Starting phenix.real_space_refine on Thu May 9 12:53:52 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8uop_42435/05_2024/8uop_42435.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8uop_42435/05_2024/8uop_42435.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8uop_42435/05_2024/8uop_42435.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8uop_42435/05_2024/8uop_42435.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8uop_42435/05_2024/8uop_42435.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8uop_42435/05_2024/8uop_42435.pdb" } resolution = 3.8 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= 0.022 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 S 22 5.16 5 C 4182 2.51 5 N 1122 2.21 5 O 1318 1.98 5 H 6544 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 162": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A PHE 175": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A ASP 204": "OD1" <-> "OD2" Residue "A PHE 242": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A TYR 250": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A TYR 286": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A GLU 297": "OE1" <-> "OE2" Residue "A PHE 321": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A TYR 408": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B ASP 204": "OD1" <-> "OD2" Residue "B PHE 242": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B GLU 376": "OE1" <-> "OE2" Residue "B ASP 384": "OD1" <-> "OD2" Residue "B TYR 424": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B PHE 430": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5322/modules/chem_data/mon_lib" Total number of atoms: 13188 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 6594 Number of conformers: 1 Conformer: "" Number of residues, atoms: 436, 6594 Classifications: {'peptide': 436} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PTRANS': 11, 'TRANS': 424} Unresolved non-hydrogen bonds: 22 Unresolved non-hydrogen angles: 28 Unresolved non-hydrogen dihedrals: 18 Planarities with less than four sites: {'PHE:plan': 1, 'GLU:plan': 3, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 21 Chain: "B" Number of atoms: 6594 Number of conformers: 1 Conformer: "" Number of residues, atoms: 436, 6594 Classifications: {'peptide': 436} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PTRANS': 11, 'TRANS': 424} Unresolved non-hydrogen bonds: 22 Unresolved non-hydrogen angles: 28 Unresolved non-hydrogen dihedrals: 18 Planarities with less than four sites: {'PHE:plan': 1, 'GLU:plan': 3, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 21 Time building chain proxies: 5.93, per 1000 atoms: 0.45 Number of scatterers: 13188 At special positions: 0 Unit cell: (99.176, 76.538, 89.474, 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 22 16.00 O 1318 8.00 N 1122 7.00 C 4182 6.00 H 6544 1.00 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: 10.13 Conformation dependent library (CDL) restraints added in 1.3 seconds 1736 Ramachandran restraints generated. 868 Oldfield, 0 Emsley, 868 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: 36 helices and 6 sheets defined 40.9% alpha, 10.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.94 Creating SS restraints... Processing helix chain 'A' and resid 64 through 73 Processing helix chain 'A' and resid 74 through 78 Processing helix chain 'A' and resid 86 through 92 Processing helix chain 'A' and resid 93 through 99 removed outlier: 4.030A pdb=" N LEU A 97 " --> pdb=" O ALA A 93 " (cutoff:3.500A) Processing helix chain 'A' and resid 107 through 120 removed outlier: 3.731A pdb=" N VAL A 118 " --> pdb=" O VAL A 114 " (cutoff:3.500A) Processing helix chain 'A' and resid 121 through 126 Processing helix chain 'A' and resid 129 through 134 Processing helix chain 'A' and resid 153 through 156 removed outlier: 3.768A pdb=" N SER A 156 " --> pdb=" O GLY A 153 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 153 through 156' Processing helix chain 'A' and resid 176 through 197 removed outlier: 4.340A pdb=" N ARG A 180 " --> pdb=" O LYS A 176 " (cutoff:3.500A) removed outlier: 5.395A pdb=" N VAL A 185 " --> pdb=" O TRP A 181 " (cutoff:3.500A) removed outlier: 4.937A pdb=" N PHE A 186 " --> pdb=" O GLY A 182 " (cutoff:3.500A) removed outlier: 4.526A pdb=" N HIS A 187 " --> pdb=" O ALA A 183 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N ALA A 188 " --> pdb=" O GLU A 184 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N ILE A 192 " --> pdb=" O ALA A 188 " (cutoff:3.500A) removed outlier: 4.768A pdb=" N GLU A 195 " --> pdb=" O LYS A 191 " (cutoff:3.500A) Processing helix chain 'A' and resid 219 through 230 removed outlier: 3.892A pdb=" N LEU A 223 " --> pdb=" O VAL A 219 " (cutoff:3.500A) removed outlier: 3.915A pdb=" N ILE A 226 " --> pdb=" O ILE A 222 " (cutoff:3.500A) Processing helix chain 'A' and resid 245 through 250 Processing helix chain 'A' and resid 271 through 286 removed outlier: 4.555A pdb=" N VAL A 276 " --> pdb=" O SER A 272 " (cutoff:3.500A) removed outlier: 5.914A pdb=" N ASP A 277 " --> pdb=" O ALA A 273 " (cutoff:3.500A) removed outlier: 4.126A pdb=" N TYR A 278 " --> pdb=" O GLU A 274 " (cutoff:3.500A) removed outlier: 3.844A pdb=" N LEU A 279 " --> pdb=" O GLN A 275 " (cutoff:3.500A) removed outlier: 4.482A pdb=" N ASN A 284 " --> pdb=" O GLU A 280 " (cutoff:3.500A) removed outlier: 4.324A pdb=" N LYS A 285 " --> pdb=" O GLU A 281 " (cutoff:3.500A) Processing helix chain 'A' and resid 305 through 310 Processing helix chain 'A' and resid 325 through 335 removed outlier: 3.618A pdb=" N GLU A 335 " --> pdb=" O ARG A 331 " (cutoff:3.500A) Processing helix chain 'A' and resid 344 through 349 Processing helix chain 'A' and resid 350 through 364 Processing helix chain 'A' and resid 380 through 389 removed outlier: 3.826A pdb=" N ASP A 384 " --> pdb=" O SER A 380 " (cutoff:3.500A) removed outlier: 3.905A pdb=" N ILE A 385 " --> pdb=" O THR A 381 " (cutoff:3.500A) removed outlier: 5.190A pdb=" N ALA A 386 " --> pdb=" O ILE A 382 " (cutoff:3.500A) removed outlier: 4.051A pdb=" N VAL A 387 " --> pdb=" O ALA A 383 " (cutoff:3.500A) Processing helix chain 'A' and resid 401 through 416 removed outlier: 4.837A pdb=" N LYS A 407 " --> pdb=" O ASP A 403 " (cutoff:3.500A) removed outlier: 4.302A pdb=" N TYR A 408 " --> pdb=" O ARG A 404 " (cutoff:3.500A) removed outlier: 4.759A pdb=" N ARG A 413 " --> pdb=" O ASN A 409 " (cutoff:3.500A) removed outlier: 3.948A pdb=" N ILE A 414 " --> pdb=" O GLN A 410 " (cutoff:3.500A) Processing helix chain 'A' and resid 425 through 429 Processing helix chain 'B' and resid 64 through 73 removed outlier: 3.856A pdb=" N ASN B 70 " --> pdb=" O LYS B 66 " (cutoff:3.500A) removed outlier: 4.355A pdb=" N VAL B 71 " --> pdb=" O ALA B 67 " (cutoff:3.500A) Processing helix chain 'B' and resid 86 through 99 removed outlier: 3.538A pdb=" N ILE B 90 " --> pdb=" O ASP B 86 " (cutoff:3.500A) removed outlier: 4.099A pdb=" N ALA B 93 " --> pdb=" O ALA B 89 " (cutoff:3.500A) removed outlier: 3.960A pdb=" N MET B 94 " --> pdb=" O ILE B 90 " (cutoff:3.500A) removed outlier: 4.312A pdb=" N ILE B 95 " --> pdb=" O ASP B 91 " (cutoff:3.500A) removed outlier: 3.993A pdb=" N ALA B 96 " --> pdb=" O ARG B 92 " (cutoff:3.500A) removed outlier: 4.675A pdb=" N LEU B 97 " --> pdb=" O ALA B 93 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N ASP B 98 " --> pdb=" O MET B 94 " (cutoff:3.500A) Processing helix chain 'B' and resid 107 through 124 removed outlier: 3.656A pdb=" N SER B 115 " --> pdb=" O ILE B 111 " (cutoff:3.500A) removed outlier: 4.705A pdb=" N ALA B 122 " --> pdb=" O VAL B 118 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N ALA B 123 " --> pdb=" O ALA B 119 " (cutoff:3.500A) removed outlier: 4.342A pdb=" N ASP B 124 " --> pdb=" O ARG B 120 " (cutoff:3.500A) Processing helix chain 'B' and resid 130 through 134 removed outlier: 4.098A pdb=" N LEU B 134 " --> pdb=" O TYR B 131 " (cutoff:3.500A) Processing helix chain 'B' and resid 153 through 156 Processing helix chain 'B' and resid 174 through 188 removed outlier: 5.006A pdb=" N ARG B 180 " --> pdb=" O LYS B 176 " (cutoff:3.500A) removed outlier: 4.232A pdb=" N TRP B 181 " --> pdb=" O GLU B 177 " (cutoff:3.500A) removed outlier: 3.829A pdb=" N GLY B 182 " --> pdb=" O GLY B 178 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N ALA B 183 " --> pdb=" O LEU B 179 " (cutoff:3.500A) Processing helix chain 'B' and resid 192 through 196 Processing helix chain 'B' and resid 214 through 218 Processing helix chain 'B' and resid 219 through 228 removed outlier: 3.619A pdb=" N LYS B 224 " --> pdb=" O GLU B 220 " (cutoff:3.500A) removed outlier: 4.590A pdb=" N ALA B 225 " --> pdb=" O THR B 221 " (cutoff:3.500A) Processing helix chain 'B' and resid 271 through 285 removed outlier: 3.803A pdb=" N LEU B 282 " --> pdb=" O TYR B 278 " (cutoff:3.500A) Processing helix chain 'B' and resid 301 through 306 removed outlier: 3.791A pdb=" N VAL B 305 " --> pdb=" O ASP B 301 " (cutoff:3.500A) removed outlier: 3.844A pdb=" N LEU B 306 " --> pdb=" O GLY B 302 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 301 through 306' Processing helix chain 'B' and resid 325 through 336 removed outlier: 4.176A pdb=" N ILE B 333 " --> pdb=" O LEU B 329 " (cutoff:3.500A) Processing helix chain 'B' and resid 344 through 348 removed outlier: 3.555A pdb=" N ILE B 348 " --> pdb=" O VAL B 345 " (cutoff:3.500A) Processing helix chain 'B' and resid 350 through 363 Processing helix chain 'B' and resid 380 through 389 Processing helix chain 'B' and resid 401 through 419 removed outlier: 3.640A pdb=" N LYS B 407 " --> pdb=" O ASP B 403 " (cutoff:3.500A) Processing helix chain 'B' and resid 425 through 430 Processing sheet with id=AA1, first strand: chain 'A' and resid 6 through 7 Processing sheet with id=AA2, first strand: chain 'A' and resid 10 through 14 removed outlier: 3.641A pdb=" N ASN A 18 " --> pdb=" O ASP A 14 " (cutoff:3.500A) removed outlier: 4.282A pdb=" N LEU A 21 " --> pdb=" O VAL A 37 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 144 through 151 removed outlier: 6.480A pdb=" N ASN A 148 " --> pdb=" O ILE A 167 " (cutoff:3.500A) removed outlier: 7.526A pdb=" N ILE A 167 " --> pdb=" O ASN A 148 " (cutoff:3.500A) removed outlier: 4.657A pdb=" N ILE A 150 " --> pdb=" O PHE A 165 " (cutoff:3.500A) removed outlier: 4.198A pdb=" N GLU A 164 " --> pdb=" O ASP A 243 " (cutoff:3.500A) removed outlier: 7.410A pdb=" N ILE A 240 " --> pdb=" O ILE A 289 " (cutoff:3.500A) removed outlier: 6.217A pdb=" N ILE A 291 " --> pdb=" O ILE A 240 " (cutoff:3.500A) removed outlier: 6.658A pdb=" N PHE A 242 " --> pdb=" O ILE A 291 " (cutoff:3.500A) removed outlier: 7.218A pdb=" N ILE A 289 " --> pdb=" O GLN A 315 " (cutoff:3.500A) removed outlier: 7.327A pdb=" N VAL A 317 " --> pdb=" O ILE A 289 " (cutoff:3.500A) removed outlier: 6.130A pdb=" N ILE A 291 " --> pdb=" O VAL A 317 " (cutoff:3.500A) removed outlier: 6.381A pdb=" N LEU A 316 " --> pdb=" O SER A 340 " (cutoff:3.500A) removed outlier: 6.847A pdb=" N LEU A 342 " --> pdb=" O LEU A 316 " (cutoff:3.500A) removed outlier: 6.667A pdb=" N GLY A 318 " --> pdb=" O LEU A 342 " (cutoff:3.500A) removed outlier: 7.240A pdb=" N ALA A 368 " --> pdb=" O GLN A 393 " (cutoff:3.500A) removed outlier: 8.283A pdb=" N LYS A 395 " --> pdb=" O ALA A 368 " (cutoff:3.500A) removed outlier: 6.913A pdb=" N VAL A 370 " --> pdb=" O LYS A 395 " (cutoff:3.500A) removed outlier: 5.573A pdb=" N THR A 144 " --> pdb=" O ILE A 394 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 8 through 12 Processing sheet with id=AA5, first strand: chain 'B' and resid 239 through 243 removed outlier: 4.523A pdb=" N MET B 239 " --> pdb=" O MET B 168 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N MET B 168 " --> pdb=" O MET B 239 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N GLU B 164 " --> pdb=" O ASP B 243 " (cutoff:3.500A) removed outlier: 6.262A pdb=" N PHE B 165 " --> pdb=" O ILE B 149 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N GLN B 393 " --> pdb=" O ALA B 368 " (cutoff:3.500A) removed outlier: 6.992A pdb=" N ILE B 341 " --> pdb=" O VAL B 369 " (cutoff:3.500A) removed outlier: 7.517A pdb=" N SER B 371 " --> pdb=" O ILE B 341 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 290 through 292 removed outlier: 6.673A pdb=" N ILE B 291 " --> pdb=" O VAL B 317 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA6 206 hydrogen bonds defined for protein. 555 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: 4.28 Time building geometry restraints manager: 10.59 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.03: 6542 1.03 - 1.23: 6 1.23 - 1.42: 2788 1.42 - 1.62: 3916 1.62 - 1.81: 42 Bond restraints: 13294 Sorted by residual: bond pdb=" C TYR A 286 " pdb=" N PRO A 287 " ideal model delta sigma weight residual 1.332 1.363 -0.031 1.34e-02 5.57e+03 5.46e+00 bond pdb=" CA TYR A 286 " pdb=" CB TYR A 286 " ideal model delta sigma weight residual 1.528 1.559 -0.031 1.41e-02 5.03e+03 4.91e+00 bond pdb=" CB ASP B 299 " pdb=" CG ASP B 299 " ideal model delta sigma weight residual 1.516 1.571 -0.055 2.50e-02 1.60e+03 4.76e+00 bond pdb=" CA ASN A 236 " pdb=" CB ASN A 236 " ideal model delta sigma weight residual 1.530 1.560 -0.030 1.39e-02 5.18e+03 4.60e+00 bond pdb=" N MET B 168 " pdb=" CA MET B 168 " ideal model delta sigma weight residual 1.453 1.469 -0.015 9.20e-03 1.18e+04 2.83e+00 ... (remaining 13289 not shown) Histogram of bond angle deviations from ideal: 98.33 - 105.48: 102 105.48 - 112.63: 15384 112.63 - 119.78: 3726 119.78 - 126.93: 4762 126.93 - 134.08: 48 Bond angle restraints: 24022 Sorted by residual: angle pdb=" N ASP B 6 " pdb=" CA ASP B 6 " pdb=" C ASP B 6 " ideal model delta sigma weight residual 108.46 114.83 -6.37 1.51e+00 4.39e-01 1.78e+01 angle pdb=" N VAL B 421 " pdb=" CA VAL B 421 " pdb=" C VAL B 421 " ideal model delta sigma weight residual 106.21 110.24 -4.03 1.07e+00 8.73e-01 1.42e+01 angle pdb=" N ALA B 48 " pdb=" CA ALA B 48 " pdb=" C ALA B 48 " ideal model delta sigma weight residual 110.70 105.07 5.63 1.55e+00 4.16e-01 1.32e+01 angle pdb=" N LEU B 97 " pdb=" CA LEU B 97 " pdb=" C LEU B 97 " ideal model delta sigma weight residual 113.18 108.37 4.81 1.33e+00 5.65e-01 1.31e+01 angle pdb=" N THR B 200 " pdb=" CA THR B 200 " pdb=" C THR B 200 " ideal model delta sigma weight residual 107.57 114.21 -6.64 1.94e+00 2.66e-01 1.17e+01 ... (remaining 24017 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.46: 5396 17.46 - 34.91: 568 34.91 - 52.37: 182 52.37 - 69.83: 55 69.83 - 87.29: 11 Dihedral angle restraints: 6212 sinusoidal: 3390 harmonic: 2822 Sorted by residual: dihedral pdb=" CA GLU A 235 " pdb=" C GLU A 235 " pdb=" N ASN A 236 " pdb=" CA ASN A 236 " ideal model delta harmonic sigma weight residual 180.00 149.98 30.02 0 5.00e+00 4.00e-02 3.60e+01 dihedral pdb=" CA ALA B 228 " pdb=" C ALA B 228 " pdb=" N ALA B 229 " pdb=" CA ALA B 229 " ideal model delta harmonic sigma weight residual 180.00 150.71 29.29 0 5.00e+00 4.00e-02 3.43e+01 dihedral pdb=" CA ALA B 225 " pdb=" C ALA B 225 " pdb=" N ILE B 226 " pdb=" CA ILE B 226 " ideal model delta harmonic sigma weight residual 180.00 153.57 26.43 0 5.00e+00 4.00e-02 2.79e+01 ... (remaining 6209 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.036: 646 0.036 - 0.072: 267 0.072 - 0.109: 87 0.109 - 0.145: 23 0.145 - 0.181: 3 Chirality restraints: 1026 Sorted by residual: chirality pdb=" CB VAL A 219 " pdb=" CA VAL A 219 " pdb=" CG1 VAL A 219 " pdb=" CG2 VAL A 219 " both_signs ideal model delta sigma weight residual False -2.63 -2.45 -0.18 2.00e-01 2.50e+01 8.18e-01 chirality pdb=" CG LEU B 198 " pdb=" CB LEU B 198 " pdb=" CD1 LEU B 198 " pdb=" CD2 LEU B 198 " both_signs ideal model delta sigma weight residual False -2.59 -2.44 -0.15 2.00e-01 2.50e+01 5.87e-01 chirality pdb=" CA ILE A 288 " pdb=" N ILE A 288 " pdb=" C ILE A 288 " pdb=" CB ILE A 288 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.15 2.00e-01 2.50e+01 5.33e-01 ... (remaining 1023 not shown) Planarity restraints: 2046 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ALA B 225 " 0.013 2.00e-02 2.50e+03 2.56e-02 6.53e+00 pdb=" C ALA B 225 " -0.044 2.00e-02 2.50e+03 pdb=" O ALA B 225 " 0.016 2.00e-02 2.50e+03 pdb=" N ILE B 226 " 0.015 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR A 286 " 0.020 2.00e-02 2.50e+03 1.21e-02 4.39e+00 pdb=" CG TYR A 286 " -0.033 2.00e-02 2.50e+03 pdb=" CD1 TYR A 286 " -0.000 2.00e-02 2.50e+03 pdb=" CD2 TYR A 286 " 0.006 2.00e-02 2.50e+03 pdb=" CE1 TYR A 286 " 0.005 2.00e-02 2.50e+03 pdb=" CE2 TYR A 286 " 0.009 2.00e-02 2.50e+03 pdb=" CZ TYR A 286 " -0.003 2.00e-02 2.50e+03 pdb=" OH TYR A 286 " -0.002 2.00e-02 2.50e+03 pdb=" HD1 TYR A 286 " 0.002 2.00e-02 2.50e+03 pdb=" HD2 TYR A 286 " -0.009 2.00e-02 2.50e+03 pdb=" HE1 TYR A 286 " 0.001 2.00e-02 2.50e+03 pdb=" HE2 TYR A 286 " 0.006 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LEU B 193 " 0.010 2.00e-02 2.50e+03 1.93e-02 3.71e+00 pdb=" C LEU B 193 " -0.033 2.00e-02 2.50e+03 pdb=" O LEU B 193 " 0.012 2.00e-02 2.50e+03 pdb=" N LYS B 194 " 0.011 2.00e-02 2.50e+03 ... (remaining 2043 not shown) Histogram of nonbonded interaction distances: 1.46 - 2.09: 348 2.09 - 2.72: 22698 2.72 - 3.34: 37656 3.34 - 3.97: 45929 3.97 - 4.60: 72127 Nonbonded interactions: 178758 Sorted by model distance: nonbonded pdb=" HH TYR B 257 " pdb=" OD2 ASP B 299 " model vdw 1.459 1.850 nonbonded pdb=" H ASP B 293 " pdb=" O VAL B 317 " model vdw 1.486 1.850 nonbonded pdb=" OG SER B 246 " pdb=" H MET B 295 " model vdw 1.530 1.850 nonbonded pdb=" O ASN B 298 " pdb=" H TRP B 300 " model vdw 1.555 1.850 nonbonded pdb="HH11 ARG B 180 " pdb=" OE2 GLU B 184 " model vdw 1.573 1.850 ... (remaining 178753 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 'A' selection = chain 'B' } 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: 0.410 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: 0.190 Extract box with map and model: 2.700 Check model and map are aligned: 0.090 Set scattering table: 0.120 Process input model: 42.430 Find NCS groups from input model: 0.450 Set up NCS constraints: 0.040 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:2.510 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 48.940 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.1503 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 : 0.005 0.055 6750 Z= 0.304 Angle : 0.905 9.735 9128 Z= 0.547 Chirality : 0.045 0.181 1026 Planarity : 0.005 0.055 1198 Dihedral : 16.453 87.286 2470 Min Nonbonded Distance : 1.954 Molprobity Statistics. All-atom Clashscore : 17.97 Ramachandran Plot: Outliers : 0.69 % Allowed : 15.67 % Favored : 83.64 % Rotamer: Outliers : 0.73 % Allowed : 17.45 % Favored : 81.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.12 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.60 (0.25), residues: 868 helix: -1.37 (0.30), residues: 264 sheet: -2.50 (0.61), residues: 64 loop : -3.09 (0.24), residues: 540 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.005 TRP A 300 HIS 0.009 0.002 HIS B 0 PHE 0.018 0.003 PHE A 175 TYR 0.034 0.003 TYR A 286 ARG 0.010 0.001 ARG A 309 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1736 Ramachandran restraints generated. 868 Oldfield, 0 Emsley, 868 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1736 Ramachandran restraints generated. 868 Oldfield, 0 Emsley, 868 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 95 residues out of total 692 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 90 time to evaluate : 0.896 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 131 TYR cc_start: 0.0860 (p90) cc_final: 0.0132 (p90) REVERT: A 359 GLU cc_start: 0.1655 (tm-30) cc_final: -0.0744 (mt-10) REVERT: B 6 ASP cc_start: 0.5409 (p0) cc_final: 0.5123 (p0) REVERT: B 92 ARG cc_start: 0.3431 (mmt180) cc_final: 0.2180 (tpt90) REVERT: B 239 MET cc_start: 0.2235 (mmp) cc_final: 0.1922 (mmt) REVERT: B 360 MET cc_start: 0.0955 (tpt) cc_final: 0.0245 (mtp) outliers start: 5 outliers final: 2 residues processed: 95 average time/residue: 0.4161 time to fit residues: 52.9432 Evaluate side-chains 68 residues out of total 692 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 66 time to evaluate : 1.033 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 403 ASP Chi-restraints excluded: chain B residue 316 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 86 random chunks: chunk 72 optimal weight: 0.6980 chunk 65 optimal weight: 10.0000 chunk 36 optimal weight: 10.0000 chunk 22 optimal weight: 0.6980 chunk 43 optimal weight: 1.9990 chunk 34 optimal weight: 10.0000 chunk 67 optimal weight: 3.9990 chunk 26 optimal weight: 2.9990 chunk 40 optimal weight: 5.9990 chunk 50 optimal weight: 0.9980 chunk 78 optimal weight: 20.0000 overall best weight: 1.4784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.1878 moved from start: 0.2109 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 6750 Z= 0.208 Angle : 0.658 7.378 9128 Z= 0.355 Chirality : 0.042 0.154 1026 Planarity : 0.004 0.041 1198 Dihedral : 6.934 56.115 950 Min Nonbonded Distance : 2.024 Molprobity Statistics. All-atom Clashscore : 12.44 Ramachandran Plot: Outliers : 0.46 % Allowed : 12.10 % Favored : 87.44 % Rotamer: Outliers : 2.05 % Allowed : 17.45 % Favored : 80.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.39 (0.25), residues: 868 helix: -1.01 (0.30), residues: 265 sheet: -2.30 (0.66), residues: 63 loop : -3.09 (0.23), residues: 540 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 181 HIS 0.006 0.002 HIS B 0 PHE 0.013 0.002 PHE B 242 TYR 0.019 0.002 TYR A 278 ARG 0.003 0.000 ARG A 331 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1736 Ramachandran restraints generated. 868 Oldfield, 0 Emsley, 868 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1736 Ramachandran restraints generated. 868 Oldfield, 0 Emsley, 868 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 86 residues out of total 692 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 72 time to evaluate : 0.887 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 94 MET cc_start: 0.3455 (tpp) cc_final: 0.2967 (ttm) REVERT: A 131 TYR cc_start: 0.1015 (p90) cc_final: 0.0371 (p90) REVERT: A 359 GLU cc_start: 0.2270 (OUTLIER) cc_final: -0.0372 (mt-10) REVERT: B 92 ARG cc_start: 0.3191 (mmt180) cc_final: 0.2350 (tpt90) REVERT: B 239 MET cc_start: 0.2415 (mmp) cc_final: 0.1779 (mmt) REVERT: B 360 MET cc_start: 0.1284 (tpt) cc_final: 0.0360 (mtp) outliers start: 14 outliers final: 11 residues processed: 81 average time/residue: 0.4045 time to fit residues: 45.7751 Evaluate side-chains 78 residues out of total 692 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 66 time to evaluate : 0.907 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 0 HIS Chi-restraints excluded: chain A residue 359 GLU Chi-restraints excluded: chain A residue 403 ASP Chi-restraints excluded: chain B residue 6 ASP Chi-restraints excluded: chain B residue 100 THR Chi-restraints excluded: chain B residue 147 MET Chi-restraints excluded: chain B residue 170 VAL Chi-restraints excluded: chain B residue 204 ASP Chi-restraints excluded: chain B residue 271 THR Chi-restraints excluded: chain B residue 274 GLU Chi-restraints excluded: chain B residue 316 LEU Chi-restraints excluded: chain B residue 367 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 86 random chunks: chunk 43 optimal weight: 1.9990 chunk 24 optimal weight: 6.9990 chunk 64 optimal weight: 5.9990 chunk 53 optimal weight: 1.9990 chunk 21 optimal weight: 1.9990 chunk 78 optimal weight: 20.0000 chunk 84 optimal weight: 2.9990 chunk 69 optimal weight: 7.9990 chunk 77 optimal weight: 10.0000 chunk 26 optimal weight: 1.9990 chunk 62 optimal weight: 2.9990 overall best weight: 2.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 187 HIS ** B 325 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 346 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.2108 moved from start: 0.3307 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 6750 Z= 0.237 Angle : 0.658 7.363 9128 Z= 0.359 Chirality : 0.043 0.156 1026 Planarity : 0.004 0.038 1198 Dihedral : 6.793 58.944 950 Min Nonbonded Distance : 2.028 Molprobity Statistics. All-atom Clashscore : 13.80 Ramachandran Plot: Outliers : 0.35 % Allowed : 13.59 % Favored : 86.06 % Rotamer: Outliers : 3.96 % Allowed : 16.42 % Favored : 79.62 % 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: -3.25 (0.26), residues: 868 helix: -0.78 (0.31), residues: 258 sheet: -2.80 (0.54), residues: 83 loop : -2.92 (0.24), residues: 527 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP B 303 HIS 0.006 0.002 HIS A 372 PHE 0.019 0.002 PHE B 242 TYR 0.021 0.001 TYR A 278 ARG 0.003 0.000 ARG A 34 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1736 Ramachandran restraints generated. 868 Oldfield, 0 Emsley, 868 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1736 Ramachandran restraints generated. 868 Oldfield, 0 Emsley, 868 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 91 residues out of total 692 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 64 time to evaluate : 0.961 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 79 ILE cc_start: 0.3035 (OUTLIER) cc_final: 0.2334 (mm) REVERT: A 94 MET cc_start: 0.3606 (tpp) cc_final: 0.3129 (ttm) REVERT: A 131 TYR cc_start: 0.1248 (p90) cc_final: 0.0742 (p90) REVERT: A 166 MET cc_start: 0.1365 (mmm) cc_final: 0.0616 (mpp) REVERT: A 235 GLU cc_start: 0.1180 (OUTLIER) cc_final: -0.0168 (tt0) REVERT: A 331 ARG cc_start: 0.0958 (ttt180) cc_final: -0.1028 (ttm-80) REVERT: A 376 GLU cc_start: 0.1189 (mm-30) cc_final: 0.0459 (mp0) REVERT: B 360 MET cc_start: 0.1142 (tpt) cc_final: -0.0334 (mtt) outliers start: 27 outliers final: 16 residues processed: 87 average time/residue: 0.3525 time to fit residues: 43.1830 Evaluate side-chains 77 residues out of total 692 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 59 time to evaluate : 0.946 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 THR Chi-restraints excluded: chain A residue 28 GLU Chi-restraints excluded: chain A residue 79 ILE Chi-restraints excluded: chain A residue 157 ASP Chi-restraints excluded: chain A residue 223 LEU Chi-restraints excluded: chain A residue 235 GLU Chi-restraints excluded: chain A residue 291 ILE Chi-restraints excluded: chain A residue 306 LEU Chi-restraints excluded: chain A residue 321 PHE Chi-restraints excluded: chain A residue 350 THR Chi-restraints excluded: chain A residue 403 ASP Chi-restraints excluded: chain B residue 100 THR Chi-restraints excluded: chain B residue 133 TYR Chi-restraints excluded: chain B residue 170 VAL Chi-restraints excluded: chain B residue 204 ASP Chi-restraints excluded: chain B residue 242 PHE Chi-restraints excluded: chain B residue 316 LEU Chi-restraints excluded: chain B residue 367 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 86 random chunks: chunk 77 optimal weight: 3.9990 chunk 58 optimal weight: 8.9990 chunk 40 optimal weight: 7.9990 chunk 8 optimal weight: 0.9980 chunk 37 optimal weight: 10.0000 chunk 52 optimal weight: 4.9990 chunk 78 optimal weight: 2.9990 chunk 83 optimal weight: 10.0000 chunk 41 optimal weight: 7.9990 chunk 74 optimal weight: 1.9990 chunk 22 optimal weight: 5.9990 overall best weight: 2.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 70 ASN ** B 325 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.2280 moved from start: 0.4300 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.062 6750 Z= 0.282 Angle : 0.714 6.528 9128 Z= 0.389 Chirality : 0.044 0.165 1026 Planarity : 0.005 0.046 1198 Dihedral : 7.219 57.167 950 Min Nonbonded Distance : 2.051 Molprobity Statistics. All-atom Clashscore : 15.55 Ramachandran Plot: Outliers : 0.46 % Allowed : 13.48 % Favored : 86.06 % Rotamer: Outliers : 5.13 % Allowed : 16.57 % Favored : 78.30 % 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: -3.46 (0.26), residues: 868 helix: -0.99 (0.29), residues: 263 sheet: -2.82 (0.53), residues: 84 loop : -3.07 (0.24), residues: 521 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.002 TRP B 303 HIS 0.007 0.002 HIS A 372 PHE 0.022 0.002 PHE B 165 TYR 0.022 0.002 TYR A 278 ARG 0.006 0.001 ARG B 85 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1736 Ramachandran restraints generated. 868 Oldfield, 0 Emsley, 868 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1736 Ramachandran restraints generated. 868 Oldfield, 0 Emsley, 868 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 98 residues out of total 692 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 63 time to evaluate : 0.891 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 79 ILE cc_start: 0.3166 (OUTLIER) cc_final: 0.2666 (tp) REVERT: A 94 MET cc_start: 0.3604 (tpp) cc_final: 0.2987 (ttm) REVERT: A 157 ASP cc_start: 0.6881 (OUTLIER) cc_final: 0.6287 (t0) REVERT: A 166 MET cc_start: 0.1389 (mmm) cc_final: 0.0687 (mpp) REVERT: A 184 GLU cc_start: 0.3613 (OUTLIER) cc_final: 0.3153 (pt0) REVERT: A 259 TYR cc_start: 0.0662 (OUTLIER) cc_final: -0.0304 (t80) REVERT: A 376 GLU cc_start: 0.1771 (mm-30) cc_final: 0.0650 (mt-10) REVERT: B 360 MET cc_start: 0.1486 (tpt) cc_final: 0.0088 (mtt) outliers start: 35 outliers final: 24 residues processed: 92 average time/residue: 0.3411 time to fit residues: 44.3304 Evaluate side-chains 91 residues out of total 692 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 63 time to evaluate : 1.011 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 THR Chi-restraints excluded: chain A residue 28 GLU Chi-restraints excluded: chain A residue 79 ILE Chi-restraints excluded: chain A residue 157 ASP Chi-restraints excluded: chain A residue 174 THR Chi-restraints excluded: chain A residue 184 GLU Chi-restraints excluded: chain A residue 223 LEU Chi-restraints excluded: chain A residue 259 TYR Chi-restraints excluded: chain A residue 291 ILE Chi-restraints excluded: chain A residue 306 LEU Chi-restraints excluded: chain A residue 321 PHE Chi-restraints excluded: chain A residue 359 GLU Chi-restraints excluded: chain A residue 402 THR Chi-restraints excluded: chain A residue 403 ASP Chi-restraints excluded: chain A residue 423 GLN Chi-restraints excluded: chain B residue 6 ASP Chi-restraints excluded: chain B residue 74 ILE Chi-restraints excluded: chain B residue 100 THR Chi-restraints excluded: chain B residue 111 ILE Chi-restraints excluded: chain B residue 133 TYR Chi-restraints excluded: chain B residue 170 VAL Chi-restraints excluded: chain B residue 204 ASP Chi-restraints excluded: chain B residue 212 PHE Chi-restraints excluded: chain B residue 238 ILE Chi-restraints excluded: chain B residue 242 PHE Chi-restraints excluded: chain B residue 274 GLU Chi-restraints excluded: chain B residue 316 LEU Chi-restraints excluded: chain B residue 367 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 86 random chunks: chunk 69 optimal weight: 10.0000 chunk 47 optimal weight: 9.9990 chunk 1 optimal weight: 10.0000 chunk 61 optimal weight: 5.9990 chunk 34 optimal weight: 10.0000 chunk 70 optimal weight: 0.9990 chunk 57 optimal weight: 6.9990 chunk 0 optimal weight: 2.9990 chunk 42 optimal weight: 4.9990 chunk 74 optimal weight: 1.9990 chunk 20 optimal weight: 9.9990 overall best weight: 3.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 315 GLN ** B 325 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.2409 moved from start: 0.5240 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.078 6750 Z= 0.308 Angle : 0.729 6.885 9128 Z= 0.400 Chirality : 0.045 0.178 1026 Planarity : 0.005 0.049 1198 Dihedral : 7.481 54.704 950 Min Nonbonded Distance : 2.034 Molprobity Statistics. All-atom Clashscore : 18.88 Ramachandran Plot: Outliers : 0.46 % Allowed : 15.09 % Favored : 84.45 % Rotamer: Outliers : 5.72 % Allowed : 18.18 % Favored : 76.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.65 (0.25), residues: 868 helix: -1.24 (0.29), residues: 257 sheet: -2.82 (0.55), residues: 80 loop : -3.15 (0.24), residues: 531 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.002 TRP B 300 HIS 0.006 0.002 HIS A 372 PHE 0.030 0.002 PHE B 165 TYR 0.021 0.002 TYR A 278 ARG 0.006 0.001 ARG B 85 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1736 Ramachandran restraints generated. 868 Oldfield, 0 Emsley, 868 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1736 Ramachandran restraints generated. 868 Oldfield, 0 Emsley, 868 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 101 residues out of total 692 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 62 time to evaluate : 1.021 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 79 ILE cc_start: 0.3350 (OUTLIER) cc_final: 0.2914 (tp) REVERT: A 157 ASP cc_start: 0.6772 (OUTLIER) cc_final: 0.6410 (t70) REVERT: A 166 MET cc_start: 0.1449 (OUTLIER) cc_final: 0.0612 (mpp) REVERT: A 259 TYR cc_start: 0.0569 (OUTLIER) cc_final: -0.0608 (t80) REVERT: A 376 GLU cc_start: 0.1702 (mm-30) cc_final: 0.0711 (mt-10) REVERT: B 85 ARG cc_start: 0.1416 (ttp-170) cc_final: 0.0736 (ttm170) REVERT: B 146 MET cc_start: 0.2803 (OUTLIER) cc_final: 0.2568 (mtp) REVERT: B 147 MET cc_start: 0.6391 (ptt) cc_final: 0.6187 (ptt) REVERT: B 221 THR cc_start: -0.0648 (OUTLIER) cc_final: -0.0850 (m) REVERT: B 286 TYR cc_start: -0.1473 (OUTLIER) cc_final: -0.2036 (t80) REVERT: B 360 MET cc_start: 0.1352 (tpt) cc_final: -0.0109 (mtt) outliers start: 39 outliers final: 24 residues processed: 93 average time/residue: 0.3778 time to fit residues: 48.3114 Evaluate side-chains 89 residues out of total 692 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 58 time to evaluate : 1.012 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 THR Chi-restraints excluded: chain A residue 79 ILE Chi-restraints excluded: chain A residue 83 ASP Chi-restraints excluded: chain A residue 157 ASP Chi-restraints excluded: chain A residue 166 MET Chi-restraints excluded: chain A residue 174 THR Chi-restraints excluded: chain A residue 239 MET Chi-restraints excluded: chain A residue 259 TYR Chi-restraints excluded: chain A residue 291 ILE Chi-restraints excluded: chain A residue 306 LEU Chi-restraints excluded: chain A residue 321 PHE Chi-restraints excluded: chain A residue 350 THR Chi-restraints excluded: chain A residue 403 ASP Chi-restraints excluded: chain B residue 6 ASP Chi-restraints excluded: chain B residue 39 SER Chi-restraints excluded: chain B residue 74 ILE Chi-restraints excluded: chain B residue 100 THR Chi-restraints excluded: chain B residue 111 ILE Chi-restraints excluded: chain B residue 146 MET Chi-restraints excluded: chain B residue 170 VAL Chi-restraints excluded: chain B residue 204 ASP Chi-restraints excluded: chain B residue 212 PHE Chi-restraints excluded: chain B residue 221 THR Chi-restraints excluded: chain B residue 242 PHE Chi-restraints excluded: chain B residue 274 GLU Chi-restraints excluded: chain B residue 286 TYR Chi-restraints excluded: chain B residue 315 GLN Chi-restraints excluded: chain B residue 316 LEU Chi-restraints excluded: chain B residue 366 TYR Chi-restraints excluded: chain B residue 367 THR Chi-restraints excluded: chain B residue 421 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 86 random chunks: chunk 27 optimal weight: 0.4980 chunk 74 optimal weight: 4.9990 chunk 16 optimal weight: 4.9990 chunk 48 optimal weight: 10.0000 chunk 20 optimal weight: 9.9990 chunk 83 optimal weight: 9.9990 chunk 69 optimal weight: 4.9990 chunk 38 optimal weight: 9.9990 chunk 6 optimal weight: 9.9990 chunk 43 optimal weight: 0.7980 chunk 80 optimal weight: 7.9990 overall best weight: 3.2586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 325 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.2431 moved from start: 0.5585 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.066 6750 Z= 0.285 Angle : 0.704 6.310 9128 Z= 0.387 Chirality : 0.044 0.180 1026 Planarity : 0.005 0.048 1198 Dihedral : 7.501 52.938 950 Min Nonbonded Distance : 1.987 Molprobity Statistics. All-atom Clashscore : 19.19 Ramachandran Plot: Outliers : 0.46 % Allowed : 15.09 % Favored : 84.45 % Rotamer: Outliers : 6.16 % Allowed : 18.91 % Favored : 74.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.12 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.71 (0.25), residues: 868 helix: -1.33 (0.29), residues: 257 sheet: -2.79 (0.56), residues: 80 loop : -3.16 (0.24), residues: 531 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.002 TRP B 300 HIS 0.006 0.002 HIS A 372 PHE 0.021 0.002 PHE B 165 TYR 0.019 0.002 TYR A 278 ARG 0.005 0.000 ARG A 313 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1736 Ramachandran restraints generated. 868 Oldfield, 0 Emsley, 868 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1736 Ramachandran restraints generated. 868 Oldfield, 0 Emsley, 868 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 99 residues out of total 692 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 57 time to evaluate : 0.959 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 235 GLU cc_start: 0.1621 (OUTLIER) cc_final: -0.2304 (mt-10) REVERT: A 259 TYR cc_start: 0.0714 (OUTLIER) cc_final: -0.0515 (t80) REVERT: B 85 ARG cc_start: 0.1481 (ttp-170) cc_final: 0.0665 (ttp-170) REVERT: B 221 THR cc_start: -0.0560 (OUTLIER) cc_final: -0.0789 (m) REVERT: B 239 MET cc_start: 0.2936 (mmp) cc_final: 0.1836 (mmt) REVERT: B 286 TYR cc_start: -0.1479 (OUTLIER) cc_final: -0.2138 (t80) REVERT: B 360 MET cc_start: 0.1393 (tpt) cc_final: -0.0150 (mtt) outliers start: 42 outliers final: 31 residues processed: 91 average time/residue: 0.3581 time to fit residues: 45.8972 Evaluate side-chains 91 residues out of total 692 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 56 time to evaluate : 1.003 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 THR Chi-restraints excluded: chain A residue 28 GLU Chi-restraints excluded: chain A residue 79 ILE Chi-restraints excluded: chain A residue 83 ASP Chi-restraints excluded: chain A residue 167 ILE Chi-restraints excluded: chain A residue 174 THR Chi-restraints excluded: chain A residue 215 THR Chi-restraints excluded: chain A residue 235 GLU Chi-restraints excluded: chain A residue 239 MET Chi-restraints excluded: chain A residue 259 TYR Chi-restraints excluded: chain A residue 291 ILE Chi-restraints excluded: chain A residue 306 LEU Chi-restraints excluded: chain A residue 321 PHE Chi-restraints excluded: chain A residue 350 THR Chi-restraints excluded: chain A residue 359 GLU Chi-restraints excluded: chain A residue 402 THR Chi-restraints excluded: chain A residue 403 ASP Chi-restraints excluded: chain B residue 6 ASP Chi-restraints excluded: chain B residue 74 ILE Chi-restraints excluded: chain B residue 100 THR Chi-restraints excluded: chain B residue 111 ILE Chi-restraints excluded: chain B residue 133 TYR Chi-restraints excluded: chain B residue 140 LYS Chi-restraints excluded: chain B residue 170 VAL Chi-restraints excluded: chain B residue 204 ASP Chi-restraints excluded: chain B residue 212 PHE Chi-restraints excluded: chain B residue 221 THR Chi-restraints excluded: chain B residue 238 ILE Chi-restraints excluded: chain B residue 242 PHE Chi-restraints excluded: chain B residue 274 GLU Chi-restraints excluded: chain B residue 286 TYR Chi-restraints excluded: chain B residue 316 LEU Chi-restraints excluded: chain B residue 366 TYR Chi-restraints excluded: chain B residue 367 THR Chi-restraints excluded: chain B residue 421 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 86 random chunks: chunk 9 optimal weight: 9.9990 chunk 47 optimal weight: 10.0000 chunk 60 optimal weight: 2.9990 chunk 70 optimal weight: 8.9990 chunk 46 optimal weight: 10.0000 chunk 82 optimal weight: 0.9980 chunk 51 optimal weight: 0.9980 chunk 50 optimal weight: 0.0070 chunk 38 optimal weight: 20.0000 chunk 33 optimal weight: 5.9990 chunk 49 optimal weight: 0.0050 overall best weight: 1.0014 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 87 GLN ** B 325 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.2283 moved from start: 0.5547 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 6750 Z= 0.160 Angle : 0.565 4.443 9128 Z= 0.310 Chirality : 0.041 0.149 1026 Planarity : 0.003 0.038 1198 Dihedral : 6.621 51.962 950 Min Nonbonded Distance : 1.996 Molprobity Statistics. All-atom Clashscore : 14.41 Ramachandran Plot: Outliers : 0.46 % Allowed : 11.06 % Favored : 88.48 % Rotamer: Outliers : 4.99 % Allowed : 20.38 % Favored : 74.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.29 (0.26), residues: 868 helix: -0.81 (0.31), residues: 254 sheet: -2.63 (0.54), residues: 93 loop : -2.98 (0.24), residues: 521 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 303 HIS 0.006 0.001 HIS A 372 PHE 0.016 0.001 PHE B 242 TYR 0.016 0.001 TYR A 278 ARG 0.003 0.000 ARG A 313 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1736 Ramachandran restraints generated. 868 Oldfield, 0 Emsley, 868 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1736 Ramachandran restraints generated. 868 Oldfield, 0 Emsley, 868 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 93 residues out of total 692 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 59 time to evaluate : 1.021 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 82 TYR cc_start: 0.2727 (OUTLIER) cc_final: 0.1958 (t80) REVERT: A 259 TYR cc_start: 0.0564 (OUTLIER) cc_final: -0.0451 (t80) REVERT: A 376 GLU cc_start: 0.1604 (mm-30) cc_final: 0.0464 (mt-10) REVERT: B 147 MET cc_start: 0.6432 (ptt) cc_final: 0.6193 (ptt) REVERT: B 239 MET cc_start: 0.2718 (mmp) cc_final: 0.1462 (mmt) REVERT: B 286 TYR cc_start: -0.1381 (OUTLIER) cc_final: -0.1942 (t80) REVERT: B 322 PHE cc_start: 0.1588 (m-10) cc_final: 0.1303 (m-10) REVERT: B 360 MET cc_start: 0.1793 (tpt) cc_final: 0.0441 (mtt) REVERT: B 405 ILE cc_start: 0.2179 (mm) cc_final: 0.1910 (mm) outliers start: 34 outliers final: 27 residues processed: 86 average time/residue: 0.3162 time to fit residues: 39.7337 Evaluate side-chains 87 residues out of total 692 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 57 time to evaluate : 1.012 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 THR Chi-restraints excluded: chain A residue 28 GLU Chi-restraints excluded: chain A residue 79 ILE Chi-restraints excluded: chain A residue 82 TYR Chi-restraints excluded: chain A residue 95 ILE Chi-restraints excluded: chain A residue 100 THR Chi-restraints excluded: chain A residue 174 THR Chi-restraints excluded: chain A residue 259 TYR Chi-restraints excluded: chain A residue 291 ILE Chi-restraints excluded: chain A residue 321 PHE Chi-restraints excluded: chain A residue 350 THR Chi-restraints excluded: chain A residue 359 GLU Chi-restraints excluded: chain A residue 402 THR Chi-restraints excluded: chain A residue 403 ASP Chi-restraints excluded: chain B residue 6 ASP Chi-restraints excluded: chain B residue 39 SER Chi-restraints excluded: chain B residue 74 ILE Chi-restraints excluded: chain B residue 80 ILE Chi-restraints excluded: chain B residue 100 THR Chi-restraints excluded: chain B residue 111 ILE Chi-restraints excluded: chain B residue 133 TYR Chi-restraints excluded: chain B residue 140 LYS Chi-restraints excluded: chain B residue 157 ASP Chi-restraints excluded: chain B residue 170 VAL Chi-restraints excluded: chain B residue 204 ASP Chi-restraints excluded: chain B residue 212 PHE Chi-restraints excluded: chain B residue 242 PHE Chi-restraints excluded: chain B residue 274 GLU Chi-restraints excluded: chain B residue 286 TYR Chi-restraints excluded: chain B residue 316 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 86 random chunks: chunk 24 optimal weight: 5.9990 chunk 16 optimal weight: 0.7980 chunk 52 optimal weight: 3.9990 chunk 56 optimal weight: 9.9990 chunk 40 optimal weight: 20.0000 chunk 7 optimal weight: 10.0000 chunk 65 optimal weight: 10.0000 chunk 75 optimal weight: 7.9990 chunk 79 optimal weight: 10.0000 chunk 72 optimal weight: 4.9990 chunk 77 optimal weight: 0.9990 overall best weight: 3.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 325 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.2447 moved from start: 0.6015 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.076 6750 Z= 0.295 Angle : 0.691 5.934 9128 Z= 0.379 Chirality : 0.044 0.164 1026 Planarity : 0.005 0.043 1198 Dihedral : 7.257 53.167 950 Min Nonbonded Distance : 1.939 Molprobity Statistics. All-atom Clashscore : 20.48 Ramachandran Plot: Outliers : 0.35 % Allowed : 14.86 % Favored : 84.79 % Rotamer: Outliers : 5.13 % Allowed : 20.53 % Favored : 74.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.54 (0.26), residues: 868 helix: -1.12 (0.30), residues: 258 sheet: -2.72 (0.57), residues: 80 loop : -3.10 (0.24), residues: 530 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP A 303 HIS 0.005 0.002 HIS A 0 PHE 0.021 0.002 PHE B 242 TYR 0.019 0.002 TYR A 278 ARG 0.005 0.000 ARG A 313 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1736 Ramachandran restraints generated. 868 Oldfield, 0 Emsley, 868 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1736 Ramachandran restraints generated. 868 Oldfield, 0 Emsley, 868 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 91 residues out of total 692 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 56 time to evaluate : 0.963 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 82 TYR cc_start: 0.3287 (OUTLIER) cc_final: 0.2277 (t80) REVERT: A 235 GLU cc_start: 0.1633 (OUTLIER) cc_final: -0.2263 (mt-10) REVERT: A 259 TYR cc_start: 0.0684 (OUTLIER) cc_final: -0.0496 (t80) REVERT: B 80 ILE cc_start: 0.3746 (OUTLIER) cc_final: 0.3415 (mm) REVERT: B 85 ARG cc_start: 0.1279 (ttp-170) cc_final: -0.0329 (ttp-170) REVERT: B 221 THR cc_start: -0.0557 (OUTLIER) cc_final: -0.0800 (m) REVERT: B 239 MET cc_start: 0.2752 (mmp) cc_final: 0.1653 (mmt) REVERT: B 286 TYR cc_start: -0.1593 (OUTLIER) cc_final: -0.2251 (t80) REVERT: B 360 MET cc_start: 0.1953 (tpt) cc_final: 0.0540 (mtt) outliers start: 35 outliers final: 25 residues processed: 84 average time/residue: 0.3650 time to fit residues: 43.6992 Evaluate side-chains 86 residues out of total 692 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 55 time to evaluate : 1.048 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 THR Chi-restraints excluded: chain A residue 79 ILE Chi-restraints excluded: chain A residue 82 TYR Chi-restraints excluded: chain A residue 100 THR Chi-restraints excluded: chain A residue 174 THR Chi-restraints excluded: chain A residue 215 THR Chi-restraints excluded: chain A residue 235 GLU Chi-restraints excluded: chain A residue 259 TYR Chi-restraints excluded: chain A residue 291 ILE Chi-restraints excluded: chain A residue 306 LEU Chi-restraints excluded: chain A residue 321 PHE Chi-restraints excluded: chain A residue 350 THR Chi-restraints excluded: chain A residue 359 GLU Chi-restraints excluded: chain A residue 402 THR Chi-restraints excluded: chain A residue 403 ASP Chi-restraints excluded: chain B residue 6 ASP Chi-restraints excluded: chain B residue 39 SER Chi-restraints excluded: chain B residue 74 ILE Chi-restraints excluded: chain B residue 79 ILE Chi-restraints excluded: chain B residue 80 ILE Chi-restraints excluded: chain B residue 100 THR Chi-restraints excluded: chain B residue 111 ILE Chi-restraints excluded: chain B residue 140 LYS Chi-restraints excluded: chain B residue 170 VAL Chi-restraints excluded: chain B residue 204 ASP Chi-restraints excluded: chain B residue 212 PHE Chi-restraints excluded: chain B residue 221 THR Chi-restraints excluded: chain B residue 242 PHE Chi-restraints excluded: chain B residue 286 TYR Chi-restraints excluded: chain B residue 316 LEU Chi-restraints excluded: chain B residue 367 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 86 random chunks: chunk 79 optimal weight: 7.9990 chunk 46 optimal weight: 10.0000 chunk 33 optimal weight: 6.9990 chunk 60 optimal weight: 2.9990 chunk 23 optimal weight: 5.9990 chunk 69 optimal weight: 9.9990 chunk 73 optimal weight: 3.9990 chunk 76 optimal weight: 0.9990 chunk 50 optimal weight: 0.9990 chunk 81 optimal weight: 9.9990 chunk 49 optimal weight: 0.7980 overall best weight: 1.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 325 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.2376 moved from start: 0.6083 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 6750 Z= 0.200 Angle : 0.602 5.012 9128 Z= 0.331 Chirality : 0.042 0.143 1026 Planarity : 0.004 0.042 1198 Dihedral : 6.921 52.912 950 Min Nonbonded Distance : 1.952 Molprobity Statistics. All-atom Clashscore : 16.68 Ramachandran Plot: Outliers : 0.35 % Allowed : 13.48 % Favored : 86.18 % Rotamer: Outliers : 4.55 % Allowed : 20.97 % Favored : 74.49 % 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: -3.39 (0.26), residues: 868 helix: -0.92 (0.31), residues: 258 sheet: -2.75 (0.55), residues: 86 loop : -3.03 (0.24), residues: 524 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP B 303 HIS 0.005 0.001 HIS A 372 PHE 0.018 0.002 PHE B 242 TYR 0.017 0.001 TYR A 278 ARG 0.004 0.000 ARG A 313 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1736 Ramachandran restraints generated. 868 Oldfield, 0 Emsley, 868 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1736 Ramachandran restraints generated. 868 Oldfield, 0 Emsley, 868 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 87 residues out of total 692 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 56 time to evaluate : 0.987 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 82 TYR cc_start: 0.3058 (OUTLIER) cc_final: 0.2115 (t80) REVERT: A 259 TYR cc_start: 0.0709 (OUTLIER) cc_final: -0.0462 (t80) REVERT: A 306 LEU cc_start: 0.1534 (OUTLIER) cc_final: 0.1302 (tp) REVERT: A 376 GLU cc_start: 0.1724 (mm-30) cc_final: 0.0644 (mt-10) REVERT: B 80 ILE cc_start: 0.3502 (OUTLIER) cc_final: 0.3173 (mm) REVERT: B 85 ARG cc_start: 0.1274 (ttp-170) cc_final: 0.0339 (ttm170) REVERT: B 147 MET cc_start: 0.6439 (ptt) cc_final: 0.6210 (ptt) REVERT: B 239 MET cc_start: 0.2798 (mmp) cc_final: 0.1561 (mmt) REVERT: B 286 TYR cc_start: -0.1772 (OUTLIER) cc_final: -0.2079 (t80) REVERT: B 360 MET cc_start: 0.1850 (tpt) cc_final: 0.0381 (mtt) outliers start: 31 outliers final: 25 residues processed: 81 average time/residue: 0.3575 time to fit residues: 40.9938 Evaluate side-chains 85 residues out of total 692 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 55 time to evaluate : 0.904 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 THR Chi-restraints excluded: chain A residue 28 GLU Chi-restraints excluded: chain A residue 79 ILE Chi-restraints excluded: chain A residue 82 TYR Chi-restraints excluded: chain A residue 100 THR Chi-restraints excluded: chain A residue 167 ILE Chi-restraints excluded: chain A residue 174 THR Chi-restraints excluded: chain A residue 215 THR Chi-restraints excluded: chain A residue 259 TYR Chi-restraints excluded: chain A residue 291 ILE Chi-restraints excluded: chain A residue 306 LEU Chi-restraints excluded: chain A residue 321 PHE Chi-restraints excluded: chain A residue 350 THR Chi-restraints excluded: chain A residue 359 GLU Chi-restraints excluded: chain A residue 402 THR Chi-restraints excluded: chain A residue 403 ASP Chi-restraints excluded: chain B residue 6 ASP Chi-restraints excluded: chain B residue 39 SER Chi-restraints excluded: chain B residue 74 ILE Chi-restraints excluded: chain B residue 80 ILE Chi-restraints excluded: chain B residue 100 THR Chi-restraints excluded: chain B residue 111 ILE Chi-restraints excluded: chain B residue 170 VAL Chi-restraints excluded: chain B residue 204 ASP Chi-restraints excluded: chain B residue 212 PHE Chi-restraints excluded: chain B residue 242 PHE Chi-restraints excluded: chain B residue 274 GLU Chi-restraints excluded: chain B residue 286 TYR Chi-restraints excluded: chain B residue 316 LEU Chi-restraints excluded: chain B residue 366 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 86 random chunks: chunk 38 optimal weight: 20.0000 chunk 56 optimal weight: 0.0040 chunk 85 optimal weight: 4.9990 chunk 78 optimal weight: 7.9990 chunk 68 optimal weight: 1.9990 chunk 7 optimal weight: 9.9990 chunk 52 optimal weight: 0.9980 chunk 41 optimal weight: 10.0000 chunk 54 optimal weight: 5.9990 chunk 72 optimal weight: 3.9990 chunk 20 optimal weight: 9.9990 overall best weight: 2.3998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 163 GLN ** B 325 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.2420 moved from start: 0.6373 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 6750 Z= 0.235 Angle : 0.633 5.138 9128 Z= 0.348 Chirality : 0.043 0.149 1026 Planarity : 0.004 0.041 1198 Dihedral : 7.046 56.076 950 Min Nonbonded Distance : 1.923 Molprobity Statistics. All-atom Clashscore : 18.50 Ramachandran Plot: Outliers : 0.35 % Allowed : 14.52 % Favored : 85.14 % Rotamer: Outliers : 4.69 % Allowed : 20.82 % Favored : 74.49 % 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: -3.45 (0.26), residues: 868 helix: -0.94 (0.31), residues: 258 sheet: -2.81 (0.53), residues: 86 loop : -3.08 (0.24), residues: 524 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 181 HIS 0.005 0.001 HIS A 372 PHE 0.020 0.002 PHE B 242 TYR 0.019 0.002 TYR A 278 ARG 0.005 0.000 ARG A 313 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1736 Ramachandran restraints generated. 868 Oldfield, 0 Emsley, 868 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1736 Ramachandran restraints generated. 868 Oldfield, 0 Emsley, 868 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 88 residues out of total 692 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 56 time to evaluate : 1.098 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 82 TYR cc_start: 0.3105 (OUTLIER) cc_final: 0.2102 (t80) REVERT: A 235 GLU cc_start: 0.1716 (OUTLIER) cc_final: -0.2203 (mt-10) REVERT: A 259 TYR cc_start: 0.0680 (OUTLIER) cc_final: -0.0560 (t80) REVERT: A 306 LEU cc_start: 0.1763 (OUTLIER) cc_final: 0.1490 (tp) REVERT: A 322 PHE cc_start: -0.0060 (m-10) cc_final: -0.0624 (m-10) REVERT: B 80 ILE cc_start: 0.3423 (OUTLIER) cc_final: 0.3012 (mm) REVERT: B 85 ARG cc_start: 0.1572 (ttp-170) cc_final: 0.0765 (ttp-170) REVERT: B 147 MET cc_start: 0.6457 (ptt) cc_final: 0.6229 (ptt) REVERT: B 239 MET cc_start: 0.2757 (mmp) cc_final: 0.1540 (mmt) REVERT: B 286 TYR cc_start: -0.1656 (OUTLIER) cc_final: -0.2089 (t80) REVERT: B 360 MET cc_start: 0.1911 (tpt) cc_final: 0.0432 (mtt) outliers start: 32 outliers final: 24 residues processed: 82 average time/residue: 0.3598 time to fit residues: 41.3644 Evaluate side-chains 83 residues out of total 692 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 53 time to evaluate : 1.042 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 THR Chi-restraints excluded: chain A residue 28 GLU Chi-restraints excluded: chain A residue 79 ILE Chi-restraints excluded: chain A residue 82 TYR Chi-restraints excluded: chain A residue 100 THR Chi-restraints excluded: chain A residue 167 ILE Chi-restraints excluded: chain A residue 174 THR Chi-restraints excluded: chain A residue 215 THR Chi-restraints excluded: chain A residue 235 GLU Chi-restraints excluded: chain A residue 259 TYR Chi-restraints excluded: chain A residue 306 LEU Chi-restraints excluded: chain A residue 321 PHE Chi-restraints excluded: chain A residue 350 THR Chi-restraints excluded: chain A residue 359 GLU Chi-restraints excluded: chain A residue 402 THR Chi-restraints excluded: chain A residue 403 ASP Chi-restraints excluded: chain B residue 6 ASP Chi-restraints excluded: chain B residue 39 SER Chi-restraints excluded: chain B residue 74 ILE Chi-restraints excluded: chain B residue 80 ILE Chi-restraints excluded: chain B residue 100 THR Chi-restraints excluded: chain B residue 111 ILE Chi-restraints excluded: chain B residue 170 VAL Chi-restraints excluded: chain B residue 204 ASP Chi-restraints excluded: chain B residue 212 PHE Chi-restraints excluded: chain B residue 242 PHE Chi-restraints excluded: chain B residue 274 GLU Chi-restraints excluded: chain B residue 286 TYR Chi-restraints excluded: chain B residue 316 LEU Chi-restraints excluded: chain B residue 366 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 86 random chunks: chunk 62 optimal weight: 0.8980 chunk 10 optimal weight: 10.0000 chunk 18 optimal weight: 10.0000 chunk 68 optimal weight: 4.9990 chunk 28 optimal weight: 0.8980 chunk 70 optimal weight: 8.9990 chunk 8 optimal weight: 0.7980 chunk 12 optimal weight: 10.0000 chunk 59 optimal weight: 0.8980 chunk 3 optimal weight: 0.9980 chunk 49 optimal weight: 9.9990 overall best weight: 0.8980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 73 ASN ** B 325 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 = 0.5304 r_free = 0.5304 target = 0.340243 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 78)----------------| | r_work = 0.5250 r_free = 0.5250 target = 0.333791 restraints weight = 41388.954| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.5264 r_free = 0.5264 target = 0.335526 restraints weight = 25705.846| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.5275 r_free = 0.5275 target = 0.336851 restraints weight = 15944.261| |-----------------------------------------------------------------------------| r_work (final): 0.5279 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.2414 moved from start: 0.6320 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 6750 Z= 0.153 Angle : 0.548 5.518 9128 Z= 0.299 Chirality : 0.041 0.148 1026 Planarity : 0.003 0.035 1198 Dihedral : 6.530 57.398 950 Min Nonbonded Distance : 1.949 Molprobity Statistics. All-atom Clashscore : 14.94 Ramachandran Plot: Outliers : 0.35 % Allowed : 11.75 % Favored : 87.90 % Rotamer: Outliers : 4.11 % Allowed : 21.26 % Favored : 74.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.15 (0.27), residues: 868 helix: -0.58 (0.32), residues: 257 sheet: -2.63 (0.53), residues: 93 loop : -2.94 (0.25), residues: 518 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 303 HIS 0.005 0.001 HIS A 372 PHE 0.016 0.001 PHE B 242 TYR 0.015 0.001 TYR A 278 ARG 0.002 0.000 ARG A 270 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2926.72 seconds wall clock time: 53 minutes 2.71 seconds (3182.71 seconds total)