Starting phenix.real_space_refine on Thu Jun 12 23:02:40 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8t5c_41048/06_2025/8t5c_41048.cif Found real_map, /net/cci-nas-00/data/ceres_data/8t5c_41048/06_2025/8t5c_41048.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8t5c_41048/06_2025/8t5c_41048.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8t5c_41048/06_2025/8t5c_41048.map" model { file = "/net/cci-nas-00/data/ceres_data/8t5c_41048/06_2025/8t5c_41048.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8t5c_41048/06_2025/8t5c_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-5710/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: 9.41, 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: 4.57 Conformation dependent library (CDL) restraints added in 1.6 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: 1.56 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: 3.98 Time building geometry restraints manager: 5.20 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: 1.700 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: 0.110 Set scattering table: 0.150 Process input model: 34.840 Find NCS groups from input model: 0.700 Set up NCS constraints: 0.080 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:2.950 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 41.180 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7169 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.058 14597 Z= 0.254 Angle : 0.895 15.219 19939 Z= 0.387 Chirality : 0.053 0.367 2415 Planarity : 0.007 0.293 2359 Dihedral : 20.844 120.607 6633 Min Nonbonded Distance : 2.044 Molprobity Statistics. All-atom Clashscore : 5.82 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 Details of bonding type rmsd link_NAG-ASN : bond 0.00700 ( 35) link_NAG-ASN : angle 2.77064 ( 105) link_ALPHA1-6 : bond 0.01163 ( 10) link_ALPHA1-6 : angle 3.33535 ( 30) link_BETA1-4 : bond 0.00519 ( 27) link_BETA1-4 : angle 2.41410 ( 81) link_ALPHA1-2 : bond 0.00743 ( 2) link_ALPHA1-2 : angle 5.60407 ( 6) link_ALPHA1-3 : bond 0.00763 ( 13) link_ALPHA1-3 : angle 2.74015 ( 39) hydrogen bonds : bond 0.29519 ( 333) hydrogen bonds : angle 8.90106 ( 906) SS BOND : bond 0.00286 ( 26) SS BOND : angle 1.05393 ( 52) covalent geometry : bond 0.00512 (14484) covalent geometry : angle 0.83906 (19626) *********************** 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 : 1.679 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: 0.2884 time to fit residues: 242.5639 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 : 1.687 ------------------------------------------------------------------------------- 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: 0.6980 chunk 40 optimal weight: 20.0000 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: 0.7980 chunk 142 optimal weight: 3.9990 overall best weight: 3.2986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 189 GLN ** B 230 HIS ** 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** C 141 HIS C 223 GLN c 305 HIS c 353 ASN c 406 GLN D 39 GLN ** H 60 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 37 GLN L 90 GLN E 76 ASN ** I 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3543 r_free = 0.3543 target = 0.088820 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3114 r_free = 0.3114 target = 0.068751 restraints weight = 52320.827| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3160 r_free = 0.3160 target = 0.070802 restraints weight = 35558.418| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3193 r_free = 0.3193 target = 0.072282 restraints weight = 27519.982| |-----------------------------------------------------------------------------| r_work (final): 0.3182 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7764 moved from start: 0.3354 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.062 14597 Z= 0.297 Angle : 0.991 12.256 19939 Z= 0.465 Chirality : 0.054 0.388 2415 Planarity : 0.005 0.063 2359 Dihedral : 17.447 112.053 3617 Min Nonbonded Distance : 2.297 Molprobity Statistics. All-atom Clashscore : 15.40 Ramachandran Plot: Outliers : 0.49 % Allowed : 14.79 % Favored : 84.71 % Rotamer: Outliers : 0.55 % Allowed : 6.44 % Favored : 93.01 % 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: -2.68 (0.20), residues: 1629 helix: -0.19 (0.30), residues: 290 sheet: -1.20 (0.32), residues: 284 loop : -2.57 (0.18), residues: 1055 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.003 TRP C 210 HIS 0.014 0.002 HIS B 170 PHE 0.026 0.002 PHE c 318 TYR 0.023 0.003 TYR c 363 ARG 0.007 0.001 ARG D 67 Details of bonding type rmsd link_NAG-ASN : bond 0.00885 ( 35) link_NAG-ASN : angle 3.82617 ( 105) link_ALPHA1-6 : bond 0.00965 ( 10) link_ALPHA1-6 : angle 2.56556 ( 30) link_BETA1-4 : bond 0.00672 ( 27) link_BETA1-4 : angle 2.80388 ( 81) link_ALPHA1-2 : bond 0.00571 ( 2) link_ALPHA1-2 : angle 4.26479 ( 6) link_ALPHA1-3 : bond 0.01206 ( 13) link_ALPHA1-3 : angle 3.39845 ( 39) hydrogen bonds : bond 0.06366 ( 333) hydrogen bonds : angle 6.58009 ( 906) SS BOND : bond 0.00963 ( 26) SS BOND : angle 1.67184 ( 52) covalent geometry : bond 0.00643 (14484) covalent geometry : angle 0.91659 (19626) *********************** 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 405 residues out of total 1448 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 397 time to evaluate : 1.673 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: B 101 THR cc_start: 0.8460 (p) cc_final: 0.8252 (t) REVERT: B 157 PHE cc_start: 0.8735 (m-80) cc_final: 0.8533 (m-80) REVERT: B 194 MET cc_start: 0.9117 (tpp) cc_final: 0.8892 (tpp) REVERT: B 232 GLN cc_start: 0.7842 (tt0) cc_final: 0.7591 (tt0) REVERT: b 270 GLU cc_start: 0.7612 (mp0) cc_final: 0.7269 (tp30) REVERT: b 311 ASP cc_start: 0.8985 (m-30) cc_final: 0.8652 (m-30) REVERT: b 345 ILE cc_start: 0.9382 (tp) cc_final: 0.9090 (tp) REVERT: b 346 ASN cc_start: 0.9343 (t0) cc_final: 0.8934 (t0) REVERT: b 380 THR cc_start: 0.9293 (p) cc_final: 0.9088 (t) REVERT: b 414 MET cc_start: 0.9041 (tmm) cc_final: 0.8220 (tmm) REVERT: A 75 MET cc_start: 0.8717 (mtp) cc_final: 0.8201 (ttm) REVERT: A 82 MET cc_start: 0.9006 (pmm) cc_final: 0.8530 (pmm) REVERT: A 133 LEU cc_start: 0.8409 (mm) cc_final: 0.7006 (mm) REVERT: A 134 MET cc_start: 0.8408 (mmm) cc_final: 0.7968 (mmm) REVERT: A 140 PHE cc_start: 0.9242 (m-80) cc_final: 0.8731 (m-80) REVERT: A 223 GLN cc_start: 0.8256 (mm110) cc_final: 0.8015 (mm-40) REVERT: a 281 THR cc_start: 0.7998 (p) cc_final: 0.7762 (t) REVERT: a 287 GLU cc_start: 0.8297 (mt-10) cc_final: 0.7697 (tm-30) REVERT: a 325 ARG cc_start: 0.8141 (ptp-170) cc_final: 0.7728 (ptp-170) REVERT: a 334 ILE cc_start: 0.9278 (mm) cc_final: 0.9011 (pt) REVERT: a 349 LEU cc_start: 0.8840 (tp) cc_final: 0.8597 (tp) REVERT: a 387 LEU cc_start: 0.8873 (mt) cc_final: 0.8610 (mm) REVERT: C 75 MET cc_start: 0.9015 (mtm) cc_final: 0.8659 (mtm) REVERT: C 82 MET cc_start: 0.8375 (mmm) cc_final: 0.8050 (mmm) REVERT: C 92 HIS cc_start: 0.8281 (m-70) cc_final: 0.8020 (m90) REVERT: C 93 HIS cc_start: 0.8428 (m90) cc_final: 0.8095 (m-70) REVERT: C 241 TYR cc_start: 0.9287 (t80) cc_final: 0.9062 (t80) REVERT: c 268 ASP cc_start: 0.7625 (p0) cc_final: 0.7187 (p0) REVERT: c 282 ARG cc_start: 0.8367 (ttt180) cc_final: 0.7183 (ptp-170) REVERT: c 285 LEU cc_start: 0.9389 (mp) cc_final: 0.9157 (mp) REVERT: c 311 ASP cc_start: 0.9279 (m-30) cc_final: 0.8978 (m-30) REVERT: c 320 LYS cc_start: 0.9324 (ttpt) cc_final: 0.8922 (ttmm) REVERT: c 337 ILE cc_start: 0.8878 (mt) cc_final: 0.7924 (mt) REVERT: c 349 LEU cc_start: 0.9264 (tp) cc_final: 0.8892 (tt) REVERT: c 369 TYR cc_start: 0.8786 (m-80) cc_final: 0.7704 (m-80) REVERT: c 387 LEU cc_start: 0.9345 (mt) cc_final: 0.8919 (mp) REVERT: D 34 MET cc_start: 0.8798 (mtm) cc_final: 0.8206 (mtp) REVERT: D 37 GLU cc_start: 0.6021 (mt-10) cc_final: 0.5594 (mt-10) REVERT: D 46 GLU cc_start: 0.8694 (pt0) cc_final: 0.7843 (pm20) REVERT: D 95 TYR cc_start: 0.7701 (m-10) cc_final: 0.7011 (m-80) REVERT: D 96 CYS cc_start: 0.5945 (t) cc_final: 0.5738 (t) REVERT: D 105 ARG cc_start: 0.8052 (ptp-110) cc_final: 0.7631 (ptp-110) REVERT: H 3 GLN cc_start: 0.8894 (mp10) cc_final: 0.8573 (mp10) REVERT: L 6 GLN cc_start: 0.7479 (mt0) cc_final: 0.6892 (mp-120) REVERT: L 23 CYS cc_start: 0.6334 (t) cc_final: 0.4679 (t) REVERT: L 37 GLN cc_start: 0.8676 (OUTLIER) cc_final: 0.8469 (tm-30) REVERT: L 53 THR cc_start: 0.8519 (OUTLIER) cc_final: 0.8301 (t) REVERT: E 67 LEU cc_start: 0.8892 (mm) cc_final: 0.8470 (mm) REVERT: E 76 ASN cc_start: 0.7882 (m-40) cc_final: 0.7559 (m-40) REVERT: E 86 ASP cc_start: 0.9120 (m-30) cc_final: 0.8562 (m-30) outliers start: 8 outliers final: 1 residues processed: 404 average time/residue: 0.2665 time to fit residues: 157.4879 Evaluate side-chains 296 residues out of total 1448 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 293 time to evaluate : 1.617 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 157 random chunks: chunk 49 optimal weight: 8.9990 chunk 155 optimal weight: 0.5980 chunk 113 optimal weight: 8.9990 chunk 38 optimal weight: 0.4980 chunk 60 optimal weight: 2.9990 chunk 151 optimal weight: 0.6980 chunk 111 optimal weight: 0.9980 chunk 58 optimal weight: 5.9990 chunk 131 optimal weight: 3.9990 chunk 17 optimal weight: 0.2980 chunk 101 optimal weight: 5.9990 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 170 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 319 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 131 HIS ** A 170 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** a 353 ASN ** a 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 148 ASN D 39 GLN ** I 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3605 r_free = 0.3605 target = 0.091993 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3195 r_free = 0.3195 target = 0.072326 restraints weight = 49686.212| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3241 r_free = 0.3241 target = 0.074459 restraints weight = 33434.776| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3276 r_free = 0.3276 target = 0.076032 restraints weight = 25523.134| |-----------------------------------------------------------------------------| r_work (final): 0.3265 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7633 moved from start: 0.3894 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.075 14597 Z= 0.165 Angle : 0.870 11.460 19939 Z= 0.409 Chirality : 0.052 0.353 2415 Planarity : 0.005 0.147 2359 Dihedral : 14.427 112.371 3617 Min Nonbonded Distance : 2.379 Molprobity Statistics. All-atom Clashscore : 12.98 Ramachandran Plot: Outliers : 0.55 % Allowed : 13.20 % Favored : 86.25 % Rotamer: Outliers : 0.21 % Allowed : 4.43 % Favored : 95.36 % 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: -2.65 (0.20), residues: 1629 helix: -0.11 (0.30), residues: 290 sheet: -1.20 (0.32), residues: 280 loop : -2.57 (0.18), residues: 1059 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.002 TRP C 210 HIS 0.012 0.002 HIS B 170 PHE 0.021 0.002 PHE C 117 TYR 0.026 0.002 TYR A 129 ARG 0.010 0.001 ARG E 30 Details of bonding type rmsd link_NAG-ASN : bond 0.00875 ( 35) link_NAG-ASN : angle 3.34477 ( 105) link_ALPHA1-6 : bond 0.01195 ( 10) link_ALPHA1-6 : angle 2.37946 ( 30) link_BETA1-4 : bond 0.00768 ( 27) link_BETA1-4 : angle 2.54428 ( 81) link_ALPHA1-2 : bond 0.01095 ( 2) link_ALPHA1-2 : angle 4.75428 ( 6) link_ALPHA1-3 : bond 0.01279 ( 13) link_ALPHA1-3 : angle 3.01229 ( 39) hydrogen bonds : bond 0.04850 ( 333) hydrogen bonds : angle 6.03957 ( 906) SS BOND : bond 0.00458 ( 26) SS BOND : angle 1.75714 ( 52) covalent geometry : bond 0.00352 (14484) covalent geometry : angle 0.80042 (19626) *********************** 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 413 residues out of total 1448 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 410 time to evaluate : 1.489 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: B 142 LEU cc_start: 0.9121 (mp) cc_final: 0.8767 (tp) REVERT: B 157 PHE cc_start: 0.8699 (m-80) cc_final: 0.8444 (m-80) REVERT: B 183 VAL cc_start: 0.8511 (t) cc_final: 0.8118 (m) REVERT: b 270 GLU cc_start: 0.7574 (mp0) cc_final: 0.7302 (tp30) REVERT: b 311 ASP cc_start: 0.8972 (m-30) cc_final: 0.8679 (m-30) REVERT: b 318 PHE cc_start: 0.9373 (t80) cc_final: 0.9171 (t80) REVERT: b 345 ILE cc_start: 0.9421 (tp) cc_final: 0.9200 (tp) REVERT: b 346 ASN cc_start: 0.9222 (t0) cc_final: 0.8759 (t0) REVERT: b 380 THR cc_start: 0.9316 (p) cc_final: 0.9099 (t) REVERT: b 414 MET cc_start: 0.8709 (tmm) cc_final: 0.7747 (tmm) REVERT: b 415 LEU cc_start: 0.9543 (tt) cc_final: 0.9227 (mm) REVERT: A 62 TYR cc_start: 0.7057 (m-10) cc_final: 0.6146 (m-10) REVERT: A 76 GLU cc_start: 0.8611 (tt0) cc_final: 0.7622 (tp30) REVERT: A 82 MET cc_start: 0.8976 (pmm) cc_final: 0.8444 (pmm) REVERT: A 134 MET cc_start: 0.8367 (mmm) cc_final: 0.8083 (mmm) REVERT: A 140 PHE cc_start: 0.9237 (m-80) cc_final: 0.8795 (m-80) REVERT: a 266 LEU cc_start: 0.8891 (mp) cc_final: 0.8554 (tp) REVERT: a 281 THR cc_start: 0.7977 (p) cc_final: 0.6975 (p) REVERT: a 283 TRP cc_start: 0.8697 (p-90) cc_final: 0.8280 (p-90) REVERT: a 287 GLU cc_start: 0.8337 (mt-10) cc_final: 0.7717 (tm-30) REVERT: a 325 ARG cc_start: 0.8189 (ptp-170) cc_final: 0.7823 (ptp-170) REVERT: a 334 ILE cc_start: 0.9241 (mm) cc_final: 0.9024 (pt) REVERT: a 372 LEU cc_start: 0.9216 (mm) cc_final: 0.8975 (tp) REVERT: a 387 LEU cc_start: 0.8689 (mt) cc_final: 0.7817 (mt) REVERT: C 68 LEU cc_start: 0.8384 (tp) cc_final: 0.7825 (tp) REVERT: C 75 MET cc_start: 0.9006 (mtm) cc_final: 0.8752 (mtm) REVERT: C 92 HIS cc_start: 0.8299 (m-70) cc_final: 0.8041 (m90) REVERT: C 93 HIS cc_start: 0.8463 (m90) cc_final: 0.7996 (m-70) REVERT: C 241 TYR cc_start: 0.9099 (t80) cc_final: 0.8560 (t80) REVERT: c 268 ASP cc_start: 0.7607 (p0) cc_final: 0.7166 (p0) REVERT: c 282 ARG cc_start: 0.8283 (ttt180) cc_final: 0.6986 (ptp-170) REVERT: c 285 LEU cc_start: 0.9230 (mp) cc_final: 0.8976 (mp) REVERT: c 311 ASP cc_start: 0.9286 (m-30) cc_final: 0.8866 (m-30) REVERT: c 320 LYS cc_start: 0.9325 (ttpt) cc_final: 0.8899 (ttmm) REVERT: c 337 ILE cc_start: 0.9015 (mt) cc_final: 0.7981 (mt) REVERT: c 349 LEU cc_start: 0.9161 (tp) cc_final: 0.8802 (tt) REVERT: c 359 MET cc_start: 0.8740 (mmm) cc_final: 0.8259 (mmm) REVERT: c 369 TYR cc_start: 0.8733 (m-80) cc_final: 0.7770 (m-80) REVERT: c 387 LEU cc_start: 0.9337 (mt) cc_final: 0.8905 (mp) REVERT: c 409 ASN cc_start: 0.9540 (t0) cc_final: 0.9170 (m-40) REVERT: D 6 GLU cc_start: 0.8422 (pt0) cc_final: 0.8076 (pm20) REVERT: D 30 SER cc_start: 0.7915 (p) cc_final: 0.7588 (m) REVERT: D 34 MET cc_start: 0.8546 (mtm) cc_final: 0.7631 (mtp) REVERT: D 37 GLU cc_start: 0.6248 (mt-10) cc_final: 0.5806 (mt-10) REVERT: D 46 GLU cc_start: 0.8775 (pt0) cc_final: 0.8095 (pm20) REVERT: D 105 ARG cc_start: 0.7906 (ptp-110) cc_final: 0.7573 (ptp90) REVERT: H 2 VAL cc_start: 0.9566 (t) cc_final: 0.9361 (t) REVERT: H 3 GLN cc_start: 0.9008 (mp10) cc_final: 0.8606 (mp10) REVERT: H 27 VAL cc_start: 0.6627 (OUTLIER) cc_final: 0.6250 (p) REVERT: H 86 ASP cc_start: 0.8353 (m-30) cc_final: 0.8142 (m-30) REVERT: H 96 PHE cc_start: 0.7754 (m-80) cc_final: 0.7508 (m-10) REVERT: H 103 TRP cc_start: 0.9147 (m100) cc_final: 0.8800 (m-10) REVERT: L 6 GLN cc_start: 0.8113 (mt0) cc_final: 0.7003 (mp-120) REVERT: L 31 ASP cc_start: 0.8691 (p0) cc_final: 0.8448 (p0) REVERT: L 74 THR cc_start: 0.8146 (m) cc_final: 0.7619 (t) REVERT: L 78 MET cc_start: 0.8580 (tmm) cc_final: 0.7869 (tmm) REVERT: L 98 PHE cc_start: 0.8550 (m-80) cc_final: 0.8346 (m-10) REVERT: E 3 GLN cc_start: 0.7782 (tm-30) cc_final: 0.7545 (tm-30) REVERT: E 47 TRP cc_start: 0.9042 (t60) cc_final: 0.8441 (t60) REVERT: E 67 LEU cc_start: 0.8754 (mm) cc_final: 0.8230 (mm) REVERT: E 76 ASN cc_start: 0.7751 (m-40) cc_final: 0.7444 (m-40) REVERT: E 86 ASP cc_start: 0.9104 (m-30) cc_final: 0.8571 (m-30) REVERT: I 37 GLN cc_start: 0.7972 (pp30) cc_final: 0.7719 (tm-30) REVERT: I 83 PHE cc_start: 0.8094 (m-80) cc_final: 0.7595 (m-80) outliers start: 3 outliers final: 2 residues processed: 412 average time/residue: 0.2632 time to fit residues: 159.5076 Evaluate side-chains 303 residues out of total 1448 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 300 time to evaluate : 1.827 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 157 random chunks: chunk 31 optimal weight: 0.9990 chunk 151 optimal weight: 2.9990 chunk 114 optimal weight: 9.9990 chunk 56 optimal weight: 5.9990 chunk 82 optimal weight: 4.9990 chunk 14 optimal weight: 6.9990 chunk 63 optimal weight: 6.9990 chunk 153 optimal weight: 9.9990 chunk 46 optimal weight: 0.6980 chunk 53 optimal weight: 1.9990 chunk 154 optimal weight: 0.9990 overall best weight: 1.5388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 170 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 319 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** b 374 HIS ** A 170 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 189 GLN D 39 GLN L 37 GLN L 89 GLN E 3 GLN ** E 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 6 GLN ** I 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3569 r_free = 0.3569 target = 0.089933 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3157 r_free = 0.3157 target = 0.070581 restraints weight = 50266.609| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3194 r_free = 0.3194 target = 0.072360 restraints weight = 35885.571| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3218 r_free = 0.3218 target = 0.073444 restraints weight = 26232.896| |-----------------------------------------------------------------------------| r_work (final): 0.3206 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7758 moved from start: 0.4395 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.067 14597 Z= 0.187 Angle : 0.880 14.028 19939 Z= 0.412 Chirality : 0.051 0.361 2415 Planarity : 0.005 0.111 2359 Dihedral : 12.948 112.396 3617 Min Nonbonded Distance : 2.335 Molprobity Statistics. All-atom Clashscore : 14.75 Ramachandran Plot: Outliers : 0.49 % Allowed : 14.36 % Favored : 85.14 % Rotamer: Outliers : 0.14 % Allowed : 3.67 % Favored : 96.19 % 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: -0.15 (0.30), residues: 299 sheet: -1.10 (0.32), residues: 273 loop : -2.63 (0.18), residues: 1057 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.002 TRP C 210 HIS 0.012 0.002 HIS B 170 PHE 0.019 0.002 PHE A 191 TYR 0.028 0.002 TYR A 62 ARG 0.013 0.001 ARG E 30 Details of bonding type rmsd link_NAG-ASN : bond 0.00780 ( 35) link_NAG-ASN : angle 3.69113 ( 105) link_ALPHA1-6 : bond 0.01160 ( 10) link_ALPHA1-6 : angle 2.27269 ( 30) link_BETA1-4 : bond 0.00654 ( 27) link_BETA1-4 : angle 2.41294 ( 81) link_ALPHA1-2 : bond 0.00954 ( 2) link_ALPHA1-2 : angle 4.32187 ( 6) link_ALPHA1-3 : bond 0.01167 ( 13) link_ALPHA1-3 : angle 3.01506 ( 39) hydrogen bonds : bond 0.04384 ( 333) hydrogen bonds : angle 5.96441 ( 906) SS BOND : bond 0.00496 ( 26) SS BOND : angle 1.79379 ( 52) covalent geometry : bond 0.00412 (14484) covalent geometry : angle 0.80626 (19626) *********************** 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 : 1.531 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 104 GLU cc_start: 0.7804 (tp30) cc_final: 0.7317 (mm-30) REVERT: B 142 LEU cc_start: 0.9132 (mp) cc_final: 0.8845 (tp) REVERT: B 157 PHE cc_start: 0.8633 (m-80) cc_final: 0.8432 (m-80) REVERT: b 270 GLU cc_start: 0.7619 (mp0) cc_final: 0.7264 (tp30) REVERT: b 317 ASP cc_start: 0.8904 (t70) cc_final: 0.8651 (t70) REVERT: b 345 ILE cc_start: 0.9450 (tp) cc_final: 0.9238 (tp) REVERT: b 346 ASN cc_start: 0.9327 (t0) cc_final: 0.8889 (t0) REVERT: b 357 ASP cc_start: 0.9039 (t70) cc_final: 0.8596 (t0) REVERT: b 414 MET cc_start: 0.8544 (tmm) cc_final: 0.8156 (tmm) REVERT: A 75 MET cc_start: 0.8651 (ttp) cc_final: 0.8410 (ttm) REVERT: A 76 GLU cc_start: 0.8611 (tt0) cc_final: 0.7754 (tp30) REVERT: A 82 MET cc_start: 0.9035 (pmm) cc_final: 0.8597 (pmm) REVERT: A 122 ASP cc_start: 0.9251 (m-30) cc_final: 0.8890 (m-30) REVERT: A 126 LYS cc_start: 0.8603 (mmtm) cc_final: 0.8335 (mmtp) REVERT: A 134 MET cc_start: 0.8706 (mmm) cc_final: 0.8310 (mmm) REVERT: A 140 PHE cc_start: 0.9262 (m-80) cc_final: 0.8790 (m-80) REVERT: A 222 ILE cc_start: 0.9162 (mt) cc_final: 0.8760 (tp) REVERT: a 281 THR cc_start: 0.8061 (p) cc_final: 0.7795 (p) REVERT: a 283 TRP cc_start: 0.8663 (p-90) cc_final: 0.8326 (p-90) REVERT: a 287 GLU cc_start: 0.8304 (mt-10) cc_final: 0.7633 (tm-30) REVERT: a 324 GLN cc_start: 0.8943 (tm-30) cc_final: 0.8731 (tm-30) REVERT: a 332 MET cc_start: 0.7234 (mtt) cc_final: 0.6404 (mtt) REVERT: a 372 LEU cc_start: 0.9348 (mm) cc_final: 0.8948 (tp) REVERT: C 75 MET cc_start: 0.9000 (mtm) cc_final: 0.8664 (mtm) REVERT: C 92 HIS cc_start: 0.8372 (m-70) cc_final: 0.8038 (m90) REVERT: C 93 HIS cc_start: 0.8487 (m90) cc_final: 0.7943 (m-70) REVERT: c 268 ASP cc_start: 0.7702 (p0) cc_final: 0.7219 (p0) REVERT: c 282 ARG cc_start: 0.8400 (ttt180) cc_final: 0.7203 (ptp-170) REVERT: c 285 LEU cc_start: 0.9175 (mp) cc_final: 0.8966 (mp) REVERT: c 311 ASP cc_start: 0.9213 (m-30) cc_final: 0.8960 (m-30) REVERT: c 314 ARG cc_start: 0.9225 (mtt90) cc_final: 0.8662 (ttm110) REVERT: c 320 LYS cc_start: 0.9345 (ttpt) cc_final: 0.8874 (ttmm) REVERT: c 337 ILE cc_start: 0.8774 (mt) cc_final: 0.8026 (mt) REVERT: c 359 MET cc_start: 0.8808 (mmm) cc_final: 0.8118 (mmm) REVERT: c 369 TYR cc_start: 0.8751 (m-80) cc_final: 0.6836 (m-80) REVERT: c 387 LEU cc_start: 0.9399 (mt) cc_final: 0.8977 (mp) REVERT: c 403 ILE cc_start: 0.9161 (mt) cc_final: 0.8838 (mt) REVERT: c 409 ASN cc_start: 0.9486 (t0) cc_final: 0.9181 (m110) REVERT: D 6 GLU cc_start: 0.8472 (pt0) cc_final: 0.7801 (pm20) REVERT: D 30 SER cc_start: 0.7885 (p) cc_final: 0.7671 (m) REVERT: D 34 MET cc_start: 0.8698 (mtm) cc_final: 0.7751 (mtp) REVERT: D 37 GLU cc_start: 0.6202 (mt-10) cc_final: 0.5835 (mt-10) REVERT: D 46 GLU cc_start: 0.8743 (pt0) cc_final: 0.8096 (pm20) REVERT: D 75 TRP cc_start: 0.8290 (t-100) cc_final: 0.7628 (t-100) REVERT: D 95 TYR cc_start: 0.7524 (m-10) cc_final: 0.6357 (m-80) REVERT: D 104 LEU cc_start: 0.7771 (pp) cc_final: 0.7509 (pp) REVERT: D 105 ARG cc_start: 0.7928 (ptp-110) cc_final: 0.7232 (ptp-110) REVERT: H 2 VAL cc_start: 0.9599 (t) cc_final: 0.9391 (t) REVERT: H 3 GLN cc_start: 0.8950 (mp10) cc_final: 0.8692 (mp10) REVERT: H 86 ASP cc_start: 0.8516 (m-30) cc_final: 0.8273 (m-30) REVERT: H 96 PHE cc_start: 0.8043 (m-80) cc_final: 0.7742 (m-10) REVERT: L 6 GLN cc_start: 0.8035 (mt0) cc_final: 0.7320 (mp-120) REVERT: L 74 THR cc_start: 0.8201 (m) cc_final: 0.7816 (t) REVERT: L 78 MET cc_start: 0.8659 (tmm) cc_final: 0.8268 (tmm) REVERT: E 47 TRP cc_start: 0.9121 (t60) cc_final: 0.8449 (t60) REVERT: E 67 LEU cc_start: 0.8946 (mm) cc_final: 0.8418 (mm) REVERT: E 76 ASN cc_start: 0.7831 (m-40) cc_final: 0.7326 (m-40) REVERT: E 86 ASP cc_start: 0.9202 (m-30) cc_final: 0.8657 (m-30) REVERT: I 37 GLN cc_start: 0.8010 (pp30) cc_final: 0.7620 (tm-30) outliers start: 2 outliers final: 1 residues processed: 373 average time/residue: 0.2867 time to fit residues: 160.6388 Evaluate side-chains 285 residues out of total 1448 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 284 time to evaluate : 1.502 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 157 random chunks: chunk 120 optimal weight: 0.1980 chunk 54 optimal weight: 5.9990 chunk 42 optimal weight: 0.6980 chunk 117 optimal weight: 6.9990 chunk 71 optimal weight: 0.7980 chunk 61 optimal weight: 0.0980 chunk 151 optimal weight: 0.4980 chunk 145 optimal weight: 10.0000 chunk 143 optimal weight: 4.9990 chunk 79 optimal weight: 3.9990 chunk 152 optimal weight: 3.9990 overall best weight: 0.4580 ------------------------------------------------------------------------------- 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 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 170 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 223 GLN ** a 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 39 GLN ** I 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3611 r_free = 0.3611 target = 0.092162 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3202 r_free = 0.3202 target = 0.072343 restraints weight = 50876.143| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3251 r_free = 0.3251 target = 0.074576 restraints weight = 33824.601| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3286 r_free = 0.3286 target = 0.076176 restraints weight = 25590.282| |-----------------------------------------------------------------------------| r_work (final): 0.3276 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7665 moved from start: 0.4630 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.068 14597 Z= 0.156 Angle : 0.849 12.206 19939 Z= 0.400 Chirality : 0.051 0.378 2415 Planarity : 0.005 0.082 2359 Dihedral : 11.930 111.765 3617 Min Nonbonded Distance : 2.334 Molprobity Statistics. All-atom Clashscore : 13.73 Ramachandran Plot: Outliers : 0.55 % Allowed : 13.51 % Favored : 85.94 % Rotamer: Outliers : 0.00 % Allowed : 2.56 % Favored : 97.44 % 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: -2.66 (0.20), residues: 1629 helix: -0.05 (0.30), residues: 294 sheet: -1.17 (0.31), residues: 277 loop : -2.62 (0.18), residues: 1058 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.035 0.002 TRP C 210 HIS 0.013 0.002 HIS B 170 PHE 0.047 0.002 PHE I 83 TYR 0.019 0.002 TYR A 129 ARG 0.008 0.001 ARG E 30 Details of bonding type rmsd link_NAG-ASN : bond 0.00783 ( 35) link_NAG-ASN : angle 3.36069 ( 105) link_ALPHA1-6 : bond 0.01207 ( 10) link_ALPHA1-6 : angle 2.21325 ( 30) link_BETA1-4 : bond 0.00701 ( 27) link_BETA1-4 : angle 2.18165 ( 81) link_ALPHA1-2 : bond 0.01158 ( 2) link_ALPHA1-2 : angle 4.36471 ( 6) link_ALPHA1-3 : bond 0.01222 ( 13) link_ALPHA1-3 : angle 3.03463 ( 39) hydrogen bonds : bond 0.04202 ( 333) hydrogen bonds : angle 5.70230 ( 906) SS BOND : bond 0.00523 ( 26) SS BOND : angle 1.86585 ( 52) covalent geometry : bond 0.00332 (14484) covalent geometry : angle 0.78227 (19626) *********************** 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 376 residues out of total 1448 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 376 time to evaluate : 1.484 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 104 GLU cc_start: 0.7816 (tp30) cc_final: 0.7186 (mm-30) REVERT: B 142 LEU cc_start: 0.9078 (mp) cc_final: 0.8682 (tp) REVERT: B 150 TYR cc_start: 0.7028 (m-80) cc_final: 0.5830 (m-80) REVERT: b 270 GLU cc_start: 0.7502 (mp0) cc_final: 0.7209 (tp30) REVERT: b 284 MET cc_start: 0.8343 (mmm) cc_final: 0.7857 (mmm) REVERT: b 317 ASP cc_start: 0.8936 (t70) cc_final: 0.8687 (t70) REVERT: b 345 ILE cc_start: 0.9409 (tp) cc_final: 0.9173 (tp) REVERT: b 346 ASN cc_start: 0.9252 (t0) cc_final: 0.8815 (t0) REVERT: A 75 MET cc_start: 0.8747 (ttp) cc_final: 0.8310 (ttm) REVERT: A 76 GLU cc_start: 0.8624 (tt0) cc_final: 0.7684 (tp30) REVERT: A 82 MET cc_start: 0.8821 (pmm) cc_final: 0.8492 (pmm) REVERT: a 287 GLU cc_start: 0.8249 (mt-10) cc_final: 0.7589 (tm-30) REVERT: a 324 GLN cc_start: 0.9004 (tm-30) cc_final: 0.8709 (tm-30) REVERT: a 332 MET cc_start: 0.7029 (mtt) cc_final: 0.6815 (mtt) REVERT: a 372 LEU cc_start: 0.9345 (mm) cc_final: 0.8914 (tp) REVERT: C 72 GLU cc_start: 0.8745 (mm-30) cc_final: 0.8225 (mm-30) REVERT: C 92 HIS cc_start: 0.8233 (m-70) cc_final: 0.7994 (m90) REVERT: C 93 HIS cc_start: 0.8300 (m90) cc_final: 0.7929 (m-70) REVERT: C 153 MET cc_start: 0.8202 (tmm) cc_final: 0.7924 (tmm) REVERT: C 192 MET cc_start: 0.8494 (mmt) cc_final: 0.8238 (mmt) REVERT: C 259 ARG cc_start: 0.8245 (mmm-85) cc_final: 0.7970 (mmm-85) REVERT: c 268 ASP cc_start: 0.7753 (p0) cc_final: 0.7276 (p0) REVERT: c 282 ARG cc_start: 0.8381 (ttt180) cc_final: 0.7179 (ptp-170) REVERT: c 311 ASP cc_start: 0.9163 (m-30) cc_final: 0.8958 (m-30) REVERT: c 314 ARG cc_start: 0.9073 (mtt90) cc_final: 0.8613 (ttm110) REVERT: c 320 LYS cc_start: 0.9358 (ttpt) cc_final: 0.8881 (ttmm) REVERT: c 337 ILE cc_start: 0.8639 (mt) cc_final: 0.8166 (mt) REVERT: c 349 LEU cc_start: 0.9216 (tp) cc_final: 0.8919 (tt) REVERT: c 359 MET cc_start: 0.8935 (mmm) cc_final: 0.8427 (mmm) REVERT: c 368 LYS cc_start: 0.9116 (mtpp) cc_final: 0.8162 (mtpp) REVERT: c 369 TYR cc_start: 0.8595 (m-80) cc_final: 0.6638 (m-80) REVERT: c 387 LEU cc_start: 0.9326 (mt) cc_final: 0.8892 (mp) REVERT: c 403 ILE cc_start: 0.9104 (mt) cc_final: 0.8741 (mt) REVERT: c 404 GLU cc_start: 0.9316 (mm-30) cc_final: 0.9063 (mm-30) REVERT: c 409 ASN cc_start: 0.9493 (t0) cc_final: 0.9158 (m110) REVERT: D 6 GLU cc_start: 0.8419 (pt0) cc_final: 0.7779 (pm20) REVERT: D 30 SER cc_start: 0.7874 (p) cc_final: 0.7580 (m) REVERT: D 34 MET cc_start: 0.8515 (mtm) cc_final: 0.7689 (mtp) REVERT: D 37 GLU cc_start: 0.6295 (mt-10) cc_final: 0.5866 (mt-10) REVERT: D 46 GLU cc_start: 0.8668 (pt0) cc_final: 0.8092 (pm20) REVERT: D 75 TRP cc_start: 0.8192 (t-100) cc_final: 0.7591 (t-100) REVERT: D 95 TYR cc_start: 0.7410 (m-10) cc_final: 0.6280 (m-80) REVERT: D 104 LEU cc_start: 0.7870 (pp) cc_final: 0.7437 (pp) REVERT: D 105 ARG cc_start: 0.7826 (ptp-110) cc_final: 0.6585 (ptp-110) REVERT: H 3 GLN cc_start: 0.8987 (mp10) cc_final: 0.8686 (mp10) REVERT: H 67 LEU cc_start: 0.7266 (mm) cc_final: 0.6879 (mm) REVERT: H 86 ASP cc_start: 0.8361 (m-30) cc_final: 0.8144 (m-30) REVERT: H 96 PHE cc_start: 0.7899 (m-80) cc_final: 0.7580 (m-10) REVERT: L 6 GLN cc_start: 0.7861 (mt0) cc_final: 0.7180 (mp-120) REVERT: L 31 ASP cc_start: 0.8562 (p0) cc_final: 0.8342 (p0) REVERT: L 74 THR cc_start: 0.8187 (m) cc_final: 0.7760 (t) REVERT: E 3 GLN cc_start: 0.7685 (tm-30) cc_final: 0.7476 (tm-30) REVERT: E 47 TRP cc_start: 0.8960 (t60) cc_final: 0.8556 (t60) REVERT: E 50 TYR cc_start: 0.8553 (p90) cc_final: 0.8213 (p90) REVERT: E 67 LEU cc_start: 0.8891 (mm) cc_final: 0.8384 (mm) REVERT: E 76 ASN cc_start: 0.7686 (m-40) cc_final: 0.7173 (m-40) REVERT: E 86 ASP cc_start: 0.9144 (m-30) cc_final: 0.8623 (m-30) REVERT: I 83 PHE cc_start: 0.7496 (m-80) cc_final: 0.7094 (m-80) REVERT: I 104 LEU cc_start: 0.8701 (tt) cc_final: 0.8463 (tp) outliers start: 0 outliers final: 0 residues processed: 376 average time/residue: 0.2610 time to fit residues: 143.4849 Evaluate side-chains 288 residues out of total 1448 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 288 time to evaluate : 1.530 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 157 random chunks: chunk 62 optimal weight: 6.9990 chunk 1 optimal weight: 2.9990 chunk 16 optimal weight: 0.4980 chunk 52 optimal weight: 9.9990 chunk 145 optimal weight: 4.9990 chunk 84 optimal weight: 10.0000 chunk 60 optimal weight: 0.5980 chunk 5 optimal weight: 7.9990 chunk 140 optimal weight: 3.9990 chunk 40 optimal weight: 9.9990 chunk 130 optimal weight: 3.9990 overall best weight: 2.4186 ------------------------------------------------------------------------------- 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 319 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 170 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 124 HIS c 331 GLN ** E 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 37 GLN ** I 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3534 r_free = 0.3534 target = 0.087556 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3099 r_free = 0.3099 target = 0.067545 restraints weight = 53646.842| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3138 r_free = 0.3138 target = 0.069549 restraints weight = 37736.005| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3166 r_free = 0.3166 target = 0.070620 restraints weight = 28394.891| |-----------------------------------------------------------------------------| r_work (final): 0.3155 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7858 moved from start: 0.4978 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.058 14597 Z= 0.232 Angle : 0.906 12.923 19939 Z= 0.425 Chirality : 0.052 0.391 2415 Planarity : 0.005 0.090 2359 Dihedral : 11.715 111.349 3617 Min Nonbonded Distance : 2.303 Molprobity Statistics. All-atom Clashscore : 17.46 Ramachandran Plot: Outliers : 0.55 % Allowed : 15.10 % Favored : 84.35 % Rotamer: Outliers : 0.07 % Allowed : 2.84 % Favored : 97.09 % 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: -0.10 (0.30), residues: 301 sheet: -1.09 (0.31), residues: 276 loop : -2.65 (0.18), residues: 1052 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.035 0.003 TRP C 210 HIS 0.014 0.002 HIS B 170 PHE 0.027 0.002 PHE I 83 TYR 0.036 0.003 TYR A 62 ARG 0.016 0.001 ARG E 30 Details of bonding type rmsd link_NAG-ASN : bond 0.00864 ( 35) link_NAG-ASN : angle 3.70501 ( 105) link_ALPHA1-6 : bond 0.01274 ( 10) link_ALPHA1-6 : angle 2.38268 ( 30) link_BETA1-4 : bond 0.00618 ( 27) link_BETA1-4 : angle 2.17684 ( 81) link_ALPHA1-2 : bond 0.00816 ( 2) link_ALPHA1-2 : angle 3.88122 ( 6) link_ALPHA1-3 : bond 0.01158 ( 13) link_ALPHA1-3 : angle 3.04166 ( 39) hydrogen bonds : bond 0.04307 ( 333) hydrogen bonds : angle 5.79184 ( 906) SS BOND : bond 0.00400 ( 26) SS BOND : angle 1.63941 ( 52) covalent geometry : bond 0.00508 (14484) covalent geometry : angle 0.83845 (19626) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3258 Ramachandran restraints generated. 1629 Oldfield, 0 Emsley, 1629 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3258 Ramachandran restraints generated. 1629 Oldfield, 0 Emsley, 1629 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 353 residues out of total 1448 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 352 time to evaluate : 1.755 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 104 GLU cc_start: 0.7940 (tp30) cc_final: 0.7334 (mm-30) REVERT: B 142 LEU cc_start: 0.9159 (mp) cc_final: 0.8856 (tp) REVERT: b 270 GLU cc_start: 0.7612 (mp0) cc_final: 0.7170 (tp30) REVERT: b 317 ASP cc_start: 0.8913 (t70) cc_final: 0.8585 (t70) REVERT: b 345 ILE cc_start: 0.9502 (tp) cc_final: 0.9244 (tp) REVERT: b 346 ASN cc_start: 0.9381 (t0) cc_final: 0.8869 (t0) REVERT: b 351 MET cc_start: 0.9200 (mmt) cc_final: 0.8845 (mmp) REVERT: b 353 ASN cc_start: 0.9273 (m-40) cc_final: 0.9065 (m-40) REVERT: b 357 ASP cc_start: 0.9008 (t70) cc_final: 0.8461 (t0) REVERT: A 62 TYR cc_start: 0.7028 (m-10) cc_final: 0.6824 (m-10) REVERT: A 75 MET cc_start: 0.8842 (ttp) cc_final: 0.8507 (ttp) REVERT: A 82 MET cc_start: 0.8931 (pmm) cc_final: 0.8590 (pmm) REVERT: A 193 ARG cc_start: 0.5933 (tmm-80) cc_final: 0.5584 (tmm-80) REVERT: a 265 THR cc_start: 0.8111 (m) cc_final: 0.7803 (p) REVERT: a 266 LEU cc_start: 0.8838 (mp) cc_final: 0.8539 (tp) REVERT: a 287 GLU cc_start: 0.8312 (mt-10) cc_final: 0.7658 (tm-30) REVERT: a 324 GLN cc_start: 0.9079 (tm-30) cc_final: 0.8800 (tm-30) REVERT: a 325 ARG cc_start: 0.8437 (ptp-170) cc_final: 0.7811 (ptp-170) REVERT: C 93 HIS cc_start: 0.8449 (m90) cc_final: 0.7963 (m-70) REVERT: C 192 MET cc_start: 0.8654 (mmt) cc_final: 0.8259 (mmt) REVERT: c 268 ASP cc_start: 0.7867 (p0) cc_final: 0.7468 (p0) REVERT: c 282 ARG cc_start: 0.8514 (ttt180) cc_final: 0.7360 (ptp-170) REVERT: c 306 ASP cc_start: 0.9149 (m-30) cc_final: 0.8929 (m-30) REVERT: c 311 ASP cc_start: 0.9252 (m-30) cc_final: 0.9023 (m-30) REVERT: c 314 ARG cc_start: 0.9191 (mtt90) cc_final: 0.8731 (ttm110) REVERT: c 337 ILE cc_start: 0.8931 (mt) cc_final: 0.8338 (mt) REVERT: c 351 MET cc_start: 0.8550 (tpt) cc_final: 0.8305 (tpt) REVERT: c 359 MET cc_start: 0.9073 (mmm) cc_final: 0.8483 (mmm) REVERT: c 369 TYR cc_start: 0.8758 (m-80) cc_final: 0.6889 (m-80) REVERT: c 387 LEU cc_start: 0.9382 (mt) cc_final: 0.8820 (mt) REVERT: c 403 ILE cc_start: 0.9164 (mt) cc_final: 0.8786 (mt) REVERT: c 404 GLU cc_start: 0.9328 (mm-30) cc_final: 0.9079 (mm-30) REVERT: c 409 ASN cc_start: 0.9505 (t0) cc_final: 0.9171 (m110) REVERT: D 6 GLU cc_start: 0.8570 (pt0) cc_final: 0.8254 (pt0) REVERT: D 34 MET cc_start: 0.8828 (mtm) cc_final: 0.8086 (mtp) REVERT: D 37 GLU cc_start: 0.6141 (mt-10) cc_final: 0.5889 (mt-10) REVERT: D 46 GLU cc_start: 0.8854 (pt0) cc_final: 0.8036 (pm20) REVERT: H 30 ARG cc_start: 0.7960 (ptt-90) cc_final: 0.7726 (ttp-170) REVERT: H 86 ASP cc_start: 0.8628 (m-30) cc_final: 0.8299 (m-30) REVERT: H 96 PHE cc_start: 0.8064 (m-80) cc_final: 0.7754 (m-10) REVERT: L 6 GLN cc_start: 0.8175 (mt0) cc_final: 0.7018 (mp-120) REVERT: L 23 CYS cc_start: 0.5598 (t) cc_final: 0.3917 (t) REVERT: L 74 THR cc_start: 0.8354 (m) cc_final: 0.8070 (t) REVERT: L 83 PHE cc_start: 0.7694 (m-80) cc_final: 0.7337 (m-80) REVERT: E 3 GLN cc_start: 0.7756 (tm-30) cc_final: 0.7492 (tm-30) REVERT: E 47 TRP cc_start: 0.9202 (t60) cc_final: 0.7980 (t60) REVERT: E 67 LEU cc_start: 0.9053 (mm) cc_final: 0.8556 (mm) REVERT: E 76 ASN cc_start: 0.8051 (m-40) cc_final: 0.7740 (m-40) REVERT: E 86 ASP cc_start: 0.9259 (m-30) cc_final: 0.8735 (m-30) REVERT: I 83 PHE cc_start: 0.7675 (m-80) cc_final: 0.7114 (m-80) outliers start: 1 outliers final: 0 residues processed: 353 average time/residue: 0.2534 time to fit residues: 131.1520 Evaluate side-chains 269 residues out of total 1448 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 269 time to evaluate : 1.660 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 157 random chunks: chunk 113 optimal weight: 3.9990 chunk 119 optimal weight: 4.9990 chunk 115 optimal weight: 0.6980 chunk 30 optimal weight: 0.6980 chunk 126 optimal weight: 0.0870 chunk 128 optimal weight: 9.9990 chunk 108 optimal weight: 5.9990 chunk 127 optimal weight: 10.0000 chunk 71 optimal weight: 1.9990 chunk 84 optimal weight: 8.9990 chunk 42 optimal weight: 5.9990 overall best weight: 1.4962 ------------------------------------------------------------------------------- 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 305 HIS ** 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 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 89 ASN ** C 124 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3548 r_free = 0.3548 target = 0.088341 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3114 r_free = 0.3114 target = 0.068346 restraints weight = 53012.330| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3155 r_free = 0.3155 target = 0.070378 restraints weight = 37101.676| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3185 r_free = 0.3185 target = 0.071553 restraints weight = 27828.292| |-----------------------------------------------------------------------------| r_work (final): 0.3171 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7823 moved from start: 0.5171 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 14597 Z= 0.177 Angle : 0.866 12.929 19939 Z= 0.406 Chirality : 0.051 0.488 2415 Planarity : 0.005 0.077 2359 Dihedral : 11.234 111.145 3617 Min Nonbonded Distance : 2.310 Molprobity Statistics. All-atom Clashscore : 16.41 Ramachandran Plot: Outliers : 0.55 % Allowed : 14.24 % Favored : 85.21 % Rotamer: Outliers : 0.00 % Allowed : 1.52 % Favored : 98.48 % 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: -0.01 (0.30), residues: 299 sheet: -0.89 (0.31), residues: 293 loop : -2.68 (0.18), residues: 1037 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.041 0.002 TRP C 210 HIS 0.013 0.002 HIS B 170 PHE 0.023 0.002 PHE I 83 TYR 0.034 0.002 TYR D 95 ARG 0.009 0.001 ARG a 282 Details of bonding type rmsd link_NAG-ASN : bond 0.00895 ( 35) link_NAG-ASN : angle 3.64080 ( 105) link_ALPHA1-6 : bond 0.01308 ( 10) link_ALPHA1-6 : angle 2.30645 ( 30) link_BETA1-4 : bond 0.00621 ( 27) link_BETA1-4 : angle 2.05065 ( 81) link_ALPHA1-2 : bond 0.00959 ( 2) link_ALPHA1-2 : angle 3.89221 ( 6) link_ALPHA1-3 : bond 0.01195 ( 13) link_ALPHA1-3 : angle 3.03669 ( 39) hydrogen bonds : bond 0.04088 ( 333) hydrogen bonds : angle 5.58568 ( 906) SS BOND : bond 0.00573 ( 26) SS BOND : angle 1.51431 ( 52) covalent geometry : bond 0.00381 (14484) covalent geometry : angle 0.79747 (19626) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3258 Ramachandran restraints generated. 1629 Oldfield, 0 Emsley, 1629 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3258 Ramachandran restraints generated. 1629 Oldfield, 0 Emsley, 1629 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 347 residues out of total 1448 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 347 time to evaluate : 1.652 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 82 MET cc_start: 0.8711 (pmm) cc_final: 0.7947 (pmm) REVERT: B 104 GLU cc_start: 0.7819 (tp30) cc_final: 0.7208 (mm-30) REVERT: B 142 LEU cc_start: 0.9139 (mp) cc_final: 0.8816 (tp) REVERT: b 270 GLU cc_start: 0.7635 (mp0) cc_final: 0.7112 (tp30) REVERT: b 345 ILE cc_start: 0.9510 (tp) cc_final: 0.9271 (tp) REVERT: b 346 ASN cc_start: 0.9263 (t0) cc_final: 0.8653 (t0) REVERT: b 351 MET cc_start: 0.9237 (mmt) cc_final: 0.8904 (mmp) REVERT: b 357 ASP cc_start: 0.8907 (t70) cc_final: 0.8405 (t0) REVERT: A 75 MET cc_start: 0.8835 (ttp) cc_final: 0.8456 (ttm) REVERT: A 76 GLU cc_start: 0.8674 (tt0) cc_final: 0.7942 (tp30) REVERT: A 82 MET cc_start: 0.8955 (pmm) cc_final: 0.8650 (pmm) REVERT: A 193 ARG cc_start: 0.5977 (tmm-80) cc_final: 0.5626 (tmm-80) REVERT: a 264 TRP cc_start: 0.6992 (m100) cc_final: 0.6296 (m-90) REVERT: a 265 THR cc_start: 0.8103 (m) cc_final: 0.7753 (p) REVERT: a 266 LEU cc_start: 0.8842 (mp) cc_final: 0.8580 (tp) REVERT: a 287 GLU cc_start: 0.8352 (mt-10) cc_final: 0.7693 (tm-30) REVERT: a 324 GLN cc_start: 0.9086 (tm-30) cc_final: 0.8833 (tm-30) REVERT: a 325 ARG cc_start: 0.8455 (ptp-170) cc_final: 0.7951 (ptp-170) REVERT: a 372 LEU cc_start: 0.9411 (mm) cc_final: 0.8963 (tp) REVERT: C 93 HIS cc_start: 0.8454 (m90) cc_final: 0.7950 (m-70) REVERT: C 164 VAL cc_start: 0.8548 (t) cc_final: 0.8253 (t) REVERT: C 192 MET cc_start: 0.8690 (mmt) cc_final: 0.8206 (mmt) REVERT: C 214 MET cc_start: 0.6835 (mtm) cc_final: 0.6165 (mtm) REVERT: c 268 ASP cc_start: 0.7795 (p0) cc_final: 0.7410 (p0) REVERT: c 282 ARG cc_start: 0.8387 (ttt180) cc_final: 0.7133 (ptp-170) REVERT: c 311 ASP cc_start: 0.9249 (m-30) cc_final: 0.8952 (m-30) REVERT: c 337 ILE cc_start: 0.8851 (mt) cc_final: 0.8437 (mt) REVERT: c 349 LEU cc_start: 0.9282 (tp) cc_final: 0.9010 (tt) REVERT: c 359 MET cc_start: 0.9024 (mmm) cc_final: 0.8604 (mmm) REVERT: c 369 TYR cc_start: 0.8761 (m-80) cc_final: 0.6953 (m-80) REVERT: c 387 LEU cc_start: 0.9365 (mt) cc_final: 0.8822 (mt) REVERT: c 403 ILE cc_start: 0.9151 (mt) cc_final: 0.8805 (mt) REVERT: c 404 GLU cc_start: 0.9309 (mm-30) cc_final: 0.9100 (mm-30) REVERT: c 409 ASN cc_start: 0.9486 (t0) cc_final: 0.9148 (m-40) REVERT: D 6 GLU cc_start: 0.8377 (pt0) cc_final: 0.8151 (pt0) REVERT: D 34 MET cc_start: 0.8813 (mtm) cc_final: 0.8054 (mtp) REVERT: D 37 GLU cc_start: 0.6232 (mt-10) cc_final: 0.5949 (mt-10) REVERT: D 46 GLU cc_start: 0.8773 (pt0) cc_final: 0.7977 (pm20) REVERT: D 95 TYR cc_start: 0.7788 (m-80) cc_final: 0.7414 (m-80) REVERT: D 105 ARG cc_start: 0.8117 (ptp-110) cc_final: 0.7572 (ptp-110) REVERT: H 30 ARG cc_start: 0.7999 (ptt-90) cc_final: 0.7750 (ttp-170) REVERT: H 86 ASP cc_start: 0.8501 (m-30) cc_final: 0.8219 (m-30) REVERT: H 96 PHE cc_start: 0.7977 (m-80) cc_final: 0.7626 (m-10) REVERT: L 6 GLN cc_start: 0.8134 (mt0) cc_final: 0.7421 (mp-120) REVERT: L 31 ASP cc_start: 0.8490 (p0) cc_final: 0.8250 (p0) REVERT: L 74 THR cc_start: 0.8323 (m) cc_final: 0.7984 (t) REVERT: E 3 GLN cc_start: 0.7677 (tm-30) cc_final: 0.7369 (tm-30) REVERT: E 67 LEU cc_start: 0.8912 (mm) cc_final: 0.8527 (mm) REVERT: E 76 ASN cc_start: 0.7936 (m-40) cc_final: 0.7724 (m-40) REVERT: E 86 ASP cc_start: 0.9241 (m-30) cc_final: 0.8735 (m-30) REVERT: I 83 PHE cc_start: 0.7788 (m-80) cc_final: 0.7263 (m-80) outliers start: 0 outliers final: 0 residues processed: 347 average time/residue: 0.2599 time to fit residues: 131.9102 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 : 1.690 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 157 random chunks: chunk 57 optimal weight: 10.0000 chunk 131 optimal weight: 0.9980 chunk 87 optimal weight: 2.9990 chunk 133 optimal weight: 1.9990 chunk 88 optimal weight: 0.9980 chunk 38 optimal weight: 0.9980 chunk 91 optimal weight: 0.0000 chunk 9 optimal weight: 0.7980 chunk 45 optimal weight: 7.9990 chunk 83 optimal weight: 9.9990 chunk 62 optimal weight: 6.9990 overall best weight: 0.7584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 92 HIS ** B 170 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 230 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 319 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 170 HIS ** C 124 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 149 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3574 r_free = 0.3574 target = 0.089710 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3148 r_free = 0.3148 target = 0.069907 restraints weight = 52289.999| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3189 r_free = 0.3189 target = 0.071983 restraints weight = 36705.978| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3217 r_free = 0.3217 target = 0.073136 restraints weight = 27432.439| |-----------------------------------------------------------------------------| r_work (final): 0.3204 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7777 moved from start: 0.5306 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 14597 Z= 0.153 Angle : 0.860 11.450 19939 Z= 0.403 Chirality : 0.051 0.428 2415 Planarity : 0.006 0.164 2359 Dihedral : 10.780 111.317 3617 Min Nonbonded Distance : 2.315 Molprobity Statistics. All-atom Clashscore : 15.90 Ramachandran Plot: Outliers : 0.55 % Allowed : 13.87 % Favored : 85.57 % Rotamer: Outliers : 0.00 % Allowed : 1.25 % Favored : 98.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % 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: -2.52 (0.20), residues: 1629 helix: 0.05 (0.30), residues: 302 sheet: -0.73 (0.33), residues: 278 loop : -2.66 (0.18), residues: 1049 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.057 0.002 TRP C 210 HIS 0.013 0.002 HIS B 170 PHE 0.024 0.002 PHE L 83 TYR 0.022 0.002 TYR A 62 ARG 0.014 0.001 ARG D 93 Details of bonding type rmsd link_NAG-ASN : bond 0.00856 ( 35) link_NAG-ASN : angle 3.60954 ( 105) link_ALPHA1-6 : bond 0.01402 ( 10) link_ALPHA1-6 : angle 2.28153 ( 30) link_BETA1-4 : bond 0.00631 ( 27) link_BETA1-4 : angle 1.97805 ( 81) link_ALPHA1-2 : bond 0.01070 ( 2) link_ALPHA1-2 : angle 3.96499 ( 6) link_ALPHA1-3 : bond 0.01248 ( 13) link_ALPHA1-3 : angle 2.99063 ( 39) hydrogen bonds : bond 0.03871 ( 333) hydrogen bonds : angle 5.42827 ( 906) SS BOND : bond 0.00492 ( 26) SS BOND : angle 1.47363 ( 52) covalent geometry : bond 0.00324 (14484) covalent geometry : angle 0.79299 (19626) *********************** 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 345 residues out of total 1448 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 345 time to evaluate : 1.693 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: 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: 0.8665 (pmm) cc_final: 0.7984 (pmm) REVERT: B 104 GLU cc_start: 0.7680 (tp30) cc_final: 0.7211 (mm-30) REVERT: B 142 LEU cc_start: 0.9160 (mp) cc_final: 0.8853 (tp) REVERT: B 149 GLN cc_start: 0.8024 (tm-30) cc_final: 0.7652 (tm-30) REVERT: b 270 GLU cc_start: 0.7564 (mp0) cc_final: 0.7102 (tp30) REVERT: b 284 MET cc_start: 0.7849 (mmp) cc_final: 0.7572 (mmp) REVERT: b 325 ARG cc_start: 0.7654 (ptp90) cc_final: 0.7271 (ptp90) REVERT: b 345 ILE cc_start: 0.9489 (tp) cc_final: 0.9266 (tp) REVERT: b 346 ASN cc_start: 0.9214 (t0) cc_final: 0.8557 (t0) REVERT: b 350 ILE cc_start: 0.9459 (pt) cc_final: 0.9246 (pt) REVERT: b 351 MET cc_start: 0.9232 (mmt) cc_final: 0.8813 (mmp) REVERT: b 357 ASP cc_start: 0.8874 (t70) cc_final: 0.8398 (t0) REVERT: b 369 TYR cc_start: 0.8701 (m-80) cc_final: 0.7976 (m-10) REVERT: A 75 MET cc_start: 0.8751 (ttp) cc_final: 0.8278 (ttm) REVERT: A 76 GLU cc_start: 0.8700 (tt0) cc_final: 0.7915 (tp30) REVERT: A 82 MET cc_start: 0.8966 (pmm) cc_final: 0.8697 (pmm) REVERT: A 193 ARG cc_start: 0.5993 (tmm-80) cc_final: 0.5658 (tmm-80) REVERT: a 264 TRP cc_start: 0.7018 (m100) cc_final: 0.6258 (m-90) REVERT: a 265 THR cc_start: 0.8218 (m) cc_final: 0.7940 (p) REVERT: a 266 LEU cc_start: 0.8812 (mp) cc_final: 0.8531 (tp) REVERT: a 324 GLN cc_start: 0.9101 (tm-30) cc_final: 0.8863 (tm-30) REVERT: a 325 ARG cc_start: 0.8452 (ptp-170) cc_final: 0.8083 (ptp-170) REVERT: a 372 LEU cc_start: 0.9381 (mm) cc_final: 0.8986 (tp) REVERT: a 404 GLU cc_start: 0.8695 (tp30) cc_final: 0.8488 (tp30) REVERT: C 93 HIS cc_start: 0.8500 (m90) cc_final: 0.7971 (m-70) REVERT: C 151 GLU cc_start: 0.8691 (pt0) cc_final: 0.8256 (pp20) REVERT: C 164 VAL cc_start: 0.8390 (t) cc_final: 0.8150 (t) REVERT: C 192 MET cc_start: 0.8663 (mmt) cc_final: 0.8151 (mmt) REVERT: c 268 ASP cc_start: 0.7932 (p0) cc_final: 0.7468 (p0) REVERT: c 282 ARG cc_start: 0.8383 (ttt180) cc_final: 0.7117 (ptp-170) REVERT: c 311 ASP cc_start: 0.9185 (m-30) cc_final: 0.8916 (m-30) REVERT: c 312 MET cc_start: 0.8241 (mmm) cc_final: 0.8020 (mmm) REVERT: c 349 LEU cc_start: 0.9257 (tp) cc_final: 0.9030 (tt) REVERT: c 359 MET cc_start: 0.9066 (mmm) cc_final: 0.8608 (mmm) REVERT: c 368 LYS cc_start: 0.9227 (mtpp) cc_final: 0.8629 (mtpp) REVERT: c 369 TYR cc_start: 0.8710 (m-80) cc_final: 0.6853 (m-80) REVERT: c 387 LEU cc_start: 0.9331 (mt) cc_final: 0.8824 (mt) REVERT: c 409 ASN cc_start: 0.9462 (t0) cc_final: 0.9116 (m-40) REVERT: D 6 GLU cc_start: 0.8366 (pt0) cc_final: 0.8145 (pt0) REVERT: D 30 SER cc_start: 0.8045 (p) cc_final: 0.7784 (m) REVERT: D 34 MET cc_start: 0.8718 (mtm) cc_final: 0.7823 (mtp) REVERT: D 37 GLU cc_start: 0.6306 (mt-10) cc_final: 0.5898 (mt-10) REVERT: D 46 GLU cc_start: 0.8741 (pt0) cc_final: 0.8054 (pm20) REVERT: H 30 ARG cc_start: 0.7907 (ptt-90) cc_final: 0.7476 (tmm-80) REVERT: H 86 ASP cc_start: 0.8439 (m-30) cc_final: 0.8161 (m-30) REVERT: L 6 GLN cc_start: 0.8098 (mt0) cc_final: 0.7400 (mp10) REVERT: L 31 ASP cc_start: 0.8580 (p0) cc_final: 0.8347 (p0) REVERT: L 74 THR cc_start: 0.8288 (m) cc_final: 0.8006 (t) REVERT: E 3 GLN cc_start: 0.7748 (tm-30) cc_final: 0.7414 (tm-30) REVERT: E 47 TRP cc_start: 0.9091 (t60) cc_final: 0.8705 (t60) REVERT: E 67 LEU cc_start: 0.8962 (mm) cc_final: 0.8557 (mm) REVERT: E 86 ASP cc_start: 0.9215 (m-30) cc_final: 0.8708 (m-30) REVERT: I 83 PHE cc_start: 0.7842 (m-80) cc_final: 0.7400 (m-80) outliers start: 0 outliers final: 0 residues processed: 345 average time/residue: 0.2612 time to fit residues: 132.4252 Evaluate side-chains 267 residues out of total 1448 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 267 time to evaluate : 1.596 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 157 random chunks: chunk 148 optimal weight: 5.9990 chunk 123 optimal weight: 0.4980 chunk 22 optimal weight: 0.8980 chunk 20 optimal weight: 4.9990 chunk 85 optimal weight: 1.9990 chunk 54 optimal weight: 5.9990 chunk 73 optimal weight: 0.7980 chunk 115 optimal weight: 7.9990 chunk 45 optimal weight: 6.9990 chunk 117 optimal weight: 2.9990 chunk 143 optimal weight: 2.9990 overall best weight: 1.4384 ------------------------------------------------------------------------------- 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 305 HIS ** b 319 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 124 HIS ** C 149 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3549 r_free = 0.3549 target = 0.088348 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3117 r_free = 0.3117 target = 0.068435 restraints weight = 52491.317| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3154 r_free = 0.3154 target = 0.070333 restraints weight = 37007.642| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3182 r_free = 0.3182 target = 0.071476 restraints weight = 27879.305| |-----------------------------------------------------------------------------| r_work (final): 0.3168 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7826 moved from start: 0.5499 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 14597 Z= 0.174 Angle : 0.861 12.601 19939 Z= 0.409 Chirality : 0.051 0.404 2415 Planarity : 0.005 0.134 2359 Dihedral : 10.524 110.379 3617 Min Nonbonded Distance : 2.307 Molprobity Statistics. All-atom Clashscore : 16.66 Ramachandran Plot: Outliers : 0.49 % Allowed : 14.86 % Favored : 84.65 % Rotamer: Outliers : 0.00 % Allowed : 0.28 % Favored : 99.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % 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: -2.58 (0.20), residues: 1629 helix: -0.02 (0.30), residues: 305 sheet: -0.70 (0.33), residues: 278 loop : -2.71 (0.18), residues: 1046 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.059 0.002 TRP C 210 HIS 0.012 0.002 HIS B 170 PHE 0.032 0.002 PHE H 96 TYR 0.022 0.002 TYR H 32 ARG 0.014 0.001 ARG D 93 Details of bonding type rmsd link_NAG-ASN : bond 0.00834 ( 35) link_NAG-ASN : angle 3.58132 ( 105) link_ALPHA1-6 : bond 0.01384 ( 10) link_ALPHA1-6 : angle 2.36442 ( 30) link_BETA1-4 : bond 0.00586 ( 27) link_BETA1-4 : angle 1.93502 ( 81) link_ALPHA1-2 : bond 0.00933 ( 2) link_ALPHA1-2 : angle 3.69000 ( 6) link_ALPHA1-3 : bond 0.01231 ( 13) link_ALPHA1-3 : angle 2.99995 ( 39) hydrogen bonds : bond 0.03963 ( 333) hydrogen bonds : angle 5.45268 ( 906) SS BOND : bond 0.00495 ( 26) SS BOND : angle 1.31397 ( 52) covalent geometry : bond 0.00377 (14484) covalent geometry : angle 0.79649 (19626) *********************** 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 339 residues out of total 1448 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 339 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: symmetry clash REVERT: B 82 MET cc_start: 0.8720 (pmm) cc_final: 0.7973 (pmm) REVERT: B 104 GLU cc_start: 0.8050 (tp30) cc_final: 0.7483 (mm-30) REVERT: B 142 LEU cc_start: 0.9157 (mp) cc_final: 0.8863 (tp) REVERT: B 149 GLN cc_start: 0.8093 (tm-30) cc_final: 0.7644 (tm-30) REVERT: b 262 PHE cc_start: 0.6248 (m-80) cc_final: 0.6019 (m-80) REVERT: b 270 GLU cc_start: 0.7630 (mp0) cc_final: 0.7114 (tp30) REVERT: b 284 MET cc_start: 0.7852 (mmp) cc_final: 0.7520 (mmp) REVERT: b 325 ARG cc_start: 0.7843 (ptp90) cc_final: 0.7364 (ptp90) REVERT: b 345 ILE cc_start: 0.9520 (tp) cc_final: 0.9299 (tp) REVERT: b 346 ASN cc_start: 0.9217 (t0) cc_final: 0.8576 (t0) REVERT: b 351 MET cc_start: 0.9241 (mmt) cc_final: 0.8842 (mmp) REVERT: b 357 ASP cc_start: 0.8945 (t70) cc_final: 0.8403 (t0) REVERT: b 369 TYR cc_start: 0.8699 (m-80) cc_final: 0.8048 (m-10) REVERT: b 410 MET cc_start: 0.9040 (mmp) cc_final: 0.8840 (mmp) REVERT: A 75 MET cc_start: 0.8908 (ttp) cc_final: 0.8487 (ttp) REVERT: A 76 GLU cc_start: 0.8681 (tt0) cc_final: 0.8074 (tp30) REVERT: A 82 MET cc_start: 0.9032 (pmm) cc_final: 0.8774 (pmm) REVERT: A 193 ARG cc_start: 0.6035 (tmm-80) cc_final: 0.5692 (tmm-80) REVERT: A 219 TYR cc_start: 0.8135 (m-80) cc_final: 0.7522 (m-80) REVERT: a 264 TRP cc_start: 0.7205 (m100) cc_final: 0.6380 (m-90) REVERT: a 265 THR cc_start: 0.8289 (m) cc_final: 0.7980 (p) REVERT: a 266 LEU cc_start: 0.8790 (mp) cc_final: 0.8507 (tp) REVERT: a 324 GLN cc_start: 0.9122 (tm-30) cc_final: 0.8748 (tm-30) REVERT: a 325 ARG cc_start: 0.8472 (ptp-170) cc_final: 0.7600 (ptp-170) REVERT: a 349 LEU cc_start: 0.8681 (tp) cc_final: 0.8378 (mt) REVERT: a 372 LEU cc_start: 0.9381 (mm) cc_final: 0.8960 (tp) REVERT: C 93 HIS cc_start: 0.8476 (m90) cc_final: 0.7987 (m-70) REVERT: C 192 MET cc_start: 0.8729 (mmt) cc_final: 0.8200 (mmt) REVERT: c 291 LYS cc_start: 0.9066 (mmtt) cc_final: 0.8815 (mmtt) REVERT: c 311 ASP cc_start: 0.9188 (m-30) cc_final: 0.8931 (m-30) REVERT: c 359 MET cc_start: 0.9037 (mmm) cc_final: 0.8613 (mmm) REVERT: c 369 TYR cc_start: 0.8757 (m-80) cc_final: 0.6940 (m-80) REVERT: c 387 LEU cc_start: 0.9319 (mt) cc_final: 0.8788 (mt) REVERT: c 403 ILE cc_start: 0.9171 (mt) cc_final: 0.8856 (mt) REVERT: c 409 ASN cc_start: 0.9470 (t0) cc_final: 0.9140 (m-40) REVERT: D 6 GLU cc_start: 0.8330 (pt0) cc_final: 0.8065 (pt0) REVERT: D 34 MET cc_start: 0.8803 (mtm) cc_final: 0.8019 (mtp) REVERT: D 37 GLU cc_start: 0.6287 (mt-10) cc_final: 0.5957 (mt-10) REVERT: D 46 GLU cc_start: 0.8812 (pt0) cc_final: 0.7979 (pm20) REVERT: H 30 ARG cc_start: 0.8119 (ptt-90) cc_final: 0.7649 (tmm-80) REVERT: H 86 ASP cc_start: 0.8551 (m-30) cc_final: 0.8250 (m-30) REVERT: H 96 PHE cc_start: 0.8080 (m-80) cc_final: 0.7625 (m-10) REVERT: L 6 GLN cc_start: 0.8177 (mt0) cc_final: 0.7570 (mp-120) REVERT: L 74 THR cc_start: 0.8346 (m) cc_final: 0.8077 (t) REVERT: E 3 GLN cc_start: 0.7693 (tm-30) cc_final: 0.7380 (tm-30) REVERT: E 18 LEU cc_start: 0.8509 (tt) cc_final: 0.8225 (mt) REVERT: E 47 TRP cc_start: 0.9152 (t60) cc_final: 0.8802 (t60) REVERT: E 53 ASN cc_start: 0.8591 (m-40) cc_final: 0.8285 (m-40) REVERT: E 67 LEU cc_start: 0.8919 (mm) cc_final: 0.8501 (mm) REVERT: E 76 ASN cc_start: 0.7883 (m-40) cc_final: 0.7547 (m-40) REVERT: E 86 ASP cc_start: 0.9232 (m-30) cc_final: 0.8755 (m-30) REVERT: I 83 PHE cc_start: 0.7879 (m-80) cc_final: 0.7125 (m-10) outliers start: 0 outliers final: 0 residues processed: 339 average time/residue: 0.2571 time to fit residues: 128.5844 Evaluate side-chains 266 residues out of total 1448 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 266 time to evaluate : 1.598 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 157 random chunks: chunk 39 optimal weight: 8.9990 chunk 9 optimal weight: 0.7980 chunk 16 optimal weight: 1.9990 chunk 116 optimal weight: 10.0000 chunk 70 optimal weight: 2.9990 chunk 156 optimal weight: 2.9990 chunk 37 optimal weight: 3.9990 chunk 76 optimal weight: 2.9990 chunk 29 optimal weight: 5.9990 chunk 14 optimal weight: 10.0000 chunk 142 optimal weight: 0.8980 overall best weight: 1.9386 ------------------------------------------------------------------------------- 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** C 158 ASN C 189 GLN ** E 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3529 r_free = 0.3529 target = 0.087282 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3078 r_free = 0.3078 target = 0.066837 restraints weight = 52924.814| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3127 r_free = 0.3127 target = 0.068891 restraints weight = 36082.332| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.3161 r_free = 0.3161 target = 0.070343 restraints weight = 27821.405| |-----------------------------------------------------------------------------| r_work (final): 0.3150 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7853 moved from start: 0.5718 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.061 14597 Z= 0.201 Angle : 0.883 11.433 19939 Z= 0.421 Chirality : 0.051 0.392 2415 Planarity : 0.006 0.113 2359 Dihedral : 10.479 109.951 3617 Min Nonbonded Distance : 2.307 Molprobity Statistics. All-atom Clashscore : 18.07 Ramachandran Plot: Outliers : 0.49 % Allowed : 14.98 % Favored : 84.53 % Rotamer: Outliers : 0.07 % Allowed : 0.21 % Favored : 99.72 % 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: -2.64 (0.20), residues: 1629 helix: -0.13 (0.30), residues: 308 sheet: -1.05 (0.31), residues: 301 loop : -2.66 (0.19), residues: 1020 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.047 0.002 TRP C 210 HIS 0.012 0.002 HIS B 170 PHE 0.068 0.002 PHE E 96 TYR 0.045 0.002 TYR b 393 ARG 0.013 0.001 ARG I 45 Details of bonding type rmsd link_NAG-ASN : bond 0.00778 ( 35) link_NAG-ASN : angle 3.51027 ( 105) link_ALPHA1-6 : bond 0.01336 ( 10) link_ALPHA1-6 : angle 2.40205 ( 30) link_BETA1-4 : bond 0.00567 ( 27) link_BETA1-4 : angle 1.90853 ( 81) link_ALPHA1-2 : bond 0.00840 ( 2) link_ALPHA1-2 : angle 3.58807 ( 6) link_ALPHA1-3 : bond 0.01185 ( 13) link_ALPHA1-3 : angle 2.99656 ( 39) hydrogen bonds : bond 0.03969 ( 333) hydrogen bonds : angle 5.56913 ( 906) SS BOND : bond 0.00538 ( 26) SS BOND : angle 2.04523 ( 52) covalent geometry : bond 0.00441 (14484) covalent geometry : angle 0.81822 (19626) ********************** 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 337 residues out of total 1448 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 336 time to evaluate : 1.438 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 82 MET cc_start: 0.8723 (pmm) cc_final: 0.7993 (pmm) REVERT: B 104 GLU cc_start: 0.8043 (tp30) cc_final: 0.7477 (mm-30) REVERT: B 142 LEU cc_start: 0.9134 (mp) cc_final: 0.8821 (tp) REVERT: B 149 GLN cc_start: 0.7787 (tm-30) cc_final: 0.7180 (tm-30) REVERT: b 262 PHE cc_start: 0.6321 (m-80) cc_final: 0.5977 (m-80) REVERT: b 270 GLU cc_start: 0.7565 (mp0) cc_final: 0.7136 (tp30) REVERT: b 284 MET cc_start: 0.7990 (mmp) cc_final: 0.7612 (mmp) REVERT: b 345 ILE cc_start: 0.9516 (tp) cc_final: 0.9290 (tp) REVERT: b 346 ASN cc_start: 0.9306 (t0) cc_final: 0.8639 (t0) REVERT: b 350 ILE cc_start: 0.9504 (pt) cc_final: 0.9300 (pt) REVERT: b 351 MET cc_start: 0.9259 (mmt) cc_final: 0.8871 (mmp) REVERT: b 357 ASP cc_start: 0.8958 (t70) cc_final: 0.8417 (t0) REVERT: b 369 TYR cc_start: 0.8829 (m-80) cc_final: 0.8310 (m-10) REVERT: b 384 LYS cc_start: 0.9184 (mtpp) cc_final: 0.8842 (tppp) REVERT: b 410 MET cc_start: 0.9035 (mmp) cc_final: 0.8822 (mmp) REVERT: A 75 MET cc_start: 0.9016 (ttp) cc_final: 0.8543 (ttp) REVERT: A 76 GLU cc_start: 0.8727 (tt0) cc_final: 0.8135 (tp30) REVERT: A 82 MET cc_start: 0.9116 (pmm) cc_final: 0.8850 (pmm) REVERT: A 134 MET cc_start: 0.8525 (mmm) cc_final: 0.7937 (mmm) REVERT: A 193 ARG cc_start: 0.6126 (tmm-80) cc_final: 0.5749 (tmm-80) REVERT: A 219 TYR cc_start: 0.8153 (m-80) cc_final: 0.7545 (m-80) REVERT: a 264 TRP cc_start: 0.7155 (m100) cc_final: 0.6439 (m-90) REVERT: a 266 LEU cc_start: 0.8670 (mp) cc_final: 0.8449 (tp) REVERT: a 324 GLN cc_start: 0.9102 (tm-30) cc_final: 0.8844 (tm-30) REVERT: a 325 ARG cc_start: 0.8499 (ptp-170) cc_final: 0.8031 (ptp-170) REVERT: a 349 LEU cc_start: 0.8731 (tp) cc_final: 0.8391 (mt) REVERT: a 372 LEU cc_start: 0.9405 (mm) cc_final: 0.9003 (tp) REVERT: C 93 HIS cc_start: 0.8466 (m90) cc_final: 0.7945 (m-70) REVERT: C 178 ASN cc_start: 0.6193 (t0) cc_final: 0.5169 (p0) REVERT: C 189 GLN cc_start: 0.8611 (mt0) cc_final: 0.8225 (mm-40) REVERT: C 192 MET cc_start: 0.8714 (mmt) cc_final: 0.8214 (mmt) REVERT: c 312 MET cc_start: 0.8108 (mmm) cc_final: 0.7480 (mmm) REVERT: c 321 GLN cc_start: 0.8903 (mm-40) cc_final: 0.8643 (mm110) REVERT: c 359 MET cc_start: 0.9023 (mmm) cc_final: 0.8499 (mmm) REVERT: c 369 TYR cc_start: 0.8762 (m-80) cc_final: 0.6889 (m-80) REVERT: c 387 LEU cc_start: 0.9327 (mt) cc_final: 0.8750 (mt) REVERT: c 409 ASN cc_start: 0.9482 (t0) cc_final: 0.9116 (m-40) REVERT: D 6 GLU cc_start: 0.8319 (pt0) cc_final: 0.8071 (pt0) REVERT: D 34 MET cc_start: 0.8844 (mtm) cc_final: 0.8113 (mtp) REVERT: D 37 GLU cc_start: 0.6404 (mt-10) cc_final: 0.5933 (mt-10) REVERT: D 46 GLU cc_start: 0.8862 (pt0) cc_final: 0.7997 (pm20) REVERT: H 30 ARG cc_start: 0.8189 (ptt-90) cc_final: 0.7825 (ttp-170) REVERT: H 86 ASP cc_start: 0.8554 (m-30) cc_final: 0.8230 (m-30) REVERT: H 96 PHE cc_start: 0.8283 (m-80) cc_final: 0.8075 (m-10) REVERT: L 6 GLN cc_start: 0.8235 (mt0) cc_final: 0.7103 (mp-120) REVERT: L 23 CYS cc_start: 0.5768 (t) cc_final: 0.3766 (t) REVERT: L 31 ASP cc_start: 0.8742 (p0) cc_final: 0.8394 (p0) REVERT: L 74 THR cc_start: 0.8323 (m) cc_final: 0.8073 (t) REVERT: E 3 GLN cc_start: 0.7626 (tm-30) cc_final: 0.7308 (tm-30) REVERT: E 18 LEU cc_start: 0.8436 (tt) cc_final: 0.8163 (mt) REVERT: E 47 TRP cc_start: 0.9117 (t60) cc_final: 0.8747 (t60) REVERT: E 53 ASN cc_start: 0.8631 (m-40) cc_final: 0.8328 (m-40) REVERT: E 67 LEU cc_start: 0.9192 (mm) cc_final: 0.8941 (mm) REVERT: E 76 ASN cc_start: 0.7969 (m-40) cc_final: 0.7671 (m110) REVERT: E 86 ASP cc_start: 0.9273 (m-30) cc_final: 0.8794 (m-30) REVERT: I 83 PHE cc_start: 0.7931 (m-80) cc_final: 0.7316 (m-80) outliers start: 1 outliers final: 0 residues processed: 337 average time/residue: 0.2437 time to fit residues: 121.2137 Evaluate side-chains 258 residues out of total 1448 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 258 time to evaluate : 1.485 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 157 random chunks: chunk 4 optimal weight: 0.5980 chunk 115 optimal weight: 9.9990 chunk 100 optimal weight: 3.9990 chunk 90 optimal weight: 5.9990 chunk 26 optimal weight: 1.9990 chunk 69 optimal weight: 2.9990 chunk 27 optimal weight: 0.6980 chunk 86 optimal weight: 5.9990 chunk 150 optimal weight: 0.9990 chunk 88 optimal weight: 7.9990 chunk 124 optimal weight: 3.9990 overall best weight: 1.4586 ------------------------------------------------------------------------------- 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** ** E 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3530 r_free = 0.3530 target = 0.087511 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3076 r_free = 0.3076 target = 0.066758 restraints weight = 53498.955| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3124 r_free = 0.3124 target = 0.068827 restraints weight = 36154.669| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3159 r_free = 0.3159 target = 0.070310 restraints weight = 27826.387| |-----------------------------------------------------------------------------| r_work (final): 0.3146 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7846 moved from start: 0.5865 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 14597 Z= 0.177 Angle : 0.878 11.598 19939 Z= 0.418 Chirality : 0.051 0.397 2415 Planarity : 0.005 0.086 2359 Dihedral : 10.263 109.711 3617 Min Nonbonded Distance : 2.320 Molprobity Statistics. All-atom Clashscore : 16.63 Ramachandran Plot: Outliers : 0.49 % Allowed : 13.87 % Favored : 85.64 % Rotamer: Outliers : 0.00 % Allowed : 0.69 % Favored : 99.31 % 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: -2.56 (0.21), residues: 1629 helix: -0.08 (0.30), residues: 311 sheet: -1.07 (0.32), residues: 291 loop : -2.57 (0.19), residues: 1027 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.047 0.002 TRP C 210 HIS 0.012 0.002 HIS B 170 PHE 0.048 0.002 PHE E 96 TYR 0.032 0.002 TYR b 393 ARG 0.010 0.001 ARG E 66 Details of bonding type rmsd link_NAG-ASN : bond 0.00771 ( 35) link_NAG-ASN : angle 3.41406 ( 105) link_ALPHA1-6 : bond 0.01389 ( 10) link_ALPHA1-6 : angle 2.39896 ( 30) link_BETA1-4 : bond 0.00577 ( 27) link_BETA1-4 : angle 1.84589 ( 81) link_ALPHA1-2 : bond 0.00883 ( 2) link_ALPHA1-2 : angle 3.65969 ( 6) link_ALPHA1-3 : bond 0.01238 ( 13) link_ALPHA1-3 : angle 2.97782 ( 39) hydrogen bonds : bond 0.03870 ( 333) hydrogen bonds : angle 5.50550 ( 906) SS BOND : bond 0.00486 ( 26) SS BOND : angle 1.91066 ( 52) covalent geometry : bond 0.00386 (14484) covalent geometry : angle 0.81669 (19626) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4677.03 seconds wall clock time: 83 minutes 19.15 seconds (4999.15 seconds total)