Starting phenix.real_space_refine on Tue Aug 6 15:55:03 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6dbu_7850/08_2024/6dbu_7850_neut.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6dbu_7850/08_2024/6dbu_7850.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6dbu_7850/08_2024/6dbu_7850.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6dbu_7850/08_2024/6dbu_7850.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6dbu_7850/08_2024/6dbu_7850_neut.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6dbu_7850/08_2024/6dbu_7850_neut.cif" } resolution = 3.9 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= 0.008 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 Ca 4 9.91 5 Zn 2 6.06 5 P 136 5.49 5 S 106 5.16 5 C 10272 2.51 5 N 3004 2.21 5 O 3486 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 490": "NH1" <-> "NH2" Residue "A ARG 505": "NH1" <-> "NH2" Residue "A GLU 637": "OE1" <-> "OE2" Residue "A ARG 641": "NH1" <-> "NH2" Residue "A ARG 756": "NH1" <-> "NH2" Residue "A GLU 777": "OE1" <-> "OE2" Residue "A ARG 795": "NH1" <-> "NH2" Residue "A GLU 833": "OE1" <-> "OE2" Residue "A ARG 870": "NH1" <-> "NH2" Residue "A ARG 971": "NH1" <-> "NH2" Residue "A ARG 991": "NH1" <-> "NH2" Residue "A ARG 999": "NH1" <-> "NH2" Residue "A GLU 1005": "OE1" <-> "OE2" Residue "B ARG 49": "NH1" <-> "NH2" Residue "B ARG 96": "NH1" <-> "NH2" Residue "B ARG 114": "NH1" <-> "NH2" Residue "B ARG 123": "NH1" <-> "NH2" Residue "B ARG 148": "NH1" <-> "NH2" Residue "B ARG 167": "NH1" <-> "NH2" Residue "B ARG 232": "NH1" <-> "NH2" Residue "B ARG 235": "NH1" <-> "NH2" Residue "B ARG 302": "NH1" <-> "NH2" Residue "B ARG 315": "NH1" <-> "NH2" Residue "C ARG 490": "NH1" <-> "NH2" Residue "C ARG 505": "NH1" <-> "NH2" Residue "C GLU 637": "OE1" <-> "OE2" Residue "C ARG 641": "NH1" <-> "NH2" Residue "C ARG 756": "NH1" <-> "NH2" Residue "C GLU 777": "OE1" <-> "OE2" Residue "C ARG 795": "NH1" <-> "NH2" Residue "C GLU 833": "OE1" <-> "OE2" Residue "C ARG 870": "NH1" <-> "NH2" Residue "C ARG 971": "NH1" <-> "NH2" Residue "C ARG 991": "NH1" <-> "NH2" Residue "C ARG 999": "NH1" <-> "NH2" Residue "D ARG 49": "NH1" <-> "NH2" Residue "D ARG 96": "NH1" <-> "NH2" Residue "D ARG 114": "NH1" <-> "NH2" Residue "D ARG 123": "NH1" <-> "NH2" Residue "D ARG 148": "NH1" <-> "NH2" Residue "D ARG 167": "NH1" <-> "NH2" Residue "D ARG 232": "NH1" <-> "NH2" Residue "D ARG 235": "NH1" <-> "NH2" Residue "D ARG 302": "NH1" <-> "NH2" Residue "D ARG 315": "NH1" <-> "NH2" Time to flip residues: 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/chem_data/mon_lib" Total number of atoms: 17010 Number of models: 1 Model: "" Number of chains: 10 Chain: "A" Number of atoms: 4394 Number of conformers: 1 Conformer: "" Number of residues, atoms: 543, 4394 Classifications: {'peptide': 543} Link IDs: {'CIS': 3, 'PCIS': 1, 'PTRANS': 19, 'TRANS': 519} Chain breaks: 1 Chain: "B" Number of atoms: 2714 Number of conformers: 1 Conformer: "" Number of residues, atoms: 351, 2714 Classifications: {'peptide': 351} Link IDs: {'CIS': 9, 'PCIS': 2, 'PTRANS': 22, 'TRANS': 317} Chain: "C" Number of atoms: 4394 Number of conformers: 1 Conformer: "" Number of residues, atoms: 543, 4394 Classifications: {'peptide': 543} Link IDs: {'CIS': 3, 'PCIS': 1, 'PTRANS': 19, 'TRANS': 519} Chain breaks: 1 Chain: "D" Number of atoms: 2714 Number of conformers: 1 Conformer: "" Number of residues, atoms: 351, 2714 Classifications: {'peptide': 351} Link IDs: {'CIS': 9, 'PCIS': 2, 'PTRANS': 22, 'TRANS': 317} Chain: "E" Number of atoms: 696 Number of conformers: 1 Conformer: "" Number of residues, atoms: 34, 696 Classifications: {'DNA': 34} Link IDs: {'rna3p': 33} Chain: "F" Number of atoms: 698 Number of conformers: 1 Conformer: "" Number of residues, atoms: 34, 698 Classifications: {'DNA': 34} Link IDs: {'rna3p': 33} Chain: "G" Number of atoms: 696 Number of conformers: 1 Conformer: "" Number of residues, atoms: 34, 696 Classifications: {'DNA': 34} Link IDs: {'rna3p': 33} Chain: "H" Number of atoms: 698 Number of conformers: 1 Conformer: "" Number of residues, atoms: 34, 698 Classifications: {'DNA': 34} Link IDs: {'rna3p': 33} Chain: "A" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Unusual residues: {' CA': 2, ' ZN': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "C" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Unusual residues: {' CA': 2, ' ZN': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 2075 SG CYS A 749 106.444 97.375 60.497 1.00 43.54 S ATOM 9183 SG CYS C 749 48.329 32.009 60.495 1.00 42.97 S Time building chain proxies: 9.31, per 1000 atoms: 0.55 Number of scatterers: 17010 At special positions: 0 Unit cell: (155.82, 130.38, 115.54, 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 2 29.99 Ca 4 19.99 S 106 16.00 P 136 15.00 O 3486 8.00 N 3004 7.00 C 10272 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: 7.60 Conformation dependent library (CDL) restraints added in 2.7 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A1101 " pdb="ZN ZN A1101 " - pdb=" NE2 HIS A 959 " pdb="ZN ZN A1101 " - pdb=" NE2 HIS A 964 " pdb="ZN ZN A1101 " - pdb=" SG CYS A 749 " pdb=" ZN C1101 " pdb="ZN ZN C1101 " - pdb=" NE2 HIS C 964 " pdb="ZN ZN C1101 " - pdb=" NE2 HIS C 959 " pdb="ZN ZN C1101 " - pdb=" SG CYS C 749 " 3552 Ramachandran restraints generated. 1776 Oldfield, 0 Emsley, 1776 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3332 Finding SS restraints... Secondary structure from input PDB file: 46 helices and 18 sheets defined 33.3% alpha, 21.9% beta 66 base pairs and 119 stacking pairs defined. Time for finding SS restraints: 6.78 Creating SS restraints... Processing helix chain 'A' and resid 482 through 492 Processing helix chain 'A' and resid 497 through 511 removed outlier: 3.547A pdb=" N SER A 511 " --> pdb=" O VAL A 507 " (cutoff:3.500A) Processing helix chain 'A' and resid 518 through 527 Processing helix chain 'A' and resid 577 through 600 removed outlier: 4.892A pdb=" N GLU A 591 " --> pdb=" O LYS A 587 " (cutoff:3.500A) removed outlier: 5.419A pdb=" N ASP A 592 " --> pdb=" O ASP A 588 " (cutoff:3.500A) Processing helix chain 'A' and resid 670 through 674 Processing helix chain 'A' and resid 686 through 705 removed outlier: 3.712A pdb=" N LEU A 690 " --> pdb=" O ASP A 686 " (cutoff:3.500A) Proline residue: A 696 - end of helix Processing helix chain 'A' and resid 730 through 739 Processing helix chain 'A' and resid 755 through 762 removed outlier: 3.687A pdb=" N ALA A 759 " --> pdb=" O THR A 755 " (cutoff:3.500A) removed outlier: 4.049A pdb=" N ASN A 762 " --> pdb=" O GLU A 758 " (cutoff:3.500A) Processing helix chain 'A' and resid 771 through 785 Processing helix chain 'A' and resid 790 through 798 Processing helix chain 'A' and resid 819 through 835 removed outlier: 4.327A pdb=" N GLY A 835 " --> pdb=" O GLN A 831 " (cutoff:3.500A) Processing helix chain 'A' and resid 846 through 863 Processing helix chain 'A' and resid 872 through 880 Processing helix chain 'A' and resid 881 through 890 removed outlier: 3.636A pdb=" N GLU A 890 " --> pdb=" O GLU A 886 " (cutoff:3.500A) Processing helix chain 'A' and resid 895 through 917 removed outlier: 3.859A pdb=" N GLU A 899 " --> pdb=" O GLU A 895 " (cutoff:3.500A) Proline residue: A 913 - end of helix Processing helix chain 'A' and resid 924 through 945 removed outlier: 3.885A pdb=" N LEU A 928 " --> pdb=" O CYS A 924 " (cutoff:3.500A) removed outlier: 4.432A pdb=" N SER A 932 " --> pdb=" O LEU A 928 " (cutoff:3.500A) removed outlier: 5.302A pdb=" N TYR A 933 " --> pdb=" O CYS A 929 " (cutoff:3.500A) Processing helix chain 'A' and resid 955 through 964 removed outlier: 3.546A pdb=" N HIS A 959 " --> pdb=" O THR A 955 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N LYS A 960 " --> pdb=" O ASN A 956 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N HIS A 964 " --> pdb=" O LYS A 960 " (cutoff:3.500A) Processing helix chain 'A' and resid 964 through 973 Processing helix chain 'A' and resid 975 through 979 removed outlier: 3.517A pdb=" N ALA A 979 " --> pdb=" O GLY A 976 " (cutoff:3.500A) Processing helix chain 'A' and resid 980 through 997 removed outlier: 4.154A pdb=" N LYS A 988 " --> pdb=" O GLU A 984 " (cutoff:3.500A) removed outlier: 3.861A pdb=" N LEU A 989 " --> pdb=" O SER A 985 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N ARG A 991 " --> pdb=" O ASN A 987 " (cutoff:3.500A) removed outlier: 3.924A pdb=" N ARG A 992 " --> pdb=" O LYS A 988 " (cutoff:3.500A) Processing helix chain 'A' and resid 1001 through 1017 removed outlier: 4.290A pdb=" N LEU A1006 " --> pdb=" O LYS A1002 " (cutoff:3.500A) removed outlier: 4.526A pdb=" N GLU A1007 " --> pdb=" O THR A1003 " (cutoff:3.500A) Processing helix chain 'A' and resid 1019 through 1024 Processing helix chain 'B' and resid 308 through 313 Processing helix chain 'C' and resid 482 through 492 Processing helix chain 'C' and resid 497 through 511 removed outlier: 3.574A pdb=" N SER C 511 " --> pdb=" O VAL C 507 " (cutoff:3.500A) Processing helix chain 'C' and resid 518 through 527 Processing helix chain 'C' and resid 577 through 600 removed outlier: 4.921A pdb=" N GLU C 591 " --> pdb=" O LYS C 587 " (cutoff:3.500A) removed outlier: 5.433A pdb=" N ASP C 592 " --> pdb=" O ASP C 588 " (cutoff:3.500A) Processing helix chain 'C' and resid 670 through 674 Processing helix chain 'C' and resid 686 through 705 removed outlier: 3.757A pdb=" N LEU C 690 " --> pdb=" O ASP C 686 " (cutoff:3.500A) Proline residue: C 696 - end of helix Processing helix chain 'C' and resid 730 through 739 Processing helix chain 'C' and resid 755 through 762 removed outlier: 3.679A pdb=" N ALA C 759 " --> pdb=" O THR C 755 " (cutoff:3.500A) removed outlier: 4.025A pdb=" N ASN C 762 " --> pdb=" O GLU C 758 " (cutoff:3.500A) Processing helix chain 'C' and resid 771 through 785 Processing helix chain 'C' and resid 790 through 798 Processing helix chain 'C' and resid 819 through 835 removed outlier: 4.371A pdb=" N GLY C 835 " --> pdb=" O GLN C 831 " (cutoff:3.500A) Processing helix chain 'C' and resid 846 through 863 Processing helix chain 'C' and resid 872 through 880 Processing helix chain 'C' and resid 881 through 890 removed outlier: 3.570A pdb=" N GLU C 890 " --> pdb=" O GLU C 886 " (cutoff:3.500A) Processing helix chain 'C' and resid 895 through 917 removed outlier: 3.855A pdb=" N GLU C 899 " --> pdb=" O GLU C 895 " (cutoff:3.500A) Proline residue: C 913 - end of helix Processing helix chain 'C' and resid 924 through 945 removed outlier: 3.879A pdb=" N LEU C 928 " --> pdb=" O CYS C 924 " (cutoff:3.500A) removed outlier: 4.471A pdb=" N SER C 932 " --> pdb=" O LEU C 928 " (cutoff:3.500A) removed outlier: 5.335A pdb=" N TYR C 933 " --> pdb=" O CYS C 929 " (cutoff:3.500A) Processing helix chain 'C' and resid 955 through 964 removed outlier: 3.548A pdb=" N HIS C 959 " --> pdb=" O THR C 955 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N LYS C 960 " --> pdb=" O ASN C 956 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N HIS C 964 " --> pdb=" O LYS C 960 " (cutoff:3.500A) Processing helix chain 'C' and resid 964 through 973 Processing helix chain 'C' and resid 975 through 979 Processing helix chain 'C' and resid 980 through 997 removed outlier: 4.429A pdb=" N LYS C 988 " --> pdb=" O GLU C 984 " (cutoff:3.500A) removed outlier: 4.311A pdb=" N LEU C 989 " --> pdb=" O SER C 985 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N MET C 996 " --> pdb=" O ARG C 992 " (cutoff:3.500A) Processing helix chain 'C' and resid 1001 through 1017 removed outlier: 4.179A pdb=" N LEU C1006 " --> pdb=" O LYS C1002 " (cutoff:3.500A) removed outlier: 4.821A pdb=" N GLU C1007 " --> pdb=" O THR C1003 " (cutoff:3.500A) Processing helix chain 'C' and resid 1019 through 1024 Processing helix chain 'D' and resid 308 through 313 Processing sheet with id=AA1, first strand: chain 'A' and resid 537 through 539 removed outlier: 6.951A pdb=" N PHE A 611 " --> pdb=" O ARG A 721 " (cutoff:3.500A) removed outlier: 7.821A pdb=" N PHE A 723 " --> pdb=" O PHE A 611 " (cutoff:3.500A) removed outlier: 6.396A pdb=" N VAL A 613 " --> pdb=" O PHE A 723 " (cutoff:3.500A) removed outlier: 6.590A pdb=" N THR A 612 " --> pdb=" O ILE A 649 " (cutoff:3.500A) removed outlier: 4.316A pdb=" N ILE A 649 " --> pdb=" O THR A 612 " (cutoff:3.500A) removed outlier: 6.779A pdb=" N VAL A 614 " --> pdb=" O MET A 647 " (cutoff:3.500A) removed outlier: 6.881A pdb=" N VAL A 640 " --> pdb=" O LEU A 679 " (cutoff:3.500A) removed outlier: 4.667A pdb=" N LEU A 679 " --> pdb=" O VAL A 640 " (cutoff:3.500A) removed outlier: 6.872A pdb=" N PHE A 642 " --> pdb=" O LEU A 677 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 537 through 539 removed outlier: 6.951A pdb=" N PHE A 611 " --> pdb=" O ARG A 721 " (cutoff:3.500A) removed outlier: 7.821A pdb=" N PHE A 723 " --> pdb=" O PHE A 611 " (cutoff:3.500A) removed outlier: 6.396A pdb=" N VAL A 613 " --> pdb=" O PHE A 723 " (cutoff:3.500A) removed outlier: 6.590A pdb=" N THR A 612 " --> pdb=" O ILE A 649 " (cutoff:3.500A) removed outlier: 4.316A pdb=" N ILE A 649 " --> pdb=" O THR A 612 " (cutoff:3.500A) removed outlier: 6.779A pdb=" N VAL A 614 " --> pdb=" O MET A 647 " (cutoff:3.500A) removed outlier: 6.619A pdb=" N ILE A 651 " --> pdb=" O THR A 661 " (cutoff:3.500A) removed outlier: 6.337A pdb=" N THR A 661 " --> pdb=" O ILE A 651 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 2 through 5 removed outlier: 5.862A pdb=" N THR B 326 " --> pdb=" O LEU B 322 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 7 through 8 removed outlier: 6.786A pdb=" N THR B 7 " --> pdb=" O LEU B 55 " (cutoff:3.500A) removed outlier: 8.423A pdb=" N LEU B 57 " --> pdb=" O THR B 7 " (cutoff:3.500A) removed outlier: 4.135A pdb=" N VAL B 28 " --> pdb=" O VAL B 48 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 76 through 80 removed outlier: 6.801A pdb=" N THR B 121 " --> pdb=" O ASP B 112 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 141 through 147 Processing sheet with id=AA7, first strand: chain 'B' and resid 159 through 161 Processing sheet with id=AA8, first strand: chain 'B' and resid 209 through 212 Processing sheet with id=AA9, first strand: chain 'B' and resid 263 through 265 Processing sheet with id=AB1, first strand: chain 'C' and resid 537 through 539 removed outlier: 6.957A pdb=" N PHE C 611 " --> pdb=" O ARG C 721 " (cutoff:3.500A) removed outlier: 7.827A pdb=" N PHE C 723 " --> pdb=" O PHE C 611 " (cutoff:3.500A) removed outlier: 6.386A pdb=" N VAL C 613 " --> pdb=" O PHE C 723 " (cutoff:3.500A) removed outlier: 6.592A pdb=" N THR C 612 " --> pdb=" O ILE C 649 " (cutoff:3.500A) removed outlier: 4.310A pdb=" N ILE C 649 " --> pdb=" O THR C 612 " (cutoff:3.500A) removed outlier: 6.767A pdb=" N VAL C 614 " --> pdb=" O MET C 647 " (cutoff:3.500A) removed outlier: 6.884A pdb=" N VAL C 640 " --> pdb=" O LEU C 679 " (cutoff:3.500A) removed outlier: 4.666A pdb=" N LEU C 679 " --> pdb=" O VAL C 640 " (cutoff:3.500A) removed outlier: 6.846A pdb=" N PHE C 642 " --> pdb=" O LEU C 677 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 537 through 539 removed outlier: 6.957A pdb=" N PHE C 611 " --> pdb=" O ARG C 721 " (cutoff:3.500A) removed outlier: 7.827A pdb=" N PHE C 723 " --> pdb=" O PHE C 611 " (cutoff:3.500A) removed outlier: 6.386A pdb=" N VAL C 613 " --> pdb=" O PHE C 723 " (cutoff:3.500A) removed outlier: 6.592A pdb=" N THR C 612 " --> pdb=" O ILE C 649 " (cutoff:3.500A) removed outlier: 4.310A pdb=" N ILE C 649 " --> pdb=" O THR C 612 " (cutoff:3.500A) removed outlier: 6.767A pdb=" N VAL C 614 " --> pdb=" O MET C 647 " (cutoff:3.500A) removed outlier: 6.595A pdb=" N ILE C 651 " --> pdb=" O THR C 661 " (cutoff:3.500A) removed outlier: 6.341A pdb=" N THR C 661 " --> pdb=" O ILE C 651 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'D' and resid 2 through 5 removed outlier: 5.853A pdb=" N THR D 326 " --> pdb=" O LEU D 322 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'D' and resid 7 through 8 removed outlier: 6.782A pdb=" N THR D 7 " --> pdb=" O LEU D 55 " (cutoff:3.500A) removed outlier: 8.424A pdb=" N LEU D 57 " --> pdb=" O THR D 7 " (cutoff:3.500A) removed outlier: 3.961A pdb=" N VAL D 28 " --> pdb=" O VAL D 48 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'D' and resid 77 through 80 removed outlier: 6.810A pdb=" N THR D 121 " --> pdb=" O ASP D 112 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'D' and resid 141 through 147 Processing sheet with id=AB7, first strand: chain 'D' and resid 159 through 161 Processing sheet with id=AB8, first strand: chain 'D' and resid 209 through 212 Processing sheet with id=AB9, first strand: chain 'D' and resid 263 through 265 624 hydrogen bonds defined for protein. 1698 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 168 hydrogen bonds 336 hydrogen bond angles 0 basepair planarities 66 basepair parallelities 119 stacking parallelities Total time for adding SS restraints: 8.26 Time building geometry restraints manager: 8.24 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.08 - 1.23: 81 1.23 - 1.37: 5748 1.37 - 1.52: 7554 1.52 - 1.67: 4115 1.67 - 1.82: 160 Bond restraints: 17658 Sorted by residual: bond pdb=" CA HIS D 222 " pdb=" CB HIS D 222 " ideal model delta sigma weight residual 1.534 1.314 0.220 2.33e-02 1.84e+03 8.94e+01 bond pdb=" CA HIS B 222 " pdb=" CB HIS B 222 " ideal model delta sigma weight residual 1.534 1.315 0.219 2.33e-02 1.84e+03 8.84e+01 bond pdb=" CG ASN D 10 " pdb=" OD1 ASN D 10 " ideal model delta sigma weight residual 1.231 1.080 0.151 1.90e-02 2.77e+03 6.28e+01 bond pdb=" CG GLN D 282 " pdb=" CD GLN D 282 " ideal model delta sigma weight residual 1.516 1.708 -0.192 2.50e-02 1.60e+03 5.88e+01 bond pdb=" CG GLN B 282 " pdb=" CD GLN B 282 " ideal model delta sigma weight residual 1.516 1.692 -0.176 2.50e-02 1.60e+03 4.96e+01 ... (remaining 17653 not shown) Histogram of bond angle deviations from ideal: 75.43 - 96.33: 9 96.33 - 117.24: 13416 117.24 - 138.15: 11013 138.15 - 159.05: 9 159.05 - 179.96: 1 Bond angle restraints: 24448 Sorted by residual: angle pdb=" CG GLN C 910 " pdb=" CD GLN C 910 " pdb=" OE1 GLN C 910 " ideal model delta sigma weight residual 120.80 179.96 -59.16 2.00e+00 2.50e-01 8.75e+02 angle pdb=" CG GLN C 910 " pdb=" CD GLN C 910 " pdb=" NE2 GLN C 910 " ideal model delta sigma weight residual 116.40 75.43 40.97 1.50e+00 4.44e-01 7.46e+02 angle pdb=" CB HIS C 687 " pdb=" CG HIS C 687 " pdb=" CD2 HIS C 687 " ideal model delta sigma weight residual 131.20 97.36 33.84 1.30e+00 5.92e-01 6.78e+02 angle pdb=" OE1 GLN C 910 " pdb=" CD GLN C 910 " pdb=" NE2 GLN C 910 " ideal model delta sigma weight residual 122.60 104.60 18.00 1.00e+00 1.00e+00 3.24e+02 angle pdb=" CB ASN B 10 " pdb=" CG ASN B 10 " pdb=" ND2 ASN B 10 " ideal model delta sigma weight residual 116.40 90.28 26.12 1.50e+00 4.44e-01 3.03e+02 ... (remaining 24443 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 32.11: 9168 32.11 - 64.21: 1066 64.21 - 96.32: 42 96.32 - 128.43: 0 128.43 - 160.53: 2 Dihedral angle restraints: 10278 sinusoidal: 5102 harmonic: 5176 Sorted by residual: dihedral pdb=" C HIS B 222 " pdb=" N HIS B 222 " pdb=" CA HIS B 222 " pdb=" CB HIS B 222 " ideal model delta harmonic sigma weight residual -122.60 -86.55 -36.05 0 2.50e+00 1.60e-01 2.08e+02 dihedral pdb=" C HIS D 222 " pdb=" N HIS D 222 " pdb=" CA HIS D 222 " pdb=" CB HIS D 222 " ideal model delta harmonic sigma weight residual -122.60 -86.75 -35.85 0 2.50e+00 1.60e-01 2.06e+02 dihedral pdb=" C GLN B 282 " pdb=" N GLN B 282 " pdb=" CA GLN B 282 " pdb=" CB GLN B 282 " ideal model delta harmonic sigma weight residual -122.60 -94.39 -28.21 0 2.50e+00 1.60e-01 1.27e+02 ... (remaining 10275 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.173: 2656 0.173 - 0.346: 13 0.346 - 0.519: 2 0.519 - 0.692: 0 0.692 - 0.864: 1 Chirality restraints: 2672 Sorted by residual: chirality pdb=" CA HIS C 687 " pdb=" N HIS C 687 " pdb=" C HIS C 687 " pdb=" CB HIS C 687 " both_signs ideal model delta sigma weight residual False 2.51 1.65 0.86 2.00e-01 2.50e+01 1.87e+01 chirality pdb=" CB VAL D 48 " pdb=" CA VAL D 48 " pdb=" CG1 VAL D 48 " pdb=" CG2 VAL D 48 " both_signs ideal model delta sigma weight residual False -2.63 -2.11 -0.52 2.00e-01 2.50e+01 6.63e+00 chirality pdb=" CA GLN B 282 " pdb=" N GLN B 282 " pdb=" C GLN B 282 " pdb=" CB GLN B 282 " both_signs ideal model delta sigma weight residual False 2.51 2.89 -0.38 2.00e-01 2.50e+01 3.64e+00 ... (remaining 2669 not shown) Planarity restraints: 2682 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB HIS C 687 " -0.155 2.00e-02 2.50e+03 1.41e-01 3.00e+02 pdb=" CG HIS C 687 " 0.252 2.00e-02 2.50e+03 pdb=" ND1 HIS C 687 " -0.103 2.00e-02 2.50e+03 pdb=" CD2 HIS C 687 " 0.087 2.00e-02 2.50e+03 pdb=" CE1 HIS C 687 " 0.032 2.00e-02 2.50e+03 pdb=" NE2 HIS C 687 " -0.114 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CG GLN C 936 " -0.085 2.00e-02 2.50e+03 1.73e-01 2.99e+02 pdb=" CD GLN C 936 " 0.297 2.00e-02 2.50e+03 pdb=" OE1 GLN C 936 " -0.135 2.00e-02 2.50e+03 pdb=" NE2 GLN C 936 " -0.077 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CG GLN A 936 " 0.085 2.00e-02 2.50e+03 1.73e-01 2.98e+02 pdb=" CD GLN A 936 " -0.296 2.00e-02 2.50e+03 pdb=" OE1 GLN A 936 " 0.136 2.00e-02 2.50e+03 pdb=" NE2 GLN A 936 " 0.075 2.00e-02 2.50e+03 ... (remaining 2679 not shown) Histogram of nonbonded interaction distances: 1.77 - 2.40: 103 2.40 - 3.02: 10150 3.02 - 3.65: 27107 3.65 - 4.27: 38341 4.27 - 4.90: 59878 Nonbonded interactions: 135579 Sorted by model distance: nonbonded pdb=" OE2 GLU A 789 " pdb=" NH1 ARG A 797 " model vdw 1.769 3.120 nonbonded pdb=" OD2 ASP A 588 " pdb=" OG SER A1018 " model vdw 1.914 3.040 nonbonded pdb=" OD2 ASP C 588 " pdb=" OG SER C1018 " model vdw 1.920 3.040 nonbonded pdb=" OE2 GLU C 789 " pdb=" NH1 ARG C 797 " model vdw 1.956 3.120 nonbonded pdb=" O ASN D 10 " pdb=" ND2 ASN D 10 " model vdw 1.966 3.120 ... (remaining 135574 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'C' } ncs_group { reference = chain 'B' selection = chain 'D' } ncs_group { reference = chain 'E' selection = chain 'G' } ncs_group { reference = chain 'F' selection = chain 'H' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.860 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.010 Extract box with map and model: 0.690 Check model and map are aligned: 0.120 Set scattering table: 0.150 Process input model: 57.510 Find NCS groups from input model: 0.510 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:2.680 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 62.620 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8158 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 0.220 17658 Z= 0.391 Angle : 1.198 59.160 24448 Z= 0.710 Chirality : 0.049 0.864 2672 Planarity : 0.011 0.173 2682 Dihedral : 22.114 160.535 6946 Min Nonbonded Distance : 1.769 Molprobity Statistics. All-atom Clashscore : 23.39 Ramachandran Plot: Outliers : 0.23 % Allowed : 8.84 % Favored : 90.93 % Rotamer: Outliers : 0.13 % Allowed : 29.19 % Favored : 70.69 % Cbeta Deviations : 0.48 % Peptide Plane: Cis-proline : 6.98 % Cis-general : 1.42 % Twisted Proline : 0.00 % Twisted General : 0.12 % 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: -4.17 (0.16), residues: 1776 helix: -2.36 (0.17), residues: 552 sheet: -2.11 (0.26), residues: 340 loop : -3.34 (0.17), residues: 884 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.049 0.002 TRP C 538 HIS 0.209 0.008 HIS D 222 PHE 0.078 0.002 PHE B 62 TYR 0.018 0.002 TYR C 747 ARG 0.034 0.001 ARG C 922 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3552 Ramachandran restraints generated. 1776 Oldfield, 0 Emsley, 1776 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3552 Ramachandran restraints generated. 1776 Oldfield, 0 Emsley, 1776 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 383 residues out of total 1576 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 381 time to evaluate : 1.772 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 582 LEU cc_start: 0.9230 (mt) cc_final: 0.8953 (tp) REVERT: A 808 GLU cc_start: 0.9271 (tt0) cc_final: 0.9023 (tt0) REVERT: A 829 ILE cc_start: 0.9001 (mt) cc_final: 0.8772 (mt) REVERT: A 836 GLU cc_start: 0.7073 (mm-30) cc_final: 0.6829 (pm20) REVERT: A 849 ARG cc_start: 0.7797 (mmt180) cc_final: 0.7570 (tpm170) REVERT: A 869 MET cc_start: 0.6668 (pp-130) cc_final: 0.6198 (ppp) REVERT: A 870 ARG cc_start: 0.7751 (ptt90) cc_final: 0.7228 (ptt180) REVERT: A 922 ARG cc_start: 0.7651 (ttt-90) cc_final: 0.7401 (mtp85) REVERT: B 210 LEU cc_start: 0.8489 (mt) cc_final: 0.8238 (mp) REVERT: B 213 GLN cc_start: 0.7882 (tp40) cc_final: 0.7653 (tm-30) REVERT: B 214 ASP cc_start: 0.7816 (p0) cc_final: 0.7410 (p0) REVERT: C 808 GLU cc_start: 0.9261 (tt0) cc_final: 0.8895 (tt0) REVERT: C 870 ARG cc_start: 0.7320 (ptt90) cc_final: 0.7115 (ptt180) REVERT: C 905 MET cc_start: 0.7456 (tpp) cc_final: 0.7237 (tpp) REVERT: C 922 ARG cc_start: 0.7605 (ttt-90) cc_final: 0.7383 (mtp85) REVERT: D 177 ASP cc_start: 0.8363 (m-30) cc_final: 0.8157 (m-30) REVERT: D 210 LEU cc_start: 0.8548 (mt) cc_final: 0.8255 (mp) REVERT: D 214 ASP cc_start: 0.7607 (p0) cc_final: 0.7262 (p0) outliers start: 2 outliers final: 1 residues processed: 383 average time/residue: 0.3450 time to fit residues: 185.6217 Evaluate side-chains 200 residues out of total 1576 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 199 time to evaluate : 1.910 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 133 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 190 random chunks: chunk 160 optimal weight: 2.9990 chunk 144 optimal weight: 5.9990 chunk 79 optimal weight: 10.0000 chunk 49 optimal weight: 9.9990 chunk 97 optimal weight: 4.9990 chunk 76 optimal weight: 6.9990 chunk 148 optimal weight: 4.9990 chunk 57 optimal weight: 6.9990 chunk 90 optimal weight: 5.9990 chunk 110 optimal weight: 1.9990 chunk 172 optimal weight: 9.9990 overall best weight: 4.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 524 ASN ** A 534 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 910 GLN A 934 ASN A 936 GLN A 937 GLN ** A 964 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 10 ASN B 146 ASN B 171 ASN B 173 ASN B 222 HIS B 282 GLN C 482 HIS ** C 534 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 761 GLN C 934 ASN C 936 GLN ** C 997 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 146 ASN ** D 181 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 282 GLN Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8300 moved from start: 0.2524 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.042 17658 Z= 0.393 Angle : 0.811 10.837 24448 Z= 0.435 Chirality : 0.046 0.219 2672 Planarity : 0.007 0.066 2682 Dihedral : 24.722 155.428 3447 Min Nonbonded Distance : 2.198 Molprobity Statistics. All-atom Clashscore : 15.55 Ramachandran Plot: Outliers : 0.11 % Allowed : 8.33 % Favored : 91.55 % Rotamer: Outliers : 9.84 % Allowed : 22.46 % Favored : 67.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.98 % Cis-general : 1.42 % Twisted Proline : 0.00 % Twisted General : 0.12 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.80 (0.18), residues: 1776 helix: -0.92 (0.21), residues: 544 sheet: -1.75 (0.27), residues: 354 loop : -2.52 (0.18), residues: 878 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP C 538 HIS 0.009 0.002 HIS D 222 PHE 0.015 0.002 PHE D 274 TYR 0.042 0.003 TYR A 908 ARG 0.010 0.001 ARG A 845 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3552 Ramachandran restraints generated. 1776 Oldfield, 0 Emsley, 1776 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3552 Ramachandran restraints generated. 1776 Oldfield, 0 Emsley, 1776 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 350 residues out of total 1576 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 155 poor density : 195 time to evaluate : 1.882 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 565 ASP cc_start: 0.8710 (p0) cc_final: 0.8331 (p0) REVERT: A 587 LYS cc_start: 0.9022 (OUTLIER) cc_final: 0.8742 (mtpp) REVERT: A 661 THR cc_start: 0.8995 (OUTLIER) cc_final: 0.8545 (p) REVERT: A 681 PHE cc_start: 0.8891 (OUTLIER) cc_final: 0.8607 (m-10) REVERT: A 694 LEU cc_start: 0.9633 (OUTLIER) cc_final: 0.9391 (mp) REVERT: A 808 GLU cc_start: 0.9135 (tt0) cc_final: 0.8868 (tt0) REVERT: A 813 LEU cc_start: 0.8831 (OUTLIER) cc_final: 0.8607 (tp) REVERT: A 825 GLU cc_start: 0.8417 (tp30) cc_final: 0.7613 (tm-30) REVERT: A 869 MET cc_start: 0.6925 (OUTLIER) cc_final: 0.6689 (ppp) REVERT: A 905 MET cc_start: 0.7368 (tpp) cc_final: 0.6992 (tpp) REVERT: A 922 ARG cc_start: 0.7756 (OUTLIER) cc_final: 0.7362 (mtp85) REVERT: B 189 PHE cc_start: 0.8264 (OUTLIER) cc_final: 0.7625 (m-80) REVERT: B 213 GLN cc_start: 0.7979 (tp40) cc_final: 0.7571 (tm-30) REVERT: C 589 LEU cc_start: 0.8398 (OUTLIER) cc_final: 0.8179 (mp) REVERT: C 661 THR cc_start: 0.9006 (OUTLIER) cc_final: 0.8492 (p) REVERT: C 733 MET cc_start: 0.8001 (tpp) cc_final: 0.7672 (tpp) REVERT: C 808 GLU cc_start: 0.9116 (tt0) cc_final: 0.8756 (tt0) REVERT: C 922 ARG cc_start: 0.7823 (OUTLIER) cc_final: 0.7310 (mtp85) REVERT: D 189 PHE cc_start: 0.8288 (OUTLIER) cc_final: 0.7761 (m-80) REVERT: D 210 LEU cc_start: 0.8667 (mt) cc_final: 0.8306 (mp) outliers start: 155 outliers final: 55 residues processed: 323 average time/residue: 0.2884 time to fit residues: 139.2327 Evaluate side-chains 239 residues out of total 1576 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 67 poor density : 172 time to evaluate : 1.733 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 485 VAL Chi-restraints excluded: chain A residue 489 ILE Chi-restraints excluded: chain A residue 497 CYS Chi-restraints excluded: chain A residue 507 VAL Chi-restraints excluded: chain A residue 587 LYS Chi-restraints excluded: chain A residue 650 SER Chi-restraints excluded: chain A residue 661 THR Chi-restraints excluded: chain A residue 681 PHE Chi-restraints excluded: chain A residue 694 LEU Chi-restraints excluded: chain A residue 750 THR Chi-restraints excluded: chain A residue 768 ILE Chi-restraints excluded: chain A residue 798 VAL Chi-restraints excluded: chain A residue 809 THR Chi-restraints excluded: chain A residue 813 LEU Chi-restraints excluded: chain A residue 817 HIS Chi-restraints excluded: chain A residue 834 ILE Chi-restraints excluded: chain A residue 869 MET Chi-restraints excluded: chain A residue 917 SER Chi-restraints excluded: chain A residue 922 ARG Chi-restraints excluded: chain A residue 928 LEU Chi-restraints excluded: chain A residue 1003 THR Chi-restraints excluded: chain B residue 24 LEU Chi-restraints excluded: chain B residue 97 THR Chi-restraints excluded: chain B residue 138 TYR Chi-restraints excluded: chain B residue 151 THR Chi-restraints excluded: chain B residue 153 CYS Chi-restraints excluded: chain B residue 189 PHE Chi-restraints excluded: chain B residue 219 LEU Chi-restraints excluded: chain B residue 247 LEU Chi-restraints excluded: chain B residue 248 THR Chi-restraints excluded: chain B residue 250 THR Chi-restraints excluded: chain B residue 311 ILE Chi-restraints excluded: chain B residue 313 HIS Chi-restraints excluded: chain C residue 485 VAL Chi-restraints excluded: chain C residue 489 ILE Chi-restraints excluded: chain C residue 497 CYS Chi-restraints excluded: chain C residue 507 VAL Chi-restraints excluded: chain C residue 560 TRP Chi-restraints excluded: chain C residue 563 SER Chi-restraints excluded: chain C residue 589 LEU Chi-restraints excluded: chain C residue 617 GLU Chi-restraints excluded: chain C residue 650 SER Chi-restraints excluded: chain C residue 661 THR Chi-restraints excluded: chain C residue 748 ILE Chi-restraints excluded: chain C residue 750 THR Chi-restraints excluded: chain C residue 798 VAL Chi-restraints excluded: chain C residue 809 THR Chi-restraints excluded: chain C residue 812 THR Chi-restraints excluded: chain C residue 817 HIS Chi-restraints excluded: chain C residue 834 ILE Chi-restraints excluded: chain C residue 922 ARG Chi-restraints excluded: chain C residue 928 LEU Chi-restraints excluded: chain C residue 1003 THR Chi-restraints excluded: chain C residue 1006 LEU Chi-restraints excluded: chain C residue 1018 SER Chi-restraints excluded: chain D residue 9 VAL Chi-restraints excluded: chain D residue 62 PHE Chi-restraints excluded: chain D residue 97 THR Chi-restraints excluded: chain D residue 133 VAL Chi-restraints excluded: chain D residue 138 TYR Chi-restraints excluded: chain D residue 146 ASN Chi-restraints excluded: chain D residue 168 THR Chi-restraints excluded: chain D residue 189 PHE Chi-restraints excluded: chain D residue 219 LEU Chi-restraints excluded: chain D residue 247 LEU Chi-restraints excluded: chain D residue 248 THR Chi-restraints excluded: chain D residue 311 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 190 random chunks: chunk 95 optimal weight: 0.0980 chunk 53 optimal weight: 0.9990 chunk 143 optimal weight: 4.9990 chunk 117 optimal weight: 0.7980 chunk 47 optimal weight: 7.9990 chunk 172 optimal weight: 4.9990 chunk 186 optimal weight: 6.9990 chunk 153 optimal weight: 0.5980 chunk 171 optimal weight: 4.9990 chunk 58 optimal weight: 4.9990 chunk 138 optimal weight: 3.9990 overall best weight: 1.2984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 964 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 983 ASN ** B 4 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 65 ASN ** B 347 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 766 HIS ** C 858 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 937 GLN C 983 ASN C 997 ASN D 146 ASN ** D 222 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8232 moved from start: 0.3107 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 17658 Z= 0.210 Angle : 0.702 8.869 24448 Z= 0.380 Chirality : 0.043 0.215 2672 Planarity : 0.005 0.054 2682 Dihedral : 24.411 155.085 3446 Min Nonbonded Distance : 2.334 Molprobity Statistics. All-atom Clashscore : 13.43 Ramachandran Plot: Outliers : 0.06 % Allowed : 5.07 % Favored : 94.88 % Rotamer: Outliers : 5.77 % Allowed : 24.30 % Favored : 69.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.98 % Cis-general : 1.42 % 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: -2.07 (0.19), residues: 1776 helix: -0.34 (0.21), residues: 548 sheet: -1.40 (0.27), residues: 352 loop : -2.04 (0.19), residues: 876 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C 915 HIS 0.014 0.002 HIS C 817 PHE 0.016 0.001 PHE C 787 TYR 0.015 0.002 TYR A 933 ARG 0.005 0.001 ARG A 845 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3552 Ramachandran restraints generated. 1776 Oldfield, 0 Emsley, 1776 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3552 Ramachandran restraints generated. 1776 Oldfield, 0 Emsley, 1776 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 292 residues out of total 1576 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 91 poor density : 201 time to evaluate : 1.762 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 565 ASP cc_start: 0.8749 (p0) cc_final: 0.8504 (p0) REVERT: A 661 THR cc_start: 0.8960 (OUTLIER) cc_final: 0.8492 (p) REVERT: A 672 LEU cc_start: 0.8564 (mp) cc_final: 0.8288 (mt) REVERT: A 681 PHE cc_start: 0.8749 (OUTLIER) cc_final: 0.8533 (m-10) REVERT: A 871 MET cc_start: 0.8387 (mmp) cc_final: 0.8047 (mmp) REVERT: A 905 MET cc_start: 0.7287 (tpp) cc_final: 0.6945 (tpp) REVERT: A 922 ARG cc_start: 0.7643 (OUTLIER) cc_final: 0.7163 (mtp85) REVERT: B 3 LEU cc_start: 0.7886 (pp) cc_final: 0.7294 (pp) REVERT: B 73 ARG cc_start: 0.8192 (OUTLIER) cc_final: 0.7883 (ttp80) REVERT: B 189 PHE cc_start: 0.8214 (OUTLIER) cc_final: 0.7650 (m-80) REVERT: B 213 GLN cc_start: 0.7943 (tp40) cc_final: 0.7560 (tm-30) REVERT: C 587 LYS cc_start: 0.8905 (OUTLIER) cc_final: 0.8629 (mtpp) REVERT: C 589 LEU cc_start: 0.8359 (OUTLIER) cc_final: 0.8102 (mp) REVERT: C 661 THR cc_start: 0.8979 (OUTLIER) cc_final: 0.8491 (p) REVERT: C 690 LEU cc_start: 0.9373 (tp) cc_final: 0.9159 (tt) REVERT: C 808 GLU cc_start: 0.8993 (tt0) cc_final: 0.8594 (tt0) REVERT: C 871 MET cc_start: 0.8324 (mmp) cc_final: 0.7833 (mmp) REVERT: C 922 ARG cc_start: 0.7705 (OUTLIER) cc_final: 0.7157 (mtp85) REVERT: D 9 VAL cc_start: 0.4803 (OUTLIER) cc_final: 0.4514 (p) REVERT: D 189 PHE cc_start: 0.8368 (OUTLIER) cc_final: 0.7799 (m-80) REVERT: D 210 LEU cc_start: 0.8491 (mt) cc_final: 0.8227 (mp) REVERT: D 240 LEU cc_start: 0.7735 (OUTLIER) cc_final: 0.7504 (mp) outliers start: 91 outliers final: 36 residues processed: 270 average time/residue: 0.2795 time to fit residues: 114.8830 Evaluate side-chains 228 residues out of total 1576 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 180 time to evaluate : 1.849 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 489 ILE Chi-restraints excluded: chain A residue 661 THR Chi-restraints excluded: chain A residue 662 ILE Chi-restraints excluded: chain A residue 681 PHE Chi-restraints excluded: chain A residue 748 ILE Chi-restraints excluded: chain A residue 750 THR Chi-restraints excluded: chain A residue 768 ILE Chi-restraints excluded: chain A residue 816 LEU Chi-restraints excluded: chain A residue 834 ILE Chi-restraints excluded: chain A residue 922 ARG Chi-restraints excluded: chain A residue 928 LEU Chi-restraints excluded: chain A residue 1018 SER Chi-restraints excluded: chain A residue 1024 PHE Chi-restraints excluded: chain B residue 73 ARG Chi-restraints excluded: chain B residue 97 THR Chi-restraints excluded: chain B residue 106 LEU Chi-restraints excluded: chain B residue 151 THR Chi-restraints excluded: chain B residue 153 CYS Chi-restraints excluded: chain B residue 189 PHE Chi-restraints excluded: chain B residue 201 THR Chi-restraints excluded: chain B residue 247 LEU Chi-restraints excluded: chain B residue 248 THR Chi-restraints excluded: chain B residue 250 THR Chi-restraints excluded: chain B residue 311 ILE Chi-restraints excluded: chain B residue 313 HIS Chi-restraints excluded: chain C residue 489 ILE Chi-restraints excluded: chain C residue 587 LYS Chi-restraints excluded: chain C residue 589 LEU Chi-restraints excluded: chain C residue 661 THR Chi-restraints excluded: chain C residue 748 ILE Chi-restraints excluded: chain C residue 771 SER Chi-restraints excluded: chain C residue 798 VAL Chi-restraints excluded: chain C residue 812 THR Chi-restraints excluded: chain C residue 834 ILE Chi-restraints excluded: chain C residue 886 GLU Chi-restraints excluded: chain C residue 922 ARG Chi-restraints excluded: chain C residue 928 LEU Chi-restraints excluded: chain C residue 1006 LEU Chi-restraints excluded: chain C residue 1018 SER Chi-restraints excluded: chain D residue 9 VAL Chi-restraints excluded: chain D residue 62 PHE Chi-restraints excluded: chain D residue 97 THR Chi-restraints excluded: chain D residue 146 ASN Chi-restraints excluded: chain D residue 189 PHE Chi-restraints excluded: chain D residue 240 LEU Chi-restraints excluded: chain D residue 248 THR Chi-restraints excluded: chain D residue 272 ILE Chi-restraints excluded: chain D residue 311 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 190 random chunks: chunk 170 optimal weight: 8.9990 chunk 129 optimal weight: 4.9990 chunk 89 optimal weight: 3.9990 chunk 19 optimal weight: 6.9990 chunk 82 optimal weight: 1.9990 chunk 116 optimal weight: 0.9980 chunk 173 optimal weight: 0.0270 chunk 183 optimal weight: 10.0000 chunk 90 optimal weight: 1.9990 chunk 164 optimal weight: 6.9990 chunk 49 optimal weight: 3.9990 overall best weight: 1.8044 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 964 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 65 ASN ** C 858 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 65 ASN D 146 ASN D 173 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8242 moved from start: 0.3509 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 17658 Z= 0.224 Angle : 0.682 8.711 24448 Z= 0.367 Chirality : 0.042 0.149 2672 Planarity : 0.005 0.063 2682 Dihedral : 24.173 155.740 3446 Min Nonbonded Distance : 2.288 Molprobity Statistics. All-atom Clashscore : 12.81 Ramachandran Plot: Outliers : 0.06 % Allowed : 5.35 % Favored : 94.59 % Rotamer: Outliers : 5.65 % Allowed : 23.92 % Favored : 70.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.98 % Cis-general : 1.42 % 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: -1.67 (0.19), residues: 1776 helix: 0.09 (0.22), residues: 546 sheet: -1.17 (0.28), residues: 352 loop : -1.86 (0.19), residues: 878 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP D 317 HIS 0.009 0.001 HIS A 817 PHE 0.026 0.001 PHE B 274 TYR 0.021 0.002 TYR A 908 ARG 0.004 0.000 ARG C 598 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3552 Ramachandran restraints generated. 1776 Oldfield, 0 Emsley, 1776 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3552 Ramachandran restraints generated. 1776 Oldfield, 0 Emsley, 1776 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 283 residues out of total 1576 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 89 poor density : 194 time to evaluate : 1.845 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 565 ASP cc_start: 0.8793 (p0) cc_final: 0.8589 (p0) REVERT: A 661 THR cc_start: 0.8989 (OUTLIER) cc_final: 0.8537 (p) REVERT: A 681 PHE cc_start: 0.8779 (OUTLIER) cc_final: 0.8515 (m-10) REVERT: A 717 LEU cc_start: 0.8892 (OUTLIER) cc_final: 0.8622 (pp) REVERT: A 825 GLU cc_start: 0.8333 (tp30) cc_final: 0.7628 (tm-30) REVERT: A 869 MET cc_start: 0.6970 (ppp) cc_final: 0.6385 (ttp) REVERT: A 871 MET cc_start: 0.8434 (mmp) cc_final: 0.8131 (mmp) REVERT: A 905 MET cc_start: 0.7178 (tpp) cc_final: 0.6913 (tpp) REVERT: A 915 TRP cc_start: 0.7526 (p90) cc_final: 0.6813 (p90) REVERT: A 922 ARG cc_start: 0.7659 (OUTLIER) cc_final: 0.7171 (mtp85) REVERT: A 996 MET cc_start: 0.8468 (mtm) cc_final: 0.8119 (mtm) REVERT: B 73 ARG cc_start: 0.8197 (OUTLIER) cc_final: 0.7887 (ttp80) REVERT: B 189 PHE cc_start: 0.8167 (OUTLIER) cc_final: 0.7566 (m-80) REVERT: C 587 LYS cc_start: 0.8834 (OUTLIER) cc_final: 0.8629 (mtpp) REVERT: C 589 LEU cc_start: 0.8380 (OUTLIER) cc_final: 0.8175 (mp) REVERT: C 661 THR cc_start: 0.8995 (OUTLIER) cc_final: 0.8545 (p) REVERT: C 690 LEU cc_start: 0.9398 (tp) cc_final: 0.9132 (tt) REVERT: C 717 LEU cc_start: 0.8871 (OUTLIER) cc_final: 0.8583 (pp) REVERT: C 882 ARG cc_start: 0.8069 (ttt180) cc_final: 0.7694 (tpp80) REVERT: C 922 ARG cc_start: 0.7728 (OUTLIER) cc_final: 0.7146 (mtp85) REVERT: D 189 PHE cc_start: 0.8392 (OUTLIER) cc_final: 0.7814 (m-80) outliers start: 89 outliers final: 46 residues processed: 261 average time/residue: 0.2964 time to fit residues: 116.9838 Evaluate side-chains 237 residues out of total 1576 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 58 poor density : 179 time to evaluate : 1.785 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 489 ILE Chi-restraints excluded: chain A residue 507 VAL Chi-restraints excluded: chain A residue 661 THR Chi-restraints excluded: chain A residue 662 ILE Chi-restraints excluded: chain A residue 681 PHE Chi-restraints excluded: chain A residue 717 LEU Chi-restraints excluded: chain A residue 748 ILE Chi-restraints excluded: chain A residue 750 THR Chi-restraints excluded: chain A residue 768 ILE Chi-restraints excluded: chain A residue 771 SER Chi-restraints excluded: chain A residue 892 VAL Chi-restraints excluded: chain A residue 917 SER Chi-restraints excluded: chain A residue 922 ARG Chi-restraints excluded: chain A residue 928 LEU Chi-restraints excluded: chain A residue 1018 SER Chi-restraints excluded: chain A residue 1024 PHE Chi-restraints excluded: chain B residue 73 ARG Chi-restraints excluded: chain B residue 97 THR Chi-restraints excluded: chain B residue 106 LEU Chi-restraints excluded: chain B residue 151 THR Chi-restraints excluded: chain B residue 153 CYS Chi-restraints excluded: chain B residue 189 PHE Chi-restraints excluded: chain B residue 201 THR Chi-restraints excluded: chain B residue 247 LEU Chi-restraints excluded: chain B residue 248 THR Chi-restraints excluded: chain B residue 250 THR Chi-restraints excluded: chain B residue 311 ILE Chi-restraints excluded: chain B residue 313 HIS Chi-restraints excluded: chain C residue 489 ILE Chi-restraints excluded: chain C residue 507 VAL Chi-restraints excluded: chain C residue 560 TRP Chi-restraints excluded: chain C residue 587 LYS Chi-restraints excluded: chain C residue 589 LEU Chi-restraints excluded: chain C residue 617 GLU Chi-restraints excluded: chain C residue 649 ILE Chi-restraints excluded: chain C residue 661 THR Chi-restraints excluded: chain C residue 662 ILE Chi-restraints excluded: chain C residue 717 LEU Chi-restraints excluded: chain C residue 745 SER Chi-restraints excluded: chain C residue 748 ILE Chi-restraints excluded: chain C residue 798 VAL Chi-restraints excluded: chain C residue 812 THR Chi-restraints excluded: chain C residue 834 ILE Chi-restraints excluded: chain C residue 886 GLU Chi-restraints excluded: chain C residue 917 SER Chi-restraints excluded: chain C residue 922 ARG Chi-restraints excluded: chain C residue 928 LEU Chi-restraints excluded: chain C residue 1003 THR Chi-restraints excluded: chain C residue 1018 SER Chi-restraints excluded: chain D residue 2 SER Chi-restraints excluded: chain D residue 62 PHE Chi-restraints excluded: chain D residue 97 THR Chi-restraints excluded: chain D residue 133 VAL Chi-restraints excluded: chain D residue 153 CYS Chi-restraints excluded: chain D residue 168 THR Chi-restraints excluded: chain D residue 189 PHE Chi-restraints excluded: chain D residue 248 THR Chi-restraints excluded: chain D residue 311 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 190 random chunks: chunk 152 optimal weight: 3.9990 chunk 104 optimal weight: 3.9990 chunk 2 optimal weight: 0.6980 chunk 136 optimal weight: 9.9990 chunk 75 optimal weight: 3.9990 chunk 156 optimal weight: 3.9990 chunk 126 optimal weight: 0.9990 chunk 0 optimal weight: 5.9990 chunk 93 optimal weight: 2.9990 chunk 164 optimal weight: 8.9990 chunk 46 optimal weight: 9.9990 overall best weight: 2.5388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 964 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 4 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 65 ASN ** B 347 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 534 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 858 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 65 ASN ** D 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8270 moved from start: 0.3805 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.093 17658 Z= 0.263 Angle : 0.672 8.844 24448 Z= 0.363 Chirality : 0.042 0.210 2672 Planarity : 0.005 0.055 2682 Dihedral : 24.020 156.871 3446 Min Nonbonded Distance : 2.266 Molprobity Statistics. All-atom Clashscore : 12.97 Ramachandran Plot: Outliers : 0.06 % Allowed : 5.63 % Favored : 94.31 % Rotamer: Outliers : 6.15 % Allowed : 24.05 % Favored : 69.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.98 % Cis-general : 1.42 % 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: -1.49 (0.19), residues: 1776 helix: 0.36 (0.22), residues: 546 sheet: -1.06 (0.27), residues: 382 loop : -1.87 (0.19), residues: 848 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP C 915 HIS 0.006 0.001 HIS D 313 PHE 0.013 0.002 PHE D 274 TYR 0.016 0.002 TYR A 933 ARG 0.005 0.000 ARG C 598 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3552 Ramachandran restraints generated. 1776 Oldfield, 0 Emsley, 1776 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3552 Ramachandran restraints generated. 1776 Oldfield, 0 Emsley, 1776 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 280 residues out of total 1576 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 97 poor density : 183 time to evaluate : 1.760 Fit side-chains revert: symmetry clash REVERT: A 565 ASP cc_start: 0.8861 (p0) cc_final: 0.8598 (p0) REVERT: A 606 MET cc_start: 0.6781 (tpt) cc_final: 0.6072 (ttt) REVERT: A 661 THR cc_start: 0.9019 (OUTLIER) cc_final: 0.8580 (p) REVERT: A 681 PHE cc_start: 0.8832 (OUTLIER) cc_final: 0.8553 (m-10) REVERT: A 717 LEU cc_start: 0.8965 (OUTLIER) cc_final: 0.8694 (pp) REVERT: A 825 GLU cc_start: 0.8333 (tp30) cc_final: 0.7618 (tm-30) REVERT: A 869 MET cc_start: 0.6979 (ppp) cc_final: 0.6516 (ttp) REVERT: A 880 MET cc_start: 0.7015 (mtt) cc_final: 0.6293 (ppp) REVERT: A 905 MET cc_start: 0.7137 (tpp) cc_final: 0.6904 (tpp) REVERT: A 915 TRP cc_start: 0.7554 (p90) cc_final: 0.6972 (p90) REVERT: A 922 ARG cc_start: 0.7697 (OUTLIER) cc_final: 0.7138 (mtp85) REVERT: B 73 ARG cc_start: 0.8363 (OUTLIER) cc_final: 0.8046 (ttp80) REVERT: B 189 PHE cc_start: 0.8132 (OUTLIER) cc_final: 0.7619 (m-80) REVERT: C 587 LYS cc_start: 0.8893 (OUTLIER) cc_final: 0.8617 (mtpp) REVERT: C 606 MET cc_start: 0.7533 (tpt) cc_final: 0.6624 (ttt) REVERT: C 661 THR cc_start: 0.9029 (OUTLIER) cc_final: 0.8614 (p) REVERT: C 717 LEU cc_start: 0.8918 (OUTLIER) cc_final: 0.8649 (pp) REVERT: C 871 MET cc_start: 0.8284 (mmp) cc_final: 0.7716 (mmp) REVERT: C 880 MET cc_start: 0.7952 (tmm) cc_final: 0.7612 (tmm) REVERT: C 922 ARG cc_start: 0.7854 (OUTLIER) cc_final: 0.7159 (mtp85) REVERT: C 992 ARG cc_start: 0.7487 (tpp80) cc_final: 0.7273 (tpp80) REVERT: D 189 PHE cc_start: 0.8338 (OUTLIER) cc_final: 0.7812 (m-80) outliers start: 97 outliers final: 58 residues processed: 259 average time/residue: 0.2795 time to fit residues: 110.4463 Evaluate side-chains 241 residues out of total 1576 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 69 poor density : 172 time to evaluate : 1.822 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 489 ILE Chi-restraints excluded: chain A residue 507 VAL Chi-restraints excluded: chain A residue 661 THR Chi-restraints excluded: chain A residue 662 ILE Chi-restraints excluded: chain A residue 681 PHE Chi-restraints excluded: chain A residue 713 VAL Chi-restraints excluded: chain A residue 717 LEU Chi-restraints excluded: chain A residue 748 ILE Chi-restraints excluded: chain A residue 750 THR Chi-restraints excluded: chain A residue 768 ILE Chi-restraints excluded: chain A residue 771 SER Chi-restraints excluded: chain A residue 809 THR Chi-restraints excluded: chain A residue 817 HIS Chi-restraints excluded: chain A residue 892 VAL Chi-restraints excluded: chain A residue 917 SER Chi-restraints excluded: chain A residue 922 ARG Chi-restraints excluded: chain A residue 928 LEU Chi-restraints excluded: chain A residue 1018 SER Chi-restraints excluded: chain A residue 1024 PHE Chi-restraints excluded: chain B residue 2 SER Chi-restraints excluded: chain B residue 62 PHE Chi-restraints excluded: chain B residue 73 ARG Chi-restraints excluded: chain B residue 97 THR Chi-restraints excluded: chain B residue 106 LEU Chi-restraints excluded: chain B residue 133 VAL Chi-restraints excluded: chain B residue 151 THR Chi-restraints excluded: chain B residue 153 CYS Chi-restraints excluded: chain B residue 189 PHE Chi-restraints excluded: chain B residue 201 THR Chi-restraints excluded: chain B residue 247 LEU Chi-restraints excluded: chain B residue 248 THR Chi-restraints excluded: chain B residue 290 VAL Chi-restraints excluded: chain B residue 311 ILE Chi-restraints excluded: chain B residue 313 HIS Chi-restraints excluded: chain C residue 489 ILE Chi-restraints excluded: chain C residue 507 VAL Chi-restraints excluded: chain C residue 560 TRP Chi-restraints excluded: chain C residue 564 VAL Chi-restraints excluded: chain C residue 587 LYS Chi-restraints excluded: chain C residue 617 GLU Chi-restraints excluded: chain C residue 649 ILE Chi-restraints excluded: chain C residue 661 THR Chi-restraints excluded: chain C residue 662 ILE Chi-restraints excluded: chain C residue 713 VAL Chi-restraints excluded: chain C residue 717 LEU Chi-restraints excluded: chain C residue 748 ILE Chi-restraints excluded: chain C residue 771 SER Chi-restraints excluded: chain C residue 798 VAL Chi-restraints excluded: chain C residue 809 THR Chi-restraints excluded: chain C residue 812 THR Chi-restraints excluded: chain C residue 817 HIS Chi-restraints excluded: chain C residue 834 ILE Chi-restraints excluded: chain C residue 886 GLU Chi-restraints excluded: chain C residue 917 SER Chi-restraints excluded: chain C residue 922 ARG Chi-restraints excluded: chain C residue 928 LEU Chi-restraints excluded: chain C residue 1003 THR Chi-restraints excluded: chain C residue 1018 SER Chi-restraints excluded: chain D residue 2 SER Chi-restraints excluded: chain D residue 62 PHE Chi-restraints excluded: chain D residue 65 ASN Chi-restraints excluded: chain D residue 97 THR Chi-restraints excluded: chain D residue 133 VAL Chi-restraints excluded: chain D residue 153 CYS Chi-restraints excluded: chain D residue 168 THR Chi-restraints excluded: chain D residue 189 PHE Chi-restraints excluded: chain D residue 201 THR Chi-restraints excluded: chain D residue 248 THR Chi-restraints excluded: chain D residue 311 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/build/../modules/phenix/phenix/command_line/real_space_refine.py", line 8, in run_program(real_space_refine.Program) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/iotbx/cli_parser.py", line 946, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/phenix/phenix/programs/real_space_refine.py", line 200, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 306, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 702, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 766, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 51, in __init__ gradients_method = gradients_method) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/mmtbx/refinement/real_space/weight.py", line 87, in __init__ rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 368, in refine rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 235, in __init__ weight = weight) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 112, in refine states_collector = self.states_accumulator) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 174, in __init__ exception_handling_params=lbfgs_exception_handling_params) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 245, in compute_functional_and_gradients compute_gradients=True) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1479, in energies_sites flags=flags, sites_cart=sites_cart, site_labels=site_labels) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1381, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1262, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 67.4663 > 50: distance: 78 - 81: 33.344 distance: 81 - 82: 58.590 distance: 82 - 83: 52.150 distance: 82 - 85: 37.411 distance: 83 - 84: 27.229 distance: 83 - 89: 31.671 distance: 85 - 86: 38.710 distance: 85 - 87: 46.163 distance: 86 - 88: 33.915 distance: 89 - 90: 57.583 distance: 90 - 91: 26.331 distance: 90 - 93: 39.940 distance: 91 - 92: 46.938 distance: 91 - 95: 33.742 distance: 93 - 94: 46.639 distance: 95 - 96: 32.993 distance: 96 - 97: 38.029 distance: 96 - 99: 22.176 distance: 97 - 98: 22.457 distance: 97 - 106: 38.798 distance: 99 - 100: 43.632 distance: 100 - 101: 27.292 distance: 100 - 102: 26.715 distance: 101 - 103: 13.622 distance: 102 - 104: 24.786 distance: 103 - 105: 24.641 distance: 104 - 105: 23.118 distance: 106 - 107: 44.717 distance: 107 - 108: 46.442 distance: 107 - 110: 31.733 distance: 108 - 109: 53.053 distance: 108 - 112: 49.898 distance: 110 - 111: 40.411 distance: 112 - 113: 43.146 distance: 113 - 114: 50.805 distance: 113 - 116: 14.541 distance: 114 - 115: 17.734 distance: 114 - 120: 48.123 distance: 116 - 117: 58.160 distance: 117 - 118: 40.311 distance: 117 - 119: 47.578 distance: 120 - 121: 56.367 distance: 121 - 122: 48.564 distance: 121 - 124: 32.177 distance: 122 - 123: 59.241 distance: 122 - 128: 52.763 distance: 124 - 125: 36.494 distance: 125 - 126: 49.517 distance: 125 - 127: 36.151 distance: 128 - 129: 37.846 distance: 129 - 130: 58.077 distance: 129 - 132: 7.415 distance: 130 - 131: 46.167 distance: 130 - 134: 48.031 distance: 132 - 133: 46.308 distance: 134 - 135: 32.833 distance: 135 - 136: 26.389 distance: 135 - 138: 51.251 distance: 136 - 137: 9.517 distance: 136 - 140: 43.252 distance: 138 - 139: 46.990 distance: 140 - 141: 45.486 distance: 141 - 142: 49.119 distance: 141 - 144: 57.974 distance: 142 - 143: 52.798 distance: 142 - 152: 58.467 distance: 144 - 145: 45.281 distance: 145 - 146: 16.545 distance: 145 - 147: 9.494 distance: 146 - 148: 22.732 distance: 147 - 149: 19.327 distance: 148 - 150: 21.263 distance: 149 - 150: 34.078 distance: 150 - 151: 9.321 distance: 152 - 153: 23.758 distance: 153 - 154: 57.735 distance: 153 - 156: 57.456 distance: 154 - 155: 57.660 distance: 154 - 160: 34.744 distance: 156 - 157: 48.787 distance: 157 - 158: 45.656 distance: 157 - 159: 25.546