Starting phenix.real_space_refine on Wed Sep 17 20:19:53 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6ip1_9697/09_2025/6ip1_9697.cif Found real_map, /net/cci-nas-00/data/ceres_data/6ip1_9697/09_2025/6ip1_9697.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/6ip1_9697/09_2025/6ip1_9697.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6ip1_9697/09_2025/6ip1_9697.map" model { file = "/net/cci-nas-00/data/ceres_data/6ip1_9697/09_2025/6ip1_9697.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6ip1_9697/09_2025/6ip1_9697.cif" } resolution = 3.9 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= 0.001 sd= 0.016 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: 4 Type Number sf(0) Gaussians S 83 5.16 5 C 7037 2.51 5 N 1901 2.21 5 O 2224 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 14 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 11245 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 509 Number of conformers: 1 Conformer: "" Number of residues, atoms: 63, 509 Classifications: {'peptide': 63} Link IDs: {'TRANS': 62} Chain: "B" Number of atoms: 509 Number of conformers: 1 Conformer: "" Number of residues, atoms: 62, 509 Classifications: {'peptide': 62} Link IDs: {'TRANS': 61} Chain: "C" Number of atoms: 520 Number of conformers: 1 Conformer: "" Number of residues, atoms: 65, 520 Classifications: {'peptide': 65} Link IDs: {'TRANS': 64} Chain: "D" Number of atoms: 495 Number of conformers: 1 Conformer: "" Number of residues, atoms: 62, 495 Classifications: {'peptide': 62} Link IDs: {'TRANS': 61} Chain: "E" Number of atoms: 2303 Number of conformers: 1 Conformer: "" Number of residues, atoms: 292, 2303 Classifications: {'peptide': 292} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 288} Chain: "F" Number of atoms: 2303 Number of conformers: 1 Conformer: "" Number of residues, atoms: 292, 2303 Classifications: {'peptide': 292} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 288} Chain: "G" Number of atoms: 2303 Number of conformers: 1 Conformer: "" Number of residues, atoms: 292, 2303 Classifications: {'peptide': 292} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 288} Chain: "H" Number of atoms: 2303 Number of conformers: 1 Conformer: "" Number of residues, atoms: 292, 2303 Classifications: {'peptide': 292} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 288} Time building chain proxies: 2.57, per 1000 atoms: 0.23 Number of scatterers: 11245 At special positions: 0 Unit cell: (117.589, 116.282, 118.895, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 83 16.00 O 2224 8.00 N 1901 7.00 C 7037 6.00 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: 1.00 Conformation dependent library (CDL) restraints added in 354.3 milliseconds Enol-peptide restraints added in 476.8 nanoseconds 2808 Ramachandran restraints generated. 1404 Oldfield, 0 Emsley, 1404 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2736 Finding SS restraints... Secondary structure from input PDB file: 76 helices and 0 sheets defined 86.1% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.25 Creating SS restraints... Processing helix chain 'A' and resid 28 through 83 removed outlier: 3.855A pdb=" N THR A 35 " --> pdb=" O ARG A 31 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N ASP A 40 " --> pdb=" O GLN A 36 " (cutoff:3.500A) removed outlier: 4.495A pdb=" N ASP A 51 " --> pdb=" O ARG A 47 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N ARG A 56 " --> pdb=" O LYS A 52 " (cutoff:3.500A) removed outlier: 3.850A pdb=" N ASP A 57 " --> pdb=" O VAL A 53 " (cutoff:3.500A) removed outlier: 4.076A pdb=" N ASP A 65 " --> pdb=" O SER A 61 " (cutoff:3.500A) removed outlier: 3.925A pdb=" N GLN A 71 " --> pdb=" O ALA A 67 " (cutoff:3.500A) Processing helix chain 'B' and resid 193 through 228 removed outlier: 4.266A pdb=" N ARG B 198 " --> pdb=" O GLU B 194 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N GLU B 201 " --> pdb=" O THR B 197 " (cutoff:3.500A) removed outlier: 3.895A pdb=" N LYS B 204 " --> pdb=" O SER B 200 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N GLU B 211 " --> pdb=" O ASN B 207 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N MET B 215 " --> pdb=" O GLU B 211 " (cutoff:3.500A) removed outlier: 3.939A pdb=" N GLU B 224 " --> pdb=" O ALA B 220 " (cutoff:3.500A) Processing helix chain 'B' and resid 230 through 252 removed outlier: 4.238A pdb=" N ASN B 236 " --> pdb=" O ARG B 232 " (cutoff:3.500A) removed outlier: 3.984A pdb=" N ASP B 242 " --> pdb=" O GLU B 238 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N SER B 249 " --> pdb=" O GLU B 245 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N ASP B 250 " --> pdb=" O ARG B 246 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N LYS B 252 " --> pdb=" O VAL B 248 " (cutoff:3.500A) Processing helix chain 'C' and resid 18 through 37 removed outlier: 3.593A pdb=" N ARG C 31 " --> pdb=" O GLU C 27 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N LEU C 33 " --> pdb=" O THR C 29 " (cutoff:3.500A) Processing helix chain 'C' and resid 37 through 67 removed outlier: 3.685A pdb=" N ASP C 41 " --> pdb=" O GLU C 37 " (cutoff:3.500A) removed outlier: 3.966A pdb=" N ALA C 42 " --> pdb=" O GLU C 38 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N LEU C 47 " --> pdb=" O GLY C 43 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N GLU C 55 " --> pdb=" O ASP C 51 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N ILE C 60 " --> pdb=" O GLN C 56 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N GLU C 61 " --> pdb=" O LEU C 57 " (cutoff:3.500A) Processing helix chain 'C' and resid 68 through 77 removed outlier: 4.032A pdb=" N ALA C 74 " --> pdb=" O ASP C 70 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N GLU C 75 " --> pdb=" O MET C 71 " (cutoff:3.500A) Processing helix chain 'C' and resid 78 through 80 No H-bonds generated for 'chain 'C' and resid 78 through 80' Processing helix chain 'D' and resid 142 through 201 removed outlier: 3.752A pdb=" N GLN D 152 " --> pdb=" O GLU D 148 " (cutoff:3.500A) removed outlier: 4.399A pdb=" N ASN D 159 " --> pdb=" O GLY D 155 " (cutoff:3.500A) removed outlier: 4.134A pdb=" N HIS D 162 " --> pdb=" O GLY D 158 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N MET D 167 " --> pdb=" O MET D 163 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N ILE D 171 " --> pdb=" O MET D 167 " (cutoff:3.500A) removed outlier: 4.415A pdb=" N ASP D 172 " --> pdb=" O GLY D 168 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N GLU D 183 " --> pdb=" O ASP D 179 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N LYS D 184 " --> pdb=" O ARG D 180 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N ILE D 192 " --> pdb=" O ASN D 188 " (cutoff:3.500A) removed outlier: 4.301A pdb=" N GLN D 197 " --> pdb=" O ASP D 193 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N ARG D 198 " --> pdb=" O GLU D 194 " (cutoff:3.500A) Processing helix chain 'E' and resid 5 through 20 removed outlier: 3.548A pdb=" N ALA E 17 " --> pdb=" O LEU E 13 " (cutoff:3.500A) removed outlier: 3.943A pdb=" N GLU E 18 " --> pdb=" O LEU E 14 " (cutoff:3.500A) removed outlier: 4.384A pdb=" N LYS E 20 " --> pdb=" O GLU E 16 " (cutoff:3.500A) Processing helix chain 'E' and resid 23 through 27 removed outlier: 3.567A pdb=" N PHE E 27 " --> pdb=" O SER E 24 " (cutoff:3.500A) Processing helix chain 'E' and resid 39 through 55 removed outlier: 4.237A pdb=" N GLU E 43 " --> pdb=" O GLU E 39 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N ILE E 44 " --> pdb=" O GLU E 40 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N TYR E 45 " --> pdb=" O ALA E 41 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N ALA E 48 " --> pdb=" O ILE E 44 " (cutoff:3.500A) removed outlier: 4.084A pdb=" N PHE E 52 " --> pdb=" O ALA E 48 " (cutoff:3.500A) removed outlier: 4.068A pdb=" N LYS E 53 " --> pdb=" O ALA E 49 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N MET E 54 " --> pdb=" O ASN E 50 " (cutoff:3.500A) Processing helix chain 'E' and resid 57 through 75 removed outlier: 3.998A pdb=" N SER E 63 " --> pdb=" O SER E 59 " (cutoff:3.500A) removed outlier: 3.876A pdb=" N ALA E 64 " --> pdb=" O ALA E 60 " (cutoff:3.500A) removed outlier: 3.980A pdb=" N GLN E 67 " --> pdb=" O SER E 63 " (cutoff:3.500A) Processing helix chain 'E' and resid 77 through 90 removed outlier: 3.643A pdb=" N ALA E 81 " --> pdb=" O SER E 77 " (cutoff:3.500A) removed outlier: 4.748A pdb=" N CYS E 84 " --> pdb=" O ASP E 80 " (cutoff:3.500A) removed outlier: 3.997A pdb=" N ASP E 87 " --> pdb=" O THR E 83 " (cutoff:3.500A) Processing helix chain 'E' and resid 91 through 95 removed outlier: 3.621A pdb=" N LYS E 94 " --> pdb=" O ALA E 91 " (cutoff:3.500A) Processing helix chain 'E' and resid 96 through 113 removed outlier: 3.603A pdb=" N ASN E 102 " --> pdb=" O GLN E 98 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N CYS E 103 " --> pdb=" O GLU E 99 " (cutoff:3.500A) removed outlier: 3.885A pdb=" N GLU E 109 " --> pdb=" O MET E 105 " (cutoff:3.500A) removed outlier: 4.227A pdb=" N ILE E 110 " --> pdb=" O ARG E 106 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N TYR E 111 " --> pdb=" O ALA E 107 " (cutoff:3.500A) removed outlier: 3.818A pdb=" N ASP E 113 " --> pdb=" O GLU E 109 " (cutoff:3.500A) Processing helix chain 'E' and resid 117 through 134 removed outlier: 3.515A pdb=" N ILE E 130 " --> pdb=" O SER E 126 " (cutoff:3.500A) Processing helix chain 'E' and resid 137 through 155 removed outlier: 3.608A pdb=" N ALA E 143 " --> pdb=" O GLU E 139 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N ASP E 150 " --> pdb=" O GLU E 146 " (cutoff:3.500A) Processing helix chain 'E' and resid 157 through 175 removed outlier: 3.879A pdb=" N ASN E 162 " --> pdb=" O ASN E 158 " (cutoff:3.500A) removed outlier: 3.972A pdb=" N LYS E 163 " --> pdb=" O SER E 159 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N CYS E 164 " --> pdb=" O SER E 160 " (cutoff:3.500A) removed outlier: 4.178A pdb=" N LYS E 167 " --> pdb=" O LYS E 163 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N ALA E 172 " --> pdb=" O VAL E 168 " (cutoff:3.500A) removed outlier: 4.158A pdb=" N GLN E 174 " --> pdb=" O GLY E 170 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N LEU E 175 " --> pdb=" O TYR E 171 " (cutoff:3.500A) Processing helix chain 'E' and resid 177 through 194 removed outlier: 4.054A pdb=" N ASP E 183 " --> pdb=" O GLN E 179 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N ILE E 184 " --> pdb=" O LYS E 180 " (cutoff:3.500A) removed outlier: 4.184A pdb=" N ASP E 194 " --> pdb=" O THR E 190 " (cutoff:3.500A) Processing helix chain 'E' and resid 201 through 212 removed outlier: 3.820A pdb=" N TYR E 205 " --> pdb=" O SER E 201 " (cutoff:3.500A) Processing helix chain 'E' and resid 221 through 232 removed outlier: 4.459A pdb=" N PHE E 232 " --> pdb=" O TYR E 228 " (cutoff:3.500A) Processing helix chain 'E' and resid 233 through 238 Processing helix chain 'E' and resid 239 through 252 removed outlier: 3.766A pdb=" N LYS E 245 " --> pdb=" O CYS E 241 " (cutoff:3.500A) removed outlier: 4.013A pdb=" N ALA E 250 " --> pdb=" O LYS E 246 " (cutoff:3.500A) Processing helix chain 'E' and resid 257 through 268 removed outlier: 3.718A pdb=" N GLU E 261 " --> pdb=" O ASP E 257 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N TYR E 266 " --> pdb=" O ALA E 262 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N SER E 268 " --> pdb=" O LYS E 264 " (cutoff:3.500A) Processing helix chain 'E' and resid 273 through 295 removed outlier: 3.533A pdb=" N THR E 278 " --> pdb=" O GLN E 274 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N GLN E 288 " --> pdb=" O LYS E 284 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N GLY E 289 " --> pdb=" O LYS E 285 " (cutoff:3.500A) removed outlier: 3.873A pdb=" N ASP E 290 " --> pdb=" O THR E 286 " (cutoff:3.500A) Processing helix chain 'F' and resid 5 through 20 removed outlier: 3.547A pdb=" N ALA F 17 " --> pdb=" O LEU F 13 " (cutoff:3.500A) removed outlier: 3.943A pdb=" N GLU F 18 " --> pdb=" O LEU F 14 " (cutoff:3.500A) removed outlier: 4.385A pdb=" N LYS F 20 " --> pdb=" O GLU F 16 " (cutoff:3.500A) Processing helix chain 'F' and resid 23 through 27 removed outlier: 3.567A pdb=" N PHE F 27 " --> pdb=" O SER F 24 " (cutoff:3.500A) Processing helix chain 'F' and resid 39 through 55 removed outlier: 4.237A pdb=" N GLU F 43 " --> pdb=" O GLU F 39 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N ILE F 44 " --> pdb=" O GLU F 40 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N TYR F 45 " --> pdb=" O ALA F 41 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N ALA F 48 " --> pdb=" O ILE F 44 " (cutoff:3.500A) removed outlier: 4.085A pdb=" N PHE F 52 " --> pdb=" O ALA F 48 " (cutoff:3.500A) removed outlier: 4.067A pdb=" N LYS F 53 " --> pdb=" O ALA F 49 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N MET F 54 " --> pdb=" O ASN F 50 " (cutoff:3.500A) Processing helix chain 'F' and resid 57 through 75 removed outlier: 3.997A pdb=" N SER F 63 " --> pdb=" O SER F 59 " (cutoff:3.500A) removed outlier: 3.876A pdb=" N ALA F 64 " --> pdb=" O ALA F 60 " (cutoff:3.500A) removed outlier: 3.980A pdb=" N GLN F 67 " --> pdb=" O SER F 63 " (cutoff:3.500A) Processing helix chain 'F' and resid 77 through 90 removed outlier: 3.643A pdb=" N ALA F 81 " --> pdb=" O SER F 77 " (cutoff:3.500A) removed outlier: 4.748A pdb=" N CYS F 84 " --> pdb=" O ASP F 80 " (cutoff:3.500A) removed outlier: 3.997A pdb=" N ASP F 87 " --> pdb=" O THR F 83 " (cutoff:3.500A) Processing helix chain 'F' and resid 91 through 95 removed outlier: 3.622A pdb=" N LYS F 94 " --> pdb=" O ALA F 91 " (cutoff:3.500A) Processing helix chain 'F' and resid 96 through 113 removed outlier: 3.604A pdb=" N ASN F 102 " --> pdb=" O GLN F 98 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N CYS F 103 " --> pdb=" O GLU F 99 " (cutoff:3.500A) removed outlier: 3.885A pdb=" N GLU F 109 " --> pdb=" O MET F 105 " (cutoff:3.500A) removed outlier: 4.228A pdb=" N ILE F 110 " --> pdb=" O ARG F 106 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N TYR F 111 " --> pdb=" O ALA F 107 " (cutoff:3.500A) removed outlier: 3.818A pdb=" N ASP F 113 " --> pdb=" O GLU F 109 " (cutoff:3.500A) Processing helix chain 'F' and resid 117 through 134 removed outlier: 3.515A pdb=" N ILE F 130 " --> pdb=" O SER F 126 " (cutoff:3.500A) Processing helix chain 'F' and resid 137 through 155 removed outlier: 3.607A pdb=" N ALA F 143 " --> pdb=" O GLU F 139 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N ASP F 150 " --> pdb=" O GLU F 146 " (cutoff:3.500A) Processing helix chain 'F' and resid 157 through 175 removed outlier: 3.879A pdb=" N ASN F 162 " --> pdb=" O ASN F 158 " (cutoff:3.500A) removed outlier: 3.973A pdb=" N LYS F 163 " --> pdb=" O SER F 159 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N CYS F 164 " --> pdb=" O SER F 160 " (cutoff:3.500A) removed outlier: 4.178A pdb=" N LYS F 167 " --> pdb=" O LYS F 163 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N ALA F 172 " --> pdb=" O VAL F 168 " (cutoff:3.500A) removed outlier: 4.157A pdb=" N GLN F 174 " --> pdb=" O GLY F 170 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N LEU F 175 " --> pdb=" O TYR F 171 " (cutoff:3.500A) Processing helix chain 'F' and resid 177 through 194 removed outlier: 4.053A pdb=" N ASP F 183 " --> pdb=" O GLN F 179 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N ILE F 184 " --> pdb=" O LYS F 180 " (cutoff:3.500A) removed outlier: 4.185A pdb=" N ASP F 194 " --> pdb=" O THR F 190 " (cutoff:3.500A) Processing helix chain 'F' and resid 201 through 212 removed outlier: 3.819A pdb=" N TYR F 205 " --> pdb=" O SER F 201 " (cutoff:3.500A) Processing helix chain 'F' and resid 221 through 232 removed outlier: 4.459A pdb=" N PHE F 232 " --> pdb=" O TYR F 228 " (cutoff:3.500A) Processing helix chain 'F' and resid 233 through 238 Processing helix chain 'F' and resid 239 through 252 removed outlier: 3.766A pdb=" N LYS F 245 " --> pdb=" O CYS F 241 " (cutoff:3.500A) removed outlier: 4.014A pdb=" N ALA F 250 " --> pdb=" O LYS F 246 " (cutoff:3.500A) Processing helix chain 'F' and resid 257 through 268 removed outlier: 3.718A pdb=" N GLU F 261 " --> pdb=" O ASP F 257 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N TYR F 266 " --> pdb=" O ALA F 262 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N SER F 268 " --> pdb=" O LYS F 264 " (cutoff:3.500A) Processing helix chain 'F' and resid 273 through 295 removed outlier: 3.533A pdb=" N THR F 278 " --> pdb=" O GLN F 274 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N GLN F 288 " --> pdb=" O LYS F 284 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N GLY F 289 " --> pdb=" O LYS F 285 " (cutoff:3.500A) removed outlier: 3.874A pdb=" N ASP F 290 " --> pdb=" O THR F 286 " (cutoff:3.500A) Processing helix chain 'G' and resid 5 through 20 removed outlier: 3.549A pdb=" N ALA G 17 " --> pdb=" O LEU G 13 " (cutoff:3.500A) removed outlier: 3.943A pdb=" N GLU G 18 " --> pdb=" O LEU G 14 " (cutoff:3.500A) removed outlier: 4.384A pdb=" N LYS G 20 " --> pdb=" O GLU G 16 " (cutoff:3.500A) Processing helix chain 'G' and resid 23 through 27 removed outlier: 3.567A pdb=" N PHE G 27 " --> pdb=" O SER G 24 " (cutoff:3.500A) Processing helix chain 'G' and resid 39 through 55 removed outlier: 4.237A pdb=" N GLU G 43 " --> pdb=" O GLU G 39 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N ILE G 44 " --> pdb=" O GLU G 40 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N TYR G 45 " --> pdb=" O ALA G 41 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N ALA G 48 " --> pdb=" O ILE G 44 " (cutoff:3.500A) removed outlier: 4.084A pdb=" N PHE G 52 " --> pdb=" O ALA G 48 " (cutoff:3.500A) removed outlier: 4.068A pdb=" N LYS G 53 " --> pdb=" O ALA G 49 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N MET G 54 " --> pdb=" O ASN G 50 " (cutoff:3.500A) Processing helix chain 'G' and resid 57 through 75 removed outlier: 3.998A pdb=" N SER G 63 " --> pdb=" O SER G 59 " (cutoff:3.500A) removed outlier: 3.876A pdb=" N ALA G 64 " --> pdb=" O ALA G 60 " (cutoff:3.500A) removed outlier: 3.979A pdb=" N GLN G 67 " --> pdb=" O SER G 63 " (cutoff:3.500A) Processing helix chain 'G' and resid 81 through 90 removed outlier: 3.997A pdb=" N ASP G 87 " --> pdb=" O THR G 83 " (cutoff:3.500A) Processing helix chain 'G' and resid 91 through 95 removed outlier: 3.621A pdb=" N LYS G 94 " --> pdb=" O ALA G 91 " (cutoff:3.500A) Processing helix chain 'G' and resid 96 through 113 removed outlier: 3.604A pdb=" N ASN G 102 " --> pdb=" O GLN G 98 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N CYS G 103 " --> pdb=" O GLU G 99 " (cutoff:3.500A) removed outlier: 3.885A pdb=" N GLU G 109 " --> pdb=" O MET G 105 " (cutoff:3.500A) removed outlier: 4.227A pdb=" N ILE G 110 " --> pdb=" O ARG G 106 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N TYR G 111 " --> pdb=" O ALA G 107 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N ASP G 113 " --> pdb=" O GLU G 109 " (cutoff:3.500A) Processing helix chain 'G' and resid 117 through 134 removed outlier: 3.514A pdb=" N ILE G 130 " --> pdb=" O SER G 126 " (cutoff:3.500A) Processing helix chain 'G' and resid 137 through 155 removed outlier: 3.608A pdb=" N ALA G 143 " --> pdb=" O GLU G 139 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N ASP G 150 " --> pdb=" O GLU G 146 " (cutoff:3.500A) Processing helix chain 'G' and resid 157 through 175 removed outlier: 3.879A pdb=" N ASN G 162 " --> pdb=" O ASN G 158 " (cutoff:3.500A) removed outlier: 3.972A pdb=" N LYS G 163 " --> pdb=" O SER G 159 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N CYS G 164 " --> pdb=" O SER G 160 " (cutoff:3.500A) removed outlier: 4.178A pdb=" N LYS G 167 " --> pdb=" O LYS G 163 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N ALA G 172 " --> pdb=" O VAL G 168 " (cutoff:3.500A) removed outlier: 4.158A pdb=" N GLN G 174 " --> pdb=" O GLY G 170 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N LEU G 175 " --> pdb=" O TYR G 171 " (cutoff:3.500A) Processing helix chain 'G' and resid 177 through 194 removed outlier: 4.054A pdb=" N ASP G 183 " --> pdb=" O GLN G 179 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N ILE G 184 " --> pdb=" O LYS G 180 " (cutoff:3.500A) removed outlier: 4.185A pdb=" N ASP G 194 " --> pdb=" O THR G 190 " (cutoff:3.500A) Processing helix chain 'G' and resid 202 through 212 removed outlier: 3.700A pdb=" N LYS G 208 " --> pdb=" O ASP G 204 " (cutoff:3.500A) Processing helix chain 'G' and resid 221 through 232 removed outlier: 4.459A pdb=" N PHE G 232 " --> pdb=" O TYR G 228 " (cutoff:3.500A) Processing helix chain 'G' and resid 233 through 238 Processing helix chain 'G' and resid 239 through 252 removed outlier: 3.766A pdb=" N LYS G 245 " --> pdb=" O CYS G 241 " (cutoff:3.500A) removed outlier: 4.014A pdb=" N ALA G 250 " --> pdb=" O LYS G 246 " (cutoff:3.500A) Processing helix chain 'G' and resid 257 through 268 removed outlier: 3.718A pdb=" N GLU G 261 " --> pdb=" O ASP G 257 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N TYR G 266 " --> pdb=" O ALA G 262 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N SER G 268 " --> pdb=" O LYS G 264 " (cutoff:3.500A) Processing helix chain 'G' and resid 273 through 295 removed outlier: 3.533A pdb=" N THR G 278 " --> pdb=" O GLN G 274 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N GLN G 288 " --> pdb=" O LYS G 284 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N GLY G 289 " --> pdb=" O LYS G 285 " (cutoff:3.500A) removed outlier: 3.873A pdb=" N ASP G 290 " --> pdb=" O THR G 286 " (cutoff:3.500A) Processing helix chain 'H' and resid 5 through 20 removed outlier: 3.548A pdb=" N ALA H 17 " --> pdb=" O LEU H 13 " (cutoff:3.500A) removed outlier: 3.943A pdb=" N GLU H 18 " --> pdb=" O LEU H 14 " (cutoff:3.500A) removed outlier: 4.384A pdb=" N LYS H 20 " --> pdb=" O GLU H 16 " (cutoff:3.500A) Processing helix chain 'H' and resid 23 through 27 removed outlier: 3.567A pdb=" N PHE H 27 " --> pdb=" O SER H 24 " (cutoff:3.500A) Processing helix chain 'H' and resid 39 through 55 removed outlier: 4.237A pdb=" N GLU H 43 " --> pdb=" O GLU H 39 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N ILE H 44 " --> pdb=" O GLU H 40 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N TYR H 45 " --> pdb=" O ALA H 41 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N ALA H 48 " --> pdb=" O ILE H 44 " (cutoff:3.500A) removed outlier: 4.085A pdb=" N PHE H 52 " --> pdb=" O ALA H 48 " (cutoff:3.500A) removed outlier: 4.068A pdb=" N LYS H 53 " --> pdb=" O ALA H 49 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N MET H 54 " --> pdb=" O ASN H 50 " (cutoff:3.500A) Processing helix chain 'H' and resid 57 through 75 removed outlier: 3.998A pdb=" N SER H 63 " --> pdb=" O SER H 59 " (cutoff:3.500A) removed outlier: 3.876A pdb=" N ALA H 64 " --> pdb=" O ALA H 60 " (cutoff:3.500A) removed outlier: 3.979A pdb=" N GLN H 67 " --> pdb=" O SER H 63 " (cutoff:3.500A) Processing helix chain 'H' and resid 77 through 90 removed outlier: 3.643A pdb=" N ALA H 81 " --> pdb=" O SER H 77 " (cutoff:3.500A) removed outlier: 4.747A pdb=" N CYS H 84 " --> pdb=" O ASP H 80 " (cutoff:3.500A) removed outlier: 3.998A pdb=" N ASP H 87 " --> pdb=" O THR H 83 " (cutoff:3.500A) Processing helix chain 'H' and resid 91 through 95 removed outlier: 3.620A pdb=" N LYS H 94 " --> pdb=" O ALA H 91 " (cutoff:3.500A) Processing helix chain 'H' and resid 96 through 113 removed outlier: 3.604A pdb=" N ASN H 102 " --> pdb=" O GLN H 98 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N CYS H 103 " --> pdb=" O GLU H 99 " (cutoff:3.500A) removed outlier: 3.885A pdb=" N GLU H 109 " --> pdb=" O MET H 105 " (cutoff:3.500A) removed outlier: 4.227A pdb=" N ILE H 110 " --> pdb=" O ARG H 106 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N TYR H 111 " --> pdb=" O ALA H 107 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N ASP H 113 " --> pdb=" O GLU H 109 " (cutoff:3.500A) Processing helix chain 'H' and resid 117 through 134 removed outlier: 3.514A pdb=" N ILE H 130 " --> pdb=" O SER H 126 " (cutoff:3.500A) Processing helix chain 'H' and resid 137 through 155 removed outlier: 3.608A pdb=" N ALA H 143 " --> pdb=" O GLU H 139 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N ASP H 150 " --> pdb=" O GLU H 146 " (cutoff:3.500A) Processing helix chain 'H' and resid 157 through 175 removed outlier: 3.879A pdb=" N ASN H 162 " --> pdb=" O ASN H 158 " (cutoff:3.500A) removed outlier: 3.972A pdb=" N LYS H 163 " --> pdb=" O SER H 159 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N CYS H 164 " --> pdb=" O SER H 160 " (cutoff:3.500A) removed outlier: 4.178A pdb=" N LYS H 167 " --> pdb=" O LYS H 163 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N ALA H 172 " --> pdb=" O VAL H 168 " (cutoff:3.500A) removed outlier: 4.158A pdb=" N GLN H 174 " --> pdb=" O GLY H 170 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N LEU H 175 " --> pdb=" O TYR H 171 " (cutoff:3.500A) Processing helix chain 'H' and resid 177 through 194 removed outlier: 4.054A pdb=" N ASP H 183 " --> pdb=" O GLN H 179 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N ILE H 184 " --> pdb=" O LYS H 180 " (cutoff:3.500A) removed outlier: 4.185A pdb=" N ASP H 194 " --> pdb=" O THR H 190 " (cutoff:3.500A) Processing helix chain 'H' and resid 201 through 212 removed outlier: 3.820A pdb=" N TYR H 205 " --> pdb=" O SER H 201 " (cutoff:3.500A) Processing helix chain 'H' and resid 221 through 232 removed outlier: 4.459A pdb=" N PHE H 232 " --> pdb=" O TYR H 228 " (cutoff:3.500A) Processing helix chain 'H' and resid 233 through 238 Processing helix chain 'H' and resid 239 through 252 removed outlier: 3.766A pdb=" N LYS H 245 " --> pdb=" O CYS H 241 " (cutoff:3.500A) removed outlier: 4.014A pdb=" N ALA H 250 " --> pdb=" O LYS H 246 " (cutoff:3.500A) Processing helix chain 'H' and resid 257 through 268 removed outlier: 3.718A pdb=" N GLU H 261 " --> pdb=" O ASP H 257 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N TYR H 266 " --> pdb=" O ALA H 262 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N SER H 268 " --> pdb=" O LYS H 264 " (cutoff:3.500A) Processing helix chain 'H' and resid 273 through 295 removed outlier: 3.533A pdb=" N THR H 278 " --> pdb=" O GLN H 274 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N GLN H 288 " --> pdb=" O LYS H 284 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N GLY H 289 " --> pdb=" O LYS H 285 " (cutoff:3.500A) removed outlier: 3.873A pdb=" N ASP H 290 " --> pdb=" O THR H 286 " (cutoff:3.500A) 702 hydrogen bonds defined for protein. 2046 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.67 Time building geometry restraints manager: 1.31 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 3669 1.34 - 1.46: 1657 1.46 - 1.57: 5952 1.57 - 1.69: 0 1.69 - 1.81: 134 Bond restraints: 11412 Sorted by residual: bond pdb=" N LYS C 69 " pdb=" CA LYS C 69 " ideal model delta sigma weight residual 1.459 1.498 -0.039 1.19e-02 7.06e+03 1.07e+01 bond pdb=" N ASP A 57 " pdb=" CA ASP A 57 " ideal model delta sigma weight residual 1.459 1.434 0.025 1.18e-02 7.18e+03 4.50e+00 bond pdb=" CA LEU F 197 " pdb=" C LEU F 197 " ideal model delta sigma weight residual 1.523 1.550 -0.027 1.28e-02 6.10e+03 4.40e+00 bond pdb=" C TRP A 89 " pdb=" O TRP A 89 " ideal model delta sigma weight residual 1.231 1.271 -0.040 2.00e-02 2.50e+03 3.96e+00 bond pdb=" N ASP A 44 " pdb=" CA ASP A 44 " ideal model delta sigma weight residual 1.459 1.437 0.022 1.17e-02 7.31e+03 3.50e+00 ... (remaining 11407 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.91: 14479 1.91 - 3.82: 661 3.82 - 5.73: 114 5.73 - 7.64: 50 7.64 - 9.55: 17 Bond angle restraints: 15321 Sorted by residual: angle pdb=" N LYS C 69 " pdb=" CA LYS C 69 " pdb=" C LYS C 69 " ideal model delta sigma weight residual 111.07 116.12 -5.05 1.07e+00 8.73e-01 2.23e+01 angle pdb=" N ASP C 70 " pdb=" CA ASP C 70 " pdb=" C ASP C 70 " ideal model delta sigma weight residual 111.28 106.52 4.76 1.09e+00 8.42e-01 1.91e+01 angle pdb=" N ASP A 57 " pdb=" CA ASP A 57 " pdb=" C ASP A 57 " ideal model delta sigma weight residual 111.03 106.21 4.82 1.11e+00 8.12e-01 1.88e+01 angle pdb=" C ALA E 17 " pdb=" N GLU E 18 " pdb=" CA GLU E 18 " ideal model delta sigma weight residual 122.07 128.25 -6.18 1.43e+00 4.89e-01 1.87e+01 angle pdb=" C ALA F 17 " pdb=" N GLU F 18 " pdb=" CA GLU F 18 " ideal model delta sigma weight residual 122.07 128.18 -6.11 1.43e+00 4.89e-01 1.83e+01 ... (remaining 15316 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.99: 6485 15.99 - 31.99: 424 31.99 - 47.98: 115 47.98 - 63.97: 3 63.97 - 79.97: 4 Dihedral angle restraints: 7031 sinusoidal: 2824 harmonic: 4207 Sorted by residual: dihedral pdb=" CA VAL C 36 " pdb=" C VAL C 36 " pdb=" N GLU C 37 " pdb=" CA GLU C 37 " ideal model delta harmonic sigma weight residual 180.00 151.74 28.26 0 5.00e+00 4.00e-02 3.19e+01 dihedral pdb=" CA ALA A 81 " pdb=" C ALA A 81 " pdb=" N ALA A 82 " pdb=" CA ALA A 82 " ideal model delta harmonic sigma weight residual 180.00 155.21 24.79 0 5.00e+00 4.00e-02 2.46e+01 dihedral pdb=" CA PHE F 232 " pdb=" C PHE F 232 " pdb=" N PRO F 233 " pdb=" CA PRO F 233 " ideal model delta harmonic sigma weight residual 180.00 -155.66 -24.34 0 5.00e+00 4.00e-02 2.37e+01 ... (remaining 7028 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.048: 1087 0.048 - 0.095: 482 0.095 - 0.143: 64 0.143 - 0.190: 29 0.190 - 0.238: 5 Chirality restraints: 1667 Sorted by residual: chirality pdb=" CB VAL C 36 " pdb=" CA VAL C 36 " pdb=" CG1 VAL C 36 " pdb=" CG2 VAL C 36 " both_signs ideal model delta sigma weight residual False -2.63 -2.39 -0.24 2.00e-01 2.50e+01 1.42e+00 chirality pdb=" CA ILE E 216 " pdb=" N ILE E 216 " pdb=" C ILE E 216 " pdb=" CB ILE E 216 " both_signs ideal model delta sigma weight residual False 2.43 2.66 -0.22 2.00e-01 2.50e+01 1.24e+00 chirality pdb=" CA ILE G 216 " pdb=" N ILE G 216 " pdb=" C ILE G 216 " pdb=" CB ILE G 216 " both_signs ideal model delta sigma weight residual False 2.43 2.66 -0.22 2.00e-01 2.50e+01 1.24e+00 ... (remaining 1664 not shown) Planarity restraints: 1998 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA PRO F 196 " -0.014 2.00e-02 2.50e+03 2.87e-02 8.21e+00 pdb=" C PRO F 196 " 0.050 2.00e-02 2.50e+03 pdb=" O PRO F 196 " -0.019 2.00e-02 2.50e+03 pdb=" N LEU F 197 " -0.017 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA PRO F 233 " 0.013 2.00e-02 2.50e+03 2.61e-02 6.81e+00 pdb=" C PRO F 233 " -0.045 2.00e-02 2.50e+03 pdb=" O PRO F 233 " 0.017 2.00e-02 2.50e+03 pdb=" N ALA F 234 " 0.015 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA PRO E 233 " -0.013 2.00e-02 2.50e+03 2.61e-02 6.81e+00 pdb=" C PRO E 233 " 0.045 2.00e-02 2.50e+03 pdb=" O PRO E 233 " -0.017 2.00e-02 2.50e+03 pdb=" N ALA E 234 " -0.015 2.00e-02 2.50e+03 ... (remaining 1995 not shown) Histogram of nonbonded interaction distances: 1.32 - 2.04: 6 2.04 - 2.75: 1825 2.75 - 3.47: 16634 3.47 - 4.18: 26466 4.18 - 4.90: 44221 Nonbonded interactions: 89152 Sorted by model distance: nonbonded pdb=" CB LYS C 69 " pdb=" CE1 HIS G 79 " model vdw 1.321 3.660 nonbonded pdb=" O MET C 64 " pdb=" CG2 ILE C 67 " model vdw 1.541 3.460 nonbonded pdb=" CA MET C 64 " pdb=" CG2 ILE C 67 " model vdw 1.752 3.890 nonbonded pdb=" C MET C 64 " pdb=" CG2 ILE C 67 " model vdw 1.768 3.690 nonbonded pdb=" CB LYS C 69 " pdb=" ND1 HIS G 79 " model vdw 1.910 3.520 ... (remaining 89147 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 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' } 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 group one per residue 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: 0.330 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.000 Extract box with map and model: 0.200 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 10.320 Find NCS groups from input model: 0.140 Set up NCS constraints: 0.020 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: 12.200 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7266 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 : 0.006 0.050 11412 Z= 0.288 Angle : 1.025 9.555 15321 Z= 0.570 Chirality : 0.053 0.238 1667 Planarity : 0.005 0.030 1998 Dihedral : 11.709 79.966 4295 Min Nonbonded Distance : 1.321 Molprobity Statistics. All-atom Clashscore : 7.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.55 % Favored : 92.45 % Rotamer: Outliers : 0.34 % Allowed : 5.50 % Favored : 94.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 aren not related in a simple way. whole: -5.85 (0.15), residues: 1404 helix: -3.86 (0.09), residues: 1073 sheet: None (None), residues: 0 loop : -2.85 (0.32), residues: 331 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG B 232 TYR 0.027 0.003 TYR H 45 PHE 0.029 0.004 PHE F 85 TRP 0.024 0.003 TRP F 275 HIS 0.012 0.003 HIS H 251 Details of bonding type rmsd covalent geometry : bond 0.00572 (11412) covalent geometry : angle 1.02506 (15321) hydrogen bonds : bond 0.32024 ( 702) hydrogen bonds : angle 9.93034 ( 2046) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2808 Ramachandran restraints generated. 1404 Oldfield, 0 Emsley, 1404 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2808 Ramachandran restraints generated. 1404 Oldfield, 0 Emsley, 1404 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 661 residues out of total 1181 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 657 time to evaluate : 0.398 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 65 ASP cc_start: 0.8179 (m-30) cc_final: 0.7772 (t0) REVERT: B 203 ILE cc_start: 0.8103 (mm) cc_final: 0.7561 (pt) REVERT: B 226 GLN cc_start: 0.8572 (tt0) cc_final: 0.8293 (tt0) REVERT: B 242 ASP cc_start: 0.7416 (t70) cc_final: 0.7178 (t70) REVERT: C 34 GLN cc_start: 0.8655 (tp40) cc_final: 0.8420 (tp40) REVERT: C 56 GLN cc_start: 0.8428 (mm110) cc_final: 0.8190 (mt0) REVERT: E 57 ASN cc_start: 0.8430 (t0) cc_final: 0.8154 (t0) REVERT: E 58 TRP cc_start: 0.8676 (m-90) cc_final: 0.7844 (m-90) REVERT: E 75 LEU cc_start: 0.8079 (OUTLIER) cc_final: 0.7640 (tp) REVERT: E 104 LEU cc_start: 0.8871 (mt) cc_final: 0.8605 (mt) REVERT: E 122 LYS cc_start: 0.8866 (tttp) cc_final: 0.8406 (tppt) REVERT: E 125 ILE cc_start: 0.8615 (pp) cc_final: 0.8240 (mt) REVERT: E 227 LYS cc_start: 0.8577 (mttm) cc_final: 0.8024 (tptt) REVERT: E 278 THR cc_start: 0.8490 (p) cc_final: 0.8109 (t) REVERT: F 67 GLN cc_start: 0.8085 (mt0) cc_final: 0.7630 (mt0) REVERT: F 78 LYS cc_start: 0.8833 (mmmm) cc_final: 0.8588 (mtpt) REVERT: F 87 ASP cc_start: 0.8699 (m-30) cc_final: 0.8371 (m-30) REVERT: F 135 LEU cc_start: 0.8856 (mt) cc_final: 0.8282 (mt) REVERT: F 175 LEU cc_start: 0.8259 (mm) cc_final: 0.8042 (tt) REVERT: F 268 SER cc_start: 0.8636 (p) cc_final: 0.8314 (m) REVERT: F 276 LEU cc_start: 0.9036 (tm) cc_final: 0.8695 (tm) REVERT: F 279 MET cc_start: 0.7967 (mmt) cc_final: 0.7749 (mmt) REVERT: F 288 GLN cc_start: 0.8289 (mt0) cc_final: 0.7931 (mt0) REVERT: G 71 LEU cc_start: 0.8336 (mt) cc_final: 0.7638 (mt) REVERT: G 93 LYS cc_start: 0.8048 (mtpt) cc_final: 0.7751 (mttt) REVERT: G 175 LEU cc_start: 0.8805 (mm) cc_final: 0.8231 (mt) REVERT: G 239 ARG cc_start: 0.7408 (tpt90) cc_final: 0.7033 (tpt170) REVERT: G 267 ASP cc_start: 0.8694 (p0) cc_final: 0.8028 (t70) REVERT: H 9 GLU cc_start: 0.7757 (tp30) cc_final: 0.7455 (tp30) REVERT: H 53 LYS cc_start: 0.8806 (mtmt) cc_final: 0.8606 (mtpp) REVERT: H 54 MET cc_start: 0.8481 (tpp) cc_final: 0.8255 (mtm) REVERT: H 99 GLU cc_start: 0.7932 (tp30) cc_final: 0.7557 (mp0) REVERT: H 106 ARG cc_start: 0.7680 (mtp85) cc_final: 0.7218 (mtm180) REVERT: H 125 ILE cc_start: 0.8414 (pp) cc_final: 0.8099 (pt) REVERT: H 138 ILE cc_start: 0.9031 (mm) cc_final: 0.8492 (mt) REVERT: H 146 GLU cc_start: 0.7578 (tt0) cc_final: 0.7301 (tp30) REVERT: H 166 LEU cc_start: 0.8344 (tt) cc_final: 0.8127 (tt) REVERT: H 175 LEU cc_start: 0.7788 (mm) cc_final: 0.7495 (mm) REVERT: H 222 LYS cc_start: 0.7666 (ttmt) cc_final: 0.7362 (ptmt) outliers start: 4 outliers final: 0 residues processed: 657 average time/residue: 0.1127 time to fit residues: 101.0745 Evaluate side-chains 394 residues out of total 1181 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 393 time to evaluate : 0.420 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 75 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 98 optimal weight: 2.9990 chunk 107 optimal weight: 9.9990 chunk 10 optimal weight: 1.9990 chunk 66 optimal weight: 2.9990 chunk 130 optimal weight: 2.9990 chunk 124 optimal weight: 8.9990 chunk 103 optimal weight: 4.9990 chunk 77 optimal weight: 0.9990 chunk 122 optimal weight: 3.9990 chunk 91 optimal weight: 4.9990 chunk 55 optimal weight: 7.9990 overall best weight: 2.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 49 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 71 GLN ** B 226 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 66 GLN C 77 ASN D 175 ASN D 188 ASN E 50 ASN E 98 GLN E 191 ASN F 25 GLN F 98 GLN F 162 ASN G 25 GLN G 50 ASN G 162 ASN ** H 50 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 67 GLN H 147 GLN ** H 213 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 226 GLN Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4038 r_free = 0.4038 target = 0.152910 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3755 r_free = 0.3755 target = 0.132001 restraints weight = 25052.455| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3799 r_free = 0.3799 target = 0.135237 restraints weight = 14146.578| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3829 r_free = 0.3829 target = 0.137452 restraints weight = 9274.574| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3847 r_free = 0.3847 target = 0.138832 restraints weight = 6790.504| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3862 r_free = 0.3862 target = 0.139938 restraints weight = 5457.379| |-----------------------------------------------------------------------------| r_work (final): 0.3807 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7500 moved from start: 0.5128 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 11412 Z= 0.194 Angle : 0.807 9.485 15321 Z= 0.435 Chirality : 0.045 0.187 1667 Planarity : 0.004 0.040 1998 Dihedral : 6.492 58.562 1530 Min Nonbonded Distance : 2.396 Molprobity Statistics. All-atom Clashscore : 14.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.34 % Favored : 92.66 % Rotamer: Outliers : 5.17 % Allowed : 18.12 % Favored : 76.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 aren not related in a simple way. whole: -3.35 (0.19), residues: 1404 helix: -1.92 (0.13), residues: 1115 sheet: None (None), residues: 0 loop : -2.56 (0.34), residues: 289 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG G 106 TYR 0.039 0.002 TYR B 235 PHE 0.024 0.003 PHE F 85 TRP 0.014 0.001 TRP E 275 HIS 0.011 0.003 HIS E 213 Details of bonding type rmsd covalent geometry : bond 0.00412 (11412) covalent geometry : angle 0.80713 (15321) hydrogen bonds : bond 0.05739 ( 702) hydrogen bonds : angle 5.45081 ( 2046) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2808 Ramachandran restraints generated. 1404 Oldfield, 0 Emsley, 1404 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2808 Ramachandran restraints generated. 1404 Oldfield, 0 Emsley, 1404 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 503 residues out of total 1181 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 442 time to evaluate : 0.392 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 41 GLU cc_start: 0.9041 (OUTLIER) cc_final: 0.8797 (tt0) REVERT: A 61 SER cc_start: 0.8509 (p) cc_final: 0.7983 (t) REVERT: A 65 ASP cc_start: 0.8293 (m-30) cc_final: 0.7914 (t0) REVERT: A 78 GLU cc_start: 0.8461 (pp20) cc_final: 0.7781 (tp30) REVERT: B 210 ARG cc_start: 0.8018 (mmm160) cc_final: 0.7761 (ttm-80) REVERT: B 229 MET cc_start: 0.8136 (mtm) cc_final: 0.7761 (ttm) REVERT: C 34 GLN cc_start: 0.8575 (tp40) cc_final: 0.8278 (tp40) REVERT: D 184 LYS cc_start: 0.8160 (mtpt) cc_final: 0.7920 (mtpt) REVERT: D 191 ARG cc_start: 0.8465 (mtp85) cc_final: 0.7824 (mtp85) REVERT: D 196 ASN cc_start: 0.8337 (p0) cc_final: 0.7993 (p0) REVERT: E 125 ILE cc_start: 0.8612 (pp) cc_final: 0.8355 (mt) REVERT: E 146 GLU cc_start: 0.7624 (pt0) cc_final: 0.7324 (pt0) REVERT: E 164 CYS cc_start: 0.8505 (m) cc_final: 0.7976 (m) REVERT: E 199 LYS cc_start: 0.8397 (ttpm) cc_final: 0.8187 (ttmt) REVERT: E 227 LYS cc_start: 0.8623 (mttm) cc_final: 0.8236 (tptt) REVERT: E 278 THR cc_start: 0.8210 (p) cc_final: 0.7974 (t) REVERT: F 11 MET cc_start: 0.7693 (ppp) cc_final: 0.7451 (ppp) REVERT: F 24 SER cc_start: 0.7439 (m) cc_final: 0.6943 (t) REVERT: F 51 MET cc_start: 0.7614 (tpp) cc_final: 0.6900 (tpp) REVERT: F 54 MET cc_start: 0.8922 (mmm) cc_final: 0.8654 (tpp) REVERT: F 78 LYS cc_start: 0.8512 (mmmm) cc_final: 0.8310 (mtmt) REVERT: F 80 ASP cc_start: 0.8024 (OUTLIER) cc_final: 0.7450 (m-30) REVERT: F 87 ASP cc_start: 0.8337 (m-30) cc_final: 0.7882 (m-30) REVERT: F 125 ILE cc_start: 0.8421 (pp) cc_final: 0.7996 (mt) REVERT: F 175 LEU cc_start: 0.8548 (mm) cc_final: 0.7828 (tt) REVERT: F 244 MET cc_start: 0.6758 (ttm) cc_final: 0.6412 (ttm) REVERT: F 260 THR cc_start: 0.8394 (p) cc_final: 0.7957 (p) REVERT: F 266 TYR cc_start: 0.8200 (t80) cc_final: 0.7836 (t80) REVERT: F 268 SER cc_start: 0.8243 (p) cc_final: 0.7861 (m) REVERT: F 271 ARG cc_start: 0.7292 (tpt-90) cc_final: 0.6619 (tpp-160) REVERT: F 279 MET cc_start: 0.8315 (mmt) cc_final: 0.7648 (mmt) REVERT: G 105 MET cc_start: 0.8614 (tpp) cc_final: 0.8272 (tpp) REVERT: G 113 ASP cc_start: 0.7422 (p0) cc_final: 0.6780 (t0) REVERT: G 114 MET cc_start: 0.8254 (ttm) cc_final: 0.7851 (ttt) REVERT: G 147 GLN cc_start: 0.7699 (tt0) cc_final: 0.7250 (mt0) REVERT: G 264 LYS cc_start: 0.8305 (tptp) cc_final: 0.7654 (tptp) REVERT: G 267 ASP cc_start: 0.8683 (p0) cc_final: 0.8335 (p0) REVERT: H 76 GLN cc_start: 0.8056 (mp10) cc_final: 0.7366 (tm-30) REVERT: H 103 CYS cc_start: 0.8297 (p) cc_final: 0.7997 (p) REVERT: H 106 ARG cc_start: 0.7927 (mtp85) cc_final: 0.7302 (mtm180) REVERT: H 140 LYS cc_start: 0.8614 (mttt) cc_final: 0.8309 (mtmt) REVERT: H 150 ASP cc_start: 0.8590 (t0) cc_final: 0.8113 (t0) REVERT: H 204 ASP cc_start: 0.8202 (OUTLIER) cc_final: 0.7616 (m-30) outliers start: 61 outliers final: 37 residues processed: 469 average time/residue: 0.1100 time to fit residues: 71.3038 Evaluate side-chains 409 residues out of total 1181 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 369 time to evaluate : 0.433 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 32 LEU Chi-restraints excluded: chain A residue 41 GLU Chi-restraints excluded: chain A residue 45 ILE Chi-restraints excluded: chain A residue 48 VAL Chi-restraints excluded: chain A residue 50 VAL Chi-restraints excluded: chain A residue 55 GLU Chi-restraints excluded: chain A residue 79 THR Chi-restraints excluded: chain B residue 236 ASN Chi-restraints excluded: chain B residue 237 VAL Chi-restraints excluded: chain C residue 26 LEU Chi-restraints excluded: chain C residue 78 LEU Chi-restraints excluded: chain C residue 79 THR Chi-restraints excluded: chain D residue 175 ASN Chi-restraints excluded: chain D residue 181 ILE Chi-restraints excluded: chain E residue 103 CYS Chi-restraints excluded: chain E residue 127 ILE Chi-restraints excluded: chain E residue 166 LEU Chi-restraints excluded: chain E residue 183 ASP Chi-restraints excluded: chain E residue 256 VAL Chi-restraints excluded: chain F residue 38 ILE Chi-restraints excluded: chain F residue 80 ASP Chi-restraints excluded: chain F residue 83 THR Chi-restraints excluded: chain F residue 84 CYS Chi-restraints excluded: chain F residue 118 THR Chi-restraints excluded: chain F residue 142 ILE Chi-restraints excluded: chain G residue 50 ASN Chi-restraints excluded: chain G residue 73 LEU Chi-restraints excluded: chain G residue 84 CYS Chi-restraints excluded: chain G residue 108 ILE Chi-restraints excluded: chain G residue 125 ILE Chi-restraints excluded: chain G residue 136 VAL Chi-restraints excluded: chain G residue 193 MET Chi-restraints excluded: chain G residue 197 LEU Chi-restraints excluded: chain G residue 219 LEU Chi-restraints excluded: chain G residue 259 TYR Chi-restraints excluded: chain H residue 38 ILE Chi-restraints excluded: chain H residue 101 ILE Chi-restraints excluded: chain H residue 110 ILE Chi-restraints excluded: chain H residue 127 ILE Chi-restraints excluded: chain H residue 204 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 82 optimal weight: 5.9990 chunk 45 optimal weight: 9.9990 chunk 29 optimal weight: 3.9990 chunk 61 optimal weight: 9.9990 chunk 81 optimal weight: 4.9990 chunk 101 optimal weight: 9.9990 chunk 46 optimal weight: 8.9990 chunk 49 optimal weight: 0.7980 chunk 63 optimal weight: 0.8980 chunk 96 optimal weight: 10.0000 chunk 27 optimal weight: 0.3980 overall best weight: 2.2184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 49 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 226 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 53 GLN C 66 GLN D 175 ASN D 188 ASN E 177 GLN E 187 GLN F 50 ASN ** F 255 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 90 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3962 r_free = 0.3962 target = 0.144018 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3664 r_free = 0.3664 target = 0.122610 restraints weight = 25823.587| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3709 r_free = 0.3709 target = 0.125776 restraints weight = 15145.890| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3739 r_free = 0.3739 target = 0.127906 restraints weight = 10189.367| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3758 r_free = 0.3758 target = 0.129310 restraints weight = 7646.987| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 39)----------------| | r_work = 0.3772 r_free = 0.3772 target = 0.130292 restraints weight = 6204.572| |-----------------------------------------------------------------------------| r_work (final): 0.3769 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7576 moved from start: 0.6003 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 11412 Z= 0.172 Angle : 0.755 14.491 15321 Z= 0.397 Chirality : 0.044 0.180 1667 Planarity : 0.003 0.045 1998 Dihedral : 6.130 64.964 1528 Min Nonbonded Distance : 2.449 Molprobity Statistics. All-atom Clashscore : 15.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.12 % Favored : 92.88 % Rotamer: Outliers : 6.69 % Allowed : 20.91 % Favored : 72.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 aren not related in a simple way. whole: -2.14 (0.21), residues: 1404 helix: -0.96 (0.15), residues: 1119 sheet: None (None), residues: 0 loop : -2.67 (0.34), residues: 285 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG G 239 TYR 0.034 0.002 TYR B 235 PHE 0.018 0.002 PHE F 85 TRP 0.009 0.001 TRP E 275 HIS 0.009 0.002 HIS E 79 Details of bonding type rmsd covalent geometry : bond 0.00366 (11412) covalent geometry : angle 0.75457 (15321) hydrogen bonds : bond 0.04713 ( 702) hydrogen bonds : angle 5.01346 ( 2046) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2808 Ramachandran restraints generated. 1404 Oldfield, 0 Emsley, 1404 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2808 Ramachandran restraints generated. 1404 Oldfield, 0 Emsley, 1404 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 475 residues out of total 1181 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 79 poor density : 396 time to evaluate : 0.357 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 56 ARG cc_start: 0.9024 (ptm160) cc_final: 0.8772 (ptm160) REVERT: A 57 ASP cc_start: 0.7950 (t0) cc_final: 0.7725 (t0) REVERT: A 61 SER cc_start: 0.8179 (p) cc_final: 0.7979 (t) REVERT: A 65 ASP cc_start: 0.8274 (m-30) cc_final: 0.7808 (t0) REVERT: A 66 ARG cc_start: 0.8321 (mmm160) cc_final: 0.8056 (mmp-170) REVERT: A 68 ASP cc_start: 0.7371 (t0) cc_final: 0.7134 (t0) REVERT: A 78 GLU cc_start: 0.8734 (pp20) cc_final: 0.7939 (tp30) REVERT: B 193 SER cc_start: 0.8582 (p) cc_final: 0.8206 (t) REVERT: B 203 ILE cc_start: 0.8185 (mm) cc_final: 0.7790 (pt) REVERT: B 210 ARG cc_start: 0.8104 (mmm160) cc_final: 0.7754 (ttm-80) REVERT: B 229 MET cc_start: 0.8055 (mtm) cc_final: 0.7717 (ttm) REVERT: B 246 ARG cc_start: 0.8472 (ttm170) cc_final: 0.8051 (mtm-85) REVERT: C 34 GLN cc_start: 0.8486 (tp40) cc_final: 0.8108 (tp40) REVERT: C 66 GLN cc_start: 0.8411 (mt0) cc_final: 0.8147 (mm-40) REVERT: D 184 LYS cc_start: 0.8322 (mtpt) cc_final: 0.8019 (mtpt) REVERT: D 196 ASN cc_start: 0.7910 (p0) cc_final: 0.7565 (p0) REVERT: E 40 GLU cc_start: 0.7582 (tp30) cc_final: 0.7064 (mp0) REVERT: E 122 LYS cc_start: 0.9325 (tppt) cc_final: 0.8929 (tppt) REVERT: E 125 ILE cc_start: 0.8759 (pp) cc_final: 0.8370 (mt) REVERT: E 164 CYS cc_start: 0.8618 (m) cc_final: 0.8077 (m) REVERT: E 227 LYS cc_start: 0.8563 (mttm) cc_final: 0.8195 (tptt) REVERT: E 246 LYS cc_start: 0.9074 (mmtt) cc_final: 0.8845 (mmmt) REVERT: E 278 THR cc_start: 0.8227 (p) cc_final: 0.7988 (t) REVERT: F 11 MET cc_start: 0.7792 (ppp) cc_final: 0.7534 (ppp) REVERT: F 24 SER cc_start: 0.7493 (m) cc_final: 0.6988 (t) REVERT: F 51 MET cc_start: 0.7718 (tpp) cc_final: 0.6996 (tpp) REVERT: F 78 LYS cc_start: 0.8619 (mmmm) cc_final: 0.8263 (mtmt) REVERT: F 80 ASP cc_start: 0.8003 (OUTLIER) cc_final: 0.7516 (m-30) REVERT: F 87 ASP cc_start: 0.8664 (m-30) cc_final: 0.8319 (m-30) REVERT: F 125 ILE cc_start: 0.8586 (OUTLIER) cc_final: 0.8236 (mt) REVERT: F 140 LYS cc_start: 0.8301 (OUTLIER) cc_final: 0.8036 (mtmm) REVERT: F 155 GLU cc_start: 0.7621 (tm-30) cc_final: 0.7413 (tm-30) REVERT: F 158 ASN cc_start: 0.9026 (p0) cc_final: 0.8729 (p0) REVERT: F 175 LEU cc_start: 0.8683 (mm) cc_final: 0.8009 (tt) REVERT: F 226 GLN cc_start: 0.7979 (tp-100) cc_final: 0.7716 (tp-100) REVERT: F 244 MET cc_start: 0.6926 (ttm) cc_final: 0.6603 (ttm) REVERT: F 266 TYR cc_start: 0.8228 (t80) cc_final: 0.7992 (t80) REVERT: F 268 SER cc_start: 0.8311 (p) cc_final: 0.7739 (m) REVERT: F 279 MET cc_start: 0.8364 (mmt) cc_final: 0.7803 (mmt) REVERT: G 37 LYS cc_start: 0.7378 (OUTLIER) cc_final: 0.7108 (tptt) REVERT: G 105 MET cc_start: 0.8476 (tpp) cc_final: 0.8111 (tpp) REVERT: G 106 ARG cc_start: 0.7069 (ttm110) cc_final: 0.6856 (ttm110) REVERT: G 113 ASP cc_start: 0.7512 (p0) cc_final: 0.6662 (t0) REVERT: G 152 TYR cc_start: 0.9101 (OUTLIER) cc_final: 0.8526 (m-10) REVERT: G 158 ASN cc_start: 0.5084 (m110) cc_final: 0.4871 (m110) REVERT: G 179 GLN cc_start: 0.8551 (tp-100) cc_final: 0.7690 (tt0) REVERT: G 239 ARG cc_start: 0.7211 (tpt170) cc_final: 0.6593 (tpt170) REVERT: G 265 GLU cc_start: 0.7706 (pp20) cc_final: 0.7407 (tp30) REVERT: G 267 ASP cc_start: 0.8679 (p0) cc_final: 0.8458 (p0) REVERT: H 40 GLU cc_start: 0.8420 (tp30) cc_final: 0.8216 (tp30) REVERT: H 51 MET cc_start: 0.8102 (mtt) cc_final: 0.7729 (mtm) REVERT: H 76 GLN cc_start: 0.8169 (mp10) cc_final: 0.7517 (tm-30) REVERT: H 103 CYS cc_start: 0.8223 (p) cc_final: 0.7981 (p) REVERT: H 105 MET cc_start: 0.8762 (tpt) cc_final: 0.8332 (tpt) REVERT: H 125 ILE cc_start: 0.8645 (OUTLIER) cc_final: 0.8161 (mt) REVERT: H 204 ASP cc_start: 0.8261 (OUTLIER) cc_final: 0.7807 (m-30) REVERT: H 271 ARG cc_start: 0.8246 (mmm-85) cc_final: 0.6933 (ttt180) outliers start: 79 outliers final: 43 residues processed: 433 average time/residue: 0.1117 time to fit residues: 66.7378 Evaluate side-chains 407 residues out of total 1181 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 357 time to evaluate : 0.426 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 32 LEU Chi-restraints excluded: chain A residue 48 VAL Chi-restraints excluded: chain A residue 55 GLU Chi-restraints excluded: chain A residue 62 GLU Chi-restraints excluded: chain B residue 209 ILE Chi-restraints excluded: chain B residue 236 ASN Chi-restraints excluded: chain B residue 237 VAL Chi-restraints excluded: chain C residue 78 LEU Chi-restraints excluded: chain C residue 79 THR Chi-restraints excluded: chain D residue 175 ASN Chi-restraints excluded: chain E residue 103 CYS Chi-restraints excluded: chain E residue 183 ASP Chi-restraints excluded: chain E residue 211 LEU Chi-restraints excluded: chain E residue 256 VAL Chi-restraints excluded: chain E residue 260 THR Chi-restraints excluded: chain F residue 38 ILE Chi-restraints excluded: chain F residue 80 ASP Chi-restraints excluded: chain F residue 83 THR Chi-restraints excluded: chain F residue 84 CYS Chi-restraints excluded: chain F residue 125 ILE Chi-restraints excluded: chain F residue 140 LYS Chi-restraints excluded: chain F residue 142 ILE Chi-restraints excluded: chain F residue 219 LEU Chi-restraints excluded: chain F residue 238 SER Chi-restraints excluded: chain G residue 21 VAL Chi-restraints excluded: chain G residue 37 LYS Chi-restraints excluded: chain G residue 84 CYS Chi-restraints excluded: chain G residue 96 ASP Chi-restraints excluded: chain G residue 108 ILE Chi-restraints excluded: chain G residue 125 ILE Chi-restraints excluded: chain G residue 136 VAL Chi-restraints excluded: chain G residue 152 TYR Chi-restraints excluded: chain G residue 197 LEU Chi-restraints excluded: chain G residue 219 LEU Chi-restraints excluded: chain G residue 256 VAL Chi-restraints excluded: chain G residue 259 TYR Chi-restraints excluded: chain H residue 45 TYR Chi-restraints excluded: chain H residue 71 LEU Chi-restraints excluded: chain H residue 101 ILE Chi-restraints excluded: chain H residue 110 ILE Chi-restraints excluded: chain H residue 116 ARG Chi-restraints excluded: chain H residue 125 ILE Chi-restraints excluded: chain H residue 127 ILE Chi-restraints excluded: chain H residue 171 TYR Chi-restraints excluded: chain H residue 194 ASP Chi-restraints excluded: chain H residue 197 LEU Chi-restraints excluded: chain H residue 204 ASP Chi-restraints excluded: chain H residue 219 LEU Chi-restraints excluded: chain H residue 228 TYR Chi-restraints excluded: chain H residue 243 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 37 optimal weight: 0.2980 chunk 135 optimal weight: 8.9990 chunk 96 optimal weight: 2.9990 chunk 107 optimal weight: 5.9990 chunk 60 optimal weight: 8.9990 chunk 35 optimal weight: 4.9990 chunk 85 optimal weight: 6.9990 chunk 72 optimal weight: 0.6980 chunk 68 optimal weight: 10.0000 chunk 124 optimal weight: 0.8980 chunk 27 optimal weight: 10.0000 overall best weight: 1.9784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 199 HIS ** B 226 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 175 ASN D 188 ASN E 254 GLN F 50 ASN F 213 HIS ** G 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 254 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4010 r_free = 0.4010 target = 0.147033 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3723 r_free = 0.3723 target = 0.125895 restraints weight = 25995.371| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3762 r_free = 0.3762 target = 0.128698 restraints weight = 15572.819| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3788 r_free = 0.3788 target = 0.130584 restraints weight = 10760.186| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3804 r_free = 0.3804 target = 0.131837 restraints weight = 8274.648| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3815 r_free = 0.3815 target = 0.132674 restraints weight = 6900.626| |-----------------------------------------------------------------------------| r_work (final): 0.3812 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7579 moved from start: 0.6484 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 11412 Z= 0.164 Angle : 0.738 11.283 15321 Z= 0.383 Chirality : 0.043 0.179 1667 Planarity : 0.003 0.048 1998 Dihedral : 6.018 66.776 1528 Min Nonbonded Distance : 2.504 Molprobity Statistics. All-atom Clashscore : 15.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.34 % Favored : 92.66 % Rotamer: Outliers : 6.35 % Allowed : 22.78 % Favored : 70.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 aren not related in a simple way. whole: -1.65 (0.22), residues: 1404 helix: -0.57 (0.15), residues: 1131 sheet: None (None), residues: 0 loop : -2.79 (0.36), residues: 273 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG E 239 TYR 0.034 0.002 TYR B 235 PHE 0.018 0.002 PHE H 85 TRP 0.008 0.001 TRP H 275 HIS 0.008 0.002 HIS E 79 Details of bonding type rmsd covalent geometry : bond 0.00344 (11412) covalent geometry : angle 0.73792 (15321) hydrogen bonds : bond 0.04252 ( 702) hydrogen bonds : angle 4.75472 ( 2046) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2808 Ramachandran restraints generated. 1404 Oldfield, 0 Emsley, 1404 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2808 Ramachandran restraints generated. 1404 Oldfield, 0 Emsley, 1404 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 463 residues out of total 1181 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 388 time to evaluate : 0.423 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 44 ASP cc_start: 0.8345 (t0) cc_final: 0.7987 (t0) REVERT: A 57 ASP cc_start: 0.7693 (t0) cc_final: 0.7472 (t0) REVERT: A 61 SER cc_start: 0.8114 (p) cc_final: 0.7872 (t) REVERT: A 65 ASP cc_start: 0.8204 (m-30) cc_final: 0.7831 (t0) REVERT: A 70 LEU cc_start: 0.9282 (tp) cc_final: 0.8931 (tt) REVERT: A 78 GLU cc_start: 0.8643 (pp20) cc_final: 0.7896 (tp30) REVERT: B 193 SER cc_start: 0.8667 (p) cc_final: 0.8314 (t) REVERT: B 200 SER cc_start: 0.8807 (t) cc_final: 0.8463 (p) REVERT: B 203 ILE cc_start: 0.8115 (mm) cc_final: 0.7332 (pt) REVERT: B 210 ARG cc_start: 0.7949 (mmm160) cc_final: 0.7646 (ttm-80) REVERT: B 215 MET cc_start: 0.8268 (ppp) cc_final: 0.8063 (ppp) REVERT: B 229 MET cc_start: 0.7978 (mtm) cc_final: 0.7727 (ttm) REVERT: B 246 ARG cc_start: 0.8411 (ttm170) cc_final: 0.7771 (mtm-85) REVERT: C 26 LEU cc_start: 0.7966 (tm) cc_final: 0.7585 (mt) REVERT: D 196 ASN cc_start: 0.7682 (p0) cc_final: 0.7353 (p0) REVERT: E 40 GLU cc_start: 0.7570 (tp30) cc_final: 0.7118 (mp0) REVERT: E 122 LYS cc_start: 0.9313 (tppt) cc_final: 0.8779 (tppt) REVERT: E 125 ILE cc_start: 0.8737 (OUTLIER) cc_final: 0.8145 (mt) REVERT: E 164 CYS cc_start: 0.8343 (m) cc_final: 0.7918 (m) REVERT: E 168 VAL cc_start: 0.8619 (OUTLIER) cc_final: 0.8400 (p) REVERT: E 227 LYS cc_start: 0.8440 (mttm) cc_final: 0.8177 (tptt) REVERT: E 246 LYS cc_start: 0.9109 (mmtt) cc_final: 0.8905 (mmmt) REVERT: E 278 THR cc_start: 0.8113 (p) cc_final: 0.7851 (t) REVERT: F 24 SER cc_start: 0.7562 (m) cc_final: 0.7096 (t) REVERT: F 51 MET cc_start: 0.7597 (tpp) cc_final: 0.7334 (tpp) REVERT: F 78 LYS cc_start: 0.8568 (mmmm) cc_final: 0.8184 (mtmt) REVERT: F 80 ASP cc_start: 0.7730 (OUTLIER) cc_final: 0.7487 (m-30) REVERT: F 87 ASP cc_start: 0.8552 (m-30) cc_final: 0.8279 (m-30) REVERT: F 103 CYS cc_start: 0.8307 (m) cc_final: 0.7879 (p) REVERT: F 158 ASN cc_start: 0.9158 (p0) cc_final: 0.8803 (p0) REVERT: F 171 TYR cc_start: 0.8280 (m-80) cc_final: 0.6877 (m-80) REVERT: F 175 LEU cc_start: 0.8647 (mm) cc_final: 0.7982 (tt) REVERT: F 193 MET cc_start: 0.7458 (OUTLIER) cc_final: 0.6875 (mmm) REVERT: F 226 GLN cc_start: 0.7834 (tp-100) cc_final: 0.7577 (tp-100) REVERT: F 244 MET cc_start: 0.6551 (ttm) cc_final: 0.6169 (ttm) REVERT: F 268 SER cc_start: 0.8293 (p) cc_final: 0.7538 (m) REVERT: G 11 MET cc_start: 0.7276 (tmm) cc_final: 0.7059 (mmp) REVERT: G 79 HIS cc_start: 0.6532 (t-90) cc_final: 0.6164 (t-170) REVERT: G 105 MET cc_start: 0.8422 (tpp) cc_final: 0.8005 (tpp) REVERT: G 106 ARG cc_start: 0.6973 (ttm110) cc_final: 0.6659 (ttm110) REVERT: G 113 ASP cc_start: 0.7273 (p0) cc_final: 0.6376 (t0) REVERT: G 152 TYR cc_start: 0.9148 (OUTLIER) cc_final: 0.8557 (m-10) REVERT: G 163 LYS cc_start: 0.8465 (mtmt) cc_final: 0.7914 (mttp) REVERT: G 227 LYS cc_start: 0.8793 (mmtt) cc_final: 0.8574 (mmtt) REVERT: H 45 TYR cc_start: 0.7347 (OUTLIER) cc_final: 0.6812 (t80) REVERT: H 51 MET cc_start: 0.8021 (mtt) cc_final: 0.7572 (mtm) REVERT: H 76 GLN cc_start: 0.7977 (mp10) cc_final: 0.7375 (tm-30) REVERT: H 125 ILE cc_start: 0.8735 (OUTLIER) cc_final: 0.8375 (mt) REVERT: H 140 LYS cc_start: 0.8349 (mttt) cc_final: 0.8071 (mtmt) REVERT: H 146 GLU cc_start: 0.7854 (tt0) cc_final: 0.7623 (tp30) REVERT: H 153 LYS cc_start: 0.8805 (mtpp) cc_final: 0.8573 (mtpt) REVERT: H 204 ASP cc_start: 0.8133 (OUTLIER) cc_final: 0.7709 (m-30) REVERT: H 222 LYS cc_start: 0.6473 (ttmt) cc_final: 0.5973 (ttmt) REVERT: H 248 LEU cc_start: 0.7328 (OUTLIER) cc_final: 0.7120 (mm) REVERT: H 271 ARG cc_start: 0.8305 (mmm-85) cc_final: 0.7165 (ttt180) outliers start: 75 outliers final: 47 residues processed: 421 average time/residue: 0.1119 time to fit residues: 64.8640 Evaluate side-chains 406 residues out of total 1181 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 350 time to evaluate : 0.465 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 32 LEU Chi-restraints excluded: chain A residue 35 THR Chi-restraints excluded: chain A residue 48 VAL Chi-restraints excluded: chain A residue 53 VAL Chi-restraints excluded: chain A residue 55 GLU Chi-restraints excluded: chain A residue 62 GLU Chi-restraints excluded: chain A residue 79 THR Chi-restraints excluded: chain B residue 209 ILE Chi-restraints excluded: chain B residue 236 ASN Chi-restraints excluded: chain B residue 237 VAL Chi-restraints excluded: chain C residue 49 MET Chi-restraints excluded: chain C residue 78 LEU Chi-restraints excluded: chain C residue 79 THR Chi-restraints excluded: chain D residue 160 LEU Chi-restraints excluded: chain D residue 175 ASN Chi-restraints excluded: chain E residue 103 CYS Chi-restraints excluded: chain E residue 125 ILE Chi-restraints excluded: chain E residue 168 VAL Chi-restraints excluded: chain E residue 211 LEU Chi-restraints excluded: chain E residue 256 VAL Chi-restraints excluded: chain E residue 272 LEU Chi-restraints excluded: chain E residue 277 THR Chi-restraints excluded: chain F residue 50 ASN Chi-restraints excluded: chain F residue 80 ASP Chi-restraints excluded: chain F residue 83 THR Chi-restraints excluded: chain F residue 84 CYS Chi-restraints excluded: chain F residue 118 THR Chi-restraints excluded: chain F residue 127 ILE Chi-restraints excluded: chain F residue 142 ILE Chi-restraints excluded: chain F residue 193 MET Chi-restraints excluded: chain F residue 219 LEU Chi-restraints excluded: chain F residue 238 SER Chi-restraints excluded: chain G residue 21 VAL Chi-restraints excluded: chain G residue 84 CYS Chi-restraints excluded: chain G residue 108 ILE Chi-restraints excluded: chain G residue 125 ILE Chi-restraints excluded: chain G residue 135 LEU Chi-restraints excluded: chain G residue 136 VAL Chi-restraints excluded: chain G residue 152 TYR Chi-restraints excluded: chain G residue 197 LEU Chi-restraints excluded: chain G residue 256 VAL Chi-restraints excluded: chain G residue 259 TYR Chi-restraints excluded: chain H residue 45 TYR Chi-restraints excluded: chain H residue 70 GLN Chi-restraints excluded: chain H residue 71 LEU Chi-restraints excluded: chain H residue 101 ILE Chi-restraints excluded: chain H residue 116 ARG Chi-restraints excluded: chain H residue 125 ILE Chi-restraints excluded: chain H residue 127 ILE Chi-restraints excluded: chain H residue 171 TYR Chi-restraints excluded: chain H residue 197 LEU Chi-restraints excluded: chain H residue 204 ASP Chi-restraints excluded: chain H residue 211 LEU Chi-restraints excluded: chain H residue 219 LEU Chi-restraints excluded: chain H residue 228 TYR Chi-restraints excluded: chain H residue 248 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 6 optimal weight: 10.0000 chunk 39 optimal weight: 5.9990 chunk 64 optimal weight: 6.9990 chunk 79 optimal weight: 0.0570 chunk 40 optimal weight: 1.9990 chunk 53 optimal weight: 5.9990 chunk 50 optimal weight: 9.9990 chunk 51 optimal weight: 2.9990 chunk 132 optimal weight: 6.9990 chunk 37 optimal weight: 9.9990 chunk 118 optimal weight: 3.9990 overall best weight: 3.0106 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 226 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 159 ASN D 175 ASN D 188 ASN E 50 ASN ** E 147 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 50 ASN ** F 255 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3965 r_free = 0.3965 target = 0.143857 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3680 r_free = 0.3680 target = 0.122705 restraints weight = 25274.555| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3724 r_free = 0.3724 target = 0.125777 restraints weight = 14336.589| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3751 r_free = 0.3751 target = 0.127793 restraints weight = 9550.716| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3770 r_free = 0.3770 target = 0.129153 restraints weight = 7170.709| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 42)----------------| | r_work = 0.3781 r_free = 0.3781 target = 0.130027 restraints weight = 5871.906| |-----------------------------------------------------------------------------| r_work (final): 0.3776 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7645 moved from start: 0.6909 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 11412 Z= 0.190 Angle : 0.755 10.683 15321 Z= 0.396 Chirality : 0.044 0.193 1667 Planarity : 0.004 0.050 1998 Dihedral : 6.034 69.361 1528 Min Nonbonded Distance : 2.443 Molprobity Statistics. All-atom Clashscore : 16.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.19 % Favored : 91.81 % Rotamer: Outliers : 6.52 % Allowed : 25.32 % Favored : 68.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 aren not related in a simple way. whole: -1.58 (0.22), residues: 1404 helix: -0.44 (0.15), residues: 1152 sheet: None (None), residues: 0 loop : -3.37 (0.34), residues: 252 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG A 56 TYR 0.039 0.002 TYR B 235 PHE 0.017 0.002 PHE H 85 TRP 0.008 0.001 TRP F 275 HIS 0.008 0.002 HIS E 123 Details of bonding type rmsd covalent geometry : bond 0.00412 (11412) covalent geometry : angle 0.75465 (15321) hydrogen bonds : bond 0.04251 ( 702) hydrogen bonds : angle 4.74620 ( 2046) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2808 Ramachandran restraints generated. 1404 Oldfield, 0 Emsley, 1404 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2808 Ramachandran restraints generated. 1404 Oldfield, 0 Emsley, 1404 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 457 residues out of total 1181 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 380 time to evaluate : 0.387 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 44 ASP cc_start: 0.8658 (t0) cc_final: 0.8128 (t0) REVERT: A 57 ASP cc_start: 0.7972 (t0) cc_final: 0.7697 (t0) REVERT: A 70 LEU cc_start: 0.9271 (tp) cc_final: 0.8957 (tt) REVERT: B 193 SER cc_start: 0.8823 (p) cc_final: 0.8468 (t) REVERT: B 199 HIS cc_start: 0.7121 (t-90) cc_final: 0.6848 (t70) REVERT: B 200 SER cc_start: 0.8575 (t) cc_final: 0.8332 (p) REVERT: B 203 ILE cc_start: 0.8139 (mm) cc_final: 0.7608 (pt) REVERT: B 210 ARG cc_start: 0.8087 (mmm160) cc_final: 0.7745 (ttm-80) REVERT: B 215 MET cc_start: 0.8358 (ppp) cc_final: 0.8034 (ppp) REVERT: B 216 PHE cc_start: 0.8422 (OUTLIER) cc_final: 0.7754 (m-80) REVERT: B 229 MET cc_start: 0.8003 (mtm) cc_final: 0.7674 (ttm) REVERT: B 246 ARG cc_start: 0.8369 (ttm170) cc_final: 0.7838 (mtm-85) REVERT: C 34 GLN cc_start: 0.8304 (tp40) cc_final: 0.7945 (tp40) REVERT: C 66 GLN cc_start: 0.8483 (mm-40) cc_final: 0.8096 (mm-40) REVERT: D 184 LYS cc_start: 0.8355 (mtpt) cc_final: 0.7822 (mtpt) REVERT: D 188 ASN cc_start: 0.9057 (m-40) cc_final: 0.8610 (m110) REVERT: D 196 ASN cc_start: 0.7694 (p0) cc_final: 0.7350 (p0) REVERT: E 50 ASN cc_start: 0.8843 (OUTLIER) cc_final: 0.8638 (t0) REVERT: E 72 HIS cc_start: 0.7206 (m90) cc_final: 0.6793 (m170) REVERT: E 122 LYS cc_start: 0.9367 (tppt) cc_final: 0.8954 (tppt) REVERT: E 125 ILE cc_start: 0.8737 (OUTLIER) cc_final: 0.8247 (mt) REVERT: E 164 CYS cc_start: 0.8491 (m) cc_final: 0.8016 (m) REVERT: E 278 THR cc_start: 0.8236 (p) cc_final: 0.7996 (t) REVERT: F 24 SER cc_start: 0.7567 (m) cc_final: 0.7085 (t) REVERT: F 51 MET cc_start: 0.7753 (tpp) cc_final: 0.7089 (tpp) REVERT: F 78 LYS cc_start: 0.8585 (mmmm) cc_final: 0.8251 (mtpt) REVERT: F 80 ASP cc_start: 0.7804 (OUTLIER) cc_final: 0.7488 (m-30) REVERT: F 87 ASP cc_start: 0.8591 (m-30) cc_final: 0.8237 (m-30) REVERT: F 114 MET cc_start: 0.8687 (tpp) cc_final: 0.8348 (ttm) REVERT: F 156 GLU cc_start: 0.8299 (tp30) cc_final: 0.7973 (tp30) REVERT: F 158 ASN cc_start: 0.9147 (p0) cc_final: 0.8939 (p0) REVERT: F 175 LEU cc_start: 0.8803 (mm) cc_final: 0.8192 (tt) REVERT: F 191 ASN cc_start: 0.8273 (t0) cc_final: 0.8065 (t0) REVERT: F 226 GLN cc_start: 0.8078 (tp-100) cc_final: 0.7837 (tp-100) REVERT: G 85 PHE cc_start: 0.8870 (OUTLIER) cc_final: 0.8589 (m-10) REVERT: G 93 LYS cc_start: 0.8480 (OUTLIER) cc_final: 0.8065 (mppt) REVERT: G 94 LYS cc_start: 0.7639 (OUTLIER) cc_final: 0.7415 (mtmm) REVERT: G 105 MET cc_start: 0.8422 (tpp) cc_final: 0.8021 (tpp) REVERT: G 113 ASP cc_start: 0.7340 (p0) cc_final: 0.6606 (t0) REVERT: G 152 TYR cc_start: 0.9147 (OUTLIER) cc_final: 0.8373 (m-10) REVERT: G 163 LYS cc_start: 0.8635 (mtmt) cc_final: 0.8016 (mttp) REVERT: G 222 LYS cc_start: 0.7398 (ttmt) cc_final: 0.7060 (tttt) REVERT: G 259 TYR cc_start: 0.8219 (OUTLIER) cc_final: 0.7872 (t80) REVERT: H 39 GLU cc_start: 0.8096 (OUTLIER) cc_final: 0.7813 (mp0) REVERT: H 51 MET cc_start: 0.8157 (mtt) cc_final: 0.7691 (mtm) REVERT: H 76 GLN cc_start: 0.7948 (mp10) cc_final: 0.7196 (tm-30) REVERT: H 87 ASP cc_start: 0.8137 (t70) cc_final: 0.7824 (t70) REVERT: H 125 ILE cc_start: 0.8706 (OUTLIER) cc_final: 0.8375 (mt) REVERT: H 140 LYS cc_start: 0.8740 (mttt) cc_final: 0.8222 (mtmt) REVERT: H 146 GLU cc_start: 0.8202 (tt0) cc_final: 0.7751 (tm-30) REVERT: H 153 LYS cc_start: 0.8906 (mtpp) cc_final: 0.8690 (mtpt) REVERT: H 204 ASP cc_start: 0.8243 (OUTLIER) cc_final: 0.7832 (m-30) REVERT: H 222 LYS cc_start: 0.6956 (ttmt) cc_final: 0.6592 (ttmt) REVERT: H 271 ARG cc_start: 0.8480 (mmm-85) cc_final: 0.7255 (ttt180) outliers start: 77 outliers final: 52 residues processed: 419 average time/residue: 0.1123 time to fit residues: 65.0085 Evaluate side-chains 407 residues out of total 1181 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 343 time to evaluate : 0.445 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 32 LEU Chi-restraints excluded: chain A residue 35 THR Chi-restraints excluded: chain A residue 48 VAL Chi-restraints excluded: chain A residue 55 GLU Chi-restraints excluded: chain A residue 79 THR Chi-restraints excluded: chain B residue 209 ILE Chi-restraints excluded: chain B residue 211 GLU Chi-restraints excluded: chain B residue 216 PHE Chi-restraints excluded: chain B residue 236 ASN Chi-restraints excluded: chain B residue 237 VAL Chi-restraints excluded: chain C residue 49 MET Chi-restraints excluded: chain C residue 78 LEU Chi-restraints excluded: chain C residue 79 THR Chi-restraints excluded: chain E residue 50 ASN Chi-restraints excluded: chain E residue 103 CYS Chi-restraints excluded: chain E residue 125 ILE Chi-restraints excluded: chain E residue 231 LEU Chi-restraints excluded: chain E residue 256 VAL Chi-restraints excluded: chain E residue 277 THR Chi-restraints excluded: chain F residue 50 ASN Chi-restraints excluded: chain F residue 80 ASP Chi-restraints excluded: chain F residue 83 THR Chi-restraints excluded: chain F residue 84 CYS Chi-restraints excluded: chain F residue 118 THR Chi-restraints excluded: chain F residue 127 ILE Chi-restraints excluded: chain F residue 142 ILE Chi-restraints excluded: chain F residue 198 LEU Chi-restraints excluded: chain F residue 238 SER Chi-restraints excluded: chain F residue 249 GLU Chi-restraints excluded: chain G residue 21 VAL Chi-restraints excluded: chain G residue 84 CYS Chi-restraints excluded: chain G residue 85 PHE Chi-restraints excluded: chain G residue 93 LYS Chi-restraints excluded: chain G residue 94 LYS Chi-restraints excluded: chain G residue 96 ASP Chi-restraints excluded: chain G residue 102 ASN Chi-restraints excluded: chain G residue 108 ILE Chi-restraints excluded: chain G residue 125 ILE Chi-restraints excluded: chain G residue 135 LEU Chi-restraints excluded: chain G residue 136 VAL Chi-restraints excluded: chain G residue 152 TYR Chi-restraints excluded: chain G residue 197 LEU Chi-restraints excluded: chain G residue 241 CYS Chi-restraints excluded: chain G residue 256 VAL Chi-restraints excluded: chain G residue 259 TYR Chi-restraints excluded: chain H residue 38 ILE Chi-restraints excluded: chain H residue 39 GLU Chi-restraints excluded: chain H residue 42 CYS Chi-restraints excluded: chain H residue 45 TYR Chi-restraints excluded: chain H residue 70 GLN Chi-restraints excluded: chain H residue 71 LEU Chi-restraints excluded: chain H residue 101 ILE Chi-restraints excluded: chain H residue 116 ARG Chi-restraints excluded: chain H residue 125 ILE Chi-restraints excluded: chain H residue 127 ILE Chi-restraints excluded: chain H residue 131 TYR Chi-restraints excluded: chain H residue 171 TYR Chi-restraints excluded: chain H residue 184 ILE Chi-restraints excluded: chain H residue 197 LEU Chi-restraints excluded: chain H residue 204 ASP Chi-restraints excluded: chain H residue 211 LEU Chi-restraints excluded: chain H residue 219 LEU Chi-restraints excluded: chain H residue 228 TYR Chi-restraints excluded: chain H residue 276 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 135 optimal weight: 5.9990 chunk 106 optimal weight: 3.9990 chunk 33 optimal weight: 0.8980 chunk 86 optimal weight: 9.9990 chunk 63 optimal weight: 3.9990 chunk 119 optimal weight: 0.0980 chunk 96 optimal weight: 6.9990 chunk 139 optimal weight: 6.9990 chunk 11 optimal weight: 2.9990 chunk 40 optimal weight: 4.9990 chunk 48 optimal weight: 2.9990 overall best weight: 2.1986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 199 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 213 HIS ** C 53 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 175 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 50 ASN F 50 ASN ** G 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 67 GLN ** H 79 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4021 r_free = 0.4021 target = 0.151020 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3738 r_free = 0.3738 target = 0.130341 restraints weight = 25726.587| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3785 r_free = 0.3785 target = 0.133613 restraints weight = 14644.461| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3814 r_free = 0.3814 target = 0.135738 restraints weight = 9678.008| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3831 r_free = 0.3831 target = 0.137077 restraints weight = 7150.108| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3845 r_free = 0.3845 target = 0.138167 restraints weight = 5809.737| |-----------------------------------------------------------------------------| r_work (final): 0.3795 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7605 moved from start: 0.7247 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 11412 Z= 0.166 Angle : 0.768 16.000 15321 Z= 0.396 Chirality : 0.043 0.199 1667 Planarity : 0.004 0.055 1998 Dihedral : 5.994 71.147 1528 Min Nonbonded Distance : 2.425 Molprobity Statistics. All-atom Clashscore : 15.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.98 % Favored : 92.02 % Rotamer: Outliers : 6.86 % Allowed : 26.50 % Favored : 66.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 aren not related in a simple way. whole: -1.37 (0.22), residues: 1404 helix: -0.31 (0.15), residues: 1152 sheet: None (None), residues: 0 loop : -3.21 (0.35), residues: 252 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG G 106 TYR 0.040 0.002 TYR B 235 PHE 0.018 0.002 PHE H 85 TRP 0.010 0.001 TRP F 275 HIS 0.008 0.002 HIS E 79 Details of bonding type rmsd covalent geometry : bond 0.00366 (11412) covalent geometry : angle 0.76844 (15321) hydrogen bonds : bond 0.04021 ( 702) hydrogen bonds : angle 4.64705 ( 2046) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2808 Ramachandran restraints generated. 1404 Oldfield, 0 Emsley, 1404 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2808 Ramachandran restraints generated. 1404 Oldfield, 0 Emsley, 1404 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 449 residues out of total 1181 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 81 poor density : 368 time to evaluate : 0.447 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 44 ASP cc_start: 0.8565 (t0) cc_final: 0.8025 (t0) REVERT: A 70 LEU cc_start: 0.9165 (tp) cc_final: 0.8813 (tt) REVERT: B 193 SER cc_start: 0.8841 (p) cc_final: 0.8489 (t) REVERT: B 199 HIS cc_start: 0.7104 (t-90) cc_final: 0.6855 (t70) REVERT: B 200 SER cc_start: 0.8681 (t) cc_final: 0.8426 (p) REVERT: B 203 ILE cc_start: 0.8149 (mm) cc_final: 0.7637 (pt) REVERT: B 210 ARG cc_start: 0.7896 (mmm160) cc_final: 0.7622 (ttm-80) REVERT: B 215 MET cc_start: 0.8130 (ppp) cc_final: 0.7819 (ppp) REVERT: B 246 ARG cc_start: 0.8176 (ttm170) cc_final: 0.7746 (ttp-110) REVERT: C 34 GLN cc_start: 0.8185 (tp40) cc_final: 0.7773 (tp40) REVERT: C 66 GLN cc_start: 0.8439 (mm-40) cc_final: 0.8103 (mm-40) REVERT: D 184 LYS cc_start: 0.8414 (mtpt) cc_final: 0.7879 (mtpt) REVERT: D 196 ASN cc_start: 0.7645 (p0) cc_final: 0.7300 (p0) REVERT: E 122 LYS cc_start: 0.9343 (tppt) cc_final: 0.8888 (tppt) REVERT: E 125 ILE cc_start: 0.8747 (OUTLIER) cc_final: 0.8232 (mt) REVERT: E 164 CYS cc_start: 0.7902 (m) cc_final: 0.7456 (m) REVERT: E 227 LYS cc_start: 0.8854 (mmmt) cc_final: 0.8416 (tptp) REVERT: E 278 THR cc_start: 0.8154 (p) cc_final: 0.7907 (t) REVERT: F 78 LYS cc_start: 0.8421 (mmmm) cc_final: 0.8185 (mtpt) REVERT: F 80 ASP cc_start: 0.7497 (OUTLIER) cc_final: 0.7137 (m-30) REVERT: F 87 ASP cc_start: 0.8408 (m-30) cc_final: 0.8182 (m-30) REVERT: F 94 LYS cc_start: 0.8402 (OUTLIER) cc_final: 0.7983 (mtmm) REVERT: F 156 GLU cc_start: 0.8205 (tp30) cc_final: 0.7911 (tp30) REVERT: F 175 LEU cc_start: 0.8703 (mm) cc_final: 0.8132 (tt) REVERT: F 226 GLN cc_start: 0.7961 (tp-100) cc_final: 0.7733 (tp-100) REVERT: F 271 ARG cc_start: 0.7477 (tpt-90) cc_final: 0.7098 (tpp-160) REVERT: F 279 MET cc_start: 0.8411 (mmm) cc_final: 0.7993 (mmt) REVERT: G 11 MET cc_start: 0.7133 (tmm) cc_final: 0.6905 (mmp) REVERT: G 51 MET cc_start: 0.7735 (tpp) cc_final: 0.7534 (tpp) REVERT: G 74 GLN cc_start: 0.8101 (pt0) cc_final: 0.7899 (pt0) REVERT: G 85 PHE cc_start: 0.8855 (OUTLIER) cc_final: 0.8617 (m-10) REVERT: G 93 LYS cc_start: 0.8358 (OUTLIER) cc_final: 0.8138 (mtmt) REVERT: G 94 LYS cc_start: 0.7335 (OUTLIER) cc_final: 0.6620 (mmtt) REVERT: G 105 MET cc_start: 0.8387 (tpp) cc_final: 0.7889 (tpp) REVERT: G 106 ARG cc_start: 0.6907 (ttm110) cc_final: 0.6698 (ttm110) REVERT: G 113 ASP cc_start: 0.6875 (p0) cc_final: 0.6122 (t0) REVERT: G 152 TYR cc_start: 0.9128 (OUTLIER) cc_final: 0.8262 (m-10) REVERT: G 163 LYS cc_start: 0.8467 (mtmt) cc_final: 0.7892 (mttp) REVERT: H 39 GLU cc_start: 0.8101 (OUTLIER) cc_final: 0.7845 (mp0) REVERT: H 51 MET cc_start: 0.7994 (mtt) cc_final: 0.7757 (ttm) REVERT: H 76 GLN cc_start: 0.7699 (mp10) cc_final: 0.7026 (tm-30) REVERT: H 87 ASP cc_start: 0.7924 (t70) cc_final: 0.7602 (t70) REVERT: H 125 ILE cc_start: 0.8754 (OUTLIER) cc_final: 0.8442 (mt) REVERT: H 146 GLU cc_start: 0.8013 (tt0) cc_final: 0.7699 (tm-30) REVERT: H 204 ASP cc_start: 0.8229 (OUTLIER) cc_final: 0.7910 (m-30) REVERT: H 271 ARG cc_start: 0.8362 (mmm-85) cc_final: 0.7275 (ttt180) outliers start: 81 outliers final: 54 residues processed: 414 average time/residue: 0.1149 time to fit residues: 65.6165 Evaluate side-chains 410 residues out of total 1181 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 346 time to evaluate : 0.431 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 32 LEU Chi-restraints excluded: chain A residue 35 THR Chi-restraints excluded: chain A residue 48 VAL Chi-restraints excluded: chain A residue 53 VAL Chi-restraints excluded: chain A residue 55 GLU Chi-restraints excluded: chain A residue 79 THR Chi-restraints excluded: chain B residue 209 ILE Chi-restraints excluded: chain B residue 211 GLU Chi-restraints excluded: chain B residue 236 ASN Chi-restraints excluded: chain B residue 237 VAL Chi-restraints excluded: chain C residue 49 MET Chi-restraints excluded: chain C residue 78 LEU Chi-restraints excluded: chain C residue 79 THR Chi-restraints excluded: chain D residue 160 LEU Chi-restraints excluded: chain E residue 85 PHE Chi-restraints excluded: chain E residue 103 CYS Chi-restraints excluded: chain E residue 125 ILE Chi-restraints excluded: chain E residue 256 VAL Chi-restraints excluded: chain E residue 272 LEU Chi-restraints excluded: chain E residue 276 LEU Chi-restraints excluded: chain E residue 277 THR Chi-restraints excluded: chain F residue 50 ASN Chi-restraints excluded: chain F residue 80 ASP Chi-restraints excluded: chain F residue 83 THR Chi-restraints excluded: chain F residue 94 LYS Chi-restraints excluded: chain F residue 118 THR Chi-restraints excluded: chain F residue 127 ILE Chi-restraints excluded: chain F residue 142 ILE Chi-restraints excluded: chain F residue 152 TYR Chi-restraints excluded: chain F residue 166 LEU Chi-restraints excluded: chain F residue 238 SER Chi-restraints excluded: chain G residue 21 VAL Chi-restraints excluded: chain G residue 45 TYR Chi-restraints excluded: chain G residue 84 CYS Chi-restraints excluded: chain G residue 85 PHE Chi-restraints excluded: chain G residue 93 LYS Chi-restraints excluded: chain G residue 94 LYS Chi-restraints excluded: chain G residue 102 ASN Chi-restraints excluded: chain G residue 108 ILE Chi-restraints excluded: chain G residue 125 ILE Chi-restraints excluded: chain G residue 135 LEU Chi-restraints excluded: chain G residue 136 VAL Chi-restraints excluded: chain G residue 152 TYR Chi-restraints excluded: chain G residue 197 LEU Chi-restraints excluded: chain G residue 256 VAL Chi-restraints excluded: chain G residue 259 TYR Chi-restraints excluded: chain H residue 38 ILE Chi-restraints excluded: chain H residue 39 GLU Chi-restraints excluded: chain H residue 42 CYS Chi-restraints excluded: chain H residue 45 TYR Chi-restraints excluded: chain H residue 70 GLN Chi-restraints excluded: chain H residue 71 LEU Chi-restraints excluded: chain H residue 101 ILE Chi-restraints excluded: chain H residue 116 ARG Chi-restraints excluded: chain H residue 125 ILE Chi-restraints excluded: chain H residue 127 ILE Chi-restraints excluded: chain H residue 131 TYR Chi-restraints excluded: chain H residue 171 TYR Chi-restraints excluded: chain H residue 184 ILE Chi-restraints excluded: chain H residue 197 LEU Chi-restraints excluded: chain H residue 204 ASP Chi-restraints excluded: chain H residue 211 LEU Chi-restraints excluded: chain H residue 228 TYR Chi-restraints excluded: chain H residue 276 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 76 optimal weight: 0.9980 chunk 136 optimal weight: 0.8980 chunk 82 optimal weight: 9.9990 chunk 61 optimal weight: 0.9990 chunk 60 optimal weight: 6.9990 chunk 83 optimal weight: 0.9980 chunk 53 optimal weight: 10.0000 chunk 74 optimal weight: 1.9990 chunk 26 optimal weight: 8.9990 chunk 62 optimal weight: 0.5980 chunk 104 optimal weight: 3.9990 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 38 GLN B 199 HIS C 53 GLN D 152 GLN ** D 175 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 188 ASN E 50 ASN ** E 213 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 50 ASN G 162 ASN ** H 79 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4064 r_free = 0.4064 target = 0.154111 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3785 r_free = 0.3785 target = 0.133468 restraints weight = 25603.216| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3829 r_free = 0.3829 target = 0.136629 restraints weight = 14936.321| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3859 r_free = 0.3859 target = 0.138752 restraints weight = 10016.776| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3876 r_free = 0.3876 target = 0.140102 restraints weight = 7447.177| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3887 r_free = 0.3887 target = 0.140941 restraints weight = 6049.944| |-----------------------------------------------------------------------------| r_work (final): 0.3844 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7556 moved from start: 0.7482 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 11412 Z= 0.145 Angle : 0.745 16.594 15321 Z= 0.382 Chirality : 0.042 0.260 1667 Planarity : 0.003 0.061 1998 Dihedral : 5.957 72.583 1528 Min Nonbonded Distance : 2.365 Molprobity Statistics. All-atom Clashscore : 13.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.41 % Favored : 92.59 % Rotamer: Outliers : 4.74 % Allowed : 29.21 % Favored : 66.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 aren not related in a simple way. whole: -1.10 (0.23), residues: 1404 helix: -0.16 (0.16), residues: 1164 sheet: None (None), residues: 0 loop : -3.05 (0.37), residues: 240 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG G 106 TYR 0.041 0.001 TYR B 235 PHE 0.020 0.002 PHE G 207 TRP 0.013 0.001 TRP F 275 HIS 0.006 0.002 HIS E 79 Details of bonding type rmsd covalent geometry : bond 0.00311 (11412) covalent geometry : angle 0.74516 (15321) hydrogen bonds : bond 0.03727 ( 702) hydrogen bonds : angle 4.47083 ( 2046) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2808 Ramachandran restraints generated. 1404 Oldfield, 0 Emsley, 1404 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2808 Ramachandran restraints generated. 1404 Oldfield, 0 Emsley, 1404 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 436 residues out of total 1181 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 380 time to evaluate : 0.430 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 44 ASP cc_start: 0.8484 (t0) cc_final: 0.7958 (t0) REVERT: A 65 ASP cc_start: 0.7953 (m-30) cc_final: 0.7547 (t0) REVERT: A 66 ARG cc_start: 0.8306 (mmp-170) cc_final: 0.7686 (mmp-170) REVERT: B 193 SER cc_start: 0.8814 (p) cc_final: 0.8469 (t) REVERT: B 199 HIS cc_start: 0.7133 (t70) cc_final: 0.5914 (t-90) REVERT: B 203 ILE cc_start: 0.7958 (mm) cc_final: 0.7348 (pt) REVERT: B 210 ARG cc_start: 0.7979 (mmm160) cc_final: 0.7544 (ttm-80) REVERT: B 217 MET cc_start: 0.6441 (mmp) cc_final: 0.6229 (mmp) REVERT: B 246 ARG cc_start: 0.8144 (ttm170) cc_final: 0.7851 (ttm110) REVERT: C 34 GLN cc_start: 0.8333 (tp40) cc_final: 0.7954 (tp40) REVERT: D 184 LYS cc_start: 0.8410 (mtpt) cc_final: 0.7878 (mtpt) REVERT: D 186 ASP cc_start: 0.8003 (m-30) cc_final: 0.7111 (m-30) REVERT: E 76 GLN cc_start: 0.8140 (mp10) cc_final: 0.7273 (pp30) REVERT: E 102 ASN cc_start: 0.7490 (p0) cc_final: 0.6924 (m110) REVERT: E 105 MET cc_start: 0.6605 (tpt) cc_final: 0.6242 (tpt) REVERT: E 122 LYS cc_start: 0.9299 (tppt) cc_final: 0.8850 (tppt) REVERT: E 125 ILE cc_start: 0.8762 (OUTLIER) cc_final: 0.8168 (mt) REVERT: E 164 CYS cc_start: 0.8125 (m) cc_final: 0.7637 (m) REVERT: E 227 LYS cc_start: 0.8877 (mmmt) cc_final: 0.8421 (tptp) REVERT: E 278 THR cc_start: 0.8117 (p) cc_final: 0.7893 (t) REVERT: F 51 MET cc_start: 0.7266 (tpp) cc_final: 0.6988 (tpp) REVERT: F 66 CYS cc_start: 0.8631 (t) cc_final: 0.7525 (p) REVERT: F 87 ASP cc_start: 0.8448 (m-30) cc_final: 0.8172 (m-30) REVERT: F 114 MET cc_start: 0.8259 (ttm) cc_final: 0.7984 (ttm) REVERT: F 175 LEU cc_start: 0.8792 (OUTLIER) cc_final: 0.8200 (tt) REVERT: F 226 GLN cc_start: 0.7858 (tp-100) cc_final: 0.7606 (tp-100) REVERT: F 240 GLU cc_start: 0.6422 (mt-10) cc_final: 0.6126 (mm-30) REVERT: F 271 ARG cc_start: 0.7465 (tpt-90) cc_final: 0.7221 (tpp-160) REVERT: G 11 MET cc_start: 0.7344 (tmm) cc_final: 0.7000 (mmp) REVERT: G 51 MET cc_start: 0.7807 (tpp) cc_final: 0.7567 (tpp) REVERT: G 74 GLN cc_start: 0.8097 (pt0) cc_final: 0.7838 (pt0) REVERT: G 85 PHE cc_start: 0.8976 (OUTLIER) cc_final: 0.8775 (m-10) REVERT: G 93 LYS cc_start: 0.8363 (OUTLIER) cc_final: 0.8101 (mtmt) REVERT: G 94 LYS cc_start: 0.7258 (OUTLIER) cc_final: 0.6337 (mmtt) REVERT: G 96 ASP cc_start: 0.6677 (t0) cc_final: 0.6402 (m-30) REVERT: G 105 MET cc_start: 0.8430 (tpp) cc_final: 0.7891 (tpp) REVERT: G 109 GLU cc_start: 0.8165 (pm20) cc_final: 0.7897 (pm20) REVERT: G 113 ASP cc_start: 0.7242 (p0) cc_final: 0.6363 (t0) REVERT: G 152 TYR cc_start: 0.8970 (OUTLIER) cc_final: 0.8400 (m-10) REVERT: G 155 GLU cc_start: 0.8353 (mm-30) cc_final: 0.8052 (mm-30) REVERT: G 162 ASN cc_start: 0.7839 (OUTLIER) cc_final: 0.7303 (m-40) REVERT: G 163 LYS cc_start: 0.8686 (mtmt) cc_final: 0.8110 (mttp) REVERT: G 227 LYS cc_start: 0.8933 (mmtt) cc_final: 0.8686 (mmtt) REVERT: G 265 GLU cc_start: 0.8121 (pp20) cc_final: 0.7462 (tm-30) REVERT: H 11 MET cc_start: 0.6245 (tpt) cc_final: 0.5882 (tpt) REVERT: H 39 GLU cc_start: 0.8074 (OUTLIER) cc_final: 0.7851 (mp0) REVERT: H 45 TYR cc_start: 0.7287 (OUTLIER) cc_final: 0.6867 (t80) REVERT: H 47 ARG cc_start: 0.7843 (ptm160) cc_final: 0.7393 (ptm160) REVERT: H 51 MET cc_start: 0.8055 (mtt) cc_final: 0.7733 (ttm) REVERT: H 76 GLN cc_start: 0.7709 (mp10) cc_final: 0.7032 (tm-30) REVERT: H 87 ASP cc_start: 0.7990 (t70) cc_final: 0.7547 (t70) REVERT: H 125 ILE cc_start: 0.8592 (pp) cc_final: 0.8321 (mt) REVERT: H 146 GLU cc_start: 0.8130 (tt0) cc_final: 0.7680 (tm-30) REVERT: H 204 ASP cc_start: 0.8314 (OUTLIER) cc_final: 0.8020 (m-30) REVERT: H 271 ARG cc_start: 0.8372 (mmm-85) cc_final: 0.7167 (ttt180) REVERT: H 284 LYS cc_start: 0.9098 (tttm) cc_final: 0.8891 (tttp) outliers start: 56 outliers final: 34 residues processed: 410 average time/residue: 0.1171 time to fit residues: 66.0410 Evaluate side-chains 386 residues out of total 1181 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 342 time to evaluate : 0.436 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 32 LEU Chi-restraints excluded: chain A residue 79 THR Chi-restraints excluded: chain B residue 209 ILE Chi-restraints excluded: chain C residue 19 ASP Chi-restraints excluded: chain C residue 33 LEU Chi-restraints excluded: chain C residue 49 MET Chi-restraints excluded: chain C residue 78 LEU Chi-restraints excluded: chain D residue 160 LEU Chi-restraints excluded: chain E residue 50 ASN Chi-restraints excluded: chain E residue 85 PHE Chi-restraints excluded: chain E residue 103 CYS Chi-restraints excluded: chain E residue 125 ILE Chi-restraints excluded: chain E residue 168 VAL Chi-restraints excluded: chain E residue 260 THR Chi-restraints excluded: chain E residue 276 LEU Chi-restraints excluded: chain E residue 277 THR Chi-restraints excluded: chain F residue 50 ASN Chi-restraints excluded: chain F residue 108 ILE Chi-restraints excluded: chain F residue 118 THR Chi-restraints excluded: chain F residue 175 LEU Chi-restraints excluded: chain F residue 238 SER Chi-restraints excluded: chain F residue 249 GLU Chi-restraints excluded: chain G residue 21 VAL Chi-restraints excluded: chain G residue 45 TYR Chi-restraints excluded: chain G residue 84 CYS Chi-restraints excluded: chain G residue 85 PHE Chi-restraints excluded: chain G residue 93 LYS Chi-restraints excluded: chain G residue 94 LYS Chi-restraints excluded: chain G residue 108 ILE Chi-restraints excluded: chain G residue 136 VAL Chi-restraints excluded: chain G residue 152 TYR Chi-restraints excluded: chain G residue 162 ASN Chi-restraints excluded: chain G residue 197 LEU Chi-restraints excluded: chain G residue 259 TYR Chi-restraints excluded: chain H residue 39 GLU Chi-restraints excluded: chain H residue 42 CYS Chi-restraints excluded: chain H residue 45 TYR Chi-restraints excluded: chain H residue 70 GLN Chi-restraints excluded: chain H residue 71 LEU Chi-restraints excluded: chain H residue 116 ARG Chi-restraints excluded: chain H residue 127 ILE Chi-restraints excluded: chain H residue 131 TYR Chi-restraints excluded: chain H residue 204 ASP Chi-restraints excluded: chain H residue 228 TYR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 139 optimal weight: 7.9990 chunk 3 optimal weight: 4.9990 chunk 88 optimal weight: 9.9990 chunk 126 optimal weight: 4.9990 chunk 100 optimal weight: 5.9990 chunk 19 optimal weight: 0.9980 chunk 135 optimal weight: 2.9990 chunk 15 optimal weight: 0.9980 chunk 30 optimal weight: 3.9990 chunk 58 optimal weight: 3.9990 chunk 4 optimal weight: 6.9990 overall best weight: 2.5986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 38 GLN D 159 ASN ** D 188 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 50 ASN ** E 72 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 213 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 50 ASN G 162 ASN ** H 79 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4018 r_free = 0.4018 target = 0.150322 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3734 r_free = 0.3734 target = 0.129718 restraints weight = 25538.790| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3778 r_free = 0.3778 target = 0.132884 restraints weight = 14738.222| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3807 r_free = 0.3807 target = 0.134998 restraints weight = 9783.699| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3828 r_free = 0.3828 target = 0.136448 restraints weight = 7244.871| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3839 r_free = 0.3839 target = 0.137333 restraints weight = 5822.589| |-----------------------------------------------------------------------------| r_work (final): 0.3832 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7626 moved from start: 0.7670 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 11412 Z= 0.182 Angle : 0.802 15.837 15321 Z= 0.410 Chirality : 0.045 0.224 1667 Planarity : 0.004 0.066 1998 Dihedral : 6.008 73.670 1528 Min Nonbonded Distance : 2.476 Molprobity Statistics. All-atom Clashscore : 16.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.05 % Favored : 91.95 % Rotamer: Outliers : 5.93 % Allowed : 28.37 % Favored : 65.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 aren not related in a simple way. whole: -1.14 (0.23), residues: 1404 helix: -0.20 (0.15), residues: 1164 sheet: None (None), residues: 0 loop : -3.00 (0.37), residues: 240 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.001 ARG D 180 TYR 0.041 0.002 TYR B 235 PHE 0.020 0.002 PHE H 85 TRP 0.007 0.001 TRP F 275 HIS 0.021 0.002 HIS G 79 Details of bonding type rmsd covalent geometry : bond 0.00402 (11412) covalent geometry : angle 0.80234 (15321) hydrogen bonds : bond 0.03966 ( 702) hydrogen bonds : angle 4.57076 ( 2046) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2808 Ramachandran restraints generated. 1404 Oldfield, 0 Emsley, 1404 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2808 Ramachandran restraints generated. 1404 Oldfield, 0 Emsley, 1404 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 423 residues out of total 1181 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 353 time to evaluate : 0.446 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 44 ASP cc_start: 0.8522 (t0) cc_final: 0.7920 (t0) REVERT: A 66 ARG cc_start: 0.8388 (mmp-170) cc_final: 0.7818 (mmp-170) REVERT: B 193 SER cc_start: 0.8884 (p) cc_final: 0.8546 (t) REVERT: B 199 HIS cc_start: 0.7164 (t70) cc_final: 0.5991 (t-90) REVERT: B 203 ILE cc_start: 0.7983 (mm) cc_final: 0.7295 (pt) REVERT: B 210 ARG cc_start: 0.8113 (mmm160) cc_final: 0.7618 (ttm-80) REVERT: C 34 GLN cc_start: 0.8373 (tp40) cc_final: 0.7957 (tp40) REVERT: D 165 LEU cc_start: 0.8987 (mt) cc_final: 0.8778 (mp) REVERT: D 184 LYS cc_start: 0.8430 (mtpt) cc_final: 0.7896 (mtpt) REVERT: E 122 LYS cc_start: 0.9342 (tppt) cc_final: 0.8990 (tppt) REVERT: E 125 ILE cc_start: 0.8716 (OUTLIER) cc_final: 0.8269 (mt) REVERT: E 164 CYS cc_start: 0.8307 (m) cc_final: 0.7881 (m) REVERT: E 226 GLN cc_start: 0.8504 (mm-40) cc_final: 0.8036 (mm-40) REVERT: F 51 MET cc_start: 0.7711 (tpp) cc_final: 0.7102 (tpp) REVERT: F 87 ASP cc_start: 0.8525 (m-30) cc_final: 0.8233 (m-30) REVERT: F 114 MET cc_start: 0.8294 (ttm) cc_final: 0.8007 (ttm) REVERT: F 175 LEU cc_start: 0.8872 (OUTLIER) cc_final: 0.8269 (tt) REVERT: F 187 GLN cc_start: 0.8739 (pt0) cc_final: 0.8084 (tp-100) REVERT: F 226 GLN cc_start: 0.8207 (tp-100) cc_final: 0.7962 (tp-100) REVERT: F 240 GLU cc_start: 0.6663 (mt-10) cc_final: 0.5960 (mm-30) REVERT: F 271 ARG cc_start: 0.7772 (tpt-90) cc_final: 0.7361 (tpp-160) REVERT: G 75 LEU cc_start: 0.9320 (tt) cc_final: 0.8655 (mp) REVERT: G 85 PHE cc_start: 0.8981 (OUTLIER) cc_final: 0.8775 (m-10) REVERT: G 93 LYS cc_start: 0.8438 (OUTLIER) cc_final: 0.8155 (mtmt) REVERT: G 94 LYS cc_start: 0.7395 (OUTLIER) cc_final: 0.6667 (mmtt) REVERT: G 96 ASP cc_start: 0.6756 (t0) cc_final: 0.6467 (m-30) REVERT: G 105 MET cc_start: 0.8469 (tpp) cc_final: 0.7764 (tpp) REVERT: G 113 ASP cc_start: 0.7382 (p0) cc_final: 0.6439 (t0) REVERT: G 152 TYR cc_start: 0.9234 (OUTLIER) cc_final: 0.8351 (m-10) REVERT: G 162 ASN cc_start: 0.8058 (OUTLIER) cc_final: 0.7438 (m-40) REVERT: G 163 LYS cc_start: 0.8737 (mtmt) cc_final: 0.8158 (mttp) REVERT: G 227 LYS cc_start: 0.8956 (mmtt) cc_final: 0.8722 (mmtt) REVERT: G 239 ARG cc_start: 0.7492 (tpt170) cc_final: 0.7212 (tpt170) REVERT: G 282 ARG cc_start: 0.8536 (ttm170) cc_final: 0.8319 (ttm170) REVERT: H 11 MET cc_start: 0.6301 (tpt) cc_final: 0.6080 (tpt) REVERT: H 39 GLU cc_start: 0.8126 (OUTLIER) cc_final: 0.7853 (mp0) REVERT: H 51 MET cc_start: 0.8289 (mtt) cc_final: 0.7734 (ttm) REVERT: H 76 GLN cc_start: 0.7708 (mp10) cc_final: 0.7192 (tm-30) REVERT: H 87 ASP cc_start: 0.8090 (t70) cc_final: 0.7640 (t70) REVERT: H 125 ILE cc_start: 0.8628 (OUTLIER) cc_final: 0.8372 (mt) REVERT: H 146 GLU cc_start: 0.8190 (tt0) cc_final: 0.7711 (tm-30) REVERT: H 153 LYS cc_start: 0.8828 (mtpp) cc_final: 0.8599 (mtpt) REVERT: H 193 MET cc_start: 0.7309 (tpp) cc_final: 0.6854 (tpp) REVERT: H 204 ASP cc_start: 0.8397 (OUTLIER) cc_final: 0.8115 (m-30) REVERT: H 213 HIS cc_start: 0.6803 (OUTLIER) cc_final: 0.6467 (m170) REVERT: H 244 MET cc_start: 0.8266 (tmm) cc_final: 0.8041 (tmm) REVERT: H 271 ARG cc_start: 0.8457 (mmm-85) cc_final: 0.7261 (ttt180) REVERT: H 284 LYS cc_start: 0.9124 (tttm) cc_final: 0.8919 (tttp) outliers start: 70 outliers final: 44 residues processed: 391 average time/residue: 0.1132 time to fit residues: 61.2487 Evaluate side-chains 398 residues out of total 1181 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 343 time to evaluate : 0.446 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 32 LEU Chi-restraints excluded: chain A residue 35 THR Chi-restraints excluded: chain A residue 50 VAL Chi-restraints excluded: chain A residue 53 VAL Chi-restraints excluded: chain A residue 79 THR Chi-restraints excluded: chain B residue 209 ILE Chi-restraints excluded: chain B residue 215 MET Chi-restraints excluded: chain C residue 33 LEU Chi-restraints excluded: chain C residue 49 MET Chi-restraints excluded: chain C residue 78 LEU Chi-restraints excluded: chain D residue 160 LEU Chi-restraints excluded: chain E residue 50 ASN Chi-restraints excluded: chain E residue 85 PHE Chi-restraints excluded: chain E residue 103 CYS Chi-restraints excluded: chain E residue 125 ILE Chi-restraints excluded: chain E residue 260 THR Chi-restraints excluded: chain E residue 261 GLU Chi-restraints excluded: chain E residue 276 LEU Chi-restraints excluded: chain E residue 277 THR Chi-restraints excluded: chain F residue 50 ASN Chi-restraints excluded: chain F residue 118 THR Chi-restraints excluded: chain F residue 127 ILE Chi-restraints excluded: chain F residue 164 CYS Chi-restraints excluded: chain F residue 166 LEU Chi-restraints excluded: chain F residue 175 LEU Chi-restraints excluded: chain F residue 238 SER Chi-restraints excluded: chain F residue 249 GLU Chi-restraints excluded: chain F residue 270 SER Chi-restraints excluded: chain G residue 21 VAL Chi-restraints excluded: chain G residue 45 TYR Chi-restraints excluded: chain G residue 84 CYS Chi-restraints excluded: chain G residue 85 PHE Chi-restraints excluded: chain G residue 93 LYS Chi-restraints excluded: chain G residue 94 LYS Chi-restraints excluded: chain G residue 108 ILE Chi-restraints excluded: chain G residue 135 LEU Chi-restraints excluded: chain G residue 136 VAL Chi-restraints excluded: chain G residue 152 TYR Chi-restraints excluded: chain G residue 162 ASN Chi-restraints excluded: chain G residue 197 LEU Chi-restraints excluded: chain G residue 259 TYR Chi-restraints excluded: chain H residue 39 GLU Chi-restraints excluded: chain H residue 45 TYR Chi-restraints excluded: chain H residue 70 GLN Chi-restraints excluded: chain H residue 71 LEU Chi-restraints excluded: chain H residue 96 ASP Chi-restraints excluded: chain H residue 116 ARG Chi-restraints excluded: chain H residue 125 ILE Chi-restraints excluded: chain H residue 127 ILE Chi-restraints excluded: chain H residue 131 TYR Chi-restraints excluded: chain H residue 184 ILE Chi-restraints excluded: chain H residue 194 ASP Chi-restraints excluded: chain H residue 204 ASP Chi-restraints excluded: chain H residue 213 HIS Chi-restraints excluded: chain H residue 228 TYR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 128 optimal weight: 0.0980 chunk 36 optimal weight: 5.9990 chunk 109 optimal weight: 0.8980 chunk 97 optimal weight: 4.9990 chunk 93 optimal weight: 3.9990 chunk 121 optimal weight: 5.9990 chunk 81 optimal weight: 8.9990 chunk 49 optimal weight: 2.9990 chunk 8 optimal weight: 0.9980 chunk 98 optimal weight: 4.9990 chunk 27 optimal weight: 0.4980 overall best weight: 1.0982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 159 ASN E 72 HIS ** E 213 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 50 ASN G 162 ASN ** H 79 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4059 r_free = 0.4059 target = 0.153662 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3778 r_free = 0.3778 target = 0.132895 restraints weight = 25448.858| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.3824 r_free = 0.3824 target = 0.136163 restraints weight = 14741.207| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3855 r_free = 0.3855 target = 0.138384 restraints weight = 9790.600| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3872 r_free = 0.3872 target = 0.139733 restraints weight = 7201.542| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3887 r_free = 0.3887 target = 0.140823 restraints weight = 5811.825| |-----------------------------------------------------------------------------| r_work (final): 0.3881 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7566 moved from start: 0.7817 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 11412 Z= 0.153 Angle : 0.812 15.443 15321 Z= 0.413 Chirality : 0.044 0.222 1667 Planarity : 0.004 0.071 1998 Dihedral : 5.995 73.806 1528 Min Nonbonded Distance : 2.481 Molprobity Statistics. All-atom Clashscore : 14.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.12 % Favored : 91.88 % Rotamer: Outliers : 5.08 % Allowed : 30.31 % Favored : 64.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 aren not related in a simple way. whole: -0.88 (0.23), residues: 1404 helix: -0.05 (0.16), residues: 1148 sheet: None (None), residues: 0 loop : -2.59 (0.38), residues: 256 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG D 180 TYR 0.044 0.001 TYR B 235 PHE 0.022 0.002 PHE H 85 TRP 0.011 0.001 TRP E 275 HIS 0.025 0.002 HIS G 79 Details of bonding type rmsd covalent geometry : bond 0.00342 (11412) covalent geometry : angle 0.81162 (15321) hydrogen bonds : bond 0.03834 ( 702) hydrogen bonds : angle 4.50945 ( 2046) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2808 Ramachandran restraints generated. 1404 Oldfield, 0 Emsley, 1404 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2808 Ramachandran restraints generated. 1404 Oldfield, 0 Emsley, 1404 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 414 residues out of total 1181 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 354 time to evaluate : 0.459 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 44 ASP cc_start: 0.8455 (t0) cc_final: 0.7977 (t0) REVERT: A 66 ARG cc_start: 0.8369 (mmp-170) cc_final: 0.7890 (mtp85) REVERT: B 193 SER cc_start: 0.8885 (p) cc_final: 0.8579 (t) REVERT: B 199 HIS cc_start: 0.7110 (t70) cc_final: 0.5985 (t-90) REVERT: B 203 ILE cc_start: 0.7865 (mm) cc_final: 0.7276 (pt) REVERT: B 210 ARG cc_start: 0.8083 (mmm160) cc_final: 0.7572 (ttm-80) REVERT: B 231 ASP cc_start: 0.7982 (t0) cc_final: 0.7609 (t0) REVERT: C 34 GLN cc_start: 0.8335 (tp40) cc_final: 0.8043 (tp40) REVERT: D 184 LYS cc_start: 0.8352 (mtpt) cc_final: 0.8000 (mtpt) REVERT: E 76 GLN cc_start: 0.8193 (mp10) cc_final: 0.7247 (pp30) REVERT: E 122 LYS cc_start: 0.9317 (tppt) cc_final: 0.8892 (tppt) REVERT: E 125 ILE cc_start: 0.8685 (OUTLIER) cc_final: 0.8206 (mt) REVERT: E 164 CYS cc_start: 0.8194 (m) cc_final: 0.7750 (m) REVERT: E 218 MET cc_start: 0.5474 (tpp) cc_final: 0.3082 (mmt) REVERT: E 222 LYS cc_start: 0.6835 (pttt) cc_final: 0.6619 (pttp) REVERT: E 227 LYS cc_start: 0.8938 (mmmt) cc_final: 0.8423 (tptp) REVERT: F 51 MET cc_start: 0.7665 (tpp) cc_final: 0.7253 (tpp) REVERT: F 66 CYS cc_start: 0.8678 (t) cc_final: 0.7671 (p) REVERT: F 87 ASP cc_start: 0.8469 (m-30) cc_final: 0.8148 (m-30) REVERT: F 175 LEU cc_start: 0.8888 (OUTLIER) cc_final: 0.8291 (tt) REVERT: F 187 GLN cc_start: 0.8700 (pt0) cc_final: 0.8003 (tp-100) REVERT: F 226 GLN cc_start: 0.8133 (tp-100) cc_final: 0.7894 (tp-100) REVERT: F 240 GLU cc_start: 0.6684 (mt-10) cc_final: 0.5926 (mm-30) REVERT: F 271 ARG cc_start: 0.7756 (tpt-90) cc_final: 0.7308 (tpp-160) REVERT: F 279 MET cc_start: 0.8176 (mmm) cc_final: 0.7875 (mmt) REVERT: G 11 MET cc_start: 0.7058 (tmm) cc_final: 0.6694 (mmp) REVERT: G 74 GLN cc_start: 0.8203 (pt0) cc_final: 0.7841 (pt0) REVERT: G 93 LYS cc_start: 0.8377 (OUTLIER) cc_final: 0.8119 (mtmt) REVERT: G 94 LYS cc_start: 0.7356 (OUTLIER) cc_final: 0.6483 (mmtt) REVERT: G 96 ASP cc_start: 0.6803 (t0) cc_final: 0.6533 (m-30) REVERT: G 113 ASP cc_start: 0.7197 (p0) cc_final: 0.6311 (t0) REVERT: G 152 TYR cc_start: 0.9202 (OUTLIER) cc_final: 0.8280 (m-10) REVERT: G 222 LYS cc_start: 0.6975 (ttpt) cc_final: 0.6590 (ttpt) REVERT: G 227 LYS cc_start: 0.8863 (mmtt) cc_final: 0.8610 (mmtt) REVERT: G 239 ARG cc_start: 0.7456 (tpt170) cc_final: 0.7233 (tpt170) REVERT: H 11 MET cc_start: 0.6442 (tpt) cc_final: 0.6188 (tpt) REVERT: H 39 GLU cc_start: 0.8115 (OUTLIER) cc_final: 0.7851 (mp0) REVERT: H 45 TYR cc_start: 0.7332 (OUTLIER) cc_final: 0.6940 (t80) REVERT: H 51 MET cc_start: 0.8165 (mtt) cc_final: 0.7744 (ttm) REVERT: H 76 GLN cc_start: 0.7635 (mp10) cc_final: 0.7230 (tm-30) REVERT: H 87 ASP cc_start: 0.8029 (t70) cc_final: 0.7525 (t70) REVERT: H 125 ILE cc_start: 0.8568 (OUTLIER) cc_final: 0.8316 (mt) REVERT: H 146 GLU cc_start: 0.8162 (tt0) cc_final: 0.7686 (tm-30) REVERT: H 193 MET cc_start: 0.7196 (tpp) cc_final: 0.6824 (tpp) REVERT: H 194 ASP cc_start: 0.7552 (OUTLIER) cc_final: 0.7146 (t0) REVERT: H 204 ASP cc_start: 0.8391 (OUTLIER) cc_final: 0.8159 (m-30) REVERT: H 284 LYS cc_start: 0.9069 (tttm) cc_final: 0.8862 (tttp) outliers start: 60 outliers final: 40 residues processed: 389 average time/residue: 0.1106 time to fit residues: 60.0755 Evaluate side-chains 391 residues out of total 1181 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 341 time to evaluate : 0.418 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 32 LEU Chi-restraints excluded: chain A residue 53 VAL Chi-restraints excluded: chain A residue 79 THR Chi-restraints excluded: chain B residue 209 ILE Chi-restraints excluded: chain B residue 215 MET Chi-restraints excluded: chain B residue 237 VAL Chi-restraints excluded: chain C residue 19 ASP Chi-restraints excluded: chain C residue 33 LEU Chi-restraints excluded: chain C residue 78 LEU Chi-restraints excluded: chain D residue 160 LEU Chi-restraints excluded: chain E residue 85 PHE Chi-restraints excluded: chain E residue 103 CYS Chi-restraints excluded: chain E residue 125 ILE Chi-restraints excluded: chain E residue 256 VAL Chi-restraints excluded: chain E residue 261 GLU Chi-restraints excluded: chain E residue 276 LEU Chi-restraints excluded: chain E residue 277 THR Chi-restraints excluded: chain F residue 50 ASN Chi-restraints excluded: chain F residue 108 ILE Chi-restraints excluded: chain F residue 127 ILE Chi-restraints excluded: chain F residue 160 SER Chi-restraints excluded: chain F residue 175 LEU Chi-restraints excluded: chain F residue 249 GLU Chi-restraints excluded: chain G residue 21 VAL Chi-restraints excluded: chain G residue 45 TYR Chi-restraints excluded: chain G residue 84 CYS Chi-restraints excluded: chain G residue 93 LYS Chi-restraints excluded: chain G residue 94 LYS Chi-restraints excluded: chain G residue 102 ASN Chi-restraints excluded: chain G residue 108 ILE Chi-restraints excluded: chain G residue 135 LEU Chi-restraints excluded: chain G residue 136 VAL Chi-restraints excluded: chain G residue 152 TYR Chi-restraints excluded: chain G residue 197 LEU Chi-restraints excluded: chain G residue 256 VAL Chi-restraints excluded: chain H residue 39 GLU Chi-restraints excluded: chain H residue 42 CYS Chi-restraints excluded: chain H residue 43 GLU Chi-restraints excluded: chain H residue 45 TYR Chi-restraints excluded: chain H residue 70 GLN Chi-restraints excluded: chain H residue 71 LEU Chi-restraints excluded: chain H residue 96 ASP Chi-restraints excluded: chain H residue 116 ARG Chi-restraints excluded: chain H residue 125 ILE Chi-restraints excluded: chain H residue 127 ILE Chi-restraints excluded: chain H residue 131 TYR Chi-restraints excluded: chain H residue 171 TYR Chi-restraints excluded: chain H residue 184 ILE Chi-restraints excluded: chain H residue 194 ASP Chi-restraints excluded: chain H residue 204 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 45 optimal weight: 0.8980 chunk 83 optimal weight: 10.0000 chunk 113 optimal weight: 9.9990 chunk 129 optimal weight: 8.9990 chunk 59 optimal weight: 8.9990 chunk 80 optimal weight: 1.9990 chunk 16 optimal weight: 0.7980 chunk 97 optimal weight: 5.9990 chunk 55 optimal weight: 20.0000 chunk 70 optimal weight: 2.9990 chunk 1 optimal weight: 0.7980 overall best weight: 1.4984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 239 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 72 HIS ** E 213 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 50 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4053 r_free = 0.4053 target = 0.153001 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 26)----------------| | r_work = 0.3773 r_free = 0.3773 target = 0.132353 restraints weight = 25518.576| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3817 r_free = 0.3817 target = 0.135499 restraints weight = 14655.587| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3848 r_free = 0.3848 target = 0.137720 restraints weight = 9773.798| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3868 r_free = 0.3868 target = 0.139201 restraints weight = 7210.103| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3879 r_free = 0.3879 target = 0.140076 restraints weight = 5771.951| |-----------------------------------------------------------------------------| r_work (final): 0.3873 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7576 moved from start: 0.7932 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 11412 Z= 0.161 Angle : 0.836 15.393 15321 Z= 0.424 Chirality : 0.045 0.229 1667 Planarity : 0.004 0.075 1998 Dihedral : 6.003 73.925 1528 Min Nonbonded Distance : 2.439 Molprobity Statistics. All-atom Clashscore : 16.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.19 % Favored : 91.81 % Rotamer: Outliers : 4.32 % Allowed : 31.84 % Favored : 63.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 aren not related in a simple way. whole: -0.98 (0.22), residues: 1404 helix: -0.12 (0.15), residues: 1156 sheet: None (None), residues: 0 loop : -2.72 (0.37), residues: 248 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG A 56 TYR 0.044 0.001 TYR B 235 PHE 0.023 0.002 PHE G 85 TRP 0.014 0.001 TRP E 275 HIS 0.027 0.002 HIS G 79 Details of bonding type rmsd covalent geometry : bond 0.00365 (11412) covalent geometry : angle 0.83634 (15321) hydrogen bonds : bond 0.03880 ( 702) hydrogen bonds : angle 4.49125 ( 2046) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2808 Ramachandran restraints generated. 1404 Oldfield, 0 Emsley, 1404 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2808 Ramachandran restraints generated. 1404 Oldfield, 0 Emsley, 1404 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 403 residues out of total 1181 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 352 time to evaluate : 0.506 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 44 ASP cc_start: 0.8684 (t0) cc_final: 0.8273 (t0) REVERT: A 66 ARG cc_start: 0.8332 (mmp-170) cc_final: 0.7851 (mtp85) REVERT: B 193 SER cc_start: 0.8751 (p) cc_final: 0.8433 (t) REVERT: B 199 HIS cc_start: 0.7112 (t70) cc_final: 0.6005 (t-90) REVERT: B 203 ILE cc_start: 0.7889 (mm) cc_final: 0.7344 (pt) REVERT: B 210 ARG cc_start: 0.8232 (mmm160) cc_final: 0.7619 (ttm-80) REVERT: B 231 ASP cc_start: 0.7951 (t0) cc_final: 0.7599 (t0) REVERT: C 34 GLN cc_start: 0.8175 (tp40) cc_final: 0.7931 (tp40) REVERT: D 176 ARG cc_start: 0.7788 (mpt180) cc_final: 0.7389 (tpp80) REVERT: D 184 LYS cc_start: 0.8415 (mtpt) cc_final: 0.8036 (mtpt) REVERT: E 40 GLU cc_start: 0.7370 (tp30) cc_final: 0.7042 (mp0) REVERT: E 76 GLN cc_start: 0.8331 (mp10) cc_final: 0.7453 (pp30) REVERT: E 122 LYS cc_start: 0.9297 (tppt) cc_final: 0.8907 (tppt) REVERT: E 125 ILE cc_start: 0.8678 (OUTLIER) cc_final: 0.8206 (mt) REVERT: E 164 CYS cc_start: 0.8186 (m) cc_final: 0.7728 (m) REVERT: E 218 MET cc_start: 0.5350 (tpp) cc_final: 0.3140 (mmt) REVERT: E 227 LYS cc_start: 0.8941 (mmmt) cc_final: 0.8396 (tptp) REVERT: F 51 MET cc_start: 0.7542 (tpp) cc_final: 0.7164 (tpt) REVERT: F 66 CYS cc_start: 0.8686 (t) cc_final: 0.7671 (p) REVERT: F 87 ASP cc_start: 0.8532 (m-30) cc_final: 0.8207 (m-30) REVERT: F 175 LEU cc_start: 0.8834 (OUTLIER) cc_final: 0.8250 (tt) REVERT: F 187 GLN cc_start: 0.8691 (pt0) cc_final: 0.8001 (tp-100) REVERT: F 203 LYS cc_start: 0.8647 (pttp) cc_final: 0.8007 (ptpp) REVERT: F 226 GLN cc_start: 0.8138 (tp-100) cc_final: 0.7886 (tp-100) REVERT: F 240 GLU cc_start: 0.6430 (mt-10) cc_final: 0.5459 (mm-30) REVERT: F 244 MET cc_start: 0.7444 (ptp) cc_final: 0.7211 (ptp) REVERT: F 271 ARG cc_start: 0.7828 (tpt-90) cc_final: 0.7382 (tpp-160) REVERT: G 11 MET cc_start: 0.6967 (tmm) cc_final: 0.6636 (mmp) REVERT: G 74 GLN cc_start: 0.8242 (pt0) cc_final: 0.7908 (pt0) REVERT: G 75 LEU cc_start: 0.9252 (tt) cc_final: 0.9041 (tp) REVERT: G 93 LYS cc_start: 0.8394 (OUTLIER) cc_final: 0.8112 (mtmt) REVERT: G 94 LYS cc_start: 0.7406 (OUTLIER) cc_final: 0.6602 (mmtt) REVERT: G 96 ASP cc_start: 0.6822 (t0) cc_final: 0.6553 (m-30) REVERT: G 105 MET cc_start: 0.8372 (tpp) cc_final: 0.8166 (tpp) REVERT: G 113 ASP cc_start: 0.7174 (p0) cc_final: 0.6222 (t0) REVERT: G 122 LYS cc_start: 0.7872 (tttp) cc_final: 0.7533 (tptp) REVERT: G 152 TYR cc_start: 0.9189 (OUTLIER) cc_final: 0.8256 (m-10) REVERT: G 227 LYS cc_start: 0.8955 (mmtt) cc_final: 0.8666 (mmtt) REVERT: G 239 ARG cc_start: 0.7487 (tpt170) cc_final: 0.7277 (tpt170) REVERT: G 265 GLU cc_start: 0.8110 (pp20) cc_final: 0.7426 (tm-30) REVERT: H 11 MET cc_start: 0.6475 (tpt) cc_final: 0.6229 (tpt) REVERT: H 39 GLU cc_start: 0.8126 (OUTLIER) cc_final: 0.7854 (mp0) REVERT: H 45 TYR cc_start: 0.7329 (OUTLIER) cc_final: 0.6927 (t80) REVERT: H 47 ARG cc_start: 0.7738 (ptm160) cc_final: 0.7340 (ptm160) REVERT: H 51 MET cc_start: 0.8174 (mtt) cc_final: 0.7754 (ttm) REVERT: H 76 GLN cc_start: 0.7584 (mp10) cc_final: 0.7248 (tm-30) REVERT: H 87 ASP cc_start: 0.7983 (t70) cc_final: 0.7459 (t70) REVERT: H 125 ILE cc_start: 0.8583 (OUTLIER) cc_final: 0.8328 (mt) REVERT: H 140 LYS cc_start: 0.8114 (mtpt) cc_final: 0.7696 (mtmt) REVERT: H 146 GLU cc_start: 0.8182 (tt0) cc_final: 0.7707 (tm-30) REVERT: H 153 LYS cc_start: 0.8849 (mtpp) cc_final: 0.8619 (mtpt) REVERT: H 193 MET cc_start: 0.7245 (tpp) cc_final: 0.6816 (tpp) REVERT: H 194 ASP cc_start: 0.7639 (OUTLIER) cc_final: 0.7228 (t0) REVERT: H 204 ASP cc_start: 0.8404 (OUTLIER) cc_final: 0.8190 (m-30) REVERT: H 284 LYS cc_start: 0.9071 (tttm) cc_final: 0.8860 (tttp) outliers start: 51 outliers final: 40 residues processed: 382 average time/residue: 0.1179 time to fit residues: 62.0046 Evaluate side-chains 391 residues out of total 1181 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 341 time to evaluate : 0.362 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 32 LEU Chi-restraints excluded: chain A residue 53 VAL Chi-restraints excluded: chain A residue 79 THR Chi-restraints excluded: chain B residue 209 ILE Chi-restraints excluded: chain B residue 215 MET Chi-restraints excluded: chain B residue 237 VAL Chi-restraints excluded: chain C residue 19 ASP Chi-restraints excluded: chain C residue 33 LEU Chi-restraints excluded: chain C residue 78 LEU Chi-restraints excluded: chain C residue 79 THR Chi-restraints excluded: chain D residue 160 LEU Chi-restraints excluded: chain E residue 85 PHE Chi-restraints excluded: chain E residue 103 CYS Chi-restraints excluded: chain E residue 125 ILE Chi-restraints excluded: chain E residue 256 VAL Chi-restraints excluded: chain E residue 261 GLU Chi-restraints excluded: chain E residue 276 LEU Chi-restraints excluded: chain E residue 277 THR Chi-restraints excluded: chain E residue 294 LEU Chi-restraints excluded: chain F residue 108 ILE Chi-restraints excluded: chain F residue 127 ILE Chi-restraints excluded: chain F residue 160 SER Chi-restraints excluded: chain F residue 175 LEU Chi-restraints excluded: chain F residue 249 GLU Chi-restraints excluded: chain G residue 21 VAL Chi-restraints excluded: chain G residue 45 TYR Chi-restraints excluded: chain G residue 84 CYS Chi-restraints excluded: chain G residue 93 LYS Chi-restraints excluded: chain G residue 94 LYS Chi-restraints excluded: chain G residue 102 ASN Chi-restraints excluded: chain G residue 108 ILE Chi-restraints excluded: chain G residue 135 LEU Chi-restraints excluded: chain G residue 136 VAL Chi-restraints excluded: chain G residue 152 TYR Chi-restraints excluded: chain G residue 197 LEU Chi-restraints excluded: chain G residue 256 VAL Chi-restraints excluded: chain H residue 39 GLU Chi-restraints excluded: chain H residue 42 CYS Chi-restraints excluded: chain H residue 45 TYR Chi-restraints excluded: chain H residue 70 GLN Chi-restraints excluded: chain H residue 71 LEU Chi-restraints excluded: chain H residue 96 ASP Chi-restraints excluded: chain H residue 116 ARG Chi-restraints excluded: chain H residue 125 ILE Chi-restraints excluded: chain H residue 127 ILE Chi-restraints excluded: chain H residue 131 TYR Chi-restraints excluded: chain H residue 171 TYR Chi-restraints excluded: chain H residue 184 ILE Chi-restraints excluded: chain H residue 194 ASP Chi-restraints excluded: chain H residue 204 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 122 optimal weight: 1.9990 chunk 37 optimal weight: 8.9990 chunk 9 optimal weight: 3.9990 chunk 12 optimal weight: 7.9990 chunk 120 optimal weight: 0.9990 chunk 95 optimal weight: 3.9990 chunk 114 optimal weight: 0.0040 chunk 46 optimal weight: 3.9990 chunk 8 optimal weight: 0.9990 chunk 134 optimal weight: 5.9990 chunk 72 optimal weight: 0.0470 overall best weight: 0.8096 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 239 HIS E 72 HIS ** E 213 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 102 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4106 r_free = 0.4106 target = 0.157804 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3819 r_free = 0.3819 target = 0.136502 restraints weight = 25617.465| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3866 r_free = 0.3866 target = 0.139901 restraints weight = 14778.461| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3897 r_free = 0.3897 target = 0.142188 restraints weight = 9790.763| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3917 r_free = 0.3917 target = 0.143724 restraints weight = 7177.659| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3930 r_free = 0.3930 target = 0.144686 restraints weight = 5721.935| |-----------------------------------------------------------------------------| r_work (final): 0.3925 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7518 moved from start: 0.8143 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 11412 Z= 0.150 Angle : 0.830 16.820 15321 Z= 0.417 Chirality : 0.043 0.220 1667 Planarity : 0.004 0.076 1998 Dihedral : 5.940 74.175 1528 Min Nonbonded Distance : 2.456 Molprobity Statistics. All-atom Clashscore : 14.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.55 % Favored : 92.45 % Rotamer: Outliers : 4.15 % Allowed : 32.43 % Favored : 63.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 aren not related in a simple way. whole: -0.84 (0.23), residues: 1404 helix: -0.04 (0.15), residues: 1148 sheet: None (None), residues: 0 loop : -2.44 (0.38), residues: 256 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG D 180 TYR 0.047 0.001 TYR B 235 PHE 0.025 0.002 PHE G 85 TRP 0.017 0.001 TRP E 275 HIS 0.025 0.002 HIS G 79 Details of bonding type rmsd covalent geometry : bond 0.00335 (11412) covalent geometry : angle 0.82981 (15321) hydrogen bonds : bond 0.03717 ( 702) hydrogen bonds : angle 4.38857 ( 2046) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2065.12 seconds wall clock time: 36 minutes 39.85 seconds (2199.85 seconds total)