Starting phenix.real_space_refine on Fri Mar 15 04:27:24 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8omq_16974/03_2024/8omq_16974_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8omq_16974/03_2024/8omq_16974.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.11 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8omq_16974/03_2024/8omq_16974.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8omq_16974/03_2024/8omq_16974.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8omq_16974/03_2024/8omq_16974_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8omq_16974/03_2024/8omq_16974_updated.pdb" } resolution = 3.11 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= 0.020 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: 6 Type Number sf(0) Gaussians P 6 5.49 5 Mg 2 5.21 5 S 54 5.16 5 C 6707 2.51 5 N 1811 2.21 5 O 2004 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "B GLU 533": "OE1" <-> "OE2" Residue "B GLU 546": "OE1" <-> "OE2" Residue "B GLU 589": "OE1" <-> "OE2" Residue "B GLU 599": "OE1" <-> "OE2" Residue "B GLU 622": "OE1" <-> "OE2" Residue "B GLU 637": "OE1" <-> "OE2" Residue "B TYR 646": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 691": "OE1" <-> "OE2" Residue "B GLU 718": "OE1" <-> "OE2" Residue "B GLU 787": "OE1" <-> "OE2" Residue "B GLU 806": "OE1" <-> "OE2" Residue "B GLU 812": "OE1" <-> "OE2" Residue "B GLU 886": "OE1" <-> "OE2" Residue "B GLU 889": "OE1" <-> "OE2" Residue "B GLU 925": "OE1" <-> "OE2" Residue "B GLU 961": "OE1" <-> "OE2" Residue "B ARG 979": "NH1" <-> "NH2" Residue "B GLU 995": "OE1" <-> "OE2" Residue "B GLU 1092": "OE1" <-> "OE2" Residue "A ARG 159": "NH1" <-> "NH2" Residue "A GLU 198": "OE1" <-> "OE2" Residue "A ARG 243": "NH1" <-> "NH2" Residue "A GLU 290": "OE1" <-> "OE2" Residue "A GLU 318": "OE1" <-> "OE2" Residue "A GLU 358": "OE1" <-> "OE2" Residue "A GLU 464": "OE1" <-> "OE2" Residue "A GLU 467": "OE1" <-> "OE2" Residue "A GLU 480": "OE1" <-> "OE2" Residue "A GLU 483": "OE1" <-> "OE2" Residue "A ARG 501": "NH1" <-> "NH2" Residue "A ARG 534": "NH1" <-> "NH2" Residue "A GLU 562": "OE1" <-> "OE2" Residue "A GLU 643": "OE1" <-> "OE2" Residue "A ARG 680": "NH1" <-> "NH2" Residue "A ARG 711": "NH1" <-> "NH2" Residue "A ARG 752": "NH1" <-> "NH2" Residue "A GLU 768": "OE1" <-> "OE2" Residue "A GLU 808": "OE1" <-> "OE2" Residue "A GLU 850": "OE1" <-> "OE2" Residue "A GLU 853": "OE1" <-> "OE2" Residue "A GLU 876": "OE1" <-> "OE2" Residue "A GLU 878": "OE1" <-> "OE2" Residue "A GLU 881": "OE1" <-> "OE2" Residue "A GLU 902": "OE1" <-> "OE2" Residue "A GLU 925": "OE1" <-> "OE2" Time to flip residues: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 10584 Number of models: 1 Model: "" Number of chains: 4 Chain: "B" Number of atoms: 4634 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 577, 4631 Classifications: {'peptide': 577} Link IDs: {'PTRANS': 17, 'TRANS': 559} Chain breaks: 1 Conformer: "B" Number of residues, atoms: 577, 4631 Classifications: {'peptide': 577} Link IDs: {'PTRANS': 17, 'TRANS': 559} Chain breaks: 1 bond proxies already assigned to first conformer: 4716 Chain: "A" Number of atoms: 5886 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 745, 5883 Classifications: {'peptide': 745} Link IDs: {'PTRANS': 22, 'TRANS': 722} Chain breaks: 6 Conformer: "B" Number of residues, atoms: 745, 5883 Classifications: {'peptide': 745} Link IDs: {'PTRANS': 22, 'TRANS': 722} Chain breaks: 6 bond proxies already assigned to first conformer: 5960 Chain: "B" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "A" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 11.05, per 1000 atoms: 1.04 Number of scatterers: 10584 At special positions: 0 Unit cell: (85.0206, 108.79, 171.87, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 54 16.00 P 6 15.00 Mg 2 11.99 O 2004 8.00 N 1811 7.00 C 6707 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: 4.44 Conformation dependent library (CDL) restraints added in 3.8 seconds 2612 Ramachandran restraints generated. 1306 Oldfield, 0 Emsley, 1306 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2514 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 53 helices and 9 sheets defined 51.2% alpha, 6.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.22 Creating SS restraints... Processing helix chain 'B' and resid 539 through 544 Processing helix chain 'B' and resid 560 through 564 Processing helix chain 'B' and resid 570 through 581 Processing helix chain 'B' and resid 587 through 602 Processing helix chain 'B' and resid 607 through 616 Processing helix chain 'B' and resid 621 through 630 Processing helix chain 'B' and resid 635 through 653 Processing helix chain 'B' and resid 656 through 662 Processing helix chain 'B' and resid 666 through 672 Processing helix chain 'B' and resid 675 through 678 No H-bonds generated for 'chain 'B' and resid 675 through 678' Processing helix chain 'B' and resid 680 through 682 No H-bonds generated for 'chain 'B' and resid 680 through 682' Processing helix chain 'B' and resid 684 through 687 No H-bonds generated for 'chain 'B' and resid 684 through 687' Processing helix chain 'B' and resid 691 through 696 removed outlier: 3.941A pdb=" N VAL B 696 " --> pdb=" O GLN B 692 " (cutoff:3.500A) Processing helix chain 'B' and resid 706 through 708 No H-bonds generated for 'chain 'B' and resid 706 through 708' Processing helix chain 'B' and resid 710 through 737 removed outlier: 3.566A pdb=" N HIS B 729 " --> pdb=" O GLU B 725 " (cutoff:3.500A) removed outlier: 4.483A pdb=" N LEU B 730 " --> pdb=" O ILE B 726 " (cutoff:3.500A) removed outlier: 5.258A pdb=" N GLN B 731 " --> pdb=" O ARG B 727 " (cutoff:3.500A) removed outlier: 5.049A pdb=" N GLU B 732 " --> pdb=" O MET B 728 " (cutoff:3.500A) Processing helix chain 'B' and resid 783 through 842 removed outlier: 3.796A pdb=" N GLU B 816 " --> pdb=" O GLU B 812 " (cutoff:3.500A) removed outlier: 4.565A pdb=" N HIS B 817 " --> pdb=" O LYS B 813 " (cutoff:3.500A) removed outlier: 4.927A pdb=" N TYR B 818 " --> pdb=" O PHE B 814 " (cutoff:3.500A) removed outlier: 5.690A pdb=" N HIS B 819 " --> pdb=" O SER B 815 " (cutoff:3.500A) removed outlier: 6.333A pdb=" N SER B 820 " --> pdb=" O GLU B 816 " (cutoff:3.500A) Processing helix chain 'B' and resid 865 through 870 Processing helix chain 'B' and resid 902 through 918 Processing helix chain 'B' and resid 945 through 947 No H-bonds generated for 'chain 'B' and resid 945 through 947' Processing helix chain 'B' and resid 951 through 964 Processing helix chain 'B' and resid 983 through 999 Processing helix chain 'B' and resid 1012 through 1017 removed outlier: 4.875A pdb=" N LEU B1017 " --> pdb=" O PRO B1013 " (cutoff:3.500A) Processing helix chain 'B' and resid 1069 through 1075 Processing helix chain 'B' and resid 1080 through 1110 Processing helix chain 'B' and resid 1116 through 1120 Processing helix chain 'A' and resid 186 through 194 Processing helix chain 'A' and resid 210 through 220 removed outlier: 3.802A pdb=" N GLY A 220 " --> pdb=" O ILE A 216 " (cutoff:3.500A) Processing helix chain 'A' and resid 237 through 243 removed outlier: 3.686A pdb=" N ARG A 243 " --> pdb=" O GLN A 239 " (cutoff:3.500A) Processing helix chain 'A' and resid 259 through 262 removed outlier: 3.568A pdb=" N GLU A 262 " --> pdb=" O PRO A 259 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 259 through 262' Processing helix chain 'A' and resid 264 through 274 Processing helix chain 'A' and resid 283 through 285 No H-bonds generated for 'chain 'A' and resid 283 through 285' Processing helix chain 'A' and resid 304 through 309 Processing helix chain 'A' and resid 327 through 330 No H-bonds generated for 'chain 'A' and resid 327 through 330' Processing helix chain 'A' and resid 336 through 347 removed outlier: 3.603A pdb=" N ARG A 340 " --> pdb=" O PRO A 336 " (cutoff:3.500A) removed outlier: 3.855A pdb=" N LEU A 341 " --> pdb=" O GLN A 337 " (cutoff:3.500A) Processing helix chain 'A' and resid 353 through 368 Processing helix chain 'A' and resid 370 through 377 Processing helix chain 'A' and resid 381 through 383 No H-bonds generated for 'chain 'A' and resid 381 through 383' Processing helix chain 'A' and resid 389 through 395 Processing helix chain 'A' and resid 401 through 423 removed outlier: 3.540A pdb=" N GLN A 413 " --> pdb=" O GLN A 409 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N LEU A 414 " --> pdb=" O GLY A 410 " (cutoff:3.500A) Proline residue: A 415 - end of helix Processing helix chain 'A' and resid 428 through 457 removed outlier: 4.290A pdb=" N LEU A 431 " --> pdb=" O HIS A 428 " (cutoff:3.500A) Proline residue: A 439 - end of helix removed outlier: 3.816A pdb=" N SER A 448 " --> pdb=" O SER A 445 " (cutoff:3.500A) removed outlier: 5.001A pdb=" N LYS A 449 " --> pdb=" O ASP A 446 " (cutoff:3.500A) removed outlier: 5.055A pdb=" N GLU A 452 " --> pdb=" O LYS A 449 " (cutoff:3.500A) removed outlier: 4.913A pdb=" N THR A 456 " --> pdb=" O MET A 453 " (cutoff:3.500A) Processing helix chain 'A' and resid 476 through 503 removed outlier: 3.551A pdb=" N ARG A 482 " --> pdb=" O LEU A 478 " (cutoff:3.500A) removed outlier: 4.089A pdb=" N GLU A 483 " --> pdb=" O SER A 479 " (cutoff:3.500A) removed outlier: 3.914A pdb=" N ILE A 484 " --> pdb=" O GLU A 480 " (cutoff:3.500A) Processing helix chain 'A' and resid 527 through 531 removed outlier: 3.927A pdb=" N GLU A 530 " --> pdb=" O CYS A 527 " (cutoff:3.500A) Processing helix chain 'A' and resid 554 through 612 removed outlier: 3.653A pdb=" N ILE A 577 " --> pdb=" O ALA A 573 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N LYS A 579 " --> pdb=" O ASP A 575 " (cutoff:3.500A) removed outlier: 4.635A pdb=" N GLU A 580 " --> pdb=" O ALA A 576 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N GLY A 587 " --> pdb=" O ASN A 583 " (cutoff:3.500A) removed outlier: 4.407A pdb=" N TYR A 588 " --> pdb=" O ILE A 584 " (cutoff:3.500A) removed outlier: 4.375A pdb=" N VAL A 589 " --> pdb=" O SER A 585 " (cutoff:3.500A) removed outlier: 5.619A pdb=" N GLU A 590 " --> pdb=" O SER A 586 " (cutoff:3.500A) Proline residue: A 591 - end of helix removed outlier: 3.873A pdb=" N VAL A 598 " --> pdb=" O THR A 594 " (cutoff:3.500A) Processing helix chain 'A' and resid 642 through 644 No H-bonds generated for 'chain 'A' and resid 642 through 644' Processing helix chain 'A' and resid 675 through 691 removed outlier: 3.852A pdb=" N GLY A 683 " --> pdb=" O ILE A 679 " (cutoff:3.500A) Processing helix chain 'A' and resid 726 through 735 Processing helix chain 'A' and resid 756 through 773 Processing helix chain 'A' and resid 785 through 793 removed outlier: 3.779A pdb=" N THR A 788 " --> pdb=" O HIS A 785 " (cutoff:3.500A) removed outlier: 4.263A pdb=" N ALA A 789 " --> pdb=" O GLU A 786 " (cutoff:3.500A) Processing helix chain 'A' and resid 827 through 833 Processing helix chain 'A' and resid 838 through 849 Processing helix chain 'A' and resid 871 through 892 removed outlier: 3.769A pdb=" N ILE A 884 " --> pdb=" O GLY A 880 " (cutoff:3.500A) removed outlier: 3.864A pdb=" N GLN A 885 " --> pdb=" O GLU A 881 " (cutoff:3.500A) Processing helix chain 'A' and resid 901 through 918 removed outlier: 4.054A pdb=" N THR A 905 " --> pdb=" O GLU A 901 " (cutoff:3.500A) removed outlier: 4.159A pdb=" N GLU A 914 " --> pdb=" O GLN A 910 " (cutoff:3.500A) removed outlier: 4.158A pdb=" N VAL A 915 " --> pdb=" O LEU A 911 " (cutoff:3.500A) removed outlier: 3.977A pdb=" N ILE A 916 " --> pdb=" O LYS A 912 " (cutoff:3.500A) Processing helix chain 'A' and resid 921 through 929 Processing sheet with id= A, first strand: chain 'B' and resid 754 through 757 Processing sheet with id= B, first strand: chain 'B' and resid 857 through 859 Processing sheet with id= C, first strand: chain 'B' and resid 1054 through 1061 removed outlier: 3.709A pdb=" N LEU B1056 " --> pdb=" O GLY B1031 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N GLY B1031 " --> pdb=" O LEU B1056 " (cutoff:3.500A) removed outlier: 5.868A pdb=" N GLN B1058 " --> pdb=" O HIS B1029 " (cutoff:3.500A) removed outlier: 5.955A pdb=" N HIS B1029 " --> pdb=" O GLN B1058 " (cutoff:3.500A) removed outlier: 6.791A pdb=" N THR B1060 " --> pdb=" O ASN B1027 " (cutoff:3.500A) removed outlier: 7.098A pdb=" N ASN B1027 " --> pdb=" O THR B1060 " (cutoff:3.500A) removed outlier: 7.104A pdb=" N TYR B1028 " --> pdb=" O VAL B 891 " (cutoff:3.500A) removed outlier: 5.697A pdb=" N ILE B 893 " --> pdb=" O TYR B1028 " (cutoff:3.500A) removed outlier: 7.539A pdb=" N MET B1030 " --> pdb=" O ILE B 893 " (cutoff:3.500A) removed outlier: 7.220A pdb=" N THR B 895 " --> pdb=" O MET B1030 " (cutoff:3.500A) removed outlier: 8.604A pdb=" N PHE B1032 " --> pdb=" O THR B 895 " (cutoff:3.500A) removed outlier: 7.163A pdb=" N THR B1005 " --> pdb=" O MET B 892 " (cutoff:3.500A) removed outlier: 7.363A pdb=" N ILE B 894 " --> pdb=" O THR B1005 " (cutoff:3.500A) removed outlier: 6.174A pdb=" N PHE B1007 " --> pdb=" O ILE B 894 " (cutoff:3.500A) removed outlier: 8.418A pdb=" N GLY B 896 " --> pdb=" O PHE B1007 " (cutoff:3.500A) removed outlier: 6.468A pdb=" N GLY B 934 " --> pdb=" O LEU B 971 " (cutoff:3.500A) removed outlier: 7.537A pdb=" N ILE B 973 " --> pdb=" O GLY B 934 " (cutoff:3.500A) removed outlier: 6.383A pdb=" N PHE B 936 " --> pdb=" O ILE B 973 " (cutoff:3.500A) removed outlier: 7.785A pdb=" N ASP B 975 " --> pdb=" O PHE B 936 " (cutoff:3.500A) removed outlier: 6.507A pdb=" N ARG B 938 " --> pdb=" O ASP B 975 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'A' and resid 147 through 153 removed outlier: 5.825A pdb=" N GLU A 290 " --> pdb=" O LEU A 173 " (cutoff:3.500A) removed outlier: 7.688A pdb=" N LEU A 175 " --> pdb=" O GLU A 290 " (cutoff:3.500A) removed outlier: 6.847A pdb=" N THR A 292 " --> pdb=" O LEU A 175 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'A' and resid 632 through 634 Processing sheet with id= F, first strand: chain 'A' and resid 665 through 667 Processing sheet with id= G, first strand: chain 'A' and resid 707 through 711 Processing sheet with id= H, first strand: chain 'A' and resid 800 through 802 Processing sheet with id= I, first strand: chain 'A' and resid 804 through 806 463 hydrogen bonds defined for protein. 1289 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: 2.92 Time building geometry restraints manager: 4.79 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 2908 1.34 - 1.46: 2840 1.46 - 1.58: 4915 1.58 - 1.70: 9 1.70 - 1.82: 86 Bond restraints: 10758 Sorted by residual: bond pdb=" CA SER B 904 " pdb=" CB SER B 904 " ideal model delta sigma weight residual 1.528 1.491 0.038 1.56e-02 4.11e+03 5.89e+00 bond pdb=" CA SER A 607 " pdb=" CB SER A 607 " ideal model delta sigma weight residual 1.529 1.491 0.038 1.58e-02 4.01e+03 5.89e+00 bond pdb=" CA SER A 825 " pdb=" CB SER A 825 " ideal model delta sigma weight residual 1.530 1.489 0.041 1.68e-02 3.54e+03 5.85e+00 bond pdb=" CA SER B 559 " pdb=" CB SER B 559 " ideal model delta sigma weight residual 1.535 1.495 0.040 1.71e-02 3.42e+03 5.58e+00 bond pdb=" CE1 HIS A 665 " pdb=" NE2 HIS A 665 " ideal model delta sigma weight residual 1.321 1.344 -0.023 1.00e-02 1.00e+04 5.27e+00 ... (remaining 10753 not shown) Histogram of bond angle deviations from ideal: 99.08 - 106.12: 218 106.12 - 113.17: 5643 113.17 - 120.21: 4478 120.21 - 127.26: 4123 127.26 - 134.30: 62 Bond angle restraints: 14524 Sorted by residual: angle pdb=" PA ATP A2000 " pdb=" O3A ATP A2000 " pdb=" PB ATP A2000 " ideal model delta sigma weight residual 136.83 116.13 20.70 1.00e+00 1.00e+00 4.29e+02 angle pdb=" PA ATP B2000 " pdb=" O3A ATP B2000 " pdb=" PB ATP B2000 " ideal model delta sigma weight residual 136.83 117.40 19.43 1.00e+00 1.00e+00 3.77e+02 angle pdb=" PB ATP A2000 " pdb=" O3B ATP A2000 " pdb=" PG ATP A2000 " ideal model delta sigma weight residual 139.87 122.47 17.40 1.00e+00 1.00e+00 3.03e+02 angle pdb=" PB ATP B2000 " pdb=" O3B ATP B2000 " pdb=" PG ATP B2000 " ideal model delta sigma weight residual 139.87 123.91 15.96 1.00e+00 1.00e+00 2.55e+02 angle pdb=" C5' ATP B2000 " pdb=" O5' ATP B2000 " pdb=" PA ATP B2000 " ideal model delta sigma weight residual 121.27 110.88 10.39 1.00e+00 1.00e+00 1.08e+02 ... (remaining 14519 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.34: 5740 17.34 - 34.68: 645 34.68 - 52.02: 177 52.02 - 69.36: 47 69.36 - 86.70: 20 Dihedral angle restraints: 6629 sinusoidal: 2763 harmonic: 3866 Sorted by residual: dihedral pdb=" CA THR A 438 " pdb=" C THR A 438 " pdb=" N PRO A 439 " pdb=" CA PRO A 439 " ideal model delta harmonic sigma weight residual 180.00 155.65 24.35 0 5.00e+00 4.00e-02 2.37e+01 dihedral pdb=" CA GLY B 900 " pdb=" C GLY B 900 " pdb=" N GLY B 901 " pdb=" CA GLY B 901 " ideal model delta harmonic sigma weight residual -180.00 -157.06 -22.94 0 5.00e+00 4.00e-02 2.10e+01 dihedral pdb=" C LYS B 738 " pdb=" N LYS B 738 " pdb=" CA LYS B 738 " pdb=" CB LYS B 738 " ideal model delta harmonic sigma weight residual -122.60 -131.89 9.29 0 2.50e+00 1.60e-01 1.38e+01 ... (remaining 6626 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.064: 872 0.064 - 0.129: 599 0.129 - 0.193: 172 0.193 - 0.258: 26 0.258 - 0.322: 2 Chirality restraints: 1671 Sorted by residual: chirality pdb=" CA LYS B 738 " pdb=" N LYS B 738 " pdb=" C LYS B 738 " pdb=" CB LYS B 738 " both_signs ideal model delta sigma weight residual False 2.51 2.19 0.32 2.00e-01 2.50e+01 2.60e+00 chirality pdb=" CA THR A 438 " pdb=" N THR A 438 " pdb=" C THR A 438 " pdb=" CB THR A 438 " both_signs ideal model delta sigma weight residual False 2.53 2.24 0.29 2.00e-01 2.50e+01 2.10e+00 chirality pdb=" CA GLU A 878 " pdb=" N GLU A 878 " pdb=" C GLU A 878 " pdb=" CB GLU A 878 " both_signs ideal model delta sigma weight residual False 2.51 2.27 0.24 2.00e-01 2.50e+01 1.45e+00 ... (remaining 1668 not shown) Planarity restraints: 1844 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' ATP A2000 " -0.026 2.00e-02 2.50e+03 1.36e-02 5.06e+00 pdb=" C2 ATP A2000 " 0.013 2.00e-02 2.50e+03 pdb=" C4 ATP A2000 " 0.002 2.00e-02 2.50e+03 pdb=" C5 ATP A2000 " 0.004 2.00e-02 2.50e+03 pdb=" C6 ATP A2000 " 0.008 2.00e-02 2.50e+03 pdb=" C8 ATP A2000 " 0.017 2.00e-02 2.50e+03 pdb=" N1 ATP A2000 " 0.002 2.00e-02 2.50e+03 pdb=" N3 ATP A2000 " -0.003 2.00e-02 2.50e+03 pdb=" N6 ATP A2000 " -0.027 2.00e-02 2.50e+03 pdb=" N7 ATP A2000 " 0.006 2.00e-02 2.50e+03 pdb=" N9 ATP A2000 " 0.005 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA THR A 438 " 0.008 2.00e-02 2.50e+03 1.52e-02 2.32e+00 pdb=" C THR A 438 " -0.026 2.00e-02 2.50e+03 pdb=" O THR A 438 " 0.010 2.00e-02 2.50e+03 pdb=" N PRO A 439 " 0.009 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP B 579 " -0.017 2.00e-02 2.50e+03 8.69e-03 1.89e+00 pdb=" CG TRP B 579 " 0.017 2.00e-02 2.50e+03 pdb=" CD1 TRP B 579 " 0.001 2.00e-02 2.50e+03 pdb=" CD2 TRP B 579 " 0.007 2.00e-02 2.50e+03 pdb=" NE1 TRP B 579 " -0.003 2.00e-02 2.50e+03 pdb=" CE2 TRP B 579 " 0.004 2.00e-02 2.50e+03 pdb=" CE3 TRP B 579 " 0.003 2.00e-02 2.50e+03 pdb=" CZ2 TRP B 579 " -0.011 2.00e-02 2.50e+03 pdb=" CZ3 TRP B 579 " -0.001 2.00e-02 2.50e+03 pdb=" CH2 TRP B 579 " 0.001 2.00e-02 2.50e+03 ... (remaining 1841 not shown) Histogram of nonbonded interaction distances: 1.85 - 2.46: 50 2.46 - 3.07: 7318 3.07 - 3.68: 17371 3.68 - 4.29: 25295 4.29 - 4.90: 40702 Nonbonded interactions: 90736 Sorted by model distance: nonbonded pdb=" O2G ATP B2000 " pdb="MG MG B2001 " model vdw 1.847 2.170 nonbonded pdb=" OG SER A 676 " pdb="MG MG A2001 " model vdw 1.944 2.170 nonbonded pdb=" O2B ATP A2000 " pdb="MG MG A2001 " model vdw 1.946 2.170 nonbonded pdb=" OG SER B 903 " pdb="MG MG B2001 " model vdw 2.087 2.170 nonbonded pdb=" O2G ATP A2000 " pdb="MG MG A2001 " model vdw 2.109 2.170 ... (remaining 90731 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=0.50 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.880 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: 7.100 Check model and map are aligned: 0.140 Set scattering table: 0.100 Process input model: 39.080 Find NCS groups from input model: 0.320 Set up NCS constraints: 0.080 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:3.150 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 51.860 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7555 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 : 0.007 0.048 10758 Z= 0.439 Angle : 1.226 20.705 14524 Z= 0.856 Chirality : 0.084 0.322 1671 Planarity : 0.004 0.034 1844 Dihedral : 16.896 86.699 4115 Min Nonbonded Distance : 1.847 Molprobity Statistics. All-atom Clashscore : 16.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.29 % Favored : 92.71 % Rotamer: Outliers : 2.99 % Allowed : 13.48 % Favored : 83.53 % 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: -3.30 (0.20), residues: 1306 helix: -1.56 (0.17), residues: 704 sheet: -3.24 (0.39), residues: 120 loop : -2.66 (0.26), residues: 482 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.004 TRP B 579 HIS 0.013 0.002 HIS A 610 PHE 0.014 0.003 PHE A 836 TYR 0.018 0.003 TYR A 405 ARG 0.005 0.001 ARG A 680 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2612 Ramachandran restraints generated. 1306 Oldfield, 0 Emsley, 1306 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2612 Ramachandran restraints generated. 1306 Oldfield, 0 Emsley, 1306 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 350 residues out of total 1168 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 315 time to evaluate : 1.123 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 532 MET cc_start: 0.7284 (ttt) cc_final: 0.6885 (ttt) REVERT: B 534 PHE cc_start: 0.8237 (m-80) cc_final: 0.7665 (m-80) REVERT: B 554 MET cc_start: 0.8315 (mmt) cc_final: 0.7982 (mmm) REVERT: B 573 ARG cc_start: 0.7730 (ttt-90) cc_final: 0.7513 (ttt-90) REVERT: B 785 ILE cc_start: 0.7398 (mt) cc_final: 0.7172 (mt) REVERT: B 809 ASP cc_start: 0.7531 (t0) cc_final: 0.7185 (t0) REVERT: B 852 GLN cc_start: 0.8695 (mt0) cc_final: 0.8404 (mt0) REVERT: B 856 LYS cc_start: 0.8500 (tttt) cc_final: 0.8168 (tttp) REVERT: B 863 ARG cc_start: 0.7842 (mtm-85) cc_final: 0.7499 (ptp-110) REVERT: B 953 MET cc_start: 0.7906 (tpt) cc_final: 0.7360 (tpt) REVERT: B 1077 ASP cc_start: 0.7865 (t0) cc_final: 0.7524 (t0) REVERT: B 1084 LYS cc_start: 0.8295 (tptp) cc_final: 0.7989 (tptp) REVERT: A 172 LYS cc_start: 0.7389 (tttp) cc_final: 0.6874 (mmmt) REVERT: A 188 GLU cc_start: 0.7390 (tm-30) cc_final: 0.7181 (tm-30) REVERT: A 244 LEU cc_start: 0.7483 (tp) cc_final: 0.6730 (tp) REVERT: A 253 MET cc_start: 0.7023 (tpt) cc_final: 0.6002 (tpt) REVERT: A 350 LEU cc_start: 0.8175 (mt) cc_final: 0.7969 (mt) REVERT: A 351 MET cc_start: 0.8008 (mmm) cc_final: 0.7693 (tpp) REVERT: A 358 GLU cc_start: 0.8077 (tt0) cc_final: 0.7480 (pt0) REVERT: A 419 GLN cc_start: 0.8458 (tt0) cc_final: 0.8223 (tt0) REVERT: A 422 GLU cc_start: 0.8126 (mt-10) cc_final: 0.7904 (mt-10) REVERT: A 605 VAL cc_start: 0.8207 (t) cc_final: 0.7938 (m) REVERT: A 619 TYR cc_start: 0.8686 (m-10) cc_final: 0.8471 (m-10) REVERT: A 620 VAL cc_start: 0.8699 (t) cc_final: 0.8457 (m) REVERT: A 635 LYS cc_start: 0.8464 (mptt) cc_final: 0.8262 (mptt) REVERT: A 638 ARG cc_start: 0.7884 (mtt180) cc_final: 0.7606 (mtm-85) REVERT: A 720 LYS cc_start: 0.8235 (mttt) cc_final: 0.7986 (mttm) REVERT: A 726 MET cc_start: 0.8256 (tpp) cc_final: 0.7904 (tpp) REVERT: A 793 GLN cc_start: 0.8215 (mt0) cc_final: 0.7967 (mp10) REVERT: A 845 LYS cc_start: 0.8448 (mtpt) cc_final: 0.8228 (mtmm) outliers start: 35 outliers final: 22 residues processed: 341 average time/residue: 0.2769 time to fit residues: 124.6969 Evaluate side-chains 300 residues out of total 1168 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 278 time to evaluate : 1.179 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 607 VAL Chi-restraints excluded: chain B residue 671 VAL Chi-restraints excluded: chain B residue 673 LEU Chi-restraints excluded: chain B residue 744 TYR Chi-restraints excluded: chain B residue 777 VAL Chi-restraints excluded: chain B residue 781 HIS Chi-restraints excluded: chain B residue 799 LEU Chi-restraints excluded: chain B residue 817 HIS Chi-restraints excluded: chain B residue 939 MET Chi-restraints excluded: chain B residue 1025 VAL Chi-restraints excluded: chain B residue 1060 THR Chi-restraints excluded: chain A residue 148 VAL Chi-restraints excluded: chain A residue 270 LEU Chi-restraints excluded: chain A residue 280 LEU Chi-restraints excluded: chain A residue 293 THR Chi-restraints excluded: chain A residue 296 PHE Chi-restraints excluded: chain A residue 435 VAL Chi-restraints excluded: chain A residue 539 PHE Chi-restraints excluded: chain A residue 677 THR Chi-restraints excluded: chain A residue 807 THR Chi-restraints excluded: chain A residue 810 THR Chi-restraints excluded: chain A residue 851 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 131 random chunks: chunk 110 optimal weight: 0.6980 chunk 99 optimal weight: 0.9980 chunk 55 optimal weight: 0.8980 chunk 33 optimal weight: 0.6980 chunk 66 optimal weight: 0.2980 chunk 53 optimal weight: 0.8980 chunk 102 optimal weight: 0.7980 chunk 39 optimal weight: 0.9980 chunk 62 optimal weight: 0.5980 chunk 76 optimal weight: 0.5980 chunk 118 optimal weight: 0.8980 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 538 ASN B 549 GLN B 582 GLN B 613 ASN B 684 HIS ** B 729 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 852 GLN B 861 ASN ** B 917 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1071 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1098 ASN B1114 HIS ** A 186 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 239 GLN A 311 ASN A 343 ASN ** A 348 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 409 GLN ** A 424 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 462 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 538 ASN A 639 HIS ** A 662 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 681 GLN A 690 GLN A 718 GLN A 793 GLN ** A 798 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 879 GLN A 924 ASN Total number of N/Q/H flips: 21 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7504 moved from start: 0.1416 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 10758 Z= 0.255 Angle : 0.625 9.653 14524 Z= 0.324 Chirality : 0.043 0.262 1671 Planarity : 0.004 0.037 1844 Dihedral : 9.630 89.036 1511 Min Nonbonded Distance : 1.928 Molprobity Statistics. All-atom Clashscore : 16.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.60 % Favored : 95.40 % Rotamer: Outliers : 2.90 % Allowed : 20.90 % Favored : 76.19 % 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: -1.94 (0.22), residues: 1306 helix: -0.34 (0.19), residues: 698 sheet: -2.76 (0.40), residues: 120 loop : -2.18 (0.27), residues: 488 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP B 562 HIS 0.015 0.002 HIS B 614 PHE 0.035 0.002 PHE A 286 TYR 0.027 0.002 TYR A 815 ARG 0.008 0.001 ARG A 406 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2612 Ramachandran restraints generated. 1306 Oldfield, 0 Emsley, 1306 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2612 Ramachandran restraints generated. 1306 Oldfield, 0 Emsley, 1306 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 315 residues out of total 1168 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 281 time to evaluate : 1.216 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 532 MET cc_start: 0.7248 (ttt) cc_final: 0.6871 (ttt) REVERT: B 534 PHE cc_start: 0.8230 (m-80) cc_final: 0.7768 (m-80) REVERT: B 651 GLU cc_start: 0.8244 (tt0) cc_final: 0.7976 (tt0) REVERT: B 809 ASP cc_start: 0.7425 (t0) cc_final: 0.7050 (t0) REVERT: B 814 PHE cc_start: 0.8130 (t80) cc_final: 0.7852 (t80) REVERT: B 852 GLN cc_start: 0.8632 (mt0) cc_final: 0.8341 (mt0) REVERT: B 856 LYS cc_start: 0.8403 (tttt) cc_final: 0.8122 (tttp) REVERT: B 949 ARG cc_start: 0.7753 (mtm-85) cc_final: 0.7442 (mtm110) REVERT: B 1077 ASP cc_start: 0.7857 (t0) cc_final: 0.7438 (t0) REVERT: B 1084 LYS cc_start: 0.8233 (tptp) cc_final: 0.7853 (tptp) REVERT: B 1092 GLU cc_start: 0.8422 (tt0) cc_final: 0.7902 (mt-10) REVERT: A 172 LYS cc_start: 0.7394 (tttp) cc_final: 0.7089 (mmmt) REVERT: A 188 GLU cc_start: 0.7374 (tm-30) cc_final: 0.7087 (tm-30) REVERT: A 244 LEU cc_start: 0.7385 (tp) cc_final: 0.7117 (tp) REVERT: A 350 LEU cc_start: 0.8151 (mt) cc_final: 0.7949 (mt) REVERT: A 351 MET cc_start: 0.7936 (mmm) cc_final: 0.7623 (tpp) REVERT: A 358 GLU cc_start: 0.8092 (tt0) cc_final: 0.7547 (pt0) REVERT: A 359 ARG cc_start: 0.8375 (ttm170) cc_final: 0.8047 (mtt180) REVERT: A 620 VAL cc_start: 0.8644 (t) cc_final: 0.8409 (m) REVERT: A 638 ARG cc_start: 0.7726 (mtt180) cc_final: 0.7504 (mtm110) REVERT: A 691 ILE cc_start: 0.8063 (mt) cc_final: 0.7821 (tt) REVERT: A 702 VAL cc_start: 0.8944 (t) cc_final: 0.8727 (m) REVERT: A 726 MET cc_start: 0.8087 (tpp) cc_final: 0.7738 (tpp) REVERT: A 749 GLU cc_start: 0.7275 (pt0) cc_final: 0.6767 (pm20) REVERT: A 819 LYS cc_start: 0.8299 (tttm) cc_final: 0.8046 (tptt) REVERT: A 845 LYS cc_start: 0.8355 (mtpt) cc_final: 0.8068 (mtmm) outliers start: 34 outliers final: 20 residues processed: 305 average time/residue: 0.2778 time to fit residues: 113.0019 Evaluate side-chains 291 residues out of total 1168 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 271 time to evaluate : 1.163 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 585 LEU Chi-restraints excluded: chain B residue 587 LEU Chi-restraints excluded: chain B residue 607 VAL Chi-restraints excluded: chain B residue 642 VAL Chi-restraints excluded: chain B residue 644 THR Chi-restraints excluded: chain B residue 671 VAL Chi-restraints excluded: chain B residue 744 TYR Chi-restraints excluded: chain B residue 799 LEU Chi-restraints excluded: chain B residue 882 THR Chi-restraints excluded: chain B residue 1000 ASP Chi-restraints excluded: chain B residue 1025 VAL Chi-restraints excluded: chain A residue 148 VAL Chi-restraints excluded: chain A residue 317 VAL Chi-restraints excluded: chain A residue 463 VAL Chi-restraints excluded: chain A residue 677 THR Chi-restraints excluded: chain A residue 690 GLN Chi-restraints excluded: chain A residue 723 SER Chi-restraints excluded: chain A residue 732 THR Chi-restraints excluded: chain A residue 803 THR Chi-restraints excluded: chain A residue 810 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 131 random chunks: chunk 66 optimal weight: 2.9990 chunk 36 optimal weight: 0.9980 chunk 99 optimal weight: 0.9990 chunk 81 optimal weight: 1.9990 chunk 32 optimal weight: 0.9980 chunk 119 optimal weight: 0.2980 chunk 128 optimal weight: 0.2980 chunk 106 optimal weight: 0.2980 chunk 118 optimal weight: 0.6980 chunk 40 optimal weight: 0.9980 chunk 95 optimal weight: 6.9990 overall best weight: 0.5180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 684 HIS ** B 729 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 917 GLN ** B1071 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 186 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 239 GLN ** A 348 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 462 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 653 ASN A 681 GLN A 690 GLN A 718 GLN ** A 798 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7486 moved from start: 0.1816 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 10758 Z= 0.232 Angle : 0.593 7.828 14524 Z= 0.308 Chirality : 0.042 0.318 1671 Planarity : 0.004 0.038 1844 Dihedral : 8.658 83.944 1487 Min Nonbonded Distance : 1.935 Molprobity Statistics. All-atom Clashscore : 15.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.14 % Favored : 95.86 % Rotamer: Outliers : 2.90 % Allowed : 21.84 % Favored : 75.26 % 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: -1.42 (0.23), residues: 1306 helix: 0.14 (0.19), residues: 698 sheet: -2.53 (0.42), residues: 120 loop : -2.05 (0.27), residues: 488 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 764 HIS 0.009 0.001 HIS B 614 PHE 0.017 0.002 PHE B 814 TYR 0.022 0.002 TYR A 815 ARG 0.006 0.001 ARG A 406 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2612 Ramachandran restraints generated. 1306 Oldfield, 0 Emsley, 1306 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2612 Ramachandran restraints generated. 1306 Oldfield, 0 Emsley, 1306 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 309 residues out of total 1168 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 275 time to evaluate : 1.251 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 532 MET cc_start: 0.7243 (ttt) cc_final: 0.6852 (ttt) REVERT: B 534 PHE cc_start: 0.8182 (m-80) cc_final: 0.7667 (m-80) REVERT: B 636 GLN cc_start: 0.8398 (tp40) cc_final: 0.8197 (tp40) REVERT: B 651 GLU cc_start: 0.8144 (tt0) cc_final: 0.7750 (tt0) REVERT: B 753 MET cc_start: 0.1783 (ptt) cc_final: 0.0136 (ptt) REVERT: B 809 ASP cc_start: 0.7428 (t0) cc_final: 0.7034 (t0) REVERT: B 852 GLN cc_start: 0.8658 (mt0) cc_final: 0.8389 (mt0) REVERT: B 856 LYS cc_start: 0.8278 (tttt) cc_final: 0.8055 (tttp) REVERT: B 915 MET cc_start: 0.8466 (mtt) cc_final: 0.8252 (mtp) REVERT: B 917 GLN cc_start: 0.8180 (OUTLIER) cc_final: 0.7448 (mt0) REVERT: B 953 MET cc_start: 0.8070 (tpt) cc_final: 0.7864 (tpt) REVERT: B 1077 ASP cc_start: 0.7776 (t0) cc_final: 0.7328 (t0) REVERT: B 1084 LYS cc_start: 0.8182 (tptp) cc_final: 0.7773 (tptp) REVERT: A 172 LYS cc_start: 0.7396 (tttp) cc_final: 0.7008 (mtpt) REVERT: A 188 GLU cc_start: 0.7412 (tm-30) cc_final: 0.7120 (tm-30) REVERT: A 358 GLU cc_start: 0.8084 (tt0) cc_final: 0.7539 (pt0) REVERT: A 359 ARG cc_start: 0.8390 (ttm170) cc_final: 0.8037 (mtt180) REVERT: A 453 MET cc_start: 0.8077 (mtt) cc_final: 0.7869 (mtt) REVERT: A 620 VAL cc_start: 0.8655 (t) cc_final: 0.8420 (m) REVERT: A 702 VAL cc_start: 0.8918 (t) cc_final: 0.8715 (m) REVERT: A 726 MET cc_start: 0.8079 (tpp) cc_final: 0.7763 (tpp) REVERT: A 737 ARG cc_start: 0.8472 (ttp-110) cc_final: 0.8216 (mtm-85) REVERT: A 749 GLU cc_start: 0.7270 (pt0) cc_final: 0.6813 (pm20) REVERT: A 819 LYS cc_start: 0.8287 (tttm) cc_final: 0.8016 (tptt) REVERT: A 845 LYS cc_start: 0.8309 (mtpt) cc_final: 0.8030 (mtmm) outliers start: 34 outliers final: 23 residues processed: 297 average time/residue: 0.2768 time to fit residues: 110.1427 Evaluate side-chains 290 residues out of total 1168 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 266 time to evaluate : 1.143 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 552 THR Chi-restraints excluded: chain B residue 587 LEU Chi-restraints excluded: chain B residue 607 VAL Chi-restraints excluded: chain B residue 642 VAL Chi-restraints excluded: chain B residue 644 THR Chi-restraints excluded: chain B residue 666 ASP Chi-restraints excluded: chain B residue 671 VAL Chi-restraints excluded: chain B residue 673 LEU Chi-restraints excluded: chain B residue 744 TYR Chi-restraints excluded: chain B residue 882 THR Chi-restraints excluded: chain B residue 917 GLN Chi-restraints excluded: chain B residue 1025 VAL Chi-restraints excluded: chain A residue 148 VAL Chi-restraints excluded: chain A residue 293 THR Chi-restraints excluded: chain A residue 317 VAL Chi-restraints excluded: chain A residue 440 LEU Chi-restraints excluded: chain A residue 463 VAL Chi-restraints excluded: chain A residue 542 VAL Chi-restraints excluded: chain A residue 732 THR Chi-restraints excluded: chain A residue 742 ASP Chi-restraints excluded: chain A residue 803 THR Chi-restraints excluded: chain A residue 810 THR Chi-restraints excluded: chain A residue 818 LYS Chi-restraints excluded: chain A residue 851 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 131 random chunks: chunk 117 optimal weight: 0.5980 chunk 89 optimal weight: 2.9990 chunk 61 optimal weight: 0.6980 chunk 13 optimal weight: 0.0470 chunk 56 optimal weight: 10.0000 chunk 80 optimal weight: 0.0770 chunk 119 optimal weight: 0.0020 chunk 126 optimal weight: 9.9990 chunk 62 optimal weight: 3.9990 chunk 113 optimal weight: 2.9990 chunk 34 optimal weight: 0.7980 overall best weight: 0.2844 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 549 GLN B 684 HIS ** B 729 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 781 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 861 ASN B 917 GLN ** B1071 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1098 ASN ** A 186 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 348 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 462 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 510 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 653 ASN ** A 662 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 798 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7455 moved from start: 0.2175 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 10758 Z= 0.184 Angle : 0.569 8.240 14524 Z= 0.295 Chirality : 0.041 0.271 1671 Planarity : 0.004 0.039 1844 Dihedral : 8.204 80.013 1484 Min Nonbonded Distance : 1.958 Molprobity Statistics. All-atom Clashscore : 15.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.06 % Favored : 95.94 % Rotamer: Outliers : 3.16 % Allowed : 22.44 % Favored : 74.40 % 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: -1.06 (0.23), residues: 1306 helix: 0.48 (0.20), residues: 700 sheet: -2.46 (0.41), residues: 125 loop : -1.92 (0.27), residues: 481 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 764 HIS 0.009 0.001 HIS B 614 PHE 0.031 0.002 PHE B 814 TYR 0.021 0.002 TYR A 815 ARG 0.009 0.001 ARG B 779 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2612 Ramachandran restraints generated. 1306 Oldfield, 0 Emsley, 1306 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2612 Ramachandran restraints generated. 1306 Oldfield, 0 Emsley, 1306 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 303 residues out of total 1168 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 266 time to evaluate : 1.274 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 532 MET cc_start: 0.7216 (ttt) cc_final: 0.6804 (ttt) REVERT: B 534 PHE cc_start: 0.8101 (m-80) cc_final: 0.7550 (m-80) REVERT: B 555 LYS cc_start: 0.7978 (mtmm) cc_final: 0.7605 (mtmm) REVERT: B 586 LYS cc_start: 0.7702 (mmmm) cc_final: 0.7500 (mmpt) REVERT: B 636 GLN cc_start: 0.8377 (tp40) cc_final: 0.8163 (tp40) REVERT: B 651 GLU cc_start: 0.8076 (tt0) cc_final: 0.7722 (tt0) REVERT: B 809 ASP cc_start: 0.7402 (t0) cc_final: 0.6993 (t0) REVERT: B 852 GLN cc_start: 0.8649 (mt0) cc_final: 0.8379 (mt0) REVERT: B 917 GLN cc_start: 0.8112 (OUTLIER) cc_final: 0.7097 (mt0) REVERT: B 953 MET cc_start: 0.8051 (tpt) cc_final: 0.7193 (tpt) REVERT: B 1084 LYS cc_start: 0.8140 (tptp) cc_final: 0.7722 (tptp) REVERT: B 1092 GLU cc_start: 0.8378 (mt-10) cc_final: 0.8039 (mt-10) REVERT: B 1103 ARG cc_start: 0.7645 (mtt180) cc_final: 0.7215 (mtt-85) REVERT: A 172 LYS cc_start: 0.7337 (tttp) cc_final: 0.7090 (mmtt) REVERT: A 188 GLU cc_start: 0.7417 (tm-30) cc_final: 0.7119 (tm-30) REVERT: A 358 GLU cc_start: 0.8114 (tt0) cc_final: 0.7565 (pt0) REVERT: A 359 ARG cc_start: 0.8390 (ttm170) cc_final: 0.8065 (mtt180) REVERT: A 393 LYS cc_start: 0.7842 (mttt) cc_final: 0.7403 (mtpp) REVERT: A 666 ILE cc_start: 0.8153 (mm) cc_final: 0.7690 (mt) REVERT: A 691 ILE cc_start: 0.8073 (OUTLIER) cc_final: 0.7861 (tt) REVERT: A 702 VAL cc_start: 0.8888 (t) cc_final: 0.8684 (m) REVERT: A 726 MET cc_start: 0.8014 (tpp) cc_final: 0.7735 (tpp) REVERT: A 737 ARG cc_start: 0.8404 (ttp-110) cc_final: 0.8193 (mtm-85) REVERT: A 845 LYS cc_start: 0.8280 (mtpt) cc_final: 0.7971 (mtmm) REVERT: A 846 GLN cc_start: 0.7766 (mp10) cc_final: 0.7474 (mp10) outliers start: 37 outliers final: 25 residues processed: 285 average time/residue: 0.2787 time to fit residues: 106.4263 Evaluate side-chains 285 residues out of total 1168 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 258 time to evaluate : 1.246 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 552 THR Chi-restraints excluded: chain B residue 587 LEU Chi-restraints excluded: chain B residue 607 VAL Chi-restraints excluded: chain B residue 644 THR Chi-restraints excluded: chain B residue 666 ASP Chi-restraints excluded: chain B residue 671 VAL Chi-restraints excluded: chain B residue 673 LEU Chi-restraints excluded: chain B residue 702 LEU Chi-restraints excluded: chain B residue 744 TYR Chi-restraints excluded: chain B residue 882 THR Chi-restraints excluded: chain B residue 917 GLN Chi-restraints excluded: chain B residue 965 LYS Chi-restraints excluded: chain B residue 1000 ASP Chi-restraints excluded: chain B residue 1025 VAL Chi-restraints excluded: chain B residue 1094 GLU Chi-restraints excluded: chain A residue 293 THR Chi-restraints excluded: chain A residue 317 VAL Chi-restraints excluded: chain A residue 440 LEU Chi-restraints excluded: chain A residue 463 VAL Chi-restraints excluded: chain A residue 526 THR Chi-restraints excluded: chain A residue 539 PHE Chi-restraints excluded: chain A residue 542 VAL Chi-restraints excluded: chain A residue 691 ILE Chi-restraints excluded: chain A residue 720 LYS Chi-restraints excluded: chain A residue 742 ASP Chi-restraints excluded: chain A residue 807 THR Chi-restraints excluded: chain A residue 851 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 131 random chunks: chunk 105 optimal weight: 1.9990 chunk 71 optimal weight: 0.9980 chunk 1 optimal weight: 0.7980 chunk 94 optimal weight: 1.9990 chunk 52 optimal weight: 2.9990 chunk 108 optimal weight: 0.5980 chunk 87 optimal weight: 3.9990 chunk 0 optimal weight: 1.9990 chunk 64 optimal weight: 0.0040 chunk 113 optimal weight: 2.9990 chunk 31 optimal weight: 0.5980 overall best weight: 0.5992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 549 GLN B 684 HIS ** B 729 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 781 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 861 ASN B 917 GLN ** B1071 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1088 HIS B1098 ASN ** A 186 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 239 GLN ** A 348 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 462 GLN ** A 510 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 653 ASN ** A 662 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 798 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7474 moved from start: 0.2266 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 10758 Z= 0.240 Angle : 0.571 8.110 14524 Z= 0.298 Chirality : 0.042 0.248 1671 Planarity : 0.004 0.040 1844 Dihedral : 8.175 83.951 1482 Min Nonbonded Distance : 1.909 Molprobity Statistics. All-atom Clashscore : 15.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.14 % Favored : 95.86 % Rotamer: Outliers : 3.41 % Allowed : 22.53 % Favored : 74.06 % 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 (0.23), residues: 1306 helix: 0.55 (0.20), residues: 701 sheet: -2.35 (0.42), residues: 131 loop : -1.79 (0.28), residues: 474 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 807 HIS 0.008 0.001 HIS B 614 PHE 0.024 0.002 PHE B 814 TYR 0.020 0.002 TYR A 678 ARG 0.009 0.001 ARG B 779 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2612 Ramachandran restraints generated. 1306 Oldfield, 0 Emsley, 1306 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2612 Ramachandran restraints generated. 1306 Oldfield, 0 Emsley, 1306 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 314 residues out of total 1168 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 274 time to evaluate : 1.223 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 532 MET cc_start: 0.7216 (ttt) cc_final: 0.6805 (ttt) REVERT: B 534 PHE cc_start: 0.8119 (m-80) cc_final: 0.7581 (m-80) REVERT: B 555 LYS cc_start: 0.8002 (mtmm) cc_final: 0.7637 (mtmm) REVERT: B 636 GLN cc_start: 0.8376 (tp40) cc_final: 0.8158 (tp40) REVERT: B 651 GLU cc_start: 0.8063 (tt0) cc_final: 0.7724 (tt0) REVERT: B 779 ARG cc_start: 0.6866 (mmm-85) cc_final: 0.6528 (mmm-85) REVERT: B 809 ASP cc_start: 0.7446 (t0) cc_final: 0.7032 (t0) REVERT: B 852 GLN cc_start: 0.8675 (mt0) cc_final: 0.8400 (mt0) REVERT: B 856 LYS cc_start: 0.8291 (tttp) cc_final: 0.7929 (tttt) REVERT: B 917 GLN cc_start: 0.8109 (OUTLIER) cc_final: 0.7108 (mt0) REVERT: B 1084 LYS cc_start: 0.8142 (tptp) cc_final: 0.7721 (tptp) REVERT: B 1092 GLU cc_start: 0.8395 (mt-10) cc_final: 0.7942 (mt-10) REVERT: B 1103 ARG cc_start: 0.7668 (mtt180) cc_final: 0.7219 (mtt-85) REVERT: A 172 LYS cc_start: 0.7431 (tttp) cc_final: 0.7057 (mtpt) REVERT: A 188 GLU cc_start: 0.7432 (tm-30) cc_final: 0.7147 (tm-30) REVERT: A 358 GLU cc_start: 0.8092 (tt0) cc_final: 0.7569 (pt0) REVERT: A 389 ARG cc_start: 0.8574 (ttt180) cc_final: 0.8272 (ttp-110) REVERT: A 393 LYS cc_start: 0.7856 (mttt) cc_final: 0.7432 (mtpp) REVERT: A 666 ILE cc_start: 0.8228 (mm) cc_final: 0.7742 (mt) REVERT: A 691 ILE cc_start: 0.8085 (OUTLIER) cc_final: 0.7843 (tt) REVERT: A 726 MET cc_start: 0.7920 (tpp) cc_final: 0.7640 (tpp) REVERT: A 749 GLU cc_start: 0.7267 (pt0) cc_final: 0.6807 (pm20) REVERT: A 768 GLU cc_start: 0.7735 (OUTLIER) cc_final: 0.7339 (pp20) REVERT: A 793 GLN cc_start: 0.8206 (mt0) cc_final: 0.7866 (tt0) REVERT: A 845 LYS cc_start: 0.8308 (mtpt) cc_final: 0.8006 (mtmm) REVERT: A 846 GLN cc_start: 0.7817 (OUTLIER) cc_final: 0.7518 (mp10) outliers start: 40 outliers final: 32 residues processed: 295 average time/residue: 0.2750 time to fit residues: 108.4447 Evaluate side-chains 300 residues out of total 1168 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 264 time to evaluate : 1.198 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 552 THR Chi-restraints excluded: chain B residue 565 ASP Chi-restraints excluded: chain B residue 577 LYS Chi-restraints excluded: chain B residue 585 LEU Chi-restraints excluded: chain B residue 587 LEU Chi-restraints excluded: chain B residue 644 THR Chi-restraints excluded: chain B residue 666 ASP Chi-restraints excluded: chain B residue 671 VAL Chi-restraints excluded: chain B residue 673 LEU Chi-restraints excluded: chain B residue 702 LEU Chi-restraints excluded: chain B residue 744 TYR Chi-restraints excluded: chain B residue 794 GLN Chi-restraints excluded: chain B residue 882 THR Chi-restraints excluded: chain B residue 917 GLN Chi-restraints excluded: chain B residue 925 GLU Chi-restraints excluded: chain B residue 965 LYS Chi-restraints excluded: chain B residue 1000 ASP Chi-restraints excluded: chain B residue 1025 VAL Chi-restraints excluded: chain A residue 148 VAL Chi-restraints excluded: chain A residue 293 THR Chi-restraints excluded: chain A residue 317 VAL Chi-restraints excluded: chain A residue 440 LEU Chi-restraints excluded: chain A residue 463 VAL Chi-restraints excluded: chain A residue 526 THR Chi-restraints excluded: chain A residue 539 PHE Chi-restraints excluded: chain A residue 542 VAL Chi-restraints excluded: chain A residue 691 ILE Chi-restraints excluded: chain A residue 723 SER Chi-restraints excluded: chain A residue 741 LYS Chi-restraints excluded: chain A residue 742 ASP Chi-restraints excluded: chain A residue 768 GLU Chi-restraints excluded: chain A residue 802 VAL Chi-restraints excluded: chain A residue 807 THR Chi-restraints excluded: chain A residue 810 THR Chi-restraints excluded: chain A residue 846 GLN Chi-restraints excluded: chain A residue 851 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 131 random chunks: chunk 42 optimal weight: 0.9980 chunk 114 optimal weight: 1.9990 chunk 25 optimal weight: 0.5980 chunk 74 optimal weight: 0.8980 chunk 31 optimal weight: 0.7980 chunk 126 optimal weight: 6.9990 chunk 105 optimal weight: 0.9990 chunk 58 optimal weight: 0.0470 chunk 10 optimal weight: 1.9990 chunk 41 optimal weight: 1.9990 chunk 66 optimal weight: 2.9990 overall best weight: 0.6678 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 549 GLN B 684 HIS ** B 729 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 781 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 917 GLN ** B1071 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 186 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 239 GLN ** A 348 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 510 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 662 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 798 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7478 moved from start: 0.2370 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 10758 Z= 0.257 Angle : 0.580 7.994 14524 Z= 0.302 Chirality : 0.042 0.234 1671 Planarity : 0.004 0.040 1844 Dihedral : 8.188 85.099 1481 Min Nonbonded Distance : 1.899 Molprobity Statistics. All-atom Clashscore : 16.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.99 % Favored : 96.01 % Rotamer: Outliers : 3.92 % Allowed : 22.44 % Favored : 73.63 % 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 (0.23), residues: 1306 helix: 0.53 (0.19), residues: 699 sheet: -2.28 (0.42), residues: 126 loop : -1.74 (0.28), residues: 481 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 807 HIS 0.008 0.001 HIS B 614 PHE 0.022 0.002 PHE B 814 TYR 0.023 0.002 TYR A 815 ARG 0.006 0.001 ARG B 779 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2612 Ramachandran restraints generated. 1306 Oldfield, 0 Emsley, 1306 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2612 Ramachandran restraints generated. 1306 Oldfield, 0 Emsley, 1306 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 316 residues out of total 1168 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 270 time to evaluate : 1.184 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 532 MET cc_start: 0.7235 (ttt) cc_final: 0.6802 (ttt) REVERT: B 534 PHE cc_start: 0.8128 (m-80) cc_final: 0.7601 (m-80) REVERT: B 636 GLN cc_start: 0.8369 (tp40) cc_final: 0.8148 (tp40) REVERT: B 651 GLU cc_start: 0.8019 (tt0) cc_final: 0.7759 (tt0) REVERT: B 809 ASP cc_start: 0.7462 (t0) cc_final: 0.7054 (t0) REVERT: B 852 GLN cc_start: 0.8678 (mt0) cc_final: 0.8394 (mt0) REVERT: B 856 LYS cc_start: 0.8222 (tttp) cc_final: 0.7890 (tttt) REVERT: B 917 GLN cc_start: 0.8145 (OUTLIER) cc_final: 0.7122 (mt0) REVERT: B 977 LEU cc_start: 0.8311 (tt) cc_final: 0.8069 (tp) REVERT: B 1084 LYS cc_start: 0.8142 (tptp) cc_final: 0.7721 (tptp) REVERT: A 172 LYS cc_start: 0.7476 (tttp) cc_final: 0.7109 (mtpt) REVERT: A 188 GLU cc_start: 0.7455 (tm-30) cc_final: 0.7181 (tm-30) REVERT: A 358 GLU cc_start: 0.8064 (tt0) cc_final: 0.7582 (pt0) REVERT: A 389 ARG cc_start: 0.8601 (ttt180) cc_final: 0.8302 (ttp-110) REVERT: A 393 LYS cc_start: 0.7849 (mttt) cc_final: 0.7429 (mtpp) REVERT: A 437 VAL cc_start: 0.6960 (OUTLIER) cc_final: 0.6624 (p) REVERT: A 666 ILE cc_start: 0.8234 (mm) cc_final: 0.7807 (mt) REVERT: A 726 MET cc_start: 0.7910 (tpp) cc_final: 0.7620 (tpp) REVERT: A 793 GLN cc_start: 0.8279 (mt0) cc_final: 0.7925 (tt0) REVERT: A 845 LYS cc_start: 0.8313 (mtpt) cc_final: 0.8009 (mtmm) REVERT: A 846 GLN cc_start: 0.7816 (OUTLIER) cc_final: 0.7492 (mp10) outliers start: 46 outliers final: 39 residues processed: 294 average time/residue: 0.2655 time to fit residues: 104.8922 Evaluate side-chains 307 residues out of total 1168 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 265 time to evaluate : 1.153 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 552 THR Chi-restraints excluded: chain B residue 565 ASP Chi-restraints excluded: chain B residue 577 LYS Chi-restraints excluded: chain B residue 585 LEU Chi-restraints excluded: chain B residue 587 LEU Chi-restraints excluded: chain B residue 607 VAL Chi-restraints excluded: chain B residue 644 THR Chi-restraints excluded: chain B residue 666 ASP Chi-restraints excluded: chain B residue 671 VAL Chi-restraints excluded: chain B residue 673 LEU Chi-restraints excluded: chain B residue 702 LEU Chi-restraints excluded: chain B residue 744 TYR Chi-restraints excluded: chain B residue 794 GLN Chi-restraints excluded: chain B residue 799 LEU Chi-restraints excluded: chain B residue 882 THR Chi-restraints excluded: chain B residue 917 GLN Chi-restraints excluded: chain B residue 925 GLU Chi-restraints excluded: chain B residue 965 LYS Chi-restraints excluded: chain B residue 1000 ASP Chi-restraints excluded: chain B residue 1025 VAL Chi-restraints excluded: chain B residue 1072 VAL Chi-restraints excluded: chain A residue 148 VAL Chi-restraints excluded: chain A residue 293 THR Chi-restraints excluded: chain A residue 317 VAL Chi-restraints excluded: chain A residue 437 VAL Chi-restraints excluded: chain A residue 440 LEU Chi-restraints excluded: chain A residue 463 VAL Chi-restraints excluded: chain A residue 526 THR Chi-restraints excluded: chain A residue 539 PHE Chi-restraints excluded: chain A residue 542 VAL Chi-restraints excluded: chain A residue 691 ILE Chi-restraints excluded: chain A residue 702 VAL Chi-restraints excluded: chain A residue 723 SER Chi-restraints excluded: chain A residue 741 LYS Chi-restraints excluded: chain A residue 742 ASP Chi-restraints excluded: chain A residue 802 VAL Chi-restraints excluded: chain A residue 807 THR Chi-restraints excluded: chain A residue 810 THR Chi-restraints excluded: chain A residue 815 TYR Chi-restraints excluded: chain A residue 819 LYS Chi-restraints excluded: chain A residue 846 GLN Chi-restraints excluded: chain A residue 851 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 131 random chunks: chunk 122 optimal weight: 1.9990 chunk 14 optimal weight: 0.9980 chunk 72 optimal weight: 0.4980 chunk 92 optimal weight: 0.0070 chunk 71 optimal weight: 0.8980 chunk 106 optimal weight: 0.6980 chunk 70 optimal weight: 1.9990 chunk 126 optimal weight: 7.9990 chunk 79 optimal weight: 0.0670 chunk 76 optimal weight: 1.9990 chunk 58 optimal weight: 0.9980 overall best weight: 0.4336 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 549 GLN B 684 HIS ** B 729 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 781 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 917 GLN ** B1071 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 186 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 239 GLN ** A 348 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 510 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 662 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 798 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7455 moved from start: 0.2514 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 10758 Z= 0.210 Angle : 0.573 8.291 14524 Z= 0.295 Chirality : 0.041 0.219 1671 Planarity : 0.004 0.039 1844 Dihedral : 7.995 82.818 1481 Min Nonbonded Distance : 1.936 Molprobity Statistics. All-atom Clashscore : 15.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.99 % Favored : 96.01 % Rotamer: Outliers : 3.84 % Allowed : 23.04 % Favored : 73.12 % 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: -0.76 (0.23), residues: 1306 helix: 0.65 (0.19), residues: 701 sheet: -2.27 (0.42), residues: 135 loop : -1.65 (0.28), residues: 470 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 764 HIS 0.009 0.001 HIS B 614 PHE 0.019 0.002 PHE B 814 TYR 0.023 0.002 TYR A 678 ARG 0.006 0.001 ARG B 779 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2612 Ramachandran restraints generated. 1306 Oldfield, 0 Emsley, 1306 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2612 Ramachandran restraints generated. 1306 Oldfield, 0 Emsley, 1306 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 309 residues out of total 1168 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 264 time to evaluate : 1.063 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 532 MET cc_start: 0.7219 (ttt) cc_final: 0.6790 (ttt) REVERT: B 534 PHE cc_start: 0.8120 (m-80) cc_final: 0.7581 (m-80) REVERT: B 651 GLU cc_start: 0.7922 (tt0) cc_final: 0.7673 (tt0) REVERT: B 809 ASP cc_start: 0.7476 (t0) cc_final: 0.7049 (t0) REVERT: B 852 GLN cc_start: 0.8668 (mt0) cc_final: 0.8447 (mt0) REVERT: B 856 LYS cc_start: 0.8172 (tttp) cc_final: 0.7836 (tttt) REVERT: B 977 LEU cc_start: 0.8309 (tt) cc_final: 0.8078 (tp) REVERT: B 1091 LYS cc_start: 0.8026 (mttt) cc_final: 0.7755 (mmtm) REVERT: A 172 LYS cc_start: 0.7464 (tttp) cc_final: 0.7088 (mtpp) REVERT: A 188 GLU cc_start: 0.7450 (tm-30) cc_final: 0.7177 (tm-30) REVERT: A 311 ASN cc_start: 0.7677 (m-40) cc_final: 0.7461 (t0) REVERT: A 358 GLU cc_start: 0.8046 (tt0) cc_final: 0.7579 (pt0) REVERT: A 393 LYS cc_start: 0.7779 (mttt) cc_final: 0.7362 (mtpp) REVERT: A 437 VAL cc_start: 0.6772 (OUTLIER) cc_final: 0.6485 (p) REVERT: A 726 MET cc_start: 0.7913 (tpp) cc_final: 0.7636 (tpp) REVERT: A 749 GLU cc_start: 0.7289 (pt0) cc_final: 0.6835 (pm20) REVERT: A 779 MET cc_start: 0.7705 (mmt) cc_final: 0.7498 (mmm) REVERT: A 793 GLN cc_start: 0.8244 (mt0) cc_final: 0.7926 (tt0) REVERT: A 845 LYS cc_start: 0.8290 (mtpt) cc_final: 0.7988 (mtmm) REVERT: A 846 GLN cc_start: 0.7774 (OUTLIER) cc_final: 0.7439 (mp10) outliers start: 45 outliers final: 35 residues processed: 290 average time/residue: 0.2739 time to fit residues: 106.6535 Evaluate side-chains 298 residues out of total 1168 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 261 time to evaluate : 1.236 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 552 THR Chi-restraints excluded: chain B residue 565 ASP Chi-restraints excluded: chain B residue 585 LEU Chi-restraints excluded: chain B residue 587 LEU Chi-restraints excluded: chain B residue 607 VAL Chi-restraints excluded: chain B residue 642 VAL Chi-restraints excluded: chain B residue 644 THR Chi-restraints excluded: chain B residue 666 ASP Chi-restraints excluded: chain B residue 671 VAL Chi-restraints excluded: chain B residue 673 LEU Chi-restraints excluded: chain B residue 680 SER Chi-restraints excluded: chain B residue 744 TYR Chi-restraints excluded: chain B residue 794 GLN Chi-restraints excluded: chain B residue 799 LEU Chi-restraints excluded: chain B residue 882 THR Chi-restraints excluded: chain B residue 917 GLN Chi-restraints excluded: chain B residue 965 LYS Chi-restraints excluded: chain B residue 1000 ASP Chi-restraints excluded: chain B residue 1025 VAL Chi-restraints excluded: chain A residue 148 VAL Chi-restraints excluded: chain A residue 293 THR Chi-restraints excluded: chain A residue 317 VAL Chi-restraints excluded: chain A residue 437 VAL Chi-restraints excluded: chain A residue 440 LEU Chi-restraints excluded: chain A residue 463 VAL Chi-restraints excluded: chain A residue 526 THR Chi-restraints excluded: chain A residue 539 PHE Chi-restraints excluded: chain A residue 542 VAL Chi-restraints excluded: chain A residue 702 VAL Chi-restraints excluded: chain A residue 723 SER Chi-restraints excluded: chain A residue 741 LYS Chi-restraints excluded: chain A residue 742 ASP Chi-restraints excluded: chain A residue 802 VAL Chi-restraints excluded: chain A residue 810 THR Chi-restraints excluded: chain A residue 819 LYS Chi-restraints excluded: chain A residue 846 GLN Chi-restraints excluded: chain A residue 851 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 131 random chunks: chunk 78 optimal weight: 0.8980 chunk 50 optimal weight: 1.9990 chunk 75 optimal weight: 0.2980 chunk 38 optimal weight: 0.9990 chunk 24 optimal weight: 7.9990 chunk 80 optimal weight: 0.0050 chunk 86 optimal weight: 1.9990 chunk 62 optimal weight: 0.0970 chunk 11 optimal weight: 1.9990 chunk 99 optimal weight: 0.7980 chunk 114 optimal weight: 1.9990 overall best weight: 0.4192 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 684 HIS B 729 HIS ** B 781 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 917 GLN ** A 186 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 239 GLN ** A 348 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 510 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 596 ASN ** A 662 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 798 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7448 moved from start: 0.2654 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 10758 Z= 0.211 Angle : 0.591 15.729 14524 Z= 0.300 Chirality : 0.041 0.209 1671 Planarity : 0.004 0.039 1844 Dihedral : 7.913 84.432 1481 Min Nonbonded Distance : 1.926 Molprobity Statistics. All-atom Clashscore : 15.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.06 % Favored : 95.94 % Rotamer: Outliers : 3.84 % Allowed : 23.21 % Favored : 72.95 % 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: -0.67 (0.23), residues: 1306 helix: 0.70 (0.19), residues: 700 sheet: -2.20 (0.42), residues: 135 loop : -1.59 (0.28), residues: 471 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 764 HIS 0.008 0.001 HIS B 614 PHE 0.019 0.001 PHE B 814 TYR 0.023 0.002 TYR A 678 ARG 0.005 0.001 ARG B 779 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2612 Ramachandran restraints generated. 1306 Oldfield, 0 Emsley, 1306 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2612 Ramachandran restraints generated. 1306 Oldfield, 0 Emsley, 1306 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 313 residues out of total 1168 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 268 time to evaluate : 1.044 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 532 MET cc_start: 0.7223 (ttt) cc_final: 0.6791 (ttt) REVERT: B 534 PHE cc_start: 0.8117 (m-80) cc_final: 0.7615 (m-80) REVERT: B 651 GLU cc_start: 0.7882 (tt0) cc_final: 0.7564 (tt0) REVERT: B 809 ASP cc_start: 0.7482 (t0) cc_final: 0.7059 (t0) REVERT: B 852 GLN cc_start: 0.8656 (mt0) cc_final: 0.8437 (mt0) REVERT: B 856 LYS cc_start: 0.8144 (tttp) cc_final: 0.7803 (tttt) REVERT: B 881 ASN cc_start: 0.8011 (m-40) cc_final: 0.7790 (m-40) REVERT: B 1091 LYS cc_start: 0.8039 (mttt) cc_final: 0.7784 (mmtm) REVERT: B 1092 GLU cc_start: 0.8327 (mt-10) cc_final: 0.8083 (mt-10) REVERT: A 172 LYS cc_start: 0.7490 (tttp) cc_final: 0.7017 (mtpt) REVERT: A 188 GLU cc_start: 0.7439 (tm-30) cc_final: 0.7167 (tm-30) REVERT: A 358 GLU cc_start: 0.8042 (tt0) cc_final: 0.7584 (pt0) REVERT: A 393 LYS cc_start: 0.7772 (mttt) cc_final: 0.7350 (mtpp) REVERT: A 437 VAL cc_start: 0.6804 (OUTLIER) cc_final: 0.6522 (p) REVERT: A 749 GLU cc_start: 0.7277 (pt0) cc_final: 0.6825 (pm20) REVERT: A 768 GLU cc_start: 0.7564 (OUTLIER) cc_final: 0.7189 (pp20) REVERT: A 769 TYR cc_start: 0.8304 (t80) cc_final: 0.7849 (t80) REVERT: A 779 MET cc_start: 0.7706 (mmt) cc_final: 0.7451 (tpp) REVERT: A 793 GLN cc_start: 0.8283 (mt0) cc_final: 0.7960 (tt0) REVERT: A 845 LYS cc_start: 0.8281 (mtpt) cc_final: 0.7978 (mtmm) REVERT: A 846 GLN cc_start: 0.7765 (OUTLIER) cc_final: 0.7435 (mp10) outliers start: 45 outliers final: 35 residues processed: 295 average time/residue: 0.2668 time to fit residues: 105.3710 Evaluate side-chains 295 residues out of total 1168 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 257 time to evaluate : 1.266 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 552 THR Chi-restraints excluded: chain B residue 565 ASP Chi-restraints excluded: chain B residue 577 LYS Chi-restraints excluded: chain B residue 585 LEU Chi-restraints excluded: chain B residue 587 LEU Chi-restraints excluded: chain B residue 607 VAL Chi-restraints excluded: chain B residue 644 THR Chi-restraints excluded: chain B residue 666 ASP Chi-restraints excluded: chain B residue 671 VAL Chi-restraints excluded: chain B residue 673 LEU Chi-restraints excluded: chain B residue 680 SER Chi-restraints excluded: chain B residue 794 GLN Chi-restraints excluded: chain B residue 799 LEU Chi-restraints excluded: chain B residue 882 THR Chi-restraints excluded: chain B residue 1000 ASP Chi-restraints excluded: chain B residue 1025 VAL Chi-restraints excluded: chain A residue 148 VAL Chi-restraints excluded: chain A residue 210 MET Chi-restraints excluded: chain A residue 293 THR Chi-restraints excluded: chain A residue 317 VAL Chi-restraints excluded: chain A residue 437 VAL Chi-restraints excluded: chain A residue 440 LEU Chi-restraints excluded: chain A residue 463 VAL Chi-restraints excluded: chain A residue 526 THR Chi-restraints excluded: chain A residue 539 PHE Chi-restraints excluded: chain A residue 542 VAL Chi-restraints excluded: chain A residue 596 ASN Chi-restraints excluded: chain A residue 702 VAL Chi-restraints excluded: chain A residue 720 LYS Chi-restraints excluded: chain A residue 723 SER Chi-restraints excluded: chain A residue 741 LYS Chi-restraints excluded: chain A residue 742 ASP Chi-restraints excluded: chain A residue 768 GLU Chi-restraints excluded: chain A residue 802 VAL Chi-restraints excluded: chain A residue 810 THR Chi-restraints excluded: chain A residue 819 LYS Chi-restraints excluded: chain A residue 846 GLN Chi-restraints excluded: chain A residue 851 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 131 random chunks: chunk 120 optimal weight: 0.6980 chunk 110 optimal weight: 1.9990 chunk 117 optimal weight: 2.9990 chunk 70 optimal weight: 0.4980 chunk 51 optimal weight: 1.9990 chunk 92 optimal weight: 4.9990 chunk 36 optimal weight: 0.9990 chunk 106 optimal weight: 0.6980 chunk 111 optimal weight: 0.9990 chunk 77 optimal weight: 0.1980 chunk 124 optimal weight: 0.9980 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 538 ASN ** B 781 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 880 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 917 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1027 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1098 ASN ** A 186 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 239 GLN ** A 348 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 596 ASN ** A 662 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 798 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7451 moved from start: 0.2672 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.144 10758 Z= 0.294 Angle : 0.858 59.200 14524 Z= 0.500 Chirality : 0.045 0.678 1671 Planarity : 0.004 0.039 1844 Dihedral : 7.890 84.479 1479 Min Nonbonded Distance : 1.660 Molprobity Statistics. All-atom Clashscore : 17.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.99 % Favored : 96.01 % Rotamer: Outliers : 3.24 % Allowed : 23.81 % Favored : 72.95 % Cbeta Deviations : 0.08 % 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: -0.67 (0.23), residues: 1306 helix: 0.70 (0.19), residues: 700 sheet: -2.19 (0.42), residues: 135 loop : -1.59 (0.28), residues: 471 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 764 HIS 0.008 0.001 HIS B 614 PHE 0.023 0.002 PHE B 936 TYR 0.021 0.002 TYR A 678 ARG 0.015 0.001 ARG A 638 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2612 Ramachandran restraints generated. 1306 Oldfield, 0 Emsley, 1306 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2612 Ramachandran restraints generated. 1306 Oldfield, 0 Emsley, 1306 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 302 residues out of total 1168 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 264 time to evaluate : 1.249 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 532 MET cc_start: 0.7222 (ttt) cc_final: 0.6785 (ttt) REVERT: B 534 PHE cc_start: 0.8128 (m-80) cc_final: 0.7603 (m-80) REVERT: B 651 GLU cc_start: 0.7887 (tt0) cc_final: 0.7566 (tt0) REVERT: B 809 ASP cc_start: 0.7483 (t0) cc_final: 0.7061 (t0) REVERT: B 852 GLN cc_start: 0.8659 (mt0) cc_final: 0.8440 (mt0) REVERT: B 856 LYS cc_start: 0.8139 (tttp) cc_final: 0.7804 (tttt) REVERT: B 881 ASN cc_start: 0.8020 (m-40) cc_final: 0.7796 (m-40) REVERT: B 1091 LYS cc_start: 0.8043 (mttt) cc_final: 0.7783 (mmtm) REVERT: B 1092 GLU cc_start: 0.8321 (mt-10) cc_final: 0.8083 (mt-10) REVERT: A 172 LYS cc_start: 0.7492 (tttp) cc_final: 0.7020 (mtpt) REVERT: A 188 GLU cc_start: 0.7442 (tm-30) cc_final: 0.7205 (tm-30) REVERT: A 286 PHE cc_start: 0.7564 (m-80) cc_final: 0.7165 (t80) REVERT: A 311 ASN cc_start: 0.7666 (m-40) cc_final: 0.7451 (t0) REVERT: A 358 GLU cc_start: 0.8043 (tt0) cc_final: 0.7585 (pt0) REVERT: A 393 LYS cc_start: 0.7783 (mttt) cc_final: 0.7359 (mtpp) REVERT: A 437 VAL cc_start: 0.6811 (OUTLIER) cc_final: 0.6528 (p) REVERT: A 749 GLU cc_start: 0.7277 (pt0) cc_final: 0.6825 (pm20) REVERT: A 768 GLU cc_start: 0.7559 (OUTLIER) cc_final: 0.7183 (pp20) REVERT: A 769 TYR cc_start: 0.8302 (t80) cc_final: 0.7847 (t80) REVERT: A 779 MET cc_start: 0.7713 (mmt) cc_final: 0.7447 (tpp) REVERT: A 793 GLN cc_start: 0.8285 (mt0) cc_final: 0.7960 (tt0) REVERT: A 845 LYS cc_start: 0.8280 (mtpt) cc_final: 0.7978 (mtmm) REVERT: A 846 GLN cc_start: 0.7765 (OUTLIER) cc_final: 0.7440 (mp10) outliers start: 38 outliers final: 34 residues processed: 287 average time/residue: 0.2692 time to fit residues: 103.5512 Evaluate side-chains 300 residues out of total 1168 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 263 time to evaluate : 1.218 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 552 THR Chi-restraints excluded: chain B residue 565 ASP Chi-restraints excluded: chain B residue 577 LYS Chi-restraints excluded: chain B residue 585 LEU Chi-restraints excluded: chain B residue 587 LEU Chi-restraints excluded: chain B residue 607 VAL Chi-restraints excluded: chain B residue 644 THR Chi-restraints excluded: chain B residue 666 ASP Chi-restraints excluded: chain B residue 671 VAL Chi-restraints excluded: chain B residue 673 LEU Chi-restraints excluded: chain B residue 680 SER Chi-restraints excluded: chain B residue 794 GLN Chi-restraints excluded: chain B residue 799 LEU Chi-restraints excluded: chain B residue 882 THR Chi-restraints excluded: chain B residue 1000 ASP Chi-restraints excluded: chain B residue 1025 VAL Chi-restraints excluded: chain A residue 148 VAL Chi-restraints excluded: chain A residue 293 THR Chi-restraints excluded: chain A residue 317 VAL Chi-restraints excluded: chain A residue 437 VAL Chi-restraints excluded: chain A residue 440 LEU Chi-restraints excluded: chain A residue 463 VAL Chi-restraints excluded: chain A residue 526 THR Chi-restraints excluded: chain A residue 539 PHE Chi-restraints excluded: chain A residue 542 VAL Chi-restraints excluded: chain A residue 596 ASN Chi-restraints excluded: chain A residue 702 VAL Chi-restraints excluded: chain A residue 720 LYS Chi-restraints excluded: chain A residue 723 SER Chi-restraints excluded: chain A residue 741 LYS Chi-restraints excluded: chain A residue 742 ASP Chi-restraints excluded: chain A residue 768 GLU Chi-restraints excluded: chain A residue 802 VAL Chi-restraints excluded: chain A residue 810 THR Chi-restraints excluded: chain A residue 819 LYS Chi-restraints excluded: chain A residue 846 GLN Chi-restraints excluded: chain A residue 851 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 131 random chunks: chunk 75 optimal weight: 0.3980 chunk 59 optimal weight: 1.9990 chunk 86 optimal weight: 0.2980 chunk 130 optimal weight: 0.8980 chunk 120 optimal weight: 0.0030 chunk 103 optimal weight: 0.8980 chunk 10 optimal weight: 0.6980 chunk 80 optimal weight: 2.9990 chunk 63 optimal weight: 4.9990 chunk 82 optimal weight: 0.5980 chunk 110 optimal weight: 2.9990 overall best weight: 0.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 781 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 880 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 917 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1027 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1098 ASN ** A 186 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 239 GLN ** A 348 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 596 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 662 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 798 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7451 moved from start: 0.2685 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.172 10758 Z= 0.298 Angle : 0.692 23.780 14524 Z= 0.410 Chirality : 0.044 0.581 1671 Planarity : 0.004 0.074 1844 Dihedral : 7.890 84.479 1479 Min Nonbonded Distance : 1.660 Molprobity Statistics. All-atom Clashscore : 18.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.99 % Favored : 96.01 % Rotamer: Outliers : 3.16 % Allowed : 23.89 % Favored : 72.95 % Cbeta Deviations : 0.08 % 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: -0.67 (0.23), residues: 1306 helix: 0.70 (0.19), residues: 700 sheet: -2.19 (0.42), residues: 135 loop : -1.59 (0.28), residues: 471 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 764 HIS 0.008 0.001 HIS B 614 PHE 0.023 0.002 PHE B 936 TYR 0.021 0.002 TYR A 678 ARG 0.015 0.001 ARG A 638 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2612 Ramachandran restraints generated. 1306 Oldfield, 0 Emsley, 1306 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2612 Ramachandran restraints generated. 1306 Oldfield, 0 Emsley, 1306 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 299 residues out of total 1168 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 262 time to evaluate : 1.206 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 532 MET cc_start: 0.7221 (ttt) cc_final: 0.6786 (ttt) REVERT: B 534 PHE cc_start: 0.8124 (m-80) cc_final: 0.7603 (m-80) REVERT: B 651 GLU cc_start: 0.7887 (tt0) cc_final: 0.7565 (tt0) REVERT: B 809 ASP cc_start: 0.7483 (t0) cc_final: 0.7061 (t0) REVERT: B 852 GLN cc_start: 0.8659 (mt0) cc_final: 0.8440 (mt0) REVERT: B 856 LYS cc_start: 0.8139 (tttp) cc_final: 0.7804 (tttt) REVERT: B 881 ASN cc_start: 0.8019 (m-40) cc_final: 0.7796 (m-40) REVERT: B 1091 LYS cc_start: 0.8043 (mttt) cc_final: 0.7783 (mmtm) REVERT: B 1092 GLU cc_start: 0.8322 (mt-10) cc_final: 0.8083 (mt-10) REVERT: A 172 LYS cc_start: 0.7492 (tttp) cc_final: 0.7020 (mtpt) REVERT: A 188 GLU cc_start: 0.7481 (tm-30) cc_final: 0.7205 (tm-30) REVERT: A 286 PHE cc_start: 0.7565 (m-80) cc_final: 0.7165 (t80) REVERT: A 311 ASN cc_start: 0.7666 (m-40) cc_final: 0.7450 (t0) REVERT: A 358 GLU cc_start: 0.8042 (tt0) cc_final: 0.7585 (pt0) REVERT: A 393 LYS cc_start: 0.7784 (mttt) cc_final: 0.7354 (mtpp) REVERT: A 437 VAL cc_start: 0.6811 (OUTLIER) cc_final: 0.6529 (p) REVERT: A 749 GLU cc_start: 0.7275 (pt0) cc_final: 0.6825 (pm20) REVERT: A 768 GLU cc_start: 0.7559 (OUTLIER) cc_final: 0.7183 (pp20) REVERT: A 769 TYR cc_start: 0.8302 (t80) cc_final: 0.7847 (t80) REVERT: A 779 MET cc_start: 0.7712 (mmt) cc_final: 0.7447 (tpp) REVERT: A 793 GLN cc_start: 0.8285 (mt0) cc_final: 0.7951 (tt0) REVERT: A 845 LYS cc_start: 0.8280 (mtpt) cc_final: 0.7978 (mtmm) REVERT: A 846 GLN cc_start: 0.7766 (OUTLIER) cc_final: 0.7440 (mp10) outliers start: 37 outliers final: 33 residues processed: 285 average time/residue: 0.2650 time to fit residues: 101.7159 Evaluate side-chains 298 residues out of total 1168 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 262 time to evaluate : 1.241 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 552 THR Chi-restraints excluded: chain B residue 565 ASP Chi-restraints excluded: chain B residue 577 LYS Chi-restraints excluded: chain B residue 585 LEU Chi-restraints excluded: chain B residue 587 LEU Chi-restraints excluded: chain B residue 607 VAL Chi-restraints excluded: chain B residue 644 THR Chi-restraints excluded: chain B residue 666 ASP Chi-restraints excluded: chain B residue 671 VAL Chi-restraints excluded: chain B residue 673 LEU Chi-restraints excluded: chain B residue 680 SER Chi-restraints excluded: chain B residue 794 GLN Chi-restraints excluded: chain B residue 799 LEU Chi-restraints excluded: chain B residue 882 THR Chi-restraints excluded: chain B residue 1000 ASP Chi-restraints excluded: chain B residue 1025 VAL Chi-restraints excluded: chain A residue 148 VAL Chi-restraints excluded: chain A residue 293 THR Chi-restraints excluded: chain A residue 317 VAL Chi-restraints excluded: chain A residue 437 VAL Chi-restraints excluded: chain A residue 440 LEU Chi-restraints excluded: chain A residue 463 VAL Chi-restraints excluded: chain A residue 526 THR Chi-restraints excluded: chain A residue 539 PHE Chi-restraints excluded: chain A residue 542 VAL Chi-restraints excluded: chain A residue 702 VAL Chi-restraints excluded: chain A residue 720 LYS Chi-restraints excluded: chain A residue 723 SER Chi-restraints excluded: chain A residue 741 LYS Chi-restraints excluded: chain A residue 742 ASP Chi-restraints excluded: chain A residue 768 GLU Chi-restraints excluded: chain A residue 802 VAL Chi-restraints excluded: chain A residue 810 THR Chi-restraints excluded: chain A residue 819 LYS Chi-restraints excluded: chain A residue 846 GLN Chi-restraints excluded: chain A residue 851 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 131 random chunks: chunk 31 optimal weight: 0.6980 chunk 95 optimal weight: 9.9990 chunk 15 optimal weight: 0.9980 chunk 28 optimal weight: 0.5980 chunk 104 optimal weight: 0.6980 chunk 43 optimal weight: 0.7980 chunk 106 optimal weight: 0.9990 chunk 13 optimal weight: 3.9990 chunk 19 optimal weight: 3.9990 chunk 91 optimal weight: 0.9990 chunk 5 optimal weight: 0.6980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 781 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1027 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1071 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1098 ASN ** A 186 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 239 GLN ** A 348 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 596 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 662 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 798 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4328 r_free = 0.4328 target = 0.181052 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3924 r_free = 0.3924 target = 0.147590 restraints weight = 30396.578| |-----------------------------------------------------------------------------| r_work (start): 0.3894 rms_B_bonded: 3.65 r_work: 0.3712 rms_B_bonded: 4.09 restraints_weight: 0.5000 r_work (final): 0.3712 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3716 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3716 r_free = 0.3716 target_work(ls_wunit_k1) = 0.131 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3715 r_free = 0.3715 target_work(ls_wunit_k1) = 0.131 | | occupancies: max = 1.00 min = 0.33 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3715 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7122 moved from start: 0.2691 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.070 10758 Z= 0.274 Angle : 0.623 16.447 14524 Z= 0.318 Chirality : 0.043 0.199 1671 Planarity : 0.004 0.041 1844 Dihedral : 8.085 89.699 1479 Min Nonbonded Distance : 1.883 Molprobity Statistics. All-atom Clashscore : 17.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.22 % Favored : 95.78 % Rotamer: Outliers : 3.16 % Allowed : 23.72 % Favored : 73.12 % 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: -0.74 (0.23), residues: 1306 helix: 0.60 (0.19), residues: 702 sheet: -2.15 (0.42), residues: 134 loop : -1.55 (0.29), residues: 470 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 764 HIS 0.008 0.001 HIS B 614 PHE 0.032 0.002 PHE A 760 TYR 0.025 0.002 TYR A 815 ARG 0.006 0.001 ARG B 779 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3093.57 seconds wall clock time: 56 minutes 8.80 seconds (3368.80 seconds total)