Starting phenix.real_space_refine on Fri Dec 8 00:58:19 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8aqt_15589/12_2023/8aqt_15589.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8aqt_15589/12_2023/8aqt_15589.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8aqt_15589/12_2023/8aqt_15589.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8aqt_15589/12_2023/8aqt_15589.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8aqt_15589/12_2023/8aqt_15589.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8aqt_15589/12_2023/8aqt_15589.pdb" } resolution = 4.4 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= -0.001 sd= 0.049 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 4033 2.51 5 N 1055 2.21 5 O 1196 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A TYR 50": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 327": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 510": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 396": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 495": "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: 6321 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 4744 Number of conformers: 1 Conformer: "" Number of residues, atoms: 584, 4744 Classifications: {'peptide': 584} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 26, 'TRANS': 557} Unresolved non-hydrogen bonds: 13 Unresolved non-hydrogen angles: 17 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 12 Chain: "B" Number of atoms: 1535 Number of conformers: 1 Conformer: "" Number of residues, atoms: 193, 1535 Classifications: {'peptide': 193} Link IDs: {'PTRANS': 10, 'TRANS': 182} Chain: "C" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "B" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 3.98, per 1000 atoms: 0.63 Number of scatterers: 6321 At special positions: 0 Unit cell: (86.086, 91.3836, 116.547, 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 1196 8.00 N 1055 7.00 C 4033 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=6, symmetry=0 Simple disulfide: pdb=" SG CYS A 133 " - pdb=" SG CYS A 141 " distance=2.03 Simple disulfide: pdb=" SG CYS A 530 " - pdb=" SG CYS A 542 " distance=2.04 Simple disulfide: pdb=" SG CYS B 336 " - pdb=" SG CYS B 361 " distance=2.03 Simple disulfide: pdb=" SG CYS B 379 " - pdb=" SG CYS B 432 " distance=2.03 Simple disulfide: pdb=" SG CYS B 391 " - pdb=" SG CYS B 525 " distance=2.03 Simple disulfide: pdb=" SG CYS B 480 " - pdb=" SG CYS B 488 " distance=2.03 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 Links applied BETA1-4 " NAG C 1 " - " NAG C 2 " NAG-ASN " NAG B1301 " - " ASN B 343 " " NAG C 1 " - " ASN A 53 " Time building additional restraints: 2.16 Conformation dependent library (CDL) restraints added in 1.2 seconds 1546 Ramachandran restraints generated. 773 Oldfield, 0 Emsley, 773 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1466 Finding SS restraints... Secondary structure from input PDB file: 36 helices and 2 sheets defined 48.9% alpha, 4.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.69 Creating SS restraints... Processing helix chain 'A' and resid 23 through 53 Processing helix chain 'A' and resid 56 through 80 Processing helix chain 'A' and resid 93 through 102 Processing helix chain 'A' and resid 111 through 117 removed outlier: 3.623A pdb=" N GLN A 115 " --> pdb=" O ASP A 111 " (cutoff:3.500A) Processing helix chain 'A' and resid 119 through 129 removed outlier: 4.350A pdb=" N ILE A 126 " --> pdb=" O THR A 122 " (cutoff:3.500A) removed outlier: 4.692A pdb=" N TYR A 127 " --> pdb=" O MET A 123 " (cutoff:3.500A) removed outlier: 3.953A pdb=" N SER A 128 " --> pdb=" O SER A 124 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N THR A 129 " --> pdb=" O THR A 125 " (cutoff:3.500A) Processing helix chain 'A' and resid 145 through 153 removed outlier: 4.222A pdb=" N GLU A 150 " --> pdb=" O PRO A 146 " (cutoff:3.500A) removed outlier: 6.004A pdb=" N ILE A 151 " --> pdb=" O GLY A 147 " (cutoff:3.500A) Processing helix chain 'A' and resid 165 through 173 removed outlier: 3.509A pdb=" N GLY A 173 " --> pdb=" O ARG A 169 " (cutoff:3.500A) Processing helix chain 'A' and resid 175 through 187 removed outlier: 3.847A pdb=" N GLU A 182 " --> pdb=" O PRO A 178 " (cutoff:3.500A) removed outlier: 4.035A pdb=" N VAL A 185 " --> pdb=" O GLU A 181 " (cutoff:3.500A) Processing helix chain 'A' and resid 187 through 193 Processing helix chain 'A' and resid 198 through 205 removed outlier: 3.827A pdb=" N TRP A 203 " --> pdb=" O TYR A 199 " (cutoff:3.500A) removed outlier: 4.144A pdb=" N ARG A 204 " --> pdb=" O GLY A 200 " (cutoff:3.500A) Processing helix chain 'A' and resid 220 through 230 removed outlier: 3.592A pdb=" N GLU A 224 " --> pdb=" O ASN A 220 " (cutoff:3.500A) removed outlier: 4.135A pdb=" N GLU A 227 " --> pdb=" O ILE A 223 " (cutoff:3.500A) removed outlier: 4.168A pdb=" N ARG A 228 " --> pdb=" O GLU A 224 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N THR A 229 " --> pdb=" O ASP A 225 " (cutoff:3.500A) Processing helix chain 'A' and resid 234 through 239 removed outlier: 4.030A pdb=" N GLU A 238 " --> pdb=" O LYS A 234 " (cutoff:3.500A) removed outlier: 4.037A pdb=" N HIS A 239 " --> pdb=" O PRO A 235 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 234 through 239' Processing helix chain 'A' and resid 239 through 252 removed outlier: 3.756A pdb=" N TYR A 243 " --> pdb=" O HIS A 239 " (cutoff:3.500A) removed outlier: 3.857A pdb=" N VAL A 244 " --> pdb=" O LEU A 240 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N ARG A 245 " --> pdb=" O HIS A 241 " (cutoff:3.500A) removed outlier: 4.063A pdb=" N ARG A 246 " --> pdb=" O ALA A 242 " (cutoff:3.500A) removed outlier: 4.664A pdb=" N LYS A 247 " --> pdb=" O TYR A 243 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N LEU A 248 " --> pdb=" O VAL A 244 " (cutoff:3.500A) removed outlier: 4.448A pdb=" N ASP A 250 " --> pdb=" O ARG A 246 " (cutoff:3.500A) removed outlier: 4.004A pdb=" N TYR A 252 " --> pdb=" O LEU A 248 " (cutoff:3.500A) Processing helix chain 'A' and resid 292 through 298 Processing helix chain 'A' and resid 303 through 308 removed outlier: 3.503A pdb=" N PHE A 308 " --> pdb=" O ALA A 304 " (cutoff:3.500A) Processing helix chain 'A' and resid 308 through 319 removed outlier: 4.330A pdb=" N GLU A 312 " --> pdb=" O PHE A 308 " (cutoff:3.500A) removed outlier: 3.820A pdb=" N SER A 317 " --> pdb=" O LYS A 313 " (cutoff:3.500A) Processing helix chain 'A' and resid 324 through 330 removed outlier: 3.733A pdb=" N TRP A 328 " --> pdb=" O THR A 324 " (cutoff:3.500A) Processing helix chain 'A' and resid 366 through 383 removed outlier: 4.368A pdb=" N LEU A 370 " --> pdb=" O MET A 366 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N HIS A 373 " --> pdb=" O PHE A 369 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N HIS A 374 " --> pdb=" O LEU A 370 " (cutoff:3.500A) removed outlier: 4.181A pdb=" N HIS A 378 " --> pdb=" O HIS A 374 " (cutoff:3.500A) removed outlier: 4.049A pdb=" N ILE A 379 " --> pdb=" O GLU A 375 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N GLN A 380 " --> pdb=" O MET A 376 " (cutoff:3.500A) Processing helix chain 'A' and resid 388 through 393 Processing helix chain 'A' and resid 399 through 413 removed outlier: 4.070A pdb=" N GLY A 405 " --> pdb=" O HIS A 401 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N MET A 408 " --> pdb=" O VAL A 404 " (cutoff:3.500A) removed outlier: 3.931A pdb=" N SER A 409 " --> pdb=" O GLY A 405 " (cutoff:3.500A) Processing helix chain 'A' and resid 414 through 421 removed outlier: 4.076A pdb=" N ILE A 421 " --> pdb=" O HIS A 417 " (cutoff:3.500A) Processing helix chain 'A' and resid 433 through 446 removed outlier: 3.995A pdb=" N ASN A 437 " --> pdb=" O GLU A 433 " (cutoff:3.500A) removed outlier: 4.615A pdb=" N LYS A 441 " --> pdb=" O ASN A 437 " (cutoff:3.500A) removed outlier: 4.399A pdb=" N GLN A 442 " --> pdb=" O PHE A 438 " (cutoff:3.500A) removed outlier: 3.907A pdb=" N ILE A 446 " --> pdb=" O GLN A 442 " (cutoff:3.500A) Processing helix chain 'A' and resid 449 through 464 removed outlier: 3.682A pdb=" N LYS A 458 " --> pdb=" O TYR A 454 " (cutoff:3.500A) removed outlier: 3.902A pdb=" N PHE A 464 " --> pdb=" O ARG A 460 " (cutoff:3.500A) Processing helix chain 'A' and resid 472 through 485 removed outlier: 3.645A pdb=" N LYS A 476 " --> pdb=" O GLN A 472 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N GLU A 479 " --> pdb=" O LYS A 475 " (cutoff:3.500A) Processing helix chain 'A' and resid 513 through 531 removed outlier: 4.258A pdb=" N ARG A 518 " --> pdb=" O ARG A 514 " (cutoff:3.500A) removed outlier: 5.913A pdb=" N THR A 519 " --> pdb=" O TYR A 515 " (cutoff:3.500A) removed outlier: 4.786A pdb=" N ILE A 520 " --> pdb=" O TYR A 516 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N TYR A 521 " --> pdb=" O THR A 517 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N GLN A 522 " --> pdb=" O ARG A 518 " (cutoff:3.500A) removed outlier: 4.092A pdb=" N PHE A 523 " --> pdb=" O THR A 519 " (cutoff:3.500A) Processing helix chain 'A' and resid 548 through 559 removed outlier: 3.777A pdb=" N LYS A 556 " --> pdb=" O GLN A 552 " (cutoff:3.500A) removed outlier: 4.015A pdb=" N MET A 557 " --> pdb=" O LYS A 553 " (cutoff:3.500A) Processing helix chain 'A' and resid 560 through 564 removed outlier: 3.968A pdb=" N GLU A 564 " --> pdb=" O GLY A 561 " (cutoff:3.500A) Processing helix chain 'A' and resid 565 through 574 Processing helix chain 'A' and resid 581 through 589 removed outlier: 3.721A pdb=" N PHE A 588 " --> pdb=" O LEU A 584 " (cutoff:3.500A) Processing helix chain 'A' and resid 592 through 598 removed outlier: 3.934A pdb=" N GLN A 598 " --> pdb=" O TRP A 594 " (cutoff:3.500A) Processing helix chain 'B' and resid 337 through 343 removed outlier: 4.210A pdb=" N VAL B 341 " --> pdb=" O PRO B 337 " (cutoff:3.500A) Processing helix chain 'B' and resid 365 through 370 Processing helix chain 'B' and resid 383 through 388 removed outlier: 3.875A pdb=" N ASN B 388 " --> pdb=" O PRO B 384 " (cutoff:3.500A) Processing helix chain 'B' and resid 405 through 408 removed outlier: 4.241A pdb=" N ARG B 408 " --> pdb=" O ASP B 405 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 405 through 408' Processing helix chain 'B' and resid 416 through 422 Processing helix chain 'B' and resid 502 through 505 Processing sheet with id=AA1, first strand: chain 'A' and resid 347 through 349 removed outlier: 3.885A pdb=" N THR A 347 " --> pdb=" O LYS A 359 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N LYS A 359 " --> pdb=" O THR A 347 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N TRP A 349 " --> pdb=" O ARG A 357 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N ARG A 357 " --> pdb=" O TRP A 349 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'B' and resid 356 through 358 removed outlier: 3.597A pdb=" N LYS B 356 " --> pdb=" O ALA B 397 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N VAL B 395 " --> pdb=" O ILE B 358 " (cutoff:3.500A) removed outlier: 4.555A pdb=" N ASN B 394 " --> pdb=" O GLU B 516 " (cutoff:3.500A) removed outlier: 4.369A pdb=" N GLU B 516 " --> pdb=" O ASN B 394 " (cutoff:3.500A) removed outlier: 3.860A pdb=" N TYR B 396 " --> pdb=" O SER B 514 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N ILE B 402 " --> pdb=" O TYR B 508 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N ILE B 434 " --> pdb=" O VAL B 511 " (cutoff:3.500A) removed outlier: 3.947A pdb=" N CYS B 432 " --> pdb=" O LEU B 513 " (cutoff:3.500A) removed outlier: 4.269A pdb=" N VAL B 433 " --> pdb=" O LYS B 378 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N LYS B 378 " --> pdb=" O VAL B 433 " (cutoff:3.500A) 191 hydrogen bonds defined for protein. 564 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: 1.48 Time building geometry restraints manager: 2.37 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 1476 1.33 - 1.45: 1554 1.45 - 1.58: 3405 1.58 - 1.70: 1 1.70 - 1.82: 58 Bond restraints: 6494 Sorted by residual: bond pdb=" C1 NAG B1301 " pdb=" O5 NAG B1301 " ideal model delta sigma weight residual 1.406 1.476 -0.070 2.00e-02 2.50e+03 1.24e+01 bond pdb=" CA SER B 477 " pdb=" CB SER B 477 " ideal model delta sigma weight residual 1.530 1.486 0.044 1.69e-02 3.50e+03 6.75e+00 bond pdb=" C PRO B 479 " pdb=" O PRO B 479 " ideal model delta sigma weight residual 1.235 1.208 0.027 1.30e-02 5.92e+03 4.40e+00 bond pdb=" CB PRO A 389 " pdb=" CG PRO A 389 " ideal model delta sigma weight residual 1.492 1.578 -0.086 5.00e-02 4.00e+02 2.95e+00 bond pdb=" N THR B 478 " pdb=" CA THR B 478 " ideal model delta sigma weight residual 1.457 1.479 -0.022 1.41e-02 5.03e+03 2.44e+00 ... (remaining 6489 not shown) Histogram of bond angle deviations from ideal: 100.23 - 106.99: 208 106.99 - 113.76: 3422 113.76 - 120.52: 2654 120.52 - 127.28: 2452 127.28 - 134.04: 83 Bond angle restraints: 8819 Sorted by residual: angle pdb=" C PRO B 479 " pdb=" CA PRO B 479 " pdb=" CB PRO B 479 " ideal model delta sigma weight residual 111.56 100.23 11.33 1.65e+00 3.67e-01 4.71e+01 angle pdb=" N PRO B 479 " pdb=" CA PRO B 479 " pdb=" C PRO B 479 " ideal model delta sigma weight residual 112.47 121.36 -8.89 2.06e+00 2.36e-01 1.86e+01 angle pdb=" N GLN A 287 " pdb=" CA GLN A 287 " pdb=" C GLN A 287 " ideal model delta sigma weight residual 114.31 109.56 4.75 1.29e+00 6.01e-01 1.35e+01 angle pdb=" N PRO A 389 " pdb=" CA PRO A 389 " pdb=" C PRO A 389 " ideal model delta sigma weight residual 112.47 119.46 -6.99 2.06e+00 2.36e-01 1.15e+01 angle pdb=" C ILE A 468 " pdb=" CA ILE A 468 " pdb=" CB ILE A 468 " ideal model delta sigma weight residual 109.33 112.46 -3.13 9.80e-01 1.04e+00 1.02e+01 ... (remaining 8814 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 24.45: 3664 24.45 - 48.90: 187 48.90 - 73.36: 28 73.36 - 97.81: 3 97.81 - 122.26: 3 Dihedral angle restraints: 3885 sinusoidal: 1600 harmonic: 2285 Sorted by residual: dihedral pdb=" CB CYS A 530 " pdb=" SG CYS A 530 " pdb=" SG CYS A 542 " pdb=" CB CYS A 542 " ideal model delta sinusoidal sigma weight residual 93.00 156.68 -63.68 1 1.00e+01 1.00e-02 5.34e+01 dihedral pdb=" CB CYS B 480 " pdb=" SG CYS B 480 " pdb=" SG CYS B 488 " pdb=" CB CYS B 488 " ideal model delta sinusoidal sigma weight residual -86.00 -139.48 53.48 1 1.00e+01 1.00e-02 3.89e+01 dihedral pdb=" CB CYS B 336 " pdb=" SG CYS B 336 " pdb=" SG CYS B 361 " pdb=" CB CYS B 361 " ideal model delta sinusoidal sigma weight residual 93.00 39.79 53.21 1 1.00e+01 1.00e-02 3.85e+01 ... (remaining 3882 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.050: 730 0.050 - 0.101: 170 0.101 - 0.151: 26 0.151 - 0.201: 2 0.201 - 0.252: 1 Chirality restraints: 929 Sorted by residual: chirality pdb=" CA PRO A 389 " pdb=" N PRO A 389 " pdb=" C PRO A 389 " pdb=" CB PRO A 389 " both_signs ideal model delta sigma weight residual False 2.72 2.47 0.25 2.00e-01 2.50e+01 1.58e+00 chirality pdb=" C2 NAG C 2 " pdb=" C1 NAG C 2 " pdb=" C3 NAG C 2 " pdb=" N2 NAG C 2 " both_signs ideal model delta sigma weight residual False -2.49 -2.33 -0.16 2.00e-01 2.50e+01 6.43e-01 chirality pdb=" CA CYS B 480 " pdb=" N CYS B 480 " pdb=" C CYS B 480 " pdb=" CB CYS B 480 " both_signs ideal model delta sigma weight residual False 2.51 2.67 -0.15 2.00e-01 2.50e+01 6.01e-01 ... (remaining 926 not shown) Planarity restraints: 1144 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLN A 388 " 0.081 5.00e-02 4.00e+02 1.22e-01 2.40e+01 pdb=" N PRO A 389 " -0.212 5.00e-02 4.00e+02 pdb=" CA PRO A 389 " 0.068 5.00e-02 4.00e+02 pdb=" CD PRO A 389 " 0.063 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA ALA B 475 " -0.012 2.00e-02 2.50e+03 2.53e-02 6.39e+00 pdb=" C ALA B 475 " 0.044 2.00e-02 2.50e+03 pdb=" O ALA B 475 " -0.017 2.00e-02 2.50e+03 pdb=" N GLY B 476 " -0.015 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ILE A 468 " 0.036 5.00e-02 4.00e+02 5.49e-02 4.82e+00 pdb=" N PRO A 469 " -0.095 5.00e-02 4.00e+02 pdb=" CA PRO A 469 " 0.028 5.00e-02 4.00e+02 pdb=" CD PRO A 469 " 0.030 5.00e-02 4.00e+02 ... (remaining 1141 not shown) Histogram of nonbonded interaction distances: 2.16 - 2.71: 207 2.71 - 3.26: 6506 3.26 - 3.81: 9278 3.81 - 4.35: 11190 4.35 - 4.90: 17785 Nonbonded interactions: 44966 Sorted by model distance: nonbonded pdb=" O LEU A 370 " pdb=" ND1 HIS A 374 " model vdw 2.165 2.520 nonbonded pdb=" OH TYR A 41 " pdb=" OG1 THR B 500 " model vdw 2.225 2.440 nonbonded pdb=" OE2 GLU A 227 " pdb=" OH TYR A 454 " model vdw 2.226 2.440 nonbonded pdb=" O LEU A 278 " pdb=" OG1 THR A 282 " model vdw 2.239 2.440 nonbonded pdb=" NZ LYS A 247 " pdb=" O LEU A 281 " model vdw 2.240 2.520 ... (remaining 44961 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: 1.100 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: 4.860 Check model and map are aligned: 0.100 Set scattering table: 0.060 Process input model: 20.900 Find NCS groups from input model: 0.160 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:2.920 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 30.130 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5934 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.086 6494 Z= 0.215 Angle : 0.695 11.326 8819 Z= 0.394 Chirality : 0.044 0.252 929 Planarity : 0.006 0.122 1142 Dihedral : 14.457 122.259 2401 Min Nonbonded Distance : 2.165 Molprobity Statistics. All-atom Clashscore : 9.80 Ramachandran Plot: Outliers : 0.78 % Allowed : 5.43 % Favored : 93.79 % Rotamer: Outliers : 0.45 % Allowed : 0.15 % Favored : 99.41 % Cbeta Deviations : 0.14 % 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: -1.80 (0.29), residues: 773 helix: -0.56 (0.30), residues: 297 sheet: 2.44 (1.08), residues: 22 loop : -1.91 (0.28), residues: 454 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP A 48 HIS 0.006 0.001 HIS A 374 PHE 0.016 0.001 PHE A 390 TYR 0.009 0.001 TYR A 215 ARG 0.005 0.000 ARG A 161 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1546 Ramachandran restraints generated. 773 Oldfield, 0 Emsley, 773 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1546 Ramachandran restraints generated. 773 Oldfield, 0 Emsley, 773 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 173 residues out of total 677 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 170 time to evaluate : 0.753 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 3 outliers final: 3 residues processed: 173 average time/residue: 0.2062 time to fit residues: 45.6937 Evaluate side-chains 94 residues out of total 677 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 91 time to evaluate : 1.051 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 1 residues processed: 3 average time/residue: 0.0564 time to fit residues: 1.2834 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 77 random chunks: chunk 65 optimal weight: 6.9990 chunk 58 optimal weight: 0.9990 chunk 32 optimal weight: 6.9990 chunk 19 optimal weight: 6.9990 chunk 39 optimal weight: 4.9990 chunk 31 optimal weight: 5.9990 chunk 60 optimal weight: 3.9990 chunk 23 optimal weight: 20.0000 chunk 36 optimal weight: 2.9990 chunk 44 optimal weight: 8.9990 chunk 69 optimal weight: 0.0770 overall best weight: 2.6146 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 30 ASN A 76 GLN ** A 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 188 ASN A 239 HIS ** A 368 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 442 GLN A 508 ASN A 572 ASN B 422 ASN ** B 448 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6351 moved from start: 0.3997 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.077 6494 Z= 0.333 Angle : 0.784 10.382 8819 Z= 0.409 Chirality : 0.048 0.255 929 Planarity : 0.006 0.126 1142 Dihedral : 9.539 113.840 913 Min Nonbonded Distance : 2.056 Molprobity Statistics. All-atom Clashscore : 18.80 Ramachandran Plot: Outliers : 0.26 % Allowed : 7.89 % Favored : 91.85 % Rotamer: Outliers : 0.74 % Allowed : 6.82 % Favored : 92.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.14 % 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: -2.20 (0.29), residues: 773 helix: -0.92 (0.29), residues: 302 sheet: 1.46 (1.07), residues: 25 loop : -2.09 (0.28), residues: 446 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP A 473 HIS 0.009 0.002 HIS A 374 PHE 0.035 0.003 PHE A 314 TYR 0.015 0.002 TYR B 501 ARG 0.015 0.001 ARG A 306 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1546 Ramachandran restraints generated. 773 Oldfield, 0 Emsley, 773 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1546 Ramachandran restraints generated. 773 Oldfield, 0 Emsley, 773 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 117 residues out of total 677 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 112 time to evaluate : 0.742 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 5 outliers final: 4 residues processed: 117 average time/residue: 0.1909 time to fit residues: 29.4552 Evaluate side-chains 81 residues out of total 677 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 77 time to evaluate : 0.707 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 1 residues processed: 4 average time/residue: 0.0634 time to fit residues: 1.4234 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 77 random chunks: chunk 38 optimal weight: 0.8980 chunk 21 optimal weight: 0.0370 chunk 58 optimal weight: 1.9990 chunk 47 optimal weight: 7.9990 chunk 19 optimal weight: 6.9990 chunk 70 optimal weight: 3.9990 chunk 75 optimal weight: 4.9990 chunk 62 optimal weight: 0.9990 chunk 69 optimal weight: 1.9990 chunk 23 optimal weight: 0.1980 chunk 56 optimal weight: 0.7980 overall best weight: 0.5860 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 30 ASN ** A 368 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 380 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 505 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 508 ASN A 526 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6229 moved from start: 0.4218 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.089 6494 Z= 0.191 Angle : 0.623 9.411 8819 Z= 0.310 Chirality : 0.046 0.342 929 Planarity : 0.005 0.121 1142 Dihedral : 8.870 110.751 913 Min Nonbonded Distance : 2.169 Molprobity Statistics. All-atom Clashscore : 11.75 Ramachandran Plot: Outliers : 0.39 % Allowed : 4.66 % Favored : 94.95 % Rotamer: Outliers : 0.30 % Allowed : 4.01 % Favored : 95.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.14 % 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: -1.70 (0.29), residues: 773 helix: -0.31 (0.31), residues: 299 sheet: 1.30 (1.03), residues: 25 loop : -1.93 (0.28), residues: 449 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 459 HIS 0.003 0.001 HIS A 374 PHE 0.014 0.002 PHE B 374 TYR 0.016 0.001 TYR A 215 ARG 0.003 0.000 ARG A 219 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1546 Ramachandran restraints generated. 773 Oldfield, 0 Emsley, 773 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1546 Ramachandran restraints generated. 773 Oldfield, 0 Emsley, 773 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 111 residues out of total 677 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 109 time to evaluate : 0.733 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 2 outliers final: 2 residues processed: 111 average time/residue: 0.1917 time to fit residues: 28.0895 Evaluate side-chains 84 residues out of total 677 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 82 time to evaluate : 0.732 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 1 residues processed: 2 average time/residue: 0.0727 time to fit residues: 1.2330 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 77 random chunks: chunk 69 optimal weight: 6.9990 chunk 52 optimal weight: 8.9990 chunk 36 optimal weight: 0.9990 chunk 7 optimal weight: 0.5980 chunk 33 optimal weight: 5.9990 chunk 47 optimal weight: 10.0000 chunk 70 optimal weight: 3.9990 chunk 74 optimal weight: 0.9980 chunk 66 optimal weight: 0.9980 chunk 20 optimal weight: 10.0000 chunk 61 optimal weight: 5.9990 overall best weight: 1.5184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 368 ASN ** A 380 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 505 HIS A 508 ASN A 526 GLN ** B 448 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6324 moved from start: 0.4806 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.083 6494 Z= 0.220 Angle : 0.657 9.211 8819 Z= 0.325 Chirality : 0.047 0.339 929 Planarity : 0.005 0.121 1142 Dihedral : 8.876 110.268 913 Min Nonbonded Distance : 2.097 Molprobity Statistics. All-atom Clashscore : 14.59 Ramachandran Plot: Outliers : 0.39 % Allowed : 7.12 % Favored : 92.50 % Rotamer: Outliers : 0.30 % Allowed : 2.82 % Favored : 96.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.14 % 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: -1.60 (0.30), residues: 773 helix: -0.29 (0.31), residues: 305 sheet: 0.95 (0.94), residues: 29 loop : -1.84 (0.29), residues: 439 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 461 HIS 0.005 0.001 HIS A 374 PHE 0.021 0.002 PHE A 452 TYR 0.013 0.001 TYR B 421 ARG 0.004 0.001 ARG A 514 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1546 Ramachandran restraints generated. 773 Oldfield, 0 Emsley, 773 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1546 Ramachandran restraints generated. 773 Oldfield, 0 Emsley, 773 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 103 residues out of total 677 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 101 time to evaluate : 0.754 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 2 outliers final: 2 residues processed: 103 average time/residue: 0.1960 time to fit residues: 26.7015 Evaluate side-chains 75 residues out of total 677 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 73 time to evaluate : 0.741 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 1 residues processed: 2 average time/residue: 0.0757 time to fit residues: 1.2496 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 77 random chunks: chunk 42 optimal weight: 2.9990 chunk 1 optimal weight: 0.7980 chunk 55 optimal weight: 5.9990 chunk 30 optimal weight: 1.9990 chunk 63 optimal weight: 1.9990 chunk 51 optimal weight: 0.7980 chunk 0 optimal weight: 4.9990 chunk 38 optimal weight: 0.9990 chunk 66 optimal weight: 9.9990 chunk 18 optimal weight: 5.9990 chunk 25 optimal weight: 0.4980 overall best weight: 1.0184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 368 ASN ** A 380 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 508 ASN A 526 GLN ** B 448 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6316 moved from start: 0.4952 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.085 6494 Z= 0.192 Angle : 0.629 9.200 8819 Z= 0.310 Chirality : 0.046 0.308 929 Planarity : 0.005 0.120 1142 Dihedral : 8.695 109.297 913 Min Nonbonded Distance : 2.130 Molprobity Statistics. All-atom Clashscore : 13.13 Ramachandran Plot: Outliers : 0.26 % Allowed : 6.08 % Favored : 93.66 % Rotamer: Outliers : 0.15 % Allowed : 2.82 % Favored : 97.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.14 % 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: -1.55 (0.30), residues: 773 helix: -0.15 (0.31), residues: 308 sheet: 0.85 (0.92), residues: 29 loop : -1.88 (0.29), residues: 436 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 459 HIS 0.004 0.001 HIS A 374 PHE 0.020 0.001 PHE A 452 TYR 0.015 0.001 TYR B 421 ARG 0.002 0.000 ARG A 514 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1546 Ramachandran restraints generated. 773 Oldfield, 0 Emsley, 773 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1546 Ramachandran restraints generated. 773 Oldfield, 0 Emsley, 773 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 103 residues out of total 677 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 102 time to evaluate : 1.066 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: 1 outliers final: 1 residues processed: 103 average time/residue: 0.2159 time to fit residues: 30.1018 Evaluate side-chains 75 residues out of total 677 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 74 time to evaluate : 0.755 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 1 residues processed: 1 average time/residue: 0.0578 time to fit residues: 1.1617 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 77 random chunks: chunk 67 optimal weight: 0.2980 chunk 14 optimal weight: 3.9990 chunk 43 optimal weight: 4.9990 chunk 18 optimal weight: 0.9980 chunk 74 optimal weight: 0.7980 chunk 61 optimal weight: 0.9990 chunk 34 optimal weight: 2.9990 chunk 6 optimal weight: 8.9990 chunk 24 optimal weight: 7.9990 chunk 39 optimal weight: 4.9990 chunk 71 optimal weight: 2.9990 overall best weight: 1.2184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 368 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 380 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 505 HIS A 508 ASN ** B 448 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6358 moved from start: 0.5441 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.084 6494 Z= 0.202 Angle : 0.652 9.143 8819 Z= 0.324 Chirality : 0.047 0.329 929 Planarity : 0.005 0.119 1142 Dihedral : 8.687 108.759 913 Min Nonbonded Distance : 2.121 Molprobity Statistics. All-atom Clashscore : 14.18 Ramachandran Plot: Outliers : 0.26 % Allowed : 7.24 % Favored : 92.50 % Rotamer: Outliers : 0.15 % Allowed : 2.37 % Favored : 97.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.14 % 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: -1.55 (0.30), residues: 773 helix: -0.24 (0.30), residues: 308 sheet: 0.92 (0.94), residues: 29 loop : -1.81 (0.30), residues: 436 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A 459 HIS 0.003 0.001 HIS A 374 PHE 0.016 0.001 PHE B 374 TYR 0.012 0.001 TYR B 421 ARG 0.004 0.000 ARG A 514 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1546 Ramachandran restraints generated. 773 Oldfield, 0 Emsley, 773 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1546 Ramachandran restraints generated. 773 Oldfield, 0 Emsley, 773 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 98 residues out of total 677 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 97 time to evaluate : 0.762 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: 1 outliers final: 1 residues processed: 98 average time/residue: 0.1921 time to fit residues: 25.1546 Evaluate side-chains 74 residues out of total 677 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 73 time to evaluate : 0.748 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 1 residues processed: 1 average time/residue: 0.0611 time to fit residues: 1.1243 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 77 random chunks: chunk 8 optimal weight: 9.9990 chunk 42 optimal weight: 0.9980 chunk 54 optimal weight: 7.9990 chunk 62 optimal weight: 4.9990 chunk 41 optimal weight: 10.0000 chunk 74 optimal weight: 0.8980 chunk 46 optimal weight: 0.9990 chunk 45 optimal weight: 0.3980 chunk 34 optimal weight: 3.9990 chunk 29 optimal weight: 0.6980 chunk 44 optimal weight: 8.9990 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 368 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 508 ASN ** B 448 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6340 moved from start: 0.5610 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.084 6494 Z= 0.186 Angle : 0.638 9.259 8819 Z= 0.316 Chirality : 0.046 0.275 929 Planarity : 0.005 0.117 1142 Dihedral : 8.487 107.434 913 Min Nonbonded Distance : 2.139 Molprobity Statistics. All-atom Clashscore : 12.64 Ramachandran Plot: Outliers : 0.26 % Allowed : 6.73 % Favored : 93.01 % Rotamer: Outliers : 0.15 % Allowed : 1.04 % Favored : 98.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.14 % 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: -1.62 (0.30), residues: 773 helix: -0.32 (0.30), residues: 311 sheet: 1.04 (0.97), residues: 29 loop : -1.85 (0.29), residues: 433 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 473 HIS 0.002 0.001 HIS A 374 PHE 0.016 0.001 PHE A 452 TYR 0.011 0.001 TYR B 421 ARG 0.004 0.000 ARG A 514 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1546 Ramachandran restraints generated. 773 Oldfield, 0 Emsley, 773 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1546 Ramachandran restraints generated. 773 Oldfield, 0 Emsley, 773 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 99 residues out of total 677 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 98 time to evaluate : 0.760 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 outliers start: 1 outliers final: 1 residues processed: 99 average time/residue: 0.2560 time to fit residues: 34.6010 Evaluate side-chains 76 residues out of total 677 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 75 time to evaluate : 0.826 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 1 residues processed: 1 average time/residue: 0.0535 time to fit residues: 1.0275 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 77 random chunks: chunk 22 optimal weight: 0.0000 chunk 14 optimal weight: 0.9990 chunk 47 optimal weight: 0.8980 chunk 50 optimal weight: 0.3980 chunk 36 optimal weight: 3.9990 chunk 6 optimal weight: 0.9990 chunk 58 optimal weight: 0.7980 chunk 67 optimal weight: 0.9990 chunk 71 optimal weight: 8.9990 chunk 64 optimal weight: 1.9990 chunk 69 optimal weight: 7.9990 overall best weight: 0.6186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 368 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 505 HIS A 508 ASN ** B 448 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6337 moved from start: 0.5841 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.083 6494 Z= 0.192 Angle : 0.660 9.138 8819 Z= 0.325 Chirality : 0.047 0.281 929 Planarity : 0.005 0.116 1142 Dihedral : 8.382 106.513 913 Min Nonbonded Distance : 2.148 Molprobity Statistics. All-atom Clashscore : 12.48 Ramachandran Plot: Outliers : 0.26 % Allowed : 6.34 % Favored : 93.40 % Rotamer: Outliers : 0.15 % Allowed : 0.59 % Favored : 99.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.14 % 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: -1.64 (0.30), residues: 773 helix: -0.39 (0.30), residues: 317 sheet: 1.13 (1.00), residues: 29 loop : -1.85 (0.29), residues: 427 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.095 0.002 TRP A 461 HIS 0.004 0.001 HIS A 505 PHE 0.013 0.001 PHE B 374 TYR 0.010 0.001 TYR B 508 ARG 0.003 0.000 ARG A 192 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1546 Ramachandran restraints generated. 773 Oldfield, 0 Emsley, 773 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1546 Ramachandran restraints generated. 773 Oldfield, 0 Emsley, 773 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 94 residues out of total 677 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 93 time to evaluate : 0.733 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: 1 outliers final: 1 residues processed: 94 average time/residue: 0.1860 time to fit residues: 23.4327 Evaluate side-chains 69 residues out of total 677 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 68 time to evaluate : 0.800 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 1 residues processed: 1 average time/residue: 0.0593 time to fit residues: 1.1583 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 77 random chunks: chunk 71 optimal weight: 0.0570 chunk 41 optimal weight: 9.9990 chunk 30 optimal weight: 0.7980 chunk 54 optimal weight: 1.9990 chunk 21 optimal weight: 1.9990 chunk 62 optimal weight: 0.6980 chunk 65 optimal weight: 4.9990 chunk 68 optimal weight: 1.9990 chunk 45 optimal weight: 0.0980 chunk 73 optimal weight: 0.0070 chunk 44 optimal weight: 0.3980 overall best weight: 0.2516 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 368 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 508 ASN ** B 448 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6291 moved from start: 0.5881 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.085 6494 Z= 0.187 Angle : 0.638 9.410 8819 Z= 0.311 Chirality : 0.046 0.267 929 Planarity : 0.005 0.114 1142 Dihedral : 8.072 104.085 913 Min Nonbonded Distance : 2.177 Molprobity Statistics. All-atom Clashscore : 10.94 Ramachandran Plot: Outliers : 0.13 % Allowed : 5.56 % Favored : 94.31 % Rotamer: Outliers : 0.15 % Allowed : 0.74 % Favored : 99.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.14 % 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: -1.54 (0.30), residues: 773 helix: -0.19 (0.31), residues: 297 sheet: 0.90 (1.10), residues: 23 loop : -1.77 (0.28), residues: 453 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.072 0.001 TRP A 461 HIS 0.001 0.000 HIS A 353 PHE 0.015 0.001 PHE A 452 TYR 0.008 0.001 TYR B 508 ARG 0.002 0.000 ARG A 192 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1546 Ramachandran restraints generated. 773 Oldfield, 0 Emsley, 773 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1546 Ramachandran restraints generated. 773 Oldfield, 0 Emsley, 773 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 98 residues out of total 677 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 97 time to evaluate : 0.748 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 1 outliers final: 1 residues processed: 98 average time/residue: 0.1869 time to fit residues: 24.4314 Evaluate side-chains 70 residues out of total 677 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 69 time to evaluate : 0.741 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 1 residues processed: 1 average time/residue: 0.0567 time to fit residues: 1.0892 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 77 random chunks: chunk 34 optimal weight: 0.4980 chunk 50 optimal weight: 4.9990 chunk 76 optimal weight: 0.0970 chunk 70 optimal weight: 8.9990 chunk 61 optimal weight: 3.9990 chunk 6 optimal weight: 1.9990 chunk 47 optimal weight: 0.0030 chunk 37 optimal weight: 0.0670 chunk 48 optimal weight: 1.9990 chunk 65 optimal weight: 0.4980 chunk 18 optimal weight: 7.9990 overall best weight: 0.2326 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 368 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 505 HIS A 508 ASN ** B 448 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6279 moved from start: 0.6021 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.084 6494 Z= 0.181 Angle : 0.646 9.414 8819 Z= 0.312 Chirality : 0.046 0.271 929 Planarity : 0.005 0.113 1142 Dihedral : 7.888 102.120 913 Min Nonbonded Distance : 2.187 Molprobity Statistics. All-atom Clashscore : 11.59 Ramachandran Plot: Outliers : 0.13 % Allowed : 5.30 % Favored : 94.57 % Rotamer: Outliers : 0.30 % Allowed : 0.00 % Favored : 99.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.14 % 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: -1.50 (0.30), residues: 773 helix: -0.17 (0.31), residues: 297 sheet: 0.95 (1.09), residues: 23 loop : -1.73 (0.28), residues: 453 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.065 0.001 TRP A 461 HIS 0.002 0.001 HIS A 505 PHE 0.011 0.001 PHE A 452 TYR 0.007 0.001 TYR B 508 ARG 0.002 0.000 ARG A 192 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1546 Ramachandran restraints generated. 773 Oldfield, 0 Emsley, 773 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1546 Ramachandran restraints generated. 773 Oldfield, 0 Emsley, 773 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 97 residues out of total 677 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 95 time to evaluate : 0.750 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 2 outliers final: 1 residues processed: 97 average time/residue: 0.1901 time to fit residues: 24.6889 Evaluate side-chains 74 residues out of total 677 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 73 time to evaluate : 0.730 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 1 residues processed: 1 average time/residue: 0.0569 time to fit residues: 1.0894 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 77 random chunks: chunk 56 optimal weight: 0.6980 chunk 9 optimal weight: 0.5980 chunk 16 optimal weight: 6.9990 chunk 61 optimal weight: 3.9990 chunk 25 optimal weight: 0.0970 chunk 62 optimal weight: 7.9990 chunk 7 optimal weight: 10.0000 chunk 11 optimal weight: 8.9990 chunk 53 optimal weight: 1.9990 chunk 3 optimal weight: 0.8980 chunk 44 optimal weight: 0.6980 overall best weight: 0.5978 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 368 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 508 ASN ** B 448 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4374 r_free = 0.4374 target = 0.141789 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.4215 r_free = 0.4215 target = 0.129307 restraints weight = 33177.107| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.4238 r_free = 0.4238 target = 0.131003 restraints weight = 23011.737| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.4256 r_free = 0.4256 target = 0.132265 restraints weight = 17114.298| |-----------------------------------------------------------------------------| r_work (final): 0.4139 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6327 moved from start: 0.6139 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.082 6494 Z= 0.185 Angle : 0.654 9.455 8819 Z= 0.321 Chirality : 0.047 0.263 929 Planarity : 0.005 0.112 1142 Dihedral : 7.866 101.687 913 Min Nonbonded Distance : 2.171 Molprobity Statistics. All-atom Clashscore : 11.91 Ramachandran Plot: Outliers : 0.13 % Allowed : 5.95 % Favored : 93.92 % Rotamer: Outliers : 0.15 % Allowed : 0.30 % Favored : 99.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.14 % 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: -1.50 (0.30), residues: 773 helix: -0.21 (0.31), residues: 301 sheet: 1.45 (1.18), residues: 19 loop : -1.72 (0.28), residues: 453 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.061 0.001 TRP A 461 HIS 0.003 0.001 HIS A 374 PHE 0.011 0.001 PHE A 452 TYR 0.009 0.001 TYR A 497 ARG 0.008 0.000 ARG A 169 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1697.89 seconds wall clock time: 32 minutes 37.73 seconds (1957.73 seconds total)