Starting phenix.real_space_refine on Wed Sep 25 04:54:32 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8eje_28179/09_2024/8eje_28179.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8eje_28179/09_2024/8eje_28179.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.69 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8eje_28179/09_2024/8eje_28179.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8eje_28179/09_2024/8eje_28179.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8eje_28179/09_2024/8eje_28179.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8eje_28179/09_2024/8eje_28179.cif" } resolution = 3.69 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= 0.001 sd= 0.026 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 87 5.16 5 C 5892 2.51 5 N 1497 2.21 5 O 1950 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 39 residue(s): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/chem_data/mon_lib" Total number of atoms: 9426 Number of models: 1 Model: "" Number of chains: 33 Chain: "A" Number of atoms: 1538 Number of conformers: 1 Conformer: "" Number of residues, atoms: 195, 1538 Classifications: {'peptide': 195} Link IDs: {'PTRANS': 4, 'TRANS': 190} Chain: "a" Number of atoms: 1308 Number of conformers: 1 Conformer: "" Number of residues, atoms: 161, 1308 Classifications: {'peptide': 161} Link IDs: {'PTRANS': 4, 'TRANS': 156} Chain: "B" Number of atoms: 1538 Number of conformers: 1 Conformer: "" Number of residues, atoms: 195, 1538 Classifications: {'peptide': 195} Link IDs: {'PTRANS': 4, 'TRANS': 190} Chain: "b" Number of atoms: 1308 Number of conformers: 1 Conformer: "" Number of residues, atoms: 161, 1308 Classifications: {'peptide': 161} Link IDs: {'PTRANS': 4, 'TRANS': 156} Chain: "C" Number of atoms: 1538 Number of conformers: 1 Conformer: "" Number of residues, atoms: 195, 1538 Classifications: {'peptide': 195} Link IDs: {'PTRANS': 4, 'TRANS': 190} Chain: "c" Number of atoms: 1308 Number of conformers: 1 Conformer: "" Number of residues, atoms: 161, 1308 Classifications: {'peptide': 161} Link IDs: {'PTRANS': 4, 'TRANS': 156} Chain: "D" 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: "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: 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: 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: 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: "J" 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: "K" 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: "L" 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: "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: 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: "P" 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: "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: 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: "S" 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: "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: 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: "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: 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: "X" 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: "A" 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: "a" 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: "B" 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: "b" 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: "C" 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: "c" 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 Time building chain proxies: 5.94, per 1000 atoms: 0.63 Number of scatterers: 9426 At special positions: 0 Unit cell: (93.005, 91.96, 100.32, 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 87 16.00 O 1950 8.00 N 1497 7.00 C 5892 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=21, symmetry=0 Simple disulfide: pdb=" SG CYS A 85 " - pdb=" SG CYS A 230 " distance=2.03 Simple disulfide: pdb=" SG CYS A 117 " - pdb=" SG CYS A 154 " distance=2.03 Simple disulfide: pdb=" SG CYS A 179 " - pdb=" SG CYS A 211 " distance=2.03 Simple disulfide: pdb=" SG CYS A 206 " - pdb=" SG CYS a 359 " distance=2.06 Simple disulfide: pdb=" SG CYS a 278 " - pdb=" SG CYS a 291 " distance=2.04 Simple disulfide: pdb=" SG CYS a 300 " - pdb=" SG CYS a 309 " distance=2.03 Simple disulfide: pdb=" SG CYS a 363 " - pdb=" SG CYS a 384 " distance=2.01 Simple disulfide: pdb=" SG CYS B 85 " - pdb=" SG CYS B 230 " distance=2.03 Simple disulfide: pdb=" SG CYS B 117 " - pdb=" SG CYS B 154 " distance=2.03 Simple disulfide: pdb=" SG CYS B 179 " - pdb=" SG CYS B 211 " distance=2.03 Simple disulfide: pdb=" SG CYS B 206 " - pdb=" SG CYS b 359 " distance=2.06 Simple disulfide: pdb=" SG CYS b 278 " - pdb=" SG CYS b 291 " distance=2.04 Simple disulfide: pdb=" SG CYS b 300 " - pdb=" SG CYS b 309 " distance=2.03 Simple disulfide: pdb=" SG CYS b 363 " - pdb=" SG CYS b 384 " distance=2.01 Simple disulfide: pdb=" SG CYS C 85 " - pdb=" SG CYS C 230 " distance=2.03 Simple disulfide: pdb=" SG CYS C 117 " - pdb=" SG CYS C 154 " distance=2.03 Simple disulfide: pdb=" SG CYS C 179 " - pdb=" SG CYS C 211 " distance=2.03 Simple disulfide: pdb=" SG CYS C 206 " - pdb=" SG CYS c 359 " distance=2.06 Simple disulfide: pdb=" SG CYS c 278 " - pdb=" SG CYS c 291 " distance=2.04 Simple disulfide: pdb=" SG CYS c 300 " - pdb=" SG CYS c 309 " distance=2.03 Simple disulfide: pdb=" SG CYS c 363 " - pdb=" SG CYS c 384 " distance=2.01 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 I 3 " - " MAN I 4 " " BMA P 3 " - " MAN P 4 " " BMA W 3 " - " MAN W 4 " ALPHA1-6 " BMA I 3 " - " MAN I 5 " " BMA P 3 " - " MAN P 5 " " BMA W 3 " - " MAN W 5 " BETA1-4 " NAG D 1 " - " NAG D 2 " " NAG D 2 " - " BMA D 3 " " NAG E 1 " - " NAG E 2 " " NAG F 1 " - " NAG F 2 " " NAG G 1 " - " NAG G 2 " " NAG H 1 " - " NAG H 2 " " NAG I 1 " - " NAG I 2 " " NAG I 2 " - " BMA I 3 " " NAG J 1 " - " NAG J 2 " " NAG K 1 " - " NAG K 2 " " NAG K 2 " - " BMA K 3 " " 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 P 1 " - " NAG P 2 " " NAG P 2 " - " BMA P 3 " " NAG Q 1 " - " NAG Q 2 " " NAG R 1 " - " NAG R 2 " " NAG R 2 " - " BMA R 3 " " NAG S 1 " - " NAG S 2 " " 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 W 2 " - " BMA W 3 " " NAG X 1 " - " NAG X 2 " NAG-ASN " NAG A 301 " - " ASN A 98 " " NAG A 302 " - " ASN A 223 " " NAG B 301 " - " ASN B 98 " " NAG B 302 " - " ASN B 223 " " NAG C 301 " - " ASN C 98 " " NAG C 302 " - " ASN C 223 " " NAG D 1 " - " ASN A 78 " " NAG E 1 " - " ASN A 88 " " NAG F 1 " - " ASN A 108 " " NAG G 1 " - " ASN A 118 " " NAG H 1 " - " ASN A 166 " " NAG I 1 " - " ASN a 364 " " NAG J 1 " - " ASN a 372 " " NAG K 1 " - " ASN B 78 " " NAG L 1 " - " ASN B 88 " " NAG M 1 " - " ASN B 108 " " NAG N 1 " - " ASN B 118 " " NAG O 1 " - " ASN B 166 " " NAG P 1 " - " ASN b 364 " " NAG Q 1 " - " ASN b 372 " " NAG R 1 " - " ASN C 78 " " NAG S 1 " - " ASN C 88 " " NAG T 1 " - " ASN C 108 " " NAG U 1 " - " ASN C 118 " " NAG V 1 " - " ASN C 166 " " NAG W 1 " - " ASN c 364 " " NAG X 1 " - " ASN c 372 " " NAG a 501 " - " ASN a 394 " " NAG a 502 " - " ASN a 389 " " NAG b 501 " - " ASN b 394 " " NAG b 502 " - " ASN b 389 " " NAG c 501 " - " ASN c 394 " " NAG c 502 " - " ASN c 389 " Time building additional restraints: 3.14 Conformation dependent library (CDL) restraints added in 997.2 milliseconds 2112 Ramachandran restraints generated. 1056 Oldfield, 0 Emsley, 1056 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2016 Finding SS restraints... Secondary structure from input PDB file: 45 helices and 12 sheets defined 40.4% alpha, 12.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.96 Creating SS restraints... Processing helix chain 'A' and resid 73 through 78 Processing helix chain 'A' and resid 118 through 126 Processing helix chain 'A' and resid 129 through 142 Processing helix chain 'A' and resid 168 through 170 No H-bonds generated for 'chain 'A' and resid 168 through 170' Processing helix chain 'A' and resid 171 through 178 Processing helix chain 'A' and resid 182 through 194 removed outlier: 3.733A pdb=" N ARG A 192 " --> pdb=" O GLN A 188 " (cutoff:3.500A) Processing helix chain 'A' and resid 201 through 205 Processing helix chain 'A' and resid 237 through 246 Processing helix chain 'a' and resid 293 through 298 Processing helix chain 'a' and resid 299 through 302 Processing helix chain 'a' and resid 306 through 325 removed outlier: 3.805A pdb=" N ASP a 310 " --> pdb=" O GLU a 306 " (cutoff:3.500A) Processing helix chain 'a' and resid 333 through 344 removed outlier: 3.551A pdb=" N ASN a 341 " --> pdb=" O ASN a 337 " (cutoff:3.500A) Processing helix chain 'a' and resid 345 through 357 Processing helix chain 'a' and resid 358 through 360 No H-bonds generated for 'chain 'a' and resid 358 through 360' Processing helix chain 'a' and resid 398 through 415 Processing helix chain 'B' and resid 73 through 78 Processing helix chain 'B' and resid 118 through 126 Processing helix chain 'B' and resid 129 through 142 Processing helix chain 'B' and resid 168 through 170 No H-bonds generated for 'chain 'B' and resid 168 through 170' Processing helix chain 'B' and resid 171 through 178 Processing helix chain 'B' and resid 182 through 194 removed outlier: 3.733A pdb=" N ARG B 192 " --> pdb=" O GLN B 188 " (cutoff:3.500A) Processing helix chain 'B' and resid 201 through 205 Processing helix chain 'B' and resid 237 through 246 Processing helix chain 'b' and resid 293 through 298 Processing helix chain 'b' and resid 299 through 302 Processing helix chain 'b' and resid 306 through 325 removed outlier: 3.805A pdb=" N ASP b 310 " --> pdb=" O GLU b 306 " (cutoff:3.500A) Processing helix chain 'b' and resid 333 through 344 removed outlier: 3.551A pdb=" N ASN b 341 " --> pdb=" O ASN b 337 " (cutoff:3.500A) Processing helix chain 'b' and resid 345 through 357 Processing helix chain 'b' and resid 358 through 360 No H-bonds generated for 'chain 'b' and resid 358 through 360' Processing helix chain 'b' and resid 398 through 415 Processing helix chain 'C' and resid 73 through 78 Processing helix chain 'C' and resid 118 through 126 Processing helix chain 'C' and resid 129 through 142 Processing helix chain 'C' and resid 168 through 170 No H-bonds generated for 'chain 'C' and resid 168 through 170' Processing helix chain 'C' and resid 171 through 178 Processing helix chain 'C' and resid 182 through 194 removed outlier: 3.732A pdb=" N ARG C 192 " --> pdb=" O GLN C 188 " (cutoff:3.500A) Processing helix chain 'C' and resid 201 through 205 Processing helix chain 'C' and resid 237 through 246 Processing helix chain 'c' and resid 293 through 298 Processing helix chain 'c' and resid 299 through 302 Processing helix chain 'c' and resid 306 through 325 removed outlier: 3.805A pdb=" N ASP c 310 " --> pdb=" O GLU c 306 " (cutoff:3.500A) Processing helix chain 'c' and resid 333 through 344 removed outlier: 3.550A pdb=" N ASN c 341 " --> pdb=" O ASN c 337 " (cutoff:3.500A) Processing helix chain 'c' and resid 345 through 357 Processing helix chain 'c' and resid 358 through 360 No H-bonds generated for 'chain 'c' and resid 358 through 360' Processing helix chain 'c' and resid 398 through 415 Processing sheet with id=AA1, first strand: chain 'A' and resid 65 through 71 Processing sheet with id=AA2, first strand: chain 'A' and resid 83 through 86 Processing sheet with id=AA3, first strand: chain 'a' and resid 277 through 279 Processing sheet with id=AA4, first strand: chain 'a' and resid 387 through 388 Processing sheet with id=AA5, first strand: chain 'B' and resid 65 through 71 Processing sheet with id=AA6, first strand: chain 'B' and resid 83 through 86 Processing sheet with id=AA7, first strand: chain 'b' and resid 277 through 279 Processing sheet with id=AA8, first strand: chain 'b' and resid 387 through 388 Processing sheet with id=AA9, first strand: chain 'C' and resid 65 through 71 Processing sheet with id=AB1, first strand: chain 'C' and resid 83 through 86 Processing sheet with id=AB2, first strand: chain 'c' and resid 277 through 279 Processing sheet with id=AB3, first strand: chain 'c' and resid 387 through 388 372 hydrogen bonds defined for protein. 990 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: 2.58 Time building geometry restraints manager: 3.51 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.33: 2322 1.33 - 1.47: 3215 1.47 - 1.62: 3946 1.62 - 1.77: 12 1.77 - 1.91: 123 Bond restraints: 9618 Sorted by residual: bond pdb=" CB ILE b 419 " pdb=" CG1 ILE b 419 " ideal model delta sigma weight residual 1.530 1.653 -0.123 2.00e-02 2.50e+03 3.78e+01 bond pdb=" CB ILE a 419 " pdb=" CG1 ILE a 419 " ideal model delta sigma weight residual 1.530 1.653 -0.123 2.00e-02 2.50e+03 3.76e+01 bond pdb=" CB ILE c 419 " pdb=" CG1 ILE c 419 " ideal model delta sigma weight residual 1.530 1.653 -0.123 2.00e-02 2.50e+03 3.76e+01 bond pdb=" NE1 TRP b 385 " pdb=" CE2 TRP b 385 " ideal model delta sigma weight residual 1.370 1.304 0.066 1.10e-02 8.26e+03 3.61e+01 bond pdb=" NE1 TRP c 385 " pdb=" CE2 TRP c 385 " ideal model delta sigma weight residual 1.370 1.304 0.066 1.10e-02 8.26e+03 3.57e+01 ... (remaining 9613 not shown) Histogram of bond angle deviations from ideal: 0.00 - 7.28: 12964 7.28 - 14.56: 59 14.56 - 21.84: 0 21.84 - 29.11: 0 29.11 - 36.39: 9 Bond angle restraints: 13032 Sorted by residual: angle pdb=" C2 NAG V 2 " pdb=" N2 NAG V 2 " pdb=" C7 NAG V 2 " ideal model delta sigma weight residual 124.56 160.95 -36.39 3.00e+00 1.11e-01 1.47e+02 angle pdb=" C2 NAG H 2 " pdb=" N2 NAG H 2 " pdb=" C7 NAG H 2 " ideal model delta sigma weight residual 124.56 160.94 -36.38 3.00e+00 1.11e-01 1.47e+02 angle pdb=" C2 NAG A 301 " pdb=" N2 NAG A 301 " pdb=" C7 NAG A 301 " ideal model delta sigma weight residual 124.56 160.94 -36.38 3.00e+00 1.11e-01 1.47e+02 angle pdb=" C2 NAG C 301 " pdb=" N2 NAG C 301 " pdb=" C7 NAG C 301 " ideal model delta sigma weight residual 124.56 160.93 -36.37 3.00e+00 1.11e-01 1.47e+02 angle pdb=" C2 NAG B 301 " pdb=" N2 NAG B 301 " pdb=" C7 NAG B 301 " ideal model delta sigma weight residual 124.56 160.93 -36.37 3.00e+00 1.11e-01 1.47e+02 ... (remaining 13027 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 21.37: 6246 21.37 - 42.73: 226 42.73 - 64.10: 44 64.10 - 85.47: 45 85.47 - 106.83: 30 Dihedral angle restraints: 6591 sinusoidal: 3456 harmonic: 3135 Sorted by residual: dihedral pdb=" CA CYS B 117 " pdb=" CB CYS B 117 " pdb=" SG CYS B 117 " pdb=" SG CYS B 154 " ideal model delta sinusoidal sigma weight residual 79.00 13.37 65.63 1 2.00e+01 2.50e-03 1.41e+01 dihedral pdb=" CA CYS C 117 " pdb=" CB CYS C 117 " pdb=" SG CYS C 117 " pdb=" SG CYS C 154 " ideal model delta sinusoidal sigma weight residual 79.00 13.39 65.61 1 2.00e+01 2.50e-03 1.41e+01 dihedral pdb=" CA CYS A 117 " pdb=" CB CYS A 117 " pdb=" SG CYS A 117 " pdb=" SG CYS A 154 " ideal model delta sinusoidal sigma weight residual 79.00 13.42 65.58 1 2.00e+01 2.50e-03 1.41e+01 ... (remaining 6588 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.121: 1072 0.121 - 0.242: 359 0.242 - 0.363: 135 0.363 - 0.483: 51 0.483 - 0.604: 15 Chirality restraints: 1632 Sorted by residual: chirality pdb=" C1 BMA D 3 " pdb=" O4 NAG D 2 " pdb=" C2 BMA D 3 " pdb=" O5 BMA D 3 " both_signs ideal model delta sigma weight residual False -2.40 -1.80 -0.60 2.00e-02 2.50e+03 9.13e+02 chirality pdb=" C1 BMA R 3 " pdb=" O4 NAG R 2 " pdb=" C2 BMA R 3 " pdb=" O5 BMA R 3 " both_signs ideal model delta sigma weight residual False -2.40 -1.80 -0.60 2.00e-02 2.50e+03 9.13e+02 chirality pdb=" C1 BMA K 3 " pdb=" O4 NAG K 2 " pdb=" C2 BMA K 3 " pdb=" O5 BMA K 3 " both_signs ideal model delta sigma weight residual False -2.40 -1.80 -0.60 2.00e-02 2.50e+03 9.08e+02 ... (remaining 1629 not shown) Planarity restraints: 1590 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 NAG K 2 " -0.226 2.00e-02 2.50e+03 1.85e-01 4.28e+02 pdb=" C7 NAG K 2 " 0.065 2.00e-02 2.50e+03 pdb=" C8 NAG K 2 " -0.163 2.00e-02 2.50e+03 pdb=" N2 NAG K 2 " 0.298 2.00e-02 2.50e+03 pdb=" O7 NAG K 2 " 0.026 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG D 2 " -0.226 2.00e-02 2.50e+03 1.85e-01 4.28e+02 pdb=" C7 NAG D 2 " 0.065 2.00e-02 2.50e+03 pdb=" C8 NAG D 2 " -0.163 2.00e-02 2.50e+03 pdb=" N2 NAG D 2 " 0.298 2.00e-02 2.50e+03 pdb=" O7 NAG D 2 " 0.026 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG R 2 " 0.226 2.00e-02 2.50e+03 1.85e-01 4.28e+02 pdb=" C7 NAG R 2 " -0.065 2.00e-02 2.50e+03 pdb=" C8 NAG R 2 " 0.163 2.00e-02 2.50e+03 pdb=" N2 NAG R 2 " -0.298 2.00e-02 2.50e+03 pdb=" O7 NAG R 2 " -0.026 2.00e-02 2.50e+03 ... (remaining 1587 not shown) Histogram of nonbonded interaction distances: 2.32 - 2.83: 2756 2.83 - 3.35: 9323 3.35 - 3.87: 15841 3.87 - 4.38: 19496 4.38 - 4.90: 30060 Nonbonded interactions: 77476 Sorted by model distance: nonbonded pdb=" N ALA B 201 " pdb=" N LEU B 202 " model vdw 2.317 2.560 nonbonded pdb=" N ALA A 201 " pdb=" N LEU A 202 " model vdw 2.317 2.560 nonbonded pdb=" N ALA C 201 " pdb=" N LEU C 202 " model vdw 2.317 2.560 nonbonded pdb=" O GLY B 207 " pdb=" C SER B 208 " model vdw 2.403 3.270 nonbonded pdb=" O GLY C 207 " pdb=" C SER C 208 " model vdw 2.403 3.270 ... (remaining 77471 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: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' } ncs_group { reference = chain 'D' selection = chain 'K' selection = chain 'R' } ncs_group { reference = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'J' selection = chain 'L' selection = chain 'M' selection = chain 'N' selection = chain 'O' selection = chain 'Q' selection = chain 'S' selection = chain 'T' selection = chain 'U' selection = chain 'V' selection = chain 'X' } ncs_group { reference = chain 'I' selection = chain 'P' selection = chain 'W' } ncs_group { reference = chain 'a' selection = chain 'b' selection = chain 'c' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.990 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.000 Extract box with map and model: 0.320 Check model and map are aligned: 0.060 Set scattering table: 0.080 Process input model: 24.030 Find NCS groups from input model: 0.470 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.920 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 28.950 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7742 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 : 0.023 0.123 9618 Z= 1.470 Angle : 2.139 36.392 13032 Z= 1.262 Chirality : 0.155 0.604 1632 Planarity : 0.012 0.185 1557 Dihedral : 15.070 106.833 4512 Min Nonbonded Distance : 2.317 Molprobity Statistics. All-atom Clashscore : 2.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.97 % Favored : 94.03 % Rotamer: Outliers : 0.00 % Allowed : 0.95 % Favored : 99.05 % 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: -0.11 (0.24), residues: 1056 helix: -0.09 (0.24), residues: 339 sheet: 1.95 (0.48), residues: 99 loop : -0.34 (0.24), residues: 618 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.005 TRP B 226 HIS 0.009 0.003 HIS C 140 PHE 0.025 0.006 PHE C 146 TYR 0.043 0.009 TYR B 218 ARG 0.006 0.001 ARG C 125 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2112 Ramachandran restraints generated. 1056 Oldfield, 0 Emsley, 1056 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2112 Ramachandran restraints generated. 1056 Oldfield, 0 Emsley, 1056 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 356 residues out of total 951 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 356 time to evaluate : 1.012 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: a 316 ASP cc_start: 0.8681 (t70) cc_final: 0.8398 (t0) REVERT: a 350 MET cc_start: 0.9295 (mmm) cc_final: 0.9083 (tpp) REVERT: a 401 ASP cc_start: 0.8451 (m-30) cc_final: 0.8054 (m-30) REVERT: B 129 ASP cc_start: 0.8208 (t0) cc_final: 0.7996 (t0) REVERT: B 182 ILE cc_start: 0.8049 (mt) cc_final: 0.7778 (mp) REVERT: b 316 ASP cc_start: 0.8636 (t70) cc_final: 0.8306 (t0) REVERT: b 350 MET cc_start: 0.9260 (mmm) cc_final: 0.9051 (tpp) REVERT: b 401 ASP cc_start: 0.8477 (m-30) cc_final: 0.7988 (m-30) REVERT: C 129 ASP cc_start: 0.8023 (t0) cc_final: 0.7811 (t0) REVERT: C 193 MET cc_start: 0.7914 (tpp) cc_final: 0.7609 (tpp) REVERT: C 210 ASP cc_start: 0.6558 (p0) cc_final: 0.6077 (t0) REVERT: c 316 ASP cc_start: 0.8627 (t70) cc_final: 0.8389 (t0) REVERT: c 401 ASP cc_start: 0.8410 (m-30) cc_final: 0.8075 (m-30) outliers start: 0 outliers final: 0 residues processed: 356 average time/residue: 0.2559 time to fit residues: 119.6856 Evaluate side-chains 195 residues out of total 951 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 195 time to evaluate : 0.979 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 88 optimal weight: 0.0980 chunk 79 optimal weight: 4.9990 chunk 44 optimal weight: 0.9980 chunk 27 optimal weight: 4.9990 chunk 53 optimal weight: 0.7980 chunk 42 optimal weight: 0.5980 chunk 82 optimal weight: 0.9990 chunk 31 optimal weight: 1.9990 chunk 50 optimal weight: 0.9980 chunk 61 optimal weight: 5.9990 chunk 95 optimal weight: 3.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 188 GLN ** a 334 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 415 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 130 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** b 334 GLN ** b 415 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 123 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 130 HIS c 330 GLN c 353 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7835 moved from start: 0.3864 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.086 9618 Z= 0.311 Angle : 1.047 12.028 13032 Z= 0.537 Chirality : 0.056 0.302 1632 Planarity : 0.004 0.029 1557 Dihedral : 13.521 85.208 2514 Min Nonbonded Distance : 2.298 Molprobity Statistics. All-atom Clashscore : 12.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.63 % Favored : 93.37 % Rotamer: Outliers : 4.42 % Allowed : 12.30 % Favored : 83.28 % Cbeta Deviations : 0.10 % 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: -0.24 (0.25), residues: 1056 helix: 0.56 (0.27), residues: 336 sheet: 0.58 (0.42), residues: 144 loop : -0.76 (0.26), residues: 576 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP A 195 HIS 0.021 0.002 HIS C 123 PHE 0.023 0.003 PHE A 116 TYR 0.020 0.001 TYR B 149 ARG 0.005 0.001 ARG B 125 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2112 Ramachandran restraints generated. 1056 Oldfield, 0 Emsley, 1056 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2112 Ramachandran restraints generated. 1056 Oldfield, 0 Emsley, 1056 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 278 residues out of total 951 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 236 time to evaluate : 1.043 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: A 171 TYR cc_start: 0.7159 (OUTLIER) cc_final: 0.5451 (p90) REVERT: a 400 ASP cc_start: 0.8427 (OUTLIER) cc_final: 0.8224 (p0) REVERT: b 331 MET cc_start: 0.5275 (ptp) cc_final: 0.4980 (ptp) REVERT: b 401 ASP cc_start: 0.8361 (m-30) cc_final: 0.8089 (m-30) REVERT: C 193 MET cc_start: 0.8162 (tpp) cc_final: 0.7710 (tpp) REVERT: C 229 HIS cc_start: 0.7986 (m-70) cc_final: 0.7592 (m-70) REVERT: c 401 ASP cc_start: 0.8349 (m-30) cc_final: 0.8143 (m-30) REVERT: c 409 MET cc_start: 0.6980 (mtp) cc_final: 0.6644 (mtp) outliers start: 42 outliers final: 22 residues processed: 258 average time/residue: 0.2525 time to fit residues: 86.4643 Evaluate side-chains 209 residues out of total 951 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 185 time to evaluate : 1.061 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 116 PHE Chi-restraints excluded: chain A residue 118 ASN Chi-restraints excluded: chain A residue 121 ASP Chi-restraints excluded: chain A residue 171 TYR Chi-restraints excluded: chain A residue 195 TRP Chi-restraints excluded: chain a residue 262 THR Chi-restraints excluded: chain a residue 291 CYS Chi-restraints excluded: chain a residue 376 THR Chi-restraints excluded: chain a residue 400 ASP Chi-restraints excluded: chain B residue 121 ASP Chi-restraints excluded: chain B residue 179 CYS Chi-restraints excluded: chain B residue 195 TRP Chi-restraints excluded: chain B residue 241 LEU Chi-restraints excluded: chain b residue 262 THR Chi-restraints excluded: chain b residue 283 MET Chi-restraints excluded: chain b residue 304 HIS Chi-restraints excluded: chain b residue 376 THR Chi-restraints excluded: chain C residue 116 PHE Chi-restraints excluded: chain C residue 121 ASP Chi-restraints excluded: chain C residue 195 TRP Chi-restraints excluded: chain C residue 241 LEU Chi-restraints excluded: chain c residue 260 THR Chi-restraints excluded: chain c residue 357 ILE Chi-restraints excluded: chain c residue 376 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 52 optimal weight: 0.8980 chunk 29 optimal weight: 0.9990 chunk 79 optimal weight: 0.0060 chunk 64 optimal weight: 0.9980 chunk 26 optimal weight: 0.6980 chunk 95 optimal weight: 0.7980 chunk 103 optimal weight: 0.9980 chunk 85 optimal weight: 3.9990 chunk 94 optimal weight: 0.5980 chunk 32 optimal weight: 3.9990 chunk 76 optimal weight: 9.9990 overall best weight: 0.5996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 123 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 169 HIS A 217 GLN B 217 GLN b 330 GLN C 217 GLN c 334 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7836 moved from start: 0.4638 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.070 9618 Z= 0.273 Angle : 0.901 9.372 13032 Z= 0.456 Chirality : 0.053 0.295 1632 Planarity : 0.003 0.020 1557 Dihedral : 11.482 75.045 2514 Min Nonbonded Distance : 2.329 Molprobity Statistics. All-atom Clashscore : 11.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.20 % Favored : 92.80 % Rotamer: Outliers : 5.99 % Allowed : 12.72 % Favored : 81.28 % Cbeta Deviations : 0.10 % 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: 1056 helix: 0.53 (0.27), residues: 333 sheet: 0.13 (0.45), residues: 144 loop : -0.87 (0.26), residues: 579 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP A 195 HIS 0.010 0.001 HIS C 123 PHE 0.015 0.002 PHE a 292 TYR 0.018 0.001 TYR B 149 ARG 0.010 0.001 ARG a 355 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2112 Ramachandran restraints generated. 1056 Oldfield, 0 Emsley, 1056 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2112 Ramachandran restraints generated. 1056 Oldfield, 0 Emsley, 1056 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 274 residues out of total 951 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 57 poor density : 217 time to evaluate : 1.012 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: A 152 MET cc_start: 0.8205 (tmm) cc_final: 0.7820 (tmm) REVERT: A 171 TYR cc_start: 0.7204 (OUTLIER) cc_final: 0.5544 (p90) REVERT: a 355 ARG cc_start: 0.8644 (mtt90) cc_final: 0.8411 (mtt180) REVERT: B 191 MET cc_start: 0.8132 (mmt) cc_final: 0.7902 (mmt) REVERT: b 262 THR cc_start: 0.9381 (OUTLIER) cc_final: 0.8496 (m) REVERT: b 331 MET cc_start: 0.5252 (ptp) cc_final: 0.4976 (ptp) REVERT: b 401 ASP cc_start: 0.8507 (m-30) cc_final: 0.8199 (m-30) REVERT: C 152 MET cc_start: 0.8309 (tmm) cc_final: 0.8035 (tmm) REVERT: C 178 HIS cc_start: 0.6945 (OUTLIER) cc_final: 0.6736 (m-70) REVERT: C 193 MET cc_start: 0.8414 (tpp) cc_final: 0.8028 (tpp) REVERT: C 230 CYS cc_start: 0.7822 (OUTLIER) cc_final: 0.7375 (m) REVERT: c 356 ASP cc_start: 0.8210 (t0) cc_final: 0.8003 (t0) REVERT: c 401 ASP cc_start: 0.8367 (m-30) cc_final: 0.8124 (m-30) outliers start: 57 outliers final: 34 residues processed: 249 average time/residue: 0.2463 time to fit residues: 81.0681 Evaluate side-chains 211 residues out of total 951 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 173 time to evaluate : 0.852 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 99 GLU Chi-restraints excluded: chain A residue 116 PHE Chi-restraints excluded: chain A residue 118 ASN Chi-restraints excluded: chain A residue 121 ASP Chi-restraints excluded: chain A residue 136 ILE Chi-restraints excluded: chain A residue 171 TYR Chi-restraints excluded: chain A residue 195 TRP Chi-restraints excluded: chain A residue 199 TYR Chi-restraints excluded: chain A residue 245 SER Chi-restraints excluded: chain a residue 266 SER Chi-restraints excluded: chain a residue 283 MET Chi-restraints excluded: chain a residue 323 ARG Chi-restraints excluded: chain a residue 376 THR Chi-restraints excluded: chain B residue 81 MET Chi-restraints excluded: chain B residue 99 GLU Chi-restraints excluded: chain B residue 116 PHE Chi-restraints excluded: chain B residue 121 ASP Chi-restraints excluded: chain B residue 179 CYS Chi-restraints excluded: chain B residue 195 TRP Chi-restraints excluded: chain B residue 230 CYS Chi-restraints excluded: chain b residue 260 THR Chi-restraints excluded: chain b residue 262 THR Chi-restraints excluded: chain b residue 266 SER Chi-restraints excluded: chain b residue 283 MET Chi-restraints excluded: chain b residue 291 CYS Chi-restraints excluded: chain b residue 376 THR Chi-restraints excluded: chain b residue 414 LEU Chi-restraints excluded: chain C residue 99 GLU Chi-restraints excluded: chain C residue 116 PHE Chi-restraints excluded: chain C residue 121 ASP Chi-restraints excluded: chain C residue 136 ILE Chi-restraints excluded: chain C residue 178 HIS Chi-restraints excluded: chain C residue 195 TRP Chi-restraints excluded: chain C residue 230 CYS Chi-restraints excluded: chain C residue 241 LEU Chi-restraints excluded: chain c residue 266 SER Chi-restraints excluded: chain c residue 291 CYS Chi-restraints excluded: chain c residue 323 ARG Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 94 optimal weight: 0.9980 chunk 71 optimal weight: 0.9980 chunk 49 optimal weight: 10.0000 chunk 10 optimal weight: 0.9980 chunk 45 optimal weight: 1.9990 chunk 64 optimal weight: 1.9990 chunk 95 optimal weight: 0.9980 chunk 101 optimal weight: 1.9990 chunk 50 optimal weight: 2.9990 chunk 90 optimal weight: 6.9990 chunk 27 optimal weight: 0.6980 overall best weight: 0.9380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 91 HIS ** A 123 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 188 GLN B 91 HIS ** B 123 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 304 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** b 334 GLN C 91 HIS ** c 337 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 415 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7881 moved from start: 0.5003 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.070 9618 Z= 0.270 Angle : 0.865 10.523 13032 Z= 0.434 Chirality : 0.052 0.315 1632 Planarity : 0.003 0.031 1557 Dihedral : 10.772 68.226 2514 Min Nonbonded Distance : 2.328 Molprobity Statistics. All-atom Clashscore : 11.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.39 % Favored : 92.61 % Rotamer: Outliers : 5.26 % Allowed : 15.25 % Favored : 79.50 % Cbeta Deviations : 0.10 % 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: -0.51 (0.25), residues: 1056 helix: 0.75 (0.27), residues: 336 sheet: -0.24 (0.43), residues: 144 loop : -1.01 (0.25), residues: 576 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP A 195 HIS 0.011 0.001 HIS C 123 PHE 0.013 0.002 PHE c 292 TYR 0.021 0.001 TYR B 149 ARG 0.005 0.001 ARG a 355 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2112 Ramachandran restraints generated. 1056 Oldfield, 0 Emsley, 1056 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2112 Ramachandran restraints generated. 1056 Oldfield, 0 Emsley, 1056 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 246 residues out of total 951 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 196 time to evaluate : 1.414 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 115 LYS cc_start: 0.8319 (mmtm) cc_final: 0.8003 (mmtm) REVERT: A 171 TYR cc_start: 0.7124 (OUTLIER) cc_final: 0.5424 (p90) REVERT: A 199 TYR cc_start: 0.6693 (OUTLIER) cc_final: 0.5171 (m-80) REVERT: b 262 THR cc_start: 0.9149 (OUTLIER) cc_final: 0.8885 (m) REVERT: b 310 ASP cc_start: 0.8579 (m-30) cc_final: 0.8162 (t0) REVERT: b 401 ASP cc_start: 0.8476 (m-30) cc_final: 0.8158 (m-30) REVERT: C 148 GLN cc_start: 0.8504 (mm110) cc_final: 0.8074 (tm-30) REVERT: C 191 MET cc_start: 0.8301 (mmm) cc_final: 0.8002 (mmm) REVERT: c 356 ASP cc_start: 0.8273 (t0) cc_final: 0.7932 (t0) outliers start: 50 outliers final: 38 residues processed: 225 average time/residue: 0.2583 time to fit residues: 76.7343 Evaluate side-chains 213 residues out of total 951 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 172 time to evaluate : 0.922 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 99 GLU Chi-restraints excluded: chain A residue 116 PHE Chi-restraints excluded: chain A residue 118 ASN Chi-restraints excluded: chain A residue 136 ILE Chi-restraints excluded: chain A residue 171 TYR Chi-restraints excluded: chain A residue 195 TRP Chi-restraints excluded: chain A residue 199 TYR Chi-restraints excluded: chain A residue 245 SER Chi-restraints excluded: chain a residue 266 SER Chi-restraints excluded: chain a residue 283 MET Chi-restraints excluded: chain a residue 295 THR Chi-restraints excluded: chain a residue 376 THR Chi-restraints excluded: chain B residue 81 MET Chi-restraints excluded: chain B residue 99 GLU Chi-restraints excluded: chain B residue 116 PHE Chi-restraints excluded: chain B residue 121 ASP Chi-restraints excluded: chain B residue 123 HIS Chi-restraints excluded: chain B residue 195 TRP Chi-restraints excluded: chain B residue 241 LEU Chi-restraints excluded: chain B residue 245 SER Chi-restraints excluded: chain b residue 262 THR Chi-restraints excluded: chain b residue 266 SER Chi-restraints excluded: chain b residue 291 CYS Chi-restraints excluded: chain b residue 360 ILE Chi-restraints excluded: chain b residue 376 THR Chi-restraints excluded: chain b residue 414 LEU Chi-restraints excluded: chain C residue 81 MET Chi-restraints excluded: chain C residue 99 GLU Chi-restraints excluded: chain C residue 116 PHE Chi-restraints excluded: chain C residue 121 ASP Chi-restraints excluded: chain C residue 136 ILE Chi-restraints excluded: chain C residue 171 TYR Chi-restraints excluded: chain C residue 195 TRP Chi-restraints excluded: chain C residue 241 LEU Chi-restraints excluded: chain c residue 260 THR Chi-restraints excluded: chain c residue 266 SER Chi-restraints excluded: chain c residue 291 CYS Chi-restraints excluded: chain c residue 323 ARG Chi-restraints excluded: chain c residue 354 LEU Chi-restraints excluded: chain c residue 360 ILE Chi-restraints excluded: chain c residue 376 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 84 optimal weight: 0.2980 chunk 57 optimal weight: 0.9990 chunk 1 optimal weight: 0.9980 chunk 75 optimal weight: 0.9990 chunk 41 optimal weight: 20.0000 chunk 86 optimal weight: 0.9990 chunk 70 optimal weight: 5.9990 chunk 0 optimal weight: 4.9990 chunk 51 optimal weight: 2.9990 chunk 91 optimal weight: 3.9990 chunk 25 optimal weight: 0.9990 overall best weight: 0.8586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 188 GLN ** B 123 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 304 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** b 330 GLN ** c 337 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 415 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7887 moved from start: 0.5346 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.072 9618 Z= 0.258 Angle : 0.849 9.882 13032 Z= 0.422 Chirality : 0.052 0.331 1632 Planarity : 0.003 0.035 1557 Dihedral : 10.366 64.633 2514 Min Nonbonded Distance : 2.335 Molprobity Statistics. All-atom Clashscore : 11.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.33 % Favored : 91.67 % Rotamer: Outliers : 5.99 % Allowed : 15.77 % Favored : 78.23 % Cbeta Deviations : 0.10 % 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: -0.49 (0.25), residues: 1056 helix: 0.83 (0.27), residues: 336 sheet: -0.25 (0.44), residues: 144 loop : -1.05 (0.26), residues: 576 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP A 195 HIS 0.007 0.001 HIS c 304 PHE 0.019 0.002 PHE B 116 TYR 0.025 0.001 TYR A 149 ARG 0.007 0.001 ARG b 383 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2112 Ramachandran restraints generated. 1056 Oldfield, 0 Emsley, 1056 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2112 Ramachandran restraints generated. 1056 Oldfield, 0 Emsley, 1056 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 256 residues out of total 951 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 57 poor density : 199 time to evaluate : 1.016 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: A 115 LYS cc_start: 0.8242 (mmtm) cc_final: 0.7956 (mmtm) REVERT: A 152 MET cc_start: 0.8328 (tmm) cc_final: 0.8091 (tmm) REVERT: A 171 TYR cc_start: 0.7166 (OUTLIER) cc_final: 0.5497 (p90) REVERT: A 193 MET cc_start: 0.8467 (tpp) cc_final: 0.8264 (tpp) REVERT: A 199 TYR cc_start: 0.6685 (OUTLIER) cc_final: 0.5168 (m-80) REVERT: b 262 THR cc_start: 0.9090 (OUTLIER) cc_final: 0.8823 (m) REVERT: b 310 ASP cc_start: 0.8488 (m-30) cc_final: 0.8185 (t0) REVERT: b 334 GLN cc_start: 0.7376 (pt0) cc_final: 0.7073 (mp10) REVERT: b 352 ASN cc_start: 0.8894 (m-40) cc_final: 0.8629 (m-40) REVERT: b 401 ASP cc_start: 0.8508 (m-30) cc_final: 0.8257 (m-30) REVERT: b 409 MET cc_start: 0.7537 (mtp) cc_final: 0.7334 (mtp) REVERT: C 148 GLN cc_start: 0.8431 (mm110) cc_final: 0.8036 (tm-30) REVERT: C 191 MET cc_start: 0.8236 (mmm) cc_final: 0.7930 (mmm) REVERT: C 210 ASP cc_start: 0.6497 (p0) cc_final: 0.5936 (p0) REVERT: c 303 LYS cc_start: 0.7702 (mmtt) cc_final: 0.7501 (mmmt) REVERT: c 356 ASP cc_start: 0.8269 (t0) cc_final: 0.7917 (t0) REVERT: c 404 GLN cc_start: 0.8038 (tp40) cc_final: 0.7311 (tp40) REVERT: c 408 ASN cc_start: 0.8578 (m-40) cc_final: 0.8325 (m-40) outliers start: 57 outliers final: 39 residues processed: 230 average time/residue: 0.2414 time to fit residues: 74.2724 Evaluate side-chains 218 residues out of total 951 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 176 time to evaluate : 0.942 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 99 GLU Chi-restraints excluded: chain A residue 116 PHE Chi-restraints excluded: chain A residue 118 ASN Chi-restraints excluded: chain A residue 123 HIS Chi-restraints excluded: chain A residue 136 ILE Chi-restraints excluded: chain A residue 171 TYR Chi-restraints excluded: chain A residue 195 TRP Chi-restraints excluded: chain A residue 199 TYR Chi-restraints excluded: chain A residue 227 GLU Chi-restraints excluded: chain A residue 245 SER Chi-restraints excluded: chain a residue 266 SER Chi-restraints excluded: chain a residue 291 CYS Chi-restraints excluded: chain a residue 323 ARG Chi-restraints excluded: chain a residue 376 THR Chi-restraints excluded: chain B residue 81 MET Chi-restraints excluded: chain B residue 99 GLU Chi-restraints excluded: chain B residue 116 PHE Chi-restraints excluded: chain B residue 121 ASP Chi-restraints excluded: chain B residue 123 HIS Chi-restraints excluded: chain B residue 195 TRP Chi-restraints excluded: chain B residue 241 LEU Chi-restraints excluded: chain B residue 245 SER Chi-restraints excluded: chain b residue 262 THR Chi-restraints excluded: chain b residue 266 SER Chi-restraints excluded: chain b residue 283 MET Chi-restraints excluded: chain b residue 291 CYS Chi-restraints excluded: chain b residue 304 HIS Chi-restraints excluded: chain b residue 360 ILE Chi-restraints excluded: chain b residue 376 THR Chi-restraints excluded: chain b residue 414 LEU Chi-restraints excluded: chain C residue 81 MET Chi-restraints excluded: chain C residue 91 HIS Chi-restraints excluded: chain C residue 116 PHE Chi-restraints excluded: chain C residue 121 ASP Chi-restraints excluded: chain C residue 136 ILE Chi-restraints excluded: chain C residue 171 TYR Chi-restraints excluded: chain C residue 195 TRP Chi-restraints excluded: chain c residue 266 SER Chi-restraints excluded: chain c residue 291 CYS Chi-restraints excluded: chain c residue 323 ARG Chi-restraints excluded: chain c residue 336 ILE Chi-restraints excluded: chain c residue 376 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 34 optimal weight: 2.9990 chunk 91 optimal weight: 2.9990 chunk 20 optimal weight: 10.0000 chunk 59 optimal weight: 0.7980 chunk 25 optimal weight: 3.9990 chunk 101 optimal weight: 3.9990 chunk 84 optimal weight: 2.9990 chunk 47 optimal weight: 6.9990 chunk 8 optimal weight: 3.9990 chunk 33 optimal weight: 0.9980 chunk 53 optimal weight: 4.9990 overall best weight: 2.1586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 123 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 169 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 304 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 337 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7991 moved from start: 0.5595 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.084 9618 Z= 0.389 Angle : 0.924 11.739 13032 Z= 0.455 Chirality : 0.056 0.358 1632 Planarity : 0.004 0.027 1557 Dihedral : 10.449 59.927 2514 Min Nonbonded Distance : 2.339 Molprobity Statistics. All-atom Clashscore : 12.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.19 % Favored : 90.81 % Rotamer: Outliers : 6.10 % Allowed : 16.72 % Favored : 77.18 % Cbeta Deviations : 0.10 % 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: -0.85 (0.25), residues: 1056 helix: 0.64 (0.26), residues: 354 sheet: -0.65 (0.42), residues: 153 loop : -1.36 (0.26), residues: 549 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP A 195 HIS 0.010 0.001 HIS B 123 PHE 0.013 0.002 PHE c 292 TYR 0.024 0.002 TYR c 418 ARG 0.008 0.001 ARG b 383 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2112 Ramachandran restraints generated. 1056 Oldfield, 0 Emsley, 1056 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2112 Ramachandran restraints generated. 1056 Oldfield, 0 Emsley, 1056 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 234 residues out of total 951 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 58 poor density : 176 time to evaluate : 1.010 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: A 95 MET cc_start: 0.7506 (ttt) cc_final: 0.7231 (ttt) REVERT: A 115 LYS cc_start: 0.8322 (mmtm) cc_final: 0.8007 (mmtm) REVERT: A 171 TYR cc_start: 0.7213 (OUTLIER) cc_final: 0.5512 (p90) REVERT: A 199 TYR cc_start: 0.6712 (OUTLIER) cc_final: 0.5327 (m-80) REVERT: b 401 ASP cc_start: 0.8593 (m-30) cc_final: 0.8263 (m-30) REVERT: C 148 GLN cc_start: 0.8536 (mm110) cc_final: 0.7980 (tm-30) REVERT: C 152 MET cc_start: 0.8120 (tmm) cc_final: 0.7851 (tmm) REVERT: C 191 MET cc_start: 0.8316 (mmm) cc_final: 0.7992 (mmt) REVERT: c 356 ASP cc_start: 0.8356 (t0) cc_final: 0.8005 (t0) outliers start: 58 outliers final: 44 residues processed: 213 average time/residue: 0.2447 time to fit residues: 69.4417 Evaluate side-chains 209 residues out of total 951 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 163 time to evaluate : 0.843 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 91 HIS Chi-restraints excluded: chain A residue 99 GLU Chi-restraints excluded: chain A residue 116 PHE Chi-restraints excluded: chain A residue 118 ASN Chi-restraints excluded: chain A residue 123 HIS Chi-restraints excluded: chain A residue 136 ILE Chi-restraints excluded: chain A residue 171 TYR Chi-restraints excluded: chain A residue 195 TRP Chi-restraints excluded: chain A residue 199 TYR Chi-restraints excluded: chain a residue 260 THR Chi-restraints excluded: chain a residue 266 SER Chi-restraints excluded: chain a residue 291 CYS Chi-restraints excluded: chain a residue 323 ARG Chi-restraints excluded: chain a residue 359 CYS Chi-restraints excluded: chain a residue 360 ILE Chi-restraints excluded: chain a residue 376 THR Chi-restraints excluded: chain B residue 81 MET Chi-restraints excluded: chain B residue 99 GLU Chi-restraints excluded: chain B residue 116 PHE Chi-restraints excluded: chain B residue 121 ASP Chi-restraints excluded: chain B residue 123 HIS Chi-restraints excluded: chain B residue 195 TRP Chi-restraints excluded: chain B residue 241 LEU Chi-restraints excluded: chain B residue 245 SER Chi-restraints excluded: chain b residue 266 SER Chi-restraints excluded: chain b residue 291 CYS Chi-restraints excluded: chain b residue 304 HIS Chi-restraints excluded: chain b residue 359 CYS Chi-restraints excluded: chain b residue 360 ILE Chi-restraints excluded: chain b residue 376 THR Chi-restraints excluded: chain b residue 414 LEU Chi-restraints excluded: chain C residue 70 LEU Chi-restraints excluded: chain C residue 81 MET Chi-restraints excluded: chain C residue 116 PHE Chi-restraints excluded: chain C residue 121 ASP Chi-restraints excluded: chain C residue 123 HIS Chi-restraints excluded: chain C residue 171 TYR Chi-restraints excluded: chain C residue 195 TRP Chi-restraints excluded: chain C residue 241 LEU Chi-restraints excluded: chain c residue 266 SER Chi-restraints excluded: chain c residue 291 CYS Chi-restraints excluded: chain c residue 323 ARG Chi-restraints excluded: chain c residue 336 ILE Chi-restraints excluded: chain c residue 359 CYS Chi-restraints excluded: chain c residue 360 ILE Chi-restraints excluded: chain c residue 376 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 97 optimal weight: 0.8980 chunk 11 optimal weight: 5.9990 chunk 57 optimal weight: 0.0470 chunk 74 optimal weight: 0.9990 chunk 85 optimal weight: 0.8980 chunk 56 optimal weight: 0.9990 chunk 101 optimal weight: 0.9980 chunk 63 optimal weight: 1.9990 chunk 61 optimal weight: 0.9980 chunk 46 optimal weight: 0.9980 chunk 62 optimal weight: 0.9980 overall best weight: 0.7678 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: a 337 ASN ** b 304 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 337 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7920 moved from start: 0.5826 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.075 9618 Z= 0.260 Angle : 0.874 13.245 13032 Z= 0.430 Chirality : 0.053 0.347 1632 Planarity : 0.003 0.025 1557 Dihedral : 9.975 57.867 2514 Min Nonbonded Distance : 2.369 Molprobity Statistics. All-atom Clashscore : 10.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.09 % Favored : 90.91 % Rotamer: Outliers : 5.05 % Allowed : 17.98 % Favored : 76.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % 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: -0.86 (0.25), residues: 1056 helix: 0.61 (0.27), residues: 357 sheet: -0.73 (0.42), residues: 153 loop : -1.34 (0.26), residues: 546 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP A 195 HIS 0.010 0.001 HIS B 123 PHE 0.014 0.001 PHE a 292 TYR 0.014 0.001 TYR c 418 ARG 0.004 0.001 ARG c 383 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2112 Ramachandran restraints generated. 1056 Oldfield, 0 Emsley, 1056 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2112 Ramachandran restraints generated. 1056 Oldfield, 0 Emsley, 1056 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 232 residues out of total 951 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 184 time to evaluate : 1.049 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 95 MET cc_start: 0.7370 (ttt) cc_final: 0.7113 (ttt) REVERT: A 115 LYS cc_start: 0.8277 (mmtm) cc_final: 0.7984 (mmtm) REVERT: A 171 TYR cc_start: 0.7178 (OUTLIER) cc_final: 0.5517 (p90) REVERT: A 193 MET cc_start: 0.8557 (tpp) cc_final: 0.8351 (tpp) REVERT: A 199 TYR cc_start: 0.6791 (OUTLIER) cc_final: 0.5274 (m-80) REVERT: a 404 GLN cc_start: 0.8058 (tp40) cc_final: 0.7705 (tp40) REVERT: B 193 MET cc_start: 0.8287 (tpp) cc_final: 0.7759 (ttm) REVERT: b 352 ASN cc_start: 0.8942 (m-40) cc_final: 0.8703 (m-40) REVERT: b 401 ASP cc_start: 0.8573 (m-30) cc_final: 0.8276 (m-30) REVERT: b 405 GLN cc_start: 0.8189 (tt0) cc_final: 0.7909 (tt0) REVERT: C 191 MET cc_start: 0.8224 (mmm) cc_final: 0.7993 (mmt) REVERT: C 193 MET cc_start: 0.8190 (tpp) cc_final: 0.7566 (ttm) REVERT: c 356 ASP cc_start: 0.8167 (t0) cc_final: 0.7957 (t0) outliers start: 48 outliers final: 38 residues processed: 216 average time/residue: 0.2537 time to fit residues: 73.4136 Evaluate side-chains 208 residues out of total 951 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 168 time to evaluate : 1.024 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 70 LEU Chi-restraints excluded: chain A residue 91 HIS Chi-restraints excluded: chain A residue 99 GLU Chi-restraints excluded: chain A residue 116 PHE Chi-restraints excluded: chain A residue 118 ASN Chi-restraints excluded: chain A residue 123 HIS Chi-restraints excluded: chain A residue 136 ILE Chi-restraints excluded: chain A residue 171 TYR Chi-restraints excluded: chain A residue 195 TRP Chi-restraints excluded: chain A residue 199 TYR Chi-restraints excluded: chain A residue 211 CYS Chi-restraints excluded: chain A residue 227 GLU Chi-restraints excluded: chain a residue 266 SER Chi-restraints excluded: chain a residue 291 CYS Chi-restraints excluded: chain a residue 323 ARG Chi-restraints excluded: chain a residue 337 ASN Chi-restraints excluded: chain B residue 99 GLU Chi-restraints excluded: chain B residue 123 HIS Chi-restraints excluded: chain B residue 195 TRP Chi-restraints excluded: chain B residue 211 CYS Chi-restraints excluded: chain B residue 245 SER Chi-restraints excluded: chain b residue 266 SER Chi-restraints excluded: chain b residue 283 MET Chi-restraints excluded: chain b residue 291 CYS Chi-restraints excluded: chain b residue 304 HIS Chi-restraints excluded: chain b residue 359 CYS Chi-restraints excluded: chain b residue 414 LEU Chi-restraints excluded: chain C residue 116 PHE Chi-restraints excluded: chain C residue 123 HIS Chi-restraints excluded: chain C residue 136 ILE Chi-restraints excluded: chain C residue 171 TYR Chi-restraints excluded: chain C residue 195 TRP Chi-restraints excluded: chain C residue 245 SER Chi-restraints excluded: chain c residue 266 SER Chi-restraints excluded: chain c residue 291 CYS Chi-restraints excluded: chain c residue 292 PHE Chi-restraints excluded: chain c residue 323 ARG Chi-restraints excluded: chain c residue 336 ILE Chi-restraints excluded: chain c residue 360 ILE Chi-restraints excluded: chain c residue 376 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 40 optimal weight: 0.6980 chunk 60 optimal weight: 0.2980 chunk 30 optimal weight: 0.6980 chunk 19 optimal weight: 0.0170 chunk 64 optimal weight: 0.9990 chunk 68 optimal weight: 0.9990 chunk 50 optimal weight: 0.9980 chunk 9 optimal weight: 4.9990 chunk 79 optimal weight: 3.9990 chunk 92 optimal weight: 0.8980 chunk 96 optimal weight: 3.9990 overall best weight: 0.5218 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 123 HIS ** A 130 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** a 337 ASN ** b 304 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 337 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7906 moved from start: 0.5960 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.074 9618 Z= 0.248 Angle : 0.878 13.282 13032 Z= 0.433 Chirality : 0.054 0.389 1632 Planarity : 0.003 0.032 1557 Dihedral : 9.793 59.826 2514 Min Nonbonded Distance : 2.394 Molprobity Statistics. All-atom Clashscore : 11.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.19 % Favored : 90.81 % Rotamer: Outliers : 4.52 % Allowed : 18.30 % Favored : 77.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.82 (0.26), residues: 1056 helix: 0.75 (0.27), residues: 354 sheet: -0.70 (0.42), residues: 153 loop : -1.38 (0.26), residues: 549 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 195 HIS 0.010 0.001 HIS C 91 PHE 0.033 0.002 PHE B 116 TYR 0.013 0.001 TYR c 418 ARG 0.006 0.001 ARG b 383 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2112 Ramachandran restraints generated. 1056 Oldfield, 0 Emsley, 1056 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2112 Ramachandran restraints generated. 1056 Oldfield, 0 Emsley, 1056 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 233 residues out of total 951 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 190 time to evaluate : 1.021 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 115 LYS cc_start: 0.8186 (mmtm) cc_final: 0.7913 (mmtm) REVERT: A 171 TYR cc_start: 0.7331 (OUTLIER) cc_final: 0.5699 (p90) REVERT: A 199 TYR cc_start: 0.6744 (OUTLIER) cc_final: 0.5218 (m-80) REVERT: a 404 GLN cc_start: 0.7977 (tp40) cc_final: 0.7581 (tp40) REVERT: B 193 MET cc_start: 0.8436 (tpp) cc_final: 0.7990 (ttm) REVERT: b 306 GLU cc_start: 0.8249 (mm-30) cc_final: 0.7822 (mm-30) REVERT: b 346 ASP cc_start: 0.7833 (t0) cc_final: 0.7381 (t0) REVERT: b 352 ASN cc_start: 0.8898 (m-40) cc_final: 0.8605 (m-40) REVERT: b 401 ASP cc_start: 0.8585 (m-30) cc_final: 0.8256 (m-30) REVERT: C 191 MET cc_start: 0.8167 (mmm) cc_final: 0.7933 (mmt) REVERT: C 193 MET cc_start: 0.8175 (tpp) cc_final: 0.7480 (ttm) outliers start: 43 outliers final: 35 residues processed: 218 average time/residue: 0.2442 time to fit residues: 71.2576 Evaluate side-chains 213 residues out of total 951 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 176 time to evaluate : 1.140 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 70 LEU Chi-restraints excluded: chain A residue 91 HIS Chi-restraints excluded: chain A residue 99 GLU Chi-restraints excluded: chain A residue 116 PHE Chi-restraints excluded: chain A residue 118 ASN Chi-restraints excluded: chain A residue 123 HIS Chi-restraints excluded: chain A residue 136 ILE Chi-restraints excluded: chain A residue 171 TYR Chi-restraints excluded: chain A residue 195 TRP Chi-restraints excluded: chain A residue 199 TYR Chi-restraints excluded: chain a residue 266 SER Chi-restraints excluded: chain a residue 291 CYS Chi-restraints excluded: chain a residue 359 CYS Chi-restraints excluded: chain a residue 376 THR Chi-restraints excluded: chain B residue 99 GLU Chi-restraints excluded: chain B residue 123 HIS Chi-restraints excluded: chain B residue 171 TYR Chi-restraints excluded: chain B residue 195 TRP Chi-restraints excluded: chain b residue 266 SER Chi-restraints excluded: chain b residue 291 CYS Chi-restraints excluded: chain b residue 304 HIS Chi-restraints excluded: chain b residue 359 CYS Chi-restraints excluded: chain b residue 387 VAL Chi-restraints excluded: chain b residue 414 LEU Chi-restraints excluded: chain C residue 116 PHE Chi-restraints excluded: chain C residue 123 HIS Chi-restraints excluded: chain C residue 130 HIS Chi-restraints excluded: chain C residue 171 TYR Chi-restraints excluded: chain C residue 195 TRP Chi-restraints excluded: chain C residue 245 SER Chi-restraints excluded: chain c residue 266 SER Chi-restraints excluded: chain c residue 291 CYS Chi-restraints excluded: chain c residue 292 PHE Chi-restraints excluded: chain c residue 336 ILE Chi-restraints excluded: chain c residue 359 CYS Chi-restraints excluded: chain c residue 360 ILE Chi-restraints excluded: chain c residue 376 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 88 optimal weight: 3.9990 chunk 94 optimal weight: 3.9990 chunk 96 optimal weight: 1.9990 chunk 56 optimal weight: 3.9990 chunk 41 optimal weight: 6.9990 chunk 74 optimal weight: 2.9990 chunk 28 optimal weight: 2.9990 chunk 85 optimal weight: 0.9980 chunk 89 optimal weight: 1.9990 chunk 93 optimal weight: 0.6980 chunk 61 optimal weight: 6.9990 overall best weight: 1.7386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 130 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 304 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 334 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 337 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7976 moved from start: 0.6103 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.081 9618 Z= 0.340 Angle : 0.930 13.559 13032 Z= 0.457 Chirality : 0.055 0.361 1632 Planarity : 0.003 0.025 1557 Dihedral : 9.929 59.978 2514 Min Nonbonded Distance : 2.416 Molprobity Statistics. All-atom Clashscore : 12.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.66 % Favored : 90.34 % Rotamer: Outliers : 4.73 % Allowed : 18.82 % Favored : 76.45 % 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: -0.85 (0.26), residues: 1056 helix: 0.87 (0.28), residues: 348 sheet: -0.73 (0.42), residues: 153 loop : -1.49 (0.26), residues: 555 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP A 195 HIS 0.022 0.001 HIS A 123 PHE 0.025 0.002 PHE B 116 TYR 0.008 0.001 TYR C 199 ARG 0.012 0.001 ARG b 355 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2112 Ramachandran restraints generated. 1056 Oldfield, 0 Emsley, 1056 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2112 Ramachandran restraints generated. 1056 Oldfield, 0 Emsley, 1056 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 231 residues out of total 951 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 186 time to evaluate : 1.062 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: A 95 MET cc_start: 0.7463 (ttt) cc_final: 0.7168 (ttt) REVERT: A 115 LYS cc_start: 0.8280 (mmtm) cc_final: 0.8010 (mmtm) REVERT: A 171 TYR cc_start: 0.7331 (OUTLIER) cc_final: 0.5665 (p90) REVERT: A 193 MET cc_start: 0.8479 (tpp) cc_final: 0.7917 (ttm) REVERT: A 199 TYR cc_start: 0.6806 (OUTLIER) cc_final: 0.5281 (m-80) REVERT: a 404 GLN cc_start: 0.8114 (tp40) cc_final: 0.7747 (tp40) REVERT: B 193 MET cc_start: 0.8494 (tpp) cc_final: 0.8057 (ttm) REVERT: b 346 ASP cc_start: 0.7643 (t0) cc_final: 0.7422 (t0) REVERT: b 401 ASP cc_start: 0.8579 (m-30) cc_final: 0.8322 (m-30) REVERT: C 191 MET cc_start: 0.8181 (mmm) cc_final: 0.7918 (mmt) REVERT: c 409 MET cc_start: 0.7587 (mtp) cc_final: 0.7120 (mtp) outliers start: 45 outliers final: 39 residues processed: 213 average time/residue: 0.2482 time to fit residues: 70.9250 Evaluate side-chains 213 residues out of total 951 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 172 time to evaluate : 1.014 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 70 LEU Chi-restraints excluded: chain A residue 91 HIS Chi-restraints excluded: chain A residue 99 GLU Chi-restraints excluded: chain A residue 116 PHE Chi-restraints excluded: chain A residue 118 ASN Chi-restraints excluded: chain A residue 136 ILE Chi-restraints excluded: chain A residue 171 TYR Chi-restraints excluded: chain A residue 195 TRP Chi-restraints excluded: chain A residue 199 TYR Chi-restraints excluded: chain A residue 211 CYS Chi-restraints excluded: chain a residue 266 SER Chi-restraints excluded: chain a residue 291 CYS Chi-restraints excluded: chain a residue 333 ILE Chi-restraints excluded: chain a residue 359 CYS Chi-restraints excluded: chain a residue 376 THR Chi-restraints excluded: chain B residue 70 LEU Chi-restraints excluded: chain B residue 99 GLU Chi-restraints excluded: chain B residue 123 HIS Chi-restraints excluded: chain B residue 171 TYR Chi-restraints excluded: chain B residue 195 TRP Chi-restraints excluded: chain b residue 266 SER Chi-restraints excluded: chain b residue 291 CYS Chi-restraints excluded: chain b residue 304 HIS Chi-restraints excluded: chain b residue 359 CYS Chi-restraints excluded: chain b residue 376 THR Chi-restraints excluded: chain b residue 387 VAL Chi-restraints excluded: chain b residue 414 LEU Chi-restraints excluded: chain C residue 81 MET Chi-restraints excluded: chain C residue 116 PHE Chi-restraints excluded: chain C residue 123 HIS Chi-restraints excluded: chain C residue 136 ILE Chi-restraints excluded: chain C residue 171 TYR Chi-restraints excluded: chain C residue 195 TRP Chi-restraints excluded: chain C residue 245 SER Chi-restraints excluded: chain c residue 266 SER Chi-restraints excluded: chain c residue 291 CYS Chi-restraints excluded: chain c residue 323 ARG Chi-restraints excluded: chain c residue 336 ILE Chi-restraints excluded: chain c residue 359 CYS Chi-restraints excluded: chain c residue 360 ILE Chi-restraints excluded: chain c residue 376 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 99 optimal weight: 0.9990 chunk 60 optimal weight: 0.9990 chunk 47 optimal weight: 4.9990 chunk 69 optimal weight: 5.9990 chunk 104 optimal weight: 5.9990 chunk 96 optimal weight: 3.9990 chunk 83 optimal weight: 4.9990 chunk 8 optimal weight: 0.9980 chunk 64 optimal weight: 0.8980 chunk 51 optimal weight: 1.9990 chunk 66 optimal weight: 2.9990 overall best weight: 1.1786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** b 304 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7952 moved from start: 0.6276 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.079 9618 Z= 0.290 Angle : 0.924 13.459 13032 Z= 0.456 Chirality : 0.054 0.370 1632 Planarity : 0.003 0.041 1557 Dihedral : 9.500 59.567 2514 Min Nonbonded Distance : 2.380 Molprobity Statistics. All-atom Clashscore : 12.07 Ramachandran Plot: Outliers : 0.09 % Allowed : 9.75 % Favored : 90.15 % Rotamer: Outliers : 4.52 % Allowed : 19.56 % Favored : 75.92 % 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: -0.82 (0.26), residues: 1056 helix: 0.93 (0.28), residues: 345 sheet: -0.46 (0.48), residues: 123 loop : -1.53 (0.25), residues: 588 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP c 282 HIS 0.003 0.001 HIS c 304 PHE 0.024 0.002 PHE B 116 TYR 0.010 0.001 TYR a 418 ARG 0.009 0.001 ARG b 383 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2112 Ramachandran restraints generated. 1056 Oldfield, 0 Emsley, 1056 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2112 Ramachandran restraints generated. 1056 Oldfield, 0 Emsley, 1056 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 220 residues out of total 951 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 177 time to evaluate : 1.016 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 95 MET cc_start: 0.7338 (ttt) cc_final: 0.7049 (ttt) REVERT: A 171 TYR cc_start: 0.7451 (OUTLIER) cc_final: 0.5869 (p90) REVERT: A 193 MET cc_start: 0.8550 (tpp) cc_final: 0.7813 (ttm) REVERT: A 199 TYR cc_start: 0.6768 (OUTLIER) cc_final: 0.5258 (m-80) REVERT: a 306 GLU cc_start: 0.8087 (mm-30) cc_final: 0.7834 (mm-30) REVERT: a 404 GLN cc_start: 0.8083 (tp40) cc_final: 0.7703 (tp40) REVERT: B 193 MET cc_start: 0.8482 (tpp) cc_final: 0.8047 (ttm) REVERT: b 302 GLU cc_start: 0.7782 (tp30) cc_final: 0.7577 (tp30) REVERT: b 306 GLU cc_start: 0.8228 (mm-30) cc_final: 0.8016 (mm-30) REVERT: b 401 ASP cc_start: 0.8570 (m-30) cc_final: 0.8287 (m-30) REVERT: C 191 MET cc_start: 0.8126 (mmm) cc_final: 0.7889 (mmt) REVERT: C 193 MET cc_start: 0.8197 (tpp) cc_final: 0.7497 (ttm) REVERT: c 404 GLN cc_start: 0.8126 (tp40) cc_final: 0.7790 (tp40) outliers start: 43 outliers final: 39 residues processed: 208 average time/residue: 0.2357 time to fit residues: 65.7304 Evaluate side-chains 208 residues out of total 951 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 167 time to evaluate : 0.936 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 70 LEU Chi-restraints excluded: chain A residue 91 HIS Chi-restraints excluded: chain A residue 99 GLU Chi-restraints excluded: chain A residue 118 ASN Chi-restraints excluded: chain A residue 123 HIS Chi-restraints excluded: chain A residue 136 ILE Chi-restraints excluded: chain A residue 171 TYR Chi-restraints excluded: chain A residue 195 TRP Chi-restraints excluded: chain A residue 199 TYR Chi-restraints excluded: chain A residue 211 CYS Chi-restraints excluded: chain A residue 227 GLU Chi-restraints excluded: chain a residue 266 SER Chi-restraints excluded: chain a residue 291 CYS Chi-restraints excluded: chain a residue 323 ARG Chi-restraints excluded: chain a residue 359 CYS Chi-restraints excluded: chain a residue 376 THR Chi-restraints excluded: chain B residue 70 LEU Chi-restraints excluded: chain B residue 99 GLU Chi-restraints excluded: chain B residue 123 HIS Chi-restraints excluded: chain B residue 130 HIS Chi-restraints excluded: chain B residue 171 TYR Chi-restraints excluded: chain B residue 195 TRP Chi-restraints excluded: chain b residue 266 SER Chi-restraints excluded: chain b residue 291 CYS Chi-restraints excluded: chain b residue 304 HIS Chi-restraints excluded: chain b residue 359 CYS Chi-restraints excluded: chain b residue 387 VAL Chi-restraints excluded: chain b residue 414 LEU Chi-restraints excluded: chain C residue 116 PHE Chi-restraints excluded: chain C residue 123 HIS Chi-restraints excluded: chain C residue 130 HIS Chi-restraints excluded: chain C residue 171 TYR Chi-restraints excluded: chain C residue 195 TRP Chi-restraints excluded: chain C residue 245 SER Chi-restraints excluded: chain c residue 266 SER Chi-restraints excluded: chain c residue 291 CYS Chi-restraints excluded: chain c residue 323 ARG Chi-restraints excluded: chain c residue 336 ILE Chi-restraints excluded: chain c residue 359 CYS Chi-restraints excluded: chain c residue 360 ILE Chi-restraints excluded: chain c residue 376 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 88 optimal weight: 0.9990 chunk 25 optimal weight: 3.9990 chunk 76 optimal weight: 6.9990 chunk 12 optimal weight: 4.9990 chunk 23 optimal weight: 8.9990 chunk 83 optimal weight: 0.9990 chunk 34 optimal weight: 0.0060 chunk 85 optimal weight: 0.0030 chunk 10 optimal weight: 5.9990 chunk 15 optimal weight: 1.9990 chunk 73 optimal weight: 0.8980 overall best weight: 0.5810 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** b 304 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3809 r_free = 0.3809 target = 0.122278 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3416 r_free = 0.3416 target = 0.096379 restraints weight = 19019.576| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3465 r_free = 0.3465 target = 0.099410 restraints weight = 12998.143| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3497 r_free = 0.3497 target = 0.101450 restraints weight = 10248.053| |-----------------------------------------------------------------------------| r_work (final): 0.3507 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7704 moved from start: 0.6417 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.067 9618 Z= 0.253 Angle : 0.910 12.429 13032 Z= 0.450 Chirality : 0.053 0.373 1632 Planarity : 0.003 0.034 1557 Dihedral : 9.094 59.976 2514 Min Nonbonded Distance : 2.401 Molprobity Statistics. All-atom Clashscore : 11.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.66 % Favored : 90.34 % Rotamer: Outliers : 4.63 % Allowed : 19.77 % Favored : 75.60 % 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: -0.65 (0.26), residues: 1056 helix: 1.25 (0.28), residues: 330 sheet: -0.61 (0.47), residues: 126 loop : -1.41 (0.26), residues: 600 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP A 195 HIS 0.009 0.001 HIS B 123 PHE 0.017 0.001 PHE B 116 TYR 0.011 0.001 TYR a 418 ARG 0.006 0.001 ARG a 383 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2188.24 seconds wall clock time: 40 minutes 18.10 seconds (2418.10 seconds total)