Starting phenix.real_space_refine on Thu Jun 26 14:50:17 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7web_32445/06_2025/7web_32445.cif Found real_map, /net/cci-nas-00/data/ceres_data/7web_32445/06_2025/7web_32445.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7web_32445/06_2025/7web_32445.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7web_32445/06_2025/7web_32445.map" model { file = "/net/cci-nas-00/data/ceres_data/7web_32445/06_2025/7web_32445.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7web_32445/06_2025/7web_32445.cif" } resolution = 3.7 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.067 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 133 5.16 5 C 19345 2.51 5 N 4984 2.21 5 O 5951 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 24 residue(s): 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib" Total number of atoms: 30413 Number of models: 1 Model: "" Number of chains: 30 Chain: "G" Number of atoms: 941 Number of conformers: 1 Conformer: "" Number of residues, atoms: 123, 941 Classifications: {'peptide': 123} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 4, 'TRANS': 118} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "H" Number of atoms: 941 Number of conformers: 1 Conformer: "" Number of residues, atoms: 123, 941 Classifications: {'peptide': 123} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 4, 'TRANS': 118} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "I" Number of atoms: 807 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 807 Classifications: {'peptide': 107} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PCIS': 1, 'PTRANS': 6, 'TRANS': 99} Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 8 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 2} Unresolved non-hydrogen planarities: 8 Chain: "L" Number of atoms: 807 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 807 Classifications: {'peptide': 107} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PCIS': 1, 'PTRANS': 6, 'TRANS': 99} Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 8 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 2} Unresolved non-hydrogen planarities: 8 Chain: "B" Number of atoms: 8632 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1098, 8632 Classifications: {'peptide': 1098} Link IDs: {'PTRANS': 55, 'TRANS': 1042} Chain breaks: 4 Chain: "C" Number of atoms: 8632 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1098, 8632 Classifications: {'peptide': 1098} Link IDs: {'PTRANS': 55, 'TRANS': 1042} Chain breaks: 4 Chain: "D" Number of atoms: 8632 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1098, 8632 Classifications: {'peptide': 1098} Link IDs: {'CIS': 1, 'PTRANS': 55, 'TRANS': 1041} Chain breaks: 4 Chain: "A" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "E" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "F" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "J" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "K" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "M" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "N" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "O" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "P" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "Q" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "R" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "S" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "T" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "U" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "V" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "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 dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "X" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "Y" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "Z" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "a" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "B" Number of atoms: 126 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 126 Unusual residues: {'NAG': 9} Classifications: {'undetermined': 9} Link IDs: {None: 8} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 27 Unresolved non-hydrogen chiralities: 9 Chain: "C" Number of atoms: 154 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 154 Unusual residues: {'NAG': 11} Classifications: {'undetermined': 11} Link IDs: {None: 10} Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 22 Unresolved non-hydrogen dihedrals: 33 Unresolved non-hydrogen chiralities: 11 Chain: "D" Number of atoms: 126 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 126 Unusual residues: {'NAG': 9} Classifications: {'undetermined': 9} Link IDs: {None: 8} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 27 Unresolved non-hydrogen chiralities: 9 Time building chain proxies: 16.58, per 1000 atoms: 0.55 Number of scatterers: 30413 At special positions: 0 Unit cell: (145.52, 143.38, 254.66, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 133 16.00 O 5951 8.00 N 4984 7.00 C 19345 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=45, symmetry=0 Simple disulfide: pdb=" SG CYS G 22 " - pdb=" SG CYS G 97 " distance=2.04 Simple disulfide: pdb=" SG CYS G 102 " - pdb=" SG CYS G 107 " distance=2.03 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 97 " distance=2.03 Simple disulfide: pdb=" SG CYS H 102 " - pdb=" SG CYS H 107 " distance=2.03 Simple disulfide: pdb=" SG CYS I 23 " - pdb=" SG CYS I 89 " distance=2.03 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 89 " distance=2.03 Simple disulfide: pdb=" SG CYS B 15 " - pdb=" SG CYS B 134 " distance=2.03 Simple disulfide: pdb=" SG CYS B 129 " - pdb=" SG CYS B 161 " distance=2.04 Simple disulfide: pdb=" SG CYS B 288 " - pdb=" SG CYS B 298 " distance=2.03 Simple disulfide: pdb=" SG CYS B 333 " - pdb=" SG CYS B 358 " distance=2.03 Simple disulfide: pdb=" SG CYS B 376 " - pdb=" SG CYS B 429 " distance=2.04 Simple disulfide: pdb=" SG CYS B 388 " - pdb=" SG CYS B 522 " distance=2.03 Simple disulfide: pdb=" SG CYS B 477 " - pdb=" SG CYS B 485 " distance=2.03 Simple disulfide: pdb=" SG CYS B 614 " - pdb=" SG CYS B 646 " distance=2.03 Simple disulfide: pdb=" SG CYS B 659 " - pdb=" SG CYS B 668 " distance=2.03 Simple disulfide: pdb=" SG CYS B 735 " - pdb=" SG CYS B 757 " distance=2.03 Simple disulfide: pdb=" SG CYS B 740 " - pdb=" SG CYS B 746 " distance=2.03 Simple disulfide: pdb=" SG CYS B1029 " - pdb=" SG CYS B1040 " distance=2.03 Simple disulfide: pdb=" SG CYS B1079 " - pdb=" SG CYS B1123 " distance=2.03 Simple disulfide: pdb=" SG CYS C 15 " - pdb=" SG CYS C 134 " distance=2.03 Simple disulfide: pdb=" SG CYS C 129 " - pdb=" SG CYS C 161 " distance=2.03 Simple disulfide: pdb=" SG CYS C 288 " - pdb=" SG CYS C 298 " distance=2.03 Simple disulfide: pdb=" SG CYS C 333 " - pdb=" SG CYS C 358 " distance=2.03 Simple disulfide: pdb=" SG CYS C 376 " - pdb=" SG CYS C 429 " distance=2.04 Simple disulfide: pdb=" SG CYS C 388 " - pdb=" SG CYS C 522 " distance=2.03 Simple disulfide: pdb=" SG CYS C 477 " - pdb=" SG CYS C 485 " distance=2.03 Simple disulfide: pdb=" SG CYS C 614 " - pdb=" SG CYS C 646 " distance=2.03 Simple disulfide: pdb=" SG CYS C 659 " - pdb=" SG CYS C 668 " distance=2.03 Simple disulfide: pdb=" SG CYS C 735 " - pdb=" SG CYS C 757 " distance=2.02 Simple disulfide: pdb=" SG CYS C 740 " - pdb=" SG CYS C 746 " distance=2.03 Simple disulfide: pdb=" SG CYS C1029 " - pdb=" SG CYS C1040 " distance=2.03 Simple disulfide: pdb=" SG CYS C1079 " - pdb=" SG CYS C1123 " distance=2.03 Simple disulfide: pdb=" SG CYS D 15 " - pdb=" SG CYS D 134 " 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=2.04 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 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 D1029 " - pdb=" SG CYS D1040 " distance=2.03 Simple disulfide: pdb=" SG CYS D1079 " - pdb=" SG CYS D1123 " 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=7, symmetry=0 Links applied BETA1-4 " NAG A 1 " - " NAG A 2 " " NAG E 1 " - " NAG E 2 " " NAG F 1 " - " NAG F 2 " " NAG J 1 " - " NAG J 2 " " NAG K 1 " - " NAG K 2 " " NAG K 2 " - " BMA K 3 " " NAG M 1 " - " NAG M 2 " " NAG M 2 " - " BMA M 3 " " 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 S 2 " - " BMA S 3 " " NAG T 1 " - " NAG T 2 " " NAG T 2 " - " BMA T 3 " " 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 Y 1 " - " NAG Y 2 " " NAG Z 1 " - " NAG Z 2 " " NAG Z 2 " - " BMA Z 3 " " NAG a 1 " - " NAG a 2 " NAG-ASN " NAG A 1 " - " ASN B 328 " " NAG B1301 " - " ASN B1155 " " NAG B1302 " - " ASN B 123 " " NAG B1303 " - " ASN B 143 " " NAG B1304 " - " ASN B 17 " " NAG B1305 " - " ASN B 61 " " NAG B1306 " - " ASN B 600 " " NAG B1307 " - " ASN B 654 " " NAG B1308 " - " ASN B 613 " " NAG B1309 " - " ASN B 706 " " NAG C1303 " - " ASN C1155 " " NAG C1304 " - " ASN C 123 " " NAG C1305 " - " ASN C 143 " " NAG C1306 " - " ASN C 17 " " NAG C1307 " - " ASN C 61 " " NAG C1308 " - " ASN C 600 " " NAG C1309 " - " ASN C 654 " " NAG C1310 " - " ASN C 613 " " NAG C1311 " - " ASN C 706 " " NAG D1302 " - " ASN D1155 " " NAG D1303 " - " ASN D 143 " " NAG D1304 " - " ASN D 17 " " NAG D1305 " - " ASN D 61 " " NAG D1306 " - " ASN D 600 " " NAG D1307 " - " ASN D 654 " " NAG D1308 " - " ASN D 613 " " NAG D1309 " - " ASN D 706 " " NAG E 1 " - " ASN B 714 " " NAG J 1 " - " ASN B 798 " " NAG K 1 " - " ASN B1095 " " NAG M 1 " - " ASN B1131 " " NAG N 1 " - " ASN C 231 " " NAG P 1 " - " ASN C 714 " " NAG R 1 " - " ASN C 798 " " NAG S 1 " - " ASN C1095 " " NAG T 1 " - " ASN C1131 " " NAG U 1 " - " ASN D 231 " " NAG W 1 " - " ASN D 714 " " NAG X 1 " - " ASN D1071 " " NAG Y 1 " - " ASN D 798 " " NAG Z 1 " - " ASN D1095 " " NAG a 1 " - " ASN D1131 " Number of additional bonds: simple=7, symmetry=0 Coordination: Other bonds: Time building additional restraints: 7.59 Conformation dependent library (CDL) restraints added in 3.7 seconds 7432 Ramachandran restraints generated. 3716 Oldfield, 0 Emsley, 3716 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7042 Finding SS restraints... Secondary structure from input PDB file: 68 helices and 61 sheets defined 21.2% alpha, 24.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 4.08 Creating SS restraints... Processing helix chain 'G' and resid 88 through 92 removed outlier: 3.613A pdb=" N THR G 92 " --> pdb=" O SER G 89 " (cutoff:3.500A) Processing helix chain 'H' and resid 88 through 92 removed outlier: 3.539A pdb=" N THR H 92 " --> pdb=" O SER H 89 " (cutoff:3.500A) Processing helix chain 'L' and resid 80 through 84 removed outlier: 3.910A pdb=" N PHE L 84 " --> pdb=" O PRO L 81 " (cutoff:3.500A) Processing helix chain 'B' and resid 291 through 300 Processing helix chain 'B' and resid 335 through 340 Processing helix chain 'B' and resid 362 through 367 removed outlier: 3.824A pdb=" N TYR B 366 " --> pdb=" O TYR B 362 " (cutoff:3.500A) Processing helix chain 'B' and resid 402 through 408 removed outlier: 4.547A pdb=" N ARG B 405 " --> pdb=" O ASP B 402 " (cutoff:3.500A) Processing helix chain 'B' and resid 539 through 543 Processing helix chain 'B' and resid 616 through 621 Processing helix chain 'B' and resid 630 through 634 removed outlier: 3.684A pdb=" N TYR B 633 " --> pdb=" O TRP B 630 " (cutoff:3.500A) Processing helix chain 'B' and resid 743 through 751 removed outlier: 3.582A pdb=" N SER B 747 " --> pdb=" O SER B 743 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N ASN B 748 " --> pdb=" O THR B 744 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N LEU B 749 " --> pdb=" O GLU B 745 " (cutoff:3.500A) Processing helix chain 'B' and resid 752 through 754 No H-bonds generated for 'chain 'B' and resid 752 through 754' Processing helix chain 'B' and resid 755 through 780 removed outlier: 3.638A pdb=" N GLN B 759 " --> pdb=" O SER B 755 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N LEU B 760 " --> pdb=" O PHE B 756 " (cutoff:3.500A) removed outlier: 3.855A pdb=" N ASP B 772 " --> pdb=" O ALA B 768 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N LYS B 773 " --> pdb=" O VAL B 769 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N THR B 775 " --> pdb=" O GLN B 771 " (cutoff:3.500A) Processing helix chain 'B' and resid 813 through 823 removed outlier: 3.824A pdb=" N LEU B 818 " --> pdb=" O PHE B 814 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N LEU B 819 " --> pdb=" O ILE B 815 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N VAL B 823 " --> pdb=" O LEU B 819 " (cutoff:3.500A) Processing helix chain 'B' and resid 847 through 851 Processing helix chain 'B' and resid 863 through 879 removed outlier: 3.596A pdb=" N ALA B 868 " --> pdb=" O ASP B 864 " (cutoff:3.500A) removed outlier: 4.086A pdb=" N GLN B 869 " --> pdb=" O GLU B 865 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N TYR B 870 " --> pdb=" O MET B 866 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N SER B 872 " --> pdb=" O ALA B 868 " (cutoff:3.500A) Processing helix chain 'B' and resid 883 through 887 removed outlier: 4.113A pdb=" N GLY B 886 " --> pdb=" O TRP B 883 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N ALA B 887 " --> pdb=" O THR B 884 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 883 through 887' Processing helix chain 'B' and resid 894 through 907 removed outlier: 4.150A pdb=" N ALA B 900 " --> pdb=" O ALA B 896 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N TYR B 901 " --> pdb=" O MET B 897 " (cutoff:3.500A) Processing helix chain 'B' and resid 910 through 915 removed outlier: 3.750A pdb=" N TYR B 914 " --> pdb=" O GLN B 910 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N GLU B 915 " --> pdb=" O ASN B 911 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 910 through 915' Processing helix chain 'B' and resid 916 through 938 removed outlier: 3.716A pdb=" N SER B 926 " --> pdb=" O ASN B 922 " (cutoff:3.500A) removed outlier: 4.017A pdb=" N ALA B 927 " --> pdb=" O GLN B 923 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N GLY B 929 " --> pdb=" O ASN B 925 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N ILE B 931 " --> pdb=" O ALA B 927 " (cutoff:3.500A) removed outlier: 3.835A pdb=" N GLN B 932 " --> pdb=" O ILE B 928 " (cutoff:3.500A) removed outlier: 3.895A pdb=" N ASP B 933 " --> pdb=" O GLY B 929 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N THR B 938 " --> pdb=" O SER B 934 " (cutoff:3.500A) Processing helix chain 'B' and resid 942 through 961 removed outlier: 4.081A pdb=" N VAL B 948 " --> pdb=" O LYS B 944 " (cutoff:3.500A) removed outlier: 4.396A pdb=" N VAL B 949 " --> pdb=" O LEU B 945 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N ASN B 952 " --> pdb=" O VAL B 948 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N ASN B 957 " --> pdb=" O ALA B 953 " (cutoff:3.500A) Processing helix chain 'B' and resid 962 through 965 Processing helix chain 'B' and resid 973 through 981 removed outlier: 4.172A pdb=" N ILE B 977 " --> pdb=" O VAL B 973 " (cutoff:3.500A) removed outlier: 3.877A pdb=" N PHE B 978 " --> pdb=" O LEU B 974 " (cutoff:3.500A) Processing helix chain 'B' and resid 985 through 1029 removed outlier: 3.596A pdb=" N GLN B 989 " --> pdb=" O GLU B 985 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N LEU B 993 " --> pdb=" O GLN B 989 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N GLY B 996 " --> pdb=" O ARG B 992 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N SER B1000 " --> pdb=" O GLY B 996 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N GLN B1002 " --> pdb=" O LEU B 998 " (cutoff:3.500A) removed outlier: 4.160A pdb=" N LEU B1021 " --> pdb=" O ALA B1017 " (cutoff:3.500A) Processing helix chain 'B' and resid 1113 through 1115 No H-bonds generated for 'chain 'B' and resid 1113 through 1115' Processing helix chain 'B' and resid 1137 through 1158 removed outlier: 3.628A pdb=" N GLU B1141 " --> pdb=" O PRO B1137 " (cutoff:3.500A) removed outlier: 4.410A pdb=" N PHE B1145 " --> pdb=" O GLU B1141 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N GLU B1147 " --> pdb=" O ASP B1143 " (cutoff:3.500A) removed outlier: 4.065A pdb=" N GLU B1148 " --> pdb=" O SER B1144 " (cutoff:3.500A) removed outlier: 4.088A pdb=" N SER B1158 " --> pdb=" O LYS B1154 " (cutoff:3.500A) Processing helix chain 'C' and resid 291 through 301 Processing helix chain 'C' and resid 334 through 340 removed outlier: 3.736A pdb=" N VAL C 338 " --> pdb=" O PRO C 334 " (cutoff:3.500A) Processing helix chain 'C' and resid 362 through 367 Processing helix chain 'C' and resid 380 through 384 removed outlier: 3.738A pdb=" N LEU C 384 " --> pdb=" O PRO C 381 " (cutoff:3.500A) Processing helix chain 'C' and resid 404 through 408 removed outlier: 3.510A pdb=" N ILE C 407 " --> pdb=" O VAL C 404 " (cutoff:3.500A) Processing helix chain 'C' and resid 414 through 419 removed outlier: 3.514A pdb=" N TYR C 418 " --> pdb=" O ASN C 414 " (cutoff:3.500A) Processing helix chain 'C' and resid 616 through 621 Processing helix chain 'C' and resid 736 through 741 Processing helix chain 'C' and resid 743 through 751 removed outlier: 3.636A pdb=" N SER C 747 " --> pdb=" O SER C 743 " (cutoff:3.500A) removed outlier: 3.908A pdb=" N ASN C 748 " --> pdb=" O THR C 744 " (cutoff:3.500A) removed outlier: 4.438A pdb=" N LEU C 749 " --> pdb=" O GLU C 745 " (cutoff:3.500A) Processing helix chain 'C' and resid 752 through 754 No H-bonds generated for 'chain 'C' and resid 752 through 754' Processing helix chain 'C' and resid 755 through 779 removed outlier: 3.850A pdb=" N LEU C 760 " --> pdb=" O PHE C 756 " (cutoff:3.500A) removed outlier: 4.000A pdb=" N ASP C 772 " --> pdb=" O ALA C 768 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N LYS C 773 " --> pdb=" O VAL C 769 " (cutoff:3.500A) removed outlier: 4.237A pdb=" N THR C 775 " --> pdb=" O GLN C 771 " (cutoff:3.500A) Processing helix chain 'C' and resid 813 through 822 removed outlier: 3.637A pdb=" N ASP C 817 " --> pdb=" O SER C 813 " (cutoff:3.500A) removed outlier: 3.947A pdb=" N LEU C 818 " --> pdb=" O PHE C 814 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N LEU C 819 " --> pdb=" O ILE C 815 " (cutoff:3.500A) Processing helix chain 'C' and resid 863 through 879 removed outlier: 3.863A pdb=" N GLN C 869 " --> pdb=" O GLU C 865 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N ALA C 876 " --> pdb=" O SER C 872 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N ILE C 879 " --> pdb=" O LEU C 875 " (cutoff:3.500A) Processing helix chain 'C' and resid 898 through 907 removed outlier: 3.720A pdb=" N ASN C 904 " --> pdb=" O ALA C 900 " (cutoff:3.500A) Processing helix chain 'C' and resid 910 through 916 removed outlier: 3.985A pdb=" N TYR C 914 " --> pdb=" O GLN C 910 " (cutoff:3.500A) Processing helix chain 'C' and resid 916 through 938 removed outlier: 3.720A pdb=" N ALA C 927 " --> pdb=" O GLN C 923 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N GLY C 929 " --> pdb=" O ASN C 925 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N LYS C 930 " --> pdb=" O SER C 926 " (cutoff:3.500A) removed outlier: 4.026A pdb=" N ILE C 931 " --> pdb=" O ALA C 927 " (cutoff:3.500A) removed outlier: 4.349A pdb=" N GLN C 932 " --> pdb=" O ILE C 928 " (cutoff:3.500A) removed outlier: 3.981A pdb=" N ASP C 933 " --> pdb=" O GLY C 929 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N THR C 938 " --> pdb=" O SER C 934 " (cutoff:3.500A) Processing helix chain 'C' and resid 942 through 963 removed outlier: 3.919A pdb=" N VAL C 948 " --> pdb=" O LYS C 944 " (cutoff:3.500A) removed outlier: 4.252A pdb=" N VAL C 949 " --> pdb=" O LEU C 945 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N ASN C 950 " --> pdb=" O GLN C 946 " (cutoff:3.500A) removed outlier: 4.189A pdb=" N ASN C 952 " --> pdb=" O VAL C 948 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N VAL C 960 " --> pdb=" O LEU C 956 " (cutoff:3.500A) removed outlier: 4.084A pdb=" N LEU C 963 " --> pdb=" O LEU C 959 " (cutoff:3.500A) Processing helix chain 'C' and resid 975 through 979 Processing helix chain 'C' and resid 982 through 1030 removed outlier: 3.875A pdb=" N GLU C 987 " --> pdb=" O LYS C 983 " (cutoff:3.500A) removed outlier: 5.806A pdb=" N VAL C 988 " --> pdb=" O VAL C 984 " (cutoff:3.500A) removed outlier: 3.854A pdb=" N GLN C 989 " --> pdb=" O GLU C 985 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N LEU C 993 " --> pdb=" O GLN C 989 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N THR C1003 " --> pdb=" O GLN C 999 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N TYR C1004 " --> pdb=" O SER C1000 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N ALA C1013 " --> pdb=" O LEU C1009 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N GLU C1014 " --> pdb=" O ILE C1010 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N LEU C1021 " --> pdb=" O ALA C1017 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N SER C1027 " --> pdb=" O ALA C1023 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N VAL C1030 " --> pdb=" O MET C1026 " (cutoff:3.500A) Processing helix chain 'C' and resid 1113 through 1115 No H-bonds generated for 'chain 'C' and resid 1113 through 1115' Processing helix chain 'C' and resid 1137 through 1144 removed outlier: 3.751A pdb=" N GLU C1141 " --> pdb=" O PRO C1137 " (cutoff:3.500A) Processing helix chain 'C' and resid 1145 through 1158 removed outlier: 3.767A pdb=" N HIS C1156 " --> pdb=" O TYR C1152 " (cutoff:3.500A) removed outlier: 3.995A pdb=" N SER C1158 " --> pdb=" O LYS C1154 " (cutoff:3.500A) Processing helix chain 'D' and resid 291 through 301 Processing helix chain 'D' and resid 334 through 340 removed outlier: 4.227A pdb=" N VAL D 338 " --> pdb=" O PRO D 334 " (cutoff:3.500A) Processing helix chain 'D' and resid 346 through 350 removed outlier: 3.578A pdb=" N TRP D 350 " --> pdb=" O VAL D 347 " (cutoff:3.500A) Processing helix chain 'D' and resid 362 through 368 removed outlier: 3.584A pdb=" N LEU D 368 " --> pdb=" O VAL D 364 " (cutoff:3.500A) Processing helix chain 'D' and resid 380 through 387 removed outlier: 3.698A pdb=" N LEU D 384 " --> pdb=" O PRO D 381 " (cutoff:3.500A) removed outlier: 4.605A pdb=" N ASN D 385 " --> pdb=" O THR D 382 " (cutoff:3.500A) removed outlier: 3.954A pdb=" N ASP D 386 " --> pdb=" O LYS D 383 " (cutoff:3.500A) removed outlier: 4.123A pdb=" N LEU D 387 " --> pdb=" O LEU D 384 " (cutoff:3.500A) Processing helix chain 'D' and resid 401 through 408 removed outlier: 3.841A pdb=" N VAL D 404 " --> pdb=" O GLY D 401 " (cutoff:3.500A) removed outlier: 4.254A pdb=" N ARG D 405 " --> pdb=" O ASP D 402 " (cutoff:3.500A) Processing helix chain 'D' and resid 630 through 634 Processing helix chain 'D' and resid 734 through 741 removed outlier: 3.812A pdb=" N CYS D 740 " --> pdb=" O THR D 736 " (cutoff:3.500A) Processing helix chain 'D' and resid 743 through 752 removed outlier: 4.090A pdb=" N SER D 747 " --> pdb=" O SER D 743 " (cutoff:3.500A) removed outlier: 4.606A pdb=" N ASN D 748 " --> pdb=" O THR D 744 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N LEU D 749 " --> pdb=" O GLU D 745 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N GLN D 752 " --> pdb=" O ASN D 748 " (cutoff:3.500A) Processing helix chain 'D' and resid 756 through 762 Processing helix chain 'D' and resid 763 through 779 removed outlier: 3.615A pdb=" N ILE D 767 " --> pdb=" O ALA D 763 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N ALA D 768 " --> pdb=" O LEU D 764 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N ASP D 772 " --> pdb=" O ALA D 768 " (cutoff:3.500A) removed outlier: 4.410A pdb=" N THR D 775 " --> pdb=" O GLN D 771 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N GLN D 776 " --> pdb=" O ASP D 772 " (cutoff:3.500A) Processing helix chain 'D' and resid 813 through 822 removed outlier: 3.963A pdb=" N LEU D 818 " --> pdb=" O PHE D 814 " (cutoff:3.500A) Processing helix chain 'D' and resid 863 through 879 removed outlier: 3.542A pdb=" N ALA D 868 " --> pdb=" O ASP D 864 " (cutoff:3.500A) removed outlier: 4.078A pdb=" N GLN D 869 " --> pdb=" O GLU D 865 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N TYR D 870 " --> pdb=" O MET D 866 " (cutoff:3.500A) Processing helix chain 'D' and resid 883 through 887 removed outlier: 3.555A pdb=" N GLY D 886 " --> pdb=" O TRP D 883 " (cutoff:3.500A) Processing helix chain 'D' and resid 894 through 907 removed outlier: 4.448A pdb=" N ALA D 900 " --> pdb=" O ALA D 896 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N TYR D 901 " --> pdb=" O MET D 897 " (cutoff:3.500A) Processing helix chain 'D' and resid 910 through 915 removed outlier: 3.923A pdb=" N TYR D 914 " --> pdb=" O GLN D 910 " (cutoff:3.500A) removed outlier: 3.868A pdb=" N GLU D 915 " --> pdb=" O ASN D 911 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 910 through 915' Processing helix chain 'D' and resid 916 through 938 removed outlier: 3.820A pdb=" N LYS D 930 " --> pdb=" O SER D 926 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N ILE D 931 " --> pdb=" O ALA D 927 " (cutoff:3.500A) removed outlier: 3.932A pdb=" N GLN D 932 " --> pdb=" O ILE D 928 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N ASP D 933 " --> pdb=" O GLY D 929 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N SER D 936 " --> pdb=" O GLN D 932 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N THR D 938 " --> pdb=" O SER D 934 " (cutoff:3.500A) Processing helix chain 'D' and resid 942 through 963 removed outlier: 4.119A pdb=" N VAL D 948 " --> pdb=" O LYS D 944 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N VAL D 949 " --> pdb=" O LEU D 945 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N ASN D 952 " --> pdb=" O VAL D 948 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N LEU D 963 " --> pdb=" O LEU D 959 " (cutoff:3.500A) Processing helix chain 'D' and resid 985 through 1029 removed outlier: 4.006A pdb=" N GLN D 989 " --> pdb=" O GLU D 985 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N GLY D 996 " --> pdb=" O ARG D 992 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N SER D1027 " --> pdb=" O ALA D1023 " (cutoff:3.500A) Processing helix chain 'D' and resid 1139 through 1158 removed outlier: 5.127A pdb=" N PHE D1145 " --> pdb=" O GLU D1141 " (cutoff:3.500A) removed outlier: 4.058A pdb=" N LYS D1151 " --> pdb=" O GLU D1147 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'G' and resid 3 through 6 removed outlier: 3.787A pdb=" N GLN G 3 " --> pdb=" O SER G 25 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'G' and resid 10 through 12 removed outlier: 6.203A pdb=" N GLU G 10 " --> pdb=" O THR G 121 " (cutoff:3.500A) removed outlier: 6.383A pdb=" N LEU G 35 " --> pdb=" O TRP G 51 " (cutoff:3.500A) removed outlier: 4.478A pdb=" N TRP G 51 " --> pdb=" O LEU G 35 " (cutoff:3.500A) removed outlier: 6.895A pdb=" N TRP G 37 " --> pdb=" O ILE G 49 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'G' and resid 10 through 12 removed outlier: 6.203A pdb=" N GLU G 10 " --> pdb=" O THR G 121 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'G' and resid 18 through 20 Processing sheet with id=AA5, first strand: chain 'H' and resid 3 through 6 removed outlier: 3.517A pdb=" N GLN H 3 " --> pdb=" O SER H 25 " (cutoff:3.500A) removed outlier: 3.994A pdb=" N CYS H 22 " --> pdb=" O ALA H 80 " (cutoff:3.500A) removed outlier: 4.712A pdb=" N ALA H 80 " --> pdb=" O CYS H 22 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'H' and resid 10 through 12 removed outlier: 3.683A pdb=" N GLY H 50 " --> pdb=" O TRP H 37 " (cutoff:3.500A) removed outlier: 6.665A pdb=" N ARG H 39 " --> pdb=" O TRP H 48 " (cutoff:3.500A) removed outlier: 5.585A pdb=" N TRP H 48 " --> pdb=" O ARG H 39 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'H' and resid 10 through 12 Processing sheet with id=AA8, first strand: chain 'I' and resid 4 through 7 Processing sheet with id=AA9, first strand: chain 'I' and resid 10 through 12 removed outlier: 5.698A pdb=" N LEU I 11 " --> pdb=" O GLU I 106 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N ILE I 49 " --> pdb=" O TRP I 36 " (cutoff:3.500A) removed outlier: 6.411A pdb=" N GLN I 38 " --> pdb=" O LEU I 47 " (cutoff:3.500A) removed outlier: 5.786A pdb=" N LEU I 47 " --> pdb=" O GLN I 38 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'L' and resid 4 through 7 Processing sheet with id=AB2, first strand: chain 'L' and resid 54 through 55 removed outlier: 3.628A pdb=" N SER L 54 " --> pdb=" O SER L 50 " (cutoff:3.500A) removed outlier: 6.659A pdb=" N TRP L 36 " --> pdb=" O LEU L 48 " (cutoff:3.500A) removed outlier: 4.430A pdb=" N SER L 50 " --> pdb=" O LEU L 34 " (cutoff:3.500A) removed outlier: 6.703A pdb=" N LEU L 34 " --> pdb=" O SER L 50 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N GLN L 39 " --> pdb=" O VAL L 86 " (cutoff:3.500A) removed outlier: 4.086A pdb=" N VAL L 86 " --> pdb=" O GLN L 39 " (cutoff:3.500A) removed outlier: 4.541A pdb=" N GLN L 91 " --> pdb=" O THR L 98 " (cutoff:3.500A) removed outlier: 4.592A pdb=" N THR L 98 " --> pdb=" O GLN L 91 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'L' and resid 54 through 55 removed outlier: 3.628A pdb=" N SER L 54 " --> pdb=" O SER L 50 " (cutoff:3.500A) removed outlier: 6.659A pdb=" N TRP L 36 " --> pdb=" O LEU L 48 " (cutoff:3.500A) removed outlier: 4.430A pdb=" N SER L 50 " --> pdb=" O LEU L 34 " (cutoff:3.500A) removed outlier: 6.703A pdb=" N LEU L 34 " --> pdb=" O SER L 50 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N GLN L 39 " --> pdb=" O VAL L 86 " (cutoff:3.500A) removed outlier: 4.086A pdb=" N VAL L 86 " --> pdb=" O GLN L 39 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'B' and resid 27 through 30 Processing sheet with id=AB5, first strand: chain 'B' and resid 42 through 43 removed outlier: 3.630A pdb=" N ALA C 572 " --> pdb=" O GLY C 563 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'B' and resid 47 through 55 removed outlier: 4.021A pdb=" N ASP B 284 " --> pdb=" O LYS B 275 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'B' and resid 99 through 103 Processing sheet with id=AB8, first strand: chain 'B' and resid 113 through 118 removed outlier: 3.523A pdb=" N VAL B 128 " --> pdb=" O PHE B 163 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N PHE B 163 " --> pdb=" O VAL B 128 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 308 through 315 removed outlier: 5.462A pdb=" N ILE B 309 " --> pdb=" O THR B 596 " (cutoff:3.500A) removed outlier: 7.192A pdb=" N THR B 596 " --> pdb=" O ILE B 309 " (cutoff:3.500A) removed outlier: 5.642A pdb=" N GLN B 311 " --> pdb=" O VAL B 594 " (cutoff:3.500A) removed outlier: 6.546A pdb=" N VAL B 594 " --> pdb=" O GLN B 311 " (cutoff:3.500A) removed outlier: 5.420A pdb=" N SER B 313 " --> pdb=" O VAL B 592 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N VAL B 592 " --> pdb=" O SER B 313 " (cutoff:3.500A) removed outlier: 3.981A pdb=" N TYR B 609 " --> pdb=" O CYS B 646 " (cutoff:3.500A) removed outlier: 3.835A pdb=" N CYS B 646 " --> pdb=" O TYR B 609 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 321 through 322 removed outlier: 7.857A pdb=" N GLU B 321 " --> pdb=" O ASN B 537 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC1 Processing sheet with id=AC2, first strand: chain 'B' and resid 351 through 355 removed outlier: 4.195A pdb=" N ASN B 351 " --> pdb=" O SER B 396 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N SER B 396 " --> pdb=" O ASN B 351 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N TYR B 393 " --> pdb=" O SER B 511 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N LEU B 510 " --> pdb=" O CYS B 429 " (cutoff:3.500A) removed outlier: 4.609A pdb=" N VAL B 430 " --> pdb=" O LYS B 375 " (cutoff:3.500A) removed outlier: 4.417A pdb=" N LYS B 375 " --> pdb=" O VAL B 430 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N ALA B 432 " --> pdb=" O THR B 373 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N THR B 373 " --> pdb=" O ALA B 432 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 388 through 389 Processing sheet with id=AC4, first strand: chain 'B' and resid 449 through 451 Processing sheet with id=AC5, first strand: chain 'B' and resid 470 through 471 removed outlier: 3.601A pdb=" N TYR B 470 " --> pdb=" O TYR B 486 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N TYR B 486 " --> pdb=" O TYR B 470 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC5 Processing sheet with id=AC6, first strand: chain 'B' and resid 548 through 551 removed outlier: 3.540A pdb=" N THR B 585 " --> pdb=" O VAL B 548 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'B' and resid 651 through 657 removed outlier: 5.476A pdb=" N THR B 693 " --> pdb=" O VAL B 653 " (cutoff:3.500A) removed outlier: 6.979A pdb=" N ASN B 655 " --> pdb=" O THR B 693 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N CYS B 668 " --> pdb=" O TYR B 692 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'B' and resid 708 through 712 Processing sheet with id=AC9, first strand: chain 'B' and resid 715 through 725 removed outlier: 3.556A pdb=" N SER B 718 " --> pdb=" O THR B1063 " (cutoff:3.500A) removed outlier: 7.108A pdb=" N VAL B1062 " --> pdb=" O LEU B1046 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'B' and resid 715 through 725 removed outlier: 3.556A pdb=" N SER B 718 " --> pdb=" O THR B1063 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'B' and resid 730 through 732 removed outlier: 4.384A pdb=" N LYS B 730 " --> pdb=" O LEU B 858 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'B' and resid 784 through 787 removed outlier: 5.302A pdb=" N ILE B 785 " --> pdb=" O ASN C 700 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD3 Processing sheet with id=AD4, first strand: chain 'B' and resid 1117 through 1119 Processing sheet with id=AD5, first strand: chain 'B' and resid 1091 through 1094 removed outlier: 3.613A pdb=" N THR B1102 " --> pdb=" O VAL B1091 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'C' and resid 27 through 31 removed outlier: 8.288A pdb=" N ASN C 61 " --> pdb=" O TYR C 266 " (cutoff:3.500A) removed outlier: 6.446A pdb=" N TYR C 266 " --> pdb=" O ASN C 61 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N ALA C 261 " --> pdb=" O ILE C 93 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N ILE C 198 " --> pdb=" O VAL C 224 " (cutoff:3.500A) removed outlier: 4.232A pdb=" N VAL C 224 " --> pdb=" O ILE C 198 " (cutoff:3.500A) removed outlier: 5.976A pdb=" N SER C 200 " --> pdb=" O PRO C 222 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'C' and resid 48 through 55 removed outlier: 4.109A pdb=" N ASP C 284 " --> pdb=" O LYS C 275 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'C' and resid 81 through 83 removed outlier: 7.561A pdb=" N ARG C 234 " --> pdb=" O PHE C 104 " (cutoff:3.500A) removed outlier: 5.699A pdb=" N PHE C 104 " --> pdb=" O ARG C 234 " (cutoff:3.500A) removed outlier: 6.883A pdb=" N GLN C 236 " --> pdb=" O TRP C 102 " (cutoff:3.500A) removed outlier: 4.961A pdb=" N TRP C 102 " --> pdb=" O GLN C 236 " (cutoff:3.500A) removed outlier: 6.907A pdb=" N LEU C 238 " --> pdb=" O ARG C 100 " (cutoff:3.500A) removed outlier: 5.261A pdb=" N THR C 112 " --> pdb=" O PHE C 131 " (cutoff:3.500A) removed outlier: 4.188A pdb=" N PHE C 131 " --> pdb=" O THR C 112 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'C' and resid 308 through 316 removed outlier: 5.452A pdb=" N ILE C 309 " --> pdb=" O THR C 596 " (cutoff:3.500A) removed outlier: 7.446A pdb=" N THR C 596 " --> pdb=" O ILE C 309 " (cutoff:3.500A) removed outlier: 5.680A pdb=" N GLN C 311 " --> pdb=" O VAL C 594 " (cutoff:3.500A) removed outlier: 6.486A pdb=" N VAL C 594 " --> pdb=" O GLN C 311 " (cutoff:3.500A) removed outlier: 4.859A pdb=" N SER C 313 " --> pdb=" O VAL C 592 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N VAL C 592 " --> pdb=" O SER C 313 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'C' and resid 321 through 323 removed outlier: 3.804A pdb=" N GLU C 321 " --> pdb=" O CYS C 535 " (cutoff:3.500A) removed outlier: 3.989A pdb=" N PHE C 540 " --> pdb=" O LEU C 543 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N THR C 585 " --> pdb=" O VAL C 548 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'C' and resid 353 through 355 removed outlier: 3.581A pdb=" N ALA C 394 " --> pdb=" O LYS C 353 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N TRP C 433 " --> pdb=" O ARG C 506 " (cutoff:3.500A) removed outlier: 4.738A pdb=" N VAL C 430 " --> pdb=" O LYS C 375 " (cutoff:3.500A) removed outlier: 4.385A pdb=" N LYS C 375 " --> pdb=" O VAL C 430 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'C' and resid 388 through 389 Processing sheet with id=AE4, first strand: chain 'C' and resid 449 through 451 Processing sheet with id=AE5, first strand: chain 'C' and resid 470 through 471 removed outlier: 3.723A pdb=" N TYR C 470 " --> pdb=" O TYR C 486 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'C' and resid 651 through 657 removed outlier: 6.187A pdb=" N GLU C 651 " --> pdb=" O ALA C 691 " (cutoff:3.500A) removed outlier: 8.619A pdb=" N THR C 693 " --> pdb=" O GLU C 651 " (cutoff:3.500A) removed outlier: 9.236A pdb=" N VAL C 653 " --> pdb=" O THR C 693 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N SER C 688 " --> pdb=" O GLN C 672 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N GLN C 672 " --> pdb=" O SER C 688 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'C' and resid 708 through 712 Processing sheet with id=AE8, first strand: chain 'C' and resid 715 through 725 removed outlier: 3.771A pdb=" N MET C1047 " --> pdb=" O VAL C1062 " (cutoff:3.500A) removed outlier: 6.191A pdb=" N TYR C1064 " --> pdb=" O HIS C1045 " (cutoff:3.500A) removed outlier: 6.051A pdb=" N HIS C1045 " --> pdb=" O TYR C1064 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'C' and resid 732 through 733 removed outlier: 3.681A pdb=" N SER C 732 " --> pdb=" O THR C 856 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'C' and resid 784 through 785 removed outlier: 3.523A pdb=" N ILE C 785 " --> pdb=" O ALA D 698 " (cutoff:3.500A) No H-bonds generated for sheet with id=AF1 Processing sheet with id=AF2, first strand: chain 'C' and resid 1078 through 1079 removed outlier: 4.717A pdb=" N ALA C1084 " --> pdb=" O SER C1120 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'C' and resid 1091 through 1094 Processing sheet with id=AF4, first strand: chain 'D' and resid 27 through 31 removed outlier: 3.933A pdb=" N SER D 60 " --> pdb=" O SER D 31 " (cutoff:3.500A) removed outlier: 8.675A pdb=" N ASN D 61 " --> pdb=" O TYR D 266 " (cutoff:3.500A) removed outlier: 6.901A pdb=" N TYR D 266 " --> pdb=" O ASN D 61 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N ALA D 261 " --> pdb=" O ILE D 93 " (cutoff:3.500A) removed outlier: 5.733A pdb=" N SER D 200 " --> pdb=" O PRO D 222 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'D' and resid 48 through 55 removed outlier: 3.621A pdb=" N ASP D 284 " --> pdb=" O LYS D 275 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'D' and resid 82 through 83 removed outlier: 4.554A pdb=" N PHE D 163 " --> pdb=" O VAL D 128 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'D' and resid 308 through 311 removed outlier: 3.562A pdb=" N GLY D 591 " --> pdb=" O GLN D 610 " (cutoff:3.500A) Processing sheet with id=AF8, first strand: chain 'D' and resid 322 through 325 removed outlier: 7.830A pdb=" N ILE D 323 " --> pdb=" O ASN D 539 " (cutoff:3.500A) removed outlier: 3.853A pdb=" N PHE D 540 " --> pdb=" O LEU D 543 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N THR D 585 " --> pdb=" O VAL D 548 " (cutoff:3.500A) Processing sheet with id=AF9, first strand: chain 'D' and resid 351 through 355 removed outlier: 3.558A pdb=" N ASN D 351 " --> pdb=" O SER D 396 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N SER D 511 " --> pdb=" O TYR D 393 " (cutoff:3.500A) removed outlier: 3.982A pdb=" N VAL D 430 " --> pdb=" O LYS D 375 " (cutoff:3.500A) removed outlier: 4.046A pdb=" N LYS D 375 " --> pdb=" O VAL D 430 " (cutoff:3.500A) Processing sheet with id=AG1, first strand: chain 'D' and resid 449 through 451 Processing sheet with id=AG2, first strand: chain 'D' and resid 470 through 471 Processing sheet with id=AG3, first strand: chain 'D' and resid 651 through 652 removed outlier: 6.463A pdb=" N GLU D 651 " --> pdb=" O ALA D 691 " (cutoff:3.500A) removed outlier: 8.681A pdb=" N THR D 693 " --> pdb=" O GLU D 651 " (cutoff:3.500A) removed outlier: 6.798A pdb=" N ILE D 667 " --> pdb=" O ILE D 663 " (cutoff:3.500A) Processing sheet with id=AG4, first strand: chain 'D' and resid 708 through 712 removed outlier: 3.810A pdb=" N THR D1073 " --> pdb=" O SER D1094 " (cutoff:3.500A) Processing sheet with id=AG5, first strand: chain 'D' and resid 715 through 724 removed outlier: 3.538A pdb=" N PHE D1049 " --> pdb=" O LEU D1060 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N MET D1047 " --> pdb=" O VAL D1062 " (cutoff:3.500A) removed outlier: 6.060A pdb=" N TYR D1064 " --> pdb=" O HIS D1045 " (cutoff:3.500A) removed outlier: 5.817A pdb=" N HIS D1045 " --> pdb=" O TYR D1064 " (cutoff:3.500A) Processing sheet with id=AG6, first strand: chain 'D' and resid 732 through 733 removed outlier: 3.502A pdb=" N SER D 732 " --> pdb=" O THR D 856 " (cutoff:3.500A) Processing sheet with id=AG7, first strand: chain 'D' and resid 1117 through 1122 removed outlier: 4.769A pdb=" N ALA D1084 " --> pdb=" O SER D1120 " (cutoff:3.500A) 991 hydrogen bonds defined for protein. 2598 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: 14.24 Time building geometry restraints manager: 9.03 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.34: 9529 1.34 - 1.46: 7670 1.46 - 1.59: 13740 1.59 - 1.71: 0 1.71 - 1.83: 167 Bond restraints: 31106 Sorted by residual: bond pdb=" C1 NAG X 2 " pdb=" O5 NAG X 2 " ideal model delta sigma weight residual 1.406 1.491 -0.085 2.00e-02 2.50e+03 1.79e+01 bond pdb=" N ILE B 323 " pdb=" CA ILE B 323 " ideal model delta sigma weight residual 1.456 1.500 -0.045 1.11e-02 8.12e+03 1.63e+01 bond pdb=" N PHE C 326 " pdb=" CA PHE C 326 " ideal model delta sigma weight residual 1.455 1.492 -0.037 9.60e-03 1.09e+04 1.49e+01 bond pdb=" C1 NAG A 2 " pdb=" O5 NAG A 2 " ideal model delta sigma weight residual 1.406 1.482 -0.076 2.00e-02 2.50e+03 1.43e+01 bond pdb=" N VAL D 317 " pdb=" CA VAL D 317 " ideal model delta sigma weight residual 1.458 1.496 -0.039 1.14e-02 7.69e+03 1.15e+01 ... (remaining 31101 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.30: 41622 2.30 - 4.61: 610 4.61 - 6.91: 58 6.91 - 9.22: 13 9.22 - 11.52: 2 Bond angle restraints: 42305 Sorted by residual: angle pdb=" CA PHE C 326 " pdb=" C PHE C 326 " pdb=" N PRO C 327 " ideal model delta sigma weight residual 117.95 123.38 -5.43 7.70e-01 1.69e+00 4.97e+01 angle pdb=" C THR C 19 " pdb=" CA THR C 19 " pdb=" CB THR C 19 " ideal model delta sigma weight residual 116.54 110.43 6.11 1.15e+00 7.56e-01 2.82e+01 angle pdb=" CA PHE C 326 " pdb=" C PHE C 326 " pdb=" O PHE C 326 " ideal model delta sigma weight residual 120.34 115.85 4.49 9.20e-01 1.18e+00 2.38e+01 angle pdb=" C THR D 19 " pdb=" CA THR D 19 " pdb=" CB THR D 19 " ideal model delta sigma weight residual 115.79 110.13 5.66 1.19e+00 7.06e-01 2.26e+01 angle pdb=" CA ASN C 143 " pdb=" C ASN C 143 " pdb=" O ASN C 143 " ideal model delta sigma weight residual 122.45 116.86 5.59 1.30e+00 5.92e-01 1.85e+01 ... (remaining 42300 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 24.95: 18309 24.95 - 49.89: 998 49.89 - 74.84: 97 74.84 - 99.79: 64 99.79 - 124.73: 42 Dihedral angle restraints: 19510 sinusoidal: 8571 harmonic: 10939 Sorted by residual: dihedral pdb=" CA ASP C 140 " pdb=" C ASP C 140 " pdb=" N HIS C 141 " pdb=" CA HIS C 141 " ideal model delta harmonic sigma weight residual 180.00 -133.47 -46.53 0 5.00e+00 4.00e-02 8.66e+01 dihedral pdb=" CA ASP D 140 " pdb=" C ASP D 140 " pdb=" N HIS D 141 " pdb=" CA HIS D 141 " ideal model delta harmonic sigma weight residual -180.00 -133.79 -46.21 0 5.00e+00 4.00e-02 8.54e+01 dihedral pdb=" CB CYS D 735 " pdb=" SG CYS D 735 " pdb=" SG CYS D 757 " pdb=" CB CYS D 757 " ideal model delta sinusoidal sigma weight residual 93.00 13.70 79.30 1 1.00e+01 1.00e-02 7.82e+01 ... (remaining 19507 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.098: 4710 0.098 - 0.197: 254 0.197 - 0.295: 14 0.295 - 0.394: 1 0.394 - 0.492: 1 Chirality restraints: 4980 Sorted by residual: chirality pdb=" CA ASN C 144 " pdb=" N ASN C 144 " pdb=" C ASN C 144 " pdb=" CB ASN C 144 " both_signs ideal model delta sigma weight residual False 2.51 2.02 0.49 2.00e-01 2.50e+01 6.06e+00 chirality pdb=" C1 NAG X 1 " pdb=" ND2 ASN D1071 " pdb=" C2 NAG X 1 " pdb=" O5 NAG X 1 " both_signs ideal model delta sigma weight residual False -2.40 -2.01 -0.39 2.00e-01 2.50e+01 3.84e+00 chirality pdb=" CA ASN C 143 " pdb=" N ASN C 143 " pdb=" C ASN C 143 " pdb=" CB ASN C 143 " both_signs ideal model delta sigma weight residual False 2.51 2.22 0.29 2.00e-01 2.50e+01 2.17e+00 ... (remaining 4977 not shown) Planarity restraints: 5395 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 NAG C1301 " 0.023 2.00e-02 2.50e+03 3.24e-02 1.31e+01 pdb=" C7 NAG C1301 " -0.057 2.00e-02 2.50e+03 pdb=" C8 NAG C1301 " 0.032 2.00e-02 2.50e+03 pdb=" N2 NAG C1301 " -0.013 2.00e-02 2.50e+03 pdb=" O7 NAG C1301 " 0.015 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLU B 321 " -0.011 2.00e-02 2.50e+03 2.16e-02 4.65e+00 pdb=" C GLU B 321 " 0.037 2.00e-02 2.50e+03 pdb=" O GLU B 321 " -0.014 2.00e-02 2.50e+03 pdb=" N SER B 322 " -0.012 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C THR B 627 " 0.030 5.00e-02 4.00e+02 4.47e-02 3.20e+00 pdb=" N PRO B 628 " -0.077 5.00e-02 4.00e+02 pdb=" CA PRO B 628 " 0.023 5.00e-02 4.00e+02 pdb=" CD PRO B 628 " 0.025 5.00e-02 4.00e+02 ... (remaining 5392 not shown) Histogram of nonbonded interaction distances: 2.11 - 2.67: 584 2.67 - 3.23: 28769 3.23 - 3.78: 44837 3.78 - 4.34: 60517 4.34 - 4.90: 98128 Nonbonded interactions: 232835 Sorted by model distance: nonbonded pdb=" CG ARG C 463 " pdb=" O7 NAG C1301 " model vdw 2.109 2.752 nonbonded pdb=" OG SER G 33 " pdb=" O CYS G 102 " model vdw 2.130 3.040 nonbonded pdb=" O PRO B 227 " pdb=" NH2 ARG C 354 " model vdw 2.143 3.120 nonbonded pdb=" O GLY C 877 " pdb=" OG SER C 881 " model vdw 2.181 3.040 nonbonded pdb=" NH2 ARG B 564 " pdb=" OD1 ASP B 565 " model vdw 2.186 3.120 ... (remaining 232830 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'E' selection = chain 'F' selection = chain 'J' selection = chain 'N' selection = chain 'O' selection = chain 'P' selection = chain 'Q' selection = chain 'R' selection = chain 'U' selection = chain 'V' selection = chain 'W' selection = chain 'X' selection = chain 'Y' selection = chain 'a' } ncs_group { reference = chain 'B' selection = (chain 'C' and (resid 14 through 1159 or resid 1301 through 1309)) selection = chain 'D' } ncs_group { reference = chain 'G' selection = chain 'H' } ncs_group { reference = chain 'I' selection = chain 'L' } ncs_group { reference = chain 'K' selection = chain 'M' selection = chain 'S' selection = chain 'T' selection = chain 'Z' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.340 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: 1.140 Check model and map are aligned: 0.200 Set scattering table: 0.240 Process input model: 68.950 Find NCS groups from input model: 1.770 Set up NCS constraints: 0.320 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: 0.020 Load rotamer database and sin/cos tables:2.710 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 78.720 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8110 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 0.085 31225 Z= 0.213 Angle : 0.661 11.521 42596 Z= 0.333 Chirality : 0.048 0.492 4980 Planarity : 0.004 0.052 5353 Dihedral : 15.998 124.733 12333 Min Nonbonded Distance : 2.109 Molprobity Statistics. All-atom Clashscore : 11.89 Ramachandran Plot: Outliers : 0.05 % Allowed : 5.71 % Favored : 94.24 % Rotamer: Outliers : 0.15 % Allowed : 0.49 % Favored : 99.36 % Cbeta Deviations : 0.03 % Peptide Plane: Cis-proline : 1.07 % Cis-general : 0.03 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.30 (0.13), residues: 3716 helix: -0.94 (0.20), residues: 675 sheet: 0.25 (0.19), residues: 776 loop : -1.27 (0.13), residues: 2265 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.001 TRP B 630 HIS 0.006 0.001 HIS C 141 PHE 0.015 0.001 PHE C 487 TYR 0.020 0.001 TYR G 96 ARG 0.008 0.000 ARG D 234 Details of bonding type rmsd link_NAG-ASN : bond 0.00452 ( 42) link_NAG-ASN : angle 1.99835 ( 126) link_BETA1-4 : bond 0.00455 ( 25) link_BETA1-4 : angle 1.13980 ( 75) hydrogen bonds : bond 0.26157 ( 963) hydrogen bonds : angle 8.58960 ( 2598) SS BOND : bond 0.00320 ( 45) SS BOND : angle 1.42107 ( 90) covalent geometry : bond 0.00420 (31106) covalent geometry : angle 0.64908 (42305) Misc. bond : bond 0.00624 ( 7) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7432 Ramachandran restraints generated. 3716 Oldfield, 0 Emsley, 3716 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7432 Ramachandran restraints generated. 3716 Oldfield, 0 Emsley, 3716 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 178 residues out of total 3284 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 173 time to evaluate : 3.432 Fit side-chains REVERT: G 67 GLU cc_start: 0.7686 (pm20) cc_final: 0.7262 (pp20) REVERT: L 96 PRO cc_start: 0.5049 (Cg_exo) cc_final: 0.4845 (Cg_endo) REVERT: B 512 PHE cc_start: 0.6940 (p90) cc_final: 0.6724 (p90) REVERT: C 335 PHE cc_start: 0.7070 (m-80) cc_final: 0.6846 (m-80) outliers start: 5 outliers final: 0 residues processed: 178 average time/residue: 0.3984 time to fit residues: 118.9102 Evaluate side-chains 116 residues out of total 3284 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 116 time to evaluate : 3.505 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 371 random chunks: chunk 313 optimal weight: 0.7980 chunk 281 optimal weight: 0.9980 chunk 156 optimal weight: 7.9990 chunk 96 optimal weight: 2.9990 chunk 189 optimal weight: 9.9990 chunk 150 optimal weight: 1.9990 chunk 290 optimal weight: 0.9980 chunk 112 optimal weight: 2.9990 chunk 176 optimal weight: 6.9990 chunk 216 optimal weight: 1.9990 chunk 336 optimal weight: 3.9990 overall best weight: 1.3584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 60 ASN G 116 GLN I 91 GLN L 39 GLN ** L 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 850 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1156 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 952 ASN C1139 GLN D 97 ASN ** D 328 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 414 ASN ** D 577 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 610 GLN D 923 GLN D1098 HIS Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4210 r_free = 0.4210 target = 0.123279 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3327 r_free = 0.3327 target = 0.076013 restraints weight = 99422.969| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3344 r_free = 0.3344 target = 0.076986 restraints weight = 75717.167| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3351 r_free = 0.3351 target = 0.077148 restraints weight = 52193.043| |-----------------------------------------------------------------------------| r_work (final): 0.3255 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8072 moved from start: 0.1121 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 31225 Z= 0.147 Angle : 0.638 10.684 42596 Z= 0.319 Chirality : 0.047 0.408 4980 Planarity : 0.004 0.044 5353 Dihedral : 10.920 110.989 5579 Min Nonbonded Distance : 2.201 Molprobity Statistics. All-atom Clashscore : 9.11 Ramachandran Plot: Outliers : 0.03 % Allowed : 5.14 % Favored : 94.83 % Rotamer: Outliers : 0.46 % Allowed : 6.96 % Favored : 92.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.07 % Cis-general : 0.03 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.21 (0.13), residues: 3716 helix: -0.65 (0.20), residues: 701 sheet: 0.22 (0.18), residues: 806 loop : -1.27 (0.13), residues: 2209 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP D 64 HIS 0.005 0.001 HIS C 141 PHE 0.031 0.001 PHE B 181 TYR 0.031 0.001 TYR C 262 ARG 0.009 0.000 ARG B 185 Details of bonding type rmsd link_NAG-ASN : bond 0.00389 ( 42) link_NAG-ASN : angle 1.84399 ( 126) link_BETA1-4 : bond 0.00592 ( 25) link_BETA1-4 : angle 1.95852 ( 75) hydrogen bonds : bond 0.06438 ( 963) hydrogen bonds : angle 6.36894 ( 2598) SS BOND : bond 0.00410 ( 45) SS BOND : angle 1.20361 ( 90) covalent geometry : bond 0.00325 (31106) covalent geometry : angle 0.62431 (42305) Misc. bond : bond 0.00408 ( 7) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7432 Ramachandran restraints generated. 3716 Oldfield, 0 Emsley, 3716 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7432 Ramachandran restraints generated. 3716 Oldfield, 0 Emsley, 3716 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 165 residues out of total 3284 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 150 time to evaluate : 3.251 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: G 2 MET cc_start: 0.4380 (ttt) cc_final: 0.4174 (ttt) REVERT: L 96 PRO cc_start: 0.4838 (Cg_exo) cc_final: 0.4617 (Cg_endo) REVERT: B 512 PHE cc_start: 0.7151 (p90) cc_final: 0.6787 (p90) REVERT: B 589 PHE cc_start: 0.7094 (p90) cc_final: 0.6698 (p90) REVERT: C 335 PHE cc_start: 0.6649 (m-80) cc_final: 0.6329 (m-80) REVERT: C 455 LYS cc_start: 0.6628 (mmtt) cc_final: 0.6362 (mmmt) REVERT: C 559 PHE cc_start: 0.7193 (p90) cc_final: 0.6985 (p90) REVERT: C 1139 GLN cc_start: 0.8966 (OUTLIER) cc_final: 0.8622 (tp-100) REVERT: D 148 MET cc_start: 0.6174 (tpp) cc_final: 0.5942 (tpp) REVERT: D 172 MET cc_start: 0.3305 (mmt) cc_final: 0.2960 (mmt) REVERT: D 181 PHE cc_start: 0.6074 (m-80) cc_final: 0.5623 (m-10) REVERT: D 999 GLN cc_start: 0.8544 (tm-30) cc_final: 0.8268 (tm-30) outliers start: 15 outliers final: 10 residues processed: 156 average time/residue: 0.4090 time to fit residues: 106.5856 Evaluate side-chains 132 residues out of total 3284 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 121 time to evaluate : 3.453 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 115 LEU Chi-restraints excluded: chain B residue 235 PHE Chi-restraints excluded: chain B residue 299 THR Chi-restraints excluded: chain B residue 325 ARG Chi-restraints excluded: chain B residue 389 PHE Chi-restraints excluded: chain B residue 393 TYR Chi-restraints excluded: chain B residue 897 MET Chi-restraints excluded: chain C residue 1139 GLN Chi-restraints excluded: chain D residue 196 PHE Chi-restraints excluded: chain D residue 366 TYR Chi-restraints excluded: chain D residue 1138 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 371 random chunks: chunk 198 optimal weight: 1.9990 chunk 178 optimal weight: 0.9980 chunk 197 optimal weight: 8.9990 chunk 79 optimal weight: 10.0000 chunk 351 optimal weight: 6.9990 chunk 155 optimal weight: 4.9990 chunk 267 optimal weight: 9.9990 chunk 173 optimal weight: 0.9980 chunk 101 optimal weight: 3.9990 chunk 92 optimal weight: 10.0000 chunk 164 optimal weight: 9.9990 overall best weight: 2.5986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: I 90 GLN L 90 GLN ** L 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1156 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C1139 GLN ** D 328 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 610 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4160 r_free = 0.4160 target = 0.120489 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3281 r_free = 0.3281 target = 0.075050 restraints weight = 97982.296| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3241 r_free = 0.3241 target = 0.072925 restraints weight = 75025.370| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3235 r_free = 0.3235 target = 0.072826 restraints weight = 65973.286| |-----------------------------------------------------------------------------| r_work (final): 0.3151 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8075 moved from start: 0.1459 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.073 31225 Z= 0.204 Angle : 0.647 10.774 42596 Z= 0.322 Chirality : 0.047 0.420 4980 Planarity : 0.004 0.059 5353 Dihedral : 9.407 114.031 5579 Min Nonbonded Distance : 2.206 Molprobity Statistics. All-atom Clashscore : 9.61 Ramachandran Plot: Outliers : 0.03 % Allowed : 5.97 % Favored : 94.00 % Rotamer: Outliers : 0.76 % Allowed : 10.87 % Favored : 88.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.07 % Cis-general : 0.03 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.29 (0.13), residues: 3716 helix: -0.54 (0.20), residues: 694 sheet: 0.15 (0.18), residues: 831 loop : -1.39 (0.13), residues: 2191 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP D 64 HIS 0.005 0.001 HIS C1085 PHE 0.020 0.001 PHE B 326 TYR 0.028 0.001 TYR C 262 ARG 0.008 0.001 ARG B 185 Details of bonding type rmsd link_NAG-ASN : bond 0.00395 ( 42) link_NAG-ASN : angle 1.95874 ( 126) link_BETA1-4 : bond 0.00513 ( 25) link_BETA1-4 : angle 1.85775 ( 75) hydrogen bonds : bond 0.05951 ( 963) hydrogen bonds : angle 6.15981 ( 2598) SS BOND : bond 0.00402 ( 45) SS BOND : angle 1.17799 ( 90) covalent geometry : bond 0.00478 (31106) covalent geometry : angle 0.63321 (42305) Misc. bond : bond 0.00347 ( 7) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7432 Ramachandran restraints generated. 3716 Oldfield, 0 Emsley, 3716 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7432 Ramachandran restraints generated. 3716 Oldfield, 0 Emsley, 3716 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 152 residues out of total 3284 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 127 time to evaluate : 3.161 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 512 PHE cc_start: 0.7242 (p90) cc_final: 0.6824 (p90) REVERT: B 589 PHE cc_start: 0.7056 (p90) cc_final: 0.6666 (p90) REVERT: C 335 PHE cc_start: 0.6733 (m-80) cc_final: 0.6360 (m-80) REVERT: C 559 PHE cc_start: 0.7263 (p90) cc_final: 0.7003 (p90) REVERT: C 1089 GLU cc_start: 0.8506 (pp20) cc_final: 0.8289 (pp20) REVERT: D 148 MET cc_start: 0.6488 (tpp) cc_final: 0.6283 (tpp) REVERT: D 181 PHE cc_start: 0.6172 (m-80) cc_final: 0.5792 (m-10) REVERT: D 999 GLN cc_start: 0.8484 (tm-30) cc_final: 0.8133 (tm-30) outliers start: 25 outliers final: 11 residues processed: 147 average time/residue: 0.4119 time to fit residues: 103.5771 Evaluate side-chains 124 residues out of total 3284 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 113 time to evaluate : 3.236 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 69 VAL Chi-restraints excluded: chain B residue 235 PHE Chi-restraints excluded: chain B residue 299 THR Chi-restraints excluded: chain B residue 325 ARG Chi-restraints excluded: chain B residue 326 PHE Chi-restraints excluded: chain B residue 897 MET Chi-restraints excluded: chain C residue 198 ILE Chi-restraints excluded: chain D residue 33 THR Chi-restraints excluded: chain D residue 366 TYR Chi-restraints excluded: chain D residue 373 THR Chi-restraints excluded: chain D residue 1138 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 371 random chunks: chunk 203 optimal weight: 0.9990 chunk 249 optimal weight: 0.0270 chunk 75 optimal weight: 6.9990 chunk 5 optimal weight: 0.0980 chunk 256 optimal weight: 2.9990 chunk 62 optimal weight: 5.9990 chunk 208 optimal weight: 2.9990 chunk 111 optimal weight: 0.9990 chunk 241 optimal weight: 4.9990 chunk 366 optimal weight: 2.9990 chunk 160 optimal weight: 9.9990 overall best weight: 1.0244 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 91 GLN ** B 191 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1156 HIS ** D 328 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4179 r_free = 0.4179 target = 0.122282 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3364 r_free = 0.3364 target = 0.078667 restraints weight = 100805.472| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3281 r_free = 0.3281 target = 0.074290 restraints weight = 71659.485| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3280 r_free = 0.3280 target = 0.074691 restraints weight = 63063.459| |-----------------------------------------------------------------------------| r_work (final): 0.3194 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8021 moved from start: 0.1652 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 31225 Z= 0.117 Angle : 0.580 10.985 42596 Z= 0.286 Chirality : 0.045 0.400 4980 Planarity : 0.004 0.047 5353 Dihedral : 8.287 112.704 5579 Min Nonbonded Distance : 2.204 Molprobity Statistics. All-atom Clashscore : 8.85 Ramachandran Plot: Outliers : 0.03 % Allowed : 5.01 % Favored : 94.97 % Rotamer: Outliers : 1.19 % Allowed : 11.87 % Favored : 86.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.07 % Cis-general : 0.03 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.10 (0.13), residues: 3716 helix: -0.26 (0.20), residues: 690 sheet: 0.27 (0.18), residues: 813 loop : -1.30 (0.13), residues: 2213 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP D 64 HIS 0.004 0.001 HIS B1156 PHE 0.019 0.001 PHE B 326 TYR 0.024 0.001 TYR C 262 ARG 0.006 0.000 ARG B 185 Details of bonding type rmsd link_NAG-ASN : bond 0.00357 ( 42) link_NAG-ASN : angle 1.81990 ( 126) link_BETA1-4 : bond 0.00513 ( 25) link_BETA1-4 : angle 1.77265 ( 75) hydrogen bonds : bond 0.04891 ( 963) hydrogen bonds : angle 5.78113 ( 2598) SS BOND : bond 0.00468 ( 45) SS BOND : angle 0.87694 ( 90) covalent geometry : bond 0.00255 (31106) covalent geometry : angle 0.56700 (42305) Misc. bond : bond 0.00330 ( 7) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7432 Ramachandran restraints generated. 3716 Oldfield, 0 Emsley, 3716 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7432 Ramachandran restraints generated. 3716 Oldfield, 0 Emsley, 3716 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 165 residues out of total 3284 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 126 time to evaluate : 3.527 Fit side-chains revert: symmetry clash REVERT: I 73 THR cc_start: 0.8465 (OUTLIER) cc_final: 0.8243 (m) REVERT: B 325 ARG cc_start: 0.5451 (OUTLIER) cc_final: 0.5151 (tmm160) REVERT: B 430 VAL cc_start: 0.4935 (OUTLIER) cc_final: 0.4583 (t) REVERT: B 512 PHE cc_start: 0.7257 (p90) cc_final: 0.6828 (p90) REVERT: B 589 PHE cc_start: 0.6770 (p90) cc_final: 0.6459 (p90) REVERT: C 335 PHE cc_start: 0.6464 (m-80) cc_final: 0.6064 (m-80) REVERT: D 148 MET cc_start: 0.6646 (tpp) cc_final: 0.6437 (tpp) REVERT: D 172 MET cc_start: 0.3370 (mmt) cc_final: 0.3158 (mmt) REVERT: D 181 PHE cc_start: 0.6220 (m-80) cc_final: 0.5782 (m-10) REVERT: D 630 TRP cc_start: 0.5499 (p90) cc_final: 0.5231 (p90) REVERT: D 999 GLN cc_start: 0.8341 (tm-30) cc_final: 0.7839 (tm-30) outliers start: 39 outliers final: 19 residues processed: 158 average time/residue: 0.3666 time to fit residues: 100.5317 Evaluate side-chains 132 residues out of total 3284 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 110 time to evaluate : 3.263 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 107 CYS Chi-restraints excluded: chain I residue 73 THR Chi-restraints excluded: chain B residue 117 ILE Chi-restraints excluded: chain B residue 235 PHE Chi-restraints excluded: chain B residue 299 THR Chi-restraints excluded: chain B residue 325 ARG Chi-restraints excluded: chain B residue 326 PHE Chi-restraints excluded: chain B residue 389 PHE Chi-restraints excluded: chain B residue 430 VAL Chi-restraints excluded: chain B residue 596 THR Chi-restraints excluded: chain B residue 897 MET Chi-restraints excluded: chain B residue 906 ILE Chi-restraints excluded: chain B residue 960 VAL Chi-restraints excluded: chain C residue 198 ILE Chi-restraints excluded: chain C residue 207 VAL Chi-restraints excluded: chain C residue 578 THR Chi-restraints excluded: chain C residue 585 THR Chi-restraints excluded: chain D residue 163 PHE Chi-restraints excluded: chain D residue 188 VAL Chi-restraints excluded: chain D residue 365 LEU Chi-restraints excluded: chain D residue 373 THR Chi-restraints excluded: chain D residue 1138 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 371 random chunks: chunk 131 optimal weight: 0.0770 chunk 152 optimal weight: 10.0000 chunk 48 optimal weight: 7.9990 chunk 263 optimal weight: 7.9990 chunk 11 optimal weight: 50.0000 chunk 31 optimal weight: 50.0000 chunk 135 optimal weight: 0.8980 chunk 275 optimal weight: 30.0000 chunk 321 optimal weight: 0.0270 chunk 18 optimal weight: 0.8980 chunk 287 optimal weight: 5.9990 overall best weight: 1.5798 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 850 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 328 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4171 r_free = 0.4171 target = 0.121753 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3335 r_free = 0.3335 target = 0.077328 restraints weight = 100661.089| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3264 r_free = 0.3264 target = 0.073502 restraints weight = 74877.054| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3267 r_free = 0.3267 target = 0.074271 restraints weight = 65312.417| |-----------------------------------------------------------------------------| r_work (final): 0.3178 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8052 moved from start: 0.1811 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 31225 Z= 0.140 Angle : 0.589 11.434 42596 Z= 0.290 Chirality : 0.045 0.400 4980 Planarity : 0.004 0.046 5353 Dihedral : 7.596 114.015 5579 Min Nonbonded Distance : 2.208 Molprobity Statistics. All-atom Clashscore : 9.03 Ramachandran Plot: Outliers : 0.05 % Allowed : 5.46 % Favored : 94.48 % Rotamer: Outliers : 1.40 % Allowed : 13.46 % Favored : 85.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.07 % Cis-general : 0.03 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.03 (0.13), residues: 3716 helix: -0.13 (0.20), residues: 692 sheet: 0.31 (0.18), residues: 810 loop : -1.28 (0.13), residues: 2214 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP D 64 HIS 0.003 0.001 HIS C1085 PHE 0.018 0.001 PHE D 559 TYR 0.023 0.001 TYR C 262 ARG 0.006 0.000 ARG B 185 Details of bonding type rmsd link_NAG-ASN : bond 0.00343 ( 42) link_NAG-ASN : angle 1.97346 ( 126) link_BETA1-4 : bond 0.00476 ( 25) link_BETA1-4 : angle 1.79041 ( 75) hydrogen bonds : bond 0.04779 ( 963) hydrogen bonds : angle 5.65685 ( 2598) SS BOND : bond 0.00305 ( 45) SS BOND : angle 1.07299 ( 90) covalent geometry : bond 0.00323 (31106) covalent geometry : angle 0.57405 (42305) Misc. bond : bond 0.00319 ( 7) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7432 Ramachandran restraints generated. 3716 Oldfield, 0 Emsley, 3716 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7432 Ramachandran restraints generated. 3716 Oldfield, 0 Emsley, 3716 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 168 residues out of total 3284 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 122 time to evaluate : 3.230 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: I 73 THR cc_start: 0.8464 (OUTLIER) cc_final: 0.8247 (m) REVERT: B 325 ARG cc_start: 0.5574 (OUTLIER) cc_final: 0.5226 (tmm160) REVERT: B 512 PHE cc_start: 0.7374 (p90) cc_final: 0.6938 (p90) REVERT: B 589 PHE cc_start: 0.6877 (p90) cc_final: 0.6577 (p90) REVERT: C 335 PHE cc_start: 0.6296 (m-80) cc_final: 0.5857 (m-80) REVERT: C 866 MET cc_start: 0.8381 (mtm) cc_final: 0.7900 (mtm) REVERT: D 148 MET cc_start: 0.6612 (tpp) cc_final: 0.6390 (tpp) REVERT: D 181 PHE cc_start: 0.6290 (m-80) cc_final: 0.5941 (m-10) REVERT: D 999 GLN cc_start: 0.8323 (tm-30) cc_final: 0.7798 (tm-30) outliers start: 46 outliers final: 27 residues processed: 160 average time/residue: 0.3808 time to fit residues: 102.9461 Evaluate side-chains 135 residues out of total 3284 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 106 time to evaluate : 3.197 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 69 VAL Chi-restraints excluded: chain G residue 107 CYS Chi-restraints excluded: chain I residue 48 LEU Chi-restraints excluded: chain I residue 73 THR Chi-restraints excluded: chain B residue 81 VAL Chi-restraints excluded: chain B residue 235 PHE Chi-restraints excluded: chain B residue 299 THR Chi-restraints excluded: chain B residue 325 ARG Chi-restraints excluded: chain B residue 326 PHE Chi-restraints excluded: chain B residue 596 THR Chi-restraints excluded: chain B residue 756 PHE Chi-restraints excluded: chain B residue 897 MET Chi-restraints excluded: chain B residue 906 ILE Chi-restraints excluded: chain B residue 960 VAL Chi-restraints excluded: chain C residue 93 ILE Chi-restraints excluded: chain C residue 195 TYR Chi-restraints excluded: chain C residue 207 VAL Chi-restraints excluded: chain C residue 578 THR Chi-restraints excluded: chain C residue 585 THR Chi-restraints excluded: chain D residue 33 THR Chi-restraints excluded: chain D residue 82 LEU Chi-restraints excluded: chain D residue 188 VAL Chi-restraints excluded: chain D residue 359 VAL Chi-restraints excluded: chain D residue 365 LEU Chi-restraints excluded: chain D residue 373 THR Chi-restraints excluded: chain D residue 702 VAL Chi-restraints excluded: chain D residue 746 CYS Chi-restraints excluded: chain D residue 973 VAL Chi-restraints excluded: chain D residue 1138 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 371 random chunks: chunk 293 optimal weight: 20.0000 chunk 42 optimal weight: 8.9990 chunk 169 optimal weight: 8.9990 chunk 116 optimal weight: 3.9990 chunk 241 optimal weight: 2.9990 chunk 44 optimal weight: 9.9990 chunk 221 optimal weight: 1.9990 chunk 260 optimal weight: 3.9990 chunk 33 optimal weight: 20.0000 chunk 367 optimal weight: 5.9990 chunk 272 optimal weight: 10.0000 overall best weight: 3.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 183 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 533 ASN B 561 GLN ** B 850 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1116 ASN ** D 328 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4137 r_free = 0.4137 target = 0.119001 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3221 r_free = 0.3221 target = 0.072717 restraints weight = 98822.539| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3202 r_free = 0.3202 target = 0.070805 restraints weight = 75949.641| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3196 r_free = 0.3196 target = 0.071058 restraints weight = 67659.121| |-----------------------------------------------------------------------------| r_work (final): 0.3110 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8132 moved from start: 0.2100 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.062 31225 Z= 0.283 Angle : 0.701 11.592 42596 Z= 0.349 Chirality : 0.048 0.430 4980 Planarity : 0.004 0.058 5353 Dihedral : 7.616 116.703 5579 Min Nonbonded Distance : 2.207 Molprobity Statistics. All-atom Clashscore : 10.51 Ramachandran Plot: Outliers : 0.05 % Allowed : 6.75 % Favored : 93.19 % Rotamer: Outliers : 1.95 % Allowed : 14.50 % Favored : 83.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.07 % Cis-general : 0.03 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.33 (0.13), residues: 3716 helix: -0.42 (0.20), residues: 697 sheet: 0.11 (0.18), residues: 837 loop : -1.48 (0.13), residues: 2182 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP G 51 HIS 0.006 0.001 HIS C1085 PHE 0.027 0.002 PHE D 559 TYR 0.024 0.002 TYR B1064 ARG 0.008 0.001 ARG C 354 Details of bonding type rmsd link_NAG-ASN : bond 0.00490 ( 42) link_NAG-ASN : angle 2.36672 ( 126) link_BETA1-4 : bond 0.00444 ( 25) link_BETA1-4 : angle 1.91718 ( 75) hydrogen bonds : bond 0.05780 ( 963) hydrogen bonds : angle 6.02247 ( 2598) SS BOND : bond 0.00390 ( 45) SS BOND : angle 1.64624 ( 90) covalent geometry : bond 0.00671 (31106) covalent geometry : angle 0.68273 (42305) Misc. bond : bond 0.00305 ( 7) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7432 Ramachandran restraints generated. 3716 Oldfield, 0 Emsley, 3716 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7432 Ramachandran restraints generated. 3716 Oldfield, 0 Emsley, 3716 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 180 residues out of total 3284 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 116 time to evaluate : 3.453 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: H 35 LEU cc_start: 0.6146 (tt) cc_final: 0.5885 (pt) REVERT: B 103 ILE cc_start: 0.7844 (OUTLIER) cc_final: 0.7643 (mm) REVERT: B 189 PHE cc_start: 0.2716 (OUTLIER) cc_final: 0.1887 (m-80) REVERT: B 325 ARG cc_start: 0.4816 (OUTLIER) cc_final: 0.4386 (tmm160) REVERT: B 430 VAL cc_start: 0.5021 (OUTLIER) cc_final: 0.4687 (t) REVERT: B 512 PHE cc_start: 0.7350 (p90) cc_final: 0.6939 (p90) REVERT: B 589 PHE cc_start: 0.6891 (p90) cc_final: 0.6535 (p90) REVERT: C 455 LYS cc_start: 0.6174 (mmtt) cc_final: 0.5858 (mmmt) REVERT: C 1089 GLU cc_start: 0.8645 (pp20) cc_final: 0.8341 (pp20) REVERT: D 148 MET cc_start: 0.6721 (tpp) cc_final: 0.6496 (tpp) REVERT: D 161 CYS cc_start: 0.2904 (OUTLIER) cc_final: 0.2692 (p) REVERT: D 999 GLN cc_start: 0.8487 (tm-30) cc_final: 0.7869 (tm-30) REVERT: D 1026 MET cc_start: 0.9256 (tpp) cc_final: 0.8953 (ttm) outliers start: 64 outliers final: 35 residues processed: 172 average time/residue: 0.3790 time to fit residues: 114.1076 Evaluate side-chains 147 residues out of total 3284 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 107 time to evaluate : 3.686 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 107 CYS Chi-restraints excluded: chain H residue 31 ASP Chi-restraints excluded: chain I residue 48 LEU Chi-restraints excluded: chain B residue 33 THR Chi-restraints excluded: chain B residue 103 ILE Chi-restraints excluded: chain B residue 117 ILE Chi-restraints excluded: chain B residue 118 VAL Chi-restraints excluded: chain B residue 189 PHE Chi-restraints excluded: chain B residue 235 PHE Chi-restraints excluded: chain B residue 299 THR Chi-restraints excluded: chain B residue 325 ARG Chi-restraints excluded: chain B residue 326 PHE Chi-restraints excluded: chain B residue 414 ASN Chi-restraints excluded: chain B residue 430 VAL Chi-restraints excluded: chain B residue 596 THR Chi-restraints excluded: chain B residue 897 MET Chi-restraints excluded: chain B residue 960 VAL Chi-restraints excluded: chain B residue 1074 THR Chi-restraints excluded: chain B residue 1098 HIS Chi-restraints excluded: chain C residue 88 VAL Chi-restraints excluded: chain C residue 93 ILE Chi-restraints excluded: chain C residue 195 TYR Chi-restraints excluded: chain C residue 198 ILE Chi-restraints excluded: chain C residue 207 VAL Chi-restraints excluded: chain C residue 578 THR Chi-restraints excluded: chain C residue 585 THR Chi-restraints excluded: chain D residue 33 THR Chi-restraints excluded: chain D residue 82 LEU Chi-restraints excluded: chain D residue 161 CYS Chi-restraints excluded: chain D residue 188 VAL Chi-restraints excluded: chain D residue 359 VAL Chi-restraints excluded: chain D residue 365 LEU Chi-restraints excluded: chain D residue 373 THR Chi-restraints excluded: chain D residue 585 THR Chi-restraints excluded: chain D residue 601 THR Chi-restraints excluded: chain D residue 702 VAL Chi-restraints excluded: chain D residue 726 VAL Chi-restraints excluded: chain D residue 746 CYS Chi-restraints excluded: chain D residue 973 VAL Chi-restraints excluded: chain D residue 1138 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 371 random chunks: chunk 311 optimal weight: 20.0000 chunk 181 optimal weight: 0.9980 chunk 237 optimal weight: 0.8980 chunk 350 optimal weight: 2.9990 chunk 352 optimal weight: 2.9990 chunk 73 optimal weight: 10.0000 chunk 90 optimal weight: 30.0000 chunk 367 optimal weight: 4.9990 chunk 52 optimal weight: 0.3980 chunk 152 optimal weight: 10.0000 chunk 370 optimal weight: 2.9990 overall best weight: 1.6584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 144 ASN ** B 183 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 191 ASN B 414 ASN ** B 850 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 328 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4161 r_free = 0.4161 target = 0.121038 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3320 r_free = 0.3320 target = 0.075917 restraints weight = 98804.861| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3257 r_free = 0.3257 target = 0.073771 restraints weight = 67347.887| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3257 r_free = 0.3257 target = 0.073834 restraints weight = 56915.593| |-----------------------------------------------------------------------------| r_work (final): 0.3173 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8051 moved from start: 0.2183 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 31225 Z= 0.146 Angle : 0.606 14.857 42596 Z= 0.302 Chirality : 0.045 0.381 4980 Planarity : 0.004 0.048 5353 Dihedral : 7.138 114.113 5579 Min Nonbonded Distance : 2.208 Molprobity Statistics. All-atom Clashscore : 9.20 Ramachandran Plot: Outliers : 0.03 % Allowed : 5.27 % Favored : 94.70 % Rotamer: Outliers : 1.74 % Allowed : 15.35 % Favored : 82.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.07 % Cis-general : 0.03 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.15 (0.13), residues: 3716 helix: -0.15 (0.20), residues: 699 sheet: 0.29 (0.18), residues: 823 loop : -1.43 (0.13), residues: 2194 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP D 147 HIS 0.003 0.001 HIS C1085 PHE 0.022 0.001 PHE D 559 TYR 0.021 0.001 TYR C 262 ARG 0.005 0.000 ARG C 354 Details of bonding type rmsd link_NAG-ASN : bond 0.00349 ( 42) link_NAG-ASN : angle 2.01443 ( 126) link_BETA1-4 : bond 0.00442 ( 25) link_BETA1-4 : angle 1.77873 ( 75) hydrogen bonds : bond 0.04831 ( 963) hydrogen bonds : angle 5.67134 ( 2598) SS BOND : bond 0.00329 ( 45) SS BOND : angle 2.07419 ( 90) covalent geometry : bond 0.00337 (31106) covalent geometry : angle 0.58509 (42305) Misc. bond : bond 0.00309 ( 7) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7432 Ramachandran restraints generated. 3716 Oldfield, 0 Emsley, 3716 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7432 Ramachandran restraints generated. 3716 Oldfield, 0 Emsley, 3716 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 171 residues out of total 3284 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 114 time to evaluate : 3.281 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 35 LEU cc_start: 0.6053 (tt) cc_final: 0.5765 (pt) REVERT: B 325 ARG cc_start: 0.5128 (OUTLIER) cc_final: 0.4804 (tmm160) REVERT: B 430 VAL cc_start: 0.5018 (OUTLIER) cc_final: 0.4672 (t) REVERT: B 512 PHE cc_start: 0.7388 (p90) cc_final: 0.6998 (p90) REVERT: B 589 PHE cc_start: 0.6955 (p90) cc_final: 0.6583 (p90) REVERT: C 335 PHE cc_start: 0.6768 (m-80) cc_final: 0.6450 (m-80) REVERT: C 866 MET cc_start: 0.8366 (mtm) cc_final: 0.7936 (mtm) REVERT: C 1089 GLU cc_start: 0.8556 (pp20) cc_final: 0.8284 (pp20) REVERT: D 148 MET cc_start: 0.6641 (tpp) cc_final: 0.6366 (tpp) REVERT: D 161 CYS cc_start: 0.2927 (OUTLIER) cc_final: 0.2647 (p) REVERT: D 181 PHE cc_start: 0.6371 (m-80) cc_final: 0.5720 (m-10) REVERT: D 999 GLN cc_start: 0.8355 (tm-30) cc_final: 0.7790 (tm-30) REVERT: D 1026 MET cc_start: 0.9283 (tpp) cc_final: 0.8971 (ttm) outliers start: 57 outliers final: 36 residues processed: 163 average time/residue: 0.3818 time to fit residues: 108.2461 Evaluate side-chains 147 residues out of total 3284 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 108 time to evaluate : 3.503 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 69 VAL Chi-restraints excluded: chain G residue 82 MET Chi-restraints excluded: chain G residue 107 CYS Chi-restraints excluded: chain I residue 48 LEU Chi-restraints excluded: chain I residue 80 GLU Chi-restraints excluded: chain L residue 80 GLU Chi-restraints excluded: chain B residue 117 ILE Chi-restraints excluded: chain B residue 118 VAL Chi-restraints excluded: chain B residue 189 PHE Chi-restraints excluded: chain B residue 235 PHE Chi-restraints excluded: chain B residue 299 THR Chi-restraints excluded: chain B residue 325 ARG Chi-restraints excluded: chain B residue 326 PHE Chi-restraints excluded: chain B residue 414 ASN Chi-restraints excluded: chain B residue 430 VAL Chi-restraints excluded: chain B residue 596 THR Chi-restraints excluded: chain B residue 694 MET Chi-restraints excluded: chain B residue 897 MET Chi-restraints excluded: chain B residue 906 ILE Chi-restraints excluded: chain B residue 960 VAL Chi-restraints excluded: chain C residue 88 VAL Chi-restraints excluded: chain C residue 192 ILE Chi-restraints excluded: chain C residue 195 TYR Chi-restraints excluded: chain C residue 198 ILE Chi-restraints excluded: chain C residue 207 VAL Chi-restraints excluded: chain C residue 578 THR Chi-restraints excluded: chain C residue 585 THR Chi-restraints excluded: chain D residue 33 THR Chi-restraints excluded: chain D residue 82 LEU Chi-restraints excluded: chain D residue 161 CYS Chi-restraints excluded: chain D residue 188 VAL Chi-restraints excluded: chain D residue 359 VAL Chi-restraints excluded: chain D residue 365 LEU Chi-restraints excluded: chain D residue 373 THR Chi-restraints excluded: chain D residue 585 THR Chi-restraints excluded: chain D residue 630 TRP Chi-restraints excluded: chain D residue 746 CYS Chi-restraints excluded: chain D residue 973 VAL Chi-restraints excluded: chain D residue 1138 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 371 random chunks: chunk 344 optimal weight: 0.7980 chunk 27 optimal weight: 20.0000 chunk 16 optimal weight: 0.0770 chunk 145 optimal weight: 3.9990 chunk 266 optimal weight: 6.9990 chunk 359 optimal weight: 3.9990 chunk 244 optimal weight: 0.0670 chunk 135 optimal weight: 0.7980 chunk 80 optimal weight: 6.9990 chunk 331 optimal weight: 5.9990 chunk 72 optimal weight: 0.9990 overall best weight: 0.5478 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 66 GLN ** B 183 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 414 ASN ** B 850 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 503 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 954 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 328 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4179 r_free = 0.4179 target = 0.121467 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3326 r_free = 0.3326 target = 0.076792 restraints weight = 97340.660| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3282 r_free = 0.3282 target = 0.074447 restraints weight = 70988.336| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3279 r_free = 0.3279 target = 0.074598 restraints weight = 63330.273| |-----------------------------------------------------------------------------| r_work (final): 0.3186 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8033 moved from start: 0.2276 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.041 31225 Z= 0.104 Angle : 0.574 12.091 42596 Z= 0.285 Chirality : 0.044 0.359 4980 Planarity : 0.004 0.054 5353 Dihedral : 6.730 112.492 5579 Min Nonbonded Distance : 2.207 Molprobity Statistics. All-atom Clashscore : 8.76 Ramachandran Plot: Outliers : 0.03 % Allowed : 5.14 % Favored : 94.83 % Rotamer: Outliers : 1.53 % Allowed : 15.60 % Favored : 82.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.07 % Cis-general : 0.03 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.94 (0.14), residues: 3716 helix: 0.09 (0.21), residues: 698 sheet: 0.42 (0.18), residues: 811 loop : -1.31 (0.13), residues: 2207 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP B 630 HIS 0.002 0.000 HIS D 502 PHE 0.019 0.001 PHE B 326 TYR 0.020 0.001 TYR C 262 ARG 0.006 0.000 ARG C 354 Details of bonding type rmsd link_NAG-ASN : bond 0.00366 ( 42) link_NAG-ASN : angle 1.88726 ( 126) link_BETA1-4 : bond 0.00463 ( 25) link_BETA1-4 : angle 1.68693 ( 75) hydrogen bonds : bond 0.04270 ( 963) hydrogen bonds : angle 5.41981 ( 2598) SS BOND : bond 0.00257 ( 45) SS BOND : angle 1.71614 ( 90) covalent geometry : bond 0.00221 (31106) covalent geometry : angle 0.55692 (42305) Misc. bond : bond 0.00313 ( 7) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7432 Ramachandran restraints generated. 3716 Oldfield, 0 Emsley, 3716 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7432 Ramachandran restraints generated. 3716 Oldfield, 0 Emsley, 3716 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 166 residues out of total 3284 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 116 time to evaluate : 3.411 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 35 LEU cc_start: 0.6015 (tt) cc_final: 0.5743 (pt) REVERT: B 325 ARG cc_start: 0.5112 (OUTLIER) cc_final: 0.4090 (tpp-160) REVERT: B 430 VAL cc_start: 0.5018 (OUTLIER) cc_final: 0.4677 (t) REVERT: B 512 PHE cc_start: 0.7372 (p90) cc_final: 0.6949 (p90) REVERT: B 589 PHE cc_start: 0.6933 (p90) cc_final: 0.6565 (p90) REVERT: C 335 PHE cc_start: 0.6629 (m-80) cc_final: 0.6277 (m-80) REVERT: C 866 MET cc_start: 0.8338 (mtm) cc_final: 0.8042 (mtm) REVERT: C 1089 GLU cc_start: 0.8549 (pp20) cc_final: 0.8270 (pp20) REVERT: D 148 MET cc_start: 0.6691 (tpp) cc_final: 0.6377 (tpp) REVERT: D 161 CYS cc_start: 0.3154 (OUTLIER) cc_final: 0.2846 (p) REVERT: D 181 PHE cc_start: 0.6253 (m-80) cc_final: 0.5731 (m-10) REVERT: D 999 GLN cc_start: 0.8301 (tm-30) cc_final: 0.7807 (tm-30) outliers start: 50 outliers final: 36 residues processed: 159 average time/residue: 0.3865 time to fit residues: 105.3758 Evaluate side-chains 149 residues out of total 3284 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 110 time to evaluate : 3.407 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 69 VAL Chi-restraints excluded: chain G residue 82 MET Chi-restraints excluded: chain G residue 107 CYS Chi-restraints excluded: chain I residue 80 GLU Chi-restraints excluded: chain L residue 80 GLU Chi-restraints excluded: chain B residue 118 VAL Chi-restraints excluded: chain B residue 235 PHE Chi-restraints excluded: chain B residue 274 LEU Chi-restraints excluded: chain B residue 299 THR Chi-restraints excluded: chain B residue 325 ARG Chi-restraints excluded: chain B residue 326 PHE Chi-restraints excluded: chain B residue 414 ASN Chi-restraints excluded: chain B residue 430 VAL Chi-restraints excluded: chain B residue 596 THR Chi-restraints excluded: chain B residue 694 MET Chi-restraints excluded: chain B residue 897 MET Chi-restraints excluded: chain B residue 906 ILE Chi-restraints excluded: chain B residue 960 VAL Chi-restraints excluded: chain B residue 1098 HIS Chi-restraints excluded: chain C residue 88 VAL Chi-restraints excluded: chain C residue 192 ILE Chi-restraints excluded: chain C residue 195 TYR Chi-restraints excluded: chain C residue 198 ILE Chi-restraints excluded: chain C residue 207 VAL Chi-restraints excluded: chain C residue 303 PHE Chi-restraints excluded: chain C residue 578 THR Chi-restraints excluded: chain C residue 585 THR Chi-restraints excluded: chain C residue 948 VAL Chi-restraints excluded: chain D residue 33 THR Chi-restraints excluded: chain D residue 82 LEU Chi-restraints excluded: chain D residue 161 CYS Chi-restraints excluded: chain D residue 188 VAL Chi-restraints excluded: chain D residue 359 VAL Chi-restraints excluded: chain D residue 366 TYR Chi-restraints excluded: chain D residue 373 THR Chi-restraints excluded: chain D residue 585 THR Chi-restraints excluded: chain D residue 726 VAL Chi-restraints excluded: chain D residue 746 CYS Chi-restraints excluded: chain D residue 973 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 371 random chunks: chunk 0 optimal weight: 40.0000 chunk 165 optimal weight: 0.0980 chunk 231 optimal weight: 8.9990 chunk 36 optimal weight: 50.0000 chunk 212 optimal weight: 0.4980 chunk 44 optimal weight: 0.6980 chunk 52 optimal weight: 2.9990 chunk 219 optimal weight: 0.8980 chunk 306 optimal weight: 6.9990 chunk 9 optimal weight: 7.9990 chunk 209 optimal weight: 4.9990 overall best weight: 1.0382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** G 116 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 183 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 414 ASN ** B 850 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 328 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4176 r_free = 0.4176 target = 0.121327 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3234 r_free = 0.3234 target = 0.072558 restraints weight = 96973.295| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3275 r_free = 0.3275 target = 0.074210 restraints weight = 62668.226| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3283 r_free = 0.3283 target = 0.074644 restraints weight = 40940.324| |-----------------------------------------------------------------------------| r_work (final): 0.3196 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8024 moved from start: 0.2323 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 31225 Z= 0.114 Angle : 0.571 10.500 42596 Z= 0.282 Chirality : 0.044 0.362 4980 Planarity : 0.004 0.055 5353 Dihedral : 6.563 111.864 5579 Min Nonbonded Distance : 2.208 Molprobity Statistics. All-atom Clashscore : 8.75 Ramachandran Plot: Outliers : 0.03 % Allowed : 5.27 % Favored : 94.70 % Rotamer: Outliers : 1.59 % Allowed : 15.72 % Favored : 82.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.07 % Cis-general : 0.03 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.90 (0.14), residues: 3716 helix: 0.16 (0.21), residues: 698 sheet: 0.46 (0.18), residues: 800 loop : -1.29 (0.13), residues: 2218 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP D 147 HIS 0.002 0.000 HIS C1085 PHE 0.020 0.001 PHE D 90 TYR 0.021 0.001 TYR C 262 ARG 0.007 0.000 ARG L 46 Details of bonding type rmsd link_NAG-ASN : bond 0.00347 ( 42) link_NAG-ASN : angle 1.90709 ( 126) link_BETA1-4 : bond 0.00453 ( 25) link_BETA1-4 : angle 1.68098 ( 75) hydrogen bonds : bond 0.04228 ( 963) hydrogen bonds : angle 5.36162 ( 2598) SS BOND : bond 0.00260 ( 45) SS BOND : angle 1.77110 ( 90) covalent geometry : bond 0.00258 (31106) covalent geometry : angle 0.55347 (42305) Misc. bond : bond 0.00315 ( 7) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7432 Ramachandran restraints generated. 3716 Oldfield, 0 Emsley, 3716 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7432 Ramachandran restraints generated. 3716 Oldfield, 0 Emsley, 3716 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 169 residues out of total 3284 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 117 time to evaluate : 3.484 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 3 GLN cc_start: 0.6296 (tm-30) cc_final: 0.5987 (tm-30) REVERT: B 430 VAL cc_start: 0.4921 (OUTLIER) cc_final: 0.4563 (t) REVERT: B 512 PHE cc_start: 0.7339 (p90) cc_final: 0.6979 (p90) REVERT: B 589 PHE cc_start: 0.6746 (p90) cc_final: 0.6443 (p90) REVERT: C 335 PHE cc_start: 0.6713 (m-80) cc_final: 0.6348 (m-80) REVERT: C 1089 GLU cc_start: 0.8453 (pp20) cc_final: 0.8191 (pp20) REVERT: D 148 MET cc_start: 0.6650 (tpp) cc_final: 0.6336 (tpp) REVERT: D 161 CYS cc_start: 0.3114 (OUTLIER) cc_final: 0.2838 (p) REVERT: D 181 PHE cc_start: 0.6217 (m-80) cc_final: 0.5619 (m-10) REVERT: D 999 GLN cc_start: 0.8265 (tm-30) cc_final: 0.7760 (tm-30) outliers start: 52 outliers final: 40 residues processed: 163 average time/residue: 0.3606 time to fit residues: 103.8906 Evaluate side-chains 153 residues out of total 3284 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 111 time to evaluate : 3.657 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 69 VAL Chi-restraints excluded: chain G residue 82 MET Chi-restraints excluded: chain G residue 107 CYS Chi-restraints excluded: chain I residue 80 GLU Chi-restraints excluded: chain L residue 80 GLU Chi-restraints excluded: chain B residue 117 ILE Chi-restraints excluded: chain B residue 118 VAL Chi-restraints excluded: chain B residue 235 PHE Chi-restraints excluded: chain B residue 274 LEU Chi-restraints excluded: chain B residue 299 THR Chi-restraints excluded: chain B residue 326 PHE Chi-restraints excluded: chain B residue 414 ASN Chi-restraints excluded: chain B residue 430 VAL Chi-restraints excluded: chain B residue 596 THR Chi-restraints excluded: chain B residue 694 MET Chi-restraints excluded: chain B residue 897 MET Chi-restraints excluded: chain B residue 960 VAL Chi-restraints excluded: chain B residue 1098 HIS Chi-restraints excluded: chain C residue 88 VAL Chi-restraints excluded: chain C residue 93 ILE Chi-restraints excluded: chain C residue 192 ILE Chi-restraints excluded: chain C residue 195 TYR Chi-restraints excluded: chain C residue 198 ILE Chi-restraints excluded: chain C residue 207 VAL Chi-restraints excluded: chain C residue 303 PHE Chi-restraints excluded: chain C residue 578 THR Chi-restraints excluded: chain C residue 585 THR Chi-restraints excluded: chain C residue 875 LEU Chi-restraints excluded: chain C residue 948 VAL Chi-restraints excluded: chain D residue 33 THR Chi-restraints excluded: chain D residue 82 LEU Chi-restraints excluded: chain D residue 161 CYS Chi-restraints excluded: chain D residue 188 VAL Chi-restraints excluded: chain D residue 230 ILE Chi-restraints excluded: chain D residue 359 VAL Chi-restraints excluded: chain D residue 365 LEU Chi-restraints excluded: chain D residue 373 THR Chi-restraints excluded: chain D residue 585 THR Chi-restraints excluded: chain D residue 630 TRP Chi-restraints excluded: chain D residue 726 VAL Chi-restraints excluded: chain D residue 746 CYS Chi-restraints excluded: chain D residue 973 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 371 random chunks: chunk 335 optimal weight: 3.9990 chunk 116 optimal weight: 3.9990 chunk 292 optimal weight: 5.9990 chunk 206 optimal weight: 0.5980 chunk 314 optimal weight: 9.9990 chunk 161 optimal weight: 1.9990 chunk 16 optimal weight: 4.9990 chunk 368 optimal weight: 0.2980 chunk 27 optimal weight: 8.9990 chunk 357 optimal weight: 3.9990 chunk 61 optimal weight: 8.9990 overall best weight: 2.1786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** G 116 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 183 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 414 ASN ** B 850 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 328 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4161 r_free = 0.4161 target = 0.120383 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3230 r_free = 0.3230 target = 0.072795 restraints weight = 97654.853| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3241 r_free = 0.3241 target = 0.072390 restraints weight = 69226.204| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3237 r_free = 0.3237 target = 0.072709 restraints weight = 54446.263| |-----------------------------------------------------------------------------| r_work (final): 0.3142 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8096 moved from start: 0.2382 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 31225 Z= 0.173 Angle : 0.611 10.476 42596 Z= 0.301 Chirality : 0.045 0.375 4980 Planarity : 0.004 0.054 5353 Dihedral : 6.657 112.364 5579 Min Nonbonded Distance : 2.209 Molprobity Statistics. All-atom Clashscore : 9.16 Ramachandran Plot: Outliers : 0.03 % Allowed : 6.00 % Favored : 93.97 % Rotamer: Outliers : 1.34 % Allowed : 16.12 % Favored : 82.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.07 % Cis-general : 0.03 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.99 (0.13), residues: 3716 helix: 0.06 (0.21), residues: 702 sheet: 0.38 (0.18), residues: 815 loop : -1.36 (0.13), residues: 2199 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP D 147 HIS 0.003 0.001 HIS C1085 PHE 0.023 0.001 PHE D 559 TYR 0.021 0.001 TYR C 262 ARG 0.006 0.000 ARG L 46 Details of bonding type rmsd link_NAG-ASN : bond 0.00538 ( 42) link_NAG-ASN : angle 2.21520 ( 126) link_BETA1-4 : bond 0.00484 ( 25) link_BETA1-4 : angle 1.79422 ( 75) hydrogen bonds : bond 0.04629 ( 963) hydrogen bonds : angle 5.47062 ( 2598) SS BOND : bond 0.00298 ( 45) SS BOND : angle 1.82192 ( 90) covalent geometry : bond 0.00406 (31106) covalent geometry : angle 0.59065 (42305) Misc. bond : bond 0.00312 ( 7) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7432 Ramachandran restraints generated. 3716 Oldfield, 0 Emsley, 3716 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7432 Ramachandran restraints generated. 3716 Oldfield, 0 Emsley, 3716 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 160 residues out of total 3284 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 116 time to evaluate : 3.483 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 3 GLN cc_start: 0.6321 (tm-30) cc_final: 0.6018 (tm-30) REVERT: B 430 VAL cc_start: 0.4990 (OUTLIER) cc_final: 0.4614 (t) REVERT: B 512 PHE cc_start: 0.7421 (p90) cc_final: 0.7076 (p90) REVERT: B 589 PHE cc_start: 0.6841 (p90) cc_final: 0.6538 (p90) REVERT: C 335 PHE cc_start: 0.6740 (m-80) cc_final: 0.6370 (m-80) REVERT: C 1089 GLU cc_start: 0.8511 (pp20) cc_final: 0.8228 (pp20) REVERT: D 148 MET cc_start: 0.6730 (tpp) cc_final: 0.6406 (tpp) REVERT: D 161 CYS cc_start: 0.2990 (OUTLIER) cc_final: 0.2726 (p) REVERT: D 181 PHE cc_start: 0.6410 (m-80) cc_final: 0.5880 (m-10) REVERT: D 999 GLN cc_start: 0.8237 (tm-30) cc_final: 0.7744 (tm-30) outliers start: 44 outliers final: 40 residues processed: 153 average time/residue: 0.3768 time to fit residues: 101.2416 Evaluate side-chains 151 residues out of total 3284 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 109 time to evaluate : 3.542 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 69 VAL Chi-restraints excluded: chain G residue 82 MET Chi-restraints excluded: chain G residue 107 CYS Chi-restraints excluded: chain I residue 80 GLU Chi-restraints excluded: chain L residue 80 GLU Chi-restraints excluded: chain B residue 117 ILE Chi-restraints excluded: chain B residue 118 VAL Chi-restraints excluded: chain B residue 235 PHE Chi-restraints excluded: chain B residue 274 LEU Chi-restraints excluded: chain B residue 299 THR Chi-restraints excluded: chain B residue 326 PHE Chi-restraints excluded: chain B residue 414 ASN Chi-restraints excluded: chain B residue 430 VAL Chi-restraints excluded: chain B residue 596 THR Chi-restraints excluded: chain B residue 694 MET Chi-restraints excluded: chain B residue 897 MET Chi-restraints excluded: chain B residue 960 VAL Chi-restraints excluded: chain B residue 1098 HIS Chi-restraints excluded: chain C residue 88 VAL Chi-restraints excluded: chain C residue 93 ILE Chi-restraints excluded: chain C residue 192 ILE Chi-restraints excluded: chain C residue 195 TYR Chi-restraints excluded: chain C residue 198 ILE Chi-restraints excluded: chain C residue 207 VAL Chi-restraints excluded: chain C residue 578 THR Chi-restraints excluded: chain C residue 585 THR Chi-restraints excluded: chain C residue 757 CYS Chi-restraints excluded: chain C residue 875 LEU Chi-restraints excluded: chain C residue 948 VAL Chi-restraints excluded: chain D residue 33 THR Chi-restraints excluded: chain D residue 82 LEU Chi-restraints excluded: chain D residue 161 CYS Chi-restraints excluded: chain D residue 188 VAL Chi-restraints excluded: chain D residue 359 VAL Chi-restraints excluded: chain D residue 365 LEU Chi-restraints excluded: chain D residue 373 THR Chi-restraints excluded: chain D residue 585 THR Chi-restraints excluded: chain D residue 630 TRP Chi-restraints excluded: chain D residue 726 VAL Chi-restraints excluded: chain D residue 746 CYS Chi-restraints excluded: chain D residue 973 VAL Chi-restraints excluded: chain D residue 1138 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 371 random chunks: chunk 368 optimal weight: 2.9990 chunk 133 optimal weight: 0.7980 chunk 289 optimal weight: 0.6980 chunk 124 optimal weight: 2.9990 chunk 277 optimal weight: 0.6980 chunk 230 optimal weight: 4.9990 chunk 199 optimal weight: 20.0000 chunk 160 optimal weight: 4.9990 chunk 188 optimal weight: 8.9990 chunk 156 optimal weight: 6.9990 chunk 265 optimal weight: 8.9990 overall best weight: 1.6384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** G 116 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 183 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 850 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 328 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4163 r_free = 0.4163 target = 0.120538 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3219 r_free = 0.3219 target = 0.072273 restraints weight = 97772.423| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3259 r_free = 0.3259 target = 0.073566 restraints weight = 62484.704| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3248 r_free = 0.3248 target = 0.073253 restraints weight = 43168.536| |-----------------------------------------------------------------------------| r_work (final): 0.3148 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8101 moved from start: 0.2442 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 31225 Z= 0.144 Angle : 0.594 10.449 42596 Z= 0.293 Chirality : 0.045 0.367 4980 Planarity : 0.004 0.058 5353 Dihedral : 6.551 111.517 5579 Min Nonbonded Distance : 2.209 Molprobity Statistics. All-atom Clashscore : 9.20 Ramachandran Plot: Outliers : 0.03 % Allowed : 5.54 % Favored : 94.43 % Rotamer: Outliers : 1.40 % Allowed : 16.30 % Favored : 82.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.07 % Cis-general : 0.03 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.99 (0.13), residues: 3716 helix: 0.07 (0.21), residues: 703 sheet: 0.41 (0.18), residues: 821 loop : -1.37 (0.13), residues: 2192 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.052 0.001 TRP B 102 HIS 0.003 0.001 HIS C1085 PHE 0.022 0.001 PHE D 559 TYR 0.020 0.001 TYR C 262 ARG 0.006 0.000 ARG L 46 Details of bonding type rmsd link_NAG-ASN : bond 0.00438 ( 42) link_NAG-ASN : angle 2.05227 ( 126) link_BETA1-4 : bond 0.00511 ( 25) link_BETA1-4 : angle 1.71993 ( 75) hydrogen bonds : bond 0.04492 ( 963) hydrogen bonds : angle 5.42184 ( 2598) SS BOND : bond 0.00290 ( 45) SS BOND : angle 1.71328 ( 90) covalent geometry : bond 0.00335 (31106) covalent geometry : angle 0.57600 (42305) Misc. bond : bond 0.00313 ( 7) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 9348.53 seconds wall clock time: 163 minutes 33.68 seconds (9813.68 seconds total)