Starting phenix.real_space_refine on Sat Feb 7 04:37:48 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7wea_32444/02_2026/7wea_32444.cif Found real_map, /net/cci-nas-00/data/ceres_data/7wea_32444/02_2026/7wea_32444.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7wea_32444/02_2026/7wea_32444.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7wea_32444/02_2026/7wea_32444.map" model { file = "/net/cci-nas-00/data/ceres_data/7wea_32444/02_2026/7wea_32444.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7wea_32444/02_2026/7wea_32444.cif" } resolution = 3.3 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.083 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 118 residue(s): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 30413 Number of models: 1 Model: "" Number of chains: 30 Chain: "A" Number of atoms: 8632 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1098, 8632 Classifications: {'peptide': 1098} Link IDs: {'CIS': 1, 'PTRANS': 55, 'TRANS': 1041} Chain breaks: 4 Chain: "B" Number of atoms: 8632 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1098, 8632 Classifications: {'peptide': 1098} Link IDs: {'PTRANS': 55, 'TRANS': 1042} Chain breaks: 4 Chain: "C" Number of atoms: 8632 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1098, 8632 Classifications: {'peptide': 1098} Link IDs: {'PTRANS': 55, 'TRANS': 1042} Chain breaks: 4 Chain: "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: "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: "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: "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: "D" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "E" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "F" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "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: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "M" Number of atoms: 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: 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: 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: "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 Time building chain proxies: 6.71, per 1000 atoms: 0.22 Number of scatterers: 30413 At special positions: 0 Unit cell: (147.66, 142.31, 255.73, 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 A 15 " - pdb=" SG CYS A 134 " distance=2.03 Simple disulfide: pdb=" SG CYS A 129 " - pdb=" SG CYS A 161 " distance=2.03 Simple disulfide: pdb=" SG CYS A 288 " - pdb=" SG CYS A 298 " distance=2.03 Simple disulfide: pdb=" SG CYS A 333 " - pdb=" SG CYS A 358 " distance=2.03 Simple disulfide: pdb=" SG CYS A 376 " - pdb=" SG CYS A 429 " distance=2.04 Simple disulfide: pdb=" SG CYS A 388 " - pdb=" SG CYS A 522 " distance=2.03 Simple disulfide: pdb=" SG CYS A 477 " - pdb=" SG CYS A 485 " distance=2.03 Simple disulfide: pdb=" SG CYS A 614 " - pdb=" SG CYS A 646 " distance=2.03 Simple disulfide: pdb=" SG CYS A 659 " - pdb=" SG CYS A 668 " distance=2.03 Simple disulfide: pdb=" SG CYS A 735 " - pdb=" SG CYS A 757 " distance=2.03 Simple disulfide: pdb=" SG CYS A 740 " - pdb=" SG CYS A 746 " distance=2.03 Simple disulfide: pdb=" SG CYS A1029 " - pdb=" SG CYS A1040 " distance=2.03 Simple disulfide: pdb=" SG CYS A1079 " - pdb=" SG CYS A1123 " distance=2.03 Simple disulfide: pdb=" SG CYS B 15 " - pdb=" SG CYS B 134 " distance=2.03 Simple disulfide: pdb=" SG CYS B 129 " - pdb=" SG CYS B 161 " distance=2.03 Simple disulfide: pdb=" SG CYS B 288 " - pdb=" SG CYS B 298 " distance=2.03 Simple disulfide: pdb=" SG CYS B 333 " - pdb=" SG CYS B 358 " distance=2.03 Simple disulfide: pdb=" SG CYS B 376 " - pdb=" SG CYS B 429 " distance=2.04 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=2.03 Simple disulfide: pdb=" SG CYS C 740 " - pdb=" SG CYS C 746 " distance=2.03 Simple disulfide: pdb=" SG CYS C1029 " - pdb=" SG CYS C1040 " distance=2.03 Simple disulfide: pdb=" SG CYS C1079 " - pdb=" SG CYS C1123 " distance=2.03 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 97 " distance=2.04 Simple disulfide: pdb=" SG CYS H 102 " - pdb=" SG CYS H 107 " distance=2.03 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 89 " distance=2.04 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 I 23 " - pdb=" SG CYS I 89 " 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=9, symmetry=0 Links applied BETA1-4 " NAG D 1 " - " NAG D 2 " " NAG E 1 " - " NAG E 2 " " NAG F 1 " - " NAG F 2 " " NAG J 1 " - " NAG J 2 " " NAG K 1 " - " NAG K 2 " " 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 a 2 " - " BMA a 3 " NAG-ASN " NAG A1302 " - " ASN A1155 " " NAG A1303 " - " ASN A 143 " " NAG A1304 " - " ASN A 17 " " NAG A1305 " - " ASN A 61 " " NAG A1306 " - " ASN A 600 " " NAG A1307 " - " ASN A 654 " " NAG A1308 " - " ASN A 613 " " NAG A1309 " - " ASN A 706 " " 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 D 1 " - " ASN A 231 " " NAG F 1 " - " ASN A 714 " " NAG J 1 " - " ASN A1071 " " NAG K 1 " - " ASN A 798 " " NAG M 1 " - " ASN A1095 " " NAG N 1 " - " ASN A1131 " " NAG P 1 " - " ASN B 714 " " NAG R 1 " - " ASN B 798 " " NAG S 1 " - " ASN B1095 " " NAG T 1 " - " ASN B1131 " " NAG U 1 " - " ASN C 231 " " NAG W 1 " - " ASN C 714 " " NAG Y 1 " - " ASN C 798 " " NAG Z 1 " - " ASN C1095 " " NAG a 1 " - " ASN C1131 " Number of additional bonds: simple=9, symmetry=0 Coordination: Other bonds: Time building additional restraints: 2.79 Conformation dependent library (CDL) restraints added in 1.1 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: 74 helices and 61 sheets defined 21.4% alpha, 22.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.34 Creating SS restraints... Processing helix chain 'A' and resid 291 through 299 Processing helix chain 'A' and resid 334 through 340 removed outlier: 4.356A pdb=" N VAL A 338 " --> pdb=" O PRO A 334 " (cutoff:3.500A) Processing helix chain 'A' and resid 346 through 350 removed outlier: 3.653A pdb=" N TRP A 350 " --> pdb=" O VAL A 347 " (cutoff:3.500A) Processing helix chain 'A' and resid 362 through 367 removed outlier: 3.607A pdb=" N ASN A 367 " --> pdb=" O SER A 363 " (cutoff:3.500A) Processing helix chain 'A' and resid 380 through 384 removed outlier: 4.123A pdb=" N LEU A 384 " --> pdb=" O PRO A 381 " (cutoff:3.500A) Processing helix chain 'A' and resid 402 through 408 removed outlier: 4.121A pdb=" N ARG A 405 " --> pdb=" O ASP A 402 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N ILE A 407 " --> pdb=" O VAL A 404 " (cutoff:3.500A) removed outlier: 3.982A pdb=" N ALA A 408 " --> pdb=" O ARG A 405 " (cutoff:3.500A) Processing helix chain 'A' and resid 414 through 419 removed outlier: 3.694A pdb=" N TYR A 418 " --> pdb=" O ASN A 414 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N ASN A 419 " --> pdb=" O ILE A 415 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 414 through 419' Processing helix chain 'A' and resid 616 through 621 Processing helix chain 'A' and resid 734 through 741 removed outlier: 3.873A pdb=" N TYR A 738 " --> pdb=" O ASP A 734 " (cutoff:3.500A) removed outlier: 4.183A pdb=" N ILE A 739 " --> pdb=" O CYS A 735 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N CYS A 740 " --> pdb=" O THR A 736 " (cutoff:3.500A) Processing helix chain 'A' and resid 743 through 754 removed outlier: 3.804A pdb=" N ASN A 748 " --> pdb=" O THR A 744 " (cutoff:3.500A) removed outlier: 4.529A pdb=" N LEU A 749 " --> pdb=" O GLU A 745 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N LEU A 751 " --> pdb=" O SER A 747 " (cutoff:3.500A) removed outlier: 4.144A pdb=" N GLN A 752 " --> pdb=" O ASN A 748 " (cutoff:3.500A) removed outlier: 4.361A pdb=" N TYR A 753 " --> pdb=" O LEU A 749 " (cutoff:3.500A) Processing helix chain 'A' and resid 755 through 780 removed outlier: 3.716A pdb=" N GLN A 759 " --> pdb=" O SER A 755 " (cutoff:3.500A) removed outlier: 3.844A pdb=" N LEU A 760 " --> pdb=" O PHE A 756 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N ILE A 767 " --> pdb=" O ALA A 763 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N ASP A 772 " --> pdb=" O ALA A 768 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N LYS A 773 " --> pdb=" O VAL A 769 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N THR A 775 " --> pdb=" O GLN A 771 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N GLN A 776 " --> pdb=" O ASP A 772 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N VAL A 778 " --> pdb=" O ASN A 774 " (cutoff:3.500A) Processing helix chain 'A' and resid 813 through 821 removed outlier: 3.915A pdb=" N LEU A 818 " --> pdb=" O PHE A 814 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N LEU A 819 " --> pdb=" O ILE A 815 " (cutoff:3.500A) Processing helix chain 'A' and resid 863 through 879 removed outlier: 3.712A pdb=" N ALA A 868 " --> pdb=" O ASP A 864 " (cutoff:3.500A) removed outlier: 3.978A pdb=" N GLN A 869 " --> pdb=" O GLU A 865 " (cutoff:3.500A) Processing helix chain 'A' and resid 883 through 887 removed outlier: 3.796A pdb=" N ALA A 887 " --> pdb=" O THR A 884 " (cutoff:3.500A) Processing helix chain 'A' and resid 894 through 907 removed outlier: 3.829A pdb=" N ALA A 900 " --> pdb=" O ALA A 896 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N TYR A 901 " --> pdb=" O MET A 897 " (cutoff:3.500A) Processing helix chain 'A' and resid 910 through 916 removed outlier: 4.070A pdb=" N TYR A 914 " --> pdb=" O GLN A 910 " (cutoff:3.500A) removed outlier: 3.894A pdb=" N GLU A 915 " --> pdb=" O ASN A 911 " (cutoff:3.500A) Processing helix chain 'A' and resid 916 through 938 removed outlier: 3.706A pdb=" N ILE A 931 " --> pdb=" O ALA A 927 " (cutoff:3.500A) removed outlier: 4.353A pdb=" N GLN A 932 " --> pdb=" O ILE A 928 " (cutoff:3.500A) removed outlier: 3.818A pdb=" N ASP A 933 " --> pdb=" O GLY A 929 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N THR A 938 " --> pdb=" O SER A 934 " (cutoff:3.500A) Processing helix chain 'A' and resid 942 through 962 removed outlier: 4.079A pdb=" N VAL A 948 " --> pdb=" O LYS A 944 " (cutoff:3.500A) removed outlier: 3.861A pdb=" N VAL A 949 " --> pdb=" O LEU A 945 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N ASN A 952 " --> pdb=" O VAL A 948 " (cutoff:3.500A) Processing helix chain 'A' and resid 963 through 965 No H-bonds generated for 'chain 'A' and resid 963 through 965' Processing helix chain 'A' and resid 973 through 981 removed outlier: 4.207A pdb=" N ILE A 977 " --> pdb=" O VAL A 973 " (cutoff:3.500A) removed outlier: 4.020A pdb=" N PHE A 978 " --> pdb=" O LEU A 974 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N SER A 979 " --> pdb=" O ASN A 975 " (cutoff:3.500A) Processing helix chain 'A' and resid 982 through 1029 removed outlier: 4.474A pdb=" N GLU A 987 " --> pdb=" O LYS A 983 " (cutoff:3.500A) removed outlier: 5.560A pdb=" N VAL A 988 " --> pdb=" O VAL A 984 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N GLN A 989 " --> pdb=" O GLU A 985 " (cutoff:3.500A) removed outlier: 4.588A pdb=" N GLY A 996 " --> pdb=" O ARG A 992 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N LEU A1001 " --> pdb=" O ARG A 997 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N LEU A1021 " --> pdb=" O ALA A1017 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N THR A1024 " --> pdb=" O ASN A1020 " (cutoff:3.500A) Processing helix chain 'A' and resid 1137 through 1147 removed outlier: 4.347A pdb=" N GLU A1141 " --> pdb=" O PRO A1137 " (cutoff:3.500A) removed outlier: 3.994A pdb=" N SER A1144 " --> pdb=" O PRO A1140 " (cutoff:3.500A) removed outlier: 4.191A pdb=" N PHE A1145 " --> pdb=" O GLU A1141 " (cutoff:3.500A) Processing helix chain 'A' and resid 1148 through 1158 removed outlier: 3.848A pdb=" N HIS A1156 " --> pdb=" O TYR A1152 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N THR A1157 " --> pdb=" O PHE A1153 " (cutoff:3.500A) removed outlier: 4.141A pdb=" N SER A1158 " --> pdb=" O LYS A1154 " (cutoff:3.500A) Processing helix chain 'B' and resid 291 through 300 removed outlier: 3.567A pdb=" N LEU B 300 " --> pdb=" O THR B 296 " (cutoff:3.500A) Processing helix chain 'B' and resid 335 through 340 Processing helix chain 'B' and resid 380 through 384 removed outlier: 3.618A pdb=" N LEU B 384 " --> pdb=" O PRO B 381 " (cutoff:3.500A) Processing helix chain 'B' and resid 404 through 408 removed outlier: 3.759A pdb=" N ILE B 407 " --> pdb=" O VAL B 404 " (cutoff:3.500A) Processing helix chain 'B' and resid 616 through 621 removed outlier: 3.753A pdb=" N VAL B 619 " --> pdb=" O GLU B 616 " (cutoff:3.500A) removed outlier: 3.851A pdb=" N ALA B 620 " --> pdb=" O VAL B 617 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N ILE B 621 " --> pdb=" O PRO B 618 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 616 through 621' Processing helix chain 'B' and resid 630 through 634 removed outlier: 3.634A pdb=" N TYR B 633 " --> pdb=" O TRP B 630 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N SER B 634 " --> pdb=" O ARG B 631 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 630 through 634' Processing helix chain 'B' and resid 734 through 741 removed outlier: 3.588A pdb=" N ILE B 739 " --> pdb=" O CYS B 735 " (cutoff:3.500A) Processing helix chain 'B' and resid 743 through 750 removed outlier: 3.659A pdb=" N ASN B 748 " --> pdb=" O THR B 744 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N LEU B 749 " --> pdb=" O GLU B 745 " (cutoff:3.500A) Processing helix chain 'B' and resid 755 through 780 removed outlier: 3.590A pdb=" N LYS B 761 " --> pdb=" O CYS B 757 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N ILE B 767 " --> pdb=" O ALA B 763 " (cutoff:3.500A) removed outlier: 3.842A pdb=" N ASP B 772 " --> pdb=" O ALA B 768 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N LYS B 773 " --> pdb=" O VAL B 769 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N THR B 775 " --> pdb=" O GLN B 771 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N GLN B 776 " --> pdb=" O ASP B 772 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N VAL B 778 " --> pdb=" O ASN B 774 " (cutoff:3.500A) Processing helix chain 'B' and resid 813 through 823 removed outlier: 3.895A pdb=" N LEU B 818 " --> pdb=" O PHE B 814 " (cutoff:3.500A) removed outlier: 3.882A 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: 3.646A pdb=" N ALA B 868 " --> pdb=" O ASP B 864 " (cutoff:3.500A) removed outlier: 3.976A pdb=" N GLN B 869 " --> pdb=" O GLU B 865 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N TYR B 870 " --> pdb=" O MET B 866 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N SER B 872 " --> pdb=" O ALA B 868 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N ALA B 876 " --> pdb=" O SER B 872 " (cutoff:3.500A) Processing helix chain 'B' and resid 883 through 887 removed outlier: 3.716A pdb=" N GLY B 886 " --> pdb=" O TRP B 883 " (cutoff:3.500A) removed outlier: 3.688A 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 897 Processing helix chain 'B' and resid 898 through 904 removed outlier: 3.569A pdb=" N ASN B 904 " --> pdb=" O ALA B 900 " (cutoff:3.500A) Processing helix chain 'B' and resid 910 through 916 removed outlier: 3.812A pdb=" N TYR B 914 " --> pdb=" O GLN B 910 " (cutoff:3.500A) Processing helix chain 'B' and resid 916 through 938 removed outlier: 3.690A pdb=" N ALA B 927 " --> pdb=" O GLN B 923 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N ILE B 931 " --> pdb=" O ALA B 927 " (cutoff:3.500A) removed outlier: 4.301A pdb=" N GLN B 932 " --> pdb=" O ILE B 928 " (cutoff:3.500A) removed outlier: 4.287A pdb=" N ASP B 933 " --> pdb=" O GLY B 929 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N THR B 938 " --> pdb=" O SER B 934 " (cutoff:3.500A) Processing helix chain 'B' and resid 942 through 962 removed outlier: 4.308A pdb=" N VAL B 948 " --> pdb=" O LYS B 944 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N VAL B 949 " --> pdb=" O LEU B 945 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N ASN B 952 " --> pdb=" O VAL B 948 " (cutoff:3.500A) Processing helix chain 'B' and resid 963 through 965 No H-bonds generated for 'chain 'B' and resid 963 through 965' Processing helix chain 'B' and resid 982 through 1029 removed outlier: 4.266A pdb=" N GLU B 987 " --> pdb=" O LYS B 983 " (cutoff:3.500A) removed outlier: 5.330A pdb=" N VAL B 988 " --> pdb=" O VAL B 984 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N GLN B 989 " --> pdb=" O GLU B 985 " (cutoff:3.500A) removed outlier: 3.916A pdb=" N GLY B 996 " --> pdb=" O ARG B 992 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N LEU B1001 " --> pdb=" O ARG B 997 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N GLN B1002 " --> pdb=" O LEU B 998 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N GLU B1014 " --> pdb=" O ILE B1010 " (cutoff:3.500A) removed outlier: 3.890A pdb=" N ALA B1017 " --> pdb=" O ALA B1013 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N SER B1018 " --> pdb=" O GLU B1014 " (cutoff:3.500A) removed outlier: 3.980A pdb=" N LEU B1021 " --> pdb=" O ALA B1017 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N THR B1024 " --> pdb=" O ASN B1020 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N SER B1027 " --> pdb=" O ALA B1023 " (cutoff:3.500A) Processing helix chain 'B' and resid 1137 through 1145 removed outlier: 4.212A pdb=" N GLU B1141 " --> pdb=" O PRO B1137 " (cutoff:3.500A) Processing helix chain 'B' and resid 1145 through 1156 removed outlier: 3.658A pdb=" N HIS B1156 " --> pdb=" O TYR B1152 " (cutoff:3.500A) Processing helix chain 'C' and resid 291 through 301 Processing helix chain 'C' and resid 334 through 340 removed outlier: 4.344A pdb=" N VAL C 338 " --> pdb=" O PRO C 334 " (cutoff:3.500A) Processing helix chain 'C' and resid 362 through 368 removed outlier: 4.276A pdb=" N LEU C 368 " --> pdb=" O VAL C 364 " (cutoff:3.500A) Processing helix chain 'C' and resid 380 through 386 removed outlier: 4.225A pdb=" N LEU C 384 " --> pdb=" O PRO C 381 " (cutoff:3.500A) removed outlier: 5.393A pdb=" N ASN C 385 " --> pdb=" O THR C 382 " (cutoff:3.500A) removed outlier: 3.846A pdb=" N ASP C 386 " --> pdb=" O LYS C 383 " (cutoff:3.500A) Processing helix chain 'C' and resid 402 through 408 removed outlier: 4.354A pdb=" N ARG C 405 " --> pdb=" O ASP C 402 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N ILE C 407 " --> pdb=" O VAL C 404 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N ALA C 408 " --> pdb=" O ARG C 405 " (cutoff:3.500A) Processing helix chain 'C' and resid 734 through 740 removed outlier: 4.126A pdb=" N TYR C 738 " --> pdb=" O ASP C 734 " (cutoff:3.500A) removed outlier: 4.070A pdb=" N ILE C 739 " --> pdb=" O CYS C 735 " (cutoff:3.500A) Processing helix chain 'C' and resid 743 through 751 removed outlier: 3.616A pdb=" N ASN C 748 " --> pdb=" O THR C 744 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N LEU C 749 " --> pdb=" O GLU C 745 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N LEU C 751 " --> pdb=" O SER C 747 " (cutoff:3.500A) Processing helix chain 'C' and resid 752 through 754 No H-bonds generated for 'chain 'C' and resid 752 through 754' Processing helix chain 'C' and resid 757 through 780 removed outlier: 3.630A pdb=" N ILE C 767 " --> pdb=" O ALA C 763 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N ALA C 768 " --> pdb=" O LEU C 764 " (cutoff:3.500A) removed outlier: 4.022A pdb=" N ASP C 772 " --> pdb=" O ALA C 768 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N LYS C 773 " --> pdb=" O VAL C 769 " (cutoff:3.500A) removed outlier: 4.054A pdb=" N THR C 775 " --> pdb=" O GLN C 771 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N VAL C 778 " --> pdb=" O ASN C 774 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N ALA C 780 " --> pdb=" O GLN C 776 " (cutoff:3.500A) Processing helix chain 'C' and resid 813 through 820 removed outlier: 3.670A pdb=" N LEU C 818 " --> pdb=" O PHE C 814 " (cutoff:3.500A) Processing helix chain 'C' and resid 850 through 853 removed outlier: 4.267A pdb=" N LYS C 853 " --> pdb=" O GLN C 850 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 850 through 853' Processing helix chain 'C' and resid 863 through 879 removed outlier: 4.085A pdb=" N GLN C 869 " --> pdb=" O GLU C 865 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N ILE C 879 " --> pdb=" O LEU C 875 " (cutoff:3.500A) Processing helix chain 'C' and resid 883 through 887 removed outlier: 3.507A pdb=" N ALA C 887 " --> pdb=" O THR C 884 " (cutoff:3.500A) Processing helix chain 'C' and resid 894 through 897 Processing helix chain 'C' and resid 898 through 905 Processing helix chain 'C' and resid 910 through 916 removed outlier: 3.980A pdb=" N TYR C 914 " --> pdb=" O GLN C 910 " (cutoff:3.500A) Processing helix chain 'C' and resid 916 through 928 Processing helix chain 'C' and resid 930 through 938 removed outlier: 3.835A pdb=" N THR C 938 " --> pdb=" O SER C 934 " (cutoff:3.500A) Processing helix chain 'C' and resid 942 through 962 removed outlier: 3.958A pdb=" N VAL C 948 " --> pdb=" O LYS C 944 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N VAL C 949 " --> pdb=" O LEU C 945 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N ASN C 952 " --> pdb=" O VAL C 948 " (cutoff:3.500A) removed outlier: 4.338A pdb=" N LEU C 956 " --> pdb=" O ASN C 952 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N LEU C 959 " --> pdb=" O ALA C 955 " (cutoff:3.500A) Processing helix chain 'C' and resid 963 through 965 No H-bonds generated for 'chain 'C' and resid 963 through 965' Processing helix chain 'C' and resid 975 through 981 Processing helix chain 'C' and resid 986 through 1029 removed outlier: 3.753A pdb=" N ASP C 991 " --> pdb=" O GLU C 987 " (cutoff:3.500A) removed outlier: 3.829A pdb=" N ARG C 992 " --> pdb=" O VAL C 988 " (cutoff:3.500A) removed outlier: 4.116A pdb=" N GLY C 996 " --> pdb=" O ARG C 992 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N GLN C 999 " --> pdb=" O THR C 995 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N GLN C1002 " --> pdb=" O LEU C 998 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N THR C1003 " --> pdb=" O GLN C 999 " (cutoff:3.500A) removed outlier: 3.974A pdb=" N TYR C1004 " --> pdb=" O SER C1000 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N GLU C1014 " --> pdb=" O ILE C1010 " (cutoff:3.500A) removed outlier: 3.982A pdb=" N LEU C1021 " --> pdb=" O ALA C1017 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N ALA C1023 " --> pdb=" O ALA C1019 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N THR C1024 " --> pdb=" O ASN C1020 " (cutoff:3.500A) Processing helix chain 'C' and resid 1138 through 1143 Processing helix chain 'C' and resid 1145 through 1158 removed outlier: 3.623A pdb=" N SER C1158 " --> pdb=" O LYS C1154 " (cutoff:3.500A) Processing helix chain 'H' and resid 62 through 66 removed outlier: 3.603A pdb=" N GLN H 66 " --> pdb=" O PRO H 63 " (cutoff:3.500A) Processing helix chain 'H' and resid 88 through 92 removed outlier: 3.521A pdb=" N THR H 92 " --> pdb=" O SER H 89 " (cutoff:3.500A) Processing helix chain 'L' and resid 80 through 84 removed outlier: 3.802A pdb=" N PHE L 84 " --> pdb=" O PRO L 81 " (cutoff:3.500A) Processing helix chain 'G' and resid 88 through 92 removed outlier: 3.908A pdb=" N THR G 92 " --> pdb=" O SER G 89 " (cutoff:3.500A) Processing helix chain 'I' and resid 80 through 84 removed outlier: 3.962A pdb=" N PHE I 84 " --> pdb=" O PRO I 81 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 27 through 31 removed outlier: 3.661A pdb=" N SER A 60 " --> pdb=" O SER A 31 " (cutoff:3.500A) removed outlier: 6.387A pdb=" N ASN A 61 " --> pdb=" O TYR A 266 " (cutoff:3.500A) removed outlier: 4.388A pdb=" N TYR A 266 " --> pdb=" O ASN A 61 " (cutoff:3.500A) removed outlier: 3.923A pdb=" N ALA A 261 " --> pdb=" O ILE A 93 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 36 through 37 removed outlier: 6.551A pdb=" N VAL A 36 " --> pdb=" O LEU A 220 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA2 Processing sheet with id=AA3, first strand: chain 'A' and resid 48 through 55 removed outlier: 4.160A pdb=" N ASP A 284 " --> pdb=" O LYS A 275 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 81 through 83 removed outlier: 6.426A pdb=" N ARG A 234 " --> pdb=" O PHE A 104 " (cutoff:3.500A) removed outlier: 4.471A pdb=" N PHE A 104 " --> pdb=" O ARG A 234 " (cutoff:3.500A) removed outlier: 7.340A pdb=" N GLN A 236 " --> pdb=" O TRP A 102 " (cutoff:3.500A) removed outlier: 5.603A pdb=" N TRP A 102 " --> pdb=" O GLN A 236 " (cutoff:3.500A) removed outlier: 6.932A pdb=" N LEU A 238 " --> pdb=" O ARG A 100 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 308 through 316 removed outlier: 4.722A pdb=" N VAL A 592 " --> pdb=" O THR A 312 " (cutoff:3.500A) removed outlier: 5.338A pdb=" N ASN A 314 " --> pdb=" O GLY A 590 " (cutoff:3.500A) removed outlier: 7.060A pdb=" N GLY A 590 " --> pdb=" O ASN A 314 " (cutoff:3.500A) removed outlier: 3.897A pdb=" N GLY A 591 " --> pdb=" O GLN A 610 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N TYR A 609 " --> pdb=" O CYS A 646 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N CYS A 646 " --> pdb=" O TYR A 609 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 321 through 322 removed outlier: 7.378A pdb=" N GLU A 321 " --> pdb=" O ASN A 537 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 351 through 355 removed outlier: 3.837A pdb=" N ASN A 351 " --> pdb=" O SER A 396 " (cutoff:3.500A) removed outlier: 4.226A pdb=" N VAL A 430 " --> pdb=" O LYS A 375 " (cutoff:3.500A) removed outlier: 4.138A pdb=" N LYS A 375 " --> pdb=" O VAL A 430 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 358 through 359 removed outlier: 6.719A pdb=" N CYS A 358 " --> pdb=" O CYS A 522 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 449 through 451 Processing sheet with id=AB1, first strand: chain 'A' and resid 470 through 471 Processing sheet with id=AB2, first strand: chain 'A' and resid 539 through 540 Processing sheet with id=AB3, first strand: chain 'A' and resid 651 through 652 removed outlier: 6.088A pdb=" N GLU A 651 " --> pdb=" O ALA A 691 " (cutoff:3.500A) removed outlier: 8.582A pdb=" N THR A 693 " --> pdb=" O GLU A 651 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 698 through 699 removed outlier: 6.760A pdb=" N ALA A 698 " --> pdb=" O ILE C 785 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB4 Processing sheet with id=AB5, first strand: chain 'A' and resid 708 through 712 Processing sheet with id=AB6, first strand: chain 'A' and resid 715 through 719 removed outlier: 3.758A pdb=" N SER A 718 " --> pdb=" O THR A1063 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'A' and resid 715 through 719 removed outlier: 3.758A pdb=" N SER A 718 " --> pdb=" O THR A1063 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N MET A1047 " --> pdb=" O VAL A1062 " (cutoff:3.500A) removed outlier: 6.107A pdb=" N TYR A1064 " --> pdb=" O HIS A1045 " (cutoff:3.500A) removed outlier: 6.000A pdb=" N HIS A1045 " --> pdb=" O TYR A1064 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'A' and resid 784 through 785 Processing sheet with id=AB9, first strand: chain 'A' and resid 1117 through 1119 Processing sheet with id=AC1, first strand: chain 'A' and resid 1091 through 1094 Processing sheet with id=AC2, first strand: chain 'B' and resid 27 through 31 removed outlier: 3.597A pdb=" N SER B 60 " --> pdb=" O SER B 31 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N ALA B 261 " --> pdb=" O ILE B 93 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N GLU B 186 " --> pdb=" O LYS B 201 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 48 through 55 removed outlier: 3.780A pdb=" N ASP B 284 " --> pdb=" O LYS B 275 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 99 through 103 removed outlier: 4.002A pdb=" N GLY B 101 " --> pdb=" O LEU B 238 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 113 through 119 removed outlier: 4.143A pdb=" N VAL B 124 " --> pdb=" O SER B 167 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N SER B 167 " --> pdb=" O VAL B 124 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N TYR B 165 " --> pdb=" O ILE B 126 " (cutoff:3.500A) removed outlier: 4.127A pdb=" N VAL B 128 " --> pdb=" O PHE B 163 " (cutoff:3.500A) removed outlier: 5.163A pdb=" N PHE B 163 " --> pdb=" O VAL B 128 " (cutoff:3.500A) removed outlier: 8.595A pdb=" N GLU B 130 " --> pdb=" O CYS B 161 " (cutoff:3.500A) removed outlier: 7.625A pdb=" N CYS B 161 " --> pdb=" O GLU B 130 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 308 through 314 removed outlier: 3.501A pdb=" N THR B 596 " --> pdb=" O GLY B 308 " (cutoff:3.500A) removed outlier: 4.748A pdb=" N VAL B 592 " --> pdb=" O THR B 312 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N TYR B 609 " --> pdb=" O CYS B 646 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N CYS B 646 " --> pdb=" O TYR B 609 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N GLY B 645 " --> pdb=" O THR B 642 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'B' and resid 351 through 355 removed outlier: 4.251A pdb=" N ASN B 351 " --> pdb=" O SER B 396 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N SER B 396 " --> pdb=" O ASN B 351 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N TYR B 393 " --> pdb=" O SER B 511 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N SER B 511 " --> pdb=" O TYR B 393 " (cutoff:3.500A) removed outlier: 3.923A pdb=" N LEU B 510 " --> pdb=" O CYS B 429 " (cutoff:3.500A) removed outlier: 3.821A pdb=" N CYS B 429 " --> pdb=" O LEU B 510 " (cutoff:3.500A) removed outlier: 7.191A pdb=" N ALA B 432 " --> pdb=" O PHE B 372 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N PHE B 372 " --> pdb=" O ALA B 432 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'B' and resid 358 through 359 removed outlier: 6.267A pdb=" N CYS B 358 " --> pdb=" O CYS B 522 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'B' and resid 449 through 451 Processing sheet with id=AD1, first strand: chain 'B' and resid 470 through 471 removed outlier: 3.646A pdb=" N TYR B 470 " --> pdb=" O TYR B 486 " (cutoff:3.500A) removed outlier: 4.188A pdb=" N TYR B 486 " --> pdb=" O TYR B 470 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD1 Processing sheet with id=AD2, first strand: chain 'B' and resid 537 through 539 removed outlier: 3.713A pdb=" N PHE B 538 " --> pdb=" O GLY B 545 " (cutoff:3.500A) removed outlier: 3.945A pdb=" N GLY B 545 " --> pdb=" O PHE B 538 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD2 Processing sheet with id=AD3, first strand: chain 'B' and resid 548 through 551 removed outlier: 3.652A pdb=" N THR B 585 " --> pdb=" O VAL B 548 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N THR B 550 " --> pdb=" O ASP B 583 " (cutoff:3.500A) removed outlier: 5.117A pdb=" N ASP B 571 " --> pdb=" O ILE B 584 " (cutoff:3.500A) removed outlier: 6.517A pdb=" N GLY B 563 " --> pdb=" O ASP B 571 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'B' and resid 651 through 652 removed outlier: 6.193A pdb=" N GLU B 651 " --> pdb=" O ALA B 691 " (cutoff:3.500A) removed outlier: 8.739A pdb=" N THR B 693 " --> pdb=" O GLU B 651 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'B' and resid 708 through 712 removed outlier: 3.836A pdb=" N THR B1073 " --> pdb=" O SER B1094 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'B' and resid 715 through 725 removed outlier: 3.525A pdb=" N SER B 718 " --> pdb=" O THR B1063 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N MET B1047 " --> pdb=" O VAL B1062 " (cutoff:3.500A) removed outlier: 6.172A pdb=" N TYR B1064 " --> pdb=" O HIS B1045 " (cutoff:3.500A) removed outlier: 6.002A pdb=" N HIS B1045 " --> pdb=" O TYR B1064 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'B' and resid 730 through 733 removed outlier: 4.645A pdb=" N LYS B 730 " --> pdb=" O LEU B 858 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'B' and resid 784 through 785 Processing sheet with id=AD9, first strand: chain 'B' and resid 1117 through 1122 removed outlier: 3.585A pdb=" N SER B1120 " --> pdb=" O ALA B1084 " (cutoff:3.500A) removed outlier: 4.734A pdb=" N ALA B1084 " --> pdb=" O SER B1120 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'C' and resid 27 through 31 removed outlier: 3.578A pdb=" N SER C 60 " --> pdb=" O SER C 31 " (cutoff:3.500A) removed outlier: 8.135A pdb=" N ASN C 61 " --> pdb=" O TYR C 266 " (cutoff:3.500A) removed outlier: 5.634A pdb=" N TYR C 266 " --> pdb=" O ASN C 61 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N VAL C 224 " --> pdb=" O ILE C 198 " (cutoff:3.500A) removed outlier: 5.792A pdb=" N SER C 200 " --> pdb=" O PRO C 222 " (cutoff:3.500A) removed outlier: 9.344A pdb=" N HIS C 202 " --> pdb=" O LEU C 220 " (cutoff:3.500A) removed outlier: 9.308A pdb=" N LEU C 220 " --> pdb=" O HIS C 202 " (cutoff:3.500A) removed outlier: 7.304A pdb=" N VAL C 36 " --> pdb=" O LEU C 220 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'C' and resid 48 through 55 removed outlier: 3.897A pdb=" N ASP C 284 " --> pdb=" O LYS C 275 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'C' and resid 102 through 104 removed outlier: 3.578A pdb=" N PHE C 104 " --> pdb=" O LEU C 115 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N VAL C 118 " --> pdb=" O VAL C 125 " (cutoff:3.500A) removed outlier: 3.904A pdb=" N PHE C 163 " --> pdb=" O VAL C 128 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'C' and resid 308 through 315 removed outlier: 4.674A pdb=" N VAL C 592 " --> pdb=" O THR C 312 " (cutoff:3.500A) removed outlier: 5.272A pdb=" N ASN C 314 " --> pdb=" O GLY C 590 " (cutoff:3.500A) removed outlier: 6.826A pdb=" N GLY C 590 " --> pdb=" O ASN C 314 " (cutoff:3.500A) removed outlier: 4.439A pdb=" N GLY C 591 " --> pdb=" O GLN C 610 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N TYR C 609 " --> pdb=" O CYS C 646 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N CYS C 646 " --> pdb=" O TYR C 609 " (cutoff:3.500A) removed outlier: 3.893A pdb=" N GLY C 645 " --> pdb=" O THR C 642 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'C' and resid 322 through 325 removed outlier: 3.880A pdb=" N PHE C 538 " --> pdb=" O GLY C 545 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N THR C 585 " --> pdb=" O VAL C 548 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'C' and resid 351 through 355 removed outlier: 3.737A pdb=" N ASN C 351 " --> pdb=" O SER C 396 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N VAL C 392 " --> pdb=" O ILE C 355 " (cutoff:3.500A) removed outlier: 4.086A pdb=" N VAL C 430 " --> pdb=" O LYS C 375 " (cutoff:3.500A) removed outlier: 4.194A pdb=" N LYS C 375 " --> pdb=" O VAL C 430 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N THR C 373 " --> pdb=" O ALA C 432 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'C' and resid 358 through 359 removed outlier: 6.675A pdb=" N CYS C 358 " --> pdb=" O CYS C 522 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'C' and resid 449 through 451 Processing sheet with id=AE9, first strand: chain 'C' and resid 470 through 471 removed outlier: 3.557A pdb=" N TYR C 470 " --> pdb=" O TYR C 486 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'C' and resid 562 through 563 removed outlier: 3.693A pdb=" N ALA C 572 " --> pdb=" O GLY C 563 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'C' and resid 651 through 657 removed outlier: 6.109A pdb=" N GLU C 651 " --> pdb=" O ALA C 691 " (cutoff:3.500A) removed outlier: 8.726A pdb=" N THR C 693 " --> pdb=" O GLU C 651 " (cutoff:3.500A) removed outlier: 9.300A pdb=" N VAL C 653 " --> pdb=" O THR C 693 " (cutoff:3.500A) removed outlier: 6.422A pdb=" N ALA C 669 " --> pdb=" O PRO C 662 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'C' and resid 709 through 712 Processing sheet with id=AF4, first strand: chain 'C' and resid 715 through 725 removed outlier: 3.714A pdb=" N MET C1047 " --> pdb=" O VAL C1062 " (cutoff:3.500A) removed outlier: 6.020A pdb=" N TYR C1064 " --> pdb=" O HIS C1045 " (cutoff:3.500A) removed outlier: 5.962A pdb=" N HIS C1045 " --> pdb=" O TYR C1064 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'C' and resid 730 through 733 removed outlier: 4.551A pdb=" N LYS C 730 " --> pdb=" O LEU C 858 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'C' and resid 1117 through 1122 removed outlier: 4.718A pdb=" N ALA C1084 " --> pdb=" O SER C1120 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'C' and resid 1091 through 1094 Processing sheet with id=AF8, first strand: chain 'H' and resid 3 through 6 removed outlier: 3.817A pdb=" N ALA H 80 " --> pdb=" O CYS H 22 " (cutoff:3.500A) Processing sheet with id=AF9, first strand: chain 'H' and resid 10 through 12 removed outlier: 6.614A pdb=" N LEU H 35 " --> pdb=" O TRP H 51 " (cutoff:3.500A) removed outlier: 4.405A pdb=" N TRP H 51 " --> pdb=" O LEU H 35 " (cutoff:3.500A) removed outlier: 6.731A pdb=" N TRP H 37 " --> pdb=" O ILE H 49 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N GLU H 47 " --> pdb=" O ARG H 39 " (cutoff:3.500A) Processing sheet with id=AG1, first strand: chain 'L' and resid 5 through 7 Processing sheet with id=AG2, first strand: chain 'L' and resid 10 through 12 removed outlier: 6.197A pdb=" N LEU L 11 " --> pdb=" O GLU L 106 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N VAL L 86 " --> pdb=" O GLN L 39 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N ILE L 49 " --> pdb=" O TRP L 36 " (cutoff:3.500A) removed outlier: 6.694A pdb=" N GLN L 38 " --> pdb=" O LEU L 47 " (cutoff:3.500A) removed outlier: 5.895A pdb=" N LEU L 47 " --> pdb=" O GLN L 38 " (cutoff:3.500A) removed outlier: 3.926A pdb=" N SER L 50 " --> pdb=" O SER L 54 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N SER L 54 " --> pdb=" O SER L 50 " (cutoff:3.500A) Processing sheet with id=AG3, first strand: chain 'G' and resid 3 through 6 Processing sheet with id=AG4, first strand: chain 'G' and resid 10 through 12 removed outlier: 3.718A pdb=" N GLY G 50 " --> pdb=" O TRP G 37 " (cutoff:3.500A) removed outlier: 7.272A pdb=" N ARG G 39 " --> pdb=" O TRP G 48 " (cutoff:3.500A) removed outlier: 6.361A pdb=" N TRP G 48 " --> pdb=" O ARG G 39 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N ASN G 60 " --> pdb=" O TRP G 51 " (cutoff:3.500A) Processing sheet with id=AG5, first strand: chain 'G' and resid 17 through 20 Processing sheet with id=AG6, first strand: chain 'I' and resid 4 through 7 Processing sheet with id=AG7, first strand: chain 'I' and resid 10 through 12 removed outlier: 5.582A pdb=" N LEU I 11 " --> pdb=" O GLU I 106 " (cutoff:3.500A) removed outlier: 4.145A pdb=" N VAL I 86 " --> pdb=" O GLN I 39 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N GLN I 39 " --> pdb=" O VAL I 86 " (cutoff:3.500A) removed outlier: 7.149A pdb=" N LEU I 34 " --> pdb=" O SER I 50 " (cutoff:3.500A) removed outlier: 5.240A pdb=" N SER I 50 " --> pdb=" O LEU I 34 " (cutoff:3.500A) removed outlier: 6.571A pdb=" N TRP I 36 " --> pdb=" O LEU I 48 " (cutoff:3.500A) removed outlier: 3.852A pdb=" N SER I 54 " --> pdb=" O SER I 50 " (cutoff:3.500A) 914 hydrogen bonds defined for protein. 2454 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: 7.34 Time building geometry restraints manager: 3.57 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 9541 1.34 - 1.46: 7695 1.46 - 1.59: 13703 1.59 - 1.71: 0 1.71 - 1.83: 167 Bond restraints: 31106 Sorted by residual: bond pdb=" C1 NAG J 2 " pdb=" O5 NAG J 2 " ideal model delta sigma weight residual 1.406 1.490 -0.084 2.00e-02 2.50e+03 1.78e+01 bond pdb=" N VAL B 324 " pdb=" CA VAL B 324 " ideal model delta sigma weight residual 1.457 1.503 -0.046 1.14e-02 7.69e+03 1.64e+01 bond pdb=" CG1 ILE C 465 " pdb=" CD1 ILE C 465 " ideal model delta sigma weight residual 1.513 1.355 0.158 3.90e-02 6.57e+02 1.63e+01 bond pdb=" N ILE B 323 " pdb=" CA ILE B 323 " ideal model delta sigma weight residual 1.458 1.506 -0.048 1.24e-02 6.50e+03 1.49e+01 bond pdb=" N PHE A 326 " pdb=" CA PHE A 326 " ideal model delta sigma weight residual 1.453 1.489 -0.035 9.20e-03 1.18e+04 1.47e+01 ... (remaining 31101 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.32: 42034 3.32 - 6.64: 253 6.64 - 9.97: 15 9.97 - 13.29: 2 13.29 - 16.61: 1 Bond angle restraints: 42305 Sorted by residual: angle pdb=" CB ILE C 465 " pdb=" CG1 ILE C 465 " pdb=" CD1 ILE C 465 " ideal model delta sigma weight residual 113.80 130.41 -16.61 2.10e+00 2.27e-01 6.26e+01 angle pdb=" CA ILE C 465 " pdb=" CB ILE C 465 " pdb=" CG1 ILE C 465 " ideal model delta sigma weight residual 110.40 98.07 12.33 1.70e+00 3.46e-01 5.26e+01 angle pdb=" N THR C 233 " pdb=" CA THR C 233 " pdb=" C THR C 233 " ideal model delta sigma weight residual 112.94 104.68 8.26 1.41e+00 5.03e-01 3.43e+01 angle pdb=" N ASP A 212 " pdb=" CA ASP A 212 " pdb=" C ASP A 212 " ideal model delta sigma weight residual 108.45 114.69 -6.24 1.26e+00 6.30e-01 2.46e+01 angle pdb=" CA PRO B 327 " pdb=" C PRO B 327 " pdb=" O PRO B 327 " ideal model delta sigma weight residual 121.98 116.06 5.92 1.23e+00 6.61e-01 2.32e+01 ... (remaining 42300 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 24.55: 18293 24.55 - 49.09: 1010 49.09 - 73.64: 117 73.64 - 98.18: 56 98.18 - 122.73: 34 Dihedral angle restraints: 19510 sinusoidal: 8571 harmonic: 10939 Sorted by residual: dihedral pdb=" CA ASP C 464 " pdb=" C ASP C 464 " pdb=" N ILE C 465 " pdb=" CA ILE C 465 " ideal model delta harmonic sigma weight residual -180.00 -130.33 -49.67 0 5.00e+00 4.00e-02 9.87e+01 dihedral pdb=" CB CYS G 22 " pdb=" SG CYS G 22 " pdb=" SG CYS G 97 " pdb=" CB CYS G 97 " ideal model delta sinusoidal sigma weight residual 93.00 166.33 -73.33 1 1.00e+01 1.00e-02 6.85e+01 dihedral pdb=" CB CYS B 288 " pdb=" SG CYS B 288 " pdb=" SG CYS B 298 " pdb=" CB CYS B 298 " ideal model delta sinusoidal sigma weight residual 93.00 159.88 -66.88 1 1.00e+01 1.00e-02 5.83e+01 ... (remaining 19507 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.083: 4475 0.083 - 0.165: 472 0.165 - 0.248: 20 0.248 - 0.330: 10 0.330 - 0.413: 2 Chirality restraints: 4979 Sorted by residual: chirality pdb=" C1 NAG J 1 " pdb=" ND2 ASN A1071 " pdb=" C2 NAG J 1 " pdb=" O5 NAG J 1 " both_signs ideal model delta sigma weight residual False -2.40 -1.99 -0.41 2.00e-01 2.50e+01 4.26e+00 chirality pdb=" C1 NAG B1302 " pdb=" ND2 ASN B 123 " pdb=" C2 NAG B1302 " pdb=" O5 NAG B1302 " both_signs ideal model delta sigma weight residual False -2.40 -2.00 -0.40 2.00e-01 2.50e+01 4.03e+00 chirality pdb=" CA GLN A 577 " pdb=" N GLN A 577 " pdb=" C GLN A 577 " pdb=" CB GLN A 577 " both_signs ideal model delta sigma weight residual False 2.51 2.80 -0.29 2.00e-01 2.50e+01 2.15e+00 ... (remaining 4976 not shown) Planarity restraints: 5394 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ASP C 464 " 0.031 2.00e-02 2.50e+03 6.18e-02 3.81e+01 pdb=" C ASP C 464 " -0.107 2.00e-02 2.50e+03 pdb=" O ASP C 464 " 0.040 2.00e-02 2.50e+03 pdb=" N ILE C 465 " 0.036 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C GLN A 268 " -0.040 5.00e-02 4.00e+02 6.05e-02 5.86e+00 pdb=" N PRO A 269 " 0.105 5.00e-02 4.00e+02 pdb=" CA PRO A 269 " -0.031 5.00e-02 4.00e+02 pdb=" CD PRO A 269 " -0.033 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB ASN C 231 " -0.022 2.00e-02 2.50e+03 2.02e-02 5.10e+00 pdb=" CG ASN C 231 " 0.018 2.00e-02 2.50e+03 pdb=" OD1 ASN C 231 " 0.004 2.00e-02 2.50e+03 pdb=" ND2 ASN C 231 " 0.025 2.00e-02 2.50e+03 pdb=" C1 NAG U 1 " -0.025 2.00e-02 2.50e+03 ... (remaining 5391 not shown) Histogram of nonbonded interaction distances: 2.11 - 2.67: 594 2.67 - 3.23: 27973 3.23 - 3.78: 43655 3.78 - 4.34: 59546 4.34 - 4.90: 99022 Nonbonded interactions: 230790 Sorted by model distance: nonbonded pdb=" O ASP C 464 " pdb=" O4 NAG C1302 " model vdw 2.111 2.432 nonbonded pdb=" OD2 ASP A 464 " pdb=" OG1 THR C 106 " model vdw 2.130 3.040 nonbonded pdb=" NH1 ARG L 78 " pdb=" O LEU L 79 " model vdw 2.134 3.120 nonbonded pdb=" OG SER I 28 " pdb=" OD1 ASN I 94 " model vdw 2.199 3.040 nonbonded pdb=" CB LEU C 184 " pdb=" CD1 LEU C 206 " model vdw 2.211 3.860 ... (remaining 230785 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = (chain 'C' and resid 14 through 1309) } ncs_group { reference = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'J' selection = chain 'K' 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' } ncs_group { reference = chain 'G' selection = chain 'H' } ncs_group { reference = chain 'I' selection = chain 'L' } ncs_group { reference = chain 'M' selection = chain 'S' selection = chain 'T' selection = chain 'Z' selection = chain 'a' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 4.100 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.030 Extract box with map and model: 0.490 Check model and map are aligned: 0.080 Set scattering table: 0.060 Process input model: 28.260 Find NCS groups from input model: 0.780 Set up NCS constraints: 0.090 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.280 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 35.180 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7906 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 0.158 31226 Z= 0.235 Angle : 0.795 16.609 42593 Z= 0.450 Chirality : 0.049 0.413 4979 Planarity : 0.004 0.062 5353 Dihedral : 15.892 122.729 12333 Min Nonbonded Distance : 2.111 Molprobity Statistics. All-atom Clashscore : 10.04 Ramachandran Plot: Outliers : 0.11 % Allowed : 5.81 % Favored : 94.08 % Rotamer: Outliers : 0.03 % Allowed : 0.24 % Favored : 99.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.07 % Cis-general : 0.03 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.05 (0.13), residues: 3716 helix: -2.08 (0.18), residues: 649 sheet: 0.11 (0.19), residues: 810 loop : -1.76 (0.12), residues: 2257 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 451 TYR 0.019 0.001 TYR C 450 PHE 0.018 0.001 PHE A 55 TRP 0.024 0.001 TRP B 630 HIS 0.004 0.001 HIS A 202 Details of bonding type rmsd covalent geometry : bond 0.00420 (31106) covalent geometry : angle 0.78283 (42305) SS BOND : bond 0.00292 ( 45) SS BOND : angle 1.09703 ( 90) hydrogen bonds : bond 0.25926 ( 911) hydrogen bonds : angle 8.68550 ( 2454) Misc. bond : bond 0.02406 ( 9) link_BETA1-4 : bond 0.00665 ( 25) link_BETA1-4 : angle 1.40302 ( 75) link_NAG-ASN : bond 0.00373 ( 41) link_NAG-ASN : angle 2.42542 ( 123) *********************** 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 218 residues out of total 3284 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 217 time to evaluate : 0.983 Fit side-chains revert: symmetry clash REVERT: A 186 GLU cc_start: 0.7930 (mp0) cc_final: 0.7307 (mp0) REVERT: A 402 ASP cc_start: 0.7957 (t0) cc_final: 0.7750 (t0) REVERT: A 1135 TYR cc_start: 0.7657 (t80) cc_final: 0.6829 (t80) REVERT: B 850 GLN cc_start: 0.7557 (tp-100) cc_final: 0.7274 (tp-100) REVERT: C 148 MET cc_start: 0.5869 (mmt) cc_final: 0.5614 (tpp) REVERT: C 415 ILE cc_start: 0.8772 (tt) cc_final: 0.8449 (tt) REVERT: H 36 GLN cc_start: 0.7018 (pt0) cc_final: 0.6624 (pt0) REVERT: H 65 PHE cc_start: 0.7829 (m-80) cc_final: 0.7596 (m-10) outliers start: 1 outliers final: 1 residues processed: 218 average time/residue: 0.2123 time to fit residues: 71.8416 Evaluate side-chains 176 residues out of total 3284 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 175 time to evaluate : 1.157 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 324 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 371 random chunks: chunk 197 optimal weight: 4.9990 chunk 215 optimal weight: 2.9990 chunk 20 optimal weight: 2.9990 chunk 132 optimal weight: 0.9990 chunk 261 optimal weight: 3.9990 chunk 248 optimal weight: 5.9990 chunk 207 optimal weight: 1.9990 chunk 155 optimal weight: 10.0000 chunk 244 optimal weight: 3.9990 chunk 183 optimal weight: 0.9980 chunk 298 optimal weight: 0.6980 overall best weight: 1.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 97 ASN A 419 ASN A 539 ASN A1103 GLN ** B 183 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 191 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 231 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 952 ASN C 577 GLN H 58 ASN ** H 116 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4162 r_free = 0.4162 target = 0.148647 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3330 r_free = 0.3330 target = 0.092350 restraints weight = 59588.615| |-----------------------------------------------------------------------------| r_work (start): 0.3284 rms_B_bonded: 3.72 r_work: 0.3130 rms_B_bonded: 3.93 restraints_weight: 0.5000 r_work (final): 0.3130 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7950 moved from start: 0.0997 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.068 31226 Z= 0.169 Angle : 0.696 20.275 42593 Z= 0.343 Chirality : 0.048 0.540 4979 Planarity : 0.005 0.072 5353 Dihedral : 10.575 111.133 5580 Min Nonbonded Distance : 2.115 Molprobity Statistics. All-atom Clashscore : 7.66 Ramachandran Plot: Outliers : 0.05 % Allowed : 6.27 % Favored : 93.68 % Rotamer: Outliers : 0.40 % Allowed : 6.78 % Favored : 92.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.07 % Cis-general : 0.03 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.74 (0.13), residues: 3716 helix: -1.09 (0.19), residues: 675 sheet: 0.13 (0.18), residues: 853 loop : -1.77 (0.13), residues: 2188 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG H 88 TYR 0.018 0.001 TYR C1064 PHE 0.021 0.001 PHE C 104 TRP 0.020 0.001 TRP B 64 HIS 0.005 0.001 HIS B 622 Details of bonding type rmsd covalent geometry : bond 0.00395 (31106) covalent geometry : angle 0.67777 (42305) SS BOND : bond 0.00319 ( 45) SS BOND : angle 1.09656 ( 90) hydrogen bonds : bond 0.06387 ( 911) hydrogen bonds : angle 6.31339 ( 2454) Misc. bond : bond 0.00874 ( 9) link_BETA1-4 : bond 0.00509 ( 25) link_BETA1-4 : angle 1.98271 ( 75) link_NAG-ASN : bond 0.00375 ( 41) link_NAG-ASN : angle 2.50809 ( 123) *********************** 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 209 residues out of total 3284 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 196 time to evaluate : 1.160 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 186 GLU cc_start: 0.8550 (mp0) cc_final: 0.7822 (mp0) REVERT: A 1135 TYR cc_start: 0.7860 (t80) cc_final: 0.6798 (t80) REVERT: B 850 GLN cc_start: 0.8364 (tp-100) cc_final: 0.8008 (tp-100) REVERT: C 498 TYR cc_start: 0.7481 (m-80) cc_final: 0.7221 (m-80) REVERT: C 820 PHE cc_start: 0.8450 (m-80) cc_final: 0.8218 (m-80) REVERT: C 866 MET cc_start: 0.9008 (mtp) cc_final: 0.8746 (mtp) REVERT: H 10 GLU cc_start: 0.8174 (tm-30) cc_final: 0.7951 (tm-30) REVERT: H 65 PHE cc_start: 0.7994 (m-80) cc_final: 0.7685 (m-10) REVERT: H 91 ASP cc_start: 0.7886 (m-30) cc_final: 0.7440 (m-30) outliers start: 13 outliers final: 11 residues processed: 207 average time/residue: 0.2169 time to fit residues: 70.1811 Evaluate side-chains 193 residues out of total 3284 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 182 time to evaluate : 1.137 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 199 TYR Chi-restraints excluded: chain B residue 188 VAL Chi-restraints excluded: chain B residue 492 TYR Chi-restraints excluded: chain B residue 824 THR Chi-restraints excluded: chain B residue 948 VAL Chi-restraints excluded: chain B residue 990 ILE Chi-restraints excluded: chain C residue 324 VAL Chi-restraints excluded: chain C residue 329 ILE Chi-restraints excluded: chain C residue 367 ASN Chi-restraints excluded: chain C residue 974 LEU Chi-restraints excluded: chain H residue 51 TRP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 371 random chunks: chunk 253 optimal weight: 3.9990 chunk 296 optimal weight: 0.0070 chunk 234 optimal weight: 2.9990 chunk 85 optimal weight: 3.9990 chunk 22 optimal weight: 50.0000 chunk 109 optimal weight: 30.0000 chunk 108 optimal weight: 5.9990 chunk 106 optimal weight: 0.0670 chunk 324 optimal weight: 0.0870 chunk 330 optimal weight: 7.9990 chunk 143 optimal weight: 0.1980 overall best weight: 0.6716 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 419 ASN A 539 ASN ** B 66 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 191 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 231 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 36 GLN H 58 ASN L 38 GLN I 39 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4184 r_free = 0.4184 target = 0.150360 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3363 r_free = 0.3363 target = 0.094579 restraints weight = 59902.428| |-----------------------------------------------------------------------------| r_work (start): 0.3298 rms_B_bonded: 3.91 r_work: 0.3139 rms_B_bonded: 3.85 restraints_weight: 0.5000 r_work (final): 0.3139 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7943 moved from start: 0.1282 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.078 31226 Z= 0.123 Angle : 0.639 19.597 42593 Z= 0.310 Chirality : 0.047 0.509 4979 Planarity : 0.004 0.073 5353 Dihedral : 8.602 110.265 5580 Min Nonbonded Distance : 2.015 Molprobity Statistics. All-atom Clashscore : 6.93 Ramachandran Plot: Outliers : 0.05 % Allowed : 5.57 % Favored : 94.38 % Rotamer: Outliers : 0.76 % Allowed : 9.80 % Favored : 89.44 % Cbeta Deviations : 0.03 % Peptide Plane: Cis-proline : 1.07 % Cis-general : 0.03 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.58 (0.13), residues: 3716 helix: -0.64 (0.20), residues: 665 sheet: 0.11 (0.18), residues: 888 loop : -1.75 (0.13), residues: 2163 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 354 TYR 0.017 0.001 TYR B 348 PHE 0.019 0.001 PHE C 104 TRP 0.030 0.002 TRP B 433 HIS 0.003 0.001 HIS B 202 Details of bonding type rmsd covalent geometry : bond 0.00266 (31106) covalent geometry : angle 0.62170 (42305) SS BOND : bond 0.00266 ( 45) SS BOND : angle 0.88012 ( 90) hydrogen bonds : bond 0.04940 ( 911) hydrogen bonds : angle 5.84224 ( 2454) Misc. bond : bond 0.00989 ( 9) link_BETA1-4 : bond 0.00538 ( 25) link_BETA1-4 : angle 1.96883 ( 75) link_NAG-ASN : bond 0.00371 ( 41) link_NAG-ASN : angle 2.35708 ( 123) *********************** 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 220 residues out of total 3284 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 195 time to evaluate : 1.181 Fit side-chains revert: symmetry clash REVERT: A 186 GLU cc_start: 0.8480 (mp0) cc_final: 0.7960 (mp0) REVERT: A 202 HIS cc_start: 0.6698 (t70) cc_final: 0.6103 (p-80) REVERT: A 1026 MET cc_start: 0.9255 (OUTLIER) cc_final: 0.9014 (ttt) REVERT: A 1135 TYR cc_start: 0.7804 (t80) cc_final: 0.7377 (t80) REVERT: B 850 GLN cc_start: 0.8331 (tp-100) cc_final: 0.8019 (tp-100) REVERT: C 1002 GLN cc_start: 0.8444 (OUTLIER) cc_final: 0.7184 (mp10) REVERT: H 3 GLN cc_start: 0.8688 (tm-30) cc_final: 0.8137 (tm-30) REVERT: H 65 PHE cc_start: 0.7824 (m-80) cc_final: 0.7561 (m-10) REVERT: L 55 ARG cc_start: 0.7952 (mtt-85) cc_final: 0.7190 (mtt180) REVERT: L 62 ARG cc_start: 0.8017 (ptt180) cc_final: 0.7390 (ptm160) REVERT: L 104 LYS cc_start: 0.8499 (ttpp) cc_final: 0.8274 (tptt) outliers start: 25 outliers final: 16 residues processed: 215 average time/residue: 0.2262 time to fit residues: 76.1177 Evaluate side-chains 197 residues out of total 3284 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 179 time to evaluate : 1.174 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 188 VAL Chi-restraints excluded: chain A residue 226 LEU Chi-restraints excluded: chain A residue 539 ASN Chi-restraints excluded: chain A residue 906 ILE Chi-restraints excluded: chain A residue 1026 MET Chi-restraints excluded: chain B residue 238 LEU Chi-restraints excluded: chain B residue 783 LYS Chi-restraints excluded: chain B residue 990 ILE Chi-restraints excluded: chain B residue 1089 GLU Chi-restraints excluded: chain C residue 237 THR Chi-restraints excluded: chain C residue 324 VAL Chi-restraints excluded: chain C residue 329 ILE Chi-restraints excluded: chain C residue 367 ASN Chi-restraints excluded: chain C residue 757 CYS Chi-restraints excluded: chain C residue 1002 GLN Chi-restraints excluded: chain H residue 51 TRP Chi-restraints excluded: chain H residue 107 CYS Chi-restraints excluded: chain L residue 47 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 371 random chunks: chunk 123 optimal weight: 30.0000 chunk 354 optimal weight: 3.9990 chunk 170 optimal weight: 0.7980 chunk 15 optimal weight: 0.9980 chunk 19 optimal weight: 0.3980 chunk 267 optimal weight: 0.2980 chunk 335 optimal weight: 9.9990 chunk 7 optimal weight: 0.8980 chunk 84 optimal weight: 2.9990 chunk 219 optimal weight: 0.9990 chunk 175 optimal weight: 3.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 539 ASN A 932 GLN ** B 66 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 183 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 191 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 231 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1139 GLN H 58 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4182 r_free = 0.4182 target = 0.150407 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3361 r_free = 0.3361 target = 0.094505 restraints weight = 59501.299| |-----------------------------------------------------------------------------| r_work (start): 0.3310 rms_B_bonded: 3.93 r_work: 0.3152 rms_B_bonded: 3.87 restraints_weight: 0.5000 r_work (final): 0.3152 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7909 moved from start: 0.1491 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.067 31226 Z= 0.115 Angle : 0.614 19.552 42593 Z= 0.298 Chirality : 0.046 0.503 4979 Planarity : 0.004 0.064 5353 Dihedral : 7.536 108.539 5580 Min Nonbonded Distance : 2.124 Molprobity Statistics. All-atom Clashscore : 6.83 Ramachandran Plot: Outliers : 0.05 % Allowed : 5.95 % Favored : 94.00 % Rotamer: Outliers : 0.98 % Allowed : 11.17 % Favored : 87.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.07 % Cis-general : 0.03 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.46 (0.13), residues: 3716 helix: -0.43 (0.20), residues: 667 sheet: 0.18 (0.18), residues: 877 loop : -1.71 (0.13), residues: 2172 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG L 78 TYR 0.014 0.001 TYR C1064 PHE 0.018 0.001 PHE C 104 TRP 0.022 0.001 TRP B 255 HIS 0.005 0.001 HIS B 622 Details of bonding type rmsd covalent geometry : bond 0.00247 (31106) covalent geometry : angle 0.59664 (42305) SS BOND : bond 0.00329 ( 45) SS BOND : angle 0.90261 ( 90) hydrogen bonds : bond 0.04445 ( 911) hydrogen bonds : angle 5.59872 ( 2454) Misc. bond : bond 0.01213 ( 9) link_BETA1-4 : bond 0.00489 ( 25) link_BETA1-4 : angle 1.97550 ( 75) link_NAG-ASN : bond 0.00352 ( 41) link_NAG-ASN : angle 2.30866 ( 123) *********************** 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 216 residues out of total 3284 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 184 time to evaluate : 1.098 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 186 GLU cc_start: 0.8442 (mp0) cc_final: 0.7854 (mp0) REVERT: A 202 HIS cc_start: 0.6243 (t70) cc_final: 0.5780 (p-80) REVERT: A 580 GLU cc_start: 0.8359 (OUTLIER) cc_final: 0.8038 (pm20) REVERT: A 1135 TYR cc_start: 0.7761 (t80) cc_final: 0.6705 (t80) REVERT: B 116 LEU cc_start: 0.7551 (OUTLIER) cc_final: 0.7176 (mp) REVERT: B 850 GLN cc_start: 0.8290 (tp-100) cc_final: 0.8044 (tp-100) REVERT: C 393 TYR cc_start: 0.7702 (m-80) cc_final: 0.7493 (m-10) REVERT: C 1002 GLN cc_start: 0.8432 (OUTLIER) cc_final: 0.7130 (mp10) REVERT: L 55 ARG cc_start: 0.7922 (mtt-85) cc_final: 0.7284 (mtt90) REVERT: L 62 ARG cc_start: 0.7957 (ptt180) cc_final: 0.7646 (ptm160) REVERT: L 104 LYS cc_start: 0.8503 (ttpp) cc_final: 0.8271 (tptt) outliers start: 32 outliers final: 20 residues processed: 208 average time/residue: 0.2177 time to fit residues: 71.6415 Evaluate side-chains 200 residues out of total 3284 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 177 time to evaluate : 1.050 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 188 VAL Chi-restraints excluded: chain A residue 199 TYR Chi-restraints excluded: chain A residue 226 LEU Chi-restraints excluded: chain A residue 393 TYR Chi-restraints excluded: chain A residue 429 CYS Chi-restraints excluded: chain A residue 548 VAL Chi-restraints excluded: chain A residue 580 GLU Chi-restraints excluded: chain B residue 116 LEU Chi-restraints excluded: chain B residue 188 VAL Chi-restraints excluded: chain B residue 492 TYR Chi-restraints excluded: chain B residue 783 LYS Chi-restraints excluded: chain B residue 990 ILE Chi-restraints excluded: chain B residue 1089 GLU Chi-restraints excluded: chain C residue 118 VAL Chi-restraints excluded: chain C residue 237 THR Chi-restraints excluded: chain C residue 315 PHE Chi-restraints excluded: chain C residue 324 VAL Chi-restraints excluded: chain C residue 329 ILE Chi-restraints excluded: chain C residue 367 ASN Chi-restraints excluded: chain C residue 1002 GLN Chi-restraints excluded: chain H residue 51 TRP Chi-restraints excluded: chain H residue 107 CYS Chi-restraints excluded: chain L residue 47 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 371 random chunks: chunk 59 optimal weight: 9.9990 chunk 221 optimal weight: 3.9990 chunk 86 optimal weight: 3.9990 chunk 9 optimal weight: 9.9990 chunk 180 optimal weight: 5.9990 chunk 366 optimal weight: 0.0270 chunk 252 optimal weight: 0.6980 chunk 204 optimal weight: 3.9990 chunk 331 optimal weight: 6.9990 chunk 232 optimal weight: 6.9990 chunk 303 optimal weight: 0.7980 overall best weight: 1.9042 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 191 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 231 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 = 0.4155 r_free = 0.4155 target = 0.148267 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3317 r_free = 0.3317 target = 0.091834 restraints weight = 59387.153| |-----------------------------------------------------------------------------| r_work (start): 0.3263 rms_B_bonded: 3.83 r_work: 0.3098 rms_B_bonded: 3.89 restraints_weight: 0.5000 r_work (final): 0.3098 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7970 moved from start: 0.1581 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.072 31226 Z= 0.187 Angle : 0.668 20.011 42593 Z= 0.327 Chirality : 0.049 0.531 4979 Planarity : 0.004 0.074 5353 Dihedral : 7.196 106.251 5580 Min Nonbonded Distance : 2.107 Molprobity Statistics. All-atom Clashscore : 7.23 Ramachandran Plot: Outliers : 0.08 % Allowed : 6.84 % Favored : 93.08 % Rotamer: Outliers : 1.53 % Allowed : 12.58 % Favored : 85.90 % Cbeta Deviations : 0.03 % Peptide Plane: Cis-proline : 1.07 % Cis-general : 0.03 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.53 (0.13), residues: 3716 helix: -0.42 (0.20), residues: 675 sheet: 0.16 (0.18), residues: 880 loop : -1.79 (0.13), residues: 2161 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG L 78 TYR 0.016 0.001 TYR C 262 PHE 0.023 0.002 PHE A 43 TRP 0.019 0.002 TRP B 433 HIS 0.004 0.001 HIS A 202 Details of bonding type rmsd covalent geometry : bond 0.00450 (31106) covalent geometry : angle 0.65011 (42305) SS BOND : bond 0.00290 ( 45) SS BOND : angle 1.06504 ( 90) hydrogen bonds : bond 0.05221 ( 911) hydrogen bonds : angle 5.71805 ( 2454) Misc. bond : bond 0.01197 ( 9) link_BETA1-4 : bond 0.00422 ( 25) link_BETA1-4 : angle 1.94299 ( 75) link_NAG-ASN : bond 0.00384 ( 41) link_NAG-ASN : angle 2.44243 ( 123) *********************** 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 237 residues out of total 3284 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 187 time to evaluate : 1.260 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 148 MET cc_start: 0.2934 (tpt) cc_final: 0.2661 (tpt) REVERT: A 185 ARG cc_start: 0.7103 (mpt180) cc_final: 0.6709 (mpt180) REVERT: A 186 GLU cc_start: 0.8675 (mp0) cc_final: 0.8056 (mp0) REVERT: A 202 HIS cc_start: 0.6390 (t70) cc_final: 0.5851 (p-80) REVERT: A 580 GLU cc_start: 0.8336 (OUTLIER) cc_final: 0.8054 (pm20) REVERT: A 1135 TYR cc_start: 0.7841 (t80) cc_final: 0.6753 (t80) REVERT: B 116 LEU cc_start: 0.7585 (OUTLIER) cc_final: 0.7230 (mp) REVERT: B 850 GLN cc_start: 0.8389 (tp-100) cc_final: 0.8098 (tp-100) REVERT: B 985 GLU cc_start: 0.8243 (tm-30) cc_final: 0.7980 (tm-30) REVERT: C 235 PHE cc_start: 0.8408 (OUTLIER) cc_final: 0.7979 (p90) REVERT: C 1002 GLN cc_start: 0.8479 (OUTLIER) cc_final: 0.7179 (mp10) REVERT: L 55 ARG cc_start: 0.7870 (mtt-85) cc_final: 0.7211 (mtt90) REVERT: L 62 ARG cc_start: 0.8094 (ptt180) cc_final: 0.7634 (ptm160) REVERT: L 104 LYS cc_start: 0.8423 (ttpp) cc_final: 0.8149 (tptt) outliers start: 50 outliers final: 29 residues processed: 231 average time/residue: 0.2148 time to fit residues: 80.1903 Evaluate side-chains 209 residues out of total 3284 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 176 time to evaluate : 1.041 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 188 VAL Chi-restraints excluded: chain A residue 220 LEU Chi-restraints excluded: chain A residue 226 LEU Chi-restraints excluded: chain A residue 393 TYR Chi-restraints excluded: chain A residue 548 VAL Chi-restraints excluded: chain A residue 580 GLU Chi-restraints excluded: chain A residue 617 VAL Chi-restraints excluded: chain A residue 906 ILE Chi-restraints excluded: chain A residue 1125 VAL Chi-restraints excluded: chain B residue 42 VAL Chi-restraints excluded: chain B residue 116 LEU Chi-restraints excluded: chain B residue 188 VAL Chi-restraints excluded: chain B residue 207 VAL Chi-restraints excluded: chain B residue 238 LEU Chi-restraints excluded: chain B residue 492 TYR Chi-restraints excluded: chain B residue 783 LYS Chi-restraints excluded: chain B residue 990 ILE Chi-restraints excluded: chain B residue 991 ASP Chi-restraints excluded: chain C residue 115 LEU Chi-restraints excluded: chain C residue 118 VAL Chi-restraints excluded: chain C residue 188 VAL Chi-restraints excluded: chain C residue 235 PHE Chi-restraints excluded: chain C residue 237 THR Chi-restraints excluded: chain C residue 315 PHE Chi-restraints excluded: chain C residue 324 VAL Chi-restraints excluded: chain C residue 329 ILE Chi-restraints excluded: chain C residue 367 ASN Chi-restraints excluded: chain C residue 578 THR Chi-restraints excluded: chain C residue 1002 GLN Chi-restraints excluded: chain H residue 51 TRP Chi-restraints excluded: chain H residue 107 CYS Chi-restraints excluded: chain L residue 63 PHE Chi-restraints excluded: chain L residue 79 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 371 random chunks: chunk 76 optimal weight: 4.9990 chunk 37 optimal weight: 0.0060 chunk 345 optimal weight: 30.0000 chunk 43 optimal weight: 0.2980 chunk 209 optimal weight: 0.2980 chunk 189 optimal weight: 1.9990 chunk 20 optimal weight: 0.8980 chunk 190 optimal weight: 0.0370 chunk 191 optimal weight: 0.5980 chunk 17 optimal weight: 0.6980 chunk 262 optimal weight: 6.9990 overall best weight: 0.2474 ------------------------------------------------------------------------------- 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 191 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 231 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 97 ASN C 952 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4191 r_free = 0.4191 target = 0.151286 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3378 r_free = 0.3378 target = 0.095361 restraints weight = 59977.810| |-----------------------------------------------------------------------------| r_work (start): 0.3317 rms_B_bonded: 3.77 r_work: 0.3158 rms_B_bonded: 3.79 restraints_weight: 0.5000 r_work (final): 0.3158 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7958 moved from start: 0.1760 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.069 31226 Z= 0.109 Angle : 0.607 19.145 42593 Z= 0.295 Chirality : 0.046 0.469 4979 Planarity : 0.004 0.069 5353 Dihedral : 6.749 105.447 5580 Min Nonbonded Distance : 2.210 Molprobity Statistics. All-atom Clashscore : 6.56 Ramachandran Plot: Outliers : 0.05 % Allowed : 5.62 % Favored : 94.32 % Rotamer: Outliers : 1.31 % Allowed : 13.25 % Favored : 85.44 % Cbeta Deviations : 0.03 % Peptide Plane: Cis-proline : 1.07 % Cis-general : 0.03 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.33 (0.14), residues: 3716 helix: -0.09 (0.21), residues: 666 sheet: 0.22 (0.18), residues: 877 loop : -1.68 (0.13), residues: 2173 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG A 454 TYR 0.018 0.001 TYR A 199 PHE 0.019 0.001 PHE C 104 TRP 0.019 0.001 TRP B 433 HIS 0.002 0.000 HIS B 202 Details of bonding type rmsd covalent geometry : bond 0.00224 (31106) covalent geometry : angle 0.58794 (42305) SS BOND : bond 0.00282 ( 45) SS BOND : angle 0.78816 ( 90) hydrogen bonds : bond 0.03915 ( 911) hydrogen bonds : angle 5.37886 ( 2454) Misc. bond : bond 0.01189 ( 9) link_BETA1-4 : bond 0.00480 ( 25) link_BETA1-4 : angle 1.93362 ( 75) link_NAG-ASN : bond 0.00424 ( 41) link_NAG-ASN : angle 2.40661 ( 123) *********************** 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 231 residues out of total 3284 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 188 time to evaluate : 1.167 Fit side-chains revert: symmetry clash REVERT: A 119 ASN cc_start: 0.7437 (p0) cc_final: 0.7187 (p0) REVERT: A 185 ARG cc_start: 0.7288 (mpt180) cc_final: 0.7007 (mpt180) REVERT: A 186 GLU cc_start: 0.8391 (mp0) cc_final: 0.7783 (mp0) REVERT: A 190 LYS cc_start: 0.4022 (OUTLIER) cc_final: 0.2387 (ttpt) REVERT: A 202 HIS cc_start: 0.6157 (t70) cc_final: 0.5761 (p-80) REVERT: A 580 GLU cc_start: 0.8327 (OUTLIER) cc_final: 0.8083 (pm20) REVERT: A 1016 ARG cc_start: 0.8754 (tpt170) cc_final: 0.7969 (ttp80) REVERT: A 1135 TYR cc_start: 0.7942 (t80) cc_final: 0.6918 (t80) REVERT: B 116 LEU cc_start: 0.7381 (OUTLIER) cc_final: 0.7000 (mp) REVERT: B 631 ARG cc_start: 0.6944 (pmt170) cc_final: 0.5762 (ptp90) REVERT: B 850 GLN cc_start: 0.8254 (tp-100) cc_final: 0.7953 (tp-100) REVERT: B 985 GLU cc_start: 0.8262 (tm-30) cc_final: 0.8024 (tm-30) REVERT: C 429 CYS cc_start: 0.7660 (OUTLIER) cc_final: 0.7449 (p) REVERT: C 1002 GLN cc_start: 0.8426 (OUTLIER) cc_final: 0.7229 (mp10) REVERT: H 68 ARG cc_start: 0.7210 (tpt170) cc_final: 0.6863 (mmm160) REVERT: L 37 TYR cc_start: 0.7454 (m-80) cc_final: 0.6966 (m-80) REVERT: L 55 ARG cc_start: 0.8023 (mtt-85) cc_final: 0.7504 (mtt90) REVERT: L 62 ARG cc_start: 0.8132 (ptt180) cc_final: 0.7684 (ptm160) outliers start: 43 outliers final: 23 residues processed: 224 average time/residue: 0.2102 time to fit residues: 74.1010 Evaluate side-chains 207 residues out of total 3284 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 179 time to evaluate : 0.945 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 188 VAL Chi-restraints excluded: chain A residue 190 LYS Chi-restraints excluded: chain A residue 207 VAL Chi-restraints excluded: chain A residue 220 LEU Chi-restraints excluded: chain A residue 226 LEU Chi-restraints excluded: chain A residue 393 TYR Chi-restraints excluded: chain A residue 429 CYS Chi-restraints excluded: chain A residue 580 GLU Chi-restraints excluded: chain A residue 906 ILE Chi-restraints excluded: chain A residue 1125 VAL Chi-restraints excluded: chain B residue 116 LEU Chi-restraints excluded: chain B residue 188 VAL Chi-restraints excluded: chain B residue 207 VAL Chi-restraints excluded: chain B residue 492 TYR Chi-restraints excluded: chain B residue 990 ILE Chi-restraints excluded: chain B residue 991 ASP Chi-restraints excluded: chain B residue 1089 GLU Chi-restraints excluded: chain C residue 118 VAL Chi-restraints excluded: chain C residue 188 VAL Chi-restraints excluded: chain C residue 315 PHE Chi-restraints excluded: chain C residue 324 VAL Chi-restraints excluded: chain C residue 367 ASN Chi-restraints excluded: chain C residue 429 CYS Chi-restraints excluded: chain C residue 1002 GLN Chi-restraints excluded: chain H residue 22 CYS Chi-restraints excluded: chain H residue 51 TRP Chi-restraints excluded: chain H residue 107 CYS Chi-restraints excluded: chain L residue 79 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 371 random chunks: chunk 143 optimal weight: 10.0000 chunk 60 optimal weight: 9.9990 chunk 17 optimal weight: 6.9990 chunk 269 optimal weight: 3.9990 chunk 31 optimal weight: 0.0970 chunk 241 optimal weight: 3.9990 chunk 204 optimal weight: 0.9980 chunk 192 optimal weight: 0.9980 chunk 210 optimal weight: 3.9990 chunk 87 optimal weight: 3.9990 chunk 40 optimal weight: 0.9980 overall best weight: 1.4180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 191 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 231 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 97 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 = 0.4166 r_free = 0.4166 target = 0.149387 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3344 r_free = 0.3344 target = 0.093809 restraints weight = 59753.202| |-----------------------------------------------------------------------------| r_work (start): 0.3290 rms_B_bonded: 3.82 r_work: 0.3120 rms_B_bonded: 3.76 restraints_weight: 0.5000 r_work (final): 0.3120 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7951 moved from start: 0.1797 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.084 31226 Z= 0.154 Angle : 0.646 19.611 42593 Z= 0.315 Chirality : 0.047 0.494 4979 Planarity : 0.004 0.069 5353 Dihedral : 6.642 103.743 5580 Min Nonbonded Distance : 2.229 Molprobity Statistics. All-atom Clashscore : 7.26 Ramachandran Plot: Outliers : 0.08 % Allowed : 6.46 % Favored : 93.46 % Rotamer: Outliers : 1.50 % Allowed : 13.80 % Favored : 84.71 % Cbeta Deviations : 0.03 % Peptide Plane: Cis-proline : 1.07 % Cis-general : 0.03 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.38 (0.14), residues: 3716 helix: -0.18 (0.20), residues: 686 sheet: 0.17 (0.18), residues: 866 loop : -1.69 (0.13), residues: 2164 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A 454 TYR 0.014 0.001 TYR C 262 PHE 0.023 0.001 PHE C 235 TRP 0.022 0.002 TRP L 36 HIS 0.003 0.001 HIS B 202 Details of bonding type rmsd covalent geometry : bond 0.00360 (31106) covalent geometry : angle 0.62685 (42305) SS BOND : bond 0.00277 ( 45) SS BOND : angle 1.35627 ( 90) hydrogen bonds : bond 0.04523 ( 911) hydrogen bonds : angle 5.48057 ( 2454) Misc. bond : bond 0.01141 ( 9) link_BETA1-4 : bond 0.00485 ( 25) link_BETA1-4 : angle 1.84489 ( 75) link_NAG-ASN : bond 0.00367 ( 41) link_NAG-ASN : angle 2.39313 ( 123) *********************** 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 230 residues out of total 3284 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 181 time to evaluate : 1.070 Fit side-chains REVERT: A 126 ILE cc_start: 0.6030 (OUTLIER) cc_final: 0.5626 (mm) REVERT: A 185 ARG cc_start: 0.7222 (mpt180) cc_final: 0.6907 (mpt180) REVERT: A 186 GLU cc_start: 0.8561 (mp0) cc_final: 0.7893 (mp0) REVERT: A 190 LYS cc_start: 0.4062 (OUTLIER) cc_final: 0.2549 (ttpt) REVERT: A 202 HIS cc_start: 0.6212 (t70) cc_final: 0.5755 (p-80) REVERT: A 580 GLU cc_start: 0.8327 (OUTLIER) cc_final: 0.8066 (pm20) REVERT: A 1135 TYR cc_start: 0.7927 (t80) cc_final: 0.6897 (t80) REVERT: B 116 LEU cc_start: 0.7391 (OUTLIER) cc_final: 0.7012 (mp) REVERT: B 631 ARG cc_start: 0.6984 (pmt170) cc_final: 0.5774 (ptp90) REVERT: B 850 GLN cc_start: 0.8335 (tp-100) cc_final: 0.8048 (tp-100) REVERT: B 985 GLU cc_start: 0.8273 (tm-30) cc_final: 0.8034 (tm-30) REVERT: C 1002 GLN cc_start: 0.8480 (OUTLIER) cc_final: 0.7245 (mp10) REVERT: H 3 GLN cc_start: 0.8643 (tm-30) cc_final: 0.8065 (tm-30) REVERT: H 88 ARG cc_start: 0.7746 (mpp-170) cc_final: 0.7543 (mtm-85) REVERT: L 47 LEU cc_start: 0.8528 (tp) cc_final: 0.8299 (mt) REVERT: L 55 ARG cc_start: 0.7952 (mtt-85) cc_final: 0.7397 (mtt90) REVERT: L 62 ARG cc_start: 0.8135 (ptt180) cc_final: 0.7423 (ptm160) REVERT: L 78 ARG cc_start: 0.8019 (tmm160) cc_final: 0.7643 (ttp80) outliers start: 49 outliers final: 35 residues processed: 222 average time/residue: 0.1965 time to fit residues: 69.3275 Evaluate side-chains 215 residues out of total 3284 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 175 time to evaluate : 0.694 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 126 ILE Chi-restraints excluded: chain A residue 188 VAL Chi-restraints excluded: chain A residue 190 LYS Chi-restraints excluded: chain A residue 203 THR Chi-restraints excluded: chain A residue 207 VAL Chi-restraints excluded: chain A residue 220 LEU Chi-restraints excluded: chain A residue 226 LEU Chi-restraints excluded: chain A residue 271 THR Chi-restraints excluded: chain A residue 393 TYR Chi-restraints excluded: chain A residue 429 CYS Chi-restraints excluded: chain A residue 548 VAL Chi-restraints excluded: chain A residue 580 GLU Chi-restraints excluded: chain A residue 617 VAL Chi-restraints excluded: chain A residue 906 ILE Chi-restraints excluded: chain A residue 1125 VAL Chi-restraints excluded: chain B residue 42 VAL Chi-restraints excluded: chain B residue 66 HIS Chi-restraints excluded: chain B residue 116 LEU Chi-restraints excluded: chain B residue 188 VAL Chi-restraints excluded: chain B residue 207 VAL Chi-restraints excluded: chain B residue 238 LEU Chi-restraints excluded: chain B residue 264 VAL Chi-restraints excluded: chain B residue 492 TYR Chi-restraints excluded: chain B residue 783 LYS Chi-restraints excluded: chain B residue 824 THR Chi-restraints excluded: chain B residue 990 ILE Chi-restraints excluded: chain B residue 991 ASP Chi-restraints excluded: chain C residue 115 LEU Chi-restraints excluded: chain C residue 118 VAL Chi-restraints excluded: chain C residue 188 VAL Chi-restraints excluded: chain C residue 237 THR Chi-restraints excluded: chain C residue 315 PHE Chi-restraints excluded: chain C residue 324 VAL Chi-restraints excluded: chain C residue 367 ASN Chi-restraints excluded: chain C residue 578 THR Chi-restraints excluded: chain C residue 1002 GLN Chi-restraints excluded: chain H residue 22 CYS Chi-restraints excluded: chain H residue 51 TRP Chi-restraints excluded: chain H residue 107 CYS Chi-restraints excluded: chain L residue 79 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 371 random chunks: chunk 165 optimal weight: 0.9990 chunk 151 optimal weight: 0.0970 chunk 363 optimal weight: 20.0000 chunk 159 optimal weight: 3.9990 chunk 71 optimal weight: 4.9990 chunk 24 optimal weight: 5.9990 chunk 237 optimal weight: 0.0980 chunk 92 optimal weight: 6.9990 chunk 226 optimal weight: 1.9990 chunk 91 optimal weight: 10.0000 chunk 8 optimal weight: 9.9990 overall best weight: 1.4384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 191 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 231 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 314 ASN C 97 ASN H 58 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4164 r_free = 0.4164 target = 0.149075 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3335 r_free = 0.3335 target = 0.092727 restraints weight = 59774.114| |-----------------------------------------------------------------------------| r_work (start): 0.3281 rms_B_bonded: 3.72 r_work: 0.3119 rms_B_bonded: 3.84 restraints_weight: 0.5000 r_work (final): 0.3119 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7963 moved from start: 0.1853 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.109 31226 Z= 0.155 Angle : 0.640 19.529 42593 Z= 0.313 Chirality : 0.047 0.489 4979 Planarity : 0.004 0.069 5353 Dihedral : 6.540 102.445 5580 Min Nonbonded Distance : 2.279 Molprobity Statistics. All-atom Clashscore : 7.28 Ramachandran Plot: Outliers : 0.05 % Allowed : 6.57 % Favored : 93.38 % Rotamer: Outliers : 1.74 % Allowed : 14.01 % Favored : 84.25 % Cbeta Deviations : 0.03 % Peptide Plane: Cis-proline : 1.07 % Cis-general : 0.03 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.39 (0.13), residues: 3716 helix: -0.17 (0.20), residues: 686 sheet: 0.19 (0.18), residues: 862 loop : -1.71 (0.13), residues: 2168 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 454 TYR 0.015 0.001 TYR C 262 PHE 0.029 0.001 PHE C 235 TRP 0.021 0.001 TRP B 433 HIS 0.003 0.001 HIS A 202 Details of bonding type rmsd covalent geometry : bond 0.00361 (31106) covalent geometry : angle 0.62212 (42305) SS BOND : bond 0.00318 ( 45) SS BOND : angle 1.20008 ( 90) hydrogen bonds : bond 0.04590 ( 911) hydrogen bonds : angle 5.49914 ( 2454) Misc. bond : bond 0.01400 ( 9) link_BETA1-4 : bond 0.00444 ( 25) link_BETA1-4 : angle 1.85983 ( 75) link_NAG-ASN : bond 0.00364 ( 41) link_NAG-ASN : angle 2.39763 ( 123) *********************** 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 238 residues out of total 3284 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 181 time to evaluate : 1.058 Fit side-chains REVERT: A 126 ILE cc_start: 0.5811 (OUTLIER) cc_final: 0.5387 (mm) REVERT: A 185 ARG cc_start: 0.7175 (mpt180) cc_final: 0.6820 (mpt180) REVERT: A 186 GLU cc_start: 0.8622 (mp0) cc_final: 0.7941 (mp0) REVERT: A 190 LYS cc_start: 0.4083 (OUTLIER) cc_final: 0.2567 (ttpt) REVERT: A 202 HIS cc_start: 0.6263 (t70) cc_final: 0.5797 (p-80) REVERT: A 236 GLN cc_start: 0.6843 (tm-30) cc_final: 0.6639 (tm-30) REVERT: A 580 GLU cc_start: 0.8313 (OUTLIER) cc_final: 0.8051 (pm20) REVERT: A 1135 TYR cc_start: 0.7960 (t80) cc_final: 0.6941 (t80) REVERT: B 116 LEU cc_start: 0.7455 (OUTLIER) cc_final: 0.7098 (mp) REVERT: B 631 ARG cc_start: 0.7057 (pmt170) cc_final: 0.5802 (ptp90) REVERT: B 850 GLN cc_start: 0.8354 (tp-100) cc_final: 0.8054 (tp-100) REVERT: B 985 GLU cc_start: 0.8302 (tm-30) cc_final: 0.8074 (tm-30) REVERT: C 1002 GLN cc_start: 0.8485 (OUTLIER) cc_final: 0.7257 (mp10) REVERT: H 3 GLN cc_start: 0.8647 (tm-30) cc_final: 0.8079 (tm-30) REVERT: H 91 ASP cc_start: 0.7794 (m-30) cc_final: 0.6763 (m-30) REVERT: L 47 LEU cc_start: 0.8506 (tp) cc_final: 0.8180 (mt) REVERT: L 55 ARG cc_start: 0.7828 (mtt-85) cc_final: 0.7133 (mtt90) REVERT: L 62 ARG cc_start: 0.8110 (ptt180) cc_final: 0.7379 (ptm160) REVERT: L 78 ARG cc_start: 0.8089 (tmm160) cc_final: 0.7779 (ttp80) outliers start: 57 outliers final: 41 residues processed: 228 average time/residue: 0.1932 time to fit residues: 69.6434 Evaluate side-chains 222 residues out of total 3284 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 176 time to evaluate : 1.179 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 126 ILE Chi-restraints excluded: chain A residue 188 VAL Chi-restraints excluded: chain A residue 190 LYS Chi-restraints excluded: chain A residue 203 THR Chi-restraints excluded: chain A residue 207 VAL Chi-restraints excluded: chain A residue 220 LEU Chi-restraints excluded: chain A residue 226 LEU Chi-restraints excluded: chain A residue 271 THR Chi-restraints excluded: chain A residue 393 TYR Chi-restraints excluded: chain A residue 548 VAL Chi-restraints excluded: chain A residue 580 GLU Chi-restraints excluded: chain A residue 617 VAL Chi-restraints excluded: chain A residue 906 ILE Chi-restraints excluded: chain A residue 1001 LEU Chi-restraints excluded: chain A residue 1026 MET Chi-restraints excluded: chain A residue 1125 VAL Chi-restraints excluded: chain B residue 42 VAL Chi-restraints excluded: chain B residue 66 HIS Chi-restraints excluded: chain B residue 116 LEU Chi-restraints excluded: chain B residue 188 VAL Chi-restraints excluded: chain B residue 207 VAL Chi-restraints excluded: chain B residue 235 PHE Chi-restraints excluded: chain B residue 238 LEU Chi-restraints excluded: chain B residue 264 VAL Chi-restraints excluded: chain B residue 824 THR Chi-restraints excluded: chain B residue 990 ILE Chi-restraints excluded: chain B residue 991 ASP Chi-restraints excluded: chain C residue 97 ASN Chi-restraints excluded: chain C residue 115 LEU Chi-restraints excluded: chain C residue 188 VAL Chi-restraints excluded: chain C residue 217 PHE Chi-restraints excluded: chain C residue 237 THR Chi-restraints excluded: chain C residue 315 PHE Chi-restraints excluded: chain C residue 324 VAL Chi-restraints excluded: chain C residue 367 ASN Chi-restraints excluded: chain C residue 415 ILE Chi-restraints excluded: chain C residue 578 THR Chi-restraints excluded: chain C residue 607 VAL Chi-restraints excluded: chain C residue 897 MET Chi-restraints excluded: chain C residue 1002 GLN Chi-restraints excluded: chain H residue 22 CYS Chi-restraints excluded: chain H residue 32 VAL Chi-restraints excluded: chain H residue 51 TRP Chi-restraints excluded: chain H residue 107 CYS Chi-restraints excluded: chain L residue 79 LEU Chi-restraints excluded: chain G residue 2 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 371 random chunks: chunk 205 optimal weight: 3.9990 chunk 272 optimal weight: 5.9990 chunk 275 optimal weight: 2.9990 chunk 343 optimal weight: 4.9990 chunk 16 optimal weight: 5.9990 chunk 273 optimal weight: 0.9980 chunk 157 optimal weight: 10.0000 chunk 298 optimal weight: 0.9980 chunk 151 optimal weight: 0.0570 chunk 162 optimal weight: 0.0270 chunk 256 optimal weight: 0.8980 overall best weight: 0.5956 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 191 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 231 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 97 ASN C 541 ASN C 561 GLN H 58 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4184 r_free = 0.4184 target = 0.150711 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3376 r_free = 0.3376 target = 0.095544 restraints weight = 59610.481| |-----------------------------------------------------------------------------| r_work (start): 0.3327 rms_B_bonded: 3.84 r_work: 0.3157 rms_B_bonded: 3.84 restraints_weight: 0.5000 r_work (final): 0.3157 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7926 moved from start: 0.1934 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.124 31226 Z= 0.119 Angle : 0.621 19.094 42593 Z= 0.303 Chirality : 0.046 0.463 4979 Planarity : 0.004 0.072 5353 Dihedral : 6.360 101.718 5580 Min Nonbonded Distance : 2.290 Molprobity Statistics. All-atom Clashscore : 6.95 Ramachandran Plot: Outliers : 0.05 % Allowed : 5.95 % Favored : 94.00 % Rotamer: Outliers : 1.43 % Allowed : 14.74 % Favored : 83.82 % Cbeta Deviations : 0.03 % Peptide Plane: Cis-proline : 1.07 % Cis-general : 0.03 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.27 (0.14), residues: 3716 helix: 0.01 (0.21), residues: 687 sheet: 0.22 (0.18), residues: 862 loop : -1.65 (0.13), residues: 2167 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG H 68 TYR 0.019 0.001 TYR B 492 PHE 0.028 0.001 PHE C 235 TRP 0.021 0.001 TRP B 433 HIS 0.003 0.000 HIS B 202 Details of bonding type rmsd covalent geometry : bond 0.00255 (31106) covalent geometry : angle 0.60302 (42305) SS BOND : bond 0.00346 ( 45) SS BOND : angle 1.27339 ( 90) hydrogen bonds : bond 0.04031 ( 911) hydrogen bonds : angle 5.34805 ( 2454) Misc. bond : bond 0.01463 ( 9) link_BETA1-4 : bond 0.00475 ( 25) link_BETA1-4 : angle 1.80596 ( 75) link_NAG-ASN : bond 0.00364 ( 41) link_NAG-ASN : angle 2.31496 ( 123) *********************** 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 232 residues out of total 3284 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 185 time to evaluate : 1.187 Fit side-chains revert: symmetry clash REVERT: A 119 ASN cc_start: 0.7496 (p0) cc_final: 0.7261 (p0) REVERT: A 126 ILE cc_start: 0.6163 (OUTLIER) cc_final: 0.5803 (mm) REVERT: A 185 ARG cc_start: 0.7275 (mpt180) cc_final: 0.6954 (mpt180) REVERT: A 186 GLU cc_start: 0.8492 (mp0) cc_final: 0.7810 (mp0) REVERT: A 190 LYS cc_start: 0.3836 (OUTLIER) cc_final: 0.2443 (ttpt) REVERT: A 202 HIS cc_start: 0.6122 (t70) cc_final: 0.5752 (p-80) REVERT: A 354 ARG cc_start: 0.7998 (OUTLIER) cc_final: 0.7751 (tpp80) REVERT: A 580 GLU cc_start: 0.8321 (OUTLIER) cc_final: 0.8057 (pm20) REVERT: A 1135 TYR cc_start: 0.7982 (t80) cc_final: 0.7000 (t80) REVERT: B 116 LEU cc_start: 0.7402 (OUTLIER) cc_final: 0.7053 (mp) REVERT: B 631 ARG cc_start: 0.7013 (pmt170) cc_final: 0.5790 (ptp90) REVERT: B 850 GLN cc_start: 0.8320 (tp-100) cc_final: 0.8019 (tp-100) REVERT: B 985 GLU cc_start: 0.8288 (tm-30) cc_final: 0.8078 (tm-30) REVERT: C 148 MET cc_start: 0.4940 (mtt) cc_final: 0.4655 (ptp) REVERT: C 1002 GLN cc_start: 0.8463 (OUTLIER) cc_final: 0.7245 (mp10) REVERT: H 91 ASP cc_start: 0.7451 (m-30) cc_final: 0.7019 (m-30) REVERT: L 47 LEU cc_start: 0.8495 (tp) cc_final: 0.8197 (mt) REVERT: L 55 ARG cc_start: 0.7808 (mtt-85) cc_final: 0.7146 (mtt90) REVERT: L 62 ARG cc_start: 0.8121 (ptt180) cc_final: 0.7379 (ptm160) REVERT: L 78 ARG cc_start: 0.8231 (tmm160) cc_final: 0.7999 (ttp80) outliers start: 47 outliers final: 37 residues processed: 223 average time/residue: 0.2190 time to fit residues: 76.8620 Evaluate side-chains 224 residues out of total 3284 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 181 time to evaluate : 1.038 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 126 ILE Chi-restraints excluded: chain A residue 188 VAL Chi-restraints excluded: chain A residue 190 LYS Chi-restraints excluded: chain A residue 199 TYR Chi-restraints excluded: chain A residue 203 THR Chi-restraints excluded: chain A residue 207 VAL Chi-restraints excluded: chain A residue 220 LEU Chi-restraints excluded: chain A residue 226 LEU Chi-restraints excluded: chain A residue 271 THR Chi-restraints excluded: chain A residue 354 ARG Chi-restraints excluded: chain A residue 393 TYR Chi-restraints excluded: chain A residue 548 VAL Chi-restraints excluded: chain A residue 580 GLU Chi-restraints excluded: chain A residue 617 VAL Chi-restraints excluded: chain A residue 906 ILE Chi-restraints excluded: chain A residue 1125 VAL Chi-restraints excluded: chain B residue 42 VAL Chi-restraints excluded: chain B residue 66 HIS Chi-restraints excluded: chain B residue 116 LEU Chi-restraints excluded: chain B residue 188 VAL Chi-restraints excluded: chain B residue 207 VAL Chi-restraints excluded: chain B residue 238 LEU Chi-restraints excluded: chain B residue 264 VAL Chi-restraints excluded: chain B residue 578 THR Chi-restraints excluded: chain B residue 990 ILE Chi-restraints excluded: chain B residue 991 ASP Chi-restraints excluded: chain B residue 1089 GLU Chi-restraints excluded: chain C residue 115 LEU Chi-restraints excluded: chain C residue 188 VAL Chi-restraints excluded: chain C residue 237 THR Chi-restraints excluded: chain C residue 315 PHE Chi-restraints excluded: chain C residue 324 VAL Chi-restraints excluded: chain C residue 367 ASN Chi-restraints excluded: chain C residue 415 ILE Chi-restraints excluded: chain C residue 578 THR Chi-restraints excluded: chain C residue 632 VAL Chi-restraints excluded: chain C residue 897 MET Chi-restraints excluded: chain C residue 1002 GLN Chi-restraints excluded: chain H residue 32 VAL Chi-restraints excluded: chain H residue 51 TRP Chi-restraints excluded: chain H residue 107 CYS Chi-restraints excluded: chain L residue 79 LEU Chi-restraints excluded: chain G residue 2 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 371 random chunks: chunk 177 optimal weight: 0.7980 chunk 144 optimal weight: 1.9990 chunk 147 optimal weight: 4.9990 chunk 343 optimal weight: 9.9990 chunk 120 optimal weight: 9.9990 chunk 299 optimal weight: 1.9990 chunk 116 optimal weight: 8.9990 chunk 334 optimal weight: 2.9990 chunk 205 optimal weight: 1.9990 chunk 316 optimal weight: 0.7980 chunk 30 optimal weight: 3.9990 overall best weight: 1.5186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 191 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 231 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 = 0.148987 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3335 r_free = 0.3335 target = 0.092769 restraints weight = 59304.306| |-----------------------------------------------------------------------------| r_work (start): 0.3286 rms_B_bonded: 3.78 r_work: 0.3119 rms_B_bonded: 3.88 restraints_weight: 0.5000 r_work (final): 0.3119 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7959 moved from start: 0.1941 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.076 31226 Z= 0.158 Angle : 0.646 19.526 42593 Z= 0.315 Chirality : 0.047 0.488 4979 Planarity : 0.004 0.051 5353 Dihedral : 6.323 100.140 5580 Min Nonbonded Distance : 2.155 Molprobity Statistics. All-atom Clashscore : 7.26 Ramachandran Plot: Outliers : 0.03 % Allowed : 6.81 % Favored : 93.16 % Rotamer: Outliers : 1.40 % Allowed : 14.99 % Favored : 83.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.07 % Cis-general : 0.03 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.34 (0.13), residues: 3716 helix: -0.05 (0.20), residues: 686 sheet: 0.19 (0.18), residues: 861 loop : -1.70 (0.13), residues: 2169 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG H 68 TYR 0.015 0.001 TYR C 262 PHE 0.029 0.001 PHE C 235 TRP 0.022 0.002 TRP B 433 HIS 0.003 0.001 HIS A 202 Details of bonding type rmsd covalent geometry : bond 0.00375 (31106) covalent geometry : angle 0.62757 (42305) SS BOND : bond 0.00325 ( 45) SS BOND : angle 1.33494 ( 90) hydrogen bonds : bond 0.04618 ( 911) hydrogen bonds : angle 5.46201 ( 2454) Misc. bond : bond 0.01046 ( 9) link_BETA1-4 : bond 0.00440 ( 25) link_BETA1-4 : angle 1.82375 ( 75) link_NAG-ASN : bond 0.00363 ( 41) link_NAG-ASN : angle 2.38457 ( 123) ********************** 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 234 residues out of total 3284 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 188 time to evaluate : 1.417 Fit side-chains REVERT: A 126 ILE cc_start: 0.5837 (OUTLIER) cc_final: 0.5395 (mm) REVERT: A 185 ARG cc_start: 0.7184 (mpt180) cc_final: 0.6823 (mpt180) REVERT: A 186 GLU cc_start: 0.8638 (mp0) cc_final: 0.7956 (mp0) REVERT: A 190 LYS cc_start: 0.4063 (OUTLIER) cc_final: 0.2539 (ttpt) REVERT: A 202 HIS cc_start: 0.6261 (t70) cc_final: 0.5818 (p-80) REVERT: A 580 GLU cc_start: 0.8306 (OUTLIER) cc_final: 0.8053 (pm20) REVERT: A 1135 TYR cc_start: 0.7949 (t80) cc_final: 0.6939 (t80) REVERT: B 116 LEU cc_start: 0.7448 (OUTLIER) cc_final: 0.7105 (mp) REVERT: B 631 ARG cc_start: 0.6891 (pmt170) cc_final: 0.5679 (ptp90) REVERT: B 850 GLN cc_start: 0.8360 (tp-100) cc_final: 0.8059 (tp-100) REVERT: B 985 GLU cc_start: 0.8332 (tm-30) cc_final: 0.8085 (tm-30) REVERT: C 1002 GLN cc_start: 0.8473 (OUTLIER) cc_final: 0.7217 (mp10) REVERT: H 3 GLN cc_start: 0.8652 (tm-30) cc_final: 0.8064 (tm-30) REVERT: H 91 ASP cc_start: 0.7359 (m-30) cc_final: 0.6808 (m-30) REVERT: L 47 LEU cc_start: 0.8463 (tp) cc_final: 0.8135 (mt) REVERT: L 55 ARG cc_start: 0.7814 (mtt-85) cc_final: 0.7124 (mtt90) REVERT: L 62 ARG cc_start: 0.8139 (ptt180) cc_final: 0.7402 (ptm160) REVERT: L 78 ARG cc_start: 0.8245 (tmm160) cc_final: 0.8038 (ttp80) outliers start: 46 outliers final: 36 residues processed: 225 average time/residue: 0.2262 time to fit residues: 80.1127 Evaluate side-chains 220 residues out of total 3284 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 179 time to evaluate : 1.152 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 126 ILE Chi-restraints excluded: chain A residue 188 VAL Chi-restraints excluded: chain A residue 190 LYS Chi-restraints excluded: chain A residue 203 THR Chi-restraints excluded: chain A residue 207 VAL Chi-restraints excluded: chain A residue 220 LEU Chi-restraints excluded: chain A residue 226 LEU Chi-restraints excluded: chain A residue 271 THR Chi-restraints excluded: chain A residue 393 TYR Chi-restraints excluded: chain A residue 548 VAL Chi-restraints excluded: chain A residue 580 GLU Chi-restraints excluded: chain A residue 617 VAL Chi-restraints excluded: chain A residue 906 ILE Chi-restraints excluded: chain A residue 1026 MET Chi-restraints excluded: chain A residue 1125 VAL Chi-restraints excluded: chain B residue 42 VAL Chi-restraints excluded: chain B residue 66 HIS Chi-restraints excluded: chain B residue 116 LEU Chi-restraints excluded: chain B residue 188 VAL Chi-restraints excluded: chain B residue 207 VAL Chi-restraints excluded: chain B residue 238 LEU Chi-restraints excluded: chain B residue 264 VAL Chi-restraints excluded: chain B residue 578 THR Chi-restraints excluded: chain B residue 990 ILE Chi-restraints excluded: chain B residue 991 ASP Chi-restraints excluded: chain C residue 115 LEU Chi-restraints excluded: chain C residue 188 VAL Chi-restraints excluded: chain C residue 237 THR Chi-restraints excluded: chain C residue 315 PHE Chi-restraints excluded: chain C residue 324 VAL Chi-restraints excluded: chain C residue 367 ASN Chi-restraints excluded: chain C residue 415 ILE Chi-restraints excluded: chain C residue 578 THR Chi-restraints excluded: chain C residue 632 VAL Chi-restraints excluded: chain C residue 897 MET Chi-restraints excluded: chain C residue 1002 GLN Chi-restraints excluded: chain H residue 32 VAL Chi-restraints excluded: chain H residue 51 TRP Chi-restraints excluded: chain H residue 107 CYS Chi-restraints excluded: chain L residue 79 LEU Chi-restraints excluded: chain G residue 2 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 371 random chunks: chunk 219 optimal weight: 0.7980 chunk 104 optimal weight: 1.9990 chunk 211 optimal weight: 4.9990 chunk 328 optimal weight: 7.9990 chunk 282 optimal weight: 3.9990 chunk 170 optimal weight: 4.9990 chunk 183 optimal weight: 0.7980 chunk 202 optimal weight: 0.6980 chunk 237 optimal weight: 0.6980 chunk 334 optimal weight: 10.0000 chunk 150 optimal weight: 10.0000 overall best weight: 0.9982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 236 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 457 ASN ** B 191 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 231 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 58 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4169 r_free = 0.4169 target = 0.149629 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3337 r_free = 0.3337 target = 0.092725 restraints weight = 59577.356| |-----------------------------------------------------------------------------| r_work (start): 0.3289 rms_B_bonded: 3.73 r_work: 0.3140 rms_B_bonded: 3.82 restraints_weight: 0.5000 r_work (final): 0.3140 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7923 moved from start: 0.1996 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.068 31226 Z= 0.127 Angle : 0.627 19.241 42593 Z= 0.305 Chirality : 0.046 0.469 4979 Planarity : 0.004 0.050 5353 Dihedral : 6.218 99.384 5580 Min Nonbonded Distance : 2.087 Molprobity Statistics. All-atom Clashscore : 7.20 Ramachandran Plot: Outliers : 0.05 % Allowed : 6.08 % Favored : 93.86 % Rotamer: Outliers : 1.43 % Allowed : 15.05 % Favored : 83.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.07 % Cis-general : 0.03 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.29 (0.14), residues: 3716 helix: 0.05 (0.21), residues: 688 sheet: 0.23 (0.18), residues: 878 loop : -1.71 (0.13), residues: 2150 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG H 68 TYR 0.021 0.001 TYR B 420 PHE 0.026 0.001 PHE C 235 TRP 0.057 0.002 TRP B 350 HIS 0.003 0.001 HIS B 202 Details of bonding type rmsd covalent geometry : bond 0.00292 (31106) covalent geometry : angle 0.60865 (42305) SS BOND : bond 0.00315 ( 45) SS BOND : angle 1.20443 ( 90) hydrogen bonds : bond 0.04257 ( 911) hydrogen bonds : angle 5.37619 ( 2454) Misc. bond : bond 0.00916 ( 9) link_BETA1-4 : bond 0.00449 ( 25) link_BETA1-4 : angle 1.80312 ( 75) link_NAG-ASN : bond 0.00358 ( 41) link_NAG-ASN : angle 2.33792 ( 123) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8264.59 seconds wall clock time: 142 minutes 15.57 seconds (8535.57 seconds total)