Starting phenix.real_space_refine on Thu Feb 15 03:20:46 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8d1v_27138/02_2024/8d1v_27138.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8d1v_27138/02_2024/8d1v_27138.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.82 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8d1v_27138/02_2024/8d1v_27138.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8d1v_27138/02_2024/8d1v_27138.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8d1v_27138/02_2024/8d1v_27138.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8d1v_27138/02_2024/8d1v_27138.pdb" } resolution = 2.82 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.003 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 7 Type Number sf(0) Gaussians Zn 4 6.06 5 P 51 5.49 5 S 47 5.16 5 C 6729 2.51 5 N 1965 2.21 5 O 2177 1.98 5 H 9 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A TYR 122": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 161": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 197": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 280": "OE1" <-> "OE2" Residue "A ASP 311": "OD1" <-> "OD2" Residue "A TYR 458": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 492": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 507": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 543": "OD1" <-> "OD2" Residue "A ASP 581": "OD1" <-> "OD2" Residue "A PHE 714": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 725": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 851": "OD1" <-> "OD2" Residue "A TYR 866": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 930": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 958": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 970": "OD1" <-> "OD2" Residue "A PHE 1348": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 1367": "OD1" <-> "OD2" Residue "A PHE 1540": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 10982 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 9875 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1229, 9875 Classifications: {'peptide': 1229} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'CIS': 4, 'PTRANS': 69, 'TRANS': 1155} Chain breaks: 5 Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 10 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 Chain: "J" Number of atoms: 716 Number of conformers: 1 Conformer: "" Number of residues, atoms: 34, 716 Classifications: {'RNA': 34} Modifications used: {'5*END': 1, 'rna2p_pur': 12, 'rna2p_pyr': 7, 'rna3p_pur': 4, 'rna3p_pyr': 11} Link IDs: {'rna2p': 19, 'rna3p': 14} Chain: "N" Number of atoms: 387 Number of conformers: 1 Conformer: "" Number of residues, atoms: 18, 387 Classifications: {'RNA': 18} Modifications used: {'rna2p_pur': 2, 'rna2p_pyr': 4, 'rna3p_pur': 9, 'rna3p_pyr': 3} Link IDs: {'rna2p': 6, 'rna3p': 11} Chain: "A" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 4 Unusual residues: {' ZN': 4} Classifications: {'undetermined': 4} Link IDs: {None: 3} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 7389 SG CYS A 965 52.610 79.489 34.405 1.00 16.18 S ATOM 7646 SG CYS A1312 54.788 76.398 34.787 1.00 42.26 S ATOM 7776 SG CYS A1342 56.145 79.835 35.770 1.00 16.46 S ATOM 7794 SG CYS A1345 53.703 78.265 37.918 1.00 42.76 S ATOM 5323 SG CYS A 706 67.274 57.736 63.303 1.00 64.50 S ATOM 5338 SG CYS A 708 66.711 61.546 63.496 1.00 47.76 S ATOM 5360 SG CYS A 711 63.819 58.979 64.304 1.00 40.08 S ATOM 3404 SG CYS A 463 56.018 42.763 85.262 1.00 49.22 S ATOM 3466 SG CYS A 472 56.667 39.772 87.611 1.00 43.87 S ATOM 3480 SG CYS A 474 56.786 43.428 88.933 1.00 31.88 S ATOM 3502 SG CYS A 477 53.532 41.954 87.701 1.00 37.68 S ATOM 704 SG CYS A 86 41.398 20.116 105.052 1.00 54.15 S ATOM 950 SG CYS A 115 39.201 17.399 106.531 1.00 59.03 S ATOM 1012 SG CYS A 123 37.966 21.095 106.260 1.00 59.56 S ATOM 1036 SG CYS A 126 38.414 19.054 103.155 1.00 54.26 S Time building chain proxies: 5.83, per 1000 atoms: 0.53 Number of scatterers: 10982 At special positions: 0 Unit cell: (84.66, 126.99, 124.5, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Zn 4 29.99 S 47 16.00 P 51 15.00 O 2177 8.00 N 1965 7.00 C 6729 6.00 H 9 1.00 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: 6.39 Conformation dependent library (CDL) restraints added in 8.7 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A1701 " pdb="ZN ZN A1701 " - pdb=" SG CYS A1312 " pdb="ZN ZN A1701 " - pdb=" SG CYS A1345 " pdb="ZN ZN A1701 " - pdb=" SG CYS A 965 " pdb="ZN ZN A1701 " - pdb=" SG CYS A1342 " pdb=" ZN A1702 " pdb="ZN ZN A1702 " - pdb=" ND1 HIS A 703 " pdb="ZN ZN A1702 " - pdb=" SG CYS A 706 " pdb="ZN ZN A1702 " - pdb=" SG CYS A 711 " pdb="ZN ZN A1702 " - pdb=" SG CYS A 708 " pdb=" ZN A1703 " pdb="ZN ZN A1703 " - pdb=" SG CYS A 477 " pdb="ZN ZN A1703 " - pdb=" SG CYS A 463 " pdb="ZN ZN A1703 " - pdb=" SG CYS A 474 " pdb="ZN ZN A1703 " - pdb=" SG CYS A 472 " pdb=" ZN A1704 " pdb="ZN ZN A1704 " - pdb=" SG CYS A 86 " pdb="ZN ZN A1704 " - pdb=" SG CYS A 126 " pdb="ZN ZN A1704 " - pdb=" SG CYS A 123 " pdb="ZN ZN A1704 " - pdb=" SG CYS A 115 " Number of angles added : 21 2434 Ramachandran restraints generated. 1217 Oldfield, 0 Emsley, 1217 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2272 Finding SS restraints... Secondary structure from input PDB file: 39 helices and 17 sheets defined 30.8% alpha, 25.1% beta 10 base pairs and 15 stacking pairs defined. Time for finding SS restraints: 2.98 Creating SS restraints... Processing helix chain 'A' and resid 30 through 36 Processing helix chain 'A' and resid 37 through 39 No H-bonds generated for 'chain 'A' and resid 37 through 39' Processing helix chain 'A' and resid 57 through 76 Processing helix chain 'A' and resid 123 through 130 Processing helix chain 'A' and resid 163 through 167 removed outlier: 3.990A pdb=" N ILE A 167 " --> pdb=" O GLY A 163 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 163 through 167' Processing helix chain 'A' and resid 211 through 225 Processing helix chain 'A' and resid 260 through 276 removed outlier: 3.678A pdb=" N ALA A 266 " --> pdb=" O ALA A 262 " (cutoff:3.500A) Processing helix chain 'A' and resid 281 through 291 Processing helix chain 'A' and resid 292 through 295 Processing helix chain 'A' and resid 328 through 337 Processing helix chain 'A' and resid 344 through 366 Processing helix chain 'A' and resid 443 through 460 Processing helix chain 'A' and resid 474 through 481 Processing helix chain 'A' and resid 542 through 554 removed outlier: 3.585A pdb=" N THR A 547 " --> pdb=" O ASP A 543 " (cutoff:3.500A) Processing helix chain 'A' and resid 562 through 566 Processing helix chain 'A' and resid 584 through 594 Processing helix chain 'A' and resid 595 through 598 Processing helix chain 'A' and resid 599 through 610 removed outlier: 4.431A pdb=" N GLU A 604 " --> pdb=" O GLU A 600 " (cutoff:3.500A) removed outlier: 4.690A pdb=" N GLU A 605 " --> pdb=" O LYS A 601 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N ARG A 609 " --> pdb=" O GLU A 605 " (cutoff:3.500A) Processing helix chain 'A' and resid 642 through 649 removed outlier: 3.578A pdb=" N ALA A 646 " --> pdb=" O ASP A 642 " (cutoff:3.500A) Processing helix chain 'A' and resid 675 through 691 removed outlier: 3.839A pdb=" N ILE A 690 " --> pdb=" O ALA A 686 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N HIS A 691 " --> pdb=" O VAL A 687 " (cutoff:3.500A) Processing helix chain 'A' and resid 710 through 715 Processing helix chain 'A' and resid 780 through 784 Processing helix chain 'A' and resid 785 through 801 Processing helix chain 'A' and resid 809 through 813 Processing helix chain 'A' and resid 829 through 833 Processing helix chain 'A' and resid 920 through 924 removed outlier: 3.559A pdb=" N ARG A 924 " --> pdb=" O LYS A 921 " (cutoff:3.500A) Processing helix chain 'A' and resid 946 through 962 removed outlier: 3.712A pdb=" N VAL A 957 " --> pdb=" O MET A 953 " (cutoff:3.500A) Processing helix chain 'A' and resid 1300 through 1304 Processing helix chain 'A' and resid 1331 through 1336 Processing helix chain 'A' and resid 1342 through 1348 Processing helix chain 'A' and resid 1395 through 1400 removed outlier: 3.604A pdb=" N SER A1399 " --> pdb=" O ARG A1395 " (cutoff:3.500A) Processing helix chain 'A' and resid 1420 through 1426 Processing helix chain 'A' and resid 1464 through 1476 Processing helix chain 'A' and resid 1488 through 1492 Processing helix chain 'A' and resid 1518 through 1535 Processing helix chain 'A' and resid 1538 through 1549 Processing helix chain 'A' and resid 1565 through 1569 Processing helix chain 'A' and resid 1575 through 1582 removed outlier: 3.872A pdb=" N ASP A1581 " --> pdb=" O GLU A1577 " (cutoff:3.500A) Processing helix chain 'A' and resid 1588 through 1594 Processing sheet with id=AA1, first strand: chain 'A' and resid 148 through 150 Processing sheet with id=AA2, first strand: chain 'A' and resid 15 through 17 removed outlier: 3.807A pdb=" N ASP A 185 " --> pdb=" O ARG A 175 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N SER A 169 " --> pdb=" O GLU A 191 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 41 through 44 Processing sheet with id=AA4, first strand: chain 'A' and resid 106 through 107 removed outlier: 6.138A pdb=" N THR A 106 " --> pdb=" O VAL A 395 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'A' and resid 483 through 485 removed outlier: 4.992A pdb=" N GLU A 409 " --> pdb=" O ASN A 574 " (cutoff:3.500A) removed outlier: 5.288A pdb=" N ASN A 574 " --> pdb=" O GLU A 409 " (cutoff:3.500A) removed outlier: 6.744A pdb=" N VAL A 411 " --> pdb=" O MET A 572 " (cutoff:3.500A) removed outlier: 5.607A pdb=" N MET A 572 " --> pdb=" O VAL A 411 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 483 through 485 removed outlier: 4.992A pdb=" N GLU A 409 " --> pdb=" O ASN A 574 " (cutoff:3.500A) removed outlier: 5.288A pdb=" N ASN A 574 " --> pdb=" O GLU A 409 " (cutoff:3.500A) removed outlier: 6.744A pdb=" N VAL A 411 " --> pdb=" O MET A 572 " (cutoff:3.500A) removed outlier: 5.607A pdb=" N MET A 572 " --> pdb=" O VAL A 411 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 441 through 442 Processing sheet with id=AA8, first strand: chain 'A' and resid 497 through 504 removed outlier: 5.593A pdb=" N ALA A 515 " --> pdb=" O ARG A 503 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 659 through 664 removed outlier: 3.557A pdb=" N GLU A 667 " --> pdb=" O GLU A 664 " (cutoff:3.500A) removed outlier: 7.434A pdb=" N CYS A 672 " --> pdb=" O PHE A 730 " (cutoff:3.500A) removed outlier: 4.068A pdb=" N PHE A 730 " --> pdb=" O CYS A 672 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 659 through 664 removed outlier: 3.557A pdb=" N GLU A 667 " --> pdb=" O GLU A 664 " (cutoff:3.500A) removed outlier: 7.434A pdb=" N CYS A 672 " --> pdb=" O PHE A 730 " (cutoff:3.500A) removed outlier: 4.068A pdb=" N PHE A 730 " --> pdb=" O CYS A 672 " (cutoff:3.500A) removed outlier: 6.512A pdb=" N SER A 631 " --> pdb=" O LEU A 820 " (cutoff:3.500A) removed outlier: 4.342A pdb=" N LEU A 820 " --> pdb=" O SER A 631 " (cutoff:3.500A) removed outlier: 6.749A pdb=" N GLU A 633 " --> pdb=" O LYS A 818 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 739 through 744 removed outlier: 6.310A pdb=" N LYS A 755 " --> pdb=" O ALA A 743 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 836 through 837 removed outlier: 6.943A pdb=" N ALA A 836 " --> pdb=" O TRP A1512 " (cutoff:3.500A) removed outlier: 8.852A pdb=" N ASN A1514 " --> pdb=" O ALA A 836 " (cutoff:3.500A) removed outlier: 6.685A pdb=" N ARG A 896 " --> pdb=" O GLU A1501 " (cutoff:3.500A) removed outlier: 4.595A pdb=" N VAL A1503 " --> pdb=" O LYS A 894 " (cutoff:3.500A) removed outlier: 6.725A pdb=" N LYS A 894 " --> pdb=" O VAL A1503 " (cutoff:3.500A) removed outlier: 4.533A pdb=" N LEU A1505 " --> pdb=" O THR A 892 " (cutoff:3.500A) removed outlier: 7.013A pdb=" N THR A 892 " --> pdb=" O LEU A1505 " (cutoff:3.500A) removed outlier: 5.411A pdb=" N LEU A 891 " --> pdb=" O ASN A1462 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 944 through 945 removed outlier: 5.411A pdb=" N LEU A 891 " --> pdb=" O ASN A1462 " (cutoff:3.500A) removed outlier: 7.013A pdb=" N THR A 892 " --> pdb=" O LEU A1505 " (cutoff:3.500A) removed outlier: 4.533A pdb=" N LEU A1505 " --> pdb=" O THR A 892 " (cutoff:3.500A) removed outlier: 6.725A pdb=" N LYS A 894 " --> pdb=" O VAL A1503 " (cutoff:3.500A) removed outlier: 4.595A pdb=" N VAL A1503 " --> pdb=" O LYS A 894 " (cutoff:3.500A) removed outlier: 6.685A pdb=" N ARG A 896 " --> pdb=" O GLU A1501 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 861 through 862 Processing sheet with id=AB6, first strand: chain 'A' and resid 865 through 868 Processing sheet with id=AB7, first strand: chain 'A' and resid 908 through 909 removed outlier: 4.284A pdb=" N ALA A 935 " --> pdb=" O ASP A 909 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'A' and resid 932 through 933 removed outlier: 6.952A pdb=" N LYS A 932 " --> pdb=" O THR A1444 " (cutoff:3.500A) removed outlier: 8.849A pdb=" N GLU A1446 " --> pdb=" O LYS A 932 " (cutoff:3.500A) removed outlier: 4.359A pdb=" N ARG A1443 " --> pdb=" O LEU A1388 " (cutoff:3.500A) 383 hydrogen bonds defined for protein. 1053 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 22 hydrogen bonds 44 hydrogen bond angles 0 basepair planarities 10 basepair parallelities 15 stacking parallelities Total time for adding SS restraints: 4.10 Time building geometry restraints manager: 4.12 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.86 - 1.05: 9 1.05 - 1.24: 1339 1.24 - 1.43: 3607 1.43 - 1.62: 6313 1.62 - 1.81: 68 Bond restraints: 11336 Sorted by residual: bond pdb=" CB PRO A 114 " pdb=" CG PRO A 114 " ideal model delta sigma weight residual 1.492 1.095 0.397 5.00e-02 4.00e+02 6.31e+01 bond pdb=" N PRO A 114 " pdb=" CD PRO A 114 " ideal model delta sigma weight residual 1.473 1.384 0.089 1.40e-02 5.10e+03 4.05e+01 bond pdb=" CA PRO A 114 " pdb=" CB PRO A 114 " ideal model delta sigma weight residual 1.533 1.606 -0.073 1.47e-02 4.63e+03 2.46e+01 bond pdb=" CB ASP A1536 " pdb=" CG ASP A1536 " ideal model delta sigma weight residual 1.516 1.549 -0.033 2.50e-02 1.60e+03 1.69e+00 bond pdb=" N LYS A 827 " pdb=" CA LYS A 827 " ideal model delta sigma weight residual 1.457 1.474 -0.016 1.29e-02 6.01e+03 1.62e+00 ... (remaining 11331 not shown) Histogram of bond angle deviations from ideal: 84.08 - 96.18: 4 96.18 - 108.27: 1025 108.27 - 120.37: 9847 120.37 - 132.47: 4614 132.47 - 144.57: 36 Bond angle restraints: 15526 Sorted by residual: angle pdb=" CA PRO A 114 " pdb=" N PRO A 114 " pdb=" CD PRO A 114 " ideal model delta sigma weight residual 112.00 87.63 24.37 1.40e+00 5.10e-01 3.03e+02 angle pdb=" N PRO A 114 " pdb=" CD PRO A 114 " pdb=" CG PRO A 114 " ideal model delta sigma weight residual 103.20 86.02 17.18 1.50e+00 4.44e-01 1.31e+02 angle pdb=" CA PRO A 114 " pdb=" CB PRO A 114 " pdb=" CG PRO A 114 " ideal model delta sigma weight residual 104.50 84.08 20.42 1.90e+00 2.77e-01 1.16e+02 angle pdb=" C GLU A 877 " pdb=" N GLU A 878 " pdb=" CA GLU A 878 " ideal model delta sigma weight residual 121.70 136.07 -14.37 1.80e+00 3.09e-01 6.37e+01 angle pdb=" CB PRO A 114 " pdb=" CG PRO A 114 " pdb=" CD PRO A 114 " ideal model delta sigma weight residual 106.10 88.47 17.63 3.20e+00 9.77e-02 3.04e+01 ... (remaining 15521 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.97: 6690 35.97 - 71.94: 215 71.94 - 107.90: 28 107.90 - 143.87: 0 143.87 - 179.84: 4 Dihedral angle restraints: 6937 sinusoidal: 3408 harmonic: 3529 Sorted by residual: dihedral pdb=" O4' C J 8 " pdb=" C1' C J 8 " pdb=" N1 C J 8 " pdb=" C2 C J 8 " ideal model delta sinusoidal sigma weight residual -160.00 14.71 -174.71 1 1.50e+01 4.44e-03 8.52e+01 dihedral pdb=" O4' C J 10 " pdb=" C1' C J 10 " pdb=" N1 C J 10 " pdb=" C2 C J 10 " ideal model delta sinusoidal sigma weight residual 232.00 70.80 161.20 1 1.70e+01 3.46e-03 6.47e+01 dihedral pdb=" CA GLY A 824 " pdb=" C GLY A 824 " pdb=" N ASP A 825 " pdb=" CA ASP A 825 " ideal model delta harmonic sigma weight residual 180.00 147.16 32.84 0 5.00e+00 4.00e-02 4.31e+01 ... (remaining 6934 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.047: 1300 0.047 - 0.093: 286 0.093 - 0.140: 83 0.140 - 0.187: 3 0.187 - 0.234: 1 Chirality restraints: 1673 Sorted by residual: chirality pdb=" C3' A N 6 " pdb=" C4' A N 6 " pdb=" O3' A N 6 " pdb=" C2' A N 6 " both_signs ideal model delta sigma weight residual False -2.74 -2.51 -0.23 2.00e-01 2.50e+01 1.37e+00 chirality pdb=" C1' G N 7 " pdb=" O4' G N 7 " pdb=" C2' G N 7 " pdb=" N9 G N 7 " both_signs ideal model delta sigma weight residual False 2.46 2.28 0.18 2.00e-01 2.50e+01 8.09e-01 chirality pdb=" C3' C N 8 " pdb=" C4' C N 8 " pdb=" O3' C N 8 " pdb=" C2' C N 8 " both_signs ideal model delta sigma weight residual False -2.74 -2.57 -0.17 2.00e-01 2.50e+01 7.23e-01 ... (remaining 1670 not shown) Planarity restraints: 1829 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASN A 113 " -0.062 5.00e-02 4.00e+02 8.24e-02 1.09e+01 pdb=" N PRO A 114 " 0.141 5.00e-02 4.00e+02 pdb=" CA PRO A 114 " -0.029 5.00e-02 4.00e+02 pdb=" CD PRO A 114 " -0.050 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C1' U J 24 " -0.032 2.00e-02 2.50e+03 1.72e-02 6.66e+00 pdb=" N1 U J 24 " 0.036 2.00e-02 2.50e+03 pdb=" C2 U J 24 " -0.001 2.00e-02 2.50e+03 pdb=" O2 U J 24 " -0.000 2.00e-02 2.50e+03 pdb=" N3 U J 24 " 0.009 2.00e-02 2.50e+03 pdb=" C4 U J 24 " -0.006 2.00e-02 2.50e+03 pdb=" O4 U J 24 " -0.013 2.00e-02 2.50e+03 pdb=" C5 U J 24 " -0.001 2.00e-02 2.50e+03 pdb=" C6 U J 24 " 0.009 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASP A 825 " 0.009 2.00e-02 2.50e+03 1.85e-02 3.43e+00 pdb=" C ASP A 825 " -0.032 2.00e-02 2.50e+03 pdb=" O ASP A 825 " 0.012 2.00e-02 2.50e+03 pdb=" N ASP A 826 " 0.011 2.00e-02 2.50e+03 ... (remaining 1826 not shown) Histogram of nonbonded interaction distances: 2.06 - 2.57: 143 2.57 - 3.08: 7593 3.08 - 3.58: 13373 3.58 - 4.09: 21124 4.09 - 4.60: 30889 Nonbonded interactions: 73122 Sorted by model distance: nonbonded pdb=" O SER A 399 " pdb=" OG SER A 583 " model vdw 2.059 2.200 nonbonded pdb=" OD2 ASP A 193 " pdb=" OG1 THR A 195 " model vdw 2.063 2.200 nonbonded pdb=" OH TYR A 863 " pdb=" OP2 A J 30 " model vdw 2.178 2.200 nonbonded pdb=" NE ARG A 951 " pdb=" OP1 U J 24 " model vdw 2.195 2.350 nonbonded pdb=" O GLY A1486 " pdb=" NZ LYS A1489 " model vdw 2.199 2.350 ... (remaining 73117 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as 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: 1.460 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: 0.250 Extract box with map and model: 6.320 Check model and map are aligned: 0.150 Set scattering table: 0.090 Process input model: 33.010 Find NCS groups from input model: 0.220 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:11.490 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 53.030 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7631 moved from start: 0.0000 Sorry: Reduce crashed with command 'molprobity.reduce -quiet -trim -'. Dumping stdin to file 'reduce_fail.pdb'. Return code: -15 Dumping stderr: