Starting phenix.real_space_refine on Thu Feb 13 19:17:12 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7sgd_25107/02_2025/7sgd_25107.cif Found real_map, /net/cci-nas-00/data/ceres_data/7sgd_25107/02_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_25107/02_2025/7sgd_25107.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7sgd_25107/02_2025/7sgd_25107.map" model { file = "/net/cci-nas-00/data/ceres_data/7sgd_25107/02_2025/7sgd_25107.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7sgd_25107/02_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-5592/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: 5.51, per 1000 atoms: 0.60 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: 3.37 Conformation dependent library (CDL) restraints added in 927.8 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: 0.76 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: 2.32 Time building geometry restraints manager: 3.62 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: 0.05 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: 1.230 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.300 Check model and map are aligned: 0.060 Set scattering table: 0.090 Process input model: 22.430 Find NCS groups from input model: 0.560 Set up NCS constraints: 0.040 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:2.720 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 27.440 ------------------------------------------------------------------------------- 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 : 0.954 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: 0.2454 time to fit residues: 152.0300 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 : 0.971 ------------------------------------------------------------------------------- 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 = 34)----------------| | r_work = 0.2960 r_free = 0.2960 target = 0.056490 restraints weight = 29137.552| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3017 r_free = 0.3017 target = 0.058989 restraints weight = 15462.768| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3056 r_free = 0.3056 target = 0.060731 restraints weight = 10684.706| |-----------------------------------------------------------------------------| 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 : 0.905 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: 0.8140 (tt0) cc_final: 0.7928 (tt0) REVERT: A 130 ASP cc_start: 0.8415 (t0) cc_final: 0.7864 (t0) REVERT: a 300 LYS cc_start: 0.9202 (mmtm) cc_final: 0.8559 (mptt) REVERT: a 307 GLU cc_start: 0.8832 (mm-30) cc_final: 0.8590 (mm-30) REVERT: a 311 ASP cc_start: 0.9236 (m-30) cc_final: 0.8999 (m-30) REVERT: a 313 LEU cc_start: 0.9777 (tp) cc_final: 0.9334 (tp) REVERT: a 357 ASP cc_start: 0.9156 (t70) cc_final: 0.8622 (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: 0.7955 (tpp) REVERT: B 130 ASP cc_start: 0.8339 (t0) cc_final: 0.7804 (t0) REVERT: B 211 ASP cc_start: 0.8477 (p0) cc_final: 0.8207 (p0) REVERT: b 261 THR cc_start: 0.8303 (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: 0.8951 (m-30) REVERT: b 313 LEU cc_start: 0.9784 (tp) cc_final: 0.9419 (tp) REVERT: b 346 ASN cc_start: 0.9357 (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: 0.8665 (m-40) cc_final: 0.8374 (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: 0.7520 (mm-30) cc_final: 0.7281 (mm-30) REVERT: C 130 ASP cc_start: 0.8281 (t0) cc_final: 0.7720 (t70) REVERT: C 227 TRP cc_start: 0.7171 (t-100) cc_final: 0.6831 (t-100) REVERT: c 278 TYR cc_start: 0.8381 (t80) cc_final: 0.7881 (t80) REVERT: c 300 LYS cc_start: 0.9164 (mmtm) cc_final: 0.8645 (mptt) REVERT: c 306 ASP cc_start: 0.8715 (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: 0.9142 (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: 0.8566 (m-40) cc_final: 0.8235 (m-40) outliers start: 43 outliers final: 19 residues processed: 327 average time/residue: 0.2118 time to fit residues: 94.6654 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 : 1.011 ------------------------------------------------------------------------------- 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: 0.8980 chunk 72 optimal weight: 10.0000 chunk 8 optimal weight: 2.9990 chunk 23 optimal weight: 1.9990 chunk 38 optimal weight: 9.9990 chunk 86 optimal weight: 3.9990 chunk 44 optimal weight: 8.9990 chunk 7 optimal weight: 6.9990 chunk 78 optimal weight: 7.9990 chunk 83 optimal weight: 0.9990 chunk 30 optimal weight: 0.0870 overall best weight: 1.3964 ------------------------------------------------------------------------------- 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 = 0.3379 r_free = 0.3379 target = 0.075474 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2945 r_free = 0.2945 target = 0.055980 restraints weight = 29816.998| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3003 r_free = 0.3003 target = 0.058427 restraints weight = 15978.053| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3040 r_free = 0.3040 target = 0.060101 restraints weight = 11170.586| |-----------------------------------------------------------------------------| r_work (final): 0.3033 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8208 moved from start: 0.5304 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 9294 Z= 0.241 Angle : 0.837 10.210 12567 Z= 0.420 Chirality : 0.048 0.271 1599 Planarity : 0.004 0.031 1482 Dihedral : 11.441 69.703 2613 Min Nonbonded Distance : 2.502 Molprobity Statistics. All-atom Clashscore : 10.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.64 % Favored : 97.36 % Rotamer: Outliers : 5.59 % Allowed : 20.29 % Favored : 74.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.44 (0.25), residues: 984 helix: 1.27 (0.26), residues: 366 sheet: 1.57 (0.50), residues: 108 loop : -0.72 (0.24), residues: 510 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.003 TRP B 227 HIS 0.003 0.001 HIS C 93 PHE 0.024 0.003 PHE A 157 TYR 0.022 0.002 TYR C 241 ARG 0.004 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 327 residues out of total 912 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 276 time to evaluate : 0.933 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: A 75 MET cc_start: 0.8567 (mtp) cc_final: 0.8241 (mtp) REVERT: A 76 GLU cc_start: 0.9085 (tt0) cc_final: 0.8248 (tm-30) REVERT: A 130 ASP cc_start: 0.8474 (t0) cc_final: 0.7899 (t70) REVERT: A 140 PHE cc_start: 0.9398 (t80) cc_final: 0.9153 (t80) REVERT: a 261 THR cc_start: 0.8142 (p) cc_final: 0.7887 (p) REVERT: a 282 ARG cc_start: 0.8881 (mmm-85) cc_final: 0.8656 (mmm-85) REVERT: a 300 LYS cc_start: 0.9284 (mmtm) cc_final: 0.8633 (mptt) REVERT: a 313 LEU cc_start: 0.9714 (tp) cc_final: 0.9172 (tp) REVERT: a 357 ASP cc_start: 0.9183 (t70) cc_final: 0.8669 (t0) REVERT: a 405 GLN cc_start: 0.9192 (tm-30) cc_final: 0.8926 (tm-30) REVERT: a 410 MET cc_start: 0.8768 (tpp) cc_final: 0.8349 (tpp) REVERT: a 417 LYS cc_start: 0.9205 (pttp) cc_final: 0.8955 (ptpp) REVERT: B 130 ASP cc_start: 0.8314 (t0) cc_final: 0.7743 (t0) REVERT: B 227 TRP cc_start: 0.6837 (t-100) cc_final: 0.6623 (t60) REVERT: b 261 THR cc_start: 0.8468 (p) cc_final: 0.8263 (p) REVERT: b 306 ASP cc_start: 0.8193 (OUTLIER) cc_final: 0.7977 (m-30) REVERT: b 307 GLU cc_start: 0.8729 (mm-30) cc_final: 0.8124 (mp0) REVERT: b 313 LEU cc_start: 0.9735 (tp) cc_final: 0.9331 (tp) REVERT: b 357 ASP cc_start: 0.9170 (t70) cc_final: 0.8695 (t0) REVERT: b 408 ASP cc_start: 0.9297 (m-30) cc_final: 0.8943 (m-30) REVERT: b 410 MET cc_start: 0.9070 (tpp) cc_final: 0.8151 (tpp) REVERT: b 413 GLU cc_start: 0.8874 (mp0) cc_final: 0.8641 (pm20) REVERT: b 416 GLN cc_start: 0.9231 (mm110) cc_final: 0.8686 (mm-40) REVERT: C 96 MET cc_start: 0.7911 (ptp) cc_final: 0.7665 (ptp) REVERT: C 100 GLU cc_start: 0.7592 (mm-30) cc_final: 0.7314 (mm-30) REVERT: C 130 ASP cc_start: 0.8237 (t0) cc_final: 0.7686 (t70) REVERT: c 278 TYR cc_start: 0.8423 (t80) cc_final: 0.8001 (t80) REVERT: c 300 LYS cc_start: 0.9276 (mmtm) cc_final: 0.8810 (mptt) REVERT: c 307 GLU cc_start: 0.8807 (mm-30) cc_final: 0.8190 (mp0) REVERT: c 313 LEU cc_start: 0.9733 (tp) cc_final: 0.9295 (tp) REVERT: c 347 ASP cc_start: 0.8946 (OUTLIER) cc_final: 0.8736 (p0) REVERT: c 348 GLN cc_start: 0.8804 (mp10) cc_final: 0.8482 (mp10) REVERT: c 402 ASP cc_start: 0.9343 (t0) cc_final: 0.8948 (t70) REVERT: c 410 MET cc_start: 0.9076 (tpp) cc_final: 0.8499 (tpp) outliers start: 51 outliers final: 29 residues processed: 307 average time/residue: 0.2315 time to fit residues: 95.4445 Evaluate side-chains 271 residues out of total 912 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 240 time to evaluate : 1.020 ------------------------------------------------------------------------------- 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 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 218 GLN Chi-restraints excluded: chain a residue 274 THR Chi-restraints excluded: chain a residue 325 ARG Chi-restraints excluded: chain a residue 337 ILE Chi-restraints excluded: chain a residue 361 ILE Chi-restraints excluded: chain a residue 380 THR 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 306 ASP Chi-restraints excluded: chain b residue 337 ILE Chi-restraints excluded: chain b residue 385 CYS Chi-restraints excluded: chain b residue 403 ILE Chi-restraints excluded: chain b residue 421 GLU Chi-restraints excluded: chain C residue 86 CYS Chi-restraints excluded: chain C residue 128 LEU Chi-restraints excluded: chain C residue 218 GLN Chi-restraints excluded: chain c residue 274 THR Chi-restraints excluded: chain c residue 337 ILE Chi-restraints excluded: chain c residue 347 ASP Chi-restraints excluded: chain c residue 380 THR Chi-restraints excluded: chain c residue 385 CYS Chi-restraints excluded: chain c residue 421 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 57 optimal weight: 0.9990 chunk 83 optimal weight: 7.9990 chunk 78 optimal weight: 6.9990 chunk 54 optimal weight: 10.0000 chunk 80 optimal weight: 9.9990 chunk 67 optimal weight: 7.9990 chunk 23 optimal weight: 7.9990 chunk 14 optimal weight: 7.9990 chunk 86 optimal weight: 5.9990 chunk 94 optimal weight: 1.9990 chunk 84 optimal weight: 5.9990 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 115 HIS ** c 406 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** c 416 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3248 r_free = 0.3248 target = 0.070273 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2787 r_free = 0.2787 target = 0.050526 restraints weight = 30855.207| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.2842 r_free = 0.2842 target = 0.052652 restraints weight = 17661.688| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.2877 r_free = 0.2877 target = 0.054100 restraints weight = 12737.355| |-----------------------------------------------------------------------------| r_work (final): 0.2867 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8363 moved from start: 0.5844 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= 0.406 Angle : 0.898 8.406 12567 Z= 0.443 Chirality : 0.050 0.325 1599 Planarity : 0.005 0.045 1482 Dihedral : 10.117 59.141 2613 Min Nonbonded Distance : 2.422 Molprobity Statistics. All-atom Clashscore : 14.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.46 % Favored : 96.54 % Rotamer: Outliers : 6.69 % Allowed : 20.83 % Favored : 72.48 % 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: 0.34 (0.25), residues: 984 helix: 1.42 (0.26), residues: 369 sheet: 0.91 (0.48), residues: 117 loop : -0.88 (0.25), residues: 498 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP c 283 HIS 0.007 0.001 HIS b 354 PHE 0.022 0.003 PHE A 157 TYR 0.021 0.002 TYR A 241 ARG 0.007 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 300 residues out of total 912 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 239 time to evaluate : 1.030 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 96 MET cc_start: 0.8340 (ttp) cc_final: 0.7950 (ttm) REVERT: A 130 ASP cc_start: 0.8622 (t0) cc_final: 0.8055 (t70) REVERT: a 300 LYS cc_start: 0.9371 (mmtm) cc_final: 0.8751 (mptt) REVERT: a 313 LEU cc_start: 0.9797 (tp) cc_final: 0.9303 (tp) REVERT: a 357 ASP cc_start: 0.9413 (t70) cc_final: 0.8881 (t0) REVERT: a 405 GLN cc_start: 0.9269 (tm-30) cc_final: 0.8991 (tm-30) REVERT: a 410 MET cc_start: 0.8886 (tpp) cc_final: 0.8549 (tpp) REVERT: B 130 ASP cc_start: 0.8309 (t0) cc_final: 0.7810 (t0) REVERT: B 245 LEU cc_start: 0.9416 (OUTLIER) cc_final: 0.9188 (tt) REVERT: b 306 ASP cc_start: 0.8259 (OUTLIER) cc_final: 0.7843 (m-30) REVERT: b 313 LEU cc_start: 0.9730 (tp) cc_final: 0.9320 (tp) REVERT: b 357 ASP cc_start: 0.9354 (t70) cc_final: 0.8774 (t0) REVERT: b 408 ASP cc_start: 0.9296 (m-30) cc_final: 0.8978 (m-30) REVERT: b 420 MET cc_start: 0.8429 (mmp) cc_final: 0.8116 (mmt) REVERT: C 76 GLU cc_start: 0.9276 (tt0) cc_final: 0.9039 (tt0) REVERT: C 96 MET cc_start: 0.8146 (ptp) cc_final: 0.7755 (ptm) REVERT: C 130 ASP cc_start: 0.8264 (t0) cc_final: 0.7833 (t0) REVERT: C 211 ASP cc_start: 0.8719 (p0) cc_final: 0.8392 (p0) REVERT: c 278 TYR cc_start: 0.8572 (t80) cc_final: 0.8247 (t80) REVERT: c 300 LYS cc_start: 0.9342 (mmtm) cc_final: 0.8902 (mptt) REVERT: c 311 ASP cc_start: 0.9163 (OUTLIER) cc_final: 0.8855 (t0) REVERT: c 313 LEU cc_start: 0.9768 (tp) cc_final: 0.9299 (tp) REVERT: c 325 ARG cc_start: 0.8634 (mmm160) cc_final: 0.8401 (mmm160) outliers start: 61 outliers final: 38 residues processed: 280 average time/residue: 0.2225 time to fit residues: 84.8723 Evaluate side-chains 240 residues out of total 912 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 199 time to evaluate : 1.025 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 86 CYS Chi-restraints excluded: chain A residue 126 LYS Chi-restraints excluded: chain A residue 128 LEU Chi-restraints excluded: chain A residue 156 ASP Chi-restraints excluded: chain A residue 218 GLN Chi-restraints excluded: chain A residue 239 ILE Chi-restraints excluded: chain A residue 245 LEU Chi-restraints excluded: chain a residue 274 THR Chi-restraints excluded: chain a residue 311 ASP Chi-restraints excluded: chain a residue 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 403 ILE Chi-restraints excluded: chain a residue 421 GLU Chi-restraints excluded: chain B residue 86 CYS Chi-restraints excluded: chain B residue 128 LEU Chi-restraints excluded: chain B residue 210 TRP 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 86 CYS Chi-restraints excluded: chain C residue 128 LEU Chi-restraints excluded: chain C residue 210 TRP 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 350 ILE Chi-restraints excluded: chain c residue 380 THR Chi-restraints excluded: chain c residue 392 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 14 optimal weight: 1.9990 chunk 54 optimal weight: 6.9990 chunk 52 optimal weight: 2.9990 chunk 47 optimal weight: 3.9990 chunk 74 optimal weight: 10.0000 chunk 59 optimal weight: 0.9980 chunk 9 optimal weight: 0.9980 chunk 18 optimal weight: 9.9990 chunk 96 optimal weight: 6.9990 chunk 48 optimal weight: 8.9990 chunk 76 optimal weight: 5.9990 overall best weight: 2.1986 ------------------------------------------------------------------------------- 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 ** B 93 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 185 ASN b 416 GLN ** c 406 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** c 423 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3324 r_free = 0.3324 target = 0.072949 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2881 r_free = 0.2881 target = 0.053721 restraints weight = 29910.717| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.2937 r_free = 0.2937 target = 0.055973 restraints weight = 16618.474| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.2973 r_free = 0.2973 target = 0.057491 restraints weight = 11808.783| |-----------------------------------------------------------------------------| r_work (final): 0.2960 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8335 moved from start: 0.6086 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 9294 Z= 0.251 Angle : 0.780 7.385 12567 Z= 0.385 Chirality : 0.048 0.290 1599 Planarity : 0.004 0.041 1482 Dihedral : 9.315 55.857 2613 Min Nonbonded Distance : 2.422 Molprobity Statistics. All-atom Clashscore : 12.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.05 % Favored : 96.95 % Rotamer: Outliers : 4.82 % Allowed : 24.01 % Favored : 71.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 0.40 (0.26), residues: 984 helix: 1.48 (0.26), residues: 369 sheet: 0.95 (0.49), residues: 117 loop : -0.85 (0.25), residues: 498 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP B 210 HIS 0.005 0.001 HIS b 354 PHE 0.022 0.002 PHE A 157 TYR 0.022 0.002 TYR B 241 ARG 0.007 0.001 ARG a 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 268 residues out of total 912 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 224 time to evaluate : 1.028 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 76 GLU cc_start: 0.9085 (tt0) cc_final: 0.8184 (tm-30) REVERT: A 130 ASP cc_start: 0.8587 (t0) cc_final: 0.8055 (t70) REVERT: A 227 TRP cc_start: 0.6672 (t-100) cc_final: 0.5977 (t60) REVERT: a 313 LEU cc_start: 0.9752 (tp) cc_final: 0.9237 (tp) REVERT: a 325 ARG cc_start: 0.8796 (mmt180) cc_final: 0.8523 (mmm160) REVERT: a 357 ASP cc_start: 0.9339 (t70) cc_final: 0.8836 (t0) REVERT: a 405 GLN cc_start: 0.9209 (tm-30) cc_final: 0.8594 (tm-30) REVERT: a 422 ARG cc_start: 0.7192 (tmm-80) cc_final: 0.6969 (ttp80) REVERT: B 130 ASP cc_start: 0.8337 (t0) cc_final: 0.7847 (t70) REVERT: B 194 MET cc_start: 0.9481 (tpp) cc_final: 0.8873 (tpp) REVERT: b 306 ASP cc_start: 0.8206 (OUTLIER) cc_final: 0.7810 (m-30) REVERT: b 313 LEU cc_start: 0.9711 (tp) cc_final: 0.9234 (tp) REVERT: b 357 ASP cc_start: 0.9290 (t70) cc_final: 0.8772 (t0) REVERT: b 408 ASP cc_start: 0.9277 (m-30) cc_final: 0.8909 (m-30) REVERT: b 420 MET cc_start: 0.8283 (mmp) cc_final: 0.7702 (mmt) REVERT: C 76 GLU cc_start: 0.9192 (tt0) cc_final: 0.8930 (tt0) REVERT: C 130 ASP cc_start: 0.8248 (t0) cc_final: 0.7704 (t70) REVERT: C 211 ASP cc_start: 0.8663 (p0) cc_final: 0.8298 (p0) REVERT: c 278 TYR cc_start: 0.8549 (t80) cc_final: 0.8215 (t80) REVERT: c 311 ASP cc_start: 0.9051 (OUTLIER) cc_final: 0.8745 (t0) REVERT: c 313 LEU cc_start: 0.9729 (tp) cc_final: 0.9223 (tp) outliers start: 44 outliers final: 28 residues processed: 260 average time/residue: 0.2187 time to fit residues: 78.0351 Evaluate side-chains 234 residues out of total 912 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 204 time to evaluate : 1.006 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 86 CYS Chi-restraints excluded: chain A residue 128 LEU Chi-restraints excluded: chain A residue 153 MET Chi-restraints excluded: chain A residue 156 ASP Chi-restraints excluded: chain A residue 185 ASN Chi-restraints excluded: chain A residue 218 GLN Chi-restraints excluded: chain A residue 245 LEU Chi-restraints excluded: chain a residue 274 THR Chi-restraints excluded: chain a residue 311 ASP Chi-restraints excluded: chain a residue 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 86 CYS Chi-restraints excluded: chain B residue 128 LEU Chi-restraints excluded: chain B residue 185 ASN Chi-restraints excluded: chain B residue 218 GLN Chi-restraints excluded: chain b residue 274 THR Chi-restraints excluded: chain b residue 306 ASP Chi-restraints excluded: chain b residue 337 ILE Chi-restraints excluded: chain b residue 349 LEU Chi-restraints excluded: chain b residue 385 CYS Chi-restraints excluded: chain b residue 403 ILE Chi-restraints excluded: chain C residue 86 CYS Chi-restraints excluded: chain C residue 128 LEU Chi-restraints excluded: chain C residue 218 GLN Chi-restraints excluded: chain C residue 245 LEU Chi-restraints excluded: chain c residue 274 THR Chi-restraints excluded: chain c residue 311 ASP Chi-restraints excluded: chain c residue 380 THR Rotamers are restrained with sigma=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: 6.9990 chunk 32 optimal weight: 1.9990 chunk 97 optimal weight: 7.9990 chunk 58 optimal weight: 4.9990 chunk 36 optimal weight: 0.9990 chunk 42 optimal weight: 1.9990 chunk 49 optimal weight: 0.9980 chunk 6 optimal weight: 9.9990 overall best weight: 1.3786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 93 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 185 ASN ** B 93 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 185 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3296 r_free = 0.3296 target = 0.072406 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2853 r_free = 0.2853 target = 0.053117 restraints weight = 29794.981| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.2907 r_free = 0.2907 target = 0.055327 restraints weight = 16891.541| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.2942 r_free = 0.2942 target = 0.056817 restraints weight = 12110.460| |-----------------------------------------------------------------------------| r_work (final): 0.2926 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8302 moved from start: 0.6303 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.068 9294 Z= 0.218 Angle : 0.787 9.781 12567 Z= 0.387 Chirality : 0.049 0.297 1599 Planarity : 0.004 0.042 1482 Dihedral : 9.076 55.207 2613 Min Nonbonded Distance : 2.467 Molprobity Statistics. All-atom Clashscore : 12.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.56 % Favored : 96.44 % Rotamer: Outliers : 5.15 % Allowed : 23.79 % Favored : 71.05 % 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: 0.52 (0.26), residues: 984 helix: 1.55 (0.26), residues: 369 sheet: 1.43 (0.51), residues: 108 loop : -0.83 (0.25), residues: 507 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP B 227 HIS 0.004 0.001 HIS b 354 PHE 0.023 0.002 PHE A 157 TYR 0.020 0.002 TYR B 241 ARG 0.006 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: 47 poor density : 211 time to evaluate : 0.966 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 76 GLU cc_start: 0.9118 (tt0) cc_final: 0.8196 (tm-30) REVERT: A 82 MET cc_start: 0.9261 (OUTLIER) cc_final: 0.8774 (ptp) REVERT: A 130 ASP cc_start: 0.8479 (t0) cc_final: 0.7928 (t70) REVERT: A 211 ASP cc_start: 0.8695 (p0) cc_final: 0.8428 (p0) REVERT: a 278 TYR cc_start: 0.8297 (t80) cc_final: 0.7886 (t80) REVERT: a 311 ASP cc_start: 0.9112 (m-30) cc_final: 0.8795 (t0) REVERT: a 313 LEU cc_start: 0.9714 (tp) cc_final: 0.9190 (tp) REVERT: a 325 ARG cc_start: 0.8806 (mmt180) cc_final: 0.8500 (mmm160) REVERT: a 357 ASP cc_start: 0.9341 (t70) cc_final: 0.8822 (t0) REVERT: a 405 GLN cc_start: 0.9231 (tm-30) cc_final: 0.8608 (tm-30) REVERT: B 76 GLU cc_start: 0.9104 (tt0) cc_final: 0.8252 (tm-30) REVERT: B 130 ASP cc_start: 0.8332 (t0) cc_final: 0.7846 (t70) REVERT: b 306 ASP cc_start: 0.8258 (OUTLIER) cc_final: 0.7951 (m-30) REVERT: b 313 LEU cc_start: 0.9684 (tp) cc_final: 0.9194 (tp) REVERT: b 357 ASP cc_start: 0.9313 (t70) cc_final: 0.8749 (t0) REVERT: b 408 ASP cc_start: 0.9264 (m-30) cc_final: 0.8879 (m-30) REVERT: b 413 GLU cc_start: 0.8840 (mp0) cc_final: 0.8345 (pm20) REVERT: b 420 MET cc_start: 0.8560 (mmp) cc_final: 0.8121 (mmt) REVERT: C 76 GLU cc_start: 0.9246 (tt0) cc_final: 0.8976 (tt0) REVERT: C 130 ASP cc_start: 0.8160 (t0) cc_final: 0.7639 (t70) REVERT: C 194 MET cc_start: 0.9038 (tpp) cc_final: 0.8805 (tpp) REVERT: C 211 ASP cc_start: 0.8729 (p0) cc_final: 0.8463 (p0) REVERT: c 278 TYR cc_start: 0.8546 (t80) cc_final: 0.8041 (t80) REVERT: c 311 ASP cc_start: 0.9104 (OUTLIER) cc_final: 0.8798 (t0) REVERT: c 313 LEU cc_start: 0.9686 (tp) cc_final: 0.9148 (tp) REVERT: c 351 MET cc_start: 0.8812 (mmp) cc_final: 0.8452 (mmp) REVERT: c 410 MET cc_start: 0.9110 (tpp) cc_final: 0.8897 (tpp) outliers start: 47 outliers final: 32 residues processed: 245 average time/residue: 0.1971 time to fit residues: 67.7624 Evaluate side-chains 231 residues out of total 912 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 196 time to evaluate : 0.971 ------------------------------------------------------------------------------- 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 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 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 128 LEU Chi-restraints excluded: chain B residue 185 ASN Chi-restraints excluded: chain B residue 245 LEU Chi-restraints excluded: chain b residue 274 THR Chi-restraints excluded: chain b residue 306 ASP Chi-restraints excluded: chain b residue 311 ASP Chi-restraints excluded: chain b residue 337 ILE Chi-restraints excluded: chain b residue 349 LEU Chi-restraints excluded: chain b residue 385 CYS Chi-restraints excluded: chain b residue 403 ILE Chi-restraints excluded: chain 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: 10.0000 chunk 96 optimal weight: 7.9990 chunk 82 optimal weight: 0.5980 chunk 2 optimal weight: 7.9990 chunk 64 optimal weight: 8.9990 chunk 24 optimal weight: 0.9980 chunk 31 optimal weight: 3.9990 chunk 78 optimal weight: 7.9990 chunk 1 optimal weight: 2.9990 chunk 4 optimal weight: 9.9990 chunk 52 optimal weight: 6.9990 overall best weight: 3.1186 ------------------------------------------------------------------------------- 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** B 185 ASN ** c 406 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 423 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3267 r_free = 0.3267 target = 0.070919 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2814 r_free = 0.2814 target = 0.051377 restraints weight = 30718.354| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.2866 r_free = 0.2866 target = 0.053529 restraints weight = 17535.267| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.2901 r_free = 0.2901 target = 0.054987 restraints weight = 12638.668| |-----------------------------------------------------------------------------| r_work (final): 0.2893 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8364 moved from start: 0.6498 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.062 9294 Z= 0.310 Angle : 0.827 16.320 12567 Z= 0.406 Chirality : 0.050 0.330 1599 Planarity : 0.004 0.040 1482 Dihedral : 9.006 55.562 2613 Min Nonbonded Distance : 2.458 Molprobity Statistics. All-atom Clashscore : 13.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.96 % Favored : 96.04 % Rotamer: Outliers : 5.04 % Allowed : 24.67 % Favored : 70.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.42 (0.26), residues: 984 helix: 1.62 (0.27), residues: 369 sheet: 0.74 (0.50), residues: 117 loop : -0.88 (0.26), residues: 498 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.036 0.002 TRP A 227 HIS 0.004 0.001 HIS b 354 PHE 0.021 0.003 PHE A 157 TYR 0.026 0.002 TYR A 241 ARG 0.007 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 241 residues out of total 912 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 195 time to evaluate : 0.973 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: 0.9144 (tt0) cc_final: 0.8216 (tm-30) REVERT: A 130 ASP cc_start: 0.8570 (t0) cc_final: 0.8042 (t70) REVERT: A 211 ASP cc_start: 0.8827 (p0) cc_final: 0.8525 (p0) REVERT: a 278 TYR cc_start: 0.8337 (t80) cc_final: 0.8048 (t80) REVERT: a 311 ASP cc_start: 0.9149 (OUTLIER) cc_final: 0.8852 (t0) REVERT: a 313 LEU cc_start: 0.9749 (tp) cc_final: 0.9236 (tp) REVERT: a 325 ARG cc_start: 0.8800 (mmt180) cc_final: 0.8593 (mmm160) REVERT: a 357 ASP cc_start: 0.9373 (t70) cc_final: 0.8900 (t0) REVERT: a 405 GLN cc_start: 0.9290 (tm-30) cc_final: 0.8686 (tm-30) REVERT: B 76 GLU cc_start: 0.9141 (tt0) cc_final: 0.8357 (tm-30) REVERT: B 96 MET cc_start: 0.8585 (ttp) cc_final: 0.8303 (ttm) REVERT: B 130 ASP cc_start: 0.8399 (t0) cc_final: 0.7930 (t70) REVERT: B 227 TRP cc_start: 0.6801 (t-100) cc_final: 0.6262 (t60) REVERT: b 306 ASP cc_start: 0.8375 (OUTLIER) cc_final: 0.8145 (m-30) REVERT: b 351 MET cc_start: 0.9060 (OUTLIER) cc_final: 0.8832 (mmp) REVERT: b 357 ASP cc_start: 0.9353 (t70) cc_final: 0.8768 (t0) REVERT: b 408 ASP cc_start: 0.9306 (m-30) cc_final: 0.8924 (m-30) REVERT: b 413 GLU cc_start: 0.8869 (mp0) cc_final: 0.8380 (pm20) REVERT: C 80 MET cc_start: 0.8981 (mmt) cc_final: 0.8476 (mmm) REVERT: C 130 ASP cc_start: 0.8258 (t0) cc_final: 0.7744 (t70) REVERT: C 211 ASP cc_start: 0.8760 (p0) cc_final: 0.8394 (p0) REVERT: c 278 TYR cc_start: 0.8355 (t80) cc_final: 0.7821 (t80) REVERT: c 311 ASP cc_start: 0.9142 (OUTLIER) cc_final: 0.8869 (t0) REVERT: c 313 LEU cc_start: 0.9729 (tp) cc_final: 0.9209 (tp) REVERT: c 325 ARG cc_start: 0.8672 (mmm160) cc_final: 0.8379 (mmm160) REVERT: c 351 MET cc_start: 0.8795 (mmp) cc_final: 0.8400 (mmp) REVERT: c 410 MET cc_start: 0.9128 (tpp) cc_final: 0.8925 (tpp) outliers start: 46 outliers final: 36 residues processed: 230 average time/residue: 0.1946 time to fit residues: 63.5120 Evaluate side-chains 222 residues out of total 912 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 182 time to evaluate : 1.042 ------------------------------------------------------------------------------- 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 210 TRP Chi-restraints excluded: chain A residue 218 GLN Chi-restraints excluded: chain A residue 239 ILE Chi-restraints excluded: chain A residue 245 LEU Chi-restraints excluded: chain a residue 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 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 351 MET Chi-restraints excluded: chain b residue 385 CYS Chi-restraints excluded: chain b residue 392 SER Chi-restraints excluded: chain b residue 403 ILE Chi-restraints excluded: chain 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 323 ILE Chi-restraints excluded: chain c residue 337 ILE Chi-restraints excluded: chain c residue 350 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: 2.9990 chunk 16 optimal weight: 2.9990 chunk 34 optimal weight: 6.9990 chunk 80 optimal weight: 8.9990 chunk 29 optimal weight: 10.0000 chunk 5 optimal weight: 6.9990 chunk 60 optimal weight: 4.9990 chunk 73 optimal weight: 1.9990 chunk 21 optimal weight: 8.9990 chunk 69 optimal weight: 1.9990 chunk 42 optimal weight: 0.8980 overall best weight: 2.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 93 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 185 ASN B 93 HIS ** 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 = 0.3279 r_free = 0.3279 target = 0.071556 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.2827 r_free = 0.2827 target = 0.051988 restraints weight = 30735.253| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.2880 r_free = 0.2880 target = 0.054161 restraints weight = 17479.132| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.2916 r_free = 0.2916 target = 0.055668 restraints weight = 12578.113| |-----------------------------------------------------------------------------| r_work (final): 0.2907 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8342 moved from start: 0.6706 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.059 9294 Z= 0.250 Angle : 0.803 13.394 12567 Z= 0.393 Chirality : 0.049 0.293 1599 Planarity : 0.004 0.062 1482 Dihedral : 8.851 55.423 2613 Min Nonbonded Distance : 2.414 Molprobity Statistics. All-atom Clashscore : 13.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.96 % Favored : 96.04 % Rotamer: Outliers : 4.71 % Allowed : 24.67 % Favored : 70.61 % 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: 0.45 (0.26), residues: 984 helix: 1.62 (0.27), residues: 369 sheet: 0.59 (0.49), residues: 117 loop : -0.80 (0.27), residues: 498 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP C 227 HIS 0.004 0.001 HIS b 354 PHE 0.024 0.002 PHE A 157 TYR 0.024 0.002 TYR C 241 ARG 0.012 0.001 ARG a 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 241 residues out of total 912 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 198 time to evaluate : 0.978 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 76 GLU cc_start: 0.9181 (tt0) cc_final: 0.8217 (tm-30) REVERT: A 130 ASP cc_start: 0.8556 (t0) cc_final: 0.8079 (t0) REVERT: a 278 TYR cc_start: 0.8366 (t80) cc_final: 0.7997 (t80) REVERT: a 311 ASP cc_start: 0.9139 (OUTLIER) cc_final: 0.8842 (t0) REVERT: a 313 LEU cc_start: 0.9731 (tp) cc_final: 0.9217 (tp) REVERT: a 357 ASP cc_start: 0.9414 (t70) cc_final: 0.8920 (t0) REVERT: a 405 GLN cc_start: 0.9295 (tm-30) cc_final: 0.8689 (tm-30) REVERT: B 76 GLU cc_start: 0.9154 (tt0) cc_final: 0.8336 (tm-30) REVERT: B 96 MET cc_start: 0.8576 (ttp) cc_final: 0.8201 (ttm) REVERT: B 130 ASP cc_start: 0.8428 (t0) cc_final: 0.7978 (t0) REVERT: B 227 TRP cc_start: 0.6786 (t-100) cc_final: 0.6161 (t60) REVERT: b 313 LEU cc_start: 0.9735 (mt) cc_final: 0.9512 (mt) REVERT: b 351 MET cc_start: 0.9084 (mmp) cc_final: 0.8856 (mmp) REVERT: b 357 ASP cc_start: 0.9340 (t70) cc_final: 0.8787 (t0) REVERT: b 408 ASP cc_start: 0.9302 (m-30) cc_final: 0.8908 (m-30) REVERT: b 413 GLU cc_start: 0.8853 (mp0) cc_final: 0.8407 (pm20) REVERT: C 130 ASP cc_start: 0.8216 (t0) cc_final: 0.7705 (t70) REVERT: c 278 TYR cc_start: 0.8354 (t80) cc_final: 0.7791 (t80) REVERT: c 311 ASP cc_start: 0.9176 (OUTLIER) cc_final: 0.8897 (t0) REVERT: c 351 MET cc_start: 0.8814 (mmp) cc_final: 0.8395 (mmp) outliers start: 43 outliers final: 35 residues processed: 234 average time/residue: 0.1804 time to fit residues: 61.2545 Evaluate side-chains 221 residues out of total 912 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 184 time to evaluate : 1.030 ------------------------------------------------------------------------------- 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 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 162 ILE Chi-restraints excluded: chain B residue 185 ASN Chi-restraints excluded: chain B residue 245 LEU Chi-restraints excluded: chain b residue 274 THR Chi-restraints excluded: chain b residue 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 350 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: 9.9990 chunk 64 optimal weight: 8.9990 chunk 67 optimal weight: 2.9990 chunk 47 optimal weight: 0.6980 chunk 61 optimal weight: 7.9990 chunk 65 optimal weight: 0.9980 chunk 55 optimal weight: 1.9990 chunk 11 optimal weight: 8.9990 chunk 16 optimal weight: 3.9990 chunk 0 optimal weight: 9.9990 overall best weight: 2.1386 ------------------------------------------------------------------------------- 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 ** B 93 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 185 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 423 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3324 r_free = 0.3324 target = 0.072577 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2871 r_free = 0.2871 target = 0.053196 restraints weight = 30395.438| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.2926 r_free = 0.2926 target = 0.055465 restraints weight = 16907.042| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.2963 r_free = 0.2963 target = 0.056973 restraints weight = 12040.121| |-----------------------------------------------------------------------------| r_work (final): 0.2957 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8350 moved from start: 0.6791 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= 0.260 Angle : 0.818 13.002 12567 Z= 0.400 Chirality : 0.051 0.337 1599 Planarity : 0.004 0.050 1482 Dihedral : 8.787 55.317 2613 Min Nonbonded Distance : 2.406 Molprobity Statistics. All-atom Clashscore : 13.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.37 % Favored : 95.63 % Rotamer: Outliers : 4.17 % Allowed : 25.77 % Favored : 70.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 0.71 (0.27), residues: 984 helix: 2.00 (0.27), residues: 345 sheet: 0.61 (0.49), residues: 117 loop : -0.62 (0.27), residues: 522 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.002 TRP C 227 HIS 0.015 0.001 HIS B 93 PHE 0.023 0.002 PHE A 157 TYR 0.041 0.002 TYR C 241 ARG 0.010 0.001 ARG a 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 234 residues out of total 912 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 196 time to evaluate : 1.040 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: 0.9168 (tt0) cc_final: 0.8195 (tm-30) REVERT: A 130 ASP cc_start: 0.8568 (t0) cc_final: 0.8097 (t0) REVERT: a 278 TYR cc_start: 0.8385 (t80) cc_final: 0.7953 (t80) REVERT: a 311 ASP cc_start: 0.9134 (OUTLIER) cc_final: 0.8848 (t0) REVERT: a 313 LEU cc_start: 0.9735 (tp) cc_final: 0.9242 (tp) REVERT: a 357 ASP cc_start: 0.9425 (t70) cc_final: 0.9009 (t0) REVERT: a 405 GLN cc_start: 0.9289 (tm-30) cc_final: 0.9053 (tm-30) REVERT: B 76 GLU cc_start: 0.9153 (tt0) cc_final: 0.8325 (tm-30) REVERT: B 96 MET cc_start: 0.8624 (ttp) cc_final: 0.8152 (ttm) REVERT: B 130 ASP cc_start: 0.8431 (t0) cc_final: 0.7992 (t0) REVERT: B 227 TRP cc_start: 0.6808 (t-100) cc_final: 0.6132 (t60) REVERT: b 351 MET cc_start: 0.9034 (OUTLIER) cc_final: 0.8798 (mmp) REVERT: b 357 ASP cc_start: 0.9332 (t70) cc_final: 0.8793 (t0) REVERT: b 408 ASP cc_start: 0.9287 (m-30) cc_final: 0.8897 (m-30) REVERT: C 130 ASP cc_start: 0.8213 (t0) cc_final: 0.7715 (t70) REVERT: c 278 TYR cc_start: 0.8394 (t80) cc_final: 0.7916 (t80) REVERT: c 311 ASP cc_start: 0.9164 (OUTLIER) cc_final: 0.8814 (t0) outliers start: 38 outliers final: 34 residues processed: 227 average time/residue: 0.1827 time to fit residues: 60.8218 Evaluate side-chains 219 residues out of total 912 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 182 time to evaluate : 0.969 ------------------------------------------------------------------------------- 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 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 162 ILE Chi-restraints excluded: chain B residue 185 ASN Chi-restraints excluded: chain b residue 274 THR Chi-restraints excluded: chain b residue 337 ILE Chi-restraints excluded: chain b residue 349 LEU Chi-restraints excluded: chain b residue 351 MET Chi-restraints excluded: chain b residue 385 CYS Chi-restraints excluded: chain b residue 392 SER Chi-restraints excluded: chain b residue 403 ILE Chi-restraints excluded: chain 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 239 ILE 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 350 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: 8.9990 chunk 7 optimal weight: 3.9990 chunk 90 optimal weight: 8.9990 chunk 36 optimal weight: 0.8980 chunk 70 optimal weight: 6.9990 chunk 28 optimal weight: 0.7980 chunk 9 optimal weight: 0.0170 chunk 13 optimal weight: 4.9990 chunk 49 optimal weight: 2.9990 chunk 95 optimal weight: 0.8980 chunk 40 optimal weight: 8.9990 overall best weight: 1.1220 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 92 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 93 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** a 416 GLN B 93 HIS ** B 185 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** c 416 GLN ** c 423 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3307 r_free = 0.3307 target = 0.072932 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2857 r_free = 0.2857 target = 0.053187 restraints weight = 30472.046| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 23)----------------| | r_work = 0.2910 r_free = 0.2910 target = 0.055411 restraints weight = 17476.061| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.2946 r_free = 0.2946 target = 0.056925 restraints weight = 12600.859| |-----------------------------------------------------------------------------| r_work (final): 0.2936 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8324 moved from start: 0.6937 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 : 0.827 12.703 12567 Z= 0.401 Chirality : 0.051 0.348 1599 Planarity : 0.004 0.043 1482 Dihedral : 8.632 54.907 2613 Min Nonbonded Distance : 2.412 Molprobity Statistics. All-atom Clashscore : 12.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.07 % Favored : 95.93 % Rotamer: Outliers : 4.17 % Allowed : 25.99 % Favored : 69.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.64 (0.27), residues: 984 helix: 1.93 (0.27), residues: 345 sheet: 0.53 (0.50), residues: 111 loop : -0.62 (0.27), residues: 528 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.044 0.003 TRP C 227 HIS 0.005 0.001 HIS B 93 PHE 0.024 0.002 PHE A 157 TYR 0.041 0.002 TYR C 241 ARG 0.010 0.001 ARG a 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 236 residues out of total 912 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 198 time to evaluate : 0.957 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: 0.9147 (tt0) cc_final: 0.8169 (tm-30) REVERT: A 96 MET cc_start: 0.8161 (ttm) cc_final: 0.7959 (tpp) REVERT: A 130 ASP cc_start: 0.8508 (t0) cc_final: 0.8040 (t0) REVERT: a 278 TYR cc_start: 0.8376 (t80) cc_final: 0.7996 (t80) REVERT: a 311 ASP cc_start: 0.9120 (OUTLIER) cc_final: 0.8833 (t0) REVERT: a 313 LEU cc_start: 0.9705 (tp) cc_final: 0.9390 (mm) REVERT: a 357 ASP cc_start: 0.9416 (t70) cc_final: 0.9033 (t0) REVERT: a 405 GLN cc_start: 0.9289 (tm-30) cc_final: 0.9050 (tm-30) REVERT: a 416 GLN cc_start: 0.9144 (tp40) cc_final: 0.8939 (tp-100) REVERT: B 76 GLU cc_start: 0.9112 (tt0) cc_final: 0.8312 (tm-30) REVERT: B 96 MET cc_start: 0.8680 (ttp) cc_final: 0.8213 (ttm) REVERT: B 130 ASP cc_start: 0.8381 (t0) cc_final: 0.7939 (t0) REVERT: B 227 TRP cc_start: 0.6905 (t-100) cc_final: 0.6163 (t60) REVERT: b 307 GLU cc_start: 0.8833 (mm-30) cc_final: 0.7988 (mp0) REVERT: b 325 ARG cc_start: 0.8692 (mmm160) cc_final: 0.8434 (mmm160) REVERT: b 351 MET cc_start: 0.9045 (OUTLIER) cc_final: 0.8805 (mmp) REVERT: b 357 ASP cc_start: 0.9320 (t70) cc_final: 0.8800 (t0) REVERT: b 410 MET cc_start: 0.9049 (tpp) cc_final: 0.8319 (mmm) REVERT: b 413 GLU cc_start: 0.8793 (mp0) cc_final: 0.8363 (pm20) REVERT: C 96 MET cc_start: 0.7501 (ttt) cc_final: 0.7095 (ttt) REVERT: C 117 PHE cc_start: 0.6578 (OUTLIER) cc_final: 0.6116 (p90) REVERT: C 130 ASP cc_start: 0.8157 (t0) cc_final: 0.7652 (t70) REVERT: c 278 TYR cc_start: 0.8415 (t80) cc_final: 0.7898 (t80) REVERT: c 311 ASP cc_start: 0.9143 (OUTLIER) cc_final: 0.8727 (t0) REVERT: c 351 MET cc_start: 0.8749 (mmp) cc_final: 0.8319 (mmp) REVERT: c 420 MET cc_start: 0.8070 (mmp) cc_final: 0.7745 (mmp) outliers start: 38 outliers final: 28 residues processed: 229 average time/residue: 0.1751 time to fit residues: 58.3275 Evaluate side-chains 219 residues out of total 912 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 187 time to evaluate : 1.038 ------------------------------------------------------------------------------- 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 311 ASP Chi-restraints excluded: chain a residue 403 ILE 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 162 ILE Chi-restraints excluded: chain B residue 185 ASN Chi-restraints excluded: chain B residue 245 LEU Chi-restraints excluded: chain b residue 274 THR Chi-restraints excluded: chain b residue 337 ILE Chi-restraints excluded: chain b residue 349 LEU Chi-restraints excluded: chain b residue 351 MET Chi-restraints excluded: chain b residue 385 CYS Chi-restraints excluded: chain b residue 403 ILE Chi-restraints excluded: chain C residue 86 CYS Chi-restraints excluded: chain C residue 117 PHE Chi-restraints excluded: chain C residue 128 LEU Chi-restraints excluded: chain C residue 218 GLN Chi-restraints excluded: chain C residue 245 LEU Chi-restraints excluded: chain c residue 274 THR Chi-restraints excluded: chain c residue 311 ASP Chi-restraints excluded: chain c residue 380 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 58 optimal weight: 1.9990 chunk 5 optimal weight: 20.0000 chunk 23 optimal weight: 4.9990 chunk 95 optimal weight: 0.5980 chunk 93 optimal weight: 4.9990 chunk 76 optimal weight: 7.9990 chunk 33 optimal weight: 10.0000 chunk 89 optimal weight: 0.9980 chunk 1 optimal weight: 7.9990 chunk 63 optimal weight: 8.9990 chunk 9 optimal weight: 10.0000 overall best weight: 2.7186 ------------------------------------------------------------------------------- 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** B 93 HIS ** B 185 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 218 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 335 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 335 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 423 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3287 r_free = 0.3287 target = 0.071885 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2835 r_free = 0.2835 target = 0.052512 restraints weight = 30487.863| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.2886 r_free = 0.2886 target = 0.054621 restraints weight = 17850.826| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.2921 r_free = 0.2921 target = 0.056089 restraints weight = 12984.900| |-----------------------------------------------------------------------------| r_work (final): 0.2907 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8364 moved from start: 0.7029 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.062 9294 Z= 0.305 Angle : 0.883 15.324 12567 Z= 0.427 Chirality : 0.051 0.441 1599 Planarity : 0.005 0.041 1482 Dihedral : 8.779 55.211 2613 Min Nonbonded Distance : 2.417 Molprobity Statistics. All-atom Clashscore : 14.49 Ramachandran Plot: Outliers : 0.10 % Allowed : 4.37 % Favored : 95.53 % Rotamer: Outliers : 3.95 % Allowed : 26.86 % Favored : 69.19 % 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: 0.57 (0.27), residues: 984 helix: 1.94 (0.27), residues: 345 sheet: 0.35 (0.50), residues: 111 loop : -0.68 (0.28), residues: 528 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.002 TRP C 227 HIS 0.009 0.001 HIS B 93 PHE 0.022 0.002 PHE C 157 TYR 0.035 0.002 TYR A 241 ARG 0.009 0.001 ARG a 422 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2696.76 seconds wall clock time: 49 minutes 39.51 seconds (2979.51 seconds total)