Starting phenix.real_space_refine on Wed Sep 25 19:36:57 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ip1_9697/09_2024/6ip1_9697.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ip1_9697/09_2024/6ip1_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/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ip1_9697/09_2024/6ip1_9697.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ip1_9697/09_2024/6ip1_9697.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ip1_9697/09_2024/6ip1_9697.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ip1_9697/09_2024/6ip1_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-5461/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: 8.52, per 1000 atoms: 0.76 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: 2.29 Conformation dependent library (CDL) restraints added in 1.6 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: 1.00 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: 3.27 Time building geometry restraints manager: 2.71 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: 0.230 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: 0.440 Check model and map are aligned: 0.090 Set scattering table: 0.120 Process input model: 29.090 Find NCS groups from input model: 0.330 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:3.060 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 33.430 ------------------------------------------------------------------------------- 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= 0.363 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 *********************** 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 fitting. rotamer outliers: 4 poor density : 657 time to evaluate : 1.265 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: 0.2698 time to fit residues: 238.7895 Evaluate side-chains 394 residues out of total 1181 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 393 time to evaluate : 1.310 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7496 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= 0.243 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 *********************** 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 fitting. rotamer outliers: 58 poor density : 448 time to evaluate : 1.364 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: 0.8918 (OUTLIER) cc_final: 0.8695 (tt0) REVERT: A 61 SER cc_start: 0.8520 (p) cc_final: 0.7992 (t) REVERT: A 65 ASP cc_start: 0.8420 (m-30) cc_final: 0.8066 (t0) REVERT: A 78 GLU cc_start: 0.8548 (pp20) cc_final: 0.7804 (tp30) REVERT: B 229 MET cc_start: 0.8060 (mtm) cc_final: 0.7687 (ttm) REVERT: B 246 ARG cc_start: 0.8034 (ttm-80) cc_final: 0.7646 (ttm170) REVERT: C 24 GLU cc_start: 0.5403 (mt-10) cc_final: 0.5178 (mt-10) REVERT: C 34 GLN cc_start: 0.8530 (tp40) cc_final: 0.8245 (tp40) REVERT: C 62 GLU cc_start: 0.8321 (tp30) cc_final: 0.8051 (tp30) REVERT: C 66 GLN cc_start: 0.8469 (mt0) cc_final: 0.7866 (mm-40) REVERT: D 191 ARG cc_start: 0.7896 (mtp85) cc_final: 0.7257 (mtp85) REVERT: E 125 ILE cc_start: 0.8488 (pp) cc_final: 0.8236 (mt) REVERT: E 146 GLU cc_start: 0.7740 (pt0) cc_final: 0.7429 (pt0) REVERT: E 164 CYS cc_start: 0.8557 (m) cc_final: 0.8075 (m) REVERT: E 227 LYS cc_start: 0.8690 (mttm) cc_final: 0.8190 (tptt) REVERT: F 11 MET cc_start: 0.7781 (ppp) cc_final: 0.7522 (ppp) REVERT: F 24 SER cc_start: 0.7450 (m) cc_final: 0.6976 (t) REVERT: F 51 MET cc_start: 0.7712 (tpp) cc_final: 0.6710 (tpp) REVERT: F 54 MET cc_start: 0.8907 (mmm) cc_final: 0.8604 (tpp) REVERT: F 78 LYS cc_start: 0.8497 (mmmm) cc_final: 0.8254 (mtpt) REVERT: F 80 ASP cc_start: 0.8063 (OUTLIER) cc_final: 0.7539 (m-30) REVERT: F 87 ASP cc_start: 0.8408 (m-30) cc_final: 0.8022 (m-30) REVERT: F 101 ILE cc_start: 0.8940 (pp) cc_final: 0.8678 (pp) REVERT: F 140 LYS cc_start: 0.8355 (OUTLIER) cc_final: 0.7892 (mtmm) REVERT: F 175 LEU cc_start: 0.8482 (mm) cc_final: 0.7791 (tt) REVERT: F 260 THR cc_start: 0.8439 (p) cc_final: 0.7837 (p) REVERT: F 266 TYR cc_start: 0.8284 (t80) cc_final: 0.8059 (t80) REVERT: F 268 SER cc_start: 0.8309 (p) cc_final: 0.7662 (m) REVERT: F 279 MET cc_start: 0.8358 (mmt) cc_final: 0.7760 (mmt) REVERT: G 93 LYS cc_start: 0.8018 (mtpt) cc_final: 0.7773 (mttt) REVERT: G 105 MET cc_start: 0.8615 (tpp) cc_final: 0.8310 (tpp) REVERT: G 113 ASP cc_start: 0.7565 (p0) cc_final: 0.6854 (t0) REVERT: G 114 MET cc_start: 0.8254 (ttm) cc_final: 0.7885 (ttt) REVERT: G 147 GLN cc_start: 0.7327 (tt0) cc_final: 0.6990 (mt0) REVERT: G 264 LYS cc_start: 0.8274 (tptp) cc_final: 0.7635 (tptp) REVERT: G 267 ASP cc_start: 0.8651 (p0) cc_final: 0.8308 (p0) REVERT: H 25 GLN cc_start: 0.6803 (mp10) cc_final: 0.6551 (mp10) REVERT: H 39 GLU cc_start: 0.8366 (pt0) cc_final: 0.8109 (mp0) REVERT: H 40 GLU cc_start: 0.8352 (tp30) cc_final: 0.7733 (tp30) REVERT: H 43 GLU cc_start: 0.8181 (OUTLIER) cc_final: 0.7869 (pm20) REVERT: H 51 MET cc_start: 0.8377 (OUTLIER) cc_final: 0.8085 (mtm) REVERT: H 54 MET cc_start: 0.8594 (tpp) cc_final: 0.8258 (mtm) REVERT: H 76 GLN cc_start: 0.7983 (mp10) cc_final: 0.7506 (tm-30) REVERT: H 103 CYS cc_start: 0.8190 (p) cc_final: 0.7928 (p) REVERT: H 106 ARG cc_start: 0.7899 (mtp85) cc_final: 0.7335 (mtm180) REVERT: H 153 LYS cc_start: 0.8869 (mtpp) cc_final: 0.8249 (mtpt) REVERT: H 204 ASP cc_start: 0.8324 (OUTLIER) cc_final: 0.7896 (m-30) REVERT: H 249 GLU cc_start: 0.7693 (tm-30) cc_final: 0.7490 (tp30) outliers start: 58 outliers final: 30 residues processed: 477 average time/residue: 0.2611 time to fit residues: 169.3926 Evaluate side-chains 403 residues out of total 1181 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 367 time to evaluate : 1.238 ------------------------------------------------------------------------------- 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 51 MET 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 70 optimal weight: 0.7980 chunk 39 optimal weight: 2.9990 chunk 105 optimal weight: 3.9990 chunk 86 optimal weight: 10.0000 chunk 35 optimal weight: 3.9990 chunk 127 optimal weight: 6.9990 chunk 137 optimal weight: 0.4980 chunk 113 optimal weight: 9.9990 chunk 126 optimal weight: 9.9990 chunk 43 optimal weight: 6.9990 chunk 102 optimal weight: 1.9990 overall best weight: 2.0586 ------------------------------------------------------------------------------- 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 H 50 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7582 moved from start: 0.6110 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 11412 Z= 0.229 Angle : 0.746 14.088 15321 Z= 0.394 Chirality : 0.043 0.177 1667 Planarity : 0.003 0.043 1998 Dihedral : 6.091 64.948 1528 Min Nonbonded Distance : 2.493 Molprobity Statistics. All-atom Clashscore : 13.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.05 % Favored : 92.95 % Rotamer: Outliers : 6.35 % Allowed : 21.51 % Favored : 72.14 % 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: -2.21 (0.21), residues: 1404 helix: -0.95 (0.14), residues: 1143 sheet: None (None), residues: 0 loop : -3.10 (0.35), residues: 261 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP E 275 HIS 0.008 0.002 HIS E 213 PHE 0.021 0.002 PHE H 28 TYR 0.034 0.002 TYR B 235 ARG 0.003 0.000 ARG G 282 *********************** 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 472 residues out of total 1181 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 75 poor density : 397 time to evaluate : 1.291 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 44 ASP cc_start: 0.8244 (t0) cc_final: 0.7844 (t0) REVERT: A 61 SER cc_start: 0.8294 (p) cc_final: 0.8028 (t) REVERT: A 65 ASP cc_start: 0.8331 (m-30) cc_final: 0.7872 (t0) REVERT: A 66 ARG cc_start: 0.8160 (mmm160) cc_final: 0.7932 (mmp-170) REVERT: A 68 ASP cc_start: 0.7664 (t0) cc_final: 0.7096 (t0) REVERT: A 70 LEU cc_start: 0.9160 (tp) cc_final: 0.8777 (tt) REVERT: B 193 SER cc_start: 0.8544 (p) cc_final: 0.8180 (t) REVERT: B 210 ARG cc_start: 0.8067 (ttm-80) cc_final: 0.7526 (mmm160) REVERT: B 216 PHE cc_start: 0.8204 (OUTLIER) cc_final: 0.7791 (m-80) REVERT: B 229 MET cc_start: 0.8059 (mtm) cc_final: 0.7682 (ttm) REVERT: C 34 GLN cc_start: 0.8490 (tp40) cc_final: 0.8168 (tp40) REVERT: C 66 GLN cc_start: 0.8352 (mt0) cc_final: 0.8129 (mm-40) REVERT: D 196 ASN cc_start: 0.8027 (p0) cc_final: 0.7579 (p0) REVERT: E 40 GLU cc_start: 0.7636 (tp30) cc_final: 0.7074 (mp0) REVERT: E 76 GLN cc_start: 0.8262 (mp10) cc_final: 0.7752 (pp30) REVERT: E 98 GLN cc_start: 0.7942 (tp-100) cc_final: 0.7719 (tp-100) REVERT: E 122 LYS cc_start: 0.9335 (tppt) cc_final: 0.8959 (tppt) REVERT: E 125 ILE cc_start: 0.8616 (pp) cc_final: 0.8245 (mt) REVERT: E 164 CYS cc_start: 0.8704 (m) cc_final: 0.8324 (m) REVERT: E 227 LYS cc_start: 0.8677 (mttm) cc_final: 0.8163 (tptt) REVERT: F 11 MET cc_start: 0.7771 (ppp) cc_final: 0.7483 (ppp) REVERT: F 24 SER cc_start: 0.7588 (m) cc_final: 0.7004 (t) REVERT: F 51 MET cc_start: 0.7883 (tpp) cc_final: 0.7278 (tpp) REVERT: F 78 LYS cc_start: 0.8539 (mmmm) cc_final: 0.8251 (mtmt) REVERT: F 80 ASP cc_start: 0.7978 (OUTLIER) cc_final: 0.7766 (m-30) REVERT: F 87 ASP cc_start: 0.8786 (m-30) cc_final: 0.8361 (m-30) REVERT: F 101 ILE cc_start: 0.8958 (pp) cc_final: 0.8711 (pp) REVERT: F 114 MET cc_start: 0.8711 (tpp) cc_final: 0.8212 (ttt) REVERT: F 158 ASN cc_start: 0.9256 (p0) cc_final: 0.8812 (p0) REVERT: F 175 LEU cc_start: 0.8728 (mm) cc_final: 0.8071 (tt) REVERT: F 193 MET cc_start: 0.7305 (OUTLIER) cc_final: 0.5978 (tpt) REVERT: F 268 SER cc_start: 0.8385 (p) cc_final: 0.7574 (m) REVERT: F 279 MET cc_start: 0.8387 (mmt) cc_final: 0.7908 (mmt) REVERT: G 105 MET cc_start: 0.8472 (tpp) cc_final: 0.8129 (tpp) REVERT: G 106 ARG cc_start: 0.6904 (ttm110) cc_final: 0.6663 (ttm110) REVERT: G 113 ASP cc_start: 0.7652 (p0) cc_final: 0.6827 (t0) REVERT: G 152 TYR cc_start: 0.9178 (OUTLIER) cc_final: 0.8635 (m-10) REVERT: G 179 GLN cc_start: 0.8392 (tp-100) cc_final: 0.7534 (tt0) REVERT: G 285 LYS cc_start: 0.8814 (mmmt) cc_final: 0.8595 (mmmt) REVERT: H 40 GLU cc_start: 0.8357 (tp30) cc_final: 0.8114 (tp30) REVERT: H 51 MET cc_start: 0.8361 (OUTLIER) cc_final: 0.8100 (mtm) REVERT: H 54 MET cc_start: 0.8526 (tpp) cc_final: 0.8305 (mtm) REVERT: H 76 GLN cc_start: 0.8031 (mp10) cc_final: 0.7448 (tm-30) REVERT: H 103 CYS cc_start: 0.8060 (p) cc_final: 0.7826 (p) REVERT: H 105 MET cc_start: 0.8704 (tpt) cc_final: 0.8305 (tpt) REVERT: H 125 ILE cc_start: 0.8715 (OUTLIER) cc_final: 0.8187 (mt) REVERT: H 153 LYS cc_start: 0.8846 (mtpp) cc_final: 0.8574 (mtpt) REVERT: H 204 ASP cc_start: 0.8356 (OUTLIER) cc_final: 0.7895 (m-30) REVERT: H 249 GLU cc_start: 0.7755 (tm-30) cc_final: 0.7549 (tp30) REVERT: H 271 ARG cc_start: 0.8318 (mmm-85) cc_final: 0.6993 (ttt180) outliers start: 75 outliers final: 38 residues processed: 435 average time/residue: 0.2531 time to fit residues: 150.8949 Evaluate side-chains 396 residues out of total 1181 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 351 time to evaluate : 1.265 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 32 LEU Chi-restraints excluded: chain A residue 48 VAL Chi-restraints excluded: chain A residue 55 GLU Chi-restraints excluded: chain A residue 62 GLU Chi-restraints excluded: chain B residue 209 ILE Chi-restraints excluded: chain B residue 211 GLU Chi-restraints excluded: chain B residue 214 ASP Chi-restraints excluded: chain B residue 216 PHE Chi-restraints excluded: chain B residue 236 ASN Chi-restraints excluded: chain B residue 237 VAL Chi-restraints excluded: chain C residue 78 LEU Chi-restraints excluded: chain C residue 79 THR Chi-restraints excluded: chain E residue 103 CYS Chi-restraints excluded: chain E residue 183 ASP Chi-restraints excluded: chain E residue 201 SER Chi-restraints excluded: chain E residue 256 VAL Chi-restraints excluded: chain E residue 277 THR Chi-restraints excluded: chain F residue 38 ILE 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 142 ILE Chi-restraints excluded: chain F residue 193 MET Chi-restraints excluded: chain G residue 21 VAL Chi-restraints excluded: chain G residue 84 CYS Chi-restraints excluded: chain G residue 108 ILE Chi-restraints excluded: chain G residue 125 ILE Chi-restraints excluded: chain G residue 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 45 TYR Chi-restraints excluded: chain H residue 51 MET Chi-restraints excluded: chain H residue 101 ILE Chi-restraints excluded: chain H residue 110 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 194 ASP Chi-restraints excluded: chain H residue 197 LEU Chi-restraints excluded: chain H residue 204 ASP 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 125 optimal weight: 3.9990 chunk 95 optimal weight: 8.9990 chunk 66 optimal weight: 4.9990 chunk 14 optimal weight: 0.3980 chunk 60 optimal weight: 6.9990 chunk 85 optimal weight: 3.9990 chunk 127 optimal weight: 8.9990 chunk 135 optimal weight: 1.9990 chunk 121 optimal weight: 2.9990 chunk 36 optimal weight: 2.9990 chunk 112 optimal weight: 9.9990 overall best weight: 2.4788 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** F 50 ASN F 213 HIS ** 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: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7628 moved from start: 0.6649 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 11412 Z= 0.239 Angle : 0.747 11.593 15321 Z= 0.392 Chirality : 0.043 0.172 1667 Planarity : 0.004 0.048 1998 Dihedral : 6.029 67.045 1528 Min Nonbonded Distance : 2.506 Molprobity Statistics. All-atom Clashscore : 16.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.76 % Favored : 92.24 % Rotamer: Outliers : 6.44 % Allowed : 22.18 % Favored : 71.38 % 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: -1.61 (0.22), residues: 1404 helix: -0.50 (0.15), residues: 1143 sheet: None (None), residues: 0 loop : -3.10 (0.35), residues: 261 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP F 275 HIS 0.008 0.002 HIS E 79 PHE 0.021 0.002 PHE H 28 TYR 0.034 0.002 TYR B 235 ARG 0.004 0.000 ARG H 106 *********************** 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 450 residues out of total 1181 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 76 poor density : 374 time to evaluate : 1.285 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: 0.8497 (t0) cc_final: 0.7793 (t0) REVERT: A 61 SER cc_start: 0.8509 (p) cc_final: 0.8301 (t) REVERT: A 70 LEU cc_start: 0.9148 (tp) cc_final: 0.8807 (tt) REVERT: A 78 GLU cc_start: 0.8759 (pp20) cc_final: 0.7919 (tp30) REVERT: B 193 SER cc_start: 0.8670 (p) cc_final: 0.8306 (t) REVERT: B 203 ILE cc_start: 0.8177 (mm) cc_final: 0.7642 (pt) REVERT: B 215 MET cc_start: 0.8365 (ppp) cc_final: 0.8080 (ppp) REVERT: B 217 MET cc_start: 0.7022 (mmp) cc_final: 0.6807 (mmp) REVERT: B 228 GLU cc_start: 0.8273 (tp30) cc_final: 0.8036 (tp30) REVERT: B 229 MET cc_start: 0.7970 (mtm) cc_final: 0.7565 (ttm) REVERT: C 26 LEU cc_start: 0.7628 (tm) cc_final: 0.7186 (mt) REVERT: C 34 GLN cc_start: 0.8348 (tp40) cc_final: 0.8050 (tp40) REVERT: C 66 GLN cc_start: 0.8405 (mt0) cc_final: 0.8199 (mm-40) REVERT: D 196 ASN cc_start: 0.7770 (p0) cc_final: 0.7440 (p0) REVERT: E 40 GLU cc_start: 0.7516 (tp30) cc_final: 0.7009 (mp0) REVERT: E 98 GLN cc_start: 0.8143 (tp-100) cc_final: 0.7837 (tp-100) REVERT: E 122 LYS cc_start: 0.9342 (tppt) cc_final: 0.8896 (tppt) REVERT: E 125 ILE cc_start: 0.8656 (OUTLIER) cc_final: 0.8126 (mt) REVERT: E 164 CYS cc_start: 0.8562 (m) cc_final: 0.8143 (m) REVERT: E 168 VAL cc_start: 0.8626 (OUTLIER) cc_final: 0.8422 (p) REVERT: E 227 LYS cc_start: 0.8668 (mttm) cc_final: 0.8188 (tptp) REVERT: F 11 MET cc_start: 0.7759 (ppp) cc_final: 0.7549 (ppp) REVERT: F 24 SER cc_start: 0.7505 (m) cc_final: 0.6977 (t) REVERT: F 51 MET cc_start: 0.7761 (tpp) cc_final: 0.7031 (tpp) REVERT: F 78 LYS cc_start: 0.8640 (mmmm) cc_final: 0.8223 (mtpt) REVERT: F 87 ASP cc_start: 0.8736 (m-30) cc_final: 0.8338 (m-30) REVERT: F 101 ILE cc_start: 0.9110 (pp) cc_final: 0.8899 (pp) REVERT: F 114 MET cc_start: 0.8733 (tpp) cc_final: 0.8175 (ttt) REVERT: F 171 TYR cc_start: 0.8332 (m-80) cc_final: 0.7109 (m-80) REVERT: F 175 LEU cc_start: 0.8816 (mm) cc_final: 0.8221 (tt) REVERT: F 193 MET cc_start: 0.7400 (OUTLIER) cc_final: 0.7099 (tpt) REVERT: F 218 MET cc_start: 0.4048 (OUTLIER) cc_final: 0.3726 (mtm) REVERT: F 268 SER cc_start: 0.8243 (p) cc_final: 0.7471 (m) REVERT: F 271 ARG cc_start: 0.7364 (tpp-160) cc_final: 0.6812 (tpp-160) REVERT: G 11 MET cc_start: 0.7394 (tmm) cc_final: 0.6986 (mmp) REVERT: G 79 HIS cc_start: 0.6887 (t-90) cc_final: 0.6341 (t-170) REVERT: G 105 MET cc_start: 0.8418 (tpp) cc_final: 0.7443 (tpp) REVERT: G 106 ARG cc_start: 0.6984 (ttm110) cc_final: 0.6496 (ttm110) REVERT: G 113 ASP cc_start: 0.7725 (p0) cc_final: 0.6822 (t0) REVERT: G 152 TYR cc_start: 0.9195 (OUTLIER) cc_final: 0.8617 (m-10) REVERT: G 163 LYS cc_start: 0.8441 (mtmt) cc_final: 0.7897 (mttp) REVERT: H 54 MET cc_start: 0.8554 (tpp) cc_final: 0.8311 (mtm) REVERT: H 76 GLN cc_start: 0.8067 (mp10) cc_final: 0.7285 (tm-30) REVERT: H 125 ILE cc_start: 0.8729 (OUTLIER) cc_final: 0.8362 (mt) REVERT: H 146 GLU cc_start: 0.8062 (tt0) cc_final: 0.7687 (tm-30) REVERT: H 153 LYS cc_start: 0.8895 (mtpp) cc_final: 0.8627 (mtpt) REVERT: H 204 ASP cc_start: 0.8355 (OUTLIER) cc_final: 0.7864 (m-30) REVERT: H 249 GLU cc_start: 0.7763 (tm-30) cc_final: 0.7506 (tp30) REVERT: H 271 ARG cc_start: 0.8461 (mmm-85) cc_final: 0.7159 (ttt180) outliers start: 76 outliers final: 48 residues processed: 408 average time/residue: 0.2449 time to fit residues: 138.5255 Evaluate side-chains 397 residues out of total 1181 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 55 poor density : 342 time to evaluate : 1.252 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 32 LEU Chi-restraints excluded: chain A residue 35 THR Chi-restraints excluded: chain A residue 48 VAL Chi-restraints excluded: chain A residue 53 VAL Chi-restraints excluded: chain A residue 55 GLU Chi-restraints excluded: chain A residue 62 GLU Chi-restraints excluded: chain A residue 79 THR Chi-restraints excluded: chain B residue 209 ILE Chi-restraints excluded: chain B residue 214 ASP Chi-restraints excluded: chain B residue 236 ASN 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 103 CYS Chi-restraints excluded: chain E residue 125 ILE Chi-restraints excluded: chain E residue 168 VAL Chi-restraints excluded: chain E residue 211 LEU Chi-restraints excluded: chain E residue 256 VAL Chi-restraints excluded: chain E residue 272 LEU Chi-restraints excluded: chain E residue 277 THR Chi-restraints excluded: chain F residue 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 193 MET 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 102 ASN Chi-restraints excluded: chain G residue 108 ILE Chi-restraints excluded: chain G residue 125 ILE Chi-restraints excluded: chain G residue 135 LEU Chi-restraints excluded: chain G residue 136 VAL Chi-restraints excluded: chain G residue 152 TYR Chi-restraints excluded: chain G residue 197 LEU Chi-restraints excluded: chain G residue 256 VAL Chi-restraints excluded: chain G residue 259 TYR Chi-restraints excluded: chain H residue 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 116 ARG Chi-restraints excluded: chain H residue 125 ILE Chi-restraints excluded: chain H residue 127 ILE Chi-restraints excluded: chain H residue 171 TYR Chi-restraints excluded: chain H residue 197 LEU Chi-restraints excluded: chain H residue 204 ASP Chi-restraints excluded: chain H residue 211 LEU Chi-restraints excluded: chain H residue 219 LEU Chi-restraints excluded: chain H residue 228 TYR Chi-restraints excluded: chain H residue 276 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 76 optimal weight: 6.9990 chunk 1 optimal weight: 0.9990 chunk 100 optimal weight: 0.9980 chunk 55 optimal weight: 2.9990 chunk 115 optimal weight: 4.9990 chunk 93 optimal weight: 2.9990 chunk 0 optimal weight: 10.0000 chunk 69 optimal weight: 5.9990 chunk 121 optimal weight: 0.9980 chunk 34 optimal weight: 7.9990 chunk 45 optimal weight: 5.9990 overall best weight: 1.7986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 199 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 213 HIS D 159 ASN D 188 ASN E 50 ASN ** F 23 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 50 ASN ** F 255 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 90 ASN ** G 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 70 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7611 moved from start: 0.7041 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 11412 Z= 0.214 Angle : 0.728 15.456 15321 Z= 0.378 Chirality : 0.042 0.195 1667 Planarity : 0.003 0.051 1998 Dihedral : 5.946 69.244 1528 Min Nonbonded Distance : 2.453 Molprobity Statistics. All-atom Clashscore : 14.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.19 % Favored : 92.81 % Rotamer: Outliers : 5.59 % Allowed : 25.32 % Favored : 69.09 % 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: -1.32 (0.22), residues: 1404 helix: -0.27 (0.15), residues: 1147 sheet: None (None), residues: 0 loop : -3.19 (0.35), residues: 257 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP F 275 HIS 0.007 0.002 HIS E 213 PHE 0.021 0.002 PHE H 28 TYR 0.039 0.002 TYR B 235 ARG 0.012 0.000 ARG D 180 *********************** 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 444 residues out of total 1181 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 66 poor density : 378 time to evaluate : 1.339 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: 0.8517 (t0) cc_final: 0.7847 (t0) REVERT: A 61 SER cc_start: 0.8561 (p) cc_final: 0.8093 (t) REVERT: A 65 ASP cc_start: 0.8235 (m-30) cc_final: 0.7651 (t0) REVERT: A 70 LEU cc_start: 0.9122 (tp) cc_final: 0.8811 (tt) REVERT: B 193 SER cc_start: 0.8753 (p) cc_final: 0.8389 (t) REVERT: B 199 HIS cc_start: 0.7023 (t-90) cc_final: 0.5958 (t-90) REVERT: B 203 ILE cc_start: 0.7991 (mm) cc_final: 0.7386 (pt) REVERT: B 210 ARG cc_start: 0.8012 (ttm-80) cc_final: 0.7625 (mmm160) REVERT: B 215 MET cc_start: 0.8266 (ppp) cc_final: 0.7941 (ppp) REVERT: B 229 MET cc_start: 0.8055 (mtm) cc_final: 0.7604 (ttm) REVERT: C 26 LEU cc_start: 0.7659 (tm) cc_final: 0.7245 (mt) REVERT: D 196 ASN cc_start: 0.7667 (p0) cc_final: 0.7391 (p0) REVERT: E 76 GLN cc_start: 0.8233 (mp10) cc_final: 0.7606 (pp30) REVERT: E 98 GLN cc_start: 0.8141 (tp-100) cc_final: 0.7868 (tp-100) REVERT: E 122 LYS cc_start: 0.9312 (tppt) cc_final: 0.8931 (tppt) REVERT: E 125 ILE cc_start: 0.8662 (pp) cc_final: 0.8150 (mt) REVERT: E 164 CYS cc_start: 0.8566 (m) cc_final: 0.8098 (m) REVERT: E 200 TYR cc_start: 0.7947 (m-80) cc_final: 0.7478 (m-80) REVERT: E 227 LYS cc_start: 0.8665 (mttm) cc_final: 0.8136 (tptt) REVERT: F 11 MET cc_start: 0.7771 (ppp) cc_final: 0.7533 (ppp) REVERT: F 24 SER cc_start: 0.7474 (m) cc_final: 0.6974 (t) REVERT: F 51 MET cc_start: 0.7893 (tpp) cc_final: 0.7276 (tpp) REVERT: F 78 LYS cc_start: 0.8529 (mmmm) cc_final: 0.8144 (mtpt) REVERT: F 87 ASP cc_start: 0.8724 (m-30) cc_final: 0.8283 (m-30) REVERT: F 114 MET cc_start: 0.8695 (tpp) cc_final: 0.8476 (ttm) REVERT: F 171 TYR cc_start: 0.8346 (m-80) cc_final: 0.7319 (m-80) REVERT: F 175 LEU cc_start: 0.8801 (mm) cc_final: 0.8211 (tt) REVERT: F 191 ASN cc_start: 0.8421 (t0) cc_final: 0.8154 (t0) REVERT: F 218 MET cc_start: 0.3567 (OUTLIER) cc_final: 0.3282 (mtm) REVERT: F 251 HIS cc_start: 0.6473 (t-90) cc_final: 0.5989 (t-90) REVERT: F 263 VAL cc_start: 0.8954 (t) cc_final: 0.8740 (m) REVERT: F 268 SER cc_start: 0.8307 (p) cc_final: 0.7336 (p) REVERT: G 87 ASP cc_start: 0.8509 (m-30) cc_final: 0.8308 (m-30) REVERT: G 105 MET cc_start: 0.8225 (tpp) cc_final: 0.7861 (tpp) REVERT: G 110 ILE cc_start: 0.8834 (mm) cc_final: 0.8564 (mm) REVERT: G 113 ASP cc_start: 0.7535 (p0) cc_final: 0.6714 (t0) REVERT: G 152 TYR cc_start: 0.9139 (OUTLIER) cc_final: 0.8370 (m-10) REVERT: G 163 LYS cc_start: 0.8520 (mtmt) cc_final: 0.7972 (mttp) REVERT: G 259 TYR cc_start: 0.8089 (OUTLIER) cc_final: 0.7777 (t80) REVERT: H 45 TYR cc_start: 0.7534 (OUTLIER) cc_final: 0.7134 (t80) REVERT: H 87 ASP cc_start: 0.8060 (t70) cc_final: 0.7785 (t70) REVERT: H 125 ILE cc_start: 0.8706 (pp) cc_final: 0.8367 (mt) REVERT: H 146 GLU cc_start: 0.8143 (tt0) cc_final: 0.7769 (tm-30) REVERT: H 153 LYS cc_start: 0.8904 (mtpp) cc_final: 0.8637 (mtpt) REVERT: H 193 MET cc_start: 0.7177 (tpp) cc_final: 0.6809 (tpp) REVERT: H 219 LEU cc_start: 0.8342 (OUTLIER) cc_final: 0.7808 (pp) REVERT: H 222 LYS cc_start: 0.6880 (ttmt) cc_final: 0.6077 (tppt) REVERT: H 271 ARG cc_start: 0.8507 (mmm-85) cc_final: 0.7187 (ttt180) outliers start: 66 outliers final: 39 residues processed: 408 average time/residue: 0.2431 time to fit residues: 136.9622 Evaluate side-chains 395 residues out of total 1181 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 351 time to evaluate : 1.256 ------------------------------------------------------------------------------- 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 79 THR Chi-restraints excluded: chain B residue 214 ASP Chi-restraints excluded: chain B residue 236 ASN Chi-restraints excluded: chain B residue 237 VAL Chi-restraints excluded: chain C residue 49 MET Chi-restraints excluded: chain C residue 78 LEU Chi-restraints excluded: chain C residue 79 THR Chi-restraints excluded: chain E residue 103 CYS Chi-restraints excluded: chain E residue 248 LEU Chi-restraints excluded: chain E residue 256 VAL Chi-restraints excluded: chain E residue 260 THR Chi-restraints excluded: chain E residue 276 LEU Chi-restraints excluded: chain E residue 277 THR Chi-restraints excluded: chain F residue 50 ASN Chi-restraints excluded: chain F residue 83 THR Chi-restraints excluded: chain F residue 102 ASN Chi-restraints excluded: chain F residue 118 THR Chi-restraints excluded: chain F residue 142 ILE Chi-restraints excluded: chain F residue 218 MET 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 108 ILE Chi-restraints excluded: chain G residue 125 ILE Chi-restraints excluded: chain G residue 136 VAL Chi-restraints excluded: chain G residue 152 TYR Chi-restraints excluded: chain G residue 197 LEU Chi-restraints excluded: chain G residue 256 VAL Chi-restraints excluded: chain G residue 259 TYR 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 116 ARG 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 Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 121 optimal weight: 5.9990 chunk 26 optimal weight: 9.9990 chunk 79 optimal weight: 0.0870 chunk 33 optimal weight: 5.9990 chunk 135 optimal weight: 4.9990 chunk 112 optimal weight: 20.0000 chunk 62 optimal weight: 2.9990 chunk 11 optimal weight: 2.9990 chunk 44 optimal weight: 3.9990 chunk 71 optimal weight: 0.0670 chunk 130 optimal weight: 0.7980 overall best weight: 1.3900 ------------------------------------------------------------------------------- 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 226 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 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** ** G 213 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 67 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7599 moved from start: 0.7316 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 11412 Z= 0.201 Angle : 0.743 15.629 15321 Z= 0.380 Chirality : 0.042 0.218 1667 Planarity : 0.003 0.056 1998 Dihedral : 5.914 71.024 1528 Min Nonbonded Distance : 2.430 Molprobity Statistics. All-atom Clashscore : 14.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.69 % Favored : 92.31 % Rotamer: Outliers : 5.42 % Allowed : 27.01 % Favored : 67.57 % 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: -0.96 (0.23), residues: 1404 helix: -0.03 (0.16), residues: 1144 sheet: None (None), residues: 0 loop : -2.95 (0.36), residues: 260 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP H 275 HIS 0.008 0.002 HIS G 79 PHE 0.023 0.002 PHE G 85 TYR 0.042 0.001 TYR B 235 ARG 0.007 0.000 ARG D 180 *********************** 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 447 residues out of total 1181 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 64 poor density : 383 time to evaluate : 1.291 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: 0.8543 (t0) cc_final: 0.7764 (t0) REVERT: A 61 SER cc_start: 0.8599 (p) cc_final: 0.8180 (t) REVERT: A 65 ASP cc_start: 0.8196 (m-30) cc_final: 0.7585 (t0) REVERT: A 70 LEU cc_start: 0.9096 (tp) cc_final: 0.8750 (tt) REVERT: B 193 SER cc_start: 0.8725 (p) cc_final: 0.8359 (t) REVERT: B 199 HIS cc_start: 0.6974 (t-90) cc_final: 0.5943 (t-90) REVERT: B 203 ILE cc_start: 0.7952 (mm) cc_final: 0.7371 (pt) REVERT: B 210 ARG cc_start: 0.8136 (ttm-80) cc_final: 0.7740 (mmm160) REVERT: B 215 MET cc_start: 0.8083 (ppp) cc_final: 0.7787 (ppp) REVERT: B 229 MET cc_start: 0.7974 (mtm) cc_final: 0.7630 (ttm) REVERT: C 34 GLN cc_start: 0.8339 (tp40) cc_final: 0.8098 (tp40) REVERT: C 66 GLN cc_start: 0.8470 (mm-40) cc_final: 0.8111 (mm-40) REVERT: C 71 MET cc_start: 0.8245 (tmm) cc_final: 0.8005 (tmm) REVERT: C 72 LYS cc_start: 0.9202 (tppt) cc_final: 0.8886 (tppp) REVERT: D 196 ASN cc_start: 0.7720 (p0) cc_final: 0.7505 (p0) REVERT: E 57 ASN cc_start: 0.8565 (t0) cc_final: 0.8243 (t0) REVERT: E 76 GLN cc_start: 0.8299 (mp10) cc_final: 0.7562 (pp30) REVERT: E 98 GLN cc_start: 0.8140 (tp-100) cc_final: 0.7900 (tp-100) REVERT: E 106 ARG cc_start: 0.8364 (mtp85) cc_final: 0.7805 (ttp-110) REVERT: E 122 LYS cc_start: 0.9308 (tppt) cc_final: 0.8884 (tppt) REVERT: E 125 ILE cc_start: 0.8625 (OUTLIER) cc_final: 0.8105 (mt) REVERT: E 164 CYS cc_start: 0.8456 (m) cc_final: 0.7779 (m) REVERT: E 200 TYR cc_start: 0.7999 (m-80) cc_final: 0.7761 (m-80) REVERT: E 227 LYS cc_start: 0.8676 (mttm) cc_final: 0.8141 (tptt) REVERT: F 66 CYS cc_start: 0.8913 (t) cc_final: 0.7841 (p) REVERT: F 78 LYS cc_start: 0.8508 (mmmm) cc_final: 0.8034 (mtpt) REVERT: F 87 ASP cc_start: 0.8681 (m-30) cc_final: 0.8295 (m-30) REVERT: F 150 ASP cc_start: 0.8348 (t0) cc_final: 0.8099 (t0) REVERT: F 175 LEU cc_start: 0.8788 (OUTLIER) cc_final: 0.8247 (tt) REVERT: F 191 ASN cc_start: 0.8370 (t0) cc_final: 0.8042 (t0) REVERT: F 218 MET cc_start: 0.3218 (OUTLIER) cc_final: 0.2978 (mtm) REVERT: F 279 MET cc_start: 0.8464 (mmm) cc_final: 0.8094 (mmt) REVERT: G 11 MET cc_start: 0.7505 (tmm) cc_final: 0.7036 (mmp) REVERT: G 39 GLU cc_start: 0.8742 (tm-30) cc_final: 0.8470 (tm-30) REVERT: G 51 MET cc_start: 0.8423 (tpp) cc_final: 0.8013 (tpp) REVERT: G 79 HIS cc_start: 0.7120 (t-170) cc_final: 0.6725 (t-170) REVERT: G 93 LYS cc_start: 0.8322 (mtmt) cc_final: 0.8103 (mtmt) REVERT: G 105 MET cc_start: 0.8436 (tpp) cc_final: 0.7833 (tpp) REVERT: G 113 ASP cc_start: 0.7584 (p0) cc_final: 0.6707 (t0) REVERT: G 152 TYR cc_start: 0.9107 (OUTLIER) cc_final: 0.8546 (m-10) REVERT: G 163 LYS cc_start: 0.8569 (mtmt) cc_final: 0.8001 (mttp) REVERT: G 282 ARG cc_start: 0.8521 (ttm170) cc_final: 0.8301 (ttm170) REVERT: H 45 TYR cc_start: 0.7472 (OUTLIER) cc_final: 0.7123 (t80) REVERT: H 87 ASP cc_start: 0.8108 (t70) cc_final: 0.7675 (t70) REVERT: H 125 ILE cc_start: 0.8691 (OUTLIER) cc_final: 0.8353 (mt) REVERT: H 146 GLU cc_start: 0.8166 (tt0) cc_final: 0.7754 (tm-30) REVERT: H 153 LYS cc_start: 0.8813 (mtpp) cc_final: 0.8572 (mtpt) REVERT: H 204 ASP cc_start: 0.8545 (OUTLIER) cc_final: 0.8183 (m-30) REVERT: H 219 LEU cc_start: 0.8394 (pt) cc_final: 0.7811 (pp) outliers start: 64 outliers final: 39 residues processed: 413 average time/residue: 0.2483 time to fit residues: 141.3192 Evaluate side-chains 401 residues out of total 1181 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 355 time to evaluate : 1.247 ------------------------------------------------------------------------------- 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 79 THR Chi-restraints excluded: chain B residue 214 ASP Chi-restraints excluded: chain C residue 19 ASP Chi-restraints excluded: chain C residue 33 LEU Chi-restraints excluded: chain C residue 49 MET Chi-restraints excluded: chain C residue 78 LEU Chi-restraints excluded: chain 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 248 LEU Chi-restraints excluded: chain E residue 256 VAL Chi-restraints excluded: chain E residue 272 LEU Chi-restraints excluded: chain E residue 276 LEU Chi-restraints excluded: chain E residue 277 THR Chi-restraints excluded: chain F residue 50 ASN Chi-restraints excluded: chain F residue 71 LEU Chi-restraints excluded: chain F residue 102 ASN Chi-restraints excluded: chain F residue 118 THR Chi-restraints excluded: chain F residue 175 LEU Chi-restraints excluded: chain F residue 218 MET 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 102 ASN Chi-restraints excluded: chain G residue 108 ILE Chi-restraints excluded: chain G residue 135 LEU Chi-restraints excluded: chain G residue 136 VAL Chi-restraints excluded: chain G residue 152 TYR Chi-restraints excluded: chain G residue 197 LEU Chi-restraints excluded: chain G residue 256 VAL Chi-restraints excluded: chain G residue 259 TYR 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 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 184 ILE Chi-restraints excluded: chain H residue 204 ASP Chi-restraints excluded: chain H residue 211 LEU Chi-restraints excluded: chain H residue 228 TYR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 15 optimal weight: 0.7980 chunk 77 optimal weight: 9.9990 chunk 98 optimal weight: 6.9990 chunk 76 optimal weight: 4.9990 chunk 114 optimal weight: 0.2980 chunk 75 optimal weight: 5.9990 chunk 134 optimal weight: 7.9990 chunk 84 optimal weight: 0.0060 chunk 82 optimal weight: 10.0000 chunk 62 optimal weight: 0.8980 chunk 83 optimal weight: 8.9990 overall best weight: 1.3998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 38 GLN ** A 49 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 199 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 188 ASN ** E 72 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 23 ASN F 50 ASN ** G 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 162 ASN ** G 213 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7597 moved from start: 0.7598 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= 0.210 Angle : 0.752 14.427 15321 Z= 0.384 Chirality : 0.043 0.259 1667 Planarity : 0.003 0.061 1998 Dihedral : 5.932 72.506 1528 Min Nonbonded Distance : 2.365 Molprobity Statistics. All-atom Clashscore : 14.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.55 % Favored : 92.45 % Rotamer: Outliers : 5.42 % Allowed : 27.94 % Favored : 66.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -0.95 (0.23), residues: 1404 helix: -0.06 (0.16), residues: 1162 sheet: None (None), residues: 0 loop : -2.97 (0.38), residues: 242 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP E 275 HIS 0.009 0.002 HIS E 79 PHE 0.025 0.002 PHE G 85 TYR 0.043 0.001 TYR B 235 ARG 0.006 0.000 ARG B 232 *********************** 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 431 residues out of total 1181 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 64 poor density : 367 time to evaluate : 1.291 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: 0.8577 (t0) cc_final: 0.7894 (t0) REVERT: A 61 SER cc_start: 0.8638 (p) cc_final: 0.8317 (t) REVERT: A 66 ARG cc_start: 0.8265 (mmp-170) cc_final: 0.7730 (mtp85) REVERT: A 70 LEU cc_start: 0.9066 (tp) cc_final: 0.8781 (tt) REVERT: B 193 SER cc_start: 0.8778 (p) cc_final: 0.8406 (t) REVERT: B 199 HIS cc_start: 0.7177 (t-90) cc_final: 0.6262 (t-90) REVERT: B 203 ILE cc_start: 0.7826 (mm) cc_final: 0.7356 (pt) REVERT: B 210 ARG cc_start: 0.8102 (ttm-80) cc_final: 0.7687 (mmm160) REVERT: B 215 MET cc_start: 0.8100 (ppp) cc_final: 0.7737 (ppp) REVERT: B 217 MET cc_start: 0.6512 (mmp) cc_final: 0.6260 (mmp) REVERT: B 229 MET cc_start: 0.8052 (mtm) cc_final: 0.7642 (ttm) REVERT: C 34 GLN cc_start: 0.8389 (tp40) cc_final: 0.8093 (tp40) REVERT: C 72 LYS cc_start: 0.9193 (tppt) cc_final: 0.8802 (tppt) REVERT: E 57 ASN cc_start: 0.8688 (t0) cc_final: 0.8452 (t0) REVERT: E 98 GLN cc_start: 0.8118 (tp-100) cc_final: 0.7907 (tp-100) REVERT: E 122 LYS cc_start: 0.9271 (tppt) cc_final: 0.8889 (tppt) REVERT: E 125 ILE cc_start: 0.8618 (OUTLIER) cc_final: 0.8111 (mt) REVERT: E 164 CYS cc_start: 0.8447 (m) cc_final: 0.7872 (m) REVERT: E 200 TYR cc_start: 0.7734 (m-80) cc_final: 0.7465 (m-80) REVERT: E 227 LYS cc_start: 0.8707 (mttm) cc_final: 0.8282 (tptp) REVERT: F 51 MET cc_start: 0.7481 (tpp) cc_final: 0.6901 (tpt) REVERT: F 66 CYS cc_start: 0.8861 (t) cc_final: 0.7760 (p) REVERT: F 87 ASP cc_start: 0.8735 (m-30) cc_final: 0.8362 (m-30) REVERT: F 114 MET cc_start: 0.8401 (ttm) cc_final: 0.8117 (ttm) REVERT: F 150 ASP cc_start: 0.8461 (t0) cc_final: 0.8217 (t0) REVERT: F 175 LEU cc_start: 0.8760 (OUTLIER) cc_final: 0.8216 (tt) REVERT: F 179 GLN cc_start: 0.8471 (tp40) cc_final: 0.8230 (tp40) REVERT: F 203 LYS cc_start: 0.8785 (pttp) cc_final: 0.8318 (ptpt) REVERT: F 218 MET cc_start: 0.3083 (OUTLIER) cc_final: 0.2854 (mtm) REVERT: F 279 MET cc_start: 0.8481 (mmm) cc_final: 0.7944 (mmt) REVERT: F 282 ARG cc_start: 0.8586 (mtp85) cc_final: 0.8283 (mtp85) REVERT: G 11 MET cc_start: 0.7681 (tmm) cc_final: 0.7219 (mmp) REVERT: G 39 GLU cc_start: 0.8827 (tm-30) cc_final: 0.8374 (tm-30) REVERT: G 42 CYS cc_start: 0.8474 (m) cc_final: 0.8058 (p) REVERT: G 75 LEU cc_start: 0.9193 (tt) cc_final: 0.8486 (mp) REVERT: G 93 LYS cc_start: 0.8366 (mtmt) cc_final: 0.8074 (mtmt) REVERT: G 94 LYS cc_start: 0.7355 (mtmm) cc_final: 0.6849 (mmtt) REVERT: G 105 MET cc_start: 0.8358 (tpp) cc_final: 0.8106 (tpp) REVERT: G 109 GLU cc_start: 0.8572 (pm20) cc_final: 0.8262 (tt0) REVERT: G 113 ASP cc_start: 0.7536 (p0) cc_final: 0.6651 (t0) REVERT: G 152 TYR cc_start: 0.9291 (OUTLIER) cc_final: 0.8531 (m-10) REVERT: G 155 GLU cc_start: 0.8494 (mm-30) cc_final: 0.7426 (tp30) REVERT: G 162 ASN cc_start: 0.7891 (OUTLIER) cc_final: 0.7369 (m-40) REVERT: G 163 LYS cc_start: 0.8592 (mtmt) cc_final: 0.8023 (mttp) REVERT: G 227 LYS cc_start: 0.8956 (mmtt) cc_final: 0.8706 (mmtt) REVERT: H 11 MET cc_start: 0.6717 (tpt) cc_final: 0.6366 (tpt) REVERT: H 76 GLN cc_start: 0.7782 (mp10) cc_final: 0.7241 (tm-30) REVERT: H 87 ASP cc_start: 0.7986 (t70) cc_final: 0.7503 (t70) REVERT: H 125 ILE cc_start: 0.8660 (OUTLIER) cc_final: 0.8383 (mt) REVERT: H 146 GLU cc_start: 0.8153 (tt0) cc_final: 0.7761 (tm-30) REVERT: H 153 LYS cc_start: 0.8781 (mtpp) cc_final: 0.8549 (mtpt) REVERT: H 194 ASP cc_start: 0.7651 (OUTLIER) cc_final: 0.7280 (t0) REVERT: H 204 ASP cc_start: 0.8541 (OUTLIER) cc_final: 0.8270 (m-30) outliers start: 64 outliers final: 41 residues processed: 395 average time/residue: 0.2518 time to fit residues: 137.7539 Evaluate side-chains 403 residues out of total 1181 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 354 time to evaluate : 1.268 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 32 LEU Chi-restraints excluded: chain A residue 35 THR Chi-restraints excluded: chain A residue 48 VAL Chi-restraints excluded: chain A residue 53 VAL Chi-restraints excluded: chain A residue 79 THR Chi-restraints excluded: chain B residue 236 ASN Chi-restraints excluded: chain B residue 237 VAL Chi-restraints excluded: chain C residue 19 ASP 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 125 ILE Chi-restraints excluded: chain E residue 256 VAL Chi-restraints excluded: chain E residue 261 GLU Chi-restraints excluded: chain E residue 276 LEU Chi-restraints excluded: chain E residue 277 THR Chi-restraints excluded: chain F residue 50 ASN Chi-restraints excluded: chain F residue 71 LEU 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 175 LEU Chi-restraints excluded: chain F residue 218 MET Chi-restraints excluded: chain G residue 21 VAL Chi-restraints excluded: chain G residue 45 TYR Chi-restraints excluded: chain G residue 86 VAL Chi-restraints excluded: chain G residue 102 ASN Chi-restraints excluded: chain G residue 108 ILE Chi-restraints excluded: chain G residue 135 LEU Chi-restraints excluded: chain G residue 136 VAL Chi-restraints excluded: chain G residue 152 TYR Chi-restraints excluded: chain G residue 162 ASN Chi-restraints excluded: chain G residue 197 LEU Chi-restraints excluded: chain G residue 256 VAL 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 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 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 219 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 53 optimal weight: 10.0000 chunk 80 optimal weight: 0.9980 chunk 40 optimal weight: 1.9990 chunk 26 optimal weight: 9.9990 chunk 85 optimal weight: 7.9990 chunk 91 optimal weight: 3.9990 chunk 66 optimal weight: 4.9990 chunk 12 optimal weight: 0.9980 chunk 106 optimal weight: 4.9990 chunk 122 optimal weight: 0.9990 chunk 129 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 ** A 49 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 199 HIS D 152 GLN D 188 ASN E 72 HIS F 50 ASN ** G 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 162 ASN ** G 213 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7592 moved from start: 0.7754 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= 0.208 Angle : 0.751 14.100 15321 Z= 0.385 Chirality : 0.043 0.235 1667 Planarity : 0.003 0.069 1998 Dihedral : 5.949 73.359 1528 Min Nonbonded Distance : 2.479 Molprobity Statistics. All-atom Clashscore : 14.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.76 % Favored : 92.24 % Rotamer: Outliers : 5.50 % Allowed : 28.20 % Favored : 66.30 % 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: -0.71 (0.23), residues: 1404 helix: 0.11 (0.16), residues: 1153 sheet: None (None), residues: 0 loop : -2.81 (0.38), residues: 251 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP E 275 HIS 0.020 0.002 HIS G 79 PHE 0.022 0.002 PHE H 28 TYR 0.045 0.001 TYR B 235 ARG 0.004 0.000 ARG D 180 *********************** 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 424 residues out of total 1181 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 65 poor density : 359 time to evaluate : 1.248 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 44 ASP cc_start: 0.8530 (t0) cc_final: 0.7852 (t0) REVERT: A 61 SER cc_start: 0.8631 (p) cc_final: 0.8313 (t) REVERT: A 66 ARG cc_start: 0.8282 (mmp-170) cc_final: 0.7837 (mtp85) REVERT: A 70 LEU cc_start: 0.9115 (tp) cc_final: 0.8855 (tt) REVERT: B 193 SER cc_start: 0.8802 (p) cc_final: 0.8464 (t) REVERT: B 203 ILE cc_start: 0.7784 (mm) cc_final: 0.7358 (pt) REVERT: B 206 GLU cc_start: 0.8044 (pp20) cc_final: 0.7730 (pp20) REVERT: B 210 ARG cc_start: 0.8033 (ttm-80) cc_final: 0.7691 (mmm160) REVERT: B 215 MET cc_start: 0.8202 (ppp) cc_final: 0.7799 (ppp) REVERT: B 216 PHE cc_start: 0.8313 (OUTLIER) cc_final: 0.7877 (m-80) REVERT: B 217 MET cc_start: 0.6698 (mmp) cc_final: 0.6463 (mmp) REVERT: B 229 MET cc_start: 0.7991 (mtm) cc_final: 0.7662 (ttm) REVERT: C 34 GLN cc_start: 0.8323 (tp40) cc_final: 0.7918 (tp40) REVERT: D 188 ASN cc_start: 0.8939 (m-40) cc_final: 0.8602 (m110) REVERT: E 40 GLU cc_start: 0.7551 (tp30) cc_final: 0.7061 (mp0) REVERT: E 57 ASN cc_start: 0.8714 (t0) cc_final: 0.8485 (t0) REVERT: E 76 GLN cc_start: 0.8296 (mp10) cc_final: 0.7855 (pp30) REVERT: E 102 ASN cc_start: 0.7337 (p0) cc_final: 0.6871 (m110) REVERT: E 122 LYS cc_start: 0.9255 (tppt) cc_final: 0.8826 (tppt) REVERT: E 125 ILE cc_start: 0.8623 (OUTLIER) cc_final: 0.8140 (mt) REVERT: E 164 CYS cc_start: 0.8448 (m) cc_final: 0.7892 (m) REVERT: E 200 TYR cc_start: 0.7812 (m-80) cc_final: 0.7596 (m-80) REVERT: E 218 MET cc_start: 0.5596 (tpp) cc_final: 0.3281 (mmt) REVERT: E 227 LYS cc_start: 0.8757 (mttm) cc_final: 0.8492 (mmmt) REVERT: F 45 TYR cc_start: 0.8283 (t80) cc_final: 0.7104 (t80) REVERT: F 51 MET cc_start: 0.7368 (tpp) cc_final: 0.6633 (tpt) REVERT: F 66 CYS cc_start: 0.8855 (t) cc_final: 0.7755 (p) REVERT: F 87 ASP cc_start: 0.8699 (m-30) cc_final: 0.8355 (m-30) REVERT: F 96 ASP cc_start: 0.8191 (t0) cc_final: 0.7873 (t0) REVERT: F 114 MET cc_start: 0.8423 (ttm) cc_final: 0.8131 (ttm) REVERT: F 132 GLU cc_start: 0.7391 (tt0) cc_final: 0.7131 (tt0) REVERT: F 150 ASP cc_start: 0.8470 (t0) cc_final: 0.8211 (t0) REVERT: F 175 LEU cc_start: 0.8785 (OUTLIER) cc_final: 0.8254 (tt) REVERT: F 218 MET cc_start: 0.3150 (OUTLIER) cc_final: 0.2938 (mtm) REVERT: G 42 CYS cc_start: 0.8516 (m) cc_final: 0.7995 (p) REVERT: G 74 GLN cc_start: 0.7948 (pt0) cc_final: 0.7744 (pt0) REVERT: G 93 LYS cc_start: 0.8381 (mtmt) cc_final: 0.8003 (mtpt) REVERT: G 94 LYS cc_start: 0.7395 (mtmm) cc_final: 0.6924 (mmtt) REVERT: G 105 MET cc_start: 0.8417 (tpp) cc_final: 0.8151 (tpp) REVERT: G 109 GLU cc_start: 0.8485 (pm20) cc_final: 0.8263 (tt0) REVERT: G 113 ASP cc_start: 0.7479 (p0) cc_final: 0.6520 (t0) REVERT: G 114 MET cc_start: 0.8775 (tpp) cc_final: 0.8386 (tpt) REVERT: G 152 TYR cc_start: 0.9270 (OUTLIER) cc_final: 0.8502 (m-10) REVERT: G 162 ASN cc_start: 0.7823 (OUTLIER) cc_final: 0.7176 (m-40) REVERT: G 163 LYS cc_start: 0.8474 (mtmt) cc_final: 0.7953 (mttp) REVERT: G 227 LYS cc_start: 0.8950 (mmtt) cc_final: 0.8696 (mmtt) REVERT: H 11 MET cc_start: 0.6716 (tpt) cc_final: 0.6365 (tpt) REVERT: H 39 GLU cc_start: 0.8232 (OUTLIER) cc_final: 0.7948 (mp0) REVERT: H 47 ARG cc_start: 0.7774 (ptm160) cc_final: 0.7352 (ptm160) REVERT: H 76 GLN cc_start: 0.7732 (mp10) cc_final: 0.7285 (tm-30) REVERT: H 87 ASP cc_start: 0.7961 (t70) cc_final: 0.7377 (t70) REVERT: H 125 ILE cc_start: 0.8649 (OUTLIER) cc_final: 0.8389 (mt) REVERT: H 146 GLU cc_start: 0.8155 (tt0) cc_final: 0.7742 (tm-30) REVERT: H 194 ASP cc_start: 0.7638 (OUTLIER) cc_final: 0.7292 (t0) REVERT: H 204 ASP cc_start: 0.8677 (OUTLIER) cc_final: 0.8443 (m-30) outliers start: 65 outliers final: 41 residues processed: 388 average time/residue: 0.2458 time to fit residues: 133.3187 Evaluate side-chains 398 residues out of total 1181 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 347 time to evaluate : 1.326 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 32 LEU Chi-restraints excluded: chain A residue 35 THR Chi-restraints excluded: chain A residue 48 VAL Chi-restraints excluded: chain A residue 53 VAL Chi-restraints excluded: chain A residue 79 THR Chi-restraints excluded: chain B residue 211 GLU Chi-restraints excluded: chain B residue 216 PHE Chi-restraints excluded: chain B residue 237 VAL Chi-restraints excluded: chain C residue 19 ASP Chi-restraints excluded: chain C residue 78 LEU Chi-restraints excluded: chain C residue 79 THR Chi-restraints excluded: chain E residue 125 ILE Chi-restraints excluded: chain E residue 256 VAL Chi-restraints excluded: chain E residue 261 GLU Chi-restraints excluded: chain E residue 276 LEU Chi-restraints excluded: chain E residue 277 THR Chi-restraints excluded: chain F residue 50 ASN Chi-restraints excluded: chain F residue 71 LEU 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 175 LEU Chi-restraints excluded: chain F residue 218 MET 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 86 VAL Chi-restraints excluded: chain G residue 108 ILE Chi-restraints excluded: chain G residue 135 LEU Chi-restraints excluded: chain G residue 136 VAL Chi-restraints excluded: chain G residue 152 TYR Chi-restraints excluded: chain G residue 162 ASN Chi-restraints excluded: chain G residue 197 LEU Chi-restraints excluded: chain G residue 256 VAL Chi-restraints excluded: chain H residue 39 GLU Chi-restraints excluded: chain H residue 42 CYS Chi-restraints excluded: chain H residue 45 TYR Chi-restraints excluded: chain H residue 51 MET 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 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 219 LEU 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 117 optimal weight: 3.9990 chunk 125 optimal weight: 1.9990 chunk 129 optimal weight: 0.9990 chunk 75 optimal weight: 3.9990 chunk 54 optimal weight: 8.9990 chunk 98 optimal weight: 3.9990 chunk 38 optimal weight: 7.9990 chunk 113 optimal weight: 5.9990 chunk 118 optimal weight: 8.9990 chunk 82 optimal weight: 8.9990 chunk 132 optimal weight: 0.6980 overall best weight: 2.3388 ------------------------------------------------------------------------------- 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** D 152 GLN D 159 ASN E 72 HIS ** E 213 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 50 ASN G 162 ASN ** G 213 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7637 moved from start: 0.7887 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 11412 Z= 0.242 Angle : 0.790 15.820 15321 Z= 0.403 Chirality : 0.044 0.238 1667 Planarity : 0.004 0.074 1998 Dihedral : 5.986 74.243 1528 Min Nonbonded Distance : 2.513 Molprobity Statistics. All-atom Clashscore : 15.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.19 % Favored : 91.81 % Rotamer: Outliers : 5.17 % Allowed : 28.87 % Favored : 65.96 % 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: -0.70 (0.23), residues: 1404 helix: 0.09 (0.16), residues: 1145 sheet: None (None), residues: 0 loop : -2.56 (0.39), residues: 259 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP F 58 HIS 0.024 0.002 HIS G 79 PHE 0.024 0.002 PHE G 85 TYR 0.041 0.002 TYR B 235 ARG 0.004 0.000 ARG D 180 *********************** 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 413 residues out of total 1181 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 61 poor density : 352 time to evaluate : 1.293 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 44 ASP cc_start: 0.8642 (t0) cc_final: 0.7915 (t0) REVERT: A 61 SER cc_start: 0.8683 (p) cc_final: 0.8309 (t) REVERT: A 66 ARG cc_start: 0.8376 (mmp-170) cc_final: 0.8059 (mtp85) REVERT: A 70 LEU cc_start: 0.9114 (tp) cc_final: 0.8887 (tt) REVERT: B 193 SER cc_start: 0.8646 (p) cc_final: 0.8292 (t) REVERT: B 199 HIS cc_start: 0.7133 (t70) cc_final: 0.6179 (t-90) REVERT: B 203 ILE cc_start: 0.7857 (mm) cc_final: 0.7244 (pt) REVERT: B 210 ARG cc_start: 0.8030 (ttm-80) cc_final: 0.7676 (mmm160) REVERT: B 216 PHE cc_start: 0.8386 (OUTLIER) cc_final: 0.7844 (m-80) REVERT: B 229 MET cc_start: 0.8094 (mtm) cc_final: 0.7696 (ttm) REVERT: C 32 MET cc_start: 0.8481 (tpp) cc_final: 0.8195 (tmm) REVERT: C 34 GLN cc_start: 0.8284 (tp40) cc_final: 0.7885 (tp40) REVERT: D 188 ASN cc_start: 0.8964 (m-40) cc_final: 0.8676 (m110) REVERT: D 196 ASN cc_start: 0.7735 (p0) cc_final: 0.7497 (p0) REVERT: E 57 ASN cc_start: 0.8800 (t0) cc_final: 0.8481 (t0) REVERT: E 76 GLN cc_start: 0.8267 (mp10) cc_final: 0.7866 (pp30) REVERT: E 106 ARG cc_start: 0.8464 (mtp85) cc_final: 0.8102 (ttp-110) REVERT: E 122 LYS cc_start: 0.9296 (tppt) cc_final: 0.8963 (tppt) REVERT: E 125 ILE cc_start: 0.8649 (OUTLIER) cc_final: 0.8183 (mt) REVERT: E 164 CYS cc_start: 0.8478 (m) cc_final: 0.8091 (m) REVERT: E 218 MET cc_start: 0.5899 (tpp) cc_final: 0.3669 (mmt) REVERT: F 51 MET cc_start: 0.7673 (tpp) cc_final: 0.7171 (tpt) REVERT: F 66 CYS cc_start: 0.8856 (t) cc_final: 0.7758 (p) REVERT: F 87 ASP cc_start: 0.8718 (m-30) cc_final: 0.8395 (m-30) REVERT: F 96 ASP cc_start: 0.8221 (t0) cc_final: 0.7882 (t0) REVERT: F 132 GLU cc_start: 0.7417 (tt0) cc_final: 0.7181 (tt0) REVERT: F 150 ASP cc_start: 0.8493 (t0) cc_final: 0.8231 (t0) REVERT: F 175 LEU cc_start: 0.8867 (OUTLIER) cc_final: 0.8347 (tt) REVERT: F 203 LYS cc_start: 0.8803 (pttp) cc_final: 0.8345 (ptpt) REVERT: F 218 MET cc_start: 0.3551 (OUTLIER) cc_final: 0.3259 (mtm) REVERT: F 279 MET cc_start: 0.8353 (mmm) cc_final: 0.7872 (mmt) REVERT: G 11 MET cc_start: 0.7128 (tmm) cc_final: 0.6668 (mmp) REVERT: G 42 CYS cc_start: 0.8510 (m) cc_final: 0.7976 (p) REVERT: G 75 LEU cc_start: 0.9295 (tt) cc_final: 0.8598 (mp) REVERT: G 93 LYS cc_start: 0.8418 (mtmt) cc_final: 0.8178 (mtmt) REVERT: G 94 LYS cc_start: 0.7378 (OUTLIER) cc_final: 0.7012 (mmtp) REVERT: G 105 MET cc_start: 0.8381 (tpp) cc_final: 0.8119 (tpp) REVERT: G 109 GLU cc_start: 0.8474 (pm20) cc_final: 0.8200 (tt0) REVERT: G 113 ASP cc_start: 0.7514 (p0) cc_final: 0.6550 (t0) REVERT: G 152 TYR cc_start: 0.9283 (OUTLIER) cc_final: 0.8441 (m-10) REVERT: G 162 ASN cc_start: 0.8007 (OUTLIER) cc_final: 0.7385 (m-40) REVERT: G 227 LYS cc_start: 0.8945 (mmtt) cc_final: 0.8672 (mmtt) REVERT: H 11 MET cc_start: 0.6824 (tpt) cc_final: 0.6486 (tpt) REVERT: H 39 GLU cc_start: 0.8258 (OUTLIER) cc_final: 0.7933 (mp0) REVERT: H 47 ARG cc_start: 0.7771 (ptm160) cc_final: 0.7360 (ptm160) REVERT: H 87 ASP cc_start: 0.8008 (t70) cc_final: 0.7420 (t70) REVERT: H 125 ILE cc_start: 0.8684 (OUTLIER) cc_final: 0.8436 (mt) REVERT: H 146 GLU cc_start: 0.8161 (tt0) cc_final: 0.7736 (tm-30) REVERT: H 194 ASP cc_start: 0.7744 (OUTLIER) cc_final: 0.7375 (t0) REVERT: H 204 ASP cc_start: 0.8546 (OUTLIER) cc_final: 0.8320 (m-30) outliers start: 61 outliers final: 44 residues processed: 380 average time/residue: 0.2437 time to fit residues: 128.7062 Evaluate side-chains 396 residues out of total 1181 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 55 poor density : 341 time to evaluate : 1.252 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 32 LEU Chi-restraints excluded: chain A residue 35 THR Chi-restraints excluded: chain A residue 48 VAL Chi-restraints excluded: chain A residue 53 VAL Chi-restraints excluded: chain A residue 79 THR Chi-restraints excluded: chain B residue 211 GLU Chi-restraints excluded: chain B residue 216 PHE 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 125 ILE Chi-restraints excluded: chain E residue 256 VAL Chi-restraints excluded: chain E residue 261 GLU Chi-restraints excluded: chain E residue 272 LEU Chi-restraints excluded: chain E residue 276 LEU Chi-restraints excluded: chain E residue 277 THR Chi-restraints excluded: chain E residue 280 LEU Chi-restraints excluded: chain F residue 50 ASN Chi-restraints excluded: chain F residue 71 LEU 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 175 LEU Chi-restraints excluded: chain F residue 218 MET 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 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 135 LEU Chi-restraints excluded: chain G residue 136 VAL Chi-restraints excluded: chain G residue 152 TYR Chi-restraints excluded: chain G residue 162 ASN Chi-restraints excluded: chain G residue 197 LEU Chi-restraints excluded: chain G residue 256 VAL Chi-restraints excluded: chain H residue 39 GLU Chi-restraints excluded: chain H residue 42 CYS Chi-restraints excluded: chain H residue 45 TYR Chi-restraints excluded: chain H residue 51 MET Chi-restraints excluded: chain H residue 96 ASP 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 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 219 LEU Chi-restraints excluded: chain H residue 228 TYR Chi-restraints excluded: chain H residue 276 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 81 optimal weight: 6.9990 chunk 63 optimal weight: 5.9990 chunk 92 optimal weight: 0.6980 chunk 139 optimal weight: 3.9990 chunk 128 optimal weight: 2.9990 chunk 111 optimal weight: 9.9990 chunk 11 optimal weight: 10.0000 chunk 85 optimal weight: 7.9990 chunk 68 optimal weight: 0.7980 chunk 88 optimal weight: 3.9990 chunk 118 optimal weight: 6.9990 overall best weight: 2.4986 ------------------------------------------------------------------------------- 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** E 72 HIS ** E 213 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 50 ASN F 226 GLN G 162 ASN ** G 213 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7647 moved from start: 0.7977 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 11412 Z= 0.256 Angle : 0.823 15.629 15321 Z= 0.419 Chirality : 0.045 0.251 1667 Planarity : 0.004 0.078 1998 Dihedral : 6.040 74.489 1528 Min Nonbonded Distance : 2.506 Molprobity Statistics. All-atom Clashscore : 16.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.48 % Favored : 91.52 % Rotamer: Outliers : 5.33 % Allowed : 29.13 % Favored : 65.54 % 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: -0.82 (0.23), residues: 1404 helix: 0.04 (0.16), residues: 1145 sheet: None (None), residues: 0 loop : -2.79 (0.37), residues: 259 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP F 58 HIS 0.024 0.002 HIS G 79 PHE 0.023 0.002 PHE G 85 TYR 0.043 0.002 TYR B 235 ARG 0.004 0.001 ARG D 161 ********************** 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 407 residues out of total 1181 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 63 poor density : 344 time to evaluate : 1.212 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 44 ASP cc_start: 0.8666 (t0) cc_final: 0.7968 (t0) REVERT: A 66 ARG cc_start: 0.8338 (mmp-170) cc_final: 0.7954 (mtp85) REVERT: B 193 SER cc_start: 0.8781 (p) cc_final: 0.8480 (t) REVERT: B 199 HIS cc_start: 0.7208 (t70) cc_final: 0.6270 (t-90) REVERT: B 203 ILE cc_start: 0.7740 (mm) cc_final: 0.7242 (pt) REVERT: B 210 ARG cc_start: 0.8024 (ttm-80) cc_final: 0.7683 (mmm160) REVERT: B 216 PHE cc_start: 0.8286 (OUTLIER) cc_final: 0.7713 (m-80) REVERT: C 34 GLN cc_start: 0.8376 (tp40) cc_final: 0.7970 (tp40) REVERT: D 188 ASN cc_start: 0.8947 (m-40) cc_final: 0.8594 (m110) REVERT: E 57 ASN cc_start: 0.8823 (t0) cc_final: 0.8552 (t0) REVERT: E 76 GLN cc_start: 0.8268 (mp10) cc_final: 0.7798 (pp30) REVERT: E 106 ARG cc_start: 0.8365 (mtp85) cc_final: 0.7983 (ttp-110) REVERT: E 122 LYS cc_start: 0.9288 (tppt) cc_final: 0.8883 (tppt) REVERT: E 125 ILE cc_start: 0.8660 (OUTLIER) cc_final: 0.8213 (mt) REVERT: E 164 CYS cc_start: 0.8485 (m) cc_final: 0.8107 (m) REVERT: E 218 MET cc_start: 0.6101 (tpp) cc_final: 0.4053 (mmt) REVERT: F 51 MET cc_start: 0.7642 (tpp) cc_final: 0.6597 (tpp) REVERT: F 66 CYS cc_start: 0.8890 (t) cc_final: 0.7774 (p) REVERT: F 87 ASP cc_start: 0.8741 (m-30) cc_final: 0.8406 (m-30) REVERT: F 96 ASP cc_start: 0.8216 (t0) cc_final: 0.7871 (t0) REVERT: F 150 ASP cc_start: 0.8502 (t0) cc_final: 0.8231 (t0) REVERT: F 175 LEU cc_start: 0.8941 (OUTLIER) cc_final: 0.8415 (tt) REVERT: F 218 MET cc_start: 0.3672 (OUTLIER) cc_final: 0.3347 (mtm) REVERT: F 226 GLN cc_start: 0.8226 (tp-100) cc_final: 0.7962 (tp-100) REVERT: F 249 GLU cc_start: 0.7836 (pt0) cc_final: 0.7282 (pp20) REVERT: F 279 MET cc_start: 0.8345 (mmm) cc_final: 0.7748 (mmt) REVERT: G 11 MET cc_start: 0.7176 (tmm) cc_final: 0.6738 (mmp) REVERT: G 42 CYS cc_start: 0.8499 (m) cc_final: 0.8016 (p) REVERT: G 75 LEU cc_start: 0.9275 (tt) cc_final: 0.8566 (mp) REVERT: G 94 LYS cc_start: 0.7410 (OUTLIER) cc_final: 0.7036 (mmtp) REVERT: G 105 MET cc_start: 0.8397 (tpp) cc_final: 0.8119 (tpp) REVERT: G 109 GLU cc_start: 0.8471 (pm20) cc_final: 0.8182 (tt0) REVERT: G 113 ASP cc_start: 0.7512 (p0) cc_final: 0.6549 (t0) REVERT: G 152 TYR cc_start: 0.9276 (OUTLIER) cc_final: 0.8440 (m-10) REVERT: G 227 LYS cc_start: 0.8966 (mmtt) cc_final: 0.8677 (mmtt) REVERT: H 11 MET cc_start: 0.6855 (tpt) cc_final: 0.6509 (tpt) REVERT: H 39 GLU cc_start: 0.8277 (OUTLIER) cc_final: 0.7963 (mp0) REVERT: H 47 ARG cc_start: 0.7840 (ptm160) cc_final: 0.7445 (ptm160) REVERT: H 76 GLN cc_start: 0.7780 (mp10) cc_final: 0.7298 (tm-30) REVERT: H 87 ASP cc_start: 0.8051 (t70) cc_final: 0.7567 (t70) REVERT: H 125 ILE cc_start: 0.8695 (OUTLIER) cc_final: 0.8429 (mt) REVERT: H 146 GLU cc_start: 0.8162 (tt0) cc_final: 0.7747 (tm-30) REVERT: H 194 ASP cc_start: 0.7683 (OUTLIER) cc_final: 0.7295 (t0) REVERT: H 204 ASP cc_start: 0.8553 (OUTLIER) cc_final: 0.8267 (m-30) outliers start: 63 outliers final: 49 residues processed: 373 average time/residue: 0.2342 time to fit residues: 122.4732 Evaluate side-chains 396 residues out of total 1181 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 59 poor density : 337 time to evaluate : 1.294 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 32 LEU Chi-restraints excluded: chain A residue 35 THR Chi-restraints excluded: chain A residue 48 VAL Chi-restraints excluded: chain A residue 53 VAL Chi-restraints excluded: chain A residue 79 THR Chi-restraints excluded: chain B residue 211 GLU Chi-restraints excluded: chain B residue 215 MET Chi-restraints excluded: chain B residue 216 PHE Chi-restraints excluded: chain B residue 237 VAL Chi-restraints excluded: chain C residue 19 ASP 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 72 HIS 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 259 TYR Chi-restraints excluded: chain E residue 261 GLU Chi-restraints excluded: chain E residue 272 LEU Chi-restraints excluded: chain E residue 276 LEU Chi-restraints excluded: chain E residue 277 THR Chi-restraints excluded: chain E residue 280 LEU Chi-restraints excluded: chain F residue 50 ASN Chi-restraints excluded: chain F residue 71 LEU 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 175 LEU Chi-restraints excluded: chain F residue 218 MET 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 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 135 LEU Chi-restraints excluded: chain G residue 136 VAL Chi-restraints excluded: chain G residue 152 TYR Chi-restraints excluded: chain G residue 197 LEU Chi-restraints excluded: chain G residue 256 VAL Chi-restraints excluded: chain H residue 39 GLU Chi-restraints excluded: chain H residue 42 CYS Chi-restraints excluded: chain H residue 45 TYR Chi-restraints excluded: chain H residue 51 MET Chi-restraints excluded: chain H residue 96 ASP 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 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 219 LEU Chi-restraints excluded: chain H residue 228 TYR Chi-restraints excluded: chain H residue 276 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 34 optimal weight: 0.4980 chunk 102 optimal weight: 5.9990 chunk 16 optimal weight: 1.9990 chunk 30 optimal weight: 2.9990 chunk 111 optimal weight: 8.9990 chunk 46 optimal weight: 6.9990 chunk 114 optimal weight: 20.0000 chunk 14 optimal weight: 1.9990 chunk 20 optimal weight: 0.9990 chunk 97 optimal weight: 0.8980 chunk 6 optimal weight: 5.9990 overall best weight: 1.2786 ------------------------------------------------------------------------------- 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 236 ASN D 152 GLN E 72 HIS ** E 213 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 50 ASN ** G 213 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4072 r_free = 0.4072 target = 0.155024 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3781 r_free = 0.3781 target = 0.133748 restraints weight = 25112.094| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3826 r_free = 0.3826 target = 0.136991 restraints weight = 14276.638| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3856 r_free = 0.3856 target = 0.139214 restraints weight = 9437.306| |-----------------------------------------------------------------------------| r_work (final): 0.3796 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7598 moved from start: 0.8104 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= 0.225 Angle : 0.814 15.598 15321 Z= 0.412 Chirality : 0.044 0.242 1667 Planarity : 0.004 0.072 1998 Dihedral : 6.028 74.156 1528 Min Nonbonded Distance : 2.487 Molprobity Statistics. All-atom Clashscore : 15.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.83 % Favored : 92.17 % Rotamer: Outliers : 4.83 % Allowed : 29.81 % Favored : 65.37 % 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: -0.84 (0.23), residues: 1404 helix: -0.01 (0.16), residues: 1153 sheet: None (None), residues: 0 loop : -2.69 (0.38), residues: 251 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP E 275 HIS 0.023 0.002 HIS G 79 PHE 0.023 0.002 PHE H 28 TYR 0.047 0.001 TYR B 235 ARG 0.004 0.000 ARG G 106 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2918.58 seconds wall clock time: 53 minutes 28.17 seconds (3208.17 seconds total)