Starting phenix.real_space_refine on Sun Jun 30 08:02:20 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8umu_42384/06_2024/8umu_42384_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8umu_42384/06_2024/8umu_42384.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.16 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8umu_42384/06_2024/8umu_42384.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8umu_42384/06_2024/8umu_42384.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8umu_42384/06_2024/8umu_42384_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8umu_42384/06_2024/8umu_42384_updated.pdb" } resolution = 3.16 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= 0.052 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: 6 Type Number sf(0) Gaussians P 11 5.49 5 Mg 3 5.21 5 S 136 5.16 5 C 12926 2.51 5 N 3528 2.21 5 O 3917 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 302": "NH1" <-> "NH2" Residue "A ARG 410": "NH1" <-> "NH2" Residue "A GLU 414": "OE1" <-> "OE2" Residue "A ARG 751": "NH1" <-> "NH2" Residue "A ARG 804": "NH1" <-> "NH2" Residue "B ASP 110": "OD1" <-> "OD2" Residue "B ARG 156": "NH1" <-> "NH2" Residue "B PHE 245": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 293": "OE1" <-> "OE2" Residue "C PHE 119": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 191": "OE1" <-> "OE2" Residue "D ARG 193": "NH1" <-> "NH2" Residue "D GLU 225": "OE1" <-> "OE2" Residue "D GLU 235": "OE1" <-> "OE2" Residue "E ARG 105": "NH1" <-> "NH2" Residue "E GLU 136": "OE1" <-> "OE2" Residue "E GLU 190": "OE1" <-> "OE2" Residue "E GLU 231": "OE1" <-> "OE2" Residue "F GLU 25": "OE1" <-> "OE2" Residue "G GLU 3": "OE1" <-> "OE2" Residue "G PHE 169": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G GLU 256": "OE1" <-> "OE2" Time to flip residues: 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5370/modules/chem_data/mon_lib" Total number of atoms: 20521 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 4074 Number of conformers: 1 Conformer: "" Number of residues, atoms: 515, 4074 Classifications: {'peptide': 515} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 32, 'TRANS': 482} Chain breaks: 5 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: "B" Number of atoms: 2492 Number of conformers: 1 Conformer: "" Number of residues, atoms: 316, 2492 Classifications: {'peptide': 316} Link IDs: {'PTRANS': 12, 'TRANS': 303} Chain: "C" Number of atoms: 2563 Number of conformers: 1 Conformer: "" Number of residues, atoms: 322, 2563 Classifications: {'peptide': 322} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 12, 'TRANS': 309} Chain: "D" Number of atoms: 2526 Number of conformers: 1 Conformer: "" Number of residues, atoms: 327, 2526 Classifications: {'peptide': 327} Link IDs: {'PTRANS': 13, 'TRANS': 313} Chain: "E" Number of atoms: 2773 Number of conformers: 1 Conformer: "" Number of residues, atoms: 348, 2773 Classifications: {'peptide': 348} Link IDs: {'PTRANS': 15, 'TRANS': 332} Chain: "F" Number of atoms: 1972 Number of conformers: 1 Conformer: "" Number of residues, atoms: 256, 1972 Classifications: {'peptide': 256} Link IDs: {'PTRANS': 7, 'TRANS': 248} Chain: "G" Number of atoms: 2009 Number of conformers: 1 Conformer: "" Number of residues, atoms: 261, 2009 Classifications: {'peptide': 261} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 253} Chain: "H" Number of atoms: 1989 Number of conformers: 1 Conformer: "" Number of residues, atoms: 258, 1989 Classifications: {'peptide': 258} Link IDs: {'PTRANS': 7, 'TRANS': 250} Chain: "A" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'AGS': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'AGS': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "C" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'AGS': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "E" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Time building chain proxies: 10.62, per 1000 atoms: 0.52 Number of scatterers: 20521 At special positions: 0 Unit cell: (117.576, 128.34, 140.76, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 136 16.00 P 11 15.00 Mg 3 11.99 O 3917 8.00 N 3528 7.00 C 12926 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 7.77 Conformation dependent library (CDL) restraints added in 3.4 seconds 5154 Ramachandran restraints generated. 2577 Oldfield, 0 Emsley, 2577 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4956 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 108 helices and 17 sheets defined 43.4% alpha, 16.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.97 Creating SS restraints... Processing helix chain 'A' and resid 282 through 285 No H-bonds generated for 'chain 'A' and resid 282 through 285' Processing helix chain 'A' and resid 291 through 293 No H-bonds generated for 'chain 'A' and resid 291 through 293' Processing helix chain 'A' and resid 298 through 315 removed outlier: 4.218A pdb=" N ASP A 312 " --> pdb=" O LEU A 308 " (cutoff:3.500A) removed outlier: 5.461A pdb=" N LEU A 313 " --> pdb=" O LYS A 309 " (cutoff:3.500A) removed outlier: 6.008A pdb=" N VAL A 314 " --> pdb=" O LEU A 310 " (cutoff:3.500A) removed outlier: 4.326A pdb=" N VAL A 315 " --> pdb=" O TRP A 311 " (cutoff:3.500A) Processing helix chain 'A' and resid 347 through 355 Processing helix chain 'A' and resid 380 through 390 Processing helix chain 'A' and resid 406 through 415 Processing helix chain 'A' and resid 442 through 452 Processing helix chain 'A' and resid 496 through 502 removed outlier: 3.725A pdb=" N ARG A 499 " --> pdb=" O PRO A 496 " (cutoff:3.500A) removed outlier: 4.627A pdb=" N GLN A 500 " --> pdb=" O SER A 497 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N LYS A 502 " --> pdb=" O ARG A 499 " (cutoff:3.500A) Processing helix chain 'A' and resid 515 through 528 Processing helix chain 'A' and resid 535 through 544 Processing helix chain 'A' and resid 549 through 559 Processing helix chain 'A' and resid 586 through 594 Processing helix chain 'A' and resid 628 through 642 Processing helix chain 'A' and resid 646 through 653 Processing helix chain 'A' and resid 667 through 689 Processing helix chain 'A' and resid 693 through 696 removed outlier: 4.060A pdb=" N ARG A 696 " --> pdb=" O GLN A 693 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 693 through 696' Processing helix chain 'A' and resid 698 through 708 Proline residue: A 702 - end of helix Processing helix chain 'A' and resid 722 through 743 Processing helix chain 'A' and resid 746 through 751 removed outlier: 3.840A pdb=" N ARG A 751 " --> pdb=" O ALA A 747 " (cutoff:3.500A) Processing helix chain 'A' and resid 754 through 760 Processing helix chain 'A' and resid 763 through 768 Processing helix chain 'A' and resid 783 through 799 Processing helix chain 'A' and resid 821 through 824 removed outlier: 3.543A pdb=" N LEU A 824 " --> pdb=" O VAL A 821 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 821 through 824' Processing helix chain 'A' and resid 838 through 862 Processing helix chain 'B' and resid 38 through 41 No H-bonds generated for 'chain 'B' and resid 38 through 41' Processing helix chain 'B' and resid 54 through 66 Processing helix chain 'B' and resid 82 through 101 Proline residue: B 96 - end of helix removed outlier: 5.422A pdb=" N LYS B 99 " --> pdb=" O GLY B 95 " (cutoff:3.500A) removed outlier: 5.968A pdb=" N ASP B 100 " --> pdb=" O PRO B 96 " (cutoff:3.500A) Processing helix chain 'B' and resid 113 through 124 removed outlier: 4.727A pdb=" N ILE B 120 " --> pdb=" O VAL B 116 " (cutoff:3.500A) removed outlier: 4.670A pdb=" N LYS B 121 " --> pdb=" O ARG B 117 " (cutoff:3.500A) Processing helix chain 'B' and resid 143 through 145 No H-bonds generated for 'chain 'B' and resid 143 through 145' Processing helix chain 'B' and resid 148 through 163 removed outlier: 4.371A pdb=" N ARG B 156 " --> pdb=" O GLN B 152 " (cutoff:3.500A) removed outlier: 4.056A pdb=" N THR B 157 " --> pdb=" O ALA B 153 " (cutoff:3.500A) removed outlier: 4.008A pdb=" N SER B 162 " --> pdb=" O MET B 158 " (cutoff:3.500A) removed outlier: 5.898A pdb=" N LYS B 163 " --> pdb=" O GLU B 159 " (cutoff:3.500A) Processing helix chain 'B' and resid 179 through 184 Processing helix chain 'B' and resid 195 through 209 Processing helix chain 'B' and resid 215 through 225 Processing helix chain 'B' and resid 229 through 243 Processing helix chain 'B' and resid 248 through 255 Processing helix chain 'B' and resid 260 through 271 Processing helix chain 'B' and resid 275 through 287 removed outlier: 3.743A pdb=" N ILE B 281 " --> pdb=" O GLU B 277 " (cutoff:3.500A) Processing helix chain 'B' and resid 292 through 304 Processing helix chain 'B' and resid 310 through 329 Processing helix chain 'B' and resid 334 through 347 Processing helix chain 'C' and resid 22 through 25 No H-bonds generated for 'chain 'C' and resid 22 through 25' Processing helix chain 'C' and resid 38 through 49 Processing helix chain 'C' and resid 66 through 77 removed outlier: 3.687A pdb=" N ILE C 70 " --> pdb=" O LYS C 66 " (cutoff:3.500A) Processing helix chain 'C' and resid 83 through 85 No H-bonds generated for 'chain 'C' and resid 83 through 85' Processing helix chain 'C' and resid 104 through 109 Processing helix chain 'C' and resid 127 through 129 No H-bonds generated for 'chain 'C' and resid 127 through 129' Processing helix chain 'C' and resid 132 through 144 Processing helix chain 'C' and resid 158 through 160 No H-bonds generated for 'chain 'C' and resid 158 through 160' Processing helix chain 'C' and resid 163 through 166 No H-bonds generated for 'chain 'C' and resid 163 through 166' Processing helix chain 'C' and resid 179 through 181 No H-bonds generated for 'chain 'C' and resid 179 through 181' Processing helix chain 'C' and resid 183 through 192 Processing helix chain 'C' and resid 199 through 208 removed outlier: 4.200A pdb=" N LYS C 203 " --> pdb=" O GLU C 199 " (cutoff:3.500A) Processing helix chain 'C' and resid 213 through 226 removed outlier: 3.543A pdb=" N GLN C 221 " --> pdb=" O LEU C 217 " (cutoff:3.500A) Processing helix chain 'C' and resid 232 through 239 Processing helix chain 'C' and resid 244 through 256 Processing helix chain 'C' and resid 259 through 273 Processing helix chain 'C' and resid 277 through 288 Processing helix chain 'C' and resid 295 through 311 Processing helix chain 'C' and resid 318 through 339 Processing helix chain 'D' and resid 56 through 68 removed outlier: 3.871A pdb=" N LEU D 62 " --> pdb=" O VAL D 58 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N GLU D 67 " --> pdb=" O LYS D 63 " (cutoff:3.500A) Processing helix chain 'D' and resid 84 through 96 Processing helix chain 'D' and resid 98 through 104 removed outlier: 4.509A pdb=" N ARG D 102 " --> pdb=" O PRO D 98 " (cutoff:3.500A) removed outlier: 4.710A pdb=" N LEU D 103 " --> pdb=" O GLU D 99 " (cutoff:3.500A) Processing helix chain 'D' and resid 116 through 119 No H-bonds generated for 'chain 'D' and resid 116 through 119' Processing helix chain 'D' and resid 122 through 128 Processing helix chain 'D' and resid 152 through 154 No H-bonds generated for 'chain 'D' and resid 152 through 154' Processing helix chain 'D' and resid 157 through 169 Processing helix chain 'D' and resid 188 through 191 No H-bonds generated for 'chain 'D' and resid 188 through 191' Processing helix chain 'D' and resid 207 through 217 Processing helix chain 'D' and resid 224 through 233 Processing helix chain 'D' and resid 238 through 252 Processing helix chain 'D' and resid 259 through 265 Processing helix chain 'D' and resid 271 through 282 Processing helix chain 'D' and resid 286 through 297 Processing helix chain 'D' and resid 303 through 315 Processing helix chain 'D' and resid 321 through 339 Processing helix chain 'D' and resid 344 through 359 Processing helix chain 'E' and resid 4 through 7 No H-bonds generated for 'chain 'E' and resid 4 through 7' Processing helix chain 'E' and resid 13 through 15 No H-bonds generated for 'chain 'E' and resid 13 through 15' Processing helix chain 'E' and resid 20 through 31 Processing helix chain 'E' and resid 48 through 59 Processing helix chain 'E' and resid 104 through 117 removed outlier: 4.263A pdb=" N LEU E 112 " --> pdb=" O ILE E 108 " (cutoff:3.500A) Processing helix chain 'E' and resid 123 through 126 No H-bonds generated for 'chain 'E' and resid 123 through 126' Processing helix chain 'E' and resid 142 through 154 Processing helix chain 'E' and resid 173 through 176 No H-bonds generated for 'chain 'E' and resid 173 through 176' Processing helix chain 'E' and resid 189 through 202 Processing helix chain 'E' and resid 209 through 219 Processing helix chain 'E' and resid 223 through 236 Processing helix chain 'E' and resid 250 through 264 Processing helix chain 'E' and resid 268 through 284 removed outlier: 4.071A pdb=" N HIS E 284 " --> pdb=" O GLU E 280 " (cutoff:3.500A) Processing helix chain 'E' and resid 288 through 299 Processing helix chain 'E' and resid 308 through 324 Processing helix chain 'E' and resid 328 through 348 Processing helix chain 'F' and resid 10 through 15 Processing helix chain 'F' and resid 19 through 22 No H-bonds generated for 'chain 'F' and resid 19 through 22' Processing helix chain 'F' and resid 76 through 79 No H-bonds generated for 'chain 'F' and resid 76 through 79' Processing helix chain 'F' and resid 141 through 150 Processing helix chain 'F' and resid 191 through 193 No H-bonds generated for 'chain 'F' and resid 191 through 193' Processing helix chain 'F' and resid 209 through 218 removed outlier: 3.881A pdb=" N LYS F 217 " --> pdb=" O ASN F 213 " (cutoff:3.500A) removed outlier: 5.215A pdb=" N ALA F 218 " --> pdb=" O PHE F 214 " (cutoff:3.500A) Processing helix chain 'G' and resid 10 through 17 Processing helix chain 'G' and resid 72 through 79 Processing helix chain 'G' and resid 141 through 154 removed outlier: 4.195A pdb=" N HIS G 153 " --> pdb=" O ARG G 149 " (cutoff:3.500A) removed outlier: 3.993A pdb=" N ILE G 154 " --> pdb=" O ASP G 150 " (cutoff:3.500A) Processing helix chain 'G' and resid 209 through 217 removed outlier: 4.019A pdb=" N LYS G 217 " --> pdb=" O ASN G 213 " (cutoff:3.500A) Processing helix chain 'G' and resid 219 through 221 No H-bonds generated for 'chain 'G' and resid 219 through 221' Processing helix chain 'H' and resid 10 through 19 Processing helix chain 'H' and resid 72 through 79 Processing helix chain 'H' and resid 141 through 152 Processing helix chain 'H' and resid 191 through 193 No H-bonds generated for 'chain 'H' and resid 191 through 193' Processing helix chain 'H' and resid 209 through 217 removed outlier: 4.130A pdb=" N LYS H 217 " --> pdb=" O ASN H 213 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'A' and resid 177 through 180 Processing sheet with id= B, first strand: chain 'A' and resid 506 through 509 removed outlier: 3.913A pdb=" N LEU A 508 " --> pdb=" O LEU A 371 " (cutoff:3.500A) removed outlier: 6.912A pdb=" N ILE A 486 " --> pdb=" O ALA A 370 " (cutoff:3.500A) removed outlier: 7.799A pdb=" N LEU A 372 " --> pdb=" O ILE A 486 " (cutoff:3.500A) removed outlier: 6.524A pdb=" N CYS A 488 " --> pdb=" O LEU A 372 " (cutoff:3.500A) removed outlier: 8.962A pdb=" N ILE A 487 " --> pdb=" O ASN A 430 " (cutoff:3.500A) removed outlier: 6.777A pdb=" N LEU A 432 " --> pdb=" O ILE A 487 " (cutoff:3.500A) removed outlier: 7.772A pdb=" N ILE A 489 " --> pdb=" O LEU A 432 " (cutoff:3.500A) removed outlier: 6.890A pdb=" N ILE A 434 " --> pdb=" O ILE A 489 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N CYS A 431 " --> pdb=" O SER A 394 " (cutoff:3.500A) removed outlier: 3.993A pdb=" N VAL A 396 " --> pdb=" O CYS A 431 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'A' and resid 803 through 807 Processing sheet with id= D, first strand: chain 'B' and resid 186 through 190 removed outlier: 6.289A pdb=" N LYS B 136 " --> pdb=" O ARG B 166 " (cutoff:3.500A) removed outlier: 7.169A pdb=" N ALA B 168 " --> pdb=" O LYS B 136 " (cutoff:3.500A) removed outlier: 6.496A pdb=" N ILE B 138 " --> pdb=" O ALA B 168 " (cutoff:3.500A) removed outlier: 7.178A pdb=" N ALA B 170 " --> pdb=" O ILE B 138 " (cutoff:3.500A) removed outlier: 6.552A pdb=" N LEU B 140 " --> pdb=" O ALA B 170 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'C' and resid 170 through 173 removed outlier: 5.955A pdb=" N LYS C 120 " --> pdb=" O ARG C 150 " (cutoff:3.500A) removed outlier: 7.261A pdb=" N CYS C 152 " --> pdb=" O LYS C 120 " (cutoff:3.500A) removed outlier: 5.994A pdb=" N VAL C 122 " --> pdb=" O CYS C 152 " (cutoff:3.500A) removed outlier: 7.157A pdb=" N ILE C 154 " --> pdb=" O VAL C 122 " (cutoff:3.500A) removed outlier: 6.350A pdb=" N LEU C 124 " --> pdb=" O ILE C 154 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'D' and resid 194 through 198 removed outlier: 7.076A pdb=" N ASN D 73 " --> pdb=" O SER D 195 " (cutoff:3.500A) removed outlier: 7.987A pdb=" N PHE D 197 " --> pdb=" O ASN D 73 " (cutoff:3.500A) removed outlier: 6.558A pdb=" N LEU D 75 " --> pdb=" O PHE D 197 " (cutoff:3.500A) removed outlier: 6.153A pdb=" N LYS D 145 " --> pdb=" O ARG D 175 " (cutoff:3.500A) removed outlier: 7.655A pdb=" N CYS D 177 " --> pdb=" O LYS D 145 " (cutoff:3.500A) removed outlier: 6.427A pdb=" N VAL D 147 " --> pdb=" O CYS D 177 " (cutoff:3.500A) removed outlier: 8.181A pdb=" N ILE D 179 " --> pdb=" O VAL D 147 " (cutoff:3.500A) removed outlier: 6.874A pdb=" N LEU D 149 " --> pdb=" O ILE D 179 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'E' and resid 180 through 184 removed outlier: 3.812A pdb=" N GLY E 42 " --> pdb=" O CYS E 165 " (cutoff:3.500A) removed outlier: 6.449A pdb=" N LYS E 130 " --> pdb=" O ARG E 160 " (cutoff:3.500A) removed outlier: 7.872A pdb=" N ILE E 162 " --> pdb=" O LYS E 130 " (cutoff:3.500A) removed outlier: 6.492A pdb=" N VAL E 132 " --> pdb=" O ILE E 162 " (cutoff:3.500A) removed outlier: 7.409A pdb=" N CYS E 164 " --> pdb=" O VAL E 132 " (cutoff:3.500A) removed outlier: 6.399A pdb=" N LEU E 134 " --> pdb=" O CYS E 164 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'E' and resid 68 through 75 Processing sheet with id= I, first strand: chain 'F' and resid 59 through 62 removed outlier: 4.232A pdb=" N THR F 59 " --> pdb=" O ARG F 5 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N GLU F 104 " --> pdb=" O ILE F 87 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'F' and resid 66 through 71 removed outlier: 6.697A pdb=" N GLU F 25 " --> pdb=" O MET F 40 " (cutoff:3.500A) removed outlier: 6.202A pdb=" N MET F 40 " --> pdb=" O GLU F 25 " (cutoff:3.500A) removed outlier: 5.333A pdb=" N CYS F 27 " --> pdb=" O GLN F 38 " (cutoff:3.500A) removed outlier: 4.224A pdb=" N GLN F 38 " --> pdb=" O CYS F 27 " (cutoff:3.500A) removed outlier: 4.745A pdb=" N LYS F 240 " --> pdb=" O THR F 224 " (cutoff:3.500A) removed outlier: 6.838A pdb=" N THR F 224 " --> pdb=" O LYS F 240 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'F' and resid 203 through 208 removed outlier: 5.374A pdb=" N ALA F 157 " --> pdb=" O SER F 172 " (cutoff:3.500A) removed outlier: 4.425A pdb=" N SER F 172 " --> pdb=" O ALA F 157 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'G' and resid 2 through 6 Processing sheet with id= M, first strand: chain 'G' and resid 66 through 71 removed outlier: 6.753A pdb=" N GLU G 25 " --> pdb=" O MET G 40 " (cutoff:3.500A) removed outlier: 6.134A pdb=" N MET G 40 " --> pdb=" O GLU G 25 " (cutoff:3.500A) removed outlier: 5.307A pdb=" N CYS G 27 " --> pdb=" O GLN G 38 " (cutoff:3.500A) removed outlier: 4.220A pdb=" N GLN G 38 " --> pdb=" O CYS G 27 " (cutoff:3.500A) removed outlier: 4.736A pdb=" N LYS G 240 " --> pdb=" O THR G 224 " (cutoff:3.500A) removed outlier: 6.860A pdb=" N THR G 224 " --> pdb=" O LYS G 240 " (cutoff:3.500A) Processing sheet with id= N, first strand: chain 'G' and resid 203 through 208 removed outlier: 6.194A pdb=" N ALA G 157 " --> pdb=" O SER G 172 " (cutoff:3.500A) removed outlier: 4.775A pdb=" N SER G 172 " --> pdb=" O ALA G 157 " (cutoff:3.500A) Processing sheet with id= O, first strand: chain 'H' and resid 59 through 62 Processing sheet with id= P, first strand: chain 'H' and resid 66 through 71 removed outlier: 7.276A pdb=" N GLU H 25 " --> pdb=" O MET H 40 " (cutoff:3.500A) removed outlier: 6.218A pdb=" N MET H 40 " --> pdb=" O GLU H 25 " (cutoff:3.500A) removed outlier: 6.041A pdb=" N CYS H 27 " --> pdb=" O GLN H 38 " (cutoff:3.500A) removed outlier: 4.536A pdb=" N GLN H 38 " --> pdb=" O CYS H 27 " (cutoff:3.500A) removed outlier: 4.403A pdb=" N LYS H 240 " --> pdb=" O THR H 224 " (cutoff:3.500A) removed outlier: 6.551A pdb=" N THR H 224 " --> pdb=" O LYS H 240 " (cutoff:3.500A) Processing sheet with id= Q, first strand: chain 'H' and resid 203 through 208 removed outlier: 5.496A pdb=" N ALA H 157 " --> pdb=" O SER H 172 " (cutoff:3.500A) removed outlier: 4.350A pdb=" N SER H 172 " --> pdb=" O ALA H 157 " (cutoff:3.500A) 988 hydrogen bonds defined for protein. 2826 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: 7.01 Time building geometry restraints manager: 8.51 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.33: 5306 1.33 - 1.49: 6129 1.49 - 1.64: 9212 1.64 - 1.79: 86 1.79 - 1.95: 120 Bond restraints: 20853 Sorted by residual: bond pdb=" CA SER B 238 " pdb=" C SER B 238 " ideal model delta sigma weight residual 1.524 1.425 0.099 1.24e-02 6.50e+03 6.38e+01 bond pdb=" CA GLN B 237 " pdb=" C GLN B 237 " ideal model delta sigma weight residual 1.524 1.440 0.084 1.24e-02 6.50e+03 4.59e+01 bond pdb=" CA ASP G 21 " pdb=" C ASP G 21 " ideal model delta sigma weight residual 1.522 1.436 0.085 1.31e-02 5.83e+03 4.25e+01 bond pdb=" N ILE G 23 " pdb=" CA ILE G 23 " ideal model delta sigma weight residual 1.460 1.527 -0.068 1.25e-02 6.40e+03 2.93e+01 bond pdb=" N LYS F 14 " pdb=" CA LYS F 14 " ideal model delta sigma weight residual 1.459 1.398 0.061 1.21e-02 6.83e+03 2.55e+01 ... (remaining 20848 not shown) Histogram of bond angle deviations from ideal: 95.04 - 103.25: 190 103.25 - 111.45: 8764 111.45 - 119.66: 9637 119.66 - 127.87: 9506 127.87 - 136.08: 126 Bond angle restraints: 28223 Sorted by residual: angle pdb=" N GLU F 17 " pdb=" CA GLU F 17 " pdb=" C GLU F 17 " ideal model delta sigma weight residual 113.23 100.51 12.72 1.24e+00 6.50e-01 1.05e+02 angle pdb=" N LYS G 20 " pdb=" CA LYS G 20 " pdb=" C LYS G 20 " ideal model delta sigma weight residual 111.71 121.98 -10.27 1.15e+00 7.56e-01 7.97e+01 angle pdb=" N ILE F 78 " pdb=" CA ILE F 78 " pdb=" C ILE F 78 " ideal model delta sigma weight residual 113.22 105.48 7.74 1.23e+00 6.61e-01 3.96e+01 angle pdb=" C GLN B 237 " pdb=" CA GLN B 237 " pdb=" CB GLN B 237 " ideal model delta sigma weight residual 110.96 101.47 9.49 1.54e+00 4.22e-01 3.80e+01 angle pdb=" C SER B 238 " pdb=" CA SER B 238 " pdb=" CB SER B 238 " ideal model delta sigma weight residual 110.96 101.65 9.31 1.54e+00 4.22e-01 3.65e+01 ... (remaining 28218 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 24.53: 11661 24.53 - 49.06: 1057 49.06 - 73.59: 136 73.59 - 98.13: 22 98.13 - 122.66: 2 Dihedral angle restraints: 12878 sinusoidal: 5265 harmonic: 7613 Sorted by residual: dihedral pdb=" C5' ADP E2000 " pdb=" O5' ADP E2000 " pdb=" PA ADP E2000 " pdb=" O2A ADP E2000 " ideal model delta sinusoidal sigma weight residual 300.00 177.35 122.66 1 2.00e+01 2.50e-03 3.70e+01 dihedral pdb=" O1B ADP E2000 " pdb=" O3A ADP E2000 " pdb=" PB ADP E2000 " pdb=" PA ADP E2000 " ideal model delta sinusoidal sigma weight residual -60.00 -175.46 115.45 1 2.00e+01 2.50e-03 3.43e+01 dihedral pdb=" C GLN B 237 " pdb=" N GLN B 237 " pdb=" CA GLN B 237 " pdb=" CB GLN B 237 " ideal model delta harmonic sigma weight residual -122.60 -109.96 -12.64 0 2.50e+00 1.60e-01 2.56e+01 ... (remaining 12875 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.104: 3025 0.104 - 0.207: 246 0.207 - 0.310: 15 0.310 - 0.414: 3 0.414 - 0.517: 3 Chirality restraints: 3292 Sorted by residual: chirality pdb=" CA PHE B 240 " pdb=" N PHE B 240 " pdb=" C PHE B 240 " pdb=" CB PHE B 240 " both_signs ideal model delta sigma weight residual False 2.51 1.99 0.52 2.00e-01 2.50e+01 6.69e+00 chirality pdb=" CA LYS G 20 " pdb=" N LYS G 20 " pdb=" C LYS G 20 " pdb=" CB LYS G 20 " both_signs ideal model delta sigma weight residual False 2.51 2.04 0.47 2.00e-01 2.50e+01 5.47e+00 chirality pdb=" CB ILE H 241 " pdb=" CA ILE H 241 " pdb=" CG1 ILE H 241 " pdb=" CG2 ILE H 241 " both_signs ideal model delta sigma weight residual False 2.64 2.18 0.46 2.00e-01 2.50e+01 5.32e+00 ... (remaining 3289 not shown) Planarity restraints: 3607 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C SER A 405 " -0.083 5.00e-02 4.00e+02 1.24e-01 2.46e+01 pdb=" N PRO A 406 " 0.214 5.00e-02 4.00e+02 pdb=" CA PRO A 406 " -0.066 5.00e-02 4.00e+02 pdb=" CD PRO A 406 " -0.065 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PRO A 698 " -0.058 5.00e-02 4.00e+02 8.67e-02 1.20e+01 pdb=" N PRO A 699 " 0.150 5.00e-02 4.00e+02 pdb=" CA PRO A 699 " -0.043 5.00e-02 4.00e+02 pdb=" CD PRO A 699 " -0.048 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASP A 360 " -0.051 5.00e-02 4.00e+02 7.82e-02 9.78e+00 pdb=" N PRO A 361 " 0.135 5.00e-02 4.00e+02 pdb=" CA PRO A 361 " -0.041 5.00e-02 4.00e+02 pdb=" CD PRO A 361 " -0.043 5.00e-02 4.00e+02 ... (remaining 3604 not shown) Histogram of nonbonded interaction distances: 2.10 - 2.66: 335 2.66 - 3.22: 17725 3.22 - 3.78: 32503 3.78 - 4.34: 43189 4.34 - 4.90: 71182 Nonbonded interactions: 164934 Sorted by model distance: nonbonded pdb="MG MG C 401 " pdb=" O3G AGS C 402 " model vdw 2.104 2.170 nonbonded pdb="MG MG B 401 " pdb=" O3G AGS B 402 " model vdw 2.167 2.170 nonbonded pdb=" O THR E 168 " pdb=" OG1 THR E 168 " model vdw 2.257 2.440 nonbonded pdb=" O TYR E 254 " pdb=" OG1 THR E 258 " model vdw 2.271 2.440 nonbonded pdb=" O GLU D 259 " pdb=" OG1 THR D 263 " model vdw 2.285 2.440 ... (remaining 164929 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'F' selection = (chain 'G' and resid 1 through 256) selection = (chain 'H' and resid 1 through 256) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.810 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: 7.470 Check model and map are aligned: 0.150 Set scattering table: 0.200 Process input model: 53.580 Find NCS groups from input model: 0.860 Set up NCS constraints: 0.110 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:3.210 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 67.410 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6961 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.099 20853 Z= 0.372 Angle : 1.015 13.336 28223 Z= 0.577 Chirality : 0.059 0.517 3292 Planarity : 0.008 0.124 3607 Dihedral : 17.808 122.657 7922 Min Nonbonded Distance : 2.104 Molprobity Statistics. All-atom Clashscore : 8.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.76 % Favored : 97.24 % Rotamer: Outliers : 0.84 % Allowed : 27.36 % Favored : 71.80 % Cbeta Deviations : 0.16 % 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: -1.89 (0.15), residues: 2577 helix: -1.65 (0.12), residues: 1169 sheet: -0.06 (0.22), residues: 555 loop : -1.15 (0.19), residues: 853 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP E 251 HIS 0.011 0.002 HIS H 246 PHE 0.049 0.003 PHE B 223 TYR 0.040 0.002 TYR F 249 ARG 0.014 0.001 ARG A 846 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5154 Ramachandran restraints generated. 2577 Oldfield, 0 Emsley, 2577 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5154 Ramachandran restraints generated. 2577 Oldfield, 0 Emsley, 2577 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 361 residues out of total 2274 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 342 time to evaluate : 2.373 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 203 MET cc_start: 0.6499 (mmm) cc_final: 0.6147 (mmm) REVERT: C 51 ASP cc_start: 0.6192 (t0) cc_final: 0.5873 (t0) REVERT: E 317 TYR cc_start: 0.8270 (t80) cc_final: 0.7417 (t80) REVERT: F 121 LEU cc_start: 0.7329 (OUTLIER) cc_final: 0.7109 (tt) REVERT: G 27 CYS cc_start: 0.7266 (m) cc_final: 0.6569 (t) REVERT: H 2 PHE cc_start: 0.5988 (t80) cc_final: 0.5520 (t80) REVERT: H 133 TYR cc_start: 0.3392 (m-80) cc_final: 0.1611 (m-10) outliers start: 19 outliers final: 5 residues processed: 353 average time/residue: 0.3453 time to fit residues: 182.3160 Evaluate side-chains 292 residues out of total 2274 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 286 time to evaluate : 2.230 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 748 THR Chi-restraints excluded: chain A residue 764 LEU Chi-restraints excluded: chain B residue 240 PHE Chi-restraints excluded: chain F residue 15 VAL Chi-restraints excluded: chain F residue 121 LEU Chi-restraints excluded: chain H residue 30 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 256 random chunks: chunk 216 optimal weight: 8.9990 chunk 194 optimal weight: 4.9990 chunk 107 optimal weight: 6.9990 chunk 66 optimal weight: 2.9990 chunk 130 optimal weight: 0.6980 chunk 103 optimal weight: 0.2980 chunk 200 optimal weight: 0.0980 chunk 77 optimal weight: 2.9990 chunk 122 optimal weight: 8.9990 chunk 149 optimal weight: 1.9990 chunk 232 optimal weight: 8.9990 overall best weight: 1.2184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 504 GLN A 509 HIS B 151 GLN ** B 172 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 182 GLN B 204 ASN B 231 GLN B 234 ASN C 300 HIS ** D 207 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 347 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 71 HIS ** E 119 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 194 HIS F 131 GLN H 200 ASN H 204 GLN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7061 moved from start: 0.1122 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 20853 Z= 0.208 Angle : 0.600 9.548 28223 Z= 0.301 Chirality : 0.041 0.163 3292 Planarity : 0.005 0.077 3607 Dihedral : 8.048 109.432 2880 Min Nonbonded Distance : 2.006 Molprobity Statistics. All-atom Clashscore : 11.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.29 % Favored : 97.71 % Rotamer: Outliers : 3.26 % Allowed : 26.00 % Favored : 70.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.73 (0.16), residues: 2577 helix: -0.40 (0.14), residues: 1172 sheet: 0.17 (0.22), residues: 561 loop : -0.78 (0.21), residues: 844 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP A 307 HIS 0.008 0.001 HIS H 246 PHE 0.019 0.001 PHE B 223 TYR 0.019 0.001 TYR F 249 ARG 0.010 0.000 ARG D 193 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5154 Ramachandran restraints generated. 2577 Oldfield, 0 Emsley, 2577 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5154 Ramachandran restraints generated. 2577 Oldfield, 0 Emsley, 2577 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 384 residues out of total 2274 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 74 poor density : 310 time to evaluate : 2.113 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 632 PHE cc_start: 0.5009 (t80) cc_final: 0.4544 (t80) REVERT: B 136 LYS cc_start: 0.8256 (OUTLIER) cc_final: 0.7582 (mtmt) REVERT: B 145 SER cc_start: 0.8029 (OUTLIER) cc_final: 0.7674 (m) REVERT: B 280 LYS cc_start: 0.7644 (mmtm) cc_final: 0.7417 (mmtm) REVERT: C 51 ASP cc_start: 0.6382 (t0) cc_final: 0.5929 (t0) REVERT: C 143 GLU cc_start: 0.6035 (mt-10) cc_final: 0.5748 (mt-10) REVERT: D 95 LEU cc_start: 0.4892 (tp) cc_final: 0.4412 (mt) REVERT: E 317 TYR cc_start: 0.8204 (t80) cc_final: 0.7295 (t80) REVERT: G 27 CYS cc_start: 0.7406 (m) cc_final: 0.6822 (t) REVERT: H 2 PHE cc_start: 0.5953 (t80) cc_final: 0.5313 (t80) REVERT: H 133 TYR cc_start: 0.3457 (m-80) cc_final: 0.1668 (m-10) outliers start: 74 outliers final: 42 residues processed: 361 average time/residue: 0.3178 time to fit residues: 174.3068 Evaluate side-chains 326 residues out of total 2274 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 282 time to evaluate : 2.431 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 179 HIS Chi-restraints excluded: chain A residue 283 VAL Chi-restraints excluded: chain A residue 369 VAL Chi-restraints excluded: chain A residue 504 GLN Chi-restraints excluded: chain A residue 695 LEU Chi-restraints excluded: chain A residue 748 THR Chi-restraints excluded: chain A residue 830 LEU Chi-restraints excluded: chain B residue 136 LYS Chi-restraints excluded: chain B residue 145 SER Chi-restraints excluded: chain B residue 192 LYS Chi-restraints excluded: chain B residue 199 LEU Chi-restraints excluded: chain B residue 240 PHE Chi-restraints excluded: chain B residue 243 PHE Chi-restraints excluded: chain B residue 251 VAL Chi-restraints excluded: chain B residue 332 ASN Chi-restraints excluded: chain C residue 90 LEU Chi-restraints excluded: chain C residue 124 LEU Chi-restraints excluded: chain C residue 207 THR Chi-restraints excluded: chain C residue 219 ILE Chi-restraints excluded: chain D residue 238 LEU Chi-restraints excluded: chain E residue 3 LEU Chi-restraints excluded: chain E residue 84 ILE Chi-restraints excluded: chain E residue 128 ASP Chi-restraints excluded: chain E residue 136 GLU Chi-restraints excluded: chain E residue 256 ARG Chi-restraints excluded: chain E residue 311 VAL Chi-restraints excluded: chain F residue 23 ILE Chi-restraints excluded: chain F residue 43 SER Chi-restraints excluded: chain F residue 72 LEU Chi-restraints excluded: chain F residue 121 LEU Chi-restraints excluded: chain F residue 131 GLN Chi-restraints excluded: chain F residue 153 HIS Chi-restraints excluded: chain F residue 247 LEU Chi-restraints excluded: chain G residue 19 LEU Chi-restraints excluded: chain G residue 39 SER Chi-restraints excluded: chain G residue 177 ASN Chi-restraints excluded: chain G residue 251 LEU Chi-restraints excluded: chain H residue 17 GLU Chi-restraints excluded: chain H residue 86 ASP Chi-restraints excluded: chain H residue 103 PHE Chi-restraints excluded: chain H residue 167 VAL Chi-restraints excluded: chain H residue 224 THR Chi-restraints excluded: chain H residue 235 LEU Chi-restraints excluded: chain H residue 247 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 256 random chunks: chunk 129 optimal weight: 0.8980 chunk 72 optimal weight: 2.9990 chunk 193 optimal weight: 7.9990 chunk 158 optimal weight: 9.9990 chunk 64 optimal weight: 2.9990 chunk 232 optimal weight: 5.9990 chunk 251 optimal weight: 8.9990 chunk 207 optimal weight: 0.3980 chunk 230 optimal weight: 4.9990 chunk 79 optimal weight: 3.9990 chunk 186 optimal weight: 5.9990 overall best weight: 2.2586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 504 GLN A 820 ASN ** B 172 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 231 GLN B 235 ASN C 55 HIS C 91 ASN ** D 207 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 246 GLN ** D 347 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 71 HIS ** E 119 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 44 HIS Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7188 moved from start: 0.1829 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.049 20853 Z= 0.305 Angle : 0.635 10.831 28223 Z= 0.320 Chirality : 0.043 0.170 3292 Planarity : 0.005 0.064 3607 Dihedral : 7.643 91.367 2875 Min Nonbonded Distance : 1.920 Molprobity Statistics. All-atom Clashscore : 14.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.87 % Favored : 97.13 % Rotamer: Outliers : 5.37 % Allowed : 25.34 % Favored : 69.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.57 (0.16), residues: 2577 helix: -0.18 (0.14), residues: 1192 sheet: 0.19 (0.22), residues: 551 loop : -0.81 (0.21), residues: 834 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP E 4 HIS 0.007 0.001 HIS H 246 PHE 0.020 0.002 PHE H 207 TYR 0.028 0.002 TYR G 249 ARG 0.005 0.000 ARG E 221 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5154 Ramachandran restraints generated. 2577 Oldfield, 0 Emsley, 2577 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5154 Ramachandran restraints generated. 2577 Oldfield, 0 Emsley, 2577 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 434 residues out of total 2274 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 122 poor density : 312 time to evaluate : 2.356 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 632 PHE cc_start: 0.5385 (t80) cc_final: 0.4780 (t80) REVERT: B 127 LYS cc_start: 0.8466 (OUTLIER) cc_final: 0.7570 (ttpt) REVERT: B 136 LYS cc_start: 0.8218 (OUTLIER) cc_final: 0.7472 (mtmt) REVERT: B 229 MET cc_start: 0.7691 (tpp) cc_final: 0.7427 (tpp) REVERT: B 245 PHE cc_start: 0.6154 (OUTLIER) cc_final: 0.5769 (t80) REVERT: B 336 GLN cc_start: 0.7623 (OUTLIER) cc_final: 0.7341 (mp10) REVERT: C 51 ASP cc_start: 0.6567 (t0) cc_final: 0.6013 (t0) REVERT: C 85 SER cc_start: 0.7521 (m) cc_final: 0.7205 (p) REVERT: C 165 LEU cc_start: 0.7914 (OUTLIER) cc_final: 0.7616 (tp) REVERT: D 193 ARG cc_start: 0.5999 (ttt-90) cc_final: 0.5681 (ttt-90) REVERT: D 272 GLU cc_start: 0.8514 (OUTLIER) cc_final: 0.8003 (pm20) REVERT: E 258 THR cc_start: 0.7884 (OUTLIER) cc_final: 0.7607 (m) REVERT: E 317 TYR cc_start: 0.8207 (t80) cc_final: 0.7765 (t80) REVERT: H 2 PHE cc_start: 0.5892 (t80) cc_final: 0.5686 (t80) REVERT: H 91 ARG cc_start: 0.7257 (tmt170) cc_final: 0.7050 (tmt170) REVERT: H 116 MET cc_start: 0.6919 (tpt) cc_final: 0.6653 (tpt) REVERT: H 133 TYR cc_start: 0.3660 (m-80) cc_final: 0.1829 (m-10) outliers start: 122 outliers final: 73 residues processed: 403 average time/residue: 0.3094 time to fit residues: 191.9877 Evaluate side-chains 360 residues out of total 2274 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 80 poor density : 280 time to evaluate : 1.885 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 179 HIS Chi-restraints excluded: chain A residue 283 VAL Chi-restraints excluded: chain A residue 315 VAL Chi-restraints excluded: chain A residue 369 VAL Chi-restraints excluded: chain A residue 383 LEU Chi-restraints excluded: chain A residue 396 VAL Chi-restraints excluded: chain A residue 413 ILE Chi-restraints excluded: chain A residue 417 THR Chi-restraints excluded: chain A residue 504 GLN Chi-restraints excluded: chain A residue 589 VAL Chi-restraints excluded: chain A residue 695 LEU Chi-restraints excluded: chain A residue 713 HIS Chi-restraints excluded: chain A residue 748 THR Chi-restraints excluded: chain A residue 830 LEU Chi-restraints excluded: chain B residue 48 ASN Chi-restraints excluded: chain B residue 116 VAL Chi-restraints excluded: chain B residue 127 LYS Chi-restraints excluded: chain B residue 136 LYS Chi-restraints excluded: chain B residue 145 SER Chi-restraints excluded: chain B residue 192 LYS Chi-restraints excluded: chain B residue 194 THR Chi-restraints excluded: chain B residue 199 LEU Chi-restraints excluded: chain B residue 240 PHE Chi-restraints excluded: chain B residue 245 PHE Chi-restraints excluded: chain B residue 248 SER Chi-restraints excluded: chain B residue 251 VAL Chi-restraints excluded: chain B residue 299 ILE Chi-restraints excluded: chain B residue 332 ASN Chi-restraints excluded: chain B residue 336 GLN Chi-restraints excluded: chain C residue 22 TRP Chi-restraints excluded: chain C residue 87 VAL Chi-restraints excluded: chain C residue 90 LEU Chi-restraints excluded: chain C residue 113 THR Chi-restraints excluded: chain C residue 124 LEU Chi-restraints excluded: chain C residue 165 LEU Chi-restraints excluded: chain C residue 207 THR Chi-restraints excluded: chain C residue 219 ILE Chi-restraints excluded: chain C residue 260 THR Chi-restraints excluded: chain C residue 271 THR Chi-restraints excluded: chain D residue 173 THR Chi-restraints excluded: chain D residue 222 ILE Chi-restraints excluded: chain D residue 238 LEU Chi-restraints excluded: chain D residue 246 GLN Chi-restraints excluded: chain D residue 272 GLU Chi-restraints excluded: chain E residue 40 VAL Chi-restraints excluded: chain E residue 54 CYS Chi-restraints excluded: chain E residue 84 ILE Chi-restraints excluded: chain E residue 86 THR Chi-restraints excluded: chain E residue 99 ASP Chi-restraints excluded: chain E residue 123 THR Chi-restraints excluded: chain E residue 127 ARG Chi-restraints excluded: chain E residue 128 ASP Chi-restraints excluded: chain E residue 136 GLU Chi-restraints excluded: chain E residue 253 VAL Chi-restraints excluded: chain E residue 258 THR Chi-restraints excluded: chain E residue 311 VAL Chi-restraints excluded: chain F residue 7 VAL Chi-restraints excluded: chain F residue 15 VAL Chi-restraints excluded: chain F residue 44 HIS Chi-restraints excluded: chain F residue 68 MET Chi-restraints excluded: chain F residue 72 LEU Chi-restraints excluded: chain F residue 121 LEU Chi-restraints excluded: chain F residue 153 HIS Chi-restraints excluded: chain F residue 195 VAL Chi-restraints excluded: chain F residue 233 VAL Chi-restraints excluded: chain F residue 236 VAL Chi-restraints excluded: chain F residue 247 LEU Chi-restraints excluded: chain F residue 255 ILE Chi-restraints excluded: chain G residue 19 LEU Chi-restraints excluded: chain G residue 39 SER Chi-restraints excluded: chain G residue 75 MET Chi-restraints excluded: chain G residue 177 ASN Chi-restraints excluded: chain G residue 243 ASP Chi-restraints excluded: chain G residue 251 LEU Chi-restraints excluded: chain H residue 30 ILE Chi-restraints excluded: chain H residue 160 ILE Chi-restraints excluded: chain H residue 167 VAL Chi-restraints excluded: chain H residue 185 THR Chi-restraints excluded: chain H residue 224 THR Chi-restraints excluded: chain H residue 241 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 256 random chunks: chunk 230 optimal weight: 0.9990 chunk 175 optimal weight: 0.6980 chunk 120 optimal weight: 0.0040 chunk 25 optimal weight: 5.9990 chunk 111 optimal weight: 1.9990 chunk 156 optimal weight: 5.9990 chunk 233 optimal weight: 1.9990 chunk 247 optimal weight: 0.7980 chunk 122 optimal weight: 3.9990 chunk 221 optimal weight: 0.8980 chunk 66 optimal weight: 3.9990 overall best weight: 0.6794 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 504 GLN ** A 738 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 151 GLN ** B 172 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 298 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 91 ASN C 132 GLN ** D 207 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 246 GLN D 347 GLN E 71 HIS ** E 119 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 194 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7109 moved from start: 0.1880 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 20853 Z= 0.169 Angle : 0.558 9.041 28223 Z= 0.280 Chirality : 0.041 0.146 3292 Planarity : 0.004 0.058 3607 Dihedral : 7.328 86.055 2875 Min Nonbonded Distance : 2.016 Molprobity Statistics. All-atom Clashscore : 12.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.13 % Favored : 97.87 % Rotamer: Outliers : 3.74 % Allowed : 27.45 % Favored : 68.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.09 (0.16), residues: 2577 helix: 0.34 (0.15), residues: 1182 sheet: 0.30 (0.23), residues: 551 loop : -0.67 (0.21), residues: 844 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP E 4 HIS 0.007 0.001 HIS H 246 PHE 0.023 0.001 PHE H 207 TYR 0.017 0.001 TYR G 249 ARG 0.004 0.000 ARG H 210 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5154 Ramachandran restraints generated. 2577 Oldfield, 0 Emsley, 2577 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5154 Ramachandran restraints generated. 2577 Oldfield, 0 Emsley, 2577 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 393 residues out of total 2274 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 85 poor density : 308 time to evaluate : 2.024 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 632 PHE cc_start: 0.5297 (t80) cc_final: 0.4706 (t80) REVERT: B 136 LYS cc_start: 0.8126 (OUTLIER) cc_final: 0.7470 (mtmt) REVERT: C 29 GLN cc_start: 0.7324 (mm-40) cc_final: 0.7097 (mm110) REVERT: C 51 ASP cc_start: 0.6470 (t0) cc_final: 0.5938 (t0) REVERT: C 85 SER cc_start: 0.7549 (m) cc_final: 0.7255 (p) REVERT: E 213 HIS cc_start: 0.6494 (t-90) cc_final: 0.6252 (m-70) REVERT: E 317 TYR cc_start: 0.8159 (t80) cc_final: 0.7726 (t80) REVERT: H 8 GLN cc_start: 0.7305 (tm-30) cc_final: 0.7080 (tm-30) REVERT: H 91 ARG cc_start: 0.7208 (tmt170) cc_final: 0.6765 (tmt170) REVERT: H 133 TYR cc_start: 0.3659 (m-80) cc_final: 0.1754 (m-10) outliers start: 85 outliers final: 54 residues processed: 366 average time/residue: 0.3168 time to fit residues: 177.5449 Evaluate side-chains 339 residues out of total 2274 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 55 poor density : 284 time to evaluate : 2.379 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 283 VAL Chi-restraints excluded: chain A residue 369 VAL Chi-restraints excluded: chain A residue 383 LEU Chi-restraints excluded: chain A residue 413 ILE Chi-restraints excluded: chain A residue 451 ILE Chi-restraints excluded: chain A residue 504 GLN Chi-restraints excluded: chain A residue 695 LEU Chi-restraints excluded: chain A residue 713 HIS Chi-restraints excluded: chain A residue 830 LEU Chi-restraints excluded: chain B residue 40 GLU Chi-restraints excluded: chain B residue 48 ASN Chi-restraints excluded: chain B residue 136 LYS Chi-restraints excluded: chain B residue 192 LYS Chi-restraints excluded: chain B residue 199 LEU Chi-restraints excluded: chain B residue 248 SER Chi-restraints excluded: chain B residue 270 CYS Chi-restraints excluded: chain B residue 271 VAL Chi-restraints excluded: chain B residue 332 ASN Chi-restraints excluded: chain B residue 335 LEU Chi-restraints excluded: chain C residue 48 ILE Chi-restraints excluded: chain C residue 90 LEU Chi-restraints excluded: chain C residue 124 LEU Chi-restraints excluded: chain C residue 219 ILE Chi-restraints excluded: chain D residue 156 THR Chi-restraints excluded: chain D residue 238 LEU Chi-restraints excluded: chain D residue 246 GLN Chi-restraints excluded: chain E residue 40 VAL Chi-restraints excluded: chain E residue 84 ILE Chi-restraints excluded: chain E residue 128 ASP Chi-restraints excluded: chain E residue 136 GLU Chi-restraints excluded: chain E residue 143 ASP Chi-restraints excluded: chain E residue 246 ILE Chi-restraints excluded: chain E residue 250 ASP Chi-restraints excluded: chain E residue 253 VAL Chi-restraints excluded: chain E residue 256 ARG Chi-restraints excluded: chain F residue 7 VAL Chi-restraints excluded: chain F residue 15 VAL Chi-restraints excluded: chain F residue 44 HIS Chi-restraints excluded: chain F residue 72 LEU Chi-restraints excluded: chain F residue 121 LEU Chi-restraints excluded: chain F residue 153 HIS Chi-restraints excluded: chain F residue 195 VAL Chi-restraints excluded: chain F residue 236 VAL Chi-restraints excluded: chain F residue 255 ILE Chi-restraints excluded: chain G residue 19 LEU Chi-restraints excluded: chain G residue 27 CYS Chi-restraints excluded: chain G residue 111 VAL Chi-restraints excluded: chain G residue 246 HIS Chi-restraints excluded: chain G residue 251 LEU Chi-restraints excluded: chain H residue 52 LEU Chi-restraints excluded: chain H residue 103 PHE Chi-restraints excluded: chain H residue 160 ILE Chi-restraints excluded: chain H residue 167 VAL Chi-restraints excluded: chain H residue 185 THR Chi-restraints excluded: chain H residue 224 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 256 random chunks: chunk 206 optimal weight: 0.8980 chunk 140 optimal weight: 7.9990 chunk 3 optimal weight: 0.0670 chunk 184 optimal weight: 4.9990 chunk 102 optimal weight: 5.9990 chunk 211 optimal weight: 0.9980 chunk 171 optimal weight: 0.9990 chunk 0 optimal weight: 10.0000 chunk 126 optimal weight: 9.9990 chunk 222 optimal weight: 7.9990 chunk 62 optimal weight: 9.9990 overall best weight: 1.5922 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 738 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 820 ASN ** B 172 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 207 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 246 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 347 GLN E 71 HIS ** E 119 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7166 moved from start: 0.2138 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 20853 Z= 0.238 Angle : 0.583 8.458 28223 Z= 0.291 Chirality : 0.042 0.215 3292 Planarity : 0.004 0.059 3607 Dihedral : 7.123 71.468 2872 Min Nonbonded Distance : 1.952 Molprobity Statistics. All-atom Clashscore : 13.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.83 % Favored : 97.17 % Rotamer: Outliers : 5.59 % Allowed : 26.13 % Favored : 68.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.05 (0.17), residues: 2577 helix: 0.36 (0.15), residues: 1186 sheet: 0.31 (0.23), residues: 551 loop : -0.63 (0.22), residues: 840 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP E 4 HIS 0.007 0.001 HIS F 44 PHE 0.015 0.001 PHE G 2 TYR 0.026 0.001 TYR G 249 ARG 0.007 0.000 ARG H 210 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5154 Ramachandran restraints generated. 2577 Oldfield, 0 Emsley, 2577 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5154 Ramachandran restraints generated. 2577 Oldfield, 0 Emsley, 2577 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 438 residues out of total 2274 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 127 poor density : 311 time to evaluate : 2.378 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 632 PHE cc_start: 0.5422 (t80) cc_final: 0.4770 (t80) REVERT: A 682 LEU cc_start: 0.7921 (tt) cc_final: 0.7718 (tp) REVERT: B 136 LYS cc_start: 0.8222 (OUTLIER) cc_final: 0.7516 (mtmt) REVERT: B 229 MET cc_start: 0.7855 (tpp) cc_final: 0.7627 (tpp) REVERT: C 29 GLN cc_start: 0.7258 (mm-40) cc_final: 0.7038 (mm110) REVERT: C 51 ASP cc_start: 0.6464 (t0) cc_final: 0.5940 (t0) REVERT: C 85 SER cc_start: 0.7551 (m) cc_final: 0.7294 (p) REVERT: C 91 ASN cc_start: 0.6510 (p0) cc_final: 0.6293 (p0) REVERT: D 272 GLU cc_start: 0.8480 (OUTLIER) cc_final: 0.7995 (pm20) REVERT: E 127 ARG cc_start: 0.7152 (OUTLIER) cc_final: 0.6798 (ttp-110) REVERT: E 213 HIS cc_start: 0.6562 (t-90) cc_final: 0.6301 (m-70) REVERT: E 258 THR cc_start: 0.7884 (OUTLIER) cc_final: 0.7583 (m) REVERT: E 317 TYR cc_start: 0.8178 (t80) cc_final: 0.7699 (t80) REVERT: H 40 MET cc_start: 0.5715 (tpt) cc_final: 0.5170 (tmm) REVERT: H 91 ARG cc_start: 0.7333 (tmt170) cc_final: 0.6912 (tmt170) REVERT: H 162 CYS cc_start: 0.6769 (t) cc_final: 0.6530 (p) outliers start: 127 outliers final: 82 residues processed: 397 average time/residue: 0.3206 time to fit residues: 193.0686 Evaluate side-chains 377 residues out of total 2274 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 86 poor density : 291 time to evaluate : 2.515 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 179 HIS Chi-restraints excluded: chain A residue 283 VAL Chi-restraints excluded: chain A residue 315 VAL Chi-restraints excluded: chain A residue 348 GLU Chi-restraints excluded: chain A residue 369 VAL Chi-restraints excluded: chain A residue 383 LEU Chi-restraints excluded: chain A residue 396 VAL Chi-restraints excluded: chain A residue 413 ILE Chi-restraints excluded: chain A residue 451 ILE Chi-restraints excluded: chain A residue 695 LEU Chi-restraints excluded: chain A residue 713 HIS Chi-restraints excluded: chain A residue 748 THR Chi-restraints excluded: chain A residue 830 LEU Chi-restraints excluded: chain B residue 40 GLU Chi-restraints excluded: chain B residue 48 ASN Chi-restraints excluded: chain B residue 100 ASP Chi-restraints excluded: chain B residue 136 LYS Chi-restraints excluded: chain B residue 144 ASP Chi-restraints excluded: chain B residue 181 ILE Chi-restraints excluded: chain B residue 192 LYS Chi-restraints excluded: chain B residue 195 ASP Chi-restraints excluded: chain B residue 199 LEU Chi-restraints excluded: chain B residue 218 LEU Chi-restraints excluded: chain B residue 248 SER Chi-restraints excluded: chain B residue 270 CYS Chi-restraints excluded: chain B residue 271 VAL Chi-restraints excluded: chain B residue 299 ILE Chi-restraints excluded: chain B residue 332 ASN Chi-restraints excluded: chain B residue 335 LEU Chi-restraints excluded: chain C residue 48 ILE Chi-restraints excluded: chain C residue 87 VAL Chi-restraints excluded: chain C residue 90 LEU Chi-restraints excluded: chain C residue 113 THR Chi-restraints excluded: chain C residue 124 LEU Chi-restraints excluded: chain C residue 153 LEU Chi-restraints excluded: chain C residue 207 THR Chi-restraints excluded: chain C residue 219 ILE Chi-restraints excluded: chain C residue 296 SER Chi-restraints excluded: chain D residue 156 THR Chi-restraints excluded: chain D residue 173 THR Chi-restraints excluded: chain D residue 202 LEU Chi-restraints excluded: chain D residue 238 LEU Chi-restraints excluded: chain D residue 272 GLU Chi-restraints excluded: chain E residue 40 VAL Chi-restraints excluded: chain E residue 54 CYS Chi-restraints excluded: chain E residue 84 ILE Chi-restraints excluded: chain E residue 99 ASP Chi-restraints excluded: chain E residue 123 THR Chi-restraints excluded: chain E residue 127 ARG Chi-restraints excluded: chain E residue 128 ASP Chi-restraints excluded: chain E residue 136 GLU Chi-restraints excluded: chain E residue 227 LEU Chi-restraints excluded: chain E residue 235 VAL Chi-restraints excluded: chain E residue 246 ILE Chi-restraints excluded: chain E residue 250 ASP Chi-restraints excluded: chain E residue 253 VAL Chi-restraints excluded: chain E residue 256 ARG Chi-restraints excluded: chain E residue 258 THR Chi-restraints excluded: chain F residue 7 VAL Chi-restraints excluded: chain F residue 15 VAL Chi-restraints excluded: chain F residue 23 ILE Chi-restraints excluded: chain F residue 72 LEU Chi-restraints excluded: chain F residue 89 THR Chi-restraints excluded: chain F residue 121 LEU Chi-restraints excluded: chain F residue 147 ILE Chi-restraints excluded: chain F residue 153 HIS Chi-restraints excluded: chain F residue 195 VAL Chi-restraints excluded: chain F residue 233 VAL Chi-restraints excluded: chain F residue 236 VAL Chi-restraints excluded: chain F residue 247 LEU Chi-restraints excluded: chain F residue 255 ILE Chi-restraints excluded: chain G residue 19 LEU Chi-restraints excluded: chain G residue 111 VAL Chi-restraints excluded: chain G residue 139 MET Chi-restraints excluded: chain G residue 177 ASN Chi-restraints excluded: chain G residue 243 ASP Chi-restraints excluded: chain G residue 246 HIS Chi-restraints excluded: chain G residue 251 LEU Chi-restraints excluded: chain H residue 2 PHE Chi-restraints excluded: chain H residue 52 LEU Chi-restraints excluded: chain H residue 103 PHE Chi-restraints excluded: chain H residue 160 ILE Chi-restraints excluded: chain H residue 167 VAL Chi-restraints excluded: chain H residue 185 THR Chi-restraints excluded: chain H residue 224 THR Chi-restraints excluded: chain H residue 241 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 256 random chunks: chunk 83 optimal weight: 4.9990 chunk 222 optimal weight: 0.6980 chunk 48 optimal weight: 0.8980 chunk 145 optimal weight: 1.9990 chunk 61 optimal weight: 2.9990 chunk 247 optimal weight: 0.8980 chunk 205 optimal weight: 0.9980 chunk 114 optimal weight: 0.6980 chunk 20 optimal weight: 0.9990 chunk 81 optimal weight: 3.9990 chunk 130 optimal weight: 5.9990 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 738 GLN ** B 172 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 298 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 207 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 246 GLN ** D 311 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 347 GLN E 71 HIS ** E 119 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 194 HIS ** E 260 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7125 moved from start: 0.2222 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 20853 Z= 0.175 Angle : 0.559 10.616 28223 Z= 0.278 Chirality : 0.041 0.261 3292 Planarity : 0.004 0.056 3607 Dihedral : 6.959 63.739 2872 Min Nonbonded Distance : 2.005 Molprobity Statistics. All-atom Clashscore : 13.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.37 % Favored : 97.63 % Rotamer: Outliers : 4.31 % Allowed : 27.58 % Favored : 68.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.13 (0.17), residues: 2577 helix: 0.56 (0.15), residues: 1181 sheet: 0.26 (0.22), residues: 560 loop : -0.52 (0.22), residues: 836 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP E 4 HIS 0.009 0.001 HIS H 246 PHE 0.027 0.001 PHE B 223 TYR 0.020 0.001 TYR G 249 ARG 0.008 0.000 ARG H 210 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5154 Ramachandran restraints generated. 2577 Oldfield, 0 Emsley, 2577 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5154 Ramachandran restraints generated. 2577 Oldfield, 0 Emsley, 2577 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 405 residues out of total 2274 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 98 poor density : 307 time to evaluate : 2.226 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 482 LEU cc_start: 0.7010 (OUTLIER) cc_final: 0.6578 (tt) REVERT: A 632 PHE cc_start: 0.5396 (t80) cc_final: 0.4737 (t80) REVERT: B 127 LYS cc_start: 0.8276 (OUTLIER) cc_final: 0.7557 (ttpt) REVERT: B 136 LYS cc_start: 0.8176 (OUTLIER) cc_final: 0.7544 (mtmt) REVERT: B 216 ASP cc_start: 0.5778 (p0) cc_final: 0.5385 (p0) REVERT: C 29 GLN cc_start: 0.7308 (mm-40) cc_final: 0.7082 (mm110) REVERT: C 51 ASP cc_start: 0.6395 (t0) cc_final: 0.5887 (t0) REVERT: C 85 SER cc_start: 0.7532 (m) cc_final: 0.7311 (p) REVERT: D 272 GLU cc_start: 0.8425 (OUTLIER) cc_final: 0.7869 (pm20) REVERT: E 258 THR cc_start: 0.7872 (OUTLIER) cc_final: 0.7570 (m) REVERT: E 317 TYR cc_start: 0.8145 (t80) cc_final: 0.7770 (t80) REVERT: H 40 MET cc_start: 0.5418 (tpt) cc_final: 0.4599 (tmm) REVERT: H 91 ARG cc_start: 0.7349 (tmt170) cc_final: 0.6921 (tmt170) REVERT: H 116 MET cc_start: 0.6111 (tpt) cc_final: 0.5691 (tpt) REVERT: H 162 CYS cc_start: 0.6721 (t) cc_final: 0.6482 (p) outliers start: 98 outliers final: 72 residues processed: 378 average time/residue: 0.3187 time to fit residues: 184.5863 Evaluate side-chains 380 residues out of total 2274 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 77 poor density : 303 time to evaluate : 2.178 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 283 VAL Chi-restraints excluded: chain A residue 348 GLU Chi-restraints excluded: chain A residue 369 VAL Chi-restraints excluded: chain A residue 383 LEU Chi-restraints excluded: chain A residue 396 VAL Chi-restraints excluded: chain A residue 413 ILE Chi-restraints excluded: chain A residue 451 ILE Chi-restraints excluded: chain A residue 482 LEU Chi-restraints excluded: chain A residue 695 LEU Chi-restraints excluded: chain A residue 713 HIS Chi-restraints excluded: chain A residue 748 THR Chi-restraints excluded: chain A residue 830 LEU Chi-restraints excluded: chain B residue 40 GLU Chi-restraints excluded: chain B residue 48 ASN Chi-restraints excluded: chain B residue 127 LYS Chi-restraints excluded: chain B residue 136 LYS Chi-restraints excluded: chain B residue 144 ASP Chi-restraints excluded: chain B residue 145 SER Chi-restraints excluded: chain B residue 181 ILE Chi-restraints excluded: chain B residue 192 LYS Chi-restraints excluded: chain B residue 199 LEU Chi-restraints excluded: chain B residue 218 LEU Chi-restraints excluded: chain B residue 270 CYS Chi-restraints excluded: chain B residue 271 VAL Chi-restraints excluded: chain B residue 332 ASN Chi-restraints excluded: chain B residue 335 LEU Chi-restraints excluded: chain C residue 48 ILE Chi-restraints excluded: chain C residue 77 LEU Chi-restraints excluded: chain C residue 90 LEU Chi-restraints excluded: chain C residue 113 THR Chi-restraints excluded: chain C residue 124 LEU Chi-restraints excluded: chain C residue 153 LEU Chi-restraints excluded: chain C residue 219 ILE Chi-restraints excluded: chain C residue 271 THR Chi-restraints excluded: chain C residue 296 SER Chi-restraints excluded: chain D residue 156 THR Chi-restraints excluded: chain D residue 173 THR Chi-restraints excluded: chain D residue 192 SER Chi-restraints excluded: chain D residue 202 LEU Chi-restraints excluded: chain D residue 246 GLN Chi-restraints excluded: chain D residue 272 GLU Chi-restraints excluded: chain E residue 40 VAL Chi-restraints excluded: chain E residue 54 CYS Chi-restraints excluded: chain E residue 84 ILE Chi-restraints excluded: chain E residue 99 ASP Chi-restraints excluded: chain E residue 123 THR Chi-restraints excluded: chain E residue 128 ASP Chi-restraints excluded: chain E residue 136 GLU Chi-restraints excluded: chain E residue 143 ASP Chi-restraints excluded: chain E residue 235 VAL Chi-restraints excluded: chain E residue 246 ILE Chi-restraints excluded: chain E residue 250 ASP Chi-restraints excluded: chain E residue 253 VAL Chi-restraints excluded: chain E residue 256 ARG Chi-restraints excluded: chain E residue 258 THR Chi-restraints excluded: chain F residue 7 VAL Chi-restraints excluded: chain F residue 15 VAL Chi-restraints excluded: chain F residue 44 HIS Chi-restraints excluded: chain F residue 72 LEU Chi-restraints excluded: chain F residue 89 THR Chi-restraints excluded: chain F residue 121 LEU Chi-restraints excluded: chain F residue 147 ILE Chi-restraints excluded: chain F residue 153 HIS Chi-restraints excluded: chain F residue 167 VAL Chi-restraints excluded: chain F residue 195 VAL Chi-restraints excluded: chain F residue 206 THR Chi-restraints excluded: chain F residue 236 VAL Chi-restraints excluded: chain F residue 247 LEU Chi-restraints excluded: chain F residue 255 ILE Chi-restraints excluded: chain G residue 19 LEU Chi-restraints excluded: chain G residue 111 VAL Chi-restraints excluded: chain G residue 251 LEU Chi-restraints excluded: chain H residue 2 PHE Chi-restraints excluded: chain H residue 103 PHE Chi-restraints excluded: chain H residue 160 ILE Chi-restraints excluded: chain H residue 167 VAL Chi-restraints excluded: chain H residue 241 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 256 random chunks: chunk 238 optimal weight: 8.9990 chunk 27 optimal weight: 9.9990 chunk 141 optimal weight: 0.9990 chunk 180 optimal weight: 6.9990 chunk 140 optimal weight: 4.9990 chunk 208 optimal weight: 9.9990 chunk 138 optimal weight: 0.7980 chunk 246 optimal weight: 3.9990 chunk 154 optimal weight: 30.0000 chunk 150 optimal weight: 2.9990 chunk 113 optimal weight: 3.9990 overall best weight: 2.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 738 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 106 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 172 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 148 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 300 HIS ** D 207 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 246 GLN D 347 GLN E 71 HIS ** E 119 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 44 HIS ** H 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7236 moved from start: 0.2602 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.047 20853 Z= 0.334 Angle : 0.656 10.408 28223 Z= 0.324 Chirality : 0.043 0.185 3292 Planarity : 0.005 0.059 3607 Dihedral : 7.011 64.361 2872 Min Nonbonded Distance : 1.914 Molprobity Statistics. All-atom Clashscore : 16.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.65 % Favored : 96.35 % Rotamer: Outliers : 5.50 % Allowed : 26.66 % Favored : 67.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.19 (0.16), residues: 2577 helix: 0.26 (0.15), residues: 1184 sheet: 0.09 (0.23), residues: 547 loop : -0.60 (0.21), residues: 846 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP E 4 HIS 0.007 0.001 HIS F 44 PHE 0.022 0.002 PHE G 2 TYR 0.032 0.002 TYR G 249 ARG 0.008 0.001 ARG H 210 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5154 Ramachandran restraints generated. 2577 Oldfield, 0 Emsley, 2577 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5154 Ramachandran restraints generated. 2577 Oldfield, 0 Emsley, 2577 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 438 residues out of total 2274 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 125 poor density : 313 time to evaluate : 2.376 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 482 LEU cc_start: 0.7145 (OUTLIER) cc_final: 0.6718 (tt) REVERT: A 507 LEU cc_start: 0.8126 (mt) cc_final: 0.7917 (mp) REVERT: A 632 PHE cc_start: 0.5543 (t80) cc_final: 0.4780 (t80) REVERT: A 682 LEU cc_start: 0.8069 (tt) cc_final: 0.7859 (tp) REVERT: A 806 GLU cc_start: 0.6307 (OUTLIER) cc_final: 0.5710 (pp20) REVERT: A 839 GLN cc_start: 0.8208 (mp10) cc_final: 0.7899 (mm-40) REVERT: B 127 LYS cc_start: 0.8403 (OUTLIER) cc_final: 0.7687 (ttpt) REVERT: B 136 LYS cc_start: 0.8334 (OUTLIER) cc_final: 0.7781 (mtmt) REVERT: B 229 MET cc_start: 0.7970 (tpp) cc_final: 0.7709 (tpp) REVERT: C 165 LEU cc_start: 0.7927 (OUTLIER) cc_final: 0.7572 (tp) REVERT: D 272 GLU cc_start: 0.8481 (OUTLIER) cc_final: 0.8007 (pm20) REVERT: E 127 ARG cc_start: 0.7165 (OUTLIER) cc_final: 0.6759 (ttp-110) REVERT: E 194 HIS cc_start: 0.8182 (t-90) cc_final: 0.7978 (t-170) REVERT: G 143 GLU cc_start: 0.7284 (tm-30) cc_final: 0.6953 (tt0) REVERT: H 91 ARG cc_start: 0.7420 (tmt170) cc_final: 0.7032 (tmt170) REVERT: H 162 CYS cc_start: 0.6831 (t) cc_final: 0.6601 (p) outliers start: 125 outliers final: 92 residues processed: 408 average time/residue: 0.3145 time to fit residues: 196.5433 Evaluate side-chains 394 residues out of total 2274 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 99 poor density : 295 time to evaluate : 2.182 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 283 VAL Chi-restraints excluded: chain A residue 313 LEU Chi-restraints excluded: chain A residue 315 VAL Chi-restraints excluded: chain A residue 348 GLU Chi-restraints excluded: chain A residue 369 VAL Chi-restraints excluded: chain A residue 383 LEU Chi-restraints excluded: chain A residue 396 VAL Chi-restraints excluded: chain A residue 413 ILE Chi-restraints excluded: chain A residue 451 ILE Chi-restraints excluded: chain A residue 482 LEU Chi-restraints excluded: chain A residue 695 LEU Chi-restraints excluded: chain A residue 713 HIS Chi-restraints excluded: chain A residue 748 THR Chi-restraints excluded: chain A residue 806 GLU Chi-restraints excluded: chain A residue 830 LEU Chi-restraints excluded: chain B residue 48 ASN Chi-restraints excluded: chain B residue 73 ILE Chi-restraints excluded: chain B residue 100 ASP Chi-restraints excluded: chain B residue 127 LYS Chi-restraints excluded: chain B residue 136 LYS Chi-restraints excluded: chain B residue 144 ASP Chi-restraints excluded: chain B residue 145 SER Chi-restraints excluded: chain B residue 165 THR Chi-restraints excluded: chain B residue 181 ILE Chi-restraints excluded: chain B residue 192 LYS Chi-restraints excluded: chain B residue 194 THR Chi-restraints excluded: chain B residue 199 LEU Chi-restraints excluded: chain B residue 218 LEU Chi-restraints excluded: chain B residue 270 CYS Chi-restraints excluded: chain B residue 271 VAL Chi-restraints excluded: chain B residue 299 ILE Chi-restraints excluded: chain B residue 335 LEU Chi-restraints excluded: chain C residue 22 TRP Chi-restraints excluded: chain C residue 48 ILE Chi-restraints excluded: chain C residue 77 LEU Chi-restraints excluded: chain C residue 87 VAL Chi-restraints excluded: chain C residue 90 LEU Chi-restraints excluded: chain C residue 113 THR Chi-restraints excluded: chain C residue 124 LEU Chi-restraints excluded: chain C residue 153 LEU Chi-restraints excluded: chain C residue 154 ILE Chi-restraints excluded: chain C residue 165 LEU Chi-restraints excluded: chain C residue 190 VAL Chi-restraints excluded: chain C residue 207 THR Chi-restraints excluded: chain C residue 219 ILE Chi-restraints excluded: chain C residue 239 THR Chi-restraints excluded: chain C residue 271 THR Chi-restraints excluded: chain C residue 291 VAL Chi-restraints excluded: chain C residue 296 SER Chi-restraints excluded: chain D residue 156 THR Chi-restraints excluded: chain D residue 173 THR Chi-restraints excluded: chain D residue 192 SER Chi-restraints excluded: chain D residue 202 LEU Chi-restraints excluded: chain D residue 230 LEU Chi-restraints excluded: chain D residue 272 GLU Chi-restraints excluded: chain D residue 361 GLN Chi-restraints excluded: chain E residue 40 VAL Chi-restraints excluded: chain E residue 54 CYS Chi-restraints excluded: chain E residue 84 ILE Chi-restraints excluded: chain E residue 99 ASP Chi-restraints excluded: chain E residue 123 THR Chi-restraints excluded: chain E residue 127 ARG Chi-restraints excluded: chain E residue 128 ASP Chi-restraints excluded: chain E residue 143 ASP Chi-restraints excluded: chain E residue 227 LEU Chi-restraints excluded: chain E residue 235 VAL Chi-restraints excluded: chain E residue 246 ILE Chi-restraints excluded: chain E residue 250 ASP Chi-restraints excluded: chain E residue 253 VAL Chi-restraints excluded: chain E residue 256 ARG Chi-restraints excluded: chain F residue 7 VAL Chi-restraints excluded: chain F residue 15 VAL Chi-restraints excluded: chain F residue 59 THR Chi-restraints excluded: chain F residue 68 MET Chi-restraints excluded: chain F residue 89 THR Chi-restraints excluded: chain F residue 121 LEU Chi-restraints excluded: chain F residue 147 ILE Chi-restraints excluded: chain F residue 152 SER Chi-restraints excluded: chain F residue 158 VAL Chi-restraints excluded: chain F residue 167 VAL Chi-restraints excluded: chain F residue 195 VAL Chi-restraints excluded: chain F residue 206 THR Chi-restraints excluded: chain F residue 233 VAL Chi-restraints excluded: chain F residue 236 VAL Chi-restraints excluded: chain F residue 255 ILE Chi-restraints excluded: chain G residue 19 LEU Chi-restraints excluded: chain G residue 111 VAL Chi-restraints excluded: chain G residue 243 ASP Chi-restraints excluded: chain G residue 246 HIS Chi-restraints excluded: chain G residue 251 LEU Chi-restraints excluded: chain H residue 15 VAL Chi-restraints excluded: chain H residue 52 LEU Chi-restraints excluded: chain H residue 98 THR Chi-restraints excluded: chain H residue 103 PHE Chi-restraints excluded: chain H residue 160 ILE Chi-restraints excluded: chain H residue 167 VAL Chi-restraints excluded: chain H residue 185 THR Chi-restraints excluded: chain H residue 224 THR Chi-restraints excluded: chain H residue 241 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 256 random chunks: chunk 152 optimal weight: 5.9990 chunk 98 optimal weight: 0.7980 chunk 147 optimal weight: 0.8980 chunk 74 optimal weight: 0.0270 chunk 48 optimal weight: 0.0170 chunk 47 optimal weight: 3.9990 chunk 156 optimal weight: 7.9990 chunk 168 optimal weight: 0.8980 chunk 121 optimal weight: 20.0000 chunk 22 optimal weight: 0.9990 chunk 193 optimal weight: 0.9990 overall best weight: 0.5276 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 724 GLN ** A 738 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 172 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 231 GLN ** B 298 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 300 HIS ** D 207 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 311 HIS D 347 GLN E 71 HIS ** E 260 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7126 moved from start: 0.2554 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.071 20853 Z= 0.166 Angle : 0.577 10.179 28223 Z= 0.284 Chirality : 0.041 0.155 3292 Planarity : 0.004 0.058 3607 Dihedral : 6.814 62.142 2872 Min Nonbonded Distance : 2.038 Molprobity Statistics. All-atom Clashscore : 13.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.37 % Favored : 97.63 % Rotamer: Outliers : 3.78 % Allowed : 28.99 % Favored : 67.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.12 (0.17), residues: 2577 helix: 0.55 (0.15), residues: 1182 sheet: 0.21 (0.23), residues: 540 loop : -0.49 (0.22), residues: 855 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP E 4 HIS 0.005 0.001 HIS G 246 PHE 0.020 0.001 PHE B 223 TYR 0.026 0.001 TYR E 155 ARG 0.005 0.000 ARG H 210 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5154 Ramachandran restraints generated. 2577 Oldfield, 0 Emsley, 2577 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5154 Ramachandran restraints generated. 2577 Oldfield, 0 Emsley, 2577 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 401 residues out of total 2274 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 86 poor density : 315 time to evaluate : 2.476 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 482 LEU cc_start: 0.7083 (OUTLIER) cc_final: 0.6628 (tt) REVERT: A 483 MET cc_start: 0.6945 (tpp) cc_final: 0.6696 (tpp) REVERT: A 632 PHE cc_start: 0.5428 (t80) cc_final: 0.4704 (t80) REVERT: B 127 LYS cc_start: 0.8233 (OUTLIER) cc_final: 0.7559 (ttpt) REVERT: B 136 LYS cc_start: 0.8152 (OUTLIER) cc_final: 0.7670 (mtmt) REVERT: B 216 ASP cc_start: 0.5691 (p0) cc_final: 0.5388 (p0) REVERT: B 325 MET cc_start: 0.8247 (mtm) cc_final: 0.7735 (mpp) REVERT: D 272 GLU cc_start: 0.8413 (OUTLIER) cc_final: 0.8054 (pm20) REVERT: E 317 TYR cc_start: 0.8237 (t80) cc_final: 0.7858 (t80) REVERT: H 91 ARG cc_start: 0.7381 (tmt170) cc_final: 0.7025 (tmt170) REVERT: H 116 MET cc_start: 0.6194 (tpt) cc_final: 0.5763 (tpt) REVERT: H 162 CYS cc_start: 0.6726 (t) cc_final: 0.6448 (p) REVERT: H 227 LEU cc_start: 0.7059 (tt) cc_final: 0.6785 (tt) outliers start: 86 outliers final: 71 residues processed: 380 average time/residue: 0.3182 time to fit residues: 185.4268 Evaluate side-chains 371 residues out of total 2274 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 75 poor density : 296 time to evaluate : 2.359 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 283 VAL Chi-restraints excluded: chain A residue 313 LEU Chi-restraints excluded: chain A residue 348 GLU Chi-restraints excluded: chain A residue 369 VAL Chi-restraints excluded: chain A residue 383 LEU Chi-restraints excluded: chain A residue 396 VAL Chi-restraints excluded: chain A residue 413 ILE Chi-restraints excluded: chain A residue 451 ILE Chi-restraints excluded: chain A residue 482 LEU Chi-restraints excluded: chain A residue 713 HIS Chi-restraints excluded: chain A residue 724 GLN Chi-restraints excluded: chain A residue 830 LEU Chi-restraints excluded: chain B residue 48 ASN Chi-restraints excluded: chain B residue 100 ASP Chi-restraints excluded: chain B residue 127 LYS Chi-restraints excluded: chain B residue 136 LYS Chi-restraints excluded: chain B residue 144 ASP Chi-restraints excluded: chain B residue 145 SER Chi-restraints excluded: chain B residue 181 ILE Chi-restraints excluded: chain B residue 192 LYS Chi-restraints excluded: chain B residue 199 LEU Chi-restraints excluded: chain B residue 218 LEU Chi-restraints excluded: chain B residue 271 VAL Chi-restraints excluded: chain B residue 335 LEU Chi-restraints excluded: chain C residue 48 ILE Chi-restraints excluded: chain C residue 77 LEU Chi-restraints excluded: chain C residue 87 VAL Chi-restraints excluded: chain C residue 90 LEU Chi-restraints excluded: chain C residue 113 THR Chi-restraints excluded: chain C residue 124 LEU Chi-restraints excluded: chain C residue 153 LEU Chi-restraints excluded: chain C residue 219 ILE Chi-restraints excluded: chain C residue 239 THR Chi-restraints excluded: chain C residue 271 THR Chi-restraints excluded: chain C residue 273 LYS Chi-restraints excluded: chain C residue 296 SER Chi-restraints excluded: chain D residue 173 THR Chi-restraints excluded: chain D residue 192 SER Chi-restraints excluded: chain D residue 272 GLU Chi-restraints excluded: chain E residue 40 VAL Chi-restraints excluded: chain E residue 54 CYS Chi-restraints excluded: chain E residue 84 ILE Chi-restraints excluded: chain E residue 99 ASP Chi-restraints excluded: chain E residue 128 ASP Chi-restraints excluded: chain E residue 136 GLU Chi-restraints excluded: chain E residue 143 ASP Chi-restraints excluded: chain E residue 246 ILE Chi-restraints excluded: chain E residue 250 ASP Chi-restraints excluded: chain E residue 253 VAL Chi-restraints excluded: chain E residue 256 ARG Chi-restraints excluded: chain F residue 7 VAL Chi-restraints excluded: chain F residue 15 VAL Chi-restraints excluded: chain F residue 72 LEU Chi-restraints excluded: chain F residue 89 THR Chi-restraints excluded: chain F residue 121 LEU Chi-restraints excluded: chain F residue 147 ILE Chi-restraints excluded: chain F residue 152 SER Chi-restraints excluded: chain F residue 167 VAL Chi-restraints excluded: chain F residue 195 VAL Chi-restraints excluded: chain F residue 206 THR Chi-restraints excluded: chain F residue 236 VAL Chi-restraints excluded: chain F residue 255 ILE Chi-restraints excluded: chain G residue 19 LEU Chi-restraints excluded: chain G residue 111 VAL Chi-restraints excluded: chain G residue 177 ASN Chi-restraints excluded: chain G residue 243 ASP Chi-restraints excluded: chain G residue 251 LEU Chi-restraints excluded: chain H residue 2 PHE Chi-restraints excluded: chain H residue 15 VAL Chi-restraints excluded: chain H residue 52 LEU Chi-restraints excluded: chain H residue 103 PHE Chi-restraints excluded: chain H residue 160 ILE Chi-restraints excluded: chain H residue 167 VAL Chi-restraints excluded: chain H residue 185 THR Chi-restraints excluded: chain H residue 241 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 256 random chunks: chunk 224 optimal weight: 6.9990 chunk 236 optimal weight: 5.9990 chunk 215 optimal weight: 2.9990 chunk 229 optimal weight: 1.9990 chunk 138 optimal weight: 0.4980 chunk 100 optimal weight: 1.9990 chunk 180 optimal weight: 6.9990 chunk 70 optimal weight: 5.9990 chunk 207 optimal weight: 3.9990 chunk 217 optimal weight: 8.9990 chunk 150 optimal weight: 3.9990 overall best weight: 2.2988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 724 GLN ** A 738 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 172 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 29 GLN C 300 HIS ** D 207 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 347 GLN E 71 HIS E 194 HIS ** H 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7224 moved from start: 0.2797 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.044 20853 Z= 0.312 Angle : 0.658 9.751 28223 Z= 0.324 Chirality : 0.043 0.166 3292 Planarity : 0.005 0.059 3607 Dihedral : 6.884 71.864 2872 Min Nonbonded Distance : 1.930 Molprobity Statistics. All-atom Clashscore : 16.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.22 % Favored : 96.78 % Rotamer: Outliers : 4.49 % Allowed : 28.82 % Favored : 66.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.07 (0.17), residues: 2577 helix: 0.37 (0.15), residues: 1183 sheet: 0.17 (0.23), residues: 532 loop : -0.57 (0.21), residues: 862 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP E 4 HIS 0.006 0.001 HIS C 55 PHE 0.025 0.002 PHE G 2 TYR 0.045 0.002 TYR E 155 ARG 0.008 0.000 ARG H 210 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5154 Ramachandran restraints generated. 2577 Oldfield, 0 Emsley, 2577 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5154 Ramachandran restraints generated. 2577 Oldfield, 0 Emsley, 2577 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 399 residues out of total 2274 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 102 poor density : 297 time to evaluate : 2.298 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 482 LEU cc_start: 0.7098 (OUTLIER) cc_final: 0.6647 (tt) REVERT: A 483 MET cc_start: 0.7051 (tpp) cc_final: 0.6711 (tpp) REVERT: A 632 PHE cc_start: 0.5404 (t80) cc_final: 0.4636 (t80) REVERT: A 839 GLN cc_start: 0.8155 (mp10) cc_final: 0.7946 (mm-40) REVERT: B 127 LYS cc_start: 0.8377 (OUTLIER) cc_final: 0.7703 (ttpt) REVERT: B 136 LYS cc_start: 0.8309 (OUTLIER) cc_final: 0.7785 (mtmt) REVERT: C 51 ASP cc_start: 0.6646 (t0) cc_final: 0.6350 (t0) REVERT: D 272 GLU cc_start: 0.8415 (OUTLIER) cc_final: 0.8112 (pt0) REVERT: E 317 TYR cc_start: 0.8341 (t80) cc_final: 0.7871 (t80) REVERT: F 243 ASP cc_start: 0.7529 (p0) cc_final: 0.7302 (p0) REVERT: H 91 ARG cc_start: 0.7368 (tmt170) cc_final: 0.7058 (tmt170) REVERT: H 116 MET cc_start: 0.6275 (tpt) cc_final: 0.5894 (tpt) REVERT: H 162 CYS cc_start: 0.6845 (t) cc_final: 0.6563 (p) outliers start: 102 outliers final: 86 residues processed: 375 average time/residue: 0.3209 time to fit residues: 184.7189 Evaluate side-chains 383 residues out of total 2274 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 90 poor density : 293 time to evaluate : 2.481 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 283 VAL Chi-restraints excluded: chain A residue 313 LEU Chi-restraints excluded: chain A residue 315 VAL Chi-restraints excluded: chain A residue 348 GLU Chi-restraints excluded: chain A residue 369 VAL Chi-restraints excluded: chain A residue 383 LEU Chi-restraints excluded: chain A residue 396 VAL Chi-restraints excluded: chain A residue 413 ILE Chi-restraints excluded: chain A residue 451 ILE Chi-restraints excluded: chain A residue 482 LEU Chi-restraints excluded: chain A residue 695 LEU Chi-restraints excluded: chain A residue 713 HIS Chi-restraints excluded: chain A residue 748 THR Chi-restraints excluded: chain A residue 830 LEU Chi-restraints excluded: chain B residue 48 ASN Chi-restraints excluded: chain B residue 100 ASP Chi-restraints excluded: chain B residue 127 LYS Chi-restraints excluded: chain B residue 136 LYS Chi-restraints excluded: chain B residue 144 ASP Chi-restraints excluded: chain B residue 145 SER Chi-restraints excluded: chain B residue 165 THR Chi-restraints excluded: chain B residue 181 ILE Chi-restraints excluded: chain B residue 192 LYS Chi-restraints excluded: chain B residue 199 LEU Chi-restraints excluded: chain B residue 218 LEU Chi-restraints excluded: chain B residue 270 CYS Chi-restraints excluded: chain B residue 271 VAL Chi-restraints excluded: chain B residue 335 LEU Chi-restraints excluded: chain B residue 340 LEU Chi-restraints excluded: chain C residue 23 VAL Chi-restraints excluded: chain C residue 48 ILE Chi-restraints excluded: chain C residue 77 LEU Chi-restraints excluded: chain C residue 87 VAL Chi-restraints excluded: chain C residue 90 LEU Chi-restraints excluded: chain C residue 113 THR Chi-restraints excluded: chain C residue 124 LEU Chi-restraints excluded: chain C residue 153 LEU Chi-restraints excluded: chain C residue 154 ILE Chi-restraints excluded: chain C residue 219 ILE Chi-restraints excluded: chain C residue 239 THR Chi-restraints excluded: chain C residue 271 THR Chi-restraints excluded: chain C residue 296 SER Chi-restraints excluded: chain D residue 149 LEU Chi-restraints excluded: chain D residue 156 THR Chi-restraints excluded: chain D residue 173 THR Chi-restraints excluded: chain D residue 192 SER Chi-restraints excluded: chain D residue 263 THR Chi-restraints excluded: chain D residue 272 GLU Chi-restraints excluded: chain D residue 361 GLN Chi-restraints excluded: chain E residue 40 VAL Chi-restraints excluded: chain E residue 54 CYS Chi-restraints excluded: chain E residue 84 ILE Chi-restraints excluded: chain E residue 99 ASP Chi-restraints excluded: chain E residue 128 ASP Chi-restraints excluded: chain E residue 143 ASP Chi-restraints excluded: chain E residue 227 LEU Chi-restraints excluded: chain E residue 235 VAL Chi-restraints excluded: chain E residue 246 ILE Chi-restraints excluded: chain E residue 250 ASP Chi-restraints excluded: chain E residue 253 VAL Chi-restraints excluded: chain E residue 256 ARG Chi-restraints excluded: chain F residue 7 VAL Chi-restraints excluded: chain F residue 15 VAL Chi-restraints excluded: chain F residue 89 THR Chi-restraints excluded: chain F residue 121 LEU Chi-restraints excluded: chain F residue 147 ILE Chi-restraints excluded: chain F residue 152 SER Chi-restraints excluded: chain F residue 167 VAL Chi-restraints excluded: chain F residue 195 VAL Chi-restraints excluded: chain F residue 206 THR Chi-restraints excluded: chain F residue 236 VAL Chi-restraints excluded: chain F residue 255 ILE Chi-restraints excluded: chain G residue 19 LEU Chi-restraints excluded: chain G residue 111 VAL Chi-restraints excluded: chain G residue 177 ASN Chi-restraints excluded: chain G residue 235 LEU Chi-restraints excluded: chain G residue 243 ASP Chi-restraints excluded: chain G residue 246 HIS Chi-restraints excluded: chain G residue 251 LEU Chi-restraints excluded: chain H residue 2 PHE Chi-restraints excluded: chain H residue 15 VAL Chi-restraints excluded: chain H residue 30 ILE Chi-restraints excluded: chain H residue 52 LEU Chi-restraints excluded: chain H residue 59 THR Chi-restraints excluded: chain H residue 103 PHE Chi-restraints excluded: chain H residue 160 ILE Chi-restraints excluded: chain H residue 167 VAL Chi-restraints excluded: chain H residue 185 THR Chi-restraints excluded: chain H residue 241 ILE Chi-restraints excluded: chain H residue 247 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 256 random chunks: chunk 243 optimal weight: 0.5980 chunk 148 optimal weight: 0.8980 chunk 115 optimal weight: 0.0060 chunk 169 optimal weight: 5.9990 chunk 255 optimal weight: 6.9990 chunk 234 optimal weight: 20.0000 chunk 203 optimal weight: 4.9990 chunk 21 optimal weight: 0.0570 chunk 156 optimal weight: 20.0000 chunk 124 optimal weight: 0.8980 chunk 161 optimal weight: 8.9990 overall best weight: 0.4914 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 738 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 172 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 300 HIS D 73 ASN ** D 207 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 71 HIS ** E 260 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7130 moved from start: 0.2752 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 20853 Z= 0.170 Angle : 0.594 11.721 28223 Z= 0.290 Chirality : 0.041 0.158 3292 Planarity : 0.004 0.058 3607 Dihedral : 6.619 74.306 2872 Min Nonbonded Distance : 2.033 Molprobity Statistics. All-atom Clashscore : 14.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.41 % Favored : 97.59 % Rotamer: Outliers : 3.43 % Allowed : 29.87 % Favored : 66.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.16 (0.17), residues: 2577 helix: 0.63 (0.15), residues: 1177 sheet: 0.22 (0.23), residues: 533 loop : -0.50 (0.21), residues: 867 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP E 4 HIS 0.006 0.001 HIS E 213 PHE 0.026 0.001 PHE B 223 TYR 0.035 0.001 TYR E 155 ARG 0.006 0.000 ARG A 854 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5154 Ramachandran restraints generated. 2577 Oldfield, 0 Emsley, 2577 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5154 Ramachandran restraints generated. 2577 Oldfield, 0 Emsley, 2577 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 385 residues out of total 2274 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 78 poor density : 307 time to evaluate : 2.254 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 482 LEU cc_start: 0.7051 (OUTLIER) cc_final: 0.6590 (tt) REVERT: A 483 MET cc_start: 0.6989 (tpp) cc_final: 0.6630 (tpp) REVERT: A 632 PHE cc_start: 0.5461 (t80) cc_final: 0.4707 (t80) REVERT: A 839 GLN cc_start: 0.8141 (mp10) cc_final: 0.7935 (mm-40) REVERT: B 127 LYS cc_start: 0.8212 (OUTLIER) cc_final: 0.7554 (ttpt) REVERT: B 136 LYS cc_start: 0.8148 (OUTLIER) cc_final: 0.7705 (mtmt) REVERT: D 272 GLU cc_start: 0.8405 (OUTLIER) cc_final: 0.7965 (pm20) REVERT: E 166 ASN cc_start: 0.7109 (p0) cc_final: 0.6544 (p0) REVERT: E 213 HIS cc_start: 0.7007 (m-70) cc_final: 0.6797 (t-90) REVERT: E 317 TYR cc_start: 0.8249 (t80) cc_final: 0.7866 (t80) REVERT: H 91 ARG cc_start: 0.7354 (tmt170) cc_final: 0.7092 (tmt170) REVERT: H 116 MET cc_start: 0.6178 (tpt) cc_final: 0.5829 (tpt) REVERT: H 162 CYS cc_start: 0.6743 (t) cc_final: 0.6456 (p) outliers start: 78 outliers final: 70 residues processed: 367 average time/residue: 0.3127 time to fit residues: 176.4411 Evaluate side-chains 373 residues out of total 2274 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 74 poor density : 299 time to evaluate : 2.259 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 283 VAL Chi-restraints excluded: chain A residue 313 LEU Chi-restraints excluded: chain A residue 348 GLU Chi-restraints excluded: chain A residue 369 VAL Chi-restraints excluded: chain A residue 383 LEU Chi-restraints excluded: chain A residue 396 VAL Chi-restraints excluded: chain A residue 413 ILE Chi-restraints excluded: chain A residue 451 ILE Chi-restraints excluded: chain A residue 482 LEU Chi-restraints excluded: chain A residue 713 HIS Chi-restraints excluded: chain A residue 748 THR Chi-restraints excluded: chain A residue 830 LEU Chi-restraints excluded: chain B residue 48 ASN Chi-restraints excluded: chain B residue 100 ASP Chi-restraints excluded: chain B residue 127 LYS Chi-restraints excluded: chain B residue 136 LYS Chi-restraints excluded: chain B residue 144 ASP Chi-restraints excluded: chain B residue 145 SER Chi-restraints excluded: chain B residue 181 ILE Chi-restraints excluded: chain B residue 192 LYS Chi-restraints excluded: chain B residue 218 LEU Chi-restraints excluded: chain B residue 270 CYS Chi-restraints excluded: chain B residue 271 VAL Chi-restraints excluded: chain B residue 335 LEU Chi-restraints excluded: chain B residue 340 LEU Chi-restraints excluded: chain C residue 23 VAL Chi-restraints excluded: chain C residue 48 ILE Chi-restraints excluded: chain C residue 77 LEU Chi-restraints excluded: chain C residue 87 VAL Chi-restraints excluded: chain C residue 90 LEU Chi-restraints excluded: chain C residue 124 LEU Chi-restraints excluded: chain C residue 153 LEU Chi-restraints excluded: chain C residue 219 ILE Chi-restraints excluded: chain C residue 239 THR Chi-restraints excluded: chain C residue 271 THR Chi-restraints excluded: chain C residue 296 SER Chi-restraints excluded: chain D residue 173 THR Chi-restraints excluded: chain D residue 192 SER Chi-restraints excluded: chain D residue 263 THR Chi-restraints excluded: chain D residue 272 GLU Chi-restraints excluded: chain E residue 40 VAL Chi-restraints excluded: chain E residue 54 CYS Chi-restraints excluded: chain E residue 84 ILE Chi-restraints excluded: chain E residue 99 ASP Chi-restraints excluded: chain E residue 128 ASP Chi-restraints excluded: chain E residue 143 ASP Chi-restraints excluded: chain E residue 246 ILE Chi-restraints excluded: chain E residue 250 ASP Chi-restraints excluded: chain E residue 253 VAL Chi-restraints excluded: chain E residue 256 ARG Chi-restraints excluded: chain F residue 7 VAL Chi-restraints excluded: chain F residue 15 VAL Chi-restraints excluded: chain F residue 89 THR Chi-restraints excluded: chain F residue 121 LEU Chi-restraints excluded: chain F residue 147 ILE Chi-restraints excluded: chain F residue 152 SER Chi-restraints excluded: chain F residue 195 VAL Chi-restraints excluded: chain F residue 206 THR Chi-restraints excluded: chain F residue 236 VAL Chi-restraints excluded: chain F residue 255 ILE Chi-restraints excluded: chain G residue 19 LEU Chi-restraints excluded: chain G residue 111 VAL Chi-restraints excluded: chain G residue 177 ASN Chi-restraints excluded: chain G residue 235 LEU Chi-restraints excluded: chain G residue 243 ASP Chi-restraints excluded: chain G residue 251 LEU Chi-restraints excluded: chain H residue 2 PHE Chi-restraints excluded: chain H residue 15 VAL Chi-restraints excluded: chain H residue 103 PHE Chi-restraints excluded: chain H residue 160 ILE Chi-restraints excluded: chain H residue 167 VAL Chi-restraints excluded: chain H residue 185 THR Chi-restraints excluded: chain H residue 241 ILE Chi-restraints excluded: chain H residue 247 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 256 random chunks: chunk 216 optimal weight: 10.0000 chunk 62 optimal weight: 5.9990 chunk 187 optimal weight: 2.9990 chunk 29 optimal weight: 10.0000 chunk 56 optimal weight: 2.9990 chunk 203 optimal weight: 4.9990 chunk 85 optimal weight: 0.8980 chunk 208 optimal weight: 9.9990 chunk 25 optimal weight: 3.9990 chunk 37 optimal weight: 0.9980 chunk 178 optimal weight: 1.9990 overall best weight: 1.9786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 738 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 172 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 300 HIS ** D 207 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 246 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 71 HIS E 194 HIS ** H 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4479 r_free = 0.4479 target = 0.199232 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3996 r_free = 0.3996 target = 0.154027 restraints weight = 29789.662| |-----------------------------------------------------------------------------| r_work (start): 0.3968 rms_B_bonded: 3.20 r_work: 0.3781 rms_B_bonded: 3.96 restraints_weight: 0.5000 r_work (final): 0.3781 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7260 moved from start: 0.2968 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 20853 Z= 0.285 Angle : 0.647 10.169 28223 Z= 0.318 Chirality : 0.043 0.164 3292 Planarity : 0.004 0.059 3607 Dihedral : 6.656 88.159 2872 Min Nonbonded Distance : 1.929 Molprobity Statistics. All-atom Clashscore : 16.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.57 % Favored : 96.43 % Rotamer: Outliers : 4.00 % Allowed : 29.34 % Favored : 66.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.06 (0.17), residues: 2577 helix: 0.41 (0.15), residues: 1184 sheet: 0.14 (0.23), residues: 532 loop : -0.58 (0.21), residues: 861 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP E 4 HIS 0.005 0.001 HIS D 311 PHE 0.023 0.002 PHE G 2 TYR 0.033 0.002 TYR G 249 ARG 0.009 0.000 ARG H 210 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4665.40 seconds wall clock time: 83 minutes 59.29 seconds (5039.29 seconds total)