Starting phenix.real_space_refine on Fri Dec 8 22:07:27 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7n5a_24184/12_2023/7n5a_24184_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7n5a_24184/12_2023/7n5a_24184.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.95 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7n5a_24184/12_2023/7n5a_24184.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7n5a_24184/12_2023/7n5a_24184.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7n5a_24184/12_2023/7n5a_24184_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7n5a_24184/12_2023/7n5a_24184_updated.pdb" } resolution = 3.95 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= 0.005 sd= 0.072 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: 7 Type Number sf(0) Gaussians V 2 8.30 5 P 4 5.49 5 Mg 2 5.21 5 S 34 5.16 5 C 5886 2.51 5 N 1586 2.21 5 O 1740 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A TYR 205": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 337": "OD1" <-> "OD2" Residue "A TYR 349": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 682": "OE1" <-> "OE2" Residue "B TYR 205": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 337": "OD1" <-> "OD2" Residue "B TYR 349": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 682": "OE1" <-> "OE2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/chem_data/mon_lib" Total number of atoms: 9254 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 4594 Number of conformers: 1 Conformer: "" Number of residues, atoms: 589, 4594 Classifications: {'peptide': 589} Link IDs: {'PTRANS': 13, 'TRANS': 575} Chain breaks: 1 Chain: "B" Number of atoms: 4594 Number of conformers: 1 Conformer: "" Number of residues, atoms: 589, 4594 Classifications: {'peptide': 589} Link IDs: {'PTRANS': 13, 'TRANS': 575} Chain breaks: 1 Chain: "A" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 33 Unusual residues: {' MG': 1, 'ADP': 1, 'VO4': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "B" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 33 Unusual residues: {' MG': 1, 'ADP': 1, 'VO4': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Time building chain proxies: 5.55, per 1000 atoms: 0.60 Number of scatterers: 9254 At special positions: 0 Unit cell: (76.26, 92.66, 139.4, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) V 2 22.97 S 34 16.00 P 4 15.00 Mg 2 11.99 O 1740 8.00 N 1586 7.00 C 5886 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 3.66 Conformation dependent library (CDL) restraints added in 1.9 seconds 2340 Ramachandran restraints generated. 1170 Oldfield, 0 Emsley, 1170 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2204 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 40 helices and 6 sheets defined 61.5% alpha, 4.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.05 Creating SS restraints... Processing helix chain 'A' and resid 118 through 131 Processing helix chain 'A' and resid 137 through 174 Proline residue: A 161 - end of helix removed outlier: 4.053A pdb=" N LEU A 166 " --> pdb=" O PHE A 162 " (cutoff:3.500A) removed outlier: 3.985A pdb=" N ALA A 167 " --> pdb=" O LEU A 163 " (cutoff:3.500A) Processing helix chain 'A' and resid 198 through 244 removed outlier: 3.785A pdb=" N ARG A 209 " --> pdb=" O TYR A 205 " (cutoff:3.500A) removed outlier: 3.829A pdb=" N THR A 220 " --> pdb=" O ASN A 216 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N ALA A 221 " --> pdb=" O GLU A 217 " (cutoff:3.500A) removed outlier: 4.090A pdb=" N LYS A 225 " --> pdb=" O ALA A 221 " (cutoff:3.500A) removed outlier: 4.132A pdb=" N VAL A 226 " --> pdb=" O VAL A 222 " (cutoff:3.500A) removed outlier: 3.912A pdb=" N HIS A 243 " --> pdb=" O PHE A 239 " (cutoff:3.500A) removed outlier: 4.109A pdb=" N ASP A 244 " --> pdb=" O SER A 240 " (cutoff:3.500A) Processing helix chain 'A' and resid 247 through 250 No H-bonds generated for 'chain 'A' and resid 247 through 250' Processing helix chain 'A' and resid 258 through 278 removed outlier: 3.726A pdb=" N ASN A 270 " --> pdb=" O SER A 266 " (cutoff:3.500A) Processing helix chain 'A' and resid 280 through 296 removed outlier: 3.772A pdb=" N ILE A 284 " --> pdb=" O VAL A 280 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N LEU A 285 " --> pdb=" O VAL A 281 " (cutoff:3.500A) removed outlier: 4.761A pdb=" N LEU A 294 " --> pdb=" O VAL A 290 " (cutoff:3.500A) removed outlier: 5.838A pdb=" N ALA A 295 " --> pdb=" O SER A 291 " (cutoff:3.500A) removed outlier: 5.502A pdb=" N TYR A 296 " --> pdb=" O GLY A 292 " (cutoff:3.500A) Processing helix chain 'A' and resid 302 through 347 removed outlier: 4.792A pdb=" N ALA A 330 " --> pdb=" O LYS A 326 " (cutoff:3.500A) removed outlier: 4.352A pdb=" N MET A 331 " --> pdb=" O PHE A 327 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N ASP A 337 " --> pdb=" O LYS A 333 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N ALA A 338 " --> pdb=" O ALA A 334 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N SER A 339 " --> pdb=" O ASP A 335 " (cutoff:3.500A) Processing helix chain 'A' and resid 349 through 355 Processing helix chain 'A' and resid 358 through 407 removed outlier: 3.721A pdb=" N SER A 382 " --> pdb=" O GLN A 378 " (cutoff:3.500A) removed outlier: 3.868A pdb=" N LEU A 386 " --> pdb=" O SER A 382 " (cutoff:3.500A) removed outlier: 4.203A pdb=" N ASN A 387 " --> pdb=" O LEU A 383 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N PHE A 388 " --> pdb=" O ALA A 384 " (cutoff:3.500A) Processing helix chain 'A' and resid 411 through 413 No H-bonds generated for 'chain 'A' and resid 411 through 413' Processing helix chain 'A' and resid 418 through 438 removed outlier: 3.623A pdb=" N LEU A 426 " --> pdb=" O VAL A 422 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N PHE A 427 " --> pdb=" O ASN A 423 " (cutoff:3.500A) Proline residue: A 432 - end of helix removed outlier: 3.926A pdb=" N PHE A 435 " --> pdb=" O LEU A 431 " (cutoff:3.500A) Processing helix chain 'A' and resid 440 through 458 removed outlier: 3.659A pdb=" N GLN A 445 " --> pdb=" O ARG A 441 " (cutoff:3.500A) removed outlier: 4.101A pdb=" N VAL A 448 " --> pdb=" O ILE A 444 " (cutoff:3.500A) removed outlier: 3.832A pdb=" N LEU A 457 " --> pdb=" O MET A 453 " (cutoff:3.500A) removed outlier: 4.121A pdb=" N GLU A 458 " --> pdb=" O PHE A 454 " (cutoff:3.500A) Processing helix chain 'A' and resid 548 through 554 removed outlier: 3.623A pdb=" N SER A 554 " --> pdb=" O SER A 550 " (cutoff:3.500A) Processing helix chain 'A' and resid 569 through 576 removed outlier: 5.312A pdb=" N GLY A 576 " --> pdb=" O ASN A 572 " (cutoff:3.500A) Processing helix chain 'A' and resid 582 through 591 Processing helix chain 'A' and resid 595 through 600 removed outlier: 4.145A pdb=" N ASN A 600 " --> pdb=" O GLU A 596 " (cutoff:3.500A) Processing helix chain 'A' and resid 618 through 632 removed outlier: 3.521A pdb=" N ALA A 625 " --> pdb=" O LYS A 621 " (cutoff:3.500A) Processing helix chain 'A' and resid 648 through 660 Processing helix chain 'A' and resid 697 through 702 removed outlier: 3.908A pdb=" N GLY A 702 " --> pdb=" O ASP A 698 " (cutoff:3.500A) Processing helix chain 'A' and resid 706 through 715 removed outlier: 3.507A pdb=" N GLN A 713 " --> pdb=" O GLN A 709 " (cutoff:3.500A) Processing helix chain 'B' and resid 118 through 131 Processing helix chain 'B' and resid 137 through 174 Proline residue: B 161 - end of helix removed outlier: 4.053A pdb=" N LEU B 166 " --> pdb=" O PHE B 162 " (cutoff:3.500A) removed outlier: 3.985A pdb=" N ALA B 167 " --> pdb=" O LEU B 163 " (cutoff:3.500A) Processing helix chain 'B' and resid 198 through 244 removed outlier: 3.786A pdb=" N ARG B 209 " --> pdb=" O TYR B 205 " (cutoff:3.500A) removed outlier: 3.829A pdb=" N THR B 220 " --> pdb=" O ASN B 216 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N ALA B 221 " --> pdb=" O GLU B 217 " (cutoff:3.500A) removed outlier: 4.091A pdb=" N LYS B 225 " --> pdb=" O ALA B 221 " (cutoff:3.500A) removed outlier: 4.133A pdb=" N VAL B 226 " --> pdb=" O VAL B 222 " (cutoff:3.500A) removed outlier: 3.912A pdb=" N HIS B 243 " --> pdb=" O PHE B 239 " (cutoff:3.500A) removed outlier: 4.108A pdb=" N ASP B 244 " --> pdb=" O SER B 240 " (cutoff:3.500A) Processing helix chain 'B' and resid 247 through 250 No H-bonds generated for 'chain 'B' and resid 247 through 250' Processing helix chain 'B' and resid 258 through 278 removed outlier: 3.725A pdb=" N ASN B 270 " --> pdb=" O SER B 266 " (cutoff:3.500A) Processing helix chain 'B' and resid 280 through 296 removed outlier: 3.772A pdb=" N ILE B 284 " --> pdb=" O VAL B 280 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N LEU B 285 " --> pdb=" O VAL B 281 " (cutoff:3.500A) removed outlier: 4.761A pdb=" N LEU B 294 " --> pdb=" O VAL B 290 " (cutoff:3.500A) removed outlier: 5.838A pdb=" N ALA B 295 " --> pdb=" O SER B 291 " (cutoff:3.500A) removed outlier: 5.502A pdb=" N TYR B 296 " --> pdb=" O GLY B 292 " (cutoff:3.500A) Processing helix chain 'B' and resid 302 through 347 removed outlier: 4.792A pdb=" N ALA B 330 " --> pdb=" O LYS B 326 " (cutoff:3.500A) removed outlier: 4.353A pdb=" N MET B 331 " --> pdb=" O PHE B 327 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N ASP B 337 " --> pdb=" O LYS B 333 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N ALA B 338 " --> pdb=" O ALA B 334 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N SER B 339 " --> pdb=" O ASP B 335 " (cutoff:3.500A) Processing helix chain 'B' and resid 349 through 355 Processing helix chain 'B' and resid 358 through 407 removed outlier: 3.722A pdb=" N SER B 382 " --> pdb=" O GLN B 378 " (cutoff:3.500A) removed outlier: 3.869A pdb=" N LEU B 386 " --> pdb=" O SER B 382 " (cutoff:3.500A) removed outlier: 4.203A pdb=" N ASN B 387 " --> pdb=" O LEU B 383 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N PHE B 388 " --> pdb=" O ALA B 384 " (cutoff:3.500A) Processing helix chain 'B' and resid 411 through 413 No H-bonds generated for 'chain 'B' and resid 411 through 413' Processing helix chain 'B' and resid 418 through 438 removed outlier: 3.624A pdb=" N LEU B 426 " --> pdb=" O VAL B 422 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N PHE B 427 " --> pdb=" O ASN B 423 " (cutoff:3.500A) Proline residue: B 432 - end of helix removed outlier: 3.927A pdb=" N PHE B 435 " --> pdb=" O LEU B 431 " (cutoff:3.500A) Processing helix chain 'B' and resid 440 through 458 removed outlier: 3.660A pdb=" N GLN B 445 " --> pdb=" O ARG B 441 " (cutoff:3.500A) removed outlier: 4.100A pdb=" N VAL B 448 " --> pdb=" O ILE B 444 " (cutoff:3.500A) removed outlier: 3.832A pdb=" N LEU B 457 " --> pdb=" O MET B 453 " (cutoff:3.500A) removed outlier: 4.122A pdb=" N GLU B 458 " --> pdb=" O PHE B 454 " (cutoff:3.500A) Processing helix chain 'B' and resid 548 through 554 removed outlier: 3.622A pdb=" N SER B 554 " --> pdb=" O SER B 550 " (cutoff:3.500A) Processing helix chain 'B' and resid 569 through 576 removed outlier: 5.312A pdb=" N GLY B 576 " --> pdb=" O ASN B 572 " (cutoff:3.500A) Processing helix chain 'B' and resid 582 through 591 Processing helix chain 'B' and resid 595 through 600 removed outlier: 4.145A pdb=" N ASN B 600 " --> pdb=" O GLU B 596 " (cutoff:3.500A) Processing helix chain 'B' and resid 618 through 632 removed outlier: 3.522A pdb=" N ALA B 625 " --> pdb=" O LYS B 621 " (cutoff:3.500A) Processing helix chain 'B' and resid 648 through 660 Processing helix chain 'B' and resid 697 through 702 removed outlier: 3.906A pdb=" N GLY B 702 " --> pdb=" O ASP B 698 " (cutoff:3.500A) Processing helix chain 'B' and resid 706 through 715 removed outlier: 3.507A pdb=" N GLN B 713 " --> pdb=" O GLN B 709 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'A' and resid 479 through 482 Processing sheet with id= B, first strand: chain 'A' and resid 682 through 685 removed outlier: 6.740A pdb=" N SER A 667 " --> pdb=" O VAL A 508 " (cutoff:3.500A) removed outlier: 8.269A pdb=" N ILE A 510 " --> pdb=" O SER A 667 " (cutoff:3.500A) removed outlier: 6.945A pdb=" N PHE A 669 " --> pdb=" O ILE A 510 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'A' and resid 484 through 486 removed outlier: 8.395A pdb=" N PHE A 486 " --> pdb=" O ASP A 496 " (cutoff:3.500A) removed outlier: 6.131A pdb=" N ASP A 496 " --> pdb=" O PHE A 486 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'B' and resid 479 through 482 Processing sheet with id= E, first strand: chain 'B' and resid 682 through 685 removed outlier: 6.740A pdb=" N SER B 667 " --> pdb=" O VAL B 508 " (cutoff:3.500A) removed outlier: 8.269A pdb=" N ILE B 510 " --> pdb=" O SER B 667 " (cutoff:3.500A) removed outlier: 6.945A pdb=" N PHE B 669 " --> pdb=" O ILE B 510 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'B' and resid 484 through 486 removed outlier: 8.394A pdb=" N PHE B 486 " --> pdb=" O ASP B 496 " (cutoff:3.500A) removed outlier: 6.132A pdb=" N ASP B 496 " --> pdb=" O PHE B 486 " (cutoff:3.500A) 514 hydrogen bonds defined for protein. 1524 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.64 Time building geometry restraints manager: 3.94 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.36: 3044 1.36 - 1.50: 2362 1.50 - 1.64: 3938 1.64 - 1.77: 0 1.77 - 1.91: 70 Bond restraints: 9414 Sorted by residual: bond pdb=" CA SER B 633 " pdb=" CB SER B 633 " ideal model delta sigma weight residual 1.522 1.531 -0.008 7.00e-03 2.04e+04 1.45e+00 bond pdb=" CA SER A 633 " pdb=" CB SER A 633 " ideal model delta sigma weight residual 1.522 1.530 -0.008 7.00e-03 2.04e+04 1.27e+00 bond pdb=" C4 ADP B 802 " pdb=" C5 ADP B 802 " ideal model delta sigma weight residual 1.490 1.469 0.021 2.00e-02 2.50e+03 1.06e+00 bond pdb=" C4 ADP A 801 " pdb=" C5 ADP A 801 " ideal model delta sigma weight residual 1.490 1.470 0.020 2.00e-02 2.50e+03 1.04e+00 bond pdb=" C LYS A 632 " pdb=" N SER A 633 " ideal model delta sigma weight residual 1.329 1.340 -0.011 1.12e-02 7.97e+03 9.64e-01 ... (remaining 9409 not shown) Histogram of bond angle deviations from ideal: 98.11 - 105.71: 118 105.71 - 113.31: 5301 113.31 - 120.91: 4863 120.91 - 128.51: 2416 128.51 - 136.11: 48 Bond angle restraints: 12746 Sorted by residual: angle pdb=" C PRO B 559 " pdb=" N GLN B 560 " pdb=" CA GLN B 560 " ideal model delta sigma weight residual 120.44 123.99 -3.55 1.30e+00 5.92e-01 7.46e+00 angle pdb=" C PRO A 559 " pdb=" N GLN A 560 " pdb=" CA GLN A 560 " ideal model delta sigma weight residual 120.44 123.92 -3.48 1.30e+00 5.92e-01 7.15e+00 angle pdb=" N VAL A 692 " pdb=" CA VAL A 692 " pdb=" C VAL A 692 " ideal model delta sigma weight residual 110.74 113.07 -2.33 9.10e-01 1.21e+00 6.56e+00 angle pdb=" N VAL B 692 " pdb=" CA VAL B 692 " pdb=" C VAL B 692 " ideal model delta sigma weight residual 110.74 113.06 -2.32 9.10e-01 1.21e+00 6.51e+00 angle pdb=" C VAL B 609 " pdb=" CA VAL B 609 " pdb=" CB VAL B 609 " ideal model delta sigma weight residual 111.88 108.80 3.08 1.37e+00 5.33e-01 5.05e+00 ... (remaining 12741 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 24.63: 5299 24.63 - 49.26: 299 49.26 - 73.89: 20 73.89 - 98.53: 2 98.53 - 123.16: 2 Dihedral angle restraints: 5622 sinusoidal: 2212 harmonic: 3410 Sorted by residual: dihedral pdb=" O1B ADP B 802 " pdb=" O3A ADP B 802 " pdb=" PB ADP B 802 " pdb=" PA ADP B 802 " ideal model delta sinusoidal sigma weight residual -60.00 63.15 -123.16 1 2.00e+01 2.50e-03 3.71e+01 dihedral pdb=" O1B ADP A 801 " pdb=" O3A ADP A 801 " pdb=" PB ADP A 801 " pdb=" PA ADP A 801 " ideal model delta sinusoidal sigma weight residual -60.00 63.13 -123.14 1 2.00e+01 2.50e-03 3.71e+01 dihedral pdb=" CA VAL B 691 " pdb=" C VAL B 691 " pdb=" N VAL B 692 " pdb=" CA VAL B 692 " ideal model delta harmonic sigma weight residual 180.00 -162.21 -17.79 0 5.00e+00 4.00e-02 1.27e+01 ... (remaining 5619 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.029: 937 0.029 - 0.058: 371 0.058 - 0.087: 110 0.087 - 0.117: 60 0.117 - 0.146: 12 Chirality restraints: 1490 Sorted by residual: chirality pdb=" CG LEU B 456 " pdb=" CB LEU B 456 " pdb=" CD1 LEU B 456 " pdb=" CD2 LEU B 456 " both_signs ideal model delta sigma weight residual False -2.59 -2.74 0.15 2.00e-01 2.50e+01 5.31e-01 chirality pdb=" CG LEU A 456 " pdb=" CB LEU A 456 " pdb=" CD1 LEU A 456 " pdb=" CD2 LEU A 456 " both_signs ideal model delta sigma weight residual False -2.59 -2.73 0.14 2.00e-01 2.50e+01 5.11e-01 chirality pdb=" CA GLN B 413 " pdb=" N GLN B 413 " pdb=" C GLN B 413 " pdb=" CB GLN B 413 " both_signs ideal model delta sigma weight residual False 2.51 2.37 0.14 2.00e-01 2.50e+01 4.78e-01 ... (remaining 1487 not shown) Planarity restraints: 1606 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB PHE B 427 " 0.015 2.00e-02 2.50e+03 1.28e-02 2.85e+00 pdb=" CG PHE B 427 " -0.028 2.00e-02 2.50e+03 pdb=" CD1 PHE B 427 " 0.006 2.00e-02 2.50e+03 pdb=" CD2 PHE B 427 " -0.002 2.00e-02 2.50e+03 pdb=" CE1 PHE B 427 " 0.000 2.00e-02 2.50e+03 pdb=" CE2 PHE B 427 " 0.008 2.00e-02 2.50e+03 pdb=" CZ PHE B 427 " 0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE A 427 " 0.015 2.00e-02 2.50e+03 1.25e-02 2.74e+00 pdb=" CG PHE A 427 " -0.028 2.00e-02 2.50e+03 pdb=" CD1 PHE A 427 " 0.006 2.00e-02 2.50e+03 pdb=" CD2 PHE A 427 " -0.002 2.00e-02 2.50e+03 pdb=" CE1 PHE A 427 " 0.000 2.00e-02 2.50e+03 pdb=" CE2 PHE A 427 " 0.008 2.00e-02 2.50e+03 pdb=" CZ PHE A 427 " 0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C LEU B 489 " -0.020 5.00e-02 4.00e+02 3.10e-02 1.54e+00 pdb=" N PRO B 490 " 0.054 5.00e-02 4.00e+02 pdb=" CA PRO B 490 " -0.016 5.00e-02 4.00e+02 pdb=" CD PRO B 490 " -0.017 5.00e-02 4.00e+02 ... (remaining 1603 not shown) Histogram of nonbonded interaction distances: 2.05 - 2.62: 116 2.62 - 3.19: 9021 3.19 - 3.76: 14846 3.76 - 4.33: 19666 4.33 - 4.90: 31555 Nonbonded interactions: 75204 Sorted by model distance: nonbonded pdb="MG MG A 803 " pdb=" O4 VO4 B 803 " model vdw 2.045 2.170 nonbonded pdb=" O4 VO4 A 802 " pdb="MG MG B 801 " model vdw 2.045 2.170 nonbonded pdb="MG MG A 803 " pdb=" O3B ADP B 802 " model vdw 2.066 2.170 nonbonded pdb=" O3B ADP A 801 " pdb="MG MG B 801 " model vdw 2.067 2.170 nonbonded pdb=" OG SER A 487 " pdb=" O ARG A 492 " model vdw 2.133 2.440 ... (remaining 75199 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'A' and resid 117 through 716) selection = (chain 'B' and resid 117 through 716) } 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: 2.320 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: 5.970 Check model and map are aligned: 0.130 Set scattering table: 0.080 Process input model: 28.680 Find NCS groups from input model: 0.580 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.630 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 40.460 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7597 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 0.029 9414 Z= 0.168 Angle : 0.613 7.847 12746 Z= 0.318 Chirality : 0.039 0.146 1490 Planarity : 0.003 0.031 1606 Dihedral : 14.007 123.157 3418 Min Nonbonded Distance : 2.045 Molprobity Statistics. All-atom Clashscore : 11.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.05 % Favored : 97.95 % Rotamer: Outliers : 0.20 % Allowed : 0.80 % Favored : 99.00 % 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: 0.92 (0.25), residues: 1170 helix: 1.49 (0.20), residues: 722 sheet: 0.68 (0.61), residues: 90 loop : -1.20 (0.31), residues: 358 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 304 HIS 0.009 0.001 HIS A 595 PHE 0.028 0.001 PHE B 427 TYR 0.008 0.001 TYR A 349 ARG 0.005 0.001 ARG A 590 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2340 Ramachandran restraints generated. 1170 Oldfield, 0 Emsley, 1170 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2340 Ramachandran restraints generated. 1170 Oldfield, 0 Emsley, 1170 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 82 residues out of total 996 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 80 time to evaluate : 1.130 Fit side-chains outliers start: 2 outliers final: 0 residues processed: 82 average time/residue: 0.2091 time to fit residues: 25.0997 Evaluate side-chains 59 residues out of total 996 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 59 time to evaluate : 1.477 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.4429 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 97 optimal weight: 0.8980 chunk 87 optimal weight: 7.9990 chunk 48 optimal weight: 5.9990 chunk 30 optimal weight: 10.0000 chunk 59 optimal weight: 2.9990 chunk 46 optimal weight: 8.9990 chunk 90 optimal weight: 2.9990 chunk 35 optimal weight: 1.9990 chunk 55 optimal weight: 2.9990 chunk 67 optimal weight: 10.0000 chunk 105 optimal weight: 0.9990 overall best weight: 1.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 390 GLN ** A 465 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 560 GLN ** A 672 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 390 GLN ** B 465 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 560 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7667 moved from start: 0.1241 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 9414 Z= 0.225 Angle : 0.637 6.497 12746 Z= 0.324 Chirality : 0.040 0.146 1490 Planarity : 0.004 0.033 1606 Dihedral : 7.314 115.514 1296 Min Nonbonded Distance : 1.844 Molprobity Statistics. All-atom Clashscore : 14.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.56 % Favored : 97.44 % Rotamer: Outliers : 0.60 % Allowed : 8.03 % Favored : 91.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.04 (0.25), residues: 1170 helix: 1.57 (0.19), residues: 728 sheet: 1.05 (0.67), residues: 76 loop : -1.21 (0.30), residues: 366 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 304 HIS 0.006 0.002 HIS B 697 PHE 0.023 0.002 PHE A 302 TYR 0.019 0.002 TYR B 360 ARG 0.004 0.001 ARG A 209 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2340 Ramachandran restraints generated. 1170 Oldfield, 0 Emsley, 1170 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2340 Ramachandran restraints generated. 1170 Oldfield, 0 Emsley, 1170 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 73 residues out of total 996 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 67 time to evaluate : 1.117 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 6 outliers final: 1 residues processed: 71 average time/residue: 0.2078 time to fit residues: 21.8322 Evaluate side-chains 60 residues out of total 996 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 59 time to evaluate : 1.144 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.0872 time to fit residues: 1.5649 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 58 optimal weight: 20.0000 chunk 32 optimal weight: 0.7980 chunk 87 optimal weight: 6.9990 chunk 71 optimal weight: 0.9990 chunk 29 optimal weight: 9.9990 chunk 105 optimal weight: 0.6980 chunk 114 optimal weight: 6.9990 chunk 93 optimal weight: 0.9980 chunk 104 optimal weight: 5.9990 chunk 35 optimal weight: 5.9990 chunk 84 optimal weight: 8.9990 overall best weight: 1.8984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 465 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 622 GLN ** A 672 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 465 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 622 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7675 moved from start: 0.1515 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 9414 Z= 0.210 Angle : 0.612 8.045 12746 Z= 0.304 Chirality : 0.039 0.151 1490 Planarity : 0.003 0.034 1606 Dihedral : 7.209 116.586 1296 Min Nonbonded Distance : 1.871 Molprobity Statistics. All-atom Clashscore : 13.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.74 % Favored : 97.26 % Rotamer: Outliers : 1.00 % Allowed : 11.65 % Favored : 87.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.04 (0.25), residues: 1170 helix: 1.60 (0.19), residues: 740 sheet: 0.91 (0.64), residues: 76 loop : -1.34 (0.31), residues: 354 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP A 132 HIS 0.005 0.001 HIS B 672 PHE 0.023 0.001 PHE A 302 TYR 0.016 0.002 TYR A 205 ARG 0.003 0.000 ARG A 209 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2340 Ramachandran restraints generated. 1170 Oldfield, 0 Emsley, 1170 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2340 Ramachandran restraints generated. 1170 Oldfield, 0 Emsley, 1170 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 77 residues out of total 996 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 67 time to evaluate : 1.142 Fit side-chains revert: symmetry clash outliers start: 10 outliers final: 2 residues processed: 76 average time/residue: 0.1628 time to fit residues: 20.1765 Evaluate side-chains 62 residues out of total 996 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 60 time to evaluate : 1.076 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.0959 time to fit residues: 1.7572 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 104 optimal weight: 3.9990 chunk 79 optimal weight: 8.9990 chunk 54 optimal weight: 8.9990 chunk 11 optimal weight: 0.6980 chunk 50 optimal weight: 10.0000 chunk 70 optimal weight: 7.9990 chunk 105 optimal weight: 1.9990 chunk 112 optimal weight: 4.9990 chunk 55 optimal weight: 0.0980 chunk 100 optimal weight: 0.9990 chunk 30 optimal weight: 5.9990 overall best weight: 1.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 465 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 672 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 434 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 465 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7666 moved from start: 0.1756 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 9414 Z= 0.187 Angle : 0.622 11.476 12746 Z= 0.303 Chirality : 0.039 0.206 1490 Planarity : 0.003 0.039 1606 Dihedral : 7.106 116.324 1296 Min Nonbonded Distance : 1.883 Molprobity Statistics. All-atom Clashscore : 13.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.39 % Favored : 97.61 % Rotamer: Outliers : 0.90 % Allowed : 13.86 % Favored : 85.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.09 (0.24), residues: 1170 helix: 1.64 (0.19), residues: 740 sheet: 0.85 (0.63), residues: 76 loop : -1.29 (0.31), residues: 354 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 132 HIS 0.005 0.001 HIS A 672 PHE 0.025 0.001 PHE A 164 TYR 0.018 0.002 TYR A 360 ARG 0.004 0.000 ARG B 236 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2340 Ramachandran restraints generated. 1170 Oldfield, 0 Emsley, 1170 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2340 Ramachandran restraints generated. 1170 Oldfield, 0 Emsley, 1170 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 73 residues out of total 996 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 64 time to evaluate : 1.103 Fit side-chains revert: symmetry clash outliers start: 9 outliers final: 6 residues processed: 69 average time/residue: 0.1737 time to fit residues: 19.1407 Evaluate side-chains 66 residues out of total 996 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 60 time to evaluate : 0.957 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 0 residues processed: 6 average time/residue: 0.1032 time to fit residues: 2.5062 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 93 optimal weight: 1.9990 chunk 63 optimal weight: 8.9990 chunk 1 optimal weight: 4.9990 chunk 83 optimal weight: 7.9990 chunk 46 optimal weight: 0.0050 chunk 95 optimal weight: 0.4980 chunk 77 optimal weight: 0.8980 chunk 0 optimal weight: 9.9990 chunk 57 optimal weight: 6.9990 chunk 100 optimal weight: 9.9990 chunk 28 optimal weight: 0.2980 overall best weight: 0.7396 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 560 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7619 moved from start: 0.1958 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 9414 Z= 0.156 Angle : 0.615 11.625 12746 Z= 0.295 Chirality : 0.039 0.307 1490 Planarity : 0.003 0.043 1606 Dihedral : 6.901 114.327 1296 Min Nonbonded Distance : 1.945 Molprobity Statistics. All-atom Clashscore : 12.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.48 % Favored : 97.52 % Rotamer: Outliers : 0.50 % Allowed : 15.46 % Favored : 84.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.30 (0.25), residues: 1170 helix: 1.72 (0.19), residues: 738 sheet: 1.57 (0.63), residues: 68 loop : -1.11 (0.32), residues: 364 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.000 TRP B 132 HIS 0.002 0.001 HIS A 241 PHE 0.023 0.001 PHE B 302 TYR 0.019 0.002 TYR A 360 ARG 0.004 0.000 ARG B 236 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2340 Ramachandran restraints generated. 1170 Oldfield, 0 Emsley, 1170 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2340 Ramachandran restraints generated. 1170 Oldfield, 0 Emsley, 1170 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 72 residues out of total 996 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 67 time to evaluate : 1.082 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 5 outliers final: 5 residues processed: 68 average time/residue: 0.1887 time to fit residues: 19.7348 Evaluate side-chains 66 residues out of total 996 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 61 time to evaluate : 1.042 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 0 residues processed: 5 average time/residue: 0.0863 time to fit residues: 2.2111 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 37 optimal weight: 30.0000 chunk 100 optimal weight: 1.9990 chunk 22 optimal weight: 0.6980 chunk 65 optimal weight: 8.9990 chunk 27 optimal weight: 8.9990 chunk 112 optimal weight: 0.6980 chunk 93 optimal weight: 3.9990 chunk 51 optimal weight: 4.9990 chunk 9 optimal weight: 5.9990 chunk 58 optimal weight: 20.0000 chunk 108 optimal weight: 0.9990 overall best weight: 1.6786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 259 ASN ** A 465 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 465 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7661 moved from start: 0.2114 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 9414 Z= 0.197 Angle : 0.624 11.475 12746 Z= 0.301 Chirality : 0.041 0.375 1490 Planarity : 0.004 0.045 1606 Dihedral : 6.948 115.920 1296 Min Nonbonded Distance : 1.872 Molprobity Statistics. All-atom Clashscore : 13.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.56 % Favored : 97.44 % Rotamer: Outliers : 1.00 % Allowed : 16.67 % Favored : 82.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.27 (0.25), residues: 1170 helix: 1.69 (0.19), residues: 750 sheet: 1.60 (0.62), residues: 68 loop : -1.18 (0.34), residues: 352 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 304 HIS 0.004 0.001 HIS A 672 PHE 0.025 0.001 PHE B 302 TYR 0.015 0.002 TYR A 205 ARG 0.003 0.000 ARG B 236 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2340 Ramachandran restraints generated. 1170 Oldfield, 0 Emsley, 1170 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2340 Ramachandran restraints generated. 1170 Oldfield, 0 Emsley, 1170 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 71 residues out of total 996 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 61 time to evaluate : 1.133 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 10 outliers final: 4 residues processed: 68 average time/residue: 0.1987 time to fit residues: 21.2426 Evaluate side-chains 61 residues out of total 996 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 57 time to evaluate : 1.184 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.1055 time to fit residues: 2.4341 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 12 optimal weight: 5.9990 chunk 63 optimal weight: 20.0000 chunk 81 optimal weight: 3.9990 chunk 94 optimal weight: 0.4980 chunk 62 optimal weight: 0.9990 chunk 111 optimal weight: 1.9990 chunk 69 optimal weight: 6.9990 chunk 68 optimal weight: 3.9990 chunk 51 optimal weight: 2.9990 chunk 44 optimal weight: 4.9990 chunk 66 optimal weight: 5.9990 overall best weight: 2.0988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 465 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 465 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 560 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7680 moved from start: 0.2235 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 9414 Z= 0.217 Angle : 0.651 12.104 12746 Z= 0.313 Chirality : 0.042 0.315 1490 Planarity : 0.004 0.046 1606 Dihedral : 6.990 117.544 1296 Min Nonbonded Distance : 1.856 Molprobity Statistics. All-atom Clashscore : 14.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.91 % Favored : 97.09 % Rotamer: Outliers : 0.80 % Allowed : 17.27 % Favored : 81.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.04 (0.25), residues: 1170 helix: 1.51 (0.19), residues: 762 sheet: 1.54 (0.63), residues: 68 loop : -1.42 (0.33), residues: 340 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 132 HIS 0.006 0.001 HIS A 672 PHE 0.033 0.001 PHE B 302 TYR 0.015 0.002 TYR B 205 ARG 0.003 0.000 ARG A 209 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2340 Ramachandran restraints generated. 1170 Oldfield, 0 Emsley, 1170 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2340 Ramachandran restraints generated. 1170 Oldfield, 0 Emsley, 1170 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 68 residues out of total 996 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 60 time to evaluate : 1.171 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 8 outliers final: 3 residues processed: 66 average time/residue: 0.1850 time to fit residues: 19.3090 Evaluate side-chains 61 residues out of total 996 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 58 time to evaluate : 1.222 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.0902 time to fit residues: 2.0342 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 33 optimal weight: 9.9990 chunk 21 optimal weight: 5.9990 chunk 71 optimal weight: 0.9980 chunk 76 optimal weight: 10.0000 chunk 55 optimal weight: 3.9990 chunk 10 optimal weight: 8.9990 chunk 87 optimal weight: 4.9990 chunk 101 optimal weight: 5.9990 chunk 107 optimal weight: 4.9990 chunk 97 optimal weight: 0.9990 chunk 104 optimal weight: 1.9990 overall best weight: 2.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 465 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 664 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 465 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 664 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7713 moved from start: 0.2365 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.029 9414 Z= 0.252 Angle : 0.674 12.962 12746 Z= 0.330 Chirality : 0.042 0.182 1490 Planarity : 0.004 0.049 1606 Dihedral : 7.150 120.410 1296 Min Nonbonded Distance : 1.847 Molprobity Statistics. All-atom Clashscore : 15.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.50 % Favored : 96.50 % Rotamer: Outliers : 0.50 % Allowed : 18.07 % Favored : 81.43 % 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: 0.90 (0.24), residues: 1170 helix: 1.54 (0.19), residues: 750 sheet: 0.87 (0.62), residues: 76 loop : -1.63 (0.31), residues: 344 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 304 HIS 0.007 0.002 HIS A 672 PHE 0.032 0.001 PHE B 302 TYR 0.014 0.002 TYR B 205 ARG 0.003 0.000 ARG A 209 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2340 Ramachandran restraints generated. 1170 Oldfield, 0 Emsley, 1170 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2340 Ramachandran restraints generated. 1170 Oldfield, 0 Emsley, 1170 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 64 residues out of total 996 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 59 time to evaluate : 1.100 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 5 outliers final: 2 residues processed: 63 average time/residue: 0.1653 time to fit residues: 17.0494 Evaluate side-chains 59 residues out of total 996 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 57 time to evaluate : 1.056 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.1017 time to fit residues: 1.7919 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 107 optimal weight: 3.9990 chunk 62 optimal weight: 0.7980 chunk 45 optimal weight: 7.9990 chunk 81 optimal weight: 1.9990 chunk 31 optimal weight: 20.0000 chunk 94 optimal weight: 2.9990 chunk 98 optimal weight: 4.9990 chunk 103 optimal weight: 6.9990 chunk 68 optimal weight: 1.9990 chunk 110 optimal weight: 0.9980 chunk 67 optimal weight: 6.9990 overall best weight: 1.7586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 465 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 465 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7680 moved from start: 0.2459 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 9414 Z= 0.201 Angle : 0.670 13.378 12746 Z= 0.321 Chirality : 0.041 0.182 1490 Planarity : 0.004 0.049 1606 Dihedral : 7.012 118.502 1296 Min Nonbonded Distance : 1.887 Molprobity Statistics. All-atom Clashscore : 14.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.33 % Favored : 96.67 % Rotamer: Outliers : 0.40 % Allowed : 18.47 % Favored : 81.12 % 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: 0.90 (0.25), residues: 1170 helix: 1.49 (0.19), residues: 758 sheet: 0.93 (0.62), residues: 76 loop : -1.56 (0.32), residues: 336 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 132 HIS 0.005 0.001 HIS B 672 PHE 0.024 0.001 PHE B 302 TYR 0.015 0.001 TYR B 205 ARG 0.003 0.000 ARG B 236 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2340 Ramachandran restraints generated. 1170 Oldfield, 0 Emsley, 1170 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2340 Ramachandran restraints generated. 1170 Oldfield, 0 Emsley, 1170 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 63 residues out of total 996 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 59 time to evaluate : 0.993 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 4 outliers final: 1 residues processed: 60 average time/residue: 0.2074 time to fit residues: 19.2957 Evaluate side-chains 57 residues out of total 996 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 56 time to evaluate : 1.137 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.1176 time to fit residues: 1.6798 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 52 optimal weight: 0.1980 chunk 76 optimal weight: 9.9990 chunk 115 optimal weight: 5.9990 chunk 106 optimal weight: 0.8980 chunk 92 optimal weight: 7.9990 chunk 9 optimal weight: 9.9990 chunk 71 optimal weight: 3.9990 chunk 56 optimal weight: 7.9990 chunk 73 optimal weight: 7.9990 chunk 98 optimal weight: 6.9990 chunk 28 optimal weight: 6.9990 overall best weight: 3.6186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 250 HIS ** A 465 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 572 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 250 HIS ** B 465 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 572 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7756 moved from start: 0.2636 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.048 9414 Z= 0.325 Angle : 0.739 12.552 12746 Z= 0.362 Chirality : 0.044 0.189 1490 Planarity : 0.004 0.049 1606 Dihedral : 7.330 123.640 1296 Min Nonbonded Distance : 1.807 Molprobity Statistics. All-atom Clashscore : 16.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.76 % Favored : 96.24 % Rotamer: Outliers : 0.30 % Allowed : 18.78 % Favored : 80.92 % 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: 0.65 (0.24), residues: 1170 helix: 1.36 (0.19), residues: 746 sheet: 0.85 (0.63), residues: 76 loop : -1.73 (0.29), residues: 348 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 132 HIS 0.009 0.002 HIS A 697 PHE 0.057 0.002 PHE B 164 TYR 0.016 0.002 TYR B 575 ARG 0.004 0.001 ARG B 209 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2340 Ramachandran restraints generated. 1170 Oldfield, 0 Emsley, 1170 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2340 Ramachandran restraints generated. 1170 Oldfield, 0 Emsley, 1170 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 61 residues out of total 996 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 58 time to evaluate : 1.153 Fit side-chains outliers start: 3 outliers final: 2 residues processed: 59 average time/residue: 0.1739 time to fit residues: 16.8209 Evaluate side-chains 58 residues out of total 996 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 56 time to evaluate : 1.091 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.0885 time to fit residues: 1.7819 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 84 optimal weight: 5.9990 chunk 13 optimal weight: 5.9990 chunk 25 optimal weight: 6.9990 chunk 92 optimal weight: 0.7980 chunk 38 optimal weight: 2.9990 chunk 94 optimal weight: 5.9990 chunk 11 optimal weight: 5.9990 chunk 16 optimal weight: 0.0010 chunk 80 optimal weight: 2.9990 chunk 5 optimal weight: 20.0000 chunk 66 optimal weight: 10.0000 overall best weight: 2.5592 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 465 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 572 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 465 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4053 r_free = 0.4053 target = 0.100771 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3567 r_free = 0.3567 target = 0.076245 restraints weight = 24984.979| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3567 r_free = 0.3567 target = 0.076451 restraints weight = 18478.812| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3576 r_free = 0.3576 target = 0.077100 restraints weight = 15316.272| |-----------------------------------------------------------------------------| r_work (final): 0.3561 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7767 moved from start: 0.2690 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 9414 Z= 0.255 Angle : 0.717 13.146 12746 Z= 0.347 Chirality : 0.042 0.171 1490 Planarity : 0.004 0.048 1606 Dihedral : 7.274 123.071 1296 Min Nonbonded Distance : 1.840 Molprobity Statistics. All-atom Clashscore : 16.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.10 % Favored : 95.90 % Rotamer: Outliers : 0.40 % Allowed : 18.78 % Favored : 80.82 % 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: 0.52 (0.24), residues: 1170 helix: 1.24 (0.19), residues: 758 sheet: 0.78 (0.62), residues: 76 loop : -1.85 (0.30), residues: 336 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 132 HIS 0.007 0.002 HIS B 672 PHE 0.051 0.002 PHE B 164 TYR 0.015 0.002 TYR A 205 ARG 0.003 0.000 ARG B 209 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1624.61 seconds wall clock time: 31 minutes 0.05 seconds (1860.05 seconds total)