Starting phenix.real_space_refine on Mon Jul 6 23:09:43 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7qti_14141/07_2026/7qti_14141.cif Found real_map, /net/cci-nas-00/data/ceres_data/7qti_14141/07_2026/7qti_14141.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.04 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7qti_14141/07_2026/7qti_14141.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7qti_14141/07_2026/7qti_14141.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7qti_14141/07_2026/7qti_14141.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7qti_14141/07_2026/7qti_14141.map" restraint_files = "/net/cci-nas-00/data/ceres_data/7qti_14141/07_2026/7qti_14141.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7qti_14141/07_2026/7qti_14141.cif" } resolution = 3.04 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= 0.024 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 165 5.16 5 C 25407 2.51 5 N 6639 2.21 5 O 7883 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 16 residue(s): 0.04s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 40094 Number of models: 1 Model: "" Number of chains: 31 Chain: "G" Number of atoms: 1729 Number of conformers: 1 Conformer: "" Number of residues, atoms: 228, 1729 Classifications: {'peptide': 228} Link IDs: {'PTRANS': 11, 'TRANS': 216} Chain: "H" Number of atoms: 1640 Number of conformers: 1 Conformer: "" Number of residues, atoms: 214, 1640 Classifications: {'peptide': 214} Link IDs: {'PTRANS': 10, 'TRANS': 203} Chain: "B" Number of atoms: 1729 Number of conformers: 1 Conformer: "" Number of residues, atoms: 228, 1729 Classifications: {'peptide': 228} Link IDs: {'PTRANS': 11, 'TRANS': 216} Chain: "C" Number of atoms: 1640 Number of conformers: 1 Conformer: "" Number of residues, atoms: 214, 1640 Classifications: {'peptide': 214} Link IDs: {'PTRANS': 10, 'TRANS': 203} Chain: "E" Number of atoms: 1645 Number of conformers: 1 Conformer: "" Number of residues, atoms: 215, 1645 Classifications: {'peptide': 215} Link IDs: {'PTRANS': 12, 'TRANS': 202} Chain: "F" Number of atoms: 1637 Number of conformers: 1 Conformer: "" Number of residues, atoms: 221, 1637 Classifications: {'peptide': 221} Link IDs: {'PTRANS': 11, 'TRANS': 209} Chain: "I" Number of atoms: 1729 Number of conformers: 1 Conformer: "" Number of residues, atoms: 228, 1729 Classifications: {'peptide': 228} Link IDs: {'PTRANS': 11, 'TRANS': 216} Chain: "J" Number of atoms: 1640 Number of conformers: 1 Conformer: "" Number of residues, atoms: 214, 1640 Classifications: {'peptide': 214} Link IDs: {'PTRANS': 10, 'TRANS': 203} Chain: "D" Number of atoms: 8623 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1103, 8623 Classifications: {'peptide': 1103} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 56, 'TRANS': 1046} Chain breaks: 4 Unresolved non-hydrogen bonds: 18 Unresolved non-hydrogen angles: 23 Unresolved non-hydrogen dihedrals: 13 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'ARG:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 8 Chain: "K" Number of atoms: 8589 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1096, 8589 Classifications: {'peptide': 1096} Link IDs: {'PTRANS': 56, 'TRANS': 1039} Chain breaks: 4 Chain: "A" Number of atoms: 8609 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1100, 8609 Classifications: {'peptide': 1100} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 56, 'TRANS': 1043} Chain breaks: 4 Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 8 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 Chain: "L" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "M" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "N" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "O" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "P" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "Q" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "R" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "S" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "T" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "U" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "V" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "W" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "X" Number of atoms: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 50 Unusual residues: {'BMA': 1, 'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen chiralities: 4 Chain: "Y" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "Z" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "a" Number of atoms: 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 chiralities: 3 Chain: "b" 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 chiralities: 3 Chain: "D" Number of atoms: 112 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 112 Unusual residues: {'NAG': 8} Classifications: {'undetermined': 8} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen chiralities: 8 Chain: "K" Number of atoms: 168 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 168 Unusual residues: {'NAG': 12} Classifications: {'undetermined': 12} Link IDs: {None: 11} Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 24 Unresolved non-hydrogen chiralities: 12 Chain: "A" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 84 Unusual residues: {'NAG': 6} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen chiralities: 6 Time building chain proxies: 8.27, per 1000 atoms: 0.21 Number of scatterers: 40094 At special positions: 0 Unit cell: (146.633, 199.2, 264.217, 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 165 16.00 O 7883 8.00 N 6639 7.00 C 25407 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=62, symmetry=0 Simple disulfide: pdb=" SG CYS G 22 " - pdb=" SG CYS G 96 " distance=2.03 Simple disulfide: pdb=" SG CYS G 152 " - pdb=" SG CYS G 208 " distance=2.03 Simple disulfide: pdb=" SG CYS G 228 " - pdb=" SG CYS H 214 " distance=2.03 Simple disulfide: pdb=" SG CYS H 23 " - pdb=" SG CYS H 88 " distance=2.03 Simple disulfide: pdb=" SG CYS H 134 " - pdb=" SG CYS H 194 " distance=2.03 Simple disulfide: pdb=" SG CYS B 22 " - pdb=" SG CYS B 96 " distance=2.03 Simple disulfide: pdb=" SG CYS B 152 " - pdb=" SG CYS B 208 " distance=2.03 Simple disulfide: pdb=" SG CYS B 228 " - pdb=" SG CYS C 214 " distance=2.03 Simple disulfide: pdb=" SG CYS C 23 " - pdb=" SG CYS C 88 " distance=2.04 Simple disulfide: pdb=" SG CYS C 134 " - pdb=" SG CYS C 194 " distance=2.03 Simple disulfide: pdb=" SG CYS E 23 " - pdb=" SG CYS E 89 " distance=2.03 Simple disulfide: pdb=" SG CYS E 135 " - pdb=" SG CYS E 195 " distance=2.03 Simple disulfide: pdb=" SG CYS F 22 " - pdb=" SG CYS F 96 " distance=2.03 Simple disulfide: pdb=" SG CYS F 101 " - pdb=" SG CYS F 106 " distance=2.03 Simple disulfide: pdb=" SG CYS F 150 " - pdb=" SG CYS F 206 " distance=2.03 Simple disulfide: pdb=" SG CYS I 22 " - pdb=" SG CYS I 96 " distance=2.03 Simple disulfide: pdb=" SG CYS I 152 " - pdb=" SG CYS I 208 " distance=2.03 Simple disulfide: pdb=" SG CYS I 228 " - pdb=" SG CYS J 214 " distance=2.03 Simple disulfide: pdb=" SG CYS J 23 " - pdb=" SG CYS J 88 " distance=2.03 Simple disulfide: pdb=" SG CYS J 134 " - pdb=" SG CYS J 194 " distance=2.03 Simple disulfide: pdb=" SG CYS D 129 " - pdb=" SG CYS D 161 " distance=2.03 Simple disulfide: pdb=" SG CYS D 288 " - pdb=" SG CYS D 298 " distance=2.03 Simple disulfide: pdb=" SG CYS D 333 " - pdb=" SG CYS D 358 " distance=2.03 Simple disulfide: pdb=" SG CYS D 376 " - pdb=" SG CYS D 429 " distance=2.03 Simple disulfide: pdb=" SG CYS D 388 " - pdb=" SG CYS D 522 " distance=2.03 Simple disulfide: pdb=" SG CYS D 477 " - pdb=" SG CYS D 485 " distance=2.03 Simple disulfide: pdb=" SG CYS D 535 " - pdb=" SG CYS D 587 " distance=2.03 Simple disulfide: pdb=" SG CYS D 614 " - pdb=" SG CYS D 646 " distance=2.03 Simple disulfide: pdb=" SG CYS D 659 " - pdb=" SG CYS D 668 " distance=2.03 Simple disulfide: pdb=" SG CYS D 735 " - pdb=" SG CYS D 757 " distance=2.03 Simple disulfide: pdb=" SG CYS D 740 " - pdb=" SG CYS D 746 " distance=2.03 Simple disulfide: pdb=" SG CYS D 837 " - pdb=" SG CYS D 848 " distance=2.03 Simple disulfide: pdb=" SG CYS D1029 " - pdb=" SG CYS D1040 " distance=2.03 Simple disulfide: pdb=" SG CYS D1079 " - pdb=" SG CYS D1123 " distance=2.03 Simple disulfide: pdb=" SG CYS K 129 " - pdb=" SG CYS K 161 " distance=2.03 Simple disulfide: pdb=" SG CYS K 288 " - pdb=" SG CYS K 298 " distance=2.03 Simple disulfide: pdb=" SG CYS K 333 " - pdb=" SG CYS K 358 " distance=2.03 Simple disulfide: pdb=" SG CYS K 376 " - pdb=" SG CYS K 429 " distance=2.03 Simple disulfide: pdb=" SG CYS K 388 " - pdb=" SG CYS K 522 " distance=2.03 Simple disulfide: pdb=" SG CYS K 477 " - pdb=" SG CYS K 485 " distance=2.03 Simple disulfide: pdb=" SG CYS K 535 " - pdb=" SG CYS K 587 " distance=2.04 Simple disulfide: pdb=" SG CYS K 614 " - pdb=" SG CYS K 646 " distance=2.03 Simple disulfide: pdb=" SG CYS K 659 " - pdb=" SG CYS K 668 " distance=2.04 Simple disulfide: pdb=" SG CYS K 735 " - pdb=" SG CYS K 757 " distance=2.03 Simple disulfide: pdb=" SG CYS K 740 " - pdb=" SG CYS K 746 " distance=2.03 Simple disulfide: pdb=" SG CYS K 837 " - pdb=" SG CYS K 848 " distance=2.03 Simple disulfide: pdb=" SG CYS K1029 " - pdb=" SG CYS K1040 " distance=2.03 Simple disulfide: pdb=" SG CYS K1079 " - pdb=" SG CYS K1123 " 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=2.04 Simple disulfide: pdb=" SG CYS A 388 " - pdb=" SG CYS A 522 " distance=2.04 Simple disulfide: pdb=" SG CYS A 477 " - pdb=" SG CYS A 485 " distance=2.03 Simple disulfide: pdb=" SG CYS A 535 " - pdb=" SG CYS A 587 " distance=2.03 Simple disulfide: pdb=" SG CYS A 614 " - pdb=" SG CYS A 646 " distance=2.03 Simple disulfide: pdb=" SG CYS A 659 " - pdb=" SG CYS A 668 " distance=2.03 Simple disulfide: pdb=" SG CYS A 735 " - pdb=" SG CYS A 757 " distance=2.03 Simple disulfide: pdb=" SG CYS A 740 " - pdb=" SG CYS A 746 " distance=2.03 Simple disulfide: pdb=" SG CYS A 837 " - pdb=" SG CYS A 848 " distance=2.03 Simple disulfide: pdb=" SG CYS A1029 " - pdb=" SG CYS A1040 " distance=2.03 Simple disulfide: pdb=" SG CYS A1079 " - pdb=" SG CYS A1123 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied ALPHA1-3 " BMA X 3 " - " MAN X 4 " BETA1-4 " NAG L 1 " - " NAG L 2 " " NAG M 1 " - " NAG M 2 " " NAG N 1 " - " NAG N 2 " " NAG O 1 " - " NAG O 2 " " NAG P 1 " - " NAG P 2 " " NAG 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 W 1 " - " NAG W 2 " " NAG X 1 " - " NAG X 2 " " NAG X 2 " - " BMA X 3 " " NAG Y 1 " - " NAG Y 2 " " NAG Z 1 " - " NAG Z 2 " " NAG a 1 " - " NAG a 2 " " NAG a 2 " - " BMA a 3 " " NAG b 1 " - " NAG b 2 " " NAG b 2 " - " BMA b 3 " NAG-ASN " NAG A1301 " - " ASN A 613 " " NAG A1302 " - " ASN A 654 " " NAG A1303 " - " ASN A1071 " " NAG A1304 " - " ASN A 706 " " NAG A1305 " - " ASN A 120 " " NAG A1306 " - " ASN A 159 " " NAG D1301 " - " ASN D 328 " " NAG D1302 " - " ASN D 613 " " NAG D1303 " - " ASN D 654 " " NAG D1304 " - " ASN D1071 " " NAG D1305 " - " ASN D1131 " " NAG D1306 " - " ASN D 120 " " NAG D1307 " - " ASN D 135 " " NAG D1308 " - " ASN D 159 " " NAG K1301 " - " ASN K 328 " " NAG K1302 " - " ASN K 706 " " NAG K1303 " - " ASN K 61 " " NAG K1304 " - " ASN K 340 " " NAG K1305 " - " ASN K 600 " " NAG K1306 " - " ASN K 613 " " NAG K1307 " - " ASN K 654 " " NAG K1308 " - " ASN K1071 " " NAG K1309 " - " ASN K 798 " " NAG K1310 " - " ASN K 120 " " NAG K1311 " - " ASN K 159 " " NAG K1312 " - " ASN K 231 " " NAG L 1 " - " ASN D 279 " " NAG M 1 " - " ASN D 340 " " NAG N 1 " - " ASN D 706 " " NAG O 1 " - " ASN D 714 " " NAG P 1 " - " ASN D 798 " " NAG Q 1 " - " ASN D1095 " " NAG R 1 " - " ASN K1095 " " NAG S 1 " - " ASN K 279 " " NAG T 1 " - " ASN K1131 " " NAG U 1 " - " ASN K 714 " " NAG V 1 " - " ASN A 279 " " NAG W 1 " - " ASN A 328 " " NAG X 1 " - " ASN A 340 " " NAG Y 1 " - " ASN A1095 " " NAG Z 1 " - " ASN A1131 " " NAG a 1 " - " ASN A 714 " " NAG b 1 " - " ASN A 798 " Time building additional restraints: 3.14 Conformation dependent library (CDL) restraints added in 1.8 seconds 10030 Ramachandran restraints generated. 5015 Oldfield, 0 Emsley, 5015 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 9424 Finding SS restraints... Secondary structure from input PDB file: 91 helices and 92 sheets defined 17.8% alpha, 28.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.48 Creating SS restraints... Processing helix chain 'G' and resid 62 through 65 removed outlier: 3.568A pdb=" N LYS G 65 " --> pdb=" O GLU G 62 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 62 through 65' Processing helix chain 'G' and resid 87 through 91 Processing helix chain 'G' and resid 168 through 170 No H-bonds generated for 'chain 'G' and resid 168 through 170' Processing helix chain 'G' and resid 199 through 201 No H-bonds generated for 'chain 'G' and resid 199 through 201' Processing helix chain 'H' and resid 79 through 83 removed outlier: 3.896A pdb=" N PHE H 83 " --> pdb=" O PRO H 80 " (cutoff:3.500A) Processing helix chain 'H' and resid 121 through 126 Processing helix chain 'H' and resid 183 through 188 Processing helix chain 'B' and resid 87 through 91 Processing helix chain 'B' and resid 139 through 141 No H-bonds generated for 'chain 'B' and resid 139 through 141' Processing helix chain 'B' and resid 199 through 201 No H-bonds generated for 'chain 'B' and resid 199 through 201' Processing helix chain 'C' and resid 79 through 83 removed outlier: 3.802A pdb=" N PHE C 83 " --> pdb=" O PRO C 80 " (cutoff:3.500A) Processing helix chain 'C' and resid 121 through 127 Processing helix chain 'C' and resid 183 through 188 Processing helix chain 'E' and resid 122 through 128 removed outlier: 3.717A pdb=" N SER E 128 " --> pdb=" O GLU E 124 " (cutoff:3.500A) Processing helix chain 'E' and resid 184 through 189 Processing helix chain 'F' and resid 28 through 31 Processing helix chain 'F' and resid 87 through 91 Processing helix chain 'F' and resid 137 through 139 No H-bonds generated for 'chain 'F' and resid 137 through 139' Processing helix chain 'F' and resid 197 through 199 No H-bonds generated for 'chain 'F' and resid 197 through 199' Processing helix chain 'I' and resid 87 through 91 Processing helix chain 'I' and resid 139 through 141 No H-bonds generated for 'chain 'I' and resid 139 through 141' Processing helix chain 'I' and resid 168 through 170 No H-bonds generated for 'chain 'I' and resid 168 through 170' Processing helix chain 'I' and resid 199 through 201 No H-bonds generated for 'chain 'I' and resid 199 through 201' Processing helix chain 'J' and resid 121 through 127 removed outlier: 3.547A pdb=" N SER J 127 " --> pdb=" O GLU J 123 " (cutoff:3.500A) Processing helix chain 'J' and resid 183 through 188 Processing helix chain 'D' and resid 69 through 73 removed outlier: 3.805A pdb=" N ASN D 72 " --> pdb=" O SER D 69 " (cutoff:3.500A) Processing helix chain 'D' and resid 150 through 155 removed outlier: 4.131A pdb=" N VAL D 154 " --> pdb=" O GLU D 151 " (cutoff:3.500A) Processing helix chain 'D' and resid 291 through 301 Processing helix chain 'D' and resid 334 through 340 removed outlier: 3.893A pdb=" N VAL D 338 " --> pdb=" O PRO D 334 " (cutoff:3.500A) Processing helix chain 'D' and resid 362 through 369 removed outlier: 3.834A pdb=" N ALA D 369 " --> pdb=" O LEU D 365 " (cutoff:3.500A) Processing helix chain 'D' and resid 380 through 384 Processing helix chain 'D' and resid 402 through 407 removed outlier: 4.133A pdb=" N ARG D 405 " --> pdb=" O ASP D 402 " (cutoff:3.500A) Processing helix chain 'D' and resid 413 through 419 Processing helix chain 'D' and resid 499 through 502 Processing helix chain 'D' and resid 540 through 543 Processing helix chain 'D' and resid 734 through 740 Processing helix chain 'D' and resid 743 through 752 removed outlier: 3.695A pdb=" N GLN D 752 " --> pdb=" O ASN D 748 " (cutoff:3.500A) Processing helix chain 'D' and resid 757 through 780 Processing helix chain 'D' and resid 813 through 824 Processing helix chain 'D' and resid 863 through 882 removed outlier: 3.607A pdb=" N ILE D 867 " --> pdb=" O THR D 863 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N ALA D 868 " --> pdb=" O ASP D 864 " (cutoff:3.500A) removed outlier: 3.954A pdb=" N GLN D 869 " --> pdb=" O GLU D 865 " (cutoff:3.500A) Processing helix chain 'D' and resid 883 through 888 removed outlier: 3.524A pdb=" N GLY D 886 " --> pdb=" O TRP D 883 " (cutoff:3.500A) removed outlier: 4.084A pdb=" N GLY D 888 " --> pdb=" O PHE D 885 " (cutoff:3.500A) Processing helix chain 'D' and resid 894 through 905 Processing helix chain 'D' and resid 910 through 937 removed outlier: 6.837A pdb=" N LYS D 918 " --> pdb=" O TYR D 914 " (cutoff:3.500A) removed outlier: 6.321A pdb=" N LEU D 919 " --> pdb=" O GLU D 915 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N ILE D 931 " --> pdb=" O ALA D 927 " (cutoff:3.500A) removed outlier: 3.953A pdb=" N GLN D 932 " --> pdb=" O ILE D 928 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N ASP D 933 " --> pdb=" O GLY D 929 " (cutoff:3.500A) Processing helix chain 'D' and resid 942 through 962 removed outlier: 3.757A pdb=" N VAL D 948 " --> pdb=" O LYS D 944 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N VAL D 949 " --> pdb=" O LEU D 945 " (cutoff:3.500A) Processing helix chain 'D' and resid 963 through 965 No H-bonds generated for 'chain 'D' and resid 963 through 965' Processing helix chain 'D' and resid 973 through 981 Processing helix chain 'D' and resid 982 through 1030 removed outlier: 4.923A pdb=" N VAL D 988 " --> pdb=" O PRO D 984 " (cutoff:3.500A) removed outlier: 3.879A pdb=" N LEU D 993 " --> pdb=" O GLN D 989 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N ALA D1013 " --> pdb=" O LEU D1009 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N GLU D1014 " --> pdb=" O ILE D1010 " (cutoff:3.500A) Processing helix chain 'K' and resid 69 through 74 removed outlier: 3.754A pdb=" N GLY K 73 " --> pdb=" O SER K 69 " (cutoff:3.500A) Processing helix chain 'K' and resid 291 through 301 Processing helix chain 'K' and resid 362 through 368 removed outlier: 3.645A pdb=" N TYR K 366 " --> pdb=" O TYR K 362 " (cutoff:3.500A) Processing helix chain 'K' and resid 380 through 384 removed outlier: 3.616A pdb=" N LEU K 384 " --> pdb=" O PRO K 381 " (cutoff:3.500A) Processing helix chain 'K' and resid 402 through 405 removed outlier: 4.208A pdb=" N ARG K 405 " --> pdb=" O ASP K 402 " (cutoff:3.500A) No H-bonds generated for 'chain 'K' and resid 402 through 405' Processing helix chain 'K' and resid 413 through 419 Processing helix chain 'K' and resid 435 through 440 removed outlier: 3.821A pdb=" N SER K 440 " --> pdb=" O ASN K 436 " (cutoff:3.500A) Processing helix chain 'K' and resid 499 through 502 Processing helix chain 'K' and resid 734 through 740 Processing helix chain 'K' and resid 743 through 752 removed outlier: 4.276A pdb=" N GLN K 752 " --> pdb=" O ASN K 748 " (cutoff:3.500A) Processing helix chain 'K' and resid 756 through 780 removed outlier: 3.860A pdb=" N LEU K 760 " --> pdb=" O PHE K 756 " (cutoff:3.500A) removed outlier: 3.988A pdb=" N ASP K 772 " --> pdb=" O ALA K 768 " (cutoff:3.500A) Processing helix chain 'K' and resid 813 through 824 Processing helix chain 'K' and resid 825 through 827 No H-bonds generated for 'chain 'K' and resid 825 through 827' Processing helix chain 'K' and resid 863 through 882 removed outlier: 3.789A pdb=" N ILE K 867 " --> pdb=" O THR K 863 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N ALA K 868 " --> pdb=" O ASP K 864 " (cutoff:3.500A) Processing helix chain 'K' and resid 883 through 887 Processing helix chain 'K' and resid 894 through 905 Processing helix chain 'K' and resid 910 through 937 removed outlier: 3.523A pdb=" N TYR K 914 " --> pdb=" O GLN K 910 " (cutoff:3.500A) removed outlier: 6.949A pdb=" N LYS K 918 " --> pdb=" O TYR K 914 " (cutoff:3.500A) removed outlier: 6.386A pdb=" N LEU K 919 " --> pdb=" O GLU K 915 " (cutoff:3.500A) removed outlier: 3.879A pdb=" N GLN K 932 " --> pdb=" O ILE K 928 " (cutoff:3.500A) removed outlier: 3.829A pdb=" N ASP K 933 " --> pdb=" O GLY K 929 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N SER K 937 " --> pdb=" O ASP K 933 " (cutoff:3.500A) Processing helix chain 'K' and resid 942 through 962 removed outlier: 3.703A pdb=" N VAL K 948 " --> pdb=" O LYS K 944 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N VAL K 949 " --> pdb=" O LEU K 945 " (cutoff:3.500A) Processing helix chain 'K' and resid 963 through 965 No H-bonds generated for 'chain 'K' and resid 963 through 965' Processing helix chain 'K' and resid 973 through 980 Processing helix chain 'K' and resid 982 through 1030 removed outlier: 4.908A pdb=" N VAL K 988 " --> pdb=" O PRO K 984 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N ALA K1013 " --> pdb=" O LEU K1009 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N GLU K1014 " --> pdb=" O ILE K1010 " (cutoff:3.500A) Processing helix chain 'A' and resid 69 through 73 removed outlier: 3.553A pdb=" N ASN A 72 " --> pdb=" O SER A 69 " (cutoff:3.500A) Processing helix chain 'A' and resid 291 through 300 Processing helix chain 'A' and resid 335 through 340 Processing helix chain 'A' and resid 361 through 368 removed outlier: 3.501A pdb=" N ASN A 367 " --> pdb=" O VAL A 364 " (cutoff:3.500A) Processing helix chain 'A' and resid 380 through 384 removed outlier: 3.518A pdb=" N LYS A 383 " --> pdb=" O SER A 380 " (cutoff:3.500A) removed outlier: 4.011A pdb=" N LEU A 384 " --> pdb=" O PRO A 381 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 380 through 384' Processing helix chain 'A' and resid 401 through 408 removed outlier: 4.135A pdb=" N ARG A 405 " --> pdb=" O GLY A 401 " (cutoff:3.500A) removed outlier: 4.124A pdb=" N ALA A 408 " --> pdb=" O VAL A 404 " (cutoff:3.500A) Processing helix chain 'A' and resid 413 through 420 Processing helix chain 'A' and resid 499 through 503 Processing helix chain 'A' and resid 616 through 621 Processing helix chain 'A' and resid 734 through 740 removed outlier: 3.626A pdb=" N CYS A 740 " --> pdb=" O THR A 736 " (cutoff:3.500A) Processing helix chain 'A' and resid 743 through 751 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 757 through 780 removed outlier: 3.671A pdb=" N THR A 775 " --> pdb=" O GLN A 771 " (cutoff:3.500A) Processing helix chain 'A' and resid 813 through 824 Processing helix chain 'A' and resid 846 through 852 Processing helix chain 'A' and resid 863 through 881 removed outlier: 3.625A pdb=" N ILE A 867 " --> pdb=" O THR A 863 " (cutoff:3.500A) Processing helix chain 'A' and resid 883 through 887 Processing helix chain 'A' and resid 894 through 905 Processing helix chain 'A' and resid 910 through 937 removed outlier: 6.969A pdb=" N LYS A 918 " --> pdb=" O TYR A 914 " (cutoff:3.500A) removed outlier: 6.363A pdb=" N LEU A 919 " --> pdb=" O GLU A 915 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N GLN A 932 " --> pdb=" O ILE A 928 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N ASP A 933 " --> pdb=" O GLY A 929 " (cutoff:3.500A) Processing helix chain 'A' and resid 942 through 962 removed outlier: 3.704A pdb=" N GLN A 946 " --> pdb=" O LEU A 942 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N VAL A 948 " --> pdb=" O LYS A 944 " (cutoff:3.500A) removed outlier: 3.864A pdb=" N VAL A 949 " --> pdb=" O LEU A 945 " (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 980 removed outlier: 3.550A pdb=" N ILE A 977 " --> pdb=" O VAL A 973 " (cutoff:3.500A) Processing helix chain 'A' and resid 982 through 1030 removed outlier: 4.406A pdb=" N VAL A 988 " --> pdb=" O PRO A 984 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N LEU A 993 " --> pdb=" O GLN A 989 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N GLU A1014 " --> pdb=" O ILE A1010 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'G' and resid 3 through 7 Processing sheet with id=AA2, first strand: chain 'G' and resid 11 through 12 removed outlier: 6.836A pdb=" N LEU G 34 " --> pdb=" O GLY G 50 " (cutoff:3.500A) removed outlier: 4.499A pdb=" N GLY G 50 " --> pdb=" O LEU G 34 " (cutoff:3.500A) removed outlier: 6.316A pdb=" N TRP G 36 " --> pdb=" O VAL G 48 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'G' and resid 11 through 12 removed outlier: 3.520A pdb=" N LYS G 98 " --> pdb=" O ILE G 114 " (cutoff:3.500A) removed outlier: 3.980A pdb=" N ILE G 114 " --> pdb=" O LYS G 98 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'G' and resid 132 through 136 removed outlier: 5.872A pdb=" N TYR G 188 " --> pdb=" O ASP G 156 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'G' and resid 143 through 144 removed outlier: 3.701A pdb=" N THR G 147 " --> pdb=" O SER G 144 " (cutoff:3.500A) removed outlier: 5.872A pdb=" N TYR G 188 " --> pdb=" O ASP G 156 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'G' and resid 163 through 166 removed outlier: 4.662A pdb=" N TYR G 206 " --> pdb=" O VAL G 223 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'H' and resid 4 through 6 Processing sheet with id=AA8, first strand: chain 'H' and resid 10 through 12 removed outlier: 6.490A pdb=" N LEU H 11 " --> pdb=" O ASP H 105 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N THR H 85 " --> pdb=" O GLN H 38 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N GLN H 89 " --> pdb=" O ALA H 34 " (cutoff:3.500A) removed outlier: 3.894A pdb=" N ALA H 34 " --> pdb=" O GLN H 89 " (cutoff:3.500A) removed outlier: 6.920A pdb=" N VAL H 33 " --> pdb=" O TYR H 49 " (cutoff:3.500A) removed outlier: 5.097A pdb=" N TYR H 49 " --> pdb=" O VAL H 33 " (cutoff:3.500A) removed outlier: 6.998A pdb=" N TRP H 35 " --> pdb=" O LEU H 47 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'H' and resid 114 through 118 removed outlier: 4.772A pdb=" N SER H 131 " --> pdb=" O LEU H 181 " (cutoff:3.500A) removed outlier: 7.074A pdb=" N LEU H 181 " --> pdb=" O SER H 131 " (cutoff:3.500A) removed outlier: 5.608A pdb=" N VAL H 133 " --> pdb=" O LEU H 179 " (cutoff:3.500A) removed outlier: 7.157A pdb=" N LEU H 179 " --> pdb=" O VAL H 133 " (cutoff:3.500A) removed outlier: 5.333A pdb=" N LEU H 135 " --> pdb=" O SER H 177 " (cutoff:3.500A) removed outlier: 7.032A pdb=" N SER H 177 " --> pdb=" O LEU H 135 " (cutoff:3.500A) removed outlier: 4.732A pdb=" N ASN H 137 " --> pdb=" O LEU H 175 " (cutoff:3.500A) removed outlier: 6.654A pdb=" N LEU H 175 " --> pdb=" O ASN H 137 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'H' and resid 153 through 155 removed outlier: 4.394A pdb=" N TRP H 148 " --> pdb=" O GLN H 155 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 3 through 7 removed outlier: 3.598A pdb=" N SER B 78 " --> pdb=" O ASP B 73 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N ASP B 73 " --> pdb=" O SER B 78 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 11 through 12 removed outlier: 6.225A pdb=" N ARG B 38 " --> pdb=" O TRP B 47 " (cutoff:3.500A) removed outlier: 5.881A pdb=" N TRP B 47 " --> pdb=" O ARG B 38 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'B' and resid 132 through 136 removed outlier: 3.639A pdb=" N ASP B 156 " --> pdb=" O TYR B 188 " (cutoff:3.500A) removed outlier: 6.673A pdb=" N TYR B 188 " --> pdb=" O ASP B 156 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'B' and resid 143 through 144 removed outlier: 3.639A pdb=" N ASP B 156 " --> pdb=" O TYR B 188 " (cutoff:3.500A) removed outlier: 6.673A pdb=" N TYR B 188 " --> pdb=" O ASP B 156 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'B' and resid 163 through 166 removed outlier: 3.777A pdb=" N THR B 163 " --> pdb=" O ASN B 211 " (cutoff:3.500A) removed outlier: 4.330A pdb=" N TYR B 206 " --> pdb=" O VAL B 223 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'C' and resid 4 through 6 removed outlier: 3.593A pdb=" N CYS C 23 " --> pdb=" O PHE C 71 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N PHE C 71 " --> pdb=" O CYS C 23 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'C' and resid 10 through 12 removed outlier: 6.132A pdb=" N LEU C 11 " --> pdb=" O ASP C 105 " (cutoff:3.500A) removed outlier: 7.568A pdb=" N VAL C 33 " --> pdb=" O TYR C 49 " (cutoff:3.500A) removed outlier: 5.367A pdb=" N TYR C 49 " --> pdb=" O VAL C 33 " (cutoff:3.500A) removed outlier: 6.854A pdb=" N TRP C 35 " --> pdb=" O LEU C 47 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'C' and resid 114 through 118 removed outlier: 5.476A pdb=" N TYR C 173 " --> pdb=" O ASN C 138 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'C' and resid 153 through 155 removed outlier: 4.374A pdb=" N TRP C 148 " --> pdb=" O GLN C 155 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N LYS C 207 " --> pdb=" O CYS C 194 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'E' and resid 4 through 5 removed outlier: 3.665A pdb=" N ALA E 19 " --> pdb=" O ILE E 76 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N ASP E 71 " --> pdb=" O SER E 68 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'E' and resid 54 through 55 removed outlier: 6.393A pdb=" N TRP E 36 " --> pdb=" O LEU E 48 " (cutoff:3.500A) removed outlier: 4.484A pdb=" N TYR E 50 " --> pdb=" O LEU E 34 " (cutoff:3.500A) removed outlier: 6.530A pdb=" N LEU E 34 " --> pdb=" O TYR E 50 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'E' and resid 115 through 119 removed outlier: 5.868A pdb=" N TYR E 174 " --> pdb=" O ASN E 139 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'E' and resid 154 through 156 removed outlier: 4.520A pdb=" N TRP E 149 " --> pdb=" O GLN E 156 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'F' and resid 3 through 6 removed outlier: 3.705A pdb=" N THR F 78 " --> pdb=" O ASP F 73 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N ASP F 73 " --> pdb=" O THR F 78 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'F' and resid 10 through 12 removed outlier: 6.706A pdb=" N VAL F 34 " --> pdb=" O TRP F 50 " (cutoff:3.500A) removed outlier: 4.404A pdb=" N TRP F 50 " --> pdb=" O VAL F 34 " (cutoff:3.500A) removed outlier: 6.255A pdb=" N TRP F 36 " --> pdb=" O ILE F 48 " (cutoff:3.500A) removed outlier: 3.883A pdb=" N TRP F 50 " --> pdb=" O ASP F 59 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N ASP F 59 " --> pdb=" O TRP F 50 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'F' and resid 10 through 12 Processing sheet with id=AC9, first strand: chain 'F' and resid 130 through 134 removed outlier: 6.034A pdb=" N TYR F 186 " --> pdb=" O ASP F 154 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'F' and resid 141 through 142 removed outlier: 6.034A pdb=" N TYR F 186 " --> pdb=" O ASP F 154 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'F' and resid 161 through 164 removed outlier: 3.652A pdb=" N CYS F 206 " --> pdb=" O LYS F 219 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'I' and resid 3 through 7 removed outlier: 3.728A pdb=" N LEU I 81 " --> pdb=" O LEU I 20 " (cutoff:3.500A) removed outlier: 3.927A pdb=" N SER I 78 " --> pdb=" O ASP I 73 " (cutoff:3.500A) removed outlier: 3.853A pdb=" N ASP I 73 " --> pdb=" O SER I 78 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'I' and resid 10 through 12 removed outlier: 6.361A pdb=" N GLY I 10 " --> pdb=" O THR I 122 " (cutoff:3.500A) removed outlier: 7.027A pdb=" N LEU I 34 " --> pdb=" O GLY I 50 " (cutoff:3.500A) removed outlier: 4.638A pdb=" N GLY I 50 " --> pdb=" O LEU I 34 " (cutoff:3.500A) removed outlier: 6.509A pdb=" N TRP I 36 " --> pdb=" O VAL I 48 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N GLY I 50 " --> pdb=" O GLY I 59 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N GLY I 59 " --> pdb=" O GLY I 50 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'I' and resid 10 through 12 removed outlier: 6.361A pdb=" N GLY I 10 " --> pdb=" O THR I 122 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N LYS I 98 " --> pdb=" O ILE I 114 " (cutoff:3.500A) removed outlier: 3.903A pdb=" N ILE I 114 " --> pdb=" O LYS I 98 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'I' and resid 132 through 136 removed outlier: 6.042A pdb=" N TYR I 188 " --> pdb=" O ASP I 156 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'I' and resid 143 through 144 removed outlier: 6.042A pdb=" N TYR I 188 " --> pdb=" O ASP I 156 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'I' and resid 163 through 166 removed outlier: 4.553A pdb=" N TYR I 206 " --> pdb=" O VAL I 223 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'J' and resid 5 through 6 removed outlier: 3.708A pdb=" N LEU J 73 " --> pdb=" O VAL J 21 " (cutoff:3.500A) removed outlier: 4.222A pdb=" N CYS J 23 " --> pdb=" O PHE J 71 " (cutoff:3.500A) removed outlier: 4.512A pdb=" N PHE J 71 " --> pdb=" O CYS J 23 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'J' and resid 10 through 12 removed outlier: 6.314A pdb=" N LEU J 11 " --> pdb=" O ASP J 105 " (cutoff:3.500A) removed outlier: 7.134A pdb=" N VAL J 33 " --> pdb=" O TYR J 49 " (cutoff:3.500A) removed outlier: 5.243A pdb=" N TYR J 49 " --> pdb=" O VAL J 33 " (cutoff:3.500A) removed outlier: 6.921A pdb=" N TRP J 35 " --> pdb=" O LEU J 47 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'J' and resid 114 through 118 Processing sheet with id=AE3, first strand: chain 'J' and resid 153 through 155 removed outlier: 4.463A pdb=" N TRP J 148 " --> pdb=" O GLN J 155 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'D' and resid 28 through 30 Processing sheet with id=AE5, first strand: chain 'D' and resid 36 through 37 removed outlier: 7.292A pdb=" N VAL D 36 " --> pdb=" O LEU D 220 " (cutoff:3.500A) removed outlier: 6.028A pdb=" N SER D 200 " --> pdb=" O PRO D 222 " (cutoff:3.500A) removed outlier: 3.919A pdb=" N VAL D 224 " --> pdb=" O ILE D 198 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N LYS D 190 " --> pdb=" O LYS D 197 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N TYR D 199 " --> pdb=" O VAL D 188 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N LYS D 201 " --> pdb=" O GLU D 186 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'D' and resid 50 through 55 removed outlier: 3.815A pdb=" N GLN D 268 " --> pdb=" O PHE D 55 " (cutoff:3.500A) removed outlier: 7.951A pdb=" N THR D 271 " --> pdb=" O ASP D 287 " (cutoff:3.500A) removed outlier: 5.484A pdb=" N ASP D 287 " --> pdb=" O THR D 271 " (cutoff:3.500A) removed outlier: 6.845A pdb=" N LEU D 273 " --> pdb=" O ALA D 285 " (cutoff:3.500A) removed outlier: 4.661A pdb=" N ALA D 285 " --> pdb=" O LEU D 273 " (cutoff:3.500A) removed outlier: 7.378A pdb=" N LYS D 275 " --> pdb=" O THR D 283 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'D' and resid 66 through 67 Processing sheet with id=AE8, first strand: chain 'D' and resid 82 through 83 removed outlier: 3.512A pdb=" N GLY D 105 " --> pdb=" O ARG D 234 " (cutoff:3.500A) removed outlier: 3.942A pdb=" N PHE D 104 " --> pdb=" O LEU D 115 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N LEU D 115 " --> pdb=" O PHE D 104 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N SER D 114 " --> pdb=" O CYS D 129 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N PHE D 163 " --> pdb=" O VAL D 128 " (cutoff:3.500A) removed outlier: 7.251A pdb=" N GLU D 130 " --> pdb=" O CYS D 161 " (cutoff:3.500A) removed outlier: 6.152A pdb=" N CYS D 161 " --> pdb=" O GLU D 130 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'D' and resid 99 through 100 removed outlier: 3.740A pdb=" N ARG D 100 " --> pdb=" O LEU D 238 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'D' and resid 308 through 316 removed outlier: 3.511A pdb=" N THR D 312 " --> pdb=" O VAL D 592 " (cutoff:3.500A) removed outlier: 7.368A pdb=" N VAL D 592 " --> pdb=" O THR D 312 " (cutoff:3.500A) removed outlier: 4.888A pdb=" N ASN D 314 " --> pdb=" O GLY D 590 " (cutoff:3.500A) removed outlier: 6.791A pdb=" N GLY D 590 " --> pdb=" O ASN D 314 " (cutoff:3.500A) removed outlier: 4.416A pdb=" N GLY D 591 " --> pdb=" O GLN D 610 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'D' and resid 322 through 323 removed outlier: 3.631A pdb=" N THR D 550 " --> pdb=" O ASP D 583 " (cutoff:3.500A) removed outlier: 5.361A pdb=" N ASP D 571 " --> pdb=" O ILE D 584 " (cutoff:3.500A) removed outlier: 6.759A pdb=" N GLY D 563 " --> pdb=" O ASP D 571 " (cutoff:3.500A) removed outlier: 3.916A pdb=" N PHE A 43 " --> pdb=" O PHE D 562 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'D' and resid 351 through 355 removed outlier: 3.829A pdb=" N ASN D 351 " --> pdb=" O SER D 396 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N SER D 396 " --> pdb=" O ASN D 351 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N VAL D 392 " --> pdb=" O ILE D 355 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'D' and resid 449 through 451 Processing sheet with id=AF5, first strand: chain 'D' and resid 470 through 471 Processing sheet with id=AF6, first strand: chain 'D' and resid 651 through 652 removed outlier: 5.951A pdb=" N GLU D 651 " --> pdb=" O ALA D 691 " (cutoff:3.500A) removed outlier: 8.457A pdb=" N THR D 693 " --> pdb=" O GLU D 651 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N SER D 688 " --> pdb=" O GLN D 672 " (cutoff:3.500A) removed outlier: 6.697A pdb=" N ILE D 667 " --> pdb=" O ILE D 663 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'D' and resid 698 through 699 removed outlier: 6.661A pdb=" N ALA D 698 " --> pdb=" O ILE A 785 " (cutoff:3.500A) No H-bonds generated for sheet with id=AF7 Processing sheet with id=AF8, first strand: chain 'D' and resid 709 through 710 removed outlier: 3.553A pdb=" N THR D1073 " --> pdb=" O SER D1094 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N ALA D1075 " --> pdb=" O PHE D1092 " (cutoff:3.500A) removed outlier: 4.600A pdb=" N PHE D1092 " --> pdb=" O ALA D1075 " (cutoff:3.500A) Processing sheet with id=AF9, first strand: chain 'D' and resid 714 through 725 removed outlier: 3.653A pdb=" N MET D1047 " --> pdb=" O VAL D1062 " (cutoff:3.500A) removed outlier: 6.012A pdb=" N TYR D1064 " --> pdb=" O HIS D1045 " (cutoff:3.500A) removed outlier: 5.911A pdb=" N HIS D1045 " --> pdb=" O TYR D1064 " (cutoff:3.500A) Processing sheet with id=AG1, first strand: chain 'D' and resid 730 through 733 removed outlier: 4.696A pdb=" N LYS D 730 " --> pdb=" O LEU D 858 " (cutoff:3.500A) Processing sheet with id=AG2, first strand: chain 'D' and resid 784 through 785 Processing sheet with id=AG3, first strand: chain 'D' and resid 1117 through 1122 removed outlier: 4.755A pdb=" N ALA D1084 " --> pdb=" O SER D1120 " (cutoff:3.500A) Processing sheet with id=AG4, first strand: chain 'K' and resid 28 through 30 Processing sheet with id=AG5, first strand: chain 'K' and resid 36 through 37 removed outlier: 6.881A pdb=" N VAL K 36 " --> pdb=" O LEU K 220 " (cutoff:3.500A) No H-bonds generated for sheet with id=AG5 Processing sheet with id=AG6, first strand: chain 'K' and resid 48 through 55 removed outlier: 3.704A pdb=" N PHE K 55 " --> pdb=" O GLN K 268 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N GLN K 268 " --> pdb=" O PHE K 55 " (cutoff:3.500A) removed outlier: 7.835A pdb=" N THR K 271 " --> pdb=" O ASP K 287 " (cutoff:3.500A) removed outlier: 5.433A pdb=" N ASP K 287 " --> pdb=" O THR K 271 " (cutoff:3.500A) removed outlier: 6.680A pdb=" N LEU K 273 " --> pdb=" O ALA K 285 " (cutoff:3.500A) removed outlier: 4.407A pdb=" N ALA K 285 " --> pdb=" O LEU K 273 " (cutoff:3.500A) removed outlier: 7.212A pdb=" N LYS K 275 " --> pdb=" O THR K 283 " (cutoff:3.500A) Processing sheet with id=AG7, first strand: chain 'K' and resid 66 through 67 Processing sheet with id=AG8, first strand: chain 'K' and resid 82 through 83 Processing sheet with id=AG9, first strand: chain 'K' and resid 87 through 88 removed outlier: 3.771A pdb=" N LYS K 190 " --> pdb=" O LYS K 197 " (cutoff:3.500A) removed outlier: 3.888A pdb=" N VAL K 224 " --> pdb=" O ILE K 198 " (cutoff:3.500A) Processing sheet with id=AH1, first strand: chain 'K' and resid 126 through 133 removed outlier: 3.973A pdb=" N TYR K 165 " --> pdb=" O ILE K 126 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N VAL K 128 " --> pdb=" O PHE K 163 " (cutoff:3.500A) removed outlier: 4.411A pdb=" N PHE K 163 " --> pdb=" O VAL K 128 " (cutoff:3.500A) removed outlier: 7.688A pdb=" N GLU K 130 " --> pdb=" O CYS K 161 " (cutoff:3.500A) removed outlier: 7.201A pdb=" N CYS K 161 " --> pdb=" O GLU K 130 " (cutoff:3.500A) removed outlier: 8.058A pdb=" N GLN K 132 " --> pdb=" O ASN K 159 " (cutoff:3.500A) removed outlier: 9.132A pdb=" N ASN K 159 " --> pdb=" O GLN K 132 " (cutoff:3.500A) Processing sheet with id=AH2, first strand: chain 'K' and resid 308 through 316 removed outlier: 7.271A pdb=" N VAL K 592 " --> pdb=" O THR K 312 " (cutoff:3.500A) removed outlier: 4.886A pdb=" N ASN K 314 " --> pdb=" O GLY K 590 " (cutoff:3.500A) removed outlier: 6.946A pdb=" N GLY K 590 " --> pdb=" O ASN K 314 " (cutoff:3.500A) removed outlier: 4.000A pdb=" N GLY K 591 " --> pdb=" O GLN K 610 " (cutoff:3.500A) Processing sheet with id=AH3, first strand: chain 'K' and resid 322 through 323 removed outlier: 3.890A pdb=" N PHE K 540 " --> pdb=" O LEU K 543 " (cutoff:3.500A) Processing sheet with id=AH4, first strand: chain 'K' and resid 351 through 355 removed outlier: 3.914A pdb=" N ASN K 351 " --> pdb=" O SER K 396 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N SER K 396 " --> pdb=" O ASN K 351 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N LYS K 353 " --> pdb=" O ALA K 394 " (cutoff:3.500A) removed outlier: 3.963A pdb=" N ALA K 394 " --> pdb=" O LYS K 353 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N ILE K 355 " --> pdb=" O VAL K 392 " (cutoff:3.500A) removed outlier: 4.208A pdb=" N VAL K 392 " --> pdb=" O ILE K 355 " (cutoff:3.500A) Processing sheet with id=AH5, first strand: chain 'K' and resid 449 through 451 removed outlier: 3.571A pdb=" N TYR K 450 " --> pdb=" O ARG K 490 " (cutoff:3.500A) Processing sheet with id=AH6, first strand: chain 'K' and resid 470 through 471 Processing sheet with id=AH7, first strand: chain 'K' and resid 550 through 551 removed outlier: 3.777A pdb=" N THR K 550 " --> pdb=" O ASP K 583 " (cutoff:3.500A) Processing sheet with id=AH8, first strand: chain 'K' and resid 651 through 652 removed outlier: 6.038A pdb=" N GLU K 651 " --> pdb=" O ALA K 691 " (cutoff:3.500A) removed outlier: 8.693A pdb=" N THR K 693 " --> pdb=" O GLU K 651 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N TYR K 692 " --> pdb=" O CYS K 668 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N ILE K 667 " --> pdb=" O ILE K 663 " (cutoff:3.500A) Processing sheet with id=AH9, first strand: chain 'K' and resid 709 through 725 removed outlier: 6.364A pdb=" N ALA K 710 " --> pdb=" O ASN K1071 " (cutoff:3.500A) removed outlier: 6.979A pdb=" N ASN K1071 " --> pdb=" O ALA K 710 " (cutoff:3.500A) removed outlier: 6.217A pdb=" N GLU K1069 " --> pdb=" O PRO K 712 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N MET K1047 " --> pdb=" O VAL K1062 " (cutoff:3.500A) removed outlier: 6.126A pdb=" N TYR K1064 " --> pdb=" O HIS K1045 " (cutoff:3.500A) removed outlier: 6.025A pdb=" N HIS K1045 " --> pdb=" O TYR K1064 " (cutoff:3.500A) Processing sheet with id=AI1, first strand: chain 'K' and resid 709 through 725 removed outlier: 6.364A pdb=" N ALA K 710 " --> pdb=" O ASN K1071 " (cutoff:3.500A) removed outlier: 6.979A pdb=" N ASN K1071 " --> pdb=" O ALA K 710 " (cutoff:3.500A) removed outlier: 6.217A pdb=" N GLU K1069 " --> pdb=" O PRO K 712 " (cutoff:3.500A) removed outlier: 3.908A pdb=" N THR K1073 " --> pdb=" O SER K1094 " (cutoff:3.500A) Processing sheet with id=AI2, first strand: chain 'K' and resid 730 through 733 removed outlier: 4.478A pdb=" N LYS K 730 " --> pdb=" O LEU K 858 " (cutoff:3.500A) Processing sheet with id=AI3, first strand: chain 'K' and resid 784 through 785 Processing sheet with id=AI4, first strand: chain 'K' and resid 1117 through 1122 removed outlier: 4.547A pdb=" N ALA K1084 " --> pdb=" O SER K1120 " (cutoff:3.500A) Processing sheet with id=AI5, first strand: chain 'A' and resid 28 through 30 Processing sheet with id=AI6, first strand: chain 'A' and resid 36 through 37 removed outlier: 7.302A pdb=" N VAL A 36 " --> pdb=" O LEU A 220 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N GLU A 221 " --> pdb=" O SER A 200 " (cutoff:3.500A) removed outlier: 6.941A pdb=" N ILE A 198 " --> pdb=" O LEU A 223 " (cutoff:3.500A) removed outlier: 4.438A pdb=" N ASP A 225 " --> pdb=" O PHE A 196 " (cutoff:3.500A) removed outlier: 6.426A pdb=" N PHE A 196 " --> pdb=" O ASP A 225 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N LYS A 201 " --> pdb=" O GLU A 186 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N VAL A 88 " --> pdb=" O PHE A 189 " (cutoff:3.500A) Processing sheet with id=AI7, first strand: chain 'A' and resid 48 through 55 removed outlier: 3.524A pdb=" N PHE A 55 " --> pdb=" O GLN A 268 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N GLN A 268 " --> pdb=" O PHE A 55 " (cutoff:3.500A) removed outlier: 3.955A pdb=" N ASP A 284 " --> pdb=" O LYS A 275 " (cutoff:3.500A) Processing sheet with id=AI8, first strand: chain 'A' and resid 66 through 67 Processing sheet with id=AI9, first strand: chain 'A' and resid 82 through 83 removed outlier: 3.613A pdb=" N GLY A 105 " --> pdb=" O ARG A 234 " (cutoff:3.500A) Processing sheet with id=AJ1, first strand: chain 'A' and resid 113 through 114 removed outlier: 3.524A pdb=" N CYS A 129 " --> pdb=" O SER A 114 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N PHE A 163 " --> pdb=" O VAL A 128 " (cutoff:3.500A) removed outlier: 7.754A pdb=" N GLU A 130 " --> pdb=" O CYS A 161 " (cutoff:3.500A) removed outlier: 7.001A pdb=" N CYS A 161 " --> pdb=" O GLU A 130 " (cutoff:3.500A) removed outlier: 10.449A pdb=" N GLN A 132 " --> pdb=" O ASN A 159 " (cutoff:3.500A) removed outlier: 9.285A pdb=" N ASN A 159 " --> pdb=" O GLN A 132 " (cutoff:3.500A) Processing sheet with id=AJ2, first strand: chain 'A' and resid 308 through 310 Processing sheet with id=AJ3, first strand: chain 'A' and resid 321 through 322 removed outlier: 6.544A pdb=" N GLU A 321 " --> pdb=" O ASN A 537 " (cutoff:3.500A) removed outlier: 8.706A pdb=" N ASN A 539 " --> pdb=" O GLU A 321 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N GLY A 547 " --> pdb=" O VAL A 536 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N THR A 585 " --> pdb=" O VAL A 548 " (cutoff:3.500A) Processing sheet with id=AJ4, first strand: chain 'A' and resid 351 through 355 removed outlier: 3.712A pdb=" N ASN A 351 " --> pdb=" O SER A 396 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N SER A 396 " --> pdb=" O ASN A 351 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N VAL A 392 " --> pdb=" O ILE A 355 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N ASN A 391 " --> pdb=" O GLU A 513 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N GLY A 428 " --> pdb=" O TYR A 377 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N TYR A 377 " --> pdb=" O GLY A 428 " (cutoff:3.500A) Processing sheet with id=AJ5, first strand: chain 'A' and resid 449 through 451 Processing sheet with id=AJ6, first strand: chain 'A' and resid 651 through 652 removed outlier: 6.074A pdb=" N GLU A 651 " --> pdb=" O ALA A 691 " (cutoff:3.500A) removed outlier: 8.759A pdb=" N THR A 693 " --> pdb=" O GLU A 651 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N GLN A 672 " --> pdb=" O SER A 688 " (cutoff:3.500A) removed outlier: 6.601A pdb=" N ILE A 667 " --> pdb=" O ILE A 663 " (cutoff:3.500A) Processing sheet with id=AJ7, first strand: chain 'A' and resid 709 through 710 Processing sheet with id=AJ8, first strand: chain 'A' and resid 714 through 725 removed outlier: 3.723A pdb=" N MET A1047 " --> pdb=" O VAL A1062 " (cutoff:3.500A) removed outlier: 6.114A pdb=" N TYR A1064 " --> pdb=" O HIS A1045 " (cutoff:3.500A) removed outlier: 6.083A pdb=" N HIS A1045 " --> pdb=" O TYR A1064 " (cutoff:3.500A) Processing sheet with id=AJ9, first strand: chain 'A' and resid 730 through 733 removed outlier: 4.608A pdb=" N LYS A 730 " --> pdb=" O LEU A 858 " (cutoff:3.500A) Processing sheet with id=AK1, first strand: chain 'A' and resid 1117 through 1119 Processing sheet with id=AK2, first strand: chain 'A' and resid 1091 through 1094 1382 hydrogen bonds defined for protein. 3621 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: 12.13 Time building geometry restraints manager: 4.21 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.33: 7275 1.33 - 1.46: 12771 1.46 - 1.59: 20763 1.59 - 1.71: 0 1.71 - 1.84: 202 Bond restraints: 41011 Sorted by residual: bond pdb=" C1 NAG S 1 " pdb=" O5 NAG S 1 " ideal model delta sigma weight residual 1.406 1.499 -0.093 2.00e-02 2.50e+03 2.17e+01 bond pdb=" C1 NAG Y 2 " pdb=" O5 NAG Y 2 " ideal model delta sigma weight residual 1.406 1.499 -0.093 2.00e-02 2.50e+03 2.16e+01 bond pdb=" C GLU B 160 " pdb=" N PRO B 161 " ideal model delta sigma weight residual 1.333 1.370 -0.037 1.01e-02 9.80e+03 1.31e+01 bond pdb=" N VAL H 96 " pdb=" CA VAL H 96 " ideal model delta sigma weight residual 1.458 1.497 -0.039 1.14e-02 7.69e+03 1.19e+01 bond pdb=" N ASP A 140 " pdb=" CA ASP A 140 " ideal model delta sigma weight residual 1.458 1.496 -0.038 1.19e-02 7.06e+03 1.03e+01 ... (remaining 41006 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.49: 54849 2.49 - 4.98: 856 4.98 - 7.48: 65 7.48 - 9.97: 8 9.97 - 12.46: 4 Bond angle restraints: 55782 Sorted by residual: angle pdb=" N PRO C 95 " pdb=" CA PRO C 95 " pdb=" C PRO C 95 " ideal model delta sigma weight residual 112.33 101.62 10.71 1.87e+00 2.86e-01 3.28e+01 angle pdb=" N ILE F 48 " pdb=" CA ILE F 48 " pdb=" C ILE F 48 " ideal model delta sigma weight residual 113.47 108.07 5.40 1.01e+00 9.80e-01 2.86e+01 angle pdb=" N PRO I 161 " pdb=" CA PRO I 161 " pdb=" C PRO I 161 " ideal model delta sigma weight residual 112.47 122.94 -10.47 2.06e+00 2.36e-01 2.58e+01 angle pdb=" CA GLU B 160 " pdb=" C GLU B 160 " pdb=" N PRO B 161 " ideal model delta sigma weight residual 118.44 126.48 -8.04 1.59e+00 3.96e-01 2.55e+01 angle pdb=" N GLU A 151 " pdb=" CA GLU A 151 " pdb=" C GLU A 151 " ideal model delta sigma weight residual 113.43 107.12 6.31 1.26e+00 6.30e-01 2.51e+01 ... (remaining 55777 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.91: 21898 17.91 - 35.82: 1644 35.82 - 53.73: 318 53.73 - 71.65: 64 71.65 - 89.56: 41 Dihedral angle restraints: 23965 sinusoidal: 9278 harmonic: 14687 Sorted by residual: dihedral pdb=" CB CYS A 837 " pdb=" SG CYS A 837 " pdb=" SG CYS A 848 " pdb=" CB CYS A 848 " ideal model delta sinusoidal sigma weight residual 93.00 177.46 -84.46 1 1.00e+01 1.00e-02 8.67e+01 dihedral pdb=" CB CYS A 288 " pdb=" SG CYS A 288 " pdb=" SG CYS A 298 " pdb=" CB CYS A 298 " ideal model delta sinusoidal sigma weight residual 93.00 162.51 -69.51 1 1.00e+01 1.00e-02 6.24e+01 dihedral pdb=" CB CYS K1079 " pdb=" SG CYS K1079 " pdb=" SG CYS K1123 " pdb=" CB CYS K1123 " ideal model delta sinusoidal sigma weight residual -86.00 -32.53 -53.47 1 1.00e+01 1.00e-02 3.89e+01 ... (remaining 23962 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.130: 6370 0.130 - 0.260: 86 0.260 - 0.390: 13 0.390 - 0.519: 1 0.519 - 0.649: 1 Chirality restraints: 6471 Sorted by residual: chirality pdb=" CA TYR J 94 " pdb=" N TYR J 94 " pdb=" C TYR J 94 " pdb=" CB TYR J 94 " both_signs ideal model delta sigma weight residual False 2.51 1.86 0.65 2.00e-01 2.50e+01 1.05e+01 chirality pdb=" C1 NAG M 1 " pdb=" ND2 ASN D 340 " pdb=" C2 NAG M 1 " pdb=" O5 NAG M 1 " both_signs ideal model delta sigma weight residual False -2.40 -1.95 -0.45 2.00e-01 2.50e+01 5.10e+00 chirality pdb=" C1 NAG K1310 " pdb=" ND2 ASN K 120 " pdb=" C2 NAG K1310 " pdb=" O5 NAG K1310 " both_signs ideal model delta sigma weight residual False -2.40 -2.05 -0.35 2.00e-01 2.50e+01 3.01e+00 ... (remaining 6468 not shown) Planarity restraints: 7159 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 NAG K1310 " -0.252 2.00e-02 2.50e+03 2.11e-01 5.59e+02 pdb=" C7 NAG K1310 " 0.065 2.00e-02 2.50e+03 pdb=" C8 NAG K1310 " -0.170 2.00e-02 2.50e+03 pdb=" N2 NAG K1310 " 0.356 2.00e-02 2.50e+03 pdb=" O7 NAG K1310 " 0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C GLU E 80 " -0.068 5.00e-02 4.00e+02 1.01e-01 1.64e+01 pdb=" N PRO E 81 " 0.175 5.00e-02 4.00e+02 pdb=" CA PRO E 81 " -0.051 5.00e-02 4.00e+02 pdb=" CD PRO E 81 " -0.056 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA LYS I 155 " -0.016 2.00e-02 2.50e+03 3.24e-02 1.05e+01 pdb=" C LYS I 155 " 0.056 2.00e-02 2.50e+03 pdb=" O LYS I 155 " -0.021 2.00e-02 2.50e+03 pdb=" N ASP I 156 " -0.019 2.00e-02 2.50e+03 ... (remaining 7156 not shown) Histogram of nonbonded interaction distances: 2.15 - 2.70: 1154 2.70 - 3.25: 38380 3.25 - 3.80: 60699 3.80 - 4.35: 77025 4.35 - 4.90: 130681 Nonbonded interactions: 307939 Sorted by model distance: nonbonded pdb=" NH2 ARG J 24 " pdb=" O PHE J 71 " model vdw 2.151 3.120 nonbonded pdb=" OH TYR D 89 " pdb=" OE1 GLU D 186 " model vdw 2.174 3.040 nonbonded pdb=" O GLN E 101 " pdb=" NH1 ARG F 44 " model vdw 2.205 3.120 nonbonded pdb=" O LEU A 290 " pdb=" OG1 THR A 629 " model vdw 2.206 3.040 nonbonded pdb=" O HIS I 101 " pdb=" ND1 HIS I 101 " model vdw 2.208 3.120 ... (remaining 307934 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 19 through 837 or resid 848 through 1306)) selection = (chain 'D' and (resid 19 through 837 or resid 848 through 1306)) selection = (chain 'K' and resid 19 through 1306) } ncs_group { reference = chain 'B' selection = chain 'G' selection = chain 'I' } ncs_group { reference = chain 'C' selection = chain 'H' selection = chain 'J' } ncs_group { reference = chain 'L' selection = chain 'M' selection = chain 'N' selection = chain 'O' selection = chain 'P' selection = chain 'Q' selection = chain 'R' selection = chain 'S' selection = chain 'T' selection = chain 'U' selection = chain 'V' selection = chain 'W' selection = chain 'Y' selection = chain 'Z' } ncs_group { reference = chain 'a' selection = chain 'b' } 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: 0.010 Normalize map: mean=0, sd=1: 1.840 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.030 Extract box with map and model: 0.550 Check model and map are aligned: 0.090 Set scattering table: 0.090 Process input model: 38.850 Find NCS groups from input model: 1.090 Set up NCS constraints: 0.120 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.220 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 43.900 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6764 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.093 41137 Z= 0.235 Angle : 0.745 20.284 56098 Z= 0.415 Chirality : 0.050 0.649 6471 Planarity : 0.005 0.211 7116 Dihedral : 13.453 89.557 14355 Min Nonbonded Distance : 2.151 Molprobity Statistics. All-atom Clashscore : 8.80 Ramachandran Plot: Outliers : 0.32 % Allowed : 5.50 % Favored : 94.18 % Rotamer: Outliers : 0.91 % Allowed : 0.89 % Favored : 98.19 % Cbeta Deviations : 0.02 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.44 (0.12), residues: 5015 helix: 1.36 (0.21), residues: 735 sheet: 0.48 (0.15), residues: 1318 loop : -1.13 (0.11), residues: 2962 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG E 18 TYR 0.029 0.001 TYR D 901 PHE 0.036 0.001 PHE K 163 TRP 0.023 0.001 TRP I 53 HIS 0.006 0.001 HIS G 35 Details of bonding type rmsd/Z covalent geometry : bond 0.00403 / 0.23 (41011) covalent geometry : angle 0.71341 / 0.41 (55782) SS BOND : bond 0.00285 / 0.21 ( 62) SS BOND : angle 0.69779 / 0.46 ( 124) hydrogen bonds : bond 0.23124 / 15.41 ( 1319) hydrogen bonds : angle 8.49211 / 5.89 ( 3621) link_ALPHA1-3 : bond 0.00418 / 0.22 ( 1) link_ALPHA1-3 : angle 1.53242 / 0.83 ( 3) link_BETA1-4 : bond 0.00843 / 0.47 ( 20) link_BETA1-4 : angle 2.79766 / 2.08 ( 60) link_NAG-ASN : bond 0.00674 / 0.42 ( 43) link_NAG-ASN : angle 4.16796 / 3.13 ( 129) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10030 Ramachandran restraints generated. 5015 Oldfield, 0 Emsley, 5015 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10030 Ramachandran restraints generated. 5015 Oldfield, 0 Emsley, 5015 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 350 residues out of total 4385 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 310 time to evaluate : 1.447 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 93 SER cc_start: 0.5995 (OUTLIER) cc_final: 0.5707 (p) REVERT: J 94 TYR cc_start: 0.7173 (OUTLIER) cc_final: 0.6573 (t80) REVERT: K 141 HIS cc_start: 0.5415 (OUTLIER) cc_final: 0.4750 (p90) REVERT: K 142 LYS cc_start: 0.4290 (OUTLIER) cc_final: 0.3776 (mmmt) REVERT: K 148 MET cc_start: 0.5914 (OUTLIER) cc_final: 0.5334 (ttp) outliers start: 40 outliers final: 10 residues processed: 346 average time/residue: 0.2477 time to fit residues: 141.9628 Evaluate side-chains 224 residues out of total 4385 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 209 time to evaluate : 1.614 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 93 SER Chi-restraints excluded: chain B residue 158 PHE Chi-restraints excluded: chain C residue 12 SER Chi-restraints excluded: chain C residue 96 VAL Chi-restraints excluded: chain C residue 108 ARG Chi-restraints excluded: chain C residue 140 TYR Chi-restraints excluded: chain J residue 94 TYR Chi-restraints excluded: chain D residue 143 ASN Chi-restraints excluded: chain D residue 526 LYS Chi-restraints excluded: chain D residue 529 ASN Chi-restraints excluded: chain K residue 141 HIS Chi-restraints excluded: chain K residue 142 LYS Chi-restraints excluded: chain K residue 146 SER Chi-restraints excluded: chain K residue 148 MET Chi-restraints excluded: chain A residue 242 HIS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 501 random chunks: chunk 432 optimal weight: 6.9990 chunk 197 optimal weight: 1.9990 chunk 388 optimal weight: 4.9990 chunk 455 optimal weight: 0.9980 chunk 215 optimal weight: 3.9990 chunk 20 optimal weight: 9.9990 chunk 132 optimal weight: 20.0000 chunk 494 optimal weight: 1.9990 chunk 261 optimal weight: 2.9990 chunk 248 optimal weight: 2.9990 chunk 207 optimal weight: 0.9990 overall best weight: 1.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 125 GLN I 35 HIS I 110 ASN D 85 ASN D 202 HIS D 357 ASN ** D 419 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 622 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 989 GLN K 801 GLN K 932 GLN A 79 ASN ** A 471 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 923 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4464 r_free = 0.4464 target = 0.156400 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 70)----------------| | r_work = 0.3624 r_free = 0.3624 target = 0.092698 restraints weight = 103510.386| |-----------------------------------------------------------------------------| r_work (start): 0.3435 rms_B_bonded: 4.78 r_work: 0.3281 rms_B_bonded: 4.85 restraints_weight: 0.5000 r_work (final): 0.3281 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7648 moved from start: 0.1197 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.061 41137 Z= 0.152 Angle : 0.650 19.161 56098 Z= 0.324 Chirality : 0.046 0.363 6471 Planarity : 0.004 0.066 7116 Dihedral : 4.740 54.974 5475 Min Nonbonded Distance : 2.347 Molprobity Statistics. All-atom Clashscore : 7.09 Ramachandran Plot: Outliers : 0.18 % Allowed : 5.70 % Favored : 94.12 % Rotamer: Outliers : 0.87 % Allowed : 6.56 % Favored : 92.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.44 (0.12), residues: 5015 helix: 1.37 (0.20), residues: 739 sheet: 0.43 (0.14), residues: 1402 loop : -1.15 (0.11), residues: 2874 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG E 30 TYR 0.029 0.002 TYR K 901 PHE 0.032 0.002 PHE K 163 TRP 0.013 0.001 TRP K 350 HIS 0.007 0.001 HIS D 622 Details of bonding type rmsd/Z covalent geometry : bond 0.00346 / 0.15 (41011) covalent geometry : angle 0.61835 / 0.32 (55782) SS BOND : bond 0.00497 / 0.38 ( 62) SS BOND : angle 0.95081 / 0.62 ( 124) hydrogen bonds : bond 0.04866 / 3.21 ( 1319) hydrogen bonds : angle 6.15393 / 4.26 ( 3621) link_ALPHA1-3 : bond 0.00413 / 0.22 ( 1) link_ALPHA1-3 : angle 1.48200 / 0.84 ( 3) link_BETA1-4 : bond 0.00764 / 0.40 ( 20) link_BETA1-4 : angle 2.38551 / 1.78 ( 60) link_NAG-ASN : bond 0.00618 / 0.39 ( 43) link_NAG-ASN : angle 3.88170 / 2.96 ( 129) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10030 Ramachandran restraints generated. 5015 Oldfield, 0 Emsley, 5015 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10030 Ramachandran restraints generated. 5015 Oldfield, 0 Emsley, 5015 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 265 residues out of total 4385 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 227 time to evaluate : 1.662 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 27 PHE cc_start: 0.6008 (p90) cc_final: 0.5780 (p90) REVERT: B 94 TYR cc_start: 0.4673 (m-10) cc_final: 0.4409 (m-10) REVERT: C 142 ARG cc_start: 0.5299 (tpt170) cc_final: 0.4234 (mpt180) REVERT: F 2 MET cc_start: 0.6443 (mtt) cc_final: 0.6228 (mmt) REVERT: F 74 MET cc_start: 0.8170 (mmp) cc_final: 0.7379 (mpp) REVERT: I 101 HIS cc_start: 0.6009 (t-90) cc_final: 0.5345 (t-90) REVERT: D 756 PHE cc_start: 0.7073 (t80) cc_final: 0.6849 (t80) REVERT: K 266 TYR cc_start: 0.7960 (m-80) cc_final: 0.7085 (m-80) REVERT: K 384 LEU cc_start: 0.8628 (mp) cc_final: 0.8396 (mp) REVERT: K 990 ILE cc_start: 0.7696 (OUTLIER) cc_final: 0.7452 (mt) REVERT: A 217 PHE cc_start: 0.7051 (m-80) cc_final: 0.6819 (t80) outliers start: 38 outliers final: 21 residues processed: 255 average time/residue: 0.2317 time to fit residues: 98.9730 Evaluate side-chains 218 residues out of total 4385 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 196 time to evaluate : 1.400 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 158 PHE Chi-restraints excluded: chain B residue 4 LEU Chi-restraints excluded: chain B residue 53 TRP Chi-restraints excluded: chain B residue 158 PHE Chi-restraints excluded: chain B residue 172 THR Chi-restraints excluded: chain C residue 5 THR Chi-restraints excluded: chain C residue 96 VAL Chi-restraints excluded: chain F residue 209 ASN Chi-restraints excluded: chain J residue 97 THR Chi-restraints excluded: chain J residue 166 GLN Chi-restraints excluded: chain D residue 143 ASN Chi-restraints excluded: chain D residue 527 SER Chi-restraints excluded: chain K residue 142 LYS Chi-restraints excluded: chain K residue 200 SER Chi-restraints excluded: chain K residue 569 THR Chi-restraints excluded: chain K residue 990 ILE Chi-restraints excluded: chain A residue 42 VAL Chi-restraints excluded: chain A residue 79 ASN Chi-restraints excluded: chain A residue 268 GLN Chi-restraints excluded: chain A residue 424 ASP Chi-restraints excluded: chain A residue 543 LEU Chi-restraints excluded: chain A residue 760 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 501 random chunks: chunk 2 optimal weight: 4.9990 chunk 320 optimal weight: 10.0000 chunk 42 optimal weight: 40.0000 chunk 185 optimal weight: 10.0000 chunk 300 optimal weight: 0.1980 chunk 217 optimal weight: 0.6980 chunk 254 optimal weight: 0.5980 chunk 77 optimal weight: 3.9990 chunk 157 optimal weight: 5.9990 chunk 265 optimal weight: 0.5980 chunk 445 optimal weight: 6.9990 overall best weight: 1.2182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 138 ASN E 101 GLN F 207 ASN ** D 419 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 168 GLN K 610 GLN K1068 GLN A 79 ASN A 144 ASN ** A 471 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 923 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4494 r_free = 0.4494 target = 0.155480 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3705 r_free = 0.3705 target = 0.096045 restraints weight = 115925.727| |-----------------------------------------------------------------------------| r_work (start): 0.3433 rms_B_bonded: 5.28 r_work: 0.3256 rms_B_bonded: 5.23 restraints_weight: 2.0000 r_work (final): 0.3256 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7764 moved from start: 0.1529 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.066 41137 Z= 0.119 Angle : 0.596 17.836 56098 Z= 0.295 Chirality : 0.045 0.344 6471 Planarity : 0.004 0.070 7116 Dihedral : 4.387 55.277 5451 Min Nonbonded Distance : 2.396 Molprobity Statistics. All-atom Clashscore : 6.23 Ramachandran Plot: Outliers : 0.16 % Allowed : 5.46 % Favored : 94.38 % Rotamer: Outliers : 1.10 % Allowed : 8.68 % Favored : 90.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.39 (0.12), residues: 5015 helix: 1.43 (0.20), residues: 741 sheet: 0.49 (0.14), residues: 1380 loop : -1.13 (0.11), residues: 2894 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A1104 TYR 0.020 0.001 TYR K 901 PHE 0.019 0.001 PHE D 131 TRP 0.015 0.001 TRP B 47 HIS 0.008 0.001 HIS K 141 Details of bonding type rmsd/Z covalent geometry : bond 0.00268 / 0.12 (41011) covalent geometry : angle 0.56539 / 0.29 (55782) SS BOND : bond 0.00330 / 0.24 ( 62) SS BOND : angle 0.83253 / 0.54 ( 124) hydrogen bonds : bond 0.04256 / 2.83 ( 1319) hydrogen bonds : angle 5.59562 / 3.87 ( 3621) link_ALPHA1-3 : bond 0.00457 / 0.24 ( 1) link_ALPHA1-3 : angle 1.40060 / 0.78 ( 3) link_BETA1-4 : bond 0.00770 / 0.41 ( 20) link_BETA1-4 : angle 2.31937 / 1.74 ( 60) link_NAG-ASN : bond 0.00607 / 0.38 ( 43) link_NAG-ASN : angle 3.61297 / 2.75 ( 129) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10030 Ramachandran restraints generated. 5015 Oldfield, 0 Emsley, 5015 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10030 Ramachandran restraints generated. 5015 Oldfield, 0 Emsley, 5015 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 268 residues out of total 4385 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 220 time to evaluate : 1.549 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 38 ARG cc_start: 0.6032 (ptt90) cc_final: 0.5747 (ptp90) REVERT: B 115 TRP cc_start: 0.5574 (m-10) cc_final: 0.5325 (m-90) REVERT: C 142 ARG cc_start: 0.5278 (tpt170) cc_final: 0.4336 (mpt180) REVERT: F 74 MET cc_start: 0.8396 (mmp) cc_final: 0.8094 (mpp) REVERT: I 101 HIS cc_start: 0.5166 (t-90) cc_final: 0.4647 (t-90) REVERT: D 375 LYS cc_start: 0.9068 (OUTLIER) cc_final: 0.8805 (ptmm) REVERT: D 391 ASN cc_start: 0.7869 (m-40) cc_final: 0.7640 (m110) REVERT: D 630 TRP cc_start: 0.7760 (m-10) cc_final: 0.7549 (m-10) REVERT: D 756 PHE cc_start: 0.6931 (t80) cc_final: 0.6710 (t80) REVERT: D 770 GLU cc_start: 0.8537 (tp30) cc_final: 0.8100 (tp30) REVERT: K 143 ASN cc_start: 0.6816 (OUTLIER) cc_final: 0.6233 (t0) REVERT: K 266 TYR cc_start: 0.8014 (m-80) cc_final: 0.7072 (m-80) REVERT: K 372 PHE cc_start: 0.4038 (m-80) cc_final: 0.3813 (m-80) REVERT: K 379 VAL cc_start: 0.7536 (t) cc_final: 0.7289 (p) REVERT: K 658 GLU cc_start: 0.8012 (tp30) cc_final: 0.7756 (tp30) REVERT: A 262 TYR cc_start: 0.8476 (p90) cc_final: 0.8269 (p90) REVERT: A 976 ASP cc_start: 0.8715 (OUTLIER) cc_final: 0.8449 (m-30) REVERT: A 982 ASP cc_start: 0.7616 (t0) cc_final: 0.7054 (t0) REVERT: A 985 GLU cc_start: 0.8506 (mp0) cc_final: 0.8171 (mp0) outliers start: 48 outliers final: 28 residues processed: 259 average time/residue: 0.2427 time to fit residues: 104.4495 Evaluate side-chains 224 residues out of total 4385 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 193 time to evaluate : 1.543 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 158 PHE Chi-restraints excluded: chain B residue 4 LEU Chi-restraints excluded: chain B residue 158 PHE Chi-restraints excluded: chain B residue 172 THR Chi-restraints excluded: chain C residue 5 THR Chi-restraints excluded: chain C residue 96 VAL Chi-restraints excluded: chain F residue 209 ASN Chi-restraints excluded: chain J residue 106 ILE Chi-restraints excluded: chain J residue 109 THR Chi-restraints excluded: chain J residue 163 VAL Chi-restraints excluded: chain J residue 166 GLN Chi-restraints excluded: chain D residue 71 THR Chi-restraints excluded: chain D residue 143 ASN Chi-restraints excluded: chain D residue 375 LYS Chi-restraints excluded: chain D residue 402 ASP Chi-restraints excluded: chain D residue 527 SER Chi-restraints excluded: chain D residue 1078 ILE Chi-restraints excluded: chain K residue 40 ASP Chi-restraints excluded: chain K residue 143 ASN Chi-restraints excluded: chain K residue 200 SER Chi-restraints excluded: chain K residue 498 TYR Chi-restraints excluded: chain A residue 42 VAL Chi-restraints excluded: chain A residue 117 ILE Chi-restraints excluded: chain A residue 124 VAL Chi-restraints excluded: chain A residue 268 GLN Chi-restraints excluded: chain A residue 320 THR Chi-restraints excluded: chain A residue 424 ASP Chi-restraints excluded: chain A residue 742 ASP Chi-restraints excluded: chain A residue 760 LEU Chi-restraints excluded: chain A residue 960 VAL Chi-restraints excluded: chain A residue 976 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 501 random chunks: chunk 438 optimal weight: 0.0770 chunk 9 optimal weight: 20.0000 chunk 261 optimal weight: 2.9990 chunk 248 optimal weight: 3.9990 chunk 157 optimal weight: 0.7980 chunk 403 optimal weight: 7.9990 chunk 419 optimal weight: 0.8980 chunk 172 optimal weight: 0.0070 chunk 209 optimal weight: 3.9990 chunk 148 optimal weight: 10.0000 chunk 299 optimal weight: 3.9990 overall best weight: 0.9558 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 160 GLN D 357 ASN ** D 419 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 471 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 923 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 962 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4495 r_free = 0.4495 target = 0.155603 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 72)----------------| | r_work = 0.3711 r_free = 0.3711 target = 0.096440 restraints weight = 115529.228| |-----------------------------------------------------------------------------| r_work (start): 0.3435 rms_B_bonded: 5.23 r_work (final): 0.3435 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7669 moved from start: 0.1784 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 41137 Z= 0.107 Angle : 0.578 16.826 56098 Z= 0.285 Chirality : 0.045 0.338 6471 Planarity : 0.004 0.064 7116 Dihedral : 4.138 51.379 5447 Min Nonbonded Distance : 2.395 Molprobity Statistics. All-atom Clashscore : 6.15 Ramachandran Plot: Outliers : 0.16 % Allowed : 5.44 % Favored : 94.40 % Rotamer: Outliers : 1.28 % Allowed : 9.73 % Favored : 88.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.31 (0.12), residues: 5015 helix: 1.48 (0.20), residues: 749 sheet: 0.50 (0.14), residues: 1392 loop : -1.05 (0.11), residues: 2874 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 405 TYR 0.025 0.001 TYR K 165 PHE 0.032 0.001 PHE K 163 TRP 0.012 0.001 TRP K 350 HIS 0.007 0.001 HIS A 242 Details of bonding type rmsd/Z covalent geometry : bond 0.00238 / 0.11 (41011) covalent geometry : angle 0.54971 / 0.28 (55782) SS BOND : bond 0.00286 / 0.22 ( 62) SS BOND : angle 0.76648 / 0.49 ( 124) hydrogen bonds : bond 0.03788 / 2.52 ( 1319) hydrogen bonds : angle 5.24608 / 3.62 ( 3621) link_ALPHA1-3 : bond 0.00433 / 0.23 ( 1) link_ALPHA1-3 : angle 1.40299 / 0.78 ( 3) link_BETA1-4 : bond 0.00761 / 0.40 ( 20) link_BETA1-4 : angle 2.25061 / 1.68 ( 60) link_NAG-ASN : bond 0.00584 / 0.37 ( 43) link_NAG-ASN : angle 3.40203 / 2.57 ( 129) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10030 Ramachandran restraints generated. 5015 Oldfield, 0 Emsley, 5015 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10030 Ramachandran restraints generated. 5015 Oldfield, 0 Emsley, 5015 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 263 residues out of total 4385 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 207 time to evaluate : 1.402 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 142 ARG cc_start: 0.5143 (tpt170) cc_final: 0.4191 (mpt180) REVERT: F 74 MET cc_start: 0.8383 (mmp) cc_final: 0.8166 (mpp) REVERT: I 101 HIS cc_start: 0.5836 (t-90) cc_final: 0.5328 (t-90) REVERT: D 226 LEU cc_start: 0.8927 (mm) cc_final: 0.8277 (tp) REVERT: D 375 LYS cc_start: 0.8999 (OUTLIER) cc_final: 0.8708 (ptmm) REVERT: D 513 GLU cc_start: 0.7514 (mt-10) cc_final: 0.7268 (pt0) REVERT: D 756 PHE cc_start: 0.6807 (t80) cc_final: 0.6552 (t80) REVERT: K 266 TYR cc_start: 0.7671 (m-80) cc_final: 0.6689 (m-80) REVERT: K 372 PHE cc_start: 0.4267 (m-80) cc_final: 0.4050 (m-80) REVERT: K 379 VAL cc_start: 0.7694 (t) cc_final: 0.7478 (p) REVERT: K 663 ILE cc_start: 0.8358 (OUTLIER) cc_final: 0.7919 (mm) REVERT: A 262 TYR cc_start: 0.8318 (p90) cc_final: 0.8100 (p90) REVERT: A 982 ASP cc_start: 0.7702 (t0) cc_final: 0.6995 (t0) REVERT: A 985 GLU cc_start: 0.8443 (mp0) cc_final: 0.8013 (mp0) outliers start: 56 outliers final: 35 residues processed: 251 average time/residue: 0.2284 time to fit residues: 97.3633 Evaluate side-chains 232 residues out of total 4385 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 195 time to evaluate : 1.651 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 158 PHE Chi-restraints excluded: chain G residue 223 VAL Chi-restraints excluded: chain B residue 53 TRP Chi-restraints excluded: chain B residue 158 PHE Chi-restraints excluded: chain B residue 163 THR Chi-restraints excluded: chain B residue 172 THR Chi-restraints excluded: chain C residue 5 THR Chi-restraints excluded: chain C residue 96 VAL Chi-restraints excluded: chain E residue 130 THR Chi-restraints excluded: chain F residue 118 MET Chi-restraints excluded: chain F residue 209 ASN Chi-restraints excluded: chain J residue 97 THR Chi-restraints excluded: chain J residue 106 ILE Chi-restraints excluded: chain J residue 163 VAL Chi-restraints excluded: chain J residue 166 GLN Chi-restraints excluded: chain D residue 71 THR Chi-restraints excluded: chain D residue 143 ASN Chi-restraints excluded: chain D residue 375 LYS Chi-restraints excluded: chain D residue 402 ASP Chi-restraints excluded: chain D residue 527 SER Chi-restraints excluded: chain D residue 1078 ILE Chi-restraints excluded: chain K residue 40 ASP Chi-restraints excluded: chain K residue 128 VAL Chi-restraints excluded: chain K residue 200 SER Chi-restraints excluded: chain K residue 498 TYR Chi-restraints excluded: chain K residue 663 ILE Chi-restraints excluded: chain A residue 42 VAL Chi-restraints excluded: chain A residue 117 ILE Chi-restraints excluded: chain A residue 124 VAL Chi-restraints excluded: chain A residue 264 VAL Chi-restraints excluded: chain A residue 268 GLN Chi-restraints excluded: chain A residue 373 THR Chi-restraints excluded: chain A residue 424 ASP Chi-restraints excluded: chain A residue 742 ASP Chi-restraints excluded: chain A residue 760 LEU Chi-restraints excluded: chain A residue 960 VAL Chi-restraints excluded: chain A residue 976 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 501 random chunks: chunk 93 optimal weight: 50.0000 chunk 15 optimal weight: 9.9990 chunk 4 optimal weight: 50.0000 chunk 273 optimal weight: 4.9990 chunk 0 optimal weight: 40.0000 chunk 482 optimal weight: 4.9990 chunk 116 optimal weight: 50.0000 chunk 123 optimal weight: 40.0000 chunk 163 optimal weight: 10.0000 chunk 362 optimal weight: 1.9990 chunk 184 optimal weight: 20.0000 overall best weight: 6.3992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 110 ASN C 6 GLN E 101 GLN E 161 GLN I 82 GLN D 113 GLN ** D 419 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D1085 HIS ** K 160 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 183 ASN K 707 ASN K 952 ASN K 954 GLN K 989 GLN ** A 79 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 141 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 242 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 471 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 561 GLN A 577 GLN A 923 GLN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4399 r_free = 0.4399 target = 0.163405 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3506 r_free = 0.3506 target = 0.100023 restraints weight = 96788.477| |-----------------------------------------------------------------------------| r_work (start): 0.3290 rms_B_bonded: 5.41 r_work: 0.3077 rms_B_bonded: 5.28 restraints_weight: 2.0000 r_work (final): 0.3077 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7811 moved from start: 0.2876 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.010 0.084 41137 Z= 0.407 Angle : 0.863 19.061 56098 Z= 0.435 Chirality : 0.053 0.397 6471 Planarity : 0.005 0.058 7116 Dihedral : 5.263 50.871 5447 Min Nonbonded Distance : 2.329 Molprobity Statistics. All-atom Clashscore : 10.22 Ramachandran Plot: Outliers : 0.18 % Allowed : 7.66 % Favored : 92.16 % Rotamer: Outliers : 1.99 % Allowed : 11.11 % Favored : 86.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % 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: -1.02 (0.12), residues: 5015 helix: 0.43 (0.19), residues: 756 sheet: 0.11 (0.14), residues: 1420 loop : -1.44 (0.11), residues: 2839 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG K1104 TYR 0.027 0.003 TYR D 89 PHE 0.032 0.003 PHE A 217 TRP 0.019 0.002 TRP G 36 HIS 0.013 0.002 HIS A 141 Details of bonding type rmsd/Z covalent geometry : bond 0.00975 / 0.41 (41011) covalent geometry : angle 0.83423 / 0.43 (55782) SS BOND : bond 0.00535 / 0.35 ( 62) SS BOND : angle 1.54475 / 1.01 ( 124) hydrogen bonds : bond 0.06872 / 4.55 ( 1319) hydrogen bonds : angle 5.93681 / 4.11 ( 3621) link_ALPHA1-3 : bond 0.00546 / 0.29 ( 1) link_ALPHA1-3 : angle 1.29130 / 0.72 ( 3) link_BETA1-4 : bond 0.00722 / 0.42 ( 20) link_BETA1-4 : angle 2.49453 / 1.77 ( 60) link_NAG-ASN : bond 0.00951 / 0.56 ( 43) link_NAG-ASN : angle 4.22550 / 3.03 ( 129) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10030 Ramachandran restraints generated. 5015 Oldfield, 0 Emsley, 5015 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10030 Ramachandran restraints generated. 5015 Oldfield, 0 Emsley, 5015 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 291 residues out of total 4385 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 87 poor density : 204 time to evaluate : 1.418 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 72 ARG cc_start: 0.5593 (OUTLIER) cc_final: 0.4811 (ttp-170) REVERT: F 74 MET cc_start: 0.7817 (mmp) cc_final: 0.7351 (mpp) REVERT: F 202 GLN cc_start: 0.3739 (tp40) cc_final: 0.3190 (mt0) REVERT: I 101 HIS cc_start: 0.5745 (t-90) cc_final: 0.5191 (t-90) REVERT: D 756 PHE cc_start: 0.7850 (t80) cc_final: 0.7488 (t80) REVERT: D 987 GLU cc_start: 0.8067 (mm-30) cc_final: 0.7785 (tm-30) REVERT: K 193 ASP cc_start: 0.8694 (t0) cc_final: 0.8485 (t0) REVERT: K 372 PHE cc_start: 0.4279 (m-80) cc_final: 0.3969 (m-80) REVERT: K 658 GLU cc_start: 0.8346 (tp30) cc_final: 0.8125 (pt0) REVERT: K 663 ILE cc_start: 0.8617 (OUTLIER) cc_final: 0.8374 (mm) REVERT: A 42 VAL cc_start: 0.8665 (OUTLIER) cc_final: 0.8430 (m) REVERT: A 286 VAL cc_start: 0.8652 (OUTLIER) cc_final: 0.8304 (p) REVERT: A 454 ARG cc_start: 0.7808 (OUTLIER) cc_final: 0.7098 (ttt180) REVERT: A 1089 GLU cc_start: 0.8854 (mt-10) cc_final: 0.8058 (tm-30) outliers start: 87 outliers final: 48 residues processed: 279 average time/residue: 0.2178 time to fit residues: 104.0697 Evaluate side-chains 226 residues out of total 4385 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 173 time to evaluate : 1.365 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 158 PHE Chi-restraints excluded: chain G residue 223 VAL Chi-restraints excluded: chain B residue 72 ARG Chi-restraints excluded: chain B residue 158 PHE Chi-restraints excluded: chain B residue 163 THR Chi-restraints excluded: chain B residue 172 THR Chi-restraints excluded: chain C residue 5 THR Chi-restraints excluded: chain F residue 209 ASN Chi-restraints excluded: chain I residue 37 VAL Chi-restraints excluded: chain J residue 97 THR Chi-restraints excluded: chain J residue 106 ILE Chi-restraints excluded: chain J residue 163 VAL Chi-restraints excluded: chain J residue 166 GLN Chi-restraints excluded: chain D residue 33 THR Chi-restraints excluded: chain D residue 71 THR Chi-restraints excluded: chain D residue 88 VAL Chi-restraints excluded: chain D residue 402 ASP Chi-restraints excluded: chain D residue 513 GLU Chi-restraints excluded: chain D residue 585 THR Chi-restraints excluded: chain D residue 596 THR Chi-restraints excluded: chain D residue 778 VAL Chi-restraints excluded: chain D residue 928 ILE Chi-restraints excluded: chain D residue 1078 ILE Chi-restraints excluded: chain K residue 33 THR Chi-restraints excluded: chain K residue 88 VAL Chi-restraints excluded: chain K residue 126 ILE Chi-restraints excluded: chain K residue 128 VAL Chi-restraints excluded: chain K residue 200 SER Chi-restraints excluded: chain K residue 392 VAL Chi-restraints excluded: chain K residue 498 TYR Chi-restraints excluded: chain K residue 543 LEU Chi-restraints excluded: chain K residue 569 THR Chi-restraints excluded: chain K residue 578 THR Chi-restraints excluded: chain K residue 663 ILE Chi-restraints excluded: chain K residue 1133 THR Chi-restraints excluded: chain A residue 42 VAL Chi-restraints excluded: chain A residue 79 ASN Chi-restraints excluded: chain A residue 117 ILE Chi-restraints excluded: chain A residue 124 VAL Chi-restraints excluded: chain A residue 264 VAL Chi-restraints excluded: chain A residue 286 VAL Chi-restraints excluded: chain A residue 320 THR Chi-restraints excluded: chain A residue 330 THR Chi-restraints excluded: chain A residue 347 VAL Chi-restraints excluded: chain A residue 359 VAL Chi-restraints excluded: chain A residue 424 ASP Chi-restraints excluded: chain A residue 435 SER Chi-restraints excluded: chain A residue 454 ARG Chi-restraints excluded: chain A residue 465 ILE Chi-restraints excluded: chain A residue 742 ASP Chi-restraints excluded: chain A residue 760 LEU Chi-restraints excluded: chain A residue 960 VAL Chi-restraints excluded: chain A residue 1078 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 501 random chunks: chunk 60 optimal weight: 0.8980 chunk 297 optimal weight: 8.9990 chunk 263 optimal weight: 0.9980 chunk 196 optimal weight: 0.9980 chunk 346 optimal weight: 2.9990 chunk 243 optimal weight: 0.9980 chunk 226 optimal weight: 1.9990 chunk 283 optimal weight: 0.9990 chunk 333 optimal weight: 3.9990 chunk 54 optimal weight: 2.9990 chunk 220 optimal weight: 0.9990 overall best weight: 0.9782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 6 GLN ** C 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 138 ASN F 181 GLN ** D 419 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 687 GLN ** A 141 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 471 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4452 r_free = 0.4452 target = 0.152513 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 70)----------------| | r_work = 0.3628 r_free = 0.3628 target = 0.092394 restraints weight = 114631.182| |-----------------------------------------------------------------------------| r_work (start): 0.3349 rms_B_bonded: 5.06 r_work (final): 0.3349 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7706 moved from start: 0.2765 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 41137 Z= 0.119 Angle : 0.618 17.243 56098 Z= 0.306 Chirality : 0.046 0.348 6471 Planarity : 0.004 0.054 7116 Dihedral : 4.564 49.483 5444 Min Nonbonded Distance : 2.326 Molprobity Statistics. All-atom Clashscore : 7.09 Ramachandran Plot: Outliers : 0.16 % Allowed : 5.08 % Favored : 94.76 % Rotamer: Outliers : 1.33 % Allowed : 12.61 % Favored : 86.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.67 (0.12), residues: 5015 helix: 1.21 (0.20), residues: 747 sheet: 0.13 (0.14), residues: 1431 loop : -1.24 (0.11), residues: 2837 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG A 405 TYR 0.028 0.001 TYR A 834 PHE 0.030 0.001 PHE K 163 TRP 0.013 0.001 TRP D 883 HIS 0.006 0.001 HIS A 242 Details of bonding type rmsd/Z covalent geometry : bond 0.00261 / 0.12 (41011) covalent geometry : angle 0.58929 / 0.30 (55782) SS BOND : bond 0.00441 / 0.29 ( 62) SS BOND : angle 0.91809 / 0.61 ( 124) hydrogen bonds : bond 0.04432 / 2.93 ( 1319) hydrogen bonds : angle 5.24091 / 3.62 ( 3621) link_ALPHA1-3 : bond 0.00369 / 0.19 ( 1) link_ALPHA1-3 : angle 1.41188 / 0.77 ( 3) link_BETA1-4 : bond 0.00795 / 0.41 ( 20) link_BETA1-4 : angle 2.25814 / 1.67 ( 60) link_NAG-ASN : bond 0.00675 / 0.41 ( 43) link_NAG-ASN : angle 3.56960 / 2.65 ( 129) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10030 Ramachandran restraints generated. 5015 Oldfield, 0 Emsley, 5015 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10030 Ramachandran restraints generated. 5015 Oldfield, 0 Emsley, 5015 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 251 residues out of total 4385 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 193 time to evaluate : 1.608 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: F 202 GLN cc_start: 0.3777 (tp40) cc_final: 0.3312 (mt0) REVERT: I 101 HIS cc_start: 0.6170 (t-90) cc_final: 0.5718 (t-90) REVERT: D 405 ARG cc_start: 0.8800 (mtm110) cc_final: 0.8469 (ptp-110) REVERT: D 737 MET cc_start: 0.8777 (ttp) cc_final: 0.8539 (tpp) REVERT: D 756 PHE cc_start: 0.7149 (t80) cc_final: 0.6846 (t80) REVERT: D 770 GLU cc_start: 0.8024 (tp30) cc_final: 0.7633 (tp30) REVERT: K 172 MET cc_start: 0.8711 (tpp) cc_final: 0.7990 (pmm) REVERT: K 266 TYR cc_start: 0.8208 (m-80) cc_final: 0.7340 (m-80) REVERT: K 372 PHE cc_start: 0.4192 (m-80) cc_final: 0.3875 (m-80) REVERT: K 658 GLU cc_start: 0.7974 (tp30) cc_final: 0.7774 (pt0) REVERT: K 663 ILE cc_start: 0.8574 (OUTLIER) cc_final: 0.8259 (mm) REVERT: K 745 GLU cc_start: 0.8782 (OUTLIER) cc_final: 0.8567 (pm20) REVERT: A 170 PHE cc_start: 0.8373 (m-10) cc_final: 0.8163 (m-10) REVERT: A 791 ILE cc_start: 0.8867 (OUTLIER) cc_final: 0.8607 (pt) REVERT: A 1089 GLU cc_start: 0.8577 (mt-10) cc_final: 0.7859 (tm-30) REVERT: A 1141 GLU cc_start: 0.8471 (mp0) cc_final: 0.8244 (pm20) outliers start: 58 outliers final: 32 residues processed: 240 average time/residue: 0.2388 time to fit residues: 97.5646 Evaluate side-chains 206 residues out of total 4385 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 171 time to evaluate : 1.541 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 158 PHE Chi-restraints excluded: chain G residue 223 VAL Chi-restraints excluded: chain B residue 158 PHE Chi-restraints excluded: chain C residue 5 THR Chi-restraints excluded: chain C residue 138 ASN Chi-restraints excluded: chain F residue 203 THR Chi-restraints excluded: chain F residue 209 ASN Chi-restraints excluded: chain I residue 37 VAL Chi-restraints excluded: chain I residue 64 VAL Chi-restraints excluded: chain I residue 120 LEU Chi-restraints excluded: chain J residue 97 THR Chi-restraints excluded: chain J residue 106 ILE Chi-restraints excluded: chain J residue 109 THR Chi-restraints excluded: chain J residue 163 VAL Chi-restraints excluded: chain J residue 166 GLN Chi-restraints excluded: chain D residue 71 THR Chi-restraints excluded: chain D residue 402 ASP Chi-restraints excluded: chain K residue 62 VAL Chi-restraints excluded: chain K residue 128 VAL Chi-restraints excluded: chain K residue 152 PHE Chi-restraints excluded: chain K residue 498 TYR Chi-restraints excluded: chain K residue 663 ILE Chi-restraints excluded: chain K residue 745 GLU Chi-restraints excluded: chain A residue 124 VAL Chi-restraints excluded: chain A residue 184 LEU Chi-restraints excluded: chain A residue 264 VAL Chi-restraints excluded: chain A residue 268 GLN Chi-restraints excluded: chain A residue 309 ILE Chi-restraints excluded: chain A residue 404 VAL Chi-restraints excluded: chain A residue 407 ILE Chi-restraints excluded: chain A residue 424 ASP Chi-restraints excluded: chain A residue 630 TRP Chi-restraints excluded: chain A residue 760 LEU Chi-restraints excluded: chain A residue 791 ILE Chi-restraints excluded: chain A residue 960 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 501 random chunks: chunk 474 optimal weight: 0.7980 chunk 244 optimal weight: 2.9990 chunk 365 optimal weight: 4.9990 chunk 40 optimal weight: 9.9990 chunk 46 optimal weight: 7.9990 chunk 231 optimal weight: 3.9990 chunk 222 optimal weight: 6.9990 chunk 145 optimal weight: 20.0000 chunk 464 optimal weight: 2.9990 chunk 90 optimal weight: 7.9990 chunk 75 optimal weight: 30.0000 overall best weight: 3.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 138 ASN ** D 419 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 687 GLN K 160 ASN ** K 202 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 141 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 471 GLN ** 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 = 0.4417 r_free = 0.4417 target = 0.158622 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 74)----------------| | r_work = 0.3530 r_free = 0.3530 target = 0.094512 restraints weight = 95476.481| |-----------------------------------------------------------------------------| r_work (start): 0.3334 rms_B_bonded: 5.05 r_work (final): 0.3334 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7584 moved from start: 0.2986 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.050 41137 Z= 0.210 Angle : 0.658 17.186 56098 Z= 0.326 Chirality : 0.047 0.357 6471 Planarity : 0.004 0.059 7116 Dihedral : 4.640 48.639 5444 Min Nonbonded Distance : 2.338 Molprobity Statistics. All-atom Clashscore : 7.88 Ramachandran Plot: Outliers : 0.14 % Allowed : 6.72 % Favored : 93.14 % Rotamer: Outliers : 1.62 % Allowed : 12.98 % Favored : 85.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.74 (0.12), residues: 5015 helix: 1.08 (0.20), residues: 752 sheet: 0.11 (0.14), residues: 1428 loop : -1.29 (0.11), residues: 2835 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG A 405 TYR 0.028 0.002 TYR K 89 PHE 0.029 0.002 PHE K 235 TRP 0.019 0.001 TRP I 53 HIS 0.007 0.001 HIS K 202 Details of bonding type rmsd/Z covalent geometry : bond 0.00498 / 0.21 (41011) covalent geometry : angle 0.63074 / 0.32 (55782) SS BOND : bond 0.00333 / 0.23 ( 62) SS BOND : angle 1.02738 / 0.66 ( 124) hydrogen bonds : bond 0.04953 / 3.28 ( 1319) hydrogen bonds : angle 5.28409 / 3.65 ( 3621) link_ALPHA1-3 : bond 0.00395 / 0.21 ( 1) link_ALPHA1-3 : angle 1.37558 / 0.77 ( 3) link_BETA1-4 : bond 0.00689 / 0.35 ( 20) link_BETA1-4 : angle 2.25707 / 1.64 ( 60) link_NAG-ASN : bond 0.00615 / 0.36 ( 43) link_NAG-ASN : angle 3.59816 / 2.64 ( 129) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10030 Ramachandran restraints generated. 5015 Oldfield, 0 Emsley, 5015 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10030 Ramachandran restraints generated. 5015 Oldfield, 0 Emsley, 5015 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 247 residues out of total 4385 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 176 time to evaluate : 1.437 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: F 202 GLN cc_start: 0.3606 (tp40) cc_final: 0.3183 (mt0) REVERT: I 101 HIS cc_start: 0.6517 (t-90) cc_final: 0.5871 (t-90) REVERT: D 405 ARG cc_start: 0.8861 (mtm110) cc_final: 0.8522 (ptp90) REVERT: D 756 PHE cc_start: 0.7374 (t80) cc_final: 0.7052 (t80) REVERT: D 770 GLU cc_start: 0.8170 (tp30) cc_final: 0.7891 (tp30) REVERT: K 172 MET cc_start: 0.8678 (tpp) cc_final: 0.7851 (pmm) REVERT: K 200 SER cc_start: 0.9400 (OUTLIER) cc_final: 0.9007 (m) REVERT: K 295 GLU cc_start: 0.8871 (OUTLIER) cc_final: 0.8244 (tp30) REVERT: K 372 PHE cc_start: 0.4537 (m-80) cc_final: 0.4192 (m-80) REVERT: K 663 ILE cc_start: 0.8553 (OUTLIER) cc_final: 0.8279 (mm) REVERT: A 170 PHE cc_start: 0.8432 (m-10) cc_final: 0.8142 (m-10) REVERT: A 454 ARG cc_start: 0.7892 (OUTLIER) cc_final: 0.7004 (ttt180) REVERT: A 791 ILE cc_start: 0.8889 (OUTLIER) cc_final: 0.8610 (pt) REVERT: A 1089 GLU cc_start: 0.8605 (mt-10) cc_final: 0.7901 (tm-30) outliers start: 71 outliers final: 50 residues processed: 235 average time/residue: 0.2372 time to fit residues: 95.4201 Evaluate side-chains 223 residues out of total 4385 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 168 time to evaluate : 1.822 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 158 PHE Chi-restraints excluded: chain G residue 223 VAL Chi-restraints excluded: chain H residue 106 ILE Chi-restraints excluded: chain B residue 158 PHE Chi-restraints excluded: chain B residue 163 THR Chi-restraints excluded: chain B residue 172 THR Chi-restraints excluded: chain C residue 5 THR Chi-restraints excluded: chain C residue 116 PHE Chi-restraints excluded: chain F residue 203 THR Chi-restraints excluded: chain F residue 209 ASN Chi-restraints excluded: chain I residue 37 VAL Chi-restraints excluded: chain I residue 64 VAL Chi-restraints excluded: chain I residue 191 SER Chi-restraints excluded: chain J residue 4 LEU Chi-restraints excluded: chain J residue 97 THR Chi-restraints excluded: chain J residue 106 ILE Chi-restraints excluded: chain J residue 163 VAL Chi-restraints excluded: chain J residue 166 GLN Chi-restraints excluded: chain D residue 33 THR Chi-restraints excluded: chain D residue 71 THR Chi-restraints excluded: chain D residue 286 VAL Chi-restraints excluded: chain D residue 402 ASP Chi-restraints excluded: chain D residue 596 THR Chi-restraints excluded: chain D residue 735 CYS Chi-restraints excluded: chain D residue 965 SER Chi-restraints excluded: chain D residue 1078 ILE Chi-restraints excluded: chain K residue 33 THR Chi-restraints excluded: chain K residue 62 VAL Chi-restraints excluded: chain K residue 128 VAL Chi-restraints excluded: chain K residue 200 SER Chi-restraints excluded: chain K residue 224 VAL Chi-restraints excluded: chain K residue 295 GLU Chi-restraints excluded: chain K residue 359 VAL Chi-restraints excluded: chain K residue 386 ASP Chi-restraints excluded: chain K residue 498 TYR Chi-restraints excluded: chain K residue 663 ILE Chi-restraints excluded: chain K residue 783 LYS Chi-restraints excluded: chain K residue 928 ILE Chi-restraints excluded: chain A residue 117 ILE Chi-restraints excluded: chain A residue 124 VAL Chi-restraints excluded: chain A residue 264 VAL Chi-restraints excluded: chain A residue 268 GLN Chi-restraints excluded: chain A residue 309 ILE Chi-restraints excluded: chain A residue 320 THR Chi-restraints excluded: chain A residue 404 VAL Chi-restraints excluded: chain A residue 407 ILE Chi-restraints excluded: chain A residue 424 ASP Chi-restraints excluded: chain A residue 454 ARG Chi-restraints excluded: chain A residue 543 LEU Chi-restraints excluded: chain A residue 630 TRP Chi-restraints excluded: chain A residue 742 ASP Chi-restraints excluded: chain A residue 760 LEU Chi-restraints excluded: chain A residue 791 ILE Chi-restraints excluded: chain A residue 960 VAL Chi-restraints excluded: chain A residue 981 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 501 random chunks: chunk 306 optimal weight: 4.9990 chunk 294 optimal weight: 6.9990 chunk 210 optimal weight: 0.7980 chunk 97 optimal weight: 40.0000 chunk 156 optimal weight: 30.0000 chunk 348 optimal weight: 0.7980 chunk 176 optimal weight: 7.9990 chunk 22 optimal weight: 0.0970 chunk 215 optimal weight: 0.1980 chunk 184 optimal weight: 9.9990 chunk 330 optimal weight: 20.0000 overall best weight: 1.3780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... H 166 GLN C 138 ASN D 23 GLN ** D 419 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 687 GLN ** A 141 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 471 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 577 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4424 r_free = 0.4424 target = 0.154572 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3555 r_free = 0.3555 target = 0.091970 restraints weight = 100401.592| |-----------------------------------------------------------------------------| r_work (start): 0.3349 rms_B_bonded: 5.39 r_work: 0.3175 rms_B_bonded: 4.74 restraints_weight: 0.5000 r_work (final): 0.3175 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7681 moved from start: 0.3029 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 41137 Z= 0.124 Angle : 0.606 15.986 56098 Z= 0.297 Chirality : 0.045 0.342 6471 Planarity : 0.004 0.067 7116 Dihedral : 4.421 48.282 5444 Min Nonbonded Distance : 2.227 Molprobity Statistics. All-atom Clashscore : 7.01 Ramachandran Plot: Outliers : 0.14 % Allowed : 5.48 % Favored : 94.38 % Rotamer: Outliers : 1.39 % Allowed : 13.44 % Favored : 85.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.59 (0.12), residues: 5015 helix: 1.34 (0.20), residues: 744 sheet: 0.17 (0.14), residues: 1425 loop : -1.20 (0.11), residues: 2846 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG A 405 TYR 0.017 0.001 TYR A1064 PHE 0.027 0.001 PHE K 235 TRP 0.012 0.001 TRP I 53 HIS 0.006 0.001 HIS A 242 Details of bonding type rmsd/Z covalent geometry : bond 0.00281 / 0.12 (41011) covalent geometry : angle 0.57976 / 0.29 (55782) SS BOND : bond 0.00299 / 0.21 ( 62) SS BOND : angle 0.87484 / 0.58 ( 124) hydrogen bonds : bond 0.04151 / 2.75 ( 1319) hydrogen bonds : angle 5.04154 / 3.48 ( 3621) link_ALPHA1-3 : bond 0.00348 / 0.18 ( 1) link_ALPHA1-3 : angle 1.41845 / 0.78 ( 3) link_BETA1-4 : bond 0.00734 / 0.39 ( 20) link_BETA1-4 : angle 2.19240 / 1.61 ( 60) link_NAG-ASN : bond 0.00611 / 0.37 ( 43) link_NAG-ASN : angle 3.37456 / 2.48 ( 129) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10030 Ramachandran restraints generated. 5015 Oldfield, 0 Emsley, 5015 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10030 Ramachandran restraints generated. 5015 Oldfield, 0 Emsley, 5015 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 244 residues out of total 4385 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 183 time to evaluate : 1.584 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: F 202 GLN cc_start: 0.3522 (tp40) cc_final: 0.3111 (mt0) REVERT: I 101 HIS cc_start: 0.5822 (t-90) cc_final: 0.5223 (t-90) REVERT: D 23 GLN cc_start: 0.5402 (OUTLIER) cc_final: 0.4433 (tp40) REVERT: D 53 ASP cc_start: 0.8033 (t0) cc_final: 0.7793 (t70) REVERT: D 405 ARG cc_start: 0.9067 (mtm110) cc_final: 0.8810 (ptp90) REVERT: D 749 LEU cc_start: 0.9517 (mm) cc_final: 0.9209 (tt) REVERT: D 756 PHE cc_start: 0.7353 (t80) cc_final: 0.7067 (t80) REVERT: D 770 GLU cc_start: 0.8543 (tp30) cc_final: 0.8291 (tp30) REVERT: K 172 MET cc_start: 0.8642 (tpp) cc_final: 0.7851 (pmm) REVERT: K 200 SER cc_start: 0.9474 (OUTLIER) cc_final: 0.9139 (m) REVERT: K 266 TYR cc_start: 0.8413 (m-80) cc_final: 0.7548 (m-80) REVERT: K 295 GLU cc_start: 0.9049 (OUTLIER) cc_final: 0.8537 (tp30) REVERT: K 372 PHE cc_start: 0.4022 (m-80) cc_final: 0.3708 (m-80) REVERT: K 663 ILE cc_start: 0.8689 (OUTLIER) cc_final: 0.8367 (mm) REVERT: A 170 PHE cc_start: 0.8409 (m-10) cc_final: 0.8127 (m-10) REVERT: A 377 TYR cc_start: 0.7754 (m-80) cc_final: 0.7491 (m-80) REVERT: A 454 ARG cc_start: 0.7983 (OUTLIER) cc_final: 0.7043 (ttt180) REVERT: A 791 ILE cc_start: 0.8976 (OUTLIER) cc_final: 0.8704 (pt) REVERT: A 1089 GLU cc_start: 0.9058 (mt-10) cc_final: 0.8215 (tm-30) outliers start: 61 outliers final: 50 residues processed: 235 average time/residue: 0.2464 time to fit residues: 98.9590 Evaluate side-chains 230 residues out of total 4385 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 174 time to evaluate : 1.576 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 158 PHE Chi-restraints excluded: chain G residue 223 VAL Chi-restraints excluded: chain B residue 158 PHE Chi-restraints excluded: chain B residue 163 THR Chi-restraints excluded: chain B residue 172 THR Chi-restraints excluded: chain C residue 5 THR Chi-restraints excluded: chain C residue 138 ASN Chi-restraints excluded: chain F residue 203 THR Chi-restraints excluded: chain F residue 209 ASN Chi-restraints excluded: chain I residue 37 VAL Chi-restraints excluded: chain I residue 64 VAL Chi-restraints excluded: chain I residue 191 SER Chi-restraints excluded: chain J residue 4 LEU Chi-restraints excluded: chain J residue 97 THR Chi-restraints excluded: chain J residue 106 ILE Chi-restraints excluded: chain J residue 163 VAL Chi-restraints excluded: chain J residue 166 GLN Chi-restraints excluded: chain D residue 23 GLN Chi-restraints excluded: chain D residue 33 THR Chi-restraints excluded: chain D residue 71 THR Chi-restraints excluded: chain D residue 402 ASP Chi-restraints excluded: chain D residue 596 THR Chi-restraints excluded: chain D residue 735 CYS Chi-restraints excluded: chain D residue 1078 ILE Chi-restraints excluded: chain K residue 33 THR Chi-restraints excluded: chain K residue 62 VAL Chi-restraints excluded: chain K residue 63 THR Chi-restraints excluded: chain K residue 128 VAL Chi-restraints excluded: chain K residue 152 PHE Chi-restraints excluded: chain K residue 200 SER Chi-restraints excluded: chain K residue 264 VAL Chi-restraints excluded: chain K residue 295 GLU Chi-restraints excluded: chain K residue 359 VAL Chi-restraints excluded: chain K residue 386 ASP Chi-restraints excluded: chain K residue 498 TYR Chi-restraints excluded: chain K residue 663 ILE Chi-restraints excluded: chain K residue 783 LYS Chi-restraints excluded: chain K residue 928 ILE Chi-restraints excluded: chain A residue 117 ILE Chi-restraints excluded: chain A residue 124 VAL Chi-restraints excluded: chain A residue 264 VAL Chi-restraints excluded: chain A residue 268 GLN Chi-restraints excluded: chain A residue 359 VAL Chi-restraints excluded: chain A residue 376 CYS Chi-restraints excluded: chain A residue 404 VAL Chi-restraints excluded: chain A residue 407 ILE Chi-restraints excluded: chain A residue 424 ASP Chi-restraints excluded: chain A residue 454 ARG Chi-restraints excluded: chain A residue 465 ILE Chi-restraints excluded: chain A residue 630 TRP Chi-restraints excluded: chain A residue 760 LEU Chi-restraints excluded: chain A residue 791 ILE Chi-restraints excluded: chain A residue 960 VAL Chi-restraints excluded: chain A residue 976 ASP Chi-restraints excluded: chain A residue 1133 THR Chi-restraints excluded: chain A residue 1138 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 501 random chunks: chunk 434 optimal weight: 0.9980 chunk 292 optimal weight: 3.9990 chunk 281 optimal weight: 4.9990 chunk 84 optimal weight: 30.0000 chunk 379 optimal weight: 0.9990 chunk 386 optimal weight: 0.8980 chunk 151 optimal weight: 0.5980 chunk 310 optimal weight: 3.9990 chunk 362 optimal weight: 0.1980 chunk 318 optimal weight: 8.9990 chunk 277 optimal weight: 0.7980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 138 ASN D 23 GLN ** D 419 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 687 GLN ** A 141 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 471 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4459 r_free = 0.4459 target = 0.152968 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3679 r_free = 0.3679 target = 0.096609 restraints weight = 114946.954| |-----------------------------------------------------------------------------| r_work (start): 0.3361 rms_B_bonded: 6.02 r_work: 0.3175 rms_B_bonded: 5.08 restraints_weight: 2.0000 r_work (final): 0.3175 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7674 moved from start: 0.3054 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 41137 Z= 0.104 Angle : 0.594 15.111 56098 Z= 0.290 Chirality : 0.045 0.336 6471 Planarity : 0.004 0.056 7116 Dihedral : 4.252 47.606 5444 Min Nonbonded Distance : 2.392 Molprobity Statistics. All-atom Clashscore : 6.58 Ramachandran Plot: Outliers : 0.12 % Allowed : 5.52 % Favored : 94.36 % Rotamer: Outliers : 1.37 % Allowed : 13.80 % Favored : 84.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.49 (0.12), residues: 5015 helix: 1.44 (0.20), residues: 746 sheet: 0.26 (0.14), residues: 1418 loop : -1.15 (0.11), residues: 2851 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.000 ARG D 21 TYR 0.017 0.001 TYR A1064 PHE 0.030 0.001 PHE K 235 TRP 0.019 0.001 TRP K 630 HIS 0.006 0.001 HIS A 242 Details of bonding type rmsd/Z covalent geometry : bond 0.00227 / 0.10 (41011) covalent geometry : angle 0.56913 / 0.28 (55782) SS BOND : bond 0.00279 / 0.20 ( 62) SS BOND : angle 0.77722 / 0.50 ( 124) hydrogen bonds : bond 0.03748 / 2.49 ( 1319) hydrogen bonds : angle 4.89622 / 3.38 ( 3621) link_ALPHA1-3 : bond 0.00350 / 0.18 ( 1) link_ALPHA1-3 : angle 1.43598 / 0.79 ( 3) link_BETA1-4 : bond 0.00728 / 0.39 ( 20) link_BETA1-4 : angle 2.15563 / 1.58 ( 60) link_NAG-ASN : bond 0.00613 / 0.38 ( 43) link_NAG-ASN : angle 3.23855 / 2.37 ( 129) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10030 Ramachandran restraints generated. 5015 Oldfield, 0 Emsley, 5015 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10030 Ramachandran restraints generated. 5015 Oldfield, 0 Emsley, 5015 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 244 residues out of total 4385 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 184 time to evaluate : 1.564 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: F 202 GLN cc_start: 0.3647 (tp40) cc_final: 0.3251 (mt0) REVERT: I 101 HIS cc_start: 0.5495 (t-90) cc_final: 0.4957 (t-90) REVERT: D 53 ASP cc_start: 0.8001 (t0) cc_final: 0.7766 (t70) REVERT: D 86 ASP cc_start: 0.8386 (m-30) cc_final: 0.7981 (t70) REVERT: D 405 ARG cc_start: 0.9055 (mtm110) cc_final: 0.8782 (ptp90) REVERT: D 749 LEU cc_start: 0.9532 (mm) cc_final: 0.9296 (tt) REVERT: D 756 PHE cc_start: 0.7283 (t80) cc_final: 0.7012 (t80) REVERT: D 770 GLU cc_start: 0.8482 (tp30) cc_final: 0.8226 (tp30) REVERT: K 172 MET cc_start: 0.8690 (tpp) cc_final: 0.7885 (pmm) REVERT: K 200 SER cc_start: 0.9500 (OUTLIER) cc_final: 0.9190 (m) REVERT: K 266 TYR cc_start: 0.8346 (m-80) cc_final: 0.7402 (m-80) REVERT: K 295 GLU cc_start: 0.9039 (OUTLIER) cc_final: 0.8570 (tp30) REVERT: K 372 PHE cc_start: 0.3838 (m-80) cc_final: 0.3542 (m-80) REVERT: K 663 ILE cc_start: 0.8649 (OUTLIER) cc_final: 0.8337 (mm) REVERT: K 1047 MET cc_start: 0.9084 (ptm) cc_final: 0.8846 (ptm) REVERT: A 170 PHE cc_start: 0.8383 (m-10) cc_final: 0.8112 (m-10) REVERT: A 377 TYR cc_start: 0.7639 (m-80) cc_final: 0.7418 (m-80) REVERT: A 454 ARG cc_start: 0.8072 (OUTLIER) cc_final: 0.7114 (ttt180) REVERT: A 791 ILE cc_start: 0.8940 (OUTLIER) cc_final: 0.8673 (pt) outliers start: 60 outliers final: 47 residues processed: 237 average time/residue: 0.2320 time to fit residues: 93.8789 Evaluate side-chains 229 residues out of total 4385 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 177 time to evaluate : 1.328 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 158 PHE Chi-restraints excluded: chain G residue 223 VAL Chi-restraints excluded: chain B residue 158 PHE Chi-restraints excluded: chain B residue 163 THR Chi-restraints excluded: chain C residue 5 THR Chi-restraints excluded: chain C residue 138 ASN Chi-restraints excluded: chain F residue 203 THR Chi-restraints excluded: chain F residue 209 ASN Chi-restraints excluded: chain I residue 37 VAL Chi-restraints excluded: chain I residue 64 VAL Chi-restraints excluded: chain J residue 4 LEU Chi-restraints excluded: chain J residue 97 THR Chi-restraints excluded: chain J residue 106 ILE Chi-restraints excluded: chain J residue 163 VAL Chi-restraints excluded: chain J residue 166 GLN Chi-restraints excluded: chain D residue 71 THR Chi-restraints excluded: chain D residue 286 VAL Chi-restraints excluded: chain D residue 402 ASP Chi-restraints excluded: chain D residue 596 THR Chi-restraints excluded: chain K residue 33 THR Chi-restraints excluded: chain K residue 62 VAL Chi-restraints excluded: chain K residue 63 THR Chi-restraints excluded: chain K residue 128 VAL Chi-restraints excluded: chain K residue 200 SER Chi-restraints excluded: chain K residue 264 VAL Chi-restraints excluded: chain K residue 295 GLU Chi-restraints excluded: chain K residue 386 ASP Chi-restraints excluded: chain K residue 498 TYR Chi-restraints excluded: chain K residue 587 CYS Chi-restraints excluded: chain K residue 663 ILE Chi-restraints excluded: chain K residue 783 LYS Chi-restraints excluded: chain K residue 1091 VAL Chi-restraints excluded: chain A residue 117 ILE Chi-restraints excluded: chain A residue 118 VAL Chi-restraints excluded: chain A residue 124 VAL Chi-restraints excluded: chain A residue 264 VAL Chi-restraints excluded: chain A residue 268 GLN Chi-restraints excluded: chain A residue 309 ILE Chi-restraints excluded: chain A residue 359 VAL Chi-restraints excluded: chain A residue 376 CYS Chi-restraints excluded: chain A residue 404 VAL Chi-restraints excluded: chain A residue 407 ILE Chi-restraints excluded: chain A residue 424 ASP Chi-restraints excluded: chain A residue 435 SER Chi-restraints excluded: chain A residue 454 ARG Chi-restraints excluded: chain A residue 630 TRP Chi-restraints excluded: chain A residue 760 LEU Chi-restraints excluded: chain A residue 791 ILE Chi-restraints excluded: chain A residue 960 VAL Chi-restraints excluded: chain A residue 976 ASP Chi-restraints excluded: chain A residue 1133 THR Chi-restraints excluded: chain A residue 1138 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 501 random chunks: chunk 133 optimal weight: 7.9990 chunk 182 optimal weight: 10.0000 chunk 89 optimal weight: 50.0000 chunk 86 optimal weight: 30.0000 chunk 242 optimal weight: 3.9990 chunk 94 optimal weight: 6.9990 chunk 265 optimal weight: 0.7980 chunk 38 optimal weight: 7.9990 chunk 212 optimal weight: 2.9990 chunk 463 optimal weight: 4.9990 chunk 452 optimal weight: 5.9990 overall best weight: 3.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 138 ASN ** D 419 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 202 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 141 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 577 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4407 r_free = 0.4407 target = 0.160974 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.3509 r_free = 0.3509 target = 0.095518 restraints weight = 94848.969| |-----------------------------------------------------------------------------| r_work (start): 0.3313 rms_B_bonded: 5.77 r_work: 0.3116 rms_B_bonded: 4.84 restraints_weight: 0.5000 r_work (final): 0.3116 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7774 moved from start: 0.3338 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.057 41137 Z= 0.243 Angle : 0.690 13.990 56098 Z= 0.342 Chirality : 0.047 0.355 6471 Planarity : 0.004 0.058 7116 Dihedral : 4.619 46.933 5444 Min Nonbonded Distance : 2.327 Molprobity Statistics. All-atom Clashscore : 8.51 Ramachandran Plot: Outliers : 0.14 % Allowed : 6.96 % Favored : 92.90 % Rotamer: Outliers : 1.49 % Allowed : 13.71 % Favored : 84.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.73 (0.12), residues: 5015 helix: 1.08 (0.20), residues: 747 sheet: 0.16 (0.14), residues: 1397 loop : -1.28 (0.11), residues: 2871 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 405 TYR 0.031 0.002 TYR K 89 PHE 0.022 0.002 PHE A 389 TRP 0.025 0.002 TRP K 630 HIS 0.008 0.001 HIS K 202 Details of bonding type rmsd/Z covalent geometry : bond 0.00577 / 0.24 (41011) covalent geometry : angle 0.66613 / 0.34 (55782) SS BOND : bond 0.00353 / 0.24 ( 62) SS BOND : angle 1.11356 / 0.72 ( 124) hydrogen bonds : bond 0.05263 / 3.49 ( 1319) hydrogen bonds : angle 5.20298 / 3.60 ( 3621) link_ALPHA1-3 : bond 0.00380 / 0.20 ( 1) link_ALPHA1-3 : angle 1.37289 / 0.76 ( 3) link_BETA1-4 : bond 0.00688 / 0.35 ( 20) link_BETA1-4 : angle 2.21942 / 1.58 ( 60) link_NAG-ASN : bond 0.00627 / 0.38 ( 43) link_NAG-ASN : angle 3.39220 / 2.40 ( 129) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10030 Ramachandran restraints generated. 5015 Oldfield, 0 Emsley, 5015 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10030 Ramachandran restraints generated. 5015 Oldfield, 0 Emsley, 5015 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 252 residues out of total 4385 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 187 time to evaluate : 1.524 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: G 83 MET cc_start: 0.0979 (mmm) cc_final: 0.0778 (mmm) REVERT: F 202 GLN cc_start: 0.3489 (tp40) cc_final: 0.2868 (mt0) REVERT: I 101 HIS cc_start: 0.5781 (t-90) cc_final: 0.5204 (t-90) REVERT: D 53 ASP cc_start: 0.8061 (t0) cc_final: 0.7832 (t70) REVERT: D 405 ARG cc_start: 0.9084 (mtm110) cc_final: 0.8768 (ptp90) REVERT: D 756 PHE cc_start: 0.7636 (t80) cc_final: 0.7335 (t80) REVERT: K 172 MET cc_start: 0.8740 (tpp) cc_final: 0.7985 (pmm) REVERT: K 200 SER cc_start: 0.9530 (OUTLIER) cc_final: 0.9181 (m) REVERT: K 295 GLU cc_start: 0.8983 (OUTLIER) cc_final: 0.8472 (tp30) REVERT: K 663 ILE cc_start: 0.8643 (OUTLIER) cc_final: 0.8377 (mm) REVERT: A 42 VAL cc_start: 0.8840 (t) cc_final: 0.8632 (m) REVERT: A 454 ARG cc_start: 0.7873 (OUTLIER) cc_final: 0.6780 (ttt180) REVERT: A 791 ILE cc_start: 0.9023 (OUTLIER) cc_final: 0.8739 (pt) REVERT: A 1089 GLU cc_start: 0.8988 (mt-10) cc_final: 0.8174 (tm-30) outliers start: 65 outliers final: 53 residues processed: 245 average time/residue: 0.2369 time to fit residues: 98.9245 Evaluate side-chains 236 residues out of total 4385 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 178 time to evaluate : 1.456 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 158 PHE Chi-restraints excluded: chain G residue 223 VAL Chi-restraints excluded: chain B residue 158 PHE Chi-restraints excluded: chain B residue 163 THR Chi-restraints excluded: chain B residue 172 THR Chi-restraints excluded: chain C residue 5 THR Chi-restraints excluded: chain F residue 203 THR Chi-restraints excluded: chain F residue 209 ASN Chi-restraints excluded: chain J residue 4 LEU Chi-restraints excluded: chain J residue 97 THR Chi-restraints excluded: chain J residue 106 ILE Chi-restraints excluded: chain J residue 109 THR Chi-restraints excluded: chain J residue 163 VAL Chi-restraints excluded: chain J residue 166 GLN Chi-restraints excluded: chain D residue 33 THR Chi-restraints excluded: chain D residue 71 THR Chi-restraints excluded: chain D residue 286 VAL Chi-restraints excluded: chain D residue 402 ASP Chi-restraints excluded: chain D residue 596 THR Chi-restraints excluded: chain D residue 735 CYS Chi-restraints excluded: chain D residue 965 SER Chi-restraints excluded: chain D residue 1078 ILE Chi-restraints excluded: chain K residue 33 THR Chi-restraints excluded: chain K residue 62 VAL Chi-restraints excluded: chain K residue 63 THR Chi-restraints excluded: chain K residue 128 VAL Chi-restraints excluded: chain K residue 200 SER Chi-restraints excluded: chain K residue 264 VAL Chi-restraints excluded: chain K residue 295 GLU Chi-restraints excluded: chain K residue 386 ASP Chi-restraints excluded: chain K residue 498 TYR Chi-restraints excluded: chain K residue 587 CYS Chi-restraints excluded: chain K residue 663 ILE Chi-restraints excluded: chain K residue 783 LYS Chi-restraints excluded: chain K residue 928 ILE Chi-restraints excluded: chain K residue 1091 VAL Chi-restraints excluded: chain A residue 117 ILE Chi-restraints excluded: chain A residue 118 VAL Chi-restraints excluded: chain A residue 124 VAL Chi-restraints excluded: chain A residue 264 VAL Chi-restraints excluded: chain A residue 309 ILE Chi-restraints excluded: chain A residue 359 VAL Chi-restraints excluded: chain A residue 376 CYS Chi-restraints excluded: chain A residue 404 VAL Chi-restraints excluded: chain A residue 407 ILE Chi-restraints excluded: chain A residue 424 ASP Chi-restraints excluded: chain A residue 435 SER Chi-restraints excluded: chain A residue 454 ARG Chi-restraints excluded: chain A residue 601 THR Chi-restraints excluded: chain A residue 630 TRP Chi-restraints excluded: chain A residue 742 ASP Chi-restraints excluded: chain A residue 760 LEU Chi-restraints excluded: chain A residue 791 ILE Chi-restraints excluded: chain A residue 960 VAL Chi-restraints excluded: chain A residue 976 ASP Chi-restraints excluded: chain A residue 981 LEU Chi-restraints excluded: chain A residue 1133 THR Chi-restraints excluded: chain A residue 1138 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 501 random chunks: chunk 76 optimal weight: 8.9990 chunk 147 optimal weight: 1.9990 chunk 373 optimal weight: 1.9990 chunk 294 optimal weight: 20.0000 chunk 382 optimal weight: 0.7980 chunk 461 optimal weight: 0.7980 chunk 445 optimal weight: 5.9990 chunk 415 optimal weight: 2.9990 chunk 230 optimal weight: 0.9990 chunk 353 optimal weight: 0.7980 chunk 475 optimal weight: 0.9990 overall best weight: 0.8784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 138 ASN D 79 ASN ** D 419 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 141 HIS ** 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 = 0.4450 r_free = 0.4450 target = 0.152331 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3643 r_free = 0.3643 target = 0.093383 restraints weight = 114549.887| |-----------------------------------------------------------------------------| r_work (start): 0.3365 rms_B_bonded: 5.09 r_work (final): 0.3365 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7698 moved from start: 0.3316 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 41137 Z= 0.110 Angle : 0.609 13.594 56098 Z= 0.298 Chirality : 0.045 0.336 6471 Planarity : 0.004 0.062 7116 Dihedral : 4.324 46.977 5444 Min Nonbonded Distance : 2.398 Molprobity Statistics. All-atom Clashscore : 6.91 Ramachandran Plot: Outliers : 0.14 % Allowed : 5.16 % Favored : 94.70 % Rotamer: Outliers : 1.33 % Allowed : 14.01 % Favored : 84.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.52 (0.12), residues: 5015 helix: 1.45 (0.21), residues: 740 sheet: 0.22 (0.14), residues: 1424 loop : -1.16 (0.11), residues: 2851 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.028 0.000 ARG K 980 TYR 0.017 0.001 TYR A1064 PHE 0.027 0.001 PHE B 27 TRP 0.028 0.001 TRP K 630 HIS 0.006 0.001 HIS A 242 Details of bonding type rmsd/Z covalent geometry : bond 0.00244 / 0.11 (41011) covalent geometry : angle 0.58702 / 0.29 (55782) SS BOND : bond 0.00286 / 0.20 ( 62) SS BOND : angle 0.81246 / 0.53 ( 124) hydrogen bonds : bond 0.03921 / 2.59 ( 1319) hydrogen bonds : angle 4.89489 / 3.38 ( 3621) link_ALPHA1-3 : bond 0.00336 / 0.18 ( 1) link_ALPHA1-3 : angle 1.43340 / 0.78 ( 3) link_BETA1-4 : bond 0.00756 / 0.39 ( 20) link_BETA1-4 : angle 2.11686 / 1.54 ( 60) link_NAG-ASN : bond 0.00612 / 0.39 ( 43) link_NAG-ASN : angle 3.11824 / 2.20 ( 129) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 17544.70 seconds wall clock time: 298 minutes 52.66 seconds (17932.66 seconds total)