Starting phenix.real_space_refine on Tue Jul 29 06:15:20 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6ip1_9697/07_2025/6ip1_9697.cif Found real_map, /net/cci-nas-00/data/ceres_data/6ip1_9697/07_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_9697/07_2025/6ip1_9697.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6ip1_9697/07_2025/6ip1_9697.map" model { file = "/net/cci-nas-00/data/ceres_data/6ip1_9697/07_2025/6ip1_9697.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6ip1_9697/07_2025/6ip1_9697.cif" } resolution = 3.9 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 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): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/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: 7.27, per 1000 atoms: 0.65 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: 2.74 Conformation dependent library (CDL) restraints added in 1.5 seconds 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: 0.92 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: 2.99 Time building geometry restraints manager: 3.26 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: 0.260 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.510 Check model and map are aligned: 0.090 Set scattering table: 0.120 Process input model: 27.740 Find NCS groups from input model: 0.340 Set up NCS constraints: 0.050 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:2.850 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 31.970 ------------------------------------------------------------------------------- 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 : 7.91 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -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 TRP 0.024 0.003 TRP F 275 HIS 0.012 0.003 HIS H 251 PHE 0.029 0.004 PHE F 85 TYR 0.027 0.003 TYR H 45 ARG 0.010 0.001 ARG B 232 Details of bonding type rmsd hydrogen bonds : bond 0.32024 ( 702) hydrogen bonds : angle 9.93034 ( 2046) covalent geometry : bond 0.00572 (11412) covalent geometry : angle 1.02506 (15321) *********************** 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 : 1.197 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 65 ASP cc_start: 0.8179 (m-30) cc_final: 0.7771 (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: 0.8294 (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: 0.8429 (tp40) REVERT: C 56 GLN cc_start: 0.8428 (mm110) cc_final: 0.8191 (mt0) REVERT: E 57 ASN cc_start: 0.8430 (t0) cc_final: 0.8155 (t0) REVERT: E 58 TRP cc_start: 0.8676 (m-90) cc_final: 0.7843 (m-90) REVERT: E 75 LEU cc_start: 0.8079 (OUTLIER) cc_final: 0.7636 (tp) REVERT: E 104 LEU cc_start: 0.8871 (mt) cc_final: 0.8607 (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: 0.8026 (tptt) REVERT: E 278 THR cc_start: 0.8490 (p) cc_final: 0.8110 (t) REVERT: F 67 GLN cc_start: 0.8085 (mt0) cc_final: 0.7657 (mt0) REVERT: F 78 LYS cc_start: 0.8833 (mmmm) cc_final: 0.8589 (mtpt) REVERT: F 87 ASP cc_start: 0.8699 (m-30) cc_final: 0.8365 (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: 0.7981 (tt) REVERT: F 203 LYS cc_start: 0.8262 (pptt) cc_final: 0.7973 (pttp) REVERT: F 268 SER cc_start: 0.8636 (p) cc_final: 0.8307 (m) REVERT: F 276 LEU cc_start: 0.9036 (tm) cc_final: 0.8585 (tm) REVERT: F 279 MET cc_start: 0.7967 (mmt) cc_final: 0.7759 (mmt) REVERT: F 288 GLN cc_start: 0.8289 (mt0) cc_final: 0.7926 (mt0) REVERT: G 71 LEU cc_start: 0.8336 (mt) cc_final: 0.7640 (mt) REVERT: G 93 LYS cc_start: 0.8048 (mtpt) cc_final: 0.7752 (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: 0.7032 (tpt170) REVERT: G 267 ASP cc_start: 0.8694 (p0) cc_final: 0.8025 (t70) REVERT: H 9 GLU cc_start: 0.7757 (tp30) cc_final: 0.7453 (tp30) REVERT: H 54 MET cc_start: 0.8481 (tpp) cc_final: 0.8256 (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: 0.8125 (tt) REVERT: H 175 LEU cc_start: 0.7788 (mm) cc_final: 0.7496 (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: 0.2660 time to fit residues: 234.9418 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 : 1.492 ------------------------------------------------------------------------------- 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 118 optimal weight: 6.9990 chunk 106 optimal weight: 1.9990 chunk 58 optimal weight: 10.0000 chunk 36 optimal weight: 0.9990 chunk 71 optimal weight: 2.9990 chunk 56 optimal weight: 9.9990 chunk 109 optimal weight: 5.9990 chunk 42 optimal weight: 0.9990 chunk 66 optimal weight: 0.9990 chunk 81 optimal weight: 9.9990 chunk 127 optimal weight: 1.9990 overall best weight: 1.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 187 GLN E 191 ASN F 23 ASN F 25 GLN F 98 GLN F 162 ASN G 25 GLN 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: 18 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4090 r_free = 0.4090 target = 0.158075 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3808 r_free = 0.3808 target = 0.136784 restraints weight = 24575.733| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3852 r_free = 0.3852 target = 0.140109 restraints weight = 14307.538| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3879 r_free = 0.3879 target = 0.142244 restraints weight = 9525.926| |-----------------------------------------------------------------------------| r_work (final): 0.3806 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7497 moved from start: 0.5146 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.072 11412 Z= 0.179 Angle : 0.794 10.071 15321 Z= 0.425 Chirality : 0.043 0.172 1667 Planarity : 0.004 0.040 1998 Dihedral : 6.453 58.293 1530 Min Nonbonded Distance : 2.423 Molprobity Statistics. All-atom Clashscore : 14.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.77 % Favored : 93.23 % Rotamer: Outliers : 4.91 % Allowed : 18.63 % Favored : 76.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.38 (0.19), residues: 1404 helix: -1.96 (0.13), residues: 1107 sheet: None (None), residues: 0 loop : -2.49 (0.34), residues: 297 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP E 275 HIS 0.010 0.002 HIS E 213 PHE 0.024 0.003 PHE F 85 TYR 0.039 0.002 TYR B 235 ARG 0.004 0.001 ARG G 106 Details of bonding type rmsd hydrogen bonds : bond 0.05528 ( 702) hydrogen bonds : angle 5.38065 ( 2046) covalent geometry : bond 0.00378 (11412) covalent geometry : angle 0.79361 (15321) *********************** 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 506 residues out of total 1181 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 448 time to evaluate : 1.361 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 41 GLU cc_start: 0.8935 (OUTLIER) cc_final: 0.8707 (tt0) REVERT: A 61 SER cc_start: 0.8520 (p) cc_final: 0.7937 (t) REVERT: A 65 ASP cc_start: 0.8322 (m-30) cc_final: 0.8005 (t0) REVERT: A 78 GLU cc_start: 0.8494 (pp20) cc_final: 0.7790 (tp30) REVERT: B 229 MET cc_start: 0.8070 (mtm) cc_final: 0.7757 (ttm) REVERT: B 246 ARG cc_start: 0.8193 (ttm-80) cc_final: 0.7700 (ttm170) REVERT: C 34 GLN cc_start: 0.8572 (tp40) cc_final: 0.8281 (tp40) REVERT: C 62 GLU cc_start: 0.8287 (tp30) cc_final: 0.8024 (tp30) REVERT: C 66 GLN cc_start: 0.8538 (mt0) cc_final: 0.7921 (mm-40) REVERT: D 191 ARG cc_start: 0.8458 (mtp85) cc_final: 0.7800 (mtp85) REVERT: E 125 ILE cc_start: 0.8527 (pp) cc_final: 0.8279 (mt) REVERT: E 146 GLU cc_start: 0.7611 (pt0) cc_final: 0.7329 (pt0) REVERT: E 164 CYS cc_start: 0.8499 (m) cc_final: 0.8008 (m) REVERT: E 227 LYS cc_start: 0.8656 (mttm) cc_final: 0.8220 (tptt) REVERT: E 278 THR cc_start: 0.8178 (p) cc_final: 0.7962 (t) REVERT: F 11 MET cc_start: 0.7793 (ppp) cc_final: 0.7533 (ppp) REVERT: F 13 LEU cc_start: 0.8165 (tp) cc_final: 0.7957 (tt) REVERT: F 24 SER cc_start: 0.7477 (m) cc_final: 0.6991 (t) REVERT: F 51 MET cc_start: 0.7714 (tpp) cc_final: 0.6740 (tpp) REVERT: F 54 MET cc_start: 0.8916 (mmm) cc_final: 0.8613 (tpp) REVERT: F 78 LYS cc_start: 0.8505 (mmmm) cc_final: 0.8246 (mtpt) REVERT: F 80 ASP cc_start: 0.8046 (OUTLIER) cc_final: 0.7451 (m-30) REVERT: F 87 ASP cc_start: 0.8263 (m-30) cc_final: 0.7948 (m-30) REVERT: F 101 ILE cc_start: 0.8990 (pp) cc_final: 0.8740 (pp) REVERT: F 140 LYS cc_start: 0.8375 (OUTLIER) cc_final: 0.7924 (mtmm) REVERT: F 175 LEU cc_start: 0.8420 (mm) cc_final: 0.7691 (tt) REVERT: F 260 THR cc_start: 0.8421 (p) cc_final: 0.7809 (p) REVERT: F 266 TYR cc_start: 0.8061 (t80) cc_final: 0.7849 (t80) REVERT: F 268 SER cc_start: 0.8286 (p) cc_final: 0.7828 (m) REVERT: F 279 MET cc_start: 0.8362 (mmt) cc_final: 0.7751 (mmt) REVERT: G 105 MET cc_start: 0.8621 (tpp) cc_final: 0.8310 (tpp) REVERT: G 113 ASP cc_start: 0.7432 (p0) cc_final: 0.6732 (t0) REVERT: G 114 MET cc_start: 0.8252 (ttm) cc_final: 0.7853 (ttt) REVERT: G 147 GLN cc_start: 0.7713 (tt0) cc_final: 0.7255 (mt0) REVERT: G 153 LYS cc_start: 0.8698 (mtpp) cc_final: 0.8482 (mtmt) REVERT: G 264 LYS cc_start: 0.8292 (tptp) cc_final: 0.7648 (tptp) REVERT: G 267 ASP cc_start: 0.8585 (p0) cc_final: 0.8230 (p0) REVERT: H 25 GLN cc_start: 0.6794 (mp10) cc_final: 0.6545 (mp10) REVERT: H 39 GLU cc_start: 0.8353 (pt0) cc_final: 0.8099 (mp0) REVERT: H 40 GLU cc_start: 0.8350 (tp30) cc_final: 0.7747 (tp30) REVERT: H 43 GLU cc_start: 0.8152 (OUTLIER) cc_final: 0.7872 (pm20) REVERT: H 76 GLN cc_start: 0.8034 (mp10) cc_final: 0.7523 (tm-30) REVERT: H 103 CYS cc_start: 0.8322 (p) cc_final: 0.8084 (p) REVERT: H 106 ARG cc_start: 0.7976 (mtp85) cc_final: 0.7345 (mtm180) REVERT: H 140 LYS cc_start: 0.8533 (mttt) cc_final: 0.8207 (mtmt) REVERT: H 153 LYS cc_start: 0.8920 (mtpp) cc_final: 0.8292 (mtpt) REVERT: H 204 ASP cc_start: 0.8305 (OUTLIER) cc_final: 0.7870 (m-30) outliers start: 58 outliers final: 30 residues processed: 477 average time/residue: 0.2621 time to fit residues: 169.5901 Evaluate side-chains 400 residues out of total 1181 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 365 time to evaluate : 1.104 ------------------------------------------------------------------------------- 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 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 80 ASP Chi-restraints excluded: chain F residue 84 CYS Chi-restraints excluded: chain F residue 118 THR Chi-restraints excluded: chain F residue 140 LYS Chi-restraints excluded: chain F residue 142 ILE 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 43 GLU 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 73 optimal weight: 0.9980 chunk 79 optimal weight: 8.9990 chunk 53 optimal weight: 6.9990 chunk 16 optimal weight: 2.9990 chunk 126 optimal weight: 10.0000 chunk 17 optimal weight: 2.9990 chunk 66 optimal weight: 4.9990 chunk 57 optimal weight: 4.9990 chunk 96 optimal weight: 9.9990 chunk 6 optimal weight: 4.9990 chunk 102 optimal weight: 6.9990 overall best weight: 3.3988 ------------------------------------------------------------------------------- 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** C 53 GLN D 188 ASN E 177 GLN F 50 ASN ** F 255 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 90 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 213 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 50 ASN ** H 213 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 = 0.3977 r_free = 0.3977 target = 0.148571 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 26)----------------| | r_work = 0.3699 r_free = 0.3699 target = 0.128450 restraints weight = 25165.631| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3746 r_free = 0.3746 target = 0.131705 restraints weight = 14187.887| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3776 r_free = 0.3776 target = 0.133885 restraints weight = 9266.235| |-----------------------------------------------------------------------------| r_work (final): 0.3718 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7638 moved from start: 0.6131 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.055 11412 Z= 0.211 Angle : 0.778 10.871 15321 Z= 0.416 Chirality : 0.045 0.182 1667 Planarity : 0.004 0.044 1998 Dihedral : 6.175 64.867 1528 Min Nonbonded Distance : 2.478 Molprobity Statistics. All-atom Clashscore : 15.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.62 % Favored : 92.38 % Rotamer: Outliers : 6.52 % Allowed : 21.51 % Favored : 71.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.20 (0.21), residues: 1404 helix: -0.95 (0.15), residues: 1127 sheet: None (None), residues: 0 loop : -2.98 (0.34), residues: 277 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP E 275 HIS 0.009 0.002 HIS E 213 PHE 0.021 0.002 PHE F 207 TYR 0.033 0.002 TYR B 235 ARG 0.005 0.001 ARG A 56 Details of bonding type rmsd hydrogen bonds : bond 0.04887 ( 702) hydrogen bonds : angle 5.08005 ( 2046) covalent geometry : bond 0.00452 (11412) covalent geometry : angle 0.77798 (15321) *********************** 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 470 residues out of total 1181 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 393 time to evaluate : 1.306 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 44 ASP cc_start: 0.8503 (t0) cc_final: 0.7989 (t0) REVERT: A 56 ARG cc_start: 0.9111 (ptm160) cc_final: 0.8844 (ptm160) REVERT: A 66 ARG cc_start: 0.8347 (mmm160) cc_final: 0.8112 (mmp-170) REVERT: A 68 ASP cc_start: 0.7552 (t0) cc_final: 0.7340 (t0) REVERT: A 70 LEU cc_start: 0.9322 (tp) cc_final: 0.8985 (tt) REVERT: B 193 SER cc_start: 0.8610 (p) cc_final: 0.8260 (t) REVERT: B 203 ILE cc_start: 0.8166 (mm) cc_final: 0.7793 (pt) REVERT: B 210 ARG cc_start: 0.8043 (ttm-80) cc_final: 0.7440 (mmm160) REVERT: B 229 MET cc_start: 0.8188 (mtm) cc_final: 0.7834 (ttm) REVERT: C 66 GLN cc_start: 0.8526 (mt0) cc_final: 0.8273 (mm-40) REVERT: D 196 ASN cc_start: 0.7731 (p0) cc_final: 0.7428 (p0) REVERT: E 40 GLU cc_start: 0.7596 (tp30) cc_final: 0.7111 (mp0) REVERT: E 76 GLN cc_start: 0.8153 (mp10) cc_final: 0.7602 (pp30) REVERT: E 98 GLN cc_start: 0.7951 (tp-100) cc_final: 0.7739 (tp-100) REVERT: E 122 LYS cc_start: 0.9341 (tppt) cc_final: 0.8940 (tppt) REVERT: E 125 ILE cc_start: 0.8684 (pp) cc_final: 0.8290 (mt) REVERT: E 164 CYS cc_start: 0.8563 (m) cc_final: 0.8137 (m) REVERT: E 227 LYS cc_start: 0.8594 (mttm) cc_final: 0.8218 (tptt) REVERT: E 278 THR cc_start: 0.8246 (p) cc_final: 0.8007 (t) REVERT: F 11 MET cc_start: 0.7804 (ppp) cc_final: 0.7563 (ppp) REVERT: F 51 MET cc_start: 0.7890 (tpp) cc_final: 0.6913 (tpp) REVERT: F 78 LYS cc_start: 0.8576 (mmmm) cc_final: 0.8338 (mtmt) REVERT: F 80 ASP cc_start: 0.8048 (OUTLIER) cc_final: 0.7555 (m-30) REVERT: F 87 ASP cc_start: 0.8676 (m-30) cc_final: 0.8314 (m-30) REVERT: F 101 ILE cc_start: 0.9090 (pp) cc_final: 0.8861 (pp) REVERT: F 114 MET cc_start: 0.8707 (tpp) cc_final: 0.8130 (ttt) REVERT: F 158 ASN cc_start: 0.9268 (p0) cc_final: 0.8820 (p0) REVERT: F 175 LEU cc_start: 0.8805 (mm) cc_final: 0.8183 (tt) REVERT: F 226 GLN cc_start: 0.8100 (tp-100) cc_final: 0.7823 (tp-100) REVERT: F 279 MET cc_start: 0.8464 (mmt) cc_final: 0.7925 (mmt) REVERT: F 282 ARG cc_start: 0.8307 (mtp85) cc_final: 0.8097 (mtp85) REVERT: G 105 MET cc_start: 0.8478 (tpp) cc_final: 0.8136 (tpp) REVERT: G 113 ASP cc_start: 0.7619 (p0) cc_final: 0.6776 (t0) REVERT: G 152 TYR cc_start: 0.9204 (OUTLIER) cc_final: 0.8553 (m-10) REVERT: G 163 LYS cc_start: 0.8515 (mtmt) cc_final: 0.7931 (mttp) REVERT: G 179 GLN cc_start: 0.8583 (tp-100) cc_final: 0.7660 (tt0) REVERT: G 265 GLU cc_start: 0.7710 (pp20) cc_final: 0.7478 (tp30) REVERT: G 285 LYS cc_start: 0.8809 (mmmt) cc_final: 0.8600 (mmmt) REVERT: H 51 MET cc_start: 0.8226 (mtm) cc_final: 0.7813 (ttp) REVERT: H 76 GLN cc_start: 0.8140 (mp10) cc_final: 0.7336 (tm-30) REVERT: H 103 CYS cc_start: 0.8319 (p) cc_final: 0.8082 (p) REVERT: H 105 MET cc_start: 0.8795 (tpt) cc_final: 0.8265 (tpt) REVERT: H 106 ARG cc_start: 0.7780 (mtp85) cc_final: 0.7543 (ttp-110) REVERT: H 125 ILE cc_start: 0.8659 (OUTLIER) cc_final: 0.8166 (mt) REVERT: H 153 LYS cc_start: 0.8855 (mtpp) cc_final: 0.8618 (mtpt) REVERT: H 204 ASP cc_start: 0.8272 (OUTLIER) cc_final: 0.7898 (m-30) REVERT: H 271 ARG cc_start: 0.8236 (mmm-85) cc_final: 0.7039 (ttt180) outliers start: 77 outliers final: 52 residues processed: 433 average time/residue: 0.2516 time to fit residues: 148.6220 Evaluate side-chains 396 residues out of total 1181 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 340 time to evaluate : 1.259 ------------------------------------------------------------------------------- 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 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 78 LEU Chi-restraints excluded: chain C residue 79 THR 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 E residue 260 THR 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 102 ASN 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 225 VAL Chi-restraints excluded: chain G residue 21 VAL 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 130 ILE Chi-restraints excluded: chain G residue 136 VAL Chi-restraints excluded: chain G residue 152 TYR Chi-restraints excluded: chain G residue 193 MET 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 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 184 ILE 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 128 optimal weight: 0.0980 chunk 104 optimal weight: 1.9990 chunk 85 optimal weight: 0.0070 chunk 131 optimal weight: 2.9990 chunk 115 optimal weight: 2.9990 chunk 39 optimal weight: 9.9990 chunk 123 optimal weight: 3.9990 chunk 90 optimal weight: 1.9990 chunk 14 optimal weight: 0.9980 chunk 56 optimal weight: 7.9990 chunk 103 optimal weight: 4.9990 overall best weight: 1.0202 ------------------------------------------------------------------------------- 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 D 177 GLN D 188 ASN E 254 GLN F 23 ASN ** F 50 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 213 HIS ** G 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 254 GLN ** H 50 ASN ** 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 = 0.4071 r_free = 0.4071 target = 0.154757 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3790 r_free = 0.3790 target = 0.133951 restraints weight = 25344.904| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3835 r_free = 0.3835 target = 0.137266 restraints weight = 14357.722| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3862 r_free = 0.3862 target = 0.139370 restraints weight = 9393.999| |-----------------------------------------------------------------------------| r_work (final): 0.3816 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7564 moved from start: 0.6559 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 : 0.728 15.973 15321 Z= 0.376 Chirality : 0.042 0.177 1667 Planarity : 0.003 0.048 1998 Dihedral : 6.008 66.707 1528 Min Nonbonded Distance : 2.511 Molprobity Statistics. All-atom Clashscore : 13.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.84 % Favored : 93.16 % Rotamer: Outliers : 4.74 % Allowed : 24.22 % Favored : 71.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.59 (0.22), residues: 1404 helix: -0.52 (0.15), residues: 1139 sheet: None (None), residues: 0 loop : -2.91 (0.36), residues: 265 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP E 275 HIS 0.007 0.002 HIS E 213 PHE 0.020 0.002 PHE H 28 TYR 0.034 0.001 TYR B 235 ARG 0.005 0.000 ARG F 239 Details of bonding type rmsd hydrogen bonds : bond 0.04112 ( 702) hydrogen bonds : angle 4.69152 ( 2046) covalent geometry : bond 0.00306 (11412) covalent geometry : angle 0.72798 (15321) *********************** 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 446 residues out of total 1181 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 390 time to evaluate : 1.287 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 44 ASP cc_start: 0.8476 (t0) cc_final: 0.7804 (t0) REVERT: A 65 ASP cc_start: 0.8088 (m-30) cc_final: 0.7652 (t0) REVERT: A 70 LEU cc_start: 0.9114 (tp) cc_final: 0.8831 (tt) REVERT: A 78 GLU cc_start: 0.8573 (pp20) cc_final: 0.7836 (tp30) REVERT: B 193 SER cc_start: 0.8642 (p) cc_final: 0.8328 (t) REVERT: B 200 SER cc_start: 0.8677 (t) cc_final: 0.8274 (p) REVERT: B 203 ILE cc_start: 0.8077 (mm) cc_final: 0.7280 (pt) REVERT: B 217 MET cc_start: 0.6280 (mmp) cc_final: 0.5643 (mtm) REVERT: C 26 LEU cc_start: 0.7959 (tm) cc_final: 0.7594 (mt) REVERT: C 34 GLN cc_start: 0.8245 (tp40) cc_final: 0.7730 (tp40) REVERT: D 196 ASN cc_start: 0.7646 (p0) cc_final: 0.7294 (p0) REVERT: E 122 LYS cc_start: 0.9332 (tppt) cc_final: 0.8801 (tppt) REVERT: E 125 ILE cc_start: 0.8765 (OUTLIER) cc_final: 0.8292 (mt) REVERT: E 164 CYS cc_start: 0.8331 (m) cc_final: 0.7972 (m) REVERT: E 168 VAL cc_start: 0.8564 (p) cc_final: 0.8344 (p) REVERT: E 200 TYR cc_start: 0.7944 (m-80) cc_final: 0.7662 (m-80) REVERT: E 226 GLN cc_start: 0.8138 (mm-40) cc_final: 0.7937 (mm-40) REVERT: E 227 LYS cc_start: 0.8455 (mttm) cc_final: 0.8098 (tptt) REVERT: E 278 THR cc_start: 0.8121 (p) cc_final: 0.7894 (t) REVERT: F 24 SER cc_start: 0.7513 (m) cc_final: 0.6977 (t) REVERT: F 51 MET cc_start: 0.7540 (tpp) cc_final: 0.6961 (tpp) REVERT: F 78 LYS cc_start: 0.8486 (mmmm) cc_final: 0.8117 (mtmt) REVERT: F 80 ASP cc_start: 0.7676 (OUTLIER) cc_final: 0.7447 (m-30) REVERT: F 87 ASP cc_start: 0.8525 (m-30) cc_final: 0.8235 (m-30) REVERT: F 114 MET cc_start: 0.8576 (tpp) cc_final: 0.8039 (ttt) REVERT: F 132 GLU cc_start: 0.7243 (tt0) cc_final: 0.7041 (tt0) REVERT: F 158 ASN cc_start: 0.9157 (p0) cc_final: 0.8876 (p0) REVERT: F 171 TYR cc_start: 0.8224 (m-80) cc_final: 0.6875 (m-80) REVERT: F 175 LEU cc_start: 0.8578 (mm) cc_final: 0.7915 (tt) REVERT: F 187 GLN cc_start: 0.8682 (pt0) cc_final: 0.7998 (tp-100) REVERT: F 193 MET cc_start: 0.7343 (mmt) cc_final: 0.6016 (tpt) REVERT: F 271 ARG cc_start: 0.7404 (tpp-160) cc_final: 0.7052 (tpt-90) REVERT: G 11 MET cc_start: 0.7370 (tmm) cc_final: 0.7145 (mmp) REVERT: G 79 HIS cc_start: 0.6659 (t-90) cc_final: 0.6392 (t-170) REVERT: G 105 MET cc_start: 0.8414 (tpp) cc_final: 0.7958 (tpp) REVERT: G 113 ASP cc_start: 0.7267 (p0) cc_final: 0.6583 (t0) REVERT: G 152 TYR cc_start: 0.9100 (OUTLIER) cc_final: 0.8511 (m-10) REVERT: G 163 LYS cc_start: 0.8397 (mtmt) cc_final: 0.7882 (mttp) REVERT: H 45 TYR cc_start: 0.7383 (OUTLIER) cc_final: 0.6764 (t80) REVERT: H 51 MET cc_start: 0.8124 (OUTLIER) cc_final: 0.7867 (ttp) REVERT: H 76 GLN cc_start: 0.7972 (mp10) cc_final: 0.7354 (tm-30) REVERT: H 125 ILE cc_start: 0.8624 (pp) cc_final: 0.8283 (mt) REVERT: H 146 GLU cc_start: 0.7922 (tt0) cc_final: 0.7664 (tp30) REVERT: H 222 LYS cc_start: 0.6342 (ttmt) cc_final: 0.5635 (ttmt) REVERT: H 271 ARG cc_start: 0.8254 (mmm-85) cc_final: 0.7075 (ttt180) outliers start: 56 outliers final: 30 residues processed: 417 average time/residue: 0.2458 time to fit residues: 140.5969 Evaluate side-chains 377 residues out of total 1181 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 342 time to evaluate : 1.235 ------------------------------------------------------------------------------- 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 55 GLU Chi-restraints excluded: chain A residue 62 GLU Chi-restraints excluded: chain B residue 214 ASP Chi-restraints excluded: chain B residue 236 ASN Chi-restraints excluded: chain C residue 36 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 103 CYS Chi-restraints excluded: chain E residue 125 ILE Chi-restraints excluded: chain E residue 211 LEU Chi-restraints excluded: chain E residue 272 LEU Chi-restraints excluded: chain E residue 277 THR Chi-restraints excluded: chain F residue 38 ILE Chi-restraints excluded: chain F residue 80 ASP Chi-restraints excluded: chain F residue 84 CYS Chi-restraints excluded: chain F residue 142 ILE 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 136 VAL Chi-restraints excluded: chain G residue 152 TYR Chi-restraints excluded: chain G residue 197 LEU Chi-restraints excluded: chain H residue 38 ILE Chi-restraints excluded: chain H residue 42 CYS Chi-restraints excluded: chain H residue 45 TYR Chi-restraints excluded: chain H residue 51 MET Chi-restraints excluded: chain H residue 101 ILE Chi-restraints excluded: chain H residue 127 ILE Chi-restraints excluded: chain H residue 171 TYR Chi-restraints excluded: chain H residue 211 LEU Chi-restraints excluded: chain H residue 219 LEU Chi-restraints excluded: chain H residue 276 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 13 optimal weight: 3.9990 chunk 21 optimal weight: 4.9990 chunk 101 optimal weight: 9.9990 chunk 25 optimal weight: 9.9990 chunk 60 optimal weight: 5.9990 chunk 19 optimal weight: 0.6980 chunk 121 optimal weight: 0.9980 chunk 55 optimal weight: 8.9990 chunk 138 optimal weight: 0.9990 chunk 113 optimal weight: 0.0020 chunk 139 optimal weight: 6.9990 overall best weight: 1.3392 ------------------------------------------------------------------------------- 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 199 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 226 GLN D 159 ASN D 188 ASN E 50 ASN ** F 23 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 50 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 70 GLN ** 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 = 0.4074 r_free = 0.4074 target = 0.154920 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3795 r_free = 0.3795 target = 0.134094 restraints weight = 25096.543| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3838 r_free = 0.3838 target = 0.137223 restraints weight = 14256.410| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3867 r_free = 0.3867 target = 0.139363 restraints weight = 9478.524| |-----------------------------------------------------------------------------| r_work (final): 0.3816 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7578 moved from start: 0.6951 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= 0.144 Angle : 0.720 12.808 15321 Z= 0.374 Chirality : 0.042 0.184 1667 Planarity : 0.003 0.050 1998 Dihedral : 5.951 68.497 1528 Min Nonbonded Distance : 2.481 Molprobity Statistics. All-atom Clashscore : 14.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.12 % Favored : 92.88 % Rotamer: Outliers : 5.08 % Allowed : 25.57 % Favored : 69.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.25 (0.23), residues: 1404 helix: -0.25 (0.15), residues: 1139 sheet: None (None), residues: 0 loop : -2.95 (0.37), residues: 265 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP H 275 HIS 0.007 0.002 HIS E 79 PHE 0.021 0.002 PHE H 28 TYR 0.039 0.001 TYR B 235 ARG 0.012 0.000 ARG D 180 Details of bonding type rmsd hydrogen bonds : bond 0.03896 ( 702) hydrogen bonds : angle 4.55843 ( 2046) covalent geometry : bond 0.00312 (11412) covalent geometry : angle 0.72009 (15321) *********************** 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 435 residues out of total 1181 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 375 time to evaluate : 1.340 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: 0.8560 (t0) cc_final: 0.7854 (t0) REVERT: A 65 ASP cc_start: 0.8105 (m-30) cc_final: 0.7616 (t0) REVERT: A 70 LEU cc_start: 0.9083 (tp) cc_final: 0.8820 (tt) REVERT: B 193 SER cc_start: 0.8740 (p) cc_final: 0.8391 (t) REVERT: B 199 HIS cc_start: 0.7067 (t-90) cc_final: 0.6786 (t70) REVERT: B 200 SER cc_start: 0.8534 (t) cc_final: 0.8264 (p) REVERT: B 203 ILE cc_start: 0.7906 (mm) cc_final: 0.7364 (pt) REVERT: B 210 ARG cc_start: 0.8087 (ttm-80) cc_final: 0.7651 (mmm160) REVERT: B 217 MET cc_start: 0.6324 (mmp) cc_final: 0.5714 (mtm) REVERT: C 26 LEU cc_start: 0.7856 (tm) cc_final: 0.7494 (mt) REVERT: C 34 GLN cc_start: 0.8284 (tp40) cc_final: 0.7955 (tp40) REVERT: C 66 GLN cc_start: 0.8495 (mm-40) cc_final: 0.8095 (mm-40) REVERT: D 196 ASN cc_start: 0.7632 (p0) cc_final: 0.7303 (p0) REVERT: E 50 ASN cc_start: 0.8693 (OUTLIER) cc_final: 0.8420 (t0) REVERT: E 76 GLN cc_start: 0.8034 (mp10) cc_final: 0.7557 (pp30) REVERT: E 122 LYS cc_start: 0.9382 (tppt) cc_final: 0.8917 (tppt) REVERT: E 125 ILE cc_start: 0.8724 (OUTLIER) cc_final: 0.8152 (mt) REVERT: E 164 CYS cc_start: 0.8314 (m) cc_final: 0.7717 (m) REVERT: E 168 VAL cc_start: 0.8568 (OUTLIER) cc_final: 0.8359 (p) REVERT: E 227 LYS cc_start: 0.8546 (mttm) cc_final: 0.8252 (tptp) REVERT: E 278 THR cc_start: 0.8142 (p) cc_final: 0.7926 (t) REVERT: F 51 MET cc_start: 0.7778 (tpp) cc_final: 0.7283 (tpp) REVERT: F 78 LYS cc_start: 0.8340 (mmmm) cc_final: 0.7938 (mtpt) REVERT: F 80 ASP cc_start: 0.7528 (OUTLIER) cc_final: 0.7303 (m-30) REVERT: F 87 ASP cc_start: 0.8535 (m-30) cc_final: 0.8213 (m-30) REVERT: F 114 MET cc_start: 0.8472 (tpp) cc_final: 0.7974 (ttt) REVERT: F 150 ASP cc_start: 0.8270 (t0) cc_final: 0.8048 (t0) REVERT: F 171 TYR cc_start: 0.8278 (m-80) cc_final: 0.7203 (m-80) REVERT: F 175 LEU cc_start: 0.8620 (mm) cc_final: 0.7998 (tt) REVERT: F 193 MET cc_start: 0.7379 (mmt) cc_final: 0.6097 (tpt) REVERT: F 218 MET cc_start: 0.3744 (OUTLIER) cc_final: 0.3436 (mtm) REVERT: G 93 LYS cc_start: 0.8327 (OUTLIER) cc_final: 0.7983 (mppt) REVERT: G 94 LYS cc_start: 0.7156 (OUTLIER) cc_final: 0.6618 (mmtt) REVERT: G 105 MET cc_start: 0.8393 (tpp) cc_final: 0.7946 (tpp) REVERT: G 113 ASP cc_start: 0.7315 (p0) cc_final: 0.6574 (t0) REVERT: G 152 TYR cc_start: 0.9074 (OUTLIER) cc_final: 0.8521 (m-10) REVERT: G 163 LYS cc_start: 0.8536 (mtmt) cc_final: 0.7995 (mttp) REVERT: G 259 TYR cc_start: 0.8213 (OUTLIER) cc_final: 0.7923 (t80) REVERT: H 45 TYR cc_start: 0.7181 (OUTLIER) cc_final: 0.6254 (t80) REVERT: H 125 ILE cc_start: 0.8629 (OUTLIER) cc_final: 0.8310 (mt) REVERT: H 146 GLU cc_start: 0.8052 (tt0) cc_final: 0.7723 (tm-30) REVERT: H 271 ARG cc_start: 0.8319 (mmm-85) cc_final: 0.7177 (ttt180) outliers start: 60 outliers final: 31 residues processed: 400 average time/residue: 0.2471 time to fit residues: 135.8250 Evaluate side-chains 393 residues out of total 1181 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 351 time to evaluate : 1.396 ------------------------------------------------------------------------------- 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 55 GLU Chi-restraints excluded: chain B residue 214 ASP Chi-restraints excluded: chain B residue 237 VAL Chi-restraints excluded: chain C residue 36 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 168 VAL Chi-restraints excluded: chain E residue 260 THR Chi-restraints excluded: chain E residue 277 THR Chi-restraints excluded: chain F residue 80 ASP Chi-restraints excluded: chain F residue 83 THR Chi-restraints excluded: chain F residue 218 MET Chi-restraints excluded: chain G residue 21 VAL 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 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 G residue 267 ASP Chi-restraints excluded: chain H residue 42 CYS Chi-restraints excluded: chain H residue 45 TYR Chi-restraints excluded: chain H residue 101 ILE 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 184 ILE Chi-restraints excluded: chain H residue 194 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 100 optimal weight: 2.9990 chunk 60 optimal weight: 10.0000 chunk 109 optimal weight: 6.9990 chunk 96 optimal weight: 3.9990 chunk 32 optimal weight: 0.9980 chunk 54 optimal weight: 8.9990 chunk 114 optimal weight: 0.0980 chunk 19 optimal weight: 0.9990 chunk 2 optimal weight: 4.9990 chunk 95 optimal weight: 3.9990 chunk 101 optimal weight: 7.9990 overall best weight: 1.8186 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** B 213 HIS D 152 GLN D 188 ASN E 50 ASN ** F 23 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 50 ASN ** G 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 50 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4059 r_free = 0.4059 target = 0.153913 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3773 r_free = 0.3773 target = 0.132812 restraints weight = 25779.459| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3817 r_free = 0.3817 target = 0.136011 restraints weight = 14781.063| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3847 r_free = 0.3847 target = 0.138183 restraints weight = 9830.075| |-----------------------------------------------------------------------------| r_work (final): 0.3797 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7609 moved from start: 0.7234 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 11412 Z= 0.155 Angle : 0.748 15.643 15321 Z= 0.386 Chirality : 0.043 0.230 1667 Planarity : 0.003 0.057 1998 Dihedral : 5.983 70.398 1528 Min Nonbonded Distance : 2.410 Molprobity Statistics. All-atom Clashscore : 14.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.69 % Favored : 92.31 % Rotamer: Outliers : 5.59 % Allowed : 26.08 % Favored : 68.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.05 (0.23), residues: 1404 helix: -0.10 (0.16), residues: 1139 sheet: None (None), residues: 0 loop : -2.94 (0.36), residues: 265 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP H 275 HIS 0.018 0.002 HIS G 79 PHE 0.024 0.002 PHE G 85 TYR 0.040 0.001 TYR B 235 ARG 0.007 0.000 ARG D 180 Details of bonding type rmsd hydrogen bonds : bond 0.03812 ( 702) hydrogen bonds : angle 4.52487 ( 2046) covalent geometry : bond 0.00342 (11412) covalent geometry : angle 0.74783 (15321) *********************** 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 436 residues out of total 1181 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 370 time to evaluate : 1.392 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: symmetry clash REVERT: A 44 ASP cc_start: 0.8658 (t0) cc_final: 0.7889 (t0) REVERT: A 65 ASP cc_start: 0.8171 (m-30) cc_final: 0.7724 (t0) REVERT: A 70 LEU cc_start: 0.9100 (tp) cc_final: 0.8831 (tt) REVERT: B 193 SER cc_start: 0.8834 (p) cc_final: 0.8492 (t) REVERT: B 199 HIS cc_start: 0.7102 (t-90) cc_final: 0.6866 (t70) REVERT: B 200 SER cc_start: 0.8627 (t) cc_final: 0.8373 (p) REVERT: B 203 ILE cc_start: 0.7843 (mm) cc_final: 0.7402 (pt) REVERT: B 210 ARG cc_start: 0.8082 (ttm-80) cc_final: 0.7674 (mmm160) REVERT: B 222 LEU cc_start: 0.9114 (tt) cc_final: 0.8553 (mt) REVERT: C 34 GLN cc_start: 0.8176 (tp40) cc_final: 0.7823 (tp40) REVERT: C 52 GLU cc_start: 0.8845 (tp30) cc_final: 0.8457 (tp30) REVERT: D 196 ASN cc_start: 0.7658 (p0) cc_final: 0.7407 (p0) REVERT: E 76 GLN cc_start: 0.8047 (mp10) cc_final: 0.7425 (pp30) REVERT: E 122 LYS cc_start: 0.9220 (tppt) cc_final: 0.8769 (tppt) REVERT: E 125 ILE cc_start: 0.8827 (OUTLIER) cc_final: 0.8075 (mt) REVERT: E 164 CYS cc_start: 0.8216 (m) cc_final: 0.7570 (m) REVERT: E 227 LYS cc_start: 0.8546 (mttm) cc_final: 0.8233 (tptp) REVERT: F 51 MET cc_start: 0.7744 (tpp) cc_final: 0.7156 (tpp) REVERT: F 66 CYS cc_start: 0.8659 (t) cc_final: 0.7712 (p) REVERT: F 78 LYS cc_start: 0.8439 (mmmm) cc_final: 0.8029 (mtpt) REVERT: F 80 ASP cc_start: 0.7530 (OUTLIER) cc_final: 0.7265 (m-30) REVERT: F 87 ASP cc_start: 0.8560 (m-30) cc_final: 0.8245 (m-30) REVERT: F 150 ASP cc_start: 0.8427 (t0) cc_final: 0.8174 (t0) REVERT: F 175 LEU cc_start: 0.8742 (mm) cc_final: 0.8110 (tt) REVERT: F 193 MET cc_start: 0.7412 (mmt) cc_final: 0.6924 (tpt) REVERT: F 271 ARG cc_start: 0.7396 (tpt-90) cc_final: 0.6927 (tpp-160) REVERT: G 11 MET cc_start: 0.7332 (tmm) cc_final: 0.6959 (mmp) REVERT: G 39 GLU cc_start: 0.8822 (tm-30) cc_final: 0.8505 (tm-30) REVERT: G 51 MET cc_start: 0.8294 (tpp) cc_final: 0.7956 (tpp) REVERT: G 93 LYS cc_start: 0.8300 (OUTLIER) cc_final: 0.7994 (mppt) REVERT: G 94 LYS cc_start: 0.7107 (OUTLIER) cc_final: 0.6559 (mmtt) REVERT: G 105 MET cc_start: 0.8377 (tpp) cc_final: 0.7843 (tpp) REVERT: G 113 ASP cc_start: 0.7400 (p0) cc_final: 0.6526 (t0) REVERT: G 152 TYR cc_start: 0.9277 (OUTLIER) cc_final: 0.8469 (m-10) REVERT: G 163 LYS cc_start: 0.8637 (mtmt) cc_final: 0.8038 (mttp) REVERT: H 11 MET cc_start: 0.6416 (tpt) cc_final: 0.6126 (tpt) REVERT: H 45 TYR cc_start: 0.7413 (OUTLIER) cc_final: 0.6733 (t80) REVERT: H 125 ILE cc_start: 0.8626 (OUTLIER) cc_final: 0.8290 (mt) REVERT: H 146 GLU cc_start: 0.8124 (tt0) cc_final: 0.7745 (tm-30) REVERT: H 194 ASP cc_start: 0.7472 (OUTLIER) cc_final: 0.7130 (t0) outliers start: 66 outliers final: 40 residues processed: 403 average time/residue: 0.2629 time to fit residues: 145.0463 Evaluate side-chains 387 residues out of total 1181 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 339 time to evaluate : 1.358 ------------------------------------------------------------------------------- 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 53 VAL Chi-restraints excluded: chain A residue 55 GLU Chi-restraints excluded: chain A residue 79 THR Chi-restraints excluded: chain B residue 192 LEU Chi-restraints excluded: chain B residue 214 ASP Chi-restraints excluded: chain B residue 215 MET 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 103 CYS Chi-restraints excluded: chain E residue 125 ILE Chi-restraints excluded: chain E residue 256 VAL 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 71 LEU Chi-restraints excluded: chain F residue 80 ASP Chi-restraints excluded: chain F residue 83 THR Chi-restraints excluded: chain F residue 118 THR Chi-restraints excluded: chain F residue 127 ILE Chi-restraints excluded: chain G residue 21 VAL 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 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 42 CYS 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 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 184 ILE Chi-restraints excluded: chain H residue 194 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 51 optimal weight: 5.9990 chunk 130 optimal weight: 7.9990 chunk 110 optimal weight: 5.9990 chunk 78 optimal weight: 5.9990 chunk 132 optimal weight: 8.9990 chunk 85 optimal weight: 8.9990 chunk 113 optimal weight: 8.9990 chunk 75 optimal weight: 1.9990 chunk 35 optimal weight: 1.9990 chunk 64 optimal weight: 6.9990 chunk 60 optimal weight: 5.9990 overall best weight: 4.3990 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** B 236 ASN ** C 53 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 152 GLN D 159 ASN D 188 ASN E 50 ASN ** E 147 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 50 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 72 HIS ** G 79 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 162 ASN G 254 GLN H 67 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3968 r_free = 0.3968 target = 0.146315 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3675 r_free = 0.3675 target = 0.125330 restraints weight = 26041.478| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3720 r_free = 0.3720 target = 0.128473 restraints weight = 14907.484| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3749 r_free = 0.3749 target = 0.130512 restraints weight = 9915.974| |-----------------------------------------------------------------------------| r_work (final): 0.3703 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7746 moved from start: 0.7536 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.056 11412 Z= 0.247 Angle : 0.852 15.842 15321 Z= 0.446 Chirality : 0.047 0.210 1667 Planarity : 0.004 0.060 1998 Dihedral : 6.244 73.280 1528 Min Nonbonded Distance : 2.466 Molprobity Statistics. All-atom Clashscore : 19.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.05 % Favored : 90.95 % Rotamer: Outliers : 6.86 % Allowed : 25.83 % Favored : 67.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.31 (0.23), residues: 1404 helix: -0.33 (0.15), residues: 1153 sheet: None (None), residues: 0 loop : -2.89 (0.38), residues: 251 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP E 58 HIS 0.018 0.003 HIS G 79 PHE 0.028 0.003 PHE G 85 TYR 0.038 0.002 TYR B 235 ARG 0.005 0.001 ARG B 232 Details of bonding type rmsd hydrogen bonds : bond 0.04523 ( 702) hydrogen bonds : angle 4.91378 ( 2046) covalent geometry : bond 0.00542 (11412) covalent geometry : angle 0.85193 (15321) *********************** 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 445 residues out of total 1181 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 81 poor density : 364 time to evaluate : 1.356 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: A 44 ASP cc_start: 0.8836 (t0) cc_final: 0.8140 (t0) REVERT: A 70 LEU cc_start: 0.9350 (tp) cc_final: 0.9086 (tt) REVERT: B 193 SER cc_start: 0.8972 (p) cc_final: 0.8598 (t) REVERT: B 199 HIS cc_start: 0.7213 (t-90) cc_final: 0.6047 (t-90) REVERT: B 203 ILE cc_start: 0.8053 (mm) cc_final: 0.7336 (pt) REVERT: B 210 ARG cc_start: 0.8004 (ttm-80) cc_final: 0.7649 (mmm160) REVERT: C 24 GLU cc_start: 0.5372 (mt-10) cc_final: 0.5020 (mt-10) REVERT: C 34 GLN cc_start: 0.8466 (tp40) cc_final: 0.7888 (tp40) REVERT: C 52 GLU cc_start: 0.8714 (tp30) cc_final: 0.8380 (tp30) REVERT: C 66 GLN cc_start: 0.8578 (mm-40) cc_final: 0.8161 (mm-40) REVERT: D 186 ASP cc_start: 0.8051 (m-30) cc_final: 0.6743 (m-30) REVERT: E 102 ASN cc_start: 0.7563 (p0) cc_final: 0.7097 (m110) REVERT: E 122 LYS cc_start: 0.9354 (tppt) cc_final: 0.8921 (tppt) REVERT: E 125 ILE cc_start: 0.8764 (OUTLIER) cc_final: 0.8335 (mt) REVERT: E 164 CYS cc_start: 0.8355 (m) cc_final: 0.7980 (m) REVERT: E 227 LYS cc_start: 0.8718 (mttm) cc_final: 0.8369 (tptp) REVERT: F 87 ASP cc_start: 0.8456 (m-30) cc_final: 0.8081 (m-30) REVERT: F 132 GLU cc_start: 0.7363 (tt0) cc_final: 0.7131 (tt0) REVERT: F 150 ASP cc_start: 0.8429 (t0) cc_final: 0.8140 (t0) REVERT: F 175 LEU cc_start: 0.8916 (OUTLIER) cc_final: 0.8329 (tt) REVERT: F 187 GLN cc_start: 0.8696 (pt0) cc_final: 0.8046 (tp-100) REVERT: F 193 MET cc_start: 0.7511 (mmt) cc_final: 0.6998 (tpt) REVERT: F 226 GLN cc_start: 0.8311 (tp-100) cc_final: 0.8016 (tp-100) REVERT: F 279 MET cc_start: 0.8408 (mmm) cc_final: 0.7838 (mmt) REVERT: F 282 ARG cc_start: 0.8690 (mtp85) cc_final: 0.8294 (mtp85) REVERT: G 11 MET cc_start: 0.7338 (tmm) cc_final: 0.6919 (mmp) REVERT: G 79 HIS cc_start: 0.6626 (t-170) cc_final: 0.6257 (t-170) REVERT: G 105 MET cc_start: 0.8462 (tpp) cc_final: 0.7970 (tpp) REVERT: G 113 ASP cc_start: 0.7475 (p0) cc_final: 0.6603 (t0) REVERT: G 152 TYR cc_start: 0.9347 (OUTLIER) cc_final: 0.8447 (m-10) REVERT: G 162 ASN cc_start: 0.8216 (OUTLIER) cc_final: 0.7654 (m-40) REVERT: G 163 LYS cc_start: 0.8818 (mtmt) cc_final: 0.8158 (mttp) REVERT: G 259 TYR cc_start: 0.8216 (OUTLIER) cc_final: 0.8004 (t80) REVERT: H 11 MET cc_start: 0.6341 (tpt) cc_final: 0.6016 (tpt) REVERT: H 116 ARG cc_start: 0.8026 (OUTLIER) cc_final: 0.7258 (mtp85) REVERT: H 125 ILE cc_start: 0.8715 (OUTLIER) cc_final: 0.8429 (mt) REVERT: H 146 GLU cc_start: 0.8189 (tt0) cc_final: 0.7773 (tm-30) REVERT: H 153 LYS cc_start: 0.8900 (mtpp) cc_final: 0.8686 (mtpt) REVERT: H 204 ASP cc_start: 0.8217 (OUTLIER) cc_final: 0.7664 (m-30) REVERT: H 271 ARG cc_start: 0.8296 (mmm-85) cc_final: 0.7038 (ttt180) outliers start: 81 outliers final: 58 residues processed: 407 average time/residue: 0.2496 time to fit residues: 138.7963 Evaluate side-chains 410 residues out of total 1181 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 344 time to evaluate : 1.246 ------------------------------------------------------------------------------- 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 50 VAL Chi-restraints excluded: chain A residue 55 GLU Chi-restraints excluded: chain A residue 79 THR Chi-restraints excluded: chain B residue 192 LEU Chi-restraints excluded: chain B residue 195 ILE Chi-restraints excluded: chain B residue 214 ASP Chi-restraints excluded: chain B residue 215 MET 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 67 ILE Chi-restraints excluded: chain C residue 78 LEU Chi-restraints excluded: chain C residue 79 THR Chi-restraints excluded: chain D residue 192 ILE 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 260 THR Chi-restraints excluded: chain E residue 261 GLU Chi-restraints excluded: chain E residue 272 LEU Chi-restraints excluded: chain E residue 277 THR Chi-restraints excluded: chain F residue 71 LEU Chi-restraints excluded: chain F residue 83 THR Chi-restraints excluded: chain F residue 84 CYS Chi-restraints excluded: chain F residue 102 ASN Chi-restraints excluded: chain F residue 127 ILE Chi-restraints excluded: chain F residue 142 ILE Chi-restraints excluded: chain F residue 166 LEU Chi-restraints excluded: chain F residue 175 LEU Chi-restraints excluded: chain F residue 219 LEU Chi-restraints excluded: chain F residue 249 GLU Chi-restraints excluded: chain F residue 260 THR Chi-restraints excluded: chain G residue 21 VAL Chi-restraints excluded: chain G residue 84 CYS Chi-restraints excluded: chain G residue 86 VAL 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 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 256 VAL Chi-restraints excluded: chain G residue 259 TYR Chi-restraints excluded: chain H residue 38 ILE Chi-restraints excluded: chain H residue 42 CYS Chi-restraints excluded: chain H residue 45 TYR Chi-restraints excluded: chain H residue 71 LEU Chi-restraints excluded: chain H residue 96 ASP Chi-restraints excluded: chain H residue 101 ILE Chi-restraints excluded: chain H residue 111 TYR 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 168 VAL 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 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 30 optimal weight: 2.9990 chunk 31 optimal weight: 5.9990 chunk 52 optimal weight: 20.0000 chunk 130 optimal weight: 0.8980 chunk 46 optimal weight: 0.9990 chunk 98 optimal weight: 3.9990 chunk 71 optimal weight: 0.0370 chunk 29 optimal weight: 5.9990 chunk 13 optimal weight: 0.6980 chunk 18 optimal weight: 5.9990 chunk 14 optimal weight: 3.9990 overall best weight: 1.1262 ------------------------------------------------------------------------------- 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 199 HIS C 53 GLN D 152 GLN D 159 ASN D 188 ASN ** E 174 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 213 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 23 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 50 ASN F 179 GLN ** G 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 162 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4044 r_free = 0.4044 target = 0.152575 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3762 r_free = 0.3762 target = 0.131682 restraints weight = 25815.837| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3807 r_free = 0.3807 target = 0.134934 restraints weight = 14718.095| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3836 r_free = 0.3836 target = 0.137091 restraints weight = 9696.730| |-----------------------------------------------------------------------------| r_work (final): 0.3827 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7611 moved from start: 0.7783 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= 0.155 Angle : 0.784 15.457 15321 Z= 0.404 Chirality : 0.043 0.217 1667 Planarity : 0.003 0.063 1998 Dihedral : 6.091 73.710 1528 Min Nonbonded Distance : 2.499 Molprobity Statistics. All-atom Clashscore : 14.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.98 % Favored : 92.02 % Rotamer: Outliers : 4.40 % Allowed : 29.13 % Favored : 66.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.03 (0.23), residues: 1404 helix: -0.17 (0.15), residues: 1154 sheet: None (None), residues: 0 loop : -2.62 (0.40), residues: 250 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP E 275 HIS 0.015 0.002 HIS G 79 PHE 0.028 0.002 PHE G 85 TYR 0.034 0.001 TYR B 235 ARG 0.005 0.000 ARG D 180 Details of bonding type rmsd hydrogen bonds : bond 0.03852 ( 702) hydrogen bonds : angle 4.56996 ( 2046) covalent geometry : bond 0.00339 (11412) covalent geometry : angle 0.78405 (15321) *********************** 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 413 residues out of total 1181 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 361 time to evaluate : 1.361 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 44 ASP cc_start: 0.8684 (t0) cc_final: 0.7890 (t0) REVERT: A 65 ASP cc_start: 0.8352 (m-30) cc_final: 0.7860 (t0) REVERT: A 70 LEU cc_start: 0.9242 (tp) cc_final: 0.9009 (tt) REVERT: B 193 SER cc_start: 0.8917 (p) cc_final: 0.8582 (t) REVERT: B 199 HIS cc_start: 0.7145 (t70) cc_final: 0.5988 (t-90) REVERT: B 203 ILE cc_start: 0.7793 (mm) cc_final: 0.7275 (pt) REVERT: B 210 ARG cc_start: 0.8116 (ttm-80) cc_final: 0.7740 (mmm160) REVERT: B 217 MET cc_start: 0.5909 (mmp) cc_final: 0.4787 (ttm) REVERT: C 34 GLN cc_start: 0.8136 (tp40) cc_final: 0.7793 (tp40) REVERT: C 38 GLU cc_start: 0.8682 (tp30) cc_final: 0.8461 (tp30) REVERT: C 41 ASP cc_start: 0.8634 (p0) cc_final: 0.8301 (p0) REVERT: C 52 GLU cc_start: 0.8718 (tp30) cc_final: 0.8412 (tp30) REVERT: D 165 LEU cc_start: 0.8971 (mt) cc_final: 0.8718 (mp) REVERT: E 72 HIS cc_start: 0.7289 (m90) cc_final: 0.7004 (m90) REVERT: E 76 GLN cc_start: 0.8140 (mp10) cc_final: 0.7758 (pp30) REVERT: E 102 ASN cc_start: 0.7296 (p0) cc_final: 0.6708 (m110) REVERT: E 122 LYS cc_start: 0.9278 (tppt) cc_final: 0.8821 (tppt) REVERT: E 125 ILE cc_start: 0.8687 (OUTLIER) cc_final: 0.8158 (mt) REVERT: E 164 CYS cc_start: 0.8229 (m) cc_final: 0.7805 (m) REVERT: E 218 MET cc_start: 0.6351 (tpp) cc_final: 0.4347 (mmt) REVERT: E 227 LYS cc_start: 0.8693 (mttm) cc_final: 0.8282 (tptp) REVERT: F 51 MET cc_start: 0.7641 (tpp) cc_final: 0.7190 (tpt) REVERT: F 66 CYS cc_start: 0.8723 (t) cc_final: 0.7629 (p) REVERT: F 87 ASP cc_start: 0.8385 (m-30) cc_final: 0.8100 (m-30) REVERT: F 150 ASP cc_start: 0.8407 (t0) cc_final: 0.8158 (t0) REVERT: F 162 ASN cc_start: 0.8683 (t0) cc_final: 0.8393 (t0) REVERT: F 175 LEU cc_start: 0.8844 (mm) cc_final: 0.8280 (tt) REVERT: F 226 GLN cc_start: 0.8031 (tp-100) cc_final: 0.7696 (tp-100) REVERT: F 279 MET cc_start: 0.8405 (mmm) cc_final: 0.7944 (mmt) REVERT: F 282 ARG cc_start: 0.8553 (mtp85) cc_final: 0.8215 (mtp85) REVERT: G 42 CYS cc_start: 0.8372 (m) cc_final: 0.7936 (p) REVERT: G 93 LYS cc_start: 0.8433 (OUTLIER) cc_final: 0.8130 (mppt) REVERT: G 94 LYS cc_start: 0.6974 (OUTLIER) cc_final: 0.6558 (mmtt) REVERT: G 105 MET cc_start: 0.8442 (tpp) cc_final: 0.8168 (tpp) REVERT: G 109 GLU cc_start: 0.8486 (pm20) cc_final: 0.8211 (tt0) REVERT: G 113 ASP cc_start: 0.7337 (p0) cc_final: 0.6416 (t0) REVERT: G 114 MET cc_start: 0.8716 (tpp) cc_final: 0.8317 (tpt) REVERT: G 152 TYR cc_start: 0.9215 (OUTLIER) cc_final: 0.8312 (m-10) REVERT: G 163 LYS cc_start: 0.8695 (mtmt) cc_final: 0.8186 (mttp) REVERT: G 222 LYS cc_start: 0.7180 (ttmt) cc_final: 0.6843 (ttpt) REVERT: G 227 LYS cc_start: 0.8995 (mmtt) cc_final: 0.8725 (mmtt) REVERT: H 11 MET cc_start: 0.6419 (tpt) cc_final: 0.6046 (tpt) REVERT: H 125 ILE cc_start: 0.8511 (pp) cc_final: 0.8268 (mt) REVERT: H 140 LYS cc_start: 0.8383 (mttt) cc_final: 0.7864 (mtmt) REVERT: H 146 GLU cc_start: 0.8117 (tt0) cc_final: 0.7700 (tm-30) REVERT: H 194 ASP cc_start: 0.7386 (OUTLIER) cc_final: 0.7052 (t0) outliers start: 52 outliers final: 31 residues processed: 388 average time/residue: 0.2470 time to fit residues: 132.2168 Evaluate side-chains 378 residues out of total 1181 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 342 time to evaluate : 1.319 ------------------------------------------------------------------------------- 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 79 THR Chi-restraints excluded: chain B residue 214 ASP Chi-restraints excluded: chain B residue 215 MET Chi-restraints excluded: chain B residue 237 VAL Chi-restraints excluded: chain C residue 49 MET Chi-restraints excluded: chain C residue 79 THR Chi-restraints excluded: chain D residue 197 GLN 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 277 THR Chi-restraints excluded: chain F residue 84 CYS Chi-restraints excluded: chain F residue 102 ASN Chi-restraints excluded: chain F residue 127 ILE Chi-restraints excluded: chain F residue 219 LEU 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 136 VAL Chi-restraints excluded: chain G residue 152 TYR Chi-restraints excluded: chain G residue 197 LEU Chi-restraints excluded: chain H residue 42 CYS Chi-restraints excluded: chain H residue 45 TYR Chi-restraints excluded: chain H residue 65 PHE Chi-restraints excluded: chain H residue 101 ILE Chi-restraints excluded: chain H residue 116 ARG 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 228 TYR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 61 optimal weight: 4.9990 chunk 92 optimal weight: 3.9990 chunk 65 optimal weight: 4.9990 chunk 62 optimal weight: 0.9980 chunk 101 optimal weight: 0.9990 chunk 115 optimal weight: 3.9990 chunk 69 optimal weight: 0.9980 chunk 106 optimal weight: 5.9990 chunk 122 optimal weight: 1.9990 chunk 0 optimal weight: 10.0000 chunk 40 optimal weight: 1.9990 overall best weight: 1.3986 ------------------------------------------------------------------------------- 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 188 ASN ** E 174 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 187 GLN ** E 213 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 23 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 50 ASN ** G 74 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4048 r_free = 0.4048 target = 0.152583 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 25)----------------| | r_work = 0.3763 r_free = 0.3763 target = 0.131663 restraints weight = 25762.574| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3808 r_free = 0.3808 target = 0.134880 restraints weight = 14618.376| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3837 r_free = 0.3837 target = 0.137035 restraints weight = 9650.756| |-----------------------------------------------------------------------------| r_work (final): 0.3829 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7616 moved from start: 0.7922 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 11412 Z= 0.156 Angle : 0.808 14.872 15321 Z= 0.411 Chirality : 0.044 0.245 1667 Planarity : 0.004 0.069 1998 Dihedral : 6.058 73.849 1528 Min Nonbonded Distance : 2.471 Molprobity Statistics. All-atom Clashscore : 14.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.40 % Favored : 91.60 % Rotamer: Outliers : 3.98 % Allowed : 30.91 % Favored : 65.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.92 (0.23), residues: 1404 helix: -0.09 (0.16), residues: 1146 sheet: None (None), residues: 0 loop : -2.54 (0.39), residues: 258 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP E 275 HIS 0.024 0.002 HIS G 79 PHE 0.023 0.002 PHE H 28 TYR 0.040 0.001 TYR B 235 ARG 0.006 0.001 ARG B 232 Details of bonding type rmsd hydrogen bonds : bond 0.03874 ( 702) hydrogen bonds : angle 4.56557 ( 2046) covalent geometry : bond 0.00350 (11412) covalent geometry : angle 0.80789 (15321) *********************** 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 399 residues out of total 1181 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 352 time to evaluate : 1.263 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 44 ASP cc_start: 0.8668 (t0) cc_final: 0.7932 (t0) REVERT: A 65 ASP cc_start: 0.8158 (m-30) cc_final: 0.7679 (t0) REVERT: A 70 LEU cc_start: 0.9356 (tp) cc_final: 0.9108 (tt) REVERT: B 193 SER cc_start: 0.8751 (p) cc_final: 0.8425 (t) REVERT: B 199 HIS cc_start: 0.7150 (t70) cc_final: 0.6163 (t-90) REVERT: B 203 ILE cc_start: 0.7628 (mm) cc_final: 0.7236 (pt) REVERT: B 210 ARG cc_start: 0.8094 (ttm-80) cc_final: 0.7678 (mmm160) REVERT: C 32 MET cc_start: 0.8483 (tpp) cc_final: 0.8155 (tmm) REVERT: C 34 GLN cc_start: 0.8156 (tp40) cc_final: 0.7831 (tp40) REVERT: C 52 GLU cc_start: 0.8690 (tp30) cc_final: 0.8419 (tp30) REVERT: D 165 LEU cc_start: 0.8960 (mt) cc_final: 0.8721 (mp) REVERT: E 76 GLN cc_start: 0.8177 (mp10) cc_final: 0.7736 (pp30) REVERT: E 122 LYS cc_start: 0.9308 (tppt) cc_final: 0.8883 (tppt) REVERT: E 125 ILE cc_start: 0.8691 (OUTLIER) cc_final: 0.8187 (mt) REVERT: E 164 CYS cc_start: 0.8208 (m) cc_final: 0.7796 (m) REVERT: E 218 MET cc_start: 0.6135 (tpp) cc_final: 0.4238 (mmt) REVERT: E 227 LYS cc_start: 0.8677 (mttm) cc_final: 0.8258 (tptp) REVERT: F 51 MET cc_start: 0.7546 (tpp) cc_final: 0.6881 (tpt) REVERT: F 87 ASP cc_start: 0.8470 (m-30) cc_final: 0.8130 (m-30) REVERT: F 132 GLU cc_start: 0.7339 (tt0) cc_final: 0.7107 (tt0) REVERT: F 150 ASP cc_start: 0.8549 (t0) cc_final: 0.8253 (t0) REVERT: F 175 LEU cc_start: 0.8772 (mm) cc_final: 0.8196 (tt) REVERT: F 218 MET cc_start: 0.3104 (mtm) cc_final: 0.2508 (mtm) REVERT: F 226 GLN cc_start: 0.8071 (tp-100) cc_final: 0.7742 (tp-100) REVERT: G 42 CYS cc_start: 0.8372 (m) cc_final: 0.7907 (p) REVERT: G 75 LEU cc_start: 0.9278 (tt) cc_final: 0.8668 (mp) REVERT: G 94 LYS cc_start: 0.7210 (OUTLIER) cc_final: 0.6580 (mmtt) REVERT: G 105 MET cc_start: 0.8412 (tpp) cc_final: 0.8169 (tpp) REVERT: G 113 ASP cc_start: 0.7260 (p0) cc_final: 0.6370 (t0) REVERT: G 122 LYS cc_start: 0.7702 (tttp) cc_final: 0.7384 (tptp) REVERT: G 152 TYR cc_start: 0.9209 (OUTLIER) cc_final: 0.8276 (m-10) REVERT: G 155 GLU cc_start: 0.8433 (mm-30) cc_final: 0.7534 (tp30) REVERT: G 163 LYS cc_start: 0.8735 (mtmt) cc_final: 0.8299 (mttp) REVERT: G 222 LYS cc_start: 0.7008 (ttmt) cc_final: 0.6614 (ttpt) REVERT: H 11 MET cc_start: 0.6497 (tpt) cc_final: 0.6115 (tpt) REVERT: H 125 ILE cc_start: 0.8541 (OUTLIER) cc_final: 0.8298 (mt) REVERT: H 140 LYS cc_start: 0.8343 (mttt) cc_final: 0.7816 (mtmt) REVERT: H 146 GLU cc_start: 0.8113 (tt0) cc_final: 0.7696 (tm-30) REVERT: H 194 ASP cc_start: 0.7309 (OUTLIER) cc_final: 0.6968 (t0) outliers start: 47 outliers final: 38 residues processed: 376 average time/residue: 0.2428 time to fit residues: 125.8056 Evaluate side-chains 378 residues out of total 1181 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 335 time to evaluate : 1.219 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 32 LEU Chi-restraints excluded: chain A residue 35 THR Chi-restraints excluded: chain B residue 215 MET Chi-restraints excluded: chain B residue 237 VAL Chi-restraints excluded: chain C residue 33 LEU Chi-restraints excluded: chain C residue 49 MET Chi-restraints excluded: chain C residue 67 ILE Chi-restraints excluded: chain C residue 79 THR Chi-restraints excluded: chain D residue 197 GLN 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 256 VAL Chi-restraints excluded: chain E residue 261 GLU Chi-restraints excluded: chain E residue 277 THR Chi-restraints excluded: chain E residue 280 LEU Chi-restraints excluded: chain E residue 294 LEU Chi-restraints excluded: chain F residue 50 ASN Chi-restraints excluded: chain F residue 102 ASN Chi-restraints excluded: chain F residue 127 ILE Chi-restraints excluded: chain F residue 160 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 94 LYS Chi-restraints excluded: chain G residue 102 ASN 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 197 LEU Chi-restraints excluded: chain G residue 256 VAL Chi-restraints excluded: chain H residue 45 TYR Chi-restraints excluded: chain H residue 65 PHE Chi-restraints excluded: chain H residue 71 LEU Chi-restraints excluded: chain H residue 101 ILE Chi-restraints excluded: chain H residue 111 TYR 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 228 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 110 optimal weight: 0.0870 chunk 115 optimal weight: 6.9990 chunk 57 optimal weight: 5.9990 chunk 4 optimal weight: 2.9990 chunk 98 optimal weight: 1.9990 chunk 60 optimal weight: 0.9990 chunk 91 optimal weight: 7.9990 chunk 7 optimal weight: 0.9980 chunk 34 optimal weight: 0.9980 chunk 18 optimal weight: 8.9990 chunk 43 optimal weight: 0.6980 overall best weight: 0.7560 ------------------------------------------------------------------------------- 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 162 HIS D 188 ASN ** E 72 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 174 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 213 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 23 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 50 ASN ** G 70 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4078 r_free = 0.4078 target = 0.155148 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3794 r_free = 0.3794 target = 0.134297 restraints weight = 25621.210| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3839 r_free = 0.3839 target = 0.137577 restraints weight = 14482.554| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3869 r_free = 0.3869 target = 0.139797 restraints weight = 9529.978| |-----------------------------------------------------------------------------| r_work (final): 0.3859 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7567 moved from start: 0.8105 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 11412 Z= 0.154 Angle : 0.822 14.524 15321 Z= 0.416 Chirality : 0.045 0.280 1667 Planarity : 0.004 0.073 1998 Dihedral : 6.063 73.664 1528 Min Nonbonded Distance : 2.477 Molprobity Statistics. All-atom Clashscore : 14.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.12 % Favored : 91.88 % Rotamer: Outliers : 3.64 % Allowed : 31.16 % Favored : 65.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.89 (0.23), residues: 1404 helix: -0.06 (0.16), residues: 1141 sheet: None (None), residues: 0 loop : -2.51 (0.38), residues: 263 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP E 275 HIS 0.027 0.002 HIS G 79 PHE 0.023 0.002 PHE H 28 TYR 0.045 0.001 TYR B 235 ARG 0.015 0.001 ARG F 239 Details of bonding type rmsd hydrogen bonds : bond 0.03851 ( 702) hydrogen bonds : angle 4.56039 ( 2046) covalent geometry : bond 0.00339 (11412) covalent geometry : angle 0.82200 (15321) ********************** 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 392 residues out of total 1181 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 349 time to evaluate : 1.230 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 44 ASP cc_start: 0.8757 (t0) cc_final: 0.8083 (t0) REVERT: A 65 ASP cc_start: 0.8127 (m-30) cc_final: 0.7664 (t0) REVERT: B 193 SER cc_start: 0.8767 (p) cc_final: 0.8448 (t) REVERT: B 199 HIS cc_start: 0.7033 (t70) cc_final: 0.6022 (t-90) REVERT: B 201 GLU cc_start: 0.7755 (tm-30) cc_final: 0.7207 (tm-30) REVERT: B 203 ILE cc_start: 0.7572 (mm) cc_final: 0.7071 (pt) REVERT: B 210 ARG cc_start: 0.8076 (ttm-80) cc_final: 0.7687 (mmm160) REVERT: C 34 GLN cc_start: 0.8122 (tp40) cc_final: 0.7782 (tp40) REVERT: C 52 GLU cc_start: 0.8679 (tp30) cc_final: 0.8449 (tp30) REVERT: D 165 LEU cc_start: 0.8955 (mt) cc_final: 0.8734 (mp) REVERT: E 72 HIS cc_start: 0.7230 (m90) cc_final: 0.6966 (m90) REVERT: E 76 GLN cc_start: 0.8144 (mp10) cc_final: 0.7586 (pp30) REVERT: E 122 LYS cc_start: 0.9286 (tppt) cc_final: 0.8828 (tppt) REVERT: E 125 ILE cc_start: 0.8640 (OUTLIER) cc_final: 0.8116 (mt) REVERT: E 132 GLU cc_start: 0.7607 (pt0) cc_final: 0.7392 (pt0) REVERT: E 164 CYS cc_start: 0.8173 (m) cc_final: 0.7660 (m) REVERT: E 218 MET cc_start: 0.5874 (tpp) cc_final: 0.3993 (mmt) REVERT: E 227 LYS cc_start: 0.8619 (mttm) cc_final: 0.8124 (tptt) REVERT: F 45 TYR cc_start: 0.7955 (t80) cc_final: 0.6915 (t80) REVERT: F 51 MET cc_start: 0.7665 (tpp) cc_final: 0.6946 (tpt) REVERT: F 66 CYS cc_start: 0.8532 (t) cc_final: 0.7510 (p) REVERT: F 67 GLN cc_start: 0.7616 (mt0) cc_final: 0.6923 (tp-100) REVERT: F 87 ASP cc_start: 0.8500 (m-30) cc_final: 0.8164 (m-30) REVERT: F 132 GLU cc_start: 0.7389 (tt0) cc_final: 0.7128 (tt0) REVERT: F 150 ASP cc_start: 0.8525 (t0) cc_final: 0.8247 (t0) REVERT: F 175 LEU cc_start: 0.8729 (mm) cc_final: 0.8110 (tt) REVERT: F 187 GLN cc_start: 0.8714 (pt0) cc_final: 0.8019 (tp-100) REVERT: F 203 LYS cc_start: 0.8744 (pttp) cc_final: 0.8385 (ptpp) REVERT: F 271 ARG cc_start: 0.7581 (tpt-90) cc_final: 0.7375 (tpm170) REVERT: G 42 CYS cc_start: 0.8298 (m) cc_final: 0.7871 (p) REVERT: G 75 LEU cc_start: 0.9349 (tt) cc_final: 0.8887 (mp) REVERT: G 94 LYS cc_start: 0.7133 (mtmm) cc_final: 0.6467 (mmtt) REVERT: G 105 MET cc_start: 0.8325 (tpp) cc_final: 0.8111 (tpp) REVERT: G 113 ASP cc_start: 0.7203 (p0) cc_final: 0.6262 (t0) REVERT: G 152 TYR cc_start: 0.9167 (OUTLIER) cc_final: 0.8277 (m-10) REVERT: G 222 LYS cc_start: 0.7044 (ttmt) cc_final: 0.6695 (ttpt) REVERT: G 227 LYS cc_start: 0.8933 (mmtt) cc_final: 0.8689 (mmtt) REVERT: H 11 MET cc_start: 0.6408 (tpt) cc_final: 0.6131 (tpt) REVERT: H 51 MET cc_start: 0.8298 (mtm) cc_final: 0.7716 (ttp) REVERT: H 76 GLN cc_start: 0.7645 (mp10) cc_final: 0.7347 (tm-30) REVERT: H 87 ASP cc_start: 0.8112 (t70) cc_final: 0.7756 (t70) REVERT: H 125 ILE cc_start: 0.8480 (OUTLIER) cc_final: 0.8238 (mt) REVERT: H 140 LYS cc_start: 0.8318 (mttt) cc_final: 0.7832 (mtmt) REVERT: H 146 GLU cc_start: 0.8131 (tt0) cc_final: 0.7708 (tm-30) REVERT: H 194 ASP cc_start: 0.7372 (OUTLIER) cc_final: 0.7058 (t0) outliers start: 43 outliers final: 33 residues processed: 372 average time/residue: 0.2425 time to fit residues: 124.5915 Evaluate side-chains 374 residues out of total 1181 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 337 time to evaluate : 1.280 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 32 LEU Chi-restraints excluded: chain B residue 215 MET Chi-restraints excluded: chain B residue 237 VAL Chi-restraints excluded: chain C residue 33 LEU Chi-restraints excluded: chain C residue 49 MET Chi-restraints excluded: chain C residue 79 THR Chi-restraints excluded: chain D residue 197 GLN 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 277 THR Chi-restraints excluded: chain E residue 280 LEU Chi-restraints excluded: chain E residue 294 LEU Chi-restraints excluded: chain F residue 50 ASN Chi-restraints excluded: chain F residue 102 ASN Chi-restraints excluded: chain F residue 127 ILE Chi-restraints excluded: chain F residue 160 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 102 ASN 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 197 LEU Chi-restraints excluded: chain H residue 42 CYS Chi-restraints excluded: chain H residue 45 TYR Chi-restraints excluded: chain H residue 101 ILE Chi-restraints excluded: chain H residue 111 TYR 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 211 LEU Chi-restraints excluded: chain H residue 228 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 47 optimal weight: 0.9980 chunk 19 optimal weight: 0.6980 chunk 89 optimal weight: 1.9990 chunk 68 optimal weight: 10.0000 chunk 110 optimal weight: 8.9990 chunk 48 optimal weight: 1.9990 chunk 133 optimal weight: 0.7980 chunk 69 optimal weight: 6.9990 chunk 35 optimal weight: 6.9990 chunk 103 optimal weight: 7.9990 chunk 122 optimal weight: 0.4980 overall best weight: 0.9982 ------------------------------------------------------------------------------- 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** ** A 49 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 239 HIS D 162 HIS D 188 ASN ** E 72 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 174 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 187 GLN ** E 213 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 23 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 50 ASN F 226 GLN ** G 70 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 79 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4094 r_free = 0.4094 target = 0.156997 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3813 r_free = 0.3813 target = 0.136032 restraints weight = 25527.068| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3857 r_free = 0.3857 target = 0.139321 restraints weight = 14656.116| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3886 r_free = 0.3886 target = 0.141516 restraints weight = 9686.261| |-----------------------------------------------------------------------------| r_work (final): 0.3863 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7573 moved from start: 0.8227 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= 0.153 Angle : 0.816 14.313 15321 Z= 0.413 Chirality : 0.044 0.275 1667 Planarity : 0.004 0.071 1998 Dihedral : 6.025 74.035 1528 Min Nonbonded Distance : 2.477 Molprobity Statistics. All-atom Clashscore : 15.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.69 % Favored : 92.31 % Rotamer: Outliers : 3.90 % Allowed : 31.16 % Favored : 64.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.87 (0.23), residues: 1404 helix: -0.06 (0.16), residues: 1145 sheet: None (None), residues: 0 loop : -2.47 (0.39), residues: 259 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP E 275 HIS 0.027 0.002 HIS G 79 PHE 0.024 0.002 PHE H 28 TYR 0.044 0.001 TYR B 235 ARG 0.014 0.001 ARG F 239 Details of bonding type rmsd hydrogen bonds : bond 0.03775 ( 702) hydrogen bonds : angle 4.52905 ( 2046) covalent geometry : bond 0.00342 (11412) covalent geometry : angle 0.81613 (15321) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4080.05 seconds wall clock time: 71 minutes 34.71 seconds (4294.71 seconds total)