Starting phenix.real_space_refine on Mon Mar 18 04:21:57 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7or0_13036/03_2024/7or0_13036_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7or0_13036/03_2024/7or0_13036.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.64 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7or0_13036/03_2024/7or0_13036.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7or0_13036/03_2024/7or0_13036.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7or0_13036/03_2024/7or0_13036_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7or0_13036/03_2024/7or0_13036_updated.pdb" } resolution = 2.64 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= 0.004 sd= 0.091 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians Ca 5 9.91 5 P 32 5.49 5 S 144 5.16 5 C 12900 2.51 5 N 3168 2.21 5 O 3620 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A TYR 658": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 696": "OE1" <-> "OE2" Residue "A PHE 778": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 823": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 877": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 1049": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 1059": "OE1" <-> "OE2" Residue "B TYR 658": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 696": "OE1" <-> "OE2" Residue "B PHE 778": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 823": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 877": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 1049": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 1059": "OE1" <-> "OE2" Residue "C TYR 658": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 696": "OE1" <-> "OE2" Residue "C PHE 778": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 823": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 877": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 1049": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 1059": "OE1" <-> "OE2" Residue "D TYR 658": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 696": "OE1" <-> "OE2" Residue "D PHE 778": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 823": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 877": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 1049": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 1059": "OE1" <-> "OE2" Time to flip residues: 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 19869 Number of models: 1 Model: "" Number of chains: 16 Chain: "A" Number of atoms: 4753 Number of conformers: 1 Conformer: "" Number of residues, atoms: 596, 4753 Classifications: {'peptide': 596} Incomplete info: {'truncation_to_alanine': 15} Link IDs: {'PTRANS': 21, 'TRANS': 574} Chain breaks: 3 Unresolved non-hydrogen bonds: 63 Unresolved non-hydrogen angles: 74 Unresolved non-hydrogen dihedrals: 54 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLN:plan1': 1, 'ASN:plan1': 1, 'ASP:plan': 2, 'PHE:plan': 1, 'GLU:plan': 2, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 31 Chain: "B" Number of atoms: 4753 Number of conformers: 1 Conformer: "" Number of residues, atoms: 596, 4753 Classifications: {'peptide': 596} Incomplete info: {'truncation_to_alanine': 15} Link IDs: {'PTRANS': 21, 'TRANS': 574} Chain breaks: 3 Unresolved non-hydrogen bonds: 63 Unresolved non-hydrogen angles: 74 Unresolved non-hydrogen dihedrals: 54 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLN:plan1': 1, 'ASN:plan1': 1, 'ASP:plan': 2, 'PHE:plan': 1, 'GLU:plan': 2, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 31 Chain: "C" Number of atoms: 4753 Number of conformers: 1 Conformer: "" Number of residues, atoms: 596, 4753 Classifications: {'peptide': 596} Incomplete info: {'truncation_to_alanine': 15} Link IDs: {'PTRANS': 21, 'TRANS': 574} Chain breaks: 3 Unresolved non-hydrogen bonds: 63 Unresolved non-hydrogen angles: 74 Unresolved non-hydrogen dihedrals: 54 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLN:plan1': 1, 'ASN:plan1': 1, 'ASP:plan': 2, 'PHE:plan': 1, 'GLU:plan': 2, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 31 Chain: "D" Number of atoms: 4753 Number of conformers: 1 Conformer: "" Number of residues, atoms: 596, 4753 Classifications: {'peptide': 596} Incomplete info: {'truncation_to_alanine': 15} Link IDs: {'PTRANS': 21, 'TRANS': 574} Chain breaks: 3 Unresolved non-hydrogen bonds: 63 Unresolved non-hydrogen angles: 74 Unresolved non-hydrogen dihedrals: 54 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLN:plan1': 1, 'ASN:plan1': 1, 'ASP:plan': 2, 'PHE:plan': 1, 'GLU:plan': 2, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 31 Chain: "E" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "F" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "G" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "H" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 173 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 173 Unusual residues: {' CA': 1, '0IG': 1, 'IHP': 1, 'NAG': 1, 'PC1': 2} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 18 Unresolved non-hydrogen angles: 22 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 1 Chain: "B" Number of atoms: 174 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 174 Unusual residues: {' CA': 2, '0IG': 1, 'IHP': 1, 'NAG': 1, 'PC1': 2} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 18 Unresolved non-hydrogen angles: 22 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 1 Chain: "C" Number of atoms: 173 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 173 Unusual residues: {' CA': 1, '0IG': 1, 'IHP': 1, 'NAG': 1, 'PC1': 2} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 18 Unresolved non-hydrogen angles: 22 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 1 Chain: "D" Number of atoms: 173 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 173 Unusual residues: {' CA': 1, '0IG': 1, 'IHP': 1, 'NAG': 1, 'PC1': 2} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 18 Unresolved non-hydrogen angles: 22 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 1 Chain: "A" Number of atoms: 13 Number of conformers: 1 Conformer: "" Number of residues, atoms: 13, 13 Classifications: {'water': 13} Link IDs: {None: 12} Chain: "B" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 14, 14 Classifications: {'water': 14} Link IDs: {None: 13} Chain: "C" Number of atoms: 13 Number of conformers: 1 Conformer: "" Number of residues, atoms: 13, 13 Classifications: {'water': 13} Link IDs: {None: 12} Chain: "D" Number of atoms: 12 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 12 Classifications: {'water': 12} Link IDs: {None: 11} Time building chain proxies: 10.35, per 1000 atoms: 0.52 Number of scatterers: 19869 At special positions: 0 Unit cell: (113.36, 114.45, 148.24, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Ca 5 19.99 S 144 16.00 P 32 15.00 O 3620 8.00 N 3168 7.00 C 12900 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 Links applied BETA1-4 " NAG E 1 " - " NAG E 2 " " NAG F 1 " - " NAG F 2 " " NAG G 1 " - " NAG G 2 " " NAG H 1 " - " NAG H 2 " NAG-ASN " NAG A1205 " - " ASN A 753 " " NAG B1205 " - " ASN B 753 " " NAG C1205 " - " ASN C 753 " " NAG D1206 " - " ASN D 753 " " NAG E 1 " - " ASN A 747 " " NAG F 1 " - " ASN B 747 " " NAG G 1 " - " ASN C 747 " " NAG H 1 " - " ASN D 747 " Time building additional restraints: 7.43 Conformation dependent library (CDL) restraints added in 3.2 seconds 4704 Ramachandran restraints generated. 2352 Oldfield, 0 Emsley, 2352 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4568 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 128 helices and 8 sheets defined 63.6% alpha, 2.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 4.11 Creating SS restraints... Processing helix chain 'A' and resid 448 through 455 Processing helix chain 'A' and resid 459 through 465 Processing helix chain 'A' and resid 485 through 492 Processing helix chain 'A' and resid 495 through 504 Processing helix chain 'A' and resid 517 through 524 Processing helix chain 'A' and resid 527 through 535 removed outlier: 3.829A pdb=" N ASP A 535 " --> pdb=" O LYS A 531 " (cutoff:3.500A) Processing helix chain 'A' and resid 551 through 558 Processing helix chain 'A' and resid 561 through 569 Processing helix chain 'A' and resid 583 through 589 Processing helix chain 'A' and resid 593 through 601 Processing helix chain 'A' and resid 605 through 610 Processing helix chain 'A' and resid 622 through 629 Processing helix chain 'A' and resid 631 through 641 removed outlier: 3.687A pdb=" N VAL A 636 " --> pdb=" O GLU A 632 " (cutoff:3.500A) removed outlier: 4.052A pdb=" N CYS A 641 " --> pdb=" O LEU A 637 " (cutoff:3.500A) Processing helix chain 'A' and resid 666 through 668 No H-bonds generated for 'chain 'A' and resid 666 through 668' Processing helix chain 'A' and resid 684 through 692 removed outlier: 3.517A pdb=" N ASN A 692 " --> pdb=" O ALA A 688 " (cutoff:3.500A) Processing helix chain 'A' and resid 695 through 698 No H-bonds generated for 'chain 'A' and resid 695 through 698' Processing helix chain 'A' and resid 701 through 739 removed outlier: 6.231A pdb=" N PHE A 716 " --> pdb=" O LEU A 712 " (cutoff:3.500A) removed outlier: 6.244A pdb=" N ARG A 717 " --> pdb=" O ALA A 713 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N ASN A 722 " --> pdb=" O ALA A 718 " (cutoff:3.500A) removed outlier: 4.291A pdb=" N GLY A 729 " --> pdb=" O SER A 725 " (cutoff:3.500A) Proline residue: A 732 - end of helix Processing helix chain 'A' and resid 767 through 791 Processing helix chain 'A' and resid 803 through 818 removed outlier: 3.655A pdb=" N ILE A 817 " --> pdb=" O THR A 813 " (cutoff:3.500A) Processing helix chain 'A' and resid 820 through 822 No H-bonds generated for 'chain 'A' and resid 820 through 822' Processing helix chain 'A' and resid 828 through 852 removed outlier: 3.919A pdb=" N ILE A 837 " --> pdb=" O GLN A 833 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N TYR A 840 " --> pdb=" O ALA A 836 " (cutoff:3.500A) removed outlier: 4.000A pdb=" N TRP A 843 " --> pdb=" O VAL A 839 " (cutoff:3.500A) removed outlier: 4.198A pdb=" N LEU A 847 " --> pdb=" O TRP A 843 " (cutoff:3.500A) removed outlier: 4.616A pdb=" N LEU A 848 " --> pdb=" O MET A 844 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N TYR A 849 " --> pdb=" O ASN A 845 " (cutoff:3.500A) removed outlier: 4.742A pdb=" N ARG A 852 " --> pdb=" O LEU A 848 " (cutoff:3.500A) Processing helix chain 'A' and resid 858 through 871 Processing helix chain 'A' and resid 874 through 877 No H-bonds generated for 'chain 'A' and resid 874 through 877' Processing helix chain 'A' and resid 879 through 891 removed outlier: 3.681A pdb=" N ILE A 890 " --> pdb=" O LEU A 886 " (cutoff:3.500A) Processing helix chain 'A' and resid 896 through 898 No H-bonds generated for 'chain 'A' and resid 896 through 898' Processing helix chain 'A' and resid 901 through 913 removed outlier: 3.661A pdb=" N MET A 912 " --> pdb=" O THR A 908 " (cutoff:3.500A) removed outlier: 5.088A pdb=" N LEU A 913 " --> pdb=" O PHE A 909 " (cutoff:3.500A) Processing helix chain 'A' and resid 918 through 921 No H-bonds generated for 'chain 'A' and resid 918 through 921' Processing helix chain 'A' and resid 923 through 927 Processing helix chain 'A' and resid 934 through 947 Processing helix chain 'A' and resid 951 through 987 removed outlier: 4.024A pdb=" N HIS A 970 " --> pdb=" O GLU A 966 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N ALA A 971 " --> pdb=" O VAL A 967 " (cutoff:3.500A) removed outlier: 5.566A pdb=" N SER A 972 " --> pdb=" O GLN A 968 " (cutoff:3.500A) removed outlier: 6.677A pdb=" N LEU A 973 " --> pdb=" O LYS A 969 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N GLN A 979 " --> pdb=" O ARG A 975 " (cutoff:3.500A) Processing helix chain 'A' and resid 992 through 998 Processing helix chain 'A' and resid 1039 through 1071 Processing helix chain 'B' and resid 448 through 455 Processing helix chain 'B' and resid 459 through 465 Processing helix chain 'B' and resid 485 through 492 Processing helix chain 'B' and resid 495 through 504 Processing helix chain 'B' and resid 517 through 524 Processing helix chain 'B' and resid 527 through 535 removed outlier: 3.828A pdb=" N ASP B 535 " --> pdb=" O LYS B 531 " (cutoff:3.500A) Processing helix chain 'B' and resid 551 through 558 Processing helix chain 'B' and resid 561 through 569 Processing helix chain 'B' and resid 583 through 589 Processing helix chain 'B' and resid 593 through 601 Processing helix chain 'B' and resid 605 through 610 Processing helix chain 'B' and resid 622 through 629 Processing helix chain 'B' and resid 631 through 641 removed outlier: 3.687A pdb=" N VAL B 636 " --> pdb=" O GLU B 632 " (cutoff:3.500A) removed outlier: 4.053A pdb=" N CYS B 641 " --> pdb=" O LEU B 637 " (cutoff:3.500A) Processing helix chain 'B' and resid 666 through 668 No H-bonds generated for 'chain 'B' and resid 666 through 668' Processing helix chain 'B' and resid 684 through 692 removed outlier: 3.518A pdb=" N ASN B 692 " --> pdb=" O ALA B 688 " (cutoff:3.500A) Processing helix chain 'B' and resid 695 through 698 No H-bonds generated for 'chain 'B' and resid 695 through 698' Processing helix chain 'B' and resid 701 through 739 removed outlier: 6.231A pdb=" N PHE B 716 " --> pdb=" O LEU B 712 " (cutoff:3.500A) removed outlier: 6.245A pdb=" N ARG B 717 " --> pdb=" O ALA B 713 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N ASN B 722 " --> pdb=" O ALA B 718 " (cutoff:3.500A) removed outlier: 4.291A pdb=" N GLY B 729 " --> pdb=" O SER B 725 " (cutoff:3.500A) Proline residue: B 732 - end of helix Processing helix chain 'B' and resid 767 through 791 Processing helix chain 'B' and resid 803 through 818 removed outlier: 3.655A pdb=" N ILE B 817 " --> pdb=" O THR B 813 " (cutoff:3.500A) Processing helix chain 'B' and resid 820 through 822 No H-bonds generated for 'chain 'B' and resid 820 through 822' Processing helix chain 'B' and resid 828 through 852 removed outlier: 3.920A pdb=" N ILE B 837 " --> pdb=" O GLN B 833 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N TYR B 840 " --> pdb=" O ALA B 836 " (cutoff:3.500A) removed outlier: 4.002A pdb=" N TRP B 843 " --> pdb=" O VAL B 839 " (cutoff:3.500A) removed outlier: 4.197A pdb=" N LEU B 847 " --> pdb=" O TRP B 843 " (cutoff:3.500A) removed outlier: 4.616A pdb=" N LEU B 848 " --> pdb=" O MET B 844 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N TYR B 849 " --> pdb=" O ASN B 845 " (cutoff:3.500A) removed outlier: 4.743A pdb=" N ARG B 852 " --> pdb=" O LEU B 848 " (cutoff:3.500A) Processing helix chain 'B' and resid 858 through 871 Processing helix chain 'B' and resid 874 through 877 No H-bonds generated for 'chain 'B' and resid 874 through 877' Processing helix chain 'B' and resid 879 through 891 removed outlier: 3.680A pdb=" N ILE B 890 " --> pdb=" O LEU B 886 " (cutoff:3.500A) Processing helix chain 'B' and resid 896 through 898 No H-bonds generated for 'chain 'B' and resid 896 through 898' Processing helix chain 'B' and resid 901 through 913 removed outlier: 3.660A pdb=" N MET B 912 " --> pdb=" O THR B 908 " (cutoff:3.500A) removed outlier: 5.088A pdb=" N LEU B 913 " --> pdb=" O PHE B 909 " (cutoff:3.500A) Processing helix chain 'B' and resid 918 through 921 No H-bonds generated for 'chain 'B' and resid 918 through 921' Processing helix chain 'B' and resid 923 through 927 Processing helix chain 'B' and resid 934 through 947 Processing helix chain 'B' and resid 951 through 987 removed outlier: 4.024A pdb=" N HIS B 970 " --> pdb=" O GLU B 966 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N ALA B 971 " --> pdb=" O VAL B 967 " (cutoff:3.500A) removed outlier: 5.566A pdb=" N SER B 972 " --> pdb=" O GLN B 968 " (cutoff:3.500A) removed outlier: 6.678A pdb=" N LEU B 973 " --> pdb=" O LYS B 969 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N GLN B 979 " --> pdb=" O ARG B 975 " (cutoff:3.500A) Processing helix chain 'B' and resid 992 through 998 Processing helix chain 'B' and resid 1039 through 1071 Processing helix chain 'C' and resid 448 through 455 Processing helix chain 'C' and resid 459 through 465 Processing helix chain 'C' and resid 485 through 492 Processing helix chain 'C' and resid 495 through 504 Processing helix chain 'C' and resid 517 through 524 Processing helix chain 'C' and resid 527 through 535 removed outlier: 3.829A pdb=" N ASP C 535 " --> pdb=" O LYS C 531 " (cutoff:3.500A) Processing helix chain 'C' and resid 551 through 558 Processing helix chain 'C' and resid 561 through 569 Processing helix chain 'C' and resid 583 through 589 Processing helix chain 'C' and resid 593 through 601 Processing helix chain 'C' and resid 605 through 610 Processing helix chain 'C' and resid 622 through 629 Processing helix chain 'C' and resid 631 through 641 removed outlier: 3.687A pdb=" N VAL C 636 " --> pdb=" O GLU C 632 " (cutoff:3.500A) removed outlier: 4.053A pdb=" N CYS C 641 " --> pdb=" O LEU C 637 " (cutoff:3.500A) Processing helix chain 'C' and resid 666 through 668 No H-bonds generated for 'chain 'C' and resid 666 through 668' Processing helix chain 'C' and resid 684 through 692 removed outlier: 3.518A pdb=" N ASN C 692 " --> pdb=" O ALA C 688 " (cutoff:3.500A) Processing helix chain 'C' and resid 695 through 698 No H-bonds generated for 'chain 'C' and resid 695 through 698' Processing helix chain 'C' and resid 701 through 739 removed outlier: 6.231A pdb=" N PHE C 716 " --> pdb=" O LEU C 712 " (cutoff:3.500A) removed outlier: 6.245A pdb=" N ARG C 717 " --> pdb=" O ALA C 713 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N ASN C 722 " --> pdb=" O ALA C 718 " (cutoff:3.500A) removed outlier: 4.290A pdb=" N GLY C 729 " --> pdb=" O SER C 725 " (cutoff:3.500A) Proline residue: C 732 - end of helix Processing helix chain 'C' and resid 767 through 791 Processing helix chain 'C' and resid 803 through 818 removed outlier: 3.655A pdb=" N ILE C 817 " --> pdb=" O THR C 813 " (cutoff:3.500A) Processing helix chain 'C' and resid 820 through 822 No H-bonds generated for 'chain 'C' and resid 820 through 822' Processing helix chain 'C' and resid 828 through 852 removed outlier: 3.920A pdb=" N ILE C 837 " --> pdb=" O GLN C 833 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N TYR C 840 " --> pdb=" O ALA C 836 " (cutoff:3.500A) removed outlier: 4.001A pdb=" N TRP C 843 " --> pdb=" O VAL C 839 " (cutoff:3.500A) removed outlier: 4.197A pdb=" N LEU C 847 " --> pdb=" O TRP C 843 " (cutoff:3.500A) removed outlier: 4.616A pdb=" N LEU C 848 " --> pdb=" O MET C 844 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N TYR C 849 " --> pdb=" O ASN C 845 " (cutoff:3.500A) removed outlier: 4.741A pdb=" N ARG C 852 " --> pdb=" O LEU C 848 " (cutoff:3.500A) Processing helix chain 'C' and resid 858 through 871 Processing helix chain 'C' and resid 874 through 877 No H-bonds generated for 'chain 'C' and resid 874 through 877' Processing helix chain 'C' and resid 879 through 891 removed outlier: 3.680A pdb=" N ILE C 890 " --> pdb=" O LEU C 886 " (cutoff:3.500A) Processing helix chain 'C' and resid 896 through 898 No H-bonds generated for 'chain 'C' and resid 896 through 898' Processing helix chain 'C' and resid 901 through 913 removed outlier: 3.661A pdb=" N MET C 912 " --> pdb=" O THR C 908 " (cutoff:3.500A) removed outlier: 5.089A pdb=" N LEU C 913 " --> pdb=" O PHE C 909 " (cutoff:3.500A) Processing helix chain 'C' and resid 918 through 921 No H-bonds generated for 'chain 'C' and resid 918 through 921' Processing helix chain 'C' and resid 923 through 927 Processing helix chain 'C' and resid 934 through 947 Processing helix chain 'C' and resid 951 through 987 removed outlier: 4.024A pdb=" N HIS C 970 " --> pdb=" O GLU C 966 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N ALA C 971 " --> pdb=" O VAL C 967 " (cutoff:3.500A) removed outlier: 5.566A pdb=" N SER C 972 " --> pdb=" O GLN C 968 " (cutoff:3.500A) removed outlier: 6.678A pdb=" N LEU C 973 " --> pdb=" O LYS C 969 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N GLN C 979 " --> pdb=" O ARG C 975 " (cutoff:3.500A) Processing helix chain 'C' and resid 992 through 998 Processing helix chain 'C' and resid 1039 through 1071 Processing helix chain 'D' and resid 448 through 455 Processing helix chain 'D' and resid 459 through 465 Processing helix chain 'D' and resid 485 through 492 Processing helix chain 'D' and resid 495 through 504 Processing helix chain 'D' and resid 517 through 524 Processing helix chain 'D' and resid 527 through 535 removed outlier: 3.829A pdb=" N ASP D 535 " --> pdb=" O LYS D 531 " (cutoff:3.500A) Processing helix chain 'D' and resid 551 through 558 Processing helix chain 'D' and resid 561 through 569 Processing helix chain 'D' and resid 583 through 589 Processing helix chain 'D' and resid 593 through 601 Processing helix chain 'D' and resid 605 through 610 Processing helix chain 'D' and resid 622 through 629 Processing helix chain 'D' and resid 631 through 641 removed outlier: 3.687A pdb=" N VAL D 636 " --> pdb=" O GLU D 632 " (cutoff:3.500A) removed outlier: 4.052A pdb=" N CYS D 641 " --> pdb=" O LEU D 637 " (cutoff:3.500A) Processing helix chain 'D' and resid 666 through 668 No H-bonds generated for 'chain 'D' and resid 666 through 668' Processing helix chain 'D' and resid 684 through 692 removed outlier: 3.518A pdb=" N ASN D 692 " --> pdb=" O ALA D 688 " (cutoff:3.500A) Processing helix chain 'D' and resid 695 through 698 No H-bonds generated for 'chain 'D' and resid 695 through 698' Processing helix chain 'D' and resid 701 through 739 removed outlier: 6.230A pdb=" N PHE D 716 " --> pdb=" O LEU D 712 " (cutoff:3.500A) removed outlier: 6.245A pdb=" N ARG D 717 " --> pdb=" O ALA D 713 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N ASN D 722 " --> pdb=" O ALA D 718 " (cutoff:3.500A) removed outlier: 4.291A pdb=" N GLY D 729 " --> pdb=" O SER D 725 " (cutoff:3.500A) Proline residue: D 732 - end of helix Processing helix chain 'D' and resid 767 through 791 Processing helix chain 'D' and resid 803 through 818 removed outlier: 3.655A pdb=" N ILE D 817 " --> pdb=" O THR D 813 " (cutoff:3.500A) Processing helix chain 'D' and resid 820 through 822 No H-bonds generated for 'chain 'D' and resid 820 through 822' Processing helix chain 'D' and resid 828 through 852 removed outlier: 3.919A pdb=" N ILE D 837 " --> pdb=" O GLN D 833 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N TYR D 840 " --> pdb=" O ALA D 836 " (cutoff:3.500A) removed outlier: 4.001A pdb=" N TRP D 843 " --> pdb=" O VAL D 839 " (cutoff:3.500A) removed outlier: 4.198A pdb=" N LEU D 847 " --> pdb=" O TRP D 843 " (cutoff:3.500A) removed outlier: 4.616A pdb=" N LEU D 848 " --> pdb=" O MET D 844 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N TYR D 849 " --> pdb=" O ASN D 845 " (cutoff:3.500A) removed outlier: 4.742A pdb=" N ARG D 852 " --> pdb=" O LEU D 848 " (cutoff:3.500A) Processing helix chain 'D' and resid 858 through 871 Processing helix chain 'D' and resid 874 through 877 No H-bonds generated for 'chain 'D' and resid 874 through 877' Processing helix chain 'D' and resid 879 through 891 removed outlier: 3.680A pdb=" N ILE D 890 " --> pdb=" O LEU D 886 " (cutoff:3.500A) Processing helix chain 'D' and resid 896 through 898 No H-bonds generated for 'chain 'D' and resid 896 through 898' Processing helix chain 'D' and resid 901 through 913 removed outlier: 3.661A pdb=" N MET D 912 " --> pdb=" O THR D 908 " (cutoff:3.500A) removed outlier: 5.088A pdb=" N LEU D 913 " --> pdb=" O PHE D 909 " (cutoff:3.500A) Processing helix chain 'D' and resid 918 through 921 No H-bonds generated for 'chain 'D' and resid 918 through 921' Processing helix chain 'D' and resid 923 through 927 Processing helix chain 'D' and resid 934 through 947 Processing helix chain 'D' and resid 951 through 987 removed outlier: 4.023A pdb=" N HIS D 970 " --> pdb=" O GLU D 966 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N ALA D 971 " --> pdb=" O VAL D 967 " (cutoff:3.500A) removed outlier: 5.565A pdb=" N SER D 972 " --> pdb=" O GLN D 968 " (cutoff:3.500A) removed outlier: 6.678A pdb=" N LEU D 973 " --> pdb=" O LYS D 969 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N GLN D 979 " --> pdb=" O ARG D 975 " (cutoff:3.500A) Processing helix chain 'D' and resid 992 through 998 Processing helix chain 'D' and resid 1039 through 1071 Processing sheet with id= A, first strand: chain 'A' and resid 642 through 644 Processing sheet with id= B, first strand: chain 'A' and resid 745 through 747 removed outlier: 4.229A pdb=" N ALA A 745 " --> pdb=" O ILE A 752 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'B' and resid 642 through 644 Processing sheet with id= D, first strand: chain 'B' and resid 745 through 747 removed outlier: 4.229A pdb=" N ALA B 745 " --> pdb=" O ILE B 752 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'C' and resid 642 through 644 Processing sheet with id= F, first strand: chain 'C' and resid 745 through 747 removed outlier: 4.228A pdb=" N ALA C 745 " --> pdb=" O ILE C 752 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'D' and resid 642 through 644 Processing sheet with id= H, first strand: chain 'D' and resid 745 through 747 removed outlier: 4.228A pdb=" N ALA D 745 " --> pdb=" O ILE D 752 " (cutoff:3.500A) 960 hydrogen bonds defined for protein. 2844 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 6.05 Time building geometry restraints manager: 8.16 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.16 - 1.29: 3044 1.29 - 1.42: 5038 1.42 - 1.55: 11882 1.55 - 1.68: 40 1.68 - 1.81: 232 Bond restraints: 20236 Sorted by residual: bond pdb=" C2 0IG B1201 " pdb=" N1 0IG B1201 " ideal model delta sigma weight residual 1.317 1.466 -0.149 2.00e-02 2.50e+03 5.52e+01 bond pdb=" C2 0IG C1201 " pdb=" N1 0IG C1201 " ideal model delta sigma weight residual 1.317 1.465 -0.148 2.00e-02 2.50e+03 5.50e+01 bond pdb=" C2 0IG A1201 " pdb=" N1 0IG A1201 " ideal model delta sigma weight residual 1.317 1.465 -0.148 2.00e-02 2.50e+03 5.49e+01 bond pdb=" C2 0IG D1202 " pdb=" N1 0IG D1202 " ideal model delta sigma weight residual 1.317 1.465 -0.148 2.00e-02 2.50e+03 5.49e+01 bond pdb=" N6 0IG C1201 " pdb=" N7 0IG C1201 " ideal model delta sigma weight residual 1.161 1.293 -0.132 2.00e-02 2.50e+03 4.33e+01 ... (remaining 20231 not shown) Histogram of bond angle deviations from ideal: 92.22 - 109.65: 2403 109.65 - 127.09: 24757 127.09 - 144.52: 248 144.52 - 161.95: 0 161.95 - 179.38: 4 Bond angle restraints: 27412 Sorted by residual: angle pdb=" C1 0IG B1201 " pdb=" N 0IG B1201 " pdb=" C2 0IG B1201 " ideal model delta sigma weight residual 127.53 109.41 18.12 3.00e+00 1.11e-01 3.65e+01 angle pdb=" C1 0IG A1201 " pdb=" N 0IG A1201 " pdb=" C2 0IG A1201 " ideal model delta sigma weight residual 127.53 109.42 18.11 3.00e+00 1.11e-01 3.64e+01 angle pdb=" C1 0IG C1201 " pdb=" N 0IG C1201 " pdb=" C2 0IG C1201 " ideal model delta sigma weight residual 127.53 109.45 18.08 3.00e+00 1.11e-01 3.63e+01 angle pdb=" C1 0IG D1202 " pdb=" N 0IG D1202 " pdb=" C2 0IG D1202 " ideal model delta sigma weight residual 127.53 109.49 18.04 3.00e+00 1.11e-01 3.62e+01 angle pdb=" C14 0IG A1201 " pdb=" N6 0IG A1201 " pdb=" N7 0IG A1201 " ideal model delta sigma weight residual 130.27 117.66 12.61 3.00e+00 1.11e-01 1.77e+01 ... (remaining 27407 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 23.95: 11726 23.95 - 47.90: 514 47.90 - 71.86: 88 71.86 - 95.81: 20 95.81 - 119.76: 48 Dihedral angle restraints: 12396 sinusoidal: 5368 harmonic: 7028 Sorted by residual: dihedral pdb=" C4 IHP D1201 " pdb=" C2 IHP D1201 " pdb=" C3 IHP D1201 " pdb=" O12 IHP D1201 " ideal model delta sinusoidal sigma weight residual 60.90 -179.34 -119.76 1 3.00e+01 1.11e-03 1.60e+01 dihedral pdb=" C4 IHP C1206 " pdb=" C2 IHP C1206 " pdb=" C3 IHP C1206 " pdb=" O12 IHP C1206 " ideal model delta sinusoidal sigma weight residual 60.90 -179.35 -119.75 1 3.00e+01 1.11e-03 1.60e+01 dihedral pdb=" C6 IHP D1201 " pdb=" C1 IHP D1201 " pdb=" C2 IHP D1201 " pdb=" O12 IHP D1201 " ideal model delta sinusoidal sigma weight residual 61.05 -179.20 -119.75 1 3.00e+01 1.11e-03 1.60e+01 ... (remaining 12393 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 1.007: 3164 1.007 - 2.013: 0 2.013 - 3.019: 0 3.019 - 4.026: 0 4.026 - 5.032: 16 Chirality restraints: 3180 Sorted by residual: chirality pdb=" C5 IHP D1201 " pdb=" C4 IHP D1201 " pdb=" C6 IHP D1201 " pdb=" O15 IHP D1201 " both_signs ideal model delta sigma weight residual False -2.42 2.62 -5.03 2.00e-01 2.50e+01 6.33e+02 chirality pdb=" C5 IHP A1206 " pdb=" C4 IHP A1206 " pdb=" C6 IHP A1206 " pdb=" O15 IHP A1206 " both_signs ideal model delta sigma weight residual False -2.42 2.61 -5.03 2.00e-01 2.50e+01 6.33e+02 chirality pdb=" C5 IHP B1206 " pdb=" C4 IHP B1206 " pdb=" C6 IHP B1206 " pdb=" O15 IHP B1206 " both_signs ideal model delta sigma weight residual False -2.42 2.61 -5.03 2.00e-01 2.50e+01 6.32e+02 ... (remaining 3177 not shown) Planarity restraints: 3304 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C10 0IG A1201 " 0.223 2.00e-02 2.50e+03 2.73e-01 1.86e+03 pdb=" C11 0IG A1201 " 0.075 2.00e-02 2.50e+03 pdb=" C12 0IG A1201 " 0.229 2.00e-02 2.50e+03 pdb=" C13 0IG A1201 " 0.082 2.00e-02 2.50e+03 pdb=" C14 0IG A1201 " -0.219 2.00e-02 2.50e+03 pdb=" C15 0IG A1201 " -0.373 2.00e-02 2.50e+03 pdb=" C16 0IG A1201 " -0.227 2.00e-02 2.50e+03 pdb=" N6 0IG A1201 " -0.371 2.00e-02 2.50e+03 pdb=" N7 0IG A1201 " 0.085 2.00e-02 2.50e+03 pdb=" N8 0IG A1201 " 0.496 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C10 0IG B1201 " -0.223 2.00e-02 2.50e+03 2.73e-01 1.86e+03 pdb=" C11 0IG B1201 " -0.075 2.00e-02 2.50e+03 pdb=" C12 0IG B1201 " -0.230 2.00e-02 2.50e+03 pdb=" C13 0IG B1201 " -0.082 2.00e-02 2.50e+03 pdb=" C14 0IG B1201 " 0.219 2.00e-02 2.50e+03 pdb=" C15 0IG B1201 " 0.373 2.00e-02 2.50e+03 pdb=" C16 0IG B1201 " 0.227 2.00e-02 2.50e+03 pdb=" N6 0IG B1201 " 0.371 2.00e-02 2.50e+03 pdb=" N7 0IG B1201 " -0.085 2.00e-02 2.50e+03 pdb=" N8 0IG B1201 " -0.496 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C10 0IG C1201 " -0.223 2.00e-02 2.50e+03 2.73e-01 1.86e+03 pdb=" C11 0IG C1201 " -0.075 2.00e-02 2.50e+03 pdb=" C12 0IG C1201 " -0.230 2.00e-02 2.50e+03 pdb=" C13 0IG C1201 " -0.082 2.00e-02 2.50e+03 pdb=" C14 0IG C1201 " 0.219 2.00e-02 2.50e+03 pdb=" C15 0IG C1201 " 0.373 2.00e-02 2.50e+03 pdb=" C16 0IG C1201 " 0.227 2.00e-02 2.50e+03 pdb=" N6 0IG C1201 " 0.371 2.00e-02 2.50e+03 pdb=" N7 0IG C1201 " -0.085 2.00e-02 2.50e+03 pdb=" N8 0IG C1201 " -0.496 2.00e-02 2.50e+03 ... (remaining 3301 not shown) Histogram of nonbonded interaction distances: 2.22 - 2.75: 3288 2.75 - 3.29: 19013 3.29 - 3.83: 30452 3.83 - 4.36: 38340 4.36 - 4.90: 65744 Nonbonded interactions: 156837 Sorted by model distance: nonbonded pdb=" ND2 ASN D 855 " pdb=" O 0IG D1202 " model vdw 2.217 2.520 nonbonded pdb=" ND2 ASN A 855 " pdb=" O 0IG A1201 " model vdw 2.217 2.520 nonbonded pdb=" ND2 ASN C 855 " pdb=" O 0IG C1201 " model vdw 2.217 2.520 nonbonded pdb=" ND2 ASN B 855 " pdb=" O 0IG B1201 " model vdw 2.218 2.520 nonbonded pdb=" O ILE B 916 " pdb=" O HOH B1301 " model vdw 2.270 2.440 ... (remaining 156832 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'A' and (resid 447 through 1079 or (resid 1203 and (name C1 or name C11 o \ r name C2 or name C21 or name C22 or name C23 or name C24 or name C25 or name C2 \ 6 or name C27 or name C28 or name C29 or name C2A or name C2B or name C2C or nam \ e C2D or name C3 or name C31 or name C32 or name C33 or name C34 or name C35 or \ name C36 or name C37 or name C38 or name C39 or name C3A or name C3B or name O11 \ or name O12 or name O13 or name O14 or name O21 or name O22 or name O31 or name \ O32 or name P )))) selection = (chain 'B' and (resid 447 through 1079 or (resid 1203 and (name C1 or name C11 o \ r name C2 or name C21 or name C22 or name C23 or name C24 or name C25 or name C2 \ 6 or name C27 or name C28 or name C29 or name C2A or name C2B or name C2C or nam \ e C2D or name C3 or name C31 or name C32 or name C33 or name C34 or name C35 or \ name C36 or name C37 or name C38 or name C39 or name C3A or name C3B or name O11 \ or name O12 or name O13 or name O14 or name O21 or name O22 or name O31 or name \ O32 or name P )))) selection = (chain 'C' and (resid 447 through 1079 or (resid 1203 and (name C1 or name C11 o \ r name C2 or name C21 or name C22 or name C23 or name C24 or name C25 or name C2 \ 6 or name C27 or name C28 or name C29 or name C2A or name C2B or name C2C or nam \ e C2D or name C3 or name C31 or name C32 or name C33 or name C34 or name C35 or \ name C36 or name C37 or name C38 or name C39 or name C3A or name C3B or name O11 \ or name O12 or name O13 or name O14 or name O21 or name O22 or name O31 or name \ O32 or name P )))) selection = (chain 'D' and (resid 447 through 1079 or (resid 1203 and (name C1 or name C11 o \ r name C2 or name C21 or name C22 or name C23 or name C24 or name C25 or name C2 \ 6 or name C27 or name C28 or name C29 or name C2A or name C2B or name C2C or nam \ e C2D or name C3 or name C31 or name C32 or name C33 or name C34 or name C35 or \ name C36 or name C37 or name C38 or name C39 or name C3A or name C3B or name O11 \ or name O12 or name O13 or name O14 or name O21 or name O22 or name O31 or name \ O32 or name P )))) } ncs_group { reference = chain 'E' selection = chain 'F' selection = chain 'G' 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 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: 1.030 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: 0.020 Extract box with map and model: 5.460 Check model and map are aligned: 0.250 Set scattering table: 0.180 Process input model: 50.830 Find NCS groups from input model: 1.270 Set up NCS constraints: 0.130 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:13.520 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 72.700 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8216 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 : 0.009 0.149 20236 Z= 0.580 Angle : 0.850 18.117 27412 Z= 0.400 Chirality : 0.354 5.032 3180 Planarity : 0.011 0.273 3296 Dihedral : 16.304 119.760 7828 Min Nonbonded Distance : 2.217 Molprobity Statistics. All-atom Clashscore : 2.61 Ramachandran Plot: Outliers : 0.34 % Allowed : 5.44 % Favored : 94.22 % Rotamer: Outliers : 1.15 % Allowed : 6.99 % Favored : 91.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.99 (0.16), residues: 2352 helix: -0.75 (0.12), residues: 1644 sheet: -0.42 (0.58), residues: 68 loop : -2.64 (0.22), residues: 640 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP C 832 HIS 0.004 0.001 HIS D 983 PHE 0.012 0.002 PHE A 583 TYR 0.013 0.002 TYR C 456 ARG 0.004 0.001 ARG B 996 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4704 Ramachandran restraints generated. 2352 Oldfield, 0 Emsley, 2352 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4704 Ramachandran restraints generated. 2352 Oldfield, 0 Emsley, 2352 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 219 residues out of total 2156 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 195 time to evaluate : 2.279 Fit side-chains REVERT: A 809 TRP cc_start: 0.7826 (t60) cc_final: 0.7617 (t60) REVERT: A 912 MET cc_start: 0.8420 (ttm) cc_final: 0.8146 (ttp) REVERT: B 508 PHE cc_start: 0.9170 (m-80) cc_final: 0.8865 (m-80) REVERT: B 953 MET cc_start: 0.8561 (mmm) cc_final: 0.8354 (mmm) REVERT: C 862 MET cc_start: 0.8879 (mtt) cc_final: 0.8412 (mtt) REVERT: C 912 MET cc_start: 0.8473 (ttm) cc_final: 0.8252 (ttp) REVERT: D 912 MET cc_start: 0.8426 (ttm) cc_final: 0.8153 (ttp) outliers start: 24 outliers final: 9 residues processed: 211 average time/residue: 1.3287 time to fit residues: 316.6723 Evaluate side-chains 177 residues out of total 2156 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 168 time to evaluate : 2.000 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 469 ILE Chi-restraints excluded: chain A residue 684 THR Chi-restraints excluded: chain A residue 785 TYR Chi-restraints excluded: chain B residue 611 ILE Chi-restraints excluded: chain C residue 469 ILE Chi-restraints excluded: chain C residue 684 THR Chi-restraints excluded: chain C residue 785 TYR Chi-restraints excluded: chain D residue 469 ILE Chi-restraints excluded: chain D residue 684 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 236 random chunks: chunk 199 optimal weight: 0.6980 chunk 178 optimal weight: 3.9990 chunk 99 optimal weight: 0.8980 chunk 61 optimal weight: 6.9990 chunk 120 optimal weight: 6.9990 chunk 95 optimal weight: 2.9990 chunk 184 optimal weight: 0.7980 chunk 71 optimal weight: 2.9990 chunk 112 optimal weight: 6.9990 chunk 137 optimal weight: 1.9990 chunk 214 optimal weight: 2.9990 overall best weight: 1.4784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 619 ASN A 664 GLN ** A 855 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1008 ASN ** A1047 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 615 ASN B 619 ASN B 664 GLN B1008 ASN ** B1047 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 619 ASN ** C 855 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C1008 ASN ** C1047 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 619 ASN D 664 GLN ** D 855 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D1008 ASN ** D1047 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8204 moved from start: 0.0924 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 20236 Z= 0.233 Angle : 0.622 11.441 27412 Z= 0.286 Chirality : 0.044 0.512 3180 Planarity : 0.004 0.049 3296 Dihedral : 9.471 73.695 3303 Min Nonbonded Distance : 2.147 Molprobity Statistics. All-atom Clashscore : 2.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.83 % Favored : 96.17 % Rotamer: Outliers : 2.11 % Allowed : 8.81 % Favored : 89.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.28 (0.17), residues: 2352 helix: 0.54 (0.13), residues: 1624 sheet: 1.73 (0.57), residues: 60 loop : -2.09 (0.24), residues: 668 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP D 832 HIS 0.004 0.001 HIS C 970 PHE 0.010 0.001 PHE B 583 TYR 0.008 0.001 TYR B 706 ARG 0.005 0.000 ARG A 996 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4704 Ramachandran restraints generated. 2352 Oldfield, 0 Emsley, 2352 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4704 Ramachandran restraints generated. 2352 Oldfield, 0 Emsley, 2352 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 235 residues out of total 2156 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 191 time to evaluate : 2.348 Fit side-chains REVERT: A 562 LYS cc_start: 0.8872 (OUTLIER) cc_final: 0.8386 (mppt) REVERT: A 912 MET cc_start: 0.8365 (ttm) cc_final: 0.8106 (ttp) REVERT: C 912 MET cc_start: 0.8397 (ttm) cc_final: 0.8173 (ttp) REVERT: C 1063 GLU cc_start: 0.8029 (OUTLIER) cc_final: 0.7751 (mp0) REVERT: D 651 CYS cc_start: 0.8393 (m) cc_final: 0.8137 (m) REVERT: D 744 MET cc_start: 0.8436 (OUTLIER) cc_final: 0.7838 (mtm) REVERT: D 912 MET cc_start: 0.8363 (ttm) cc_final: 0.8102 (ttp) REVERT: D 1063 GLU cc_start: 0.7927 (OUTLIER) cc_final: 0.7443 (mp0) outliers start: 44 outliers final: 20 residues processed: 217 average time/residue: 1.2595 time to fit residues: 310.1154 Evaluate side-chains 199 residues out of total 2156 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 175 time to evaluate : 2.159 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 469 ILE Chi-restraints excluded: chain A residue 495 ASP Chi-restraints excluded: chain A residue 562 LYS Chi-restraints excluded: chain A residue 684 THR Chi-restraints excluded: chain A residue 721 MET Chi-restraints excluded: chain A residue 785 TYR Chi-restraints excluded: chain A residue 875 VAL Chi-restraints excluded: chain B residue 469 ILE Chi-restraints excluded: chain B residue 684 THR Chi-restraints excluded: chain B residue 785 TYR Chi-restraints excluded: chain B residue 1045 LEU Chi-restraints excluded: chain C residue 469 ILE Chi-restraints excluded: chain C residue 607 GLU Chi-restraints excluded: chain C residue 684 THR Chi-restraints excluded: chain C residue 785 TYR Chi-restraints excluded: chain C residue 992 LEU Chi-restraints excluded: chain C residue 1063 GLU Chi-restraints excluded: chain D residue 469 ILE Chi-restraints excluded: chain D residue 607 GLU Chi-restraints excluded: chain D residue 684 THR Chi-restraints excluded: chain D residue 744 MET Chi-restraints excluded: chain D residue 785 TYR Chi-restraints excluded: chain D residue 839 VAL Chi-restraints excluded: chain D residue 1063 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 236 random chunks: chunk 119 optimal weight: 4.9990 chunk 66 optimal weight: 1.9990 chunk 178 optimal weight: 2.9990 chunk 145 optimal weight: 0.9980 chunk 59 optimal weight: 8.9990 chunk 214 optimal weight: 0.8980 chunk 231 optimal weight: 3.9990 chunk 191 optimal weight: 0.0040 chunk 212 optimal weight: 1.9990 chunk 73 optimal weight: 0.0870 chunk 172 optimal weight: 3.9990 overall best weight: 0.7972 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 664 GLN A1008 ASN A1047 GLN B 664 GLN B1008 ASN B1047 GLN C1008 ASN C1047 GLN D 664 GLN D1008 ASN D1047 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8168 moved from start: 0.1457 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 20236 Z= 0.144 Angle : 0.489 8.374 27412 Z= 0.237 Chirality : 0.038 0.191 3180 Planarity : 0.004 0.047 3296 Dihedral : 8.519 71.235 3301 Min Nonbonded Distance : 2.190 Molprobity Statistics. All-atom Clashscore : 2.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.87 % Favored : 96.13 % Rotamer: Outliers : 2.30 % Allowed : 8.76 % Favored : 88.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.65 (0.18), residues: 2352 helix: 1.19 (0.13), residues: 1624 sheet: 2.45 (0.62), residues: 60 loop : -1.64 (0.25), residues: 668 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 832 HIS 0.003 0.001 HIS B 481 PHE 0.007 0.001 PHE A 716 TYR 0.008 0.001 TYR A 662 ARG 0.006 0.000 ARG B 996 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4704 Ramachandran restraints generated. 2352 Oldfield, 0 Emsley, 2352 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4704 Ramachandran restraints generated. 2352 Oldfield, 0 Emsley, 2352 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 240 residues out of total 2156 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 192 time to evaluate : 2.137 Fit side-chains REVERT: A 1059 GLU cc_start: 0.8106 (mt-10) cc_final: 0.7863 (mt-10) REVERT: B 721 MET cc_start: 0.7521 (mmp) cc_final: 0.7232 (mmt) REVERT: C 912 MET cc_start: 0.8324 (ttm) cc_final: 0.8120 (ttp) REVERT: D 651 CYS cc_start: 0.8374 (m) cc_final: 0.8143 (m) outliers start: 48 outliers final: 20 residues processed: 225 average time/residue: 1.2304 time to fit residues: 314.5752 Evaluate side-chains 199 residues out of total 2156 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 179 time to evaluate : 2.113 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 469 ILE Chi-restraints excluded: chain A residue 684 THR Chi-restraints excluded: chain A residue 719 HIS Chi-restraints excluded: chain A residue 721 MET Chi-restraints excluded: chain A residue 785 TYR Chi-restraints excluded: chain A residue 992 LEU Chi-restraints excluded: chain B residue 495 ASP Chi-restraints excluded: chain B residue 607 GLU Chi-restraints excluded: chain C residue 469 ILE Chi-restraints excluded: chain C residue 607 GLU Chi-restraints excluded: chain C residue 684 THR Chi-restraints excluded: chain C residue 785 TYR Chi-restraints excluded: chain C residue 992 LEU Chi-restraints excluded: chain D residue 469 ILE Chi-restraints excluded: chain D residue 495 ASP Chi-restraints excluded: chain D residue 573 ASP Chi-restraints excluded: chain D residue 607 GLU Chi-restraints excluded: chain D residue 684 THR Chi-restraints excluded: chain D residue 719 HIS Chi-restraints excluded: chain D residue 785 TYR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 236 random chunks: chunk 212 optimal weight: 4.9990 chunk 161 optimal weight: 2.9990 chunk 111 optimal weight: 2.9990 chunk 23 optimal weight: 0.9980 chunk 102 optimal weight: 0.5980 chunk 144 optimal weight: 2.9990 chunk 215 optimal weight: 0.9980 chunk 228 optimal weight: 3.9990 chunk 112 optimal weight: 0.5980 chunk 204 optimal weight: 0.8980 chunk 61 optimal weight: 0.9980 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 664 GLN B 664 GLN B1008 ASN C 494 HIS D 664 GLN D1008 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8170 moved from start: 0.1619 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 20236 Z= 0.149 Angle : 0.480 10.105 27412 Z= 0.232 Chirality : 0.038 0.191 3180 Planarity : 0.004 0.045 3296 Dihedral : 8.315 68.572 3301 Min Nonbonded Distance : 2.216 Molprobity Statistics. All-atom Clashscore : 2.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.70 % Favored : 96.30 % Rotamer: Outliers : 1.96 % Allowed : 10.01 % Favored : 88.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.97 (0.18), residues: 2352 helix: 1.44 (0.13), residues: 1624 sheet: 1.50 (0.67), residues: 68 loop : -1.45 (0.25), residues: 660 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP D 832 HIS 0.004 0.001 HIS D 494 PHE 0.007 0.001 PHE B 583 TYR 0.007 0.001 TYR B 706 ARG 0.003 0.000 ARG C 996 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4704 Ramachandran restraints generated. 2352 Oldfield, 0 Emsley, 2352 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4704 Ramachandran restraints generated. 2352 Oldfield, 0 Emsley, 2352 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 227 residues out of total 2156 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 186 time to evaluate : 2.179 Fit side-chains REVERT: A 607 GLU cc_start: 0.7860 (OUTLIER) cc_final: 0.7599 (pt0) REVERT: A 1059 GLU cc_start: 0.8115 (mt-10) cc_final: 0.7873 (mt-10) REVERT: C 912 MET cc_start: 0.8327 (ttm) cc_final: 0.8099 (ttp) REVERT: D 651 CYS cc_start: 0.8412 (m) cc_final: 0.8192 (m) outliers start: 41 outliers final: 25 residues processed: 215 average time/residue: 1.2718 time to fit residues: 310.2679 Evaluate side-chains 196 residues out of total 2156 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 170 time to evaluate : 2.164 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 469 ILE Chi-restraints excluded: chain A residue 573 ASP Chi-restraints excluded: chain A residue 607 GLU Chi-restraints excluded: chain A residue 684 THR Chi-restraints excluded: chain A residue 719 HIS Chi-restraints excluded: chain A residue 721 MET Chi-restraints excluded: chain A residue 785 TYR Chi-restraints excluded: chain A residue 992 LEU Chi-restraints excluded: chain B residue 495 ASP Chi-restraints excluded: chain B residue 607 GLU Chi-restraints excluded: chain B residue 684 THR Chi-restraints excluded: chain B residue 785 TYR Chi-restraints excluded: chain B residue 833 GLN Chi-restraints excluded: chain B residue 912 MET Chi-restraints excluded: chain C residue 469 ILE Chi-restraints excluded: chain C residue 573 ASP Chi-restraints excluded: chain C residue 607 GLU Chi-restraints excluded: chain C residue 684 THR Chi-restraints excluded: chain C residue 785 TYR Chi-restraints excluded: chain C residue 992 LEU Chi-restraints excluded: chain D residue 469 ILE Chi-restraints excluded: chain D residue 573 ASP Chi-restraints excluded: chain D residue 607 GLU Chi-restraints excluded: chain D residue 684 THR Chi-restraints excluded: chain D residue 719 HIS Chi-restraints excluded: chain D residue 785 TYR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 236 random chunks: chunk 189 optimal weight: 6.9990 chunk 129 optimal weight: 3.9990 chunk 3 optimal weight: 4.9990 chunk 169 optimal weight: 3.9990 chunk 94 optimal weight: 1.9990 chunk 194 optimal weight: 5.9990 chunk 157 optimal weight: 0.9990 chunk 0 optimal weight: 4.9990 chunk 116 optimal weight: 2.9990 chunk 204 optimal weight: 0.6980 chunk 57 optimal weight: 0.6980 overall best weight: 1.4786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 664 GLN B 664 GLN B1008 ASN C 481 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8198 moved from start: 0.1743 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 20236 Z= 0.219 Angle : 0.508 10.324 27412 Z= 0.248 Chirality : 0.039 0.189 3180 Planarity : 0.004 0.041 3296 Dihedral : 8.313 65.857 3301 Min Nonbonded Distance : 2.217 Molprobity Statistics. All-atom Clashscore : 2.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.29 % Favored : 95.71 % Rotamer: Outliers : 2.49 % Allowed : 10.20 % Favored : 87.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.11 (0.18), residues: 2352 helix: 1.51 (0.13), residues: 1628 sheet: 1.59 (0.68), residues: 68 loop : -1.32 (0.25), residues: 656 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 832 HIS 0.004 0.001 HIS C 983 PHE 0.009 0.001 PHE B 583 TYR 0.008 0.001 TYR C 706 ARG 0.004 0.000 ARG B 996 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4704 Ramachandran restraints generated. 2352 Oldfield, 0 Emsley, 2352 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4704 Ramachandran restraints generated. 2352 Oldfield, 0 Emsley, 2352 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 238 residues out of total 2156 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 186 time to evaluate : 2.255 Fit side-chains REVERT: A 664 GLN cc_start: 0.8622 (pt0) cc_final: 0.8189 (pm20) REVERT: A 1059 GLU cc_start: 0.8128 (mt-10) cc_final: 0.7916 (mt-10) REVERT: B 664 GLN cc_start: 0.8588 (pt0) cc_final: 0.8102 (pm20) REVERT: B 1063 GLU cc_start: 0.8002 (OUTLIER) cc_final: 0.7488 (mp0) REVERT: C 483 MET cc_start: 0.8688 (mtp) cc_final: 0.8386 (mtm) REVERT: C 530 MET cc_start: 0.8660 (mtp) cc_final: 0.8160 (mtp) REVERT: D 651 CYS cc_start: 0.8459 (m) cc_final: 0.8225 (m) REVERT: D 664 GLN cc_start: 0.8564 (pt0) cc_final: 0.8141 (pm20) REVERT: D 864 GLU cc_start: 0.7730 (OUTLIER) cc_final: 0.7452 (tm-30) outliers start: 52 outliers final: 30 residues processed: 224 average time/residue: 1.2633 time to fit residues: 321.3633 Evaluate side-chains 209 residues out of total 2156 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 177 time to evaluate : 2.042 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 469 ILE Chi-restraints excluded: chain A residue 495 ASP Chi-restraints excluded: chain A residue 607 GLU Chi-restraints excluded: chain A residue 684 THR Chi-restraints excluded: chain A residue 719 HIS Chi-restraints excluded: chain A residue 721 MET Chi-restraints excluded: chain A residue 785 TYR Chi-restraints excluded: chain A residue 839 VAL Chi-restraints excluded: chain A residue 992 LEU Chi-restraints excluded: chain B residue 495 ASP Chi-restraints excluded: chain B residue 607 GLU Chi-restraints excluded: chain B residue 719 HIS Chi-restraints excluded: chain B residue 785 TYR Chi-restraints excluded: chain B residue 839 VAL Chi-restraints excluded: chain B residue 912 MET Chi-restraints excluded: chain B residue 1063 GLU Chi-restraints excluded: chain C residue 469 ILE Chi-restraints excluded: chain C residue 573 ASP Chi-restraints excluded: chain C residue 607 GLU Chi-restraints excluded: chain C residue 684 THR Chi-restraints excluded: chain C residue 785 TYR Chi-restraints excluded: chain C residue 839 VAL Chi-restraints excluded: chain C residue 992 LEU Chi-restraints excluded: chain D residue 469 ILE Chi-restraints excluded: chain D residue 573 ASP Chi-restraints excluded: chain D residue 607 GLU Chi-restraints excluded: chain D residue 684 THR Chi-restraints excluded: chain D residue 719 HIS Chi-restraints excluded: chain D residue 785 TYR Chi-restraints excluded: chain D residue 864 GLU Chi-restraints excluded: chain D residue 875 VAL Chi-restraints excluded: chain D residue 992 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 236 random chunks: chunk 76 optimal weight: 7.9990 chunk 205 optimal weight: 0.5980 chunk 45 optimal weight: 0.9980 chunk 133 optimal weight: 0.8980 chunk 56 optimal weight: 6.9990 chunk 228 optimal weight: 0.9990 chunk 189 optimal weight: 0.3980 chunk 105 optimal weight: 0.6980 chunk 18 optimal weight: 3.9990 chunk 75 optimal weight: 0.6980 chunk 119 optimal weight: 4.9990 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 494 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8163 moved from start: 0.1934 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 20236 Z= 0.133 Angle : 0.461 9.150 27412 Z= 0.225 Chirality : 0.037 0.190 3180 Planarity : 0.003 0.040 3296 Dihedral : 7.999 63.869 3301 Min Nonbonded Distance : 2.220 Molprobity Statistics. All-atom Clashscore : 3.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.66 % Favored : 96.34 % Rotamer: Outliers : 1.87 % Allowed : 11.35 % Favored : 86.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.29 (0.18), residues: 2352 helix: 1.59 (0.13), residues: 1652 sheet: 3.24 (0.75), residues: 48 loop : -1.24 (0.25), residues: 652 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 832 HIS 0.002 0.000 HIS D 983 PHE 0.008 0.001 PHE C 877 TYR 0.007 0.001 TYR B 706 ARG 0.004 0.000 ARG A1050 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4704 Ramachandran restraints generated. 2352 Oldfield, 0 Emsley, 2352 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4704 Ramachandran restraints generated. 2352 Oldfield, 0 Emsley, 2352 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 222 residues out of total 2156 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 183 time to evaluate : 2.360 Fit side-chains REVERT: A 483 MET cc_start: 0.8835 (mtp) cc_final: 0.8519 (mtm) REVERT: A 530 MET cc_start: 0.8755 (mtp) cc_final: 0.8296 (mtp) REVERT: A 864 GLU cc_start: 0.7757 (OUTLIER) cc_final: 0.7497 (tm-30) REVERT: B 1059 GLU cc_start: 0.8020 (mt-10) cc_final: 0.7782 (mt-10) REVERT: C 483 MET cc_start: 0.8683 (mtp) cc_final: 0.8388 (mtm) REVERT: C 530 MET cc_start: 0.8626 (mtp) cc_final: 0.8146 (mtp) REVERT: C 721 MET cc_start: 0.7646 (OUTLIER) cc_final: 0.7424 (mmt) outliers start: 39 outliers final: 19 residues processed: 213 average time/residue: 1.3209 time to fit residues: 318.0303 Evaluate side-chains 195 residues out of total 2156 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 174 time to evaluate : 2.395 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 469 ILE Chi-restraints excluded: chain A residue 684 THR Chi-restraints excluded: chain A residue 785 TYR Chi-restraints excluded: chain A residue 864 GLU Chi-restraints excluded: chain A residue 992 LEU Chi-restraints excluded: chain B residue 469 ILE Chi-restraints excluded: chain B residue 607 GLU Chi-restraints excluded: chain B residue 719 HIS Chi-restraints excluded: chain B residue 785 TYR Chi-restraints excluded: chain C residue 469 ILE Chi-restraints excluded: chain C residue 495 ASP Chi-restraints excluded: chain C residue 607 GLU Chi-restraints excluded: chain C residue 684 THR Chi-restraints excluded: chain C residue 721 MET Chi-restraints excluded: chain C residue 785 TYR Chi-restraints excluded: chain C residue 992 LEU Chi-restraints excluded: chain D residue 469 ILE Chi-restraints excluded: chain D residue 607 GLU Chi-restraints excluded: chain D residue 684 THR Chi-restraints excluded: chain D residue 785 TYR Chi-restraints excluded: chain D residue 992 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 236 random chunks: chunk 220 optimal weight: 2.9990 chunk 25 optimal weight: 4.9990 chunk 130 optimal weight: 6.9990 chunk 166 optimal weight: 1.9990 chunk 129 optimal weight: 2.9990 chunk 192 optimal weight: 1.9990 chunk 127 optimal weight: 6.9990 chunk 227 optimal weight: 0.7980 chunk 142 optimal weight: 2.9990 chunk 138 optimal weight: 0.1980 chunk 105 optimal weight: 2.9990 overall best weight: 1.5986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8196 moved from start: 0.1932 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 20236 Z= 0.232 Angle : 0.504 9.151 27412 Z= 0.246 Chirality : 0.039 0.187 3180 Planarity : 0.003 0.035 3296 Dihedral : 8.100 61.365 3301 Min Nonbonded Distance : 2.214 Molprobity Statistics. All-atom Clashscore : 3.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.38 % Favored : 95.62 % Rotamer: Outliers : 1.72 % Allowed : 12.16 % Favored : 86.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.33 (0.18), residues: 2352 helix: 1.65 (0.13), residues: 1632 sheet: 3.22 (0.75), residues: 48 loop : -1.24 (0.25), residues: 672 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP D 832 HIS 0.003 0.001 HIS D 983 PHE 0.009 0.001 PHE B 583 TYR 0.009 0.001 TYR D 706 ARG 0.005 0.000 ARG A1050 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4704 Ramachandran restraints generated. 2352 Oldfield, 0 Emsley, 2352 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4704 Ramachandran restraints generated. 2352 Oldfield, 0 Emsley, 2352 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 213 residues out of total 2156 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 177 time to evaluate : 2.595 Fit side-chains REVERT: A 864 GLU cc_start: 0.7779 (OUTLIER) cc_final: 0.7518 (tm-30) REVERT: B 1059 GLU cc_start: 0.8036 (mt-10) cc_final: 0.7799 (mt-10) REVERT: C 483 MET cc_start: 0.8717 (mtp) cc_final: 0.8398 (mtm) REVERT: D 664 GLN cc_start: 0.8533 (pt0) cc_final: 0.7748 (pm20) outliers start: 36 outliers final: 27 residues processed: 204 average time/residue: 1.3044 time to fit residues: 302.2847 Evaluate side-chains 202 residues out of total 2156 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 174 time to evaluate : 2.366 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 611 ILE Chi-restraints excluded: chain A residue 684 THR Chi-restraints excluded: chain A residue 719 HIS Chi-restraints excluded: chain A residue 721 MET Chi-restraints excluded: chain A residue 785 TYR Chi-restraints excluded: chain A residue 864 GLU Chi-restraints excluded: chain A residue 992 LEU Chi-restraints excluded: chain B residue 469 ILE Chi-restraints excluded: chain B residue 607 GLU Chi-restraints excluded: chain B residue 611 ILE Chi-restraints excluded: chain B residue 684 THR Chi-restraints excluded: chain B residue 719 HIS Chi-restraints excluded: chain B residue 785 TYR Chi-restraints excluded: chain B residue 912 MET Chi-restraints excluded: chain C residue 469 ILE Chi-restraints excluded: chain C residue 607 GLU Chi-restraints excluded: chain C residue 611 ILE Chi-restraints excluded: chain C residue 684 THR Chi-restraints excluded: chain C residue 719 HIS Chi-restraints excluded: chain C residue 785 TYR Chi-restraints excluded: chain C residue 992 LEU Chi-restraints excluded: chain D residue 469 ILE Chi-restraints excluded: chain D residue 607 GLU Chi-restraints excluded: chain D residue 611 ILE Chi-restraints excluded: chain D residue 684 THR Chi-restraints excluded: chain D residue 719 HIS Chi-restraints excluded: chain D residue 785 TYR Chi-restraints excluded: chain D residue 992 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 236 random chunks: chunk 140 optimal weight: 8.9990 chunk 90 optimal weight: 0.0970 chunk 135 optimal weight: 0.7980 chunk 68 optimal weight: 6.9990 chunk 44 optimal weight: 0.2980 chunk 144 optimal weight: 1.9990 chunk 154 optimal weight: 0.8980 chunk 112 optimal weight: 0.0170 chunk 21 optimal weight: 0.0470 chunk 178 optimal weight: 2.9990 chunk 206 optimal weight: 0.7980 overall best weight: 0.2514 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 664 GLN D 494 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8140 moved from start: 0.2176 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 20236 Z= 0.111 Angle : 0.450 8.386 27412 Z= 0.220 Chirality : 0.037 0.190 3180 Planarity : 0.003 0.035 3296 Dihedral : 7.622 58.264 3299 Min Nonbonded Distance : 2.209 Molprobity Statistics. All-atom Clashscore : 3.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.19 % Favored : 96.81 % Rotamer: Outliers : 1.72 % Allowed : 12.31 % Favored : 85.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.55 (0.18), residues: 2352 helix: 1.74 (0.13), residues: 1656 sheet: 3.40 (0.77), residues: 48 loop : -1.03 (0.25), residues: 648 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 832 HIS 0.002 0.000 HIS A 719 PHE 0.009 0.001 PHE C 877 TYR 0.007 0.001 TYR B 706 ARG 0.004 0.000 ARG C1050 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4704 Ramachandran restraints generated. 2352 Oldfield, 0 Emsley, 2352 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4704 Ramachandran restraints generated. 2352 Oldfield, 0 Emsley, 2352 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 226 residues out of total 2156 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 190 time to evaluate : 2.402 Fit side-chains REVERT: B 571 ASN cc_start: 0.8249 (t0) cc_final: 0.8039 (t0) REVERT: B 1059 GLU cc_start: 0.7999 (mt-10) cc_final: 0.7771 (mt-10) REVERT: C 483 MET cc_start: 0.8715 (mtp) cc_final: 0.8411 (mtm) REVERT: C 530 MET cc_start: 0.8667 (mtp) cc_final: 0.8282 (mtp) REVERT: C 721 MET cc_start: 0.7643 (mmt) cc_final: 0.7420 (mmt) REVERT: D 469 ILE cc_start: 0.8111 (OUTLIER) cc_final: 0.7910 (pp) REVERT: D 571 ASN cc_start: 0.8242 (t0) cc_final: 0.7995 (t0) REVERT: D 664 GLN cc_start: 0.8531 (pt0) cc_final: 0.7715 (pm20) outliers start: 36 outliers final: 20 residues processed: 214 average time/residue: 1.3357 time to fit residues: 322.5697 Evaluate side-chains 203 residues out of total 2156 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 182 time to evaluate : 2.246 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 469 ILE Chi-restraints excluded: chain A residue 684 THR Chi-restraints excluded: chain A residue 721 MET Chi-restraints excluded: chain A residue 785 TYR Chi-restraints excluded: chain B residue 607 GLU Chi-restraints excluded: chain B residue 684 THR Chi-restraints excluded: chain B residue 785 TYR Chi-restraints excluded: chain C residue 469 ILE Chi-restraints excluded: chain C residue 495 ASP Chi-restraints excluded: chain C residue 607 GLU Chi-restraints excluded: chain C residue 611 ILE Chi-restraints excluded: chain C residue 684 THR Chi-restraints excluded: chain C residue 719 HIS Chi-restraints excluded: chain C residue 785 TYR Chi-restraints excluded: chain C residue 992 LEU Chi-restraints excluded: chain D residue 469 ILE Chi-restraints excluded: chain D residue 607 GLU Chi-restraints excluded: chain D residue 684 THR Chi-restraints excluded: chain D residue 719 HIS Chi-restraints excluded: chain D residue 785 TYR Chi-restraints excluded: chain D residue 992 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/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-5265/modules/cctbx_project/iotbx/cli_parser.py", line 944, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/phenix/phenix/programs/real_space_refine.py", line 189, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/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-5265/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 700, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 764, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/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-5265/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-5265/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-5265/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-5265/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-5265/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-5265/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/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-5265/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-5265/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-5265/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-5265/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: 71.0031 > 50: distance: 28 - 65: 29.523 distance: 31 - 62: 23.637 distance: 48 - 54: 14.622 distance: 54 - 55: 10.061 distance: 54 - 251: 11.340 distance: 55 - 56: 23.757 distance: 55 - 58: 10.235 distance: 56 - 57: 18.128 distance: 56 - 62: 29.116 distance: 57 - 248: 20.009 distance: 58 - 59: 31.209 distance: 58 - 60: 31.615 distance: 59 - 61: 11.909 distance: 62 - 63: 16.574 distance: 63 - 64: 18.190 distance: 63 - 66: 32.408 distance: 64 - 65: 9.791 distance: 64 - 71: 11.583 distance: 66 - 67: 14.538 distance: 67 - 68: 30.279 distance: 68 - 69: 9.846 distance: 68 - 70: 8.071 distance: 71 - 72: 16.878 distance: 71 - 236: 33.446 distance: 72 - 73: 34.327 distance: 72 - 75: 20.039 distance: 73 - 74: 42.580 distance: 73 - 83: 16.773 distance: 74 - 233: 35.433 distance: 75 - 76: 24.967 distance: 76 - 77: 12.507 distance: 76 - 78: 7.198 distance: 77 - 79: 17.093 distance: 78 - 80: 29.790 distance: 79 - 81: 32.532 distance: 80 - 81: 21.691 distance: 81 - 82: 12.554 distance: 83 - 84: 9.357 distance: 84 - 85: 32.479 distance: 84 - 87: 16.294 distance: 85 - 86: 6.895 distance: 85 - 91: 7.390 distance: 87 - 88: 10.256 distance: 88 - 89: 10.813 distance: 88 - 90: 29.346 distance: 91 - 92: 36.186 distance: 92 - 93: 7.141 distance: 92 - 95: 20.752 distance: 93 - 94: 39.723 distance: 93 - 102: 11.308 distance: 95 - 96: 44.055 distance: 96 - 97: 10.093 distance: 96 - 98: 6.760 distance: 97 - 99: 11.525 distance: 98 - 100: 14.517 distance: 100 - 101: 4.429 distance: 102 - 103: 30.850 distance: 103 - 104: 32.286 distance: 103 - 106: 4.171 distance: 104 - 105: 37.414 distance: 104 - 111: 5.949 distance: 106 - 107: 35.432 distance: 108 - 109: 28.132 distance: 109 - 110: 41.252 distance: 111 - 112: 21.523 distance: 112 - 113: 5.231 distance: 112 - 115: 14.947 distance: 113 - 114: 9.994 distance: 113 - 123: 24.437 distance: 115 - 116: 12.048 distance: 116 - 117: 17.793 distance: 116 - 118: 10.789 distance: 117 - 119: 19.783 distance: 118 - 120: 20.974 distance: 119 - 121: 5.425 distance: 120 - 121: 13.382 distance: 121 - 122: 11.703 distance: 123 - 124: 22.693 distance: 124 - 125: 11.875 distance: 124 - 127: 23.841 distance: 125 - 126: 10.417 distance: 125 - 131: 5.817 distance: 127 - 128: 13.273 distance: 128 - 129: 7.429 distance: 128 - 130: 11.235 distance: 131 - 132: 7.819 distance: 132 - 133: 8.143 distance: 132 - 135: 8.728 distance: 133 - 134: 32.525 distance: 133 - 140: 19.652 distance: 135 - 136: 20.049 distance: 136 - 137: 7.199 distance: 140 - 141: 22.735 distance: 141 - 142: 46.006 distance: 141 - 144: 45.483 distance: 142 - 143: 24.638 distance: 142 - 146: 19.331 distance: 144 - 145: 14.586