Starting phenix.real_space_refine on Fri Feb 16 05:09:31 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8g3l_29701/02_2024/8g3l_29701_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8g3l_29701/02_2024/8g3l_29701.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8g3l_29701/02_2024/8g3l_29701.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8g3l_29701/02_2024/8g3l_29701.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8g3l_29701/02_2024/8g3l_29701_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8g3l_29701/02_2024/8g3l_29701_updated.pdb" } resolution = 3.5 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.020 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 2 5.49 5 S 62 5.16 5 C 9385 2.51 5 N 2374 2.21 5 O 2619 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 251": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 351": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 547": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 125": "OE1" <-> "OE2" Residue "B GLU 135": "OE1" <-> "OE2" Residue "D GLU 141": "OE1" <-> "OE2" Residue "E GLU 99": "OE1" <-> "OE2" Residue "E TYR 151": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 152": "OE1" <-> "OE2" Time to flip residues: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 14442 Number of models: 1 Model: "" Number of chains: 7 Chain: "A" Number of atoms: 5000 Number of conformers: 1 Conformer: "" Number of residues, atoms: 635, 5000 Classifications: {'peptide': 635} Link IDs: {'PTRANS': 10, 'TRANS': 624} Chain breaks: 1 Chain: "B" Number of atoms: 1915 Number of conformers: 1 Conformer: "" Number of residues, atoms: 244, 1915 Classifications: {'peptide': 244} Link IDs: {'PTRANS': 5, 'TRANS': 238} Chain: "C" Number of atoms: 1915 Number of conformers: 1 Conformer: "" Number of residues, atoms: 244, 1915 Classifications: {'peptide': 244} Link IDs: {'PTRANS': 5, 'TRANS': 238} Chain: "D" Number of atoms: 2738 Number of conformers: 1 Conformer: "" Number of residues, atoms: 334, 2738 Classifications: {'peptide': 334} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 9, 'TRANS': 324} Chain: "E" Number of atoms: 2738 Number of conformers: 1 Conformer: "" Number of residues, atoms: 334, 2738 Classifications: {'peptide': 334} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 9, 'TRANS': 324} Chain: "A" Number of atoms: 116 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 116 Unusual residues: {'6OU': 2, 'PLM': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "E" Number of atoms: 20 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 20 Unusual residues: {'OLA': 1} Classifications: {'undetermined': 1} Time building chain proxies: 7.82, per 1000 atoms: 0.54 Number of scatterers: 14442 At special positions: 0 Unit cell: (93.304, 117.72, 197.072, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 62 16.00 P 2 15.00 O 2619 8.00 N 2374 7.00 C 9385 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: 5.73 Conformation dependent library (CDL) restraints added in 2.9 seconds 3558 Ramachandran restraints generated. 1779 Oldfield, 0 Emsley, 1779 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3374 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 69 helices and 10 sheets defined 54.5% alpha, 6.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.85 Creating SS restraints... Processing helix chain 'A' and resid 3 through 17 Processing helix chain 'A' and resid 20 through 40 removed outlier: 3.665A pdb=" N TYR A 40 " --> pdb=" O VAL A 36 " (cutoff:3.500A) Processing helix chain 'A' and resid 42 through 46 Processing helix chain 'A' and resid 56 through 93 removed outlier: 3.741A pdb=" N ALA A 66 " --> pdb=" O ILE A 62 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N VAL A 67 " --> pdb=" O LEU A 63 " (cutoff:3.500A) removed outlier: 3.909A pdb=" N LYS A 81 " --> pdb=" O THR A 77 " (cutoff:3.500A) removed outlier: 3.911A pdb=" N ARG A 82 " --> pdb=" O ILE A 78 " (cutoff:3.500A) removed outlier: 4.308A pdb=" N ARG A 83 " --> pdb=" O PHE A 79 " (cutoff:3.500A) removed outlier: 4.324A pdb=" N SER A 84 " --> pdb=" O ILE A 80 " (cutoff:3.500A) removed outlier: 5.947A pdb=" N LYS A 85 " --> pdb=" O LYS A 81 " (cutoff:3.500A) removed outlier: 6.182A pdb=" N GLU A 86 " --> pdb=" O ARG A 82 " (cutoff:3.500A) Processing helix chain 'A' and resid 101 through 104 No H-bonds generated for 'chain 'A' and resid 101 through 104' Processing helix chain 'A' and resid 111 through 121 Processing helix chain 'A' and resid 127 through 138 removed outlier: 3.632A pdb=" N ILE A 137 " --> pdb=" O ILE A 133 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N VAL A 138 " --> pdb=" O LEU A 134 " (cutoff:3.500A) Processing helix chain 'A' and resid 150 through 177 removed outlier: 4.008A pdb=" N VAL A 154 " --> pdb=" O GLU A 150 " (cutoff:3.500A) removed outlier: 3.904A pdb=" N VAL A 159 " --> pdb=" O GLN A 155 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N THR A 173 " --> pdb=" O ILE A 169 " (cutoff:3.500A) removed outlier: 3.863A pdb=" N PHE A 174 " --> pdb=" O MET A 170 " (cutoff:3.500A) Processing helix chain 'A' and resid 200 through 221 removed outlier: 4.031A pdb=" N GLY A 205 " --> pdb=" O GLN A 201 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N GLY A 208 " --> pdb=" O ILE A 204 " (cutoff:3.500A) removed outlier: 3.942A pdb=" N ILE A 209 " --> pdb=" O GLY A 205 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N LEU A 213 " --> pdb=" O ILE A 209 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N THR A 214 " --> pdb=" O VAL A 210 " (cutoff:3.500A) removed outlier: 3.935A pdb=" N GLY A 215 " --> pdb=" O LEU A 211 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N TYR A 216 " --> pdb=" O ILE A 212 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N GLU A 221 " --> pdb=" O TYR A 217 " (cutoff:3.500A) Processing helix chain 'A' and resid 234 through 252 Processing helix chain 'A' and resid 255 through 266 Processing helix chain 'A' and resid 273 through 285 removed outlier: 3.777A pdb=" N SER A 280 " --> pdb=" O VAL A 276 " (cutoff:3.500A) removed outlier: 4.463A pdb=" N SER A 281 " --> pdb=" O LEU A 277 " (cutoff:3.500A) removed outlier: 3.898A pdb=" N MET A 283 " --> pdb=" O LEU A 279 " (cutoff:3.500A) removed outlier: 5.115A pdb=" N PHE A 284 " --> pdb=" O SER A 280 " (cutoff:3.500A) Processing helix chain 'A' and resid 293 through 324 removed outlier: 3.783A pdb=" N TYR A 314 " --> pdb=" O ALA A 310 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N TYR A 315 " --> pdb=" O TYR A 311 " (cutoff:3.500A) removed outlier: 4.096A pdb=" N SER A 316 " --> pdb=" O ILE A 312 " (cutoff:3.500A) removed outlier: 4.736A pdb=" N SER A 317 " --> pdb=" O SER A 313 " (cutoff:3.500A) removed outlier: 5.142A pdb=" N GLU A 318 " --> pdb=" O TYR A 314 " (cutoff:3.500A) removed outlier: 4.737A pdb=" N LYS A 319 " --> pdb=" O TYR A 315 " (cutoff:3.500A) Processing helix chain 'A' and resid 334 through 347 removed outlier: 3.905A pdb=" N GLU A 346 " --> pdb=" O ASN A 342 " (cutoff:3.500A) Processing helix chain 'A' and resid 366 through 368 No H-bonds generated for 'chain 'A' and resid 366 through 368' Processing helix chain 'A' and resid 410 through 415 removed outlier: 3.599A pdb=" N LYS A 414 " --> pdb=" O ASP A 410 " (cutoff:3.500A) Processing helix chain 'A' and resid 462 through 471 removed outlier: 3.835A pdb=" N GLN A 467 " --> pdb=" O SER A 463 " (cutoff:3.500A) removed outlier: 3.902A pdb=" N LYS A 470 " --> pdb=" O LYS A 466 " (cutoff:3.500A) Processing helix chain 'A' and resid 495 through 504 Processing helix chain 'A' and resid 519 through 556 removed outlier: 3.622A pdb=" N LYS A 549 " --> pdb=" O ILE A 545 " (cutoff:3.500A) removed outlier: 3.879A pdb=" N GLN A 550 " --> pdb=" O LEU A 546 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N MET A 551 " --> pdb=" O TYR A 547 " (cutoff:3.500A) removed outlier: 4.420A pdb=" N GLY A 552 " --> pdb=" O PHE A 548 " (cutoff:3.500A) Processing helix chain 'A' and resid 558 through 565 Processing helix chain 'A' and resid 571 through 601 removed outlier: 3.856A pdb=" N ILE A 580 " --> pdb=" O LYS A 576 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N ILE A 588 " --> pdb=" O TYR A 584 " (cutoff:3.500A) Proline residue: A 589 - end of helix Processing helix chain 'A' and resid 615 through 632 removed outlier: 4.306A pdb=" N ILE A 629 " --> pdb=" O ALA A 625 " (cutoff:3.500A) removed outlier: 5.224A pdb=" N PHE A 630 " --> pdb=" O LEU A 626 " (cutoff:3.500A) removed outlier: 4.181A pdb=" N GLY A 631 " --> pdb=" O TYR A 627 " (cutoff:3.500A) Processing helix chain 'A' and resid 634 through 643 Processing helix chain 'B' and resid 46 through 53 Processing helix chain 'B' and resid 76 through 85 Processing helix chain 'B' and resid 102 through 107 Processing helix chain 'B' and resid 109 through 111 No H-bonds generated for 'chain 'B' and resid 109 through 111' Processing helix chain 'B' and resid 118 through 128 Processing helix chain 'B' and resid 134 through 136 No H-bonds generated for 'chain 'B' and resid 134 through 136' Processing helix chain 'B' and resid 141 through 143 No H-bonds generated for 'chain 'B' and resid 141 through 143' Processing helix chain 'B' and resid 146 through 157 removed outlier: 4.034A pdb=" N GLN B 150 " --> pdb=" O GLY B 146 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N ARG B 151 " --> pdb=" O GLY B 147 " (cutoff:3.500A) Processing helix chain 'B' and resid 176 through 192 Processing helix chain 'B' and resid 204 through 209 removed outlier: 4.159A pdb=" N TYR B 209 " --> pdb=" O VAL B 205 " (cutoff:3.500A) Processing helix chain 'B' and resid 232 through 245 Processing helix chain 'C' and resid 46 through 54 Processing helix chain 'C' and resid 76 through 86 Processing helix chain 'C' and resid 102 through 110 Proline residue: C 109 - end of helix Processing helix chain 'C' and resid 117 through 131 Processing helix chain 'C' and resid 146 through 158 removed outlier: 3.673A pdb=" N ALA C 157 " --> pdb=" O SER C 153 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N PHE C 158 " --> pdb=" O ALA C 154 " (cutoff:3.500A) Processing helix chain 'C' and resid 176 through 192 removed outlier: 3.609A pdb=" N GLN C 191 " --> pdb=" O SER C 187 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N LYS C 192 " --> pdb=" O GLN C 188 " (cutoff:3.500A) Processing helix chain 'C' and resid 204 through 209 removed outlier: 4.195A pdb=" N TYR C 209 " --> pdb=" O VAL C 205 " (cutoff:3.500A) Processing helix chain 'C' and resid 234 through 245 Processing helix chain 'D' and resid 2 through 8 Processing helix chain 'D' and resid 12 through 29 removed outlier: 3.590A pdb=" N ALA D 27 " --> pdb=" O MET D 23 " (cutoff:3.500A) Processing helix chain 'D' and resid 35 through 60 removed outlier: 3.549A pdb=" N LEU D 47 " --> pdb=" O TYR D 43 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N PHE D 48 " --> pdb=" O LEU D 44 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N ILE D 50 " --> pdb=" O ILE D 46 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N ILE D 51 " --> pdb=" O LEU D 47 " (cutoff:3.500A) Processing helix chain 'D' and resid 63 through 70 Processing helix chain 'D' and resid 85 through 138 removed outlier: 4.065A pdb=" N MET D 89 " --> pdb=" O PRO D 85 " (cutoff:3.500A) removed outlier: 4.780A pdb=" N VAL D 90 " --> pdb=" O PHE D 86 " (cutoff:3.500A) removed outlier: 3.891A pdb=" N LYS D 102 " --> pdb=" O THR D 98 " (cutoff:3.500A) Proline residue: D 129 - end of helix Processing helix chain 'D' and resid 143 through 170 removed outlier: 4.327A pdb=" N SER D 170 " --> pdb=" O GLN D 166 " (cutoff:3.500A) Processing helix chain 'D' and resid 172 through 174 No H-bonds generated for 'chain 'D' and resid 172 through 174' Processing helix chain 'D' and resid 183 through 193 Processing helix chain 'D' and resid 195 through 201 Processing helix chain 'D' and resid 218 through 234 Processing helix chain 'D' and resid 265 through 268 No H-bonds generated for 'chain 'D' and resid 265 through 268' Processing helix chain 'D' and resid 282 through 284 No H-bonds generated for 'chain 'D' and resid 282 through 284' Processing helix chain 'D' and resid 290 through 302 Proline residue: D 301 - end of helix Processing helix chain 'D' and resid 325 through 333 removed outlier: 4.074A pdb=" N HIS D 330 " --> pdb=" O GLN D 327 " (cutoff:3.500A) Processing helix chain 'E' and resid 2 through 8 Processing helix chain 'E' and resid 12 through 29 removed outlier: 3.546A pdb=" N PHE E 16 " --> pdb=" O TRP E 12 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N LEU E 17 " --> pdb=" O ILE E 13 " (cutoff:3.500A) removed outlier: 4.680A pdb=" N GLN E 19 " --> pdb=" O ALA E 15 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N GLN E 20 " --> pdb=" O PHE E 16 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N ALA E 21 " --> pdb=" O LEU E 17 " (cutoff:3.500A) removed outlier: 4.113A pdb=" N PHE E 28 " --> pdb=" O LEU E 24 " (cutoff:3.500A) removed outlier: 3.951A pdb=" N VAL E 29 " --> pdb=" O PHE E 25 " (cutoff:3.500A) Processing helix chain 'E' and resid 39 through 60 removed outlier: 3.951A pdb=" N ARG E 58 " --> pdb=" O TRP E 54 " (cutoff:3.500A) removed outlier: 4.184A pdb=" N LYS E 59 " --> pdb=" O PHE E 55 " (cutoff:3.500A) Processing helix chain 'E' and resid 63 through 70 Processing helix chain 'E' and resid 85 through 137 Proline residue: E 129 - end of helix Processing helix chain 'E' and resid 144 through 169 Processing helix chain 'E' and resid 172 through 174 No H-bonds generated for 'chain 'E' and resid 172 through 174' Processing helix chain 'E' and resid 183 through 201 removed outlier: 5.078A pdb=" N SER E 196 " --> pdb=" O LYS E 192 " (cutoff:3.500A) removed outlier: 5.758A pdb=" N TRP E 197 " --> pdb=" O ASP E 193 " (cutoff:3.500A) Processing helix chain 'E' and resid 218 through 234 Processing helix chain 'E' and resid 265 through 268 No H-bonds generated for 'chain 'E' and resid 265 through 268' Processing helix chain 'E' and resid 282 through 286 Processing helix chain 'E' and resid 290 through 302 removed outlier: 3.870A pdb=" N ALA E 300 " --> pdb=" O LYS E 296 " (cutoff:3.500A) Proline residue: E 301 - end of helix Processing helix chain 'E' and resid 325 through 332 removed outlier: 3.938A pdb=" N HIS E 330 " --> pdb=" O GLN E 327 " (cutoff:3.500A) removed outlier: 3.889A pdb=" N ILE E 332 " --> pdb=" O GLU E 329 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'A' and resid 359 through 363 removed outlier: 3.891A pdb=" N MET A 383 " --> pdb=" O VAL A 363 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N VAL A 388 " --> pdb=" O VAL A 458 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N ALA A 457 " --> pdb=" O SER A 406 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N VAL A 404 " --> pdb=" O ILE A 459 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'B' and resid 4 through 7 Processing sheet with id= C, first strand: chain 'B' and resid 12 through 14 Processing sheet with id= D, first strand: chain 'B' and resid 212 through 215 removed outlier: 3.757A pdb=" N ARG B 212 " --> pdb=" O PHE B 35 " (cutoff:3.500A) removed outlier: 6.361A pdb=" N ILE B 197 " --> pdb=" O VAL B 36 " (cutoff:3.500A) removed outlier: 7.837A pdb=" N ILE B 38 " --> pdb=" O ILE B 197 " (cutoff:3.500A) removed outlier: 6.614A pdb=" N MET B 199 " --> pdb=" O ILE B 38 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N VAL B 200 " --> pdb=" O ALA B 167 " (cutoff:3.500A) removed outlier: 7.515A pdb=" N GLY B 88 " --> pdb=" O PHE B 166 " (cutoff:3.500A) removed outlier: 8.149A pdb=" N ASP B 168 " --> pdb=" O GLY B 88 " (cutoff:3.500A) removed outlier: 7.190A pdb=" N ILE B 90 " --> pdb=" O ASP B 168 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'C' and resid 36 through 39 removed outlier: 6.252A pdb=" N ARG C 212 " --> pdb=" O SER C 37 " (cutoff:3.500A) removed outlier: 7.564A pdb=" N MET C 39 " --> pdb=" O ARG C 212 " (cutoff:3.500A) removed outlier: 5.931A pdb=" N ILE C 214 " --> pdb=" O MET C 39 " (cutoff:3.500A) No H-bonds generated for sheet with id= E Processing sheet with id= F, first strand: chain 'C' and resid 164 through 167 removed outlier: 6.618A pdb=" N THR C 196 " --> pdb=" O ILE C 165 " (cutoff:3.500A) removed outlier: 7.349A pdb=" N ALA C 167 " --> pdb=" O THR C 196 " (cutoff:3.500A) removed outlier: 6.116A pdb=" N ILE C 198 " --> pdb=" O ALA C 167 " (cutoff:3.500A) No H-bonds generated for sheet with id= F Processing sheet with id= G, first strand: chain 'D' and resid 205 through 209 removed outlier: 6.151A pdb=" N ILE D 241 " --> pdb=" O ASP D 206 " (cutoff:3.500A) removed outlier: 7.209A pdb=" N GLN D 208 " --> pdb=" O ILE D 241 " (cutoff:3.500A) removed outlier: 5.986A pdb=" N ILE D 243 " --> pdb=" O GLN D 208 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'D' and resid 305 through 311 Processing sheet with id= I, first strand: chain 'E' and resid 179 through 182 removed outlier: 4.006A pdb=" N GLU E 179 " --> pdb=" O SER E 216 " (cutoff:3.500A) removed outlier: 3.821A pdb=" N SER E 216 " --> pdb=" O GLU E 179 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N VAL E 214 " --> pdb=" O ILE E 181 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'E' and resid 205 through 209 removed outlier: 6.933A pdb=" N ILE E 241 " --> pdb=" O ASP E 206 " (cutoff:3.500A) removed outlier: 7.954A pdb=" N GLN E 208 " --> pdb=" O ILE E 241 " (cutoff:3.500A) removed outlier: 6.970A pdb=" N ILE E 243 " --> pdb=" O GLN E 208 " (cutoff:3.500A) 673 hydrogen bonds defined for protein. 1959 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: 4.16 Time building geometry restraints manager: 6.16 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.31: 2344 1.31 - 1.44: 3764 1.44 - 1.56: 8465 1.56 - 1.69: 22 1.69 - 1.81: 114 Bond restraints: 14709 Sorted by residual: bond pdb=" C10 OLA E 401 " pdb=" C9 OLA E 401 " ideal model delta sigma weight residual 1.332 1.470 -0.138 2.00e-02 2.50e+03 4.75e+01 bond pdb=" C16 6OU A 702 " pdb=" O18 6OU A 702 " ideal model delta sigma weight residual 1.327 1.455 -0.128 2.00e-02 2.50e+03 4.08e+01 bond pdb=" C16 6OU A 703 " pdb=" O18 6OU A 703 " ideal model delta sigma weight residual 1.327 1.454 -0.127 2.00e-02 2.50e+03 4.02e+01 bond pdb=" C14 6OU A 702 " pdb=" C15 6OU A 702 " ideal model delta sigma weight residual 1.521 1.607 -0.086 2.00e-02 2.50e+03 1.85e+01 bond pdb=" C31 6OU A 703 " pdb=" O30 6OU A 703 " ideal model delta sigma weight residual 1.331 1.417 -0.086 2.00e-02 2.50e+03 1.84e+01 ... (remaining 14704 not shown) Histogram of bond angle deviations from ideal: 98.01 - 109.10: 841 109.10 - 120.19: 12965 120.19 - 131.28: 5953 131.28 - 142.37: 17 142.37 - 153.46: 2 Bond angle restraints: 19778 Sorted by residual: angle pdb=" C40 6OU A 702 " pdb=" C41 6OU A 702 " pdb=" C42 6OU A 702 " ideal model delta sigma weight residual 127.56 153.46 -25.90 3.00e+00 1.11e-01 7.45e+01 angle pdb=" C40 6OU A 703 " pdb=" C41 6OU A 703 " pdb=" C42 6OU A 703 " ideal model delta sigma weight residual 127.56 151.55 -23.99 3.00e+00 1.11e-01 6.40e+01 angle pdb=" O22 6OU A 702 " pdb=" P23 6OU A 702 " pdb=" O26 6OU A 702 " ideal model delta sigma weight residual 93.95 110.61 -16.66 3.00e+00 1.11e-01 3.08e+01 angle pdb=" C39 6OU A 703 " pdb=" C40 6OU A 703 " pdb=" C41 6OU A 703 " ideal model delta sigma weight residual 127.60 111.71 15.89 3.00e+00 1.11e-01 2.81e+01 angle pdb=" O22 6OU A 703 " pdb=" P23 6OU A 703 " pdb=" O26 6OU A 703 " ideal model delta sigma weight residual 93.95 108.87 -14.92 3.00e+00 1.11e-01 2.47e+01 ... (remaining 19773 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.85: 8672 35.85 - 71.70: 202 71.70 - 107.55: 21 107.55 - 143.40: 4 143.40 - 179.25: 2 Dihedral angle restraints: 8901 sinusoidal: 3689 harmonic: 5212 Sorted by residual: dihedral pdb=" C19 6OU A 703 " pdb=" C20 6OU A 703 " pdb=" O30 6OU A 703 " pdb=" C31 6OU A 703 " ideal model delta sinusoidal sigma weight residual 212.33 33.08 179.25 1 3.00e+01 1.11e-03 2.13e+01 dihedral pdb=" C21 6OU A 703 " pdb=" C20 6OU A 703 " pdb=" O30 6OU A 703 " pdb=" C31 6OU A 703 " ideal model delta sinusoidal sigma weight residual 85.49 -88.88 174.37 1 3.00e+01 1.11e-03 2.13e+01 dihedral pdb=" C19 6OU A 703 " pdb=" C20 6OU A 703 " pdb=" C21 6OU A 703 " pdb=" O22 6OU A 703 " ideal model delta sinusoidal sigma weight residual 301.00 158.85 142.15 1 3.00e+01 1.11e-03 1.91e+01 ... (remaining 8898 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.060: 1880 0.060 - 0.120: 335 0.120 - 0.180: 28 0.180 - 0.240: 2 0.240 - 0.300: 1 Chirality restraints: 2246 Sorted by residual: chirality pdb=" C20 6OU A 702 " pdb=" C19 6OU A 702 " pdb=" C21 6OU A 702 " pdb=" O30 6OU A 702 " both_signs ideal model delta sigma weight residual False 2.35 2.65 -0.30 2.00e-01 2.50e+01 2.25e+00 chirality pdb=" CB ILE C 198 " pdb=" CA ILE C 198 " pdb=" CG1 ILE C 198 " pdb=" CG2 ILE C 198 " both_signs ideal model delta sigma weight residual False 2.64 2.43 0.21 2.00e-01 2.50e+01 1.13e+00 chirality pdb=" CA ILE A 563 " pdb=" N ILE A 563 " pdb=" C ILE A 563 " pdb=" CB ILE A 563 " both_signs ideal model delta sigma weight residual False 2.43 2.62 -0.19 2.00e-01 2.50e+01 8.78e-01 ... (remaining 2243 not shown) Planarity restraints: 2468 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C10 OLA E 401 " 0.287 2.00e-02 2.50e+03 2.20e-01 4.82e+02 pdb=" C11 OLA E 401 " -0.112 2.00e-02 2.50e+03 pdb=" C8 OLA E 401 " 0.116 2.00e-02 2.50e+03 pdb=" C9 OLA E 401 " -0.291 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP D 153 " 0.031 2.00e-02 2.50e+03 2.44e-02 1.49e+01 pdb=" CG TRP D 153 " -0.065 2.00e-02 2.50e+03 pdb=" CD1 TRP D 153 " 0.026 2.00e-02 2.50e+03 pdb=" CD2 TRP D 153 " 0.000 2.00e-02 2.50e+03 pdb=" NE1 TRP D 153 " -0.000 2.00e-02 2.50e+03 pdb=" CE2 TRP D 153 " -0.001 2.00e-02 2.50e+03 pdb=" CE3 TRP D 153 " -0.000 2.00e-02 2.50e+03 pdb=" CZ2 TRP D 153 " -0.001 2.00e-02 2.50e+03 pdb=" CZ3 TRP D 153 " 0.001 2.00e-02 2.50e+03 pdb=" CH2 TRP D 153 " 0.009 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP D 197 " -0.008 2.00e-02 2.50e+03 1.56e-02 6.06e+00 pdb=" CG TRP D 197 " 0.036 2.00e-02 2.50e+03 pdb=" CD1 TRP D 197 " -0.030 2.00e-02 2.50e+03 pdb=" CD2 TRP D 197 " -0.001 2.00e-02 2.50e+03 pdb=" NE1 TRP D 197 " 0.011 2.00e-02 2.50e+03 pdb=" CE2 TRP D 197 " 0.000 2.00e-02 2.50e+03 pdb=" CE3 TRP D 197 " -0.004 2.00e-02 2.50e+03 pdb=" CZ2 TRP D 197 " -0.001 2.00e-02 2.50e+03 pdb=" CZ3 TRP D 197 " -0.005 2.00e-02 2.50e+03 pdb=" CH2 TRP D 197 " 0.001 2.00e-02 2.50e+03 ... (remaining 2465 not shown) Histogram of nonbonded interaction distances: 2.19 - 2.73: 988 2.73 - 3.27: 14552 3.27 - 3.82: 22790 3.82 - 4.36: 25655 4.36 - 4.90: 44554 Nonbonded interactions: 108539 Sorted by model distance: nonbonded pdb=" ND2 ASN A 362 " pdb=" OD1 ASN A 382 " model vdw 2.191 2.520 nonbonded pdb=" NH2 ARG D 9 " pdb=" OE2 GLU D 60 " model vdw 2.226 2.520 nonbonded pdb=" OG SER C 145 " pdb=" OE1 GLN C 148 " model vdw 2.227 2.440 nonbonded pdb=" OG SER A 406 " pdb=" O ALA A 457 " model vdw 2.241 2.440 nonbonded pdb=" OG1 THR A 451 " pdb=" O MET A 455 " model vdw 2.268 2.440 ... (remaining 108534 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 'B' selection = chain 'C' } ncs_group { reference = chain 'D' selection = (chain 'E' and resid 1 through 334) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.540 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: 9.980 Check model and map are aligned: 0.200 Set scattering table: 0.140 Process input model: 39.970 Find NCS groups from input model: 0.660 Set up NCS constraints: 0.080 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.870 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 56.450 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7015 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 0.138 14709 Z= 0.405 Angle : 0.805 25.896 19778 Z= 0.387 Chirality : 0.045 0.300 2246 Planarity : 0.006 0.220 2468 Dihedral : 16.626 179.254 5527 Min Nonbonded Distance : 2.191 Molprobity Statistics. All-atom Clashscore : 7.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.51 % Favored : 94.49 % Rotamer: Outliers : 0.00 % Allowed : 0.51 % Favored : 99.49 % 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 (0.21), residues: 1779 helix: 0.99 (0.17), residues: 1003 sheet: -1.02 (0.45), residues: 169 loop : -1.60 (0.25), residues: 607 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.065 0.004 TRP D 153 HIS 0.008 0.001 HIS A 596 PHE 0.026 0.002 PHE A 529 TYR 0.023 0.002 TYR A 315 ARG 0.010 0.001 ARG D 226 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3558 Ramachandran restraints generated. 1779 Oldfield, 0 Emsley, 1779 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3558 Ramachandran restraints generated. 1779 Oldfield, 0 Emsley, 1779 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 167 residues out of total 1563 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 167 time to evaluate : 1.640 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: E 57 TYR cc_start: 0.8347 (t80) cc_final: 0.8086 (t80) outliers start: 0 outliers final: 0 residues processed: 167 average time/residue: 0.2752 time to fit residues: 67.0721 Evaluate side-chains 144 residues out of total 1563 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 144 time to evaluate : 1.824 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 177 random chunks: chunk 149 optimal weight: 0.7980 chunk 134 optimal weight: 8.9990 chunk 74 optimal weight: 0.6980 chunk 45 optimal weight: 0.5980 chunk 90 optimal weight: 8.9990 chunk 71 optimal weight: 0.9990 chunk 138 optimal weight: 7.9990 chunk 53 optimal weight: 0.7980 chunk 84 optimal weight: 3.9990 chunk 103 optimal weight: 1.9990 chunk 160 optimal weight: 9.9990 overall best weight: 0.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 503 GLN ** A 510 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 165 HIS D 255 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6965 moved from start: 0.0796 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 14709 Z= 0.186 Angle : 0.548 12.159 19778 Z= 0.276 Chirality : 0.042 0.252 2246 Planarity : 0.003 0.038 2468 Dihedral : 11.876 165.451 2018 Min Nonbonded Distance : 2.221 Molprobity Statistics. All-atom Clashscore : 7.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.50 % Favored : 95.50 % Rotamer: Outliers : 0.58 % Allowed : 6.78 % Favored : 92.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.10 (0.21), residues: 1779 helix: 1.21 (0.17), residues: 1004 sheet: -1.03 (0.43), residues: 170 loop : -1.54 (0.25), residues: 605 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP D 153 HIS 0.007 0.001 HIS D 134 PHE 0.021 0.001 PHE A 529 TYR 0.032 0.002 TYR E 151 ARG 0.005 0.000 ARG D 226 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3558 Ramachandran restraints generated. 1779 Oldfield, 0 Emsley, 1779 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3558 Ramachandran restraints generated. 1779 Oldfield, 0 Emsley, 1779 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 161 residues out of total 1563 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 152 time to evaluate : 1.786 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 202 MET cc_start: 0.5556 (mtt) cc_final: 0.5343 (mtm) REVERT: D 41 MET cc_start: 0.5531 (mmp) cc_final: 0.5323 (mmp) outliers start: 9 outliers final: 8 residues processed: 154 average time/residue: 0.2681 time to fit residues: 61.0699 Evaluate side-chains 151 residues out of total 1563 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 143 time to evaluate : 1.742 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 281 SER Chi-restraints excluded: chain A residue 486 VAL Chi-restraints excluded: chain B residue 52 VAL Chi-restraints excluded: chain B residue 161 ASP Chi-restraints excluded: chain C residue 49 LEU Chi-restraints excluded: chain D residue 113 GLU Chi-restraints excluded: chain E residue 130 LEU Chi-restraints excluded: chain E residue 290 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 177 random chunks: chunk 89 optimal weight: 4.9990 chunk 49 optimal weight: 0.6980 chunk 133 optimal weight: 8.9990 chunk 109 optimal weight: 3.9990 chunk 44 optimal weight: 7.9990 chunk 161 optimal weight: 40.0000 chunk 173 optimal weight: 5.9990 chunk 143 optimal weight: 0.9980 chunk 159 optimal weight: 0.9980 chunk 54 optimal weight: 1.9990 chunk 129 optimal weight: 0.0370 overall best weight: 0.9460 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 510 HIS D 124 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6982 moved from start: 0.1038 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 14709 Z= 0.197 Angle : 0.527 11.182 19778 Z= 0.265 Chirality : 0.041 0.266 2246 Planarity : 0.003 0.038 2468 Dihedral : 11.118 169.981 2018 Min Nonbonded Distance : 2.197 Molprobity Statistics. All-atom Clashscore : 6.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.06 % Favored : 94.94 % Rotamer: Outliers : 0.58 % Allowed : 10.75 % Favored : 88.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 0.14 (0.21), residues: 1779 helix: 1.23 (0.17), residues: 1007 sheet: -1.05 (0.44), residues: 156 loop : -1.51 (0.25), residues: 616 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP E 122 HIS 0.005 0.001 HIS A 596 PHE 0.024 0.001 PHE A 529 TYR 0.027 0.002 TYR E 151 ARG 0.005 0.000 ARG D 107 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3558 Ramachandran restraints generated. 1779 Oldfield, 0 Emsley, 1779 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3558 Ramachandran restraints generated. 1779 Oldfield, 0 Emsley, 1779 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 161 residues out of total 1563 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 152 time to evaluate : 1.673 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 9 outliers final: 7 residues processed: 156 average time/residue: 0.2567 time to fit residues: 59.8347 Evaluate side-chains 146 residues out of total 1563 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 139 time to evaluate : 1.939 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 281 SER Chi-restraints excluded: chain B residue 52 VAL Chi-restraints excluded: chain B residue 161 ASP Chi-restraints excluded: chain C residue 49 LEU Chi-restraints excluded: chain C residue 86 HIS Chi-restraints excluded: chain D residue 113 GLU Chi-restraints excluded: chain E residue 130 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 177 random chunks: chunk 159 optimal weight: 3.9990 chunk 121 optimal weight: 2.9990 chunk 83 optimal weight: 4.9990 chunk 17 optimal weight: 0.4980 chunk 76 optimal weight: 0.6980 chunk 108 optimal weight: 0.9990 chunk 161 optimal weight: 20.0000 chunk 171 optimal weight: 50.0000 chunk 84 optimal weight: 4.9990 chunk 153 optimal weight: 0.8980 chunk 46 optimal weight: 0.0970 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 510 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6950 moved from start: 0.1307 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 14709 Z= 0.161 Angle : 0.516 13.757 19778 Z= 0.256 Chirality : 0.040 0.217 2246 Planarity : 0.003 0.037 2468 Dihedral : 10.621 167.964 2018 Min Nonbonded Distance : 2.201 Molprobity Statistics. All-atom Clashscore : 6.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.61 % Favored : 95.39 % Rotamer: Outliers : 1.34 % Allowed : 12.54 % Favored : 86.12 % 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: 0.26 (0.21), residues: 1779 helix: 1.41 (0.17), residues: 994 sheet: -1.22 (0.44), residues: 150 loop : -1.47 (0.24), residues: 635 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP D 122 HIS 0.003 0.001 HIS A 596 PHE 0.021 0.001 PHE A 529 TYR 0.025 0.001 TYR E 151 ARG 0.005 0.000 ARG D 107 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3558 Ramachandran restraints generated. 1779 Oldfield, 0 Emsley, 1779 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3558 Ramachandran restraints generated. 1779 Oldfield, 0 Emsley, 1779 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 165 residues out of total 1563 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 144 time to evaluate : 1.604 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: E 140 MET cc_start: 0.6110 (pmm) cc_final: 0.5592 (pmm) outliers start: 21 outliers final: 10 residues processed: 154 average time/residue: 0.2639 time to fit residues: 60.8653 Evaluate side-chains 143 residues out of total 1563 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 133 time to evaluate : 1.558 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 281 SER Chi-restraints excluded: chain B residue 52 VAL Chi-restraints excluded: chain B residue 161 ASP Chi-restraints excluded: chain B residue 171 THR Chi-restraints excluded: chain C residue 49 LEU Chi-restraints excluded: chain C residue 86 HIS Chi-restraints excluded: chain D residue 30 ASP Chi-restraints excluded: chain D residue 113 GLU Chi-restraints excluded: chain E residue 130 LEU Chi-restraints excluded: chain E residue 308 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 177 random chunks: chunk 142 optimal weight: 1.9990 chunk 97 optimal weight: 1.9990 chunk 2 optimal weight: 0.3980 chunk 127 optimal weight: 0.3980 chunk 70 optimal weight: 0.2980 chunk 145 optimal weight: 0.5980 chunk 118 optimal weight: 2.9990 chunk 0 optimal weight: 3.9990 chunk 87 optimal weight: 20.0000 chunk 153 optimal weight: 1.9990 chunk 43 optimal weight: 0.1980 overall best weight: 0.3780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 502 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 510 HIS ** B 20 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6910 moved from start: 0.1578 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.051 14709 Z= 0.136 Angle : 0.508 12.832 19778 Z= 0.251 Chirality : 0.040 0.193 2246 Planarity : 0.003 0.036 2468 Dihedral : 10.217 171.240 2018 Min Nonbonded Distance : 2.209 Molprobity Statistics. All-atom Clashscore : 6.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.67 % Favored : 95.33 % Rotamer: Outliers : 1.02 % Allowed : 13.56 % Favored : 85.41 % 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: 0.48 (0.21), residues: 1779 helix: 1.58 (0.17), residues: 991 sheet: -1.01 (0.43), residues: 156 loop : -1.40 (0.24), residues: 632 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP D 122 HIS 0.003 0.000 HIS B 86 PHE 0.018 0.001 PHE A 529 TYR 0.022 0.001 TYR E 151 ARG 0.006 0.000 ARG D 107 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3558 Ramachandran restraints generated. 1779 Oldfield, 0 Emsley, 1779 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3558 Ramachandran restraints generated. 1779 Oldfield, 0 Emsley, 1779 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 156 residues out of total 1563 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 140 time to evaluate : 1.688 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 315 TYR cc_start: 0.6276 (m-80) cc_final: 0.6001 (m-80) outliers start: 16 outliers final: 13 residues processed: 150 average time/residue: 0.2558 time to fit residues: 57.6523 Evaluate side-chains 146 residues out of total 1563 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 133 time to evaluate : 1.656 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 77 THR Chi-restraints excluded: chain A residue 109 VAL Chi-restraints excluded: chain A residue 229 THR Chi-restraints excluded: chain A residue 281 SER Chi-restraints excluded: chain B residue 52 VAL Chi-restraints excluded: chain B residue 171 THR Chi-restraints excluded: chain C residue 49 LEU Chi-restraints excluded: chain C residue 50 LEU Chi-restraints excluded: chain C residue 86 HIS Chi-restraints excluded: chain D residue 113 GLU Chi-restraints excluded: chain D residue 128 THR Chi-restraints excluded: chain E residue 130 LEU Chi-restraints excluded: chain E residue 308 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 177 random chunks: chunk 57 optimal weight: 0.5980 chunk 154 optimal weight: 3.9990 chunk 33 optimal weight: 6.9990 chunk 100 optimal weight: 2.9990 chunk 42 optimal weight: 7.9990 chunk 171 optimal weight: 50.0000 chunk 142 optimal weight: 5.9990 chunk 79 optimal weight: 0.5980 chunk 14 optimal weight: 0.1980 chunk 56 optimal weight: 0.8980 chunk 89 optimal weight: 0.9980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 510 HIS ** B 20 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 231 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6940 moved from start: 0.1661 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 14709 Z= 0.161 Angle : 0.519 12.417 19778 Z= 0.257 Chirality : 0.040 0.215 2246 Planarity : 0.003 0.036 2468 Dihedral : 10.138 172.364 2018 Min Nonbonded Distance : 2.203 Molprobity Statistics. All-atom Clashscore : 6.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.78 % Favored : 95.22 % Rotamer: Outliers : 1.73 % Allowed : 14.14 % Favored : 84.13 % 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: 0.48 (0.21), residues: 1779 helix: 1.53 (0.17), residues: 1000 sheet: -0.87 (0.44), residues: 155 loop : -1.37 (0.25), residues: 624 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP D 122 HIS 0.005 0.001 HIS D 124 PHE 0.023 0.001 PHE A 529 TYR 0.021 0.001 TYR E 151 ARG 0.006 0.000 ARG D 107 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3558 Ramachandran restraints generated. 1779 Oldfield, 0 Emsley, 1779 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3558 Ramachandran restraints generated. 1779 Oldfield, 0 Emsley, 1779 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 165 residues out of total 1563 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 138 time to evaluate : 1.718 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 27 outliers final: 17 residues processed: 153 average time/residue: 0.2469 time to fit residues: 57.3559 Evaluate side-chains 149 residues out of total 1563 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 132 time to evaluate : 1.565 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 77 THR Chi-restraints excluded: chain A residue 109 VAL Chi-restraints excluded: chain A residue 229 THR Chi-restraints excluded: chain A residue 281 SER Chi-restraints excluded: chain A residue 445 LEU Chi-restraints excluded: chain A residue 616 MET Chi-restraints excluded: chain B residue 52 VAL Chi-restraints excluded: chain B residue 161 ASP Chi-restraints excluded: chain B residue 171 THR Chi-restraints excluded: chain C residue 49 LEU Chi-restraints excluded: chain C residue 50 LEU Chi-restraints excluded: chain C residue 86 HIS Chi-restraints excluded: chain C residue 94 TYR Chi-restraints excluded: chain D residue 30 ASP Chi-restraints excluded: chain D residue 113 GLU Chi-restraints excluded: chain E residue 290 MET Chi-restraints excluded: chain E residue 308 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 177 random chunks: chunk 165 optimal weight: 30.0000 chunk 19 optimal weight: 0.8980 chunk 97 optimal weight: 0.7980 chunk 125 optimal weight: 6.9990 chunk 96 optimal weight: 2.9990 chunk 144 optimal weight: 0.8980 chunk 95 optimal weight: 0.6980 chunk 170 optimal weight: 0.0070 chunk 106 optimal weight: 0.9990 chunk 104 optimal weight: 0.8980 chunk 78 optimal weight: 0.4980 overall best weight: 0.5798 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 503 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 510 HIS ** B 20 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6927 moved from start: 0.1781 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.049 14709 Z= 0.156 Angle : 0.532 13.197 19778 Z= 0.259 Chirality : 0.040 0.255 2246 Planarity : 0.003 0.036 2468 Dihedral : 9.985 170.563 2018 Min Nonbonded Distance : 2.212 Molprobity Statistics. All-atom Clashscore : 6.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.89 % Favored : 95.11 % Rotamer: Outliers : 1.47 % Allowed : 14.91 % Favored : 83.62 % 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: 0.55 (0.21), residues: 1779 helix: 1.60 (0.17), residues: 994 sheet: -0.92 (0.43), residues: 159 loop : -1.31 (0.25), residues: 626 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.058 0.002 TRP E 122 HIS 0.003 0.000 HIS A 510 PHE 0.021 0.001 PHE A 529 TYR 0.020 0.001 TYR E 151 ARG 0.007 0.000 ARG D 107 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3558 Ramachandran restraints generated. 1779 Oldfield, 0 Emsley, 1779 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3558 Ramachandran restraints generated. 1779 Oldfield, 0 Emsley, 1779 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 161 residues out of total 1563 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 138 time to evaluate : 1.728 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 23 outliers final: 17 residues processed: 152 average time/residue: 0.2789 time to fit residues: 65.2586 Evaluate side-chains 148 residues out of total 1563 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 131 time to evaluate : 1.519 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 77 THR Chi-restraints excluded: chain A residue 109 VAL Chi-restraints excluded: chain A residue 229 THR Chi-restraints excluded: chain A residue 281 SER Chi-restraints excluded: chain A residue 445 LEU Chi-restraints excluded: chain B residue 52 VAL Chi-restraints excluded: chain B residue 161 ASP Chi-restraints excluded: chain B residue 171 THR Chi-restraints excluded: chain C residue 49 LEU Chi-restraints excluded: chain C residue 50 LEU Chi-restraints excluded: chain C residue 86 HIS Chi-restraints excluded: chain C residue 94 TYR Chi-restraints excluded: chain D residue 30 ASP Chi-restraints excluded: chain D residue 113 GLU Chi-restraints excluded: chain D residue 321 THR Chi-restraints excluded: chain E residue 290 MET Chi-restraints excluded: chain E residue 308 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 177 random chunks: chunk 105 optimal weight: 0.9990 chunk 68 optimal weight: 3.9990 chunk 101 optimal weight: 1.9990 chunk 51 optimal weight: 0.5980 chunk 33 optimal weight: 6.9990 chunk 108 optimal weight: 0.0870 chunk 116 optimal weight: 1.9990 chunk 84 optimal weight: 0.8980 chunk 15 optimal weight: 2.9990 chunk 134 optimal weight: 7.9990 chunk 155 optimal weight: 6.9990 overall best weight: 0.9162 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 503 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 510 HIS ** B 20 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6975 moved from start: 0.1802 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 14709 Z= 0.194 Angle : 0.543 13.143 19778 Z= 0.266 Chirality : 0.041 0.266 2246 Planarity : 0.003 0.037 2468 Dihedral : 10.108 172.616 2018 Min Nonbonded Distance : 2.208 Molprobity Statistics. All-atom Clashscore : 6.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.83 % Favored : 95.17 % Rotamer: Outliers : 1.34 % Allowed : 15.36 % Favored : 83.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.44 (0.21), residues: 1779 helix: 1.47 (0.17), residues: 1004 sheet: -0.95 (0.42), residues: 159 loop : -1.33 (0.25), residues: 616 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.002 TRP E 122 HIS 0.003 0.000 HIS A 596 PHE 0.026 0.001 PHE A 529 TYR 0.018 0.001 TYR E 151 ARG 0.007 0.000 ARG D 107 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3558 Ramachandran restraints generated. 1779 Oldfield, 0 Emsley, 1779 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3558 Ramachandran restraints generated. 1779 Oldfield, 0 Emsley, 1779 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 160 residues out of total 1563 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 139 time to evaluate : 1.528 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 21 outliers final: 18 residues processed: 149 average time/residue: 0.2449 time to fit residues: 55.2099 Evaluate side-chains 155 residues out of total 1563 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 137 time to evaluate : 1.708 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 77 THR Chi-restraints excluded: chain A residue 95 MET Chi-restraints excluded: chain A residue 109 VAL Chi-restraints excluded: chain A residue 229 THR Chi-restraints excluded: chain A residue 281 SER Chi-restraints excluded: chain A residue 283 MET Chi-restraints excluded: chain A residue 445 LEU Chi-restraints excluded: chain A residue 510 HIS Chi-restraints excluded: chain B residue 52 VAL Chi-restraints excluded: chain B residue 161 ASP Chi-restraints excluded: chain B residue 171 THR Chi-restraints excluded: chain C residue 49 LEU Chi-restraints excluded: chain C residue 86 HIS Chi-restraints excluded: chain D residue 30 ASP Chi-restraints excluded: chain D residue 113 GLU Chi-restraints excluded: chain D residue 321 THR Chi-restraints excluded: chain E residue 290 MET Chi-restraints excluded: chain E residue 308 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 177 random chunks: chunk 163 optimal weight: 5.9990 chunk 149 optimal weight: 1.9990 chunk 158 optimal weight: 10.0000 chunk 95 optimal weight: 0.9980 chunk 69 optimal weight: 0.9990 chunk 124 optimal weight: 5.9990 chunk 48 optimal weight: 0.7980 chunk 143 optimal weight: 10.0000 chunk 150 optimal weight: 0.9980 chunk 104 optimal weight: 5.9990 chunk 168 optimal weight: 6.9990 overall best weight: 1.1584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 503 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 510 HIS ** B 20 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6996 moved from start: 0.1805 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 14709 Z= 0.231 Angle : 0.571 13.442 19778 Z= 0.277 Chirality : 0.042 0.248 2246 Planarity : 0.003 0.038 2468 Dihedral : 10.196 172.497 2018 Min Nonbonded Distance : 2.194 Molprobity Statistics. All-atom Clashscore : 6.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.00 % Favored : 95.00 % Rotamer: Outliers : 1.60 % Allowed : 15.61 % Favored : 82.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.36 (0.21), residues: 1779 helix: 1.38 (0.17), residues: 1004 sheet: -0.93 (0.42), residues: 159 loop : -1.33 (0.25), residues: 616 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.036 0.002 TRP E 122 HIS 0.014 0.001 HIS A 510 PHE 0.027 0.001 PHE A 529 TYR 0.018 0.002 TYR E 151 ARG 0.006 0.000 ARG D 107 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3558 Ramachandran restraints generated. 1779 Oldfield, 0 Emsley, 1779 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3558 Ramachandran restraints generated. 1779 Oldfield, 0 Emsley, 1779 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 166 residues out of total 1563 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 141 time to evaluate : 1.682 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 25 outliers final: 19 residues processed: 154 average time/residue: 0.2621 time to fit residues: 61.0732 Evaluate side-chains 159 residues out of total 1563 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 140 time to evaluate : 1.650 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 77 THR Chi-restraints excluded: chain A residue 95 MET Chi-restraints excluded: chain A residue 109 VAL Chi-restraints excluded: chain A residue 229 THR Chi-restraints excluded: chain A residue 281 SER Chi-restraints excluded: chain A residue 445 LEU Chi-restraints excluded: chain A residue 510 HIS Chi-restraints excluded: chain A residue 616 MET Chi-restraints excluded: chain B residue 52 VAL Chi-restraints excluded: chain B residue 161 ASP Chi-restraints excluded: chain B residue 171 THR Chi-restraints excluded: chain C residue 49 LEU Chi-restraints excluded: chain C residue 86 HIS Chi-restraints excluded: chain D residue 30 ASP Chi-restraints excluded: chain D residue 113 GLU Chi-restraints excluded: chain D residue 320 LEU Chi-restraints excluded: chain D residue 321 THR Chi-restraints excluded: chain E residue 290 MET Chi-restraints excluded: chain E residue 308 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 177 random chunks: chunk 102 optimal weight: 0.0970 chunk 79 optimal weight: 2.9990 chunk 116 optimal weight: 1.9990 chunk 176 optimal weight: 2.9990 chunk 162 optimal weight: 7.9990 chunk 140 optimal weight: 9.9990 chunk 14 optimal weight: 0.9980 chunk 108 optimal weight: 0.9990 chunk 86 optimal weight: 0.4980 chunk 111 optimal weight: 0.0000 chunk 149 optimal weight: 0.9980 overall best weight: 0.5182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 503 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 20 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6941 moved from start: 0.1948 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.051 14709 Z= 0.157 Angle : 0.550 14.004 19778 Z= 0.266 Chirality : 0.041 0.308 2246 Planarity : 0.003 0.036 2468 Dihedral : 9.941 171.149 2018 Min Nonbonded Distance : 2.215 Molprobity Statistics. All-atom Clashscore : 6.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.72 % Favored : 95.28 % Rotamer: Outliers : 1.34 % Allowed : 15.80 % Favored : 82.85 % 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: 0.49 (0.21), residues: 1779 helix: 1.48 (0.17), residues: 999 sheet: -0.83 (0.42), residues: 156 loop : -1.27 (0.25), residues: 624 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.036 0.002 TRP E 122 HIS 0.017 0.001 HIS A 510 PHE 0.020 0.001 PHE A 529 TYR 0.017 0.001 TYR E 151 ARG 0.006 0.000 ARG D 107 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3558 Ramachandran restraints generated. 1779 Oldfield, 0 Emsley, 1779 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3558 Ramachandran restraints generated. 1779 Oldfield, 0 Emsley, 1779 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 159 residues out of total 1563 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 138 time to evaluate : 1.703 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 21 outliers final: 16 residues processed: 147 average time/residue: 0.2855 time to fit residues: 64.5449 Evaluate side-chains 152 residues out of total 1563 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 136 time to evaluate : 1.760 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 77 THR Chi-restraints excluded: chain A residue 109 VAL Chi-restraints excluded: chain A residue 229 THR Chi-restraints excluded: chain A residue 281 SER Chi-restraints excluded: chain A residue 445 LEU Chi-restraints excluded: chain B residue 52 VAL Chi-restraints excluded: chain B residue 161 ASP Chi-restraints excluded: chain B residue 171 THR Chi-restraints excluded: chain C residue 49 LEU Chi-restraints excluded: chain C residue 86 HIS Chi-restraints excluded: chain D residue 30 ASP Chi-restraints excluded: chain D residue 113 GLU Chi-restraints excluded: chain D residue 320 LEU Chi-restraints excluded: chain D residue 321 THR Chi-restraints excluded: chain E residue 290 MET Chi-restraints excluded: chain E residue 308 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 177 random chunks: chunk 43 optimal weight: 0.6980 chunk 129 optimal weight: 0.0000 chunk 20 optimal weight: 1.9990 chunk 39 optimal weight: 6.9990 chunk 140 optimal weight: 20.0000 chunk 58 optimal weight: 1.9990 chunk 144 optimal weight: 0.7980 chunk 17 optimal weight: 0.6980 chunk 25 optimal weight: 0.6980 chunk 123 optimal weight: 6.9990 chunk 8 optimal weight: 0.8980 overall best weight: 0.5784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 503 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 510 HIS ** B 20 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4504 r_free = 0.4504 target = 0.228408 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.4169 r_free = 0.4169 target = 0.192208 restraints weight = 18619.829| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.4120 r_free = 0.4120 target = 0.187648 restraints weight = 39386.938| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.4090 r_free = 0.4090 target = 0.184931 restraints weight = 35198.831| |-----------------------------------------------------------------------------| r_work (final): 0.4094 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6976 moved from start: 0.2028 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 14709 Z= 0.162 Angle : 0.549 13.479 19778 Z= 0.264 Chirality : 0.041 0.259 2246 Planarity : 0.003 0.037 2468 Dihedral : 9.787 170.876 2018 Min Nonbonded Distance : 2.214 Molprobity Statistics. All-atom Clashscore : 6.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.72 % Favored : 95.28 % Rotamer: Outliers : 1.15 % Allowed : 16.06 % Favored : 82.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.55 (0.21), residues: 1779 helix: 1.53 (0.17), residues: 998 sheet: -0.79 (0.42), residues: 156 loop : -1.24 (0.25), residues: 625 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.002 TRP E 122 HIS 0.005 0.000 HIS A 510 PHE 0.022 0.001 PHE A 529 TYR 0.017 0.001 TYR E 151 ARG 0.006 0.000 ARG D 107 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2675.01 seconds wall clock time: 50 minutes 5.45 seconds (3005.45 seconds total)