Starting phenix.real_space_refine on Sat Oct 11 11:56:47 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8t5c_41048/10_2025/8t5c_41048.cif Found real_map, /net/cci-nas-00/data/ceres_data/8t5c_41048/10_2025/8t5c_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 { model { file = "/net/cci-nas-00/data/ceres_data/8t5c_41048/10_2025/8t5c_41048.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8t5c_41048/10_2025/8t5c_41048.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8t5c_41048/10_2025/8t5c_41048.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8t5c_41048/10_2025/8t5c_41048.map" } 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-2.0-5842/lib/python3.9/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: 24 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: 18 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: 15 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: 15 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 dihedrals: 9 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: 18 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: 15 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: 18 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: 18 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: 3.62, per 1000 atoms: 0.26 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: 1.61 Conformation dependent library (CDL) restraints added in 615.7 milliseconds Enol-peptide restraints added in 715.3 nanoseconds 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: 0.47 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: 2.17 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 - 24.12: 8916 24.12 - 48.24: 584 48.24 - 72.36: 86 72.36 - 96.49: 108 96.49 - 120.61: 75 Dihedral angle restraints: 9769 sinusoidal: 4987 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 9766 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: 1.870 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: 0.150 Check model and map are aligned: 0.040 Set scattering table: 0.030 Process input model: 14.010 Find NCS groups from input model: 0.310 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:1.370 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 17.840 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7169 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 : 20.844 120.607 6633 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 aren 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 covalent geometry : bond 0.00512 (14484) covalent geometry : angle 0.83906 (19626) SS BOND : bond 0.00286 ( 26) SS BOND : angle 1.05393 ( 52) hydrogen bonds : bond 0.29519 ( 333) hydrogen bonds : angle 8.90106 ( 906) link_ALPHA1-2 : bond 0.00743 ( 2) link_ALPHA1-2 : angle 5.60407 ( 6) link_ALPHA1-3 : bond 0.00763 ( 13) link_ALPHA1-3 : angle 2.74015 ( 39) link_ALPHA1-6 : bond 0.01163 ( 10) link_ALPHA1-6 : angle 3.33535 ( 30) link_BETA1-4 : bond 0.00519 ( 27) link_BETA1-4 : angle 2.41410 ( 81) link_NAG-ASN : bond 0.00700 ( 35) link_NAG-ASN : angle 2.77064 ( 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 : 0.521 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: 0.7890 (ptp) cc_final: 0.7661 (ptp) REVERT: B 101 THR cc_start: 0.8735 (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: 0.7142 (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: 0.8716 (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: 0.8522 (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: 0.8165 (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: 0.7275 (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: 0.7736 (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: 0.8907 (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: 0.6676 (t) cc_final: 0.4958 (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: 0.8092 (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: 0.7902 (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: 0.8481 (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: 0.1139 time to fit residues: 96.3699 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 : 0.527 ------------------------------------------------------------------------------- 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... Flipped N/Q/H residues before XYZ refinement: 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 = 0.3678 r_free = 0.3678 target = 0.096078 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3290 r_free = 0.3290 target = 0.076864 restraints weight = 49087.118| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3341 r_free = 0.3341 target = 0.079242 restraints weight = 32130.018| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3377 r_free = 0.3377 target = 0.080929 restraints weight = 23948.028| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.3401 r_free = 0.3401 target = 0.082099 restraints weight = 19339.296| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3416 r_free = 0.3416 target = 0.082840 restraints weight = 16598.589| |-----------------------------------------------------------------------------| r_work (final): 0.3412 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7446 moved from start: 0.2970 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.070 14597 Z= 0.180 Angle : 0.904 11.927 19939 Z= 0.424 Chirality : 0.052 0.341 2415 Planarity : 0.005 0.059 2359 Dihedral : 17.668 113.529 3617 Min Nonbonded Distance : 2.339 Molprobity Statistics. All-atom Clashscore : 10.23 Ramachandran Plot: Outliers : 0.55 % Allowed : 13.75 % Favored : 85.70 % Rotamer: Outliers : 0.42 % Allowed : 4.50 % Favored : 95.08 % 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 aren not related in a simple way. whole: -2.60 (0.20), residues: 1629 helix: -0.08 (0.30), residues: 283 sheet: -1.18 (0.32), residues: 294 loop : -2.52 (0.18), residues: 1052 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG D 67 TYR 0.020 0.002 TYR c 363 PHE 0.028 0.002 PHE B 191 TRP 0.027 0.002 TRP C 210 HIS 0.013 0.001 HIS B 170 Details of bonding type rmsd covalent geometry : bond 0.00379 (14484) covalent geometry : angle 0.82641 (19626) SS BOND : bond 0.00541 ( 26) SS BOND : angle 1.83725 ( 52) hydrogen bonds : bond 0.06690 ( 333) hydrogen bonds : angle 6.32813 ( 906) link_ALPHA1-2 : bond 0.01050 ( 2) link_ALPHA1-2 : angle 4.78568 ( 6) link_ALPHA1-3 : bond 0.01191 ( 13) link_ALPHA1-3 : angle 3.18442 ( 39) link_ALPHA1-6 : bond 0.01087 ( 10) link_ALPHA1-6 : angle 2.40504 ( 30) link_BETA1-4 : bond 0.00869 ( 27) link_BETA1-4 : angle 2.69850 ( 81) link_NAG-ASN : bond 0.00776 ( 35) link_NAG-ASN : angle 3.69759 ( 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 439 residues out of total 1448 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 433 time to evaluate : 0.548 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 189 GLN cc_start: 0.9101 (tp40) cc_final: 0.8837 (mm-40) REVERT: B 200 TYR cc_start: 0.6727 (p90) cc_final: 0.5787 (p90) REVERT: B 232 GLN cc_start: 0.7762 (tt0) cc_final: 0.6807 (mm-40) REVERT: b 270 GLU cc_start: 0.7458 (mp0) cc_final: 0.7203 (tp30) REVERT: b 289 GLU cc_start: 0.8764 (tp30) cc_final: 0.8471 (tp30) REVERT: b 311 ASP cc_start: 0.8950 (m-30) cc_final: 0.8567 (m-30) REVERT: b 317 ASP cc_start: 0.8882 (t70) cc_final: 0.8506 (t0) REVERT: b 346 ASN cc_start: 0.9210 (t0) cc_final: 0.8852 (t0) REVERT: b 414 MET cc_start: 0.8835 (tmm) cc_final: 0.7783 (tmm) REVERT: A 75 MET cc_start: 0.8538 (mtp) cc_final: 0.8062 (ttm) REVERT: A 82 MET cc_start: 0.8833 (pmm) cc_final: 0.8426 (pmm) REVERT: A 134 MET cc_start: 0.7988 (mmm) cc_final: 0.7707 (mmm) REVERT: A 140 PHE cc_start: 0.9165 (m-80) cc_final: 0.8671 (m-80) REVERT: A 247 GLN cc_start: 0.6926 (mp10) cc_final: 0.6199 (mp10) REVERT: a 266 LEU cc_start: 0.8744 (mp) cc_final: 0.8504 (tp) REVERT: a 281 THR cc_start: 0.7967 (p) cc_final: 0.6827 (p) REVERT: a 287 GLU cc_start: 0.8109 (mt-10) cc_final: 0.7315 (tm-30) REVERT: a 325 ARG cc_start: 0.7842 (ptp-170) cc_final: 0.7562 (ptp-170) REVERT: a 363 TYR cc_start: 0.8637 (p90) cc_final: 0.8094 (p90) REVERT: a 387 LEU cc_start: 0.8710 (mt) cc_final: 0.8155 (mt) REVERT: a 410 MET cc_start: 0.9142 (mmt) cc_final: 0.8679 (mmt) REVERT: C 68 LEU cc_start: 0.8295 (tp) cc_final: 0.7934 (tp) REVERT: C 82 MET cc_start: 0.8272 (mmm) cc_final: 0.7979 (mmm) REVERT: C 93 HIS cc_start: 0.8285 (m90) cc_final: 0.8008 (m-70) REVERT: C 241 TYR cc_start: 0.9096 (t80) cc_final: 0.8689 (t80) REVERT: c 268 ASP cc_start: 0.7520 (p0) cc_final: 0.7080 (p0) REVERT: c 282 ARG cc_start: 0.8176 (ttt180) cc_final: 0.7075 (ptp-170) REVERT: c 311 ASP cc_start: 0.9144 (m-30) cc_final: 0.8873 (m-30) REVERT: c 312 MET cc_start: 0.8260 (mmm) cc_final: 0.7727 (mmm) REVERT: c 320 LYS cc_start: 0.9218 (ttpt) cc_final: 0.8847 (ttmm) REVERT: c 337 ILE cc_start: 0.8918 (mt) cc_final: 0.8122 (mt) REVERT: c 349 LEU cc_start: 0.9124 (tp) cc_final: 0.8748 (tt) REVERT: c 369 TYR cc_start: 0.8560 (m-80) cc_final: 0.6589 (m-10) REVERT: c 387 LEU cc_start: 0.9219 (mt) cc_final: 0.8814 (mp) REVERT: c 403 ILE cc_start: 0.9051 (mt) cc_final: 0.8836 (mt) REVERT: D 6 GLU cc_start: 0.8245 (pt0) cc_final: 0.8006 (pm20) REVERT: D 34 MET cc_start: 0.8608 (mtm) cc_final: 0.7762 (mtp) REVERT: D 37 GLU cc_start: 0.5731 (mt-10) cc_final: 0.5424 (mt-10) REVERT: D 96 CYS cc_start: 0.6116 (t) cc_final: 0.5710 (t) REVERT: D 107 GLN cc_start: 0.8088 (pt0) cc_final: 0.7751 (pt0) REVERT: H 96 PHE cc_start: 0.7757 (m-80) cc_final: 0.7443 (m-80) REVERT: H 103 TRP cc_start: 0.9010 (m100) cc_final: 0.8787 (m100) REVERT: H 107 THR cc_start: 0.7807 (t) cc_final: 0.7428 (t) REVERT: L 6 GLN cc_start: 0.7191 (mt0) cc_final: 0.6769 (mp-120) REVERT: L 35 TRP cc_start: 0.8630 (m100) cc_final: 0.8224 (m100) REVERT: L 53 THR cc_start: 0.8435 (OUTLIER) cc_final: 0.8116 (t) REVERT: L 98 PHE cc_start: 0.8485 (m-80) cc_final: 0.8117 (m-80) REVERT: E 67 LEU cc_start: 0.8701 (mm) cc_final: 0.8181 (mm) REVERT: E 76 ASN cc_start: 0.7420 (m-40) cc_final: 0.7099 (m-40) REVERT: E 86 ASP cc_start: 0.8835 (m-30) cc_final: 0.8414 (m-30) REVERT: I 37 GLN cc_start: 0.7664 (pp30) cc_final: 0.7412 (pp30) REVERT: I 38 GLN cc_start: 0.8312 (tt0) cc_final: 0.8013 (mt0) REVERT: I 75 ILE cc_start: 0.9420 (mt) cc_final: 0.8995 (tt) outliers start: 6 outliers final: 1 residues processed: 438 average time/residue: 0.1139 time to fit residues: 74.3850 Evaluate side-chains 308 residues out of total 1448 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 306 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: 2.9990 chunk 94 optimal weight: 0.8980 chunk 11 optimal weight: 3.9990 chunk 81 optimal weight: 8.9990 chunk 103 optimal weight: 1.9990 chunk 26 optimal weight: 5.9990 chunk 149 optimal weight: 3.9990 chunk 42 optimal weight: 4.9990 chunk 23 optimal weight: 0.9990 chunk 107 optimal weight: 5.9990 chunk 141 optimal weight: 5.9990 overall best weight: 2.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 170 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 319 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** b 342 ASN b 374 HIS ** A 170 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 223 GLN c 331 GLN D 84 ASN L 37 GLN L 89 GLN E 3 GLN E 77 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 = 0.3591 r_free = 0.3591 target = 0.091198 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3181 r_free = 0.3181 target = 0.071719 restraints weight = 50819.648| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3228 r_free = 0.3228 target = 0.073822 restraints weight = 34515.898| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3260 r_free = 0.3260 target = 0.075284 restraints weight = 26413.545| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 42)----------------| | r_work = 0.3283 r_free = 0.3283 target = 0.076327 restraints weight = 21886.460| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3296 r_free = 0.3296 target = 0.076944 restraints weight = 19117.846| |-----------------------------------------------------------------------------| r_work (final): 0.3286 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7649 moved from start: 0.3826 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.073 14597 Z= 0.224 Angle : 0.910 10.515 19939 Z= 0.431 Chirality : 0.053 0.442 2415 Planarity : 0.006 0.141 2359 Dihedral : 15.023 112.463 3617 Min Nonbonded Distance : 2.384 Molprobity Statistics. All-atom Clashscore : 13.73 Ramachandran Plot: Outliers : 0.49 % Allowed : 13.75 % Favored : 85.76 % Rotamer: Outliers : 0.28 % Allowed : 5.68 % Favored : 94.04 % 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 aren not related in a simple way. whole: -2.72 (0.20), residues: 1629 helix: -0.22 (0.30), residues: 289 sheet: -1.16 (0.30), residues: 292 loop : -2.64 (0.18), residues: 1048 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.022 0.001 ARG E 30 TYR 0.029 0.002 TYR A 62 PHE 0.026 0.002 PHE b 318 TRP 0.035 0.003 TRP D 75 HIS 0.015 0.002 HIS B 170 Details of bonding type rmsd covalent geometry : bond 0.00483 (14484) covalent geometry : angle 0.83449 (19626) SS BOND : bond 0.00531 ( 26) SS BOND : angle 1.88096 ( 52) hydrogen bonds : bond 0.05278 ( 333) hydrogen bonds : angle 6.17155 ( 906) link_ALPHA1-2 : bond 0.00866 ( 2) link_ALPHA1-2 : angle 4.53621 ( 6) link_ALPHA1-3 : bond 0.01198 ( 13) link_ALPHA1-3 : angle 3.04249 ( 39) link_ALPHA1-6 : bond 0.01034 ( 10) link_ALPHA1-6 : angle 2.45010 ( 30) link_BETA1-4 : bond 0.00657 ( 27) link_BETA1-4 : angle 2.52446 ( 81) link_NAG-ASN : bond 0.01009 ( 35) link_NAG-ASN : angle 3.74533 ( 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 398 residues out of total 1448 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 394 time to evaluate : 0.549 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: 0.9199 (mp) cc_final: 0.8739 (tp) REVERT: B 183 VAL cc_start: 0.8513 (t) cc_final: 0.8139 (m) REVERT: B 194 MET cc_start: 0.9065 (tpp) cc_final: 0.8663 (tpp) REVERT: B 248 ARG cc_start: 0.8156 (tpp80) cc_final: 0.7807 (tpp80) REVERT: b 289 GLU cc_start: 0.8898 (tp30) cc_final: 0.8561 (tp30) REVERT: b 311 ASP cc_start: 0.8827 (m-30) cc_final: 0.8530 (m-30) REVERT: b 345 ILE cc_start: 0.9365 (tp) cc_final: 0.9156 (tp) REVERT: b 346 ASN cc_start: 0.9341 (t0) cc_final: 0.8895 (t0) REVERT: b 414 MET cc_start: 0.8798 (tmm) cc_final: 0.8569 (tmm) REVERT: A 75 MET cc_start: 0.8780 (mtp) cc_final: 0.8481 (ttm) REVERT: A 82 MET cc_start: 0.8830 (pmm) cc_final: 0.8337 (pmm) REVERT: A 122 ASP cc_start: 0.9318 (m-30) cc_final: 0.8899 (m-30) REVERT: A 126 LYS cc_start: 0.8438 (mmtm) cc_final: 0.8174 (mmtp) REVERT: A 140 PHE cc_start: 0.9214 (m-80) cc_final: 0.8817 (m-80) REVERT: A 219 TYR cc_start: 0.7739 (m-80) cc_final: 0.7193 (m-80) REVERT: A 241 TYR cc_start: 0.8635 (t80) cc_final: 0.8389 (t80) REVERT: A 247 GLN cc_start: 0.6346 (mp10) cc_final: 0.5931 (mp10) REVERT: a 281 THR cc_start: 0.8013 (p) cc_final: 0.6893 (p) REVERT: a 283 TRP cc_start: 0.8892 (p-90) cc_final: 0.8669 (p-90) REVERT: a 287 GLU cc_start: 0.8345 (mt-10) cc_final: 0.7698 (tm-30) REVERT: a 307 GLU cc_start: 0.8417 (tm-30) cc_final: 0.8109 (tm-30) REVERT: a 325 ARG cc_start: 0.8121 (ptp-170) cc_final: 0.7784 (ptp-170) REVERT: a 410 MET cc_start: 0.9248 (mmp) cc_final: 0.9000 (mmt) REVERT: C 68 LEU cc_start: 0.8322 (tp) cc_final: 0.7799 (tp) REVERT: C 93 HIS cc_start: 0.8487 (m90) cc_final: 0.7966 (m-70) REVERT: C 115 HIS cc_start: 0.8123 (m90) cc_final: 0.7874 (m90) REVERT: C 142 LEU cc_start: 0.8899 (mp) cc_final: 0.8500 (tp) REVERT: C 241 TYR cc_start: 0.9179 (t80) cc_final: 0.8713 (t80) REVERT: c 268 ASP cc_start: 0.7658 (p0) cc_final: 0.7193 (p0) REVERT: c 282 ARG cc_start: 0.8380 (ttt180) cc_final: 0.7162 (ptp-170) REVERT: c 285 LEU cc_start: 0.9279 (mp) cc_final: 0.8966 (mp) REVERT: c 311 ASP cc_start: 0.9242 (m-30) cc_final: 0.8903 (m-30) REVERT: c 312 MET cc_start: 0.8594 (mmm) cc_final: 0.7929 (mmm) REVERT: c 320 LYS cc_start: 0.9330 (ttpt) cc_final: 0.8871 (ttmm) REVERT: c 337 ILE cc_start: 0.8886 (mt) cc_final: 0.7834 (mt) REVERT: c 369 TYR cc_start: 0.8683 (m-80) cc_final: 0.7808 (m-80) REVERT: c 387 LEU cc_start: 0.9369 (mt) cc_final: 0.8932 (mp) REVERT: c 401 ASP cc_start: 0.8967 (p0) cc_final: 0.8507 (p0) REVERT: c 404 GLU cc_start: 0.9472 (mp0) cc_final: 0.9165 (pp20) REVERT: c 408 ASP cc_start: 0.9542 (p0) cc_final: 0.9327 (p0) REVERT: D 6 GLU cc_start: 0.8289 (pt0) cc_final: 0.7895 (pm20) REVERT: D 30 SER cc_start: 0.7782 (p) cc_final: 0.7175 (m) REVERT: D 34 MET cc_start: 0.8790 (mtm) cc_final: 0.7904 (mtp) REVERT: D 37 GLU cc_start: 0.6267 (mt-10) cc_final: 0.5780 (mt-10) REVERT: D 46 GLU cc_start: 0.8475 (pm20) cc_final: 0.7589 (pm20) REVERT: D 104 LEU cc_start: 0.7942 (pp) cc_final: 0.7716 (pp) REVERT: D 105 ARG cc_start: 0.8127 (ptp-110) cc_final: 0.7719 (ptp90) REVERT: H 96 PHE cc_start: 0.8065 (m-80) cc_final: 0.7641 (m-80) REVERT: L 6 GLN cc_start: 0.7958 (mt0) cc_final: 0.6901 (mp-120) REVERT: L 23 CYS cc_start: 0.6209 (t) cc_final: 0.4615 (t) REVERT: L 31 ASP cc_start: 0.8355 (p0) cc_final: 0.8100 (p0) REVERT: L 74 THR cc_start: 0.8010 (p) cc_final: 0.7683 (t) REVERT: L 78 MET cc_start: 0.8563 (tmm) cc_final: 0.8016 (tmm) REVERT: E 47 TRP cc_start: 0.8798 (t60) cc_final: 0.8475 (t60) REVERT: E 67 LEU cc_start: 0.8825 (mm) cc_final: 0.8218 (mm) REVERT: E 76 ASN cc_start: 0.7646 (m-40) cc_final: 0.7356 (m-40) REVERT: E 86 ASP cc_start: 0.9068 (m-30) cc_final: 0.8537 (m-30) REVERT: I 37 GLN cc_start: 0.7752 (pp30) cc_final: 0.7360 (tm-30) REVERT: I 83 PHE cc_start: 0.8045 (m-80) cc_final: 0.7610 (m-80) outliers start: 4 outliers final: 1 residues processed: 397 average time/residue: 0.1228 time to fit residues: 71.9284 Evaluate side-chains 285 residues out of total 1448 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 284 time to evaluate : 0.669 ------------------------------------------------------------------------------- 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: 0.9990 chunk 151 optimal weight: 0.8980 chunk 133 optimal weight: 4.9990 chunk 81 optimal weight: 0.9990 chunk 12 optimal weight: 2.9990 chunk 140 optimal weight: 0.3980 chunk 61 optimal weight: 7.9990 chunk 54 optimal weight: 0.0050 chunk 139 optimal weight: 2.9990 chunk 72 optimal weight: 5.9990 chunk 55 optimal weight: 0.0670 overall best weight: 0.4734 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 ** both conformations clash, **PLEASE CHECK MANUALLY** A 93 HIS ** A 170 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** a 353 ASN C 189 GLN D 39 GLN E 3 GLN ** 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: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3631 r_free = 0.3631 target = 0.093295 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3219 r_free = 0.3219 target = 0.073425 restraints weight = 50538.821| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3267 r_free = 0.3267 target = 0.075616 restraints weight = 33986.012| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3301 r_free = 0.3301 target = 0.077176 restraints weight = 25945.759| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3323 r_free = 0.3323 target = 0.078203 restraints weight = 21410.908| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3339 r_free = 0.3339 target = 0.078982 restraints weight = 18764.538| |-----------------------------------------------------------------------------| r_work (final): 0.3331 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7575 moved from start: 0.4285 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= 0.161 Angle : 0.882 11.510 19939 Z= 0.414 Chirality : 0.053 0.402 2415 Planarity : 0.005 0.098 2359 Dihedral : 12.991 112.745 3617 Min Nonbonded Distance : 2.377 Molprobity Statistics. All-atom Clashscore : 13.19 Ramachandran Plot: Outliers : 0.55 % Allowed : 13.20 % Favored : 86.25 % Rotamer: Outliers : 0.07 % Allowed : 3.32 % Favored : 96.61 % 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 aren not related in a simple way. whole: -2.66 (0.20), residues: 1629 helix: -0.14 (0.30), residues: 296 sheet: -1.01 (0.31), residues: 277 loop : -2.65 (0.18), residues: 1056 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG a 282 TYR 0.022 0.002 TYR A 62 PHE 0.026 0.002 PHE L 98 TRP 0.030 0.002 TRP C 210 HIS 0.016 0.002 HIS B 92 Details of bonding type rmsd covalent geometry : bond 0.00336 (14484) covalent geometry : angle 0.80418 (19626) SS BOND : bond 0.00439 ( 26) SS BOND : angle 2.00564 ( 52) hydrogen bonds : bond 0.04436 ( 333) hydrogen bonds : angle 5.82046 ( 906) link_ALPHA1-2 : bond 0.01207 ( 2) link_ALPHA1-2 : angle 4.57968 ( 6) link_ALPHA1-3 : bond 0.01250 ( 13) link_ALPHA1-3 : angle 3.02638 ( 39) link_ALPHA1-6 : bond 0.01179 ( 10) link_ALPHA1-6 : angle 2.24512 ( 30) link_BETA1-4 : bond 0.00718 ( 27) link_BETA1-4 : angle 2.41305 ( 81) link_NAG-ASN : bond 0.01037 ( 35) link_NAG-ASN : angle 3.78866 ( 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 390 residues out of total 1448 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 389 time to evaluate : 0.525 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 77 THR cc_start: 0.9085 (m) cc_final: 0.8844 (t) REVERT: B 104 GLU cc_start: 0.8328 (tp30) cc_final: 0.7949 (mm-30) REVERT: B 142 LEU cc_start: 0.9174 (mp) cc_final: 0.8551 (tp) REVERT: B 150 TYR cc_start: 0.6934 (m-80) cc_final: 0.6034 (m-80) REVERT: B 248 ARG cc_start: 0.7873 (tpp80) cc_final: 0.7578 (tpp80) REVERT: b 289 GLU cc_start: 0.8710 (tp30) cc_final: 0.8372 (tp30) REVERT: b 311 ASP cc_start: 0.8881 (m-30) cc_final: 0.8592 (m-30) REVERT: b 346 ASN cc_start: 0.9231 (t0) cc_final: 0.8765 (t0) REVERT: b 414 MET cc_start: 0.8712 (tmm) cc_final: 0.8506 (tmm) REVERT: A 62 TYR cc_start: 0.6290 (m-10) cc_final: 0.5794 (m-80) REVERT: A 75 MET cc_start: 0.8745 (mtp) cc_final: 0.8491 (ttm) REVERT: A 76 GLU cc_start: 0.8663 (tt0) cc_final: 0.7713 (tp30) REVERT: A 82 MET cc_start: 0.8714 (pmm) cc_final: 0.8214 (pmm) REVERT: A 104 GLU cc_start: 0.7650 (tp30) cc_final: 0.7387 (tp30) REVERT: A 140 PHE cc_start: 0.9196 (m-80) cc_final: 0.8713 (m-80) REVERT: A 219 TYR cc_start: 0.7779 (m-80) cc_final: 0.7221 (m-80) REVERT: A 241 TYR cc_start: 0.8551 (t80) cc_final: 0.8102 (t80) REVERT: a 265 THR cc_start: 0.8113 (m) cc_final: 0.7760 (p) REVERT: a 266 LEU cc_start: 0.8709 (mp) cc_final: 0.8427 (tp) REVERT: a 281 THR cc_start: 0.7929 (p) cc_final: 0.7069 (p) REVERT: a 283 TRP cc_start: 0.8667 (p-90) cc_final: 0.8125 (p-90) REVERT: a 287 GLU cc_start: 0.8195 (mt-10) cc_final: 0.7653 (tm-30) REVERT: a 325 ARG cc_start: 0.8176 (ptp-170) cc_final: 0.7514 (ptp-170) REVERT: a 332 MET cc_start: 0.6687 (mtt) cc_final: 0.5886 (mtt) REVERT: a 387 LEU cc_start: 0.8694 (mt) cc_final: 0.8388 (mm) REVERT: a 404 GLU cc_start: 0.8621 (tp30) cc_final: 0.8412 (tp30) REVERT: C 164 VAL cc_start: 0.8693 (t) cc_final: 0.8483 (t) REVERT: c 268 ASP cc_start: 0.7678 (p0) cc_final: 0.7143 (p0) REVERT: c 282 ARG cc_start: 0.8258 (ttt180) cc_final: 0.7147 (ptp-170) REVERT: c 314 ARG cc_start: 0.9146 (mtt90) cc_final: 0.8539 (ttm110) REVERT: c 320 LYS cc_start: 0.9331 (ttpt) cc_final: 0.8879 (ttmm) REVERT: c 337 ILE cc_start: 0.8738 (mt) cc_final: 0.8111 (mt) REVERT: c 349 LEU cc_start: 0.9160 (tp) cc_final: 0.8753 (tt) REVERT: c 369 TYR cc_start: 0.8563 (m-80) cc_final: 0.7789 (m-80) REVERT: c 387 LEU cc_start: 0.9288 (mt) cc_final: 0.8833 (mp) REVERT: c 401 ASP cc_start: 0.8894 (p0) cc_final: 0.8396 (p0) REVERT: c 402 ASP cc_start: 0.9122 (t0) cc_final: 0.8858 (t0) REVERT: c 404 GLU cc_start: 0.9455 (mp0) cc_final: 0.9074 (pp20) REVERT: D 34 MET cc_start: 0.8638 (mtm) cc_final: 0.7830 (mtp) REVERT: D 37 GLU cc_start: 0.6095 (mt-10) cc_final: 0.5669 (mt-10) REVERT: D 104 LEU cc_start: 0.7874 (pp) cc_final: 0.7325 (pp) REVERT: H 86 ASP cc_start: 0.8294 (m-30) cc_final: 0.8081 (m-30) REVERT: H 96 PHE cc_start: 0.7936 (m-80) cc_final: 0.7580 (m-10) REVERT: L 6 GLN cc_start: 0.7678 (mt0) cc_final: 0.7082 (mp-120) REVERT: L 31 ASP cc_start: 0.8444 (p0) cc_final: 0.8164 (p0) REVERT: L 74 THR cc_start: 0.7917 (p) cc_final: 0.7595 (t) REVERT: L 78 MET cc_start: 0.8567 (tmm) cc_final: 0.7872 (tmm) REVERT: E 67 LEU cc_start: 0.8735 (mm) cc_final: 0.8228 (mm) REVERT: E 76 ASN cc_start: 0.7571 (m-40) cc_final: 0.7062 (m-40) REVERT: E 86 ASP cc_start: 0.9048 (m-30) cc_final: 0.8689 (m-30) REVERT: I 37 GLN cc_start: 0.7754 (pp30) cc_final: 0.7477 (tm-30) REVERT: I 78 MET cc_start: 0.8573 (tpt) cc_final: 0.8344 (tpt) REVERT: I 83 PHE cc_start: 0.7770 (m-80) cc_final: 0.7399 (m-80) outliers start: 1 outliers final: 1 residues processed: 389 average time/residue: 0.1106 time to fit residues: 64.9501 Evaluate side-chains 301 residues out of total 1448 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 300 time to evaluate : 0.549 ------------------------------------------------------------------------------- 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: 9.9990 chunk 5 optimal weight: 7.9990 chunk 97 optimal weight: 0.0000 chunk 44 optimal weight: 6.9990 chunk 22 optimal weight: 0.5980 chunk 33 optimal weight: 0.7980 chunk 70 optimal weight: 0.9990 chunk 142 optimal weight: 0.2980 chunk 67 optimal weight: 0.6980 chunk 140 optimal weight: 1.9990 chunk 150 optimal weight: 1.9990 overall best weight: 0.4784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 92 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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** ** C 93 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 37 GLN E 3 GLN E 77 GLN ** 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 = 0.3635 r_free = 0.3635 target = 0.093424 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3220 r_free = 0.3220 target = 0.073406 restraints weight = 51264.233| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3269 r_free = 0.3269 target = 0.075647 restraints weight = 34127.259| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3304 r_free = 0.3304 target = 0.077253 restraints weight = 25895.428| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 22)----------------| | r_work = 0.3327 r_free = 0.3327 target = 0.078343 restraints weight = 21271.451| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3339 r_free = 0.3339 target = 0.078929 restraints weight = 18487.411| |-----------------------------------------------------------------------------| r_work (final): 0.3330 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7580 moved from start: 0.4596 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.072 14597 Z= 0.155 Angle : 0.855 11.459 19939 Z= 0.402 Chirality : 0.051 0.373 2415 Planarity : 0.005 0.062 2359 Dihedral : 12.070 112.586 3617 Min Nonbonded Distance : 2.366 Molprobity Statistics. All-atom Clashscore : 13.77 Ramachandran Plot: Outliers : 0.55 % Allowed : 13.20 % Favored : 86.25 % Rotamer: Outliers : 0.00 % Allowed : 2.77 % Favored : 97.23 % 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 aren not related in a simple way. whole: -2.59 (0.20), residues: 1629 helix: -0.08 (0.30), residues: 298 sheet: -0.91 (0.31), residues: 292 loop : -2.64 (0.18), residues: 1039 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG E 30 TYR 0.020 0.002 TYR A 62 PHE 0.018 0.002 PHE C 117 TRP 0.028 0.002 TRP C 210 HIS 0.015 0.002 HIS B 170 Details of bonding type rmsd covalent geometry : bond 0.00333 (14484) covalent geometry : angle 0.78275 (19626) SS BOND : bond 0.00433 ( 26) SS BOND : angle 1.85655 ( 52) hydrogen bonds : bond 0.04094 ( 333) hydrogen bonds : angle 5.70101 ( 906) link_ALPHA1-2 : bond 0.01134 ( 2) link_ALPHA1-2 : angle 4.51516 ( 6) link_ALPHA1-3 : bond 0.01251 ( 13) link_ALPHA1-3 : angle 3.02266 ( 39) link_ALPHA1-6 : bond 0.01228 ( 10) link_ALPHA1-6 : angle 2.23951 ( 30) link_BETA1-4 : bond 0.00702 ( 27) link_BETA1-4 : angle 2.25399 ( 81) link_NAG-ASN : bond 0.00889 ( 35) link_NAG-ASN : angle 3.57112 ( 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 369 residues out of total 1448 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 369 time to evaluate : 0.549 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 77 THR cc_start: 0.9191 (m) cc_final: 0.8986 (t) REVERT: B 104 GLU cc_start: 0.8376 (tp30) cc_final: 0.7705 (mm-30) REVERT: B 142 LEU cc_start: 0.9137 (mp) cc_final: 0.8600 (tp) REVERT: B 150 TYR cc_start: 0.6731 (m-80) cc_final: 0.6056 (m-80) REVERT: B 194 MET cc_start: 0.8987 (tpp) cc_final: 0.8772 (tpp) REVERT: B 248 ARG cc_start: 0.7893 (tpp80) cc_final: 0.7629 (tpp80) REVERT: b 284 MET cc_start: 0.8412 (mmt) cc_final: 0.7995 (mmp) REVERT: b 289 GLU cc_start: 0.8780 (tp30) cc_final: 0.8384 (tp30) REVERT: b 311 ASP cc_start: 0.8885 (m-30) cc_final: 0.8637 (m-30) REVERT: b 325 ARG cc_start: 0.7379 (ptp90) cc_final: 0.6720 (ptp90) REVERT: b 344 LEU cc_start: 0.9124 (mp) cc_final: 0.8702 (mp) REVERT: b 346 ASN cc_start: 0.9245 (t0) cc_final: 0.8800 (t0) REVERT: A 62 TYR cc_start: 0.6495 (m-10) cc_final: 0.6086 (m-10) REVERT: A 75 MET cc_start: 0.8739 (mtp) cc_final: 0.8300 (ttm) REVERT: A 76 GLU cc_start: 0.8728 (tt0) cc_final: 0.7761 (tp30) REVERT: A 82 MET cc_start: 0.8739 (pmm) cc_final: 0.8344 (pmm) REVERT: A 140 PHE cc_start: 0.9261 (m-80) cc_final: 0.8732 (m-80) REVERT: A 219 TYR cc_start: 0.7846 (m-80) cc_final: 0.7287 (m-80) REVERT: a 265 THR cc_start: 0.8114 (m) cc_final: 0.7681 (p) REVERT: a 266 LEU cc_start: 0.8692 (mp) cc_final: 0.8407 (tp) REVERT: a 287 GLU cc_start: 0.8118 (mt-10) cc_final: 0.7643 (tm-30) REVERT: a 324 GLN cc_start: 0.8998 (tm-30) cc_final: 0.8736 (tm-30) REVERT: a 349 LEU cc_start: 0.8434 (tp) cc_final: 0.8207 (mt) REVERT: a 363 TYR cc_start: 0.8397 (p90) cc_final: 0.8088 (p90) REVERT: a 404 GLU cc_start: 0.8678 (tp30) cc_final: 0.8473 (tp30) REVERT: c 268 ASP cc_start: 0.7737 (p0) cc_final: 0.7344 (p0) REVERT: c 282 ARG cc_start: 0.8369 (ttt180) cc_final: 0.7164 (ptp-170) REVERT: c 314 ARG cc_start: 0.9075 (mtt90) cc_final: 0.8621 (ttm110) REVERT: c 320 LYS cc_start: 0.9376 (ttpt) cc_final: 0.8902 (ttmm) REVERT: c 349 LEU cc_start: 0.9172 (tp) cc_final: 0.8900 (tt) REVERT: c 368 LYS cc_start: 0.8970 (mtpp) cc_final: 0.8454 (mtpp) REVERT: c 369 TYR cc_start: 0.8562 (m-80) cc_final: 0.6737 (m-80) REVERT: c 387 LEU cc_start: 0.9268 (mt) cc_final: 0.8805 (mp) REVERT: D 34 MET cc_start: 0.8519 (mtm) cc_final: 0.7720 (mtp) REVERT: D 37 GLU cc_start: 0.6402 (mt-10) cc_final: 0.5968 (tt0) REVERT: H 86 ASP cc_start: 0.8330 (m-30) cc_final: 0.8115 (m-30) REVERT: H 96 PHE cc_start: 0.7985 (m-80) cc_final: 0.7521 (m-10) REVERT: H 101 ASP cc_start: 0.8221 (p0) cc_final: 0.7757 (p0) REVERT: L 6 GLN cc_start: 0.7585 (mt0) cc_final: 0.7160 (mp-120) REVERT: L 31 ASP cc_start: 0.8441 (p0) cc_final: 0.8121 (p0) REVERT: L 74 THR cc_start: 0.7962 (p) cc_final: 0.7709 (t) REVERT: L 78 MET cc_start: 0.8517 (tmm) cc_final: 0.8031 (tmm) REVERT: E 67 LEU cc_start: 0.8760 (mm) cc_final: 0.8230 (mm) REVERT: E 76 ASN cc_start: 0.7622 (m-40) cc_final: 0.7388 (m-40) REVERT: E 86 ASP cc_start: 0.9081 (m-30) cc_final: 0.8716 (m-30) REVERT: I 23 CYS cc_start: 0.3388 (t) cc_final: 0.3130 (t) REVERT: I 37 GLN cc_start: 0.7893 (pp30) cc_final: 0.7368 (tm-30) REVERT: I 83 PHE cc_start: 0.7806 (m-80) cc_final: 0.7511 (m-80) outliers start: 0 outliers final: 0 residues processed: 369 average time/residue: 0.1197 time to fit residues: 65.3638 Evaluate side-chains 290 residues out of total 1448 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 290 time to evaluate : 0.553 ------------------------------------------------------------------------------- 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: 0.0980 chunk 105 optimal weight: 9.9990 chunk 141 optimal weight: 5.9990 chunk 118 optimal weight: 0.9980 chunk 109 optimal weight: 7.9990 chunk 45 optimal weight: 10.0000 chunk 18 optimal weight: 0.9980 chunk 121 optimal weight: 0.0370 chunk 99 optimal weight: 3.9990 chunk 0 optimal weight: 9.9990 chunk 6 optimal weight: 0.9990 overall best weight: 0.6260 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 170 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 319 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** b 405 GLN ** A 170 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 93 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: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3630 r_free = 0.3630 target = 0.093111 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3210 r_free = 0.3210 target = 0.072754 restraints weight = 50731.951| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3264 r_free = 0.3264 target = 0.075251 restraints weight = 32443.200| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3302 r_free = 0.3302 target = 0.077004 restraints weight = 23846.652| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3328 r_free = 0.3328 target = 0.078220 restraints weight = 19159.583| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3345 r_free = 0.3345 target = 0.079018 restraints weight = 16411.319| |-----------------------------------------------------------------------------| r_work (final): 0.3338 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7556 moved from start: 0.4809 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 14597 Z= 0.152 Angle : 0.857 13.605 19939 Z= 0.404 Chirality : 0.051 0.375 2415 Planarity : 0.005 0.063 2359 Dihedral : 11.431 112.413 3617 Min Nonbonded Distance : 2.361 Molprobity Statistics. All-atom Clashscore : 13.16 Ramachandran Plot: Outliers : 0.49 % Allowed : 13.57 % Favored : 85.94 % Rotamer: Outliers : 0.00 % Allowed : 1.94 % Favored : 98.06 % 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 aren not related in a simple way. whole: -2.54 (0.20), residues: 1629 helix: -0.05 (0.30), residues: 298 sheet: -0.85 (0.31), residues: 298 loop : -2.62 (0.18), residues: 1033 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG E 30 TYR 0.023 0.002 TYR H 59 PHE 0.040 0.002 PHE A 140 TRP 0.034 0.002 TRP C 210 HIS 0.013 0.002 HIS B 170 Details of bonding type rmsd covalent geometry : bond 0.00318 (14484) covalent geometry : angle 0.79079 (19626) SS BOND : bond 0.00682 ( 26) SS BOND : angle 1.50139 ( 52) hydrogen bonds : bond 0.04029 ( 333) hydrogen bonds : angle 5.58527 ( 906) link_ALPHA1-2 : bond 0.01194 ( 2) link_ALPHA1-2 : angle 4.28284 ( 6) link_ALPHA1-3 : bond 0.01229 ( 13) link_ALPHA1-3 : angle 3.01570 ( 39) link_ALPHA1-6 : bond 0.01319 ( 10) link_ALPHA1-6 : angle 2.26415 ( 30) link_BETA1-4 : bond 0.00660 ( 27) link_BETA1-4 : angle 2.15003 ( 81) link_NAG-ASN : bond 0.00808 ( 35) link_NAG-ASN : angle 3.46570 ( 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 368 residues out of total 1448 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 368 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: B 77 THR cc_start: 0.9228 (m) cc_final: 0.9021 (t) REVERT: B 104 GLU cc_start: 0.8361 (tp30) cc_final: 0.7601 (mm-30) REVERT: B 142 LEU cc_start: 0.9174 (mp) cc_final: 0.8642 (tp) REVERT: B 194 MET cc_start: 0.9007 (tpp) cc_final: 0.8247 (tmm) REVERT: B 248 ARG cc_start: 0.7890 (tpp80) cc_final: 0.7672 (tpp80) REVERT: b 284 MET cc_start: 0.8351 (mmt) cc_final: 0.7935 (mmp) REVERT: b 289 GLU cc_start: 0.8720 (tp30) cc_final: 0.8386 (tp30) REVERT: b 311 ASP cc_start: 0.8977 (m-30) cc_final: 0.8709 (m-30) REVERT: b 317 ASP cc_start: 0.8992 (t0) cc_final: 0.8725 (t70) REVERT: b 325 ARG cc_start: 0.7433 (ptp90) cc_final: 0.7064 (ptp90) REVERT: b 346 ASN cc_start: 0.9236 (t0) cc_final: 0.8731 (t0) REVERT: A 75 MET cc_start: 0.8803 (mtp) cc_final: 0.8374 (ttm) REVERT: A 76 GLU cc_start: 0.8831 (tt0) cc_final: 0.7861 (tp30) REVERT: A 82 MET cc_start: 0.8826 (pmm) cc_final: 0.8411 (pmm) REVERT: A 219 TYR cc_start: 0.7919 (m-80) cc_final: 0.7517 (m-80) REVERT: a 265 THR cc_start: 0.8101 (m) cc_final: 0.7512 (p) REVERT: a 266 LEU cc_start: 0.8649 (mp) cc_final: 0.8443 (tp) REVERT: a 324 GLN cc_start: 0.9055 (tm-30) cc_final: 0.8745 (tm-30) REVERT: a 363 TYR cc_start: 0.8362 (p90) cc_final: 0.8016 (p90) REVERT: C 192 MET cc_start: 0.8478 (mmt) cc_final: 0.8225 (mmt) REVERT: c 268 ASP cc_start: 0.7653 (p0) cc_final: 0.7219 (p0) REVERT: c 282 ARG cc_start: 0.8324 (ttt180) cc_final: 0.7196 (ptp-170) REVERT: c 314 ARG cc_start: 0.9044 (mtt90) cc_final: 0.8579 (ttm110) REVERT: c 320 LYS cc_start: 0.9372 (ttpt) cc_final: 0.8918 (ttmm) REVERT: c 349 LEU cc_start: 0.9233 (tp) cc_final: 0.8914 (tt) REVERT: c 369 TYR cc_start: 0.8518 (m-80) cc_final: 0.6715 (m-80) REVERT: c 387 LEU cc_start: 0.9257 (mt) cc_final: 0.8815 (mp) REVERT: c 401 ASP cc_start: 0.8979 (p0) cc_final: 0.8376 (p0) REVERT: c 404 GLU cc_start: 0.9524 (mp0) cc_final: 0.9127 (pp20) REVERT: c 409 ASN cc_start: 0.9447 (t0) cc_final: 0.9016 (m110) REVERT: D 34 MET cc_start: 0.8489 (mtm) cc_final: 0.7767 (mtp) REVERT: D 37 GLU cc_start: 0.6512 (mt-10) cc_final: 0.6075 (mt-10) REVERT: D 95 TYR cc_start: 0.7466 (m-10) cc_final: 0.6794 (m-80) REVERT: D 105 ARG cc_start: 0.7627 (ptp-110) cc_final: 0.7034 (ptp-110) REVERT: H 86 ASP cc_start: 0.8396 (m-30) cc_final: 0.8132 (m-30) REVERT: H 96 PHE cc_start: 0.7803 (m-80) cc_final: 0.7315 (m-80) REVERT: L 6 GLN cc_start: 0.7998 (mt0) cc_final: 0.7323 (mp-120) REVERT: L 31 ASP cc_start: 0.8496 (p0) cc_final: 0.8074 (p0) REVERT: L 102 THR cc_start: 0.9048 (p) cc_final: 0.8810 (p) REVERT: E 3 GLN cc_start: 0.7603 (tm130) cc_final: 0.7368 (tm-30) REVERT: E 47 TRP cc_start: 0.8690 (t60) cc_final: 0.8365 (t60) REVERT: E 50 TYR cc_start: 0.8639 (p90) cc_final: 0.8372 (p90) REVERT: E 67 LEU cc_start: 0.8859 (mm) cc_final: 0.8314 (mm) REVERT: E 76 ASN cc_start: 0.7712 (m-40) cc_final: 0.7310 (m-40) REVERT: E 86 ASP cc_start: 0.8987 (m-30) cc_final: 0.8590 (m-30) REVERT: E 89 VAL cc_start: 0.7591 (t) cc_final: 0.7239 (p) REVERT: E 91 TYR cc_start: 0.7939 (m-10) cc_final: 0.7736 (m-80) REVERT: I 37 GLN cc_start: 0.7862 (pp30) cc_final: 0.7619 (tm-30) REVERT: I 83 PHE cc_start: 0.7900 (m-80) cc_final: 0.7541 (m-80) outliers start: 0 outliers final: 0 residues processed: 368 average time/residue: 0.1148 time to fit residues: 62.4747 Evaluate side-chains 278 residues out of total 1448 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 278 time to evaluate : 0.479 ------------------------------------------------------------------------------- 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: 1.9990 chunk 116 optimal weight: 6.9990 chunk 56 optimal weight: 4.9990 chunk 96 optimal weight: 0.0020 chunk 78 optimal weight: 0.0370 chunk 40 optimal weight: 10.0000 chunk 84 optimal weight: 7.9990 chunk 47 optimal weight: 20.0000 chunk 22 optimal weight: 0.5980 chunk 46 optimal weight: 2.9990 chunk 24 optimal weight: 10.0000 overall best weight: 1.1270 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 170 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** b 305 HIS ** 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** ** E 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 53 ASN ** 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 = 0.3607 r_free = 0.3607 target = 0.091905 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3194 r_free = 0.3194 target = 0.072017 restraints weight = 50346.626| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3243 r_free = 0.3243 target = 0.074196 restraints weight = 34194.694| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3277 r_free = 0.3277 target = 0.075731 restraints weight = 26017.727| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3297 r_free = 0.3297 target = 0.076707 restraints weight = 21468.797| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 44)----------------| | r_work = 0.3316 r_free = 0.3316 target = 0.077542 restraints weight = 18839.589| |-----------------------------------------------------------------------------| r_work (final): 0.3308 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7617 moved from start: 0.5054 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.065 14597 Z= 0.162 Angle : 0.844 13.505 19939 Z= 0.397 Chirality : 0.051 0.373 2415 Planarity : 0.005 0.063 2359 Dihedral : 11.007 111.779 3617 Min Nonbonded Distance : 2.352 Molprobity Statistics. All-atom Clashscore : 15.14 Ramachandran Plot: Outliers : 0.49 % Allowed : 13.51 % Favored : 86.00 % Rotamer: Outliers : 0.00 % Allowed : 1.59 % Favored : 98.41 % 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 aren not related in a simple way. whole: -2.50 (0.20), residues: 1629 helix: -0.10 (0.30), residues: 306 sheet: -0.76 (0.31), residues: 298 loop : -2.60 (0.18), residues: 1025 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG a 282 TYR 0.018 0.002 TYR H 59 PHE 0.018 0.002 PHE C 117 TRP 0.055 0.002 TRP L 35 HIS 0.012 0.002 HIS B 170 Details of bonding type rmsd covalent geometry : bond 0.00350 (14484) covalent geometry : angle 0.78034 (19626) SS BOND : bond 0.00480 ( 26) SS BOND : angle 1.30636 ( 52) hydrogen bonds : bond 0.03867 ( 333) hydrogen bonds : angle 5.53862 ( 906) link_ALPHA1-2 : bond 0.01102 ( 2) link_ALPHA1-2 : angle 4.02784 ( 6) link_ALPHA1-3 : bond 0.01245 ( 13) link_ALPHA1-3 : angle 3.01644 ( 39) link_ALPHA1-6 : bond 0.01347 ( 10) link_ALPHA1-6 : angle 2.29441 ( 30) link_BETA1-4 : bond 0.00615 ( 27) link_BETA1-4 : angle 2.05139 ( 81) link_NAG-ASN : bond 0.00796 ( 35) link_NAG-ASN : angle 3.42131 ( 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 352 residues out of total 1448 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 352 time to evaluate : 0.473 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: B 77 THR cc_start: 0.9270 (m) cc_final: 0.9035 (t) REVERT: B 82 MET cc_start: 0.8418 (ptp) cc_final: 0.7609 (pmm) REVERT: B 104 GLU cc_start: 0.8323 (tp30) cc_final: 0.7376 (mm-30) REVERT: B 142 LEU cc_start: 0.9109 (mp) cc_final: 0.8660 (tp) REVERT: B 194 MET cc_start: 0.9027 (tpp) cc_final: 0.8770 (tpp) REVERT: b 284 MET cc_start: 0.8403 (mmt) cc_final: 0.8027 (mmp) REVERT: b 289 GLU cc_start: 0.8728 (tp30) cc_final: 0.8415 (tp30) REVERT: b 317 ASP cc_start: 0.8900 (t0) cc_final: 0.8588 (t70) REVERT: b 325 ARG cc_start: 0.7482 (ptp90) cc_final: 0.7057 (ptp90) REVERT: b 346 ASN cc_start: 0.9321 (t0) cc_final: 0.8891 (t0) REVERT: b 414 MET cc_start: 0.8739 (tmm) cc_final: 0.7707 (tmm) REVERT: b 415 LEU cc_start: 0.9565 (tt) cc_final: 0.9193 (tt) REVERT: A 75 MET cc_start: 0.8752 (mtp) cc_final: 0.8414 (ttm) REVERT: A 76 GLU cc_start: 0.8799 (tt0) cc_final: 0.7829 (tp30) REVERT: A 82 MET cc_start: 0.8924 (pmm) cc_final: 0.8449 (pmm) REVERT: A 134 MET cc_start: 0.8514 (mmm) cc_final: 0.8019 (mmm) REVERT: A 219 TYR cc_start: 0.7925 (m-80) cc_final: 0.7502 (m-80) REVERT: A 241 TYR cc_start: 0.8610 (t80) cc_final: 0.8195 (t80) REVERT: A 247 GLN cc_start: 0.6510 (mp10) cc_final: 0.6199 (tt0) REVERT: a 265 THR cc_start: 0.8084 (m) cc_final: 0.6879 (p) REVERT: a 266 LEU cc_start: 0.8656 (mp) cc_final: 0.8419 (tp) REVERT: a 268 ASP cc_start: 0.8426 (m-30) cc_final: 0.8086 (m-30) REVERT: a 324 GLN cc_start: 0.9058 (tm-30) cc_final: 0.8747 (tm-30) REVERT: a 347 ASP cc_start: 0.8676 (m-30) cc_final: 0.8236 (t0) REVERT: a 363 TYR cc_start: 0.8357 (p90) cc_final: 0.8146 (p90) REVERT: C 103 LEU cc_start: 0.8220 (mm) cc_final: 0.8014 (mt) REVERT: C 192 MET cc_start: 0.8535 (mmt) cc_final: 0.8218 (mmt) REVERT: C 241 TYR cc_start: 0.9212 (t80) cc_final: 0.8717 (t80) REVERT: c 268 ASP cc_start: 0.7627 (p0) cc_final: 0.7185 (p0) REVERT: c 282 ARG cc_start: 0.8374 (ttt180) cc_final: 0.7168 (ptp-170) REVERT: c 314 ARG cc_start: 0.9024 (mtt90) cc_final: 0.8522 (ttm110) REVERT: c 320 LYS cc_start: 0.9409 (ttpt) cc_final: 0.8912 (ttmt) REVERT: c 359 MET cc_start: 0.8947 (mmp) cc_final: 0.8732 (mmp) REVERT: c 369 TYR cc_start: 0.8643 (m-80) cc_final: 0.6863 (m-80) REVERT: c 387 LEU cc_start: 0.9323 (mt) cc_final: 0.8929 (mp) REVERT: c 406 GLN cc_start: 0.9010 (tp40) cc_final: 0.8800 (tp40) REVERT: c 409 ASN cc_start: 0.9431 (t0) cc_final: 0.9129 (m110) REVERT: D 34 MET cc_start: 0.8572 (mtm) cc_final: 0.7863 (mtp) REVERT: D 37 GLU cc_start: 0.6430 (mt-10) cc_final: 0.5865 (mt-10) REVERT: D 105 ARG cc_start: 0.7619 (ptp-110) cc_final: 0.7392 (ptp90) REVERT: H 86 ASP cc_start: 0.8429 (m-30) cc_final: 0.8168 (m-30) REVERT: H 101 ASP cc_start: 0.8062 (p0) cc_final: 0.7203 (p0) REVERT: H 102 TYR cc_start: 0.8014 (m-10) cc_final: 0.7454 (m-10) REVERT: L 6 GLN cc_start: 0.7951 (mt0) cc_final: 0.7033 (mp-120) REVERT: L 23 CYS cc_start: 0.6060 (t) cc_final: 0.4367 (t) REVERT: L 31 ASP cc_start: 0.8519 (p0) cc_final: 0.8193 (p0) REVERT: L 83 PHE cc_start: 0.7545 (m-80) cc_final: 0.7283 (m-80) REVERT: E 47 TRP cc_start: 0.8766 (t60) cc_final: 0.8262 (t60) REVERT: E 67 LEU cc_start: 0.9225 (mm) cc_final: 0.8885 (mm) REVERT: E 76 ASN cc_start: 0.7719 (m-40) cc_final: 0.7466 (m-40) REVERT: E 86 ASP cc_start: 0.9029 (m-30) cc_final: 0.8613 (m-30) REVERT: E 89 VAL cc_start: 0.7620 (t) cc_final: 0.7308 (p) REVERT: E 91 TYR cc_start: 0.8007 (m-10) cc_final: 0.7784 (m-80) REVERT: I 37 GLN cc_start: 0.8003 (pp30) cc_final: 0.7543 (tm-30) REVERT: I 78 MET cc_start: 0.8961 (tpt) cc_final: 0.8681 (tpt) REVERT: I 83 PHE cc_start: 0.7919 (m-80) cc_final: 0.7626 (m-80) outliers start: 0 outliers final: 0 residues processed: 352 average time/residue: 0.1095 time to fit residues: 57.3055 Evaluate side-chains 273 residues out of total 1448 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 273 time to evaluate : 0.522 ------------------------------------------------------------------------------- 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: 4.9990 chunk 36 optimal weight: 3.9990 chunk 105 optimal weight: 7.9990 chunk 135 optimal weight: 0.4980 chunk 118 optimal weight: 1.9990 chunk 102 optimal weight: 1.9990 chunk 113 optimal weight: 4.9990 chunk 27 optimal weight: 2.9990 chunk 108 optimal weight: 9.9990 chunk 139 optimal weight: 2.9990 chunk 49 optimal weight: 0.0980 overall best weight: 1.5186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 92 HIS ** B 170 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 230 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** ** 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: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3584 r_free = 0.3584 target = 0.090687 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3175 r_free = 0.3175 target = 0.071067 restraints weight = 51570.844| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3215 r_free = 0.3215 target = 0.073127 restraints weight = 37090.264| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3244 r_free = 0.3244 target = 0.074351 restraints weight = 27504.517| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3258 r_free = 0.3258 target = 0.075004 restraints weight = 22933.257| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3264 r_free = 0.3264 target = 0.075264 restraints weight = 21351.524| |-----------------------------------------------------------------------------| r_work (final): 0.3254 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7709 moved from start: 0.5314 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 14597 Z= 0.181 Angle : 0.879 12.198 19939 Z= 0.415 Chirality : 0.052 0.427 2415 Planarity : 0.005 0.063 2359 Dihedral : 10.801 111.252 3617 Min Nonbonded Distance : 2.343 Molprobity Statistics. All-atom Clashscore : 15.43 Ramachandran Plot: Outliers : 0.49 % Allowed : 14.00 % Favored : 85.51 % Rotamer: Outliers : 0.00 % Allowed : 1.25 % Favored : 98.75 % 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 aren not related in a simple way. whole: -2.50 (0.20), residues: 1629 helix: -0.07 (0.29), residues: 307 sheet: -0.81 (0.31), residues: 293 loop : -2.58 (0.19), residues: 1029 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG L 66 TYR 0.030 0.002 TYR B 94 PHE 0.023 0.002 PHE H 96 TRP 0.041 0.003 TRP C 210 HIS 0.016 0.002 HIS B 92 Details of bonding type rmsd covalent geometry : bond 0.00393 (14484) covalent geometry : angle 0.81391 (19626) SS BOND : bond 0.00447 ( 26) SS BOND : angle 1.25497 ( 52) hydrogen bonds : bond 0.04017 ( 333) hydrogen bonds : angle 5.63536 ( 906) link_ALPHA1-2 : bond 0.01037 ( 2) link_ALPHA1-2 : angle 3.78809 ( 6) link_ALPHA1-3 : bond 0.01216 ( 13) link_ALPHA1-3 : angle 3.00883 ( 39) link_ALPHA1-6 : bond 0.01390 ( 10) link_ALPHA1-6 : angle 2.35451 ( 30) link_BETA1-4 : bond 0.00591 ( 27) link_BETA1-4 : angle 1.99233 ( 81) link_NAG-ASN : bond 0.00880 ( 35) link_NAG-ASN : angle 3.62656 ( 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 355 residues out of total 1448 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 355 time to evaluate : 0.553 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 77 THR cc_start: 0.9274 (m) cc_final: 0.8977 (t) REVERT: B 82 MET cc_start: 0.8511 (ptp) cc_final: 0.7706 (pmm) REVERT: B 104 GLU cc_start: 0.8791 (tp30) cc_final: 0.8370 (tp30) REVERT: B 142 LEU cc_start: 0.9017 (mp) cc_final: 0.8707 (tp) REVERT: B 194 MET cc_start: 0.9045 (tpp) cc_final: 0.8797 (tpp) REVERT: b 284 MET cc_start: 0.8466 (mmt) cc_final: 0.8058 (mmp) REVERT: b 317 ASP cc_start: 0.8799 (t0) cc_final: 0.8512 (t70) REVERT: b 344 LEU cc_start: 0.9067 (mm) cc_final: 0.8690 (mp) REVERT: b 346 ASN cc_start: 0.9317 (t0) cc_final: 0.8931 (t0) REVERT: b 348 GLN cc_start: 0.8167 (pt0) cc_final: 0.7838 (mp10) REVERT: b 416 GLN cc_start: 0.9155 (tp-100) cc_final: 0.8868 (tp-100) REVERT: A 75 MET cc_start: 0.8795 (mtp) cc_final: 0.8505 (ttm) REVERT: A 76 GLU cc_start: 0.8776 (tt0) cc_final: 0.7855 (tp30) REVERT: A 82 MET cc_start: 0.8984 (pmm) cc_final: 0.8544 (pmm) REVERT: A 219 TYR cc_start: 0.7988 (m-80) cc_final: 0.7527 (m-80) REVERT: A 241 TYR cc_start: 0.8709 (t80) cc_final: 0.8390 (t80) REVERT: a 265 THR cc_start: 0.8129 (m) cc_final: 0.6940 (p) REVERT: a 266 LEU cc_start: 0.8667 (mp) cc_final: 0.8352 (tp) REVERT: a 268 ASP cc_start: 0.8430 (m-30) cc_final: 0.8218 (m-30) REVERT: a 332 MET cc_start: 0.6509 (mtt) cc_final: 0.6288 (mtt) REVERT: a 347 ASP cc_start: 0.8710 (m-30) cc_final: 0.8254 (t0) REVERT: a 363 TYR cc_start: 0.8390 (p90) cc_final: 0.8107 (p90) REVERT: C 164 VAL cc_start: 0.8371 (t) cc_final: 0.8151 (t) REVERT: C 192 MET cc_start: 0.8519 (mmt) cc_final: 0.8153 (mmt) REVERT: C 241 TYR cc_start: 0.9235 (t80) cc_final: 0.8854 (t80) REVERT: c 268 ASP cc_start: 0.7584 (p0) cc_final: 0.7104 (p0) REVERT: c 282 ARG cc_start: 0.8304 (ttt180) cc_final: 0.7113 (ptp-170) REVERT: c 314 ARG cc_start: 0.9074 (mtt90) cc_final: 0.8588 (ttm110) REVERT: c 320 LYS cc_start: 0.9429 (ttpt) cc_final: 0.8884 (ttmt) REVERT: c 321 GLN cc_start: 0.8822 (mm-40) cc_final: 0.8570 (mm110) REVERT: c 359 MET cc_start: 0.8919 (mmp) cc_final: 0.8719 (mmp) REVERT: c 369 TYR cc_start: 0.8662 (m-80) cc_final: 0.6897 (m-80) REVERT: c 387 LEU cc_start: 0.9356 (mt) cc_final: 0.8860 (mt) REVERT: D 34 MET cc_start: 0.8720 (mtm) cc_final: 0.7965 (mtp) REVERT: D 37 GLU cc_start: 0.6375 (mt-10) cc_final: 0.5804 (mt-10) REVERT: H 86 ASP cc_start: 0.8460 (m-30) cc_final: 0.8197 (m-30) REVERT: L 6 GLN cc_start: 0.8129 (mt0) cc_final: 0.6996 (mp-120) REVERT: L 23 CYS cc_start: 0.6157 (t) cc_final: 0.4322 (t) REVERT: L 83 PHE cc_start: 0.7645 (m-80) cc_final: 0.7368 (m-80) REVERT: E 3 GLN cc_start: 0.7641 (tm-30) cc_final: 0.7431 (tm-30) REVERT: E 47 TRP cc_start: 0.8939 (t60) cc_final: 0.8209 (t60) REVERT: E 67 LEU cc_start: 0.9310 (mm) cc_final: 0.8965 (mm) REVERT: E 76 ASN cc_start: 0.7743 (m-40) cc_final: 0.7516 (m-40) REVERT: E 86 ASP cc_start: 0.9151 (m-30) cc_final: 0.8788 (m-30) REVERT: E 91 TYR cc_start: 0.8197 (m-10) cc_final: 0.7989 (m-80) REVERT: I 23 CYS cc_start: 0.3108 (t) cc_final: 0.2858 (t) REVERT: I 37 GLN cc_start: 0.8032 (pp30) cc_final: 0.7650 (pp30) outliers start: 0 outliers final: 0 residues processed: 355 average time/residue: 0.1138 time to fit residues: 59.7679 Evaluate side-chains 269 residues out of total 1448 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 269 time to evaluate : 0.566 ------------------------------------------------------------------------------- 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: 2.9990 chunk 63 optimal weight: 2.9990 chunk 114 optimal weight: 9.9990 chunk 116 optimal weight: 7.9990 chunk 45 optimal weight: 0.9980 chunk 129 optimal weight: 10.0000 chunk 97 optimal weight: 2.9990 chunk 69 optimal weight: 10.0000 chunk 140 optimal weight: 0.7980 chunk 15 optimal weight: 10.0000 chunk 43 optimal weight: 10.0000 overall best weight: 2.1586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 170 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 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** ** 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: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3529 r_free = 0.3529 target = 0.087863 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3095 r_free = 0.3095 target = 0.067338 restraints weight = 51041.859| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3145 r_free = 0.3145 target = 0.069532 restraints weight = 33204.696| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3182 r_free = 0.3182 target = 0.071159 restraints weight = 24937.123| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3205 r_free = 0.3205 target = 0.072214 restraints weight = 20343.726| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3223 r_free = 0.3223 target = 0.073032 restraints weight = 17666.215| |-----------------------------------------------------------------------------| r_work (final): 0.3214 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7748 moved from start: 0.5568 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.076 14597 Z= 0.213 Angle : 0.896 13.717 19939 Z= 0.427 Chirality : 0.052 0.374 2415 Planarity : 0.006 0.125 2359 Dihedral : 10.731 110.317 3617 Min Nonbonded Distance : 2.315 Molprobity Statistics. All-atom Clashscore : 16.91 Ramachandran Plot: Outliers : 0.55 % Allowed : 14.86 % Favored : 84.59 % Rotamer: Outliers : 0.00 % Allowed : 1.04 % Favored : 98.96 % 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 aren not related in a simple way. whole: -2.58 (0.20), residues: 1629 helix: -0.11 (0.29), residues: 308 sheet: -0.83 (0.31), residues: 291 loop : -2.66 (0.18), residues: 1030 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG L 66 TYR 0.029 0.003 TYR B 94 PHE 0.026 0.002 PHE B 191 TRP 0.047 0.003 TRP E 103 HIS 0.011 0.002 HIS B 92 Details of bonding type rmsd covalent geometry : bond 0.00469 (14484) covalent geometry : angle 0.83409 (19626) SS BOND : bond 0.00506 ( 26) SS BOND : angle 1.37262 ( 52) hydrogen bonds : bond 0.04169 ( 333) hydrogen bonds : angle 5.63657 ( 906) link_ALPHA1-2 : bond 0.00928 ( 2) link_ALPHA1-2 : angle 3.52671 ( 6) link_ALPHA1-3 : bond 0.01170 ( 13) link_ALPHA1-3 : angle 3.02414 ( 39) link_ALPHA1-6 : bond 0.01388 ( 10) link_ALPHA1-6 : angle 2.42306 ( 30) link_BETA1-4 : bond 0.00574 ( 27) link_BETA1-4 : angle 1.97005 ( 81) link_NAG-ASN : bond 0.00770 ( 35) link_NAG-ASN : angle 3.57149 ( 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 326 residues out of total 1448 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 326 time to evaluate : 0.533 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: B 82 MET cc_start: 0.8520 (ptp) cc_final: 0.7650 (pmm) REVERT: B 104 GLU cc_start: 0.8697 (tp30) cc_final: 0.8204 (tp30) REVERT: B 142 LEU cc_start: 0.9045 (mp) cc_final: 0.8805 (tp) REVERT: B 150 TYR cc_start: 0.7106 (m-80) cc_final: 0.6744 (m-80) REVERT: B 192 MET cc_start: 0.9296 (mmt) cc_final: 0.8927 (mmm) REVERT: B 194 MET cc_start: 0.9122 (tpp) cc_final: 0.8890 (tpp) REVERT: b 284 MET cc_start: 0.8558 (mmt) cc_final: 0.8111 (mmp) REVERT: b 317 ASP cc_start: 0.8980 (t0) cc_final: 0.8691 (t70) REVERT: b 344 LEU cc_start: 0.9080 (mm) cc_final: 0.8687 (mp) REVERT: b 346 ASN cc_start: 0.9281 (t0) cc_final: 0.8726 (t0) REVERT: b 348 GLN cc_start: 0.8126 (pt0) cc_final: 0.7760 (mp10) REVERT: b 351 MET cc_start: 0.9262 (mmt) cc_final: 0.9058 (mmp) REVERT: b 369 TYR cc_start: 0.8797 (m-80) cc_final: 0.7992 (m-10) REVERT: b 410 MET cc_start: 0.9165 (mmp) cc_final: 0.8905 (mmt) REVERT: b 416 GLN cc_start: 0.9064 (tp-100) cc_final: 0.8841 (tp-100) REVERT: A 75 MET cc_start: 0.8860 (mtp) cc_final: 0.8542 (ttm) REVERT: A 76 GLU cc_start: 0.8893 (tt0) cc_final: 0.8012 (tp30) REVERT: A 82 MET cc_start: 0.8973 (pmm) cc_final: 0.8581 (pmm) REVERT: A 219 TYR cc_start: 0.8024 (m-80) cc_final: 0.7529 (m-80) REVERT: A 241 TYR cc_start: 0.8888 (t80) cc_final: 0.8586 (t80) REVERT: a 265 THR cc_start: 0.8016 (m) cc_final: 0.6857 (p) REVERT: a 266 LEU cc_start: 0.8567 (mp) cc_final: 0.8288 (tp) REVERT: a 268 ASP cc_start: 0.8553 (m-30) cc_final: 0.8264 (m-30) REVERT: a 347 ASP cc_start: 0.8692 (m-30) cc_final: 0.8222 (t0) REVERT: a 363 TYR cc_start: 0.8419 (p90) cc_final: 0.8015 (p90) REVERT: C 82 MET cc_start: 0.8826 (mmm) cc_final: 0.8430 (mmp) REVERT: C 103 LEU cc_start: 0.8602 (mm) cc_final: 0.8396 (mm) REVERT: C 164 VAL cc_start: 0.8341 (t) cc_final: 0.8058 (t) REVERT: C 192 MET cc_start: 0.8657 (mmt) cc_final: 0.8123 (mmt) REVERT: C 214 MET cc_start: 0.6208 (mtm) cc_final: 0.5083 (mtm) REVERT: C 241 TYR cc_start: 0.9291 (t80) cc_final: 0.8963 (t80) REVERT: c 268 ASP cc_start: 0.7604 (p0) cc_final: 0.7121 (p0) REVERT: c 282 ARG cc_start: 0.8445 (ttt180) cc_final: 0.7231 (ptp-170) REVERT: c 311 ASP cc_start: 0.9196 (m-30) cc_final: 0.8718 (m-30) REVERT: c 320 LYS cc_start: 0.9429 (ttpt) cc_final: 0.8897 (ttmt) REVERT: c 321 GLN cc_start: 0.8875 (mm-40) cc_final: 0.8574 (mm110) REVERT: c 369 TYR cc_start: 0.8774 (m-80) cc_final: 0.7986 (m-80) REVERT: c 387 LEU cc_start: 0.9349 (mt) cc_final: 0.8797 (mt) REVERT: c 401 ASP cc_start: 0.8923 (p0) cc_final: 0.8219 (p0) REVERT: c 404 GLU cc_start: 0.9573 (mp0) cc_final: 0.9135 (pp20) REVERT: c 410 MET cc_start: 0.8473 (tpt) cc_final: 0.7349 (tpt) REVERT: c 414 MET cc_start: 0.8459 (ptp) cc_final: 0.8057 (ptp) REVERT: D 34 MET cc_start: 0.8688 (mtm) cc_final: 0.8020 (mtp) REVERT: D 37 GLU cc_start: 0.6208 (mt-10) cc_final: 0.5931 (mt-10) REVERT: D 81 LEU cc_start: 0.8644 (mm) cc_final: 0.8368 (mm) REVERT: D 104 LEU cc_start: 0.7960 (pp) cc_final: 0.7707 (pp) REVERT: H 86 ASP cc_start: 0.8547 (m-30) cc_final: 0.8257 (m-30) REVERT: L 6 GLN cc_start: 0.8089 (mt0) cc_final: 0.7490 (mp-120) REVERT: E 3 GLN cc_start: 0.7633 (tm-30) cc_final: 0.7422 (tm-30) REVERT: E 47 TRP cc_start: 0.9055 (t60) cc_final: 0.8182 (t60) REVERT: E 67 LEU cc_start: 0.9348 (mm) cc_final: 0.9000 (mm) REVERT: E 76 ASN cc_start: 0.7957 (m-40) cc_final: 0.7740 (m-40) REVERT: E 86 ASP cc_start: 0.9291 (m-30) cc_final: 0.8767 (m-30) REVERT: I 37 GLN cc_start: 0.8197 (pp30) cc_final: 0.7707 (tm-30) REVERT: I 53 THR cc_start: 0.9488 (m) cc_final: 0.9071 (p) REVERT: I 78 MET cc_start: 0.8979 (tpt) cc_final: 0.8752 (tpt) REVERT: I 83 PHE cc_start: 0.8165 (m-80) cc_final: 0.7689 (m-80) outliers start: 0 outliers final: 0 residues processed: 326 average time/residue: 0.1165 time to fit residues: 57.0273 Evaluate side-chains 255 residues out of total 1448 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 255 time to evaluate : 0.586 ------------------------------------------------------------------------------- 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: 0.9980 chunk 113 optimal weight: 6.9990 chunk 132 optimal weight: 0.4980 chunk 77 optimal weight: 0.9990 chunk 80 optimal weight: 9.9990 chunk 54 optimal weight: 1.9990 chunk 154 optimal weight: 2.9990 chunk 67 optimal weight: 4.9990 chunk 36 optimal weight: 4.9990 chunk 91 optimal weight: 0.0020 chunk 75 optimal weight: 3.9990 overall best weight: 0.8992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 131 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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** D 84 ASN E 3 GLN ** I 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3580 r_free = 0.3580 target = 0.090417 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3157 r_free = 0.3157 target = 0.070201 restraints weight = 51262.802| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3206 r_free = 0.3206 target = 0.072379 restraints weight = 34698.877| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3240 r_free = 0.3240 target = 0.073881 restraints weight = 26532.905| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3264 r_free = 0.3264 target = 0.074986 restraints weight = 21948.385| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3281 r_free = 0.3281 target = 0.075754 restraints weight = 19095.737| |-----------------------------------------------------------------------------| r_work (final): 0.3270 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7687 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 : 0.003 0.037 14597 Z= 0.157 Angle : 0.871 12.823 19939 Z= 0.413 Chirality : 0.051 0.384 2415 Planarity : 0.005 0.062 2359 Dihedral : 10.313 110.796 3617 Min Nonbonded Distance : 2.348 Molprobity Statistics. All-atom Clashscore : 15.90 Ramachandran Plot: Outliers : 0.55 % Allowed : 13.69 % Favored : 85.76 % Rotamer: Outliers : 0.00 % Allowed : 0.42 % Favored : 99.58 % 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 aren not related in a simple way. whole: -2.50 (0.20), residues: 1629 helix: -0.14 (0.29), residues: 304 sheet: -0.83 (0.32), residues: 280 loop : -2.54 (0.19), residues: 1045 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG L 66 TYR 0.019 0.002 TYR A 62 PHE 0.017 0.001 PHE C 117 TRP 0.051 0.002 TRP C 210 HIS 0.011 0.002 HIS B 170 Details of bonding type rmsd covalent geometry : bond 0.00332 (14484) covalent geometry : angle 0.81083 (19626) SS BOND : bond 0.00615 ( 26) SS BOND : angle 1.48407 ( 52) hydrogen bonds : bond 0.03876 ( 333) hydrogen bonds : angle 5.49793 ( 906) link_ALPHA1-2 : bond 0.01134 ( 2) link_ALPHA1-2 : angle 3.69981 ( 6) link_ALPHA1-3 : bond 0.01269 ( 13) link_ALPHA1-3 : angle 2.99679 ( 39) link_ALPHA1-6 : bond 0.01401 ( 10) link_ALPHA1-6 : angle 2.35355 ( 30) link_BETA1-4 : bond 0.00599 ( 27) link_BETA1-4 : angle 1.88596 ( 81) link_NAG-ASN : bond 0.00803 ( 35) link_NAG-ASN : angle 3.42827 ( 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 343 residues out of total 1448 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 343 time to evaluate : 0.540 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: B 77 THR cc_start: 0.9252 (m) cc_final: 0.8939 (t) REVERT: B 82 MET cc_start: 0.8418 (ptp) cc_final: 0.7575 (pmm) REVERT: B 104 GLU cc_start: 0.8665 (tp30) cc_final: 0.8092 (tp30) REVERT: B 142 LEU cc_start: 0.8966 (mp) cc_final: 0.8669 (tp) REVERT: B 150 TYR cc_start: 0.6839 (m-80) cc_final: 0.6035 (m-80) REVERT: B 194 MET cc_start: 0.9006 (tpp) cc_final: 0.8403 (tmm) REVERT: b 273 ASP cc_start: 0.7101 (p0) cc_final: 0.6892 (p0) REVERT: b 284 MET cc_start: 0.8415 (mmt) cc_final: 0.7991 (mmp) REVERT: b 317 ASP cc_start: 0.8859 (t0) cc_final: 0.8518 (t70) REVERT: b 321 GLN cc_start: 0.8264 (tt0) cc_final: 0.7975 (tt0) REVERT: b 344 LEU cc_start: 0.9086 (mm) cc_final: 0.8712 (mp) REVERT: b 346 ASN cc_start: 0.9255 (t0) cc_final: 0.8704 (t0) REVERT: b 348 GLN cc_start: 0.8150 (pt0) cc_final: 0.7759 (mp10) REVERT: b 369 TYR cc_start: 0.8739 (m-80) cc_final: 0.8126 (m-10) REVERT: b 410 MET cc_start: 0.9067 (mmp) cc_final: 0.8852 (mmt) REVERT: b 416 GLN cc_start: 0.9032 (tp-100) cc_final: 0.8825 (tp-100) REVERT: A 75 MET cc_start: 0.8747 (mtp) cc_final: 0.8403 (ttm) REVERT: A 76 GLU cc_start: 0.8789 (tt0) cc_final: 0.7903 (tp30) REVERT: A 82 MET cc_start: 0.8986 (pmm) cc_final: 0.8591 (pmm) REVERT: A 134 MET cc_start: 0.8388 (mmm) cc_final: 0.7867 (mmm) REVERT: A 191 PHE cc_start: 0.8461 (t80) cc_final: 0.8244 (t80) REVERT: A 219 TYR cc_start: 0.7976 (m-80) cc_final: 0.7464 (m-80) REVERT: A 241 TYR cc_start: 0.8831 (t80) cc_final: 0.8539 (t80) REVERT: a 264 TRP cc_start: 0.7036 (m100) cc_final: 0.6354 (m-90) REVERT: a 265 THR cc_start: 0.8136 (m) cc_final: 0.7660 (p) REVERT: a 266 LEU cc_start: 0.8495 (mp) cc_final: 0.8252 (tp) REVERT: a 347 ASP cc_start: 0.8591 (m-30) cc_final: 0.8189 (t0) REVERT: C 82 MET cc_start: 0.8730 (mmm) cc_final: 0.8405 (mmp) REVERT: C 153 MET cc_start: 0.8221 (tmm) cc_final: 0.7955 (tmm) REVERT: C 164 VAL cc_start: 0.8163 (t) cc_final: 0.7890 (t) REVERT: C 192 MET cc_start: 0.8634 (mmt) cc_final: 0.8028 (mmt) REVERT: C 214 MET cc_start: 0.6186 (mtm) cc_final: 0.4988 (mtm) REVERT: C 241 TYR cc_start: 0.9188 (t80) cc_final: 0.8923 (t80) REVERT: c 268 ASP cc_start: 0.7708 (p0) cc_final: 0.7221 (p0) REVERT: c 282 ARG cc_start: 0.8209 (ttt180) cc_final: 0.7019 (ptp-170) REVERT: c 311 ASP cc_start: 0.8890 (m-30) cc_final: 0.8559 (m-30) REVERT: c 321 GLN cc_start: 0.8855 (mm-40) cc_final: 0.8528 (mm110) REVERT: c 359 MET cc_start: 0.8863 (mmp) cc_final: 0.8498 (mmm) REVERT: c 363 TYR cc_start: 0.7438 (p90) cc_final: 0.7180 (p90) REVERT: c 369 TYR cc_start: 0.8592 (m-80) cc_final: 0.6912 (m-80) REVERT: c 387 LEU cc_start: 0.9294 (mt) cc_final: 0.8811 (mt) REVERT: c 401 ASP cc_start: 0.8820 (p0) cc_final: 0.8088 (p0) REVERT: c 404 GLU cc_start: 0.9522 (mp0) cc_final: 0.9122 (pp20) REVERT: c 410 MET cc_start: 0.8383 (tpt) cc_final: 0.7242 (tpt) REVERT: c 414 MET cc_start: 0.8413 (ptp) cc_final: 0.7906 (ptp) REVERT: D 34 MET cc_start: 0.8626 (mtm) cc_final: 0.7932 (mtp) REVERT: D 37 GLU cc_start: 0.6157 (mt-10) cc_final: 0.5900 (mt-10) REVERT: D 75 TRP cc_start: 0.8073 (t-100) cc_final: 0.7699 (t-100) REVERT: H 86 ASP cc_start: 0.8361 (m-30) cc_final: 0.8070 (m-30) REVERT: L 6 GLN cc_start: 0.8056 (mt0) cc_final: 0.7142 (mp-120) REVERT: L 23 CYS cc_start: 0.5949 (t) cc_final: 0.4569 (t) REVERT: E 3 GLN cc_start: 0.7577 (tm130) cc_final: 0.7302 (tm-30) REVERT: E 47 TRP cc_start: 0.8914 (t60) cc_final: 0.8090 (t60) REVERT: E 67 LEU cc_start: 0.9266 (mm) cc_final: 0.8940 (mm) REVERT: E 76 ASN cc_start: 0.7713 (m-40) cc_final: 0.7507 (m-40) REVERT: E 86 ASP cc_start: 0.9247 (m-30) cc_final: 0.8736 (m-30) REVERT: E 89 VAL cc_start: 0.7588 (t) cc_final: 0.7369 (p) REVERT: I 37 GLN cc_start: 0.8036 (pp30) cc_final: 0.7668 (tm-30) outliers start: 0 outliers final: 0 residues processed: 343 average time/residue: 0.1184 time to fit residues: 60.7399 Evaluate side-chains 266 residues out of total 1448 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 266 time to evaluate : 0.557 ------------------------------------------------------------------------------- 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: 5.9990 chunk 136 optimal weight: 0.9980 chunk 101 optimal weight: 0.7980 chunk 75 optimal weight: 5.9990 chunk 103 optimal weight: 4.9990 chunk 156 optimal weight: 0.7980 chunk 98 optimal weight: 0.9980 chunk 41 optimal weight: 8.9990 chunk 28 optimal weight: 0.7980 chunk 62 optimal weight: 7.9990 chunk 21 optimal weight: 5.9990 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 131 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 170 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 319 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 324 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 170 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 189 GLN ** C 93 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 6 GLN 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 = 0.3580 r_free = 0.3580 target = 0.090168 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3162 r_free = 0.3162 target = 0.070273 restraints weight = 51183.611| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3211 r_free = 0.3211 target = 0.072666 restraints weight = 35290.229| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3236 r_free = 0.3236 target = 0.073719 restraints weight = 25195.669| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3263 r_free = 0.3263 target = 0.074907 restraints weight = 21074.084| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3267 r_free = 0.3267 target = 0.075073 restraints weight = 18726.836| |-----------------------------------------------------------------------------| r_work (final): 0.3255 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7700 moved from start: 0.5816 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 14597 Z= 0.158 Angle : 0.861 12.584 19939 Z= 0.408 Chirality : 0.051 0.369 2415 Planarity : 0.005 0.098 2359 Dihedral : 10.024 110.079 3617 Min Nonbonded Distance : 2.349 Molprobity Statistics. All-atom Clashscore : 15.61 Ramachandran Plot: Outliers : 0.55 % Allowed : 13.32 % Favored : 86.13 % Rotamer: Outliers : 0.00 % Allowed : 0.62 % Favored : 99.38 % 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 aren not related in a simple way. whole: -2.38 (0.21), residues: 1629 helix: -0.04 (0.30), residues: 303 sheet: -0.73 (0.33), residues: 280 loop : -2.46 (0.19), residues: 1046 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG I 66 TYR 0.025 0.002 TYR B 94 PHE 0.025 0.002 PHE I 83 TRP 0.047 0.003 TRP C 210 HIS 0.011 0.001 HIS B 170 Details of bonding type rmsd covalent geometry : bond 0.00336 (14484) covalent geometry : angle 0.79674 (19626) SS BOND : bond 0.00452 ( 26) SS BOND : angle 2.02119 ( 52) hydrogen bonds : bond 0.03774 ( 333) hydrogen bonds : angle 5.46263 ( 906) link_ALPHA1-2 : bond 0.01100 ( 2) link_ALPHA1-2 : angle 3.65761 ( 6) link_ALPHA1-3 : bond 0.01292 ( 13) link_ALPHA1-3 : angle 2.97742 ( 39) link_ALPHA1-6 : bond 0.01378 ( 10) link_ALPHA1-6 : angle 2.36295 ( 30) link_BETA1-4 : bond 0.00590 ( 27) link_BETA1-4 : angle 1.84742 ( 81) link_NAG-ASN : bond 0.00812 ( 35) link_NAG-ASN : angle 3.45683 ( 105) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2363.18 seconds wall clock time: 42 minutes 4.06 seconds (2524.06 seconds total)