091) hydrogen bonds : bond 0.04253 / 2.75 ( 822) hydrogen bonds : angle 4.81322 / 3.34 ( 2337) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7006.76 seconds wall clock time: 119 minutes 17.19 seconds (7157.19 seconds total)