Starting phenix.real_space_refine on Mon Jul 6 10:06:05 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7q9f_13868/07_2026/7q9f_13868.cif Found real_map, /net/cci-nas-00/data/ceres_data/7q9f_13868/07_2026/7q9f_13868.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/cci-nas-00/data/ceres_data/7q9f_13868/07_2026/7q9f_13868.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7q9f_13868/07_2026/7q9f_13868.cif" model { file = "/net/cci-nas-00/data/ceres_data/7q9f_13868/07_2026/7q9f_13868.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7q9f_13868/07_2026/7q9f_13868.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7q9f_13868/07_2026/7q9f_13868.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7q9f_13868/07_2026/7q9f_13868.map" } resolution = 3.6 write_initial_geo_file = False refinement { macro_cycles = 10 } 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= 0.003 sd= 0.020 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 148 5.16 5 C 21751 2.51 5 N 5609 2.21 5 O 6756 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 5 residue(s): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 34264 Number of models: 1 Model: "" Number of chains: 29 Chain: "A" Number of atoms: 7874 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1009, 7874 Classifications: {'peptide': 1009} Link IDs: {'PTRANS': 50, 'TRANS': 958} Chain breaks: 7 Chain: "B" Number of atoms: 7848 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1005, 7848 Classifications: {'peptide': 1005} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 50, 'TRANS': 954} Chain breaks: 7 Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Unresolved non-hydrogen chiralities: 1 Chain: "C" Number of atoms: 7926 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1014, 7926 Classifications: {'peptide': 1014} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 51, 'TRANS': 962} Chain breaks: 7 Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Unresolved non-hydrogen chiralities: 1 Chain: "L" Number of atoms: 1668 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 216, 1661 Classifications: {'peptide': 216} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 2, 'PTRANS': 10, 'TRANS': 203} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Conformer: "B" Number of residues, atoms: 216, 1661 Classifications: {'peptide': 216} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 2, 'PTRANS': 10, 'TRANS': 203} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 bond proxies already assigned to first conformer: 1689 Chain: "H" Number of atoms: 1578 Number of conformers: 1 Conformer: "" Number of residues, atoms: 212, 1578 Classifications: {'peptide': 212} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PCIS': 2, 'PTRANS': 11, 'TRANS': 198} Chain breaks: 1 Unresolved non-hydrogen bonds: 14 Unresolved non-hydrogen angles: 15 Unresolved non-hydrogen dihedrals: 13 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "F" Number of atoms: 1668 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 216, 1661 Classifications: {'peptide': 216} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 2, 'PTRANS': 10, 'TRANS': 203} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Conformer: "B" Number of residues, atoms: 216, 1661 Classifications: {'peptide': 216} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 2, 'PTRANS': 10, 'TRANS': 203} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 bond proxies already assigned to first conformer: 1689 Chain: "E" Number of atoms: 1578 Number of conformers: 1 Conformer: "" Number of residues, atoms: 212, 1578 Classifications: {'peptide': 212} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PCIS': 2, 'PTRANS': 11, 'TRANS': 198} Chain breaks: 1 Unresolved non-hydrogen bonds: 14 Unresolved non-hydrogen angles: 15 Unresolved non-hydrogen dihedrals: 13 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "K" Number of atoms: 1668 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 216, 1661 Classifications: {'peptide': 216} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 2, 'PTRANS': 10, 'TRANS': 203} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Conformer: "B" Number of residues, atoms: 216, 1661 Classifications: {'peptide': 216} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 2, 'PTRANS': 10, 'TRANS': 203} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 bond proxies already assigned to first conformer: 1689 Chain: "J" Number of atoms: 1578 Number of conformers: 1 Conformer: "" Number of residues, atoms: 212, 1578 Classifications: {'peptide': 212} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PCIS': 2, 'PTRANS': 11, 'TRANS': 198} Chain breaks: 1 Unresolved non-hydrogen bonds: 14 Unresolved non-hydrogen angles: 15 Unresolved non-hydrogen dihedrals: 13 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "D" Number of atoms: 38 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 38 Unusual residues: {'FUC': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen chiralities: 3 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 chiralities: 2 Chain: "I" 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 chiralities: 2 Chain: "M" 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 chiralities: 2 Chain: "N" 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 chiralities: 2 Chain: "O" 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 chiralities: 2 Chain: "P" Number of atoms: 49 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 49 Unusual residues: {'BMA': 1, 'FUC': 1, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen chiralities: 4 Chain: "Q" 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 chiralities: 2 Chain: "R" 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 chiralities: 2 Chain: "S" 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 chiralities: 2 Chain: "T" 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 chiralities: 2 Chain: "U" 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 chiralities: 2 Chain: "V" Number of atoms: 49 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 49 Unusual residues: {'BMA': 1, 'FUC': 1, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen chiralities: 4 Chain: "W" 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 chiralities: 2 Chain: "X" 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 chiralities: 2 Chain: "Y" 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 chiralities: 2 Chain: "Z" 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 chiralities: 2 Chain: "A" Number of atoms: 112 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 112 Unusual residues: {'NAG': 8} Classifications: {'undetermined': 8} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen chiralities: 8 Chain: "B" Number of atoms: 126 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 126 Unusual residues: {'NAG': 9} Classifications: {'undetermined': 9} Link IDs: {None: 8} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen chiralities: 9 Chain: "C" Number of atoms: 112 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 112 Unusual residues: {'NAG': 8} Classifications: {'undetermined': 8} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen chiralities: 8 Time building chain proxies: 7.10, per 1000 atoms: 0.21 Number of scatterers: 34264 At special positions: 0 Unit cell: (160.72, 168.92, 215.66, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 148 16.00 O 6756 8.00 N 5609 7.00 C 21751 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=54, symmetry=0 Simple disulfide: pdb=" SG CYS A 131 " - pdb=" SG CYS A 166 " distance=2.03 Simple disulfide: pdb=" SG CYS A 288 " - pdb=" SG CYS A 298 " distance=2.03 Simple disulfide: pdb=" SG CYS A 333 " - pdb=" SG CYS A 358 " distance=2.03 Simple disulfide: pdb=" SG CYS A 376 " - pdb=" SG CYS A 429 " distance=2.03 Simple disulfide: pdb=" SG CYS A 388 " - pdb=" SG CYS A 522 " distance=2.03 Simple disulfide: pdb=" SG CYS A 477 " - pdb=" SG CYS A 485 " distance=2.03 Simple disulfide: pdb=" SG CYS A 535 " - pdb=" SG CYS A 587 " distance=2.03 Simple disulfide: pdb=" SG CYS A 614 " - pdb=" SG CYS A 646 " distance=2.03 Simple disulfide: pdb=" SG CYS A 659 " - pdb=" SG CYS A 668 " distance=2.03 Simple disulfide: pdb=" SG CYS A 735 " - pdb=" SG CYS A 757 " distance=2.03 Simple disulfide: pdb=" SG CYS A 740 " - pdb=" SG CYS A 746 " distance=2.03 Simple disulfide: pdb=" SG CYS A1029 " - pdb=" SG CYS A1040 " distance=2.03 Simple disulfide: pdb=" SG CYS A1079 " - pdb=" SG CYS A1123 " distance=2.03 Simple disulfide: pdb=" SG CYS B 131 " - pdb=" SG CYS B 166 " distance=2.03 Simple disulfide: pdb=" SG CYS B 288 " - pdb=" SG CYS B 298 " distance=2.03 Simple disulfide: pdb=" SG CYS B 333 " - pdb=" SG CYS B 358 " distance=2.03 Simple disulfide: pdb=" SG CYS B 376 " - pdb=" SG CYS B 429 " distance=2.03 Simple disulfide: pdb=" SG CYS B 388 " - pdb=" SG CYS B 522 " distance=2.03 Simple disulfide: pdb=" SG CYS B 477 " - pdb=" SG CYS B 485 " distance=2.03 Simple disulfide: pdb=" SG CYS B 535 " - pdb=" SG CYS B 587 " distance=2.03 Simple disulfide: pdb=" SG CYS B 614 " - pdb=" SG CYS B 646 " distance=2.03 Simple disulfide: pdb=" SG CYS B 659 " - pdb=" SG CYS B 668 " distance=2.03 Simple disulfide: pdb=" SG CYS B 735 " - pdb=" SG CYS B 757 " distance=2.03 Simple disulfide: pdb=" SG CYS B 740 " - pdb=" SG CYS B 746 " distance=2.03 Simple disulfide: pdb=" SG CYS B1029 " - pdb=" SG CYS B1040 " distance=2.03 Simple disulfide: pdb=" SG CYS B1079 " - pdb=" SG CYS B1123 " distance=2.03 Simple disulfide: pdb=" SG CYS C 131 " - pdb=" SG CYS C 166 " distance=2.03 Simple disulfide: pdb=" SG CYS C 288 " - pdb=" SG CYS C 298 " distance=2.03 Simple disulfide: pdb=" SG CYS C 333 " - pdb=" SG CYS C 358 " distance=2.03 Simple disulfide: pdb=" SG CYS C 376 " - pdb=" SG CYS C 429 " distance=2.03 Simple disulfide: pdb=" SG CYS C 388 " - pdb=" SG CYS C 522 " distance=2.03 Simple disulfide: pdb=" SG CYS C 477 " - pdb=" SG CYS C 485 " distance=2.03 Simple disulfide: pdb=" SG CYS C 535 " - pdb=" SG CYS C 587 " distance=2.03 Simple disulfide: pdb=" SG CYS C 614 " - pdb=" SG CYS C 646 " distance=2.03 Simple disulfide: pdb=" SG CYS C 659 " - pdb=" SG CYS C 668 " distance=2.03 Simple disulfide: pdb=" SG CYS C 735 " - pdb=" SG CYS C 757 " distance=2.03 Simple disulfide: pdb=" SG CYS C 740 " - pdb=" SG CYS C 746 " distance=2.03 Simple disulfide: pdb=" SG CYS C1029 " - pdb=" SG CYS C1040 " distance=2.03 Simple disulfide: pdb=" SG CYS C1079 " - pdb=" SG CYS C1123 " distance=2.03 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 89 " distance=2.03 Simple disulfide: pdb=" SG CYS L 137 " - pdb=" SG ACYS L 197 " distance=2.03 Simple disulfide: pdb=" SG CYS L 137 " - pdb=" SG BCYS L 197 " distance=2.03 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 96 " distance=2.03 Simple disulfide: pdb=" SG CYS H 145 " - pdb=" SG CYS H 201 " distance=2.03 Simple disulfide: pdb=" SG CYS F 23 " - pdb=" SG CYS F 89 " distance=2.03 Simple disulfide: pdb=" SG CYS F 137 " - pdb=" SG ACYS F 197 " distance=2.03 Simple disulfide: pdb=" SG CYS F 137 " - pdb=" SG BCYS F 197 " distance=2.03 Simple disulfide: pdb=" SG CYS E 22 " - pdb=" SG CYS E 96 " distance=2.03 Simple disulfide: pdb=" SG CYS E 145 " - pdb=" SG CYS E 201 " distance=2.03 Simple disulfide: pdb=" SG CYS K 23 " - pdb=" SG CYS K 89 " distance=2.03 Simple disulfide: pdb=" SG CYS K 137 " - pdb=" SG ACYS K 197 " distance=2.03 Simple disulfide: pdb=" SG CYS K 137 " - pdb=" SG BCYS K 197 " distance=2.03 Simple disulfide: pdb=" SG CYS J 22 " - pdb=" SG CYS J 96 " distance=2.03 Simple disulfide: pdb=" SG CYS J 145 " - pdb=" SG CYS J 201 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 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 D 1 " - " NAG D 2 " " NAG G 1 " - " NAG G 2 " " NAG I 1 " - " NAG I 2 " " NAG M 1 " - " NAG M 2 " " NAG N 1 " - " NAG N 2 " " NAG O 1 " - " NAG O 2 " " NAG P 1 " - " NAG P 2 " " NAG P 2 " - " BMA P 3 " " NAG Q 1 " - " NAG Q 2 " " NAG R 1 " - " NAG R 2 " " NAG S 1 " - " NAG S 2 " " NAG T 1 " - " NAG T 2 " " NAG U 1 " - " NAG U 2 " " NAG V 1 " - " NAG V 2 " " NAG V 2 " - " BMA V 3 " " NAG W 1 " - " NAG W 2 " " NAG X 1 " - " NAG X 2 " " NAG Y 1 " - " NAG Y 2 " " NAG Z 1 " - " NAG Z 2 " BETA1-6 " NAG D 1 " - " FUC D 3 " ~> Even though FUC is an alpha isomer, a beta linkage is required... " NAG P 1 " - " FUC P 4 " " NAG V 1 " - " FUC V 4 " NAG-ASN " NAG A1301 " - " ASN A 61 " " NAG A1302 " - " ASN A 279 " " NAG A1303 " - " ASN A 600 " " NAG A1304 " - " ASN A 613 " " NAG A1305 " - " ASN A 654 " " NAG A1306 " - " ASN A 706 " " NAG A1307 " - " ASN A1071 " " NAG A1308 " - " ASN A 328 " " NAG B1301 " - " ASN B 61 " " NAG B1302 " - " ASN B 279 " " NAG B1303 " - " ASN B 328 " " NAG B1304 " - " ASN B 600 " " NAG B1305 " - " ASN B 613 " " NAG B1306 " - " ASN B 654 " " NAG B1307 " - " ASN B 706 " " NAG B1308 " - " ASN B1071 " " NAG B1309 " - " ASN B 165 " " NAG C1301 " - " ASN C 61 " " NAG C1302 " - " ASN C 279 " " NAG C1303 " - " ASN C 600 " " NAG C1304 " - " ASN C 613 " " NAG C1305 " - " ASN C 654 " " NAG C1306 " - " ASN C 706 " " NAG C1307 " - " ASN C1071 " " NAG C1308 " - " ASN C 328 " " NAG D 1 " - " ASN A 340 " " NAG G 1 " - " ASN A 234 " " NAG I 1 " - " ASN A 714 " " NAG M 1 " - " ASN A 798 " " NAG N 1 " - " ASN A1095 " " NAG O 1 " - " ASN A1131 " " NAG P 1 " - " ASN B 340 " " NAG Q 1 " - " ASN B 234 " " NAG R 1 " - " ASN B 714 " " NAG S 1 " - " ASN B 798 " " NAG T 1 " - " ASN B1095 " " NAG U 1 " - " ASN B1131 " " NAG V 1 " - " ASN C 340 " " NAG W 1 " - " ASN C 714 " " NAG X 1 " - " ASN C 798 " " NAG Y 1 " - " ASN C1095 " " NAG Z 1 " - " ASN C1131 " Time building additional restraints: 2.79 Conformation dependent library (CDL) restraints added in 1.2 seconds 8504 Ramachandran restraints generated. 4252 Oldfield, 0 Emsley, 4252 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 8046 Finding SS restraints... Secondary structure from input PDB file: 86 helices and 85 sheets defined 20.3% alpha, 33.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.18 Creating SS restraints... Processing helix chain 'A' and resid 291 through 301 Processing helix chain 'A' and resid 335 through 340 Processing helix chain 'A' and resid 346 through 350 Processing helix chain 'A' and resid 362 through 368 removed outlier: 3.878A pdb=" N TYR A 366 " --> pdb=" O TYR A 362 " (cutoff:3.500A) Processing helix chain 'A' and resid 402 through 407 Processing helix chain 'A' and resid 413 through 419 Processing helix chain 'A' and resid 734 through 740 Processing helix chain 'A' and resid 743 through 752 removed outlier: 3.671A pdb=" N GLN A 752 " --> pdb=" O ASN A 748 " (cutoff:3.500A) Processing helix chain 'A' and resid 759 through 780 Processing helix chain 'A' and resid 813 through 823 Processing helix chain 'A' and resid 863 through 882 Processing helix chain 'A' and resid 883 through 888 removed outlier: 3.679A pdb=" N ALA A 887 " --> pdb=" O TRP A 883 " (cutoff:3.500A) Processing helix chain 'A' and resid 894 through 906 removed outlier: 3.559A pdb=" N ALA A 900 " --> pdb=" O ALA A 896 " (cutoff:3.500A) Processing helix chain 'A' and resid 909 through 916 removed outlier: 4.122A pdb=" N LEU A 913 " --> pdb=" O THR A 909 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N GLU A 915 " --> pdb=" O ASN A 911 " (cutoff:3.500A) Processing helix chain 'A' and resid 916 through 938 Processing helix chain 'A' and resid 942 through 962 Processing helix chain 'A' and resid 963 through 965 No H-bonds generated for 'chain 'A' and resid 963 through 965' Processing helix chain 'A' and resid 973 through 979 Processing helix chain 'A' and resid 982 through 1030 removed outlier: 5.022A pdb=" N VAL A 988 " --> pdb=" O PRO A 984 " (cutoff:3.500A) removed outlier: 4.187A pdb=" N GLN A 989 " --> pdb=" O GLU A 985 " (cutoff:3.500A) Processing helix chain 'A' and resid 1137 through 1144 removed outlier: 4.276A pdb=" N GLU A1141 " --> pdb=" O PRO A1137 " (cutoff:3.500A) Processing helix chain 'B' and resid 291 through 301 Processing helix chain 'B' and resid 335 through 340 Processing helix chain 'B' and resid 346 through 350 Processing helix chain 'B' and resid 362 through 368 removed outlier: 3.663A pdb=" N TYR B 366 " --> pdb=" O TYR B 362 " (cutoff:3.500A) Processing helix chain 'B' and resid 380 through 385 removed outlier: 4.100A pdb=" N ASN B 385 " --> pdb=" O PRO B 381 " (cutoff:3.500A) Processing helix chain 'B' and resid 402 through 407 removed outlier: 3.994A pdb=" N ARG B 405 " --> pdb=" O ASP B 402 " (cutoff:3.500A) Processing helix chain 'B' and resid 413 through 419 Processing helix chain 'B' and resid 499 through 502 Processing helix chain 'B' and resid 734 through 740 Processing helix chain 'B' and resid 743 through 751 Processing helix chain 'B' and resid 752 through 754 No H-bonds generated for 'chain 'B' and resid 752 through 754' Processing helix chain 'B' and resid 759 through 780 Processing helix chain 'B' and resid 798 through 802 removed outlier: 4.433A pdb=" N GLN B 801 " --> pdb=" O ASN B 798 " (cutoff:3.500A) Processing helix chain 'B' and resid 813 through 823 Processing helix chain 'B' and resid 863 through 882 Processing helix chain 'B' and resid 883 through 888 removed outlier: 3.776A pdb=" N ALA B 887 " --> pdb=" O TRP B 883 " (cutoff:3.500A) Processing helix chain 'B' and resid 894 through 907 Processing helix chain 'B' and resid 910 through 915 Processing helix chain 'B' and resid 916 through 938 removed outlier: 3.862A pdb=" N ASN B 922 " --> pdb=" O LYS B 918 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N GLN B 932 " --> pdb=" O ILE B 928 " (cutoff:3.500A) Processing helix chain 'B' and resid 942 through 962 removed outlier: 4.031A pdb=" N VAL B 948 " --> pdb=" O LYS B 944 " (cutoff:3.500A) Processing helix chain 'B' and resid 963 through 965 No H-bonds generated for 'chain 'B' and resid 963 through 965' Processing helix chain 'B' and resid 973 through 981 Processing helix chain 'B' and resid 982 through 1029 removed outlier: 4.442A pdb=" N VAL B 988 " --> pdb=" O PRO B 984 " (cutoff:3.500A) removed outlier: 3.942A pdb=" N GLN B 989 " --> pdb=" O GLU B 985 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N ARG B 992 " --> pdb=" O VAL B 988 " (cutoff:3.500A) Processing helix chain 'B' and resid 1137 through 1144 removed outlier: 3.983A pdb=" N GLU B1141 " --> pdb=" O PRO B1137 " (cutoff:3.500A) Processing helix chain 'C' and resid 291 through 301 Processing helix chain 'C' and resid 335 through 340 Processing helix chain 'C' and resid 346 through 350 Processing helix chain 'C' and resid 362 through 368 removed outlier: 3.588A pdb=" N TYR C 366 " --> pdb=" O TYR C 362 " (cutoff:3.500A) Processing helix chain 'C' and resid 381 through 385 removed outlier: 3.954A pdb=" N ASN C 385 " --> pdb=" O THR C 382 " (cutoff:3.500A) Processing helix chain 'C' and resid 402 through 407 removed outlier: 4.318A pdb=" N ARG C 405 " --> pdb=" O ASP C 402 " (cutoff:3.500A) Processing helix chain 'C' and resid 413 through 419 Processing helix chain 'C' and resid 734 through 740 Processing helix chain 'C' and resid 743 through 751 Processing helix chain 'C' and resid 752 through 754 No H-bonds generated for 'chain 'C' and resid 752 through 754' Processing helix chain 'C' and resid 759 through 780 Processing helix chain 'C' and resid 813 through 823 Processing helix chain 'C' and resid 863 through 882 removed outlier: 3.837A pdb=" N GLN C 869 " --> pdb=" O GLU C 865 " (cutoff:3.500A) Processing helix chain 'C' and resid 883 through 887 Processing helix chain 'C' and resid 894 through 906 removed outlier: 3.696A pdb=" N ALA C 900 " --> pdb=" O ALA C 896 " (cutoff:3.500A) removed outlier: 3.884A pdb=" N TYR C 901 " --> pdb=" O MET C 897 " (cutoff:3.500A) Processing helix chain 'C' and resid 909 through 938 removed outlier: 4.166A pdb=" N LEU C 913 " --> pdb=" O THR C 909 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N TYR C 914 " --> pdb=" O GLN C 910 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N GLU C 915 " --> pdb=" O ASN C 911 " (cutoff:3.500A) removed outlier: 4.947A pdb=" N LYS C 918 " --> pdb=" O TYR C 914 " (cutoff:3.500A) removed outlier: 6.520A pdb=" N LEU C 919 " --> pdb=" O GLU C 915 " (cutoff:3.500A) Processing helix chain 'C' and resid 939 through 941 No H-bonds generated for 'chain 'C' and resid 939 through 941' Processing helix chain 'C' and resid 942 through 962 removed outlier: 3.912A pdb=" N VAL C 948 " --> pdb=" O LYS C 944 " (cutoff:3.500A) Processing helix chain 'C' and resid 963 through 965 No H-bonds generated for 'chain 'C' and resid 963 through 965' Processing helix chain 'C' and resid 973 through 981 removed outlier: 3.650A pdb=" N ILE C 977 " --> pdb=" O VAL C 973 " (cutoff:3.500A) Processing helix chain 'C' and resid 982 through 1029 removed outlier: 5.121A pdb=" N VAL C 988 " --> pdb=" O PRO C 984 " (cutoff:3.500A) removed outlier: 4.276A pdb=" N GLN C 989 " --> pdb=" O GLU C 985 " (cutoff:3.500A) Processing helix chain 'C' and resid 1137 through 1144 removed outlier: 3.717A pdb=" N GLU C1141 " --> pdb=" O PRO C1137 " (cutoff:3.500A) Processing helix chain 'L' and resid 80 through 84 removed outlier: 3.509A pdb=" N PHE L 84 " --> pdb=" O PRO L 81 " (cutoff:3.500A) Processing helix chain 'L' and resid 95 through 99 Processing helix chain 'L' and resid 124 through 130 removed outlier: 3.521A pdb=" N SER L 130 " --> pdb=" O GLU L 126 " (cutoff:3.500A) Processing helix chain 'L' and resid 186 through 191 Processing helix chain 'H' and resid 62 through 65 Processing helix chain 'H' and resid 87 through 91 Processing helix chain 'H' and resid 192 through 194 No H-bonds generated for 'chain 'H' and resid 192 through 194' Processing helix chain 'F' and resid 80 through 84 Processing helix chain 'F' and resid 95 through 99 Processing helix chain 'F' and resid 124 through 130 removed outlier: 3.608A pdb=" N SER F 130 " --> pdb=" O GLU F 126 " (cutoff:3.500A) Processing helix chain 'F' and resid 186 through 191 Processing helix chain 'E' and resid 62 through 65 removed outlier: 3.555A pdb=" N GLN E 65 " --> pdb=" O GLN E 62 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 62 through 65' Processing helix chain 'E' and resid 87 through 91 Processing helix chain 'E' and resid 192 through 194 No H-bonds generated for 'chain 'E' and resid 192 through 194' Processing helix chain 'K' and resid 80 through 84 removed outlier: 3.596A pdb=" N PHE K 84 " --> pdb=" O PRO K 81 " (cutoff:3.500A) Processing helix chain 'K' and resid 95 through 99 Processing helix chain 'K' and resid 124 through 130 Processing helix chain 'K' and resid 186 through 191 Processing helix chain 'J' and resid 87 through 91 Processing helix chain 'J' and resid 192 through 194 No H-bonds generated for 'chain 'J' and resid 192 through 194' Processing sheet with id=AA1, first strand: chain 'A' and resid 27 through 30 removed outlier: 3.576A pdb=" N THR A 63 " --> pdb=" O VAL A 264 " (cutoff:3.500A) removed outlier: 5.749A pdb=" N SER A 205 " --> pdb=" O PRO A 225 " (cutoff:3.500A) removed outlier: 9.176A pdb=" N HIS A 207 " --> pdb=" O LEU A 223 " (cutoff:3.500A) removed outlier: 9.198A pdb=" N LEU A 223 " --> pdb=" O HIS A 207 " (cutoff:3.500A) removed outlier: 6.961A pdb=" N VAL A 36 " --> pdb=" O LEU A 223 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 50 through 55 Processing sheet with id=AA3, first strand: chain 'A' and resid 84 through 85 Processing sheet with id=AA4, first strand: chain 'A' and resid 127 through 129 Processing sheet with id=AA5, first strand: chain 'A' and resid 132 through 141 removed outlier: 6.458A pdb=" N GLU A 132 " --> pdb=" O ALA A 163 " (cutoff:3.500A) removed outlier: 4.859A pdb=" N ALA A 163 " --> pdb=" O GLU A 132 " (cutoff:3.500A) removed outlier: 6.204A pdb=" N GLN A 134 " --> pdb=" O SER A 161 " (cutoff:3.500A) removed outlier: 8.246A pdb=" N VAL A 159 " --> pdb=" O CYS A 136 " (cutoff:3.500A) removed outlier: 12.382A pdb=" N ASP A 138 " --> pdb=" O PHE A 157 " (cutoff:3.500A) removed outlier: 10.681A pdb=" N PHE A 157 " --> pdb=" O ASP A 138 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 308 through 316 removed outlier: 3.570A pdb=" N TYR A 310 " --> pdb=" O VAL A 594 " (cutoff:3.500A) removed outlier: 6.876A pdb=" N VAL A 592 " --> pdb=" O THR A 312 " (cutoff:3.500A) removed outlier: 4.439A pdb=" N ASN A 314 " --> pdb=" O GLY A 590 " (cutoff:3.500A) removed outlier: 6.159A pdb=" N GLY A 590 " --> pdb=" O ASN A 314 " (cutoff:3.500A) removed outlier: 4.247A pdb=" N GLY A 591 " --> pdb=" O GLN A 610 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 322 through 325 removed outlier: 3.770A pdb=" N PHE A 540 " --> pdb=" O LEU A 543 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 351 through 355 Processing sheet with id=AA9, first strand: chain 'A' and resid 358 through 359 removed outlier: 6.937A pdb=" N CYS A 358 " --> pdb=" O CYS A 522 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA9 Processing sheet with id=AB1, first strand: chain 'A' and resid 449 through 451 Processing sheet with id=AB2, first strand: chain 'A' and resid 470 through 471 Processing sheet with id=AB3, first strand: chain 'A' and resid 651 through 652 removed outlier: 3.587A pdb=" N ALA A 691 " --> pdb=" O GLU A 651 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N GLN A 672 " --> pdb=" O SER A 688 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N TYR A 692 " --> pdb=" O CYS A 668 " (cutoff:3.500A) removed outlier: 5.813A pdb=" N ALA A 669 " --> pdb=" O PRO A 662 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 708 through 712 removed outlier: 3.574A pdb=" N THR A1073 " --> pdb=" O SER A1094 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N ALA A1075 " --> pdb=" O PHE A1092 " (cutoff:3.500A) removed outlier: 4.565A pdb=" N PHE A1092 " --> pdb=" O ALA A1075 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 716 through 725 removed outlier: 3.555A pdb=" N MET A1047 " --> pdb=" O VAL A1062 " (cutoff:3.500A) removed outlier: 6.040A pdb=" N TYR A1064 " --> pdb=" O HIS A1045 " (cutoff:3.500A) removed outlier: 5.453A pdb=" N HIS A1045 " --> pdb=" O TYR A1064 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 731 through 733 Processing sheet with id=AB7, first strand: chain 'A' and resid 785 through 787 removed outlier: 6.064A pdb=" N ILE A 785 " --> pdb=" O ASN C 700 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB7 Processing sheet with id=AB8, first strand: chain 'A' and resid 1117 through 1122 removed outlier: 4.378A pdb=" N ALA A1084 " --> pdb=" O SER A1120 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 27 through 30 removed outlier: 7.729A pdb=" N ASN B 61 " --> pdb=" O TYR B 266 " (cutoff:3.500A) removed outlier: 6.174A pdb=" N TYR B 266 " --> pdb=" O ASN B 61 " (cutoff:3.500A) removed outlier: 5.567A pdb=" N SER B 205 " --> pdb=" O PRO B 225 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 48 through 55 removed outlier: 3.534A pdb=" N ASP B 53 " --> pdb=" O ARG B 270 " (cutoff:3.500A) removed outlier: 3.919A pdb=" N ASP B 284 " --> pdb=" O LYS B 275 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 84 through 85 removed outlier: 3.521A pdb=" N GLY B 103 " --> pdb=" O LEU B 241 " (cutoff:3.500A) removed outlier: 5.633A pdb=" N ARG B 102 " --> pdb=" O ASN B 121 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 132 through 141 removed outlier: 6.129A pdb=" N GLU B 132 " --> pdb=" O ALA B 163 " (cutoff:3.500A) removed outlier: 4.587A pdb=" N ALA B 163 " --> pdb=" O GLU B 132 " (cutoff:3.500A) removed outlier: 6.299A pdb=" N GLN B 134 " --> pdb=" O SER B 161 " (cutoff:3.500A) removed outlier: 8.386A pdb=" N VAL B 159 " --> pdb=" O CYS B 136 " (cutoff:3.500A) removed outlier: 12.788A pdb=" N ASP B 138 " --> pdb=" O PHE B 157 " (cutoff:3.500A) removed outlier: 11.501A pdb=" N PHE B 157 " --> pdb=" O ASP B 138 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 308 through 314 removed outlier: 3.714A pdb=" N TYR B 310 " --> pdb=" O VAL B 594 " (cutoff:3.500A) removed outlier: 6.830A pdb=" N VAL B 592 " --> pdb=" O THR B 312 " (cutoff:3.500A) removed outlier: 4.248A pdb=" N GLY B 591 " --> pdb=" O GLN B 610 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 322 through 325 Processing sheet with id=AC6, first strand: chain 'B' and resid 322 through 325 removed outlier: 3.802A pdb=" N THR B 585 " --> pdb=" O VAL B 548 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N THR B 550 " --> pdb=" O ASP B 583 " (cutoff:3.500A) removed outlier: 6.944A pdb=" N PHE B 562 " --> pdb=" O PHE C 43 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'B' and resid 351 through 355 Processing sheet with id=AC8, first strand: chain 'B' and resid 358 through 359 removed outlier: 6.705A pdb=" N CYS B 358 " --> pdb=" O CYS B 522 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'B' and resid 449 through 451 Processing sheet with id=AD1, first strand: chain 'B' and resid 470 through 471 Processing sheet with id=AD2, first strand: chain 'B' and resid 651 through 652 removed outlier: 3.743A pdb=" N TYR B 692 " --> pdb=" O CYS B 668 " (cutoff:3.500A) removed outlier: 6.648A pdb=" N ILE B 667 " --> pdb=" O ILE B 663 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'B' and resid 699 through 701 Processing sheet with id=AD4, first strand: chain 'B' and resid 708 through 712 Processing sheet with id=AD5, first strand: chain 'B' and resid 715 through 725 removed outlier: 6.925A pdb=" N VAL B1062 " --> pdb=" O LEU B1046 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'B' and resid 715 through 725 Processing sheet with id=AD7, first strand: chain 'B' and resid 731 through 733 Processing sheet with id=AD8, first strand: chain 'B' and resid 1083 through 1087 removed outlier: 4.282A pdb=" N ALA B1084 " --> pdb=" O SER B1120 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'B' and resid 1091 through 1094 Processing sheet with id=AE1, first strand: chain 'C' and resid 27 through 30 removed outlier: 7.733A pdb=" N ASN C 61 " --> pdb=" O TYR C 266 " (cutoff:3.500A) removed outlier: 6.053A pdb=" N TYR C 266 " --> pdb=" O ASN C 61 " (cutoff:3.500A) removed outlier: 6.519A pdb=" N PHE C 201 " --> pdb=" O ASP C 228 " (cutoff:3.500A) removed outlier: 4.229A pdb=" N ASP C 228 " --> pdb=" O PHE C 201 " (cutoff:3.500A) removed outlier: 6.818A pdb=" N ILE C 203 " --> pdb=" O LEU C 226 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'C' and resid 50 through 55 Processing sheet with id=AE3, first strand: chain 'C' and resid 84 through 85 removed outlier: 4.176A pdb=" N GLY C 103 " --> pdb=" O LEU C 241 " (cutoff:3.500A) removed outlier: 6.695A pdb=" N ILE C 128 " --> pdb=" O GLU C 169 " (cutoff:3.500A) removed outlier: 4.218A pdb=" N GLU C 169 " --> pdb=" O ILE C 128 " (cutoff:3.500A) removed outlier: 6.686A pdb=" N VAL C 130 " --> pdb=" O THR C 167 " (cutoff:3.500A) removed outlier: 4.283A pdb=" N GLU C 132 " --> pdb=" O ASN C 165 " (cutoff:3.500A) removed outlier: 5.543A pdb=" N ASN C 165 " --> pdb=" O GLU C 132 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'C' and resid 135 through 142 removed outlier: 6.804A pdb=" N VAL C 159 " --> pdb=" O CYS C 136 " (cutoff:3.500A) removed outlier: 11.280A pdb=" N ASP C 138 " --> pdb=" O PHE C 157 " (cutoff:3.500A) removed outlier: 9.427A pdb=" N PHE C 157 " --> pdb=" O ASP C 138 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'C' and resid 275 through 276 removed outlier: 7.083A pdb=" N LYS C 275 " --> pdb=" O THR C 283 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'C' and resid 308 through 316 removed outlier: 3.754A pdb=" N TYR C 310 " --> pdb=" O VAL C 594 " (cutoff:3.500A) removed outlier: 6.821A pdb=" N VAL C 592 " --> pdb=" O THR C 312 " (cutoff:3.500A) removed outlier: 4.781A pdb=" N ASN C 314 " --> pdb=" O GLY C 590 " (cutoff:3.500A) removed outlier: 6.496A pdb=" N GLY C 590 " --> pdb=" O ASN C 314 " (cutoff:3.500A) removed outlier: 4.416A pdb=" N GLY C 591 " --> pdb=" O GLN C 610 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'C' and resid 321 through 322 removed outlier: 7.229A pdb=" N GLU C 321 " --> pdb=" O ASN C 537 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N THR C 585 " --> pdb=" O VAL C 548 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'C' and resid 351 through 355 Processing sheet with id=AE9, first strand: chain 'C' and resid 358 through 359 removed outlier: 6.536A pdb=" N CYS C 358 " --> pdb=" O CYS C 522 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'C' and resid 449 through 451 Processing sheet with id=AF2, first strand: chain 'C' and resid 470 through 471 Processing sheet with id=AF3, first strand: chain 'C' and resid 539 through 540 removed outlier: 3.828A pdb=" N PHE C 540 " --> pdb=" O LEU C 543 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'C' and resid 651 through 652 removed outlier: 6.237A pdb=" N GLU C 651 " --> pdb=" O ALA C 691 " (cutoff:3.500A) removed outlier: 8.453A pdb=" N THR C 693 " --> pdb=" O GLU C 651 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N GLN C 672 " --> pdb=" O SER C 688 " (cutoff:3.500A) removed outlier: 5.827A pdb=" N ALA C 669 " --> pdb=" O PRO C 662 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'C' and resid 708 through 725 removed outlier: 6.783A pdb=" N SER C 708 " --> pdb=" O THR C1073 " (cutoff:3.500A) removed outlier: 6.971A pdb=" N THR C1073 " --> pdb=" O SER C 708 " (cutoff:3.500A) removed outlier: 6.366A pdb=" N ALA C 710 " --> pdb=" O ASN C1071 " (cutoff:3.500A) removed outlier: 6.659A pdb=" N ASN C1071 " --> pdb=" O ALA C 710 " (cutoff:3.500A) removed outlier: 6.380A pdb=" N GLU C1069 " --> pdb=" O PRO C 712 " (cutoff:3.500A) removed outlier: 6.694A pdb=" N ASN C 714 " --> pdb=" O ALA C1067 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N MET C1047 " --> pdb=" O VAL C1062 " (cutoff:3.500A) removed outlier: 5.821A pdb=" N TYR C1064 " --> pdb=" O HIS C1045 " (cutoff:3.500A) removed outlier: 5.280A pdb=" N HIS C1045 " --> pdb=" O TYR C1064 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'C' and resid 708 through 725 removed outlier: 6.783A pdb=" N SER C 708 " --> pdb=" O THR C1073 " (cutoff:3.500A) removed outlier: 6.971A pdb=" N THR C1073 " --> pdb=" O SER C 708 " (cutoff:3.500A) removed outlier: 6.366A pdb=" N ALA C 710 " --> pdb=" O ASN C1071 " (cutoff:3.500A) removed outlier: 6.659A pdb=" N ASN C1071 " --> pdb=" O ALA C 710 " (cutoff:3.500A) removed outlier: 6.380A pdb=" N GLU C1069 " --> pdb=" O PRO C 712 " (cutoff:3.500A) removed outlier: 6.694A pdb=" N ASN C 714 " --> pdb=" O ALA C1067 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'C' and resid 731 through 733 Processing sheet with id=AF8, first strand: chain 'C' and resid 1117 through 1119 Processing sheet with id=AF9, first strand: chain 'C' and resid 1091 through 1094 Processing sheet with id=AG1, first strand: chain 'L' and resid 4 through 7 Processing sheet with id=AG2, first strand: chain 'L' and resid 10 through 12 removed outlier: 7.250A pdb=" N LEU L 34 " --> pdb=" O TYR L 50 " (cutoff:3.500A) removed outlier: 5.341A pdb=" N TYR L 50 " --> pdb=" O LEU L 34 " (cutoff:3.500A) removed outlier: 6.532A pdb=" N TRP L 36 " --> pdb=" O LEU L 48 " (cutoff:3.500A) Processing sheet with id=AG3, first strand: chain 'L' and resid 10 through 12 Processing sheet with id=AG4, first strand: chain 'L' and resid 117 through 121 removed outlier: 5.290A pdb=" N SER L 134 " --> pdb=" O LEU L 184 " (cutoff:3.500A) removed outlier: 7.446A pdb=" N LEU L 184 " --> pdb=" O SER L 134 " (cutoff:3.500A) removed outlier: 5.665A pdb=" N VAL L 136 " --> pdb=" O LEU L 182 " (cutoff:3.500A) removed outlier: 7.142A pdb=" N LEU L 182 " --> pdb=" O VAL L 136 " (cutoff:3.500A) removed outlier: 5.584A pdb=" N LEU L 138 " --> pdb=" O SER L 180 " (cutoff:3.500A) removed outlier: 7.349A pdb=" N SER L 180 " --> pdb=" O LEU L 138 " (cutoff:3.500A) removed outlier: 5.086A pdb=" N ASN L 140 " --> pdb=" O LEU L 178 " (cutoff:3.500A) removed outlier: 7.021A pdb=" N LEU L 178 " --> pdb=" O ASN L 140 " (cutoff:3.500A) Processing sheet with id=AG5, first strand: chain 'L' and resid 156 through 158 removed outlier: 4.531A pdb=" N TRP L 151 " --> pdb=" O GLN L 158 " (cutoff:3.500A) Processing sheet with id=AG6, first strand: chain 'H' and resid 5 through 6 Processing sheet with id=AG7, first strand: chain 'H' and resid 10 through 12 removed outlier: 3.590A pdb=" N VAL H 33 " --> pdb=" O LEU H 99 " (cutoff:3.500A) removed outlier: 6.821A pdb=" N PHE H 34 " --> pdb=" O GLY H 50 " (cutoff:3.500A) removed outlier: 4.548A pdb=" N GLY H 50 " --> pdb=" O PHE H 34 " (cutoff:3.500A) removed outlier: 6.652A pdb=" N TRP H 36 " --> pdb=" O MET H 48 " (cutoff:3.500A) Processing sheet with id=AG8, first strand: chain 'H' and resid 10 through 12 Processing sheet with id=AG9, first strand: chain 'H' and resid 125 through 129 removed outlier: 6.062A pdb=" N TYR H 181 " --> pdb=" O ASP H 149 " (cutoff:3.500A) Processing sheet with id=AH1, first strand: chain 'H' and resid 125 through 129 removed outlier: 6.062A pdb=" N TYR H 181 " --> pdb=" O ASP H 149 " (cutoff:3.500A) Processing sheet with id=AH2, first strand: chain 'H' and resid 156 through 159 removed outlier: 4.355A pdb=" N TYR H 199 " --> pdb=" O VAL H 216 " (cutoff:3.500A) Processing sheet with id=AH3, first strand: chain 'F' and resid 4 through 7 Processing sheet with id=AH4, first strand: chain 'F' and resid 10 through 12 removed outlier: 7.122A pdb=" N LEU F 34 " --> pdb=" O TYR F 50 " (cutoff:3.500A) removed outlier: 5.169A pdb=" N TYR F 50 " --> pdb=" O LEU F 34 " (cutoff:3.500A) removed outlier: 6.437A pdb=" N TRP F 36 " --> pdb=" O LEU F 48 " (cutoff:3.500A) Processing sheet with id=AH5, first strand: chain 'F' and resid 117 through 121 removed outlier: 5.549A pdb=" N TYR F 176 " --> pdb=" O ASN F 141 " (cutoff:3.500A) Processing sheet with id=AH6, first strand: chain 'F' and resid 157 through 158 removed outlier: 4.689A pdb=" N TRP F 151 " --> pdb=" O GLN F 158 " (cutoff:3.500A) Processing sheet with id=AH7, first strand: chain 'E' and resid 5 through 6 Processing sheet with id=AH8, first strand: chain 'E' and resid 10 through 12 removed outlier: 5.827A pdb=" N ARG E 38 " --> pdb=" O TRP E 47 " (cutoff:3.500A) removed outlier: 4.721A pdb=" N TRP E 47 " --> pdb=" O ARG E 38 " (cutoff:3.500A) Processing sheet with id=AH9, first strand: chain 'E' and resid 10 through 12 Processing sheet with id=AI1, first strand: chain 'E' and resid 125 through 129 removed outlier: 6.056A pdb=" N TYR E 181 " --> pdb=" O ASP E 149 " (cutoff:3.500A) Processing sheet with id=AI2, first strand: chain 'E' and resid 125 through 129 removed outlier: 6.056A pdb=" N TYR E 181 " --> pdb=" O ASP E 149 " (cutoff:3.500A) Processing sheet with id=AI3, first strand: chain 'E' and resid 155 through 159 removed outlier: 4.336A pdb=" N TYR E 199 " --> pdb=" O VAL E 216 " (cutoff:3.500A) Processing sheet with id=AI4, first strand: chain 'K' and resid 4 through 7 Processing sheet with id=AI5, first strand: chain 'K' and resid 10 through 12 removed outlier: 7.322A pdb=" N LEU K 34 " --> pdb=" O TYR K 50 " (cutoff:3.500A) removed outlier: 5.367A pdb=" N TYR K 50 " --> pdb=" O LEU K 34 " (cutoff:3.500A) removed outlier: 6.533A pdb=" N TRP K 36 " --> pdb=" O LEU K 48 " (cutoff:3.500A) Processing sheet with id=AI6, first strand: chain 'K' and resid 10 through 12 Processing sheet with id=AI7, first strand: chain 'K' and resid 117 through 121 removed outlier: 5.307A pdb=" N SER K 134 " --> pdb=" O LEU K 184 " (cutoff:3.500A) removed outlier: 7.432A pdb=" N LEU K 184 " --> pdb=" O SER K 134 " (cutoff:3.500A) removed outlier: 5.653A pdb=" N VAL K 136 " --> pdb=" O LEU K 182 " (cutoff:3.500A) removed outlier: 7.056A pdb=" N LEU K 182 " --> pdb=" O VAL K 136 " (cutoff:3.500A) removed outlier: 5.553A pdb=" N LEU K 138 " --> pdb=" O SER K 180 " (cutoff:3.500A) removed outlier: 7.323A pdb=" N SER K 180 " --> pdb=" O LEU K 138 " (cutoff:3.500A) removed outlier: 5.106A pdb=" N ASN K 140 " --> pdb=" O LEU K 178 " (cutoff:3.500A) removed outlier: 7.058A pdb=" N LEU K 178 " --> pdb=" O ASN K 140 " (cutoff:3.500A) Processing sheet with id=AI8, first strand: chain 'K' and resid 156 through 158 removed outlier: 4.521A pdb=" N TRP K 151 " --> pdb=" O GLN K 158 " (cutoff:3.500A) Processing sheet with id=AI9, first strand: chain 'J' and resid 5 through 6 Processing sheet with id=AJ1, first strand: chain 'J' and resid 10 through 12 removed outlier: 6.778A pdb=" N PHE J 34 " --> pdb=" O GLY J 50 " (cutoff:3.500A) removed outlier: 4.512A pdb=" N GLY J 50 " --> pdb=" O PHE J 34 " (cutoff:3.500A) removed outlier: 6.585A pdb=" N TRP J 36 " --> pdb=" O MET J 48 " (cutoff:3.500A) Processing sheet with id=AJ2, first strand: chain 'J' and resid 125 through 129 removed outlier: 6.134A pdb=" N TYR J 181 " --> pdb=" O ASP J 149 " (cutoff:3.500A) Processing sheet with id=AJ3, first strand: chain 'J' and resid 125 through 129 removed outlier: 6.134A pdb=" N TYR J 181 " --> pdb=" O ASP J 149 " (cutoff:3.500A) Processing sheet with id=AJ4, first strand: chain 'J' and resid 156 through 159 removed outlier: 4.377A pdb=" N TYR J 199 " --> pdb=" O VAL J 216 " (cutoff:3.500A) 1478 hydrogen bonds defined for protein. 3846 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: 9.13 Time building geometry restraints manager: 3.78 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 10853 1.34 - 1.46: 8539 1.46 - 1.58: 15460 1.58 - 1.70: 0 1.70 - 1.82: 188 Bond restraints: 35040 Sorted by residual: bond pdb=" N ASP K 1 " pdb=" CA ASP K 1 " ideal model delta sigma weight residual 1.458 1.489 -0.031 1.90e-02 2.77e+03 2.58e+00 bond pdb=" N ASP F 1 " pdb=" CA ASP F 1 " ideal model delta sigma weight residual 1.458 1.488 -0.030 1.90e-02 2.77e+03 2.56e+00 bond pdb=" N ASP L 1 " pdb=" CA ASP L 1 " ideal model delta sigma weight residual 1.458 1.488 -0.030 1.90e-02 2.77e+03 2.49e+00 bond pdb=" C1 NAG B1309 " pdb=" O5 NAG B1309 " ideal model delta sigma weight residual 1.406 1.437 -0.031 2.00e-02 2.50e+03 2.48e+00 bond pdb=" C1 BMA P 3 " pdb=" C2 BMA P 3 " ideal model delta sigma weight residual 1.519 1.550 -0.031 2.00e-02 2.50e+03 2.37e+00 ... (remaining 35035 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.27: 46334 1.27 - 2.53: 1035 2.53 - 3.80: 289 3.80 - 5.07: 34 5.07 - 6.33: 7 Bond angle restraints: 47699 Sorted by residual: angle pdb=" N THR C 615 " pdb=" CA THR C 615 " pdb=" C THR C 615 " ideal model delta sigma weight residual 114.62 110.79 3.83 1.14e+00 7.69e-01 1.13e+01 angle pdb=" N THR B 615 " pdb=" CA THR B 615 " pdb=" C THR B 615 " ideal model delta sigma weight residual 114.62 111.17 3.45 1.14e+00 7.69e-01 9.18e+00 angle pdb=" CA THR C 615 " pdb=" C THR C 615 " pdb=" N GLU C 616 " ideal model delta sigma weight residual 119.71 116.84 2.87 1.17e+00 7.31e-01 6.03e+00 angle pdb=" C GLY K 51 " pdb=" N ALA K 52 " pdb=" CA ALA K 52 " ideal model delta sigma weight residual 121.54 126.05 -4.51 1.91e+00 2.74e-01 5.58e+00 angle pdb=" C3 BMA P 3 " pdb=" C2 BMA P 3 " pdb=" O2 BMA P 3 " ideal model delta sigma weight residual 112.95 106.62 6.33 3.00e+00 1.11e-01 4.45e+00 ... (remaining 47694 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.71: 19639 17.71 - 35.43: 623 35.43 - 53.14: 103 53.14 - 70.85: 17 70.85 - 88.57: 15 Dihedral angle restraints: 20397 sinusoidal: 7868 harmonic: 12529 Sorted by residual: dihedral pdb=" CB CYS B1079 " pdb=" SG CYS B1079 " pdb=" SG CYS B1123 " pdb=" CB CYS B1123 " ideal model delta sinusoidal sigma weight residual -86.00 -125.08 39.08 1 1.00e+01 1.00e-02 2.15e+01 dihedral pdb=" CA THR B 596 " pdb=" C THR B 596 " pdb=" N PRO B 597 " pdb=" CA PRO B 597 " ideal model delta harmonic sigma weight residual 180.00 163.73 16.27 0 5.00e+00 4.00e-02 1.06e+01 dihedral pdb=" CA PRO F 116 " pdb=" C PRO F 116 " pdb=" N SER F 117 " pdb=" CA SER F 117 " ideal model delta harmonic sigma weight residual 180.00 164.18 15.82 0 5.00e+00 4.00e-02 1.00e+01 ... (remaining 20394 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.055: 4763 0.055 - 0.111: 689 0.111 - 0.166: 153 0.166 - 0.222: 3 0.222 - 0.277: 2 Chirality restraints: 5610 Sorted by residual: chirality pdb=" C5 BMA P 3 " pdb=" C4 BMA P 3 " pdb=" C6 BMA P 3 " pdb=" O5 BMA P 3 " both_signs ideal model delta sigma weight residual False -2.27 -2.55 0.28 2.00e-01 2.50e+01 1.92e+00 chirality pdb=" C5 BMA V 3 " pdb=" C4 BMA V 3 " pdb=" C6 BMA V 3 " pdb=" O5 BMA V 3 " both_signs ideal model delta sigma weight residual False -2.27 -2.54 0.27 2.00e-01 2.50e+01 1.80e+00 chirality pdb=" C1 NAG Q 1 " pdb=" ND2 ASN B 234 " pdb=" C2 NAG Q 1 " pdb=" O5 NAG Q 1 " both_signs ideal model delta sigma weight residual False -2.40 -2.20 -0.20 2.00e-01 2.50e+01 9.90e-01 ... (remaining 5607 not shown) Planarity restraints: 6107 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLU E 153 " 0.031 5.00e-02 4.00e+02 4.73e-02 3.59e+00 pdb=" N PRO E 154 " -0.082 5.00e-02 4.00e+02 pdb=" CA PRO E 154 " 0.027 5.00e-02 4.00e+02 pdb=" CD PRO E 154 " 0.024 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLU J 153 " 0.030 5.00e-02 4.00e+02 4.51e-02 3.25e+00 pdb=" N PRO J 154 " -0.078 5.00e-02 4.00e+02 pdb=" CA PRO J 154 " 0.026 5.00e-02 4.00e+02 pdb=" CD PRO J 154 " 0.022 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLU H 153 " -0.027 5.00e-02 4.00e+02 4.06e-02 2.64e+00 pdb=" N PRO H 154 " 0.070 5.00e-02 4.00e+02 pdb=" CA PRO H 154 " -0.023 5.00e-02 4.00e+02 pdb=" CD PRO H 154 " -0.020 5.00e-02 4.00e+02 ... (remaining 6104 not shown) Histogram of nonbonded interaction distances: 1.94 - 2.53: 305 2.53 - 3.12: 27264 3.12 - 3.72: 51836 3.72 - 4.31: 75264 4.31 - 4.90: 126249 Nonbonded interactions: 280918 Sorted by model distance: nonbonded pdb=" OG1 THR A 390 " pdb=" O GLU A 513 " model vdw 1.941 3.040 nonbonded pdb=" OG1 THR B 390 " pdb=" O GLU B 513 " model vdw 2.012 3.040 nonbonded pdb=" OG SER B 356 " pdb=" OD1 ASN B 391 " model vdw 2.037 3.040 nonbonded pdb=" O TYR F 189 " pdb=" OH TYR F 195 " model vdw 2.060 3.040 nonbonded pdb=" OD1 ASP B 361 " pdb=" N TYR B 362 " model vdw 2.110 3.120 ... (remaining 280913 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' and (resid 25 through 242 or (resid 243 and (name N or name CA or nam \ e C or name O or name CB )) or resid 262 through 617 or resid 638 through 1308)) \ selection = (chain 'B' and resid 25 through 1308) selection = (chain 'C' and (resid 25 through 143 or resid 156 through 617 or resid 638 throu \ gh 1308)) } ncs_group { reference = chain 'E' selection = chain 'H' selection = chain 'J' } ncs_group { reference = (chain 'F' and (resid 1 through 165 or resid 167 through 196 or resid 198 throug \ h 216)) selection = (chain 'K' and (resid 1 through 165 or resid 167 through 196 or resid 198 throug \ h 216)) selection = (chain 'L' and (resid 1 through 165 or resid 167 through 196 or resid 198 throug \ h 216)) } ncs_group { reference = chain 'G' selection = chain 'I' selection = chain 'M' selection = chain 'N' selection = chain 'O' selection = chain 'Q' selection = chain 'R' selection = chain 'S' selection = chain 'T' selection = chain 'U' selection = chain 'W' selection = chain 'X' selection = chain 'Y' selection = chain 'Z' } ncs_group { reference = chain 'P' selection = chain 'V' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.01 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: 4.820 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: 0.030 Extract box with map and model: 0.640 Check model and map are aligned: 0.080 Set scattering table: 0.070 Process input model: 31.620 Find NCS groups from input model: 0.790 Set up NCS constraints: 0.120 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:1.250 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 39.420 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8558 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 : 0.004 0.031 35158 Z= 0.168 Angle : 0.516 7.090 47999 Z= 0.255 Chirality : 0.044 0.277 5610 Planarity : 0.003 0.047 6065 Dihedral : 9.258 88.569 12189 Min Nonbonded Distance : 1.941 Molprobity Statistics. All-atom Clashscore : 4.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.93 % Favored : 96.07 % Rotamer: Outliers : 0.45 % Allowed : 3.77 % Favored : 95.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.31 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.15 (0.13), residues: 4252 helix: 0.93 (0.20), residues: 730 sheet: 0.37 (0.15), residues: 1276 loop : -0.27 (0.14), residues: 2246 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG J 98 TYR 0.015 0.001 TYR B1064 PHE 0.009 0.001 PHE B 92 TRP 0.006 0.001 TRP E 102 HIS 0.003 0.001 HIS A 652 Details of bonding type rmsd/Z covalent geometry : bond 0.00353 / 0.17 (35040) covalent geometry : angle 0.50868 / 0.25 (47699) SS BOND : bond 0.00219 / 0.14 ( 54) SS BOND : angle 0.65372 / 0.43 ( 108) hydrogen bonds : bond 0.12485 / 8.26 ( 1387) hydrogen bonds : angle 6.61575 / 4.62 ( 3846) link_BETA1-4 : bond 0.00237 / 0.12 ( 19) link_BETA1-4 : angle 1.11207 / 0.76 ( 57) link_BETA1-6 : bond 0.00266 / 0.13 ( 3) link_BETA1-6 : angle 2.18120 / 1.21 ( 9) link_NAG-ASN : bond 0.00226 / 0.14 ( 42) link_NAG-ASN : angle 1.50384 / 1.13 ( 126) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8504 Ramachandran restraints generated. 4252 Oldfield, 0 Emsley, 4252 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8504 Ramachandran restraints generated. 4252 Oldfield, 0 Emsley, 4252 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 404 residues out of total 3747 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 387 time to evaluate : 1.384 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 486 TYR cc_start: 0.8782 (m-80) cc_final: 0.8335 (m-80) REVERT: B 220 PHE cc_start: 0.7251 (t80) cc_final: 0.6613 (t80) REVERT: B 520 THR cc_start: 0.7611 (p) cc_final: 0.7327 (p) REVERT: B 899 MET cc_start: 0.9067 (mmm) cc_final: 0.8650 (tpt) REVERT: C 168 PHE cc_start: 0.8345 (t80) cc_final: 0.8144 (t80) REVERT: C 267 LEU cc_start: 0.8583 (mt) cc_final: 0.7929 (mt) REVERT: C 350 TRP cc_start: 0.8205 (p-90) cc_final: 0.7678 (p-90) REVERT: C 399 ILE cc_start: 0.8366 (pt) cc_final: 0.8083 (pt) REVERT: C 449 LEU cc_start: 0.9260 (mt) cc_final: 0.9053 (mm) REVERT: C 502 TYR cc_start: 0.9028 (m-80) cc_final: 0.8717 (m-10) REVERT: C 866 MET cc_start: 0.8831 (mtt) cc_final: 0.8515 (ttm) REVERT: C 899 MET cc_start: 0.8942 (mmm) cc_final: 0.8633 (tpt) REVERT: L 33 TYR cc_start: 0.8672 (m-80) cc_final: 0.8029 (m-80) REVERT: L 91 GLN cc_start: 0.9003 (OUTLIER) cc_final: 0.8736 (pp30) REVERT: L 119 PHE cc_start: 0.8395 (m-80) cc_final: 0.8187 (t80) REVERT: H 32 TYR cc_start: 0.8840 (m-10) cc_final: 0.8580 (m-80) REVERT: H 48 MET cc_start: 0.8615 (mtp) cc_final: 0.8297 (mtp) REVERT: H 82 GLU cc_start: 0.9207 (tt0) cc_final: 0.8988 (tp30) REVERT: H 107 MET cc_start: 0.9106 (mmm) cc_final: 0.8888 (mmm) REVERT: F 4 MET cc_start: 0.7907 (mmm) cc_final: 0.7292 (mmm) REVERT: F 36 TRP cc_start: 0.8321 (m100) cc_final: 0.7932 (m100) REVERT: E 46 GLU cc_start: 0.8533 (tt0) cc_final: 0.8042 (pt0) REVERT: E 48 MET cc_start: 0.8650 (mtp) cc_final: 0.8268 (mtp) REVERT: E 197 GLN cc_start: 0.8337 (tp40) cc_final: 0.7744 (tm-30) REVERT: E 211 LYS cc_start: 0.9169 (mttm) cc_final: 0.8915 (tptp) REVERT: K 61 ASP cc_start: 0.9140 (p0) cc_final: 0.8811 (p0) outliers start: 17 outliers final: 7 residues processed: 404 average time/residue: 0.2493 time to fit residues: 150.1659 Evaluate side-chains 201 residues out of total 3747 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 193 time to evaluate : 1.091 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 913 LEU Chi-restraints excluded: chain B residue 480 VAL Chi-restraints excluded: chain B residue 1078 ILE Chi-restraints excluded: chain B residue 1119 VAL Chi-restraints excluded: chain C residue 756 PHE Chi-restraints excluded: chain L residue 91 GLN Chi-restraints excluded: chain K residue 91 GLN Chi-restraints excluded: chain J residue 98 ARG Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 427 random chunks: chunk 197 optimal weight: 0.3980 chunk 388 optimal weight: 20.0000 chunk 215 optimal weight: 7.9990 chunk 20 optimal weight: 1.9990 chunk 132 optimal weight: 6.9990 chunk 261 optimal weight: 0.7980 chunk 248 optimal weight: 4.9990 chunk 207 optimal weight: 10.0000 chunk 401 optimal weight: 0.7980 chunk 424 optimal weight: 4.9990 chunk 155 optimal weight: 5.9990 overall best weight: 1.7984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 447 ASN A 560 GLN A 610 GLN B 196 ASN B 447 ASN C 484 ASN C 801 GLN C 904 ASN C1008 GLN ** H 110 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 176 GLN ** F 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 6 GLN E 65 GLN E 176 GLN ** K 192 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 65 GLN J 176 GLN J 204 ASN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4268 r_free = 0.4268 target = 0.119530 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 68)----------------| | r_work = 0.3742 r_free = 0.3742 target = 0.086966 restraints weight = 117039.385| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 59)----------------| | r_work = 0.3606 r_free = 0.3606 target = 0.081354 restraints weight = 82031.358| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3552 r_free = 0.3552 target = 0.078841 restraints weight = 79721.226| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3565 r_free = 0.3565 target = 0.079670 restraints weight = 62629.703| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.3564 r_free = 0.3564 target = 0.079678 restraints weight = 51890.630| |-----------------------------------------------------------------------------| r_work (final): 0.3312 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3308 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3308 r_free = 0.3308 target_work(ls_wunit_k1) = 0.069 | | occupancies: max = 1.00 min = 0.01 number of occupancies < 0.1: 9 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3308 r_free = 0.3308 target_work(ls_wunit_k1) = 0.069 | | occupancies: max = 1.00 min = 0.25 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (6 function evaluations) r_final: 0.3308 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8479 moved from start: 0.1476 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.063 35158 Z= 0.165 Angle : 0.581 10.204 47999 Z= 0.297 Chirality : 0.044 0.182 5610 Planarity : 0.004 0.052 6065 Dihedral : 4.312 49.455 4643 Min Nonbonded Distance : 2.402 Molprobity Statistics. All-atom Clashscore : 6.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.58 % Favored : 96.42 % Rotamer: Outliers : 1.42 % Allowed : 7.18 % Favored : 91.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.31 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.30 (0.13), residues: 4252 helix: 1.45 (0.19), residues: 753 sheet: 0.42 (0.14), residues: 1307 loop : -0.32 (0.14), residues: 2192 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG E 87 TYR 0.023 0.001 TYR B1064 PHE 0.037 0.002 PHE C 135 TRP 0.011 0.001 TRP H 108 HIS 0.005 0.001 HIS F 192 Details of bonding type rmsd/Z covalent geometry : bond 0.00380 / 0.16 (35040) covalent geometry : angle 0.57253 / 0.30 (47699) SS BOND : bond 0.00294 / 0.20 ( 54) SS BOND : angle 1.30690 / 1.21 ( 108) hydrogen bonds : bond 0.04090 / 2.64 ( 1387) hydrogen bonds : angle 5.62229 / 3.89 ( 3846) link_BETA1-4 : bond 0.00400 / 0.21 ( 19) link_BETA1-4 : angle 1.07398 / 0.75 ( 57) link_BETA1-6 : bond 0.00315 / 0.15 ( 3) link_BETA1-6 : angle 1.48126 / 0.87 ( 9) link_NAG-ASN : bond 0.00225 / 0.14 ( 42) link_NAG-ASN : angle 1.57653 / 1.14 ( 126) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8504 Ramachandran restraints generated. 4252 Oldfield, 0 Emsley, 4252 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8504 Ramachandran restraints generated. 4252 Oldfield, 0 Emsley, 4252 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 296 residues out of total 3747 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 243 time to evaluate : 1.229 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 118 LEU cc_start: 0.9548 (tp) cc_final: 0.9223 (mp) REVERT: A 486 TYR cc_start: 0.8541 (m-80) cc_final: 0.7912 (m-10) REVERT: A 1026 MET cc_start: 0.9120 (tpp) cc_final: 0.8274 (ttm) REVERT: B 133 PHE cc_start: 0.6650 (OUTLIER) cc_final: 0.6143 (m-80) REVERT: B 210 ILE cc_start: 0.8249 (OUTLIER) cc_final: 0.7844 (tp) REVERT: B 220 PHE cc_start: 0.7356 (t80) cc_final: 0.6724 (t80) REVERT: B 875 LEU cc_start: 0.9080 (OUTLIER) cc_final: 0.8878 (tt) REVERT: B 897 MET cc_start: 0.8841 (mtp) cc_final: 0.8547 (mtp) REVERT: B 899 MET cc_start: 0.9071 (mmm) cc_final: 0.8530 (tpt) REVERT: C 229 LEU cc_start: 0.8471 (OUTLIER) cc_final: 0.7985 (tp) REVERT: C 350 TRP cc_start: 0.8342 (p-90) cc_final: 0.8042 (p-90) REVERT: C 399 ILE cc_start: 0.8216 (pt) cc_final: 0.7970 (pt) REVERT: C 502 TYR cc_start: 0.8909 (m-80) cc_final: 0.8672 (m-10) REVERT: C 737 MET cc_start: 0.8010 (tpp) cc_final: 0.7695 (tpt) REVERT: C 866 MET cc_start: 0.8981 (mtt) cc_final: 0.8612 (ttm) REVERT: H 10 GLU cc_start: 0.6596 (mm-30) cc_final: 0.6362 (mm-30) REVERT: H 65 GLN cc_start: 0.8215 (mm-40) cc_final: 0.7936 (mm-40) REVERT: H 80 TYR cc_start: 0.8732 (m-80) cc_final: 0.8389 (m-10) REVERT: H 81 MET cc_start: 0.7950 (ppp) cc_final: 0.7471 (ppp) REVERT: H 149 ASP cc_start: 0.8860 (m-30) cc_final: 0.8615 (m-30) REVERT: F 4 MET cc_start: 0.7932 (mmm) cc_final: 0.7126 (mmm) REVERT: E 29 PHE cc_start: 0.7746 (t80) cc_final: 0.7512 (t80) REVERT: E 48 MET cc_start: 0.8362 (mtp) cc_final: 0.7724 (mtp) REVERT: E 67 ARG cc_start: 0.8248 (mtp180) cc_final: 0.6965 (mtp180) REVERT: E 94 TYR cc_start: 0.8342 (m-80) cc_final: 0.7933 (m-80) REVERT: K 24 ARG cc_start: 0.8425 (mtm-85) cc_final: 0.8186 (mtm-85) REVERT: K 61 ASP cc_start: 0.9087 (p0) cc_final: 0.8788 (p0) REVERT: J 10 GLU cc_start: 0.7895 (mm-30) cc_final: 0.7434 (mm-30) REVERT: J 48 MET cc_start: 0.8234 (mtt) cc_final: 0.8006 (mmt) REVERT: J 107 MET cc_start: 0.8321 (mtt) cc_final: 0.8079 (mtt) outliers start: 53 outliers final: 28 residues processed: 285 average time/residue: 0.2506 time to fit residues: 107.5103 Evaluate side-chains 221 residues out of total 3747 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 189 time to evaluate : 1.144 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 THR Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 131 CYS Chi-restraints excluded: chain A residue 514 LEU Chi-restraints excluded: chain A residue 546 THR Chi-restraints excluded: chain A residue 653 VAL Chi-restraints excluded: chain A residue 788 THR Chi-restraints excluded: chain A residue 863 THR Chi-restraints excluded: chain A residue 913 LEU Chi-restraints excluded: chain B residue 133 PHE Chi-restraints excluded: chain B residue 200 TYR Chi-restraints excluded: chain B residue 210 ILE Chi-restraints excluded: chain B residue 223 LEU Chi-restraints excluded: chain B residue 233 ILE Chi-restraints excluded: chain B residue 317 VAL Chi-restraints excluded: chain B residue 347 VAL Chi-restraints excluded: chain B residue 480 VAL Chi-restraints excluded: chain B residue 698 VAL Chi-restraints excluded: chain B residue 875 LEU Chi-restraints excluded: chain B residue 937 SER Chi-restraints excluded: chain B residue 1078 ILE Chi-restraints excluded: chain B residue 1101 VAL Chi-restraints excluded: chain B residue 1119 VAL Chi-restraints excluded: chain C residue 229 LEU Chi-restraints excluded: chain C residue 756 PHE Chi-restraints excluded: chain C residue 913 LEU Chi-restraints excluded: chain F residue 192 HIS Chi-restraints excluded: chain E residue 6 GLN Chi-restraints excluded: chain K residue 91 GLN Chi-restraints excluded: chain J residue 98 ARG Chi-restraints excluded: chain J residue 213 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 427 random chunks: chunk 107 optimal weight: 40.0000 chunk 250 optimal weight: 6.9990 chunk 50 optimal weight: 6.9990 chunk 168 optimal weight: 2.9990 chunk 391 optimal weight: 20.0000 chunk 146 optimal weight: 1.9990 chunk 143 optimal weight: 9.9990 chunk 363 optimal weight: 8.9990 chunk 217 optimal weight: 0.9990 chunk 180 optimal weight: 3.9990 chunk 253 optimal weight: 0.8980 overall best weight: 2.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 687 GLN A 962 GLN C 447 ASN C 484 ASN ** H 110 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 38 GLN E 6 GLN ** K 192 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4262 r_free = 0.4262 target = 0.119154 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 116)---------------| | r_work = 0.3466 r_free = 0.3466 target = 0.076211 restraints weight = 116440.512| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3506 r_free = 0.3506 target = 0.077379 restraints weight = 75929.348| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3483 r_free = 0.3483 target = 0.076555 restraints weight = 60097.315| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3486 r_free = 0.3486 target = 0.076712 restraints weight = 64594.909| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3489 r_free = 0.3489 target = 0.076851 restraints weight = 59105.714| |-----------------------------------------------------------------------------| r_work (final): 0.3249 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3245 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3245 r_free = 0.3245 target_work(ls_wunit_k1) = 0.066 | | occupancies: max = 1.00 min = 0.25 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3245 r_free = 0.3245 target_work(ls_wunit_k1) = 0.066 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3245 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8601 moved from start: 0.1853 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.068 35158 Z= 0.180 Angle : 0.575 12.097 47999 Z= 0.291 Chirality : 0.044 0.238 5610 Planarity : 0.004 0.062 6065 Dihedral : 4.329 48.178 4640 Min Nonbonded Distance : 2.398 Molprobity Statistics. All-atom Clashscore : 6.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.84 % Favored : 96.16 % Rotamer: Outliers : 1.58 % Allowed : 8.41 % Favored : 90.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.31 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.19 (0.13), residues: 4252 helix: 1.50 (0.20), residues: 747 sheet: 0.34 (0.14), residues: 1299 loop : -0.44 (0.14), residues: 2206 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.018 0.001 ARG F 55 TYR 0.034 0.001 TYR L 99 PHE 0.039 0.002 PHE C 135 TRP 0.030 0.001 TRP F 36 HIS 0.005 0.001 HIS A 652 Details of bonding type rmsd/Z covalent geometry : bond 0.00422 / 0.18 (35040) covalent geometry : angle 0.56419 / 0.29 (47699) SS BOND : bond 0.00318 / 0.19 ( 54) SS BOND : angle 1.62707 / 1.42 ( 108) hydrogen bonds : bond 0.03883 / 2.51 ( 1387) hydrogen bonds : angle 5.50287 / 3.80 ( 3846) link_BETA1-4 : bond 0.00242 / 0.14 ( 19) link_BETA1-4 : angle 1.06967 / 0.73 ( 57) link_BETA1-6 : bond 0.00133 / 0.09 ( 3) link_BETA1-6 : angle 1.40687 / 0.82 ( 9) link_NAG-ASN : bond 0.00252 / 0.16 ( 42) link_NAG-ASN : angle 1.52901 / 1.10 ( 126) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8504 Ramachandran restraints generated. 4252 Oldfield, 0 Emsley, 4252 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8504 Ramachandran restraints generated. 4252 Oldfield, 0 Emsley, 4252 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 274 residues out of total 3747 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 215 time to evaluate : 1.166 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 92 PHE cc_start: 0.7498 (t80) cc_final: 0.7089 (t80) REVERT: A 118 LEU cc_start: 0.9803 (tp) cc_final: 0.9495 (mp) REVERT: A 486 TYR cc_start: 0.9072 (m-80) cc_final: 0.8536 (m-80) REVERT: A 1026 MET cc_start: 0.8852 (tpp) cc_final: 0.8186 (ttm) REVERT: B 133 PHE cc_start: 0.7956 (OUTLIER) cc_final: 0.7506 (m-80) REVERT: B 210 ILE cc_start: 0.8724 (OUTLIER) cc_final: 0.8486 (tp) REVERT: B 220 PHE cc_start: 0.7355 (t80) cc_final: 0.6738 (t80) REVERT: B 422 LEU cc_start: 0.9292 (tp) cc_final: 0.9047 (tp) REVERT: B 897 MET cc_start: 0.8861 (mtp) cc_final: 0.8548 (mtp) REVERT: B 899 MET cc_start: 0.9083 (mmm) cc_final: 0.8534 (tpt) REVERT: C 51 THR cc_start: 0.8925 (OUTLIER) cc_final: 0.8680 (p) REVERT: C 229 LEU cc_start: 0.8483 (OUTLIER) cc_final: 0.7931 (tp) REVERT: C 350 TRP cc_start: 0.8455 (p-90) cc_final: 0.7983 (p-90) REVERT: C 399 ILE cc_start: 0.8355 (pt) cc_final: 0.8023 (pt) REVERT: C 502 TYR cc_start: 0.9413 (m-80) cc_final: 0.9131 (m-10) REVERT: C 737 MET cc_start: 0.8006 (tpp) cc_final: 0.7699 (tpt) REVERT: L 55 ARG cc_start: 0.9121 (ttp80) cc_final: 0.8864 (tmt170) REVERT: H 10 GLU cc_start: 0.7528 (mm-30) cc_final: 0.7254 (mm-30) REVERT: H 32 TYR cc_start: 0.8652 (m-80) cc_final: 0.8149 (m-80) REVERT: H 80 TYR cc_start: 0.9101 (m-80) cc_final: 0.8575 (m-10) REVERT: F 4 MET cc_start: 0.8334 (mmm) cc_final: 0.7644 (mmm) REVERT: F 97 ARG cc_start: 0.8957 (mtp-110) cc_final: 0.8627 (mtp85) REVERT: E 29 PHE cc_start: 0.7553 (t80) cc_final: 0.7308 (t80) REVERT: E 48 MET cc_start: 0.8894 (mtp) cc_final: 0.8053 (mtp) REVERT: E 68 VAL cc_start: 0.8615 (OUTLIER) cc_final: 0.8177 (p) REVERT: K 61 ASP cc_start: 0.9489 (p0) cc_final: 0.9207 (p0) REVERT: J 10 GLU cc_start: 0.8646 (mm-30) cc_final: 0.8162 (mm-30) REVERT: J 48 MET cc_start: 0.8915 (mtt) cc_final: 0.8388 (tpp) REVERT: J 107 MET cc_start: 0.8244 (mtt) cc_final: 0.8022 (mtt) outliers start: 59 outliers final: 33 residues processed: 266 average time/residue: 0.2439 time to fit residues: 99.2653 Evaluate side-chains 222 residues out of total 3747 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 184 time to evaluate : 1.257 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 THR Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 309 ILE Chi-restraints excluded: chain A residue 514 LEU Chi-restraints excluded: chain A residue 544 THR Chi-restraints excluded: chain A residue 546 THR Chi-restraints excluded: chain A residue 596 THR Chi-restraints excluded: chain A residue 653 VAL Chi-restraints excluded: chain A residue 788 THR Chi-restraints excluded: chain A residue 863 THR Chi-restraints excluded: chain A residue 913 LEU Chi-restraints excluded: chain B residue 133 PHE Chi-restraints excluded: chain B residue 200 TYR Chi-restraints excluded: chain B residue 210 ILE Chi-restraints excluded: chain B residue 223 LEU Chi-restraints excluded: chain B residue 233 ILE Chi-restraints excluded: chain B residue 317 VAL Chi-restraints excluded: chain B residue 347 VAL Chi-restraints excluded: chain B residue 356 SER Chi-restraints excluded: chain B residue 480 VAL Chi-restraints excluded: chain B residue 698 VAL Chi-restraints excluded: chain B residue 783 LYS Chi-restraints excluded: chain B residue 863 THR Chi-restraints excluded: chain B residue 913 LEU Chi-restraints excluded: chain B residue 937 SER Chi-restraints excluded: chain B residue 1078 ILE Chi-restraints excluded: chain B residue 1101 VAL Chi-restraints excluded: chain B residue 1119 VAL Chi-restraints excluded: chain C residue 51 THR Chi-restraints excluded: chain C residue 229 LEU Chi-restraints excluded: chain C residue 717 ILE Chi-restraints excluded: chain C residue 756 PHE Chi-restraints excluded: chain C residue 913 LEU Chi-restraints excluded: chain L residue 91 GLN Chi-restraints excluded: chain F residue 61 ASP Chi-restraints excluded: chain E residue 68 VAL Chi-restraints excluded: chain J residue 98 ARG Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/phenix/command_line/real_space_refine.py", line 9, in run_program(real_space_refine.Program) File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/iotbx/cli_parser.py", line 987, in run_program task.run() File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/phenix/programs/real_space_refine.py", line 206, in run self.rsr_result = rsr_wrappers.run_real_space_refine( ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/phenix/refinement/rsr/wrappers.py", line 52, in __init__ self._refined = macro_cycle_real_space.run( ^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/phenix/refinement/macro_cycle_real_space.py", line 306, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/phenix/refinement/macro_cycle_real_space.py", line 702, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/phenix/refinement/macro_cycle_real_space.py", line 755, in minimization_no_ncs ro = mmtbx.refinement.real_space.individual_sites.easy( ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 44, in __init__ self.weight = mmtbx.refinement.real_space.weight.run( ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/mmtbx/refinement/real_space/weight.py", line 84, in __init__ ro.refine( File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 362, in refine real_space_result = refinery( ^^^^^^^^^ File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 233, in __init__ refiner.refine( File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 100, in refine self.refined = maptbx.real_space_refinement_simple.lbfgs( ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/cctbx/maptbx/real_space_refinement_simple.py", line 168, in __init__ O.minimizer = scitbx.lbfgs.run( ^^^^^^^^^^^^^^^^^ File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/scitbx/lbfgs/__init__.py", line 270, in run return run_c_plus_plus( ^^^^^^^^^^^^^^^^ File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/cctbx/maptbx/real_space_refinement_simple.py", line 243, in compute_functional_and_gradients gr_e = O.geometry_restraints_manager.energies_sites( ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/cctbx/geometry_restraints/manager.py", line 1602, in energies_sites pair_proxies = self.pair_proxies( ^^^^^^^^^^^^^^^^^^ File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/cctbx/geometry_restraints/manager.py", line 1505, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/cctbx/geometry_restraints/manager.py", line 1386, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 68.3917 > 50: distance: 65 - 176: 33.882 distance: 68 - 173: 31.701 distance: 81 - 161: 31.443 distance: 84 - 158: 23.435 distance: 117 - 121: 23.193 distance: 121 - 122: 9.561 distance: 122 - 123: 10.617 distance: 122 - 125: 13.511 distance: 123 - 124: 47.941 distance: 123 - 126: 14.178 distance: 126 - 127: 27.628 distance: 127 - 128: 22.039 distance: 127 - 130: 13.326 distance: 128 - 129: 44.774 distance: 128 - 134: 17.645 distance: 130 - 131: 32.067 distance: 131 - 132: 47.202 distance: 131 - 133: 12.173 distance: 134 - 135: 14.538 distance: 135 - 136: 33.703 distance: 135 - 138: 48.488 distance: 136 - 137: 33.290 distance: 136 - 143: 29.169 distance: 138 - 139: 17.617 distance: 139 - 140: 16.094 distance: 140 - 141: 9.910 distance: 140 - 142: 13.939 distance: 143 - 144: 36.337 distance: 144 - 145: 19.320 distance: 144 - 147: 41.601 distance: 145 - 150: 35.910 distance: 147 - 148: 16.408 distance: 148 - 149: 57.570 distance: 150 - 151: 19.445 distance: 151 - 152: 29.506 distance: 151 - 154: 42.789 distance: 152 - 153: 7.416 distance: 152 - 158: 22.207 distance: 154 - 155: 19.517 distance: 155 - 156: 9.745 distance: 155 - 157: 31.165 distance: 158 - 159: 13.723 distance: 159 - 160: 23.663 distance: 159 - 162: 27.393 distance: 160 - 161: 8.611 distance: 160 - 165: 14.740 distance: 162 - 163: 58.983 distance: 162 - 164: 48.960 distance: 165 - 166: 21.790 distance: 166 - 167: 15.265 distance: 166 - 169: 7.541 distance: 167 - 168: 35.926 distance: 167 - 173: 37.383 distance: 169 - 170: 42.028 distance: 170 - 171: 21.304 distance: 170 - 172: 17.211 distance: 173 - 174: 10.575 distance: 174 - 175: 17.038 distance: 174 - 177: 26.276 distance: 175 - 176: 37.530 distance: 175 - 181: 39.809 distance: 177 - 178: 31.900 distance: 178 - 179: 22.873 distance: 178 - 180: 42.055 distance: 181 - 182: 6.772 distance: 181 - 187: 39.176 distance: 182 - 183: 20.825 distance: 182 - 185: 6.885 distance: 183 - 184: 19.421 distance: 183 - 188: 22.781 distance: 185 - 186: 35.536 distance: 186 - 187: 26.585 distance: 188 - 189: 6.406 distance: 189 - 190: 34.820 distance: 190 - 191: 28.733 distance: 190 - 196: 22.209 distance: 192 - 193: 33.191 distance: 192 - 194: 53.879 distance: 193 - 195: 7.041