Starting phenix.real_space_refine on Sat Aug 23 05:32:23 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8tye_41715/08_2025/8tye_41715.cif Found real_map, /net/cci-nas-00/data/ceres_data/8tye_41715/08_2025/8tye_41715.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8tye_41715/08_2025/8tye_41715.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8tye_41715/08_2025/8tye_41715.map" model { file = "/net/cci-nas-00/data/ceres_data/8tye_41715/08_2025/8tye_41715.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8tye_41715/08_2025/8tye_41715.cif" } resolution = 3.8 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.008 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 90 5.16 5 C 6178 2.51 5 N 1630 2.21 5 O 2023 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 9921 Number of models: 1 Model: "" Number of chains: 33 Chain: "H" Number of atoms: 580 Number of conformers: 1 Conformer: "" Number of residues, atoms: 116, 580 Classifications: {'peptide': 116} Incomplete info: {'truncation_to_alanine': 116} Link IDs: {'TRANS': 115} Unresolved non-hydrogen bonds: 232 Unresolved non-hydrogen angles: 348 Unresolved non-hydrogen dihedrals: 116 Planarities with less than four sites: {'UNK:plan-1': 116} Unresolved non-hydrogen planarities: 116 Chain: "L" Number of atoms: 510 Number of conformers: 1 Conformer: "" Number of residues, atoms: 102, 510 Classifications: {'peptide': 102} Incomplete info: {'truncation_to_alanine': 102} Link IDs: {'TRANS': 101} Chain breaks: 1 Unresolved non-hydrogen bonds: 204 Unresolved non-hydrogen angles: 306 Unresolved non-hydrogen dihedrals: 102 Planarities with less than four sites: {'UNK:plan-1': 102} Unresolved non-hydrogen planarities: 102 Chain: "C" Number of atoms: 1459 Number of conformers: 1 Conformer: "" Number of residues, atoms: 182, 1459 Classifications: {'peptide': 182} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 177} Chain breaks: 2 Chain: "A" Number of atoms: 1459 Number of conformers: 1 Conformer: "" Number of residues, atoms: 182, 1459 Classifications: {'peptide': 182} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 177} Chain breaks: 2 Chain: "B" Number of atoms: 1463 Number of conformers: 1 Conformer: "" Number of residues, atoms: 183, 1463 Classifications: {'peptide': 183} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 178} Chain breaks: 2 Chain: "c" Number of atoms: 1251 Number of conformers: 1 Conformer: "" Number of residues, atoms: 155, 1251 Classifications: {'peptide': 155} Link IDs: {'PTRANS': 4, 'TRANS': 150} Chain: "a" Number of atoms: 1189 Number of conformers: 1 Conformer: "" Number of residues, atoms: 146, 1189 Classifications: {'peptide': 146} Link IDs: {'PTRANS': 3, 'TRANS': 142} Chain breaks: 1 Chain: "b" Number of atoms: 1189 Number of conformers: 1 Conformer: "" Number of residues, atoms: 146, 1189 Classifications: {'peptide': 146} Link IDs: {'PTRANS': 3, 'TRANS': 142} Chain breaks: 1 Chain: "D" Number of atoms: 24 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 24 Unusual residues: {'FUC': 1, 'NAG': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "E" Number of atoms: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 50 Unusual residues: {'BMA': 1, 'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "F" Number of atoms: 38 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 38 Unusual residues: {'FUC': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "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: "I" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "J" Number of atoms: 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: 38 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 38 Unusual residues: {'FUC': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "M" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "N" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "O" Number of atoms: 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: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "Q" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "R" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "S" Number of atoms: 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: "T" 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: "U" Number of atoms: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 50 Unusual residues: {'BMA': 1, 'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 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: 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: "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: "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: "A" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 42 Unusual residues: {'NAG': 3} 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: "B" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 42 Unusual residues: {'NAG': 3} 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: "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: "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 Time building chain proxies: 2.26, per 1000 atoms: 0.23 Number of scatterers: 9921 At special positions: 0 Unit cell: (104.4, 97.15, 103.675, 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 90 16.00 O 2023 8.00 N 1630 7.00 C 6178 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=21, symmetry=0 Simple disulfide: pdb=" SG CYS C 86 " - pdb=" SG CYS C 231 " distance=1.66 Simple disulfide: pdb=" SG CYS C 118 " - pdb=" SG CYS C 155 " distance=2.03 Simple disulfide: pdb=" SG CYS C 180 " - pdb=" SG CYS C 212 " distance=2.03 Simple disulfide: pdb=" SG CYS C 207 " - pdb=" SG CYS c 360 " distance=2.03 Simple disulfide: pdb=" SG CYS A 86 " - pdb=" SG CYS A 231 " distance=2.03 Simple disulfide: pdb=" SG CYS A 118 " - pdb=" SG CYS A 155 " distance=2.02 Simple disulfide: pdb=" SG CYS A 180 " - pdb=" SG CYS A 212 " distance=2.03 Simple disulfide: pdb=" SG CYS A 207 " - pdb=" SG CYS a 360 " distance=2.03 Simple disulfide: pdb=" SG CYS B 86 " - pdb=" SG CYS B 231 " distance=2.03 Simple disulfide: pdb=" SG CYS B 118 " - pdb=" SG CYS B 155 " distance=2.03 Simple disulfide: pdb=" SG CYS B 180 " - pdb=" SG CYS B 212 " distance=2.02 Simple disulfide: pdb=" SG CYS B 207 " - pdb=" SG CYS b 360 " distance=2.04 Simple disulfide: pdb=" SG CYS c 279 " - pdb=" SG CYS c 292 " distance=2.03 Simple disulfide: pdb=" SG CYS c 301 " - pdb=" SG CYS c 310 " distance=2.03 Simple disulfide: pdb=" SG CYS c 364 " - pdb=" SG CYS c 385 " distance=2.02 Simple disulfide: pdb=" SG CYS a 279 " - pdb=" SG CYS a 292 " distance=2.03 Simple disulfide: pdb=" SG CYS a 301 " - pdb=" SG CYS a 310 " distance=2.03 Simple disulfide: pdb=" SG CYS a 364 " - pdb=" SG CYS a 385 " distance=2.03 Simple disulfide: pdb=" SG CYS b 279 " - pdb=" SG CYS b 292 " distance=2.03 Simple disulfide: pdb=" SG CYS b 301 " - pdb=" SG CYS b 310 " distance=2.03 Simple disulfide: pdb=" SG CYS b 364 " - pdb=" SG CYS b 385 " distance=2.02 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 ALPHA1-6 " BMA E 3 " - " MAN E 4 " " BMA U 3 " - " MAN U 4 " BETA1-4 " NAG E 1 " - " NAG E 2 " " NAG E 2 " - " BMA E 3 " " NAG F 1 " - " NAG F 2 " " NAG G 1 " - " NAG G 2 " " NAG I 1 " - " NAG I 2 " " NAG J 1 " - " NAG J 2 " " NAG K 1 " - " NAG K 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 Q 1 " - " NAG Q 2 " " NAG R 1 " - " NAG R 2 " " NAG S 1 " - " NAG S 2 " " NAG S 2 " - " BMA S 3 " " NAG T 1 " - " NAG T 2 " " NAG T 2 " - " BMA T 3 " " NAG U 1 " - " NAG U 2 " " NAG U 2 " - " BMA U 3 " " NAG V 1 " - " NAG V 2 " " NAG W 1 " - " NAG W 2 " " NAG W 2 " - " BMA W 3 " " NAG X 1 " - " NAG X 2 " BETA1-6 " NAG D 1 " - " FUC D 2 " ~> Even though FUC is an alpha isomer, a beta linkage is required... " NAG F 1 " - " FUC F 3 " " NAG K 1 " - " FUC K 3 " NAG-ASN " NAG A 301 " - " ASN A 109 " " NAG A 302 " - " ASN A 89 " " NAG A 303 " - " ASN A 99 " " NAG B 301 " - " ASN B 89 " " NAG B 302 " - " ASN B 99 " " NAG B 303 " - " ASN B 119 " " NAG C 301 " - " ASN C 89 " " NAG C 302 " - " ASN C 99 " " NAG D 1 " - " ASN C 109 " " NAG E 1 " - " ASN C 79 " " NAG F 1 " - " ASN C 119 " " NAG G 1 " - " ASN C 167 " " NAG I 1 " - " ASN C 224 " " NAG J 1 " - " ASN A 79 " " NAG K 1 " - " ASN A 119 " " NAG M 1 " - " ASN A 167 " " NAG N 1 " - " ASN A 224 " " NAG O 1 " - " ASN B 79 " " NAG P 1 " - " ASN B 109 " " NAG Q 1 " - " ASN B 167 " " NAG R 1 " - " ASN B 224 " " NAG S 1 " - " ASN c 365 " " NAG T 1 " - " ASN c 373 " " NAG U 1 " - " ASN a 365 " " NAG V 1 " - " ASN a 373 " " NAG W 1 " - " ASN b 365 " " NAG X 1 " - " ASN b 373 " " NAG a 701 " - " ASN a 395 " " NAG a 702 " - " ASN a 390 " " NAG b 701 " - " ASN b 390 " " NAG b 702 " - " ASN b 395 " " NAG c 701 " - " ASN c 390 " " NAG c 702 " - " ASN c 395 " Time building additional restraints: 0.94 Conformation dependent library (CDL) restraints added in 267.4 milliseconds Enol-peptide restraints added in 715.3 nanoseconds 1932 Ramachandran restraints generated. 966 Oldfield, 0 Emsley, 966 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2322 Finding SS restraints... Secondary structure from input PDB file: 37 helices and 14 sheets defined 39.1% alpha, 15.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.32 Creating SS restraints... Processing helix chain 'H' and resid 69 through 73 Processing helix chain 'L' and resid 50 through 52 No H-bonds generated for 'chain 'L' and resid 50 through 52' Processing helix chain 'C' and resid 75 through 80 removed outlier: 4.345A pdb=" N MET C 80 " --> pdb=" O THR C 77 " (cutoff:3.500A) Processing helix chain 'C' and resid 119 through 127 Processing helix chain 'C' and resid 130 through 143 Processing helix chain 'C' and resid 157 through 161 removed outlier: 3.987A pdb=" N LYS C 161 " --> pdb=" O ASN C 158 " (cutoff:3.500A) Processing helix chain 'C' and resid 182 through 195 removed outlier: 4.054A pdb=" N GLY C 186 " --> pdb=" O THR C 182 " (cutoff:3.500A) Processing helix chain 'C' and resid 238 through 247 removed outlier: 3.949A pdb=" N SER C 246 " --> pdb=" O LEU C 242 " (cutoff:3.500A) removed outlier: 3.892A pdb=" N GLN C 247 " --> pdb=" O GLY C 243 " (cutoff:3.500A) Processing helix chain 'A' and resid 74 through 80 removed outlier: 3.793A pdb=" N THR A 77 " --> pdb=" O ASN A 74 " (cutoff:3.500A) removed outlier: 4.414A pdb=" N MET A 80 " --> pdb=" O THR A 77 " (cutoff:3.500A) Processing helix chain 'A' and resid 119 through 127 Processing helix chain 'A' and resid 130 through 143 Processing helix chain 'A' and resid 157 through 161 removed outlier: 3.867A pdb=" N GLY A 160 " --> pdb=" O PHE A 157 " (cutoff:3.500A) Processing helix chain 'A' and resid 182 through 195 removed outlier: 4.049A pdb=" N GLY A 186 " --> pdb=" O THR A 182 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N ARG A 193 " --> pdb=" O GLN A 189 " (cutoff:3.500A) Processing helix chain 'A' and resid 238 through 245 removed outlier: 3.669A pdb=" N LEU A 245 " --> pdb=" O TYR A 241 " (cutoff:3.500A) Processing helix chain 'A' and resid 246 through 249 removed outlier: 4.476A pdb=" N THR A 249 " --> pdb=" O SER A 246 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 246 through 249' Processing helix chain 'B' and resid 74 through 81 removed outlier: 4.042A pdb=" N THR B 77 " --> pdb=" O ASN B 74 " (cutoff:3.500A) removed outlier: 4.254A pdb=" N MET B 80 " --> pdb=" O THR B 77 " (cutoff:3.500A) Processing helix chain 'B' and resid 119 through 127 Processing helix chain 'B' and resid 130 through 143 Processing helix chain 'B' and resid 157 through 161 removed outlier: 3.588A pdb=" N GLY B 160 " --> pdb=" O PHE B 157 " (cutoff:3.500A) Processing helix chain 'B' and resid 182 through 195 removed outlier: 3.943A pdb=" N GLY B 186 " --> pdb=" O THR B 182 " (cutoff:3.500A) Processing helix chain 'B' and resid 238 through 246 removed outlier: 4.061A pdb=" N SER B 246 " --> pdb=" O LEU B 242 " (cutoff:3.500A) Processing helix chain 'c' and resid 294 through 301 removed outlier: 3.802A pdb=" N LYS c 300 " --> pdb=" O THR c 296 " (cutoff:3.500A) removed outlier: 3.853A pdb=" N CYS c 301 " --> pdb=" O ALA c 297 " (cutoff:3.500A) Processing helix chain 'c' and resid 307 through 325 removed outlier: 3.674A pdb=" N ASP c 311 " --> pdb=" O GLU c 307 " (cutoff:3.500A) Processing helix chain 'c' and resid 334 through 345 removed outlier: 6.162A pdb=" N ASN c 342 " --> pdb=" O ASN c 338 " (cutoff:3.500A) removed outlier: 5.351A pdb=" N ALA c 343 " --> pdb=" O LYS c 339 " (cutoff:3.500A) Processing helix chain 'c' and resid 346 through 359 removed outlier: 3.950A pdb=" N ILE c 350 " --> pdb=" O ASN c 346 " (cutoff:3.500A) Processing helix chain 'c' and resid 399 through 414 removed outlier: 3.590A pdb=" N ILE c 403 " --> pdb=" O PHE c 399 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N THR c 412 " --> pdb=" O ASP c 408 " (cutoff:3.500A) removed outlier: 3.992A pdb=" N GLU c 413 " --> pdb=" O ASN c 409 " (cutoff:3.500A) removed outlier: 4.068A pdb=" N MET c 414 " --> pdb=" O MET c 410 " (cutoff:3.500A) Processing helix chain 'a' and resid 294 through 302 removed outlier: 3.548A pdb=" N VAL a 298 " --> pdb=" O GLY a 294 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N CYS a 301 " --> pdb=" O ALA a 297 " (cutoff:3.500A) removed outlier: 4.032A pdb=" N ASN a 302 " --> pdb=" O VAL a 298 " (cutoff:3.500A) Processing helix chain 'a' and resid 308 through 326 Processing helix chain 'a' and resid 334 through 339 Processing helix chain 'a' and resid 346 through 359 removed outlier: 3.827A pdb=" N ILE a 350 " --> pdb=" O ASN a 346 " (cutoff:3.500A) Processing helix chain 'a' and resid 399 through 413 removed outlier: 4.039A pdb=" N GLU a 413 " --> pdb=" O ASN a 409 " (cutoff:3.500A) Processing helix chain 'b' and resid 294 through 304 removed outlier: 3.577A pdb=" N VAL b 298 " --> pdb=" O GLY b 294 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N ASN b 302 " --> pdb=" O VAL b 298 " (cutoff:3.500A) removed outlier: 4.234A pdb=" N GLU b 303 " --> pdb=" O ALA b 299 " (cutoff:3.500A) Processing helix chain 'b' and resid 307 through 326 removed outlier: 3.822A pdb=" N GLN b 324 " --> pdb=" O LYS b 320 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N LEU b 326 " --> pdb=" O ALA b 322 " (cutoff:3.500A) Processing helix chain 'b' and resid 334 through 340 removed outlier: 3.669A pdb=" N ALA b 340 " --> pdb=" O LEU b 336 " (cutoff:3.500A) Processing helix chain 'b' and resid 346 through 359 removed outlier: 3.533A pdb=" N ILE b 350 " --> pdb=" O ASN b 346 " (cutoff:3.500A) Processing helix chain 'b' and resid 396 through 398 No H-bonds generated for 'chain 'b' and resid 396 through 398' Processing helix chain 'b' and resid 399 through 414 removed outlier: 4.007A pdb=" N GLU b 413 " --> pdb=" O ASN b 409 " (cutoff:3.500A) removed outlier: 4.092A pdb=" N MET b 414 " --> pdb=" O MET b 410 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'H' and resid 35A through 38 Processing sheet with id=AA2, first strand: chain 'H' and resid 65 through 68 Processing sheet with id=AA3, first strand: chain 'L' and resid 35 through 37 Processing sheet with id=AA4, first strand: chain 'L' and resid 48 through 49 Processing sheet with id=AA5, first strand: chain 'C' and resid 61 through 62 removed outlier: 3.518A pdb=" N TYR C 66 " --> pdb=" O TYR C 62 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N TYR c 371 " --> pdb=" O GLN C 69 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 84 through 85 Processing sheet with id=AA7, first strand: chain 'A' and resid 66 through 72 removed outlier: 4.008A pdb=" N ASN a 365 " --> pdb=" O TRP a 386 " (cutoff:3.500A) removed outlier: 8.142A pdb=" N TRP a 386 " --> pdb=" O ASN a 365 " (cutoff:3.500A) removed outlier: 8.999A pdb=" N SER a 367 " --> pdb=" O LYS a 384 " (cutoff:3.500A) removed outlier: 10.446A pdb=" N LYS a 384 " --> pdb=" O SER a 367 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 84 through 86 Processing sheet with id=AA9, first strand: chain 'B' and resid 61 through 62 Processing sheet with id=AB1, first strand: chain 'B' and resid 84 through 87 Processing sheet with id=AB2, first strand: chain 'c' and resid 278 through 280 Processing sheet with id=AB3, first strand: chain 'c' and resid 388 through 389 Processing sheet with id=AB4, first strand: chain 'b' and resid 278 through 280 Processing sheet with id=AB5, first strand: chain 'b' and resid 388 through 389 removed outlier: 3.540A pdb=" N SER b 389 " --> pdb=" O SER b 392 " (cutoff:3.500A) 331 hydrogen bonds defined for protein. 873 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.33 Time building geometry restraints manager: 1.14 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.34: 3035 1.34 - 1.46: 2528 1.46 - 1.59: 4387 1.59 - 1.71: 0 1.71 - 1.83: 138 Bond restraints: 10088 Sorted by residual: bond pdb=" C SER C 237 " pdb=" N PRO C 238 " ideal model delta sigma weight residual 1.331 1.354 -0.023 7.90e-03 1.60e+04 8.27e+00 bond pdb=" N TRP a 264 " pdb=" CA TRP a 264 " ideal model delta sigma weight residual 1.456 1.491 -0.035 1.23e-02 6.61e+03 8.21e+00 bond pdb=" N ILE b 286 " pdb=" CA ILE b 286 " ideal model delta sigma weight residual 1.459 1.492 -0.034 1.19e-02 7.06e+03 8.01e+00 bond pdb=" N ILE b 337 " pdb=" CA ILE b 337 " ideal model delta sigma weight residual 1.460 1.494 -0.034 1.21e-02 6.83e+03 7.95e+00 bond pdb=" N PHE b 262 " pdb=" CA PHE b 262 " ideal model delta sigma weight residual 1.455 1.490 -0.036 1.27e-02 6.20e+03 7.85e+00 ... (remaining 10083 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.89: 12801 1.89 - 3.78: 728 3.78 - 5.67: 128 5.67 - 7.56: 30 7.56 - 9.45: 7 Bond angle restraints: 13694 Sorted by residual: angle pdb=" CB LYS A 63 " pdb=" CG LYS A 63 " pdb=" CD LYS A 63 " ideal model delta sigma weight residual 111.30 120.18 -8.88 2.30e+00 1.89e-01 1.49e+01 angle pdb=" CA CYS C 86 " pdb=" CB CYS C 86 " pdb=" SG CYS C 86 " ideal model delta sigma weight residual 114.40 122.70 -8.30 2.30e+00 1.89e-01 1.30e+01 angle pdb=" N ILE b 334 " pdb=" CA ILE b 334 " pdb=" C ILE b 334 " ideal model delta sigma weight residual 113.07 108.19 4.88 1.36e+00 5.41e-01 1.29e+01 angle pdb=" N ASN a 365 " pdb=" CA ASN a 365 " pdb=" C ASN a 365 " ideal model delta sigma weight residual 113.28 109.01 4.27 1.22e+00 6.72e-01 1.22e+01 angle pdb=" N ALA b 330 " pdb=" CA ALA b 330 " pdb=" C ALA b 330 " ideal model delta sigma weight residual 111.28 107.48 3.80 1.09e+00 8.42e-01 1.22e+01 ... (remaining 13689 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 22.26: 6360 22.26 - 44.52: 337 44.52 - 66.78: 63 66.78 - 89.04: 43 89.04 - 111.30: 22 Dihedral angle restraints: 6825 sinusoidal: 3260 harmonic: 3565 Sorted by residual: dihedral pdb=" CB CYS a 364 " pdb=" SG CYS a 364 " pdb=" SG CYS a 385 " pdb=" CB CYS a 385 " ideal model delta sinusoidal sigma weight residual -86.00 -169.64 83.64 1 1.00e+01 1.00e-02 8.54e+01 dihedral pdb=" CB CYS B 207 " pdb=" SG CYS B 207 " pdb=" SG CYS b 360 " pdb=" CB CYS b 360 " ideal model delta sinusoidal sigma weight residual -86.00 -32.94 -53.06 1 1.00e+01 1.00e-02 3.83e+01 dihedral pdb=" CB CYS C 207 " pdb=" SG CYS C 207 " pdb=" SG CYS c 360 " pdb=" CB CYS c 360 " ideal model delta sinusoidal sigma weight residual 93.00 130.83 -37.83 1 1.00e+01 1.00e-02 2.02e+01 ... (remaining 6822 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.148: 1695 0.148 - 0.296: 42 0.296 - 0.444: 6 0.444 - 0.592: 1 0.592 - 0.741: 2 Chirality restraints: 1746 Sorted by residual: chirality pdb=" C1 NAG T 2 " pdb=" O4 NAG T 1 " pdb=" C2 NAG T 2 " pdb=" O5 NAG T 2 " both_signs ideal model delta sigma weight residual False -2.40 -1.74 -0.66 2.00e-02 2.50e+03 1.10e+03 chirality pdb=" C1 BMA E 3 " pdb=" O4 NAG E 2 " pdb=" C2 BMA E 3 " pdb=" O5 BMA E 3 " both_signs ideal model delta sigma weight residual False -2.40 -1.99 -0.41 2.00e-02 2.50e+03 4.11e+02 chirality pdb=" C1 BMA U 3 " pdb=" O4 NAG U 2 " pdb=" C2 BMA U 3 " pdb=" O5 BMA U 3 " both_signs ideal model delta sigma weight residual False -2.40 -2.09 -0.31 2.00e-02 2.50e+03 2.33e+02 ... (remaining 1743 not shown) Planarity restraints: 1697 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 NAG T 2 " -0.370 2.00e-02 2.50e+03 3.17e-01 1.25e+03 pdb=" C7 NAG T 2 " 0.091 2.00e-02 2.50e+03 pdb=" C8 NAG T 2 " -0.124 2.00e-02 2.50e+03 pdb=" N2 NAG T 2 " 0.562 2.00e-02 2.50e+03 pdb=" O7 NAG T 2 " -0.159 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG E 2 " -0.346 2.00e-02 2.50e+03 2.97e-01 1.10e+03 pdb=" C7 NAG E 2 " 0.080 2.00e-02 2.50e+03 pdb=" C8 NAG E 2 " -0.035 2.00e-02 2.50e+03 pdb=" N2 NAG E 2 " 0.516 2.00e-02 2.50e+03 pdb=" O7 NAG E 2 " -0.215 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG U 1 " 0.334 2.00e-02 2.50e+03 2.88e-01 1.04e+03 pdb=" C7 NAG U 1 " -0.083 2.00e-02 2.50e+03 pdb=" C8 NAG U 1 " 0.148 2.00e-02 2.50e+03 pdb=" N2 NAG U 1 " -0.512 2.00e-02 2.50e+03 pdb=" O7 NAG U 1 " 0.113 2.00e-02 2.50e+03 ... (remaining 1694 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 838 2.74 - 3.28: 10384 3.28 - 3.82: 15616 3.82 - 4.36: 18268 4.36 - 4.90: 31112 Nonbonded interactions: 76218 Sorted by model distance: nonbonded pdb=" OG1 THR C 81 " pdb=" OD1 ASN c 319 " model vdw 2.202 3.040 nonbonded pdb=" OD1 ASP b 311 " pdb=" NH2 ARG b 314 " model vdw 2.247 3.120 nonbonded pdb=" NZ LYS A 116 " pdb=" O7 NAG M 1 " model vdw 2.248 3.120 nonbonded pdb=" N GLY a 277 " pdb=" OD1 ASN a 295 " model vdw 2.253 3.120 nonbonded pdb=" NH2 ARG C 256 " pdb=" OG SER A 255 " model vdw 2.256 3.120 ... (remaining 76213 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' and resid 60 through 302) selection = (chain 'B' and (resid 60 through 197 or resid 207 through 302)) selection = chain 'C' } ncs_group { reference = (chain 'D' and resid 1) selection = (chain 'G' and resid 1) selection = (chain 'I' and resid 1) selection = (chain 'J' and resid 1) selection = (chain 'M' and resid 1) selection = (chain 'N' and resid 1) selection = (chain 'O' and resid 1) selection = (chain 'P' and resid 1) selection = (chain 'Q' and resid 1) selection = (chain 'R' and resid 1) selection = (chain 'V' and resid 1) selection = (chain 'X' and resid 1) } ncs_group { reference = chain 'E' selection = chain 'U' } ncs_group { reference = (chain 'F' and resid 1 through 2) selection = (chain 'K' and resid 1 through 2) selection = (chain 'S' and resid 1 through 2) selection = (chain 'T' and resid 1 through 2) selection = (chain 'W' and resid 1 through 2) } ncs_group { reference = (chain 'H' and resid 15 through 109) selection = chain 'L' } ncs_group { reference = chain 'a' selection = chain 'b' selection = (chain 'c' and (resid 260 through 267 or resid 277 through 702)) } 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=0.00 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: 7.950 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.170 Check model and map are aligned: 0.020 Set scattering table: 0.030 Process input model: 9.180 Find NCS groups from input model: 0.150 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.440 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 18.960 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7478 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 : 0.007 0.371 10170 Z= 0.356 Angle : 1.116 33.157 13919 Z= 0.534 Chirality : 0.064 0.741 1746 Planarity : 0.025 0.317 1664 Dihedral : 16.149 111.296 4440 Min Nonbonded Distance : 2.202 Molprobity Statistics. All-atom Clashscore : 5.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.73 % Favored : 96.27 % Rotamer: Outliers : 0.00 % Allowed : 0.78 % Favored : 99.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.26 (0.26), residues: 966 helix: -0.10 (0.27), residues: 309 sheet: -1.70 (0.40), residues: 158 loop : -0.92 (0.28), residues: 499 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG B 248 TYR 0.025 0.002 TYR a 363 PHE 0.019 0.002 PHE a 318 TRP 0.055 0.003 TRP a 386 HIS 0.014 0.002 HIS c 354 Details of bonding type rmsd covalent geometry : bond 0.00597 (10088) covalent geometry : angle 1.01734 (13694) SS BOND : bond 0.08105 ( 21) SS BOND : angle 6.03196 ( 42) hydrogen bonds : bond 0.17996 ( 331) hydrogen bonds : angle 6.83614 ( 873) link_ALPHA1-6 : bond 0.00298 ( 2) link_ALPHA1-6 : angle 2.39482 ( 6) link_BETA1-4 : bond 0.00797 ( 23) link_BETA1-4 : angle 3.21603 ( 69) link_BETA1-6 : bond 0.00429 ( 3) link_BETA1-6 : angle 1.32919 ( 9) link_NAG-ASN : bond 0.00550 ( 33) link_NAG-ASN : angle 2.96456 ( 99) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1932 Ramachandran restraints generated. 966 Oldfield, 0 Emsley, 966 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1932 Ramachandran restraints generated. 966 Oldfield, 0 Emsley, 966 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 321 residues out of total 901 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 321 time to evaluate : 0.346 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 211 ASP cc_start: 0.8193 (t0) cc_final: 0.7896 (t0) REVERT: A 129 TYR cc_start: 0.7807 (p90) cc_final: 0.7553 (p90) REVERT: A 193 ARG cc_start: 0.8223 (mtp180) cc_final: 0.7683 (mtp180) REVERT: A 194 MET cc_start: 0.7239 (tpp) cc_final: 0.6654 (tpp) REVERT: B 76 GLU cc_start: 0.8296 (mt-10) cc_final: 0.7995 (mp0) REVERT: B 151 GLU cc_start: 0.8432 (mm-30) cc_final: 0.8043 (mm-30) REVERT: B 153 MET cc_start: 0.8447 (ttm) cc_final: 0.8245 (ttm) REVERT: B 245 LEU cc_start: 0.9402 (mt) cc_final: 0.8993 (tt) REVERT: c 286 ILE cc_start: 0.8907 (pt) cc_final: 0.7969 (pt) REVERT: c 295 ASN cc_start: 0.8628 (t0) cc_final: 0.8226 (t0) REVERT: c 379 ARG cc_start: 0.8248 (mmp80) cc_final: 0.7884 (mmm160) REVERT: a 357 ASP cc_start: 0.8690 (t70) cc_final: 0.8330 (t0) REVERT: a 363 TYR cc_start: 0.7670 (p90) cc_final: 0.7463 (p90) REVERT: a 398 HIS cc_start: 0.7501 (m-70) cc_final: 0.7151 (m-70) REVERT: b 358 ILE cc_start: 0.9104 (tt) cc_final: 0.8876 (tt) REVERT: b 381 SER cc_start: 0.8877 (p) cc_final: 0.8623 (t) REVERT: b 400 SER cc_start: 0.8552 (p) cc_final: 0.8327 (m) REVERT: b 414 MET cc_start: 0.6937 (mpp) cc_final: 0.6639 (mpp) outliers start: 0 outliers final: 0 residues processed: 321 average time/residue: 0.1042 time to fit residues: 44.9927 Evaluate side-chains 254 residues out of total 901 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 254 time to evaluate : 0.245 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 108 optimal weight: 0.9980 chunk 49 optimal weight: 1.9990 chunk 97 optimal weight: 0.6980 chunk 113 optimal weight: 4.9990 chunk 53 optimal weight: 0.9980 chunk 5 optimal weight: 10.0000 chunk 33 optimal weight: 3.9990 chunk 65 optimal weight: 0.7980 chunk 62 optimal weight: 5.9990 chunk 51 optimal weight: 2.9990 chunk 117 optimal weight: 0.5980 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 146 ASN c 354 HIS c 409 ASN a 335 GLN a 374 HIS b 335 GLN b 409 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3762 r_free = 0.3762 target = 0.129319 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3460 r_free = 0.3460 target = 0.108821 restraints weight = 21025.889| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3514 r_free = 0.3514 target = 0.112174 restraints weight = 11487.078| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3551 r_free = 0.3551 target = 0.114578 restraints weight = 7490.628| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.3576 r_free = 0.3576 target = 0.116255 restraints weight = 5457.435| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3591 r_free = 0.3591 target = 0.117296 restraints weight = 4285.013| |-----------------------------------------------------------------------------| r_work (final): 0.3592 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7732 moved from start: 0.1680 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 10170 Z= 0.154 Angle : 0.841 9.876 13919 Z= 0.373 Chirality : 0.046 0.349 1746 Planarity : 0.004 0.036 1664 Dihedral : 11.962 82.210 2534 Min Nonbonded Distance : 2.477 Molprobity Statistics. All-atom Clashscore : 5.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.69 % Favored : 97.31 % Rotamer: Outliers : 1.44 % Allowed : 11.43 % Favored : 87.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.86 (0.26), residues: 966 helix: 0.30 (0.28), residues: 333 sheet: -1.49 (0.41), residues: 143 loop : -0.81 (0.28), residues: 490 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG C 248 TYR 0.020 0.001 TYR B 241 PHE 0.021 0.002 PHE b 399 TRP 0.028 0.002 TRP C 227 HIS 0.009 0.001 HIS B 93 Details of bonding type rmsd covalent geometry : bond 0.00333 (10088) covalent geometry : angle 0.79160 (13694) SS BOND : bond 0.00499 ( 21) SS BOND : angle 1.33023 ( 42) hydrogen bonds : bond 0.04771 ( 331) hydrogen bonds : angle 5.47833 ( 873) link_ALPHA1-6 : bond 0.00964 ( 2) link_ALPHA1-6 : angle 3.21416 ( 6) link_BETA1-4 : bond 0.00970 ( 23) link_BETA1-4 : angle 2.79665 ( 69) link_BETA1-6 : bond 0.00480 ( 3) link_BETA1-6 : angle 1.37090 ( 9) link_NAG-ASN : bond 0.00451 ( 33) link_NAG-ASN : angle 2.39440 ( 99) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1932 Ramachandran restraints generated. 966 Oldfield, 0 Emsley, 966 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1932 Ramachandran restraints generated. 966 Oldfield, 0 Emsley, 966 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 284 residues out of total 901 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 271 time to evaluate : 0.297 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 247 GLN cc_start: 0.8522 (tm-30) cc_final: 0.8270 (tm-30) REVERT: A 129 TYR cc_start: 0.8009 (p90) cc_final: 0.7669 (p90) REVERT: A 194 MET cc_start: 0.7038 (tpp) cc_final: 0.6456 (tpp) REVERT: B 67 GLU cc_start: 0.8318 (tp30) cc_final: 0.8004 (tp30) REVERT: B 76 GLU cc_start: 0.8291 (mt-10) cc_final: 0.7928 (mp0) REVERT: B 245 LEU cc_start: 0.9511 (mt) cc_final: 0.9010 (tt) REVERT: B 257 ARG cc_start: 0.8439 (mtm180) cc_final: 0.8232 (mtm-85) REVERT: c 295 ASN cc_start: 0.8421 (t0) cc_final: 0.8206 (t0) REVERT: a 357 ASP cc_start: 0.8712 (t70) cc_final: 0.8408 (t0) REVERT: a 398 HIS cc_start: 0.7545 (m-70) cc_final: 0.7181 (m-70) REVERT: a 402 ASP cc_start: 0.8731 (t70) cc_final: 0.8488 (t70) REVERT: a 410 MET cc_start: 0.8600 (tpp) cc_final: 0.8177 (tpp) REVERT: b 358 ILE cc_start: 0.9142 (tt) cc_final: 0.8910 (tt) REVERT: b 381 SER cc_start: 0.8939 (p) cc_final: 0.8435 (t) REVERT: b 400 SER cc_start: 0.8520 (p) cc_final: 0.8168 (m) outliers start: 13 outliers final: 10 residues processed: 275 average time/residue: 0.0973 time to fit residues: 36.7343 Evaluate side-chains 254 residues out of total 901 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 244 time to evaluate : 0.335 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 97 VAL Chi-restraints excluded: chain A residue 110 THR Chi-restraints excluded: chain A residue 137 ILE Chi-restraints excluded: chain B residue 188 LEU Chi-restraints excluded: chain c residue 298 VAL Chi-restraints excluded: chain c residue 344 LEU Chi-restraints excluded: chain a residue 380 THR Chi-restraints excluded: chain a residue 389 SER Chi-restraints excluded: chain a residue 392 SER Chi-restraints excluded: chain b residue 321 GLN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 97 optimal weight: 0.6980 chunk 27 optimal weight: 0.4980 chunk 94 optimal weight: 1.9990 chunk 22 optimal weight: 4.9990 chunk 90 optimal weight: 5.9990 chunk 14 optimal weight: 9.9990 chunk 80 optimal weight: 0.8980 chunk 106 optimal weight: 4.9990 chunk 44 optimal weight: 2.9990 chunk 16 optimal weight: 9.9990 chunk 100 optimal weight: 1.9990 overall best weight: 1.2184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 179 HIS A 209 ASN c 354 HIS c 409 ASN a 374 HIS a 405 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3719 r_free = 0.3719 target = 0.126274 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3409 r_free = 0.3409 target = 0.105744 restraints weight = 21301.459| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 22)----------------| | r_work = 0.3460 r_free = 0.3460 target = 0.108948 restraints weight = 11858.193| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3496 r_free = 0.3496 target = 0.111302 restraints weight = 7898.457| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 46)----------------| | r_work = 0.3522 r_free = 0.3522 target = 0.112953 restraints weight = 5841.798| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3537 r_free = 0.3537 target = 0.114004 restraints weight = 4646.636| |-----------------------------------------------------------------------------| r_work (final): 0.3534 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7800 moved from start: 0.2193 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.059 10170 Z= 0.174 Angle : 0.787 10.021 13919 Z= 0.354 Chirality : 0.045 0.320 1746 Planarity : 0.003 0.030 1664 Dihedral : 10.102 78.984 2534 Min Nonbonded Distance : 2.517 Molprobity Statistics. All-atom Clashscore : 7.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.52 % Favored : 96.48 % Rotamer: Outliers : 3.11 % Allowed : 14.32 % Favored : 82.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.65 (0.27), residues: 966 helix: 0.59 (0.29), residues: 331 sheet: -1.54 (0.40), residues: 160 loop : -0.66 (0.29), residues: 475 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG C 248 TYR 0.018 0.001 TYR B 253 PHE 0.015 0.002 PHE b 399 TRP 0.035 0.002 TRP C 227 HIS 0.009 0.001 HIS B 93 Details of bonding type rmsd covalent geometry : bond 0.00391 (10088) covalent geometry : angle 0.73628 (13694) SS BOND : bond 0.00382 ( 21) SS BOND : angle 1.73396 ( 42) hydrogen bonds : bond 0.04219 ( 331) hydrogen bonds : angle 5.21964 ( 873) link_ALPHA1-6 : bond 0.01116 ( 2) link_ALPHA1-6 : angle 1.88930 ( 6) link_BETA1-4 : bond 0.00913 ( 23) link_BETA1-4 : angle 2.56267 ( 69) link_BETA1-6 : bond 0.00476 ( 3) link_BETA1-6 : angle 1.39527 ( 9) link_NAG-ASN : bond 0.00402 ( 33) link_NAG-ASN : angle 2.40596 ( 99) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1932 Ramachandran restraints generated. 966 Oldfield, 0 Emsley, 966 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1932 Ramachandran restraints generated. 966 Oldfield, 0 Emsley, 966 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 284 residues out of total 901 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 256 time to evaluate : 0.341 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 129 TYR cc_start: 0.7706 (p90) cc_final: 0.7478 (p90) REVERT: C 250 ARG cc_start: 0.8647 (mmm-85) cc_final: 0.8306 (ttp-170) REVERT: A 72 GLU cc_start: 0.7909 (mp0) cc_final: 0.7299 (mp0) REVERT: A 129 TYR cc_start: 0.8127 (p90) cc_final: 0.7826 (p90) REVERT: A 194 MET cc_start: 0.7320 (tpp) cc_final: 0.6837 (tpp) REVERT: B 76 GLU cc_start: 0.8315 (mt-10) cc_final: 0.7976 (mp0) REVERT: B 245 LEU cc_start: 0.9510 (mt) cc_final: 0.8994 (tt) REVERT: B 257 ARG cc_start: 0.8470 (mtm180) cc_final: 0.8210 (mtm-85) REVERT: c 295 ASN cc_start: 0.8434 (t0) cc_final: 0.8195 (t0) REVERT: c 321 GLN cc_start: 0.8285 (mt0) cc_final: 0.7970 (mt0) REVERT: a 398 HIS cc_start: 0.7661 (m-70) cc_final: 0.7259 (m-70) REVERT: a 402 ASP cc_start: 0.8765 (t70) cc_final: 0.8456 (t70) REVERT: a 409 ASN cc_start: 0.8782 (m-40) cc_final: 0.8568 (m-40) REVERT: b 358 ILE cc_start: 0.9156 (tt) cc_final: 0.8906 (tt) REVERT: b 400 SER cc_start: 0.8582 (p) cc_final: 0.8227 (m) outliers start: 28 outliers final: 19 residues processed: 269 average time/residue: 0.0846 time to fit residues: 31.6258 Evaluate side-chains 257 residues out of total 901 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 238 time to evaluate : 0.225 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 97 VAL Chi-restraints excluded: chain C residue 180 CYS Chi-restraints excluded: chain C residue 213 ILE Chi-restraints excluded: chain C residue 255 SER Chi-restraints excluded: chain A residue 101 THR Chi-restraints excluded: chain A residue 137 ILE Chi-restraints excluded: chain A residue 182 THR Chi-restraints excluded: chain A residue 229 ASP Chi-restraints excluded: chain B residue 118 CYS Chi-restraints excluded: chain B residue 188 LEU Chi-restraints excluded: chain B residue 258 LEU Chi-restraints excluded: chain c residue 298 VAL Chi-restraints excluded: chain c residue 400 SER Chi-restraints excluded: chain a residue 281 THR Chi-restraints excluded: chain a residue 389 SER Chi-restraints excluded: chain a residue 411 ILE Chi-restraints excluded: chain b residue 321 GLN Chi-restraints excluded: chain b residue 349 LEU Chi-restraints excluded: chain b residue 380 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 78 optimal weight: 1.9990 chunk 62 optimal weight: 4.9990 chunk 39 optimal weight: 4.9990 chunk 23 optimal weight: 2.9990 chunk 110 optimal weight: 0.9990 chunk 88 optimal weight: 4.9990 chunk 83 optimal weight: 2.9990 chunk 10 optimal weight: 9.9990 chunk 59 optimal weight: 0.0770 chunk 44 optimal weight: 1.9990 chunk 52 optimal weight: 5.9990 overall best weight: 1.6146 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 179 HIS ** B 93 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 141 HIS a 405 GLN b 374 HIS b 405 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3693 r_free = 0.3693 target = 0.124353 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3376 r_free = 0.3376 target = 0.103576 restraints weight = 21383.390| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3429 r_free = 0.3429 target = 0.106786 restraints weight = 12052.357| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3463 r_free = 0.3463 target = 0.108983 restraints weight = 8012.376| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3489 r_free = 0.3489 target = 0.110657 restraints weight = 6013.191| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3504 r_free = 0.3504 target = 0.111698 restraints weight = 4792.895| |-----------------------------------------------------------------------------| r_work (final): 0.3504 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7851 moved from start: 0.2575 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.040 10170 Z= 0.206 Angle : 0.833 16.726 13919 Z= 0.372 Chirality : 0.046 0.306 1746 Planarity : 0.003 0.034 1664 Dihedral : 9.518 80.329 2534 Min Nonbonded Distance : 2.465 Molprobity Statistics. All-atom Clashscore : 9.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.83 % Favored : 96.17 % Rotamer: Outliers : 3.22 % Allowed : 17.09 % Favored : 79.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.67 (0.27), residues: 966 helix: 0.46 (0.29), residues: 331 sheet: -1.22 (0.40), residues: 162 loop : -0.73 (0.29), residues: 473 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG B 250 TYR 0.023 0.002 TYR B 241 PHE 0.017 0.002 PHE A 157 TRP 0.053 0.002 TRP C 227 HIS 0.009 0.001 HIS B 93 Details of bonding type rmsd covalent geometry : bond 0.00462 (10088) covalent geometry : angle 0.78676 (13694) SS BOND : bond 0.00430 ( 21) SS BOND : angle 1.50714 ( 42) hydrogen bonds : bond 0.04167 ( 331) hydrogen bonds : angle 5.26827 ( 873) link_ALPHA1-6 : bond 0.01094 ( 2) link_ALPHA1-6 : angle 1.95116 ( 6) link_BETA1-4 : bond 0.00847 ( 23) link_BETA1-4 : angle 2.49788 ( 69) link_BETA1-6 : bond 0.00445 ( 3) link_BETA1-6 : angle 1.46413 ( 9) link_NAG-ASN : bond 0.00410 ( 33) link_NAG-ASN : angle 2.47665 ( 99) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1932 Ramachandran restraints generated. 966 Oldfield, 0 Emsley, 966 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1932 Ramachandran restraints generated. 966 Oldfield, 0 Emsley, 966 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 280 residues out of total 901 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 251 time to evaluate : 0.349 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 81 THR cc_start: 0.9084 (m) cc_final: 0.8572 (t) REVERT: C 82 MET cc_start: 0.8839 (pmm) cc_final: 0.8233 (pmm) REVERT: C 250 ARG cc_start: 0.8664 (mmm-85) cc_final: 0.8355 (ttp-170) REVERT: A 76 GLU cc_start: 0.7863 (mp0) cc_final: 0.7555 (mp0) REVERT: A 129 TYR cc_start: 0.8171 (p90) cc_final: 0.7857 (p90) REVERT: B 76 GLU cc_start: 0.8357 (mt-10) cc_final: 0.8007 (mp0) REVERT: B 245 LEU cc_start: 0.9502 (mt) cc_final: 0.8963 (tt) REVERT: B 257 ARG cc_start: 0.8502 (mtm180) cc_final: 0.8201 (mtm-85) REVERT: c 295 ASN cc_start: 0.8433 (t0) cc_final: 0.8198 (t0) REVERT: c 321 GLN cc_start: 0.8400 (mt0) cc_final: 0.8140 (mt0) REVERT: a 398 HIS cc_start: 0.7759 (m-70) cc_final: 0.7276 (m-70) REVERT: a 402 ASP cc_start: 0.8761 (t70) cc_final: 0.8510 (t0) REVERT: b 358 ILE cc_start: 0.9145 (tt) cc_final: 0.8930 (tt) REVERT: b 400 SER cc_start: 0.8608 (p) cc_final: 0.8231 (m) outliers start: 29 outliers final: 21 residues processed: 269 average time/residue: 0.0967 time to fit residues: 35.6423 Evaluate side-chains 262 residues out of total 901 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 241 time to evaluate : 0.330 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 97 VAL Chi-restraints excluded: chain C residue 118 CYS Chi-restraints excluded: chain C residue 180 CYS Chi-restraints excluded: chain C residue 255 SER Chi-restraints excluded: chain A residue 65 VAL Chi-restraints excluded: chain A residue 101 THR Chi-restraints excluded: chain A residue 110 THR Chi-restraints excluded: chain A residue 137 ILE Chi-restraints excluded: chain A residue 182 THR Chi-restraints excluded: chain A residue 229 ASP Chi-restraints excluded: chain B residue 118 CYS Chi-restraints excluded: chain B residue 188 LEU Chi-restraints excluded: chain c residue 298 VAL Chi-restraints excluded: chain c residue 400 SER Chi-restraints excluded: chain a residue 281 THR Chi-restraints excluded: chain a residue 380 THR Chi-restraints excluded: chain a residue 389 SER Chi-restraints excluded: chain a residue 399 PHE Chi-restraints excluded: chain b residue 321 GLN Chi-restraints excluded: chain b residue 349 LEU Chi-restraints excluded: chain b residue 380 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 78 optimal weight: 3.9990 chunk 16 optimal weight: 9.9990 chunk 95 optimal weight: 0.6980 chunk 15 optimal weight: 6.9990 chunk 0 optimal weight: 10.0000 chunk 32 optimal weight: 4.9990 chunk 14 optimal weight: 10.0000 chunk 42 optimal weight: 1.9990 chunk 87 optimal weight: 2.9990 chunk 113 optimal weight: 3.9990 chunk 86 optimal weight: 0.7980 overall best weight: 2.0986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 93 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 230 HIS A 74 ASN ** B 93 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 319 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** a 324 GLN a 405 GLN b 321 GLN b 406 GLN b 409 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3665 r_free = 0.3665 target = 0.122114 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3349 r_free = 0.3349 target = 0.101413 restraints weight = 21520.136| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3400 r_free = 0.3400 target = 0.104571 restraints weight = 12165.229| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3436 r_free = 0.3436 target = 0.106863 restraints weight = 8141.907| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3461 r_free = 0.3461 target = 0.108455 restraints weight = 6069.759| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3477 r_free = 0.3477 target = 0.109474 restraints weight = 4878.486| |-----------------------------------------------------------------------------| r_work (final): 0.3476 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7920 moved from start: 0.3010 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.077 10170 Z= 0.253 Angle : 0.884 15.220 13919 Z= 0.396 Chirality : 0.047 0.315 1746 Planarity : 0.004 0.033 1664 Dihedral : 9.477 82.601 2534 Min Nonbonded Distance : 2.438 Molprobity Statistics. All-atom Clashscore : 10.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.35 % Favored : 95.65 % Rotamer: Outliers : 3.11 % Allowed : 18.65 % Favored : 78.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.77 (0.27), residues: 966 helix: 0.39 (0.28), residues: 332 sheet: -1.19 (0.40), residues: 162 loop : -0.84 (0.29), residues: 472 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 250 TYR 0.027 0.002 TYR B 253 PHE 0.022 0.002 PHE a 309 TRP 0.024 0.002 TRP C 210 HIS 0.008 0.002 HIS C 141 Details of bonding type rmsd covalent geometry : bond 0.00568 (10088) covalent geometry : angle 0.83706 (13694) SS BOND : bond 0.00489 ( 21) SS BOND : angle 1.99797 ( 42) hydrogen bonds : bond 0.04237 ( 331) hydrogen bonds : angle 5.38143 ( 873) link_ALPHA1-6 : bond 0.01182 ( 2) link_ALPHA1-6 : angle 2.10344 ( 6) link_BETA1-4 : bond 0.00837 ( 23) link_BETA1-4 : angle 2.53631 ( 69) link_BETA1-6 : bond 0.00437 ( 3) link_BETA1-6 : angle 1.64326 ( 9) link_NAG-ASN : bond 0.00472 ( 33) link_NAG-ASN : angle 2.52162 ( 99) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1932 Ramachandran restraints generated. 966 Oldfield, 0 Emsley, 966 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1932 Ramachandran restraints generated. 966 Oldfield, 0 Emsley, 966 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 288 residues out of total 901 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 260 time to evaluate : 0.280 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 75 MET cc_start: 0.8616 (mmm) cc_final: 0.8198 (mmt) REVERT: C 153 MET cc_start: 0.9365 (ppp) cc_final: 0.9116 (ppp) REVERT: C 248 ARG cc_start: 0.8696 (ttt90) cc_final: 0.8460 (ttt90) REVERT: C 250 ARG cc_start: 0.8649 (mmm-85) cc_final: 0.8390 (ttp-170) REVERT: A 76 GLU cc_start: 0.7886 (mp0) cc_final: 0.7633 (mp0) REVERT: A 129 TYR cc_start: 0.8247 (p90) cc_final: 0.7954 (p90) REVERT: B 76 GLU cc_start: 0.8333 (mt-10) cc_final: 0.7981 (mp0) REVERT: B 88 LYS cc_start: 0.8594 (tmtt) cc_final: 0.8002 (tmtt) REVERT: B 245 LEU cc_start: 0.9528 (mt) cc_final: 0.9008 (tt) REVERT: c 295 ASN cc_start: 0.8396 (t0) cc_final: 0.8181 (t0) REVERT: c 321 GLN cc_start: 0.8475 (mt0) cc_final: 0.8255 (mt0) REVERT: a 398 HIS cc_start: 0.7792 (m-70) cc_final: 0.7253 (m-70) REVERT: a 402 ASP cc_start: 0.8711 (t70) cc_final: 0.8489 (t0) REVERT: b 358 ILE cc_start: 0.9131 (tt) cc_final: 0.8854 (tp) REVERT: b 400 SER cc_start: 0.8577 (p) cc_final: 0.8209 (m) outliers start: 28 outliers final: 21 residues processed: 276 average time/residue: 0.0972 time to fit residues: 36.2792 Evaluate side-chains 265 residues out of total 901 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 244 time to evaluate : 0.271 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 97 VAL Chi-restraints excluded: chain C residue 118 CYS Chi-restraints excluded: chain C residue 180 CYS Chi-restraints excluded: chain C residue 187 VAL Chi-restraints excluded: chain C residue 255 SER Chi-restraints excluded: chain A residue 65 VAL Chi-restraints excluded: chain A residue 101 THR Chi-restraints excluded: chain A residue 137 ILE Chi-restraints excluded: chain A residue 182 THR Chi-restraints excluded: chain B residue 118 CYS Chi-restraints excluded: chain B residue 188 LEU Chi-restraints excluded: chain B residue 247 GLN Chi-restraints excluded: chain c residue 298 VAL Chi-restraints excluded: chain c residue 400 SER Chi-restraints excluded: chain a residue 281 THR Chi-restraints excluded: chain a residue 315 LEU Chi-restraints excluded: chain a residue 380 THR Chi-restraints excluded: chain a residue 389 SER Chi-restraints excluded: chain a residue 399 PHE Chi-restraints excluded: chain b residue 371 TYR Chi-restraints excluded: chain b residue 380 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 99 optimal weight: 0.5980 chunk 50 optimal weight: 0.9990 chunk 14 optimal weight: 9.9990 chunk 23 optimal weight: 0.0980 chunk 117 optimal weight: 0.6980 chunk 21 optimal weight: 0.6980 chunk 47 optimal weight: 0.0060 chunk 55 optimal weight: 0.7980 chunk 100 optimal weight: 0.8980 chunk 89 optimal weight: 0.9980 chunk 5 optimal weight: 10.0000 overall best weight: 0.4196 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 185 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 141 HIS a 319 ASN a 405 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3726 r_free = 0.3726 target = 0.126779 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3421 r_free = 0.3421 target = 0.106263 restraints weight = 21168.461| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3474 r_free = 0.3474 target = 0.109621 restraints weight = 11564.419| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3510 r_free = 0.3510 target = 0.111982 restraints weight = 7574.228| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3532 r_free = 0.3532 target = 0.113547 restraints weight = 5566.393| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.3552 r_free = 0.3552 target = 0.114778 restraints weight = 4458.583| |-----------------------------------------------------------------------------| r_work (final): 0.3547 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7811 moved from start: 0.3113 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.067 10170 Z= 0.138 Angle : 0.813 14.539 13919 Z= 0.364 Chirality : 0.045 0.313 1746 Planarity : 0.003 0.034 1664 Dihedral : 8.930 79.066 2534 Min Nonbonded Distance : 2.465 Molprobity Statistics. All-atom Clashscore : 10.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.73 % Favored : 96.27 % Rotamer: Outliers : 2.66 % Allowed : 21.09 % Favored : 76.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.56 (0.27), residues: 966 helix: 0.67 (0.29), residues: 331 sheet: -1.30 (0.42), residues: 144 loop : -0.73 (0.28), residues: 491 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 250 TYR 0.029 0.001 TYR B 253 PHE 0.021 0.002 PHE a 293 TRP 0.050 0.002 TRP C 227 HIS 0.003 0.001 HIS C 141 Details of bonding type rmsd covalent geometry : bond 0.00312 (10088) covalent geometry : angle 0.76571 (13694) SS BOND : bond 0.00549 ( 21) SS BOND : angle 2.43027 ( 42) hydrogen bonds : bond 0.03714 ( 331) hydrogen bonds : angle 5.02765 ( 873) link_ALPHA1-6 : bond 0.01340 ( 2) link_ALPHA1-6 : angle 2.04982 ( 6) link_BETA1-4 : bond 0.00847 ( 23) link_BETA1-4 : angle 2.41543 ( 69) link_BETA1-6 : bond 0.00461 ( 3) link_BETA1-6 : angle 1.45981 ( 9) link_NAG-ASN : bond 0.00452 ( 33) link_NAG-ASN : angle 2.19858 ( 99) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1932 Ramachandran restraints generated. 966 Oldfield, 0 Emsley, 966 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1932 Ramachandran restraints generated. 966 Oldfield, 0 Emsley, 966 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 292 residues out of total 901 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 268 time to evaluate : 0.222 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 75 MET cc_start: 0.8603 (mmm) cc_final: 0.8215 (mmt) REVERT: C 81 THR cc_start: 0.9015 (m) cc_final: 0.8574 (t) REVERT: C 82 MET cc_start: 0.8908 (pmm) cc_final: 0.8274 (pmm) REVERT: C 129 TYR cc_start: 0.7880 (p90) cc_final: 0.7595 (p90) REVERT: C 153 MET cc_start: 0.9323 (ppp) cc_final: 0.9117 (ppp) REVERT: C 250 ARG cc_start: 0.8535 (mmm-85) cc_final: 0.8333 (ttp-170) REVERT: A 76 GLU cc_start: 0.7849 (mp0) cc_final: 0.7622 (mp0) REVERT: A 129 TYR cc_start: 0.8125 (p90) cc_final: 0.7824 (p90) REVERT: A 134 MET cc_start: 0.9176 (tpp) cc_final: 0.8788 (tpp) REVERT: A 196 TRP cc_start: 0.7800 (OUTLIER) cc_final: 0.6972 (t60) REVERT: B 76 GLU cc_start: 0.8383 (mt-10) cc_final: 0.8028 (mp0) REVERT: B 245 LEU cc_start: 0.9452 (mt) cc_final: 0.8950 (tt) REVERT: c 284 MET cc_start: 0.9068 (mtt) cc_final: 0.8332 (mtm) REVERT: c 379 ARG cc_start: 0.8099 (mmp80) cc_final: 0.7880 (mmm160) REVERT: a 321 GLN cc_start: 0.9014 (mm-40) cc_final: 0.8475 (mm-40) REVERT: a 379 ARG cc_start: 0.7103 (ttp-170) cc_final: 0.6805 (ttt-90) REVERT: a 398 HIS cc_start: 0.7579 (m-70) cc_final: 0.7044 (m-70) REVERT: a 402 ASP cc_start: 0.8661 (t70) cc_final: 0.8436 (t0) REVERT: b 358 ILE cc_start: 0.9000 (tt) cc_final: 0.8715 (tp) REVERT: b 400 SER cc_start: 0.8539 (p) cc_final: 0.8210 (m) outliers start: 24 outliers final: 13 residues processed: 284 average time/residue: 0.1023 time to fit residues: 39.2320 Evaluate side-chains 257 residues out of total 901 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 243 time to evaluate : 0.213 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 118 CYS Chi-restraints excluded: chain C residue 213 ILE Chi-restraints excluded: chain A residue 117 PHE Chi-restraints excluded: chain A residue 137 ILE Chi-restraints excluded: chain A residue 182 THR Chi-restraints excluded: chain A residue 196 TRP Chi-restraints excluded: chain A residue 229 ASP Chi-restraints excluded: chain B residue 118 CYS Chi-restraints excluded: chain c residue 298 VAL Chi-restraints excluded: chain c residue 400 SER Chi-restraints excluded: chain a residue 292 CYS Chi-restraints excluded: chain a residue 389 SER Chi-restraints excluded: chain b residue 341 VAL Chi-restraints excluded: chain b residue 364 CYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 2 optimal weight: 8.9990 chunk 109 optimal weight: 0.2980 chunk 63 optimal weight: 4.9990 chunk 106 optimal weight: 4.9990 chunk 31 optimal weight: 0.7980 chunk 54 optimal weight: 1.9990 chunk 41 optimal weight: 0.3980 chunk 24 optimal weight: 3.9990 chunk 73 optimal weight: 0.6980 chunk 39 optimal weight: 3.9990 chunk 76 optimal weight: 6.9990 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 74 ASN ** C 93 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 93 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** c 295 ASN c 321 GLN a 405 GLN b 409 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3725 r_free = 0.3725 target = 0.126144 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3419 r_free = 0.3419 target = 0.105529 restraints weight = 21065.116| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3472 r_free = 0.3472 target = 0.108924 restraints weight = 11342.410| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3509 r_free = 0.3509 target = 0.111299 restraints weight = 7372.337| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3531 r_free = 0.3531 target = 0.112804 restraints weight = 5395.807| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3549 r_free = 0.3549 target = 0.113974 restraints weight = 4316.887| |-----------------------------------------------------------------------------| r_work (final): 0.3548 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7817 moved from start: 0.3304 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 10170 Z= 0.153 Angle : 0.809 13.227 13919 Z= 0.365 Chirality : 0.045 0.310 1746 Planarity : 0.003 0.034 1664 Dihedral : 8.759 78.746 2534 Min Nonbonded Distance : 2.459 Molprobity Statistics. All-atom Clashscore : 10.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.35 % Favored : 95.65 % Rotamer: Outliers : 2.66 % Allowed : 21.98 % Favored : 75.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.61 (0.27), residues: 966 helix: 0.60 (0.29), residues: 331 sheet: -1.15 (0.42), residues: 144 loop : -0.81 (0.28), residues: 491 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 250 TYR 0.019 0.001 TYR A 241 PHE 0.015 0.001 PHE B 140 TRP 0.035 0.002 TRP C 227 HIS 0.005 0.001 HIS B 93 Details of bonding type rmsd covalent geometry : bond 0.00351 (10088) covalent geometry : angle 0.76732 (13694) SS BOND : bond 0.00463 ( 21) SS BOND : angle 1.63804 ( 42) hydrogen bonds : bond 0.03870 ( 331) hydrogen bonds : angle 4.97730 ( 873) link_ALPHA1-6 : bond 0.01287 ( 2) link_ALPHA1-6 : angle 2.01594 ( 6) link_BETA1-4 : bond 0.00889 ( 23) link_BETA1-4 : angle 2.42571 ( 69) link_BETA1-6 : bond 0.00459 ( 3) link_BETA1-6 : angle 1.43781 ( 9) link_NAG-ASN : bond 0.00353 ( 33) link_NAG-ASN : angle 2.19681 ( 99) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1932 Ramachandran restraints generated. 966 Oldfield, 0 Emsley, 966 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1932 Ramachandran restraints generated. 966 Oldfield, 0 Emsley, 966 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 284 residues out of total 901 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 260 time to evaluate : 0.273 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 75 MET cc_start: 0.8602 (mmm) cc_final: 0.8165 (mmt) REVERT: C 129 TYR cc_start: 0.7810 (p90) cc_final: 0.7489 (p90) REVERT: C 151 GLU cc_start: 0.8901 (OUTLIER) cc_final: 0.8258 (mp0) REVERT: C 153 MET cc_start: 0.9339 (ppp) cc_final: 0.9123 (ppp) REVERT: C 194 MET cc_start: 0.7200 (tpt) cc_final: 0.6974 (tpp) REVERT: A 76 GLU cc_start: 0.7826 (mp0) cc_final: 0.7581 (mp0) REVERT: A 129 TYR cc_start: 0.8188 (p90) cc_final: 0.7899 (p90) REVERT: A 248 ARG cc_start: 0.9004 (ptm160) cc_final: 0.8663 (ptm160) REVERT: B 76 GLU cc_start: 0.8375 (mt-10) cc_final: 0.8044 (mp0) REVERT: B 245 LEU cc_start: 0.9451 (mt) cc_final: 0.8926 (tt) REVERT: c 321 GLN cc_start: 0.8290 (OUTLIER) cc_final: 0.7931 (mt0) REVERT: c 348 GLN cc_start: 0.9094 (mm-40) cc_final: 0.8387 (mm-40) REVERT: c 351 MET cc_start: 0.9123 (tpp) cc_final: 0.8764 (tpp) REVERT: a 325 ARG cc_start: 0.8395 (mtt-85) cc_final: 0.8107 (mtt-85) REVERT: a 379 ARG cc_start: 0.7178 (ttp-170) cc_final: 0.6924 (ttt-90) REVERT: a 398 HIS cc_start: 0.7603 (m-70) cc_final: 0.7021 (m-70) REVERT: a 402 ASP cc_start: 0.8671 (t70) cc_final: 0.8454 (t0) REVERT: b 358 ILE cc_start: 0.8981 (tt) cc_final: 0.8722 (tp) REVERT: b 400 SER cc_start: 0.8523 (p) cc_final: 0.8180 (m) outliers start: 24 outliers final: 15 residues processed: 271 average time/residue: 0.1041 time to fit residues: 37.9672 Evaluate side-chains 263 residues out of total 901 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 246 time to evaluate : 0.301 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 118 CYS Chi-restraints excluded: chain C residue 151 GLU Chi-restraints excluded: chain C residue 239 ILE Chi-restraints excluded: chain A residue 117 PHE Chi-restraints excluded: chain A residue 137 ILE Chi-restraints excluded: chain A residue 182 THR Chi-restraints excluded: chain A residue 229 ASP Chi-restraints excluded: chain B residue 118 CYS Chi-restraints excluded: chain B residue 247 GLN Chi-restraints excluded: chain c residue 298 VAL Chi-restraints excluded: chain c residue 321 GLN Chi-restraints excluded: chain c residue 344 LEU Chi-restraints excluded: chain c residue 400 SER Chi-restraints excluded: chain a residue 315 LEU Chi-restraints excluded: chain a residue 389 SER Chi-restraints excluded: chain b residue 283 TRP Chi-restraints excluded: chain b residue 321 GLN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 105 optimal weight: 0.0270 chunk 49 optimal weight: 1.9990 chunk 57 optimal weight: 0.0030 chunk 56 optimal weight: 0.3980 chunk 90 optimal weight: 5.9990 chunk 58 optimal weight: 0.7980 chunk 115 optimal weight: 3.9990 chunk 84 optimal weight: 2.9990 chunk 92 optimal weight: 1.9990 chunk 67 optimal weight: 2.9990 chunk 16 optimal weight: 10.0000 overall best weight: 0.6450 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 230 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** c 321 GLN a 405 GLN b 319 ASN b 409 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3715 r_free = 0.3715 target = 0.125935 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3414 r_free = 0.3414 target = 0.105429 restraints weight = 20874.965| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3466 r_free = 0.3466 target = 0.108728 restraints weight = 11304.330| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3502 r_free = 0.3502 target = 0.111064 restraints weight = 7391.233| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3525 r_free = 0.3525 target = 0.112651 restraints weight = 5422.985| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3544 r_free = 0.3544 target = 0.113858 restraints weight = 4336.474| |-----------------------------------------------------------------------------| r_work (final): 0.3541 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7798 moved from start: 0.3434 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.066 10170 Z= 0.148 Angle : 0.836 22.976 13919 Z= 0.372 Chirality : 0.044 0.306 1746 Planarity : 0.003 0.036 1664 Dihedral : 8.578 78.152 2534 Min Nonbonded Distance : 2.453 Molprobity Statistics. All-atom Clashscore : 11.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.14 % Favored : 95.86 % Rotamer: Outliers : 2.89 % Allowed : 22.75 % Favored : 74.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.57 (0.27), residues: 966 helix: 0.55 (0.29), residues: 329 sheet: -0.90 (0.40), residues: 162 loop : -0.78 (0.29), residues: 475 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG b 356 TYR 0.019 0.001 TYR A 150 PHE 0.023 0.002 PHE c 399 TRP 0.033 0.002 TRP C 227 HIS 0.007 0.001 HIS C 179 Details of bonding type rmsd covalent geometry : bond 0.00341 (10088) covalent geometry : angle 0.76524 (13694) SS BOND : bond 0.00370 ( 21) SS BOND : angle 1.42142 ( 42) hydrogen bonds : bond 0.03777 ( 331) hydrogen bonds : angle 4.95831 ( 873) link_ALPHA1-6 : bond 0.01187 ( 2) link_ALPHA1-6 : angle 1.95380 ( 6) link_BETA1-4 : bond 0.00864 ( 23) link_BETA1-4 : angle 2.39554 ( 69) link_BETA1-6 : bond 0.00468 ( 3) link_BETA1-6 : angle 1.41656 ( 9) link_NAG-ASN : bond 0.00397 ( 33) link_NAG-ASN : angle 3.45222 ( 99) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1932 Ramachandran restraints generated. 966 Oldfield, 0 Emsley, 966 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1932 Ramachandran restraints generated. 966 Oldfield, 0 Emsley, 966 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 278 residues out of total 901 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 252 time to evaluate : 0.321 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 75 MET cc_start: 0.8619 (mmm) cc_final: 0.8169 (mmt) REVERT: C 129 TYR cc_start: 0.7711 (p90) cc_final: 0.7448 (p90) REVERT: C 153 MET cc_start: 0.9349 (ppp) cc_final: 0.9127 (ppp) REVERT: C 194 MET cc_start: 0.7274 (tpt) cc_final: 0.7053 (tpp) REVERT: A 76 GLU cc_start: 0.7831 (mp0) cc_final: 0.7582 (mp0) REVERT: A 129 TYR cc_start: 0.8167 (p90) cc_final: 0.7865 (p90) REVERT: A 196 TRP cc_start: 0.7760 (OUTLIER) cc_final: 0.6955 (t60) REVERT: A 248 ARG cc_start: 0.8999 (ptm160) cc_final: 0.8677 (ptm160) REVERT: B 76 GLU cc_start: 0.8379 (mt-10) cc_final: 0.8040 (mp0) REVERT: B 245 LEU cc_start: 0.9381 (mt) cc_final: 0.8980 (tt) REVERT: c 284 MET cc_start: 0.9183 (mtm) cc_final: 0.8337 (mtm) REVERT: c 321 GLN cc_start: 0.8317 (OUTLIER) cc_final: 0.7932 (mt0) REVERT: c 348 GLN cc_start: 0.9104 (mm-40) cc_final: 0.8359 (mm-40) REVERT: c 351 MET cc_start: 0.9108 (tpp) cc_final: 0.8806 (tpp) REVERT: a 352 LYS cc_start: 0.8524 (pttm) cc_final: 0.8306 (ptpp) REVERT: a 379 ARG cc_start: 0.7172 (ttp-170) cc_final: 0.6963 (ttt-90) REVERT: a 398 HIS cc_start: 0.7549 (m-70) cc_final: 0.6945 (m-70) REVERT: a 402 ASP cc_start: 0.8661 (t70) cc_final: 0.8442 (t0) REVERT: b 358 ILE cc_start: 0.8940 (tt) cc_final: 0.8690 (tp) REVERT: b 368 LYS cc_start: 0.8382 (tttm) cc_final: 0.8145 (tttm) REVERT: b 400 SER cc_start: 0.8529 (p) cc_final: 0.8203 (m) outliers start: 26 outliers final: 17 residues processed: 266 average time/residue: 0.0950 time to fit residues: 34.8386 Evaluate side-chains 261 residues out of total 901 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 242 time to evaluate : 0.309 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 63 LYS Chi-restraints excluded: chain C residue 118 CYS Chi-restraints excluded: chain C residue 239 ILE Chi-restraints excluded: chain C residue 255 SER Chi-restraints excluded: chain A residue 117 PHE Chi-restraints excluded: chain A residue 137 ILE Chi-restraints excluded: chain A residue 182 THR Chi-restraints excluded: chain A residue 196 TRP Chi-restraints excluded: chain A residue 229 ASP Chi-restraints excluded: chain B residue 118 CYS Chi-restraints excluded: chain B residue 247 GLN Chi-restraints excluded: chain c residue 298 VAL Chi-restraints excluded: chain c residue 321 GLN Chi-restraints excluded: chain c residue 344 LEU Chi-restraints excluded: chain a residue 292 CYS Chi-restraints excluded: chain a residue 315 LEU Chi-restraints excluded: chain a residue 389 SER Chi-restraints excluded: chain b residue 283 TRP Chi-restraints excluded: chain b residue 321 GLN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 103 optimal weight: 2.9990 chunk 30 optimal weight: 3.9990 chunk 46 optimal weight: 3.9990 chunk 97 optimal weight: 0.9980 chunk 41 optimal weight: 4.9990 chunk 84 optimal weight: 0.7980 chunk 50 optimal weight: 0.0870 chunk 33 optimal weight: 3.9990 chunk 62 optimal weight: 7.9990 chunk 38 optimal weight: 0.0970 chunk 99 optimal weight: 0.8980 overall best weight: 0.5756 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 69 GLN ** A 230 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 93 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** c 321 GLN a 405 GLN a 409 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3722 r_free = 0.3722 target = 0.126420 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3425 r_free = 0.3425 target = 0.106038 restraints weight = 20989.308| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3477 r_free = 0.3477 target = 0.109370 restraints weight = 11275.337| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3512 r_free = 0.3512 target = 0.111705 restraints weight = 7333.398| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 44)----------------| | r_work = 0.3538 r_free = 0.3538 target = 0.113374 restraints weight = 5363.152| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3554 r_free = 0.3554 target = 0.114456 restraints weight = 4244.060| |-----------------------------------------------------------------------------| r_work (final): 0.3546 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7784 moved from start: 0.3503 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.072 10170 Z= 0.143 Angle : 0.828 18.244 13919 Z= 0.372 Chirality : 0.044 0.310 1746 Planarity : 0.003 0.038 1664 Dihedral : 8.468 77.563 2534 Min Nonbonded Distance : 2.478 Molprobity Statistics. All-atom Clashscore : 11.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.04 % Favored : 95.96 % Rotamer: Outliers : 2.22 % Allowed : 23.31 % Favored : 74.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.55 (0.27), residues: 966 helix: 0.57 (0.29), residues: 329 sheet: -0.84 (0.40), residues: 164 loop : -0.78 (0.29), residues: 473 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 250 TYR 0.016 0.001 TYR A 241 PHE 0.014 0.002 PHE c 399 TRP 0.027 0.002 TRP C 210 HIS 0.005 0.001 HIS B 93 Details of bonding type rmsd covalent geometry : bond 0.00332 (10088) covalent geometry : angle 0.77151 (13694) SS BOND : bond 0.00370 ( 21) SS BOND : angle 1.51303 ( 42) hydrogen bonds : bond 0.03708 ( 331) hydrogen bonds : angle 4.92590 ( 873) link_ALPHA1-6 : bond 0.01245 ( 2) link_ALPHA1-6 : angle 1.94686 ( 6) link_BETA1-4 : bond 0.00875 ( 23) link_BETA1-4 : angle 2.38372 ( 69) link_BETA1-6 : bond 0.00461 ( 3) link_BETA1-6 : angle 1.39135 ( 9) link_NAG-ASN : bond 0.00342 ( 33) link_NAG-ASN : angle 2.95189 ( 99) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1932 Ramachandran restraints generated. 966 Oldfield, 0 Emsley, 966 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1932 Ramachandran restraints generated. 966 Oldfield, 0 Emsley, 966 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 279 residues out of total 901 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 259 time to evaluate : 0.270 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 75 MET cc_start: 0.8635 (mmm) cc_final: 0.8177 (mmt) REVERT: C 129 TYR cc_start: 0.7687 (p90) cc_final: 0.7407 (p90) REVERT: C 153 MET cc_start: 0.9333 (ppp) cc_final: 0.9119 (ppp) REVERT: C 194 MET cc_start: 0.7245 (tpt) cc_final: 0.7009 (tpp) REVERT: A 76 GLU cc_start: 0.7801 (mp0) cc_final: 0.7581 (mp0) REVERT: A 129 TYR cc_start: 0.8137 (p90) cc_final: 0.7861 (p90) REVERT: A 134 MET cc_start: 0.9434 (tpt) cc_final: 0.9141 (tpp) REVERT: A 196 TRP cc_start: 0.7698 (OUTLIER) cc_final: 0.6912 (t60) REVERT: A 248 ARG cc_start: 0.8942 (ptm160) cc_final: 0.8248 (ttm170) REVERT: B 82 MET cc_start: 0.8965 (ptp) cc_final: 0.8571 (ptp) REVERT: B 245 LEU cc_start: 0.9340 (mt) cc_final: 0.8958 (tt) REVERT: c 284 MET cc_start: 0.9222 (mtm) cc_final: 0.8598 (mtm) REVERT: c 309 PHE cc_start: 0.9166 (t80) cc_final: 0.8840 (t80) REVERT: c 321 GLN cc_start: 0.8270 (OUTLIER) cc_final: 0.7881 (mt0) REVERT: c 348 GLN cc_start: 0.9101 (mm-40) cc_final: 0.8357 (mm-40) REVERT: c 351 MET cc_start: 0.9135 (tpp) cc_final: 0.8853 (tpp) REVERT: a 321 GLN cc_start: 0.9123 (mm-40) cc_final: 0.8774 (mm-40) REVERT: a 352 LYS cc_start: 0.8515 (pttm) cc_final: 0.8276 (ptpp) REVERT: a 398 HIS cc_start: 0.7524 (m-70) cc_final: 0.6926 (m-70) REVERT: b 358 ILE cc_start: 0.8925 (tt) cc_final: 0.8677 (tp) REVERT: b 368 LYS cc_start: 0.8279 (tttm) cc_final: 0.8019 (tttm) REVERT: b 400 SER cc_start: 0.8550 (p) cc_final: 0.8229 (m) outliers start: 20 outliers final: 17 residues processed: 269 average time/residue: 0.0992 time to fit residues: 36.5824 Evaluate side-chains 267 residues out of total 901 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 248 time to evaluate : 0.333 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 63 LYS Chi-restraints excluded: chain C residue 118 CYS Chi-restraints excluded: chain C residue 239 ILE Chi-restraints excluded: chain C residue 255 SER Chi-restraints excluded: chain A residue 117 PHE Chi-restraints excluded: chain A residue 137 ILE Chi-restraints excluded: chain A residue 182 THR Chi-restraints excluded: chain A residue 196 TRP Chi-restraints excluded: chain A residue 229 ASP Chi-restraints excluded: chain B residue 118 CYS Chi-restraints excluded: chain B residue 247 GLN Chi-restraints excluded: chain c residue 298 VAL Chi-restraints excluded: chain c residue 321 GLN Chi-restraints excluded: chain c residue 344 LEU Chi-restraints excluded: chain a residue 292 CYS Chi-restraints excluded: chain a residue 315 LEU Chi-restraints excluded: chain a residue 389 SER Chi-restraints excluded: chain b residue 283 TRP Chi-restraints excluded: chain b residue 321 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 31 optimal weight: 1.9990 chunk 59 optimal weight: 0.8980 chunk 65 optimal weight: 0.8980 chunk 84 optimal weight: 0.7980 chunk 15 optimal weight: 8.9990 chunk 108 optimal weight: 2.9990 chunk 66 optimal weight: 0.4980 chunk 93 optimal weight: 4.9990 chunk 6 optimal weight: 10.0000 chunk 14 optimal weight: 9.9990 chunk 22 optimal weight: 4.9990 overall best weight: 1.0182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 93 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 93 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** c 321 GLN a 409 ASN b 409 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3706 r_free = 0.3706 target = 0.125563 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3408 r_free = 0.3408 target = 0.105127 restraints weight = 20955.550| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3460 r_free = 0.3460 target = 0.108348 restraints weight = 11727.270| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3495 r_free = 0.3495 target = 0.110618 restraints weight = 7714.320| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3518 r_free = 0.3518 target = 0.112190 restraints weight = 5694.881| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.3536 r_free = 0.3536 target = 0.113360 restraints weight = 4558.907| |-----------------------------------------------------------------------------| r_work (final): 0.3533 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7808 moved from start: 0.3631 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.077 10170 Z= 0.170 Angle : 0.851 15.323 13919 Z= 0.382 Chirality : 0.045 0.303 1746 Planarity : 0.004 0.037 1664 Dihedral : 8.523 78.578 2534 Min Nonbonded Distance : 2.449 Molprobity Statistics. All-atom Clashscore : 11.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.45 % Favored : 95.55 % Rotamer: Outliers : 2.33 % Allowed : 24.53 % Favored : 73.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.60 (0.27), residues: 966 helix: 0.50 (0.29), residues: 331 sheet: -0.88 (0.40), residues: 168 loop : -0.78 (0.29), residues: 467 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 250 TYR 0.020 0.001 TYR A 150 PHE 0.017 0.002 PHE A 233 TRP 0.071 0.003 TRP C 227 HIS 0.007 0.001 HIS B 93 Details of bonding type rmsd covalent geometry : bond 0.00395 (10088) covalent geometry : angle 0.78954 (13694) SS BOND : bond 0.00529 ( 21) SS BOND : angle 1.40737 ( 42) hydrogen bonds : bond 0.03779 ( 331) hydrogen bonds : angle 4.94494 ( 873) link_ALPHA1-6 : bond 0.01130 ( 2) link_ALPHA1-6 : angle 1.94255 ( 6) link_BETA1-4 : bond 0.00846 ( 23) link_BETA1-4 : angle 2.40046 ( 69) link_BETA1-6 : bond 0.00451 ( 3) link_BETA1-6 : angle 1.41499 ( 9) link_NAG-ASN : bond 0.00399 ( 33) link_NAG-ASN : angle 3.19575 ( 99) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1932 Ramachandran restraints generated. 966 Oldfield, 0 Emsley, 966 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1932 Ramachandran restraints generated. 966 Oldfield, 0 Emsley, 966 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 270 residues out of total 901 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 249 time to evaluate : 0.222 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 75 MET cc_start: 0.8655 (mmm) cc_final: 0.8209 (mmt) REVERT: C 129 TYR cc_start: 0.7707 (p90) cc_final: 0.7405 (p90) REVERT: C 153 MET cc_start: 0.9327 (ppp) cc_final: 0.9099 (ppp) REVERT: C 250 ARG cc_start: 0.8495 (mmm-85) cc_final: 0.7946 (ttp-170) REVERT: A 76 GLU cc_start: 0.7849 (mp0) cc_final: 0.7570 (mp0) REVERT: A 129 TYR cc_start: 0.8155 (p90) cc_final: 0.7852 (p90) REVERT: A 134 MET cc_start: 0.9469 (tpt) cc_final: 0.9161 (tpp) REVERT: A 196 TRP cc_start: 0.7758 (OUTLIER) cc_final: 0.6922 (t60) REVERT: A 248 ARG cc_start: 0.8967 (ptm160) cc_final: 0.8290 (ttm170) REVERT: B 82 MET cc_start: 0.8988 (ptp) cc_final: 0.8610 (ptp) REVERT: B 245 LEU cc_start: 0.9323 (mt) cc_final: 0.8911 (tt) REVERT: c 284 MET cc_start: 0.9283 (mtm) cc_final: 0.8786 (mtm) REVERT: a 321 GLN cc_start: 0.9121 (mm-40) cc_final: 0.8882 (mm-40) REVERT: a 352 LYS cc_start: 0.8539 (pttm) cc_final: 0.8272 (ptpp) REVERT: a 398 HIS cc_start: 0.7499 (m-70) cc_final: 0.7194 (m-70) REVERT: b 289 GLU cc_start: 0.8104 (mp0) cc_final: 0.7853 (mp0) REVERT: b 358 ILE cc_start: 0.8931 (tt) cc_final: 0.8684 (tp) REVERT: b 368 LYS cc_start: 0.8339 (tttm) cc_final: 0.8028 (tttm) REVERT: b 400 SER cc_start: 0.8538 (p) cc_final: 0.8205 (m) outliers start: 21 outliers final: 18 residues processed: 258 average time/residue: 0.0967 time to fit residues: 34.2823 Evaluate side-chains 266 residues out of total 901 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 247 time to evaluate : 0.356 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 63 LYS Chi-restraints excluded: chain C residue 118 CYS Chi-restraints excluded: chain C residue 239 ILE Chi-restraints excluded: chain C residue 255 SER Chi-restraints excluded: chain A residue 117 PHE Chi-restraints excluded: chain A residue 137 ILE Chi-restraints excluded: chain A residue 182 THR Chi-restraints excluded: chain A residue 196 TRP Chi-restraints excluded: chain A residue 229 ASP Chi-restraints excluded: chain B residue 118 CYS Chi-restraints excluded: chain B residue 247 GLN Chi-restraints excluded: chain c residue 298 VAL Chi-restraints excluded: chain c residue 344 LEU Chi-restraints excluded: chain a residue 281 THR Chi-restraints excluded: chain a residue 292 CYS Chi-restraints excluded: chain a residue 315 LEU Chi-restraints excluded: chain a residue 389 SER Chi-restraints excluded: chain b residue 321 GLN Chi-restraints excluded: chain b residue 332 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 117 optimal weight: 0.5980 chunk 50 optimal weight: 7.9990 chunk 47 optimal weight: 0.0030 chunk 37 optimal weight: 0.0970 chunk 6 optimal weight: 10.0000 chunk 20 optimal weight: 20.0000 chunk 24 optimal weight: 2.9990 chunk 87 optimal weight: 3.9990 chunk 107 optimal weight: 2.9990 chunk 14 optimal weight: 10.0000 chunk 70 optimal weight: 2.9990 overall best weight: 1.3392 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 93 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 93 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** a 405 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3685 r_free = 0.3685 target = 0.123974 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3383 r_free = 0.3383 target = 0.103474 restraints weight = 21012.340| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3435 r_free = 0.3435 target = 0.106668 restraints weight = 11692.510| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3470 r_free = 0.3470 target = 0.108913 restraints weight = 7700.073| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3494 r_free = 0.3494 target = 0.110492 restraints weight = 5710.841| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.3511 r_free = 0.3511 target = 0.111636 restraints weight = 4578.350| |-----------------------------------------------------------------------------| r_work (final): 0.3503 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7845 moved from start: 0.3773 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.077 10170 Z= 0.193 Angle : 0.859 12.511 13919 Z= 0.390 Chirality : 0.046 0.299 1746 Planarity : 0.004 0.036 1664 Dihedral : 8.709 80.662 2534 Min Nonbonded Distance : 2.467 Molprobity Statistics. All-atom Clashscore : 13.00 Ramachandran Plot: Outliers : 0.10 % Allowed : 4.66 % Favored : 95.24 % Rotamer: Outliers : 2.33 % Allowed : 24.86 % Favored : 72.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.69 (0.27), residues: 966 helix: 0.43 (0.29), residues: 333 sheet: -0.95 (0.42), residues: 150 loop : -0.85 (0.28), residues: 483 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 250 TYR 0.023 0.002 TYR A 241 PHE 0.013 0.002 PHE B 157 TRP 0.043 0.002 TRP C 227 HIS 0.007 0.001 HIS B 93 Details of bonding type rmsd covalent geometry : bond 0.00447 (10088) covalent geometry : angle 0.80975 (13694) SS BOND : bond 0.00417 ( 21) SS BOND : angle 1.39223 ( 42) hydrogen bonds : bond 0.04007 ( 331) hydrogen bonds : angle 5.05128 ( 873) link_ALPHA1-6 : bond 0.01118 ( 2) link_ALPHA1-6 : angle 1.98012 ( 6) link_BETA1-4 : bond 0.00843 ( 23) link_BETA1-4 : angle 2.42131 ( 69) link_BETA1-6 : bond 0.00431 ( 3) link_BETA1-6 : angle 1.48510 ( 9) link_NAG-ASN : bond 0.00380 ( 33) link_NAG-ASN : angle 2.79363 ( 99) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1615.81 seconds wall clock time: 28 minutes 49.48 seconds (1729.48 seconds total)