Starting phenix.real_space_refine on Mon Mar 11 02:09:04 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xf2_33168/03_2024/7xf2_33168.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xf2_33168/03_2024/7xf2_33168.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.73 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xf2_33168/03_2024/7xf2_33168.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xf2_33168/03_2024/7xf2_33168.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xf2_33168/03_2024/7xf2_33168.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xf2_33168/03_2024/7xf2_33168.pdb" } resolution = 3.73 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= 0.016 sd= 0.082 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 46 5.16 5 C 4165 2.51 5 N 1109 2.21 5 O 1271 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 9": "OE1" <-> "OE2" Residue "A ASP 23": "OD1" <-> "OD2" Residue "A GLU 31": "OE1" <-> "OE2" Residue "A GLU 36": "OE1" <-> "OE2" Residue "A TYR 72": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 100": "OD1" <-> "OD2" Residue "A GLU 101": "OE1" <-> "OE2" Residue "A ARG 103": "NH1" <-> "NH2" Residue "A ARG 118": "NH1" <-> "NH2" Residue "A GLU 124": "OE1" <-> "OE2" Residue "A GLU 155": "OE1" <-> "OE2" Residue "A PHE 162": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 179": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 183": "OD1" <-> "OD2" Residue "A PHE 190": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 208": "OD1" <-> "OD2" Residue "A GLU 214": "OE1" <-> "OE2" Residue "A ASP 246": "OD1" <-> "OD2" Residue "A PHE 264": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 285": "OD1" <-> "OD2" Residue "A PHE 296": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 297": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 300": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 325": "NH1" <-> "NH2" Residue "A GLU 336": "OE1" <-> "OE2" Residue "A GLU 337": "OE1" <-> "OE2" Residue "A GLU 352": "OE1" <-> "OE2" Residue "A PHE 353": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 373": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 384": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 396": "OE1" <-> "OE2" Residue "A GLU 397": "OE1" <-> "OE2" Residue "A ASP 420": "OD1" <-> "OD2" Residue "A TYR 430": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 453": "OE1" <-> "OE2" Residue "A GLU 456": "OE1" <-> "OE2" Residue "A ARG 463": "NH1" <-> "NH2" Residue "B ASP 8": "OD1" <-> "OD2" Residue "B ASP 20": "OD1" <-> "OD2" Residue "B ASP 23": "OD1" <-> "OD2" Residue "B ARG 92": "NH1" <-> "NH2" Residue "B GLU 124": "OE1" <-> "OE2" Residue "B GLU 126": "OE1" <-> "OE2" Residue "B ASP 161": "OD1" <-> "OD2" Residue "B PHE 193": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 202": "OD1" <-> "OD2" Residue "B ASP 221": "OD1" <-> "OD2" Residue "B ARG 235": "NH1" <-> "NH2" Residue "B TYR 255": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 257": "NH1" <-> "NH2" Residue "B GLU 280": "OE1" <-> "OE2" Residue "B GLU 288": "OE1" <-> "OE2" Residue "B GLU 293": "OE1" <-> "OE2" Residue "B GLU 302": "OE1" <-> "OE2" Residue "B ARG 325": "NH1" <-> "NH2" Residue "B PHE 346": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 352": "OE1" <-> "OE2" Residue "B ARG 382": "NH1" <-> "NH2" Residue "B TYR 384": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 389": "OE1" <-> "OE2" Residue "B PHE 395": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 401": "OE1" <-> "OE2" Residue "B GLU 453": "OE1" <-> "OE2" Residue "B TYR 458": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 6591 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 3450 Number of conformers: 1 Conformer: "" Number of residues, atoms: 440, 3450 Classifications: {'peptide': 440} Link IDs: {'PTRANS': 19, 'TRANS': 420} Chain breaks: 2 Chain: "B" Number of atoms: 3141 Number of conformers: 1 Conformer: "" Number of residues, atoms: 400, 3141 Classifications: {'peptide': 400} Link IDs: {'PTRANS': 15, 'TRANS': 384} Chain breaks: 4 Time building chain proxies: 4.16, per 1000 atoms: 0.63 Number of scatterers: 6591 At special positions: 0 Unit cell: (96.48, 109.88, 88.44, 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 46 16.00 O 1271 8.00 N 1109 7.00 C 4165 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: 2.77 Conformation dependent library (CDL) restraints added in 1.3 seconds 1648 Ramachandran restraints generated. 824 Oldfield, 0 Emsley, 824 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1624 Finding SS restraints... Secondary structure from input PDB file: 34 helices and 4 sheets defined 65.8% alpha, 2.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.05 Creating SS restraints... Processing helix chain 'A' and resid 2 through 25 Processing helix chain 'A' and resid 76 through 85 Processing helix chain 'A' and resid 92 through 110 removed outlier: 3.570A pdb=" N ASP A 96 " --> pdb=" O ARG A 92 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N ALA A 99 " --> pdb=" O ALA A 95 " (cutoff:3.500A) removed outlier: 4.385A pdb=" N THR A 104 " --> pdb=" O ASP A 100 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N GLU A 107 " --> pdb=" O ARG A 103 " (cutoff:3.500A) Processing helix chain 'A' and resid 123 through 128 removed outlier: 4.158A pdb=" N ASN A 127 " --> pdb=" O LEU A 123 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N LYS A 128 " --> pdb=" O GLU A 124 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 123 through 128' Processing helix chain 'A' and resid 158 through 163 Processing helix chain 'A' and resid 164 through 179 removed outlier: 3.868A pdb=" N ILE A 168 " --> pdb=" O ASN A 164 " (cutoff:3.500A) removed outlier: 3.977A pdb=" N ALA A 169 " --> pdb=" O PRO A 165 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N THR A 172 " --> pdb=" O ILE A 168 " (cutoff:3.500A) removed outlier: 3.826A pdb=" N SER A 177 " --> pdb=" O LYS A 173 " (cutoff:3.500A) Processing helix chain 'A' and resid 190 through 200 Processing helix chain 'A' and resid 202 through 219 removed outlier: 3.518A pdb=" N SER A 206 " --> pdb=" O ASP A 202 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N GLU A 214 " --> pdb=" O ALA A 210 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N ASN A 215 " --> pdb=" O ASN A 211 " (cutoff:3.500A) removed outlier: 4.041A pdb=" N VAL A 216 " --> pdb=" O MET A 212 " (cutoff:3.500A) Processing helix chain 'A' and resid 236 through 248 removed outlier: 3.562A pdb=" N ALA A 243 " --> pdb=" O VAL A 239 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N TYR A 248 " --> pdb=" O VAL A 244 " (cutoff:3.500A) Processing helix chain 'A' and resid 264 through 299 removed outlier: 3.591A pdb=" N LEU A 282 " --> pdb=" O CYS A 278 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N PHE A 296 " --> pdb=" O VAL A 292 " (cutoff:3.500A) Processing helix chain 'A' and resid 308 through 322 removed outlier: 3.626A pdb=" N GLN A 314 " --> pdb=" O LYS A 310 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N SER A 319 " --> pdb=" O ASN A 315 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N MET A 320 " --> pdb=" O LYS A 316 " (cutoff:3.500A) Processing helix chain 'A' and resid 334 through 349 removed outlier: 3.682A pdb=" N MET A 349 " --> pdb=" O MET A 345 " (cutoff:3.500A) Processing helix chain 'A' and resid 352 through 357 removed outlier: 3.595A pdb=" N CYS A 356 " --> pdb=" O GLU A 352 " (cutoff:3.500A) Processing helix chain 'A' and resid 376 through 382 removed outlier: 4.161A pdb=" N LEU A 380 " --> pdb=" O CYS A 376 " (cutoff:3.500A) Processing helix chain 'A' and resid 387 through 409 removed outlier: 4.178A pdb=" N ALA A 393 " --> pdb=" O GLU A 389 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N ILE A 398 " --> pdb=" O HIS A 394 " (cutoff:3.500A) Processing helix chain 'A' and resid 415 through 424 removed outlier: 4.268A pdb=" N ALA A 421 " --> pdb=" O ASP A 417 " (cutoff:3.500A) Processing helix chain 'A' and resid 425 through 427 No H-bonds generated for 'chain 'A' and resid 425 through 427' Processing helix chain 'A' and resid 428 through 466 removed outlier: 4.189A pdb=" N LEU A 434 " --> pdb=" O TYR A 430 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N LEU A 436 " --> pdb=" O LEU A 432 " (cutoff:3.500A) removed outlier: 3.999A pdb=" N VAL A 437 " --> pdb=" O ILE A 433 " (cutoff:3.500A) removed outlier: 3.971A pdb=" N ALA A 442 " --> pdb=" O ARG A 438 " (cutoff:3.500A) removed outlier: 3.975A pdb=" N LYS A 449 " --> pdb=" O SER A 445 " (cutoff:3.500A) removed outlier: 3.977A pdb=" N PHE A 464 " --> pdb=" O LEU A 460 " (cutoff:3.500A) Processing helix chain 'B' and resid 2 through 24 removed outlier: 3.671A pdb=" N LEU B 7 " --> pdb=" O ALA B 3 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N TYR B 10 " --> pdb=" O ILE B 6 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N VAL B 18 " --> pdb=" O THR B 14 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N ALA B 22 " --> pdb=" O VAL B 18 " (cutoff:3.500A) Processing helix chain 'B' and resid 82 through 110 removed outlier: 3.781A pdb=" N GLY B 87 " --> pdb=" O VAL B 83 " (cutoff:3.500A) removed outlier: 4.059A pdb=" N GLN B 88 " --> pdb=" O ALA B 84 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N ASN B 91 " --> pdb=" O GLY B 87 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N LYS B 93 " --> pdb=" O GLU B 89 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N ALA B 99 " --> pdb=" O ALA B 95 " (cutoff:3.500A) removed outlier: 3.844A pdb=" N ILE B 105 " --> pdb=" O GLU B 101 " (cutoff:3.500A) Processing helix chain 'B' and resid 123 through 127 removed outlier: 4.122A pdb=" N ASN B 127 " --> pdb=" O LEU B 123 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 123 through 127' Processing helix chain 'B' and resid 158 through 164 removed outlier: 3.569A pdb=" N PHE B 162 " --> pdb=" O SER B 158 " (cutoff:3.500A) Processing helix chain 'B' and resid 164 through 180 removed outlier: 4.221A pdb=" N VAL B 171 " --> pdb=" O VAL B 167 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N LYS B 173 " --> pdb=" O ALA B 169 " (cutoff:3.500A) removed outlier: 3.913A pdb=" N GLU B 176 " --> pdb=" O THR B 172 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N ILE B 178 " --> pdb=" O ARG B 174 " (cutoff:3.500A) Processing helix chain 'B' and resid 184 through 188 Processing helix chain 'B' and resid 189 through 200 removed outlier: 4.510A pdb=" N PHE B 193 " --> pdb=" O ARG B 189 " (cutoff:3.500A) Processing helix chain 'B' and resid 201 through 219 removed outlier: 4.469A pdb=" N SER B 205 " --> pdb=" O MET B 201 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N VAL B 216 " --> pdb=" O MET B 212 " (cutoff:3.500A) removed outlier: 4.250A pdb=" N ILE B 217 " --> pdb=" O VAL B 213 " (cutoff:3.500A) removed outlier: 3.863A pdb=" N LYS B 218 " --> pdb=" O GLU B 214 " (cutoff:3.500A) Processing helix chain 'B' and resid 236 through 254 removed outlier: 3.547A pdb=" N VAL B 240 " --> pdb=" O ASP B 236 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N ALA B 243 " --> pdb=" O VAL B 239 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N ASN B 245 " --> pdb=" O LYS B 241 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N ASP B 246 " --> pdb=" O THR B 242 " (cutoff:3.500A) Processing helix chain 'B' and resid 264 through 299 removed outlier: 3.722A pdb=" N GLU B 269 " --> pdb=" O MET B 265 " (cutoff:3.500A) removed outlier: 4.334A pdb=" N ALA B 274 " --> pdb=" O LYS B 270 " (cutoff:3.500A) removed outlier: 3.979A pdb=" N PHE B 296 " --> pdb=" O VAL B 292 " (cutoff:3.500A) Processing helix chain 'B' and resid 311 through 322 Processing helix chain 'B' and resid 334 through 349 removed outlier: 3.652A pdb=" N MET B 349 " --> pdb=" O MET B 345 " (cutoff:3.500A) Processing helix chain 'B' and resid 351 through 357 removed outlier: 4.243A pdb=" N ASN B 355 " --> pdb=" O PRO B 351 " (cutoff:3.500A) Processing helix chain 'B' and resid 377 through 383 removed outlier: 4.373A pdb=" N LYS B 383 " --> pdb=" O PRO B 379 " (cutoff:3.500A) Processing helix chain 'B' and resid 389 through 409 removed outlier: 3.837A pdb=" N HIS B 394 " --> pdb=" O LYS B 390 " (cutoff:3.500A) removed outlier: 3.900A pdb=" N PHE B 395 " --> pdb=" O SER B 391 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N LYS B 408 " --> pdb=" O ASN B 404 " (cutoff:3.500A) Processing helix chain 'B' and resid 427 through 466 removed outlier: 3.712A pdb=" N VAL B 431 " --> pdb=" O GLY B 427 " (cutoff:3.500A) removed outlier: 4.186A pdb=" N ARG B 438 " --> pdb=" O LEU B 434 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N ALA B 442 " --> pdb=" O ARG B 438 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N LYS B 449 " --> pdb=" O SER B 445 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N ARG B 463 " --> pdb=" O LEU B 459 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N VAL B 465 " --> pdb=" O TRP B 461 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 131 through 133 Processing sheet with id=AA2, first strand: chain 'A' and resid 147 through 148 removed outlier: 6.601A pdb=" N THR A 147 " --> pdb=" O LEU A 330 " (cutoff:3.500A) removed outlier: 8.307A pdb=" N ARG A 332 " --> pdb=" O THR A 147 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 132 through 133 Processing sheet with id=AA4, first strand: chain 'B' and resid 146 through 148 removed outlier: 6.753A pdb=" N THR B 147 " --> pdb=" O LEU B 330 " (cutoff:3.500A) 354 hydrogen bonds defined for protein. 1050 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: 3.39 Time building geometry restraints manager: 2.95 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 2150 1.34 - 1.46: 1428 1.46 - 1.58: 3051 1.58 - 1.69: 0 1.69 - 1.81: 74 Bond restraints: 6703 Sorted by residual: bond pdb=" CA TYR A 46 " pdb=" CB TYR A 46 " ideal model delta sigma weight residual 1.526 1.490 0.036 1.76e-02 3.23e+03 4.26e+00 bond pdb=" CG ARG B 103 " pdb=" CD ARG B 103 " ideal model delta sigma weight residual 1.520 1.558 -0.038 3.00e-02 1.11e+03 1.63e+00 bond pdb=" CA ASN B 424 " pdb=" CB ASN B 424 " ideal model delta sigma weight residual 1.539 1.483 0.056 4.88e-02 4.20e+02 1.33e+00 bond pdb=" NE ARG B 103 " pdb=" CZ ARG B 103 " ideal model delta sigma weight residual 1.326 1.338 -0.012 1.10e-02 8.26e+03 1.12e+00 bond pdb=" CB ARG B 103 " pdb=" CG ARG B 103 " ideal model delta sigma weight residual 1.520 1.549 -0.029 3.00e-02 1.11e+03 9.58e-01 ... (remaining 6698 not shown) Histogram of bond angle deviations from ideal: 99.71 - 106.56: 170 106.56 - 113.41: 3694 113.41 - 120.26: 2603 120.26 - 127.11: 2542 127.11 - 133.96: 43 Bond angle restraints: 9052 Sorted by residual: angle pdb=" CA LEU A 45 " pdb=" CB LEU A 45 " pdb=" CG LEU A 45 " ideal model delta sigma weight residual 116.30 125.83 -9.53 3.50e+00 8.16e-02 7.41e+00 angle pdb=" C CYS B 418 " pdb=" N LEU B 419 " pdb=" CA LEU B 419 " ideal model delta sigma weight residual 121.54 126.51 -4.97 1.91e+00 2.74e-01 6.76e+00 angle pdb=" N GLY A 252 " pdb=" CA GLY A 252 " pdb=" C GLY A 252 " ideal model delta sigma weight residual 113.37 116.74 -3.37 1.34e+00 5.57e-01 6.31e+00 angle pdb=" N LEU B 425 " pdb=" CA LEU B 425 " pdb=" C LEU B 425 " ideal model delta sigma weight residual 112.72 109.71 3.01 1.28e+00 6.10e-01 5.54e+00 angle pdb=" CA LEU B 434 " pdb=" CB LEU B 434 " pdb=" CG LEU B 434 " ideal model delta sigma weight residual 116.30 124.47 -8.17 3.50e+00 8.16e-02 5.45e+00 ... (remaining 9047 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.02: 3638 16.02 - 32.04: 388 32.04 - 48.06: 83 48.06 - 64.09: 15 64.09 - 80.11: 7 Dihedral angle restraints: 4131 sinusoidal: 1651 harmonic: 2480 Sorted by residual: dihedral pdb=" CA VAL A 251 " pdb=" C VAL A 251 " pdb=" N GLY A 252 " pdb=" CA GLY A 252 " ideal model delta harmonic sigma weight residual 180.00 -152.05 -27.95 0 5.00e+00 4.00e-02 3.12e+01 dihedral pdb=" CA CYS B 256 " pdb=" C CYS B 256 " pdb=" N ARG B 257 " pdb=" CA ARG B 257 " ideal model delta harmonic sigma weight residual 180.00 156.13 23.87 0 5.00e+00 4.00e-02 2.28e+01 dihedral pdb=" CA GLN B 261 " pdb=" C GLN B 261 " pdb=" N LEU B 262 " pdb=" CA LEU B 262 " ideal model delta harmonic sigma weight residual 180.00 156.54 23.46 0 5.00e+00 4.00e-02 2.20e+01 ... (remaining 4128 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.028: 547 0.028 - 0.055: 331 0.055 - 0.083: 113 0.083 - 0.111: 41 0.111 - 0.138: 10 Chirality restraints: 1042 Sorted by residual: chirality pdb=" CA THR A 378 " pdb=" N THR A 378 " pdb=" C THR A 378 " pdb=" CB THR A 378 " both_signs ideal model delta sigma weight residual False 2.53 2.39 0.14 2.00e-01 2.50e+01 4.77e-01 chirality pdb=" CA ILE A 131 " pdb=" N ILE A 131 " pdb=" C ILE A 131 " pdb=" CB ILE A 131 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 4.24e-01 chirality pdb=" CA ILE A 363 " pdb=" N ILE A 363 " pdb=" C ILE A 363 " pdb=" CB ILE A 363 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 4.12e-01 ... (remaining 1039 not shown) Planarity restraints: 1159 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ARG B 257 " 0.053 5.00e-02 4.00e+02 8.04e-02 1.03e+01 pdb=" N PRO B 258 " -0.139 5.00e-02 4.00e+02 pdb=" CA PRO B 258 " 0.041 5.00e-02 4.00e+02 pdb=" CD PRO B 258 " 0.045 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU A 219 " 0.037 5.00e-02 4.00e+02 5.60e-02 5.02e+00 pdb=" N PRO A 220 " -0.097 5.00e-02 4.00e+02 pdb=" CA PRO A 220 " 0.029 5.00e-02 4.00e+02 pdb=" CD PRO A 220 " 0.031 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PRO A 49 " -0.035 5.00e-02 4.00e+02 5.25e-02 4.41e+00 pdb=" N PRO A 50 " 0.091 5.00e-02 4.00e+02 pdb=" CA PRO A 50 " -0.024 5.00e-02 4.00e+02 pdb=" CD PRO A 50 " -0.031 5.00e-02 4.00e+02 ... (remaining 1156 not shown) Histogram of nonbonded interaction distances: 2.13 - 2.69: 202 2.69 - 3.24: 7912 3.24 - 3.79: 10301 3.79 - 4.35: 13389 4.35 - 4.90: 19871 Nonbonded interactions: 51675 Sorted by model distance: nonbonded pdb=" O ILE B 168 " pdb=" OG1 THR B 172 " model vdw 2.133 2.440 nonbonded pdb=" O ALA A 169 " pdb=" OG1 THR A 172 " model vdw 2.164 2.440 nonbonded pdb=" O ILE B 203 " pdb=" OG SER B 206 " model vdw 2.200 2.440 nonbonded pdb=" O ALA B 304 " pdb=" OG1 THR B 307 " model vdw 2.208 2.440 nonbonded pdb=" O ARG A 174 " pdb=" OG SER A 177 " model vdw 2.226 2.440 ... (remaining 51670 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' and (resid 1 through 38 or resid 80 through 116 or resid 122 through \ 360 or resid 373 through 409 or resid 418 through 466)) 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: 14.870 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: 0.000 Extract box with map and model: 53.790 Check model and map are aligned: 0.080 Set scattering table: 0.060 Process input model: 24.560 Find NCS groups from input model: 0.770 Set up NCS constraints: 0.120 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: 0.030 Load rotamer database and sin/cos tables:3.280 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 97.560 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8014 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 6703 Z= 0.234 Angle : 0.653 9.529 9052 Z= 0.357 Chirality : 0.041 0.138 1042 Planarity : 0.005 0.080 1159 Dihedral : 14.121 80.108 2507 Min Nonbonded Distance : 2.133 Molprobity Statistics. All-atom Clashscore : 14.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.50 % Favored : 91.50 % Rotamer: Outliers : 0.13 % Allowed : 5.36 % Favored : 94.50 % 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: -4.97 (0.22), residues: 824 helix: -3.30 (0.16), residues: 486 sheet: -4.06 (1.92), residues: 6 loop : -3.06 (0.30), residues: 332 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 392 HIS 0.007 0.002 HIS A 130 PHE 0.009 0.001 PHE B 358 TYR 0.016 0.002 TYR B 255 ARG 0.007 0.001 ARG A 103 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1648 Ramachandran restraints generated. 824 Oldfield, 0 Emsley, 824 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1648 Ramachandran restraints generated. 824 Oldfield, 0 Emsley, 824 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 88 residues out of total 746 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 87 time to evaluate : 0.859 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: A 297 TYR cc_start: 0.8488 (m-10) cc_final: 0.8062 (m-80) REVERT: A 345 MET cc_start: 0.8785 (tpp) cc_final: 0.8403 (tpp) REVERT: A 436 LEU cc_start: 0.9350 (tp) cc_final: 0.9143 (tt) REVERT: B 88 GLN cc_start: 0.7579 (tt0) cc_final: 0.7336 (tt0) outliers start: 1 outliers final: 0 residues processed: 88 average time/residue: 0.3281 time to fit residues: 35.0126 Evaluate side-chains 57 residues out of total 746 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 57 time to evaluate : 0.782 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 70 optimal weight: 0.8980 chunk 63 optimal weight: 2.9990 chunk 35 optimal weight: 5.9990 chunk 21 optimal weight: 5.9990 chunk 42 optimal weight: 4.9990 chunk 34 optimal weight: 6.9990 chunk 65 optimal weight: 9.9990 chunk 25 optimal weight: 4.9990 chunk 40 optimal weight: 5.9990 chunk 49 optimal weight: 6.9990 chunk 76 optimal weight: 10.0000 overall best weight: 3.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 211 ASN ** B 33 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 91 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 130 HIS B 163 GLN ** B 164 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 195 ASN ** B 199 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 245 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 314 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 323 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8096 moved from start: 0.2556 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 6703 Z= 0.225 Angle : 0.718 10.457 9052 Z= 0.373 Chirality : 0.041 0.138 1042 Planarity : 0.006 0.059 1159 Dihedral : 5.211 27.774 900 Min Nonbonded Distance : 2.124 Molprobity Statistics. All-atom Clashscore : 18.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.28 % Favored : 92.72 % Rotamer: Outliers : 0.94 % Allowed : 11.13 % Favored : 87.94 % 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: -2.63 (0.27), residues: 824 helix: -1.13 (0.21), residues: 491 sheet: None (None), residues: 0 loop : -2.63 (0.32), residues: 333 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 209 HIS 0.009 0.002 HIS A 130 PHE 0.014 0.001 PHE B 179 TYR 0.025 0.002 TYR B 297 ARG 0.004 0.001 ARG A 463 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1648 Ramachandran restraints generated. 824 Oldfield, 0 Emsley, 824 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1648 Ramachandran restraints generated. 824 Oldfield, 0 Emsley, 824 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 67 residues out of total 746 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 60 time to evaluate : 0.897 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 93 LYS cc_start: 0.8665 (tppt) cc_final: 0.8250 (tppt) REVERT: A 103 ARG cc_start: 0.7644 (mtp180) cc_final: 0.7375 (mmm-85) REVERT: A 436 LEU cc_start: 0.9259 (tp) cc_final: 0.8969 (tt) REVERT: B 320 MET cc_start: 0.8729 (mmp) cc_final: 0.8459 (mmm) outliers start: 7 outliers final: 2 residues processed: 65 average time/residue: 0.2797 time to fit residues: 23.0042 Evaluate side-chains 49 residues out of total 746 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 47 time to evaluate : 0.844 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 130 HIS Chi-restraints excluded: chain B residue 260 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 42 optimal weight: 5.9990 chunk 23 optimal weight: 0.3980 chunk 63 optimal weight: 4.9990 chunk 51 optimal weight: 8.9990 chunk 21 optimal weight: 6.9990 chunk 76 optimal weight: 8.9990 chunk 82 optimal weight: 5.9990 chunk 68 optimal weight: 0.9990 chunk 75 optimal weight: 8.9990 chunk 26 optimal weight: 6.9990 chunk 61 optimal weight: 20.0000 overall best weight: 3.6788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 457 ASN B 33 GLN ** B 91 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 164 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 199 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 245 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 314 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8113 moved from start: 0.3397 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 6703 Z= 0.196 Angle : 0.640 10.923 9052 Z= 0.330 Chirality : 0.039 0.133 1042 Planarity : 0.005 0.055 1159 Dihedral : 5.013 24.621 900 Min Nonbonded Distance : 2.111 Molprobity Statistics. All-atom Clashscore : 17.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.67 % Favored : 93.33 % Rotamer: Outliers : 1.88 % Allowed : 14.34 % Favored : 83.78 % 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: -1.56 (0.29), residues: 824 helix: -0.22 (0.23), residues: 504 sheet: -3.65 (1.91), residues: 6 loop : -2.30 (0.34), residues: 314 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 392 HIS 0.008 0.002 HIS A 130 PHE 0.009 0.001 PHE B 179 TYR 0.016 0.001 TYR A 72 ARG 0.006 0.001 ARG B 186 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1648 Ramachandran restraints generated. 824 Oldfield, 0 Emsley, 824 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1648 Ramachandran restraints generated. 824 Oldfield, 0 Emsley, 824 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 62 residues out of total 746 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 48 time to evaluate : 0.879 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 103 ARG cc_start: 0.7769 (mtp180) cc_final: 0.7475 (mmm-85) REVERT: A 345 MET cc_start: 0.8889 (tpp) cc_final: 0.8682 (tpp) REVERT: A 436 LEU cc_start: 0.9292 (tp) cc_final: 0.9081 (tt) REVERT: A 457 ASN cc_start: 0.9121 (OUTLIER) cc_final: 0.8754 (t0) REVERT: B 297 TYR cc_start: 0.8376 (m-80) cc_final: 0.8131 (m-80) outliers start: 14 outliers final: 4 residues processed: 59 average time/residue: 0.2095 time to fit residues: 16.8330 Evaluate side-chains 48 residues out of total 746 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 43 time to evaluate : 0.852 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 105 ILE Chi-restraints excluded: chain A residue 229 VAL Chi-restraints excluded: chain A residue 378 THR Chi-restraints excluded: chain A residue 457 ASN Chi-restraints excluded: chain B residue 81 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 75 optimal weight: 10.0000 chunk 57 optimal weight: 20.0000 chunk 39 optimal weight: 5.9990 chunk 8 optimal weight: 5.9990 chunk 36 optimal weight: 20.0000 chunk 51 optimal weight: 0.9980 chunk 76 optimal weight: 7.9990 chunk 81 optimal weight: 4.9990 chunk 40 optimal weight: 0.7980 chunk 72 optimal weight: 30.0000 chunk 21 optimal weight: 0.0040 overall best weight: 2.5596 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 457 ASN ** B 164 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 199 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 245 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 314 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8107 moved from start: 0.3756 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 6703 Z= 0.172 Angle : 0.633 10.388 9052 Z= 0.317 Chirality : 0.039 0.137 1042 Planarity : 0.005 0.059 1159 Dihedral : 4.859 22.945 900 Min Nonbonded Distance : 2.114 Molprobity Statistics. All-atom Clashscore : 15.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.67 % Favored : 93.33 % Rotamer: Outliers : 2.01 % Allowed : 16.62 % Favored : 81.37 % 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: -1.13 (0.29), residues: 824 helix: 0.12 (0.23), residues: 509 sheet: -3.60 (1.82), residues: 6 loop : -2.14 (0.36), residues: 309 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 461 HIS 0.007 0.001 HIS A 130 PHE 0.008 0.001 PHE A 360 TYR 0.010 0.001 TYR A 430 ARG 0.005 0.000 ARG A 289 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1648 Ramachandran restraints generated. 824 Oldfield, 0 Emsley, 824 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1648 Ramachandran restraints generated. 824 Oldfield, 0 Emsley, 824 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 60 residues out of total 746 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 45 time to evaluate : 0.789 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 103 ARG cc_start: 0.7614 (mtp180) cc_final: 0.7384 (mmm-85) REVERT: A 162 PHE cc_start: 0.8685 (OUTLIER) cc_final: 0.8316 (m-80) REVERT: A 221 ASP cc_start: 0.5968 (OUTLIER) cc_final: 0.5686 (t0) REVERT: A 436 LEU cc_start: 0.9293 (tp) cc_final: 0.9063 (tt) REVERT: A 457 ASN cc_start: 0.9047 (OUTLIER) cc_final: 0.8826 (t0) REVERT: B 186 ARG cc_start: 0.8812 (mpp-170) cc_final: 0.8561 (ptt-90) REVERT: B 297 TYR cc_start: 0.8344 (m-80) cc_final: 0.8125 (m-80) REVERT: B 320 MET cc_start: 0.8510 (mmm) cc_final: 0.8259 (tpt) outliers start: 15 outliers final: 7 residues processed: 58 average time/residue: 0.1967 time to fit residues: 15.5929 Evaluate side-chains 54 residues out of total 746 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 44 time to evaluate : 0.817 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 105 ILE Chi-restraints excluded: chain A residue 162 PHE Chi-restraints excluded: chain A residue 221 ASP Chi-restraints excluded: chain A residue 236 ASP Chi-restraints excluded: chain A residue 378 THR Chi-restraints excluded: chain A residue 437 VAL Chi-restraints excluded: chain A residue 457 ASN Chi-restraints excluded: chain B residue 81 MET Chi-restraints excluded: chain B residue 260 THR Chi-restraints excluded: chain B residue 399 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 67 optimal weight: 3.9990 chunk 46 optimal weight: 10.0000 chunk 1 optimal weight: 3.9990 chunk 60 optimal weight: 5.9990 chunk 33 optimal weight: 20.0000 chunk 69 optimal weight: 0.9980 chunk 56 optimal weight: 6.9990 chunk 0 optimal weight: 9.9990 chunk 41 optimal weight: 6.9990 chunk 72 optimal weight: 40.0000 chunk 20 optimal weight: 2.9990 overall best weight: 3.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 88 GLN A 457 ASN ** B 33 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 91 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 164 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 199 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 245 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 314 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8124 moved from start: 0.4058 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 6703 Z= 0.188 Angle : 0.600 9.743 9052 Z= 0.306 Chirality : 0.038 0.135 1042 Planarity : 0.005 0.052 1159 Dihedral : 4.797 21.907 900 Min Nonbonded Distance : 2.127 Molprobity Statistics. All-atom Clashscore : 17.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.92 % Favored : 93.08 % Rotamer: Outliers : 2.55 % Allowed : 17.29 % Favored : 80.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.89 (0.30), residues: 824 helix: 0.33 (0.23), residues: 510 sheet: -3.65 (1.76), residues: 6 loop : -2.09 (0.36), residues: 308 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 461 HIS 0.008 0.002 HIS A 130 PHE 0.009 0.001 PHE A 360 TYR 0.014 0.001 TYR A 72 ARG 0.003 0.000 ARG A 103 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1648 Ramachandran restraints generated. 824 Oldfield, 0 Emsley, 824 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1648 Ramachandran restraints generated. 824 Oldfield, 0 Emsley, 824 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 62 residues out of total 746 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 43 time to evaluate : 0.730 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 45 LEU cc_start: 0.7083 (OUTLIER) cc_final: 0.6881 (pp) REVERT: A 162 PHE cc_start: 0.8722 (OUTLIER) cc_final: 0.8352 (m-80) REVERT: A 212 MET cc_start: 0.8952 (ptp) cc_final: 0.8738 (tmm) REVERT: A 221 ASP cc_start: 0.6164 (OUTLIER) cc_final: 0.5929 (t0) REVERT: A 345 MET cc_start: 0.8897 (tpp) cc_final: 0.7737 (tpp) REVERT: A 436 LEU cc_start: 0.9309 (tp) cc_final: 0.9094 (tt) REVERT: A 457 ASN cc_start: 0.8831 (OUTLIER) cc_final: 0.8311 (t0) REVERT: B 297 TYR cc_start: 0.8339 (m-80) cc_final: 0.8097 (m-80) REVERT: B 345 MET cc_start: 0.9062 (mmp) cc_final: 0.8630 (mmm) outliers start: 19 outliers final: 9 residues processed: 60 average time/residue: 0.1649 time to fit residues: 13.9191 Evaluate side-chains 56 residues out of total 746 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 43 time to evaluate : 0.720 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 LEU Chi-restraints excluded: chain A residue 105 ILE Chi-restraints excluded: chain A residue 162 PHE Chi-restraints excluded: chain A residue 221 ASP Chi-restraints excluded: chain A residue 229 VAL Chi-restraints excluded: chain A residue 236 ASP Chi-restraints excluded: chain A residue 378 THR Chi-restraints excluded: chain A residue 437 VAL Chi-restraints excluded: chain A residue 457 ASN Chi-restraints excluded: chain B residue 81 MET Chi-restraints excluded: chain B residue 134 MET Chi-restraints excluded: chain B residue 260 THR Chi-restraints excluded: chain B residue 399 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 27 optimal weight: 3.9990 chunk 73 optimal weight: 9.9990 chunk 16 optimal weight: 9.9990 chunk 47 optimal weight: 10.0000 chunk 20 optimal weight: 30.0000 chunk 81 optimal weight: 2.9990 chunk 67 optimal weight: 6.9990 chunk 37 optimal weight: 9.9990 chunk 6 optimal weight: 6.9990 chunk 26 optimal weight: 5.9990 chunk 42 optimal weight: 8.9990 overall best weight: 5.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 457 ASN ** B 33 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 91 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 164 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 199 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 245 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 314 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 323 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8160 moved from start: 0.4315 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 6703 Z= 0.228 Angle : 0.623 9.806 9052 Z= 0.317 Chirality : 0.039 0.133 1042 Planarity : 0.005 0.061 1159 Dihedral : 4.772 21.871 900 Min Nonbonded Distance : 2.146 Molprobity Statistics. All-atom Clashscore : 18.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.89 % Favored : 92.11 % Rotamer: Outliers : 2.95 % Allowed : 17.56 % Favored : 79.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.76 (0.30), residues: 824 helix: 0.42 (0.23), residues: 510 sheet: -3.57 (1.78), residues: 6 loop : -2.01 (0.36), residues: 308 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 461 HIS 0.009 0.002 HIS A 130 PHE 0.010 0.001 PHE A 360 TYR 0.015 0.001 TYR A 72 ARG 0.003 0.000 ARG A 438 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1648 Ramachandran restraints generated. 824 Oldfield, 0 Emsley, 824 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1648 Ramachandran restraints generated. 824 Oldfield, 0 Emsley, 824 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 64 residues out of total 746 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 42 time to evaluate : 0.814 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 162 PHE cc_start: 0.8742 (OUTLIER) cc_final: 0.8401 (m-80) REVERT: A 190 PHE cc_start: 0.7960 (OUTLIER) cc_final: 0.7701 (p90) REVERT: A 221 ASP cc_start: 0.6144 (OUTLIER) cc_final: 0.5877 (t0) REVERT: A 345 MET cc_start: 0.8955 (tpp) cc_final: 0.7991 (tpp) REVERT: A 436 LEU cc_start: 0.9343 (tp) cc_final: 0.9124 (tt) REVERT: A 457 ASN cc_start: 0.8869 (OUTLIER) cc_final: 0.8259 (t0) REVERT: B 297 TYR cc_start: 0.8415 (m-80) cc_final: 0.8207 (m-80) REVERT: B 345 MET cc_start: 0.9048 (mmp) cc_final: 0.8623 (mmm) outliers start: 22 outliers final: 11 residues processed: 61 average time/residue: 0.1725 time to fit residues: 14.9008 Evaluate side-chains 56 residues out of total 746 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 41 time to evaluate : 0.803 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 105 ILE Chi-restraints excluded: chain A residue 162 PHE Chi-restraints excluded: chain A residue 190 PHE Chi-restraints excluded: chain A residue 221 ASP Chi-restraints excluded: chain A residue 229 VAL Chi-restraints excluded: chain A residue 236 ASP Chi-restraints excluded: chain A residue 255 TYR Chi-restraints excluded: chain A residue 320 MET Chi-restraints excluded: chain A residue 378 THR Chi-restraints excluded: chain A residue 437 VAL Chi-restraints excluded: chain A residue 457 ASN Chi-restraints excluded: chain B residue 81 MET Chi-restraints excluded: chain B residue 134 MET Chi-restraints excluded: chain B residue 178 ILE Chi-restraints excluded: chain B residue 399 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 78 optimal weight: 8.9990 chunk 9 optimal weight: 2.9990 chunk 46 optimal weight: 5.9990 chunk 59 optimal weight: 0.0050 chunk 45 optimal weight: 2.9990 chunk 68 optimal weight: 6.9990 chunk 80 optimal weight: 8.9990 chunk 50 optimal weight: 5.9990 chunk 49 optimal weight: 6.9990 chunk 37 optimal weight: 10.0000 chunk 32 optimal weight: 5.9990 overall best weight: 3.6002 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 195 ASN A 457 ASN ** B 91 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 164 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 199 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 245 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 314 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8146 moved from start: 0.4493 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 6703 Z= 0.186 Angle : 0.632 12.320 9052 Z= 0.313 Chirality : 0.039 0.165 1042 Planarity : 0.005 0.058 1159 Dihedral : 4.783 23.656 900 Min Nonbonded Distance : 2.114 Molprobity Statistics. All-atom Clashscore : 17.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.80 % Favored : 93.20 % Rotamer: Outliers : 2.01 % Allowed : 18.77 % Favored : 79.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.63 (0.30), residues: 824 helix: 0.53 (0.23), residues: 510 sheet: -3.48 (1.74), residues: 6 loop : -1.98 (0.36), residues: 308 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 461 HIS 0.007 0.002 HIS A 130 PHE 0.010 0.001 PHE B 395 TYR 0.013 0.001 TYR B 255 ARG 0.003 0.000 ARG A 438 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1648 Ramachandran restraints generated. 824 Oldfield, 0 Emsley, 824 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1648 Ramachandran restraints generated. 824 Oldfield, 0 Emsley, 824 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 56 residues out of total 746 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 41 time to evaluate : 0.842 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 162 PHE cc_start: 0.8725 (OUTLIER) cc_final: 0.8359 (m-80) REVERT: A 190 PHE cc_start: 0.7997 (OUTLIER) cc_final: 0.7766 (p90) REVERT: A 221 ASP cc_start: 0.6344 (OUTLIER) cc_final: 0.6054 (t0) REVERT: A 345 MET cc_start: 0.8942 (tpp) cc_final: 0.7865 (tpp) REVERT: A 436 LEU cc_start: 0.9332 (tp) cc_final: 0.9121 (tt) REVERT: A 457 ASN cc_start: 0.8946 (OUTLIER) cc_final: 0.8387 (t0) REVERT: B 106 MET cc_start: 0.8512 (mmm) cc_final: 0.8225 (mmm) REVERT: B 138 THR cc_start: 0.9204 (OUTLIER) cc_final: 0.8697 (p) REVERT: B 297 TYR cc_start: 0.8381 (m-80) cc_final: 0.8172 (m-80) REVERT: B 345 MET cc_start: 0.9048 (mmp) cc_final: 0.8626 (mmm) outliers start: 15 outliers final: 8 residues processed: 53 average time/residue: 0.2003 time to fit residues: 15.1447 Evaluate side-chains 52 residues out of total 746 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 39 time to evaluate : 0.848 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 162 PHE Chi-restraints excluded: chain A residue 190 PHE Chi-restraints excluded: chain A residue 221 ASP Chi-restraints excluded: chain A residue 229 VAL Chi-restraints excluded: chain A residue 236 ASP Chi-restraints excluded: chain A residue 320 MET Chi-restraints excluded: chain A residue 378 THR Chi-restraints excluded: chain A residue 437 VAL Chi-restraints excluded: chain A residue 457 ASN Chi-restraints excluded: chain B residue 81 MET Chi-restraints excluded: chain B residue 138 THR Chi-restraints excluded: chain B residue 178 ILE Chi-restraints excluded: chain B residue 399 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 48 optimal weight: 6.9990 chunk 24 optimal weight: 5.9990 chunk 15 optimal weight: 1.9990 chunk 51 optimal weight: 0.0870 chunk 55 optimal weight: 0.8980 chunk 40 optimal weight: 5.9990 chunk 7 optimal weight: 6.9990 chunk 63 optimal weight: 6.9990 chunk 73 optimal weight: 7.9990 chunk 77 optimal weight: 7.9990 chunk 70 optimal weight: 9.9990 overall best weight: 2.9964 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 457 ASN B 33 GLN ** B 91 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 164 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 199 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 245 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 314 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8138 moved from start: 0.4669 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 6703 Z= 0.172 Angle : 0.650 11.485 9052 Z= 0.317 Chirality : 0.039 0.170 1042 Planarity : 0.005 0.061 1159 Dihedral : 4.718 22.114 900 Min Nonbonded Distance : 2.134 Molprobity Statistics. All-atom Clashscore : 17.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.92 % Favored : 93.08 % Rotamer: Outliers : 2.14 % Allowed : 19.97 % Favored : 77.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.48 (0.30), residues: 824 helix: 0.66 (0.23), residues: 509 sheet: -3.32 (1.72), residues: 6 loop : -1.93 (0.36), residues: 309 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 461 HIS 0.006 0.002 HIS A 130 PHE 0.010 0.001 PHE B 395 TYR 0.012 0.001 TYR B 255 ARG 0.008 0.000 ARG A 103 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1648 Ramachandran restraints generated. 824 Oldfield, 0 Emsley, 824 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1648 Ramachandran restraints generated. 824 Oldfield, 0 Emsley, 824 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 56 residues out of total 746 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 40 time to evaluate : 0.832 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 162 PHE cc_start: 0.8724 (OUTLIER) cc_final: 0.8336 (m-80) REVERT: A 190 PHE cc_start: 0.7994 (OUTLIER) cc_final: 0.7769 (p90) REVERT: A 221 ASP cc_start: 0.6748 (OUTLIER) cc_final: 0.6369 (t0) REVERT: A 345 MET cc_start: 0.8935 (tpp) cc_final: 0.7945 (tpp) REVERT: A 436 LEU cc_start: 0.9344 (tp) cc_final: 0.9131 (tt) REVERT: A 457 ASN cc_start: 0.8804 (OUTLIER) cc_final: 0.8197 (t0) REVERT: B 297 TYR cc_start: 0.8445 (m-80) cc_final: 0.8183 (m-80) REVERT: B 345 MET cc_start: 0.9045 (mmp) cc_final: 0.8638 (mmm) outliers start: 16 outliers final: 8 residues processed: 54 average time/residue: 0.1680 time to fit residues: 13.1399 Evaluate side-chains 51 residues out of total 746 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 39 time to evaluate : 0.821 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 105 ILE Chi-restraints excluded: chain A residue 162 PHE Chi-restraints excluded: chain A residue 190 PHE Chi-restraints excluded: chain A residue 221 ASP Chi-restraints excluded: chain A residue 229 VAL Chi-restraints excluded: chain A residue 236 ASP Chi-restraints excluded: chain A residue 320 MET Chi-restraints excluded: chain A residue 378 THR Chi-restraints excluded: chain A residue 437 VAL Chi-restraints excluded: chain A residue 457 ASN Chi-restraints excluded: chain B residue 178 ILE Chi-restraints excluded: chain B residue 399 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 75 optimal weight: 7.9990 chunk 77 optimal weight: 7.9990 chunk 45 optimal weight: 4.9990 chunk 32 optimal weight: 20.0000 chunk 59 optimal weight: 20.0000 chunk 23 optimal weight: 8.9990 chunk 68 optimal weight: 0.9980 chunk 71 optimal weight: 0.0070 chunk 49 optimal weight: 3.9990 chunk 79 optimal weight: 0.7980 chunk 48 optimal weight: 6.9990 overall best weight: 2.1602 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 457 ASN ** B 91 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 164 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 199 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 245 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 314 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8122 moved from start: 0.4842 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 6703 Z= 0.158 Angle : 0.656 11.292 9052 Z= 0.316 Chirality : 0.039 0.143 1042 Planarity : 0.005 0.059 1159 Dihedral : 4.675 21.328 900 Min Nonbonded Distance : 2.137 Molprobity Statistics. All-atom Clashscore : 17.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.43 % Favored : 93.57 % Rotamer: Outliers : 1.61 % Allowed : 20.78 % Favored : 77.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.37 (0.30), residues: 824 helix: 0.74 (0.23), residues: 509 sheet: -3.13 (1.72), residues: 6 loop : -1.88 (0.37), residues: 309 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 461 HIS 0.006 0.001 HIS A 130 PHE 0.010 0.001 PHE B 395 TYR 0.011 0.001 TYR B 255 ARG 0.007 0.000 ARG A 103 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1648 Ramachandran restraints generated. 824 Oldfield, 0 Emsley, 824 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1648 Ramachandran restraints generated. 824 Oldfield, 0 Emsley, 824 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 51 residues out of total 746 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 39 time to evaluate : 0.794 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 190 PHE cc_start: 0.8045 (OUTLIER) cc_final: 0.7843 (p90) REVERT: A 221 ASP cc_start: 0.6938 (OUTLIER) cc_final: 0.6527 (t0) REVERT: A 345 MET cc_start: 0.8922 (tpp) cc_final: 0.8064 (tpp) REVERT: A 436 LEU cc_start: 0.9316 (tp) cc_final: 0.9096 (tt) REVERT: A 457 ASN cc_start: 0.9061 (OUTLIER) cc_final: 0.8541 (t0) REVERT: B 297 TYR cc_start: 0.8449 (m-80) cc_final: 0.8149 (m-80) REVERT: B 345 MET cc_start: 0.9038 (mmp) cc_final: 0.8642 (mmm) outliers start: 12 outliers final: 7 residues processed: 50 average time/residue: 0.1649 time to fit residues: 11.9015 Evaluate side-chains 49 residues out of total 746 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 39 time to evaluate : 0.743 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 105 ILE Chi-restraints excluded: chain A residue 190 PHE Chi-restraints excluded: chain A residue 221 ASP Chi-restraints excluded: chain A residue 229 VAL Chi-restraints excluded: chain A residue 320 MET Chi-restraints excluded: chain A residue 378 THR Chi-restraints excluded: chain A residue 437 VAL Chi-restraints excluded: chain A residue 457 ASN Chi-restraints excluded: chain B residue 178 ILE Chi-restraints excluded: chain B residue 399 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/build/../modules/phenix/phenix/command_line/real_space_refine.py", line 8, in run_program(real_space_refine.Program) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/iotbx/cli_parser.py", line 944, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/phenix/phenix/programs/real_space_refine.py", line 189, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 306, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 700, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 764, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 51, in __init__ gradients_method = gradients_method) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/mmtbx/refinement/real_space/weight.py", line 87, in __init__ rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 368, in refine rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 235, in __init__ weight = weight) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 112, in refine states_collector = self.states_accumulator) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 174, in __init__ exception_handling_params=lbfgs_exception_handling_params) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 245, in compute_functional_and_gradients compute_gradients=True) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1479, in energies_sites flags=flags, sites_cart=sites_cart, site_labels=site_labels) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1381, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1262, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 51.4575 > 50: distance: 16 - 40: 19.757 distance: 24 - 49: 10.079 distance: 35 - 40: 19.102 distance: 40 - 41: 11.341 distance: 41 - 42: 20.065 distance: 41 - 44: 20.826 distance: 42 - 43: 17.121 distance: 42 - 49: 15.700 distance: 44 - 45: 34.593 distance: 45 - 46: 8.649 distance: 46 - 47: 10.847 distance: 47 - 48: 40.036 distance: 49 - 50: 8.372 distance: 50 - 51: 4.917 distance: 50 - 53: 7.598 distance: 51 - 52: 13.938 distance: 51 - 57: 9.913 distance: 53 - 54: 7.036 distance: 54 - 55: 18.739 distance: 54 - 56: 19.096 distance: 57 - 58: 16.531 distance: 57 - 63: 27.441 distance: 58 - 59: 12.036 distance: 58 - 61: 22.058 distance: 59 - 60: 25.069 distance: 59 - 64: 13.462 distance: 61 - 62: 44.183 distance: 62 - 63: 18.857 distance: 64 - 65: 14.974 distance: 65 - 66: 12.569 distance: 65 - 68: 29.781 distance: 66 - 67: 45.242 distance: 66 - 72: 21.250 distance: 68 - 69: 30.916 distance: 69 - 70: 40.447 distance: 69 - 71: 38.483 distance: 72 - 73: 26.060 distance: 73 - 74: 21.999 distance: 73 - 76: 26.183 distance: 74 - 75: 42.557 distance: 74 - 78: 48.900 distance: 76 - 77: 28.541 distance: 78 - 79: 21.559 distance: 79 - 80: 14.636 distance: 79 - 82: 18.348 distance: 80 - 81: 4.792 distance: 80 - 85: 15.978 distance: 82 - 83: 12.221 distance: 82 - 84: 27.695 distance: 85 - 86: 5.109 distance: 85 - 91: 12.537 distance: 86 - 87: 19.940 distance: 86 - 89: 15.181 distance: 87 - 88: 19.697 distance: 87 - 92: 29.187 distance: 89 - 90: 11.775 distance: 90 - 91: 7.917 distance: 92 - 93: 22.028 distance: 93 - 94: 8.826 distance: 93 - 96: 8.622 distance: 94 - 95: 25.670 distance: 94 - 100: 27.853 distance: 96 - 97: 14.180 distance: 97 - 98: 5.524 distance: 97 - 99: 9.356 distance: 100 - 101: 13.314 distance: 100 - 106: 32.007 distance: 101 - 102: 27.080 distance: 101 - 104: 26.397 distance: 102 - 103: 24.744 distance: 102 - 107: 16.592 distance: 104 - 105: 26.578 distance: 105 - 106: 23.707 distance: 107 - 108: 11.469 distance: 108 - 109: 6.711 distance: 108 - 111: 24.391 distance: 109 - 110: 38.993 distance: 109 - 113: 34.403 distance: 111 - 112: 40.821