Starting phenix.real_space_refine on Fri Mar 6 16:11:22 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7wec_32446/03_2026/7wec_32446.cif Found real_map, /net/cci-nas-00/data/ceres_data/7wec_32446/03_2026/7wec_32446.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7wec_32446/03_2026/7wec_32446.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7wec_32446/03_2026/7wec_32446.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7wec_32446/03_2026/7wec_32446.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7wec_32446/03_2026/7wec_32446.map" } resolution = 3.3 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= -0.000 sd= 0.092 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 141 5.16 5 C 20471 2.51 5 N 5287 2.21 5 O 6318 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 17 residue(s): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 32217 Number of models: 1 Model: "" Number of chains: 33 Chain: "G" Number of atoms: 941 Number of conformers: 1 Conformer: "" Number of residues, atoms: 123, 941 Classifications: {'peptide': 123} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 4, 'TRANS': 118} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "H" Number of atoms: 941 Number of conformers: 1 Conformer: "" Number of residues, atoms: 123, 941 Classifications: {'peptide': 123} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 4, 'TRANS': 118} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "I" Number of atoms: 941 Number of conformers: 1 Conformer: "" Number of residues, atoms: 123, 941 Classifications: {'peptide': 123} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 4, 'TRANS': 118} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "J" Number of atoms: 807 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 807 Classifications: {'peptide': 107} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PCIS': 1, 'PTRANS': 6, 'TRANS': 99} Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 8 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 2} Unresolved non-hydrogen planarities: 8 Chain: "K" Number of atoms: 807 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 807 Classifications: {'peptide': 107} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PCIS': 1, 'PTRANS': 6, 'TRANS': 99} Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 8 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 2} Unresolved non-hydrogen planarities: 8 Chain: "L" Number of atoms: 807 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 807 Classifications: {'peptide': 107} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PCIS': 1, 'PTRANS': 6, 'TRANS': 99} Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 8 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 2} Unresolved non-hydrogen planarities: 8 Chain: "A" Number of atoms: 8632 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1098, 8632 Classifications: {'peptide': 1098} Link IDs: {'CIS': 1, 'PTRANS': 55, 'TRANS': 1041} Chain breaks: 4 Chain: "B" Number of atoms: 8632 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1098, 8632 Classifications: {'peptide': 1098} Link IDs: {'PTRANS': 55, 'TRANS': 1042} Chain breaks: 4 Chain: "C" Number of atoms: 8632 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1098, 8632 Classifications: {'peptide': 1098} Link IDs: {'PTRANS': 55, 'TRANS': 1042} Chain breaks: 4 Chain: "D" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "E" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "F" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "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 dihedrals: 6 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 dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "O" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "P" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "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 dihedrals: 6 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 dihedrals: 6 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 dihedrals: 6 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 dihedrals: 6 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 dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "V" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "W" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 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 dihedrals: 6 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 dihedrals: 6 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 dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "a" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "b" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "c" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "d" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "A" Number of atoms: 140 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 140 Unusual residues: {'NAG': 10} Classifications: {'undetermined': 10} Link IDs: {None: 9} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 30 Unresolved non-hydrogen chiralities: 10 Chain: "B" Number of atoms: 154 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 154 Unusual residues: {'NAG': 11} Classifications: {'undetermined': 11} Link IDs: {None: 10} Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 22 Unresolved non-hydrogen dihedrals: 33 Unresolved non-hydrogen chiralities: 11 Chain: "C" Number of atoms: 140 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 140 Unusual residues: {'NAG': 10} Classifications: {'undetermined': 10} Link IDs: {None: 9} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 30 Unresolved non-hydrogen chiralities: 10 Time building chain proxies: 8.57, per 1000 atoms: 0.27 Number of scatterers: 32217 At special positions: 0 Unit cell: (163.71, 164.78, 208.65, 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 141 16.00 O 6318 8.00 N 5287 7.00 C 20471 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=48, symmetry=0 Simple disulfide: pdb=" SG CYS G 22 " - pdb=" SG CYS G 97 " distance=2.04 Simple disulfide: pdb=" SG CYS G 102 " - pdb=" SG CYS G 107 " distance=2.04 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 97 " distance=2.04 Simple disulfide: pdb=" SG CYS H 102 " - pdb=" SG CYS H 107 " distance=2.04 Simple disulfide: pdb=" SG CYS I 22 " - pdb=" SG CYS I 97 " distance=2.04 Simple disulfide: pdb=" SG CYS I 102 " - pdb=" SG CYS I 107 " distance=2.04 Simple disulfide: pdb=" SG CYS J 23 " - pdb=" SG CYS J 89 " distance=2.04 Simple disulfide: pdb=" SG CYS K 23 " - pdb=" SG CYS K 89 " distance=2.04 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 89 " distance=2.04 Simple disulfide: pdb=" SG CYS A 15 " - pdb=" SG CYS A 134 " distance=2.03 Simple disulfide: pdb=" SG CYS A 129 " - pdb=" SG CYS A 161 " 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=2.05 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=2.04 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=2.04 Simple disulfide: pdb=" SG CYS B 15 " - pdb=" SG CYS B 134 " distance=2.03 Simple disulfide: pdb=" SG CYS B 129 " - pdb=" SG CYS B 161 " 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=2.05 Simple disulfide: pdb=" SG CYS B 388 " - pdb=" SG CYS B 522 " distance=2.02 Simple disulfide: pdb=" SG CYS B 477 " - pdb=" SG CYS B 485 " 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 15 " - pdb=" SG CYS C 134 " distance=2.03 Simple disulfide: pdb=" SG CYS C 129 " - pdb=" SG CYS C 161 " 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=2.05 Simple disulfide: pdb=" SG CYS C 388 " - pdb=" SG CYS C 522 " distance=2.02 Simple disulfide: pdb=" SG CYS C 477 " - pdb=" SG CYS C 485 " 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=2.04 Simple disulfide: pdb=" SG CYS C1029 " - pdb=" SG CYS C1040 " distance=2.03 Simple disulfide: pdb=" SG CYS C1079 " - pdb=" SG CYS C1123 " distance=2.04 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=12, symmetry=0 Links applied BETA1-4 " NAG D 1 " - " NAG D 2 " " NAG E 1 " - " NAG E 2 " " NAG F 1 " - " NAG F 2 " " NAG M 1 " - " NAG M 2 " " NAG N 1 " - " NAG N 2 " " NAG O 1 " - " NAG O 2 " " NAG O 2 " - " BMA O 3 " " NAG P 1 " - " NAG P 2 " " 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 W 2 " - " BMA W 3 " " NAG X 1 " - " NAG X 2 " " NAG Y 1 " - " NAG Y 2 " " NAG Z 1 " - " NAG Z 2 " " NAG a 1 " - " NAG a 2 " " NAG b 1 " - " NAG b 2 " " NAG c 1 " - " NAG c 2 " " NAG c 2 " - " BMA c 3 " " NAG d 1 " - " NAG d 2 " " NAG d 2 " - " BMA d 3 " NAG-ASN " NAG A1302 " - " ASN A1155 " " NAG A1303 " - " ASN A 143 " " NAG A1304 " - " ASN A 17 " " NAG A1306 " - " ASN A 61 " " NAG A1307 " - " ASN A 600 " " NAG A1308 " - " ASN A 654 " " NAG A1309 " - " ASN A 613 " " NAG A1310 " - " ASN A 706 " " NAG B1302 " - " ASN B1155 " " NAG B1303 " - " ASN B 123 " " NAG B1304 " - " ASN B 143 " " NAG B1305 " - " ASN B 17 " " NAG B1307 " - " ASN B 61 " " NAG B1308 " - " ASN B 600 " " NAG B1309 " - " ASN B 654 " " NAG B1310 " - " ASN B 613 " " NAG B1311 " - " ASN B 706 " " NAG C1301 " - " ASN C1155 " " NAG C1302 " - " ASN C 123 " " NAG C1303 " - " ASN C 143 " " NAG C1304 " - " ASN C 17 " " NAG C1306 " - " ASN C 61 " " NAG C1307 " - " ASN C 600 " " NAG C1308 " - " ASN C 654 " " NAG C1309 " - " ASN C 613 " " NAG C1310 " - " ASN C 706 " " NAG D 1 " - " ASN A 231 " " NAG F 1 " - " ASN A 714 " " NAG M 1 " - " ASN A1071 " " NAG N 1 " - " ASN A 798 " " NAG O 1 " - " ASN A1095 " " NAG P 1 " - " ASN A1131 " " NAG S 1 " - " ASN B 714 " " NAG U 1 " - " ASN B 798 " " NAG V 1 " - " ASN B1095 " " NAG W 1 " - " ASN B1131 " " NAG X 1 " - " ASN C 231 " " NAG Z 1 " - " ASN C 714 " " NAG b 1 " - " ASN C 798 " " NAG c 1 " - " ASN C1095 " " NAG d 1 " - " ASN C1131 " Number of additional bonds: simple=12, symmetry=0 Coordination: Other bonds: Time building additional restraints: 3.05 Conformation dependent library (CDL) restraints added in 1.4 seconds 7884 Ramachandran restraints generated. 3942 Oldfield, 0 Emsley, 3942 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7464 Finding SS restraints... Secondary structure from input PDB file: 77 helices and 69 sheets defined 20.3% alpha, 24.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.54 Creating SS restraints... Processing helix chain 'G' and resid 88 through 92 Processing helix chain 'H' and resid 63 through 66 removed outlier: 3.691A pdb=" N GLN H 66 " --> pdb=" O PRO H 63 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 63 through 66' Processing helix chain 'H' and resid 88 through 92 removed outlier: 3.687A pdb=" N THR H 92 " --> pdb=" O SER H 89 " (cutoff:3.500A) Processing helix chain 'I' and resid 88 through 92 Processing helix chain 'A' and resid 291 through 301 Processing helix chain 'A' and resid 334 through 341 removed outlier: 4.119A pdb=" N VAL A 338 " --> pdb=" O PRO A 334 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N PHE A 339 " --> pdb=" O PHE A 335 " (cutoff:3.500A) Processing helix chain 'A' and resid 362 through 367 Processing helix chain 'A' and resid 380 through 384 removed outlier: 3.819A pdb=" N LEU A 384 " --> pdb=" O PRO A 381 " (cutoff:3.500A) Processing helix chain 'A' and resid 402 through 408 removed outlier: 5.199A pdb=" N ARG A 405 " --> pdb=" O ASP A 402 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N ALA A 408 " --> pdb=" O ARG A 405 " (cutoff:3.500A) Processing helix chain 'A' and resid 630 through 634 Processing helix chain 'A' and resid 734 through 740 removed outlier: 3.637A pdb=" N ILE A 739 " --> pdb=" O CYS A 735 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N CYS A 740 " --> pdb=" O THR A 736 " (cutoff:3.500A) Processing helix chain 'A' and resid 743 through 751 removed outlier: 3.734A pdb=" N SER A 747 " --> pdb=" O SER A 743 " (cutoff:3.500A) removed outlier: 4.151A pdb=" N ASN A 748 " --> pdb=" O THR A 744 " (cutoff:3.500A) removed outlier: 4.359A pdb=" N LEU A 749 " --> pdb=" O GLU A 745 " (cutoff:3.500A) Processing helix chain 'A' and resid 752 through 754 No H-bonds generated for 'chain 'A' and resid 752 through 754' Processing helix chain 'A' and resid 755 through 777 removed outlier: 3.787A pdb=" N ASP A 772 " --> pdb=" O ALA A 768 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N LYS A 773 " --> pdb=" O VAL A 769 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N THR A 775 " --> pdb=" O GLN A 771 " (cutoff:3.500A) Processing helix chain 'A' and resid 813 through 821 removed outlier: 3.589A pdb=" N LEU A 818 " --> pdb=" O PHE A 814 " (cutoff:3.500A) Processing helix chain 'A' and resid 846 through 851 removed outlier: 3.738A pdb=" N LYS A 851 " --> pdb=" O CYS A 848 " (cutoff:3.500A) Processing helix chain 'A' and resid 863 through 878 removed outlier: 4.066A pdb=" N GLN A 869 " --> pdb=" O GLU A 865 " (cutoff:3.500A) Processing helix chain 'A' and resid 883 through 887 removed outlier: 3.885A pdb=" N GLY A 886 " --> pdb=" O TRP A 883 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N ALA A 887 " --> pdb=" O THR A 884 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 883 through 887' Processing helix chain 'A' and resid 894 through 905 removed outlier: 4.046A pdb=" N ALA A 900 " --> pdb=" O ALA A 896 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N TYR A 901 " --> pdb=" O MET A 897 " (cutoff:3.500A) Processing helix chain 'A' and resid 910 through 916 removed outlier: 3.980A pdb=" N TYR A 914 " --> pdb=" O GLN A 910 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N GLU A 915 " --> pdb=" O ASN A 911 " (cutoff:3.500A) Processing helix chain 'A' and resid 916 through 936 removed outlier: 3.781A pdb=" N GLN A 932 " --> pdb=" O ILE A 928 " (cutoff:3.500A) removed outlier: 3.893A pdb=" N ASP A 933 " --> pdb=" O GLY A 929 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N SER A 936 " --> pdb=" O GLN A 932 " (cutoff:3.500A) Processing helix chain 'A' and resid 942 through 962 removed outlier: 4.016A pdb=" N VAL A 948 " --> pdb=" O LYS A 944 " (cutoff:3.500A) removed outlier: 3.936A pdb=" N VAL A 949 " --> pdb=" O LEU A 945 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N ASN A 952 " --> pdb=" O VAL A 948 " (cutoff:3.500A) removed outlier: 4.425A pdb=" N LEU A 956 " --> pdb=" O ASN A 952 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N ASN A 957 " --> pdb=" O ALA A 953 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N THR A 958 " --> pdb=" O GLN A 954 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N LEU A 959 " --> pdb=" O ALA A 955 " (cutoff:3.500A) 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 removed outlier: 3.823A pdb=" N ILE A 977 " --> pdb=" O VAL A 973 " (cutoff:3.500A) removed outlier: 3.982A pdb=" N PHE A 978 " --> pdb=" O LEU A 974 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N SER A 979 " --> pdb=" O ASN A 975 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 973 through 979' Processing helix chain 'A' and resid 985 through 1029 removed outlier: 3.827A pdb=" N GLN A 989 " --> pdb=" O GLU A 985 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N ASP A 991 " --> pdb=" O GLU A 987 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N ARG A 992 " --> pdb=" O VAL A 988 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N GLY A 996 " --> pdb=" O ARG A 992 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N LEU A 998 " --> pdb=" O ILE A 994 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N LEU A1001 " --> pdb=" O ARG A 997 " (cutoff:3.500A) removed outlier: 4.011A pdb=" N TYR A1004 " --> pdb=" O SER A1000 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N ALA A1017 " --> pdb=" O ALA A1013 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N SER A1018 " --> pdb=" O GLU A1014 " (cutoff:3.500A) removed outlier: 3.956A pdb=" N LEU A1021 " --> pdb=" O ALA A1017 " (cutoff:3.500A) removed outlier: 3.967A pdb=" N THR A1024 " --> pdb=" O ASN A1020 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N SER A1027 " --> pdb=" O ALA A1023 " (cutoff:3.500A) Processing helix chain 'A' and resid 1137 through 1147 removed outlier: 3.695A pdb=" N GLU A1141 " --> pdb=" O PRO A1137 " (cutoff:3.500A) removed outlier: 4.553A pdb=" N PHE A1145 " --> pdb=" O GLU A1141 " (cutoff:3.500A) Processing helix chain 'A' and resid 1148 through 1158 removed outlier: 3.727A pdb=" N SER A1158 " --> pdb=" O LYS A1154 " (cutoff:3.500A) Processing helix chain 'B' and resid 291 through 300 Processing helix chain 'B' and resid 334 through 340 removed outlier: 4.195A pdb=" N VAL B 338 " --> pdb=" O PRO B 334 " (cutoff:3.500A) Processing helix chain 'B' and resid 362 through 367 Processing helix chain 'B' and resid 380 through 384 removed outlier: 4.150A pdb=" N LEU B 384 " --> pdb=" O PRO B 381 " (cutoff:3.500A) Processing helix chain 'B' and resid 400 through 408 removed outlier: 4.686A pdb=" N ARG B 405 " --> pdb=" O ASP B 402 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N ILE B 407 " --> pdb=" O VAL B 404 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N ALA B 408 " --> pdb=" O ARG B 405 " (cutoff:3.500A) Processing helix chain 'B' and resid 414 through 419 Processing helix chain 'B' and resid 617 through 621 Processing helix chain 'B' and resid 630 through 634 Processing helix chain 'B' and resid 735 through 740 removed outlier: 4.313A pdb=" N ILE B 739 " --> pdb=" O CYS B 735 " (cutoff:3.500A) Processing helix chain 'B' and resid 743 through 748 removed outlier: 3.715A pdb=" N SER B 747 " --> pdb=" O SER B 743 " (cutoff:3.500A) removed outlier: 4.210A pdb=" N ASN B 748 " --> pdb=" O THR B 744 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 743 through 748' Processing helix chain 'B' and resid 750 through 754 Processing helix chain 'B' and resid 755 through 777 removed outlier: 3.548A pdb=" N GLN B 759 " --> pdb=" O SER B 755 " (cutoff:3.500A) removed outlier: 3.867A pdb=" N ASP B 772 " --> pdb=" O ALA B 768 " (cutoff:3.500A) removed outlier: 3.884A pdb=" N LYS B 773 " --> pdb=" O VAL B 769 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N THR B 775 " --> pdb=" O GLN B 771 " (cutoff:3.500A) Processing helix chain 'B' and resid 813 through 822 removed outlier: 3.632A pdb=" N LEU B 818 " --> pdb=" O PHE B 814 " (cutoff:3.500A) Processing helix chain 'B' and resid 846 through 851 removed outlier: 3.730A pdb=" N LYS B 851 " --> pdb=" O CYS B 848 " (cutoff:3.500A) Processing helix chain 'B' and resid 863 through 878 removed outlier: 3.525A pdb=" N SER B 872 " --> pdb=" O ALA B 868 " (cutoff:3.500A) Processing helix chain 'B' and resid 894 through 897 Processing helix chain 'B' and resid 898 through 905 Processing helix chain 'B' and resid 910 through 915 removed outlier: 3.945A pdb=" N TYR B 914 " --> pdb=" O GLN B 910 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N GLU B 915 " --> pdb=" O ASN B 911 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 910 through 915' Processing helix chain 'B' and resid 916 through 936 removed outlier: 3.698A pdb=" N GLN B 932 " --> pdb=" O ILE B 928 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N ASP B 933 " --> pdb=" O GLY B 929 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N SER B 936 " --> pdb=" O GLN B 932 " (cutoff:3.500A) Processing helix chain 'B' and resid 942 through 962 removed outlier: 3.987A pdb=" N VAL B 948 " --> pdb=" O LYS B 944 " (cutoff:3.500A) removed outlier: 3.896A pdb=" N VAL B 949 " --> pdb=" O LEU B 945 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N ASN B 952 " --> pdb=" O VAL B 948 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N LEU B 956 " --> pdb=" O ASN B 952 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N LEU B 959 " --> pdb=" O ALA B 955 " (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 985 through 1016 removed outlier: 3.808A pdb=" N GLN B 989 " --> pdb=" O GLU B 985 " (cutoff:3.500A) removed outlier: 3.903A pdb=" N GLY B 996 " --> pdb=" O ARG B 992 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N LEU B1001 " --> pdb=" O ARG B 997 " (cutoff:3.500A) Processing helix chain 'B' and resid 1018 through 1029 removed outlier: 3.951A pdb=" N THR B1024 " --> pdb=" O ASN B1020 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N SER B1027 " --> pdb=" O ALA B1023 " (cutoff:3.500A) Processing helix chain 'B' and resid 1137 through 1144 removed outlier: 3.982A pdb=" N GLU B1141 " --> pdb=" O PRO B1137 " (cutoff:3.500A) Processing helix chain 'B' and resid 1145 through 1158 removed outlier: 3.775A pdb=" N SER B1158 " --> pdb=" O LYS B1154 " (cutoff:3.500A) Processing helix chain 'C' and resid 291 through 300 Processing helix chain 'C' and resid 334 through 340 removed outlier: 4.207A pdb=" N VAL C 338 " --> pdb=" O PRO C 334 " (cutoff:3.500A) Processing helix chain 'C' and resid 346 through 350 removed outlier: 3.663A pdb=" N ALA C 349 " --> pdb=" O SER C 346 " (cutoff:3.500A) removed outlier: 3.973A pdb=" N TRP C 350 " --> pdb=" O VAL C 347 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 346 through 350' Processing helix chain 'C' and resid 362 through 367 Processing helix chain 'C' and resid 380 through 384 removed outlier: 4.085A pdb=" N LEU C 384 " --> pdb=" O PRO C 381 " (cutoff:3.500A) Processing helix chain 'C' and resid 402 through 408 removed outlier: 4.925A pdb=" N ARG C 405 " --> pdb=" O ASP C 402 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N ALA C 408 " --> pdb=" O ARG C 405 " (cutoff:3.500A) Processing helix chain 'C' and resid 414 through 419 removed outlier: 3.895A pdb=" N TYR C 418 " --> pdb=" O ASN C 414 " (cutoff:3.500A) Processing helix chain 'C' and resid 615 through 620 removed outlier: 4.117A pdb=" N VAL C 619 " --> pdb=" O THR C 615 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N ALA C 620 " --> pdb=" O GLU C 616 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 615 through 620' Processing helix chain 'C' and resid 630 through 636 removed outlier: 3.747A pdb=" N TYR C 633 " --> pdb=" O TRP C 630 " (cutoff:3.500A) Processing helix chain 'C' and resid 734 through 740 removed outlier: 4.206A pdb=" N TYR C 738 " --> pdb=" O ASP C 734 " (cutoff:3.500A) removed outlier: 4.196A pdb=" N ILE C 739 " --> pdb=" O CYS C 735 " (cutoff:3.500A) Processing helix chain 'C' and resid 743 through 751 removed outlier: 3.518A pdb=" N SER C 747 " --> pdb=" O SER C 743 " (cutoff:3.500A) removed outlier: 4.006A pdb=" N ASN C 748 " --> pdb=" O THR C 744 " (cutoff:3.500A) removed outlier: 4.506A pdb=" N LEU C 749 " --> pdb=" O GLU C 745 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N LEU C 751 " --> pdb=" O SER C 747 " (cutoff:3.500A) 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 757 through 779 removed outlier: 3.762A pdb=" N ASP C 772 " --> pdb=" O ALA C 768 " (cutoff:3.500A) removed outlier: 3.898A pdb=" N LYS C 773 " --> pdb=" O VAL C 769 " (cutoff:3.500A) removed outlier: 3.873A pdb=" N THR C 775 " --> pdb=" O GLN C 771 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N VAL C 778 " --> pdb=" O ASN C 774 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N PHE C 779 " --> pdb=" O THR C 775 " (cutoff:3.500A) Processing helix chain 'C' and resid 813 through 821 removed outlier: 3.630A pdb=" N LEU C 818 " --> pdb=" O PHE C 814 " (cutoff:3.500A) Processing helix chain 'C' and resid 846 through 851 removed outlier: 3.781A pdb=" N GLN C 850 " --> pdb=" O ILE C 847 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N LYS C 851 " --> pdb=" O CYS C 848 " (cutoff:3.500A) Processing helix chain 'C' and resid 863 through 878 removed outlier: 4.271A pdb=" N GLN C 869 " --> pdb=" O GLU C 865 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N TYR C 870 " --> pdb=" O MET C 866 " (cutoff:3.500A) Processing helix chain 'C' and resid 883 through 887 removed outlier: 3.950A pdb=" N GLY C 886 " --> pdb=" O TRP C 883 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N ALA C 887 " --> pdb=" O THR C 884 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 883 through 887' Processing helix chain 'C' and resid 894 through 905 removed outlier: 4.160A pdb=" N ALA C 900 " --> pdb=" O ALA C 896 " (cutoff:3.500A) removed outlier: 4.036A pdb=" N TYR C 901 " --> pdb=" O MET C 897 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N ARG C 902 " --> pdb=" O GLN C 898 " (cutoff:3.500A) Processing helix chain 'C' and resid 910 through 916 removed outlier: 4.047A pdb=" N TYR C 914 " --> pdb=" O GLN C 910 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N ASN C 916 " --> pdb=" O VAL C 912 " (cutoff:3.500A) Processing helix chain 'C' and resid 916 through 936 removed outlier: 3.770A pdb=" N GLN C 932 " --> pdb=" O ILE C 928 " (cutoff:3.500A) removed outlier: 3.927A pdb=" N ASP C 933 " --> pdb=" O GLY C 929 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N SER C 936 " --> pdb=" O GLN C 932 " (cutoff:3.500A) Processing helix chain 'C' and resid 942 through 963 removed outlier: 4.038A pdb=" N VAL C 948 " --> pdb=" O LYS C 944 " (cutoff:3.500A) removed outlier: 3.917A pdb=" N VAL C 949 " --> pdb=" O LEU C 945 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N ASN C 952 " --> pdb=" O VAL C 948 " (cutoff:3.500A) removed outlier: 4.525A pdb=" N LEU C 956 " --> pdb=" O ASN C 952 " (cutoff:3.500A) removed outlier: 4.114A pdb=" N LEU C 963 " --> pdb=" O LEU C 959 " (cutoff:3.500A) Processing helix chain 'C' and resid 973 through 979 removed outlier: 3.553A pdb=" N ILE C 977 " --> pdb=" O VAL C 973 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N PHE C 978 " --> pdb=" O LEU C 974 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N SER C 979 " --> pdb=" O ASN C 975 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 973 through 979' Processing helix chain 'C' and resid 982 through 1029 removed outlier: 3.736A pdb=" N GLU C 987 " --> pdb=" O LYS C 983 " (cutoff:3.500A) removed outlier: 4.906A pdb=" N VAL C 988 " --> pdb=" O VAL C 984 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N GLN C 989 " --> pdb=" O GLU C 985 " (cutoff:3.500A) removed outlier: 3.916A pdb=" N ASP C 991 " --> pdb=" O GLU C 987 " (cutoff:3.500A) removed outlier: 4.190A pdb=" N GLY C 996 " --> pdb=" O ARG C 992 " (cutoff:3.500A) removed outlier: 3.999A pdb=" N TYR C1004 " --> pdb=" O SER C1000 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N ALA C1017 " --> pdb=" O ALA C1013 " (cutoff:3.500A) removed outlier: 3.974A pdb=" N LEU C1021 " --> pdb=" O ALA C1017 " (cutoff:3.500A) removed outlier: 4.064A pdb=" N THR C1024 " --> pdb=" O ASN C1020 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N SER C1027 " --> pdb=" O ALA C1023 " (cutoff:3.500A) Processing helix chain 'C' and resid 1137 through 1144 removed outlier: 4.199A pdb=" N GLU C1141 " --> pdb=" O PRO C1137 " (cutoff:3.500A) Processing helix chain 'C' and resid 1145 through 1158 removed outlier: 3.873A pdb=" N SER C1158 " --> pdb=" O LYS C1154 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'G' and resid 4 through 6 removed outlier: 3.889A pdb=" N CYS G 22 " --> pdb=" O ALA G 80 " (cutoff:3.500A) removed outlier: 4.087A pdb=" N ALA G 80 " --> pdb=" O CYS G 22 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'G' and resid 10 through 12 removed outlier: 6.327A pdb=" N GLU G 10 " --> pdb=" O THR G 121 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N LEU G 35 " --> pdb=" O THR G 52 " (cutoff:3.500A) removed outlier: 3.923A pdb=" N GLY G 50 " --> pdb=" O TRP G 37 " (cutoff:3.500A) removed outlier: 6.869A pdb=" N ARG G 39 " --> pdb=" O TRP G 48 " (cutoff:3.500A) removed outlier: 6.002A pdb=" N TRP G 48 " --> pdb=" O ARG G 39 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'H' and resid 3 through 6 removed outlier: 3.799A pdb=" N GLN H 3 " --> pdb=" O SER H 25 " (cutoff:3.500A) removed outlier: 3.990A pdb=" N CYS H 22 " --> pdb=" O ALA H 80 " (cutoff:3.500A) removed outlier: 4.273A pdb=" N ALA H 80 " --> pdb=" O CYS H 22 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'H' and resid 10 through 12 removed outlier: 6.379A pdb=" N GLU H 10 " --> pdb=" O THR H 121 " (cutoff:3.500A) removed outlier: 3.868A pdb=" N LEU H 35 " --> pdb=" O THR H 52 " (cutoff:3.500A) removed outlier: 3.949A pdb=" N GLY H 50 " --> pdb=" O TRP H 37 " (cutoff:3.500A) removed outlier: 6.777A pdb=" N ARG H 39 " --> pdb=" O TRP H 48 " (cutoff:3.500A) removed outlier: 5.820A pdb=" N TRP H 48 " --> pdb=" O ARG H 39 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'I' and resid 10 through 12 removed outlier: 6.300A pdb=" N GLU I 10 " --> pdb=" O THR I 121 " (cutoff:3.500A) removed outlier: 6.817A pdb=" N LEU I 35 " --> pdb=" O TRP I 51 " (cutoff:3.500A) removed outlier: 4.456A pdb=" N TRP I 51 " --> pdb=" O LEU I 35 " (cutoff:3.500A) removed outlier: 6.871A pdb=" N TRP I 37 " --> pdb=" O ILE I 49 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N GLU I 47 " --> pdb=" O ARG I 39 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'I' and resid 10 through 12 removed outlier: 6.300A pdb=" N GLU I 10 " --> pdb=" O THR I 121 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N ALA I 99 " --> pdb=" O LEU I 113 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N LEU I 113 " --> pdb=" O ALA I 99 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'I' and resid 17 through 21 Processing sheet with id=AA8, first strand: chain 'J' and resid 5 through 7 removed outlier: 3.577A pdb=" N THR J 73 " --> pdb=" O SER J 66 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'J' and resid 10 through 12 removed outlier: 5.834A pdb=" N LEU J 11 " --> pdb=" O GLU J 106 " (cutoff:3.500A) removed outlier: 4.155A pdb=" N VAL J 86 " --> pdb=" O GLN J 39 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N GLN J 39 " --> pdb=" O VAL J 86 " (cutoff:3.500A) removed outlier: 6.641A pdb=" N LEU J 34 " --> pdb=" O SER J 50 " (cutoff:3.500A) removed outlier: 4.742A pdb=" N SER J 50 " --> pdb=" O LEU J 34 " (cutoff:3.500A) removed outlier: 6.677A pdb=" N TRP J 36 " --> pdb=" O LEU J 48 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N SER J 54 " --> pdb=" O SER J 50 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'K' and resid 5 through 7 removed outlier: 3.737A pdb=" N THR K 73 " --> pdb=" O SER K 66 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'K' and resid 10 through 12 removed outlier: 6.010A pdb=" N LEU K 11 " --> pdb=" O GLU K 106 " (cutoff:3.500A) removed outlier: 4.127A pdb=" N VAL K 86 " --> pdb=" O GLN K 39 " (cutoff:3.500A) removed outlier: 6.380A pdb=" N LEU K 34 " --> pdb=" O SER K 50 " (cutoff:3.500A) removed outlier: 4.432A pdb=" N SER K 50 " --> pdb=" O LEU K 34 " (cutoff:3.500A) removed outlier: 6.730A pdb=" N TRP K 36 " --> pdb=" O LEU K 48 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N SER K 54 " --> pdb=" O SER K 50 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'L' and resid 5 through 7 removed outlier: 3.708A pdb=" N THR L 73 " --> pdb=" O SER L 66 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'L' and resid 10 through 12 removed outlier: 5.854A pdb=" N LEU L 11 " --> pdb=" O GLU L 106 " (cutoff:3.500A) removed outlier: 4.030A pdb=" N VAL L 86 " --> pdb=" O GLN L 39 " (cutoff:3.500A) removed outlier: 6.621A pdb=" N LEU L 34 " --> pdb=" O SER L 50 " (cutoff:3.500A) removed outlier: 4.743A pdb=" N SER L 50 " --> pdb=" O LEU L 34 " (cutoff:3.500A) removed outlier: 6.583A pdb=" N TRP L 36 " --> pdb=" O LEU L 48 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 27 through 31 removed outlier: 3.567A pdb=" N SER A 60 " --> pdb=" O SER A 31 " (cutoff:3.500A) removed outlier: 7.699A pdb=" N ASN A 61 " --> pdb=" O TYR A 266 " (cutoff:3.500A) removed outlier: 5.736A pdb=" N TYR A 266 " --> pdb=" O ASN A 61 " (cutoff:3.500A) removed outlier: 3.941A pdb=" N ALA A 261 " --> pdb=" O ILE A 93 " (cutoff:3.500A) removed outlier: 5.652A pdb=" N SER A 200 " --> pdb=" O PRO A 222 " (cutoff:3.500A) removed outlier: 9.408A pdb=" N HIS A 202 " --> pdb=" O LEU A 220 " (cutoff:3.500A) removed outlier: 9.561A pdb=" N LEU A 220 " --> pdb=" O HIS A 202 " (cutoff:3.500A) removed outlier: 7.012A pdb=" N VAL A 36 " --> pdb=" O LEU A 220 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 48 through 55 removed outlier: 3.943A pdb=" N ASP A 284 " --> pdb=" O LYS A 275 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'A' and resid 82 through 83 Processing sheet with id=AB8, first strand: chain 'A' and resid 308 through 312 removed outlier: 4.737A pdb=" N VAL A 592 " --> pdb=" O THR A 312 " (cutoff:3.500A) removed outlier: 3.952A pdb=" N TYR A 609 " --> pdb=" O CYS A 646 " (cutoff:3.500A) removed outlier: 3.888A pdb=" N CYS A 646 " --> pdb=" O TYR A 609 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'A' and resid 321 through 322 removed outlier: 7.366A pdb=" N GLU A 321 " --> pdb=" O ASN A 537 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB9 Processing sheet with id=AC1, first strand: chain 'A' and resid 351 through 355 removed outlier: 3.633A pdb=" N ASN A 351 " --> pdb=" O SER A 396 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N SER A 396 " --> pdb=" O ASN A 351 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N SER A 511 " --> pdb=" O TYR A 393 " (cutoff:3.500A) removed outlier: 3.927A pdb=" N VAL A 430 " --> pdb=" O LYS A 375 " (cutoff:3.500A) removed outlier: 3.950A pdb=" N LYS A 375 " --> pdb=" O VAL A 430 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'A' and resid 449 through 451 Processing sheet with id=AC3, first strand: chain 'A' and resid 470 through 471 removed outlier: 3.653A pdb=" N TYR A 470 " --> pdb=" O TYR A 486 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'A' and resid 539 through 540 removed outlier: 3.661A pdb=" N PHE A 540 " --> pdb=" O LEU A 543 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'A' and resid 548 through 551 removed outlier: 5.384A pdb=" N ASP A 571 " --> pdb=" O ILE A 584 " (cutoff:3.500A) removed outlier: 4.169A pdb=" N ALA A 572 " --> pdb=" O GLY A 563 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'A' and resid 651 through 652 removed outlier: 5.747A pdb=" N GLU A 651 " --> pdb=" O ALA A 691 " (cutoff:3.500A) removed outlier: 8.277A pdb=" N THR A 693 " --> pdb=" O GLU A 651 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'A' and resid 698 through 699 removed outlier: 7.156A pdb=" N ALA A 698 " --> pdb=" O ILE C 785 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC7 Processing sheet with id=AC8, first strand: chain 'A' and resid 708 through 712 Processing sheet with id=AC9, first strand: chain 'A' and resid 715 through 725 removed outlier: 6.911A pdb=" N VAL A1062 " --> pdb=" O LEU A1046 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'A' and resid 715 through 725 removed outlier: 3.562A pdb=" N ALA A1053 " --> pdb=" O GLY A1056 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'A' and resid 732 through 733 Processing sheet with id=AD3, first strand: chain 'A' and resid 1117 through 1122 removed outlier: 3.602A pdb=" N SER A1120 " --> pdb=" O ALA A1084 " (cutoff:3.500A) removed outlier: 5.071A pdb=" N ALA A1084 " --> pdb=" O SER A1120 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'A' and resid 1091 through 1094 Processing sheet with id=AD5, first strand: chain 'B' and resid 27 through 31 removed outlier: 3.620A pdb=" N SER B 60 " --> pdb=" O SER B 31 " (cutoff:3.500A) removed outlier: 7.514A pdb=" N ASN B 61 " --> pdb=" O TYR B 266 " (cutoff:3.500A) removed outlier: 5.874A pdb=" N TYR B 266 " --> pdb=" O ASN B 61 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N ALA B 261 " --> pdb=" O ILE B 93 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N ILE B 198 " --> pdb=" O VAL B 224 " (cutoff:3.500A) removed outlier: 3.941A pdb=" N VAL B 224 " --> pdb=" O ILE B 198 " (cutoff:3.500A) removed outlier: 6.133A pdb=" N SER B 200 " --> pdb=" O PRO B 222 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'B' and resid 48 through 55 removed outlier: 3.946A pdb=" N ASP B 284 " --> pdb=" O LYS B 275 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'B' and resid 99 through 104 removed outlier: 6.395A pdb=" N LEU B 238 " --> pdb=" O ARG B 100 " (cutoff:3.500A) removed outlier: 5.594A pdb=" N TRP B 102 " --> pdb=" O GLN B 236 " (cutoff:3.500A) removed outlier: 7.683A pdb=" N GLN B 236 " --> pdb=" O TRP B 102 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'B' and resid 113 through 114 Processing sheet with id=AD9, first strand: chain 'B' and resid 113 through 114 removed outlier: 6.413A pdb=" N ILE B 126 " --> pdb=" O GLU B 164 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N GLU B 164 " --> pdb=" O ILE B 126 " (cutoff:3.500A) removed outlier: 6.577A pdb=" N VAL B 128 " --> pdb=" O THR B 162 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'B' and resid 308 through 315 removed outlier: 4.702A pdb=" N VAL B 592 " --> pdb=" O THR B 312 " (cutoff:3.500A) removed outlier: 5.200A pdb=" N ASN B 314 " --> pdb=" O GLY B 590 " (cutoff:3.500A) removed outlier: 6.608A pdb=" N GLY B 590 " --> pdb=" O ASN B 314 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'B' and resid 321 through 322 removed outlier: 7.480A pdb=" N GLU B 321 " --> pdb=" O ASN B 537 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE2 Processing sheet with id=AE3, first strand: chain 'B' and resid 351 through 355 removed outlier: 3.762A pdb=" N ASN B 351 " --> pdb=" O SER B 396 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N VAL B 392 " --> pdb=" O ILE B 355 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N ILE B 399 " --> pdb=" O TYR B 505 " (cutoff:3.500A) removed outlier: 7.336A pdb=" N GLY B 428 " --> pdb=" O CYS B 376 " (cutoff:3.500A) removed outlier: 5.386A pdb=" N CYS B 376 " --> pdb=" O GLY B 428 " (cutoff:3.500A) removed outlier: 7.380A pdb=" N VAL B 430 " --> pdb=" O PHE B 374 " (cutoff:3.500A) removed outlier: 4.414A pdb=" N PHE B 374 " --> pdb=" O VAL B 430 " (cutoff:3.500A) removed outlier: 6.514A pdb=" N ALA B 432 " --> pdb=" O PHE B 372 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'B' and resid 358 through 359 removed outlier: 7.267A pdb=" N CYS B 358 " --> pdb=" O CYS B 522 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE4 Processing sheet with id=AE5, first strand: chain 'B' and resid 449 through 451 Processing sheet with id=AE6, first strand: chain 'B' and resid 470 through 471 Processing sheet with id=AE7, first strand: chain 'B' and resid 539 through 540 removed outlier: 3.743A pdb=" N PHE B 540 " --> pdb=" O LEU B 543 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'B' and resid 548 through 551 removed outlier: 3.503A pdb=" N ASP B 583 " --> pdb=" O THR B 550 " (cutoff:3.500A) removed outlier: 5.551A pdb=" N ASP B 571 " --> pdb=" O ILE B 584 " (cutoff:3.500A) removed outlier: 4.145A pdb=" N ALA B 572 " --> pdb=" O GLY B 563 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'B' and resid 651 through 657 removed outlier: 6.024A pdb=" N GLU B 651 " --> pdb=" O ALA B 691 " (cutoff:3.500A) removed outlier: 8.371A pdb=" N THR B 693 " --> pdb=" O GLU B 651 " (cutoff:3.500A) removed outlier: 9.076A pdb=" N VAL B 653 " --> pdb=" O THR B 693 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'B' and resid 708 through 712 Processing sheet with id=AF2, first strand: chain 'B' and resid 715 through 725 removed outlier: 3.523A pdb=" N MET B1047 " --> pdb=" O VAL B1062 " (cutoff:3.500A) removed outlier: 5.798A pdb=" N TYR B1064 " --> pdb=" O HIS B1045 " (cutoff:3.500A) removed outlier: 5.839A pdb=" N HIS B1045 " --> pdb=" O TYR B1064 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'B' and resid 715 through 725 Processing sheet with id=AF4, first strand: chain 'B' and resid 732 through 733 Processing sheet with id=AF5, first strand: chain 'B' and resid 1117 through 1122 removed outlier: 3.554A pdb=" N SER B1120 " --> pdb=" O ALA B1084 " (cutoff:3.500A) removed outlier: 4.835A pdb=" N ALA B1084 " --> pdb=" O SER B1120 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'B' and resid 1091 through 1094 Processing sheet with id=AF7, first strand: chain 'C' and resid 27 through 31 removed outlier: 3.697A pdb=" N SER C 60 " --> pdb=" O SER C 31 " (cutoff:3.500A) removed outlier: 8.124A pdb=" N ASN C 61 " --> pdb=" O TYR C 266 " (cutoff:3.500A) removed outlier: 5.709A pdb=" N TYR C 266 " --> pdb=" O ASN C 61 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N ALA C 261 " --> pdb=" O ILE C 93 " (cutoff:3.500A) removed outlier: 6.110A pdb=" N SER C 200 " --> pdb=" O PRO C 222 " (cutoff:3.500A) removed outlier: 9.561A pdb=" N HIS C 202 " --> pdb=" O LEU C 220 " (cutoff:3.500A) removed outlier: 9.603A pdb=" N LEU C 220 " --> pdb=" O HIS C 202 " (cutoff:3.500A) removed outlier: 6.977A pdb=" N VAL C 36 " --> pdb=" O LEU C 220 " (cutoff:3.500A) Processing sheet with id=AF8, first strand: chain 'C' and resid 48 through 55 removed outlier: 3.905A pdb=" N ASP C 284 " --> pdb=" O LYS C 275 " (cutoff:3.500A) Processing sheet with id=AF9, first strand: chain 'C' and resid 102 through 104 Processing sheet with id=AG1, first strand: chain 'C' and resid 308 through 311 Processing sheet with id=AG2, first strand: chain 'C' and resid 315 through 316 Processing sheet with id=AG3, first strand: chain 'C' and resid 321 through 322 removed outlier: 7.433A pdb=" N GLU C 321 " --> pdb=" O ASN C 537 " (cutoff:3.500A) No H-bonds generated for sheet with id=AG3 Processing sheet with id=AG4, first strand: chain 'C' and resid 351 through 355 removed outlier: 3.871A pdb=" N ASN C 351 " --> pdb=" O SER C 396 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N SER C 396 " --> pdb=" O ASN C 351 " (cutoff:3.500A) removed outlier: 3.871A pdb=" N ALA C 394 " --> pdb=" O LYS C 353 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N ILE C 355 " --> pdb=" O VAL C 392 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N VAL C 392 " --> pdb=" O ILE C 355 " (cutoff:3.500A) removed outlier: 3.939A pdb=" N VAL C 430 " --> pdb=" O LYS C 375 " (cutoff:3.500A) removed outlier: 3.927A pdb=" N LYS C 375 " --> pdb=" O VAL C 430 " (cutoff:3.500A) Processing sheet with id=AG5, first strand: chain 'C' and resid 358 through 359 removed outlier: 7.449A pdb=" N CYS C 358 " --> pdb=" O CYS C 522 " (cutoff:3.500A) No H-bonds generated for sheet with id=AG5 Processing sheet with id=AG6, first strand: chain 'C' and resid 449 through 451 removed outlier: 3.501A pdb=" N TYR C 450 " --> pdb=" O ARG C 490 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N ARG C 490 " --> pdb=" O TYR C 450 " (cutoff:3.500A) No H-bonds generated for sheet with id=AG6 Processing sheet with id=AG7, first strand: chain 'C' and resid 470 through 471 Processing sheet with id=AG8, first strand: chain 'C' and resid 539 through 540 Processing sheet with id=AG9, first strand: chain 'C' and resid 548 through 551 Processing sheet with id=AH1, first strand: chain 'C' and resid 562 through 564 removed outlier: 4.137A pdb=" N ALA C 572 " --> pdb=" O GLY C 563 " (cutoff:3.500A) Processing sheet with id=AH2, first strand: chain 'C' and resid 651 through 657 removed outlier: 5.894A pdb=" N GLU C 651 " --> pdb=" O ALA C 691 " (cutoff:3.500A) removed outlier: 8.457A pdb=" N THR C 693 " --> pdb=" O GLU C 651 " (cutoff:3.500A) removed outlier: 9.150A pdb=" N VAL C 653 " --> pdb=" O THR C 693 " (cutoff:3.500A) Processing sheet with id=AH3, first strand: chain 'C' and resid 708 through 712 removed outlier: 3.748A pdb=" N THR C1073 " --> pdb=" O SER C1094 " (cutoff:3.500A) Processing sheet with id=AH4, first strand: chain 'C' and resid 715 through 725 removed outlier: 3.543A pdb=" N ALA C1053 " --> pdb=" O GLY C1056 " (cutoff:3.500A) removed outlier: 5.752A pdb=" N TYR C1064 " --> pdb=" O HIS C1045 " (cutoff:3.500A) removed outlier: 5.812A pdb=" N HIS C1045 " --> pdb=" O TYR C1064 " (cutoff:3.500A) Processing sheet with id=AH5, first strand: chain 'C' and resid 732 through 733 Processing sheet with id=AH6, first strand: chain 'C' and resid 1078 through 1079 removed outlier: 4.912A pdb=" N ALA C1084 " --> pdb=" O SER C1120 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N SER C1120 " --> pdb=" O ALA C1084 " (cutoff:3.500A) 989 hydrogen bonds defined for protein. 2589 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: 8.29 Time building geometry restraints manager: 3.96 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 5156 1.31 - 1.44: 9396 1.44 - 1.58: 18220 1.58 - 1.71: 0 1.71 - 1.84: 177 Bond restraints: 32949 Sorted by residual: bond pdb=" C PRO C 576 " pdb=" O PRO C 576 " ideal model delta sigma weight residual 1.235 1.180 0.056 1.30e-02 5.92e+03 1.82e+01 bond pdb=" C1 NAG M 2 " pdb=" O5 NAG M 2 " ideal model delta sigma weight residual 1.406 1.488 -0.082 2.00e-02 2.50e+03 1.69e+01 bond pdb=" N PHE A 326 " pdb=" CA PHE A 326 " ideal model delta sigma weight residual 1.453 1.486 -0.033 8.30e-03 1.45e+04 1.56e+01 bond pdb=" C PRO B 576 " pdb=" O PRO B 576 " ideal model delta sigma weight residual 1.235 1.190 0.045 1.30e-02 5.92e+03 1.19e+01 bond pdb=" N VAL A 305 " pdb=" CA VAL A 305 " ideal model delta sigma weight residual 1.454 1.496 -0.042 1.28e-02 6.10e+03 1.06e+01 ... (remaining 32944 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.68: 44127 2.68 - 5.35: 618 5.35 - 8.03: 61 8.03 - 10.70: 4 10.70 - 13.38: 2 Bond angle restraints: 44812 Sorted by residual: angle pdb=" N LEU C 139 " pdb=" CA LEU C 139 " pdb=" C LEU C 139 " ideal model delta sigma weight residual 112.92 99.54 13.38 1.23e+00 6.61e-01 1.18e+02 angle pdb=" C GLU B 211 " pdb=" CA GLU B 211 " pdb=" CB GLU B 211 " ideal model delta sigma weight residual 116.54 110.21 6.33 1.15e+00 7.56e-01 3.03e+01 angle pdb=" N ASP C 140 " pdb=" CA ASP C 140 " pdb=" C ASP C 140 " ideal model delta sigma weight residual 111.07 116.72 -5.65 1.07e+00 8.73e-01 2.79e+01 angle pdb=" N LEU B 139 " pdb=" CA LEU B 139 " pdb=" C LEU B 139 " ideal model delta sigma weight residual 113.17 106.59 6.58 1.26e+00 6.30e-01 2.72e+01 angle pdb=" N GLN B 577 " pdb=" CA GLN B 577 " pdb=" C GLN B 577 " ideal model delta sigma weight residual 113.43 106.87 6.56 1.26e+00 6.30e-01 2.71e+01 ... (remaining 44807 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 23.07: 19208 23.07 - 46.13: 1201 46.13 - 69.20: 156 69.20 - 92.26: 61 92.26 - 115.33: 31 Dihedral angle restraints: 20657 sinusoidal: 9059 harmonic: 11598 Sorted by residual: dihedral pdb=" CA SER J 95 " pdb=" C SER J 95 " pdb=" N PRO J 96 " pdb=" CA PRO J 96 " ideal model delta harmonic sigma weight residual -180.00 -141.06 -38.94 0 5.00e+00 4.00e-02 6.07e+01 dihedral pdb=" CB CYS G 22 " pdb=" SG CYS G 22 " pdb=" SG CYS G 97 " pdb=" CB CYS G 97 " ideal model delta sinusoidal sigma weight residual 93.00 146.26 -53.26 1 1.00e+01 1.00e-02 3.86e+01 dihedral pdb=" CA CYS A 161 " pdb=" C CYS A 161 " pdb=" N THR A 162 " pdb=" CA THR A 162 " ideal model delta harmonic sigma weight residual -180.00 -149.45 -30.55 0 5.00e+00 4.00e-02 3.73e+01 ... (remaining 20654 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.156: 5228 0.156 - 0.311: 37 0.311 - 0.467: 3 0.467 - 0.622: 0 0.622 - 0.778: 1 Chirality restraints: 5269 Sorted by residual: chirality pdb=" C1 NAG B1303 " pdb=" ND2 ASN B 123 " pdb=" C2 NAG B1303 " pdb=" O5 NAG B1303 " both_signs ideal model delta sigma weight residual False -2.40 -1.62 -0.78 2.00e-01 2.50e+01 1.51e+01 chirality pdb=" CA HIS C 141 " pdb=" N HIS C 141 " pdb=" C HIS C 141 " pdb=" CB HIS C 141 " both_signs ideal model delta sigma weight residual False 2.51 2.12 0.39 2.00e-01 2.50e+01 3.80e+00 chirality pdb=" CA LEU C 139 " pdb=" N LEU C 139 " pdb=" C LEU C 139 " pdb=" CB LEU C 139 " both_signs ideal model delta sigma weight residual False 2.51 2.89 -0.38 2.00e-01 2.50e+01 3.61e+00 ... (remaining 5266 not shown) Planarity restraints: 5709 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASP B 336 " -0.023 2.00e-02 2.50e+03 4.83e-02 2.34e+01 pdb=" CG ASP B 336 " 0.084 2.00e-02 2.50e+03 pdb=" OD1 ASP B 336 " -0.031 2.00e-02 2.50e+03 pdb=" OD2 ASP B 336 " -0.030 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG B1306 " 0.014 2.00e-02 2.50e+03 3.86e-02 1.86e+01 pdb=" C7 NAG B1306 " -0.075 2.00e-02 2.50e+03 pdb=" C8 NAG B1306 " 0.032 2.00e-02 2.50e+03 pdb=" N2 NAG B1306 " 0.004 2.00e-02 2.50e+03 pdb=" O7 NAG B1306 " 0.025 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C SER L 95 " 0.065 5.00e-02 4.00e+02 9.80e-02 1.54e+01 pdb=" N PRO L 96 " -0.170 5.00e-02 4.00e+02 pdb=" CA PRO L 96 " 0.051 5.00e-02 4.00e+02 pdb=" CD PRO L 96 " 0.054 5.00e-02 4.00e+02 ... (remaining 5706 not shown) Histogram of nonbonded interaction distances: 1.78 - 2.41: 97 2.41 - 3.03: 18949 3.03 - 3.65: 45387 3.65 - 4.28: 66571 4.28 - 4.90: 113306 Nonbonded interactions: 244310 Sorted by model distance: nonbonded pdb=" OD2 ASP B 336 " pdb=" O7 NAG B1306 " model vdw 1.785 2.432 nonbonded pdb=" OD1 ASP B 336 " pdb=" N2 NAG B1306 " model vdw 2.012 2.496 nonbonded pdb=" OD1 ASP B 336 " pdb=" C8 NAG B1306 " model vdw 2.095 2.768 nonbonded pdb=" OH TYR B 633 " pdb=" O ILE B 648 " model vdw 2.121 3.040 nonbonded pdb=" O PRO B 460 " pdb=" O3 NAG B1301 " model vdw 2.157 3.040 ... (remaining 244305 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = (chain 'B' and resid 14 through 1310) selection = chain 'C' } ncs_group { reference = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'M' selection = chain 'N' selection = chain 'P' selection = chain 'Q' selection = chain 'R' selection = chain 'S' selection = chain 'T' selection = chain 'U' selection = chain 'X' selection = chain 'Y' selection = chain 'Z' selection = chain 'a' selection = chain 'b' } ncs_group { reference = chain 'G' selection = chain 'H' selection = chain 'I' } ncs_group { reference = chain 'J' selection = chain 'K' selection = chain 'L' } ncs_group { reference = chain 'O' selection = chain 'V' selection = chain 'W' selection = chain 'c' selection = chain 'd' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 5.290 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: 0.050 Extract box with map and model: 0.730 Check model and map are aligned: 0.130 Set scattering table: 0.100 Process input model: 33.680 Find NCS groups from input model: 0.870 Set up NCS constraints: 0.130 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.370 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 42.350 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7901 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 : 0.005 0.082 33076 Z= 0.249 Angle : 0.748 13.380 45109 Z= 0.392 Chirality : 0.052 0.778 5269 Planarity : 0.005 0.098 5668 Dihedral : 15.351 115.331 13049 Min Nonbonded Distance : 1.785 Molprobity Statistics. All-atom Clashscore : 9.83 Ramachandran Plot: Outliers : 0.13 % Allowed : 6.65 % Favored : 93.23 % Rotamer: Outliers : 0.26 % Allowed : 0.69 % Favored : 99.05 % Cbeta Deviations : 0.03 % Peptide Plane: Cis-proline : 1.52 % Cis-general : 0.03 % Twisted Proline : 0.51 % Twisted General : 0.03 % 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: -1.96 (0.13), residues: 3942 helix: -2.31 (0.17), residues: 704 sheet: -0.00 (0.17), residues: 979 loop : -1.58 (0.13), residues: 2259 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A 316 TYR 0.018 0.001 TYR C 450 PHE 0.022 0.001 PHE C 196 TRP 0.026 0.002 TRP H 51 HIS 0.005 0.001 HIS C 141 Details of bonding type rmsd covalent geometry : bond 0.00501 (32949) covalent geometry : angle 0.73482 (44812) SS BOND : bond 0.00525 ( 48) SS BOND : angle 1.49058 ( 96) hydrogen bonds : bond 0.25430 ( 963) hydrogen bonds : angle 8.62154 ( 2589) Misc. bond : bond 0.02292 ( 12) link_BETA1-4 : bond 0.00701 ( 26) link_BETA1-4 : angle 2.01805 ( 78) link_NAG-ASN : bond 0.00524 ( 41) link_NAG-ASN : angle 2.08818 ( 123) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7884 Ramachandran restraints generated. 3942 Oldfield, 0 Emsley, 3942 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7884 Ramachandran restraints generated. 3942 Oldfield, 0 Emsley, 3942 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 273 residues out of total 3480 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 264 time to evaluate : 1.153 Fit side-chains revert: symmetry clash REVERT: H 112 ASP cc_start: 0.7566 (m-30) cc_final: 0.7297 (m-30) REVERT: K 92 TYR cc_start: 0.7520 (m-10) cc_final: 0.7300 (m-80) REVERT: A 357 ASN cc_start: 0.8047 (m-40) cc_final: 0.7765 (t0) REVERT: A 777 GLU cc_start: 0.8071 (mt-10) cc_final: 0.7804 (mt-10) REVERT: B 386 ASP cc_start: 0.7850 (OUTLIER) cc_final: 0.7408 (p0) REVERT: B 777 GLU cc_start: 0.7977 (mt-10) cc_final: 0.7564 (mt-10) REVERT: C 255 TRP cc_start: 0.3711 (OUTLIER) cc_final: 0.3193 (p-90) outliers start: 9 outliers final: 1 residues processed: 270 average time/residue: 0.2175 time to fit residues: 94.4141 Evaluate side-chains 212 residues out of total 3480 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 209 time to evaluate : 1.093 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 386 ASP Chi-restraints excluded: chain C residue 255 TRP Chi-restraints excluded: chain C residue 329 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 393 random chunks: chunk 197 optimal weight: 6.9990 chunk 388 optimal weight: 5.9990 chunk 215 optimal weight: 6.9990 chunk 20 optimal weight: 20.0000 chunk 132 optimal weight: 0.9980 chunk 261 optimal weight: 1.9990 chunk 248 optimal weight: 2.9990 chunk 207 optimal weight: 5.9990 chunk 155 optimal weight: 0.9990 chunk 244 optimal weight: 1.9990 chunk 183 optimal weight: 6.9990 overall best weight: 1.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** I 40 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 116 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 90 GLN ** K 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 414 ASN A 759 GLN A1139 GLN ** A1156 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 183 ASN ** B 191 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 314 ASN C 52 GLN C1116 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4131 r_free = 0.4131 target = 0.150224 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 75)----------------| | r_work = 0.3380 r_free = 0.3380 target = 0.095886 restraints weight = 60621.305| |-----------------------------------------------------------------------------| r_work (start): 0.3360 rms_B_bonded: 3.26 r_work: 0.3234 rms_B_bonded: 3.47 restraints_weight: 0.5000 r_work (final): 0.3234 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7847 moved from start: 0.0960 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.069 33076 Z= 0.181 Angle : 0.682 19.093 45109 Z= 0.338 Chirality : 0.048 0.484 5269 Planarity : 0.005 0.062 5668 Dihedral : 9.900 107.019 5918 Min Nonbonded Distance : 1.791 Molprobity Statistics. All-atom Clashscore : 7.74 Ramachandran Plot: Outliers : 0.03 % Allowed : 6.16 % Favored : 93.81 % Rotamer: Outliers : 0.66 % Allowed : 8.82 % Favored : 90.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.52 % Cis-general : 0.03 % Twisted Proline : 0.51 % 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: -1.70 (0.13), residues: 3942 helix: -1.49 (0.18), residues: 711 sheet: -0.01 (0.17), residues: 1007 loop : -1.56 (0.13), residues: 2224 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 902 TYR 0.026 0.001 TYR A 393 PHE 0.025 0.002 PHE G 101 TRP 0.017 0.001 TRP A 64 HIS 0.010 0.001 HIS C 202 Details of bonding type rmsd covalent geometry : bond 0.00425 (32949) covalent geometry : angle 0.66867 (44812) SS BOND : bond 0.00452 ( 48) SS BOND : angle 1.30271 ( 96) hydrogen bonds : bond 0.06149 ( 963) hydrogen bonds : angle 6.03790 ( 2589) Misc. bond : bond 0.00989 ( 12) link_BETA1-4 : bond 0.00601 ( 26) link_BETA1-4 : angle 2.11464 ( 78) link_NAG-ASN : bond 0.00321 ( 41) link_NAG-ASN : angle 1.84018 ( 123) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7884 Ramachandran restraints generated. 3942 Oldfield, 0 Emsley, 3942 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7884 Ramachandran restraints generated. 3942 Oldfield, 0 Emsley, 3942 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 247 residues out of total 3480 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 224 time to evaluate : 1.227 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 12 LYS cc_start: 0.6771 (mmmm) cc_final: 0.5764 (mptt) REVERT: H 112 ASP cc_start: 0.7453 (m-30) cc_final: 0.7213 (m-30) REVERT: I 65 PHE cc_start: 0.6731 (m-10) cc_final: 0.6457 (m-10) REVERT: K 39 GLN cc_start: 0.7085 (tt0) cc_final: 0.6771 (tp40) REVERT: K 71 ASP cc_start: 0.8722 (p0) cc_final: 0.8257 (t0) REVERT: A 483 PHE cc_start: 0.7857 (t80) cc_final: 0.7308 (t80) REVERT: B 139 LEU cc_start: 0.8122 (OUTLIER) cc_final: 0.7395 (tt) REVERT: B 777 GLU cc_start: 0.8918 (mt-10) cc_final: 0.8620 (mt-10) REVERT: C 526 LYS cc_start: 0.9217 (mptt) cc_final: 0.8810 (tttt) outliers start: 23 outliers final: 19 residues processed: 240 average time/residue: 0.2145 time to fit residues: 83.0221 Evaluate side-chains 228 residues out of total 3480 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 208 time to evaluate : 1.199 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 51 TRP Chi-restraints excluded: chain I residue 4 LEU Chi-restraints excluded: chain I residue 51 TRP Chi-restraints excluded: chain J residue 62 ARG Chi-restraints excluded: chain K residue 95 SER Chi-restraints excluded: chain L residue 3 VAL Chi-restraints excluded: chain A residue 224 VAL Chi-restraints excluded: chain A residue 430 VAL Chi-restraints excluded: chain B residue 139 LEU Chi-restraints excluded: chain B residue 332 LEU Chi-restraints excluded: chain B residue 430 VAL Chi-restraints excluded: chain B residue 579 LEU Chi-restraints excluded: chain B residue 1037 VAL Chi-restraints excluded: chain B residue 1120 SER Chi-restraints excluded: chain C residue 86 ASP Chi-restraints excluded: chain C residue 255 TRP Chi-restraints excluded: chain C residue 309 ILE Chi-restraints excluded: chain C residue 329 ILE Chi-restraints excluded: chain C residue 364 VAL Chi-restraints excluded: chain C residue 430 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 393 random chunks: chunk 270 optimal weight: 3.9990 chunk 227 optimal weight: 0.0870 chunk 151 optimal weight: 2.9990 chunk 296 optimal weight: 20.0000 chunk 186 optimal weight: 9.9990 chunk 315 optimal weight: 7.9990 chunk 140 optimal weight: 3.9990 chunk 261 optimal weight: 1.9990 chunk 238 optimal weight: 1.9990 chunk 256 optimal weight: 1.9990 chunk 83 optimal weight: 3.9990 overall best weight: 1.8166 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** I 40 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 116 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 97 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 759 GLN A 999 GLN ** A1156 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 183 ASN ** B 191 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 759 GLN C 85 ASN C 144 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4127 r_free = 0.4127 target = 0.150607 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.3360 r_free = 0.3360 target = 0.094903 restraints weight = 60475.514| |-----------------------------------------------------------------------------| r_work (start): 0.3328 rms_B_bonded: 3.51 r_work: 0.3194 rms_B_bonded: 3.75 restraints_weight: 0.5000 r_work (final): 0.3194 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7947 moved from start: 0.1286 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.067 33076 Z= 0.175 Angle : 0.650 18.875 45109 Z= 0.321 Chirality : 0.047 0.463 5269 Planarity : 0.004 0.067 5668 Dihedral : 8.464 106.216 5916 Min Nonbonded Distance : 1.792 Molprobity Statistics. All-atom Clashscore : 7.33 Ramachandran Plot: Outliers : 0.03 % Allowed : 6.16 % Favored : 93.81 % Rotamer: Outliers : 1.70 % Allowed : 10.99 % Favored : 87.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.52 % Cis-general : 0.03 % Twisted Proline : 0.51 % 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: -1.68 (0.13), residues: 3942 helix: -1.28 (0.18), residues: 727 sheet: -0.00 (0.17), residues: 1009 loop : -1.62 (0.13), residues: 2206 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 354 TYR 0.019 0.001 TYR C1064 PHE 0.021 0.001 PHE C1118 TRP 0.017 0.001 TRP A 64 HIS 0.009 0.001 HIS C 202 Details of bonding type rmsd covalent geometry : bond 0.00416 (32949) covalent geometry : angle 0.63757 (44812) SS BOND : bond 0.00406 ( 48) SS BOND : angle 1.23247 ( 96) hydrogen bonds : bond 0.05473 ( 963) hydrogen bonds : angle 5.62780 ( 2589) Misc. bond : bond 0.00987 ( 12) link_BETA1-4 : bond 0.00557 ( 26) link_BETA1-4 : angle 2.05521 ( 78) link_NAG-ASN : bond 0.00286 ( 41) link_NAG-ASN : angle 1.78346 ( 123) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7884 Ramachandran restraints generated. 3942 Oldfield, 0 Emsley, 3942 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7884 Ramachandran restraints generated. 3942 Oldfield, 0 Emsley, 3942 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 281 residues out of total 3480 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 222 time to evaluate : 1.089 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: G 12 LYS cc_start: 0.6639 (mmmm) cc_final: 0.5682 (mptt) REVERT: H 112 ASP cc_start: 0.7443 (m-30) cc_final: 0.7213 (m-30) REVERT: I 36 GLN cc_start: 0.6963 (pt0) cc_final: 0.6456 (pt0) REVERT: K 39 GLN cc_start: 0.7221 (tt0) cc_final: 0.6914 (tp40) REVERT: K 71 ASP cc_start: 0.8728 (p0) cc_final: 0.8285 (t0) REVERT: A 483 PHE cc_start: 0.8006 (t80) cc_final: 0.7582 (t80) REVERT: A 498 TYR cc_start: 0.6909 (m-10) cc_final: 0.6706 (m-80) REVERT: B 139 LEU cc_start: 0.8128 (OUTLIER) cc_final: 0.7471 (tp) REVERT: B 386 ASP cc_start: 0.8234 (OUTLIER) cc_final: 0.7840 (p0) REVERT: B 777 GLU cc_start: 0.8943 (mt-10) cc_final: 0.8710 (mt-10) REVERT: C 41 LYS cc_start: 0.9091 (OUTLIER) cc_final: 0.8434 (mtpp) REVERT: C 526 LYS cc_start: 0.9223 (mptt) cc_final: 0.8835 (tttt) outliers start: 59 outliers final: 35 residues processed: 264 average time/residue: 0.2137 time to fit residues: 91.1701 Evaluate side-chains 249 residues out of total 3480 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 211 time to evaluate : 1.127 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 51 TRP Chi-restraints excluded: chain I residue 4 LEU Chi-restraints excluded: chain I residue 51 TRP Chi-restraints excluded: chain J residue 62 ARG Chi-restraints excluded: chain K residue 31 ILE Chi-restraints excluded: chain K residue 95 SER Chi-restraints excluded: chain L residue 3 VAL Chi-restraints excluded: chain A residue 224 VAL Chi-restraints excluded: chain A residue 226 LEU Chi-restraints excluded: chain A residue 264 VAL Chi-restraints excluded: chain A residue 271 THR Chi-restraints excluded: chain A residue 315 PHE Chi-restraints excluded: chain A residue 430 VAL Chi-restraints excluded: chain A residue 585 THR Chi-restraints excluded: chain A residue 720 THR Chi-restraints excluded: chain A residue 1037 VAL Chi-restraints excluded: chain A residue 1074 THR Chi-restraints excluded: chain B residue 139 LEU Chi-restraints excluded: chain B residue 190 LYS Chi-restraints excluded: chain B residue 264 VAL Chi-restraints excluded: chain B residue 309 ILE Chi-restraints excluded: chain B residue 332 LEU Chi-restraints excluded: chain B residue 386 ASP Chi-restraints excluded: chain B residue 430 VAL Chi-restraints excluded: chain B residue 579 LEU Chi-restraints excluded: chain B residue 749 LEU Chi-restraints excluded: chain B residue 756 PHE Chi-restraints excluded: chain B residue 973 VAL Chi-restraints excluded: chain B residue 1037 VAL Chi-restraints excluded: chain B residue 1120 SER Chi-restraints excluded: chain C residue 41 LYS Chi-restraints excluded: chain C residue 81 VAL Chi-restraints excluded: chain C residue 206 LEU Chi-restraints excluded: chain C residue 255 TRP Chi-restraints excluded: chain C residue 264 VAL Chi-restraints excluded: chain C residue 329 ILE Chi-restraints excluded: chain C residue 430 VAL Chi-restraints excluded: chain C residue 585 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 393 random chunks: chunk 16 optimal weight: 20.0000 chunk 97 optimal weight: 5.9990 chunk 338 optimal weight: 5.9990 chunk 120 optimal weight: 5.9990 chunk 143 optimal weight: 0.5980 chunk 249 optimal weight: 2.9990 chunk 77 optimal weight: 0.0670 chunk 92 optimal weight: 4.9990 chunk 301 optimal weight: 0.2980 chunk 361 optimal weight: 0.1980 chunk 280 optimal weight: 3.9990 overall best weight: 0.8320 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** G 116 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 3 GLN ** I 40 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 116 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 97 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 414 ASN ** A1156 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 191 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 419 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4150 r_free = 0.4150 target = 0.152763 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3395 r_free = 0.3395 target = 0.097174 restraints weight = 60008.286| |-----------------------------------------------------------------------------| r_work (start): 0.3361 rms_B_bonded: 3.54 r_work: 0.3226 rms_B_bonded: 3.77 restraints_weight: 0.5000 r_work (final): 0.3226 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7916 moved from start: 0.1515 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.065 33076 Z= 0.121 Angle : 0.609 19.027 45109 Z= 0.297 Chirality : 0.045 0.457 5269 Planarity : 0.004 0.064 5668 Dihedral : 7.583 104.678 5916 Min Nonbonded Distance : 1.790 Molprobity Statistics. All-atom Clashscore : 6.91 Ramachandran Plot: Outliers : 0.03 % Allowed : 5.40 % Favored : 94.57 % Rotamer: Outliers : 1.87 % Allowed : 12.75 % Favored : 85.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.52 % Cis-general : 0.03 % Twisted Proline : 0.51 % 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: -1.52 (0.13), residues: 3942 helix: -0.98 (0.19), residues: 722 sheet: 0.07 (0.17), residues: 990 loop : -1.55 (0.13), residues: 2230 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 354 TYR 0.018 0.001 TYR B 498 PHE 0.022 0.001 PHE H 101 TRP 0.015 0.001 TRP A 64 HIS 0.008 0.001 HIS C 202 Details of bonding type rmsd covalent geometry : bond 0.00267 (32949) covalent geometry : angle 0.59569 (44812) SS BOND : bond 0.00406 ( 48) SS BOND : angle 1.29579 ( 96) hydrogen bonds : bond 0.04334 ( 963) hydrogen bonds : angle 5.28933 ( 2589) Misc. bond : bond 0.00979 ( 12) link_BETA1-4 : bond 0.00507 ( 26) link_BETA1-4 : angle 1.98597 ( 78) link_NAG-ASN : bond 0.00306 ( 41) link_NAG-ASN : angle 1.69599 ( 123) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7884 Ramachandran restraints generated. 3942 Oldfield, 0 Emsley, 3942 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7884 Ramachandran restraints generated. 3942 Oldfield, 0 Emsley, 3942 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 294 residues out of total 3480 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 229 time to evaluate : 1.345 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 12 LYS cc_start: 0.6604 (mmmm) cc_final: 0.5631 (mptt) REVERT: H 112 ASP cc_start: 0.7423 (m-30) cc_final: 0.7198 (m-30) REVERT: I 65 PHE cc_start: 0.6552 (m-10) cc_final: 0.6259 (m-10) REVERT: K 39 GLN cc_start: 0.7169 (tt0) cc_final: 0.6919 (tp40) REVERT: L 39 GLN cc_start: 0.6989 (tt0) cc_final: 0.6737 (tp40) REVERT: L 97 TRP cc_start: 0.5375 (m-10) cc_final: 0.3932 (m-90) REVERT: A 483 PHE cc_start: 0.8033 (t80) cc_final: 0.7626 (t80) REVERT: A 498 TYR cc_start: 0.6935 (m-10) cc_final: 0.6654 (m-10) REVERT: A 549 LEU cc_start: 0.8947 (OUTLIER) cc_final: 0.8608 (mt) REVERT: B 139 LEU cc_start: 0.8187 (OUTLIER) cc_final: 0.7485 (tp) REVERT: B 386 ASP cc_start: 0.8198 (OUTLIER) cc_final: 0.7798 (p0) REVERT: B 777 GLU cc_start: 0.8912 (mt-10) cc_final: 0.8709 (mt-10) REVERT: C 41 LYS cc_start: 0.9030 (OUTLIER) cc_final: 0.8438 (mtpp) REVERT: C 526 LYS cc_start: 0.9163 (mptt) cc_final: 0.8805 (tttt) outliers start: 65 outliers final: 37 residues processed: 281 average time/residue: 0.1990 time to fit residues: 92.0234 Evaluate side-chains 248 residues out of total 3480 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 207 time to evaluate : 1.069 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 51 TRP Chi-restraints excluded: chain H residue 107 CYS Chi-restraints excluded: chain I residue 4 LEU Chi-restraints excluded: chain I residue 32 VAL Chi-restraints excluded: chain J residue 62 ARG Chi-restraints excluded: chain L residue 3 VAL Chi-restraints excluded: chain A residue 188 VAL Chi-restraints excluded: chain A residue 263 TYR Chi-restraints excluded: chain A residue 286 VAL Chi-restraints excluded: chain A residue 315 PHE Chi-restraints excluded: chain A residue 393 TYR Chi-restraints excluded: chain A residue 430 VAL Chi-restraints excluded: chain A residue 438 LEU Chi-restraints excluded: chain A residue 549 LEU Chi-restraints excluded: chain A residue 585 THR Chi-restraints excluded: chain A residue 982 ASP Chi-restraints excluded: chain A residue 1037 VAL Chi-restraints excluded: chain A residue 1074 THR Chi-restraints excluded: chain A residue 1101 VAL Chi-restraints excluded: chain B residue 139 LEU Chi-restraints excluded: chain B residue 188 VAL Chi-restraints excluded: chain B residue 332 LEU Chi-restraints excluded: chain B residue 386 ASP Chi-restraints excluded: chain B residue 430 VAL Chi-restraints excluded: chain B residue 579 LEU Chi-restraints excluded: chain B residue 585 THR Chi-restraints excluded: chain B residue 756 PHE Chi-restraints excluded: chain B residue 912 VAL Chi-restraints excluded: chain B residue 990 ILE Chi-restraints excluded: chain B residue 1101 VAL Chi-restraints excluded: chain B residue 1120 SER Chi-restraints excluded: chain C residue 33 THR Chi-restraints excluded: chain C residue 41 LYS Chi-restraints excluded: chain C residue 188 VAL Chi-restraints excluded: chain C residue 255 TRP Chi-restraints excluded: chain C residue 309 ILE Chi-restraints excluded: chain C residue 329 ILE Chi-restraints excluded: chain C residue 430 VAL Chi-restraints excluded: chain C residue 585 THR Chi-restraints excluded: chain C residue 973 VAL Chi-restraints excluded: chain C residue 982 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 393 random chunks: chunk 390 optimal weight: 6.9990 chunk 113 optimal weight: 5.9990 chunk 226 optimal weight: 4.9990 chunk 245 optimal weight: 3.9990 chunk 177 optimal weight: 4.9990 chunk 355 optimal weight: 5.9990 chunk 186 optimal weight: 8.9990 chunk 83 optimal weight: 3.9990 chunk 63 optimal weight: 5.9990 chunk 291 optimal weight: 5.9990 chunk 384 optimal weight: 3.9990 overall best weight: 4.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** G 116 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 3 GLN ** I 40 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 116 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 97 ASN ** A1156 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 191 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 759 GLN C 202 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4073 r_free = 0.4073 target = 0.146305 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 71)----------------| | r_work = 0.3289 r_free = 0.3289 target = 0.090713 restraints weight = 60778.198| |-----------------------------------------------------------------------------| r_work (start): 0.3271 rms_B_bonded: 3.41 r_work: 0.3137 rms_B_bonded: 3.65 restraints_weight: 0.5000 r_work (final): 0.3137 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8001 moved from start: 0.1842 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.071 33076 Z= 0.355 Angle : 0.813 18.831 45109 Z= 0.404 Chirality : 0.053 0.466 5269 Planarity : 0.005 0.070 5668 Dihedral : 8.094 104.435 5916 Min Nonbonded Distance : 1.785 Molprobity Statistics. All-atom Clashscore : 8.78 Ramachandran Plot: Outliers : 0.05 % Allowed : 8.04 % Favored : 91.91 % Rotamer: Outliers : 2.94 % Allowed : 14.79 % Favored : 82.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.52 % Cis-general : 0.03 % Twisted Proline : 0.00 % Twisted General : 0.03 % 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: -1.94 (0.13), residues: 3942 helix: -1.42 (0.18), residues: 730 sheet: -0.09 (0.17), residues: 964 loop : -1.83 (0.12), residues: 2248 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG B 902 TYR 0.020 0.002 TYR C1064 PHE 0.036 0.002 PHE A1118 TRP 0.022 0.002 TRP A 64 HIS 0.008 0.002 HIS C 202 Details of bonding type rmsd covalent geometry : bond 0.00872 (32949) covalent geometry : angle 0.79901 (44812) SS BOND : bond 0.00628 ( 48) SS BOND : angle 1.91128 ( 96) hydrogen bonds : bond 0.06699 ( 963) hydrogen bonds : angle 5.86071 ( 2589) Misc. bond : bond 0.00997 ( 12) link_BETA1-4 : bond 0.00479 ( 26) link_BETA1-4 : angle 1.99940 ( 78) link_NAG-ASN : bond 0.00432 ( 41) link_NAG-ASN : angle 2.05425 ( 123) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7884 Ramachandran restraints generated. 3942 Oldfield, 0 Emsley, 3942 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7884 Ramachandran restraints generated. 3942 Oldfield, 0 Emsley, 3942 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 326 residues out of total 3480 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 102 poor density : 224 time to evaluate : 1.239 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 12 LYS cc_start: 0.6736 (mmmm) cc_final: 0.5793 (mptt) REVERT: H 112 ASP cc_start: 0.7267 (m-30) cc_final: 0.7048 (m-30) REVERT: K 39 GLN cc_start: 0.7174 (tt0) cc_final: 0.6942 (tp40) REVERT: L 39 GLN cc_start: 0.7024 (tt0) cc_final: 0.6751 (tp40) REVERT: L 97 TRP cc_start: 0.5416 (m-10) cc_final: 0.4626 (m-90) REVERT: A 498 TYR cc_start: 0.6863 (m-10) cc_final: 0.6554 (m-10) REVERT: A 912 VAL cc_start: 0.8194 (OUTLIER) cc_final: 0.7894 (m) REVERT: B 386 ASP cc_start: 0.8256 (OUTLIER) cc_final: 0.7867 (p0) REVERT: C 526 LYS cc_start: 0.9212 (mptt) cc_final: 0.8871 (tttt) outliers start: 102 outliers final: 72 residues processed: 312 average time/residue: 0.2085 time to fit residues: 106.4302 Evaluate side-chains 289 residues out of total 3480 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 215 time to evaluate : 1.231 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 2 MET Chi-restraints excluded: chain G residue 51 TRP Chi-restraints excluded: chain H residue 107 CYS Chi-restraints excluded: chain I residue 3 GLN Chi-restraints excluded: chain I residue 4 LEU Chi-restraints excluded: chain I residue 18 VAL Chi-restraints excluded: chain I residue 51 TRP Chi-restraints excluded: chain I residue 107 CYS Chi-restraints excluded: chain J residue 62 ARG Chi-restraints excluded: chain K residue 31 ILE Chi-restraints excluded: chain K residue 62 ARG Chi-restraints excluded: chain K residue 95 SER Chi-restraints excluded: chain L residue 3 VAL Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 188 VAL Chi-restraints excluded: chain A residue 224 VAL Chi-restraints excluded: chain A residue 263 TYR Chi-restraints excluded: chain A residue 264 VAL Chi-restraints excluded: chain A residue 271 THR Chi-restraints excluded: chain A residue 286 VAL Chi-restraints excluded: chain A residue 315 PHE Chi-restraints excluded: chain A residue 393 TYR Chi-restraints excluded: chain A residue 430 VAL Chi-restraints excluded: chain A residue 512 PHE Chi-restraints excluded: chain A residue 585 THR Chi-restraints excluded: chain A residue 720 THR Chi-restraints excluded: chain A residue 744 THR Chi-restraints excluded: chain A residue 819 LEU Chi-restraints excluded: chain A residue 912 VAL Chi-restraints excluded: chain A residue 1037 VAL Chi-restraints excluded: chain A residue 1074 THR Chi-restraints excluded: chain A residue 1101 VAL Chi-restraints excluded: chain A residue 1130 VAL Chi-restraints excluded: chain A residue 1139 GLN Chi-restraints excluded: chain B residue 53 ASP Chi-restraints excluded: chain B residue 107 THR Chi-restraints excluded: chain B residue 188 VAL Chi-restraints excluded: chain B residue 264 VAL Chi-restraints excluded: chain B residue 309 ILE Chi-restraints excluded: chain B residue 332 LEU Chi-restraints excluded: chain B residue 386 ASP Chi-restraints excluded: chain B residue 430 VAL Chi-restraints excluded: chain B residue 585 THR Chi-restraints excluded: chain B residue 749 LEU Chi-restraints excluded: chain B residue 874 LEU Chi-restraints excluded: chain B residue 912 VAL Chi-restraints excluded: chain B residue 973 VAL Chi-restraints excluded: chain B residue 1037 VAL Chi-restraints excluded: chain B residue 1078 ILE Chi-restraints excluded: chain B residue 1101 VAL Chi-restraints excluded: chain B residue 1120 SER Chi-restraints excluded: chain C residue 33 THR Chi-restraints excluded: chain C residue 81 VAL Chi-restraints excluded: chain C residue 86 ASP Chi-restraints excluded: chain C residue 126 ILE Chi-restraints excluded: chain C residue 188 VAL Chi-restraints excluded: chain C residue 206 LEU Chi-restraints excluded: chain C residue 233 THR Chi-restraints excluded: chain C residue 255 TRP Chi-restraints excluded: chain C residue 264 VAL Chi-restraints excluded: chain C residue 286 VAL Chi-restraints excluded: chain C residue 309 ILE Chi-restraints excluded: chain C residue 329 ILE Chi-restraints excluded: chain C residue 364 VAL Chi-restraints excluded: chain C residue 430 VAL Chi-restraints excluded: chain C residue 465 ILE Chi-restraints excluded: chain C residue 570 THR Chi-restraints excluded: chain C residue 585 THR Chi-restraints excluded: chain C residue 723 ILE Chi-restraints excluded: chain C residue 897 MET Chi-restraints excluded: chain C residue 912 VAL Chi-restraints excluded: chain C residue 973 VAL Chi-restraints excluded: chain C residue 982 ASP Chi-restraints excluded: chain C residue 1126 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 393 random chunks: chunk 144 optimal weight: 1.9990 chunk 313 optimal weight: 0.8980 chunk 341 optimal weight: 2.9990 chunk 25 optimal weight: 10.0000 chunk 214 optimal weight: 0.7980 chunk 15 optimal weight: 9.9990 chunk 257 optimal weight: 0.9990 chunk 143 optimal weight: 0.6980 chunk 295 optimal weight: 3.9990 chunk 296 optimal weight: 7.9990 chunk 277 optimal weight: 0.6980 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** G 116 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 1 GLN ** I 116 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 414 ASN A 850 GLN ** A1156 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 191 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4126 r_free = 0.4126 target = 0.150060 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 67)----------------| | r_work = 0.3370 r_free = 0.3370 target = 0.095108 restraints weight = 60160.727| |-----------------------------------------------------------------------------| r_work (start): 0.3339 rms_B_bonded: 3.47 r_work: 0.3205 rms_B_bonded: 3.74 restraints_weight: 0.5000 r_work (final): 0.3205 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7940 moved from start: 0.1870 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.065 33076 Z= 0.124 Angle : 0.633 19.037 45109 Z= 0.311 Chirality : 0.046 0.443 5269 Planarity : 0.004 0.073 5668 Dihedral : 7.441 104.158 5916 Min Nonbonded Distance : 1.788 Molprobity Statistics. All-atom Clashscore : 7.25 Ramachandran Plot: Outliers : 0.03 % Allowed : 5.20 % Favored : 94.77 % Rotamer: Outliers : 2.13 % Allowed : 16.15 % Favored : 81.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.52 % Cis-general : 0.03 % 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: -1.64 (0.13), residues: 3942 helix: -0.95 (0.19), residues: 726 sheet: -0.04 (0.16), residues: 1010 loop : -1.69 (0.13), residues: 2206 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG G 88 TYR 0.017 0.001 TYR A1064 PHE 0.027 0.001 PHE H 101 TRP 0.012 0.001 TRP I 48 HIS 0.004 0.001 HIS C 141 Details of bonding type rmsd covalent geometry : bond 0.00271 (32949) covalent geometry : angle 0.62132 (44812) SS BOND : bond 0.00460 ( 48) SS BOND : angle 1.21003 ( 96) hydrogen bonds : bond 0.04501 ( 963) hydrogen bonds : angle 5.32877 ( 2589) Misc. bond : bond 0.00993 ( 12) link_BETA1-4 : bond 0.00517 ( 26) link_BETA1-4 : angle 1.86271 ( 78) link_NAG-ASN : bond 0.00318 ( 41) link_NAG-ASN : angle 1.68984 ( 123) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7884 Ramachandran restraints generated. 3942 Oldfield, 0 Emsley, 3942 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7884 Ramachandran restraints generated. 3942 Oldfield, 0 Emsley, 3942 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 294 residues out of total 3480 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 220 time to evaluate : 1.235 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: G 12 LYS cc_start: 0.6720 (mmmm) cc_final: 0.5771 (mptt) REVERT: H 112 ASP cc_start: 0.7295 (m-30) cc_final: 0.7094 (m-30) REVERT: I 36 GLN cc_start: 0.7045 (pt0) cc_final: 0.6464 (pt0) REVERT: J 90 GLN cc_start: 0.5743 (tp-100) cc_final: 0.5225 (tp40) REVERT: K 39 GLN cc_start: 0.7159 (tt0) cc_final: 0.6953 (tp40) REVERT: L 39 GLN cc_start: 0.6995 (tt0) cc_final: 0.6727 (tp40) REVERT: L 92 TYR cc_start: 0.7502 (m-10) cc_final: 0.6562 (m-80) REVERT: L 97 TRP cc_start: 0.5481 (m-10) cc_final: 0.4488 (m-90) REVERT: A 498 TYR cc_start: 0.6822 (m-10) cc_final: 0.6502 (m-10) REVERT: A 549 LEU cc_start: 0.8941 (OUTLIER) cc_final: 0.8529 (mt) REVERT: A 883 TRP cc_start: 0.8436 (p90) cc_final: 0.8227 (p90) REVERT: B 386 ASP cc_start: 0.8187 (OUTLIER) cc_final: 0.7811 (p0) REVERT: B 469 ILE cc_start: 0.8106 (pt) cc_final: 0.7716 (tt) REVERT: B 478 ASN cc_start: 0.8620 (t0) cc_final: 0.8345 (p0) REVERT: C 526 LYS cc_start: 0.9135 (mptt) cc_final: 0.8846 (tttt) outliers start: 74 outliers final: 49 residues processed: 285 average time/residue: 0.2118 time to fit residues: 98.3650 Evaluate side-chains 257 residues out of total 3480 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 206 time to evaluate : 1.215 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 51 TRP Chi-restraints excluded: chain H residue 107 CYS Chi-restraints excluded: chain I residue 4 LEU Chi-restraints excluded: chain I residue 107 CYS Chi-restraints excluded: chain K residue 62 ARG Chi-restraints excluded: chain K residue 95 SER Chi-restraints excluded: chain L residue 3 VAL Chi-restraints excluded: chain A residue 188 VAL Chi-restraints excluded: chain A residue 263 TYR Chi-restraints excluded: chain A residue 393 TYR Chi-restraints excluded: chain A residue 430 VAL Chi-restraints excluded: chain A residue 512 PHE Chi-restraints excluded: chain A residue 549 LEU Chi-restraints excluded: chain A residue 585 THR Chi-restraints excluded: chain A residue 874 LEU Chi-restraints excluded: chain A residue 1037 VAL Chi-restraints excluded: chain A residue 1078 ILE Chi-restraints excluded: chain A residue 1101 VAL Chi-restraints excluded: chain A residue 1125 VAL Chi-restraints excluded: chain A residue 1130 VAL Chi-restraints excluded: chain B residue 107 THR Chi-restraints excluded: chain B residue 188 VAL Chi-restraints excluded: chain B residue 309 ILE Chi-restraints excluded: chain B residue 330 THR Chi-restraints excluded: chain B residue 332 LEU Chi-restraints excluded: chain B residue 386 ASP Chi-restraints excluded: chain B residue 430 VAL Chi-restraints excluded: chain B residue 585 THR Chi-restraints excluded: chain B residue 617 VAL Chi-restraints excluded: chain B residue 726 VAL Chi-restraints excluded: chain B residue 973 VAL Chi-restraints excluded: chain B residue 990 ILE Chi-restraints excluded: chain B residue 998 LEU Chi-restraints excluded: chain B residue 1037 VAL Chi-restraints excluded: chain B residue 1130 VAL Chi-restraints excluded: chain C residue 33 THR Chi-restraints excluded: chain C residue 81 VAL Chi-restraints excluded: chain C residue 126 ILE Chi-restraints excluded: chain C residue 188 VAL Chi-restraints excluded: chain C residue 233 THR Chi-restraints excluded: chain C residue 255 TRP Chi-restraints excluded: chain C residue 309 ILE Chi-restraints excluded: chain C residue 329 ILE Chi-restraints excluded: chain C residue 430 VAL Chi-restraints excluded: chain C residue 465 ILE Chi-restraints excluded: chain C residue 585 THR Chi-restraints excluded: chain C residue 973 VAL Chi-restraints excluded: chain C residue 982 ASP Chi-restraints excluded: chain C residue 998 LEU Chi-restraints excluded: chain C residue 1078 ILE Chi-restraints excluded: chain C residue 1098 HIS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 393 random chunks: chunk 275 optimal weight: 0.5980 chunk 47 optimal weight: 0.8980 chunk 285 optimal weight: 1.9990 chunk 164 optimal weight: 0.7980 chunk 74 optimal weight: 6.9990 chunk 130 optimal weight: 1.9990 chunk 144 optimal weight: 7.9990 chunk 35 optimal weight: 20.0000 chunk 20 optimal weight: 20.0000 chunk 180 optimal weight: 2.9990 chunk 370 optimal weight: 5.9990 overall best weight: 1.2584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** G 116 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 1 GLN ** I 116 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 38 GLN A 759 GLN A 850 GLN ** A1156 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 191 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 314 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4134 r_free = 0.4134 target = 0.151643 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3375 r_free = 0.3375 target = 0.096229 restraints weight = 59921.609| |-----------------------------------------------------------------------------| r_work (start): 0.3335 rms_B_bonded: 3.49 r_work: 0.3203 rms_B_bonded: 3.72 restraints_weight: 0.5000 r_work (final): 0.3203 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7929 moved from start: 0.1941 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.067 33076 Z= 0.141 Angle : 0.624 18.787 45109 Z= 0.305 Chirality : 0.046 0.428 5269 Planarity : 0.004 0.076 5668 Dihedral : 7.229 104.678 5916 Min Nonbonded Distance : 1.790 Molprobity Statistics. All-atom Clashscore : 7.41 Ramachandran Plot: Outliers : 0.03 % Allowed : 6.27 % Favored : 93.71 % Rotamer: Outliers : 2.65 % Allowed : 15.92 % Favored : 81.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.52 % Cis-general : 0.03 % 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: -1.53 (0.13), residues: 3942 helix: -0.78 (0.19), residues: 725 sheet: 0.07 (0.17), residues: 977 loop : -1.64 (0.13), residues: 2240 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG K 24 TYR 0.017 0.001 TYR C1064 PHE 0.024 0.001 PHE G 101 TRP 0.014 0.001 TRP I 48 HIS 0.004 0.001 HIS C 141 Details of bonding type rmsd covalent geometry : bond 0.00327 (32949) covalent geometry : angle 0.61259 (44812) SS BOND : bond 0.00422 ( 48) SS BOND : angle 1.25123 ( 96) hydrogen bonds : bond 0.04489 ( 963) hydrogen bonds : angle 5.20524 ( 2589) Misc. bond : bond 0.00978 ( 12) link_BETA1-4 : bond 0.00493 ( 26) link_BETA1-4 : angle 1.89098 ( 78) link_NAG-ASN : bond 0.00261 ( 41) link_NAG-ASN : angle 1.67653 ( 123) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7884 Ramachandran restraints generated. 3942 Oldfield, 0 Emsley, 3942 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7884 Ramachandran restraints generated. 3942 Oldfield, 0 Emsley, 3942 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 303 residues out of total 3480 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 92 poor density : 211 time to evaluate : 1.240 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 12 LYS cc_start: 0.6624 (mmmm) cc_final: 0.5624 (mptt) REVERT: J 90 GLN cc_start: 0.5675 (tp-100) cc_final: 0.5358 (tp40) REVERT: J 92 TYR cc_start: 0.7567 (m-80) cc_final: 0.7270 (m-80) REVERT: L 39 GLN cc_start: 0.6860 (tt0) cc_final: 0.6605 (tp40) REVERT: L 71 ASP cc_start: 0.8642 (p0) cc_final: 0.8245 (t0) REVERT: L 97 TRP cc_start: 0.5411 (m-10) cc_final: 0.4482 (m-90) REVERT: A 498 TYR cc_start: 0.7054 (m-10) cc_final: 0.6740 (m-10) REVERT: B 139 LEU cc_start: 0.8132 (OUTLIER) cc_final: 0.7446 (tp) REVERT: B 354 ARG cc_start: 0.8364 (mtp85) cc_final: 0.8013 (ttm-80) REVERT: B 386 ASP cc_start: 0.8227 (OUTLIER) cc_final: 0.7834 (p0) REVERT: C 526 LYS cc_start: 0.9114 (mptt) cc_final: 0.8802 (tttt) outliers start: 92 outliers final: 73 residues processed: 289 average time/residue: 0.2037 time to fit residues: 96.6182 Evaluate side-chains 282 residues out of total 3480 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 207 time to evaluate : 1.215 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 2 MET Chi-restraints excluded: chain G residue 51 TRP Chi-restraints excluded: chain H residue 107 CYS Chi-restraints excluded: chain I residue 4 LEU Chi-restraints excluded: chain I residue 107 CYS Chi-restraints excluded: chain J residue 62 ARG Chi-restraints excluded: chain J residue 82 GLU Chi-restraints excluded: chain K residue 13 LEU Chi-restraints excluded: chain K residue 31 ILE Chi-restraints excluded: chain K residue 62 ARG Chi-restraints excluded: chain K residue 95 SER Chi-restraints excluded: chain L residue 3 VAL Chi-restraints excluded: chain A residue 186 GLU Chi-restraints excluded: chain A residue 188 VAL Chi-restraints excluded: chain A residue 263 TYR Chi-restraints excluded: chain A residue 271 THR Chi-restraints excluded: chain A residue 286 VAL Chi-restraints excluded: chain A residue 315 PHE Chi-restraints excluded: chain A residue 393 TYR Chi-restraints excluded: chain A residue 430 VAL Chi-restraints excluded: chain A residue 512 PHE Chi-restraints excluded: chain A residue 585 THR Chi-restraints excluded: chain A residue 720 THR Chi-restraints excluded: chain A residue 874 LEU Chi-restraints excluded: chain A residue 928 ILE Chi-restraints excluded: chain A residue 982 ASP Chi-restraints excluded: chain A residue 1037 VAL Chi-restraints excluded: chain A residue 1074 THR Chi-restraints excluded: chain A residue 1078 ILE Chi-restraints excluded: chain A residue 1101 VAL Chi-restraints excluded: chain A residue 1125 VAL Chi-restraints excluded: chain A residue 1130 VAL Chi-restraints excluded: chain A residue 1139 GLN Chi-restraints excluded: chain B residue 107 THR Chi-restraints excluded: chain B residue 139 LEU Chi-restraints excluded: chain B residue 188 VAL Chi-restraints excluded: chain B residue 309 ILE Chi-restraints excluded: chain B residue 330 THR Chi-restraints excluded: chain B residue 332 LEU Chi-restraints excluded: chain B residue 386 ASP Chi-restraints excluded: chain B residue 415 ILE Chi-restraints excluded: chain B residue 430 VAL Chi-restraints excluded: chain B residue 579 LEU Chi-restraints excluded: chain B residue 585 THR Chi-restraints excluded: chain B residue 617 VAL Chi-restraints excluded: chain B residue 723 ILE Chi-restraints excluded: chain B residue 726 VAL Chi-restraints excluded: chain B residue 912 VAL Chi-restraints excluded: chain B residue 973 VAL Chi-restraints excluded: chain B residue 990 ILE Chi-restraints excluded: chain B residue 998 LEU Chi-restraints excluded: chain B residue 1037 VAL Chi-restraints excluded: chain B residue 1078 ILE Chi-restraints excluded: chain B residue 1098 HIS Chi-restraints excluded: chain B residue 1101 VAL Chi-restraints excluded: chain C residue 33 THR Chi-restraints excluded: chain C residue 68 ILE Chi-restraints excluded: chain C residue 81 VAL Chi-restraints excluded: chain C residue 126 ILE Chi-restraints excluded: chain C residue 188 VAL Chi-restraints excluded: chain C residue 233 THR Chi-restraints excluded: chain C residue 255 TRP Chi-restraints excluded: chain C residue 264 VAL Chi-restraints excluded: chain C residue 309 ILE Chi-restraints excluded: chain C residue 329 ILE Chi-restraints excluded: chain C residue 430 VAL Chi-restraints excluded: chain C residue 465 ILE Chi-restraints excluded: chain C residue 585 THR Chi-restraints excluded: chain C residue 617 VAL Chi-restraints excluded: chain C residue 897 MET Chi-restraints excluded: chain C residue 973 VAL Chi-restraints excluded: chain C residue 982 ASP Chi-restraints excluded: chain C residue 998 LEU Chi-restraints excluded: chain C residue 1078 ILE Chi-restraints excluded: chain C residue 1098 HIS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 393 random chunks: chunk 325 optimal weight: 8.9990 chunk 96 optimal weight: 5.9990 chunk 217 optimal weight: 7.9990 chunk 114 optimal weight: 0.5980 chunk 353 optimal weight: 3.9990 chunk 151 optimal weight: 3.9990 chunk 48 optimal weight: 7.9990 chunk 237 optimal weight: 5.9990 chunk 51 optimal weight: 7.9990 chunk 313 optimal weight: 0.1980 chunk 339 optimal weight: 3.9990 overall best weight: 2.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** G 116 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 116 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 414 ASN ** A1156 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 191 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4093 r_free = 0.4093 target = 0.147734 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3322 r_free = 0.3322 target = 0.092451 restraints weight = 60674.124| |-----------------------------------------------------------------------------| r_work (start): 0.3301 rms_B_bonded: 3.43 r_work: 0.3170 rms_B_bonded: 3.63 restraints_weight: 0.5000 r_work (final): 0.3170 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7955 moved from start: 0.2039 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.070 33076 Z= 0.223 Angle : 0.690 18.732 45109 Z= 0.340 Chirality : 0.048 0.438 5269 Planarity : 0.004 0.073 5668 Dihedral : 7.395 104.359 5916 Min Nonbonded Distance : 1.787 Molprobity Statistics. All-atom Clashscore : 8.07 Ramachandran Plot: Outliers : 0.05 % Allowed : 6.85 % Favored : 93.10 % Rotamer: Outliers : 3.14 % Allowed : 16.15 % Favored : 80.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.52 % Cis-general : 0.03 % 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: -1.71 (0.13), residues: 3942 helix: -0.99 (0.19), residues: 733 sheet: -0.05 (0.17), residues: 986 loop : -1.75 (0.13), residues: 2223 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 354 TYR 0.019 0.001 TYR C1064 PHE 0.028 0.002 PHE C1118 TRP 0.018 0.002 TRP A 64 HIS 0.004 0.001 HIS A1045 Details of bonding type rmsd covalent geometry : bond 0.00545 (32949) covalent geometry : angle 0.67823 (44812) SS BOND : bond 0.00472 ( 48) SS BOND : angle 1.45136 ( 96) hydrogen bonds : bond 0.05356 ( 963) hydrogen bonds : angle 5.41404 ( 2589) Misc. bond : bond 0.00989 ( 12) link_BETA1-4 : bond 0.00478 ( 26) link_BETA1-4 : angle 1.94121 ( 78) link_NAG-ASN : bond 0.00282 ( 41) link_NAG-ASN : angle 1.79165 ( 123) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7884 Ramachandran restraints generated. 3942 Oldfield, 0 Emsley, 3942 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7884 Ramachandran restraints generated. 3942 Oldfield, 0 Emsley, 3942 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 330 residues out of total 3480 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 109 poor density : 221 time to evaluate : 1.192 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 12 LYS cc_start: 0.6667 (mmmm) cc_final: 0.5698 (mptt) REVERT: J 4 LEU cc_start: 0.5754 (mt) cc_final: 0.5507 (mt) REVERT: J 90 GLN cc_start: 0.5647 (tp-100) cc_final: 0.5323 (tp40) REVERT: L 39 GLN cc_start: 0.7000 (tt0) cc_final: 0.6715 (tp40) REVERT: L 71 ASP cc_start: 0.8593 (p0) cc_final: 0.8193 (t0) REVERT: L 97 TRP cc_start: 0.5444 (m-10) cc_final: 0.4447 (m-90) REVERT: A 498 TYR cc_start: 0.7068 (m-10) cc_final: 0.6747 (m-10) REVERT: A 549 LEU cc_start: 0.8937 (OUTLIER) cc_final: 0.8529 (mt) REVERT: A 749 LEU cc_start: 0.9127 (OUTLIER) cc_final: 0.8784 (tt) REVERT: A 883 TRP cc_start: 0.8487 (p90) cc_final: 0.8188 (p90) REVERT: B 354 ARG cc_start: 0.8361 (mtp85) cc_final: 0.8021 (ttm-80) REVERT: B 386 ASP cc_start: 0.8236 (OUTLIER) cc_final: 0.7848 (p0) REVERT: B 459 LYS cc_start: 0.8121 (mtpp) cc_final: 0.7921 (mtpp) REVERT: C 526 LYS cc_start: 0.9169 (mptt) cc_final: 0.8832 (tttt) outliers start: 109 outliers final: 87 residues processed: 312 average time/residue: 0.2041 time to fit residues: 104.3617 Evaluate side-chains 305 residues out of total 3480 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 90 poor density : 215 time to evaluate : 1.176 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 2 MET Chi-restraints excluded: chain G residue 51 TRP Chi-restraints excluded: chain H residue 107 CYS Chi-restraints excluded: chain I residue 4 LEU Chi-restraints excluded: chain I residue 107 CYS Chi-restraints excluded: chain J residue 62 ARG Chi-restraints excluded: chain J residue 82 GLU Chi-restraints excluded: chain K residue 31 ILE Chi-restraints excluded: chain K residue 62 ARG Chi-restraints excluded: chain K residue 71 ASP Chi-restraints excluded: chain K residue 95 SER Chi-restraints excluded: chain L residue 3 VAL Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 186 GLU Chi-restraints excluded: chain A residue 188 VAL Chi-restraints excluded: chain A residue 228 ILE Chi-restraints excluded: chain A residue 263 TYR Chi-restraints excluded: chain A residue 264 VAL Chi-restraints excluded: chain A residue 271 THR Chi-restraints excluded: chain A residue 286 VAL Chi-restraints excluded: chain A residue 393 TYR Chi-restraints excluded: chain A residue 414 ASN Chi-restraints excluded: chain A residue 430 VAL Chi-restraints excluded: chain A residue 512 PHE Chi-restraints excluded: chain A residue 549 LEU Chi-restraints excluded: chain A residue 585 THR Chi-restraints excluded: chain A residue 720 THR Chi-restraints excluded: chain A residue 749 LEU Chi-restraints excluded: chain A residue 874 LEU Chi-restraints excluded: chain A residue 928 ILE Chi-restraints excluded: chain A residue 982 ASP Chi-restraints excluded: chain A residue 1037 VAL Chi-restraints excluded: chain A residue 1074 THR Chi-restraints excluded: chain A residue 1078 ILE Chi-restraints excluded: chain A residue 1101 VAL Chi-restraints excluded: chain A residue 1125 VAL Chi-restraints excluded: chain A residue 1130 VAL Chi-restraints excluded: chain A residue 1139 GLN Chi-restraints excluded: chain B residue 107 THR Chi-restraints excluded: chain B residue 188 VAL Chi-restraints excluded: chain B residue 264 VAL Chi-restraints excluded: chain B residue 309 ILE Chi-restraints excluded: chain B residue 315 PHE Chi-restraints excluded: chain B residue 330 THR Chi-restraints excluded: chain B residue 332 LEU Chi-restraints excluded: chain B residue 386 ASP Chi-restraints excluded: chain B residue 415 ILE Chi-restraints excluded: chain B residue 430 VAL Chi-restraints excluded: chain B residue 485 CYS Chi-restraints excluded: chain B residue 570 THR Chi-restraints excluded: chain B residue 579 LEU Chi-restraints excluded: chain B residue 585 THR Chi-restraints excluded: chain B residue 617 VAL Chi-restraints excluded: chain B residue 723 ILE Chi-restraints excluded: chain B residue 726 VAL Chi-restraints excluded: chain B residue 912 VAL Chi-restraints excluded: chain B residue 928 ILE Chi-restraints excluded: chain B residue 973 VAL Chi-restraints excluded: chain B residue 990 ILE Chi-restraints excluded: chain B residue 998 LEU Chi-restraints excluded: chain B residue 1037 VAL Chi-restraints excluded: chain B residue 1078 ILE Chi-restraints excluded: chain B residue 1101 VAL Chi-restraints excluded: chain B residue 1125 VAL Chi-restraints excluded: chain C residue 33 THR Chi-restraints excluded: chain C residue 68 ILE Chi-restraints excluded: chain C residue 81 VAL Chi-restraints excluded: chain C residue 126 ILE Chi-restraints excluded: chain C residue 188 VAL Chi-restraints excluded: chain C residue 233 THR Chi-restraints excluded: chain C residue 255 TRP Chi-restraints excluded: chain C residue 264 VAL Chi-restraints excluded: chain C residue 286 VAL Chi-restraints excluded: chain C residue 309 ILE Chi-restraints excluded: chain C residue 329 ILE Chi-restraints excluded: chain C residue 430 VAL Chi-restraints excluded: chain C residue 465 ILE Chi-restraints excluded: chain C residue 490 ARG Chi-restraints excluded: chain C residue 570 THR Chi-restraints excluded: chain C residue 585 THR Chi-restraints excluded: chain C residue 617 VAL Chi-restraints excluded: chain C residue 723 ILE Chi-restraints excluded: chain C residue 897 MET Chi-restraints excluded: chain C residue 960 VAL Chi-restraints excluded: chain C residue 973 VAL Chi-restraints excluded: chain C residue 982 ASP Chi-restraints excluded: chain C residue 998 LEU Chi-restraints excluded: chain C residue 1078 ILE Chi-restraints excluded: chain C residue 1098 HIS Chi-restraints excluded: chain C residue 1126 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 393 random chunks: chunk 204 optimal weight: 0.0980 chunk 25 optimal weight: 20.0000 chunk 135 optimal weight: 2.9990 chunk 343 optimal weight: 4.9990 chunk 104 optimal weight: 0.9990 chunk 161 optimal weight: 0.6980 chunk 308 optimal weight: 0.7980 chunk 5 optimal weight: 9.9990 chunk 371 optimal weight: 5.9990 chunk 107 optimal weight: 8.9990 chunk 197 optimal weight: 20.0000 overall best weight: 1.1184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** G 116 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 116 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 414 ASN ** A1156 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 191 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4117 r_free = 0.4117 target = 0.149439 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.3359 r_free = 0.3359 target = 0.094548 restraints weight = 60290.161| |-----------------------------------------------------------------------------| r_work (start): 0.3340 rms_B_bonded: 3.40 r_work: 0.3213 rms_B_bonded: 3.61 restraints_weight: 0.5000 r_work (final): 0.3213 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7900 moved from start: 0.2100 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.066 33076 Z= 0.134 Angle : 0.633 18.869 45109 Z= 0.309 Chirality : 0.046 0.422 5269 Planarity : 0.004 0.078 5668 Dihedral : 7.022 104.143 5916 Min Nonbonded Distance : 1.787 Molprobity Statistics. All-atom Clashscore : 7.27 Ramachandran Plot: Outliers : 0.03 % Allowed : 5.83 % Favored : 94.14 % Rotamer: Outliers : 2.60 % Allowed : 16.78 % Favored : 80.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.52 % Cis-general : 0.03 % 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: -1.56 (0.13), residues: 3942 helix: -0.76 (0.19), residues: 725 sheet: 0.01 (0.16), residues: 992 loop : -1.66 (0.13), residues: 2225 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG K 24 TYR 0.017 0.001 TYR C1064 PHE 0.025 0.001 PHE G 101 TRP 0.015 0.001 TRP I 48 HIS 0.003 0.001 HIS C 141 Details of bonding type rmsd covalent geometry : bond 0.00309 (32949) covalent geometry : angle 0.62063 (44812) SS BOND : bond 0.00531 ( 48) SS BOND : angle 1.47221 ( 96) hydrogen bonds : bond 0.04334 ( 963) hydrogen bonds : angle 5.18066 ( 2589) Misc. bond : bond 0.00981 ( 12) link_BETA1-4 : bond 0.00477 ( 26) link_BETA1-4 : angle 1.93679 ( 78) link_NAG-ASN : bond 0.00275 ( 41) link_NAG-ASN : angle 1.64472 ( 123) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7884 Ramachandran restraints generated. 3942 Oldfield, 0 Emsley, 3942 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7884 Ramachandran restraints generated. 3942 Oldfield, 0 Emsley, 3942 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 305 residues out of total 3480 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 90 poor density : 215 time to evaluate : 1.143 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 12 LYS cc_start: 0.6715 (mmmm) cc_final: 0.5716 (mptt) REVERT: J 39 GLN cc_start: 0.7238 (tt0) cc_final: 0.6839 (tp40) REVERT: L 39 GLN cc_start: 0.6836 (tt0) cc_final: 0.6614 (tp40) REVERT: L 71 ASP cc_start: 0.8589 (p0) cc_final: 0.8191 (t0) REVERT: L 97 TRP cc_start: 0.5470 (m-10) cc_final: 0.4567 (m-90) REVERT: A 498 TYR cc_start: 0.7049 (m-10) cc_final: 0.6705 (m-10) REVERT: A 549 LEU cc_start: 0.8903 (OUTLIER) cc_final: 0.8499 (mt) REVERT: A 749 LEU cc_start: 0.9097 (OUTLIER) cc_final: 0.8751 (tt) REVERT: A 883 TRP cc_start: 0.8488 (p90) cc_final: 0.8193 (p90) REVERT: B 139 LEU cc_start: 0.8074 (OUTLIER) cc_final: 0.7460 (tp) REVERT: B 148 MET cc_start: 0.1369 (ptp) cc_final: 0.0597 (ptp) REVERT: B 354 ARG cc_start: 0.8330 (mtp85) cc_final: 0.8005 (ttm-80) REVERT: B 386 ASP cc_start: 0.8215 (OUTLIER) cc_final: 0.7821 (p0) REVERT: B 459 LYS cc_start: 0.8002 (mtpp) cc_final: 0.7775 (mtpp) REVERT: B 490 ARG cc_start: 0.6633 (OUTLIER) cc_final: 0.5931 (tpt170) REVERT: C 526 LYS cc_start: 0.9113 (mptt) cc_final: 0.8831 (tttt) REVERT: C 723 ILE cc_start: 0.9071 (OUTLIER) cc_final: 0.8829 (mt) outliers start: 90 outliers final: 76 residues processed: 292 average time/residue: 0.1984 time to fit residues: 95.0808 Evaluate side-chains 287 residues out of total 3480 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 82 poor density : 205 time to evaluate : 1.137 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 2 MET Chi-restraints excluded: chain G residue 51 TRP Chi-restraints excluded: chain H residue 107 CYS Chi-restraints excluded: chain I residue 4 LEU Chi-restraints excluded: chain I residue 107 CYS Chi-restraints excluded: chain J residue 62 ARG Chi-restraints excluded: chain J residue 82 GLU Chi-restraints excluded: chain K residue 62 ARG Chi-restraints excluded: chain K residue 95 SER Chi-restraints excluded: chain L residue 3 VAL Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 186 GLU Chi-restraints excluded: chain A residue 188 VAL Chi-restraints excluded: chain A residue 228 ILE Chi-restraints excluded: chain A residue 263 TYR Chi-restraints excluded: chain A residue 264 VAL Chi-restraints excluded: chain A residue 271 THR Chi-restraints excluded: chain A residue 286 VAL Chi-restraints excluded: chain A residue 309 ILE Chi-restraints excluded: chain A residue 393 TYR Chi-restraints excluded: chain A residue 430 VAL Chi-restraints excluded: chain A residue 463 ARG Chi-restraints excluded: chain A residue 512 PHE Chi-restraints excluded: chain A residue 549 LEU Chi-restraints excluded: chain A residue 585 THR Chi-restraints excluded: chain A residue 749 LEU Chi-restraints excluded: chain A residue 874 LEU Chi-restraints excluded: chain A residue 982 ASP Chi-restraints excluded: chain A residue 1037 VAL Chi-restraints excluded: chain A residue 1074 THR Chi-restraints excluded: chain A residue 1078 ILE Chi-restraints excluded: chain A residue 1101 VAL Chi-restraints excluded: chain A residue 1125 VAL Chi-restraints excluded: chain A residue 1130 VAL Chi-restraints excluded: chain B residue 107 THR Chi-restraints excluded: chain B residue 139 LEU Chi-restraints excluded: chain B residue 188 VAL Chi-restraints excluded: chain B residue 264 VAL Chi-restraints excluded: chain B residue 309 ILE Chi-restraints excluded: chain B residue 330 THR Chi-restraints excluded: chain B residue 332 LEU Chi-restraints excluded: chain B residue 386 ASP Chi-restraints excluded: chain B residue 415 ILE Chi-restraints excluded: chain B residue 430 VAL Chi-restraints excluded: chain B residue 485 CYS Chi-restraints excluded: chain B residue 490 ARG Chi-restraints excluded: chain B residue 570 THR Chi-restraints excluded: chain B residue 579 LEU Chi-restraints excluded: chain B residue 585 THR Chi-restraints excluded: chain B residue 617 VAL Chi-restraints excluded: chain B residue 723 ILE Chi-restraints excluded: chain B residue 973 VAL Chi-restraints excluded: chain B residue 990 ILE Chi-restraints excluded: chain B residue 998 LEU Chi-restraints excluded: chain B residue 1037 VAL Chi-restraints excluded: chain B residue 1078 ILE Chi-restraints excluded: chain B residue 1101 VAL Chi-restraints excluded: chain B residue 1125 VAL Chi-restraints excluded: chain C residue 33 THR Chi-restraints excluded: chain C residue 68 ILE Chi-restraints excluded: chain C residue 81 VAL Chi-restraints excluded: chain C residue 126 ILE Chi-restraints excluded: chain C residue 188 VAL Chi-restraints excluded: chain C residue 233 THR Chi-restraints excluded: chain C residue 255 TRP Chi-restraints excluded: chain C residue 264 VAL Chi-restraints excluded: chain C residue 286 VAL Chi-restraints excluded: chain C residue 309 ILE Chi-restraints excluded: chain C residue 315 PHE Chi-restraints excluded: chain C residue 329 ILE Chi-restraints excluded: chain C residue 430 VAL Chi-restraints excluded: chain C residue 465 ILE Chi-restraints excluded: chain C residue 585 THR Chi-restraints excluded: chain C residue 617 VAL Chi-restraints excluded: chain C residue 723 ILE Chi-restraints excluded: chain C residue 897 MET Chi-restraints excluded: chain C residue 960 VAL Chi-restraints excluded: chain C residue 973 VAL Chi-restraints excluded: chain C residue 982 ASP Chi-restraints excluded: chain C residue 998 LEU Chi-restraints excluded: chain C residue 1078 ILE Chi-restraints excluded: chain C residue 1098 HIS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 393 random chunks: chunk 174 optimal weight: 10.0000 chunk 269 optimal weight: 0.9990 chunk 44 optimal weight: 9.9990 chunk 306 optimal weight: 20.0000 chunk 351 optimal weight: 5.9990 chunk 197 optimal weight: 0.0770 chunk 43 optimal weight: 5.9990 chunk 331 optimal weight: 4.9990 chunk 128 optimal weight: 3.9990 chunk 45 optimal weight: 1.9990 chunk 40 optimal weight: 20.0000 overall best weight: 2.4146 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** G 116 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 3 GLN ** I 116 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 850 GLN ** A1156 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 191 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4105 r_free = 0.4105 target = 0.148198 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.3342 r_free = 0.3342 target = 0.093459 restraints weight = 61044.491| |-----------------------------------------------------------------------------| r_work (start): 0.3306 rms_B_bonded: 3.39 r_work: 0.3175 rms_B_bonded: 3.64 restraints_weight: 0.5000 r_work (final): 0.3175 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7944 moved from start: 0.2157 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.069 33076 Z= 0.214 Angle : 0.691 18.741 45109 Z= 0.339 Chirality : 0.048 0.423 5269 Planarity : 0.005 0.078 5668 Dihedral : 7.097 104.683 5916 Min Nonbonded Distance : 1.788 Molprobity Statistics. All-atom Clashscore : 8.17 Ramachandran Plot: Outliers : 0.03 % Allowed : 7.23 % Favored : 92.74 % Rotamer: Outliers : 2.74 % Allowed : 16.90 % Favored : 80.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.52 % Cis-general : 0.03 % 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: -1.70 (0.13), residues: 3942 helix: -0.93 (0.19), residues: 736 sheet: -0.04 (0.17), residues: 986 loop : -1.75 (0.13), residues: 2220 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG K 24 TYR 0.018 0.001 TYR C1064 PHE 0.026 0.002 PHE C1118 TRP 0.018 0.001 TRP A 64 HIS 0.004 0.001 HIS B1098 Details of bonding type rmsd covalent geometry : bond 0.00521 (32949) covalent geometry : angle 0.67753 (44812) SS BOND : bond 0.00534 ( 48) SS BOND : angle 1.55787 ( 96) hydrogen bonds : bond 0.05138 ( 963) hydrogen bonds : angle 5.35011 ( 2589) Misc. bond : bond 0.00981 ( 12) link_BETA1-4 : bond 0.00472 ( 26) link_BETA1-4 : angle 2.01588 ( 78) link_NAG-ASN : bond 0.00278 ( 41) link_NAG-ASN : angle 1.77478 ( 123) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7884 Ramachandran restraints generated. 3942 Oldfield, 0 Emsley, 3942 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7884 Ramachandran restraints generated. 3942 Oldfield, 0 Emsley, 3942 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 308 residues out of total 3480 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 95 poor density : 213 time to evaluate : 1.271 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 12 LYS cc_start: 0.6722 (mmmm) cc_final: 0.5777 (mptt) REVERT: J 4 LEU cc_start: 0.5813 (mt) cc_final: 0.5595 (mt) REVERT: L 39 GLN cc_start: 0.6874 (tt0) cc_final: 0.6624 (tp40) REVERT: L 71 ASP cc_start: 0.8589 (p0) cc_final: 0.8200 (t0) REVERT: L 97 TRP cc_start: 0.5422 (m-10) cc_final: 0.4600 (m-90) REVERT: A 498 TYR cc_start: 0.7047 (m-10) cc_final: 0.6703 (m-10) REVERT: A 549 LEU cc_start: 0.8922 (OUTLIER) cc_final: 0.8516 (mt) REVERT: A 749 LEU cc_start: 0.9126 (OUTLIER) cc_final: 0.8781 (tt) REVERT: A 883 TRP cc_start: 0.8488 (p90) cc_final: 0.8148 (p90) REVERT: B 354 ARG cc_start: 0.8347 (mtp85) cc_final: 0.8016 (ttm-80) REVERT: B 386 ASP cc_start: 0.8229 (OUTLIER) cc_final: 0.7844 (p0) REVERT: B 459 LYS cc_start: 0.8068 (mtpp) cc_final: 0.7810 (mtpp) REVERT: B 490 ARG cc_start: 0.6488 (OUTLIER) cc_final: 0.5809 (tpt170) REVERT: C 490 ARG cc_start: 0.7743 (OUTLIER) cc_final: 0.7107 (tpt170) REVERT: C 526 LYS cc_start: 0.9164 (mptt) cc_final: 0.8815 (tttt) REVERT: C 723 ILE cc_start: 0.9090 (OUTLIER) cc_final: 0.8850 (mt) REVERT: C 874 LEU cc_start: 0.8870 (OUTLIER) cc_final: 0.8549 (mm) outliers start: 95 outliers final: 83 residues processed: 293 average time/residue: 0.2111 time to fit residues: 100.9094 Evaluate side-chains 297 residues out of total 3480 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 90 poor density : 207 time to evaluate : 1.266 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 2 MET Chi-restraints excluded: chain G residue 51 TRP Chi-restraints excluded: chain H residue 107 CYS Chi-restraints excluded: chain I residue 3 GLN Chi-restraints excluded: chain I residue 4 LEU Chi-restraints excluded: chain I residue 107 CYS Chi-restraints excluded: chain J residue 62 ARG Chi-restraints excluded: chain J residue 82 GLU Chi-restraints excluded: chain K residue 62 ARG Chi-restraints excluded: chain K residue 95 SER Chi-restraints excluded: chain L residue 3 VAL Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 186 GLU Chi-restraints excluded: chain A residue 188 VAL Chi-restraints excluded: chain A residue 228 ILE Chi-restraints excluded: chain A residue 263 TYR Chi-restraints excluded: chain A residue 264 VAL Chi-restraints excluded: chain A residue 271 THR Chi-restraints excluded: chain A residue 286 VAL Chi-restraints excluded: chain A residue 309 ILE Chi-restraints excluded: chain A residue 393 TYR Chi-restraints excluded: chain A residue 430 VAL Chi-restraints excluded: chain A residue 512 PHE Chi-restraints excluded: chain A residue 549 LEU Chi-restraints excluded: chain A residue 585 THR Chi-restraints excluded: chain A residue 720 THR Chi-restraints excluded: chain A residue 749 LEU Chi-restraints excluded: chain A residue 874 LEU Chi-restraints excluded: chain A residue 928 ILE Chi-restraints excluded: chain A residue 982 ASP Chi-restraints excluded: chain A residue 1037 VAL Chi-restraints excluded: chain A residue 1074 THR Chi-restraints excluded: chain A residue 1078 ILE Chi-restraints excluded: chain A residue 1101 VAL Chi-restraints excluded: chain A residue 1125 VAL Chi-restraints excluded: chain A residue 1130 VAL Chi-restraints excluded: chain B residue 107 THR Chi-restraints excluded: chain B residue 188 VAL Chi-restraints excluded: chain B residue 264 VAL Chi-restraints excluded: chain B residue 309 ILE Chi-restraints excluded: chain B residue 315 PHE Chi-restraints excluded: chain B residue 330 THR Chi-restraints excluded: chain B residue 332 LEU Chi-restraints excluded: chain B residue 386 ASP Chi-restraints excluded: chain B residue 415 ILE Chi-restraints excluded: chain B residue 430 VAL Chi-restraints excluded: chain B residue 485 CYS Chi-restraints excluded: chain B residue 490 ARG Chi-restraints excluded: chain B residue 570 THR Chi-restraints excluded: chain B residue 579 LEU Chi-restraints excluded: chain B residue 585 THR Chi-restraints excluded: chain B residue 617 VAL Chi-restraints excluded: chain B residue 646 CYS Chi-restraints excluded: chain B residue 723 ILE Chi-restraints excluded: chain B residue 726 VAL Chi-restraints excluded: chain B residue 912 VAL Chi-restraints excluded: chain B residue 928 ILE Chi-restraints excluded: chain B residue 973 VAL Chi-restraints excluded: chain B residue 990 ILE Chi-restraints excluded: chain B residue 998 LEU Chi-restraints excluded: chain B residue 1037 VAL Chi-restraints excluded: chain B residue 1078 ILE Chi-restraints excluded: chain B residue 1101 VAL Chi-restraints excluded: chain B residue 1125 VAL Chi-restraints excluded: chain C residue 33 THR Chi-restraints excluded: chain C residue 68 ILE Chi-restraints excluded: chain C residue 81 VAL Chi-restraints excluded: chain C residue 126 ILE Chi-restraints excluded: chain C residue 188 VAL Chi-restraints excluded: chain C residue 233 THR Chi-restraints excluded: chain C residue 255 TRP Chi-restraints excluded: chain C residue 264 VAL Chi-restraints excluded: chain C residue 286 VAL Chi-restraints excluded: chain C residue 309 ILE Chi-restraints excluded: chain C residue 315 PHE Chi-restraints excluded: chain C residue 329 ILE Chi-restraints excluded: chain C residue 430 VAL Chi-restraints excluded: chain C residue 465 ILE Chi-restraints excluded: chain C residue 490 ARG Chi-restraints excluded: chain C residue 585 THR Chi-restraints excluded: chain C residue 617 VAL Chi-restraints excluded: chain C residue 723 ILE Chi-restraints excluded: chain C residue 874 LEU Chi-restraints excluded: chain C residue 897 MET Chi-restraints excluded: chain C residue 960 VAL Chi-restraints excluded: chain C residue 973 VAL Chi-restraints excluded: chain C residue 982 ASP Chi-restraints excluded: chain C residue 998 LEU Chi-restraints excluded: chain C residue 1078 ILE Chi-restraints excluded: chain C residue 1098 HIS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 393 random chunks: chunk 231 optimal weight: 3.9990 chunk 58 optimal weight: 6.9990 chunk 302 optimal weight: 0.7980 chunk 61 optimal weight: 6.9990 chunk 301 optimal weight: 0.5980 chunk 387 optimal weight: 0.5980 chunk 145 optimal weight: 3.9990 chunk 225 optimal weight: 0.9990 chunk 187 optimal weight: 9.9990 chunk 330 optimal weight: 5.9990 chunk 228 optimal weight: 3.9990 overall best weight: 1.3984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** G 116 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 116 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 414 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1156 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 191 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4099 r_free = 0.4099 target = 0.147933 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3333 r_free = 0.3333 target = 0.093007 restraints weight = 60804.502| |-----------------------------------------------------------------------------| r_work (start): 0.3309 rms_B_bonded: 3.40 r_work: 0.3183 rms_B_bonded: 3.59 restraints_weight: 0.5000 r_work (final): 0.3183 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7935 moved from start: 0.2166 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.107 33076 Z= 0.198 Angle : 0.780 59.200 45109 Z= 0.405 Chirality : 0.049 0.938 5269 Planarity : 0.004 0.076 5668 Dihedral : 7.095 104.648 5916 Min Nonbonded Distance : 1.788 Molprobity Statistics. All-atom Clashscore : 8.75 Ramachandran Plot: Outliers : 0.03 % Allowed : 7.18 % Favored : 92.80 % Rotamer: Outliers : 2.80 % Allowed : 16.81 % Favored : 80.39 % Cbeta Deviations : 0.03 % Peptide Plane: Cis-proline : 1.52 % Cis-general : 0.03 % 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: -1.69 (0.13), residues: 3942 helix: -0.93 (0.19), residues: 736 sheet: -0.04 (0.17), residues: 986 loop : -1.75 (0.13), residues: 2220 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG K 24 TYR 0.018 0.001 TYR C1064 PHE 0.025 0.001 PHE C1118 TRP 0.017 0.001 TRP A 64 HIS 0.004 0.001 HIS B1098 Details of bonding type rmsd covalent geometry : bond 0.00469 (32949) covalent geometry : angle 0.76844 (44812) SS BOND : bond 0.00527 ( 48) SS BOND : angle 1.66459 ( 96) hydrogen bonds : bond 0.05029 ( 963) hydrogen bonds : angle 5.34759 ( 2589) Misc. bond : bond 0.00987 ( 12) link_BETA1-4 : bond 0.00457 ( 26) link_BETA1-4 : angle 2.02174 ( 78) link_NAG-ASN : bond 0.00283 ( 41) link_NAG-ASN : angle 1.77995 ( 123) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 9332.30 seconds wall clock time: 160 minutes 25.51 seconds (9625.51 seconds total)