Starting phenix.real_space_refine on Mon Jul 6 10:11:41 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7q6e_13857/07_2026/7q6e_13857.cif Found real_map, /net/cci-nas-00/data/ceres_data/7q6e_13857/07_2026/7q6e_13857.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7q6e_13857/07_2026/7q6e_13857.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7q6e_13857/07_2026/7q6e_13857.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7q6e_13857/07_2026/7q6e_13857.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7q6e_13857/07_2026/7q6e_13857.map" restraint_files = "/net/cci-nas-00/data/ceres_data/7q6e_13857/07_2026/7q6e_13857.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7q6e_13857/07_2026/7q6e_13857.cif" } resolution = 2.7 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= 0.002 sd= 0.034 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 144 5.16 5 C 21773 2.51 5 N 5619 2.21 5 O 6805 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 2 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 34341 Number of models: 1 Model: "" Number of chains: 29 Chain: "A" Number of atoms: 7903 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1013, 7903 Classifications: {'peptide': 1013} Link IDs: {'PTRANS': 51, 'TRANS': 961} Chain breaks: 7 Chain: "B" Number of atoms: 7871 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1008, 7871 Classifications: {'peptide': 1008} Link IDs: {'PTRANS': 51, 'TRANS': 956} Chain breaks: 7 Chain: "C" Number of atoms: 7811 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1001, 7811 Classifications: {'peptide': 1001} Link IDs: {'PTRANS': 51, 'TRANS': 949} Chain breaks: 7 Chain: "L" Number of atoms: 1652 Number of conformers: 1 Conformer: "" Number of residues, atoms: 216, 1652 Classifications: {'peptide': 216} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 2, 'PTRANS': 10, 'TRANS': 203} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "H" Number of atoms: 1603 Number of conformers: 1 Conformer: "" Number of residues, atoms: 219, 1603 Classifications: {'peptide': 219} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PCIS': 2, 'PTRANS': 10, 'TRANS': 206} Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 13 Unresolved non-hydrogen dihedrals: 11 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "F" Number of atoms: 1652 Number of conformers: 1 Conformer: "" Number of residues, atoms: 216, 1652 Classifications: {'peptide': 216} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 2, 'PTRANS': 10, 'TRANS': 203} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "E" Number of atoms: 1603 Number of conformers: 1 Conformer: "" Number of residues, atoms: 219, 1603 Classifications: {'peptide': 219} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PCIS': 2, 'PTRANS': 10, 'TRANS': 206} Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 13 Unresolved non-hydrogen dihedrals: 11 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "K" Number of atoms: 1652 Number of conformers: 1 Conformer: "" Number of residues, atoms: 216, 1652 Classifications: {'peptide': 216} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 2, 'PTRANS': 10, 'TRANS': 203} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "J" Number of atoms: 1603 Number of conformers: 1 Conformer: "" Number of residues, atoms: 219, 1603 Classifications: {'peptide': 219} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PCIS': 2, 'PTRANS': 10, 'TRANS': 206} Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 13 Unresolved non-hydrogen dihedrals: 11 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "D" Number of atoms: 82 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 82 Unusual residues: {'BMA': 1, 'FUC': 1, 'MAN': 3, 'NAG': 2} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen chiralities: 7 Chain: "G" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "I" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "M" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "N" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "O" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "P" Number of atoms: 71 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 71 Unusual residues: {'BMA': 1, 'FUC': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen chiralities: 6 Chain: "Q" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "R" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "S" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "T" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "U" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "V" Number of atoms: 82 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 82 Unusual residues: {'BMA': 1, 'FUC': 1, 'MAN': 3, 'NAG': 2} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen chiralities: 7 Chain: "W" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "X" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "Y" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "Z" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 126 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 126 Unusual residues: {'NAG': 9} Classifications: {'undetermined': 9} Link IDs: {None: 8} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen chiralities: 9 Chain: "B" Number of atoms: 126 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 126 Unusual residues: {'NAG': 9} Classifications: {'undetermined': 9} Link IDs: {None: 8} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen chiralities: 9 Chain: "C" Number of atoms: 112 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 112 Unusual residues: {'NAG': 8} Classifications: {'undetermined': 8} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen chiralities: 8 Time building chain proxies: 7.17, per 1000 atoms: 0.21 Number of scatterers: 34341 At special positions: 0 Unit cell: (162.36, 166.46, 214.02, 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 144 16.00 O 6805 8.00 N 5619 7.00 C 21773 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=51, symmetry=0 Simple disulfide: pdb=" SG CYS A 131 " - pdb=" SG CYS A 166 " distance=2.03 Simple disulfide: pdb=" SG CYS A 288 " - pdb=" SG CYS A 298 " distance=2.03 Simple disulfide: pdb=" SG CYS A 333 " - pdb=" SG CYS A 358 " distance=2.03 Simple disulfide: pdb=" SG CYS A 376 " - pdb=" SG CYS A 429 " distance=2.03 Simple disulfide: pdb=" SG CYS A 388 " - pdb=" SG CYS A 522 " distance=2.03 Simple disulfide: pdb=" SG CYS A 477 " - pdb=" SG CYS A 485 " distance=2.03 Simple disulfide: pdb=" SG CYS A 535 " - pdb=" SG CYS A 587 " distance=2.03 Simple disulfide: pdb=" SG CYS A 614 " - pdb=" SG CYS A 646 " distance=2.03 Simple disulfide: pdb=" SG CYS A 659 " - pdb=" SG CYS A 668 " distance=2.03 Simple disulfide: pdb=" SG CYS A 735 " - pdb=" SG CYS A 757 " distance=2.03 Simple disulfide: pdb=" SG CYS A 740 " - pdb=" SG CYS A 746 " distance=2.03 Simple disulfide: pdb=" SG CYS A1029 " - pdb=" SG CYS A1040 " distance=2.03 Simple disulfide: pdb=" SG CYS A1079 " - pdb=" SG CYS A1123 " distance=2.03 Simple disulfide: pdb=" SG CYS B 131 " - pdb=" SG CYS B 166 " distance=2.03 Simple disulfide: pdb=" SG CYS B 288 " - pdb=" SG CYS B 298 " distance=2.03 Simple disulfide: pdb=" SG CYS B 333 " - pdb=" SG CYS B 358 " distance=2.03 Simple disulfide: pdb=" SG CYS B 376 " - pdb=" SG CYS B 429 " distance=2.03 Simple disulfide: pdb=" SG CYS B 388 " - pdb=" SG CYS B 522 " distance=2.03 Simple disulfide: pdb=" SG CYS B 477 " - pdb=" SG CYS B 485 " distance=2.03 Simple disulfide: pdb=" SG CYS B 535 " - pdb=" SG CYS B 587 " distance=2.03 Simple disulfide: pdb=" SG CYS B 614 " - pdb=" SG CYS B 646 " distance=2.03 Simple disulfide: pdb=" SG CYS B 659 " - pdb=" SG CYS B 668 " distance=2.03 Simple disulfide: pdb=" SG CYS B 735 " - pdb=" SG CYS B 757 " distance=2.03 Simple disulfide: pdb=" SG CYS B 740 " - pdb=" SG CYS B 746 " distance=2.03 Simple disulfide: pdb=" SG CYS B1029 " - pdb=" SG CYS B1040 " distance=2.03 Simple disulfide: pdb=" SG CYS B1079 " - pdb=" SG CYS B1123 " distance=2.03 Simple disulfide: pdb=" SG CYS C 131 " - pdb=" SG CYS C 166 " distance=2.03 Simple disulfide: pdb=" SG CYS C 288 " - pdb=" SG CYS C 298 " distance=2.03 Simple disulfide: pdb=" SG CYS C 333 " - pdb=" SG CYS C 358 " distance=2.03 Simple disulfide: pdb=" SG CYS C 376 " - pdb=" SG CYS C 429 " distance=2.03 Simple disulfide: pdb=" SG CYS C 388 " - pdb=" SG CYS C 522 " distance=2.03 Simple disulfide: pdb=" SG CYS C 477 " - pdb=" SG CYS C 485 " distance=2.03 Simple disulfide: pdb=" SG CYS C 535 " - pdb=" SG CYS C 587 " distance=2.02 Simple disulfide: pdb=" SG CYS C 614 " - pdb=" SG CYS C 646 " distance=2.03 Simple disulfide: pdb=" SG CYS C 659 " - pdb=" SG CYS C 668 " distance=2.03 Simple disulfide: pdb=" SG CYS C 735 " - pdb=" SG CYS C 757 " distance=2.02 Simple disulfide: pdb=" SG CYS C 740 " - pdb=" SG CYS C 746 " distance=2.03 Simple disulfide: pdb=" SG CYS C1029 " - pdb=" SG CYS C1040 " distance=2.03 Simple disulfide: pdb=" SG CYS C1079 " - pdb=" SG CYS C1123 " distance=2.03 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 89 " distance=2.03 Simple disulfide: pdb=" SG CYS L 136 " - pdb=" SG CYS L 196 " distance=2.03 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 96 " distance=2.03 Simple disulfide: pdb=" SG CYS H 145 " - pdb=" SG CYS H 201 " distance=2.03 Simple disulfide: pdb=" SG CYS F 23 " - pdb=" SG CYS F 89 " distance=2.03 Simple disulfide: pdb=" SG CYS F 136 " - pdb=" SG CYS F 196 " distance=2.03 Simple disulfide: pdb=" SG CYS E 22 " - pdb=" SG CYS E 96 " distance=2.03 Simple disulfide: pdb=" SG CYS E 145 " - pdb=" SG CYS E 201 " distance=2.03 Simple disulfide: pdb=" SG CYS K 23 " - pdb=" SG CYS K 89 " distance=2.03 Simple disulfide: pdb=" SG CYS K 136 " - pdb=" SG CYS K 196 " distance=2.03 Simple disulfide: pdb=" SG CYS J 22 " - pdb=" SG CYS J 96 " distance=2.03 Simple disulfide: pdb=" SG CYS J 145 " - pdb=" SG CYS J 201 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied ALPHA1-2 " MAN D 4 " - " MAN D 5 " " MAN P 4 " - " MAN P 5 " " MAN V 4 " - " MAN V 5 " ALPHA1-3 " BMA D 3 " - " MAN D 4 " " BMA P 3 " - " MAN P 4 " " BMA V 3 " - " MAN V 4 " ALPHA1-6 " BMA D 3 " - " MAN D 6 " " BMA V 3 " - " MAN V 6 " BETA1-4 " NAG D 1 " - " NAG D 2 " " NAG D 2 " - " BMA D 3 " " NAG G 1 " - " NAG G 2 " " NAG I 1 " - " NAG I 2 " " NAG M 1 " - " NAG M 2 " " NAG N 1 " - " NAG N 2 " " NAG O 1 " - " NAG O 2 " " NAG P 1 " - " NAG P 2 " " NAG P 2 " - " BMA P 3 " " NAG Q 1 " - " NAG Q 2 " " NAG R 1 " - " NAG R 2 " " NAG S 1 " - " NAG S 2 " " NAG T 1 " - " NAG T 2 " " NAG U 1 " - " NAG U 2 " " NAG V 1 " - " NAG V 2 " " NAG V 2 " - " BMA V 3 " " NAG W 1 " - " NAG W 2 " " NAG X 1 " - " NAG X 2 " " NAG Y 1 " - " NAG Y 2 " " NAG Z 1 " - " NAG Z 2 " BETA1-6 " NAG D 1 " - " FUC D 7 " ~> Even though FUC is an alpha isomer, a beta linkage is required... " NAG P 1 " - " FUC P 6 " " NAG V 1 " - " FUC V 7 " NAG-ASN " NAG A1301 " - " ASN A 61 " " NAG A1302 " - " ASN A 279 " " NAG A1303 " - " ASN A 600 " " NAG A1304 " - " ASN A 613 " " NAG A1305 " - " ASN A 654 " " NAG A1306 " - " ASN A 706 " " NAG A1307 " - " ASN A1071 " " NAG A1308 " - " ASN A 165 " " NAG A1309 " - " ASN A 328 " " NAG B1301 " - " ASN B 61 " " NAG B1302 " - " ASN B 279 " " NAG B1303 " - " ASN B 328 " " NAG B1304 " - " ASN B 600 " " NAG B1305 " - " ASN B 613 " " NAG B1306 " - " ASN B 654 " " NAG B1307 " - " ASN B 706 " " NAG B1308 " - " ASN B1071 " " NAG B1309 " - " ASN B 165 " " NAG C1301 " - " ASN C 61 " " NAG C1302 " - " ASN C 279 " " NAG C1303 " - " ASN C 600 " " NAG C1304 " - " ASN C 613 " " NAG C1305 " - " ASN C 654 " " NAG C1306 " - " ASN C 706 " " NAG C1307 " - " ASN C1071 " " NAG C1308 " - " ASN C 328 " " NAG D 1 " - " ASN A 340 " " NAG G 1 " - " ASN A 234 " " NAG I 1 " - " ASN A 714 " " NAG M 1 " - " ASN A 798 " " NAG N 1 " - " ASN A1095 " " NAG O 1 " - " ASN A1131 " " NAG P 1 " - " ASN B 340 " " NAG Q 1 " - " ASN B 234 " " NAG R 1 " - " ASN B 714 " " NAG S 1 " - " ASN B 798 " " NAG T 1 " - " ASN B1095 " " NAG U 1 " - " ASN B1131 " " NAG V 1 " - " ASN C 340 " " NAG W 1 " - " ASN C 714 " " NAG X 1 " - " ASN C 798 " " NAG Y 1 " - " ASN C1095 " " NAG Z 1 " - " ASN C1131 " Time building additional restraints: 3.01 Conformation dependent library (CDL) restraints added in 1.5 seconds 8534 Ramachandran restraints generated. 4267 Oldfield, 0 Emsley, 4267 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 8052 Finding SS restraints... Secondary structure from input PDB file: 88 helices and 82 sheets defined 20.7% alpha, 34.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.80 Creating SS restraints... Processing helix chain 'A' and resid 291 through 301 Processing helix chain 'A' and resid 335 through 340 Processing helix chain 'A' and resid 346 through 350 Processing helix chain 'A' and resid 361 through 368 removed outlier: 4.256A pdb=" N LEU A 365 " --> pdb=" O ASP A 361 " (cutoff:3.500A) Processing helix chain 'A' and resid 380 through 386 removed outlier: 3.623A pdb=" N LEU A 384 " --> pdb=" O PRO A 381 " (cutoff:3.500A) removed outlier: 4.668A pdb=" N ASN A 385 " --> pdb=" O THR A 382 " (cutoff:3.500A) Processing helix chain 'A' and resid 401 through 405 removed outlier: 4.351A pdb=" N ARG A 405 " --> pdb=" O GLY A 401 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 401 through 405' Processing helix chain 'A' and resid 413 through 419 Processing helix chain 'A' and resid 435 through 440 removed outlier: 3.511A pdb=" N SER A 440 " --> pdb=" O ASN A 436 " (cutoff:3.500A) Processing helix chain 'A' and resid 734 through 741 Processing helix chain 'A' and resid 743 through 751 Processing helix chain 'A' and resid 752 through 754 No H-bonds generated for 'chain 'A' and resid 752 through 754' Processing helix chain 'A' and resid 755 through 780 removed outlier: 3.612A pdb=" N ASP A 772 " --> pdb=" O ALA A 768 " (cutoff:3.500A) Processing helix chain 'A' and resid 813 through 823 Processing helix chain 'A' and resid 863 through 882 Processing helix chain 'A' and resid 894 through 906 Processing helix chain 'A' and resid 909 through 916 removed outlier: 4.077A pdb=" N LEU A 913 " --> pdb=" O THR A 909 " (cutoff:3.500A) Processing helix chain 'A' and resid 916 through 938 Processing helix chain 'A' and resid 939 through 941 No H-bonds generated for 'chain 'A' and resid 939 through 941' Processing helix chain 'A' and resid 942 through 962 Processing helix chain 'A' and resid 963 through 965 No H-bonds generated for 'chain 'A' and resid 963 through 965' Processing helix chain 'A' and resid 973 through 981 Processing helix chain 'A' and resid 982 through 1030 removed outlier: 4.270A pdb=" N VAL A 988 " --> pdb=" O PRO A 984 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N GLN A 989 " --> pdb=" O GLU A 985 " (cutoff:3.500A) Processing helix chain 'A' and resid 1137 through 1144 removed outlier: 4.200A pdb=" N GLU A1141 " --> pdb=" O PRO A1137 " (cutoff:3.500A) Processing helix chain 'B' and resid 291 through 301 Processing helix chain 'B' and resid 335 through 340 Processing helix chain 'B' and resid 346 through 350 Processing helix chain 'B' and resid 362 through 367 Processing helix chain 'B' and resid 380 through 386 removed outlier: 3.761A pdb=" N LEU B 384 " --> pdb=" O PRO B 381 " (cutoff:3.500A) removed outlier: 4.630A pdb=" N ASN B 385 " --> pdb=" O THR B 382 " (cutoff:3.500A) Processing helix chain 'B' and resid 402 through 407 removed outlier: 4.161A pdb=" N ARG B 405 " --> pdb=" O ASP B 402 " (cutoff:3.500A) Processing helix chain 'B' and resid 413 through 419 Processing helix chain 'B' and resid 435 through 440 Processing helix chain 'B' and resid 734 through 741 Processing helix chain 'B' and resid 743 through 751 Processing helix chain 'B' and resid 752 through 754 No H-bonds generated for 'chain 'B' and resid 752 through 754' Processing helix chain 'B' and resid 755 through 780 removed outlier: 3.582A pdb=" N GLN B 759 " --> pdb=" O SER B 755 " (cutoff:3.500A) Processing helix chain 'B' and resid 813 through 823 Processing helix chain 'B' and resid 863 through 882 Processing helix chain 'B' and resid 883 through 888 removed outlier: 3.899A pdb=" N ALA B 887 " --> pdb=" O TRP B 883 " (cutoff:3.500A) Processing helix chain 'B' and resid 894 through 907 Processing helix chain 'B' and resid 910 through 916 Processing helix chain 'B' and resid 916 through 938 Processing helix chain 'B' and resid 939 through 941 No H-bonds generated for 'chain 'B' and resid 939 through 941' Processing helix chain 'B' and resid 942 through 963 removed outlier: 3.635A pdb=" N LEU B 963 " --> pdb=" O LEU B 959 " (cutoff:3.500A) Processing helix chain 'B' and resid 973 through 981 Processing helix chain 'B' and resid 982 through 1030 removed outlier: 4.057A pdb=" N VAL B 988 " --> pdb=" O PRO B 984 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N GLN B 989 " --> pdb=" O GLU B 985 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N ARG B 992 " --> pdb=" O VAL B 988 " (cutoff:3.500A) Processing helix chain 'B' and resid 1137 through 1144 removed outlier: 3.965A pdb=" N GLU B1141 " --> pdb=" O PRO B1137 " (cutoff:3.500A) Processing helix chain 'C' and resid 291 through 301 Processing helix chain 'C' and resid 335 through 340 Processing helix chain 'C' and resid 362 through 367 Processing helix chain 'C' and resid 380 through 386 removed outlier: 3.536A pdb=" N LEU C 384 " --> pdb=" O PRO C 381 " (cutoff:3.500A) removed outlier: 4.333A pdb=" N ASN C 385 " --> pdb=" O THR C 382 " (cutoff:3.500A) Processing helix chain 'C' and resid 402 through 407 removed outlier: 4.609A pdb=" N ARG C 405 " --> pdb=" O ASP C 402 " (cutoff:3.500A) Processing helix chain 'C' and resid 413 through 419 Processing helix chain 'C' and resid 435 through 440 Processing helix chain 'C' and resid 734 through 741 Processing helix chain 'C' and resid 743 through 751 Processing helix chain 'C' and resid 752 through 754 No H-bonds generated for 'chain 'C' and resid 752 through 754' Processing helix chain 'C' and resid 755 through 780 removed outlier: 3.908A pdb=" N GLN C 759 " --> pdb=" O SER C 755 " (cutoff:3.500A) Processing helix chain 'C' and resid 813 through 823 Processing helix chain 'C' and resid 863 through 882 Processing helix chain 'C' and resid 883 through 887 Processing helix chain 'C' and resid 894 through 907 Processing helix chain 'C' and resid 909 through 916 removed outlier: 4.013A pdb=" N LEU C 913 " --> pdb=" O THR C 909 " (cutoff:3.500A) Processing helix chain 'C' and resid 916 through 938 Processing helix chain 'C' and resid 939 through 941 No H-bonds generated for 'chain 'C' and resid 939 through 941' Processing helix chain 'C' and resid 942 through 962 removed outlier: 3.743A pdb=" N VAL C 948 " --> pdb=" O LYS C 944 " (cutoff:3.500A) Processing helix chain 'C' and resid 963 through 965 No H-bonds generated for 'chain 'C' and resid 963 through 965' Processing helix chain 'C' and resid 973 through 981 Processing helix chain 'C' and resid 982 through 1030 removed outlier: 4.334A pdb=" N VAL C 988 " --> pdb=" O PRO C 984 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N GLN C 989 " --> pdb=" O GLU C 985 " (cutoff:3.500A) removed outlier: 3.855A pdb=" N ARG C 992 " --> pdb=" O VAL C 988 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N LEU C 993 " --> pdb=" O GLN C 989 " (cutoff:3.500A) Processing helix chain 'C' and resid 1137 through 1144 removed outlier: 3.825A pdb=" N GLU C1141 " --> pdb=" O PRO C1137 " (cutoff:3.500A) Processing helix chain 'L' and resid 30 through 32 No H-bonds generated for 'chain 'L' and resid 30 through 32' Processing helix chain 'L' and resid 123 through 129 removed outlier: 3.713A pdb=" N SER L 129 " --> pdb=" O GLU L 125 " (cutoff:3.500A) Processing helix chain 'L' and resid 185 through 190 Processing helix chain 'H' and resid 62 through 65 removed outlier: 3.712A pdb=" N GLN H 65 " --> pdb=" O GLN H 62 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 62 through 65' Processing helix chain 'H' and resid 87 through 91 removed outlier: 3.642A pdb=" N THR H 91 " --> pdb=" O SER H 88 " (cutoff:3.500A) Processing helix chain 'H' and resid 192 through 194 No H-bonds generated for 'chain 'H' and resid 192 through 194' Processing helix chain 'F' and resid 30 through 32 No H-bonds generated for 'chain 'F' and resid 30 through 32' Processing helix chain 'F' and resid 80 through 84 removed outlier: 4.013A pdb=" N PHE F 84 " --> pdb=" O PRO F 81 " (cutoff:3.500A) Processing helix chain 'F' and resid 123 through 128 removed outlier: 3.525A pdb=" N LYS F 128 " --> pdb=" O ASP F 124 " (cutoff:3.500A) Processing helix chain 'F' and resid 185 through 190 Processing helix chain 'E' and resid 87 through 91 removed outlier: 3.568A pdb=" N THR E 91 " --> pdb=" O SER E 88 " (cutoff:3.500A) Processing helix chain 'E' and resid 161 through 163 No H-bonds generated for 'chain 'E' and resid 161 through 163' Processing helix chain 'E' and resid 192 through 194 No H-bonds generated for 'chain 'E' and resid 192 through 194' Processing helix chain 'K' and resid 30 through 32 No H-bonds generated for 'chain 'K' and resid 30 through 32' Processing helix chain 'K' and resid 123 through 128 Processing helix chain 'K' and resid 185 through 190 removed outlier: 3.550A pdb=" N LYS K 190 " --> pdb=" O ALA K 186 " (cutoff:3.500A) Processing helix chain 'J' and resid 87 through 91 Processing helix chain 'J' and resid 161 through 163 No H-bonds generated for 'chain 'J' and resid 161 through 163' Processing helix chain 'J' and resid 192 through 194 No H-bonds generated for 'chain 'J' and resid 192 through 194' Processing sheet with id=AA1, first strand: chain 'A' and resid 27 through 30 removed outlier: 7.832A pdb=" N ASN A 61 " --> pdb=" O TYR A 266 " (cutoff:3.500A) removed outlier: 6.285A pdb=" N TYR A 266 " --> pdb=" O ASN A 61 " (cutoff:3.500A) removed outlier: 5.965A pdb=" N SER A 205 " --> pdb=" O PRO A 225 " (cutoff:3.500A) removed outlier: 9.034A pdb=" N HIS A 207 " --> pdb=" O LEU A 223 " (cutoff:3.500A) removed outlier: 9.324A pdb=" N LEU A 223 " --> pdb=" O HIS A 207 " (cutoff:3.500A) removed outlier: 7.058A pdb=" N VAL A 36 " --> pdb=" O LEU A 223 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 47 through 55 removed outlier: 3.900A pdb=" N ASP A 284 " --> pdb=" O LYS A 275 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 84 through 85 removed outlier: 3.522A pdb=" N GLY A 103 " --> pdb=" O LEU A 241 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 127 through 129 Processing sheet with id=AA5, first strand: chain 'A' and resid 135 through 140 removed outlier: 3.608A pdb=" N CYS A 136 " --> pdb=" O VAL A 159 " (cutoff:3.500A) removed outlier: 8.474A pdb=" N VAL A 159 " --> pdb=" O CYS A 136 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA5 Processing sheet with id=AA6, first strand: chain 'A' and resid 308 through 316 removed outlier: 6.972A pdb=" N VAL A 592 " --> pdb=" O THR A 312 " (cutoff:3.500A) removed outlier: 4.838A pdb=" N ASN A 314 " --> pdb=" O GLY A 590 " (cutoff:3.500A) removed outlier: 6.420A pdb=" N GLY A 590 " --> pdb=" O ASN A 314 " (cutoff:3.500A) removed outlier: 4.411A pdb=" N GLY A 591 " --> pdb=" O GLN A 610 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 321 through 325 removed outlier: 4.101A pdb=" N GLU A 321 " --> pdb=" O CYS A 535 " (cutoff:3.500A) removed outlier: 5.465A pdb=" N ASP A 571 " --> pdb=" O ILE A 584 " (cutoff:3.500A) removed outlier: 6.798A pdb=" N PHE A 562 " --> pdb=" O PHE B 43 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 351 through 355 Processing sheet with id=AA9, first strand: chain 'A' and resid 358 through 359 removed outlier: 6.618A pdb=" N CYS A 358 " --> pdb=" O CYS A 522 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 449 through 451 Processing sheet with id=AB2, first strand: chain 'A' and resid 470 through 471 Processing sheet with id=AB3, first strand: chain 'A' and resid 651 through 652 removed outlier: 6.277A pdb=" N ILE A 667 " --> pdb=" O ILE A 663 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 699 through 701 removed outlier: 3.549A pdb=" N LYS B 787 " --> pdb=" O ASN A 700 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 708 through 712 removed outlier: 3.808A pdb=" N ALA A1075 " --> pdb=" O PHE A1092 " (cutoff:3.500A) removed outlier: 4.531A pdb=" N PHE A1092 " --> pdb=" O ALA A1075 " (cutoff:3.500A) removed outlier: 4.652A pdb=" N GLN A1103 " --> pdb=" O GLU A1108 " (cutoff:3.500A) removed outlier: 5.210A pdb=" N GLU A1108 " --> pdb=" O GLN A1103 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 715 through 725 removed outlier: 7.009A pdb=" N GLY A1056 " --> pdb=" O SER A1052 " (cutoff:3.500A) removed outlier: 5.246A pdb=" N SER A1052 " --> pdb=" O GLY A1056 " (cutoff:3.500A) removed outlier: 6.659A pdb=" N VAL A1058 " --> pdb=" O PRO A1050 " (cutoff:3.500A) removed outlier: 6.346A pdb=" N LEU A1060 " --> pdb=" O SER A1048 " (cutoff:3.500A) removed outlier: 4.285A pdb=" N SER A1048 " --> pdb=" O LEU A1060 " (cutoff:3.500A) removed outlier: 6.835A pdb=" N VAL A1062 " --> pdb=" O LEU A1046 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'A' and resid 730 through 733 removed outlier: 4.448A pdb=" N LYS A 730 " --> pdb=" O LEU A 858 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'A' and resid 785 through 787 removed outlier: 5.819A pdb=" N ILE A 785 " --> pdb=" O ASN C 700 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB8 Processing sheet with id=AB9, first strand: chain 'A' and resid 1117 through 1119 Processing sheet with id=AC1, first strand: chain 'B' and resid 27 through 30 removed outlier: 7.842A pdb=" N ASN B 61 " --> pdb=" O TYR B 266 " (cutoff:3.500A) removed outlier: 5.865A pdb=" N TYR B 266 " --> pdb=" O ASN B 61 " (cutoff:3.500A) removed outlier: 6.489A pdb=" N PHE B 201 " --> pdb=" O ASP B 228 " (cutoff:3.500A) removed outlier: 4.251A pdb=" N ASP B 228 " --> pdb=" O PHE B 201 " (cutoff:3.500A) removed outlier: 6.747A pdb=" N ILE B 203 " --> pdb=" O LEU B 226 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 47 through 55 removed outlier: 3.605A pdb=" N VAL B 47 " --> pdb=" O TYR B 276 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N ASP B 284 " --> pdb=" O LYS B 275 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 84 through 85 removed outlier: 3.518A pdb=" N GLY B 103 " --> pdb=" O LEU B 241 " (cutoff:3.500A) removed outlier: 5.853A pdb=" N ARG B 102 " --> pdb=" O ASN B 121 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 132 through 140 removed outlier: 6.302A pdb=" N GLU B 132 " --> pdb=" O ALA B 163 " (cutoff:3.500A) removed outlier: 4.647A pdb=" N ALA B 163 " --> pdb=" O GLU B 132 " (cutoff:3.500A) removed outlier: 6.264A pdb=" N GLN B 134 " --> pdb=" O SER B 161 " (cutoff:3.500A) removed outlier: 8.495A pdb=" N VAL B 159 " --> pdb=" O CYS B 136 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 308 through 316 removed outlier: 5.329A pdb=" N ILE B 309 " --> pdb=" O THR B 596 " (cutoff:3.500A) removed outlier: 7.235A pdb=" N THR B 596 " --> pdb=" O ILE B 309 " (cutoff:3.500A) removed outlier: 5.885A pdb=" N GLN B 311 " --> pdb=" O VAL B 594 " (cutoff:3.500A) removed outlier: 6.655A pdb=" N VAL B 594 " --> pdb=" O GLN B 311 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N SER B 313 " --> pdb=" O VAL B 592 " (cutoff:3.500A) removed outlier: 4.212A pdb=" N GLY B 591 " --> pdb=" O GLN B 610 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 321 through 325 removed outlier: 6.779A pdb=" N GLU B 321 " --> pdb=" O ASN B 537 " (cutoff:3.500A) removed outlier: 7.818A pdb=" N ASN B 539 " --> pdb=" O GLU B 321 " (cutoff:3.500A) removed outlier: 6.478A pdb=" N ILE B 323 " --> pdb=" O ASN B 539 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'B' and resid 321 through 325 removed outlier: 6.779A pdb=" N GLU B 321 " --> pdb=" O ASN B 537 " (cutoff:3.500A) removed outlier: 7.818A pdb=" N ASN B 539 " --> pdb=" O GLU B 321 " (cutoff:3.500A) removed outlier: 6.478A pdb=" N ILE B 323 " --> pdb=" O ASN B 539 " (cutoff:3.500A) removed outlier: 7.006A pdb=" N PHE B 562 " --> pdb=" O PHE C 43 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'B' and resid 351 through 355 Processing sheet with id=AC9, first strand: chain 'B' and resid 358 through 359 removed outlier: 6.620A pdb=" N CYS B 358 " --> pdb=" O CYS B 522 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'B' and resid 449 through 451 Processing sheet with id=AD2, first strand: chain 'B' and resid 470 through 471 removed outlier: 3.705A pdb=" N TYR B 486 " --> pdb=" O TYR B 470 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'B' and resid 651 through 652 removed outlier: 5.878A pdb=" N GLU B 651 " --> pdb=" O ALA B 691 " (cutoff:3.500A) removed outlier: 8.349A pdb=" N THR B 693 " --> pdb=" O GLU B 651 " (cutoff:3.500A) removed outlier: 6.315A pdb=" N ALA B 669 " --> pdb=" O PRO B 662 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'B' and resid 699 through 701 Processing sheet with id=AD5, first strand: chain 'B' and resid 708 through 712 removed outlier: 3.763A pdb=" N ALA B1075 " --> pdb=" O PHE B1092 " (cutoff:3.500A) removed outlier: 4.481A pdb=" N PHE B1092 " --> pdb=" O ALA B1075 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'B' and resid 715 through 725 removed outlier: 7.027A pdb=" N GLY B1056 " --> pdb=" O SER B1052 " (cutoff:3.500A) removed outlier: 5.226A pdb=" N SER B1052 " --> pdb=" O GLY B1056 " (cutoff:3.500A) removed outlier: 6.661A pdb=" N VAL B1058 " --> pdb=" O PRO B1050 " (cutoff:3.500A) removed outlier: 6.349A pdb=" N LEU B1060 " --> pdb=" O SER B1048 " (cutoff:3.500A) removed outlier: 4.315A pdb=" N SER B1048 " --> pdb=" O LEU B1060 " (cutoff:3.500A) removed outlier: 6.834A pdb=" N VAL B1062 " --> pdb=" O LEU B1046 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'B' and resid 730 through 733 removed outlier: 4.405A pdb=" N LYS B 730 " --> pdb=" O LEU B 858 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'B' and resid 1117 through 1122 removed outlier: 4.602A pdb=" N ALA B1084 " --> pdb=" O SER B1120 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'C' and resid 27 through 30 removed outlier: 8.075A pdb=" N ASN C 61 " --> pdb=" O TYR C 266 " (cutoff:3.500A) removed outlier: 6.144A pdb=" N TYR C 266 " --> pdb=" O ASN C 61 " (cutoff:3.500A) removed outlier: 6.442A pdb=" N PHE C 201 " --> pdb=" O ASP C 228 " (cutoff:3.500A) removed outlier: 4.119A pdb=" N ASP C 228 " --> pdb=" O PHE C 201 " (cutoff:3.500A) removed outlier: 6.646A pdb=" N ILE C 203 " --> pdb=" O LEU C 226 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'C' and resid 47 through 55 removed outlier: 3.950A pdb=" N ASP C 284 " --> pdb=" O LYS C 275 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'C' and resid 84 through 85 removed outlier: 3.530A pdb=" N GLY C 103 " --> pdb=" O LEU C 241 " (cutoff:3.500A) removed outlier: 5.818A pdb=" N ARG C 102 " --> pdb=" O ASN C 121 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'C' and resid 308 through 316 removed outlier: 7.013A pdb=" N VAL C 592 " --> pdb=" O THR C 312 " (cutoff:3.500A) removed outlier: 4.934A pdb=" N ASN C 314 " --> pdb=" O GLY C 590 " (cutoff:3.500A) removed outlier: 6.591A pdb=" N GLY C 590 " --> pdb=" O ASN C 314 " (cutoff:3.500A) removed outlier: 4.270A pdb=" N GLY C 591 " --> pdb=" O GLN C 610 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'C' and resid 322 through 325 removed outlier: 5.488A pdb=" N ASP C 571 " --> pdb=" O ILE C 584 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'C' and resid 351 through 355 removed outlier: 3.717A pdb=" N ASN C 391 " --> pdb=" O GLU C 513 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'C' and resid 358 through 359 removed outlier: 6.760A pdb=" N CYS C 358 " --> pdb=" O CYS C 522 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'C' and resid 449 through 451 Processing sheet with id=AE8, first strand: chain 'C' and resid 470 through 471 Processing sheet with id=AE9, first strand: chain 'C' and resid 651 through 652 removed outlier: 6.377A pdb=" N ILE C 667 " --> pdb=" O ILE C 663 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'C' and resid 708 through 712 removed outlier: 3.801A pdb=" N ALA C1075 " --> pdb=" O PHE C1092 " (cutoff:3.500A) removed outlier: 4.453A pdb=" N PHE C1092 " --> pdb=" O ALA C1075 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'C' and resid 715 through 725 removed outlier: 7.036A pdb=" N GLY C1056 " --> pdb=" O SER C1052 " (cutoff:3.500A) removed outlier: 5.256A pdb=" N SER C1052 " --> pdb=" O GLY C1056 " (cutoff:3.500A) removed outlier: 6.660A pdb=" N VAL C1058 " --> pdb=" O PRO C1050 " (cutoff:3.500A) removed outlier: 6.329A pdb=" N LEU C1060 " --> pdb=" O SER C1048 " (cutoff:3.500A) removed outlier: 4.322A pdb=" N SER C1048 " --> pdb=" O LEU C1060 " (cutoff:3.500A) removed outlier: 6.813A pdb=" N VAL C1062 " --> pdb=" O LEU C1046 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'C' and resid 730 through 733 removed outlier: 4.394A pdb=" N LYS C 730 " --> pdb=" O LEU C 858 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'C' and resid 1117 through 1122 removed outlier: 4.619A pdb=" N ALA C1084 " --> pdb=" O SER C1120 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'L' and resid 4 through 7 Processing sheet with id=AF6, first strand: chain 'L' and resid 10 through 13 removed outlier: 6.571A pdb=" N LEU L 34 " --> pdb=" O TYR L 50 " (cutoff:3.500A) removed outlier: 4.495A pdb=" N TYR L 50 " --> pdb=" O LEU L 34 " (cutoff:3.500A) removed outlier: 6.343A pdb=" N TRP L 36 " --> pdb=" O LEU L 48 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'L' and resid 10 through 13 Processing sheet with id=AF8, first strand: chain 'L' and resid 116 through 120 removed outlier: 5.938A pdb=" N TYR L 175 " --> pdb=" O ASN L 140 " (cutoff:3.500A) Processing sheet with id=AF9, first strand: chain 'L' and resid 156 through 157 removed outlier: 4.442A pdb=" N TRP L 150 " --> pdb=" O GLN L 157 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N LYS L 209 " --> pdb=" O CYS L 196 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N VAL L 198 " --> pdb=" O VAL L 207 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N VAL L 207 " --> pdb=" O VAL L 198 " (cutoff:3.500A) Processing sheet with id=AG1, first strand: chain 'H' and resid 3 through 6 Processing sheet with id=AG2, first strand: chain 'H' and resid 10 through 12 removed outlier: 6.751A pdb=" N GLU H 10 " --> pdb=" O THR H 115 " (cutoff:3.500A) removed outlier: 6.611A pdb=" N ILE H 34 " --> pdb=" O GLY H 50 " (cutoff:3.500A) removed outlier: 4.467A pdb=" N GLY H 50 " --> pdb=" O ILE H 34 " (cutoff:3.500A) removed outlier: 6.769A pdb=" N TRP H 36 " --> pdb=" O MET H 48 " (cutoff:3.500A) Processing sheet with id=AG3, first strand: chain 'H' and resid 10 through 12 removed outlier: 6.751A pdb=" N GLU H 10 " --> pdb=" O THR H 115 " (cutoff:3.500A) Processing sheet with id=AG4, first strand: chain 'H' and resid 125 through 129 removed outlier: 3.925A pdb=" N GLY H 144 " --> pdb=" O LEU H 129 " (cutoff:3.500A) removed outlier: 6.551A pdb=" N TYR H 181 " --> pdb=" O ASP H 149 " (cutoff:3.500A) Processing sheet with id=AG5, first strand: chain 'H' and resid 125 through 129 removed outlier: 3.925A pdb=" N GLY H 144 " --> pdb=" O LEU H 129 " (cutoff:3.500A) removed outlier: 6.551A pdb=" N TYR H 181 " --> pdb=" O ASP H 149 " (cutoff:3.500A) Processing sheet with id=AG6, first strand: chain 'H' and resid 156 through 159 removed outlier: 4.408A pdb=" N TYR H 199 " --> pdb=" O VAL H 216 " (cutoff:3.500A) Processing sheet with id=AG7, first strand: chain 'F' and resid 4 through 7 Processing sheet with id=AG8, first strand: chain 'F' and resid 10 through 12 removed outlier: 3.682A pdb=" N TYR F 88 " --> pdb=" O TYR F 37 " (cutoff:3.500A) removed outlier: 6.726A pdb=" N LEU F 34 " --> pdb=" O TYR F 50 " (cutoff:3.500A) removed outlier: 4.626A pdb=" N TYR F 50 " --> pdb=" O LEU F 34 " (cutoff:3.500A) removed outlier: 6.324A pdb=" N TRP F 36 " --> pdb=" O LEU F 48 " (cutoff:3.500A) Processing sheet with id=AG9, first strand: chain 'F' and resid 10 through 12 Processing sheet with id=AH1, first strand: chain 'F' and resid 116 through 120 removed outlier: 5.660A pdb=" N TYR F 175 " --> pdb=" O ASN F 140 " (cutoff:3.500A) Processing sheet with id=AH2, first strand: chain 'F' and resid 156 through 157 removed outlier: 4.678A pdb=" N TRP F 150 " --> pdb=" O GLN F 157 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N LYS F 209 " --> pdb=" O CYS F 196 " (cutoff:3.500A) Processing sheet with id=AH3, first strand: chain 'E' and resid 3 through 6 Processing sheet with id=AH4, first strand: chain 'E' and resid 10 through 12 removed outlier: 6.683A pdb=" N GLU E 10 " --> pdb=" O THR E 115 " (cutoff:3.500A) removed outlier: 6.589A pdb=" N ILE E 34 " --> pdb=" O GLY E 50 " (cutoff:3.500A) removed outlier: 4.405A pdb=" N GLY E 50 " --> pdb=" O ILE E 34 " (cutoff:3.500A) removed outlier: 6.764A pdb=" N TRP E 36 " --> pdb=" O MET E 48 " (cutoff:3.500A) Processing sheet with id=AH5, first strand: chain 'E' and resid 10 through 12 removed outlier: 6.683A pdb=" N GLU E 10 " --> pdb=" O THR E 115 " (cutoff:3.500A) Processing sheet with id=AH6, first strand: chain 'E' and resid 125 through 129 removed outlier: 3.880A pdb=" N GLY E 144 " --> pdb=" O LEU E 129 " (cutoff:3.500A) removed outlier: 6.117A pdb=" N TYR E 181 " --> pdb=" O ASP E 149 " (cutoff:3.500A) Processing sheet with id=AH7, first strand: chain 'E' and resid 125 through 129 removed outlier: 3.880A pdb=" N GLY E 144 " --> pdb=" O LEU E 129 " (cutoff:3.500A) removed outlier: 6.117A pdb=" N TYR E 181 " --> pdb=" O ASP E 149 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N SER E 182 " --> pdb=" O VAL E 174 " (cutoff:3.500A) Processing sheet with id=AH8, first strand: chain 'E' and resid 156 through 159 removed outlier: 4.287A pdb=" N TYR E 199 " --> pdb=" O VAL E 216 " (cutoff:3.500A) Processing sheet with id=AH9, first strand: chain 'K' and resid 4 through 7 Processing sheet with id=AI1, first strand: chain 'K' and resid 10 through 13 removed outlier: 6.532A pdb=" N LEU K 34 " --> pdb=" O TYR K 50 " (cutoff:3.500A) removed outlier: 4.430A pdb=" N TYR K 50 " --> pdb=" O LEU K 34 " (cutoff:3.500A) removed outlier: 6.329A pdb=" N TRP K 36 " --> pdb=" O LEU K 48 " (cutoff:3.500A) Processing sheet with id=AI2, first strand: chain 'K' and resid 10 through 13 Processing sheet with id=AI3, first strand: chain 'K' and resid 116 through 120 removed outlier: 3.620A pdb=" N VAL K 135 " --> pdb=" O PHE K 120 " (cutoff:3.500A) removed outlier: 5.212A pdb=" N SER K 133 " --> pdb=" O LEU K 183 " (cutoff:3.500A) removed outlier: 7.300A pdb=" N LEU K 183 " --> pdb=" O SER K 133 " (cutoff:3.500A) removed outlier: 5.704A pdb=" N VAL K 135 " --> pdb=" O LEU K 181 " (cutoff:3.500A) removed outlier: 7.252A pdb=" N LEU K 181 " --> pdb=" O VAL K 135 " (cutoff:3.500A) removed outlier: 5.356A pdb=" N LEU K 137 " --> pdb=" O SER K 179 " (cutoff:3.500A) removed outlier: 7.173A pdb=" N SER K 179 " --> pdb=" O LEU K 137 " (cutoff:3.500A) removed outlier: 5.238A pdb=" N ASN K 139 " --> pdb=" O LEU K 177 " (cutoff:3.500A) removed outlier: 7.078A pdb=" N LEU K 177 " --> pdb=" O ASN K 139 " (cutoff:3.500A) Processing sheet with id=AI4, first strand: chain 'K' and resid 156 through 157 removed outlier: 4.668A pdb=" N TRP K 150 " --> pdb=" O GLN K 157 " (cutoff:3.500A) Processing sheet with id=AI5, first strand: chain 'J' and resid 3 through 6 removed outlier: 3.590A pdb=" N GLN J 3 " --> pdb=" O SER J 25 " (cutoff:3.500A) Processing sheet with id=AI6, first strand: chain 'J' and resid 10 through 12 removed outlier: 6.790A pdb=" N GLU J 10 " --> pdb=" O THR J 115 " (cutoff:3.500A) removed outlier: 6.659A pdb=" N ILE J 34 " --> pdb=" O GLY J 50 " (cutoff:3.500A) removed outlier: 4.548A pdb=" N GLY J 50 " --> pdb=" O ILE J 34 " (cutoff:3.500A) removed outlier: 6.779A pdb=" N TRP J 36 " --> pdb=" O MET J 48 " (cutoff:3.500A) Processing sheet with id=AI7, first strand: chain 'J' and resid 10 through 12 removed outlier: 6.790A pdb=" N GLU J 10 " --> pdb=" O THR J 115 " (cutoff:3.500A) Processing sheet with id=AI8, first strand: chain 'J' and resid 125 through 129 removed outlier: 3.910A pdb=" N GLY J 144 " --> pdb=" O LEU J 129 " (cutoff:3.500A) removed outlier: 6.114A pdb=" N TYR J 181 " --> pdb=" O ASP J 149 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N VAL J 186 " --> pdb=" O HIS J 169 " (cutoff:3.500A) Processing sheet with id=AI9, first strand: chain 'J' and resid 125 through 129 removed outlier: 3.910A pdb=" N GLY J 144 " --> pdb=" O LEU J 129 " (cutoff:3.500A) removed outlier: 6.114A pdb=" N TYR J 181 " --> pdb=" O ASP J 149 " (cutoff:3.500A) Processing sheet with id=AJ1, first strand: chain 'J' and resid 156 through 159 removed outlier: 4.355A pdb=" N TYR J 199 " --> pdb=" O VAL J 216 " (cutoff:3.500A) 1503 hydrogen bonds defined for protein. 3981 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 14.39 Time building geometry restraints manager: 4.06 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: 10862 1.34 - 1.46: 8828 1.46 - 1.58: 15229 1.58 - 1.70: 2 1.70 - 1.82: 180 Bond restraints: 35101 Sorted by residual: bond pdb=" C1 MAN P 5 " pdb=" C2 MAN P 5 " ideal model delta sigma weight residual 1.526 1.607 -0.081 2.00e-02 2.50e+03 1.63e+01 bond pdb=" C1 MAN P 5 " pdb=" O5 MAN P 5 " ideal model delta sigma weight residual 1.399 1.467 -0.068 2.00e-02 2.50e+03 1.14e+01 bond pdb=" C1 MAN D 5 " pdb=" C2 MAN D 5 " ideal model delta sigma weight residual 1.526 1.586 -0.060 2.00e-02 2.50e+03 9.10e+00 bond pdb=" C2 MAN V 4 " pdb=" O2 MAN V 4 " ideal model delta sigma weight residual 1.407 1.453 -0.046 2.00e-02 2.50e+03 5.24e+00 bond pdb=" C2 MAN V 4 " pdb=" C3 MAN V 4 " ideal model delta sigma weight residual 1.525 1.570 -0.045 2.00e-02 2.50e+03 5.14e+00 ... (remaining 35096 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.44: 46545 1.44 - 2.89: 943 2.89 - 4.33: 245 4.33 - 5.77: 27 5.77 - 7.21: 10 Bond angle restraints: 47770 Sorted by residual: angle pdb=" N ALA F 52 " pdb=" CA ALA F 52 " pdb=" CB ALA F 52 " ideal model delta sigma weight residual 114.17 110.27 3.90 1.14e+00 7.69e-01 1.17e+01 angle pdb=" N THR B 615 " pdb=" CA THR B 615 " pdb=" C THR B 615 " ideal model delta sigma weight residual 114.75 110.60 4.15 1.26e+00 6.30e-01 1.08e+01 angle pdb=" N THR B 520 " pdb=" CA THR B 520 " pdb=" C THR B 520 " ideal model delta sigma weight residual 114.56 110.86 3.70 1.27e+00 6.20e-01 8.48e+00 angle pdb=" CA VAL E 189 " pdb=" C VAL E 189 " pdb=" N PRO E 190 " ideal model delta sigma weight residual 117.00 119.36 -2.36 9.50e-01 1.11e+00 6.15e+00 angle pdb=" CA GLY A 473 " pdb=" C GLY A 473 " pdb=" N SER A 474 " ideal model delta sigma weight residual 114.65 116.87 -2.22 9.20e-01 1.18e+00 5.85e+00 ... (remaining 47765 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 18.00: 19555 18.00 - 35.99: 634 35.99 - 53.99: 128 53.99 - 71.99: 30 71.99 - 89.98: 13 Dihedral angle restraints: 20360 sinusoidal: 7826 harmonic: 12534 Sorted by residual: dihedral pdb=" CB CYS B1079 " pdb=" SG CYS B1079 " pdb=" SG CYS B1123 " pdb=" CB CYS B1123 " ideal model delta sinusoidal sigma weight residual -86.00 -133.28 47.28 1 1.00e+01 1.00e-02 3.09e+01 dihedral pdb=" CB CYS C1079 " pdb=" SG CYS C1079 " pdb=" SG CYS C1123 " pdb=" CB CYS C1123 " ideal model delta sinusoidal sigma weight residual -86.00 -133.14 47.14 1 1.00e+01 1.00e-02 3.07e+01 dihedral pdb=" CA THR B 596 " pdb=" C THR B 596 " pdb=" N PRO B 597 " pdb=" CA PRO B 597 " ideal model delta harmonic sigma weight residual 180.00 153.11 26.89 0 5.00e+00 4.00e-02 2.89e+01 ... (remaining 20357 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.055: 4767 0.055 - 0.111: 724 0.111 - 0.166: 170 0.166 - 0.221: 1 0.221 - 0.277: 3 Chirality restraints: 5665 Sorted by residual: chirality pdb=" C5 BMA D 3 " pdb=" C4 BMA D 3 " pdb=" C6 BMA D 3 " pdb=" O5 BMA D 3 " both_signs ideal model delta sigma weight residual False -2.27 -2.55 0.28 2.00e-01 2.50e+01 1.91e+00 chirality pdb=" C5 BMA V 3 " pdb=" C4 BMA V 3 " pdb=" C6 BMA V 3 " pdb=" O5 BMA V 3 " both_signs ideal model delta sigma weight residual False -2.27 -2.55 0.27 2.00e-01 2.50e+01 1.84e+00 chirality pdb=" C5 BMA P 3 " pdb=" C4 BMA P 3 " pdb=" C6 BMA P 3 " pdb=" O5 BMA P 3 " both_signs ideal model delta sigma weight residual False -2.27 -2.55 0.27 2.00e-01 2.50e+01 1.83e+00 ... (remaining 5662 not shown) Planarity restraints: 6092 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLU H 153 " 0.030 5.00e-02 4.00e+02 4.55e-02 3.32e+00 pdb=" N PRO H 154 " -0.079 5.00e-02 4.00e+02 pdb=" CA PRO H 154 " 0.026 5.00e-02 4.00e+02 pdb=" CD PRO H 154 " 0.023 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLU E 153 " 0.029 5.00e-02 4.00e+02 4.34e-02 3.02e+00 pdb=" N PRO E 154 " -0.075 5.00e-02 4.00e+02 pdb=" CA PRO E 154 " 0.025 5.00e-02 4.00e+02 pdb=" CD PRO E 154 " 0.022 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLU J 153 " -0.028 5.00e-02 4.00e+02 4.23e-02 2.86e+00 pdb=" N PRO J 154 " 0.073 5.00e-02 4.00e+02 pdb=" CA PRO J 154 " -0.024 5.00e-02 4.00e+02 pdb=" CD PRO J 154 " -0.021 5.00e-02 4.00e+02 ... (remaining 6089 not shown) Histogram of nonbonded interaction distances: 2.13 - 2.68: 662 2.68 - 3.24: 32132 3.24 - 3.79: 52843 3.79 - 4.35: 75441 4.35 - 4.90: 124005 Nonbonded interactions: 285083 Sorted by model distance: nonbonded pdb=" NH1 ARG A1088 " pdb=" O THR A1117 " model vdw 2.127 3.120 nonbonded pdb=" O THR J 28 " pdb=" OG SER J 32 " model vdw 2.191 3.040 nonbonded pdb=" OH TYR L 37 " pdb=" OE1 GLN L 90 " model vdw 2.191 3.040 nonbonded pdb=" OG SER E 30 " pdb=" OE2 GLU E 74 " model vdw 2.206 3.040 nonbonded pdb=" OG SER H 30 " pdb=" OE2 GLU H 74 " model vdw 2.209 3.040 ... (remaining 285078 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 22 through 143 or resid 165 through 617 or resid 638 throu \ gh 1308)) selection = (chain 'B' and (resid 22 through 143 or resid 165 through 1308)) selection = (chain 'C' and (resid 22 through 617 or resid 638 through 1308)) } ncs_group { reference = (chain 'D' and (resid 2 or resid 5 through 7)) selection = (chain 'P' and (resid 1 or resid 4 through 6)) selection = (chain 'V' and (resid 2 or resid 5 through 7)) } ncs_group { reference = chain 'E' selection = chain 'H' selection = chain 'J' } ncs_group { reference = chain 'F' selection = chain 'K' selection = chain 'L' } ncs_group { reference = chain 'G' selection = chain 'I' selection = chain 'M' selection = chain 'N' selection = chain 'O' selection = chain 'Q' selection = chain 'R' selection = chain 'S' selection = chain 'T' selection = chain 'U' selection = chain 'W' selection = chain 'X' selection = chain 'Y' selection = chain 'Z' } 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: 7.040 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.060 Extract box with map and model: 0.870 Check model and map are aligned: 0.110 Set scattering table: 0.060 Process input model: 39.020 Find NCS groups from input model: 1.200 Set up NCS constraints: 0.150 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:7.970 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 56.490 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8374 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 : 0.003 0.081 35226 Z= 0.171 Angle : 0.550 7.214 48094 Z= 0.271 Chirality : 0.045 0.277 5665 Planarity : 0.003 0.046 6049 Dihedral : 9.838 89.984 12155 Min Nonbonded Distance : 2.127 Molprobity Statistics. All-atom Clashscore : 3.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.72 % Favored : 97.28 % Rotamer: Outliers : 0.48 % Allowed : 3.21 % Favored : 96.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.33 (0.13), residues: 4267 helix: 1.04 (0.20), residues: 731 sheet: 0.46 (0.14), residues: 1259 loop : -0.10 (0.13), residues: 2277 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C1104 TYR 0.015 0.001 TYR C1064 PHE 0.011 0.001 PHE C 756 TRP 0.006 0.001 TRP C 883 HIS 0.002 0.001 HIS A1061 Details of bonding type rmsd/Z covalent geometry : bond 0.00349 / 0.17 (35101) covalent geometry : angle 0.54061 / 0.27 (47770) SS BOND : bond 0.00261 / 0.17 ( 51) SS BOND : angle 0.71549 / 0.46 ( 102) hydrogen bonds : bond 0.12349 / 7.93 ( 1435) hydrogen bonds : angle 7.01539 / 4.86 ( 3981) link_ALPHA1-2 : bond 0.00939 / 0.46 ( 3) link_ALPHA1-2 : angle 2.63379 / 1.44 ( 9) link_ALPHA1-3 : bond 0.00351 / 0.17 ( 3) link_ALPHA1-3 : angle 1.96474 / 1.02 ( 9) link_ALPHA1-6 : bond 0.00435 / 0.21 ( 2) link_ALPHA1-6 : angle 1.56513 / 0.79 ( 6) link_BETA1-4 : bond 0.00298 / 0.20 ( 20) link_BETA1-4 : angle 1.19797 / 0.83 ( 60) link_BETA1-6 : bond 0.00315 / 0.14 ( 3) link_BETA1-6 : angle 1.53306 / 0.80 ( 9) link_NAG-ASN : bond 0.00174 / 0.13 ( 43) link_NAG-ASN : angle 1.59051 / 1.02 ( 129) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8534 Ramachandran restraints generated. 4267 Oldfield, 0 Emsley, 4267 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8534 Ramachandran restraints generated. 4267 Oldfield, 0 Emsley, 4267 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 576 residues out of total 3751 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 558 time to evaluate : 1.304 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 203 ILE cc_start: 0.6610 (mt) cc_final: 0.6397 (mt) REVERT: A 449 LEU cc_start: 0.8376 (mt) cc_final: 0.8097 (mt) REVERT: A 787 LYS cc_start: 0.8388 (ptmt) cc_final: 0.7813 (mmpt) REVERT: A 926 SER cc_start: 0.8432 (OUTLIER) cc_final: 0.8189 (m) REVERT: B 129 LYS cc_start: 0.7605 (mttt) cc_final: 0.7205 (mmpt) REVERT: B 207 HIS cc_start: 0.7762 (m170) cc_final: 0.7513 (m-70) REVERT: B 239 GLN cc_start: 0.6894 (tt0) cc_final: 0.6551 (tm-30) REVERT: B 375 LYS cc_start: 0.8245 (mttt) cc_final: 0.7559 (mtmt) REVERT: B 526 LYS cc_start: 0.8807 (mttt) cc_final: 0.8508 (mmpt) REVERT: L 80 GLU cc_start: 0.7513 (mm-30) cc_final: 0.6648 (mp0) REVERT: F 80 GLU cc_start: 0.6667 (mm-30) cc_final: 0.6451 (mm-30) REVERT: E 23 LYS cc_start: 0.8613 (mttt) cc_final: 0.7749 (mtpm) REVERT: K 55 ARG cc_start: 0.8106 (mtm110) cc_final: 0.7864 (mtm-85) REVERT: K 168 GLN cc_start: 0.7483 (tt0) cc_final: 0.6244 (tt0) REVERT: J 23 LYS cc_start: 0.8888 (mttp) cc_final: 0.8668 (mttp) REVERT: J 81 MET cc_start: 0.8034 (tmm) cc_final: 0.7723 (tmm) REVERT: J 180 LEU cc_start: 0.8563 (mt) cc_final: 0.8343 (tt) outliers start: 18 outliers final: 11 residues processed: 574 average time/residue: 0.7383 time to fit residues: 503.4325 Evaluate side-chains 371 residues out of total 3751 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 359 time to evaluate : 1.551 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 612 VAL Chi-restraints excluded: chain A residue 875 LEU Chi-restraints excluded: chain A residue 926 SER Chi-restraints excluded: chain B residue 612 VAL Chi-restraints excluded: chain B residue 788 THR Chi-restraints excluded: chain B residue 875 LEU Chi-restraints excluded: chain C residue 424 ASP Chi-restraints excluded: chain C residue 612 VAL Chi-restraints excluded: chain C residue 875 LEU Chi-restraints excluded: chain L residue 61 ASP Chi-restraints excluded: chain F residue 43 GLN Chi-restraints excluded: chain K residue 34 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 427 random chunks: chunk 197 optimal weight: 0.9980 chunk 388 optimal weight: 2.9990 chunk 215 optimal weight: 6.9990 chunk 20 optimal weight: 4.9990 chunk 132 optimal weight: 7.9990 chunk 261 optimal weight: 1.9990 chunk 248 optimal weight: 3.9990 chunk 207 optimal weight: 20.0000 chunk 401 optimal weight: 2.9990 chunk 424 optimal weight: 30.0000 chunk 155 optimal weight: 0.0870 overall best weight: 1.8164 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 801 GLN A1007 GLN B 81 ASN ** B 391 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 516 HIS B 761 ASN B 776 GLN B1116 ASN C 391 ASN C 490 GLN C 954 GLN C 966 ASN H 59 ASN F 39 GLN ** F 201 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 6 GLN E 39 GLN K 39 GLN J 39 GLN Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4344 r_free = 0.4344 target = 0.201908 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 74)----------------| | r_work = 0.3747 r_free = 0.3747 target = 0.140233 restraints weight = 41368.174| |-----------------------------------------------------------------------------| r_work (start): 0.3592 rms_B_bonded: 3.00 r_work: 0.3268 rms_B_bonded: 2.27 restraints_weight: 0.5000 r_work: 0.3148 rms_B_bonded: 3.58 restraints_weight: 0.2500 r_work (final): 0.3148 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8683 moved from start: 0.1312 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.051 35226 Z= 0.211 Angle : 0.601 9.595 48094 Z= 0.307 Chirality : 0.047 0.404 5665 Planarity : 0.004 0.048 6049 Dihedral : 5.174 93.386 4639 Min Nonbonded Distance : 2.418 Molprobity Statistics. All-atom Clashscore : 4.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.23 % Favored : 96.77 % Rotamer: Outliers : 1.90 % Allowed : 8.37 % Favored : 89.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.44 (0.13), residues: 4267 helix: 1.26 (0.19), residues: 740 sheet: 0.58 (0.14), residues: 1292 loop : -0.13 (0.13), residues: 2235 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG J 87 TYR 0.025 0.002 TYR C 393 PHE 0.013 0.002 PHE B 895 TRP 0.008 0.001 TRP C 433 HIS 0.006 0.001 HIS F 200 Details of bonding type rmsd/Z covalent geometry : bond 0.00496 / 0.21 (35101) covalent geometry : angle 0.58689 / 0.30 (47770) SS BOND : bond 0.00451 / 0.29 ( 51) SS BOND : angle 1.03482 / 0.70 ( 102) hydrogen bonds : bond 0.04899 / 3.16 ( 1435) hydrogen bonds : angle 5.96864 / 4.13 ( 3981) link_ALPHA1-2 : bond 0.01669 / 0.79 ( 3) link_ALPHA1-2 : angle 3.64688 / 1.92 ( 9) link_ALPHA1-3 : bond 0.00710 / 0.33 ( 3) link_ALPHA1-3 : angle 1.70412 / 0.91 ( 9) link_ALPHA1-6 : bond 0.00454 / 0.23 ( 2) link_ALPHA1-6 : angle 1.65014 / 0.90 ( 6) link_BETA1-4 : bond 0.00408 / 0.25 ( 20) link_BETA1-4 : angle 1.03027 / 0.68 ( 60) link_BETA1-6 : bond 0.00104 / 0.05 ( 3) link_BETA1-6 : angle 1.41633 / 0.74 ( 9) link_NAG-ASN : bond 0.00334 / 0.19 ( 43) link_NAG-ASN : angle 2.08522 / 1.53 ( 129) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8534 Ramachandran restraints generated. 4267 Oldfield, 0 Emsley, 4267 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8534 Ramachandran restraints generated. 4267 Oldfield, 0 Emsley, 4267 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 439 residues out of total 3751 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 368 time to evaluate : 1.433 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 52 GLN cc_start: 0.8520 (OUTLIER) cc_final: 0.8089 (tt0) REVERT: A 311 GLN cc_start: 0.8696 (OUTLIER) cc_final: 0.8439 (tm-30) REVERT: A 449 LEU cc_start: 0.8125 (mt) cc_final: 0.7769 (mt) REVERT: A 555 LYS cc_start: 0.8094 (mptp) cc_final: 0.7894 (mptp) REVERT: A 787 LYS cc_start: 0.8902 (ptmt) cc_final: 0.7889 (mmpt) REVERT: A 954 GLN cc_start: 0.8267 (OUTLIER) cc_final: 0.8052 (tp40) REVERT: A 961 LYS cc_start: 0.8590 (mttt) cc_final: 0.8335 (mtpp) REVERT: B 46 SER cc_start: 0.8923 (m) cc_final: 0.8723 (p) REVERT: B 129 LYS cc_start: 0.7617 (mttt) cc_final: 0.6966 (mmpt) REVERT: B 239 GLN cc_start: 0.7204 (tt0) cc_final: 0.6716 (pp30) REVERT: B 375 LYS cc_start: 0.8164 (mttt) cc_final: 0.7215 (mtmt) REVERT: B 526 LYS cc_start: 0.9015 (mttt) cc_final: 0.8374 (mmtt) REVERT: B 1089 GLU cc_start: 0.7761 (OUTLIER) cc_final: 0.7154 (mp0) REVERT: B 1139 GLN cc_start: 0.7656 (tm-30) cc_final: 0.7377 (pt0) REVERT: C 487 PHE cc_start: 0.7157 (t80) cc_final: 0.6940 (t80) REVERT: C 490 GLN cc_start: 0.7478 (tp40) cc_final: 0.7234 (tm-30) REVERT: C 801 GLN cc_start: 0.8218 (mm110) cc_final: 0.7856 (mm-40) REVERT: C 982 ASP cc_start: 0.7422 (m-30) cc_final: 0.6999 (p0) REVERT: L 24 ARG cc_start: 0.8203 (tpp-160) cc_final: 0.7970 (tpp-160) REVERT: L 27 GLN cc_start: 0.8256 (mt0) cc_final: 0.7826 (mt0) REVERT: L 80 GLU cc_start: 0.7207 (mm-30) cc_final: 0.6336 (mp0) REVERT: L 109 LYS cc_start: 0.8039 (tppp) cc_final: 0.7824 (tppp) REVERT: H 180 LEU cc_start: 0.9326 (mm) cc_final: 0.8555 (tp) REVERT: F 80 GLU cc_start: 0.6423 (mm-30) cc_final: 0.6220 (mm-30) REVERT: F 107 GLU cc_start: 0.7694 (pt0) cc_final: 0.7007 (tt0) REVERT: E 23 LYS cc_start: 0.8467 (mttt) cc_final: 0.7411 (mtpm) REVERT: K 55 ARG cc_start: 0.8491 (mtm110) cc_final: 0.7980 (mtm-85) REVERT: K 145 GLU cc_start: 0.8587 (mp0) cc_final: 0.8130 (pm20) REVERT: K 181 LEU cc_start: 0.7842 (mt) cc_final: 0.7587 (mt) REVERT: J 83 MET cc_start: 0.8100 (ttp) cc_final: 0.7885 (ttt) REVERT: J 180 LEU cc_start: 0.8996 (mt) cc_final: 0.8261 (tt) outliers start: 71 outliers final: 35 residues processed: 408 average time/residue: 0.7666 time to fit residues: 369.8218 Evaluate side-chains 363 residues out of total 3751 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 324 time to evaluate : 1.143 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 52 GLN Chi-restraints excluded: chain A residue 268 GLN Chi-restraints excluded: chain A residue 311 GLN Chi-restraints excluded: chain A residue 612 VAL Chi-restraints excluded: chain A residue 639 VAL Chi-restraints excluded: chain A residue 716 THR Chi-restraints excluded: chain A residue 720 THR Chi-restraints excluded: chain A residue 758 THR Chi-restraints excluded: chain A residue 777 GLU Chi-restraints excluded: chain A residue 875 LEU Chi-restraints excluded: chain A residue 954 GLN Chi-restraints excluded: chain B residue 51 THR Chi-restraints excluded: chain B residue 221 SER Chi-restraints excluded: chain B residue 281 THR Chi-restraints excluded: chain B residue 317 VAL Chi-restraints excluded: chain B residue 320 THR Chi-restraints excluded: chain B residue 347 VAL Chi-restraints excluded: chain B residue 599 THR Chi-restraints excluded: chain B residue 612 VAL Chi-restraints excluded: chain B residue 737 MET Chi-restraints excluded: chain B residue 788 THR Chi-restraints excluded: chain B residue 875 LEU Chi-restraints excluded: chain B residue 1089 GLU Chi-restraints excluded: chain C residue 48 LEU Chi-restraints excluded: chain C residue 295 GLU Chi-restraints excluded: chain C residue 304 THR Chi-restraints excluded: chain C residue 322 SER Chi-restraints excluded: chain C residue 359 VAL Chi-restraints excluded: chain C residue 412 THR Chi-restraints excluded: chain C residue 543 LEU Chi-restraints excluded: chain C residue 573 VAL Chi-restraints excluded: chain C residue 612 VAL Chi-restraints excluded: chain C residue 716 THR Chi-restraints excluded: chain C residue 875 LEU Chi-restraints excluded: chain C residue 991 ASP Chi-restraints excluded: chain L residue 22 SER Chi-restraints excluded: chain H residue 89 GLU Chi-restraints excluded: chain E residue 5 VAL Chi-restraints excluded: chain K residue 34 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 427 random chunks: chunk 258 optimal weight: 0.6980 chunk 399 optimal weight: 8.9990 chunk 151 optimal weight: 3.9990 chunk 227 optimal weight: 0.9980 chunk 67 optimal weight: 0.8980 chunk 215 optimal weight: 0.9980 chunk 69 optimal weight: 0.9990 chunk 175 optimal weight: 0.0970 chunk 412 optimal weight: 2.9990 chunk 73 optimal weight: 0.7980 chunk 54 optimal weight: 4.9990 overall best weight: 0.6978 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A1116 ASN B 196 ASN B 391 ASN B 759 GLN B1098 HIS C 242 HIS ** C 801 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 954 GLN C 999 GLN C1007 GLN C1116 ASN H 59 ASN ** F 201 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4359 r_free = 0.4359 target = 0.202768 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 75)----------------| | r_work = 0.3781 r_free = 0.3781 target = 0.141910 restraints weight = 41575.348| |-----------------------------------------------------------------------------| r_work (start): 0.3621 rms_B_bonded: 2.88 r_work: 0.3301 rms_B_bonded: 2.32 restraints_weight: 0.5000 r_work: 0.3179 rms_B_bonded: 3.64 restraints_weight: 0.2500 r_work (final): 0.3179 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8657 moved from start: 0.1579 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 35226 Z= 0.120 Angle : 0.534 9.586 48094 Z= 0.272 Chirality : 0.044 0.383 5665 Planarity : 0.004 0.045 6049 Dihedral : 4.635 59.140 4631 Min Nonbonded Distance : 2.420 Molprobity Statistics. All-atom Clashscore : 4.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.70 % Favored : 97.30 % Rotamer: Outliers : 1.82 % Allowed : 9.63 % Favored : 88.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.60 (0.13), residues: 4267 helix: 1.54 (0.19), residues: 747 sheet: 0.64 (0.14), residues: 1304 loop : -0.07 (0.13), residues: 2216 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A 316 TYR 0.022 0.001 TYR A 366 PHE 0.020 0.001 PHE B 397 TRP 0.007 0.001 TRP C 433 HIS 0.003 0.001 HIS B1098 Details of bonding type rmsd/Z covalent geometry : bond 0.00270 / 0.12 (35101) covalent geometry : angle 0.52106 / 0.27 (47770) SS BOND : bond 0.00255 / 0.17 ( 51) SS BOND : angle 0.90708 / 0.60 ( 102) hydrogen bonds : bond 0.03945 / 2.55 ( 1435) hydrogen bonds : angle 5.57987 / 3.85 ( 3981) link_ALPHA1-2 : bond 0.01498 / 0.71 ( 3) link_ALPHA1-2 : angle 3.48269 / 1.81 ( 9) link_ALPHA1-3 : bond 0.00597 / 0.29 ( 3) link_ALPHA1-3 : angle 1.73838 / 0.92 ( 9) link_ALPHA1-6 : bond 0.00559 / 0.28 ( 2) link_ALPHA1-6 : angle 1.45891 / 0.80 ( 6) link_BETA1-4 : bond 0.00439 / 0.26 ( 20) link_BETA1-4 : angle 1.01103 / 0.69 ( 60) link_BETA1-6 : bond 0.00153 / 0.07 ( 3) link_BETA1-6 : angle 1.30665 / 0.69 ( 9) link_NAG-ASN : bond 0.00357 / 0.22 ( 43) link_NAG-ASN : angle 1.81287 / 1.25 ( 129) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8534 Ramachandran restraints generated. 4267 Oldfield, 0 Emsley, 4267 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8534 Ramachandran restraints generated. 4267 Oldfield, 0 Emsley, 4267 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 436 residues out of total 3751 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 368 time to evaluate : 1.318 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 52 GLN cc_start: 0.8494 (OUTLIER) cc_final: 0.8048 (tt0) REVERT: A 268 GLN cc_start: 0.8072 (OUTLIER) cc_final: 0.7724 (mt0) REVERT: A 449 LEU cc_start: 0.8088 (mt) cc_final: 0.7704 (mt) REVERT: A 787 LYS cc_start: 0.8891 (ptmt) cc_final: 0.7935 (mmpt) REVERT: A 805 ASP cc_start: 0.7481 (OUTLIER) cc_final: 0.6747 (m-30) REVERT: A 954 GLN cc_start: 0.8254 (OUTLIER) cc_final: 0.8029 (tp40) REVERT: A 1042 LYS cc_start: 0.8877 (tttm) cc_final: 0.8429 (mptt) REVERT: B 81 ASN cc_start: 0.7616 (OUTLIER) cc_final: 0.7305 (p0) REVERT: B 129 LYS cc_start: 0.7560 (mttt) cc_final: 0.6914 (mmpt) REVERT: B 239 GLN cc_start: 0.7089 (tt0) cc_final: 0.6521 (pp30) REVERT: B 375 LYS cc_start: 0.8149 (mttt) cc_final: 0.7205 (mtmt) REVERT: B 526 LYS cc_start: 0.9038 (mttt) cc_final: 0.8389 (mmpt) REVERT: B 1002 GLN cc_start: 0.8666 (mm-40) cc_final: 0.8395 (mm-40) REVERT: B 1089 GLU cc_start: 0.7706 (OUTLIER) cc_final: 0.7099 (mp0) REVERT: C 311 GLN cc_start: 0.7930 (pm20) cc_final: 0.7581 (tm-30) REVERT: C 490 GLN cc_start: 0.7412 (tp40) cc_final: 0.7169 (tm-30) REVERT: C 672 GLN cc_start: 0.7992 (mt0) cc_final: 0.7675 (mt0) REVERT: C 733 VAL cc_start: 0.7882 (t) cc_final: 0.7613 (p) REVERT: C 897 MET cc_start: 0.9165 (OUTLIER) cc_final: 0.8879 (mtm) REVERT: C 1141 GLU cc_start: 0.8672 (mm-30) cc_final: 0.8288 (mm-30) REVERT: L 24 ARG cc_start: 0.8275 (tpp-160) cc_final: 0.8027 (tpp-160) REVERT: L 27 GLN cc_start: 0.8271 (mt0) cc_final: 0.7922 (mt0) REVERT: L 80 GLU cc_start: 0.7108 (mm-30) cc_final: 0.6156 (mp0) REVERT: L 82 GLU cc_start: 0.8579 (pm20) cc_final: 0.8282 (pm20) REVERT: L 109 LYS cc_start: 0.8074 (tppp) cc_final: 0.7837 (tppp) REVERT: H 82 GLU cc_start: 0.8226 (tt0) cc_final: 0.7939 (tt0) REVERT: H 180 LEU cc_start: 0.9256 (mm) cc_final: 0.8584 (mt) REVERT: F 107 GLU cc_start: 0.7669 (pt0) cc_final: 0.7041 (tt0) REVERT: E 23 LYS cc_start: 0.8433 (mttt) cc_final: 0.7384 (mtpm) REVERT: E 81 MET cc_start: 0.8508 (ttp) cc_final: 0.8289 (ttp) REVERT: E 183 LEU cc_start: 0.9169 (OUTLIER) cc_final: 0.8886 (mp) REVERT: K 46 ARG cc_start: 0.8195 (ttt-90) cc_final: 0.7932 (ttt-90) REVERT: K 55 ARG cc_start: 0.8483 (mtm110) cc_final: 0.7972 (mtm-85) REVERT: K 145 GLU cc_start: 0.8550 (mp0) cc_final: 0.8116 (pm20) REVERT: J 180 LEU cc_start: 0.8936 (mt) cc_final: 0.8194 (tt) outliers start: 68 outliers final: 32 residues processed: 405 average time/residue: 0.7356 time to fit residues: 353.2705 Evaluate side-chains 376 residues out of total 3751 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 336 time to evaluate : 1.163 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 52 GLN Chi-restraints excluded: chain A residue 268 GLN Chi-restraints excluded: chain A residue 520 THR Chi-restraints excluded: chain A residue 550 THR Chi-restraints excluded: chain A residue 612 VAL Chi-restraints excluded: chain A residue 639 VAL Chi-restraints excluded: chain A residue 716 THR Chi-restraints excluded: chain A residue 720 THR Chi-restraints excluded: chain A residue 758 THR Chi-restraints excluded: chain A residue 777 GLU Chi-restraints excluded: chain A residue 805 ASP Chi-restraints excluded: chain A residue 875 LEU Chi-restraints excluded: chain A residue 926 SER Chi-restraints excluded: chain A residue 954 GLN Chi-restraints excluded: chain A residue 1138 LEU Chi-restraints excluded: chain B residue 81 ASN Chi-restraints excluded: chain B residue 347 VAL Chi-restraints excluded: chain B residue 612 VAL Chi-restraints excluded: chain B residue 737 MET Chi-restraints excluded: chain B residue 744 THR Chi-restraints excluded: chain B residue 788 THR Chi-restraints excluded: chain B residue 875 LEU Chi-restraints excluded: chain B residue 961 LYS Chi-restraints excluded: chain B residue 1089 GLU Chi-restraints excluded: chain C residue 46 SER Chi-restraints excluded: chain C residue 48 LEU Chi-restraints excluded: chain C residue 295 GLU Chi-restraints excluded: chain C residue 322 SER Chi-restraints excluded: chain C residue 359 VAL Chi-restraints excluded: chain C residue 412 THR Chi-restraints excluded: chain C residue 543 LEU Chi-restraints excluded: chain C residue 612 VAL Chi-restraints excluded: chain C residue 716 THR Chi-restraints excluded: chain C residue 875 LEU Chi-restraints excluded: chain C residue 897 MET Chi-restraints excluded: chain C residue 991 ASP Chi-restraints excluded: chain L residue 22 SER Chi-restraints excluded: chain E residue 183 LEU Chi-restraints excluded: chain K residue 34 LEU Chi-restraints excluded: chain K residue 94 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 427 random chunks: chunk 188 optimal weight: 0.8980 chunk 177 optimal weight: 1.9990 chunk 87 optimal weight: 0.9980 chunk 324 optimal weight: 1.9990 chunk 342 optimal weight: 30.0000 chunk 150 optimal weight: 3.9990 chunk 279 optimal weight: 3.9990 chunk 217 optimal weight: 10.0000 chunk 44 optimal weight: 0.0370 chunk 336 optimal weight: 30.0000 chunk 214 optimal weight: 3.9990 overall best weight: 1.1862 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 81 ASN A 752 GLN B 196 ASN ** B 391 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 761 ASN B 952 ASN ** C 801 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 954 GLN C 999 GLN ** F 201 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 3 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4355 r_free = 0.4355 target = 0.202993 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 74)----------------| | r_work = 0.3758 r_free = 0.3758 target = 0.141251 restraints weight = 41136.781| |-----------------------------------------------------------------------------| r_work (start): 0.3610 rms_B_bonded: 3.15 r_work: 0.3289 rms_B_bonded: 2.33 restraints_weight: 0.5000 r_work: 0.3164 rms_B_bonded: 3.66 restraints_weight: 0.2500 r_work (final): 0.3164 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8659 moved from start: 0.1709 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 35226 Z= 0.154 Angle : 0.546 10.074 48094 Z= 0.277 Chirality : 0.045 0.385 5665 Planarity : 0.004 0.064 6049 Dihedral : 4.672 58.999 4631 Min Nonbonded Distance : 2.419 Molprobity Statistics. All-atom Clashscore : 4.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.14 % Favored : 96.86 % Rotamer: Outliers : 2.19 % Allowed : 10.11 % Favored : 87.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.59 (0.13), residues: 4267 helix: 1.48 (0.19), residues: 753 sheet: 0.66 (0.14), residues: 1300 loop : -0.09 (0.13), residues: 2214 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG B 316 TYR 0.023 0.001 TYR C 366 PHE 0.022 0.001 PHE B 168 TRP 0.012 0.001 TRP E 159 HIS 0.005 0.001 HIS B 207 Details of bonding type rmsd/Z covalent geometry : bond 0.00358 / 0.15 (35101) covalent geometry : angle 0.53310 / 0.27 (47770) SS BOND : bond 0.00283 / 0.19 ( 51) SS BOND : angle 0.79820 / 0.53 ( 102) hydrogen bonds : bond 0.04094 / 2.64 ( 1435) hydrogen bonds : angle 5.51158 / 3.80 ( 3981) link_ALPHA1-2 : bond 0.01311 / 0.62 ( 3) link_ALPHA1-2 : angle 3.45715 / 1.81 ( 9) link_ALPHA1-3 : bond 0.00555 / 0.27 ( 3) link_ALPHA1-3 : angle 1.73546 / 0.91 ( 9) link_ALPHA1-6 : bond 0.00543 / 0.27 ( 2) link_ALPHA1-6 : angle 1.45051 / 0.79 ( 6) link_BETA1-4 : bond 0.00362 / 0.22 ( 20) link_BETA1-4 : angle 1.02123 / 0.68 ( 60) link_BETA1-6 : bond 0.00116 / 0.06 ( 3) link_BETA1-6 : angle 1.36203 / 0.71 ( 9) link_NAG-ASN : bond 0.00198 / 0.11 ( 43) link_NAG-ASN : angle 1.87421 / 1.27 ( 129) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8534 Ramachandran restraints generated. 4267 Oldfield, 0 Emsley, 4267 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8534 Ramachandran restraints generated. 4267 Oldfield, 0 Emsley, 4267 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 439 residues out of total 3751 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 82 poor density : 357 time to evaluate : 1.324 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 52 GLN cc_start: 0.8515 (OUTLIER) cc_final: 0.8113 (tt0) REVERT: A 63 THR cc_start: 0.7458 (OUTLIER) cc_final: 0.6813 (p) REVERT: A 268 GLN cc_start: 0.8106 (OUTLIER) cc_final: 0.7889 (mt0) REVERT: A 311 GLN cc_start: 0.8714 (OUTLIER) cc_final: 0.8410 (tm-30) REVERT: A 449 LEU cc_start: 0.8060 (mt) cc_final: 0.7661 (mt) REVERT: A 787 LYS cc_start: 0.8906 (ptmt) cc_final: 0.7925 (mmpt) REVERT: A 805 ASP cc_start: 0.7487 (OUTLIER) cc_final: 0.6736 (m-30) REVERT: A 954 GLN cc_start: 0.8241 (OUTLIER) cc_final: 0.8016 (tp40) REVERT: A 1042 LYS cc_start: 0.8836 (tttm) cc_final: 0.8436 (tppt) REVERT: B 81 ASN cc_start: 0.7521 (OUTLIER) cc_final: 0.7303 (p0) REVERT: B 129 LYS cc_start: 0.7523 (mttt) cc_final: 0.6859 (mmpt) REVERT: B 239 GLN cc_start: 0.7108 (tt0) cc_final: 0.6643 (pp30) REVERT: B 375 LYS cc_start: 0.8122 (mttt) cc_final: 0.7167 (mtmt) REVERT: B 526 LYS cc_start: 0.9025 (mttt) cc_final: 0.8359 (mmpt) REVERT: B 658 GLU cc_start: 0.8560 (tt0) cc_final: 0.8181 (tt0) REVERT: B 932 GLN cc_start: 0.7827 (OUTLIER) cc_final: 0.7490 (tt0) REVERT: B 1089 GLU cc_start: 0.7729 (OUTLIER) cc_final: 0.7126 (mp0) REVERT: C 487 PHE cc_start: 0.6984 (t80) cc_final: 0.6634 (t80) REVERT: C 490 GLN cc_start: 0.7352 (tp40) cc_final: 0.7067 (tm-30) REVERT: C 672 GLN cc_start: 0.8026 (mt0) cc_final: 0.7705 (mt0) REVERT: C 752 GLN cc_start: 0.8322 (mm-40) cc_final: 0.7766 (mm-40) REVERT: C 801 GLN cc_start: 0.8153 (mm110) cc_final: 0.7779 (mm-40) REVERT: C 897 MET cc_start: 0.9219 (OUTLIER) cc_final: 0.8910 (mtp) REVERT: C 1089 GLU cc_start: 0.7597 (OUTLIER) cc_final: 0.6994 (pp20) REVERT: C 1141 GLU cc_start: 0.8659 (mm-30) cc_final: 0.8284 (mm-30) REVERT: L 24 ARG cc_start: 0.8290 (tpp-160) cc_final: 0.8062 (tpp-160) REVERT: L 27 GLN cc_start: 0.8255 (mt0) cc_final: 0.7903 (mt0) REVERT: L 80 GLU cc_start: 0.7003 (mm-30) cc_final: 0.6038 (mp0) REVERT: L 82 GLU cc_start: 0.8461 (pm20) cc_final: 0.8220 (pm20) REVERT: L 109 LYS cc_start: 0.8097 (tppp) cc_final: 0.7835 (tppp) REVERT: L 147 LYS cc_start: 0.8642 (tptt) cc_final: 0.8294 (tptt) REVERT: L 197 GLU cc_start: 0.8680 (tt0) cc_final: 0.7960 (pp20) REVERT: H 82 GLU cc_start: 0.8216 (tt0) cc_final: 0.7948 (tt0) REVERT: H 180 LEU cc_start: 0.9243 (mm) cc_final: 0.8549 (mt) REVERT: H 183 LEU cc_start: 0.7806 (pp) cc_final: 0.7570 (pt) REVERT: F 107 GLU cc_start: 0.7661 (pt0) cc_final: 0.7061 (tt0) REVERT: E 23 LYS cc_start: 0.8417 (mttt) cc_final: 0.7397 (mtpm) REVERT: E 81 MET cc_start: 0.8504 (ttp) cc_final: 0.8236 (ttp) REVERT: E 183 LEU cc_start: 0.9138 (OUTLIER) cc_final: 0.8704 (mp) REVERT: K 27 GLN cc_start: 0.8216 (OUTLIER) cc_final: 0.7901 (mp10) REVERT: K 55 ARG cc_start: 0.8504 (mtm110) cc_final: 0.7964 (mtm-85) REVERT: K 145 GLU cc_start: 0.8578 (mp0) cc_final: 0.8214 (pm20) REVERT: J 43 GLN cc_start: 0.8572 (mt0) cc_final: 0.8280 (mp10) REVERT: J 180 LEU cc_start: 0.8909 (mt) cc_final: 0.8148 (tt) outliers start: 82 outliers final: 44 residues processed: 404 average time/residue: 0.7406 time to fit residues: 354.5138 Evaluate side-chains 388 residues out of total 3751 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 331 time to evaluate : 1.269 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 46 SER Chi-restraints excluded: chain A residue 52 GLN Chi-restraints excluded: chain A residue 63 THR Chi-restraints excluded: chain A residue 268 GLN Chi-restraints excluded: chain A residue 299 THR Chi-restraints excluded: chain A residue 311 GLN Chi-restraints excluded: chain A residue 520 THR Chi-restraints excluded: chain A residue 550 THR Chi-restraints excluded: chain A residue 612 VAL Chi-restraints excluded: chain A residue 639 VAL Chi-restraints excluded: chain A residue 716 THR Chi-restraints excluded: chain A residue 720 THR Chi-restraints excluded: chain A residue 777 GLU Chi-restraints excluded: chain A residue 805 ASP Chi-restraints excluded: chain A residue 875 LEU Chi-restraints excluded: chain A residue 897 MET Chi-restraints excluded: chain A residue 926 SER Chi-restraints excluded: chain A residue 954 GLN Chi-restraints excluded: chain A residue 1007 GLN Chi-restraints excluded: chain A residue 1138 LEU Chi-restraints excluded: chain B residue 51 THR Chi-restraints excluded: chain B residue 81 ASN Chi-restraints excluded: chain B residue 317 VAL Chi-restraints excluded: chain B residue 347 VAL Chi-restraints excluded: chain B residue 390 THR Chi-restraints excluded: chain B residue 550 THR Chi-restraints excluded: chain B residue 599 THR Chi-restraints excluded: chain B residue 612 VAL Chi-restraints excluded: chain B residue 737 MET Chi-restraints excluded: chain B residue 744 THR Chi-restraints excluded: chain B residue 788 THR Chi-restraints excluded: chain B residue 875 LEU Chi-restraints excluded: chain B residue 932 GLN Chi-restraints excluded: chain B residue 961 LYS Chi-restraints excluded: chain B residue 1089 GLU Chi-restraints excluded: chain C residue 48 LEU Chi-restraints excluded: chain C residue 295 GLU Chi-restraints excluded: chain C residue 322 SER Chi-restraints excluded: chain C residue 359 VAL Chi-restraints excluded: chain C residue 412 THR Chi-restraints excluded: chain C residue 543 LEU Chi-restraints excluded: chain C residue 568 ASP Chi-restraints excluded: chain C residue 612 VAL Chi-restraints excluded: chain C residue 716 THR Chi-restraints excluded: chain C residue 875 LEU Chi-restraints excluded: chain C residue 897 MET Chi-restraints excluded: chain C residue 991 ASP Chi-restraints excluded: chain C residue 1089 GLU Chi-restraints excluded: chain L residue 22 SER Chi-restraints excluded: chain L residue 34 LEU Chi-restraints excluded: chain F residue 167 GLU Chi-restraints excluded: chain E residue 183 LEU Chi-restraints excluded: chain K residue 27 GLN Chi-restraints excluded: chain K residue 34 LEU Chi-restraints excluded: chain K residue 94 THR Chi-restraints excluded: chain J residue 112 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 427 random chunks: chunk 274 optimal weight: 3.9990 chunk 196 optimal weight: 0.8980 chunk 144 optimal weight: 9.9990 chunk 118 optimal weight: 7.9990 chunk 340 optimal weight: 40.0000 chunk 250 optimal weight: 2.9990 chunk 87 optimal weight: 0.9980 chunk 389 optimal weight: 4.9990 chunk 143 optimal weight: 8.9990 chunk 39 optimal weight: 5.9990 chunk 111 optimal weight: 8.9990 overall best weight: 2.7786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 81 ASN A 484 ASN A 752 GLN B 196 ASN B 391 ASN B 759 GLN ** C 801 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 954 GLN C 999 GLN ** F 201 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4330 r_free = 0.4330 target = 0.200619 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 79)----------------| | r_work = 0.3727 r_free = 0.3727 target = 0.138630 restraints weight = 41142.733| |-----------------------------------------------------------------------------| r_work (start): 0.3580 rms_B_bonded: 3.05 r_work: 0.3239 rms_B_bonded: 2.33 restraints_weight: 0.5000 r_work: 0.3115 rms_B_bonded: 3.64 restraints_weight: 0.2500 r_work (final): 0.3115 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8702 moved from start: 0.1808 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.067 35226 Z= 0.289 Angle : 0.635 11.816 48094 Z= 0.325 Chirality : 0.049 0.386 5665 Planarity : 0.005 0.048 6049 Dihedral : 5.059 58.228 4631 Min Nonbonded Distance : 2.413 Molprobity Statistics. All-atom Clashscore : 5.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.61 % Favored : 96.39 % Rotamer: Outliers : 2.97 % Allowed : 10.30 % Favored : 86.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.32 (0.13), residues: 4267 helix: 1.09 (0.19), residues: 742 sheet: 0.55 (0.14), residues: 1291 loop : -0.22 (0.13), residues: 2234 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 316 TYR 0.026 0.002 TYR C 366 PHE 0.020 0.002 PHE A 65 TRP 0.011 0.002 TRP J 102 HIS 0.006 0.001 HIS C1061 Details of bonding type rmsd/Z covalent geometry : bond 0.00692 / 0.29 (35101) covalent geometry : angle 0.62011 / 0.32 (47770) SS BOND : bond 0.00463 / 0.31 ( 51) SS BOND : angle 1.08247 / 0.71 ( 102) hydrogen bonds : bond 0.05049 / 3.25 ( 1435) hydrogen bonds : angle 5.72007 / 3.96 ( 3981) link_ALPHA1-2 : bond 0.01007 / 0.48 ( 3) link_ALPHA1-2 : angle 3.49183 / 1.84 ( 9) link_ALPHA1-3 : bond 0.00542 / 0.27 ( 3) link_ALPHA1-3 : angle 1.88504 / 1.00 ( 9) link_ALPHA1-6 : bond 0.00521 / 0.26 ( 2) link_ALPHA1-6 : angle 1.45502 / 0.79 ( 6) link_BETA1-4 : bond 0.00284 / 0.18 ( 20) link_BETA1-4 : angle 1.10840 / 0.72 ( 60) link_BETA1-6 : bond 0.00091 / 0.05 ( 3) link_BETA1-6 : angle 1.51597 / 0.79 ( 9) link_NAG-ASN : bond 0.00324 / 0.20 ( 43) link_NAG-ASN : angle 2.20141 / 1.48 ( 129) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8534 Ramachandran restraints generated. 4267 Oldfield, 0 Emsley, 4267 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8534 Ramachandran restraints generated. 4267 Oldfield, 0 Emsley, 4267 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 460 residues out of total 3751 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 111 poor density : 349 time to evaluate : 1.393 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 52 GLN cc_start: 0.8528 (OUTLIER) cc_final: 0.8114 (tt0) REVERT: A 268 GLN cc_start: 0.8066 (OUTLIER) cc_final: 0.7817 (mt0) REVERT: A 311 GLN cc_start: 0.8742 (OUTLIER) cc_final: 0.8380 (tm-30) REVERT: A 402 ASP cc_start: 0.8121 (m-30) cc_final: 0.7910 (m-30) REVERT: A 449 LEU cc_start: 0.8073 (mt) cc_final: 0.7688 (mt) REVERT: A 787 LYS cc_start: 0.8975 (ptmt) cc_final: 0.7996 (mmpt) REVERT: A 805 ASP cc_start: 0.7515 (OUTLIER) cc_final: 0.6707 (m-30) REVERT: A 954 GLN cc_start: 0.8266 (OUTLIER) cc_final: 0.8036 (tp40) REVERT: A 1135 TYR cc_start: 0.8331 (t80) cc_final: 0.8095 (t80) REVERT: B 81 ASN cc_start: 0.7538 (OUTLIER) cc_final: 0.7187 (p0) REVERT: B 129 LYS cc_start: 0.7486 (mttt) cc_final: 0.6832 (mmpt) REVERT: B 237 ARG cc_start: 0.7592 (mtp85) cc_final: 0.7357 (mtm110) REVERT: B 239 GLN cc_start: 0.7254 (tt0) cc_final: 0.6584 (pp30) REVERT: B 375 LYS cc_start: 0.8121 (mttt) cc_final: 0.7198 (mtmt) REVERT: B 445 ASN cc_start: 0.8290 (t0) cc_final: 0.6868 (m110) REVERT: B 526 LYS cc_start: 0.9024 (mttt) cc_final: 0.8344 (mmtt) REVERT: B 658 GLU cc_start: 0.8617 (tt0) cc_final: 0.8265 (tt0) REVERT: B 932 GLN cc_start: 0.7936 (OUTLIER) cc_final: 0.7598 (tt0) REVERT: B 1089 GLU cc_start: 0.7801 (OUTLIER) cc_final: 0.7204 (mp0) REVERT: C 45 SER cc_start: 0.8723 (p) cc_final: 0.8239 (t) REVERT: C 311 GLN cc_start: 0.7688 (pm20) cc_final: 0.7484 (tm-30) REVERT: C 405 ARG cc_start: 0.8111 (OUTLIER) cc_final: 0.7661 (ptm-80) REVERT: C 490 GLN cc_start: 0.7407 (tp40) cc_final: 0.7149 (tm-30) REVERT: C 672 GLN cc_start: 0.8013 (mt0) cc_final: 0.7758 (mt0) REVERT: C 801 GLN cc_start: 0.8292 (mm110) cc_final: 0.7907 (mm110) REVERT: C 982 ASP cc_start: 0.7686 (m-30) cc_final: 0.7236 (m-30) REVERT: C 985 GLU cc_start: 0.7613 (mp0) cc_final: 0.6960 (tm-30) REVERT: C 1141 GLU cc_start: 0.8645 (mm-30) cc_final: 0.8357 (mm-30) REVERT: L 24 ARG cc_start: 0.8321 (tpp-160) cc_final: 0.7954 (ttm110) REVERT: L 27 GLN cc_start: 0.8272 (mt0) cc_final: 0.7893 (mt0) REVERT: L 80 GLU cc_start: 0.7033 (mm-30) cc_final: 0.6072 (mp0) REVERT: L 82 GLU cc_start: 0.8446 (pm20) cc_final: 0.8174 (pm20) REVERT: L 109 LYS cc_start: 0.8134 (tppp) cc_final: 0.7873 (tppp) REVERT: H 3 GLN cc_start: 0.8273 (tt0) cc_final: 0.8035 (tt0) REVERT: H 82 GLU cc_start: 0.8226 (tt0) cc_final: 0.7951 (tt0) REVERT: H 180 LEU cc_start: 0.9258 (mm) cc_final: 0.9038 (mm) REVERT: F 107 GLU cc_start: 0.7725 (pt0) cc_final: 0.7147 (tt0) REVERT: E 23 LYS cc_start: 0.8376 (mttt) cc_final: 0.7339 (mtpm) REVERT: E 81 MET cc_start: 0.8565 (ttp) cc_final: 0.8331 (ttp) REVERT: E 183 LEU cc_start: 0.9107 (OUTLIER) cc_final: 0.8630 (mp) REVERT: K 27 GLN cc_start: 0.8280 (OUTLIER) cc_final: 0.7953 (mp10) REVERT: K 46 ARG cc_start: 0.8251 (ttp80) cc_final: 0.7899 (ttt-90) REVERT: K 55 ARG cc_start: 0.8525 (mtm110) cc_final: 0.8034 (mtm-85) REVERT: K 94 THR cc_start: 0.8834 (OUTLIER) cc_final: 0.8296 (p) REVERT: K 107 GLU cc_start: 0.7728 (pt0) cc_final: 0.7513 (pm20) REVERT: K 145 GLU cc_start: 0.8619 (mp0) cc_final: 0.8298 (pm20) REVERT: J 38 ARG cc_start: 0.8670 (OUTLIER) cc_final: 0.6947 (ttt180) REVERT: J 43 GLN cc_start: 0.8539 (mt0) cc_final: 0.8261 (mp10) REVERT: J 180 LEU cc_start: 0.8916 (mt) cc_final: 0.8174 (tt) outliers start: 111 outliers final: 62 residues processed: 415 average time/residue: 0.7501 time to fit residues: 370.2314 Evaluate side-chains 399 residues out of total 3751 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 324 time to evaluate : 1.352 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 46 SER Chi-restraints excluded: chain A residue 52 GLN Chi-restraints excluded: chain A residue 63 THR Chi-restraints excluded: chain A residue 81 ASN Chi-restraints excluded: chain A residue 84 LEU Chi-restraints excluded: chain A residue 268 GLN Chi-restraints excluded: chain A residue 299 THR Chi-restraints excluded: chain A residue 311 GLN Chi-restraints excluded: chain A residue 373 THR Chi-restraints excluded: chain A residue 520 THR Chi-restraints excluded: chain A residue 550 THR Chi-restraints excluded: chain A residue 612 VAL Chi-restraints excluded: chain A residue 639 VAL Chi-restraints excluded: chain A residue 716 THR Chi-restraints excluded: chain A residue 720 THR Chi-restraints excluded: chain A residue 721 THR Chi-restraints excluded: chain A residue 777 GLU Chi-restraints excluded: chain A residue 788 THR Chi-restraints excluded: chain A residue 805 ASP Chi-restraints excluded: chain A residue 875 LEU Chi-restraints excluded: chain A residue 897 MET Chi-restraints excluded: chain A residue 926 SER Chi-restraints excluded: chain A residue 954 GLN Chi-restraints excluded: chain A residue 1007 GLN Chi-restraints excluded: chain A residue 1133 THR Chi-restraints excluded: chain A residue 1138 LEU Chi-restraints excluded: chain B residue 51 THR Chi-restraints excluded: chain B residue 54 LEU Chi-restraints excluded: chain B residue 81 ASN Chi-restraints excluded: chain B residue 281 THR Chi-restraints excluded: chain B residue 317 VAL Chi-restraints excluded: chain B residue 320 THR Chi-restraints excluded: chain B residue 347 VAL Chi-restraints excluded: chain B residue 390 THR Chi-restraints excluded: chain B residue 511 SER Chi-restraints excluded: chain B residue 599 THR Chi-restraints excluded: chain B residue 612 VAL Chi-restraints excluded: chain B residue 737 MET Chi-restraints excluded: chain B residue 744 THR Chi-restraints excluded: chain B residue 788 THR Chi-restraints excluded: chain B residue 875 LEU Chi-restraints excluded: chain B residue 932 GLN Chi-restraints excluded: chain B residue 961 LYS Chi-restraints excluded: chain B residue 1089 GLU Chi-restraints excluded: chain C residue 48 LEU Chi-restraints excluded: chain C residue 295 GLU Chi-restraints excluded: chain C residue 304 THR Chi-restraints excluded: chain C residue 322 SER Chi-restraints excluded: chain C residue 359 VAL Chi-restraints excluded: chain C residue 403 GLU Chi-restraints excluded: chain C residue 405 ARG Chi-restraints excluded: chain C residue 412 THR Chi-restraints excluded: chain C residue 466 SER Chi-restraints excluded: chain C residue 543 LEU Chi-restraints excluded: chain C residue 568 ASP Chi-restraints excluded: chain C residue 612 VAL Chi-restraints excluded: chain C residue 698 VAL Chi-restraints excluded: chain C residue 716 THR Chi-restraints excluded: chain C residue 856 THR Chi-restraints excluded: chain C residue 875 LEU Chi-restraints excluded: chain C residue 991 ASP Chi-restraints excluded: chain C residue 1007 GLN Chi-restraints excluded: chain L residue 22 SER Chi-restraints excluded: chain L residue 34 LEU Chi-restraints excluded: chain F residue 167 GLU Chi-restraints excluded: chain E residue 5 VAL Chi-restraints excluded: chain E residue 93 VAL Chi-restraints excluded: chain E residue 183 LEU Chi-restraints excluded: chain K residue 27 GLN Chi-restraints excluded: chain K residue 34 LEU Chi-restraints excluded: chain K residue 94 THR Chi-restraints excluded: chain J residue 38 ARG Chi-restraints excluded: chain J residue 74 GLU Chi-restraints excluded: chain J residue 112 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 427 random chunks: chunk 137 optimal weight: 20.0000 chunk 152 optimal weight: 3.9990 chunk 343 optimal weight: 9.9990 chunk 283 optimal weight: 0.6980 chunk 31 optimal weight: 0.8980 chunk 98 optimal weight: 0.6980 chunk 60 optimal weight: 1.9990 chunk 39 optimal weight: 10.0000 chunk 118 optimal weight: 1.9990 chunk 370 optimal weight: 7.9990 chunk 156 optimal weight: 0.9990 overall best weight: 1.0584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 81 ASN A 752 GLN B 196 ASN B 391 ASN B 759 GLN C 999 GLN ** F 201 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4349 r_free = 0.4349 target = 0.202694 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 76)----------------| | r_work = 0.3760 r_free = 0.3760 target = 0.141088 restraints weight = 41146.918| |-----------------------------------------------------------------------------| r_work (start): 0.3600 rms_B_bonded: 2.86 r_work: 0.3273 rms_B_bonded: 2.35 restraints_weight: 0.5000 r_work: 0.3150 rms_B_bonded: 3.68 restraints_weight: 0.2500 r_work (final): 0.3150 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8657 moved from start: 0.1880 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 35226 Z= 0.144 Angle : 0.555 10.310 48094 Z= 0.281 Chirality : 0.044 0.385 5665 Planarity : 0.004 0.044 6049 Dihedral : 4.757 58.008 4631 Min Nonbonded Distance : 2.388 Molprobity Statistics. All-atom Clashscore : 5.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.86 % Favored : 97.14 % Rotamer: Outliers : 2.51 % Allowed : 11.21 % Favored : 86.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.50 (0.13), residues: 4267 helix: 1.41 (0.19), residues: 746 sheet: 0.59 (0.14), residues: 1293 loop : -0.12 (0.13), residues: 2228 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A 316 TYR 0.028 0.001 TYR C 366 PHE 0.022 0.001 PHE B 168 TRP 0.010 0.001 TRP E 108 HIS 0.005 0.001 HIS B 207 Details of bonding type rmsd/Z covalent geometry : bond 0.00334 / 0.14 (35101) covalent geometry : angle 0.54164 / 0.28 (47770) SS BOND : bond 0.00268 / 0.18 ( 51) SS BOND : angle 0.78292 / 0.52 ( 102) hydrogen bonds : bond 0.03997 / 2.57 ( 1435) hydrogen bonds : angle 5.45197 / 3.77 ( 3981) link_ALPHA1-2 : bond 0.00958 / 0.47 ( 3) link_ALPHA1-2 : angle 3.26887 / 1.70 ( 9) link_ALPHA1-3 : bond 0.00507 / 0.25 ( 3) link_ALPHA1-3 : angle 1.76697 / 0.91 ( 9) link_ALPHA1-6 : bond 0.00534 / 0.27 ( 2) link_ALPHA1-6 : angle 1.43173 / 0.77 ( 6) link_BETA1-4 : bond 0.00344 / 0.21 ( 20) link_BETA1-4 : angle 1.00372 / 0.68 ( 60) link_BETA1-6 : bond 0.00156 / 0.08 ( 3) link_BETA1-6 : angle 1.29601 / 0.68 ( 9) link_NAG-ASN : bond 0.00242 / 0.17 ( 43) link_NAG-ASN : angle 2.01893 / 1.39 ( 129) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8534 Ramachandran restraints generated. 4267 Oldfield, 0 Emsley, 4267 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8534 Ramachandran restraints generated. 4267 Oldfield, 0 Emsley, 4267 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 457 residues out of total 3751 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 94 poor density : 363 time to evaluate : 1.324 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 52 GLN cc_start: 0.8521 (OUTLIER) cc_final: 0.8083 (tt0) REVERT: A 63 THR cc_start: 0.7478 (OUTLIER) cc_final: 0.6812 (p) REVERT: A 266 TYR cc_start: 0.7656 (m-80) cc_final: 0.7334 (m-80) REVERT: A 268 GLN cc_start: 0.8058 (OUTLIER) cc_final: 0.7773 (mt0) REVERT: A 311 GLN cc_start: 0.8713 (OUTLIER) cc_final: 0.8382 (tm-30) REVERT: A 402 ASP cc_start: 0.8097 (m-30) cc_final: 0.7880 (m-30) REVERT: A 449 LEU cc_start: 0.8048 (mt) cc_final: 0.7648 (mt) REVERT: A 787 LYS cc_start: 0.8929 (ptmt) cc_final: 0.7907 (mmpt) REVERT: A 805 ASP cc_start: 0.7453 (OUTLIER) cc_final: 0.6688 (m-30) REVERT: A 954 GLN cc_start: 0.8232 (OUTLIER) cc_final: 0.8006 (tp40) REVERT: A 1007 GLN cc_start: 0.8428 (OUTLIER) cc_final: 0.7616 (mp10) REVERT: A 1042 LYS cc_start: 0.8848 (tttm) cc_final: 0.8423 (tppt) REVERT: B 129 LYS cc_start: 0.7480 (mttt) cc_final: 0.6828 (mmpt) REVERT: B 239 GLN cc_start: 0.7231 (tt0) cc_final: 0.6514 (pp30) REVERT: B 375 LYS cc_start: 0.8140 (mttt) cc_final: 0.7215 (mtmt) REVERT: B 526 LYS cc_start: 0.8997 (mttt) cc_final: 0.8340 (mmtt) REVERT: B 658 GLU cc_start: 0.8585 (tt0) cc_final: 0.8210 (tt0) REVERT: B 1089 GLU cc_start: 0.7742 (OUTLIER) cc_final: 0.7131 (mp0) REVERT: C 45 SER cc_start: 0.8745 (OUTLIER) cc_final: 0.8277 (t) REVERT: C 268 GLN cc_start: 0.7371 (OUTLIER) cc_final: 0.7167 (mt0) REVERT: C 311 GLN cc_start: 0.7795 (pm20) cc_final: 0.7542 (tm-30) REVERT: C 455 LYS cc_start: 0.8123 (OUTLIER) cc_final: 0.7874 (tppt) REVERT: C 487 PHE cc_start: 0.7036 (t80) cc_final: 0.6618 (t80) REVERT: C 490 GLN cc_start: 0.7364 (tp40) cc_final: 0.7099 (tm-30) REVERT: C 733 VAL cc_start: 0.7828 (t) cc_final: 0.7505 (p) REVERT: C 897 MET cc_start: 0.9188 (OUTLIER) cc_final: 0.8911 (mtp) REVERT: C 961 LYS cc_start: 0.8398 (mtpt) cc_final: 0.8185 (mmmt) REVERT: C 982 ASP cc_start: 0.7592 (m-30) cc_final: 0.7153 (m-30) REVERT: C 985 GLU cc_start: 0.7656 (mp0) cc_final: 0.7014 (tm-30) REVERT: C 1141 GLU cc_start: 0.8655 (mm-30) cc_final: 0.8379 (mm-30) REVERT: L 24 ARG cc_start: 0.8303 (tpp-160) cc_final: 0.7938 (ttm110) REVERT: L 27 GLN cc_start: 0.8250 (mt0) cc_final: 0.7903 (mt0) REVERT: L 80 GLU cc_start: 0.6986 (mm-30) cc_final: 0.6022 (mp0) REVERT: L 82 GLU cc_start: 0.8453 (pm20) cc_final: 0.8237 (pm20) REVERT: L 109 LYS cc_start: 0.8164 (tppp) cc_final: 0.7908 (tppp) REVERT: H 82 GLU cc_start: 0.8231 (tt0) cc_final: 0.7972 (tt0) REVERT: H 180 LEU cc_start: 0.9234 (mm) cc_final: 0.9010 (mm) REVERT: H 183 LEU cc_start: 0.7733 (pp) cc_final: 0.7508 (pt) REVERT: F 107 GLU cc_start: 0.7679 (pt0) cc_final: 0.7096 (tt0) REVERT: E 23 LYS cc_start: 0.8388 (mttt) cc_final: 0.7327 (mtpm) REVERT: E 63 LYS cc_start: 0.8986 (mtpp) cc_final: 0.8700 (mttp) REVERT: K 27 GLN cc_start: 0.8278 (OUTLIER) cc_final: 0.7939 (mp10) REVERT: K 55 ARG cc_start: 0.8512 (mtm110) cc_final: 0.8001 (mtm-85) REVERT: K 94 THR cc_start: 0.8766 (OUTLIER) cc_final: 0.8132 (p) REVERT: K 145 GLU cc_start: 0.8570 (mp0) cc_final: 0.8285 (pm20) REVERT: J 67 ARG cc_start: 0.8238 (ptm160) cc_final: 0.8008 (ptm160) REVERT: J 180 LEU cc_start: 0.8919 (mt) cc_final: 0.8190 (tt) outliers start: 94 outliers final: 49 residues processed: 416 average time/residue: 0.7528 time to fit residues: 371.5755 Evaluate side-chains 399 residues out of total 3751 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 336 time to evaluate : 1.421 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 52 GLN Chi-restraints excluded: chain A residue 63 THR Chi-restraints excluded: chain A residue 81 ASN Chi-restraints excluded: chain A residue 84 LEU Chi-restraints excluded: chain A residue 268 GLN Chi-restraints excluded: chain A residue 299 THR Chi-restraints excluded: chain A residue 311 GLN Chi-restraints excluded: chain A residue 520 THR Chi-restraints excluded: chain A residue 544 THR Chi-restraints excluded: chain A residue 550 THR Chi-restraints excluded: chain A residue 612 VAL Chi-restraints excluded: chain A residue 639 VAL Chi-restraints excluded: chain A residue 716 THR Chi-restraints excluded: chain A residue 720 THR Chi-restraints excluded: chain A residue 721 THR Chi-restraints excluded: chain A residue 777 GLU Chi-restraints excluded: chain A residue 805 ASP Chi-restraints excluded: chain A residue 875 LEU Chi-restraints excluded: chain A residue 897 MET Chi-restraints excluded: chain A residue 926 SER Chi-restraints excluded: chain A residue 954 GLN Chi-restraints excluded: chain A residue 1007 GLN Chi-restraints excluded: chain A residue 1138 LEU Chi-restraints excluded: chain B residue 51 THR Chi-restraints excluded: chain B residue 281 THR Chi-restraints excluded: chain B residue 322 SER Chi-restraints excluded: chain B residue 347 VAL Chi-restraints excluded: chain B residue 431 ILE Chi-restraints excluded: chain B residue 579 LEU Chi-restraints excluded: chain B residue 612 VAL Chi-restraints excluded: chain B residue 737 MET Chi-restraints excluded: chain B residue 744 THR Chi-restraints excluded: chain B residue 788 THR Chi-restraints excluded: chain B residue 875 LEU Chi-restraints excluded: chain B residue 961 LYS Chi-restraints excluded: chain B residue 1089 GLU Chi-restraints excluded: chain C residue 45 SER Chi-restraints excluded: chain C residue 46 SER Chi-restraints excluded: chain C residue 48 LEU Chi-restraints excluded: chain C residue 268 GLN Chi-restraints excluded: chain C residue 304 THR Chi-restraints excluded: chain C residue 322 SER Chi-restraints excluded: chain C residue 359 VAL Chi-restraints excluded: chain C residue 412 THR Chi-restraints excluded: chain C residue 424 ASP Chi-restraints excluded: chain C residue 455 LYS Chi-restraints excluded: chain C residue 543 LEU Chi-restraints excluded: chain C residue 568 ASP Chi-restraints excluded: chain C residue 612 VAL Chi-restraints excluded: chain C residue 716 THR Chi-restraints excluded: chain C residue 875 LEU Chi-restraints excluded: chain C residue 897 MET Chi-restraints excluded: chain C residue 991 ASP Chi-restraints excluded: chain L residue 34 LEU Chi-restraints excluded: chain L residue 86 VAL Chi-restraints excluded: chain F residue 167 GLU Chi-restraints excluded: chain E residue 183 LEU Chi-restraints excluded: chain K residue 27 GLN Chi-restraints excluded: chain K residue 34 LEU Chi-restraints excluded: chain K residue 94 THR Chi-restraints excluded: chain J residue 112 THR Chi-restraints excluded: chain J residue 214 LYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 427 random chunks: chunk 18 optimal weight: 9.9990 chunk 15 optimal weight: 0.2980 chunk 416 optimal weight: 0.9980 chunk 5 optimal weight: 0.8980 chunk 114 optimal weight: 5.9990 chunk 6 optimal weight: 5.9990 chunk 187 optimal weight: 2.9990 chunk 193 optimal weight: 2.9990 chunk 61 optimal weight: 0.6980 chunk 243 optimal weight: 3.9990 chunk 312 optimal weight: 30.0000 overall best weight: 1.1782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 81 ASN B 196 ASN B 391 ASN B 761 ASN B1116 ASN C 999 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4351 r_free = 0.4351 target = 0.202871 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 70)----------------| | r_work = 0.3765 r_free = 0.3765 target = 0.141347 restraints weight = 41399.925| |-----------------------------------------------------------------------------| r_work (start): 0.3600 rms_B_bonded: 2.87 r_work: 0.3275 rms_B_bonded: 2.33 restraints_weight: 0.5000 r_work: 0.3151 rms_B_bonded: 3.68 restraints_weight: 0.2500 r_work (final): 0.3151 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8684 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 0.047 35226 Z= 0.153 Angle : 0.564 11.499 48094 Z= 0.283 Chirality : 0.045 0.398 5665 Planarity : 0.004 0.069 6049 Dihedral : 4.724 57.641 4631 Min Nonbonded Distance : 2.287 Molprobity Statistics. All-atom Clashscore : 5.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.05 % Favored : 96.95 % Rotamer: Outliers : 2.06 % Allowed : 11.96 % Favored : 85.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.33 % Cis-general : 0.00 % Twisted Proline : 0.44 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.53 (0.13), residues: 4267 helix: 1.42 (0.19), residues: 752 sheet: 0.59 (0.14), residues: 1305 loop : -0.10 (0.13), residues: 2210 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.017 0.000 ARG K 3 TYR 0.025 0.001 TYR C 366 PHE 0.023 0.001 PHE B 397 TRP 0.013 0.001 TRP E 108 HIS 0.005 0.001 HIS B 207 Details of bonding type rmsd/Z covalent geometry : bond 0.00357 / 0.15 (35101) covalent geometry : angle 0.54787 / 0.28 (47770) SS BOND : bond 0.00275 / 0.18 ( 51) SS BOND : angle 0.94044 / 0.63 ( 102) hydrogen bonds : bond 0.04025 / 2.59 ( 1435) hydrogen bonds : angle 5.38102 / 3.71 ( 3981) link_ALPHA1-2 : bond 0.00776 / 0.38 ( 3) link_ALPHA1-2 : angle 3.02642 / 1.54 ( 9) link_ALPHA1-3 : bond 0.00508 / 0.25 ( 3) link_ALPHA1-3 : angle 1.82095 / 0.94 ( 9) link_ALPHA1-6 : bond 0.00522 / 0.26 ( 2) link_ALPHA1-6 : angle 1.42338 / 0.77 ( 6) link_BETA1-4 : bond 0.00334 / 0.20 ( 20) link_BETA1-4 : angle 1.01374 / 0.68 ( 60) link_BETA1-6 : bond 0.00149 / 0.07 ( 3) link_BETA1-6 : angle 1.31302 / 0.69 ( 9) link_NAG-ASN : bond 0.00185 / 0.12 ( 43) link_NAG-ASN : angle 2.24316 / 1.56 ( 129) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8534 Ramachandran restraints generated. 4267 Oldfield, 0 Emsley, 4267 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8534 Ramachandran restraints generated. 4267 Oldfield, 0 Emsley, 4267 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 430 residues out of total 3751 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 353 time to evaluate : 1.160 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 52 GLN cc_start: 0.8508 (OUTLIER) cc_final: 0.8100 (tt0) REVERT: A 63 THR cc_start: 0.7506 (OUTLIER) cc_final: 0.6855 (p) REVERT: A 266 TYR cc_start: 0.7668 (m-80) cc_final: 0.7332 (m-80) REVERT: A 268 GLN cc_start: 0.8066 (OUTLIER) cc_final: 0.7774 (mt0) REVERT: A 311 GLN cc_start: 0.8719 (OUTLIER) cc_final: 0.8384 (tm-30) REVERT: A 402 ASP cc_start: 0.8082 (m-30) cc_final: 0.7873 (m-30) REVERT: A 449 LEU cc_start: 0.8093 (mt) cc_final: 0.7693 (mt) REVERT: A 787 LYS cc_start: 0.8941 (ptmt) cc_final: 0.7946 (mmpt) REVERT: A 805 ASP cc_start: 0.7441 (OUTLIER) cc_final: 0.6702 (m-30) REVERT: A 954 GLN cc_start: 0.8260 (OUTLIER) cc_final: 0.8040 (tp40) REVERT: A 1007 GLN cc_start: 0.8450 (OUTLIER) cc_final: 0.7653 (mp10) REVERT: B 81 ASN cc_start: 0.7617 (OUTLIER) cc_final: 0.7395 (p0) REVERT: B 129 LYS cc_start: 0.7486 (mttt) cc_final: 0.6826 (mmpt) REVERT: B 237 ARG cc_start: 0.7520 (mtp85) cc_final: 0.7284 (mtm110) REVERT: B 239 GLN cc_start: 0.7248 (tt0) cc_final: 0.6550 (pp30) REVERT: B 375 LYS cc_start: 0.8161 (mttt) cc_final: 0.7246 (mtmt) REVERT: B 445 ASN cc_start: 0.8249 (t0) cc_final: 0.6981 (m110) REVERT: B 526 LYS cc_start: 0.9007 (mttt) cc_final: 0.8360 (mmtt) REVERT: B 658 GLU cc_start: 0.8610 (tt0) cc_final: 0.8247 (tt0) REVERT: B 1089 GLU cc_start: 0.7705 (OUTLIER) cc_final: 0.7123 (mp0) REVERT: C 45 SER cc_start: 0.8761 (OUTLIER) cc_final: 0.8318 (t) REVERT: C 268 GLN cc_start: 0.7370 (OUTLIER) cc_final: 0.7152 (mt0) REVERT: C 403 GLU cc_start: 0.8353 (mt-10) cc_final: 0.7925 (pt0) REVERT: C 490 GLN cc_start: 0.7409 (tp40) cc_final: 0.7160 (tm-30) REVERT: C 733 VAL cc_start: 0.7824 (t) cc_final: 0.7535 (p) REVERT: C 752 GLN cc_start: 0.8359 (mm-40) cc_final: 0.7765 (mm-40) REVERT: C 897 MET cc_start: 0.9211 (OUTLIER) cc_final: 0.8924 (mtp) REVERT: C 982 ASP cc_start: 0.7610 (m-30) cc_final: 0.7177 (m-30) REVERT: C 985 GLU cc_start: 0.7714 (mp0) cc_final: 0.7027 (tm-30) REVERT: C 1141 GLU cc_start: 0.8673 (mm-30) cc_final: 0.8396 (mm-30) REVERT: L 24 ARG cc_start: 0.8311 (tpp-160) cc_final: 0.7969 (ttm110) REVERT: L 27 GLN cc_start: 0.8257 (mt0) cc_final: 0.7930 (mt0) REVERT: L 80 GLU cc_start: 0.7027 (mm-30) cc_final: 0.6104 (mp0) REVERT: L 82 GLU cc_start: 0.8466 (pm20) cc_final: 0.8238 (pm20) REVERT: L 109 LYS cc_start: 0.8194 (tppp) cc_final: 0.7935 (tppp) REVERT: H 82 GLU cc_start: 0.8208 (tt0) cc_final: 0.7970 (tt0) REVERT: H 180 LEU cc_start: 0.9197 (mm) cc_final: 0.8972 (mm) REVERT: H 183 LEU cc_start: 0.7700 (pp) cc_final: 0.7493 (pt) REVERT: F 107 GLU cc_start: 0.7689 (pt0) cc_final: 0.7114 (tt0) REVERT: E 23 LYS cc_start: 0.8405 (mttt) cc_final: 0.7348 (mtpm) REVERT: E 63 LYS cc_start: 0.8969 (mtpp) cc_final: 0.8651 (mttp) REVERT: E 148 LYS cc_start: 0.8513 (tppp) cc_final: 0.8219 (tppt) REVERT: E 183 LEU cc_start: 0.9070 (OUTLIER) cc_final: 0.8343 (mt) REVERT: K 27 GLN cc_start: 0.8315 (OUTLIER) cc_final: 0.8066 (mp10) REVERT: K 55 ARG cc_start: 0.8538 (mtm110) cc_final: 0.8015 (mtm-85) REVERT: K 94 THR cc_start: 0.8772 (OUTLIER) cc_final: 0.8158 (p) REVERT: K 145 GLU cc_start: 0.8571 (mp0) cc_final: 0.8289 (pm20) REVERT: J 81 MET cc_start: 0.8627 (tmm) cc_final: 0.7783 (tmm) REVERT: J 180 LEU cc_start: 0.8913 (mt) cc_final: 0.8183 (tt) outliers start: 77 outliers final: 43 residues processed: 394 average time/residue: 0.7311 time to fit residues: 340.6135 Evaluate side-chains 397 residues out of total 3751 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 339 time to evaluate : 1.241 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 52 GLN Chi-restraints excluded: chain A residue 63 THR Chi-restraints excluded: chain A residue 84 LEU Chi-restraints excluded: chain A residue 268 GLN Chi-restraints excluded: chain A residue 299 THR Chi-restraints excluded: chain A residue 311 GLN Chi-restraints excluded: chain A residue 520 THR Chi-restraints excluded: chain A residue 544 THR Chi-restraints excluded: chain A residue 550 THR Chi-restraints excluded: chain A residue 612 VAL Chi-restraints excluded: chain A residue 639 VAL Chi-restraints excluded: chain A residue 716 THR Chi-restraints excluded: chain A residue 720 THR Chi-restraints excluded: chain A residue 721 THR Chi-restraints excluded: chain A residue 777 GLU Chi-restraints excluded: chain A residue 805 ASP Chi-restraints excluded: chain A residue 875 LEU Chi-restraints excluded: chain A residue 897 MET Chi-restraints excluded: chain A residue 926 SER Chi-restraints excluded: chain A residue 954 GLN Chi-restraints excluded: chain A residue 1007 GLN Chi-restraints excluded: chain A residue 1138 LEU Chi-restraints excluded: chain B residue 51 THR Chi-restraints excluded: chain B residue 81 ASN Chi-restraints excluded: chain B residue 281 THR Chi-restraints excluded: chain B residue 347 VAL Chi-restraints excluded: chain B residue 579 LEU Chi-restraints excluded: chain B residue 599 THR Chi-restraints excluded: chain B residue 612 VAL Chi-restraints excluded: chain B residue 737 MET Chi-restraints excluded: chain B residue 744 THR Chi-restraints excluded: chain B residue 788 THR Chi-restraints excluded: chain B residue 875 LEU Chi-restraints excluded: chain B residue 961 LYS Chi-restraints excluded: chain B residue 1089 GLU Chi-restraints excluded: chain C residue 45 SER Chi-restraints excluded: chain C residue 48 LEU Chi-restraints excluded: chain C residue 268 GLN Chi-restraints excluded: chain C residue 295 GLU Chi-restraints excluded: chain C residue 304 THR Chi-restraints excluded: chain C residue 322 SER Chi-restraints excluded: chain C residue 359 VAL Chi-restraints excluded: chain C residue 412 THR Chi-restraints excluded: chain C residue 543 LEU Chi-restraints excluded: chain C residue 568 ASP Chi-restraints excluded: chain C residue 716 THR Chi-restraints excluded: chain C residue 875 LEU Chi-restraints excluded: chain C residue 897 MET Chi-restraints excluded: chain C residue 991 ASP Chi-restraints excluded: chain L residue 34 LEU Chi-restraints excluded: chain L residue 86 VAL Chi-restraints excluded: chain F residue 167 GLU Chi-restraints excluded: chain E residue 183 LEU Chi-restraints excluded: chain K residue 27 GLN Chi-restraints excluded: chain K residue 34 LEU Chi-restraints excluded: chain K residue 94 THR Chi-restraints excluded: chain J residue 214 LYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 427 random chunks: chunk 417 optimal weight: 0.0670 chunk 268 optimal weight: 0.6980 chunk 70 optimal weight: 6.9990 chunk 247 optimal weight: 4.9990 chunk 13 optimal weight: 0.8980 chunk 28 optimal weight: 0.7980 chunk 42 optimal weight: 0.7980 chunk 301 optimal weight: 7.9990 chunk 400 optimal weight: 0.0060 chunk 80 optimal weight: 1.9990 chunk 378 optimal weight: 30.0000 overall best weight: 0.4734 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 81 ASN B 196 ASN B 391 ASN B1116 ASN C 801 GLN C 932 GLN C 999 GLN L 162 GLN ** F 200 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4365 r_free = 0.4365 target = 0.203433 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 73)----------------| | r_work = 0.3794 r_free = 0.3794 target = 0.142797 restraints weight = 41425.308| |-----------------------------------------------------------------------------| r_work (start): 0.3658 rms_B_bonded: 2.83 r_work: 0.3358 rms_B_bonded: 2.29 restraints_weight: 0.5000 r_work: 0.3238 rms_B_bonded: 3.60 restraints_weight: 0.2500 r_work (final): 0.3238 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8624 moved from start: 0.2109 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.059 35226 Z= 0.106 Angle : 0.536 14.852 48094 Z= 0.270 Chirality : 0.044 0.442 5665 Planarity : 0.004 0.049 6049 Dihedral : 4.460 56.443 4630 Min Nonbonded Distance : 2.385 Molprobity Statistics. All-atom Clashscore : 4.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.62 % Favored : 97.38 % Rotamer: Outliers : 1.77 % Allowed : 12.49 % Favored : 85.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.68 (0.13), residues: 4267 helix: 1.69 (0.20), residues: 746 sheet: 0.70 (0.14), residues: 1294 loop : -0.05 (0.13), residues: 2227 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG A 316 TYR 0.028 0.001 TYR C 366 PHE 0.021 0.001 PHE B 397 TRP 0.017 0.001 TRP E 108 HIS 0.003 0.001 HIS B 207 Details of bonding type rmsd/Z covalent geometry : bond 0.00241 / 0.11 (35101) covalent geometry : angle 0.52187 / 0.27 (47770) SS BOND : bond 0.00208 / 0.14 ( 51) SS BOND : angle 0.78859 / 0.52 ( 102) hydrogen bonds : bond 0.03458 / 2.23 ( 1435) hydrogen bonds : angle 5.17099 / 3.57 ( 3981) link_ALPHA1-2 : bond 0.00828 / 0.40 ( 3) link_ALPHA1-2 : angle 2.77322 / 1.37 ( 9) link_ALPHA1-3 : bond 0.00504 / 0.24 ( 3) link_ALPHA1-3 : angle 1.74768 / 0.90 ( 9) link_ALPHA1-6 : bond 0.00519 / 0.26 ( 2) link_ALPHA1-6 : angle 1.41497 / 0.76 ( 6) link_BETA1-4 : bond 0.00379 / 0.23 ( 20) link_BETA1-4 : angle 0.97923 / 0.66 ( 60) link_BETA1-6 : bond 0.00191 / 0.09 ( 3) link_BETA1-6 : angle 1.21919 / 0.64 ( 9) link_NAG-ASN : bond 0.00212 / 0.13 ( 43) link_NAG-ASN : angle 2.10567 / 1.38 ( 129) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8534 Ramachandran restraints generated. 4267 Oldfield, 0 Emsley, 4267 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8534 Ramachandran restraints generated. 4267 Oldfield, 0 Emsley, 4267 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 442 residues out of total 3751 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 376 time to evaluate : 1.366 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 52 GLN cc_start: 0.8477 (OUTLIER) cc_final: 0.8062 (tt0) REVERT: A 63 THR cc_start: 0.7492 (OUTLIER) cc_final: 0.6908 (p) REVERT: A 266 TYR cc_start: 0.7605 (m-80) cc_final: 0.7346 (m-80) REVERT: A 268 GLN cc_start: 0.8075 (OUTLIER) cc_final: 0.7825 (mt0) REVERT: A 311 GLN cc_start: 0.8672 (OUTLIER) cc_final: 0.8339 (tm-30) REVERT: A 402 ASP cc_start: 0.8070 (m-30) cc_final: 0.7836 (m-30) REVERT: A 449 LEU cc_start: 0.8094 (mt) cc_final: 0.7690 (mt) REVERT: A 787 LYS cc_start: 0.8879 (ptmt) cc_final: 0.7934 (mmpt) REVERT: A 805 ASP cc_start: 0.7363 (m-30) cc_final: 0.6685 (m-30) REVERT: A 918 LYS cc_start: 0.8641 (mmpt) cc_final: 0.8370 (mtpp) REVERT: A 954 GLN cc_start: 0.8221 (OUTLIER) cc_final: 0.7999 (tp40) REVERT: A 1007 GLN cc_start: 0.8428 (OUTLIER) cc_final: 0.7567 (mp10) REVERT: B 81 ASN cc_start: 0.7634 (OUTLIER) cc_final: 0.7393 (p0) REVERT: B 129 LYS cc_start: 0.7584 (mttt) cc_final: 0.6894 (mmpt) REVERT: B 237 ARG cc_start: 0.7467 (mtp85) cc_final: 0.7235 (mtm110) REVERT: B 239 GLN cc_start: 0.7224 (tt0) cc_final: 0.6741 (pp30) REVERT: B 375 LYS cc_start: 0.8167 (mttt) cc_final: 0.7236 (mtmt) REVERT: B 445 ASN cc_start: 0.8265 (t0) cc_final: 0.7001 (m110) REVERT: B 526 LYS cc_start: 0.8976 (mttt) cc_final: 0.8344 (mmpt) REVERT: B 658 GLU cc_start: 0.8569 (tt0) cc_final: 0.8085 (tm-30) REVERT: B 947 ASP cc_start: 0.8275 (t0) cc_final: 0.7794 (m-30) REVERT: B 1089 GLU cc_start: 0.7582 (OUTLIER) cc_final: 0.7000 (mp0) REVERT: B 1125 VAL cc_start: 0.9054 (t) cc_final: 0.8791 (p) REVERT: C 45 SER cc_start: 0.8797 (OUTLIER) cc_final: 0.8380 (t) REVERT: C 403 GLU cc_start: 0.8268 (mt-10) cc_final: 0.7832 (pt0) REVERT: C 487 PHE cc_start: 0.7043 (t80) cc_final: 0.6556 (t80) REVERT: C 490 GLN cc_start: 0.7344 (tp40) cc_final: 0.7052 (tm-30) REVERT: C 564 ARG cc_start: 0.8327 (mtt90) cc_final: 0.8026 (mmt90) REVERT: C 733 VAL cc_start: 0.7903 (t) cc_final: 0.7580 (p) REVERT: C 737 MET cc_start: 0.8511 (OUTLIER) cc_final: 0.8048 (ttt) REVERT: C 752 GLN cc_start: 0.8336 (mm-40) cc_final: 0.7776 (mm-40) REVERT: C 985 GLU cc_start: 0.7715 (mp0) cc_final: 0.6957 (tm-30) REVERT: L 24 ARG cc_start: 0.8314 (tpp-160) cc_final: 0.7980 (ttm110) REVERT: L 27 GLN cc_start: 0.8267 (mt0) cc_final: 0.7973 (mt0) REVERT: L 80 GLU cc_start: 0.7005 (mm-30) cc_final: 0.6060 (mp0) REVERT: L 147 LYS cc_start: 0.8773 (tppt) cc_final: 0.8288 (tptt) REVERT: H 82 GLU cc_start: 0.8186 (tt0) cc_final: 0.7961 (tt0) REVERT: H 180 LEU cc_start: 0.9169 (mm) cc_final: 0.8496 (mt) REVERT: F 82 GLU cc_start: 0.7467 (mm-30) cc_final: 0.7208 (mm-30) REVERT: F 107 GLU cc_start: 0.7677 (pt0) cc_final: 0.7069 (tt0) REVERT: E 23 LYS cc_start: 0.8383 (mttt) cc_final: 0.7328 (mtpm) REVERT: E 63 LYS cc_start: 0.8943 (mtpp) cc_final: 0.8662 (mttp) REVERT: E 148 LYS cc_start: 0.8668 (tppp) cc_final: 0.8405 (tppt) REVERT: E 183 LEU cc_start: 0.9066 (OUTLIER) cc_final: 0.8318 (mt) REVERT: K 145 GLU cc_start: 0.8510 (mp0) cc_final: 0.8290 (pm20) REVERT: J 81 MET cc_start: 0.8615 (tmm) cc_final: 0.7739 (tmm) REVERT: J 180 LEU cc_start: 0.8915 (mt) cc_final: 0.8201 (tt) outliers start: 66 outliers final: 31 residues processed: 414 average time/residue: 0.7092 time to fit residues: 348.3557 Evaluate side-chains 379 residues out of total 3751 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 337 time to evaluate : 1.274 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 THR Chi-restraints excluded: chain A residue 52 GLN Chi-restraints excluded: chain A residue 63 THR Chi-restraints excluded: chain A residue 268 GLN Chi-restraints excluded: chain A residue 311 GLN Chi-restraints excluded: chain A residue 550 THR Chi-restraints excluded: chain A residue 612 VAL Chi-restraints excluded: chain A residue 639 VAL Chi-restraints excluded: chain A residue 720 THR Chi-restraints excluded: chain A residue 777 GLU Chi-restraints excluded: chain A residue 788 THR Chi-restraints excluded: chain A residue 875 LEU Chi-restraints excluded: chain A residue 897 MET Chi-restraints excluded: chain A residue 954 GLN Chi-restraints excluded: chain A residue 1007 GLN Chi-restraints excluded: chain A residue 1138 LEU Chi-restraints excluded: chain B residue 51 THR Chi-restraints excluded: chain B residue 81 ASN Chi-restraints excluded: chain B residue 347 VAL Chi-restraints excluded: chain B residue 599 THR Chi-restraints excluded: chain B residue 612 VAL Chi-restraints excluded: chain B residue 737 MET Chi-restraints excluded: chain B residue 788 THR Chi-restraints excluded: chain B residue 875 LEU Chi-restraints excluded: chain B residue 961 LYS Chi-restraints excluded: chain B residue 1089 GLU Chi-restraints excluded: chain C residue 45 SER Chi-restraints excluded: chain C residue 46 SER Chi-restraints excluded: chain C residue 48 LEU Chi-restraints excluded: chain C residue 322 SER Chi-restraints excluded: chain C residue 359 VAL Chi-restraints excluded: chain C residue 543 LEU Chi-restraints excluded: chain C residue 737 MET Chi-restraints excluded: chain C residue 875 LEU Chi-restraints excluded: chain C residue 991 ASP Chi-restraints excluded: chain L residue 34 LEU Chi-restraints excluded: chain L residue 86 VAL Chi-restraints excluded: chain E residue 183 LEU Chi-restraints excluded: chain K residue 34 LEU Chi-restraints excluded: chain K residue 94 THR Chi-restraints excluded: chain J residue 112 THR Chi-restraints excluded: chain J residue 214 LYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 427 random chunks: chunk 375 optimal weight: 20.0000 chunk 162 optimal weight: 0.4980 chunk 252 optimal weight: 8.9990 chunk 303 optimal weight: 0.6980 chunk 406 optimal weight: 6.9990 chunk 188 optimal weight: 0.7980 chunk 135 optimal weight: 6.9990 chunk 195 optimal weight: 0.7980 chunk 22 optimal weight: 0.8980 chunk 25 optimal weight: 0.0970 chunk 328 optimal weight: 0.5980 overall best weight: 0.5378 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 196 ASN ** B 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 391 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 561 GLN C 999 GLN ** F 200 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4379 r_free = 0.4379 target = 0.204445 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 68)----------------| | r_work = 0.3809 r_free = 0.3809 target = 0.144180 restraints weight = 41285.400| |-----------------------------------------------------------------------------| r_work (start): 0.3665 rms_B_bonded: 2.67 r_work: 0.3358 rms_B_bonded: 2.30 restraints_weight: 0.5000 r_work: 0.3239 rms_B_bonded: 3.62 restraints_weight: 0.2500 r_work (final): 0.3239 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8627 moved from start: 0.2220 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 35226 Z= 0.110 Angle : 0.546 16.778 48094 Z= 0.274 Chirality : 0.044 0.589 5665 Planarity : 0.004 0.057 6049 Dihedral : 4.415 55.250 4630 Min Nonbonded Distance : 2.368 Molprobity Statistics. All-atom Clashscore : 5.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.74 % Favored : 97.26 % Rotamer: Outliers : 1.44 % Allowed : 13.19 % Favored : 85.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.74 (0.13), residues: 4267 helix: 1.78 (0.20), residues: 739 sheet: 0.72 (0.14), residues: 1308 loop : -0.02 (0.13), residues: 2220 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.000 ARG A 316 TYR 0.023 0.001 TYR B 450 PHE 0.025 0.001 PHE B 397 TRP 0.010 0.001 TRP E 108 HIS 0.003 0.001 HIS B 207 Details of bonding type rmsd/Z covalent geometry : bond 0.00251 / 0.11 (35101) covalent geometry : angle 0.53087 / 0.27 (47770) SS BOND : bond 0.00211 / 0.15 ( 51) SS BOND : angle 0.77408 / 0.52 ( 102) hydrogen bonds : bond 0.03461 / 2.23 ( 1435) hydrogen bonds : angle 5.09439 / 3.52 ( 3981) link_ALPHA1-2 : bond 0.00832 / 0.40 ( 3) link_ALPHA1-2 : angle 2.76760 / 1.37 ( 9) link_ALPHA1-3 : bond 0.00510 / 0.25 ( 3) link_ALPHA1-3 : angle 1.72124 / 0.89 ( 9) link_ALPHA1-6 : bond 0.00514 / 0.26 ( 2) link_ALPHA1-6 : angle 1.40837 / 0.75 ( 6) link_BETA1-4 : bond 0.00369 / 0.23 ( 20) link_BETA1-4 : angle 0.98441 / 0.66 ( 60) link_BETA1-6 : bond 0.00196 / 0.09 ( 3) link_BETA1-6 : angle 1.23854 / 0.65 ( 9) link_NAG-ASN : bond 0.00195 / 0.12 ( 43) link_NAG-ASN : angle 2.22333 / 1.45 ( 129) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8534 Ramachandran restraints generated. 4267 Oldfield, 0 Emsley, 4267 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8534 Ramachandran restraints generated. 4267 Oldfield, 0 Emsley, 4267 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 401 residues out of total 3751 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 347 time to evaluate : 1.263 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 52 GLN cc_start: 0.8499 (OUTLIER) cc_final: 0.8087 (tt0) REVERT: A 63 THR cc_start: 0.7524 (OUTLIER) cc_final: 0.6952 (p) REVERT: A 266 TYR cc_start: 0.7591 (m-80) cc_final: 0.7371 (m-80) REVERT: A 268 GLN cc_start: 0.8091 (OUTLIER) cc_final: 0.7857 (mt0) REVERT: A 311 GLN cc_start: 0.8694 (OUTLIER) cc_final: 0.8367 (tm-30) REVERT: A 402 ASP cc_start: 0.8046 (m-30) cc_final: 0.7823 (m-30) REVERT: A 449 LEU cc_start: 0.8135 (mt) cc_final: 0.7726 (mt) REVERT: A 787 LYS cc_start: 0.8897 (ptmt) cc_final: 0.7985 (mmpt) REVERT: A 805 ASP cc_start: 0.7351 (m-30) cc_final: 0.6691 (m-30) REVERT: A 918 LYS cc_start: 0.8641 (mmpt) cc_final: 0.8379 (mtpp) REVERT: A 954 GLN cc_start: 0.8255 (OUTLIER) cc_final: 0.8042 (tp40) REVERT: A 1007 GLN cc_start: 0.8426 (OUTLIER) cc_final: 0.7560 (mp10) REVERT: B 81 ASN cc_start: 0.7659 (OUTLIER) cc_final: 0.7404 (p0) REVERT: B 129 LYS cc_start: 0.7533 (mttt) cc_final: 0.6890 (mmpt) REVERT: B 237 ARG cc_start: 0.7463 (mtp85) cc_final: 0.7222 (mtm110) REVERT: B 239 GLN cc_start: 0.7237 (tt0) cc_final: 0.6763 (pp30) REVERT: B 375 LYS cc_start: 0.8124 (mttt) cc_final: 0.7190 (mtmt) REVERT: B 526 LYS cc_start: 0.8989 (mttt) cc_final: 0.8379 (mmpt) REVERT: B 658 GLU cc_start: 0.8589 (tt0) cc_final: 0.8224 (tt0) REVERT: B 947 ASP cc_start: 0.8321 (t0) cc_final: 0.7857 (m-30) REVERT: B 1125 VAL cc_start: 0.9044 (t) cc_final: 0.8800 (p) REVERT: C 45 SER cc_start: 0.8791 (OUTLIER) cc_final: 0.8402 (t) REVERT: C 268 GLN cc_start: 0.7368 (OUTLIER) cc_final: 0.7135 (mt0) REVERT: C 403 GLU cc_start: 0.8266 (mt-10) cc_final: 0.7844 (pt0) REVERT: C 490 GLN cc_start: 0.7342 (tp40) cc_final: 0.7104 (tm-30) REVERT: C 564 ARG cc_start: 0.8311 (mtt90) cc_final: 0.8030 (mmt90) REVERT: C 733 VAL cc_start: 0.7768 (t) cc_final: 0.7470 (p) REVERT: C 737 MET cc_start: 0.8572 (OUTLIER) cc_final: 0.8137 (ttt) REVERT: C 752 GLN cc_start: 0.8325 (mm-40) cc_final: 0.7773 (mm-40) REVERT: C 985 GLU cc_start: 0.7733 (mp0) cc_final: 0.7018 (tm-30) REVERT: C 1141 GLU cc_start: 0.8700 (mm-30) cc_final: 0.8334 (mm-30) REVERT: L 24 ARG cc_start: 0.8321 (tpp-160) cc_final: 0.7990 (ttm110) REVERT: L 27 GLN cc_start: 0.8267 (mt0) cc_final: 0.8010 (mt0) REVERT: L 80 GLU cc_start: 0.7034 (mm-30) cc_final: 0.6127 (mp0) REVERT: L 147 LYS cc_start: 0.8760 (tppt) cc_final: 0.8291 (tptt) REVERT: H 180 LEU cc_start: 0.9167 (mm) cc_final: 0.8501 (mt) REVERT: F 82 GLU cc_start: 0.7468 (mm-30) cc_final: 0.7214 (mm-30) REVERT: F 107 GLU cc_start: 0.7684 (pt0) cc_final: 0.7031 (tt0) REVERT: E 183 LEU cc_start: 0.9069 (OUTLIER) cc_final: 0.8334 (mt) REVERT: J 180 LEU cc_start: 0.8918 (mt) cc_final: 0.8206 (tt) outliers start: 54 outliers final: 33 residues processed: 383 average time/residue: 0.7441 time to fit residues: 337.9222 Evaluate side-chains 377 residues out of total 3751 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 333 time to evaluate : 1.319 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 THR Chi-restraints excluded: chain A residue 52 GLN Chi-restraints excluded: chain A residue 63 THR Chi-restraints excluded: chain A residue 268 GLN Chi-restraints excluded: chain A residue 311 GLN Chi-restraints excluded: chain A residue 550 THR Chi-restraints excluded: chain A residue 612 VAL Chi-restraints excluded: chain A residue 639 VAL Chi-restraints excluded: chain A residue 701 SER Chi-restraints excluded: chain A residue 720 THR Chi-restraints excluded: chain A residue 777 GLU Chi-restraints excluded: chain A residue 788 THR Chi-restraints excluded: chain A residue 875 LEU Chi-restraints excluded: chain A residue 897 MET Chi-restraints excluded: chain A residue 954 GLN Chi-restraints excluded: chain A residue 1007 GLN Chi-restraints excluded: chain A residue 1138 LEU Chi-restraints excluded: chain B residue 51 THR Chi-restraints excluded: chain B residue 81 ASN Chi-restraints excluded: chain B residue 322 SER Chi-restraints excluded: chain B residue 347 VAL Chi-restraints excluded: chain B residue 599 THR Chi-restraints excluded: chain B residue 612 VAL Chi-restraints excluded: chain B residue 737 MET Chi-restraints excluded: chain B residue 875 LEU Chi-restraints excluded: chain B residue 961 LYS Chi-restraints excluded: chain C residue 45 SER Chi-restraints excluded: chain C residue 46 SER Chi-restraints excluded: chain C residue 48 LEU Chi-restraints excluded: chain C residue 268 GLN Chi-restraints excluded: chain C residue 295 GLU Chi-restraints excluded: chain C residue 322 SER Chi-restraints excluded: chain C residue 359 VAL Chi-restraints excluded: chain C residue 543 LEU Chi-restraints excluded: chain C residue 737 MET Chi-restraints excluded: chain C residue 875 LEU Chi-restraints excluded: chain C residue 991 ASP Chi-restraints excluded: chain L residue 34 LEU Chi-restraints excluded: chain L residue 86 VAL Chi-restraints excluded: chain E residue 183 LEU Chi-restraints excluded: chain K residue 34 LEU Chi-restraints excluded: chain K residue 94 THR Chi-restraints excluded: chain J residue 112 THR Chi-restraints excluded: chain J residue 214 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 427 random chunks: chunk 20 optimal weight: 3.9990 chunk 149 optimal weight: 7.9990 chunk 206 optimal weight: 9.9990 chunk 86 optimal weight: 1.9990 chunk 132 optimal weight: 7.9990 chunk 123 optimal weight: 3.9990 chunk 171 optimal weight: 0.3980 chunk 272 optimal weight: 0.0040 chunk 15 optimal weight: 0.0010 chunk 211 optimal weight: 5.9990 chunk 276 optimal weight: 0.7980 overall best weight: 0.6400 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 196 ASN ** B 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 391 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 951 GLN C 561 GLN C 801 GLN C 952 ASN C 999 GLN ** F 200 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4379 r_free = 0.4379 target = 0.204492 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 82)----------------| | r_work = 0.3787 r_free = 0.3787 target = 0.142580 restraints weight = 41334.269| |-----------------------------------------------------------------------------| r_work (start): 0.3603 rms_B_bonded: 2.89 r_work: 0.3315 rms_B_bonded: 2.27 restraints_weight: 0.5000 r_work: 0.3197 rms_B_bonded: 3.59 restraints_weight: 0.2500 r_work (final): 0.3197 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8622 moved from start: 0.2259 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 35226 Z= 0.116 Angle : 0.556 15.450 48094 Z= 0.279 Chirality : 0.044 0.555 5665 Planarity : 0.004 0.060 6049 Dihedral : 4.388 53.835 4629 Min Nonbonded Distance : 2.392 Molprobity Statistics. All-atom Clashscore : 5.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.74 % Favored : 97.26 % Rotamer: Outliers : 1.28 % Allowed : 13.37 % Favored : 85.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.76 (0.13), residues: 4267 helix: 1.82 (0.20), residues: 733 sheet: 0.75 (0.14), residues: 1309 loop : -0.02 (0.13), residues: 2225 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.000 ARG A 316 TYR 0.025 0.001 TYR B 450 PHE 0.023 0.001 PHE B 397 TRP 0.010 0.001 TRP E 108 HIS 0.007 0.001 HIS A 207 Details of bonding type rmsd/Z covalent geometry : bond 0.00269 / 0.12 (35101) covalent geometry : angle 0.54178 / 0.28 (47770) SS BOND : bond 0.00216 / 0.15 ( 51) SS BOND : angle 0.76614 / 0.52 ( 102) hydrogen bonds : bond 0.03482 / 2.24 ( 1435) hydrogen bonds : angle 5.06619 / 3.50 ( 3981) link_ALPHA1-2 : bond 0.00824 / 0.40 ( 3) link_ALPHA1-2 : angle 2.74967 / 1.36 ( 9) link_ALPHA1-3 : bond 0.00515 / 0.25 ( 3) link_ALPHA1-3 : angle 1.72162 / 0.89 ( 9) link_ALPHA1-6 : bond 0.00508 / 0.26 ( 2) link_ALPHA1-6 : angle 1.40582 / 0.75 ( 6) link_BETA1-4 : bond 0.00370 / 0.23 ( 20) link_BETA1-4 : angle 0.98055 / 0.66 ( 60) link_BETA1-6 : bond 0.00208 / 0.10 ( 3) link_BETA1-6 : angle 1.23591 / 0.65 ( 9) link_NAG-ASN : bond 0.00253 / 0.15 ( 43) link_NAG-ASN : angle 2.12766 / 1.40 ( 129) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8534 Ramachandran restraints generated. 4267 Oldfield, 0 Emsley, 4267 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8534 Ramachandran restraints generated. 4267 Oldfield, 0 Emsley, 4267 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 398 residues out of total 3751 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 350 time to evaluate : 1.389 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 52 GLN cc_start: 0.8489 (OUTLIER) cc_final: 0.8109 (tt0) REVERT: A 63 THR cc_start: 0.7546 (OUTLIER) cc_final: 0.7003 (p) REVERT: A 266 TYR cc_start: 0.7581 (m-80) cc_final: 0.7338 (m-80) REVERT: A 268 GLN cc_start: 0.8070 (OUTLIER) cc_final: 0.7755 (mt0) REVERT: A 311 GLN cc_start: 0.8684 (OUTLIER) cc_final: 0.8351 (tm-30) REVERT: A 402 ASP cc_start: 0.8014 (m-30) cc_final: 0.7794 (m-30) REVERT: A 449 LEU cc_start: 0.8154 (mt) cc_final: 0.7774 (mt) REVERT: A 787 LYS cc_start: 0.8892 (ptmt) cc_final: 0.7988 (mmpt) REVERT: A 805 ASP cc_start: 0.7366 (m-30) cc_final: 0.6719 (m-30) REVERT: A 918 LYS cc_start: 0.8642 (mmpt) cc_final: 0.8376 (mtpp) REVERT: A 954 GLN cc_start: 0.8264 (OUTLIER) cc_final: 0.8054 (tp40) REVERT: A 1007 GLN cc_start: 0.8423 (OUTLIER) cc_final: 0.7564 (mp10) REVERT: B 81 ASN cc_start: 0.7681 (OUTLIER) cc_final: 0.7425 (p0) REVERT: B 129 LYS cc_start: 0.7587 (mttt) cc_final: 0.6942 (mmpt) REVERT: B 237 ARG cc_start: 0.7462 (mtp85) cc_final: 0.7215 (mtm110) REVERT: B 239 GLN cc_start: 0.7238 (tt0) cc_final: 0.6523 (pp30) REVERT: B 375 LYS cc_start: 0.8134 (mttt) cc_final: 0.7178 (mtmt) REVERT: B 526 LYS cc_start: 0.8998 (mttt) cc_final: 0.8383 (mmpt) REVERT: B 640 PHE cc_start: 0.7702 (t80) cc_final: 0.7496 (t80) REVERT: B 658 GLU cc_start: 0.8572 (tt0) cc_final: 0.8202 (tt0) REVERT: B 947 ASP cc_start: 0.8330 (t0) cc_final: 0.7883 (m-30) REVERT: B 1125 VAL cc_start: 0.9009 (t) cc_final: 0.8782 (p) REVERT: C 45 SER cc_start: 0.8774 (OUTLIER) cc_final: 0.8428 (t) REVERT: C 268 GLN cc_start: 0.7357 (OUTLIER) cc_final: 0.7119 (mt0) REVERT: C 403 GLU cc_start: 0.8279 (mt-10) cc_final: 0.7836 (pt0) REVERT: C 490 GLN cc_start: 0.7328 (tp40) cc_final: 0.7101 (tm-30) REVERT: C 564 ARG cc_start: 0.8248 (mtt90) cc_final: 0.7987 (mmt90) REVERT: C 733 VAL cc_start: 0.7813 (t) cc_final: 0.7512 (p) REVERT: C 737 MET cc_start: 0.8562 (OUTLIER) cc_final: 0.8122 (ttt) REVERT: C 752 GLN cc_start: 0.8335 (mm-40) cc_final: 0.7786 (mm-40) REVERT: C 985 GLU cc_start: 0.7759 (mp0) cc_final: 0.7082 (tm-30) REVERT: C 1141 GLU cc_start: 0.8684 (mm-30) cc_final: 0.8413 (mm-30) REVERT: L 24 ARG cc_start: 0.8294 (tpp-160) cc_final: 0.7973 (ttm110) REVERT: L 27 GLN cc_start: 0.8253 (mt0) cc_final: 0.7987 (mt0) REVERT: L 80 GLU cc_start: 0.7018 (mm-30) cc_final: 0.6167 (mp0) REVERT: L 147 LYS cc_start: 0.8737 (tppt) cc_final: 0.8275 (tptt) REVERT: H 180 LEU cc_start: 0.9169 (mm) cc_final: 0.8960 (mm) REVERT: F 82 GLU cc_start: 0.7439 (mm-30) cc_final: 0.7182 (mm-30) REVERT: F 107 GLU cc_start: 0.7694 (pt0) cc_final: 0.7052 (tt0) REVERT: E 23 LYS cc_start: 0.8411 (mttt) cc_final: 0.7372 (mtpm) REVERT: E 63 LYS cc_start: 0.8903 (mtpp) cc_final: 0.8638 (mttp) REVERT: E 183 LEU cc_start: 0.9034 (OUTLIER) cc_final: 0.8280 (mt) REVERT: K 27 GLN cc_start: 0.8152 (mp10) cc_final: 0.7936 (mp10) REVERT: J 180 LEU cc_start: 0.8917 (mt) cc_final: 0.8211 (tt) outliers start: 48 outliers final: 33 residues processed: 383 average time/residue: 0.7542 time to fit residues: 342.0569 Evaluate side-chains 375 residues out of total 3751 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 331 time to evaluate : 1.262 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 THR Chi-restraints excluded: chain A residue 52 GLN Chi-restraints excluded: chain A residue 63 THR Chi-restraints excluded: chain A residue 268 GLN Chi-restraints excluded: chain A residue 311 GLN Chi-restraints excluded: chain A residue 550 THR Chi-restraints excluded: chain A residue 612 VAL Chi-restraints excluded: chain A residue 639 VAL Chi-restraints excluded: chain A residue 701 SER Chi-restraints excluded: chain A residue 720 THR Chi-restraints excluded: chain A residue 777 GLU Chi-restraints excluded: chain A residue 788 THR Chi-restraints excluded: chain A residue 875 LEU Chi-restraints excluded: chain A residue 897 MET Chi-restraints excluded: chain A residue 954 GLN Chi-restraints excluded: chain A residue 1007 GLN Chi-restraints excluded: chain A residue 1138 LEU Chi-restraints excluded: chain B residue 51 THR Chi-restraints excluded: chain B residue 81 ASN Chi-restraints excluded: chain B residue 322 SER Chi-restraints excluded: chain B residue 347 VAL Chi-restraints excluded: chain B residue 599 THR Chi-restraints excluded: chain B residue 612 VAL Chi-restraints excluded: chain B residue 737 MET Chi-restraints excluded: chain B residue 875 LEU Chi-restraints excluded: chain B residue 961 LYS Chi-restraints excluded: chain C residue 45 SER Chi-restraints excluded: chain C residue 46 SER Chi-restraints excluded: chain C residue 48 LEU Chi-restraints excluded: chain C residue 268 GLN Chi-restraints excluded: chain C residue 295 GLU Chi-restraints excluded: chain C residue 322 SER Chi-restraints excluded: chain C residue 359 VAL Chi-restraints excluded: chain C residue 716 THR Chi-restraints excluded: chain C residue 737 MET Chi-restraints excluded: chain C residue 875 LEU Chi-restraints excluded: chain C residue 991 ASP Chi-restraints excluded: chain L residue 34 LEU Chi-restraints excluded: chain L residue 86 VAL Chi-restraints excluded: chain E residue 183 LEU Chi-restraints excluded: chain K residue 34 LEU Chi-restraints excluded: chain K residue 94 THR Chi-restraints excluded: chain J residue 112 THR Chi-restraints excluded: chain J residue 214 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 427 random chunks: chunk 344 optimal weight: 30.0000 chunk 120 optimal weight: 0.9980 chunk 101 optimal weight: 10.0000 chunk 338 optimal weight: 0.0870 chunk 407 optimal weight: 4.9990 chunk 158 optimal weight: 3.9990 chunk 224 optimal weight: 0.9990 chunk 32 optimal weight: 3.9990 chunk 397 optimal weight: 2.9990 chunk 295 optimal weight: 1.9990 chunk 110 optimal weight: 10.0000 overall best weight: 1.4164 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 196 ASN ** B 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 391 ASN C 561 GLN C 801 GLN C 932 GLN C 999 GLN ** F 200 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 204 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4363 r_free = 0.4363 target = 0.202930 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 82)----------------| | r_work = 0.3771 r_free = 0.3771 target = 0.141305 restraints weight = 41091.093| |-----------------------------------------------------------------------------| r_work (start): 0.3600 rms_B_bonded: 2.86 r_work: 0.3283 rms_B_bonded: 2.31 restraints_weight: 0.5000 r_work: 0.3161 rms_B_bonded: 3.62 restraints_weight: 0.2500 r_work (final): 0.3161 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8674 moved from start: 0.2214 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 35226 Z= 0.172 Angle : 0.590 14.984 48094 Z= 0.299 Chirality : 0.045 0.490 5665 Planarity : 0.004 0.061 6049 Dihedral : 4.593 53.325 4629 Min Nonbonded Distance : 2.402 Molprobity Statistics. All-atom Clashscore : 5.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.93 % Favored : 97.07 % Rotamer: Outliers : 1.44 % Allowed : 13.45 % Favored : 85.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.66 (0.13), residues: 4267 helix: 1.59 (0.19), residues: 741 sheet: 0.71 (0.14), residues: 1317 loop : -0.06 (0.13), residues: 2209 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG A 316 TYR 0.023 0.001 TYR B 450 PHE 0.022 0.001 PHE C 589 TRP 0.008 0.001 TRP B 433 HIS 0.008 0.001 HIS A 207 Details of bonding type rmsd/Z covalent geometry : bond 0.00410 / 0.17 (35101) covalent geometry : angle 0.57598 / 0.30 (47770) SS BOND : bond 0.00288 / 0.19 ( 51) SS BOND : angle 0.85801 / 0.58 ( 102) hydrogen bonds : bond 0.04000 / 2.57 ( 1435) hydrogen bonds : angle 5.19874 / 3.59 ( 3981) link_ALPHA1-2 : bond 0.00745 / 0.36 ( 3) link_ALPHA1-2 : angle 2.79358 / 1.40 ( 9) link_ALPHA1-3 : bond 0.00524 / 0.26 ( 3) link_ALPHA1-3 : angle 1.75434 / 0.91 ( 9) link_ALPHA1-6 : bond 0.00492 / 0.25 ( 2) link_ALPHA1-6 : angle 1.40937 / 0.75 ( 6) link_BETA1-4 : bond 0.00328 / 0.20 ( 20) link_BETA1-4 : angle 1.01605 / 0.67 ( 60) link_BETA1-6 : bond 0.00152 / 0.07 ( 3) link_BETA1-6 : angle 1.31059 / 0.69 ( 9) link_NAG-ASN : bond 0.00238 / 0.14 ( 43) link_NAG-ASN : angle 2.17996 / 1.42 ( 129) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 18660.09 seconds wall clock time: 316 minutes 59.66 seconds (19019.66 seconds total)