Starting phenix.real_space_refine on Tue Sep 24 20:33:57 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6m1i_30048/09_2024/6m1i_30048.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6m1i_30048/09_2024/6m1i_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/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6m1i_30048/09_2024/6m1i_30048.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6m1i_30048/09_2024/6m1i_30048.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6m1i_30048/09_2024/6m1i_30048.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6m1i_30048/09_2024/6m1i_30048.cif" } resolution = 3.5 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.003 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): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/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: {'GLN:plan1': 2, 'ASP:plan': 1, 'HIS:plan': 1, 'PHE:plan': 2, 'GLU:plan': 2, 'ARG:plan': 2} 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: 5.17, per 1000 atoms: 0.58 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: 2.32 Conformation dependent library (CDL) restraints added in 1.1 seconds 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: 1.11 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: 2.38 Time building geometry restraints manager: 2.71 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 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: 0.500 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: 0.000 Extract box with map and model: 0.330 Check model and map are aligned: 0.060 Set scattering table: 0.070 Process input model: 22.850 Find NCS groups from input model: 0.110 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.850 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 26.800 ------------------------------------------------------------------------------- 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 9114 Z= 0.516 Angle : 0.968 12.046 12345 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.80 (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 TRP 0.014 0.003 TRP F 234 HIS 0.013 0.002 HIS F 357 PHE 0.024 0.003 PHE E 241 TYR 0.030 0.003 TYR E 105 ARG 0.005 0.001 ARG F 385 *********************** 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 fitting. rotamer outliers: 3 poor density : 189 time to evaluate : 1.064 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: 0.2805 time to fit residues: 68.3910 Evaluate side-chains 135 residues out of total 970 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 132 time to evaluate : 1.018 ------------------------------------------------------------------------------- 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 92 optimal weight: 7.9990 chunk 82 optimal weight: 1.9990 chunk 45 optimal weight: 1.9990 chunk 28 optimal weight: 0.8980 chunk 55 optimal weight: 6.9990 chunk 44 optimal weight: 1.9990 chunk 85 optimal weight: 0.9980 chunk 33 optimal weight: 0.9990 chunk 51 optimal weight: 8.9990 chunk 63 optimal weight: 8.9990 chunk 98 optimal weight: 0.2980 overall best weight: 1.0384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 234 HIS A 392 GLN A 404 ASN E 88 ASN F 41 HIS ** F 220 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 292 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7985 moved from start: 0.2136 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 9114 Z= 0.192 Angle : 0.629 7.225 12345 Z= 0.345 Chirality : 0.045 0.203 1364 Planarity : 0.005 0.050 1574 Dihedral : 6.180 32.717 1229 Min Nonbonded Distance : 2.506 Molprobity Statistics. All-atom Clashscore : 8.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.26 % Favored : 95.74 % Rotamer: Outliers : 1.79 % Allowed : 17.65 % Favored : 80.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.28 (0.22), residues: 1102 helix: -2.29 (0.21), residues: 408 sheet: -1.06 (0.34), residues: 232 loop : -2.54 (0.25), residues: 462 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 243 HIS 0.005 0.001 HIS F 220 PHE 0.027 0.002 PHE F 222 TYR 0.017 0.001 TYR A 157 ARG 0.004 0.000 ARG F 317 *********************** 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 fitting. rotamer outliers: 17 poor density : 162 time to evaluate : 0.986 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 213 GLU cc_start: 0.5663 (OUTLIER) cc_final: 0.5002 (pm20) REVERT: A 225 GLU cc_start: 0.6475 (tt0) cc_final: 0.6169 (tp30) REVERT: A 361 LEU cc_start: 0.8446 (tt) cc_final: 0.8199 (tt) REVERT: B 3 ASP cc_start: 0.8935 (m-30) cc_final: 0.8726 (m-30) REVERT: C 18 LEU cc_start: 0.8895 (tp) cc_final: 0.8549 (tt) REVERT: C 20 LEU cc_start: 0.8358 (mt) cc_final: 0.8038 (mt) REVERT: C 33 LYS cc_start: 0.8316 (tttt) cc_final: 0.8113 (ttmt) REVERT: C 83 MET cc_start: 0.8551 (mtm) cc_final: 0.8186 (mtp) REVERT: D 18 GLN cc_start: 0.8916 (tp-100) cc_final: 0.8433 (tp40) outliers start: 17 outliers final: 9 residues processed: 172 average time/residue: 0.2523 time to fit residues: 56.6747 Evaluate side-chains 148 residues out of total 970 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 138 time to evaluate : 1.064 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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 F residue 325 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 55 optimal weight: 4.9990 chunk 30 optimal weight: 1.9990 chunk 82 optimal weight: 0.8980 chunk 67 optimal weight: 10.0000 chunk 27 optimal weight: 0.0870 chunk 99 optimal weight: 0.3980 chunk 107 optimal weight: 1.9990 chunk 88 optimal weight: 4.9990 chunk 98 optimal weight: 1.9990 chunk 33 optimal weight: 8.9990 chunk 79 optimal weight: 10.0000 overall best weight: 1.0762 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 230 ASN F 23 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7976 moved from start: 0.2859 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 9114 Z= 0.178 Angle : 0.591 6.898 12345 Z= 0.318 Chirality : 0.043 0.199 1364 Planarity : 0.004 0.042 1574 Dihedral : 5.427 23.272 1226 Min Nonbonded Distance : 2.565 Molprobity Statistics. All-atom Clashscore : 8.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.54 % Favored : 95.46 % Rotamer: Outliers : 2.10 % Allowed : 20.17 % Favored : 77.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.61 (0.23), residues: 1102 helix: -1.46 (0.23), residues: 411 sheet: -0.62 (0.36), residues: 207 loop : -2.43 (0.25), residues: 484 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 243 HIS 0.004 0.001 HIS F 357 PHE 0.022 0.001 PHE F 222 TYR 0.020 0.001 TYR A 211 ARG 0.007 0.000 ARG F 317 *********************** 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 184 residues out of total 970 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 164 time to evaluate : 1.016 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 213 GLU cc_start: 0.5847 (OUTLIER) cc_final: 0.5228 (pm20) REVERT: A 225 GLU cc_start: 0.6532 (tt0) cc_final: 0.6240 (tp30) REVERT: A 230 MET cc_start: 0.8607 (tpp) cc_final: 0.8363 (tpt) REVERT: A 361 LEU cc_start: 0.8584 (tt) cc_final: 0.8273 (tt) REVERT: C 18 LEU cc_start: 0.8731 (tp) cc_final: 0.8324 (tt) REVERT: C 20 LEU cc_start: 0.8462 (mt) cc_final: 0.8079 (mt) REVERT: C 33 LYS cc_start: 0.8159 (tttt) cc_final: 0.7957 (ttmt) REVERT: C 67 ARG cc_start: 0.7695 (ptp90) cc_final: 0.7136 (ptp90) REVERT: C 83 MET cc_start: 0.8481 (mtm) cc_final: 0.7901 (mtm) REVERT: E 217 MET cc_start: 0.7442 (ppp) cc_final: 0.7234 (ppp) REVERT: E 241 PHE cc_start: 0.9031 (p90) cc_final: 0.8484 (p90) REVERT: F 13 ARG cc_start: 0.8922 (mtt180) cc_final: 0.8679 (mpp80) REVERT: F 342 ARG cc_start: 0.8758 (tmm-80) cc_final: 0.8386 (tmm-80) outliers start: 20 outliers final: 11 residues processed: 179 average time/residue: 0.2359 time to fit residues: 56.1902 Evaluate side-chains 152 residues out of total 970 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 140 time to evaluate : 1.016 ------------------------------------------------------------------------------- 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 B residue 26 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 F residue 241 VAL Chi-restraints excluded: chain F residue 325 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 97 optimal weight: 3.9990 chunk 74 optimal weight: 10.0000 chunk 51 optimal weight: 6.9990 chunk 10 optimal weight: 0.8980 chunk 47 optimal weight: 0.9990 chunk 66 optimal weight: 0.7980 chunk 99 optimal weight: 0.9980 chunk 105 optimal weight: 9.9990 chunk 94 optimal weight: 0.9980 chunk 28 optimal weight: 0.6980 chunk 87 optimal weight: 0.9980 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 300 ASN E 125 ASN E 230 ASN F 279 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7964 moved from start: 0.3261 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 9114 Z= 0.165 Angle : 0.578 6.863 12345 Z= 0.305 Chirality : 0.043 0.185 1364 Planarity : 0.004 0.041 1574 Dihedral : 5.094 20.430 1226 Min Nonbonded Distance : 2.565 Molprobity Statistics. All-atom Clashscore : 9.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.54 % Favored : 95.46 % Rotamer: Outliers : 2.84 % Allowed : 20.69 % Favored : 76.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.13 (0.24), residues: 1102 helix: -0.95 (0.24), residues: 418 sheet: -0.43 (0.35), residues: 221 loop : -2.29 (0.25), residues: 463 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 243 HIS 0.003 0.001 HIS F 357 PHE 0.012 0.001 PHE F 376 TYR 0.025 0.001 TYR A 211 ARG 0.011 0.000 ARG F 333 *********************** 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 186 residues out of total 970 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 159 time to evaluate : 1.032 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 146 GLN cc_start: 0.7810 (pt0) cc_final: 0.7578 (pm20) REVERT: A 211 TYR cc_start: 0.7313 (t80) cc_final: 0.6738 (t80) REVERT: A 213 GLU cc_start: 0.5912 (OUTLIER) cc_final: 0.5549 (pm20) REVERT: A 230 MET cc_start: 0.8690 (tpp) cc_final: 0.8190 (tpp) REVERT: A 361 LEU cc_start: 0.8633 (tt) cc_final: 0.8346 (tt) REVERT: C 18 LEU cc_start: 0.8708 (tp) cc_final: 0.8315 (tt) REVERT: C 20 LEU cc_start: 0.8515 (mt) cc_final: 0.8171 (mt) REVERT: C 83 MET cc_start: 0.8448 (mtm) cc_final: 0.7883 (mtm) REVERT: D 18 GLN cc_start: 0.8981 (tp-100) cc_final: 0.8558 (tp40) REVERT: D 20 LYS cc_start: 0.8615 (tmmt) cc_final: 0.8412 (tmmt) REVERT: E 241 PHE cc_start: 0.8986 (p90) cc_final: 0.8561 (p90) REVERT: F 13 ARG cc_start: 0.8943 (mtt180) cc_final: 0.8691 (mpp80) outliers start: 27 outliers final: 17 residues processed: 176 average time/residue: 0.2326 time to fit residues: 54.8059 Evaluate side-chains 159 residues out of total 970 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 141 time to evaluate : 0.937 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 85 ASN 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 211 LYS 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 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 59 optimal weight: 8.9990 chunk 1 optimal weight: 5.9990 chunk 78 optimal weight: 0.7980 chunk 43 optimal weight: 8.9990 chunk 89 optimal weight: 2.9990 chunk 72 optimal weight: 10.0000 chunk 0 optimal weight: 10.0000 chunk 53 optimal weight: 0.0770 chunk 94 optimal weight: 0.8980 chunk 26 optimal weight: 2.9990 chunk 35 optimal weight: 7.9990 overall best weight: 1.5542 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 9 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7990 moved from start: 0.3376 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 9114 Z= 0.200 Angle : 0.590 9.601 12345 Z= 0.310 Chirality : 0.043 0.184 1364 Planarity : 0.004 0.039 1574 Dihedral : 4.999 21.193 1226 Min Nonbonded Distance : 2.549 Molprobity Statistics. All-atom Clashscore : 8.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.99 % Favored : 95.01 % Rotamer: Outliers : 3.57 % Allowed : 21.22 % Favored : 75.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.85 (0.24), residues: 1102 helix: -0.67 (0.25), residues: 423 sheet: -0.29 (0.35), residues: 215 loop : -2.18 (0.26), residues: 464 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 243 HIS 0.004 0.001 HIS F 357 PHE 0.014 0.001 PHE F 376 TYR 0.018 0.001 TYR A 211 ARG 0.004 0.000 ARG F 333 *********************** 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 182 residues out of total 970 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 148 time to evaluate : 1.054 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 146 GLN cc_start: 0.7918 (pt0) cc_final: 0.7648 (pm20) REVERT: C 18 LEU cc_start: 0.8704 (tp) cc_final: 0.8278 (tt) REVERT: C 20 LEU cc_start: 0.8508 (mt) cc_final: 0.8178 (mt) REVERT: C 83 MET cc_start: 0.8532 (mtm) cc_final: 0.7913 (mtm) REVERT: D 18 GLN cc_start: 0.9002 (tp-100) cc_final: 0.8579 (tp40) REVERT: D 20 LYS cc_start: 0.8664 (tmmt) cc_final: 0.8462 (tmmt) REVERT: E 118 ASP cc_start: 0.8056 (p0) cc_final: 0.7851 (p0) REVERT: E 241 PHE cc_start: 0.9026 (p90) cc_final: 0.8630 (p90) REVERT: F 13 ARG cc_start: 0.8954 (mtt180) cc_final: 0.8695 (mpp80) outliers start: 34 outliers final: 24 residues processed: 171 average time/residue: 0.2115 time to fit residues: 49.3960 Evaluate side-chains 159 residues out of total 970 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 135 time to evaluate : 0.966 ------------------------------------------------------------------------------- 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 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 5 ILE 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 157 ILE 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 291 LEU Chi-restraints excluded: chain F residue 325 THR 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: 0.7980 chunk 20 optimal weight: 0.8980 chunk 61 optimal weight: 6.9990 chunk 26 optimal weight: 0.9990 chunk 105 optimal weight: 10.0000 chunk 87 optimal weight: 2.9990 chunk 48 optimal weight: 0.0980 chunk 8 optimal weight: 0.0040 chunk 34 optimal weight: 1.9990 chunk 55 optimal weight: 4.9990 chunk 101 optimal weight: 6.9990 overall best weight: 0.5594 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 9 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7955 moved from start: 0.3681 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 9114 Z= 0.152 Angle : 0.568 8.023 12345 Z= 0.297 Chirality : 0.042 0.179 1364 Planarity : 0.003 0.038 1574 Dihedral : 4.744 19.521 1226 Min Nonbonded Distance : 2.553 Molprobity Statistics. All-atom Clashscore : 8.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.17 % Favored : 95.83 % Rotamer: Outliers : 2.84 % Allowed : 21.74 % Favored : 75.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.57 (0.24), residues: 1102 helix: -0.35 (0.25), residues: 421 sheet: -0.23 (0.35), residues: 215 loop : -2.05 (0.26), residues: 466 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 297 HIS 0.003 0.001 HIS E 54 PHE 0.010 0.001 PHE A 362 TYR 0.016 0.001 TYR F 318 ARG 0.008 0.000 ARG E 96 *********************** 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 187 residues out of total 970 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 160 time to evaluate : 1.078 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 165 LEU cc_start: 0.8925 (tp) cc_final: 0.8524 (tt) REVERT: A 197 MET cc_start: 0.8398 (mtt) cc_final: 0.8007 (mtt) REVERT: C 19 ARG cc_start: 0.8698 (ttm-80) cc_final: 0.8206 (tpp80) REVERT: C 20 LEU cc_start: 0.8468 (mt) cc_final: 0.8115 (mt) REVERT: C 34 MET cc_start: 0.7966 (mtp) cc_final: 0.7653 (mtt) REVERT: C 83 MET cc_start: 0.8520 (mtm) cc_final: 0.8048 (mtm) REVERT: D 18 GLN cc_start: 0.9000 (tp-100) cc_final: 0.8588 (tp40) REVERT: E 118 ASP cc_start: 0.7887 (p0) cc_final: 0.7649 (p0) REVERT: E 209 LYS cc_start: 0.8150 (mmtp) cc_final: 0.7900 (mttm) REVERT: E 241 PHE cc_start: 0.8967 (p90) cc_final: 0.8673 (p90) REVERT: F 13 ARG cc_start: 0.8964 (mtt180) cc_final: 0.8702 (mpp80) outliers start: 27 outliers final: 18 residues processed: 179 average time/residue: 0.2223 time to fit residues: 54.2114 Evaluate side-chains 159 residues out of total 970 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 141 time to evaluate : 0.954 ------------------------------------------------------------------------------- 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 203 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 B residue 26 VAL Chi-restraints excluded: chain C residue 37 VAL 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 E residue 317 CYS Chi-restraints excluded: chain F residue 241 VAL Chi-restraints excluded: chain F residue 325 THR 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 11 optimal weight: 0.0070 chunk 60 optimal weight: 6.9990 chunk 77 optimal weight: 0.9990 chunk 59 optimal weight: 0.9990 chunk 88 optimal weight: 3.9990 chunk 58 optimal weight: 2.9990 chunk 105 optimal weight: 0.5980 chunk 65 optimal weight: 4.9990 chunk 64 optimal weight: 0.0370 chunk 48 optimal weight: 1.9990 chunk 41 optimal weight: 0.9990 overall best weight: 0.5280 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 186 ASN E 9 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7944 moved from start: 0.3918 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 9114 Z= 0.156 Angle : 0.603 10.011 12345 Z= 0.311 Chirality : 0.043 0.206 1364 Planarity : 0.003 0.037 1574 Dihedral : 4.578 18.399 1226 Min Nonbonded Distance : 2.499 Molprobity Statistics. All-atom Clashscore : 8.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.90 % Favored : 96.10 % Rotamer: Outliers : 2.73 % Allowed : 23.84 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.45 (0.25), residues: 1102 helix: -0.24 (0.25), residues: 428 sheet: -0.09 (0.36), residues: 208 loop : -2.04 (0.26), residues: 466 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 243 HIS 0.003 0.001 HIS F 357 PHE 0.011 0.001 PHE A 362 TYR 0.024 0.001 TYR A 211 ARG 0.006 0.000 ARG F 342 *********************** 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 181 residues out of total 970 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 155 time to evaluate : 1.038 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 85 ASN cc_start: 0.7020 (OUTLIER) cc_final: 0.6723 (m-40) REVERT: A 197 MET cc_start: 0.8402 (mtt) cc_final: 0.8026 (mtt) REVERT: C 19 ARG cc_start: 0.8628 (ttm-80) cc_final: 0.8196 (tpp80) REVERT: C 20 LEU cc_start: 0.8453 (mt) cc_final: 0.8132 (mt) REVERT: C 34 MET cc_start: 0.7959 (mtp) cc_final: 0.7664 (mtt) REVERT: C 83 MET cc_start: 0.8515 (mtm) cc_final: 0.7997 (mtm) REVERT: D 18 GLN cc_start: 0.9007 (tp-100) cc_final: 0.8704 (tp40) REVERT: E 209 LYS cc_start: 0.8253 (mmtp) cc_final: 0.8041 (mttm) REVERT: E 241 PHE cc_start: 0.8941 (p90) cc_final: 0.8681 (p90) REVERT: F 13 ARG cc_start: 0.8960 (mtt180) cc_final: 0.8706 (mpp80) REVERT: F 318 TYR cc_start: 0.7652 (t80) cc_final: 0.7284 (t80) outliers start: 26 outliers final: 17 residues processed: 177 average time/residue: 0.2072 time to fit residues: 50.4303 Evaluate side-chains 158 residues out of total 970 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 140 time to evaluate : 0.983 ------------------------------------------------------------------------------- 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 332 VAL Chi-restraints excluded: chain A residue 347 ILE Chi-restraints excluded: chain B residue 26 VAL Chi-restraints excluded: chain C residue 37 VAL Chi-restraints excluded: chain D residue 16 VAL Chi-restraints excluded: chain E residue 7 LEU 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 317 CYS Chi-restraints excluded: chain F residue 211 LYS Chi-restraints excluded: chain F residue 241 VAL Chi-restraints excluded: chain F residue 325 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 62 optimal weight: 2.9990 chunk 31 optimal weight: 6.9990 chunk 20 optimal weight: 3.9990 chunk 66 optimal weight: 3.9990 chunk 71 optimal weight: 5.9990 chunk 51 optimal weight: 6.9990 chunk 9 optimal weight: 3.9990 chunk 82 optimal weight: 0.9990 chunk 95 optimal weight: 0.5980 chunk 100 optimal weight: 7.9990 chunk 91 optimal weight: 0.0020 overall best weight: 1.7194 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7983 moved from start: 0.3948 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 9114 Z= 0.214 Angle : 0.627 9.354 12345 Z= 0.327 Chirality : 0.044 0.178 1364 Planarity : 0.004 0.037 1574 Dihedral : 4.665 19.341 1226 Min Nonbonded Distance : 2.500 Molprobity Statistics. All-atom Clashscore : 10.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.99 % Favored : 95.01 % Rotamer: Outliers : 2.73 % Allowed : 23.95 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.38 (0.25), residues: 1102 helix: -0.18 (0.25), residues: 430 sheet: -0.09 (0.36), residues: 210 loop : -2.00 (0.26), residues: 462 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP E 211 HIS 0.005 0.001 HIS F 357 PHE 0.017 0.001 PHE A 362 TYR 0.022 0.001 TYR F 391 ARG 0.007 0.000 ARG B 12 *********************** 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 162 residues out of total 970 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 136 time to evaluate : 0.999 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 85 ASN cc_start: 0.7019 (OUTLIER) cc_final: 0.6742 (m-40) REVERT: A 197 MET cc_start: 0.8492 (mtt) cc_final: 0.8086 (mtt) REVERT: C 20 LEU cc_start: 0.8497 (mt) cc_final: 0.8255 (mt) REVERT: C 34 MET cc_start: 0.8054 (mtp) cc_final: 0.7740 (mtt) REVERT: C 83 MET cc_start: 0.8566 (mtm) cc_final: 0.8043 (mtm) REVERT: D 21 MET cc_start: 0.8458 (mtp) cc_final: 0.8019 (mmt) REVERT: E 8 ARG cc_start: 0.8686 (mtt180) cc_final: 0.8193 (tpm170) REVERT: E 118 ASP cc_start: 0.7901 (p0) cc_final: 0.7682 (p0) REVERT: E 241 PHE cc_start: 0.9018 (p90) cc_final: 0.8797 (p90) REVERT: F 13 ARG cc_start: 0.9032 (mtt180) cc_final: 0.8740 (mpp80) REVERT: F 318 TYR cc_start: 0.7807 (t80) cc_final: 0.7400 (t80) outliers start: 26 outliers final: 20 residues processed: 155 average time/residue: 0.2204 time to fit residues: 47.0443 Evaluate side-chains 149 residues out of total 970 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 128 time to evaluate : 1.000 ------------------------------------------------------------------------------- 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 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 D residue 16 VAL Chi-restraints excluded: chain D residue 25 ILE Chi-restraints excluded: chain E residue 7 LEU Chi-restraints excluded: chain E residue 59 TYR Chi-restraints excluded: chain E residue 93 ILE Chi-restraints excluded: chain E residue 187 VAL Chi-restraints excluded: chain E residue 234 PHE Chi-restraints excluded: chain E residue 317 CYS Chi-restraints excluded: chain F residue 241 VAL Chi-restraints excluded: chain F residue 325 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 97 optimal weight: 0.5980 chunk 100 optimal weight: 5.9990 chunk 58 optimal weight: 2.9990 chunk 42 optimal weight: 2.9990 chunk 76 optimal weight: 9.9990 chunk 30 optimal weight: 0.5980 chunk 88 optimal weight: 0.8980 chunk 92 optimal weight: 5.9990 chunk 64 optimal weight: 0.9980 chunk 103 optimal weight: 3.9990 chunk 63 optimal weight: 0.0070 overall best weight: 0.6198 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7945 moved from start: 0.4116 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 9114 Z= 0.164 Angle : 0.613 10.631 12345 Z= 0.316 Chirality : 0.043 0.184 1364 Planarity : 0.003 0.036 1574 Dihedral : 4.507 18.112 1226 Min Nonbonded Distance : 2.509 Molprobity Statistics. All-atom Clashscore : 8.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.17 % Favored : 95.83 % Rotamer: Outliers : 2.63 % Allowed : 24.16 % Favored : 73.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.24 (0.25), residues: 1102 helix: -0.02 (0.26), residues: 427 sheet: -0.01 (0.36), residues: 208 loop : -1.95 (0.26), residues: 467 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 243 HIS 0.002 0.001 HIS F 357 PHE 0.015 0.001 PHE A 362 TYR 0.021 0.001 TYR A 211 ARG 0.008 0.000 ARG F 342 *********************** 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 171 residues out of total 970 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 146 time to evaluate : 1.054 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 197 MET cc_start: 0.8448 (mtt) cc_final: 0.8052 (mtt) REVERT: C 19 ARG cc_start: 0.8590 (ttm-80) cc_final: 0.8265 (tpp80) REVERT: C 20 LEU cc_start: 0.8453 (mt) cc_final: 0.8172 (mt) REVERT: C 34 MET cc_start: 0.7997 (mtp) cc_final: 0.7700 (mtt) REVERT: C 83 MET cc_start: 0.8554 (mtm) cc_final: 0.8064 (mtm) REVERT: E 8 ARG cc_start: 0.8701 (mtt180) cc_final: 0.8176 (tpm170) REVERT: E 93 ILE cc_start: 0.9060 (OUTLIER) cc_final: 0.8851 (tt) REVERT: F 13 ARG cc_start: 0.8968 (mtt180) cc_final: 0.8713 (mpp80) REVERT: F 318 TYR cc_start: 0.7670 (t80) cc_final: 0.7223 (t80) outliers start: 25 outliers final: 20 residues processed: 165 average time/residue: 0.2194 time to fit residues: 49.2299 Evaluate side-chains 160 residues out of total 970 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 139 time to evaluate : 1.024 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 MET 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 332 VAL Chi-restraints excluded: chain A residue 347 ILE 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 7 LEU Chi-restraints excluded: chain E residue 59 TYR Chi-restraints excluded: chain E residue 93 ILE Chi-restraints excluded: chain E residue 187 VAL Chi-restraints excluded: chain E residue 234 PHE Chi-restraints excluded: chain E residue 317 CYS 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 Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 49 optimal weight: 5.9990 chunk 71 optimal weight: 0.3980 chunk 108 optimal weight: 3.9990 chunk 99 optimal weight: 0.8980 chunk 86 optimal weight: 0.0570 chunk 8 optimal weight: 5.9990 chunk 66 optimal weight: 1.9990 chunk 53 optimal weight: 4.9990 chunk 68 optimal weight: 8.9990 chunk 92 optimal weight: 4.9990 chunk 26 optimal weight: 0.3980 overall best weight: 0.7500 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7944 moved from start: 0.4227 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 9114 Z= 0.172 Angle : 0.633 9.902 12345 Z= 0.326 Chirality : 0.044 0.185 1364 Planarity : 0.003 0.036 1574 Dihedral : 4.430 17.180 1226 Min Nonbonded Distance : 2.500 Molprobity Statistics. All-atom Clashscore : 9.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.54 % Favored : 95.46 % Rotamer: Outliers : 2.21 % Allowed : 24.37 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.21 (0.25), residues: 1102 helix: 0.02 (0.26), residues: 427 sheet: 0.12 (0.37), residues: 196 loop : -1.97 (0.26), residues: 479 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 243 HIS 0.003 0.001 HIS F 357 PHE 0.012 0.001 PHE A 362 TYR 0.043 0.001 TYR F 391 ARG 0.007 0.000 ARG F 342 ********************** 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 168 residues out of total 970 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 147 time to evaluate : 1.133 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 197 MET cc_start: 0.8450 (mtt) cc_final: 0.8011 (mtt) REVERT: A 299 MET cc_start: 0.4578 (mmp) cc_final: 0.4169 (mmp) REVERT: C 19 ARG cc_start: 0.8603 (ttm-80) cc_final: 0.8297 (tpp80) REVERT: C 20 LEU cc_start: 0.8485 (mt) cc_final: 0.8185 (mt) REVERT: C 34 MET cc_start: 0.7999 (mtp) cc_final: 0.7709 (mtt) REVERT: C 83 MET cc_start: 0.8575 (mtm) cc_final: 0.8054 (mtm) REVERT: D 18 GLN cc_start: 0.8894 (tp40) cc_final: 0.8380 (tp40) REVERT: D 20 LYS cc_start: 0.8456 (pptt) cc_final: 0.8063 (ttpp) REVERT: E 8 ARG cc_start: 0.8707 (mtt180) cc_final: 0.8193 (tpm170) REVERT: E 93 ILE cc_start: 0.9039 (OUTLIER) cc_final: 0.8811 (tt) REVERT: E 209 LYS cc_start: 0.8242 (mmtp) cc_final: 0.8024 (mttm) REVERT: F 13 ARG cc_start: 0.8971 (mtt180) cc_final: 0.8635 (mpp80) REVERT: F 318 TYR cc_start: 0.7712 (t80) cc_final: 0.7327 (t80) outliers start: 21 outliers final: 20 residues processed: 162 average time/residue: 0.2142 time to fit residues: 47.7652 Evaluate side-chains 160 residues out of total 970 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 139 time to evaluate : 1.043 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 MET 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 332 VAL Chi-restraints excluded: chain A residue 347 ILE 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 E residue 7 LEU Chi-restraints excluded: chain E residue 59 TYR Chi-restraints excluded: chain E residue 93 ILE Chi-restraints excluded: chain E residue 187 VAL Chi-restraints excluded: chain E residue 234 PHE Chi-restraints excluded: chain E residue 317 CYS 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 Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 79 optimal weight: 7.9990 chunk 12 optimal weight: 0.7980 chunk 24 optimal weight: 0.9990 chunk 86 optimal weight: 0.9980 chunk 36 optimal weight: 2.9990 chunk 88 optimal weight: 2.9990 chunk 10 optimal weight: 0.6980 chunk 15 optimal weight: 3.9990 chunk 76 optimal weight: 4.9990 chunk 4 optimal weight: 20.0000 chunk 62 optimal weight: 3.9990 overall best weight: 1.2984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3697 r_free = 0.3697 target = 0.095225 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3252 r_free = 0.3252 target = 0.072756 restraints weight = 26423.565| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3296 r_free = 0.3296 target = 0.074958 restraints weight = 13798.229| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 46)----------------| | r_work = 0.3325 r_free = 0.3325 target = 0.076385 restraints weight = 9341.704| |-----------------------------------------------------------------------------| r_work (final): 0.3314 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3312 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3312 r_free = 0.3312 target_work(ls_wunit_k1) = 0.075 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3311 r_free = 0.3311 target_work(ls_wunit_k1) = 0.075 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| r_final: 0.3311 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7932 moved from start: 0.4236 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 9114 Z= 0.200 Angle : 0.667 13.157 12345 Z= 0.345 Chirality : 0.044 0.184 1364 Planarity : 0.004 0.036 1574 Dihedral : 4.532 21.377 1226 Min Nonbonded Distance : 2.357 Molprobity Statistics. All-atom Clashscore : 9.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.17 % Favored : 94.83 % Rotamer: Outliers : 2.52 % Allowed : 24.68 % Favored : 72.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.19 (0.25), residues: 1102 helix: 0.05 (0.26), residues: 427 sheet: -0.01 (0.36), residues: 208 loop : -1.94 (0.26), residues: 467 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 243 HIS 0.003 0.001 HIS F 357 PHE 0.014 0.001 PHE A 362 TYR 0.041 0.002 TYR F 391 ARG 0.008 0.000 ARG F 333 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2034.16 seconds wall clock time: 36 minutes 48.52 seconds (2208.52 seconds total)