Starting phenix.real_space_refine on Fri Jul 3 13:37:21 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/8t5c_41048/07_2026/8t5c_41048.cif Found real_map, /net/cci-nas-00/data/ceres_data/8t5c_41048/07_2026/8t5c_41048.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8t5c_41048/07_2026/8t5c_41048.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8t5c_41048/07_2026/8t5c_41048.map" restraint_files = "/net/cci-nas-00/data/ceres_data/8t5c_41048/07_2026/8t5c_41048.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/8t5c_41048/07_2026/8t5c_41048.cif" model { file = "/net/cci-nas-00/data/ceres_data/8t5c_41048/07_2026/8t5c_41048.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8t5c_41048/07_2026/8t5c_41048.cif" } resolution = 4.7 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.005 sd= 0.066 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 104 5.16 5 C 8835 2.51 5 N 2277 2.21 5 O 2973 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 12 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 14189 Number of models: 1 Model: "" Number of chains: 35 Chain: "B" Number of atoms: 1581 Number of conformers: 1 Conformer: "" Number of residues, atoms: 202, 1581 Classifications: {'peptide': 202} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 4, 'TRANS': 197} Unresolved non-hydrogen bonds: 18 Unresolved non-hydrogen angles: 21 Unresolved non-hydrogen dihedrals: 15 Planarities with less than four sites: {'ARG:plan': 3} Unresolved non-hydrogen planarities: 15 Chain: "b" Number of atoms: 1282 Number of conformers: 1 Conformer: "" Number of residues, atoms: 159, 1282 Classifications: {'peptide': 159} Link IDs: {'PTRANS': 4, 'TRANS': 154} Chain: "A" Number of atoms: 1548 Number of conformers: 1 Conformer: "" Number of residues, atoms: 198, 1548 Classifications: {'peptide': 198} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 4, 'TRANS': 193} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 8 Planarities with less than four sites: {'TYR:plan': 1} Unresolved non-hydrogen planarities: 7 Chain: "a" Number of atoms: 1282 Number of conformers: 1 Conformer: "" Number of residues, atoms: 159, 1282 Classifications: {'peptide': 159} Link IDs: {'PTRANS': 4, 'TRANS': 154} Chain: "C" Number of atoms: 1599 Number of conformers: 1 Conformer: "" Number of residues, atoms: 202, 1599 Classifications: {'peptide': 202} Link IDs: {'PTRANS': 4, 'TRANS': 197} Chain: "c" Number of atoms: 1282 Number of conformers: 1 Conformer: "" Number of residues, atoms: 159, 1282 Classifications: {'peptide': 159} Link IDs: {'PTRANS': 4, 'TRANS': 154} Chain: "D" Number of atoms: 906 Number of conformers: 1 Conformer: "" Number of residues, atoms: 116, 906 Classifications: {'peptide': 116} Link IDs: {'PTRANS': 2, 'TRANS': 113} Chain: "H" Number of atoms: 928 Number of conformers: 1 Conformer: "" Number of residues, atoms: 119, 928 Classifications: {'peptide': 119} Link IDs: {'PTRANS': 5, 'TRANS': 113} Chain: "L" Number of atoms: 851 Number of conformers: 1 Conformer: "" Number of residues, atoms: 109, 851 Classifications: {'peptide': 109} Link IDs: {'PTRANS': 6, 'TRANS': 102} Chain: "E" Number of atoms: 928 Number of conformers: 1 Conformer: "" Number of residues, atoms: 119, 928 Classifications: {'peptide': 119} Link IDs: {'PTRANS': 5, 'TRANS': 113} Chain: "I" Number of atoms: 851 Number of conformers: 1 Conformer: "" Number of residues, atoms: 109, 851 Classifications: {'peptide': 109} Link IDs: {'PTRANS': 6, 'TRANS': 102} Chain: "F" Number of atoms: 94 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 94 Unusual residues: {'BMA': 1, 'MAN': 5, 'NAG': 2} Classifications: {'undetermined': 8} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 8 Chain: "G" 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: "J" Number of atoms: 25 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 25 Unusual residues: {'BMA': 1, 'NAG': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "K" Number of atoms: 25 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 25 Unusual residues: {'BMA': 1, 'NAG': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "M" Number of atoms: 72 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 72 Unusual residues: {'BMA': 1, 'MAN': 3, 'NAG': 2} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 6 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: 9 Unresolved non-hydrogen chiralities: 5 Chain: "O" 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: 9 Unresolved non-hydrogen chiralities: 5 Chain: "P" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 33 Unusual residues: {'MAN': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen chiralities: 3 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: 72 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 72 Unusual residues: {'BMA': 1, 'MAN': 3, 'NAG': 2} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 6 Chain: "S" 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: 9 Unresolved non-hydrogen chiralities: 5 Chain: "T" Number of atoms: 72 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 72 Unusual residues: {'BMA': 1, 'MAN': 3, 'NAG': 2} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 6 Chain: "U" 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: "V" Number of atoms: 25 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 25 Unusual residues: {'BMA': 1, 'NAG': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "W" Number of atoms: 72 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 72 Unusual residues: {'BMA': 1, 'MAN': 3, 'NAG': 2} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 6 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: "B" 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: 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: "a" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "C" Number of atoms: 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: "c" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "L" 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: "I" 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: 3.33, per 1000 atoms: 0.23 Number of scatterers: 14189 At special positions: 0 Unit cell: (109.752, 125.892, 139.88, 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 104 16.00 O 2973 8.00 N 2277 7.00 C 8835 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=26, symmetry=0 Simple disulfide: pdb=" SG CYS B 86 " - pdb=" SG CYS B 231 " distance=2.03 Simple disulfide: pdb=" SG CYS B 118 " - pdb=" SG CYS B 155 " distance=2.03 Simple disulfide: pdb=" SG CYS B 180 " - pdb=" SG CYS B 212 " distance=2.04 Simple disulfide: pdb=" SG CYS B 207 " - pdb=" SG CYS a 326 " distance=2.03 Simple disulfide: pdb=" SG CYS b 279 " - pdb=" SG CYS b 292 " distance=2.03 Simple disulfide: pdb=" SG CYS b 301 " - pdb=" SG CYS b 310 " distance=2.03 Simple disulfide: pdb=" SG CYS b 326 " - pdb=" SG CYS C 207 " distance=2.03 Simple disulfide: pdb=" SG CYS b 364 " - pdb=" SG CYS b 385 " distance=2.03 Simple disulfide: pdb=" SG CYS A 86 " - pdb=" SG CYS A 231 " distance=2.02 Simple disulfide: pdb=" SG CYS A 118 " - pdb=" SG CYS A 155 " distance=2.03 Simple disulfide: pdb=" SG CYS A 180 " - pdb=" SG CYS A 212 " distance=2.03 Simple disulfide: pdb=" SG CYS A 207 " - pdb=" SG CYS c 326 " distance=2.03 Simple disulfide: pdb=" SG CYS a 279 " - pdb=" SG CYS a 292 " distance=2.04 Simple disulfide: pdb=" SG CYS a 301 " - pdb=" SG CYS a 310 " distance=2.03 Simple disulfide: pdb=" SG CYS a 364 " - pdb=" SG CYS a 385 " distance=2.03 Simple disulfide: pdb=" SG CYS C 86 " - pdb=" SG CYS C 231 " distance=2.03 Simple disulfide: pdb=" SG CYS C 118 " - pdb=" SG CYS C 155 " distance=2.03 Simple disulfide: pdb=" SG CYS C 180 " - pdb=" SG CYS C 212 " distance=2.02 Simple disulfide: pdb=" SG CYS c 279 " - pdb=" SG CYS c 292 " distance=2.03 Simple disulfide: pdb=" SG CYS c 301 " - pdb=" SG CYS c 310 " distance=2.03 Simple disulfide: pdb=" SG CYS c 364 " - pdb=" SG CYS c 385 " distance=2.03 Simple disulfide: pdb=" SG CYS D 22 " - pdb=" SG CYS D 96 " distance=2.03 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 92 " distance=2.03 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 88 " distance=2.03 Simple disulfide: pdb=" SG CYS E 22 " - pdb=" SG CYS E 92 " distance=2.03 Simple disulfide: pdb=" SG CYS I 23 " - pdb=" SG CYS I 88 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied ALPHA1-2 " MAN F 4 " - " MAN F 5 " " MAN O 4 " - " MAN O 5 " ALPHA1-3 " BMA F 3 " - " MAN F 4 " " MAN F 6 " - " MAN F 7 " " BMA M 3 " - " MAN M 6 " " MAN M 4 " - " MAN M 5 " " BMA N 3 " - " MAN N 4 " " BMA O 3 " - " MAN O 4 " " MAN P 1 " - " MAN P 2 " " BMA R 3 " - " MAN R 6 " " MAN R 4 " - " MAN R 5 " " BMA S 3 " - " MAN S 4 " " BMA T 3 " - " MAN T 6 " " BMA W 3 " - " MAN W 6 " " MAN W 4 " - " MAN W 5 " ALPHA1-6 " BMA F 3 " - " MAN F 6 " " MAN F 6 " - " MAN F 8 " " BMA M 3 " - " MAN M 4 " " BMA N 3 " - " MAN N 5 " " MAN P 1 " - " MAN P 3 " " BMA R 3 " - " MAN R 4 " " BMA S 3 " - " MAN S 5 " " BMA T 3 " - " MAN T 4 " " MAN T 4 " - " MAN T 5 " " BMA W 3 " - " MAN W 4 " BETA1-4 " NAG F 1 " - " NAG F 2 " " NAG F 2 " - " BMA F 3 " " NAG G 1 " - " NAG G 2 " " NAG G 2 " - " BMA G 3 " " NAG J 1 " - " BMA J 2 " " NAG K 1 " - " BMA K 2 " " 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 Q 1 " - " NAG Q 2 " " NAG Q 2 " - " BMA Q 3 " " NAG R 1 " - " NAG R 2 " " NAG R 2 " - " BMA R 3 " " NAG S 1 " - " NAG S 2 " " NAG S 2 " - " BMA S 3 " " NAG T 1 " - " NAG T 2 " " NAG T 2 " - " BMA T 3 " " NAG U 1 " - " NAG U 2 " " NAG U 2 " - " BMA U 3 " " NAG V 1 " - " BMA V 2 " " NAG W 1 " - " NAG W 2 " " NAG W 2 " - " BMA W 3 " " NAG X 1 " - " NAG X 2 " " NAG X 2 " - " BMA X 3 " NAG-ASN " NAG A 301 " - " ASN A 99 " " NAG A 302 " - " ASN A 167 " " NAG A 303 " - " ASN A 224 " " NAG A 304 " - " ASN A 90 " " NAG A 305 " - " ASN A 109 " " NAG B 301 " - " ASN B 99 " " NAG B 302 " - " ASN B 224 " " NAG B 303 " - " ASN B 90 " " NAG B 304 " - " ASN B 109 " " NAG B 305 " - " ASN B 167 " " NAG C 301 " - " ASN C 99 " " NAG C 302 " - " ASN C 224 " " NAG C 303 " - " ASN C 90 " " NAG C 304 " - " ASN C 109 " " NAG C 305 " - " ASN C 167 " " NAG F 1 " - " ASN B 79 " " NAG G 1 " - " ASN B 119 " " NAG I 201 " - " ASN I 72 " " NAG L 201 " - " ASN L 72 " " NAG M 1 " - " ASN b 365 " " NAG N 1 " - " ASN b 373 " " NAG O 1 " - " ASN A 79 " " NAG Q 1 " - " ASN A 119 " " NAG R 1 " - " ASN a 365 " " NAG S 1 " - " ASN a 373 " " NAG T 1 " - " ASN C 79 " " NAG U 1 " - " ASN C 119 " " NAG W 1 " - " ASN c 365 " " NAG X 1 " - " ASN c 373 " " NAG a 501 " - " ASN a 390 " " NAG a 502 " - " ASN a 395 " " NAG b 501 " - " ASN b 390 " " NAG b 502 " - " ASN b 395 " " NAG c 501 " - " ASN c 390 " " NAG c 502 " - " ASN c 395 " Time building additional restraints: 1.63 Conformation dependent library (CDL) restraints added in 703.5 milliseconds 3258 Ramachandran restraints generated. 1629 Oldfield, 0 Emsley, 1629 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3058 Finding SS restraints... Secondary structure from input PDB file: 37 helices and 23 sheets defined 22.2% alpha, 15.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.30 Creating SS restraints... Processing helix chain 'B' and resid 120 through 127 Processing helix chain 'B' and resid 131 through 143 removed outlier: 4.077A pdb=" N SER B 135 " --> pdb=" O HIS B 131 " (cutoff:3.500A) removed outlier: 4.220A pdb=" N ILE B 136 " --> pdb=" O ALA B 132 " (cutoff:3.500A) Processing helix chain 'B' and resid 185 through 195 removed outlier: 3.531A pdb=" N ARG B 193 " --> pdb=" O GLN B 189 " (cutoff:3.500A) Processing helix chain 'B' and resid 238 through 249 removed outlier: 3.820A pdb=" N LEU B 244 " --> pdb=" O GLY B 240 " (cutoff:3.500A) Processing helix chain 'b' and resid 294 through 303 removed outlier: 3.926A pdb=" N LYS b 300 " --> pdb=" O THR b 296 " (cutoff:3.500A) removed outlier: 4.669A pdb=" N CYS b 301 " --> pdb=" O ALA b 297 " (cutoff:3.500A) Processing helix chain 'b' and resid 307 through 324 removed outlier: 3.713A pdb=" N ASP b 311 " --> pdb=" O GLU b 307 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N ASN b 319 " --> pdb=" O LEU b 315 " (cutoff:3.500A) Processing helix chain 'b' and resid 334 through 340 removed outlier: 4.257A pdb=" N ASN b 338 " --> pdb=" O ILE b 334 " (cutoff:3.500A) removed outlier: 4.275A pdb=" N LYS b 339 " --> pdb=" O GLN b 335 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N ALA b 340 " --> pdb=" O LEU b 336 " (cutoff:3.500A) No H-bonds generated for 'chain 'b' and resid 334 through 340' Processing helix chain 'b' and resid 340 through 345 removed outlier: 3.979A pdb=" N ILE b 345 " --> pdb=" O VAL b 341 " (cutoff:3.500A) Processing helix chain 'b' and resid 346 through 360 removed outlier: 3.610A pdb=" N MET b 351 " --> pdb=" O ASP b 347 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N ILE b 358 " --> pdb=" O HIS b 354 " (cutoff:3.500A) Processing helix chain 'b' and resid 399 through 418 removed outlier: 3.584A pdb=" N ILE b 411 " --> pdb=" O ALA b 407 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N GLN b 416 " --> pdb=" O THR b 412 " (cutoff:3.500A) Processing helix chain 'A' and resid 119 through 126 removed outlier: 3.738A pdb=" N HIS A 124 " --> pdb=" O LEU A 120 " (cutoff:3.500A) Processing helix chain 'A' and resid 136 through 143 removed outlier: 3.748A pdb=" N HIS A 141 " --> pdb=" O ILE A 137 " (cutoff:3.500A) Processing helix chain 'A' and resid 184 through 195 removed outlier: 3.787A pdb=" N LEU A 188 " --> pdb=" O ALA A 184 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N MET A 194 " --> pdb=" O THR A 190 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N ALA A 195 " --> pdb=" O PHE A 191 " (cutoff:3.500A) Processing helix chain 'A' and resid 238 through 247 removed outlier: 3.550A pdb=" N LEU A 244 " --> pdb=" O GLY A 240 " (cutoff:3.500A) Processing helix chain 'a' and resid 281 through 285 Processing helix chain 'a' and resid 294 through 305 removed outlier: 3.698A pdb=" N VAL a 298 " --> pdb=" O GLY a 294 " (cutoff:3.500A) removed outlier: 5.270A pdb=" N CYS a 301 " --> pdb=" O ALA a 297 " (cutoff:3.500A) removed outlier: 5.163A pdb=" N ASN a 302 " --> pdb=" O VAL a 298 " (cutoff:3.500A) removed outlier: 4.353A pdb=" N GLU a 303 " --> pdb=" O ALA a 299 " (cutoff:3.500A) Processing helix chain 'a' and resid 307 through 325 removed outlier: 3.984A pdb=" N ARG a 325 " --> pdb=" O GLN a 321 " (cutoff:3.500A) Processing helix chain 'a' and resid 335 through 339 removed outlier: 3.889A pdb=" N LYS a 339 " --> pdb=" O LEU a 336 " (cutoff:3.500A) Processing helix chain 'a' and resid 340 through 345 Processing helix chain 'a' and resid 346 through 354 removed outlier: 3.526A pdb=" N ILE a 350 " --> pdb=" O ASN a 346 " (cutoff:3.500A) Processing helix chain 'a' and resid 399 through 418 removed outlier: 3.569A pdb=" N ILE a 403 " --> pdb=" O PHE a 399 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N ILE a 411 " --> pdb=" O ALA a 407 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N GLN a 416 " --> pdb=" O THR a 412 " (cutoff:3.500A) Processing helix chain 'C' and resid 120 through 124 Processing helix chain 'C' and resid 131 through 133 No H-bonds generated for 'chain 'C' and resid 131 through 133' Processing helix chain 'C' and resid 134 through 143 Processing helix chain 'C' and resid 171 through 175 removed outlier: 3.579A pdb=" N GLY C 174 " --> pdb=" O SER C 171 " (cutoff:3.500A) Processing helix chain 'C' and resid 186 through 195 removed outlier: 3.625A pdb=" N MET C 192 " --> pdb=" O LEU C 188 " (cutoff:3.500A) removed outlier: 3.912A pdb=" N ARG C 193 " --> pdb=" O GLN C 189 " (cutoff:3.500A) Processing helix chain 'C' and resid 238 through 247 removed outlier: 3.710A pdb=" N LEU C 244 " --> pdb=" O GLY C 240 " (cutoff:3.500A) Processing helix chain 'c' and resid 281 through 285 removed outlier: 3.533A pdb=" N MET c 284 " --> pdb=" O THR c 281 " (cutoff:3.500A) Processing helix chain 'c' and resid 299 through 303 Processing helix chain 'c' and resid 307 through 323 Processing helix chain 'c' and resid 333 through 339 removed outlier: 3.870A pdb=" N ILE c 337 " --> pdb=" O SER c 333 " (cutoff:3.500A) removed outlier: 3.866A pdb=" N LYS c 339 " --> pdb=" O GLN c 335 " (cutoff:3.500A) Processing helix chain 'c' and resid 340 through 345 removed outlier: 3.597A pdb=" N LEU c 344 " --> pdb=" O ALA c 340 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N ILE c 345 " --> pdb=" O VAL c 341 " (cutoff:3.500A) No H-bonds generated for 'chain 'c' and resid 340 through 345' Processing helix chain 'c' and resid 346 through 359 removed outlier: 3.516A pdb=" N ILE c 350 " --> pdb=" O ASN c 346 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N HIS c 354 " --> pdb=" O ILE c 350 " (cutoff:3.500A) removed outlier: 4.211A pdb=" N MET c 359 " --> pdb=" O LEU c 355 " (cutoff:3.500A) Processing helix chain 'c' and resid 399 through 418 Processing helix chain 'D' and resid 87 through 91 Processing helix chain 'H' and resid 83 through 87 Processing helix chain 'E' and resid 83 through 87 removed outlier: 3.514A pdb=" N THR E 87 " --> pdb=" O ALA E 84 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'b' and resid 285 through 286 removed outlier: 4.423A pdb=" N GLU B 72 " --> pdb=" O ILE b 286 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N TRP b 370 " --> pdb=" O LYS b 384 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 84 through 87 Processing sheet with id=AA3, first strand: chain 'B' and resid 106 through 108 Processing sheet with id=AA4, first strand: chain 'b' and resid 279 through 280 removed outlier: 3.920A pdb=" N LEU b 280 " --> pdb=" O LYS b 291 " (cutoff:3.500A) removed outlier: 4.057A pdb=" N LYS b 291 " --> pdb=" O LEU b 280 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'A' and resid 61 through 62 removed outlier: 3.791A pdb=" N TYR A 62 " --> pdb=" O TYR A 66 " (cutoff:3.500A) removed outlier: 3.876A pdb=" N TYR A 66 " --> pdb=" O TYR A 62 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 84 through 85 Processing sheet with id=AA7, first strand: chain 'A' and resid 154 through 155 Processing sheet with id=AA8, first strand: chain 'C' and resid 61 through 62 Processing sheet with id=AA9, first strand: chain 'C' and resid 84 through 86 removed outlier: 3.633A pdb=" N VAL C 97 " --> pdb=" O THR C 101 " (cutoff:3.500A) removed outlier: 4.027A pdb=" N THR C 101 " --> pdb=" O VAL C 97 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 106 through 108 removed outlier: 3.612A pdb=" N LEU C 220 " --> pdb=" O TYR C 166 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'c' and resid 279 through 280 removed outlier: 3.625A pdb=" N LYS c 291 " --> pdb=" O LEU c 280 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'D' and resid 6 through 7 removed outlier: 3.526A pdb=" N LEU D 18 " --> pdb=" O MET D 83 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N GLN D 82 " --> pdb=" O THR D 69 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'D' and resid 11 through 12 removed outlier: 3.837A pdb=" N THR D 109 " --> pdb=" O TYR D 94 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N VAL D 111 " --> pdb=" O ALA D 92 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N ALA D 92 " --> pdb=" O VAL D 111 " (cutoff:3.500A) removed outlier: 6.172A pdb=" N ARG D 38 " --> pdb=" O PHE D 47 " (cutoff:3.500A) removed outlier: 5.923A pdb=" N PHE D 47 " --> pdb=" O ARG D 38 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'H' and resid 3 through 7 removed outlier: 4.255A pdb=" N GLN H 3 " --> pdb=" O SER H 25 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N SER H 7 " --> pdb=" O THR H 21 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N THR H 21 " --> pdb=" O SER H 7 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N PHE H 78 " --> pdb=" O CYS H 22 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N GLN H 77 " --> pdb=" O ASP H 72 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'H' and resid 46 through 52 removed outlier: 6.209A pdb=" N TRP H 47 " --> pdb=" O ARG H 38 " (cutoff:3.500A) removed outlier: 7.437A pdb=" N ARG H 38 " --> pdb=" O TRP H 47 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N GLY H 49 " --> pdb=" O TRP H 36 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N SER H 94 " --> pdb=" O TYR H 102 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'H' and resid 46 through 52 removed outlier: 6.209A pdb=" N TRP H 47 " --> pdb=" O ARG H 38 " (cutoff:3.500A) removed outlier: 7.437A pdb=" N ARG H 38 " --> pdb=" O TRP H 47 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N GLY H 49 " --> pdb=" O TRP H 36 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N THR H 107 " --> pdb=" O TYR H 90 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'L' and resid 4 through 5 removed outlier: 4.047A pdb=" N THR L 5 " --> pdb=" O ARG L 24 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'L' and resid 53 through 54 removed outlier: 3.587A pdb=" N THR L 53 " --> pdb=" O TYR L 49 " (cutoff:3.500A) removed outlier: 5.165A pdb=" N LEU L 46 " --> pdb=" O GLN L 37 " (cutoff:3.500A) removed outlier: 5.579A pdb=" N GLN L 37 " --> pdb=" O LEU L 46 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N ILE L 48 " --> pdb=" O TRP L 35 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'E' and resid 3 through 7 removed outlier: 4.275A pdb=" N GLN E 3 " --> pdb=" O SER E 25 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N SER E 25 " --> pdb=" O GLN E 3 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'E' and resid 11 through 12 removed outlier: 7.820A pdb=" N VAL E 12 " --> pdb=" O PRO E 108 " (cutoff:3.500A) removed outlier: 5.721A pdb=" N THR E 110 " --> pdb=" O VAL E 12 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N THR E 107 " --> pdb=" O TYR E 90 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'E' and resid 45 through 47 removed outlier: 3.850A pdb=" N GLU E 46 " --> pdb=" O ARG E 38 " (cutoff:3.500A) removed outlier: 3.894A pdb=" N ARG E 38 " --> pdb=" O GLU E 46 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'I' and resid 19 through 24 removed outlier: 3.617A pdb=" N ALA I 19 " --> pdb=" O ILE I 75 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N ILE I 75 " --> pdb=" O ALA I 19 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'I' and resid 53 through 54 removed outlier: 5.321A pdb=" N LEU I 46 " --> pdb=" O GLN I 37 " (cutoff:3.500A) removed outlier: 5.857A pdb=" N GLN I 37 " --> pdb=" O LEU I 46 " (cutoff:3.500A) 348 hydrogen bonds defined for protein. 906 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: 2.31 Time building geometry restraints manager: 2.02 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 4322 1.34 - 1.46: 3863 1.46 - 1.58: 6143 1.58 - 1.71: 0 1.71 - 1.83: 156 Bond restraints: 14484 Sorted by residual: bond pdb=" C6 BMA T 3 " pdb=" O6 BMA T 3 " ideal model delta sigma weight residual 1.411 1.469 -0.058 2.00e-02 2.50e+03 8.39e+00 bond pdb=" C2 MAN O 4 " pdb=" O2 MAN O 4 " ideal model delta sigma weight residual 1.407 1.462 -0.055 2.00e-02 2.50e+03 7.55e+00 bond pdb=" C1 BMA K 2 " pdb=" C2 BMA K 2 " ideal model delta sigma weight residual 1.519 1.573 -0.054 2.00e-02 2.50e+03 7.41e+00 bond pdb=" N HIS b 374 " pdb=" CA HIS b 374 " ideal model delta sigma weight residual 1.462 1.496 -0.035 1.46e-02 4.69e+03 5.62e+00 bond pdb=" C3 BMA N 3 " pdb=" O3 BMA N 3 " ideal model delta sigma weight residual 1.406 1.453 -0.047 2.00e-02 2.50e+03 5.53e+00 ... (remaining 14479 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.04: 19314 3.04 - 6.09: 281 6.09 - 9.13: 30 9.13 - 12.18: 0 12.18 - 15.22: 1 Bond angle restraints: 19626 Sorted by residual: angle pdb=" CA CYS a 292 " pdb=" CB CYS a 292 " pdb=" SG CYS a 292 " ideal model delta sigma weight residual 114.40 129.62 -15.22 2.30e+00 1.89e-01 4.38e+01 angle pdb=" CA THR b 375 " pdb=" C THR b 375 " pdb=" O THR b 375 " ideal model delta sigma weight residual 120.96 115.34 5.62 1.09e+00 8.42e-01 2.66e+01 angle pdb=" C THR b 375 " pdb=" CA THR b 375 " pdb=" CB THR b 375 " ideal model delta sigma weight residual 109.84 116.61 -6.77 1.50e+00 4.44e-01 2.04e+01 angle pdb=" N ILE E 54 " pdb=" CA ILE E 54 " pdb=" C ILE E 54 " ideal model delta sigma weight residual 113.20 109.41 3.79 9.60e-01 1.09e+00 1.55e+01 angle pdb=" C HIS b 374 " pdb=" CA HIS b 374 " pdb=" CB HIS b 374 " ideal model delta sigma weight residual 111.41 105.55 5.86 1.70e+00 3.46e-01 1.19e+01 ... (remaining 19621 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 23.06: 8405 23.06 - 46.13: 611 46.13 - 69.19: 91 69.19 - 92.26: 108 92.26 - 115.32: 60 Dihedral angle restraints: 9275 sinusoidal: 4493 harmonic: 4782 Sorted by residual: dihedral pdb=" CB CYS b 326 " pdb=" SG CYS b 326 " pdb=" SG CYS C 207 " pdb=" CB CYS C 207 " ideal model delta sinusoidal sigma weight residual 93.00 166.94 -73.94 1 1.00e+01 1.00e-02 6.94e+01 dihedral pdb=" CB CYS B 180 " pdb=" SG CYS B 180 " pdb=" SG CYS B 212 " pdb=" CB CYS B 212 " ideal model delta sinusoidal sigma weight residual -86.00 -27.61 -58.39 1 1.00e+01 1.00e-02 4.57e+01 dihedral pdb=" CB CYS a 364 " pdb=" SG CYS a 364 " pdb=" SG CYS a 385 " pdb=" CB CYS a 385 " ideal model delta sinusoidal sigma weight residual -86.00 -140.89 54.89 1 1.00e+01 1.00e-02 4.08e+01 ... (remaining 9272 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.073: 2130 0.073 - 0.147: 248 0.147 - 0.220: 14 0.220 - 0.294: 20 0.294 - 0.367: 3 Chirality restraints: 2415 Sorted by residual: chirality pdb=" C1 NAG B 303 " pdb=" ND2 ASN B 90 " pdb=" C2 NAG B 303 " pdb=" O5 NAG B 303 " both_signs ideal model delta sigma weight residual False -2.40 -2.03 -0.37 2.00e-01 2.50e+01 3.37e+00 chirality pdb=" C5 BMA N 3 " pdb=" C4 BMA N 3 " pdb=" C6 BMA N 3 " pdb=" O5 BMA N 3 " both_signs ideal model delta sigma weight residual False -2.27 -2.59 0.31 2.00e-01 2.50e+01 2.42e+00 chirality pdb=" C5 BMA F 3 " pdb=" C4 BMA F 3 " pdb=" C6 BMA F 3 " pdb=" O5 BMA F 3 " both_signs ideal model delta sigma weight residual False -2.27 -2.58 0.31 2.00e-01 2.50e+01 2.36e+00 ... (remaining 2412 not shown) Planarity restraints: 2394 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG b 379 " -0.653 9.50e-02 1.11e+02 2.93e-01 5.23e+01 pdb=" NE ARG b 379 " 0.040 2.00e-02 2.50e+03 pdb=" CZ ARG b 379 " 0.003 2.00e-02 2.50e+03 pdb=" NH1 ARG b 379 " 0.005 2.00e-02 2.50e+03 pdb=" NH2 ARG b 379 " -0.019 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C TRP L 94 " 0.041 5.00e-02 4.00e+02 6.27e-02 6.30e+00 pdb=" N PRO L 95 " -0.109 5.00e-02 4.00e+02 pdb=" CA PRO L 95 " 0.032 5.00e-02 4.00e+02 pdb=" CD PRO L 95 " 0.035 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ILE a 361 " 0.038 5.00e-02 4.00e+02 5.80e-02 5.38e+00 pdb=" N PRO a 362 " -0.100 5.00e-02 4.00e+02 pdb=" CA PRO a 362 " 0.030 5.00e-02 4.00e+02 pdb=" CD PRO a 362 " 0.032 5.00e-02 4.00e+02 ... (remaining 2391 not shown) Histogram of nonbonded interaction distances: 2.04 - 2.61: 222 2.61 - 3.19: 13550 3.19 - 3.76: 20846 3.76 - 4.33: 28942 4.33 - 4.90: 46350 Nonbonded interactions: 109910 Sorted by model distance: nonbonded pdb=" O ALA I 25 " pdb=" OG1 THR I 69 " model vdw 2.044 3.040 nonbonded pdb=" O SER L 20 " pdb=" O6 NAG L 201 " model vdw 2.070 3.040 nonbonded pdb=" O LEU A 245 " pdb=" OG1 THR A 249 " model vdw 2.080 3.040 nonbonded pdb=" O GLN L 6 " pdb=" OG1 THR L 102 " model vdw 2.124 3.040 nonbonded pdb=" OD2 ASP A 229 " pdb=" NH2 ARG L 61 " model vdw 2.130 3.120 ... (remaining 109905 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = (chain 'B' and (resid 59 through 252 or (resid 253 and (name N or name CA or nam \ e C or name O or name CB )) or resid 254 through 255 or resid 301 through 305)) selection = (chain 'C' and (resid 59 through 252 or (resid 253 and (name N or name CA or nam \ e C or name O or name CB )) or resid 254 through 255 or resid 301 through 305)) } ncs_group { reference = chain 'E' selection = chain 'H' } ncs_group { reference = chain 'G' selection = chain 'Q' selection = chain 'U' selection = chain 'X' } ncs_group { reference = chain 'I' selection = chain 'L' } ncs_group { reference = chain 'J' selection = chain 'K' selection = chain 'V' } ncs_group { reference = chain 'M' selection = chain 'R' selection = chain 'T' selection = chain 'W' } ncs_group { reference = chain 'N' selection = chain 'O' selection = chain 'S' } ncs_group { reference = chain 'a' selection = chain 'b' selection = chain 'c' } 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: 2.360 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: 0.170 Check model and map are aligned: 0.030 Set scattering table: 0.020 Process input model: 13.700 Find NCS groups from input model: 0.570 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.430 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 18.340 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7153 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.058 14597 Z= 0.254 Angle : 0.895 15.219 19939 Z= 0.387 Chirality : 0.053 0.367 2415 Planarity : 0.007 0.293 2359 Dihedral : 20.302 115.320 6139 Min Nonbonded Distance : 2.044 Molprobity Statistics. All-atom Clashscore : 5.75 Ramachandran Plot: Outliers : 0.55 % Allowed : 13.51 % Favored : 85.94 % Rotamer: Outliers : 1.11 % Allowed : 1.11 % Favored : 97.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -2.26 (0.21), residues: 1629 helix: 0.83 (0.34), residues: 281 sheet: -1.15 (0.34), residues: 286 loop : -2.43 (0.18), residues: 1062 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG b 379 TYR 0.033 0.001 TYR b 363 PHE 0.015 0.001 PHE C 117 TRP 0.021 0.001 TRP E 103 HIS 0.004 0.001 HIS B 92 Details of bonding type rmsd/Z covalent geometry : bond 0.00512 / 0.25 (14484) covalent geometry : angle 0.83906 / 0.37 (19626) SS BOND : bond 0.00286 / 0.20 ( 26) SS BOND : angle 1.05393 / 0.62 ( 52) hydrogen bonds : bond 0.29519 / 19.58 ( 333) hydrogen bonds : angle 8.90106 / 6.22 ( 906) link_ALPHA1-2 : bond 0.00743 / 0.39 ( 2) link_ALPHA1-2 : angle 5.60407 / 2.90 ( 6) link_ALPHA1-3 : bond 0.00763 / 0.51 ( 13) link_ALPHA1-3 : angle 2.74015 / 1.68 ( 39) link_ALPHA1-6 : bond 0.01163 / 0.86 ( 10) link_ALPHA1-6 : angle 3.33535 / 2.41 ( 30) link_BETA1-4 : bond 0.00519 / 0.35 ( 27) link_BETA1-4 : angle 2.41410 / 1.53 ( 81) link_NAG-ASN : bond 0.00700 / 0.46 ( 35) link_NAG-ASN : angle 2.77064 / 1.70 ( 105) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3258 Ramachandran restraints generated. 1629 Oldfield, 0 Emsley, 1629 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3258 Ramachandran restraints generated. 1629 Oldfield, 0 Emsley, 1629 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 584 residues out of total 1448 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 568 time to evaluate : 0.539 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: B 82 MET cc_start: 0.7889 (ptp) cc_final: 0.7660 (ptp) REVERT: B 101 THR cc_start: 0.8734 (p) cc_final: 0.8364 (t) REVERT: B 104 GLU cc_start: 0.8762 (tt0) cc_final: 0.7788 (tt0) REVERT: B 119 ASN cc_start: 0.8002 (OUTLIER) cc_final: 0.7141 (m-40) REVERT: B 130 ASP cc_start: 0.9080 (p0) cc_final: 0.8747 (p0) REVERT: B 133 LEU cc_start: 0.8898 (mt) cc_final: 0.8305 (mp) REVERT: B 187 VAL cc_start: 0.8715 (t) cc_final: 0.8503 (p) REVERT: B 232 GLN cc_start: 0.7532 (tt0) cc_final: 0.6835 (mm-40) REVERT: b 270 GLU cc_start: 0.7855 (mp0) cc_final: 0.7241 (tp30) REVERT: b 284 MET cc_start: 0.8116 (mmm) cc_final: 0.7868 (mmm) REVERT: b 302 ASN cc_start: 0.9073 (OUTLIER) cc_final: 0.8521 (m110) REVERT: b 325 ARG cc_start: 0.7924 (ptt180) cc_final: 0.7690 (ptp90) REVERT: b 344 LEU cc_start: 0.8314 (mp) cc_final: 0.7468 (mp) REVERT: b 372 LEU cc_start: 0.8260 (mt) cc_final: 0.7877 (tp) REVERT: b 380 THR cc_start: 0.9545 (p) cc_final: 0.9046 (t) REVERT: A 73 LEU cc_start: 0.8644 (mt) cc_final: 0.8164 (mp) REVERT: A 82 MET cc_start: 0.8452 (pmm) cc_final: 0.8112 (pmm) REVERT: A 140 PHE cc_start: 0.9454 (m-80) cc_final: 0.9066 (m-80) REVERT: A 179 HIS cc_start: 0.7862 (t70) cc_final: 0.7635 (t70) REVERT: a 325 ARG cc_start: 0.8266 (ptp-170) cc_final: 0.7276 (ptp-170) REVERT: a 344 LEU cc_start: 0.9338 (mt) cc_final: 0.9011 (mt) REVERT: a 363 TYR cc_start: 0.8643 (p90) cc_final: 0.8298 (p90) REVERT: a 369 TYR cc_start: 0.8672 (m-80) cc_final: 0.7280 (m-80) REVERT: a 372 LEU cc_start: 0.8886 (mt) cc_final: 0.8659 (tp) REVERT: a 387 LEU cc_start: 0.8574 (mt) cc_final: 0.7928 (tp) REVERT: C 75 MET cc_start: 0.8858 (mtm) cc_final: 0.8599 (mtm) REVERT: C 80 MET cc_start: 0.7185 (mtt) cc_final: 0.6745 (mtt) REVERT: C 92 HIS cc_start: 0.8218 (m-70) cc_final: 0.7776 (m-70) REVERT: c 268 ASP cc_start: 0.7462 (p0) cc_final: 0.6886 (p0) REVERT: c 282 ARG cc_start: 0.7594 (ttt180) cc_final: 0.6465 (ptp-170) REVERT: c 321 GLN cc_start: 0.8802 (mm-40) cc_final: 0.8427 (mm110) REVERT: c 338 ASN cc_start: 0.8756 (OUTLIER) cc_final: 0.8273 (t0) REVERT: c 356 ARG cc_start: 0.7352 (mtt180) cc_final: 0.6725 (mmm-85) REVERT: c 361 ILE cc_start: 0.8690 (tp) cc_final: 0.8060 (tp) REVERT: c 369 TYR cc_start: 0.7737 (m-80) cc_final: 0.6100 (m-10) REVERT: c 387 LEU cc_start: 0.9031 (mt) cc_final: 0.8611 (mp) REVERT: c 404 GLU cc_start: 0.9408 (mm-30) cc_final: 0.9079 (mm-30) REVERT: c 410 MET cc_start: 0.9022 (mmt) cc_final: 0.8534 (tpt) REVERT: c 416 GLN cc_start: 0.8502 (tt0) cc_final: 0.8180 (tt0) REVERT: D 37 GLU cc_start: 0.6292 (mt-10) cc_final: 0.5755 (mm-30) REVERT: D 46 GLU cc_start: 0.8520 (pt0) cc_final: 0.7580 (pm20) REVERT: D 107 GLN cc_start: 0.8366 (pt0) cc_final: 0.8123 (pt0) REVERT: H 67 LEU cc_start: 0.8212 (mt) cc_final: 0.7968 (mm) REVERT: H 91 TYR cc_start: 0.7697 (m-80) cc_final: 0.7377 (m-80) REVERT: H 102 TYR cc_start: 0.8906 (m-80) cc_final: 0.7246 (m-80) REVERT: H 103 TRP cc_start: 0.9161 (m100) cc_final: 0.8779 (m-10) REVERT: H 105 GLN cc_start: 0.9041 (mm-40) cc_final: 0.8563 (pm20) REVERT: L 6 GLN cc_start: 0.6431 (mt0) cc_final: 0.5798 (mp-120) REVERT: L 23 CYS cc_start: 0.6675 (t) cc_final: 0.4957 (t) REVERT: L 47 VAL cc_start: 0.9026 (m) cc_final: 0.8805 (m) REVERT: L 48 ILE cc_start: 0.9498 (mm) cc_final: 0.9179 (tt) REVERT: L 57 ASP cc_start: 0.8468 (t0) cc_final: 0.8267 (t0) REVERT: L 58 ILE cc_start: 0.9288 (mm) cc_final: 0.8791 (mt) REVERT: L 98 PHE cc_start: 0.8542 (m-80) cc_final: 0.8323 (m-10) REVERT: E 3 GLN cc_start: 0.8539 (tt0) cc_final: 0.8091 (tm-30) REVERT: E 77 GLN cc_start: 0.8740 (tt0) cc_final: 0.8324 (tm-30) REVERT: E 86 ASP cc_start: 0.8665 (m-30) cc_final: 0.8223 (m-30) REVERT: I 38 GLN cc_start: 0.7901 (tt0) cc_final: 0.7537 (tt0) REVERT: I 75 ILE cc_start: 0.9250 (mt) cc_final: 0.8509 (tt) REVERT: I 78 MET cc_start: 0.8871 (tpp) cc_final: 0.8480 (tpt) REVERT: I 93 ASN cc_start: 0.9082 (m-40) cc_final: 0.8571 (p0) outliers start: 16 outliers final: 3 residues processed: 578 average time/residue: 0.1162 time to fit residues: 99.0052 Evaluate side-chains 334 residues out of total 1448 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 328 time to evaluate : 0.563 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 157 random chunks: chunk 98 optimal weight: 0.8980 chunk 107 optimal weight: 0.0670 chunk 10 optimal weight: 0.0170 chunk 66 optimal weight: 0.6980 chunk 130 optimal weight: 0.3980 chunk 124 optimal weight: 4.9990 chunk 103 optimal weight: 1.9990 chunk 77 optimal weight: 2.9990 chunk 122 optimal weight: 2.9990 chunk 91 optimal weight: 0.7980 chunk 149 optimal weight: 5.9990 overall best weight: 0.3956 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 189 GLN B 230 HIS B 247 GLN ** b 319 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** b 321 GLN b 342 ASN b 354 HIS A 93 HIS A 131 HIS ** A 170 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 115 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** c 305 HIS c 353 ASN c 406 GLN D 39 GLN ** H 60 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 37 GLN L 90 GLN E 76 ASN ** I 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3680 r_free = 0.3680 target = 0.096178 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3293 r_free = 0.3293 target = 0.076987 restraints weight = 49622.040| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3342 r_free = 0.3342 target = 0.079302 restraints weight = 32679.882| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3378 r_free = 0.3378 target = 0.080982 restraints weight = 24494.561| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3402 r_free = 0.3402 target = 0.082154 restraints weight = 19868.694| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 38)----------------| | r_work = 0.3419 r_free = 0.3419 target = 0.082968 restraints weight = 17053.995| |-----------------------------------------------------------------------------| r_work (final): 0.3414 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7430 moved from start: 0.3028 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.069 14597 Z= 0.177 Angle : 0.896 10.045 19939 Z= 0.422 Chirality : 0.053 0.351 2415 Planarity : 0.005 0.060 2359 Dihedral : 16.595 94.373 3123 Min Nonbonded Distance : 2.342 Molprobity Statistics. All-atom Clashscore : 10.16 Ramachandran Plot: Outliers : 0.49 % Allowed : 13.87 % Favored : 85.64 % Rotamer: Outliers : 0.48 % Allowed : 4.78 % Favored : 94.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -2.66 (0.20), residues: 1629 helix: -0.23 (0.30), residues: 290 sheet: -1.17 (0.32), residues: 296 loop : -2.56 (0.18), residues: 1043 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG D 67 TYR 0.023 0.002 TYR L 49 PHE 0.029 0.002 PHE B 191 TRP 0.025 0.002 TRP C 210 HIS 0.013 0.001 HIS B 170 Details of bonding type rmsd/Z covalent geometry : bond 0.00370 / 0.17 (14484) covalent geometry : angle 0.82348 / 0.41 (19626) SS BOND : bond 0.00898 / 0.43 ( 26) SS BOND : angle 1.73477 / 1.05 ( 52) hydrogen bonds : bond 0.06375 / 4.04 ( 333) hydrogen bonds : angle 6.30574 / 4.36 ( 906) link_ALPHA1-2 : bond 0.00983 / 0.51 ( 2) link_ALPHA1-2 : angle 4.51672 / 2.19 ( 6) link_ALPHA1-3 : bond 0.01071 / 0.71 ( 13) link_ALPHA1-3 : angle 2.93060 / 1.91 ( 39) link_ALPHA1-6 : bond 0.01024 / 0.78 ( 10) link_ALPHA1-6 : angle 2.23723 / 1.51 ( 30) link_BETA1-4 : bond 0.00884 / 0.57 ( 27) link_BETA1-4 : angle 2.68932 / 1.73 ( 81) link_NAG-ASN : bond 0.00874 / 0.53 ( 35) link_NAG-ASN : angle 3.57513 / 2.31 ( 105) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3258 Ramachandran restraints generated. 1629 Oldfield, 0 Emsley, 1629 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3258 Ramachandran restraints generated. 1629 Oldfield, 0 Emsley, 1629 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 438 residues out of total 1448 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 431 time to evaluate : 0.522 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: B 150 TYR cc_start: 0.6730 (m-80) cc_final: 0.6362 (m-80) REVERT: B 189 GLN cc_start: 0.9120 (tp40) cc_final: 0.8905 (mm-40) REVERT: B 200 TYR cc_start: 0.6730 (p90) cc_final: 0.5877 (p90) REVERT: B 232 GLN cc_start: 0.7751 (tt0) cc_final: 0.7035 (tp40) REVERT: b 270 GLU cc_start: 0.7459 (mp0) cc_final: 0.7226 (tp30) REVERT: b 289 GLU cc_start: 0.8759 (tp30) cc_final: 0.8489 (tp30) REVERT: b 311 ASP cc_start: 0.8945 (m-30) cc_final: 0.8553 (m-30) REVERT: b 317 ASP cc_start: 0.8910 (t70) cc_final: 0.8498 (t0) REVERT: b 346 ASN cc_start: 0.9188 (t0) cc_final: 0.8851 (t0) REVERT: b 414 MET cc_start: 0.8853 (tmm) cc_final: 0.7781 (tmm) REVERT: A 75 MET cc_start: 0.8566 (mtp) cc_final: 0.8140 (ttm) REVERT: A 76 GLU cc_start: 0.8549 (tt0) cc_final: 0.7398 (tp30) REVERT: A 82 MET cc_start: 0.8818 (pmm) cc_final: 0.8437 (pmm) REVERT: A 134 MET cc_start: 0.8021 (mmm) cc_final: 0.7721 (mmm) REVERT: A 140 PHE cc_start: 0.9200 (m-80) cc_final: 0.8662 (m-80) REVERT: A 247 GLN cc_start: 0.6962 (mp10) cc_final: 0.6169 (mp10) REVERT: a 266 LEU cc_start: 0.8756 (mp) cc_final: 0.8518 (tp) REVERT: a 281 THR cc_start: 0.8053 (p) cc_final: 0.6988 (p) REVERT: a 287 GLU cc_start: 0.8156 (mt-10) cc_final: 0.7307 (tm-30) REVERT: a 325 ARG cc_start: 0.7943 (ptp-170) cc_final: 0.7636 (ptp-170) REVERT: a 363 TYR cc_start: 0.8665 (p90) cc_final: 0.8110 (p90) REVERT: a 366 TYR cc_start: 0.9068 (m-10) cc_final: 0.8811 (m-10) REVERT: a 387 LEU cc_start: 0.8706 (mt) cc_final: 0.8142 (mt) REVERT: a 410 MET cc_start: 0.9182 (mmt) cc_final: 0.8720 (mmt) REVERT: C 68 LEU cc_start: 0.8320 (tp) cc_final: 0.7922 (tp) REVERT: C 82 MET cc_start: 0.8259 (mmm) cc_final: 0.7973 (mmm) REVERT: C 93 HIS cc_start: 0.8306 (m90) cc_final: 0.8025 (m-70) REVERT: C 241 TYR cc_start: 0.9078 (t80) cc_final: 0.8647 (t80) REVERT: c 268 ASP cc_start: 0.7521 (p0) cc_final: 0.7068 (p0) REVERT: c 282 ARG cc_start: 0.8190 (ttt180) cc_final: 0.7044 (ptp-170) REVERT: c 285 LEU cc_start: 0.9258 (mp) cc_final: 0.9053 (mp) REVERT: c 311 ASP cc_start: 0.9143 (m-30) cc_final: 0.8750 (m-30) REVERT: c 312 MET cc_start: 0.8244 (mmm) cc_final: 0.7781 (mmm) REVERT: c 314 ARG cc_start: 0.9255 (mtt90) cc_final: 0.8485 (ttm110) REVERT: c 320 LYS cc_start: 0.9226 (ttpt) cc_final: 0.8855 (ttmm) REVERT: c 337 ILE cc_start: 0.8876 (mt) cc_final: 0.8065 (mt) REVERT: c 349 LEU cc_start: 0.9118 (tp) cc_final: 0.8914 (tt) REVERT: c 359 MET cc_start: 0.8088 (mtp) cc_final: 0.7500 (mmm) REVERT: c 369 TYR cc_start: 0.8559 (m-80) cc_final: 0.6568 (m-10) REVERT: c 387 LEU cc_start: 0.9218 (mt) cc_final: 0.8810 (mp) REVERT: c 403 ILE cc_start: 0.9032 (mt) cc_final: 0.8674 (mt) REVERT: D 6 GLU cc_start: 0.8315 (pt0) cc_final: 0.8050 (pm20) REVERT: D 34 MET cc_start: 0.8573 (mtm) cc_final: 0.7735 (mtp) REVERT: D 37 GLU cc_start: 0.5773 (mt-10) cc_final: 0.5507 (mt-10) REVERT: D 81 LEU cc_start: 0.8002 (mp) cc_final: 0.7797 (mp) REVERT: D 90 ASP cc_start: 0.7159 (m-30) cc_final: 0.6949 (m-30) REVERT: D 96 CYS cc_start: 0.6122 (t) cc_final: 0.5770 (t) REVERT: D 104 LEU cc_start: 0.7863 (pp) cc_final: 0.7409 (pp) REVERT: D 107 GLN cc_start: 0.8113 (pt0) cc_final: 0.7729 (pt0) REVERT: H 69 ILE cc_start: 0.8963 (mm) cc_final: 0.8698 (pt) REVERT: H 96 PHE cc_start: 0.7792 (m-80) cc_final: 0.7478 (m-10) REVERT: H 103 TRP cc_start: 0.9028 (m100) cc_final: 0.8767 (m100) REVERT: H 107 THR cc_start: 0.7875 (t) cc_final: 0.7498 (t) REVERT: L 6 GLN cc_start: 0.7157 (mt0) cc_final: 0.6723 (mp-120) REVERT: L 35 TRP cc_start: 0.8676 (m100) cc_final: 0.8183 (m100) REVERT: L 53 THR cc_start: 0.8477 (OUTLIER) cc_final: 0.8219 (t) REVERT: L 98 PHE cc_start: 0.8497 (m-80) cc_final: 0.7939 (m-10) REVERT: E 67 LEU cc_start: 0.8694 (mm) cc_final: 0.8166 (mm) REVERT: E 76 ASN cc_start: 0.7358 (m-40) cc_final: 0.7022 (m-40) REVERT: E 86 ASP cc_start: 0.8844 (m-30) cc_final: 0.8436 (m-30) REVERT: I 38 GLN cc_start: 0.8342 (tt0) cc_final: 0.8002 (mt0) REVERT: I 75 ILE cc_start: 0.9415 (mt) cc_final: 0.8966 (tt) outliers start: 7 outliers final: 2 residues processed: 437 average time/residue: 0.1131 time to fit residues: 74.1326 Evaluate side-chains 311 residues out of total 1448 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 308 time to evaluate : 0.532 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 157 random chunks: chunk 24 optimal weight: 1.9990 chunk 94 optimal weight: 2.9990 chunk 11 optimal weight: 1.9990 chunk 81 optimal weight: 4.9990 chunk 103 optimal weight: 2.9990 chunk 26 optimal weight: 6.9990 chunk 149 optimal weight: 2.9990 chunk 42 optimal weight: 5.9990 chunk 23 optimal weight: 1.9990 chunk 107 optimal weight: 6.9990 chunk 141 optimal weight: 5.9990 overall best weight: 2.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 170 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 319 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** b 374 HIS ** A 170 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** a 353 ASN ** a 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 141 HIS C 223 GLN c 331 GLN D 84 ASN L 37 GLN L 89 GLN E 3 GLN ** I 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3563 r_free = 0.3563 target = 0.089798 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3150 r_free = 0.3150 target = 0.070312 restraints weight = 50888.925| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3188 r_free = 0.3188 target = 0.072136 restraints weight = 35039.869| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3213 r_free = 0.3213 target = 0.073271 restraints weight = 25244.621| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3232 r_free = 0.3232 target = 0.074065 restraints weight = 22438.066| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3237 r_free = 0.3237 target = 0.074333 restraints weight = 20119.974| |-----------------------------------------------------------------------------| r_work (final): 0.3226 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7717 moved from start: 0.3926 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.083 14597 Z= 0.232 Angle : 0.897 9.938 19939 Z= 0.430 Chirality : 0.053 0.376 2415 Planarity : 0.006 0.154 2359 Dihedral : 13.919 86.628 3123 Min Nonbonded Distance : 2.364 Molprobity Statistics. All-atom Clashscore : 14.10 Ramachandran Plot: Outliers : 0.49 % Allowed : 13.63 % Favored : 85.88 % Rotamer: Outliers : 0.21 % Allowed : 5.89 % Favored : 93.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.68 (0.20), residues: 1629 helix: -0.17 (0.30), residues: 284 sheet: -1.24 (0.31), residues: 286 loop : -2.56 (0.18), residues: 1059 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.019 0.001 ARG E 30 TYR 0.029 0.002 TYR A 62 PHE 0.028 0.002 PHE b 318 TRP 0.029 0.003 TRP C 210 HIS 0.015 0.002 HIS B 170 Details of bonding type rmsd/Z covalent geometry : bond 0.00503 / 0.23 (14484) covalent geometry : angle 0.82996 / 0.42 (19626) SS BOND : bond 0.00463 / 0.28 ( 26) SS BOND : angle 1.90999 / 1.15 ( 52) hydrogen bonds : bond 0.05140 / 3.24 ( 333) hydrogen bonds : angle 6.12895 / 4.20 ( 906) link_ALPHA1-2 : bond 0.00715 / 0.36 ( 2) link_ALPHA1-2 : angle 4.23280 / 2.04 ( 6) link_ALPHA1-3 : bond 0.00982 / 0.65 ( 13) link_ALPHA1-3 : angle 2.68866 / 1.79 ( 39) link_ALPHA1-6 : bond 0.00915 / 0.72 ( 10) link_ALPHA1-6 : angle 2.39321 / 1.61 ( 30) link_BETA1-4 : bond 0.00802 / 0.53 ( 27) link_BETA1-4 : angle 2.49067 / 1.60 ( 81) link_NAG-ASN : bond 0.00814 / 0.51 ( 35) link_NAG-ASN : angle 3.49770 / 2.22 ( 105) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3258 Ramachandran restraints generated. 1629 Oldfield, 0 Emsley, 1629 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3258 Ramachandran restraints generated. 1629 Oldfield, 0 Emsley, 1629 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 396 residues out of total 1448 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 393 time to evaluate : 0.529 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: B 75 MET cc_start: 0.8561 (mtm) cc_final: 0.8271 (mtm) REVERT: B 142 LEU cc_start: 0.9204 (mp) cc_final: 0.8756 (tp) REVERT: B 183 VAL cc_start: 0.8671 (t) cc_final: 0.8290 (m) REVERT: B 194 MET cc_start: 0.9055 (tpp) cc_final: 0.8808 (tpp) REVERT: B 200 TYR cc_start: 0.6724 (p90) cc_final: 0.5706 (p90) REVERT: B 248 ARG cc_start: 0.8189 (tpp80) cc_final: 0.7936 (tpp80) REVERT: b 270 GLU cc_start: 0.7583 (mp0) cc_final: 0.7304 (tp30) REVERT: b 289 GLU cc_start: 0.8888 (tp30) cc_final: 0.8501 (tp30) REVERT: b 311 ASP cc_start: 0.8943 (m-30) cc_final: 0.8670 (m-30) REVERT: b 346 ASN cc_start: 0.9351 (t0) cc_final: 0.8921 (t0) REVERT: b 414 MET cc_start: 0.8890 (tmm) cc_final: 0.8647 (tmm) REVERT: A 75 MET cc_start: 0.8809 (mtp) cc_final: 0.8597 (ttm) REVERT: A 82 MET cc_start: 0.8882 (pmm) cc_final: 0.8354 (pmm) REVERT: A 122 ASP cc_start: 0.9332 (m-30) cc_final: 0.8934 (m-30) REVERT: A 126 LYS cc_start: 0.8477 (mmtm) cc_final: 0.8209 (mmtp) REVERT: A 140 PHE cc_start: 0.9230 (m-80) cc_final: 0.8819 (m-80) REVERT: A 219 TYR cc_start: 0.7767 (m-80) cc_final: 0.7259 (m-80) REVERT: A 241 TYR cc_start: 0.8708 (t80) cc_final: 0.8444 (t80) REVERT: a 281 THR cc_start: 0.8128 (p) cc_final: 0.7058 (p) REVERT: a 283 TRP cc_start: 0.8877 (p-90) cc_final: 0.8554 (p-90) REVERT: a 287 GLU cc_start: 0.8324 (mt-10) cc_final: 0.7864 (tm-30) REVERT: a 307 GLU cc_start: 0.8476 (tm-30) cc_final: 0.8144 (tm-30) REVERT: a 325 ARG cc_start: 0.8161 (ptp-170) cc_final: 0.7791 (ptp-170) REVERT: a 372 LEU cc_start: 0.9227 (tp) cc_final: 0.8997 (tp) REVERT: a 410 MET cc_start: 0.9222 (mmp) cc_final: 0.9012 (mmt) REVERT: C 68 LEU cc_start: 0.8305 (tp) cc_final: 0.7815 (tp) REVERT: C 93 HIS cc_start: 0.8531 (m90) cc_final: 0.8002 (m-70) REVERT: C 115 HIS cc_start: 0.8156 (m90) cc_final: 0.7931 (m90) REVERT: C 241 TYR cc_start: 0.9179 (t80) cc_final: 0.8753 (t80) REVERT: c 268 ASP cc_start: 0.7607 (p0) cc_final: 0.7149 (p0) REVERT: c 282 ARG cc_start: 0.8355 (ttt180) cc_final: 0.7129 (ptp-170) REVERT: c 285 LEU cc_start: 0.9290 (mp) cc_final: 0.8900 (mp) REVERT: c 312 MET cc_start: 0.8482 (mmm) cc_final: 0.7785 (mmm) REVERT: c 314 ARG cc_start: 0.9254 (mtt90) cc_final: 0.8636 (ttm110) REVERT: c 320 LYS cc_start: 0.9309 (ttpt) cc_final: 0.8848 (ttmm) REVERT: c 337 ILE cc_start: 0.8952 (mt) cc_final: 0.7792 (mt) REVERT: c 369 TYR cc_start: 0.8714 (m-80) cc_final: 0.6784 (m-80) REVERT: c 387 LEU cc_start: 0.9383 (mt) cc_final: 0.8972 (mp) REVERT: c 401 ASP cc_start: 0.9041 (p0) cc_final: 0.8449 (p0) REVERT: c 404 GLU cc_start: 0.9365 (mp0) cc_final: 0.9094 (pp20) REVERT: D 6 GLU cc_start: 0.8578 (pt0) cc_final: 0.7838 (pt0) REVERT: D 30 SER cc_start: 0.7871 (p) cc_final: 0.7605 (m) REVERT: D 34 MET cc_start: 0.8822 (mtm) cc_final: 0.7987 (mtp) REVERT: D 37 GLU cc_start: 0.6224 (mt-10) cc_final: 0.5666 (mt-10) REVERT: D 46 GLU cc_start: 0.8495 (pm20) cc_final: 0.7629 (pm20) REVERT: D 95 TYR cc_start: 0.7804 (m-10) cc_final: 0.7113 (m-80) REVERT: D 105 ARG cc_start: 0.8012 (ptp-110) cc_final: 0.7139 (ptp-110) REVERT: L 6 GLN cc_start: 0.8049 (mt0) cc_final: 0.6938 (mp-120) REVERT: L 23 CYS cc_start: 0.6296 (t) cc_final: 0.4666 (t) REVERT: L 74 THR cc_start: 0.8088 (p) cc_final: 0.7766 (t) REVERT: L 78 MET cc_start: 0.8599 (tmm) cc_final: 0.8125 (tmm) REVERT: E 47 TRP cc_start: 0.8900 (t60) cc_final: 0.8484 (t60) REVERT: E 67 LEU cc_start: 0.8894 (mm) cc_final: 0.8267 (mm) REVERT: E 76 ASN cc_start: 0.7663 (m-40) cc_final: 0.7397 (m-40) REVERT: E 86 ASP cc_start: 0.9149 (m-30) cc_final: 0.8585 (m-30) REVERT: I 37 GLN cc_start: 0.7862 (pp30) cc_final: 0.7432 (pp30) REVERT: I 77 ARG cc_start: 0.8605 (ptp90) cc_final: 0.8355 (ptp-170) REVERT: I 78 MET cc_start: 0.8635 (tpp) cc_final: 0.8337 (tpp) REVERT: I 83 PHE cc_start: 0.8089 (m-80) cc_final: 0.7706 (m-80) outliers start: 3 outliers final: 1 residues processed: 395 average time/residue: 0.1144 time to fit residues: 66.7089 Evaluate side-chains 293 residues out of total 1448 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 292 time to evaluate : 0.385 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 157 random chunks: chunk 3 optimal weight: 2.9990 chunk 151 optimal weight: 1.9990 chunk 133 optimal weight: 4.9990 chunk 81 optimal weight: 2.9990 chunk 12 optimal weight: 0.2980 chunk 140 optimal weight: 2.9990 chunk 61 optimal weight: 2.9990 chunk 54 optimal weight: 6.9990 chunk 139 optimal weight: 0.9990 chunk 72 optimal weight: 6.9990 chunk 55 optimal weight: 5.9990 overall best weight: 1.8588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 170 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 189 GLN ** b 319 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 170 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 124 HIS c 406 GLN D 39 GLN ** E 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 6 GLN ** I 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3553 r_free = 0.3553 target = 0.089156 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3137 r_free = 0.3137 target = 0.069581 restraints weight = 50755.795| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3187 r_free = 0.3187 target = 0.071993 restraints weight = 34797.804| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3210 r_free = 0.3210 target = 0.072937 restraints weight = 24689.429| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3222 r_free = 0.3222 target = 0.073477 restraints weight = 21854.625| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3228 r_free = 0.3228 target = 0.073707 restraints weight = 19830.453| |-----------------------------------------------------------------------------| r_work (final): 0.3218 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7735 moved from start: 0.4476 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.069 14597 Z= 0.199 Angle : 0.891 11.152 19939 Z= 0.421 Chirality : 0.054 0.529 2415 Planarity : 0.005 0.088 2359 Dihedral : 12.198 82.388 3123 Min Nonbonded Distance : 2.347 Molprobity Statistics. All-atom Clashscore : 15.65 Ramachandran Plot: Outliers : 0.55 % Allowed : 13.38 % Favored : 86.07 % Rotamer: Outliers : 0.07 % Allowed : 4.43 % Favored : 95.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.68 (0.20), residues: 1629 helix: -0.24 (0.30), residues: 297 sheet: -0.91 (0.31), residues: 280 loop : -2.67 (0.18), residues: 1052 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG E 30 TYR 0.026 0.002 TYR b 393 PHE 0.029 0.002 PHE L 98 TRP 0.030 0.002 TRP C 210 HIS 0.018 0.002 HIS B 170 Details of bonding type rmsd/Z covalent geometry : bond 0.00437 / 0.20 (14484) covalent geometry : angle 0.81257 / 0.40 (19626) SS BOND : bond 0.00462 / 0.29 ( 26) SS BOND : angle 2.02135 / 1.20 ( 52) hydrogen bonds : bond 0.04413 / 2.74 ( 333) hydrogen bonds : angle 5.78602 / 3.92 ( 906) link_ALPHA1-2 : bond 0.00950 / 0.49 ( 2) link_ALPHA1-2 : angle 3.97988 / 1.94 ( 6) link_ALPHA1-3 : bond 0.00922 / 0.62 ( 13) link_ALPHA1-3 : angle 2.72864 / 1.82 ( 39) link_ALPHA1-6 : bond 0.00963 / 0.71 ( 10) link_ALPHA1-6 : angle 2.28109 / 1.52 ( 30) link_BETA1-4 : bond 0.00650 / 0.41 ( 27) link_BETA1-4 : angle 2.35505 / 1.49 ( 81) link_NAG-ASN : bond 0.00980 / 0.54 ( 35) link_NAG-ASN : angle 3.97441 / 2.54 ( 105) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3258 Ramachandran restraints generated. 1629 Oldfield, 0 Emsley, 1629 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3258 Ramachandran restraints generated. 1629 Oldfield, 0 Emsley, 1629 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 364 residues out of total 1448 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 363 time to evaluate : 0.542 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: B 75 MET cc_start: 0.8537 (mtm) cc_final: 0.8300 (mtm) REVERT: B 77 THR cc_start: 0.9172 (m) cc_final: 0.8965 (t) REVERT: B 142 LEU cc_start: 0.9227 (mp) cc_final: 0.8770 (tp) REVERT: B 150 TYR cc_start: 0.7128 (m-80) cc_final: 0.6459 (m-80) REVERT: B 157 PHE cc_start: 0.8614 (m-80) cc_final: 0.8387 (m-80) REVERT: B 248 ARG cc_start: 0.8155 (tpp80) cc_final: 0.7933 (tpp80) REVERT: b 264 TRP cc_start: 0.7731 (m-10) cc_final: 0.7426 (m-10) REVERT: b 270 GLU cc_start: 0.7670 (mp0) cc_final: 0.7233 (tp30) REVERT: b 311 ASP cc_start: 0.8982 (m-30) cc_final: 0.8742 (m-30) REVERT: b 346 ASN cc_start: 0.9385 (t0) cc_final: 0.8937 (t0) REVERT: A 75 MET cc_start: 0.8847 (mtp) cc_final: 0.8489 (ttm) REVERT: A 82 MET cc_start: 0.8775 (pmm) cc_final: 0.8458 (pmm) REVERT: A 122 ASP cc_start: 0.9305 (m-30) cc_final: 0.8945 (m-30) REVERT: A 126 LYS cc_start: 0.8571 (mmtm) cc_final: 0.8292 (mmtp) REVERT: A 140 PHE cc_start: 0.9254 (m-80) cc_final: 0.8812 (m-80) REVERT: A 219 TYR cc_start: 0.7946 (m-80) cc_final: 0.7323 (m-80) REVERT: A 241 TYR cc_start: 0.8737 (t80) cc_final: 0.8460 (t80) REVERT: a 266 LEU cc_start: 0.8808 (mp) cc_final: 0.8509 (tp) REVERT: a 287 GLU cc_start: 0.8226 (mt-10) cc_final: 0.7805 (tm-30) REVERT: a 324 GLN cc_start: 0.8979 (tm-30) cc_final: 0.8710 (tm-30) REVERT: a 332 MET cc_start: 0.6880 (mtt) cc_final: 0.6023 (mtt) REVERT: a 349 LEU cc_start: 0.8771 (tp) cc_final: 0.8466 (mt) REVERT: C 93 HIS cc_start: 0.8470 (m90) cc_final: 0.7869 (m-70) REVERT: C 164 VAL cc_start: 0.8674 (t) cc_final: 0.8389 (t) REVERT: C 259 ARG cc_start: 0.8274 (mmm-85) cc_final: 0.8028 (mmm-85) REVERT: c 268 ASP cc_start: 0.7603 (p0) cc_final: 0.7153 (p0) REVERT: c 282 ARG cc_start: 0.8418 (ttt180) cc_final: 0.7224 (ptp-170) REVERT: c 285 LEU cc_start: 0.9223 (mp) cc_final: 0.9013 (mp) REVERT: c 312 MET cc_start: 0.8362 (mmm) cc_final: 0.7589 (mmm) REVERT: c 314 ARG cc_start: 0.9155 (mtt90) cc_final: 0.8635 (ttm110) REVERT: c 320 LYS cc_start: 0.9360 (ttpt) cc_final: 0.8914 (ttmm) REVERT: c 337 ILE cc_start: 0.8775 (mt) cc_final: 0.8078 (mt) REVERT: c 349 LEU cc_start: 0.9245 (tp) cc_final: 0.8894 (tt) REVERT: c 359 MET cc_start: 0.8889 (mmm) cc_final: 0.8287 (mmm) REVERT: c 369 TYR cc_start: 0.8712 (m-80) cc_final: 0.6935 (m-80) REVERT: c 387 LEU cc_start: 0.9404 (mt) cc_final: 0.8988 (mp) REVERT: c 401 ASP cc_start: 0.9013 (p0) cc_final: 0.8363 (p0) REVERT: c 402 ASP cc_start: 0.9202 (t0) cc_final: 0.8885 (t0) REVERT: c 404 GLU cc_start: 0.9440 (mp0) cc_final: 0.9113 (pp20) REVERT: D 6 GLU cc_start: 0.8310 (pt0) cc_final: 0.7961 (pt0) REVERT: D 34 MET cc_start: 0.8750 (mtm) cc_final: 0.7788 (mtp) REVERT: D 37 GLU cc_start: 0.6363 (mt-10) cc_final: 0.5834 (mt-10) REVERT: D 75 TRP cc_start: 0.8338 (t-100) cc_final: 0.7563 (t-100) REVERT: D 105 ARG cc_start: 0.8023 (ptp-110) cc_final: 0.7342 (ptp90) REVERT: H 86 ASP cc_start: 0.8551 (m-30) cc_final: 0.8279 (m-30) REVERT: H 96 PHE cc_start: 0.8088 (m-80) cc_final: 0.7785 (m-10) REVERT: L 6 GLN cc_start: 0.7863 (mt0) cc_final: 0.7022 (mp-120) REVERT: L 35 TRP cc_start: 0.9220 (m100) cc_final: 0.8158 (m100) REVERT: L 74 THR cc_start: 0.8216 (p) cc_final: 0.7763 (t) REVERT: L 78 MET cc_start: 0.8767 (tmm) cc_final: 0.8240 (tmm) REVERT: E 47 TRP cc_start: 0.8844 (t60) cc_final: 0.8469 (t60) REVERT: E 67 LEU cc_start: 0.8889 (mm) cc_final: 0.8419 (mm) REVERT: E 76 ASN cc_start: 0.7832 (m-40) cc_final: 0.7328 (m-40) REVERT: E 86 ASP cc_start: 0.9169 (m-30) cc_final: 0.8637 (m-30) REVERT: I 66 ARG cc_start: 0.8081 (tmt170) cc_final: 0.7699 (tmt170) REVERT: I 77 ARG cc_start: 0.8509 (ptp90) cc_final: 0.8295 (ptp-170) REVERT: I 83 PHE cc_start: 0.8077 (m-80) cc_final: 0.7455 (m-80) outliers start: 1 outliers final: 1 residues processed: 363 average time/residue: 0.1100 time to fit residues: 59.4799 Evaluate side-chains 283 residues out of total 1448 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 282 time to evaluate : 0.349 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 157 random chunks: chunk 100 optimal weight: 4.9990 chunk 5 optimal weight: 10.0000 chunk 97 optimal weight: 3.9990 chunk 44 optimal weight: 10.0000 chunk 22 optimal weight: 0.4980 chunk 33 optimal weight: 0.3980 chunk 70 optimal weight: 0.5980 chunk 142 optimal weight: 0.0670 chunk 67 optimal weight: 0.0670 chunk 140 optimal weight: 2.9990 chunk 150 optimal weight: 5.9990 overall best weight: 0.3256 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 92 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 170 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 189 GLN ** b 319 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** b 374 HIS ** A 170 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 189 GLN E 3 GLN I 37 GLN ** I 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3605 r_free = 0.3605 target = 0.091889 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3195 r_free = 0.3195 target = 0.072118 restraints weight = 50148.274| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3243 r_free = 0.3243 target = 0.074332 restraints weight = 33560.128| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3278 r_free = 0.3278 target = 0.075903 restraints weight = 25439.876| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3300 r_free = 0.3300 target = 0.076948 restraints weight = 20924.776| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3314 r_free = 0.3314 target = 0.077647 restraints weight = 18279.545| |-----------------------------------------------------------------------------| r_work (final): 0.3305 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7610 moved from start: 0.4672 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.073 14597 Z= 0.151 Angle : 0.848 11.655 19939 Z= 0.402 Chirality : 0.052 0.421 2415 Planarity : 0.004 0.057 2359 Dihedral : 11.204 79.488 3123 Min Nonbonded Distance : 2.345 Molprobity Statistics. All-atom Clashscore : 14.02 Ramachandran Plot: Outliers : 0.55 % Allowed : 13.14 % Favored : 86.31 % Rotamer: Outliers : 0.00 % Allowed : 2.84 % Favored : 97.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.62 (0.20), residues: 1629 helix: -0.08 (0.30), residues: 302 sheet: -1.02 (0.30), residues: 293 loop : -2.64 (0.18), residues: 1034 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG E 30 TYR 0.023 0.002 TYR A 62 PHE 0.019 0.002 PHE L 83 TRP 0.035 0.002 TRP C 210 HIS 0.016 0.002 HIS B 170 Details of bonding type rmsd/Z covalent geometry : bond 0.00319 / 0.15 (14484) covalent geometry : angle 0.78013 / 0.39 (19626) SS BOND : bond 0.00519 / 0.30 ( 26) SS BOND : angle 1.78309 / 1.07 ( 52) hydrogen bonds : bond 0.04084 / 2.52 ( 333) hydrogen bonds : angle 5.54782 / 3.78 ( 906) link_ALPHA1-2 : bond 0.01162 / 0.60 ( 2) link_ALPHA1-2 : angle 4.06787 / 2.04 ( 6) link_ALPHA1-3 : bond 0.01024 / 0.66 ( 13) link_ALPHA1-3 : angle 2.68126 / 1.79 ( 39) link_ALPHA1-6 : bond 0.01073 / 0.76 ( 10) link_ALPHA1-6 : angle 2.12149 / 1.42 ( 30) link_BETA1-4 : bond 0.00672 / 0.43 ( 27) link_BETA1-4 : angle 2.12455 / 1.35 ( 81) link_NAG-ASN : bond 0.00930 / 0.53 ( 35) link_NAG-ASN : angle 3.56263 / 2.25 ( 105) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3258 Ramachandran restraints generated. 1629 Oldfield, 0 Emsley, 1629 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3258 Ramachandran restraints generated. 1629 Oldfield, 0 Emsley, 1629 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 377 residues out of total 1448 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 377 time to evaluate : 0.494 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: B 82 MET cc_start: 0.7936 (ptt) cc_final: 0.7517 (pmm) REVERT: B 104 GLU cc_start: 0.7959 (tp30) cc_final: 0.7287 (mm-30) REVERT: B 142 LEU cc_start: 0.9117 (mp) cc_final: 0.8732 (tp) REVERT: B 157 PHE cc_start: 0.8612 (m-80) cc_final: 0.8376 (m-80) REVERT: B 194 MET cc_start: 0.8907 (tpp) cc_final: 0.8222 (tmm) REVERT: B 221 ILE cc_start: 0.9155 (mt) cc_final: 0.8926 (mt) REVERT: B 223 GLN cc_start: 0.8027 (mp10) cc_final: 0.7583 (mp10) REVERT: b 270 GLU cc_start: 0.7456 (mp0) cc_final: 0.7206 (tp30) REVERT: b 284 MET cc_start: 0.8292 (mmt) cc_final: 0.7887 (mmp) REVERT: b 311 ASP cc_start: 0.9059 (m-30) cc_final: 0.8738 (m-30) REVERT: b 325 ARG cc_start: 0.7462 (ptp90) cc_final: 0.6971 (ptp90) REVERT: b 346 ASN cc_start: 0.9276 (t0) cc_final: 0.8655 (t0) REVERT: b 351 MET cc_start: 0.9086 (mmm) cc_final: 0.8809 (mmp) REVERT: A 75 MET cc_start: 0.8794 (mtp) cc_final: 0.8416 (ttm) REVERT: A 82 MET cc_start: 0.8722 (pmm) cc_final: 0.8434 (pmm) REVERT: A 140 PHE cc_start: 0.9265 (m-80) cc_final: 0.8780 (m-80) REVERT: A 219 TYR cc_start: 0.7975 (m-80) cc_final: 0.7350 (m-80) REVERT: A 241 TYR cc_start: 0.8604 (t80) cc_final: 0.8270 (t80) REVERT: a 265 THR cc_start: 0.8070 (m) cc_final: 0.7828 (p) REVERT: a 266 LEU cc_start: 0.8693 (mp) cc_final: 0.8442 (tp) REVERT: a 287 GLU cc_start: 0.8161 (mt-10) cc_final: 0.7738 (tm-30) REVERT: a 324 GLN cc_start: 0.9047 (tm-30) cc_final: 0.8737 (tm-30) REVERT: a 363 TYR cc_start: 0.8395 (p90) cc_final: 0.8014 (p90) REVERT: a 404 GLU cc_start: 0.8631 (tp30) cc_final: 0.8368 (tp30) REVERT: C 93 HIS cc_start: 0.8531 (m90) cc_final: 0.7984 (m-70) REVERT: C 259 ARG cc_start: 0.8290 (mmm-85) cc_final: 0.8041 (mmm-85) REVERT: c 268 ASP cc_start: 0.7747 (p0) cc_final: 0.7307 (p0) REVERT: c 282 ARG cc_start: 0.8358 (ttt180) cc_final: 0.7156 (ptp-170) REVERT: c 289 GLU cc_start: 0.8038 (tt0) cc_final: 0.7822 (tt0) REVERT: c 312 MET cc_start: 0.8224 (mmm) cc_final: 0.7672 (mmm) REVERT: c 314 ARG cc_start: 0.9017 (mtt90) cc_final: 0.8578 (ttm110) REVERT: c 320 LYS cc_start: 0.9379 (ttpt) cc_final: 0.8927 (ttmt) REVERT: c 349 LEU cc_start: 0.9182 (tp) cc_final: 0.8860 (tt) REVERT: c 359 MET cc_start: 0.8986 (mmm) cc_final: 0.8456 (mmm) REVERT: c 369 TYR cc_start: 0.8660 (m-80) cc_final: 0.6718 (m-80) REVERT: c 387 LEU cc_start: 0.9334 (mt) cc_final: 0.8884 (mp) REVERT: c 403 ILE cc_start: 0.8870 (mm) cc_final: 0.8638 (mt) REVERT: D 6 GLU cc_start: 0.8114 (pt0) cc_final: 0.7319 (pt0) REVERT: D 30 SER cc_start: 0.7910 (p) cc_final: 0.7693 (m) REVERT: D 34 MET cc_start: 0.8680 (mtm) cc_final: 0.7906 (mtp) REVERT: D 36 TRP cc_start: 0.8069 (m100) cc_final: 0.7724 (m100) REVERT: D 37 GLU cc_start: 0.6485 (mt-10) cc_final: 0.5851 (mt-10) REVERT: D 75 TRP cc_start: 0.8248 (t-100) cc_final: 0.7725 (t-100) REVERT: D 105 ARG cc_start: 0.7832 (ptp-110) cc_final: 0.7103 (ptp-170) REVERT: H 86 ASP cc_start: 0.8392 (m-30) cc_final: 0.8140 (m-30) REVERT: H 96 PHE cc_start: 0.7950 (m-80) cc_final: 0.7514 (m-80) REVERT: H 101 ASP cc_start: 0.8212 (p0) cc_final: 0.7903 (p0) REVERT: L 6 GLN cc_start: 0.7722 (mt0) cc_final: 0.6966 (mp-120) REVERT: L 31 ASP cc_start: 0.8601 (p0) cc_final: 0.8378 (p0) REVERT: L 35 TRP cc_start: 0.9053 (m100) cc_final: 0.7955 (m100) REVERT: L 74 THR cc_start: 0.8166 (p) cc_final: 0.7688 (t) REVERT: E 3 GLN cc_start: 0.7603 (tm130) cc_final: 0.7397 (tm-30) REVERT: E 47 TRP cc_start: 0.8763 (t60) cc_final: 0.8436 (t60) REVERT: E 67 LEU cc_start: 0.8866 (mm) cc_final: 0.8370 (mm) REVERT: E 76 ASN cc_start: 0.7731 (m-40) cc_final: 0.7237 (m-40) REVERT: E 86 ASP cc_start: 0.9122 (m-30) cc_final: 0.8607 (m-30) REVERT: I 78 MET cc_start: 0.8676 (tpt) cc_final: 0.8423 (tpt) REVERT: I 83 PHE cc_start: 0.7700 (m-80) cc_final: 0.7419 (m-80) outliers start: 0 outliers final: 0 residues processed: 377 average time/residue: 0.1157 time to fit residues: 64.4575 Evaluate side-chains 295 residues out of total 1448 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 295 time to evaluate : 0.531 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 157 random chunks: chunk 112 optimal weight: 9.9990 chunk 105 optimal weight: 30.0000 chunk 141 optimal weight: 6.9990 chunk 118 optimal weight: 4.9990 chunk 109 optimal weight: 5.9990 chunk 45 optimal weight: 10.0000 chunk 18 optimal weight: 0.6980 chunk 121 optimal weight: 0.0770 chunk 99 optimal weight: 2.9990 chunk 0 optimal weight: 9.9990 chunk 6 optimal weight: 0.9990 overall best weight: 1.9544 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 92 HIS B 141 HIS ** B 170 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 189 GLN B 230 HIS b 305 HIS ** b 319 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** b 405 GLN b 406 GLN ** A 170 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 189 GLN ** E 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3542 r_free = 0.3542 target = 0.088286 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3115 r_free = 0.3115 target = 0.068293 restraints weight = 50980.106| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3166 r_free = 0.3166 target = 0.070808 restraints weight = 34423.878| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3189 r_free = 0.3189 target = 0.071784 restraints weight = 24118.645| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3214 r_free = 0.3214 target = 0.072782 restraints weight = 20793.580| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3218 r_free = 0.3218 target = 0.072933 restraints weight = 18632.400| |-----------------------------------------------------------------------------| r_work (final): 0.3209 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7753 moved from start: 0.5025 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 14597 Z= 0.200 Angle : 0.868 13.430 19939 Z= 0.413 Chirality : 0.052 0.371 2415 Planarity : 0.005 0.064 2359 Dihedral : 10.812 76.577 3123 Min Nonbonded Distance : 2.321 Molprobity Statistics. All-atom Clashscore : 16.34 Ramachandran Plot: Outliers : 0.55 % Allowed : 14.18 % Favored : 85.27 % Rotamer: Outliers : 0.00 % Allowed : 2.35 % Favored : 97.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.56 (0.20), residues: 1629 helix: -0.02 (0.30), residues: 298 sheet: -0.95 (0.30), residues: 302 loop : -2.62 (0.19), residues: 1029 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG a 282 TYR 0.021 0.002 TYR A 62 PHE 0.032 0.002 PHE A 140 TRP 0.031 0.002 TRP C 210 HIS 0.015 0.002 HIS B 170 Details of bonding type rmsd/Z covalent geometry : bond 0.00436 / 0.20 (14484) covalent geometry : angle 0.80368 / 0.40 (19626) SS BOND : bond 0.00649 / 0.36 ( 26) SS BOND : angle 1.57573 / 0.93 ( 52) hydrogen bonds : bond 0.04221 / 2.59 ( 333) hydrogen bonds : angle 5.57552 / 3.82 ( 906) link_ALPHA1-2 : bond 0.00820 / 0.41 ( 2) link_ALPHA1-2 : angle 3.47232 / 1.71 ( 6) link_ALPHA1-3 : bond 0.00862 / 0.57 ( 13) link_ALPHA1-3 : angle 2.67426 / 1.78 ( 39) link_ALPHA1-6 : bond 0.00993 / 0.71 ( 10) link_ALPHA1-6 : angle 2.21711 / 1.46 ( 30) link_BETA1-4 : bond 0.00681 / 0.45 ( 27) link_BETA1-4 : angle 2.08579 / 1.32 ( 81) link_NAG-ASN : bond 0.00798 / 0.47 ( 35) link_NAG-ASN : angle 3.62673 / 2.25 ( 105) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3258 Ramachandran restraints generated. 1629 Oldfield, 0 Emsley, 1629 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3258 Ramachandran restraints generated. 1629 Oldfield, 0 Emsley, 1629 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 353 residues out of total 1448 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 353 time to evaluate : 0.534 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: B 142 LEU cc_start: 0.9122 (mp) cc_final: 0.8830 (tp) REVERT: B 157 PHE cc_start: 0.8688 (m-80) cc_final: 0.8388 (m-80) REVERT: B 185 ASN cc_start: 0.8540 (p0) cc_final: 0.8332 (p0) REVERT: b 270 GLU cc_start: 0.7640 (mp0) cc_final: 0.7162 (tp30) REVERT: b 284 MET cc_start: 0.8451 (mmt) cc_final: 0.8107 (mmp) REVERT: b 311 ASP cc_start: 0.8936 (m-30) cc_final: 0.8662 (m-30) REVERT: b 325 ARG cc_start: 0.7608 (ptp90) cc_final: 0.7194 (ptp90) REVERT: b 346 ASN cc_start: 0.9359 (t0) cc_final: 0.8717 (t0) REVERT: b 351 MET cc_start: 0.9210 (mmm) cc_final: 0.8872 (mmp) REVERT: b 414 MET cc_start: 0.8868 (tmm) cc_final: 0.8147 (tmm) REVERT: A 72 GLU cc_start: 0.8926 (mm-30) cc_final: 0.8641 (tp30) REVERT: A 75 MET cc_start: 0.8992 (mtp) cc_final: 0.8581 (ttm) REVERT: A 76 GLU cc_start: 0.8808 (tt0) cc_final: 0.7837 (tp30) REVERT: A 82 MET cc_start: 0.8887 (pmm) cc_final: 0.8609 (pmm) REVERT: A 134 MET cc_start: 0.8758 (mmm) cc_final: 0.8304 (mmm) REVERT: A 219 TYR cc_start: 0.8048 (m-80) cc_final: 0.7608 (m-80) REVERT: a 265 THR cc_start: 0.8159 (m) cc_final: 0.7726 (p) REVERT: a 266 LEU cc_start: 0.8591 (mp) cc_final: 0.8349 (tp) REVERT: a 324 GLN cc_start: 0.9060 (tm-30) cc_final: 0.8745 (tm-30) REVERT: a 363 TYR cc_start: 0.8569 (p90) cc_final: 0.8221 (p90) REVERT: a 404 GLU cc_start: 0.8728 (tp30) cc_final: 0.8515 (tp30) REVERT: C 192 MET cc_start: 0.8653 (mmt) cc_final: 0.8291 (mmt) REVERT: C 241 TYR cc_start: 0.9315 (t80) cc_final: 0.9073 (t80) REVERT: c 268 ASP cc_start: 0.7782 (p0) cc_final: 0.7392 (p0) REVERT: c 282 ARG cc_start: 0.8574 (ttt180) cc_final: 0.7382 (ptp-170) REVERT: c 314 ARG cc_start: 0.9051 (mtt90) cc_final: 0.8671 (ttm110) REVERT: c 320 LYS cc_start: 0.9393 (ttpt) cc_final: 0.8921 (ttmt) REVERT: c 349 LEU cc_start: 0.9271 (tp) cc_final: 0.8967 (tt) REVERT: c 359 MET cc_start: 0.9123 (mmm) cc_final: 0.8573 (mmm) REVERT: c 369 TYR cc_start: 0.8797 (m-80) cc_final: 0.6723 (m-80) REVERT: c 387 LEU cc_start: 0.9376 (mt) cc_final: 0.8960 (mp) REVERT: c 401 ASP cc_start: 0.8989 (p0) cc_final: 0.8323 (p0) REVERT: c 402 ASP cc_start: 0.9165 (t0) cc_final: 0.8936 (t0) REVERT: c 404 GLU cc_start: 0.9468 (mp0) cc_final: 0.9152 (pp20) REVERT: D 6 GLU cc_start: 0.8264 (pt0) cc_final: 0.7788 (pt0) REVERT: D 37 GLU cc_start: 0.6583 (mt-10) cc_final: 0.5987 (mt-10) REVERT: D 104 LEU cc_start: 0.8011 (pp) cc_final: 0.7692 (pp) REVERT: H 86 ASP cc_start: 0.8609 (m-30) cc_final: 0.8284 (m-30) REVERT: H 96 PHE cc_start: 0.8178 (m-80) cc_final: 0.7626 (m-80) REVERT: L 6 GLN cc_start: 0.7902 (mt0) cc_final: 0.6854 (mp-120) REVERT: L 23 CYS cc_start: 0.5931 (t) cc_final: 0.4168 (t) REVERT: L 35 TRP cc_start: 0.9275 (m100) cc_final: 0.8160 (m100) REVERT: L 73 LEU cc_start: 0.9353 (tp) cc_final: 0.9068 (tp) REVERT: L 74 THR cc_start: 0.8309 (p) cc_final: 0.7966 (t) REVERT: L 83 PHE cc_start: 0.7706 (m-80) cc_final: 0.7337 (m-80) REVERT: L 102 THR cc_start: 0.9085 (p) cc_final: 0.8833 (p) REVERT: E 3 GLN cc_start: 0.7704 (tm-30) cc_final: 0.7455 (tm-30) REVERT: E 47 TRP cc_start: 0.8980 (t60) cc_final: 0.7910 (t60) REVERT: E 50 TYR cc_start: 0.8740 (p90) cc_final: 0.7811 (p90) REVERT: E 67 LEU cc_start: 0.8980 (mm) cc_final: 0.8414 (mm) REVERT: E 76 ASN cc_start: 0.7973 (m-40) cc_final: 0.7746 (m-40) REVERT: E 86 ASP cc_start: 0.9214 (m-30) cc_final: 0.8688 (m-30) REVERT: E 100 ASP cc_start: 0.7762 (t70) cc_final: 0.7422 (t0) REVERT: I 37 GLN cc_start: 0.8222 (pp30) cc_final: 0.7880 (tm-30) REVERT: I 66 ARG cc_start: 0.8049 (tmt170) cc_final: 0.7762 (tmt170) REVERT: I 83 PHE cc_start: 0.8039 (m-80) cc_final: 0.7602 (m-80) outliers start: 0 outliers final: 0 residues processed: 353 average time/residue: 0.1161 time to fit residues: 60.3319 Evaluate side-chains 265 residues out of total 1448 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 265 time to evaluate : 0.554 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 157 random chunks: chunk 145 optimal weight: 9.9990 chunk 116 optimal weight: 0.3980 chunk 56 optimal weight: 1.9990 chunk 96 optimal weight: 2.9990 chunk 78 optimal weight: 0.4980 chunk 40 optimal weight: 10.0000 chunk 84 optimal weight: 20.0000 chunk 47 optimal weight: 0.0970 chunk 22 optimal weight: 1.9990 chunk 46 optimal weight: 10.0000 chunk 24 optimal weight: 9.9990 overall best weight: 0.9982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 170 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 189 GLN ** b 319 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** b 348 GLN b 405 GLN ** A 170 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 93 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 124 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 189 GLN ** E 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3570 r_free = 0.3570 target = 0.089939 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3165 r_free = 0.3165 target = 0.070789 restraints weight = 50313.895| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3197 r_free = 0.3197 target = 0.072306 restraints weight = 35423.614| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3224 r_free = 0.3224 target = 0.073541 restraints weight = 25743.606| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3236 r_free = 0.3236 target = 0.074062 restraints weight = 23376.172| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3239 r_free = 0.3239 target = 0.074179 restraints weight = 20918.867| |-----------------------------------------------------------------------------| r_work (final): 0.3229 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7721 moved from start: 0.5246 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 14597 Z= 0.154 Angle : 0.827 12.155 19939 Z= 0.395 Chirality : 0.051 0.389 2415 Planarity : 0.005 0.119 2359 Dihedral : 10.197 73.646 3123 Min Nonbonded Distance : 2.330 Molprobity Statistics. All-atom Clashscore : 15.87 Ramachandran Plot: Outliers : 0.55 % Allowed : 13.26 % Favored : 86.19 % Rotamer: Outliers : 0.00 % Allowed : 2.08 % Favored : 97.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.48 (0.21), residues: 1629 helix: 0.13 (0.31), residues: 298 sheet: -0.89 (0.31), residues: 292 loop : -2.59 (0.19), residues: 1039 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG E 30 TYR 0.020 0.002 TYR A 241 PHE 0.020 0.001 PHE I 83 TRP 0.039 0.002 TRP C 210 HIS 0.012 0.001 HIS B 170 Details of bonding type rmsd/Z covalent geometry : bond 0.00331 / 0.15 (14484) covalent geometry : angle 0.76716 / 0.38 (19626) SS BOND : bond 0.00548 / 0.32 ( 26) SS BOND : angle 1.30061 / 0.78 ( 52) hydrogen bonds : bond 0.04030 / 2.42 ( 333) hydrogen bonds : angle 5.40410 / 3.69 ( 906) link_ALPHA1-2 : bond 0.01032 / 0.53 ( 2) link_ALPHA1-2 : angle 3.49763 / 1.75 ( 6) link_ALPHA1-3 : bond 0.00958 / 0.62 ( 13) link_ALPHA1-3 : angle 2.65266 / 1.76 ( 39) link_ALPHA1-6 : bond 0.01049 / 0.73 ( 10) link_ALPHA1-6 : angle 2.08357 / 1.38 ( 30) link_BETA1-4 : bond 0.00616 / 0.39 ( 27) link_BETA1-4 : angle 1.93267 / 1.22 ( 81) link_NAG-ASN : bond 0.00780 / 0.46 ( 35) link_NAG-ASN : angle 3.41520 / 2.12 ( 105) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3258 Ramachandran restraints generated. 1629 Oldfield, 0 Emsley, 1629 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3258 Ramachandran restraints generated. 1629 Oldfield, 0 Emsley, 1629 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 347 residues out of total 1448 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 347 time to evaluate : 0.384 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: B 142 LEU cc_start: 0.9064 (mp) cc_final: 0.8742 (tp) REVERT: B 153 MET cc_start: 0.7867 (tpp) cc_final: 0.7666 (tpp) REVERT: B 157 PHE cc_start: 0.8609 (m-80) cc_final: 0.8321 (m-80) REVERT: b 270 GLU cc_start: 0.7559 (mp0) cc_final: 0.7214 (tp30) REVERT: b 284 MET cc_start: 0.8525 (mmt) cc_final: 0.8184 (mmp) REVERT: b 311 ASP cc_start: 0.8981 (m-30) cc_final: 0.8756 (m-30) REVERT: b 317 ASP cc_start: 0.8899 (t0) cc_final: 0.8621 (t70) REVERT: b 325 ARG cc_start: 0.7599 (ptp90) cc_final: 0.7227 (ptp90) REVERT: b 346 ASN cc_start: 0.9389 (t0) cc_final: 0.8755 (t0) REVERT: b 351 MET cc_start: 0.9311 (mmt) cc_final: 0.9025 (mmp) REVERT: b 369 TYR cc_start: 0.8719 (m-80) cc_final: 0.7869 (m-10) REVERT: b 416 GLN cc_start: 0.9112 (tp-100) cc_final: 0.8876 (tp-100) REVERT: A 72 GLU cc_start: 0.8816 (mm-30) cc_final: 0.8585 (tp30) REVERT: A 75 MET cc_start: 0.8838 (mtp) cc_final: 0.8601 (ttm) REVERT: A 76 GLU cc_start: 0.8741 (tt0) cc_final: 0.7820 (tp30) REVERT: A 82 MET cc_start: 0.8951 (pmm) cc_final: 0.8692 (pmm) REVERT: A 104 GLU cc_start: 0.6854 (tt0) cc_final: 0.6150 (tt0) REVERT: A 191 PHE cc_start: 0.8226 (t80) cc_final: 0.7905 (t80) REVERT: A 219 TYR cc_start: 0.8021 (m-80) cc_final: 0.7550 (m-80) REVERT: A 241 TYR cc_start: 0.8784 (t80) cc_final: 0.8390 (t80) REVERT: a 265 THR cc_start: 0.8160 (m) cc_final: 0.7674 (p) REVERT: a 266 LEU cc_start: 0.8628 (mp) cc_final: 0.8297 (tp) REVERT: a 347 ASP cc_start: 0.8535 (m-30) cc_final: 0.8160 (t0) REVERT: a 363 TYR cc_start: 0.8530 (p90) cc_final: 0.8218 (p90) REVERT: a 404 GLU cc_start: 0.8737 (tp30) cc_final: 0.8467 (tp30) REVERT: C 82 MET cc_start: 0.8507 (mmm) cc_final: 0.8263 (mmm) REVERT: C 164 VAL cc_start: 0.8417 (t) cc_final: 0.8061 (t) REVERT: C 192 MET cc_start: 0.8542 (mmt) cc_final: 0.8109 (mmt) REVERT: c 268 ASP cc_start: 0.7668 (p0) cc_final: 0.7214 (p0) REVERT: c 282 ARG cc_start: 0.8517 (ttt180) cc_final: 0.7308 (ptp-170) REVERT: c 314 ARG cc_start: 0.8947 (mtt90) cc_final: 0.8579 (ttm110) REVERT: c 320 LYS cc_start: 0.9403 (ttpt) cc_final: 0.8917 (ttmt) REVERT: c 359 MET cc_start: 0.9089 (mmm) cc_final: 0.8456 (mmm) REVERT: c 369 TYR cc_start: 0.8800 (m-80) cc_final: 0.6848 (m-80) REVERT: c 387 LEU cc_start: 0.9305 (mt) cc_final: 0.8802 (mt) REVERT: c 403 ILE cc_start: 0.9038 (mm) cc_final: 0.8797 (mt) REVERT: D 6 GLU cc_start: 0.8133 (pt0) cc_final: 0.7899 (pt0) REVERT: D 37 GLU cc_start: 0.6448 (mt-10) cc_final: 0.5999 (mt-10) REVERT: H 86 ASP cc_start: 0.8463 (m-30) cc_final: 0.8244 (m-30) REVERT: H 96 PHE cc_start: 0.7968 (m-80) cc_final: 0.7592 (m-10) REVERT: H 101 ASP cc_start: 0.8003 (p0) cc_final: 0.7698 (p0) REVERT: L 6 GLN cc_start: 0.7860 (mt0) cc_final: 0.7132 (mp-120) REVERT: L 31 ASP cc_start: 0.8460 (p0) cc_final: 0.8177 (p0) REVERT: L 35 TRP cc_start: 0.9192 (m100) cc_final: 0.8117 (m100) REVERT: L 74 THR cc_start: 0.8227 (p) cc_final: 0.7834 (t) REVERT: E 3 GLN cc_start: 0.7638 (tm-30) cc_final: 0.7408 (tm-30) REVERT: E 47 TRP cc_start: 0.8818 (t60) cc_final: 0.7757 (t60) REVERT: E 50 TYR cc_start: 0.8634 (p90) cc_final: 0.8336 (p90) REVERT: E 67 LEU cc_start: 0.8961 (mm) cc_final: 0.8437 (mm) REVERT: E 76 ASN cc_start: 0.7772 (m-40) cc_final: 0.7571 (m-40) REVERT: E 86 ASP cc_start: 0.9166 (m-30) cc_final: 0.8654 (m-30) REVERT: I 37 GLN cc_start: 0.8325 (pp30) cc_final: 0.8009 (tm-30) outliers start: 0 outliers final: 0 residues processed: 347 average time/residue: 0.1063 time to fit residues: 54.2543 Evaluate side-chains 270 residues out of total 1448 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 270 time to evaluate : 0.550 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 157 random chunks: chunk 119 optimal weight: 5.9990 chunk 36 optimal weight: 2.9990 chunk 105 optimal weight: 0.8980 chunk 135 optimal weight: 0.7980 chunk 118 optimal weight: 0.7980 chunk 102 optimal weight: 10.0000 chunk 113 optimal weight: 9.9990 chunk 27 optimal weight: 0.3980 chunk 108 optimal weight: 9.9990 chunk 139 optimal weight: 1.9990 chunk 49 optimal weight: 8.9990 overall best weight: 0.9782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 170 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 247 GLN b 305 HIS ** b 319 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 170 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 93 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 124 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 3 GLN ** I 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3574 r_free = 0.3574 target = 0.090004 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3145 r_free = 0.3145 target = 0.069714 restraints weight = 50465.805| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3197 r_free = 0.3197 target = 0.072057 restraints weight = 33003.618| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3230 r_free = 0.3230 target = 0.073603 restraints weight = 24624.983| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3258 r_free = 0.3258 target = 0.074825 restraints weight = 20171.714| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 40)----------------| | r_work = 0.3277 r_free = 0.3277 target = 0.075684 restraints weight = 17319.040| |-----------------------------------------------------------------------------| r_work (final): 0.3268 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7669 moved from start: 0.5386 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 14597 Z= 0.156 Angle : 0.844 11.081 19939 Z= 0.403 Chirality : 0.051 0.379 2415 Planarity : 0.005 0.094 2359 Dihedral : 9.896 71.492 3123 Min Nonbonded Distance : 2.323 Molprobity Statistics. All-atom Clashscore : 15.83 Ramachandran Plot: Outliers : 0.55 % Allowed : 13.87 % Favored : 85.57 % Rotamer: Outliers : 0.00 % Allowed : 1.11 % Favored : 98.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.42 (0.21), residues: 1629 helix: 0.09 (0.31), residues: 299 sheet: -0.82 (0.31), residues: 292 loop : -2.53 (0.19), residues: 1038 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG C 259 TYR 0.035 0.002 TYR A 62 PHE 0.031 0.002 PHE B 191 TRP 0.049 0.002 TRP C 210 HIS 0.012 0.002 HIS B 170 Details of bonding type rmsd/Z covalent geometry : bond 0.00338 / 0.15 (14484) covalent geometry : angle 0.78148 / 0.39 (19626) SS BOND : bond 0.00487 / 0.29 ( 26) SS BOND : angle 1.45520 / 0.85 ( 52) hydrogen bonds : bond 0.04029 / 2.44 ( 333) hydrogen bonds : angle 5.36433 / 3.69 ( 906) link_ALPHA1-2 : bond 0.00949 / 0.49 ( 2) link_ALPHA1-2 : angle 3.44318 / 1.73 ( 6) link_ALPHA1-3 : bond 0.00941 / 0.61 ( 13) link_ALPHA1-3 : angle 2.62017 / 1.73 ( 39) link_ALPHA1-6 : bond 0.01072 / 0.75 ( 10) link_ALPHA1-6 : angle 2.05953 / 1.36 ( 30) link_BETA1-4 : bond 0.00616 / 0.40 ( 27) link_BETA1-4 : angle 1.89281 / 1.19 ( 81) link_NAG-ASN : bond 0.00777 / 0.46 ( 35) link_NAG-ASN : angle 3.60431 / 2.30 ( 105) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3258 Ramachandran restraints generated. 1629 Oldfield, 0 Emsley, 1629 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3258 Ramachandran restraints generated. 1629 Oldfield, 0 Emsley, 1629 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 342 residues out of total 1448 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 342 time to evaluate : 0.573 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: B 82 MET cc_start: 0.8115 (ptt) cc_final: 0.7372 (pmm) REVERT: B 142 LEU cc_start: 0.9061 (mp) cc_final: 0.8730 (tp) REVERT: B 150 TYR cc_start: 0.7071 (m-80) cc_final: 0.6775 (m-80) REVERT: B 157 PHE cc_start: 0.8635 (m-80) cc_final: 0.8331 (m-80) REVERT: b 270 GLU cc_start: 0.7481 (mp0) cc_final: 0.7220 (tp30) REVERT: b 284 MET cc_start: 0.8419 (mmt) cc_final: 0.8130 (mmp) REVERT: b 311 ASP cc_start: 0.9002 (m-30) cc_final: 0.8791 (m-30) REVERT: b 317 ASP cc_start: 0.8983 (t0) cc_final: 0.8636 (t70) REVERT: b 325 ARG cc_start: 0.7698 (ptp90) cc_final: 0.7328 (ptp90) REVERT: b 346 ASN cc_start: 0.9291 (t0) cc_final: 0.8708 (t0) REVERT: b 348 GLN cc_start: 0.8082 (pt0) cc_final: 0.7785 (mp10) REVERT: b 351 MET cc_start: 0.9357 (mmt) cc_final: 0.9056 (mmp) REVERT: b 369 TYR cc_start: 0.8787 (m-80) cc_final: 0.7979 (m-10) REVERT: A 72 GLU cc_start: 0.8809 (mm-30) cc_final: 0.8523 (tp30) REVERT: A 75 MET cc_start: 0.8866 (mtp) cc_final: 0.8531 (ttm) REVERT: A 76 GLU cc_start: 0.8881 (tt0) cc_final: 0.7906 (tp30) REVERT: A 82 MET cc_start: 0.8993 (pmm) cc_final: 0.8659 (pmm) REVERT: A 241 TYR cc_start: 0.8856 (t80) cc_final: 0.8486 (t80) REVERT: a 265 THR cc_start: 0.8142 (m) cc_final: 0.7674 (p) REVERT: a 266 LEU cc_start: 0.8505 (mp) cc_final: 0.8196 (tp) REVERT: a 347 ASP cc_start: 0.8513 (m-30) cc_final: 0.8091 (t0) REVERT: a 363 TYR cc_start: 0.8503 (p90) cc_final: 0.8082 (p90) REVERT: C 82 MET cc_start: 0.8450 (mmm) cc_final: 0.8185 (mmm) REVERT: C 164 VAL cc_start: 0.8159 (t) cc_final: 0.7901 (t) REVERT: C 192 MET cc_start: 0.8607 (mmt) cc_final: 0.8154 (mmt) REVERT: c 268 ASP cc_start: 0.7842 (p0) cc_final: 0.7350 (p0) REVERT: c 282 ARG cc_start: 0.8436 (ttt180) cc_final: 0.7210 (ptp-170) REVERT: c 311 ASP cc_start: 0.9112 (m-30) cc_final: 0.8812 (m-30) REVERT: c 320 LYS cc_start: 0.9389 (ttpt) cc_final: 0.8902 (ttmt) REVERT: c 321 GLN cc_start: 0.8933 (mm-40) cc_final: 0.8675 (mm110) REVERT: c 359 MET cc_start: 0.9043 (mmm) cc_final: 0.8551 (mmm) REVERT: c 369 TYR cc_start: 0.8734 (m-80) cc_final: 0.6791 (m-80) REVERT: c 387 LEU cc_start: 0.9305 (mt) cc_final: 0.8803 (mt) REVERT: c 403 ILE cc_start: 0.8954 (mm) cc_final: 0.8716 (mt) REVERT: D 6 GLU cc_start: 0.8366 (pt0) cc_final: 0.7742 (pt0) REVERT: D 37 GLU cc_start: 0.6212 (mt-10) cc_final: 0.5815 (mt-10) REVERT: D 75 TRP cc_start: 0.8364 (t-100) cc_final: 0.7741 (t-100) REVERT: H 86 ASP cc_start: 0.8456 (m-30) cc_final: 0.8178 (m-30) REVERT: H 96 PHE cc_start: 0.8021 (m-80) cc_final: 0.7448 (m-80) REVERT: L 6 GLN cc_start: 0.7935 (mt0) cc_final: 0.7274 (mp-120) REVERT: L 31 ASP cc_start: 0.8586 (p0) cc_final: 0.8356 (p0) REVERT: L 35 TRP cc_start: 0.9224 (m100) cc_final: 0.8111 (m100) REVERT: L 74 THR cc_start: 0.8321 (p) cc_final: 0.7876 (t) REVERT: L 83 PHE cc_start: 0.7732 (m-80) cc_final: 0.7418 (m-80) REVERT: E 3 GLN cc_start: 0.7687 (tm130) cc_final: 0.7368 (tm-30) REVERT: E 67 LEU cc_start: 0.8972 (mm) cc_final: 0.8475 (mm) REVERT: E 76 ASN cc_start: 0.7766 (m-40) cc_final: 0.7546 (m-40) REVERT: E 86 ASP cc_start: 0.9199 (m-30) cc_final: 0.8682 (m-30) REVERT: I 37 GLN cc_start: 0.8176 (pp30) cc_final: 0.7891 (tm-30) REVERT: I 83 PHE cc_start: 0.8178 (m-80) cc_final: 0.7677 (m-80) outliers start: 0 outliers final: 0 residues processed: 342 average time/residue: 0.0897 time to fit residues: 46.1787 Evaluate side-chains 268 residues out of total 1448 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 268 time to evaluate : 0.385 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 157 random chunks: chunk 76 optimal weight: 4.9990 chunk 63 optimal weight: 1.9990 chunk 114 optimal weight: 1.9990 chunk 116 optimal weight: 0.0010 chunk 45 optimal weight: 0.7980 chunk 129 optimal weight: 8.9990 chunk 97 optimal weight: 1.9990 chunk 69 optimal weight: 9.9990 chunk 140 optimal weight: 0.8980 chunk 15 optimal weight: 4.9990 chunk 43 optimal weight: 5.9990 overall best weight: 1.1390 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 170 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 319 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 170 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 93 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 124 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 77 GLN ** I 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 90 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 = 0.3565 r_free = 0.3565 target = 0.089522 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3132 r_free = 0.3132 target = 0.069087 restraints weight = 50480.735| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3184 r_free = 0.3184 target = 0.071391 restraints weight = 33162.864| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3219 r_free = 0.3219 target = 0.072972 restraints weight = 24850.100| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3245 r_free = 0.3245 target = 0.074137 restraints weight = 20403.504| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.3263 r_free = 0.3263 target = 0.074957 restraints weight = 17612.417| |-----------------------------------------------------------------------------| r_work (final): 0.3256 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7688 moved from start: 0.5577 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 14597 Z= 0.162 Angle : 0.857 12.447 19939 Z= 0.409 Chirality : 0.051 0.398 2415 Planarity : 0.005 0.087 2359 Dihedral : 9.653 69.271 3123 Min Nonbonded Distance : 2.324 Molprobity Statistics. All-atom Clashscore : 15.94 Ramachandran Plot: Outliers : 0.49 % Allowed : 14.18 % Favored : 85.33 % Rotamer: Outliers : 0.00 % Allowed : 0.48 % Favored : 99.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.42 (0.21), residues: 1629 helix: 0.09 (0.31), residues: 298 sheet: -0.80 (0.32), residues: 292 loop : -2.54 (0.19), residues: 1039 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG C 259 TYR 0.023 0.002 TYR A 62 PHE 0.021 0.002 PHE L 83 TRP 0.052 0.002 TRP C 210 HIS 0.013 0.002 HIS B 93 Details of bonding type rmsd/Z covalent geometry : bond 0.00349 / 0.16 (14484) covalent geometry : angle 0.79257 / 0.39 (19626) SS BOND : bond 0.00564 / 0.37 ( 26) SS BOND : angle 2.16500 / 1.23 ( 52) hydrogen bonds : bond 0.03900 / 2.38 ( 333) hydrogen bonds : angle 5.39866 / 3.72 ( 906) link_ALPHA1-2 : bond 0.00947 / 0.49 ( 2) link_ALPHA1-2 : angle 3.30196 / 1.65 ( 6) link_ALPHA1-3 : bond 0.00916 / 0.60 ( 13) link_ALPHA1-3 : angle 2.60022 / 1.72 ( 39) link_ALPHA1-6 : bond 0.01050 / 0.75 ( 10) link_ALPHA1-6 : angle 2.07627 / 1.36 ( 30) link_BETA1-4 : bond 0.00566 / 0.37 ( 27) link_BETA1-4 : angle 1.87223 / 1.18 ( 81) link_NAG-ASN : bond 0.00817 / 0.46 ( 35) link_NAG-ASN : angle 3.56247 / 2.25 ( 105) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3258 Ramachandran restraints generated. 1629 Oldfield, 0 Emsley, 1629 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3258 Ramachandran restraints generated. 1629 Oldfield, 0 Emsley, 1629 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 328 residues out of total 1448 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 328 time to evaluate : 0.534 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: B 82 MET cc_start: 0.8130 (ptt) cc_final: 0.7364 (pmm) REVERT: B 142 LEU cc_start: 0.9074 (mp) cc_final: 0.8791 (tp) REVERT: B 157 PHE cc_start: 0.8576 (m-80) cc_final: 0.8228 (m-80) REVERT: b 270 GLU cc_start: 0.7486 (mp0) cc_final: 0.7233 (tp30) REVERT: b 284 MET cc_start: 0.8392 (mmt) cc_final: 0.8131 (mmp) REVERT: b 317 ASP cc_start: 0.8910 (t0) cc_final: 0.8570 (t70) REVERT: b 325 ARG cc_start: 0.7467 (ptp90) cc_final: 0.6906 (ptp90) REVERT: b 346 ASN cc_start: 0.9288 (t0) cc_final: 0.8725 (t0) REVERT: b 348 GLN cc_start: 0.8051 (pt0) cc_final: 0.7757 (mp10) REVERT: b 351 MET cc_start: 0.9364 (mmt) cc_final: 0.9104 (mmp) REVERT: b 369 TYR cc_start: 0.8776 (m-80) cc_final: 0.8088 (m-10) REVERT: b 410 MET cc_start: 0.9356 (mmm) cc_final: 0.9141 (mmm) REVERT: A 72 GLU cc_start: 0.8841 (mm-30) cc_final: 0.8516 (tp30) REVERT: A 75 MET cc_start: 0.8932 (mtp) cc_final: 0.8518 (ttm) REVERT: A 76 GLU cc_start: 0.8870 (tt0) cc_final: 0.7876 (tp30) REVERT: A 82 MET cc_start: 0.8927 (pmm) cc_final: 0.8702 (pmm) REVERT: A 104 GLU cc_start: 0.6102 (tt0) cc_final: 0.5898 (tt0) REVERT: A 134 MET cc_start: 0.8435 (mmm) cc_final: 0.7947 (mmm) REVERT: A 219 TYR cc_start: 0.8056 (m-80) cc_final: 0.7502 (m-80) REVERT: A 241 TYR cc_start: 0.8877 (t80) cc_final: 0.8547 (t80) REVERT: a 264 TRP cc_start: 0.6831 (m100) cc_final: 0.6106 (m-90) REVERT: a 265 THR cc_start: 0.8214 (m) cc_final: 0.7779 (p) REVERT: a 266 LEU cc_start: 0.8513 (mp) cc_final: 0.8255 (tp) REVERT: a 347 ASP cc_start: 0.8381 (m-30) cc_final: 0.8063 (t0) REVERT: a 363 TYR cc_start: 0.8541 (p90) cc_final: 0.8075 (p90) REVERT: C 82 MET cc_start: 0.8452 (mmm) cc_final: 0.8247 (mmm) REVERT: C 164 VAL cc_start: 0.8157 (t) cc_final: 0.7909 (t) REVERT: C 192 MET cc_start: 0.8622 (mmt) cc_final: 0.8142 (mmt) REVERT: c 268 ASP cc_start: 0.7696 (p0) cc_final: 0.7239 (p0) REVERT: c 311 ASP cc_start: 0.9093 (m-30) cc_final: 0.8785 (m-30) REVERT: c 320 LYS cc_start: 0.9380 (ttpt) cc_final: 0.8912 (ttmt) REVERT: c 321 GLN cc_start: 0.8941 (mm-40) cc_final: 0.8614 (mm110) REVERT: c 359 MET cc_start: 0.9034 (mmm) cc_final: 0.8579 (mmm) REVERT: c 369 TYR cc_start: 0.8743 (m-80) cc_final: 0.6788 (m-80) REVERT: c 370 TRP cc_start: 0.8624 (p-90) cc_final: 0.8316 (p-90) REVERT: c 387 LEU cc_start: 0.9307 (mt) cc_final: 0.8778 (mt) REVERT: c 401 ASP cc_start: 0.8896 (p0) cc_final: 0.8261 (p0) REVERT: c 404 GLU cc_start: 0.9453 (mp0) cc_final: 0.9087 (pp20) REVERT: D 6 GLU cc_start: 0.8398 (pt0) cc_final: 0.7892 (pt0) REVERT: D 34 MET cc_start: 0.8971 (mtm) cc_final: 0.8170 (mtp) REVERT: D 37 GLU cc_start: 0.6167 (mt-10) cc_final: 0.5846 (mt-10) REVERT: D 75 TRP cc_start: 0.8436 (t-100) cc_final: 0.7808 (t-100) REVERT: H 86 ASP cc_start: 0.8414 (m-30) cc_final: 0.8161 (m-30) REVERT: H 96 PHE cc_start: 0.8023 (m-80) cc_final: 0.7608 (m-80) REVERT: L 6 GLN cc_start: 0.7897 (mt0) cc_final: 0.7287 (mp-120) REVERT: L 31 ASP cc_start: 0.8586 (p0) cc_final: 0.8290 (p0) REVERT: L 35 TRP cc_start: 0.9238 (m100) cc_final: 0.8129 (m100) REVERT: L 73 LEU cc_start: 0.9387 (tp) cc_final: 0.9115 (tp) REVERT: L 74 THR cc_start: 0.8333 (p) cc_final: 0.7942 (t) REVERT: E 3 GLN cc_start: 0.7610 (tm-30) cc_final: 0.7305 (tm-30) REVERT: E 50 TYR cc_start: 0.8474 (p90) cc_final: 0.8158 (p90) REVERT: E 67 LEU cc_start: 0.8978 (mm) cc_final: 0.8507 (mm) REVERT: E 86 ASP cc_start: 0.9206 (m-30) cc_final: 0.8695 (m-30) REVERT: E 89 VAL cc_start: 0.7613 (p) cc_final: 0.7242 (p) REVERT: I 83 PHE cc_start: 0.8146 (m-80) cc_final: 0.7748 (m-80) outliers start: 0 outliers final: 0 residues processed: 328 average time/residue: 0.1027 time to fit residues: 50.7557 Evaluate side-chains 264 residues out of total 1448 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 264 time to evaluate : 0.448 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 157 random chunks: chunk 31 optimal weight: 0.9990 chunk 113 optimal weight: 0.9990 chunk 132 optimal weight: 3.9990 chunk 77 optimal weight: 0.9990 chunk 80 optimal weight: 10.0000 chunk 54 optimal weight: 1.9990 chunk 154 optimal weight: 6.9990 chunk 67 optimal weight: 3.9990 chunk 36 optimal weight: 0.8980 chunk 91 optimal weight: 2.9990 chunk 75 optimal weight: 2.9990 overall best weight: 1.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 170 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 319 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 170 HIS ** C 93 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 124 HIS ** E 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 37 GLN ** I 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3564 r_free = 0.3564 target = 0.089420 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3127 r_free = 0.3127 target = 0.068924 restraints weight = 52117.222| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3176 r_free = 0.3176 target = 0.071072 restraints weight = 35432.362| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3210 r_free = 0.3210 target = 0.072605 restraints weight = 27208.958| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3235 r_free = 0.3235 target = 0.073697 restraints weight = 22589.564| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 20)----------------| | r_work = 0.3241 r_free = 0.3241 target = 0.073972 restraints weight = 19730.504| |-----------------------------------------------------------------------------| r_work (final): 0.3229 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7730 moved from start: 0.5707 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 14597 Z= 0.162 Angle : 0.870 14.182 19939 Z= 0.412 Chirality : 0.051 0.372 2415 Planarity : 0.005 0.083 2359 Dihedral : 9.436 67.140 3123 Min Nonbonded Distance : 2.331 Molprobity Statistics. All-atom Clashscore : 15.54 Ramachandran Plot: Outliers : 0.55 % Allowed : 14.18 % Favored : 85.27 % Rotamer: Outliers : 0.00 % Allowed : 0.28 % Favored : 99.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.41 (0.21), residues: 1629 helix: -0.05 (0.30), residues: 310 sheet: -0.76 (0.32), residues: 292 loop : -2.51 (0.19), residues: 1027 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG E 66 TYR 0.019 0.002 TYR C 253 PHE 0.030 0.002 PHE B 191 TRP 0.055 0.002 TRP C 210 HIS 0.012 0.002 HIS B 93 Details of bonding type rmsd/Z covalent geometry : bond 0.00349 / 0.16 (14484) covalent geometry : angle 0.80605 / 0.40 (19626) SS BOND : bond 0.00466 / 0.30 ( 26) SS BOND : angle 1.84669 / 1.04 ( 52) hydrogen bonds : bond 0.03851 / 2.31 ( 333) hydrogen bonds : angle 5.31705 / 3.66 ( 906) link_ALPHA1-2 : bond 0.00954 / 0.49 ( 2) link_ALPHA1-2 : angle 3.25600 / 1.63 ( 6) link_ALPHA1-3 : bond 0.00909 / 0.59 ( 13) link_ALPHA1-3 : angle 2.58892 / 1.71 ( 39) link_ALPHA1-6 : bond 0.01050 / 0.74 ( 10) link_ALPHA1-6 : angle 2.06499 / 1.36 ( 30) link_BETA1-4 : bond 0.00576 / 0.38 ( 27) link_BETA1-4 : angle 1.83837 / 1.15 ( 81) link_NAG-ASN : bond 0.00819 / 0.47 ( 35) link_NAG-ASN : angle 3.68848 / 2.25 ( 105) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3258 Ramachandran restraints generated. 1629 Oldfield, 0 Emsley, 1629 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3258 Ramachandran restraints generated. 1629 Oldfield, 0 Emsley, 1629 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 323 residues out of total 1448 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 323 time to evaluate : 0.512 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: B 82 MET cc_start: 0.8126 (ptt) cc_final: 0.7382 (pmm) REVERT: B 142 LEU cc_start: 0.9049 (mp) cc_final: 0.8745 (tp) REVERT: B 150 TYR cc_start: 0.7075 (m-80) cc_final: 0.6697 (m-80) REVERT: B 157 PHE cc_start: 0.8551 (m-80) cc_final: 0.8179 (m-80) REVERT: B 221 ILE cc_start: 0.9137 (mt) cc_final: 0.8869 (mt) REVERT: B 223 GLN cc_start: 0.7893 (mp10) cc_final: 0.7410 (mp10) REVERT: b 270 GLU cc_start: 0.7548 (mp0) cc_final: 0.7250 (tp30) REVERT: b 284 MET cc_start: 0.8435 (mmt) cc_final: 0.8130 (mmp) REVERT: b 317 ASP cc_start: 0.8890 (t0) cc_final: 0.8525 (t70) REVERT: b 325 ARG cc_start: 0.7453 (ptp90) cc_final: 0.6806 (ptp90) REVERT: b 346 ASN cc_start: 0.9305 (t0) cc_final: 0.8751 (t0) REVERT: b 348 GLN cc_start: 0.8005 (pt0) cc_final: 0.7732 (mp10) REVERT: b 351 MET cc_start: 0.9392 (mmt) cc_final: 0.9124 (mmp) REVERT: b 357 ASP cc_start: 0.8844 (t70) cc_final: 0.8378 (t0) REVERT: b 369 TYR cc_start: 0.8782 (m-80) cc_final: 0.8095 (m-10) REVERT: A 72 GLU cc_start: 0.8893 (mm-30) cc_final: 0.8582 (tp30) REVERT: A 75 MET cc_start: 0.8851 (mtp) cc_final: 0.8549 (ttm) REVERT: A 76 GLU cc_start: 0.8849 (tt0) cc_final: 0.7898 (tp30) REVERT: A 82 MET cc_start: 0.9007 (pmm) cc_final: 0.8708 (pmm) REVERT: A 134 MET cc_start: 0.8470 (mmm) cc_final: 0.7984 (mmm) REVERT: A 219 TYR cc_start: 0.8006 (m-80) cc_final: 0.7401 (m-80) REVERT: A 241 TYR cc_start: 0.8896 (t80) cc_final: 0.8557 (t80) REVERT: a 264 TRP cc_start: 0.6922 (m100) cc_final: 0.6169 (m-90) REVERT: a 265 THR cc_start: 0.8308 (m) cc_final: 0.7842 (p) REVERT: a 266 LEU cc_start: 0.8528 (mp) cc_final: 0.8234 (tp) REVERT: a 347 ASP cc_start: 0.8413 (m-30) cc_final: 0.8116 (t0) REVERT: a 348 GLN cc_start: 0.7555 (tt0) cc_final: 0.6667 (tp40) REVERT: a 363 TYR cc_start: 0.8590 (p90) cc_final: 0.8068 (p90) REVERT: C 153 MET cc_start: 0.8253 (tmm) cc_final: 0.8025 (tmm) REVERT: C 164 VAL cc_start: 0.8173 (t) cc_final: 0.7888 (t) REVERT: C 192 MET cc_start: 0.8643 (mmt) cc_final: 0.8128 (mmt) REVERT: c 268 ASP cc_start: 0.7724 (p0) cc_final: 0.7240 (p0) REVERT: c 311 ASP cc_start: 0.9049 (m-30) cc_final: 0.8695 (m-30) REVERT: c 320 LYS cc_start: 0.9392 (ttpt) cc_final: 0.8987 (ttmm) REVERT: c 321 GLN cc_start: 0.8948 (mm-40) cc_final: 0.8629 (mm110) REVERT: c 359 MET cc_start: 0.9026 (mmm) cc_final: 0.8519 (mmm) REVERT: c 369 TYR cc_start: 0.8729 (m-80) cc_final: 0.6837 (m-80) REVERT: c 387 LEU cc_start: 0.9293 (mt) cc_final: 0.8786 (mt) REVERT: c 401 ASP cc_start: 0.8953 (p0) cc_final: 0.8256 (p0) REVERT: c 404 GLU cc_start: 0.9465 (mp0) cc_final: 0.9101 (pp20) REVERT: D 6 GLU cc_start: 0.8393 (pt0) cc_final: 0.8089 (pt0) REVERT: D 37 GLU cc_start: 0.6151 (mt-10) cc_final: 0.5936 (mt-10) REVERT: D 75 TRP cc_start: 0.8415 (t-100) cc_final: 0.7797 (t-100) REVERT: H 86 ASP cc_start: 0.8329 (m-30) cc_final: 0.7965 (m-30) REVERT: H 96 PHE cc_start: 0.8035 (m-80) cc_final: 0.7712 (m-10) REVERT: L 6 GLN cc_start: 0.7957 (mt0) cc_final: 0.7307 (mp-120) REVERT: L 31 ASP cc_start: 0.8573 (p0) cc_final: 0.8321 (p0) REVERT: L 35 TRP cc_start: 0.9253 (m100) cc_final: 0.8189 (m100) REVERT: L 73 LEU cc_start: 0.9388 (tp) cc_final: 0.9076 (tp) REVERT: L 74 THR cc_start: 0.8410 (p) cc_final: 0.8059 (t) REVERT: E 3 GLN cc_start: 0.7523 (tm-30) cc_final: 0.7264 (tm-30) REVERT: E 50 TYR cc_start: 0.8478 (p90) cc_final: 0.8171 (p90) REVERT: E 67 LEU cc_start: 0.9259 (mm) cc_final: 0.8917 (mm) REVERT: E 76 ASN cc_start: 0.7777 (m-40) cc_final: 0.7407 (m110) REVERT: E 86 ASP cc_start: 0.9208 (m-30) cc_final: 0.8712 (m-30) REVERT: I 53 THR cc_start: 0.9396 (m) cc_final: 0.9046 (p) REVERT: I 78 MET cc_start: 0.8833 (tpt) cc_final: 0.8474 (tpt) REVERT: I 83 PHE cc_start: 0.8138 (m-80) cc_final: 0.7493 (m-80) outliers start: 0 outliers final: 0 residues processed: 323 average time/residue: 0.1032 time to fit residues: 50.5798 Evaluate side-chains 259 residues out of total 1448 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 259 time to evaluate : 0.304 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 157 random chunks: chunk 84 optimal weight: 2.9990 chunk 136 optimal weight: 0.8980 chunk 101 optimal weight: 0.9990 chunk 75 optimal weight: 3.9990 chunk 103 optimal weight: 5.9990 chunk 156 optimal weight: 3.9990 chunk 98 optimal weight: 0.9980 chunk 41 optimal weight: 8.9990 chunk 28 optimal weight: 0.0870 chunk 62 optimal weight: 1.9990 chunk 21 optimal weight: 2.9990 overall best weight: 0.9962 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** b 319 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 93 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 90 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 = 0.3572 r_free = 0.3572 target = 0.089603 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3155 r_free = 0.3155 target = 0.070089 restraints weight = 52638.492| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3191 r_free = 0.3191 target = 0.071782 restraints weight = 35012.269| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3215 r_free = 0.3215 target = 0.072803 restraints weight = 26720.584| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3234 r_free = 0.3234 target = 0.073668 restraints weight = 23258.645| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3237 r_free = 0.3237 target = 0.073791 restraints weight = 20886.719| |-----------------------------------------------------------------------------| r_work (final): 0.3225 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7739 moved from start: 0.5817 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 14597 Z= 0.154 Angle : 0.854 16.005 19939 Z= 0.405 Chirality : 0.050 0.369 2415 Planarity : 0.005 0.079 2359 Dihedral : 9.196 64.816 3123 Min Nonbonded Distance : 2.343 Molprobity Statistics. All-atom Clashscore : 15.47 Ramachandran Plot: Outliers : 0.55 % Allowed : 14.06 % Favored : 85.39 % Rotamer: Outliers : 0.00 % Allowed : 0.21 % Favored : 99.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.13 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.38 (0.21), residues: 1629 helix: 0.00 (0.30), residues: 310 sheet: -0.72 (0.32), residues: 294 loop : -2.51 (0.19), residues: 1025 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG E 66 TYR 0.018 0.002 TYR C 253 PHE 0.019 0.001 PHE D 29 TRP 0.053 0.002 TRP C 210 HIS 0.010 0.001 HIS A 93 Details of bonding type rmsd/Z covalent geometry : bond 0.00330 / 0.15 (14484) covalent geometry : angle 0.79247 / 0.39 (19626) SS BOND : bond 0.00391 / 0.26 ( 26) SS BOND : angle 1.70561 / 0.98 ( 52) hydrogen bonds : bond 0.03740 / 2.26 ( 333) hydrogen bonds : angle 5.23766 / 3.62 ( 906) link_ALPHA1-2 : bond 0.00936 / 0.48 ( 2) link_ALPHA1-2 : angle 3.17347 / 1.59 ( 6) link_ALPHA1-3 : bond 0.00931 / 0.61 ( 13) link_ALPHA1-3 : angle 2.56308 / 1.69 ( 39) link_ALPHA1-6 : bond 0.01004 / 0.69 ( 10) link_ALPHA1-6 : angle 2.03709 / 1.34 ( 30) link_BETA1-4 : bond 0.00580 / 0.38 ( 27) link_BETA1-4 : angle 1.80282 / 1.13 ( 81) link_NAG-ASN : bond 0.00808 / 0.46 ( 35) link_NAG-ASN : angle 3.58309 / 2.19 ( 105) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2219.67 seconds wall clock time: 39 minutes 38.23 seconds (2378.23 seconds total)