Starting phenix.real_space_refine on Thu Mar 5 06:07:20 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6vo3_21258/03_2026/6vo3_21258.cif Found real_map, /net/cci-nas-00/data/ceres_data/6vo3_21258/03_2026/6vo3_21258.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.25 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/6vo3_21258/03_2026/6vo3_21258.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6vo3_21258/03_2026/6vo3_21258.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/6vo3_21258/03_2026/6vo3_21258.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6vo3_21258/03_2026/6vo3_21258.map" } resolution = 4.25 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.002 sd= 0.049 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 120 5.16 5 C 12300 2.51 5 N 3300 2.21 5 O 3834 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 60 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 19554 Number of models: 1 Model: "" Number of chains: 39 Chain: "H" Number of atoms: 994 Number of conformers: 1 Conformer: "" Number of residues, atoms: 125, 994 Classifications: {'peptide': 125} Link IDs: {'PTRANS': 3, 'TRANS': 121} Chain: "L" Number of atoms: 784 Number of conformers: 1 Conformer: "" Number of residues, atoms: 100, 784 Classifications: {'peptide': 100} Link IDs: {'PCIS': 1, 'PTRANS': 6, 'TRANS': 92} Chain: "A" Number of atoms: 3402 Number of conformers: 1 Conformer: "" Number of residues, atoms: 429, 3402 Classifications: {'peptide': 429} Link IDs: {'PTRANS': 22, 'TRANS': 406} Chain breaks: 4 Chain: "B" Number of atoms: 992 Number of conformers: 1 Conformer: "" Number of residues, atoms: 124, 992 Classifications: {'peptide': 124} Link IDs: {'PTRANS': 1, 'TRANS': 122} Chain breaks: 1 Chain: "G" Number of atoms: 994 Number of conformers: 1 Conformer: "" Number of residues, atoms: 125, 994 Classifications: {'peptide': 125} Link IDs: {'PTRANS': 3, 'TRANS': 121} Chain: "J" Number of atoms: 784 Number of conformers: 1 Conformer: "" Number of residues, atoms: 100, 784 Classifications: {'peptide': 100} Link IDs: {'PCIS': 1, 'PTRANS': 6, 'TRANS': 92} Chain: "C" Number of atoms: 3402 Number of conformers: 1 Conformer: "" Number of residues, atoms: 429, 3402 Classifications: {'peptide': 429} Link IDs: {'PTRANS': 22, 'TRANS': 406} Chain breaks: 4 Chain: "E" Number of atoms: 992 Number of conformers: 1 Conformer: "" Number of residues, atoms: 124, 992 Classifications: {'peptide': 124} Link IDs: {'PTRANS': 1, 'TRANS': 122} Chain breaks: 1 Chain: "I" Number of atoms: 994 Number of conformers: 1 Conformer: "" Number of residues, atoms: 125, 994 Classifications: {'peptide': 125} Link IDs: {'PTRANS': 3, 'TRANS': 121} Chain: "K" Number of atoms: 784 Number of conformers: 1 Conformer: "" Number of residues, atoms: 100, 784 Classifications: {'peptide': 100} Link IDs: {'PCIS': 1, 'PTRANS': 6, 'TRANS': 92} Chain: "D" Number of atoms: 3402 Number of conformers: 1 Conformer: "" Number of residues, atoms: 429, 3402 Classifications: {'peptide': 429} Link IDs: {'PTRANS': 22, 'TRANS': 406} Chain breaks: 4 Chain: "F" Number of atoms: 992 Number of conformers: 1 Conformer: "" Number of residues, atoms: 124, 992 Classifications: {'peptide': 124} Link IDs: {'PTRANS': 1, 'TRANS': 122} Chain breaks: 1 Chain: "M" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "N" Number of atoms: 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: "O" 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: "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: 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: "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: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "U" Number of atoms: 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: "V" 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: "W" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "X" Number of atoms: 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: "Y" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "Z" Number of atoms: 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: 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: "b" 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: "c" 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: "d" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "e" Number of atoms: 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: 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: "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: "A" Number of atoms: 70 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 70 Unusual residues: {'NAG': 5} 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: "B" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "C" Number of atoms: 70 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 70 Unusual residues: {'NAG': 5} 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: "E" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "D" Number of atoms: 70 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 70 Unusual residues: {'NAG': 5} 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: "F" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 4.78, per 1000 atoms: 0.24 Number of scatterers: 19554 At special positions: 0 Unit cell: (144.1, 148.03, 116.59, 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 120 16.00 O 3834 8.00 N 3300 7.00 C 12300 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=36, symmetry=0 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 92 " distance=2.05 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 88 " distance=2.02 Simple disulfide: pdb=" SG CYS A 54 " - pdb=" SG CYS A 74 " distance=2.04 Simple disulfide: pdb=" SG CYS A 119 " - pdb=" SG CYS A 205 " distance=2.04 Simple disulfide: pdb=" SG CYS A 126 " - pdb=" SG CYS A 196 " distance=2.13 Simple disulfide: pdb=" SG CYS A 131 " - pdb=" SG CYS A 157 " distance=2.04 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=2.03 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=2.03 Simple disulfide: pdb=" SG CYS B 598 " - pdb=" SG CYS B 604 " distance=2.04 Simple disulfide: pdb=" SG CYS G 22 " - pdb=" SG CYS G 92 " distance=2.05 Simple disulfide: pdb=" SG CYS J 23 " - pdb=" SG CYS J 88 " distance=2.02 Simple disulfide: pdb=" SG CYS C 54 " - pdb=" SG CYS C 74 " distance=2.04 Simple disulfide: pdb=" SG CYS C 119 " - pdb=" SG CYS C 205 " distance=2.04 Simple disulfide: pdb=" SG CYS C 126 " - pdb=" SG CYS C 196 " distance=2.13 Simple disulfide: pdb=" SG CYS C 131 " - pdb=" SG CYS C 157 " distance=2.04 Simple disulfide: pdb=" SG CYS C 218 " - pdb=" SG CYS C 247 " distance=2.02 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=2.03 Simple disulfide: pdb=" SG CYS C 385 " - pdb=" SG CYS C 418 " distance=2.03 Simple disulfide: pdb=" SG CYS E 598 " - pdb=" SG CYS E 604 " distance=2.04 Simple disulfide: pdb=" SG CYS I 22 " - pdb=" SG CYS I 92 " distance=2.05 Simple disulfide: pdb=" SG CYS K 23 " - pdb=" SG CYS K 88 " distance=2.02 Simple disulfide: pdb=" SG CYS D 54 " - pdb=" SG CYS D 74 " distance=2.04 Simple disulfide: pdb=" SG CYS D 119 " - pdb=" SG CYS D 205 " distance=2.04 Simple disulfide: pdb=" SG CYS D 126 " - pdb=" SG CYS D 196 " distance=2.13 Simple disulfide: pdb=" SG CYS D 131 " - pdb=" SG CYS D 157 " distance=2.04 Simple disulfide: pdb=" SG CYS D 218 " - pdb=" SG CYS D 247 " distance=2.02 Simple disulfide: pdb=" SG CYS D 228 " - pdb=" SG CYS D 239 " distance=2.03 Simple disulfide: pdb=" SG CYS D 296 " - pdb=" SG CYS D 331 " distance=2.03 Simple disulfide: pdb=" SG CYS D 378 " - pdb=" SG CYS D 445 " distance=2.03 Simple disulfide: pdb=" SG CYS D 385 " - pdb=" SG CYS D 418 " distance=2.03 Simple disulfide: pdb=" SG CYS F 598 " - pdb=" SG CYS F 604 " distance=2.04 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied ALPHA1-3 " BMA N 3 " - " MAN N 4 " " BMA U 3 " - " MAN U 4 " " BMA b 3 " - " MAN b 4 " ALPHA1-6 " BMA N 3 " - " MAN N 5 " " BMA U 3 " - " MAN U 5 " " BMA b 3 " - " MAN b 5 " BETA1-4 " NAG M 1 " - " NAG M 2 " " NAG M 2 " - " BMA M 3 " " NAG N 1 " - " NAG N 2 " " NAG N 2 " - " BMA N 3 " " NAG O 1 " - " NAG O 2 " " NAG O 2 " - " BMA O 3 " " NAG P 1 " - " NAG P 2 " " NAG Q 1 " - " NAG Q 2 " " NAG Q 2 " - " BMA Q 3 " " NAG R 1 " - " NAG R 2 " " NAG S 1 " - " NAG S 2 " " NAG T 1 " - " NAG T 2 " " NAG T 2 " - " BMA T 3 " " NAG U 1 " - " NAG U 2 " " NAG U 2 " - " BMA U 3 " " NAG V 1 " - " NAG V 2 " " NAG V 2 " - " BMA V 3 " " NAG W 1 " - " NAG W 2 " " NAG X 1 " - " NAG X 2 " " NAG X 2 " - " BMA X 3 " " NAG Y 1 " - " NAG Y 2 " " NAG Z 1 " - " NAG Z 2 " " NAG a 1 " - " NAG a 2 " " NAG a 2 " - " BMA a 3 " " NAG b 1 " - " NAG b 2 " " NAG b 2 " - " BMA b 3 " " NAG c 1 " - " NAG c 2 " " NAG c 2 " - " BMA c 3 " " NAG d 1 " - " NAG d 2 " " NAG e 1 " - " NAG e 2 " " NAG e 2 " - " BMA e 3 " " NAG f 1 " - " NAG f 2 " " NAG g 1 " - " NAG g 2 " NAG-ASN " NAG A 614 " - " ASN A 396 " " NAG A 615 " - " ASN A 448 " " NAG A 619 " - " ASN A 463 " " NAG A 622 " - " ASN A 234 " " NAG A 623 " - " ASN A 197 " " NAG B 701 " - " ASN B 625 " " NAG C 614 " - " ASN C 396 " " NAG C 615 " - " ASN C 448 " " NAG C 619 " - " ASN C 463 " " NAG C 622 " - " ASN C 234 " " NAG C 623 " - " ASN C 197 " " NAG D 614 " - " ASN D 396 " " NAG D 615 " - " ASN D 448 " " NAG D 619 " - " ASN D 463 " " NAG D 622 " - " ASN D 234 " " NAG D 623 " - " ASN D 197 " " NAG E 701 " - " ASN E 625 " " NAG F 701 " - " ASN F 625 " " NAG M 1 " - " ASN A 262 " " NAG N 1 " - " ASN A 276 " " NAG O 1 " - " ASN A 386 " " NAG P 1 " - " ASN A 392 " " NAG Q 1 " - " ASN A 362 " " NAG R 1 " - " ASN A 241 " " NAG S 1 " - " ASN A 88 " " NAG T 1 " - " ASN C 262 " " NAG U 1 " - " ASN C 276 " " NAG V 1 " - " ASN C 386 " " NAG W 1 " - " ASN C 392 " " NAG X 1 " - " ASN C 362 " " NAG Y 1 " - " ASN C 241 " " NAG Z 1 " - " ASN C 88 " " NAG a 1 " - " ASN D 262 " " NAG b 1 " - " ASN D 276 " " NAG c 1 " - " ASN D 386 " " NAG d 1 " - " ASN D 392 " " NAG e 1 " - " ASN D 362 " " NAG f 1 " - " ASN D 241 " " NAG g 1 " - " ASN D 88 " Time building additional restraints: 1.93 Conformation dependent library (CDL) restraints added in 815.4 milliseconds 4560 Ramachandran restraints generated. 2280 Oldfield, 0 Emsley, 2280 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4338 Finding SS restraints... Secondary structure from input PDB file: 57 helices and 45 sheets defined 24.4% alpha, 34.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.94 Creating SS restraints... Processing helix chain 'H' and resid 25 through 31 Processing helix chain 'H' and resid 60 through 66 Processing helix chain 'H' and resid 83 through 87 Processing helix chain 'L' and resid 77 through 83 Proline residue: L 80 - end of helix Processing helix chain 'A' and resid 70 through 74 Processing helix chain 'A' and resid 98 through 117 removed outlier: 4.206A 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 334 through 353 Processing helix chain 'A' and resid 368 through 373 Processing helix chain 'A' and resid 387 through 390 Processing helix chain 'A' and resid 425 through 429 Processing helix chain 'A' and resid 474 through 484 removed outlier: 4.032A pdb=" N ASN A 478 " --> pdb=" O ASP A 474 " (cutoff:3.500A) removed outlier: 4.068A pdb=" N GLU A 482 " --> pdb=" O ASN A 478 " (cutoff:3.500A) Processing helix chain 'B' and resid 523 through 528 Processing helix chain 'B' and resid 532 through 541 removed outlier: 4.764A pdb=" N THR B 538 " --> pdb=" O SER B 534 " (cutoff:3.500A) Processing helix chain 'B' and resid 570 through 596 Processing helix chain 'B' and resid 618 through 624 removed outlier: 3.560A pdb=" N ILE B 622 " --> pdb=" O SER B 618 " (cutoff:3.500A) Processing helix chain 'B' and resid 627 through 636 removed outlier: 3.885A pdb=" N ARG B 633 " --> pdb=" O ILE B 629 " (cutoff:3.500A) removed outlier: 4.257A pdb=" N GLU B 634 " --> pdb=" O GLU B 630 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N ILE B 635 " --> pdb=" O TRP B 631 " (cutoff:3.500A) Processing helix chain 'B' and resid 638 through 651 Processing helix chain 'B' and resid 651 through 664 Processing helix chain 'G' and resid 25 through 31 Processing helix chain 'G' and resid 60 through 66 Processing helix chain 'G' and resid 83 through 87 Processing helix chain 'J' and resid 77 through 83 Proline residue: J 80 - end of helix Processing helix chain 'C' and resid 70 through 74 Processing helix chain 'C' and resid 98 through 117 removed outlier: 4.206A 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 334 through 353 Processing helix chain 'C' and resid 368 through 373 Processing helix chain 'C' and resid 387 through 390 Processing helix chain 'C' and resid 425 through 429 Processing helix chain 'C' and resid 474 through 484 removed outlier: 4.032A pdb=" N ASN C 478 " --> pdb=" O ASP C 474 " (cutoff:3.500A) removed outlier: 4.068A pdb=" N GLU C 482 " --> pdb=" O ASN C 478 " (cutoff:3.500A) Processing helix chain 'E' and resid 523 through 528 Processing helix chain 'E' and resid 532 through 541 removed outlier: 4.764A pdb=" N THR E 538 " --> pdb=" O SER E 534 " (cutoff:3.500A) Processing helix chain 'E' and resid 570 through 596 Processing helix chain 'E' and resid 618 through 624 removed outlier: 3.561A pdb=" N ILE E 622 " --> pdb=" O SER E 618 " (cutoff:3.500A) Processing helix chain 'E' and resid 627 through 636 removed outlier: 3.885A pdb=" N ARG E 633 " --> pdb=" O ILE E 629 " (cutoff:3.500A) removed outlier: 4.256A pdb=" N GLU E 634 " --> pdb=" O GLU E 630 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N ILE E 635 " --> pdb=" O TRP E 631 " (cutoff:3.500A) Processing helix chain 'E' and resid 638 through 651 Processing helix chain 'E' and resid 651 through 664 Processing helix chain 'I' and resid 25 through 31 Processing helix chain 'I' and resid 60 through 66 Processing helix chain 'I' and resid 83 through 87 Processing helix chain 'K' and resid 77 through 83 Proline residue: K 80 - end of helix Processing helix chain 'D' and resid 70 through 74 Processing helix chain 'D' and resid 98 through 117 removed outlier: 4.207A pdb=" N GLU D 102 " --> pdb=" O ASN D 98 " (cutoff:3.500A) Processing helix chain 'D' and resid 122 through 126 Processing helix chain 'D' and resid 334 through 353 Processing helix chain 'D' and resid 368 through 373 Processing helix chain 'D' and resid 387 through 390 Processing helix chain 'D' and resid 425 through 429 Processing helix chain 'D' and resid 474 through 484 removed outlier: 4.032A pdb=" N ASN D 478 " --> pdb=" O ASP D 474 " (cutoff:3.500A) removed outlier: 4.068A pdb=" N GLU D 482 " --> pdb=" O ASN D 478 " (cutoff:3.500A) Processing helix chain 'F' and resid 523 through 528 Processing helix chain 'F' and resid 532 through 541 removed outlier: 4.764A pdb=" N THR F 538 " --> pdb=" O SER F 534 " (cutoff:3.500A) Processing helix chain 'F' and resid 570 through 596 Processing helix chain 'F' and resid 618 through 624 removed outlier: 3.560A pdb=" N ILE F 622 " --> pdb=" O SER F 618 " (cutoff:3.500A) Processing helix chain 'F' and resid 627 through 636 removed outlier: 3.885A pdb=" N ARG F 633 " --> pdb=" O ILE F 629 " (cutoff:3.500A) removed outlier: 4.257A pdb=" N GLU F 634 " --> pdb=" O GLU F 630 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N ILE F 635 " --> pdb=" O TRP F 631 " (cutoff:3.500A) Processing helix chain 'F' and resid 638 through 651 Processing helix chain 'F' and resid 651 through 664 Processing sheet with id=AA1, first strand: chain 'H' and resid 10 through 12 removed outlier: 6.671A pdb=" N ILE H 35 " --> pdb=" O TRP H 50 " (cutoff:3.500A) removed outlier: 4.460A pdb=" N TRP H 50 " --> pdb=" O ILE H 35 " (cutoff:3.500A) removed outlier: 6.866A pdb=" N TRP H 36 " --> pdb=" O ILE H 48 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'H' and resid 10 through 12 removed outlier: 5.688A pdb=" N CYS H 92 " --> pdb=" O GLY H 104 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'L' and resid 4 through 7 Processing sheet with id=AA4, first strand: chain 'L' and resid 10 through 12 removed outlier: 5.951A pdb=" N LEU L 11 " --> pdb=" O GLU L 105 " (cutoff:3.500A) removed outlier: 6.615A pdb=" N TRP L 35 " --> pdb=" O LEU L 47 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'L' and resid 10 through 12 removed outlier: 5.951A pdb=" N LEU L 11 " --> pdb=" O GLU L 105 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 494 through 498 Processing sheet with id=AA7, first strand: chain 'A' and resid 45 through 47 Processing sheet with id=AA8, first strand: chain 'A' and resid 75 through 76 removed outlier: 6.830A pdb=" N CYS A 54 " --> pdb=" O VAL A 75 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 91 through 94 Processing sheet with id=AB1, first strand: chain 'A' and resid 170 through 177 Processing sheet with id=AB2, first strand: chain 'A' and resid 200 through 203 removed outlier: 6.160A pdb=" N VAL A 200 " --> pdb=" O ALA A 433 " (cutoff:3.500A) removed outlier: 7.280A pdb=" N TYR A 435 " --> pdb=" O VAL A 200 " (cutoff:3.500A) removed outlier: 6.625A pdb=" N LYS A 202 " --> pdb=" O TYR A 435 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 259 through 260 removed outlier: 3.785A pdb=" N GLY A 451 " --> pdb=" O LEU A 260 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 259 through 260 removed outlier: 3.785A pdb=" N GLY A 451 " --> pdb=" O LEU A 260 " (cutoff:3.500A) removed outlier: 6.684A pdb=" N ALA A 360 " --> pdb=" O PHE A 468 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 315 through 323A removed outlier: 7.394A pdb=" N TRP A 316 " --> pdb=" O ILE A 309 " (cutoff:3.500A) removed outlier: 6.262A pdb=" N ILE A 309 " --> pdb=" O TRP A 316 " (cutoff:3.500A) removed outlier: 5.544A pdb=" N TYR A 318 " --> pdb=" O ILE A 307 " (cutoff:3.500A) removed outlier: 7.181A pdb=" N ILE A 307 " --> pdb=" O TYR A 318 " (cutoff:3.500A) removed outlier: 5.402A pdb=" N THR A 320 " --> pdb=" O LYS A 305 " (cutoff:3.500A) removed outlier: 4.907A pdb=" N LYS A 305 " --> pdb=" O THR A 320 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N ALA A 322 " --> pdb=" O THR A 303 " (cutoff:3.500A) removed outlier: 4.529A pdb=" N PHE A 382 " --> pdb=" O LYS A 421 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 315 through 323A removed outlier: 7.394A pdb=" N TRP A 316 " --> pdb=" O ILE A 309 " (cutoff:3.500A) removed outlier: 6.262A pdb=" N ILE A 309 " --> pdb=" O TRP A 316 " (cutoff:3.500A) removed outlier: 5.544A pdb=" N TYR A 318 " --> pdb=" O ILE A 307 " (cutoff:3.500A) removed outlier: 7.181A pdb=" N ILE A 307 " --> pdb=" O TYR A 318 " (cutoff:3.500A) removed outlier: 5.402A pdb=" N THR A 320 " --> pdb=" O LYS A 305 " (cutoff:3.500A) removed outlier: 4.907A pdb=" N LYS A 305 " --> pdb=" O THR A 320 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N ALA A 322 " --> pdb=" O THR A 303 " (cutoff:3.500A) removed outlier: 6.925A pdb=" N ASN A 300 " --> pdb=" O GLY A 441 " (cutoff:3.500A) removed outlier: 4.790A pdb=" N GLY A 441 " --> pdb=" O ASN A 300 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'G' and resid 10 through 12 removed outlier: 6.671A pdb=" N ILE G 35 " --> pdb=" O TRP G 50 " (cutoff:3.500A) removed outlier: 4.460A pdb=" N TRP G 50 " --> pdb=" O ILE G 35 " (cutoff:3.500A) removed outlier: 6.867A pdb=" N TRP G 36 " --> pdb=" O ILE G 48 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'G' and resid 10 through 12 removed outlier: 5.688A pdb=" N CYS G 92 " --> pdb=" O GLY G 104 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'J' and resid 4 through 7 Processing sheet with id=AC1, first strand: chain 'J' and resid 10 through 12 removed outlier: 5.950A pdb=" N LEU J 11 " --> pdb=" O GLU J 105 " (cutoff:3.500A) removed outlier: 6.615A pdb=" N TRP J 35 " --> pdb=" O LEU J 47 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'J' and resid 10 through 12 removed outlier: 5.950A pdb=" N LEU J 11 " --> pdb=" O GLU J 105 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'C' and resid 494 through 498 Processing sheet with id=AC4, first strand: chain 'C' and resid 45 through 47 Processing sheet with id=AC5, first strand: chain 'C' and resid 75 through 76 removed outlier: 6.830A pdb=" N CYS C 54 " --> pdb=" O VAL C 75 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'C' and resid 91 through 94 Processing sheet with id=AC7, first strand: chain 'C' and resid 170 through 177 Processing sheet with id=AC8, first strand: chain 'C' and resid 200 through 203 removed outlier: 6.161A pdb=" N VAL C 200 " --> pdb=" O ALA C 433 " (cutoff:3.500A) removed outlier: 7.281A pdb=" N TYR C 435 " --> pdb=" O VAL C 200 " (cutoff:3.500A) removed outlier: 6.625A pdb=" N LYS C 202 " --> pdb=" O TYR C 435 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'C' and resid 259 through 260 removed outlier: 3.785A pdb=" N GLY C 451 " --> pdb=" O LEU C 260 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'C' and resid 259 through 260 removed outlier: 3.785A pdb=" N GLY C 451 " --> pdb=" O LEU C 260 " (cutoff:3.500A) removed outlier: 6.684A pdb=" N ALA C 360 " --> pdb=" O PHE C 468 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'C' and resid 315 through 323A removed outlier: 7.394A pdb=" N TRP C 316 " --> pdb=" O ILE C 309 " (cutoff:3.500A) removed outlier: 6.262A pdb=" N ILE C 309 " --> pdb=" O TRP C 316 " (cutoff:3.500A) removed outlier: 5.544A pdb=" N TYR C 318 " --> pdb=" O ILE C 307 " (cutoff:3.500A) removed outlier: 7.182A pdb=" N ILE C 307 " --> pdb=" O TYR C 318 " (cutoff:3.500A) removed outlier: 5.402A pdb=" N THR C 320 " --> pdb=" O LYS C 305 " (cutoff:3.500A) removed outlier: 4.907A pdb=" N LYS C 305 " --> pdb=" O THR C 320 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N ALA C 322 " --> pdb=" O THR C 303 " (cutoff:3.500A) removed outlier: 4.529A pdb=" N PHE C 382 " --> pdb=" O LYS C 421 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'C' and resid 315 through 323A removed outlier: 7.394A pdb=" N TRP C 316 " --> pdb=" O ILE C 309 " (cutoff:3.500A) removed outlier: 6.262A pdb=" N ILE C 309 " --> pdb=" O TRP C 316 " (cutoff:3.500A) removed outlier: 5.544A pdb=" N TYR C 318 " --> pdb=" O ILE C 307 " (cutoff:3.500A) removed outlier: 7.182A pdb=" N ILE C 307 " --> pdb=" O TYR C 318 " (cutoff:3.500A) removed outlier: 5.402A pdb=" N THR C 320 " --> pdb=" O LYS C 305 " (cutoff:3.500A) removed outlier: 4.907A pdb=" N LYS C 305 " --> pdb=" O THR C 320 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N ALA C 322 " --> pdb=" O THR C 303 " (cutoff:3.500A) removed outlier: 6.925A pdb=" N ASN C 300 " --> pdb=" O GLY C 441 " (cutoff:3.500A) removed outlier: 4.790A pdb=" N GLY C 441 " --> pdb=" O ASN C 300 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'I' and resid 10 through 12 removed outlier: 6.671A pdb=" N ILE I 35 " --> pdb=" O TRP I 50 " (cutoff:3.500A) removed outlier: 4.460A pdb=" N TRP I 50 " --> pdb=" O ILE I 35 " (cutoff:3.500A) removed outlier: 6.866A pdb=" N TRP I 36 " --> pdb=" O ILE I 48 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'I' and resid 10 through 12 removed outlier: 5.687A pdb=" N CYS I 92 " --> pdb=" O GLY I 104 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'K' and resid 4 through 7 Processing sheet with id=AD7, first strand: chain 'K' and resid 10 through 12 removed outlier: 5.951A pdb=" N LEU K 11 " --> pdb=" O GLU K 105 " (cutoff:3.500A) removed outlier: 6.615A pdb=" N TRP K 35 " --> pdb=" O LEU K 47 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'K' and resid 10 through 12 removed outlier: 5.951A pdb=" N LEU K 11 " --> pdb=" O GLU K 105 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'D' and resid 494 through 498 Processing sheet with id=AE1, first strand: chain 'D' and resid 45 through 47 Processing sheet with id=AE2, first strand: chain 'D' and resid 75 through 76 removed outlier: 6.830A pdb=" N CYS D 54 " --> pdb=" O VAL D 75 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'D' and resid 91 through 94 Processing sheet with id=AE4, first strand: chain 'D' and resid 170 through 177 Processing sheet with id=AE5, first strand: chain 'D' and resid 200 through 203 removed outlier: 6.161A pdb=" N VAL D 200 " --> pdb=" O ALA D 433 " (cutoff:3.500A) removed outlier: 7.280A pdb=" N TYR D 435 " --> pdb=" O VAL D 200 " (cutoff:3.500A) removed outlier: 6.625A pdb=" N LYS D 202 " --> pdb=" O TYR D 435 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'D' and resid 259 through 260 removed outlier: 3.786A pdb=" N GLY D 451 " --> pdb=" O LEU D 260 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'D' and resid 259 through 260 removed outlier: 3.786A pdb=" N GLY D 451 " --> pdb=" O LEU D 260 " (cutoff:3.500A) removed outlier: 6.684A pdb=" N ALA D 360 " --> pdb=" O PHE D 468 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'D' and resid 315 through 323A removed outlier: 7.393A pdb=" N TRP D 316 " --> pdb=" O ILE D 309 " (cutoff:3.500A) removed outlier: 6.262A pdb=" N ILE D 309 " --> pdb=" O TRP D 316 " (cutoff:3.500A) removed outlier: 5.543A pdb=" N TYR D 318 " --> pdb=" O ILE D 307 " (cutoff:3.500A) removed outlier: 7.182A pdb=" N ILE D 307 " --> pdb=" O TYR D 318 " (cutoff:3.500A) removed outlier: 5.402A pdb=" N THR D 320 " --> pdb=" O LYS D 305 " (cutoff:3.500A) removed outlier: 4.907A pdb=" N LYS D 305 " --> pdb=" O THR D 320 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N ALA D 322 " --> pdb=" O THR D 303 " (cutoff:3.500A) removed outlier: 4.529A pdb=" N PHE D 382 " --> pdb=" O LYS D 421 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'D' and resid 315 through 323A removed outlier: 7.393A pdb=" N TRP D 316 " --> pdb=" O ILE D 309 " (cutoff:3.500A) removed outlier: 6.262A pdb=" N ILE D 309 " --> pdb=" O TRP D 316 " (cutoff:3.500A) removed outlier: 5.543A pdb=" N TYR D 318 " --> pdb=" O ILE D 307 " (cutoff:3.500A) removed outlier: 7.182A pdb=" N ILE D 307 " --> pdb=" O TYR D 318 " (cutoff:3.500A) removed outlier: 5.402A pdb=" N THR D 320 " --> pdb=" O LYS D 305 " (cutoff:3.500A) removed outlier: 4.907A pdb=" N LYS D 305 " --> pdb=" O THR D 320 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N ALA D 322 " --> pdb=" O THR D 303 " (cutoff:3.500A) removed outlier: 6.925A pdb=" N ASN D 300 " --> pdb=" O GLY D 441 " (cutoff:3.500A) removed outlier: 4.791A pdb=" N GLY D 441 " --> pdb=" O ASN D 300 " (cutoff:3.500A) 807 hydrogen bonds defined for protein. 2016 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: 3.94 Time building geometry restraints manager: 2.48 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.33: 4975 1.33 - 1.47: 6369 1.47 - 1.61: 8444 1.61 - 1.74: 12 1.74 - 1.88: 159 Bond restraints: 19959 Sorted by residual: bond pdb=" CB CYS L 88 " pdb=" SG CYS L 88 " ideal model delta sigma weight residual 1.808 1.635 0.173 3.30e-02 9.18e+02 2.75e+01 bond pdb=" CB CYS J 88 " pdb=" SG CYS J 88 " ideal model delta sigma weight residual 1.808 1.635 0.173 3.30e-02 9.18e+02 2.75e+01 bond pdb=" CB CYS K 88 " pdb=" SG CYS K 88 " ideal model delta sigma weight residual 1.808 1.635 0.173 3.30e-02 9.18e+02 2.74e+01 bond pdb=" CB HIS C 330 " pdb=" CG HIS C 330 " ideal model delta sigma weight residual 1.497 1.427 0.070 1.40e-02 5.10e+03 2.49e+01 bond pdb=" CB TYR H 100E" pdb=" CG TYR H 100E" ideal model delta sigma weight residual 1.512 1.402 0.110 2.20e-02 2.07e+03 2.49e+01 ... (remaining 19954 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.18: 22093 2.18 - 4.36: 3949 4.36 - 6.53: 836 6.53 - 8.71: 176 8.71 - 10.89: 18 Bond angle restraints: 27072 Sorted by residual: angle pdb=" CA PHE A 53 " pdb=" CB PHE A 53 " pdb=" CG PHE A 53 " ideal model delta sigma weight residual 113.80 121.92 -8.12 1.00e+00 1.00e+00 6.59e+01 angle pdb=" CA PHE D 53 " pdb=" CB PHE D 53 " pdb=" CG PHE D 53 " ideal model delta sigma weight residual 113.80 121.91 -8.11 1.00e+00 1.00e+00 6.57e+01 angle pdb=" CA PHE C 53 " pdb=" CB PHE C 53 " pdb=" CG PHE C 53 " ideal model delta sigma weight residual 113.80 121.90 -8.10 1.00e+00 1.00e+00 6.56e+01 angle pdb=" N ILE A 181 " pdb=" CA ILE A 181 " pdb=" C ILE A 181 " ideal model delta sigma weight residual 108.17 119.06 -10.89 1.40e+00 5.10e-01 6.05e+01 angle pdb=" N ILE C 181 " pdb=" CA ILE C 181 " pdb=" C ILE C 181 " ideal model delta sigma weight residual 108.17 119.06 -10.89 1.40e+00 5.10e-01 6.05e+01 ... (remaining 27067 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 21.68: 12256 21.68 - 43.35: 437 43.35 - 65.03: 135 65.03 - 86.70: 66 86.70 - 108.38: 57 Dihedral angle restraints: 12951 sinusoidal: 6237 harmonic: 6714 Sorted by residual: dihedral pdb=" C LEU E 537 " pdb=" N LEU E 537 " pdb=" CA LEU E 537 " pdb=" CB LEU E 537 " ideal model delta harmonic sigma weight residual -122.60 -112.27 -10.33 0 2.50e+00 1.60e-01 1.71e+01 dihedral pdb=" C LEU F 537 " pdb=" N LEU F 537 " pdb=" CA LEU F 537 " pdb=" CB LEU F 537 " ideal model delta harmonic sigma weight residual -122.60 -112.28 -10.32 0 2.50e+00 1.60e-01 1.70e+01 dihedral pdb=" C LEU B 537 " pdb=" N LEU B 537 " pdb=" CA LEU B 537 " pdb=" CB LEU B 537 " ideal model delta harmonic sigma weight residual -122.60 -112.30 -10.30 0 2.50e+00 1.60e-01 1.70e+01 ... (remaining 12948 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.113: 2392 0.113 - 0.226: 729 0.226 - 0.339: 101 0.339 - 0.452: 3 0.452 - 0.565: 12 Chirality restraints: 3237 Sorted by residual: chirality pdb=" C1 BMA a 3 " pdb=" O4 NAG a 2 " pdb=" C2 BMA a 3 " pdb=" O5 BMA a 3 " both_signs ideal model delta sigma weight residual False -2.40 -2.57 0.17 2.00e-02 2.50e+03 7.33e+01 chirality pdb=" C1 BMA M 3 " pdb=" O4 NAG M 2 " pdb=" C2 BMA M 3 " pdb=" O5 BMA M 3 " both_signs ideal model delta sigma weight residual False -2.40 -2.57 0.17 2.00e-02 2.50e+03 7.26e+01 chirality pdb=" C1 BMA T 3 " pdb=" O4 NAG T 2 " pdb=" C2 BMA T 3 " pdb=" O5 BMA T 3 " both_signs ideal model delta sigma weight residual False -2.40 -2.57 0.17 2.00e-02 2.50e+03 7.18e+01 ... (remaining 3234 not shown) Planarity restraints: 3375 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 NAG T 2 " -0.088 2.00e-02 2.50e+03 7.24e-02 6.55e+01 pdb=" C7 NAG T 2 " 0.023 2.00e-02 2.50e+03 pdb=" C8 NAG T 2 " -0.066 2.00e-02 2.50e+03 pdb=" N2 NAG T 2 " 0.115 2.00e-02 2.50e+03 pdb=" O7 NAG T 2 " 0.017 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG a 2 " -0.088 2.00e-02 2.50e+03 7.24e-02 6.54e+01 pdb=" C7 NAG a 2 " 0.023 2.00e-02 2.50e+03 pdb=" C8 NAG a 2 " -0.066 2.00e-02 2.50e+03 pdb=" N2 NAG a 2 " 0.115 2.00e-02 2.50e+03 pdb=" O7 NAG a 2 " 0.017 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG M 2 " -0.088 2.00e-02 2.50e+03 7.23e-02 6.54e+01 pdb=" C7 NAG M 2 " 0.023 2.00e-02 2.50e+03 pdb=" C8 NAG M 2 " -0.066 2.00e-02 2.50e+03 pdb=" N2 NAG M 2 " 0.115 2.00e-02 2.50e+03 pdb=" O7 NAG M 2 " 0.017 2.00e-02 2.50e+03 ... (remaining 3372 not shown) Histogram of nonbonded interaction distances: 2.38 - 2.89: 7888 2.89 - 3.39: 17911 3.39 - 3.89: 34105 3.89 - 4.40: 39417 4.40 - 4.90: 62034 Nonbonded interactions: 161355 Sorted by model distance: nonbonded pdb=" N ASP C 57 " pdb=" OD1 ASP C 57 " model vdw 2.385 3.120 nonbonded pdb=" N ASP A 57 " pdb=" OD1 ASP A 57 " model vdw 2.385 3.120 nonbonded pdb=" N ASP D 57 " pdb=" OD1 ASP D 57 " model vdw 2.385 3.120 nonbonded pdb=" OD1 ASP H 27 " pdb=" NZ LYS C 207 " model vdw 2.387 3.120 nonbonded pdb=" NZ LYS A 207 " pdb=" OD1 ASP I 27 " model vdw 2.387 3.120 ... (remaining 161350 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: 0.04 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'C' selection = chain 'D' } ncs_group { reference = chain 'B' selection = chain 'E' selection = chain 'F' } ncs_group { reference = chain 'G' selection = chain 'H' selection = chain 'I' } ncs_group { reference = chain 'J' selection = chain 'K' selection = chain 'L' } ncs_group { reference = chain 'M' selection = chain 'O' selection = chain 'Q' selection = chain 'T' selection = chain 'V' selection = chain 'X' selection = chain 'a' selection = chain 'c' selection = chain 'e' } ncs_group { reference = chain 'N' selection = chain 'U' selection = chain 'b' } ncs_group { reference = chain 'P' selection = chain 'R' selection = chain 'S' selection = chain 'W' selection = chain 'Y' selection = chain 'Z' selection = chain 'd' selection = chain 'f' 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: 1.080 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: 0.300 Check model and map are aligned: 0.050 Set scattering table: 0.040 Process input model: 19.480 Find NCS groups from input model: 0.460 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: 0.000 Load rotamer database and sin/cos tables:1.350 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 22.830 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7550 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 : 0.019 0.173 20073 Z= 1.012 Angle : 1.858 10.890 27378 Z= 1.171 Chirality : 0.106 0.565 3237 Planarity : 0.009 0.072 3336 Dihedral : 15.585 108.378 8505 Min Nonbonded Distance : 2.385 Molprobity Statistics. All-atom Clashscore : 1.91 Ramachandran Plot: Outliers : 0.53 % Allowed : 3.82 % Favored : 95.66 % Rotamer: Outliers : 0.44 % Allowed : 1.32 % Favored : 98.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.21 (0.17), residues: 2280 helix: -0.25 (0.23), residues: 429 sheet: 0.78 (0.19), residues: 642 loop : 0.05 (0.18), residues: 1209 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG H 94 TYR 0.042 0.009 TYR C 486 PHE 0.032 0.006 PHE D 53 TRP 0.040 0.011 TRP B 571 HIS 0.016 0.004 HIS A 374 Details of bonding type rmsd covalent geometry : bond 0.01915 (19959) covalent geometry : angle 1.84077 (27072) SS BOND : bond 0.02869 ( 36) SS BOND : angle 2.11563 ( 72) hydrogen bonds : bond 0.15913 ( 768) hydrogen bonds : angle 8.13255 ( 2016) link_ALPHA1-3 : bond 0.04758 ( 3) link_ALPHA1-3 : angle 6.02560 ( 9) link_ALPHA1-6 : bond 0.04450 ( 3) link_ALPHA1-6 : angle 3.79895 ( 9) link_BETA1-4 : bond 0.03794 ( 33) link_BETA1-4 : angle 3.87154 ( 99) link_NAG-ASN : bond 0.03225 ( 39) link_NAG-ASN : angle 2.18944 ( 117) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4560 Ramachandran restraints generated. 2280 Oldfield, 0 Emsley, 2280 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4560 Ramachandran restraints generated. 2280 Oldfield, 0 Emsley, 2280 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 692 residues out of total 2046 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 683 time to evaluate : 0.751 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 4 LEU cc_start: 0.8039 (mt) cc_final: 0.7023 (mt) REVERT: H 36 TRP cc_start: 0.9324 (m100) cc_final: 0.8905 (m100) REVERT: H 72 ASP cc_start: 0.7945 (t0) cc_final: 0.7462 (t0) REVERT: H 75 LEU cc_start: 0.9001 (mt) cc_final: 0.8752 (mt) REVERT: H 80 MET cc_start: 0.8778 (ttp) cc_final: 0.8493 (ttt) REVERT: H 81 ASP cc_start: 0.7892 (m-30) cc_final: 0.7628 (p0) REVERT: L 86 TYR cc_start: 0.8245 (m-80) cc_final: 0.7760 (m-10) REVERT: A 69 TRP cc_start: 0.7677 (m-90) cc_final: 0.6699 (m-90) REVERT: A 95 MET cc_start: 0.8697 (ptm) cc_final: 0.8492 (ptm) REVERT: A 195 ASN cc_start: 0.7968 (m-40) cc_final: 0.7672 (m110) REVERT: A 434 MET cc_start: 0.8486 (ttp) cc_final: 0.7924 (tmm) REVERT: A 494 LEU cc_start: 0.8870 (mt) cc_final: 0.8521 (pp) REVERT: B 622 ILE cc_start: 0.8882 (pt) cc_final: 0.8528 (mp) REVERT: G 4 LEU cc_start: 0.7919 (mt) cc_final: 0.7130 (mt) REVERT: G 13 LYS cc_start: 0.8714 (mmtt) cc_final: 0.8480 (mmmt) REVERT: G 36 TRP cc_start: 0.9353 (m100) cc_final: 0.9024 (m100) REVERT: G 72 ASP cc_start: 0.7949 (t0) cc_final: 0.7646 (t0) REVERT: G 80 MET cc_start: 0.8817 (ttp) cc_final: 0.6552 (ttp) REVERT: G 81 ASP cc_start: 0.8264 (m-30) cc_final: 0.7909 (p0) REVERT: J 86 TYR cc_start: 0.8331 (m-80) cc_final: 0.7812 (m-10) REVERT: J 102 THR cc_start: 0.8060 (p) cc_final: 0.7836 (m) REVERT: C 69 TRP cc_start: 0.7949 (m-90) cc_final: 0.7479 (m-90) REVERT: C 181 ILE cc_start: 0.8666 (mt) cc_final: 0.8423 (pt) REVERT: C 195 ASN cc_start: 0.8151 (m-40) cc_final: 0.7850 (m110) REVERT: C 475 MET cc_start: 0.8325 (mmt) cc_final: 0.7992 (mmt) REVERT: C 494 LEU cc_start: 0.8901 (mt) cc_final: 0.8603 (mt) REVERT: E 658 GLN cc_start: 0.8204 (tp40) cc_final: 0.8002 (tp40) REVERT: I 4 LEU cc_start: 0.8395 (mt) cc_final: 0.7691 (mt) REVERT: I 13 LYS cc_start: 0.8881 (mmtt) cc_final: 0.8655 (mmmt) REVERT: I 80 MET cc_start: 0.8728 (ttp) cc_final: 0.8138 (ttp) REVERT: I 81 ASP cc_start: 0.8262 (m-30) cc_final: 0.7859 (p0) REVERT: I 100 GLN cc_start: 0.5169 (mt0) cc_final: 0.4708 (mm110) REVERT: K 86 TYR cc_start: 0.8272 (m-80) cc_final: 0.7705 (m-10) REVERT: K 104 LEU cc_start: 0.8265 (mt) cc_final: 0.8018 (mt) REVERT: D 69 TRP cc_start: 0.8116 (m-90) cc_final: 0.7187 (m-90) REVERT: D 181 ILE cc_start: 0.8570 (mt) cc_final: 0.8331 (pt) REVERT: D 475 MET cc_start: 0.8386 (mmt) cc_final: 0.8137 (mmt) REVERT: D 494 LEU cc_start: 0.8740 (mt) cc_final: 0.8479 (mp) REVERT: F 576 LEU cc_start: 0.8748 (tp) cc_final: 0.8539 (tt) outliers start: 9 outliers final: 6 residues processed: 692 average time/residue: 0.1672 time to fit residues: 168.1425 Evaluate side-chains 340 residues out of total 2046 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 334 time to evaluate : 0.893 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 216 optimal weight: 2.9990 chunk 98 optimal weight: 0.7980 chunk 194 optimal weight: 5.9990 chunk 227 optimal weight: 0.9990 chunk 107 optimal weight: 6.9990 chunk 10 optimal weight: 5.9990 chunk 66 optimal weight: 2.9990 chunk 130 optimal weight: 0.9980 chunk 124 optimal weight: 20.0000 chunk 103 optimal weight: 2.9990 chunk 200 optimal weight: 5.9990 overall best weight: 1.7586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 43 GLN A 72 HIS A 105 HIS A 195 ASN A 229 ASN A 377 ASN ** B 591 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 43 GLN ** J 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 72 HIS C 105 HIS C 195 ASN C 229 ASN C 377 ASN I 43 GLN K 100 GLN D 72 HIS D 105 HIS D 229 ASN Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3540 r_free = 0.3540 target = 0.077263 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3190 r_free = 0.3190 target = 0.062101 restraints weight = 84886.886| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3243 r_free = 0.3243 target = 0.064202 restraints weight = 50686.251| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3278 r_free = 0.3278 target = 0.065640 restraints weight = 35237.638| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3301 r_free = 0.3301 target = 0.066626 restraints weight = 27243.173| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 38)----------------| | r_work = 0.3318 r_free = 0.3318 target = 0.067328 restraints weight = 22650.669| |-----------------------------------------------------------------------------| r_work (final): 0.3312 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7597 moved from start: 0.3640 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.067 20073 Z= 0.240 Angle : 1.032 24.277 27378 Z= 0.499 Chirality : 0.054 0.353 3237 Planarity : 0.005 0.068 3336 Dihedral : 12.511 85.347 4098 Min Nonbonded Distance : 2.491 Molprobity Statistics. All-atom Clashscore : 13.37 Ramachandran Plot: Outliers : 0.70 % Allowed : 4.82 % Favored : 94.47 % Rotamer: Outliers : 0.05 % Allowed : 2.64 % Favored : 97.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.21 (0.17), residues: 2280 helix: 0.78 (0.24), residues: 429 sheet: 0.60 (0.19), residues: 654 loop : -0.29 (0.18), residues: 1197 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG I 94 TYR 0.046 0.003 TYR F 643 PHE 0.033 0.003 PHE G 76 TRP 0.035 0.003 TRP C 112 HIS 0.006 0.001 HIS D 374 Details of bonding type rmsd covalent geometry : bond 0.00498 (19959) covalent geometry : angle 0.91960 (27072) SS BOND : bond 0.00451 ( 36) SS BOND : angle 1.40416 ( 72) hydrogen bonds : bond 0.06220 ( 768) hydrogen bonds : angle 6.90345 ( 2016) link_ALPHA1-3 : bond 0.00528 ( 3) link_ALPHA1-3 : angle 4.79208 ( 9) link_ALPHA1-6 : bond 0.01297 ( 3) link_ALPHA1-6 : angle 1.19813 ( 9) link_BETA1-4 : bond 0.00811 ( 33) link_BETA1-4 : angle 3.67741 ( 99) link_NAG-ASN : bond 0.00956 ( 39) link_NAG-ASN : angle 6.23170 ( 117) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4560 Ramachandran restraints generated. 2280 Oldfield, 0 Emsley, 2280 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4560 Ramachandran restraints generated. 2280 Oldfield, 0 Emsley, 2280 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 480 residues out of total 2046 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 479 time to evaluate : 0.695 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 4 LEU cc_start: 0.8348 (mt) cc_final: 0.6107 (mt) REVERT: H 28 ILE cc_start: 0.9558 (mm) cc_final: 0.9112 (mm) REVERT: H 34 LEU cc_start: 0.8943 (mt) cc_final: 0.8727 (mt) REVERT: H 72 ASP cc_start: 0.7517 (t0) cc_final: 0.6860 (t0) REVERT: H 75 LEU cc_start: 0.8949 (mt) cc_final: 0.8500 (mp) REVERT: H 81 ASP cc_start: 0.8157 (m-30) cc_final: 0.7706 (p0) REVERT: H 108 LEU cc_start: 0.8843 (tp) cc_final: 0.8612 (tp) REVERT: L 4 LEU cc_start: 0.8551 (tp) cc_final: 0.8266 (tp) REVERT: L 47 LEU cc_start: 0.9011 (mm) cc_final: 0.8475 (pp) REVERT: L 86 TYR cc_start: 0.8421 (m-80) cc_final: 0.7953 (m-10) REVERT: L 97 PHE cc_start: 0.8317 (m-10) cc_final: 0.8054 (m-80) REVERT: A 95 MET cc_start: 0.8738 (ptm) cc_final: 0.8369 (ptm) REVERT: A 154 ILE cc_start: 0.9503 (tp) cc_final: 0.8882 (tp) REVERT: A 342 LEU cc_start: 0.9212 (mp) cc_final: 0.8981 (mm) REVERT: A 373 MET cc_start: 0.8818 (mtp) cc_final: 0.8477 (mtp) REVERT: B 584 GLU cc_start: 0.8654 (tm-30) cc_final: 0.8292 (tm-30) REVERT: B 628 TRP cc_start: 0.7834 (m100) cc_final: 0.7140 (m100) REVERT: B 630 GLU cc_start: 0.8628 (pt0) cc_final: 0.7989 (pt0) REVERT: B 647 GLU cc_start: 0.8336 (OUTLIER) cc_final: 0.8102 (pm20) REVERT: G 34 LEU cc_start: 0.8779 (mt) cc_final: 0.8431 (mt) REVERT: G 36 TRP cc_start: 0.9408 (m100) cc_final: 0.8638 (m-10) REVERT: G 72 ASP cc_start: 0.7400 (t0) cc_final: 0.7141 (t0) REVERT: G 81 ASP cc_start: 0.8057 (m-30) cc_final: 0.7819 (p0) REVERT: J 47 LEU cc_start: 0.8893 (mp) cc_final: 0.8513 (pp) REVERT: J 86 TYR cc_start: 0.8641 (m-80) cc_final: 0.8095 (m-10) REVERT: J 104 LEU cc_start: 0.8571 (mt) cc_final: 0.8333 (mt) REVERT: C 69 TRP cc_start: 0.7559 (m-90) cc_final: 0.7308 (m-90) REVERT: C 95 MET cc_start: 0.9064 (ppp) cc_final: 0.8765 (ppp) REVERT: C 373 MET cc_start: 0.8724 (mtp) cc_final: 0.8225 (mtp) REVERT: E 530 MET cc_start: 0.7328 (ptm) cc_final: 0.6625 (ptm) REVERT: E 546 SER cc_start: 0.8254 (t) cc_final: 0.7720 (p) REVERT: E 628 TRP cc_start: 0.7598 (m100) cc_final: 0.7335 (m100) REVERT: E 659 GLU cc_start: 0.9004 (tt0) cc_final: 0.8603 (tt0) REVERT: I 4 LEU cc_start: 0.7891 (mt) cc_final: 0.7527 (mt) REVERT: I 72 ASP cc_start: 0.6676 (t0) cc_final: 0.6282 (t0) REVERT: I 80 MET cc_start: 0.8699 (ttp) cc_final: 0.8268 (ttp) REVERT: I 81 ASP cc_start: 0.8356 (m-30) cc_final: 0.7731 (p0) REVERT: I 100 GLN cc_start: 0.5202 (mt0) cc_final: 0.4607 (mm110) REVERT: I 108 LEU cc_start: 0.8744 (tp) cc_final: 0.8525 (tp) REVERT: K 33 MET cc_start: 0.7765 (ptp) cc_final: 0.6918 (tmm) REVERT: K 47 LEU cc_start: 0.9095 (mm) cc_final: 0.8509 (pp) REVERT: K 71 TYR cc_start: 0.6317 (t80) cc_final: 0.5919 (t80) REVERT: K 86 TYR cc_start: 0.8179 (m-80) cc_final: 0.7878 (m-10) REVERT: D 104 MET cc_start: 0.8993 (mmt) cc_final: 0.8673 (mmp) REVERT: D 373 MET cc_start: 0.8959 (mtp) cc_final: 0.8475 (mtp) REVERT: D 475 MET cc_start: 0.8234 (mmt) cc_final: 0.7765 (mmt) REVERT: F 530 MET cc_start: 0.6838 (ptt) cc_final: 0.6401 (ptt) REVERT: F 546 SER cc_start: 0.8163 (t) cc_final: 0.7910 (p) REVERT: F 574 LYS cc_start: 0.9282 (mttt) cc_final: 0.8865 (ttmm) REVERT: F 628 TRP cc_start: 0.7393 (m100) cc_final: 0.6798 (m100) outliers start: 1 outliers final: 0 residues processed: 479 average time/residue: 0.1453 time to fit residues: 105.8944 Evaluate side-chains 301 residues out of total 2046 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 300 time to evaluate : 0.796 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 148 optimal weight: 1.9990 chunk 162 optimal weight: 2.9990 chunk 103 optimal weight: 8.9990 chunk 82 optimal weight: 0.7980 chunk 51 optimal weight: 7.9990 chunk 119 optimal weight: 0.8980 chunk 39 optimal weight: 10.0000 chunk 23 optimal weight: 0.9990 chunk 188 optimal weight: 5.9990 chunk 138 optimal weight: 0.7980 chunk 53 optimal weight: 5.9990 overall best weight: 1.0984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 90 GLN G 95 GLN ** J 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 302 ASN C 425 ASN ** I 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 43 GLN D 302 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3528 r_free = 0.3528 target = 0.076568 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3178 r_free = 0.3178 target = 0.061521 restraints weight = 85046.369| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3231 r_free = 0.3231 target = 0.063635 restraints weight = 50260.976| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3266 r_free = 0.3266 target = 0.065079 restraints weight = 34839.196| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3291 r_free = 0.3291 target = 0.066079 restraints weight = 26917.367| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3306 r_free = 0.3306 target = 0.066732 restraints weight = 22286.308| |-----------------------------------------------------------------------------| r_work (final): 0.3301 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7635 moved from start: 0.4478 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 20073 Z= 0.171 Angle : 0.881 21.797 27378 Z= 0.421 Chirality : 0.052 0.354 3237 Planarity : 0.005 0.047 3336 Dihedral : 9.791 73.879 4098 Min Nonbonded Distance : 2.492 Molprobity Statistics. All-atom Clashscore : 14.38 Ramachandran Plot: Outliers : 0.53 % Allowed : 5.13 % Favored : 94.34 % Rotamer: Outliers : 0.15 % Allowed : 2.83 % Favored : 97.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.04 (0.17), residues: 2280 helix: 0.76 (0.24), residues: 447 sheet: 0.53 (0.19), residues: 675 loop : -0.52 (0.18), residues: 1158 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG H 94 TYR 0.019 0.002 TYR E 643 PHE 0.029 0.002 PHE G 76 TRP 0.038 0.002 TRP A 479 HIS 0.005 0.001 HIS D 105 Details of bonding type rmsd covalent geometry : bond 0.00361 (19959) covalent geometry : angle 0.78444 (27072) SS BOND : bond 0.00614 ( 36) SS BOND : angle 1.38683 ( 72) hydrogen bonds : bond 0.04975 ( 768) hydrogen bonds : angle 6.43389 ( 2016) link_ALPHA1-3 : bond 0.00561 ( 3) link_ALPHA1-3 : angle 4.47010 ( 9) link_ALPHA1-6 : bond 0.01174 ( 3) link_ALPHA1-6 : angle 1.11825 ( 9) link_BETA1-4 : bond 0.00658 ( 33) link_BETA1-4 : angle 2.83092 ( 99) link_NAG-ASN : bond 0.00793 ( 39) link_NAG-ASN : angle 5.43953 ( 117) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4560 Ramachandran restraints generated. 2280 Oldfield, 0 Emsley, 2280 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4560 Ramachandran restraints generated. 2280 Oldfield, 0 Emsley, 2280 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 414 residues out of total 2046 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 411 time to evaluate : 0.932 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 27 ASP cc_start: 0.9346 (p0) cc_final: 0.9015 (p0) REVERT: H 28 ILE cc_start: 0.9446 (mm) cc_final: 0.9019 (mm) REVERT: H 46 GLU cc_start: 0.8379 (mm-30) cc_final: 0.8159 (mp0) REVERT: H 72 ASP cc_start: 0.7573 (t0) cc_final: 0.7009 (t0) REVERT: H 75 LEU cc_start: 0.8718 (mt) cc_final: 0.8407 (mp) REVERT: H 80 MET cc_start: 0.9028 (ttp) cc_final: 0.7467 (ttp) REVERT: H 81 ASP cc_start: 0.8142 (m-30) cc_final: 0.7882 (p0) REVERT: H 108 LEU cc_start: 0.8870 (tp) cc_final: 0.8643 (tp) REVERT: L 4 LEU cc_start: 0.8467 (tp) cc_final: 0.8111 (tp) REVERT: L 33 MET cc_start: 0.7792 (pmm) cc_final: 0.7405 (pmm) REVERT: L 47 LEU cc_start: 0.9035 (mm) cc_final: 0.8442 (pp) REVERT: L 86 TYR cc_start: 0.8620 (m-80) cc_final: 0.8164 (m-10) REVERT: L 97 PHE cc_start: 0.8281 (m-10) cc_final: 0.8055 (m-80) REVERT: A 104 MET cc_start: 0.9290 (tpp) cc_final: 0.9035 (tpp) REVERT: A 373 MET cc_start: 0.8844 (mtp) cc_final: 0.8283 (mtm) REVERT: B 584 GLU cc_start: 0.8753 (tm-30) cc_final: 0.8470 (tm-30) REVERT: B 588 ARG cc_start: 0.8819 (tpp80) cc_final: 0.8463 (tpp80) REVERT: B 626 MET cc_start: 0.7387 (tpp) cc_final: 0.6071 (tpp) REVERT: B 647 GLU cc_start: 0.8190 (OUTLIER) cc_final: 0.7913 (pm20) REVERT: G 4 LEU cc_start: 0.8326 (mt) cc_final: 0.7849 (mt) REVERT: G 6 GLN cc_start: 0.8401 (pm20) cc_final: 0.7964 (pm20) REVERT: G 27 ASP cc_start: 0.9327 (p0) cc_final: 0.9067 (p0) REVERT: G 34 LEU cc_start: 0.8735 (mt) cc_final: 0.8254 (mt) REVERT: G 36 TRP cc_start: 0.9322 (m100) cc_final: 0.8575 (m-10) REVERT: G 46 GLU cc_start: 0.8154 (mm-30) cc_final: 0.7769 (mp0) REVERT: G 72 ASP cc_start: 0.7882 (t0) cc_final: 0.7495 (t0) REVERT: G 81 ASP cc_start: 0.8086 (m-30) cc_final: 0.7732 (p0) REVERT: G 108 LEU cc_start: 0.9038 (tp) cc_final: 0.8822 (tp) REVERT: J 33 MET cc_start: 0.7901 (pmm) cc_final: 0.7604 (pmm) REVERT: J 86 TYR cc_start: 0.8641 (m-80) cc_final: 0.8319 (m-10) REVERT: C 69 TRP cc_start: 0.7983 (m-90) cc_final: 0.7572 (m-90) REVERT: C 95 MET cc_start: 0.8978 (ppp) cc_final: 0.8660 (ppp) REVERT: C 100 MET cc_start: 0.9339 (mtt) cc_final: 0.9075 (mtt) REVERT: C 373 MET cc_start: 0.8701 (mtp) cc_final: 0.8289 (mtp) REVERT: C 420 ILE cc_start: 0.9032 (mm) cc_final: 0.8828 (mm) REVERT: C 475 MET cc_start: 0.8124 (mmm) cc_final: 0.7703 (mmt) REVERT: E 530 MET cc_start: 0.7157 (ptm) cc_final: 0.6493 (ptp) REVERT: E 588 ARG cc_start: 0.8937 (tpp80) cc_final: 0.8492 (tpp80) REVERT: E 630 GLU cc_start: 0.8538 (pt0) cc_final: 0.7963 (pt0) REVERT: E 659 GLU cc_start: 0.9112 (tt0) cc_final: 0.8857 (tp30) REVERT: E 662 GLU cc_start: 0.8164 (pt0) cc_final: 0.6051 (pt0) REVERT: I 46 GLU cc_start: 0.8285 (mm-30) cc_final: 0.8013 (mp0) REVERT: I 72 ASP cc_start: 0.7364 (t0) cc_final: 0.7100 (t0) REVERT: I 81 ASP cc_start: 0.8079 (m-30) cc_final: 0.7672 (p0) REVERT: I 100 GLN cc_start: 0.5279 (mt0) cc_final: 0.4680 (mp10) REVERT: I 108 LEU cc_start: 0.8748 (tp) cc_final: 0.8449 (tp) REVERT: K 33 MET cc_start: 0.7324 (ptp) cc_final: 0.6695 (tmm) REVERT: K 47 LEU cc_start: 0.8849 (mm) cc_final: 0.8490 (pp) REVERT: D 104 MET cc_start: 0.8993 (mmt) cc_final: 0.8536 (mmt) REVERT: D 373 MET cc_start: 0.9004 (mtp) cc_final: 0.8658 (mtp) REVERT: D 457 ASP cc_start: 0.6089 (m-30) cc_final: 0.5820 (m-30) REVERT: D 475 MET cc_start: 0.8232 (mmt) cc_final: 0.7979 (mmt) REVERT: D 492 GLU cc_start: 0.8777 (tp30) cc_final: 0.7847 (tm-30) REVERT: F 530 MET cc_start: 0.7250 (ptt) cc_final: 0.6632 (ptt) REVERT: F 537 LEU cc_start: 0.8353 (mt) cc_final: 0.8121 (mt) REVERT: F 546 SER cc_start: 0.8289 (t) cc_final: 0.8004 (p) REVERT: F 588 ARG cc_start: 0.8844 (tpp80) cc_final: 0.8577 (tpp80) REVERT: F 628 TRP cc_start: 0.7622 (m100) cc_final: 0.7107 (m100) REVERT: F 647 GLU cc_start: 0.7986 (OUTLIER) cc_final: 0.7733 (pm20) outliers start: 3 outliers final: 1 residues processed: 412 average time/residue: 0.1525 time to fit residues: 95.5174 Evaluate side-chains 272 residues out of total 2046 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 269 time to evaluate : 0.698 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 7 optimal weight: 0.7980 chunk 169 optimal weight: 6.9990 chunk 150 optimal weight: 8.9990 chunk 34 optimal weight: 10.0000 chunk 219 optimal weight: 4.9990 chunk 98 optimal weight: 7.9990 chunk 194 optimal weight: 9.9990 chunk 205 optimal weight: 5.9990 chunk 100 optimal weight: 30.0000 chunk 210 optimal weight: 7.9990 chunk 171 optimal weight: 0.9980 overall best weight: 3.9586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 79 HIS A 302 ASN ** A 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 590 GLN ** G 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 79 HIS G 95 GLN ** J 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 590 GLN I 79 HIS ** D 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 590 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3416 r_free = 0.3416 target = 0.071399 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3042 r_free = 0.3042 target = 0.056011 restraints weight = 87340.494| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3092 r_free = 0.3092 target = 0.057921 restraints weight = 52398.804| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3127 r_free = 0.3127 target = 0.059267 restraints weight = 36961.663| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3149 r_free = 0.3149 target = 0.060157 restraints weight = 28876.950| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3165 r_free = 0.3165 target = 0.060804 restraints weight = 24327.776| |-----------------------------------------------------------------------------| r_work (final): 0.3160 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7836 moved from start: 0.5356 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.091 20073 Z= 0.293 Angle : 0.960 21.792 27378 Z= 0.466 Chirality : 0.053 0.405 3237 Planarity : 0.005 0.070 3336 Dihedral : 8.741 61.166 4098 Min Nonbonded Distance : 2.449 Molprobity Statistics. All-atom Clashscore : 18.80 Ramachandran Plot: Outliers : 0.53 % Allowed : 6.40 % Favored : 93.07 % Rotamer: Outliers : 0.24 % Allowed : 2.59 % Favored : 97.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.31 (0.17), residues: 2280 helix: 0.46 (0.24), residues: 429 sheet: 0.29 (0.20), residues: 615 loop : -0.66 (0.17), residues: 1236 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG A 315 TYR 0.023 0.003 TYR D 191 PHE 0.033 0.003 PHE A 391 TRP 0.041 0.003 TRP A 479 HIS 0.009 0.002 HIS G 79 Details of bonding type rmsd covalent geometry : bond 0.00638 (19959) covalent geometry : angle 0.87205 (27072) SS BOND : bond 0.00567 ( 36) SS BOND : angle 1.47028 ( 72) hydrogen bonds : bond 0.05418 ( 768) hydrogen bonds : angle 6.57385 ( 2016) link_ALPHA1-3 : bond 0.00242 ( 3) link_ALPHA1-3 : angle 4.79105 ( 9) link_ALPHA1-6 : bond 0.00819 ( 3) link_ALPHA1-6 : angle 1.37827 ( 9) link_BETA1-4 : bond 0.00344 ( 33) link_BETA1-4 : angle 2.85240 ( 99) link_NAG-ASN : bond 0.00861 ( 39) link_NAG-ASN : angle 5.44510 ( 117) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4560 Ramachandran restraints generated. 2280 Oldfield, 0 Emsley, 2280 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4560 Ramachandran restraints generated. 2280 Oldfield, 0 Emsley, 2280 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 343 residues out of total 2046 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 338 time to evaluate : 0.739 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 27 ASP cc_start: 0.9417 (p0) cc_final: 0.9187 (p0) REVERT: H 28 ILE cc_start: 0.9372 (mm) cc_final: 0.8476 (mm) REVERT: H 46 GLU cc_start: 0.8509 (mm-30) cc_final: 0.7917 (mm-30) REVERT: H 72 ASP cc_start: 0.7700 (t0) cc_final: 0.7238 (t0) REVERT: H 80 MET cc_start: 0.8661 (ttp) cc_final: 0.8332 (ttp) REVERT: H 100 TRP cc_start: 0.7933 (m-10) cc_final: 0.7437 (m-10) REVERT: H 108 LEU cc_start: 0.8914 (tp) cc_final: 0.8593 (tp) REVERT: L 33 MET cc_start: 0.7218 (pmm) cc_final: 0.6800 (pmm) REVERT: L 47 LEU cc_start: 0.9155 (mm) cc_final: 0.8614 (pp) REVERT: L 75 ILE cc_start: 0.9052 (mm) cc_final: 0.8834 (mp) REVERT: L 96 GLU cc_start: 0.8769 (pm20) cc_final: 0.8002 (pm20) REVERT: L 97 PHE cc_start: 0.8511 (m-10) cc_final: 0.7964 (m-80) REVERT: A 95 MET cc_start: 0.9179 (ppp) cc_final: 0.8970 (ppp) REVERT: A 104 MET cc_start: 0.9296 (tpp) cc_final: 0.8915 (tpp) REVERT: A 342 LEU cc_start: 0.9306 (mp) cc_final: 0.9082 (mm) REVERT: A 373 MET cc_start: 0.9028 (mtp) cc_final: 0.7840 (mmm) REVERT: B 530 MET cc_start: 0.8022 (ttm) cc_final: 0.7698 (ttm) REVERT: B 584 GLU cc_start: 0.8931 (tm-30) cc_final: 0.8460 (tm-30) REVERT: B 588 ARG cc_start: 0.8819 (ttm170) cc_final: 0.8209 (ttm170) REVERT: B 626 MET cc_start: 0.7238 (tpp) cc_final: 0.6211 (tpp) REVERT: G 4 LEU cc_start: 0.8556 (mt) cc_final: 0.8033 (mp) REVERT: G 13 LYS cc_start: 0.8743 (mmtt) cc_final: 0.8277 (mmmt) REVERT: G 28 ILE cc_start: 0.9439 (mm) cc_final: 0.9236 (mt) REVERT: G 34 LEU cc_start: 0.8716 (mt) cc_final: 0.8312 (mt) REVERT: G 36 TRP cc_start: 0.9267 (m100) cc_final: 0.8579 (m-10) REVERT: G 46 GLU cc_start: 0.8266 (mm-30) cc_final: 0.7872 (mm-30) REVERT: G 72 ASP cc_start: 0.7873 (t0) cc_final: 0.7413 (t0) REVERT: G 81 ASP cc_start: 0.8310 (m-30) cc_final: 0.7970 (p0) REVERT: G 97 PHE cc_start: 0.6874 (m-80) cc_final: 0.6536 (m-80) REVERT: J 33 MET cc_start: 0.7863 (pmm) cc_final: 0.7466 (pmm) REVERT: C 316 TRP cc_start: 0.8022 (m-90) cc_final: 0.7675 (m-90) REVERT: C 373 MET cc_start: 0.8979 (mtp) cc_final: 0.8051 (ttm) REVERT: C 475 MET cc_start: 0.8096 (mmm) cc_final: 0.7614 (mmt) REVERT: E 546 SER cc_start: 0.8691 (t) cc_final: 0.8299 (p) REVERT: E 628 TRP cc_start: 0.8342 (m100) cc_final: 0.8129 (m100) REVERT: E 630 GLU cc_start: 0.8693 (pt0) cc_final: 0.8390 (pt0) REVERT: E 659 GLU cc_start: 0.9351 (tt0) cc_final: 0.8935 (tt0) REVERT: I 13 LYS cc_start: 0.8887 (mmtt) cc_final: 0.8409 (mmmt) REVERT: I 26 GLU cc_start: 0.8956 (tm-30) cc_final: 0.8549 (tm-30) REVERT: I 28 ILE cc_start: 0.9246 (mm) cc_final: 0.9012 (mm) REVERT: I 46 GLU cc_start: 0.8448 (mm-30) cc_final: 0.7824 (mm-30) REVERT: I 72 ASP cc_start: 0.7528 (t0) cc_final: 0.7248 (t0) REVERT: I 100 GLN cc_start: 0.5934 (mt0) cc_final: 0.5277 (mm-40) REVERT: I 108 LEU cc_start: 0.8919 (tp) cc_final: 0.8560 (tp) REVERT: K 47 LEU cc_start: 0.9044 (mm) cc_final: 0.8598 (pp) REVERT: K 86 TYR cc_start: 0.8473 (m-10) cc_final: 0.8245 (m-10) REVERT: D 95 MET cc_start: 0.9172 (ppp) cc_final: 0.8912 (ppp) REVERT: D 373 MET cc_start: 0.9030 (mtp) cc_final: 0.7816 (mtt) REVERT: F 535 MET cc_start: 0.7972 (tpp) cc_final: 0.7696 (tpp) REVERT: F 546 SER cc_start: 0.8763 (t) cc_final: 0.8396 (p) REVERT: F 574 LYS cc_start: 0.9314 (mttt) cc_final: 0.8940 (ttmm) REVERT: F 628 TRP cc_start: 0.8206 (m100) cc_final: 0.7660 (m100) outliers start: 5 outliers final: 1 residues processed: 342 average time/residue: 0.1487 time to fit residues: 77.6082 Evaluate side-chains 252 residues out of total 2046 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 251 time to evaluate : 0.755 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 42 optimal weight: 10.0000 chunk 170 optimal weight: 7.9990 chunk 61 optimal weight: 0.7980 chunk 36 optimal weight: 6.9990 chunk 160 optimal weight: 3.9990 chunk 103 optimal weight: 0.8980 chunk 108 optimal weight: 5.9990 chunk 91 optimal weight: 3.9990 chunk 46 optimal weight: 5.9990 chunk 13 optimal weight: 9.9990 chunk 37 optimal weight: 0.6980 overall best weight: 2.0784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 66 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 591 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 425 ASN ** I 6 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 = 0.3438 r_free = 0.3438 target = 0.072432 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3067 r_free = 0.3067 target = 0.057177 restraints weight = 85471.235| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3117 r_free = 0.3117 target = 0.059073 restraints weight = 52253.395| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3152 r_free = 0.3152 target = 0.060414 restraints weight = 37077.202| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3175 r_free = 0.3175 target = 0.061349 restraints weight = 29038.029| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.3192 r_free = 0.3192 target = 0.061995 restraints weight = 24379.637| |-----------------------------------------------------------------------------| r_work (final): 0.3191 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7840 moved from start: 0.5689 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.068 20073 Z= 0.195 Angle : 0.849 20.879 27378 Z= 0.409 Chirality : 0.051 0.631 3237 Planarity : 0.005 0.053 3336 Dihedral : 8.372 56.573 4098 Min Nonbonded Distance : 2.484 Molprobity Statistics. All-atom Clashscore : 16.61 Ramachandran Plot: Outliers : 0.31 % Allowed : 6.05 % Favored : 93.64 % Rotamer: Outliers : 0.10 % Allowed : 2.15 % Favored : 97.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.27 (0.17), residues: 2280 helix: 0.70 (0.24), residues: 426 sheet: 0.31 (0.20), residues: 612 loop : -0.71 (0.18), residues: 1242 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG I 64 TYR 0.020 0.002 TYR F 638 PHE 0.031 0.002 PHE I 76 TRP 0.041 0.003 TRP A 479 HIS 0.007 0.001 HIS D 105 Details of bonding type rmsd covalent geometry : bond 0.00427 (19959) covalent geometry : angle 0.76146 (27072) SS BOND : bond 0.00459 ( 36) SS BOND : angle 1.63494 ( 72) hydrogen bonds : bond 0.04872 ( 768) hydrogen bonds : angle 6.35810 ( 2016) link_ALPHA1-3 : bond 0.00238 ( 3) link_ALPHA1-3 : angle 4.50841 ( 9) link_ALPHA1-6 : bond 0.01087 ( 3) link_ALPHA1-6 : angle 1.17939 ( 9) link_BETA1-4 : bond 0.00397 ( 33) link_BETA1-4 : angle 2.49063 ( 99) link_NAG-ASN : bond 0.00718 ( 39) link_NAG-ASN : angle 5.08803 ( 117) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4560 Ramachandran restraints generated. 2280 Oldfield, 0 Emsley, 2280 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4560 Ramachandran restraints generated. 2280 Oldfield, 0 Emsley, 2280 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 338 residues out of total 2046 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 336 time to evaluate : 0.708 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 31 ARG cc_start: 0.7990 (tpm170) cc_final: 0.7670 (tpm170) REVERT: H 46 GLU cc_start: 0.8277 (mm-30) cc_final: 0.7819 (mm-30) REVERT: H 72 ASP cc_start: 0.7755 (t0) cc_final: 0.7182 (t0) REVERT: H 75 LEU cc_start: 0.9112 (mt) cc_final: 0.8892 (mm) REVERT: H 100 TRP cc_start: 0.7972 (m-10) cc_final: 0.7616 (m-10) REVERT: L 33 MET cc_start: 0.7382 (pmm) cc_final: 0.6990 (pmm) REVERT: L 47 LEU cc_start: 0.8860 (mm) cc_final: 0.8539 (pp) REVERT: L 96 GLU cc_start: 0.8769 (pm20) cc_final: 0.7798 (pm20) REVERT: L 97 PHE cc_start: 0.8571 (m-10) cc_final: 0.7434 (m-10) REVERT: A 95 MET cc_start: 0.9138 (ppp) cc_final: 0.8896 (ppp) REVERT: A 195 ASN cc_start: 0.8534 (m110) cc_final: 0.8331 (m110) REVERT: A 308 HIS cc_start: 0.8742 (m90) cc_final: 0.7777 (m90) REVERT: A 373 MET cc_start: 0.8967 (mtp) cc_final: 0.7979 (mmm) REVERT: B 530 MET cc_start: 0.7758 (ttm) cc_final: 0.7083 (mtp) REVERT: B 584 GLU cc_start: 0.8771 (tm-30) cc_final: 0.8245 (tm-30) REVERT: B 588 ARG cc_start: 0.8716 (ttm170) cc_final: 0.8011 (ttm170) REVERT: B 628 TRP cc_start: 0.8579 (m100) cc_final: 0.7625 (m100) REVERT: G 28 ILE cc_start: 0.9395 (mm) cc_final: 0.8848 (mt) REVERT: G 34 LEU cc_start: 0.8795 (mt) cc_final: 0.8419 (mt) REVERT: G 36 TRP cc_start: 0.9117 (m100) cc_final: 0.8504 (m-10) REVERT: G 46 GLU cc_start: 0.8379 (mm-30) cc_final: 0.7704 (mm-30) REVERT: G 72 ASP cc_start: 0.7920 (t0) cc_final: 0.7464 (t0) REVERT: G 81 ASP cc_start: 0.8147 (m-30) cc_final: 0.7746 (p0) REVERT: G 108 LEU cc_start: 0.9138 (tp) cc_final: 0.8911 (tp) REVERT: J 33 MET cc_start: 0.7833 (pmm) cc_final: 0.7397 (pmm) REVERT: J 47 LEU cc_start: 0.9264 (mp) cc_final: 0.8545 (pp) REVERT: J 86 TYR cc_start: 0.8837 (m-10) cc_final: 0.8486 (m-10) REVERT: C 69 TRP cc_start: 0.7973 (m-90) cc_final: 0.7733 (m-90) REVERT: C 95 MET cc_start: 0.9169 (ppp) cc_final: 0.8925 (ppp) REVERT: C 104 MET cc_start: 0.9368 (mmt) cc_final: 0.8999 (mmt) REVERT: C 373 MET cc_start: 0.8909 (mtp) cc_final: 0.7683 (mmm) REVERT: C 434 MET cc_start: 0.8434 (mtm) cc_final: 0.8199 (mtm) REVERT: C 475 MET cc_start: 0.8039 (mmm) cc_final: 0.7721 (mmt) REVERT: C 479 TRP cc_start: 0.9122 (m100) cc_final: 0.8913 (m100) REVERT: E 630 GLU cc_start: 0.8882 (pt0) cc_final: 0.8610 (pt0) REVERT: E 647 GLU cc_start: 0.8309 (pp20) cc_final: 0.8097 (pp20) REVERT: E 655 LYS cc_start: 0.9040 (ptpp) cc_final: 0.8736 (mmtp) REVERT: E 659 GLU cc_start: 0.9198 (tt0) cc_final: 0.8642 (pt0) REVERT: I 31 ARG cc_start: 0.7671 (tpm170) cc_final: 0.6864 (tpm170) REVERT: I 46 GLU cc_start: 0.8331 (mm-30) cc_final: 0.7855 (mm-30) REVERT: I 72 ASP cc_start: 0.7795 (t0) cc_final: 0.7366 (t0) REVERT: I 81 ASP cc_start: 0.7317 (p0) cc_final: 0.7065 (p0) REVERT: I 108 LEU cc_start: 0.8895 (tp) cc_final: 0.8574 (tp) REVERT: D 69 TRP cc_start: 0.8188 (m-90) cc_final: 0.7256 (m-90) REVERT: D 95 MET cc_start: 0.9033 (ppp) cc_final: 0.8686 (ppp) REVERT: D 316 TRP cc_start: 0.7882 (m-90) cc_final: 0.7576 (m-90) REVERT: D 373 MET cc_start: 0.8987 (mtp) cc_final: 0.7720 (mmm) REVERT: D 475 MET cc_start: 0.8472 (mmm) cc_final: 0.7857 (mmt) REVERT: F 574 LYS cc_start: 0.9377 (mttt) cc_final: 0.8949 (ttmm) REVERT: F 628 TRP cc_start: 0.8380 (m100) cc_final: 0.6819 (m100) outliers start: 2 outliers final: 0 residues processed: 336 average time/residue: 0.1437 time to fit residues: 74.5292 Evaluate side-chains 249 residues out of total 2046 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 249 time to evaluate : 0.705 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 157 optimal weight: 7.9990 chunk 199 optimal weight: 5.9990 chunk 42 optimal weight: 9.9990 chunk 183 optimal weight: 0.8980 chunk 16 optimal weight: 0.8980 chunk 3 optimal weight: 0.8980 chunk 86 optimal weight: 0.9980 chunk 44 optimal weight: 6.9990 chunk 203 optimal weight: 8.9990 chunk 15 optimal weight: 3.9990 chunk 173 optimal weight: 5.9990 overall best weight: 1.5382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 66 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3444 r_free = 0.3444 target = 0.072694 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3072 r_free = 0.3072 target = 0.057443 restraints weight = 86389.692| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3121 r_free = 0.3121 target = 0.059332 restraints weight = 53222.456| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3155 r_free = 0.3155 target = 0.060657 restraints weight = 38008.665| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3178 r_free = 0.3178 target = 0.061565 restraints weight = 29924.773| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 51)----------------| | r_work = 0.3193 r_free = 0.3193 target = 0.062187 restraints weight = 25204.762| |-----------------------------------------------------------------------------| r_work (final): 0.3191 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7840 moved from start: 0.6016 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.066 20073 Z= 0.177 Angle : 0.836 20.565 27378 Z= 0.402 Chirality : 0.051 0.357 3237 Planarity : 0.005 0.168 3336 Dihedral : 8.154 54.245 4098 Min Nonbonded Distance : 2.451 Molprobity Statistics. All-atom Clashscore : 16.97 Ramachandran Plot: Outliers : 0.31 % Allowed : 6.14 % Favored : 93.55 % Rotamer: Outliers : 0.00 % Allowed : 1.52 % Favored : 98.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.23 (0.17), residues: 2280 helix: 0.79 (0.25), residues: 411 sheet: 0.24 (0.20), residues: 621 loop : -0.63 (0.18), residues: 1248 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG H 94 TYR 0.022 0.002 TYR F 638 PHE 0.024 0.002 PHE G 76 TRP 0.068 0.002 TRP B 596 HIS 0.007 0.001 HIS D 105 Details of bonding type rmsd covalent geometry : bond 0.00389 (19959) covalent geometry : angle 0.74791 (27072) SS BOND : bond 0.00496 ( 36) SS BOND : angle 1.65224 ( 72) hydrogen bonds : bond 0.04712 ( 768) hydrogen bonds : angle 6.29116 ( 2016) link_ALPHA1-3 : bond 0.00269 ( 3) link_ALPHA1-3 : angle 4.51744 ( 9) link_ALPHA1-6 : bond 0.01119 ( 3) link_ALPHA1-6 : angle 1.17327 ( 9) link_BETA1-4 : bond 0.00380 ( 33) link_BETA1-4 : angle 2.42871 ( 99) link_NAG-ASN : bond 0.00726 ( 39) link_NAG-ASN : angle 5.07608 ( 117) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4560 Ramachandran restraints generated. 2280 Oldfield, 0 Emsley, 2280 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4560 Ramachandran restraints generated. 2280 Oldfield, 0 Emsley, 2280 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 338 residues out of total 2046 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 338 time to evaluate : 0.706 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 46 GLU cc_start: 0.8297 (mm-30) cc_final: 0.7895 (mm-30) REVERT: H 72 ASP cc_start: 0.7917 (t0) cc_final: 0.7135 (t0) REVERT: H 75 LEU cc_start: 0.9027 (mt) cc_final: 0.8823 (mm) REVERT: H 81 ASP cc_start: 0.7725 (p0) cc_final: 0.7492 (p0) REVERT: H 100 TRP cc_start: 0.8026 (m-10) cc_final: 0.7667 (m-10) REVERT: L 4 LEU cc_start: 0.8638 (tp) cc_final: 0.8255 (tp) REVERT: L 33 MET cc_start: 0.7394 (pmm) cc_final: 0.6954 (pmm) REVERT: L 47 LEU cc_start: 0.8877 (mm) cc_final: 0.8512 (pp) REVERT: L 96 GLU cc_start: 0.8761 (pm20) cc_final: 0.7746 (pm20) REVERT: L 97 PHE cc_start: 0.8642 (m-80) cc_final: 0.7523 (m-10) REVERT: A 69 TRP cc_start: 0.7642 (m-90) cc_final: 0.6885 (m-90) REVERT: A 95 MET cc_start: 0.9142 (ppp) cc_final: 0.8851 (ppp) REVERT: A 104 MET cc_start: 0.8968 (tpp) cc_final: 0.8714 (tpp) REVERT: A 308 HIS cc_start: 0.8748 (m90) cc_final: 0.7773 (m90) REVERT: A 373 MET cc_start: 0.9051 (mtp) cc_final: 0.8693 (mtp) REVERT: A 475 MET cc_start: 0.8508 (mmm) cc_final: 0.8129 (mmt) REVERT: B 530 MET cc_start: 0.7528 (ttm) cc_final: 0.6688 (ttp) REVERT: B 584 GLU cc_start: 0.8815 (tm-30) cc_final: 0.8337 (tm-30) REVERT: B 588 ARG cc_start: 0.8717 (ttm170) cc_final: 0.7964 (ttm170) REVERT: B 626 MET cc_start: 0.7575 (tpp) cc_final: 0.7351 (tpp) REVERT: B 628 TRP cc_start: 0.8670 (m100) cc_final: 0.7636 (m100) REVERT: B 655 LYS cc_start: 0.9320 (mmmt) cc_final: 0.8908 (mmmm) REVERT: G 4 LEU cc_start: 0.8876 (mp) cc_final: 0.8454 (mp) REVERT: G 28 ILE cc_start: 0.9391 (mm) cc_final: 0.9144 (mm) REVERT: G 34 LEU cc_start: 0.8830 (mt) cc_final: 0.8432 (mt) REVERT: G 36 TRP cc_start: 0.9047 (m100) cc_final: 0.8291 (m-10) REVERT: G 46 GLU cc_start: 0.8331 (mm-30) cc_final: 0.7679 (mm-30) REVERT: G 72 ASP cc_start: 0.8031 (t0) cc_final: 0.7559 (t0) REVERT: G 81 ASP cc_start: 0.8060 (m-30) cc_final: 0.7729 (p0) REVERT: G 96 LYS cc_start: 0.7400 (mtmm) cc_final: 0.6731 (mttm) REVERT: G 108 LEU cc_start: 0.9120 (tp) cc_final: 0.8893 (tp) REVERT: J 33 MET cc_start: 0.7888 (pmm) cc_final: 0.7499 (pmm) REVERT: J 47 LEU cc_start: 0.9217 (mp) cc_final: 0.8566 (pp) REVERT: J 78 MET cc_start: 0.6625 (ptp) cc_final: 0.6333 (ptm) REVERT: J 86 TYR cc_start: 0.8790 (m-10) cc_final: 0.8433 (m-10) REVERT: C 95 MET cc_start: 0.9147 (ppp) cc_final: 0.8923 (ppp) REVERT: C 316 TRP cc_start: 0.8002 (m-90) cc_final: 0.7668 (m-90) REVERT: C 349 LEU cc_start: 0.9749 (mt) cc_final: 0.9537 (mp) REVERT: C 373 MET cc_start: 0.9014 (mtp) cc_final: 0.7889 (mmm) REVERT: C 475 MET cc_start: 0.7971 (mmm) cc_final: 0.7674 (mmt) REVERT: E 659 GLU cc_start: 0.9209 (tt0) cc_final: 0.8640 (pt0) REVERT: I 4 LEU cc_start: 0.8303 (mt) cc_final: 0.8006 (mt) REVERT: I 27 ASP cc_start: 0.9337 (p0) cc_final: 0.9099 (p0) REVERT: I 28 ILE cc_start: 0.9201 (mm) cc_final: 0.8968 (mm) REVERT: I 46 GLU cc_start: 0.8240 (mm-30) cc_final: 0.7826 (mm-30) REVERT: I 72 ASP cc_start: 0.7624 (t0) cc_final: 0.7205 (t0) REVERT: I 108 LEU cc_start: 0.8921 (tp) cc_final: 0.8584 (tp) REVERT: K 47 LEU cc_start: 0.8979 (mp) cc_final: 0.8431 (pp) REVERT: K 86 TYR cc_start: 0.8324 (m-10) cc_final: 0.7522 (m-10) REVERT: K 104 LEU cc_start: 0.8764 (mt) cc_final: 0.8523 (mt) REVERT: D 69 TRP cc_start: 0.8172 (m-90) cc_final: 0.7213 (m-90) REVERT: D 95 MET cc_start: 0.8987 (ppp) cc_final: 0.8664 (ppp) REVERT: D 308 HIS cc_start: 0.8682 (m90) cc_final: 0.7846 (m90) REVERT: D 373 MET cc_start: 0.9006 (mtp) cc_final: 0.7692 (mmm) REVERT: D 475 MET cc_start: 0.8360 (mmm) cc_final: 0.7703 (mmt) REVERT: F 530 MET cc_start: 0.7198 (ttp) cc_final: 0.6145 (ttp) REVERT: F 574 LYS cc_start: 0.9367 (mttt) cc_final: 0.9043 (ttmt) REVERT: F 575 GLN cc_start: 0.8805 (pp30) cc_final: 0.8547 (pp30) REVERT: F 583 VAL cc_start: 0.9639 (t) cc_final: 0.9433 (p) REVERT: F 596 TRP cc_start: 0.8545 (m-10) cc_final: 0.8237 (m-90) REVERT: F 628 TRP cc_start: 0.8401 (m100) cc_final: 0.7517 (m100) outliers start: 0 outliers final: 0 residues processed: 338 average time/residue: 0.1474 time to fit residues: 77.8568 Evaluate side-chains 256 residues out of total 2046 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 256 time to evaluate : 0.740 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 144 optimal weight: 0.7980 chunk 4 optimal weight: 0.5980 chunk 183 optimal weight: 0.6980 chunk 98 optimal weight: 6.9990 chunk 58 optimal weight: 10.0000 chunk 88 optimal weight: 10.0000 chunk 36 optimal weight: 10.0000 chunk 83 optimal weight: 0.9980 chunk 8 optimal weight: 3.9990 chunk 17 optimal weight: 6.9990 chunk 91 optimal weight: 0.9990 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 66 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 66 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 66 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 616 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3467 r_free = 0.3467 target = 0.073765 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3103 r_free = 0.3103 target = 0.058687 restraints weight = 86059.629| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3153 r_free = 0.3153 target = 0.060648 restraints weight = 51588.850| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3188 r_free = 0.3188 target = 0.062003 restraints weight = 36232.703| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.3212 r_free = 0.3212 target = 0.062948 restraints weight = 28204.428| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3226 r_free = 0.3226 target = 0.063561 restraints weight = 23526.093| |-----------------------------------------------------------------------------| r_work (final): 0.3222 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7778 moved from start: 0.6266 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.066 20073 Z= 0.152 Angle : 0.821 20.269 27378 Z= 0.394 Chirality : 0.051 0.396 3237 Planarity : 0.005 0.103 3336 Dihedral : 7.896 59.254 4098 Min Nonbonded Distance : 2.439 Molprobity Statistics. All-atom Clashscore : 14.80 Ramachandran Plot: Outliers : 0.31 % Allowed : 6.05 % Favored : 93.64 % Rotamer: Outliers : 0.00 % Allowed : 1.27 % Favored : 98.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.14 (0.18), residues: 2280 helix: 0.70 (0.25), residues: 408 sheet: 0.32 (0.20), residues: 612 loop : -0.52 (0.18), residues: 1260 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG D 66 TYR 0.031 0.001 TYR H 100E PHE 0.035 0.002 PHE H 97 TRP 0.044 0.002 TRP B 596 HIS 0.006 0.001 HIS D 105 Details of bonding type rmsd covalent geometry : bond 0.00329 (19959) covalent geometry : angle 0.73604 (27072) SS BOND : bond 0.00572 ( 36) SS BOND : angle 1.67662 ( 72) hydrogen bonds : bond 0.04415 ( 768) hydrogen bonds : angle 6.21988 ( 2016) link_ALPHA1-3 : bond 0.00319 ( 3) link_ALPHA1-3 : angle 4.45522 ( 9) link_ALPHA1-6 : bond 0.00943 ( 3) link_ALPHA1-6 : angle 1.15392 ( 9) link_BETA1-4 : bond 0.00430 ( 33) link_BETA1-4 : angle 2.30419 ( 99) link_NAG-ASN : bond 0.00747 ( 39) link_NAG-ASN : angle 4.94428 ( 117) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4560 Ramachandran restraints generated. 2280 Oldfield, 0 Emsley, 2280 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4560 Ramachandran restraints generated. 2280 Oldfield, 0 Emsley, 2280 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 361 residues out of total 2046 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 361 time to evaluate : 0.612 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 46 GLU cc_start: 0.8286 (mm-30) cc_final: 0.7784 (mm-30) REVERT: H 72 ASP cc_start: 0.7793 (t0) cc_final: 0.7216 (t0) REVERT: H 75 LEU cc_start: 0.9011 (mt) cc_final: 0.8633 (mp) REVERT: H 81 ASP cc_start: 0.7822 (p0) cc_final: 0.7543 (p0) REVERT: L 4 LEU cc_start: 0.8508 (tp) cc_final: 0.8186 (tp) REVERT: L 33 MET cc_start: 0.7673 (pmm) cc_final: 0.7404 (pmm) REVERT: L 47 LEU cc_start: 0.8850 (mm) cc_final: 0.8507 (pp) REVERT: L 96 GLU cc_start: 0.8666 (pm20) cc_final: 0.8025 (pm20) REVERT: L 97 PHE cc_start: 0.8581 (m-80) cc_final: 0.7518 (m-10) REVERT: A 69 TRP cc_start: 0.7668 (m-90) cc_final: 0.7118 (m-90) REVERT: A 95 MET cc_start: 0.9107 (ppp) cc_final: 0.8754 (ppp) REVERT: A 217 TYR cc_start: 0.6462 (m-80) cc_final: 0.5880 (m-10) REVERT: A 308 HIS cc_start: 0.8903 (m90) cc_final: 0.7858 (m90) REVERT: A 373 MET cc_start: 0.9056 (mtp) cc_final: 0.8710 (mtp) REVERT: B 530 MET cc_start: 0.7419 (ttm) cc_final: 0.7166 (ttp) REVERT: B 574 LYS cc_start: 0.9249 (mttt) cc_final: 0.8958 (ttmt) REVERT: B 584 GLU cc_start: 0.8961 (tm-30) cc_final: 0.8613 (tm-30) REVERT: B 626 MET cc_start: 0.7746 (tpp) cc_final: 0.7489 (tpp) REVERT: B 655 LYS cc_start: 0.9177 (mmmt) cc_final: 0.8471 (mmmm) REVERT: G 4 LEU cc_start: 0.8827 (mp) cc_final: 0.8186 (mp) REVERT: G 28 ILE cc_start: 0.9357 (mm) cc_final: 0.9078 (mm) REVERT: G 34 LEU cc_start: 0.8790 (mt) cc_final: 0.8369 (mt) REVERT: G 36 TRP cc_start: 0.9089 (m100) cc_final: 0.8208 (m-10) REVERT: G 46 GLU cc_start: 0.8385 (mm-30) cc_final: 0.7670 (mm-30) REVERT: G 72 ASP cc_start: 0.8051 (t0) cc_final: 0.7490 (t0) REVERT: G 75 LEU cc_start: 0.8960 (mm) cc_final: 0.8740 (mp) REVERT: G 81 ASP cc_start: 0.7969 (m-30) cc_final: 0.7581 (p0) REVERT: G 108 LEU cc_start: 0.9037 (tp) cc_final: 0.8795 (tp) REVERT: J 33 MET cc_start: 0.7765 (pmm) cc_final: 0.7428 (pmm) REVERT: J 47 LEU cc_start: 0.9271 (mp) cc_final: 0.8605 (pp) REVERT: J 78 MET cc_start: 0.6665 (ptp) cc_final: 0.5867 (ptp) REVERT: J 86 TYR cc_start: 0.8862 (m-10) cc_final: 0.8603 (m-10) REVERT: C 69 TRP cc_start: 0.7636 (m-90) cc_final: 0.7417 (m-90) REVERT: C 95 MET cc_start: 0.9149 (ppp) cc_final: 0.8932 (ppp) REVERT: C 373 MET cc_start: 0.9021 (mtp) cc_final: 0.7872 (mmm) REVERT: C 475 MET cc_start: 0.8119 (mmm) cc_final: 0.7778 (mmt) REVERT: E 596 TRP cc_start: 0.8480 (m-10) cc_final: 0.8131 (m-90) REVERT: E 655 LYS cc_start: 0.9216 (pttt) cc_final: 0.8729 (pttm) REVERT: E 659 GLU cc_start: 0.9223 (tt0) cc_final: 0.8600 (pt0) REVERT: I 4 LEU cc_start: 0.8053 (mt) cc_final: 0.7815 (mt) REVERT: I 28 ILE cc_start: 0.9294 (mm) cc_final: 0.9082 (mt) REVERT: I 46 GLU cc_start: 0.8247 (mm-30) cc_final: 0.7948 (mm-30) REVERT: I 60 SER cc_start: 0.9081 (t) cc_final: 0.8827 (p) REVERT: I 72 ASP cc_start: 0.7768 (t0) cc_final: 0.7132 (t0) REVERT: I 108 LEU cc_start: 0.8865 (tp) cc_final: 0.8516 (tp) REVERT: K 33 MET cc_start: 0.7698 (pmm) cc_final: 0.7465 (pmm) REVERT: D 95 MET cc_start: 0.9000 (ppp) cc_final: 0.8593 (ppp) REVERT: D 308 HIS cc_start: 0.8766 (m90) cc_final: 0.7878 (m90) REVERT: D 316 TRP cc_start: 0.8092 (m-90) cc_final: 0.7642 (m-90) REVERT: D 373 MET cc_start: 0.9018 (mtp) cc_final: 0.7707 (mmm) REVERT: D 475 MET cc_start: 0.8405 (mmm) cc_final: 0.7739 (mmt) REVERT: F 530 MET cc_start: 0.7123 (ttp) cc_final: 0.6010 (ttp) REVERT: F 574 LYS cc_start: 0.9320 (mttt) cc_final: 0.9016 (ttpp) REVERT: F 596 TRP cc_start: 0.8244 (m-10) cc_final: 0.7932 (m-90) REVERT: F 628 TRP cc_start: 0.8225 (m100) cc_final: 0.7392 (m100) outliers start: 0 outliers final: 0 residues processed: 361 average time/residue: 0.1480 time to fit residues: 82.6061 Evaluate side-chains 254 residues out of total 2046 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 254 time to evaluate : 0.706 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 162 optimal weight: 3.9990 chunk 175 optimal weight: 1.9990 chunk 69 optimal weight: 0.8980 chunk 225 optimal weight: 0.9980 chunk 37 optimal weight: 8.9990 chunk 46 optimal weight: 3.9990 chunk 49 optimal weight: 8.9990 chunk 73 optimal weight: 5.9990 chunk 86 optimal weight: 7.9990 chunk 51 optimal weight: 5.9990 chunk 160 optimal weight: 10.0000 overall best weight: 2.3786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 66 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 80 ASN ** B 658 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 66 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 66 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 70 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3424 r_free = 0.3424 target = 0.071697 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3052 r_free = 0.3052 target = 0.056540 restraints weight = 88433.675| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3103 r_free = 0.3103 target = 0.058440 restraints weight = 53661.289| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3137 r_free = 0.3137 target = 0.059750 restraints weight = 37906.638| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3160 r_free = 0.3160 target = 0.060650 restraints weight = 29644.230| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 40)----------------| | r_work = 0.3176 r_free = 0.3176 target = 0.061270 restraints weight = 24874.315| |-----------------------------------------------------------------------------| r_work (final): 0.3171 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7879 moved from start: 0.6566 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 20073 Z= 0.201 Angle : 0.838 20.408 27378 Z= 0.407 Chirality : 0.051 0.418 3237 Planarity : 0.006 0.177 3336 Dihedral : 7.781 55.851 4098 Min Nonbonded Distance : 2.260 Molprobity Statistics. All-atom Clashscore : 16.71 Ramachandran Plot: Outliers : 0.31 % Allowed : 6.89 % Favored : 92.81 % Rotamer: Outliers : 0.10 % Allowed : 0.78 % Favored : 99.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.30 (0.17), residues: 2280 helix: 0.55 (0.25), residues: 411 sheet: 0.22 (0.20), residues: 615 loop : -0.63 (0.18), residues: 1254 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG I 64 TYR 0.023 0.002 TYR H 100E PHE 0.020 0.003 PHE D 53 TRP 0.040 0.003 TRP B 596 HIS 0.006 0.001 HIS A 105 Details of bonding type rmsd covalent geometry : bond 0.00441 (19959) covalent geometry : angle 0.75597 (27072) SS BOND : bond 0.00478 ( 36) SS BOND : angle 1.50134 ( 72) hydrogen bonds : bond 0.04744 ( 768) hydrogen bonds : angle 6.21588 ( 2016) link_ALPHA1-3 : bond 0.00287 ( 3) link_ALPHA1-3 : angle 4.51775 ( 9) link_ALPHA1-6 : bond 0.00771 ( 3) link_ALPHA1-6 : angle 1.27693 ( 9) link_BETA1-4 : bond 0.00325 ( 33) link_BETA1-4 : angle 2.41774 ( 99) link_NAG-ASN : bond 0.00727 ( 39) link_NAG-ASN : angle 4.88739 ( 117) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4560 Ramachandran restraints generated. 2280 Oldfield, 0 Emsley, 2280 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4560 Ramachandran restraints generated. 2280 Oldfield, 0 Emsley, 2280 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 328 residues out of total 2046 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 326 time to evaluate : 0.553 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 46 GLU cc_start: 0.8406 (mm-30) cc_final: 0.7950 (mm-30) REVERT: H 60 SER cc_start: 0.9227 (t) cc_final: 0.8969 (p) REVERT: H 72 ASP cc_start: 0.7847 (t0) cc_final: 0.7363 (t0) REVERT: H 75 LEU cc_start: 0.9126 (mt) cc_final: 0.8690 (mp) REVERT: H 81 ASP cc_start: 0.7419 (p0) cc_final: 0.7142 (p0) REVERT: L 4 LEU cc_start: 0.8601 (tp) cc_final: 0.8317 (tp) REVERT: L 33 MET cc_start: 0.7531 (pmm) cc_final: 0.7164 (pmm) REVERT: L 47 LEU cc_start: 0.8944 (mm) cc_final: 0.8502 (pp) REVERT: L 86 TYR cc_start: 0.8329 (m-10) cc_final: 0.7890 (m-10) REVERT: L 96 GLU cc_start: 0.8653 (pm20) cc_final: 0.8045 (pm20) REVERT: L 97 PHE cc_start: 0.8603 (m-80) cc_final: 0.7735 (m-80) REVERT: A 69 TRP cc_start: 0.7560 (m-90) cc_final: 0.6715 (m-90) REVERT: A 95 MET cc_start: 0.9169 (ppp) cc_final: 0.8774 (ppp) REVERT: A 308 HIS cc_start: 0.8930 (m90) cc_final: 0.7907 (m90) REVERT: A 373 MET cc_start: 0.9035 (mtp) cc_final: 0.8260 (ttm) REVERT: B 530 MET cc_start: 0.7486 (ttm) cc_final: 0.6633 (ttp) REVERT: B 574 LYS cc_start: 0.9260 (mttt) cc_final: 0.8955 (ttmt) REVERT: B 584 GLU cc_start: 0.8973 (tm-30) cc_final: 0.8540 (tm-30) REVERT: B 588 ARG cc_start: 0.8744 (ttm170) cc_final: 0.7667 (ttm-80) REVERT: B 628 TRP cc_start: 0.8552 (m100) cc_final: 0.7225 (m100) REVERT: G 4 LEU cc_start: 0.8813 (mp) cc_final: 0.8338 (mp) REVERT: G 28 ILE cc_start: 0.9476 (mm) cc_final: 0.9161 (mm) REVERT: G 34 LEU cc_start: 0.8749 (mt) cc_final: 0.8483 (mt) REVERT: G 36 TRP cc_start: 0.9079 (m100) cc_final: 0.8386 (m-10) REVERT: G 46 GLU cc_start: 0.8307 (mm-30) cc_final: 0.7739 (mm-30) REVERT: G 60 SER cc_start: 0.9011 (t) cc_final: 0.8650 (p) REVERT: G 72 ASP cc_start: 0.8011 (t0) cc_final: 0.7296 (t0) REVERT: G 75 LEU cc_start: 0.9068 (mm) cc_final: 0.8660 (mp) REVERT: G 81 ASP cc_start: 0.8041 (m-30) cc_final: 0.7786 (p0) REVERT: G 108 LEU cc_start: 0.9097 (tp) cc_final: 0.8868 (tp) REVERT: J 33 MET cc_start: 0.7969 (pmm) cc_final: 0.7600 (pmm) REVERT: J 78 MET cc_start: 0.7385 (ptp) cc_final: 0.6334 (ptm) REVERT: J 86 TYR cc_start: 0.8857 (m-10) cc_final: 0.8399 (m-10) REVERT: C 95 MET cc_start: 0.9166 (ppp) cc_final: 0.8699 (ppp) REVERT: C 316 TRP cc_start: 0.8108 (m-90) cc_final: 0.7832 (m-90) REVERT: C 373 MET cc_start: 0.9086 (mtp) cc_final: 0.7913 (mmm) REVERT: C 475 MET cc_start: 0.8147 (mmm) cc_final: 0.7790 (mmt) REVERT: E 596 TRP cc_start: 0.8694 (m-10) cc_final: 0.8192 (m-90) REVERT: E 659 GLU cc_start: 0.9125 (tt0) cc_final: 0.8801 (tp30) REVERT: I 4 LEU cc_start: 0.8255 (mt) cc_final: 0.8015 (mt) REVERT: I 37 VAL cc_start: 0.9351 (t) cc_final: 0.9094 (p) REVERT: I 46 GLU cc_start: 0.8242 (mm-30) cc_final: 0.7850 (mm-30) REVERT: I 72 ASP cc_start: 0.8028 (t0) cc_final: 0.7513 (t0) REVERT: I 108 LEU cc_start: 0.8891 (tp) cc_final: 0.8556 (tp) REVERT: D 69 TRP cc_start: 0.7784 (m-90) cc_final: 0.7103 (m-90) REVERT: D 95 MET cc_start: 0.9157 (ppp) cc_final: 0.8647 (ppp) REVERT: D 308 HIS cc_start: 0.8858 (m90) cc_final: 0.8069 (m-70) REVERT: D 373 MET cc_start: 0.9033 (mtp) cc_final: 0.7705 (mmm) REVERT: D 475 MET cc_start: 0.8324 (mmm) cc_final: 0.7463 (mmt) REVERT: F 530 MET cc_start: 0.6973 (ttp) cc_final: 0.6169 (ttp) REVERT: F 574 LYS cc_start: 0.9280 (mttt) cc_final: 0.9009 (ptmm) REVERT: F 596 TRP cc_start: 0.8476 (m-10) cc_final: 0.8092 (m-90) REVERT: F 628 TRP cc_start: 0.8485 (m100) cc_final: 0.7426 (m100) REVERT: F 655 LYS cc_start: 0.9071 (pttp) cc_final: 0.8662 (pttm) outliers start: 2 outliers final: 0 residues processed: 328 average time/residue: 0.1385 time to fit residues: 70.5762 Evaluate side-chains 242 residues out of total 2046 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 242 time to evaluate : 0.578 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 0 optimal weight: 7.9990 chunk 51 optimal weight: 9.9990 chunk 214 optimal weight: 0.4980 chunk 152 optimal weight: 7.9990 chunk 204 optimal weight: 2.9990 chunk 1 optimal weight: 0.0770 chunk 197 optimal weight: 9.9990 chunk 46 optimal weight: 9.9990 chunk 100 optimal weight: 6.9990 chunk 188 optimal weight: 5.9990 chunk 177 optimal weight: 0.8980 overall best weight: 2.0942 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 66 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 70 GLN A 105 HIS ** J 66 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 70 GLN ** C 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 66 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 105 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3422 r_free = 0.3422 target = 0.071643 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3054 r_free = 0.3054 target = 0.056615 restraints weight = 87285.031| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3104 r_free = 0.3104 target = 0.058505 restraints weight = 52591.603| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3137 r_free = 0.3137 target = 0.059800 restraints weight = 37124.076| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 43)----------------| | r_work = 0.3160 r_free = 0.3160 target = 0.060698 restraints weight = 29059.917| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3175 r_free = 0.3175 target = 0.061289 restraints weight = 24393.017| |-----------------------------------------------------------------------------| r_work (final): 0.3171 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7864 moved from start: 0.6801 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.063 20073 Z= 0.184 Angle : 0.838 20.273 27378 Z= 0.407 Chirality : 0.052 0.541 3237 Planarity : 0.005 0.149 3336 Dihedral : 7.663 55.304 4098 Min Nonbonded Distance : 2.373 Molprobity Statistics. All-atom Clashscore : 16.79 Ramachandran Plot: Outliers : 0.31 % Allowed : 7.06 % Favored : 92.63 % Rotamer: Outliers : 0.10 % Allowed : 0.44 % Favored : 99.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.34 (0.17), residues: 2280 helix: 0.43 (0.25), residues: 414 sheet: 0.17 (0.20), residues: 582 loop : -0.58 (0.18), residues: 1284 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG D 315 TYR 0.017 0.002 TYR H 100E PHE 0.022 0.002 PHE G 76 TRP 0.036 0.003 TRP B 596 HIS 0.006 0.001 HIS C 105 Details of bonding type rmsd covalent geometry : bond 0.00404 (19959) covalent geometry : angle 0.75916 (27072) SS BOND : bond 0.00473 ( 36) SS BOND : angle 1.59783 ( 72) hydrogen bonds : bond 0.04596 ( 768) hydrogen bonds : angle 6.13549 ( 2016) link_ALPHA1-3 : bond 0.00275 ( 3) link_ALPHA1-3 : angle 4.37059 ( 9) link_ALPHA1-6 : bond 0.00796 ( 3) link_ALPHA1-6 : angle 1.25838 ( 9) link_BETA1-4 : bond 0.00361 ( 33) link_BETA1-4 : angle 2.35970 ( 99) link_NAG-ASN : bond 0.00713 ( 39) link_NAG-ASN : angle 4.81396 ( 117) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4560 Ramachandran restraints generated. 2280 Oldfield, 0 Emsley, 2280 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4560 Ramachandran restraints generated. 2280 Oldfield, 0 Emsley, 2280 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 321 residues out of total 2046 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 319 time to evaluate : 0.772 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 46 GLU cc_start: 0.8453 (mm-30) cc_final: 0.7928 (mm-30) REVERT: H 72 ASP cc_start: 0.7727 (t0) cc_final: 0.7238 (t0) REVERT: H 75 LEU cc_start: 0.9114 (mt) cc_final: 0.8734 (mp) REVERT: H 81 ASP cc_start: 0.7401 (p0) cc_final: 0.7094 (p0) REVERT: L 4 LEU cc_start: 0.8591 (tp) cc_final: 0.8257 (tp) REVERT: L 33 MET cc_start: 0.7546 (pmm) cc_final: 0.7217 (pmm) REVERT: L 47 LEU cc_start: 0.8993 (mm) cc_final: 0.8523 (pp) REVERT: L 86 TYR cc_start: 0.8572 (m-10) cc_final: 0.8306 (m-10) REVERT: L 96 GLU cc_start: 0.8662 (pm20) cc_final: 0.8082 (pm20) REVERT: L 97 PHE cc_start: 0.8602 (m-80) cc_final: 0.7580 (m-10) REVERT: A 69 TRP cc_start: 0.7633 (m-90) cc_final: 0.6769 (m-90) REVERT: A 95 MET cc_start: 0.9191 (ppp) cc_final: 0.8702 (ppp) REVERT: A 308 HIS cc_start: 0.8968 (m90) cc_final: 0.7908 (m90) REVERT: A 373 MET cc_start: 0.9069 (mtp) cc_final: 0.8269 (ttm) REVERT: A 475 MET cc_start: 0.8560 (mmm) cc_final: 0.8177 (mmt) REVERT: B 574 LYS cc_start: 0.9316 (mttt) cc_final: 0.9037 (ttmt) REVERT: B 584 GLU cc_start: 0.9024 (tm-30) cc_final: 0.8403 (tm-30) REVERT: B 588 ARG cc_start: 0.8747 (ttm170) cc_final: 0.7618 (ttm-80) REVERT: B 626 MET cc_start: 0.7823 (tpp) cc_final: 0.7467 (tpp) REVERT: B 651 ASN cc_start: 0.7621 (m-40) cc_final: 0.6729 (m-40) REVERT: G 28 ILE cc_start: 0.9379 (mm) cc_final: 0.8910 (mt) REVERT: G 36 TRP cc_start: 0.9077 (m100) cc_final: 0.8380 (m-10) REVERT: G 46 GLU cc_start: 0.8368 (mm-30) cc_final: 0.7721 (mm-30) REVERT: G 72 ASP cc_start: 0.8105 (t0) cc_final: 0.7518 (t0) REVERT: G 75 LEU cc_start: 0.8586 (mm) cc_final: 0.7655 (mm) REVERT: G 81 ASP cc_start: 0.8112 (m-30) cc_final: 0.7808 (p0) REVERT: G 108 LEU cc_start: 0.9055 (tp) cc_final: 0.8847 (tp) REVERT: J 30 TYR cc_start: 0.8128 (m-80) cc_final: 0.7269 (m-80) REVERT: J 33 MET cc_start: 0.8022 (pmm) cc_final: 0.7597 (pmm) REVERT: J 70 GLN cc_start: 0.8172 (OUTLIER) cc_final: 0.7938 (pp30) REVERT: J 78 MET cc_start: 0.7345 (ptp) cc_final: 0.6635 (ptm) REVERT: J 86 TYR cc_start: 0.8895 (m-10) cc_final: 0.8536 (m-10) REVERT: C 95 MET cc_start: 0.9201 (ppp) cc_final: 0.8673 (ppp) REVERT: C 316 TRP cc_start: 0.8201 (m-90) cc_final: 0.7918 (m-90) REVERT: C 373 MET cc_start: 0.9124 (mtp) cc_final: 0.7974 (mmm) REVERT: C 434 MET cc_start: 0.8516 (mtm) cc_final: 0.8301 (mtm) REVERT: C 475 MET cc_start: 0.8234 (mmm) cc_final: 0.7912 (mmt) REVERT: E 588 ARG cc_start: 0.8790 (ttm170) cc_final: 0.8436 (ttm170) REVERT: E 596 TRP cc_start: 0.8692 (m-10) cc_final: 0.8164 (m-90) REVERT: I 4 LEU cc_start: 0.8152 (mt) cc_final: 0.7860 (mt) REVERT: I 37 VAL cc_start: 0.9402 (t) cc_final: 0.9056 (p) REVERT: I 46 GLU cc_start: 0.8322 (mm-30) cc_final: 0.7848 (mm-30) REVERT: I 72 ASP cc_start: 0.7958 (t0) cc_final: 0.7633 (t0) REVERT: I 94 ARG cc_start: 0.7836 (ppt170) cc_final: 0.7270 (tmt170) REVERT: I 108 LEU cc_start: 0.8872 (tp) cc_final: 0.8539 (tp) REVERT: D 69 TRP cc_start: 0.7749 (m-90) cc_final: 0.6967 (m-90) REVERT: D 95 MET cc_start: 0.9219 (ppp) cc_final: 0.8749 (ppp) REVERT: D 217 TYR cc_start: 0.6890 (m-80) cc_final: 0.6668 (m-80) REVERT: D 308 HIS cc_start: 0.8895 (m90) cc_final: 0.7997 (m90) REVERT: D 316 TRP cc_start: 0.8155 (m-90) cc_final: 0.7707 (m-90) REVERT: D 373 MET cc_start: 0.9023 (mtp) cc_final: 0.7695 (mmm) REVERT: D 475 MET cc_start: 0.8378 (mmm) cc_final: 0.7449 (mmt) REVERT: F 574 LYS cc_start: 0.9251 (mttt) cc_final: 0.8970 (ttpt) REVERT: F 596 TRP cc_start: 0.8414 (m-10) cc_final: 0.8127 (m-90) REVERT: F 632 GLU cc_start: 0.9138 (pt0) cc_final: 0.8838 (pp20) outliers start: 2 outliers final: 0 residues processed: 321 average time/residue: 0.1379 time to fit residues: 68.7784 Evaluate side-chains 241 residues out of total 2046 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 240 time to evaluate : 0.830 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 111 optimal weight: 7.9990 chunk 86 optimal weight: 3.9990 chunk 225 optimal weight: 0.0470 chunk 84 optimal weight: 10.0000 chunk 133 optimal weight: 0.7980 chunk 176 optimal weight: 5.9990 chunk 216 optimal weight: 0.7980 chunk 165 optimal weight: 20.0000 chunk 213 optimal weight: 0.9990 chunk 12 optimal weight: 9.9990 chunk 163 optimal weight: 3.9990 overall best weight: 1.3282 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 66 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 70 GLN A 80 ASN ** B 658 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 66 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 66 GLN ** 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 = 0.3432 r_free = 0.3432 target = 0.072222 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3069 r_free = 0.3069 target = 0.057257 restraints weight = 87631.692| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3118 r_free = 0.3118 target = 0.059139 restraints weight = 52835.738| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3151 r_free = 0.3151 target = 0.060447 restraints weight = 37359.824| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3174 r_free = 0.3174 target = 0.061352 restraints weight = 29212.035| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3189 r_free = 0.3189 target = 0.061966 restraints weight = 24471.877| |-----------------------------------------------------------------------------| r_work (final): 0.3185 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7829 moved from start: 0.6936 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.066 20073 Z= 0.159 Angle : 0.820 20.144 27378 Z= 0.398 Chirality : 0.051 0.465 3237 Planarity : 0.005 0.145 3336 Dihedral : 7.524 55.078 4098 Min Nonbonded Distance : 2.255 Molprobity Statistics. All-atom Clashscore : 16.42 Ramachandran Plot: Outliers : 0.31 % Allowed : 6.62 % Favored : 93.07 % Rotamer: Outliers : 0.10 % Allowed : 0.29 % Favored : 99.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.29 (0.17), residues: 2280 helix: 0.62 (0.25), residues: 393 sheet: 0.23 (0.20), residues: 582 loop : -0.61 (0.18), residues: 1305 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG I 31 TYR 0.019 0.001 TYR H 100E PHE 0.025 0.002 PHE H 100F TRP 0.033 0.003 TRP A 427 HIS 0.005 0.001 HIS H 79 Details of bonding type rmsd covalent geometry : bond 0.00349 (19959) covalent geometry : angle 0.74133 (27072) SS BOND : bond 0.00452 ( 36) SS BOND : angle 1.63382 ( 72) hydrogen bonds : bond 0.04506 ( 768) hydrogen bonds : angle 6.11788 ( 2016) link_ALPHA1-3 : bond 0.00322 ( 3) link_ALPHA1-3 : angle 4.32398 ( 9) link_ALPHA1-6 : bond 0.00825 ( 3) link_ALPHA1-6 : angle 1.18918 ( 9) link_BETA1-4 : bond 0.00372 ( 33) link_BETA1-4 : angle 2.33259 ( 99) link_NAG-ASN : bond 0.00707 ( 39) link_NAG-ASN : angle 4.73580 ( 117) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4560 Ramachandran restraints generated. 2280 Oldfield, 0 Emsley, 2280 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4560 Ramachandran restraints generated. 2280 Oldfield, 0 Emsley, 2280 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 325 residues out of total 2046 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 323 time to evaluate : 0.523 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 46 GLU cc_start: 0.8449 (mm-30) cc_final: 0.7908 (mm-30) REVERT: H 72 ASP cc_start: 0.7672 (t0) cc_final: 0.7163 (t0) REVERT: H 75 LEU cc_start: 0.9134 (mt) cc_final: 0.8880 (mp) REVERT: H 81 ASP cc_start: 0.7391 (p0) cc_final: 0.7126 (p0) REVERT: L 4 LEU cc_start: 0.8631 (tp) cc_final: 0.8294 (tp) REVERT: L 33 MET cc_start: 0.7708 (pmm) cc_final: 0.7386 (pmm) REVERT: L 47 LEU cc_start: 0.8967 (mm) cc_final: 0.8579 (pp) REVERT: L 96 GLU cc_start: 0.8664 (pm20) cc_final: 0.8049 (pm20) REVERT: L 97 PHE cc_start: 0.8614 (m-80) cc_final: 0.7576 (m-10) REVERT: A 69 TRP cc_start: 0.7618 (m-90) cc_final: 0.6767 (m-90) REVERT: A 95 MET cc_start: 0.9158 (ppp) cc_final: 0.8710 (ppp) REVERT: A 308 HIS cc_start: 0.8983 (m90) cc_final: 0.7935 (m90) REVERT: A 373 MET cc_start: 0.9023 (mtp) cc_final: 0.8718 (mtm) REVERT: A 475 MET cc_start: 0.8214 (mmm) cc_final: 0.7961 (mmt) REVERT: A 478 ASN cc_start: 0.9242 (m-40) cc_final: 0.8994 (m-40) REVERT: B 574 LYS cc_start: 0.9296 (mttt) cc_final: 0.9036 (ttmt) REVERT: B 584 GLU cc_start: 0.9045 (tm-30) cc_final: 0.8251 (tm-30) REVERT: B 588 ARG cc_start: 0.8784 (ttm170) cc_final: 0.7643 (ttm-80) REVERT: B 626 MET cc_start: 0.7811 (tpp) cc_final: 0.7386 (tpp) REVERT: B 628 TRP cc_start: 0.8508 (m100) cc_final: 0.8147 (m100) REVERT: G 4 LEU cc_start: 0.8530 (mp) cc_final: 0.8074 (mp) REVERT: G 36 TRP cc_start: 0.9095 (m100) cc_final: 0.8293 (m-10) REVERT: G 46 GLU cc_start: 0.8364 (mm-30) cc_final: 0.7705 (mm-30) REVERT: G 72 ASP cc_start: 0.8102 (t0) cc_final: 0.7368 (t0) REVERT: G 75 LEU cc_start: 0.8668 (mm) cc_final: 0.7760 (mp) REVERT: G 81 ASP cc_start: 0.8135 (m-30) cc_final: 0.7840 (p0) REVERT: G 102 LEU cc_start: 0.7358 (mt) cc_final: 0.6929 (mt) REVERT: J 33 MET cc_start: 0.7804 (pmm) cc_final: 0.7448 (pmm) REVERT: J 78 MET cc_start: 0.7325 (ptp) cc_final: 0.6646 (ptm) REVERT: J 86 TYR cc_start: 0.8914 (m-10) cc_final: 0.8602 (m-10) REVERT: C 95 MET cc_start: 0.9201 (ppp) cc_final: 0.8752 (ppp) REVERT: C 316 TRP cc_start: 0.8190 (m-90) cc_final: 0.7928 (m-90) REVERT: C 373 MET cc_start: 0.8933 (mtp) cc_final: 0.7807 (mmm) REVERT: C 434 MET cc_start: 0.8572 (mtm) cc_final: 0.8255 (mtm) REVERT: C 475 MET cc_start: 0.8264 (mmm) cc_final: 0.6435 (mmt) REVERT: C 479 TRP cc_start: 0.8784 (m100) cc_final: 0.8422 (m-90) REVERT: E 584 GLU cc_start: 0.8950 (tm-30) cc_final: 0.8728 (tm-30) REVERT: E 596 TRP cc_start: 0.8588 (m-10) cc_final: 0.8147 (m-90) REVERT: E 626 MET cc_start: 0.7189 (tpt) cc_final: 0.6960 (tpp) REVERT: I 4 LEU cc_start: 0.8185 (mt) cc_final: 0.7429 (mt) REVERT: I 37 VAL cc_start: 0.9343 (t) cc_final: 0.8982 (p) REVERT: I 46 GLU cc_start: 0.8299 (mm-30) cc_final: 0.7801 (mm-30) REVERT: I 72 ASP cc_start: 0.7897 (t0) cc_final: 0.7533 (t0) REVERT: I 108 LEU cc_start: 0.8817 (tp) cc_final: 0.8496 (tp) REVERT: D 69 TRP cc_start: 0.7818 (m-90) cc_final: 0.6960 (m-90) REVERT: D 78 ASP cc_start: 0.8149 (p0) cc_final: 0.7903 (t70) REVERT: D 95 MET cc_start: 0.9239 (ppp) cc_final: 0.8750 (ppp) REVERT: D 217 TYR cc_start: 0.6952 (m-80) cc_final: 0.6698 (m-80) REVERT: D 308 HIS cc_start: 0.8942 (m90) cc_final: 0.8021 (m90) REVERT: D 316 TRP cc_start: 0.8111 (m-90) cc_final: 0.7861 (m-90) REVERT: D 373 MET cc_start: 0.9008 (mtp) cc_final: 0.7858 (mmm) REVERT: D 475 MET cc_start: 0.8384 (mmm) cc_final: 0.7433 (mmt) REVERT: F 530 MET cc_start: 0.6577 (ttm) cc_final: 0.6357 (ttt) REVERT: F 574 LYS cc_start: 0.9230 (mttt) cc_final: 0.8969 (ptmm) REVERT: F 628 TRP cc_start: 0.8492 (m100) cc_final: 0.7545 (m100) REVERT: F 632 GLU cc_start: 0.9195 (pt0) cc_final: 0.8834 (pp20) REVERT: F 655 LYS cc_start: 0.9187 (pttp) cc_final: 0.8585 (pttm) outliers start: 2 outliers final: 0 residues processed: 325 average time/residue: 0.1466 time to fit residues: 73.6651 Evaluate side-chains 233 residues out of total 2046 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 233 time to evaluate : 0.696 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 222 optimal weight: 7.9990 chunk 14 optimal weight: 3.9990 chunk 206 optimal weight: 3.9990 chunk 201 optimal weight: 4.9990 chunk 62 optimal weight: 2.9990 chunk 158 optimal weight: 3.9990 chunk 154 optimal weight: 0.9990 chunk 226 optimal weight: 0.6980 chunk 22 optimal weight: 0.8980 chunk 63 optimal weight: 0.8980 chunk 124 optimal weight: 10.0000 overall best weight: 1.2984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 66 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 70 GLN ** J 66 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 66 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 = 0.3441 r_free = 0.3441 target = 0.072502 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3085 r_free = 0.3085 target = 0.057664 restraints weight = 87111.735| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3133 r_free = 0.3133 target = 0.059543 restraints weight = 52772.037| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3167 r_free = 0.3167 target = 0.060856 restraints weight = 37243.570| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3189 r_free = 0.3189 target = 0.061755 restraints weight = 29119.073| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3203 r_free = 0.3203 target = 0.062330 restraints weight = 24452.914| |-----------------------------------------------------------------------------| r_work (final): 0.3197 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7856 moved from start: 0.7085 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.071 20073 Z= 0.156 Angle : 0.814 20.103 27378 Z= 0.396 Chirality : 0.050 0.404 3237 Planarity : 0.005 0.150 3336 Dihedral : 7.413 54.859 4098 Min Nonbonded Distance : 2.465 Molprobity Statistics. All-atom Clashscore : 16.14 Ramachandran Plot: Outliers : 0.31 % Allowed : 6.71 % Favored : 92.98 % Rotamer: Outliers : 0.05 % Allowed : 0.20 % Favored : 99.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.26 (0.17), residues: 2280 helix: 0.67 (0.26), residues: 393 sheet: 0.43 (0.21), residues: 528 loop : -0.66 (0.17), residues: 1359 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG I 64 TYR 0.016 0.001 TYR A 191 PHE 0.029 0.002 PHE I 76 TRP 0.034 0.002 TRP A 427 HIS 0.005 0.001 HIS H 79 Details of bonding type rmsd covalent geometry : bond 0.00340 (19959) covalent geometry : angle 0.73671 (27072) SS BOND : bond 0.00437 ( 36) SS BOND : angle 1.44771 ( 72) hydrogen bonds : bond 0.04417 ( 768) hydrogen bonds : angle 6.07156 ( 2016) link_ALPHA1-3 : bond 0.00332 ( 3) link_ALPHA1-3 : angle 4.23644 ( 9) link_ALPHA1-6 : bond 0.00854 ( 3) link_ALPHA1-6 : angle 1.25304 ( 9) link_BETA1-4 : bond 0.00391 ( 33) link_BETA1-4 : angle 2.30507 ( 99) link_NAG-ASN : bond 0.00702 ( 39) link_NAG-ASN : angle 4.69301 ( 117) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3192.14 seconds wall clock time: 56 minutes 15.01 seconds (3375.01 seconds total)