Starting phenix.real_space_refine on Thu Feb 15 19:10:14 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6o5b_0626/02_2024/6o5b_0626.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6o5b_0626/02_2024/6o5b_0626.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6o5b_0626/02_2024/6o5b_0626.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6o5b_0626/02_2024/6o5b_0626.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6o5b_0626/02_2024/6o5b_0626.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6o5b_0626/02_2024/6o5b_0626.pdb" } resolution = 3.6 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= -0.000 sd= 0.002 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: 5 Type Number sf(0) Gaussians Ca 1 9.91 5 S 40 5.16 5 C 8472 2.51 5 N 2279 2.21 5 O 2377 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "J ARG 89": "NH1" <-> "NH2" Residue "K ARG 89": "NH1" <-> "NH2" Residue "E ARG 93": "NH1" <-> "NH2" Residue "E ARG 124": "NH1" <-> "NH2" Residue "C ARG 93": "NH1" <-> "NH2" Residue "C ARG 124": "NH1" <-> "NH2" Residue "A ARG 96": "NH1" <-> "NH2" Residue "A ARG 113": "NH1" <-> "NH2" Residue "A ARG 120": "NH1" <-> "NH2" Residue "A ARG 201": "NH1" <-> "NH2" Residue "L ARG 89": "NH1" <-> "NH2" Residue "L ARG 93": "NH1" <-> "NH2" Residue "L ARG 124": "NH1" <-> "NH2" Residue "I ARG 89": "NH1" <-> "NH2" Residue "I ARG 93": "NH1" <-> "NH2" Residue "I ARG 120": "NH1" <-> "NH2" Residue "G ARG 93": "NH1" <-> "NH2" Residue "G ARG 96": "NH1" <-> "NH2" Residue "G ARG 124": "NH1" <-> "NH2" Residue "G ARG 134": "NH1" <-> "NH2" Residue "G ARG 295": "NH1" <-> "NH2" Time to flip residues: 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 13169 Number of models: 1 Model: "" Number of chains: 13 Chain: "J" Number of atoms: 723 Number of conformers: 1 Conformer: "" Number of residues, atoms: 91, 723 Classifications: {'peptide': 91} Link IDs: {'PTRANS': 6, 'TRANS': 84} Chain: "K" Number of atoms: 723 Number of conformers: 1 Conformer: "" Number of residues, atoms: 91, 723 Classifications: {'peptide': 91} Link IDs: {'PTRANS': 6, 'TRANS': 84} Chain: "E" Number of atoms: 2226 Number of conformers: 1 Conformer: "" Number of residues, atoms: 270, 2226 Classifications: {'peptide': 270} Link IDs: {'PTRANS': 11, 'TRANS': 258} Chain: "F" Number of atoms: 381 Number of conformers: 1 Conformer: "" Number of residues, atoms: 49, 381 Classifications: {'peptide': 49} Link IDs: {'PTRANS': 3, 'TRANS': 45} Chain: "C" Number of atoms: 2211 Number of conformers: 1 Conformer: "" Number of residues, atoms: 268, 2211 Classifications: {'peptide': 268} Link IDs: {'PTRANS': 10, 'TRANS': 257} Chain: "D" Number of atoms: 381 Number of conformers: 1 Conformer: "" Number of residues, atoms: 49, 381 Classifications: {'peptide': 49} Link IDs: {'PTRANS': 3, 'TRANS': 45} Chain: "A" Number of atoms: 2254 Number of conformers: 1 Conformer: "" Number of residues, atoms: 273, 2254 Classifications: {'peptide': 273} Link IDs: {'PTRANS': 11, 'TRANS': 261} Chain: "B" Number of atoms: 381 Number of conformers: 1 Conformer: "" Number of residues, atoms: 49, 381 Classifications: {'peptide': 49} Link IDs: {'PTRANS': 3, 'TRANS': 45} Chain: "L" Number of atoms: 723 Number of conformers: 1 Conformer: "" Number of residues, atoms: 91, 723 Classifications: {'peptide': 91} Link IDs: {'PTRANS': 6, 'TRANS': 84} Chain: "I" Number of atoms: 723 Number of conformers: 1 Conformer: "" Number of residues, atoms: 91, 723 Classifications: {'peptide': 91} Link IDs: {'PTRANS': 6, 'TRANS': 84} Chain: "G" Number of atoms: 2069 Number of conformers: 1 Conformer: "" Number of residues, atoms: 250, 2069 Classifications: {'peptide': 250} Link IDs: {'PTRANS': 9, 'TRANS': 240} Chain breaks: 1 Chain: "H" Number of atoms: 373 Number of conformers: 1 Conformer: "" Number of residues, atoms: 48, 373 Classifications: {'peptide': 48} Link IDs: {'PTRANS': 3, 'TRANS': 44} Chain: "G" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' CA': 1} Classifications: {'undetermined': 1} Time building chain proxies: 7.19, per 1000 atoms: 0.55 Number of scatterers: 13169 At special positions: 0 Unit cell: (103.32, 150.36, 136.92, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) Ca 1 19.99 S 40 16.00 O 2377 8.00 N 2279 7.00 C 8472 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 - 3.50 Amino acid : False - 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: 4.40 Conformation dependent library (CDL) restraints added in 2.2 seconds 3188 Ramachandran restraints generated. 1594 Oldfield, 0 Emsley, 1594 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3096 Finding SS restraints... Secondary structure from input PDB file: 51 helices and 17 sheets defined 53.8% alpha, 10.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.20 Creating SS restraints... Processing helix chain 'J' and resid 107 through 112 Processing helix chain 'J' and resid 140 through 147 removed outlier: 4.519A pdb=" N ASP J 147 " --> pdb=" O LEU J 143 " (cutoff:3.500A) Processing helix chain 'K' and resid 107 through 119 removed outlier: 3.675A pdb=" N ARG K 113 " --> pdb=" O GLY K 109 " (cutoff:3.500A) Processing helix chain 'K' and resid 140 through 145 Processing helix chain 'E' and resid 107 through 119 removed outlier: 3.822A pdb=" N ARG E 113 " --> pdb=" O GLY E 109 " (cutoff:3.500A) removed outlier: 3.877A pdb=" N ASP E 119 " --> pdb=" O LEU E 115 " (cutoff:3.500A) Processing helix chain 'E' and resid 140 through 144 Processing helix chain 'E' and resid 169 through 190 removed outlier: 4.643A pdb=" N LEU E 176 " --> pdb=" O ASN E 172 " (cutoff:3.500A) removed outlier: 3.983A pdb=" N ASN E 177 " --> pdb=" O ALA E 173 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N LEU E 182 " --> pdb=" O ASP E 178 " (cutoff:3.500A) removed outlier: 4.097A pdb=" N LEU E 190 " --> pdb=" O LEU E 186 " (cutoff:3.500A) Processing helix chain 'E' and resid 191 through 253 removed outlier: 3.733A pdb=" N GLU E 200 " --> pdb=" O GLN E 196 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N GLU E 208 " --> pdb=" O ILE E 204 " (cutoff:3.500A) Proline residue: E 216 - end of helix removed outlier: 4.317A pdb=" N LYS E 219 " --> pdb=" O ALA E 215 " (cutoff:3.500A) removed outlier: 4.036A pdb=" N VAL E 220 " --> pdb=" O PRO E 216 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N ILE E 224 " --> pdb=" O VAL E 220 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N LEU E 240 " --> pdb=" O LEU E 236 " (cutoff:3.500A) removed outlier: 3.918A pdb=" N PHE E 247 " --> pdb=" O MET E 243 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N ILE E 249 " --> pdb=" O THR E 245 " (cutoff:3.500A) Processing helix chain 'E' and resid 263 through 285 removed outlier: 3.986A pdb=" N THR E 267 " --> pdb=" O MET E 263 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N TYR E 268 " --> pdb=" O GLU E 264 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N ALA E 275 " --> pdb=" O THR E 271 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N TYR E 279 " --> pdb=" O ALA E 275 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N PHE E 282 " --> pdb=" O MET E 278 " (cutoff:3.500A) Processing helix chain 'E' and resid 292 through 310 removed outlier: 3.912A pdb=" N ARG E 297 " --> pdb=" O GLU E 293 " (cutoff:3.500A) removed outlier: 4.497A pdb=" N GLN E 298 " --> pdb=" O ALA E 294 " (cutoff:3.500A) removed outlier: 4.179A pdb=" N LYS E 309 " --> pdb=" O LYS E 305 " (cutoff:3.500A) Processing helix chain 'E' and resid 313 through 328 removed outlier: 3.662A pdb=" N TYR E 317 " --> pdb=" O ASP E 313 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N LEU E 320 " --> pdb=" O LYS E 316 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N ALA E 325 " --> pdb=" O LYS E 321 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N GLN E 326 " --> pdb=" O ASP E 322 " (cutoff:3.500A) Processing helix chain 'E' and resid 328 through 335 Processing helix chain 'F' and resid 65 through 96 removed outlier: 3.732A pdb=" N PHE F 71 " --> pdb=" O LEU F 67 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N ILE F 73 " --> pdb=" O ARG F 69 " (cutoff:3.500A) Proline residue: F 76 - end of helix removed outlier: 4.103A pdb=" N SER F 85 " --> pdb=" O GLY F 81 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N ASN F 87 " --> pdb=" O LEU F 83 " (cutoff:3.500A) removed outlier: 4.407A pdb=" N PHE F 88 " --> pdb=" O ILE F 84 " (cutoff:3.500A) removed outlier: 4.078A pdb=" N ALA F 89 " --> pdb=" O SER F 85 " (cutoff:3.500A) removed outlier: 4.072A pdb=" N ALA F 90 " --> pdb=" O LYS F 86 " (cutoff:3.500A) removed outlier: 4.101A pdb=" N LEU F 91 " --> pdb=" O ASN F 87 " (cutoff:3.500A) Processing helix chain 'C' and resid 91 through 94 removed outlier: 3.550A pdb=" N ARG C 94 " --> pdb=" O PRO C 91 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 91 through 94' Processing helix chain 'C' and resid 107 through 119 removed outlier: 3.691A pdb=" N PHE C 111 " --> pdb=" O SER C 107 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N LEU C 112 " --> pdb=" O VAL C 108 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N GLN C 116 " --> pdb=" O LEU C 112 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N GLU C 118 " --> pdb=" O GLN C 114 " (cutoff:3.500A) Processing helix chain 'C' and resid 140 through 145 Processing helix chain 'C' and resid 172 through 177 Processing helix chain 'C' and resid 178 through 190 removed outlier: 3.537A pdb=" N THR C 188 " --> pdb=" O GLN C 184 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N LEU C 190 " --> pdb=" O LEU C 186 " (cutoff:3.500A) Processing helix chain 'C' and resid 191 through 214 removed outlier: 3.503A pdb=" N HIS C 195 " --> pdb=" O CYS C 191 " (cutoff:3.500A) removed outlier: 3.932A pdb=" N ILE C 204 " --> pdb=" O GLU C 200 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N ASP C 209 " --> pdb=" O GLU C 205 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N LEU C 214 " --> pdb=" O LEU C 210 " (cutoff:3.500A) Processing helix chain 'C' and resid 217 through 257 removed outlier: 3.661A pdb=" N ARG C 221 " --> pdb=" O LEU C 217 " (cutoff:3.500A) removed outlier: 4.334A pdb=" N GLU C 223 " --> pdb=" O LYS C 219 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N LYS C 227 " --> pdb=" O GLU C 223 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N LYS C 230 " --> pdb=" O ARG C 226 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N GLY C 248 " --> pdb=" O ALA C 244 " (cutoff:3.500A) removed outlier: 3.866A pdb=" N LEU C 250 " --> pdb=" O GLN C 246 " (cutoff:3.500A) removed outlier: 4.157A pdb=" N TRP C 255 " --> pdb=" O ALA C 251 " (cutoff:3.500A) removed outlier: 4.439A pdb=" N TRP C 256 " --> pdb=" O ARG C 252 " (cutoff:3.500A) Processing helix chain 'C' and resid 262 through 284 removed outlier: 4.235A pdb=" N VAL C 266 " --> pdb=" O ILE C 262 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N ALA C 275 " --> pdb=" O THR C 271 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N PHE C 282 " --> pdb=" O MET C 278 " (cutoff:3.500A) Processing helix chain 'C' and resid 294 through 311 removed outlier: 3.682A pdb=" N LYS C 305 " --> pdb=" O LEU C 301 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N LYS C 309 " --> pdb=" O LYS C 305 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N SER C 310 " --> pdb=" O GLY C 306 " (cutoff:3.500A) Processing helix chain 'C' and resid 313 through 335 removed outlier: 3.799A pdb=" N ASN C 318 " --> pdb=" O LEU C 314 " (cutoff:3.500A) removed outlier: 4.067A pdb=" N ASP C 322 " --> pdb=" O ASN C 318 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N ALA C 323 " --> pdb=" O GLN C 319 " (cutoff:3.500A) removed outlier: 4.375A pdb=" N GLN C 326 " --> pdb=" O ASP C 322 " (cutoff:3.500A) removed outlier: 4.156A pdb=" N MET C 329 " --> pdb=" O ALA C 325 " (cutoff:3.500A) Processing helix chain 'D' and resid 65 through 96 removed outlier: 3.947A pdb=" N ARG D 69 " --> pdb=" O PHE D 65 " (cutoff:3.500A) removed outlier: 4.023A pdb=" N VAL D 70 " --> pdb=" O GLY D 66 " (cutoff:3.500A) removed outlier: 3.986A pdb=" N ILE D 75 " --> pdb=" O PHE D 71 " (cutoff:3.500A) Proline residue: D 76 - end of helix removed outlier: 3.643A pdb=" N SER D 85 " --> pdb=" O GLY D 81 " (cutoff:3.500A) removed outlier: 3.858A pdb=" N LYS D 86 " --> pdb=" O THR D 82 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N PHE D 88 " --> pdb=" O ILE D 84 " (cutoff:3.500A) removed outlier: 4.819A pdb=" N LEU D 91 " --> pdb=" O ASN D 87 " (cutoff:3.500A) removed outlier: 4.641A pdb=" N GLU D 94 " --> pdb=" O ALA D 90 " (cutoff:3.500A) removed outlier: 3.870A pdb=" N HIS D 95 " --> pdb=" O LEU D 91 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N ASP D 96 " --> pdb=" O LEU D 92 " (cutoff:3.500A) Processing helix chain 'A' and resid 107 through 118 removed outlier: 3.607A pdb=" N ARG A 113 " --> pdb=" O GLY A 109 " (cutoff:3.500A) Processing helix chain 'A' and resid 140 through 145 removed outlier: 3.601A pdb=" N LEU A 144 " --> pdb=" O GLY A 140 " (cutoff:3.500A) Processing helix chain 'A' and resid 171 through 174 removed outlier: 3.591A pdb=" N ALA A 174 " --> pdb=" O GLU A 171 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 171 through 174' Processing helix chain 'A' and resid 175 through 192 removed outlier: 3.827A pdb=" N THR A 181 " --> pdb=" O ASN A 177 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N LEU A 190 " --> pdb=" O LEU A 186 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N ILE A 192 " --> pdb=" O THR A 188 " (cutoff:3.500A) Processing helix chain 'A' and resid 192 through 215 removed outlier: 3.908A pdb=" N LEU A 197 " --> pdb=" O GLU A 193 " (cutoff:3.500A) removed outlier: 4.393A pdb=" N ASN A 198 " --> pdb=" O GLN A 194 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N GLU A 208 " --> pdb=" O ILE A 204 " (cutoff:3.500A) Processing helix chain 'A' and resid 217 through 226 removed outlier: 3.898A pdb=" N ARG A 221 " --> pdb=" O LEU A 217 " (cutoff:3.500A) Processing helix chain 'A' and resid 227 through 256 removed outlier: 3.634A pdb=" N THR A 232 " --> pdb=" O ALA A 228 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N PHE A 247 " --> pdb=" O MET A 243 " (cutoff:3.500A) removed outlier: 3.935A pdb=" N LEU A 250 " --> pdb=" O GLN A 246 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N ALA A 251 " --> pdb=" O PHE A 247 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N LEU A 253 " --> pdb=" O ILE A 249 " (cutoff:3.500A) Processing helix chain 'A' and resid 263 through 285 removed outlier: 3.699A pdb=" N THR A 267 " --> pdb=" O MET A 263 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N THR A 271 " --> pdb=" O THR A 267 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N TYR A 279 " --> pdb=" O ALA A 275 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N PHE A 282 " --> pdb=" O MET A 278 " (cutoff:3.500A) Processing helix chain 'A' and resid 291 through 310 removed outlier: 3.796A pdb=" N ARG A 295 " --> pdb=" O TYR A 291 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N ASP A 296 " --> pdb=" O PRO A 292 " (cutoff:3.500A) removed outlier: 4.139A pdb=" N ARG A 297 " --> pdb=" O GLU A 293 " (cutoff:3.500A) removed outlier: 4.309A pdb=" N LEU A 300 " --> pdb=" O ASP A 296 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N LYS A 308 " --> pdb=" O HIS A 304 " (cutoff:3.500A) Processing helix chain 'A' and resid 314 through 340 removed outlier: 3.653A pdb=" N ALA A 327 " --> pdb=" O ALA A 323 " (cutoff:3.500A) removed outlier: 4.338A pdb=" N ASP A 336 " --> pdb=" O LYS A 332 " (cutoff:3.500A) Proline residue: A 337 - end of helix Processing helix chain 'B' and resid 66 through 71 removed outlier: 3.657A pdb=" N PHE B 71 " --> pdb=" O LEU B 67 " (cutoff:3.500A) Processing helix chain 'B' and resid 73 through 96 removed outlier: 4.057A pdb=" N PHE B 77 " --> pdb=" O ILE B 73 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N LEU B 78 " --> pdb=" O VAL B 74 " (cutoff:3.500A) removed outlier: 4.145A pdb=" N GLU B 93 " --> pdb=" O ALA B 89 " (cutoff:3.500A) Processing helix chain 'L' and resid 107 through 119 removed outlier: 3.701A pdb=" N GLN L 116 " --> pdb=" O LEU L 112 " (cutoff:3.500A) Processing helix chain 'L' and resid 140 through 145 Processing helix chain 'I' and resid 107 through 117 removed outlier: 3.571A pdb=" N PHE I 111 " --> pdb=" O SER I 107 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N LEU I 115 " --> pdb=" O PHE I 111 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N GLN I 116 " --> pdb=" O LEU I 112 " (cutoff:3.500A) Processing helix chain 'I' and resid 140 through 144 Processing helix chain 'G' and resid 107 through 117 removed outlier: 3.549A pdb=" N PHE G 111 " --> pdb=" O SER G 107 " (cutoff:3.500A) Processing helix chain 'G' and resid 140 through 145 Processing helix chain 'G' and resid 179 through 189 Processing helix chain 'G' and resid 192 through 257 removed outlier: 4.001A pdb=" N LEU G 197 " --> pdb=" O GLU G 193 " (cutoff:3.500A) removed outlier: 3.881A pdb=" N ARG G 201 " --> pdb=" O LEU G 197 " (cutoff:3.500A) removed outlier: 4.269A pdb=" N GLU G 202 " --> pdb=" O ASN G 198 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N LYS G 211 " --> pdb=" O LEU G 207 " (cutoff:3.500A) removed outlier: 3.936A pdb=" N ALA G 215 " --> pdb=" O LYS G 211 " (cutoff:3.500A) Proline residue: G 216 - end of helix removed outlier: 4.196A pdb=" N VAL G 220 " --> pdb=" O PRO G 216 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N GLU G 223 " --> pdb=" O LYS G 219 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N VAL G 235 " --> pdb=" O ARG G 231 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N GLY G 238 " --> pdb=" O LEU G 234 " (cutoff:3.500A) removed outlier: 3.845A pdb=" N PHE G 247 " --> pdb=" O MET G 243 " (cutoff:3.500A) removed outlier: 3.933A pdb=" N GLY G 248 " --> pdb=" O ALA G 244 " (cutoff:3.500A) removed outlier: 4.173A pdb=" N LEU G 253 " --> pdb=" O ILE G 249 " (cutoff:3.500A) removed outlier: 3.993A pdb=" N THR G 254 " --> pdb=" O LEU G 250 " (cutoff:3.500A) removed outlier: 3.869A pdb=" N TRP G 255 " --> pdb=" O ALA G 251 " (cutoff:3.500A) Processing helix chain 'G' and resid 259 through 262 Processing helix chain 'G' and resid 263 through 286 removed outlier: 3.901A pdb=" N THR G 271 " --> pdb=" O THR G 267 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N MET G 278 " --> pdb=" O SER G 274 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N PHE G 282 " --> pdb=" O MET G 278 " (cutoff:3.500A) Processing helix chain 'G' and resid 290 through 305 removed outlier: 3.551A pdb=" N ARG G 295 " --> pdb=" O TYR G 291 " (cutoff:3.500A) removed outlier: 4.035A pdb=" N ASP G 296 " --> pdb=" O PRO G 292 " (cutoff:3.500A) removed outlier: 3.934A pdb=" N LEU G 300 " --> pdb=" O ASP G 296 " (cutoff:3.500A) Processing helix chain 'G' and resid 305 through 310 removed outlier: 3.673A pdb=" N LYS G 309 " --> pdb=" O LYS G 305 " (cutoff:3.500A) Processing helix chain 'G' and resid 313 through 334 removed outlier: 3.787A pdb=" N GLN G 319 " --> pdb=" O GLU G 315 " (cutoff:3.500A) removed outlier: 3.924A pdb=" N ASP G 322 " --> pdb=" O ASN G 318 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N ALA G 325 " --> pdb=" O LYS G 321 " (cutoff:3.500A) Processing helix chain 'H' and resid 65 through 75 removed outlier: 3.783A pdb=" N ARG H 69 " --> pdb=" O PHE H 65 " (cutoff:3.500A) removed outlier: 4.372A pdb=" N ILE H 73 " --> pdb=" O ARG H 69 " (cutoff:3.500A) removed outlier: 4.145A pdb=" N VAL H 74 " --> pdb=" O VAL H 70 " (cutoff:3.500A) removed outlier: 4.074A pdb=" N ILE H 75 " --> pdb=" O PHE H 71 " (cutoff:3.500A) Processing helix chain 'H' and resid 75 through 93 removed outlier: 3.661A pdb=" N GLY H 81 " --> pdb=" O PHE H 77 " (cutoff:3.500A) removed outlier: 4.015A pdb=" N ILE H 84 " --> pdb=" O VAL H 80 " (cutoff:3.500A) removed outlier: 4.152A pdb=" N SER H 85 " --> pdb=" O GLY H 81 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N LYS H 86 " --> pdb=" O THR H 82 " (cutoff:3.500A) removed outlier: 4.108A pdb=" N LEU H 91 " --> pdb=" O ASN H 87 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'J' and resid 76 through 80 Processing sheet with id=AA2, first strand: chain 'J' and resid 125 through 128 removed outlier: 3.610A pdb=" N PHE J 149 " --> pdb=" O VAL J 160 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'J' and resid 134 through 135 removed outlier: 6.427A pdb=" N ARG J 134 " --> pdb=" O GLN I 98 " (cutoff:3.500A) removed outlier: 3.971A pdb=" N GLU I 95 " --> pdb=" O LEU I 90 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N LEU I 90 " --> pdb=" O GLU I 95 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N VAL I 78 " --> pdb=" O VAL I 85 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N THR I 76 " --> pdb=" O SER I 87 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'K' and resid 76 through 80 Processing sheet with id=AA5, first strand: chain 'K' and resid 126 through 128 removed outlier: 3.674A pdb=" N PHE K 149 " --> pdb=" O VAL K 160 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N VAL K 160 " --> pdb=" O PHE K 149 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'E' and resid 76 through 80 removed outlier: 3.910A pdb=" N ARG G 134 " --> pdb=" O ARG E 96 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'E' and resid 125 through 127 Processing sheet with id=AA8, first strand: chain 'E' and resid 134 through 135 removed outlier: 6.569A pdb=" N ARG E 134 " --> pdb=" O GLN C 98 " (cutoff:3.500A) removed outlier: 7.988A pdb=" N THR C 100 " --> pdb=" O ARG E 134 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 125 through 128 removed outlier: 3.578A pdb=" N ILE C 153 " --> pdb=" O LEU C 156 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 134 through 135 removed outlier: 3.784A pdb=" N THR A 76 " --> pdb=" O SER A 87 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 126 through 128 Processing sheet with id=AB3, first strand: chain 'L' and resid 78 through 80 removed outlier: 3.533A pdb=" N VAL L 78 " --> pdb=" O VAL L 85 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'L' and resid 87 through 90 removed outlier: 3.664A pdb=" N GLU L 95 " --> pdb=" O LEU L 90 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'L' and resid 125 through 128 Processing sheet with id=AB6, first strand: chain 'I' and resid 126 through 128 removed outlier: 3.556A pdb=" N ALA I 126 " --> pdb=" O VAL I 152 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'G' and resid 86 through 88 removed outlier: 3.707A pdb=" N ILE G 86 " --> pdb=" O PHE G 99 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'G' and resid 125 through 128 644 hydrogen bonds defined for protein. 1830 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: 3.52 Time building geometry restraints manager: 4.84 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: 4172 1.34 - 1.46: 2547 1.46 - 1.58: 6639 1.58 - 1.70: 0 1.70 - 1.82: 68 Bond restraints: 13426 Sorted by residual: bond pdb=" N ILE J 153 " pdb=" CA ILE J 153 " ideal model delta sigma weight residual 1.459 1.494 -0.035 1.29e-02 6.01e+03 7.22e+00 bond pdb=" N ILE C 153 " pdb=" CA ILE C 153 " ideal model delta sigma weight residual 1.459 1.492 -0.033 1.24e-02 6.50e+03 7.09e+00 bond pdb=" CA PRO C 162 " pdb=" C PRO C 162 " ideal model delta sigma weight residual 1.517 1.539 -0.022 9.30e-03 1.16e+04 5.78e+00 bond pdb=" N LEU G 101 " pdb=" CA LEU G 101 " ideal model delta sigma weight residual 1.457 1.485 -0.029 1.24e-02 6.50e+03 5.39e+00 bond pdb=" N ILE E 153 " pdb=" CA ILE E 153 " ideal model delta sigma weight residual 1.460 1.492 -0.033 1.42e-02 4.96e+03 5.25e+00 ... (remaining 13421 not shown) Histogram of bond angle deviations from ideal: 98.54 - 105.66: 313 105.66 - 112.78: 6904 112.78 - 119.89: 5058 119.89 - 127.01: 5769 127.01 - 134.13: 146 Bond angle restraints: 18190 Sorted by residual: angle pdb=" C ARG C 161 " pdb=" N PRO C 162 " pdb=" CA PRO C 162 " ideal model delta sigma weight residual 120.38 129.92 -9.54 1.03e+00 9.43e-01 8.58e+01 angle pdb=" N ASP J 155 " pdb=" CA ASP J 155 " pdb=" C ASP J 155 " ideal model delta sigma weight residual 113.16 123.39 -10.23 1.24e+00 6.50e-01 6.81e+01 angle pdb=" N ILE B 49 " pdb=" CA ILE B 49 " pdb=" C ILE B 49 " ideal model delta sigma weight residual 113.71 107.23 6.48 9.50e-01 1.11e+00 4.65e+01 angle pdb=" N ILE H 49 " pdb=" CA ILE H 49 " pdb=" C ILE H 49 " ideal model delta sigma weight residual 112.96 106.70 6.26 1.00e+00 1.00e+00 3.92e+01 angle pdb=" N ASP C 155 " pdb=" CA ASP C 155 " pdb=" C ASP C 155 " ideal model delta sigma weight residual 112.90 119.73 -6.83 1.31e+00 5.83e-01 2.72e+01 ... (remaining 18185 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.25: 7617 15.25 - 30.51: 434 30.51 - 45.76: 126 45.76 - 61.02: 6 61.02 - 76.27: 11 Dihedral angle restraints: 8194 sinusoidal: 3419 harmonic: 4775 Sorted by residual: dihedral pdb=" CA MET B 63 " pdb=" C MET B 63 " pdb=" N SER B 64 " pdb=" CA SER B 64 " ideal model delta harmonic sigma weight residual 180.00 150.54 29.46 0 5.00e+00 4.00e-02 3.47e+01 dihedral pdb=" CA ILE G 153 " pdb=" C ILE G 153 " pdb=" N ASN G 154 " pdb=" CA ASN G 154 " ideal model delta harmonic sigma weight residual 180.00 -151.81 -28.19 0 5.00e+00 4.00e-02 3.18e+01 dihedral pdb=" CA LEU C 253 " pdb=" C LEU C 253 " pdb=" N THR C 254 " pdb=" CA THR C 254 " ideal model delta harmonic sigma weight residual 180.00 -152.60 -27.40 0 5.00e+00 4.00e-02 3.00e+01 ... (remaining 8191 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.062: 1505 0.062 - 0.125: 465 0.125 - 0.187: 97 0.187 - 0.249: 23 0.249 - 0.311: 3 Chirality restraints: 2093 Sorted by residual: chirality pdb=" CA ASP J 155 " pdb=" N ASP J 155 " pdb=" C ASP J 155 " pdb=" CB ASP J 155 " both_signs ideal model delta sigma weight residual False 2.51 2.20 0.31 2.00e-01 2.50e+01 2.42e+00 chirality pdb=" CB ILE E 122 " pdb=" CA ILE E 122 " pdb=" CG1 ILE E 122 " pdb=" CG2 ILE E 122 " both_signs ideal model delta sigma weight residual False 2.64 2.37 0.28 2.00e-01 2.50e+01 1.90e+00 chirality pdb=" CB THR D 82 " pdb=" CA THR D 82 " pdb=" OG1 THR D 82 " pdb=" CG2 THR D 82 " both_signs ideal model delta sigma weight residual False 2.55 2.30 0.25 2.00e-01 2.50e+01 1.61e+00 ... (remaining 2090 not shown) Planarity restraints: 2309 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ARG C 161 " -0.015 2.00e-02 2.50e+03 3.05e-02 9.31e+00 pdb=" C ARG C 161 " 0.053 2.00e-02 2.50e+03 pdb=" O ARG C 161 " -0.020 2.00e-02 2.50e+03 pdb=" N PRO C 162 " -0.018 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C LYS G 102 " 0.048 5.00e-02 4.00e+02 7.23e-02 8.37e+00 pdb=" N PRO G 103 " -0.125 5.00e-02 4.00e+02 pdb=" CA PRO G 103 " 0.038 5.00e-02 4.00e+02 pdb=" CD PRO G 103 " 0.040 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU J 90 " 0.042 5.00e-02 4.00e+02 6.38e-02 6.51e+00 pdb=" N PRO J 91 " -0.110 5.00e-02 4.00e+02 pdb=" CA PRO J 91 " 0.033 5.00e-02 4.00e+02 pdb=" CD PRO J 91 " 0.035 5.00e-02 4.00e+02 ... (remaining 2306 not shown) Histogram of nonbonded interaction distances: 2.31 - 2.83: 3811 2.83 - 3.34: 11556 3.34 - 3.86: 20186 3.86 - 4.38: 22074 4.38 - 4.90: 38001 Nonbonded interactions: 95628 Sorted by model distance: nonbonded pdb=" O GLN E 185 " pdb=" OG1 THR E 189 " model vdw 2.307 2.440 nonbonded pdb=" NH1 ARG E 221 " pdb=" OH TYR E 317 " model vdw 2.378 2.520 nonbonded pdb=" OG SER E 138 " pdb=" NE2 GLN C 114 " model vdw 2.387 2.520 nonbonded pdb=" O TYR G 281 " pdb=" OG1 THR G 285 " model vdw 2.393 2.440 nonbonded pdb=" OE1 GLN C 196 " pdb=" NE2 GLN G 184 " model vdw 2.398 2.520 ... (remaining 95623 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'A' and (resid 75 through 164 or resid 177 through 336)) selection = (chain 'C' and (resid 75 through 164 or resid 177 through 336)) selection = (chain 'E' and (resid 75 through 164 or resid 177 through 336)) selection = (chain 'G' and resid 75 through 336) } ncs_group { reference = (chain 'B' and resid 48 through 95) selection = (chain 'D' and resid 48 through 95) selection = (chain 'F' and resid 48 through 95) selection = chain 'H' } ncs_group { reference = chain 'I' selection = chain 'J' selection = chain 'K' selection = chain 'L' } 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: 1.110 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: 6.350 Check model and map are aligned: 0.200 Set scattering table: 0.130 Process input model: 33.910 Find NCS groups from input model: 0.920 Set up NCS constraints: 0.070 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.980 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 45.690 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7799 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 : 0.007 0.071 13426 Z= 0.416 Angle : 1.128 12.605 18190 Z= 0.614 Chirality : 0.064 0.311 2093 Planarity : 0.007 0.072 2309 Dihedral : 11.132 76.271 5098 Min Nonbonded Distance : 2.307 Molprobity Statistics. All-atom Clashscore : 4.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.09 % Favored : 93.91 % Rotamer: Outliers : 0.41 % Allowed : 6.26 % Favored : 93.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.21 (0.17), residues: 1594 helix: -2.99 (0.12), residues: 840 sheet: -0.94 (0.37), residues: 175 loop : -2.80 (0.23), residues: 579 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.003 TRP E 255 HIS 0.008 0.002 HIS H 95 PHE 0.030 0.003 PHE I 149 TYR 0.027 0.002 TYR G 79 ARG 0.013 0.001 ARG C 297 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3188 Ramachandran restraints generated. 1594 Oldfield, 0 Emsley, 1594 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3188 Ramachandran restraints generated. 1594 Oldfield, 0 Emsley, 1594 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 341 residues out of total 1454 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 335 time to evaluate : 1.616 Fit side-chains REVERT: J 105 SER cc_start: 0.6994 (p) cc_final: 0.6772 (p) REVERT: J 133 VAL cc_start: 0.8541 (m) cc_final: 0.8329 (m) REVERT: E 104 ILE cc_start: 0.7994 (pt) cc_final: 0.7638 (mp) REVERT: E 243 MET cc_start: 0.8082 (tpt) cc_final: 0.7788 (tpp) REVERT: C 148 ASP cc_start: 0.8022 (p0) cc_final: 0.7746 (m-30) REVERT: A 161 ARG cc_start: 0.7858 (ppp80) cc_final: 0.7604 (mtt90) REVERT: A 165 ARG cc_start: 0.7133 (tpt170) cc_final: 0.6830 (mtm-85) REVERT: A 177 ASN cc_start: 0.8106 (t160) cc_final: 0.7588 (p0) REVERT: A 278 MET cc_start: 0.8349 (mtt) cc_final: 0.8116 (mtm) REVERT: B 83 LEU cc_start: 0.8030 (tp) cc_final: 0.7695 (mp) REVERT: L 115 LEU cc_start: 0.6485 (mt) cc_final: 0.6272 (mp) REVERT: I 120 ARG cc_start: 0.7935 (pmm150) cc_final: 0.7539 (mtt90) outliers start: 6 outliers final: 1 residues processed: 340 average time/residue: 0.3278 time to fit residues: 147.9442 Evaluate side-chains 173 residues out of total 1454 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 172 time to evaluate : 1.415 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 77 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 157 random chunks: chunk 132 optimal weight: 8.9990 chunk 118 optimal weight: 3.9990 chunk 66 optimal weight: 10.0000 chunk 40 optimal weight: 0.9980 chunk 80 optimal weight: 0.8980 chunk 63 optimal weight: 8.9990 chunk 123 optimal weight: 5.9990 chunk 47 optimal weight: 1.9990 chunk 74 optimal weight: 0.8980 chunk 91 optimal weight: 0.9980 chunk 142 optimal weight: 8.9990 overall best weight: 1.1582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: K 116 GLN E 184 GLN F 95 HIS C 81 ASN C 114 GLN C 246 GLN A 98 GLN A 177 ASN ** I 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 184 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 196 GLN H 95 HIS Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7822 moved from start: 0.2247 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 13426 Z= 0.183 Angle : 0.653 8.302 18190 Z= 0.334 Chirality : 0.044 0.168 2093 Planarity : 0.005 0.059 2309 Dihedral : 5.567 24.566 1812 Min Nonbonded Distance : 2.180 Molprobity Statistics. All-atom Clashscore : 8.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.45 % Favored : 95.55 % Rotamer: Outliers : 2.68 % Allowed : 13.34 % Favored : 83.98 % 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: -2.39 (0.20), residues: 1594 helix: -1.27 (0.16), residues: 847 sheet: -0.39 (0.39), residues: 165 loop : -2.25 (0.25), residues: 582 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP E 255 HIS 0.006 0.001 HIS H 95 PHE 0.023 0.002 PHE L 111 TYR 0.018 0.001 TYR K 79 ARG 0.006 0.000 ARG A 221 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3188 Ramachandran restraints generated. 1594 Oldfield, 0 Emsley, 1594 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3188 Ramachandran restraints generated. 1594 Oldfield, 0 Emsley, 1594 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 237 residues out of total 1454 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 198 time to evaluate : 1.520 Fit side-chains revert: symmetry clash REVERT: J 164 LYS cc_start: 0.2203 (mttp) cc_final: 0.1448 (mtpt) REVERT: E 104 ILE cc_start: 0.7970 (pt) cc_final: 0.7647 (mp) REVERT: C 148 ASP cc_start: 0.8011 (p0) cc_final: 0.7804 (p0) REVERT: C 164 LYS cc_start: 0.7656 (pmtt) cc_final: 0.6960 (ptmm) REVERT: A 177 ASN cc_start: 0.7947 (t0) cc_final: 0.7561 (p0) REVERT: B 83 LEU cc_start: 0.8105 (tp) cc_final: 0.7837 (mp) REVERT: L 122 ILE cc_start: 0.4698 (OUTLIER) cc_final: 0.4389 (tt) REVERT: L 158 TYR cc_start: 0.5650 (m-80) cc_final: 0.5405 (m-80) REVERT: I 120 ARG cc_start: 0.7818 (pmm150) cc_final: 0.7399 (mtt90) outliers start: 39 outliers final: 20 residues processed: 226 average time/residue: 0.2680 time to fit residues: 86.6533 Evaluate side-chains 176 residues out of total 1454 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 155 time to evaluate : 1.566 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain J residue 101 LEU Chi-restraints excluded: chain J residue 133 VAL Chi-restraints excluded: chain E residue 105 SER Chi-restraints excluded: chain E residue 142 ASP Chi-restraints excluded: chain F residue 67 LEU Chi-restraints excluded: chain C residue 77 VAL Chi-restraints excluded: chain C residue 138 SER Chi-restraints excluded: chain C residue 144 LEU Chi-restraints excluded: chain C residue 160 VAL Chi-restraints excluded: chain D residue 61 VAL Chi-restraints excluded: chain D residue 67 LEU Chi-restraints excluded: chain D residue 70 VAL Chi-restraints excluded: chain D residue 71 PHE Chi-restraints excluded: chain A residue 133 VAL Chi-restraints excluded: chain A residue 146 LEU Chi-restraints excluded: chain B residue 87 ASN Chi-restraints excluded: chain L residue 122 ILE Chi-restraints excluded: chain L residue 153 ILE Chi-restraints excluded: chain G residue 81 ASN Chi-restraints excluded: chain G residue 138 SER Chi-restraints excluded: chain G residue 290 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 157 random chunks: chunk 79 optimal weight: 8.9990 chunk 44 optimal weight: 6.9990 chunk 118 optimal weight: 8.9990 chunk 97 optimal weight: 7.9990 chunk 39 optimal weight: 5.9990 chunk 142 optimal weight: 10.0000 chunk 154 optimal weight: 1.9990 chunk 127 optimal weight: 2.9990 chunk 141 optimal weight: 2.9990 chunk 48 optimal weight: 7.9990 chunk 114 optimal weight: 9.9990 overall best weight: 4.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: J 116 GLN E 159 HIS E 194 GLN A 114 GLN ** I 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 116 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 184 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7962 moved from start: 0.2914 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.069 13426 Z= 0.365 Angle : 0.744 10.291 18190 Z= 0.374 Chirality : 0.048 0.213 2093 Planarity : 0.006 0.084 2309 Dihedral : 5.653 25.005 1812 Min Nonbonded Distance : 2.083 Molprobity Statistics. All-atom Clashscore : 9.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.71 % Favored : 93.29 % Rotamer: Outliers : 5.36 % Allowed : 13.96 % Favored : 80.67 % 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: -1.79 (0.21), residues: 1594 helix: -0.69 (0.18), residues: 849 sheet: -0.35 (0.39), residues: 176 loop : -2.09 (0.26), residues: 569 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP E 255 HIS 0.007 0.002 HIS E 304 PHE 0.018 0.002 PHE L 111 TYR 0.020 0.002 TYR C 258 ARG 0.007 0.001 ARG J 161 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3188 Ramachandran restraints generated. 1594 Oldfield, 0 Emsley, 1594 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3188 Ramachandran restraints generated. 1594 Oldfield, 0 Emsley, 1594 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 235 residues out of total 1454 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 78 poor density : 157 time to evaluate : 1.461 Fit side-chains revert: symmetry clash REVERT: E 104 ILE cc_start: 0.8099 (pt) cc_final: 0.7741 (mp) REVERT: F 91 LEU cc_start: 0.7350 (OUTLIER) cc_final: 0.7109 (pp) REVERT: C 164 LYS cc_start: 0.7829 (pmtt) cc_final: 0.6990 (ptmm) REVERT: C 176 LEU cc_start: 0.8324 (OUTLIER) cc_final: 0.8118 (mt) REVERT: A 177 ASN cc_start: 0.8028 (t0) cc_final: 0.7616 (p0) REVERT: A 242 TYR cc_start: 0.7895 (t80) cc_final: 0.7655 (t80) REVERT: A 263 MET cc_start: 0.7129 (mmm) cc_final: 0.6890 (tpp) REVERT: B 83 LEU cc_start: 0.8161 (tp) cc_final: 0.7933 (mp) REVERT: L 158 TYR cc_start: 0.5631 (m-80) cc_final: 0.5350 (m-80) REVERT: I 120 ARG cc_start: 0.7967 (pmm150) cc_final: 0.7430 (mtt90) REVERT: G 120 ARG cc_start: 0.7580 (mmt180) cc_final: 0.7348 (mmp80) outliers start: 78 outliers final: 43 residues processed: 211 average time/residue: 0.2517 time to fit residues: 78.3728 Evaluate side-chains 189 residues out of total 1454 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 144 time to evaluate : 1.613 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain J residue 101 LEU Chi-restraints excluded: chain J residue 105 SER Chi-restraints excluded: chain J residue 133 VAL Chi-restraints excluded: chain J residue 142 ASP Chi-restraints excluded: chain K residue 104 ILE Chi-restraints excluded: chain K residue 129 SER Chi-restraints excluded: chain K residue 160 VAL Chi-restraints excluded: chain E residue 105 SER Chi-restraints excluded: chain E residue 117 GLU Chi-restraints excluded: chain E residue 142 ASP Chi-restraints excluded: chain E residue 143 LEU Chi-restraints excluded: chain E residue 300 LEU Chi-restraints excluded: chain F residue 48 VAL Chi-restraints excluded: chain F residue 50 VAL Chi-restraints excluded: chain F residue 61 VAL Chi-restraints excluded: chain F residue 67 LEU Chi-restraints excluded: chain F residue 91 LEU Chi-restraints excluded: chain F residue 94 GLU Chi-restraints excluded: chain C residue 105 SER Chi-restraints excluded: chain C residue 138 SER Chi-restraints excluded: chain C residue 144 LEU Chi-restraints excluded: chain C residue 160 VAL Chi-restraints excluded: chain C residue 176 LEU Chi-restraints excluded: chain C residue 199 LYS Chi-restraints excluded: chain C residue 225 SER Chi-restraints excluded: chain D residue 51 THR Chi-restraints excluded: chain D residue 61 VAL Chi-restraints excluded: chain D residue 64 SER Chi-restraints excluded: chain D residue 67 LEU Chi-restraints excluded: chain D residue 71 PHE Chi-restraints excluded: chain A residue 110 VAL Chi-restraints excluded: chain A residue 133 VAL Chi-restraints excluded: chain A residue 145 LEU Chi-restraints excluded: chain A residue 160 VAL Chi-restraints excluded: chain A residue 290 VAL Chi-restraints excluded: chain B residue 87 ASN Chi-restraints excluded: chain L residue 90 LEU Chi-restraints excluded: chain I residue 138 SER Chi-restraints excluded: chain G residue 81 ASN Chi-restraints excluded: chain G residue 138 SER Chi-restraints excluded: chain G residue 178 ASP Chi-restraints excluded: chain G residue 290 VAL Chi-restraints excluded: chain H residue 78 LEU Chi-restraints excluded: chain H residue 82 THR Chi-restraints excluded: chain H residue 84 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 157 random chunks: chunk 141 optimal weight: 0.9990 chunk 107 optimal weight: 9.9990 chunk 74 optimal weight: 8.9990 chunk 15 optimal weight: 6.9990 chunk 68 optimal weight: 1.9990 chunk 95 optimal weight: 3.9990 chunk 143 optimal weight: 6.9990 chunk 151 optimal weight: 5.9990 chunk 135 optimal weight: 9.9990 chunk 40 optimal weight: 1.9990 chunk 126 optimal weight: 4.9990 overall best weight: 2.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 114 GLN ** I 116 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 184 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7931 moved from start: 0.3131 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 13426 Z= 0.253 Angle : 0.661 8.904 18190 Z= 0.329 Chirality : 0.046 0.283 2093 Planarity : 0.005 0.060 2309 Dihedral : 5.254 23.503 1811 Min Nonbonded Distance : 2.139 Molprobity Statistics. All-atom Clashscore : 8.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.02 % Favored : 93.98 % Rotamer: Outliers : 4.68 % Allowed : 16.44 % Favored : 78.89 % 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: -1.28 (0.21), residues: 1594 helix: -0.23 (0.18), residues: 850 sheet: -0.05 (0.40), residues: 176 loop : -1.97 (0.26), residues: 568 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP C 256 HIS 0.005 0.001 HIS C 159 PHE 0.021 0.002 PHE L 111 TYR 0.016 0.001 TYR C 268 ARG 0.007 0.000 ARG J 161 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3188 Ramachandran restraints generated. 1594 Oldfield, 0 Emsley, 1594 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3188 Ramachandran restraints generated. 1594 Oldfield, 0 Emsley, 1594 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 213 residues out of total 1454 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 68 poor density : 145 time to evaluate : 1.690 Fit side-chains revert: symmetry clash REVERT: K 94 ARG cc_start: 0.7278 (OUTLIER) cc_final: 0.5921 (mtm180) REVERT: E 104 ILE cc_start: 0.8077 (pt) cc_final: 0.7728 (mp) REVERT: E 284 MET cc_start: 0.7458 (tpp) cc_final: 0.6994 (mtt) REVERT: F 91 LEU cc_start: 0.7323 (OUTLIER) cc_final: 0.7075 (pp) REVERT: C 164 LYS cc_start: 0.7804 (pmtt) cc_final: 0.7012 (ptmm) REVERT: C 176 LEU cc_start: 0.8328 (OUTLIER) cc_final: 0.8119 (mt) REVERT: A 177 ASN cc_start: 0.7943 (t0) cc_final: 0.7535 (p0) REVERT: B 83 LEU cc_start: 0.8168 (tp) cc_final: 0.7924 (mp) REVERT: I 120 ARG cc_start: 0.7944 (pmm150) cc_final: 0.7389 (mtt90) REVERT: G 120 ARG cc_start: 0.7575 (mmt180) cc_final: 0.7351 (mmp80) REVERT: G 153 ILE cc_start: 0.5806 (OUTLIER) cc_final: 0.5551 (mt) outliers start: 68 outliers final: 48 residues processed: 193 average time/residue: 0.2387 time to fit residues: 67.7784 Evaluate side-chains 193 residues out of total 1454 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 141 time to evaluate : 1.584 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain J residue 88 VAL Chi-restraints excluded: chain J residue 101 LEU Chi-restraints excluded: chain J residue 105 SER Chi-restraints excluded: chain J residue 110 VAL Chi-restraints excluded: chain J residue 133 VAL Chi-restraints excluded: chain J residue 142 ASP Chi-restraints excluded: chain K residue 94 ARG Chi-restraints excluded: chain K residue 131 ASP Chi-restraints excluded: chain K residue 160 VAL Chi-restraints excluded: chain E residue 105 SER Chi-restraints excluded: chain E residue 142 ASP Chi-restraints excluded: chain E residue 300 LEU Chi-restraints excluded: chain E residue 331 LEU Chi-restraints excluded: chain F residue 48 VAL Chi-restraints excluded: chain F residue 50 VAL Chi-restraints excluded: chain F residue 61 VAL Chi-restraints excluded: chain F residue 67 LEU Chi-restraints excluded: chain F residue 72 SER Chi-restraints excluded: chain F residue 91 LEU Chi-restraints excluded: chain F residue 94 GLU Chi-restraints excluded: chain C residue 105 SER Chi-restraints excluded: chain C residue 125 VAL Chi-restraints excluded: chain C residue 133 VAL Chi-restraints excluded: chain C residue 142 ASP Chi-restraints excluded: chain C residue 144 LEU Chi-restraints excluded: chain C residue 159 HIS Chi-restraints excluded: chain C residue 160 VAL Chi-restraints excluded: chain C residue 176 LEU Chi-restraints excluded: chain C residue 225 SER Chi-restraints excluded: chain C residue 255 TRP Chi-restraints excluded: chain D residue 51 THR Chi-restraints excluded: chain D residue 61 VAL Chi-restraints excluded: chain D residue 67 LEU Chi-restraints excluded: chain D residue 71 PHE Chi-restraints excluded: chain D residue 82 THR Chi-restraints excluded: chain A residue 110 VAL Chi-restraints excluded: chain A residue 133 VAL Chi-restraints excluded: chain A residue 146 LEU Chi-restraints excluded: chain A residue 160 VAL Chi-restraints excluded: chain B residue 87 ASN Chi-restraints excluded: chain L residue 90 LEU Chi-restraints excluded: chain L residue 160 VAL Chi-restraints excluded: chain I residue 138 SER Chi-restraints excluded: chain G residue 81 ASN Chi-restraints excluded: chain G residue 138 SER Chi-restraints excluded: chain G residue 153 ILE Chi-restraints excluded: chain G residue 192 ILE Chi-restraints excluded: chain G residue 284 MET Chi-restraints excluded: chain H residue 70 VAL Chi-restraints excluded: chain H residue 80 VAL Chi-restraints excluded: chain H residue 82 THR Chi-restraints excluded: chain H residue 84 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 157 random chunks: chunk 86 optimal weight: 0.2980 chunk 2 optimal weight: 1.9990 chunk 112 optimal weight: 5.9990 chunk 62 optimal weight: 7.9990 chunk 129 optimal weight: 2.9990 chunk 104 optimal weight: 7.9990 chunk 0 optimal weight: 10.0000 chunk 77 optimal weight: 0.4980 chunk 136 optimal weight: 0.7980 chunk 38 optimal weight: 8.9990 chunk 51 optimal weight: 6.9990 overall best weight: 1.3184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** I 116 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 184 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7873 moved from start: 0.3320 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 13426 Z= 0.169 Angle : 0.599 7.583 18190 Z= 0.297 Chirality : 0.044 0.279 2093 Planarity : 0.004 0.063 2309 Dihedral : 4.805 23.072 1811 Min Nonbonded Distance : 2.180 Molprobity Statistics. All-atom Clashscore : 7.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.65 % Favored : 94.35 % Rotamer: Outliers : 4.26 % Allowed : 17.68 % Favored : 78.06 % 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: -0.78 (0.22), residues: 1594 helix: 0.25 (0.18), residues: 848 sheet: 0.04 (0.41), residues: 166 loop : -1.77 (0.26), residues: 580 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP C 256 HIS 0.004 0.001 HIS C 159 PHE 0.024 0.001 PHE L 111 TYR 0.017 0.001 TYR A 242 ARG 0.003 0.000 ARG C 297 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3188 Ramachandran restraints generated. 1594 Oldfield, 0 Emsley, 1594 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3188 Ramachandran restraints generated. 1594 Oldfield, 0 Emsley, 1594 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 215 residues out of total 1454 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 62 poor density : 153 time to evaluate : 1.708 Fit side-chains revert: symmetry clash REVERT: J 118 GLU cc_start: 0.7918 (tp30) cc_final: 0.7686 (tp30) REVERT: K 102 LYS cc_start: 0.7571 (mptt) cc_final: 0.6535 (mptt) REVERT: E 104 ILE cc_start: 0.8061 (pt) cc_final: 0.7709 (mp) REVERT: E 284 MET cc_start: 0.7444 (tpp) cc_final: 0.7024 (mtt) REVERT: F 91 LEU cc_start: 0.7393 (tt) cc_final: 0.7095 (pp) REVERT: C 164 LYS cc_start: 0.7701 (OUTLIER) cc_final: 0.7000 (ptmm) REVERT: C 176 LEU cc_start: 0.8288 (OUTLIER) cc_final: 0.8082 (mt) REVERT: C 278 MET cc_start: 0.7805 (mtp) cc_final: 0.7570 (mtp) REVERT: A 177 ASN cc_start: 0.7849 (t0) cc_final: 0.7434 (p0) REVERT: B 83 LEU cc_start: 0.8128 (tp) cc_final: 0.7904 (mp) REVERT: I 120 ARG cc_start: 0.7903 (pmm150) cc_final: 0.7314 (mtt90) REVERT: G 153 ILE cc_start: 0.5736 (OUTLIER) cc_final: 0.5476 (mt) outliers start: 62 outliers final: 38 residues processed: 197 average time/residue: 0.2607 time to fit residues: 74.4782 Evaluate side-chains 184 residues out of total 1454 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 143 time to evaluate : 1.577 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain J residue 88 VAL Chi-restraints excluded: chain J residue 101 LEU Chi-restraints excluded: chain J residue 133 VAL Chi-restraints excluded: chain K residue 160 VAL Chi-restraints excluded: chain E residue 105 SER Chi-restraints excluded: chain E residue 142 ASP Chi-restraints excluded: chain E residue 331 LEU Chi-restraints excluded: chain F residue 48 VAL Chi-restraints excluded: chain F residue 61 VAL Chi-restraints excluded: chain F residue 67 LEU Chi-restraints excluded: chain F residue 72 SER Chi-restraints excluded: chain F residue 94 GLU Chi-restraints excluded: chain C residue 105 SER Chi-restraints excluded: chain C residue 144 LEU Chi-restraints excluded: chain C residue 159 HIS Chi-restraints excluded: chain C residue 164 LYS Chi-restraints excluded: chain C residue 176 LEU Chi-restraints excluded: chain C residue 225 SER Chi-restraints excluded: chain C residue 255 TRP Chi-restraints excluded: chain C residue 338 LEU Chi-restraints excluded: chain D residue 51 THR Chi-restraints excluded: chain D residue 61 VAL Chi-restraints excluded: chain D residue 71 PHE Chi-restraints excluded: chain D residue 82 THR Chi-restraints excluded: chain A residue 110 VAL Chi-restraints excluded: chain A residue 133 VAL Chi-restraints excluded: chain A residue 160 VAL Chi-restraints excluded: chain A residue 167 LEU Chi-restraints excluded: chain A residue 210 LEU Chi-restraints excluded: chain L residue 90 LEU Chi-restraints excluded: chain L residue 160 VAL Chi-restraints excluded: chain I residue 138 SER Chi-restraints excluded: chain I residue 157 THR Chi-restraints excluded: chain G residue 81 ASN Chi-restraints excluded: chain G residue 138 SER Chi-restraints excluded: chain G residue 153 ILE Chi-restraints excluded: chain G residue 178 ASP Chi-restraints excluded: chain G residue 192 ILE Chi-restraints excluded: chain G residue 284 MET Chi-restraints excluded: chain H residue 70 VAL Chi-restraints excluded: chain H residue 84 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 157 random chunks: chunk 136 optimal weight: 1.9990 chunk 29 optimal weight: 7.9990 chunk 89 optimal weight: 0.9980 chunk 37 optimal weight: 5.9990 chunk 151 optimal weight: 5.9990 chunk 126 optimal weight: 1.9990 chunk 70 optimal weight: 0.7980 chunk 12 optimal weight: 8.9990 chunk 50 optimal weight: 2.9990 chunk 79 optimal weight: 7.9990 chunk 146 optimal weight: 6.9990 overall best weight: 1.7586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 172 ASN ** I 116 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 184 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7884 moved from start: 0.3473 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 13426 Z= 0.194 Angle : 0.605 8.233 18190 Z= 0.301 Chirality : 0.044 0.263 2093 Planarity : 0.004 0.064 2309 Dihedral : 4.680 22.198 1811 Min Nonbonded Distance : 2.137 Molprobity Statistics. All-atom Clashscore : 7.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.58 % Favored : 94.42 % Rotamer: Outliers : 3.85 % Allowed : 18.43 % Favored : 77.72 % 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: -0.54 (0.22), residues: 1594 helix: 0.47 (0.19), residues: 845 sheet: 0.17 (0.41), residues: 166 loop : -1.71 (0.26), residues: 583 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP C 256 HIS 0.005 0.001 HIS C 159 PHE 0.021 0.001 PHE L 149 TYR 0.012 0.001 TYR C 268 ARG 0.005 0.000 ARG G 201 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3188 Ramachandran restraints generated. 1594 Oldfield, 0 Emsley, 1594 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3188 Ramachandran restraints generated. 1594 Oldfield, 0 Emsley, 1594 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 208 residues out of total 1454 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 56 poor density : 152 time to evaluate : 2.165 Fit side-chains REVERT: J 118 GLU cc_start: 0.7988 (tp30) cc_final: 0.7720 (tp30) REVERT: E 104 ILE cc_start: 0.8063 (pt) cc_final: 0.7715 (mp) REVERT: E 284 MET cc_start: 0.7516 (tpp) cc_final: 0.7028 (mtt) REVERT: F 91 LEU cc_start: 0.7397 (tt) cc_final: 0.7061 (pp) REVERT: C 164 LYS cc_start: 0.7679 (pmtt) cc_final: 0.6953 (ptmm) REVERT: C 176 LEU cc_start: 0.8270 (OUTLIER) cc_final: 0.8068 (mt) REVERT: A 177 ASN cc_start: 0.7828 (t0) cc_final: 0.7414 (p0) REVERT: B 83 LEU cc_start: 0.8143 (tp) cc_final: 0.7822 (mp) REVERT: L 158 TYR cc_start: 0.5724 (m-80) cc_final: 0.5459 (m-80) REVERT: I 120 ARG cc_start: 0.7915 (pmm150) cc_final: 0.7308 (mtt90) REVERT: G 153 ILE cc_start: 0.5799 (OUTLIER) cc_final: 0.5553 (mt) outliers start: 56 outliers final: 46 residues processed: 193 average time/residue: 0.2394 time to fit residues: 68.7008 Evaluate side-chains 193 residues out of total 1454 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 145 time to evaluate : 1.595 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain J residue 88 VAL Chi-restraints excluded: chain J residue 101 LEU Chi-restraints excluded: chain J residue 133 VAL Chi-restraints excluded: chain J residue 142 ASP Chi-restraints excluded: chain K residue 131 ASP Chi-restraints excluded: chain K residue 138 SER Chi-restraints excluded: chain K residue 160 VAL Chi-restraints excluded: chain E residue 105 SER Chi-restraints excluded: chain E residue 142 ASP Chi-restraints excluded: chain E residue 258 TYR Chi-restraints excluded: chain E residue 312 PHE Chi-restraints excluded: chain E residue 331 LEU Chi-restraints excluded: chain F residue 48 VAL Chi-restraints excluded: chain F residue 61 VAL Chi-restraints excluded: chain F residue 67 LEU Chi-restraints excluded: chain F residue 94 GLU Chi-restraints excluded: chain C residue 105 SER Chi-restraints excluded: chain C residue 125 VAL Chi-restraints excluded: chain C residue 138 SER Chi-restraints excluded: chain C residue 144 LEU Chi-restraints excluded: chain C residue 159 HIS Chi-restraints excluded: chain C residue 176 LEU Chi-restraints excluded: chain C residue 255 TRP Chi-restraints excluded: chain D residue 51 THR Chi-restraints excluded: chain D residue 61 VAL Chi-restraints excluded: chain D residue 67 LEU Chi-restraints excluded: chain D residue 71 PHE Chi-restraints excluded: chain D residue 82 THR Chi-restraints excluded: chain A residue 110 VAL Chi-restraints excluded: chain A residue 125 VAL Chi-restraints excluded: chain A residue 133 VAL Chi-restraints excluded: chain A residue 146 LEU Chi-restraints excluded: chain A residue 160 VAL Chi-restraints excluded: chain A residue 167 LEU Chi-restraints excluded: chain A residue 210 LEU Chi-restraints excluded: chain L residue 90 LEU Chi-restraints excluded: chain L residue 138 SER Chi-restraints excluded: chain L residue 153 ILE Chi-restraints excluded: chain L residue 160 VAL Chi-restraints excluded: chain I residue 138 SER Chi-restraints excluded: chain I residue 157 THR Chi-restraints excluded: chain G residue 81 ASN Chi-restraints excluded: chain G residue 138 SER Chi-restraints excluded: chain G residue 153 ILE Chi-restraints excluded: chain G residue 178 ASP Chi-restraints excluded: chain G residue 192 ILE Chi-restraints excluded: chain G residue 284 MET Chi-restraints excluded: chain H residue 84 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 157 random chunks: chunk 17 optimal weight: 0.9990 chunk 86 optimal weight: 0.8980 chunk 110 optimal weight: 20.0000 chunk 85 optimal weight: 10.0000 chunk 127 optimal weight: 6.9990 chunk 84 optimal weight: 8.9990 chunk 151 optimal weight: 9.9990 chunk 94 optimal weight: 9.9990 chunk 92 optimal weight: 5.9990 chunk 69 optimal weight: 8.9990 chunk 93 optimal weight: 5.9990 overall best weight: 4.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** I 116 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 184 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7982 moved from start: 0.3600 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.077 13426 Z= 0.358 Angle : 0.707 10.569 18190 Z= 0.355 Chirality : 0.048 0.252 2093 Planarity : 0.005 0.062 2309 Dihedral : 5.164 24.068 1811 Min Nonbonded Distance : 2.079 Molprobity Statistics. All-atom Clashscore : 9.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.96 % Favored : 93.04 % Rotamer: Outliers : 5.09 % Allowed : 17.74 % Favored : 77.17 % 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: -0.81 (0.22), residues: 1594 helix: 0.20 (0.18), residues: 849 sheet: -0.07 (0.40), residues: 170 loop : -1.72 (0.27), residues: 575 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP C 256 HIS 0.006 0.001 HIS E 304 PHE 0.020 0.002 PHE L 149 TYR 0.019 0.002 TYR C 258 ARG 0.005 0.000 ARG G 201 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3188 Ramachandran restraints generated. 1594 Oldfield, 0 Emsley, 1594 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3188 Ramachandran restraints generated. 1594 Oldfield, 0 Emsley, 1594 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 212 residues out of total 1454 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 74 poor density : 138 time to evaluate : 1.727 Fit side-chains REVERT: J 118 GLU cc_start: 0.8208 (tp30) cc_final: 0.7850 (tp30) REVERT: E 104 ILE cc_start: 0.8066 (pt) cc_final: 0.7687 (mp) REVERT: E 320 LEU cc_start: 0.8801 (OUTLIER) cc_final: 0.8453 (tt) REVERT: C 164 LYS cc_start: 0.7784 (OUTLIER) cc_final: 0.6980 (ptmm) REVERT: C 176 LEU cc_start: 0.8332 (OUTLIER) cc_final: 0.8124 (mt) REVERT: C 258 TYR cc_start: 0.7260 (OUTLIER) cc_final: 0.5063 (t80) REVERT: C 295 ARG cc_start: 0.8673 (OUTLIER) cc_final: 0.7997 (ptt-90) REVERT: A 177 ASN cc_start: 0.7891 (t0) cc_final: 0.7464 (p0) REVERT: B 83 LEU cc_start: 0.8201 (tp) cc_final: 0.7884 (mp) REVERT: L 158 TYR cc_start: 0.5618 (m-80) cc_final: 0.5284 (m-80) REVERT: I 120 ARG cc_start: 0.8014 (pmm150) cc_final: 0.7393 (mtt90) REVERT: G 94 ARG cc_start: 0.7333 (OUTLIER) cc_final: 0.6691 (ptt-90) REVERT: G 153 ILE cc_start: 0.5753 (OUTLIER) cc_final: 0.5507 (mt) REVERT: H 67 LEU cc_start: 0.7826 (OUTLIER) cc_final: 0.7601 (tt) outliers start: 74 outliers final: 58 residues processed: 188 average time/residue: 0.2806 time to fit residues: 78.8835 Evaluate side-chains 199 residues out of total 1454 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 66 poor density : 133 time to evaluate : 1.644 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain J residue 88 VAL Chi-restraints excluded: chain J residue 101 LEU Chi-restraints excluded: chain J residue 105 SER Chi-restraints excluded: chain J residue 133 VAL Chi-restraints excluded: chain J residue 142 ASP Chi-restraints excluded: chain K residue 80 GLN Chi-restraints excluded: chain K residue 129 SER Chi-restraints excluded: chain K residue 131 ASP Chi-restraints excluded: chain K residue 133 VAL Chi-restraints excluded: chain K residue 138 SER Chi-restraints excluded: chain K residue 160 VAL Chi-restraints excluded: chain E residue 105 SER Chi-restraints excluded: chain E residue 142 ASP Chi-restraints excluded: chain E residue 217 LEU Chi-restraints excluded: chain E residue 320 LEU Chi-restraints excluded: chain E residue 331 LEU Chi-restraints excluded: chain F residue 48 VAL Chi-restraints excluded: chain F residue 50 VAL Chi-restraints excluded: chain F residue 61 VAL Chi-restraints excluded: chain F residue 67 LEU Chi-restraints excluded: chain F residue 72 SER Chi-restraints excluded: chain F residue 94 GLU Chi-restraints excluded: chain C residue 105 SER Chi-restraints excluded: chain C residue 125 VAL Chi-restraints excluded: chain C residue 138 SER Chi-restraints excluded: chain C residue 142 ASP Chi-restraints excluded: chain C residue 144 LEU Chi-restraints excluded: chain C residue 159 HIS Chi-restraints excluded: chain C residue 160 VAL Chi-restraints excluded: chain C residue 164 LYS Chi-restraints excluded: chain C residue 176 LEU Chi-restraints excluded: chain C residue 255 TRP Chi-restraints excluded: chain C residue 258 TYR Chi-restraints excluded: chain C residue 295 ARG Chi-restraints excluded: chain C residue 338 LEU Chi-restraints excluded: chain D residue 51 THR Chi-restraints excluded: chain D residue 61 VAL Chi-restraints excluded: chain D residue 64 SER Chi-restraints excluded: chain D residue 67 LEU Chi-restraints excluded: chain D residue 71 PHE Chi-restraints excluded: chain D residue 82 THR Chi-restraints excluded: chain A residue 110 VAL Chi-restraints excluded: chain A residue 125 VAL Chi-restraints excluded: chain A residue 133 VAL Chi-restraints excluded: chain A residue 146 LEU Chi-restraints excluded: chain A residue 160 VAL Chi-restraints excluded: chain A residue 167 LEU Chi-restraints excluded: chain A residue 210 LEU Chi-restraints excluded: chain B residue 87 ASN Chi-restraints excluded: chain L residue 90 LEU Chi-restraints excluded: chain L residue 138 SER Chi-restraints excluded: chain L residue 160 VAL Chi-restraints excluded: chain I residue 138 SER Chi-restraints excluded: chain I residue 157 THR Chi-restraints excluded: chain G residue 81 ASN Chi-restraints excluded: chain G residue 94 ARG Chi-restraints excluded: chain G residue 131 ASP Chi-restraints excluded: chain G residue 138 SER Chi-restraints excluded: chain G residue 153 ILE Chi-restraints excluded: chain G residue 178 ASP Chi-restraints excluded: chain G residue 192 ILE Chi-restraints excluded: chain G residue 284 MET Chi-restraints excluded: chain H residue 67 LEU Chi-restraints excluded: chain H residue 70 VAL Chi-restraints excluded: chain H residue 82 THR Chi-restraints excluded: chain H residue 84 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 157 random chunks: chunk 60 optimal weight: 0.2980 chunk 90 optimal weight: 1.9990 chunk 45 optimal weight: 1.9990 chunk 29 optimal weight: 5.9990 chunk 96 optimal weight: 2.9990 chunk 103 optimal weight: 0.9980 chunk 74 optimal weight: 7.9990 chunk 14 optimal weight: 0.9980 chunk 118 optimal weight: 0.8980 chunk 137 optimal weight: 0.8980 chunk 144 optimal weight: 0.8980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** G 184 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7875 moved from start: 0.3698 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 13426 Z= 0.159 Angle : 0.591 7.472 18190 Z= 0.294 Chirality : 0.043 0.260 2093 Planarity : 0.004 0.067 2309 Dihedral : 4.613 22.710 1811 Min Nonbonded Distance : 2.189 Molprobity Statistics. All-atom Clashscore : 7.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.77 % Favored : 95.23 % Rotamer: Outliers : 3.99 % Allowed : 19.46 % Favored : 76.55 % 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: -0.34 (0.22), residues: 1594 helix: 0.68 (0.19), residues: 844 sheet: 0.22 (0.41), residues: 165 loop : -1.69 (0.26), residues: 585 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP C 260 HIS 0.005 0.001 HIS C 159 PHE 0.024 0.001 PHE L 149 TYR 0.011 0.001 TYR C 268 ARG 0.003 0.000 ARG G 201 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3188 Ramachandran restraints generated. 1594 Oldfield, 0 Emsley, 1594 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3188 Ramachandran restraints generated. 1594 Oldfield, 0 Emsley, 1594 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 206 residues out of total 1454 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 58 poor density : 148 time to evaluate : 1.504 Fit side-chains REVERT: J 118 GLU cc_start: 0.8065 (tp30) cc_final: 0.7727 (tp30) REVERT: E 104 ILE cc_start: 0.8044 (pt) cc_final: 0.7663 (mp) REVERT: E 284 MET cc_start: 0.7458 (tpp) cc_final: 0.7006 (mtt) REVERT: E 320 LEU cc_start: 0.8669 (OUTLIER) cc_final: 0.8421 (tt) REVERT: C 164 LYS cc_start: 0.7622 (OUTLIER) cc_final: 0.6887 (ptmm) REVERT: C 258 TYR cc_start: 0.7053 (OUTLIER) cc_final: 0.4808 (t80) REVERT: A 177 ASN cc_start: 0.7845 (t0) cc_final: 0.7432 (p0) REVERT: B 83 LEU cc_start: 0.8159 (tp) cc_final: 0.7832 (mp) REVERT: L 158 TYR cc_start: 0.5524 (m-80) cc_final: 0.5180 (m-80) REVERT: I 120 ARG cc_start: 0.7908 (pmm150) cc_final: 0.7296 (mtt90) REVERT: G 94 ARG cc_start: 0.7168 (OUTLIER) cc_final: 0.6418 (ptt-90) REVERT: G 153 ILE cc_start: 0.5865 (OUTLIER) cc_final: 0.5591 (mt) outliers start: 58 outliers final: 44 residues processed: 189 average time/residue: 0.2360 time to fit residues: 65.6131 Evaluate side-chains 185 residues out of total 1454 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 136 time to evaluate : 1.422 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain J residue 88 VAL Chi-restraints excluded: chain J residue 101 LEU Chi-restraints excluded: chain J residue 133 VAL Chi-restraints excluded: chain J residue 142 ASP Chi-restraints excluded: chain K residue 80 GLN Chi-restraints excluded: chain K residue 129 SER Chi-restraints excluded: chain K residue 133 VAL Chi-restraints excluded: chain K residue 138 SER Chi-restraints excluded: chain E residue 105 SER Chi-restraints excluded: chain E residue 142 ASP Chi-restraints excluded: chain E residue 258 TYR Chi-restraints excluded: chain E residue 312 PHE Chi-restraints excluded: chain E residue 320 LEU Chi-restraints excluded: chain E residue 331 LEU Chi-restraints excluded: chain F residue 61 VAL Chi-restraints excluded: chain F residue 67 LEU Chi-restraints excluded: chain C residue 105 SER Chi-restraints excluded: chain C residue 125 VAL Chi-restraints excluded: chain C residue 144 LEU Chi-restraints excluded: chain C residue 159 HIS Chi-restraints excluded: chain C residue 164 LYS Chi-restraints excluded: chain C residue 255 TRP Chi-restraints excluded: chain C residue 258 TYR Chi-restraints excluded: chain C residue 338 LEU Chi-restraints excluded: chain D residue 51 THR Chi-restraints excluded: chain D residue 61 VAL Chi-restraints excluded: chain D residue 71 PHE Chi-restraints excluded: chain D residue 82 THR Chi-restraints excluded: chain A residue 76 THR Chi-restraints excluded: chain A residue 125 VAL Chi-restraints excluded: chain A residue 133 VAL Chi-restraints excluded: chain A residue 160 VAL Chi-restraints excluded: chain A residue 210 LEU Chi-restraints excluded: chain L residue 90 LEU Chi-restraints excluded: chain L residue 138 SER Chi-restraints excluded: chain L residue 160 VAL Chi-restraints excluded: chain I residue 138 SER Chi-restraints excluded: chain I residue 157 THR Chi-restraints excluded: chain G residue 81 ASN Chi-restraints excluded: chain G residue 94 ARG Chi-restraints excluded: chain G residue 131 ASP Chi-restraints excluded: chain G residue 138 SER Chi-restraints excluded: chain G residue 153 ILE Chi-restraints excluded: chain G residue 178 ASP Chi-restraints excluded: chain G residue 192 ILE Chi-restraints excluded: chain G residue 259 SER Chi-restraints excluded: chain G residue 290 VAL Chi-restraints excluded: chain H residue 70 VAL Chi-restraints excluded: chain H residue 82 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 157 random chunks: chunk 132 optimal weight: 7.9990 chunk 141 optimal weight: 7.9990 chunk 144 optimal weight: 3.9990 chunk 84 optimal weight: 3.9990 chunk 61 optimal weight: 10.0000 chunk 110 optimal weight: 20.0000 chunk 43 optimal weight: 7.9990 chunk 127 optimal weight: 7.9990 chunk 133 optimal weight: 6.9990 chunk 140 optimal weight: 4.9990 chunk 92 optimal weight: 4.9990 overall best weight: 4.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** I 116 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 184 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7992 moved from start: 0.3741 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.089 13426 Z= 0.412 Angle : 0.732 10.342 18190 Z= 0.366 Chirality : 0.049 0.248 2093 Planarity : 0.005 0.063 2309 Dihedral : 5.127 23.491 1811 Min Nonbonded Distance : 2.062 Molprobity Statistics. All-atom Clashscore : 8.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.96 % Favored : 93.04 % Rotamer: Outliers : 4.88 % Allowed : 19.26 % Favored : 75.86 % 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: -0.66 (0.22), residues: 1594 helix: 0.36 (0.18), residues: 846 sheet: 0.10 (0.41), residues: 165 loop : -1.72 (0.26), residues: 583 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP C 256 HIS 0.006 0.002 HIS E 304 PHE 0.018 0.002 PHE L 149 TYR 0.021 0.002 TYR C 258 ARG 0.005 0.001 ARG G 201 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3188 Ramachandran restraints generated. 1594 Oldfield, 0 Emsley, 1594 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3188 Ramachandran restraints generated. 1594 Oldfield, 0 Emsley, 1594 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 203 residues out of total 1454 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 71 poor density : 132 time to evaluate : 1.631 Fit side-chains revert: symmetry clash REVERT: J 118 GLU cc_start: 0.8233 (tp30) cc_final: 0.7887 (tp30) REVERT: E 104 ILE cc_start: 0.8089 (pt) cc_final: 0.7687 (mp) REVERT: E 320 LEU cc_start: 0.8772 (OUTLIER) cc_final: 0.8420 (tt) REVERT: C 164 LYS cc_start: 0.7814 (OUTLIER) cc_final: 0.6987 (ptmm) REVERT: C 258 TYR cc_start: 0.7320 (OUTLIER) cc_final: 0.5215 (t80) REVERT: A 177 ASN cc_start: 0.7857 (t0) cc_final: 0.7474 (p0) REVERT: B 83 LEU cc_start: 0.8230 (tp) cc_final: 0.7899 (mp) REVERT: I 120 ARG cc_start: 0.8025 (pmm150) cc_final: 0.7388 (mtt90) REVERT: G 94 ARG cc_start: 0.7305 (OUTLIER) cc_final: 0.6539 (ptt-90) REVERT: G 153 ILE cc_start: 0.5727 (OUTLIER) cc_final: 0.5485 (mt) outliers start: 71 outliers final: 59 residues processed: 181 average time/residue: 0.2373 time to fit residues: 63.5036 Evaluate side-chains 196 residues out of total 1454 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 64 poor density : 132 time to evaluate : 1.848 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain J residue 88 VAL Chi-restraints excluded: chain J residue 101 LEU Chi-restraints excluded: chain J residue 133 VAL Chi-restraints excluded: chain J residue 142 ASP Chi-restraints excluded: chain J residue 160 VAL Chi-restraints excluded: chain K residue 80 GLN Chi-restraints excluded: chain K residue 86 ILE Chi-restraints excluded: chain K residue 129 SER Chi-restraints excluded: chain K residue 131 ASP Chi-restraints excluded: chain K residue 133 VAL Chi-restraints excluded: chain K residue 138 SER Chi-restraints excluded: chain E residue 105 SER Chi-restraints excluded: chain E residue 142 ASP Chi-restraints excluded: chain E residue 143 LEU Chi-restraints excluded: chain E residue 312 PHE Chi-restraints excluded: chain E residue 320 LEU Chi-restraints excluded: chain E residue 331 LEU Chi-restraints excluded: chain F residue 48 VAL Chi-restraints excluded: chain F residue 61 VAL Chi-restraints excluded: chain F residue 67 LEU Chi-restraints excluded: chain F residue 72 SER Chi-restraints excluded: chain F residue 91 LEU Chi-restraints excluded: chain F residue 94 GLU Chi-restraints excluded: chain C residue 105 SER Chi-restraints excluded: chain C residue 125 VAL Chi-restraints excluded: chain C residue 138 SER Chi-restraints excluded: chain C residue 142 ASP Chi-restraints excluded: chain C residue 144 LEU Chi-restraints excluded: chain C residue 159 HIS Chi-restraints excluded: chain C residue 164 LYS Chi-restraints excluded: chain C residue 255 TRP Chi-restraints excluded: chain C residue 258 TYR Chi-restraints excluded: chain C residue 338 LEU Chi-restraints excluded: chain D residue 51 THR Chi-restraints excluded: chain D residue 61 VAL Chi-restraints excluded: chain D residue 64 SER Chi-restraints excluded: chain D residue 67 LEU Chi-restraints excluded: chain D residue 71 PHE Chi-restraints excluded: chain D residue 82 THR Chi-restraints excluded: chain A residue 110 VAL Chi-restraints excluded: chain A residue 125 VAL Chi-restraints excluded: chain A residue 133 VAL Chi-restraints excluded: chain A residue 146 LEU Chi-restraints excluded: chain A residue 160 VAL Chi-restraints excluded: chain A residue 210 LEU Chi-restraints excluded: chain B residue 61 VAL Chi-restraints excluded: chain L residue 90 LEU Chi-restraints excluded: chain L residue 138 SER Chi-restraints excluded: chain L residue 155 ASP Chi-restraints excluded: chain L residue 160 VAL Chi-restraints excluded: chain I residue 138 SER Chi-restraints excluded: chain I residue 157 THR Chi-restraints excluded: chain G residue 81 ASN Chi-restraints excluded: chain G residue 94 ARG Chi-restraints excluded: chain G residue 131 ASP Chi-restraints excluded: chain G residue 138 SER Chi-restraints excluded: chain G residue 153 ILE Chi-restraints excluded: chain G residue 178 ASP Chi-restraints excluded: chain G residue 192 ILE Chi-restraints excluded: chain G residue 259 SER Chi-restraints excluded: chain G residue 290 VAL Chi-restraints excluded: chain H residue 70 VAL Chi-restraints excluded: chain H residue 82 THR Chi-restraints excluded: chain H residue 84 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 157 random chunks: chunk 149 optimal weight: 0.9990 chunk 91 optimal weight: 10.0000 chunk 70 optimal weight: 4.9990 chunk 103 optimal weight: 3.9990 chunk 156 optimal weight: 8.9990 chunk 143 optimal weight: 3.9990 chunk 124 optimal weight: 10.0000 chunk 12 optimal weight: 0.7980 chunk 96 optimal weight: 2.9990 chunk 76 optimal weight: 10.0000 chunk 98 optimal weight: 0.9990 overall best weight: 1.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** G 184 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7919 moved from start: 0.3783 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 13426 Z= 0.211 Angle : 0.629 8.208 18190 Z= 0.312 Chirality : 0.045 0.252 2093 Planarity : 0.004 0.067 2309 Dihedral : 4.827 23.196 1811 Min Nonbonded Distance : 2.137 Molprobity Statistics. All-atom Clashscore : 8.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.33 % Favored : 94.67 % Rotamer: Outliers : 4.20 % Allowed : 20.01 % Favored : 75.79 % 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: -0.37 (0.22), residues: 1594 helix: 0.63 (0.18), residues: 847 sheet: 0.11 (0.41), residues: 165 loop : -1.62 (0.27), residues: 582 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP C 256 HIS 0.005 0.001 HIS C 159 PHE 0.024 0.001 PHE L 149 TYR 0.012 0.001 TYR C 258 ARG 0.003 0.000 ARG G 201 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3188 Ramachandran restraints generated. 1594 Oldfield, 0 Emsley, 1594 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3188 Ramachandran restraints generated. 1594 Oldfield, 0 Emsley, 1594 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 197 residues out of total 1454 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 61 poor density : 136 time to evaluate : 1.500 Fit side-chains REVERT: J 118 GLU cc_start: 0.8116 (tp30) cc_final: 0.7800 (tp30) REVERT: E 104 ILE cc_start: 0.8063 (pt) cc_final: 0.7660 (mp) REVERT: E 284 MET cc_start: 0.7455 (tpp) cc_final: 0.7030 (mtt) REVERT: E 320 LEU cc_start: 0.8706 (OUTLIER) cc_final: 0.8342 (tt) REVERT: C 164 LYS cc_start: 0.7717 (OUTLIER) cc_final: 0.6912 (ptmm) REVERT: C 258 TYR cc_start: 0.7184 (OUTLIER) cc_final: 0.5082 (t80) REVERT: A 177 ASN cc_start: 0.7853 (t0) cc_final: 0.7447 (p0) REVERT: B 83 LEU cc_start: 0.8196 (tp) cc_final: 0.7859 (mp) REVERT: I 120 ARG cc_start: 0.7957 (pmm150) cc_final: 0.7344 (mtt90) REVERT: G 94 ARG cc_start: 0.7229 (OUTLIER) cc_final: 0.6609 (ptt-90) REVERT: G 153 ILE cc_start: 0.5909 (OUTLIER) cc_final: 0.5644 (mt) REVERT: G 284 MET cc_start: 0.8316 (OUTLIER) cc_final: 0.7987 (mtp) outliers start: 61 outliers final: 52 residues processed: 177 average time/residue: 0.2423 time to fit residues: 63.1962 Evaluate side-chains 190 residues out of total 1454 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 58 poor density : 132 time to evaluate : 1.444 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain J residue 88 VAL Chi-restraints excluded: chain J residue 101 LEU Chi-restraints excluded: chain J residue 105 SER Chi-restraints excluded: chain J residue 133 VAL Chi-restraints excluded: chain J residue 142 ASP Chi-restraints excluded: chain K residue 80 GLN Chi-restraints excluded: chain K residue 86 ILE Chi-restraints excluded: chain K residue 129 SER Chi-restraints excluded: chain K residue 131 ASP Chi-restraints excluded: chain K residue 133 VAL Chi-restraints excluded: chain K residue 138 SER Chi-restraints excluded: chain E residue 105 SER Chi-restraints excluded: chain E residue 142 ASP Chi-restraints excluded: chain E residue 312 PHE Chi-restraints excluded: chain E residue 320 LEU Chi-restraints excluded: chain E residue 331 LEU Chi-restraints excluded: chain F residue 61 VAL Chi-restraints excluded: chain F residue 67 LEU Chi-restraints excluded: chain F residue 72 SER Chi-restraints excluded: chain F residue 91 LEU Chi-restraints excluded: chain C residue 105 SER Chi-restraints excluded: chain C residue 125 VAL Chi-restraints excluded: chain C residue 142 ASP Chi-restraints excluded: chain C residue 144 LEU Chi-restraints excluded: chain C residue 159 HIS Chi-restraints excluded: chain C residue 164 LYS Chi-restraints excluded: chain C residue 255 TRP Chi-restraints excluded: chain C residue 258 TYR Chi-restraints excluded: chain C residue 338 LEU Chi-restraints excluded: chain D residue 51 THR Chi-restraints excluded: chain D residue 61 VAL Chi-restraints excluded: chain D residue 71 PHE Chi-restraints excluded: chain D residue 82 THR Chi-restraints excluded: chain A residue 110 VAL Chi-restraints excluded: chain A residue 125 VAL Chi-restraints excluded: chain A residue 133 VAL Chi-restraints excluded: chain A residue 146 LEU Chi-restraints excluded: chain A residue 160 VAL Chi-restraints excluded: chain A residue 210 LEU Chi-restraints excluded: chain L residue 90 LEU Chi-restraints excluded: chain L residue 138 SER Chi-restraints excluded: chain L residue 155 ASP Chi-restraints excluded: chain L residue 160 VAL Chi-restraints excluded: chain I residue 138 SER Chi-restraints excluded: chain I residue 157 THR Chi-restraints excluded: chain G residue 81 ASN Chi-restraints excluded: chain G residue 94 ARG Chi-restraints excluded: chain G residue 131 ASP Chi-restraints excluded: chain G residue 138 SER Chi-restraints excluded: chain G residue 153 ILE Chi-restraints excluded: chain G residue 178 ASP Chi-restraints excluded: chain G residue 192 ILE Chi-restraints excluded: chain G residue 259 SER Chi-restraints excluded: chain G residue 284 MET Chi-restraints excluded: chain G residue 290 VAL Chi-restraints excluded: chain H residue 78 LEU Chi-restraints excluded: chain H residue 82 THR Chi-restraints excluded: chain H residue 84 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 157 random chunks: chunk 132 optimal weight: 0.0770 chunk 38 optimal weight: 5.9990 chunk 114 optimal weight: 7.9990 chunk 18 optimal weight: 10.0000 chunk 34 optimal weight: 0.9980 chunk 124 optimal weight: 10.0000 chunk 52 optimal weight: 3.9990 chunk 128 optimal weight: 0.6980 chunk 15 optimal weight: 0.8980 chunk 22 optimal weight: 7.9990 chunk 109 optimal weight: 1.9990 overall best weight: 0.9340 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: J 116 GLN K 116 GLN ** G 184 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3679 r_free = 0.3679 target = 0.111491 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3481 r_free = 0.3481 target = 0.099325 restraints weight = 35294.903| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3510 r_free = 0.3510 target = 0.101043 restraints weight = 19650.767| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3530 r_free = 0.3530 target = 0.102187 restraints weight = 12962.776| |-----------------------------------------------------------------------------| r_work (final): 0.3527 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7855 moved from start: 0.3930 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 13426 Z= 0.157 Angle : 0.600 10.662 18190 Z= 0.295 Chirality : 0.043 0.256 2093 Planarity : 0.004 0.069 2309 Dihedral : 4.427 21.878 1811 Min Nonbonded Distance : 2.196 Molprobity Statistics. All-atom Clashscore : 7.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.40 % Favored : 94.60 % Rotamer: Outliers : 3.65 % Allowed : 20.98 % Favored : 75.38 % 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: 0.03 (0.22), residues: 1594 helix: 1.06 (0.19), residues: 843 sheet: 0.20 (0.42), residues: 165 loop : -1.58 (0.26), residues: 586 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP C 260 HIS 0.005 0.001 HIS L 159 PHE 0.024 0.001 PHE L 149 TYR 0.012 0.001 TYR A 242 ARG 0.003 0.000 ARG G 201 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2696.83 seconds wall clock time: 49 minutes 29.33 seconds (2969.33 seconds total)