Starting phenix.real_space_refine on Sat Sep 12 14:27:25 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/6his_0228/09_2026/6his_0228.cif Found real_map, /net/cci-nas-00/data/ceres_data/6his_0228/09_2026/6his_0228.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/cci-nas-00/data/ceres_data/6his_0228/09_2026/6his_0228.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/6his_0228/09_2026/6his_0228.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/6his_0228/09_2026/6his_0228.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6his_0228/09_2026/6his_0228.map" model { file = "/net/cci-nas-00/data/ceres_data/6his_0228/09_2026/6his_0228.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6his_0228/09_2026/6his_0228.cif" } resolution = 4.5 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= 0.001 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 45 5.16 5 C 10655 2.51 5 N 2595 2.21 5 O 2945 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-2.2.1-6174/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 16240 Number of models: 1 Model: "" Number of chains: 25 Chain: "A" Number of atoms: 3132 Number of conformers: 1 Conformer: "" Number of residues, atoms: 387, 3132 Classifications: {'peptide': 387} Incomplete info: {'truncation_to_alanine': 19} Link IDs: {'PTRANS': 20, 'TRANS': 366} Chain breaks: 1 Unresolved non-hydrogen bonds: 71 Unresolved non-hydrogen angles: 94 Unresolved non-hydrogen dihedrals: 57 Unresolved non-hydrogen chiralities: 10 Planarities with less than four sites: {'ASP:plan': 3, 'ARG:plan': 3, 'HIS:plan': 1, 'TRP:plan': 1} Unresolved non-hydrogen planarities: 38 Chain: "E" Number of atoms: 3132 Number of conformers: 1 Conformer: "" Number of residues, atoms: 387, 3132 Classifications: {'peptide': 387} Incomplete info: {'truncation_to_alanine': 19} Link IDs: {'PTRANS': 20, 'TRANS': 366} Chain breaks: 1 Unresolved non-hydrogen bonds: 71 Unresolved non-hydrogen angles: 94 Unresolved non-hydrogen dihedrals: 57 Unresolved non-hydrogen chiralities: 10 Planarities with less than four sites: {'ASP:plan': 3, 'ARG:plan': 3, 'HIS:plan': 1, 'TRP:plan': 1} Unresolved non-hydrogen planarities: 38 Chain: "B" Number of atoms: 3132 Number of conformers: 1 Conformer: "" Number of residues, atoms: 387, 3132 Classifications: {'peptide': 387} Incomplete info: {'truncation_to_alanine': 19} Link IDs: {'PTRANS': 20, 'TRANS': 366} Chain breaks: 1 Unresolved non-hydrogen bonds: 71 Unresolved non-hydrogen angles: 94 Unresolved non-hydrogen dihedrals: 57 Unresolved non-hydrogen chiralities: 10 Planarities with less than four sites: {'ASP:plan': 3, 'ARG:plan': 3, 'HIS:plan': 1, 'TRP:plan': 1} Unresolved non-hydrogen planarities: 38 Chain: "C" Number of atoms: 3132 Number of conformers: 1 Conformer: "" Number of residues, atoms: 387, 3132 Classifications: {'peptide': 387} Incomplete info: {'truncation_to_alanine': 19} Link IDs: {'PTRANS': 20, 'TRANS': 366} Chain breaks: 1 Unresolved non-hydrogen bonds: 71 Unresolved non-hydrogen angles: 94 Unresolved non-hydrogen dihedrals: 57 Unresolved non-hydrogen chiralities: 10 Planarities with less than four sites: {'ASP:plan': 3, 'ARG:plan': 3, 'HIS:plan': 1, 'TRP:plan': 1} Unresolved non-hydrogen planarities: 38 Chain: "D" Number of atoms: 3132 Number of conformers: 1 Conformer: "" Number of residues, atoms: 387, 3132 Classifications: {'peptide': 387} Incomplete info: {'truncation_to_alanine': 19} Link IDs: {'PTRANS': 20, 'TRANS': 366} Chain breaks: 1 Unresolved non-hydrogen bonds: 71 Unresolved non-hydrogen angles: 94 Unresolved non-hydrogen dihedrals: 57 Unresolved non-hydrogen chiralities: 10 Planarities with less than four sites: {'ASP:plan': 3, 'ARG:plan': 3, 'HIS:plan': 1, 'TRP:plan': 1} Unresolved non-hydrogen planarities: 38 Chain: "F" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "G" 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 chiralities: 3 Chain: "H" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen 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 chiralities: 2 Chain: "J" 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 chiralities: 3 Chain: "K" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "L" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "M" 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 chiralities: 3 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 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 chiralities: 2 Chain: "P" 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 chiralities: 3 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 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 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 chiralities: 3 Chain: "T" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 21 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 21 Unusual residues: {'TKT': 1} Classifications: {'undetermined': 1} Chain: "E" Number of atoms: 21 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 21 Unusual residues: {'TKT': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 21 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 21 Unusual residues: {'TKT': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 21 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 21 Unusual residues: {'TKT': 1} Classifications: {'undetermined': 1} Chain: "D" Number of atoms: 21 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 21 Unusual residues: {'TKT': 1} Classifications: {'undetermined': 1} Time building chain proxies: 3.95, per 1000 atoms: 0.24 Number of scatterers: 16240 At special positions: 0 Unit cell: (105.978, 104.939, 169.357, 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 45 16.00 O 2945 8.00 N 2595 7.00 C 10655 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=5, symmetry=0 Simple disulfide: pdb=" SG CYS A 135 " - pdb=" SG CYS A 149 " distance=2.03 Simple disulfide: pdb=" SG CYS E 135 " - pdb=" SG CYS E 149 " distance=2.03 Simple disulfide: pdb=" SG CYS B 135 " - pdb=" SG CYS B 149 " distance=2.03 Simple disulfide: pdb=" SG CYS C 135 " - pdb=" SG CYS C 149 " distance=2.03 Simple disulfide: pdb=" SG CYS D 135 " - pdb=" SG CYS D 149 " distance=2.03 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 BETA1-4 " NAG F 1 " - " NAG F 2 " " NAG G 1 " - " NAG G 2 " " NAG G 2 " - " BMA G 3 " " NAG H 1 " - " NAG H 2 " " NAG I 1 " - " NAG I 2 " " NAG J 1 " - " NAG J 2 " " NAG J 2 " - " BMA J 3 " " NAG K 1 " - " NAG K 2 " " NAG L 1 " - " NAG L 2 " " NAG M 1 " - " NAG M 2 " " NAG M 2 " - " BMA M 3 " " NAG N 1 " - " NAG N 2 " " NAG O 1 " - " NAG O 2 " " NAG P 1 " - " NAG P 2 " " NAG P 2 " - " BMA P 3 " " NAG Q 1 " - " NAG Q 2 " " NAG R 1 " - " NAG R 2 " " NAG S 1 " - " NAG S 2 " " NAG S 2 " - " BMA S 3 " " NAG T 1 " - " NAG T 2 " NAG-ASN " NAG F 1 " - " ASN A 82 " " NAG G 1 " - " ASN A 164 " " NAG H 1 " - " ASN A 148 " " NAG I 1 " - " ASN E 82 " " NAG J 1 " - " ASN E 164 " " NAG K 1 " - " ASN E 148 " " NAG L 1 " - " ASN B 82 " " NAG M 1 " - " ASN B 164 " " NAG N 1 " - " ASN B 148 " " NAG O 1 " - " ASN C 82 " " NAG P 1 " - " ASN C 164 " " NAG Q 1 " - " ASN C 148 " " NAG R 1 " - " ASN D 82 " " NAG S 1 " - " ASN D 164 " " NAG T 1 " - " ASN D 148 " Time building additional restraints: 1.89 Conformation dependent library (CDL) restraints added in 765.7 milliseconds 3830 Ramachandran restraints generated. 1915 Oldfield, 0 Emsley, 1915 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3760 Finding SS restraints... Secondary structure from input PDB file: 65 helices and 10 sheets defined 45.0% alpha, 24.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.42 Creating SS restraints... Processing helix chain 'A' and resid 12 through 21 Processing helix chain 'A' and resid 71 through 74 removed outlier: 4.042A pdb=" N GLN A 74 " --> pdb=" O GLU A 71 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 71 through 74' Processing helix chain 'A' and resid 91 through 93 No H-bonds generated for 'chain 'A' and resid 91 through 93' Processing helix chain 'A' and resid 170 through 177 removed outlier: 3.968A pdb=" N VAL A 174 " --> pdb=" O SER A 170 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N ARG A 175 " --> pdb=" O PRO A 171 " (cutoff:3.500A) Processing helix chain 'A' and resid 221 through 226 removed outlier: 3.685A pdb=" N VAL A 225 " --> pdb=" O LEU A 221 " (cutoff:3.500A) Processing helix chain 'A' and resid 227 through 242 removed outlier: 3.544A pdb=" N SER A 231 " --> pdb=" O LEU A 227 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N VAL A 240 " --> pdb=" O VAL A 236 " (cutoff:3.500A) Processing helix chain 'A' and resid 249 through 269 removed outlier: 4.603A pdb=" N SER A 253 " --> pdb=" O GLY A 249 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N LYS A 255 " --> pdb=" O ARG A 251 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N THR A 257 " --> pdb=" O SER A 253 " (cutoff:3.500A) Processing helix chain 'A' and resid 270 through 272 No H-bonds generated for 'chain 'A' and resid 270 through 272' Processing helix chain 'A' and resid 281 through 283 No H-bonds generated for 'chain 'A' and resid 281 through 283' Processing helix chain 'A' and resid 284 through 308 removed outlier: 4.939A pdb=" N CYS A 290 " --> pdb=" O TYR A 286 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N VAL A 295 " --> pdb=" O MET A 291 " (cutoff:3.500A) Processing helix chain 'A' and resid 317 through 325 removed outlier: 3.602A pdb=" N HIS A 323 " --> pdb=" O ASP A 319 " (cutoff:3.500A) Processing helix chain 'A' and resid 326 through 334 Processing helix chain 'A' and resid 402 through 458 removed outlier: 3.682A pdb=" N SER A 408 " --> pdb=" O GLN A 404 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N ARG A 410 " --> pdb=" O LEU A 406 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N ARG A 416 " --> pdb=" O PHE A 412 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N VAL A 432 " --> pdb=" O ARG A 428 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N TYR A 441 " --> pdb=" O LEU A 437 " (cutoff:3.500A) Processing helix chain 'E' and resid 12 through 21 Processing helix chain 'E' and resid 71 through 74 removed outlier: 4.043A pdb=" N GLN E 74 " --> pdb=" O GLU E 71 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 71 through 74' Processing helix chain 'E' and resid 91 through 93 No H-bonds generated for 'chain 'E' and resid 91 through 93' Processing helix chain 'E' and resid 170 through 177 removed outlier: 3.967A pdb=" N VAL E 174 " --> pdb=" O SER E 170 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N ARG E 175 " --> pdb=" O PRO E 171 " (cutoff:3.500A) Processing helix chain 'E' and resid 221 through 226 removed outlier: 3.684A pdb=" N VAL E 225 " --> pdb=" O LEU E 221 " (cutoff:3.500A) Processing helix chain 'E' and resid 227 through 242 removed outlier: 3.544A pdb=" N SER E 231 " --> pdb=" O LEU E 227 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N VAL E 240 " --> pdb=" O VAL E 236 " (cutoff:3.500A) Processing helix chain 'E' and resid 249 through 269 removed outlier: 4.603A pdb=" N SER E 253 " --> pdb=" O GLY E 249 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N LYS E 255 " --> pdb=" O ARG E 251 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N THR E 257 " --> pdb=" O SER E 253 " (cutoff:3.500A) Processing helix chain 'E' and resid 270 through 272 No H-bonds generated for 'chain 'E' and resid 270 through 272' Processing helix chain 'E' and resid 281 through 283 No H-bonds generated for 'chain 'E' and resid 281 through 283' Processing helix chain 'E' and resid 284 through 308 removed outlier: 4.938A pdb=" N CYS E 290 " --> pdb=" O TYR E 286 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N VAL E 295 " --> pdb=" O MET E 291 " (cutoff:3.500A) Processing helix chain 'E' and resid 317 through 325 removed outlier: 3.602A pdb=" N HIS E 323 " --> pdb=" O ASP E 319 " (cutoff:3.500A) Processing helix chain 'E' and resid 326 through 334 Processing helix chain 'E' and resid 402 through 458 removed outlier: 3.682A pdb=" N SER E 408 " --> pdb=" O GLN E 404 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N ARG E 410 " --> pdb=" O LEU E 406 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N ARG E 416 " --> pdb=" O PHE E 412 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N VAL E 432 " --> pdb=" O ARG E 428 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N TYR E 441 " --> pdb=" O LEU E 437 " (cutoff:3.500A) Processing helix chain 'B' and resid 12 through 21 Processing helix chain 'B' and resid 71 through 74 removed outlier: 4.043A pdb=" N GLN B 74 " --> pdb=" O GLU B 71 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 71 through 74' Processing helix chain 'B' and resid 91 through 93 No H-bonds generated for 'chain 'B' and resid 91 through 93' Processing helix chain 'B' and resid 170 through 177 removed outlier: 3.968A pdb=" N VAL B 174 " --> pdb=" O SER B 170 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N ARG B 175 " --> pdb=" O PRO B 171 " (cutoff:3.500A) Processing helix chain 'B' and resid 221 through 226 removed outlier: 3.684A pdb=" N VAL B 225 " --> pdb=" O LEU B 221 " (cutoff:3.500A) Processing helix chain 'B' and resid 227 through 242 removed outlier: 3.545A pdb=" N SER B 231 " --> pdb=" O LEU B 227 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N VAL B 240 " --> pdb=" O VAL B 236 " (cutoff:3.500A) Processing helix chain 'B' and resid 249 through 269 removed outlier: 4.603A pdb=" N SER B 253 " --> pdb=" O GLY B 249 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N LYS B 255 " --> pdb=" O ARG B 251 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N THR B 257 " --> pdb=" O SER B 253 " (cutoff:3.500A) Processing helix chain 'B' and resid 270 through 272 No H-bonds generated for 'chain 'B' and resid 270 through 272' Processing helix chain 'B' and resid 281 through 283 No H-bonds generated for 'chain 'B' and resid 281 through 283' Processing helix chain 'B' and resid 284 through 308 removed outlier: 4.939A pdb=" N CYS B 290 " --> pdb=" O TYR B 286 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N VAL B 295 " --> pdb=" O MET B 291 " (cutoff:3.500A) Processing helix chain 'B' and resid 317 through 325 removed outlier: 3.602A pdb=" N HIS B 323 " --> pdb=" O ASP B 319 " (cutoff:3.500A) Processing helix chain 'B' and resid 326 through 334 Processing helix chain 'B' and resid 402 through 458 removed outlier: 3.682A pdb=" N SER B 408 " --> pdb=" O GLN B 404 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N ARG B 410 " --> pdb=" O LEU B 406 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N ARG B 416 " --> pdb=" O PHE B 412 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N VAL B 432 " --> pdb=" O ARG B 428 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N TYR B 441 " --> pdb=" O LEU B 437 " (cutoff:3.500A) Processing helix chain 'C' and resid 12 through 21 Processing helix chain 'C' and resid 71 through 74 removed outlier: 4.044A pdb=" N GLN C 74 " --> pdb=" O GLU C 71 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 71 through 74' Processing helix chain 'C' and resid 91 through 93 No H-bonds generated for 'chain 'C' and resid 91 through 93' Processing helix chain 'C' and resid 170 through 177 removed outlier: 3.967A pdb=" N VAL C 174 " --> pdb=" O SER C 170 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N ARG C 175 " --> pdb=" O PRO C 171 " (cutoff:3.500A) Processing helix chain 'C' and resid 221 through 226 removed outlier: 3.683A pdb=" N VAL C 225 " --> pdb=" O LEU C 221 " (cutoff:3.500A) Processing helix chain 'C' and resid 227 through 242 removed outlier: 3.544A pdb=" N SER C 231 " --> pdb=" O LEU C 227 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N VAL C 240 " --> pdb=" O VAL C 236 " (cutoff:3.500A) Processing helix chain 'C' and resid 249 through 269 removed outlier: 4.603A pdb=" N SER C 253 " --> pdb=" O GLY C 249 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N LYS C 255 " --> pdb=" O ARG C 251 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N THR C 257 " --> pdb=" O SER C 253 " (cutoff:3.500A) Processing helix chain 'C' and resid 270 through 272 No H-bonds generated for 'chain 'C' and resid 270 through 272' Processing helix chain 'C' and resid 281 through 283 No H-bonds generated for 'chain 'C' and resid 281 through 283' Processing helix chain 'C' and resid 284 through 308 removed outlier: 4.939A pdb=" N CYS C 290 " --> pdb=" O TYR C 286 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N VAL C 295 " --> pdb=" O MET C 291 " (cutoff:3.500A) Processing helix chain 'C' and resid 317 through 325 removed outlier: 3.602A pdb=" N HIS C 323 " --> pdb=" O ASP C 319 " (cutoff:3.500A) Processing helix chain 'C' and resid 326 through 334 Processing helix chain 'C' and resid 402 through 458 removed outlier: 3.684A pdb=" N SER C 408 " --> pdb=" O GLN C 404 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N ARG C 410 " --> pdb=" O LEU C 406 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N ARG C 416 " --> pdb=" O PHE C 412 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N VAL C 432 " --> pdb=" O ARG C 428 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N TYR C 441 " --> pdb=" O LEU C 437 " (cutoff:3.500A) Processing helix chain 'D' and resid 12 through 21 Processing helix chain 'D' and resid 71 through 74 removed outlier: 4.043A pdb=" N GLN D 74 " --> pdb=" O GLU D 71 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 71 through 74' Processing helix chain 'D' and resid 91 through 93 No H-bonds generated for 'chain 'D' and resid 91 through 93' Processing helix chain 'D' and resid 170 through 177 removed outlier: 3.966A pdb=" N VAL D 174 " --> pdb=" O SER D 170 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N ARG D 175 " --> pdb=" O PRO D 171 " (cutoff:3.500A) Processing helix chain 'D' and resid 221 through 226 removed outlier: 3.684A pdb=" N VAL D 225 " --> pdb=" O LEU D 221 " (cutoff:3.500A) Processing helix chain 'D' and resid 227 through 242 removed outlier: 3.545A pdb=" N SER D 231 " --> pdb=" O LEU D 227 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N VAL D 240 " --> pdb=" O VAL D 236 " (cutoff:3.500A) Processing helix chain 'D' and resid 249 through 269 removed outlier: 4.604A pdb=" N SER D 253 " --> pdb=" O GLY D 249 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N LYS D 255 " --> pdb=" O ARG D 251 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N THR D 257 " --> pdb=" O SER D 253 " (cutoff:3.500A) Processing helix chain 'D' and resid 270 through 272 No H-bonds generated for 'chain 'D' and resid 270 through 272' Processing helix chain 'D' and resid 281 through 283 No H-bonds generated for 'chain 'D' and resid 281 through 283' Processing helix chain 'D' and resid 284 through 308 removed outlier: 4.939A pdb=" N CYS D 290 " --> pdb=" O TYR D 286 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N VAL D 295 " --> pdb=" O MET D 291 " (cutoff:3.500A) Processing helix chain 'D' and resid 317 through 325 removed outlier: 3.602A pdb=" N HIS D 323 " --> pdb=" O ASP D 319 " (cutoff:3.500A) Processing helix chain 'D' and resid 326 through 334 Processing helix chain 'D' and resid 402 through 458 removed outlier: 3.682A pdb=" N SER D 408 " --> pdb=" O GLN D 404 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N ARG D 410 " --> pdb=" O LEU D 406 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N ARG D 416 " --> pdb=" O PHE D 412 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N VAL D 432 " --> pdb=" O ARG D 428 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N TYR D 441 " --> pdb=" O LEU D 437 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 85 through 89 removed outlier: 6.845A pdb=" N TYR A 114 " --> pdb=" O TYR A 126 " (cutoff:3.500A) removed outlier: 5.513A pdb=" N TYR A 126 " --> pdb=" O TYR A 114 " (cutoff:3.500A) removed outlier: 4.212A pdb=" N GLU A 122 " --> pdb=" O HIS A 118 " (cutoff:3.500A) removed outlier: 7.054A pdb=" N VAL A 57 " --> pdb=" O ASN A 50 " (cutoff:3.500A) removed outlier: 6.951A pdb=" N ASN A 50 " --> pdb=" O VAL A 57 " (cutoff:3.500A) removed outlier: 7.606A pdb=" N THR A 59 " --> pdb=" O ILE A 48 " (cutoff:3.500A) removed outlier: 5.301A pdb=" N ILE A 48 " --> pdb=" O THR A 59 " (cutoff:3.500A) removed outlier: 6.633A pdb=" N TYR A 61 " --> pdb=" O TYR A 46 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N ASP A 42 " --> pdb=" O ARG A 65 " (cutoff:3.500A) removed outlier: 4.387A pdb=" N THR A 69 " --> pdb=" O THR A 38 " (cutoff:3.500A) removed outlier: 6.212A pdb=" N THR A 38 " --> pdb=" O THR A 69 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 98 through 100 removed outlier: 3.987A pdb=" N SER A 155 " --> pdb=" O ALA A 208 " (cutoff:3.500A) removed outlier: 5.233A pdb=" N ALA A 208 " --> pdb=" O SER A 155 " (cutoff:3.500A) removed outlier: 9.011A pdb=" N LEU A 157 " --> pdb=" O SER A 206 " (cutoff:3.500A) removed outlier: 8.081A pdb=" N SER A 206 " --> pdb=" O LEU A 157 " (cutoff:3.500A) removed outlier: 7.439A pdb=" N ASN A 205 " --> pdb=" O ILE A 201 " (cutoff:3.500A) removed outlier: 3.923A pdb=" N ILE A 201 " --> pdb=" O ASN A 205 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N PHE A 199 " --> pdb=" O TYR A 207 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N GLU A 209 " --> pdb=" O LYS A 197 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N GLU A 191 " --> pdb=" O ILE A 215 " (cutoff:3.500A) removed outlier: 6.650A pdb=" N ARG A 217 " --> pdb=" O LEU A 189 " (cutoff:3.500A) removed outlier: 5.347A pdb=" N LEU A 189 " --> pdb=" O ARG A 217 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'E' and resid 85 through 89 removed outlier: 6.846A pdb=" N TYR E 114 " --> pdb=" O TYR E 126 " (cutoff:3.500A) removed outlier: 5.513A pdb=" N TYR E 126 " --> pdb=" O TYR E 114 " (cutoff:3.500A) removed outlier: 4.212A pdb=" N GLU E 122 " --> pdb=" O HIS E 118 " (cutoff:3.500A) removed outlier: 7.054A pdb=" N VAL E 57 " --> pdb=" O ASN E 50 " (cutoff:3.500A) removed outlier: 6.953A pdb=" N ASN E 50 " --> pdb=" O VAL E 57 " (cutoff:3.500A) removed outlier: 7.607A pdb=" N THR E 59 " --> pdb=" O ILE E 48 " (cutoff:3.500A) removed outlier: 5.302A pdb=" N ILE E 48 " --> pdb=" O THR E 59 " (cutoff:3.500A) removed outlier: 6.633A pdb=" N TYR E 61 " --> pdb=" O TYR E 46 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N ASP E 42 " --> pdb=" O ARG E 65 " (cutoff:3.500A) removed outlier: 4.388A pdb=" N THR E 69 " --> pdb=" O THR E 38 " (cutoff:3.500A) removed outlier: 6.212A pdb=" N THR E 38 " --> pdb=" O THR E 69 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'E' and resid 98 through 100 removed outlier: 3.986A pdb=" N SER E 155 " --> pdb=" O ALA E 208 " (cutoff:3.500A) removed outlier: 5.234A pdb=" N ALA E 208 " --> pdb=" O SER E 155 " (cutoff:3.500A) removed outlier: 9.011A pdb=" N LEU E 157 " --> pdb=" O SER E 206 " (cutoff:3.500A) removed outlier: 8.081A pdb=" N SER E 206 " --> pdb=" O LEU E 157 " (cutoff:3.500A) removed outlier: 7.439A pdb=" N ASN E 205 " --> pdb=" O ILE E 201 " (cutoff:3.500A) removed outlier: 3.924A pdb=" N ILE E 201 " --> pdb=" O ASN E 205 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N PHE E 199 " --> pdb=" O TYR E 207 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N GLU E 209 " --> pdb=" O LYS E 197 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N GLU E 191 " --> pdb=" O ILE E 215 " (cutoff:3.500A) removed outlier: 6.651A pdb=" N ARG E 217 " --> pdb=" O LEU E 189 " (cutoff:3.500A) removed outlier: 5.347A pdb=" N LEU E 189 " --> pdb=" O ARG E 217 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 85 through 89 removed outlier: 6.845A pdb=" N TYR B 114 " --> pdb=" O TYR B 126 " (cutoff:3.500A) removed outlier: 5.514A pdb=" N TYR B 126 " --> pdb=" O TYR B 114 " (cutoff:3.500A) removed outlier: 4.212A pdb=" N GLU B 122 " --> pdb=" O HIS B 118 " (cutoff:3.500A) removed outlier: 7.054A pdb=" N VAL B 57 " --> pdb=" O ASN B 50 " (cutoff:3.500A) removed outlier: 6.951A pdb=" N ASN B 50 " --> pdb=" O VAL B 57 " (cutoff:3.500A) removed outlier: 7.606A pdb=" N THR B 59 " --> pdb=" O ILE B 48 " (cutoff:3.500A) removed outlier: 5.301A pdb=" N ILE B 48 " --> pdb=" O THR B 59 " (cutoff:3.500A) removed outlier: 6.633A pdb=" N TYR B 61 " --> pdb=" O TYR B 46 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N ASP B 42 " --> pdb=" O ARG B 65 " (cutoff:3.500A) removed outlier: 4.388A pdb=" N THR B 69 " --> pdb=" O THR B 38 " (cutoff:3.500A) removed outlier: 6.212A pdb=" N THR B 38 " --> pdb=" O THR B 69 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 98 through 100 removed outlier: 3.987A pdb=" N SER B 155 " --> pdb=" O ALA B 208 " (cutoff:3.500A) removed outlier: 5.234A pdb=" N ALA B 208 " --> pdb=" O SER B 155 " (cutoff:3.500A) removed outlier: 9.011A pdb=" N LEU B 157 " --> pdb=" O SER B 206 " (cutoff:3.500A) removed outlier: 8.083A pdb=" N SER B 206 " --> pdb=" O LEU B 157 " (cutoff:3.500A) removed outlier: 7.439A pdb=" N ASN B 205 " --> pdb=" O ILE B 201 " (cutoff:3.500A) removed outlier: 3.925A pdb=" N ILE B 201 " --> pdb=" O ASN B 205 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N PHE B 199 " --> pdb=" O TYR B 207 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N GLU B 209 " --> pdb=" O LYS B 197 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N GLU B 191 " --> pdb=" O ILE B 215 " (cutoff:3.500A) removed outlier: 6.650A pdb=" N ARG B 217 " --> pdb=" O LEU B 189 " (cutoff:3.500A) removed outlier: 5.348A pdb=" N LEU B 189 " --> pdb=" O ARG B 217 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 85 through 89 removed outlier: 6.845A pdb=" N TYR C 114 " --> pdb=" O TYR C 126 " (cutoff:3.500A) removed outlier: 5.513A pdb=" N TYR C 126 " --> pdb=" O TYR C 114 " (cutoff:3.500A) removed outlier: 4.212A pdb=" N GLU C 122 " --> pdb=" O HIS C 118 " (cutoff:3.500A) removed outlier: 7.054A pdb=" N VAL C 57 " --> pdb=" O ASN C 50 " (cutoff:3.500A) removed outlier: 6.951A pdb=" N ASN C 50 " --> pdb=" O VAL C 57 " (cutoff:3.500A) removed outlier: 7.607A pdb=" N THR C 59 " --> pdb=" O ILE C 48 " (cutoff:3.500A) removed outlier: 5.302A pdb=" N ILE C 48 " --> pdb=" O THR C 59 " (cutoff:3.500A) removed outlier: 6.634A pdb=" N TYR C 61 " --> pdb=" O TYR C 46 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N ASP C 42 " --> pdb=" O ARG C 65 " (cutoff:3.500A) removed outlier: 4.389A pdb=" N THR C 69 " --> pdb=" O THR C 38 " (cutoff:3.500A) removed outlier: 6.213A pdb=" N THR C 38 " --> pdb=" O THR C 69 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 98 through 100 removed outlier: 3.987A pdb=" N SER C 155 " --> pdb=" O ALA C 208 " (cutoff:3.500A) removed outlier: 5.235A pdb=" N ALA C 208 " --> pdb=" O SER C 155 " (cutoff:3.500A) removed outlier: 9.011A pdb=" N LEU C 157 " --> pdb=" O SER C 206 " (cutoff:3.500A) removed outlier: 8.081A pdb=" N SER C 206 " --> pdb=" O LEU C 157 " (cutoff:3.500A) removed outlier: 7.440A pdb=" N ASN C 205 " --> pdb=" O ILE C 201 " (cutoff:3.500A) removed outlier: 3.923A pdb=" N ILE C 201 " --> pdb=" O ASN C 205 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N PHE C 199 " --> pdb=" O TYR C 207 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N GLU C 209 " --> pdb=" O LYS C 197 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N GLU C 191 " --> pdb=" O ILE C 215 " (cutoff:3.500A) removed outlier: 6.650A pdb=" N ARG C 217 " --> pdb=" O LEU C 189 " (cutoff:3.500A) removed outlier: 5.347A pdb=" N LEU C 189 " --> pdb=" O ARG C 217 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'D' and resid 85 through 89 removed outlier: 6.844A pdb=" N TYR D 114 " --> pdb=" O TYR D 126 " (cutoff:3.500A) removed outlier: 5.513A pdb=" N TYR D 126 " --> pdb=" O TYR D 114 " (cutoff:3.500A) removed outlier: 4.212A pdb=" N GLU D 122 " --> pdb=" O HIS D 118 " (cutoff:3.500A) removed outlier: 7.055A pdb=" N VAL D 57 " --> pdb=" O ASN D 50 " (cutoff:3.500A) removed outlier: 6.951A pdb=" N ASN D 50 " --> pdb=" O VAL D 57 " (cutoff:3.500A) removed outlier: 7.607A pdb=" N THR D 59 " --> pdb=" O ILE D 48 " (cutoff:3.500A) removed outlier: 5.302A pdb=" N ILE D 48 " --> pdb=" O THR D 59 " (cutoff:3.500A) removed outlier: 6.633A pdb=" N TYR D 61 " --> pdb=" O TYR D 46 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N ASP D 42 " --> pdb=" O ARG D 65 " (cutoff:3.500A) removed outlier: 4.387A pdb=" N THR D 69 " --> pdb=" O THR D 38 " (cutoff:3.500A) removed outlier: 6.212A pdb=" N THR D 38 " --> pdb=" O THR D 69 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'D' and resid 98 through 100 removed outlier: 3.986A pdb=" N SER D 155 " --> pdb=" O ALA D 208 " (cutoff:3.500A) removed outlier: 5.235A pdb=" N ALA D 208 " --> pdb=" O SER D 155 " (cutoff:3.500A) removed outlier: 9.011A pdb=" N LEU D 157 " --> pdb=" O SER D 206 " (cutoff:3.500A) removed outlier: 8.082A pdb=" N SER D 206 " --> pdb=" O LEU D 157 " (cutoff:3.500A) removed outlier: 7.438A pdb=" N ASN D 205 " --> pdb=" O ILE D 201 " (cutoff:3.500A) removed outlier: 3.924A pdb=" N ILE D 201 " --> pdb=" O ASN D 205 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N PHE D 199 " --> pdb=" O TYR D 207 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N GLU D 209 " --> pdb=" O LYS D 197 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N GLU D 191 " --> pdb=" O ILE D 215 " (cutoff:3.500A) removed outlier: 6.650A pdb=" N ARG D 217 " --> pdb=" O LEU D 189 " (cutoff:3.500A) removed outlier: 5.348A pdb=" N LEU D 189 " --> pdb=" O ARG D 217 " (cutoff:3.500A) 775 hydrogen bonds defined for protein. 2325 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.82 Time building geometry restraints manager: 2.32 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 2510 1.31 - 1.44: 4734 1.44 - 1.57: 9336 1.57 - 1.70: 20 1.70 - 1.83: 70 Bond restraints: 16670 Sorted by residual: bond pdb=" C5 TKT C 501 " pdb=" N1 TKT C 501 " ideal model delta sigma weight residual 1.463 1.282 0.181 2.00e-02 2.50e+03 8.22e+01 bond pdb=" C5 TKT B 501 " pdb=" N1 TKT B 501 " ideal model delta sigma weight residual 1.463 1.282 0.181 2.00e-02 2.50e+03 8.19e+01 bond pdb=" C5 TKT E 501 " pdb=" N1 TKT E 501 " ideal model delta sigma weight residual 1.463 1.282 0.181 2.00e-02 2.50e+03 8.17e+01 bond pdb=" C5 TKT A 501 " pdb=" N1 TKT A 501 " ideal model delta sigma weight residual 1.463 1.282 0.181 2.00e-02 2.50e+03 8.17e+01 bond pdb=" C5 TKT D 501 " pdb=" N1 TKT D 501 " ideal model delta sigma weight residual 1.463 1.282 0.181 2.00e-02 2.50e+03 8.15e+01 ... (remaining 16665 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.09: 22240 4.09 - 8.19: 460 8.19 - 12.28: 50 12.28 - 16.38: 35 16.38 - 20.47: 5 Bond angle restraints: 22790 Sorted by residual: angle pdb=" CA LEU C 73 " pdb=" CB LEU C 73 " pdb=" CG LEU C 73 " ideal model delta sigma weight residual 116.30 136.77 -20.47 3.50e+00 8.16e-02 3.42e+01 angle pdb=" CA LEU B 73 " pdb=" CB LEU B 73 " pdb=" CG LEU B 73 " ideal model delta sigma weight residual 116.30 136.77 -20.47 3.50e+00 8.16e-02 3.42e+01 angle pdb=" CA LEU A 73 " pdb=" CB LEU A 73 " pdb=" CG LEU A 73 " ideal model delta sigma weight residual 116.30 136.74 -20.44 3.50e+00 8.16e-02 3.41e+01 angle pdb=" CA LEU D 73 " pdb=" CB LEU D 73 " pdb=" CG LEU D 73 " ideal model delta sigma weight residual 116.30 136.73 -20.43 3.50e+00 8.16e-02 3.41e+01 angle pdb=" CA LEU E 73 " pdb=" CB LEU E 73 " pdb=" CG LEU E 73 " ideal model delta sigma weight residual 116.30 136.71 -20.41 3.50e+00 8.16e-02 3.40e+01 ... (remaining 22785 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.99: 8816 16.99 - 33.98: 594 33.98 - 50.97: 100 50.97 - 67.96: 10 67.96 - 84.95: 5 Dihedral angle restraints: 9525 sinusoidal: 3755 harmonic: 5770 Sorted by residual: dihedral pdb=" CA SER C 179 " pdb=" C SER C 179 " pdb=" N ILE C 180 " pdb=" CA ILE C 180 " ideal model delta harmonic sigma weight residual -180.00 -115.57 -64.43 0 5.00e+00 4.00e-02 1.66e+02 dihedral pdb=" CA SER B 179 " pdb=" C SER B 179 " pdb=" N ILE B 180 " pdb=" CA ILE B 180 " ideal model delta harmonic sigma weight residual -180.00 -115.60 -64.40 0 5.00e+00 4.00e-02 1.66e+02 dihedral pdb=" CA SER D 179 " pdb=" C SER D 179 " pdb=" N ILE D 180 " pdb=" CA ILE D 180 " ideal model delta harmonic sigma weight residual -180.00 -115.67 -64.33 0 5.00e+00 4.00e-02 1.66e+02 ... (remaining 9522 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.062: 1687 0.062 - 0.124: 760 0.124 - 0.186: 192 0.186 - 0.248: 71 0.248 - 0.310: 45 Chirality restraints: 2755 Sorted by residual: chirality pdb=" CB VAL C 252 " pdb=" CA VAL C 252 " pdb=" CG1 VAL C 252 " pdb=" CG2 VAL C 252 " both_signs ideal model delta sigma weight residual False -2.63 -2.32 -0.31 2.00e-01 2.50e+01 2.40e+00 chirality pdb=" CB VAL A 252 " pdb=" CA VAL A 252 " pdb=" CG1 VAL A 252 " pdb=" CG2 VAL A 252 " both_signs ideal model delta sigma weight residual False -2.63 -2.32 -0.31 2.00e-01 2.50e+01 2.37e+00 chirality pdb=" CB VAL E 252 " pdb=" CA VAL E 252 " pdb=" CG1 VAL E 252 " pdb=" CG2 VAL E 252 " both_signs ideal model delta sigma weight residual False -2.63 -2.32 -0.31 2.00e-01 2.50e+01 2.37e+00 ... (remaining 2752 not shown) Planarity restraints: 2775 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CG GLU D 209 " 0.013 2.00e-02 2.50e+03 2.63e-02 6.90e+00 pdb=" CD GLU D 209 " -0.045 2.00e-02 2.50e+03 pdb=" OE1 GLU D 209 " 0.016 2.00e-02 2.50e+03 pdb=" OE2 GLU D 209 " 0.016 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CG GLU A 209 " 0.013 2.00e-02 2.50e+03 2.63e-02 6.90e+00 pdb=" CD GLU A 209 " -0.045 2.00e-02 2.50e+03 pdb=" OE1 GLU A 209 " 0.016 2.00e-02 2.50e+03 pdb=" OE2 GLU A 209 " 0.016 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CG GLU B 209 " 0.013 2.00e-02 2.50e+03 2.62e-02 6.84e+00 pdb=" CD GLU B 209 " -0.045 2.00e-02 2.50e+03 pdb=" OE1 GLU B 209 " 0.016 2.00e-02 2.50e+03 pdb=" OE2 GLU B 209 " 0.016 2.00e-02 2.50e+03 ... (remaining 2772 not shown) Histogram of nonbonded interaction distances: 2.23 - 2.76: 2340 2.76 - 3.30: 15745 3.30 - 3.83: 27640 3.83 - 4.37: 30305 4.37 - 4.90: 51557 Nonbonded interactions: 127587 Sorted by model distance: nonbonded pdb=" NZ LYS D 197 " pdb=" O7 NAG T 2 " model vdw 2.228 3.120 nonbonded pdb=" NZ LYS B 197 " pdb=" O7 NAG N 2 " model vdw 2.228 3.120 nonbonded pdb=" NZ LYS A 197 " pdb=" O7 NAG H 2 " model vdw 2.229 3.120 nonbonded pdb=" NZ LYS C 197 " pdb=" O7 NAG Q 2 " model vdw 2.229 3.120 nonbonded pdb=" NZ LYS E 197 " pdb=" O7 NAG K 2 " model vdw 2.229 3.120 ... (remaining 127582 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.05 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' } ncs_group { reference = chain 'F' selection = chain 'H' selection = chain 'I' selection = chain 'K' selection = chain 'L' selection = chain 'N' selection = chain 'O' selection = chain 'Q' selection = chain 'R' selection = chain 'T' } ncs_group { reference = chain 'G' selection = chain 'J' selection = chain 'M' selection = chain 'P' selection = chain 'S' } Set up NCS constraints Number of NCS constrained groups: 3 pdb_interpretation.ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' } pdb_interpretation.ncs_group { reference = chain 'F' selection = chain 'H' selection = chain 'I' selection = chain 'K' selection = chain 'L' selection = chain 'N' selection = chain 'O' selection = chain 'Q' selection = chain 'R' selection = chain 'T' } pdb_interpretation.ncs_group { reference = chain 'G' selection = chain 'J' selection = chain 'M' selection = chain 'P' selection = chain 'S' } Set refine NCS operators NCS operators will be refined. Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.280 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: 0.020 Extract box with map and model: 0.230 Check model and map are aligned: 0.040 Set scattering table: 0.040 Process input model: 17.060 Find NCS groups from input model: 0.450 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.550 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 20.710 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7655 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 : 0.011 0.181 16710 Z= 0.493 Angle : 1.581 20.472 22905 Z= 0.803 Chirality : 0.082 0.310 2755 Planarity : 0.007 0.031 2760 Dihedral : 11.988 84.950 5750 Min Nonbonded Distance : 2.228 Molprobity Statistics. All-atom Clashscore : 16.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.86 % Favored : 95.14 % Rotamer: Outliers : 0.29 % Allowed : 11.08 % Favored : 88.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.27 % 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 are not related in a simple way. whole: -2.60 (0.17), residues: 1915 helix: -1.30 (0.16), residues: 715 sheet: -1.77 (0.20), residues: 475 loop : -1.90 (0.22), residues: 725 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 28 TYR 0.031 0.004 TYR A 207 PHE 0.025 0.004 PHE B 196 TRP 0.039 0.005 TRP A 456 HIS 0.012 0.004 HIS A 411 Details of bonding type rmsd/Z covalent geometry : bond 0.01071 / 0.49 (16670) covalent geometry : angle 1.57273 / 0.80 (22790) SS BOND : bond 0.00247 / 0.13 ( 5) SS BOND : angle 2.28766 / 1.40 ( 10) hydrogen bonds : bond 0.26321 / 17.30 ( 775) hydrogen bonds : angle 8.38771 / 5.82 ( 2325) link_BETA1-4 : bond 0.00714 / 0.47 ( 20) link_BETA1-4 : angle 2.25341 / 1.50 ( 60) link_NAG-ASN : bond 0.01142 / 0.83 ( 15) link_NAG-ASN : angle 3.45101 / 2.26 ( 45) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3830 Ramachandran restraints generated. 1915 Oldfield, 0 Emsley, 1915 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3830 Ramachandran restraints generated. 1915 Oldfield, 0 Emsley, 1915 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 96 residues out of total 362 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 95 time to evaluate : 0.133 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 102 GLU cc_start: 0.8490 (mp0) cc_final: 0.8130 (mp0) REVERT: A 144 PHE cc_start: 0.6705 (m-10) cc_final: 0.6443 (m-80) REVERT: A 152 THR cc_start: 0.8350 (m) cc_final: 0.7959 (p) REVERT: A 156 TRP cc_start: 0.7710 (t-100) cc_final: 0.7032 (t60) REVERT: A 211 LYS cc_start: 0.8437 (mttm) cc_final: 0.7957 (ptpp) REVERT: A 247 ASP cc_start: 0.7438 (t70) cc_final: 0.6697 (m-30) REVERT: A 286 TYR cc_start: 0.8007 (m-10) cc_final: 0.7599 (t80) REVERT: A 422 VAL cc_start: 0.8794 (t) cc_final: 0.8509 (t) REVERT: A 426 TRP cc_start: 0.8388 (m100) cc_final: 0.8111 (m100) REVERT: A 428 ARG cc_start: 0.8503 (tmt90) cc_final: 0.7697 (tpt170) REVERT: A 441 TYR cc_start: 0.8472 (t80) cc_final: 0.7966 (t80) outliers start: 1 outliers final: 0 residues processed: 96 average time/residue: 0.0800 time to fit residues: 9.0712 Evaluate side-chains 57 residues out of total 362 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 57 time to evaluate : 0.124 Evaluate side-chains 0 residues out of total 0 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 0 time to evaluate : 0.001 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.0009 Evaluate side-chains 0 residues out of total 0 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 0 time to evaluate : 0.001 Evaluate side-chains 0 residues out of total 0 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 0 time to evaluate : 0.001 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.0014 Evaluate side-chains 0 residues out of total 0 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 0 time to evaluate : 0.001 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 190 random chunks: chunk 98 optimal weight: 1.9990 chunk 107 optimal weight: 3.9990 chunk 10 optimal weight: 0.0050 chunk 66 optimal weight: 0.8980 chunk 130 optimal weight: 2.9990 chunk 124 optimal weight: 3.9990 chunk 103 optimal weight: 3.9990 chunk 77 optimal weight: 4.9990 chunk 122 optimal weight: 4.9990 chunk 91 optimal weight: 0.9990 chunk 149 optimal weight: 10.0000 overall best weight: 1.3800 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 119 HIS A 124 GLN A 205 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3570 r_free = 0.3570 target = 0.095429 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3319 r_free = 0.3319 target = 0.082258 restraints weight = 12808.038| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3357 r_free = 0.3357 target = 0.084087 restraints weight = 7343.631| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3383 r_free = 0.3383 target = 0.085349 restraints weight = 4802.505| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3401 r_free = 0.3401 target = 0.086206 restraints weight = 3429.484| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3410 r_free = 0.3410 target = 0.086689 restraints weight = 2658.484| |-----------------------------------------------------------------------------| r_work (final): 0.3382 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2431 r_free = 0.2431 target = 0.043798 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 25)----------------| | r_work = 0.2441 r_free = 0.2441 target = 0.043701 restraints weight = 202.640| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.2443 r_free = 0.2443 target = 0.043704 restraints weight = 2.586 | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 22)----------------| | r_work = 0.2443 r_free = 0.2443 target = 0.043704 restraints weight = 0.006 | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 22)----------------| | r_work = 0.2443 r_free = 0.2443 target = 0.043704 restraints weight = 0.006 | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.2443 r_free = 0.2443 target = 0.043704 restraints weight = 0.006 | |-----------------------------------------------------------------------------| r_work (final): 0.2478 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2805 r_free = 0.2805 target = 0.062774 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 26)----------------| | r_work = 0.2807 r_free = 0.2807 target = 0.060133 restraints weight = 370.907| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.2798 r_free = 0.2798 target = 0.060749 restraints weight = 158.233| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.2795 r_free = 0.2795 target = 0.061081 restraints weight = 104.417| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.2793 r_free = 0.2793 target = 0.061333 restraints weight = 79.440| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.2794 r_free = 0.2794 target = 0.061377 restraints weight = 65.064| |-----------------------------------------------------------------------------| r_work (final): 0.2766 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7618 moved from start: 0.2867 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.062 16710 Z= 0.202 Angle : 0.906 12.844 22905 Z= 0.465 Chirality : 0.066 1.023 2755 Planarity : 0.008 0.133 2760 Dihedral : 7.407 76.390 2125 Min Nonbonded Distance : 2.423 Molprobity Statistics. All-atom Clashscore : 13.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.05 % Favored : 92.95 % Rotamer: Outliers : 0.58 % Allowed : 5.54 % Favored : 93.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.27 % 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 are not related in a simple way. whole: -1.75 (0.19), residues: 1915 helix: -0.61 (0.17), residues: 725 sheet: -0.96 (0.23), residues: 445 loop : -1.68 (0.25), residues: 745 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG B 410 TYR 0.015 0.002 TYR A 207 PHE 0.018 0.002 PHE B 233 TRP 0.013 0.001 TRP E 63 HIS 0.008 0.002 HIS D 411 Details of bonding type rmsd/Z covalent geometry : bond 0.00422 / 0.20 (16670) covalent geometry : angle 0.89256 / 0.46 (22790) SS BOND : bond 0.00207 / 0.11 ( 5) SS BOND : angle 1.61564 / 1.02 ( 10) hydrogen bonds : bond 0.06406 / 4.13 ( 775) hydrogen bonds : angle 6.12794 / 4.23 ( 2325) link_BETA1-4 : bond 0.00375 / 0.26 ( 20) link_BETA1-4 : angle 1.55313 / 1.08 ( 60) link_NAG-ASN : bond 0.00350 / 0.24 ( 15) link_NAG-ASN : angle 3.28792 / 2.26 ( 45) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3830 Ramachandran restraints generated. 1915 Oldfield, 0 Emsley, 1915 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3830 Ramachandran restraints generated. 1915 Oldfield, 0 Emsley, 1915 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 79 residues out of total 362 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 77 time to evaluate : 0.122 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 152 THR cc_start: 0.8993 (m) cc_final: 0.8207 (m) REVERT: E 157 LEU cc_start: 0.9034 (OUTLIER) cc_final: 0.7923 (pp) REVERT: E 247 ASP cc_start: 0.7516 (t70) cc_final: 0.6958 (m-30) REVERT: E 286 TYR cc_start: 0.7942 (m-10) cc_final: 0.7543 (t80) REVERT: E 307 LEU cc_start: 0.8753 (tt) cc_final: 0.8181 (mm) REVERT: E 426 TRP cc_start: 0.8548 (m100) cc_final: 0.8214 (m-10) REVERT: E 428 ARG cc_start: 0.8296 (ttt-90) cc_final: 0.7999 (tpt170) REVERT: E 431 TYR cc_start: 0.8730 (m-80) cc_final: 0.8315 (m-80) outliers start: 2 outliers final: 1 residues processed: 78 average time/residue: 0.0687 time to fit residues: 6.5147 Evaluate side-chains 47 residues out of total 362 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 45 time to evaluate : 0.084 Evaluate side-chains 0 residues out of total 0 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 0 time to evaluate : 0.001 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.0006 Evaluate side-chains 0 residues out of total 0 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 0 time to evaluate : 0.000 Evaluate side-chains 0 residues out of total 0 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 0 time to evaluate : 0.001 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.0012 Evaluate side-chains 0 residues out of total 0 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 0 time to evaluate : 0.001 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 190 random chunks: chunk 129 optimal weight: 0.8980 chunk 28 optimal weight: 1.9990 chunk 10 optimal weight: 1.9990 chunk 145 optimal weight: 9.9990 chunk 91 optimal weight: 8.9990 chunk 93 optimal weight: 0.0170 chunk 46 optimal weight: 6.9990 chunk 87 optimal weight: 0.8980 chunk 68 optimal weight: 3.9990 chunk 124 optimal weight: 2.9990 chunk 123 optimal weight: 0.9990 overall best weight: 0.9622 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... E 119 HIS E 124 GLN E 183 ASN E 205 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3571 r_free = 0.3571 target = 0.096864 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3317 r_free = 0.3317 target = 0.083356 restraints weight = 12448.109| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3352 r_free = 0.3352 target = 0.085058 restraints weight = 7362.851| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3376 r_free = 0.3376 target = 0.086210 restraints weight = 4902.700| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3389 r_free = 0.3389 target = 0.086896 restraints weight = 3585.212| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3402 r_free = 0.3402 target = 0.087462 restraints weight = 2867.389| |-----------------------------------------------------------------------------| r_work (final): 0.3378 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2448 r_free = 0.2448 target = 0.044914 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 26)----------------| | r_work = 0.2441 r_free = 0.2441 target = 0.044673 restraints weight = 183.140| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.2456 r_free = 0.2456 target = 0.044773 restraints weight = 18.310| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.2458 r_free = 0.2458 target = 0.044805 restraints weight = 3.826 | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.2459 r_free = 0.2459 target = 0.044824 restraints weight = 0.927 | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.2459 r_free = 0.2459 target = 0.044828 restraints weight = 0.227 | |-----------------------------------------------------------------------------| r_work (final): 0.2424 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2498 r_free = 0.2498 target = 0.050336 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.2415 r_free = 0.2415 target = 0.046430 restraints weight = 301.940| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.2441 r_free = 0.2441 target = 0.047623 restraints weight = 214.202| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.2456 r_free = 0.2456 target = 0.048462 restraints weight = 148.105| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.2472 r_free = 0.2472 target = 0.049034 restraints weight = 98.427| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.2482 r_free = 0.2482 target = 0.049452 restraints weight = 65.877| |-----------------------------------------------------------------------------| r_work (final): 0.2475 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7646 moved from start: 0.3484 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 16710 Z= 0.172 Angle : 0.824 13.418 22905 Z= 0.411 Chirality : 0.060 0.825 2755 Planarity : 0.005 0.034 2760 Dihedral : 7.045 74.947 2125 Min Nonbonded Distance : 2.421 Molprobity Statistics. All-atom Clashscore : 14.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.05 % Favored : 92.95 % Rotamer: Outliers : 0.00 % Allowed : 4.37 % Favored : 95.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.27 % 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 are not related in a simple way. whole: -1.46 (0.19), residues: 1915 helix: -0.25 (0.17), residues: 725 sheet: -0.98 (0.23), residues: 445 loop : -1.55 (0.25), residues: 745 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 169 TYR 0.018 0.002 TYR B 223 PHE 0.040 0.002 PHE C 103 TRP 0.012 0.001 TRP B 68 HIS 0.012 0.002 HIS C 411 Details of bonding type rmsd/Z covalent geometry : bond 0.00374 / 0.17 (16670) covalent geometry : angle 0.81145 / 0.41 (22790) SS BOND : bond 0.00152 / 0.08 ( 5) SS BOND : angle 0.83198 / 0.53 ( 10) hydrogen bonds : bond 0.05420 / 3.48 ( 775) hydrogen bonds : angle 5.76585 / 4.00 ( 2325) link_BETA1-4 : bond 0.00511 / 0.35 ( 20) link_BETA1-4 : angle 1.38983 / 0.98 ( 60) link_NAG-ASN : bond 0.00273 / 0.21 ( 15) link_NAG-ASN : angle 3.00463 / 2.04 ( 45) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3830 Ramachandran restraints generated. 1915 Oldfield, 0 Emsley, 1915 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3830 Ramachandran restraints generated. 1915 Oldfield, 0 Emsley, 1915 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 66 residues out of total 362 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 66 time to evaluate : 0.135 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 68 TRP cc_start: 0.9170 (p90) cc_final: 0.8911 (p90) REVERT: B 101 ASN cc_start: 0.8079 (m110) cc_final: 0.7812 (m110) REVERT: B 212 PHE cc_start: 0.8117 (m-80) cc_final: 0.7490 (m-80) REVERT: B 247 ASP cc_start: 0.7532 (t70) cc_final: 0.6950 (m-30) REVERT: B 286 TYR cc_start: 0.7602 (m-10) cc_final: 0.7181 (t80) REVERT: B 307 LEU cc_start: 0.8751 (tt) cc_final: 0.8312 (mm) REVERT: B 426 TRP cc_start: 0.8668 (m100) cc_final: 0.8154 (m100) REVERT: B 428 ARG cc_start: 0.8306 (ttt-90) cc_final: 0.7911 (tpt170) REVERT: B 431 TYR cc_start: 0.8730 (m-80) cc_final: 0.8229 (m-80) outliers start: 0 outliers final: 0 residues processed: 66 average time/residue: 0.0536 time to fit residues: 4.5422 Evaluate side-chains 50 residues out of total 362 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 50 time to evaluate : 0.132 Evaluate side-chains 0 residues out of total 0 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 0 time to evaluate : 0.001 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.0010 Evaluate side-chains 0 residues out of total 0 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 0 time to evaluate : 0.001 Evaluate side-chains 0 residues out of total 0 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 0 time to evaluate : 0.001 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.0013 Evaluate side-chains 0 residues out of total 0 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 0 time to evaluate : 0.001 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 190 random chunks: chunk 108 optimal weight: 9.9990 chunk 35 optimal weight: 7.9990 chunk 129 optimal weight: 0.0370 chunk 74 optimal weight: 6.9990 chunk 124 optimal weight: 3.9990 chunk 63 optimal weight: 0.8980 chunk 163 optimal weight: 0.7980 chunk 19 optimal weight: 3.9990 chunk 68 optimal weight: 0.9980 chunk 37 optimal weight: 10.0000 chunk 158 optimal weight: 5.9990 overall best weight: 1.3460 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 119 HIS B 124 GLN B 183 ASN B 205 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3549 r_free = 0.3549 target = 0.096060 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3323 r_free = 0.3323 target = 0.083287 restraints weight = 11381.573| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3355 r_free = 0.3355 target = 0.084864 restraints weight = 6994.173| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3375 r_free = 0.3375 target = 0.085885 restraints weight = 4781.533| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3390 r_free = 0.3390 target = 0.086631 restraints weight = 3589.486| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3399 r_free = 0.3399 target = 0.087101 restraints weight = 2870.926| |-----------------------------------------------------------------------------| r_work (final): 0.3377 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2479 r_free = 0.2479 target = 0.044930 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 26)----------------| | r_work = 0.2487 r_free = 0.2487 target = 0.044686 restraints weight = 212.798| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.2491 r_free = 0.2491 target = 0.044728 restraints weight = 9.709 | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 22)----------------| | r_work = 0.2491 r_free = 0.2491 target = 0.044728 restraints weight = 1.222 | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 22)----------------| | r_work = 0.2491 r_free = 0.2491 target = 0.044728 restraints weight = 1.200 | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.2491 r_free = 0.2491 target = 0.044728 restraints weight = 1.200 | |-----------------------------------------------------------------------------| r_work (final): 0.2436 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2491 r_free = 0.2491 target = 0.049704 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.2410 r_free = 0.2410 target = 0.045871 restraints weight = 312.882| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.2436 r_free = 0.2436 target = 0.047076 restraints weight = 216.575| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.2451 r_free = 0.2451 target = 0.047803 restraints weight = 145.032| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.2467 r_free = 0.2467 target = 0.048448 restraints weight = 97.242| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.2476 r_free = 0.2476 target = 0.048849 restraints weight = 63.537| |-----------------------------------------------------------------------------| r_work (final): 0.2469 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7653 moved from start: 0.3919 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.068 16710 Z= 0.184 Angle : 0.792 14.456 22905 Z= 0.401 Chirality : 0.057 0.723 2755 Planarity : 0.006 0.080 2760 Dihedral : 6.958 75.044 2125 Min Nonbonded Distance : 2.236 Molprobity Statistics. All-atom Clashscore : 16.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.09 % Favored : 91.91 % Rotamer: Outliers : 0.00 % Allowed : 3.79 % Favored : 96.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.27 % 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 are not related in a simple way. whole: -1.42 (0.19), residues: 1915 helix: -0.21 (0.18), residues: 725 sheet: -0.74 (0.23), residues: 420 loop : -1.66 (0.24), residues: 770 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG D 410 TYR 0.017 0.002 TYR B 223 PHE 0.018 0.002 PHE C 103 TRP 0.012 0.001 TRP B 68 HIS 0.009 0.002 HIS C 411 Details of bonding type rmsd/Z covalent geometry : bond 0.00423 / 0.18 (16670) covalent geometry : angle 0.77929 / 0.40 (22790) SS BOND : bond 0.00132 / 0.07 ( 5) SS BOND : angle 0.56624 / 0.36 ( 10) hydrogen bonds : bond 0.04944 / 3.18 ( 775) hydrogen bonds : angle 5.52017 / 3.85 ( 2325) link_BETA1-4 : bond 0.00262 / 0.18 ( 20) link_BETA1-4 : angle 1.37733 / 0.96 ( 60) link_NAG-ASN : bond 0.00271 / 0.19 ( 15) link_NAG-ASN : angle 3.07271 / 2.08 ( 45) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3830 Ramachandran restraints generated. 1915 Oldfield, 0 Emsley, 1915 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3830 Ramachandran restraints generated. 1915 Oldfield, 0 Emsley, 1915 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 67 residues out of total 362 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 67 time to evaluate : 0.130 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 101 ASN cc_start: 0.7924 (m110) cc_final: 0.7679 (m110) REVERT: B 144 PHE cc_start: 0.7100 (m-10) cc_final: 0.6614 (m-80) REVERT: B 247 ASP cc_start: 0.7432 (t70) cc_final: 0.7025 (m-30) REVERT: B 286 TYR cc_start: 0.7468 (m-10) cc_final: 0.7152 (t80) REVERT: B 301 THR cc_start: 0.8962 (m) cc_final: 0.8761 (m) REVERT: B 307 LEU cc_start: 0.8691 (tt) cc_final: 0.8289 (mm) REVERT: B 426 TRP cc_start: 0.8536 (m100) cc_final: 0.8067 (m100) REVERT: B 428 ARG cc_start: 0.8255 (ttt-90) cc_final: 0.7929 (tpt170) outliers start: 0 outliers final: 0 residues processed: 67 average time/residue: 0.0493 time to fit residues: 4.3544 Evaluate side-chains 44 residues out of total 362 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 44 time to evaluate : 0.124 Evaluate side-chains 0 residues out of total 0 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 0 time to evaluate : 0.001 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.0011 Evaluate side-chains 0 residues out of total 0 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 0 time to evaluate : 0.001 Evaluate side-chains 0 residues out of total 0 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 0 time to evaluate : 0.001 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.0012 Evaluate side-chains 0 residues out of total 0 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 0 time to evaluate : 0.001 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 190 random chunks: chunk 0 optimal weight: 9.9990 chunk 147 optimal weight: 8.9990 chunk 99 optimal weight: 7.9990 chunk 61 optimal weight: 0.8980 chunk 117 optimal weight: 0.0170 chunk 175 optimal weight: 10.0000 chunk 171 optimal weight: 0.9980 chunk 123 optimal weight: 0.1980 chunk 74 optimal weight: 5.9990 chunk 32 optimal weight: 10.0000 chunk 98 optimal weight: 0.4980 overall best weight: 0.5218 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3585 r_free = 0.3585 target = 0.097798 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3330 r_free = 0.3330 target = 0.084156 restraints weight = 11961.748| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3365 r_free = 0.3365 target = 0.085890 restraints weight = 7094.225| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3390 r_free = 0.3390 target = 0.087134 restraints weight = 4767.222| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3407 r_free = 0.3407 target = 0.087974 restraints weight = 3486.646| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3417 r_free = 0.3417 target = 0.088466 restraints weight = 2728.250| |-----------------------------------------------------------------------------| r_work (final): 0.3402 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2467 r_free = 0.2467 target = 0.044721 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 24)----------------| | r_work = 0.2469 r_free = 0.2469 target = 0.044711 restraints weight = 230.303| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.2468 r_free = 0.2468 target = 0.044712 restraints weight = 1.145 | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 22)----------------| | r_work = 0.2468 r_free = 0.2468 target = 0.044712 restraints weight = 223.855| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 22)----------------| | r_work = 0.2468 r_free = 0.2468 target = 0.044712 restraints weight = 192.692| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.2468 r_free = 0.2468 target = 0.044712 restraints weight = 199.379| |-----------------------------------------------------------------------------| r_work (final): 0.2452 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2418 r_free = 0.2418 target = 0.047652 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.2354 r_free = 0.2354 target = 0.044427 restraints weight = 304.577| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.2377 r_free = 0.2377 target = 0.045324 restraints weight = 199.141| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.2390 r_free = 0.2390 target = 0.046075 restraints weight = 136.274| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.2401 r_free = 0.2401 target = 0.046579 restraints weight = 88.425| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.2408 r_free = 0.2408 target = 0.046935 restraints weight = 58.381| |-----------------------------------------------------------------------------| r_work (final): 0.2401 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7642 moved from start: 0.4149 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 16710 Z= 0.146 Angle : 0.731 10.454 22905 Z= 0.359 Chirality : 0.049 0.233 2755 Planarity : 0.005 0.065 2760 Dihedral : 6.755 76.459 2125 Min Nonbonded Distance : 2.441 Molprobity Statistics. All-atom Clashscore : 11.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.53 % Favored : 93.47 % Rotamer: Outliers : 0.00 % Allowed : 3.21 % Favored : 96.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.27 % 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 are not related in a simple way. whole: -0.99 (0.20), residues: 1915 helix: 0.24 (0.18), residues: 755 sheet: -0.71 (0.23), residues: 420 loop : -1.47 (0.26), residues: 740 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG C 410 TYR 0.012 0.002 TYR A 223 PHE 0.015 0.002 PHE C 103 TRP 0.015 0.001 TRP C 456 HIS 0.006 0.001 HIS C 411 Details of bonding type rmsd/Z covalent geometry : bond 0.00332 / 0.15 (16670) covalent geometry : angle 0.71825 / 0.36 (22790) SS BOND : bond 0.00128 / 0.07 ( 5) SS BOND : angle 0.46208 / 0.29 ( 10) hydrogen bonds : bond 0.04283 / 2.74 ( 775) hydrogen bonds : angle 5.08232 / 3.59 ( 2325) link_BETA1-4 : bond 0.00321 / 0.22 ( 20) link_BETA1-4 : angle 1.30906 / 0.92 ( 60) link_NAG-ASN : bond 0.00093 / 0.06 ( 15) link_NAG-ASN : angle 2.94737 / 1.99 ( 45) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3830 Ramachandran restraints generated. 1915 Oldfield, 0 Emsley, 1915 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3830 Ramachandran restraints generated. 1915 Oldfield, 0 Emsley, 1915 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 69 residues out of total 362 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 69 time to evaluate : 0.137 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 66 GLN cc_start: 0.7583 (mm110) cc_final: 0.7185 (mm110) REVERT: B 101 ASN cc_start: 0.7782 (m110) cc_final: 0.7512 (m110) REVERT: B 144 PHE cc_start: 0.7079 (m-10) cc_final: 0.6464 (m-80) REVERT: B 247 ASP cc_start: 0.7379 (t70) cc_final: 0.6917 (m-30) REVERT: B 286 TYR cc_start: 0.7518 (m-10) cc_final: 0.7120 (t80) REVERT: B 301 THR cc_start: 0.8948 (m) cc_final: 0.8732 (m) REVERT: B 307 LEU cc_start: 0.8766 (tt) cc_final: 0.8339 (mm) REVERT: B 426 TRP cc_start: 0.8493 (m100) cc_final: 0.8038 (m100) REVERT: B 428 ARG cc_start: 0.8113 (ttt-90) cc_final: 0.7347 (ttt180) REVERT: B 431 TYR cc_start: 0.8792 (m-80) cc_final: 0.8192 (m-80) outliers start: 0 outliers final: 0 residues processed: 69 average time/residue: 0.0452 time to fit residues: 4.1650 Evaluate side-chains 52 residues out of total 362 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 52 time to evaluate : 0.123 Evaluate side-chains 0 residues out of total 0 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 0 time to evaluate : 0.001 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.0009 Evaluate side-chains 0 residues out of total 0 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 0 time to evaluate : 0.001 Evaluate side-chains 0 residues out of total 0 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 0 time to evaluate : 0.001 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.0015 Evaluate side-chains 0 residues out of total 0 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 0 time to evaluate : 0.001 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 190 random chunks: chunk 111 optimal weight: 3.9990 chunk 124 optimal weight: 0.0970 chunk 21 optimal weight: 0.8980 chunk 35 optimal weight: 0.1980 chunk 72 optimal weight: 5.9990 chunk 17 optimal weight: 0.0980 chunk 29 optimal weight: 0.9980 chunk 115 optimal weight: 2.9990 chunk 112 optimal weight: 2.9990 chunk 183 optimal weight: 20.0000 chunk 117 optimal weight: 7.9990 overall best weight: 0.4578 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3673 r_free = 0.3673 target = 0.102539 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3452 r_free = 0.3452 target = 0.090458 restraints weight = 13093.029| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3482 r_free = 0.3482 target = 0.091989 restraints weight = 8107.779| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3501 r_free = 0.3501 target = 0.092942 restraints weight = 5580.965| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3514 r_free = 0.3514 target = 0.093631 restraints weight = 4235.657| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3522 r_free = 0.3522 target = 0.094027 restraints weight = 3474.464| |-----------------------------------------------------------------------------| r_work (final): 0.3417 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2431 r_free = 0.2431 target = 0.045158 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 25)----------------| | r_work = 0.2415 r_free = 0.2415 target = 0.045023 restraints weight = 242.820| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.2429 r_free = 0.2429 target = 0.045100 restraints weight = 21.169| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.2431 r_free = 0.2431 target = 0.045131 restraints weight = 3.231 | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.2432 r_free = 0.2432 target = 0.045141 restraints weight = 0.535 | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.2432 r_free = 0.2432 target = 0.045140 restraints weight = 0.088 | |-----------------------------------------------------------------------------| r_work (final): 0.2464 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2424 r_free = 0.2424 target = 0.047114 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.2362 r_free = 0.2362 target = 0.043827 restraints weight = 289.527| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.2384 r_free = 0.2384 target = 0.044777 restraints weight = 186.110| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.2396 r_free = 0.2396 target = 0.045426 restraints weight = 123.087| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.2406 r_free = 0.2406 target = 0.045950 restraints weight = 83.606| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.2413 r_free = 0.2413 target = 0.046324 restraints weight = 56.963| |-----------------------------------------------------------------------------| r_work (final): 0.2407 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7616 moved from start: 0.4465 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 16710 Z= 0.132 Angle : 0.685 6.757 22905 Z= 0.336 Chirality : 0.047 0.221 2755 Planarity : 0.005 0.050 2760 Dihedral : 6.573 77.031 2125 Min Nonbonded Distance : 2.444 Molprobity Statistics. All-atom Clashscore : 13.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.05 % Favored : 92.95 % Rotamer: Outliers : 0.00 % Allowed : 2.33 % Favored : 97.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.27 % 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 are not related in a simple way. whole: -0.80 (0.20), residues: 1915 helix: 0.46 (0.18), residues: 755 sheet: -0.62 (0.24), residues: 420 loop : -1.43 (0.26), residues: 740 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 315 TYR 0.017 0.002 TYR D 441 PHE 0.023 0.002 PHE A 233 TRP 0.015 0.001 TRP D 68 HIS 0.004 0.001 HIS A 411 Details of bonding type rmsd/Z covalent geometry : bond 0.00294 / 0.13 (16670) covalent geometry : angle 0.67221 / 0.33 (22790) SS BOND : bond 0.00106 / 0.05 ( 5) SS BOND : angle 0.32851 / 0.21 ( 10) hydrogen bonds : bond 0.03999 / 2.55 ( 775) hydrogen bonds : angle 4.87464 / 3.44 ( 2325) link_BETA1-4 : bond 0.00289 / 0.20 ( 20) link_BETA1-4 : angle 1.27413 / 0.89 ( 60) link_NAG-ASN : bond 0.00133 / 0.09 ( 15) link_NAG-ASN : angle 2.75424 / 1.86 ( 45) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3830 Ramachandran restraints generated. 1915 Oldfield, 0 Emsley, 1915 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3830 Ramachandran restraints generated. 1915 Oldfield, 0 Emsley, 1915 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 68 residues out of total 362 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 68 time to evaluate : 0.130 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 101 ASN cc_start: 0.7904 (m110) cc_final: 0.7494 (m110) REVERT: B 247 ASP cc_start: 0.7469 (t70) cc_final: 0.6873 (m-30) REVERT: B 286 TYR cc_start: 0.7709 (m-10) cc_final: 0.6948 (t80) REVERT: B 287 PHE cc_start: 0.8223 (m-80) cc_final: 0.7987 (m-10) REVERT: B 301 THR cc_start: 0.8958 (m) cc_final: 0.8730 (m) REVERT: B 307 LEU cc_start: 0.8832 (tt) cc_final: 0.8432 (mm) REVERT: B 426 TRP cc_start: 0.8618 (m100) cc_final: 0.8119 (m100) REVERT: B 428 ARG cc_start: 0.8053 (ttt-90) cc_final: 0.7450 (tpt170) REVERT: B 431 TYR cc_start: 0.8790 (m-80) cc_final: 0.8171 (m-80) outliers start: 0 outliers final: 0 residues processed: 68 average time/residue: 0.0473 time to fit residues: 4.2351 Evaluate side-chains 52 residues out of total 362 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 52 time to evaluate : 0.125 Evaluate side-chains 0 residues out of total 0 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 0 time to evaluate : 0.001 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.0010 Evaluate side-chains 0 residues out of total 0 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 0 time to evaluate : 0.001 Evaluate side-chains 0 residues out of total 0 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 0 time to evaluate : 0.001 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.0012 Evaluate side-chains 0 residues out of total 0 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 0 time to evaluate : 0.001 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 190 random chunks: chunk 137 optimal weight: 5.9990 chunk 10 optimal weight: 0.8980 chunk 3 optimal weight: 7.9990 chunk 118 optimal weight: 0.0370 chunk 19 optimal weight: 6.9990 chunk 14 optimal weight: 3.9990 chunk 89 optimal weight: 0.9990 chunk 163 optimal weight: 0.5980 chunk 139 optimal weight: 3.9990 chunk 9 optimal weight: 2.9990 chunk 105 optimal weight: 0.9980 overall best weight: 0.7060 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3659 r_free = 0.3659 target = 0.101739 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3439 r_free = 0.3439 target = 0.089771 restraints weight = 13525.779| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3470 r_free = 0.3470 target = 0.091340 restraints weight = 8544.784| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3492 r_free = 0.3492 target = 0.092429 restraints weight = 5828.304| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3504 r_free = 0.3504 target = 0.093050 restraints weight = 4320.588| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 49)----------------| | r_work = 0.3515 r_free = 0.3515 target = 0.093607 restraints weight = 3513.458| |-----------------------------------------------------------------------------| r_work (final): 0.3406 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2451 r_free = 0.2451 target = 0.045385 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.2449 r_free = 0.2449 target = 0.045271 restraints weight = 193.510| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.2455 r_free = 0.2455 target = 0.045301 restraints weight = 8.945 | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.2455 r_free = 0.2455 target = 0.045305 restraints weight = 0.904 | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 22)----------------| | r_work = 0.2455 r_free = 0.2455 target = 0.045305 restraints weight = 0.093 | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.2455 r_free = 0.2455 target = 0.045305 restraints weight = 0.093 | |-----------------------------------------------------------------------------| r_work (final): 0.2473 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2492 r_free = 0.2492 target = 0.048841 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 26)----------------| | r_work = 0.2418 r_free = 0.2418 target = 0.045842 restraints weight = 265.628| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.2446 r_free = 0.2446 target = 0.046897 restraints weight = 152.051| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.2466 r_free = 0.2466 target = 0.047652 restraints weight = 90.650| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.2478 r_free = 0.2478 target = 0.048133 restraints weight = 53.989| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.2484 r_free = 0.2484 target = 0.048419 restraints weight = 33.262| |-----------------------------------------------------------------------------| r_work (final): 0.2482 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7631 moved from start: 0.4626 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 16710 Z= 0.127 Angle : 0.695 7.362 22905 Z= 0.341 Chirality : 0.048 0.231 2755 Planarity : 0.004 0.042 2760 Dihedral : 6.495 77.239 2125 Min Nonbonded Distance : 2.441 Molprobity Statistics. All-atom Clashscore : 10.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.74 % Favored : 94.26 % Rotamer: Outliers : 0.00 % Allowed : 1.75 % Favored : 98.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.27 % 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 are not related in a simple way. whole: -0.53 (0.20), residues: 1915 helix: 0.59 (0.19), residues: 760 sheet: -0.48 (0.25), residues: 420 loop : -1.17 (0.27), residues: 735 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 416 TYR 0.021 0.002 TYR E 441 PHE 0.019 0.002 PHE A 233 TRP 0.017 0.001 TRP C 456 HIS 0.004 0.001 HIS C 411 Details of bonding type rmsd/Z covalent geometry : bond 0.00286 / 0.13 (16670) covalent geometry : angle 0.68429 / 0.34 (22790) SS BOND : bond 0.00118 / 0.06 ( 5) SS BOND : angle 0.34893 / 0.22 ( 10) hydrogen bonds : bond 0.03830 / 2.45 ( 775) hydrogen bonds : angle 4.78686 / 3.38 ( 2325) link_BETA1-4 : bond 0.00252 / 0.17 ( 20) link_BETA1-4 : angle 1.23508 / 0.88 ( 60) link_NAG-ASN : bond 0.00118 / 0.09 ( 15) link_NAG-ASN : angle 2.63133 / 1.77 ( 45) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3830 Ramachandran restraints generated. 1915 Oldfield, 0 Emsley, 1915 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3830 Ramachandran restraints generated. 1915 Oldfield, 0 Emsley, 1915 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 67 residues out of total 362 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 67 time to evaluate : 0.150 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 66 GLN cc_start: 0.7382 (mm110) cc_final: 0.7087 (mm110) REVERT: B 101 ASN cc_start: 0.8007 (m110) cc_final: 0.7536 (m110) REVERT: B 212 PHE cc_start: 0.8494 (m-80) cc_final: 0.8189 (m-80) REVERT: B 247 ASP cc_start: 0.7381 (t70) cc_final: 0.6831 (m-30) REVERT: B 286 TYR cc_start: 0.7653 (m-10) cc_final: 0.6861 (t80) REVERT: B 301 THR cc_start: 0.8960 (m) cc_final: 0.8730 (m) REVERT: B 307 LEU cc_start: 0.8795 (tt) cc_final: 0.8442 (mm) REVERT: B 426 TRP cc_start: 0.8625 (m100) cc_final: 0.8107 (m100) REVERT: B 428 ARG cc_start: 0.8051 (ttt-90) cc_final: 0.7452 (tpt170) REVERT: B 431 TYR cc_start: 0.8802 (m-80) cc_final: 0.8288 (m-80) REVERT: B 452 LEU cc_start: 0.7736 (mt) cc_final: 0.7462 (mt) outliers start: 0 outliers final: 0 residues processed: 67 average time/residue: 0.0467 time to fit residues: 4.1708 Evaluate side-chains 50 residues out of total 362 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 50 time to evaluate : 0.125 Evaluate side-chains 0 residues out of total 0 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 0 time to evaluate : 0.001 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.0010 Evaluate side-chains 0 residues out of total 0 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 0 time to evaluate : 0.001 Evaluate side-chains 0 residues out of total 0 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 0 time to evaluate : 0.001 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.0012 Evaluate side-chains 0 residues out of total 0 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 0 time to evaluate : 0.001 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 190 random chunks: chunk 92 optimal weight: 0.9990 chunk 107 optimal weight: 7.9990 chunk 50 optimal weight: 4.9990 chunk 18 optimal weight: 0.4980 chunk 97 optimal weight: 0.9980 chunk 45 optimal weight: 0.4980 chunk 149 optimal weight: 7.9990 chunk 164 optimal weight: 3.9990 chunk 32 optimal weight: 7.9990 chunk 129 optimal weight: 4.9990 chunk 51 optimal weight: 0.0470 overall best weight: 0.6080 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 183 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3657 r_free = 0.3657 target = 0.101581 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3440 r_free = 0.3440 target = 0.089817 restraints weight = 13535.241| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3472 r_free = 0.3472 target = 0.091396 restraints weight = 8346.354| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3492 r_free = 0.3492 target = 0.092441 restraints weight = 5683.200| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.3505 r_free = 0.3505 target = 0.093166 restraints weight = 4228.983| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3512 r_free = 0.3512 target = 0.093529 restraints weight = 3385.433| |-----------------------------------------------------------------------------| r_work (final): 0.3406 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2464 r_free = 0.2464 target = 0.046203 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2469 r_free = 0.2469 target = 0.046048 restraints weight = 212.178| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.2473 r_free = 0.2473 target = 0.046095 restraints weight = 10.508| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.2474 r_free = 0.2474 target = 0.046113 restraints weight = 0.926 | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 4)-----------------| | r_work = 0.2474 r_free = 0.2474 target = 0.046115 restraints weight = 0.102 | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 4)-----------------| | r_work = 0.2474 r_free = 0.2474 target = 0.046113 restraints weight = 0.010 | |-----------------------------------------------------------------------------| r_work (final): 0.2448 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2482 r_free = 0.2482 target = 0.048802 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.2404 r_free = 0.2404 target = 0.045560 restraints weight = 299.914| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.2432 r_free = 0.2432 target = 0.046767 restraints weight = 162.462| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.2454 r_free = 0.2454 target = 0.047549 restraints weight = 93.163| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.2468 r_free = 0.2468 target = 0.048109 restraints weight = 54.786| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.2474 r_free = 0.2474 target = 0.048391 restraints weight = 31.999| |-----------------------------------------------------------------------------| r_work (final): 0.2471 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7626 moved from start: 0.4824 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 16710 Z= 0.121 Angle : 0.669 6.877 22905 Z= 0.331 Chirality : 0.047 0.217 2755 Planarity : 0.004 0.041 2760 Dihedral : 6.416 77.776 2125 Min Nonbonded Distance : 2.442 Molprobity Statistics. All-atom Clashscore : 10.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.57 % Favored : 92.43 % Rotamer: Outliers : 0.00 % Allowed : 0.87 % Favored : 99.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.27 % 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 are not related in a simple way. whole: -0.54 (0.20), residues: 1915 helix: 0.65 (0.19), residues: 730 sheet: -0.49 (0.25), residues: 420 loop : -1.17 (0.26), residues: 765 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 410 TYR 0.015 0.001 TYR C 64 PHE 0.022 0.002 PHE D 103 TRP 0.016 0.001 TRP B 68 HIS 0.003 0.001 HIS A 411 Details of bonding type rmsd/Z covalent geometry : bond 0.00268 / 0.12 (16670) covalent geometry : angle 0.65843 / 0.33 (22790) SS BOND : bond 0.00058 / 0.03 ( 5) SS BOND : angle 0.27100 / 0.17 ( 10) hydrogen bonds : bond 0.03698 / 2.36 ( 775) hydrogen bonds : angle 4.67264 / 3.31 ( 2325) link_BETA1-4 : bond 0.00290 / 0.20 ( 20) link_BETA1-4 : angle 1.20269 / 0.86 ( 60) link_NAG-ASN : bond 0.00078 / 0.05 ( 15) link_NAG-ASN : angle 2.49153 / 1.67 ( 45) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3830 Ramachandran restraints generated. 1915 Oldfield, 0 Emsley, 1915 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3830 Ramachandran restraints generated. 1915 Oldfield, 0 Emsley, 1915 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 66 residues out of total 362 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 66 time to evaluate : 0.134 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 30 VAL cc_start: 0.8940 (m) cc_final: 0.8733 (m) REVERT: B 66 GLN cc_start: 0.7381 (mm110) cc_final: 0.6994 (mm110) REVERT: B 101 ASN cc_start: 0.7914 (m110) cc_final: 0.7427 (m110) REVERT: B 152 THR cc_start: 0.9051 (m) cc_final: 0.7885 (m) REVERT: B 210 MET cc_start: 0.8631 (tpp) cc_final: 0.8204 (tpp) REVERT: B 212 PHE cc_start: 0.8534 (m-80) cc_final: 0.8217 (m-80) REVERT: B 247 ASP cc_start: 0.7414 (t70) cc_final: 0.6838 (m-30) REVERT: B 286 TYR cc_start: 0.7633 (m-10) cc_final: 0.6818 (t80) REVERT: B 301 THR cc_start: 0.8979 (m) cc_final: 0.8722 (m) REVERT: B 307 LEU cc_start: 0.8782 (tt) cc_final: 0.8445 (mm) REVERT: B 426 TRP cc_start: 0.8649 (m100) cc_final: 0.8130 (m100) REVERT: B 428 ARG cc_start: 0.8060 (ttt-90) cc_final: 0.7484 (tpt170) REVERT: B 431 TYR cc_start: 0.8848 (m-80) cc_final: 0.8517 (m-80) REVERT: B 452 LEU cc_start: 0.7754 (mt) cc_final: 0.7450 (mt) outliers start: 0 outliers final: 0 residues processed: 66 average time/residue: 0.0419 time to fit residues: 3.7936 Evaluate side-chains 51 residues out of total 362 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 51 time to evaluate : 0.124 Evaluate side-chains 0 residues out of total 0 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 0 time to evaluate : 0.001 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.0010 Evaluate side-chains 0 residues out of total 0 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 0 time to evaluate : 0.001 Evaluate side-chains 0 residues out of total 0 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 0 time to evaluate : 0.001 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.0013 Evaluate side-chains 0 residues out of total 0 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 0 time to evaluate : 0.001 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 190 random chunks: chunk 47 optimal weight: 3.9990 chunk 186 optimal weight: 3.9990 chunk 180 optimal weight: 3.9990 chunk 141 optimal weight: 0.9990 chunk 96 optimal weight: 5.9990 chunk 32 optimal weight: 10.0000 chunk 169 optimal weight: 6.9990 chunk 55 optimal weight: 3.9990 chunk 142 optimal weight: 1.9990 chunk 118 optimal weight: 0.3980 chunk 137 optimal weight: 4.9990 overall best weight: 2.2788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3539 r_free = 0.3539 target = 0.094726 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3283 r_free = 0.3283 target = 0.081575 restraints weight = 12516.909| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3320 r_free = 0.3320 target = 0.083327 restraints weight = 7318.078| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3345 r_free = 0.3345 target = 0.084483 restraints weight = 4829.516| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3362 r_free = 0.3362 target = 0.085245 restraints weight = 3520.318| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.3373 r_free = 0.3373 target = 0.085818 restraints weight = 2776.735| |-----------------------------------------------------------------------------| r_work (final): 0.3352 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2092 r_free = 0.2092 target = 0.036027 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 24)----------------| | r_work = 0.2089 r_free = 0.2089 target = 0.036011 restraints weight = 176.506| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.2089 r_free = 0.2089 target = 0.036012 restraints weight = 4.813 | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 22)----------------| | r_work = 0.2089 r_free = 0.2089 target = 0.036012 restraints weight = 0.097 | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 22)----------------| | r_work = 0.2089 r_free = 0.2089 target = 0.036012 restraints weight = 0.095 | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.2089 r_free = 0.2089 target = 0.036012 restraints weight = 0.095 | |-----------------------------------------------------------------------------| r_work (final): 0.2158 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2498 r_free = 0.2498 target = 0.049472 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.2432 r_free = 0.2432 target = 0.046636 restraints weight = 235.809| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.2453 r_free = 0.2453 target = 0.047568 restraints weight = 138.670| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.2472 r_free = 0.2472 target = 0.048292 restraints weight = 84.964| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.2483 r_free = 0.2483 target = 0.048748 restraints weight = 52.007| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.2486 r_free = 0.2486 target = 0.048910 restraints weight = 32.923| |-----------------------------------------------------------------------------| r_work (final): 0.2483 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7730 moved from start: 0.4920 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 16710 Z= 0.154 Angle : 0.668 6.726 22905 Z= 0.333 Chirality : 0.046 0.210 2755 Planarity : 0.004 0.039 2760 Dihedral : 6.287 76.179 2125 Min Nonbonded Distance : 2.409 Molprobity Statistics. All-atom Clashscore : 11.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.31 % Favored : 92.69 % Rotamer: Outliers : 0.00 % Allowed : 0.87 % Favored : 99.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.27 % 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 are not related in a simple way. whole: -0.27 (0.21), residues: 1915 helix: 0.81 (0.20), residues: 730 sheet: -0.39 (0.25), residues: 420 loop : -0.92 (0.26), residues: 765 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 410 TYR 0.017 0.002 TYR E 64 PHE 0.017 0.002 PHE A 233 TRP 0.016 0.002 TRP E 68 HIS 0.004 0.001 HIS C 411 Details of bonding type rmsd/Z covalent geometry : bond 0.00338 / 0.15 (16670) covalent geometry : angle 0.65567 / 0.33 (22790) SS BOND : bond 0.00198 / 0.10 ( 5) SS BOND : angle 0.46499 / 0.30 ( 10) hydrogen bonds : bond 0.03704 / 2.38 ( 775) hydrogen bonds : angle 4.70486 / 3.33 ( 2325) link_BETA1-4 : bond 0.00247 / 0.17 ( 20) link_BETA1-4 : angle 1.35311 / 0.98 ( 60) link_NAG-ASN : bond 0.00340 / 0.24 ( 15) link_NAG-ASN : angle 2.63661 / 1.78 ( 45) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3830 Ramachandran restraints generated. 1915 Oldfield, 0 Emsley, 1915 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3830 Ramachandran restraints generated. 1915 Oldfield, 0 Emsley, 1915 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 60 residues out of total 362 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 60 time to evaluate : 0.150 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 66 GLN cc_start: 0.7533 (mm110) cc_final: 0.7097 (mm110) REVERT: B 101 ASN cc_start: 0.8018 (m110) cc_final: 0.7535 (m110) REVERT: B 210 MET cc_start: 0.8649 (tpp) cc_final: 0.8327 (tpp) REVERT: B 247 ASP cc_start: 0.7469 (t70) cc_final: 0.6934 (m-30) REVERT: B 286 TYR cc_start: 0.7606 (m-10) cc_final: 0.7031 (t80) REVERT: B 307 LEU cc_start: 0.8777 (tt) cc_final: 0.8458 (mm) REVERT: B 426 TRP cc_start: 0.8600 (m100) cc_final: 0.8093 (m100) REVERT: B 428 ARG cc_start: 0.8241 (ttt-90) cc_final: 0.7851 (tpt170) REVERT: B 431 TYR cc_start: 0.8929 (m-80) cc_final: 0.8506 (m-80) REVERT: B 452 LEU cc_start: 0.7727 (mt) cc_final: 0.7492 (mt) outliers start: 0 outliers final: 0 residues processed: 60 average time/residue: 0.0503 time to fit residues: 3.9718 Evaluate side-chains 48 residues out of total 362 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 48 time to evaluate : 0.137 Evaluate side-chains 0 residues out of total 0 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 0 time to evaluate : 0.001 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.0009 Evaluate side-chains 0 residues out of total 0 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 0 time to evaluate : 0.001 Evaluate side-chains 0 residues out of total 0 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 0 time to evaluate : 0.001 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.0011 Evaluate side-chains 0 residues out of total 0 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 0 time to evaluate : 0.001 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 190 random chunks: chunk 89 optimal weight: 0.0170 chunk 57 optimal weight: 0.0980 chunk 126 optimal weight: 0.8980 chunk 21 optimal weight: 0.0470 chunk 61 optimal weight: 10.0000 chunk 33 optimal weight: 10.0000 chunk 19 optimal weight: 0.0570 chunk 59 optimal weight: 0.9990 chunk 32 optimal weight: 9.9990 chunk 73 optimal weight: 5.9990 chunk 118 optimal weight: 0.6980 overall best weight: 0.1834 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3642 r_free = 0.3642 target = 0.100720 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3431 r_free = 0.3431 target = 0.089267 restraints weight = 13409.189| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3462 r_free = 0.3462 target = 0.090836 restraints weight = 8257.786| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3480 r_free = 0.3480 target = 0.091812 restraints weight = 5541.914| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 42)----------------| | r_work = 0.3493 r_free = 0.3493 target = 0.092495 restraints weight = 4098.594| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.3501 r_free = 0.3501 target = 0.092979 restraints weight = 3267.697| |-----------------------------------------------------------------------------| r_work (final): 0.3397 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2427 r_free = 0.2427 target = 0.043951 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2443 r_free = 0.2443 target = 0.042556 restraints weight = 212.831| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.2450 r_free = 0.2450 target = 0.042863 restraints weight = 27.374| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.2456 r_free = 0.2456 target = 0.043026 restraints weight = 9.194 | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.2458 r_free = 0.2458 target = 0.043059 restraints weight = 3.735 | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.2458 r_free = 0.2458 target = 0.043058 restraints weight = 1.593 | |-----------------------------------------------------------------------------| r_work (final): 0.2426 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2500 r_free = 0.2500 target = 0.049840 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.2429 r_free = 0.2429 target = 0.046689 restraints weight = 275.168| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.2452 r_free = 0.2452 target = 0.047842 restraints weight = 152.351| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.2473 r_free = 0.2473 target = 0.048612 restraints weight = 88.801| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.2484 r_free = 0.2484 target = 0.049112 restraints weight = 52.465| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.2487 r_free = 0.2487 target = 0.049293 restraints weight = 31.711| |-----------------------------------------------------------------------------| r_work (final): 0.2485 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7659 moved from start: 0.5127 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.066 16710 Z= 0.140 Angle : 0.740 10.583 22905 Z= 0.378 Chirality : 0.049 0.253 2755 Planarity : 0.005 0.059 2760 Dihedral : 6.474 76.961 2125 Min Nonbonded Distance : 2.398 Molprobity Statistics. All-atom Clashscore : 12.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.31 % Favored : 92.69 % Rotamer: Outliers : 0.00 % Allowed : 0.58 % Favored : 99.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.27 % 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 are not related in a simple way. whole: -0.40 (0.20), residues: 1915 helix: 0.59 (0.19), residues: 730 sheet: -0.26 (0.25), residues: 450 loop : -1.03 (0.26), residues: 735 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG D 410 TYR 0.015 0.002 TYR E 116 PHE 0.039 0.002 PHE C 103 TRP 0.013 0.001 TRP E 456 HIS 0.001 0.001 HIS C 411 Details of bonding type rmsd/Z covalent geometry : bond 0.00308 / 0.14 (16670) covalent geometry : angle 0.73149 / 0.38 (22790) SS BOND : bond 0.00010 / 0.01 ( 5) SS BOND : angle 0.27066 / 0.17 ( 10) hydrogen bonds : bond 0.03648 / 2.33 ( 775) hydrogen bonds : angle 4.90704 / 3.46 ( 2325) link_BETA1-4 : bond 0.00267 / 0.18 ( 20) link_BETA1-4 : angle 1.12844 / 0.80 ( 60) link_NAG-ASN : bond 0.00089 / 0.05 ( 15) link_NAG-ASN : angle 2.39537 / 1.59 ( 45) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3830 Ramachandran restraints generated. 1915 Oldfield, 0 Emsley, 1915 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3830 Ramachandran restraints generated. 1915 Oldfield, 0 Emsley, 1915 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 65 residues out of total 362 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 65 time to evaluate : 0.129 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 30 VAL cc_start: 0.8981 (m) cc_final: 0.8780 (m) REVERT: B 56 GLN cc_start: 0.9127 (mm-40) cc_final: 0.8896 (mm-40) REVERT: B 66 GLN cc_start: 0.7602 (mm110) cc_final: 0.7068 (mm110) REVERT: B 101 ASN cc_start: 0.7856 (m110) cc_final: 0.7362 (m110) REVERT: B 152 THR cc_start: 0.9100 (m) cc_final: 0.7792 (m) REVERT: B 210 MET cc_start: 0.8576 (tpp) cc_final: 0.8206 (tpp) REVERT: B 212 PHE cc_start: 0.8404 (m-80) cc_final: 0.8172 (m-80) REVERT: B 247 ASP cc_start: 0.7397 (t70) cc_final: 0.6923 (m-30) REVERT: B 307 LEU cc_start: 0.8801 (tt) cc_final: 0.8490 (mm) REVERT: B 426 TRP cc_start: 0.8645 (m100) cc_final: 0.8107 (m100) REVERT: B 428 ARG cc_start: 0.8287 (ttt-90) cc_final: 0.7741 (tpt170) REVERT: B 431 TYR cc_start: 0.8843 (m-80) cc_final: 0.8596 (m-80) outliers start: 0 outliers final: 0 residues processed: 65 average time/residue: 0.0416 time to fit residues: 3.7012 Evaluate side-chains 52 residues out of total 362 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 52 time to evaluate : 0.129 Evaluate side-chains 0 residues out of total 0 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 0 time to evaluate : 0.001 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.0011 Evaluate side-chains 0 residues out of total 0 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 0 time to evaluate : 0.001 Evaluate side-chains 0 residues out of total 0 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 0 time to evaluate : 0.001 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.0013 Evaluate side-chains 0 residues out of total 0 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 0 time to evaluate : 0.001 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 190 random chunks: chunk 126 optimal weight: 7.9990 chunk 69 optimal weight: 7.9990 chunk 23 optimal weight: 9.9990 chunk 10 optimal weight: 0.8980 chunk 114 optimal weight: 9.9990 chunk 112 optimal weight: 0.5980 chunk 167 optimal weight: 5.9990 chunk 180 optimal weight: 3.9990 chunk 186 optimal weight: 0.8980 chunk 107 optimal weight: 20.0000 chunk 70 optimal weight: 10.0000 overall best weight: 2.4784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3587 r_free = 0.3587 target = 0.097351 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3362 r_free = 0.3362 target = 0.085742 restraints weight = 14002.026| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3394 r_free = 0.3394 target = 0.087320 restraints weight = 8642.044| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3414 r_free = 0.3414 target = 0.088311 restraints weight = 5805.514| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.3426 r_free = 0.3426 target = 0.088991 restraints weight = 4291.177| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.3434 r_free = 0.3434 target = 0.089427 restraints weight = 3439.943| |-----------------------------------------------------------------------------| r_work (final): 0.3333 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2428 r_free = 0.2428 target = 0.040814 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 26)----------------| | r_work = 0.2454 r_free = 0.2454 target = 0.040034 restraints weight = 222.744| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.2457 r_free = 0.2457 target = 0.040169 restraints weight = 21.418| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.2460 r_free = 0.2460 target = 0.040297 restraints weight = 5.652 | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.2457 r_free = 0.2457 target = 0.040290 restraints weight = 1.984 | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.2457 r_free = 0.2457 target = 0.040293 restraints weight = 0.796 | |-----------------------------------------------------------------------------| r_work (final): 0.2357 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2503 r_free = 0.2503 target = 0.049984 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.2441 r_free = 0.2441 target = 0.046580 restraints weight = 300.602| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.2467 r_free = 0.2467 target = 0.047688 restraints weight = 186.043| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.2481 r_free = 0.2481 target = 0.048491 restraints weight = 118.853| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.2491 r_free = 0.2491 target = 0.049078 restraints weight = 76.082| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.2490 r_free = 0.2490 target = 0.049224 restraints weight = 47.520| |-----------------------------------------------------------------------------| r_work (final): 0.2484 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7740 moved from start: 0.5230 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.068 16710 Z= 0.170 Angle : 0.687 6.647 22905 Z= 0.356 Chirality : 0.047 0.213 2755 Planarity : 0.005 0.068 2760 Dihedral : 6.363 75.288 2125 Min Nonbonded Distance : 2.403 Molprobity Statistics. All-atom Clashscore : 13.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.36 % Favored : 91.64 % Rotamer: Outliers : 0.00 % Allowed : 0.29 % Favored : 99.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.27 % 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 are not related in a simple way. whole: -0.36 (0.20), residues: 1915 helix: 0.63 (0.19), residues: 730 sheet: -0.26 (0.26), residues: 420 loop : -0.97 (0.26), residues: 765 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 410 TYR 0.020 0.002 TYR E 61 PHE 0.026 0.002 PHE C 103 TRP 0.014 0.002 TRP C 68 HIS 0.004 0.001 HIS B 158 Details of bonding type rmsd/Z covalent geometry : bond 0.00383 / 0.17 (16670) covalent geometry : angle 0.67451 / 0.35 (22790) SS BOND : bond 0.00234 / 0.12 ( 5) SS BOND : angle 0.55464 / 0.35 ( 10) hydrogen bonds : bond 0.03763 / 2.43 ( 775) hydrogen bonds : angle 4.78585 / 3.37 ( 2325) link_BETA1-4 : bond 0.00163 / 0.11 ( 20) link_BETA1-4 : angle 1.34298 / 0.97 ( 60) link_NAG-ASN : bond 0.00419 / 0.29 ( 15) link_NAG-ASN : angle 2.67962 / 1.79 ( 45) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1643.68 seconds wall clock time: 29 minutes 32.39 seconds (1772.39 seconds total)