Starting phenix.real_space_refine on Thu Feb 5 17:41:44 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9nc6_49241/02_2026/9nc6_49241.cif Found real_map, /net/cci-nas-00/data/ceres_data/9nc6_49241/02_2026/9nc6_49241.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.52 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9nc6_49241/02_2026/9nc6_49241.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9nc6_49241/02_2026/9nc6_49241.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9nc6_49241/02_2026/9nc6_49241.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9nc6_49241/02_2026/9nc6_49241.map" } resolution = 3.52 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= -0.001 sd= 0.034 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 125 5.16 5 C 11778 2.51 5 N 3124 2.21 5 O 3802 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 57 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 18829 Number of models: 1 Model: "" Number of chains: 36 Chain: "E" Number of atoms: 3594 Number of conformers: 1 Conformer: "" Number of residues, atoms: 454, 3594 Classifications: {'peptide': 454} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 22, 'TRANS': 431} Chain breaks: 1 Chain: "F" Number of atoms: 1133 Number of conformers: 1 Conformer: "" Number of residues, atoms: 143, 1133 Classifications: {'peptide': 143} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 141} Chain breaks: 1 Chain: "A" Number of atoms: 3594 Number of conformers: 1 Conformer: "" Number of residues, atoms: 454, 3594 Classifications: {'peptide': 454} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 22, 'TRANS': 431} Chain breaks: 1 Chain: "B" Number of atoms: 1133 Number of conformers: 1 Conformer: "" Number of residues, atoms: 143, 1133 Classifications: {'peptide': 143} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 141} Chain breaks: 1 Chain: "C" Number of atoms: 3511 Number of conformers: 1 Conformer: "" Number of residues, atoms: 444, 3511 Classifications: {'peptide': 444} Link IDs: {'PTRANS': 22, 'TRANS': 421} Chain breaks: 3 Chain: "D" Number of atoms: 1022 Number of conformers: 1 Conformer: "" Number of residues, atoms: 128, 1022 Classifications: {'peptide': 128} Link IDs: {'PTRANS': 1, 'TRANS': 126} Chain breaks: 1 Chain: "H" Number of atoms: 1007 Number of conformers: 1 Conformer: "" Number of residues, atoms: 128, 1007 Classifications: {'peptide': 128} Link IDs: {'PTRANS': 4, 'TRANS': 123} Chain: "L" Number of atoms: 808 Number of conformers: 1 Conformer: "" Number of residues, atoms: 109, 808 Classifications: {'peptide': 109} Link IDs: {'CIS': 1, 'PTRANS': 6, 'TRANS': 101} Chain: "G" Number of atoms: 1007 Number of conformers: 1 Conformer: "" Number of residues, atoms: 128, 1007 Classifications: {'peptide': 128} Link IDs: {'PTRANS': 4, 'TRANS': 123} Chain: "I" Number of atoms: 808 Number of conformers: 1 Conformer: "" Number of residues, atoms: 109, 808 Classifications: {'peptide': 109} Link IDs: {'CIS': 1, 'PTRANS': 6, 'TRANS': 101} Chain: "J" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "K" Number of atoms: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 50 Unusual residues: {'BMA': 1, 'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 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: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "O" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "P" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "Q" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "R" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "S" Number of atoms: 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: 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: "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: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "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: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "Z" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "a" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "b" Number of atoms: 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: "c" 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: "d" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "e" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "f" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "g" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "E" Number of atoms: 126 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 126 Unusual residues: {'NAG': 9} Classifications: {'undetermined': 9} Link IDs: {None: 8} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 27 Unresolved non-hydrogen chiralities: 9 Chain: "A" Number of atoms: 140 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 140 Unusual residues: {'NAG': 10} Classifications: {'undetermined': 10} Link IDs: {None: 9} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 30 Unresolved non-hydrogen chiralities: 10 Chain: "C" Number of atoms: 182 Number of conformers: 1 Conformer: "" Number of residues, atoms: 13, 182 Unusual residues: {'NAG': 13} Classifications: {'undetermined': 13} Link IDs: {None: 12} Unresolved non-hydrogen bonds: 13 Unresolved non-hydrogen angles: 26 Unresolved non-hydrogen dihedrals: 39 Unresolved non-hydrogen chiralities: 13 Time building chain proxies: 4.72, per 1000 atoms: 0.25 Number of scatterers: 18829 At special positions: 0 Unit cell: (128.588, 139.128, 135.966, 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 125 16.00 O 3802 8.00 N 3124 7.00 C 11778 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=37, symmetry=0 Simple disulfide: pdb=" SG CYS E 54 " - pdb=" SG CYS E 74 " distance=2.03 Simple disulfide: pdb=" SG CYS E 119 " - pdb=" SG CYS E 205 " distance=2.13 Simple disulfide: pdb=" SG CYS E 126 " - pdb=" SG CYS E 196 " distance=2.18 Simple disulfide: pdb=" SG CYS E 131 " - pdb=" SG CYS E 157 " distance=2.03 Simple disulfide: pdb=" SG CYS E 218 " - pdb=" SG CYS E 247 " distance=2.03 Simple disulfide: pdb=" SG CYS E 228 " - pdb=" SG CYS E 239 " distance=2.04 Simple disulfide: pdb=" SG CYS E 296 " - pdb=" SG CYS E 331 " distance=2.03 Simple disulfide: pdb=" SG CYS E 378 " - pdb=" SG CYS E 445 " distance=2.03 Simple disulfide: pdb=" SG CYS E 385 " - pdb=" SG CYS E 418 " distance=2.03 Simple disulfide: pdb=" SG CYS E 501 " - pdb=" SG CYS F 605 " distance=2.11 Simple disulfide: pdb=" SG CYS F 598 " - pdb=" SG CYS F 604 " distance=2.06 Simple disulfide: pdb=" SG CYS A 54 " - pdb=" SG CYS A 74 " distance=2.03 Simple disulfide: pdb=" SG CYS A 119 " - pdb=" SG CYS A 205 " distance=2.12 Simple disulfide: pdb=" SG CYS A 126 " - pdb=" SG CYS A 196 " distance=2.19 Simple disulfide: pdb=" SG CYS A 131 " - pdb=" SG CYS A 157 " distance=2.07 Simple disulfide: pdb=" SG CYS A 218 " - pdb=" SG CYS A 247 " distance=2.02 Simple disulfide: pdb=" SG CYS A 228 " - pdb=" SG CYS A 239 " distance=2.03 Simple disulfide: pdb=" SG CYS A 296 " - pdb=" SG CYS A 331 " distance=2.07 Simple disulfide: pdb=" SG CYS A 378 " - pdb=" SG CYS A 445 " distance=2.03 Simple disulfide: pdb=" SG CYS A 385 " - pdb=" SG CYS A 418 " distance=2.04 Simple disulfide: pdb=" SG CYS A 501 " - pdb=" SG CYS B 605 " distance=2.06 Simple disulfide: pdb=" SG CYS B 598 " - pdb=" SG CYS B 604 " distance=2.04 Simple disulfide: pdb=" SG CYS C 54 " - pdb=" SG CYS C 74 " distance=2.03 Simple disulfide: pdb=" SG CYS C 119 " - pdb=" SG CYS C 205 " distance=2.10 Simple disulfide: pdb=" SG CYS C 126 " - pdb=" SG CYS C 196 " distance=2.04 Simple disulfide: pdb=" SG CYS C 131 " - pdb=" SG CYS C 157 " distance=2.22 Simple disulfide: pdb=" SG CYS C 218 " - pdb=" SG CYS C 247 " distance=2.03 Simple disulfide: pdb=" SG CYS C 228 " - pdb=" SG CYS C 239 " distance=2.03 Simple disulfide: pdb=" SG CYS C 296 " - pdb=" SG CYS C 331 " distance=2.03 Simple disulfide: pdb=" SG CYS C 378 " - pdb=" SG CYS C 445 " distance=2.05 Simple disulfide: pdb=" SG CYS C 385 " - pdb=" SG CYS C 418 " distance=2.03 Simple disulfide: pdb=" SG CYS C 501 " - pdb=" SG CYS D 605 " distance=2.02 Simple disulfide: pdb=" SG CYS D 598 " - pdb=" SG CYS D 604 " distance=2.04 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 92 " distance=2.04 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 88 " distance=2.03 Simple disulfide: pdb=" SG CYS G 22 " - pdb=" SG CYS G 92 " distance=2.03 Simple disulfide: pdb=" SG CYS I 23 " - pdb=" SG CYS I 88 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied ALPHA1-3 " BMA K 3 " - " MAN K 4 " " BMA Y 3 " - " MAN Y 4 " ALPHA1-6 " BMA Y 3 " - " MAN Y 5 " BETA1-4 " NAG J 1 " - " NAG J 2 " " NAG J 2 " - " BMA J 3 " " NAG K 1 " - " NAG K 2 " " NAG K 2 " - " BMA K 3 " " NAG M 1 " - " NAG M 2 " " NAG N 1 " - " NAG N 2 " " NAG O 1 " - " NAG O 2 " " NAG P 1 " - " NAG P 2 " " NAG Q 1 " - " NAG Q 2 " " NAG R 1 " - " NAG R 2 " " NAG S 1 " - " NAG S 2 " " NAG T 1 " - " NAG T 2 " " NAG U 1 " - " NAG U 2 " " NAG V 1 " - " NAG V 2 " " NAG W 1 " - " NAG W 2 " " NAG W 2 " - " BMA W 3 " " NAG X 1 " - " NAG X 2 " " NAG Y 1 " - " NAG Y 2 " " NAG Y 2 " - " BMA Y 3 " " NAG Z 1 " - " NAG Z 2 " " NAG a 1 " - " NAG a 2 " " NAG b 1 " - " NAG b 2 " " NAG c 1 " - " NAG c 2 " " NAG d 1 " - " NAG d 2 " " NAG d 2 " - " BMA d 3 " " NAG e 1 " - " NAG e 2 " " NAG e 2 " - " BMA e 3 " " NAG f 1 " - " NAG f 2 " " NAG f 2 " - " BMA f 3 " " NAG g 1 " - " NAG g 2 " BETA1-6 " NAG b 1 " - " FUC b 3 " ~> Even though FUC is an alpha isomer, a beta linkage is required... NAG-ASN " NAG A 601 " - " ASN A 160 " " NAG A 602 " - " ASN A 276 " " NAG A 603 " - " ASN A 295 " " NAG A 604 " - " ASN A 301 " " NAG A 605 " - " ASN A 332 " " NAG A 606 " - " ASN A 339 " " NAG A 607 " - " ASN A 356 " " NAG A 608 " - " ASN A 362 " " NAG A 609 " - " ASN A 392 " " NAG A 610 " - " ASN A 448 " " NAG C 601 " - " ASN C 88 " " NAG C 602 " - " ASN C 130 " " NAG C 603 " - " ASN C 156 " " NAG C 604 " - " ASN C 160 " " NAG C 605 " - " ASN C 276 " " NAG C 606 " - " ASN C 301 " " NAG C 607 " - " ASN C 332 " " NAG C 608 " - " ASN C 339 " " NAG C 609 " - " ASN C 356 " " NAG C 610 " - " ASN C 386 " " NAG C 611 " - " ASN C 362 " " NAG C 612 " - " ASN C 392 " " NAG C 613 " - " ASN C 448 " " NAG E 601 " - " ASN E 130 " " NAG E 602 " - " ASN E 156 " " NAG E 603 " - " ASN E 160 " " NAG E 604 " - " ASN E 197 " " NAG E 605 " - " ASN E 295 " " NAG E 606 " - " ASN E 301 " " NAG E 607 " - " ASN E 356 " " NAG E 608 " - " ASN E 362 " " NAG E 609 " - " ASN E 392 " " NAG J 1 " - " ASN E 241 " " NAG K 1 " - " ASN E 262 " " NAG M 1 " - " ASN E 276 " " NAG N 1 " - " ASN E 289 " " NAG O 1 " - " ASN E 332 " " NAG P 1 " - " ASN E 386 " " NAG Q 1 " - " ASN E 448 " " NAG R 1 " - " ASN E 88 " " NAG S 1 " - " ASN F 625 " " NAG T 1 " - " ASN A 88 " " NAG U 1 " - " ASN A 130 " " NAG V 1 " - " ASN A 156 " " NAG W 1 " - " ASN A 197 " " NAG X 1 " - " ASN A 241 " " NAG Y 1 " - " ASN A 262 " " NAG Z 1 " - " ASN A 289 " " NAG a 1 " - " ASN A 386 " " NAG b 1 " - " ASN B 625 " " NAG c 1 " - " ASN C 197 " " NAG d 1 " - " ASN C 241 " " NAG e 1 " - " ASN C 262 " " NAG f 1 " - " ASN C 289 " " NAG g 1 " - " ASN C 295 " Time building additional restraints: 1.99 Conformation dependent library (CDL) restraints added in 836.4 milliseconds 4408 Ramachandran restraints generated. 2204 Oldfield, 0 Emsley, 2204 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4148 Finding SS restraints... Secondary structure from input PDB file: 58 helices and 31 sheets defined 25.6% alpha, 21.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.65 Creating SS restraints... Processing helix chain 'E' and resid 70 through 74 Processing helix chain 'E' and resid 98 through 117 removed outlier: 3.637A pdb=" N GLU E 102 " --> pdb=" O ASN E 98 " (cutoff:3.500A) Processing helix chain 'E' and resid 122 through 126 Processing helix chain 'E' and resid 335 through 353 removed outlier: 3.553A pdb=" N LYS E 348 " --> pdb=" O GLN E 344 " (cutoff:3.500A) Processing helix chain 'E' and resid 368 through 373 Processing helix chain 'E' and resid 387 through 391 Processing helix chain 'E' and resid 396 through 401 Processing helix chain 'E' and resid 475 through 484 removed outlier: 3.670A pdb=" N TRP E 479 " --> pdb=" O MET E 475 " (cutoff:3.500A) removed outlier: 3.991A pdb=" N GLU E 482 " --> pdb=" O ASN E 478 " (cutoff:3.500A) Processing helix chain 'F' and resid 519 through 528 removed outlier: 3.542A pdb=" N PHE F 522 " --> pdb=" O PHE F 519 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N GLY F 524 " --> pdb=" O GLY F 521 " (cutoff:3.500A) removed outlier: 4.449A pdb=" N GLY F 527 " --> pdb=" O GLY F 524 " (cutoff:3.500A) Processing helix chain 'F' and resid 529 through 537 removed outlier: 3.624A pdb=" N LEU F 537 " --> pdb=" O ALA F 533 " (cutoff:3.500A) Processing helix chain 'F' and resid 545 through 550 Processing helix chain 'F' and resid 551 through 555 removed outlier: 3.888A pdb=" N LEU F 555 " --> pdb=" O GLN F 552 " (cutoff:3.500A) Processing helix chain 'F' and resid 569 through 596 Processing helix chain 'F' and resid 618 through 626 removed outlier: 3.787A pdb=" N MET F 626 " --> pdb=" O ILE F 622 " (cutoff:3.500A) Processing helix chain 'F' and resid 627 through 635 Processing helix chain 'F' and resid 638 through 662 Processing helix chain 'A' and resid 70 through 74 Processing helix chain 'A' and resid 98 through 117 removed outlier: 4.046A pdb=" N GLU A 102 " --> pdb=" O ASN A 98 " (cutoff:3.500A) Processing helix chain 'A' and resid 122 through 126 Processing helix chain 'A' and resid 335 through 352 removed outlier: 3.824A pdb=" N GLN A 352 " --> pdb=" O LYS A 348 " (cutoff:3.500A) Processing helix chain 'A' and resid 368 through 373 Processing helix chain 'A' and resid 396 through 401 Processing helix chain 'A' and resid 475 through 484 removed outlier: 3.587A pdb=" N TRP A 479 " --> pdb=" O MET A 475 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N SER A 481 " --> pdb=" O ASP A 477 " (cutoff:3.500A) removed outlier: 4.059A pdb=" N GLU A 482 " --> pdb=" O ASN A 478 " (cutoff:3.500A) Processing helix chain 'B' and resid 519 through 528 removed outlier: 3.948A pdb=" N GLY B 524 " --> pdb=" O GLY B 521 " (cutoff:3.500A) removed outlier: 4.481A pdb=" N GLY B 527 " --> pdb=" O GLY B 524 " (cutoff:3.500A) Processing helix chain 'B' and resid 529 through 539 Processing helix chain 'B' and resid 545 through 550 Processing helix chain 'B' and resid 551 through 555 removed outlier: 3.728A pdb=" N LEU B 555 " --> pdb=" O GLN B 552 " (cutoff:3.500A) Processing helix chain 'B' and resid 569 through 597 Processing helix chain 'B' and resid 618 through 625 Processing helix chain 'B' and resid 627 through 635 Processing helix chain 'B' and resid 638 through 664 Processing helix chain 'C' and resid 70 through 74 Processing helix chain 'C' and resid 98 through 117 removed outlier: 4.150A pdb=" N GLU C 102 " --> pdb=" O ASN C 98 " (cutoff:3.500A) Processing helix chain 'C' and resid 122 through 126 Processing helix chain 'C' and resid 335 through 353 removed outlier: 3.515A pdb=" N GLU C 351 " --> pdb=" O ILE C 347 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N GLN C 352 " --> pdb=" O LYS C 348 " (cutoff:3.500A) Processing helix chain 'C' and resid 368 through 373 Processing helix chain 'C' and resid 387 through 390 Processing helix chain 'C' and resid 396 through 405 Processing helix chain 'C' and resid 476 through 484 removed outlier: 4.129A pdb=" N GLU C 482 " --> pdb=" O ASN C 478 " (cutoff:3.500A) Processing helix chain 'D' and resid 516 through 520 Processing helix chain 'D' and resid 523 through 528 removed outlier: 3.503A pdb=" N GLY D 527 " --> pdb=" O GLY D 524 " (cutoff:3.500A) Processing helix chain 'D' and resid 529 through 534 removed outlier: 3.680A pdb=" N SER D 534 " --> pdb=" O MET D 530 " (cutoff:3.500A) Processing helix chain 'D' and resid 536 through 542 removed outlier: 3.549A pdb=" N GLN D 540 " --> pdb=" O THR D 536 " (cutoff:3.500A) Processing helix chain 'D' and resid 569 through 596 removed outlier: 3.800A pdb=" N LYS D 574 " --> pdb=" O VAL D 570 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N LEU D 576 " --> pdb=" O GLY D 572 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N GLN D 577 " --> pdb=" O ILE D 573 " (cutoff:3.500A) Processing helix chain 'D' and resid 618 through 625 Processing helix chain 'D' and resid 627 through 635 Processing helix chain 'D' and resid 638 through 663 removed outlier: 3.653A pdb=" N GLN D 658 " --> pdb=" O GLU D 654 " (cutoff:3.500A) removed outlier: 4.397A pdb=" N GLU D 659 " --> pdb=" O LYS D 655 " (cutoff:3.500A) removed outlier: 4.558A pdb=" N LEU D 660 " --> pdb=" O ASN D 656 " (cutoff:3.500A) removed outlier: 3.915A pdb=" N LEU D 661 " --> pdb=" O GLU D 657 " (cutoff:3.500A) removed outlier: 3.931A pdb=" N GLU D 662 " --> pdb=" O GLN D 658 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N LEU D 663 " --> pdb=" O GLU D 659 " (cutoff:3.500A) Processing helix chain 'H' and resid 28 through 32 removed outlier: 3.594A pdb=" N TYR H 32 " --> pdb=" O PHE H 29 " (cutoff:3.500A) Processing helix chain 'H' and resid 61 through 64 Processing helix chain 'H' and resid 83 through 87 Processing helix chain 'H' and resid 100E through 100I Processing helix chain 'L' and resid 79 through 83 Processing helix chain 'G' and resid 28 through 32 removed outlier: 3.878A pdb=" N TYR G 32 " --> pdb=" O PHE G 29 " (cutoff:3.500A) Processing helix chain 'G' and resid 61 through 64 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 83 through 87 removed outlier: 3.528A pdb=" N THR G 87 " --> pdb=" O PHE G 84 " (cutoff:3.500A) Processing helix chain 'G' and resid 100E through 100I Processing helix chain 'I' and resid 79 through 83 Processing sheet with id=AA1, first strand: chain 'E' and resid 494 through 499 removed outlier: 5.136A pdb=" N VAL F 608 " --> pdb=" O VAL E 36 " (cutoff:3.500A) removed outlier: 7.616A pdb=" N VAL E 38 " --> pdb=" O THR F 606 " (cutoff:3.500A) removed outlier: 7.336A pdb=" N THR F 606 " --> pdb=" O VAL E 38 " (cutoff:3.500A) removed outlier: 8.096A pdb=" N TYR E 40 " --> pdb=" O CYS F 604 " (cutoff:3.500A) removed outlier: 8.174A pdb=" N CYS F 604 " --> pdb=" O TYR E 40 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'E' and resid 45 through 47 removed outlier: 4.554A pdb=" N VAL E 242 " --> pdb=" O LEU E 86 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'E' and resid 53 through 55 Processing sheet with id=AA4, first strand: chain 'E' and resid 91 through 94 Processing sheet with id=AA5, first strand: chain 'E' and resid 169 through 177 Processing sheet with id=AA6, first strand: chain 'E' and resid 200 through 203 removed outlier: 6.170A pdb=" N VAL E 200 " --> pdb=" O ALA E 433 " (cutoff:3.500A) removed outlier: 7.183A pdb=" N TYR E 435 " --> pdb=" O VAL E 200 " (cutoff:3.500A) removed outlier: 6.432A pdb=" N THR E 202 " --> pdb=" O TYR E 435 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'E' and resid 259 through 261 WARNING: can't find start of bonding for strands! previous: chain 'E' and resid 259 through 261 current: chain 'E' and resid 284 through 298 removed outlier: 7.391A pdb=" N VAL E 293 " --> pdb=" O SER E 334 " (cutoff:3.500A) removed outlier: 4.388A pdb=" N SER E 334 " --> pdb=" O VAL E 293 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'E' and resid 330 through 334 current: chain 'E' and resid 381 through 385 WARNING: can't find start of bonding for strands! previous: chain 'E' and resid 381 through 385 current: chain 'E' and resid 465 through 470 Processing sheet with id=AA8, first strand: chain 'E' and resid 302 through 308 removed outlier: 6.943A pdb=" N THR E 303 " --> pdb=" O GLY E 321 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 494 through 499 removed outlier: 5.239A pdb=" N VAL B 608 " --> pdb=" O VAL A 36 " (cutoff:3.500A) removed outlier: 7.741A pdb=" N VAL A 38 " --> pdb=" O THR B 606 " (cutoff:3.500A) removed outlier: 7.280A pdb=" N THR B 606 " --> pdb=" O VAL A 38 " (cutoff:3.500A) removed outlier: 7.959A pdb=" N TYR A 40 " --> pdb=" O CYS B 604 " (cutoff:3.500A) removed outlier: 8.049A pdb=" N CYS B 604 " --> pdb=" O TYR A 40 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 45 through 47 removed outlier: 4.566A pdb=" N VAL A 242 " --> pdb=" O LEU A 86 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 75 through 76 removed outlier: 3.953A pdb=" N VAL A 75 " --> pdb=" O CYS A 54 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 91 through 94 Processing sheet with id=AB4, first strand: chain 'A' and resid 169 through 177 Processing sheet with id=AB5, first strand: chain 'A' and resid 200 through 203 removed outlier: 5.971A pdb=" N VAL A 200 " --> pdb=" O ALA A 433 " (cutoff:3.500A) removed outlier: 7.085A pdb=" N TYR A 435 " --> pdb=" O VAL A 200 " (cutoff:3.500A) removed outlier: 6.310A pdb=" N THR A 202 " --> pdb=" O TYR A 435 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 259 through 261 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 259 through 261 current: chain 'A' and resid 284 through 312 removed outlier: 6.593A pdb=" N ASN A 301 " --> pdb=" O ILE A 322A" (cutoff:3.500A) removed outlier: 4.520A pdb=" N ILE A 322A" --> pdb=" O ASN A 301 " (cutoff:3.500A) removed outlier: 6.772A pdb=" N THR A 303 " --> pdb=" O GLY A 321 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N ILE A 309 " --> pdb=" O ARG A 315 " (cutoff:3.500A) removed outlier: 7.237A pdb=" N ARG A 315 " --> pdb=" O ILE A 309 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 315 through 322A current: chain 'A' and resid 381 through 385 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 381 through 385 current: chain 'A' and resid 465 through 470 Processing sheet with id=AB7, first strand: chain 'C' and resid 494 through 499 removed outlier: 5.254A pdb=" N VAL D 608 " --> pdb=" O VAL C 36 " (cutoff:3.500A) removed outlier: 7.846A pdb=" N VAL C 38 " --> pdb=" O THR D 606 " (cutoff:3.500A) removed outlier: 7.365A pdb=" N THR D 606 " --> pdb=" O VAL C 38 " (cutoff:3.500A) removed outlier: 7.865A pdb=" N TYR C 40 " --> pdb=" O CYS D 604 " (cutoff:3.500A) removed outlier: 7.956A pdb=" N CYS D 604 " --> pdb=" O TYR C 40 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'C' and resid 45 through 47 removed outlier: 3.553A pdb=" N ILE C 225 " --> pdb=" O VAL C 245 " (cutoff:3.500A) removed outlier: 8.098A pdb=" N LYS C 236 " --> pdb=" O ASN C 92 " (cutoff:3.500A) removed outlier: 7.847A pdb=" N ASN C 92 " --> pdb=" O LYS C 236 " (cutoff:3.500A) removed outlier: 8.343A pdb=" N THR C 90 " --> pdb=" O PRO C 238 " (cutoff:3.500A) removed outlier: 8.420A pdb=" N THR C 240 " --> pdb=" O ASN C 88 " (cutoff:3.500A) removed outlier: 4.281A pdb=" N ASN C 88 " --> pdb=" O THR C 240 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N VAL C 242 " --> pdb=" O LEU C 86 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'C' and resid 75 through 76 Processing sheet with id=AC1, first strand: chain 'C' and resid 66 through 67 removed outlier: 6.795A pdb=" N ARG C 66 " --> pdb=" O THR C 209 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC1 Processing sheet with id=AC2, first strand: chain 'C' and resid 154 through 162 Processing sheet with id=AC3, first strand: chain 'C' and resid 181 through 183 Processing sheet with id=AC4, first strand: chain 'C' and resid 200 through 203 removed outlier: 6.084A pdb=" N VAL C 200 " --> pdb=" O ALA C 433 " (cutoff:3.500A) removed outlier: 7.150A pdb=" N TYR C 435 " --> pdb=" O VAL C 200 " (cutoff:3.500A) removed outlier: 6.401A pdb=" N THR C 202 " --> pdb=" O TYR C 435 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'C' and resid 259 through 261 WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 259 through 261 current: chain 'C' and resid 284 through 312 removed outlier: 3.722A pdb=" N ASN C 301 " --> pdb=" O ILE C 323 " (cutoff:3.500A) removed outlier: 4.359A pdb=" N GLU C 322 " --> pdb=" O THR C 303 " (cutoff:3.500A) removed outlier: 5.507A pdb=" N LYS C 305 " --> pdb=" O THR C 320 " (cutoff:3.500A) removed outlier: 5.371A pdb=" N THR C 320 " --> pdb=" O LYS C 305 " (cutoff:3.500A) removed outlier: 7.096A pdb=" N ILE C 307 " --> pdb=" O TYR C 318 " (cutoff:3.500A) removed outlier: 5.455A pdb=" N TYR C 318 " --> pdb=" O ILE C 307 " (cutoff:3.500A) removed outlier: 6.059A pdb=" N ILE C 309 " --> pdb=" O TRP C 316 " (cutoff:3.500A) removed outlier: 7.617A pdb=" N TRP C 316 " --> pdb=" O ILE C 309 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 315 through 323 current: chain 'C' and resid 381 through 385 WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 381 through 385 current: chain 'C' and resid 465 through 470 Processing sheet with id=AC6, first strand: chain 'H' and resid 5 through 6 Processing sheet with id=AC7, first strand: chain 'H' and resid 10 through 12 WARNING: can't find start of bonding for strands! previous: chain 'H' and resid 10 through 12 current: chain 'H' and resid 45 through 51 WARNING: can't find start of bonding for strands! previous: chain 'H' and resid 57 through 59 current: chain 'H' and resid 102 through 103 Processing sheet with id=AC8, first strand: chain 'L' and resid 9 through 13 WARNING: can't find start of bonding for strands! previous: chain 'L' and resid 9 through 13 current: chain 'L' and resid 45 through 48 WARNING: can't find start of bonding for strands! previous: chain 'L' and resid 45 through 48 current: chain 'L' and resid 95A through 98 No H-bonds generated for sheet with id=AC8 Processing sheet with id=AC9, first strand: chain 'L' and resid 19 through 24 Processing sheet with id=AD1, first strand: chain 'G' and resid 3 through 6 Processing sheet with id=AD2, first strand: chain 'G' and resid 10 through 12 WARNING: can't find start of bonding for strands! previous: chain 'G' and resid 10 through 12 current: chain 'G' and resid 45 through 51 WARNING: can't find start of bonding for strands! previous: chain 'G' and resid 57 through 59 current: chain 'G' and resid 100K through 103 Processing sheet with id=AD3, first strand: chain 'I' and resid 9 through 13 WARNING: can't find start of bonding for strands! previous: chain 'I' and resid 9 through 13 current: chain 'I' and resid 45 through 48 WARNING: can't find start of bonding for strands! previous: chain 'I' and resid 45 through 48 current: chain 'I' and resid 95A through 98 No H-bonds generated for sheet with id=AD3 Processing sheet with id=AD4, first strand: chain 'I' and resid 19 through 24 529 hydrogen bonds defined for protein. 1380 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: 3.40 Time building geometry restraints manager: 2.54 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 3731 1.32 - 1.45: 5015 1.45 - 1.58: 10269 1.58 - 1.71: 0 1.71 - 1.83: 174 Bond restraints: 19189 Sorted by residual: bond pdb=" N GLY C 263 " pdb=" CA GLY C 263 " ideal model delta sigma weight residual 1.442 1.465 -0.023 7.70e-03 1.69e+04 9.29e+00 bond pdb=" N PRO E 253 " pdb=" CA PRO E 253 " ideal model delta sigma weight residual 1.469 1.433 0.036 1.22e-02 6.72e+03 8.79e+00 bond pdb=" NE ARG I 27 " pdb=" CZ ARG I 27 " ideal model delta sigma weight residual 1.326 1.358 -0.032 1.10e-02 8.26e+03 8.50e+00 bond pdb=" CG ASP I 27B" pdb=" OD1 ASP I 27B" ideal model delta sigma weight residual 1.249 1.197 0.052 1.90e-02 2.77e+03 7.54e+00 bond pdb=" NE ARG C 401 " pdb=" CZ ARG C 401 " ideal model delta sigma weight residual 1.326 1.356 -0.030 1.10e-02 8.26e+03 7.26e+00 ... (remaining 19184 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.33: 24209 2.33 - 4.66: 1563 4.66 - 6.99: 244 6.99 - 9.32: 30 9.32 - 11.65: 6 Bond angle restraints: 26052 Sorted by residual: angle pdb=" C ALA A 436 " pdb=" N PRO A 437 " pdb=" CA PRO A 437 " ideal model delta sigma weight residual 119.66 126.07 -6.41 7.30e-01 1.88e+00 7.71e+01 angle pdb=" C ALA E 436 " pdb=" N PRO E 437 " pdb=" CA PRO E 437 " ideal model delta sigma weight residual 119.66 125.75 -6.09 7.30e-01 1.88e+00 6.96e+01 angle pdb=" C ALA C 436 " pdb=" N PRO C 437 " pdb=" CA PRO C 437 " ideal model delta sigma weight residual 119.66 125.58 -5.92 7.30e-01 1.88e+00 6.57e+01 angle pdb=" C ARG H 94 " pdb=" N PRO H 95 " pdb=" CA PRO H 95 " ideal model delta sigma weight residual 119.78 127.91 -8.13 1.03e+00 9.43e-01 6.24e+01 angle pdb=" C GLU E 492 " pdb=" N PRO E 493 " pdb=" CA PRO E 493 " ideal model delta sigma weight residual 119.56 127.46 -7.90 1.01e+00 9.80e-01 6.12e+01 ... (remaining 26047 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 22.36: 12233 22.36 - 44.72: 255 44.72 - 67.08: 84 67.08 - 89.44: 61 89.44 - 111.79: 28 Dihedral angle restraints: 12661 sinusoidal: 6224 harmonic: 6437 Sorted by residual: dihedral pdb=" CB CYS C 126 " pdb=" SG CYS C 126 " pdb=" SG CYS C 196 " pdb=" CB CYS C 196 " ideal model delta sinusoidal sigma weight residual -86.00 -165.35 79.35 1 1.00e+01 1.00e-02 7.83e+01 dihedral pdb=" CB CYS A 378 " pdb=" SG CYS A 378 " pdb=" SG CYS A 445 " pdb=" CB CYS A 445 " ideal model delta sinusoidal sigma weight residual -86.00 -141.39 55.39 1 1.00e+01 1.00e-02 4.15e+01 dihedral pdb=" CB CYS E 378 " pdb=" SG CYS E 378 " pdb=" SG CYS E 445 " pdb=" CB CYS E 445 " ideal model delta sinusoidal sigma weight residual -86.00 -131.52 45.52 1 1.00e+01 1.00e-02 2.87e+01 ... (remaining 12658 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.258: 3158 0.258 - 0.515: 27 0.515 - 0.773: 3 0.773 - 1.031: 2 1.031 - 1.289: 1 Chirality restraints: 3191 Sorted by residual: chirality pdb=" C1 NAG U 2 " pdb=" O4 NAG U 1 " pdb=" C2 NAG U 2 " pdb=" O5 NAG U 2 " both_signs ideal model delta sigma weight residual False -2.40 -1.72 -0.68 2.00e-02 2.50e+03 1.14e+03 chirality pdb=" C1 NAG S 2 " pdb=" O4 NAG S 1 " pdb=" C2 NAG S 2 " pdb=" O5 NAG S 2 " both_signs ideal model delta sigma weight residual False -2.40 -1.76 -0.64 2.00e-02 2.50e+03 1.03e+03 chirality pdb=" C1 BMA W 3 " pdb=" O4 NAG W 2 " pdb=" C2 BMA W 3 " pdb=" O5 BMA W 3 " both_signs ideal model delta sigma weight residual False -2.40 -2.03 -0.37 2.00e-02 2.50e+03 3.35e+02 ... (remaining 3188 not shown) Planarity restraints: 3267 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN A 356 " -0.071 2.00e-02 2.50e+03 7.42e-02 6.88e+01 pdb=" CG ASN A 356 " 0.031 2.00e-02 2.50e+03 pdb=" OD1 ASN A 356 " 0.012 2.00e-02 2.50e+03 pdb=" ND2 ASN A 356 " 0.116 2.00e-02 2.50e+03 pdb=" C1 NAG A 607 " -0.088 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN C 362 " 0.070 2.00e-02 2.50e+03 7.16e-02 6.41e+01 pdb=" CG ASN C 362 " -0.030 2.00e-02 2.50e+03 pdb=" OD1 ASN C 362 " -0.019 2.00e-02 2.50e+03 pdb=" ND2 ASN C 362 " -0.109 2.00e-02 2.50e+03 pdb=" C1 NAG C 611 " 0.087 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN E 197 " 0.067 2.00e-02 2.50e+03 6.79e-02 5.77e+01 pdb=" CG ASN E 197 " -0.033 2.00e-02 2.50e+03 pdb=" OD1 ASN E 197 " -0.013 2.00e-02 2.50e+03 pdb=" ND2 ASN E 197 " -0.103 2.00e-02 2.50e+03 pdb=" C1 NAG E 604 " 0.082 2.00e-02 2.50e+03 ... (remaining 3264 not shown) Histogram of nonbonded interaction distances: 2.25 - 2.78: 3902 2.78 - 3.31: 16953 3.31 - 3.84: 30630 3.84 - 4.37: 36294 4.37 - 4.90: 61237 Nonbonded interactions: 149016 Sorted by model distance: nonbonded pdb=" O3 NAG Q 1 " pdb=" O7 NAG Q 1 " model vdw 2.247 3.040 nonbonded pdb=" O3 NAG a 2 " pdb=" O7 NAG a 2 " model vdw 2.290 3.040 nonbonded pdb=" O3 NAG X 1 " pdb=" O5 NAG X 2 " model vdw 2.307 3.040 nonbonded pdb=" O3 NAG P 1 " pdb=" O5 NAG P 2 " model vdw 2.331 3.040 nonbonded pdb=" C3 NAG Q 1 " pdb=" O7 NAG Q 1 " model vdw 2.336 3.470 ... (remaining 149011 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 32 through 57 or resid 65 through 184 or resid 189 through \ 506 or resid 601 through 609)) selection = (chain 'C' and (resid 32 through 132 or resid 152 through 506 or resid 602 throu \ gh 610)) selection = (chain 'E' and (resid 32 through 57 or resid 65 through 184 or resid 189 through \ 506 or resid 601 through 609)) } ncs_group { reference = (chain 'B' and (resid 516 through 546 or resid 568 through 663 or (resid 664 and \ (name N or name CA or name C or name O or name CB or name CG or name OD1 or nam \ e OD2)))) selection = chain 'D' selection = (chain 'F' and (resid 516 through 546 or resid 568 through 663 or (resid 664 and \ (name N or name CA or name C or name O or name CB or name CG or name OD1 or nam \ e OD2)))) } ncs_group { reference = chain 'G' selection = chain 'H' } ncs_group { reference = chain 'I' selection = chain 'L' } ncs_group { reference = (chain 'J' and resid 1 through 2) selection = (chain 'W' and resid 1 through 2) selection = (chain 'b' and resid 1 through 2) selection = (chain 'd' and resid 1 through 2) selection = (chain 'e' and resid 1 through 2) selection = (chain 'f' and resid 1 through 2) } ncs_group { reference = chain 'M' selection = chain 'N' selection = chain 'O' selection = chain 'P' selection = chain 'Q' selection = chain 'R' selection = chain 'S' selection = chain 'T' selection = chain 'U' selection = chain 'V' selection = chain 'X' selection = chain 'Z' selection = chain 'a' selection = chain 'c' selection = chain 'g' } 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: 5.960 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: 0.010 Extract box with map and model: 0.280 Check model and map are aligned: 0.060 Set scattering table: 0.050 Process input model: 18.970 Find NCS groups from input model: 0.540 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.540 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 27.480 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7171 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 : 0.013 0.187 19315 Z= 0.674 Angle : 1.353 13.135 26393 Z= 0.833 Chirality : 0.082 1.289 3191 Planarity : 0.005 0.041 3212 Dihedral : 13.064 111.795 8402 Min Nonbonded Distance : 2.247 Molprobity Statistics. All-atom Clashscore : 0.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.82 % Favored : 99.18 % Rotamer: Outliers : 0.15 % Allowed : 0.51 % Favored : 99.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.09 % 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: 2.74 (0.18), residues: 2204 helix: 0.13 (0.21), residues: 430 sheet: 1.65 (0.21), residues: 536 loop : 2.90 (0.19), residues: 1238 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 298 TYR 0.038 0.005 TYR L 36 PHE 0.018 0.003 PHE A 317 TRP 0.032 0.006 TRP C 69 HIS 0.007 0.001 HIS A 374 Details of bonding type rmsd covalent geometry : bond 0.01185 (19189) covalent geometry : angle 1.30030 (26052) SS BOND : bond 0.05567 ( 37) SS BOND : angle 2.95525 ( 74) hydrogen bonds : bond 0.20652 ( 529) hydrogen bonds : angle 7.10138 ( 1380) link_ALPHA1-3 : bond 0.00463 ( 2) link_ALPHA1-3 : angle 2.35397 ( 6) link_ALPHA1-6 : bond 0.00359 ( 1) link_ALPHA1-6 : angle 0.76103 ( 3) link_BETA1-4 : bond 0.00786 ( 30) link_BETA1-4 : angle 3.07665 ( 90) link_BETA1-6 : bond 0.00258 ( 1) link_BETA1-6 : angle 5.83880 ( 3) link_NAG-ASN : bond 0.07032 ( 55) link_NAG-ASN : angle 3.97975 ( 165) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4408 Ramachandran restraints generated. 2204 Oldfield, 0 Emsley, 2204 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4408 Ramachandran restraints generated. 2204 Oldfield, 0 Emsley, 2204 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 538 residues out of total 1971 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 535 time to evaluate : 0.710 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 209 THR cc_start: 0.7701 (m) cc_final: 0.7375 (p) REVERT: E 504 ARG cc_start: 0.6963 (mtp85) cc_final: 0.6585 (mtm110) REVERT: F 553 ASN cc_start: 0.6593 (m110) cc_final: 0.6202 (p0) REVERT: A 170 GLN cc_start: 0.6709 (tp40) cc_final: 0.6105 (mm110) REVERT: C 39 TYR cc_start: 0.6236 (m-80) cc_final: 0.5789 (m-80) REVERT: C 477 ASP cc_start: 0.7338 (m-30) cc_final: 0.7082 (t0) REVERT: G 50 TRP cc_start: 0.6654 (m-90) cc_final: 0.6220 (m100) REVERT: G 89 MET cc_start: 0.6432 (mmm) cc_final: 0.6079 (mmt) outliers start: 3 outliers final: 2 residues processed: 538 average time/residue: 0.1806 time to fit residues: 138.2991 Evaluate side-chains 246 residues out of total 1971 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 244 time to evaluate : 0.730 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 197 ASN Chi-restraints excluded: chain A residue 448 ASN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 218 random chunks: chunk 216 optimal weight: 0.6980 chunk 98 optimal weight: 2.9990 chunk 194 optimal weight: 6.9990 chunk 107 optimal weight: 3.9990 chunk 10 optimal weight: 0.6980 chunk 66 optimal weight: 0.8980 chunk 130 optimal weight: 0.9980 chunk 124 optimal weight: 0.9980 chunk 103 optimal weight: 0.9990 chunk 200 optimal weight: 0.8980 chunk 212 optimal weight: 3.9990 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 249 HIS A 330 HIS B 540 GLN B 624 ASN B 653 GLN ** C 302 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 377 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 653 GLN H 1 GLN ** H 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 38 GLN G 100AHIS I 93 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4226 r_free = 0.4226 target = 0.152987 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3994 r_free = 0.3994 target = 0.134940 restraints weight = 37999.534| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.4036 r_free = 0.4036 target = 0.138127 restraints weight = 22282.270| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.4063 r_free = 0.4063 target = 0.140245 restraints weight = 15358.038| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.4080 r_free = 0.4080 target = 0.141676 restraints weight = 11921.373| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.4091 r_free = 0.4091 target = 0.142588 restraints weight = 9873.653| |-----------------------------------------------------------------------------| r_work (final): 0.4092 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7041 moved from start: 0.2827 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 19315 Z= 0.172 Angle : 0.748 12.962 26393 Z= 0.361 Chirality : 0.049 0.439 3191 Planarity : 0.005 0.037 3212 Dihedral : 9.566 79.825 4245 Min Nonbonded Distance : 2.386 Molprobity Statistics. All-atom Clashscore : 6.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.77 % Favored : 99.23 % Rotamer: Outliers : 2.03 % Allowed : 9.23 % Favored : 88.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.09 % 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: 2.37 (0.17), residues: 2204 helix: 1.36 (0.24), residues: 421 sheet: 1.29 (0.19), residues: 615 loop : 2.10 (0.18), residues: 1168 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG I 54 TYR 0.028 0.002 TYR H 32 PHE 0.022 0.002 PHE G 29 TRP 0.019 0.002 TRP A 45 HIS 0.006 0.001 HIS E 249 Details of bonding type rmsd covalent geometry : bond 0.00385 (19189) covalent geometry : angle 0.69952 (26052) SS BOND : bond 0.00310 ( 37) SS BOND : angle 1.18773 ( 74) hydrogen bonds : bond 0.05591 ( 529) hydrogen bonds : angle 5.45191 ( 1380) link_ALPHA1-3 : bond 0.01385 ( 2) link_ALPHA1-3 : angle 1.77343 ( 6) link_ALPHA1-6 : bond 0.01296 ( 1) link_ALPHA1-6 : angle 2.12180 ( 3) link_BETA1-4 : bond 0.00762 ( 30) link_BETA1-4 : angle 2.41219 ( 90) link_BETA1-6 : bond 0.00861 ( 1) link_BETA1-6 : angle 4.08054 ( 3) link_NAG-ASN : bond 0.00581 ( 55) link_NAG-ASN : angle 2.79476 ( 165) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4408 Ramachandran restraints generated. 2204 Oldfield, 0 Emsley, 2204 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4408 Ramachandran restraints generated. 2204 Oldfield, 0 Emsley, 2204 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 324 residues out of total 1971 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 284 time to evaluate : 0.738 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 154 MET cc_start: 0.5687 (mmt) cc_final: 0.5367 (mmm) REVERT: E 373 MET cc_start: 0.7277 (mmm) cc_final: 0.6252 (ttm) REVERT: F 553 ASN cc_start: 0.6390 (m110) cc_final: 0.6177 (p0) REVERT: F 654 GLU cc_start: 0.7004 (mm-30) cc_final: 0.6784 (mm-30) REVERT: A 349 LEU cc_start: 0.7709 (OUTLIER) cc_final: 0.7503 (mm) REVERT: A 357 LYS cc_start: 0.7279 (mmtp) cc_final: 0.6559 (mmtp) REVERT: C 39 TYR cc_start: 0.6073 (m-80) cc_final: 0.5468 (m-80) REVERT: H 89 MET cc_start: 0.7959 (mmm) cc_final: 0.7694 (mtp) REVERT: H 96 MET cc_start: 0.8390 (ttm) cc_final: 0.8007 (ttm) REVERT: G 50 TRP cc_start: 0.5865 (m-90) cc_final: 0.5473 (m100) REVERT: I 82 ASP cc_start: 0.5824 (m-30) cc_final: 0.5554 (m-30) REVERT: I 91 TYR cc_start: 0.7735 (t80) cc_final: 0.7481 (t80) REVERT: I 94 TYR cc_start: 0.7875 (m-80) cc_final: 0.7652 (m-80) outliers start: 40 outliers final: 27 residues processed: 307 average time/residue: 0.1440 time to fit residues: 68.2027 Evaluate side-chains 246 residues out of total 1971 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 218 time to evaluate : 0.746 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 51 THR Chi-restraints excluded: chain E residue 169 VAL Chi-restraints excluded: chain E residue 194 ILE Chi-restraints excluded: chain E residue 197 ASN Chi-restraints excluded: chain E residue 280 ASN Chi-restraints excluded: chain E residue 386 ASN Chi-restraints excluded: chain E residue 464 THR Chi-restraints excluded: chain A residue 54 CYS Chi-restraints excluded: chain A residue 114 GLN Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain A residue 316 TRP Chi-restraints excluded: chain A residue 349 LEU Chi-restraints excluded: chain A residue 446 SER Chi-restraints excluded: chain A residue 448 ASN Chi-restraints excluded: chain A residue 504 ARG Chi-restraints excluded: chain B residue 603 ILE Chi-restraints excluded: chain B residue 612 THR Chi-restraints excluded: chain B residue 625 ASN Chi-restraints excluded: chain C residue 123 THR Chi-restraints excluded: chain C residue 132 ASN Chi-restraints excluded: chain C residue 450 THR Chi-restraints excluded: chain C residue 496 VAL Chi-restraints excluded: chain C residue 505 VAL Chi-restraints excluded: chain D residue 544 LEU Chi-restraints excluded: chain H residue 100 VAL Chi-restraints excluded: chain L residue 21 ILE Chi-restraints excluded: chain G residue 82 LEU Chi-restraints excluded: chain I residue 88 CYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 218 random chunks: chunk 107 optimal weight: 4.9990 chunk 16 optimal weight: 1.9990 chunk 17 optimal weight: 2.9990 chunk 103 optimal weight: 0.5980 chunk 47 optimal weight: 0.6980 chunk 181 optimal weight: 2.9990 chunk 113 optimal weight: 1.9990 chunk 67 optimal weight: 1.9990 chunk 183 optimal weight: 3.9990 chunk 9 optimal weight: 0.5980 chunk 141 optimal weight: 1.9990 overall best weight: 1.1784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 105 HIS A 99 ASN B 624 ASN ** C 377 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 442 GLN L 38 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4175 r_free = 0.4175 target = 0.148431 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3927 r_free = 0.3927 target = 0.129552 restraints weight = 38403.008| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3971 r_free = 0.3971 target = 0.132824 restraints weight = 22242.408| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 48)----------------| | r_work = 0.4000 r_free = 0.4000 target = 0.135008 restraints weight = 15367.683| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.4019 r_free = 0.4019 target = 0.136474 restraints weight = 11880.561| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 42)----------------| | r_work = 0.4031 r_free = 0.4031 target = 0.137441 restraints weight = 9898.217| |-----------------------------------------------------------------------------| r_work (final): 0.4025 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7170 moved from start: 0.3605 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 19315 Z= 0.171 Angle : 0.670 12.946 26393 Z= 0.325 Chirality : 0.047 0.255 3191 Planarity : 0.004 0.043 3212 Dihedral : 7.288 59.902 4245 Min Nonbonded Distance : 2.453 Molprobity Statistics. All-atom Clashscore : 6.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.13 % Favored : 98.87 % Rotamer: Outliers : 2.99 % Allowed : 9.79 % Favored : 87.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.09 % 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: 1.75 (0.17), residues: 2204 helix: 1.31 (0.25), residues: 437 sheet: 0.92 (0.20), residues: 608 loop : 1.47 (0.18), residues: 1159 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG G 38 TYR 0.029 0.002 TYR G 33 PHE 0.046 0.002 PHE H 29 TRP 0.018 0.002 TRP H 50 HIS 0.005 0.001 HIS E 249 Details of bonding type rmsd covalent geometry : bond 0.00397 (19189) covalent geometry : angle 0.63104 (26052) SS BOND : bond 0.00279 ( 37) SS BOND : angle 0.81880 ( 74) hydrogen bonds : bond 0.04460 ( 529) hydrogen bonds : angle 5.04828 ( 1380) link_ALPHA1-3 : bond 0.01228 ( 2) link_ALPHA1-3 : angle 1.34339 ( 6) link_ALPHA1-6 : bond 0.01092 ( 1) link_ALPHA1-6 : angle 1.37073 ( 3) link_BETA1-4 : bond 0.00685 ( 30) link_BETA1-4 : angle 2.18067 ( 90) link_BETA1-6 : bond 0.00781 ( 1) link_BETA1-6 : angle 3.53435 ( 3) link_NAG-ASN : bond 0.00321 ( 55) link_NAG-ASN : angle 2.38309 ( 165) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4408 Ramachandran restraints generated. 2204 Oldfield, 0 Emsley, 2204 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4408 Ramachandran restraints generated. 2204 Oldfield, 0 Emsley, 2204 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 309 residues out of total 1971 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 250 time to evaluate : 0.677 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 154 MET cc_start: 0.5946 (mmt) cc_final: 0.5503 (mmm) REVERT: F 553 ASN cc_start: 0.6597 (m110) cc_final: 0.6214 (p0) REVERT: F 654 GLU cc_start: 0.7203 (mm-30) cc_final: 0.6923 (mm-30) REVERT: A 349 LEU cc_start: 0.7524 (OUTLIER) cc_final: 0.7017 (mm) REVERT: A 357 LYS cc_start: 0.7076 (mmtp) cc_final: 0.6551 (mmtp) REVERT: A 359 ILE cc_start: 0.6931 (mm) cc_final: 0.6699 (mm) REVERT: C 154 MET cc_start: 0.6312 (mtm) cc_final: 0.6069 (mtm) REVERT: C 477 ASP cc_start: 0.7563 (m-30) cc_final: 0.6862 (t0) REVERT: D 630 GLU cc_start: 0.7349 (tm-30) cc_final: 0.6465 (pt0) REVERT: L 35 TRP cc_start: 0.7288 (m100) cc_final: 0.6995 (m-90) outliers start: 59 outliers final: 42 residues processed: 289 average time/residue: 0.1463 time to fit residues: 65.1083 Evaluate side-chains 257 residues out of total 1971 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 214 time to evaluate : 0.638 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 116 LEU Chi-restraints excluded: chain E residue 122 LEU Chi-restraints excluded: chain E residue 169 VAL Chi-restraints excluded: chain E residue 197 ASN Chi-restraints excluded: chain E residue 265 LEU Chi-restraints excluded: chain E residue 280 ASN Chi-restraints excluded: chain E residue 323 ILE Chi-restraints excluded: chain E residue 386 ASN Chi-restraints excluded: chain E residue 455 THR Chi-restraints excluded: chain E residue 464 THR Chi-restraints excluded: chain A residue 51 THR Chi-restraints excluded: chain A residue 54 CYS Chi-restraints excluded: chain A residue 114 GLN Chi-restraints excluded: chain A residue 316 TRP Chi-restraints excluded: chain A residue 349 LEU Chi-restraints excluded: chain A residue 371 ILE Chi-restraints excluded: chain A residue 446 SER Chi-restraints excluded: chain A residue 448 ASN Chi-restraints excluded: chain A residue 504 ARG Chi-restraints excluded: chain B residue 603 ILE Chi-restraints excluded: chain B residue 612 THR Chi-restraints excluded: chain B residue 625 ASN Chi-restraints excluded: chain B residue 659 GLU Chi-restraints excluded: chain C residue 42 VAL Chi-restraints excluded: chain C residue 104 MET Chi-restraints excluded: chain C residue 132 ASN Chi-restraints excluded: chain C residue 255 VAL Chi-restraints excluded: chain C residue 274 SER Chi-restraints excluded: chain C residue 450 THR Chi-restraints excluded: chain C residue 496 VAL Chi-restraints excluded: chain C residue 505 VAL Chi-restraints excluded: chain D residue 544 LEU Chi-restraints excluded: chain D residue 589 ASP Chi-restraints excluded: chain H residue 51 VAL Chi-restraints excluded: chain H residue 82 SER Chi-restraints excluded: chain H residue 100 VAL Chi-restraints excluded: chain H residue 102 PHE Chi-restraints excluded: chain L residue 104 LEU Chi-restraints excluded: chain G residue 11 MET Chi-restraints excluded: chain G residue 68 THR Chi-restraints excluded: chain G residue 80 LEU Chi-restraints excluded: chain G residue 82 LEU Chi-restraints excluded: chain G residue 100 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 218 random chunks: chunk 130 optimal weight: 3.9990 chunk 192 optimal weight: 8.9990 chunk 90 optimal weight: 0.9980 chunk 139 optimal weight: 0.7980 chunk 162 optimal weight: 0.6980 chunk 177 optimal weight: 0.9990 chunk 138 optimal weight: 3.9990 chunk 49 optimal weight: 5.9990 chunk 166 optimal weight: 3.9990 chunk 186 optimal weight: 5.9990 chunk 56 optimal weight: 0.5980 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 258 GLN ** C 377 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4182 r_free = 0.4182 target = 0.148828 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3940 r_free = 0.3940 target = 0.130465 restraints weight = 38364.564| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3981 r_free = 0.3981 target = 0.133634 restraints weight = 22475.021| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.4009 r_free = 0.4009 target = 0.135745 restraints weight = 15629.648| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 43)----------------| | r_work = 0.4027 r_free = 0.4027 target = 0.137140 restraints weight = 12134.272| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.4038 r_free = 0.4038 target = 0.138053 restraints weight = 10174.291| |-----------------------------------------------------------------------------| r_work (final): 0.4033 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7174 moved from start: 0.3971 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 19315 Z= 0.135 Angle : 0.601 8.520 26393 Z= 0.291 Chirality : 0.045 0.242 3191 Planarity : 0.004 0.046 3212 Dihedral : 6.146 59.438 4245 Min Nonbonded Distance : 2.497 Molprobity Statistics. All-atom Clashscore : 6.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.18 % Favored : 98.82 % Rotamer: Outliers : 2.44 % Allowed : 11.31 % Favored : 86.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.09 % 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: 1.56 (0.17), residues: 2204 helix: 1.51 (0.25), residues: 431 sheet: 0.71 (0.20), residues: 605 loop : 1.25 (0.18), residues: 1168 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG L 27 TYR 0.019 0.002 TYR H 100E PHE 0.023 0.001 PHE H 29 TRP 0.017 0.001 TRP H 50 HIS 0.004 0.001 HIS E 249 Details of bonding type rmsd covalent geometry : bond 0.00304 (19189) covalent geometry : angle 0.56498 (26052) SS BOND : bond 0.00225 ( 37) SS BOND : angle 0.75366 ( 74) hydrogen bonds : bond 0.03883 ( 529) hydrogen bonds : angle 4.89025 ( 1380) link_ALPHA1-3 : bond 0.01242 ( 2) link_ALPHA1-3 : angle 1.41795 ( 6) link_ALPHA1-6 : bond 0.01084 ( 1) link_ALPHA1-6 : angle 1.29112 ( 3) link_BETA1-4 : bond 0.00640 ( 30) link_BETA1-4 : angle 2.02225 ( 90) link_BETA1-6 : bond 0.00675 ( 1) link_BETA1-6 : angle 3.34937 ( 3) link_NAG-ASN : bond 0.00318 ( 55) link_NAG-ASN : angle 2.14711 ( 165) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4408 Ramachandran restraints generated. 2204 Oldfield, 0 Emsley, 2204 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4408 Ramachandran restraints generated. 2204 Oldfield, 0 Emsley, 2204 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 284 residues out of total 1971 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 236 time to evaluate : 0.693 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 154 MET cc_start: 0.5691 (mmt) cc_final: 0.5360 (mmm) REVERT: E 449 ILE cc_start: 0.8566 (mm) cc_final: 0.8365 (mm) REVERT: F 553 ASN cc_start: 0.6435 (m110) cc_final: 0.6192 (p0) REVERT: F 575 GLN cc_start: 0.8082 (OUTLIER) cc_final: 0.7877 (tt0) REVERT: F 654 GLU cc_start: 0.7113 (mm-30) cc_final: 0.6701 (mm-30) REVERT: A 357 LYS cc_start: 0.6931 (mmtp) cc_final: 0.6488 (mmtp) REVERT: B 634 GLU cc_start: 0.7295 (tp30) cc_final: 0.7004 (tt0) REVERT: B 654 GLU cc_start: 0.7183 (pp20) cc_final: 0.6971 (pp20) REVERT: B 658 GLN cc_start: 0.7374 (tp40) cc_final: 0.6714 (mt0) REVERT: C 154 MET cc_start: 0.6264 (mtm) cc_final: 0.6006 (mtm) REVERT: H 89 MET cc_start: 0.7739 (OUTLIER) cc_final: 0.7428 (ttm) REVERT: L 35 TRP cc_start: 0.7252 (m100) cc_final: 0.7015 (m-90) REVERT: L 36 TYR cc_start: 0.8103 (m-80) cc_final: 0.7886 (m-80) REVERT: I 60 GLN cc_start: 0.6971 (tp-100) cc_final: 0.6761 (tp-100) REVERT: I 90 SER cc_start: 0.7545 (t) cc_final: 0.7320 (p) outliers start: 48 outliers final: 35 residues processed: 271 average time/residue: 0.1396 time to fit residues: 59.5765 Evaluate side-chains 251 residues out of total 1971 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 214 time to evaluate : 0.731 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 116 LEU Chi-restraints excluded: chain E residue 169 VAL Chi-restraints excluded: chain E residue 197 ASN Chi-restraints excluded: chain E residue 265 LEU Chi-restraints excluded: chain E residue 280 ASN Chi-restraints excluded: chain E residue 386 ASN Chi-restraints excluded: chain E residue 464 THR Chi-restraints excluded: chain F residue 575 GLN Chi-restraints excluded: chain A residue 75 VAL Chi-restraints excluded: chain A residue 114 GLN Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain A residue 316 TRP Chi-restraints excluded: chain A residue 446 SER Chi-restraints excluded: chain A residue 504 ARG Chi-restraints excluded: chain B residue 514 THR Chi-restraints excluded: chain B residue 535 MET Chi-restraints excluded: chain B residue 603 ILE Chi-restraints excluded: chain B residue 612 THR Chi-restraints excluded: chain B residue 625 ASN Chi-restraints excluded: chain B residue 659 GLU Chi-restraints excluded: chain C residue 34 LEU Chi-restraints excluded: chain C residue 104 MET Chi-restraints excluded: chain C residue 132 ASN Chi-restraints excluded: chain C residue 255 VAL Chi-restraints excluded: chain C residue 274 SER Chi-restraints excluded: chain C residue 450 THR Chi-restraints excluded: chain C residue 496 VAL Chi-restraints excluded: chain C residue 505 VAL Chi-restraints excluded: chain D residue 534 SER Chi-restraints excluded: chain D residue 544 LEU Chi-restraints excluded: chain D residue 589 ASP Chi-restraints excluded: chain H residue 51 VAL Chi-restraints excluded: chain H residue 89 MET Chi-restraints excluded: chain H residue 100 VAL Chi-restraints excluded: chain L residue 104 LEU Chi-restraints excluded: chain G residue 11 MET Chi-restraints excluded: chain G residue 82 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 218 random chunks: chunk 13 optimal weight: 0.0270 chunk 38 optimal weight: 1.9990 chunk 94 optimal weight: 3.9990 chunk 143 optimal weight: 0.5980 chunk 66 optimal weight: 1.9990 chunk 138 optimal weight: 3.9990 chunk 41 optimal weight: 0.0270 chunk 177 optimal weight: 0.7980 chunk 102 optimal weight: 1.9990 chunk 14 optimal weight: 3.9990 chunk 204 optimal weight: 5.9990 overall best weight: 0.6898 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 258 GLN C 308 ASN ** C 377 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 38 GLN ** I 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4181 r_free = 0.4181 target = 0.148775 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3940 r_free = 0.3940 target = 0.130530 restraints weight = 38243.278| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3982 r_free = 0.3982 target = 0.133695 restraints weight = 22400.740| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.4009 r_free = 0.4009 target = 0.135779 restraints weight = 15582.272| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 45)----------------| | r_work = 0.4028 r_free = 0.4028 target = 0.137187 restraints weight = 12142.640| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 41)----------------| | r_work = 0.4040 r_free = 0.4040 target = 0.138123 restraints weight = 10164.423| |-----------------------------------------------------------------------------| r_work (final): 0.4032 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7169 moved from start: 0.4146 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 19315 Z= 0.123 Angle : 0.577 8.748 26393 Z= 0.283 Chirality : 0.045 0.240 3191 Planarity : 0.004 0.041 3212 Dihedral : 5.685 58.569 4243 Min Nonbonded Distance : 2.415 Molprobity Statistics. All-atom Clashscore : 6.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.18 % Favored : 98.82 % Rotamer: Outliers : 2.69 % Allowed : 11.67 % Favored : 85.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.09 % Twisted Proline : 1.12 % 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: 1.42 (0.17), residues: 2204 helix: 1.56 (0.25), residues: 431 sheet: 0.65 (0.20), residues: 582 loop : 1.06 (0.18), residues: 1191 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG L 27 TYR 0.017 0.001 TYR A 177 PHE 0.018 0.001 PHE H 29 TRP 0.016 0.001 TRP H 50 HIS 0.005 0.001 HIS E 249 Details of bonding type rmsd covalent geometry : bond 0.00277 (19189) covalent geometry : angle 0.53996 (26052) SS BOND : bond 0.00538 ( 37) SS BOND : angle 1.12283 ( 74) hydrogen bonds : bond 0.03624 ( 529) hydrogen bonds : angle 4.79408 ( 1380) link_ALPHA1-3 : bond 0.01175 ( 2) link_ALPHA1-3 : angle 1.29995 ( 6) link_ALPHA1-6 : bond 0.01039 ( 1) link_ALPHA1-6 : angle 1.29616 ( 3) link_BETA1-4 : bond 0.00612 ( 30) link_BETA1-4 : angle 1.91875 ( 90) link_BETA1-6 : bond 0.00613 ( 1) link_BETA1-6 : angle 3.21271 ( 3) link_NAG-ASN : bond 0.00299 ( 55) link_NAG-ASN : angle 2.06945 ( 165) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4408 Ramachandran restraints generated. 2204 Oldfield, 0 Emsley, 2204 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4408 Ramachandran restraints generated. 2204 Oldfield, 0 Emsley, 2204 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 280 residues out of total 1971 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 227 time to evaluate : 0.722 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 154 MET cc_start: 0.5511 (mmt) cc_final: 0.5311 (mmm) REVERT: F 553 ASN cc_start: 0.6456 (m110) cc_final: 0.6198 (p0) REVERT: F 575 GLN cc_start: 0.8017 (OUTLIER) cc_final: 0.7814 (tt0) REVERT: A 357 LYS cc_start: 0.7000 (mmtp) cc_final: 0.6568 (mmtp) REVERT: B 634 GLU cc_start: 0.7270 (tp30) cc_final: 0.7054 (tt0) REVERT: B 658 GLN cc_start: 0.7444 (tp40) cc_final: 0.6748 (mt0) REVERT: C 154 MET cc_start: 0.6228 (mtm) cc_final: 0.5989 (mtm) REVERT: D 630 GLU cc_start: 0.7246 (tm-30) cc_final: 0.6301 (pt0) REVERT: H 89 MET cc_start: 0.7814 (OUTLIER) cc_final: 0.7517 (ttm) REVERT: L 36 TYR cc_start: 0.8121 (m-80) cc_final: 0.7897 (m-80) outliers start: 53 outliers final: 36 residues processed: 265 average time/residue: 0.1464 time to fit residues: 59.7316 Evaluate side-chains 249 residues out of total 1971 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 211 time to evaluate : 0.755 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 85 ILE Chi-restraints excluded: chain E residue 116 LEU Chi-restraints excluded: chain E residue 125 LEU Chi-restraints excluded: chain E residue 169 VAL Chi-restraints excluded: chain E residue 197 ASN Chi-restraints excluded: chain E residue 280 ASN Chi-restraints excluded: chain E residue 386 ASN Chi-restraints excluded: chain E residue 394 THR Chi-restraints excluded: chain E residue 464 THR Chi-restraints excluded: chain F residue 575 GLN Chi-restraints excluded: chain A residue 51 THR Chi-restraints excluded: chain A residue 114 GLN Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain A residue 316 TRP Chi-restraints excluded: chain A residue 446 SER Chi-restraints excluded: chain A residue 504 ARG Chi-restraints excluded: chain B residue 514 THR Chi-restraints excluded: chain B residue 535 MET Chi-restraints excluded: chain B residue 603 ILE Chi-restraints excluded: chain B residue 612 THR Chi-restraints excluded: chain B residue 625 ASN Chi-restraints excluded: chain B residue 659 GLU Chi-restraints excluded: chain C residue 34 LEU Chi-restraints excluded: chain C residue 104 MET Chi-restraints excluded: chain C residue 132 ASN Chi-restraints excluded: chain C residue 274 SER Chi-restraints excluded: chain C residue 450 THR Chi-restraints excluded: chain C residue 496 VAL Chi-restraints excluded: chain C residue 505 VAL Chi-restraints excluded: chain D residue 544 LEU Chi-restraints excluded: chain D residue 589 ASP Chi-restraints excluded: chain H residue 51 VAL Chi-restraints excluded: chain H residue 89 MET Chi-restraints excluded: chain H residue 100 VAL Chi-restraints excluded: chain L residue 104 LEU Chi-restraints excluded: chain G residue 80 LEU Chi-restraints excluded: chain G residue 82 LEU Chi-restraints excluded: chain I residue 85 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 218 random chunks: chunk 57 optimal weight: 4.9990 chunk 180 optimal weight: 2.9990 chunk 82 optimal weight: 4.9990 chunk 209 optimal weight: 6.9990 chunk 154 optimal weight: 3.9990 chunk 47 optimal weight: 2.9990 chunk 139 optimal weight: 4.9990 chunk 107 optimal weight: 6.9990 chunk 170 optimal weight: 0.5980 chunk 14 optimal weight: 0.9980 chunk 55 optimal weight: 1.9990 overall best weight: 1.9186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 552 GLN ** A 302 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 374 HIS ** C 302 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 377 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3996 r_free = 0.3996 target = 0.134458 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3729 r_free = 0.3729 target = 0.115156 restraints weight = 38190.479| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3772 r_free = 0.3772 target = 0.118207 restraints weight = 22528.801| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3801 r_free = 0.3801 target = 0.120250 restraints weight = 15788.551| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 42)----------------| | r_work = 0.3820 r_free = 0.3820 target = 0.121627 restraints weight = 12409.479| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.3832 r_free = 0.3832 target = 0.122559 restraints weight = 10455.796| |-----------------------------------------------------------------------------| r_work (final): 0.3837 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7298 moved from start: 0.4575 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.046 19315 Z= 0.232 Angle : 0.695 9.141 26393 Z= 0.341 Chirality : 0.048 0.262 3191 Planarity : 0.004 0.060 3212 Dihedral : 5.922 59.890 4243 Min Nonbonded Distance : 2.482 Molprobity Statistics. All-atom Clashscore : 8.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.31 % Favored : 97.69 % Rotamer: Outliers : 3.35 % Allowed : 11.72 % Favored : 84.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.09 % Twisted Proline : 1.12 % 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: 0.90 (0.17), residues: 2204 helix: 1.24 (0.25), residues: 433 sheet: 0.22 (0.20), residues: 600 loop : 0.75 (0.18), residues: 1171 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG C 273 TYR 0.019 0.002 TYR C 39 PHE 0.019 0.002 PHE A 317 TRP 0.027 0.002 TRP A 45 HIS 0.006 0.001 HIS A 374 Details of bonding type rmsd covalent geometry : bond 0.00550 (19189) covalent geometry : angle 0.65970 (26052) SS BOND : bond 0.00419 ( 37) SS BOND : angle 1.32135 ( 74) hydrogen bonds : bond 0.04365 ( 529) hydrogen bonds : angle 5.09507 ( 1380) link_ALPHA1-3 : bond 0.01085 ( 2) link_ALPHA1-3 : angle 1.19747 ( 6) link_ALPHA1-6 : bond 0.00926 ( 1) link_ALPHA1-6 : angle 1.26986 ( 3) link_BETA1-4 : bond 0.00560 ( 30) link_BETA1-4 : angle 1.95643 ( 90) link_BETA1-6 : bond 0.00765 ( 1) link_BETA1-6 : angle 3.38429 ( 3) link_NAG-ASN : bond 0.00337 ( 55) link_NAG-ASN : angle 2.30834 ( 165) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4408 Ramachandran restraints generated. 2204 Oldfield, 0 Emsley, 2204 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4408 Ramachandran restraints generated. 2204 Oldfield, 0 Emsley, 2204 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 289 residues out of total 1971 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 223 time to evaluate : 0.675 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 113 ASP cc_start: 0.8158 (t70) cc_final: 0.7875 (m-30) REVERT: F 575 GLN cc_start: 0.8293 (OUTLIER) cc_final: 0.8090 (tt0) REVERT: F 626 MET cc_start: 0.7790 (OUTLIER) cc_final: 0.7397 (mtm) REVERT: A 357 LYS cc_start: 0.7154 (mmtp) cc_final: 0.6700 (mmtp) REVERT: B 658 GLN cc_start: 0.7502 (tp40) cc_final: 0.6699 (mt0) REVERT: C 154 MET cc_start: 0.6424 (mtm) cc_final: 0.6108 (mtm) REVERT: C 426 MET cc_start: 0.5960 (mtp) cc_final: 0.5718 (mtp) REVERT: C 477 ASP cc_start: 0.7456 (m-30) cc_final: 0.7213 (t70) REVERT: H 10 GLU cc_start: 0.6666 (tm-30) cc_final: 0.6447 (tm-30) REVERT: H 89 MET cc_start: 0.8102 (OUTLIER) cc_final: 0.7665 (ttm) REVERT: L 27 ASP cc_start: 0.8212 (p0) cc_final: 0.7872 (p0) REVERT: G 50 TRP cc_start: 0.6597 (m-90) cc_final: 0.6004 (m-90) REVERT: I 69 ASN cc_start: 0.8186 (p0) cc_final: 0.7829 (p0) outliers start: 66 outliers final: 50 residues processed: 272 average time/residue: 0.1524 time to fit residues: 63.0026 Evaluate side-chains 253 residues out of total 1971 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 200 time to evaluate : 0.995 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 50 THR Chi-restraints excluded: chain E residue 85 ILE Chi-restraints excluded: chain E residue 94 ASN Chi-restraints excluded: chain E residue 116 LEU Chi-restraints excluded: chain E residue 122 LEU Chi-restraints excluded: chain E residue 125 LEU Chi-restraints excluded: chain E residue 169 VAL Chi-restraints excluded: chain E residue 197 ASN Chi-restraints excluded: chain E residue 209 THR Chi-restraints excluded: chain E residue 265 LEU Chi-restraints excluded: chain E residue 280 ASN Chi-restraints excluded: chain E residue 333 LEU Chi-restraints excluded: chain E residue 386 ASN Chi-restraints excluded: chain E residue 394 THR Chi-restraints excluded: chain E residue 455 THR Chi-restraints excluded: chain E residue 464 THR Chi-restraints excluded: chain F residue 575 GLN Chi-restraints excluded: chain F residue 583 VAL Chi-restraints excluded: chain F residue 626 MET Chi-restraints excluded: chain A residue 51 THR Chi-restraints excluded: chain A residue 54 CYS Chi-restraints excluded: chain A residue 65 VAL Chi-restraints excluded: chain A residue 114 GLN Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain A residue 316 TRP Chi-restraints excluded: chain A residue 390 LEU Chi-restraints excluded: chain A residue 446 SER Chi-restraints excluded: chain A residue 504 ARG Chi-restraints excluded: chain B residue 514 THR Chi-restraints excluded: chain B residue 603 ILE Chi-restraints excluded: chain B residue 612 THR Chi-restraints excluded: chain B residue 659 GLU Chi-restraints excluded: chain C residue 34 LEU Chi-restraints excluded: chain C residue 42 VAL Chi-restraints excluded: chain C residue 104 MET Chi-restraints excluded: chain C residue 132 ASN Chi-restraints excluded: chain C residue 274 SER Chi-restraints excluded: chain C residue 450 THR Chi-restraints excluded: chain C residue 496 VAL Chi-restraints excluded: chain C residue 505 VAL Chi-restraints excluded: chain D residue 535 MET Chi-restraints excluded: chain D residue 544 LEU Chi-restraints excluded: chain D residue 589 ASP Chi-restraints excluded: chain H residue 51 VAL Chi-restraints excluded: chain H residue 82 SER Chi-restraints excluded: chain H residue 89 MET Chi-restraints excluded: chain H residue 100 VAL Chi-restraints excluded: chain H residue 102 PHE Chi-restraints excluded: chain L residue 104 LEU Chi-restraints excluded: chain G residue 11 MET Chi-restraints excluded: chain G residue 48 VAL Chi-restraints excluded: chain G residue 68 THR Chi-restraints excluded: chain G residue 82 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 218 random chunks: chunk 2 optimal weight: 1.9990 chunk 108 optimal weight: 3.9990 chunk 216 optimal weight: 4.9990 chunk 67 optimal weight: 2.9990 chunk 132 optimal weight: 0.6980 chunk 215 optimal weight: 1.9990 chunk 71 optimal weight: 0.6980 chunk 202 optimal weight: 3.9990 chunk 179 optimal weight: 2.9990 chunk 23 optimal weight: 2.9990 chunk 18 optimal weight: 0.8980 overall best weight: 1.2584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 195 ASN ** C 302 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 377 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 38 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4009 r_free = 0.4009 target = 0.136311 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3737 r_free = 0.3737 target = 0.116374 restraints weight = 38852.896| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3782 r_free = 0.3782 target = 0.119592 restraints weight = 22723.883| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3811 r_free = 0.3811 target = 0.121720 restraints weight = 15844.586| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 44)----------------| | r_work = 0.3830 r_free = 0.3830 target = 0.123146 restraints weight = 12404.042| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.3843 r_free = 0.3843 target = 0.124100 restraints weight = 10447.987| |-----------------------------------------------------------------------------| r_work (final): 0.3850 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7274 moved from start: 0.4804 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 19315 Z= 0.167 Angle : 0.618 9.272 26393 Z= 0.303 Chirality : 0.045 0.250 3191 Planarity : 0.004 0.054 3212 Dihedral : 5.748 59.229 4243 Min Nonbonded Distance : 2.389 Molprobity Statistics. All-atom Clashscore : 8.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.86 % Favored : 98.14 % Rotamer: Outliers : 3.20 % Allowed : 12.53 % Favored : 84.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.09 % Twisted Proline : 1.12 % 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: 0.81 (0.17), residues: 2204 helix: 1.33 (0.25), residues: 433 sheet: 0.16 (0.21), residues: 581 loop : 0.60 (0.18), residues: 1190 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG L 27 TYR 0.024 0.002 TYR A 177 PHE 0.017 0.002 PHE G 100I TRP 0.021 0.002 TRP A 45 HIS 0.004 0.001 HIS E 249 Details of bonding type rmsd covalent geometry : bond 0.00395 (19189) covalent geometry : angle 0.58566 (26052) SS BOND : bond 0.00399 ( 37) SS BOND : angle 1.04746 ( 74) hydrogen bonds : bond 0.03864 ( 529) hydrogen bonds : angle 4.95165 ( 1380) link_ALPHA1-3 : bond 0.01015 ( 2) link_ALPHA1-3 : angle 1.22924 ( 6) link_ALPHA1-6 : bond 0.00815 ( 1) link_ALPHA1-6 : angle 1.29885 ( 3) link_BETA1-4 : bond 0.00552 ( 30) link_BETA1-4 : angle 1.82668 ( 90) link_BETA1-6 : bond 0.00637 ( 1) link_BETA1-6 : angle 3.37360 ( 3) link_NAG-ASN : bond 0.00280 ( 55) link_NAG-ASN : angle 2.09664 ( 165) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4408 Ramachandran restraints generated. 2204 Oldfield, 0 Emsley, 2204 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4408 Ramachandran restraints generated. 2204 Oldfield, 0 Emsley, 2204 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 280 residues out of total 1971 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 217 time to evaluate : 0.737 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 113 ASP cc_start: 0.8114 (t70) cc_final: 0.7799 (m-30) REVERT: F 575 GLN cc_start: 0.8177 (OUTLIER) cc_final: 0.7970 (tt0) REVERT: F 626 MET cc_start: 0.7767 (OUTLIER) cc_final: 0.7406 (mtm) REVERT: F 654 GLU cc_start: 0.7320 (mm-30) cc_final: 0.7026 (mm-30) REVERT: F 657 GLU cc_start: 0.7086 (pp20) cc_final: 0.6851 (mt-10) REVERT: A 357 LYS cc_start: 0.7151 (mmtp) cc_final: 0.6690 (mmtp) REVERT: B 634 GLU cc_start: 0.7444 (tp30) cc_final: 0.7032 (tt0) REVERT: B 658 GLN cc_start: 0.7486 (tp40) cc_final: 0.6651 (mt0) REVERT: C 117 LYS cc_start: 0.8421 (tppt) cc_final: 0.7911 (pttm) REVERT: C 154 MET cc_start: 0.6361 (mtm) cc_final: 0.6059 (mtm) REVERT: H 89 MET cc_start: 0.8155 (OUTLIER) cc_final: 0.7625 (ttm) REVERT: G 50 TRP cc_start: 0.6549 (m-90) cc_final: 0.5920 (m-90) REVERT: I 69 ASN cc_start: 0.8192 (p0) cc_final: 0.7760 (p0) outliers start: 63 outliers final: 48 residues processed: 264 average time/residue: 0.1406 time to fit residues: 57.7964 Evaluate side-chains 247 residues out of total 1971 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 196 time to evaluate : 0.756 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 85 ILE Chi-restraints excluded: chain E residue 114 GLN Chi-restraints excluded: chain E residue 116 LEU Chi-restraints excluded: chain E residue 122 LEU Chi-restraints excluded: chain E residue 125 LEU Chi-restraints excluded: chain E residue 169 VAL Chi-restraints excluded: chain E residue 197 ASN Chi-restraints excluded: chain E residue 209 THR Chi-restraints excluded: chain E residue 280 ASN Chi-restraints excluded: chain E residue 333 LEU Chi-restraints excluded: chain E residue 386 ASN Chi-restraints excluded: chain E residue 464 THR Chi-restraints excluded: chain F residue 575 GLN Chi-restraints excluded: chain F residue 626 MET Chi-restraints excluded: chain A residue 51 THR Chi-restraints excluded: chain A residue 65 VAL Chi-restraints excluded: chain A residue 114 GLN Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain A residue 169 VAL Chi-restraints excluded: chain A residue 181 ILE Chi-restraints excluded: chain A residue 316 TRP Chi-restraints excluded: chain A residue 446 SER Chi-restraints excluded: chain A residue 504 ARG Chi-restraints excluded: chain B residue 514 THR Chi-restraints excluded: chain B residue 535 MET Chi-restraints excluded: chain B residue 551 GLN Chi-restraints excluded: chain B residue 603 ILE Chi-restraints excluded: chain B residue 612 THR Chi-restraints excluded: chain B residue 659 GLU Chi-restraints excluded: chain C residue 34 LEU Chi-restraints excluded: chain C residue 42 VAL Chi-restraints excluded: chain C residue 86 LEU Chi-restraints excluded: chain C residue 104 MET Chi-restraints excluded: chain C residue 132 ASN Chi-restraints excluded: chain C residue 272 ILE Chi-restraints excluded: chain C residue 274 SER Chi-restraints excluded: chain C residue 450 THR Chi-restraints excluded: chain C residue 496 VAL Chi-restraints excluded: chain C residue 505 VAL Chi-restraints excluded: chain D residue 535 MET Chi-restraints excluded: chain D residue 544 LEU Chi-restraints excluded: chain D residue 589 ASP Chi-restraints excluded: chain H residue 51 VAL Chi-restraints excluded: chain H residue 82 SER Chi-restraints excluded: chain H residue 89 MET Chi-restraints excluded: chain H residue 100 VAL Chi-restraints excluded: chain L residue 75 ILE Chi-restraints excluded: chain L residue 104 LEU Chi-restraints excluded: chain G residue 11 MET Chi-restraints excluded: chain G residue 68 THR Chi-restraints excluded: chain G residue 82 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 218 random chunks: chunk 144 optimal weight: 7.9990 chunk 169 optimal weight: 3.9990 chunk 6 optimal weight: 3.9990 chunk 87 optimal weight: 6.9990 chunk 124 optimal weight: 3.9990 chunk 45 optimal weight: 4.9990 chunk 63 optimal weight: 3.9990 chunk 75 optimal weight: 2.9990 chunk 205 optimal weight: 3.9990 chunk 141 optimal weight: 1.9990 chunk 96 optimal weight: 3.9990 overall best weight: 3.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 478 ASN ** F 552 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 258 GLN ** C 302 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3932 r_free = 0.3932 target = 0.130141 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3644 r_free = 0.3644 target = 0.109828 restraints weight = 39232.916| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3688 r_free = 0.3688 target = 0.112837 restraints weight = 23297.753| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3717 r_free = 0.3717 target = 0.114873 restraints weight = 16521.186| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 46)----------------| | r_work = 0.3736 r_free = 0.3736 target = 0.116233 restraints weight = 13064.555| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.3749 r_free = 0.3749 target = 0.117146 restraints weight = 11113.881| |-----------------------------------------------------------------------------| r_work (final): 0.3745 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7455 moved from start: 0.5300 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.070 19315 Z= 0.382 Angle : 0.875 12.329 26393 Z= 0.431 Chirality : 0.054 0.281 3191 Planarity : 0.005 0.088 3212 Dihedral : 7.001 60.229 4243 Min Nonbonded Distance : 2.473 Molprobity Statistics. All-atom Clashscore : 11.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.22 % Favored : 95.78 % Rotamer: Outliers : 3.81 % Allowed : 12.48 % Favored : 83.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.09 % Twisted Proline : 1.12 % 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: -0.07 (0.17), residues: 2204 helix: 0.57 (0.24), residues: 433 sheet: -0.36 (0.21), residues: 571 loop : 0.03 (0.17), residues: 1200 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG H 94 TYR 0.026 0.003 TYR A 177 PHE 0.026 0.003 PHE G 100I TRP 0.039 0.003 TRP A 45 HIS 0.005 0.002 HIS E 105 Details of bonding type rmsd covalent geometry : bond 0.00906 (19189) covalent geometry : angle 0.84210 (26052) SS BOND : bond 0.00534 ( 37) SS BOND : angle 1.35038 ( 74) hydrogen bonds : bond 0.05283 ( 529) hydrogen bonds : angle 5.72930 ( 1380) link_ALPHA1-3 : bond 0.00896 ( 2) link_ALPHA1-3 : angle 1.18650 ( 6) link_ALPHA1-6 : bond 0.00614 ( 1) link_ALPHA1-6 : angle 1.33847 ( 3) link_BETA1-4 : bond 0.00569 ( 30) link_BETA1-4 : angle 2.11046 ( 90) link_BETA1-6 : bond 0.00884 ( 1) link_BETA1-6 : angle 3.78198 ( 3) link_NAG-ASN : bond 0.00507 ( 55) link_NAG-ASN : angle 2.65130 ( 165) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4408 Ramachandran restraints generated. 2204 Oldfield, 0 Emsley, 2204 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4408 Ramachandran restraints generated. 2204 Oldfield, 0 Emsley, 2204 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 288 residues out of total 1971 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 213 time to evaluate : 0.698 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 129 LEU cc_start: 0.6219 (OUTLIER) cc_final: 0.5929 (mt) REVERT: F 575 GLN cc_start: 0.8502 (OUTLIER) cc_final: 0.8276 (tt0) REVERT: A 129 LEU cc_start: 0.5685 (OUTLIER) cc_final: 0.5304 (mt) REVERT: A 154 MET cc_start: 0.5959 (mtt) cc_final: 0.5740 (mtm) REVERT: A 165 ILE cc_start: 0.8654 (mp) cc_final: 0.8346 (mt) REVERT: A 357 LYS cc_start: 0.7163 (mmtp) cc_final: 0.6591 (mmtp) REVERT: A 475 MET cc_start: 0.7915 (OUTLIER) cc_final: 0.7534 (mmm) REVERT: B 658 GLN cc_start: 0.7488 (tp40) cc_final: 0.6746 (mt0) REVERT: C 117 LYS cc_start: 0.8548 (tppt) cc_final: 0.7982 (pttm) REVERT: C 154 MET cc_start: 0.6475 (mtm) cc_final: 0.6230 (mtm) REVERT: C 477 ASP cc_start: 0.7558 (m-30) cc_final: 0.7342 (t70) REVERT: H 89 MET cc_start: 0.8251 (OUTLIER) cc_final: 0.7852 (ttm) REVERT: L 27 ASP cc_start: 0.8223 (p0) cc_final: 0.7913 (p0) REVERT: G 72 ASP cc_start: 0.7539 (m-30) cc_final: 0.7276 (m-30) REVERT: I 69 ASN cc_start: 0.8281 (p0) cc_final: 0.7750 (p0) outliers start: 75 outliers final: 55 residues processed: 264 average time/residue: 0.1408 time to fit residues: 58.0349 Evaluate side-chains 253 residues out of total 1971 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 193 time to evaluate : 0.730 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 94 ASN Chi-restraints excluded: chain E residue 114 GLN Chi-restraints excluded: chain E residue 116 LEU Chi-restraints excluded: chain E residue 122 LEU Chi-restraints excluded: chain E residue 129 LEU Chi-restraints excluded: chain E residue 154 MET Chi-restraints excluded: chain E residue 169 VAL Chi-restraints excluded: chain E residue 197 ASN Chi-restraints excluded: chain E residue 209 THR Chi-restraints excluded: chain E residue 280 ASN Chi-restraints excluded: chain E residue 294 ILE Chi-restraints excluded: chain E residue 333 LEU Chi-restraints excluded: chain E residue 386 ASN Chi-restraints excluded: chain E residue 464 THR Chi-restraints excluded: chain E residue 466 GLU Chi-restraints excluded: chain F residue 520 LEU Chi-restraints excluded: chain F residue 575 GLN Chi-restraints excluded: chain A residue 51 THR Chi-restraints excluded: chain A residue 54 CYS Chi-restraints excluded: chain A residue 65 VAL Chi-restraints excluded: chain A residue 114 GLN Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain A residue 129 LEU Chi-restraints excluded: chain A residue 169 VAL Chi-restraints excluded: chain A residue 316 TRP Chi-restraints excluded: chain A residue 446 SER Chi-restraints excluded: chain A residue 475 MET Chi-restraints excluded: chain A residue 504 ARG Chi-restraints excluded: chain B residue 513 VAL Chi-restraints excluded: chain B residue 603 ILE Chi-restraints excluded: chain B residue 612 THR Chi-restraints excluded: chain B residue 659 GLU Chi-restraints excluded: chain C residue 34 LEU Chi-restraints excluded: chain C residue 42 VAL Chi-restraints excluded: chain C residue 86 LEU Chi-restraints excluded: chain C residue 104 MET Chi-restraints excluded: chain C residue 132 ASN Chi-restraints excluded: chain C residue 272 ILE Chi-restraints excluded: chain C residue 274 SER Chi-restraints excluded: chain C residue 450 THR Chi-restraints excluded: chain C residue 496 VAL Chi-restraints excluded: chain D residue 535 MET Chi-restraints excluded: chain D residue 544 LEU Chi-restraints excluded: chain D residue 589 ASP Chi-restraints excluded: chain H residue 11 MET Chi-restraints excluded: chain H residue 32 TYR Chi-restraints excluded: chain H residue 51 VAL Chi-restraints excluded: chain H residue 89 MET Chi-restraints excluded: chain H residue 100 VAL Chi-restraints excluded: chain H residue 102 PHE Chi-restraints excluded: chain L residue 75 ILE Chi-restraints excluded: chain L residue 104 LEU Chi-restraints excluded: chain L residue 106 LEU Chi-restraints excluded: chain G residue 48 VAL Chi-restraints excluded: chain G residue 68 THR Chi-restraints excluded: chain G residue 74 SER Chi-restraints excluded: chain G residue 82 LEU Chi-restraints excluded: chain G residue 100 SER Chi-restraints excluded: chain G residue 100 LEU Chi-restraints excluded: chain I residue 58 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 218 random chunks: chunk 168 optimal weight: 0.8980 chunk 191 optimal weight: 0.6980 chunk 175 optimal weight: 0.6980 chunk 63 optimal weight: 3.9990 chunk 108 optimal weight: 0.7980 chunk 126 optimal weight: 0.1980 chunk 32 optimal weight: 0.9980 chunk 18 optimal weight: 0.6980 chunk 159 optimal weight: 0.5980 chunk 100 optimal weight: 0.9980 chunk 111 optimal weight: 0.9980 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 552 GLN H 100AHIS ** G 1 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 37 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4008 r_free = 0.4008 target = 0.135967 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3744 r_free = 0.3744 target = 0.116484 restraints weight = 38573.841| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3787 r_free = 0.3787 target = 0.119655 restraints weight = 22380.142| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 49)----------------| | r_work = 0.3816 r_free = 0.3816 target = 0.121756 restraints weight = 15586.161| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3835 r_free = 0.3835 target = 0.123156 restraints weight = 12154.571| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3845 r_free = 0.3845 target = 0.123959 restraints weight = 10218.622| |-----------------------------------------------------------------------------| r_work (final): 0.3849 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7282 moved from start: 0.5287 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 19315 Z= 0.133 Angle : 0.622 10.845 26393 Z= 0.305 Chirality : 0.045 0.245 3191 Planarity : 0.004 0.057 3212 Dihedral : 6.078 59.421 4243 Min Nonbonded Distance : 2.530 Molprobity Statistics. All-atom Clashscore : 8.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.86 % Favored : 98.14 % Rotamer: Outliers : 2.33 % Allowed : 14.10 % Favored : 83.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.09 % 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: 0.36 (0.18), residues: 2204 helix: 1.15 (0.25), residues: 431 sheet: -0.11 (0.21), residues: 583 loop : 0.22 (0.18), residues: 1190 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG L 27 TYR 0.017 0.002 TYR A 177 PHE 0.029 0.002 PHE G 100K TRP 0.026 0.002 TRP A 395 HIS 0.005 0.001 HIS E 249 Details of bonding type rmsd covalent geometry : bond 0.00301 (19189) covalent geometry : angle 0.59174 (26052) SS BOND : bond 0.00280 ( 37) SS BOND : angle 1.09808 ( 74) hydrogen bonds : bond 0.03701 ( 529) hydrogen bonds : angle 5.01906 ( 1380) link_ALPHA1-3 : bond 0.00961 ( 2) link_ALPHA1-3 : angle 1.33355 ( 6) link_ALPHA1-6 : bond 0.00624 ( 1) link_ALPHA1-6 : angle 1.33326 ( 3) link_BETA1-4 : bond 0.00576 ( 30) link_BETA1-4 : angle 1.76504 ( 90) link_BETA1-6 : bond 0.00615 ( 1) link_BETA1-6 : angle 3.29720 ( 3) link_NAG-ASN : bond 0.00315 ( 55) link_NAG-ASN : angle 2.03084 ( 165) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4408 Ramachandran restraints generated. 2204 Oldfield, 0 Emsley, 2204 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4408 Ramachandran restraints generated. 2204 Oldfield, 0 Emsley, 2204 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 258 residues out of total 1971 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 212 time to evaluate : 0.633 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 475 MET cc_start: 0.8464 (tpp) cc_final: 0.8207 (tpp) REVERT: F 575 GLN cc_start: 0.8103 (OUTLIER) cc_final: 0.7627 (tt0) REVERT: F 626 MET cc_start: 0.7833 (OUTLIER) cc_final: 0.7540 (mtm) REVERT: F 654 GLU cc_start: 0.7314 (mm-30) cc_final: 0.6858 (mm-30) REVERT: F 657 GLU cc_start: 0.7192 (pp20) cc_final: 0.6718 (mt-10) REVERT: A 165 ILE cc_start: 0.8626 (mp) cc_final: 0.8307 (mt) REVERT: A 357 LYS cc_start: 0.7090 (mmtp) cc_final: 0.6636 (mmtp) REVERT: B 530 MET cc_start: 0.8043 (mtp) cc_final: 0.7657 (mtp) REVERT: B 634 GLU cc_start: 0.7480 (tp30) cc_final: 0.7094 (tt0) REVERT: B 658 GLN cc_start: 0.7387 (tp40) cc_final: 0.6571 (mt0) REVERT: C 97 THR cc_start: 0.8645 (p) cc_final: 0.8411 (t) REVERT: C 117 LYS cc_start: 0.8376 (tppt) cc_final: 0.7895 (pttm) REVERT: H 89 MET cc_start: 0.8190 (OUTLIER) cc_final: 0.7733 (ttm) REVERT: I 69 ASN cc_start: 0.8114 (p0) cc_final: 0.7724 (p0) outliers start: 46 outliers final: 35 residues processed: 241 average time/residue: 0.1495 time to fit residues: 55.2251 Evaluate side-chains 239 residues out of total 1971 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 201 time to evaluate : 0.718 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 85 ILE Chi-restraints excluded: chain E residue 94 ASN Chi-restraints excluded: chain E residue 114 GLN Chi-restraints excluded: chain E residue 116 LEU Chi-restraints excluded: chain E residue 122 LEU Chi-restraints excluded: chain E residue 169 VAL Chi-restraints excluded: chain E residue 197 ASN Chi-restraints excluded: chain E residue 280 ASN Chi-restraints excluded: chain E residue 386 ASN Chi-restraints excluded: chain E residue 466 GLU Chi-restraints excluded: chain F residue 575 GLN Chi-restraints excluded: chain F residue 626 MET Chi-restraints excluded: chain A residue 65 VAL Chi-restraints excluded: chain A residue 169 VAL Chi-restraints excluded: chain A residue 181 ILE Chi-restraints excluded: chain A residue 316 TRP Chi-restraints excluded: chain A residue 446 SER Chi-restraints excluded: chain A residue 504 ARG Chi-restraints excluded: chain B residue 513 VAL Chi-restraints excluded: chain B residue 553 ASN Chi-restraints excluded: chain B residue 603 ILE Chi-restraints excluded: chain B residue 659 GLU Chi-restraints excluded: chain C residue 34 LEU Chi-restraints excluded: chain C residue 104 MET Chi-restraints excluded: chain C residue 132 ASN Chi-restraints excluded: chain C residue 272 ILE Chi-restraints excluded: chain C residue 450 THR Chi-restraints excluded: chain D residue 520 LEU Chi-restraints excluded: chain D residue 535 MET Chi-restraints excluded: chain D residue 544 LEU Chi-restraints excluded: chain H residue 51 VAL Chi-restraints excluded: chain H residue 82 SER Chi-restraints excluded: chain H residue 89 MET Chi-restraints excluded: chain L residue 75 ILE Chi-restraints excluded: chain L residue 106 LEU Chi-restraints excluded: chain G residue 82 LEU Chi-restraints excluded: chain G residue 100 SER Chi-restraints excluded: chain I residue 52 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 218 random chunks: chunk 203 optimal weight: 0.8980 chunk 102 optimal weight: 1.9990 chunk 208 optimal weight: 0.7980 chunk 22 optimal weight: 1.9990 chunk 123 optimal weight: 0.5980 chunk 110 optimal weight: 2.9990 chunk 121 optimal weight: 8.9990 chunk 176 optimal weight: 0.6980 chunk 6 optimal weight: 3.9990 chunk 179 optimal weight: 0.8980 chunk 18 optimal weight: 0.7980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 553 ASN ** C 377 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 1 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 = 0.4006 r_free = 0.4006 target = 0.135964 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3738 r_free = 0.3738 target = 0.116249 restraints weight = 38637.581| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3782 r_free = 0.3782 target = 0.119375 restraints weight = 22731.719| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3810 r_free = 0.3810 target = 0.121451 restraints weight = 15900.106| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.3829 r_free = 0.3829 target = 0.122846 restraints weight = 12476.402| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.3841 r_free = 0.3841 target = 0.123762 restraints weight = 10529.360| |-----------------------------------------------------------------------------| r_work (final): 0.3844 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7287 moved from start: 0.5341 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 19315 Z= 0.137 Angle : 0.618 11.534 26393 Z= 0.301 Chirality : 0.045 0.238 3191 Planarity : 0.004 0.055 3212 Dihedral : 5.832 59.555 4243 Min Nonbonded Distance : 2.488 Molprobity Statistics. All-atom Clashscore : 8.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.72 % Favored : 97.28 % Rotamer: Outliers : 1.88 % Allowed : 14.66 % Favored : 83.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.09 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.44 (0.18), residues: 2204 helix: 1.31 (0.25), residues: 431 sheet: -0.06 (0.21), residues: 581 loop : 0.23 (0.18), residues: 1192 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG L 27 TYR 0.017 0.002 TYR G 33 PHE 0.027 0.002 PHE G 100I TRP 0.021 0.001 TRP H 50 HIS 0.004 0.001 HIS E 249 Details of bonding type rmsd covalent geometry : bond 0.00321 (19189) covalent geometry : angle 0.58853 (26052) SS BOND : bond 0.00267 ( 37) SS BOND : angle 1.09451 ( 74) hydrogen bonds : bond 0.03590 ( 529) hydrogen bonds : angle 4.90547 ( 1380) link_ALPHA1-3 : bond 0.00889 ( 2) link_ALPHA1-3 : angle 1.19962 ( 6) link_ALPHA1-6 : bond 0.00638 ( 1) link_ALPHA1-6 : angle 1.35029 ( 3) link_BETA1-4 : bond 0.00510 ( 30) link_BETA1-4 : angle 1.72563 ( 90) link_BETA1-6 : bond 0.00545 ( 1) link_BETA1-6 : angle 3.17113 ( 3) link_NAG-ASN : bond 0.00278 ( 55) link_NAG-ASN : angle 2.01683 ( 165) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4408 Ramachandran restraints generated. 2204 Oldfield, 0 Emsley, 2204 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4408 Ramachandran restraints generated. 2204 Oldfield, 0 Emsley, 2204 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 241 residues out of total 1971 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 204 time to evaluate : 0.789 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: F 626 MET cc_start: 0.7755 (OUTLIER) cc_final: 0.7477 (mtm) REVERT: F 654 GLU cc_start: 0.7282 (mm-30) cc_final: 0.6822 (mm-30) REVERT: F 657 GLU cc_start: 0.7028 (pp20) cc_final: 0.6653 (mt-10) REVERT: A 165 ILE cc_start: 0.8633 (mp) cc_final: 0.8296 (mt) REVERT: B 530 MET cc_start: 0.8047 (mtp) cc_final: 0.7583 (mtp) REVERT: B 634 GLU cc_start: 0.7505 (tp30) cc_final: 0.7045 (tt0) REVERT: B 658 GLN cc_start: 0.7464 (tp40) cc_final: 0.6669 (mt0) REVERT: C 97 THR cc_start: 0.8663 (p) cc_final: 0.8426 (t) REVERT: C 117 LYS cc_start: 0.8352 (tppt) cc_final: 0.7890 (pttm) REVERT: C 434 MET cc_start: 0.7667 (ttp) cc_final: 0.7386 (ttp) REVERT: H 89 MET cc_start: 0.8208 (OUTLIER) cc_final: 0.7759 (ttm) REVERT: L 27 ASP cc_start: 0.8155 (p0) cc_final: 0.7826 (p0) REVERT: I 69 ASN cc_start: 0.8189 (p0) cc_final: 0.7795 (p0) outliers start: 37 outliers final: 29 residues processed: 230 average time/residue: 0.1380 time to fit residues: 49.7650 Evaluate side-chains 228 residues out of total 1971 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 197 time to evaluate : 0.740 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 85 ILE Chi-restraints excluded: chain E residue 94 ASN Chi-restraints excluded: chain E residue 114 GLN Chi-restraints excluded: chain E residue 116 LEU Chi-restraints excluded: chain E residue 122 LEU Chi-restraints excluded: chain E residue 169 VAL Chi-restraints excluded: chain E residue 280 ASN Chi-restraints excluded: chain E residue 386 ASN Chi-restraints excluded: chain E residue 466 GLU Chi-restraints excluded: chain F residue 626 MET Chi-restraints excluded: chain A residue 65 VAL Chi-restraints excluded: chain A residue 169 VAL Chi-restraints excluded: chain A residue 181 ILE Chi-restraints excluded: chain A residue 316 TRP Chi-restraints excluded: chain A residue 446 SER Chi-restraints excluded: chain A residue 504 ARG Chi-restraints excluded: chain B residue 513 VAL Chi-restraints excluded: chain B residue 553 ASN Chi-restraints excluded: chain B residue 603 ILE Chi-restraints excluded: chain B residue 659 GLU Chi-restraints excluded: chain C residue 34 LEU Chi-restraints excluded: chain C residue 104 MET Chi-restraints excluded: chain C residue 132 ASN Chi-restraints excluded: chain C residue 272 ILE Chi-restraints excluded: chain C residue 450 THR Chi-restraints excluded: chain D residue 535 MET Chi-restraints excluded: chain D residue 544 LEU Chi-restraints excluded: chain H residue 51 VAL Chi-restraints excluded: chain H residue 89 MET Chi-restraints excluded: chain L residue 106 LEU Chi-restraints excluded: chain G residue 100 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 218 random chunks: chunk 93 optimal weight: 0.7980 chunk 67 optimal weight: 2.9990 chunk 72 optimal weight: 0.2980 chunk 20 optimal weight: 3.9990 chunk 167 optimal weight: 0.6980 chunk 38 optimal weight: 0.0770 chunk 208 optimal weight: 0.0370 chunk 168 optimal weight: 2.9990 chunk 34 optimal weight: 0.9990 chunk 1 optimal weight: 0.7980 chunk 160 optimal weight: 0.6980 overall best weight: 0.3616 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 195 ASN C 258 GLN D 543 ASN ** G 1 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4034 r_free = 0.4034 target = 0.138137 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3772 r_free = 0.3772 target = 0.118623 restraints weight = 38731.302| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3817 r_free = 0.3817 target = 0.121908 restraints weight = 22311.040| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3847 r_free = 0.3847 target = 0.124049 restraints weight = 15373.432| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3866 r_free = 0.3866 target = 0.125493 restraints weight = 11937.635| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3876 r_free = 0.3876 target = 0.126293 restraints weight = 9991.135| |-----------------------------------------------------------------------------| r_work (final): 0.3885 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7217 moved from start: 0.5404 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 19315 Z= 0.110 Angle : 0.587 11.058 26393 Z= 0.287 Chirality : 0.044 0.241 3191 Planarity : 0.004 0.041 3212 Dihedral : 5.551 58.838 4241 Min Nonbonded Distance : 2.445 Molprobity Statistics. All-atom Clashscore : 7.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.91 % Favored : 98.09 % Rotamer: Outliers : 1.78 % Allowed : 14.92 % Favored : 83.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.09 % 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: 0.56 (0.18), residues: 2204 helix: 1.53 (0.26), residues: 431 sheet: -0.04 (0.20), residues: 617 loop : 0.31 (0.18), residues: 1156 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG L 27 TYR 0.014 0.001 TYR G 33 PHE 0.017 0.001 PHE G 100K TRP 0.022 0.001 TRP H 50 HIS 0.004 0.001 HIS E 249 Details of bonding type rmsd covalent geometry : bond 0.00250 (19189) covalent geometry : angle 0.55773 (26052) SS BOND : bond 0.00267 ( 37) SS BOND : angle 1.14245 ( 74) hydrogen bonds : bond 0.03204 ( 529) hydrogen bonds : angle 4.70675 ( 1380) link_ALPHA1-3 : bond 0.00887 ( 2) link_ALPHA1-3 : angle 1.23762 ( 6) link_ALPHA1-6 : bond 0.00660 ( 1) link_ALPHA1-6 : angle 1.34685 ( 3) link_BETA1-4 : bond 0.00528 ( 30) link_BETA1-4 : angle 1.61367 ( 90) link_BETA1-6 : bond 0.00528 ( 1) link_BETA1-6 : angle 2.97287 ( 3) link_NAG-ASN : bond 0.00383 ( 55) link_NAG-ASN : angle 1.94556 ( 165) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3264.18 seconds wall clock time: 57 minutes 35.25 seconds (3455.25 seconds total)