Starting phenix.real_space_refine on Thu Sep 18 11:28:12 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6his_0228/09_2025/6his_0228.cif Found real_map, /net/cci-nas-00/data/ceres_data/6his_0228/09_2025/6his_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/6his_0228/09_2025/6his_0228.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6his_0228/09_2025/6his_0228.map" model { file = "/net/cci-nas-00/data/ceres_data/6his_0228/09_2025/6his_0228.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6his_0228/09_2025/6his_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-2.0-5805/lib/python3.9/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 dihedrals: 6 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 dihedrals: 9 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 dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "I" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "J" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "K" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "L" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "M" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "N" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "O" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "P" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "Q" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "R" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "S" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "T" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 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: 3.36, per 1000 atoms: 0.21 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: 1.43 Conformation dependent library (CDL) restraints added in 739.2 milliseconds Enol-peptide restraints added in 238.4 nanoseconds 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: 0.37 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: 2.01 Time building geometry restraints manager: 1.83 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 - 21.02: 9742 21.02 - 42.05: 493 42.05 - 63.07: 75 63.07 - 84.09: 35 84.09 - 105.11: 25 Dihedral angle restraints: 10370 sinusoidal: 4600 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 10367 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: 0.860 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.250 Check model and map are aligned: 0.050 Set scattering table: 0.030 Process input model: 13.220 Find NCS groups from input model: 0.420 Set up NCS constraints: 0.030 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:1.380 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 16.240 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7687 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 : 14.279 105.113 6595 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 aren 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 covalent geometry : bond 0.01071 (16670) covalent geometry : angle 1.57273 (22790) SS BOND : bond 0.00247 ( 5) SS BOND : angle 2.28766 ( 10) hydrogen bonds : bond 0.26321 ( 775) hydrogen bonds : angle 8.38771 ( 2325) link_BETA1-4 : bond 0.00714 ( 20) link_BETA1-4 : angle 2.25341 ( 60) link_NAG-ASN : bond 0.01142 ( 15) link_NAG-ASN : angle 3.45101 ( 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 : 0.098 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: 0.0697 time to fit residues: 7.8815 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 : 0.130 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=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... Flipped N/Q/H residues before XYZ refinement: E 119 HIS E 124 GLN E 205 ASN Total number of N/Q/H flips: 3 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3573 r_free = 0.3573 target = 0.095534 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3317 r_free = 0.3317 target = 0.082168 restraints weight = 12771.357| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3357 r_free = 0.3357 target = 0.084094 restraints weight = 7243.942| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3384 r_free = 0.3384 target = 0.085402 restraints weight = 4658.602| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3401 r_free = 0.3401 target = 0.086198 restraints weight = 3307.585| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.3414 r_free = 0.3414 target = 0.086822 restraints weight = 2586.928| |-----------------------------------------------------------------------------| r_work (final): 0.3386 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2430 r_free = 0.2430 target = 0.044557 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.2445 r_free = 0.2445 target = 0.044189 restraints weight = 181.527| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.2444 r_free = 0.2444 target = 0.044201 restraints weight = 0.847 | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 4)-----------------| | r_work = 0.2444 r_free = 0.2444 target = 0.044200 restraints weight = 0.006 | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.2445 r_free = 0.2445 target = 0.044188 restraints weight = 175.100| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.2444 r_free = 0.2444 target = 0.044202 restraints weight = 0.768 | |-----------------------------------------------------------------------------| r_work (final): 0.2426 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2818 r_free = 0.2818 target = 0.063527 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.2802 r_free = 0.2802 target = 0.060978 restraints weight = 423.333| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 21)----------------| | r_work = 0.2795 r_free = 0.2795 target = 0.061586 restraints weight = 173.180| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.2796 r_free = 0.2796 target = 0.061928 restraints weight = 114.851| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 20)----------------| | r_work = 0.2797 r_free = 0.2797 target = 0.062202 restraints weight = 88.042| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.2794 r_free = 0.2794 target = 0.062369 restraints weight = 71.817| |-----------------------------------------------------------------------------| r_work (final): 0.2781 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7646 moved from start: 0.2931 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 16710 Z= 0.203 Angle : 0.911 12.228 22905 Z= 0.467 Chirality : 0.063 0.888 2755 Planarity : 0.009 0.166 2760 Dihedral : 11.172 77.223 2970 Min Nonbonded Distance : 2.435 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 aren not related in a simple way. whole: -1.78 (0.19), residues: 1915 helix: -0.66 (0.17), residues: 725 sheet: -0.94 (0.23), residues: 445 loop : -1.69 (0.25), residues: 745 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 65 TYR 0.015 0.002 TYR A 207 PHE 0.018 0.002 PHE E 233 TRP 0.014 0.001 TRP A 63 HIS 0.007 0.002 HIS D 411 Details of bonding type rmsd covalent geometry : bond 0.00428 (16670) covalent geometry : angle 0.89606 (22790) SS BOND : bond 0.00263 ( 5) SS BOND : angle 1.60821 ( 10) hydrogen bonds : bond 0.06589 ( 775) hydrogen bonds : angle 6.10981 ( 2325) link_BETA1-4 : bond 0.00127 ( 20) link_BETA1-4 : angle 1.94364 ( 60) link_NAG-ASN : bond 0.00317 ( 15) link_NAG-ASN : angle 3.19763 ( 45) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3064 Ramachandran restraints generated. 1532 Oldfield, 0 Emsley, 1532 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3064 Ramachandran restraints generated. 1532 Oldfield, 0 Emsley, 1532 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 77 residues out of total 362 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 75 time to evaluate : 0.076 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 152 THR cc_start: 0.8989 (m) cc_final: 0.8211 (m) REVERT: E 157 LEU cc_start: 0.9021 (OUTLIER) cc_final: 0.7874 (pp) REVERT: E 247 ASP cc_start: 0.7438 (t70) cc_final: 0.6902 (m-30) REVERT: E 286 TYR cc_start: 0.7930 (m-10) cc_final: 0.7560 (t80) REVERT: E 307 LEU cc_start: 0.8749 (tt) cc_final: 0.8183 (mm) REVERT: E 426 TRP cc_start: 0.8536 (m100) cc_final: 0.8204 (m-10) REVERT: E 428 ARG cc_start: 0.8264 (ttt-90) cc_final: 0.7986 (tpt170) REVERT: E 431 TYR cc_start: 0.8729 (m-80) cc_final: 0.8323 (m-80) outliers start: 2 outliers final: 1 residues processed: 76 average time/residue: 0.0643 time to fit residues: 5.8684 Evaluate side-chains 46 residues out of total 362 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 44 time to evaluate : 0.122 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 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 134 optimal weight: 8.9990 chunk 168 optimal weight: 3.9990 chunk 42 optimal weight: 1.9990 chunk 98 optimal weight: 0.0470 chunk 178 optimal weight: 0.7980 chunk 73 optimal weight: 9.9990 chunk 175 optimal weight: 5.9990 chunk 148 optimal weight: 5.9990 chunk 123 optimal weight: 0.9980 chunk 54 optimal weight: 1.9990 chunk 6 optimal weight: 2.9990 overall best weight: 1.1682 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 183 ASN Total number of N/Q/H flips: 1 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3569 r_free = 0.3569 target = 0.096659 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3315 r_free = 0.3315 target = 0.083123 restraints weight = 12453.172| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3351 r_free = 0.3351 target = 0.084855 restraints weight = 7370.718| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3375 r_free = 0.3375 target = 0.086018 restraints weight = 4900.826| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3391 r_free = 0.3391 target = 0.086779 restraints weight = 3572.946| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3400 r_free = 0.3400 target = 0.087226 restraints weight = 2824.060| |-----------------------------------------------------------------------------| r_work (final): 0.3376 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2400 r_free = 0.2400 target = 0.044268 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 24)----------------| | r_work = 0.2410 r_free = 0.2410 target = 0.044126 restraints weight = 160.761| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.2410 r_free = 0.2410 target = 0.044220 restraints weight = 12.923| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.2410 r_free = 0.2410 target = 0.044240 restraints weight = 2.312 | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.2411 r_free = 0.2411 target = 0.044247 restraints weight = 0.372 | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.2411 r_free = 0.2411 target = 0.044248 restraints weight = 0.052 | |-----------------------------------------------------------------------------| r_work (final): 0.2394 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2915 r_free = 0.2915 target = 0.068990 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.2917 r_free = 0.2917 target = 0.064496 restraints weight = 437.962| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 54)----------------| | r_work = 0.2924 r_free = 0.2924 target = 0.065887 restraints weight = 227.600| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.2922 r_free = 0.2922 target = 0.066377 restraints weight = 156.299| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.2920 r_free = 0.2920 target = 0.066697 restraints weight = 126.243| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.2918 r_free = 0.2918 target = 0.066860 restraints weight = 109.537| |-----------------------------------------------------------------------------| r_work (final): 0.2889 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7683 moved from start: 0.3646 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 16710 Z= 0.164 Angle : 0.808 13.378 22905 Z= 0.402 Chirality : 0.053 0.412 2755 Planarity : 0.005 0.035 2760 Dihedral : 8.954 74.243 2970 Min Nonbonded Distance : 2.478 Molprobity Statistics. All-atom Clashscore : 13.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.79 % Favored : 93.21 % Rotamer: Outliers : 0.00 % Allowed : 4.08 % Favored : 95.92 % 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 aren not related in a simple way. whole: -1.61 (0.19), residues: 1915 helix: -0.43 (0.17), residues: 725 sheet: -1.04 (0.22), residues: 445 loop : -1.58 (0.25), residues: 745 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG C 410 TYR 0.018 0.002 TYR A 223 PHE 0.030 0.003 PHE A 103 TRP 0.013 0.001 TRP E 456 HIS 0.011 0.002 HIS C 411 Details of bonding type rmsd covalent geometry : bond 0.00357 (16670) covalent geometry : angle 0.79423 (22790) SS BOND : bond 0.00162 ( 5) SS BOND : angle 0.80514 ( 10) hydrogen bonds : bond 0.05122 ( 775) hydrogen bonds : angle 5.62431 ( 2325) link_BETA1-4 : bond 0.00213 ( 20) link_BETA1-4 : angle 1.88786 ( 60) link_NAG-ASN : bond 0.00330 ( 15) link_NAG-ASN : angle 2.86585 ( 45) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2298 Ramachandran restraints generated. 1149 Oldfield, 0 Emsley, 1149 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2298 Ramachandran restraints generated. 1149 Oldfield, 0 Emsley, 1149 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 : 0.117 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 68 TRP cc_start: 0.9189 (p90) cc_final: 0.8978 (p90) REVERT: B 101 ASN cc_start: 0.7951 (m110) cc_final: 0.7675 (m110) REVERT: B 212 PHE cc_start: 0.8167 (m-80) cc_final: 0.7574 (m-80) REVERT: B 247 ASP cc_start: 0.7522 (t70) cc_final: 0.6963 (m-30) REVERT: B 286 TYR cc_start: 0.7569 (m-10) cc_final: 0.7146 (t80) REVERT: B 307 LEU cc_start: 0.8749 (tt) cc_final: 0.8314 (mm) REVERT: B 426 TRP cc_start: 0.8643 (m100) cc_final: 0.8134 (m100) REVERT: B 428 ARG cc_start: 0.8305 (ttt-90) cc_final: 0.7928 (tpt170) REVERT: B 431 TYR cc_start: 0.8763 (m-80) cc_final: 0.8238 (m-80) outliers start: 0 outliers final: 0 residues processed: 65 average time/residue: 0.0509 time to fit residues: 4.1676 Evaluate side-chains 46 residues out of total 362 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 46 time to evaluate : 0.110 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 : 0.000 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: 0.0019 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 42 optimal weight: 0.0870 chunk 9 optimal weight: 5.9990 chunk 167 optimal weight: 4.9990 chunk 2 optimal weight: 9.9990 chunk 133 optimal weight: 0.0470 chunk 102 optimal weight: 0.1980 chunk 90 optimal weight: 0.1980 chunk 23 optimal weight: 2.9990 chunk 80 optimal weight: 0.0870 chunk 6 optimal weight: 6.9990 chunk 173 optimal weight: 2.9990 overall best weight: 0.1234 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3600 r_free = 0.3600 target = 0.098918 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3346 r_free = 0.3346 target = 0.085043 restraints weight = 12224.828| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3384 r_free = 0.3384 target = 0.086879 restraints weight = 7159.375| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3410 r_free = 0.3410 target = 0.088154 restraints weight = 4750.693| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.3427 r_free = 0.3427 target = 0.088988 restraints weight = 3449.154| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3438 r_free = 0.3438 target = 0.089610 restraints weight = 2708.926| |-----------------------------------------------------------------------------| r_work (final): 0.3412 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2195 r_free = 0.2195 target = 0.037056 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.2186 r_free = 0.2186 target = 0.036907 restraints weight = 270.325| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.2193 r_free = 0.2193 target = 0.037010 restraints weight = 27.465| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.2195 r_free = 0.2195 target = 0.037045 restraints weight = 5.772 | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.2195 r_free = 0.2195 target = 0.037048 restraints weight = 1.278 | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.2195 r_free = 0.2195 target = 0.037048 restraints weight = 0.302 | |-----------------------------------------------------------------------------| r_work (final): 0.2204 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2899 r_free = 0.2899 target = 0.069020 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.2878 r_free = 0.2878 target = 0.064017 restraints weight = 366.146| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.2885 r_free = 0.2885 target = 0.065375 restraints weight = 185.251| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.2884 r_free = 0.2884 target = 0.065818 restraints weight = 140.896| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.2883 r_free = 0.2883 target = 0.066137 restraints weight = 119.265| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.2882 r_free = 0.2882 target = 0.066268 restraints weight = 106.859| |-----------------------------------------------------------------------------| r_work (final): 0.2852 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7637 moved from start: 0.4090 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.092 16710 Z= 0.171 Angle : 0.788 12.774 22905 Z= 0.391 Chirality : 0.055 0.601 2755 Planarity : 0.008 0.138 2760 Dihedral : 7.711 76.386 2970 Min Nonbonded Distance : 2.263 Molprobity Statistics. All-atom Clashscore : 13.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.36 % Favored : 91.64 % Rotamer: Outliers : 0.00 % Allowed : 5.25 % Favored : 94.75 % 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 aren not related in a simple way. whole: -1.93 (0.18), residues: 1915 helix: -0.74 (0.17), residues: 725 sheet: -0.95 (0.23), residues: 420 loop : -1.88 (0.23), residues: 770 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG B 410 TYR 0.015 0.002 TYR B 223 PHE 0.022 0.002 PHE A 103 TRP 0.013 0.001 TRP B 68 HIS 0.010 0.002 HIS C 411 Details of bonding type rmsd covalent geometry : bond 0.00389 (16670) covalent geometry : angle 0.77296 (22790) SS BOND : bond 0.00018 ( 5) SS BOND : angle 0.41365 ( 10) hydrogen bonds : bond 0.04711 ( 775) hydrogen bonds : angle 5.42696 ( 2325) link_BETA1-4 : bond 0.00338 ( 20) link_BETA1-4 : angle 1.77451 ( 60) link_NAG-ASN : bond 0.00113 ( 15) link_NAG-ASN : angle 3.01808 ( 45) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2298 Ramachandran restraints generated. 1149 Oldfield, 0 Emsley, 1149 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2298 Ramachandran restraints generated. 1149 Oldfield, 0 Emsley, 1149 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 : 0.089 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 101 ASN cc_start: 0.7825 (m110) cc_final: 0.7509 (m110) REVERT: B 247 ASP cc_start: 0.7391 (t70) cc_final: 0.6918 (m-30) REVERT: B 286 TYR cc_start: 0.7493 (m-10) cc_final: 0.7072 (t80) REVERT: B 307 LEU cc_start: 0.8767 (tt) cc_final: 0.8345 (mm) REVERT: B 426 TRP cc_start: 0.8607 (m100) cc_final: 0.8113 (m100) REVERT: B 428 ARG cc_start: 0.8282 (ttt-90) cc_final: 0.7864 (tpt170) outliers start: 0 outliers final: 0 residues processed: 66 average time/residue: 0.0536 time to fit residues: 4.5657 Evaluate side-chains 46 residues out of total 362 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 46 time to evaluate : 0.126 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 26 optimal weight: 5.9990 chunk 44 optimal weight: 5.9990 chunk 49 optimal weight: 0.7980 chunk 51 optimal weight: 0.0170 chunk 137 optimal weight: 0.0060 chunk 94 optimal weight: 2.9990 chunk 20 optimal weight: 2.9990 chunk 134 optimal weight: 4.9990 chunk 63 optimal weight: 2.9990 chunk 168 optimal weight: 3.9990 chunk 172 optimal weight: 4.9990 overall best weight: 1.3638 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3581 r_free = 0.3581 target = 0.097654 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3325 r_free = 0.3325 target = 0.084125 restraints weight = 12257.631| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3362 r_free = 0.3362 target = 0.085885 restraints weight = 7269.268| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3387 r_free = 0.3387 target = 0.087137 restraints weight = 4833.208| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.3404 r_free = 0.3404 target = 0.087941 restraints weight = 3499.478| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3414 r_free = 0.3414 target = 0.088444 restraints weight = 2745.641| |-----------------------------------------------------------------------------| r_work (final): 0.3388 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2322 r_free = 0.2322 target = 0.043329 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.2330 r_free = 0.2330 target = 0.043028 restraints weight = 233.000| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.2318 r_free = 0.2318 target = 0.043290 restraints weight = 38.840| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.2318 r_free = 0.2318 target = 0.043304 restraints weight = 6.346 | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.2317 r_free = 0.2317 target = 0.043299 restraints weight = 0.537 | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.2318 r_free = 0.2318 target = 0.043300 restraints weight = 0.428 | |-----------------------------------------------------------------------------| r_work (final): 0.2322 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2534 r_free = 0.2534 target = 0.049046 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2496 r_free = 0.2496 target = 0.046345 restraints weight = 255.022| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.2510 r_free = 0.2510 target = 0.047194 restraints weight = 153.405| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.2517 r_free = 0.2517 target = 0.047775 restraints weight = 95.329| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.2522 r_free = 0.2522 target = 0.048179 restraints weight = 62.465| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.2527 r_free = 0.2527 target = 0.048525 restraints weight = 41.346| |-----------------------------------------------------------------------------| r_work (final): 0.2527 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7681 moved from start: 0.4310 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 16710 Z= 0.144 Angle : 0.712 9.757 22905 Z= 0.348 Chirality : 0.048 0.234 2755 Planarity : 0.005 0.061 2760 Dihedral : 6.921 76.193 2970 Min Nonbonded Distance : 2.470 Molprobity Statistics. All-atom Clashscore : 12.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.36 % Favored : 91.64 % Rotamer: Outliers : 0.00 % Allowed : 3.50 % Favored : 96.50 % 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 aren not related in a simple way. whole: -1.57 (0.19), residues: 1915 helix: -0.33 (0.18), residues: 725 sheet: -1.04 (0.23), residues: 420 loop : -1.60 (0.24), residues: 770 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 315 TYR 0.013 0.002 TYR E 223 PHE 0.013 0.002 PHE E 233 TRP 0.012 0.001 TRP B 68 HIS 0.005 0.001 HIS C 411 Details of bonding type rmsd covalent geometry : bond 0.00326 (16670) covalent geometry : angle 0.69655 (22790) SS BOND : bond 0.00262 ( 5) SS BOND : angle 0.54459 ( 10) hydrogen bonds : bond 0.04161 ( 775) hydrogen bonds : angle 4.96783 ( 2325) link_BETA1-4 : bond 0.00203 ( 20) link_BETA1-4 : angle 1.71973 ( 60) link_NAG-ASN : bond 0.00210 ( 15) link_NAG-ASN : angle 2.92046 ( 45) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2298 Ramachandran restraints generated. 1149 Oldfield, 0 Emsley, 1149 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2298 Ramachandran restraints generated. 1149 Oldfield, 0 Emsley, 1149 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 : 0.127 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 101 ASN cc_start: 0.7922 (m110) cc_final: 0.7551 (m110) REVERT: B 247 ASP cc_start: 0.7344 (t70) cc_final: 0.6882 (m-30) REVERT: B 286 TYR cc_start: 0.7473 (m-10) cc_final: 0.6993 (t80) REVERT: B 301 THR cc_start: 0.8918 (m) cc_final: 0.8712 (m) REVERT: B 307 LEU cc_start: 0.8766 (tt) cc_final: 0.8356 (mm) REVERT: B 426 TRP cc_start: 0.8490 (m100) cc_final: 0.8057 (m100) REVERT: B 428 ARG cc_start: 0.8118 (ttt-90) cc_final: 0.7354 (ttt180) REVERT: B 431 TYR cc_start: 0.8863 (m-80) cc_final: 0.8194 (m-80) outliers start: 0 outliers final: 0 residues processed: 65 average time/residue: 0.0440 time to fit residues: 3.8178 Evaluate side-chains 47 residues out of total 362 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 47 time to evaluate : 0.134 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 190 random chunks: chunk 19 optimal weight: 0.8980 chunk 163 optimal weight: 0.9990 chunk 132 optimal weight: 3.9990 chunk 177 optimal weight: 0.8980 chunk 148 optimal weight: 0.8980 chunk 64 optimal weight: 0.4980 chunk 176 optimal weight: 0.7980 chunk 50 optimal weight: 5.9990 chunk 188 optimal weight: 3.9990 chunk 89 optimal weight: 3.9990 chunk 83 optimal weight: 9.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3667 r_free = 0.3667 target = 0.102112 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3440 r_free = 0.3440 target = 0.089991 restraints weight = 13172.392| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3470 r_free = 0.3470 target = 0.091489 restraints weight = 8283.110| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3491 r_free = 0.3491 target = 0.092517 restraints weight = 5706.595| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 41)----------------| | r_work = 0.3505 r_free = 0.3505 target = 0.093225 restraints weight = 4274.384| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3512 r_free = 0.3512 target = 0.093600 restraints weight = 3426.158| |-----------------------------------------------------------------------------| r_work (final): 0.3407 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2283 r_free = 0.2283 target = 0.042683 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 26)----------------| | r_work = 0.2313 r_free = 0.2313 target = 0.041845 restraints weight = 207.293| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.2286 r_free = 0.2286 target = 0.042331 restraints weight = 40.080| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.2281 r_free = 0.2281 target = 0.042507 restraints weight = 14.569| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.2279 r_free = 0.2279 target = 0.042597 restraints weight = 6.132 | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 9)-----------------| | r_work = 0.2279 r_free = 0.2279 target = 0.042632 restraints weight = 2.695 | |-----------------------------------------------------------------------------| r_work (final): 0.2289 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2543 r_free = 0.2543 target = 0.049462 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2497 r_free = 0.2497 target = 0.046483 restraints weight = 304.599| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.2515 r_free = 0.2515 target = 0.047468 restraints weight = 173.464| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.2525 r_free = 0.2525 target = 0.048121 restraints weight = 103.651| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.2530 r_free = 0.2530 target = 0.048558 restraints weight = 66.118| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.2534 r_free = 0.2534 target = 0.048861 restraints weight = 43.611| |-----------------------------------------------------------------------------| r_work (final): 0.2530 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7634 moved from start: 0.4512 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 16710 Z= 0.135 Angle : 0.683 6.997 22905 Z= 0.336 Chirality : 0.047 0.236 2755 Planarity : 0.005 0.045 2760 Dihedral : 6.629 76.607 2970 Min Nonbonded Distance : 2.493 Molprobity Statistics. All-atom Clashscore : 12.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.36 % Favored : 91.64 % 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 aren not related in a simple way. whole: -1.50 (0.19), residues: 1915 helix: -0.25 (0.18), residues: 725 sheet: -0.95 (0.23), residues: 420 loop : -1.64 (0.24), residues: 770 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG E 315 TYR 0.016 0.002 TYR A 64 PHE 0.014 0.001 PHE E 103 TRP 0.015 0.001 TRP B 68 HIS 0.008 0.001 HIS A 411 Details of bonding type rmsd covalent geometry : bond 0.00304 (16670) covalent geometry : angle 0.66952 (22790) SS BOND : bond 0.00162 ( 5) SS BOND : angle 0.46193 ( 10) hydrogen bonds : bond 0.04048 ( 775) hydrogen bonds : angle 4.85393 ( 2325) link_BETA1-4 : bond 0.00257 ( 20) link_BETA1-4 : angle 1.57986 ( 60) link_NAG-ASN : bond 0.00143 ( 15) link_NAG-ASN : angle 2.69095 ( 45) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2298 Ramachandran restraints generated. 1149 Oldfield, 0 Emsley, 1149 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2298 Ramachandran restraints generated. 1149 Oldfield, 0 Emsley, 1149 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 : 0.126 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 66 GLN cc_start: 0.7322 (mm110) cc_final: 0.6662 (mm110) REVERT: B 101 ASN cc_start: 0.7949 (m110) cc_final: 0.7528 (m110) REVERT: B 154 THR cc_start: 0.8763 (p) cc_final: 0.8541 (p) REVERT: B 212 PHE cc_start: 0.8570 (m-80) cc_final: 0.8320 (m-10) REVERT: B 247 ASP cc_start: 0.7460 (t70) cc_final: 0.6835 (m-30) REVERT: B 286 TYR cc_start: 0.7628 (m-10) cc_final: 0.7011 (t80) REVERT: B 301 THR cc_start: 0.8921 (m) cc_final: 0.8712 (m) REVERT: B 307 LEU cc_start: 0.8857 (tt) cc_final: 0.8428 (mm) REVERT: B 426 TRP cc_start: 0.8613 (m100) cc_final: 0.8111 (m100) REVERT: B 428 ARG cc_start: 0.8077 (ttt-90) cc_final: 0.7285 (ttt180) REVERT: B 431 TYR cc_start: 0.8828 (m-80) cc_final: 0.8209 (m-80) outliers start: 0 outliers final: 0 residues processed: 67 average time/residue: 0.0526 time to fit residues: 4.4635 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 : 0.124 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: 0.0013 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 190 random chunks: chunk 171 optimal weight: 0.9980 chunk 157 optimal weight: 0.6980 chunk 127 optimal weight: 5.9990 chunk 28 optimal weight: 2.9990 chunk 143 optimal weight: 4.9990 chunk 119 optimal weight: 1.9990 chunk 71 optimal weight: 7.9990 chunk 188 optimal weight: 2.9990 chunk 160 optimal weight: 6.9990 chunk 137 optimal weight: 6.9990 chunk 166 optimal weight: 0.9980 overall best weight: 1.5384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3644 r_free = 0.3644 target = 0.100866 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3418 r_free = 0.3418 target = 0.088961 restraints weight = 13517.116| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3449 r_free = 0.3449 target = 0.090458 restraints weight = 8428.565| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3471 r_free = 0.3471 target = 0.091529 restraints weight = 5784.632| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 48)----------------| | r_work = 0.3485 r_free = 0.3485 target = 0.092239 restraints weight = 4296.325| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3491 r_free = 0.3491 target = 0.092572 restraints weight = 3424.619| |-----------------------------------------------------------------------------| r_work (final): 0.3383 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2340 r_free = 0.2340 target = 0.043666 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 26)----------------| | r_work = 0.2374 r_free = 0.2374 target = 0.042701 restraints weight = 198.917| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.2350 r_free = 0.2350 target = 0.043215 restraints weight = 35.777| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.2345 r_free = 0.2345 target = 0.043411 restraints weight = 13.771| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 22)----------------| | r_work = 0.2345 r_free = 0.2345 target = 0.043411 restraints weight = 5.708 | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.2345 r_free = 0.2345 target = 0.043411 restraints weight = 5.707 | |-----------------------------------------------------------------------------| r_work (final): 0.2327 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2520 r_free = 0.2520 target = 0.047939 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.2456 r_free = 0.2456 target = 0.044924 restraints weight = 269.456| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.2473 r_free = 0.2473 target = 0.045857 restraints weight = 157.560| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.2490 r_free = 0.2490 target = 0.046569 restraints weight = 97.150| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.2501 r_free = 0.2501 target = 0.047012 restraints weight = 61.262| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 17)----------------| | r_work = 0.2508 r_free = 0.2508 target = 0.047345 restraints weight = 39.261| |-----------------------------------------------------------------------------| r_work (final): 0.2508 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7651 moved from start: 0.4693 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= 0.152 Angle : 0.733 9.726 22905 Z= 0.370 Chirality : 0.051 0.400 2755 Planarity : 0.005 0.042 2760 Dihedral : 6.586 76.545 2970 Min Nonbonded Distance : 2.347 Molprobity Statistics. All-atom Clashscore : 13.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.62 % Favored : 91.38 % 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 aren not related in a simple way. whole: -1.35 (0.19), residues: 1915 helix: -0.20 (0.18), residues: 730 sheet: -0.93 (0.23), residues: 420 loop : -1.43 (0.25), residues: 765 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 410 TYR 0.018 0.002 TYR E 441 PHE 0.014 0.002 PHE A 103 TRP 0.015 0.001 TRP B 68 HIS 0.006 0.001 HIS A 411 Details of bonding type rmsd covalent geometry : bond 0.00348 (16670) covalent geometry : angle 0.72133 (22790) SS BOND : bond 0.00207 ( 5) SS BOND : angle 0.50170 ( 10) hydrogen bonds : bond 0.04161 ( 775) hydrogen bonds : angle 4.88754 ( 2325) link_BETA1-4 : bond 0.00356 ( 20) link_BETA1-4 : angle 1.57712 ( 60) link_NAG-ASN : bond 0.00209 ( 15) link_NAG-ASN : angle 2.61747 ( 45) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2298 Ramachandran restraints generated. 1149 Oldfield, 0 Emsley, 1149 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2298 Ramachandran restraints generated. 1149 Oldfield, 0 Emsley, 1149 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 : 0.132 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 66 GLN cc_start: 0.7383 (mm110) cc_final: 0.6755 (mm-40) REVERT: B 101 ASN cc_start: 0.8010 (m110) cc_final: 0.7483 (m110) REVERT: B 247 ASP cc_start: 0.7552 (t70) cc_final: 0.6889 (m-30) REVERT: B 286 TYR cc_start: 0.7624 (m-10) cc_final: 0.6907 (t80) REVERT: B 301 THR cc_start: 0.8963 (m) cc_final: 0.8734 (m) REVERT: B 307 LEU cc_start: 0.8845 (tt) cc_final: 0.8411 (mm) REVERT: B 426 TRP cc_start: 0.8647 (m100) cc_final: 0.8118 (m100) REVERT: B 428 ARG cc_start: 0.8134 (ttt-90) cc_final: 0.7643 (tpt170) REVERT: B 431 TYR cc_start: 0.8846 (m-80) cc_final: 0.8267 (m-80) outliers start: 0 outliers final: 0 residues processed: 69 average time/residue: 0.0476 time to fit residues: 4.3690 Evaluate side-chains 49 residues out of total 362 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 49 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: 0.0012 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 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 50 optimal weight: 3.9990 chunk 26 optimal weight: 0.0050 chunk 38 optimal weight: 9.9990 chunk 161 optimal weight: 3.9990 chunk 22 optimal weight: 0.1980 chunk 79 optimal weight: 6.9990 chunk 76 optimal weight: 9.9990 chunk 133 optimal weight: 0.0370 chunk 110 optimal weight: 5.9990 chunk 119 optimal weight: 0.0670 chunk 145 optimal weight: 3.9990 overall best weight: 0.8612 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 183 ASN Total number of N/Q/H flips: 1 Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3578 r_free = 0.3578 target = 0.097104 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3318 r_free = 0.3318 target = 0.083135 restraints weight = 12276.698| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.3357 r_free = 0.3357 target = 0.085017 restraints weight = 7241.905| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3383 r_free = 0.3383 target = 0.086314 restraints weight = 4799.521| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3398 r_free = 0.3398 target = 0.087082 restraints weight = 3451.973| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.3410 r_free = 0.3410 target = 0.087719 restraints weight = 2712.139| |-----------------------------------------------------------------------------| r_work (final): 0.3401 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2260 r_free = 0.2260 target = 0.038623 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 26)----------------| | r_work = 0.2257 r_free = 0.2257 target = 0.038261 restraints weight = 221.344| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.2260 r_free = 0.2260 target = 0.038345 restraints weight = 8.092 | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.2260 r_free = 0.2260 target = 0.038353 restraints weight = 0.662 | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 22)----------------| | r_work = 0.2260 r_free = 0.2260 target = 0.038353 restraints weight = 0.054 | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.2260 r_free = 0.2260 target = 0.038353 restraints weight = 0.054 | |-----------------------------------------------------------------------------| r_work (final): 0.2153 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2522 r_free = 0.2522 target = 0.048262 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.2469 r_free = 0.2469 target = 0.045462 restraints weight = 235.160| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.2485 r_free = 0.2485 target = 0.046380 restraints weight = 136.201| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 18)----------------| | r_work = 0.2498 r_free = 0.2498 target = 0.047027 restraints weight = 81.377| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.2506 r_free = 0.2506 target = 0.047410 restraints weight = 51.115| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.2511 r_free = 0.2511 target = 0.047666 restraints weight = 34.148| |-----------------------------------------------------------------------------| r_work (final): 0.2508 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7685 moved from start: 0.4826 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= 0.127 Angle : 0.679 6.823 22905 Z= 0.336 Chirality : 0.048 0.240 2755 Planarity : 0.005 0.040 2760 Dihedral : 6.431 77.306 2970 Min Nonbonded Distance : 2.514 Molprobity Statistics. All-atom Clashscore : 11.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.09 % Favored : 91.91 % 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 aren not related in a simple way. whole: -1.37 (0.19), residues: 1915 helix: -0.11 (0.18), residues: 725 sheet: -0.93 (0.23), residues: 420 loop : -1.55 (0.24), residues: 770 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG E 410 TYR 0.016 0.001 TYR B 64 PHE 0.021 0.002 PHE E 103 TRP 0.015 0.001 TRP B 68 HIS 0.002 0.001 HIS B 411 Details of bonding type rmsd covalent geometry : bond 0.00280 (16670) covalent geometry : angle 0.66618 (22790) SS BOND : bond 0.00094 ( 5) SS BOND : angle 0.31216 ( 10) hydrogen bonds : bond 0.03925 ( 775) hydrogen bonds : angle 4.76426 ( 2325) link_BETA1-4 : bond 0.00256 ( 20) link_BETA1-4 : angle 1.40361 ( 60) link_NAG-ASN : bond 0.00098 ( 15) link_NAG-ASN : angle 2.67251 ( 45) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2298 Ramachandran restraints generated. 1149 Oldfield, 0 Emsley, 1149 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2298 Ramachandran restraints generated. 1149 Oldfield, 0 Emsley, 1149 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 : 0.131 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 66 GLN cc_start: 0.7381 (mm110) cc_final: 0.7004 (mm110) REVERT: B 101 ASN cc_start: 0.7803 (m110) cc_final: 0.7369 (m110) REVERT: B 210 MET cc_start: 0.8659 (tpp) cc_final: 0.8277 (tpp) REVERT: B 212 PHE cc_start: 0.8472 (m-80) cc_final: 0.8132 (m-80) REVERT: B 247 ASP cc_start: 0.7474 (t70) cc_final: 0.6980 (m-30) REVERT: B 286 TYR cc_start: 0.7544 (m-10) cc_final: 0.6940 (t80) REVERT: B 301 THR cc_start: 0.8906 (m) cc_final: 0.8690 (m) REVERT: B 307 LEU cc_start: 0.8780 (tt) cc_final: 0.8417 (mm) REVERT: B 408 SER cc_start: 0.8890 (m) cc_final: 0.8637 (p) REVERT: B 419 MET cc_start: 0.8598 (ptt) cc_final: 0.7916 (tpp) REVERT: B 426 TRP cc_start: 0.8579 (m100) cc_final: 0.8093 (m100) REVERT: B 428 ARG cc_start: 0.8049 (ttt-90) cc_final: 0.7507 (tpt170) REVERT: B 431 TYR cc_start: 0.8825 (m-80) cc_final: 0.8494 (m-80) REVERT: B 452 LEU cc_start: 0.7686 (mt) cc_final: 0.7443 (mt) outliers start: 0 outliers final: 0 residues processed: 67 average time/residue: 0.0489 time to fit residues: 4.3573 Evaluate side-chains 54 residues out of total 362 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 54 time to evaluate : 0.143 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 161 optimal weight: 0.0470 chunk 85 optimal weight: 0.7980 chunk 138 optimal weight: 5.9990 chunk 189 optimal weight: 7.9990 chunk 142 optimal weight: 2.9990 chunk 40 optimal weight: 0.9990 chunk 101 optimal weight: 4.9990 chunk 125 optimal weight: 0.6980 chunk 24 optimal weight: 0.9990 chunk 29 optimal weight: 1.9990 chunk 65 optimal weight: 0.8980 overall best weight: 0.6880 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3648 r_free = 0.3648 target = 0.101052 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3429 r_free = 0.3429 target = 0.089228 restraints weight = 13620.904| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3460 r_free = 0.3460 target = 0.090851 restraints weight = 8384.660| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 46)----------------| | r_work = 0.3481 r_free = 0.3481 target = 0.091921 restraints weight = 5662.234| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3493 r_free = 0.3493 target = 0.092579 restraints weight = 4153.829| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3499 r_free = 0.3499 target = 0.092912 restraints weight = 3309.005| |-----------------------------------------------------------------------------| r_work (final): 0.3394 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2136 r_free = 0.2136 target = 0.037372 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 24)----------------| | r_work = 0.2131 r_free = 0.2131 target = 0.037209 restraints weight = 264.914| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.2137 r_free = 0.2137 target = 0.037328 restraints weight = 16.671| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.2138 r_free = 0.2138 target = 0.037349 restraints weight = 3.027 | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.2138 r_free = 0.2138 target = 0.037347 restraints weight = 0.541 | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.2138 r_free = 0.2138 target = 0.037347 restraints weight = 0.345 | |-----------------------------------------------------------------------------| r_work (final): 0.2137 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2532 r_free = 0.2532 target = 0.048745 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2470 r_free = 0.2470 target = 0.045482 restraints weight = 285.444| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.2492 r_free = 0.2492 target = 0.046587 restraints weight = 159.204| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 23)----------------| | r_work = 0.2507 r_free = 0.2507 target = 0.047354 restraints weight = 89.822| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 21)----------------| | r_work = 0.2515 r_free = 0.2515 target = 0.047825 restraints weight = 54.501| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.2521 r_free = 0.2521 target = 0.048154 restraints weight = 36.260| |-----------------------------------------------------------------------------| r_work (final): 0.2519 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7674 moved from start: 0.4986 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 16710 Z= 0.122 Angle : 0.658 7.295 22905 Z= 0.327 Chirality : 0.047 0.228 2755 Planarity : 0.004 0.041 2760 Dihedral : 6.239 77.162 2970 Min Nonbonded Distance : 2.514 Molprobity Statistics. All-atom Clashscore : 10.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.83 % Favored : 92.17 % 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 aren not related in a simple way. whole: -1.29 (0.19), residues: 1915 helix: -0.10 (0.18), residues: 730 sheet: -0.96 (0.24), residues: 420 loop : -1.41 (0.24), residues: 765 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 410 TYR 0.015 0.002 TYR A 64 PHE 0.013 0.001 PHE C 103 TRP 0.013 0.001 TRP A 68 HIS 0.002 0.001 HIS A 411 Details of bonding type rmsd covalent geometry : bond 0.00267 (16670) covalent geometry : angle 0.64693 (22790) SS BOND : bond 0.00051 ( 5) SS BOND : angle 0.29242 ( 10) hydrogen bonds : bond 0.03761 ( 775) hydrogen bonds : angle 4.73837 ( 2325) link_BETA1-4 : bond 0.00220 ( 20) link_BETA1-4 : angle 1.35650 ( 60) link_NAG-ASN : bond 0.00167 ( 15) link_NAG-ASN : angle 2.46957 ( 45) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2298 Ramachandran restraints generated. 1149 Oldfield, 0 Emsley, 1149 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2298 Ramachandran restraints generated. 1149 Oldfield, 0 Emsley, 1149 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 63 residues out of total 362 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 63 time to evaluate : 0.130 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 66 GLN cc_start: 0.7509 (mm110) cc_final: 0.7089 (mm110) REVERT: B 101 ASN cc_start: 0.7964 (m110) cc_final: 0.7429 (m110) REVERT: B 152 THR cc_start: 0.9108 (m) cc_final: 0.7805 (m) REVERT: B 210 MET cc_start: 0.8625 (tpp) cc_final: 0.8256 (tpp) REVERT: B 247 ASP cc_start: 0.7455 (t70) cc_final: 0.6940 (m-30) REVERT: B 286 TYR cc_start: 0.7570 (m-10) cc_final: 0.6913 (t80) REVERT: B 307 LEU cc_start: 0.8795 (tt) cc_final: 0.8453 (mm) REVERT: B 408 SER cc_start: 0.8493 (m) cc_final: 0.8160 (p) REVERT: B 426 TRP cc_start: 0.8644 (m100) cc_final: 0.8110 (m100) REVERT: B 428 ARG cc_start: 0.8029 (ttt-90) cc_final: 0.7481 (tpt170) REVERT: B 431 TYR cc_start: 0.8848 (m-80) cc_final: 0.8605 (m-80) REVERT: B 452 LEU cc_start: 0.7721 (mt) cc_final: 0.7463 (mt) outliers start: 0 outliers final: 0 residues processed: 63 average time/residue: 0.0462 time to fit residues: 3.8766 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 : 0.128 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: 0.0014 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 190 random chunks: chunk 76 optimal weight: 10.0000 chunk 90 optimal weight: 0.4980 chunk 117 optimal weight: 0.3980 chunk 59 optimal weight: 0.9980 chunk 58 optimal weight: 6.9990 chunk 28 optimal weight: 0.9980 chunk 186 optimal weight: 6.9990 chunk 151 optimal weight: 0.9980 chunk 21 optimal weight: 0.9980 chunk 112 optimal weight: 5.9990 chunk 54 optimal weight: 0.6980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3649 r_free = 0.3649 target = 0.101137 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3429 r_free = 0.3429 target = 0.089346 restraints weight = 13498.389| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3459 r_free = 0.3459 target = 0.090873 restraints weight = 8219.848| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3480 r_free = 0.3480 target = 0.091971 restraints weight = 5565.421| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3492 r_free = 0.3492 target = 0.092629 restraints weight = 4102.740| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3500 r_free = 0.3500 target = 0.093040 restraints weight = 3284.849| |-----------------------------------------------------------------------------| r_work (final): 0.3397 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2365 r_free = 0.2365 target = 0.039944 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 26)----------------| | r_work = 0.2374 r_free = 0.2374 target = 0.039318 restraints weight = 308.969| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.2375 r_free = 0.2375 target = 0.039366 restraints weight = 14.438| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 22)----------------| | r_work = 0.2375 r_free = 0.2375 target = 0.039366 restraints weight = 2.330 | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 22)----------------| | r_work = 0.2375 r_free = 0.2375 target = 0.039366 restraints weight = 2.330 | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.2375 r_free = 0.2375 target = 0.039366 restraints weight = 2.330 | |-----------------------------------------------------------------------------| r_work (final): 0.2330 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2528 r_free = 0.2528 target = 0.048671 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.2488 r_free = 0.2488 target = 0.046217 restraints weight = 247.722| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.2504 r_free = 0.2504 target = 0.047190 restraints weight = 134.087| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.2514 r_free = 0.2514 target = 0.047859 restraints weight = 74.903| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.2523 r_free = 0.2523 target = 0.048307 restraints weight = 46.923| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.2529 r_free = 0.2529 target = 0.048607 restraints weight = 29.351| |-----------------------------------------------------------------------------| r_work (final): 0.2526 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7681 moved from start: 0.5140 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 16710 Z= 0.117 Angle : 0.659 7.302 22905 Z= 0.325 Chirality : 0.047 0.229 2755 Planarity : 0.004 0.040 2760 Dihedral : 6.092 76.215 2970 Min Nonbonded Distance : 2.518 Molprobity Statistics. All-atom Clashscore : 10.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.88 % Favored : 91.12 % 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 aren not related in a simple way. whole: -1.35 (0.19), residues: 1915 helix: -0.07 (0.19), residues: 730 sheet: -0.92 (0.24), residues: 420 loop : -1.59 (0.24), residues: 765 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 410 TYR 0.015 0.001 TYR D 64 PHE 0.019 0.001 PHE E 103 TRP 0.012 0.001 TRP A 68 HIS 0.003 0.001 HIS D 411 Details of bonding type rmsd covalent geometry : bond 0.00256 (16670) covalent geometry : angle 0.64796 (22790) SS BOND : bond 0.00067 ( 5) SS BOND : angle 0.34371 ( 10) hydrogen bonds : bond 0.03658 ( 775) hydrogen bonds : angle 4.66086 ( 2325) link_BETA1-4 : bond 0.00254 ( 20) link_BETA1-4 : angle 1.32180 ( 60) link_NAG-ASN : bond 0.00064 ( 15) link_NAG-ASN : angle 2.49802 ( 45) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2298 Ramachandran restraints generated. 1149 Oldfield, 0 Emsley, 1149 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2298 Ramachandran restraints generated. 1149 Oldfield, 0 Emsley, 1149 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 : 0.138 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 56 GLN cc_start: 0.9089 (mm-40) cc_final: 0.8864 (mm-40) REVERT: B 66 GLN cc_start: 0.7506 (mm110) cc_final: 0.7101 (mm110) REVERT: B 101 ASN cc_start: 0.7927 (m110) cc_final: 0.7459 (m110) REVERT: B 152 THR cc_start: 0.9046 (m) cc_final: 0.7916 (m) REVERT: B 210 MET cc_start: 0.8581 (tpp) cc_final: 0.8296 (tpp) REVERT: B 247 ASP cc_start: 0.7447 (t70) cc_final: 0.7070 (m-30) REVERT: B 286 TYR cc_start: 0.7539 (m-10) cc_final: 0.7019 (t80) REVERT: B 307 LEU cc_start: 0.8783 (tt) cc_final: 0.8492 (mm) REVERT: B 408 SER cc_start: 0.8432 (m) cc_final: 0.8139 (p) REVERT: B 426 TRP cc_start: 0.8674 (m100) cc_final: 0.8118 (m100) REVERT: B 428 ARG cc_start: 0.8158 (ttt-90) cc_final: 0.7600 (tpt170) REVERT: B 431 TYR cc_start: 0.8851 (m-80) cc_final: 0.8630 (m-80) REVERT: B 452 LEU cc_start: 0.7731 (mt) cc_final: 0.7434 (mt) outliers start: 0 outliers final: 0 residues processed: 68 average time/residue: 0.0495 time to fit residues: 4.4276 Evaluate side-chains 53 residues out of total 362 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 53 time to evaluate : 0.130 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: 0.0012 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 190 random chunks: chunk 133 optimal weight: 4.9990 chunk 162 optimal weight: 0.1980 chunk 147 optimal weight: 10.0000 chunk 107 optimal weight: 7.9990 chunk 149 optimal weight: 0.8980 chunk 120 optimal weight: 3.9990 chunk 106 optimal weight: 0.0010 chunk 148 optimal weight: 1.9990 chunk 187 optimal weight: 10.0000 chunk 41 optimal weight: 7.9990 chunk 137 optimal weight: 5.9990 overall best weight: 1.4190 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3575 r_free = 0.3575 target = 0.096830 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3332 r_free = 0.3332 target = 0.083925 restraints weight = 12557.705| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3369 r_free = 0.3369 target = 0.085703 restraints weight = 7363.766| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3394 r_free = 0.3394 target = 0.086899 restraints weight = 4790.650| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3409 r_free = 0.3409 target = 0.087689 restraints weight = 3443.395| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.3420 r_free = 0.3420 target = 0.088242 restraints weight = 2693.243| |-----------------------------------------------------------------------------| r_work (final): 0.3384 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2324 r_free = 0.2324 target = 0.038881 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.2325 r_free = 0.2325 target = 0.038780 restraints weight = 261.423| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.2328 r_free = 0.2328 target = 0.038815 restraints weight = 12.867| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.2329 r_free = 0.2329 target = 0.038821 restraints weight = 2.373 | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.2329 r_free = 0.2329 target = 0.038815 restraints weight = 0.464 | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.2329 r_free = 0.2329 target = 0.038815 restraints weight = 0.329 | |-----------------------------------------------------------------------------| r_work (final): 0.2334 |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2502 r_free = 0.2502 target = 0.048073 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2463 r_free = 0.2463 target = 0.045495 restraints weight = 253.207| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.2475 r_free = 0.2475 target = 0.046360 restraints weight = 118.845| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.2490 r_free = 0.2490 target = 0.047083 restraints weight = 73.664| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.2494 r_free = 0.2494 target = 0.047417 restraints weight = 46.339| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.2499 r_free = 0.2499 target = 0.047747 restraints weight = 34.165| |-----------------------------------------------------------------------------| r_work (final): 0.2493 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7697 moved from start: 0.5257 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 16710 Z= 0.130 Angle : 0.664 7.153 22905 Z= 0.332 Chirality : 0.047 0.220 2755 Planarity : 0.004 0.038 2760 Dihedral : 6.086 75.802 2970 Min Nonbonded Distance : 2.512 Molprobity Statistics. All-atom Clashscore : 11.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.88 % Favored : 91.12 % 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 aren not related in a simple way. whole: -1.33 (0.19), residues: 1915 helix: -0.07 (0.19), residues: 735 sheet: -0.90 (0.24), residues: 420 loop : -1.57 (0.24), residues: 760 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 410 TYR 0.020 0.002 TYR D 61 PHE 0.032 0.002 PHE D 196 TRP 0.013 0.001 TRP C 68 HIS 0.002 0.001 HIS E 118 Details of bonding type rmsd covalent geometry : bond 0.00290 (16670) covalent geometry : angle 0.65105 (22790) SS BOND : bond 0.00101 ( 5) SS BOND : angle 0.49773 ( 10) hydrogen bonds : bond 0.03543 ( 775) hydrogen bonds : angle 4.73648 ( 2325) link_BETA1-4 : bond 0.00117 ( 20) link_BETA1-4 : angle 1.41361 ( 60) link_NAG-ASN : bond 0.00132 ( 15) link_NAG-ASN : angle 2.62302 ( 45) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1528.24 seconds wall clock time: 27 minutes 58.82 seconds (1678.82 seconds total)