Starting phenix.real_space_refine on Thu Mar 13 22:27:13 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7sgd_25107/03_2025/7sgd_25107.cif Found real_map, /net/cci-nas-00/data/ceres_data/7sgd_25107/03_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_25107/03_2025/7sgd_25107.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7sgd_25107/03_2025/7sgd_25107.map" model { file = "/net/cci-nas-00/data/ceres_data/7sgd_25107/03_2025/7sgd_25107.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7sgd_25107/03_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-5624/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: 5.97, per 1000 atoms: 0.65 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: 3.47 Conformation dependent library (CDL) restraints added in 941.5 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: 0.91 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: 2.36 Time building geometry restraints manager: 3.91 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: 0.940 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: 0.000 Extract box with map and model: 0.350 Check model and map are aligned: 0.070 Set scattering table: 0.100 Process input model: 24.290 Find NCS groups from input model: 0.610 Set up NCS constraints: 0.050 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:2.800 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 29.210 ------------------------------------------------------------------------------- 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 : 0.024 0.115 9294 Z= 1.497 Angle : 1.797 10.537 12567 Z= 1.150 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 *********************** 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 : 1.429 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: 0.2734 time to fit residues: 169.7525 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 : 1.132 ------------------------------------------------------------------------------- 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: 0.9990 overall best weight: 1.3990 ------------------------------------------------------------------------------- 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 = 0.3396 r_free = 0.3396 target = 0.076031 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2960 r_free = 0.2960 target = 0.056489 restraints weight = 29137.552| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3017 r_free = 0.3017 target = 0.058992 restraints weight = 15465.074| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3056 r_free = 0.3056 target = 0.060723 restraints weight = 10689.825| |-----------------------------------------------------------------------------| r_work (final): 0.3051 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8138 moved from start: 0.4532 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.043 9294 Z= 0.294 Angle : 0.927 14.199 12567 Z= 0.477 Chirality : 0.051 0.320 1599 Planarity : 0.005 0.029 1482 Dihedral : 13.361 82.734 2613 Min Nonbonded Distance : 2.415 Molprobity Statistics. All-atom Clashscore : 11.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.13 % Favored : 97.87 % Rotamer: Outliers : 4.71 % Allowed : 18.53 % 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: 0.53 (0.25), residues: 984 helix: 1.34 (0.26), residues: 366 sheet: 1.90 (0.51), residues: 108 loop : -0.75 (0.23), 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 0.006 0.001 ARG a 282 *********************** 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 349 residues out of total 912 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 306 time to evaluate : 0.920 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 72 GLU cc_start: 0.8139 (tt0) cc_final: 0.7926 (tt0) REVERT: A 130 ASP cc_start: 0.8416 (t0) cc_final: 0.7863 (t0) REVERT: a 300 LYS cc_start: 0.9203 (mmtm) cc_final: 0.8559 (mptt) REVERT: a 307 GLU cc_start: 0.8832 (mm-30) cc_final: 0.8589 (mm-30) REVERT: a 311 ASP cc_start: 0.9236 (m-30) cc_final: 0.9000 (m-30) REVERT: a 313 LEU cc_start: 0.9777 (tp) cc_final: 0.9334 (tp) REVERT: a 357 ASP cc_start: 0.9161 (t70) cc_final: 0.8626 (t0) REVERT: a 405 GLN cc_start: 0.9145 (tm-30) cc_final: 0.8822 (tm-30) REVERT: a 410 MET cc_start: 0.8585 (tpp) cc_final: 0.7954 (tpp) REVERT: B 130 ASP cc_start: 0.8338 (t0) cc_final: 0.7802 (t0) REVERT: B 211 ASP cc_start: 0.8479 (p0) cc_final: 0.8208 (p0) REVERT: b 261 THR cc_start: 0.8304 (p) cc_final: 0.8076 (p) REVERT: b 307 GLU cc_start: 0.8767 (mm-30) cc_final: 0.8385 (mp0) REVERT: b 311 ASP cc_start: 0.9222 (m-30) cc_final: 0.8952 (m-30) REVERT: b 313 LEU cc_start: 0.9784 (tp) cc_final: 0.9420 (tp) REVERT: b 346 ASN cc_start: 0.9358 (t0) cc_final: 0.9154 (t0) REVERT: b 357 ASP cc_start: 0.9104 (t70) cc_final: 0.8583 (t0) REVERT: b 369 TYR cc_start: 0.9280 (m-10) cc_final: 0.9039 (m-80) REVERT: b 405 GLN cc_start: 0.9096 (tm-30) cc_final: 0.8852 (tm-30) REVERT: b 409 ASN cc_start: 0.8664 (m-40) cc_final: 0.8372 (m-40) REVERT: C 72 GLU cc_start: 0.8239 (tt0) cc_final: 0.7986 (tt0) REVERT: C 76 GLU cc_start: 0.9152 (tt0) cc_final: 0.8938 (tt0) REVERT: C 100 GLU cc_start: 0.7519 (mm-30) cc_final: 0.7281 (mm-30) REVERT: C 130 ASP cc_start: 0.8282 (t0) cc_final: 0.7722 (t70) REVERT: C 227 TRP cc_start: 0.7171 (t-100) cc_final: 0.6832 (t-100) REVERT: c 278 TYR cc_start: 0.8381 (t80) cc_final: 0.7880 (t80) REVERT: c 300 LYS cc_start: 0.9164 (mmtm) cc_final: 0.8646 (mptt) REVERT: c 306 ASP cc_start: 0.8716 (t0) cc_final: 0.8281 (t70) REVERT: c 307 GLU cc_start: 0.8802 (mm-30) cc_final: 0.7900 (mp0) REVERT: c 313 LEU cc_start: 0.9762 (tp) cc_final: 0.9351 (tp) REVERT: c 359 MET cc_start: 0.9144 (mtt) cc_final: 0.8901 (mtt) REVERT: c 401 ASP cc_start: 0.9217 (p0) cc_final: 0.8968 (p0) REVERT: c 408 ASP cc_start: 0.9016 (m-30) cc_final: 0.8359 (m-30) REVERT: c 409 ASN cc_start: 0.8565 (m-40) cc_final: 0.8235 (m-40) outliers start: 43 outliers final: 19 residues processed: 327 average time/residue: 0.2165 time to fit residues: 97.5252 Evaluate side-chains 265 residues out of total 912 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 246 time to evaluate : 0.999 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 86 CYS Chi-restraints excluded: chain A residue 126 LYS Chi-restraints excluded: chain A residue 156 ASP Chi-restraints excluded: chain a residue 269 SER Chi-restraints excluded: chain a residue 273 ASP Chi-restraints excluded: chain a residue 337 ILE Chi-restraints excluded: chain a residue 361 ILE Chi-restraints excluded: chain a residue 380 THR 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 421 GLU Chi-restraints excluded: chain C residue 86 CYS Chi-restraints excluded: chain c residue 269 SER Chi-restraints excluded: chain c residue 337 ILE Chi-restraints excluded: chain c residue 421 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 22 optimal weight: 0.7980 chunk 72 optimal weight: 8.9990 chunk 8 optimal weight: 0.4980 chunk 23 optimal weight: 2.9990 chunk 38 optimal weight: 9.9990 chunk 86 optimal weight: 3.9990 chunk 44 optimal weight: 10.0000 chunk 7 optimal weight: 6.9990 chunk 78 optimal weight: 7.9990 chunk 83 optimal weight: 0.9990 chunk 30 optimal weight: 0.5980 overall best weight: 1.1784 ------------------------------------------------------------------------------- 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 93 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3385 r_free = 0.3385 target = 0.075823 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2954 r_free = 0.2954 target = 0.056419 restraints weight = 29508.445| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3013 r_free = 0.3013 target = 0.058905 restraints weight = 15653.622| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3051 r_free = 0.3051 target = 0.060588 restraints weight = 10870.339| |-----------------------------------------------------------------------------| r_work (final): 0.3044 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8185 moved from start: 0.5205 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 9294 Z= 0.235 Angle : 0.831 11.305 12567 Z= 0.420 Chirality : 0.048 0.286 1599 Planarity : 0.004 0.030 1482 Dihedral : 11.837 72.770 2613 Min Nonbonded Distance : 2.493 Molprobity Statistics. All-atom Clashscore : 12.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.24 % Favored : 97.76 % Rotamer: Outliers : 5.37 % Allowed : 21.16 % Favored : 73.46 % 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: 0.48 (0.25), residues: 984 helix: 1.31 (0.26), residues: 366 sheet: 1.63 (0.50), residues: 108 loop : -0.71 (0.24), residues: 510 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.003 TRP B 227 HIS 0.004 0.001 HIS C 93 PHE 0.025 0.003 PHE A 157 TYR 0.019 0.002 TYR C 166 ARG 0.005 0.000 ARG a 325 *********************** 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 : 1.367 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 75 MET cc_start: 0.8535 (mtp) cc_final: 0.8173 (mtp) REVERT: A 76 GLU cc_start: 0.9068 (tt0) cc_final: 0.8285 (tm-30) REVERT: A 130 ASP cc_start: 0.8459 (t0) cc_final: 0.7879 (t70) REVERT: A 211 ASP cc_start: 0.8836 (p0) cc_final: 0.8482 (p0) REVERT: a 261 THR cc_start: 0.8158 (p) cc_final: 0.7894 (p) REVERT: a 282 ARG cc_start: 0.8864 (mmm-85) cc_final: 0.8580 (mmm-85) REVERT: a 300 LYS cc_start: 0.9257 (mmtm) cc_final: 0.8615 (mptt) REVERT: a 311 ASP cc_start: 0.9236 (m-30) cc_final: 0.9025 (m-30) REVERT: a 313 LEU cc_start: 0.9735 (tp) cc_final: 0.9321 (tp) REVERT: a 357 ASP cc_start: 0.9175 (t70) cc_final: 0.8630 (t0) REVERT: a 405 GLN cc_start: 0.9194 (tm-30) cc_final: 0.8951 (tm-30) REVERT: a 416 GLN cc_start: 0.9159 (mt0) cc_final: 0.8949 (mt0) REVERT: a 417 LYS cc_start: 0.9130 (pttp) cc_final: 0.8870 (ptpp) REVERT: B 130 ASP cc_start: 0.8172 (t0) cc_final: 0.7715 (t0) REVERT: B 227 TRP cc_start: 0.6817 (t-100) cc_final: 0.6048 (t60) REVERT: b 261 THR cc_start: 0.8418 (p) cc_final: 0.8205 (p) REVERT: b 313 LEU cc_start: 0.9725 (tp) cc_final: 0.9296 (tp) REVERT: b 357 ASP cc_start: 0.9131 (t70) cc_final: 0.8655 (t0) REVERT: b 408 ASP cc_start: 0.9323 (m-30) cc_final: 0.8963 (m-30) REVERT: b 410 MET cc_start: 0.9049 (tpp) cc_final: 0.8166 (tpp) REVERT: b 413 GLU cc_start: 0.8854 (mp0) cc_final: 0.8609 (pm20) REVERT: C 96 MET cc_start: 0.7961 (ptp) cc_final: 0.7697 (ptp) REVERT: C 100 GLU cc_start: 0.7585 (mm-30) cc_final: 0.7317 (mm-30) REVERT: C 130 ASP cc_start: 0.8198 (t0) cc_final: 0.7646 (t70) REVERT: c 278 TYR cc_start: 0.8411 (t80) cc_final: 0.7962 (t80) REVERT: c 300 LYS cc_start: 0.9238 (mmtm) cc_final: 0.8710 (mptt) REVERT: c 313 LEU cc_start: 0.9733 (tp) cc_final: 0.9291 (tp) REVERT: c 410 MET cc_start: 0.9006 (tpp) cc_final: 0.8647 (tpp) REVERT: c 413 GLU cc_start: 0.8746 (mp0) cc_final: 0.8542 (tm-30) outliers start: 49 outliers final: 28 residues processed: 291 average time/residue: 0.2579 time to fit residues: 103.0033 Evaluate side-chains 260 residues out of total 912 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 232 time to evaluate : 1.243 ------------------------------------------------------------------------------- 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 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 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 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 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: 4.9990 chunk 83 optimal weight: 6.9990 chunk 78 optimal weight: 0.9990 chunk 54 optimal weight: 6.9990 chunk 80 optimal weight: 9.9990 chunk 67 optimal weight: 6.9990 chunk 23 optimal weight: 6.9990 chunk 14 optimal weight: 6.9990 chunk 86 optimal weight: 6.9990 chunk 94 optimal weight: 5.9990 chunk 84 optimal weight: 2.9990 overall best weight: 4.3990 ------------------------------------------------------------------------------- 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 115 HIS A 185 ASN ** B 93 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 115 HIS C 69 GLN ** C 93 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 115 HIS c 406 GLN c 416 GLN ** c 423 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3291 r_free = 0.3291 target = 0.071270 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2842 r_free = 0.2842 target = 0.052044 restraints weight = 30604.016| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.2898 r_free = 0.2898 target = 0.054274 restraints weight = 16902.307| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.2934 r_free = 0.2934 target = 0.055754 restraints weight = 11985.085| |-----------------------------------------------------------------------------| r_work (final): 0.2923 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8364 moved from start: 0.5879 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.049 9294 Z= 0.407 Angle : 0.909 9.318 12567 Z= 0.447 Chirality : 0.050 0.325 1599 Planarity : 0.005 0.043 1482 Dihedral : 10.205 59.287 2613 Min Nonbonded Distance : 2.412 Molprobity Statistics. All-atom Clashscore : 13.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.56 % Favored : 96.44 % Rotamer: Outliers : 6.14 % Allowed : 20.72 % Favored : 73.14 % 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: 0.09 (0.25), residues: 984 helix: 1.15 (0.26), residues: 369 sheet: 0.77 (0.48), residues: 117 loop : -0.96 (0.25), residues: 498 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP c 283 HIS 0.005 0.001 HIS B 92 PHE 0.020 0.003 PHE c 309 TYR 0.023 0.002 TYR A 241 ARG 0.010 0.001 ARG b 422 *********************** 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 286 residues out of total 912 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 230 time to evaluate : 1.349 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 96 MET cc_start: 0.8371 (ttp) cc_final: 0.8129 (ttm) REVERT: A 130 ASP cc_start: 0.8655 (t0) cc_final: 0.8075 (t70) REVERT: A 211 ASP cc_start: 0.8835 (p0) cc_final: 0.8366 (p0) REVERT: a 300 LYS cc_start: 0.9373 (mmtm) cc_final: 0.8760 (mptt) REVERT: a 313 LEU cc_start: 0.9798 (tp) cc_final: 0.9328 (tp) REVERT: a 325 ARG cc_start: 0.8758 (mmt90) cc_final: 0.8511 (mmm160) REVERT: a 351 MET cc_start: 0.9064 (mmp) cc_final: 0.8668 (mmp) REVERT: a 357 ASP cc_start: 0.9419 (t70) cc_final: 0.8887 (t0) REVERT: a 405 GLN cc_start: 0.9263 (tm-30) cc_final: 0.8986 (tm-30) REVERT: B 96 MET cc_start: 0.8946 (ttp) cc_final: 0.8511 (ttm) REVERT: B 130 ASP cc_start: 0.8292 (t0) cc_final: 0.7794 (t0) REVERT: B 245 LEU cc_start: 0.9440 (OUTLIER) cc_final: 0.9229 (tt) REVERT: b 306 ASP cc_start: 0.8284 (OUTLIER) cc_final: 0.7867 (m-30) REVERT: b 313 LEU cc_start: 0.9749 (tp) cc_final: 0.9349 (tp) REVERT: b 357 ASP cc_start: 0.9398 (t70) cc_final: 0.8818 (t0) REVERT: b 408 ASP cc_start: 0.9271 (m-30) cc_final: 0.8962 (m-30) REVERT: b 420 MET cc_start: 0.8159 (mmp) cc_final: 0.7902 (mmt) REVERT: C 76 GLU cc_start: 0.9249 (tt0) cc_final: 0.9010 (tt0) REVERT: C 80 MET cc_start: 0.8987 (mmt) cc_final: 0.8759 (mmm) REVERT: C 82 MET cc_start: 0.9148 (OUTLIER) cc_final: 0.8857 (pmm) REVERT: C 96 MET cc_start: 0.8157 (ptp) cc_final: 0.7858 (ptm) REVERT: C 130 ASP cc_start: 0.8263 (t0) cc_final: 0.7713 (t70) REVERT: c 278 TYR cc_start: 0.8560 (t80) cc_final: 0.8245 (t80) REVERT: c 300 LYS cc_start: 0.9342 (mmtm) cc_final: 0.8903 (mptt) REVERT: c 311 ASP cc_start: 0.9218 (OUTLIER) cc_final: 0.8913 (t0) REVERT: c 313 LEU cc_start: 0.9778 (tp) cc_final: 0.9301 (tp) REVERT: c 325 ARG cc_start: 0.8665 (mmm160) cc_final: 0.8055 (mmm160) REVERT: c 413 GLU cc_start: 0.8842 (mp0) cc_final: 0.8600 (tm-30) outliers start: 56 outliers final: 35 residues processed: 271 average time/residue: 0.2705 time to fit residues: 100.4667 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 : 1.051 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 86 CYS Chi-restraints excluded: chain A residue 100 GLU Chi-restraints excluded: chain A residue 128 LEU Chi-restraints excluded: chain A residue 156 ASP Chi-restraints excluded: chain A residue 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 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 218 GLN Chi-restraints excluded: chain B residue 239 ILE Chi-restraints excluded: chain B residue 245 LEU Chi-restraints excluded: chain b residue 274 THR Chi-restraints excluded: chain b residue 306 ASP Chi-restraints excluded: chain b residue 337 ILE Chi-restraints excluded: chain b residue 349 LEU Chi-restraints excluded: chain b residue 385 CYS Chi-restraints excluded: chain b residue 388 VAL Chi-restraints excluded: chain b residue 392 SER Chi-restraints excluded: chain b residue 403 ILE Chi-restraints excluded: chain 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 239 ILE 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 392 SER 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: 6.9990 chunk 54 optimal weight: 7.9990 chunk 52 optimal weight: 0.9980 chunk 47 optimal weight: 6.9990 chunk 74 optimal weight: 9.9990 chunk 59 optimal weight: 0.9980 chunk 9 optimal weight: 1.9990 chunk 18 optimal weight: 9.9990 chunk 96 optimal weight: 5.9990 chunk 48 optimal weight: 8.9990 chunk 76 optimal weight: 5.9990 overall best weight: 3.1986 ------------------------------------------------------------------------------- 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 416 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 93 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 93 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 406 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** c 423 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3260 r_free = 0.3260 target = 0.070530 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2793 r_free = 0.2793 target = 0.050792 restraints weight = 30524.481| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.2848 r_free = 0.2848 target = 0.052975 restraints weight = 17336.132| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.2885 r_free = 0.2885 target = 0.054482 restraints weight = 12420.850| |-----------------------------------------------------------------------------| r_work (final): 0.2874 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8345 moved from start: 0.6122 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.040 9294 Z= 0.302 Angle : 0.809 7.281 12567 Z= 0.402 Chirality : 0.049 0.301 1599 Planarity : 0.004 0.042 1482 Dihedral : 9.407 56.529 2613 Min Nonbonded Distance : 2.442 Molprobity Statistics. All-atom Clashscore : 12.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.35 % Favored : 96.65 % Rotamer: Outliers : 5.59 % Allowed : 22.48 % Favored : 71.93 % 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: 0.08 (0.26), residues: 984 helix: 1.19 (0.27), residues: 369 sheet: 0.79 (0.49), residues: 117 loop : -1.02 (0.25), residues: 498 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP A 210 HIS 0.004 0.001 HIS B 93 PHE 0.021 0.003 PHE A 157 TYR 0.028 0.002 TYR B 241 ARG 0.006 0.001 ARG c 422 *********************** 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 269 residues out of total 912 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 218 time to evaluate : 1.027 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 130 ASP cc_start: 0.8634 (t0) cc_final: 0.8080 (t70) REVERT: A 211 ASP cc_start: 0.8793 (p0) cc_final: 0.8314 (p0) REVERT: A 227 TRP cc_start: 0.6648 (t-100) cc_final: 0.5664 (t60) REVERT: a 313 LEU cc_start: 0.9769 (tp) cc_final: 0.9279 (tp) REVERT: a 325 ARG cc_start: 0.8797 (mmt90) cc_final: 0.8494 (mmm160) REVERT: a 357 ASP cc_start: 0.9429 (t70) cc_final: 0.8880 (t0) REVERT: a 405 GLN cc_start: 0.9256 (tm-30) cc_final: 0.8654 (tm-30) REVERT: a 410 MET cc_start: 0.8841 (tpp) cc_final: 0.8523 (tpp) REVERT: a 422 ARG cc_start: 0.7415 (tmm-80) cc_final: 0.7122 (ttp80) REVERT: B 80 MET cc_start: 0.8974 (mmt) cc_final: 0.8450 (mmm) REVERT: B 96 MET cc_start: 0.8934 (ttp) cc_final: 0.8675 (ttm) REVERT: B 130 ASP cc_start: 0.8329 (t0) cc_final: 0.7840 (t0) REVERT: B 194 MET cc_start: 0.9520 (tpp) cc_final: 0.8815 (tpp) REVERT: B 227 TRP cc_start: 0.6956 (t-100) cc_final: 0.6260 (t60) REVERT: b 306 ASP cc_start: 0.8416 (OUTLIER) cc_final: 0.8082 (m-30) REVERT: b 313 LEU cc_start: 0.9704 (tp) cc_final: 0.9262 (tp) REVERT: b 357 ASP cc_start: 0.9380 (t70) cc_final: 0.8767 (t0) REVERT: b 408 ASP cc_start: 0.9317 (m-30) cc_final: 0.8968 (m-30) REVERT: b 410 MET cc_start: 0.9107 (tpp) cc_final: 0.8821 (tpp) REVERT: b 420 MET cc_start: 0.8537 (mmp) cc_final: 0.8007 (mmt) REVERT: C 76 GLU cc_start: 0.9271 (tt0) cc_final: 0.8993 (tt0) REVERT: C 96 MET cc_start: 0.8173 (ptp) cc_final: 0.7870 (ptm) REVERT: C 130 ASP cc_start: 0.8281 (t0) cc_final: 0.7726 (t70) REVERT: c 278 TYR cc_start: 0.8534 (t80) cc_final: 0.8244 (t80) REVERT: c 300 LYS cc_start: 0.9338 (mmtm) cc_final: 0.8880 (mptt) REVERT: c 311 ASP cc_start: 0.9209 (OUTLIER) cc_final: 0.8913 (t0) REVERT: c 313 LEU cc_start: 0.9747 (tp) cc_final: 0.9247 (tp) REVERT: c 325 ARG cc_start: 0.8636 (mmm160) cc_final: 0.7906 (mmm160) REVERT: c 351 MET cc_start: 0.8835 (mmp) cc_final: 0.8467 (mmp) REVERT: c 368 LYS cc_start: 0.9326 (ptmt) cc_final: 0.9037 (pttt) REVERT: c 413 GLU cc_start: 0.8897 (mp0) cc_final: 0.8678 (tm-30) REVERT: c 422 ARG cc_start: 0.7026 (ttp80) cc_final: 0.6760 (ttp80) outliers start: 51 outliers final: 32 residues processed: 255 average time/residue: 0.2174 time to fit residues: 75.3503 Evaluate side-chains 227 residues out of total 912 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 193 time to evaluate : 0.931 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 86 CYS Chi-restraints excluded: chain A residue 100 GLU Chi-restraints excluded: chain A residue 126 LYS Chi-restraints excluded: chain A residue 128 LEU Chi-restraints excluded: chain A residue 156 ASP Chi-restraints excluded: chain A residue 185 ASN Chi-restraints excluded: chain A residue 210 TRP 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 361 ILE 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 161 LYS Chi-restraints excluded: chain B residue 210 TRP Chi-restraints excluded: chain B residue 218 GLN Chi-restraints excluded: chain B residue 239 ILE Chi-restraints excluded: chain b residue 306 ASP Chi-restraints excluded: chain b residue 337 ILE Chi-restraints excluded: chain b residue 349 LEU Chi-restraints excluded: chain b residue 385 CYS Chi-restraints excluded: chain b residue 388 VAL Chi-restraints excluded: chain b residue 403 ILE Chi-restraints excluded: chain C residue 86 CYS Chi-restraints excluded: chain C residue 128 LEU Chi-restraints excluded: chain C residue 245 LEU Chi-restraints excluded: chain c residue 274 THR Chi-restraints excluded: chain c residue 311 ASP Chi-restraints excluded: chain c residue 337 ILE Chi-restraints excluded: chain c residue 380 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 82 optimal weight: 0.8980 chunk 25 optimal weight: 7.9990 chunk 81 optimal weight: 9.9990 chunk 35 optimal weight: 8.9990 chunk 32 optimal weight: 6.9990 chunk 97 optimal weight: 0.9990 chunk 58 optimal weight: 2.9990 chunk 36 optimal weight: 2.9990 chunk 42 optimal weight: 0.7980 chunk 49 optimal weight: 0.7980 chunk 6 optimal weight: 10.0000 overall best weight: 1.2984 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** B 93 HIS ** C 93 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3291 r_free = 0.3291 target = 0.072248 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2828 r_free = 0.2828 target = 0.052080 restraints weight = 30205.619| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.2882 r_free = 0.2882 target = 0.054347 restraints weight = 17280.847| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.2919 r_free = 0.2919 target = 0.055878 restraints weight = 12456.072| |-----------------------------------------------------------------------------| r_work (final): 0.2915 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8323 moved from start: 0.6331 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.064 9294 Z= 0.214 Angle : 0.789 10.165 12567 Z= 0.388 Chirality : 0.049 0.290 1599 Planarity : 0.004 0.042 1482 Dihedral : 9.029 55.401 2613 Min Nonbonded Distance : 2.451 Molprobity Statistics. All-atom Clashscore : 11.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.35 % Favored : 96.65 % Rotamer: Outliers : 5.37 % Allowed : 23.68 % Favored : 70.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 0.25 (0.26), residues: 984 helix: 1.28 (0.27), residues: 369 sheet: 1.31 (0.51), residues: 108 loop : -0.97 (0.25), residues: 507 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP A 210 HIS 0.005 0.001 HIS B 93 PHE 0.023 0.002 PHE A 157 TYR 0.023 0.002 TYR B 241 ARG 0.010 0.001 ARG c 422 *********************** 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 258 residues out of total 912 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 209 time to evaluate : 0.969 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: 0.9131 (tt0) cc_final: 0.8242 (tm-30) REVERT: A 130 ASP cc_start: 0.8564 (t0) cc_final: 0.8020 (t70) REVERT: a 278 TYR cc_start: 0.8279 (t80) cc_final: 0.7863 (t80) REVERT: a 311 ASP cc_start: 0.9092 (m-30) cc_final: 0.8755 (t0) REVERT: a 313 LEU cc_start: 0.9718 (tp) cc_final: 0.9210 (tp) REVERT: a 357 ASP cc_start: 0.9312 (t70) cc_final: 0.8810 (t0) REVERT: a 405 GLN cc_start: 0.9245 (tm-30) cc_final: 0.8636 (tm-30) REVERT: a 410 MET cc_start: 0.8865 (tpp) cc_final: 0.8518 (tpp) REVERT: B 80 MET cc_start: 0.8903 (mmt) cc_final: 0.8378 (mmm) REVERT: B 130 ASP cc_start: 0.8349 (t0) cc_final: 0.7853 (t70) REVERT: B 194 MET cc_start: 0.9483 (tpp) cc_final: 0.9044 (tpt) REVERT: B 218 GLN cc_start: 0.9010 (OUTLIER) cc_final: 0.8675 (pm20) REVERT: B 227 TRP cc_start: 0.6971 (t-100) cc_final: 0.6294 (t60) REVERT: b 306 ASP cc_start: 0.8343 (OUTLIER) cc_final: 0.8053 (m-30) REVERT: b 357 ASP cc_start: 0.9309 (t70) cc_final: 0.8763 (t0) REVERT: b 408 ASP cc_start: 0.9271 (m-30) cc_final: 0.8886 (m-30) REVERT: b 413 GLU cc_start: 0.8880 (mp0) cc_final: 0.8439 (pm20) REVERT: b 420 MET cc_start: 0.8568 (mmp) cc_final: 0.8150 (mmt) REVERT: C 76 GLU cc_start: 0.9206 (tt0) cc_final: 0.8927 (tt0) REVERT: C 130 ASP cc_start: 0.8240 (t0) cc_final: 0.7713 (t70) REVERT: c 278 TYR cc_start: 0.8528 (t80) cc_final: 0.7894 (t80) REVERT: c 311 ASP cc_start: 0.9094 (OUTLIER) cc_final: 0.8790 (t0) REVERT: c 313 LEU cc_start: 0.9693 (tp) cc_final: 0.9138 (tp) REVERT: c 351 MET cc_start: 0.8760 (mmp) cc_final: 0.8435 (mmp) REVERT: c 422 ARG cc_start: 0.7318 (ttp80) cc_final: 0.7078 (ttp80) outliers start: 49 outliers final: 32 residues processed: 246 average time/residue: 0.1888 time to fit residues: 65.8231 Evaluate side-chains 225 residues out of total 912 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 190 time to evaluate : 0.974 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 86 CYS Chi-restraints excluded: chain A residue 100 GLU Chi-restraints excluded: chain A residue 126 LYS Chi-restraints excluded: chain A residue 128 LEU Chi-restraints excluded: chain A residue 156 ASP Chi-restraints excluded: chain A residue 185 ASN Chi-restraints excluded: chain A residue 218 GLN Chi-restraints excluded: chain A residue 245 LEU Chi-restraints excluded: chain a residue 261 THR Chi-restraints excluded: chain a residue 274 THR Chi-restraints excluded: chain a residue 361 ILE Chi-restraints excluded: chain a residue 403 ILE 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 93 HIS Chi-restraints excluded: chain B residue 128 LEU Chi-restraints excluded: chain B residue 210 TRP Chi-restraints excluded: chain B residue 218 GLN Chi-restraints excluded: chain b residue 306 ASP Chi-restraints excluded: chain b residue 337 ILE Chi-restraints excluded: chain b residue 349 LEU Chi-restraints excluded: chain b residue 385 CYS Chi-restraints excluded: chain b residue 392 SER Chi-restraints excluded: chain b residue 403 ILE Chi-restraints excluded: chain C residue 86 CYS Chi-restraints excluded: chain C residue 128 LEU Chi-restraints excluded: chain C residue 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 361 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: 8.9990 chunk 82 optimal weight: 6.9990 chunk 2 optimal weight: 3.9990 chunk 64 optimal weight: 2.9990 chunk 24 optimal weight: 5.9990 chunk 31 optimal weight: 1.9990 chunk 78 optimal weight: 0.9980 chunk 1 optimal weight: 3.9990 chunk 4 optimal weight: 6.9990 chunk 52 optimal weight: 7.9990 overall best weight: 2.7988 ------------------------------------------------------------------------------- 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 416 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 93 HIS ** c 335 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 406 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 423 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3275 r_free = 0.3275 target = 0.071534 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2816 r_free = 0.2816 target = 0.051740 restraints weight = 30622.368| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.2870 r_free = 0.2870 target = 0.053905 restraints weight = 17531.233| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.2905 r_free = 0.2905 target = 0.055379 restraints weight = 12666.007| |-----------------------------------------------------------------------------| r_work (final): 0.2895 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8354 moved from start: 0.6526 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.069 9294 Z= 0.288 Angle : 0.832 16.184 12567 Z= 0.406 Chirality : 0.050 0.349 1599 Planarity : 0.004 0.072 1482 Dihedral : 9.011 55.594 2613 Min Nonbonded Distance : 2.463 Molprobity Statistics. All-atom Clashscore : 13.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.27 % Favored : 95.73 % Rotamer: Outliers : 5.26 % Allowed : 24.78 % Favored : 69.96 % 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: 0.22 (0.26), residues: 984 helix: 1.38 (0.27), residues: 369 sheet: 0.61 (0.50), residues: 117 loop : -0.92 (0.26), residues: 498 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.048 0.002 TRP A 227 HIS 0.013 0.001 HIS B 93 PHE 0.023 0.002 PHE A 157 TYR 0.019 0.002 TYR B 241 ARG 0.012 0.001 ARG a 422 *********************** 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 240 residues out of total 912 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 192 time to evaluate : 1.156 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: A 76 GLU cc_start: 0.9173 (tt0) cc_final: 0.8261 (tm-30) REVERT: A 130 ASP cc_start: 0.8585 (t0) cc_final: 0.8063 (t70) REVERT: a 278 TYR cc_start: 0.8344 (t80) cc_final: 0.7994 (t80) REVERT: a 311 ASP cc_start: 0.9157 (OUTLIER) cc_final: 0.8857 (t0) REVERT: a 313 LEU cc_start: 0.9749 (tp) cc_final: 0.9243 (tp) REVERT: a 325 ARG cc_start: 0.8585 (mmm160) cc_final: 0.7827 (mmm-85) REVERT: a 357 ASP cc_start: 0.9369 (t70) cc_final: 0.8891 (t0) REVERT: a 359 MET cc_start: 0.9186 (mtt) cc_final: 0.8165 (mtm) REVERT: a 405 GLN cc_start: 0.9296 (tm-30) cc_final: 0.8708 (tm-30) REVERT: a 410 MET cc_start: 0.8863 (tpp) cc_final: 0.8530 (tpp) REVERT: B 80 MET cc_start: 0.8981 (mmt) cc_final: 0.8522 (mmm) REVERT: B 94 TYR cc_start: 0.8122 (t80) cc_final: 0.7896 (t80) REVERT: B 130 ASP cc_start: 0.8415 (t0) cc_final: 0.7918 (t70) REVERT: B 194 MET cc_start: 0.9502 (tpp) cc_final: 0.8737 (tpp) REVERT: b 306 ASP cc_start: 0.8530 (OUTLIER) cc_final: 0.8329 (m-30) REVERT: b 313 LEU cc_start: 0.9741 (mt) cc_final: 0.9483 (mt) REVERT: b 357 ASP cc_start: 0.9375 (t70) cc_final: 0.8780 (t0) REVERT: b 408 ASP cc_start: 0.9300 (m-30) cc_final: 0.8921 (m-30) REVERT: b 413 GLU cc_start: 0.8859 (mp0) cc_final: 0.8345 (pm20) REVERT: C 76 GLU cc_start: 0.9261 (tt0) cc_final: 0.8981 (tt0) REVERT: C 80 MET cc_start: 0.9141 (mmm) cc_final: 0.8936 (mmt) REVERT: C 130 ASP cc_start: 0.8289 (t0) cc_final: 0.7772 (t70) REVERT: C 194 MET cc_start: 0.9071 (tpp) cc_final: 0.8800 (tpp) REVERT: c 278 TYR cc_start: 0.8355 (t80) cc_final: 0.7810 (t80) REVERT: c 311 ASP cc_start: 0.9177 (OUTLIER) cc_final: 0.8899 (t0) REVERT: c 313 LEU cc_start: 0.9730 (tp) cc_final: 0.9215 (tp) REVERT: c 325 ARG cc_start: 0.8627 (mmm160) cc_final: 0.7749 (mmm160) REVERT: c 408 ASP cc_start: 0.9073 (m-30) cc_final: 0.8703 (m-30) outliers start: 48 outliers final: 37 residues processed: 229 average time/residue: 0.1972 time to fit residues: 64.6896 Evaluate side-chains 223 residues out of total 912 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 183 time to evaluate : 1.066 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 86 CYS Chi-restraints excluded: chain A residue 100 GLU Chi-restraints excluded: chain A residue 126 LYS Chi-restraints excluded: chain A residue 128 LEU Chi-restraints excluded: chain A residue 156 ASP Chi-restraints excluded: chain A residue 185 ASN Chi-restraints excluded: chain A residue 210 TRP Chi-restraints excluded: chain A residue 218 GLN Chi-restraints excluded: chain A residue 245 LEU Chi-restraints excluded: chain a residue 261 THR Chi-restraints excluded: chain a residue 274 THR Chi-restraints excluded: chain a residue 311 ASP Chi-restraints excluded: chain a residue 361 ILE Chi-restraints excluded: chain a residue 388 VAL Chi-restraints excluded: chain a residue 403 ILE 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 210 TRP Chi-restraints excluded: chain B residue 218 GLN Chi-restraints excluded: chain b residue 306 ASP Chi-restraints excluded: chain b residue 311 ASP Chi-restraints excluded: chain b residue 337 ILE Chi-restraints excluded: chain b residue 349 LEU Chi-restraints excluded: chain b residue 385 CYS Chi-restraints excluded: chain b residue 388 VAL Chi-restraints excluded: chain b residue 392 SER Chi-restraints excluded: chain b residue 403 ILE Chi-restraints excluded: chain C residue 86 CYS Chi-restraints excluded: chain C residue 128 LEU Chi-restraints excluded: chain C residue 245 LEU Chi-restraints excluded: chain c residue 274 THR 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 361 ILE Chi-restraints excluded: chain c residue 380 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 6 optimal weight: 6.9990 chunk 16 optimal weight: 0.8980 chunk 34 optimal weight: 6.9990 chunk 80 optimal weight: 0.7980 chunk 29 optimal weight: 5.9990 chunk 5 optimal weight: 0.8980 chunk 60 optimal weight: 0.9980 chunk 73 optimal weight: 2.9990 chunk 21 optimal weight: 8.9990 chunk 69 optimal weight: 0.9990 chunk 42 optimal weight: 0.9980 overall best weight: 0.9180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 93 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** a 416 GLN ** a 423 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 93 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 335 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3313 r_free = 0.3313 target = 0.073155 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2851 r_free = 0.2851 target = 0.053163 restraints weight = 30420.936| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.2908 r_free = 0.2908 target = 0.055463 restraints weight = 17162.530| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.2946 r_free = 0.2946 target = 0.057025 restraints weight = 12252.359| |-----------------------------------------------------------------------------| r_work (final): 0.2942 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8313 moved from start: 0.6678 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 9294 Z= 0.203 Angle : 0.798 16.701 12567 Z= 0.388 Chirality : 0.049 0.306 1599 Planarity : 0.004 0.042 1482 Dihedral : 8.748 54.971 2613 Min Nonbonded Distance : 2.496 Molprobity Statistics. All-atom Clashscore : 11.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.17 % Favored : 95.83 % Rotamer: Outliers : 5.04 % Allowed : 25.44 % Favored : 69.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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 (0.26), residues: 984 helix: 1.35 (0.27), residues: 369 sheet: 0.56 (0.50), residues: 117 loop : -0.78 (0.27), residues: 498 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.040 0.002 TRP B 227 HIS 0.003 0.001 HIS A 92 PHE 0.026 0.002 PHE A 157 TYR 0.023 0.002 TYR A 241 ARG 0.010 0.001 ARG c 422 *********************** 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 245 residues out of total 912 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 199 time to evaluate : 0.974 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: 0.9142 (tt0) cc_final: 0.8197 (tm-30) REVERT: A 130 ASP cc_start: 0.8467 (t0) cc_final: 0.7991 (t0) REVERT: A 211 ASP cc_start: 0.8866 (OUTLIER) cc_final: 0.8534 (p0) REVERT: a 278 TYR cc_start: 0.8331 (t80) cc_final: 0.7968 (t80) REVERT: a 311 ASP cc_start: 0.9102 (OUTLIER) cc_final: 0.8782 (t0) REVERT: a 313 LEU cc_start: 0.9720 (tp) cc_final: 0.9203 (tp) REVERT: a 325 ARG cc_start: 0.8537 (mmm160) cc_final: 0.7800 (mmm-85) REVERT: a 357 ASP cc_start: 0.9303 (t70) cc_final: 0.8867 (t0) REVERT: a 405 GLN cc_start: 0.9280 (tm-30) cc_final: 0.8689 (tm-30) REVERT: a 420 MET cc_start: 0.7560 (OUTLIER) cc_final: 0.7005 (mmt) REVERT: B 130 ASP cc_start: 0.8345 (t0) cc_final: 0.7835 (t70) REVERT: B 194 MET cc_start: 0.9440 (tpp) cc_final: 0.8972 (tpt) REVERT: B 218 GLN cc_start: 0.8951 (OUTLIER) cc_final: 0.8705 (pm20) REVERT: b 357 ASP cc_start: 0.9346 (t70) cc_final: 0.8807 (t0) REVERT: b 359 MET cc_start: 0.8804 (mtp) cc_final: 0.8392 (mtm) REVERT: b 408 ASP cc_start: 0.9258 (m-30) cc_final: 0.8845 (m-30) REVERT: b 413 GLU cc_start: 0.8865 (mp0) cc_final: 0.8415 (pm20) REVERT: b 420 MET cc_start: 0.8082 (mmt) cc_final: 0.7880 (mmt) REVERT: C 76 GLU cc_start: 0.9255 (tt0) cc_final: 0.8953 (tt0) REVERT: C 80 MET cc_start: 0.9148 (mmm) cc_final: 0.8867 (mmm) REVERT: C 130 ASP cc_start: 0.8165 (t0) cc_final: 0.7655 (t70) REVERT: C 194 MET cc_start: 0.9060 (tpp) cc_final: 0.8779 (tpp) REVERT: C 211 ASP cc_start: 0.8487 (p0) cc_final: 0.7857 (p0) REVERT: C 227 TRP cc_start: 0.7452 (t-100) cc_final: 0.6417 (t-100) REVERT: c 278 TYR cc_start: 0.8304 (t80) cc_final: 0.7781 (t80) REVERT: c 311 ASP cc_start: 0.9103 (OUTLIER) cc_final: 0.8823 (t0) REVERT: c 313 LEU cc_start: 0.9664 (tp) cc_final: 0.9412 (mm) REVERT: c 351 MET cc_start: 0.8789 (mmp) cc_final: 0.8481 (mmp) REVERT: c 408 ASP cc_start: 0.9128 (m-30) cc_final: 0.8689 (m-30) REVERT: c 420 MET cc_start: 0.8456 (mmp) cc_final: 0.8243 (mmp) outliers start: 46 outliers final: 31 residues processed: 235 average time/residue: 0.1852 time to fit residues: 62.3186 Evaluate side-chains 219 residues out of total 912 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 183 time to evaluate : 0.926 ------------------------------------------------------------------------------- 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 185 ASN Chi-restraints excluded: chain A residue 211 ASP Chi-restraints excluded: chain A residue 218 GLN Chi-restraints excluded: chain A residue 245 LEU Chi-restraints excluded: chain a residue 261 THR Chi-restraints excluded: chain a residue 311 ASP Chi-restraints excluded: chain a residue 361 ILE Chi-restraints excluded: chain a residue 388 VAL Chi-restraints excluded: chain a residue 403 ILE 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 311 ASP Chi-restraints excluded: chain b residue 337 ILE Chi-restraints excluded: chain b residue 349 LEU Chi-restraints excluded: chain b residue 385 CYS Chi-restraints excluded: chain b residue 392 SER Chi-restraints excluded: chain b residue 403 ILE Chi-restraints excluded: chain C residue 86 CYS Chi-restraints excluded: chain C residue 128 LEU Chi-restraints excluded: chain C residue 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 361 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: 9.9990 chunk 79 optimal weight: 0.0980 chunk 64 optimal weight: 5.9990 chunk 67 optimal weight: 1.9990 chunk 47 optimal weight: 3.9990 chunk 61 optimal weight: 0.9980 chunk 65 optimal weight: 1.9990 chunk 55 optimal weight: 4.9990 chunk 11 optimal weight: 5.9990 chunk 16 optimal weight: 4.9990 chunk 0 optimal weight: 10.0000 overall best weight: 1.8186 ------------------------------------------------------------------------------- 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** ** c 335 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3336 r_free = 0.3336 target = 0.073414 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2894 r_free = 0.2894 target = 0.054071 restraints weight = 30316.445| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.2950 r_free = 0.2950 target = 0.056362 restraints weight = 17076.580| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.2987 r_free = 0.2987 target = 0.057891 restraints weight = 12196.441| |-----------------------------------------------------------------------------| r_work (final): 0.2977 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8353 moved from start: 0.6878 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.058 9294 Z= 0.244 Angle : 0.804 13.749 12567 Z= 0.393 Chirality : 0.049 0.291 1599 Planarity : 0.004 0.045 1482 Dihedral : 8.664 55.058 2613 Min Nonbonded Distance : 2.476 Molprobity Statistics. All-atom Clashscore : 12.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.27 % Favored : 95.73 % Rotamer: Outliers : 3.95 % Allowed : 25.88 % Favored : 70.18 % 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: 0.63 (0.27), residues: 984 helix: 1.91 (0.28), residues: 345 sheet: 0.44 (0.50), residues: 111 loop : -0.61 (0.27), residues: 528 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.003 TRP A 210 HIS 0.004 0.001 HIS B 93 PHE 0.028 0.002 PHE A 157 TYR 0.027 0.002 TYR A 241 ARG 0.007 0.001 ARG c 422 *********************** 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 219 residues out of total 912 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 183 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: A 76 GLU cc_start: 0.9120 (tt0) cc_final: 0.8218 (tm-30) REVERT: A 130 ASP cc_start: 0.8515 (t0) cc_final: 0.8052 (t0) REVERT: a 278 TYR cc_start: 0.8373 (t80) cc_final: 0.7936 (t80) REVERT: a 311 ASP cc_start: 0.9093 (OUTLIER) cc_final: 0.8806 (t0) REVERT: a 313 LEU cc_start: 0.9732 (tp) cc_final: 0.9243 (tp) REVERT: a 325 ARG cc_start: 0.8498 (mmm160) cc_final: 0.7739 (mmm-85) REVERT: a 357 ASP cc_start: 0.9353 (t70) cc_final: 0.8970 (t0) REVERT: a 405 GLN cc_start: 0.9266 (tm-30) cc_final: 0.9036 (tm-30) REVERT: a 420 MET cc_start: 0.7413 (OUTLIER) cc_final: 0.6736 (mmt) REVERT: B 130 ASP cc_start: 0.8382 (t0) cc_final: 0.7917 (t0) REVERT: b 357 ASP cc_start: 0.9343 (t70) cc_final: 0.8857 (t0) REVERT: b 408 ASP cc_start: 0.9221 (m-30) cc_final: 0.8817 (m-30) REVERT: b 420 MET cc_start: 0.7928 (mmt) cc_final: 0.7698 (mmt) REVERT: C 76 GLU cc_start: 0.9229 (tt0) cc_final: 0.8923 (tt0) REVERT: C 130 ASP cc_start: 0.8144 (t0) cc_final: 0.7673 (t70) REVERT: C 194 MET cc_start: 0.9067 (tpp) cc_final: 0.8808 (tpp) REVERT: c 278 TYR cc_start: 0.8346 (t80) cc_final: 0.7789 (t80) REVERT: c 311 ASP cc_start: 0.9091 (OUTLIER) cc_final: 0.8806 (t0) REVERT: c 351 MET cc_start: 0.8729 (mmp) cc_final: 0.8439 (mmp) REVERT: c 408 ASP cc_start: 0.9108 (m-30) cc_final: 0.8561 (m-30) REVERT: c 420 MET cc_start: 0.8321 (mmp) cc_final: 0.7800 (mmp) outliers start: 36 outliers final: 32 residues processed: 212 average time/residue: 0.1728 time to fit residues: 54.0113 Evaluate side-chains 210 residues out of total 912 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 175 time to evaluate : 0.988 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 86 CYS Chi-restraints excluded: chain A residue 105 LEU 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 261 THR Chi-restraints excluded: chain a residue 279 CYS Chi-restraints excluded: chain a residue 311 ASP Chi-restraints excluded: chain a residue 361 ILE Chi-restraints excluded: chain a residue 388 VAL Chi-restraints excluded: chain a residue 403 ILE 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 210 TRP Chi-restraints excluded: chain B residue 218 GLN Chi-restraints excluded: chain b residue 337 ILE Chi-restraints excluded: chain b residue 349 LEU Chi-restraints excluded: chain b residue 385 CYS Chi-restraints excluded: chain b residue 403 ILE Chi-restraints excluded: chain C residue 86 CYS Chi-restraints excluded: chain C residue 128 LEU Chi-restraints excluded: chain C residue 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 361 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: 0.7980 chunk 7 optimal weight: 4.9990 chunk 90 optimal weight: 6.9990 chunk 36 optimal weight: 6.9990 chunk 70 optimal weight: 0.0870 chunk 28 optimal weight: 0.3980 chunk 9 optimal weight: 6.9990 chunk 13 optimal weight: 6.9990 chunk 49 optimal weight: 1.9990 chunk 95 optimal weight: 2.9990 chunk 40 optimal weight: 6.9990 overall best weight: 1.2562 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 93 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 423 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 335 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3353 r_free = 0.3353 target = 0.074105 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2913 r_free = 0.2913 target = 0.054745 restraints weight = 30596.007| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.2969 r_free = 0.2969 target = 0.057074 restraints weight = 17123.780| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3006 r_free = 0.3006 target = 0.058636 restraints weight = 12165.233| |-----------------------------------------------------------------------------| r_work (final): 0.3000 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8338 moved from start: 0.6967 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 9294 Z= 0.220 Angle : 0.813 13.540 12567 Z= 0.395 Chirality : 0.049 0.304 1599 Planarity : 0.004 0.041 1482 Dihedral : 8.535 54.853 2613 Min Nonbonded Distance : 2.488 Molprobity Statistics. All-atom Clashscore : 11.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.27 % Favored : 95.73 % Rotamer: Outliers : 3.95 % Allowed : 26.43 % Favored : 69.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 0.61 (0.27), residues: 984 helix: 1.91 (0.28), residues: 345 sheet: 0.37 (0.50), residues: 111 loop : -0.61 (0.27), residues: 528 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.035 0.003 TRP A 210 HIS 0.003 0.001 HIS B 93 PHE 0.025 0.002 PHE A 157 TYR 0.029 0.002 TYR A 241 ARG 0.008 0.001 ARG c 422 ********************** 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 225 residues out of total 912 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 189 time to evaluate : 0.941 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: 0.9125 (tt0) cc_final: 0.8231 (tm-30) REVERT: A 130 ASP cc_start: 0.8493 (t0) cc_final: 0.8043 (t0) REVERT: A 211 ASP cc_start: 0.8371 (p0) cc_final: 0.8149 (p0) REVERT: a 278 TYR cc_start: 0.8355 (t80) cc_final: 0.7915 (t80) REVERT: a 311 ASP cc_start: 0.9080 (OUTLIER) cc_final: 0.8793 (t0) REVERT: a 313 LEU cc_start: 0.9714 (tp) cc_final: 0.9206 (tp) REVERT: a 325 ARG cc_start: 0.8522 (mmm160) cc_final: 0.7861 (mmm-85) REVERT: a 357 ASP cc_start: 0.9347 (t70) cc_final: 0.8967 (t0) REVERT: a 405 GLN cc_start: 0.9266 (tm-30) cc_final: 0.9033 (tm-30) REVERT: a 420 MET cc_start: 0.7384 (OUTLIER) cc_final: 0.6667 (mmt) REVERT: B 75 MET cc_start: 0.9019 (mmt) cc_final: 0.8650 (mmm) REVERT: B 130 ASP cc_start: 0.8318 (t0) cc_final: 0.7862 (t0) REVERT: B 194 MET cc_start: 0.9377 (tpt) cc_final: 0.9050 (tpp) REVERT: b 307 GLU cc_start: 0.8788 (mm-30) cc_final: 0.8107 (mp0) REVERT: b 357 ASP cc_start: 0.9323 (t70) cc_final: 0.8848 (t0) REVERT: b 359 MET cc_start: 0.8792 (mtp) cc_final: 0.8358 (mtm) REVERT: b 410 MET cc_start: 0.8967 (tpp) cc_final: 0.8297 (mmm) REVERT: b 413 GLU cc_start: 0.8758 (mp0) cc_final: 0.8349 (pm20) REVERT: b 420 MET cc_start: 0.7919 (mmt) cc_final: 0.7709 (mmt) REVERT: C 76 GLU cc_start: 0.9219 (tt0) cc_final: 0.8922 (tt0) REVERT: C 130 ASP cc_start: 0.8069 (t0) cc_final: 0.7596 (t70) REVERT: c 278 TYR cc_start: 0.8381 (t80) cc_final: 0.7905 (t80) REVERT: c 311 ASP cc_start: 0.9119 (OUTLIER) cc_final: 0.8843 (t0) REVERT: c 351 MET cc_start: 0.8700 (mmp) cc_final: 0.8402 (mmp) REVERT: c 408 ASP cc_start: 0.9141 (m-30) cc_final: 0.8595 (m-30) REVERT: c 420 MET cc_start: 0.8224 (mmp) cc_final: 0.7700 (mmp) outliers start: 36 outliers final: 29 residues processed: 219 average time/residue: 0.1776 time to fit residues: 56.3392 Evaluate side-chains 213 residues out of total 912 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 181 time to evaluate : 0.938 ------------------------------------------------------------------------------- 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 261 THR Chi-restraints excluded: chain a residue 279 CYS Chi-restraints excluded: chain a residue 311 ASP Chi-restraints excluded: chain a residue 361 ILE Chi-restraints excluded: chain a residue 388 VAL Chi-restraints excluded: chain a residue 403 ILE 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 210 TRP Chi-restraints excluded: chain b residue 261 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 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 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: 3.9990 chunk 5 optimal weight: 20.0000 chunk 23 optimal weight: 3.9990 chunk 95 optimal weight: 3.9990 chunk 93 optimal weight: 0.9990 chunk 76 optimal weight: 20.0000 chunk 33 optimal weight: 10.0000 chunk 89 optimal weight: 1.9990 chunk 1 optimal weight: 8.9990 chunk 63 optimal weight: 0.7980 chunk 9 optimal weight: 7.9990 overall best weight: 2.3588 ------------------------------------------------------------------------------- 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 185 ASN ** a 423 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 335 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3335 r_free = 0.3335 target = 0.073056 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2887 r_free = 0.2887 target = 0.053614 restraints weight = 30447.555| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.2944 r_free = 0.2944 target = 0.055893 restraints weight = 17076.985| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.2981 r_free = 0.2981 target = 0.057413 restraints weight = 12166.371| |-----------------------------------------------------------------------------| r_work (final): 0.2971 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8358 moved from start: 0.7050 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.060 9294 Z= 0.278 Angle : 0.844 13.503 12567 Z= 0.410 Chirality : 0.051 0.359 1599 Planarity : 0.004 0.041 1482 Dihedral : 8.577 55.055 2613 Min Nonbonded Distance : 2.469 Molprobity Statistics. All-atom Clashscore : 12.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.57 % Favored : 95.43 % Rotamer: Outliers : 3.84 % Allowed : 26.21 % Favored : 69.96 % 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: 0.54 (0.27), residues: 984 helix: 1.88 (0.28), residues: 345 sheet: 0.18 (0.49), residues: 111 loop : -0.63 (0.28), residues: 528 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.053 0.003 TRP C 227 HIS 0.005 0.001 HIS B 93 PHE 0.023 0.002 PHE A 157 TYR 0.031 0.002 TYR C 241 ARG 0.008 0.001 ARG a 422 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2965.88 seconds wall clock time: 54 minutes 36.95 seconds (3276.95 seconds total)