Starting phenix.real_space_refine on Fri Dec 8 01:12:47 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wk6_32560/12_2023/7wk6_32560.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wk6_32560/12_2023/7wk6_32560.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.67 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wk6_32560/12_2023/7wk6_32560.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wk6_32560/12_2023/7wk6_32560.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wk6_32560/12_2023/7wk6_32560.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wk6_32560/12_2023/7wk6_32560.pdb" } resolution = 3.67 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= 0.016 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 37 5.16 5 C 4119 2.51 5 N 1069 2.21 5 O 1203 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "E ASP 442": "OD1" <-> "OD2" Residue "E ARG 493": "NH1" <-> "NH2" Residue "E ARG 498": "NH1" <-> "NH2" Residue "E GLU 516": "OE1" <-> "OE2" Residue "A GLU 22": "OE1" <-> "OE2" Residue "A GLU 23": "OE1" <-> "OE2" Residue "A GLU 35": "OE1" <-> "OE2" Residue "A GLU 56": "OE1" <-> "OE2" Residue "A GLU 87": "OE1" <-> "OE2" Residue "A GLU 166": "OE1" <-> "OE2" Residue "A GLU 171": "OE1" <-> "OE2" Residue "A GLU 182": "OE1" <-> "OE2" Residue "A GLU 189": "OE1" <-> "OE2" Residue "A GLU 232": "OE1" <-> "OE2" Residue "A GLU 238": "OE1" <-> "OE2" Residue "A ARG 245": "NH1" <-> "NH2" Residue "A GLU 398": "OE1" <-> "OE2" Residue "A GLU 402": "OE1" <-> "OE2" Residue "A GLU 433": "OE1" <-> "OE2" Residue "A GLU 435": "OE1" <-> "OE2" Residue "A GLU 467": "OE1" <-> "OE2" Residue "A GLU 483": "OE1" <-> "OE2" Residue "A GLU 495": "OE1" <-> "OE2" Residue "A GLU 527": "OE1" <-> "OE2" Residue "A GLU 536": "OE1" <-> "OE2" Residue "A GLU 564": "OE1" <-> "OE2" Residue "A GLU 571": "OE1" <-> "OE2" Residue "A GLU 589": "OE1" <-> "OE2" Residue "A TYR 613": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/chem_data/mon_lib" Total number of atoms: 6428 Number of models: 1 Model: "" Number of chains: 2 Chain: "E" Number of atoms: 1558 Number of conformers: 1 Conformer: "" Number of residues, atoms: 194, 1558 Classifications: {'peptide': 194} Link IDs: {'PTRANS': 11, 'TRANS': 182} Chain: "A" Number of atoms: 4870 Number of conformers: 1 Conformer: "" Number of residues, atoms: 597, 4870 Classifications: {'peptide': 597} Link IDs: {'PTRANS': 27, 'TRANS': 569} Time building chain proxies: 3.97, per 1000 atoms: 0.62 Number of scatterers: 6428 At special positions: 0 Unit cell: (76.51, 99.463, 113.672, 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 37 16.00 O 1203 8.00 N 1069 7.00 C 4119 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=7, symmetry=0 Simple disulfide: pdb=" SG CYS E 336 " - pdb=" SG CYS E 361 " distance=2.03 Simple disulfide: pdb=" SG CYS E 379 " - pdb=" SG CYS E 432 " distance=2.06 Simple disulfide: pdb=" SG CYS E 391 " - pdb=" SG CYS E 525 " distance=2.04 Simple disulfide: pdb=" SG CYS E 480 " - pdb=" SG CYS E 488 " distance=2.03 Simple disulfide: pdb=" SG CYS A 133 " - pdb=" SG CYS A 141 " distance=2.01 Simple disulfide: pdb=" SG CYS A 344 " - pdb=" SG CYS A 361 " distance=2.03 Simple disulfide: pdb=" SG CYS A 530 " - pdb=" SG CYS A 542 " distance=2.02 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: 2.29 Conformation dependent library (CDL) restraints added in 1.3 seconds 1574 Ramachandran restraints generated. 787 Oldfield, 0 Emsley, 787 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1494 Finding SS restraints... Secondary structure from input PDB file: 37 helices and 5 sheets defined 47.7% alpha, 5.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.66 Creating SS restraints... Processing helix chain 'E' and resid 349 through 353 removed outlier: 4.154A pdb=" N TRP E 353 " --> pdb=" O VAL E 350 " (cutoff:3.500A) Processing helix chain 'E' and resid 364 through 372 removed outlier: 4.096A pdb=" N LEU E 368 " --> pdb=" O ASP E 364 " (cutoff:3.500A) Processing helix chain 'E' and resid 417 through 422 Processing helix chain 'A' and resid 20 through 49 removed outlier: 3.770A pdb=" N HIS A 34 " --> pdb=" O ASP A 30 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N SER A 43 " --> pdb=" O LEU A 39 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N ALA A 46 " --> pdb=" O GLN A 42 " (cutoff:3.500A) Processing helix chain 'A' and resid 55 through 80 removed outlier: 4.025A pdb=" N GLN A 60 " --> pdb=" O GLU A 56 " (cutoff:3.500A) removed outlier: 4.123A pdb=" N ASN A 61 " --> pdb=" O GLU A 57 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N ASP A 67 " --> pdb=" O ASN A 63 " (cutoff:3.500A) removed outlier: 3.859A pdb=" N LYS A 68 " --> pdb=" O ASN A 64 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N TRP A 69 " --> pdb=" O ALA A 65 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N PHE A 72 " --> pdb=" O LYS A 68 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N GLU A 75 " --> pdb=" O ALA A 71 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N THR A 78 " --> pdb=" O LYS A 74 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N LEU A 79 " --> pdb=" O GLU A 75 " (cutoff:3.500A) Processing helix chain 'A' and resid 81 through 83 No H-bonds generated for 'chain 'A' and resid 81 through 83' Processing helix chain 'A' and resid 90 through 98 Processing helix chain 'A' and resid 109 through 129 removed outlier: 3.680A pdb=" N ARG A 115 " --> pdb=" O ASP A 111 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N LEU A 116 " --> pdb=" O LYS A 112 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N ASN A 121 " --> pdb=" O ASN A 117 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N THR A 122 " --> pdb=" O THR A 118 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N THR A 125 " --> pdb=" O ASN A 121 " (cutoff:3.500A) removed outlier: 3.989A pdb=" N ILE A 126 " --> pdb=" O THR A 122 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N SER A 128 " --> pdb=" O SER A 124 " (cutoff:3.500A) Processing helix chain 'A' and resid 158 through 167 removed outlier: 3.662A pdb=" N ALA A 164 " --> pdb=" O GLU A 160 " (cutoff:3.500A) Processing helix chain 'A' and resid 168 through 170 No H-bonds generated for 'chain 'A' and resid 168 through 170' Processing helix chain 'A' and resid 176 through 192 removed outlier: 3.707A pdb=" N GLU A 181 " --> pdb=" O ARG A 177 " (cutoff:3.500A) removed outlier: 4.524A pdb=" N GLU A 182 " --> pdb=" O PRO A 178 " (cutoff:3.500A) removed outlier: 3.886A pdb=" N TYR A 183 " --> pdb=" O LEU A 179 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N VAL A 185 " --> pdb=" O GLU A 181 " (cutoff:3.500A) removed outlier: 4.027A pdb=" N GLU A 189 " --> pdb=" O VAL A 185 " (cutoff:3.500A) Processing helix chain 'A' and resid 199 through 204 Processing helix chain 'A' and resid 219 through 231 removed outlier: 4.243A pdb=" N ILE A 223 " --> pdb=" O ARG A 219 " (cutoff:3.500A) removed outlier: 4.010A pdb=" N GLU A 224 " --> pdb=" O GLY A 220 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N HIS A 228 " --> pdb=" O GLU A 224 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N GLU A 231 " --> pdb=" O GLU A 227 " (cutoff:3.500A) Processing helix chain 'A' and resid 233 through 248 removed outlier: 3.508A pdb=" N ARG A 245 " --> pdb=" O HIS A 241 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N ALA A 246 " --> pdb=" O ALA A 242 " (cutoff:3.500A) Processing helix chain 'A' and resid 265 through 267 No H-bonds generated for 'chain 'A' and resid 265 through 267' Processing helix chain 'A' and resid 275 through 279 Processing helix chain 'A' and resid 293 through 298 removed outlier: 3.577A pdb=" N VAL A 298 " --> pdb=" O THR A 294 " (cutoff:3.500A) Processing helix chain 'A' and resid 303 through 316 removed outlier: 3.961A pdb=" N PHE A 308 " --> pdb=" O ALA A 304 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N PHE A 314 " --> pdb=" O GLU A 310 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N PHE A 315 " --> pdb=" O ALA A 311 " (cutoff:3.500A) Processing helix chain 'A' and resid 326 through 331 removed outlier: 3.637A pdb=" N SER A 331 " --> pdb=" O PHE A 327 " (cutoff:3.500A) Processing helix chain 'A' and resid 365 through 383 removed outlier: 3.956A pdb=" N THR A 371 " --> pdb=" O ASP A 367 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N HIS A 373 " --> pdb=" O PHE A 369 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N HIS A 374 " --> pdb=" O LEU A 370 " (cutoff:3.500A) Processing helix chain 'A' and resid 384 through 388 removed outlier: 4.463A pdb=" N ALA A 387 " --> pdb=" O ALA A 384 " (cutoff:3.500A) Processing helix chain 'A' and resid 389 through 393 Processing helix chain 'A' and resid 400 through 412 removed outlier: 3.549A pdb=" N GLY A 405 " --> pdb=" O HIS A 401 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N GLU A 406 " --> pdb=" O GLU A 402 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N ILE A 407 " --> pdb=" O ALA A 403 " (cutoff:3.500A) removed outlier: 4.270A pdb=" N MET A 408 " --> pdb=" O VAL A 404 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N ALA A 412 " --> pdb=" O MET A 408 " (cutoff:3.500A) Processing helix chain 'A' and resid 414 through 419 Processing helix chain 'A' and resid 434 through 447 removed outlier: 3.532A pdb=" N PHE A 438 " --> pdb=" O THR A 434 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N THR A 445 " --> pdb=" O LYS A 441 " (cutoff:3.500A) Processing helix chain 'A' and resid 448 through 465 removed outlier: 4.211A pdb=" N PHE A 452 " --> pdb=" O GLY A 448 " (cutoff:3.500A) removed outlier: 3.835A pdb=" N LEU A 456 " --> pdb=" O PHE A 452 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N LYS A 465 " --> pdb=" O TRP A 461 " (cutoff:3.500A) Processing helix chain 'A' and resid 469 through 473 Processing helix chain 'A' and resid 474 through 479 removed outlier: 3.627A pdb=" N TRP A 478 " --> pdb=" O MET A 474 " (cutoff:3.500A) Processing helix chain 'A' and resid 498 through 502 removed outlier: 3.817A pdb=" N SER A 502 " --> pdb=" O ASP A 499 " (cutoff:3.500A) Processing helix chain 'A' and resid 503 through 508 removed outlier: 3.707A pdb=" N ASN A 508 " --> pdb=" O PHE A 504 " (cutoff:3.500A) Processing helix chain 'A' and resid 513 through 523 removed outlier: 3.831A pdb=" N THR A 519 " --> pdb=" O TYR A 515 " (cutoff:3.500A) Processing helix chain 'A' and resid 523 through 533 Processing helix chain 'A' and resid 538 through 542 removed outlier: 3.755A pdb=" N LYS A 541 " --> pdb=" O PRO A 538 " (cutoff:3.500A) Processing helix chain 'A' and resid 548 through 559 removed outlier: 3.615A pdb=" N GLN A 552 " --> pdb=" O THR A 548 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N LYS A 553 " --> pdb=" O GLU A 549 " (cutoff:3.500A) removed outlier: 4.557A pdb=" N MET A 557 " --> pdb=" O LYS A 553 " (cutoff:3.500A) Processing helix chain 'A' and resid 565 through 572 removed outlier: 3.574A pdb=" N GLU A 571 " --> pdb=" O THR A 567 " (cutoff:3.500A) Processing helix chain 'A' and resid 581 through 588 Processing helix chain 'A' and resid 588 through 599 removed outlier: 3.514A pdb=" N TRP A 594 " --> pdb=" O PRO A 590 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'E' and resid 354 through 358 removed outlier: 3.810A pdb=" N ASN E 354 " --> pdb=" O SER E 399 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N SER E 399 " --> pdb=" O ASN E 354 " (cutoff:3.500A) removed outlier: 4.026A pdb=" N VAL E 433 " --> pdb=" O LYS E 378 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N LYS E 378 " --> pdb=" O VAL E 433 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'E' and resid 452 through 454 Processing sheet with id=AA3, first strand: chain 'E' and resid 473 through 474 Processing sheet with id=AA4, first strand: chain 'A' and resid 262 through 263 removed outlier: 6.158A pdb=" N LEU A 262 " --> pdb=" O VAL A 488 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'A' and resid 347 through 352 removed outlier: 5.396A pdb=" N ALA A 348 " --> pdb=" O LEU A 359 " (cutoff:3.500A) removed outlier: 7.057A pdb=" N LEU A 359 " --> pdb=" O ALA A 348 " (cutoff:3.500A) removed outlier: 4.996A pdb=" N ASP A 350 " --> pdb=" O ARG A 357 " (cutoff:3.500A) removed outlier: 7.222A pdb=" N ARG A 357 " --> pdb=" O ASP A 350 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N GLY A 352 " --> pdb=" O ASP A 355 " (cutoff:3.500A) 200 hydrogen bonds defined for protein. 555 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.60 Time building geometry restraints manager: 2.50 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.32: 1106 1.32 - 1.45: 1931 1.45 - 1.58: 3516 1.58 - 1.71: 0 1.71 - 1.84: 58 Bond restraints: 6611 Sorted by residual: bond pdb=" CA SER E 366 " pdb=" C SER E 366 " ideal model delta sigma weight residual 1.523 1.436 0.087 1.30e-02 5.92e+03 4.52e+01 bond pdb=" CA LYS A 31 " pdb=" C LYS A 31 " ideal model delta sigma weight residual 1.524 1.454 0.070 1.26e-02 6.30e+03 3.09e+01 bond pdb=" CA TYR E 365 " pdb=" C TYR E 365 " ideal model delta sigma weight residual 1.522 1.449 0.073 1.41e-02 5.03e+03 2.67e+01 bond pdb=" CA ASN A 33 " pdb=" C ASN A 33 " ideal model delta sigma weight residual 1.524 1.460 0.064 1.27e-02 6.20e+03 2.51e+01 bond pdb=" CA GLU A 35 " pdb=" CB GLU A 35 " ideal model delta sigma weight residual 1.528 1.452 0.077 1.59e-02 3.96e+03 2.33e+01 ... (remaining 6606 not shown) Histogram of bond angle deviations from ideal: 90.89 - 99.58: 1 99.58 - 108.26: 380 108.26 - 116.94: 3998 116.94 - 125.63: 4455 125.63 - 134.31: 152 Bond angle restraints: 8986 Sorted by residual: angle pdb=" N CYS A 141 " pdb=" CA CYS A 141 " pdb=" C CYS A 141 " ideal model delta sigma weight residual 109.29 122.96 -13.67 1.41e+00 5.03e-01 9.40e+01 angle pdb=" N CYS E 488 " pdb=" CA CYS E 488 " pdb=" C CYS E 488 " ideal model delta sigma weight residual 107.20 90.89 16.31 1.70e+00 3.46e-01 9.20e+01 angle pdb=" N LEU A 142 " pdb=" CA LEU A 142 " pdb=" C LEU A 142 " ideal model delta sigma weight residual 109.50 124.40 -14.90 1.58e+00 4.01e-01 8.89e+01 angle pdb=" N LEU E 371 " pdb=" CA LEU E 371 " pdb=" C LEU E 371 " ideal model delta sigma weight residual 113.20 103.39 9.81 1.21e+00 6.83e-01 6.57e+01 angle pdb=" N PRO E 373 " pdb=" CA PRO E 373 " pdb=" C PRO E 373 " ideal model delta sigma weight residual 113.53 102.47 11.06 1.39e+00 5.18e-01 6.33e+01 ... (remaining 8981 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 18.99: 3458 18.99 - 37.99: 372 37.99 - 56.98: 59 56.98 - 75.97: 12 75.97 - 94.97: 4 Dihedral angle restraints: 3905 sinusoidal: 1579 harmonic: 2326 Sorted by residual: dihedral pdb=" CA GLU A 145 " pdb=" C GLU A 145 " pdb=" N PRO A 146 " pdb=" CA PRO A 146 " ideal model delta harmonic sigma weight residual -180.00 -85.03 -94.97 0 5.00e+00 4.00e-02 3.61e+02 dihedral pdb=" CB CYS E 391 " pdb=" SG CYS E 391 " pdb=" SG CYS E 525 " pdb=" CB CYS E 525 " ideal model delta sinusoidal sigma weight residual 93.00 17.56 75.44 1 1.00e+01 1.00e-02 7.19e+01 dihedral pdb=" CA CYS A 344 " pdb=" C CYS A 344 " pdb=" N HIS A 345 " pdb=" CA HIS A 345 " ideal model delta harmonic sigma weight residual 180.00 153.20 26.80 0 5.00e+00 4.00e-02 2.87e+01 ... (remaining 3902 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.099: 846 0.099 - 0.198: 75 0.198 - 0.297: 11 0.297 - 0.395: 3 0.395 - 0.494: 4 Chirality restraints: 939 Sorted by residual: chirality pdb=" CA LYS A 353 " pdb=" N LYS A 353 " pdb=" C LYS A 353 " pdb=" CB LYS A 353 " both_signs ideal model delta sigma weight residual False 2.51 2.02 0.49 2.00e-01 2.50e+01 6.11e+00 chirality pdb=" CA PHE E 375 " pdb=" N PHE E 375 " pdb=" C PHE E 375 " pdb=" CB PHE E 375 " both_signs ideal model delta sigma weight residual False 2.51 2.03 0.48 2.00e-01 2.50e+01 5.66e+00 chirality pdb=" CA ALA E 372 " pdb=" N ALA E 372 " pdb=" C ALA E 372 " pdb=" CB ALA E 372 " both_signs ideal model delta sigma weight residual False 2.48 2.02 0.47 2.00e-01 2.50e+01 5.45e+00 ... (remaining 936 not shown) Planarity restraints: 1166 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA LEU E 368 " -0.023 2.00e-02 2.50e+03 4.46e-02 1.99e+01 pdb=" C LEU E 368 " 0.077 2.00e-02 2.50e+03 pdb=" O LEU E 368 " -0.029 2.00e-02 2.50e+03 pdb=" N TYR E 369 " -0.026 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA THR E 500 " 0.021 2.00e-02 2.50e+03 4.21e-02 1.77e+01 pdb=" C THR E 500 " -0.073 2.00e-02 2.50e+03 pdb=" O THR E 500 " 0.027 2.00e-02 2.50e+03 pdb=" N TYR E 501 " 0.025 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA VAL E 367 " 0.019 2.00e-02 2.50e+03 3.69e-02 1.36e+01 pdb=" C VAL E 367 " -0.064 2.00e-02 2.50e+03 pdb=" O VAL E 367 " 0.023 2.00e-02 2.50e+03 pdb=" N LEU E 368 " 0.022 2.00e-02 2.50e+03 ... (remaining 1163 not shown) Histogram of nonbonded interaction distances: 2.33 - 2.84: 2240 2.84 - 3.36: 5639 3.36 - 3.87: 10703 3.87 - 4.39: 12421 4.39 - 4.90: 20478 Nonbonded interactions: 51481 Sorted by model distance: nonbonded pdb=" O THR A 449 " pdb=" OG1 THR A 453 " model vdw 2.328 2.440 nonbonded pdb=" O SER A 254 " pdb=" OG SER A 254 " model vdw 2.333 2.440 nonbonded pdb=" OD1 ASP A 431 " pdb=" OG1 THR A 434 " model vdw 2.337 2.440 nonbonded pdb=" O ASN A 121 " pdb=" OG1 THR A 125 " model vdw 2.351 2.440 nonbonded pdb=" OG1 THR E 500 " pdb=" OH TYR A 41 " model vdw 2.371 2.440 ... (remaining 51476 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.640 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 9.470 Check model and map are aligned: 0.100 Set scattering table: 0.060 Process input model: 21.060 Find NCS groups from input model: 0.170 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.810 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 36.350 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7514 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 : 0.008 0.087 6611 Z= 0.485 Angle : 1.068 16.306 8986 Z= 0.647 Chirality : 0.071 0.494 939 Planarity : 0.007 0.062 1166 Dihedral : 15.403 94.965 2390 Min Nonbonded Distance : 2.328 Molprobity Statistics. All-atom Clashscore : 5.81 Ramachandran Plot: Outliers : 0.38 % Allowed : 4.70 % Favored : 94.92 % Rotamer: Outliers : 0.57 % Allowed : 7.90 % Favored : 91.52 % Cbeta Deviations : 0.13 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.63 % 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: -5.05 (0.22), residues: 787 helix: -4.47 (0.12), residues: 325 sheet: -2.25 (0.93), residues: 35 loop : -2.50 (0.25), residues: 427 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP A 478 HIS 0.018 0.002 HIS A 34 PHE 0.020 0.002 PHE A 32 TYR 0.016 0.002 TYR A 183 ARG 0.006 0.001 ARG A 482 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1574 Ramachandran restraints generated. 787 Oldfield, 0 Emsley, 787 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1574 Ramachandran restraints generated. 787 Oldfield, 0 Emsley, 787 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 254 residues out of total 696 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 250 time to evaluate : 0.749 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 4 outliers final: 3 residues processed: 252 average time/residue: 0.2370 time to fit residues: 74.4912 Evaluate side-chains 219 residues out of total 696 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 216 time to evaluate : 0.754 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.0652 time to fit residues: 1.3663 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 65 optimal weight: 0.0870 chunk 59 optimal weight: 0.9990 chunk 32 optimal weight: 0.9990 chunk 20 optimal weight: 0.1980 chunk 39 optimal weight: 0.5980 chunk 31 optimal weight: 0.0980 chunk 61 optimal weight: 0.0770 chunk 23 optimal weight: 0.8980 chunk 37 optimal weight: 0.9980 chunk 45 optimal weight: 0.9980 chunk 70 optimal weight: 0.5980 overall best weight: 0.2116 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 417 ASN E 477 ASN A 33 ASN ** A 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 101 GLN A 121 ASN A 330 ASN A 373 HIS A 417 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7516 moved from start: 0.3033 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 6611 Z= 0.197 Angle : 0.655 9.034 8986 Z= 0.338 Chirality : 0.044 0.178 939 Planarity : 0.005 0.037 1166 Dihedral : 5.270 64.392 861 Min Nonbonded Distance : 2.241 Molprobity Statistics. All-atom Clashscore : 11.23 Ramachandran Plot: Outliers : 0.13 % Allowed : 3.30 % Favored : 96.57 % Rotamer: Outliers : 3.30 % Allowed : 19.54 % Favored : 77.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.63 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.68 (0.26), residues: 787 helix: -3.19 (0.20), residues: 353 sheet: -1.95 (0.83), residues: 34 loop : -1.66 (0.29), residues: 400 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP A 168 HIS 0.005 0.001 HIS A 265 PHE 0.015 0.001 PHE A 327 TYR 0.019 0.001 TYR A 158 ARG 0.003 0.000 ARG A 219 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1574 Ramachandran restraints generated. 787 Oldfield, 0 Emsley, 787 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1574 Ramachandran restraints generated. 787 Oldfield, 0 Emsley, 787 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 233 residues out of total 696 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 210 time to evaluate : 0.789 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 23 outliers final: 9 residues processed: 224 average time/residue: 0.2170 time to fit residues: 61.4209 Evaluate side-chains 202 residues out of total 696 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 193 time to evaluate : 0.728 Switching outliers to nearest non-outliers outliers start: 9 outliers final: 0 residues processed: 9 average time/residue: 0.0622 time to fit residues: 2.0034 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 39 optimal weight: 1.9990 chunk 21 optimal weight: 0.9980 chunk 58 optimal weight: 0.2980 chunk 48 optimal weight: 0.0980 chunk 19 optimal weight: 0.5980 chunk 70 optimal weight: 1.9990 chunk 76 optimal weight: 0.0970 chunk 63 optimal weight: 0.8980 chunk 24 optimal weight: 0.8980 chunk 56 optimal weight: 1.9990 chunk 53 optimal weight: 0.5980 overall best weight: 0.3378 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 360 ASN ** E 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 33 ASN ** A 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7551 moved from start: 0.3750 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 6611 Z= 0.221 Angle : 0.658 10.160 8986 Z= 0.330 Chirality : 0.044 0.130 939 Planarity : 0.004 0.044 1166 Dihedral : 4.932 53.618 861 Min Nonbonded Distance : 2.275 Molprobity Statistics. All-atom Clashscore : 12.66 Ramachandran Plot: Outliers : 0.13 % Allowed : 3.05 % Favored : 96.82 % Rotamer: Outliers : 2.87 % Allowed : 24.28 % Favored : 72.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.63 % 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: -2.96 (0.27), residues: 787 helix: -2.53 (0.23), residues: 362 sheet: -2.11 (0.72), residues: 48 loop : -1.16 (0.32), residues: 377 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP A 168 HIS 0.005 0.001 HIS A 265 PHE 0.029 0.002 PHE A 428 TYR 0.020 0.001 TYR A 158 ARG 0.006 0.001 ARG A 219 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1574 Ramachandran restraints generated. 787 Oldfield, 0 Emsley, 787 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1574 Ramachandran restraints generated. 787 Oldfield, 0 Emsley, 787 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 220 residues out of total 696 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 200 time to evaluate : 0.768 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 20 outliers final: 10 residues processed: 208 average time/residue: 0.2346 time to fit residues: 61.2586 Evaluate side-chains 209 residues out of total 696 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 199 time to evaluate : 0.636 Switching outliers to nearest non-outliers outliers start: 10 outliers final: 0 residues processed: 10 average time/residue: 0.0651 time to fit residues: 2.2712 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 36 optimal weight: 0.8980 chunk 7 optimal weight: 0.4980 chunk 33 optimal weight: 0.4980 chunk 47 optimal weight: 0.9990 chunk 71 optimal weight: 0.9980 chunk 75 optimal weight: 0.2980 chunk 37 optimal weight: 0.9980 chunk 67 optimal weight: 1.9990 chunk 20 optimal weight: 0.9980 chunk 62 optimal weight: 0.9990 chunk 42 optimal weight: 0.0670 overall best weight: 0.4518 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 360 ASN ** E 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 194 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7587 moved from start: 0.4271 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 6611 Z= 0.259 Angle : 0.685 10.191 8986 Z= 0.342 Chirality : 0.046 0.153 939 Planarity : 0.004 0.029 1166 Dihedral : 4.951 49.418 861 Min Nonbonded Distance : 2.248 Molprobity Statistics. All-atom Clashscore : 13.14 Ramachandran Plot: Outliers : 0.13 % Allowed : 3.68 % Favored : 96.19 % Rotamer: Outliers : 3.30 % Allowed : 27.01 % Favored : 69.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.63 % 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: -2.38 (0.29), residues: 787 helix: -1.99 (0.24), residues: 361 sheet: -2.23 (0.73), residues: 48 loop : -0.87 (0.33), residues: 378 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP A 168 HIS 0.004 0.001 HIS A 401 PHE 0.019 0.002 PHE A 400 TYR 0.028 0.002 TYR A 158 ARG 0.006 0.001 ARG E 357 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1574 Ramachandran restraints generated. 787 Oldfield, 0 Emsley, 787 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1574 Ramachandran restraints generated. 787 Oldfield, 0 Emsley, 787 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 228 residues out of total 696 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 205 time to evaluate : 0.827 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 23 outliers final: 12 residues processed: 212 average time/residue: 0.2370 time to fit residues: 63.3725 Evaluate side-chains 221 residues out of total 696 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 209 time to evaluate : 0.806 Switching outliers to nearest non-outliers outliers start: 12 outliers final: 0 residues processed: 12 average time/residue: 0.0704 time to fit residues: 2.5196 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 1 optimal weight: 0.9980 chunk 56 optimal weight: 0.6980 chunk 31 optimal weight: 0.5980 chunk 64 optimal weight: 0.3980 chunk 52 optimal weight: 0.9990 chunk 0 optimal weight: 0.9980 chunk 38 optimal weight: 0.0980 chunk 67 optimal weight: 0.4980 chunk 19 optimal weight: 0.9990 chunk 25 optimal weight: 0.9980 chunk 14 optimal weight: 0.1980 overall best weight: 0.3580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 360 ASN ** E 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 439 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 474 GLN ** A 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 101 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7572 moved from start: 0.4589 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 6611 Z= 0.237 Angle : 0.686 11.470 8986 Z= 0.340 Chirality : 0.045 0.146 939 Planarity : 0.004 0.038 1166 Dihedral : 4.859 45.821 861 Min Nonbonded Distance : 2.206 Molprobity Statistics. All-atom Clashscore : 12.98 Ramachandran Plot: Outliers : 0.13 % Allowed : 3.68 % Favored : 96.19 % Rotamer: Outliers : 2.16 % Allowed : 29.89 % Favored : 67.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.63 % 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: -1.97 (0.29), residues: 787 helix: -1.62 (0.25), residues: 369 sheet: -2.19 (0.74), residues: 48 loop : -0.64 (0.34), residues: 370 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP A 168 HIS 0.003 0.001 HIS E 505 PHE 0.015 0.002 PHE A 400 TYR 0.028 0.002 TYR A 255 ARG 0.005 0.001 ARG E 403 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1574 Ramachandran restraints generated. 787 Oldfield, 0 Emsley, 787 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1574 Ramachandran restraints generated. 787 Oldfield, 0 Emsley, 787 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 214 residues out of total 696 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 199 time to evaluate : 0.791 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 15 outliers final: 4 residues processed: 203 average time/residue: 0.2253 time to fit residues: 57.7970 Evaluate side-chains 194 residues out of total 696 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 190 time to evaluate : 0.766 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.1327 time to fit residues: 1.7961 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 44 optimal weight: 0.9990 chunk 18 optimal weight: 0.5980 chunk 75 optimal weight: 0.9980 chunk 62 optimal weight: 0.0980 chunk 34 optimal weight: 0.5980 chunk 6 optimal weight: 0.9990 chunk 24 optimal weight: 0.9990 chunk 39 optimal weight: 0.5980 chunk 72 optimal weight: 0.9990 chunk 8 optimal weight: 1.9990 chunk 42 optimal weight: 0.0970 overall best weight: 0.3978 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 360 ASN ** E 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 439 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 474 GLN ** A 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7585 moved from start: 0.4879 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 6611 Z= 0.251 Angle : 0.714 10.827 8986 Z= 0.349 Chirality : 0.046 0.166 939 Planarity : 0.004 0.029 1166 Dihedral : 4.791 41.376 861 Min Nonbonded Distance : 2.196 Molprobity Statistics. All-atom Clashscore : 14.33 Ramachandran Plot: Outliers : 0.13 % Allowed : 3.18 % Favored : 96.70 % Rotamer: Outliers : 2.73 % Allowed : 31.47 % Favored : 65.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.63 % 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: -1.57 (0.30), residues: 787 helix: -1.28 (0.26), residues: 370 sheet: -2.21 (0.71), residues: 46 loop : -0.41 (0.34), residues: 371 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP A 168 HIS 0.004 0.001 HIS E 505 PHE 0.018 0.002 PHE A 428 TYR 0.033 0.002 TYR A 255 ARG 0.003 0.001 ARG E 357 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1574 Ramachandran restraints generated. 787 Oldfield, 0 Emsley, 787 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1574 Ramachandran restraints generated. 787 Oldfield, 0 Emsley, 787 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 213 residues out of total 696 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 194 time to evaluate : 0.801 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 19 outliers final: 9 residues processed: 202 average time/residue: 0.2392 time to fit residues: 60.4482 Evaluate side-chains 202 residues out of total 696 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 193 time to evaluate : 0.788 Switching outliers to nearest non-outliers outliers start: 9 outliers final: 0 residues processed: 9 average time/residue: 0.0674 time to fit residues: 2.1335 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 55 optimal weight: 0.5980 chunk 42 optimal weight: 0.0010 chunk 63 optimal weight: 0.3980 chunk 75 optimal weight: 0.9980 chunk 47 optimal weight: 1.9990 chunk 45 optimal weight: 0.9980 chunk 34 optimal weight: 0.5980 chunk 46 optimal weight: 0.5980 chunk 30 optimal weight: 1.9990 chunk 44 optimal weight: 0.5980 chunk 22 optimal weight: 0.9990 overall best weight: 0.4386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 360 ASN ** E 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 439 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 103 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 472 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7589 moved from start: 0.5070 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 6611 Z= 0.265 Angle : 0.730 10.393 8986 Z= 0.358 Chirality : 0.046 0.183 939 Planarity : 0.004 0.036 1166 Dihedral : 4.887 38.265 861 Min Nonbonded Distance : 2.177 Molprobity Statistics. All-atom Clashscore : 14.97 Ramachandran Plot: Outliers : 0.13 % Allowed : 3.43 % Favored : 96.44 % Rotamer: Outliers : 2.16 % Allowed : 31.47 % Favored : 66.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.63 % 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: -1.39 (0.31), residues: 787 helix: -1.07 (0.26), residues: 370 sheet: -2.15 (0.72), residues: 48 loop : -0.36 (0.35), residues: 369 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP A 168 HIS 0.003 0.001 HIS A 265 PHE 0.016 0.002 PHE A 428 TYR 0.035 0.002 TYR A 255 ARG 0.004 0.001 ARG E 493 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1574 Ramachandran restraints generated. 787 Oldfield, 0 Emsley, 787 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1574 Ramachandran restraints generated. 787 Oldfield, 0 Emsley, 787 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 212 residues out of total 696 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 197 time to evaluate : 0.730 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 15 outliers final: 6 residues processed: 203 average time/residue: 0.2375 time to fit residues: 60.4331 Evaluate side-chains 194 residues out of total 696 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 188 time to evaluate : 0.785 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 0 residues processed: 6 average time/residue: 0.0660 time to fit residues: 1.7262 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 14 optimal weight: 0.9990 chunk 47 optimal weight: 0.0570 chunk 51 optimal weight: 0.8980 chunk 37 optimal weight: 0.1980 chunk 7 optimal weight: 0.9990 chunk 59 optimal weight: 0.3980 chunk 68 optimal weight: 0.8980 chunk 72 optimal weight: 0.9980 chunk 65 optimal weight: 0.9980 chunk 70 optimal weight: 0.9990 chunk 42 optimal weight: 0.0970 overall best weight: 0.3296 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 439 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 474 GLN ** A 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 103 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 241 HIS A 535 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7565 moved from start: 0.5368 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 6611 Z= 0.239 Angle : 0.755 11.017 8986 Z= 0.371 Chirality : 0.046 0.163 939 Planarity : 0.004 0.036 1166 Dihedral : 4.909 34.703 861 Min Nonbonded Distance : 2.173 Molprobity Statistics. All-atom Clashscore : 15.21 Ramachandran Plot: Outliers : 0.13 % Allowed : 4.19 % Favored : 95.68 % Rotamer: Outliers : 1.87 % Allowed : 31.75 % Favored : 66.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.63 % 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: -1.15 (0.31), residues: 787 helix: -0.81 (0.27), residues: 367 sheet: -2.18 (0.70), residues: 46 loop : -0.31 (0.35), residues: 374 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP A 271 HIS 0.003 0.001 HIS A 265 PHE 0.014 0.001 PHE A 40 TYR 0.020 0.002 TYR E 501 ARG 0.007 0.001 ARG A 219 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1574 Ramachandran restraints generated. 787 Oldfield, 0 Emsley, 787 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1574 Ramachandran restraints generated. 787 Oldfield, 0 Emsley, 787 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 208 residues out of total 696 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 195 time to evaluate : 0.782 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 13 outliers final: 7 residues processed: 202 average time/residue: 0.2365 time to fit residues: 60.7639 Evaluate side-chains 193 residues out of total 696 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 186 time to evaluate : 0.798 Switching outliers to nearest non-outliers outliers start: 7 outliers final: 0 residues processed: 7 average time/residue: 0.0761 time to fit residues: 2.0005 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 30 optimal weight: 0.6980 chunk 55 optimal weight: 1.9990 chunk 21 optimal weight: 0.8980 chunk 63 optimal weight: 0.9990 chunk 66 optimal weight: 1.9990 chunk 69 optimal weight: 0.0670 chunk 46 optimal weight: 0.6980 chunk 74 optimal weight: 0.6980 chunk 45 optimal weight: 0.0980 chunk 35 optimal weight: 0.3980 chunk 51 optimal weight: 0.0980 overall best weight: 0.2718 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 439 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 474 GLN ** A 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 103 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7535 moved from start: 0.5608 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 6611 Z= 0.229 Angle : 0.761 11.016 8986 Z= 0.376 Chirality : 0.046 0.211 939 Planarity : 0.004 0.032 1166 Dihedral : 5.028 30.539 861 Min Nonbonded Distance : 2.174 Molprobity Statistics. All-atom Clashscore : 15.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.92 % Favored : 97.08 % Rotamer: Outliers : 1.15 % Allowed : 31.61 % Favored : 67.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.63 % 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: -1.04 (0.31), residues: 787 helix: -0.62 (0.27), residues: 364 sheet: -2.06 (0.71), residues: 48 loop : -0.37 (0.35), residues: 375 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP A 566 HIS 0.004 0.001 HIS A 265 PHE 0.024 0.002 PHE A 315 TYR 0.023 0.002 TYR E 473 ARG 0.008 0.001 ARG A 161 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1574 Ramachandran restraints generated. 787 Oldfield, 0 Emsley, 787 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1574 Ramachandran restraints generated. 787 Oldfield, 0 Emsley, 787 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 204 residues out of total 696 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 196 time to evaluate : 0.762 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 8 outliers final: 3 residues processed: 198 average time/residue: 0.2276 time to fit residues: 56.8311 Evaluate side-chains 196 residues out of total 696 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 193 time to evaluate : 0.765 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.0735 time to fit residues: 1.4789 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 77 optimal weight: 0.0770 chunk 71 optimal weight: 0.9980 chunk 61 optimal weight: 0.9980 chunk 6 optimal weight: 0.0980 chunk 47 optimal weight: 0.0020 chunk 37 optimal weight: 0.9990 chunk 49 optimal weight: 0.9980 chunk 65 optimal weight: 0.0070 chunk 18 optimal weight: 0.4980 chunk 57 optimal weight: 0.5980 chunk 9 optimal weight: 0.5980 overall best weight: 0.1364 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 439 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 175 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 241 HIS ** A 380 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7485 moved from start: 0.5939 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 6611 Z= 0.214 Angle : 0.787 14.373 8986 Z= 0.383 Chirality : 0.045 0.152 939 Planarity : 0.004 0.033 1166 Dihedral : 4.834 27.793 861 Min Nonbonded Distance : 2.178 Molprobity Statistics. All-atom Clashscore : 15.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.56 % Favored : 96.44 % Rotamer: Outliers : 0.72 % Allowed : 31.90 % Favored : 67.39 % 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: -0.94 (0.31), residues: 787 helix: -0.50 (0.28), residues: 366 sheet: -1.74 (0.74), residues: 46 loop : -0.42 (0.34), residues: 375 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP A 594 HIS 0.004 0.001 HIS A 378 PHE 0.022 0.002 PHE A 428 TYR 0.018 0.001 TYR A 158 ARG 0.009 0.001 ARG E 357 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1574 Ramachandran restraints generated. 787 Oldfield, 0 Emsley, 787 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1574 Ramachandran restraints generated. 787 Oldfield, 0 Emsley, 787 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 207 residues out of total 696 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 202 time to evaluate : 0.803 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 5 outliers final: 2 residues processed: 203 average time/residue: 0.2314 time to fit residues: 59.5537 Evaluate side-chains 199 residues out of total 696 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 197 time to evaluate : 0.735 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.0647 time to fit residues: 1.3147 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 17 optimal weight: 0.9990 chunk 61 optimal weight: 0.9980 chunk 25 optimal weight: 0.3980 chunk 63 optimal weight: 0.8980 chunk 7 optimal weight: 0.8980 chunk 11 optimal weight: 0.9980 chunk 54 optimal weight: 0.9980 chunk 3 optimal weight: 0.9980 chunk 44 optimal weight: 0.8980 chunk 70 optimal weight: 0.9980 chunk 41 optimal weight: 0.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 439 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 175 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 522 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3449 r_free = 0.3449 target = 0.109131 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 25)----------------| | r_work = 0.3200 r_free = 0.3200 target = 0.093807 restraints weight = 12251.652| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3255 r_free = 0.3255 target = 0.097197 restraints weight = 5744.421| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3291 r_free = 0.3291 target = 0.099393 restraints weight = 3275.007| |-----------------------------------------------------------------------------| r_work (final): 0.3292 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7676 moved from start: 0.5893 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.046 6611 Z= 0.439 Angle : 0.882 10.745 8986 Z= 0.442 Chirality : 0.053 0.219 939 Planarity : 0.005 0.040 1166 Dihedral : 5.519 33.776 861 Min Nonbonded Distance : 2.115 Molprobity Statistics. All-atom Clashscore : 21.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.21 % Favored : 94.79 % Rotamer: Outliers : 0.72 % Allowed : 31.90 % Favored : 67.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.13 % 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: -1.19 (0.30), residues: 787 helix: -0.80 (0.27), residues: 370 sheet: -2.01 (0.70), residues: 49 loop : -0.40 (0.34), residues: 368 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.040 0.003 TRP A 566 HIS 0.008 0.002 HIS A 265 PHE 0.017 0.002 PHE A 40 TYR 0.039 0.003 TYR E 473 ARG 0.010 0.001 ARG E 403 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2061.31 seconds wall clock time: 40 minutes 5.74 seconds (2405.74 seconds total)