Starting phenix.real_space_refine on Tue Sep 24 02:54:41 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7qud_14148/09_2024/7qud_14148.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7qud_14148/09_2024/7qud_14148.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.47 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7qud_14148/09_2024/7qud_14148.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7qud_14148/09_2024/7qud_14148.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7qud_14148/09_2024/7qud_14148.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7qud_14148/09_2024/7qud_14148.cif" } resolution = 3.47 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= 0.008 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 6 5.49 5 Mg 1 5.21 5 S 47 5.16 5 C 4214 2.51 5 N 1137 2.21 5 O 1291 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 11 residue(s): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/chem_data/mon_lib" Total number of atoms: 6696 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 3350 Number of conformers: 1 Conformer: "" Number of residues, atoms: 427, 3350 Classifications: {'peptide': 427} Link IDs: {'PCIS': 1, 'PTRANS': 19, 'TRANS': 406} Chain breaks: 1 Chain: "B" Number of atoms: 3281 Number of conformers: 1 Conformer: "" Number of residues, atoms: 417, 3281 Classifications: {'peptide': 417} Link IDs: {'PCIS': 1, 'PTRANS': 18, 'TRANS': 397} Chain breaks: 2 Chain: "A" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 33 Unusual residues: {' MG': 1, 'GTP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 32 Unusual residues: {'GTP': 1} Classifications: {'undetermined': 1} Time building chain proxies: 5.33, per 1000 atoms: 0.80 Number of scatterers: 6696 At special positions: 0 Unit cell: (97.032, 74.64, 101.386, 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 47 16.00 P 6 15.00 Mg 1 11.99 O 1291 8.00 N 1137 7.00 C 4214 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 - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.54 Conformation dependent library (CDL) restraints added in 911.8 milliseconds 1668 Ramachandran restraints generated. 834 Oldfield, 0 Emsley, 834 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1564 Finding SS restraints... Secondary structure from input PDB file: 38 helices and 6 sheets defined 53.6% alpha, 12.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.69 Creating SS restraints... Processing helix chain 'A' and resid 10 through 29 Processing helix chain 'A' and resid 47 through 51 removed outlier: 3.951A pdb=" N THR A 51 " --> pdb=" O SER A 48 " (cutoff:3.500A) Processing helix chain 'A' and resid 72 through 80 Processing helix chain 'A' and resid 88 through 90 No H-bonds generated for 'chain 'A' and resid 88 through 90' Processing helix chain 'A' and resid 102 through 108 Processing helix chain 'A' and resid 109 through 128 removed outlier: 4.513A pdb=" N GLU A 113 " --> pdb=" O THR A 109 " (cutoff:3.500A) removed outlier: 3.976A pdb=" N ILE A 114 " --> pdb=" O ILE A 110 " (cutoff:3.500A) removed outlier: 4.493A pdb=" N ASP A 116 " --> pdb=" O LYS A 112 " (cutoff:3.500A) removed outlier: 5.309A pdb=" N LEU A 117 " --> pdb=" O GLU A 113 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N GLN A 128 " --> pdb=" O LYS A 124 " (cutoff:3.500A) Processing helix chain 'A' and resid 143 through 161 removed outlier: 4.475A pdb=" N THR A 150 " --> pdb=" O GLY A 146 " (cutoff:3.500A) Processing helix chain 'A' and resid 182 through 195 Processing helix chain 'A' and resid 206 through 216 Processing helix chain 'A' and resid 223 through 244 removed outlier: 3.505A pdb=" N LEU A 227 " --> pdb=" O THR A 223 " (cutoff:3.500A) removed outlier: 4.976A pdb=" N SER A 241 " --> pdb=" O SER A 237 " (cutoff:3.500A) removed outlier: 5.086A pdb=" N LEU A 242 " --> pdb=" O ILE A 238 " (cutoff:3.500A) Processing helix chain 'A' and resid 251 through 260 removed outlier: 3.741A pdb=" N PHE A 255 " --> pdb=" O ASP A 251 " (cutoff:3.500A) removed outlier: 3.869A pdb=" N GLN A 256 " --> pdb=" O LEU A 252 " (cutoff:3.500A) Processing helix chain 'A' and resid 277 through 281 Processing helix chain 'A' and resid 287 through 296 removed outlier: 3.910A pdb=" N PHE A 296 " --> pdb=" O THR A 292 " (cutoff:3.500A) Processing helix chain 'A' and resid 297 through 301 removed outlier: 4.132A pdb=" N GLN A 301 " --> pdb=" O PRO A 298 " (cutoff:3.500A) Processing helix chain 'A' and resid 306 through 310 Processing helix chain 'A' and resid 324 through 337 removed outlier: 3.508A pdb=" N THR A 337 " --> pdb=" O ALA A 333 " (cutoff:3.500A) Processing helix chain 'A' and resid 383 through 400 removed outlier: 4.264A pdb=" N ALA A 387 " --> pdb=" O ALA A 383 " (cutoff:3.500A) removed outlier: 4.238A pdb=" N LEU A 391 " --> pdb=" O ALA A 387 " (cutoff:3.500A) removed outlier: 3.989A pdb=" N ALA A 400 " --> pdb=" O ASP A 396 " (cutoff:3.500A) Processing helix chain 'A' and resid 404 through 410 removed outlier: 3.945A pdb=" N TYR A 408 " --> pdb=" O PHE A 404 " (cutoff:3.500A) Processing helix chain 'A' and resid 415 through 436 removed outlier: 4.200A pdb=" N SER A 419 " --> pdb=" O GLU A 415 " (cutoff:3.500A) Processing helix chain 'B' and resid 10 through 29 Processing helix chain 'B' and resid 41 through 45 Processing helix chain 'B' and resid 46 through 49 removed outlier: 3.719A pdb=" N VAL B 49 " --> pdb=" O ARG B 46 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 46 through 49' Processing helix chain 'B' and resid 71 through 79 removed outlier: 3.744A pdb=" N SER B 75 " --> pdb=" O GLY B 71 " (cutoff:3.500A) Processing helix chain 'B' and resid 86 through 88 No H-bonds generated for 'chain 'B' and resid 86 through 88' Processing helix chain 'B' and resid 100 through 106 Processing helix chain 'B' and resid 108 through 125 removed outlier: 3.787A pdb=" N LEU B 112 " --> pdb=" O GLU B 108 " (cutoff:3.500A) removed outlier: 4.876A pdb=" N ASP B 114 " --> pdb=" O ALA B 110 " (cutoff:3.500A) removed outlier: 4.662A pdb=" N SER B 115 " --> pdb=" O GLU B 111 " (cutoff:3.500A) Processing helix chain 'B' and resid 143 through 159 Processing helix chain 'B' and resid 180 through 195 removed outlier: 3.983A pdb=" N ASN B 184 " --> pdb=" O VAL B 180 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N GLN B 191 " --> pdb=" O LEU B 187 " (cutoff:3.500A) Processing helix chain 'B' and resid 204 through 214 Processing helix chain 'B' and resid 222 through 242 removed outlier: 4.678A pdb=" N CYS B 239 " --> pdb=" O GLY B 235 " (cutoff:3.500A) removed outlier: 5.091A pdb=" N LEU B 240 " --> pdb=" O VAL B 236 " (cutoff:3.500A) Processing helix chain 'B' and resid 249 through 258 Processing helix chain 'B' and resid 285 through 294 removed outlier: 3.954A pdb=" N PHE B 294 " --> pdb=" O THR B 290 " (cutoff:3.500A) Processing helix chain 'B' and resid 295 through 299 removed outlier: 3.790A pdb=" N MET B 299 " --> pdb=" O ALA B 296 " (cutoff:3.500A) Processing helix chain 'B' and resid 304 through 308 removed outlier: 3.500A pdb=" N GLY B 308 " --> pdb=" O PRO B 305 " (cutoff:3.500A) Processing helix chain 'B' and resid 322 through 337 Processing helix chain 'B' and resid 373 through 390 removed outlier: 4.053A pdb=" N LEU B 377 " --> pdb=" O ALA B 373 " (cutoff:3.500A) removed outlier: 3.947A pdb=" N ARG B 390 " --> pdb=" O THR B 386 " (cutoff:3.500A) Processing helix chain 'B' and resid 395 through 400 Processing helix chain 'B' and resid 404 through 428 removed outlier: 3.895A pdb=" N PHE B 408 " --> pdb=" O ASP B 404 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 92 through 93 removed outlier: 7.899A pdb=" N ILE A 93 " --> pdb=" O ALA A 65 " (cutoff:3.500A) removed outlier: 6.429A pdb=" N PHE A 67 " --> pdb=" O ILE A 93 " (cutoff:3.500A) removed outlier: 8.637A pdb=" N VAL A 66 " --> pdb=" O CYS A 4 " (cutoff:3.500A) removed outlier: 6.814A pdb=" N SER A 6 " --> pdb=" O VAL A 66 " (cutoff:3.500A) removed outlier: 7.700A pdb=" N VAL A 68 " --> pdb=" O SER A 6 " (cutoff:3.500A) removed outlier: 6.203A pdb=" N HIS A 8 " --> pdb=" O VAL A 68 " (cutoff:3.500A) removed outlier: 7.464A pdb=" N GLU A 3 " --> pdb=" O GLY A 134 " (cutoff:3.500A) removed outlier: 8.581A pdb=" N LEU A 136 " --> pdb=" O GLU A 3 " (cutoff:3.500A) removed outlier: 7.134A pdb=" N ILE A 5 " --> pdb=" O LEU A 136 " (cutoff:3.500A) removed outlier: 7.819A pdb=" N PHE A 138 " --> pdb=" O ILE A 5 " (cutoff:3.500A) removed outlier: 6.669A pdb=" N ILE A 7 " --> pdb=" O PHE A 138 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N PHE A 135 " --> pdb=" O SER A 165 " (cutoff:3.500A) removed outlier: 3.923A pdb=" N CYS A 200 " --> pdb=" O LYS A 166 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 53 through 55 Processing sheet with id=AA3, first strand: chain 'A' and resid 171 through 172 Processing sheet with id=AA4, first strand: chain 'A' and resid 269 through 273 removed outlier: 6.779A pdb=" N ALA A 374 " --> pdb=" O TYR A 319 " (cutoff:3.500A) removed outlier: 4.901A pdb=" N TYR A 319 " --> pdb=" O ALA A 374 " (cutoff:3.500A) removed outlier: 6.750A pdb=" N CYS A 376 " --> pdb=" O MET A 317 " (cutoff:3.500A) removed outlier: 4.763A pdb=" N MET A 317 " --> pdb=" O CYS A 376 " (cutoff:3.500A) removed outlier: 6.808A pdb=" N LEU A 378 " --> pdb=" O CYS A 315 " (cutoff:3.500A) removed outlier: 4.309A pdb=" N CYS A 315 " --> pdb=" O LEU A 378 " (cutoff:3.500A) removed outlier: 6.642A pdb=" N ASN A 380 " --> pdb=" O MET A 313 " (cutoff:3.500A) removed outlier: 9.573A pdb=" N LYS A 352 " --> pdb=" O MET A 313 " (cutoff:3.500A) removed outlier: 7.174A pdb=" N CYS A 315 " --> pdb=" O LYS A 352 " (cutoff:3.500A) removed outlier: 8.025A pdb=" N GLY A 354 " --> pdb=" O CYS A 315 " (cutoff:3.500A) removed outlier: 5.798A pdb=" N MET A 317 " --> pdb=" O GLY A 354 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 90 through 92 removed outlier: 8.134A pdb=" N VAL B 91 " --> pdb=" O ALA B 63 " (cutoff:3.500A) removed outlier: 6.221A pdb=" N LEU B 65 " --> pdb=" O VAL B 91 " (cutoff:3.500A) removed outlier: 8.280A pdb=" N VAL B 64 " --> pdb=" O ILE B 4 " (cutoff:3.500A) removed outlier: 6.883A pdb=" N HIS B 6 " --> pdb=" O VAL B 64 " (cutoff:3.500A) removed outlier: 8.193A pdb=" N VAL B 66 " --> pdb=" O HIS B 6 " (cutoff:3.500A) removed outlier: 6.277A pdb=" N GLN B 8 " --> pdb=" O VAL B 66 " (cutoff:3.500A) removed outlier: 5.790A pdb=" N GLU B 3 " --> pdb=" O LEU B 130 " (cutoff:3.500A) removed outlier: 3.912A pdb=" N GLY B 132 " --> pdb=" O GLU B 3 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N GLN B 134 " --> pdb=" O VAL B 5 " (cutoff:3.500A) removed outlier: 6.947A pdb=" N GLN B 131 " --> pdb=" O ILE B 163 " (cutoff:3.500A) removed outlier: 7.507A pdb=" N ASN B 165 " --> pdb=" O GLN B 131 " (cutoff:3.500A) removed outlier: 5.570A pdb=" N PHE B 133 " --> pdb=" O ASN B 165 " (cutoff:3.500A) removed outlier: 7.492A pdb=" N TYR B 167 " --> pdb=" O PHE B 133 " (cutoff:3.500A) removed outlier: 6.064A pdb=" N LEU B 135 " --> pdb=" O TYR B 167 " (cutoff:3.500A) removed outlier: 7.709A pdb=" N VAL B 169 " --> pdb=" O LEU B 135 " (cutoff:3.500A) removed outlier: 8.319A pdb=" N TYR B 200 " --> pdb=" O MET B 164 " (cutoff:3.500A) removed outlier: 7.595A pdb=" N THR B 166 " --> pdb=" O TYR B 200 " (cutoff:3.500A) removed outlier: 7.745A pdb=" N ILE B 202 " --> pdb=" O THR B 166 " (cutoff:3.500A) removed outlier: 6.115A pdb=" N SER B 168 " --> pdb=" O ILE B 202 " (cutoff:3.500A) removed outlier: 6.979A pdb=" N THR B 199 " --> pdb=" O PHE B 266 " (cutoff:3.500A) removed outlier: 8.209A pdb=" N CYS B 201 " --> pdb=" O PRO B 268 " (cutoff:3.500A) removed outlier: 10.884A pdb=" N PHE B 270 " --> pdb=" O CYS B 201 " (cutoff:3.500A) removed outlier: 13.208A pdb=" N ASP B 203 " --> pdb=" O PHE B 270 " (cutoff:3.500A) removed outlier: 6.868A pdb=" N PHE B 265 " --> pdb=" O SER B 371 " (cutoff:3.500A) removed outlier: 4.710A pdb=" N SER B 371 " --> pdb=" O PHE B 265 " (cutoff:3.500A) removed outlier: 6.913A pdb=" N SER B 364 " --> pdb=" O PHE B 317 " (cutoff:3.500A) removed outlier: 4.830A pdb=" N PHE B 317 " --> pdb=" O SER B 364 " (cutoff:3.500A) removed outlier: 6.665A pdb=" N THR B 366 " --> pdb=" O ALA B 315 " (cutoff:3.500A) removed outlier: 4.600A pdb=" N ALA B 315 " --> pdb=" O THR B 366 " (cutoff:3.500A) removed outlier: 6.780A pdb=" N ILE B 368 " --> pdb=" O VAL B 313 " (cutoff:3.500A) removed outlier: 4.501A pdb=" N VAL B 313 " --> pdb=" O ILE B 368 " (cutoff:3.500A) removed outlier: 6.751A pdb=" N ASN B 370 " --> pdb=" O LEU B 311 " (cutoff:3.500A) removed outlier: 8.545A pdb=" N LYS B 350 " --> pdb=" O LEU B 311 " (cutoff:3.500A) removed outlier: 6.471A pdb=" N VAL B 313 " --> pdb=" O LYS B 350 " (cutoff:3.500A) removed outlier: 8.000A pdb=" N ALA B 352 " --> pdb=" O VAL B 313 " (cutoff:3.500A) removed outlier: 6.319A pdb=" N ALA B 315 " --> pdb=" O ALA B 352 " (cutoff:3.500A) removed outlier: 7.762A pdb=" N CYS B 354 " --> pdb=" O ALA B 315 " (cutoff:3.500A) removed outlier: 6.306A pdb=" N PHE B 317 " --> pdb=" O CYS B 354 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 51 through 52 303 hydrogen bonds defined for protein. 870 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: 1.96 Time building geometry restraints manager: 1.85 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 2212 1.34 - 1.46: 1547 1.46 - 1.58: 3004 1.58 - 1.70: 10 1.70 - 1.82: 74 Bond restraints: 6847 Sorted by residual: bond pdb=" CG1 ILE A 122 " pdb=" CD1 ILE A 122 " ideal model delta sigma weight residual 1.513 1.456 0.057 3.90e-02 6.57e+02 2.16e+00 bond pdb=" CG1 ILE A 234 " pdb=" CD1 ILE A 234 " ideal model delta sigma weight residual 1.513 1.468 0.045 3.90e-02 6.57e+02 1.34e+00 bond pdb=" CA THR B 219 " pdb=" C THR B 219 " ideal model delta sigma weight residual 1.531 1.524 0.007 7.40e-03 1.83e+04 9.16e-01 bond pdb=" CB GLN A 35 " pdb=" CG GLN A 35 " ideal model delta sigma weight residual 1.520 1.546 -0.026 3.00e-02 1.11e+03 7.53e-01 bond pdb=" CG GLN B 245 " pdb=" CD GLN B 245 " ideal model delta sigma weight residual 1.516 1.537 -0.021 2.50e-02 1.60e+03 7.31e-01 ... (remaining 6842 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.38: 8946 1.38 - 2.75: 291 2.75 - 4.13: 47 4.13 - 5.51: 11 5.51 - 6.89: 7 Bond angle restraints: 9302 Sorted by residual: angle pdb=" C THR B 218 " pdb=" N THR B 219 " pdb=" CA THR B 219 " ideal model delta sigma weight residual 122.83 126.19 -3.36 1.08e+00 8.57e-01 9.67e+00 angle pdb=" C PRO B 261 " pdb=" N ARG B 262 " pdb=" CA ARG B 262 " ideal model delta sigma weight residual 124.82 129.55 -4.73 1.78e+00 3.16e-01 7.07e+00 angle pdb=" CA MET A 317 " pdb=" CB MET A 317 " pdb=" CG MET A 317 " ideal model delta sigma weight residual 114.10 119.02 -4.92 2.00e+00 2.50e-01 6.06e+00 angle pdb=" CB MET B 300 " pdb=" CG MET B 300 " pdb=" SD MET B 300 " ideal model delta sigma weight residual 112.70 119.59 -6.89 3.00e+00 1.11e-01 5.27e+00 angle pdb=" C2' GTP A 501 " pdb=" C3' GTP A 501 " pdb=" C4' GTP A 501 " ideal model delta sigma weight residual 111.00 104.56 6.44 3.00e+00 1.11e-01 4.60e+00 ... (remaining 9297 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 33.24: 3956 33.24 - 66.49: 85 66.49 - 99.73: 21 99.73 - 132.97: 2 132.97 - 166.22: 3 Dihedral angle restraints: 4067 sinusoidal: 1630 harmonic: 2437 Sorted by residual: dihedral pdb=" C8 GTP A 501 " pdb=" C1' GTP A 501 " pdb=" N9 GTP A 501 " pdb=" O4' GTP A 501 " ideal model delta sinusoidal sigma weight residual 104.59 -61.62 166.22 1 2.00e+01 2.50e-03 4.73e+01 dihedral pdb=" C5' GTP B 501 " pdb=" O5' GTP B 501 " pdb=" PA GTP B 501 " pdb=" O3A GTP B 501 " ideal model delta sinusoidal sigma weight residual 69.27 -128.12 -162.61 1 2.00e+01 2.50e-03 4.69e+01 dihedral pdb=" C5' GTP A 501 " pdb=" O5' GTP A 501 " pdb=" PA GTP A 501 " pdb=" O3A GTP A 501 " ideal model delta sinusoidal sigma weight residual 69.27 -82.06 151.33 1 2.00e+01 2.50e-03 4.51e+01 ... (remaining 4064 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.050: 792 0.050 - 0.100: 190 0.100 - 0.150: 38 0.150 - 0.200: 0 0.200 - 0.250: 1 Chirality restraints: 1021 Sorted by residual: chirality pdb=" CG LEU A 425 " pdb=" CB LEU A 425 " pdb=" CD1 LEU A 425 " pdb=" CD2 LEU A 425 " both_signs ideal model delta sigma weight residual False -2.59 -2.34 -0.25 2.00e-01 2.50e+01 1.57e+00 chirality pdb=" CA GLU B 181 " pdb=" N GLU B 181 " pdb=" C GLU B 181 " pdb=" CB GLU B 181 " both_signs ideal model delta sigma weight residual False 2.51 2.37 0.14 2.00e-01 2.50e+01 5.02e-01 chirality pdb=" CA LEU A 425 " pdb=" N LEU A 425 " pdb=" C LEU A 425 " pdb=" CB LEU A 425 " both_signs ideal model delta sigma weight residual False 2.51 2.38 0.13 2.00e-01 2.50e+01 4.47e-01 ... (remaining 1018 not shown) Planarity restraints: 1206 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C PHE B 260 " -0.044 5.00e-02 4.00e+02 6.68e-02 7.14e+00 pdb=" N PRO B 261 " 0.116 5.00e-02 4.00e+02 pdb=" CA PRO B 261 " -0.035 5.00e-02 4.00e+02 pdb=" CD PRO B 261 " -0.037 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C MET B 267 " 0.044 5.00e-02 4.00e+02 6.64e-02 7.06e+00 pdb=" N PRO B 268 " -0.115 5.00e-02 4.00e+02 pdb=" CA PRO B 268 " 0.035 5.00e-02 4.00e+02 pdb=" CD PRO B 268 " 0.036 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ALA B 271 " -0.032 5.00e-02 4.00e+02 4.93e-02 3.88e+00 pdb=" N PRO B 272 " 0.085 5.00e-02 4.00e+02 pdb=" CA PRO B 272 " -0.028 5.00e-02 4.00e+02 pdb=" CD PRO B 272 " -0.025 5.00e-02 4.00e+02 ... (remaining 1203 not shown) Histogram of nonbonded interaction distances: 2.03 - 2.61: 88 2.61 - 3.18: 6002 3.18 - 3.75: 10602 3.75 - 4.33: 14901 4.33 - 4.90: 24707 Nonbonded interactions: 56300 Sorted by model distance: nonbonded pdb=" O2B GTP A 501 " pdb="MG MG A 502 " model vdw 2.033 2.170 nonbonded pdb=" O GLY B 141 " pdb=" OG SER B 145 " model vdw 2.143 3.040 nonbonded pdb=" OD1 ASN A 186 " pdb=" OH TYR A 408 " model vdw 2.184 3.040 nonbonded pdb=" O GLY A 416 " pdb=" OG SER A 419 " model vdw 2.184 3.040 nonbonded pdb=" OH TYR A 210 " pdb=" NH1 ARG A 221 " model vdw 2.185 3.120 ... (remaining 56295 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=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: 6.210 Set stop_for_unknowns flag: 0.010 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.320 Check model and map are aligned: 0.050 Set scattering table: 0.070 Process input model: 20.040 Find NCS groups from input model: 0.110 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.960 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 29.800 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7560 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 : 0.004 0.057 6847 Z= 0.270 Angle : 0.616 6.887 9302 Z= 0.324 Chirality : 0.044 0.250 1021 Planarity : 0.005 0.067 1206 Dihedral : 16.741 166.216 2503 Min Nonbonded Distance : 2.033 Molprobity Statistics. All-atom Clashscore : 11.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.48 % Favored : 96.52 % Rotamer: Outliers : 0.00 % Allowed : 0.56 % Favored : 99.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.13 % 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 (0.29), residues: 834 helix: 0.70 (0.27), residues: 362 sheet: -0.69 (0.45), residues: 127 loop : -0.56 (0.34), residues: 345 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 21 HIS 0.006 0.001 HIS A 266 PHE 0.011 0.002 PHE A 138 TYR 0.017 0.002 TYR B 36 ARG 0.003 0.000 ARG A 79 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1668 Ramachandran restraints generated. 834 Oldfield, 0 Emsley, 834 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1668 Ramachandran restraints generated. 834 Oldfield, 0 Emsley, 834 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 179 residues out of total 718 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 179 time to evaluate : 0.830 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1 MET cc_start: 0.3969 (tmm) cc_final: 0.3313 (tmm) REVERT: A 27 GLU cc_start: 0.6970 (tp30) cc_final: 0.6656 (tp30) REVERT: A 155 GLU cc_start: 0.6877 (mt-10) cc_final: 0.6578 (mt-10) REVERT: A 311 LYS cc_start: 0.7075 (mtpp) cc_final: 0.6317 (mmtp) REVERT: B 23 ILE cc_start: 0.8787 (mm) cc_final: 0.8586 (mm) REVERT: B 30 ILE cc_start: 0.6442 (mt) cc_final: 0.6235 (mt) REVERT: B 69 GLU cc_start: 0.6817 (pt0) cc_final: 0.6412 (pm20) REVERT: B 108 GLU cc_start: 0.6631 (mm-30) cc_final: 0.6351 (tt0) REVERT: B 202 ILE cc_start: 0.8107 (mm) cc_final: 0.7907 (mt) REVERT: B 207 LEU cc_start: 0.8440 (mm) cc_final: 0.8202 (mm) REVERT: B 256 ASN cc_start: 0.7642 (t160) cc_final: 0.7439 (t0) REVERT: B 257 MET cc_start: 0.8263 (mmm) cc_final: 0.7295 (mmt) outliers start: 0 outliers final: 0 residues processed: 179 average time/residue: 0.1858 time to fit residues: 44.2089 Evaluate side-chains 130 residues out of total 718 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 130 time to evaluate : 0.741 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 83 random chunks: chunk 70 optimal weight: 8.9990 chunk 62 optimal weight: 1.9990 chunk 34 optimal weight: 6.9990 chunk 21 optimal weight: 3.9990 chunk 42 optimal weight: 8.9990 chunk 33 optimal weight: 8.9990 chunk 65 optimal weight: 3.9990 chunk 25 optimal weight: 7.9990 chunk 39 optimal weight: 0.5980 chunk 48 optimal weight: 2.9990 chunk 75 optimal weight: 0.9990 overall best weight: 2.1188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 206 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 8 GLN B 48 ASN B 134 GLN B 375 GLN ** B 414 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7571 moved from start: 0.1299 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.058 6847 Z= 0.240 Angle : 0.607 6.376 9302 Z= 0.313 Chirality : 0.045 0.220 1021 Planarity : 0.005 0.067 1206 Dihedral : 12.453 165.904 942 Min Nonbonded Distance : 1.945 Molprobity Statistics. All-atom Clashscore : 8.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.88 % Favored : 97.12 % Rotamer: Outliers : 1.67 % Allowed : 10.45 % Favored : 87.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.13 % 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: 0.11 (0.29), residues: 834 helix: 1.03 (0.27), residues: 365 sheet: -0.64 (0.45), residues: 132 loop : -0.58 (0.34), residues: 337 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A 346 HIS 0.006 0.001 HIS A 309 PHE 0.021 0.002 PHE A 49 TYR 0.015 0.001 TYR A 262 ARG 0.004 0.000 ARG B 309 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1668 Ramachandran restraints generated. 834 Oldfield, 0 Emsley, 834 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1668 Ramachandran restraints generated. 834 Oldfield, 0 Emsley, 834 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 156 residues out of total 718 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 144 time to evaluate : 0.768 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 1 MET cc_start: 0.3745 (tmm) cc_final: 0.2946 (tmm) REVERT: A 155 GLU cc_start: 0.6867 (mt-10) cc_final: 0.6540 (mt-10) REVERT: A 311 LYS cc_start: 0.7042 (mtpp) cc_final: 0.6543 (mmtm) REVERT: B 69 GLU cc_start: 0.6835 (pt0) cc_final: 0.6269 (pm20) REVERT: B 108 GLU cc_start: 0.6604 (mm-30) cc_final: 0.6300 (tt0) REVERT: B 154 LYS cc_start: 0.8385 (mmtt) cc_final: 0.8073 (mmtm) REVERT: B 207 LEU cc_start: 0.8473 (mm) cc_final: 0.8263 (mm) REVERT: B 256 ASN cc_start: 0.7602 (t0) cc_final: 0.7353 (t0) REVERT: B 257 MET cc_start: 0.8203 (mmm) cc_final: 0.7175 (mmt) REVERT: B 412 GLU cc_start: 0.7999 (pt0) cc_final: 0.7686 (pt0) outliers start: 12 outliers final: 7 residues processed: 151 average time/residue: 0.1743 time to fit residues: 36.0225 Evaluate side-chains 138 residues out of total 718 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 131 time to evaluate : 0.754 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 73 THR Chi-restraints excluded: chain A residue 150 THR Chi-restraints excluded: chain A residue 308 ARG Chi-restraints excluded: chain B residue 72 THR Chi-restraints excluded: chain B residue 135 LEU Chi-restraints excluded: chain B residue 180 VAL Chi-restraints excluded: chain B residue 193 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 83 random chunks: chunk 41 optimal weight: 2.9990 chunk 23 optimal weight: 6.9990 chunk 62 optimal weight: 5.9990 chunk 51 optimal weight: 10.0000 chunk 20 optimal weight: 6.9990 chunk 75 optimal weight: 1.9990 chunk 81 optimal weight: 6.9990 chunk 67 optimal weight: 3.9990 chunk 74 optimal weight: 2.9990 chunk 25 optimal weight: 0.4980 chunk 60 optimal weight: 1.9990 overall best weight: 2.0988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 15 GLN A 206 ASN ** B 414 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7570 moved from start: 0.1607 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 6847 Z= 0.224 Angle : 0.578 7.274 9302 Z= 0.298 Chirality : 0.044 0.177 1021 Planarity : 0.005 0.067 1206 Dihedral : 12.410 166.288 942 Min Nonbonded Distance : 1.954 Molprobity Statistics. All-atom Clashscore : 8.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.52 % Favored : 97.48 % Rotamer: Outliers : 1.95 % Allowed : 12.40 % Favored : 85.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.13 % 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: 0.15 (0.29), residues: 834 helix: 1.15 (0.27), residues: 367 sheet: -0.57 (0.44), residues: 136 loop : -0.70 (0.33), residues: 331 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 101 HIS 0.004 0.001 HIS A 283 PHE 0.014 0.001 PHE A 49 TYR 0.011 0.001 TYR A 210 ARG 0.003 0.000 ARG A 79 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1668 Ramachandran restraints generated. 834 Oldfield, 0 Emsley, 834 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1668 Ramachandran restraints generated. 834 Oldfield, 0 Emsley, 834 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 159 residues out of total 718 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 145 time to evaluate : 0.703 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 1 MET cc_start: 0.3574 (tmm) cc_final: 0.2668 (tmm) REVERT: A 155 GLU cc_start: 0.6844 (mt-10) cc_final: 0.6563 (mt-10) REVERT: A 311 LYS cc_start: 0.7070 (mtpp) cc_final: 0.6528 (mmtp) REVERT: B 69 GLU cc_start: 0.6801 (pt0) cc_final: 0.6121 (pm20) REVERT: B 108 GLU cc_start: 0.6658 (mm-30) cc_final: 0.6295 (tt0) REVERT: B 154 LYS cc_start: 0.8366 (mmtt) cc_final: 0.8060 (mmtm) REVERT: B 207 LEU cc_start: 0.8500 (mm) cc_final: 0.8221 (mm) REVERT: B 256 ASN cc_start: 0.7541 (t0) cc_final: 0.7274 (t0) REVERT: B 257 MET cc_start: 0.8158 (mmm) cc_final: 0.7126 (mmt) REVERT: B 293 MET cc_start: 0.7065 (ptm) cc_final: 0.6804 (ttp) REVERT: B 412 GLU cc_start: 0.8043 (pt0) cc_final: 0.7687 (pt0) outliers start: 14 outliers final: 10 residues processed: 155 average time/residue: 0.1834 time to fit residues: 38.2820 Evaluate side-chains 136 residues out of total 718 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 126 time to evaluate : 0.863 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain A residue 73 THR Chi-restraints excluded: chain A residue 150 THR Chi-restraints excluded: chain A residue 207 GLU Chi-restraints excluded: chain A residue 308 ARG Chi-restraints excluded: chain A residue 382 THR Chi-restraints excluded: chain B residue 72 THR Chi-restraints excluded: chain B residue 135 LEU Chi-restraints excluded: chain B residue 180 VAL Chi-restraints excluded: chain B residue 193 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 83 random chunks: chunk 74 optimal weight: 2.9990 chunk 56 optimal weight: 5.9990 chunk 39 optimal weight: 7.9990 chunk 8 optimal weight: 7.9990 chunk 36 optimal weight: 2.9990 chunk 50 optimal weight: 7.9990 chunk 75 optimal weight: 6.9990 chunk 80 optimal weight: 0.0870 chunk 71 optimal weight: 3.9990 chunk 21 optimal weight: 6.9990 chunk 66 optimal weight: 0.7980 overall best weight: 2.1764 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 100 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 190 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7572 moved from start: 0.1891 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 6847 Z= 0.229 Angle : 0.577 8.757 9302 Z= 0.297 Chirality : 0.044 0.175 1021 Planarity : 0.005 0.066 1206 Dihedral : 12.383 166.539 942 Min Nonbonded Distance : 1.951 Molprobity Statistics. All-atom Clashscore : 8.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.40 % Favored : 97.60 % Rotamer: Outliers : 2.65 % Allowed : 13.79 % Favored : 83.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.13 % 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: 0.18 (0.29), residues: 834 helix: 1.17 (0.27), residues: 367 sheet: -0.48 (0.44), residues: 136 loop : -0.73 (0.33), residues: 331 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 101 HIS 0.005 0.001 HIS A 8 PHE 0.020 0.001 PHE B 367 TYR 0.010 0.001 TYR A 210 ARG 0.009 0.001 ARG A 320 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1668 Ramachandran restraints generated. 834 Oldfield, 0 Emsley, 834 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1668 Ramachandran restraints generated. 834 Oldfield, 0 Emsley, 834 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 160 residues out of total 718 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 141 time to evaluate : 0.678 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 1 MET cc_start: 0.3392 (tmm) cc_final: 0.2514 (tmm) REVERT: A 155 GLU cc_start: 0.6805 (mt-10) cc_final: 0.6532 (mt-10) REVERT: A 234 ILE cc_start: 0.8873 (mp) cc_final: 0.8623 (mp) REVERT: A 262 TYR cc_start: 0.7080 (m-80) cc_final: 0.6803 (m-80) REVERT: A 311 LYS cc_start: 0.7016 (mtpp) cc_final: 0.6695 (mmtm) REVERT: B 108 GLU cc_start: 0.6681 (mm-30) cc_final: 0.6397 (mm-30) REVERT: B 154 LYS cc_start: 0.8371 (mmtt) cc_final: 0.8068 (mmtm) REVERT: B 207 LEU cc_start: 0.8538 (mm) cc_final: 0.8237 (mm) REVERT: B 412 GLU cc_start: 0.8064 (OUTLIER) cc_final: 0.7646 (pt0) outliers start: 19 outliers final: 12 residues processed: 154 average time/residue: 0.1615 time to fit residues: 34.4077 Evaluate side-chains 143 residues out of total 718 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 130 time to evaluate : 0.737 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain A residue 73 THR Chi-restraints excluded: chain A residue 150 THR Chi-restraints excluded: chain A residue 181 VAL Chi-restraints excluded: chain A residue 207 GLU Chi-restraints excluded: chain A residue 308 ARG Chi-restraints excluded: chain A residue 375 VAL Chi-restraints excluded: chain A residue 425 LEU Chi-restraints excluded: chain A residue 433 GLU Chi-restraints excluded: chain B residue 72 THR Chi-restraints excluded: chain B residue 180 VAL Chi-restraints excluded: chain B residue 193 VAL Chi-restraints excluded: chain B residue 412 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 83 random chunks: chunk 45 optimal weight: 6.9990 chunk 1 optimal weight: 3.9990 chunk 59 optimal weight: 9.9990 chunk 33 optimal weight: 0.6980 chunk 68 optimal weight: 2.9990 chunk 55 optimal weight: 9.9990 chunk 0 optimal weight: 10.0000 chunk 40 optimal weight: 7.9990 chunk 72 optimal weight: 4.9990 chunk 20 optimal weight: 6.9990 chunk 26 optimal weight: 10.0000 overall best weight: 3.9388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 100 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 190 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 256 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7628 moved from start: 0.2140 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.049 6847 Z= 0.354 Angle : 0.655 9.323 9302 Z= 0.340 Chirality : 0.047 0.204 1021 Planarity : 0.006 0.072 1206 Dihedral : 12.739 168.044 942 Min Nonbonded Distance : 1.940 Molprobity Statistics. All-atom Clashscore : 11.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.08 % Favored : 95.92 % Rotamer: Outliers : 3.20 % Allowed : 15.74 % Favored : 81.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.13 % 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: -0.08 (0.29), residues: 834 helix: 0.93 (0.27), residues: 366 sheet: -0.46 (0.46), residues: 132 loop : -0.91 (0.33), residues: 336 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 101 HIS 0.007 0.001 HIS A 266 PHE 0.016 0.002 PHE B 20 TYR 0.013 0.002 TYR B 51 ARG 0.005 0.001 ARG A 79 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1668 Ramachandran restraints generated. 834 Oldfield, 0 Emsley, 834 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1668 Ramachandran restraints generated. 834 Oldfield, 0 Emsley, 834 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 156 residues out of total 718 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 133 time to evaluate : 0.739 Fit side-chains revert: symmetry clash REVERT: A 1 MET cc_start: 0.3480 (tmm) cc_final: 0.2762 (tmm) REVERT: A 154 MET cc_start: 0.7854 (mmt) cc_final: 0.7590 (mmt) REVERT: A 155 GLU cc_start: 0.6860 (mt-10) cc_final: 0.6626 (mt-10) REVERT: A 234 ILE cc_start: 0.8870 (OUTLIER) cc_final: 0.8582 (mp) REVERT: A 255 PHE cc_start: 0.7651 (OUTLIER) cc_final: 0.7350 (m-10) REVERT: A 262 TYR cc_start: 0.7074 (m-80) cc_final: 0.6852 (m-80) REVERT: A 311 LYS cc_start: 0.7183 (mtpp) cc_final: 0.6736 (mmtm) REVERT: B 154 LYS cc_start: 0.8387 (mmtt) cc_final: 0.8084 (mmtm) REVERT: B 207 LEU cc_start: 0.8563 (OUTLIER) cc_final: 0.8254 (mm) REVERT: B 412 GLU cc_start: 0.8087 (OUTLIER) cc_final: 0.7686 (pt0) outliers start: 23 outliers final: 16 residues processed: 146 average time/residue: 0.1695 time to fit residues: 33.9714 Evaluate side-chains 145 residues out of total 718 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 125 time to evaluate : 0.772 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 23 LEU Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain A residue 73 THR Chi-restraints excluded: chain A residue 150 THR Chi-restraints excluded: chain A residue 181 VAL Chi-restraints excluded: chain A residue 195 LEU Chi-restraints excluded: chain A residue 206 ASN Chi-restraints excluded: chain A residue 207 GLU Chi-restraints excluded: chain A residue 234 ILE Chi-restraints excluded: chain A residue 255 PHE Chi-restraints excluded: chain A residue 308 ARG Chi-restraints excluded: chain A residue 375 VAL Chi-restraints excluded: chain A residue 425 LEU Chi-restraints excluded: chain A residue 433 GLU Chi-restraints excluded: chain B residue 72 THR Chi-restraints excluded: chain B residue 135 LEU Chi-restraints excluded: chain B residue 180 VAL Chi-restraints excluded: chain B residue 207 LEU Chi-restraints excluded: chain B residue 335 ASN Chi-restraints excluded: chain B residue 412 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 83 random chunks: chunk 72 optimal weight: 2.9990 chunk 15 optimal weight: 4.9990 chunk 47 optimal weight: 6.9990 chunk 19 optimal weight: 0.9990 chunk 80 optimal weight: 1.9990 chunk 66 optimal weight: 4.9990 chunk 37 optimal weight: 2.9990 chunk 6 optimal weight: 3.9990 chunk 26 optimal weight: 0.9980 chunk 42 optimal weight: 0.9990 chunk 77 optimal weight: 7.9990 overall best weight: 1.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 100 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 256 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 332 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7564 moved from start: 0.2259 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 6847 Z= 0.194 Angle : 0.569 7.460 9302 Z= 0.295 Chirality : 0.043 0.176 1021 Planarity : 0.005 0.065 1206 Dihedral : 12.490 166.180 942 Min Nonbonded Distance : 1.974 Molprobity Statistics. All-atom Clashscore : 9.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.40 % Favored : 97.60 % Rotamer: Outliers : 2.51 % Allowed : 17.69 % Favored : 79.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.13 % 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: 0.11 (0.29), residues: 834 helix: 1.13 (0.27), residues: 368 sheet: -0.37 (0.46), residues: 136 loop : -0.89 (0.33), residues: 330 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 101 HIS 0.005 0.001 HIS A 8 PHE 0.022 0.001 PHE B 367 TYR 0.016 0.001 TYR A 210 ARG 0.004 0.000 ARG A 320 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1668 Ramachandran restraints generated. 834 Oldfield, 0 Emsley, 834 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1668 Ramachandran restraints generated. 834 Oldfield, 0 Emsley, 834 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 155 residues out of total 718 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 137 time to evaluate : 0.805 Fit side-chains revert: symmetry clash REVERT: A 1 MET cc_start: 0.3371 (tmm) cc_final: 0.2675 (tmm) REVERT: A 155 GLU cc_start: 0.6818 (mt-10) cc_final: 0.6589 (mt-10) REVERT: A 234 ILE cc_start: 0.8860 (OUTLIER) cc_final: 0.8565 (mp) REVERT: A 255 PHE cc_start: 0.7701 (OUTLIER) cc_final: 0.7448 (m-10) REVERT: A 279 GLU cc_start: 0.7292 (mp0) cc_final: 0.7060 (mp0) REVERT: A 311 LYS cc_start: 0.7140 (mtpp) cc_final: 0.6719 (mmtm) REVERT: A 433 GLU cc_start: 0.7530 (OUTLIER) cc_final: 0.7000 (mp0) REVERT: B 154 LYS cc_start: 0.8374 (mmtt) cc_final: 0.8063 (mmtm) REVERT: B 207 LEU cc_start: 0.8536 (mm) cc_final: 0.8239 (mm) REVERT: B 412 GLU cc_start: 0.8034 (OUTLIER) cc_final: 0.7621 (pt0) outliers start: 18 outliers final: 12 residues processed: 149 average time/residue: 0.1676 time to fit residues: 34.5971 Evaluate side-chains 147 residues out of total 718 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 131 time to evaluate : 0.898 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain A residue 73 THR Chi-restraints excluded: chain A residue 181 VAL Chi-restraints excluded: chain A residue 207 GLU Chi-restraints excluded: chain A residue 234 ILE Chi-restraints excluded: chain A residue 255 PHE Chi-restraints excluded: chain A residue 271 THR Chi-restraints excluded: chain A residue 308 ARG Chi-restraints excluded: chain A residue 375 VAL Chi-restraints excluded: chain A residue 409 VAL Chi-restraints excluded: chain A residue 425 LEU Chi-restraints excluded: chain A residue 433 GLU Chi-restraints excluded: chain B residue 69 GLU Chi-restraints excluded: chain B residue 72 THR Chi-restraints excluded: chain B residue 180 VAL Chi-restraints excluded: chain B residue 412 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 83 random chunks: chunk 9 optimal weight: 9.9990 chunk 45 optimal weight: 6.9990 chunk 58 optimal weight: 0.8980 chunk 67 optimal weight: 3.9990 chunk 44 optimal weight: 6.9990 chunk 79 optimal weight: 6.9990 chunk 50 optimal weight: 4.9990 chunk 48 optimal weight: 0.9990 chunk 36 optimal weight: 6.9990 chunk 49 optimal weight: 5.9990 chunk 31 optimal weight: 0.9980 overall best weight: 2.3786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 28 HIS ** B 100 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 190 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 256 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 332 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7585 moved from start: 0.2357 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 6847 Z= 0.245 Angle : 0.592 10.034 9302 Z= 0.305 Chirality : 0.044 0.176 1021 Planarity : 0.005 0.067 1206 Dihedral : 12.504 166.729 942 Min Nonbonded Distance : 1.951 Molprobity Statistics. All-atom Clashscore : 10.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.60 % Favored : 96.40 % Rotamer: Outliers : 3.34 % Allowed : 17.41 % Favored : 79.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.13 % 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: 0.11 (0.29), residues: 834 helix: 1.16 (0.27), residues: 367 sheet: -0.33 (0.46), residues: 136 loop : -0.93 (0.34), residues: 331 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP B 101 HIS 0.005 0.001 HIS A 8 PHE 0.016 0.001 PHE B 20 TYR 0.015 0.001 TYR A 210 ARG 0.004 0.000 ARG B 86 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1668 Ramachandran restraints generated. 834 Oldfield, 0 Emsley, 834 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1668 Ramachandran restraints generated. 834 Oldfield, 0 Emsley, 834 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 158 residues out of total 718 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 134 time to evaluate : 0.733 Fit side-chains REVERT: A 1 MET cc_start: 0.3245 (tmm) cc_final: 0.2620 (tmm) REVERT: A 155 GLU cc_start: 0.6853 (mt-10) cc_final: 0.6620 (mt-10) REVERT: A 234 ILE cc_start: 0.8848 (OUTLIER) cc_final: 0.8560 (mp) REVERT: A 255 PHE cc_start: 0.7705 (OUTLIER) cc_final: 0.7419 (m-10) REVERT: A 311 LYS cc_start: 0.7175 (mtpp) cc_final: 0.6767 (mmtm) REVERT: A 433 GLU cc_start: 0.7612 (OUTLIER) cc_final: 0.7044 (mp0) REVERT: B 154 LYS cc_start: 0.8380 (mmtt) cc_final: 0.8053 (mmtm) REVERT: B 207 LEU cc_start: 0.8537 (OUTLIER) cc_final: 0.8233 (mm) REVERT: B 412 GLU cc_start: 0.8044 (OUTLIER) cc_final: 0.7643 (pt0) outliers start: 24 outliers final: 18 residues processed: 149 average time/residue: 0.1718 time to fit residues: 34.9655 Evaluate side-chains 152 residues out of total 718 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 129 time to evaluate : 0.720 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain A residue 73 THR Chi-restraints excluded: chain A residue 150 THR Chi-restraints excluded: chain A residue 181 VAL Chi-restraints excluded: chain A residue 206 ASN Chi-restraints excluded: chain A residue 207 GLU Chi-restraints excluded: chain A residue 234 ILE Chi-restraints excluded: chain A residue 255 PHE Chi-restraints excluded: chain A residue 271 THR Chi-restraints excluded: chain A residue 308 ARG Chi-restraints excluded: chain A residue 375 VAL Chi-restraints excluded: chain A residue 409 VAL Chi-restraints excluded: chain A residue 425 LEU Chi-restraints excluded: chain A residue 433 GLU Chi-restraints excluded: chain B residue 69 GLU Chi-restraints excluded: chain B residue 72 THR Chi-restraints excluded: chain B residue 135 LEU Chi-restraints excluded: chain B residue 139 LEU Chi-restraints excluded: chain B residue 180 VAL Chi-restraints excluded: chain B residue 193 VAL Chi-restraints excluded: chain B residue 207 LEU Chi-restraints excluded: chain B residue 335 ASN Chi-restraints excluded: chain B residue 412 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 83 random chunks: chunk 47 optimal weight: 10.0000 chunk 24 optimal weight: 7.9990 chunk 15 optimal weight: 7.9990 chunk 50 optimal weight: 1.9990 chunk 54 optimal weight: 7.9990 chunk 39 optimal weight: 0.0870 chunk 7 optimal weight: 5.9990 chunk 62 optimal weight: 4.9990 chunk 72 optimal weight: 4.9990 chunk 76 optimal weight: 9.9990 chunk 69 optimal weight: 0.2980 overall best weight: 2.4764 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 100 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 190 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 256 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 332 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7587 moved from start: 0.2435 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 6847 Z= 0.247 Angle : 0.600 8.706 9302 Z= 0.310 Chirality : 0.044 0.175 1021 Planarity : 0.006 0.068 1206 Dihedral : 12.523 166.698 942 Min Nonbonded Distance : 1.960 Molprobity Statistics. All-atom Clashscore : 10.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.88 % Favored : 97.12 % Rotamer: Outliers : 3.34 % Allowed : 17.55 % Favored : 79.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.13 % 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 (0.29), residues: 834 helix: 1.15 (0.27), residues: 367 sheet: -0.39 (0.47), residues: 133 loop : -0.91 (0.34), residues: 334 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP B 101 HIS 0.005 0.001 HIS A 8 PHE 0.024 0.002 PHE B 367 TYR 0.014 0.001 TYR A 210 ARG 0.007 0.000 ARG A 221 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1668 Ramachandran restraints generated. 834 Oldfield, 0 Emsley, 834 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1668 Ramachandran restraints generated. 834 Oldfield, 0 Emsley, 834 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 157 residues out of total 718 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 133 time to evaluate : 0.771 Fit side-chains REVERT: A 1 MET cc_start: 0.3331 (tmm) cc_final: 0.2672 (tmm) REVERT: A 234 ILE cc_start: 0.8838 (OUTLIER) cc_final: 0.8536 (mp) REVERT: A 255 PHE cc_start: 0.7722 (OUTLIER) cc_final: 0.7434 (m-10) REVERT: A 311 LYS cc_start: 0.7195 (mtpp) cc_final: 0.6778 (mmtm) REVERT: A 433 GLU cc_start: 0.7601 (OUTLIER) cc_final: 0.7029 (mp0) REVERT: B 154 LYS cc_start: 0.8396 (mmtt) cc_final: 0.8071 (mmtm) REVERT: B 207 LEU cc_start: 0.8551 (OUTLIER) cc_final: 0.8242 (mm) REVERT: B 412 GLU cc_start: 0.8042 (OUTLIER) cc_final: 0.7650 (pt0) outliers start: 24 outliers final: 17 residues processed: 148 average time/residue: 0.1582 time to fit residues: 32.5497 Evaluate side-chains 155 residues out of total 718 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 133 time to evaluate : 0.742 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain A residue 73 THR Chi-restraints excluded: chain A residue 150 THR Chi-restraints excluded: chain A residue 181 VAL Chi-restraints excluded: chain A residue 206 ASN Chi-restraints excluded: chain A residue 207 GLU Chi-restraints excluded: chain A residue 234 ILE Chi-restraints excluded: chain A residue 255 PHE Chi-restraints excluded: chain A residue 271 THR Chi-restraints excluded: chain A residue 308 ARG Chi-restraints excluded: chain A residue 375 VAL Chi-restraints excluded: chain A residue 409 VAL Chi-restraints excluded: chain A residue 433 GLU Chi-restraints excluded: chain B residue 69 GLU Chi-restraints excluded: chain B residue 72 THR Chi-restraints excluded: chain B residue 135 LEU Chi-restraints excluded: chain B residue 139 LEU Chi-restraints excluded: chain B residue 180 VAL Chi-restraints excluded: chain B residue 193 VAL Chi-restraints excluded: chain B residue 207 LEU Chi-restraints excluded: chain B residue 335 ASN Chi-restraints excluded: chain B residue 412 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 83 random chunks: chunk 74 optimal weight: 6.9990 chunk 76 optimal weight: 0.5980 chunk 44 optimal weight: 7.9990 chunk 32 optimal weight: 6.9990 chunk 58 optimal weight: 2.9990 chunk 22 optimal weight: 2.9990 chunk 67 optimal weight: 1.9990 chunk 70 optimal weight: 2.9990 chunk 48 optimal weight: 9.9990 chunk 78 optimal weight: 0.9990 chunk 37 optimal weight: 5.9990 overall best weight: 1.9188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 100 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 256 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 332 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7569 moved from start: 0.2501 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 6847 Z= 0.212 Angle : 0.600 10.230 9302 Z= 0.307 Chirality : 0.044 0.181 1021 Planarity : 0.005 0.066 1206 Dihedral : 12.445 166.189 942 Min Nonbonded Distance : 1.964 Molprobity Statistics. All-atom Clashscore : 10.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.12 % Favored : 96.88 % Rotamer: Outliers : 3.48 % Allowed : 18.25 % Favored : 78.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.13 % 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 (0.29), residues: 834 helix: 1.19 (0.27), residues: 367 sheet: -0.34 (0.48), residues: 133 loop : -0.93 (0.33), residues: 334 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP B 101 HIS 0.005 0.001 HIS A 8 PHE 0.021 0.001 PHE A 49 TYR 0.011 0.001 TYR A 210 ARG 0.003 0.000 ARG B 86 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1668 Ramachandran restraints generated. 834 Oldfield, 0 Emsley, 834 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1668 Ramachandran restraints generated. 834 Oldfield, 0 Emsley, 834 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 158 residues out of total 718 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 133 time to evaluate : 0.757 Fit side-chains REVERT: A 1 MET cc_start: 0.3334 (tmm) cc_final: 0.2705 (tmm) REVERT: A 234 ILE cc_start: 0.8829 (OUTLIER) cc_final: 0.8536 (mp) REVERT: A 255 PHE cc_start: 0.7742 (OUTLIER) cc_final: 0.7510 (m-10) REVERT: A 279 GLU cc_start: 0.7100 (mp0) cc_final: 0.6867 (mp0) REVERT: A 311 LYS cc_start: 0.7178 (mtpp) cc_final: 0.6943 (mptt) REVERT: A 433 GLU cc_start: 0.7585 (OUTLIER) cc_final: 0.7017 (mp0) REVERT: B 154 LYS cc_start: 0.8395 (mmtt) cc_final: 0.8069 (mmtm) REVERT: B 207 LEU cc_start: 0.8549 (OUTLIER) cc_final: 0.8239 (mm) REVERT: B 412 GLU cc_start: 0.8024 (OUTLIER) cc_final: 0.7628 (pt0) outliers start: 25 outliers final: 18 residues processed: 148 average time/residue: 0.1609 time to fit residues: 32.8716 Evaluate side-chains 152 residues out of total 718 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 129 time to evaluate : 0.739 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain A residue 73 THR Chi-restraints excluded: chain A residue 150 THR Chi-restraints excluded: chain A residue 181 VAL Chi-restraints excluded: chain A residue 206 ASN Chi-restraints excluded: chain A residue 207 GLU Chi-restraints excluded: chain A residue 234 ILE Chi-restraints excluded: chain A residue 255 PHE Chi-restraints excluded: chain A residue 271 THR Chi-restraints excluded: chain A residue 308 ARG Chi-restraints excluded: chain A residue 375 VAL Chi-restraints excluded: chain A residue 409 VAL Chi-restraints excluded: chain A residue 425 LEU Chi-restraints excluded: chain A residue 433 GLU Chi-restraints excluded: chain B residue 69 GLU Chi-restraints excluded: chain B residue 72 THR Chi-restraints excluded: chain B residue 135 LEU Chi-restraints excluded: chain B residue 139 LEU Chi-restraints excluded: chain B residue 166 THR Chi-restraints excluded: chain B residue 180 VAL Chi-restraints excluded: chain B residue 193 VAL Chi-restraints excluded: chain B residue 207 LEU Chi-restraints excluded: chain B residue 412 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 83 random chunks: chunk 54 optimal weight: 7.9990 chunk 82 optimal weight: 4.9990 chunk 76 optimal weight: 0.9980 chunk 65 optimal weight: 3.9990 chunk 6 optimal weight: 0.9980 chunk 50 optimal weight: 8.9990 chunk 40 optimal weight: 7.9990 chunk 52 optimal weight: 10.0000 chunk 70 optimal weight: 7.9990 chunk 20 optimal weight: 1.9990 chunk 60 optimal weight: 5.9990 overall best weight: 2.5986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 206 ASN ** B 100 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 256 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 332 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7590 moved from start: 0.2536 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 6847 Z= 0.258 Angle : 0.632 10.759 9302 Z= 0.324 Chirality : 0.045 0.209 1021 Planarity : 0.005 0.068 1206 Dihedral : 12.525 166.729 942 Min Nonbonded Distance : 1.957 Molprobity Statistics. All-atom Clashscore : 10.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.72 % Favored : 96.28 % Rotamer: Outliers : 3.62 % Allowed : 18.38 % Favored : 77.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.13 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.03 (0.29), residues: 834 helix: 1.08 (0.26), residues: 367 sheet: -0.30 (0.48), residues: 132 loop : -0.99 (0.33), residues: 335 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP B 101 HIS 0.005 0.001 HIS A 8 PHE 0.025 0.002 PHE B 367 TYR 0.009 0.001 TYR A 161 ARG 0.004 0.000 ARG B 86 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1668 Ramachandran restraints generated. 834 Oldfield, 0 Emsley, 834 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1668 Ramachandran restraints generated. 834 Oldfield, 0 Emsley, 834 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 159 residues out of total 718 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 133 time to evaluate : 0.754 Fit side-chains REVERT: A 1 MET cc_start: 0.3400 (tmm) cc_final: 0.2788 (tmm) REVERT: A 234 ILE cc_start: 0.8830 (OUTLIER) cc_final: 0.8523 (mp) REVERT: A 255 PHE cc_start: 0.7745 (OUTLIER) cc_final: 0.7475 (m-10) REVERT: A 279 GLU cc_start: 0.7093 (mp0) cc_final: 0.6887 (mp0) REVERT: A 311 LYS cc_start: 0.7185 (mtpp) cc_final: 0.6788 (mmtm) REVERT: A 433 GLU cc_start: 0.7575 (OUTLIER) cc_final: 0.7002 (mp0) REVERT: B 154 LYS cc_start: 0.8399 (mmtt) cc_final: 0.8067 (mmtm) REVERT: B 207 LEU cc_start: 0.8555 (OUTLIER) cc_final: 0.8226 (mm) REVERT: B 412 GLU cc_start: 0.8018 (OUTLIER) cc_final: 0.7641 (pt0) outliers start: 26 outliers final: 19 residues processed: 149 average time/residue: 0.1755 time to fit residues: 35.6281 Evaluate side-chains 153 residues out of total 718 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 129 time to evaluate : 0.751 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain A residue 73 THR Chi-restraints excluded: chain A residue 150 THR Chi-restraints excluded: chain A residue 181 VAL Chi-restraints excluded: chain A residue 206 ASN Chi-restraints excluded: chain A residue 207 GLU Chi-restraints excluded: chain A residue 234 ILE Chi-restraints excluded: chain A residue 255 PHE Chi-restraints excluded: chain A residue 271 THR Chi-restraints excluded: chain A residue 308 ARG Chi-restraints excluded: chain A residue 375 VAL Chi-restraints excluded: chain A residue 409 VAL Chi-restraints excluded: chain A residue 425 LEU Chi-restraints excluded: chain A residue 433 GLU Chi-restraints excluded: chain B residue 69 GLU Chi-restraints excluded: chain B residue 72 THR Chi-restraints excluded: chain B residue 135 LEU Chi-restraints excluded: chain B residue 139 LEU Chi-restraints excluded: chain B residue 166 THR Chi-restraints excluded: chain B residue 180 VAL Chi-restraints excluded: chain B residue 193 VAL Chi-restraints excluded: chain B residue 207 LEU Chi-restraints excluded: chain B residue 335 ASN Chi-restraints excluded: chain B residue 412 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 83 random chunks: chunk 9 optimal weight: 4.9990 chunk 18 optimal weight: 8.9990 chunk 65 optimal weight: 4.9990 chunk 27 optimal weight: 20.0000 chunk 67 optimal weight: 5.9990 chunk 8 optimal weight: 6.9990 chunk 12 optimal weight: 0.0770 chunk 57 optimal weight: 0.9980 chunk 3 optimal weight: 6.9990 chunk 47 optimal weight: 0.8980 chunk 75 optimal weight: 6.9990 overall best weight: 2.3942 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 216 ASN ** B 100 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 256 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 332 ASN ** 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 = 0.4160 r_free = 0.4160 target = 0.164351 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3858 r_free = 0.3858 target = 0.139868 restraints weight = 10435.563| |-----------------------------------------------------------------------------| r_work (start): 0.3856 rms_B_bonded: 2.66 r_work: 0.3742 rms_B_bonded: 3.40 restraints_weight: 0.5000 r_work (final): 0.3742 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7772 moved from start: 0.2584 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 6847 Z= 0.245 Angle : 0.629 10.545 9302 Z= 0.321 Chirality : 0.045 0.201 1021 Planarity : 0.006 0.068 1206 Dihedral : 12.528 166.656 942 Min Nonbonded Distance : 1.963 Molprobity Statistics. All-atom Clashscore : 10.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.84 % Favored : 96.16 % Rotamer: Outliers : 3.48 % Allowed : 18.66 % Favored : 77.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.13 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.03 (0.29), residues: 834 helix: 1.09 (0.26), residues: 367 sheet: -0.31 (0.48), residues: 132 loop : -0.99 (0.33), residues: 335 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP B 101 HIS 0.005 0.001 HIS A 8 PHE 0.021 0.002 PHE A 49 TYR 0.015 0.001 TYR A 210 ARG 0.006 0.000 ARG A 229 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1874.45 seconds wall clock time: 34 minutes 34.18 seconds (2074.18 seconds total)