Starting phenix.real_space_refine on Sun Apr 7 04:03:28 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8j5d_35985/04_2024/8j5d_35985.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8j5d_35985/04_2024/8j5d_35985.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8j5d_35985/04_2024/8j5d_35985.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8j5d_35985/04_2024/8j5d_35985.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8j5d_35985/04_2024/8j5d_35985.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8j5d_35985/04_2024/8j5d_35985.pdb" } resolution = 3.0 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= 0.084 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 39 5.16 5 C 6088 2.51 5 N 1599 2.21 5 O 1805 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 168": "OE1" <-> "OE2" Residue "A GLU 207": "OE1" <-> "OE2" Residue "A ASP 219": "OD1" <-> "OD2" Residue "A TYR 306": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 343": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 413": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 422": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 442": "OE1" <-> "OE2" Residue "A PHE 534": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 170": "OD1" <-> "OD2" Residue "B PHE 172": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 211": "OE1" <-> "OE2" Residue "B TYR 219": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 283": "OE1" <-> "OE2" Residue "B TYR 311": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 342": "OD1" <-> "OD2" Residue "B TYR 371": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 382": "OE1" <-> "OE2" Residue "B ASP 388": "OD1" <-> "OD2" Residue "D ASP 94": "OD1" <-> "OD2" Residue "D PHE 151": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 254": "OD1" <-> "OD2" Residue "D ASP 276": "OD1" <-> "OD2" Residue "C ASP 137": "OD1" <-> "OD2" Residue "C PHE 138": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 297": "OD1" <-> "OD2" Residue "C PHE 316": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 335": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 358": "OE1" <-> "OE2" Residue "C GLU 362": "OE1" <-> "OE2" Residue "C GLU 370": "OE1" <-> "OE2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5288/modules/chem_data/mon_lib" Total number of atoms: 9531 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 3340 Number of conformers: 1 Conformer: "" Number of residues, atoms: 422, 3340 Classifications: {'peptide': 422} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 21, 'TRANS': 398} Chain breaks: 1 Chain: "B" Number of atoms: 2356 Number of conformers: 1 Conformer: "" Number of residues, atoms: 316, 2356 Classifications: {'peptide': 316} Link IDs: {'PCIS': 1, 'PTRANS': 14, 'TRANS': 300} Chain: "D" Number of atoms: 1488 Number of conformers: 1 Conformer: "" Number of residues, atoms: 191, 1488 Classifications: {'peptide': 191} Link IDs: {'PCIS': 1, 'PTRANS': 7, 'TRANS': 182} Chain breaks: 1 Chain: "C" Number of atoms: 2347 Number of conformers: 1 Conformer: "" Number of residues, atoms: 315, 2347 Classifications: {'peptide': 315} Link IDs: {'PCIS': 1, 'PTRANS': 14, 'TRANS': 299} Time building chain proxies: 5.23, per 1000 atoms: 0.55 Number of scatterers: 9531 At special positions: 0 Unit cell: (70.62, 92.02, 146.59, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 39 16.00 O 1805 8.00 N 1599 7.00 C 6088 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 3.57 Conformation dependent library (CDL) restraints added in 1.8 seconds 2464 Ramachandran restraints generated. 1232 Oldfield, 0 Emsley, 1232 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2288 Finding SS restraints... Secondary structure from input PDB file: 48 helices and 9 sheets defined 47.0% alpha, 13.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.01 Creating SS restraints... Processing helix chain 'A' and resid 125 through 139 Processing helix chain 'A' and resid 163 through 176 Processing helix chain 'A' and resid 202 through 212 Processing helix chain 'A' and resid 243 through 259 Processing helix chain 'A' and resid 275 through 279 Processing helix chain 'A' and resid 287 through 291 Processing helix chain 'A' and resid 304 through 318 removed outlier: 4.452A pdb=" N SER A 310 " --> pdb=" O TYR A 306 " (cutoff:3.500A) Processing helix chain 'A' and resid 337 through 341 removed outlier: 3.530A pdb=" N THR A 341 " --> pdb=" O PRO A 338 " (cutoff:3.500A) Processing helix chain 'A' and resid 349 through 352 Processing helix chain 'A' and resid 353 through 382 Processing helix chain 'A' and resid 405 through 411 Processing helix chain 'A' and resid 421 through 433 removed outlier: 4.251A pdb=" N ILE A 425 " --> pdb=" O GLY A 421 " (cutoff:3.500A) Processing helix chain 'A' and resid 455 through 471 Processing helix chain 'A' and resid 484 through 497 Processing helix chain 'A' and resid 519 through 523 Processing helix chain 'A' and resid 524 through 539 Processing helix chain 'B' and resid 94 through 104 Processing helix chain 'B' and resid 119 through 128 removed outlier: 3.789A pdb=" N HIS B 128 " --> pdb=" O ALA B 124 " (cutoff:3.500A) Processing helix chain 'B' and resid 140 through 148 removed outlier: 3.634A pdb=" N ALA B 145 " --> pdb=" O PRO B 141 " (cutoff:3.500A) removed outlier: 4.283A pdb=" N ASP B 146 " --> pdb=" O SER B 142 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N LEU B 148 " --> pdb=" O LEU B 144 " (cutoff:3.500A) Processing helix chain 'B' and resid 167 through 190 removed outlier: 4.165A pdb=" N GLU B 188 " --> pdb=" O GLU B 184 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N ASN B 189 " --> pdb=" O ALA B 185 " (cutoff:3.500A) Processing helix chain 'B' and resid 201 through 215 Proline residue: B 207 - end of helix Processing helix chain 'B' and resid 220 through 222 No H-bonds generated for 'chain 'B' and resid 220 through 222' Processing helix chain 'B' and resid 228 through 244 removed outlier: 3.663A pdb=" N VAL B 232 " --> pdb=" O THR B 228 " (cutoff:3.500A) Processing helix chain 'B' and resid 267 through 270 Processing helix chain 'B' and resid 277 through 282 Processing helix chain 'B' and resid 283 through 299 removed outlier: 5.363A pdb=" N GLY B 292 " --> pdb=" O ILE B 288 " (cutoff:3.500A) removed outlier: 5.529A pdb=" N THR B 293 " --> pdb=" O GLN B 289 " (cutoff:3.500A) Processing helix chain 'B' and resid 306 through 325 Processing helix chain 'B' and resid 362 through 366 Processing helix chain 'B' and resid 369 through 396 removed outlier: 4.590A pdb=" N VAL B 381 " --> pdb=" O GLU B 377 " (cutoff:3.500A) removed outlier: 4.373A pdb=" N GLU B 382 " --> pdb=" O ALA B 378 " (cutoff:3.500A) Processing helix chain 'D' and resid 106 through 111 Processing helix chain 'D' and resid 136 through 146 removed outlier: 3.773A pdb=" N THR D 140 " --> pdb=" O ASP D 136 " (cutoff:3.500A) removed outlier: 3.953A pdb=" N LYS D 142 " --> pdb=" O GLY D 138 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N MET D 143 " --> pdb=" O ASP D 139 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N GLU D 146 " --> pdb=" O LYS D 142 " (cutoff:3.500A) Processing helix chain 'D' and resid 163 through 170 removed outlier: 4.080A pdb=" N LEU D 167 " --> pdb=" O PRO D 163 " (cutoff:3.500A) Processing helix chain 'D' and resid 212 through 216 removed outlier: 3.642A pdb=" N PHE D 215 " --> pdb=" O SER D 212 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N PHE D 216 " --> pdb=" O SER D 213 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 212 through 216' Processing helix chain 'D' and resid 217 through 225 Processing helix chain 'D' and resid 267 through 280 Processing helix chain 'C' and resid 94 through 104 Processing helix chain 'C' and resid 118 through 127 Processing helix chain 'C' and resid 140 through 148 removed outlier: 4.029A pdb=" N ASP C 146 " --> pdb=" O SER C 142 " (cutoff:3.500A) Processing helix chain 'C' and resid 167 through 190 Processing helix chain 'C' and resid 201 through 217 Proline residue: C 207 - end of helix Processing helix chain 'C' and resid 220 through 224 removed outlier: 3.883A pdb=" N LEU C 224 " --> pdb=" O PRO C 221 " (cutoff:3.500A) Processing helix chain 'C' and resid 228 through 243 removed outlier: 3.636A pdb=" N VAL C 232 " --> pdb=" O THR C 228 " (cutoff:3.500A) Processing helix chain 'C' and resid 267 through 270 Processing helix chain 'C' and resid 277 through 289 Processing helix chain 'C' and resid 291 through 299 Processing helix chain 'C' and resid 306 through 325 Processing helix chain 'C' and resid 362 through 366 Processing helix chain 'C' and resid 369 through 395 Processing sheet with id=AA1, first strand: chain 'A' and resid 108 through 111 removed outlier: 6.273A pdb=" N VAL A 108 " --> pdb=" O GLY A 143 " (cutoff:3.500A) removed outlier: 7.764A pdb=" N MET A 145 " --> pdb=" O VAL A 108 " (cutoff:3.500A) removed outlier: 6.608A pdb=" N VAL A 110 " --> pdb=" O MET A 145 " (cutoff:3.500A) removed outlier: 8.553A pdb=" N ASP A 147 " --> pdb=" O VAL A 110 " (cutoff:3.500A) removed outlier: 6.891A pdb=" N ILE A 144 " --> pdb=" O GLN A 181 " (cutoff:3.500A) removed outlier: 7.779A pdb=" N VAL A 183 " --> pdb=" O ILE A 144 " (cutoff:3.500A) removed outlier: 6.683A pdb=" N ILE A 146 " --> pdb=" O VAL A 183 " (cutoff:3.500A) removed outlier: 6.654A pdb=" N SER A 185 " --> pdb=" O ILE A 146 " (cutoff:3.500A) removed outlier: 6.192A pdb=" N VAL A 148 " --> pdb=" O SER A 185 " (cutoff:3.500A) removed outlier: 6.049A pdb=" N VAL A 180 " --> pdb=" O ILE A 267 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N GLU A 269 " --> pdb=" O VAL A 180 " (cutoff:3.500A) removed outlier: 6.727A pdb=" N VAL A 268 " --> pdb=" O LYS A 388 " (cutoff:3.500A) removed outlier: 7.765A pdb=" N SER A 390 " --> pdb=" O VAL A 268 " (cutoff:3.500A) removed outlier: 6.320A pdb=" N ILE A 270 " --> pdb=" O SER A 390 " (cutoff:3.500A) removed outlier: 7.715A pdb=" N LYS A 392 " --> pdb=" O ILE A 270 " (cutoff:3.500A) removed outlier: 7.743A pdb=" N VAL A 272 " --> pdb=" O LYS A 392 " (cutoff:3.500A) removed outlier: 8.160A pdb=" N ALA A 475 " --> pdb=" O ALA A 434 " (cutoff:3.500A) removed outlier: 6.132A pdb=" N PHE A 436 " --> pdb=" O ALA A 475 " (cutoff:3.500A) removed outlier: 7.717A pdb=" N GLU A 477 " --> pdb=" O PHE A 436 " (cutoff:3.500A) removed outlier: 6.317A pdb=" N PHE A 438 " --> pdb=" O GLU A 477 " (cutoff:3.500A) removed outlier: 9.100A pdb=" N THR A 514 " --> pdb=" O LEU A 474 " (cutoff:3.500A) removed outlier: 6.809A pdb=" N GLY A 476 " --> pdb=" O THR A 514 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 216 through 218 removed outlier: 3.737A pdb=" N TYR A 217 " --> pdb=" O ASN A 225 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 134 through 138 removed outlier: 6.543A pdb=" N SER B 109 " --> pdb=" O GLN B 134 " (cutoff:3.500A) removed outlier: 8.157A pdb=" N ARG B 136 " --> pdb=" O SER B 109 " (cutoff:3.500A) removed outlier: 6.486A pdb=" N LEU B 111 " --> pdb=" O ARG B 136 " (cutoff:3.500A) removed outlier: 7.845A pdb=" N PHE B 138 " --> pdb=" O LEU B 111 " (cutoff:3.500A) removed outlier: 6.441A pdb=" N LEU B 113 " --> pdb=" O PHE B 138 " (cutoff:3.500A) removed outlier: 6.116A pdb=" N TYR B 83 " --> pdb=" O VAL B 108 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N THR B 110 " --> pdb=" O TYR B 83 " (cutoff:3.500A) removed outlier: 6.345A pdb=" N VAL B 154 " --> pdb=" O HIS B 196 " (cutoff:3.500A) removed outlier: 6.147A pdb=" N ILE B 195 " --> pdb=" O PHE B 225 " (cutoff:3.500A) removed outlier: 6.852A pdb=" N VAL B 227 " --> pdb=" O ILE B 195 " (cutoff:3.500A) removed outlier: 6.999A pdb=" N ILE B 197 " --> pdb=" O VAL B 227 " (cutoff:3.500A) removed outlier: 8.049A pdb=" N ARG B 349 " --> pdb=" O VAL B 360 " (cutoff:3.500A) removed outlier: 5.728A pdb=" N VAL B 360 " --> pdb=" O ARG B 349 " (cutoff:3.500A) removed outlier: 6.871A pdb=" N LYS B 351 " --> pdb=" O GLU B 358 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 254 through 256 Processing sheet with id=AA5, first strand: chain 'D' and resid 76 through 82 removed outlier: 6.395A pdb=" N SER D 152 " --> pdb=" O ALA D 123 " (cutoff:3.500A) removed outlier: 4.317A pdb=" N ALA D 123 " --> pdb=" O SER D 152 " (cutoff:3.500A) removed outlier: 6.741A pdb=" N VAL D 154 " --> pdb=" O LYS D 121 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'D' and resid 247 through 251 removed outlier: 6.582A pdb=" N ARG D 88 " --> pdb=" O HIS D 100 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'D' and resid 184 through 186 Processing sheet with id=AA8, first strand: chain 'C' and resid 134 through 139 removed outlier: 6.455A pdb=" N SER C 109 " --> pdb=" O GLN C 134 " (cutoff:3.500A) removed outlier: 8.180A pdb=" N ARG C 136 " --> pdb=" O SER C 109 " (cutoff:3.500A) removed outlier: 6.542A pdb=" N LEU C 111 " --> pdb=" O ARG C 136 " (cutoff:3.500A) removed outlier: 7.956A pdb=" N PHE C 138 " --> pdb=" O LEU C 111 " (cutoff:3.500A) removed outlier: 6.261A pdb=" N LEU C 113 " --> pdb=" O PHE C 138 " (cutoff:3.500A) removed outlier: 6.954A pdb=" N TYR C 83 " --> pdb=" O SER C 109 " (cutoff:3.500A) removed outlier: 6.120A pdb=" N LEU C 111 " --> pdb=" O TYR C 83 " (cutoff:3.500A) removed outlier: 6.920A pdb=" N VAL C 85 " --> pdb=" O LEU C 111 " (cutoff:3.500A) removed outlier: 5.832A pdb=" N LEU C 113 " --> pdb=" O VAL C 85 " (cutoff:3.500A) removed outlier: 6.416A pdb=" N VAL C 87 " --> pdb=" O LEU C 113 " (cutoff:3.500A) removed outlier: 5.484A pdb=" N ASP C 115 " --> pdb=" O VAL C 87 " (cutoff:3.500A) removed outlier: 5.629A pdb=" N ILE C 195 " --> pdb=" O PHE C 225 " (cutoff:3.500A) removed outlier: 6.199A pdb=" N VAL C 227 " --> pdb=" O ILE C 195 " (cutoff:3.500A) removed outlier: 6.727A pdb=" N ILE C 197 " --> pdb=" O VAL C 227 " (cutoff:3.500A) removed outlier: 8.222A pdb=" N ARG C 349 " --> pdb=" O VAL C 360 " (cutoff:3.500A) removed outlier: 5.736A pdb=" N VAL C 360 " --> pdb=" O ARG C 349 " (cutoff:3.500A) removed outlier: 6.870A pdb=" N LYS C 351 " --> pdb=" O GLU C 358 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 254 through 256 451 hydrogen bonds defined for protein. 1281 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.64 Time building geometry restraints manager: 3.91 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.35: 3109 1.35 - 1.47: 2180 1.47 - 1.59: 4374 1.59 - 1.71: 0 1.71 - 1.83: 64 Bond restraints: 9727 Sorted by residual: bond pdb=" C MET A 111 " pdb=" N MET A 112 " ideal model delta sigma weight residual 1.328 1.360 -0.032 1.44e-02 4.82e+03 4.79e+00 bond pdb=" CG PRO B 207 " pdb=" CD PRO B 207 " ideal model delta sigma weight residual 1.503 1.447 0.056 3.40e-02 8.65e+02 2.73e+00 bond pdb=" C MET A 112 " pdb=" N PRO A 113 " ideal model delta sigma weight residual 1.331 1.350 -0.019 1.21e-02 6.83e+03 2.36e+00 bond pdb=" C CYS A 189 " pdb=" N GLY A 190 " ideal model delta sigma weight residual 1.335 1.324 0.011 7.50e-03 1.78e+04 2.07e+00 bond pdb=" CB ASP B 342 " pdb=" CG ASP B 342 " ideal model delta sigma weight residual 1.516 1.552 -0.036 2.50e-02 1.60e+03 2.04e+00 ... (remaining 9722 not shown) Histogram of bond angle deviations from ideal: 92.52 - 101.00: 20 101.00 - 109.49: 836 109.49 - 117.97: 6542 117.97 - 126.46: 5647 126.46 - 134.94: 146 Bond angle restraints: 13191 Sorted by residual: angle pdb=" N PRO B 207 " pdb=" CD PRO B 207 " pdb=" CG PRO B 207 " ideal model delta sigma weight residual 103.20 95.04 8.16 1.50e+00 4.44e-01 2.96e+01 angle pdb=" C SER A 196 " pdb=" CA SER A 196 " pdb=" CB SER A 196 " ideal model delta sigma weight residual 116.54 110.70 5.84 1.15e+00 7.56e-01 2.58e+01 angle pdb=" CA PRO B 207 " pdb=" N PRO B 207 " pdb=" CD PRO B 207 " ideal model delta sigma weight residual 112.00 104.99 7.01 1.40e+00 5.10e-01 2.51e+01 angle pdb=" CB MET A 112 " pdb=" CG MET A 112 " pdb=" SD MET A 112 " ideal model delta sigma weight residual 112.70 127.71 -15.01 3.00e+00 1.11e-01 2.50e+01 angle pdb=" CB PRO B 207 " pdb=" CG PRO B 207 " pdb=" CD PRO B 207 " ideal model delta sigma weight residual 106.10 92.52 13.58 3.20e+00 9.77e-02 1.80e+01 ... (remaining 13186 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.19: 5185 17.19 - 34.38: 454 34.38 - 51.57: 140 51.57 - 68.76: 43 68.76 - 85.96: 12 Dihedral angle restraints: 5834 sinusoidal: 2270 harmonic: 3564 Sorted by residual: dihedral pdb=" CA ALA D 198 " pdb=" C ALA D 198 " pdb=" N SER D 199 " pdb=" CA SER D 199 " ideal model delta harmonic sigma weight residual 180.00 159.94 20.06 0 5.00e+00 4.00e-02 1.61e+01 dihedral pdb=" CA ARG D 179 " pdb=" C ARG D 179 " pdb=" N GLY D 180 " pdb=" CA GLY D 180 " ideal model delta harmonic sigma weight residual 180.00 163.48 16.52 0 5.00e+00 4.00e-02 1.09e+01 dihedral pdb=" CA SER D 194 " pdb=" C SER D 194 " pdb=" N ASN D 195 " pdb=" CA ASN D 195 " ideal model delta harmonic sigma weight residual 180.00 163.49 16.51 0 5.00e+00 4.00e-02 1.09e+01 ... (remaining 5831 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.039: 1052 0.039 - 0.077: 308 0.077 - 0.116: 122 0.116 - 0.154: 15 0.154 - 0.193: 4 Chirality restraints: 1501 Sorted by residual: chirality pdb=" CB VAL B 286 " pdb=" CA VAL B 286 " pdb=" CG1 VAL B 286 " pdb=" CG2 VAL B 286 " both_signs ideal model delta sigma weight residual False -2.63 -2.44 -0.19 2.00e-01 2.50e+01 9.27e-01 chirality pdb=" CB THR B 285 " pdb=" CA THR B 285 " pdb=" OG1 THR B 285 " pdb=" CG2 THR B 285 " both_signs ideal model delta sigma weight residual False 2.55 2.38 0.17 2.00e-01 2.50e+01 7.56e-01 chirality pdb=" CB VAL B 391 " pdb=" CA VAL B 391 " pdb=" CG1 VAL B 391 " pdb=" CG2 VAL B 391 " both_signs ideal model delta sigma weight residual False -2.63 -2.46 -0.16 2.00e-01 2.50e+01 6.77e-01 ... (remaining 1498 not shown) Planarity restraints: 1699 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA GLU B 283 " -0.020 2.00e-02 2.50e+03 4.01e-02 1.61e+01 pdb=" C GLU B 283 " 0.069 2.00e-02 2.50e+03 pdb=" O GLU B 283 " -0.026 2.00e-02 2.50e+03 pdb=" N LEU B 284 " -0.023 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C PHE D 266 " -0.043 5.00e-02 4.00e+02 6.60e-02 6.96e+00 pdb=" N PRO D 267 " 0.114 5.00e-02 4.00e+02 pdb=" CA PRO D 267 " -0.034 5.00e-02 4.00e+02 pdb=" CD PRO D 267 " -0.036 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASN C 200 " 0.034 5.00e-02 4.00e+02 5.18e-02 4.29e+00 pdb=" N PRO C 201 " -0.090 5.00e-02 4.00e+02 pdb=" CA PRO C 201 " 0.029 5.00e-02 4.00e+02 pdb=" CD PRO C 201 " 0.026 5.00e-02 4.00e+02 ... (remaining 1696 not shown) Histogram of nonbonded interaction distances: 2.14 - 2.69: 254 2.69 - 3.25: 9598 3.25 - 3.80: 15723 3.80 - 4.35: 21185 4.35 - 4.90: 34873 Nonbonded interactions: 81633 Sorted by model distance: nonbonded pdb=" OH TYR D 177 " pdb=" OD1 ASN D 225 " model vdw 2.144 2.440 nonbonded pdb=" OE1 GLN A 220 " pdb=" OH TYR A 303 " model vdw 2.153 2.440 nonbonded pdb=" OH TYR A 400 " pdb=" OE1 GLN A 462 " model vdw 2.156 2.440 nonbonded pdb=" OH TYR D 77 " pdb=" OD2 ASP D 118 " model vdw 2.162 2.440 nonbonded pdb=" OE1 GLU A 372 " pdb=" NE2 HIS A 432 " model vdw 2.168 2.520 ... (remaining 81628 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'B' and resid 81 through 395) selection = chain 'C' } 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: 0.770 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 3.490 Check model and map are aligned: 0.130 Set scattering table: 0.070 Process input model: 27.280 Find NCS groups from input model: 0.400 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: 0.010 Load rotamer database and sin/cos tables:12.440 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 44.630 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7145 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 : 0.003 0.058 9727 Z= 0.218 Angle : 0.709 15.012 13191 Z= 0.365 Chirality : 0.043 0.193 1501 Planarity : 0.005 0.066 1699 Dihedral : 15.673 85.956 3546 Min Nonbonded Distance : 2.144 Molprobity Statistics. All-atom Clashscore : 12.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.03 % Favored : 94.97 % Rotamer: Outliers : 2.43 % Allowed : 20.51 % Favored : 77.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % Cis-general : 0.08 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.07 (0.24), residues: 1232 helix: 1.35 (0.22), residues: 513 sheet: -0.08 (0.45), residues: 142 loop : -1.12 (0.26), residues: 577 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 163 HIS 0.005 0.001 HIS A 370 PHE 0.010 0.001 PHE A 359 TYR 0.033 0.002 TYR B 219 ARG 0.015 0.001 ARG A 126 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2464 Ramachandran restraints generated. 1232 Oldfield, 0 Emsley, 1232 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2464 Ramachandran restraints generated. 1232 Oldfield, 0 Emsley, 1232 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 147 residues out of total 1029 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 122 time to evaluate : 1.052 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 143 MET cc_start: 0.7255 (ttt) cc_final: 0.6810 (ttp) outliers start: 25 outliers final: 16 residues processed: 142 average time/residue: 0.9643 time to fit residues: 149.9950 Evaluate side-chains 133 residues out of total 1029 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 117 time to evaluate : 1.077 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 215 LEU Chi-restraints excluded: chain A residue 291 THR Chi-restraints excluded: chain A residue 368 LEU Chi-restraints excluded: chain A residue 376 SER Chi-restraints excluded: chain A residue 514 THR Chi-restraints excluded: chain B residue 258 HIS Chi-restraints excluded: chain D residue 139 ASP Chi-restraints excluded: chain D residue 140 THR Chi-restraints excluded: chain D residue 190 ASN Chi-restraints excluded: chain D residue 244 ILE Chi-restraints excluded: chain D residue 248 VAL Chi-restraints excluded: chain C residue 120 LYS Chi-restraints excluded: chain C residue 133 SER Chi-restraints excluded: chain C residue 199 SER Chi-restraints excluded: chain C residue 285 THR Chi-restraints excluded: chain C residue 306 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 103 optimal weight: 6.9990 chunk 93 optimal weight: 3.9990 chunk 51 optimal weight: 6.9990 chunk 31 optimal weight: 5.9990 chunk 62 optimal weight: 0.7980 chunk 49 optimal weight: 0.0870 chunk 96 optimal weight: 1.9990 chunk 37 optimal weight: 8.9990 chunk 58 optimal weight: 6.9990 chunk 71 optimal weight: 6.9990 chunk 111 optimal weight: 2.9990 overall best weight: 1.9764 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 271 GLN A 352 ASN A 427 GLN ** B 189 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 205 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 128 HIS ** C 196 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7267 moved from start: 0.0982 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.140 9727 Z= 0.356 Angle : 0.666 10.534 13191 Z= 0.335 Chirality : 0.045 0.160 1501 Planarity : 0.005 0.068 1699 Dihedral : 5.883 52.742 1340 Min Nonbonded Distance : 2.062 Molprobity Statistics. All-atom Clashscore : 13.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.93 % Favored : 94.07 % Rotamer: Outliers : 5.83 % Allowed : 17.40 % Favored : 76.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % Cis-general : 0.08 % 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: -0.33 (0.23), residues: 1232 helix: 0.99 (0.22), residues: 509 sheet: -0.52 (0.42), residues: 142 loop : -1.24 (0.26), residues: 581 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP A 398 HIS 0.004 0.001 HIS A 405 PHE 0.021 0.002 PHE C 335 TYR 0.026 0.002 TYR A 363 ARG 0.008 0.001 ARG A 126 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2464 Ramachandran restraints generated. 1232 Oldfield, 0 Emsley, 1232 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2464 Ramachandran restraints generated. 1232 Oldfield, 0 Emsley, 1232 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 178 residues out of total 1029 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 60 poor density : 118 time to evaluate : 1.038 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 285 TYR cc_start: 0.6733 (OUTLIER) cc_final: 0.5150 (m-80) REVERT: A 304 ASP cc_start: 0.6638 (OUTLIER) cc_final: 0.6259 (m-30) REVERT: B 180 LYS cc_start: 0.7785 (OUTLIER) cc_final: 0.7189 (mtmm) REVERT: B 337 GLU cc_start: 0.6007 (OUTLIER) cc_final: 0.5393 (pt0) REVERT: B 372 GLU cc_start: 0.8024 (OUTLIER) cc_final: 0.7341 (mt-10) REVERT: D 195 ASN cc_start: 0.7442 (OUTLIER) cc_final: 0.7134 (p0) REVERT: C 362 GLU cc_start: 0.6561 (OUTLIER) cc_final: 0.6004 (pm20) outliers start: 60 outliers final: 26 residues processed: 165 average time/residue: 1.0238 time to fit residues: 183.9099 Evaluate side-chains 140 residues out of total 1029 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 107 time to evaluate : 1.008 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 114 LEU Chi-restraints excluded: chain A residue 145 MET Chi-restraints excluded: chain A residue 210 ASP Chi-restraints excluded: chain A residue 285 TYR Chi-restraints excluded: chain A residue 304 ASP Chi-restraints excluded: chain A residue 326 THR Chi-restraints excluded: chain A residue 341 THR Chi-restraints excluded: chain A residue 376 SER Chi-restraints excluded: chain A residue 439 THR Chi-restraints excluded: chain A residue 443 MET Chi-restraints excluded: chain A residue 514 THR Chi-restraints excluded: chain A residue 536 LYS Chi-restraints excluded: chain B residue 131 THR Chi-restraints excluded: chain B residue 151 VAL Chi-restraints excluded: chain B residue 180 LYS Chi-restraints excluded: chain B residue 232 VAL Chi-restraints excluded: chain B residue 240 SER Chi-restraints excluded: chain B residue 297 ASP Chi-restraints excluded: chain B residue 337 GLU Chi-restraints excluded: chain B residue 372 GLU Chi-restraints excluded: chain D residue 125 ASP Chi-restraints excluded: chain D residue 132 VAL Chi-restraints excluded: chain D residue 139 ASP Chi-restraints excluded: chain D residue 140 THR Chi-restraints excluded: chain D residue 195 ASN Chi-restraints excluded: chain D residue 248 VAL Chi-restraints excluded: chain C residue 120 LYS Chi-restraints excluded: chain C residue 199 SER Chi-restraints excluded: chain C residue 285 THR Chi-restraints excluded: chain C residue 339 THR Chi-restraints excluded: chain C residue 348 SER Chi-restraints excluded: chain C residue 362 GLU Chi-restraints excluded: chain C residue 379 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 62 optimal weight: 0.9990 chunk 34 optimal weight: 10.0000 chunk 92 optimal weight: 0.8980 chunk 76 optimal weight: 0.7980 chunk 30 optimal weight: 1.9990 chunk 111 optimal weight: 5.9990 chunk 120 optimal weight: 5.9990 chunk 99 optimal weight: 0.9980 chunk 110 optimal weight: 2.9990 chunk 38 optimal weight: 2.9990 chunk 89 optimal weight: 0.9980 overall best weight: 0.9382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 258 ASN ** A 333 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 352 ASN A 427 GLN ** B 189 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 205 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 196 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7212 moved from start: 0.1011 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.077 9727 Z= 0.215 Angle : 0.591 10.777 13191 Z= 0.296 Chirality : 0.042 0.177 1501 Planarity : 0.005 0.069 1699 Dihedral : 4.931 36.339 1327 Min Nonbonded Distance : 2.125 Molprobity Statistics. All-atom Clashscore : 12.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.36 % Favored : 94.64 % Rotamer: Outliers : 4.08 % Allowed : 20.41 % Favored : 75.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % Cis-general : 0.08 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.05 (0.24), residues: 1232 helix: 1.35 (0.23), residues: 509 sheet: -0.51 (0.43), residues: 141 loop : -1.18 (0.26), residues: 582 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 398 HIS 0.004 0.001 HIS A 370 PHE 0.014 0.001 PHE D 137 TYR 0.020 0.001 TYR A 363 ARG 0.008 0.000 ARG A 126 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2464 Ramachandran restraints generated. 1232 Oldfield, 0 Emsley, 1232 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2464 Ramachandran restraints generated. 1232 Oldfield, 0 Emsley, 1232 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 166 residues out of total 1029 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 124 time to evaluate : 1.105 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 111 MET cc_start: 0.5182 (ppp) cc_final: 0.4903 (ppp) REVERT: A 227 GLU cc_start: 0.7612 (mt-10) cc_final: 0.7390 (mm-30) REVERT: A 304 ASP cc_start: 0.6419 (OUTLIER) cc_final: 0.6118 (m-30) REVERT: B 337 GLU cc_start: 0.6288 (OUTLIER) cc_final: 0.5631 (pt0) REVERT: B 372 GLU cc_start: 0.7859 (OUTLIER) cc_final: 0.7145 (mt-10) REVERT: D 143 MET cc_start: 0.7198 (ttt) cc_final: 0.6751 (ttp) REVERT: C 252 VAL cc_start: 0.7014 (OUTLIER) cc_final: 0.6774 (m) outliers start: 42 outliers final: 19 residues processed: 159 average time/residue: 1.0191 time to fit residues: 177.0222 Evaluate side-chains 136 residues out of total 1029 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 113 time to evaluate : 1.105 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 145 MET Chi-restraints excluded: chain A residue 210 ASP Chi-restraints excluded: chain A residue 215 LEU Chi-restraints excluded: chain A residue 304 ASP Chi-restraints excluded: chain A residue 341 THR Chi-restraints excluded: chain A residue 439 THR Chi-restraints excluded: chain A residue 514 THR Chi-restraints excluded: chain A residue 536 LYS Chi-restraints excluded: chain A residue 538 MET Chi-restraints excluded: chain B residue 151 VAL Chi-restraints excluded: chain B residue 170 ASP Chi-restraints excluded: chain B residue 297 ASP Chi-restraints excluded: chain B residue 337 GLU Chi-restraints excluded: chain B residue 372 GLU Chi-restraints excluded: chain D residue 91 LEU Chi-restraints excluded: chain D residue 139 ASP Chi-restraints excluded: chain D residue 140 THR Chi-restraints excluded: chain D residue 244 ILE Chi-restraints excluded: chain D residue 248 VAL Chi-restraints excluded: chain C residue 252 VAL Chi-restraints excluded: chain C residue 262 THR Chi-restraints excluded: chain C residue 348 SER Chi-restraints excluded: chain C residue 379 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 110 optimal weight: 1.9990 chunk 84 optimal weight: 1.9990 chunk 58 optimal weight: 0.1980 chunk 12 optimal weight: 1.9990 chunk 53 optimal weight: 0.1980 chunk 75 optimal weight: 4.9990 chunk 112 optimal weight: 4.9990 chunk 118 optimal weight: 2.9990 chunk 106 optimal weight: 0.6980 chunk 32 optimal weight: 2.9990 chunk 99 optimal weight: 1.9990 overall best weight: 1.0184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 333 HIS A 427 GLN A 448 GLN ** B 189 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 205 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 173 ASN ** C 196 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7217 moved from start: 0.1130 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.084 9727 Z= 0.227 Angle : 0.615 10.930 13191 Z= 0.303 Chirality : 0.043 0.168 1501 Planarity : 0.005 0.068 1699 Dihedral : 4.581 31.545 1320 Min Nonbonded Distance : 2.114 Molprobity Statistics. All-atom Clashscore : 12.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.36 % Favored : 94.64 % Rotamer: Outliers : 5.44 % Allowed : 19.24 % Favored : 75.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % Cis-general : 0.08 % 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 (0.24), residues: 1232 helix: 1.40 (0.23), residues: 510 sheet: -0.49 (0.43), residues: 143 loop : -1.21 (0.26), residues: 579 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 398 HIS 0.003 0.001 HIS A 370 PHE 0.014 0.001 PHE C 335 TYR 0.021 0.002 TYR A 363 ARG 0.006 0.000 ARG A 126 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2464 Ramachandran restraints generated. 1232 Oldfield, 0 Emsley, 1232 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2464 Ramachandran restraints generated. 1232 Oldfield, 0 Emsley, 1232 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 177 residues out of total 1029 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 56 poor density : 121 time to evaluate : 1.002 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 227 GLU cc_start: 0.7608 (mt-10) cc_final: 0.7354 (mm-30) REVERT: A 285 TYR cc_start: 0.7033 (OUTLIER) cc_final: 0.5512 (m-80) REVERT: A 304 ASP cc_start: 0.6389 (OUTLIER) cc_final: 0.6054 (m-30) REVERT: B 337 GLU cc_start: 0.6283 (OUTLIER) cc_final: 0.5539 (pt0) REVERT: B 372 GLU cc_start: 0.7891 (OUTLIER) cc_final: 0.7203 (mt-10) REVERT: D 143 MET cc_start: 0.7142 (ttt) cc_final: 0.6733 (ttp) REVERT: D 195 ASN cc_start: 0.7386 (OUTLIER) cc_final: 0.7071 (p0) REVERT: C 252 VAL cc_start: 0.7036 (OUTLIER) cc_final: 0.6794 (m) REVERT: C 263 ILE cc_start: 0.7882 (OUTLIER) cc_final: 0.7466 (mm) outliers start: 56 outliers final: 24 residues processed: 162 average time/residue: 0.9603 time to fit residues: 170.6846 Evaluate side-chains 147 residues out of total 1029 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 116 time to evaluate : 1.185 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 145 MET Chi-restraints excluded: chain A residue 197 VAL Chi-restraints excluded: chain A residue 210 ASP Chi-restraints excluded: chain A residue 215 LEU Chi-restraints excluded: chain A residue 285 TYR Chi-restraints excluded: chain A residue 304 ASP Chi-restraints excluded: chain A residue 341 THR Chi-restraints excluded: chain A residue 439 THR Chi-restraints excluded: chain A residue 514 THR Chi-restraints excluded: chain A residue 536 LYS Chi-restraints excluded: chain B residue 133 SER Chi-restraints excluded: chain B residue 151 VAL Chi-restraints excluded: chain B residue 170 ASP Chi-restraints excluded: chain B residue 297 ASP Chi-restraints excluded: chain B residue 337 GLU Chi-restraints excluded: chain B residue 372 GLU Chi-restraints excluded: chain D residue 91 LEU Chi-restraints excluded: chain D residue 125 ASP Chi-restraints excluded: chain D residue 139 ASP Chi-restraints excluded: chain D residue 140 THR Chi-restraints excluded: chain D residue 195 ASN Chi-restraints excluded: chain D residue 244 ILE Chi-restraints excluded: chain C residue 99 SER Chi-restraints excluded: chain C residue 252 VAL Chi-restraints excluded: chain C residue 262 THR Chi-restraints excluded: chain C residue 263 ILE Chi-restraints excluded: chain C residue 306 THR Chi-restraints excluded: chain C residue 339 THR Chi-restraints excluded: chain C residue 348 SER Chi-restraints excluded: chain C residue 369 THR Chi-restraints excluded: chain C residue 379 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 67 optimal weight: 6.9990 chunk 1 optimal weight: 4.9990 chunk 88 optimal weight: 3.9990 chunk 49 optimal weight: 4.9990 chunk 101 optimal weight: 10.0000 chunk 82 optimal weight: 4.9990 chunk 0 optimal weight: 9.9990 chunk 60 optimal weight: 4.9990 chunk 106 optimal weight: 0.6980 chunk 30 optimal weight: 0.8980 chunk 40 optimal weight: 3.9990 overall best weight: 2.9186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 352 ASN A 397 HIS A 427 GLN ** D 205 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 173 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7338 moved from start: 0.1782 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.174 9727 Z= 0.484 Angle : 0.772 11.013 13191 Z= 0.388 Chirality : 0.049 0.187 1501 Planarity : 0.006 0.071 1699 Dihedral : 5.274 35.098 1319 Min Nonbonded Distance : 2.041 Molprobity Statistics. All-atom Clashscore : 17.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.22 % Favored : 92.78 % Rotamer: Outliers : 6.22 % Allowed : 19.63 % Favored : 74.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % Cis-general : 0.08 % 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: -0.84 (0.23), residues: 1232 helix: 0.59 (0.22), residues: 508 sheet: -0.97 (0.42), residues: 150 loop : -1.48 (0.25), residues: 574 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP A 163 HIS 0.007 0.002 HIS A 405 PHE 0.026 0.002 PHE C 335 TYR 0.031 0.003 TYR A 363 ARG 0.008 0.001 ARG A 126 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2464 Ramachandran restraints generated. 1232 Oldfield, 0 Emsley, 1232 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2464 Ramachandran restraints generated. 1232 Oldfield, 0 Emsley, 1232 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 184 residues out of total 1029 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 64 poor density : 120 time to evaluate : 1.126 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 129 MET cc_start: 0.8350 (OUTLIER) cc_final: 0.8126 (mmm) REVERT: A 184 MET cc_start: 0.8051 (OUTLIER) cc_final: 0.7252 (tpp) REVERT: A 285 TYR cc_start: 0.7464 (OUTLIER) cc_final: 0.5626 (m-80) REVERT: A 304 ASP cc_start: 0.7001 (OUTLIER) cc_final: 0.6680 (m-30) REVERT: B 337 GLU cc_start: 0.5954 (OUTLIER) cc_final: 0.5523 (pt0) REVERT: B 372 GLU cc_start: 0.8073 (OUTLIER) cc_final: 0.7397 (mt-10) REVERT: D 133 GLU cc_start: 0.8111 (OUTLIER) cc_final: 0.7206 (tm-30) REVERT: D 195 ASN cc_start: 0.7459 (OUTLIER) cc_final: 0.7157 (p0) REVERT: C 252 VAL cc_start: 0.7244 (OUTLIER) cc_final: 0.6972 (m) REVERT: C 263 ILE cc_start: 0.8243 (OUTLIER) cc_final: 0.7912 (mm) REVERT: C 362 GLU cc_start: 0.6394 (OUTLIER) cc_final: 0.5883 (pm20) outliers start: 64 outliers final: 28 residues processed: 168 average time/residue: 1.0154 time to fit residues: 185.7862 Evaluate side-chains 154 residues out of total 1029 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 115 time to evaluate : 1.007 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 129 MET Chi-restraints excluded: chain A residue 145 MET Chi-restraints excluded: chain A residue 184 MET Chi-restraints excluded: chain A residue 197 VAL Chi-restraints excluded: chain A residue 285 TYR Chi-restraints excluded: chain A residue 304 ASP Chi-restraints excluded: chain A residue 341 THR Chi-restraints excluded: chain A residue 439 THR Chi-restraints excluded: chain A residue 514 THR Chi-restraints excluded: chain A residue 538 MET Chi-restraints excluded: chain B residue 131 THR Chi-restraints excluded: chain B residue 133 SER Chi-restraints excluded: chain B residue 150 ASP Chi-restraints excluded: chain B residue 151 VAL Chi-restraints excluded: chain B residue 232 VAL Chi-restraints excluded: chain B residue 240 SER Chi-restraints excluded: chain B residue 297 ASP Chi-restraints excluded: chain B residue 337 GLU Chi-restraints excluded: chain B residue 350 VAL Chi-restraints excluded: chain B residue 360 VAL Chi-restraints excluded: chain B residue 372 GLU Chi-restraints excluded: chain D residue 91 LEU Chi-restraints excluded: chain D residue 125 ASP Chi-restraints excluded: chain D residue 133 GLU Chi-restraints excluded: chain D residue 139 ASP Chi-restraints excluded: chain D residue 140 THR Chi-restraints excluded: chain D residue 195 ASN Chi-restraints excluded: chain D residue 244 ILE Chi-restraints excluded: chain D residue 248 VAL Chi-restraints excluded: chain C residue 99 SER Chi-restraints excluded: chain C residue 120 LYS Chi-restraints excluded: chain C residue 252 VAL Chi-restraints excluded: chain C residue 262 THR Chi-restraints excluded: chain C residue 263 ILE Chi-restraints excluded: chain C residue 306 THR Chi-restraints excluded: chain C residue 339 THR Chi-restraints excluded: chain C residue 362 GLU Chi-restraints excluded: chain C residue 369 THR Chi-restraints excluded: chain C residue 379 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 107 optimal weight: 0.6980 chunk 23 optimal weight: 0.0060 chunk 69 optimal weight: 3.9990 chunk 29 optimal weight: 0.7980 chunk 119 optimal weight: 0.5980 chunk 98 optimal weight: 0.6980 chunk 55 optimal weight: 2.9990 chunk 9 optimal weight: 0.9990 chunk 39 optimal weight: 4.9990 chunk 62 optimal weight: 0.3980 chunk 114 optimal weight: 0.9990 overall best weight: 0.4796 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 352 ASN A 427 GLN A 437 ASN ** B 189 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 205 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 196 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7209 moved from start: 0.1518 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 9727 Z= 0.190 Angle : 0.648 12.552 13191 Z= 0.322 Chirality : 0.043 0.172 1501 Planarity : 0.005 0.068 1699 Dihedral : 4.636 31.638 1319 Min Nonbonded Distance : 2.126 Molprobity Statistics. All-atom Clashscore : 12.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.36 % Favored : 94.64 % Rotamer: Outliers : 4.66 % Allowed : 21.67 % Favored : 73.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % Cis-general : 0.08 % 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: -0.20 (0.24), residues: 1232 helix: 1.30 (0.23), residues: 510 sheet: -0.53 (0.42), residues: 143 loop : -1.36 (0.25), residues: 579 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 163 HIS 0.006 0.001 HIS A 370 PHE 0.011 0.001 PHE A 359 TYR 0.022 0.001 TYR B 371 ARG 0.011 0.000 ARG A 126 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2464 Ramachandran restraints generated. 1232 Oldfield, 0 Emsley, 1232 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2464 Ramachandran restraints generated. 1232 Oldfield, 0 Emsley, 1232 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 178 residues out of total 1029 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 130 time to evaluate : 0.998 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 111 MET cc_start: 0.5129 (ppp) cc_final: 0.4257 (ppp) REVERT: A 184 MET cc_start: 0.7913 (OUTLIER) cc_final: 0.7104 (tpp) REVERT: A 227 GLU cc_start: 0.7609 (mt-10) cc_final: 0.7331 (mm-30) REVERT: A 285 TYR cc_start: 0.7201 (OUTLIER) cc_final: 0.5644 (m-80) REVERT: A 304 ASP cc_start: 0.6464 (OUTLIER) cc_final: 0.6200 (m-30) REVERT: B 337 GLU cc_start: 0.6029 (OUTLIER) cc_final: 0.5389 (pt0) REVERT: B 372 GLU cc_start: 0.7840 (OUTLIER) cc_final: 0.7091 (mt-10) REVERT: D 195 ASN cc_start: 0.7356 (OUTLIER) cc_final: 0.7056 (p0) REVERT: C 252 VAL cc_start: 0.7078 (OUTLIER) cc_final: 0.6800 (m) REVERT: C 263 ILE cc_start: 0.7995 (OUTLIER) cc_final: 0.7582 (mm) outliers start: 48 outliers final: 18 residues processed: 164 average time/residue: 1.0154 time to fit residues: 181.7092 Evaluate side-chains 143 residues out of total 1029 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 117 time to evaluate : 1.077 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 145 MET Chi-restraints excluded: chain A residue 184 MET Chi-restraints excluded: chain A residue 197 VAL Chi-restraints excluded: chain A residue 285 TYR Chi-restraints excluded: chain A residue 304 ASP Chi-restraints excluded: chain A residue 437 ASN Chi-restraints excluded: chain A residue 439 THR Chi-restraints excluded: chain B residue 131 THR Chi-restraints excluded: chain B residue 133 SER Chi-restraints excluded: chain B residue 337 GLU Chi-restraints excluded: chain B residue 341 THR Chi-restraints excluded: chain B residue 360 VAL Chi-restraints excluded: chain B residue 372 GLU Chi-restraints excluded: chain D residue 91 LEU Chi-restraints excluded: chain D residue 125 ASP Chi-restraints excluded: chain D residue 139 ASP Chi-restraints excluded: chain D residue 140 THR Chi-restraints excluded: chain D residue 195 ASN Chi-restraints excluded: chain C residue 120 LYS Chi-restraints excluded: chain C residue 252 VAL Chi-restraints excluded: chain C residue 262 THR Chi-restraints excluded: chain C residue 263 ILE Chi-restraints excluded: chain C residue 339 THR Chi-restraints excluded: chain C residue 369 THR Chi-restraints excluded: chain C residue 379 LEU Chi-restraints excluded: chain C residue 380 LYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 13 optimal weight: 0.6980 chunk 67 optimal weight: 4.9990 chunk 86 optimal weight: 8.9990 chunk 100 optimal weight: 10.0000 chunk 66 optimal weight: 2.9990 chunk 118 optimal weight: 3.9990 chunk 74 optimal weight: 7.9990 chunk 72 optimal weight: 3.9990 chunk 54 optimal weight: 0.0970 chunk 73 optimal weight: 1.9990 chunk 47 optimal weight: 0.9980 overall best weight: 1.3582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 352 ASN A 427 GLN ** D 205 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 196 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 236 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7255 moved from start: 0.1574 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.105 9727 Z= 0.279 Angle : 0.673 11.557 13191 Z= 0.337 Chirality : 0.044 0.169 1501 Planarity : 0.005 0.068 1699 Dihedral : 4.685 31.777 1318 Min Nonbonded Distance : 2.101 Molprobity Statistics. All-atom Clashscore : 14.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.49 % Favored : 93.51 % Rotamer: Outliers : 4.66 % Allowed : 22.64 % Favored : 72.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % Cis-general : 0.08 % 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: -0.32 (0.24), residues: 1232 helix: 1.17 (0.22), residues: 510 sheet: -0.75 (0.42), residues: 142 loop : -1.35 (0.25), residues: 580 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 163 HIS 0.005 0.001 HIS A 333 PHE 0.017 0.002 PHE C 335 TYR 0.024 0.002 TYR A 363 ARG 0.010 0.001 ARG A 126 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2464 Ramachandran restraints generated. 1232 Oldfield, 0 Emsley, 1232 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2464 Ramachandran restraints generated. 1232 Oldfield, 0 Emsley, 1232 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 168 residues out of total 1029 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 120 time to evaluate : 1.067 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 111 MET cc_start: 0.5085 (ppp) cc_final: 0.4253 (ppp) REVERT: A 184 MET cc_start: 0.7967 (OUTLIER) cc_final: 0.7170 (tpp) REVERT: A 227 GLU cc_start: 0.7603 (mt-10) cc_final: 0.7350 (mm-30) REVERT: A 285 TYR cc_start: 0.7463 (OUTLIER) cc_final: 0.5812 (m-80) REVERT: B 337 GLU cc_start: 0.5719 (OUTLIER) cc_final: 0.5067 (pt0) REVERT: B 372 GLU cc_start: 0.7870 (OUTLIER) cc_final: 0.7148 (mt-10) REVERT: D 195 ASN cc_start: 0.7424 (OUTLIER) cc_final: 0.7124 (p0) REVERT: C 252 VAL cc_start: 0.7163 (OUTLIER) cc_final: 0.6901 (m) REVERT: C 263 ILE cc_start: 0.8045 (OUTLIER) cc_final: 0.7604 (mm) outliers start: 48 outliers final: 26 residues processed: 156 average time/residue: 1.0090 time to fit residues: 171.8938 Evaluate side-chains 149 residues out of total 1029 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 116 time to evaluate : 1.145 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 145 MET Chi-restraints excluded: chain A residue 184 MET Chi-restraints excluded: chain A residue 197 VAL Chi-restraints excluded: chain A residue 285 TYR Chi-restraints excluded: chain A residue 341 THR Chi-restraints excluded: chain A residue 439 THR Chi-restraints excluded: chain A residue 514 THR Chi-restraints excluded: chain A residue 516 LEU Chi-restraints excluded: chain B residue 131 THR Chi-restraints excluded: chain B residue 133 SER Chi-restraints excluded: chain B residue 151 VAL Chi-restraints excluded: chain B residue 232 VAL Chi-restraints excluded: chain B residue 337 GLU Chi-restraints excluded: chain B residue 341 THR Chi-restraints excluded: chain B residue 350 VAL Chi-restraints excluded: chain B residue 360 VAL Chi-restraints excluded: chain B residue 372 GLU Chi-restraints excluded: chain D residue 91 LEU Chi-restraints excluded: chain D residue 125 ASP Chi-restraints excluded: chain D residue 139 ASP Chi-restraints excluded: chain D residue 140 THR Chi-restraints excluded: chain D residue 195 ASN Chi-restraints excluded: chain D residue 196 LEU Chi-restraints excluded: chain D residue 248 VAL Chi-restraints excluded: chain C residue 99 SER Chi-restraints excluded: chain C residue 120 LYS Chi-restraints excluded: chain C residue 252 VAL Chi-restraints excluded: chain C residue 262 THR Chi-restraints excluded: chain C residue 263 ILE Chi-restraints excluded: chain C residue 306 THR Chi-restraints excluded: chain C residue 339 THR Chi-restraints excluded: chain C residue 369 THR Chi-restraints excluded: chain C residue 379 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 70 optimal weight: 6.9990 chunk 35 optimal weight: 0.7980 chunk 23 optimal weight: 1.9990 chunk 22 optimal weight: 3.9990 chunk 75 optimal weight: 2.9990 chunk 80 optimal weight: 7.9990 chunk 58 optimal weight: 3.9990 chunk 11 optimal weight: 4.9990 chunk 93 optimal weight: 1.9990 chunk 107 optimal weight: 1.9990 chunk 113 optimal weight: 5.9990 overall best weight: 1.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 427 GLN A 437 ASN ** D 205 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 173 ASN ** C 196 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 258 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7296 moved from start: 0.1810 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.134 9727 Z= 0.356 Angle : 0.723 11.968 13191 Z= 0.363 Chirality : 0.046 0.170 1501 Planarity : 0.005 0.067 1699 Dihedral : 4.941 32.847 1318 Min Nonbonded Distance : 2.087 Molprobity Statistics. All-atom Clashscore : 14.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.49 % Favored : 93.51 % Rotamer: Outliers : 5.44 % Allowed : 22.25 % Favored : 72.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % Cis-general : 0.08 % 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: -0.63 (0.23), residues: 1232 helix: 0.87 (0.22), residues: 510 sheet: -0.80 (0.41), residues: 154 loop : -1.52 (0.25), residues: 568 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP A 398 HIS 0.005 0.001 HIS A 405 PHE 0.021 0.002 PHE C 335 TYR 0.026 0.002 TYR A 363 ARG 0.013 0.001 ARG A 126 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2464 Ramachandran restraints generated. 1232 Oldfield, 0 Emsley, 1232 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2464 Ramachandran restraints generated. 1232 Oldfield, 0 Emsley, 1232 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 181 residues out of total 1029 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 56 poor density : 125 time to evaluate : 1.132 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 111 MET cc_start: 0.5087 (ppp) cc_final: 0.4223 (ppp) REVERT: A 184 MET cc_start: 0.7995 (OUTLIER) cc_final: 0.7189 (tpp) REVERT: A 227 GLU cc_start: 0.7590 (mt-10) cc_final: 0.7307 (mm-30) REVERT: A 285 TYR cc_start: 0.7534 (OUTLIER) cc_final: 0.5830 (m-80) REVERT: B 337 GLU cc_start: 0.5851 (OUTLIER) cc_final: 0.5331 (pt0) REVERT: B 372 GLU cc_start: 0.7957 (OUTLIER) cc_final: 0.7254 (mt-10) REVERT: D 195 ASN cc_start: 0.7499 (OUTLIER) cc_final: 0.7197 (p0) REVERT: C 252 VAL cc_start: 0.7178 (OUTLIER) cc_final: 0.6898 (m) REVERT: C 263 ILE cc_start: 0.8150 (OUTLIER) cc_final: 0.7722 (mm) REVERT: C 377 GLU cc_start: 0.8328 (OUTLIER) cc_final: 0.7931 (mp0) outliers start: 56 outliers final: 34 residues processed: 170 average time/residue: 0.9998 time to fit residues: 185.7327 Evaluate side-chains 158 residues out of total 1029 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 116 time to evaluate : 1.064 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 145 MET Chi-restraints excluded: chain A residue 184 MET Chi-restraints excluded: chain A residue 197 VAL Chi-restraints excluded: chain A residue 210 ASP Chi-restraints excluded: chain A residue 285 TYR Chi-restraints excluded: chain A residue 341 THR Chi-restraints excluded: chain A residue 376 SER Chi-restraints excluded: chain A residue 439 THR Chi-restraints excluded: chain A residue 514 THR Chi-restraints excluded: chain A residue 516 LEU Chi-restraints excluded: chain B residue 116 ILE Chi-restraints excluded: chain B residue 131 THR Chi-restraints excluded: chain B residue 133 SER Chi-restraints excluded: chain B residue 150 ASP Chi-restraints excluded: chain B residue 151 VAL Chi-restraints excluded: chain B residue 232 VAL Chi-restraints excluded: chain B residue 240 SER Chi-restraints excluded: chain B residue 297 ASP Chi-restraints excluded: chain B residue 337 GLU Chi-restraints excluded: chain B residue 341 THR Chi-restraints excluded: chain B residue 350 VAL Chi-restraints excluded: chain B residue 360 VAL Chi-restraints excluded: chain B residue 372 GLU Chi-restraints excluded: chain D residue 91 LEU Chi-restraints excluded: chain D residue 125 ASP Chi-restraints excluded: chain D residue 139 ASP Chi-restraints excluded: chain D residue 140 THR Chi-restraints excluded: chain D residue 195 ASN Chi-restraints excluded: chain D residue 196 LEU Chi-restraints excluded: chain D residue 244 ILE Chi-restraints excluded: chain D residue 248 VAL Chi-restraints excluded: chain C residue 99 SER Chi-restraints excluded: chain C residue 120 LYS Chi-restraints excluded: chain C residue 252 VAL Chi-restraints excluded: chain C residue 262 THR Chi-restraints excluded: chain C residue 263 ILE Chi-restraints excluded: chain C residue 285 THR Chi-restraints excluded: chain C residue 306 THR Chi-restraints excluded: chain C residue 339 THR Chi-restraints excluded: chain C residue 369 THR Chi-restraints excluded: chain C residue 377 GLU Chi-restraints excluded: chain C residue 379 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 103 optimal weight: 4.9990 chunk 110 optimal weight: 0.8980 chunk 113 optimal weight: 0.6980 chunk 66 optimal weight: 2.9990 chunk 48 optimal weight: 0.8980 chunk 86 optimal weight: 4.9990 chunk 33 optimal weight: 3.9990 chunk 99 optimal weight: 2.9990 chunk 104 optimal weight: 0.7980 chunk 72 optimal weight: 0.9990 chunk 116 optimal weight: 0.6980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 427 GLN B 128 HIS ** B 189 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 205 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 196 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7230 moved from start: 0.1694 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.075 9727 Z= 0.217 Angle : 0.674 12.395 13191 Z= 0.335 Chirality : 0.043 0.172 1501 Planarity : 0.005 0.069 1699 Dihedral : 4.632 30.543 1318 Min Nonbonded Distance : 2.120 Molprobity Statistics. All-atom Clashscore : 13.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.01 % Favored : 93.99 % Rotamer: Outliers : 4.18 % Allowed : 23.91 % Favored : 71.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % Cis-general : 0.08 % 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: -0.28 (0.24), residues: 1232 helix: 1.22 (0.23), residues: 511 sheet: -0.58 (0.42), residues: 143 loop : -1.39 (0.25), residues: 578 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.001 TRP A 163 HIS 0.005 0.001 HIS A 370 PHE 0.013 0.001 PHE C 335 TYR 0.021 0.001 TYR C 114 ARG 0.012 0.001 ARG A 126 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2464 Ramachandran restraints generated. 1232 Oldfield, 0 Emsley, 1232 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2464 Ramachandran restraints generated. 1232 Oldfield, 0 Emsley, 1232 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 163 residues out of total 1029 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 120 time to evaluate : 1.065 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 111 MET cc_start: 0.5078 (ppp) cc_final: 0.4265 (ppp) REVERT: A 184 MET cc_start: 0.7928 (OUTLIER) cc_final: 0.7131 (tpp) REVERT: A 227 GLU cc_start: 0.7605 (mt-10) cc_final: 0.7330 (mm-30) REVERT: A 285 TYR cc_start: 0.7324 (OUTLIER) cc_final: 0.5919 (m-80) REVERT: B 337 GLU cc_start: 0.5815 (OUTLIER) cc_final: 0.5126 (pt0) REVERT: B 372 GLU cc_start: 0.7835 (OUTLIER) cc_final: 0.7105 (mt-10) REVERT: D 195 ASN cc_start: 0.7383 (OUTLIER) cc_final: 0.7084 (p0) REVERT: C 252 VAL cc_start: 0.7076 (OUTLIER) cc_final: 0.6792 (m) REVERT: C 263 ILE cc_start: 0.7991 (OUTLIER) cc_final: 0.7579 (mm) outliers start: 43 outliers final: 28 residues processed: 153 average time/residue: 0.9538 time to fit residues: 160.0273 Evaluate side-chains 150 residues out of total 1029 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 115 time to evaluate : 1.079 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 145 MET Chi-restraints excluded: chain A residue 184 MET Chi-restraints excluded: chain A residue 197 VAL Chi-restraints excluded: chain A residue 210 ASP Chi-restraints excluded: chain A residue 215 LEU Chi-restraints excluded: chain A residue 285 TYR Chi-restraints excluded: chain A residue 304 ASP Chi-restraints excluded: chain A residue 341 THR Chi-restraints excluded: chain A residue 376 SER Chi-restraints excluded: chain A residue 439 THR Chi-restraints excluded: chain A residue 514 THR Chi-restraints excluded: chain A residue 516 LEU Chi-restraints excluded: chain B residue 116 ILE Chi-restraints excluded: chain B residue 131 THR Chi-restraints excluded: chain B residue 133 SER Chi-restraints excluded: chain B residue 240 SER Chi-restraints excluded: chain B residue 337 GLU Chi-restraints excluded: chain B residue 350 VAL Chi-restraints excluded: chain B residue 360 VAL Chi-restraints excluded: chain B residue 372 GLU Chi-restraints excluded: chain D residue 91 LEU Chi-restraints excluded: chain D residue 125 ASP Chi-restraints excluded: chain D residue 139 ASP Chi-restraints excluded: chain D residue 140 THR Chi-restraints excluded: chain D residue 195 ASN Chi-restraints excluded: chain D residue 196 LEU Chi-restraints excluded: chain D residue 248 VAL Chi-restraints excluded: chain C residue 120 LYS Chi-restraints excluded: chain C residue 218 VAL Chi-restraints excluded: chain C residue 252 VAL Chi-restraints excluded: chain C residue 262 THR Chi-restraints excluded: chain C residue 263 ILE Chi-restraints excluded: chain C residue 339 THR Chi-restraints excluded: chain C residue 369 THR Chi-restraints excluded: chain C residue 379 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 71 optimal weight: 8.9990 chunk 55 optimal weight: 2.9990 chunk 81 optimal weight: 0.8980 chunk 122 optimal weight: 0.9980 chunk 112 optimal weight: 3.9990 chunk 97 optimal weight: 4.9990 chunk 10 optimal weight: 2.9990 chunk 75 optimal weight: 2.9990 chunk 59 optimal weight: 1.9990 chunk 77 optimal weight: 2.9990 chunk 103 optimal weight: 0.8980 overall best weight: 1.5584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 427 GLN ** D 205 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 196 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 236 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7272 moved from start: 0.1818 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.116 9727 Z= 0.306 Angle : 0.719 14.000 13191 Z= 0.358 Chirality : 0.045 0.168 1501 Planarity : 0.005 0.070 1699 Dihedral : 4.763 31.293 1318 Min Nonbonded Distance : 2.094 Molprobity Statistics. All-atom Clashscore : 14.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.57 % Favored : 93.43 % Rotamer: Outliers : 4.66 % Allowed : 23.81 % Favored : 71.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % Cis-general : 0.08 % 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: -0.47 (0.24), residues: 1232 helix: 1.03 (0.22), residues: 510 sheet: -0.72 (0.41), residues: 153 loop : -1.46 (0.25), residues: 569 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP A 163 HIS 0.005 0.001 HIS A 333 PHE 0.018 0.002 PHE C 335 TYR 0.024 0.002 TYR C 114 ARG 0.016 0.001 ARG A 126 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2464 Ramachandran restraints generated. 1232 Oldfield, 0 Emsley, 1232 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2464 Ramachandran restraints generated. 1232 Oldfield, 0 Emsley, 1232 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 169 residues out of total 1029 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 121 time to evaluate : 1.051 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 111 MET cc_start: 0.5069 (ppp) cc_final: 0.4243 (ppp) REVERT: A 184 MET cc_start: 0.7918 (OUTLIER) cc_final: 0.7160 (tpp) REVERT: A 227 GLU cc_start: 0.7560 (mt-10) cc_final: 0.7270 (mm-30) REVERT: A 285 TYR cc_start: 0.7457 (OUTLIER) cc_final: 0.5929 (m-80) REVERT: B 337 GLU cc_start: 0.5717 (OUTLIER) cc_final: 0.5139 (pt0) REVERT: B 372 GLU cc_start: 0.7890 (OUTLIER) cc_final: 0.7185 (mt-10) REVERT: D 195 ASN cc_start: 0.7469 (OUTLIER) cc_final: 0.7169 (p0) REVERT: C 252 VAL cc_start: 0.7129 (OUTLIER) cc_final: 0.6864 (m) REVERT: C 263 ILE cc_start: 0.8075 (OUTLIER) cc_final: 0.7648 (mm) outliers start: 48 outliers final: 33 residues processed: 158 average time/residue: 1.0242 time to fit residues: 176.9948 Evaluate side-chains 161 residues out of total 1029 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 121 time to evaluate : 1.005 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 145 MET Chi-restraints excluded: chain A residue 184 MET Chi-restraints excluded: chain A residue 197 VAL Chi-restraints excluded: chain A residue 210 ASP Chi-restraints excluded: chain A residue 215 LEU Chi-restraints excluded: chain A residue 285 TYR Chi-restraints excluded: chain A residue 304 ASP Chi-restraints excluded: chain A residue 341 THR Chi-restraints excluded: chain A residue 376 SER Chi-restraints excluded: chain A residue 439 THR Chi-restraints excluded: chain A residue 514 THR Chi-restraints excluded: chain A residue 516 LEU Chi-restraints excluded: chain A residue 538 MET Chi-restraints excluded: chain B residue 116 ILE Chi-restraints excluded: chain B residue 131 THR Chi-restraints excluded: chain B residue 133 SER Chi-restraints excluded: chain B residue 232 VAL Chi-restraints excluded: chain B residue 240 SER Chi-restraints excluded: chain B residue 337 GLU Chi-restraints excluded: chain B residue 350 VAL Chi-restraints excluded: chain B residue 360 VAL Chi-restraints excluded: chain B residue 372 GLU Chi-restraints excluded: chain D residue 91 LEU Chi-restraints excluded: chain D residue 125 ASP Chi-restraints excluded: chain D residue 139 ASP Chi-restraints excluded: chain D residue 140 THR Chi-restraints excluded: chain D residue 195 ASN Chi-restraints excluded: chain D residue 196 LEU Chi-restraints excluded: chain D residue 244 ILE Chi-restraints excluded: chain D residue 248 VAL Chi-restraints excluded: chain C residue 99 SER Chi-restraints excluded: chain C residue 120 LYS Chi-restraints excluded: chain C residue 218 VAL Chi-restraints excluded: chain C residue 252 VAL Chi-restraints excluded: chain C residue 262 THR Chi-restraints excluded: chain C residue 263 ILE Chi-restraints excluded: chain C residue 285 THR Chi-restraints excluded: chain C residue 339 THR Chi-restraints excluded: chain C residue 369 THR Chi-restraints excluded: chain C residue 379 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 29 optimal weight: 1.9990 chunk 89 optimal weight: 2.9990 chunk 14 optimal weight: 0.7980 chunk 27 optimal weight: 1.9990 chunk 97 optimal weight: 2.9990 chunk 40 optimal weight: 0.7980 chunk 100 optimal weight: 10.0000 chunk 12 optimal weight: 2.9990 chunk 18 optimal weight: 1.9990 chunk 85 optimal weight: 0.9980 chunk 5 optimal weight: 0.6980 overall best weight: 1.0582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 427 GLN ** B 189 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 205 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 196 HIS ** 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 = 0.4181 r_free = 0.4181 target = 0.176009 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3770 r_free = 0.3770 target = 0.138771 restraints weight = 11249.363| |-----------------------------------------------------------------------------| r_work (start): 0.3770 rms_B_bonded: 2.46 r_work: 0.3632 rms_B_bonded: 3.22 restraints_weight: 0.5000 r_work (final): 0.3632 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7097 moved from start: 0.1754 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.086 9727 Z= 0.241 Angle : 0.684 14.040 13191 Z= 0.340 Chirality : 0.044 0.168 1501 Planarity : 0.005 0.072 1699 Dihedral : 4.644 30.195 1318 Min Nonbonded Distance : 2.112 Molprobity Statistics. All-atom Clashscore : 13.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.17 % Favored : 93.83 % Rotamer: Outliers : 4.57 % Allowed : 24.00 % Favored : 71.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % Cis-general : 0.08 % 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: -0.33 (0.24), residues: 1232 helix: 1.13 (0.23), residues: 510 sheet: -0.72 (0.43), residues: 142 loop : -1.32 (0.25), residues: 580 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP A 163 HIS 0.005 0.001 HIS A 333 PHE 0.015 0.001 PHE C 335 TYR 0.023 0.002 TYR C 114 ARG 0.016 0.001 ARG A 126 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3366.94 seconds wall clock time: 61 minutes 36.59 seconds (3696.59 seconds total)