Starting phenix.real_space_refine on Sun Nov 17 18:55:55 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8t5c_41048/11_2024/8t5c_41048.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8t5c_41048/11_2024/8t5c_41048.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8t5c_41048/11_2024/8t5c_41048.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8t5c_41048/11_2024/8t5c_41048.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8t5c_41048/11_2024/8t5c_41048.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8t5c_41048/11_2024/8t5c_41048.cif" } resolution = 4.7 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } 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): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5513/modules/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: 9.33, per 1000 atoms: 0.66 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: 4.44 Conformation dependent library (CDL) restraints added in 1.9 seconds 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: 1.25 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: 3.68 Time building geometry restraints manager: 4.94 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: 1.650 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: 0.640 Check model and map are aligned: 0.100 Set scattering table: 0.160 Process input model: 34.420 Find NCS groups from input model: 0.720 Set up NCS constraints: 0.090 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.850 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 40.640 ------------------------------------------------------------------------------- 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 14484 Z= 0.301 Angle : 0.839 15.219 19626 Z= 0.374 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 : 5.82 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. 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 TRP 0.021 0.001 TRP E 103 HIS 0.004 0.001 HIS B 92 PHE 0.015 0.001 PHE C 117 TYR 0.033 0.001 TYR b 363 ARG 0.004 0.000 ARG b 379 *********************** 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 : 1.575 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: 0.7240 (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: 0.9045 (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: 0.7636 (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: 0.6885 (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: 0.8612 (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: 0.7579 (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: 0.7245 (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: 0.8222 (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: 0.2794 time to fit residues: 232.2293 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 : 1.717 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 157 random chunks: chunk 132 optimal weight: 7.9990 chunk 118 optimal weight: 5.9990 chunk 66 optimal weight: 2.9990 chunk 40 optimal weight: 8.9990 chunk 80 optimal weight: 8.9990 chunk 63 optimal weight: 4.9990 chunk 123 optimal weight: 10.0000 chunk 47 optimal weight: 5.9990 chunk 74 optimal weight: 7.9990 chunk 91 optimal weight: 0.9990 chunk 142 optimal weight: 3.9990 overall best weight: 3.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 141 HIS B 189 GLN ** B 230 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 247 GLN ** b 319 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** b 321 GLN b 342 ASN b 354 HIS ** A 131 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 170 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 189 GLN C 141 HIS C 223 GLN c 305 HIS c 406 GLN D 39 GLN D 84 ASN ** H 60 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 37 GLN L 90 GLN E 76 ASN ** I 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7470 moved from start: 0.3664 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.095 14484 Z= 0.464 Angle : 0.982 12.213 19626 Z= 0.478 Chirality : 0.055 0.412 2415 Planarity : 0.006 0.063 2359 Dihedral : 16.930 112.516 3617 Min Nonbonded Distance : 2.279 Molprobity Statistics. All-atom Clashscore : 17.35 Ramachandran Plot: Outliers : 0.49 % Allowed : 15.47 % Favored : 84.04 % Rotamer: Outliers : 0.69 % Allowed : 8.31 % Favored : 91.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.83 (0.20), residues: 1629 helix: -0.58 (0.29), residues: 296 sheet: -1.20 (0.32), residues: 278 loop : -2.63 (0.18), residues: 1055 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.003 TRP E 103 HIS 0.015 0.002 HIS B 170 PHE 0.025 0.003 PHE c 318 TYR 0.026 0.003 TYR c 363 ARG 0.007 0.001 ARG D 57 *********************** 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 402 residues out of total 1448 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 392 time to evaluate : 1.512 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 75 MET cc_start: 0.8593 (mtm) cc_final: 0.8312 (mtm) REVERT: B 101 THR cc_start: 0.8795 (p) cc_final: 0.8499 (t) REVERT: B 104 GLU cc_start: 0.8438 (tt0) cc_final: 0.8165 (tt0) REVERT: B 142 LEU cc_start: 0.9271 (mp) cc_final: 0.8983 (tp) REVERT: B 157 PHE cc_start: 0.9093 (m-80) cc_final: 0.8696 (m-80) REVERT: B 248 ARG cc_start: 0.7842 (tpp80) cc_final: 0.7636 (tpp80) REVERT: B 251 ASP cc_start: 0.8186 (t0) cc_final: 0.7686 (p0) REVERT: b 270 GLU cc_start: 0.7847 (mp0) cc_final: 0.7267 (tp30) REVERT: b 311 ASP cc_start: 0.9042 (m-30) cc_final: 0.8626 (m-30) REVERT: b 325 ARG cc_start: 0.7739 (ptt180) cc_final: 0.7341 (ptp90) REVERT: b 345 ILE cc_start: 0.9540 (tp) cc_final: 0.9249 (tp) REVERT: b 346 ASN cc_start: 0.9007 (t0) cc_final: 0.8499 (t0) REVERT: b 357 ASP cc_start: 0.9127 (t70) cc_final: 0.8639 (t0) REVERT: b 380 THR cc_start: 0.9554 (p) cc_final: 0.9331 (t) REVERT: b 414 MET cc_start: 0.9282 (tmm) cc_final: 0.8618 (tmm) REVERT: A 75 MET cc_start: 0.8879 (mtp) cc_final: 0.8067 (ttm) REVERT: A 82 MET cc_start: 0.8625 (pmm) cc_final: 0.8226 (pmm) REVERT: A 133 LEU cc_start: 0.8686 (mm) cc_final: 0.7348 (mm) REVERT: A 134 MET cc_start: 0.8575 (mmm) cc_final: 0.8093 (mmm) REVERT: A 140 PHE cc_start: 0.9244 (m-80) cc_final: 0.8819 (m-80) REVERT: A 223 GLN cc_start: 0.8667 (mm110) cc_final: 0.8219 (mm110) REVERT: a 281 THR cc_start: 0.8131 (p) cc_final: 0.7747 (t) REVERT: a 283 TRP cc_start: 0.8760 (p-90) cc_final: 0.8054 (p-90) REVERT: a 284 MET cc_start: 0.9247 (mtm) cc_final: 0.8484 (mtm) REVERT: a 287 GLU cc_start: 0.8744 (mt-10) cc_final: 0.7860 (tm-30) REVERT: a 307 GLU cc_start: 0.8094 (tm-30) cc_final: 0.7759 (tm-30) REVERT: a 308 GLU cc_start: 0.9007 (mp0) cc_final: 0.8742 (pm20) REVERT: a 325 ARG cc_start: 0.8305 (ptp-170) cc_final: 0.7846 (ptp-170) REVERT: a 369 TYR cc_start: 0.9045 (m-80) cc_final: 0.8575 (m-80) REVERT: a 397 THR cc_start: 0.8865 (p) cc_final: 0.8540 (p) REVERT: C 75 MET cc_start: 0.9069 (mtm) cc_final: 0.8713 (mtm) REVERT: C 82 MET cc_start: 0.8195 (mmm) cc_final: 0.7654 (mmm) REVERT: C 92 HIS cc_start: 0.8450 (m-70) cc_final: 0.8016 (m90) REVERT: C 93 HIS cc_start: 0.8586 (m90) cc_final: 0.8383 (m-70) REVERT: C 149 GLN cc_start: 0.9279 (tp-100) cc_final: 0.8435 (tp-100) REVERT: C 241 TYR cc_start: 0.8788 (t80) cc_final: 0.8487 (t80) REVERT: c 268 ASP cc_start: 0.7374 (p0) cc_final: 0.6974 (p0) REVERT: c 282 ARG cc_start: 0.7954 (ttt180) cc_final: 0.6776 (ptp-170) REVERT: c 311 ASP cc_start: 0.9392 (m-30) cc_final: 0.9055 (m-30) REVERT: c 320 LYS cc_start: 0.9215 (ttpt) cc_final: 0.8984 (ttmm) REVERT: c 337 ILE cc_start: 0.9006 (mt) cc_final: 0.8068 (mt) REVERT: c 349 LEU cc_start: 0.9217 (tp) cc_final: 0.8938 (tp) REVERT: c 369 TYR cc_start: 0.8601 (m-80) cc_final: 0.7246 (m-80) REVERT: c 387 LEU cc_start: 0.9082 (mt) cc_final: 0.8666 (mp) REVERT: c 409 ASN cc_start: 0.9616 (t0) cc_final: 0.9244 (m110) REVERT: D 37 GLU cc_start: 0.6207 (mt-10) cc_final: 0.5782 (mt-10) REVERT: D 46 GLU cc_start: 0.8344 (pt0) cc_final: 0.7582 (pm20) REVERT: D 95 TYR cc_start: 0.7922 (m-10) cc_final: 0.7130 (m-80) REVERT: D 99 LEU cc_start: 0.9404 (mp) cc_final: 0.9160 (mp) REVERT: D 105 ARG cc_start: 0.8183 (ptp-110) cc_final: 0.7739 (ptp-110) REVERT: H 13 LYS cc_start: 0.9682 (tppt) cc_final: 0.9459 (tppt) REVERT: L 6 GLN cc_start: 0.7766 (mt0) cc_final: 0.7049 (mp-120) REVERT: L 23 CYS cc_start: 0.7311 (t) cc_final: 0.5425 (t) REVERT: L 37 GLN cc_start: 0.7734 (OUTLIER) cc_final: 0.7522 (tm-30) REVERT: L 78 MET cc_start: 0.8343 (tmm) cc_final: 0.8092 (tmm) REVERT: E 3 GLN cc_start: 0.8776 (tt0) cc_final: 0.8151 (tm-30) REVERT: E 67 LEU cc_start: 0.8479 (mm) cc_final: 0.7986 (mm) REVERT: E 86 ASP cc_start: 0.9024 (m-30) cc_final: 0.8466 (m-30) REVERT: I 66 ARG cc_start: 0.8869 (tmt170) cc_final: 0.8649 (tmt170) REVERT: I 78 MET cc_start: 0.8818 (tpp) cc_final: 0.8395 (tpp) REVERT: I 93 ASN cc_start: 0.9303 (m-40) cc_final: 0.8741 (p0) outliers start: 10 outliers final: 3 residues processed: 401 average time/residue: 0.2655 time to fit residues: 154.3404 Evaluate side-chains 298 residues out of total 1448 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 294 time to evaluate : 1.544 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 157 random chunks: chunk 79 optimal weight: 0.9990 chunk 44 optimal weight: 3.9990 chunk 118 optimal weight: 3.9990 chunk 97 optimal weight: 0.5980 chunk 39 optimal weight: 7.9990 chunk 142 optimal weight: 0.9980 chunk 154 optimal weight: 1.9990 chunk 127 optimal weight: 4.9990 chunk 141 optimal weight: 0.1980 chunk 48 optimal weight: 8.9990 chunk 114 optimal weight: 8.9990 overall best weight: 0.9584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 148 ASN ** B 170 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 319 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** b 342 ASN b 405 GLN A 131 HIS ** A 170 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 189 GLN a 353 ASN ** a 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 124 HIS c 353 ASN D 39 GLN ** I 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7383 moved from start: 0.4087 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.064 14484 Z= 0.238 Angle : 0.805 12.118 19626 Z= 0.396 Chirality : 0.052 0.351 2415 Planarity : 0.005 0.143 2359 Dihedral : 14.171 111.917 3617 Min Nonbonded Distance : 2.327 Molprobity Statistics. All-atom Clashscore : 13.34 Ramachandran Plot: Outliers : 0.49 % Allowed : 13.32 % Favored : 86.19 % Rotamer: Outliers : 0.35 % Allowed : 3.53 % Favored : 96.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.67 (0.20), residues: 1629 helix: -0.24 (0.30), residues: 292 sheet: -1.26 (0.31), residues: 281 loop : -2.53 (0.18), residues: 1056 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.002 TRP C 210 HIS 0.014 0.002 HIS B 170 PHE 0.017 0.002 PHE C 117 TYR 0.024 0.002 TYR A 129 ARG 0.015 0.001 ARG E 30 *********************** 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 407 residues out of total 1448 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 402 time to evaluate : 1.698 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 75 MET cc_start: 0.8493 (mtm) cc_final: 0.8198 (mtm) REVERT: B 101 THR cc_start: 0.8599 (p) cc_final: 0.8335 (t) REVERT: B 142 LEU cc_start: 0.9318 (mp) cc_final: 0.8984 (tp) REVERT: B 157 PHE cc_start: 0.9056 (m-80) cc_final: 0.8640 (m-80) REVERT: B 183 VAL cc_start: 0.8520 (t) cc_final: 0.8156 (m) REVERT: B 248 ARG cc_start: 0.7673 (tpp80) cc_final: 0.7374 (tpp80) REVERT: b 270 GLU cc_start: 0.7833 (mp0) cc_final: 0.7210 (tp30) REVERT: b 303 GLU cc_start: 0.8783 (tm-30) cc_final: 0.8444 (tm-30) REVERT: b 311 ASP cc_start: 0.9034 (m-30) cc_final: 0.8661 (m-30) REVERT: b 317 ASP cc_start: 0.9392 (t0) cc_final: 0.9171 (t70) REVERT: b 345 ILE cc_start: 0.9571 (tp) cc_final: 0.9357 (tp) REVERT: b 346 ASN cc_start: 0.8868 (t0) cc_final: 0.8340 (t0) REVERT: b 357 ASP cc_start: 0.9110 (t70) cc_final: 0.8674 (t0) REVERT: A 73 LEU cc_start: 0.8267 (mt) cc_final: 0.8028 (mt) REVERT: A 75 MET cc_start: 0.8968 (mtp) cc_final: 0.8528 (ttm) REVERT: A 82 MET cc_start: 0.8470 (pmm) cc_final: 0.8075 (pmm) REVERT: A 140 PHE cc_start: 0.9276 (m-80) cc_final: 0.8822 (m-80) REVERT: A 223 GLN cc_start: 0.8496 (mm110) cc_final: 0.8267 (mm110) REVERT: A 247 GLN cc_start: 0.7462 (mm-40) cc_final: 0.6736 (tt0) REVERT: a 266 LEU cc_start: 0.8798 (mp) cc_final: 0.8567 (tp) REVERT: a 281 THR cc_start: 0.7905 (p) cc_final: 0.6834 (p) REVERT: a 287 GLU cc_start: 0.8782 (mt-10) cc_final: 0.7841 (tm-30) REVERT: a 323 ILE cc_start: 0.9542 (tp) cc_final: 0.9333 (tp) REVERT: a 324 GLN cc_start: 0.9167 (tm-30) cc_final: 0.8827 (tm-30) REVERT: a 332 MET cc_start: 0.6741 (mtt) cc_final: 0.6507 (mtt) REVERT: a 351 MET cc_start: 0.8616 (mmm) cc_final: 0.8263 (mmm) REVERT: a 372 LEU cc_start: 0.9199 (mm) cc_final: 0.8709 (tp) REVERT: a 387 LEU cc_start: 0.8617 (mt) cc_final: 0.7763 (mt) REVERT: C 68 LEU cc_start: 0.8445 (tp) cc_final: 0.8067 (tp) REVERT: C 75 MET cc_start: 0.8989 (mtm) cc_final: 0.8704 (mtm) REVERT: C 92 HIS cc_start: 0.8328 (m-70) cc_final: 0.7948 (m90) REVERT: C 93 HIS cc_start: 0.8711 (m90) cc_final: 0.8349 (m-70) REVERT: C 242 LEU cc_start: 0.8671 (mm) cc_final: 0.8397 (tp) REVERT: c 268 ASP cc_start: 0.7431 (p0) cc_final: 0.7025 (p0) REVERT: c 282 ARG cc_start: 0.7802 (ttt180) cc_final: 0.6528 (ptp-170) REVERT: c 285 LEU cc_start: 0.9251 (mp) cc_final: 0.9048 (mp) REVERT: c 311 ASP cc_start: 0.9358 (m-30) cc_final: 0.9008 (m-30) REVERT: c 314 ARG cc_start: 0.9066 (mtt90) cc_final: 0.8369 (ttm110) REVERT: c 320 LYS cc_start: 0.9211 (ttpt) cc_final: 0.8965 (ttmm) REVERT: c 337 ILE cc_start: 0.9025 (mt) cc_final: 0.8518 (mt) REVERT: c 349 LEU cc_start: 0.9128 (tp) cc_final: 0.8779 (tt) REVERT: c 359 MET cc_start: 0.9110 (mmm) cc_final: 0.8697 (mmm) REVERT: c 369 TYR cc_start: 0.8538 (m-80) cc_final: 0.6481 (m-80) REVERT: c 387 LEU cc_start: 0.9153 (mt) cc_final: 0.8779 (mp) REVERT: D 6 GLU cc_start: 0.8811 (pt0) cc_final: 0.8202 (pm20) REVERT: D 30 SER cc_start: 0.8263 (p) cc_final: 0.7871 (m) REVERT: D 34 MET cc_start: 0.7845 (mtm) cc_final: 0.7096 (mtp) REVERT: D 37 GLU cc_start: 0.6167 (mt-10) cc_final: 0.5774 (mt-10) REVERT: D 46 GLU cc_start: 0.8255 (pt0) cc_final: 0.7810 (pm20) REVERT: D 95 TYR cc_start: 0.7714 (m-10) cc_final: 0.7194 (m-80) REVERT: D 96 CYS cc_start: 0.5985 (t) cc_final: 0.5699 (t) REVERT: D 99 LEU cc_start: 0.9369 (mp) cc_final: 0.9120 (mp) REVERT: D 105 ARG cc_start: 0.8028 (ptp-110) cc_final: 0.7500 (ptp-110) REVERT: H 3 GLN cc_start: 0.9017 (mp10) cc_final: 0.8591 (mp10) REVERT: H 27 VAL cc_start: 0.6479 (OUTLIER) cc_final: 0.5894 (p) REVERT: H 86 ASP cc_start: 0.8551 (m-30) cc_final: 0.8133 (m-30) REVERT: H 96 PHE cc_start: 0.8172 (m-80) cc_final: 0.7720 (m-80) REVERT: H 97 GLU cc_start: 0.6987 (mt-10) cc_final: 0.6650 (mt-10) REVERT: L 6 GLN cc_start: 0.8066 (mt0) cc_final: 0.7026 (mp-120) REVERT: L 31 ASP cc_start: 0.8625 (p0) cc_final: 0.8395 (p0) REVERT: L 74 THR cc_start: 0.8213 (m) cc_final: 0.7695 (t) REVERT: L 78 MET cc_start: 0.8566 (tmm) cc_final: 0.8339 (tmm) REVERT: L 79 GLN cc_start: 0.9139 (tt0) cc_final: 0.8840 (tm-30) REVERT: E 3 GLN cc_start: 0.8704 (tt0) cc_final: 0.8040 (tm-30) REVERT: E 46 GLU cc_start: 0.7725 (pm20) cc_final: 0.7363 (pm20) REVERT: E 47 TRP cc_start: 0.9114 (t60) cc_final: 0.7684 (t60) REVERT: E 67 LEU cc_start: 0.8361 (mm) cc_final: 0.7831 (mm) REVERT: E 86 ASP cc_start: 0.9009 (m-30) cc_final: 0.8456 (m-30) REVERT: I 23 CYS cc_start: 0.4863 (t) cc_final: 0.4552 (t) REVERT: I 48 ILE cc_start: 0.8782 (tp) cc_final: 0.8539 (tp) REVERT: I 66 ARG cc_start: 0.8757 (tmt170) cc_final: 0.8533 (tmm160) REVERT: I 75 ILE cc_start: 0.9213 (mt) cc_final: 0.8502 (tt) REVERT: I 77 ARG cc_start: 0.8863 (ptp90) cc_final: 0.8398 (ptp-170) REVERT: I 78 MET cc_start: 0.8770 (tpp) cc_final: 0.8304 (tpp) REVERT: I 93 ASN cc_start: 0.9252 (m-40) cc_final: 0.8180 (p0) outliers start: 5 outliers final: 2 residues processed: 406 average time/residue: 0.2662 time to fit residues: 157.2984 Evaluate side-chains 308 residues out of total 1448 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 305 time to evaluate : 1.691 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 157 random chunks: chunk 141 optimal weight: 0.8980 chunk 107 optimal weight: 0.7980 chunk 74 optimal weight: 10.0000 chunk 15 optimal weight: 10.0000 chunk 68 optimal weight: 7.9990 chunk 95 optimal weight: 10.0000 chunk 143 optimal weight: 3.9990 chunk 151 optimal weight: 0.5980 chunk 135 optimal weight: 2.9990 chunk 40 optimal weight: 5.9990 chunk 126 optimal weight: 0.8980 overall best weight: 1.2382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 141 HIS ** B 170 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 319 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** b 374 HIS b 405 GLN ** A 170 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 189 GLN ** a 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 189 GLN L 37 GLN L 89 GLN I 6 GLN ** I 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7411 moved from start: 0.4453 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.065 14484 Z= 0.243 Angle : 0.790 11.335 19626 Z= 0.388 Chirality : 0.051 0.354 2415 Planarity : 0.005 0.112 2359 Dihedral : 12.961 112.156 3617 Min Nonbonded Distance : 2.328 Molprobity Statistics. All-atom Clashscore : 13.95 Ramachandran Plot: Outliers : 0.49 % Allowed : 13.63 % Favored : 85.88 % Rotamer: Outliers : 0.14 % Allowed : 3.05 % Favored : 96.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.68 (0.20), residues: 1629 helix: -0.20 (0.30), residues: 300 sheet: -1.13 (0.32), residues: 276 loop : -2.61 (0.18), residues: 1053 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.002 TRP C 210 HIS 0.014 0.002 HIS B 170 PHE 0.019 0.002 PHE D 68 TYR 0.016 0.002 TYR E 91 ARG 0.013 0.001 ARG a 282 *********************** 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 374 residues out of total 1448 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 372 time to evaluate : 1.635 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 75 MET cc_start: 0.8458 (mtm) cc_final: 0.8168 (mtm) REVERT: B 101 THR cc_start: 0.8650 (p) cc_final: 0.8338 (t) REVERT: B 142 LEU cc_start: 0.9228 (mp) cc_final: 0.8907 (tp) REVERT: B 150 TYR cc_start: 0.7404 (m-80) cc_final: 0.6641 (m-80) REVERT: B 157 PHE cc_start: 0.9051 (m-80) cc_final: 0.8669 (m-80) REVERT: B 248 ARG cc_start: 0.7684 (tpp80) cc_final: 0.7462 (tpp80) REVERT: b 270 GLU cc_start: 0.7863 (mp0) cc_final: 0.7210 (tp30) REVERT: b 303 GLU cc_start: 0.8795 (tm-30) cc_final: 0.8481 (tm-30) REVERT: b 311 ASP cc_start: 0.8976 (m-30) cc_final: 0.8639 (m-30) REVERT: b 317 ASP cc_start: 0.9393 (t0) cc_final: 0.9131 (t70) REVERT: b 324 GLN cc_start: 0.8686 (tm-30) cc_final: 0.8390 (tm-30) REVERT: b 346 ASN cc_start: 0.8928 (t0) cc_final: 0.8356 (t0) REVERT: b 414 MET cc_start: 0.8902 (tmm) cc_final: 0.8352 (tmm) REVERT: A 62 TYR cc_start: 0.7854 (m-10) cc_final: 0.7420 (m-10) REVERT: A 75 MET cc_start: 0.9020 (mtp) cc_final: 0.8282 (ttm) REVERT: A 82 MET cc_start: 0.8591 (pmm) cc_final: 0.8197 (pmm) REVERT: A 122 ASP cc_start: 0.9425 (m-30) cc_final: 0.9067 (m-30) REVERT: A 126 LYS cc_start: 0.8722 (mmtm) cc_final: 0.8408 (mmtp) REVERT: A 140 PHE cc_start: 0.9262 (m-80) cc_final: 0.8836 (m-80) REVERT: A 223 GLN cc_start: 0.8550 (mm110) cc_final: 0.8290 (mm110) REVERT: A 247 GLN cc_start: 0.7404 (mm-40) cc_final: 0.6761 (tt0) REVERT: a 266 LEU cc_start: 0.8776 (mp) cc_final: 0.8474 (tp) REVERT: a 281 THR cc_start: 0.8103 (p) cc_final: 0.7058 (p) REVERT: a 283 TRP cc_start: 0.8540 (p-90) cc_final: 0.8186 (p-90) REVERT: a 284 MET cc_start: 0.9309 (mtm) cc_final: 0.9005 (mtt) REVERT: a 286 ILE cc_start: 0.8934 (tt) cc_final: 0.8691 (tt) REVERT: a 287 GLU cc_start: 0.8688 (mt-10) cc_final: 0.7860 (tm-30) REVERT: a 324 GLN cc_start: 0.9175 (tm-30) cc_final: 0.8768 (tm-30) REVERT: a 369 TYR cc_start: 0.8903 (m-80) cc_final: 0.8664 (m-80) REVERT: a 372 LEU cc_start: 0.9225 (mm) cc_final: 0.8754 (tp) REVERT: a 387 LEU cc_start: 0.8612 (mt) cc_final: 0.8251 (mm) REVERT: C 75 MET cc_start: 0.8988 (mtm) cc_final: 0.8645 (mtm) REVERT: C 82 MET cc_start: 0.8281 (mmm) cc_final: 0.7921 (mmm) REVERT: C 92 HIS cc_start: 0.8283 (m-70) cc_final: 0.7912 (m90) REVERT: C 93 HIS cc_start: 0.8765 (m90) cc_final: 0.8347 (m-70) REVERT: c 268 ASP cc_start: 0.7356 (p0) cc_final: 0.6884 (p0) REVERT: c 282 ARG cc_start: 0.7941 (ttt180) cc_final: 0.6725 (ptp-170) REVERT: c 311 ASP cc_start: 0.9407 (m-30) cc_final: 0.9155 (m-30) REVERT: c 314 ARG cc_start: 0.9049 (mtt90) cc_final: 0.8322 (ttm110) REVERT: c 320 LYS cc_start: 0.9212 (ttpt) cc_final: 0.8977 (ttmm) REVERT: c 337 ILE cc_start: 0.9113 (mt) cc_final: 0.8333 (mt) REVERT: c 349 LEU cc_start: 0.9152 (tp) cc_final: 0.8824 (tt) REVERT: c 359 MET cc_start: 0.9143 (mmm) cc_final: 0.8664 (mmm) REVERT: c 368 LYS cc_start: 0.8347 (mtpt) cc_final: 0.7780 (mtpt) REVERT: c 369 TYR cc_start: 0.8427 (m-80) cc_final: 0.6415 (m-80) REVERT: c 387 LEU cc_start: 0.9134 (mt) cc_final: 0.8743 (mp) REVERT: c 410 MET cc_start: 0.8793 (tpt) cc_final: 0.8315 (tpt) REVERT: D 6 GLU cc_start: 0.8930 (pt0) cc_final: 0.8221 (pm20) REVERT: D 30 SER cc_start: 0.8206 (p) cc_final: 0.7888 (m) REVERT: D 34 MET cc_start: 0.7881 (mtm) cc_final: 0.7490 (mtp) REVERT: D 37 GLU cc_start: 0.6396 (mt-10) cc_final: 0.5978 (mt-10) REVERT: D 46 GLU cc_start: 0.8689 (pt0) cc_final: 0.7918 (pm20) REVERT: D 95 TYR cc_start: 0.7821 (m-10) cc_final: 0.7259 (m-80) REVERT: D 96 CYS cc_start: 0.5711 (t) cc_final: 0.5403 (t) REVERT: D 99 LEU cc_start: 0.9375 (mp) cc_final: 0.9076 (mp) REVERT: D 104 LEU cc_start: 0.8052 (pp) cc_final: 0.7355 (pp) REVERT: D 105 ARG cc_start: 0.8252 (ptp-110) cc_final: 0.6939 (ptp-110) REVERT: H 13 LYS cc_start: 0.9709 (tppt) cc_final: 0.9467 (tppt) REVERT: H 86 ASP cc_start: 0.8686 (m-30) cc_final: 0.8290 (m-30) REVERT: L 6 GLN cc_start: 0.8035 (mt0) cc_final: 0.7201 (mp-120) REVERT: L 31 ASP cc_start: 0.8640 (p0) cc_final: 0.8369 (p0) REVERT: L 74 THR cc_start: 0.8183 (m) cc_final: 0.7765 (t) REVERT: L 79 GLN cc_start: 0.9150 (tt0) cc_final: 0.8870 (tm-30) REVERT: E 3 GLN cc_start: 0.8599 (tt0) cc_final: 0.7880 (tm-30) REVERT: E 47 TRP cc_start: 0.9097 (t60) cc_final: 0.7550 (t60) REVERT: E 67 LEU cc_start: 0.8410 (mm) cc_final: 0.7872 (mm) REVERT: E 86 ASP cc_start: 0.9073 (m-30) cc_final: 0.8511 (m-30) REVERT: I 23 CYS cc_start: 0.4492 (t) cc_final: 0.4139 (t) REVERT: I 37 GLN cc_start: 0.7915 (pp30) cc_final: 0.7629 (tm-30) REVERT: I 75 ILE cc_start: 0.9207 (mt) cc_final: 0.8463 (tt) REVERT: I 77 ARG cc_start: 0.8840 (ptp90) cc_final: 0.8377 (ptp-170) REVERT: I 78 MET cc_start: 0.8909 (tpp) cc_final: 0.8250 (tpp) REVERT: I 93 ASN cc_start: 0.9148 (m-40) cc_final: 0.8372 (p0) outliers start: 2 outliers final: 1 residues processed: 373 average time/residue: 0.2657 time to fit residues: 145.4221 Evaluate side-chains 298 residues out of total 1448 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 297 time to evaluate : 1.727 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 157 random chunks: chunk 86 optimal weight: 6.9990 chunk 2 optimal weight: 2.9990 chunk 112 optimal weight: 0.9980 chunk 62 optimal weight: 5.9990 chunk 129 optimal weight: 10.0000 chunk 104 optimal weight: 8.9990 chunk 0 optimal weight: 10.0000 chunk 77 optimal weight: 3.9990 chunk 136 optimal weight: 5.9990 chunk 38 optimal weight: 0.9980 chunk 51 optimal weight: 10.0000 overall best weight: 2.9986 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 319 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 170 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 179 HIS A 189 GLN ** a 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 189 GLN c 331 GLN E 53 ASN ** I 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7521 moved from start: 0.4994 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.082 14484 Z= 0.379 Angle : 0.863 12.956 19626 Z= 0.428 Chirality : 0.052 0.354 2415 Planarity : 0.005 0.103 2359 Dihedral : 12.397 110.898 3617 Min Nonbonded Distance : 2.290 Molprobity Statistics. All-atom Clashscore : 19.26 Ramachandran Plot: Outliers : 0.55 % Allowed : 14.86 % Favored : 84.59 % Rotamer: Outliers : 0.14 % Allowed : 4.02 % Favored : 95.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.78 (0.20), residues: 1629 helix: -0.19 (0.29), residues: 299 sheet: -1.26 (0.31), residues: 289 loop : -2.70 (0.18), residues: 1041 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.043 0.003 TRP C 210 HIS 0.017 0.002 HIS B 170 PHE 0.034 0.003 PHE L 98 TYR 0.021 0.003 TYR E 98 ARG 0.012 0.001 ARG a 282 *********************** 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 346 residues out of total 1448 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 344 time to evaluate : 1.628 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 75 MET cc_start: 0.8660 (mtm) cc_final: 0.8335 (mtm) REVERT: B 82 MET cc_start: 0.8233 (ptp) cc_final: 0.7980 (ptp) REVERT: B 101 THR cc_start: 0.8761 (p) cc_final: 0.8416 (t) REVERT: B 104 GLU cc_start: 0.8106 (tp30) cc_final: 0.7562 (mm-30) REVERT: B 142 LEU cc_start: 0.9309 (mp) cc_final: 0.9106 (tp) REVERT: B 150 TYR cc_start: 0.7550 (m-80) cc_final: 0.7126 (m-80) REVERT: B 157 PHE cc_start: 0.8960 (m-80) cc_final: 0.8549 (m-80) REVERT: B 185 ASN cc_start: 0.8571 (p0) cc_final: 0.8276 (p0) REVERT: B 223 GLN cc_start: 0.8108 (mp-120) cc_final: 0.7683 (mp10) REVERT: b 270 GLU cc_start: 0.7984 (mp0) cc_final: 0.7231 (tp30) REVERT: b 311 ASP cc_start: 0.9070 (m-30) cc_final: 0.8808 (m-30) REVERT: b 317 ASP cc_start: 0.9382 (t0) cc_final: 0.9136 (t0) REVERT: b 324 GLN cc_start: 0.8671 (tm-30) cc_final: 0.8418 (tm-30) REVERT: b 346 ASN cc_start: 0.9028 (t0) cc_final: 0.8392 (t0) REVERT: b 351 MET cc_start: 0.9396 (mmm) cc_final: 0.9048 (mmp) REVERT: b 357 ASP cc_start: 0.9291 (t70) cc_final: 0.8768 (t0) REVERT: A 75 MET cc_start: 0.9103 (mtp) cc_final: 0.8394 (ttm) REVERT: A 82 MET cc_start: 0.8573 (pmm) cc_final: 0.8246 (pmm) REVERT: A 93 HIS cc_start: 0.6356 (m90) cc_final: 0.6016 (m90) REVERT: A 104 GLU cc_start: 0.7536 (tt0) cc_final: 0.6729 (tp30) REVERT: A 105 LEU cc_start: 0.8823 (mt) cc_final: 0.8529 (tt) REVERT: A 122 ASP cc_start: 0.9416 (m-30) cc_final: 0.9003 (m-30) REVERT: A 126 LYS cc_start: 0.8879 (mmtm) cc_final: 0.8515 (mmtp) REVERT: A 191 PHE cc_start: 0.8662 (t80) cc_final: 0.8053 (t80) REVERT: A 219 TYR cc_start: 0.8098 (m-80) cc_final: 0.7883 (m-80) REVERT: A 247 GLN cc_start: 0.7236 (mm-40) cc_final: 0.6603 (tt0) REVERT: a 264 TRP cc_start: 0.7690 (m100) cc_final: 0.7084 (m100) REVERT: a 266 LEU cc_start: 0.8662 (mp) cc_final: 0.8354 (tp) REVERT: a 281 THR cc_start: 0.8242 (p) cc_final: 0.7222 (p) REVERT: a 283 TRP cc_start: 0.8731 (p-90) cc_final: 0.8141 (p-90) REVERT: a 284 MET cc_start: 0.9440 (mtm) cc_final: 0.9131 (mtt) REVERT: a 287 GLU cc_start: 0.8689 (mt-10) cc_final: 0.7907 (tm-30) REVERT: a 317 ASP cc_start: 0.9439 (t0) cc_final: 0.9033 (t0) REVERT: a 324 GLN cc_start: 0.9236 (tm-30) cc_final: 0.8795 (tm-30) REVERT: C 75 MET cc_start: 0.9035 (mtm) cc_final: 0.8777 (mtm) REVERT: C 93 HIS cc_start: 0.8716 (m90) cc_final: 0.8245 (m-70) REVERT: C 122 ASP cc_start: 0.8184 (p0) cc_final: 0.7929 (p0) REVERT: C 124 HIS cc_start: 0.8285 (m170) cc_final: 0.7940 (m-70) REVERT: C 164 VAL cc_start: 0.8137 (t) cc_final: 0.7781 (t) REVERT: C 189 GLN cc_start: 0.8281 (mt0) cc_final: 0.8036 (mm-40) REVERT: C 192 MET cc_start: 0.8714 (mmt) cc_final: 0.8377 (mmt) REVERT: c 268 ASP cc_start: 0.7481 (p0) cc_final: 0.7075 (p0) REVERT: c 282 ARG cc_start: 0.8237 (ttt180) cc_final: 0.6909 (ptp-170) REVERT: c 289 GLU cc_start: 0.8377 (tt0) cc_final: 0.7956 (tp30) REVERT: c 311 ASP cc_start: 0.9442 (m-30) cc_final: 0.9114 (m-30) REVERT: c 320 LYS cc_start: 0.9260 (ttpt) cc_final: 0.9046 (ttmt) REVERT: c 337 ILE cc_start: 0.9263 (mt) cc_final: 0.8828 (mt) REVERT: c 351 MET cc_start: 0.9115 (tpt) cc_final: 0.8880 (tpt) REVERT: c 359 MET cc_start: 0.9255 (mmm) cc_final: 0.8926 (mmm) REVERT: c 369 TYR cc_start: 0.8542 (m-80) cc_final: 0.6656 (m-80) REVERT: c 387 LEU cc_start: 0.9114 (mt) cc_final: 0.8548 (mt) REVERT: c 410 MET cc_start: 0.8854 (tpt) cc_final: 0.8346 (tpt) REVERT: D 34 MET cc_start: 0.7940 (mtm) cc_final: 0.7283 (mtp) REVERT: D 37 GLU cc_start: 0.6157 (mt-10) cc_final: 0.5769 (mt-10) REVERT: D 46 GLU cc_start: 0.8673 (pt0) cc_final: 0.7779 (pm20) REVERT: D 99 LEU cc_start: 0.9451 (mp) cc_final: 0.9022 (mm) REVERT: D 104 LEU cc_start: 0.8146 (pp) cc_final: 0.7822 (pp) REVERT: H 30 ARG cc_start: 0.8325 (ptt-90) cc_final: 0.7974 (ttp-170) REVERT: H 48 ILE cc_start: 0.9218 (mt) cc_final: 0.9014 (mt) REVERT: H 86 ASP cc_start: 0.8870 (m-30) cc_final: 0.8416 (m-30) REVERT: L 6 GLN cc_start: 0.7920 (mt0) cc_final: 0.6694 (mp-120) REVERT: L 23 CYS cc_start: 0.7146 (t) cc_final: 0.4901 (t) REVERT: L 74 THR cc_start: 0.8340 (m) cc_final: 0.8092 (t) REVERT: L 78 MET cc_start: 0.9006 (tmm) cc_final: 0.8729 (tmm) REVERT: E 3 GLN cc_start: 0.8533 (tt0) cc_final: 0.7941 (tm-30) REVERT: E 47 TRP cc_start: 0.9033 (t60) cc_final: 0.6956 (t60) REVERT: E 67 LEU cc_start: 0.8551 (mm) cc_final: 0.8035 (mm) REVERT: I 23 CYS cc_start: 0.4543 (t) cc_final: 0.4323 (t) REVERT: I 66 ARG cc_start: 0.8672 (tmt170) cc_final: 0.8414 (tmm160) REVERT: I 77 ARG cc_start: 0.8817 (ptp90) cc_final: 0.8431 (ptp-170) REVERT: I 78 MET cc_start: 0.8938 (tpp) cc_final: 0.8447 (tpp) outliers start: 2 outliers final: 0 residues processed: 346 average time/residue: 0.2674 time to fit residues: 134.8215 Evaluate side-chains 283 residues out of total 1448 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 283 time to evaluate : 1.676 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 157 random chunks: chunk 136 optimal weight: 5.9990 chunk 29 optimal weight: 0.8980 chunk 89 optimal weight: 9.9990 chunk 37 optimal weight: 5.9990 chunk 151 optimal weight: 0.0870 chunk 126 optimal weight: 6.9990 chunk 70 optimal weight: 1.9990 chunk 12 optimal weight: 5.9990 chunk 50 optimal weight: 9.9990 chunk 79 optimal weight: 1.9990 chunk 146 optimal weight: 0.7980 overall best weight: 1.1562 ------------------------------------------------------------------------------- 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 189 GLN b 305 HIS ** b 319 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** b 374 HIS ** A 170 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 189 GLN ** a 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 89 ASN C 170 HIS C 189 GLN ** I 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 93 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7462 moved from start: 0.5115 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 14484 Z= 0.240 Angle : 0.805 15.863 19626 Z= 0.395 Chirality : 0.051 0.386 2415 Planarity : 0.005 0.085 2359 Dihedral : 11.674 111.506 3617 Min Nonbonded Distance : 2.315 Molprobity Statistics. All-atom Clashscore : 15.72 Ramachandran Plot: Outliers : 0.49 % Allowed : 14.00 % Favored : 85.51 % Rotamer: Outliers : 0.07 % Allowed : 2.42 % Favored : 97.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.61 (0.20), residues: 1629 helix: -0.15 (0.29), residues: 306 sheet: -0.92 (0.31), residues: 287 loop : -2.65 (0.19), residues: 1036 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.002 TRP C 210 HIS 0.017 0.002 HIS B 170 PHE 0.022 0.002 PHE L 98 TYR 0.029 0.002 TYR D 95 ARG 0.008 0.001 ARG a 282 *********************** 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 361 residues out of total 1448 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 360 time to evaluate : 2.876 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 75 MET cc_start: 0.8587 (mtm) cc_final: 0.8216 (mtm) REVERT: B 101 THR cc_start: 0.8733 (p) cc_final: 0.8427 (t) REVERT: B 104 GLU cc_start: 0.7685 (tp30) cc_final: 0.7138 (mm-30) REVERT: B 142 LEU cc_start: 0.9214 (mp) cc_final: 0.9004 (tp) REVERT: B 157 PHE cc_start: 0.8916 (m-80) cc_final: 0.8498 (m-80) REVERT: B 185 ASN cc_start: 0.8577 (p0) cc_final: 0.8283 (p0) REVERT: B 223 GLN cc_start: 0.8082 (mp-120) cc_final: 0.7708 (mp10) REVERT: b 270 GLU cc_start: 0.7939 (mp0) cc_final: 0.7201 (tp30) REVERT: b 324 GLN cc_start: 0.8669 (tm-30) cc_final: 0.8402 (tm-30) REVERT: b 346 ASN cc_start: 0.8719 (t0) cc_final: 0.8100 (t0) REVERT: b 353 ASN cc_start: 0.8884 (m-40) cc_final: 0.8528 (m-40) REVERT: b 357 ASP cc_start: 0.9218 (t70) cc_final: 0.7583 (t0) REVERT: A 62 TYR cc_start: 0.8188 (m-10) cc_final: 0.7927 (m-10) REVERT: A 75 MET cc_start: 0.8988 (mtp) cc_final: 0.8345 (ttm) REVERT: A 82 MET cc_start: 0.8610 (pmm) cc_final: 0.8279 (pmm) REVERT: A 93 HIS cc_start: 0.6158 (m90) cc_final: 0.5523 (m90) REVERT: A 104 GLU cc_start: 0.7412 (tt0) cc_final: 0.6591 (tt0) REVERT: A 105 LEU cc_start: 0.8789 (mt) cc_final: 0.8556 (tt) REVERT: A 191 PHE cc_start: 0.8614 (t80) cc_final: 0.7958 (t80) REVERT: A 219 TYR cc_start: 0.8036 (m-80) cc_final: 0.7834 (m-80) REVERT: A 241 TYR cc_start: 0.8768 (t80) cc_final: 0.8567 (t80) REVERT: A 247 GLN cc_start: 0.7411 (mm-40) cc_final: 0.6663 (tt0) REVERT: a 265 THR cc_start: 0.7837 (m) cc_final: 0.7399 (p) REVERT: a 266 LEU cc_start: 0.8578 (mp) cc_final: 0.8157 (tp) REVERT: a 284 MET cc_start: 0.9338 (mtm) cc_final: 0.9058 (mtt) REVERT: a 287 GLU cc_start: 0.8710 (mt-10) cc_final: 0.7865 (tm-30) REVERT: a 317 ASP cc_start: 0.9358 (t0) cc_final: 0.9106 (t0) REVERT: a 324 GLN cc_start: 0.9243 (tm-30) cc_final: 0.8825 (tm-30) REVERT: a 332 MET cc_start: 0.7036 (mtt) cc_final: 0.6799 (mtt) REVERT: a 372 LEU cc_start: 0.9273 (mm) cc_final: 0.8794 (tp) REVERT: a 387 LEU cc_start: 0.8606 (mt) cc_final: 0.8238 (mm) REVERT: C 75 MET cc_start: 0.8929 (mtm) cc_final: 0.8728 (mtm) REVERT: C 82 MET cc_start: 0.8015 (mmm) cc_final: 0.7757 (mmm) REVERT: C 93 HIS cc_start: 0.8742 (m90) cc_final: 0.8266 (m-70) REVERT: C 122 ASP cc_start: 0.8142 (p0) cc_final: 0.7886 (p0) REVERT: C 124 HIS cc_start: 0.8264 (m170) cc_final: 0.7923 (m-70) REVERT: C 192 MET cc_start: 0.8673 (mmt) cc_final: 0.8257 (mmt) REVERT: C 241 TYR cc_start: 0.8989 (t80) cc_final: 0.8711 (t80) REVERT: c 268 ASP cc_start: 0.7591 (p0) cc_final: 0.7219 (p0) REVERT: c 282 ARG cc_start: 0.8052 (ttt180) cc_final: 0.6821 (ptp-170) REVERT: c 311 ASP cc_start: 0.9397 (m-30) cc_final: 0.9015 (m-30) REVERT: c 320 LYS cc_start: 0.9273 (ttpt) cc_final: 0.9004 (ttmt) REVERT: c 337 ILE cc_start: 0.9070 (mt) cc_final: 0.8351 (mt) REVERT: c 359 MET cc_start: 0.9203 (mmm) cc_final: 0.8865 (mmm) REVERT: c 369 TYR cc_start: 0.8579 (m-80) cc_final: 0.6575 (m-80) REVERT: c 370 TRP cc_start: 0.8153 (p-90) cc_final: 0.7773 (p-90) REVERT: c 387 LEU cc_start: 0.9172 (mt) cc_final: 0.8851 (mt) REVERT: c 406 GLN cc_start: 0.9164 (tp40) cc_final: 0.8745 (tp40) REVERT: c 409 ASN cc_start: 0.9477 (t0) cc_final: 0.9118 (m-40) REVERT: D 6 GLU cc_start: 0.8907 (pt0) cc_final: 0.8576 (pm20) REVERT: D 34 MET cc_start: 0.7843 (mtm) cc_final: 0.7454 (mtp) REVERT: D 37 GLU cc_start: 0.6238 (mt-10) cc_final: 0.5744 (mt-10) REVERT: D 46 GLU cc_start: 0.8694 (pt0) cc_final: 0.7789 (pm20) REVERT: D 95 TYR cc_start: 0.8202 (m-80) cc_final: 0.7885 (m-80) REVERT: D 96 CYS cc_start: 0.5800 (t) cc_final: 0.5588 (t) REVERT: D 99 LEU cc_start: 0.9410 (mp) cc_final: 0.8935 (mm) REVERT: D 105 ARG cc_start: 0.8664 (ptp-110) cc_final: 0.7728 (ptp-170) REVERT: H 13 LYS cc_start: 0.9682 (tppt) cc_final: 0.9469 (tppt) REVERT: H 30 ARG cc_start: 0.8256 (ptt-90) cc_final: 0.7882 (ttp-170) REVERT: H 86 ASP cc_start: 0.8721 (m-30) cc_final: 0.8281 (m-30) REVERT: L 6 GLN cc_start: 0.7993 (mt0) cc_final: 0.6659 (mp-120) REVERT: L 23 CYS cc_start: 0.6961 (t) cc_final: 0.4560 (t) REVERT: L 31 ASP cc_start: 0.8500 (p0) cc_final: 0.8020 (p0) REVERT: L 73 LEU cc_start: 0.9467 (tp) cc_final: 0.9247 (tp) REVERT: L 74 THR cc_start: 0.8245 (m) cc_final: 0.7874 (t) REVERT: E 3 GLN cc_start: 0.8472 (tt0) cc_final: 0.7955 (tm-30) REVERT: E 46 GLU cc_start: 0.7582 (pm20) cc_final: 0.7353 (pm20) REVERT: E 50 TYR cc_start: 0.8689 (p90) cc_final: 0.8432 (p90) REVERT: E 67 LEU cc_start: 0.8502 (mm) cc_final: 0.8031 (mm) REVERT: E 86 ASP cc_start: 0.9207 (m-30) cc_final: 0.8664 (m-30) REVERT: I 53 THR cc_start: 0.8987 (m) cc_final: 0.8379 (p) REVERT: I 75 ILE cc_start: 0.9237 (mt) cc_final: 0.8505 (tt) REVERT: I 77 ARG cc_start: 0.8787 (ptp90) cc_final: 0.8323 (ptp-170) REVERT: I 78 MET cc_start: 0.8785 (tpp) cc_final: 0.8096 (tpp) outliers start: 1 outliers final: 0 residues processed: 361 average time/residue: 0.2691 time to fit residues: 141.0690 Evaluate side-chains 296 residues out of total 1448 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 296 time to evaluate : 1.671 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 157 random chunks: chunk 17 optimal weight: 5.9990 chunk 86 optimal weight: 1.9990 chunk 110 optimal weight: 1.9990 chunk 85 optimal weight: 0.8980 chunk 127 optimal weight: 9.9990 chunk 84 optimal weight: 6.9990 chunk 151 optimal weight: 0.9980 chunk 94 optimal weight: 1.9990 chunk 92 optimal weight: 8.9990 chunk 69 optimal weight: 10.0000 chunk 93 optimal weight: 0.6980 overall best weight: 1.3184 ------------------------------------------------------------------------------- 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** A 170 HIS A 189 GLN ** a 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** c 406 GLN ** I 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 93 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7467 moved from start: 0.5323 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 14484 Z= 0.239 Angle : 0.800 12.818 19626 Z= 0.392 Chirality : 0.051 0.384 2415 Planarity : 0.005 0.082 2359 Dihedral : 11.257 111.313 3617 Min Nonbonded Distance : 2.304 Molprobity Statistics. All-atom Clashscore : 16.52 Ramachandran Plot: Outliers : 0.49 % Allowed : 14.24 % Favored : 85.27 % Rotamer: Outliers : 0.07 % Allowed : 1.59 % Favored : 98.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.60 (0.20), residues: 1629 helix: -0.09 (0.29), residues: 304 sheet: -0.85 (0.31), residues: 292 loop : -2.68 (0.18), residues: 1033 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.045 0.002 TRP C 210 HIS 0.015 0.002 HIS B 170 PHE 0.024 0.002 PHE A 140 TYR 0.023 0.002 TYR c 393 ARG 0.008 0.001 ARG E 30 *********************** 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: 1 poor density : 351 time to evaluate : 1.688 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 101 THR cc_start: 0.8772 (p) cc_final: 0.8404 (t) REVERT: B 104 GLU cc_start: 0.7745 (tp30) cc_final: 0.7516 (tp30) REVERT: B 157 PHE cc_start: 0.8893 (m-80) cc_final: 0.8432 (m-80) REVERT: B 185 ASN cc_start: 0.8590 (p0) cc_final: 0.8325 (p0) REVERT: b 270 GLU cc_start: 0.7949 (mp0) cc_final: 0.7185 (tp30) REVERT: b 311 ASP cc_start: 0.9364 (m-30) cc_final: 0.9121 (m-30) REVERT: b 324 GLN cc_start: 0.8687 (tm-30) cc_final: 0.8412 (tm-30) REVERT: b 345 ILE cc_start: 0.9525 (tp) cc_final: 0.9323 (tp) REVERT: b 346 ASN cc_start: 0.8682 (t0) cc_final: 0.7948 (t0) REVERT: b 353 ASN cc_start: 0.8938 (m-40) cc_final: 0.8654 (m-40) REVERT: b 357 ASP cc_start: 0.9094 (t70) cc_final: 0.8583 (t0) REVERT: b 369 TYR cc_start: 0.8662 (m-80) cc_final: 0.8202 (m-10) REVERT: b 410 MET cc_start: 0.9520 (mmm) cc_final: 0.8962 (mmp) REVERT: A 75 MET cc_start: 0.9082 (mtp) cc_final: 0.8383 (ttm) REVERT: A 76 GLU cc_start: 0.8978 (tt0) cc_final: 0.7779 (tp30) REVERT: A 82 MET cc_start: 0.8616 (pmm) cc_final: 0.8318 (pmm) REVERT: A 134 MET cc_start: 0.8791 (mmm) cc_final: 0.8334 (mmm) REVERT: A 191 PHE cc_start: 0.8680 (t80) cc_final: 0.8299 (t80) REVERT: A 219 TYR cc_start: 0.8039 (m-80) cc_final: 0.7751 (m-80) REVERT: A 247 GLN cc_start: 0.7245 (mm-40) cc_final: 0.6603 (tt0) REVERT: a 265 THR cc_start: 0.7814 (m) cc_final: 0.7336 (p) REVERT: a 266 LEU cc_start: 0.8525 (mp) cc_final: 0.8123 (tp) REVERT: a 284 MET cc_start: 0.9284 (mtm) cc_final: 0.9027 (mtt) REVERT: a 287 GLU cc_start: 0.8747 (mt-10) cc_final: 0.7883 (tm-30) REVERT: a 317 ASP cc_start: 0.9415 (t0) cc_final: 0.9156 (t0) REVERT: a 324 GLN cc_start: 0.9268 (tm-30) cc_final: 0.8867 (tm-30) REVERT: a 325 ARG cc_start: 0.8602 (ptp-170) cc_final: 0.7956 (ptp-170) REVERT: a 372 LEU cc_start: 0.9280 (mm) cc_final: 0.8849 (tp) REVERT: C 93 HIS cc_start: 0.8739 (m90) cc_final: 0.8244 (m-70) REVERT: C 122 ASP cc_start: 0.8157 (p0) cc_final: 0.7932 (p0) REVERT: C 124 HIS cc_start: 0.8301 (m170) cc_final: 0.7971 (m-70) REVERT: C 142 LEU cc_start: 0.8841 (mp) cc_final: 0.8536 (tp) REVERT: C 164 VAL cc_start: 0.7826 (t) cc_final: 0.7576 (t) REVERT: C 192 MET cc_start: 0.8661 (mmt) cc_final: 0.8247 (mmt) REVERT: c 268 ASP cc_start: 0.7511 (p0) cc_final: 0.7155 (p0) REVERT: c 311 ASP cc_start: 0.9412 (m-30) cc_final: 0.8911 (m-30) REVERT: c 320 LYS cc_start: 0.9310 (ttpt) cc_final: 0.9044 (ttmt) REVERT: c 337 ILE cc_start: 0.9121 (mt) cc_final: 0.8746 (mt) REVERT: c 369 TYR cc_start: 0.8692 (m-80) cc_final: 0.6670 (m-80) REVERT: c 387 LEU cc_start: 0.9140 (mt) cc_final: 0.8629 (mt) REVERT: c 404 GLU cc_start: 0.9528 (mm-30) cc_final: 0.9303 (mm-30) REVERT: D 6 GLU cc_start: 0.8954 (pt0) cc_final: 0.8696 (pm20) REVERT: D 34 MET cc_start: 0.7830 (mtm) cc_final: 0.7426 (mtp) REVERT: D 37 GLU cc_start: 0.6082 (mt-10) cc_final: 0.5672 (mt-10) REVERT: D 46 GLU cc_start: 0.8730 (pt0) cc_final: 0.7781 (pm20) REVERT: D 99 LEU cc_start: 0.9386 (mp) cc_final: 0.8933 (mm) REVERT: D 104 LEU cc_start: 0.8248 (pp) cc_final: 0.7965 (pp) REVERT: D 105 ARG cc_start: 0.8713 (ptp-110) cc_final: 0.8190 (ptm160) REVERT: H 13 LYS cc_start: 0.9695 (tppt) cc_final: 0.9463 (tppt) REVERT: H 30 ARG cc_start: 0.8289 (ptt-90) cc_final: 0.7829 (ttp-170) REVERT: H 86 ASP cc_start: 0.8729 (m-30) cc_final: 0.8286 (m-30) REVERT: H 96 PHE cc_start: 0.8305 (m-80) cc_final: 0.8103 (m-10) REVERT: L 6 GLN cc_start: 0.8031 (mt0) cc_final: 0.6690 (mp-120) REVERT: L 23 CYS cc_start: 0.6946 (t) cc_final: 0.4576 (t) REVERT: L 31 ASP cc_start: 0.8396 (p0) cc_final: 0.7979 (p0) REVERT: L 74 THR cc_start: 0.8250 (m) cc_final: 0.7916 (t) REVERT: E 3 GLN cc_start: 0.8405 (tt0) cc_final: 0.7873 (tm-30) REVERT: E 46 GLU cc_start: 0.7581 (pm20) cc_final: 0.7128 (pm20) REVERT: E 47 TRP cc_start: 0.9032 (t60) cc_final: 0.7126 (t60) REVERT: E 67 LEU cc_start: 0.8508 (mm) cc_final: 0.8018 (mm) REVERT: E 89 VAL cc_start: 0.8341 (p) cc_final: 0.8005 (p) REVERT: I 66 ARG cc_start: 0.8512 (tmt170) cc_final: 0.7995 (tmm160) REVERT: I 75 ILE cc_start: 0.9188 (mt) cc_final: 0.8489 (tt) REVERT: I 77 ARG cc_start: 0.8772 (ptp90) cc_final: 0.8352 (ptp-170) REVERT: I 78 MET cc_start: 0.8747 (tpp) cc_final: 0.8229 (tpt) outliers start: 1 outliers final: 0 residues processed: 352 average time/residue: 0.2669 time to fit residues: 136.9244 Evaluate side-chains 287 residues out of total 1448 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 287 time to evaluate : 1.511 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 157 random chunks: chunk 60 optimal weight: 1.9990 chunk 90 optimal weight: 5.9990 chunk 45 optimal weight: 9.9990 chunk 29 optimal weight: 0.9990 chunk 96 optimal weight: 1.9990 chunk 103 optimal weight: 8.9990 chunk 74 optimal weight: 9.9990 chunk 14 optimal weight: 5.9990 chunk 118 optimal weight: 3.9990 chunk 137 optimal weight: 0.2980 chunk 144 optimal weight: 2.9990 overall best weight: 1.6588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 141 HIS ** B 170 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 230 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** b 305 HIS ** b 319 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 189 GLN ** a 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 189 GLN ** I 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 93 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7492 moved from start: 0.5559 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 14484 Z= 0.257 Angle : 0.796 13.141 19626 Z= 0.391 Chirality : 0.051 0.385 2415 Planarity : 0.005 0.073 2359 Dihedral : 10.888 110.640 3617 Min Nonbonded Distance : 2.297 Molprobity Statistics. All-atom Clashscore : 16.66 Ramachandran Plot: Outliers : 0.49 % Allowed : 14.24 % Favored : 85.27 % Rotamer: Outliers : 0.07 % Allowed : 1.25 % Favored : 98.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.55 (0.20), residues: 1629 helix: -0.27 (0.29), residues: 314 sheet: -0.76 (0.32), residues: 290 loop : -2.61 (0.19), residues: 1025 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.061 0.002 TRP C 210 HIS 0.015 0.002 HIS B 170 PHE 0.028 0.002 PHE L 83 TYR 0.019 0.002 TYR c 393 ARG 0.008 0.001 ARG C 259 *********************** 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 338 residues out of total 1448 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 337 time to evaluate : 1.681 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 75 MET cc_start: 0.8659 (mtm) cc_final: 0.8277 (mtm) REVERT: B 82 MET cc_start: 0.8305 (ptp) cc_final: 0.7235 (pmm) REVERT: B 101 THR cc_start: 0.8772 (p) cc_final: 0.8422 (t) REVERT: B 104 GLU cc_start: 0.7632 (tp30) cc_final: 0.7077 (mm-30) REVERT: B 157 PHE cc_start: 0.8887 (m-80) cc_final: 0.8435 (m-80) REVERT: B 185 ASN cc_start: 0.8592 (p0) cc_final: 0.8313 (p0) REVERT: B 223 GLN cc_start: 0.7845 (mp10) cc_final: 0.7402 (mp10) REVERT: b 270 GLU cc_start: 0.7902 (mp0) cc_final: 0.7172 (tp30) REVERT: b 311 ASP cc_start: 0.9339 (m-30) cc_final: 0.9105 (m-30) REVERT: b 324 GLN cc_start: 0.8697 (tm-30) cc_final: 0.8452 (tm-30) REVERT: b 345 ILE cc_start: 0.9533 (tp) cc_final: 0.9312 (tp) REVERT: b 346 ASN cc_start: 0.8639 (t0) cc_final: 0.7974 (t0) REVERT: b 357 ASP cc_start: 0.9122 (t70) cc_final: 0.8654 (t0) REVERT: b 369 TYR cc_start: 0.8721 (m-80) cc_final: 0.8449 (m-10) REVERT: A 75 MET cc_start: 0.9089 (mtp) cc_final: 0.8465 (ttm) REVERT: A 76 GLU cc_start: 0.9019 (tt0) cc_final: 0.7847 (tp30) REVERT: A 82 MET cc_start: 0.8700 (pmm) cc_final: 0.8383 (pmm) REVERT: A 104 GLU cc_start: 0.7368 (tt0) cc_final: 0.6595 (tt0) REVERT: A 105 LEU cc_start: 0.8924 (mt) cc_final: 0.8632 (tp) REVERT: A 134 MET cc_start: 0.8854 (mmm) cc_final: 0.8341 (mmm) REVERT: A 191 PHE cc_start: 0.8959 (t80) cc_final: 0.8151 (t80) REVERT: A 219 TYR cc_start: 0.7999 (m-80) cc_final: 0.7671 (m-80) REVERT: A 247 GLN cc_start: 0.7330 (mm-40) cc_final: 0.6622 (tt0) REVERT: a 265 THR cc_start: 0.7762 (m) cc_final: 0.6757 (p) REVERT: a 266 LEU cc_start: 0.8456 (mp) cc_final: 0.8039 (tp) REVERT: a 284 MET cc_start: 0.9313 (mtm) cc_final: 0.9086 (mtt) REVERT: a 317 ASP cc_start: 0.9356 (t0) cc_final: 0.9089 (t0) REVERT: a 324 GLN cc_start: 0.9243 (tm-30) cc_final: 0.8839 (tm-30) REVERT: a 325 ARG cc_start: 0.8638 (ptp-170) cc_final: 0.8005 (ptp-170) REVERT: a 349 LEU cc_start: 0.8358 (tp) cc_final: 0.8113 (mt) REVERT: C 93 HIS cc_start: 0.8748 (m90) cc_final: 0.8243 (m-70) REVERT: C 124 HIS cc_start: 0.8332 (m170) cc_final: 0.7988 (m-70) REVERT: C 164 VAL cc_start: 0.7645 (t) cc_final: 0.7431 (t) REVERT: C 192 MET cc_start: 0.8656 (mmt) cc_final: 0.8234 (mmt) REVERT: c 311 ASP cc_start: 0.9267 (m-30) cc_final: 0.8921 (m-30) REVERT: c 359 MET cc_start: 0.9196 (mmm) cc_final: 0.8949 (mmm) REVERT: c 369 TYR cc_start: 0.8670 (m-80) cc_final: 0.6636 (m-80) REVERT: c 387 LEU cc_start: 0.9108 (mt) cc_final: 0.8598 (mt) REVERT: c 410 MET cc_start: 0.8846 (tpt) cc_final: 0.7880 (tpt) REVERT: c 414 MET cc_start: 0.8794 (ptp) cc_final: 0.8298 (ptp) REVERT: D 6 GLU cc_start: 0.8928 (pt0) cc_final: 0.8657 (pm20) REVERT: D 34 MET cc_start: 0.8019 (mtm) cc_final: 0.7506 (mtp) REVERT: D 37 GLU cc_start: 0.6043 (mt-10) cc_final: 0.5594 (mt-10) REVERT: D 46 GLU cc_start: 0.8763 (pt0) cc_final: 0.7727 (pm20) REVERT: D 99 LEU cc_start: 0.9324 (mp) cc_final: 0.8920 (mp) REVERT: D 104 LEU cc_start: 0.8244 (pp) cc_final: 0.7930 (pp) REVERT: D 105 ARG cc_start: 0.8691 (ptp-110) cc_final: 0.8177 (ptm160) REVERT: H 13 LYS cc_start: 0.9711 (tppt) cc_final: 0.9477 (tppt) REVERT: H 30 ARG cc_start: 0.8372 (ptt-90) cc_final: 0.7842 (ttp-170) REVERT: H 86 ASP cc_start: 0.8760 (m-30) cc_final: 0.8278 (m-30) REVERT: H 96 PHE cc_start: 0.8345 (m-80) cc_final: 0.7616 (m-10) REVERT: L 6 GLN cc_start: 0.7967 (mt0) cc_final: 0.6820 (mp-120) REVERT: L 23 CYS cc_start: 0.6984 (t) cc_final: 0.4638 (t) REVERT: L 31 ASP cc_start: 0.8534 (p0) cc_final: 0.8170 (p0) REVERT: L 74 THR cc_start: 0.8290 (m) cc_final: 0.8062 (t) REVERT: E 3 GLN cc_start: 0.8355 (tt0) cc_final: 0.7839 (tm-30) REVERT: E 46 GLU cc_start: 0.7679 (pm20) cc_final: 0.7182 (pm20) REVERT: E 47 TRP cc_start: 0.9024 (t60) cc_final: 0.6955 (t60) REVERT: E 50 TYR cc_start: 0.8760 (p90) cc_final: 0.7989 (p90) REVERT: E 67 LEU cc_start: 0.8547 (mm) cc_final: 0.8031 (mm) REVERT: I 75 ILE cc_start: 0.9203 (mt) cc_final: 0.8465 (tp) REVERT: I 78 MET cc_start: 0.8766 (tpp) cc_final: 0.8075 (tpp) outliers start: 1 outliers final: 0 residues processed: 338 average time/residue: 0.2652 time to fit residues: 131.9440 Evaluate side-chains 270 residues out of total 1448 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 270 time to evaluate : 1.618 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 157 random chunks: chunk 132 optimal weight: 2.9990 chunk 141 optimal weight: 2.9990 chunk 144 optimal weight: 5.9990 chunk 84 optimal weight: 7.9990 chunk 61 optimal weight: 6.9990 chunk 110 optimal weight: 9.9990 chunk 43 optimal weight: 5.9990 chunk 127 optimal weight: 9.9990 chunk 133 optimal weight: 0.9990 chunk 140 optimal weight: 0.0470 chunk 92 optimal weight: 7.9990 overall best weight: 2.6086 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 230 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 247 GLN ** b 319 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** b 405 GLN b 406 GLN A 189 GLN ** a 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 158 ASN I 37 GLN ** I 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 93 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7547 moved from start: 0.5870 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.061 14484 Z= 0.337 Angle : 0.864 13.903 19626 Z= 0.427 Chirality : 0.052 0.391 2415 Planarity : 0.005 0.097 2359 Dihedral : 10.914 109.715 3617 Min Nonbonded Distance : 2.283 Molprobity Statistics. All-atom Clashscore : 19.59 Ramachandran Plot: Outliers : 0.55 % Allowed : 15.10 % Favored : 84.35 % Rotamer: Outliers : 0.14 % Allowed : 1.18 % Favored : 98.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.68 (0.20), residues: 1629 helix: -0.35 (0.29), residues: 315 sheet: -0.95 (0.32), residues: 274 loop : -2.64 (0.18), residues: 1040 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.060 0.003 TRP C 210 HIS 0.015 0.002 HIS B 170 PHE 0.024 0.002 PHE L 83 TYR 0.034 0.002 TYR b 393 ARG 0.012 0.001 ARG a 282 *********************** 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 324 residues out of total 1448 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 322 time to evaluate : 1.507 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 75 MET cc_start: 0.8751 (mtm) cc_final: 0.8363 (mtm) REVERT: B 82 MET cc_start: 0.8383 (ptp) cc_final: 0.7324 (pmm) REVERT: B 101 THR cc_start: 0.8824 (p) cc_final: 0.8484 (t) REVERT: B 185 ASN cc_start: 0.8630 (p0) cc_final: 0.8381 (p0) REVERT: B 223 GLN cc_start: 0.7764 (mp10) cc_final: 0.7300 (mp10) REVERT: b 270 GLU cc_start: 0.7829 (mp0) cc_final: 0.7124 (tp30) REVERT: b 311 ASP cc_start: 0.9322 (m-30) cc_final: 0.9061 (m-30) REVERT: b 324 GLN cc_start: 0.8697 (tm-30) cc_final: 0.8298 (tm-30) REVERT: b 345 ILE cc_start: 0.9535 (tp) cc_final: 0.9303 (tp) REVERT: b 346 ASN cc_start: 0.8767 (t0) cc_final: 0.8065 (t0) REVERT: b 369 TYR cc_start: 0.8811 (m-80) cc_final: 0.8492 (m-10) REVERT: b 410 MET cc_start: 0.9521 (mmm) cc_final: 0.9302 (mmm) REVERT: A 75 MET cc_start: 0.9116 (mtp) cc_final: 0.8535 (ttm) REVERT: A 76 GLU cc_start: 0.9043 (tt0) cc_final: 0.8007 (tp30) REVERT: A 82 MET cc_start: 0.8809 (pmm) cc_final: 0.8448 (pmm) REVERT: A 93 HIS cc_start: 0.6292 (m90) cc_final: 0.5793 (m90) REVERT: A 104 GLU cc_start: 0.7481 (tt0) cc_final: 0.6763 (tt0) REVERT: A 105 LEU cc_start: 0.9074 (mt) cc_final: 0.8640 (tt) REVERT: A 134 MET cc_start: 0.8979 (mmm) cc_final: 0.8541 (mmm) REVERT: A 191 PHE cc_start: 0.8880 (t80) cc_final: 0.8000 (t80) REVERT: A 217 TYR cc_start: 0.8332 (m-80) cc_final: 0.8093 (m-10) REVERT: A 219 TYR cc_start: 0.7932 (m-80) cc_final: 0.7549 (m-80) REVERT: A 247 GLN cc_start: 0.7386 (mm-40) cc_final: 0.6680 (tt0) REVERT: a 264 TRP cc_start: 0.7776 (m100) cc_final: 0.6659 (m100) REVERT: a 265 THR cc_start: 0.8034 (m) cc_final: 0.7207 (p) REVERT: a 266 LEU cc_start: 0.8512 (mp) cc_final: 0.8031 (tp) REVERT: a 317 ASP cc_start: 0.9337 (t0) cc_final: 0.8872 (t70) REVERT: a 324 GLN cc_start: 0.9252 (tm-30) cc_final: 0.8850 (tm-30) REVERT: a 325 ARG cc_start: 0.8636 (ptp-170) cc_final: 0.7980 (ptp-170) REVERT: a 394 LEU cc_start: 0.8833 (mt) cc_final: 0.8620 (mt) REVERT: C 124 HIS cc_start: 0.8244 (m170) cc_final: 0.7882 (m-70) REVERT: C 164 VAL cc_start: 0.7690 (t) cc_final: 0.7474 (t) REVERT: C 189 GLN cc_start: 0.8410 (mt0) cc_final: 0.7760 (mm110) REVERT: C 192 MET cc_start: 0.8657 (mmt) cc_final: 0.8307 (mmt) REVERT: c 311 ASP cc_start: 0.9318 (m-30) cc_final: 0.8974 (m-30) REVERT: c 359 MET cc_start: 0.9123 (mmm) cc_final: 0.8882 (mmm) REVERT: c 369 TYR cc_start: 0.8709 (m-80) cc_final: 0.6653 (m-80) REVERT: c 387 LEU cc_start: 0.9146 (mt) cc_final: 0.8645 (mm) REVERT: c 401 ASP cc_start: 0.9274 (p0) cc_final: 0.9058 (p0) REVERT: c 404 GLU cc_start: 0.9605 (mp0) cc_final: 0.9251 (pm20) REVERT: c 410 MET cc_start: 0.8888 (tpt) cc_final: 0.8327 (tpt) REVERT: D 6 GLU cc_start: 0.8917 (pt0) cc_final: 0.8708 (pm20) REVERT: D 34 MET cc_start: 0.8192 (mtm) cc_final: 0.7536 (mtp) REVERT: D 37 GLU cc_start: 0.6019 (mt-10) cc_final: 0.5605 (mt-10) REVERT: D 46 GLU cc_start: 0.8652 (pt0) cc_final: 0.7528 (pm20) REVERT: D 99 LEU cc_start: 0.9274 (mp) cc_final: 0.8879 (mp) REVERT: D 105 ARG cc_start: 0.8686 (ptp-110) cc_final: 0.8278 (ptm160) REVERT: H 13 LYS cc_start: 0.9711 (tppt) cc_final: 0.9493 (tppt) REVERT: H 30 ARG cc_start: 0.8382 (ptt-90) cc_final: 0.7931 (ttp-170) REVERT: H 86 ASP cc_start: 0.8867 (m-30) cc_final: 0.8326 (m-30) REVERT: L 6 GLN cc_start: 0.7982 (mt0) cc_final: 0.7470 (pm20) REVERT: L 31 ASP cc_start: 0.8344 (p0) cc_final: 0.8063 (p0) REVERT: E 3 GLN cc_start: 0.8334 (tt0) cc_final: 0.7844 (tm-30) REVERT: E 50 TYR cc_start: 0.8800 (p90) cc_final: 0.8518 (p90) REVERT: E 67 LEU cc_start: 0.8576 (mm) cc_final: 0.8081 (mm) REVERT: I 53 THR cc_start: 0.9102 (m) cc_final: 0.8442 (p) REVERT: I 75 ILE cc_start: 0.9237 (mt) cc_final: 0.8453 (tp) REVERT: I 78 MET cc_start: 0.8823 (tpp) cc_final: 0.8330 (tpt) REVERT: I 93 ASN cc_start: 0.9059 (m110) cc_final: 0.8841 (m110) outliers start: 2 outliers final: 0 residues processed: 324 average time/residue: 0.2718 time to fit residues: 131.1573 Evaluate side-chains 259 residues out of total 1448 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 259 time to evaluate : 1.735 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 157 random chunks: chunk 149 optimal weight: 8.9990 chunk 91 optimal weight: 0.9990 chunk 70 optimal weight: 0.9990 chunk 103 optimal weight: 2.9990 chunk 156 optimal weight: 2.9990 chunk 143 optimal weight: 6.9990 chunk 124 optimal weight: 0.9980 chunk 12 optimal weight: 1.9990 chunk 96 optimal weight: 4.9990 chunk 76 optimal weight: 0.3980 chunk 98 optimal weight: 0.9980 overall best weight: 0.8784 ------------------------------------------------------------------------------- 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 230 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 319 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 93 HIS ** I 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7480 moved from start: 0.5944 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.066 14484 Z= 0.223 Angle : 0.829 15.354 19626 Z= 0.407 Chirality : 0.051 0.389 2415 Planarity : 0.005 0.083 2359 Dihedral : 10.475 110.313 3617 Min Nonbonded Distance : 2.319 Molprobity Statistics. All-atom Clashscore : 16.19 Ramachandran Plot: Outliers : 0.55 % Allowed : 13.63 % Favored : 85.82 % Rotamer: Outliers : 0.00 % Allowed : 0.55 % Favored : 99.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.50 (0.21), residues: 1629 helix: -0.21 (0.30), residues: 309 sheet: -0.75 (0.32), residues: 280 loop : -2.55 (0.19), residues: 1040 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.054 0.002 TRP C 210 HIS 0.012 0.002 HIS A 93 PHE 0.023 0.002 PHE L 83 TYR 0.027 0.002 TYR C 253 ARG 0.007 0.001 ARG C 259 ********************** 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 344 residues out of total 1448 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 344 time to evaluate : 1.785 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 101 THR cc_start: 0.8767 (p) cc_final: 0.8421 (t) REVERT: B 149 GLN cc_start: 0.8429 (tm-30) cc_final: 0.7875 (tm-30) REVERT: B 185 ASN cc_start: 0.8560 (p0) cc_final: 0.8294 (p0) REVERT: B 223 GLN cc_start: 0.7662 (mp10) cc_final: 0.7288 (mp10) REVERT: b 270 GLU cc_start: 0.7768 (mp0) cc_final: 0.7095 (tp30) REVERT: b 311 ASP cc_start: 0.9325 (m-30) cc_final: 0.9055 (m-30) REVERT: b 324 GLN cc_start: 0.8633 (tm-30) cc_final: 0.8249 (tm-30) REVERT: b 346 ASN cc_start: 0.8653 (t0) cc_final: 0.7926 (t0) REVERT: b 357 ASP cc_start: 0.9063 (t70) cc_final: 0.8610 (t0) REVERT: b 410 MET cc_start: 0.9505 (mmm) cc_final: 0.9301 (mmm) REVERT: A 75 MET cc_start: 0.8999 (mtp) cc_final: 0.8384 (ttm) REVERT: A 76 GLU cc_start: 0.9023 (tt0) cc_final: 0.7880 (tp30) REVERT: A 82 MET cc_start: 0.8787 (pmm) cc_final: 0.8426 (pmm) REVERT: A 93 HIS cc_start: 0.6023 (m90) cc_final: 0.5669 (m90) REVERT: A 104 GLU cc_start: 0.7426 (tt0) cc_final: 0.6764 (tt0) REVERT: A 105 LEU cc_start: 0.9086 (mt) cc_final: 0.8646 (tt) REVERT: A 134 MET cc_start: 0.8904 (mmm) cc_final: 0.8576 (mmm) REVERT: A 191 PHE cc_start: 0.8869 (t80) cc_final: 0.7954 (t80) REVERT: A 217 TYR cc_start: 0.8127 (m-80) cc_final: 0.7859 (m-10) REVERT: A 219 TYR cc_start: 0.8012 (m-80) cc_final: 0.7682 (m-80) REVERT: A 247 GLN cc_start: 0.7392 (mm-40) cc_final: 0.6770 (tt0) REVERT: a 265 THR cc_start: 0.7971 (m) cc_final: 0.7228 (p) REVERT: a 266 LEU cc_start: 0.8452 (mp) cc_final: 0.7973 (tp) REVERT: a 317 ASP cc_start: 0.9345 (t0) cc_final: 0.9078 (t0) REVERT: a 324 GLN cc_start: 0.9228 (tm-30) cc_final: 0.8808 (tm-30) REVERT: a 325 ARG cc_start: 0.8665 (ptp-170) cc_final: 0.7997 (ptp-170) REVERT: a 348 GLN cc_start: 0.7605 (tt0) cc_final: 0.7071 (tp40) REVERT: a 349 LEU cc_start: 0.8319 (tp) cc_final: 0.7932 (mt) REVERT: a 372 LEU cc_start: 0.9213 (mm) cc_final: 0.8791 (tp) REVERT: a 394 LEU cc_start: 0.8778 (mt) cc_final: 0.8574 (mt) REVERT: C 124 HIS cc_start: 0.8226 (m170) cc_final: 0.7882 (m-70) REVERT: C 164 VAL cc_start: 0.7511 (t) cc_final: 0.7278 (t) REVERT: C 189 GLN cc_start: 0.8302 (mt0) cc_final: 0.7636 (mm110) REVERT: C 192 MET cc_start: 0.8624 (mmt) cc_final: 0.8215 (mmt) REVERT: c 311 ASP cc_start: 0.9304 (m-30) cc_final: 0.8933 (m-30) REVERT: c 359 MET cc_start: 0.9081 (mmm) cc_final: 0.7459 (tpt) REVERT: c 369 TYR cc_start: 0.8726 (m-80) cc_final: 0.6559 (m-80) REVERT: c 387 LEU cc_start: 0.9136 (mt) cc_final: 0.8611 (mm) REVERT: c 401 ASP cc_start: 0.9247 (p0) cc_final: 0.8916 (p0) REVERT: c 403 ILE cc_start: 0.8884 (mm) cc_final: 0.8447 (mt) REVERT: c 404 GLU cc_start: 0.9570 (mp0) cc_final: 0.9197 (pm20) REVERT: c 410 MET cc_start: 0.8790 (tpt) cc_final: 0.8261 (tpt) REVERT: c 414 MET cc_start: 0.8856 (ptp) cc_final: 0.8580 (ptp) REVERT: D 6 GLU cc_start: 0.8893 (pt0) cc_final: 0.8424 (pm20) REVERT: D 34 MET cc_start: 0.7833 (mtm) cc_final: 0.7401 (mtp) REVERT: D 37 GLU cc_start: 0.6008 (mt-10) cc_final: 0.5560 (mt-10) REVERT: D 46 GLU cc_start: 0.8683 (pt0) cc_final: 0.7696 (pm20) REVERT: D 99 LEU cc_start: 0.9227 (mp) cc_final: 0.8801 (mp) REVERT: D 105 ARG cc_start: 0.8701 (ptp-110) cc_final: 0.8385 (ptm160) REVERT: H 13 LYS cc_start: 0.9719 (tppt) cc_final: 0.9479 (tppt) REVERT: H 20 LEU cc_start: 0.9320 (mm) cc_final: 0.9051 (mt) REVERT: H 30 ARG cc_start: 0.8336 (ptt-90) cc_final: 0.7808 (ttp-170) REVERT: H 86 ASP cc_start: 0.8626 (m-30) cc_final: 0.8114 (m-30) REVERT: L 6 GLN cc_start: 0.7077 (mt0) cc_final: 0.5950 (mt0) REVERT: L 31 ASP cc_start: 0.8553 (p0) cc_final: 0.8198 (p0) REVERT: E 3 GLN cc_start: 0.8258 (tt0) cc_final: 0.7777 (tm-30) REVERT: E 67 LEU cc_start: 0.8503 (mm) cc_final: 0.7839 (mm) REVERT: I 74 THR cc_start: 0.8406 (t) cc_final: 0.7833 (t) REVERT: I 75 ILE cc_start: 0.9250 (mt) cc_final: 0.8482 (tp) REVERT: I 78 MET cc_start: 0.8811 (tpp) cc_final: 0.8059 (tpp) REVERT: I 93 ASN cc_start: 0.8967 (m110) cc_final: 0.8721 (m110) outliers start: 0 outliers final: 0 residues processed: 344 average time/residue: 0.2627 time to fit residues: 132.1658 Evaluate side-chains 274 residues out of total 1448 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 274 time to evaluate : 1.773 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 157 random chunks: chunk 132 optimal weight: 3.9990 chunk 38 optimal weight: 2.9990 chunk 114 optimal weight: 9.9990 chunk 18 optimal weight: 0.9990 chunk 34 optimal weight: 0.9980 chunk 124 optimal weight: 4.9990 chunk 52 optimal weight: 4.9990 chunk 128 optimal weight: 8.9990 chunk 15 optimal weight: 7.9990 chunk 22 optimal weight: 0.0030 chunk 109 optimal weight: 0.9990 overall best weight: 1.1996 ------------------------------------------------------------------------------- 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 230 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 319 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3509 r_free = 0.3509 target = 0.086325 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3085 r_free = 0.3085 target = 0.066893 restraints weight = 53248.493| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3107 r_free = 0.3107 target = 0.067985 restraints weight = 35431.920| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3133 r_free = 0.3133 target = 0.069073 restraints weight = 28261.551| |-----------------------------------------------------------------------------| r_work (final): 0.3117 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7884 moved from start: 0.6069 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 14484 Z= 0.236 Angle : 0.816 13.889 19626 Z= 0.402 Chirality : 0.050 0.374 2415 Planarity : 0.005 0.099 2359 Dihedral : 10.352 109.501 3617 Min Nonbonded Distance : 2.301 Molprobity Statistics. All-atom Clashscore : 17.35 Ramachandran Plot: Outliers : 0.49 % Allowed : 14.61 % Favored : 84.90 % 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 : 0.06 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.48 (0.21), residues: 1629 helix: -0.10 (0.30), residues: 305 sheet: -0.76 (0.32), residues: 292 loop : -2.57 (0.19), residues: 1032 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.050 0.002 TRP C 210 HIS 0.011 0.002 HIS B 170 PHE 0.025 0.002 PHE L 83 TYR 0.045 0.002 TYR b 369 ARG 0.008 0.001 ARG C 259 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3343.81 seconds wall clock time: 62 minutes 27.81 seconds (3747.81 seconds total)