Starting phenix.real_space_refine on Thu Jul 2 16:33:58 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7sgd_25107/07_2026/7sgd_25107.cif Found real_map, /net/cci-nas-00/data/ceres_data/7sgd_25107/07_2026/7sgd_25107.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.97 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7sgd_25107/07_2026/7sgd_25107.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7sgd_25107/07_2026/7sgd_25107.cif" restraint_files = "/net/cci-nas-00/data/ceres_data/7sgd_25107/07_2026/7sgd_25107.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7sgd_25107/07_2026/7sgd_25107.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7sgd_25107/07_2026/7sgd_25107.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7sgd_25107/07_2026/7sgd_25107.map" } resolution = 3.97 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= -0.000 sd= 0.003 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 93 5.16 5 C 5679 2.51 5 N 1428 2.21 5 O 1920 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 6 residue(s): 0.00s 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: 9120 Number of models: 1 Model: "" Number of chains: 39 Chain: "A" Number of atoms: 1371 Number of conformers: 1 Conformer: "" Number of residues, atoms: 174, 1371 Classifications: {'peptide': 174} Link IDs: {'PTRANS': 4, 'TRANS': 169} Chain breaks: 3 Chain: "a" Number of atoms: 1335 Number of conformers: 1 Conformer: "" Number of residues, atoms: 164, 1335 Classifications: {'peptide': 164} Link IDs: {'PTRANS': 4, 'TRANS': 159} Chain: "B" Number of atoms: 1371 Number of conformers: 1 Conformer: "" Number of residues, atoms: 174, 1371 Classifications: {'peptide': 174} Link IDs: {'PTRANS': 4, 'TRANS': 169} Chain breaks: 3 Chain: "b" Number of atoms: 1335 Number of conformers: 1 Conformer: "" Number of residues, atoms: 164, 1335 Classifications: {'peptide': 164} Link IDs: {'PTRANS': 4, 'TRANS': 159} Chain: "C" Number of atoms: 1371 Number of conformers: 1 Conformer: "" Number of residues, atoms: 174, 1371 Classifications: {'peptide': 174} Link IDs: {'PTRANS': 4, 'TRANS': 169} Chain breaks: 3 Chain: "c" Number of atoms: 1335 Number of conformers: 1 Conformer: "" Number of residues, atoms: 164, 1335 Classifications: {'peptide': 164} Link IDs: {'PTRANS': 4, 'TRANS': 159} Chain: "D" 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: "E" 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: "F" 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: "G" 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: "H" 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: "I" 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: "J" 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: "K" 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: "L" Number of atoms: 38 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 38 Unusual residues: {'FUC': 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: 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: "N" 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: "O" 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: "P" 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: "Q" 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: "R" 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: "S" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen chiralities: 5 Chain: "T" 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: "U" Number of atoms: 38 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 38 Unusual residues: {'FUC': 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: 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: "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: 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: "Z" 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: "d" 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: "e" 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: "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: 38 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 38 Unusual residues: {'FUC': 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: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen chiralities: 1 Chain: "a" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen chiralities: 1 Chain: "B" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen chiralities: 1 Chain: "b" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen chiralities: 1 Chain: "C" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen chiralities: 1 Chain: "c" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 1.75, per 1000 atoms: 0.19 Number of scatterers: 9120 At special positions: 0 Unit cell: (99.91, 93.73, 101.97, 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 93 16.00 O 1920 8.00 N 1428 7.00 C 5679 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=21, symmetry=0 Simple disulfide: pdb=" SG CYS A 86 " - pdb=" SG CYS A 231 " distance=2.04 Simple disulfide: pdb=" SG CYS A 118 " - pdb=" SG CYS A 155 " distance=2.02 Simple disulfide: pdb=" SG CYS A 180 " - pdb=" SG CYS A 212 " distance=2.03 Simple disulfide: pdb=" SG CYS A 207 " - pdb=" SG CYS a 360 " distance=2.03 Simple disulfide: pdb=" SG CYS a 279 " - pdb=" SG CYS a 292 " distance=2.03 Simple disulfide: pdb=" SG CYS a 301 " - pdb=" SG CYS a 310 " distance=2.03 Simple disulfide: pdb=" SG CYS a 364 " - pdb=" SG CYS a 385 " distance=2.02 Simple disulfide: pdb=" SG CYS B 86 " - pdb=" SG CYS B 231 " distance=2.04 Simple disulfide: pdb=" SG CYS B 118 " - pdb=" SG CYS B 155 " distance=2.02 Simple disulfide: pdb=" SG CYS B 180 " - pdb=" SG CYS B 212 " distance=2.03 Simple disulfide: pdb=" SG CYS B 207 " - pdb=" SG CYS b 360 " distance=2.03 Simple disulfide: pdb=" SG CYS b 279 " - pdb=" SG CYS b 292 " distance=2.03 Simple disulfide: pdb=" SG CYS b 301 " - pdb=" SG CYS b 310 " distance=2.03 Simple disulfide: pdb=" SG CYS b 364 " - pdb=" SG CYS b 385 " distance=2.02 Simple disulfide: pdb=" SG CYS C 86 " - pdb=" SG CYS C 231 " distance=2.04 Simple disulfide: pdb=" SG CYS C 118 " - pdb=" SG CYS C 155 " distance=2.02 Simple disulfide: pdb=" SG CYS C 180 " - pdb=" SG CYS C 212 " distance=2.03 Simple disulfide: pdb=" SG CYS C 207 " - pdb=" SG CYS c 360 " distance=2.03 Simple disulfide: pdb=" SG CYS c 279 " - pdb=" SG CYS c 292 " distance=2.04 Simple disulfide: pdb=" SG CYS c 301 " - pdb=" SG CYS c 310 " distance=2.03 Simple disulfide: pdb=" SG CYS c 364 " - pdb=" SG CYS c 385 " distance=2.02 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 ALPHA1-3 " BMA J 3 " - " MAN J 4 " " BMA S 3 " - " MAN S 4 " " BMA e 3 " - " MAN e 4 " ALPHA1-6 " BMA J 3 " - " MAN J 5 " " BMA S 3 " - " MAN S 5 " " BMA e 3 " - " MAN e 5 " BETA1-4 " NAG D 1 " - " NAG D 2 " " NAG E 1 " - " NAG E 2 " " NAG F 1 " - " NAG F 2 " " NAG F 2 " - " BMA F 3 " " NAG G 1 " - " NAG G 2 " " NAG H 1 " - " NAG H 2 " " NAG I 1 " - " NAG I 2 " " NAG J 1 " - " NAG J 2 " " NAG J 2 " - " BMA J 3 " " NAG K 1 " - " NAG K 2 " " NAG L 1 " - " NAG L 2 " " NAG M 1 " - " NAG M 2 " " NAG N 1 " - " NAG N 2 " " NAG O 1 " - " NAG O 2 " " NAG O 2 " - " BMA O 3 " " NAG P 1 " - " NAG P 2 " " NAG Q 1 " - " NAG Q 2 " " NAG R 1 " - " NAG R 2 " " NAG S 1 " - " NAG S 2 " " NAG S 2 " - " BMA S 3 " " NAG T 1 " - " NAG T 2 " " NAG U 1 " - " NAG U 2 " " NAG V 1 " - " NAG V 2 " " NAG W 1 " - " NAG W 2 " " NAG X 1 " - " NAG X 2 " " NAG X 2 " - " BMA X 3 " " NAG Y 1 " - " NAG Y 2 " " NAG Z 1 " - " NAG Z 2 " " NAG d 1 " - " NAG d 2 " " NAG e 1 " - " NAG e 2 " " NAG e 2 " - " BMA e 3 " " NAG f 1 " - " NAG f 2 " " NAG g 1 " - " NAG g 2 " BETA1-6 " NAG L 1 " - " FUC L 3 " ~> Even though FUC is an alpha isomer, a beta linkage is required... " NAG U 1 " - " FUC U 3 " " NAG g 1 " - " FUC g 3 " NAG-ASN " NAG A 701 " - " ASN A 167 " " NAG B 701 " - " ASN B 167 " " NAG C 701 " - " ASN C 167 " " NAG D 1 " - " ASN A 99 " " NAG E 1 " - " ASN A 224 " " NAG F 1 " - " ASN A 79 " " NAG G 1 " - " ASN A 89 " " NAG H 1 " - " ASN A 109 " " NAG I 1 " - " ASN A 119 " " NAG J 1 " - " ASN a 365 " " NAG K 1 " - " ASN a 373 " " NAG L 1 " - " ASN a 395 " " NAG M 1 " - " ASN B 99 " " NAG N 1 " - " ASN B 224 " " NAG O 1 " - " ASN B 79 " " NAG P 1 " - " ASN B 89 " " NAG Q 1 " - " ASN B 109 " " NAG R 1 " - " ASN B 119 " " NAG S 1 " - " ASN b 365 " " NAG T 1 " - " ASN b 373 " " NAG U 1 " - " ASN b 395 " " NAG V 1 " - " ASN C 99 " " NAG W 1 " - " ASN C 224 " " NAG X 1 " - " ASN C 79 " " NAG Y 1 " - " ASN C 89 " " NAG Z 1 " - " ASN C 109 " " NAG a 701 " - " ASN a 390 " " NAG b 701 " - " ASN b 390 " " NAG c 701 " - " ASN c 390 " " NAG d 1 " - " ASN C 119 " " NAG e 1 " - " ASN c 365 " " NAG f 1 " - " ASN c 373 " " NAG g 1 " - " ASN c 395 " Time building additional restraints: 0.93 Conformation dependent library (CDL) restraints added in 230.1 milliseconds 1968 Ramachandran restraints generated. 984 Oldfield, 0 Emsley, 984 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1908 Finding SS restraints... Secondary structure from input PDB file: 39 helices and 12 sheets defined 42.3% alpha, 14.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.31 Creating SS restraints... Processing helix chain 'A' and resid 74 through 79 removed outlier: 3.951A pdb=" N THR A 77 " --> pdb=" O ASN A 74 " (cutoff:3.500A) Processing helix chain 'A' and resid 121 through 126 Processing helix chain 'A' and resid 130 through 144 Processing helix chain 'A' and resid 182 through 194 Processing helix chain 'A' and resid 238 through 247 Processing helix chain 'a' and resid 269 through 274 removed outlier: 3.822A pdb=" N ASP a 273 " --> pdb=" O SER a 269 " (cutoff:3.500A) removed outlier: 4.160A pdb=" N THR a 274 " --> pdb=" O GLU a 270 " (cutoff:3.500A) No H-bonds generated for 'chain 'a' and resid 269 through 274' Processing helix chain 'a' and resid 281 through 285 Processing helix chain 'a' and resid 294 through 299 Processing helix chain 'a' and resid 300 through 303 Processing helix chain 'a' and resid 307 through 326 Processing helix chain 'a' and resid 333 through 345 removed outlier: 4.878A pdb=" N ASN a 342 " --> pdb=" O ASN a 338 " (cutoff:3.500A) removed outlier: 4.774A pdb=" N ALA a 343 " --> pdb=" O LYS a 339 " (cutoff:3.500A) Processing helix chain 'a' and resid 346 through 359 removed outlier: 3.529A pdb=" N ILE a 350 " --> pdb=" O ASN a 346 " (cutoff:3.500A) Processing helix chain 'a' and resid 399 through 423 Processing helix chain 'B' and resid 74 through 79 removed outlier: 3.950A pdb=" N THR B 77 " --> pdb=" O ASN B 74 " (cutoff:3.500A) Processing helix chain 'B' and resid 121 through 126 Processing helix chain 'B' and resid 130 through 144 Processing helix chain 'B' and resid 182 through 194 Processing helix chain 'B' and resid 238 through 247 Processing helix chain 'b' and resid 269 through 274 removed outlier: 3.822A pdb=" N ASP b 273 " --> pdb=" O SER b 269 " (cutoff:3.500A) removed outlier: 4.160A pdb=" N THR b 274 " --> pdb=" O GLU b 270 " (cutoff:3.500A) No H-bonds generated for 'chain 'b' and resid 269 through 274' Processing helix chain 'b' and resid 281 through 285 Processing helix chain 'b' and resid 294 through 299 Processing helix chain 'b' and resid 300 through 303 Processing helix chain 'b' and resid 307 through 326 Processing helix chain 'b' and resid 333 through 345 removed outlier: 4.878A pdb=" N ASN b 342 " --> pdb=" O ASN b 338 " (cutoff:3.500A) removed outlier: 4.773A pdb=" N ALA b 343 " --> pdb=" O LYS b 339 " (cutoff:3.500A) Processing helix chain 'b' and resid 346 through 359 removed outlier: 3.529A pdb=" N ILE b 350 " --> pdb=" O ASN b 346 " (cutoff:3.500A) Processing helix chain 'b' and resid 399 through 423 Processing helix chain 'C' and resid 74 through 79 removed outlier: 3.951A pdb=" N THR C 77 " --> pdb=" O ASN C 74 " (cutoff:3.500A) Processing helix chain 'C' and resid 121 through 126 Processing helix chain 'C' and resid 130 through 144 Processing helix chain 'C' and resid 182 through 194 Processing helix chain 'C' and resid 238 through 247 Processing helix chain 'c' and resid 269 through 274 removed outlier: 3.822A pdb=" N ASP c 273 " --> pdb=" O SER c 269 " (cutoff:3.500A) removed outlier: 4.159A pdb=" N THR c 274 " --> pdb=" O GLU c 270 " (cutoff:3.500A) No H-bonds generated for 'chain 'c' and resid 269 through 274' Processing helix chain 'c' and resid 281 through 285 Processing helix chain 'c' and resid 294 through 299 Processing helix chain 'c' and resid 300 through 303 Processing helix chain 'c' and resid 307 through 326 Processing helix chain 'c' and resid 333 through 345 removed outlier: 4.878A pdb=" N ASN c 342 " --> pdb=" O ASN c 338 " (cutoff:3.500A) removed outlier: 4.773A pdb=" N ALA c 343 " --> pdb=" O LYS c 339 " (cutoff:3.500A) Processing helix chain 'c' and resid 346 through 359 removed outlier: 3.530A pdb=" N ILE c 350 " --> pdb=" O ASN c 346 " (cutoff:3.500A) Processing helix chain 'c' and resid 399 through 423 Processing sheet with id=AA1, first strand: chain 'A' and resid 61 through 62 Processing sheet with id=AA2, first strand: chain 'A' and resid 84 through 89 removed outlier: 6.667A pdb=" N HIS A 92 " --> pdb=" O LYS A 88 " (cutoff:3.500A) removed outlier: 3.975A pdb=" N GLY A 102 " --> pdb=" O THR A 225 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'a' and resid 278 through 280 Processing sheet with id=AA4, first strand: chain 'a' and resid 388 through 389 Processing sheet with id=AA5, first strand: chain 'B' and resid 61 through 62 Processing sheet with id=AA6, first strand: chain 'B' and resid 84 through 89 removed outlier: 6.666A pdb=" N HIS B 92 " --> pdb=" O LYS B 88 " (cutoff:3.500A) removed outlier: 3.975A pdb=" N GLY B 102 " --> pdb=" O THR B 225 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'b' and resid 278 through 280 Processing sheet with id=AA8, first strand: chain 'b' and resid 388 through 389 Processing sheet with id=AA9, first strand: chain 'C' and resid 61 through 62 Processing sheet with id=AB1, first strand: chain 'C' and resid 84 through 89 removed outlier: 6.666A pdb=" N HIS C 92 " --> pdb=" O LYS C 88 " (cutoff:3.500A) removed outlier: 3.975A pdb=" N GLY C 102 " --> pdb=" O THR C 225 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'c' and resid 278 through 280 Processing sheet with id=AB3, first strand: chain 'c' and resid 388 through 389 384 hydrogen bonds defined for protein. 1035 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: 1.01 Time building geometry restraints manager: 1.08 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.33: 2406 1.33 - 1.47: 2804 1.47 - 1.61: 3934 1.61 - 1.75: 16 1.75 - 1.88: 134 Bond restraints: 9294 Sorted by residual: bond pdb=" CG TYR C 150 " pdb=" CD2 TYR C 150 " ideal model delta sigma weight residual 1.389 1.489 -0.100 2.10e-02 2.27e+03 2.27e+01 bond pdb=" CG TYR A 150 " pdb=" CD2 TYR A 150 " ideal model delta sigma weight residual 1.389 1.489 -0.100 2.10e-02 2.27e+03 2.25e+01 bond pdb=" CG TYR B 150 " pdb=" CD2 TYR B 150 " ideal model delta sigma weight residual 1.389 1.488 -0.099 2.10e-02 2.27e+03 2.24e+01 bond pdb=" CB ASN B 178 " pdb=" CG ASN B 178 " ideal model delta sigma weight residual 1.516 1.631 -0.115 2.50e-02 1.60e+03 2.12e+01 bond pdb=" CB ASN C 178 " pdb=" CG ASN C 178 " ideal model delta sigma weight residual 1.516 1.631 -0.115 2.50e-02 1.60e+03 2.12e+01 ... (remaining 9289 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.11: 10170 2.11 - 4.21: 1968 4.21 - 6.32: 332 6.32 - 8.43: 88 8.43 - 10.54: 9 Bond angle restraints: 12567 Sorted by residual: angle pdb=" N ASN A 224 " pdb=" CA ASN A 224 " pdb=" CB ASN A 224 " ideal model delta sigma weight residual 110.26 120.80 -10.54 1.43e+00 4.89e-01 5.43e+01 angle pdb=" N ASN C 224 " pdb=" CA ASN C 224 " pdb=" CB ASN C 224 " ideal model delta sigma weight residual 110.26 120.78 -10.52 1.43e+00 4.89e-01 5.41e+01 angle pdb=" N ASN B 224 " pdb=" CA ASN B 224 " pdb=" CB ASN B 224 " ideal model delta sigma weight residual 110.26 120.77 -10.51 1.43e+00 4.89e-01 5.40e+01 angle pdb=" N VAL C 65 " pdb=" CA VAL C 65 " pdb=" C VAL C 65 " ideal model delta sigma weight residual 113.43 121.13 -7.70 1.09e+00 8.42e-01 5.00e+01 angle pdb=" N VAL B 65 " pdb=" CA VAL B 65 " pdb=" C VAL B 65 " ideal model delta sigma weight residual 113.43 121.11 -7.68 1.09e+00 8.42e-01 4.96e+01 ... (remaining 12562 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 13.35: 4623 13.35 - 26.70: 267 26.70 - 40.05: 45 40.05 - 53.40: 27 53.40 - 66.75: 15 Dihedral angle restraints: 4977 sinusoidal: 2019 harmonic: 2958 Sorted by residual: dihedral pdb=" CB CYS B 86 " pdb=" SG CYS B 86 " pdb=" SG CYS B 231 " pdb=" CB CYS B 231 " ideal model delta sinusoidal sigma weight residual 93.00 155.46 -62.46 1 1.00e+01 1.00e-02 5.16e+01 dihedral pdb=" CB CYS C 86 " pdb=" SG CYS C 86 " pdb=" SG CYS C 231 " pdb=" CB CYS C 231 " ideal model delta sinusoidal sigma weight residual 93.00 155.45 -62.45 1 1.00e+01 1.00e-02 5.16e+01 dihedral pdb=" CB CYS A 86 " pdb=" SG CYS A 86 " pdb=" SG CYS A 231 " pdb=" CB CYS A 231 " ideal model delta sinusoidal sigma weight residual 93.00 155.45 -62.45 1 1.00e+01 1.00e-02 5.16e+01 ... (remaining 4974 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.294: 1474 0.294 - 0.589: 119 0.589 - 0.883: 3 0.883 - 1.177: 0 1.177 - 1.472: 3 Chirality restraints: 1599 Sorted by residual: chirality pdb=" C1 NAG I 2 " pdb=" O4 NAG I 1 " pdb=" C2 NAG I 2 " pdb=" O5 NAG I 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.63 0.23 2.00e-02 2.50e+03 1.36e+02 chirality pdb=" C1 NAG d 2 " pdb=" O4 NAG d 1 " pdb=" C2 NAG d 2 " pdb=" O5 NAG d 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.63 0.23 2.00e-02 2.50e+03 1.36e+02 chirality pdb=" C1 NAG R 2 " pdb=" O4 NAG R 1 " pdb=" C2 NAG R 2 " pdb=" O5 NAG R 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.63 0.23 2.00e-02 2.50e+03 1.36e+02 ... (remaining 1596 not shown) Planarity restraints: 1515 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 NAG N 2 " 0.173 2.00e-02 2.50e+03 1.43e-01 2.56e+02 pdb=" C7 NAG N 2 " -0.046 2.00e-02 2.50e+03 pdb=" C8 NAG N 2 " 0.126 2.00e-02 2.50e+03 pdb=" N2 NAG N 2 " -0.233 2.00e-02 2.50e+03 pdb=" O7 NAG N 2 " -0.019 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG E 2 " 0.173 2.00e-02 2.50e+03 1.43e-01 2.56e+02 pdb=" C7 NAG E 2 " -0.046 2.00e-02 2.50e+03 pdb=" C8 NAG E 2 " 0.126 2.00e-02 2.50e+03 pdb=" N2 NAG E 2 " -0.233 2.00e-02 2.50e+03 pdb=" O7 NAG E 2 " -0.019 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG W 2 " 0.173 2.00e-02 2.50e+03 1.43e-01 2.56e+02 pdb=" C7 NAG W 2 " -0.046 2.00e-02 2.50e+03 pdb=" C8 NAG W 2 " 0.126 2.00e-02 2.50e+03 pdb=" N2 NAG W 2 " -0.233 2.00e-02 2.50e+03 pdb=" O7 NAG W 2 " -0.019 2.00e-02 2.50e+03 ... (remaining 1512 not shown) Histogram of nonbonded interaction distances: 2.48 - 2.96: 4657 2.96 - 3.45: 8715 3.45 - 3.93: 15253 3.93 - 4.42: 17664 4.42 - 4.90: 26323 Nonbonded interactions: 72612 Sorted by model distance: nonbonded pdb=" NZ LYS a 304 " pdb=" OE2 GLU c 303 " model vdw 2.477 3.120 nonbonded pdb=" OE2 GLU b 303 " pdb=" NZ LYS c 304 " model vdw 2.477 3.120 nonbonded pdb=" OE2 GLU a 303 " pdb=" NZ LYS b 304 " model vdw 2.477 3.120 nonbonded pdb=" OG SER b 367 " pdb=" N LYS b 368 " model vdw 2.486 3.120 nonbonded pdb=" OG SER c 367 " pdb=" N LYS c 368 " model vdw 2.487 3.120 ... (remaining 72607 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: 0.02 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' } ncs_group { reference = chain 'D' selection = chain 'E' selection = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'K' selection = chain 'M' selection = chain 'N' selection = chain 'P' selection = chain 'Q' selection = chain 'R' selection = chain 'T' selection = chain 'V' selection = chain 'W' selection = chain 'Y' selection = chain 'Z' selection = chain 'd' selection = chain 'f' } ncs_group { reference = (chain 'F' and resid 1 through 2) selection = (chain 'L' and resid 1 through 2) selection = (chain 'O' and resid 1 through 2) selection = (chain 'U' and resid 1 through 2) selection = (chain 'X' and resid 1 through 2) selection = (chain 'g' and resid 1 through 2) } ncs_group { reference = chain 'J' selection = chain 'S' selection = chain 'e' } ncs_group { reference = chain 'a' selection = chain 'b' selection = chain 'c' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.560 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: 0.080 Check model and map are aligned: 0.030 Set scattering table: 0.010 Process input model: 7.240 Find NCS groups from input model: 0.220 Set up NCS constraints: 0.020 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:0.930 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 9.100 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8102 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 : 0.025 0.115 9390 Z= 1.316 Angle : 1.889 15.662 12834 Z= 1.159 Chirality : 0.166 1.472 1599 Planarity : 0.012 0.143 1482 Dihedral : 9.972 66.753 3006 Min Nonbonded Distance : 2.477 Molprobity Statistics. All-atom Clashscore : 1.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.83 % Favored : 98.17 % Rotamer: Outliers : 0.00 % Allowed : 1.32 % Favored : 98.68 % Cbeta Deviations : 0.31 % 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: 0.20 (0.24), residues: 984 helix: 0.43 (0.24), residues: 354 sheet: 0.82 (0.44), residues: 141 loop : -0.19 (0.25), residues: 489 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG a 356 TYR 0.051 0.009 TYR b 363 PHE 0.016 0.005 PHE a 399 TRP 0.031 0.006 TRP a 283 HIS 0.006 0.002 HIS B 124 Details of bonding type rmsd/Z covalent geometry : bond 0.02384 / 1.28 ( 9294) covalent geometry : angle 1.79736 / 1.15 (12567) SS BOND : bond 0.00890 / 0.58 ( 21) SS BOND : angle 2.81040 / 1.73 ( 42) hydrogen bonds : bond 0.16051 / 10.62 ( 384) hydrogen bonds : angle 6.47171 / 4.51 ( 1035) link_ALPHA1-3 : bond 0.08716 / 4.37 ( 3) link_ALPHA1-3 : angle 4.33137 / 2.03 ( 9) link_ALPHA1-6 : bond 0.07039 / 3.53 ( 3) link_ALPHA1-6 : angle 3.83579 / 1.79 ( 9) link_BETA1-4 : bond 0.06947 / 4.29 ( 33) link_BETA1-4 : angle 5.62681 / 3.61 ( 99) link_BETA1-6 : bond 0.06593 / 3.30 ( 3) link_BETA1-6 : angle 4.74660 / 2.23 ( 9) link_NAG-ASN : bond 0.07397 / 4.25 ( 33) link_NAG-ASN : angle 3.52360 / 2.33 ( 99) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1968 Ramachandran restraints generated. 984 Oldfield, 0 Emsley, 984 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1968 Ramachandran restraints generated. 984 Oldfield, 0 Emsley, 984 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 469 residues out of total 912 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 469 time to evaluate : 0.279 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 130 ASP cc_start: 0.8548 (t0) cc_final: 0.8037 (t0) REVERT: A 220 LEU cc_start: 0.9229 (tp) cc_final: 0.8983 (tt) REVERT: a 311 ASP cc_start: 0.9105 (m-30) cc_final: 0.8877 (m-30) REVERT: a 313 LEU cc_start: 0.9765 (tp) cc_final: 0.9549 (tp) REVERT: a 357 ASP cc_start: 0.9090 (t70) cc_final: 0.8867 (t0) REVERT: a 408 ASP cc_start: 0.8719 (m-30) cc_final: 0.8201 (m-30) REVERT: a 409 ASN cc_start: 0.9153 (m-40) cc_final: 0.8831 (t0) REVERT: a 416 GLN cc_start: 0.9186 (mm-40) cc_final: 0.8890 (mt0) REVERT: a 417 LYS cc_start: 0.9380 (mttt) cc_final: 0.9012 (ttpp) REVERT: B 78 LEU cc_start: 0.9633 (mt) cc_final: 0.9382 (mp) REVERT: B 130 ASP cc_start: 0.8480 (t0) cc_final: 0.8030 (t0) REVERT: B 220 LEU cc_start: 0.9271 (tp) cc_final: 0.9005 (tt) REVERT: b 267 SER cc_start: 0.8975 (p) cc_final: 0.8589 (t) REVERT: b 311 ASP cc_start: 0.9045 (m-30) cc_final: 0.8821 (m-30) REVERT: b 313 LEU cc_start: 0.9758 (tp) cc_final: 0.9489 (tp) REVERT: b 346 ASN cc_start: 0.9314 (t0) cc_final: 0.9065 (t0) REVERT: b 357 ASP cc_start: 0.9077 (t70) cc_final: 0.8848 (t0) REVERT: b 408 ASP cc_start: 0.8772 (m-30) cc_final: 0.8414 (m-30) REVERT: b 409 ASN cc_start: 0.9123 (m-40) cc_final: 0.8144 (m-40) REVERT: b 411 ILE cc_start: 0.9472 (mt) cc_final: 0.9252 (mm) REVERT: b 416 GLN cc_start: 0.9212 (mm-40) cc_final: 0.8979 (mm-40) REVERT: b 417 LYS cc_start: 0.9354 (mttt) cc_final: 0.9041 (ttpp) REVERT: C 78 LEU cc_start: 0.9615 (mt) cc_final: 0.9394 (mp) REVERT: C 130 ASP cc_start: 0.8407 (t0) cc_final: 0.7960 (t0) REVERT: C 220 LEU cc_start: 0.9267 (tp) cc_final: 0.9025 (tt) REVERT: c 313 LEU cc_start: 0.9775 (tp) cc_final: 0.9493 (tp) REVERT: c 346 ASN cc_start: 0.9278 (t0) cc_final: 0.8887 (t0) REVERT: c 347 ASP cc_start: 0.8914 (p0) cc_final: 0.8519 (p0) REVERT: c 409 ASN cc_start: 0.9162 (m-40) cc_final: 0.8244 (m-40) REVERT: c 416 GLN cc_start: 0.9219 (mm-40) cc_final: 0.8838 (tp-100) REVERT: c 417 LYS cc_start: 0.9356 (mttt) cc_final: 0.8994 (ttpp) outliers start: 0 outliers final: 0 residues processed: 469 average time/residue: 0.0792 time to fit residues: 50.1563 Evaluate side-chains 283 residues out of total 912 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 283 time to evaluate : 0.233 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 49 optimal weight: 0.8980 chunk 97 optimal weight: 0.9990 chunk 53 optimal weight: 0.9980 chunk 5 optimal weight: 20.0000 chunk 33 optimal weight: 0.8980 chunk 65 optimal weight: 2.9990 chunk 62 optimal weight: 0.9980 chunk 51 optimal weight: 8.9990 chunk 38 optimal weight: 9.9990 chunk 61 optimal weight: 0.8980 chunk 45 optimal weight: 1.9990 overall best weight: 0.9380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 158 ASN A 230 HIS B 158 ASN B 230 HIS B 232 GLN b 406 GLN C 158 ASN C 230 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3411 r_free = 0.3411 target = 0.076720 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2981 r_free = 0.2981 target = 0.057260 restraints weight = 29131.971| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3038 r_free = 0.3038 target = 0.059812 restraints weight = 15320.334| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3078 r_free = 0.3078 target = 0.061575 restraints weight = 10540.064| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3102 r_free = 0.3102 target = 0.062699 restraints weight = 8363.727| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3119 r_free = 0.3119 target = 0.063465 restraints weight = 7198.375| |-----------------------------------------------------------------------------| r_work (final): 0.3119 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8035 moved from start: 0.4605 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 9390 Z= 0.203 Angle : 1.018 13.906 12834 Z= 0.491 Chirality : 0.050 0.322 1599 Planarity : 0.005 0.032 1482 Dihedral : 5.959 45.023 1074 Min Nonbonded Distance : 2.432 Molprobity Statistics. All-atom Clashscore : 10.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.03 % Favored : 97.97 % Rotamer: Outliers : 5.04 % Allowed : 17.98 % Favored : 76.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.10 % 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: 0.36 (0.25), residues: 984 helix: 1.17 (0.26), residues: 366 sheet: 1.86 (0.50), residues: 108 loop : -0.83 (0.23), residues: 510 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG a 325 TYR 0.026 0.002 TYR C 166 PHE 0.027 0.003 PHE A 157 TRP 0.015 0.002 TRP c 386 HIS 0.007 0.001 HIS C 124 Details of bonding type rmsd/Z covalent geometry : bond 0.00421 / 0.20 ( 9294) covalent geometry : angle 0.92515 / 0.47 (12567) SS BOND : bond 0.00510 / 0.33 ( 21) SS BOND : angle 2.85876 / 1.71 ( 42) hydrogen bonds : bond 0.05874 / 3.92 ( 384) hydrogen bonds : angle 5.15762 / 3.57 ( 1035) link_ALPHA1-3 : bond 0.00491 / 0.25 ( 3) link_ALPHA1-3 : angle 1.71003 / 1.00 ( 9) link_ALPHA1-6 : bond 0.01215 / 0.61 ( 3) link_ALPHA1-6 : angle 1.51031 / 0.83 ( 9) link_BETA1-4 : bond 0.01563 / 1.01 ( 33) link_BETA1-4 : angle 3.58892 / 2.37 ( 99) link_BETA1-6 : bond 0.00520 / 0.26 ( 3) link_BETA1-6 : angle 1.22056 / 0.73 ( 9) link_NAG-ASN : bond 0.00297 / 0.20 ( 33) link_NAG-ASN : angle 2.93624 / 1.91 ( 99) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1968 Ramachandran restraints generated. 984 Oldfield, 0 Emsley, 984 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1968 Ramachandran restraints generated. 984 Oldfield, 0 Emsley, 984 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 355 residues out of total 912 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 309 time to evaluate : 0.353 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 72 GLU cc_start: 0.8085 (tt0) cc_final: 0.7847 (tt0) REVERT: A 130 ASP cc_start: 0.8488 (t0) cc_final: 0.7910 (t70) REVERT: a 300 LYS cc_start: 0.9182 (mmtm) cc_final: 0.8540 (mptt) REVERT: a 307 GLU cc_start: 0.8814 (mm-30) cc_final: 0.8591 (mm-30) REVERT: a 311 ASP cc_start: 0.9208 (m-30) cc_final: 0.8967 (m-30) REVERT: a 313 LEU cc_start: 0.9764 (tp) cc_final: 0.9381 (tp) REVERT: a 357 ASP cc_start: 0.9114 (t70) cc_final: 0.8583 (t0) REVERT: a 405 GLN cc_start: 0.9123 (tm-30) cc_final: 0.8788 (tm-30) REVERT: a 409 ASN cc_start: 0.8788 (m-40) cc_final: 0.8556 (m-40) REVERT: a 410 MET cc_start: 0.8584 (tpp) cc_final: 0.7911 (tpp) REVERT: a 413 GLU cc_start: 0.8402 (pp20) cc_final: 0.8014 (pp20) REVERT: a 416 GLN cc_start: 0.8996 (mm-40) cc_final: 0.8710 (mm-40) REVERT: B 130 ASP cc_start: 0.8242 (t0) cc_final: 0.7695 (t0) REVERT: b 261 THR cc_start: 0.8221 (p) cc_final: 0.7996 (p) REVERT: b 307 GLU cc_start: 0.8738 (mm-30) cc_final: 0.8227 (mp0) REVERT: b 311 ASP cc_start: 0.9193 (m-30) cc_final: 0.8941 (m-30) REVERT: b 313 LEU cc_start: 0.9775 (tp) cc_final: 0.9411 (tp) REVERT: b 346 ASN cc_start: 0.9352 (t0) cc_final: 0.9144 (t0) REVERT: b 357 ASP cc_start: 0.9071 (t70) cc_final: 0.8555 (t0) REVERT: b 369 TYR cc_start: 0.9279 (m-10) cc_final: 0.9003 (m-80) REVERT: b 405 GLN cc_start: 0.9074 (tm-30) cc_final: 0.8616 (tm-30) REVERT: b 410 MET cc_start: 0.8929 (OUTLIER) cc_final: 0.8368 (tpp) REVERT: b 413 GLU cc_start: 0.8819 (OUTLIER) cc_final: 0.8580 (pm20) REVERT: b 416 GLN cc_start: 0.9074 (mm-40) cc_final: 0.8863 (mm110) REVERT: C 72 GLU cc_start: 0.8185 (tt0) cc_final: 0.7918 (tt0) REVERT: C 76 GLU cc_start: 0.9118 (tt0) cc_final: 0.8900 (tt0) REVERT: C 100 GLU cc_start: 0.7520 (mm-30) cc_final: 0.7285 (mm-30) REVERT: C 130 ASP cc_start: 0.8204 (t0) cc_final: 0.7668 (t70) REVERT: C 227 TRP cc_start: 0.7092 (t-100) cc_final: 0.6797 (t-100) REVERT: c 278 TYR cc_start: 0.8303 (t80) cc_final: 0.7856 (t80) REVERT: c 300 LYS cc_start: 0.9151 (mmtm) cc_final: 0.8652 (mptt) REVERT: c 306 ASP cc_start: 0.8715 (t0) cc_final: 0.8315 (t70) REVERT: c 307 GLU cc_start: 0.8779 (mm-30) cc_final: 0.8483 (mm-30) REVERT: c 313 LEU cc_start: 0.9764 (tp) cc_final: 0.9367 (tp) REVERT: c 408 ASP cc_start: 0.8989 (m-30) cc_final: 0.8281 (m-30) REVERT: c 409 ASN cc_start: 0.8561 (m-40) cc_final: 0.8326 (m-40) outliers start: 46 outliers final: 18 residues processed: 331 average time/residue: 0.0727 time to fit residues: 33.7056 Evaluate side-chains 290 residues out of total 912 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 270 time to evaluate : 0.204 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 86 CYS Chi-restraints excluded: chain A residue 126 LYS Chi-restraints excluded: chain A residue 156 ASP Chi-restraints excluded: chain a residue 269 SER Chi-restraints excluded: chain a residue 325 ARG Chi-restraints excluded: chain a residue 337 ILE Chi-restraints excluded: chain a residue 361 ILE Chi-restraints excluded: chain a residue 421 GLU Chi-restraints excluded: chain B residue 86 CYS Chi-restraints excluded: chain B residue 207 CYS Chi-restraints excluded: chain B residue 239 ILE Chi-restraints excluded: chain b residue 269 SER Chi-restraints excluded: chain b residue 337 ILE Chi-restraints excluded: chain b residue 385 CYS Chi-restraints excluded: chain b residue 410 MET Chi-restraints excluded: chain b residue 413 GLU Chi-restraints excluded: chain C residue 86 CYS Chi-restraints excluded: chain c residue 269 SER Chi-restraints excluded: chain c residue 337 ILE Chi-restraints excluded: chain c residue 421 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 61 optimal weight: 3.9990 chunk 55 optimal weight: 2.9990 chunk 30 optimal weight: 0.8980 chunk 90 optimal weight: 0.8980 chunk 80 optimal weight: 3.9990 chunk 22 optimal weight: 0.6980 chunk 85 optimal weight: 0.9990 chunk 58 optimal weight: 9.9990 chunk 36 optimal weight: 6.9990 chunk 17 optimal weight: 6.9990 chunk 12 optimal weight: 6.9990 overall best weight: 1.2984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 185 ASN C 185 ASN c 416 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3382 r_free = 0.3382 target = 0.075555 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.2960 r_free = 0.2960 target = 0.056665 restraints weight = 29133.738| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 22)----------------| | r_work = 0.3017 r_free = 0.3017 target = 0.059082 restraints weight = 15693.876| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 47)----------------| | r_work = 0.3056 r_free = 0.3056 target = 0.060755 restraints weight = 10880.806| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3081 r_free = 0.3081 target = 0.061884 restraints weight = 8658.381| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3098 r_free = 0.3098 target = 0.062633 restraints weight = 7452.328| |-----------------------------------------------------------------------------| r_work (final): 0.3095 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8122 moved from start: 0.5296 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 9390 Z= 0.174 Angle : 0.873 11.002 12834 Z= 0.421 Chirality : 0.046 0.270 1599 Planarity : 0.004 0.031 1482 Dihedral : 5.722 27.693 1074 Min Nonbonded Distance : 2.492 Molprobity Statistics. All-atom Clashscore : 10.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.44 % Favored : 97.56 % Rotamer: Outliers : 5.37 % Allowed : 20.83 % Favored : 73.79 % 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: 0.30 (0.25), residues: 984 helix: 1.20 (0.26), residues: 366 sheet: 0.91 (0.49), residues: 117 loop : -0.72 (0.24), residues: 501 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG a 325 TYR 0.024 0.002 TYR B 241 PHE 0.025 0.003 PHE B 157 TRP 0.028 0.002 TRP B 227 HIS 0.002 0.001 HIS b 354 Details of bonding type rmsd/Z covalent geometry : bond 0.00364 / 0.17 ( 9294) covalent geometry : angle 0.80882 / 0.41 (12567) SS BOND : bond 0.00379 / 0.25 ( 21) SS BOND : angle 1.42270 / 0.84 ( 42) hydrogen bonds : bond 0.05129 / 3.39 ( 384) hydrogen bonds : angle 4.73785 / 3.25 ( 1035) link_ALPHA1-3 : bond 0.00682 / 0.34 ( 3) link_ALPHA1-3 : angle 1.39765 / 0.86 ( 9) link_ALPHA1-6 : bond 0.01082 / 0.54 ( 3) link_ALPHA1-6 : angle 1.41346 / 0.76 ( 9) link_BETA1-4 : bond 0.01401 / 0.91 ( 33) link_BETA1-4 : angle 3.07971 / 1.99 ( 99) link_BETA1-6 : bond 0.00384 / 0.19 ( 3) link_BETA1-6 : angle 1.21699 / 0.74 ( 9) link_NAG-ASN : bond 0.00373 / 0.22 ( 33) link_NAG-ASN : angle 2.21181 / 1.46 ( 99) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1968 Ramachandran restraints generated. 984 Oldfield, 0 Emsley, 984 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1968 Ramachandran restraints generated. 984 Oldfield, 0 Emsley, 984 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 326 residues out of total 912 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 277 time to evaluate : 0.314 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 75 MET cc_start: 0.8484 (mtp) cc_final: 0.8171 (mtp) REVERT: A 76 GLU cc_start: 0.9042 (tt0) cc_final: 0.8135 (tm-30) REVERT: A 130 ASP cc_start: 0.8412 (t0) cc_final: 0.7841 (t70) REVERT: a 261 THR cc_start: 0.8111 (p) cc_final: 0.7875 (p) REVERT: a 300 LYS cc_start: 0.9293 (mmtm) cc_final: 0.8708 (mptt) REVERT: a 313 LEU cc_start: 0.9708 (tp) cc_final: 0.9168 (tp) REVERT: a 357 ASP cc_start: 0.9185 (t70) cc_final: 0.8652 (t0) REVERT: a 417 LYS cc_start: 0.9179 (pttp) cc_final: 0.8897 (pttp) REVERT: B 130 ASP cc_start: 0.8203 (t0) cc_final: 0.7746 (t0) REVERT: B 194 MET cc_start: 0.9400 (tpp) cc_final: 0.8701 (tpt) REVERT: B 227 TRP cc_start: 0.6788 (t-100) cc_final: 0.5958 (t60) REVERT: b 261 THR cc_start: 0.8398 (p) cc_final: 0.8182 (p) REVERT: b 306 ASP cc_start: 0.8257 (OUTLIER) cc_final: 0.7727 (m-30) REVERT: b 313 LEU cc_start: 0.9721 (tp) cc_final: 0.9330 (tp) REVERT: b 357 ASP cc_start: 0.9167 (t70) cc_final: 0.8662 (t0) REVERT: b 416 GLN cc_start: 0.9205 (mm-40) cc_final: 0.8999 (tp40) REVERT: C 96 MET cc_start: 0.7906 (ptp) cc_final: 0.7636 (ptp) REVERT: C 100 GLU cc_start: 0.7586 (mm-30) cc_final: 0.7310 (mm-30) REVERT: C 130 ASP cc_start: 0.8175 (t0) cc_final: 0.7612 (t70) REVERT: c 278 TYR cc_start: 0.8384 (t80) cc_final: 0.8071 (t80) REVERT: c 300 LYS cc_start: 0.9263 (mmtm) cc_final: 0.8781 (mptt) REVERT: c 313 LEU cc_start: 0.9732 (tp) cc_final: 0.9295 (tp) REVERT: c 348 GLN cc_start: 0.8828 (mp10) cc_final: 0.8356 (mp10) REVERT: c 410 MET cc_start: 0.8954 (tpp) cc_final: 0.8638 (tpp) outliers start: 49 outliers final: 25 residues processed: 308 average time/residue: 0.0726 time to fit residues: 31.0085 Evaluate side-chains 252 residues out of total 912 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 226 time to evaluate : 0.248 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 86 CYS Chi-restraints excluded: chain A residue 126 LYS Chi-restraints excluded: chain A residue 128 LEU Chi-restraints excluded: chain A residue 156 ASP Chi-restraints excluded: chain A residue 218 GLN Chi-restraints excluded: chain a residue 274 THR Chi-restraints excluded: chain a residue 325 ARG Chi-restraints excluded: chain a residue 337 ILE Chi-restraints excluded: chain a residue 361 ILE Chi-restraints excluded: chain a residue 421 GLU Chi-restraints excluded: chain B residue 86 CYS Chi-restraints excluded: chain B residue 128 LEU Chi-restraints excluded: chain B residue 207 CYS Chi-restraints excluded: chain B residue 218 GLN Chi-restraints excluded: chain b residue 306 ASP Chi-restraints excluded: chain b residue 337 ILE Chi-restraints excluded: chain b residue 349 LEU Chi-restraints excluded: chain b residue 385 CYS Chi-restraints excluded: chain b residue 403 ILE Chi-restraints excluded: chain C residue 86 CYS Chi-restraints excluded: chain C residue 128 LEU Chi-restraints excluded: chain c residue 269 SER Chi-restraints excluded: chain c residue 337 ILE Chi-restraints excluded: chain c residue 380 THR Chi-restraints excluded: chain c residue 385 CYS Chi-restraints excluded: chain c residue 421 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 29 optimal weight: 7.9990 chunk 69 optimal weight: 9.9990 chunk 88 optimal weight: 4.9990 chunk 95 optimal weight: 3.9990 chunk 60 optimal weight: 0.8980 chunk 62 optimal weight: 0.9990 chunk 65 optimal weight: 7.9990 chunk 12 optimal weight: 5.9990 chunk 45 optimal weight: 0.9990 chunk 42 optimal weight: 9.9990 chunk 25 optimal weight: 4.9990 overall best weight: 2.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 185 ASN ** b 405 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 406 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 = 0.3298 r_free = 0.3298 target = 0.072503 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2857 r_free = 0.2857 target = 0.052974 restraints weight = 30505.073| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.2914 r_free = 0.2914 target = 0.055297 restraints weight = 16598.641| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.2951 r_free = 0.2951 target = 0.056868 restraints weight = 11595.915| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.2976 r_free = 0.2976 target = 0.057947 restraints weight = 9298.710| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.2992 r_free = 0.2992 target = 0.058659 restraints weight = 8050.822| |-----------------------------------------------------------------------------| r_work (final): 0.2986 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8184 moved from start: 0.5662 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 9390 Z= 0.194 Angle : 0.854 10.242 12834 Z= 0.409 Chirality : 0.046 0.275 1599 Planarity : 0.004 0.036 1482 Dihedral : 5.561 24.655 1074 Min Nonbonded Distance : 2.424 Molprobity Statistics. All-atom Clashscore : 12.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.05 % Favored : 96.95 % Rotamer: Outliers : 5.48 % Allowed : 21.27 % Favored : 73.25 % 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: 0.43 (0.25), residues: 984 helix: 1.33 (0.27), residues: 372 sheet: 0.91 (0.49), residues: 117 loop : -0.68 (0.24), residues: 495 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG c 422 TYR 0.018 0.002 TYR A 241 PHE 0.022 0.003 PHE A 157 TRP 0.014 0.002 TRP A 210 HIS 0.007 0.001 HIS b 354 Details of bonding type rmsd/Z covalent geometry : bond 0.00410 / 0.19 ( 9294) covalent geometry : angle 0.80004 / 0.40 (12567) SS BOND : bond 0.00332 / 0.21 ( 21) SS BOND : angle 1.01306 / 0.63 ( 42) hydrogen bonds : bond 0.04651 / 3.06 ( 384) hydrogen bonds : angle 4.63539 / 3.16 ( 1035) link_ALPHA1-3 : bond 0.00202 / 0.10 ( 3) link_ALPHA1-3 : angle 1.79599 / 1.08 ( 9) link_ALPHA1-6 : bond 0.00999 / 0.50 ( 3) link_ALPHA1-6 : angle 1.35793 / 0.75 ( 9) link_BETA1-4 : bond 0.01227 / 0.78 ( 33) link_BETA1-4 : angle 2.80391 / 1.82 ( 99) link_BETA1-6 : bond 0.00295 / 0.15 ( 3) link_BETA1-6 : angle 1.35145 / 0.83 ( 9) link_NAG-ASN : bond 0.00307 / 0.15 ( 33) link_NAG-ASN : angle 2.10537 / 1.40 ( 99) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1968 Ramachandran restraints generated. 984 Oldfield, 0 Emsley, 984 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1968 Ramachandran restraints generated. 984 Oldfield, 0 Emsley, 984 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 284 residues out of total 912 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 234 time to evaluate : 0.362 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 76 GLU cc_start: 0.9023 (tt0) cc_final: 0.8207 (tm-30) REVERT: A 130 ASP cc_start: 0.8449 (t0) cc_final: 0.7895 (t70) REVERT: A 211 ASP cc_start: 0.8697 (p0) cc_final: 0.8404 (p0) REVERT: A 227 TRP cc_start: 0.6577 (t-100) cc_final: 0.6064 (t60) REVERT: a 300 LYS cc_start: 0.9335 (mmtm) cc_final: 0.8728 (mptt) REVERT: a 313 LEU cc_start: 0.9757 (tp) cc_final: 0.9229 (tp) REVERT: a 357 ASP cc_start: 0.9297 (t70) cc_final: 0.8746 (t0) REVERT: a 410 MET cc_start: 0.8982 (tpp) cc_final: 0.8769 (tpp) REVERT: B 76 GLU cc_start: 0.9098 (tt0) cc_final: 0.8225 (tm-30) REVERT: B 96 MET cc_start: 0.8935 (ttp) cc_final: 0.8606 (ttm) REVERT: B 130 ASP cc_start: 0.8197 (t0) cc_final: 0.7660 (t70) REVERT: B 211 ASP cc_start: 0.8648 (p0) cc_final: 0.8294 (p0) REVERT: B 227 TRP cc_start: 0.6820 (t-100) cc_final: 0.6162 (t60) REVERT: b 306 ASP cc_start: 0.8193 (OUTLIER) cc_final: 0.7653 (m-30) REVERT: b 313 LEU cc_start: 0.9704 (tp) cc_final: 0.9262 (tp) REVERT: b 325 ARG cc_start: 0.8706 (mmm160) cc_final: 0.8446 (mmm160) REVERT: b 357 ASP cc_start: 0.9249 (t70) cc_final: 0.8699 (t0) REVERT: C 76 GLU cc_start: 0.9204 (tt0) cc_final: 0.8937 (tt0) REVERT: C 82 MET cc_start: 0.9303 (ptt) cc_final: 0.8954 (ptp) REVERT: C 96 MET cc_start: 0.8031 (ptp) cc_final: 0.7697 (ptm) REVERT: C 100 GLU cc_start: 0.7684 (mm-30) cc_final: 0.7418 (mm-30) REVERT: C 130 ASP cc_start: 0.8162 (t0) cc_final: 0.7641 (t70) REVERT: C 211 ASP cc_start: 0.8583 (p0) cc_final: 0.8273 (p0) REVERT: c 278 TYR cc_start: 0.8421 (t80) cc_final: 0.8008 (t80) REVERT: c 300 LYS cc_start: 0.9306 (mmtm) cc_final: 0.8843 (mptt) REVERT: c 311 ASP cc_start: 0.9073 (OUTLIER) cc_final: 0.8757 (t0) REVERT: c 313 LEU cc_start: 0.9719 (tp) cc_final: 0.9204 (tp) REVERT: c 410 MET cc_start: 0.9086 (tpp) cc_final: 0.8812 (tpp) REVERT: c 417 LYS cc_start: 0.9209 (pttp) cc_final: 0.8992 (pttp) outliers start: 50 outliers final: 31 residues processed: 271 average time/residue: 0.0938 time to fit residues: 35.3408 Evaluate side-chains 248 residues out of total 912 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 215 time to evaluate : 0.308 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 86 CYS Chi-restraints excluded: chain A residue 126 LYS Chi-restraints excluded: chain A residue 128 LEU Chi-restraints excluded: chain A residue 156 ASP Chi-restraints excluded: chain A residue 185 ASN Chi-restraints excluded: chain A residue 218 GLN Chi-restraints excluded: chain A residue 245 LEU Chi-restraints excluded: chain a residue 274 THR Chi-restraints excluded: chain a residue 311 ASP Chi-restraints excluded: chain a residue 325 ARG Chi-restraints excluded: chain a residue 337 ILE Chi-restraints excluded: chain a residue 361 ILE Chi-restraints excluded: chain a residue 388 VAL Chi-restraints excluded: chain a residue 421 GLU Chi-restraints excluded: chain B residue 86 CYS Chi-restraints excluded: chain B residue 128 LEU Chi-restraints excluded: chain B residue 185 ASN Chi-restraints excluded: chain B residue 218 GLN Chi-restraints excluded: chain B residue 239 ILE Chi-restraints excluded: chain b residue 274 THR Chi-restraints excluded: chain b residue 306 ASP Chi-restraints excluded: chain b residue 337 ILE Chi-restraints excluded: chain b residue 349 LEU Chi-restraints excluded: chain b residue 385 CYS Chi-restraints excluded: chain b residue 403 ILE Chi-restraints excluded: chain C residue 86 CYS Chi-restraints excluded: chain C residue 128 LEU Chi-restraints excluded: chain C residue 245 LEU Chi-restraints excluded: chain c residue 311 ASP Chi-restraints excluded: chain c residue 337 ILE Chi-restraints excluded: chain c residue 350 ILE Chi-restraints excluded: chain c residue 380 THR Chi-restraints excluded: chain c residue 385 CYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 94 optimal weight: 4.9990 chunk 35 optimal weight: 10.0000 chunk 57 optimal weight: 1.9990 chunk 43 optimal weight: 10.0000 chunk 20 optimal weight: 8.9990 chunk 12 optimal weight: 2.9990 chunk 37 optimal weight: 10.0000 chunk 59 optimal weight: 5.9990 chunk 73 optimal weight: 2.9990 chunk 31 optimal weight: 8.9990 chunk 64 optimal weight: 0.9990 overall best weight: 2.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... a 416 GLN b 405 GLN ** c 406 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 = 0.3278 r_free = 0.3278 target = 0.071302 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2830 r_free = 0.2830 target = 0.051873 restraints weight = 30401.021| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.2885 r_free = 0.2885 target = 0.054119 restraints weight = 17126.267| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.2922 r_free = 0.2922 target = 0.055641 restraints weight = 12246.179| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.2945 r_free = 0.2945 target = 0.056639 restraints weight = 9948.083| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.2961 r_free = 0.2961 target = 0.057304 restraints weight = 8708.766| |-----------------------------------------------------------------------------| r_work (final): 0.2956 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8249 moved from start: 0.5887 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 9390 Z= 0.207 Angle : 0.848 10.638 12834 Z= 0.406 Chirality : 0.046 0.280 1599 Planarity : 0.004 0.037 1482 Dihedral : 5.428 23.808 1074 Min Nonbonded Distance : 2.437 Molprobity Statistics. All-atom Clashscore : 12.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.15 % Favored : 96.85 % Rotamer: Outliers : 5.81 % Allowed : 22.15 % Favored : 72.04 % 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: 0.35 (0.25), residues: 984 helix: 1.45 (0.27), residues: 369 sheet: 0.84 (0.49), residues: 117 loop : -0.87 (0.25), residues: 498 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG a 422 TYR 0.021 0.002 TYR B 241 PHE 0.022 0.003 PHE A 157 TRP 0.018 0.002 TRP B 210 HIS 0.005 0.001 HIS b 354 Details of bonding type rmsd/Z covalent geometry : bond 0.00442 / 0.20 ( 9294) covalent geometry : angle 0.79713 / 0.40 (12567) SS BOND : bond 0.00376 / 0.25 ( 21) SS BOND : angle 0.92151 / 0.56 ( 42) hydrogen bonds : bond 0.04547 / 2.98 ( 384) hydrogen bonds : angle 4.71370 / 3.23 ( 1035) link_ALPHA1-3 : bond 0.00078 / 0.04 ( 3) link_ALPHA1-3 : angle 1.84617 / 1.13 ( 9) link_ALPHA1-6 : bond 0.01061 / 0.53 ( 3) link_ALPHA1-6 : angle 1.38963 / 0.76 ( 9) link_BETA1-4 : bond 0.01227 / 0.79 ( 33) link_BETA1-4 : angle 2.74393 / 1.79 ( 99) link_BETA1-6 : bond 0.00439 / 0.22 ( 3) link_BETA1-6 : angle 1.50479 / 0.92 ( 9) link_NAG-ASN : bond 0.00272 / 0.14 ( 33) link_NAG-ASN : angle 2.01393 / 1.34 ( 99) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1968 Ramachandran restraints generated. 984 Oldfield, 0 Emsley, 984 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1968 Ramachandran restraints generated. 984 Oldfield, 0 Emsley, 984 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 277 residues out of total 912 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 224 time to evaluate : 0.339 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 76 GLU cc_start: 0.9038 (tt0) cc_final: 0.8188 (tm-30) REVERT: A 130 ASP cc_start: 0.8419 (t0) cc_final: 0.7862 (t70) REVERT: A 211 ASP cc_start: 0.8750 (p0) cc_final: 0.8453 (p0) REVERT: a 300 LYS cc_start: 0.9366 (mmtm) cc_final: 0.8764 (mptt) REVERT: a 313 LEU cc_start: 0.9766 (tp) cc_final: 0.9253 (tp) REVERT: a 357 ASP cc_start: 0.9312 (t70) cc_final: 0.8819 (t0) REVERT: a 408 ASP cc_start: 0.9151 (m-30) cc_final: 0.8924 (m-30) REVERT: B 80 MET cc_start: 0.8918 (mmt) cc_final: 0.8350 (mmm) REVERT: B 96 MET cc_start: 0.8886 (ttp) cc_final: 0.8603 (ttm) REVERT: B 130 ASP cc_start: 0.8195 (t0) cc_final: 0.7720 (t70) REVERT: B 211 ASP cc_start: 0.8348 (p0) cc_final: 0.8129 (p0) REVERT: B 227 TRP cc_start: 0.6916 (t-100) cc_final: 0.6250 (t60) REVERT: b 306 ASP cc_start: 0.8298 (OUTLIER) cc_final: 0.7884 (m-30) REVERT: b 313 LEU cc_start: 0.9705 (tp) cc_final: 0.9257 (tp) REVERT: b 325 ARG cc_start: 0.8737 (mmm160) cc_final: 0.8521 (mmm160) REVERT: b 357 ASP cc_start: 0.9292 (t70) cc_final: 0.8727 (t0) REVERT: b 410 MET cc_start: 0.9034 (tpp) cc_final: 0.8715 (tpp) REVERT: b 416 GLN cc_start: 0.9236 (mt0) cc_final: 0.9027 (mt0) REVERT: C 76 GLU cc_start: 0.9202 (tt0) cc_final: 0.8920 (tt0) REVERT: C 82 MET cc_start: 0.9292 (OUTLIER) cc_final: 0.9013 (ptp) REVERT: C 96 MET cc_start: 0.7990 (ptp) cc_final: 0.7733 (ptm) REVERT: C 130 ASP cc_start: 0.8096 (t0) cc_final: 0.7545 (t70) REVERT: C 194 MET cc_start: 0.9346 (OUTLIER) cc_final: 0.9109 (tpp) REVERT: C 211 ASP cc_start: 0.8640 (p0) cc_final: 0.8268 (p0) REVERT: c 278 TYR cc_start: 0.8501 (t80) cc_final: 0.8110 (t80) REVERT: c 311 ASP cc_start: 0.9056 (OUTLIER) cc_final: 0.8740 (t0) REVERT: c 313 LEU cc_start: 0.9736 (tp) cc_final: 0.9212 (tp) REVERT: c 410 MET cc_start: 0.9100 (tpp) cc_final: 0.8852 (tpp) REVERT: c 417 LYS cc_start: 0.9270 (pttp) cc_final: 0.9015 (pttp) REVERT: c 422 ARG cc_start: 0.7424 (ttp80) cc_final: 0.7066 (ttp80) outliers start: 53 outliers final: 34 residues processed: 265 average time/residue: 0.0826 time to fit residues: 30.5172 Evaluate side-chains 243 residues out of total 912 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 205 time to evaluate : 0.326 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 86 CYS Chi-restraints excluded: chain A residue 100 GLU Chi-restraints excluded: chain A residue 128 LEU Chi-restraints excluded: chain A residue 156 ASP Chi-restraints excluded: chain A residue 185 ASN Chi-restraints excluded: chain A residue 210 TRP Chi-restraints excluded: chain A residue 218 GLN Chi-restraints excluded: chain A residue 239 ILE Chi-restraints excluded: chain A residue 245 LEU Chi-restraints excluded: chain a residue 274 THR Chi-restraints excluded: chain a residue 311 ASP Chi-restraints excluded: chain a residue 325 ARG Chi-restraints excluded: chain a residue 337 ILE Chi-restraints excluded: chain a residue 361 ILE Chi-restraints excluded: chain a residue 388 VAL Chi-restraints excluded: chain a residue 421 GLU Chi-restraints excluded: chain B residue 86 CYS Chi-restraints excluded: chain B residue 128 LEU Chi-restraints excluded: chain B residue 185 ASN Chi-restraints excluded: chain B residue 218 GLN Chi-restraints excluded: chain B residue 239 ILE Chi-restraints excluded: chain B residue 245 LEU Chi-restraints excluded: chain b residue 274 THR Chi-restraints excluded: chain b residue 306 ASP Chi-restraints excluded: chain b residue 311 ASP Chi-restraints excluded: chain b residue 337 ILE Chi-restraints excluded: chain b residue 349 LEU Chi-restraints excluded: chain b residue 385 CYS Chi-restraints excluded: chain b residue 388 VAL Chi-restraints excluded: chain b residue 403 ILE Chi-restraints excluded: chain C residue 82 MET Chi-restraints excluded: chain C residue 86 CYS Chi-restraints excluded: chain C residue 128 LEU Chi-restraints excluded: chain C residue 194 MET Chi-restraints excluded: chain C residue 245 LEU Chi-restraints excluded: chain c residue 311 ASP Chi-restraints excluded: chain c residue 337 ILE Chi-restraints excluded: chain c residue 380 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 63 optimal weight: 0.9990 chunk 60 optimal weight: 0.5980 chunk 11 optimal weight: 7.9990 chunk 58 optimal weight: 5.9990 chunk 81 optimal weight: 6.9990 chunk 33 optimal weight: 8.9990 chunk 85 optimal weight: 0.1980 chunk 96 optimal weight: 0.0870 chunk 52 optimal weight: 0.0980 chunk 70 optimal weight: 0.8980 chunk 48 optimal weight: 7.9990 overall best weight: 0.3758 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 209 ASN ** a 416 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 93 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 185 ASN b 405 GLN ** c 406 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 = 0.3339 r_free = 0.3339 target = 0.074318 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2884 r_free = 0.2884 target = 0.054272 restraints weight = 30324.583| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.2942 r_free = 0.2942 target = 0.056657 restraints weight = 16885.136| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.2980 r_free = 0.2980 target = 0.058283 restraints weight = 11975.712| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3005 r_free = 0.3005 target = 0.059361 restraints weight = 9669.883| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.3023 r_free = 0.3023 target = 0.060110 restraints weight = 8404.592| |-----------------------------------------------------------------------------| r_work (final): 0.3026 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8169 moved from start: 0.6173 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.069 9390 Z= 0.147 Angle : 0.829 10.025 12834 Z= 0.393 Chirality : 0.046 0.300 1599 Planarity : 0.004 0.039 1482 Dihedral : 5.245 24.243 1074 Min Nonbonded Distance : 2.380 Molprobity Statistics. All-atom Clashscore : 11.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.35 % Favored : 96.65 % Rotamer: Outliers : 4.61 % Allowed : 23.68 % Favored : 71.71 % 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: 0.35 (0.26), residues: 984 helix: 1.42 (0.27), residues: 369 sheet: 0.63 (0.48), residues: 120 loop : -0.80 (0.25), residues: 495 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG c 422 TYR 0.021 0.002 TYR B 241 PHE 0.025 0.002 PHE B 157 TRP 0.034 0.002 TRP A 227 HIS 0.004 0.001 HIS b 354 Details of bonding type rmsd/Z covalent geometry : bond 0.00313 / 0.14 ( 9294) covalent geometry : angle 0.78183 / 0.38 (12567) SS BOND : bond 0.00248 / 0.17 ( 21) SS BOND : angle 1.22823 / 0.76 ( 42) hydrogen bonds : bond 0.04219 / 2.74 ( 384) hydrogen bonds : angle 4.59786 / 3.16 ( 1035) link_ALPHA1-3 : bond 0.00256 / 0.13 ( 3) link_ALPHA1-3 : angle 1.57390 / 0.97 ( 9) link_ALPHA1-6 : bond 0.01071 / 0.54 ( 3) link_ALPHA1-6 : angle 1.42388 / 0.79 ( 9) link_BETA1-4 : bond 0.01237 / 0.78 ( 33) link_BETA1-4 : angle 2.64145 / 1.71 ( 99) link_BETA1-6 : bond 0.00558 / 0.28 ( 3) link_BETA1-6 : angle 1.18971 / 0.71 ( 9) link_NAG-ASN : bond 0.00243 / 0.17 ( 33) link_NAG-ASN : angle 1.79947 / 1.17 ( 99) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1968 Ramachandran restraints generated. 984 Oldfield, 0 Emsley, 984 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1968 Ramachandran restraints generated. 984 Oldfield, 0 Emsley, 984 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 280 residues out of total 912 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 238 time to evaluate : 0.215 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 76 GLU cc_start: 0.9057 (tt0) cc_final: 0.8165 (tm-30) REVERT: A 130 ASP cc_start: 0.8313 (t0) cc_final: 0.7783 (t0) REVERT: A 211 ASP cc_start: 0.8746 (p0) cc_final: 0.8387 (p0) REVERT: a 278 TYR cc_start: 0.8156 (t80) cc_final: 0.7848 (t80) REVERT: a 300 LYS cc_start: 0.9377 (mmtm) cc_final: 0.8887 (mptt) REVERT: a 311 ASP cc_start: 0.9034 (m-30) cc_final: 0.8712 (t0) REVERT: a 357 ASP cc_start: 0.9239 (t70) cc_final: 0.8741 (t0) REVERT: a 408 ASP cc_start: 0.9152 (m-30) cc_final: 0.8811 (m-30) REVERT: a 416 GLN cc_start: 0.8979 (mm-40) cc_final: 0.8259 (mm-40) REVERT: B 76 GLU cc_start: 0.9105 (tt0) cc_final: 0.8308 (tm-30) REVERT: B 96 MET cc_start: 0.8848 (ttp) cc_final: 0.8577 (ttm) REVERT: B 100 GLU cc_start: 0.8365 (mm-30) cc_final: 0.7640 (mm-30) REVERT: B 130 ASP cc_start: 0.8153 (t0) cc_final: 0.7707 (t0) REVERT: B 227 TRP cc_start: 0.6928 (t-100) cc_final: 0.6213 (t60) REVERT: b 306 ASP cc_start: 0.8359 (OUTLIER) cc_final: 0.8063 (m-30) REVERT: b 325 ARG cc_start: 0.8667 (mmm160) cc_final: 0.8446 (mmm160) REVERT: b 357 ASP cc_start: 0.9208 (t70) cc_final: 0.8707 (t0) REVERT: b 413 GLU cc_start: 0.8987 (mp0) cc_final: 0.8335 (pm20) REVERT: b 420 MET cc_start: 0.7534 (mmt) cc_final: 0.7241 (mmt) REVERT: C 76 GLU cc_start: 0.9224 (tt0) cc_final: 0.8928 (tt0) REVERT: C 82 MET cc_start: 0.9271 (OUTLIER) cc_final: 0.8873 (ptp) REVERT: C 130 ASP cc_start: 0.8123 (t0) cc_final: 0.7618 (t70) REVERT: C 194 MET cc_start: 0.9304 (OUTLIER) cc_final: 0.9055 (tpp) REVERT: C 211 ASP cc_start: 0.8727 (p0) cc_final: 0.8387 (p0) REVERT: c 278 TYR cc_start: 0.8496 (t80) cc_final: 0.8133 (t80) REVERT: c 311 ASP cc_start: 0.9035 (OUTLIER) cc_final: 0.8715 (t0) REVERT: c 351 MET cc_start: 0.8766 (mmp) cc_final: 0.8222 (mmp) REVERT: c 410 MET cc_start: 0.9072 (tpp) cc_final: 0.8813 (tpp) REVERT: c 417 LYS cc_start: 0.9281 (pttp) cc_final: 0.8947 (pttp) REVERT: c 420 MET cc_start: 0.7868 (mmp) cc_final: 0.7437 (mmp) outliers start: 42 outliers final: 28 residues processed: 269 average time/residue: 0.0795 time to fit residues: 30.0500 Evaluate side-chains 239 residues out of total 912 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 207 time to evaluate : 0.334 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 86 CYS Chi-restraints excluded: chain A residue 126 LYS Chi-restraints excluded: chain A residue 128 LEU Chi-restraints excluded: chain A residue 156 ASP Chi-restraints excluded: chain A residue 185 ASN Chi-restraints excluded: chain A residue 209 ASN Chi-restraints excluded: chain A residue 218 GLN Chi-restraints excluded: chain A residue 245 LEU Chi-restraints excluded: chain a residue 274 THR Chi-restraints excluded: chain a residue 325 ARG Chi-restraints excluded: chain a residue 337 ILE Chi-restraints excluded: chain a residue 361 ILE Chi-restraints excluded: chain B residue 86 CYS Chi-restraints excluded: chain B residue 128 LEU Chi-restraints excluded: chain B residue 162 ILE Chi-restraints excluded: chain B residue 185 ASN Chi-restraints excluded: chain B residue 245 LEU Chi-restraints excluded: chain b residue 274 THR Chi-restraints excluded: chain b residue 306 ASP Chi-restraints excluded: chain b residue 337 ILE Chi-restraints excluded: chain b residue 349 LEU Chi-restraints excluded: chain b residue 367 SER Chi-restraints excluded: chain b residue 385 CYS Chi-restraints excluded: chain b residue 392 SER Chi-restraints excluded: chain b residue 403 ILE Chi-restraints excluded: chain C residue 82 MET Chi-restraints excluded: chain C residue 86 CYS Chi-restraints excluded: chain C residue 128 LEU Chi-restraints excluded: chain C residue 194 MET Chi-restraints excluded: chain C residue 245 LEU Chi-restraints excluded: chain c residue 311 ASP Chi-restraints excluded: chain c residue 380 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 43 optimal weight: 0.2980 chunk 1 optimal weight: 8.9990 chunk 75 optimal weight: 8.9990 chunk 24 optimal weight: 3.9990 chunk 68 optimal weight: 3.9990 chunk 42 optimal weight: 0.0970 chunk 57 optimal weight: 0.8980 chunk 22 optimal weight: 0.9980 chunk 14 optimal weight: 7.9990 chunk 17 optimal weight: 0.7980 chunk 44 optimal weight: 6.9990 overall best weight: 0.6178 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 93 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 209 ASN ** a 416 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 185 ASN ** c 406 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 = 0.3334 r_free = 0.3334 target = 0.074108 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2889 r_free = 0.2889 target = 0.054378 restraints weight = 29947.089| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.2944 r_free = 0.2944 target = 0.056680 restraints weight = 16847.190| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.2981 r_free = 0.2981 target = 0.058269 restraints weight = 12009.084| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3006 r_free = 0.3006 target = 0.059312 restraints weight = 9714.014| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3021 r_free = 0.3021 target = 0.059991 restraints weight = 8464.526| |-----------------------------------------------------------------------------| r_work (final): 0.3019 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8192 moved from start: 0.6364 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.078 9390 Z= 0.156 Angle : 0.862 17.278 12834 Z= 0.410 Chirality : 0.047 0.326 1599 Planarity : 0.004 0.041 1482 Dihedral : 5.143 25.319 1074 Min Nonbonded Distance : 2.423 Molprobity Statistics. All-atom Clashscore : 11.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.56 % Favored : 96.44 % Rotamer: Outliers : 4.28 % Allowed : 25.44 % Favored : 70.29 % 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: 0.39 (0.26), residues: 984 helix: 1.47 (0.27), residues: 369 sheet: 0.63 (0.48), residues: 117 loop : -0.76 (0.25), residues: 498 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG c 422 TYR 0.019 0.002 TYR B 241 PHE 0.024 0.002 PHE C 157 TRP 0.045 0.002 TRP A 227 HIS 0.005 0.001 HIS b 354 Details of bonding type rmsd/Z covalent geometry : bond 0.00350 / 0.15 ( 9294) covalent geometry : angle 0.81543 / 0.40 (12567) SS BOND : bond 0.00565 / 0.39 ( 21) SS BOND : angle 1.97578 / 1.28 ( 42) hydrogen bonds : bond 0.04120 / 2.70 ( 384) hydrogen bonds : angle 4.58332 / 3.14 ( 1035) link_ALPHA1-3 : bond 0.00263 / 0.13 ( 3) link_ALPHA1-3 : angle 1.59116 / 0.98 ( 9) link_ALPHA1-6 : bond 0.01065 / 0.53 ( 3) link_ALPHA1-6 : angle 1.40855 / 0.79 ( 9) link_BETA1-4 : bond 0.01197 / 0.76 ( 33) link_BETA1-4 : angle 2.59639 / 1.69 ( 99) link_BETA1-6 : bond 0.00511 / 0.26 ( 3) link_BETA1-6 : angle 1.17859 / 0.71 ( 9) link_NAG-ASN : bond 0.00240 / 0.16 ( 33) link_NAG-ASN : angle 1.70798 / 1.10 ( 99) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1968 Ramachandran restraints generated. 984 Oldfield, 0 Emsley, 984 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1968 Ramachandran restraints generated. 984 Oldfield, 0 Emsley, 984 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 254 residues out of total 912 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 215 time to evaluate : 0.253 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 76 GLU cc_start: 0.9040 (tt0) cc_final: 0.8155 (tm-30) REVERT: A 129 TYR cc_start: 0.6587 (m-10) cc_final: 0.6382 (m-10) REVERT: A 130 ASP cc_start: 0.8277 (t0) cc_final: 0.7776 (t0) REVERT: A 210 TRP cc_start: 0.6755 (OUTLIER) cc_final: 0.6549 (t60) REVERT: A 211 ASP cc_start: 0.8667 (p0) cc_final: 0.8068 (p0) REVERT: a 278 TYR cc_start: 0.8207 (t80) cc_final: 0.7913 (t80) REVERT: a 300 LYS cc_start: 0.9414 (mmtm) cc_final: 0.8909 (mptt) REVERT: a 311 ASP cc_start: 0.9035 (OUTLIER) cc_final: 0.8723 (t0) REVERT: a 357 ASP cc_start: 0.9241 (t70) cc_final: 0.8801 (t0) REVERT: a 408 ASP cc_start: 0.9150 (m-30) cc_final: 0.8756 (m-30) REVERT: B 76 GLU cc_start: 0.9082 (tt0) cc_final: 0.8280 (tm-30) REVERT: B 100 GLU cc_start: 0.8385 (mm-30) cc_final: 0.7658 (mm-30) REVERT: B 130 ASP cc_start: 0.8132 (t0) cc_final: 0.7702 (t0) REVERT: B 227 TRP cc_start: 0.6940 (t-100) cc_final: 0.6300 (t-100) REVERT: b 306 ASP cc_start: 0.8257 (OUTLIER) cc_final: 0.7935 (m-30) REVERT: b 357 ASP cc_start: 0.9254 (t70) cc_final: 0.8782 (t0) REVERT: b 405 GLN cc_start: 0.9553 (tp40) cc_final: 0.9340 (tp-100) REVERT: b 410 MET cc_start: 0.8985 (tpp) cc_final: 0.7951 (tpp) REVERT: b 413 GLU cc_start: 0.8853 (mp0) cc_final: 0.8410 (pm20) REVERT: b 414 MET cc_start: 0.9200 (tpp) cc_final: 0.8948 (tpp) REVERT: C 82 MET cc_start: 0.9223 (OUTLIER) cc_final: 0.8846 (ptp) REVERT: C 130 ASP cc_start: 0.8006 (t0) cc_final: 0.7555 (t70) REVERT: C 194 MET cc_start: 0.9267 (OUTLIER) cc_final: 0.9032 (tpp) REVERT: c 278 TYR cc_start: 0.8230 (t80) cc_final: 0.7678 (t80) REVERT: c 311 ASP cc_start: 0.9081 (OUTLIER) cc_final: 0.8770 (t0) REVERT: c 351 MET cc_start: 0.8628 (mmp) cc_final: 0.8156 (mmp) REVERT: c 410 MET cc_start: 0.9066 (tpp) cc_final: 0.8809 (tpp) outliers start: 39 outliers final: 23 residues processed: 240 average time/residue: 0.0627 time to fit residues: 21.4890 Evaluate side-chains 237 residues out of total 912 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 208 time to evaluate : 0.211 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 86 CYS Chi-restraints excluded: chain A residue 128 LEU Chi-restraints excluded: chain A residue 156 ASP Chi-restraints excluded: chain A residue 185 ASN Chi-restraints excluded: chain A residue 209 ASN Chi-restraints excluded: chain A residue 210 TRP Chi-restraints excluded: chain A residue 218 GLN Chi-restraints excluded: chain A residue 245 LEU Chi-restraints excluded: chain a residue 311 ASP Chi-restraints excluded: chain a residue 325 ARG Chi-restraints excluded: chain a residue 337 ILE Chi-restraints excluded: chain B residue 82 MET Chi-restraints excluded: chain B residue 86 CYS Chi-restraints excluded: chain B residue 128 LEU Chi-restraints excluded: chain B residue 185 ASN Chi-restraints excluded: chain B residue 210 TRP Chi-restraints excluded: chain B residue 245 LEU Chi-restraints excluded: chain b residue 274 THR Chi-restraints excluded: chain b residue 306 ASP Chi-restraints excluded: chain b residue 349 LEU Chi-restraints excluded: chain b residue 385 CYS Chi-restraints excluded: chain b residue 403 ILE Chi-restraints excluded: chain C residue 82 MET Chi-restraints excluded: chain C residue 86 CYS Chi-restraints excluded: chain C residue 128 LEU Chi-restraints excluded: chain C residue 194 MET Chi-restraints excluded: chain C residue 245 LEU Chi-restraints excluded: chain c residue 311 ASP Chi-restraints excluded: chain c residue 380 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 80 optimal weight: 6.9990 chunk 67 optimal weight: 0.9990 chunk 40 optimal weight: 6.9990 chunk 16 optimal weight: 0.9980 chunk 38 optimal weight: 3.9990 chunk 24 optimal weight: 0.8980 chunk 95 optimal weight: 3.9990 chunk 33 optimal weight: 8.9990 chunk 21 optimal weight: 0.8980 chunk 12 optimal weight: 0.8980 chunk 72 optimal weight: 0.0470 overall best weight: 0.7478 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 93 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 209 ASN B 185 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3341 r_free = 0.3341 target = 0.074680 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2889 r_free = 0.2889 target = 0.054481 restraints weight = 30101.766| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.2944 r_free = 0.2944 target = 0.056839 restraints weight = 17148.447| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.2982 r_free = 0.2982 target = 0.058431 restraints weight = 12298.482| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3006 r_free = 0.3006 target = 0.059492 restraints weight = 10005.593| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3022 r_free = 0.3022 target = 0.060210 restraints weight = 8730.354| |-----------------------------------------------------------------------------| r_work (final): 0.3017 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8195 moved from start: 0.6505 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.079 9390 Z= 0.160 Angle : 0.888 17.026 12834 Z= 0.423 Chirality : 0.048 0.334 1599 Planarity : 0.004 0.038 1482 Dihedral : 5.060 23.692 1074 Min Nonbonded Distance : 2.365 Molprobity Statistics. All-atom Clashscore : 12.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.56 % Favored : 96.44 % Rotamer: Outliers : 3.95 % Allowed : 25.99 % Favored : 70.07 % 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: 0.41 (0.26), residues: 984 helix: 1.49 (0.26), residues: 369 sheet: 0.47 (0.48), residues: 117 loop : -0.70 (0.26), residues: 498 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG a 422 TYR 0.019 0.002 TYR B 166 PHE 0.024 0.002 PHE A 157 TRP 0.028 0.002 TRP A 227 HIS 0.005 0.001 HIS b 354 Details of bonding type rmsd/Z covalent geometry : bond 0.00365 / 0.16 ( 9294) covalent geometry : angle 0.84223 / 0.41 (12567) SS BOND : bond 0.00695 / 0.44 ( 21) SS BOND : angle 2.31878 / 1.53 ( 42) hydrogen bonds : bond 0.04127 / 2.73 ( 384) hydrogen bonds : angle 4.63839 / 3.22 ( 1035) link_ALPHA1-3 : bond 0.00238 / 0.12 ( 3) link_ALPHA1-3 : angle 1.58849 / 0.97 ( 9) link_ALPHA1-6 : bond 0.01062 / 0.53 ( 3) link_ALPHA1-6 : angle 1.40531 / 0.79 ( 9) link_BETA1-4 : bond 0.01194 / 0.76 ( 33) link_BETA1-4 : angle 2.54686 / 1.66 ( 99) link_BETA1-6 : bond 0.00496 / 0.25 ( 3) link_BETA1-6 : angle 1.19010 / 0.72 ( 9) link_NAG-ASN : bond 0.00199 / 0.13 ( 33) link_NAG-ASN : angle 1.67130 / 1.07 ( 99) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1968 Ramachandran restraints generated. 984 Oldfield, 0 Emsley, 984 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1968 Ramachandran restraints generated. 984 Oldfield, 0 Emsley, 984 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 251 residues out of total 912 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 215 time to evaluate : 0.256 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 76 GLU cc_start: 0.9061 (tt0) cc_final: 0.8177 (tm-30) REVERT: A 80 MET cc_start: 0.8954 (mmt) cc_final: 0.8309 (mmm) REVERT: A 130 ASP cc_start: 0.8273 (t0) cc_final: 0.7786 (t0) REVERT: A 211 ASP cc_start: 0.8740 (p0) cc_final: 0.8353 (p0) REVERT: a 278 TYR cc_start: 0.8279 (t80) cc_final: 0.7887 (t80) REVERT: a 300 LYS cc_start: 0.9421 (mmtm) cc_final: 0.8909 (mptt) REVERT: a 311 ASP cc_start: 0.9021 (OUTLIER) cc_final: 0.8718 (t0) REVERT: a 357 ASP cc_start: 0.9249 (t70) cc_final: 0.8806 (t0) REVERT: a 408 ASP cc_start: 0.9169 (m-30) cc_final: 0.8760 (m-30) REVERT: B 76 GLU cc_start: 0.9127 (tt0) cc_final: 0.8301 (tm-30) REVERT: B 100 GLU cc_start: 0.8415 (mm-30) cc_final: 0.7750 (mm-30) REVERT: B 130 ASP cc_start: 0.8118 (t0) cc_final: 0.7698 (t0) REVERT: b 306 ASP cc_start: 0.8331 (OUTLIER) cc_final: 0.8087 (m-30) REVERT: b 357 ASP cc_start: 0.9255 (t70) cc_final: 0.8789 (t0) REVERT: b 405 GLN cc_start: 0.9568 (tp40) cc_final: 0.9318 (tp-100) REVERT: b 410 MET cc_start: 0.9017 (tpp) cc_final: 0.7947 (tpp) REVERT: b 413 GLU cc_start: 0.8858 (mp0) cc_final: 0.8584 (pm20) REVERT: b 414 MET cc_start: 0.9212 (tpp) cc_final: 0.8936 (tpp) REVERT: b 420 MET cc_start: 0.7671 (mmt) cc_final: 0.7263 (mmt) REVERT: C 80 MET cc_start: 0.9056 (mmt) cc_final: 0.8774 (mpp) REVERT: C 82 MET cc_start: 0.9263 (OUTLIER) cc_final: 0.8941 (ptp) REVERT: C 130 ASP cc_start: 0.8064 (t0) cc_final: 0.7606 (t70) REVERT: C 227 TRP cc_start: 0.7354 (t-100) cc_final: 0.7125 (t-100) REVERT: c 278 TYR cc_start: 0.8244 (t80) cc_final: 0.7794 (t80) REVERT: c 311 ASP cc_start: 0.9098 (OUTLIER) cc_final: 0.8721 (t0) REVERT: c 351 MET cc_start: 0.8628 (mmp) cc_final: 0.8170 (mmp) REVERT: c 410 MET cc_start: 0.9083 (tpp) cc_final: 0.8823 (tpp) outliers start: 36 outliers final: 22 residues processed: 237 average time/residue: 0.0675 time to fit residues: 22.6801 Evaluate side-chains 229 residues out of total 912 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 203 time to evaluate : 0.265 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 86 CYS Chi-restraints excluded: chain A residue 128 LEU Chi-restraints excluded: chain A residue 156 ASP Chi-restraints excluded: chain A residue 185 ASN Chi-restraints excluded: chain A residue 209 ASN Chi-restraints excluded: chain A residue 218 GLN Chi-restraints excluded: chain A residue 245 LEU Chi-restraints excluded: chain a residue 311 ASP Chi-restraints excluded: chain a residue 337 ILE Chi-restraints excluded: chain B residue 82 MET Chi-restraints excluded: chain B residue 86 CYS Chi-restraints excluded: chain B residue 128 LEU Chi-restraints excluded: chain B residue 185 ASN Chi-restraints excluded: chain B residue 245 LEU Chi-restraints excluded: chain b residue 274 THR Chi-restraints excluded: chain b residue 306 ASP Chi-restraints excluded: chain b residue 349 LEU Chi-restraints excluded: chain b residue 385 CYS Chi-restraints excluded: chain b residue 403 ILE Chi-restraints excluded: chain C residue 82 MET Chi-restraints excluded: chain C residue 86 CYS Chi-restraints excluded: chain C residue 128 LEU Chi-restraints excluded: chain C residue 245 LEU Chi-restraints excluded: chain c residue 279 CYS Chi-restraints excluded: chain c residue 285 LEU Chi-restraints excluded: chain c residue 311 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 46 optimal weight: 0.0040 chunk 8 optimal weight: 0.1980 chunk 76 optimal weight: 5.9990 chunk 90 optimal weight: 0.1980 chunk 62 optimal weight: 6.9990 chunk 80 optimal weight: 6.9990 chunk 29 optimal weight: 0.9980 chunk 48 optimal weight: 5.9990 chunk 70 optimal weight: 0.8980 chunk 37 optimal weight: 0.9990 chunk 24 optimal weight: 1.9990 overall best weight: 0.4592 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 93 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 209 ASN ** b 335 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 335 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 = 0.3359 r_free = 0.3359 target = 0.075459 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 24)----------------| | r_work = 0.2904 r_free = 0.2904 target = 0.055360 restraints weight = 30030.941| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.2959 r_free = 0.2959 target = 0.057686 restraints weight = 17352.195| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.2995 r_free = 0.2995 target = 0.059229 restraints weight = 12539.517| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3019 r_free = 0.3019 target = 0.060286 restraints weight = 10241.979| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 39)----------------| | r_work = 0.3035 r_free = 0.3035 target = 0.060986 restraints weight = 8965.723| |-----------------------------------------------------------------------------| r_work (final): 0.3028 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8190 moved from start: 0.6665 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.069 9390 Z= 0.159 Angle : 0.934 21.202 12834 Z= 0.447 Chirality : 0.050 0.450 1599 Planarity : 0.004 0.039 1482 Dihedral : 5.112 23.218 1074 Min Nonbonded Distance : 2.358 Molprobity Statistics. All-atom Clashscore : 12.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.66 % Favored : 96.34 % Rotamer: Outliers : 3.18 % Allowed : 26.32 % Favored : 70.50 % 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: 0.39 (0.26), residues: 984 helix: 1.49 (0.27), residues: 369 sheet: 0.31 (0.48), residues: 117 loop : -0.68 (0.26), residues: 498 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG c 422 TYR 0.019 0.002 TYR C 166 PHE 0.024 0.002 PHE A 157 TRP 0.041 0.003 TRP B 227 HIS 0.007 0.001 HIS b 354 Details of bonding type rmsd/Z covalent geometry : bond 0.00354 / 0.15 ( 9294) covalent geometry : angle 0.88541 / 0.43 (12567) SS BOND : bond 0.00769 / 0.51 ( 21) SS BOND : angle 3.09639 / 2.11 ( 42) hydrogen bonds : bond 0.04061 / 2.67 ( 384) hydrogen bonds : angle 4.61579 / 3.20 ( 1035) link_ALPHA1-3 : bond 0.00272 / 0.14 ( 3) link_ALPHA1-3 : angle 1.55316 / 0.95 ( 9) link_ALPHA1-6 : bond 0.01064 / 0.53 ( 3) link_ALPHA1-6 : angle 1.40679 / 0.79 ( 9) link_BETA1-4 : bond 0.01198 / 0.76 ( 33) link_BETA1-4 : angle 2.51533 / 1.63 ( 99) link_BETA1-6 : bond 0.00513 / 0.26 ( 3) link_BETA1-6 : angle 1.17011 / 0.71 ( 9) link_NAG-ASN : bond 0.00240 / 0.15 ( 33) link_NAG-ASN : angle 1.61276 / 1.02 ( 99) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1968 Ramachandran restraints generated. 984 Oldfield, 0 Emsley, 984 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1968 Ramachandran restraints generated. 984 Oldfield, 0 Emsley, 984 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 238 residues out of total 912 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 209 time to evaluate : 0.336 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 76 GLU cc_start: 0.9060 (tt0) cc_final: 0.8191 (tm-30) REVERT: A 130 ASP cc_start: 0.8237 (t0) cc_final: 0.7748 (t0) REVERT: A 211 ASP cc_start: 0.8489 (p0) cc_final: 0.8067 (p0) REVERT: a 278 TYR cc_start: 0.8274 (t80) cc_final: 0.7880 (t80) REVERT: a 300 LYS cc_start: 0.9422 (mmtm) cc_final: 0.8899 (mptt) REVERT: a 311 ASP cc_start: 0.9017 (OUTLIER) cc_final: 0.8723 (t0) REVERT: a 357 ASP cc_start: 0.9236 (t70) cc_final: 0.8836 (t0) REVERT: a 408 ASP cc_start: 0.9169 (m-30) cc_final: 0.8740 (m-30) REVERT: B 76 GLU cc_start: 0.9091 (tt0) cc_final: 0.8314 (tm-30) REVERT: B 130 ASP cc_start: 0.8315 (t0) cc_final: 0.7857 (t0) REVERT: b 284 MET cc_start: 0.9046 (mpp) cc_final: 0.8820 (pmm) REVERT: b 357 ASP cc_start: 0.9266 (t70) cc_final: 0.8815 (t0) REVERT: b 405 GLN cc_start: 0.9565 (tp40) cc_final: 0.9297 (tp-100) REVERT: b 410 MET cc_start: 0.8960 (tpp) cc_final: 0.8719 (tpp) REVERT: b 420 MET cc_start: 0.7154 (mmt) cc_final: 0.6922 (mmt) REVERT: C 80 MET cc_start: 0.9051 (mmt) cc_final: 0.8581 (mmm) REVERT: C 82 MET cc_start: 0.9201 (OUTLIER) cc_final: 0.8887 (ptp) REVERT: C 130 ASP cc_start: 0.8008 (t0) cc_final: 0.7577 (t70) REVERT: C 227 TRP cc_start: 0.7574 (t-100) cc_final: 0.6411 (t-100) REVERT: c 278 TYR cc_start: 0.8237 (t80) cc_final: 0.7872 (t80) REVERT: c 311 ASP cc_start: 0.9080 (OUTLIER) cc_final: 0.8659 (t0) REVERT: c 351 MET cc_start: 0.8601 (mmp) cc_final: 0.8143 (mmp) REVERT: c 410 MET cc_start: 0.9038 (tpp) cc_final: 0.8790 (tpp) outliers start: 29 outliers final: 23 residues processed: 228 average time/residue: 0.0768 time to fit residues: 24.8885 Evaluate side-chains 221 residues out of total 912 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 195 time to evaluate : 0.340 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 86 CYS Chi-restraints excluded: chain A residue 128 LEU Chi-restraints excluded: chain A residue 156 ASP Chi-restraints excluded: chain A residue 185 ASN Chi-restraints excluded: chain A residue 209 ASN Chi-restraints excluded: chain A residue 218 GLN Chi-restraints excluded: chain A residue 245 LEU Chi-restraints excluded: chain a residue 311 ASP Chi-restraints excluded: chain a residue 337 ILE Chi-restraints excluded: chain B residue 82 MET Chi-restraints excluded: chain B residue 86 CYS Chi-restraints excluded: chain B residue 128 LEU Chi-restraints excluded: chain B residue 185 ASN Chi-restraints excluded: chain B residue 245 LEU Chi-restraints excluded: chain b residue 274 THR Chi-restraints excluded: chain b residue 279 CYS Chi-restraints excluded: chain b residue 351 MET Chi-restraints excluded: chain b residue 385 CYS Chi-restraints excluded: chain b residue 403 ILE Chi-restraints excluded: chain C residue 82 MET Chi-restraints excluded: chain C residue 86 CYS Chi-restraints excluded: chain C residue 128 LEU Chi-restraints excluded: chain C residue 245 LEU Chi-restraints excluded: chain c residue 279 CYS Chi-restraints excluded: chain c residue 285 LEU Chi-restraints excluded: chain c residue 311 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 21 optimal weight: 4.9990 chunk 47 optimal weight: 0.0470 chunk 48 optimal weight: 9.9990 chunk 54 optimal weight: 0.9990 chunk 33 optimal weight: 9.9990 chunk 77 optimal weight: 2.9990 chunk 79 optimal weight: 7.9990 chunk 40 optimal weight: 1.9990 chunk 66 optimal weight: 9.9990 chunk 96 optimal weight: 0.9990 chunk 7 optimal weight: 0.9990 overall best weight: 1.0086 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 93 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 185 ASN ** b 335 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 335 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 = 0.3344 r_free = 0.3344 target = 0.074670 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2904 r_free = 0.2904 target = 0.054973 restraints weight = 30407.129| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.2957 r_free = 0.2957 target = 0.057234 restraints weight = 17527.280| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.2992 r_free = 0.2992 target = 0.058763 restraints weight = 12614.790| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 21)----------------| | r_work = 0.3014 r_free = 0.3014 target = 0.059757 restraints weight = 10277.826| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3029 r_free = 0.3029 target = 0.060396 restraints weight = 9017.095| |-----------------------------------------------------------------------------| r_work (final): 0.3017 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8208 moved from start: 0.6779 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 9390 Z= 0.162 Angle : 0.936 20.217 12834 Z= 0.448 Chirality : 0.049 0.379 1599 Planarity : 0.004 0.039 1482 Dihedral : 5.057 23.312 1074 Min Nonbonded Distance : 2.374 Molprobity Statistics. All-atom Clashscore : 12.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.07 % Favored : 95.93 % Rotamer: Outliers : 2.74 % Allowed : 26.32 % Favored : 70.94 % 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: 0.59 (0.26), residues: 984 helix: 1.95 (0.27), residues: 345 sheet: 0.25 (0.48), residues: 117 loop : -0.66 (0.26), residues: 522 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG c 422 TYR 0.049 0.002 TYR C 241 PHE 0.024 0.002 PHE C 157 TRP 0.041 0.003 TRP A 210 HIS 0.009 0.001 HIS b 354 Details of bonding type rmsd/Z covalent geometry : bond 0.00360 / 0.16 ( 9294) covalent geometry : angle 0.88954 / 0.44 (12567) SS BOND : bond 0.00827 / 0.53 ( 21) SS BOND : angle 3.02036 / 2.06 ( 42) hydrogen bonds : bond 0.04078 / 2.66 ( 384) hydrogen bonds : angle 4.67679 / 3.24 ( 1035) link_ALPHA1-3 : bond 0.00219 / 0.11 ( 3) link_ALPHA1-3 : angle 1.59702 / 0.98 ( 9) link_ALPHA1-6 : bond 0.01052 / 0.53 ( 3) link_ALPHA1-6 : angle 1.39524 / 0.78 ( 9) link_BETA1-4 : bond 0.01158 / 0.74 ( 33) link_BETA1-4 : angle 2.48523 / 1.62 ( 99) link_BETA1-6 : bond 0.00469 / 0.24 ( 3) link_BETA1-6 : angle 1.20826 / 0.73 ( 9) link_NAG-ASN : bond 0.00206 / 0.13 ( 33) link_NAG-ASN : angle 1.61407 / 1.02 ( 99) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1968 Ramachandran restraints generated. 984 Oldfield, 0 Emsley, 984 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1968 Ramachandran restraints generated. 984 Oldfield, 0 Emsley, 984 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 220 residues out of total 912 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 195 time to evaluate : 0.354 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: A 76 GLU cc_start: 0.9060 (tt0) cc_final: 0.8184 (tm-30) REVERT: A 80 MET cc_start: 0.8851 (mmt) cc_final: 0.8566 (mpp) REVERT: A 130 ASP cc_start: 0.8263 (t0) cc_final: 0.7825 (t0) REVERT: A 218 GLN cc_start: 0.8899 (OUTLIER) cc_final: 0.8465 (pm20) REVERT: a 278 TYR cc_start: 0.8222 (t80) cc_final: 0.7883 (t80) REVERT: a 300 LYS cc_start: 0.9435 (mmtm) cc_final: 0.8920 (mptt) REVERT: a 311 ASP cc_start: 0.9038 (OUTLIER) cc_final: 0.8776 (t0) REVERT: a 357 ASP cc_start: 0.9335 (t70) cc_final: 0.8933 (t0) REVERT: a 408 ASP cc_start: 0.9188 (m-30) cc_final: 0.8836 (m-30) REVERT: B 76 GLU cc_start: 0.9103 (tt0) cc_final: 0.8310 (tm-30) REVERT: B 130 ASP cc_start: 0.8249 (t0) cc_final: 0.7802 (t0) REVERT: b 357 ASP cc_start: 0.9276 (t70) cc_final: 0.8849 (t0) REVERT: b 405 GLN cc_start: 0.9566 (tp40) cc_final: 0.9288 (tp-100) REVERT: b 413 GLU cc_start: 0.8833 (mp0) cc_final: 0.8524 (pm20) REVERT: b 420 MET cc_start: 0.7518 (mmt) cc_final: 0.7095 (mmt) REVERT: C 80 MET cc_start: 0.9078 (mmt) cc_final: 0.8618 (mmm) REVERT: C 130 ASP cc_start: 0.8023 (t0) cc_final: 0.7599 (t70) REVERT: C 194 MET cc_start: 0.9217 (tpp) cc_final: 0.8893 (tpp) REVERT: c 278 TYR cc_start: 0.8211 (t80) cc_final: 0.7803 (t80) REVERT: c 311 ASP cc_start: 0.9092 (OUTLIER) cc_final: 0.8695 (t0) REVERT: c 351 MET cc_start: 0.8565 (mmp) cc_final: 0.8150 (mmp) REVERT: c 410 MET cc_start: 0.9070 (tpp) cc_final: 0.8836 (tpp) REVERT: c 417 LYS cc_start: 0.9255 (pttp) cc_final: 0.8930 (pttp) outliers start: 25 outliers final: 22 residues processed: 214 average time/residue: 0.0813 time to fit residues: 25.1790 Evaluate side-chains 212 residues out of total 912 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 187 time to evaluate : 0.340 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 86 CYS Chi-restraints excluded: chain A residue 128 LEU Chi-restraints excluded: chain A residue 156 ASP Chi-restraints excluded: chain A residue 185 ASN Chi-restraints excluded: chain A residue 218 GLN Chi-restraints excluded: chain A residue 245 LEU Chi-restraints excluded: chain a residue 311 ASP Chi-restraints excluded: chain a residue 337 ILE Chi-restraints excluded: chain B residue 82 MET Chi-restraints excluded: chain B residue 86 CYS Chi-restraints excluded: chain B residue 128 LEU Chi-restraints excluded: chain B residue 185 ASN Chi-restraints excluded: chain B residue 245 LEU Chi-restraints excluded: chain b residue 274 THR Chi-restraints excluded: chain b residue 279 CYS Chi-restraints excluded: chain b residue 349 LEU Chi-restraints excluded: chain b residue 351 MET Chi-restraints excluded: chain b residue 385 CYS Chi-restraints excluded: chain b residue 403 ILE Chi-restraints excluded: chain C residue 86 CYS Chi-restraints excluded: chain C residue 128 LEU Chi-restraints excluded: chain C residue 245 LEU Chi-restraints excluded: chain c residue 279 CYS Chi-restraints excluded: chain c residue 285 LEU Chi-restraints excluded: chain c residue 311 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 97 optimal weight: 6.9990 chunk 91 optimal weight: 7.9990 chunk 82 optimal weight: 0.8980 chunk 70 optimal weight: 10.0000 chunk 63 optimal weight: 0.9980 chunk 40 optimal weight: 6.9990 chunk 60 optimal weight: 4.9990 chunk 80 optimal weight: 6.9990 chunk 15 optimal weight: 4.9990 chunk 59 optimal weight: 3.9990 chunk 3 optimal weight: 0.9990 overall best weight: 2.3786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 93 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 185 ASN ** B 218 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 335 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 335 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 = 0.3315 r_free = 0.3315 target = 0.072979 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2859 r_free = 0.2859 target = 0.053108 restraints weight = 30341.955| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.2912 r_free = 0.2912 target = 0.055288 restraints weight = 17670.472| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.2948 r_free = 0.2948 target = 0.056801 restraints weight = 12829.282| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.2971 r_free = 0.2971 target = 0.057762 restraints weight = 10505.998| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.2986 r_free = 0.2986 target = 0.058434 restraints weight = 9243.788| |-----------------------------------------------------------------------------| r_work (final): 0.2983 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8259 moved from start: 0.6828 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 9390 Z= 0.198 Angle : 0.950 19.456 12834 Z= 0.454 Chirality : 0.049 0.367 1599 Planarity : 0.004 0.039 1482 Dihedral : 5.078 23.724 1074 Min Nonbonded Distance : 2.374 Molprobity Statistics. All-atom Clashscore : 13.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.37 % Favored : 95.63 % Rotamer: Outliers : 2.96 % Allowed : 26.64 % Favored : 70.39 % 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: 0.62 (0.27), residues: 984 helix: 1.98 (0.28), residues: 345 sheet: 0.21 (0.48), residues: 117 loop : -0.61 (0.26), residues: 522 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG a 422 TYR 0.029 0.002 TYR A 241 PHE 0.022 0.002 PHE C 157 TRP 0.044 0.003 TRP C 227 HIS 0.011 0.001 HIS b 354 Details of bonding type rmsd/Z covalent geometry : bond 0.00440 / 0.20 ( 9294) covalent geometry : angle 0.90229 / 0.44 (12567) SS BOND : bond 0.00805 / 0.51 ( 21) SS BOND : angle 3.00761 / 2.04 ( 42) hydrogen bonds : bond 0.04125 / 2.70 ( 384) hydrogen bonds : angle 4.77926 / 3.29 ( 1035) link_ALPHA1-3 : bond 0.00078 / 0.04 ( 3) link_ALPHA1-3 : angle 1.73502 / 1.06 ( 9) link_ALPHA1-6 : bond 0.01027 / 0.51 ( 3) link_ALPHA1-6 : angle 1.36941 / 0.76 ( 9) link_BETA1-4 : bond 0.01163 / 0.74 ( 33) link_BETA1-4 : angle 2.47744 / 1.62 ( 99) link_BETA1-6 : bond 0.00379 / 0.19 ( 3) link_BETA1-6 : angle 1.33377 / 0.82 ( 9) link_NAG-ASN : bond 0.00223 / 0.12 ( 33) link_NAG-ASN : angle 1.78000 / 1.12 ( 99) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1345.74 seconds wall clock time: 24 minutes 14.94 seconds (1454.94 seconds total)