Starting phenix.real_space_refine on Tue Mar 3 21:24:25 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6m1i_30048/03_2026/6m1i_30048.cif Found real_map, /net/cci-nas-00/data/ceres_data/6m1i_30048/03_2026/6m1i_30048.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/6m1i_30048/03_2026/6m1i_30048.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6m1i_30048/03_2026/6m1i_30048.map" model { file = "/net/cci-nas-00/data/ceres_data/6m1i_30048/03_2026/6m1i_30048.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6m1i_30048/03_2026/6m1i_30048.cif" } resolution = 3.5 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.003 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 58 5.16 5 C 5682 2.51 5 N 1537 2.21 5 O 1639 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 19 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 8916 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 2841 Number of conformers: 1 Conformer: "" Number of residues, atoms: 353, 2841 Classifications: {'peptide': 353} Incomplete info: {'truncation_to_alanine': 15} Link IDs: {'PTRANS': 13, 'TRANS': 339} Chain breaks: 4 Unresolved non-hydrogen bonds: 69 Unresolved non-hydrogen angles: 82 Unresolved non-hydrogen dihedrals: 62 Planarities with less than four sites: {'ASP:plan': 1, 'PHE:plan': 2, 'GLN:plan1': 2, 'GLU:plan': 2, 'ARG:plan': 2, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 46 Chain: "B" Number of atoms: 221 Number of conformers: 1 Conformer: "" Number of residues, atoms: 27, 221 Classifications: {'peptide': 27} Link IDs: {'TRANS': 26} Chain: "C" Number of atoms: 961 Number of conformers: 1 Conformer: "" Number of residues, atoms: 126, 961 Classifications: {'peptide': 126} Link IDs: {'PTRANS': 5, 'TRANS': 120} Chain: "D" Number of atoms: 436 Number of conformers: 1 Conformer: "" Number of residues, atoms: 57, 436 Classifications: {'peptide': 57} Link IDs: {'PTRANS': 4, 'TRANS': 52} Chain: "E" Number of atoms: 2595 Number of conformers: 1 Conformer: "" Number of residues, atoms: 338, 2595 Classifications: {'peptide': 338} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 5, 'TRANS': 332} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "F" Number of atoms: 1862 Number of conformers: 1 Conformer: "" Number of residues, atoms: 225, 1862 Classifications: {'peptide': 225} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 6, 'TRANS': 218} Chain breaks: 2 Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 1.89, per 1000 atoms: 0.21 Number of scatterers: 8916 At special positions: 0 Unit cell: (84.007, 105.827, 153.831, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 58 16.00 O 1639 8.00 N 1537 7.00 C 5682 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=5, symmetry=0 Simple disulfide: pdb=" SG CYS A 34 " - pdb=" SG CYS A 63 " distance=2.03 Simple disulfide: pdb=" SG CYS A 54 " - pdb=" SG CYS A 118 " distance=2.03 Simple disulfide: pdb=" SG CYS A 226 " - pdb=" SG CYS A 296 " distance=2.04 Simple disulfide: pdb=" SG CYS C 22 " - pdb=" SG CYS C 96 " distance=2.03 Simple disulfide: pdb=" SG CYS C 99 " - pdb=" SG CYS C 107 " distance=2.02 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.73 Conformation dependent library (CDL) restraints added in 268.0 milliseconds 2204 Ramachandran restraints generated. 1102 Oldfield, 0 Emsley, 1102 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2112 Finding SS restraints... Secondary structure from input PDB file: 36 helices and 11 sheets defined 39.1% alpha, 18.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.21 Creating SS restraints... Processing helix chain 'A' and resid 25 through 41 removed outlier: 4.274A pdb=" N GLN A 31 " --> pdb=" O PHE A 27 " (cutoff:3.500A) Processing helix chain 'A' and resid 78 through 82 Processing helix chain 'A' and resid 87 through 111 removed outlier: 3.504A pdb=" N MET A 111 " --> pdb=" O ASP A 87 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 87 through 111' Processing helix chain 'A' and resid 129 through 135 removed outlier: 3.573A pdb=" N CYS A 134 " --> pdb=" O TYR A 130 " (cutoff:3.500A) Processing helix chain 'A' and resid 146 through 170 removed outlier: 4.044A pdb=" N TYR A 157 " --> pdb=" O VAL A 153 " (cutoff:3.500A) removed outlier: 4.245A pdb=" N VAL A 159 " --> pdb=" O ALA A 155 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N LEU A 163 " --> pdb=" O VAL A 159 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N SER A 164 " --> pdb=" O GLY A 160 " (cutoff:3.500A) removed outlier: 3.847A pdb=" N LEU A 170 " --> pdb=" O VAL A 166 " (cutoff:3.500A) Processing helix chain 'A' and resid 170 through 176 removed outlier: 3.675A pdb=" N ILE A 174 " --> pdb=" O LEU A 170 " (cutoff:3.500A) removed outlier: 4.194A pdb=" N LEU A 175 " --> pdb=" O ALA A 171 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N CYS A 176 " --> pdb=" O MET A 172 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 170 through 176' Processing helix chain 'A' and resid 185 through 209 removed outlier: 3.580A pdb=" N MET A 190 " --> pdb=" O ASN A 186 " (cutoff:3.500A) removed outlier: 4.946A pdb=" N ASN A 191 " --> pdb=" O PHE A 187 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N MET A 197 " --> pdb=" O PHE A 193 " (cutoff:3.500A) removed outlier: 3.985A pdb=" N ARG A 199 " --> pdb=" O SER A 195 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N ILE A 205 " --> pdb=" O ILE A 201 " (cutoff:3.500A) removed outlier: 4.013A pdb=" N ILE A 209 " --> pdb=" O ILE A 205 " (cutoff:3.500A) Processing helix chain 'A' and resid 214 through 219 removed outlier: 3.536A pdb=" N HIS A 218 " --> pdb=" O GLN A 214 " (cutoff:3.500A) Processing helix chain 'A' and resid 224 through 239 removed outlier: 4.279A pdb=" N MET A 230 " --> pdb=" O CYS A 226 " (cutoff:3.500A) Processing helix chain 'A' and resid 244 through 254 removed outlier: 3.622A pdb=" N GLY A 248 " --> pdb=" O LEU A 244 " (cutoff:3.500A) Processing helix chain 'A' and resid 261 through 286 removed outlier: 3.756A pdb=" N TYR A 265 " --> pdb=" O PRO A 261 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N PHE A 266 " --> pdb=" O GLU A 262 " (cutoff:3.500A) removed outlier: 4.194A pdb=" N TYR A 267 " --> pdb=" O ARG A 263 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N TRP A 268 " --> pdb=" O ARG A 264 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N ILE A 271 " --> pdb=" O TYR A 267 " (cutoff:3.500A) removed outlier: 4.636A pdb=" N ILE A 272 " --> pdb=" O TRP A 268 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N TRP A 274 " --> pdb=" O THR A 270 " (cutoff:3.500A) removed outlier: 4.463A pdb=" N ALA A 276 " --> pdb=" O ILE A 272 " (cutoff:3.500A) Proline residue: A 277 - end of helix removed outlier: 3.712A pdb=" N PHE A 280 " --> pdb=" O ALA A 276 " (cutoff:3.500A) removed outlier: 3.990A pdb=" N THR A 282 " --> pdb=" O LEU A 278 " (cutoff:3.500A) Processing helix chain 'A' and resid 305 through 309 removed outlier: 3.667A pdb=" N VAL A 308 " --> pdb=" O LEU A 305 " (cutoff:3.500A) Processing helix chain 'A' and resid 310 through 329 removed outlier: 4.101A pdb=" N SER A 316 " --> pdb=" O PRO A 312 " (cutoff:3.500A) removed outlier: 4.152A pdb=" N ASN A 320 " --> pdb=" O SER A 316 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N VAL A 322 " --> pdb=" O MET A 318 " (cutoff:3.500A) removed outlier: 4.077A pdb=" N LEU A 323 " --> pdb=" O VAL A 319 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N ILE A 327 " --> pdb=" O LEU A 323 " (cutoff:3.500A) Processing helix chain 'A' and resid 329 through 336 Processing helix chain 'A' and resid 347 through 351 Processing helix chain 'A' and resid 351 through 356 Processing helix chain 'A' and resid 358 through 363 removed outlier: 3.586A pdb=" N GLY A 363 " --> pdb=" O ILE A 359 " (cutoff:3.500A) Processing helix chain 'A' and resid 364 through 370 removed outlier: 4.606A pdb=" N VAL A 368 " --> pdb=" O HIS A 365 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N PHE A 369 " --> pdb=" O TYR A 366 " (cutoff:3.500A) Processing helix chain 'A' and resid 373 through 378 removed outlier: 3.615A pdb=" N LYS A 378 " --> pdb=" O GLU A 374 " (cutoff:3.500A) Processing helix chain 'A' and resid 380 through 388 removed outlier: 3.685A pdb=" N PHE A 384 " --> pdb=" O GLU A 380 " (cutoff:3.500A) Processing helix chain 'A' and resid 391 through 400 removed outlier: 3.821A pdb=" N ALA A 397 " --> pdb=" O GLY A 393 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N VAL A 398 " --> pdb=" O PHE A 394 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N TYR A 400 " --> pdb=" O VAL A 396 " (cutoff:3.500A) Processing helix chain 'A' and resid 407 through 419 removed outlier: 3.584A pdb=" N LYS A 412 " --> pdb=" O GLN A 408 " (cutoff:3.500A) removed outlier: 4.106A pdb=" N ARG A 413 " --> pdb=" O ALA A 409 " (cutoff:3.500A) removed outlier: 3.906A pdb=" N LYS A 414 " --> pdb=" O GLU A 410 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N ARG A 416 " --> pdb=" O LYS A 412 " (cutoff:3.500A) Processing helix chain 'B' and resid 2 through 24 removed outlier: 3.670A pdb=" N SER B 11 " --> pdb=" O THR B 7 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N MET B 17 " --> pdb=" O TYR B 13 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N ALA B 18 " --> pdb=" O ARG B 14 " (cutoff:3.500A) Processing helix chain 'C' and resid 28 through 32 removed outlier: 3.865A pdb=" N TYR C 32 " --> pdb=" O PHE C 29 " (cutoff:3.500A) Processing helix chain 'C' and resid 62 through 65 removed outlier: 3.594A pdb=" N LYS C 65 " --> pdb=" O GLY C 62 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 62 through 65' Processing helix chain 'C' and resid 87 through 91 removed outlier: 3.575A pdb=" N ASP C 90 " --> pdb=" O LYS C 87 " (cutoff:3.500A) removed outlier: 4.153A pdb=" N THR C 91 " --> pdb=" O PRO C 88 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 87 through 91' Processing helix chain 'D' and resid 7 through 22 removed outlier: 3.504A pdb=" N VAL D 16 " --> pdb=" O ALA D 12 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N MET D 21 " --> pdb=" O GLU D 17 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N GLU D 22 " --> pdb=" O GLN D 18 " (cutoff:3.500A) Processing helix chain 'D' and resid 29 through 44 removed outlier: 3.773A pdb=" N ASP D 36 " --> pdb=" O LYS D 32 " (cutoff:3.500A) removed outlier: 4.437A pdb=" N LEU D 37 " --> pdb=" O ALA D 33 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N ALA D 43 " --> pdb=" O ALA D 39 " (cutoff:3.500A) Processing helix chain 'E' and resid 4 through 26 removed outlier: 3.526A pdb=" N ARG E 22 " --> pdb=" O ILE E 18 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N LYS E 23 " --> pdb=" O ARG E 19 " (cutoff:3.500A) Processing helix chain 'E' and resid 29 through 34 removed outlier: 3.657A pdb=" N ILE E 33 " --> pdb=" O THR E 29 " (cutoff:3.500A) Processing helix chain 'F' and resid 13 through 38 removed outlier: 3.786A pdb=" N ALA F 18 " --> pdb=" O ASN F 14 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N ASN F 23 " --> pdb=" O GLN F 19 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N GLN F 29 " --> pdb=" O LYS F 25 " (cutoff:3.500A) removed outlier: 4.450A pdb=" N GLN F 35 " --> pdb=" O GLN F 31 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N VAL F 36 " --> pdb=" O LYS F 32 " (cutoff:3.500A) Processing helix chain 'F' and resid 49 through 59 removed outlier: 3.550A pdb=" N ASN F 54 " --> pdb=" O GLU F 50 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N ILE F 56 " --> pdb=" O GLY F 52 " (cutoff:3.500A) removed outlier: 4.525A pdb=" N VAL F 57 " --> pdb=" O LYS F 53 " (cutoff:3.500A) removed outlier: 3.968A pdb=" N LYS F 58 " --> pdb=" O ASN F 54 " (cutoff:3.500A) Processing helix chain 'F' and resid 265 through 278 removed outlier: 3.689A pdb=" N SER F 275 " --> pdb=" O LYS F 271 " (cutoff:3.500A) Processing helix chain 'F' and resid 294 through 299 removed outlier: 3.601A pdb=" N GLU F 299 " --> pdb=" O ASP F 295 " (cutoff:3.500A) Processing helix chain 'F' and resid 331 through 350 removed outlier: 3.749A pdb=" N ARG F 347 " --> pdb=" O ASP F 343 " (cutoff:3.500A) removed outlier: 4.235A pdb=" N ILE F 348 " --> pdb=" O GLU F 344 " (cutoff:3.500A) Processing helix chain 'F' and resid 370 through 390 removed outlier: 4.015A pdb=" N ASP F 381 " --> pdb=" O ASN F 377 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N ILE F 383 " --> pdb=" O CYS F 379 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 72 through 76 removed outlier: 4.428A pdb=" N VAL A 75 " --> pdb=" O VAL A 114 " (cutoff:3.500A) removed outlier: 4.209A pdb=" N VAL A 114 " --> pdb=" O VAL A 75 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'C' and resid 5 through 8 removed outlier: 3.552A pdb=" N SER C 21 " --> pdb=" O SER C 7 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N THR C 78 " --> pdb=" O ASP C 73 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 58 through 60 removed outlier: 3.521A pdb=" N SER C 59 " --> pdb=" O ASP C 50 " (cutoff:3.500A) removed outlier: 5.024A pdb=" N TRP C 47 " --> pdb=" O ARG C 38 " (cutoff:3.500A) removed outlier: 5.917A pdb=" N ARG C 38 " --> pdb=" O TRP C 47 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N VAL C 124 " --> pdb=" O ALA C 92 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'E' and resid 46 through 51 removed outlier: 6.672A pdb=" N ILE E 338 " --> pdb=" O ARG E 48 " (cutoff:3.500A) removed outlier: 4.450A pdb=" N THR E 50 " --> pdb=" O LEU E 336 " (cutoff:3.500A) removed outlier: 6.196A pdb=" N LEU E 336 " --> pdb=" O THR E 50 " (cutoff:3.500A) removed outlier: 6.999A pdb=" N ALA E 328 " --> pdb=" O LEU E 318 " (cutoff:3.500A) removed outlier: 4.571A pdb=" N LEU E 318 " --> pdb=" O ALA E 328 " (cutoff:3.500A) removed outlier: 7.009A pdb=" N GLY E 330 " --> pdb=" O SER E 316 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'E' and resid 58 through 62 removed outlier: 3.560A pdb=" N ALA E 60 " --> pdb=" O ALA E 73 " (cutoff:3.500A) removed outlier: 3.894A pdb=" N LYS E 78 " --> pdb=" O SER E 74 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N HIS E 91 " --> pdb=" O ILE E 81 " (cutoff:3.500A) removed outlier: 6.437A pdb=" N ASP E 83 " --> pdb=" O LYS E 89 " (cutoff:3.500A) removed outlier: 5.898A pdb=" N LYS E 89 " --> pdb=" O ASP E 83 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'E' and resid 100 through 105 removed outlier: 3.697A pdb=" N ARG E 137 " --> pdb=" O ILE E 123 " (cutoff:3.500A) removed outlier: 6.386A pdb=" N ASN E 125 " --> pdb=" O VAL E 135 " (cutoff:3.500A) removed outlier: 6.746A pdb=" N VAL E 135 " --> pdb=" O ASN E 125 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'E' and resid 146 through 151 removed outlier: 3.979A pdb=" N ILE E 157 " --> pdb=" O TRP E 169 " (cutoff:3.500A) removed outlier: 6.746A pdb=" N CYS E 166 " --> pdb=" O THR E 179 " (cutoff:3.500A) removed outlier: 4.705A pdb=" N THR E 179 " --> pdb=" O CYS E 166 " (cutoff:3.500A) removed outlier: 6.608A pdb=" N LEU E 168 " --> pdb=" O THR E 177 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N GLN E 175 " --> pdb=" O ASP E 170 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'E' and resid 187 through 192 removed outlier: 6.855A pdb=" N GLY E 202 " --> pdb=" O MET E 188 " (cutoff:3.500A) removed outlier: 4.589A pdb=" N LEU E 190 " --> pdb=" O VAL E 200 " (cutoff:3.500A) removed outlier: 6.719A pdb=" N VAL E 200 " --> pdb=" O LEU E 190 " (cutoff:3.500A) removed outlier: 4.570A pdb=" N PHE E 199 " --> pdb=" O TRP E 211 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N ALA E 203 " --> pdb=" O SER E 207 " (cutoff:3.500A) removed outlier: 4.441A pdb=" N SER E 207 " --> pdb=" O ALA E 203 " (cutoff:3.500A) removed outlier: 6.157A pdb=" N ALA E 208 " --> pdb=" O THR E 221 " (cutoff:3.500A) removed outlier: 4.385A pdb=" N THR E 221 " --> pdb=" O ALA E 208 " (cutoff:3.500A) removed outlier: 6.598A pdb=" N LEU E 210 " --> pdb=" O ARG E 219 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'E' and resid 229 through 234 removed outlier: 3.820A pdb=" N MET E 262 " --> pdb=" O LEU E 252 " (cutoff:3.500A) removed outlier: 6.328A pdb=" N ASP E 254 " --> pdb=" O GLU E 260 " (cutoff:3.500A) removed outlier: 6.184A pdb=" N GLU E 260 " --> pdb=" O ASP E 254 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'E' and resid 275 through 278 removed outlier: 3.806A pdb=" N SER E 275 " --> pdb=" O GLY E 288 " (cutoff:3.500A) removed outlier: 6.499A pdb=" N ASP E 298 " --> pdb=" O ARG E 304 " (cutoff:3.500A) removed outlier: 6.171A pdb=" N ARG E 304 " --> pdb=" O ASP E 298 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'F' and resid 207 through 214 removed outlier: 4.370A pdb=" N VAL F 224 " --> pdb=" O LEU F 45 " (cutoff:3.500A) removed outlier: 9.564A pdb=" N ALA F 243 " --> pdb=" O THR F 40 " (cutoff:3.500A) removed outlier: 7.104A pdb=" N ARG F 42 " --> pdb=" O ALA F 243 " (cutoff:3.500A) removed outlier: 7.987A pdb=" N ILE F 245 " --> pdb=" O ARG F 42 " (cutoff:3.500A) removed outlier: 6.530A pdb=" N LEU F 44 " --> pdb=" O ILE F 245 " (cutoff:3.500A) removed outlier: 5.919A pdb=" N ILE F 244 " --> pdb=" O ILE F 288 " (cutoff:3.500A) removed outlier: 7.147A pdb=" N PHE F 290 " --> pdb=" O ILE F 244 " (cutoff:3.500A) removed outlier: 6.786A pdb=" N PHE F 246 " --> pdb=" O PHE F 290 " (cutoff:3.500A) 333 hydrogen bonds defined for protein. 951 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: 0.97 Time building geometry restraints manager: 0.97 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 2643 1.33 - 1.45: 2009 1.45 - 1.58: 4382 1.58 - 1.70: 0 1.70 - 1.82: 80 Bond restraints: 9114 Sorted by residual: bond pdb=" N PHE A 402 " pdb=" CA PHE A 402 " ideal model delta sigma weight residual 1.459 1.492 -0.032 1.20e-02 6.94e+03 7.29e+00 bond pdb=" N TYR A 400 " pdb=" CA TYR A 400 " ideal model delta sigma weight residual 1.455 1.487 -0.032 1.29e-02 6.01e+03 6.16e+00 bond pdb=" N GLU A 247 " pdb=" CA GLU A 247 " ideal model delta sigma weight residual 1.459 1.487 -0.028 1.21e-02 6.83e+03 5.17e+00 bond pdb=" N ARG A 379 " pdb=" CA ARG A 379 " ideal model delta sigma weight residual 1.459 1.483 -0.024 1.15e-02 7.56e+03 4.20e+00 bond pdb=" N ARG A 263 " pdb=" CA ARG A 263 " ideal model delta sigma weight residual 1.456 1.482 -0.026 1.33e-02 5.65e+03 3.81e+00 ... (remaining 9109 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.41: 11983 2.41 - 4.82: 314 4.82 - 7.23: 34 7.23 - 9.64: 12 9.64 - 12.05: 2 Bond angle restraints: 12345 Sorted by residual: angle pdb=" N ARG A 263 " pdb=" CA ARG A 263 " pdb=" C ARG A 263 " ideal model delta sigma weight residual 113.28 105.28 8.00 1.22e+00 6.72e-01 4.31e+01 angle pdb=" C TYR A 400 " pdb=" N CYS A 401 " pdb=" CA CYS A 401 " ideal model delta sigma weight residual 122.79 114.01 8.78 1.70e+00 3.46e-01 2.67e+01 angle pdb=" N ILE A 309 " pdb=" CA ILE A 309 " pdb=" C ILE A 309 " ideal model delta sigma weight residual 111.56 107.22 4.34 8.60e-01 1.35e+00 2.55e+01 angle pdb=" C LYS C 76 " pdb=" N ASN C 77 " pdb=" CA ASN C 77 " ideal model delta sigma weight residual 122.46 129.04 -6.58 1.41e+00 5.03e-01 2.18e+01 angle pdb=" C SER A 302 " pdb=" N THR A 303 " pdb=" CA THR A 303 " ideal model delta sigma weight residual 121.54 130.14 -8.60 1.91e+00 2.74e-01 2.03e+01 ... (remaining 12340 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.77: 4728 17.77 - 35.53: 546 35.53 - 53.30: 82 53.30 - 71.07: 23 71.07 - 88.84: 6 Dihedral angle restraints: 5385 sinusoidal: 2116 harmonic: 3269 Sorted by residual: dihedral pdb=" CB CYS A 54 " pdb=" SG CYS A 54 " pdb=" SG CYS A 118 " pdb=" CB CYS A 118 " ideal model delta sinusoidal sigma weight residual -86.00 -144.22 58.22 1 1.00e+01 1.00e-02 4.54e+01 dihedral pdb=" CA PHE A 127 " pdb=" C PHE A 127 " pdb=" N PRO A 128 " pdb=" CA PRO A 128 " ideal model delta harmonic sigma weight residual 180.00 146.56 33.44 0 5.00e+00 4.00e-02 4.47e+01 dihedral pdb=" CA THR C 114 " pdb=" C THR C 114 " pdb=" N TYR C 115 " pdb=" CA TYR C 115 " ideal model delta harmonic sigma weight residual 180.00 148.82 31.18 0 5.00e+00 4.00e-02 3.89e+01 ... (remaining 5382 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.058: 968 0.058 - 0.117: 314 0.117 - 0.175: 70 0.175 - 0.233: 7 0.233 - 0.292: 5 Chirality restraints: 1364 Sorted by residual: chirality pdb=" CB VAL F 241 " pdb=" CA VAL F 241 " pdb=" CG1 VAL F 241 " pdb=" CG2 VAL F 241 " both_signs ideal model delta sigma weight residual False -2.63 -2.34 -0.29 2.00e-01 2.50e+01 2.13e+00 chirality pdb=" CB ILE A 221 " pdb=" CA ILE A 221 " pdb=" CG1 ILE A 221 " pdb=" CG2 ILE A 221 " both_signs ideal model delta sigma weight residual False 2.64 2.37 0.28 2.00e-01 2.50e+01 1.92e+00 chirality pdb=" CB THR C 91 " pdb=" CA THR C 91 " pdb=" OG1 THR C 91 " pdb=" CG2 THR C 91 " both_signs ideal model delta sigma weight residual False 2.55 2.29 0.26 2.00e-01 2.50e+01 1.69e+00 ... (remaining 1361 not shown) Planarity restraints: 1574 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLY A 311 " 0.056 5.00e-02 4.00e+02 8.57e-02 1.17e+01 pdb=" N PRO A 312 " -0.148 5.00e-02 4.00e+02 pdb=" CA PRO A 312 " 0.045 5.00e-02 4.00e+02 pdb=" CD PRO A 312 " 0.047 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PHE E 235 " 0.045 5.00e-02 4.00e+02 6.77e-02 7.34e+00 pdb=" N PRO E 236 " -0.117 5.00e-02 4.00e+02 pdb=" CA PRO E 236 " 0.035 5.00e-02 4.00e+02 pdb=" CD PRO E 236 " 0.038 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LYS C 87 " -0.037 5.00e-02 4.00e+02 5.68e-02 5.15e+00 pdb=" N PRO C 88 " 0.098 5.00e-02 4.00e+02 pdb=" CA PRO C 88 " -0.029 5.00e-02 4.00e+02 pdb=" CD PRO C 88 " -0.031 5.00e-02 4.00e+02 ... (remaining 1571 not shown) Histogram of nonbonded interaction distances: 2.21 - 2.75: 1376 2.75 - 3.29: 8293 3.29 - 3.82: 14927 3.82 - 4.36: 17396 4.36 - 4.90: 29175 Nonbonded interactions: 71167 Sorted by model distance: nonbonded pdb=" ND1 HIS A 189 " pdb=" OE2 GLU A 247 " model vdw 2.210 3.120 nonbonded pdb=" OG SER E 245 " pdb=" OD1 ASP E 247 " model vdw 2.222 3.040 nonbonded pdb=" OH TYR A 150 " pdb=" OG SER B 9 " model vdw 2.274 3.040 nonbonded pdb=" O ARG C 98 " pdb=" OH TYR C 115 " model vdw 2.283 3.040 nonbonded pdb=" O THR C 111 " pdb=" NH2 ARG C 118 " model vdw 2.299 3.120 ... (remaining 71162 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. 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=0.50 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.370 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.130 Check model and map are aligned: 0.020 Set scattering table: 0.030 Process input model: 8.460 Find NCS groups from input model: 0.040 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.120 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 10.200 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8033 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 : 0.008 0.076 9119 Z= 0.365 Angle : 0.970 12.046 12355 Z= 0.554 Chirality : 0.061 0.292 1364 Planarity : 0.007 0.086 1574 Dihedral : 15.399 88.836 3258 Min Nonbonded Distance : 2.210 Molprobity Statistics. All-atom Clashscore : 8.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.08 % Favored : 92.92 % Rotamer: Outliers : 0.32 % Allowed : 12.61 % Favored : 87.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 3.12 % Twisted General : 0.09 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -4.80 (0.20), residues: 1102 helix: -4.08 (0.13), residues: 400 sheet: -1.74 (0.34), residues: 229 loop : -2.96 (0.23), residues: 473 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG F 385 TYR 0.030 0.003 TYR E 105 PHE 0.024 0.003 PHE E 241 TRP 0.014 0.003 TRP F 234 HIS 0.013 0.002 HIS F 357 Details of bonding type rmsd covalent geometry : bond 0.00792 ( 9114) covalent geometry : angle 0.96782 (12345) SS BOND : bond 0.00516 ( 5) SS BOND : angle 2.38307 ( 10) hydrogen bonds : bond 0.31054 ( 333) hydrogen bonds : angle 10.77469 ( 951) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2204 Ramachandran restraints generated. 1102 Oldfield, 0 Emsley, 1102 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2204 Ramachandran restraints generated. 1102 Oldfield, 0 Emsley, 1102 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 192 residues out of total 970 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 189 time to evaluate : 0.383 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 361 LEU cc_start: 0.8332 (tt) cc_final: 0.7946 (tp) REVERT: B 3 ASP cc_start: 0.8810 (m-30) cc_final: 0.8562 (m-30) REVERT: B 12 ARG cc_start: 0.8951 (ttp-170) cc_final: 0.8239 (ttp-110) REVERT: B 14 ARG cc_start: 0.9146 (tpp80) cc_final: 0.8920 (tpp80) REVERT: C 19 ARG cc_start: 0.7997 (ppt170) cc_final: 0.7761 (ppt170) REVERT: C 20 LEU cc_start: 0.8164 (mt) cc_final: 0.7883 (mm) REVERT: C 33 LYS cc_start: 0.8316 (tttt) cc_final: 0.8108 (ttmt) REVERT: C 83 MET cc_start: 0.8713 (mtm) cc_final: 0.8051 (mtm) REVERT: E 8 ARG cc_start: 0.7593 (ttt180) cc_final: 0.7214 (tpm170) REVERT: E 118 ASP cc_start: 0.8325 (p0) cc_final: 0.8021 (p0) REVERT: F 221 MET cc_start: 0.7727 (ttp) cc_final: 0.7372 (ttp) REVERT: F 342 ARG cc_start: 0.8503 (ttp80) cc_final: 0.8283 (ttp80) REVERT: F 386 MET cc_start: 0.7687 (tmm) cc_final: 0.7468 (tpp) outliers start: 3 outliers final: 3 residues processed: 190 average time/residue: 0.1249 time to fit residues: 30.4661 Evaluate side-chains 135 residues out of total 970 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 132 time to evaluate : 0.331 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 113 VAL Chi-restraints excluded: chain A residue 269 TYR Chi-restraints excluded: chain F residue 325 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 108 optimal weight: 0.8980 chunk 49 optimal weight: 6.9990 chunk 97 optimal weight: 1.9990 chunk 53 optimal weight: 6.9990 chunk 5 optimal weight: 0.2980 chunk 33 optimal weight: 0.9990 chunk 65 optimal weight: 0.7980 chunk 62 optimal weight: 0.7980 chunk 51 optimal weight: 8.9990 chunk 100 optimal weight: 0.1980 chunk 106 optimal weight: 4.9990 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 392 GLN A 404 ASN E 125 ASN F 41 HIS F 292 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3682 r_free = 0.3682 target = 0.094230 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3226 r_free = 0.3226 target = 0.071600 restraints weight = 26375.068| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3271 r_free = 0.3271 target = 0.073796 restraints weight = 13704.653| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.3302 r_free = 0.3302 target = 0.075264 restraints weight = 9256.116| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.3321 r_free = 0.3321 target = 0.076172 restraints weight = 7249.213| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3330 r_free = 0.3330 target = 0.076615 restraints weight = 6248.208| |-----------------------------------------------------------------------------| r_work (final): 0.3320 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3319 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3319 r_free = 0.3319 target_work(ls_wunit_k1) = 0.076 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3318 r_free = 0.3318 target_work(ls_wunit_k1) = 0.076 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| r_final: 0.3318 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7911 moved from start: 0.2250 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 9119 Z= 0.129 Angle : 0.621 7.498 12355 Z= 0.340 Chirality : 0.044 0.206 1364 Planarity : 0.005 0.048 1574 Dihedral : 6.053 32.152 1229 Min Nonbonded Distance : 2.507 Molprobity Statistics. All-atom Clashscore : 7.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.08 % Favored : 95.92 % Rotamer: Outliers : 1.58 % Allowed : 17.44 % Favored : 80.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.25 (0.22), residues: 1102 helix: -2.28 (0.21), residues: 403 sheet: -1.05 (0.35), residues: 218 loop : -2.47 (0.24), residues: 481 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG F 317 TYR 0.018 0.001 TYR A 157 PHE 0.023 0.001 PHE F 222 TRP 0.015 0.001 TRP A 243 HIS 0.003 0.001 HIS F 357 Details of bonding type rmsd covalent geometry : bond 0.00274 ( 9114) covalent geometry : angle 0.62053 (12345) SS BOND : bond 0.00401 ( 5) SS BOND : angle 1.23872 ( 10) hydrogen bonds : bond 0.05069 ( 333) hydrogen bonds : angle 6.14855 ( 951) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2204 Ramachandran restraints generated. 1102 Oldfield, 0 Emsley, 1102 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2204 Ramachandran restraints generated. 1102 Oldfield, 0 Emsley, 1102 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 179 residues out of total 970 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 164 time to evaluate : 0.372 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 213 GLU cc_start: 0.5623 (OUTLIER) cc_final: 0.4944 (pm20) REVERT: A 225 GLU cc_start: 0.6443 (tt0) cc_final: 0.6157 (tp30) REVERT: A 299 MET cc_start: 0.6059 (tpt) cc_final: 0.5832 (tpt) REVERT: A 361 LEU cc_start: 0.8422 (tt) cc_final: 0.8068 (tp) REVERT: B 3 ASP cc_start: 0.8974 (m-30) cc_final: 0.8770 (m-30) REVERT: B 12 ARG cc_start: 0.8929 (ttp-170) cc_final: 0.8619 (ttm170) REVERT: C 18 LEU cc_start: 0.8887 (tp) cc_final: 0.8525 (tt) REVERT: C 20 LEU cc_start: 0.8362 (mt) cc_final: 0.8005 (mt) REVERT: C 33 LYS cc_start: 0.8323 (tttt) cc_final: 0.8108 (ttmt) REVERT: C 83 MET cc_start: 0.8610 (mtm) cc_final: 0.8221 (mtp) REVERT: D 18 GLN cc_start: 0.8927 (tp-100) cc_final: 0.8465 (tp40) outliers start: 15 outliers final: 8 residues processed: 174 average time/residue: 0.1133 time to fit residues: 25.9149 Evaluate side-chains 149 residues out of total 970 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 140 time to evaluate : 0.343 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 213 GLU Chi-restraints excluded: chain A residue 368 VAL Chi-restraints excluded: chain A residue 398 VAL Chi-restraints excluded: chain A residue 406 GLU Chi-restraints excluded: chain D residue 16 VAL Chi-restraints excluded: chain D residue 25 ILE Chi-restraints excluded: chain E residue 59 TYR Chi-restraints excluded: chain E residue 187 VAL Chi-restraints excluded: chain F residue 325 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 62 optimal weight: 4.9990 chunk 27 optimal weight: 0.7980 chunk 29 optimal weight: 0.0870 chunk 42 optimal weight: 5.9990 chunk 11 optimal weight: 0.2980 chunk 13 optimal weight: 0.9980 chunk 33 optimal weight: 2.9990 chunk 59 optimal weight: 7.9990 chunk 39 optimal weight: 0.8980 chunk 53 optimal weight: 0.2980 chunk 101 optimal weight: 0.7980 overall best weight: 0.4558 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 234 HIS F 23 ASN F 279 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3703 r_free = 0.3703 target = 0.095388 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3253 r_free = 0.3253 target = 0.072845 restraints weight = 26444.518| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3298 r_free = 0.3298 target = 0.075040 restraints weight = 13654.639| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3329 r_free = 0.3329 target = 0.076538 restraints weight = 9182.231| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3345 r_free = 0.3345 target = 0.077365 restraints weight = 7180.496| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 48)----------------| | r_work = 0.3359 r_free = 0.3359 target = 0.078026 restraints weight = 6231.479| |-----------------------------------------------------------------------------| r_work (final): 0.3352 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3349 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3349 r_free = 0.3349 target_work(ls_wunit_k1) = 0.077 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3349 r_free = 0.3349 target_work(ls_wunit_k1) = 0.077 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| r_final: 0.3349 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7885 moved from start: 0.3044 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 9119 Z= 0.109 Angle : 0.577 7.060 12355 Z= 0.309 Chirality : 0.043 0.195 1364 Planarity : 0.004 0.041 1574 Dihedral : 5.232 22.067 1226 Min Nonbonded Distance : 2.565 Molprobity Statistics. All-atom Clashscore : 7.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.45 % Favored : 95.55 % Rotamer: Outliers : 1.47 % Allowed : 19.64 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.58 (0.23), residues: 1102 helix: -1.42 (0.23), residues: 415 sheet: -0.60 (0.36), residues: 205 loop : -2.43 (0.25), residues: 482 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG C 67 TYR 0.019 0.001 TYR A 211 PHE 0.015 0.001 PHE F 222 TRP 0.013 0.001 TRP A 243 HIS 0.003 0.001 HIS F 357 Details of bonding type rmsd covalent geometry : bond 0.00234 ( 9114) covalent geometry : angle 0.57714 (12345) SS BOND : bond 0.00179 ( 5) SS BOND : angle 0.86956 ( 10) hydrogen bonds : bond 0.04001 ( 333) hydrogen bonds : angle 5.27023 ( 951) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2204 Ramachandran restraints generated. 1102 Oldfield, 0 Emsley, 1102 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2204 Ramachandran restraints generated. 1102 Oldfield, 0 Emsley, 1102 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 190 residues out of total 970 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 176 time to evaluate : 0.276 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 213 GLU cc_start: 0.5825 (OUTLIER) cc_final: 0.5210 (pm20) REVERT: A 230 MET cc_start: 0.8609 (tpp) cc_final: 0.8270 (tpt) REVERT: A 361 LEU cc_start: 0.8564 (tt) cc_final: 0.8280 (tt) REVERT: C 18 LEU cc_start: 0.8709 (tp) cc_final: 0.8193 (tt) REVERT: C 20 LEU cc_start: 0.8431 (mt) cc_final: 0.8037 (mt) REVERT: C 33 LYS cc_start: 0.8063 (tttt) cc_final: 0.7852 (ttmt) REVERT: C 34 MET cc_start: 0.7931 (mtp) cc_final: 0.7703 (mtt) REVERT: C 67 ARG cc_start: 0.7663 (ptp90) cc_final: 0.7071 (ptp90) REVERT: C 83 MET cc_start: 0.8479 (mtm) cc_final: 0.7755 (mtm) REVERT: C 95 TYR cc_start: 0.8639 (m-10) cc_final: 0.8405 (m-10) REVERT: E 209 LYS cc_start: 0.8082 (mmtp) cc_final: 0.7823 (mttm) REVERT: E 241 PHE cc_start: 0.8978 (p90) cc_final: 0.8348 (p90) REVERT: F 342 ARG cc_start: 0.8736 (tmm-80) cc_final: 0.8531 (tmm-80) outliers start: 14 outliers final: 7 residues processed: 186 average time/residue: 0.1079 time to fit residues: 26.6928 Evaluate side-chains 151 residues out of total 970 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 143 time to evaluate : 0.323 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 213 GLU Chi-restraints excluded: chain A residue 406 GLU Chi-restraints excluded: chain D residue 16 VAL Chi-restraints excluded: chain E residue 59 TYR Chi-restraints excluded: chain E residue 187 VAL Chi-restraints excluded: chain F residue 241 VAL Chi-restraints excluded: chain F residue 325 THR Chi-restraints excluded: chain F residue 371 ASN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 67 optimal weight: 1.9990 chunk 63 optimal weight: 6.9990 chunk 51 optimal weight: 7.9990 chunk 52 optimal weight: 3.9990 chunk 64 optimal weight: 7.9990 chunk 69 optimal weight: 5.9990 chunk 27 optimal weight: 0.0870 chunk 39 optimal weight: 0.9990 chunk 60 optimal weight: 3.9990 chunk 45 optimal weight: 2.9990 chunk 76 optimal weight: 10.0000 overall best weight: 2.0166 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 300 ASN C 123 GLN E 88 ASN E 311 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3658 r_free = 0.3658 target = 0.092883 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3203 r_free = 0.3203 target = 0.070326 restraints weight = 27180.758| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3247 r_free = 0.3247 target = 0.072492 restraints weight = 14071.206| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3277 r_free = 0.3277 target = 0.073919 restraints weight = 9515.845| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3291 r_free = 0.3291 target = 0.074600 restraints weight = 7489.137| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 45)----------------| | r_work = 0.3306 r_free = 0.3306 target = 0.075299 restraints weight = 6593.426| |-----------------------------------------------------------------------------| r_work (final): 0.3298 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7942 moved from start: 0.3231 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.059 9119 Z= 0.163 Angle : 0.615 7.415 12355 Z= 0.325 Chirality : 0.044 0.186 1364 Planarity : 0.004 0.041 1574 Dihedral : 5.232 21.554 1226 Min Nonbonded Distance : 2.559 Molprobity Statistics. All-atom Clashscore : 9.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.63 % Favored : 95.37 % Rotamer: Outliers : 2.84 % Allowed : 21.11 % Favored : 76.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.16 (0.24), residues: 1102 helix: -1.01 (0.24), residues: 418 sheet: -0.46 (0.35), residues: 219 loop : -2.26 (0.26), residues: 465 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG F 333 TYR 0.023 0.001 TYR A 211 PHE 0.021 0.002 PHE F 222 TRP 0.011 0.001 TRP A 243 HIS 0.006 0.001 HIS E 54 Details of bonding type rmsd covalent geometry : bond 0.00367 ( 9114) covalent geometry : angle 0.61198 (12345) SS BOND : bond 0.00430 ( 5) SS BOND : angle 2.17926 ( 10) hydrogen bonds : bond 0.03867 ( 333) hydrogen bonds : angle 5.15109 ( 951) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2204 Ramachandran restraints generated. 1102 Oldfield, 0 Emsley, 1102 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2204 Ramachandran restraints generated. 1102 Oldfield, 0 Emsley, 1102 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 177 residues out of total 970 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 150 time to evaluate : 0.303 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 211 TYR cc_start: 0.7260 (t80) cc_final: 0.6711 (t80) REVERT: A 213 GLU cc_start: 0.5910 (OUTLIER) cc_final: 0.5587 (pm20) REVERT: A 230 MET cc_start: 0.8672 (tpp) cc_final: 0.8157 (tpp) REVERT: A 299 MET cc_start: 0.6042 (tpt) cc_final: 0.5773 (tpp) REVERT: C 18 LEU cc_start: 0.8754 (tp) cc_final: 0.8291 (tt) REVERT: C 20 LEU cc_start: 0.8411 (mt) cc_final: 0.8008 (mt) REVERT: C 67 ARG cc_start: 0.7533 (ptp90) cc_final: 0.7119 (ptp90) REVERT: C 83 MET cc_start: 0.8541 (mtm) cc_final: 0.7895 (mtm) REVERT: D 20 LYS cc_start: 0.8595 (tmmt) cc_final: 0.8391 (tmmt) REVERT: E 241 PHE cc_start: 0.9061 (p90) cc_final: 0.8529 (p90) REVERT: F 378 ASP cc_start: 0.8504 (m-30) cc_final: 0.8258 (t0) outliers start: 27 outliers final: 18 residues processed: 169 average time/residue: 0.1052 time to fit residues: 23.8799 Evaluate side-chains 155 residues out of total 970 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 136 time to evaluate : 0.327 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 85 ASN Chi-restraints excluded: chain A residue 203 VAL Chi-restraints excluded: chain A residue 213 GLU Chi-restraints excluded: chain A residue 368 VAL Chi-restraints excluded: chain A residue 398 VAL Chi-restraints excluded: chain B residue 26 VAL Chi-restraints excluded: chain C residue 37 VAL Chi-restraints excluded: chain C residue 113 THR Chi-restraints excluded: chain D residue 16 VAL Chi-restraints excluded: chain D residue 25 ILE Chi-restraints excluded: chain E residue 59 TYR Chi-restraints excluded: chain E residue 187 VAL Chi-restraints excluded: chain E residue 234 PHE Chi-restraints excluded: chain F residue 241 VAL Chi-restraints excluded: chain F residue 325 THR Chi-restraints excluded: chain F residue 334 VAL Chi-restraints excluded: chain F residue 349 SER Chi-restraints excluded: chain F residue 364 THR Chi-restraints excluded: chain F residue 371 ASN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 107 optimal weight: 0.4980 chunk 101 optimal weight: 3.9990 chunk 106 optimal weight: 0.9990 chunk 62 optimal weight: 3.9990 chunk 6 optimal weight: 10.0000 chunk 15 optimal weight: 0.3980 chunk 48 optimal weight: 0.9990 chunk 58 optimal weight: 5.9990 chunk 82 optimal weight: 0.8980 chunk 39 optimal weight: 0.8980 chunk 78 optimal weight: 0.9990 overall best weight: 0.7382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 77 ASN E 88 ASN E 311 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3689 r_free = 0.3689 target = 0.094768 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3242 r_free = 0.3242 target = 0.072213 restraints weight = 26635.403| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3287 r_free = 0.3287 target = 0.074424 restraints weight = 13823.622| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3317 r_free = 0.3317 target = 0.075854 restraints weight = 9313.829| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3333 r_free = 0.3333 target = 0.076667 restraints weight = 7319.173| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.3348 r_free = 0.3348 target = 0.077360 restraints weight = 6375.627| |-----------------------------------------------------------------------------| r_work (final): 0.3337 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7899 moved from start: 0.3551 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 9119 Z= 0.109 Angle : 0.579 8.561 12355 Z= 0.301 Chirality : 0.043 0.185 1364 Planarity : 0.004 0.038 1574 Dihedral : 4.919 20.387 1226 Min Nonbonded Distance : 2.380 Molprobity Statistics. All-atom Clashscore : 8.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.08 % Favored : 95.92 % Rotamer: Outliers : 2.52 % Allowed : 21.95 % Favored : 75.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.79 (0.24), residues: 1102 helix: -0.61 (0.25), residues: 415 sheet: -0.32 (0.35), residues: 215 loop : -2.09 (0.26), residues: 472 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG F 317 TYR 0.018 0.001 TYR A 211 PHE 0.016 0.001 PHE F 222 TRP 0.011 0.001 TRP A 243 HIS 0.003 0.001 HIS F 357 Details of bonding type rmsd covalent geometry : bond 0.00245 ( 9114) covalent geometry : angle 0.57876 (12345) SS BOND : bond 0.00197 ( 5) SS BOND : angle 1.08011 ( 10) hydrogen bonds : bond 0.03413 ( 333) hydrogen bonds : angle 4.86570 ( 951) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2204 Ramachandran restraints generated. 1102 Oldfield, 0 Emsley, 1102 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2204 Ramachandran restraints generated. 1102 Oldfield, 0 Emsley, 1102 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 185 residues out of total 970 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 161 time to evaluate : 0.417 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 19 ARG cc_start: 0.8654 (ttm-80) cc_final: 0.8081 (tpp80) REVERT: C 20 LEU cc_start: 0.8459 (mt) cc_final: 0.8151 (mt) REVERT: C 83 MET cc_start: 0.8596 (mtm) cc_final: 0.8133 (mtm) REVERT: D 18 GLN cc_start: 0.8989 (tp-100) cc_final: 0.8576 (tp40) REVERT: D 20 LYS cc_start: 0.8633 (tmmt) cc_final: 0.8424 (tmmt) REVERT: E 209 LYS cc_start: 0.8091 (mmtp) cc_final: 0.7773 (mttm) REVERT: E 241 PHE cc_start: 0.9012 (p90) cc_final: 0.8497 (p90) REVERT: F 350 THR cc_start: 0.8400 (p) cc_final: 0.8162 (p) REVERT: F 378 ASP cc_start: 0.8539 (m-30) cc_final: 0.8326 (t0) outliers start: 24 outliers final: 21 residues processed: 177 average time/residue: 0.1016 time to fit residues: 24.4947 Evaluate side-chains 168 residues out of total 970 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 147 time to evaluate : 0.313 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 85 ASN Chi-restraints excluded: chain A residue 159 VAL Chi-restraints excluded: chain A residue 332 VAL Chi-restraints excluded: chain A residue 359 ILE Chi-restraints excluded: chain A residue 368 VAL Chi-restraints excluded: chain A residue 406 GLU Chi-restraints excluded: chain B residue 26 VAL Chi-restraints excluded: chain C residue 37 VAL Chi-restraints excluded: chain C residue 77 ASN Chi-restraints excluded: chain C residue 113 THR Chi-restraints excluded: chain D residue 16 VAL Chi-restraints excluded: chain E residue 59 TYR Chi-restraints excluded: chain E residue 187 VAL Chi-restraints excluded: chain E residue 234 PHE Chi-restraints excluded: chain F residue 211 LYS Chi-restraints excluded: chain F residue 241 VAL Chi-restraints excluded: chain F residue 291 LEU Chi-restraints excluded: chain F residue 325 THR Chi-restraints excluded: chain F residue 349 SER Chi-restraints excluded: chain F residue 364 THR Chi-restraints excluded: chain F residue 371 ASN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 94 optimal weight: 2.9990 chunk 28 optimal weight: 0.9990 chunk 83 optimal weight: 0.6980 chunk 106 optimal weight: 3.9990 chunk 20 optimal weight: 5.9990 chunk 24 optimal weight: 0.7980 chunk 44 optimal weight: 6.9990 chunk 93 optimal weight: 8.9990 chunk 8 optimal weight: 4.9990 chunk 63 optimal weight: 0.2980 chunk 33 optimal weight: 7.9990 overall best weight: 1.1584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 88 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3685 r_free = 0.3685 target = 0.094561 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3233 r_free = 0.3233 target = 0.071809 restraints weight = 26584.272| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3278 r_free = 0.3278 target = 0.073971 restraints weight = 13906.185| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3307 r_free = 0.3307 target = 0.075414 restraints weight = 9456.187| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3325 r_free = 0.3325 target = 0.076262 restraints weight = 7466.564| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.3337 r_free = 0.3337 target = 0.076844 restraints weight = 6499.279| |-----------------------------------------------------------------------------| r_work (final): 0.3328 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7914 moved from start: 0.3649 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 9119 Z= 0.121 Angle : 0.587 9.755 12355 Z= 0.305 Chirality : 0.043 0.176 1364 Planarity : 0.004 0.038 1574 Dihedral : 4.787 19.837 1226 Min Nonbonded Distance : 2.502 Molprobity Statistics. All-atom Clashscore : 9.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.90 % Favored : 96.10 % Rotamer: Outliers : 3.26 % Allowed : 22.06 % Favored : 74.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.54 (0.24), residues: 1102 helix: -0.29 (0.25), residues: 417 sheet: -0.24 (0.35), residues: 213 loop : -2.03 (0.26), residues: 472 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG E 96 TYR 0.018 0.001 TYR F 318 PHE 0.013 0.001 PHE F 376 TRP 0.012 0.001 TRP E 99 HIS 0.003 0.001 HIS F 357 Details of bonding type rmsd covalent geometry : bond 0.00274 ( 9114) covalent geometry : angle 0.58628 (12345) SS BOND : bond 0.00203 ( 5) SS BOND : angle 0.88617 ( 10) hydrogen bonds : bond 0.03343 ( 333) hydrogen bonds : angle 4.79592 ( 951) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2204 Ramachandran restraints generated. 1102 Oldfield, 0 Emsley, 1102 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2204 Ramachandran restraints generated. 1102 Oldfield, 0 Emsley, 1102 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 176 residues out of total 970 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 145 time to evaluate : 0.278 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 197 MET cc_start: 0.8487 (mtt) cc_final: 0.8097 (mtt) REVERT: A 361 LEU cc_start: 0.8798 (tp) cc_final: 0.8572 (tt) REVERT: C 20 LEU cc_start: 0.8444 (mt) cc_final: 0.8186 (mt) REVERT: C 34 MET cc_start: 0.8032 (mtp) cc_final: 0.7681 (mtt) REVERT: C 83 MET cc_start: 0.8581 (mtm) cc_final: 0.8051 (mtm) REVERT: D 18 GLN cc_start: 0.8977 (tp-100) cc_final: 0.8555 (tp40) REVERT: D 20 LYS cc_start: 0.8682 (tmmt) cc_final: 0.8480 (tmtt) REVERT: E 209 LYS cc_start: 0.8119 (mmtp) cc_final: 0.7811 (mttm) REVERT: E 241 PHE cc_start: 0.9019 (p90) cc_final: 0.8568 (p90) REVERT: F 378 ASP cc_start: 0.8490 (m-30) cc_final: 0.8275 (t0) outliers start: 31 outliers final: 25 residues processed: 166 average time/residue: 0.0890 time to fit residues: 20.3518 Evaluate side-chains 161 residues out of total 970 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 136 time to evaluate : 0.333 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 MET Chi-restraints excluded: chain A residue 85 ASN Chi-restraints excluded: chain A residue 159 VAL Chi-restraints excluded: chain A residue 203 VAL Chi-restraints excluded: chain A residue 271 ILE Chi-restraints excluded: chain A residue 332 VAL Chi-restraints excluded: chain A residue 359 ILE Chi-restraints excluded: chain A residue 368 VAL Chi-restraints excluded: chain A residue 398 VAL Chi-restraints excluded: chain A residue 406 GLU Chi-restraints excluded: chain B residue 26 VAL Chi-restraints excluded: chain C residue 37 VAL Chi-restraints excluded: chain C residue 113 THR Chi-restraints excluded: chain D residue 16 VAL Chi-restraints excluded: chain D residue 25 ILE Chi-restraints excluded: chain E residue 59 TYR Chi-restraints excluded: chain E residue 187 VAL Chi-restraints excluded: chain E residue 234 PHE Chi-restraints excluded: chain F residue 211 LYS Chi-restraints excluded: chain F residue 241 VAL Chi-restraints excluded: chain F residue 291 LEU Chi-restraints excluded: chain F residue 325 THR Chi-restraints excluded: chain F residue 349 SER Chi-restraints excluded: chain F residue 364 THR Chi-restraints excluded: chain F residue 371 ASN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 58 optimal weight: 10.0000 chunk 47 optimal weight: 8.9990 chunk 76 optimal weight: 9.9990 chunk 100 optimal weight: 1.9990 chunk 66 optimal weight: 9.9990 chunk 3 optimal weight: 0.7980 chunk 40 optimal weight: 1.9990 chunk 94 optimal weight: 0.2980 chunk 15 optimal weight: 2.9990 chunk 27 optimal weight: 4.9990 chunk 96 optimal weight: 5.9990 overall best weight: 1.6186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 77 ASN E 311 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3669 r_free = 0.3669 target = 0.093396 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3214 r_free = 0.3214 target = 0.070875 restraints weight = 26926.916| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3260 r_free = 0.3260 target = 0.073082 restraints weight = 13866.070| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3290 r_free = 0.3290 target = 0.074523 restraints weight = 9340.990| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3308 r_free = 0.3308 target = 0.075431 restraints weight = 7333.090| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 18)----------------| | r_work = 0.3314 r_free = 0.3314 target = 0.075756 restraints weight = 6335.819| |-----------------------------------------------------------------------------| r_work (final): 0.3307 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7937 moved from start: 0.3757 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 9119 Z= 0.138 Angle : 0.613 9.500 12355 Z= 0.320 Chirality : 0.044 0.198 1364 Planarity : 0.003 0.038 1574 Dihedral : 4.771 20.179 1226 Min Nonbonded Distance : 2.418 Molprobity Statistics. All-atom Clashscore : 10.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.99 % Favored : 95.01 % Rotamer: Outliers : 3.47 % Allowed : 22.90 % Favored : 73.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.50 (0.24), residues: 1102 helix: -0.16 (0.26), residues: 418 sheet: -0.27 (0.35), residues: 210 loop : -2.09 (0.26), residues: 474 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 12 TYR 0.023 0.001 TYR A 211 PHE 0.018 0.001 PHE A 362 TRP 0.010 0.001 TRP E 211 HIS 0.004 0.001 HIS F 357 Details of bonding type rmsd covalent geometry : bond 0.00315 ( 9114) covalent geometry : angle 0.61280 (12345) SS BOND : bond 0.00233 ( 5) SS BOND : angle 0.82387 ( 10) hydrogen bonds : bond 0.03500 ( 333) hydrogen bonds : angle 4.82750 ( 951) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2204 Ramachandran restraints generated. 1102 Oldfield, 0 Emsley, 1102 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2204 Ramachandran restraints generated. 1102 Oldfield, 0 Emsley, 1102 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 167 residues out of total 970 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 134 time to evaluate : 0.331 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 197 MET cc_start: 0.8477 (mtt) cc_final: 0.8073 (mtt) REVERT: A 230 MET cc_start: 0.8144 (tpp) cc_final: 0.7609 (tpp) REVERT: A 361 LEU cc_start: 0.8901 (tp) cc_final: 0.8665 (tt) REVERT: C 20 LEU cc_start: 0.8434 (mt) cc_final: 0.8168 (mt) REVERT: C 34 MET cc_start: 0.8078 (mtp) cc_final: 0.7730 (mtt) REVERT: C 83 MET cc_start: 0.8626 (mtm) cc_final: 0.8110 (mtm) REVERT: D 18 GLN cc_start: 0.9001 (tp-100) cc_final: 0.8574 (tp40) REVERT: D 20 LYS cc_start: 0.8732 (tmmt) cc_final: 0.8532 (tmtt) REVERT: F 318 TYR cc_start: 0.7707 (t80) cc_final: 0.7228 (t80) REVERT: F 378 ASP cc_start: 0.8502 (m-30) cc_final: 0.8268 (t0) outliers start: 33 outliers final: 28 residues processed: 157 average time/residue: 0.0837 time to fit residues: 18.7262 Evaluate side-chains 155 residues out of total 970 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 127 time to evaluate : 0.337 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 MET Chi-restraints excluded: chain A residue 85 ASN Chi-restraints excluded: chain A residue 148 TYR Chi-restraints excluded: chain A residue 159 VAL Chi-restraints excluded: chain A residue 203 VAL Chi-restraints excluded: chain A residue 271 ILE Chi-restraints excluded: chain A residue 332 VAL Chi-restraints excluded: chain A residue 347 ILE Chi-restraints excluded: chain A residue 359 ILE Chi-restraints excluded: chain A residue 368 VAL Chi-restraints excluded: chain A residue 398 VAL Chi-restraints excluded: chain B residue 26 VAL Chi-restraints excluded: chain C residue 37 VAL Chi-restraints excluded: chain C residue 77 ASN Chi-restraints excluded: chain C residue 113 THR Chi-restraints excluded: chain D residue 16 VAL Chi-restraints excluded: chain D residue 25 ILE Chi-restraints excluded: chain E residue 59 TYR Chi-restraints excluded: chain E residue 157 ILE Chi-restraints excluded: chain E residue 187 VAL Chi-restraints excluded: chain E residue 234 PHE Chi-restraints excluded: chain E residue 286 LEU Chi-restraints excluded: chain E residue 317 CYS Chi-restraints excluded: chain F residue 241 VAL Chi-restraints excluded: chain F residue 266 LEU Chi-restraints excluded: chain F residue 325 THR Chi-restraints excluded: chain F residue 349 SER Chi-restraints excluded: chain F residue 371 ASN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 65 optimal weight: 5.9990 chunk 13 optimal weight: 1.9990 chunk 11 optimal weight: 0.0270 chunk 9 optimal weight: 2.9990 chunk 64 optimal weight: 2.9990 chunk 83 optimal weight: 0.6980 chunk 96 optimal weight: 6.9990 chunk 84 optimal weight: 3.9990 chunk 87 optimal weight: 3.9990 chunk 36 optimal weight: 4.9990 chunk 45 optimal weight: 5.9990 overall best weight: 1.7444 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 311 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3662 r_free = 0.3662 target = 0.093258 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3213 r_free = 0.3213 target = 0.070767 restraints weight = 26581.858| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3258 r_free = 0.3258 target = 0.072949 restraints weight = 13721.929| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3288 r_free = 0.3288 target = 0.074374 restraints weight = 9236.901| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3303 r_free = 0.3303 target = 0.075167 restraints weight = 7261.301| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 38)----------------| | r_work = 0.3317 r_free = 0.3317 target = 0.075816 restraints weight = 6341.329| |-----------------------------------------------------------------------------| r_work (final): 0.3308 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7935 moved from start: 0.3793 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 9119 Z= 0.142 Angle : 0.610 9.815 12355 Z= 0.319 Chirality : 0.044 0.171 1364 Planarity : 0.003 0.037 1574 Dihedral : 4.753 19.973 1226 Min Nonbonded Distance : 2.505 Molprobity Statistics. All-atom Clashscore : 10.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.63 % Favored : 95.37 % Rotamer: Outliers : 3.36 % Allowed : 23.21 % Favored : 73.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.35 (0.25), residues: 1102 helix: -0.02 (0.26), residues: 416 sheet: -0.17 (0.35), residues: 220 loop : -2.07 (0.26), residues: 466 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 12 TYR 0.014 0.001 TYR F 318 PHE 0.017 0.001 PHE A 362 TRP 0.010 0.001 TRP A 243 HIS 0.004 0.001 HIS F 357 Details of bonding type rmsd covalent geometry : bond 0.00326 ( 9114) covalent geometry : angle 0.60987 (12345) SS BOND : bond 0.00251 ( 5) SS BOND : angle 0.89160 ( 10) hydrogen bonds : bond 0.03501 ( 333) hydrogen bonds : angle 4.80947 ( 951) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2204 Ramachandran restraints generated. 1102 Oldfield, 0 Emsley, 1102 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2204 Ramachandran restraints generated. 1102 Oldfield, 0 Emsley, 1102 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 163 residues out of total 970 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 131 time to evaluate : 0.304 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 197 MET cc_start: 0.8494 (mtt) cc_final: 0.8084 (mtt) REVERT: A 230 MET cc_start: 0.8233 (tpp) cc_final: 0.7659 (tpp) REVERT: C 20 LEU cc_start: 0.8431 (mt) cc_final: 0.8219 (mt) REVERT: C 34 MET cc_start: 0.8087 (mtp) cc_final: 0.7752 (mtt) REVERT: C 67 ARG cc_start: 0.7600 (ptp90) cc_final: 0.7264 (ptp90) REVERT: C 83 MET cc_start: 0.8607 (mtm) cc_final: 0.8107 (mtm) REVERT: D 18 GLN cc_start: 0.9003 (tp-100) cc_final: 0.8577 (tp40) REVERT: D 20 LYS cc_start: 0.8727 (tmmt) cc_final: 0.8512 (tmtt) REVERT: F 318 TYR cc_start: 0.7715 (t80) cc_final: 0.7113 (t80) REVERT: F 378 ASP cc_start: 0.8447 (m-30) cc_final: 0.8126 (m-30) outliers start: 32 outliers final: 29 residues processed: 155 average time/residue: 0.0960 time to fit residues: 20.6980 Evaluate side-chains 155 residues out of total 970 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 126 time to evaluate : 0.333 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 MET Chi-restraints excluded: chain A residue 85 ASN Chi-restraints excluded: chain A residue 148 TYR Chi-restraints excluded: chain A residue 159 VAL Chi-restraints excluded: chain A residue 181 LEU Chi-restraints excluded: chain A residue 203 VAL Chi-restraints excluded: chain A residue 271 ILE Chi-restraints excluded: chain A residue 332 VAL Chi-restraints excluded: chain A residue 347 ILE Chi-restraints excluded: chain A residue 368 VAL Chi-restraints excluded: chain A residue 398 VAL Chi-restraints excluded: chain B residue 26 VAL Chi-restraints excluded: chain C residue 37 VAL Chi-restraints excluded: chain C residue 113 THR Chi-restraints excluded: chain C residue 125 THR Chi-restraints excluded: chain D residue 16 VAL Chi-restraints excluded: chain D residue 25 ILE Chi-restraints excluded: chain E residue 59 TYR Chi-restraints excluded: chain E residue 157 ILE Chi-restraints excluded: chain E residue 187 VAL Chi-restraints excluded: chain E residue 234 PHE Chi-restraints excluded: chain E residue 286 LEU Chi-restraints excluded: chain E residue 317 CYS Chi-restraints excluded: chain F residue 241 VAL Chi-restraints excluded: chain F residue 266 LEU Chi-restraints excluded: chain F residue 291 LEU Chi-restraints excluded: chain F residue 325 THR Chi-restraints excluded: chain F residue 349 SER Chi-restraints excluded: chain F residue 371 ASN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 17 optimal weight: 1.9990 chunk 79 optimal weight: 9.9990 chunk 21 optimal weight: 0.3980 chunk 30 optimal weight: 3.9990 chunk 71 optimal weight: 0.7980 chunk 32 optimal weight: 4.9990 chunk 15 optimal weight: 10.0000 chunk 92 optimal weight: 6.9990 chunk 35 optimal weight: 0.9990 chunk 14 optimal weight: 3.9990 chunk 45 optimal weight: 6.9990 overall best weight: 1.6386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 77 ASN E 311 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3664 r_free = 0.3664 target = 0.093423 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3214 r_free = 0.3214 target = 0.070859 restraints weight = 26550.200| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3259 r_free = 0.3259 target = 0.073027 restraints weight = 13890.600| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3288 r_free = 0.3288 target = 0.074447 restraints weight = 9431.544| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 43)----------------| | r_work = 0.3306 r_free = 0.3306 target = 0.075329 restraints weight = 7442.742| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3315 r_free = 0.3315 target = 0.075798 restraints weight = 6457.551| |-----------------------------------------------------------------------------| r_work (final): 0.3308 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7939 moved from start: 0.3864 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 9119 Z= 0.138 Angle : 0.612 10.916 12355 Z= 0.319 Chirality : 0.044 0.188 1364 Planarity : 0.003 0.037 1574 Dihedral : 4.740 20.166 1226 Min Nonbonded Distance : 2.423 Molprobity Statistics. All-atom Clashscore : 9.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.17 % Favored : 94.83 % Rotamer: Outliers : 3.05 % Allowed : 23.63 % Favored : 73.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.26 (0.25), residues: 1102 helix: 0.06 (0.26), residues: 418 sheet: -0.07 (0.36), residues: 215 loop : -2.04 (0.26), residues: 469 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 12 TYR 0.022 0.001 TYR A 211 PHE 0.018 0.001 PHE F 222 TRP 0.010 0.001 TRP A 243 HIS 0.004 0.001 HIS F 357 Details of bonding type rmsd covalent geometry : bond 0.00317 ( 9114) covalent geometry : angle 0.61179 (12345) SS BOND : bond 0.00271 ( 5) SS BOND : angle 0.85236 ( 10) hydrogen bonds : bond 0.03451 ( 333) hydrogen bonds : angle 4.80806 ( 951) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2204 Ramachandran restraints generated. 1102 Oldfield, 0 Emsley, 1102 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2204 Ramachandran restraints generated. 1102 Oldfield, 0 Emsley, 1102 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 157 residues out of total 970 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 128 time to evaluate : 0.538 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 197 MET cc_start: 0.8542 (mtt) cc_final: 0.8121 (mtt) REVERT: A 230 MET cc_start: 0.8248 (tpp) cc_final: 0.7706 (tpp) REVERT: C 20 LEU cc_start: 0.8433 (mt) cc_final: 0.8194 (mt) REVERT: C 34 MET cc_start: 0.8129 (mtp) cc_final: 0.7716 (mtt) REVERT: C 67 ARG cc_start: 0.7565 (ptp90) cc_final: 0.7248 (ptp90) REVERT: C 83 MET cc_start: 0.8616 (mtm) cc_final: 0.8078 (mtm) REVERT: D 18 GLN cc_start: 0.8984 (tp-100) cc_final: 0.8571 (tp40) REVERT: E 8 ARG cc_start: 0.8773 (mtt180) cc_final: 0.8107 (tpm170) REVERT: F 318 TYR cc_start: 0.7773 (t80) cc_final: 0.7225 (t80) outliers start: 29 outliers final: 29 residues processed: 150 average time/residue: 0.0831 time to fit residues: 17.6703 Evaluate side-chains 150 residues out of total 970 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 121 time to evaluate : 0.326 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 MET Chi-restraints excluded: chain A residue 85 ASN Chi-restraints excluded: chain A residue 148 TYR Chi-restraints excluded: chain A residue 159 VAL Chi-restraints excluded: chain A residue 203 VAL Chi-restraints excluded: chain A residue 271 ILE Chi-restraints excluded: chain A residue 332 VAL Chi-restraints excluded: chain A residue 347 ILE Chi-restraints excluded: chain A residue 368 VAL Chi-restraints excluded: chain A residue 398 VAL Chi-restraints excluded: chain B residue 26 VAL Chi-restraints excluded: chain C residue 37 VAL Chi-restraints excluded: chain C residue 77 ASN Chi-restraints excluded: chain C residue 113 THR Chi-restraints excluded: chain C residue 125 THR Chi-restraints excluded: chain D residue 16 VAL Chi-restraints excluded: chain D residue 25 ILE Chi-restraints excluded: chain E residue 59 TYR Chi-restraints excluded: chain E residue 157 ILE Chi-restraints excluded: chain E residue 187 VAL Chi-restraints excluded: chain E residue 234 PHE Chi-restraints excluded: chain E residue 286 LEU Chi-restraints excluded: chain E residue 317 CYS Chi-restraints excluded: chain F residue 241 VAL Chi-restraints excluded: chain F residue 266 LEU Chi-restraints excluded: chain F residue 325 THR Chi-restraints excluded: chain F residue 349 SER Chi-restraints excluded: chain F residue 364 THR Chi-restraints excluded: chain F residue 371 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 9 optimal weight: 0.8980 chunk 23 optimal weight: 0.3980 chunk 68 optimal weight: 8.9990 chunk 67 optimal weight: 7.9990 chunk 37 optimal weight: 8.9990 chunk 39 optimal weight: 0.9990 chunk 62 optimal weight: 3.9990 chunk 36 optimal weight: 0.8980 chunk 75 optimal weight: 5.9990 chunk 31 optimal weight: 8.9990 chunk 87 optimal weight: 0.9980 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 88 ASN E 311 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3685 r_free = 0.3685 target = 0.094593 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3238 r_free = 0.3238 target = 0.072037 restraints weight = 26474.405| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3284 r_free = 0.3284 target = 0.074259 restraints weight = 13728.758| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3313 r_free = 0.3313 target = 0.075681 restraints weight = 9261.871| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3333 r_free = 0.3333 target = 0.076642 restraints weight = 7288.728| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 21)----------------| | r_work = 0.3340 r_free = 0.3340 target = 0.077039 restraints weight = 6278.347| |-----------------------------------------------------------------------------| r_work (final): 0.3332 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7910 moved from start: 0.4014 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 9119 Z= 0.116 Angle : 0.618 11.692 12355 Z= 0.319 Chirality : 0.043 0.186 1364 Planarity : 0.003 0.038 1574 Dihedral : 4.596 18.708 1226 Min Nonbonded Distance : 2.495 Molprobity Statistics. All-atom Clashscore : 9.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.26 % Favored : 95.74 % Rotamer: Outliers : 2.94 % Allowed : 23.42 % Favored : 73.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.19 (0.25), residues: 1102 helix: 0.08 (0.26), residues: 423 sheet: -0.03 (0.36), residues: 213 loop : -1.96 (0.27), residues: 466 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 12 TYR 0.014 0.001 TYR F 318 PHE 0.012 0.001 PHE A 362 TRP 0.011 0.001 TRP A 243 HIS 0.003 0.001 HIS F 357 Details of bonding type rmsd covalent geometry : bond 0.00265 ( 9114) covalent geometry : angle 0.61756 (12345) SS BOND : bond 0.00227 ( 5) SS BOND : angle 0.77200 ( 10) hydrogen bonds : bond 0.03272 ( 333) hydrogen bonds : angle 4.71832 ( 951) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2204 Ramachandran restraints generated. 1102 Oldfield, 0 Emsley, 1102 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2204 Ramachandran restraints generated. 1102 Oldfield, 0 Emsley, 1102 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 163 residues out of total 970 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 135 time to evaluate : 0.326 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 85 ASN cc_start: 0.7066 (OUTLIER) cc_final: 0.6730 (m-40) REVERT: A 197 MET cc_start: 0.8537 (mtt) cc_final: 0.8112 (mtt) REVERT: A 230 MET cc_start: 0.8265 (tpp) cc_final: 0.7736 (tpp) REVERT: C 34 MET cc_start: 0.8121 (mtp) cc_final: 0.7776 (mtt) REVERT: C 67 ARG cc_start: 0.7713 (ptp90) cc_final: 0.7476 (ptp90) REVERT: C 83 MET cc_start: 0.8609 (mtm) cc_final: 0.8107 (mtm) REVERT: D 18 GLN cc_start: 0.8959 (tp-100) cc_final: 0.8611 (tp40) REVERT: F 318 TYR cc_start: 0.7734 (t80) cc_final: 0.7236 (t80) outliers start: 28 outliers final: 25 residues processed: 157 average time/residue: 0.0875 time to fit residues: 19.4077 Evaluate side-chains 155 residues out of total 970 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 129 time to evaluate : 0.354 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 MET Chi-restraints excluded: chain A residue 85 ASN Chi-restraints excluded: chain A residue 148 TYR Chi-restraints excluded: chain A residue 159 VAL Chi-restraints excluded: chain A residue 181 LEU Chi-restraints excluded: chain A residue 203 VAL Chi-restraints excluded: chain A residue 271 ILE Chi-restraints excluded: chain A residue 332 VAL Chi-restraints excluded: chain A residue 347 ILE Chi-restraints excluded: chain A residue 398 VAL Chi-restraints excluded: chain B residue 26 VAL Chi-restraints excluded: chain C residue 37 VAL Chi-restraints excluded: chain C residue 113 THR Chi-restraints excluded: chain C residue 125 THR Chi-restraints excluded: chain D residue 16 VAL Chi-restraints excluded: chain E residue 59 TYR Chi-restraints excluded: chain E residue 187 VAL Chi-restraints excluded: chain E residue 234 PHE Chi-restraints excluded: chain E residue 286 LEU Chi-restraints excluded: chain E residue 317 CYS Chi-restraints excluded: chain F residue 241 VAL Chi-restraints excluded: chain F residue 266 LEU Chi-restraints excluded: chain F residue 291 LEU Chi-restraints excluded: chain F residue 325 THR Chi-restraints excluded: chain F residue 349 SER Chi-restraints excluded: chain F residue 371 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 20 optimal weight: 0.9990 chunk 73 optimal weight: 7.9990 chunk 52 optimal weight: 2.9990 chunk 103 optimal weight: 4.9990 chunk 102 optimal weight: 1.9990 chunk 14 optimal weight: 0.9990 chunk 64 optimal weight: 0.4980 chunk 81 optimal weight: 6.9990 chunk 30 optimal weight: 1.9990 chunk 99 optimal weight: 0.7980 chunk 8 optimal weight: 4.9990 overall best weight: 1.0586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 88 ASN E 311 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3681 r_free = 0.3681 target = 0.094354 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3232 r_free = 0.3232 target = 0.071766 restraints weight = 26450.981| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3277 r_free = 0.3277 target = 0.073962 restraints weight = 13791.368| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3306 r_free = 0.3306 target = 0.075381 restraints weight = 9356.243| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 42)----------------| | r_work = 0.3325 r_free = 0.3325 target = 0.076306 restraints weight = 7385.495| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3334 r_free = 0.3334 target = 0.076756 restraints weight = 6380.734| |-----------------------------------------------------------------------------| r_work (final): 0.3326 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7915 moved from start: 0.4095 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 9119 Z= 0.120 Angle : 0.619 11.042 12355 Z= 0.319 Chirality : 0.044 0.183 1364 Planarity : 0.003 0.038 1574 Dihedral : 4.575 18.775 1226 Min Nonbonded Distance : 2.489 Molprobity Statistics. All-atom Clashscore : 9.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.63 % Favored : 95.37 % Rotamer: Outliers : 3.05 % Allowed : 23.95 % Favored : 73.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.13 (0.25), residues: 1102 helix: 0.11 (0.26), residues: 425 sheet: -0.06 (0.36), residues: 213 loop : -1.89 (0.27), residues: 464 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 12 TYR 0.020 0.001 TYR A 211 PHE 0.015 0.001 PHE F 222 TRP 0.011 0.001 TRP C 36 HIS 0.003 0.001 HIS F 357 Details of bonding type rmsd covalent geometry : bond 0.00276 ( 9114) covalent geometry : angle 0.61873 (12345) SS BOND : bond 0.00243 ( 5) SS BOND : angle 0.78483 ( 10) hydrogen bonds : bond 0.03257 ( 333) hydrogen bonds : angle 4.69190 ( 951) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1664.86 seconds wall clock time: 29 minutes 19.61 seconds (1759.61 seconds total)