Starting phenix.real_space_refine on Fri Mar 6 15:13:09 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7akj_11813/03_2026/7akj_11813_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/7akj_11813/03_2026/7akj_11813.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7akj_11813/03_2026/7akj_11813_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7akj_11813/03_2026/7akj_11813_neut.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7akj_11813/03_2026/7akj_11813.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7akj_11813/03_2026/7akj_11813.map" } resolution = 3.8 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.002 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 156 5.16 5 C 20211 2.51 5 N 5127 2.21 5 O 6318 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 57 residue(s): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 31812 Number of models: 1 Model: "" Number of chains: 30 Chain: "C" Number of atoms: 8459 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1084, 8459 Classifications: {'peptide': 1084} Link IDs: {'PCIS': 2, 'PTRANS': 53, 'TRANS': 1028} Chain breaks: 4 Chain: "B" Number of atoms: 8459 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1084, 8459 Classifications: {'peptide': 1084} Link IDs: {'PCIS': 2, 'PTRANS': 53, 'TRANS': 1028} Chain breaks: 4 Chain: "G" Number of atoms: 925 Number of conformers: 1 Conformer: "" Number of residues, atoms: 120, 925 Classifications: {'peptide': 120} Link IDs: {'PTRANS': 6, 'TRANS': 113} Chain: "F" Number of atoms: 798 Number of conformers: 1 Conformer: "" Number of residues, atoms: 106, 798 Classifications: {'peptide': 106} Link IDs: {'PCIS': 1, 'PTRANS': 6, 'TRANS': 98} Chain: "E" Number of atoms: 925 Number of conformers: 1 Conformer: "" Number of residues, atoms: 120, 925 Classifications: {'peptide': 120} Link IDs: {'PTRANS': 6, 'TRANS': 113} Chain: "D" Number of atoms: 798 Number of conformers: 1 Conformer: "" Number of residues, atoms: 106, 798 Classifications: {'peptide': 106} Link IDs: {'PCIS': 1, 'PTRANS': 6, 'TRANS': 98} Chain: "A" Number of atoms: 8459 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1084, 8459 Classifications: {'peptide': 1084} Link IDs: {'PCIS': 2, 'PTRANS': 53, 'TRANS': 1028} Chain breaks: 4 Chain: "H" Number of atoms: 925 Number of conformers: 1 Conformer: "" Number of residues, atoms: 120, 925 Classifications: {'peptide': 120} Link IDs: {'PTRANS': 6, 'TRANS': 113} Chain: "L" Number of atoms: 798 Number of conformers: 1 Conformer: "" Number of residues, atoms: 106, 798 Classifications: {'peptide': 106} Link IDs: {'PCIS': 1, 'PTRANS': 6, 'TRANS': 98} 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 dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "J" Number of atoms: 38 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 38 Unusual residues: {'FUC': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "K" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "M" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "N" Number of atoms: 104 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 104 Unusual residues: {'BMA': 1, 'FUC': 1, 'MAN': 5, 'NAG': 2} Classifications: {'undetermined': 9} Link IDs: {None: 8} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 27 Unresolved non-hydrogen chiralities: 9 Chain: "O" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "P" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "Q" Number of atoms: 38 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 38 Unusual residues: {'FUC': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "R" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "S" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "T" Number of atoms: 104 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 104 Unusual residues: {'BMA': 1, 'FUC': 1, 'MAN': 5, 'NAG': 2} Classifications: {'undetermined': 9} Link IDs: {None: 8} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 27 Unresolved non-hydrogen chiralities: 9 Chain: "U" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "V" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "W" Number of atoms: 38 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 38 Unusual residues: {'FUC': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "X" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "Y" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "Z" Number of atoms: 104 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 104 Unusual residues: {'BMA': 1, 'FUC': 1, 'MAN': 5, 'NAG': 2} Classifications: {'undetermined': 9} Link IDs: {None: 8} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 27 Unresolved non-hydrogen chiralities: 9 Chain: "a" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "C" Number of atoms: 168 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 168 Unusual residues: {'NAG': 12} Classifications: {'undetermined': 12} Link IDs: {None: 11} Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 24 Unresolved non-hydrogen dihedrals: 36 Unresolved non-hydrogen chiralities: 12 Chain: "B" Number of atoms: 168 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 168 Unusual residues: {'NAG': 12} Classifications: {'undetermined': 12} Link IDs: {None: 11} Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 24 Unresolved non-hydrogen dihedrals: 36 Unresolved non-hydrogen chiralities: 12 Chain: "A" Number of atoms: 168 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 168 Unusual residues: {'NAG': 12} Classifications: {'undetermined': 12} Link IDs: {None: 11} Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 24 Unresolved non-hydrogen dihedrals: 36 Unresolved non-hydrogen chiralities: 12 Time building chain proxies: 7.28, per 1000 atoms: 0.23 Number of scatterers: 31812 At special positions: 0 Unit cell: (160.92, 163.08, 183.6, 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 156 16.00 O 6318 8.00 N 5127 7.00 C 20211 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=51, symmetry=0 Simple disulfide: pdb=" SG CYS C 19 " - pdb=" SG CYS C 133 " distance=2.03 Simple disulfide: pdb=" SG CYS C 128 " - pdb=" SG CYS C 159 " distance=2.03 Simple disulfide: pdb=" SG CYS C 278 " - pdb=" SG CYS C 288 " distance=2.03 Simple disulfide: pdb=" SG CYS C 323 " - pdb=" SG CYS C 348 " distance=2.03 Simple disulfide: pdb=" SG CYS C 366 " - pdb=" SG CYS C 419 " distance=2.03 Simple disulfide: pdb=" SG CYS C 378 " - pdb=" SG CYS C 511 " distance=2.03 Simple disulfide: pdb=" SG CYS C 467 " - pdb=" SG CYS C 474 " distance=2.03 Simple disulfide: pdb=" SG CYS C 524 " - pdb=" SG CYS C 576 " distance=2.03 Simple disulfide: pdb=" SG CYS C 603 " - pdb=" SG CYS C 635 " distance=2.03 Simple disulfide: pdb=" SG CYS C 648 " - pdb=" SG CYS C 657 " distance=2.03 Simple disulfide: pdb=" SG CYS C 720 " - pdb=" SG CYS C 742 " distance=2.04 Simple disulfide: pdb=" SG CYS C 725 " - pdb=" SG CYS C 731 " distance=2.03 Simple disulfide: pdb=" SG CYS C 822 " - pdb=" SG CYS C 833 " distance=2.05 Simple disulfide: pdb=" SG CYS C1014 " - pdb=" SG CYS C1025 " distance=2.03 Simple disulfide: pdb=" SG CYS C1064 " - pdb=" SG CYS C1108 " distance=2.03 Simple disulfide: pdb=" SG CYS B 19 " - pdb=" SG CYS B 133 " distance=2.03 Simple disulfide: pdb=" SG CYS B 128 " - pdb=" SG CYS B 159 " distance=2.03 Simple disulfide: pdb=" SG CYS B 278 " - pdb=" SG CYS B 288 " distance=2.03 Simple disulfide: pdb=" SG CYS B 323 " - pdb=" SG CYS B 348 " distance=2.03 Simple disulfide: pdb=" SG CYS B 366 " - pdb=" SG CYS B 419 " distance=2.03 Simple disulfide: pdb=" SG CYS B 378 " - pdb=" SG CYS B 511 " distance=2.03 Simple disulfide: pdb=" SG CYS B 467 " - pdb=" SG CYS B 474 " distance=2.03 Simple disulfide: pdb=" SG CYS B 524 " - pdb=" SG CYS B 576 " distance=2.03 Simple disulfide: pdb=" SG CYS B 603 " - pdb=" SG CYS B 635 " distance=2.03 Simple disulfide: pdb=" SG CYS B 648 " - pdb=" SG CYS B 657 " distance=2.03 Simple disulfide: pdb=" SG CYS B 720 " - pdb=" SG CYS B 742 " distance=2.04 Simple disulfide: pdb=" SG CYS B 725 " - pdb=" SG CYS B 731 " distance=2.03 Simple disulfide: pdb=" SG CYS B 822 " - pdb=" SG CYS B 833 " distance=2.05 Simple disulfide: pdb=" SG CYS B1014 " - pdb=" SG CYS B1025 " distance=2.03 Simple disulfide: pdb=" SG CYS B1064 " - pdb=" SG CYS B1108 " distance=2.03 Simple disulfide: pdb=" SG CYS G 22 " - pdb=" SG CYS G 95 " distance=2.04 Simple disulfide: pdb=" SG CYS F 23 " - pdb=" SG CYS F 88 " distance=2.04 Simple disulfide: pdb=" SG CYS E 22 " - pdb=" SG CYS E 95 " distance=2.04 Simple disulfide: pdb=" SG CYS D 23 " - pdb=" SG CYS D 88 " distance=2.04 Simple disulfide: pdb=" SG CYS A 19 " - pdb=" SG CYS A 133 " distance=2.03 Simple disulfide: pdb=" SG CYS A 128 " - pdb=" SG CYS A 159 " distance=2.03 Simple disulfide: pdb=" SG CYS A 278 " - pdb=" SG CYS A 288 " distance=2.03 Simple disulfide: pdb=" SG CYS A 323 " - pdb=" SG CYS A 348 " distance=2.03 Simple disulfide: pdb=" SG CYS A 366 " - pdb=" SG CYS A 419 " distance=2.03 Simple disulfide: pdb=" SG CYS A 378 " - pdb=" SG CYS A 511 " distance=2.03 Simple disulfide: pdb=" SG CYS A 467 " - pdb=" SG CYS A 474 " distance=2.03 Simple disulfide: pdb=" SG CYS A 524 " - pdb=" SG CYS A 576 " distance=2.03 Simple disulfide: pdb=" SG CYS A 603 " - pdb=" SG CYS A 635 " distance=2.03 Simple disulfide: pdb=" SG CYS A 648 " - pdb=" SG CYS A 657 " distance=2.03 Simple disulfide: pdb=" SG CYS A 720 " - pdb=" SG CYS A 742 " distance=2.04 Simple disulfide: pdb=" SG CYS A 725 " - pdb=" SG CYS A 731 " distance=2.03 Simple disulfide: pdb=" SG CYS A 822 " - pdb=" SG CYS A 833 " distance=2.05 Simple disulfide: pdb=" SG CYS A1014 " - pdb=" SG CYS A1025 " distance=2.03 Simple disulfide: pdb=" SG CYS A1064 " - pdb=" SG CYS A1108 " distance=2.03 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 95 " distance=2.04 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 88 " distance=2.04 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied ALPHA1-2 " MAN N 6 " - " MAN N 7 " " MAN T 6 " - " MAN T 7 " " MAN Z 6 " - " MAN Z 7 " ALPHA1-3 " BMA N 3 " - " MAN N 4 " " MAN N 4 " - " MAN N 5 " " MAN N 6 " - " MAN N 8 " " BMA T 3 " - " MAN T 4 " " MAN T 4 " - " MAN T 5 " " MAN T 6 " - " MAN T 8 " " BMA Z 3 " - " MAN Z 4 " " MAN Z 4 " - " MAN Z 5 " " MAN Z 6 " - " MAN Z 8 " ALPHA1-6 " BMA N 3 " - " MAN N 6 " " BMA T 3 " - " MAN T 6 " " BMA Z 3 " - " MAN Z 6 " BETA1-4 " NAG I 1 " - " NAG I 2 " " NAG J 1 " - " NAG J 2 " " NAG K 1 " - " NAG K 2 " " NAG M 1 " - " NAG M 2 " " NAG N 1 " - " NAG N 2 " " NAG N 2 " - " BMA N 3 " " NAG O 1 " - " NAG O 2 " " NAG P 1 " - " NAG P 2 " " NAG Q 1 " - " NAG Q 2 " " NAG R 1 " - " NAG R 2 " " NAG S 1 " - " NAG S 2 " " NAG T 1 " - " NAG T 2 " " NAG T 2 " - " BMA T 3 " " NAG U 1 " - " NAG U 2 " " NAG V 1 " - " NAG V 2 " " NAG W 1 " - " NAG W 2 " " NAG X 1 " - " NAG X 2 " " NAG Y 1 " - " NAG Y 2 " " NAG Z 1 " - " NAG Z 2 " " NAG Z 2 " - " BMA Z 3 " " NAG a 1 " - " NAG a 2 " BETA1-6 " NAG J 1 " - " FUC J 3 " ~> Even though FUC is an alpha isomer, a beta linkage is required... " NAG N 1 " - " FUC N 9 " " NAG Q 1 " - " FUC Q 3 " " NAG T 1 " - " FUC T 9 " " NAG W 1 " - " FUC W 3 " " NAG Z 1 " - " FUC Z 9 " NAG-ASN " NAG A1301 " - " ASN A 65 " " NAG A1303 " - " ASN A 158 " " NAG A1304 " - " ASN A 318 " " NAG A1305 " - " ASN A 357 " " NAG A1308 " - " ASN A 691 " " NAG A1309 " - " ASN A 699 " " NAG A1310 " - " ASN A1056 " " NAG A1311 " - " ASN A1080 " " NAG A1312 " - " ASN A1116 " " NAG B1301 " - " ASN B 65 " " NAG B1303 " - " ASN B 158 " " NAG B1304 " - " ASN B 318 " " NAG B1305 " - " ASN B 357 " " NAG B1308 " - " ASN B 691 " " NAG B1309 " - " ASN B 699 " " NAG B1310 " - " ASN B1056 " " NAG B1311 " - " ASN B1080 " " NAG B1312 " - " ASN B1116 " " NAG C1301 " - " ASN C 65 " " NAG C1303 " - " ASN C 158 " " NAG C1304 " - " ASN C 318 " " NAG C1305 " - " ASN C 357 " " NAG C1308 " - " ASN C 691 " " NAG C1309 " - " ASN C 699 " " NAG C1310 " - " ASN C1056 " " NAG C1311 " - " ASN C1080 " " NAG C1312 " - " ASN C1116 " " NAG I 1 " - " ASN C 109 " " NAG J 1 " - " ASN C 119 " " NAG K 1 " - " ASN C 227 " " NAG M 1 " - " ASN C 269 " " NAG N 1 " - " ASN C 330 " " NAG O 1 " - " ASN C 783 " " NAG P 1 " - " ASN B 109 " " NAG Q 1 " - " ASN B 119 " " NAG R 1 " - " ASN B 227 " " NAG S 1 " - " ASN B 269 " " NAG T 1 " - " ASN B 330 " " NAG U 1 " - " ASN B 783 " " NAG V 1 " - " ASN A 109 " " NAG W 1 " - " ASN A 119 " " NAG X 1 " - " ASN A 227 " " NAG Y 1 " - " ASN A 269 " " NAG Z 1 " - " ASN A 330 " " NAG a 1 " - " ASN A 783 " Time building additional restraints: 2.91 Conformation dependent library (CDL) restraints added in 1.3 seconds 7776 Ramachandran restraints generated. 3888 Oldfield, 0 Emsley, 3888 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7320 Finding SS restraints... Secondary structure from input PDB file: 93 helices and 66 sheets defined 22.4% alpha, 30.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.41 Creating SS restraints... Processing helix chain 'C' and resid 281 through 291 removed outlier: 3.813A pdb=" N GLU C 285 " --> pdb=" O ASN C 281 " (cutoff:3.500A) Processing helix chain 'C' and resid 325 through 330 Processing helix chain 'C' and resid 336 through 340 removed outlier: 3.715A pdb=" N TRP C 340 " --> pdb=" O VAL C 337 " (cutoff:3.500A) Processing helix chain 'C' and resid 352 through 357 removed outlier: 3.571A pdb=" N TYR C 356 " --> pdb=" O TYR C 352 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N ASN C 357 " --> pdb=" O SER C 353 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 352 through 357' Processing helix chain 'C' and resid 370 through 376 removed outlier: 3.611A pdb=" N LEU C 374 " --> pdb=" O ALA C 371 " (cutoff:3.500A) removed outlier: 4.593A pdb=" N ASN C 375 " --> pdb=" O THR C 372 " (cutoff:3.500A) Processing helix chain 'C' and resid 392 through 397 Processing helix chain 'C' and resid 403 through 408 Processing helix chain 'C' and resid 425 through 430 removed outlier: 3.608A pdb=" N ALA C 430 " --> pdb=" O ARG C 426 " (cutoff:3.500A) Processing helix chain 'C' and resid 555 through 557 No H-bonds generated for 'chain 'C' and resid 555 through 557' Processing helix chain 'C' and resid 602 through 611 removed outlier: 3.850A pdb=" N VAL C 606 " --> pdb=" O ASN C 602 " (cutoff:3.500A) Processing helix chain 'C' and resid 719 through 725 removed outlier: 3.605A pdb=" N TYR C 723 " --> pdb=" O ASP C 719 " (cutoff:3.500A) Processing helix chain 'C' and resid 731 through 736 Processing helix chain 'C' and resid 737 through 739 No H-bonds generated for 'chain 'C' and resid 737 through 739' Processing helix chain 'C' and resid 740 through 765 removed outlier: 3.638A pdb=" N ASP C 757 " --> pdb=" O ALA C 753 " (cutoff:3.500A) Processing helix chain 'C' and resid 798 through 808 removed outlier: 3.794A pdb=" N ASN C 806 " --> pdb=" O ASP C 802 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N LYS C 807 " --> pdb=" O LEU C 803 " (cutoff:3.500A) removed outlier: 4.185A pdb=" N VAL C 808 " --> pdb=" O LEU C 804 " (cutoff:3.500A) Processing helix chain 'C' and resid 848 through 866 removed outlier: 3.831A pdb=" N THR C 865 " --> pdb=" O SER C 861 " (cutoff:3.500A) Processing helix chain 'C' and resid 868 through 872 removed outlier: 3.525A pdb=" N GLY C 871 " --> pdb=" O TRP C 868 " (cutoff:3.500A) Processing helix chain 'C' and resid 879 through 890 removed outlier: 4.029A pdb=" N ALA C 885 " --> pdb=" O ALA C 881 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N TYR C 886 " --> pdb=" O MET C 882 " (cutoff:3.500A) Processing helix chain 'C' and resid 895 through 901 removed outlier: 4.328A pdb=" N TYR C 899 " --> pdb=" O GLN C 895 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N GLU C 900 " --> pdb=" O ASN C 896 " (cutoff:3.500A) removed outlier: 3.960A pdb=" N ASN C 901 " --> pdb=" O VAL C 897 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 895 through 901' Processing helix chain 'C' and resid 901 through 923 removed outlier: 3.806A pdb=" N ILE C 905 " --> pdb=" O ASN C 901 " (cutoff:3.500A) Processing helix chain 'C' and resid 924 through 926 No H-bonds generated for 'chain 'C' and resid 924 through 926' Processing helix chain 'C' and resid 927 through 947 Processing helix chain 'C' and resid 948 through 950 No H-bonds generated for 'chain 'C' and resid 948 through 950' Processing helix chain 'C' and resid 958 through 966 Processing helix chain 'C' and resid 967 through 1015 removed outlier: 4.570A pdb=" N VAL C 973 " --> pdb=" O PRO C 969 " (cutoff:3.500A) removed outlier: 4.186A pdb=" N GLN C 974 " --> pdb=" O GLU C 970 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N ARG C 977 " --> pdb=" O VAL C 973 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N ALA C 998 " --> pdb=" O LEU C 994 " (cutoff:3.500A) removed outlier: 3.820A pdb=" N GLU C 999 " --> pdb=" O ILE C 995 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N SER C1003 " --> pdb=" O GLU C 999 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N VAL C1015 " --> pdb=" O MET C1011 " (cutoff:3.500A) Processing helix chain 'C' and resid 1098 through 1100 No H-bonds generated for 'chain 'C' and resid 1098 through 1100' Processing helix chain 'C' and resid 1107 through 1111 Processing helix chain 'B' and resid 281 through 291 removed outlier: 3.813A pdb=" N GLU B 285 " --> pdb=" O ASN B 281 " (cutoff:3.500A) Processing helix chain 'B' and resid 325 through 330 Processing helix chain 'B' and resid 336 through 340 removed outlier: 3.715A pdb=" N TRP B 340 " --> pdb=" O VAL B 337 " (cutoff:3.500A) Processing helix chain 'B' and resid 352 through 357 removed outlier: 3.571A pdb=" N TYR B 356 " --> pdb=" O TYR B 352 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N ASN B 357 " --> pdb=" O SER B 353 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 352 through 357' Processing helix chain 'B' and resid 370 through 376 removed outlier: 3.613A pdb=" N LEU B 374 " --> pdb=" O ALA B 371 " (cutoff:3.500A) removed outlier: 4.594A pdb=" N ASN B 375 " --> pdb=" O THR B 372 " (cutoff:3.500A) Processing helix chain 'B' and resid 392 through 397 Processing helix chain 'B' and resid 403 through 408 Processing helix chain 'B' and resid 425 through 430 removed outlier: 3.608A pdb=" N ALA B 430 " --> pdb=" O ARG B 426 " (cutoff:3.500A) Processing helix chain 'B' and resid 555 through 557 No H-bonds generated for 'chain 'B' and resid 555 through 557' Processing helix chain 'B' and resid 602 through 611 removed outlier: 3.849A pdb=" N VAL B 606 " --> pdb=" O ASN B 602 " (cutoff:3.500A) Processing helix chain 'B' and resid 719 through 725 removed outlier: 3.605A pdb=" N TYR B 723 " --> pdb=" O ASP B 719 " (cutoff:3.500A) Processing helix chain 'B' and resid 731 through 736 Processing helix chain 'B' and resid 737 through 739 No H-bonds generated for 'chain 'B' and resid 737 through 739' Processing helix chain 'B' and resid 740 through 765 removed outlier: 3.638A pdb=" N ASP B 757 " --> pdb=" O ALA B 753 " (cutoff:3.500A) Processing helix chain 'B' and resid 798 through 808 removed outlier: 3.793A pdb=" N ASN B 806 " --> pdb=" O ASP B 802 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N LYS B 807 " --> pdb=" O LEU B 803 " (cutoff:3.500A) removed outlier: 4.186A pdb=" N VAL B 808 " --> pdb=" O LEU B 804 " (cutoff:3.500A) Processing helix chain 'B' and resid 848 through 866 removed outlier: 3.832A pdb=" N THR B 865 " --> pdb=" O SER B 861 " (cutoff:3.500A) Processing helix chain 'B' and resid 868 through 872 removed outlier: 3.524A pdb=" N GLY B 871 " --> pdb=" O TRP B 868 " (cutoff:3.500A) Processing helix chain 'B' and resid 879 through 890 removed outlier: 4.028A pdb=" N ALA B 885 " --> pdb=" O ALA B 881 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N TYR B 886 " --> pdb=" O MET B 882 " (cutoff:3.500A) Processing helix chain 'B' and resid 895 through 901 removed outlier: 4.328A pdb=" N TYR B 899 " --> pdb=" O GLN B 895 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N GLU B 900 " --> pdb=" O ASN B 896 " (cutoff:3.500A) removed outlier: 3.960A pdb=" N ASN B 901 " --> pdb=" O VAL B 897 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 895 through 901' Processing helix chain 'B' and resid 901 through 923 removed outlier: 3.807A pdb=" N ILE B 905 " --> pdb=" O ASN B 901 " (cutoff:3.500A) Processing helix chain 'B' and resid 924 through 926 No H-bonds generated for 'chain 'B' and resid 924 through 926' Processing helix chain 'B' and resid 927 through 947 Processing helix chain 'B' and resid 948 through 950 No H-bonds generated for 'chain 'B' and resid 948 through 950' Processing helix chain 'B' and resid 958 through 966 Processing helix chain 'B' and resid 967 through 1015 removed outlier: 4.569A pdb=" N VAL B 973 " --> pdb=" O PRO B 969 " (cutoff:3.500A) removed outlier: 4.185A pdb=" N GLN B 974 " --> pdb=" O GLU B 970 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N ARG B 977 " --> pdb=" O VAL B 973 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N ALA B 998 " --> pdb=" O LEU B 994 " (cutoff:3.500A) removed outlier: 3.820A pdb=" N GLU B 999 " --> pdb=" O ILE B 995 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N SER B1003 " --> pdb=" O GLU B 999 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N VAL B1015 " --> pdb=" O MET B1011 " (cutoff:3.500A) Processing helix chain 'B' and resid 1098 through 1100 No H-bonds generated for 'chain 'B' and resid 1098 through 1100' Processing helix chain 'B' and resid 1107 through 1111 Processing helix chain 'G' and resid 63 through 65 No H-bonds generated for 'chain 'G' and resid 63 through 65' Processing helix chain 'G' and resid 73 through 75 No H-bonds generated for 'chain 'G' and resid 73 through 75' Processing helix chain 'G' and resid 86 through 90 Processing helix chain 'F' and resid 79 through 83 Processing helix chain 'E' and resid 63 through 65 No H-bonds generated for 'chain 'E' and resid 63 through 65' Processing helix chain 'E' and resid 73 through 75 No H-bonds generated for 'chain 'E' and resid 73 through 75' Processing helix chain 'E' and resid 86 through 90 Processing helix chain 'D' and resid 79 through 83 Processing helix chain 'A' and resid 281 through 291 removed outlier: 3.812A pdb=" N GLU A 285 " --> pdb=" O ASN A 281 " (cutoff:3.500A) Processing helix chain 'A' and resid 325 through 330 Processing helix chain 'A' and resid 336 through 340 removed outlier: 3.714A pdb=" N TRP A 340 " --> pdb=" O VAL A 337 " (cutoff:3.500A) Processing helix chain 'A' and resid 352 through 357 removed outlier: 3.571A pdb=" N TYR A 356 " --> pdb=" O TYR A 352 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N ASN A 357 " --> pdb=" O SER A 353 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 352 through 357' Processing helix chain 'A' and resid 370 through 376 removed outlier: 3.612A pdb=" N LEU A 374 " --> pdb=" O ALA A 371 " (cutoff:3.500A) removed outlier: 4.594A pdb=" N ASN A 375 " --> pdb=" O THR A 372 " (cutoff:3.500A) Processing helix chain 'A' and resid 392 through 397 Processing helix chain 'A' and resid 403 through 408 Processing helix chain 'A' and resid 425 through 430 removed outlier: 3.608A pdb=" N ALA A 430 " --> pdb=" O ARG A 426 " (cutoff:3.500A) Processing helix chain 'A' and resid 555 through 557 No H-bonds generated for 'chain 'A' and resid 555 through 557' Processing helix chain 'A' and resid 602 through 611 removed outlier: 3.849A pdb=" N VAL A 606 " --> pdb=" O ASN A 602 " (cutoff:3.500A) Processing helix chain 'A' and resid 719 through 725 removed outlier: 3.605A pdb=" N TYR A 723 " --> pdb=" O ASP A 719 " (cutoff:3.500A) Processing helix chain 'A' and resid 731 through 736 Processing helix chain 'A' and resid 737 through 739 No H-bonds generated for 'chain 'A' and resid 737 through 739' Processing helix chain 'A' and resid 740 through 765 removed outlier: 3.637A pdb=" N ASP A 757 " --> pdb=" O ALA A 753 " (cutoff:3.500A) Processing helix chain 'A' and resid 798 through 808 removed outlier: 3.793A pdb=" N ASN A 806 " --> pdb=" O ASP A 802 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N LYS A 807 " --> pdb=" O LEU A 803 " (cutoff:3.500A) removed outlier: 4.186A pdb=" N VAL A 808 " --> pdb=" O LEU A 804 " (cutoff:3.500A) Processing helix chain 'A' and resid 848 through 866 removed outlier: 3.832A pdb=" N THR A 865 " --> pdb=" O SER A 861 " (cutoff:3.500A) Processing helix chain 'A' and resid 868 through 872 removed outlier: 3.525A pdb=" N GLY A 871 " --> pdb=" O TRP A 868 " (cutoff:3.500A) Processing helix chain 'A' and resid 879 through 890 removed outlier: 4.029A pdb=" N ALA A 885 " --> pdb=" O ALA A 881 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N TYR A 886 " --> pdb=" O MET A 882 " (cutoff:3.500A) Processing helix chain 'A' and resid 895 through 901 removed outlier: 4.327A pdb=" N TYR A 899 " --> pdb=" O GLN A 895 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N GLU A 900 " --> pdb=" O ASN A 896 " (cutoff:3.500A) removed outlier: 3.960A pdb=" N ASN A 901 " --> pdb=" O VAL A 897 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 895 through 901' Processing helix chain 'A' and resid 901 through 923 removed outlier: 3.807A pdb=" N ILE A 905 " --> pdb=" O ASN A 901 " (cutoff:3.500A) Processing helix chain 'A' and resid 924 through 926 No H-bonds generated for 'chain 'A' and resid 924 through 926' Processing helix chain 'A' and resid 927 through 947 Processing helix chain 'A' and resid 948 through 950 No H-bonds generated for 'chain 'A' and resid 948 through 950' Processing helix chain 'A' and resid 958 through 966 Processing helix chain 'A' and resid 967 through 1015 removed outlier: 4.569A pdb=" N VAL A 973 " --> pdb=" O PRO A 969 " (cutoff:3.500A) removed outlier: 4.186A pdb=" N GLN A 974 " --> pdb=" O GLU A 970 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N ARG A 977 " --> pdb=" O VAL A 973 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N ALA A 998 " --> pdb=" O LEU A 994 " (cutoff:3.500A) removed outlier: 3.820A pdb=" N GLU A 999 " --> pdb=" O ILE A 995 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N SER A1003 " --> pdb=" O GLU A 999 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N VAL A1015 " --> pdb=" O MET A1011 " (cutoff:3.500A) Processing helix chain 'A' and resid 1098 through 1100 No H-bonds generated for 'chain 'A' and resid 1098 through 1100' Processing helix chain 'A' and resid 1107 through 1111 Processing helix chain 'H' and resid 63 through 65 No H-bonds generated for 'chain 'H' and resid 63 through 65' Processing helix chain 'H' and resid 73 through 75 No H-bonds generated for 'chain 'H' and resid 73 through 75' Processing helix chain 'H' and resid 86 through 90 Processing helix chain 'L' and resid 79 through 83 Processing sheet with id=AA1, first strand: chain 'C' and resid 31 through 34 removed outlier: 3.582A pdb=" N THR C 31 " --> pdb=" O GLY C 68 " (cutoff:3.500A) removed outlier: 7.763A pdb=" N ASN C 65 " --> pdb=" O TYR C 256 " (cutoff:3.500A) removed outlier: 5.729A pdb=" N TYR C 256 " --> pdb=" O ASN C 65 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N VAL C 254 " --> pdb=" O THR C 67 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N ALA C 251 " --> pdb=" O THR C 92 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N ALA C 90 " --> pdb=" O PHE C 253 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N ILE C 87 " --> pdb=" O PHE C 187 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N HIS C 181 " --> pdb=" O GLU C 93 " (cutoff:3.500A) removed outlier: 4.034A pdb=" N GLU C 184 " --> pdb=" O GLY C 199 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N VAL C 186 " --> pdb=" O TYR C 197 " (cutoff:3.500A) removed outlier: 6.842A pdb=" N LYS C 198 " --> pdb=" O PRO C 218 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'C' and resid 52 through 59 removed outlier: 4.185A pdb=" N ASP C 274 " --> pdb=" O LYS C 265 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 81 through 82 removed outlier: 12.392A pdb=" N LEU C 132 " --> pdb=" O PHE C 231 " (cutoff:3.500A) removed outlier: 11.919A pdb=" N ALA C 233 " --> pdb=" O LEU C 132 " (cutoff:3.500A) removed outlier: 10.304A pdb=" N ASP C 134 " --> pdb=" O ALA C 233 " (cutoff:3.500A) removed outlier: 9.655A pdb=" N LEU C 235 " --> pdb=" O ASP C 134 " (cutoff:3.500A) removed outlier: 7.402A pdb=" N ALA C 237 " --> pdb=" O PRO C 136 " (cutoff:3.500A) removed outlier: 5.540A pdb=" N PHE C 138 " --> pdb=" O ALA C 237 " (cutoff:3.500A) removed outlier: 6.880A pdb=" N ILE C 152 " --> pdb=" O CYS C 133 " (cutoff:3.500A) removed outlier: 10.644A pdb=" N ASN C 135 " --> pdb=" O THR C 150 " (cutoff:3.500A) removed outlier: 9.523A pdb=" N THR C 150 " --> pdb=" O ASN C 135 " (cutoff:3.500A) removed outlier: 11.306A pdb=" N PHE C 137 " --> pdb=" O THR C 148 " (cutoff:3.500A) removed outlier: 8.548A pdb=" N THR C 148 " --> pdb=" O PHE C 137 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'C' and resid 81 through 82 removed outlier: 3.985A pdb=" N GLY C 100 " --> pdb=" O ILE C 234 " (cutoff:3.500A) removed outlier: 7.071A pdb=" N THR C 236 " --> pdb=" O VAL C 98 " (cutoff:3.500A) removed outlier: 6.782A pdb=" N VAL C 98 " --> pdb=" O THR C 236 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N SER C 113 " --> pdb=" O CYS C 128 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N ILE C 117 " --> pdb=" O VAL C 124 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N VAL C 124 " --> pdb=" O ILE C 117 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 615 through 616 removed outlier: 3.678A pdb=" N GLY C 298 " --> pdb=" O THR C 585 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N THR C 585 " --> pdb=" O GLY C 298 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N THR C 302 " --> pdb=" O VAL C 581 " (cutoff:3.500A) removed outlier: 7.309A pdb=" N VAL C 581 " --> pdb=" O THR C 302 " (cutoff:3.500A) removed outlier: 4.547A pdb=" N ASN C 304 " --> pdb=" O GLY C 579 " (cutoff:3.500A) removed outlier: 6.765A pdb=" N GLY C 579 " --> pdb=" O ASN C 304 " (cutoff:3.500A) removed outlier: 4.980A pdb=" N GLY C 580 " --> pdb=" O GLN C 599 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 312 through 314 removed outlier: 7.017A pdb=" N VAL C 313 " --> pdb=" O ASN C 528 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 341 through 345 removed outlier: 3.744A pdb=" N GLU C 341 " --> pdb=" O SER C 386 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N ASN C 381 " --> pdb=" O GLU C 502 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N ALA C 422 " --> pdb=" O THR C 363 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N THR C 363 " --> pdb=" O ALA C 422 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 378 through 379 Processing sheet with id=AA9, first strand: chain 'C' and resid 435 through 441 removed outlier: 6.155A pdb=" N TYR C 436 " --> pdb=" O PHE C 483 " (cutoff:3.500A) removed outlier: 7.726A pdb=" N PHE C 483 " --> pdb=" O TYR C 436 " (cutoff:3.500A) removed outlier: 4.161A pdb=" N TYR C 438 " --> pdb=" O TYR C 481 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 539 through 540 removed outlier: 3.720A pdb=" N THR C 539 " --> pdb=" O ASP C 572 " (cutoff:3.500A) removed outlier: 6.875A pdb=" N GLY C 552 " --> pdb=" O ASP C 560 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 640 through 641 removed outlier: 6.267A pdb=" N GLU C 640 " --> pdb=" O ALA C 676 " (cutoff:3.500A) removed outlier: 8.832A pdb=" N THR C 678 " --> pdb=" O GLU C 640 " (cutoff:3.500A) removed outlier: 6.350A pdb=" N ALA C 658 " --> pdb=" O PRO C 651 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 693 through 710 removed outlier: 6.701A pdb=" N THR C 693 " --> pdb=" O THR C1058 " (cutoff:3.500A) removed outlier: 6.922A pdb=" N THR C1058 " --> pdb=" O THR C 693 " (cutoff:3.500A) removed outlier: 6.766A pdb=" N ALA C 695 " --> pdb=" O ASN C1056 " (cutoff:3.500A) removed outlier: 6.811A pdb=" N ASN C1056 " --> pdb=" O ALA C 695 " (cutoff:3.500A) removed outlier: 6.108A pdb=" N GLU C1054 " --> pdb=" O PRO C 697 " (cutoff:3.500A) removed outlier: 7.353A pdb=" N GLY C1041 " --> pdb=" O ALA C1037 " (cutoff:3.500A) removed outlier: 5.927A pdb=" N ALA C1037 " --> pdb=" O GLY C1041 " (cutoff:3.500A) removed outlier: 6.850A pdb=" N VAL C1043 " --> pdb=" O PRO C1035 " (cutoff:3.500A) removed outlier: 6.639A pdb=" N LEU C1045 " --> pdb=" O SER C1033 " (cutoff:3.500A) removed outlier: 4.560A pdb=" N SER C1033 " --> pdb=" O LEU C1045 " (cutoff:3.500A) removed outlier: 6.832A pdb=" N VAL C1047 " --> pdb=" O LEU C1031 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N TYR C1029 " --> pdb=" O TYR C1049 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 716 through 718 Processing sheet with id=AB5, first strand: chain 'C' and resid 778 through 779 Processing sheet with id=AB6, first strand: chain 'C' and resid 1102 through 1104 removed outlier: 3.611A pdb=" N ILE C1063 " --> pdb=" O TYR C1070 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'C' and resid 1076 through 1079 Processing sheet with id=AB8, first strand: chain 'B' and resid 31 through 34 removed outlier: 3.581A pdb=" N THR B 31 " --> pdb=" O GLY B 68 " (cutoff:3.500A) removed outlier: 7.762A pdb=" N ASN B 65 " --> pdb=" O TYR B 256 " (cutoff:3.500A) removed outlier: 5.730A pdb=" N TYR B 256 " --> pdb=" O ASN B 65 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N VAL B 254 " --> pdb=" O THR B 67 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N ALA B 251 " --> pdb=" O THR B 92 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N ALA B 90 " --> pdb=" O PHE B 253 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N ILE B 87 " --> pdb=" O PHE B 187 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N HIS B 181 " --> pdb=" O GLU B 93 " (cutoff:3.500A) removed outlier: 4.034A pdb=" N GLU B 184 " --> pdb=" O GLY B 199 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N VAL B 186 " --> pdb=" O TYR B 197 " (cutoff:3.500A) removed outlier: 6.842A pdb=" N LYS B 198 " --> pdb=" O PRO B 218 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 52 through 59 removed outlier: 4.185A pdb=" N ASP B 274 " --> pdb=" O LYS B 265 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 81 through 82 removed outlier: 12.392A pdb=" N LEU B 132 " --> pdb=" O PHE B 231 " (cutoff:3.500A) removed outlier: 11.919A pdb=" N ALA B 233 " --> pdb=" O LEU B 132 " (cutoff:3.500A) removed outlier: 10.304A pdb=" N ASP B 134 " --> pdb=" O ALA B 233 " (cutoff:3.500A) removed outlier: 9.655A pdb=" N LEU B 235 " --> pdb=" O ASP B 134 " (cutoff:3.500A) removed outlier: 7.402A pdb=" N ALA B 237 " --> pdb=" O PRO B 136 " (cutoff:3.500A) removed outlier: 5.539A pdb=" N PHE B 138 " --> pdb=" O ALA B 237 " (cutoff:3.500A) removed outlier: 6.880A pdb=" N ILE B 152 " --> pdb=" O CYS B 133 " (cutoff:3.500A) removed outlier: 10.643A pdb=" N ASN B 135 " --> pdb=" O THR B 150 " (cutoff:3.500A) removed outlier: 9.523A pdb=" N THR B 150 " --> pdb=" O ASN B 135 " (cutoff:3.500A) removed outlier: 11.305A pdb=" N PHE B 137 " --> pdb=" O THR B 148 " (cutoff:3.500A) removed outlier: 8.547A pdb=" N THR B 148 " --> pdb=" O PHE B 137 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 81 through 82 removed outlier: 3.985A pdb=" N GLY B 100 " --> pdb=" O ILE B 234 " (cutoff:3.500A) removed outlier: 7.070A pdb=" N THR B 236 " --> pdb=" O VAL B 98 " (cutoff:3.500A) removed outlier: 6.782A pdb=" N VAL B 98 " --> pdb=" O THR B 236 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N SER B 113 " --> pdb=" O CYS B 128 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N ILE B 117 " --> pdb=" O VAL B 124 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N VAL B 124 " --> pdb=" O ILE B 117 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 615 through 616 removed outlier: 3.678A pdb=" N GLY B 298 " --> pdb=" O THR B 585 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N THR B 585 " --> pdb=" O GLY B 298 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N THR B 302 " --> pdb=" O VAL B 581 " (cutoff:3.500A) removed outlier: 7.309A pdb=" N VAL B 581 " --> pdb=" O THR B 302 " (cutoff:3.500A) removed outlier: 4.547A pdb=" N ASN B 304 " --> pdb=" O GLY B 579 " (cutoff:3.500A) removed outlier: 6.765A pdb=" N GLY B 579 " --> pdb=" O ASN B 304 " (cutoff:3.500A) removed outlier: 4.980A pdb=" N GLY B 580 " --> pdb=" O GLN B 599 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 312 through 314 removed outlier: 7.017A pdb=" N VAL B 313 " --> pdb=" O ASN B 528 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 341 through 345 removed outlier: 3.745A pdb=" N GLU B 341 " --> pdb=" O SER B 386 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N ASN B 381 " --> pdb=" O GLU B 502 " (cutoff:3.500A) removed outlier: 3.782A pdb=" N ALA B 422 " --> pdb=" O THR B 363 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N THR B 363 " --> pdb=" O ALA B 422 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 378 through 379 Processing sheet with id=AC7, first strand: chain 'B' and resid 435 through 441 removed outlier: 6.156A pdb=" N TYR B 436 " --> pdb=" O PHE B 483 " (cutoff:3.500A) removed outlier: 7.726A pdb=" N PHE B 483 " --> pdb=" O TYR B 436 " (cutoff:3.500A) removed outlier: 4.162A pdb=" N TYR B 438 " --> pdb=" O TYR B 481 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'B' and resid 539 through 540 removed outlier: 3.720A pdb=" N THR B 539 " --> pdb=" O ASP B 572 " (cutoff:3.500A) removed outlier: 6.874A pdb=" N GLY B 552 " --> pdb=" O ASP B 560 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'B' and resid 640 through 641 removed outlier: 6.267A pdb=" N GLU B 640 " --> pdb=" O ALA B 676 " (cutoff:3.500A) removed outlier: 8.832A pdb=" N THR B 678 " --> pdb=" O GLU B 640 " (cutoff:3.500A) removed outlier: 6.350A pdb=" N ALA B 658 " --> pdb=" O PRO B 651 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'B' and resid 693 through 710 removed outlier: 6.701A pdb=" N THR B 693 " --> pdb=" O THR B1058 " (cutoff:3.500A) removed outlier: 6.923A pdb=" N THR B1058 " --> pdb=" O THR B 693 " (cutoff:3.500A) removed outlier: 6.765A pdb=" N ALA B 695 " --> pdb=" O ASN B1056 " (cutoff:3.500A) removed outlier: 6.811A pdb=" N ASN B1056 " --> pdb=" O ALA B 695 " (cutoff:3.500A) removed outlier: 6.109A pdb=" N GLU B1054 " --> pdb=" O PRO B 697 " (cutoff:3.500A) removed outlier: 7.353A pdb=" N GLY B1041 " --> pdb=" O ALA B1037 " (cutoff:3.500A) removed outlier: 5.927A pdb=" N ALA B1037 " --> pdb=" O GLY B1041 " (cutoff:3.500A) removed outlier: 6.850A pdb=" N VAL B1043 " --> pdb=" O PRO B1035 " (cutoff:3.500A) removed outlier: 6.639A pdb=" N LEU B1045 " --> pdb=" O SER B1033 " (cutoff:3.500A) removed outlier: 4.560A pdb=" N SER B1033 " --> pdb=" O LEU B1045 " (cutoff:3.500A) removed outlier: 6.831A pdb=" N VAL B1047 " --> pdb=" O LEU B1031 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N TYR B1029 " --> pdb=" O TYR B1049 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'B' and resid 716 through 718 Processing sheet with id=AD3, first strand: chain 'B' and resid 778 through 779 Processing sheet with id=AD4, first strand: chain 'B' and resid 1102 through 1104 removed outlier: 3.611A pdb=" N ILE B1063 " --> pdb=" O TYR B1070 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'B' and resid 1076 through 1079 Processing sheet with id=AD6, first strand: chain 'G' and resid 3 through 7 Processing sheet with id=AD7, first strand: chain 'G' and resid 11 through 12 removed outlier: 3.607A pdb=" N GLY G 49 " --> pdb=" O TRP G 36 " (cutoff:3.500A) removed outlier: 6.812A pdb=" N ARG G 38 " --> pdb=" O TRP G 47 " (cutoff:3.500A) removed outlier: 5.195A pdb=" N TRP G 47 " --> pdb=" O ARG G 38 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'G' and resid 11 through 12 removed outlier: 6.990A pdb=" N CYS G 95 " --> pdb=" O TRP G 111 " (cutoff:3.500A) removed outlier: 4.961A pdb=" N TRP G 111 " --> pdb=" O CYS G 95 " (cutoff:3.500A) removed outlier: 7.025A pdb=" N ARG G 97 " --> pdb=" O GLU G 109 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'F' and resid 4 through 7 removed outlier: 3.502A pdb=" N CYS F 23 " --> pdb=" O PHE F 71 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N PHE F 71 " --> pdb=" O CYS F 23 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N SER F 63 " --> pdb=" O THR F 74 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'F' and resid 10 through 12 removed outlier: 6.549A pdb=" N LEU F 11 " --> pdb=" O GLU F 105 " (cutoff:3.500A) removed outlier: 4.637A pdb=" N LEU F 33 " --> pdb=" O TYR F 49 " (cutoff:3.500A) removed outlier: 4.973A pdb=" N TYR F 49 " --> pdb=" O LEU F 33 " (cutoff:3.500A) removed outlier: 6.562A pdb=" N TRP F 35 " --> pdb=" O LEU F 47 " (cutoff:3.500A) removed outlier: 6.367A pdb=" N THR F 53 " --> pdb=" O TYR F 49 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'F' and resid 10 through 12 removed outlier: 6.549A pdb=" N LEU F 11 " --> pdb=" O GLU F 105 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N GLN F 90 " --> pdb=" O THR F 97 " (cutoff:3.500A) removed outlier: 4.260A pdb=" N THR F 97 " --> pdb=" O GLN F 90 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'E' and resid 3 through 7 Processing sheet with id=AE4, first strand: chain 'E' and resid 11 through 12 removed outlier: 3.607A pdb=" N GLY E 49 " --> pdb=" O TRP E 36 " (cutoff:3.500A) removed outlier: 6.810A pdb=" N ARG E 38 " --> pdb=" O TRP E 47 " (cutoff:3.500A) removed outlier: 5.194A pdb=" N TRP E 47 " --> pdb=" O ARG E 38 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'E' and resid 11 through 12 removed outlier: 6.989A pdb=" N CYS E 95 " --> pdb=" O TRP E 111 " (cutoff:3.500A) removed outlier: 4.962A pdb=" N TRP E 111 " --> pdb=" O CYS E 95 " (cutoff:3.500A) removed outlier: 7.012A pdb=" N ARG E 97 " --> pdb=" O GLU E 109 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'D' and resid 4 through 7 removed outlier: 3.501A pdb=" N CYS D 23 " --> pdb=" O PHE D 71 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N PHE D 71 " --> pdb=" O CYS D 23 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N SER D 63 " --> pdb=" O THR D 74 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'D' and resid 10 through 12 removed outlier: 6.550A pdb=" N LEU D 11 " --> pdb=" O GLU D 105 " (cutoff:3.500A) removed outlier: 4.638A pdb=" N LEU D 33 " --> pdb=" O TYR D 49 " (cutoff:3.500A) removed outlier: 4.973A pdb=" N TYR D 49 " --> pdb=" O LEU D 33 " (cutoff:3.500A) removed outlier: 6.562A pdb=" N TRP D 35 " --> pdb=" O LEU D 47 " (cutoff:3.500A) removed outlier: 6.367A pdb=" N THR D 53 " --> pdb=" O TYR D 49 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'D' and resid 10 through 12 removed outlier: 6.550A pdb=" N LEU D 11 " --> pdb=" O GLU D 105 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N GLN D 90 " --> pdb=" O THR D 97 " (cutoff:3.500A) removed outlier: 4.259A pdb=" N THR D 97 " --> pdb=" O GLN D 90 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'A' and resid 31 through 34 removed outlier: 3.582A pdb=" N THR A 31 " --> pdb=" O GLY A 68 " (cutoff:3.500A) removed outlier: 7.763A pdb=" N ASN A 65 " --> pdb=" O TYR A 256 " (cutoff:3.500A) removed outlier: 5.729A pdb=" N TYR A 256 " --> pdb=" O ASN A 65 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N VAL A 254 " --> pdb=" O THR A 67 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N ALA A 251 " --> pdb=" O THR A 92 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N ALA A 90 " --> pdb=" O PHE A 253 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N ILE A 87 " --> pdb=" O PHE A 187 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N HIS A 181 " --> pdb=" O GLU A 93 " (cutoff:3.500A) removed outlier: 4.034A pdb=" N GLU A 184 " --> pdb=" O GLY A 199 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N VAL A 186 " --> pdb=" O TYR A 197 " (cutoff:3.500A) removed outlier: 6.842A pdb=" N LYS A 198 " --> pdb=" O PRO A 218 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'A' and resid 52 through 59 removed outlier: 4.185A pdb=" N ASP A 274 " --> pdb=" O LYS A 265 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'A' and resid 81 through 82 removed outlier: 12.392A pdb=" N LEU A 132 " --> pdb=" O PHE A 231 " (cutoff:3.500A) removed outlier: 11.919A pdb=" N ALA A 233 " --> pdb=" O LEU A 132 " (cutoff:3.500A) removed outlier: 10.304A pdb=" N ASP A 134 " --> pdb=" O ALA A 233 " (cutoff:3.500A) removed outlier: 9.655A pdb=" N LEU A 235 " --> pdb=" O ASP A 134 " (cutoff:3.500A) removed outlier: 7.402A pdb=" N ALA A 237 " --> pdb=" O PRO A 136 " (cutoff:3.500A) removed outlier: 5.540A pdb=" N PHE A 138 " --> pdb=" O ALA A 237 " (cutoff:3.500A) removed outlier: 6.880A pdb=" N ILE A 152 " --> pdb=" O CYS A 133 " (cutoff:3.500A) removed outlier: 10.643A pdb=" N ASN A 135 " --> pdb=" O THR A 150 " (cutoff:3.500A) removed outlier: 9.522A pdb=" N THR A 150 " --> pdb=" O ASN A 135 " (cutoff:3.500A) removed outlier: 11.305A pdb=" N PHE A 137 " --> pdb=" O THR A 148 " (cutoff:3.500A) removed outlier: 8.547A pdb=" N THR A 148 " --> pdb=" O PHE A 137 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'A' and resid 81 through 82 removed outlier: 3.985A pdb=" N GLY A 100 " --> pdb=" O ILE A 234 " (cutoff:3.500A) removed outlier: 7.071A pdb=" N THR A 236 " --> pdb=" O VAL A 98 " (cutoff:3.500A) removed outlier: 6.781A pdb=" N VAL A 98 " --> pdb=" O THR A 236 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N SER A 113 " --> pdb=" O CYS A 128 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N ILE A 117 " --> pdb=" O VAL A 124 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N VAL A 124 " --> pdb=" O ILE A 117 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'A' and resid 615 through 616 removed outlier: 3.679A pdb=" N GLY A 298 " --> pdb=" O THR A 585 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N THR A 585 " --> pdb=" O GLY A 298 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N THR A 302 " --> pdb=" O VAL A 581 " (cutoff:3.500A) removed outlier: 7.309A pdb=" N VAL A 581 " --> pdb=" O THR A 302 " (cutoff:3.500A) removed outlier: 4.548A pdb=" N ASN A 304 " --> pdb=" O GLY A 579 " (cutoff:3.500A) removed outlier: 6.765A pdb=" N GLY A 579 " --> pdb=" O ASN A 304 " (cutoff:3.500A) removed outlier: 4.980A pdb=" N GLY A 580 " --> pdb=" O GLN A 599 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'A' and resid 312 through 314 removed outlier: 7.017A pdb=" N VAL A 313 " --> pdb=" O ASN A 528 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'A' and resid 341 through 345 removed outlier: 3.744A pdb=" N GLU A 341 " --> pdb=" O SER A 386 " (cutoff:3.500A) removed outlier: 3.826A pdb=" N ASN A 381 " --> pdb=" O GLU A 502 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N ALA A 422 " --> pdb=" O THR A 363 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N THR A 363 " --> pdb=" O ALA A 422 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'A' and resid 378 through 379 Processing sheet with id=AF8, first strand: chain 'A' and resid 435 through 441 removed outlier: 6.156A pdb=" N TYR A 436 " --> pdb=" O PHE A 483 " (cutoff:3.500A) removed outlier: 7.726A pdb=" N PHE A 483 " --> pdb=" O TYR A 436 " (cutoff:3.500A) removed outlier: 4.161A pdb=" N TYR A 438 " --> pdb=" O TYR A 481 " (cutoff:3.500A) Processing sheet with id=AF9, first strand: chain 'A' and resid 539 through 540 removed outlier: 3.721A pdb=" N THR A 539 " --> pdb=" O ASP A 572 " (cutoff:3.500A) removed outlier: 6.874A pdb=" N GLY A 552 " --> pdb=" O ASP A 560 " (cutoff:3.500A) Processing sheet with id=AG1, first strand: chain 'A' and resid 640 through 641 removed outlier: 6.268A pdb=" N GLU A 640 " --> pdb=" O ALA A 676 " (cutoff:3.500A) removed outlier: 8.832A pdb=" N THR A 678 " --> pdb=" O GLU A 640 " (cutoff:3.500A) removed outlier: 6.351A pdb=" N ALA A 658 " --> pdb=" O PRO A 651 " (cutoff:3.500A) Processing sheet with id=AG2, first strand: chain 'A' and resid 693 through 710 removed outlier: 6.700A pdb=" N THR A 693 " --> pdb=" O THR A1058 " (cutoff:3.500A) removed outlier: 6.922A pdb=" N THR A1058 " --> pdb=" O THR A 693 " (cutoff:3.500A) removed outlier: 6.766A pdb=" N ALA A 695 " --> pdb=" O ASN A1056 " (cutoff:3.500A) removed outlier: 6.810A pdb=" N ASN A1056 " --> pdb=" O ALA A 695 " (cutoff:3.500A) removed outlier: 6.109A pdb=" N GLU A1054 " --> pdb=" O PRO A 697 " (cutoff:3.500A) removed outlier: 7.353A pdb=" N GLY A1041 " --> pdb=" O ALA A1037 " (cutoff:3.500A) removed outlier: 5.927A pdb=" N ALA A1037 " --> pdb=" O GLY A1041 " (cutoff:3.500A) removed outlier: 6.851A pdb=" N VAL A1043 " --> pdb=" O PRO A1035 " (cutoff:3.500A) removed outlier: 6.639A pdb=" N LEU A1045 " --> pdb=" O SER A1033 " (cutoff:3.500A) removed outlier: 4.561A pdb=" N SER A1033 " --> pdb=" O LEU A1045 " (cutoff:3.500A) removed outlier: 6.831A pdb=" N VAL A1047 " --> pdb=" O LEU A1031 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N TYR A1029 " --> pdb=" O TYR A1049 " (cutoff:3.500A) Processing sheet with id=AG3, first strand: chain 'A' and resid 716 through 718 Processing sheet with id=AG4, first strand: chain 'A' and resid 778 through 779 Processing sheet with id=AG5, first strand: chain 'A' and resid 1102 through 1104 removed outlier: 3.611A pdb=" N ILE A1063 " --> pdb=" O TYR A1070 " (cutoff:3.500A) Processing sheet with id=AG6, first strand: chain 'A' and resid 1076 through 1079 Processing sheet with id=AG7, first strand: chain 'H' and resid 3 through 7 Processing sheet with id=AG8, first strand: chain 'H' and resid 11 through 12 removed outlier: 3.606A pdb=" N GLY H 49 " --> pdb=" O TRP H 36 " (cutoff:3.500A) removed outlier: 6.812A pdb=" N ARG H 38 " --> pdb=" O TRP H 47 " (cutoff:3.500A) removed outlier: 5.195A pdb=" N TRP H 47 " --> pdb=" O ARG H 38 " (cutoff:3.500A) Processing sheet with id=AG9, first strand: chain 'H' and resid 11 through 12 removed outlier: 6.989A pdb=" N CYS H 95 " --> pdb=" O TRP H 111 " (cutoff:3.500A) removed outlier: 4.962A pdb=" N TRP H 111 " --> pdb=" O CYS H 95 " (cutoff:3.500A) removed outlier: 7.038A pdb=" N ARG H 97 " --> pdb=" O GLU H 109 " (cutoff:3.500A) Processing sheet with id=AH1, first strand: chain 'L' and resid 4 through 7 removed outlier: 3.502A pdb=" N CYS L 23 " --> pdb=" O PHE L 71 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N PHE L 71 " --> pdb=" O CYS L 23 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N SER L 63 " --> pdb=" O THR L 74 " (cutoff:3.500A) Processing sheet with id=AH2, first strand: chain 'L' and resid 10 through 12 removed outlier: 6.550A pdb=" N LEU L 11 " --> pdb=" O GLU L 105 " (cutoff:3.500A) removed outlier: 4.637A pdb=" N LEU L 33 " --> pdb=" O TYR L 49 " (cutoff:3.500A) removed outlier: 4.974A pdb=" N TYR L 49 " --> pdb=" O LEU L 33 " (cutoff:3.500A) removed outlier: 6.562A pdb=" N TRP L 35 " --> pdb=" O LEU L 47 " (cutoff:3.500A) removed outlier: 6.367A pdb=" N THR L 53 " --> pdb=" O TYR L 49 " (cutoff:3.500A) Processing sheet with id=AH3, first strand: chain 'L' and resid 10 through 12 removed outlier: 6.550A pdb=" N LEU L 11 " --> pdb=" O GLU L 105 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N GLN L 90 " --> pdb=" O THR L 97 " (cutoff:3.500A) removed outlier: 4.259A pdb=" N THR L 97 " --> pdb=" O GLN L 90 " (cutoff:3.500A) 1119 hydrogen bonds defined for protein. 2988 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 8.13 Time building geometry restraints manager: 3.83 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.35: 9939 1.35 - 1.48: 8879 1.48 - 1.61: 13525 1.61 - 1.73: 3 1.73 - 1.86: 210 Bond restraints: 32556 Sorted by residual: bond pdb=" C1 MAN N 5 " pdb=" C2 MAN N 5 " ideal model delta sigma weight residual 1.526 1.629 -0.103 2.00e-02 2.50e+03 2.66e+01 bond pdb=" C1 MAN Z 5 " pdb=" C2 MAN Z 5 " ideal model delta sigma weight residual 1.526 1.629 -0.103 2.00e-02 2.50e+03 2.66e+01 bond pdb=" C1 MAN T 5 " pdb=" C2 MAN T 5 " ideal model delta sigma weight residual 1.526 1.629 -0.103 2.00e-02 2.50e+03 2.64e+01 bond pdb=" C1 MAN Z 5 " pdb=" O5 MAN Z 5 " ideal model delta sigma weight residual 1.399 1.488 -0.089 2.00e-02 2.50e+03 1.97e+01 bond pdb=" C1 MAN N 5 " pdb=" O5 MAN N 5 " ideal model delta sigma weight residual 1.399 1.488 -0.089 2.00e-02 2.50e+03 1.96e+01 ... (remaining 32551 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.35: 43029 2.35 - 4.70: 1110 4.70 - 7.04: 148 7.04 - 9.39: 26 9.39 - 11.74: 12 Bond angle restraints: 44325 Sorted by residual: angle pdb=" CA CYS B 635 " pdb=" CB CYS B 635 " pdb=" SG CYS B 635 " ideal model delta sigma weight residual 114.40 126.14 -11.74 2.30e+00 1.89e-01 2.61e+01 angle pdb=" CA CYS A 635 " pdb=" CB CYS A 635 " pdb=" SG CYS A 635 " ideal model delta sigma weight residual 114.40 126.14 -11.74 2.30e+00 1.89e-01 2.61e+01 angle pdb=" CA CYS C 635 " pdb=" CB CYS C 635 " pdb=" SG CYS C 635 " ideal model delta sigma weight residual 114.40 126.13 -11.73 2.30e+00 1.89e-01 2.60e+01 angle pdb=" CA CYS B 720 " pdb=" CB CYS B 720 " pdb=" SG CYS B 720 " ideal model delta sigma weight residual 114.40 125.27 -10.87 2.30e+00 1.89e-01 2.23e+01 angle pdb=" CA CYS A 720 " pdb=" CB CYS A 720 " pdb=" SG CYS A 720 " ideal model delta sigma weight residual 114.40 125.25 -10.85 2.30e+00 1.89e-01 2.23e+01 ... (remaining 44320 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 23.51: 19434 23.51 - 47.03: 702 47.03 - 70.54: 219 70.54 - 94.05: 123 94.05 - 117.56: 66 Dihedral angle restraints: 20544 sinusoidal: 9135 harmonic: 11409 Sorted by residual: dihedral pdb=" CB CYS C 648 " pdb=" SG CYS C 648 " pdb=" SG CYS C 657 " pdb=" CB CYS C 657 " ideal model delta sinusoidal sigma weight residual 93.00 -178.48 -88.52 1 1.00e+01 1.00e-02 9.35e+01 dihedral pdb=" CB CYS B 648 " pdb=" SG CYS B 648 " pdb=" SG CYS B 657 " pdb=" CB CYS B 657 " ideal model delta sinusoidal sigma weight residual 93.00 -178.48 -88.52 1 1.00e+01 1.00e-02 9.35e+01 dihedral pdb=" CB CYS A 648 " pdb=" SG CYS A 648 " pdb=" SG CYS A 657 " pdb=" CB CYS A 657 " ideal model delta sinusoidal sigma weight residual 93.00 -178.50 -88.50 1 1.00e+01 1.00e-02 9.35e+01 ... (remaining 20541 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.215: 5226 0.215 - 0.430: 27 0.430 - 0.644: 6 0.644 - 0.859: 3 0.859 - 1.074: 3 Chirality restraints: 5265 Sorted by residual: chirality pdb=" C1 NAG J 1 " pdb=" ND2 ASN C 119 " pdb=" C2 NAG J 1 " pdb=" O5 NAG J 1 " both_signs ideal model delta sigma weight residual False -2.40 -1.33 -1.07 2.00e-01 2.50e+01 2.88e+01 chirality pdb=" C1 NAG W 1 " pdb=" ND2 ASN A 119 " pdb=" C2 NAG W 1 " pdb=" O5 NAG W 1 " both_signs ideal model delta sigma weight residual False -2.40 -1.33 -1.07 2.00e-01 2.50e+01 2.87e+01 chirality pdb=" C1 NAG Q 1 " pdb=" ND2 ASN B 119 " pdb=" C2 NAG Q 1 " pdb=" O5 NAG Q 1 " both_signs ideal model delta sigma weight residual False -2.40 -1.33 -1.07 2.00e-01 2.50e+01 2.86e+01 ... (remaining 5262 not shown) Planarity restraints: 5622 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN B 119 " -0.047 2.00e-02 2.50e+03 4.73e-02 2.79e+01 pdb=" CG ASN B 119 " 0.038 2.00e-02 2.50e+03 pdb=" OD1 ASN B 119 " -0.005 2.00e-02 2.50e+03 pdb=" ND2 ASN B 119 " 0.068 2.00e-02 2.50e+03 pdb=" C1 NAG Q 1 " -0.054 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN A 119 " -0.046 2.00e-02 2.50e+03 4.70e-02 2.76e+01 pdb=" CG ASN A 119 " 0.038 2.00e-02 2.50e+03 pdb=" OD1 ASN A 119 " -0.005 2.00e-02 2.50e+03 pdb=" ND2 ASN A 119 " 0.067 2.00e-02 2.50e+03 pdb=" C1 NAG W 1 " -0.054 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN C 119 " 0.046 2.00e-02 2.50e+03 4.70e-02 2.76e+01 pdb=" CG ASN C 119 " -0.038 2.00e-02 2.50e+03 pdb=" OD1 ASN C 119 " 0.005 2.00e-02 2.50e+03 pdb=" ND2 ASN C 119 " -0.067 2.00e-02 2.50e+03 pdb=" C1 NAG J 1 " 0.054 2.00e-02 2.50e+03 ... (remaining 5619 not shown) Histogram of nonbonded interaction distances: 2.14 - 2.69: 852 2.69 - 3.25: 30936 3.25 - 3.80: 43714 3.80 - 4.35: 57195 4.35 - 4.90: 97605 Nonbonded interactions: 230302 Sorted by model distance: nonbonded pdb=" OG1 THR C 693 " pdb=" OE1 GLN A 877 " model vdw 2.143 3.040 nonbonded pdb=" OE1 GLN B 877 " pdb=" OG1 THR A 693 " model vdw 2.147 3.040 nonbonded pdb=" OE1 GLN C 877 " pdb=" OG1 THR B 693 " model vdw 2.153 3.040 nonbonded pdb=" O2 MAN T 4 " pdb=" O5 MAN T 5 " model vdw 2.161 3.040 nonbonded pdb=" O2 MAN Z 4 " pdb=" O5 MAN Z 5 " model vdw 2.162 3.040 ... (remaining 230297 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: 0.05 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' } ncs_group { reference = chain 'D' selection = chain 'F' selection = chain 'L' } ncs_group { reference = chain 'E' selection = chain 'G' selection = chain 'H' } ncs_group { reference = chain 'I' selection = chain 'K' selection = chain 'M' selection = chain 'O' selection = chain 'P' selection = chain 'R' selection = chain 'S' selection = chain 'U' selection = chain 'V' selection = chain 'X' selection = chain 'Y' selection = chain 'a' } ncs_group { reference = chain 'J' selection = chain 'Q' selection = chain 'W' } ncs_group { reference = chain 'N' selection = chain 'T' selection = chain 'Z' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 4.950 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: 0.020 Extract box with map and model: 0.450 Check model and map are aligned: 0.090 Set scattering table: 0.090 Process input model: 30.630 Find NCS groups from input model: 0.690 Set up NCS constraints: 0.130 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.130 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 38.180 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7803 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.103 32694 Z= 0.244 Angle : 1.043 22.392 44688 Z= 0.503 Chirality : 0.068 1.074 5265 Planarity : 0.005 0.080 5577 Dihedral : 16.704 117.563 13071 Min Nonbonded Distance : 2.143 Molprobity Statistics. All-atom Clashscore : 6.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.88 % Favored : 97.12 % Rotamer: Outliers : 0.09 % Allowed : 0.35 % Favored : 99.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.41 % 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: -1.03 (0.12), residues: 3888 helix: -1.38 (0.18), residues: 657 sheet: 0.66 (0.16), residues: 939 loop : -1.06 (0.11), residues: 2292 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.023 0.003 ARG B 232 TYR 0.027 0.002 TYR H 52 PHE 0.045 0.002 PHE A 130 TRP 0.013 0.001 TRP A 245 HIS 0.006 0.001 HIS C1030 Details of bonding type rmsd covalent geometry : bond 0.00519 (32556) covalent geometry : angle 0.88883 (44325) SS BOND : bond 0.00635 ( 51) SS BOND : angle 3.22657 ( 102) hydrogen bonds : bond 0.23656 ( 1092) hydrogen bonds : angle 8.39559 ( 2988) link_ALPHA1-2 : bond 0.01085 ( 3) link_ALPHA1-2 : angle 0.76379 ( 9) link_ALPHA1-3 : bond 0.02379 ( 9) link_ALPHA1-3 : angle 5.66933 ( 27) link_ALPHA1-6 : bond 0.01350 ( 3) link_ALPHA1-6 : angle 1.20922 ( 9) link_BETA1-4 : bond 0.00443 ( 21) link_BETA1-4 : angle 2.32040 ( 63) link_BETA1-6 : bond 0.01225 ( 6) link_BETA1-6 : angle 1.30354 ( 18) link_NAG-ASN : bond 0.01267 ( 45) link_NAG-ASN : angle 9.15909 ( 135) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7776 Ramachandran restraints generated. 3888 Oldfield, 0 Emsley, 3888 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7776 Ramachandran restraints generated. 3888 Oldfield, 0 Emsley, 3888 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 308 residues out of total 3396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 305 time to evaluate : 0.966 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 151 MET cc_start: 0.6983 (mmt) cc_final: 0.6129 (mmt) REVERT: G 52 TYR cc_start: 0.8014 (p90) cc_final: 0.7796 (p90) REVERT: A 151 MET cc_start: 0.6931 (mmt) cc_final: 0.6274 (mmt) REVERT: H 14 PRO cc_start: 0.2936 (Cg_endo) cc_final: 0.2350 (Cg_exo) outliers start: 3 outliers final: 0 residues processed: 308 average time/residue: 0.1714 time to fit residues: 89.1339 Evaluate side-chains 212 residues out of total 3396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 212 time to evaluate : 1.070 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 390 random chunks: chunk 197 optimal weight: 2.9990 chunk 388 optimal weight: 7.9990 chunk 215 optimal weight: 0.3980 chunk 20 optimal weight: 1.9990 chunk 132 optimal weight: 0.9980 chunk 261 optimal weight: 5.9990 chunk 248 optimal weight: 0.9980 chunk 207 optimal weight: 3.9990 chunk 155 optimal weight: 6.9990 chunk 244 optimal weight: 0.0270 chunk 183 optimal weight: 0.9990 overall best weight: 0.6840 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 32 GLN ** C 409 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 939 GLN B 32 GLN B 409 ASN G 58 ASN A 32 GLN A 939 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3639 r_free = 0.3639 target = 0.107889 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3297 r_free = 0.3297 target = 0.087098 restraints weight = 69959.428| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3291 r_free = 0.3291 target = 0.087131 restraints weight = 63693.794| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3298 r_free = 0.3298 target = 0.087667 restraints weight = 70868.227| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3305 r_free = 0.3305 target = 0.088129 restraints weight = 52719.026| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3308 r_free = 0.3308 target = 0.088382 restraints weight = 47375.812| |-----------------------------------------------------------------------------| r_work (final): 0.3308 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7787 moved from start: 0.1284 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 32694 Z= 0.153 Angle : 0.871 18.706 44688 Z= 0.400 Chirality : 0.054 0.528 5265 Planarity : 0.004 0.055 5577 Dihedral : 13.071 82.116 6177 Min Nonbonded Distance : 2.380 Molprobity Statistics. All-atom Clashscore : 3.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.26 % Favored : 98.74 % Rotamer: Outliers : 0.88 % Allowed : 4.42 % Favored : 94.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.41 % 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: -0.12 (0.13), residues: 3888 helix: 0.43 (0.20), residues: 672 sheet: 1.22 (0.18), residues: 858 loop : -0.75 (0.12), residues: 2358 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A 747 TYR 0.018 0.001 TYR C1049 PHE 0.020 0.002 PHE C 130 TRP 0.028 0.001 TRP B 245 HIS 0.006 0.001 HIS C1030 Details of bonding type rmsd covalent geometry : bond 0.00307 (32556) covalent geometry : angle 0.75502 (44325) SS BOND : bond 0.00397 ( 51) SS BOND : angle 2.36773 ( 102) hydrogen bonds : bond 0.06104 ( 1092) hydrogen bonds : angle 5.98201 ( 2988) link_ALPHA1-2 : bond 0.01540 ( 3) link_ALPHA1-2 : angle 2.55515 ( 9) link_ALPHA1-3 : bond 0.03016 ( 9) link_ALPHA1-3 : angle 6.18437 ( 27) link_ALPHA1-6 : bond 0.00341 ( 3) link_ALPHA1-6 : angle 1.50402 ( 9) link_BETA1-4 : bond 0.00646 ( 21) link_BETA1-4 : angle 1.93173 ( 63) link_BETA1-6 : bond 0.01030 ( 6) link_BETA1-6 : angle 1.23019 ( 18) link_NAG-ASN : bond 0.01099 ( 45) link_NAG-ASN : angle 7.04818 ( 135) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7776 Ramachandran restraints generated. 3888 Oldfield, 0 Emsley, 3888 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7776 Ramachandran restraints generated. 3888 Oldfield, 0 Emsley, 3888 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 281 residues out of total 3396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 251 time to evaluate : 1.155 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 130 PHE cc_start: 0.5680 (m-10) cc_final: 0.5339 (m-10) REVERT: B 151 MET cc_start: 0.7107 (mmt) cc_final: 0.6278 (mmt) REVERT: B 157 PHE cc_start: 0.6469 (p90) cc_final: 0.6265 (p90) REVERT: B 295 ILE cc_start: 0.8473 (mp) cc_final: 0.8192 (mm) REVERT: E 38 ARG cc_start: 0.7464 (ptt180) cc_final: 0.7005 (ptt-90) REVERT: D 72 THR cc_start: 0.8165 (m) cc_final: 0.7948 (p) REVERT: A 130 PHE cc_start: 0.6061 (m-10) cc_final: 0.5815 (m-10) REVERT: A 144 MET cc_start: 0.8030 (mpp) cc_final: 0.7280 (mpp) outliers start: 30 outliers final: 21 residues processed: 267 average time/residue: 0.1767 time to fit residues: 79.7523 Evaluate side-chains 245 residues out of total 3396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 224 time to evaluate : 1.054 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 179 PHE Chi-restraints excluded: chain C residue 205 VAL Chi-restraints excluded: chain C residue 389 VAL Chi-restraints excluded: chain C residue 433 THR Chi-restraints excluded: chain C residue 823 LEU Chi-restraints excluded: chain B residue 179 PHE Chi-restraints excluded: chain B residue 205 VAL Chi-restraints excluded: chain B residue 389 VAL Chi-restraints excluded: chain B residue 976 ASP Chi-restraints excluded: chain G residue 57 THR Chi-restraints excluded: chain G residue 76 ASN Chi-restraints excluded: chain F residue 106 ILE Chi-restraints excluded: chain E residue 57 THR Chi-restraints excluded: chain E residue 76 ASN Chi-restraints excluded: chain D residue 106 ILE Chi-restraints excluded: chain A residue 205 VAL Chi-restraints excluded: chain A residue 389 VAL Chi-restraints excluded: chain H residue 57 THR Chi-restraints excluded: chain L residue 33 LEU Chi-restraints excluded: chain L residue 69 THR Chi-restraints excluded: chain L residue 106 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 390 random chunks: chunk 110 optimal weight: 2.9990 chunk 111 optimal weight: 2.9990 chunk 99 optimal weight: 0.9980 chunk 321 optimal weight: 0.9980 chunk 210 optimal weight: 5.9990 chunk 18 optimal weight: 3.9990 chunk 132 optimal weight: 0.9980 chunk 282 optimal weight: 10.0000 chunk 227 optimal weight: 0.8980 chunk 155 optimal weight: 8.9990 chunk 157 optimal weight: 5.9990 overall best weight: 1.3782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 409 ASN C 939 GLN E 58 ASN A 409 ASN A 939 GLN H 58 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3602 r_free = 0.3602 target = 0.105632 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3261 r_free = 0.3261 target = 0.085388 restraints weight = 70780.967| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3239 r_free = 0.3239 target = 0.084717 restraints weight = 69801.956| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3254 r_free = 0.3254 target = 0.085746 restraints weight = 77777.736| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3258 r_free = 0.3258 target = 0.085953 restraints weight = 52947.649| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3272 r_free = 0.3272 target = 0.086843 restraints weight = 48116.395| |-----------------------------------------------------------------------------| r_work (final): 0.3268 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7844 moved from start: 0.1696 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 32694 Z= 0.167 Angle : 0.816 17.942 44688 Z= 0.377 Chirality : 0.053 0.519 5265 Planarity : 0.004 0.045 5577 Dihedral : 10.408 60.343 6177 Min Nonbonded Distance : 2.425 Molprobity Statistics. All-atom Clashscore : 3.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.60 % Favored : 97.40 % Rotamer: Outliers : 1.47 % Allowed : 6.60 % Favored : 91.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.41 % 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: 0.01 (0.13), residues: 3888 helix: 1.00 (0.21), residues: 657 sheet: 1.43 (0.18), residues: 825 loop : -0.83 (0.12), residues: 2406 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A1021 TYR 0.020 0.002 TYR C1049 PHE 0.015 0.002 PHE A 909 TRP 0.009 0.001 TRP A 423 HIS 0.004 0.001 HIS B1030 Details of bonding type rmsd covalent geometry : bond 0.00373 (32556) covalent geometry : angle 0.70443 (44325) SS BOND : bond 0.00536 ( 51) SS BOND : angle 2.24647 ( 102) hydrogen bonds : bond 0.06071 ( 1092) hydrogen bonds : angle 5.56135 ( 2988) link_ALPHA1-2 : bond 0.01999 ( 3) link_ALPHA1-2 : angle 2.55395 ( 9) link_ALPHA1-3 : bond 0.02876 ( 9) link_ALPHA1-3 : angle 6.52002 ( 27) link_ALPHA1-6 : bond 0.00094 ( 3) link_ALPHA1-6 : angle 2.85944 ( 9) link_BETA1-4 : bond 0.00511 ( 21) link_BETA1-4 : angle 1.86869 ( 63) link_BETA1-6 : bond 0.00952 ( 6) link_BETA1-6 : angle 1.00708 ( 18) link_NAG-ASN : bond 0.00955 ( 45) link_NAG-ASN : angle 6.53174 ( 135) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7776 Ramachandran restraints generated. 3888 Oldfield, 0 Emsley, 3888 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7776 Ramachandran restraints generated. 3888 Oldfield, 0 Emsley, 3888 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 284 residues out of total 3396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 234 time to evaluate : 1.069 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 130 PHE cc_start: 0.6217 (m-10) cc_final: 0.5903 (m-10) REVERT: C 144 MET cc_start: 0.8110 (mpp) cc_final: 0.7702 (mpp) REVERT: C 151 MET cc_start: 0.7281 (mmt) cc_final: 0.6940 (mmt) REVERT: C 770 MET cc_start: 0.7711 (mtm) cc_final: 0.7480 (mtm) REVERT: B 130 PHE cc_start: 0.5999 (m-10) cc_final: 0.5639 (m-10) REVERT: B 144 MET cc_start: 0.7824 (mpp) cc_final: 0.7595 (mpp) REVERT: B 151 MET cc_start: 0.7259 (mmt) cc_final: 0.6519 (mmt) REVERT: B 295 ILE cc_start: 0.8532 (mp) cc_final: 0.8234 (mm) REVERT: B 1045 LEU cc_start: 0.8599 (OUTLIER) cc_final: 0.8200 (pp) REVERT: E 38 ARG cc_start: 0.7554 (ptt180) cc_final: 0.7104 (ptt-90) REVERT: E 50 TYR cc_start: 0.8196 (p90) cc_final: 0.7833 (p90) REVERT: D 18 ARG cc_start: 0.6583 (ptm160) cc_final: 0.6344 (ptm160) outliers start: 50 outliers final: 28 residues processed: 260 average time/residue: 0.1755 time to fit residues: 76.6773 Evaluate side-chains 244 residues out of total 3396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 215 time to evaluate : 1.024 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 66 VAL Chi-restraints excluded: chain C residue 205 VAL Chi-restraints excluded: chain C residue 389 VAL Chi-restraints excluded: chain C residue 433 THR Chi-restraints excluded: chain C residue 869 THR Chi-restraints excluded: chain C residue 1063 ILE Chi-restraints excluded: chain B residue 66 VAL Chi-restraints excluded: chain B residue 117 ILE Chi-restraints excluded: chain B residue 205 VAL Chi-restraints excluded: chain B residue 389 VAL Chi-restraints excluded: chain B residue 869 THR Chi-restraints excluded: chain B residue 976 ASP Chi-restraints excluded: chain B residue 1045 LEU Chi-restraints excluded: chain B residue 1063 ILE Chi-restraints excluded: chain G residue 57 THR Chi-restraints excluded: chain F residue 69 THR Chi-restraints excluded: chain F residue 106 ILE Chi-restraints excluded: chain E residue 57 THR Chi-restraints excluded: chain E residue 76 ASN Chi-restraints excluded: chain D residue 106 ILE Chi-restraints excluded: chain A residue 66 VAL Chi-restraints excluded: chain A residue 205 VAL Chi-restraints excluded: chain A residue 389 VAL Chi-restraints excluded: chain A residue 869 THR Chi-restraints excluded: chain A residue 1063 ILE Chi-restraints excluded: chain H residue 57 THR Chi-restraints excluded: chain L residue 33 LEU Chi-restraints excluded: chain L residue 69 THR Chi-restraints excluded: chain L residue 106 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 390 random chunks: chunk 229 optimal weight: 4.9990 chunk 335 optimal weight: 2.9990 chunk 161 optimal weight: 3.9990 chunk 348 optimal weight: 4.9990 chunk 276 optimal weight: 5.9990 chunk 34 optimal weight: 4.9990 chunk 90 optimal weight: 3.9990 chunk 169 optimal weight: 1.9990 chunk 74 optimal weight: 1.9990 chunk 12 optimal weight: 0.9980 chunk 371 optimal weight: 6.9990 overall best weight: 2.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 409 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 756 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3547 r_free = 0.3547 target = 0.102281 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3199 r_free = 0.3199 target = 0.082064 restraints weight = 71038.949| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3178 r_free = 0.3178 target = 0.081490 restraints weight = 71167.523| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3190 r_free = 0.3190 target = 0.082306 restraints weight = 83470.120| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3198 r_free = 0.3198 target = 0.082722 restraints weight = 53591.420| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3211 r_free = 0.3211 target = 0.083573 restraints weight = 48279.743| |-----------------------------------------------------------------------------| r_work (final): 0.3209 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7929 moved from start: 0.2136 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.107 32694 Z= 0.227 Angle : 0.875 17.375 44688 Z= 0.411 Chirality : 0.057 0.518 5265 Planarity : 0.005 0.041 5577 Dihedral : 10.246 59.916 6177 Min Nonbonded Distance : 2.418 Molprobity Statistics. All-atom Clashscore : 3.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.34 % Favored : 96.66 % Rotamer: Outliers : 2.21 % Allowed : 8.69 % Favored : 89.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.41 % 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: -0.42 (0.13), residues: 3888 helix: 0.81 (0.21), residues: 654 sheet: 1.13 (0.18), residues: 837 loop : -1.18 (0.11), residues: 2397 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A1021 TYR 0.026 0.002 TYR C1049 PHE 0.020 0.002 PHE A 89 TRP 0.031 0.002 TRP A 245 HIS 0.006 0.001 HIS C1046 Details of bonding type rmsd covalent geometry : bond 0.00542 (32556) covalent geometry : angle 0.77039 (44325) SS BOND : bond 0.00602 ( 51) SS BOND : angle 2.27904 ( 102) hydrogen bonds : bond 0.06756 ( 1092) hydrogen bonds : angle 5.64543 ( 2988) link_ALPHA1-2 : bond 0.01918 ( 3) link_ALPHA1-2 : angle 2.65046 ( 9) link_ALPHA1-3 : bond 0.02460 ( 9) link_ALPHA1-3 : angle 6.33124 ( 27) link_ALPHA1-6 : bond 0.00847 ( 3) link_ALPHA1-6 : angle 2.40244 ( 9) link_BETA1-4 : bond 0.00460 ( 21) link_BETA1-4 : angle 1.92083 ( 63) link_BETA1-6 : bond 0.00978 ( 6) link_BETA1-6 : angle 1.02602 ( 18) link_NAG-ASN : bond 0.00899 ( 45) link_NAG-ASN : angle 6.62529 ( 135) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7776 Ramachandran restraints generated. 3888 Oldfield, 0 Emsley, 3888 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7776 Ramachandran restraints generated. 3888 Oldfield, 0 Emsley, 3888 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 298 residues out of total 3396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 223 time to evaluate : 1.100 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 144 MET cc_start: 0.8033 (mpp) cc_final: 0.7745 (mpp) REVERT: C 151 MET cc_start: 0.7266 (mmt) cc_final: 0.6519 (mmt) REVERT: C 770 MET cc_start: 0.7812 (mtm) cc_final: 0.7481 (mtm) REVERT: C 1045 LEU cc_start: 0.8686 (OUTLIER) cc_final: 0.8362 (pp) REVERT: B 130 PHE cc_start: 0.6435 (m-10) cc_final: 0.6046 (m-10) REVERT: B 151 MET cc_start: 0.7464 (mmt) cc_final: 0.6696 (mmt) REVERT: B 295 ILE cc_start: 0.8706 (mp) cc_final: 0.8428 (mm) REVERT: B 1045 LEU cc_start: 0.8677 (OUTLIER) cc_final: 0.8429 (pp) REVERT: G 38 ARG cc_start: 0.7505 (ptt-90) cc_final: 0.7248 (ptt-90) REVERT: E 50 TYR cc_start: 0.8292 (p90) cc_final: 0.7930 (p90) REVERT: A 144 MET cc_start: 0.7988 (mpp) cc_final: 0.7375 (mpp) REVERT: A 708 VAL cc_start: 0.8771 (OUTLIER) cc_final: 0.8553 (m) outliers start: 75 outliers final: 39 residues processed: 276 average time/residue: 0.1713 time to fit residues: 80.0778 Evaluate side-chains 252 residues out of total 3396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 210 time to evaluate : 1.166 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 66 VAL Chi-restraints excluded: chain C residue 205 VAL Chi-restraints excluded: chain C residue 389 VAL Chi-restraints excluded: chain C residue 433 THR Chi-restraints excluded: chain C residue 581 VAL Chi-restraints excluded: chain C residue 648 CYS Chi-restraints excluded: chain C residue 679 MET Chi-restraints excluded: chain C residue 708 VAL Chi-restraints excluded: chain C residue 869 THR Chi-restraints excluded: chain C residue 1045 LEU Chi-restraints excluded: chain C residue 1063 ILE Chi-restraints excluded: chain C residue 1110 VAL Chi-restraints excluded: chain B residue 66 VAL Chi-restraints excluded: chain B residue 117 ILE Chi-restraints excluded: chain B residue 205 VAL Chi-restraints excluded: chain B residue 299 ILE Chi-restraints excluded: chain B residue 389 VAL Chi-restraints excluded: chain B residue 648 CYS Chi-restraints excluded: chain B residue 679 MET Chi-restraints excluded: chain B residue 869 THR Chi-restraints excluded: chain B residue 976 ASP Chi-restraints excluded: chain B residue 1045 LEU Chi-restraints excluded: chain B residue 1063 ILE Chi-restraints excluded: chain G residue 57 THR Chi-restraints excluded: chain F residue 5 THR Chi-restraints excluded: chain F residue 47 LEU Chi-restraints excluded: chain F residue 69 THR Chi-restraints excluded: chain F residue 106 ILE Chi-restraints excluded: chain E residue 57 THR Chi-restraints excluded: chain E residue 76 ASN Chi-restraints excluded: chain D residue 106 ILE Chi-restraints excluded: chain A residue 66 VAL Chi-restraints excluded: chain A residue 205 VAL Chi-restraints excluded: chain A residue 389 VAL Chi-restraints excluded: chain A residue 648 CYS Chi-restraints excluded: chain A residue 708 VAL Chi-restraints excluded: chain A residue 869 THR Chi-restraints excluded: chain A residue 1063 ILE Chi-restraints excluded: chain H residue 57 THR Chi-restraints excluded: chain L residue 33 LEU Chi-restraints excluded: chain L residue 47 LEU Chi-restraints excluded: chain L residue 106 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 390 random chunks: chunk 243 optimal weight: 3.9990 chunk 23 optimal weight: 1.9990 chunk 201 optimal weight: 3.9990 chunk 366 optimal weight: 0.7980 chunk 156 optimal weight: 3.9990 chunk 163 optimal weight: 1.9990 chunk 68 optimal weight: 0.6980 chunk 388 optimal weight: 3.9990 chunk 389 optimal weight: 1.9990 chunk 95 optimal weight: 2.9990 chunk 321 optimal weight: 0.3980 overall best weight: 1.1784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 70 HIS ** C 409 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 70 HIS A 70 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3576 r_free = 0.3576 target = 0.104123 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3232 r_free = 0.3232 target = 0.083879 restraints weight = 70616.469| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3210 r_free = 0.3210 target = 0.083165 restraints weight = 70036.988| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3225 r_free = 0.3225 target = 0.084196 restraints weight = 79043.508| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3229 r_free = 0.3229 target = 0.084438 restraints weight = 52876.140| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3243 r_free = 0.3243 target = 0.085268 restraints weight = 48385.503| |-----------------------------------------------------------------------------| r_work (final): 0.3244 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7885 moved from start: 0.2316 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 32694 Z= 0.149 Angle : 0.783 16.732 44688 Z= 0.362 Chirality : 0.053 0.519 5265 Planarity : 0.004 0.038 5577 Dihedral : 9.524 59.947 6177 Min Nonbonded Distance : 2.437 Molprobity Statistics. All-atom Clashscore : 3.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.93 % Favored : 97.07 % Rotamer: Outliers : 2.33 % Allowed : 9.36 % Favored : 88.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.41 % 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: -0.28 (0.13), residues: 3888 helix: 1.07 (0.21), residues: 654 sheet: 1.22 (0.18), residues: 843 loop : -1.15 (0.12), residues: 2391 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A1021 TYR 0.017 0.001 TYR C1049 PHE 0.015 0.002 PHE C 130 TRP 0.035 0.001 TRP A 245 HIS 0.004 0.001 HIS B1030 Details of bonding type rmsd covalent geometry : bond 0.00325 (32556) covalent geometry : angle 0.68337 (44325) SS BOND : bond 0.00430 ( 51) SS BOND : angle 1.92979 ( 102) hydrogen bonds : bond 0.05658 ( 1092) hydrogen bonds : angle 5.39207 ( 2988) link_ALPHA1-2 : bond 0.02187 ( 3) link_ALPHA1-2 : angle 2.15520 ( 9) link_ALPHA1-3 : bond 0.02484 ( 9) link_ALPHA1-3 : angle 6.34610 ( 27) link_ALPHA1-6 : bond 0.00538 ( 3) link_ALPHA1-6 : angle 2.13570 ( 9) link_BETA1-4 : bond 0.00459 ( 21) link_BETA1-4 : angle 1.84070 ( 63) link_BETA1-6 : bond 0.00826 ( 6) link_BETA1-6 : angle 1.09258 ( 18) link_NAG-ASN : bond 0.00909 ( 45) link_NAG-ASN : angle 6.04631 ( 135) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7776 Ramachandran restraints generated. 3888 Oldfield, 0 Emsley, 3888 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7776 Ramachandran restraints generated. 3888 Oldfield, 0 Emsley, 3888 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 298 residues out of total 3396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 79 poor density : 219 time to evaluate : 1.144 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 144 MET cc_start: 0.7978 (mpp) cc_final: 0.7676 (mpp) REVERT: C 151 MET cc_start: 0.7292 (mmt) cc_final: 0.7074 (mmt) REVERT: C 1045 LEU cc_start: 0.8608 (OUTLIER) cc_final: 0.8239 (pp) REVERT: B 130 PHE cc_start: 0.6306 (m-10) cc_final: 0.6066 (m-10) REVERT: B 144 MET cc_start: 0.7714 (mpp) cc_final: 0.7091 (mpp) REVERT: B 151 MET cc_start: 0.7534 (mmt) cc_final: 0.6782 (mmt) REVERT: B 295 ILE cc_start: 0.8661 (mp) cc_final: 0.8390 (mm) REVERT: B 1045 LEU cc_start: 0.8646 (OUTLIER) cc_final: 0.8297 (pp) REVERT: G 38 ARG cc_start: 0.7437 (ptt-90) cc_final: 0.7176 (ptt-90) REVERT: E 50 TYR cc_start: 0.8125 (p90) cc_final: 0.7858 (p90) REVERT: A 144 MET cc_start: 0.7881 (mpp) cc_final: 0.7326 (mpp) REVERT: H 64 LYS cc_start: 0.6320 (OUTLIER) cc_final: 0.5621 (pttp) outliers start: 79 outliers final: 46 residues processed: 275 average time/residue: 0.1782 time to fit residues: 82.4111 Evaluate side-chains 251 residues out of total 3396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 202 time to evaluate : 0.968 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 66 VAL Chi-restraints excluded: chain C residue 114 VAL Chi-restraints excluded: chain C residue 205 VAL Chi-restraints excluded: chain C residue 389 VAL Chi-restraints excluded: chain C residue 433 THR Chi-restraints excluded: chain C residue 581 VAL Chi-restraints excluded: chain C residue 648 CYS Chi-restraints excluded: chain C residue 678 THR Chi-restraints excluded: chain C residue 679 MET Chi-restraints excluded: chain C residue 865 THR Chi-restraints excluded: chain C residue 869 THR Chi-restraints excluded: chain C residue 1045 LEU Chi-restraints excluded: chain C residue 1063 ILE Chi-restraints excluded: chain B residue 66 VAL Chi-restraints excluded: chain B residue 117 ILE Chi-restraints excluded: chain B residue 205 VAL Chi-restraints excluded: chain B residue 299 ILE Chi-restraints excluded: chain B residue 389 VAL Chi-restraints excluded: chain B residue 581 VAL Chi-restraints excluded: chain B residue 648 CYS Chi-restraints excluded: chain B residue 678 THR Chi-restraints excluded: chain B residue 708 VAL Chi-restraints excluded: chain B residue 865 THR Chi-restraints excluded: chain B residue 869 THR Chi-restraints excluded: chain B residue 888 PHE Chi-restraints excluded: chain B residue 976 ASP Chi-restraints excluded: chain B residue 1045 LEU Chi-restraints excluded: chain B residue 1063 ILE Chi-restraints excluded: chain G residue 57 THR Chi-restraints excluded: chain F residue 106 ILE Chi-restraints excluded: chain E residue 48 ILE Chi-restraints excluded: chain E residue 57 THR Chi-restraints excluded: chain D residue 13 VAL Chi-restraints excluded: chain D residue 53 THR Chi-restraints excluded: chain D residue 106 ILE Chi-restraints excluded: chain A residue 66 VAL Chi-restraints excluded: chain A residue 205 VAL Chi-restraints excluded: chain A residue 299 ILE Chi-restraints excluded: chain A residue 389 VAL Chi-restraints excluded: chain A residue 648 CYS Chi-restraints excluded: chain A residue 865 THR Chi-restraints excluded: chain A residue 869 THR Chi-restraints excluded: chain A residue 1045 LEU Chi-restraints excluded: chain A residue 1063 ILE Chi-restraints excluded: chain H residue 48 ILE Chi-restraints excluded: chain H residue 57 THR Chi-restraints excluded: chain H residue 64 LYS Chi-restraints excluded: chain L residue 33 LEU Chi-restraints excluded: chain L residue 106 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 390 random chunks: chunk 37 optimal weight: 4.9990 chunk 180 optimal weight: 4.9990 chunk 195 optimal weight: 0.7980 chunk 106 optimal weight: 3.9990 chunk 351 optimal weight: 0.0030 chunk 139 optimal weight: 3.9990 chunk 134 optimal weight: 0.9990 chunk 102 optimal weight: 6.9990 chunk 249 optimal weight: 4.9990 chunk 346 optimal weight: 1.9990 chunk 142 optimal weight: 0.6980 overall best weight: 0.8994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3587 r_free = 0.3587 target = 0.104797 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3245 r_free = 0.3245 target = 0.084533 restraints weight = 70395.292| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3226 r_free = 0.3226 target = 0.083768 restraints weight = 71124.618| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3240 r_free = 0.3240 target = 0.084821 restraints weight = 71875.672| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3247 r_free = 0.3247 target = 0.085275 restraints weight = 52534.776| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3250 r_free = 0.3250 target = 0.085435 restraints weight = 49854.680| |-----------------------------------------------------------------------------| r_work (final): 0.3252 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7871 moved from start: 0.2527 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 32694 Z= 0.133 Angle : 0.741 16.282 44688 Z= 0.340 Chirality : 0.052 0.500 5265 Planarity : 0.004 0.040 5577 Dihedral : 8.783 59.992 6177 Min Nonbonded Distance : 2.426 Molprobity Statistics. All-atom Clashscore : 3.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.52 % Favored : 96.48 % Rotamer: Outliers : 2.24 % Allowed : 10.22 % Favored : 87.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.41 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % 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: -0.24 (0.13), residues: 3888 helix: 1.18 (0.21), residues: 660 sheet: 1.15 (0.18), residues: 834 loop : -1.09 (0.12), residues: 2394 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 747 TYR 0.016 0.001 TYR B1049 PHE 0.016 0.001 PHE B 157 TRP 0.015 0.001 TRP A 245 HIS 0.004 0.001 HIS B1030 Details of bonding type rmsd covalent geometry : bond 0.00285 (32556) covalent geometry : angle 0.64670 (44325) SS BOND : bond 0.00340 ( 51) SS BOND : angle 1.47999 ( 102) hydrogen bonds : bond 0.05114 ( 1092) hydrogen bonds : angle 5.11749 ( 2988) link_ALPHA1-2 : bond 0.02272 ( 3) link_ALPHA1-2 : angle 1.62233 ( 9) link_ALPHA1-3 : bond 0.02469 ( 9) link_ALPHA1-3 : angle 6.33422 ( 27) link_ALPHA1-6 : bond 0.00127 ( 3) link_ALPHA1-6 : angle 1.76700 ( 9) link_BETA1-4 : bond 0.00444 ( 21) link_BETA1-4 : angle 1.80173 ( 63) link_BETA1-6 : bond 0.00822 ( 6) link_BETA1-6 : angle 1.11814 ( 18) link_NAG-ASN : bond 0.00853 ( 45) link_NAG-ASN : angle 5.71410 ( 135) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7776 Ramachandran restraints generated. 3888 Oldfield, 0 Emsley, 3888 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7776 Ramachandran restraints generated. 3888 Oldfield, 0 Emsley, 3888 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 298 residues out of total 3396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 222 time to evaluate : 1.145 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 144 MET cc_start: 0.7994 (mpp) cc_final: 0.7719 (mpp) REVERT: C 151 MET cc_start: 0.7324 (mmt) cc_final: 0.7115 (mmt) REVERT: C 484 TYR cc_start: 0.5498 (m-80) cc_final: 0.5246 (m-80) REVERT: C 884 MET cc_start: 0.8687 (mmp) cc_final: 0.8177 (mmp) REVERT: C 1045 LEU cc_start: 0.8569 (OUTLIER) cc_final: 0.8188 (pp) REVERT: B 130 PHE cc_start: 0.6267 (m-10) cc_final: 0.6044 (m-10) REVERT: B 144 MET cc_start: 0.7781 (mpp) cc_final: 0.7090 (mpp) REVERT: B 151 MET cc_start: 0.7390 (mmt) cc_final: 0.6956 (mmt) REVERT: B 295 ILE cc_start: 0.8580 (mp) cc_final: 0.8301 (mm) REVERT: B 1045 LEU cc_start: 0.8670 (OUTLIER) cc_final: 0.8249 (pp) REVERT: G 38 ARG cc_start: 0.7420 (ptt-90) cc_final: 0.7134 (ptt-90) REVERT: A 144 MET cc_start: 0.7865 (mpp) cc_final: 0.7414 (mpp) outliers start: 76 outliers final: 49 residues processed: 279 average time/residue: 0.1760 time to fit residues: 82.8900 Evaluate side-chains 263 residues out of total 3396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 212 time to evaluate : 1.132 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 66 VAL Chi-restraints excluded: chain C residue 132 LEU Chi-restraints excluded: chain C residue 205 VAL Chi-restraints excluded: chain C residue 389 VAL Chi-restraints excluded: chain C residue 404 VAL Chi-restraints excluded: chain C residue 433 THR Chi-restraints excluded: chain C residue 648 CYS Chi-restraints excluded: chain C residue 678 THR Chi-restraints excluded: chain C residue 679 MET Chi-restraints excluded: chain C residue 708 VAL Chi-restraints excluded: chain C residue 865 THR Chi-restraints excluded: chain C residue 869 THR Chi-restraints excluded: chain C residue 1045 LEU Chi-restraints excluded: chain C residue 1063 ILE Chi-restraints excluded: chain C residue 1110 VAL Chi-restraints excluded: chain B residue 66 VAL Chi-restraints excluded: chain B residue 132 LEU Chi-restraints excluded: chain B residue 205 VAL Chi-restraints excluded: chain B residue 299 ILE Chi-restraints excluded: chain B residue 389 VAL Chi-restraints excluded: chain B residue 581 VAL Chi-restraints excluded: chain B residue 648 CYS Chi-restraints excluded: chain B residue 678 THR Chi-restraints excluded: chain B residue 851 MET Chi-restraints excluded: chain B residue 865 THR Chi-restraints excluded: chain B residue 869 THR Chi-restraints excluded: chain B residue 888 PHE Chi-restraints excluded: chain B residue 1045 LEU Chi-restraints excluded: chain B residue 1063 ILE Chi-restraints excluded: chain G residue 57 THR Chi-restraints excluded: chain F residue 53 THR Chi-restraints excluded: chain F residue 106 ILE Chi-restraints excluded: chain E residue 57 THR Chi-restraints excluded: chain D residue 33 LEU Chi-restraints excluded: chain D residue 53 THR Chi-restraints excluded: chain D residue 106 ILE Chi-restraints excluded: chain A residue 66 VAL Chi-restraints excluded: chain A residue 205 VAL Chi-restraints excluded: chain A residue 299 ILE Chi-restraints excluded: chain A residue 389 VAL Chi-restraints excluded: chain A residue 648 CYS Chi-restraints excluded: chain A residue 678 THR Chi-restraints excluded: chain A residue 865 THR Chi-restraints excluded: chain A residue 869 THR Chi-restraints excluded: chain A residue 888 PHE Chi-restraints excluded: chain A residue 1045 LEU Chi-restraints excluded: chain A residue 1063 ILE Chi-restraints excluded: chain H residue 57 THR Chi-restraints excluded: chain L residue 33 LEU Chi-restraints excluded: chain L residue 53 THR Chi-restraints excluded: chain L residue 106 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 390 random chunks: chunk 160 optimal weight: 3.9990 chunk 283 optimal weight: 1.9990 chunk 373 optimal weight: 6.9990 chunk 97 optimal weight: 2.9990 chunk 358 optimal weight: 3.9990 chunk 26 optimal weight: 1.9990 chunk 271 optimal weight: 6.9990 chunk 138 optimal weight: 3.9990 chunk 314 optimal weight: 2.9990 chunk 48 optimal weight: 7.9990 chunk 240 optimal weight: 7.9990 overall best weight: 2.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 744 GLN A 409 ASN A 756 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3520 r_free = 0.3520 target = 0.100734 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3169 r_free = 0.3169 target = 0.080552 restraints weight = 71118.857| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3145 r_free = 0.3145 target = 0.079998 restraints weight = 73245.501| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3157 r_free = 0.3157 target = 0.080796 restraints weight = 85617.111| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3163 r_free = 0.3163 target = 0.081109 restraints weight = 55076.675| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3174 r_free = 0.3174 target = 0.081771 restraints weight = 48919.851| |-----------------------------------------------------------------------------| r_work (final): 0.3169 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7976 moved from start: 0.2747 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.129 32694 Z= 0.258 Angle : 0.882 16.358 44688 Z= 0.418 Chirality : 0.058 0.774 5265 Planarity : 0.005 0.039 5577 Dihedral : 9.127 59.956 6177 Min Nonbonded Distance : 2.424 Molprobity Statistics. All-atom Clashscore : 4.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.45 % Favored : 94.55 % Rotamer: Outliers : 2.50 % Allowed : 10.69 % Favored : 86.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.41 % 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: -0.75 (0.13), residues: 3888 helix: 0.76 (0.21), residues: 657 sheet: 0.81 (0.18), residues: 861 loop : -1.45 (0.11), residues: 2370 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A1021 TYR 0.027 0.002 TYR C1049 PHE 0.021 0.003 PHE A 89 TRP 0.017 0.002 TRP A 245 HIS 0.006 0.001 HIS C1046 Details of bonding type rmsd covalent geometry : bond 0.00628 (32556) covalent geometry : angle 0.78886 (44325) SS BOND : bond 0.00645 ( 51) SS BOND : angle 2.14739 ( 102) hydrogen bonds : bond 0.06938 ( 1092) hydrogen bonds : angle 5.57328 ( 2988) link_ALPHA1-2 : bond 0.01900 ( 3) link_ALPHA1-2 : angle 1.50184 ( 9) link_ALPHA1-3 : bond 0.02343 ( 9) link_ALPHA1-3 : angle 6.56596 ( 27) link_ALPHA1-6 : bond 0.00094 ( 3) link_ALPHA1-6 : angle 2.16624 ( 9) link_BETA1-4 : bond 0.00468 ( 21) link_BETA1-4 : angle 1.87964 ( 63) link_BETA1-6 : bond 0.00923 ( 6) link_BETA1-6 : angle 1.12265 ( 18) link_NAG-ASN : bond 0.00849 ( 45) link_NAG-ASN : angle 6.22103 ( 135) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7776 Ramachandran restraints generated. 3888 Oldfield, 0 Emsley, 3888 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7776 Ramachandran restraints generated. 3888 Oldfield, 0 Emsley, 3888 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 309 residues out of total 3396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 85 poor density : 224 time to evaluate : 1.121 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 144 MET cc_start: 0.7986 (mpp) cc_final: 0.7685 (mpp) REVERT: C 884 MET cc_start: 0.8822 (mmp) cc_final: 0.8038 (mmt) REVERT: C 1045 LEU cc_start: 0.8779 (OUTLIER) cc_final: 0.8409 (pp) REVERT: B 130 PHE cc_start: 0.6637 (m-10) cc_final: 0.6394 (m-10) REVERT: B 144 MET cc_start: 0.7914 (mpp) cc_final: 0.7192 (mpp) REVERT: B 151 MET cc_start: 0.7537 (mmt) cc_final: 0.6956 (mmt) REVERT: B 295 ILE cc_start: 0.8643 (mp) cc_final: 0.8386 (mm) REVERT: B 1032 MET cc_start: 0.8456 (mtt) cc_final: 0.8078 (mtt) REVERT: B 1045 LEU cc_start: 0.8701 (OUTLIER) cc_final: 0.8483 (pp) REVERT: G 64 LYS cc_start: 0.6447 (OUTLIER) cc_final: 0.5704 (pttp) REVERT: G 77 GLN cc_start: 0.8263 (mt0) cc_final: 0.7982 (mt0) REVERT: E 64 LYS cc_start: 0.6372 (OUTLIER) cc_final: 0.5312 (pttp) REVERT: A 144 MET cc_start: 0.7908 (mpp) cc_final: 0.7537 (mpp) REVERT: H 50 TYR cc_start: 0.7955 (p90) cc_final: 0.7487 (p90) REVERT: H 64 LYS cc_start: 0.6370 (OUTLIER) cc_final: 0.5654 (pttp) outliers start: 85 outliers final: 55 residues processed: 286 average time/residue: 0.1744 time to fit residues: 83.9772 Evaluate side-chains 270 residues out of total 3396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 210 time to evaluate : 1.174 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 66 VAL Chi-restraints excluded: chain C residue 114 VAL Chi-restraints excluded: chain C residue 119 ASN Chi-restraints excluded: chain C residue 205 VAL Chi-restraints excluded: chain C residue 389 VAL Chi-restraints excluded: chain C residue 404 VAL Chi-restraints excluded: chain C residue 433 THR Chi-restraints excluded: chain C residue 581 VAL Chi-restraints excluded: chain C residue 648 CYS Chi-restraints excluded: chain C residue 678 THR Chi-restraints excluded: chain C residue 679 MET Chi-restraints excluded: chain C residue 708 VAL Chi-restraints excluded: chain C residue 865 THR Chi-restraints excluded: chain C residue 869 THR Chi-restraints excluded: chain C residue 1045 LEU Chi-restraints excluded: chain C residue 1063 ILE Chi-restraints excluded: chain B residue 56 GLN Chi-restraints excluded: chain B residue 66 VAL Chi-restraints excluded: chain B residue 132 LEU Chi-restraints excluded: chain B residue 205 VAL Chi-restraints excluded: chain B residue 299 ILE Chi-restraints excluded: chain B residue 389 VAL Chi-restraints excluded: chain B residue 581 VAL Chi-restraints excluded: chain B residue 648 CYS Chi-restraints excluded: chain B residue 678 THR Chi-restraints excluded: chain B residue 708 VAL Chi-restraints excluded: chain B residue 851 MET Chi-restraints excluded: chain B residue 865 THR Chi-restraints excluded: chain B residue 869 THR Chi-restraints excluded: chain B residue 888 PHE Chi-restraints excluded: chain B residue 1045 LEU Chi-restraints excluded: chain B residue 1063 ILE Chi-restraints excluded: chain G residue 57 THR Chi-restraints excluded: chain G residue 64 LYS Chi-restraints excluded: chain F residue 53 THR Chi-restraints excluded: chain F residue 106 ILE Chi-restraints excluded: chain E residue 57 THR Chi-restraints excluded: chain E residue 64 LYS Chi-restraints excluded: chain D residue 13 VAL Chi-restraints excluded: chain D residue 33 LEU Chi-restraints excluded: chain D residue 53 THR Chi-restraints excluded: chain D residue 106 ILE Chi-restraints excluded: chain A residue 66 VAL Chi-restraints excluded: chain A residue 205 VAL Chi-restraints excluded: chain A residue 389 VAL Chi-restraints excluded: chain A residue 648 CYS Chi-restraints excluded: chain A residue 678 THR Chi-restraints excluded: chain A residue 787 ILE Chi-restraints excluded: chain A residue 865 THR Chi-restraints excluded: chain A residue 869 THR Chi-restraints excluded: chain A residue 1045 LEU Chi-restraints excluded: chain A residue 1063 ILE Chi-restraints excluded: chain H residue 48 ILE Chi-restraints excluded: chain H residue 57 THR Chi-restraints excluded: chain H residue 64 LYS Chi-restraints excluded: chain L residue 13 VAL Chi-restraints excluded: chain L residue 18 ARG Chi-restraints excluded: chain L residue 33 LEU Chi-restraints excluded: chain L residue 47 LEU Chi-restraints excluded: chain L residue 53 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 390 random chunks: chunk 151 optimal weight: 0.7980 chunk 224 optimal weight: 9.9990 chunk 103 optimal weight: 0.0770 chunk 146 optimal weight: 6.9990 chunk 334 optimal weight: 0.9990 chunk 19 optimal weight: 0.9980 chunk 348 optimal weight: 4.9990 chunk 80 optimal weight: 5.9990 chunk 64 optimal weight: 3.9990 chunk 152 optimal weight: 4.9990 chunk 208 optimal weight: 0.9980 overall best weight: 0.7740 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 280 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 744 GLN ** A 280 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3572 r_free = 0.3572 target = 0.103873 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3230 r_free = 0.3230 target = 0.083740 restraints weight = 70577.601| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3207 r_free = 0.3207 target = 0.082901 restraints weight = 71248.448| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3219 r_free = 0.3219 target = 0.083758 restraints weight = 77721.916| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3232 r_free = 0.3232 target = 0.084570 restraints weight = 53563.421| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3235 r_free = 0.3235 target = 0.084734 restraints weight = 48105.276| |-----------------------------------------------------------------------------| r_work (final): 0.3238 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7893 moved from start: 0.2820 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 32694 Z= 0.136 Angle : 0.772 16.212 44688 Z= 0.357 Chirality : 0.053 0.709 5265 Planarity : 0.004 0.041 5577 Dihedral : 8.610 59.661 6177 Min Nonbonded Distance : 2.395 Molprobity Statistics. All-atom Clashscore : 4.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.32 % Favored : 96.68 % Rotamer: Outliers : 1.71 % Allowed : 11.57 % Favored : 86.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.41 % 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: -0.48 (0.13), residues: 3888 helix: 1.07 (0.21), residues: 663 sheet: 1.01 (0.18), residues: 840 loop : -1.30 (0.12), residues: 2385 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 747 TYR 0.019 0.001 TYR G 50 PHE 0.016 0.001 PHE B 22 TRP 0.037 0.001 TRP B 245 HIS 0.005 0.001 HIS B1030 Details of bonding type rmsd covalent geometry : bond 0.00282 (32556) covalent geometry : angle 0.67272 (44325) SS BOND : bond 0.00589 ( 51) SS BOND : angle 2.26535 ( 102) hydrogen bonds : bond 0.05246 ( 1092) hydrogen bonds : angle 5.22701 ( 2988) link_ALPHA1-2 : bond 0.01894 ( 3) link_ALPHA1-2 : angle 1.90373 ( 9) link_ALPHA1-3 : bond 0.02248 ( 9) link_ALPHA1-3 : angle 6.40109 ( 27) link_ALPHA1-6 : bond 0.00195 ( 3) link_ALPHA1-6 : angle 1.45483 ( 9) link_BETA1-4 : bond 0.00447 ( 21) link_BETA1-4 : angle 1.78574 ( 63) link_BETA1-6 : bond 0.00755 ( 6) link_BETA1-6 : angle 1.24068 ( 18) link_NAG-ASN : bond 0.00903 ( 45) link_NAG-ASN : angle 5.86160 ( 135) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7776 Ramachandran restraints generated. 3888 Oldfield, 0 Emsley, 3888 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7776 Ramachandran restraints generated. 3888 Oldfield, 0 Emsley, 3888 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 285 residues out of total 3396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 227 time to evaluate : 1.063 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 144 MET cc_start: 0.7920 (mpp) cc_final: 0.7635 (mpp) REVERT: C 884 MET cc_start: 0.8766 (mmp) cc_final: 0.8190 (mmp) REVERT: C 1045 LEU cc_start: 0.8662 (OUTLIER) cc_final: 0.8332 (pp) REVERT: B 144 MET cc_start: 0.7892 (mpp) cc_final: 0.7209 (mpp) REVERT: B 151 MET cc_start: 0.7490 (mmt) cc_final: 0.7118 (mmt) REVERT: B 295 ILE cc_start: 0.8514 (mp) cc_final: 0.8247 (mm) REVERT: B 1032 MET cc_start: 0.8459 (mtt) cc_final: 0.8149 (mtt) REVERT: B 1045 LEU cc_start: 0.8625 (OUTLIER) cc_final: 0.8218 (pp) REVERT: G 77 GLN cc_start: 0.8179 (mt0) cc_final: 0.7963 (mt0) REVERT: E 64 LYS cc_start: 0.6468 (OUTLIER) cc_final: 0.5437 (pttp) REVERT: A 151 MET cc_start: 0.7539 (mmt) cc_final: 0.7230 (mmt) REVERT: H 50 TYR cc_start: 0.7964 (p90) cc_final: 0.7614 (p90) REVERT: H 64 LYS cc_start: 0.6325 (OUTLIER) cc_final: 0.5629 (pttp) outliers start: 58 outliers final: 43 residues processed: 266 average time/residue: 0.1819 time to fit residues: 80.7879 Evaluate side-chains 262 residues out of total 3396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 215 time to evaluate : 1.136 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 114 VAL Chi-restraints excluded: chain C residue 132 LEU Chi-restraints excluded: chain C residue 205 VAL Chi-restraints excluded: chain C residue 389 VAL Chi-restraints excluded: chain C residue 404 VAL Chi-restraints excluded: chain C residue 679 MET Chi-restraints excluded: chain C residue 708 VAL Chi-restraints excluded: chain C residue 865 THR Chi-restraints excluded: chain C residue 1045 LEU Chi-restraints excluded: chain C residue 1063 ILE Chi-restraints excluded: chain B residue 56 GLN Chi-restraints excluded: chain B residue 132 LEU Chi-restraints excluded: chain B residue 205 VAL Chi-restraints excluded: chain B residue 299 ILE Chi-restraints excluded: chain B residue 389 VAL Chi-restraints excluded: chain B residue 581 VAL Chi-restraints excluded: chain B residue 648 CYS Chi-restraints excluded: chain B residue 851 MET Chi-restraints excluded: chain B residue 865 THR Chi-restraints excluded: chain B residue 869 THR Chi-restraints excluded: chain B residue 1045 LEU Chi-restraints excluded: chain B residue 1063 ILE Chi-restraints excluded: chain G residue 48 ILE Chi-restraints excluded: chain G residue 57 THR Chi-restraints excluded: chain F residue 5 THR Chi-restraints excluded: chain F residue 13 VAL Chi-restraints excluded: chain F residue 106 ILE Chi-restraints excluded: chain E residue 57 THR Chi-restraints excluded: chain E residue 64 LYS Chi-restraints excluded: chain D residue 13 VAL Chi-restraints excluded: chain D residue 33 LEU Chi-restraints excluded: chain D residue 106 ILE Chi-restraints excluded: chain A residue 119 ASN Chi-restraints excluded: chain A residue 205 VAL Chi-restraints excluded: chain A residue 299 ILE Chi-restraints excluded: chain A residue 389 VAL Chi-restraints excluded: chain A residue 648 CYS Chi-restraints excluded: chain A residue 708 VAL Chi-restraints excluded: chain A residue 787 ILE Chi-restraints excluded: chain A residue 865 THR Chi-restraints excluded: chain A residue 869 THR Chi-restraints excluded: chain A residue 1045 LEU Chi-restraints excluded: chain A residue 1063 ILE Chi-restraints excluded: chain H residue 57 THR Chi-restraints excluded: chain H residue 64 LYS Chi-restraints excluded: chain L residue 13 VAL Chi-restraints excluded: chain L residue 33 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 390 random chunks: chunk 104 optimal weight: 0.9980 chunk 309 optimal weight: 0.9980 chunk 139 optimal weight: 4.9990 chunk 59 optimal weight: 0.9980 chunk 349 optimal weight: 3.9990 chunk 30 optimal weight: 0.8980 chunk 43 optimal weight: 3.9990 chunk 231 optimal weight: 6.9990 chunk 386 optimal weight: 9.9990 chunk 179 optimal weight: 0.4980 chunk 334 optimal weight: 2.9990 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 280 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 280 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3575 r_free = 0.3575 target = 0.104121 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3234 r_free = 0.3234 target = 0.083872 restraints weight = 70241.031| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3212 r_free = 0.3212 target = 0.083053 restraints weight = 71275.203| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3226 r_free = 0.3226 target = 0.084059 restraints weight = 74576.422| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3235 r_free = 0.3235 target = 0.084630 restraints weight = 52666.962| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3237 r_free = 0.3237 target = 0.084767 restraints weight = 50055.214| |-----------------------------------------------------------------------------| r_work (final): 0.3238 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7888 moved from start: 0.2894 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 32694 Z= 0.132 Angle : 0.756 15.944 44688 Z= 0.347 Chirality : 0.052 0.560 5265 Planarity : 0.004 0.042 5577 Dihedral : 8.366 59.861 6177 Min Nonbonded Distance : 2.468 Molprobity Statistics. All-atom Clashscore : 4.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.48 % Favored : 95.52 % Rotamer: Outliers : 1.68 % Allowed : 11.96 % Favored : 86.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.41 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.39 (0.13), residues: 3888 helix: 1.21 (0.21), residues: 663 sheet: 1.07 (0.18), residues: 840 loop : -1.26 (0.12), residues: 2385 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 18 TYR 0.017 0.001 TYR G 50 PHE 0.031 0.001 PHE A 741 TRP 0.013 0.001 TRP B 245 HIS 0.004 0.001 HIS B1030 Details of bonding type rmsd covalent geometry : bond 0.00284 (32556) covalent geometry : angle 0.65935 (44325) SS BOND : bond 0.00421 ( 51) SS BOND : angle 2.17579 ( 102) hydrogen bonds : bond 0.05074 ( 1092) hydrogen bonds : angle 5.09985 ( 2988) link_ALPHA1-2 : bond 0.01659 ( 3) link_ALPHA1-2 : angle 2.06620 ( 9) link_ALPHA1-3 : bond 0.02268 ( 9) link_ALPHA1-3 : angle 6.36593 ( 27) link_ALPHA1-6 : bond 0.00231 ( 3) link_ALPHA1-6 : angle 1.49978 ( 9) link_BETA1-4 : bond 0.00435 ( 21) link_BETA1-4 : angle 1.74837 ( 63) link_BETA1-6 : bond 0.00805 ( 6) link_BETA1-6 : angle 1.18494 ( 18) link_NAG-ASN : bond 0.00854 ( 45) link_NAG-ASN : angle 5.72800 ( 135) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7776 Ramachandran restraints generated. 3888 Oldfield, 0 Emsley, 3888 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7776 Ramachandran restraints generated. 3888 Oldfield, 0 Emsley, 3888 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 275 residues out of total 3396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 218 time to evaluate : 0.931 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 144 MET cc_start: 0.7876 (mpp) cc_final: 0.7591 (mpp) REVERT: C 884 MET cc_start: 0.8741 (mmp) cc_final: 0.8194 (mmp) REVERT: C 1045 LEU cc_start: 0.8654 (OUTLIER) cc_final: 0.8324 (pp) REVERT: B 144 MET cc_start: 0.7843 (mpp) cc_final: 0.7021 (mpp) REVERT: B 151 MET cc_start: 0.7295 (mmt) cc_final: 0.6998 (mmt) REVERT: B 295 ILE cc_start: 0.8500 (mp) cc_final: 0.8225 (mm) REVERT: B 1032 MET cc_start: 0.8526 (mtt) cc_final: 0.8245 (mtt) REVERT: B 1045 LEU cc_start: 0.8632 (OUTLIER) cc_final: 0.8212 (pp) REVERT: G 64 LYS cc_start: 0.6603 (OUTLIER) cc_final: 0.5839 (pttp) REVERT: G 77 GLN cc_start: 0.8188 (mt0) cc_final: 0.7965 (mt0) REVERT: E 50 TYR cc_start: 0.8213 (p90) cc_final: 0.7899 (p90) REVERT: E 64 LYS cc_start: 0.6403 (OUTLIER) cc_final: 0.5392 (pttp) REVERT: A 151 MET cc_start: 0.7450 (mmt) cc_final: 0.7122 (mmt) REVERT: H 50 TYR cc_start: 0.7968 (p90) cc_final: 0.7585 (p90) REVERT: H 64 LYS cc_start: 0.6332 (OUTLIER) cc_final: 0.5646 (pttp) outliers start: 57 outliers final: 44 residues processed: 257 average time/residue: 0.1833 time to fit residues: 78.1221 Evaluate side-chains 261 residues out of total 3396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 212 time to evaluate : 0.964 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 114 VAL Chi-restraints excluded: chain C residue 205 VAL Chi-restraints excluded: chain C residue 389 VAL Chi-restraints excluded: chain C residue 404 VAL Chi-restraints excluded: chain C residue 679 MET Chi-restraints excluded: chain C residue 708 VAL Chi-restraints excluded: chain C residue 865 THR Chi-restraints excluded: chain C residue 869 THR Chi-restraints excluded: chain C residue 1045 LEU Chi-restraints excluded: chain C residue 1063 ILE Chi-restraints excluded: chain B residue 132 LEU Chi-restraints excluded: chain B residue 205 VAL Chi-restraints excluded: chain B residue 299 ILE Chi-restraints excluded: chain B residue 389 VAL Chi-restraints excluded: chain B residue 581 VAL Chi-restraints excluded: chain B residue 648 CYS Chi-restraints excluded: chain B residue 678 THR Chi-restraints excluded: chain B residue 708 VAL Chi-restraints excluded: chain B residue 851 MET Chi-restraints excluded: chain B residue 865 THR Chi-restraints excluded: chain B residue 869 THR Chi-restraints excluded: chain B residue 888 PHE Chi-restraints excluded: chain B residue 1045 LEU Chi-restraints excluded: chain B residue 1063 ILE Chi-restraints excluded: chain G residue 48 ILE Chi-restraints excluded: chain G residue 57 THR Chi-restraints excluded: chain G residue 64 LYS Chi-restraints excluded: chain F residue 13 VAL Chi-restraints excluded: chain F residue 53 THR Chi-restraints excluded: chain F residue 106 ILE Chi-restraints excluded: chain E residue 57 THR Chi-restraints excluded: chain E residue 64 LYS Chi-restraints excluded: chain D residue 13 VAL Chi-restraints excluded: chain D residue 33 LEU Chi-restraints excluded: chain D residue 106 ILE Chi-restraints excluded: chain A residue 119 ASN Chi-restraints excluded: chain A residue 205 VAL Chi-restraints excluded: chain A residue 299 ILE Chi-restraints excluded: chain A residue 389 VAL Chi-restraints excluded: chain A residue 678 THR Chi-restraints excluded: chain A residue 787 ILE Chi-restraints excluded: chain A residue 865 THR Chi-restraints excluded: chain A residue 869 THR Chi-restraints excluded: chain A residue 1045 LEU Chi-restraints excluded: chain A residue 1063 ILE Chi-restraints excluded: chain H residue 57 THR Chi-restraints excluded: chain H residue 64 LYS Chi-restraints excluded: chain L residue 13 VAL Chi-restraints excluded: chain L residue 33 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 390 random chunks: chunk 335 optimal weight: 3.9990 chunk 299 optimal weight: 0.9990 chunk 80 optimal weight: 3.9990 chunk 8 optimal weight: 5.9990 chunk 98 optimal weight: 3.9990 chunk 94 optimal weight: 3.9990 chunk 278 optimal weight: 2.9990 chunk 189 optimal weight: 0.9980 chunk 86 optimal weight: 3.9990 chunk 308 optimal weight: 0.9990 chunk 212 optimal weight: 1.9990 overall best weight: 1.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3556 r_free = 0.3556 target = 0.102965 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3212 r_free = 0.3212 target = 0.082771 restraints weight = 71047.510| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3192 r_free = 0.3192 target = 0.082543 restraints weight = 71895.783| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3200 r_free = 0.3200 target = 0.083071 restraints weight = 84175.512| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3209 r_free = 0.3209 target = 0.083520 restraints weight = 53436.281| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3228 r_free = 0.3228 target = 0.084673 restraints weight = 47036.010| |-----------------------------------------------------------------------------| r_work (final): 0.3221 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7905 moved from start: 0.2956 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.065 32694 Z= 0.168 Angle : 0.782 15.783 44688 Z= 0.362 Chirality : 0.053 0.515 5265 Planarity : 0.004 0.039 5577 Dihedral : 8.419 58.952 6177 Min Nonbonded Distance : 2.492 Molprobity Statistics. All-atom Clashscore : 4.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.84 % Favored : 95.16 % Rotamer: Outliers : 1.83 % Allowed : 11.98 % Favored : 86.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.41 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.52 (0.13), residues: 3888 helix: 1.29 (0.21), residues: 645 sheet: 0.81 (0.18), residues: 879 loop : -1.35 (0.12), residues: 2364 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 18 TYR 0.018 0.002 TYR B1049 PHE 0.032 0.002 PHE A 741 TRP 0.016 0.001 TRP B 245 HIS 0.004 0.001 HIS A1030 Details of bonding type rmsd covalent geometry : bond 0.00392 (32556) covalent geometry : angle 0.68652 (44325) SS BOND : bond 0.00533 ( 51) SS BOND : angle 2.30885 ( 102) hydrogen bonds : bond 0.05558 ( 1092) hydrogen bonds : angle 5.18571 ( 2988) link_ALPHA1-2 : bond 0.01427 ( 3) link_ALPHA1-2 : angle 2.17921 ( 9) link_ALPHA1-3 : bond 0.02149 ( 9) link_ALPHA1-3 : angle 6.38774 ( 27) link_ALPHA1-6 : bond 0.00197 ( 3) link_ALPHA1-6 : angle 1.55985 ( 9) link_BETA1-4 : bond 0.00427 ( 21) link_BETA1-4 : angle 1.74107 ( 63) link_BETA1-6 : bond 0.00828 ( 6) link_BETA1-6 : angle 1.19641 ( 18) link_NAG-ASN : bond 0.00829 ( 45) link_NAG-ASN : angle 5.75996 ( 135) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7776 Ramachandran restraints generated. 3888 Oldfield, 0 Emsley, 3888 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7776 Ramachandran restraints generated. 3888 Oldfield, 0 Emsley, 3888 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 276 residues out of total 3396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 214 time to evaluate : 1.007 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 144 MET cc_start: 0.7879 (mpp) cc_final: 0.7602 (mpp) REVERT: C 151 MET cc_start: 0.7102 (mmt) cc_final: 0.6857 (tpp) REVERT: C 1045 LEU cc_start: 0.8697 (OUTLIER) cc_final: 0.8341 (pp) REVERT: B 144 MET cc_start: 0.7857 (mpp) cc_final: 0.7155 (mpp) REVERT: B 295 ILE cc_start: 0.8544 (mp) cc_final: 0.8284 (mm) REVERT: B 770 MET cc_start: 0.7937 (OUTLIER) cc_final: 0.7296 (mtm) REVERT: B 1032 MET cc_start: 0.8624 (mtt) cc_final: 0.8311 (mtt) REVERT: B 1045 LEU cc_start: 0.8686 (OUTLIER) cc_final: 0.8348 (pp) REVERT: G 64 LYS cc_start: 0.6635 (OUTLIER) cc_final: 0.5924 (pttp) REVERT: G 77 GLN cc_start: 0.8223 (mt0) cc_final: 0.7985 (mt0) REVERT: E 36 TRP cc_start: 0.8132 (m100) cc_final: 0.7444 (m100) REVERT: E 50 TYR cc_start: 0.8324 (p90) cc_final: 0.7934 (p90) REVERT: E 64 LYS cc_start: 0.6479 (OUTLIER) cc_final: 0.5473 (pttp) REVERT: H 64 LYS cc_start: 0.6386 (OUTLIER) cc_final: 0.5675 (pttp) outliers start: 62 outliers final: 48 residues processed: 260 average time/residue: 0.1881 time to fit residues: 81.3743 Evaluate side-chains 265 residues out of total 3396 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 211 time to evaluate : 0.799 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 114 VAL Chi-restraints excluded: chain C residue 132 LEU Chi-restraints excluded: chain C residue 205 VAL Chi-restraints excluded: chain C residue 389 VAL Chi-restraints excluded: chain C residue 404 VAL Chi-restraints excluded: chain C residue 678 THR Chi-restraints excluded: chain C residue 708 VAL Chi-restraints excluded: chain C residue 865 THR Chi-restraints excluded: chain C residue 869 THR Chi-restraints excluded: chain C residue 1045 LEU Chi-restraints excluded: chain C residue 1063 ILE Chi-restraints excluded: chain B residue 132 LEU Chi-restraints excluded: chain B residue 205 VAL Chi-restraints excluded: chain B residue 299 ILE Chi-restraints excluded: chain B residue 389 VAL Chi-restraints excluded: chain B residue 581 VAL Chi-restraints excluded: chain B residue 648 CYS Chi-restraints excluded: chain B residue 678 THR Chi-restraints excluded: chain B residue 708 VAL Chi-restraints excluded: chain B residue 770 MET Chi-restraints excluded: chain B residue 851 MET Chi-restraints excluded: chain B residue 865 THR Chi-restraints excluded: chain B residue 869 THR Chi-restraints excluded: chain B residue 888 PHE Chi-restraints excluded: chain B residue 1045 LEU Chi-restraints excluded: chain B residue 1063 ILE Chi-restraints excluded: chain G residue 48 ILE Chi-restraints excluded: chain G residue 57 THR Chi-restraints excluded: chain G residue 64 LYS Chi-restraints excluded: chain F residue 5 THR Chi-restraints excluded: chain F residue 13 VAL Chi-restraints excluded: chain F residue 53 THR Chi-restraints excluded: chain F residue 106 ILE Chi-restraints excluded: chain E residue 57 THR Chi-restraints excluded: chain E residue 64 LYS Chi-restraints excluded: chain D residue 13 VAL Chi-restraints excluded: chain D residue 33 LEU Chi-restraints excluded: chain D residue 106 ILE Chi-restraints excluded: chain A residue 66 VAL Chi-restraints excluded: chain A residue 119 ASN Chi-restraints excluded: chain A residue 205 VAL Chi-restraints excluded: chain A residue 299 ILE Chi-restraints excluded: chain A residue 389 VAL Chi-restraints excluded: chain A residue 678 THR Chi-restraints excluded: chain A residue 787 ILE Chi-restraints excluded: chain A residue 865 THR Chi-restraints excluded: chain A residue 869 THR Chi-restraints excluded: chain A residue 1045 LEU Chi-restraints excluded: chain A residue 1063 ILE Chi-restraints excluded: chain H residue 57 THR Chi-restraints excluded: chain H residue 64 LYS Chi-restraints excluded: chain L residue 13 VAL Chi-restraints excluded: chain L residue 18 ARG Chi-restraints excluded: chain L residue 33 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 390 random chunks: chunk 382 optimal weight: 10.0000 chunk 180 optimal weight: 0.6980 chunk 67 optimal weight: 4.9990 chunk 279 optimal weight: 4.9990 chunk 196 optimal weight: 4.9990 chunk 327 optimal weight: 5.9990 chunk 281 optimal weight: 0.8980 chunk 182 optimal weight: 2.9990 chunk 77 optimal weight: 2.9990 chunk 95 optimal weight: 0.9980 chunk 117 optimal weight: 3.9990 overall best weight: 1.7184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3548 r_free = 0.3548 target = 0.102512 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3203 r_free = 0.3203 target = 0.082282 restraints weight = 71111.760| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3183 r_free = 0.3183 target = 0.081947 restraints weight = 72847.334| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3194 r_free = 0.3194 target = 0.082609 restraints weight = 83482.781| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3200 r_free = 0.3200 target = 0.082977 restraints weight = 53859.886| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3215 r_free = 0.3215 target = 0.083867 restraints weight = 47671.811| |-----------------------------------------------------------------------------| r_work (final): 0.3209 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7923 moved from start: 0.3033 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.071 32694 Z= 0.175 Angle : 0.792 15.708 44688 Z= 0.368 Chirality : 0.053 0.495 5265 Planarity : 0.004 0.038 5577 Dihedral : 8.473 59.288 6177 Min Nonbonded Distance : 2.516 Molprobity Statistics. All-atom Clashscore : 4.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.99 % Favored : 95.01 % Rotamer: Outliers : 1.94 % Allowed : 12.04 % Favored : 86.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.41 % 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: 3888 helix: 1.24 (0.21), residues: 645 sheet: 0.76 (0.18), residues: 879 loop : -1.41 (0.12), residues: 2364 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A1021 TYR 0.019 0.002 TYR B1049 PHE 0.032 0.002 PHE A 741 TRP 0.016 0.001 TRP B 245 HIS 0.004 0.001 HIS B1030 Details of bonding type rmsd covalent geometry : bond 0.00410 (32556) covalent geometry : angle 0.69754 (44325) SS BOND : bond 0.00498 ( 51) SS BOND : angle 2.40750 ( 102) hydrogen bonds : bond 0.05756 ( 1092) hydrogen bonds : angle 5.24830 ( 2988) link_ALPHA1-2 : bond 0.01251 ( 3) link_ALPHA1-2 : angle 2.37708 ( 9) link_ALPHA1-3 : bond 0.02028 ( 9) link_ALPHA1-3 : angle 6.40287 ( 27) link_ALPHA1-6 : bond 0.00120 ( 3) link_ALPHA1-6 : angle 1.51644 ( 9) link_BETA1-4 : bond 0.00432 ( 21) link_BETA1-4 : angle 1.74169 ( 63) link_BETA1-6 : bond 0.00831 ( 6) link_BETA1-6 : angle 1.22928 ( 18) link_NAG-ASN : bond 0.00818 ( 45) link_NAG-ASN : angle 5.74621 ( 135) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3856.87 seconds wall clock time: 68 minutes 7.23 seconds (4087.23 seconds total)