Starting phenix.real_space_refine on Thu Jul 2 20:19:02 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/8ejg_28181/07_2026/8ejg_28181.cif Found real_map, /net/cci-nas-00/data/ceres_data/8ejg_28181/07_2026/8ejg_28181.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.13 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8ejg_28181/07_2026/8ejg_28181.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8ejg_28181/07_2026/8ejg_28181.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8ejg_28181/07_2026/8ejg_28181.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8ejg_28181/07_2026/8ejg_28181.map" restraint_files = "/net/cci-nas-00/data/ceres_data/8ejg_28181/07_2026/8ejg_28181.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/8ejg_28181/07_2026/8ejg_28181.cif" } resolution = 3.13 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.025 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 90 5.16 5 C 6174 2.51 5 N 1530 2.21 5 O 2172 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 49 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 9966 Number of models: 1 Model: "" Number of chains: 36 Chain: "A" Number of atoms: 1551 Number of conformers: 1 Conformer: "" Number of residues, atoms: 196, 1551 Classifications: {'peptide': 196} Link IDs: {'PTRANS': 4, 'TRANS': 191} Chain: "a" Number of atoms: 1337 Number of conformers: 1 Conformer: "" Number of residues, atoms: 165, 1337 Classifications: {'peptide': 165} Link IDs: {'PTRANS': 4, 'TRANS': 160} Chain: "B" Number of atoms: 1551 Number of conformers: 1 Conformer: "" Number of residues, atoms: 196, 1551 Classifications: {'peptide': 196} Link IDs: {'PTRANS': 4, 'TRANS': 191} Chain: "C" Number of atoms: 1551 Number of conformers: 1 Conformer: "" Number of residues, atoms: 196, 1551 Classifications: {'peptide': 196} Link IDs: {'PTRANS': 4, 'TRANS': 191} Chain: "b" Number of atoms: 1337 Number of conformers: 1 Conformer: "" Number of residues, atoms: 165, 1337 Classifications: {'peptide': 165} Link IDs: {'PTRANS': 4, 'TRANS': 160} Chain: "c" Number of atoms: 1337 Number of conformers: 1 Conformer: "" Number of residues, atoms: 165, 1337 Classifications: {'peptide': 165} Link IDs: {'PTRANS': 4, 'TRANS': 160} Chain: "D" 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 chiralities: 5 Chain: "E" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen chiralities: 3 Chain: "F" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "G" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BGC': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen chiralities: 3 Chain: "H" 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 chiralities: 3 Chain: "I" 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 chiralities: 3 Chain: "J" 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 chiralities: 3 Chain: "K" Number of atoms: 83 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 83 Unusual residues: {'BMA': 1, 'MAN': 4, 'NAG': 2} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen chiralities: 7 Chain: "L" 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 chiralities: 3 Chain: "M" 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 chiralities: 5 Chain: "N" 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 chiralities: 3 Chain: "O" 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 chiralities: 2 Chain: "P" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BGC': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen chiralities: 3 Chain: "Q" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen chiralities: 3 Chain: "R" 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 chiralities: 3 Chain: "S" 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 chiralities: 3 Chain: "T" 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 chiralities: 5 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 chiralities: 3 Chain: "V" 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 chiralities: 2 Chain: "W" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BGC': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen chiralities: 3 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 chiralities: 3 Chain: "Y" 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 chiralities: 3 Chain: "Z" 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 chiralities: 3 Chain: "d" Number of atoms: 83 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 83 Unusual residues: {'BMA': 1, 'MAN': 4, 'NAG': 2} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen chiralities: 7 Chain: "e" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen chiralities: 3 Chain: "f" Number of atoms: 83 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 83 Unusual residues: {'BMA': 1, 'MAN': 4, 'NAG': 2} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen chiralities: 7 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 chiralities: 3 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 chiralities: 2 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 chiralities: 2 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 chiralities: 2 Time building chain proxies: 2.41, per 1000 atoms: 0.24 Number of scatterers: 9966 At special positions: 0 Unit cell: (101.2, 102.35, 104.65, 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 90 16.00 O 2172 8.00 N 1530 7.00 C 6174 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=21, symmetry=0 Simple disulfide: pdb=" SG CYS A 85 " - pdb=" SG CYS A 230 " distance=2.04 Simple disulfide: pdb=" SG CYS A 117 " - pdb=" SG CYS A 154 " distance=2.16 Simple disulfide: pdb=" SG CYS A 179 " - pdb=" SG CYS A 211 " distance=2.03 Simple disulfide: pdb=" SG CYS A 206 " - pdb=" SG CYS a 359 " distance=2.02 Simple disulfide: pdb=" SG CYS a 278 " - pdb=" SG CYS a 291 " distance=2.03 Simple disulfide: pdb=" SG CYS a 300 " - pdb=" SG CYS a 309 " distance=2.03 Simple disulfide: pdb=" SG CYS a 363 " - pdb=" SG CYS a 384 " distance=2.01 Simple disulfide: pdb=" SG CYS B 85 " - pdb=" SG CYS B 230 " distance=2.04 Simple disulfide: pdb=" SG CYS B 117 " - pdb=" SG CYS B 154 " distance=2.16 Simple disulfide: pdb=" SG CYS B 179 " - pdb=" SG CYS B 211 " distance=2.03 Simple disulfide: pdb=" SG CYS B 206 " - pdb=" SG CYS b 359 " distance=2.02 Simple disulfide: pdb=" SG CYS C 85 " - pdb=" SG CYS C 230 " distance=2.04 Simple disulfide: pdb=" SG CYS C 117 " - pdb=" SG CYS C 154 " distance=2.16 Simple disulfide: pdb=" SG CYS C 179 " - pdb=" SG CYS C 211 " distance=2.04 Simple disulfide: pdb=" SG CYS C 206 " - pdb=" SG CYS c 359 " distance=2.02 Simple disulfide: pdb=" SG CYS b 278 " - pdb=" SG CYS b 291 " distance=2.03 Simple disulfide: pdb=" SG CYS b 300 " - pdb=" SG CYS b 309 " distance=2.03 Simple disulfide: pdb=" SG CYS b 363 " - pdb=" SG CYS b 384 " distance=2.01 Simple disulfide: pdb=" SG CYS c 278 " - pdb=" SG CYS c 291 " distance=2.03 Simple disulfide: pdb=" SG CYS c 300 " - pdb=" SG CYS c 309 " distance=2.03 Simple disulfide: pdb=" SG CYS c 363 " - pdb=" SG CYS c 384 " distance=2.01 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 K 4 " - " MAN K 5 " " MAN d 4 " - " MAN d 5 " " MAN f 4 " - " MAN f 5 " ALPHA1-3 " BMA D 3 " - " MAN D 4 " " BMA K 3 " - " MAN K 4 " " MAN K 6 " - " MAN K 7 " " BMA M 3 " - " MAN M 4 " " BMA T 3 " - " MAN T 4 " " BMA d 3 " - " MAN d 4 " " MAN d 6 " - " MAN d 7 " " BMA f 3 " - " MAN f 4 " " MAN f 6 " - " MAN f 7 " ALPHA1-6 " BMA D 3 " - " MAN D 5 " " BMA K 3 " - " MAN K 6 " " BMA M 3 " - " MAN M 5 " " BMA T 3 " - " MAN T 5 " " BMA d 3 " - " MAN d 6 " " BMA f 3 " - " MAN f 6 " BETA1-4 " NAG D 1 " - " NAG D 2 " " NAG D 2 " - " BMA D 3 " " NAG E 1 " - " NAG E 2 " " NAG E 2 " - " BMA E 3 " " NAG F 1 " - " NAG F 2 " " NAG G 1 " - " NAG G 2 " " NAG G 2 " - " BGC G 3 " " NAG H 1 " - " NAG H 2 " " NAG H 2 " - " BMA H 3 " " NAG I 1 " - " NAG I 2 " " NAG I 2 " - " BMA I 3 " " NAG J 1 " - " NAG J 2 " " NAG J 2 " - " BMA J 3 " " NAG K 1 " - " NAG K 2 " " NAG K 2 " - " BMA K 3 " " NAG L 1 " - " NAG L 2 " " NAG L 2 " - " BMA L 3 " " 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 P 1 " - " NAG P 2 " " NAG P 2 " - " BGC P 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 " - " NAG V 2 " " NAG W 1 " - " NAG W 2 " " NAG W 2 " - " BGC W 3 " " NAG X 1 " - " NAG X 2 " " NAG X 2 " - " BMA X 3 " " NAG Y 1 " - " NAG Y 2 " " NAG Y 2 " - " BMA Y 3 " " NAG Z 1 " - " NAG Z 2 " " NAG Z 2 " - " BMA Z 3 " " NAG d 1 " - " NAG d 2 " " NAG d 2 " - " BMA d 3 " " NAG e 1 " - " NAG e 2 " " NAG e 2 " - " BMA e 3 " " 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-ASN " NAG D 1 " - " ASN A 78 " " NAG E 1 " - " ASN A 88 " " NAG F 1 " - " ASN A 98 " " NAG G 1 " - " ASN A 108 " " NAG H 1 " - " ASN A 118 " " NAG I 1 " - " ASN A 166 " " NAG J 1 " - " ASN A 223 " " NAG K 1 " - " ASN a 364 " " NAG L 1 " - " ASN a 372 " " NAG M 1 " - " ASN B 78 " " NAG N 1 " - " ASN B 88 " " NAG O 1 " - " ASN B 98 " " NAG P 1 " - " ASN B 108 " " NAG Q 1 " - " ASN B 118 " " NAG R 1 " - " ASN B 166 " " NAG S 1 " - " ASN B 223 " " NAG T 1 " - " ASN C 78 " " NAG U 1 " - " ASN C 88 " " NAG V 1 " - " ASN C 98 " " NAG W 1 " - " ASN C 108 " " NAG X 1 " - " ASN C 118 " " NAG Y 1 " - " ASN C 166 " " NAG Z 1 " - " ASN C 223 " " NAG a 501 " - " ASN a 389 " " NAG a 502 " - " ASN a 394 " " NAG b 501 " - " ASN b 389 " " NAG b 502 " - " ASN b 394 " " NAG c 501 " - " ASN c 389 " " NAG c 502 " - " ASN c 394 " " NAG d 1 " - " ASN b 364 " " NAG e 1 " - " ASN b 372 " " NAG f 1 " - " ASN c 364 " " NAG g 1 " - " ASN c 372 " Time building additional restraints: 1.42 Conformation dependent library (CDL) restraints added in 231.5 milliseconds 2142 Ramachandran restraints generated. 1071 Oldfield, 0 Emsley, 1071 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2040 Finding SS restraints... Secondary structure from input PDB file: 48 helices and 9 sheets defined 41.0% alpha, 13.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.25 Creating SS restraints... Processing helix chain 'A' and resid 73 through 78 removed outlier: 3.680A pdb=" N THR A 76 " --> pdb=" O ASN A 73 " (cutoff:3.500A) Processing helix chain 'A' and resid 118 through 126 Processing helix chain 'A' and resid 129 through 142 Processing helix chain 'A' and resid 148 through 150 No H-bonds generated for 'chain 'A' and resid 148 through 150' Processing helix chain 'A' and resid 156 through 160 Processing helix chain 'A' and resid 181 through 194 Processing helix chain 'A' and resid 197 through 201 Processing helix chain 'A' and resid 237 through 245 Processing helix chain 'a' and resid 263 through 269 Processing helix chain 'a' and resid 293 through 298 Processing helix chain 'a' and resid 299 through 302 Processing helix chain 'a' and resid 306 through 324 Processing helix chain 'a' and resid 335 through 340 Processing helix chain 'a' and resid 341 through 343 No H-bonds generated for 'chain 'a' and resid 341 through 343' Processing helix chain 'a' and resid 345 through 358 removed outlier: 3.649A pdb=" N ILE a 349 " --> pdb=" O ASN a 345 " (cutoff:3.500A) Processing helix chain 'a' and resid 398 through 421 Processing helix chain 'B' and resid 73 through 78 removed outlier: 3.682A pdb=" N THR B 76 " --> pdb=" O ASN B 73 " (cutoff:3.500A) Processing helix chain 'B' and resid 118 through 126 Processing helix chain 'B' and resid 129 through 142 Processing helix chain 'B' and resid 148 through 150 No H-bonds generated for 'chain 'B' and resid 148 through 150' Processing helix chain 'B' and resid 156 through 160 Processing helix chain 'B' and resid 181 through 194 Processing helix chain 'B' and resid 197 through 201 Processing helix chain 'B' and resid 237 through 245 Processing helix chain 'C' and resid 73 through 78 removed outlier: 3.681A pdb=" N THR C 76 " --> pdb=" O ASN C 73 " (cutoff:3.500A) Processing helix chain 'C' and resid 118 through 126 Processing helix chain 'C' and resid 129 through 142 Processing helix chain 'C' and resid 148 through 150 No H-bonds generated for 'chain 'C' and resid 148 through 150' Processing helix chain 'C' and resid 156 through 160 Processing helix chain 'C' and resid 181 through 194 Processing helix chain 'C' and resid 197 through 201 Processing helix chain 'C' and resid 237 through 245 Processing helix chain 'b' and resid 263 through 269 Processing helix chain 'b' and resid 293 through 298 Processing helix chain 'b' and resid 299 through 302 Processing helix chain 'b' and resid 306 through 324 Processing helix chain 'b' and resid 335 through 340 Processing helix chain 'b' and resid 341 through 343 No H-bonds generated for 'chain 'b' and resid 341 through 343' Processing helix chain 'b' and resid 345 through 358 removed outlier: 3.648A pdb=" N ILE b 349 " --> pdb=" O ASN b 345 " (cutoff:3.500A) Processing helix chain 'b' and resid 398 through 421 Processing helix chain 'c' and resid 263 through 269 Processing helix chain 'c' and resid 293 through 298 Processing helix chain 'c' and resid 299 through 302 Processing helix chain 'c' and resid 306 through 324 Processing helix chain 'c' and resid 335 through 340 Processing helix chain 'c' and resid 341 through 343 No H-bonds generated for 'chain 'c' and resid 341 through 343' Processing helix chain 'c' and resid 345 through 358 removed outlier: 3.648A pdb=" N ILE c 349 " --> pdb=" O ASN c 345 " (cutoff:3.500A) Processing helix chain 'c' and resid 398 through 421 Processing sheet with id=AA1, first strand: chain 'A' and resid 60 through 61 Processing sheet with id=AA2, first strand: chain 'A' and resid 152 through 154 removed outlier: 6.854A pdb=" N HIS A 91 " --> pdb=" O LYS A 87 " (cutoff:3.500A) removed outlier: 5.352A pdb=" N THR A 86 " --> pdb=" O ARG A 234 " (cutoff:3.500A) removed outlier: 5.919A pdb=" N ARG A 234 " --> pdb=" O THR A 86 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'a' and resid 387 through 388 Processing sheet with id=AA4, first strand: chain 'B' and resid 60 through 61 Processing sheet with id=AA5, first strand: chain 'B' and resid 152 through 154 removed outlier: 6.854A pdb=" N HIS B 91 " --> pdb=" O LYS B 87 " (cutoff:3.500A) removed outlier: 5.353A pdb=" N THR B 86 " --> pdb=" O ARG B 234 " (cutoff:3.500A) removed outlier: 5.918A pdb=" N ARG B 234 " --> pdb=" O THR B 86 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 60 through 61 Processing sheet with id=AA7, first strand: chain 'C' and resid 152 through 154 removed outlier: 6.854A pdb=" N HIS C 91 " --> pdb=" O LYS C 87 " (cutoff:3.500A) removed outlier: 5.352A pdb=" N THR C 86 " --> pdb=" O ARG C 234 " (cutoff:3.500A) removed outlier: 5.919A pdb=" N ARG C 234 " --> pdb=" O THR C 86 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'b' and resid 387 through 388 Processing sheet with id=AA9, first strand: chain 'c' and resid 387 through 388 378 hydrogen bonds defined for protein. 990 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: 1.31 Time building geometry restraints manager: 1.64 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.33: 2577 1.33 - 1.47: 3187 1.47 - 1.60: 4251 1.60 - 1.74: 11 1.74 - 1.88: 132 Bond restraints: 10158 Sorted by residual: bond pdb=" NE1 TRP c 385 " pdb=" CE2 TRP c 385 " ideal model delta sigma weight residual 1.370 1.284 0.086 1.10e-02 8.26e+03 6.15e+01 bond pdb=" NE1 TRP a 385 " pdb=" CE2 TRP a 385 " ideal model delta sigma weight residual 1.370 1.284 0.086 1.10e-02 8.26e+03 6.15e+01 bond pdb=" NE1 TRP b 385 " pdb=" CE2 TRP b 385 " ideal model delta sigma weight residual 1.370 1.284 0.086 1.10e-02 8.26e+03 6.13e+01 bond pdb=" CB LEU A 59 " pdb=" CG LEU A 59 " ideal model delta sigma weight residual 1.530 1.668 -0.138 2.00e-02 2.50e+03 4.77e+01 bond pdb=" CB LEU C 59 " pdb=" CG LEU C 59 " ideal model delta sigma weight residual 1.530 1.668 -0.138 2.00e-02 2.50e+03 4.75e+01 ... (remaining 10153 not shown) Histogram of bond angle deviations from ideal: 0.00 - 7.42: 13719 7.42 - 14.84: 30 14.84 - 22.26: 3 22.26 - 29.67: 0 29.67 - 37.09: 3 Bond angle restraints: 13755 Sorted by residual: angle pdb=" C2 NAG b 502 " pdb=" N2 NAG b 502 " pdb=" C7 NAG b 502 " ideal model delta sigma weight residual 124.56 161.65 -37.09 3.00e+00 1.11e-01 1.53e+02 angle pdb=" C2 NAG c 502 " pdb=" N2 NAG c 502 " pdb=" C7 NAG c 502 " ideal model delta sigma weight residual 124.56 161.59 -37.03 3.00e+00 1.11e-01 1.52e+02 angle pdb=" C2 NAG a 502 " pdb=" N2 NAG a 502 " pdb=" C7 NAG a 502 " ideal model delta sigma weight residual 124.56 161.59 -37.03 3.00e+00 1.11e-01 1.52e+02 angle pdb=" CA PHE a 398 " pdb=" CB PHE a 398 " pdb=" CG PHE a 398 " ideal model delta sigma weight residual 113.80 122.30 -8.50 1.00e+00 1.00e+00 7.23e+01 angle pdb=" CA PHE b 398 " pdb=" CB PHE b 398 " pdb=" CG PHE b 398 " ideal model delta sigma weight residual 113.80 122.30 -8.50 1.00e+00 1.00e+00 7.22e+01 ... (remaining 13750 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 14.20: 4935 14.20 - 28.39: 249 28.39 - 42.59: 66 42.59 - 56.78: 39 56.78 - 70.98: 27 Dihedral angle restraints: 5316 sinusoidal: 2142 harmonic: 3174 Sorted by residual: dihedral pdb=" C PHE a 398 " pdb=" N PHE a 398 " pdb=" CA PHE a 398 " pdb=" CB PHE a 398 " ideal model delta harmonic sigma weight residual -122.60 -111.92 -10.68 0 2.50e+00 1.60e-01 1.83e+01 dihedral pdb=" C PHE b 398 " pdb=" N PHE b 398 " pdb=" CA PHE b 398 " pdb=" CB PHE b 398 " ideal model delta harmonic sigma weight residual -122.60 -111.94 -10.66 0 2.50e+00 1.60e-01 1.82e+01 dihedral pdb=" C PHE c 398 " pdb=" N PHE c 398 " pdb=" CA PHE c 398 " pdb=" CB PHE c 398 " ideal model delta harmonic sigma weight residual -122.60 -111.95 -10.65 0 2.50e+00 1.60e-01 1.82e+01 ... (remaining 5313 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.108: 1047 0.108 - 0.216: 410 0.216 - 0.325: 211 0.325 - 0.433: 100 0.433 - 0.541: 44 Chirality restraints: 1812 Sorted by residual: chirality pdb=" C1 NAG V 2 " pdb=" O4 NAG V 1 " pdb=" C2 NAG V 2 " pdb=" O5 NAG V 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.65 0.25 2.00e-02 2.50e+03 1.61e+02 chirality pdb=" C1 NAG O 2 " pdb=" O4 NAG O 1 " pdb=" C2 NAG O 2 " pdb=" O5 NAG O 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.65 0.25 2.00e-02 2.50e+03 1.59e+02 chirality pdb=" C1 NAG F 2 " pdb=" O4 NAG F 1 " pdb=" C2 NAG F 2 " pdb=" O5 NAG F 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.65 0.25 2.00e-02 2.50e+03 1.58e+02 ... (remaining 1809 not shown) Planarity restraints: 1629 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN C 98 " -0.038 2.00e-02 2.50e+03 4.19e-02 2.19e+01 pdb=" CG ASN C 98 " 0.013 2.00e-02 2.50e+03 pdb=" OD1 ASN C 98 " 0.008 2.00e-02 2.50e+03 pdb=" ND2 ASN C 98 " 0.067 2.00e-02 2.50e+03 pdb=" C1 NAG V 1 " -0.050 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN A 98 " -0.038 2.00e-02 2.50e+03 4.19e-02 2.19e+01 pdb=" CG ASN A 98 " 0.013 2.00e-02 2.50e+03 pdb=" OD1 ASN A 98 " 0.008 2.00e-02 2.50e+03 pdb=" ND2 ASN A 98 " 0.068 2.00e-02 2.50e+03 pdb=" C1 NAG F 1 " -0.050 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN B 98 " -0.038 2.00e-02 2.50e+03 4.18e-02 2.18e+01 pdb=" CG ASN B 98 " 0.013 2.00e-02 2.50e+03 pdb=" OD1 ASN B 98 " 0.008 2.00e-02 2.50e+03 pdb=" ND2 ASN B 98 " 0.067 2.00e-02 2.50e+03 pdb=" C1 NAG O 1 " -0.050 2.00e-02 2.50e+03 ... (remaining 1626 not shown) Histogram of nonbonded interaction distances: 2.11 - 2.66: 303 2.66 - 3.22: 9737 3.22 - 3.78: 15061 3.78 - 4.34: 21516 4.34 - 4.90: 33333 Nonbonded interactions: 79950 Sorted by model distance: nonbonded pdb=" NH1 ARG a 378 " pdb=" O THR a 379 " model vdw 2.106 3.120 nonbonded pdb=" NH1 ARG b 378 " pdb=" O THR b 379 " model vdw 2.107 3.120 nonbonded pdb=" NH1 ARG c 378 " pdb=" O THR c 379 " model vdw 2.109 3.120 nonbonded pdb=" N HIS c 397 " pdb=" O HIS c 397 " model vdw 2.286 2.496 nonbonded pdb=" N HIS a 397 " pdb=" O HIS a 397 " model vdw 2.286 2.496 ... (remaining 79945 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: 0.03 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' } ncs_group { reference = chain 'D' selection = chain 'M' selection = chain 'T' } ncs_group { reference = (chain 'E' and resid 1 through 2) selection = (chain 'G' and resid 1 through 2) selection = (chain 'H' and resid 1 through 2) selection = (chain 'I' and resid 1 through 2) selection = (chain 'J' and resid 1 through 2) selection = (chain 'L' and resid 1 through 2) selection = (chain 'N' and resid 1 through 2) selection = (chain 'P' and resid 1 through 2) selection = (chain 'Q' and resid 1 through 2) selection = (chain 'R' and resid 1 through 2) selection = (chain 'S' and resid 1 through 2) selection = (chain 'U' and resid 1 through 2) selection = (chain 'W' and resid 1 through 2) selection = (chain 'X' and resid 1 through 2) selection = (chain 'Y' and resid 1 through 2) selection = (chain 'Z' and resid 1 through 2) selection = (chain 'e' and resid 1 through 2) selection = (chain 'g' and resid 1 through 2) } ncs_group { reference = chain 'F' selection = chain 'O' selection = chain 'V' } ncs_group { reference = chain 'K' selection = chain 'd' selection = chain 'f' } 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 individual isotropic 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: 0.480 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: 0.160 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 10.240 Find NCS groups from input model: 0.250 Set up NCS constraints: 0.030 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:0.940 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 12.170 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8096 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 : 0.026 0.138 10281 Z= 1.388 Angle : 2.059 37.092 14103 Z= 1.161 Chirality : 0.172 0.541 1812 Planarity : 0.009 0.051 1596 Dihedral : 11.410 70.976 3213 Min Nonbonded Distance : 2.106 Molprobity Statistics. All-atom Clashscore : 0.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.44 % Favored : 93.56 % Rotamer: Outliers : 0.00 % Allowed : 1.24 % Favored : 98.76 % Cbeta Deviations : 0.29 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.09 (0.24), residues: 1071 helix: -1.09 (0.22), residues: 423 sheet: 1.26 (0.50), residues: 102 loop : -0.71 (0.26), residues: 546 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 95 TYR 0.055 0.008 TYR A 240 PHE 0.024 0.006 PHE b 261 TRP 0.027 0.007 TRP A 226 HIS 0.008 0.002 HIS B 91 Details of bonding type rmsd/Z covalent geometry : bond 0.02537 / 1.34 (10158) covalent geometry : angle 1.94434 / 1.15 (13755) SS BOND : bond 0.04909 / 3.37 ( 21) SS BOND : angle 3.77771 / 2.33 ( 42) hydrogen bonds : bond 0.16477 / 11.18 ( 378) hydrogen bonds : angle 7.06040 / 4.95 ( 990) link_ALPHA1-2 : bond 0.07660 / 3.84 ( 3) link_ALPHA1-2 : angle 4.26510 / 1.93 ( 9) link_ALPHA1-3 : bond 0.07983 / 4.41 ( 9) link_ALPHA1-3 : angle 4.50889 / 2.74 ( 27) link_ALPHA1-6 : bond 0.05259 / 2.85 ( 6) link_ALPHA1-6 : angle 3.46290 / 1.79 ( 18) link_BETA1-4 : bond 0.07505 / 4.70 ( 51) link_BETA1-4 : angle 6.04600 / 3.73 ( 153) link_NAG-ASN : bond 0.07530 / 4.63 ( 33) link_NAG-ASN : angle 2.60422 / 1.61 ( 99) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2142 Ramachandran restraints generated. 1071 Oldfield, 0 Emsley, 1071 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2142 Ramachandran restraints generated. 1071 Oldfield, 0 Emsley, 1071 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 322 residues out of total 966 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 322 time to evaluate : 0.250 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: a 305 ASP cc_start: 0.6570 (p0) cc_final: 0.6359 (p0) REVERT: a 330 GLN cc_start: 0.7109 (mp10) cc_final: 0.6559 (pp30) REVERT: b 305 ASP cc_start: 0.6440 (p0) cc_final: 0.6091 (p0) REVERT: c 305 ASP cc_start: 0.6753 (p0) cc_final: 0.6429 (p0) outliers start: 0 outliers final: 0 residues processed: 322 average time/residue: 0.1120 time to fit residues: 48.1319 Evaluate side-chains 180 residues out of total 966 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 180 time to evaluate : 0.362 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 49 optimal weight: 7.9990 chunk 97 optimal weight: 1.9990 chunk 53 optimal weight: 0.9990 chunk 5 optimal weight: 6.9990 chunk 33 optimal weight: 0.9990 chunk 65 optimal weight: 6.9990 chunk 62 optimal weight: 2.9990 chunk 51 optimal weight: 2.9990 chunk 100 optimal weight: 1.9990 chunk 38 optimal weight: 3.9990 chunk 61 optimal weight: 0.9980 overall best weight: 1.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 91 HIS A 145 ASN A 222 GLN a 304 HIS ** a 334 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** a 341 ASN B 91 HIS C 91 HIS b 304 HIS b 404 GLN c 304 HIS c 347 GLN c 404 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3760 r_free = 0.3760 target = 0.090436 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3224 r_free = 0.3224 target = 0.064402 restraints weight = 28155.034| |-----------------------------------------------------------------------------| r_work (start): 0.3158 rms_B_bonded: 4.41 r_work (final): 0.3158 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8016 moved from start: 0.3489 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.048 10281 Z= 0.215 Angle : 1.091 18.642 14103 Z= 0.488 Chirality : 0.052 0.426 1812 Planarity : 0.005 0.037 1596 Dihedral : 5.455 34.347 1170 Min Nonbonded Distance : 2.387 Molprobity Statistics. All-atom Clashscore : 7.55 Ramachandran Plot: Outliers : 0.28 % Allowed : 5.88 % Favored : 93.84 % Rotamer: Outliers : 2.17 % Allowed : 11.90 % Favored : 85.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.28 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.73 (0.25), residues: 1071 helix: -0.34 (0.24), residues: 426 sheet: 1.89 (0.52), residues: 114 loop : -1.10 (0.27), residues: 531 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG c 378 TYR 0.021 0.002 TYR c 277 PHE 0.021 0.002 PHE b 261 TRP 0.022 0.002 TRP a 263 HIS 0.007 0.002 HIS B 123 Details of bonding type rmsd/Z covalent geometry : bond 0.00434 / 0.20 (10158) covalent geometry : angle 0.94032 / 0.45 (13755) SS BOND : bond 0.00371 / 0.24 ( 21) SS BOND : angle 1.67407 / 1.02 ( 42) hydrogen bonds : bond 0.05650 / 3.83 ( 378) hydrogen bonds : angle 5.25327 / 3.71 ( 990) link_ALPHA1-2 : bond 0.00384 / 0.19 ( 3) link_ALPHA1-2 : angle 1.68121 / 0.84 ( 9) link_ALPHA1-3 : bond 0.01225 / 0.71 ( 9) link_ALPHA1-3 : angle 1.51120 / 0.94 ( 27) link_ALPHA1-6 : bond 0.00655 / 0.34 ( 6) link_ALPHA1-6 : angle 1.36045 / 0.78 ( 18) link_BETA1-4 : bond 0.01788 / 1.03 ( 51) link_BETA1-4 : angle 4.87633 / 2.99 ( 153) link_NAG-ASN : bond 0.00690 / 0.40 ( 33) link_NAG-ASN : angle 2.72294 / 1.74 ( 99) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2142 Ramachandran restraints generated. 1071 Oldfield, 0 Emsley, 1071 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2142 Ramachandran restraints generated. 1071 Oldfield, 0 Emsley, 1071 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 238 residues out of total 966 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 217 time to evaluate : 0.258 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 99 GLU cc_start: 0.8239 (tp30) cc_final: 0.7737 (mm-30) REVERT: A 152 MET cc_start: 0.8006 (ttt) cc_final: 0.7695 (ttt) REVERT: a 323 GLN cc_start: 0.8593 (tt0) cc_final: 0.8388 (tm-30) REVERT: a 330 GLN cc_start: 0.7667 (mp10) cc_final: 0.7436 (pp30) REVERT: a 355 ARG cc_start: 0.8555 (mtt180) cc_final: 0.8322 (mtt180) REVERT: B 94 ILE cc_start: 0.9055 (mt) cc_final: 0.8838 (tt) REVERT: B 133 MET cc_start: 0.9248 (tpt) cc_final: 0.9037 (tpt) REVERT: C 81 MET cc_start: 0.8819 (mtt) cc_final: 0.8613 (mtm) REVERT: C 94 ILE cc_start: 0.8977 (mt) cc_final: 0.8722 (tt) REVERT: C 99 GLU cc_start: 0.8404 (tp30) cc_final: 0.8146 (mm-30) REVERT: C 193 MET cc_start: 0.8801 (mmm) cc_final: 0.8520 (tpp) REVERT: b 326 LYS cc_start: 0.8009 (tppt) cc_final: 0.7656 (tppt) REVERT: b 341 ASN cc_start: 0.9188 (m-40) cc_final: 0.8763 (m-40) REVERT: b 404 GLN cc_start: 0.8708 (tp40) cc_final: 0.8391 (tp-100) REVERT: c 305 ASP cc_start: 0.7582 (p0) cc_final: 0.7280 (p0) REVERT: c 378 ARG cc_start: 0.7959 (ttm-80) cc_final: 0.7598 (ttm-80) REVERT: c 400 ASP cc_start: 0.8125 (p0) cc_final: 0.7844 (p0) REVERT: c 404 GLN cc_start: 0.8497 (OUTLIER) cc_final: 0.8255 (tp-100) outliers start: 21 outliers final: 10 residues processed: 231 average time/residue: 0.0926 time to fit residues: 29.7479 Evaluate side-chains 189 residues out of total 966 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 178 time to evaluate : 0.294 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 211 CYS Chi-restraints excluded: chain a residue 341 ASN Chi-restraints excluded: chain a residue 398 PHE Chi-restraints excluded: chain B residue 211 CYS Chi-restraints excluded: chain C residue 210 ASP Chi-restraints excluded: chain C residue 211 CYS Chi-restraints excluded: chain b residue 288 GLU Chi-restraints excluded: chain b residue 375 SER Chi-restraints excluded: chain b residue 398 PHE Chi-restraints excluded: chain c residue 375 SER Chi-restraints excluded: chain c residue 404 GLN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 87 optimal weight: 0.9990 chunk 60 optimal weight: 0.0050 chunk 54 optimal weight: 6.9990 chunk 69 optimal weight: 2.9990 chunk 35 optimal weight: 5.9990 chunk 79 optimal weight: 4.9990 chunk 4 optimal weight: 7.9990 chunk 9 optimal weight: 0.9990 chunk 11 optimal weight: 40.0000 chunk 29 optimal weight: 0.9990 chunk 24 optimal weight: 1.9990 overall best weight: 1.0002 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 169 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 145 ASN ** B 169 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 178 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 140 HIS ** C 169 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 415 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** b 422 GLN c 404 GLN c 422 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3756 r_free = 0.3756 target = 0.090084 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3232 r_free = 0.3232 target = 0.064517 restraints weight = 28353.969| |-----------------------------------------------------------------------------| r_work (start): 0.3163 rms_B_bonded: 4.27 r_work (final): 0.3163 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8039 moved from start: 0.3995 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 10281 Z= 0.182 Angle : 0.980 18.050 14103 Z= 0.429 Chirality : 0.049 0.416 1812 Planarity : 0.004 0.039 1596 Dihedral : 5.201 34.999 1170 Min Nonbonded Distance : 2.348 Molprobity Statistics. All-atom Clashscore : 8.43 Ramachandran Plot: Outliers : 0.28 % Allowed : 7.66 % Favored : 92.06 % Rotamer: Outliers : 2.80 % Allowed : 13.15 % Favored : 84.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.19 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.78 (0.25), residues: 1071 helix: -0.07 (0.25), residues: 414 sheet: 2.45 (0.53), residues: 96 loop : -1.44 (0.25), residues: 561 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG b 421 TYR 0.013 0.001 TYR A 149 PHE 0.016 0.002 PHE b 398 TRP 0.018 0.001 TRP c 263 HIS 0.008 0.001 HIS A 178 Details of bonding type rmsd/Z covalent geometry : bond 0.00361 / 0.17 (10158) covalent geometry : angle 0.82964 / 0.39 (13755) SS BOND : bond 0.00534 / 0.33 ( 21) SS BOND : angle 1.75423 / 0.99 ( 42) hydrogen bonds : bond 0.04630 / 3.15 ( 378) hydrogen bonds : angle 5.18370 / 3.66 ( 990) link_ALPHA1-2 : bond 0.00319 / 0.16 ( 3) link_ALPHA1-2 : angle 1.55746 / 0.75 ( 9) link_ALPHA1-3 : bond 0.01143 / 0.65 ( 9) link_ALPHA1-3 : angle 1.70804 / 1.08 ( 27) link_ALPHA1-6 : bond 0.00630 / 0.33 ( 6) link_ALPHA1-6 : angle 1.44659 / 0.80 ( 18) link_BETA1-4 : bond 0.01788 / 1.03 ( 51) link_BETA1-4 : angle 4.45443 / 2.74 ( 153) link_NAG-ASN : bond 0.00445 / 0.25 ( 33) link_NAG-ASN : angle 2.79836 / 1.78 ( 99) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2142 Ramachandran restraints generated. 1071 Oldfield, 0 Emsley, 1071 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2142 Ramachandran restraints generated. 1071 Oldfield, 0 Emsley, 1071 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 226 residues out of total 966 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 199 time to evaluate : 0.377 Fit side-chains revert: symmetry clash REVERT: A 99 GLU cc_start: 0.8231 (tp30) cc_final: 0.7716 (mm-30) REVERT: A 155 ASP cc_start: 0.8439 (p0) cc_final: 0.8009 (p0) REVERT: A 169 HIS cc_start: 0.6890 (t70) cc_final: 0.6495 (t-90) REVERT: A 188 GLN cc_start: 0.8739 (mm-40) cc_final: 0.8465 (mm-40) REVERT: a 400 ASP cc_start: 0.8357 (p0) cc_final: 0.7903 (p0) REVERT: B 79 MET cc_start: 0.8536 (mmm) cc_final: 0.8146 (mmm) REVERT: B 99 GLU cc_start: 0.8412 (tp30) cc_final: 0.8102 (mm-30) REVERT: B 133 MET cc_start: 0.9261 (OUTLIER) cc_final: 0.9037 (tpt) REVERT: B 249 ARG cc_start: 0.7053 (ttm-80) cc_final: 0.6505 (mtm-85) REVERT: C 66 GLU cc_start: 0.7879 (pt0) cc_final: 0.7668 (pm20) REVERT: C 94 ILE cc_start: 0.8948 (mt) cc_final: 0.8690 (tt) REVERT: C 99 GLU cc_start: 0.8476 (tp30) cc_final: 0.8173 (mm-30) REVERT: C 141 LEU cc_start: 0.9663 (OUTLIER) cc_final: 0.9420 (mm) REVERT: C 193 MET cc_start: 0.8765 (mmm) cc_final: 0.8373 (tpp) REVERT: C 213 MET cc_start: 0.7934 (mmt) cc_final: 0.7619 (mmp) REVERT: C 227 GLU cc_start: 0.8084 (mm-30) cc_final: 0.7866 (mm-30) REVERT: C 246 GLN cc_start: 0.7882 (pp30) cc_final: 0.7546 (pp30) REVERT: b 341 ASN cc_start: 0.9236 (m-40) cc_final: 0.8856 (m-40) REVERT: b 404 GLN cc_start: 0.8844 (tp40) cc_final: 0.8389 (tp-100) REVERT: c 305 ASP cc_start: 0.7514 (p0) cc_final: 0.7195 (p0) REVERT: c 330 GLN cc_start: 0.8879 (mp10) cc_final: 0.8614 (mp10) REVERT: c 331 MET cc_start: 0.6585 (mmp) cc_final: 0.6259 (mmp) REVERT: c 378 ARG cc_start: 0.8127 (ttm-80) cc_final: 0.7875 (ttm-80) REVERT: c 409 MET cc_start: 0.8389 (mtp) cc_final: 0.8062 (mtp) outliers start: 27 outliers final: 12 residues processed: 218 average time/residue: 0.1062 time to fit residues: 32.1808 Evaluate side-chains 195 residues out of total 966 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 181 time to evaluate : 0.320 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 211 CYS Chi-restraints excluded: chain a residue 322 ILE Chi-restraints excluded: chain a residue 398 PHE Chi-restraints excluded: chain B residue 133 MET Chi-restraints excluded: chain B residue 211 CYS Chi-restraints excluded: chain C residue 141 LEU Chi-restraints excluded: chain C residue 142 SER Chi-restraints excluded: chain C residue 211 CYS Chi-restraints excluded: chain b residue 288 GLU Chi-restraints excluded: chain b residue 332 SER Chi-restraints excluded: chain c residue 322 ILE Chi-restraints excluded: chain c residue 341 ASN Chi-restraints excluded: chain c residue 375 SER Chi-restraints excluded: chain c residue 398 PHE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 71 optimal weight: 8.9990 chunk 56 optimal weight: 6.9990 chunk 1 optimal weight: 2.9990 chunk 67 optimal weight: 5.9990 chunk 77 optimal weight: 10.0000 chunk 13 optimal weight: 6.9990 chunk 21 optimal weight: 0.8980 chunk 82 optimal weight: 0.9990 chunk 0 optimal weight: 6.9990 chunk 27 optimal weight: 10.0000 chunk 38 optimal weight: 0.6980 overall best weight: 2.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** a 334 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** a 422 GLN B 140 HIS ** B 169 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 178 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 169 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 334 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 415 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 = 0.3722 r_free = 0.3722 target = 0.088129 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3181 r_free = 0.3181 target = 0.062416 restraints weight = 28823.735| |-----------------------------------------------------------------------------| r_work (start): 0.3113 rms_B_bonded: 4.29 r_work (final): 0.3113 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8126 moved from start: 0.4406 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.047 10281 Z= 0.214 Angle : 0.945 17.906 14103 Z= 0.416 Chirality : 0.048 0.393 1812 Planarity : 0.004 0.045 1596 Dihedral : 5.188 33.347 1170 Min Nonbonded Distance : 2.337 Molprobity Statistics. All-atom Clashscore : 7.91 Ramachandran Plot: Outliers : 0.28 % Allowed : 8.50 % Favored : 91.22 % Rotamer: Outliers : 3.00 % Allowed : 14.60 % Favored : 82.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.19 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.75 (0.25), residues: 1071 helix: 0.11 (0.25), residues: 414 sheet: 2.16 (0.53), residues: 96 loop : -1.49 (0.25), residues: 561 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 192 TYR 0.010 0.001 TYR C 65 PHE 0.018 0.002 PHE b 398 TRP 0.016 0.001 TRP b 263 HIS 0.005 0.001 HIS B 92 Details of bonding type rmsd/Z covalent geometry : bond 0.00445 / 0.21 (10158) covalent geometry : angle 0.80595 / 0.38 (13755) SS BOND : bond 0.00523 / 0.33 ( 21) SS BOND : angle 1.51161 / 0.91 ( 42) hydrogen bonds : bond 0.04393 / 2.98 ( 378) hydrogen bonds : angle 4.97989 / 3.52 ( 990) link_ALPHA1-2 : bond 0.00155 / 0.08 ( 3) link_ALPHA1-2 : angle 1.52981 / 0.73 ( 9) link_ALPHA1-3 : bond 0.00962 / 0.56 ( 9) link_ALPHA1-3 : angle 1.67751 / 1.06 ( 27) link_ALPHA1-6 : bond 0.00581 / 0.30 ( 6) link_ALPHA1-6 : angle 1.47284 / 0.80 ( 18) link_BETA1-4 : bond 0.01687 / 0.96 ( 51) link_BETA1-4 : angle 4.25965 / 2.63 ( 153) link_NAG-ASN : bond 0.00338 / 0.20 ( 33) link_NAG-ASN : angle 2.54938 / 1.58 ( 99) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2142 Ramachandran restraints generated. 1071 Oldfield, 0 Emsley, 1071 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2142 Ramachandran restraints generated. 1071 Oldfield, 0 Emsley, 1071 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 220 residues out of total 966 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 191 time to evaluate : 0.372 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 99 GLU cc_start: 0.8335 (tp30) cc_final: 0.7819 (mm-30) REVERT: A 188 GLN cc_start: 0.8685 (mm-40) cc_final: 0.8355 (mm-40) REVERT: a 323 GLN cc_start: 0.8258 (tm-30) cc_final: 0.8029 (tm-30) REVERT: a 326 LYS cc_start: 0.8272 (tppt) cc_final: 0.8026 (tptp) REVERT: a 346 ASP cc_start: 0.9127 (p0) cc_final: 0.8780 (p0) REVERT: a 357 MET cc_start: 0.8956 (mtp) cc_final: 0.8700 (mtm) REVERT: a 400 ASP cc_start: 0.8343 (p0) cc_final: 0.8037 (p0) REVERT: a 418 TYR cc_start: 0.5179 (t80) cc_final: 0.4842 (t80) REVERT: B 74 MET cc_start: 0.9017 (mmt) cc_final: 0.8650 (mmt) REVERT: B 99 GLU cc_start: 0.8481 (tp30) cc_final: 0.8160 (mm-30) REVERT: B 124 LYS cc_start: 0.8810 (mtmm) cc_final: 0.8586 (mtmm) REVERT: B 227 GLU cc_start: 0.7924 (mm-30) cc_final: 0.7693 (mm-30) REVERT: C 79 MET cc_start: 0.8835 (mtp) cc_final: 0.8526 (mmt) REVERT: C 94 ILE cc_start: 0.9081 (mt) cc_final: 0.8780 (tt) REVERT: C 99 GLU cc_start: 0.8429 (tp30) cc_final: 0.8121 (mm-30) REVERT: C 156 PHE cc_start: 0.9217 (m-80) cc_final: 0.8966 (m-80) REVERT: C 193 MET cc_start: 0.8882 (mmm) cc_final: 0.8379 (tpp) REVERT: C 213 MET cc_start: 0.7902 (mmt) cc_final: 0.7635 (mmp) REVERT: C 227 GLU cc_start: 0.8261 (mm-30) cc_final: 0.7968 (mm-30) REVERT: C 246 GLN cc_start: 0.7851 (pp30) cc_final: 0.7487 (pp30) REVERT: b 341 ASN cc_start: 0.9264 (m-40) cc_final: 0.8853 (m-40) REVERT: b 404 GLN cc_start: 0.8910 (tp40) cc_final: 0.8426 (tp-100) REVERT: c 330 GLN cc_start: 0.8837 (mp10) cc_final: 0.8527 (mp10) REVERT: c 331 MET cc_start: 0.6903 (mmp) cc_final: 0.6687 (mmp) REVERT: c 338 LYS cc_start: 0.9167 (mtmm) cc_final: 0.8849 (mptt) REVERT: c 404 GLN cc_start: 0.8618 (tp-100) cc_final: 0.7928 (tp-100) REVERT: c 408 ASN cc_start: 0.9305 (m-40) cc_final: 0.9006 (m-40) REVERT: c 409 MET cc_start: 0.8418 (mtp) cc_final: 0.8083 (mtp) outliers start: 29 outliers final: 19 residues processed: 207 average time/residue: 0.1061 time to fit residues: 30.5199 Evaluate side-chains 192 residues out of total 966 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 173 time to evaluate : 0.360 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 211 CYS Chi-restraints excluded: chain a residue 295 THR Chi-restraints excluded: chain a residue 304 HIS Chi-restraints excluded: chain a residue 322 ILE Chi-restraints excluded: chain a residue 398 PHE Chi-restraints excluded: chain a residue 420 ASP Chi-restraints excluded: chain B residue 211 CYS Chi-restraints excluded: chain C residue 81 MET Chi-restraints excluded: chain C residue 142 SER Chi-restraints excluded: chain C residue 211 CYS Chi-restraints excluded: chain b residue 332 SER Chi-restraints excluded: chain b residue 375 SER Chi-restraints excluded: chain b residue 398 PHE Chi-restraints excluded: chain c residue 295 THR Chi-restraints excluded: chain c residue 322 ILE Chi-restraints excluded: chain c residue 341 ASN Chi-restraints excluded: chain c residue 375 SER Chi-restraints excluded: chain c residue 398 PHE Chi-restraints excluded: chain c residue 400 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 84 optimal weight: 2.9990 chunk 21 optimal weight: 0.9980 chunk 95 optimal weight: 3.9990 chunk 87 optimal weight: 1.9990 chunk 72 optimal weight: 7.9990 chunk 5 optimal weight: 9.9990 chunk 63 optimal weight: 7.9990 chunk 15 optimal weight: 0.9990 chunk 86 optimal weight: 1.9990 chunk 46 optimal weight: 30.0000 chunk 10 optimal weight: 0.9980 overall best weight: 1.3986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 169 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 169 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 178 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 169 HIS c 404 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3733 r_free = 0.3733 target = 0.088335 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3188 r_free = 0.3188 target = 0.062472 restraints weight = 28526.958| |-----------------------------------------------------------------------------| r_work (start): 0.3121 rms_B_bonded: 4.33 r_work (final): 0.3121 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8120 moved from start: 0.4663 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 10281 Z= 0.170 Angle : 0.900 17.799 14103 Z= 0.395 Chirality : 0.047 0.391 1812 Planarity : 0.004 0.041 1596 Dihedral : 5.046 30.954 1170 Min Nonbonded Distance : 2.324 Molprobity Statistics. All-atom Clashscore : 7.45 Ramachandran Plot: Outliers : 0.28 % Allowed : 7.94 % Favored : 91.78 % Rotamer: Outliers : 2.59 % Allowed : 14.70 % Favored : 82.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.68 (0.25), residues: 1071 helix: 0.29 (0.26), residues: 417 sheet: 2.00 (0.53), residues: 96 loop : -1.53 (0.25), residues: 558 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 192 TYR 0.015 0.001 TYR B 65 PHE 0.017 0.001 PHE b 398 TRP 0.015 0.001 TRP b 263 HIS 0.005 0.001 HIS B 92 Details of bonding type rmsd/Z covalent geometry : bond 0.00338 / 0.16 (10158) covalent geometry : angle 0.76429 / 0.36 (13755) SS BOND : bond 0.00480 / 0.30 ( 21) SS BOND : angle 1.28688 / 0.79 ( 42) hydrogen bonds : bond 0.04007 / 2.74 ( 378) hydrogen bonds : angle 4.84630 / 3.43 ( 990) link_ALPHA1-2 : bond 0.00172 / 0.09 ( 3) link_ALPHA1-2 : angle 1.54597 / 0.73 ( 9) link_ALPHA1-3 : bond 0.01022 / 0.59 ( 9) link_ALPHA1-3 : angle 1.73132 / 1.09 ( 27) link_ALPHA1-6 : bond 0.00567 / 0.29 ( 6) link_ALPHA1-6 : angle 1.47156 / 0.80 ( 18) link_BETA1-4 : bond 0.01660 / 0.94 ( 51) link_BETA1-4 : angle 4.11923 / 2.54 ( 153) link_NAG-ASN : bond 0.00359 / 0.24 ( 33) link_NAG-ASN : angle 2.40796 / 1.48 ( 99) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2142 Ramachandran restraints generated. 1071 Oldfield, 0 Emsley, 1071 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2142 Ramachandran restraints generated. 1071 Oldfield, 0 Emsley, 1071 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 219 residues out of total 966 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 194 time to evaluate : 0.354 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 99 GLU cc_start: 0.8329 (tp30) cc_final: 0.7861 (mm-30) REVERT: A 188 GLN cc_start: 0.8664 (mm-40) cc_final: 0.8303 (mm-40) REVERT: a 323 GLN cc_start: 0.8338 (tm-30) cc_final: 0.8047 (tm-30) REVERT: a 326 LYS cc_start: 0.8315 (tppt) cc_final: 0.8063 (tptp) REVERT: a 346 ASP cc_start: 0.9123 (p0) cc_final: 0.8757 (p0) REVERT: a 400 ASP cc_start: 0.8418 (p0) cc_final: 0.8002 (p0) REVERT: a 418 TYR cc_start: 0.5348 (t80) cc_final: 0.5135 (t80) REVERT: B 99 GLU cc_start: 0.8515 (tp30) cc_final: 0.8131 (mm-30) REVERT: B 124 LYS cc_start: 0.8854 (mtmm) cc_final: 0.8636 (mtmm) REVERT: B 188 GLN cc_start: 0.8867 (mm-40) cc_final: 0.8561 (mm-40) REVERT: B 227 GLU cc_start: 0.7909 (mm-30) cc_final: 0.7654 (mm-30) REVERT: C 94 ILE cc_start: 0.8975 (mt) cc_final: 0.8683 (tt) REVERT: C 99 GLU cc_start: 0.8447 (tp30) cc_final: 0.8208 (mm-30) REVERT: C 142 SER cc_start: 0.9075 (OUTLIER) cc_final: 0.8693 (p) REVERT: C 156 PHE cc_start: 0.9238 (m-80) cc_final: 0.8967 (m-80) REVERT: C 193 MET cc_start: 0.8835 (mmm) cc_final: 0.8538 (tpp) REVERT: C 227 GLU cc_start: 0.8228 (mm-30) cc_final: 0.7896 (mm-30) REVERT: C 246 GLN cc_start: 0.7895 (pp30) cc_final: 0.7611 (pp30) REVERT: b 326 LYS cc_start: 0.8119 (tppt) cc_final: 0.7801 (tppt) REVERT: b 341 ASN cc_start: 0.9283 (m-40) cc_final: 0.8900 (m-40) REVERT: b 404 GLN cc_start: 0.8923 (tp40) cc_final: 0.8455 (tp-100) REVERT: c 330 GLN cc_start: 0.8807 (mp10) cc_final: 0.8480 (mp10) REVERT: c 338 LYS cc_start: 0.9174 (mtmm) cc_final: 0.8794 (mptt) REVERT: c 408 ASN cc_start: 0.9310 (m-40) cc_final: 0.9073 (m-40) REVERT: c 409 MET cc_start: 0.8406 (mtp) cc_final: 0.8030 (mtp) outliers start: 25 outliers final: 9 residues processed: 210 average time/residue: 0.1056 time to fit residues: 30.8020 Evaluate side-chains 187 residues out of total 966 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 177 time to evaluate : 0.339 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 211 CYS Chi-restraints excluded: chain a residue 322 ILE Chi-restraints excluded: chain B residue 211 CYS Chi-restraints excluded: chain C residue 81 MET Chi-restraints excluded: chain C residue 142 SER Chi-restraints excluded: chain C residue 211 CYS Chi-restraints excluded: chain b residue 375 SER Chi-restraints excluded: chain c residue 375 SER Chi-restraints excluded: chain c residue 398 PHE Chi-restraints excluded: chain c residue 420 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 99 optimal weight: 0.7980 chunk 68 optimal weight: 1.9990 chunk 61 optimal weight: 1.9990 chunk 55 optimal weight: 1.9990 chunk 31 optimal weight: 8.9990 chunk 3 optimal weight: 3.9990 chunk 102 optimal weight: 3.9990 chunk 73 optimal weight: 3.9990 chunk 29 optimal weight: 1.9990 chunk 86 optimal weight: 6.9990 chunk 33 optimal weight: 0.8980 overall best weight: 1.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 169 HIS ** B 169 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 178 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 334 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 334 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3727 r_free = 0.3727 target = 0.088662 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3184 r_free = 0.3184 target = 0.062799 restraints weight = 28692.829| |-----------------------------------------------------------------------------| r_work (start): 0.3115 rms_B_bonded: 4.39 r_work (final): 0.3115 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8134 moved from start: 0.4801 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 10281 Z= 0.176 Angle : 0.903 17.715 14103 Z= 0.399 Chirality : 0.047 0.387 1812 Planarity : 0.004 0.042 1596 Dihedral : 5.054 29.221 1170 Min Nonbonded Distance : 2.362 Molprobity Statistics. All-atom Clashscore : 7.50 Ramachandran Plot: Outliers : 0.28 % Allowed : 8.40 % Favored : 91.32 % Rotamer: Outliers : 3.11 % Allowed : 16.15 % Favored : 80.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.73 (0.25), residues: 1071 helix: 0.34 (0.26), residues: 417 sheet: 1.82 (0.53), residues: 96 loop : -1.61 (0.25), residues: 558 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 192 TYR 0.025 0.001 TYR B 65 PHE 0.018 0.002 PHE b 398 TRP 0.013 0.001 TRP c 263 HIS 0.004 0.001 HIS A 123 Details of bonding type rmsd/Z covalent geometry : bond 0.00353 / 0.17 (10158) covalent geometry : angle 0.77225 / 0.37 (13755) SS BOND : bond 0.00584 / 0.36 ( 21) SS BOND : angle 1.26707 / 0.79 ( 42) hydrogen bonds : bond 0.03951 / 2.71 ( 378) hydrogen bonds : angle 4.72987 / 3.34 ( 990) link_ALPHA1-2 : bond 0.00160 / 0.08 ( 3) link_ALPHA1-2 : angle 1.54549 / 0.74 ( 9) link_ALPHA1-3 : bond 0.00995 / 0.57 ( 9) link_ALPHA1-3 : angle 1.71409 / 1.08 ( 27) link_ALPHA1-6 : bond 0.00542 / 0.28 ( 6) link_ALPHA1-6 : angle 1.45809 / 0.80 ( 18) link_BETA1-4 : bond 0.01635 / 0.93 ( 51) link_BETA1-4 : angle 4.06318 / 2.51 ( 153) link_NAG-ASN : bond 0.00342 / 0.24 ( 33) link_NAG-ASN : angle 2.39392 / 1.46 ( 99) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2142 Ramachandran restraints generated. 1071 Oldfield, 0 Emsley, 1071 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2142 Ramachandran restraints generated. 1071 Oldfield, 0 Emsley, 1071 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 215 residues out of total 966 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 185 time to evaluate : 0.276 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 99 GLU cc_start: 0.8351 (tp30) cc_final: 0.7879 (mm-30) REVERT: A 188 GLN cc_start: 0.8662 (mm-40) cc_final: 0.8300 (mm-40) REVERT: a 323 GLN cc_start: 0.8412 (tm-30) cc_final: 0.8092 (tm-30) REVERT: a 326 LYS cc_start: 0.8342 (tppt) cc_final: 0.8125 (tptp) REVERT: a 346 ASP cc_start: 0.9142 (p0) cc_final: 0.8781 (p0) REVERT: a 400 ASP cc_start: 0.8477 (p0) cc_final: 0.7992 (p0) REVERT: a 418 TYR cc_start: 0.5258 (t80) cc_final: 0.5040 (t80) REVERT: B 99 GLU cc_start: 0.8523 (tp30) cc_final: 0.8137 (mm-30) REVERT: B 124 LYS cc_start: 0.8892 (mtmm) cc_final: 0.8647 (mtmm) REVERT: B 188 GLN cc_start: 0.8895 (mm-40) cc_final: 0.8577 (mm-40) REVERT: B 227 GLU cc_start: 0.7879 (mm-30) cc_final: 0.7623 (mm-30) REVERT: C 94 ILE cc_start: 0.8981 (mt) cc_final: 0.8673 (tt) REVERT: C 99 GLU cc_start: 0.8432 (tp30) cc_final: 0.8192 (mm-30) REVERT: C 142 SER cc_start: 0.9069 (OUTLIER) cc_final: 0.8597 (p) REVERT: C 156 PHE cc_start: 0.9233 (m-80) cc_final: 0.9000 (m-80) REVERT: C 193 MET cc_start: 0.8794 (mmm) cc_final: 0.8461 (tpp) REVERT: C 213 MET cc_start: 0.8043 (OUTLIER) cc_final: 0.7607 (mmp) REVERT: C 227 GLU cc_start: 0.8245 (mm-30) cc_final: 0.8026 (mm-30) REVERT: C 246 GLN cc_start: 0.7931 (pp30) cc_final: 0.7588 (pp30) REVERT: b 341 ASN cc_start: 0.9176 (m-40) cc_final: 0.8803 (m-40) REVERT: b 404 GLN cc_start: 0.8936 (tp40) cc_final: 0.8459 (tp-100) REVERT: c 330 GLN cc_start: 0.8634 (mp10) cc_final: 0.8415 (mp10) REVERT: c 338 LYS cc_start: 0.9190 (mtmm) cc_final: 0.8769 (mptt) REVERT: c 409 MET cc_start: 0.8453 (mtp) cc_final: 0.8169 (mtp) outliers start: 30 outliers final: 20 residues processed: 203 average time/residue: 0.1052 time to fit residues: 29.5882 Evaluate side-chains 197 residues out of total 966 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 175 time to evaluate : 0.326 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 96 VAL Chi-restraints excluded: chain A residue 210 ASP Chi-restraints excluded: chain A residue 211 CYS Chi-restraints excluded: chain A residue 213 MET Chi-restraints excluded: chain a residue 295 THR Chi-restraints excluded: chain a residue 304 HIS Chi-restraints excluded: chain a residue 322 ILE Chi-restraints excluded: chain a residue 375 SER Chi-restraints excluded: chain a residue 398 PHE Chi-restraints excluded: chain a residue 420 ASP Chi-restraints excluded: chain C residue 81 MET Chi-restraints excluded: chain C residue 142 SER Chi-restraints excluded: chain C residue 211 CYS Chi-restraints excluded: chain C residue 213 MET Chi-restraints excluded: chain b residue 332 SER Chi-restraints excluded: chain b residue 375 SER Chi-restraints excluded: chain c residue 295 THR Chi-restraints excluded: chain c residue 341 ASN Chi-restraints excluded: chain c residue 375 SER Chi-restraints excluded: chain c residue 398 PHE Chi-restraints excluded: chain c residue 400 ASP Chi-restraints excluded: chain c residue 420 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 13 optimal weight: 4.9990 chunk 6 optimal weight: 5.9990 chunk 102 optimal weight: 0.0970 chunk 38 optimal weight: 3.9990 chunk 69 optimal weight: 3.9990 chunk 12 optimal weight: 5.9990 chunk 18 optimal weight: 5.9990 chunk 0 optimal weight: 8.9990 chunk 61 optimal weight: 1.9990 chunk 103 optimal weight: 4.9990 chunk 21 optimal weight: 2.9990 overall best weight: 2.6186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 169 HIS B 169 HIS ** B 178 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** b 323 GLN ** c 334 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3701 r_free = 0.3701 target = 0.086841 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3152 r_free = 0.3152 target = 0.061050 restraints weight = 28825.741| |-----------------------------------------------------------------------------| r_work (start): 0.3084 rms_B_bonded: 4.35 r_work (final): 0.3084 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8175 moved from start: 0.4991 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.047 10281 Z= 0.225 Angle : 0.923 17.680 14103 Z= 0.410 Chirality : 0.048 0.384 1812 Planarity : 0.004 0.042 1596 Dihedral : 5.049 26.889 1170 Min Nonbonded Distance : 2.334 Molprobity Statistics. All-atom Clashscore : 7.76 Ramachandran Plot: Outliers : 0.28 % Allowed : 8.78 % Favored : 90.94 % Rotamer: Outliers : 3.62 % Allowed : 16.25 % Favored : 80.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.81 (0.26), residues: 1071 helix: 0.42 (0.26), residues: 411 sheet: 0.92 (0.51), residues: 114 loop : -1.67 (0.26), residues: 546 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 192 TYR 0.021 0.001 TYR B 65 PHE 0.016 0.002 PHE b 398 TRP 0.011 0.001 TRP a 263 HIS 0.011 0.001 HIS C 169 Details of bonding type rmsd/Z covalent geometry : bond 0.00474 / 0.22 (10158) covalent geometry : angle 0.79765 / 0.38 (13755) SS BOND : bond 0.00575 / 0.36 ( 21) SS BOND : angle 1.31391 / 0.86 ( 42) hydrogen bonds : bond 0.04131 / 2.84 ( 378) hydrogen bonds : angle 4.68332 / 3.30 ( 990) link_ALPHA1-2 : bond 0.00037 / 0.02 ( 3) link_ALPHA1-2 : angle 1.59332 / 0.75 ( 9) link_ALPHA1-3 : bond 0.00918 / 0.53 ( 9) link_ALPHA1-3 : angle 1.74341 / 1.11 ( 27) link_ALPHA1-6 : bond 0.00510 / 0.26 ( 6) link_ALPHA1-6 : angle 1.50743 / 0.82 ( 18) link_BETA1-4 : bond 0.01618 / 0.92 ( 51) link_BETA1-4 : angle 4.05060 / 2.50 ( 153) link_NAG-ASN : bond 0.00435 / 0.30 ( 33) link_NAG-ASN : angle 2.33902 / 1.43 ( 99) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2142 Ramachandran restraints generated. 1071 Oldfield, 0 Emsley, 1071 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2142 Ramachandran restraints generated. 1071 Oldfield, 0 Emsley, 1071 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 222 residues out of total 966 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 187 time to evaluate : 0.383 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 99 GLU cc_start: 0.8391 (tp30) cc_final: 0.7919 (mm-30) REVERT: A 188 GLN cc_start: 0.8677 (mm-40) cc_final: 0.8304 (mm-40) REVERT: a 323 GLN cc_start: 0.8468 (tm-30) cc_final: 0.8167 (tm-30) REVERT: a 346 ASP cc_start: 0.9143 (p0) cc_final: 0.8797 (p0) REVERT: a 400 ASP cc_start: 0.8494 (p0) cc_final: 0.8138 (p0) REVERT: B 74 MET cc_start: 0.9074 (mmt) cc_final: 0.8780 (mmt) REVERT: B 99 GLU cc_start: 0.8511 (tp30) cc_final: 0.8256 (mm-30) REVERT: B 124 LYS cc_start: 0.8942 (mtmm) cc_final: 0.8658 (mtmm) REVERT: B 188 GLN cc_start: 0.8894 (mm-40) cc_final: 0.8546 (mm-40) REVERT: B 227 GLU cc_start: 0.7917 (mm-30) cc_final: 0.7655 (mm-30) REVERT: C 94 ILE cc_start: 0.9069 (mt) cc_final: 0.8749 (tt) REVERT: C 99 GLU cc_start: 0.8474 (tp30) cc_final: 0.8184 (mm-30) REVERT: C 142 SER cc_start: 0.9081 (OUTLIER) cc_final: 0.8656 (p) REVERT: C 156 PHE cc_start: 0.9221 (m-80) cc_final: 0.9014 (m-80) REVERT: C 227 GLU cc_start: 0.8302 (mm-30) cc_final: 0.8095 (mm-30) REVERT: b 341 ASN cc_start: 0.9115 (m-40) cc_final: 0.8789 (m-40) REVERT: b 404 GLN cc_start: 0.8983 (tp40) cc_final: 0.8546 (tp-100) REVERT: c 338 LYS cc_start: 0.9184 (mtmm) cc_final: 0.8741 (mptt) REVERT: c 409 MET cc_start: 0.8469 (mtp) cc_final: 0.8140 (mtp) outliers start: 35 outliers final: 28 residues processed: 205 average time/residue: 0.1063 time to fit residues: 30.3164 Evaluate side-chains 202 residues out of total 966 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 173 time to evaluate : 0.382 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 96 VAL Chi-restraints excluded: chain A residue 210 ASP Chi-restraints excluded: chain A residue 211 CYS Chi-restraints excluded: chain a residue 295 THR Chi-restraints excluded: chain a residue 304 HIS Chi-restraints excluded: chain a residue 322 ILE Chi-restraints excluded: chain a residue 375 SER Chi-restraints excluded: chain a residue 398 PHE Chi-restraints excluded: chain a residue 420 ASP Chi-restraints excluded: chain C residue 81 MET Chi-restraints excluded: chain C residue 142 SER Chi-restraints excluded: chain C residue 178 HIS Chi-restraints excluded: chain C residue 211 CYS Chi-restraints excluded: chain C residue 213 MET Chi-restraints excluded: chain b residue 295 THR Chi-restraints excluded: chain b residue 304 HIS Chi-restraints excluded: chain b residue 323 GLN Chi-restraints excluded: chain b residue 332 SER Chi-restraints excluded: chain b residue 348 LEU Chi-restraints excluded: chain b residue 375 SER Chi-restraints excluded: chain b residue 398 PHE Chi-restraints excluded: chain c residue 295 THR Chi-restraints excluded: chain c residue 304 HIS Chi-restraints excluded: chain c residue 322 ILE Chi-restraints excluded: chain c residue 332 SER Chi-restraints excluded: chain c residue 341 ASN Chi-restraints excluded: chain c residue 375 SER Chi-restraints excluded: chain c residue 398 PHE Chi-restraints excluded: chain c residue 420 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 24 optimal weight: 0.8980 chunk 69 optimal weight: 10.0000 chunk 86 optimal weight: 3.9990 chunk 26 optimal weight: 0.6980 chunk 81 optimal weight: 6.9990 chunk 92 optimal weight: 7.9990 chunk 57 optimal weight: 3.9990 chunk 93 optimal weight: 8.9990 chunk 78 optimal weight: 2.9990 chunk 16 optimal weight: 2.9990 chunk 97 optimal weight: 9.9990 overall best weight: 2.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 169 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 178 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 169 HIS ** b 334 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** b 373 HIS ** c 334 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** c 373 HIS c 404 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3704 r_free = 0.3704 target = 0.086879 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3153 r_free = 0.3153 target = 0.061077 restraints weight = 28619.088| |-----------------------------------------------------------------------------| r_work (start): 0.3088 rms_B_bonded: 4.31 r_work (final): 0.3088 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8179 moved from start: 0.5140 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.047 10281 Z= 0.210 Angle : 0.932 17.675 14103 Z= 0.413 Chirality : 0.048 0.384 1812 Planarity : 0.004 0.043 1596 Dihedral : 5.072 25.494 1170 Min Nonbonded Distance : 2.334 Molprobity Statistics. All-atom Clashscore : 7.91 Ramachandran Plot: Outliers : 0.28 % Allowed : 8.22 % Favored : 91.50 % Rotamer: Outliers : 3.11 % Allowed : 16.87 % Favored : 80.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.86 (0.25), residues: 1071 helix: 0.48 (0.26), residues: 411 sheet: 1.08 (0.53), residues: 96 loop : -1.74 (0.25), residues: 564 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 192 TYR 0.019 0.001 TYR B 65 PHE 0.015 0.002 PHE b 398 TRP 0.012 0.001 TRP a 263 HIS 0.005 0.001 HIS A 123 Details of bonding type rmsd/Z covalent geometry : bond 0.00442 / 0.20 (10158) covalent geometry : angle 0.80340 / 0.38 (13755) SS BOND : bond 0.00559 / 0.36 ( 21) SS BOND : angle 1.25306 / 0.83 ( 42) hydrogen bonds : bond 0.03994 / 2.72 ( 378) hydrogen bonds : angle 4.66415 / 3.29 ( 990) link_ALPHA1-2 : bond 0.00038 / 0.02 ( 3) link_ALPHA1-2 : angle 1.60504 / 0.76 ( 9) link_ALPHA1-3 : bond 0.00943 / 0.54 ( 9) link_ALPHA1-3 : angle 1.75301 / 1.11 ( 27) link_ALPHA1-6 : bond 0.00514 / 0.26 ( 6) link_ALPHA1-6 : angle 1.51891 / 0.82 ( 18) link_BETA1-4 : bond 0.01613 / 0.91 ( 51) link_BETA1-4 : angle 4.01408 / 2.47 ( 153) link_NAG-ASN : bond 0.00358 / 0.24 ( 33) link_NAG-ASN : angle 2.64951 / 1.57 ( 99) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2142 Ramachandran restraints generated. 1071 Oldfield, 0 Emsley, 1071 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2142 Ramachandran restraints generated. 1071 Oldfield, 0 Emsley, 1071 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 215 residues out of total 966 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 185 time to evaluate : 0.373 Fit side-chains revert: symmetry clash REVERT: A 99 GLU cc_start: 0.8399 (tp30) cc_final: 0.7915 (mm-30) REVERT: A 188 GLN cc_start: 0.8665 (mm-40) cc_final: 0.8285 (mm-40) REVERT: A 249 ARG cc_start: 0.6305 (mtt90) cc_final: 0.5966 (mpt90) REVERT: a 323 GLN cc_start: 0.8514 (tm-30) cc_final: 0.8249 (tm-30) REVERT: a 346 ASP cc_start: 0.9059 (p0) cc_final: 0.8723 (p0) REVERT: a 400 ASP cc_start: 0.8549 (p0) cc_final: 0.8015 (p0) REVERT: B 74 MET cc_start: 0.9035 (mmt) cc_final: 0.8731 (mmt) REVERT: B 99 GLU cc_start: 0.8524 (tp30) cc_final: 0.8267 (mm-30) REVERT: B 156 PHE cc_start: 0.9211 (m-80) cc_final: 0.8937 (m-80) REVERT: B 188 GLN cc_start: 0.8900 (mm-40) cc_final: 0.8550 (mm-40) REVERT: B 227 GLU cc_start: 0.7895 (mm-30) cc_final: 0.7624 (mm-30) REVERT: C 94 ILE cc_start: 0.9059 (mt) cc_final: 0.8738 (tt) REVERT: C 99 GLU cc_start: 0.8466 (tp30) cc_final: 0.8188 (mm-30) REVERT: C 152 MET cc_start: 0.8189 (tmm) cc_final: 0.7837 (tmm) REVERT: C 193 MET cc_start: 0.9034 (tpp) cc_final: 0.8734 (tpp) REVERT: C 227 GLU cc_start: 0.8311 (mm-30) cc_final: 0.8087 (mm-30) REVERT: b 323 GLN cc_start: 0.8827 (tt0) cc_final: 0.8548 (tm-30) REVERT: b 341 ASN cc_start: 0.9116 (m-40) cc_final: 0.8802 (m-40) REVERT: b 404 GLN cc_start: 0.9001 (tp40) cc_final: 0.8558 (tp-100) REVERT: c 326 LYS cc_start: 0.8372 (tppt) cc_final: 0.7993 (tppt) REVERT: c 338 LYS cc_start: 0.9179 (mtmm) cc_final: 0.8711 (mptt) REVERT: c 409 MET cc_start: 0.8429 (mtp) cc_final: 0.8110 (mtp) outliers start: 30 outliers final: 23 residues processed: 199 average time/residue: 0.1123 time to fit residues: 30.6975 Evaluate side-chains 197 residues out of total 966 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 174 time to evaluate : 0.372 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 96 VAL Chi-restraints excluded: chain A residue 210 ASP Chi-restraints excluded: chain A residue 211 CYS Chi-restraints excluded: chain A residue 213 MET Chi-restraints excluded: chain a residue 295 THR Chi-restraints excluded: chain a residue 304 HIS Chi-restraints excluded: chain a residue 322 ILE Chi-restraints excluded: chain a residue 375 SER Chi-restraints excluded: chain a residue 398 PHE Chi-restraints excluded: chain a residue 420 ASP Chi-restraints excluded: chain C residue 81 MET Chi-restraints excluded: chain C residue 136 LEU Chi-restraints excluded: chain C residue 178 HIS Chi-restraints excluded: chain C residue 211 CYS Chi-restraints excluded: chain b residue 332 SER Chi-restraints excluded: chain b residue 348 LEU Chi-restraints excluded: chain b residue 398 PHE Chi-restraints excluded: chain c residue 295 THR Chi-restraints excluded: chain c residue 322 ILE Chi-restraints excluded: chain c residue 341 ASN Chi-restraints excluded: chain c residue 398 PHE Chi-restraints excluded: chain c residue 400 ASP Chi-restraints excluded: chain c residue 420 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 79 optimal weight: 0.9990 chunk 74 optimal weight: 10.0000 chunk 76 optimal weight: 0.9990 chunk 55 optimal weight: 3.9990 chunk 24 optimal weight: 0.9980 chunk 7 optimal weight: 0.9990 chunk 20 optimal weight: 0.7980 chunk 68 optimal weight: 2.9990 chunk 23 optimal weight: 0.5980 chunk 21 optimal weight: 0.9990 chunk 28 optimal weight: 0.8980 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... a 373 HIS B 169 HIS ** B 178 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 145 ASN ** b 415 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 334 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3725 r_free = 0.3725 target = 0.087963 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3184 r_free = 0.3184 target = 0.062371 restraints weight = 28432.870| |-----------------------------------------------------------------------------| r_work (start): 0.3118 rms_B_bonded: 4.30 r_work: 0.2922 rms_B_bonded: 5.00 restraints_weight: 0.5000 r_work (final): 0.2922 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8252 moved from start: 0.5282 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 10281 Z= 0.160 Angle : 0.924 17.665 14103 Z= 0.412 Chirality : 0.047 0.381 1812 Planarity : 0.004 0.044 1596 Dihedral : 5.033 24.779 1170 Min Nonbonded Distance : 2.340 Molprobity Statistics. All-atom Clashscore : 7.29 Ramachandran Plot: Outliers : 0.28 % Allowed : 8.12 % Favored : 91.60 % Rotamer: Outliers : 2.07 % Allowed : 18.84 % Favored : 79.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.81 (0.26), residues: 1071 helix: 0.46 (0.26), residues: 417 sheet: 0.73 (0.51), residues: 114 loop : -1.67 (0.26), residues: 540 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG a 421 TYR 0.015 0.001 TYR B 65 PHE 0.016 0.002 PHE b 398 TRP 0.015 0.001 TRP a 263 HIS 0.005 0.001 HIS A 123 Details of bonding type rmsd/Z covalent geometry : bond 0.00316 / 0.15 (10158) covalent geometry : angle 0.80245 / 0.38 (13755) SS BOND : bond 0.00430 / 0.27 ( 21) SS BOND : angle 1.21161 / 0.81 ( 42) hydrogen bonds : bond 0.03682 / 2.49 ( 378) hydrogen bonds : angle 4.58841 / 3.24 ( 990) link_ALPHA1-2 : bond 0.00126 / 0.06 ( 3) link_ALPHA1-2 : angle 1.60081 / 0.76 ( 9) link_ALPHA1-3 : bond 0.01034 / 0.59 ( 9) link_ALPHA1-3 : angle 1.75557 / 1.10 ( 27) link_ALPHA1-6 : bond 0.00540 / 0.28 ( 6) link_ALPHA1-6 : angle 1.46474 / 0.80 ( 18) link_BETA1-4 : bond 0.01629 / 0.92 ( 51) link_BETA1-4 : angle 3.95997 / 2.44 ( 153) link_NAG-ASN : bond 0.00306 / 0.20 ( 33) link_NAG-ASN : angle 2.41983 / 1.44 ( 99) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2142 Ramachandran restraints generated. 1071 Oldfield, 0 Emsley, 1071 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2142 Ramachandran restraints generated. 1071 Oldfield, 0 Emsley, 1071 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 213 residues out of total 966 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 193 time to evaluate : 0.438 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 99 GLU cc_start: 0.8760 (tp30) cc_final: 0.8271 (mm-30) REVERT: A 188 GLN cc_start: 0.8877 (mm-40) cc_final: 0.8578 (mm-40) REVERT: A 192 ARG cc_start: 0.9041 (mtp85) cc_final: 0.8777 (mtp85) REVERT: A 249 ARG cc_start: 0.6352 (mtt90) cc_final: 0.6011 (mpt90) REVERT: a 323 GLN cc_start: 0.8686 (tm-30) cc_final: 0.8419 (tm-30) REVERT: a 346 ASP cc_start: 0.9184 (p0) cc_final: 0.8850 (p0) REVERT: a 400 ASP cc_start: 0.8604 (p0) cc_final: 0.8230 (p0) REVERT: B 99 GLU cc_start: 0.8894 (tp30) cc_final: 0.8498 (mm-30) REVERT: B 156 PHE cc_start: 0.9224 (m-80) cc_final: 0.8972 (m-80) REVERT: B 188 GLN cc_start: 0.9034 (mm-40) cc_final: 0.8721 (mm-40) REVERT: B 227 GLU cc_start: 0.8140 (mm-30) cc_final: 0.7859 (mm-30) REVERT: C 94 ILE cc_start: 0.9090 (mt) cc_final: 0.8777 (tt) REVERT: C 99 GLU cc_start: 0.8844 (tp30) cc_final: 0.8611 (mm-30) REVERT: C 152 MET cc_start: 0.8384 (tmm) cc_final: 0.8044 (tmm) REVERT: C 169 HIS cc_start: 0.6969 (t-90) cc_final: 0.6609 (t-90) REVERT: C 193 MET cc_start: 0.9328 (tpp) cc_final: 0.8891 (tpp) REVERT: C 227 GLU cc_start: 0.8613 (mm-30) cc_final: 0.8354 (mm-30) REVERT: b 341 ASN cc_start: 0.9266 (m-40) cc_final: 0.8976 (m-40) REVERT: b 404 GLN cc_start: 0.9101 (tp40) cc_final: 0.8696 (tp-100) REVERT: c 338 LYS cc_start: 0.9238 (mtmm) cc_final: 0.8799 (mptt) REVERT: c 398 PHE cc_start: 0.6358 (OUTLIER) cc_final: 0.5960 (m-80) REVERT: c 409 MET cc_start: 0.8326 (mtp) cc_final: 0.8003 (mtp) outliers start: 20 outliers final: 14 residues processed: 200 average time/residue: 0.1134 time to fit residues: 31.1292 Evaluate side-chains 195 residues out of total 966 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 180 time to evaluate : 0.383 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 96 VAL Chi-restraints excluded: chain A residue 210 ASP Chi-restraints excluded: chain A residue 211 CYS Chi-restraints excluded: chain A residue 213 MET Chi-restraints excluded: chain a residue 398 PHE Chi-restraints excluded: chain C residue 81 MET Chi-restraints excluded: chain C residue 178 HIS Chi-restraints excluded: chain C residue 211 CYS Chi-restraints excluded: chain b residue 332 SER Chi-restraints excluded: chain b residue 398 PHE Chi-restraints excluded: chain c residue 295 THR Chi-restraints excluded: chain c residue 332 SER Chi-restraints excluded: chain c residue 341 ASN Chi-restraints excluded: chain c residue 398 PHE Chi-restraints excluded: chain c residue 400 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 90 optimal weight: 10.0000 chunk 53 optimal weight: 5.9990 chunk 98 optimal weight: 2.9990 chunk 96 optimal weight: 5.9990 chunk 70 optimal weight: 1.9990 chunk 42 optimal weight: 1.9990 chunk 49 optimal weight: 2.9990 chunk 34 optimal weight: 2.9990 chunk 20 optimal weight: 7.9990 chunk 38 optimal weight: 1.9990 chunk 29 optimal weight: 0.9980 overall best weight: 1.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 169 HIS ** B 178 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** b 323 GLN ** b 334 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 334 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 = 0.3715 r_free = 0.3715 target = 0.087299 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3168 r_free = 0.3168 target = 0.061522 restraints weight = 28413.910| |-----------------------------------------------------------------------------| r_work (start): 0.3095 rms_B_bonded: 4.30 r_work: 0.2897 rms_B_bonded: 4.99 restraints_weight: 0.5000 r_work (final): 0.2897 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8295 moved from start: 0.5386 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 10281 Z= 0.200 Angle : 0.961 17.614 14103 Z= 0.427 Chirality : 0.048 0.384 1812 Planarity : 0.004 0.043 1596 Dihedral : 5.073 25.699 1170 Min Nonbonded Distance : 2.341 Molprobity Statistics. All-atom Clashscore : 7.86 Ramachandran Plot: Outliers : 0.28 % Allowed : 8.31 % Favored : 91.41 % Rotamer: Outliers : 2.38 % Allowed : 19.05 % Favored : 78.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.88 (0.26), residues: 1071 helix: 0.48 (0.26), residues: 411 sheet: 0.68 (0.51), residues: 114 loop : -1.76 (0.26), residues: 546 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG a 421 TYR 0.015 0.001 TYR B 65 PHE 0.016 0.002 PHE b 398 TRP 0.010 0.001 TRP a 263 HIS 0.005 0.001 HIS A 123 Details of bonding type rmsd/Z covalent geometry : bond 0.00423 / 0.19 (10158) covalent geometry : angle 0.84589 / 0.40 (13755) SS BOND : bond 0.00495 / 0.31 ( 21) SS BOND : angle 1.22479 / 0.79 ( 42) hydrogen bonds : bond 0.03861 / 2.59 ( 378) hydrogen bonds : angle 4.57594 / 3.24 ( 990) link_ALPHA1-2 : bond 0.00056 / 0.03 ( 3) link_ALPHA1-2 : angle 1.59577 / 0.75 ( 9) link_ALPHA1-3 : bond 0.00934 / 0.54 ( 9) link_ALPHA1-3 : angle 1.73322 / 1.10 ( 27) link_ALPHA1-6 : bond 0.00492 / 0.25 ( 6) link_ALPHA1-6 : angle 1.47591 / 0.81 ( 18) link_BETA1-4 : bond 0.01595 / 0.90 ( 51) link_BETA1-4 : angle 3.96473 / 2.44 ( 153) link_NAG-ASN : bond 0.00344 / 0.23 ( 33) link_NAG-ASN : angle 2.37903 / 1.42 ( 99) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2142 Ramachandran restraints generated. 1071 Oldfield, 0 Emsley, 1071 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2142 Ramachandran restraints generated. 1071 Oldfield, 0 Emsley, 1071 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 207 residues out of total 966 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 184 time to evaluate : 0.379 Fit side-chains revert: symmetry clash REVERT: A 99 GLU cc_start: 0.8769 (tp30) cc_final: 0.8287 (mm-30) REVERT: A 150 GLU cc_start: 0.8650 (pm20) cc_final: 0.7887 (tm-30) REVERT: A 188 GLN cc_start: 0.8874 (mm-40) cc_final: 0.8566 (mm-40) REVERT: A 192 ARG cc_start: 0.9077 (mtp85) cc_final: 0.8849 (mtp85) REVERT: A 249 ARG cc_start: 0.6571 (mtt90) cc_final: 0.6194 (mpt90) REVERT: a 323 GLN cc_start: 0.8708 (tm-30) cc_final: 0.8436 (tm-30) REVERT: a 331 MET cc_start: 0.6908 (tmm) cc_final: 0.5957 (tmm) REVERT: a 346 ASP cc_start: 0.9177 (p0) cc_final: 0.8840 (p0) REVERT: a 400 ASP cc_start: 0.8641 (p0) cc_final: 0.8242 (p0) REVERT: B 99 GLU cc_start: 0.8881 (tp30) cc_final: 0.8527 (mm-30) REVERT: B 156 PHE cc_start: 0.9196 (m-80) cc_final: 0.8964 (m-80) REVERT: B 188 GLN cc_start: 0.9051 (mm-40) cc_final: 0.8743 (mm-40) REVERT: B 227 GLU cc_start: 0.8178 (mm-30) cc_final: 0.7895 (mm-30) REVERT: C 94 ILE cc_start: 0.9210 (mt) cc_final: 0.8859 (tt) REVERT: C 99 GLU cc_start: 0.8855 (tp30) cc_final: 0.8415 (mm-30) REVERT: C 152 MET cc_start: 0.8308 (tmm) cc_final: 0.7986 (tmm) REVERT: C 193 MET cc_start: 0.9335 (tpp) cc_final: 0.9016 (tpp) REVERT: C 213 MET cc_start: 0.8448 (mmm) cc_final: 0.7762 (mmm) REVERT: C 227 GLU cc_start: 0.8648 (mm-30) cc_final: 0.8437 (mm-30) REVERT: b 341 ASN cc_start: 0.9287 (m-40) cc_final: 0.9011 (m-40) REVERT: b 404 GLN cc_start: 0.9098 (tp40) cc_final: 0.8677 (tp-100) REVERT: c 338 LYS cc_start: 0.9243 (mtmm) cc_final: 0.8774 (mptt) REVERT: c 409 MET cc_start: 0.8346 (mtp) cc_final: 0.8004 (mtp) outliers start: 23 outliers final: 16 residues processed: 193 average time/residue: 0.1085 time to fit residues: 28.8237 Evaluate side-chains 194 residues out of total 966 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 178 time to evaluate : 0.362 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 96 VAL Chi-restraints excluded: chain A residue 211 CYS Chi-restraints excluded: chain A residue 213 MET Chi-restraints excluded: chain a residue 398 PHE Chi-restraints excluded: chain B residue 213 MET Chi-restraints excluded: chain C residue 81 MET Chi-restraints excluded: chain C residue 178 HIS Chi-restraints excluded: chain C residue 211 CYS Chi-restraints excluded: chain b residue 323 GLN Chi-restraints excluded: chain b residue 332 SER Chi-restraints excluded: chain b residue 348 LEU Chi-restraints excluded: chain b residue 398 PHE Chi-restraints excluded: chain c residue 295 THR Chi-restraints excluded: chain c residue 304 HIS Chi-restraints excluded: chain c residue 332 SER Chi-restraints excluded: chain c residue 341 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 59 optimal weight: 8.9990 chunk 81 optimal weight: 6.9990 chunk 49 optimal weight: 0.9990 chunk 16 optimal weight: 8.9990 chunk 45 optimal weight: 10.0000 chunk 54 optimal weight: 7.9990 chunk 76 optimal weight: 4.9990 chunk 74 optimal weight: 4.9990 chunk 43 optimal weight: 2.9990 chunk 26 optimal weight: 0.7980 chunk 57 optimal weight: 7.9990 overall best weight: 2.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 178 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** b 323 GLN ** b 334 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 334 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3692 r_free = 0.3692 target = 0.086542 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3149 r_free = 0.3149 target = 0.060839 restraints weight = 29011.113| |-----------------------------------------------------------------------------| r_work (start): 0.3082 rms_B_bonded: 4.31 r_work: 0.2886 rms_B_bonded: 4.98 restraints_weight: 0.5000 r_work (final): 0.2886 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8314 moved from start: 0.5454 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.046 10281 Z= 0.244 Angle : 0.970 17.596 14103 Z= 0.435 Chirality : 0.049 0.379 1812 Planarity : 0.005 0.043 1596 Dihedral : 5.170 24.689 1170 Min Nonbonded Distance : 2.345 Molprobity Statistics. All-atom Clashscore : 8.07 Ramachandran Plot: Outliers : 0.28 % Allowed : 7.84 % Favored : 91.88 % Rotamer: Outliers : 2.07 % Allowed : 19.25 % Favored : 78.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.94 (0.25), residues: 1071 helix: 0.40 (0.26), residues: 411 sheet: 0.65 (0.50), residues: 114 loop : -1.78 (0.26), residues: 546 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.001 ARG b 324 TYR 0.015 0.001 TYR B 65 PHE 0.015 0.002 PHE b 398 TRP 0.009 0.001 TRP c 385 HIS 0.007 0.001 HIS C 169 Details of bonding type rmsd/Z covalent geometry : bond 0.00527 / 0.24 (10158) covalent geometry : angle 0.85610 / 0.41 (13755) SS BOND : bond 0.00555 / 0.35 ( 21) SS BOND : angle 1.20162 / 0.77 ( 42) hydrogen bonds : bond 0.04013 / 2.69 ( 378) hydrogen bonds : angle 4.58121 / 3.24 ( 990) link_ALPHA1-2 : bond 0.00046 / 0.02 ( 3) link_ALPHA1-2 : angle 1.61067 / 0.76 ( 9) link_ALPHA1-3 : bond 0.00898 / 0.52 ( 9) link_ALPHA1-3 : angle 1.74751 / 1.11 ( 27) link_ALPHA1-6 : bond 0.00471 / 0.24 ( 6) link_ALPHA1-6 : angle 1.53803 / 0.83 ( 18) link_BETA1-4 : bond 0.01579 / 0.89 ( 51) link_BETA1-4 : angle 3.97177 / 2.45 ( 153) link_NAG-ASN : bond 0.00422 / 0.28 ( 33) link_NAG-ASN : angle 2.39924 / 1.44 ( 99) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2042.43 seconds wall clock time: 36 minutes 15.69 seconds (2175.69 seconds total)