Starting phenix.real_space_refine on Tue Mar 3 23:35:12 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7sgd_25107/03_2026/7sgd_25107.cif Found real_map, /net/cci-nas-00/data/ceres_data/7sgd_25107/03_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_25107/03_2026/7sgd_25107.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7sgd_25107/03_2026/7sgd_25107.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7sgd_25107/03_2026/7sgd_25107.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7sgd_25107/03_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): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/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 dihedrals: 6 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 dihedrals: 6 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 dihedrals: 9 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 dihedrals: 6 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 dihedrals: 6 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 dihedrals: 6 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 dihedrals: 15 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 dihedrals: 6 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 dihedrals: 9 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 dihedrals: 6 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 dihedrals: 6 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 dihedrals: 9 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 dihedrals: 6 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 dihedrals: 6 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 dihedrals: 6 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 dihedrals: 15 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 dihedrals: 6 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 dihedrals: 9 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 dihedrals: 6 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 dihedrals: 6 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 dihedrals: 9 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 dihedrals: 6 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 dihedrals: 6 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 dihedrals: 6 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 dihedrals: 15 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 dihedrals: 6 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 dihedrals: 9 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 dihedrals: 3 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 dihedrals: 3 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 dihedrals: 3 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 dihedrals: 3 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 dihedrals: 3 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 dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 2.07, per 1000 atoms: 0.23 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: 0.81 Conformation dependent library (CDL) restraints added in 225.7 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: 0.24 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: 1.08 Time building geometry restraints manager: 1.00 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 - 21.39: 6222 21.39 - 42.78: 174 42.78 - 64.17: 54 64.17 - 85.56: 42 85.56 - 106.95: 24 Dihedral angle restraints: 6516 sinusoidal: 3558 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 6513 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: 0.680 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.000 Extract box with map and model: 0.130 Check model and map are aligned: 0.020 Set scattering table: 0.030 Process input model: 8.380 Find NCS groups from input model: 0.200 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:1.130 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 10.600 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8148 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 : 14.410 106.948 4545 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 covalent geometry : bond 0.02384 ( 9294) covalent geometry : angle 1.79736 (12567) SS BOND : bond 0.00890 ( 21) SS BOND : angle 2.81040 ( 42) hydrogen bonds : bond 0.16051 ( 384) hydrogen bonds : angle 6.47171 ( 1035) link_ALPHA1-3 : bond 0.08716 ( 3) link_ALPHA1-3 : angle 4.33137 ( 9) link_ALPHA1-6 : bond 0.07039 ( 3) link_ALPHA1-6 : angle 3.83579 ( 9) link_BETA1-4 : bond 0.06947 ( 33) link_BETA1-4 : angle 5.62681 ( 99) link_BETA1-6 : bond 0.06593 ( 3) link_BETA1-6 : angle 4.74660 ( 9) link_NAG-ASN : bond 0.07397 ( 33) link_NAG-ASN : angle 3.52360 ( 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 : 0.295 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: 0.1020 time to fit residues: 64.1686 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 : 0.346 ------------------------------------------------------------------------------- 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... Flipped N/Q/H residues before XYZ refinement: 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 = 0.3410 r_free = 0.3410 target = 0.076556 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2978 r_free = 0.2978 target = 0.057065 restraints weight = 29163.699| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3035 r_free = 0.3035 target = 0.059596 restraints weight = 15325.258| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3075 r_free = 0.3075 target = 0.061360 restraints weight = 10567.400| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3099 r_free = 0.3099 target = 0.062479 restraints weight = 8406.303| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3116 r_free = 0.3116 target = 0.063243 restraints weight = 7244.512| |-----------------------------------------------------------------------------| r_work (final): 0.3115 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8082 moved from start: 0.4598 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 9390 Z= 0.215 Angle : 1.030 13.294 12834 Z= 0.497 Chirality : 0.052 0.316 1599 Planarity : 0.005 0.028 1482 Dihedral : 13.349 82.284 2613 Min Nonbonded Distance : 2.417 Molprobity Statistics. All-atom Clashscore : 10.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.03 % Favored : 97.97 % Rotamer: Outliers : 4.71 % Allowed : 18.42 % Favored : 76.86 % 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: 0.41 (0.25), residues: 984 helix: 1.23 (0.26), residues: 366 sheet: 1.81 (0.50), residues: 108 loop : -0.80 (0.23), residues: 510 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG a 325 TYR 0.025 0.002 TYR C 166 PHE 0.026 0.002 PHE A 157 TRP 0.014 0.002 TRP A 227 HIS 0.007 0.001 HIS C 230 Details of bonding type rmsd covalent geometry : bond 0.00437 ( 9294) covalent geometry : angle 0.92479 (12567) SS BOND : bond 0.00883 ( 21) SS BOND : angle 2.97075 ( 42) hydrogen bonds : bond 0.05889 ( 384) hydrogen bonds : angle 5.15783 ( 1035) link_ALPHA1-3 : bond 0.00849 ( 3) link_ALPHA1-3 : angle 2.88229 ( 9) link_ALPHA1-6 : bond 0.01184 ( 3) link_ALPHA1-6 : angle 1.38377 ( 9) link_BETA1-4 : bond 0.01738 ( 33) link_BETA1-4 : angle 3.93032 ( 99) link_BETA1-6 : bond 0.00510 ( 3) link_BETA1-6 : angle 1.29602 ( 9) link_NAG-ASN : bond 0.00358 ( 33) link_NAG-ASN : angle 2.93779 ( 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 351 residues out of total 912 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 308 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: A 72 GLU cc_start: 0.8131 (tt0) cc_final: 0.7894 (tt0) REVERT: A 130 ASP cc_start: 0.8496 (t0) cc_final: 0.7918 (t70) REVERT: a 300 LYS cc_start: 0.9190 (mmtm) cc_final: 0.8538 (mptt) REVERT: a 307 GLU cc_start: 0.8812 (mm-30) cc_final: 0.8573 (mm-30) REVERT: a 311 ASP cc_start: 0.9205 (m-30) cc_final: 0.8960 (m-30) REVERT: a 313 LEU cc_start: 0.9767 (tp) cc_final: 0.9325 (tp) REVERT: a 357 ASP cc_start: 0.9128 (t70) cc_final: 0.8598 (t0) REVERT: a 405 GLN cc_start: 0.9138 (tm-30) cc_final: 0.8795 (tm-30) REVERT: a 409 ASN cc_start: 0.8798 (m-40) cc_final: 0.8564 (m-40) REVERT: a 410 MET cc_start: 0.8631 (tpp) cc_final: 0.7975 (tpp) REVERT: a 413 GLU cc_start: 0.8415 (pp20) cc_final: 0.8010 (pp20) REVERT: a 416 GLN cc_start: 0.9003 (mm-40) cc_final: 0.8715 (mm-40) REVERT: B 130 ASP cc_start: 0.8239 (t0) cc_final: 0.7699 (t0) REVERT: B 211 ASP cc_start: 0.8411 (p0) cc_final: 0.8192 (p0) REVERT: b 261 THR cc_start: 0.8222 (p) cc_final: 0.7996 (p) REVERT: b 307 GLU cc_start: 0.8735 (mm-30) cc_final: 0.8231 (mp0) REVERT: b 311 ASP cc_start: 0.9194 (m-30) cc_final: 0.8927 (m-30) REVERT: b 313 LEU cc_start: 0.9778 (tp) cc_final: 0.9413 (tp) REVERT: b 346 ASN cc_start: 0.9351 (t0) cc_final: 0.9146 (t0) REVERT: b 357 ASP cc_start: 0.9077 (t70) cc_final: 0.8560 (t0) REVERT: b 369 TYR cc_start: 0.9257 (m-10) cc_final: 0.9001 (m-80) REVERT: b 405 GLN cc_start: 0.9085 (tm-30) cc_final: 0.8617 (tm-30) REVERT: b 410 MET cc_start: 0.8935 (OUTLIER) cc_final: 0.8302 (tpp) REVERT: b 413 GLU cc_start: 0.8774 (OUTLIER) cc_final: 0.8280 (pm20) REVERT: b 416 GLN cc_start: 0.9109 (mm-40) cc_final: 0.8758 (mm-40) REVERT: C 72 GLU cc_start: 0.8234 (tt0) cc_final: 0.7969 (tt0) REVERT: C 76 GLU cc_start: 0.9117 (tt0) cc_final: 0.8904 (tt0) REVERT: C 100 GLU cc_start: 0.7528 (mm-30) cc_final: 0.7287 (mm-30) REVERT: C 130 ASP cc_start: 0.8207 (t0) cc_final: 0.7677 (t70) REVERT: C 227 TRP cc_start: 0.7124 (t-100) cc_final: 0.6859 (t-100) REVERT: c 261 THR cc_start: 0.8134 (p) cc_final: 0.7932 (p) REVERT: c 278 TYR cc_start: 0.8322 (t80) cc_final: 0.7890 (t80) REVERT: c 300 LYS cc_start: 0.9150 (mmtm) cc_final: 0.8629 (mptt) REVERT: c 306 ASP cc_start: 0.8746 (t0) cc_final: 0.8458 (t70) REVERT: c 307 GLU cc_start: 0.8775 (mm-30) cc_final: 0.7990 (mp0) REVERT: c 313 LEU cc_start: 0.9749 (tp) cc_final: 0.9339 (tp) REVERT: c 401 ASP cc_start: 0.9203 (p0) cc_final: 0.8949 (p0) REVERT: c 408 ASP cc_start: 0.8992 (m-30) cc_final: 0.8346 (m-30) REVERT: c 409 ASN cc_start: 0.8582 (m-40) cc_final: 0.8206 (m-40) outliers start: 43 outliers final: 18 residues processed: 328 average time/residue: 0.0926 time to fit residues: 42.2797 Evaluate side-chains 280 residues out of total 912 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 260 time to evaluate : 0.325 ------------------------------------------------------------------------------- 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 273 ASP 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 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 b residue 421 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: 0.6980 chunk 30 optimal weight: 0.9990 chunk 90 optimal weight: 0.6980 chunk 80 optimal weight: 10.0000 chunk 22 optimal weight: 0.7980 chunk 85 optimal weight: 2.9990 chunk 58 optimal weight: 3.9990 chunk 36 optimal weight: 6.9990 chunk 17 optimal weight: 0.0050 chunk 12 optimal weight: 6.9990 overall best weight: 0.6396 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 185 ASN B 185 ASN C 69 GLN C 185 ASN C 232 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3409 r_free = 0.3409 target = 0.076908 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2991 r_free = 0.2991 target = 0.057896 restraints weight = 28949.893| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3048 r_free = 0.3048 target = 0.060348 restraints weight = 15673.441| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3086 r_free = 0.3086 target = 0.062046 restraints weight = 10921.143| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3111 r_free = 0.3111 target = 0.063189 restraints weight = 8697.971| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3127 r_free = 0.3127 target = 0.063963 restraints weight = 7511.219| |-----------------------------------------------------------------------------| r_work (final): 0.3122 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8129 moved from start: 0.5367 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 9390 Z= 0.172 Angle : 0.895 12.052 12834 Z= 0.427 Chirality : 0.049 0.252 1599 Planarity : 0.004 0.030 1482 Dihedral : 11.309 68.938 2613 Min Nonbonded Distance : 2.513 Molprobity Statistics. All-atom Clashscore : 9.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.54 % Favored : 97.46 % Rotamer: Outliers : 5.26 % Allowed : 21.05 % Favored : 73.68 % 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: 0.21 (0.25), residues: 984 helix: 1.09 (0.26), residues: 366 sheet: 0.97 (0.48), residues: 117 loop : -0.78 (0.24), residues: 501 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG a 282 TYR 0.025 0.002 TYR B 241 PHE 0.026 0.003 PHE A 157 TRP 0.029 0.003 TRP B 227 HIS 0.003 0.001 HIS a 305 Details of bonding type rmsd covalent geometry : bond 0.00354 ( 9294) covalent geometry : angle 0.82652 (12567) SS BOND : bond 0.00359 ( 21) SS BOND : angle 1.36434 ( 42) hydrogen bonds : bond 0.05082 ( 384) hydrogen bonds : angle 4.78493 ( 1035) link_ALPHA1-3 : bond 0.01188 ( 3) link_ALPHA1-3 : angle 2.09920 ( 9) link_ALPHA1-6 : bond 0.01502 ( 3) link_ALPHA1-6 : angle 1.48646 ( 9) link_BETA1-4 : bond 0.01509 ( 33) link_BETA1-4 : angle 3.29459 ( 99) link_BETA1-6 : bond 0.00483 ( 3) link_BETA1-6 : angle 1.22835 ( 9) link_NAG-ASN : bond 0.00454 ( 33) link_NAG-ASN : angle 2.19470 ( 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 339 residues out of total 912 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 291 time to evaluate : 0.294 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: 0.8383 (mtp) cc_final: 0.8055 (mtp) REVERT: A 76 GLU cc_start: 0.9016 (tt0) cc_final: 0.8192 (tm-30) REVERT: A 130 ASP cc_start: 0.8363 (t0) cc_final: 0.7806 (t70) REVERT: a 300 LYS cc_start: 0.9302 (mmtm) cc_final: 0.8761 (mptt) REVERT: a 357 ASP cc_start: 0.9140 (t70) cc_final: 0.8625 (t0) REVERT: a 416 GLN cc_start: 0.9107 (mm-40) cc_final: 0.8880 (mt0) REVERT: a 417 LYS cc_start: 0.9204 (pttp) cc_final: 0.8713 (pttm) REVERT: B 76 GLU cc_start: 0.9058 (tt0) cc_final: 0.8193 (tm-30) REVERT: B 130 ASP cc_start: 0.8204 (t0) cc_final: 0.7712 (t0) REVERT: B 227 TRP cc_start: 0.6836 (t-100) cc_final: 0.6528 (t60) REVERT: b 261 THR cc_start: 0.8324 (p) cc_final: 0.8120 (p) REVERT: b 306 ASP cc_start: 0.8227 (OUTLIER) cc_final: 0.7948 (m-30) REVERT: b 307 GLU cc_start: 0.8702 (mm-30) cc_final: 0.7841 (mp0) REVERT: b 313 LEU cc_start: 0.9708 (tp) cc_final: 0.9292 (tp) REVERT: b 357 ASP cc_start: 0.9108 (t70) cc_final: 0.8697 (t0) REVERT: b 404 GLU cc_start: 0.9124 (mm-30) cc_final: 0.8823 (mm-30) REVERT: b 406 GLN cc_start: 0.9764 (tp40) cc_final: 0.9554 (tp40) REVERT: b 416 GLN cc_start: 0.9164 (mm-40) cc_final: 0.8829 (mt0) REVERT: C 100 GLU cc_start: 0.7629 (mm-30) cc_final: 0.7336 (mm-30) REVERT: C 130 ASP cc_start: 0.8213 (t0) cc_final: 0.7661 (t70) REVERT: c 261 THR cc_start: 0.8270 (p) cc_final: 0.8047 (p) REVERT: c 278 TYR cc_start: 0.8329 (t80) cc_final: 0.7989 (t80) REVERT: c 300 LYS cc_start: 0.9259 (mmtm) cc_final: 0.8773 (mptt) REVERT: c 313 LEU cc_start: 0.9707 (tp) cc_final: 0.9237 (tp) REVERT: c 348 GLN cc_start: 0.8657 (mp10) cc_final: 0.8305 (mp10) REVERT: c 402 ASP cc_start: 0.9308 (t0) cc_final: 0.8991 (t70) REVERT: c 410 MET cc_start: 0.9000 (tpp) cc_final: 0.8650 (tpp) REVERT: c 413 GLU cc_start: 0.8801 (mp0) cc_final: 0.8436 (tm-30) REVERT: c 417 LYS cc_start: 0.9277 (pttp) cc_final: 0.8778 (pttm) outliers start: 48 outliers final: 25 residues processed: 321 average time/residue: 0.0876 time to fit residues: 38.7336 Evaluate side-chains 255 residues out of total 912 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 229 time to evaluate : 0.285 ------------------------------------------------------------------------------- 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 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 b residue 421 GLU 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: 6.9990 chunk 69 optimal weight: 9.9990 chunk 88 optimal weight: 4.9990 chunk 95 optimal weight: 6.9990 chunk 60 optimal weight: 1.9990 chunk 62 optimal weight: 0.9990 chunk 65 optimal weight: 0.9990 chunk 12 optimal weight: 7.9990 chunk 45 optimal weight: 7.9990 chunk 42 optimal weight: 0.9980 chunk 25 optimal weight: 10.0000 overall best weight: 1.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** a 423 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 185 ASN ** b 405 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 406 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 423 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 = 0.3366 r_free = 0.3366 target = 0.074536 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2926 r_free = 0.2926 target = 0.055271 restraints weight = 29966.873| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.2984 r_free = 0.2984 target = 0.057610 restraints weight = 16663.460| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3021 r_free = 0.3021 target = 0.059168 restraints weight = 11827.579| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3045 r_free = 0.3045 target = 0.060232 restraints weight = 9578.066| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3061 r_free = 0.3061 target = 0.060925 restraints weight = 8354.449| |-----------------------------------------------------------------------------| r_work (final): 0.3055 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8233 moved from start: 0.5753 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 9390 Z= 0.184 Angle : 0.860 10.695 12834 Z= 0.408 Chirality : 0.048 0.262 1599 Planarity : 0.004 0.042 1482 Dihedral : 10.070 59.668 2613 Min Nonbonded Distance : 2.430 Molprobity Statistics. All-atom Clashscore : 12.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.05 % Favored : 96.95 % Rotamer: Outliers : 5.26 % Allowed : 23.57 % Favored : 71.16 % 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: 0.24 (0.25), residues: 984 helix: 1.19 (0.26), residues: 375 sheet: 1.44 (0.50), residues: 108 loop : -0.96 (0.23), residues: 501 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.020 0.001 ARG a 422 TYR 0.020 0.002 TYR A 166 PHE 0.024 0.003 PHE A 157 TRP 0.016 0.002 TRP A 210 HIS 0.008 0.001 HIS b 354 Details of bonding type rmsd covalent geometry : bond 0.00391 ( 9294) covalent geometry : angle 0.79504 (12567) SS BOND : bond 0.00299 ( 21) SS BOND : angle 0.97091 ( 42) hydrogen bonds : bond 0.04586 ( 384) hydrogen bonds : angle 4.62531 ( 1035) link_ALPHA1-3 : bond 0.00885 ( 3) link_ALPHA1-3 : angle 2.97033 ( 9) link_ALPHA1-6 : bond 0.01304 ( 3) link_ALPHA1-6 : angle 1.41283 ( 9) link_BETA1-4 : bond 0.01217 ( 33) link_BETA1-4 : angle 3.09047 ( 99) link_BETA1-6 : bond 0.00327 ( 3) link_BETA1-6 : angle 1.34386 ( 9) link_NAG-ASN : bond 0.00295 ( 33) link_NAG-ASN : angle 2.12045 ( 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 281 residues out of total 912 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 233 time to evaluate : 0.218 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: A 130 ASP cc_start: 0.8335 (t0) cc_final: 0.7789 (t70) REVERT: A 140 PHE cc_start: 0.9452 (t80) cc_final: 0.9130 (t80) REVERT: A 194 MET cc_start: 0.9430 (OUTLIER) cc_final: 0.9114 (tpp) REVERT: A 211 ASP cc_start: 0.8648 (p0) cc_final: 0.7905 (p0) REVERT: A 227 TRP cc_start: 0.6564 (t-100) cc_final: 0.5967 (t60) REVERT: a 300 LYS cc_start: 0.9367 (mmtm) cc_final: 0.8826 (mptt) REVERT: a 357 ASP cc_start: 0.9237 (t70) cc_final: 0.8737 (t0) REVERT: B 130 ASP cc_start: 0.8129 (t0) cc_final: 0.7662 (t70) REVERT: b 261 THR cc_start: 0.8488 (p) cc_final: 0.8272 (p) REVERT: b 306 ASP cc_start: 0.8134 (OUTLIER) cc_final: 0.7592 (m-30) REVERT: b 313 LEU cc_start: 0.9725 (tp) cc_final: 0.9339 (tp) REVERT: b 357 ASP cc_start: 0.9208 (t70) cc_final: 0.8732 (t0) REVERT: b 410 MET cc_start: 0.8864 (tpp) cc_final: 0.7941 (tpp) REVERT: b 413 GLU cc_start: 0.8700 (OUTLIER) cc_final: 0.8254 (pm20) REVERT: C 76 GLU cc_start: 0.9151 (tt0) cc_final: 0.8920 (tt0) REVERT: C 82 MET cc_start: 0.9009 (OUTLIER) cc_final: 0.8795 (pmm) REVERT: C 100 GLU cc_start: 0.7620 (mm-30) cc_final: 0.7327 (mm-30) REVERT: C 130 ASP cc_start: 0.8182 (t0) cc_final: 0.7755 (t70) REVERT: c 278 TYR cc_start: 0.8364 (t80) cc_final: 0.7968 (t80) REVERT: c 300 LYS cc_start: 0.9317 (mmtm) cc_final: 0.8847 (mptt) REVERT: c 311 ASP cc_start: 0.9021 (OUTLIER) cc_final: 0.8701 (t0) REVERT: c 313 LEU cc_start: 0.9729 (tp) cc_final: 0.9186 (tp) REVERT: c 351 MET cc_start: 0.8841 (mmp) cc_final: 0.8416 (mmp) REVERT: c 410 MET cc_start: 0.9064 (tpp) cc_final: 0.8740 (tpp) REVERT: c 413 GLU cc_start: 0.8818 (OUTLIER) cc_final: 0.8542 (tm-30) REVERT: c 416 GLN cc_start: 0.9308 (tp-100) cc_final: 0.8750 (tp-100) outliers start: 48 outliers final: 25 residues processed: 266 average time/residue: 0.0886 time to fit residues: 32.7738 Evaluate side-chains 245 residues out of total 912 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 214 time to evaluate : 0.262 ------------------------------------------------------------------------------- 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 194 MET 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 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 185 ASN 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 403 ILE Chi-restraints excluded: chain b residue 413 GLU Chi-restraints excluded: chain b residue 421 GLU 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 311 ASP Chi-restraints excluded: chain c residue 380 THR Chi-restraints excluded: chain c residue 413 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 94 optimal weight: 5.9990 chunk 35 optimal weight: 1.9990 chunk 57 optimal weight: 3.9990 chunk 43 optimal weight: 5.9990 chunk 20 optimal weight: 10.0000 chunk 12 optimal weight: 5.9990 chunk 37 optimal weight: 3.9990 chunk 59 optimal weight: 5.9990 chunk 73 optimal weight: 3.9990 chunk 31 optimal weight: 6.9990 chunk 64 optimal weight: 6.9990 overall best weight: 3.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 115 HIS ** a 423 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 115 HIS b 405 GLN b 416 GLN C 115 HIS ** c 406 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** c 416 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3266 r_free = 0.3266 target = 0.070529 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2811 r_free = 0.2811 target = 0.051104 restraints weight = 30679.618| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.2863 r_free = 0.2863 target = 0.053184 restraints weight = 17721.409| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.2899 r_free = 0.2899 target = 0.054648 restraints weight = 12840.924| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.2921 r_free = 0.2921 target = 0.055574 restraints weight = 10524.397| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.2938 r_free = 0.2938 target = 0.056237 restraints weight = 9295.560| |-----------------------------------------------------------------------------| r_work (final): 0.2929 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8328 moved from start: 0.6046 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.046 9390 Z= 0.268 Angle : 0.908 10.853 12834 Z= 0.432 Chirality : 0.049 0.295 1599 Planarity : 0.004 0.037 1482 Dihedral : 9.570 56.075 2613 Min Nonbonded Distance : 2.436 Molprobity Statistics. All-atom Clashscore : 14.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.76 % Favored : 96.24 % Rotamer: Outliers : 5.59 % Allowed : 23.57 % Favored : 70.83 % 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: 0.18 (0.25), residues: 984 helix: 1.19 (0.27), residues: 372 sheet: 1.28 (0.50), residues: 108 loop : -0.99 (0.24), residues: 504 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG a 422 TYR 0.020 0.002 TYR C 241 PHE 0.020 0.003 PHE A 157 TRP 0.029 0.003 TRP A 210 HIS 0.005 0.001 HIS b 354 Details of bonding type rmsd covalent geometry : bond 0.00568 ( 9294) covalent geometry : angle 0.84896 (12567) SS BOND : bond 0.00378 ( 21) SS BOND : angle 0.92071 ( 42) hydrogen bonds : bond 0.04639 ( 384) hydrogen bonds : angle 4.82053 ( 1035) link_ALPHA1-3 : bond 0.00788 ( 3) link_ALPHA1-3 : angle 3.05537 ( 9) link_ALPHA1-6 : bond 0.01426 ( 3) link_ALPHA1-6 : angle 1.55992 ( 9) link_BETA1-4 : bond 0.01186 ( 33) link_BETA1-4 : angle 2.98215 ( 99) link_BETA1-6 : bond 0.00228 ( 3) link_BETA1-6 : angle 1.56277 ( 9) link_NAG-ASN : bond 0.00402 ( 33) link_NAG-ASN : angle 2.20203 ( 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 261 residues out of total 912 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 210 time to evaluate : 0.334 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: A 76 GLU cc_start: 0.9047 (tt0) cc_final: 0.8194 (tm-30) REVERT: A 130 ASP cc_start: 0.8385 (t0) cc_final: 0.7887 (t0) REVERT: A 211 ASP cc_start: 0.8232 (p0) cc_final: 0.7897 (p0) REVERT: a 300 LYS cc_start: 0.9395 (mmtm) cc_final: 0.8845 (mptt) REVERT: a 357 ASP cc_start: 0.9371 (t70) cc_final: 0.8845 (t0) REVERT: B 80 MET cc_start: 0.8982 (mmt) cc_final: 0.8461 (mmm) REVERT: B 130 ASP cc_start: 0.8218 (t0) cc_final: 0.7740 (t70) REVERT: b 306 ASP cc_start: 0.8354 (OUTLIER) cc_final: 0.7972 (m-30) REVERT: b 313 LEU cc_start: 0.9735 (tp) cc_final: 0.9351 (tp) REVERT: b 357 ASP cc_start: 0.9378 (t70) cc_final: 0.8825 (t0) REVERT: b 413 GLU cc_start: 0.8642 (OUTLIER) cc_final: 0.8225 (pm20) REVERT: C 76 GLU cc_start: 0.9230 (tt0) cc_final: 0.8931 (tt0) REVERT: C 96 MET cc_start: 0.8052 (ptp) cc_final: 0.7776 (ptp) REVERT: C 130 ASP cc_start: 0.8108 (t0) cc_final: 0.7580 (t70) REVERT: c 278 TYR cc_start: 0.8555 (t80) cc_final: 0.8125 (t80) REVERT: c 311 ASP cc_start: 0.9132 (OUTLIER) cc_final: 0.8819 (t0) REVERT: c 313 LEU cc_start: 0.9713 (tp) cc_final: 0.9167 (tp) REVERT: c 325 ARG cc_start: 0.8649 (mmm160) cc_final: 0.8402 (mmm160) REVERT: c 413 GLU cc_start: 0.8821 (mp0) cc_final: 0.8608 (tm-30) outliers start: 51 outliers final: 34 residues processed: 251 average time/residue: 0.0868 time to fit residues: 30.7268 Evaluate side-chains 234 residues out of total 912 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 197 time to evaluate : 0.216 ------------------------------------------------------------------------------- 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 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 239 ILE Chi-restraints excluded: chain a residue 274 THR 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 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 218 GLN 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 392 SER Chi-restraints excluded: chain b residue 403 ILE Chi-restraints excluded: chain b residue 413 GLU Chi-restraints excluded: chain b residue 421 GLU 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 392 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 63 optimal weight: 4.9990 chunk 60 optimal weight: 3.9990 chunk 11 optimal weight: 9.9990 chunk 58 optimal weight: 4.9990 chunk 81 optimal weight: 10.0000 chunk 33 optimal weight: 8.9990 chunk 85 optimal weight: 6.9990 chunk 96 optimal weight: 0.8980 chunk 52 optimal weight: 2.9990 chunk 70 optimal weight: 10.0000 chunk 48 optimal weight: 9.9990 overall best weight: 3.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 93 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 209 ASN a 416 GLN ** a 423 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** c 416 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3249 r_free = 0.3249 target = 0.070372 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2785 r_free = 0.2785 target = 0.050419 restraints weight = 31298.390| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 23)----------------| | r_work = 0.2839 r_free = 0.2839 target = 0.052606 restraints weight = 17642.248| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.2875 r_free = 0.2875 target = 0.054089 restraints weight = 12656.522| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.2899 r_free = 0.2899 target = 0.055082 restraints weight = 10345.091| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.2915 r_free = 0.2915 target = 0.055734 restraints weight = 9081.389| |-----------------------------------------------------------------------------| r_work (final): 0.2914 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8341 moved from start: 0.6361 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.047 9390 Z= 0.240 Angle : 0.885 11.021 12834 Z= 0.419 Chirality : 0.049 0.302 1599 Planarity : 0.004 0.040 1482 Dihedral : 9.304 56.180 2613 Min Nonbonded Distance : 2.356 Molprobity Statistics. All-atom Clashscore : 13.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.96 % Favored : 96.04 % Rotamer: Outliers : 5.70 % Allowed : 23.36 % 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: 0.10 (0.26), residues: 984 helix: 1.27 (0.27), residues: 369 sheet: 0.66 (0.49), residues: 117 loop : -1.03 (0.25), residues: 498 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG a 422 TYR 0.025 0.002 TYR B 241 PHE 0.021 0.003 PHE A 157 TRP 0.027 0.002 TRP A 227 HIS 0.005 0.001 HIS b 354 Details of bonding type rmsd covalent geometry : bond 0.00515 ( 9294) covalent geometry : angle 0.82837 (12567) SS BOND : bond 0.00329 ( 21) SS BOND : angle 0.89311 ( 42) hydrogen bonds : bond 0.04440 ( 384) hydrogen bonds : angle 4.73027 ( 1035) link_ALPHA1-3 : bond 0.00785 ( 3) link_ALPHA1-3 : angle 2.93181 ( 9) link_ALPHA1-6 : bond 0.01452 ( 3) link_ALPHA1-6 : angle 1.67633 ( 9) link_BETA1-4 : bond 0.01210 ( 33) link_BETA1-4 : angle 2.90028 ( 99) link_BETA1-6 : bond 0.00359 ( 3) link_BETA1-6 : angle 1.43905 ( 9) link_NAG-ASN : bond 0.00304 ( 33) link_NAG-ASN : angle 2.10086 ( 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 261 residues out of total 912 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 209 time to evaluate : 0.258 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: A 130 ASP cc_start: 0.8558 (t0) cc_final: 0.8042 (t0) REVERT: A 211 ASP cc_start: 0.8433 (p0) cc_final: 0.8047 (p0) REVERT: a 300 LYS cc_start: 0.9396 (mmtm) cc_final: 0.8887 (mptt) REVERT: a 357 ASP cc_start: 0.9445 (t70) cc_final: 0.8886 (t0) REVERT: B 80 MET cc_start: 0.9007 (mmt) cc_final: 0.8513 (mmm) REVERT: B 130 ASP cc_start: 0.8367 (t0) cc_final: 0.7880 (t70) REVERT: B 194 MET cc_start: 0.9556 (tpp) cc_final: 0.9311 (tpp) REVERT: b 306 ASP cc_start: 0.8390 (OUTLIER) cc_final: 0.8081 (m-30) REVERT: b 313 LEU cc_start: 0.9734 (tp) cc_final: 0.9350 (tp) REVERT: b 357 ASP cc_start: 0.9427 (t70) cc_final: 0.8878 (t0) REVERT: b 410 MET cc_start: 0.9110 (tpp) cc_final: 0.8872 (tpp) REVERT: C 76 GLU cc_start: 0.9269 (tt0) cc_final: 0.8973 (tt0) REVERT: C 82 MET cc_start: 0.9272 (ptt) cc_final: 0.9018 (ptp) REVERT: C 96 MET cc_start: 0.8253 (ptp) cc_final: 0.7847 (ptm) REVERT: C 130 ASP cc_start: 0.8186 (t0) cc_final: 0.7648 (t70) REVERT: c 278 TYR cc_start: 0.8548 (t80) cc_final: 0.8188 (t80) REVERT: c 300 LYS cc_start: 0.9380 (mmtm) cc_final: 0.8955 (mptt) REVERT: c 311 ASP cc_start: 0.9177 (OUTLIER) cc_final: 0.8889 (t0) REVERT: c 313 LEU cc_start: 0.9730 (tp) cc_final: 0.9223 (tp) REVERT: c 351 MET cc_start: 0.8811 (mmp) cc_final: 0.8456 (mmp) REVERT: c 413 GLU cc_start: 0.8854 (mp0) cc_final: 0.8545 (tm-30) outliers start: 52 outliers final: 39 residues processed: 249 average time/residue: 0.0900 time to fit residues: 31.1195 Evaluate side-chains 232 residues out of total 912 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 191 time to evaluate : 0.245 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 72 GLU 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 239 ILE Chi-restraints excluded: chain A residue 245 LEU Chi-restraints excluded: chain a residue 274 THR Chi-restraints excluded: chain a residue 337 ILE Chi-restraints excluded: chain a residue 341 VAL Chi-restraints excluded: chain a residue 361 ILE Chi-restraints excluded: chain a residue 388 VAL Chi-restraints excluded: chain B residue 72 GLU 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 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 311 ASP Chi-restraints excluded: chain b residue 323 ILE 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 392 SER Chi-restraints excluded: chain b residue 403 ILE Chi-restraints excluded: chain b residue 421 GLU 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 392 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 43 optimal weight: 10.0000 chunk 1 optimal weight: 0.9980 chunk 75 optimal weight: 0.0870 chunk 24 optimal weight: 0.9990 chunk 68 optimal weight: 2.9990 chunk 42 optimal weight: 0.9980 chunk 57 optimal weight: 4.9990 chunk 22 optimal weight: 0.9980 chunk 14 optimal weight: 6.9990 chunk 17 optimal weight: 2.9990 chunk 44 optimal weight: 8.9990 overall best weight: 0.8160 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 93 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** a 416 GLN ** a 423 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 93 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 185 ASN b 405 GLN b 416 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3338 r_free = 0.3338 target = 0.073566 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2894 r_free = 0.2894 target = 0.054132 restraints weight = 29904.673| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 20)----------------| | r_work = 0.2950 r_free = 0.2950 target = 0.056425 restraints weight = 16655.460| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.2987 r_free = 0.2987 target = 0.057982 restraints weight = 11823.189| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3011 r_free = 0.3011 target = 0.059032 restraints weight = 9575.358| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3027 r_free = 0.3027 target = 0.059737 restraints weight = 8350.620| |-----------------------------------------------------------------------------| r_work (final): 0.3022 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8289 moved from start: 0.6521 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.091 9390 Z= 0.151 Angle : 0.837 11.138 12834 Z= 0.397 Chirality : 0.048 0.324 1599 Planarity : 0.004 0.043 1482 Dihedral : 8.961 55.213 2613 Min Nonbonded Distance : 2.486 Molprobity Statistics. All-atom Clashscore : 11.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.56 % Favored : 96.44 % Rotamer: Outliers : 5.04 % Allowed : 24.45 % 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: 0.25 (0.26), residues: 984 helix: 1.31 (0.27), residues: 369 sheet: 0.75 (0.49), residues: 117 loop : -0.87 (0.26), residues: 498 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG c 422 TYR 0.019 0.002 TYR C 241 PHE 0.025 0.002 PHE A 157 TRP 0.022 0.002 TRP B 210 HIS 0.004 0.001 HIS b 354 Details of bonding type rmsd covalent geometry : bond 0.00330 ( 9294) covalent geometry : angle 0.78221 (12567) SS BOND : bond 0.00415 ( 21) SS BOND : angle 1.43429 ( 42) hydrogen bonds : bond 0.04297 ( 384) hydrogen bonds : angle 4.60525 ( 1035) link_ALPHA1-3 : bond 0.00959 ( 3) link_ALPHA1-3 : angle 2.53484 ( 9) link_ALPHA1-6 : bond 0.01488 ( 3) link_ALPHA1-6 : angle 1.61658 ( 9) link_BETA1-4 : bond 0.01199 ( 33) link_BETA1-4 : angle 2.85257 ( 99) link_BETA1-6 : bond 0.00529 ( 3) link_BETA1-6 : angle 1.23519 ( 9) link_NAG-ASN : bond 0.00176 ( 33) link_NAG-ASN : angle 1.79372 ( 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 259 residues out of total 912 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 213 time to evaluate : 0.312 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: 0.9071 (tt0) cc_final: 0.8259 (tm-30) REVERT: A 130 ASP cc_start: 0.8452 (t0) cc_final: 0.7950 (t0) REVERT: A 211 ASP cc_start: 0.8338 (p0) cc_final: 0.7932 (p0) REVERT: a 278 TYR cc_start: 0.8066 (t80) cc_final: 0.7720 (t80) REVERT: a 300 LYS cc_start: 0.9410 (mmtm) cc_final: 0.8957 (mptt) REVERT: a 357 ASP cc_start: 0.9320 (t70) cc_final: 0.8779 (t0) REVERT: B 80 MET cc_start: 0.8916 (mmt) cc_final: 0.8476 (mmm) REVERT: B 96 MET cc_start: 0.8185 (ptp) cc_final: 0.7501 (ptp) REVERT: B 130 ASP cc_start: 0.8291 (t0) cc_final: 0.7811 (t70) REVERT: B 218 GLN cc_start: 0.8863 (OUTLIER) cc_final: 0.8570 (pm20) REVERT: B 227 TRP cc_start: 0.6819 (t60) cc_final: 0.6256 (t-100) REVERT: b 306 ASP cc_start: 0.8501 (OUTLIER) cc_final: 0.8289 (m-30) REVERT: b 313 LEU cc_start: 0.9739 (tp) cc_final: 0.9376 (tp) REVERT: b 357 ASP cc_start: 0.9331 (t70) cc_final: 0.8859 (t0) REVERT: b 413 GLU cc_start: 0.8779 (OUTLIER) cc_final: 0.8482 (pm20) REVERT: C 76 GLU cc_start: 0.9209 (tt0) cc_final: 0.8916 (tt0) REVERT: C 130 ASP cc_start: 0.8063 (t0) cc_final: 0.7566 (t70) REVERT: C 218 GLN cc_start: 0.9060 (OUTLIER) cc_final: 0.8263 (pm20) REVERT: c 278 TYR cc_start: 0.8498 (t80) cc_final: 0.8035 (t80) REVERT: c 311 ASP cc_start: 0.9085 (OUTLIER) cc_final: 0.8784 (t0) REVERT: c 351 MET cc_start: 0.8748 (mmp) cc_final: 0.8359 (mmp) REVERT: c 413 GLU cc_start: 0.8849 (mt-10) cc_final: 0.8596 (tm-30) outliers start: 46 outliers final: 32 residues processed: 247 average time/residue: 0.0802 time to fit residues: 28.5818 Evaluate side-chains 233 residues out of total 912 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 196 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 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 218 GLN 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 323 ILE 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 b residue 413 GLU Chi-restraints excluded: chain b residue 421 GLU Chi-restraints excluded: chain C residue 86 CYS Chi-restraints excluded: chain C residue 128 LEU Chi-restraints excluded: chain C residue 218 GLN Chi-restraints excluded: chain C residue 245 LEU Chi-restraints excluded: chain c residue 285 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 Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 80 optimal weight: 2.9990 chunk 67 optimal weight: 2.9990 chunk 40 optimal weight: 4.9990 chunk 16 optimal weight: 0.9980 chunk 38 optimal weight: 7.9990 chunk 24 optimal weight: 2.9990 chunk 95 optimal weight: 2.9990 chunk 33 optimal weight: 9.9990 chunk 21 optimal weight: 5.9990 chunk 12 optimal weight: 0.9990 chunk 72 optimal weight: 0.9980 overall best weight: 1.7986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 93 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 423 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: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3335 r_free = 0.3335 target = 0.073010 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2890 r_free = 0.2890 target = 0.053937 restraints weight = 29888.333| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.2946 r_free = 0.2946 target = 0.056195 restraints weight = 16633.968| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.2983 r_free = 0.2983 target = 0.057730 restraints weight = 11792.271| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3008 r_free = 0.3008 target = 0.058779 restraints weight = 9531.091| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 21)----------------| | r_work = 0.3024 r_free = 0.3024 target = 0.059431 restraints weight = 8286.567| |-----------------------------------------------------------------------------| r_work (final): 0.3017 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8300 moved from start: 0.6701 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.086 9390 Z= 0.178 Angle : 0.882 16.851 12834 Z= 0.416 Chirality : 0.050 0.342 1599 Planarity : 0.004 0.041 1482 Dihedral : 8.809 55.089 2613 Min Nonbonded Distance : 2.468 Molprobity Statistics. All-atom Clashscore : 12.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.17 % Favored : 95.83 % Rotamer: Outliers : 4.93 % Allowed : 25.33 % Favored : 69.74 % 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: 0.34 (0.26), residues: 984 helix: 1.46 (0.27), residues: 369 sheet: 0.72 (0.49), residues: 117 loop : -0.86 (0.26), residues: 498 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG c 422 TYR 0.022 0.002 TYR C 241 PHE 0.024 0.002 PHE A 157 TRP 0.034 0.002 TRP A 227 HIS 0.004 0.001 HIS b 354 Details of bonding type rmsd covalent geometry : bond 0.00404 ( 9294) covalent geometry : angle 0.82816 (12567) SS BOND : bond 0.00537 ( 21) SS BOND : angle 1.92757 ( 42) hydrogen bonds : bond 0.04217 ( 384) hydrogen bonds : angle 4.63358 ( 1035) link_ALPHA1-3 : bond 0.00919 ( 3) link_ALPHA1-3 : angle 2.55226 ( 9) link_ALPHA1-6 : bond 0.01435 ( 3) link_ALPHA1-6 : angle 1.58602 ( 9) link_BETA1-4 : bond 0.01172 ( 33) link_BETA1-4 : angle 2.85098 ( 99) link_BETA1-6 : bond 0.00482 ( 3) link_BETA1-6 : angle 1.27102 ( 9) link_NAG-ASN : bond 0.00161 ( 33) link_NAG-ASN : angle 1.78235 ( 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 241 residues out of total 912 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 196 time to evaluate : 0.210 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: 0.9120 (tt0) cc_final: 0.8274 (tm-30) REVERT: A 130 ASP cc_start: 0.8433 (t0) cc_final: 0.7945 (t0) REVERT: A 211 ASP cc_start: 0.8310 (p0) cc_final: 0.7966 (p0) REVERT: a 278 TYR cc_start: 0.8156 (t80) cc_final: 0.7759 (t80) REVERT: a 300 LYS cc_start: 0.9418 (mmtm) cc_final: 0.8956 (mptt) REVERT: a 325 ARG cc_start: 0.8594 (mmm160) cc_final: 0.8121 (mmm160) REVERT: a 357 ASP cc_start: 0.9384 (t70) cc_final: 0.8859 (t0) REVERT: B 80 MET cc_start: 0.8950 (mmt) cc_final: 0.8527 (mmm) REVERT: B 96 MET cc_start: 0.8273 (ptp) cc_final: 0.7520 (ptp) REVERT: B 130 ASP cc_start: 0.8266 (t0) cc_final: 0.7831 (t0) REVERT: B 227 TRP cc_start: 0.6876 (t-100) cc_final: 0.6205 (t-100) REVERT: b 313 LEU cc_start: 0.9724 (tp) cc_final: 0.9360 (tp) REVERT: b 357 ASP cc_start: 0.9374 (t70) cc_final: 0.8907 (t0) REVERT: b 413 GLU cc_start: 0.8755 (OUTLIER) cc_final: 0.8447 (pm20) REVERT: C 76 GLU cc_start: 0.9253 (tt0) cc_final: 0.8950 (tt0) REVERT: C 130 ASP cc_start: 0.8064 (t0) cc_final: 0.7585 (t70) REVERT: C 194 MET cc_start: 0.9009 (tpp) cc_final: 0.8772 (tpp) REVERT: C 218 GLN cc_start: 0.9009 (OUTLIER) cc_final: 0.8192 (pm20) REVERT: c 278 TYR cc_start: 0.8308 (t80) cc_final: 0.7848 (t80) REVERT: c 311 ASP cc_start: 0.9145 (OUTLIER) cc_final: 0.8797 (t0) REVERT: c 351 MET cc_start: 0.8767 (mmp) cc_final: 0.8360 (mmp) REVERT: c 413 GLU cc_start: 0.8813 (mt-10) cc_final: 0.8572 (tm-30) REVERT: c 420 MET cc_start: 0.7667 (mmp) cc_final: 0.7462 (mmt) outliers start: 45 outliers final: 29 residues processed: 230 average time/residue: 0.0741 time to fit residues: 24.8127 Evaluate side-chains 224 residues out of total 912 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 192 time to evaluate : 0.203 ------------------------------------------------------------------------------- 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 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 185 ASN Chi-restraints excluded: chain b residue 274 THR Chi-restraints excluded: chain b residue 311 ASP Chi-restraints excluded: chain b residue 323 ILE 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 392 SER Chi-restraints excluded: chain b residue 403 ILE Chi-restraints excluded: chain b residue 413 GLU Chi-restraints excluded: chain b residue 421 GLU Chi-restraints excluded: chain C residue 86 CYS Chi-restraints excluded: chain C residue 128 LEU Chi-restraints excluded: chain C residue 218 GLN 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 Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 46 optimal weight: 9.9990 chunk 8 optimal weight: 3.9990 chunk 76 optimal weight: 6.9990 chunk 90 optimal weight: 0.9980 chunk 62 optimal weight: 6.9990 chunk 80 optimal weight: 1.9990 chunk 29 optimal weight: 3.9990 chunk 48 optimal weight: 5.9990 chunk 70 optimal weight: 6.9990 chunk 37 optimal weight: 1.9990 chunk 24 optimal weight: 6.9990 overall best weight: 2.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 92 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 93 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 423 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 185 ASN b 405 GLN b 416 GLN C 69 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3323 r_free = 0.3323 target = 0.072303 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2882 r_free = 0.2882 target = 0.053563 restraints weight = 30319.798| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.2936 r_free = 0.2936 target = 0.055728 restraints weight = 17357.121| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.2972 r_free = 0.2972 target = 0.057183 restraints weight = 12501.806| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.2996 r_free = 0.2996 target = 0.058173 restraints weight = 10177.586| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3007 r_free = 0.3007 target = 0.058632 restraints weight = 8904.920| |-----------------------------------------------------------------------------| r_work (final): 0.2998 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8337 moved from start: 0.6823 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.066 9390 Z= 0.204 Angle : 0.895 16.553 12834 Z= 0.424 Chirality : 0.050 0.326 1599 Planarity : 0.004 0.041 1482 Dihedral : 8.750 55.317 2613 Min Nonbonded Distance : 2.463 Molprobity Statistics. All-atom Clashscore : 14.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.67 % Favored : 95.33 % Rotamer: Outliers : 4.06 % Allowed : 26.32 % Favored : 69.63 % 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 (0.27), residues: 984 helix: 1.90 (0.28), residues: 345 sheet: 0.62 (0.48), residues: 117 loop : -0.71 (0.27), residues: 522 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG c 422 TYR 0.038 0.002 TYR C 241 PHE 0.022 0.002 PHE A 157 TRP 0.024 0.002 TRP A 227 HIS 0.004 0.001 HIS b 354 Details of bonding type rmsd covalent geometry : bond 0.00457 ( 9294) covalent geometry : angle 0.84141 (12567) SS BOND : bond 0.00530 ( 21) SS BOND : angle 1.85083 ( 42) hydrogen bonds : bond 0.04264 ( 384) hydrogen bonds : angle 4.65012 ( 1035) link_ALPHA1-3 : bond 0.00839 ( 3) link_ALPHA1-3 : angle 2.61208 ( 9) link_ALPHA1-6 : bond 0.01397 ( 3) link_ALPHA1-6 : angle 1.61516 ( 9) link_BETA1-4 : bond 0.01161 ( 33) link_BETA1-4 : angle 2.81613 ( 99) link_BETA1-6 : bond 0.00452 ( 3) link_BETA1-6 : angle 1.33486 ( 9) link_NAG-ASN : bond 0.00210 ( 33) link_NAG-ASN : angle 1.86515 ( 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 231 residues out of total 912 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 194 time to evaluate : 0.281 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: 0.9103 (tt0) cc_final: 0.8242 (tm-30) REVERT: A 130 ASP cc_start: 0.8464 (t0) cc_final: 0.7994 (t0) REVERT: A 211 ASP cc_start: 0.8376 (p0) cc_final: 0.8118 (p0) REVERT: a 278 TYR cc_start: 0.8201 (t80) cc_final: 0.7596 (t80) REVERT: a 300 LYS cc_start: 0.9441 (mmtm) cc_final: 0.8995 (mptt) REVERT: a 357 ASP cc_start: 0.9430 (t70) cc_final: 0.8899 (t0) REVERT: B 96 MET cc_start: 0.8249 (ptp) cc_final: 0.7383 (ptp) REVERT: B 130 ASP cc_start: 0.8244 (t0) cc_final: 0.7844 (t0) REVERT: B 227 TRP cc_start: 0.6903 (t-100) cc_final: 0.6163 (t-100) REVERT: b 313 LEU cc_start: 0.9750 (tp) cc_final: 0.9395 (tp) REVERT: b 325 ARG cc_start: 0.8631 (mmm160) cc_final: 0.8369 (mmm160) REVERT: b 357 ASP cc_start: 0.9380 (t70) cc_final: 0.8918 (t0) REVERT: b 413 GLU cc_start: 0.8735 (OUTLIER) cc_final: 0.8443 (pm20) REVERT: C 76 GLU cc_start: 0.9229 (tt0) cc_final: 0.8905 (tt0) REVERT: C 130 ASP cc_start: 0.7982 (t0) cc_final: 0.7515 (t70) REVERT: C 218 GLN cc_start: 0.8962 (OUTLIER) cc_final: 0.8154 (pm20) REVERT: c 278 TYR cc_start: 0.8340 (t80) cc_final: 0.7996 (t80) REVERT: c 311 ASP cc_start: 0.9171 (OUTLIER) cc_final: 0.8773 (t0) REVERT: c 413 GLU cc_start: 0.8816 (mt-10) cc_final: 0.8588 (tm-30) REVERT: c 420 MET cc_start: 0.7730 (mmp) cc_final: 0.7491 (mmt) outliers start: 37 outliers final: 31 residues processed: 224 average time/residue: 0.0721 time to fit residues: 23.6436 Evaluate side-chains 218 residues out of total 912 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 184 time to evaluate : 0.321 ------------------------------------------------------------------------------- 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 311 ASP Chi-restraints excluded: chain a residue 313 LEU 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 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 274 THR Chi-restraints excluded: chain b residue 311 ASP Chi-restraints excluded: chain b residue 323 ILE 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 392 SER Chi-restraints excluded: chain b residue 403 ILE Chi-restraints excluded: chain b residue 413 GLU Chi-restraints excluded: chain b residue 421 GLU Chi-restraints excluded: chain C residue 86 CYS Chi-restraints excluded: chain C residue 128 LEU Chi-restraints excluded: chain C residue 218 GLN 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 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: 10.0000 chunk 48 optimal weight: 6.9990 chunk 54 optimal weight: 0.9990 chunk 33 optimal weight: 8.9990 chunk 77 optimal weight: 10.0000 chunk 79 optimal weight: 0.0970 chunk 40 optimal weight: 0.9980 chunk 66 optimal weight: 10.0000 chunk 96 optimal weight: 0.9990 chunk 7 optimal weight: 6.9990 overall best weight: 1.6184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 92 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 93 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 423 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 335 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3340 r_free = 0.3340 target = 0.073373 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2880 r_free = 0.2880 target = 0.053555 restraints weight = 31028.478| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.2935 r_free = 0.2935 target = 0.055826 restraints weight = 17713.473| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.2971 r_free = 0.2971 target = 0.057311 restraints weight = 12818.570| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.2996 r_free = 0.2996 target = 0.058346 restraints weight = 10509.615| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3012 r_free = 0.3012 target = 0.059011 restraints weight = 9215.573| |-----------------------------------------------------------------------------| r_work (final): 0.3014 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8326 moved from start: 0.6951 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= 0.170 Angle : 0.892 15.744 12834 Z= 0.420 Chirality : 0.049 0.266 1599 Planarity : 0.004 0.041 1482 Dihedral : 8.618 55.008 2613 Min Nonbonded Distance : 2.393 Molprobity Statistics. All-atom Clashscore : 13.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.67 % Favored : 95.33 % Rotamer: Outliers : 3.84 % Allowed : 26.64 % Favored : 69.52 % 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 (0.27), residues: 984 helix: 1.83 (0.28), residues: 345 sheet: 0.65 (0.48), residues: 117 loop : -0.67 (0.27), residues: 522 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG c 422 TYR 0.044 0.002 TYR C 241 PHE 0.021 0.002 PHE C 157 TRP 0.032 0.002 TRP C 227 HIS 0.004 0.001 HIS b 354 Details of bonding type rmsd covalent geometry : bond 0.00385 ( 9294) covalent geometry : angle 0.84474 (12567) SS BOND : bond 0.00648 ( 21) SS BOND : angle 1.50010 ( 42) hydrogen bonds : bond 0.04193 ( 384) hydrogen bonds : angle 4.73944 ( 1035) link_ALPHA1-3 : bond 0.00879 ( 3) link_ALPHA1-3 : angle 2.42615 ( 9) link_ALPHA1-6 : bond 0.01396 ( 3) link_ALPHA1-6 : angle 1.60567 ( 9) link_BETA1-4 : bond 0.01157 ( 33) link_BETA1-4 : angle 2.77925 ( 99) link_BETA1-6 : bond 0.00524 ( 3) link_BETA1-6 : angle 1.25877 ( 9) link_NAG-ASN : bond 0.00172 ( 33) link_NAG-ASN : angle 1.75008 ( 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 231 residues out of total 912 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 196 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: symmetry clash REVERT: A 76 GLU cc_start: 0.9126 (tt0) cc_final: 0.8199 (tm-30) REVERT: A 130 ASP cc_start: 0.8454 (t0) cc_final: 0.7983 (t0) REVERT: A 211 ASP cc_start: 0.8349 (p0) cc_final: 0.8106 (p0) REVERT: a 300 LYS cc_start: 0.9436 (mmtm) cc_final: 0.8976 (mptt) REVERT: a 325 ARG cc_start: 0.8624 (mmm160) cc_final: 0.8156 (mmm160) REVERT: a 357 ASP cc_start: 0.9404 (t70) cc_final: 0.8939 (t70) REVERT: B 75 MET cc_start: 0.9059 (mmt) cc_final: 0.8630 (mmm) REVERT: B 96 MET cc_start: 0.8211 (ptp) cc_final: 0.7434 (ptp) REVERT: B 130 ASP cc_start: 0.8258 (t0) cc_final: 0.7840 (t0) REVERT: B 227 TRP cc_start: 0.6937 (t-100) cc_final: 0.6208 (t-100) REVERT: b 313 LEU cc_start: 0.9727 (tp) cc_final: 0.9370 (tp) REVERT: b 357 ASP cc_start: 0.9348 (t70) cc_final: 0.8890 (t0) REVERT: b 413 GLU cc_start: 0.8740 (OUTLIER) cc_final: 0.8440 (pm20) REVERT: C 76 GLU cc_start: 0.9207 (tt0) cc_final: 0.8889 (tt0) REVERT: C 130 ASP cc_start: 0.8020 (t0) cc_final: 0.7570 (t70) REVERT: c 311 ASP cc_start: 0.9136 (OUTLIER) cc_final: 0.8720 (t0) REVERT: c 413 GLU cc_start: 0.8850 (mt-10) cc_final: 0.8601 (tm-30) outliers start: 35 outliers final: 31 residues processed: 224 average time/residue: 0.0780 time to fit residues: 25.6306 Evaluate side-chains 221 residues out of total 912 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 188 time to evaluate : 0.349 ------------------------------------------------------------------------------- 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 279 CYS Chi-restraints excluded: chain a residue 311 ASP Chi-restraints excluded: chain a residue 313 LEU Chi-restraints excluded: chain a residue 337 ILE Chi-restraints excluded: chain a residue 361 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 274 THR 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 351 MET 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 b residue 413 GLU Chi-restraints excluded: chain b residue 421 GLU 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 Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 97 optimal weight: 0.9990 chunk 91 optimal weight: 0.9990 chunk 82 optimal weight: 5.9990 chunk 70 optimal weight: 10.0000 chunk 63 optimal weight: 0.8980 chunk 40 optimal weight: 2.9990 chunk 60 optimal weight: 4.9990 chunk 80 optimal weight: 1.9990 chunk 15 optimal weight: 7.9990 chunk 59 optimal weight: 0.8980 chunk 3 optimal weight: 1.9990 overall best weight: 1.1586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 92 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 93 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 335 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 423 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 185 ASN b 405 GLN b 416 GLN ** c 335 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 = 0.3362 r_free = 0.3362 target = 0.074381 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2923 r_free = 0.2923 target = 0.055137 restraints weight = 29943.044| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.2980 r_free = 0.2980 target = 0.057401 restraints weight = 16684.065| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3017 r_free = 0.3017 target = 0.058959 restraints weight = 11823.298| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3043 r_free = 0.3043 target = 0.060014 restraints weight = 9553.274| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.3059 r_free = 0.3059 target = 0.060701 restraints weight = 8296.586| |-----------------------------------------------------------------------------| r_work (final): 0.3048 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8284 moved from start: 0.7059 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.060 9390 Z= 0.160 Angle : 0.897 14.716 12834 Z= 0.419 Chirality : 0.048 0.260 1599 Planarity : 0.004 0.042 1482 Dihedral : 8.611 54.658 2613 Min Nonbonded Distance : 2.393 Molprobity Statistics. All-atom Clashscore : 12.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.78 % Favored : 95.22 % Rotamer: Outliers : 3.62 % Allowed : 27.08 % Favored : 69.30 % 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: 0.51 (0.27), residues: 984 helix: 1.72 (0.28), residues: 345 sheet: 0.63 (0.48), residues: 117 loop : -0.68 (0.27), residues: 522 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG c 422 TYR 0.040 0.002 TYR B 241 PHE 0.023 0.002 PHE C 157 TRP 0.040 0.002 TRP C 227 HIS 0.004 0.001 HIS b 354 Details of bonding type rmsd covalent geometry : bond 0.00360 ( 9294) covalent geometry : angle 0.85205 (12567) SS BOND : bond 0.00623 ( 21) SS BOND : angle 1.47309 ( 42) hydrogen bonds : bond 0.04090 ( 384) hydrogen bonds : angle 4.74404 ( 1035) link_ALPHA1-3 : bond 0.00902 ( 3) link_ALPHA1-3 : angle 2.25549 ( 9) link_ALPHA1-6 : bond 0.01361 ( 3) link_ALPHA1-6 : angle 1.57430 ( 9) link_BETA1-4 : bond 0.01161 ( 33) link_BETA1-4 : angle 2.73238 ( 99) link_BETA1-6 : bond 0.00556 ( 3) link_BETA1-6 : angle 1.22576 ( 9) link_NAG-ASN : bond 0.00168 ( 33) link_NAG-ASN : angle 1.71102 ( 99) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1401.49 seconds wall clock time: 25 minutes 9.12 seconds (1509.12 seconds total)