Starting phenix.real_space_refine on Sun Jul 27 11:23:26 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7sgd_25107/07_2025/7sgd_25107.cif Found real_map, /net/cci-nas-00/data/ceres_data/7sgd_25107/07_2025/7sgd_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/7sgd_25107/07_2025/7sgd_25107.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7sgd_25107/07_2025/7sgd_25107.map" model { file = "/net/cci-nas-00/data/ceres_data/7sgd_25107/07_2025/7sgd_25107.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7sgd_25107/07_2025/7sgd_25107.cif" } resolution = 3.97 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 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): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/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: 6.45, per 1000 atoms: 0.71 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: 3.34 Conformation dependent library (CDL) restraints added in 906.0 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: 0.92 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: 2.41 Time building geometry restraints manager: 3.79 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: 0.06 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: 0.900 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.390 Check model and map are aligned: 0.070 Set scattering table: 0.090 Process input model: 24.870 Find NCS groups from input model: 0.550 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.900 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 29.840 ------------------------------------------------------------------------------- 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 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 TRP 0.031 0.006 TRP a 283 HIS 0.006 0.002 HIS B 124 PHE 0.016 0.005 PHE a 399 TYR 0.051 0.009 TYR b 363 ARG 0.004 0.001 ARG a 356 Details of bonding type rmsd link_NAG-ASN : bond 0.07397 ( 33) link_NAG-ASN : angle 3.52360 ( 99) 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_ALPHA1-3 : bond 0.08716 ( 3) link_ALPHA1-3 : angle 4.33137 ( 9) hydrogen bonds : bond 0.16051 ( 384) hydrogen bonds : angle 6.47171 ( 1035) link_BETA1-6 : bond 0.06593 ( 3) link_BETA1-6 : angle 4.74660 ( 9) SS BOND : bond 0.00890 ( 21) SS BOND : angle 2.81040 ( 42) covalent geometry : bond 0.02384 ( 9294) covalent geometry : angle 1.79736 (12567) *********************** 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 : 1.011 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: 0.8036 (t0) REVERT: A 220 LEU cc_start: 0.9228 (tp) cc_final: 0.8993 (tt) REVERT: a 311 ASP cc_start: 0.9105 (m-30) cc_final: 0.8876 (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: 0.8202 (m-30) REVERT: a 409 ASN cc_start: 0.9153 (m-40) cc_final: 0.8832 (t0) REVERT: a 416 GLN cc_start: 0.9186 (mm-40) cc_final: 0.8889 (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: 0.9381 (mp) REVERT: B 130 ASP cc_start: 0.8481 (t0) cc_final: 0.8032 (t0) REVERT: B 220 LEU cc_start: 0.9271 (tp) cc_final: 0.9007 (tt) REVERT: b 267 SER cc_start: 0.8975 (p) cc_final: 0.8588 (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: 0.9064 (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: 0.8143 (m-40) REVERT: b 411 ILE cc_start: 0.9472 (mt) cc_final: 0.9253 (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: 0.9392 (mp) REVERT: C 130 ASP cc_start: 0.8407 (t0) cc_final: 0.7960 (t0) REVERT: C 191 PHE cc_start: 0.9267 (t80) cc_final: 0.9057 (t80) REVERT: C 220 LEU cc_start: 0.9267 (tp) cc_final: 0.9030 (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: 0.2564 time to fit residues: 158.6513 Evaluate side-chains 284 residues out of total 912 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 284 time to evaluate : 1.144 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 83 optimal weight: 3.9990 chunk 75 optimal weight: 7.9990 chunk 41 optimal weight: 2.9990 chunk 25 optimal weight: 1.9990 chunk 50 optimal weight: 3.9990 chunk 40 optimal weight: 0.9990 chunk 77 optimal weight: 5.9990 chunk 30 optimal weight: 1.9990 chunk 47 optimal weight: 6.9990 chunk 57 optimal weight: 0.9990 chunk 89 optimal weight: 6.9990 overall best weight: 1.7990 ------------------------------------------------------------------------------- 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 = 0.3387 r_free = 0.3387 target = 0.075616 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2950 r_free = 0.2950 target = 0.056110 restraints weight = 29208.232| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3007 r_free = 0.3007 target = 0.058582 restraints weight = 15496.980| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 23)----------------| | r_work = 0.3045 r_free = 0.3045 target = 0.060284 restraints weight = 10740.926| |-----------------------------------------------------------------------------| r_work (final): 0.3042 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8153 moved from start: 0.4508 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.046 9390 Z= 0.221 Angle : 1.031 14.583 12834 Z= 0.501 Chirality : 0.052 0.359 1599 Planarity : 0.005 0.030 1482 Dihedral : 13.419 83.372 2613 Min Nonbonded Distance : 2.430 Molprobity Statistics. All-atom Clashscore : 11.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.13 % Favored : 97.87 % Rotamer: Outliers : 4.82 % Allowed : 18.42 % Favored : 76.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.10 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.55 (0.25), residues: 984 helix: 1.38 (0.26), residues: 366 sheet: 1.85 (0.50), residues: 108 loop : -0.73 (0.24), residues: 510 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP A 227 HIS 0.010 0.002 HIS C 93 PHE 0.027 0.003 PHE A 191 TYR 0.024 0.002 TYR C 166 ARG 0.005 0.001 ARG a 282 Details of bonding type rmsd link_NAG-ASN : bond 0.00470 ( 33) link_NAG-ASN : angle 3.00940 ( 99) link_ALPHA1-6 : bond 0.01380 ( 3) link_ALPHA1-6 : angle 1.53053 ( 9) link_BETA1-4 : bond 0.01643 ( 33) link_BETA1-4 : angle 3.92238 ( 99) link_ALPHA1-3 : bond 0.00922 ( 3) link_ALPHA1-3 : angle 2.69491 ( 9) hydrogen bonds : bond 0.05954 ( 384) hydrogen bonds : angle 5.17665 ( 1035) link_BETA1-6 : bond 0.00485 ( 3) link_BETA1-6 : angle 1.32187 ( 9) SS BOND : bond 0.00476 ( 21) SS BOND : angle 2.93590 ( 42) covalent geometry : bond 0.00468 ( 9294) covalent geometry : angle 0.92575 (12567) *********************** 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 344 residues out of total 912 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 300 time to evaluate : 1.244 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 72 GLU cc_start: 0.8114 (tt0) cc_final: 0.7886 (tt0) REVERT: A 130 ASP cc_start: 0.8455 (t0) cc_final: 0.7910 (t0) REVERT: a 300 LYS cc_start: 0.9211 (mmtm) cc_final: 0.8561 (mptt) REVERT: a 307 GLU cc_start: 0.8831 (mm-30) cc_final: 0.8609 (mm-30) REVERT: a 311 ASP cc_start: 0.9231 (m-30) cc_final: 0.8968 (m-30) REVERT: a 313 LEU cc_start: 0.9780 (tp) cc_final: 0.9387 (tp) REVERT: a 357 ASP cc_start: 0.9179 (t70) cc_final: 0.8649 (t0) REVERT: a 405 GLN cc_start: 0.9139 (tm-30) cc_final: 0.8810 (tm-30) REVERT: B 130 ASP cc_start: 0.8382 (t0) cc_final: 0.7845 (t0) REVERT: B 211 ASP cc_start: 0.8504 (p0) cc_final: 0.8221 (p0) REVERT: b 261 THR cc_start: 0.8357 (p) cc_final: 0.8136 (p) REVERT: b 307 GLU cc_start: 0.8775 (mm-30) cc_final: 0.8430 (mp0) REVERT: b 311 ASP cc_start: 0.9233 (m-30) cc_final: 0.8956 (m-30) REVERT: b 313 LEU cc_start: 0.9788 (tp) cc_final: 0.9423 (tp) REVERT: b 357 ASP cc_start: 0.9134 (t70) cc_final: 0.8613 (t0) REVERT: b 405 GLN cc_start: 0.9098 (tm-30) cc_final: 0.8858 (tm-30) REVERT: b 410 MET cc_start: 0.8988 (OUTLIER) cc_final: 0.8407 (tpp) REVERT: b 413 GLU cc_start: 0.8818 (OUTLIER) cc_final: 0.8577 (pm20) REVERT: C 72 GLU cc_start: 0.8214 (tt0) cc_final: 0.7960 (tt0) REVERT: C 76 GLU cc_start: 0.9157 (tt0) cc_final: 0.8938 (tt0) REVERT: C 100 GLU cc_start: 0.7539 (mm-30) cc_final: 0.7306 (mm-30) REVERT: C 130 ASP cc_start: 0.8324 (t0) cc_final: 0.7849 (t0) REVERT: C 191 PHE cc_start: 0.9179 (t80) cc_final: 0.8913 (t80) REVERT: C 211 ASP cc_start: 0.8580 (p0) cc_final: 0.8357 (p0) REVERT: C 227 TRP cc_start: 0.7189 (t-100) cc_final: 0.6818 (t-100) REVERT: c 261 THR cc_start: 0.8229 (p) cc_final: 0.8025 (p) REVERT: c 278 TYR cc_start: 0.8400 (t80) cc_final: 0.7921 (t80) REVERT: c 300 LYS cc_start: 0.9171 (mmtm) cc_final: 0.8668 (mptt) REVERT: c 306 ASP cc_start: 0.8683 (t0) cc_final: 0.8270 (t70) REVERT: c 307 GLU cc_start: 0.8815 (mm-30) cc_final: 0.7909 (mp0) REVERT: c 313 LEU cc_start: 0.9780 (tp) cc_final: 0.9386 (tp) REVERT: c 403 ILE cc_start: 0.9629 (mt) cc_final: 0.9425 (tt) outliers start: 44 outliers final: 20 residues processed: 322 average time/residue: 0.2968 time to fit residues: 131.9893 Evaluate side-chains 265 residues out of total 912 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 243 time to evaluate : 1.210 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 86 CYS Chi-restraints excluded: chain A residue 126 LYS Chi-restraints excluded: chain A residue 156 ASP Chi-restraints excluded: chain a residue 269 SER Chi-restraints excluded: chain a residue 325 ARG Chi-restraints excluded: chain a residue 337 ILE Chi-restraints excluded: chain a residue 361 ILE Chi-restraints excluded: chain a residue 421 GLU Chi-restraints excluded: chain B residue 86 CYS Chi-restraints excluded: chain B residue 207 CYS Chi-restraints excluded: chain B residue 239 ILE Chi-restraints excluded: chain b residue 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 305 HIS Chi-restraints excluded: chain c residue 337 ILE Chi-restraints excluded: chain c residue 385 CYS 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 22 optimal weight: 0.9980 chunk 72 optimal weight: 8.9990 chunk 8 optimal weight: 0.9980 chunk 23 optimal weight: 0.4980 chunk 38 optimal weight: 8.9990 chunk 86 optimal weight: 3.9990 chunk 44 optimal weight: 10.0000 chunk 7 optimal weight: 6.9990 chunk 78 optimal weight: 4.9990 chunk 83 optimal weight: 0.7980 chunk 30 optimal weight: 5.9990 overall best weight: 1.4582 ------------------------------------------------------------------------------- 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** ** B 93 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 69 GLN C 232 GLN ** c 406 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3371 r_free = 0.3371 target = 0.075149 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2939 r_free = 0.2939 target = 0.055838 restraints weight = 29614.198| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.2997 r_free = 0.2997 target = 0.058240 restraints weight = 15901.166| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3035 r_free = 0.3035 target = 0.059896 restraints weight = 11090.872| |-----------------------------------------------------------------------------| r_work (final): 0.3024 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8208 moved from start: 0.5187 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 9390 Z= 0.180 Angle : 0.906 12.086 12834 Z= 0.434 Chirality : 0.048 0.300 1599 Planarity : 0.004 0.031 1482 Dihedral : 11.813 72.671 2613 Min Nonbonded Distance : 2.490 Molprobity Statistics. All-atom Clashscore : 11.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.24 % Favored : 97.76 % Rotamer: Outliers : 5.37 % Allowed : 20.72 % Favored : 73.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.10 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.50 (0.25), residues: 984 helix: 1.40 (0.26), residues: 366 sheet: 1.61 (0.50), residues: 108 loop : -0.76 (0.24), residues: 510 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.003 TRP A 227 HIS 0.004 0.001 HIS A 93 PHE 0.025 0.003 PHE B 157 TYR 0.019 0.002 TYR C 241 ARG 0.005 0.000 ARG a 325 Details of bonding type rmsd link_NAG-ASN : bond 0.00352 ( 33) link_NAG-ASN : angle 2.34359 ( 99) link_ALPHA1-6 : bond 0.01507 ( 3) link_ALPHA1-6 : angle 1.44343 ( 9) link_BETA1-4 : bond 0.01429 ( 33) link_BETA1-4 : angle 3.42542 ( 99) link_ALPHA1-3 : bond 0.00960 ( 3) link_ALPHA1-3 : angle 2.42028 ( 9) hydrogen bonds : bond 0.05270 ( 384) hydrogen bonds : angle 4.81966 ( 1035) link_BETA1-6 : bond 0.00414 ( 3) link_BETA1-6 : angle 1.28718 ( 9) SS BOND : bond 0.00400 ( 21) SS BOND : angle 1.48618 ( 42) covalent geometry : bond 0.00379 ( 9294) covalent geometry : angle 0.82914 (12567) *********************** 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 308 residues out of total 912 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 259 time to evaluate : 1.073 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 75 MET cc_start: 0.8583 (mtp) cc_final: 0.8274 (mtp) REVERT: A 130 ASP cc_start: 0.8463 (t0) cc_final: 0.7859 (t70) REVERT: A 211 ASP cc_start: 0.8824 (p0) cc_final: 0.8510 (p0) REVERT: a 261 THR cc_start: 0.8124 (p) cc_final: 0.7912 (p) REVERT: a 300 LYS cc_start: 0.9266 (mmtm) cc_final: 0.8634 (mptt) REVERT: a 311 ASP cc_start: 0.9219 (m-30) cc_final: 0.9015 (m-30) REVERT: a 313 LEU cc_start: 0.9749 (tp) cc_final: 0.9344 (tp) REVERT: a 325 ARG cc_start: 0.8693 (OUTLIER) cc_final: 0.8469 (mmm160) REVERT: a 357 ASP cc_start: 0.9207 (t70) cc_final: 0.8682 (t0) REVERT: a 405 GLN cc_start: 0.9225 (tm-30) cc_final: 0.8996 (tm-30) REVERT: a 416 GLN cc_start: 0.9101 (mt0) cc_final: 0.8883 (mt0) REVERT: a 417 LYS cc_start: 0.9196 (pttp) cc_final: 0.8990 (ptpp) REVERT: B 130 ASP cc_start: 0.8257 (t0) cc_final: 0.7714 (t0) REVERT: B 227 TRP cc_start: 0.6795 (t-100) cc_final: 0.5932 (t60) REVERT: b 261 THR cc_start: 0.8460 (p) cc_final: 0.8252 (p) REVERT: b 311 ASP cc_start: 0.9219 (m-30) cc_final: 0.9017 (m-30) REVERT: b 313 LEU cc_start: 0.9719 (tp) cc_final: 0.9289 (tp) REVERT: b 357 ASP cc_start: 0.9159 (t70) cc_final: 0.8668 (t0) REVERT: b 408 ASP cc_start: 0.9317 (m-30) cc_final: 0.8964 (m-30) REVERT: C 82 MET cc_start: 0.9341 (OUTLIER) cc_final: 0.9093 (ptp) REVERT: C 96 MET cc_start: 0.7965 (ptp) cc_final: 0.7729 (ptp) REVERT: C 100 GLU cc_start: 0.7599 (mm-30) cc_final: 0.7324 (mm-30) REVERT: C 130 ASP cc_start: 0.8248 (t0) cc_final: 0.7699 (t70) REVERT: c 278 TYR cc_start: 0.8419 (t80) cc_final: 0.7989 (t80) REVERT: c 300 LYS cc_start: 0.9250 (mmtm) cc_final: 0.8758 (mptt) REVERT: c 313 LEU cc_start: 0.9764 (tp) cc_final: 0.9342 (tp) REVERT: c 410 MET cc_start: 0.9037 (tpp) cc_final: 0.8695 (tpp) REVERT: c 413 GLU cc_start: 0.8759 (mp0) cc_final: 0.8557 (tm-30) outliers start: 49 outliers final: 30 residues processed: 293 average time/residue: 0.2188 time to fit residues: 87.1590 Evaluate side-chains 262 residues out of total 912 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 230 time to evaluate : 0.998 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 82 MET 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 269 SER 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 380 THR 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 239 ILE Chi-restraints excluded: chain b residue 306 ASP Chi-restraints excluded: chain b residue 337 ILE Chi-restraints excluded: chain b residue 385 CYS 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 218 GLN Chi-restraints excluded: chain c residue 269 SER Chi-restraints excluded: chain c residue 274 THR Chi-restraints excluded: chain c residue 305 HIS 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 57 optimal weight: 0.9990 chunk 83 optimal weight: 0.3980 chunk 78 optimal weight: 5.9990 chunk 54 optimal weight: 8.9990 chunk 80 optimal weight: 9.9990 chunk 67 optimal weight: 0.4980 chunk 23 optimal weight: 4.9990 chunk 14 optimal weight: 8.9990 chunk 86 optimal weight: 5.9990 chunk 94 optimal weight: 0.8980 chunk 84 optimal weight: 4.9990 overall best weight: 1.5584 ------------------------------------------------------------------------------- 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 185 ASN ** a 423 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 93 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** b 405 GLN ** b 423 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 69 GLN ** C 93 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 406 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** c 416 GLN c 423 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3365 r_free = 0.3365 target = 0.074718 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.2932 r_free = 0.2932 target = 0.055648 restraints weight = 29617.134| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.2989 r_free = 0.2989 target = 0.058014 restraints weight = 15983.832| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3026 r_free = 0.3026 target = 0.059602 restraints weight = 11179.441| |-----------------------------------------------------------------------------| r_work (final): 0.3021 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8241 moved from start: 0.5645 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 9390 Z= 0.168 Angle : 0.846 11.047 12834 Z= 0.403 Chirality : 0.048 0.271 1599 Planarity : 0.004 0.042 1482 Dihedral : 10.145 61.216 2613 Min Nonbonded Distance : 2.456 Molprobity Statistics. All-atom Clashscore : 11.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.64 % Favored : 97.36 % Rotamer: Outliers : 5.48 % Allowed : 20.72 % Favored : 73.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.26 (0.25), residues: 984 helix: 1.27 (0.26), residues: 369 sheet: 1.04 (0.49), residues: 117 loop : -0.90 (0.24), residues: 498 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP A 210 HIS 0.007 0.001 HIS b 354 PHE 0.024 0.002 PHE B 157 TYR 0.021 0.002 TYR B 241 ARG 0.004 0.001 ARG a 325 Details of bonding type rmsd link_NAG-ASN : bond 0.00273 ( 33) link_NAG-ASN : angle 2.11502 ( 99) link_ALPHA1-6 : bond 0.01454 ( 3) link_ALPHA1-6 : angle 1.43254 ( 9) link_BETA1-4 : bond 0.01312 ( 33) link_BETA1-4 : angle 3.10033 ( 99) link_ALPHA1-3 : bond 0.00952 ( 3) link_ALPHA1-3 : angle 2.77705 ( 9) hydrogen bonds : bond 0.04634 ( 384) hydrogen bonds : angle 4.70443 ( 1035) link_BETA1-6 : bond 0.00379 ( 3) link_BETA1-6 : angle 1.29599 ( 9) SS BOND : bond 0.00264 ( 21) SS BOND : angle 0.94770 ( 42) covalent geometry : bond 0.00347 ( 9294) covalent geometry : angle 0.78048 (12567) *********************** 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 293 residues out of total 912 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 243 time to evaluate : 0.945 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 76 GLU cc_start: 0.9035 (tt0) cc_final: 0.8126 (tm-30) REVERT: A 130 ASP cc_start: 0.8443 (t0) cc_final: 0.7862 (t70) REVERT: A 211 ASP cc_start: 0.8811 (p0) cc_final: 0.8319 (p0) REVERT: A 227 TRP cc_start: 0.6651 (t-100) cc_final: 0.6240 (t60) REVERT: a 300 LYS cc_start: 0.9360 (mmtm) cc_final: 0.8819 (mptt) REVERT: a 313 LEU cc_start: 0.9765 (tp) cc_final: 0.9387 (tp) REVERT: a 357 ASP cc_start: 0.9231 (t70) cc_final: 0.8743 (t0) REVERT: a 405 GLN cc_start: 0.9230 (tm-30) cc_final: 0.9011 (tm-30) REVERT: a 413 GLU cc_start: 0.8884 (pp20) cc_final: 0.8671 (tm-30) REVERT: a 416 GLN cc_start: 0.9058 (mt0) cc_final: 0.8792 (mm-40) REVERT: B 96 MET cc_start: 0.8842 (ttp) cc_final: 0.8562 (ttm) REVERT: B 130 ASP cc_start: 0.8181 (t0) cc_final: 0.7673 (t70) REVERT: B 227 TRP cc_start: 0.6823 (t-100) cc_final: 0.6271 (t60) REVERT: b 306 ASP cc_start: 0.8199 (OUTLIER) cc_final: 0.7654 (m-30) REVERT: b 313 LEU cc_start: 0.9705 (tp) cc_final: 0.9277 (tp) REVERT: b 357 ASP cc_start: 0.9217 (t70) cc_final: 0.8692 (t0) REVERT: b 359 MET cc_start: 0.9197 (mtm) cc_final: 0.8637 (mtp) REVERT: b 408 ASP cc_start: 0.9288 (m-30) cc_final: 0.8957 (m-30) REVERT: b 413 GLU cc_start: 0.8884 (OUTLIER) cc_final: 0.8482 (pm20) REVERT: C 67 GLU cc_start: 0.8735 (tp30) cc_final: 0.8533 (tp30) REVERT: C 76 GLU cc_start: 0.9184 (tt0) cc_final: 0.8934 (tt0) REVERT: C 96 MET cc_start: 0.7959 (ptp) cc_final: 0.7694 (ptm) REVERT: C 100 GLU cc_start: 0.7655 (mm-30) cc_final: 0.7360 (mm-30) REVERT: C 130 ASP cc_start: 0.8130 (t0) cc_final: 0.7620 (t70) REVERT: C 245 LEU cc_start: 0.9396 (OUTLIER) cc_final: 0.9134 (mm) REVERT: c 278 TYR cc_start: 0.8451 (t80) cc_final: 0.8090 (t80) REVERT: c 300 LYS cc_start: 0.9301 (mmtm) cc_final: 0.8846 (mptt) REVERT: c 313 LEU cc_start: 0.9756 (tp) cc_final: 0.9296 (tp) REVERT: c 410 MET cc_start: 0.9091 (tpp) cc_final: 0.8796 (tpp) REVERT: c 413 GLU cc_start: 0.8850 (mp0) cc_final: 0.8604 (tm-30) outliers start: 50 outliers final: 28 residues processed: 275 average time/residue: 0.2104 time to fit residues: 78.9238 Evaluate side-chains 243 residues out of total 912 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 212 time to evaluate : 1.045 ------------------------------------------------------------------------------- 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 245 LEU 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 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 239 ILE Chi-restraints excluded: chain b residue 274 THR Chi-restraints excluded: chain b residue 306 ASP Chi-restraints excluded: chain b residue 337 ILE Chi-restraints excluded: chain b residue 367 SER Chi-restraints excluded: chain b residue 385 CYS Chi-restraints excluded: chain b residue 388 VAL Chi-restraints excluded: chain b residue 413 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 274 THR Chi-restraints excluded: chain c residue 305 HIS Chi-restraints excluded: chain c residue 311 ASP Chi-restraints excluded: chain c residue 337 ILE Chi-restraints excluded: chain c residue 380 THR Chi-restraints excluded: chain c residue 421 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 14 optimal weight: 0.9990 chunk 54 optimal weight: 10.0000 chunk 52 optimal weight: 6.9990 chunk 47 optimal weight: 0.8980 chunk 74 optimal weight: 9.9990 chunk 59 optimal weight: 0.5980 chunk 9 optimal weight: 0.5980 chunk 18 optimal weight: 0.7980 chunk 96 optimal weight: 0.7980 chunk 48 optimal weight: 9.9990 chunk 76 optimal weight: 9.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- 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 185 ASN B 93 HIS B 185 ASN b 405 GLN ** C 93 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 406 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3384 r_free = 0.3384 target = 0.075906 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2952 r_free = 0.2952 target = 0.056567 restraints weight = 29202.192| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3009 r_free = 0.3009 target = 0.058990 restraints weight = 15881.005| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3047 r_free = 0.3047 target = 0.060597 restraints weight = 11119.422| |-----------------------------------------------------------------------------| r_work (final): 0.3038 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8237 moved from start: 0.5960 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 9390 Z= 0.143 Angle : 0.820 10.743 12834 Z= 0.386 Chirality : 0.047 0.247 1599 Planarity : 0.004 0.038 1482 Dihedral : 9.381 54.812 2613 Min Nonbonded Distance : 2.466 Molprobity Statistics. All-atom Clashscore : 11.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.05 % Favored : 96.95 % Rotamer: Outliers : 4.82 % Allowed : 23.90 % Favored : 71.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.29 (0.25), residues: 984 helix: 1.38 (0.26), residues: 369 sheet: 0.98 (0.50), residues: 117 loop : -0.93 (0.24), residues: 498 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP A 210 HIS 0.006 0.001 HIS b 354 PHE 0.024 0.002 PHE B 157 TYR 0.017 0.002 TYR C 166 ARG 0.009 0.001 ARG c 422 Details of bonding type rmsd link_NAG-ASN : bond 0.00205 ( 33) link_NAG-ASN : angle 1.90331 ( 99) link_ALPHA1-6 : bond 0.01489 ( 3) link_ALPHA1-6 : angle 1.47040 ( 9) link_BETA1-4 : bond 0.01292 ( 33) link_BETA1-4 : angle 3.00563 ( 99) link_ALPHA1-3 : bond 0.01067 ( 3) link_ALPHA1-3 : angle 2.57906 ( 9) hydrogen bonds : bond 0.04259 ( 384) hydrogen bonds : angle 4.55208 ( 1035) link_BETA1-6 : bond 0.00458 ( 3) link_BETA1-6 : angle 1.24240 ( 9) SS BOND : bond 0.00185 ( 21) SS BOND : angle 0.85196 ( 42) covalent geometry : bond 0.00295 ( 9294) covalent geometry : angle 0.75934 (12567) *********************** 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 293 residues out of total 912 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 249 time to evaluate : 1.110 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 76 GLU cc_start: 0.9005 (tt0) cc_final: 0.8139 (tm-30) REVERT: A 130 ASP cc_start: 0.8239 (t0) cc_final: 0.7700 (t0) REVERT: A 194 MET cc_start: 0.9173 (tpp) cc_final: 0.8959 (tpp) REVERT: A 211 ASP cc_start: 0.8753 (p0) cc_final: 0.8187 (p0) REVERT: a 300 LYS cc_start: 0.9363 (mmtm) cc_final: 0.8812 (mptt) REVERT: a 313 LEU cc_start: 0.9742 (tp) cc_final: 0.9245 (tp) REVERT: a 325 ARG cc_start: 0.8700 (mmm160) cc_final: 0.8305 (mmm160) REVERT: a 357 ASP cc_start: 0.9230 (t70) cc_final: 0.8736 (t0) REVERT: a 405 GLN cc_start: 0.9263 (tm-30) cc_final: 0.9058 (tm-30) REVERT: a 413 GLU cc_start: 0.8985 (pp20) cc_final: 0.8711 (tm-30) REVERT: B 76 GLU cc_start: 0.9068 (tt0) cc_final: 0.8298 (tm-30) REVERT: B 80 MET cc_start: 0.8823 (mmt) cc_final: 0.8258 (mmm) REVERT: B 96 MET cc_start: 0.8776 (ttp) cc_final: 0.8491 (ttm) REVERT: B 130 ASP cc_start: 0.8107 (t0) cc_final: 0.7659 (t70) REVERT: B 194 MET cc_start: 0.9446 (tpp) cc_final: 0.8921 (tpp) REVERT: B 218 GLN cc_start: 0.9025 (OUTLIER) cc_final: 0.8771 (pm20) REVERT: B 227 TRP cc_start: 0.6837 (t-100) cc_final: 0.6234 (t60) REVERT: b 307 GLU cc_start: 0.8783 (mm-30) cc_final: 0.8080 (mp0) REVERT: b 325 ARG cc_start: 0.8699 (mmm160) cc_final: 0.8447 (mmm160) REVERT: b 357 ASP cc_start: 0.9224 (t70) cc_final: 0.8736 (t0) REVERT: b 359 MET cc_start: 0.9003 (mtm) cc_final: 0.8745 (mtm) REVERT: b 408 ASP cc_start: 0.9266 (m-30) cc_final: 0.8883 (m-30) REVERT: b 410 MET cc_start: 0.8982 (tpp) cc_final: 0.7997 (tpp) REVERT: b 413 GLU cc_start: 0.8824 (mp0) cc_final: 0.8350 (pm20) REVERT: C 76 GLU cc_start: 0.9144 (tt0) cc_final: 0.8862 (tt0) REVERT: C 100 GLU cc_start: 0.7762 (mm-30) cc_final: 0.7442 (mm-30) REVERT: C 130 ASP cc_start: 0.8164 (t0) cc_final: 0.7663 (t70) REVERT: C 194 MET cc_start: 0.9307 (OUTLIER) cc_final: 0.9075 (tpp) REVERT: c 278 TYR cc_start: 0.8444 (t80) cc_final: 0.8134 (t80) REVERT: c 300 LYS cc_start: 0.9316 (mmtm) cc_final: 0.8839 (mptt) REVERT: c 307 GLU cc_start: 0.8686 (mm-30) cc_final: 0.8166 (mp0) REVERT: c 311 ASP cc_start: 0.9079 (OUTLIER) cc_final: 0.8736 (t0) REVERT: c 313 LEU cc_start: 0.9704 (tp) cc_final: 0.9434 (mm) REVERT: c 408 ASP cc_start: 0.9284 (m-30) cc_final: 0.8836 (m-30) REVERT: c 410 MET cc_start: 0.9104 (tpp) cc_final: 0.8772 (tpp) REVERT: c 413 GLU cc_start: 0.8881 (OUTLIER) cc_final: 0.8660 (tm-30) outliers start: 44 outliers final: 27 residues processed: 281 average time/residue: 0.2211 time to fit residues: 84.9056 Evaluate side-chains 249 residues out of total 912 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 218 time to evaluate : 1.553 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 86 CYS Chi-restraints excluded: chain A residue 128 LEU Chi-restraints excluded: chain A residue 156 ASP Chi-restraints excluded: chain A residue 185 ASN Chi-restraints excluded: chain A residue 218 GLN Chi-restraints excluded: chain A residue 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 361 ILE Chi-restraints excluded: chain a residue 421 GLU Chi-restraints excluded: chain B residue 86 CYS Chi-restraints excluded: chain B residue 93 HIS Chi-restraints excluded: chain B residue 128 LEU Chi-restraints excluded: chain B residue 218 GLN Chi-restraints excluded: chain b residue 274 THR Chi-restraints excluded: chain b residue 337 ILE Chi-restraints excluded: chain b residue 367 SER Chi-restraints excluded: chain b residue 385 CYS Chi-restraints excluded: chain C residue 86 CYS Chi-restraints excluded: chain C residue 128 LEU Chi-restraints excluded: chain C residue 194 MET Chi-restraints excluded: chain C residue 218 GLN Chi-restraints excluded: chain C residue 245 LEU Chi-restraints excluded: chain c residue 274 THR Chi-restraints excluded: chain c residue 311 ASP Chi-restraints excluded: chain c residue 337 ILE Chi-restraints excluded: chain c residue 341 VAL Chi-restraints excluded: chain c residue 380 THR Chi-restraints excluded: chain c residue 413 GLU Chi-restraints excluded: chain c residue 420 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 82 optimal weight: 2.9990 chunk 25 optimal weight: 10.0000 chunk 81 optimal weight: 9.9990 chunk 35 optimal weight: 10.0000 chunk 32 optimal weight: 1.9990 chunk 97 optimal weight: 9.9990 chunk 58 optimal weight: 6.9990 chunk 36 optimal weight: 5.9990 chunk 42 optimal weight: 0.4980 chunk 49 optimal weight: 1.9990 chunk 6 optimal weight: 5.9990 overall best weight: 2.6988 ------------------------------------------------------------------------------- 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** B 93 HIS B 185 ASN b 405 GLN ** C 93 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 406 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** c 416 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3341 r_free = 0.3341 target = 0.073534 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2906 r_free = 0.2906 target = 0.054391 restraints weight = 29645.039| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.2960 r_free = 0.2960 target = 0.056668 restraints weight = 16286.245| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.2996 r_free = 0.2996 target = 0.058207 restraints weight = 11542.153| |-----------------------------------------------------------------------------| r_work (final): 0.2989 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8313 moved from start: 0.6158 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.071 9390 Z= 0.206 Angle : 0.870 10.766 12834 Z= 0.414 Chirality : 0.048 0.271 1599 Planarity : 0.004 0.047 1482 Dihedral : 9.211 55.063 2613 Min Nonbonded Distance : 2.449 Molprobity Statistics. All-atom Clashscore : 12.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.46 % Favored : 96.54 % Rotamer: Outliers : 5.37 % Allowed : 25.22 % Favored : 69.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.35 (0.26), residues: 984 helix: 1.49 (0.27), residues: 369 sheet: 0.74 (0.49), residues: 120 loop : -0.88 (0.25), residues: 495 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.035 0.002 TRP A 227 HIS 0.007 0.001 HIS B 93 PHE 0.021 0.002 PHE C 157 TYR 0.019 0.002 TYR B 241 ARG 0.010 0.001 ARG c 422 Details of bonding type rmsd link_NAG-ASN : bond 0.00223 ( 33) link_NAG-ASN : angle 1.92285 ( 99) link_ALPHA1-6 : bond 0.01408 ( 3) link_ALPHA1-6 : angle 1.47287 ( 9) link_BETA1-4 : bond 0.01179 ( 33) link_BETA1-4 : angle 2.91955 ( 99) link_ALPHA1-3 : bond 0.00922 ( 3) link_ALPHA1-3 : angle 2.82215 ( 9) hydrogen bonds : bond 0.04195 ( 384) hydrogen bonds : angle 4.64397 ( 1035) link_BETA1-6 : bond 0.00317 ( 3) link_BETA1-6 : angle 1.38681 ( 9) SS BOND : bond 0.00375 ( 21) SS BOND : angle 1.39896 ( 42) covalent geometry : bond 0.00450 ( 9294) covalent geometry : angle 0.81359 (12567) *********************** 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 263 residues out of total 912 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 214 time to evaluate : 1.018 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 76 GLU cc_start: 0.9048 (tt0) cc_final: 0.8212 (tm-30) REVERT: A 82 MET cc_start: 0.9353 (ptp) cc_final: 0.8678 (ptp) REVERT: A 130 ASP cc_start: 0.8329 (t0) cc_final: 0.7812 (t0) REVERT: A 211 ASP cc_start: 0.8846 (p0) cc_final: 0.8431 (p0) REVERT: a 278 TYR cc_start: 0.8266 (t80) cc_final: 0.7794 (t80) REVERT: a 300 LYS cc_start: 0.9405 (mmtm) cc_final: 0.8872 (mptt) REVERT: a 313 LEU cc_start: 0.9777 (tp) cc_final: 0.9310 (tp) REVERT: a 357 ASP cc_start: 0.9316 (t70) cc_final: 0.8814 (t0) REVERT: a 405 GLN cc_start: 0.9277 (tm-30) cc_final: 0.9064 (tm-30) REVERT: a 416 GLN cc_start: 0.8886 (mm-40) cc_final: 0.8074 (tp40) REVERT: a 420 MET cc_start: 0.7994 (OUTLIER) cc_final: 0.7451 (mmp) REVERT: B 76 GLU cc_start: 0.9083 (tt0) cc_final: 0.8338 (tm-30) REVERT: B 96 MET cc_start: 0.8764 (ttp) cc_final: 0.8499 (ttm) REVERT: B 130 ASP cc_start: 0.8186 (t0) cc_final: 0.7731 (t70) REVERT: B 194 MET cc_start: 0.9475 (tpp) cc_final: 0.8878 (tpp) REVERT: B 227 TRP cc_start: 0.6931 (t-100) cc_final: 0.6282 (t-100) REVERT: b 312 MET cc_start: 0.9207 (OUTLIER) cc_final: 0.8943 (mpp) REVERT: b 325 ARG cc_start: 0.8701 (mmm160) cc_final: 0.8491 (mmm160) REVERT: b 357 ASP cc_start: 0.9304 (t70) cc_final: 0.8790 (t0) REVERT: b 408 ASP cc_start: 0.9284 (m-30) cc_final: 0.8919 (m-30) REVERT: C 76 GLU cc_start: 0.9190 (tt0) cc_final: 0.8922 (tt0) REVERT: C 130 ASP cc_start: 0.8142 (t0) cc_final: 0.7663 (t70) REVERT: c 278 TYR cc_start: 0.8529 (t80) cc_final: 0.8210 (t80) REVERT: c 311 ASP cc_start: 0.9136 (OUTLIER) cc_final: 0.8837 (t0) REVERT: c 313 LEU cc_start: 0.9735 (tp) cc_final: 0.9256 (tp) REVERT: c 351 MET cc_start: 0.8800 (mmp) cc_final: 0.8423 (mmp) REVERT: c 408 ASP cc_start: 0.9305 (m-30) cc_final: 0.8824 (m-30) REVERT: c 410 MET cc_start: 0.9154 (tpp) cc_final: 0.8860 (tpp) outliers start: 49 outliers final: 32 residues processed: 249 average time/residue: 0.2112 time to fit residues: 72.6323 Evaluate side-chains 233 residues out of total 912 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 198 time to evaluate : 1.020 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 86 CYS Chi-restraints excluded: chain A residue 128 LEU Chi-restraints excluded: chain A residue 156 ASP Chi-restraints excluded: chain A residue 185 ASN Chi-restraints excluded: chain A residue 218 GLN Chi-restraints excluded: chain A residue 245 LEU Chi-restraints excluded: chain a residue 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 a residue 380 THR Chi-restraints excluded: chain a residue 388 VAL Chi-restraints excluded: chain a residue 420 MET 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 210 TRP Chi-restraints excluded: chain B residue 218 GLN Chi-restraints excluded: chain b residue 274 THR Chi-restraints excluded: chain b residue 312 MET 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 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 274 THR Chi-restraints excluded: chain c residue 305 HIS Chi-restraints excluded: chain c residue 311 ASP Chi-restraints excluded: chain c residue 350 ILE Chi-restraints excluded: chain c residue 380 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 74 optimal weight: 9.9990 chunk 96 optimal weight: 3.9990 chunk 82 optimal weight: 0.2980 chunk 2 optimal weight: 0.7980 chunk 64 optimal weight: 0.8980 chunk 24 optimal weight: 3.9990 chunk 31 optimal weight: 0.8980 chunk 78 optimal weight: 3.9990 chunk 1 optimal weight: 2.9990 chunk 4 optimal weight: 0.9990 chunk 52 optimal weight: 8.9990 overall best weight: 0.7782 ------------------------------------------------------------------------------- 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 185 ASN b 405 GLN ** c 406 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** c 416 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3373 r_free = 0.3373 target = 0.075147 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2941 r_free = 0.2941 target = 0.055919 restraints weight = 29573.846| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.2997 r_free = 0.2997 target = 0.058285 restraints weight = 16058.601| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3035 r_free = 0.3035 target = 0.059891 restraints weight = 11285.533| |-----------------------------------------------------------------------------| r_work (final): 0.3026 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8267 moved from start: 0.6365 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.067 9390 Z= 0.151 Angle : 0.851 17.157 12834 Z= 0.404 Chirality : 0.048 0.305 1599 Planarity : 0.004 0.050 1482 Dihedral : 8.954 54.625 2613 Min Nonbonded Distance : 2.452 Molprobity Statistics. All-atom Clashscore : 12.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.66 % Favored : 96.34 % Rotamer: Outliers : 4.17 % Allowed : 25.99 % Favored : 69.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.39 (0.26), residues: 984 helix: 1.47 (0.27), residues: 369 sheet: 0.76 (0.50), residues: 117 loop : -0.81 (0.25), residues: 498 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP A 210 HIS 0.005 0.001 HIS b 354 PHE 0.025 0.002 PHE A 157 TYR 0.025 0.002 TYR B 241 ARG 0.008 0.001 ARG a 422 Details of bonding type rmsd link_NAG-ASN : bond 0.00200 ( 33) link_NAG-ASN : angle 1.73600 ( 99) link_ALPHA1-6 : bond 0.01449 ( 3) link_ALPHA1-6 : angle 1.48665 ( 9) link_BETA1-4 : bond 0.01219 ( 33) link_BETA1-4 : angle 2.85144 ( 99) link_ALPHA1-3 : bond 0.01036 ( 3) link_ALPHA1-3 : angle 2.50437 ( 9) hydrogen bonds : bond 0.04089 ( 384) hydrogen bonds : angle 4.55382 ( 1035) link_BETA1-6 : bond 0.00468 ( 3) link_BETA1-6 : angle 1.24205 ( 9) SS BOND : bond 0.00430 ( 21) SS BOND : angle 1.60088 ( 42) covalent geometry : bond 0.00325 ( 9294) covalent geometry : angle 0.79745 (12567) *********************** 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 250 residues out of total 912 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 212 time to evaluate : 0.961 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: A 76 GLU cc_start: 0.9056 (tt0) cc_final: 0.8228 (tm-30) REVERT: A 130 ASP cc_start: 0.8314 (t0) cc_final: 0.7809 (t0) REVERT: A 211 ASP cc_start: 0.8779 (p0) cc_final: 0.8486 (p0) REVERT: a 278 TYR cc_start: 0.8191 (t80) cc_final: 0.7798 (t80) REVERT: a 300 LYS cc_start: 0.9421 (mmtm) cc_final: 0.8930 (mptt) REVERT: a 313 LEU cc_start: 0.9734 (tp) cc_final: 0.9239 (tp) REVERT: a 357 ASP cc_start: 0.9275 (t70) cc_final: 0.8811 (t0) REVERT: a 405 GLN cc_start: 0.9289 (tm-30) cc_final: 0.9072 (tm-30) REVERT: a 416 GLN cc_start: 0.8907 (mm-40) cc_final: 0.8527 (tp40) REVERT: a 420 MET cc_start: 0.8082 (OUTLIER) cc_final: 0.7592 (mmp) REVERT: B 76 GLU cc_start: 0.9082 (tt0) cc_final: 0.8328 (tm-30) REVERT: B 80 MET cc_start: 0.8812 (mmt) cc_final: 0.8169 (mmm) REVERT: B 96 MET cc_start: 0.8757 (ttp) cc_final: 0.8494 (ttm) REVERT: B 130 ASP cc_start: 0.8111 (t0) cc_final: 0.7680 (t0) REVERT: B 194 MET cc_start: 0.9431 (tpp) cc_final: 0.8901 (tpp) REVERT: B 227 TRP cc_start: 0.6909 (t-100) cc_final: 0.6294 (t-100) REVERT: b 325 ARG cc_start: 0.8690 (mmm160) cc_final: 0.8469 (mmm160) REVERT: b 357 ASP cc_start: 0.9266 (t70) cc_final: 0.8817 (t0) REVERT: b 408 ASP cc_start: 0.9260 (m-30) cc_final: 0.8862 (m-30) REVERT: C 76 GLU cc_start: 0.9196 (tt0) cc_final: 0.8914 (tt0) REVERT: C 130 ASP cc_start: 0.8037 (t0) cc_final: 0.7587 (t70) REVERT: C 218 GLN cc_start: 0.9082 (OUTLIER) cc_final: 0.8304 (pm20) REVERT: C 227 TRP cc_start: 0.7422 (t-100) cc_final: 0.6089 (t-100) REVERT: c 278 TYR cc_start: 0.8489 (t80) cc_final: 0.8258 (t80) REVERT: c 311 ASP cc_start: 0.9078 (OUTLIER) cc_final: 0.8786 (t0) REVERT: c 351 MET cc_start: 0.8727 (mmp) cc_final: 0.8305 (mmp) REVERT: c 408 ASP cc_start: 0.9306 (m-30) cc_final: 0.8809 (m-30) REVERT: c 410 MET cc_start: 0.9061 (tpp) cc_final: 0.8802 (tpp) outliers start: 38 outliers final: 27 residues processed: 242 average time/residue: 0.2017 time to fit residues: 67.4466 Evaluate side-chains 228 residues out of total 912 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 198 time to evaluate : 1.062 ------------------------------------------------------------------------------- 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 380 THR Chi-restraints excluded: chain a residue 420 MET Chi-restraints excluded: chain a residue 421 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 274 THR Chi-restraints excluded: chain b residue 313 LEU 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 420 MET 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 274 THR Chi-restraints excluded: chain c residue 311 ASP Chi-restraints excluded: chain c residue 380 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 6 optimal weight: 4.9990 chunk 16 optimal weight: 0.6980 chunk 34 optimal weight: 8.9990 chunk 80 optimal weight: 9.9990 chunk 29 optimal weight: 3.9990 chunk 5 optimal weight: 5.9990 chunk 60 optimal weight: 3.9990 chunk 73 optimal weight: 0.0470 chunk 21 optimal weight: 6.9990 chunk 69 optimal weight: 8.9990 chunk 42 optimal weight: 3.9990 overall best weight: 2.5484 ------------------------------------------------------------------------------- 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 ** B 92 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 185 ASN ** B 218 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 335 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3342 r_free = 0.3342 target = 0.073527 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2895 r_free = 0.2895 target = 0.054043 restraints weight = 30502.902| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.2952 r_free = 0.2952 target = 0.056387 restraints weight = 16655.815| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.2988 r_free = 0.2988 target = 0.057945 restraints weight = 11782.242| |-----------------------------------------------------------------------------| r_work (final): 0.2978 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8321 moved from start: 0.6524 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.062 9390 Z= 0.198 Angle : 0.880 16.298 12834 Z= 0.415 Chirality : 0.049 0.313 1599 Planarity : 0.004 0.062 1482 Dihedral : 8.898 55.031 2613 Min Nonbonded Distance : 2.459 Molprobity Statistics. All-atom Clashscore : 12.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.96 % Favored : 96.04 % Rotamer: Outliers : 4.28 % Allowed : 25.33 % Favored : 70.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.37 (0.26), residues: 984 helix: 1.50 (0.27), residues: 369 sheet: 0.59 (0.49), residues: 117 loop : -0.80 (0.26), residues: 498 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.002 TRP A 210 HIS 0.005 0.001 HIS b 354 PHE 0.022 0.002 PHE c 309 TYR 0.023 0.002 TYR A 241 ARG 0.008 0.001 ARG c 422 Details of bonding type rmsd link_NAG-ASN : bond 0.00197 ( 33) link_NAG-ASN : angle 1.82708 ( 99) link_ALPHA1-6 : bond 0.01364 ( 3) link_ALPHA1-6 : angle 1.50365 ( 9) link_BETA1-4 : bond 0.01158 ( 33) link_BETA1-4 : angle 2.85760 ( 99) link_ALPHA1-3 : bond 0.00903 ( 3) link_ALPHA1-3 : angle 2.67133 ( 9) hydrogen bonds : bond 0.04109 ( 384) hydrogen bonds : angle 4.64633 ( 1035) link_BETA1-6 : bond 0.00366 ( 3) link_BETA1-6 : angle 1.36194 ( 9) SS BOND : bond 0.00631 ( 21) SS BOND : angle 1.49176 ( 42) covalent geometry : bond 0.00434 ( 9294) covalent geometry : angle 0.82735 (12567) *********************** 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 237 residues out of total 912 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 198 time to evaluate : 0.981 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: 0.9113 (tt0) cc_final: 0.8239 (tm-30) REVERT: A 80 MET cc_start: 0.9028 (mmt) cc_final: 0.8426 (mmm) REVERT: A 129 TYR cc_start: 0.6405 (m-10) cc_final: 0.6159 (m-10) REVERT: A 130 ASP cc_start: 0.8386 (t0) cc_final: 0.7906 (t0) REVERT: A 211 ASP cc_start: 0.8888 (p0) cc_final: 0.8534 (p0) REVERT: a 278 TYR cc_start: 0.8247 (t80) cc_final: 0.7773 (t80) REVERT: a 300 LYS cc_start: 0.9443 (mmtm) cc_final: 0.8971 (mptt) REVERT: a 311 ASP cc_start: 0.9137 (OUTLIER) cc_final: 0.8844 (t0) REVERT: a 313 LEU cc_start: 0.9750 (tp) cc_final: 0.9263 (tp) REVERT: a 357 ASP cc_start: 0.9415 (t70) cc_final: 0.8962 (t0) REVERT: a 405 GLN cc_start: 0.9319 (tm-30) cc_final: 0.8992 (tm-30) REVERT: a 420 MET cc_start: 0.7875 (OUTLIER) cc_final: 0.7444 (mmp) REVERT: B 76 GLU cc_start: 0.9129 (tt0) cc_final: 0.8342 (tm-30) REVERT: B 96 MET cc_start: 0.8758 (ttp) cc_final: 0.8526 (ttm) REVERT: B 130 ASP cc_start: 0.8190 (t0) cc_final: 0.7759 (t0) REVERT: B 194 MET cc_start: 0.9491 (tpp) cc_final: 0.8881 (tpp) REVERT: B 227 TRP cc_start: 0.6981 (t-100) cc_final: 0.6295 (t-100) REVERT: b 325 ARG cc_start: 0.8716 (mmm160) cc_final: 0.8486 (mmm160) REVERT: b 357 ASP cc_start: 0.9372 (t70) cc_final: 0.8847 (t0) REVERT: b 408 ASP cc_start: 0.9305 (m-30) cc_final: 0.8908 (m-30) REVERT: b 413 GLU cc_start: 0.8847 (mp0) cc_final: 0.8496 (pm20) REVERT: C 130 ASP cc_start: 0.8112 (t0) cc_final: 0.7664 (t70) REVERT: c 278 TYR cc_start: 0.8589 (t80) cc_final: 0.8374 (t80) REVERT: c 311 ASP cc_start: 0.9174 (OUTLIER) cc_final: 0.8860 (t0) REVERT: c 325 ARG cc_start: 0.8750 (mmm160) cc_final: 0.8193 (mmm160) REVERT: c 408 ASP cc_start: 0.9342 (m-30) cc_final: 0.8832 (m-30) REVERT: c 410 MET cc_start: 0.9126 (tpp) cc_final: 0.8894 (tpp) outliers start: 39 outliers final: 31 residues processed: 226 average time/residue: 0.2072 time to fit residues: 65.1552 Evaluate side-chains 223 residues out of total 912 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 189 time to evaluate : 1.026 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 86 CYS Chi-restraints excluded: chain A residue 128 LEU Chi-restraints excluded: chain A residue 156 ASP Chi-restraints excluded: chain A residue 185 ASN Chi-restraints excluded: chain A residue 218 GLN Chi-restraints excluded: chain A residue 245 LEU Chi-restraints excluded: chain a residue 311 ASP Chi-restraints excluded: chain a residue 334 ILE Chi-restraints excluded: chain a residue 351 MET Chi-restraints excluded: chain a residue 380 THR Chi-restraints excluded: chain a residue 420 MET Chi-restraints excluded: chain a residue 421 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 269 SER Chi-restraints excluded: chain b residue 274 THR Chi-restraints excluded: chain b residue 313 LEU 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 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 274 THR Chi-restraints excluded: chain c residue 305 HIS Chi-restraints excluded: chain c residue 311 ASP Chi-restraints excluded: chain c residue 323 ILE 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 21 optimal weight: 0.7980 chunk 79 optimal weight: 3.9990 chunk 64 optimal weight: 6.9990 chunk 67 optimal weight: 1.9990 chunk 47 optimal weight: 4.9990 chunk 61 optimal weight: 1.9990 chunk 65 optimal weight: 3.9990 chunk 55 optimal weight: 0.8980 chunk 11 optimal weight: 8.9990 chunk 16 optimal weight: 0.0980 chunk 0 optimal weight: 9.9990 overall best weight: 1.1584 ------------------------------------------------------------------------------- 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 185 ASN ** B 92 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 218 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** b 405 GLN ** c 335 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** c 416 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3370 r_free = 0.3370 target = 0.074950 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2929 r_free = 0.2929 target = 0.055411 restraints weight = 29667.999| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.2986 r_free = 0.2986 target = 0.057746 restraints weight = 16511.066| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3023 r_free = 0.3023 target = 0.059328 restraints weight = 11773.643| |-----------------------------------------------------------------------------| r_work (final): 0.3012 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8304 moved from start: 0.6656 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 9390 Z= 0.153 Angle : 0.854 16.627 12834 Z= 0.402 Chirality : 0.048 0.287 1599 Planarity : 0.004 0.058 1482 Dihedral : 8.707 54.735 2613 Min Nonbonded Distance : 2.443 Molprobity Statistics. All-atom Clashscore : 12.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.96 % Favored : 96.04 % Rotamer: Outliers : 3.73 % Allowed : 25.44 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.35 (0.26), residues: 984 helix: 1.44 (0.27), residues: 369 sheet: 0.57 (0.49), residues: 117 loop : -0.78 (0.26), residues: 498 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.035 0.002 TRP A 210 HIS 0.005 0.001 HIS b 354 PHE 0.022 0.002 PHE c 309 TYR 0.034 0.002 TYR C 241 ARG 0.009 0.001 ARG c 422 Details of bonding type rmsd link_NAG-ASN : bond 0.00161 ( 33) link_NAG-ASN : angle 1.70228 ( 99) link_ALPHA1-6 : bond 0.01369 ( 3) link_ALPHA1-6 : angle 1.51551 ( 9) link_BETA1-4 : bond 0.01186 ( 33) link_BETA1-4 : angle 2.79982 ( 99) link_ALPHA1-3 : bond 0.00964 ( 3) link_ALPHA1-3 : angle 2.41205 ( 9) hydrogen bonds : bond 0.04051 ( 384) hydrogen bonds : angle 4.57556 ( 1035) link_BETA1-6 : bond 0.00468 ( 3) link_BETA1-6 : angle 1.25334 ( 9) SS BOND : bond 0.00476 ( 21) SS BOND : angle 1.35203 ( 42) covalent geometry : bond 0.00337 ( 9294) covalent geometry : angle 0.80472 (12567) *********************** 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 232 residues out of total 912 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 198 time to evaluate : 0.971 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: 0.9099 (tt0) cc_final: 0.8241 (tm-30) REVERT: A 82 MET cc_start: 0.9094 (mtm) cc_final: 0.8812 (mpp) REVERT: A 130 ASP cc_start: 0.8361 (t0) cc_final: 0.7905 (t0) REVERT: A 211 ASP cc_start: 0.8796 (p0) cc_final: 0.8421 (p0) REVERT: A 218 GLN cc_start: 0.8891 (OUTLIER) cc_final: 0.8507 (pm20) REVERT: a 278 TYR cc_start: 0.8312 (t80) cc_final: 0.7822 (t80) REVERT: a 300 LYS cc_start: 0.9442 (mmtm) cc_final: 0.8958 (mptt) REVERT: a 311 ASP cc_start: 0.9076 (OUTLIER) cc_final: 0.8796 (t0) REVERT: a 313 LEU cc_start: 0.9726 (tp) cc_final: 0.9220 (tp) REVERT: a 357 ASP cc_start: 0.9384 (t70) cc_final: 0.8997 (t0) REVERT: a 405 GLN cc_start: 0.9309 (tm-30) cc_final: 0.8988 (tm-30) REVERT: a 420 MET cc_start: 0.7805 (OUTLIER) cc_final: 0.7435 (mmp) REVERT: B 76 GLU cc_start: 0.9115 (tt0) cc_final: 0.8366 (tm-30) REVERT: B 96 MET cc_start: 0.8710 (ttp) cc_final: 0.8494 (ttm) REVERT: B 130 ASP cc_start: 0.8118 (t0) cc_final: 0.7704 (t0) REVERT: B 194 MET cc_start: 0.9439 (tpp) cc_final: 0.9104 (tpt) REVERT: B 227 TRP cc_start: 0.6918 (t-100) cc_final: 0.6252 (t-100) REVERT: b 325 ARG cc_start: 0.8680 (mmm160) cc_final: 0.8474 (mmm160) REVERT: b 357 ASP cc_start: 0.9302 (t70) cc_final: 0.8824 (t0) REVERT: b 408 ASP cc_start: 0.9281 (m-30) cc_final: 0.8908 (m-30) REVERT: b 413 GLU cc_start: 0.8812 (OUTLIER) cc_final: 0.8539 (pm20) REVERT: C 80 MET cc_start: 0.9026 (mmm) cc_final: 0.8762 (mmm) REVERT: C 96 MET cc_start: 0.8165 (ttt) cc_final: 0.7871 (mtp) REVERT: C 130 ASP cc_start: 0.8041 (t0) cc_final: 0.7623 (t70) REVERT: C 218 GLN cc_start: 0.8998 (OUTLIER) cc_final: 0.8523 (pm20) REVERT: c 278 TYR cc_start: 0.8545 (t80) cc_final: 0.8290 (t80) REVERT: c 311 ASP cc_start: 0.9138 (OUTLIER) cc_final: 0.8734 (t0) REVERT: c 408 ASP cc_start: 0.9330 (m-30) cc_final: 0.8822 (m-30) REVERT: c 410 MET cc_start: 0.9067 (tpp) cc_final: 0.8828 (tpp) outliers start: 34 outliers final: 22 residues processed: 225 average time/residue: 0.1830 time to fit residues: 58.1190 Evaluate side-chains 216 residues out of total 912 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 188 time to evaluate : 0.948 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 86 CYS Chi-restraints excluded: chain A residue 128 LEU Chi-restraints excluded: chain A residue 156 ASP Chi-restraints excluded: chain A residue 185 ASN Chi-restraints excluded: chain A residue 218 GLN Chi-restraints excluded: chain A residue 245 LEU Chi-restraints excluded: chain a residue 311 ASP Chi-restraints excluded: chain a residue 420 MET Chi-restraints excluded: chain a residue 421 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 269 SER Chi-restraints excluded: chain b residue 274 THR 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 413 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 274 THR Chi-restraints excluded: chain c residue 305 HIS Chi-restraints excluded: chain c residue 311 ASP Chi-restraints excluded: chain c residue 337 ILE Chi-restraints excluded: chain c residue 380 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 58 optimal weight: 0.8980 chunk 7 optimal weight: 0.9990 chunk 90 optimal weight: 3.9990 chunk 36 optimal weight: 3.9990 chunk 70 optimal weight: 10.0000 chunk 28 optimal weight: 7.9990 chunk 9 optimal weight: 10.0000 chunk 13 optimal weight: 10.0000 chunk 49 optimal weight: 0.9990 chunk 95 optimal weight: 2.9990 chunk 40 optimal weight: 5.9990 overall best weight: 1.9788 ------------------------------------------------------------------------------- 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 416 GLN ** B 92 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 185 ASN ** B 218 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 335 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3355 r_free = 0.3355 target = 0.074209 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2906 r_free = 0.2906 target = 0.054535 restraints weight = 30409.397| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.2964 r_free = 0.2964 target = 0.056884 restraints weight = 16733.006| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3002 r_free = 0.3002 target = 0.058461 restraints weight = 11852.935| |-----------------------------------------------------------------------------| r_work (final): 0.2991 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8315 moved from start: 0.6763 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.064 9390 Z= 0.179 Angle : 0.883 16.063 12834 Z= 0.416 Chirality : 0.048 0.275 1599 Planarity : 0.004 0.060 1482 Dihedral : 8.644 54.809 2613 Min Nonbonded Distance : 2.473 Molprobity Statistics. All-atom Clashscore : 12.80 Ramachandran Plot: Outliers : 0.10 % Allowed : 4.17 % Favored : 95.73 % Rotamer: Outliers : 2.96 % Allowed : 26.21 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.53 (0.26), residues: 984 helix: 1.88 (0.28), residues: 345 sheet: 0.44 (0.48), residues: 117 loop : -0.74 (0.26), residues: 522 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.046 0.003 TRP A 227 HIS 0.005 0.001 HIS b 354 PHE 0.020 0.002 PHE B 157 TYR 0.035 0.002 TYR C 241 ARG 0.008 0.001 ARG c 422 Details of bonding type rmsd link_NAG-ASN : bond 0.00228 ( 33) link_NAG-ASN : angle 1.72885 ( 99) link_ALPHA1-6 : bond 0.01333 ( 3) link_ALPHA1-6 : angle 1.50493 ( 9) link_BETA1-4 : bond 0.01157 ( 33) link_BETA1-4 : angle 2.77999 ( 99) link_ALPHA1-3 : bond 0.00923 ( 3) link_ALPHA1-3 : angle 2.47729 ( 9) hydrogen bonds : bond 0.04044 ( 384) hydrogen bonds : angle 4.60392 ( 1035) link_BETA1-6 : bond 0.00440 ( 3) link_BETA1-6 : angle 1.29677 ( 9) SS BOND : bond 0.00468 ( 21) SS BOND : angle 1.29519 ( 42) covalent geometry : bond 0.00404 ( 9294) covalent geometry : angle 0.83597 (12567) ********************** 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 224 residues out of total 912 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 197 time to evaluate : 1.093 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: 0.9139 (tt0) cc_final: 0.8225 (tm-30) REVERT: A 80 MET cc_start: 0.8982 (mmt) cc_final: 0.8697 (mpp) REVERT: A 96 MET cc_start: 0.8260 (ttm) cc_final: 0.8043 (tpp) REVERT: A 130 ASP cc_start: 0.8384 (t0) cc_final: 0.7930 (t0) REVERT: A 211 ASP cc_start: 0.8867 (p0) cc_final: 0.8495 (p0) REVERT: A 218 GLN cc_start: 0.8901 (OUTLIER) cc_final: 0.8521 (pm20) REVERT: a 278 TYR cc_start: 0.8392 (t80) cc_final: 0.8123 (t80) REVERT: a 300 LYS cc_start: 0.9446 (mmtm) cc_final: 0.8959 (mptt) REVERT: a 311 ASP cc_start: 0.9137 (OUTLIER) cc_final: 0.8850 (t0) REVERT: a 313 LEU cc_start: 0.9733 (tp) cc_final: 0.9263 (tp) REVERT: a 325 ARG cc_start: 0.8782 (mmm160) cc_final: 0.8468 (mmm160) REVERT: a 357 ASP cc_start: 0.9429 (t70) cc_final: 0.9023 (t0) REVERT: a 405 GLN cc_start: 0.9335 (tm-30) cc_final: 0.9047 (tm-30) REVERT: a 420 MET cc_start: 0.7843 (OUTLIER) cc_final: 0.7431 (mmp) REVERT: B 76 GLU cc_start: 0.9152 (tt0) cc_final: 0.8376 (tm-30) REVERT: B 96 MET cc_start: 0.8758 (ttp) cc_final: 0.8522 (ttm) REVERT: B 130 ASP cc_start: 0.8161 (t0) cc_final: 0.7749 (t0) REVERT: B 194 MET cc_start: 0.9465 (tpp) cc_final: 0.8828 (tpp) REVERT: B 227 TRP cc_start: 0.6957 (t-100) cc_final: 0.6260 (t-100) REVERT: b 325 ARG cc_start: 0.8710 (mmm160) cc_final: 0.8508 (mmm160) REVERT: b 357 ASP cc_start: 0.9360 (t70) cc_final: 0.8856 (t0) REVERT: b 408 ASP cc_start: 0.9305 (m-30) cc_final: 0.8951 (m-30) REVERT: b 410 MET cc_start: 0.9055 (tpp) cc_final: 0.8334 (mmm) REVERT: b 413 GLU cc_start: 0.8838 (OUTLIER) cc_final: 0.8504 (pm20) REVERT: b 420 MET cc_start: 0.7526 (mmp) cc_final: 0.6790 (mmp) REVERT: C 80 MET cc_start: 0.9035 (mmm) cc_final: 0.8825 (mmm) REVERT: C 96 MET cc_start: 0.8213 (ttt) cc_final: 0.7996 (mtp) REVERT: C 130 ASP cc_start: 0.8074 (t0) cc_final: 0.7627 (t70) REVERT: C 218 GLN cc_start: 0.9012 (OUTLIER) cc_final: 0.8571 (pm20) REVERT: c 278 TYR cc_start: 0.8546 (t80) cc_final: 0.8309 (t80) REVERT: c 311 ASP cc_start: 0.9177 (OUTLIER) cc_final: 0.8797 (t0) REVERT: c 408 ASP cc_start: 0.9346 (m-30) cc_final: 0.8844 (m-30) REVERT: c 410 MET cc_start: 0.9101 (tpp) cc_final: 0.8876 (tpp) REVERT: c 420 MET cc_start: 0.6780 (mmt) cc_final: 0.6553 (mmt) outliers start: 27 outliers final: 20 residues processed: 219 average time/residue: 0.2092 time to fit residues: 65.0254 Evaluate side-chains 215 residues out of total 912 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 189 time to evaluate : 1.051 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 86 CYS Chi-restraints excluded: chain A residue 128 LEU Chi-restraints excluded: chain A residue 156 ASP Chi-restraints excluded: chain A residue 185 ASN Chi-restraints excluded: chain A residue 218 GLN Chi-restraints excluded: chain A residue 245 LEU Chi-restraints excluded: chain a residue 311 ASP Chi-restraints excluded: chain a residue 420 MET Chi-restraints excluded: chain a residue 421 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 269 SER Chi-restraints excluded: chain b residue 274 THR Chi-restraints excluded: chain b residue 349 LEU Chi-restraints excluded: chain b residue 385 CYS Chi-restraints excluded: chain b residue 413 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 274 THR Chi-restraints excluded: chain c residue 305 HIS Chi-restraints excluded: chain c residue 311 ASP 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 58 optimal weight: 4.9990 chunk 5 optimal weight: 10.0000 chunk 23 optimal weight: 0.5980 chunk 95 optimal weight: 2.9990 chunk 93 optimal weight: 5.9990 chunk 76 optimal weight: 9.9990 chunk 33 optimal weight: 10.0000 chunk 89 optimal weight: 1.9990 chunk 1 optimal weight: 6.9990 chunk 63 optimal weight: 6.9990 chunk 9 optimal weight: 8.9990 overall best weight: 3.3188 ------------------------------------------------------------------------------- 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 185 ASN ** B 92 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 218 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** b 405 GLN ** b 423 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 92 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 335 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3325 r_free = 0.3325 target = 0.072731 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2875 r_free = 0.2875 target = 0.053287 restraints weight = 30352.762| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.2931 r_free = 0.2931 target = 0.055521 restraints weight = 17144.254| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 23)----------------| | r_work = 0.2968 r_free = 0.2968 target = 0.057004 restraints weight = 12324.840| |-----------------------------------------------------------------------------| r_work (final): 0.2956 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8372 moved from start: 0.6840 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.081 9390 Z= 0.237 Angle : 0.925 15.513 12834 Z= 0.436 Chirality : 0.050 0.279 1599 Planarity : 0.005 0.056 1482 Dihedral : 8.699 55.322 2613 Min Nonbonded Distance : 2.429 Molprobity Statistics. All-atom Clashscore : 14.43 Ramachandran Plot: Outliers : 0.10 % Allowed : 4.27 % Favored : 95.63 % Rotamer: Outliers : 3.18 % Allowed : 26.54 % Favored : 70.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.44 (0.27), residues: 984 helix: 1.86 (0.28), residues: 345 sheet: 0.33 (0.48), residues: 117 loop : -0.82 (0.26), residues: 522 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.002 TRP A 210 HIS 0.004 0.001 HIS B 93 PHE 0.019 0.003 PHE B 157 TYR 0.030 0.002 TYR A 241 ARG 0.008 0.001 ARG c 422 Details of bonding type rmsd link_NAG-ASN : bond 0.00322 ( 33) link_NAG-ASN : angle 1.89068 ( 99) link_ALPHA1-6 : bond 0.01311 ( 3) link_ALPHA1-6 : angle 1.57373 ( 9) link_BETA1-4 : bond 0.01134 ( 33) link_BETA1-4 : angle 2.76412 ( 99) link_ALPHA1-3 : bond 0.00778 ( 3) link_ALPHA1-3 : angle 2.66023 ( 9) hydrogen bonds : bond 0.04123 ( 384) hydrogen bonds : angle 4.76824 ( 1035) link_BETA1-6 : bond 0.00397 ( 3) link_BETA1-6 : angle 1.40317 ( 9) SS BOND : bond 0.00490 ( 21) SS BOND : angle 1.30328 ( 42) covalent geometry : bond 0.00529 ( 9294) covalent geometry : angle 0.87832 (12567) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3051.29 seconds wall clock time: 54 minutes 46.72 seconds (3286.72 seconds total)