Starting phenix.real_space_refine on Wed Mar 4 18:25:54 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8dg9_27419/03_2026/8dg9_27419.cif Found real_map, /net/cci-nas-00/data/ceres_data/8dg9_27419/03_2026/8dg9_27419.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.24 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8dg9_27419/03_2026/8dg9_27419.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8dg9_27419/03_2026/8dg9_27419.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8dg9_27419/03_2026/8dg9_27419.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8dg9_27419/03_2026/8dg9_27419.map" } resolution = 2.24 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= 0.003 sd= 0.368 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 84 5.16 5 C 9762 2.51 5 N 2568 2.21 5 O 3036 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 60 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 15450 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 3399 Number of conformers: 1 Conformer: "" Number of residues, atoms: 438, 3399 Classifications: {'peptide': 438} Link IDs: {'PCIS': 1, 'PTRANS': 11, 'TRANS': 425} Chain breaks: 3 Chain: "H" Number of atoms: 906 Number of conformers: 1 Conformer: "" Number of residues, atoms: 120, 906 Classifications: {'peptide': 120} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 4, 'TRANS': 115} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "L" Number of atoms: 817 Number of conformers: 1 Conformer: "" Number of residues, atoms: 111, 817 Classifications: {'peptide': 111} Link IDs: {'PTRANS': 7, 'TRANS': 103} Chain: "B" Number of atoms: 3399 Number of conformers: 1 Conformer: "" Number of residues, atoms: 438, 3399 Classifications: {'peptide': 438} Link IDs: {'PCIS': 1, 'PTRANS': 11, 'TRANS': 425} Chain breaks: 3 Chain: "F" Number of atoms: 906 Number of conformers: 1 Conformer: "" Number of residues, atoms: 120, 906 Classifications: {'peptide': 120} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 4, 'TRANS': 115} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "G" Number of atoms: 817 Number of conformers: 1 Conformer: "" Number of residues, atoms: 111, 817 Classifications: {'peptide': 111} Link IDs: {'PTRANS': 7, 'TRANS': 103} Chain: "C" Number of atoms: 3399 Number of conformers: 1 Conformer: "" Number of residues, atoms: 438, 3399 Classifications: {'peptide': 438} Link IDs: {'PCIS': 1, 'PTRANS': 11, 'TRANS': 425} Chain breaks: 3 Chain: "D" Number of atoms: 906 Number of conformers: 1 Conformer: "" Number of residues, atoms: 120, 906 Classifications: {'peptide': 120} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 4, 'TRANS': 115} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "E" Number of atoms: 817 Number of conformers: 1 Conformer: "" Number of residues, atoms: 111, 817 Classifications: {'peptide': 111} Link IDs: {'PTRANS': 7, 'TRANS': 103} Chain: "A" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "B" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "C" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Time building chain proxies: 3.59, per 1000 atoms: 0.23 Number of scatterers: 15450 At special positions: 0 Unit cell: (146.097, 140.952, 125.52, 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 84 16.00 O 3036 8.00 N 2568 7.00 C 9762 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=24, symmetry=0 Simple disulfide: pdb=" SG CYS A 37 " - pdb=" SG CYS A 439 " distance=2.03 Simple disulfide: pdb=" SG CYS A 313 " - pdb=" SG CYS A 343 " distance=2.04 Simple disulfide: pdb=" SG CYS A 322 " - pdb=" SG CYS A 333 " distance=2.03 Simple disulfide: pdb=" SG CYS A 358 " - pdb=" SG CYS A 367 " distance=2.03 Simple disulfide: pdb=" SG CYS A 382 " - pdb=" SG CYS A 393 " distance=2.03 Simple disulfide: pdb=" SG CYS A 416 " - pdb=" SG CYS A 422 " distance=2.03 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 92 " distance=2.04 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 88 " distance=2.04 Simple disulfide: pdb=" SG CYS B 37 " - pdb=" SG CYS B 439 " distance=2.03 Simple disulfide: pdb=" SG CYS B 313 " - pdb=" SG CYS B 343 " distance=2.04 Simple disulfide: pdb=" SG CYS B 322 " - pdb=" SG CYS B 333 " distance=2.03 Simple disulfide: pdb=" SG CYS B 358 " - pdb=" SG CYS B 367 " distance=2.03 Simple disulfide: pdb=" SG CYS B 382 " - pdb=" SG CYS B 393 " distance=2.03 Simple disulfide: pdb=" SG CYS B 416 " - pdb=" SG CYS B 422 " distance=2.03 Simple disulfide: pdb=" SG CYS F 22 " - pdb=" SG CYS F 92 " distance=2.04 Simple disulfide: pdb=" SG CYS G 23 " - pdb=" SG CYS G 88 " distance=2.04 Simple disulfide: pdb=" SG CYS C 37 " - pdb=" SG CYS C 439 " distance=2.03 Simple disulfide: pdb=" SG CYS C 313 " - pdb=" SG CYS C 343 " distance=2.07 Simple disulfide: pdb=" SG CYS C 322 " - pdb=" SG CYS C 333 " distance=2.03 Simple disulfide: pdb=" SG CYS C 358 " - pdb=" SG CYS C 367 " distance=2.03 Simple disulfide: pdb=" SG CYS C 382 " - pdb=" SG CYS C 393 " distance=2.03 Simple disulfide: pdb=" SG CYS C 416 " - pdb=" SG CYS C 422 " distance=2.03 Simple disulfide: pdb=" SG CYS D 22 " - pdb=" SG CYS D 92 " distance=2.04 Simple disulfide: pdb=" SG CYS E 23 " - pdb=" SG CYS E 88 " 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 NAG-ASN " NAG A5001 " - " ASN A 500 " " NAG A5002 " - " ASN A 27 " " NAG B 601 " - " ASN B 500 " " NAG B 602 " - " ASN B 27 " " NAG C 601 " - " ASN C 500 " " NAG C 602 " - " ASN C 27 " Time building additional restraints: 1.32 Conformation dependent library (CDL) restraints added in 774.8 milliseconds 3942 Ramachandran restraints generated. 1971 Oldfield, 0 Emsley, 1971 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3714 Finding SS restraints... Secondary structure from input PDB file: 50 helices and 36 sheets defined 24.9% alpha, 35.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.70 Creating SS restraints... Processing helix chain 'A' and resid 74 through 97 Processing helix chain 'A' and resid 138 through 142 Processing helix chain 'A' and resid 148 through 159 removed outlier: 3.503A pdb=" N HIS A 159 " --> pdb=" O CYS A 155 " (cutoff:3.500A) Processing helix chain 'A' and resid 162 through 171 Processing helix chain 'A' and resid 195 through 203 Processing helix chain 'A' and resid 217 through 239 removed outlier: 4.439A pdb=" N ARG A 229 " --> pdb=" O GLN A 225 " (cutoff:3.500A) removed outlier: 4.629A pdb=" N LEU A 230 " --> pdb=" O LYS A 226 " (cutoff:3.500A) Processing helix chain 'A' and resid 253 through 264 Processing helix chain 'A' and resid 267 through 276 Processing helix chain 'A' and resid 277 through 284 Processing helix chain 'A' and resid 370 through 372 No H-bonds generated for 'chain 'A' and resid 370 through 372' Processing helix chain 'A' and resid 380 through 385 removed outlier: 3.932A pdb=" N VAL A 384 " --> pdb=" O ASN A 380 " (cutoff:3.500A) Processing helix chain 'A' and resid 473 through 478 removed outlier: 3.530A pdb=" N TYR A 478 " --> pdb=" O ILE A 475 " (cutoff:3.500A) Processing helix chain 'A' and resid 492 through 513 Processing helix chain 'H' and resid 28 through 32 Processing helix chain 'H' and resid 83 through 87 removed outlier: 3.620A pdb=" N THR H 87 " --> pdb=" O ALA H 84 " (cutoff:3.500A) Processing helix chain 'L' and resid 79 through 83 removed outlier: 3.601A pdb=" N GLU L 83 " --> pdb=" O ALA L 80 " (cutoff:3.500A) Processing helix chain 'B' and resid 74 through 97 Processing helix chain 'B' and resid 138 through 142 Processing helix chain 'B' and resid 148 through 159 Processing helix chain 'B' and resid 162 through 171 Processing helix chain 'B' and resid 195 through 202 Processing helix chain 'B' and resid 217 through 239 removed outlier: 4.325A pdb=" N ARG B 229 " --> pdb=" O GLN B 225 " (cutoff:3.500A) removed outlier: 4.615A pdb=" N LEU B 230 " --> pdb=" O LYS B 226 " (cutoff:3.500A) Processing helix chain 'B' and resid 253 through 263 Processing helix chain 'B' and resid 267 through 276 Processing helix chain 'B' and resid 277 through 284 Processing helix chain 'B' and resid 370 through 372 No H-bonds generated for 'chain 'B' and resid 370 through 372' Processing helix chain 'B' and resid 376 through 379 Processing helix chain 'B' and resid 380 through 385 removed outlier: 3.974A pdb=" N VAL B 384 " --> pdb=" O ASN B 380 " (cutoff:3.500A) Processing helix chain 'B' and resid 473 through 478 removed outlier: 3.553A pdb=" N TYR B 478 " --> pdb=" O ILE B 475 " (cutoff:3.500A) Processing helix chain 'B' and resid 492 through 513 Processing helix chain 'F' and resid 28 through 32 Processing helix chain 'F' and resid 83 through 87 Processing helix chain 'G' and resid 79 through 83 Processing helix chain 'C' and resid 74 through 97 Processing helix chain 'C' and resid 138 through 142 Processing helix chain 'C' and resid 148 through 159 Processing helix chain 'C' and resid 162 through 171 Processing helix chain 'C' and resid 195 through 202 Processing helix chain 'C' and resid 217 through 239 removed outlier: 4.464A pdb=" N ARG C 229 " --> pdb=" O GLN C 225 " (cutoff:3.500A) removed outlier: 4.613A pdb=" N LEU C 230 " --> pdb=" O LYS C 226 " (cutoff:3.500A) Processing helix chain 'C' and resid 253 through 263 Processing helix chain 'C' and resid 267 through 276 Processing helix chain 'C' and resid 277 through 284 Processing helix chain 'C' and resid 370 through 372 No H-bonds generated for 'chain 'C' and resid 370 through 372' Processing helix chain 'C' and resid 376 through 379 Processing helix chain 'C' and resid 380 through 385 removed outlier: 3.945A pdb=" N VAL C 384 " --> pdb=" O ASN C 380 " (cutoff:3.500A) Processing helix chain 'C' and resid 473 through 478 removed outlier: 3.613A pdb=" N TYR C 478 " --> pdb=" O ILE C 475 " (cutoff:3.500A) Processing helix chain 'C' and resid 492 through 513 Processing helix chain 'D' and resid 28 through 32 Processing helix chain 'D' and resid 83 through 87 Processing helix chain 'E' and resid 79 through 83 Processing sheet with id=AA1, first strand: chain 'A' and resid 358 through 361 removed outlier: 8.316A pdb=" N VAL A 365 " --> pdb=" O GLY A 43 " (cutoff:3.500A) removed outlier: 6.436A pdb=" N LEU A 45 " --> pdb=" O VAL A 365 " (cutoff:3.500A) removed outlier: 7.399A pdb=" N CYS A 367 " --> pdb=" O LEU A 45 " (cutoff:3.500A) removed outlier: 6.330A pdb=" N ALA A 47 " --> pdb=" O CYS A 367 " (cutoff:3.500A) removed outlier: 3.963A pdb=" N GLY A 43 " --> pdb=" O CYS A 313 " (cutoff:3.500A) removed outlier: 6.310A pdb=" N CYS A 313 " --> pdb=" O GLY A 43 " (cutoff:3.500A) removed outlier: 4.445A pdb=" N LEU A 45 " --> pdb=" O THR A 311 " (cutoff:3.500A) removed outlier: 6.049A pdb=" N THR A 311 " --> pdb=" O LEU A 45 " (cutoff:3.500A) removed outlier: 6.469A pdb=" N ALA A 47 " --> pdb=" O ILE A 309 " (cutoff:3.500A) removed outlier: 6.910A pdb=" N ILE A 309 " --> pdb=" O ALA A 47 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 358 through 361 removed outlier: 8.316A pdb=" N VAL A 365 " --> pdb=" O GLY A 43 " (cutoff:3.500A) removed outlier: 6.436A pdb=" N LEU A 45 " --> pdb=" O VAL A 365 " (cutoff:3.500A) removed outlier: 7.399A pdb=" N CYS A 367 " --> pdb=" O LEU A 45 " (cutoff:3.500A) removed outlier: 6.330A pdb=" N ALA A 47 " --> pdb=" O CYS A 367 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 176 through 180 removed outlier: 10.733A pdb=" N SER A 186 " --> pdb=" O TRP A 52 " (cutoff:3.500A) removed outlier: 7.061A pdb=" N THR A 54 " --> pdb=" O SER A 186 " (cutoff:3.500A) removed outlier: 4.512A pdb=" N LEU A 188 " --> pdb=" O THR A 54 " (cutoff:3.500A) removed outlier: 7.925A pdb=" N GLU A 60 " --> pdb=" O VAL A 192 " (cutoff:3.500A) removed outlier: 4.975A pdb=" N ASP A 194 " --> pdb=" O GLU A 60 " (cutoff:3.500A) removed outlier: 6.653A pdb=" N VAL A 296 " --> pdb=" O ILE A 292 " (cutoff:3.500A) removed outlier: 4.537A pdb=" N ILE A 292 " --> pdb=" O VAL A 296 " (cutoff:3.500A) removed outlier: 7.025A pdb=" N ALA A 298 " --> pdb=" O CYS A 290 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 321 through 322 removed outlier: 6.445A pdb=" N ILE A 395 " --> pdb=" O ASP A 489 " (cutoff:3.500A) removed outlier: 4.716A pdb=" N ASP A 489 " --> pdb=" O ILE A 395 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 404 through 407 Processing sheet with id=AA6, first strand: chain 'A' and resid 430 through 434 removed outlier: 5.268A pdb=" N ILE A 431 " --> pdb=" O ASN A 426 " (cutoff:3.500A) removed outlier: 6.730A pdb=" N ASN A 426 " --> pdb=" O ILE A 431 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'H' and resid 5 through 7 Processing sheet with id=AA8, first strand: chain 'H' and resid 11 through 12 removed outlier: 6.903A pdb=" N MET H 34 " --> pdb=" O SER H 50 " (cutoff:3.500A) removed outlier: 4.552A pdb=" N SER H 50 " --> pdb=" O MET H 34 " (cutoff:3.500A) removed outlier: 6.592A pdb=" N TRP H 36 " --> pdb=" O VAL H 48 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'H' and resid 11 through 12 Processing sheet with id=AB1, first strand: chain 'L' and resid 9 through 13 removed outlier: 6.416A pdb=" N TRP L 35 " --> pdb=" O VAL L 47 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'L' and resid 9 through 13 removed outlier: 3.528A pdb=" N GLY L 95B" --> pdb=" O ASP L 92 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'L' and resid 19 through 24 Processing sheet with id=AB4, first strand: chain 'B' and resid 358 through 361 removed outlier: 8.323A pdb=" N VAL B 365 " --> pdb=" O GLY B 43 " (cutoff:3.500A) removed outlier: 6.509A pdb=" N LEU B 45 " --> pdb=" O VAL B 365 " (cutoff:3.500A) removed outlier: 7.519A pdb=" N CYS B 367 " --> pdb=" O LEU B 45 " (cutoff:3.500A) removed outlier: 6.414A pdb=" N ALA B 47 " --> pdb=" O CYS B 367 " (cutoff:3.500A) removed outlier: 4.002A pdb=" N GLY B 43 " --> pdb=" O CYS B 313 " (cutoff:3.500A) removed outlier: 6.274A pdb=" N CYS B 313 " --> pdb=" O GLY B 43 " (cutoff:3.500A) removed outlier: 4.388A pdb=" N LEU B 45 " --> pdb=" O THR B 311 " (cutoff:3.500A) removed outlier: 6.009A pdb=" N THR B 311 " --> pdb=" O LEU B 45 " (cutoff:3.500A) removed outlier: 6.621A pdb=" N ALA B 47 " --> pdb=" O ILE B 309 " (cutoff:3.500A) removed outlier: 7.095A pdb=" N ILE B 309 " --> pdb=" O ALA B 47 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'B' and resid 358 through 361 removed outlier: 8.323A pdb=" N VAL B 365 " --> pdb=" O GLY B 43 " (cutoff:3.500A) removed outlier: 6.509A pdb=" N LEU B 45 " --> pdb=" O VAL B 365 " (cutoff:3.500A) removed outlier: 7.519A pdb=" N CYS B 367 " --> pdb=" O LEU B 45 " (cutoff:3.500A) removed outlier: 6.414A pdb=" N ALA B 47 " --> pdb=" O CYS B 367 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'B' and resid 176 through 180 removed outlier: 10.802A pdb=" N SER B 186 " --> pdb=" O TRP B 52 " (cutoff:3.500A) removed outlier: 7.070A pdb=" N THR B 54 " --> pdb=" O SER B 186 " (cutoff:3.500A) removed outlier: 4.683A pdb=" N LEU B 188 " --> pdb=" O THR B 54 " (cutoff:3.500A) removed outlier: 7.879A pdb=" N GLU B 60 " --> pdb=" O VAL B 192 " (cutoff:3.500A) removed outlier: 5.036A pdb=" N ASP B 194 " --> pdb=" O GLU B 60 " (cutoff:3.500A) removed outlier: 6.681A pdb=" N VAL B 296 " --> pdb=" O ILE B 292 " (cutoff:3.500A) removed outlier: 4.539A pdb=" N ILE B 292 " --> pdb=" O VAL B 296 " (cutoff:3.500A) removed outlier: 7.029A pdb=" N ALA B 298 " --> pdb=" O CYS B 290 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'B' and resid 321 through 322 Processing sheet with id=AB8, first strand: chain 'B' and resid 404 through 407 Processing sheet with id=AB9, first strand: chain 'B' and resid 430 through 434 removed outlier: 5.181A pdb=" N ILE B 431 " --> pdb=" O ASN B 426 " (cutoff:3.500A) removed outlier: 6.565A pdb=" N ASN B 426 " --> pdb=" O ILE B 431 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'F' and resid 5 through 7 Processing sheet with id=AC2, first strand: chain 'F' and resid 11 through 12 removed outlier: 6.956A pdb=" N MET F 34 " --> pdb=" O SER F 50 " (cutoff:3.500A) removed outlier: 4.554A pdb=" N SER F 50 " --> pdb=" O MET F 34 " (cutoff:3.500A) removed outlier: 6.551A pdb=" N TRP F 36 " --> pdb=" O VAL F 48 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'F' and resid 11 through 12 Processing sheet with id=AC4, first strand: chain 'G' and resid 9 through 13 removed outlier: 6.468A pdb=" N TRP G 35 " --> pdb=" O VAL G 47 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'G' and resid 9 through 13 Processing sheet with id=AC6, first strand: chain 'G' and resid 19 through 24 Processing sheet with id=AC7, first strand: chain 'C' and resid 358 through 361 removed outlier: 8.263A pdb=" N VAL C 365 " --> pdb=" O GLY C 43 " (cutoff:3.500A) removed outlier: 6.414A pdb=" N LEU C 45 " --> pdb=" O VAL C 365 " (cutoff:3.500A) removed outlier: 7.418A pdb=" N CYS C 367 " --> pdb=" O LEU C 45 " (cutoff:3.500A) removed outlier: 6.373A pdb=" N ALA C 47 " --> pdb=" O CYS C 367 " (cutoff:3.500A) removed outlier: 3.966A pdb=" N GLY C 43 " --> pdb=" O CYS C 313 " (cutoff:3.500A) removed outlier: 6.378A pdb=" N CYS C 313 " --> pdb=" O GLY C 43 " (cutoff:3.500A) removed outlier: 4.385A pdb=" N LEU C 45 " --> pdb=" O THR C 311 " (cutoff:3.500A) removed outlier: 5.990A pdb=" N THR C 311 " --> pdb=" O LEU C 45 " (cutoff:3.500A) removed outlier: 6.523A pdb=" N ALA C 47 " --> pdb=" O ILE C 309 " (cutoff:3.500A) removed outlier: 6.947A pdb=" N ILE C 309 " --> pdb=" O ALA C 47 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'C' and resid 358 through 361 removed outlier: 8.263A pdb=" N VAL C 365 " --> pdb=" O GLY C 43 " (cutoff:3.500A) removed outlier: 6.414A pdb=" N LEU C 45 " --> pdb=" O VAL C 365 " (cutoff:3.500A) removed outlier: 7.418A pdb=" N CYS C 367 " --> pdb=" O LEU C 45 " (cutoff:3.500A) removed outlier: 6.373A pdb=" N ALA C 47 " --> pdb=" O CYS C 367 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'C' and resid 176 through 180 removed outlier: 10.767A pdb=" N SER C 186 " --> pdb=" O TRP C 52 " (cutoff:3.500A) removed outlier: 7.050A pdb=" N THR C 54 " --> pdb=" O SER C 186 " (cutoff:3.500A) removed outlier: 4.428A pdb=" N LEU C 188 " --> pdb=" O THR C 54 " (cutoff:3.500A) removed outlier: 7.781A pdb=" N GLU C 60 " --> pdb=" O VAL C 192 " (cutoff:3.500A) removed outlier: 4.941A pdb=" N ASP C 194 " --> pdb=" O GLU C 60 " (cutoff:3.500A) removed outlier: 6.361A pdb=" N VAL C 296 " --> pdb=" O ILE C 292 " (cutoff:3.500A) removed outlier: 4.230A pdb=" N ILE C 292 " --> pdb=" O VAL C 296 " (cutoff:3.500A) removed outlier: 7.025A pdb=" N ALA C 298 " --> pdb=" O CYS C 290 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'C' and resid 321 through 322 Processing sheet with id=AD2, first strand: chain 'C' and resid 404 through 407 Processing sheet with id=AD3, first strand: chain 'C' and resid 430 through 434 removed outlier: 6.719A pdb=" N ALA C 424 " --> pdb=" O ILE C 432 " (cutoff:3.500A) removed outlier: 4.846A pdb=" N THR C 434 " --> pdb=" O CYS C 422 " (cutoff:3.500A) removed outlier: 7.298A pdb=" N CYS C 422 " --> pdb=" O THR C 434 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'D' and resid 5 through 7 Processing sheet with id=AD5, first strand: chain 'D' and resid 11 through 12 removed outlier: 6.901A pdb=" N MET D 34 " --> pdb=" O SER D 50 " (cutoff:3.500A) removed outlier: 4.536A pdb=" N SER D 50 " --> pdb=" O MET D 34 " (cutoff:3.500A) removed outlier: 6.560A pdb=" N TRP D 36 " --> pdb=" O VAL D 48 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'D' and resid 11 through 12 Processing sheet with id=AD7, first strand: chain 'E' and resid 9 through 13 removed outlier: 6.625A pdb=" N VAL E 11 " --> pdb=" O THR E 105 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N ALA E 84 " --> pdb=" O LEU E 104 " (cutoff:3.500A) removed outlier: 6.499A pdb=" N TRP E 35 " --> pdb=" O VAL E 47 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'E' and resid 9 through 13 removed outlier: 6.625A pdb=" N VAL E 11 " --> pdb=" O THR E 105 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N ALA E 84 " --> pdb=" O LEU E 104 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'E' and resid 19 through 24 768 hydrogen bonds defined for protein. 1917 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: 2.89 Time building geometry restraints manager: 1.82 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.17 - 1.30: 2571 1.30 - 1.43: 3856 1.43 - 1.56: 9169 1.56 - 1.69: 1 1.69 - 1.82: 111 Bond restraints: 15708 Sorted by residual: bond pdb=" C VAL C 349 " pdb=" O VAL C 349 " ideal model delta sigma weight residual 1.236 1.167 0.069 1.04e-02 9.25e+03 4.38e+01 bond pdb=" C PRO E 7 " pdb=" O PRO E 7 " ideal model delta sigma weight residual 1.240 1.175 0.065 1.12e-02 7.97e+03 3.37e+01 bond pdb=" C GLY C 347 " pdb=" O GLY C 347 " ideal model delta sigma weight residual 1.237 1.188 0.048 9.40e-03 1.13e+04 2.66e+01 bond pdb=" C PRO E 8 " pdb=" O PRO E 8 " ideal model delta sigma weight residual 1.238 1.178 0.060 1.24e-02 6.50e+03 2.31e+01 bond pdb=" C ALA C 346 " pdb=" N GLY C 347 " ideal model delta sigma weight residual 1.330 1.289 0.041 1.24e-02 6.50e+03 1.07e+01 ... (remaining 15703 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.81: 20820 1.81 - 3.62: 400 3.62 - 5.43: 52 5.43 - 7.24: 5 7.24 - 9.05: 5 Bond angle restraints: 21282 Sorted by residual: angle pdb=" C ASP C 344 " pdb=" CA ASP C 344 " pdb=" CB ASP C 344 " ideal model delta sigma weight residual 109.72 118.77 -9.05 1.66e+00 3.63e-01 2.97e+01 angle pdb=" C ALA C 346 " pdb=" N GLY C 347 " pdb=" CA GLY C 347 " ideal model delta sigma weight residual 122.83 114.60 8.23 1.80e+00 3.09e-01 2.09e+01 angle pdb=" C ASP E 50 " pdb=" N ASN E 51 " pdb=" CA ASN E 51 " ideal model delta sigma weight residual 121.54 128.71 -7.17 1.91e+00 2.74e-01 1.41e+01 angle pdb=" N ILE C 432 " pdb=" CA ILE C 432 " pdb=" C ILE C 432 " ideal model delta sigma weight residual 112.96 109.26 3.70 1.00e+00 1.00e+00 1.37e+01 angle pdb=" N VAL E 11 " pdb=" CA VAL E 11 " pdb=" C VAL E 11 " ideal model delta sigma weight residual 108.45 103.04 5.41 1.48e+00 4.57e-01 1.33e+01 ... (remaining 21277 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 21.44: 8578 21.44 - 42.88: 824 42.88 - 64.32: 151 64.32 - 85.75: 34 85.75 - 107.19: 10 Dihedral angle restraints: 9597 sinusoidal: 3813 harmonic: 5784 Sorted by residual: dihedral pdb=" CB CYS B 37 " pdb=" SG CYS B 37 " pdb=" SG CYS B 439 " pdb=" CB CYS B 439 " ideal model delta sinusoidal sigma weight residual 93.00 145.99 -52.99 1 1.00e+01 1.00e-02 3.82e+01 dihedral pdb=" CA ASN A 27 " pdb=" C ASN A 27 " pdb=" N ILE A 28 " pdb=" CA ILE A 28 " ideal model delta harmonic sigma weight residual -180.00 -154.81 -25.19 0 5.00e+00 4.00e-02 2.54e+01 dihedral pdb=" CA ARG D 98 " pdb=" C ARG D 98 " pdb=" N GLU D 99 " pdb=" CA GLU D 99 " ideal model delta harmonic sigma weight residual 180.00 -156.01 -23.99 0 5.00e+00 4.00e-02 2.30e+01 ... (remaining 9594 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.149: 2501 0.149 - 0.298: 5 0.298 - 0.447: 1 0.447 - 0.596: 0 0.596 - 0.745: 1 Chirality restraints: 2508 Sorted by residual: chirality pdb=" C1 NAG A5001 " pdb=" ND2 ASN A 500 " pdb=" C2 NAG A5001 " pdb=" O5 NAG A5001 " both_signs ideal model delta sigma weight residual False -2.40 -1.65 -0.75 2.00e-01 2.50e+01 1.39e+01 chirality pdb=" C1 NAG B 601 " pdb=" ND2 ASN B 500 " pdb=" C2 NAG B 601 " pdb=" O5 NAG B 601 " both_signs ideal model delta sigma weight residual False -2.40 -1.99 -0.41 2.00e-01 2.50e+01 4.27e+00 chirality pdb=" C1 NAG C 601 " pdb=" ND2 ASN C 500 " pdb=" C2 NAG C 601 " pdb=" O5 NAG C 601 " both_signs ideal model delta sigma weight residual False -2.40 -2.12 -0.28 2.00e-01 2.50e+01 2.01e+00 ... (remaining 2505 not shown) Planarity restraints: 2691 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C PRO L 7 " -0.069 5.00e-02 4.00e+02 1.04e-01 1.71e+01 pdb=" N PRO L 8 " 0.179 5.00e-02 4.00e+02 pdb=" CA PRO L 8 " -0.054 5.00e-02 4.00e+02 pdb=" CD PRO L 8 " -0.056 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA SER E 9 " -0.012 2.00e-02 2.50e+03 2.44e-02 5.96e+00 pdb=" C SER E 9 " 0.042 2.00e-02 2.50e+03 pdb=" O SER E 9 " -0.016 2.00e-02 2.50e+03 pdb=" N VAL E 11 " -0.015 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASP C 344 " -0.011 2.00e-02 2.50e+03 2.29e-02 5.25e+00 pdb=" C ASP C 344 " 0.040 2.00e-02 2.50e+03 pdb=" O ASP C 344 " -0.015 2.00e-02 2.50e+03 pdb=" N ASN C 345 " -0.014 2.00e-02 2.50e+03 ... (remaining 2688 not shown) Histogram of nonbonded interaction distances: 2.12 - 2.67: 223 2.67 - 3.23: 13860 3.23 - 3.79: 24569 3.79 - 4.34: 35667 4.34 - 4.90: 56600 Nonbonded interactions: 130919 Sorted by model distance: nonbonded pdb=" N GLN B 26 " pdb=" OD1 ASN B 363 " model vdw 2.116 3.120 nonbonded pdb=" OE2 GLU C 30 " pdb=" OG1 THR C 408 " model vdw 2.211 3.040 nonbonded pdb=" O PRO E 7 " pdb=" OG1 THR E 102 " model vdw 2.253 3.040 nonbonded pdb=" N GLN A 26 " pdb=" O GLY A 43 " model vdw 2.266 3.120 nonbonded pdb=" NH1 ARG F 66 " pdb=" OD2 ASP F 86 " model vdw 2.266 3.120 ... (remaining 130914 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: 0.01 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' } ncs_group { reference = chain 'D' selection = chain 'F' selection = chain 'H' } ncs_group { reference = chain 'E' selection = chain 'G' selection = chain 'L' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic 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: 5.290 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.000 Extract box with map and model: 0.260 Check model and map are aligned: 0.050 Set scattering table: 0.040 Process input model: 15.480 Find NCS groups from input model: 0.210 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:6.260 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 27.630 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8091 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 : 0.004 0.093 15738 Z= 0.205 Angle : 0.666 19.956 21348 Z= 0.357 Chirality : 0.048 0.745 2508 Planarity : 0.005 0.104 2685 Dihedral : 17.358 107.193 5811 Min Nonbonded Distance : 2.116 Molprobity Statistics. All-atom Clashscore : 5.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.69 % Favored : 97.31 % Rotamer: Outliers : 0.91 % Allowed : 23.76 % Favored : 75.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.16 (0.18), residues: 1971 helix: 0.60 (0.25), residues: 432 sheet: 0.27 (0.21), residues: 594 loop : -0.61 (0.19), residues: 945 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 235 TYR 0.019 0.002 TYR A 457 PHE 0.017 0.002 PHE H 67 TRP 0.021 0.002 TRP L 96 HIS 0.003 0.001 HIS C 317 Details of bonding type rmsd covalent geometry : bond 0.00381 (15708) covalent geometry : angle 0.63454 (21282) SS BOND : bond 0.00846 ( 24) SS BOND : angle 1.26597 ( 48) hydrogen bonds : bond 0.19648 ( 728) hydrogen bonds : angle 7.69496 ( 1917) link_NAG-ASN : bond 0.01523 ( 6) link_NAG-ASN : angle 6.78604 ( 18) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3942 Ramachandran restraints generated. 1971 Oldfield, 0 Emsley, 1971 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3942 Ramachandran restraints generated. 1971 Oldfield, 0 Emsley, 1971 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 258 residues out of total 1758 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 242 time to evaluate : 0.628 Fit side-chains revert: symmetry clash REVERT: L 18 ARG cc_start: 0.7831 (ttp-170) cc_final: 0.7583 (ttp-170) REVERT: B 176 LYS cc_start: 0.8119 (ttpp) cc_final: 0.7880 (tttp) REVERT: B 295 GLU cc_start: 0.7046 (mt-10) cc_final: 0.6829 (mp0) REVERT: G 5 THR cc_start: 0.8872 (m) cc_final: 0.8647 (m) REVERT: G 67 SER cc_start: 0.8059 (p) cc_final: 0.7798 (t) REVERT: C 217 ILE cc_start: 0.8422 (tp) cc_final: 0.8175 (tp) REVERT: D 43 LYS cc_start: 0.7796 (mptt) cc_final: 0.6963 (pptt) outliers start: 16 outliers final: 12 residues processed: 253 average time/residue: 0.6255 time to fit residues: 173.4911 Evaluate side-chains 228 residues out of total 1758 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 216 time to evaluate : 0.584 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 THR Chi-restraints excluded: chain A residue 296 VAL Chi-restraints excluded: chain A residue 402 VAL Chi-restraints excluded: chain H residue 68 THR Chi-restraints excluded: chain H residue 113 SER Chi-restraints excluded: chain L residue 12 SER Chi-restraints excluded: chain B residue 41 SER Chi-restraints excluded: chain B residue 296 VAL Chi-restraints excluded: chain B residue 450 VAL Chi-restraints excluded: chain C residue 384 VAL Chi-restraints excluded: chain C residue 455 THR Chi-restraints excluded: chain D residue 68 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 198 random chunks: chunk 98 optimal weight: 6.9990 chunk 194 optimal weight: 9.9990 chunk 107 optimal weight: 0.3980 chunk 10 optimal weight: 0.9980 chunk 66 optimal weight: 5.9990 chunk 130 optimal weight: 0.6980 chunk 124 optimal weight: 0.8980 chunk 103 optimal weight: 0.9990 chunk 77 optimal weight: 4.9990 chunk 122 optimal weight: 1.9990 chunk 91 optimal weight: 0.6980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 363 ASN A 426 ASN F 76 ASN F 81 GLN C 197 ASN C 428 ASN D 76 ASN ** E 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3688 r_free = 0.3688 target = 0.151529 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3315 r_free = 0.3315 target = 0.120701 restraints weight = 13648.030| |-----------------------------------------------------------------------------| r_work (start): 0.3322 rms_B_bonded: 1.23 r_work: 0.3222 rms_B_bonded: 1.60 restraints_weight: 0.5000 r_work: 0.3119 rms_B_bonded: 2.60 restraints_weight: 0.2500 r_work (final): 0.3119 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8230 moved from start: 0.1117 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.067 15738 Z= 0.132 Angle : 0.609 18.256 21348 Z= 0.312 Chirality : 0.047 0.602 2508 Planarity : 0.004 0.063 2685 Dihedral : 6.109 54.589 2265 Min Nonbonded Distance : 2.522 Molprobity Statistics. All-atom Clashscore : 4.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.44 % Favored : 97.56 % Rotamer: Outliers : 2.91 % Allowed : 20.57 % Favored : 76.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.30 (0.18), residues: 1971 helix: 1.95 (0.25), residues: 414 sheet: 0.21 (0.20), residues: 597 loop : -0.55 (0.19), residues: 960 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 282 TYR 0.019 0.002 TYR B 457 PHE 0.014 0.002 PHE F 29 TRP 0.006 0.001 TRP D 103 HIS 0.003 0.001 HIS C 317 Details of bonding type rmsd covalent geometry : bond 0.00285 (15708) covalent geometry : angle 0.58150 (21282) SS BOND : bond 0.00326 ( 24) SS BOND : angle 0.70831 ( 48) hydrogen bonds : bond 0.04160 ( 728) hydrogen bonds : angle 5.49268 ( 1917) link_NAG-ASN : bond 0.01107 ( 6) link_NAG-ASN : angle 6.16583 ( 18) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3942 Ramachandran restraints generated. 1971 Oldfield, 0 Emsley, 1971 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3942 Ramachandran restraints generated. 1971 Oldfield, 0 Emsley, 1971 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 287 residues out of total 1758 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 236 time to evaluate : 0.513 Fit side-chains revert: symmetry clash REVERT: A 498 LYS cc_start: 0.7802 (mttp) cc_final: 0.7590 (mttp) REVERT: L 18 ARG cc_start: 0.7764 (ttp80) cc_final: 0.7496 (ttp80) REVERT: L 27 ASN cc_start: 0.8024 (m-40) cc_final: 0.7500 (p0) REVERT: B 176 LYS cc_start: 0.8558 (ttpp) cc_final: 0.8159 (tttm) REVERT: B 295 GLU cc_start: 0.7617 (mt-10) cc_final: 0.7087 (mp0) REVERT: B 489 ASP cc_start: 0.8082 (t0) cc_final: 0.7851 (t0) REVERT: F 64 LYS cc_start: 0.8247 (ttmt) cc_final: 0.7994 (ttmt) REVERT: G 38 GLN cc_start: 0.8620 (OUTLIER) cc_final: 0.7970 (tt0) REVERT: G 67 SER cc_start: 0.7951 (p) cc_final: 0.7612 (t) REVERT: C 489 ASP cc_start: 0.8143 (t0) cc_final: 0.7894 (t0) REVERT: D 76 ASN cc_start: 0.8371 (m-40) cc_final: 0.8164 (m-40) outliers start: 51 outliers final: 23 residues processed: 271 average time/residue: 0.5618 time to fit residues: 168.7245 Evaluate side-chains 239 residues out of total 1758 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 215 time to evaluate : 0.601 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 64 ILE Chi-restraints excluded: chain A residue 239 VAL Chi-restraints excluded: chain A residue 296 VAL Chi-restraints excluded: chain A residue 319 SER Chi-restraints excluded: chain A residue 455 THR Chi-restraints excluded: chain H residue 4 VAL Chi-restraints excluded: chain H residue 68 THR Chi-restraints excluded: chain H residue 85 ASP Chi-restraints excluded: chain H residue 87 THR Chi-restraints excluded: chain H residue 101 GLU Chi-restraints excluded: chain L residue 2 SER Chi-restraints excluded: chain L residue 20 THR Chi-restraints excluded: chain L residue 46 VAL Chi-restraints excluded: chain B residue 180 SER Chi-restraints excluded: chain B residue 296 VAL Chi-restraints excluded: chain B residue 348 SER Chi-restraints excluded: chain G residue 38 GLN Chi-restraints excluded: chain C residue 239 VAL Chi-restraints excluded: chain C residue 384 VAL Chi-restraints excluded: chain C residue 402 VAL Chi-restraints excluded: chain D residue 12 VAL Chi-restraints excluded: chain D residue 21 SER Chi-restraints excluded: chain D residue 68 THR Chi-restraints excluded: chain E residue 52 ASN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 198 random chunks: chunk 149 optimal weight: 3.9990 chunk 73 optimal weight: 2.9990 chunk 174 optimal weight: 0.9980 chunk 15 optimal weight: 2.9990 chunk 52 optimal weight: 2.9990 chunk 71 optimal weight: 5.9990 chunk 13 optimal weight: 0.0070 chunk 72 optimal weight: 1.9990 chunk 144 optimal weight: 4.9990 chunk 66 optimal weight: 5.9990 chunk 19 optimal weight: 1.9990 overall best weight: 1.6004 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 27BASN ** B 363 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 3 GLN F 76 ASN F 81 GLN C 81 GLN C 197 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3645 r_free = 0.3645 target = 0.147700 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3265 r_free = 0.3265 target = 0.116831 restraints weight = 13700.462| |-----------------------------------------------------------------------------| r_work (start): 0.3267 rms_B_bonded: 1.23 r_work: 0.3166 rms_B_bonded: 1.59 restraints_weight: 0.5000 r_work: 0.3061 rms_B_bonded: 2.57 restraints_weight: 0.2500 r_work (final): 0.3061 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8285 moved from start: 0.1347 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.102 15738 Z= 0.201 Angle : 0.682 18.013 21348 Z= 0.355 Chirality : 0.049 0.586 2508 Planarity : 0.005 0.052 2685 Dihedral : 5.690 53.913 2258 Min Nonbonded Distance : 2.496 Molprobity Statistics. All-atom Clashscore : 4.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.69 % Favored : 97.31 % Rotamer: Outliers : 3.36 % Allowed : 19.77 % Favored : 76.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.21 (0.18), residues: 1971 helix: 1.93 (0.25), residues: 414 sheet: 0.18 (0.21), residues: 567 loop : -0.64 (0.18), residues: 990 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG F 98 TYR 0.023 0.002 TYR B 457 PHE 0.016 0.002 PHE A 387 TRP 0.009 0.002 TRP D 103 HIS 0.004 0.002 HIS C 317 Details of bonding type rmsd covalent geometry : bond 0.00451 (15708) covalent geometry : angle 0.65987 (21282) SS BOND : bond 0.00601 ( 24) SS BOND : angle 0.83146 ( 48) hydrogen bonds : bond 0.04880 ( 728) hydrogen bonds : angle 5.63364 ( 1917) link_NAG-ASN : bond 0.01307 ( 6) link_NAG-ASN : angle 5.90831 ( 18) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3942 Ramachandran restraints generated. 1971 Oldfield, 0 Emsley, 1971 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3942 Ramachandran restraints generated. 1971 Oldfield, 0 Emsley, 1971 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 276 residues out of total 1758 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 217 time to evaluate : 0.534 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 472 GLU cc_start: 0.8328 (OUTLIER) cc_final: 0.7970 (tt0) REVERT: H 107 ILE cc_start: 0.8502 (OUTLIER) cc_final: 0.8192 (tt) REVERT: L 27 ASN cc_start: 0.8169 (m-40) cc_final: 0.7597 (p0) REVERT: B 176 LYS cc_start: 0.8569 (ttpp) cc_final: 0.8210 (tttp) REVERT: B 295 GLU cc_start: 0.7678 (mt-10) cc_final: 0.7134 (mp0) REVERT: B 489 ASP cc_start: 0.8057 (t0) cc_final: 0.7850 (t0) REVERT: G 50 ASP cc_start: 0.8671 (m-30) cc_final: 0.8456 (m-30) REVERT: C 489 ASP cc_start: 0.8047 (t0) cc_final: 0.7790 (t0) outliers start: 59 outliers final: 34 residues processed: 253 average time/residue: 0.5596 time to fit residues: 156.6106 Evaluate side-chains 241 residues out of total 1758 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 205 time to evaluate : 0.584 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 THR Chi-restraints excluded: chain A residue 76 VAL Chi-restraints excluded: chain A residue 217 ILE Chi-restraints excluded: chain A residue 239 VAL Chi-restraints excluded: chain A residue 255 SER Chi-restraints excluded: chain A residue 296 VAL Chi-restraints excluded: chain A residue 319 SER Chi-restraints excluded: chain A residue 384 VAL Chi-restraints excluded: chain A residue 455 THR Chi-restraints excluded: chain A residue 472 GLU Chi-restraints excluded: chain H residue 4 VAL Chi-restraints excluded: chain H residue 68 THR Chi-restraints excluded: chain H residue 101 GLU Chi-restraints excluded: chain H residue 107 ILE Chi-restraints excluded: chain L residue 2 SER Chi-restraints excluded: chain L residue 20 THR Chi-restraints excluded: chain B residue 76 VAL Chi-restraints excluded: chain B residue 180 SER Chi-restraints excluded: chain B residue 196 LYS Chi-restraints excluded: chain B residue 217 ILE Chi-restraints excluded: chain B residue 296 VAL Chi-restraints excluded: chain B residue 319 SER Chi-restraints excluded: chain B residue 348 SER Chi-restraints excluded: chain B residue 384 VAL Chi-restraints excluded: chain B residue 402 VAL Chi-restraints excluded: chain B residue 465 LYS Chi-restraints excluded: chain B residue 500 ASN Chi-restraints excluded: chain F residue 111 VAL Chi-restraints excluded: chain G residue 93 LYS Chi-restraints excluded: chain C residue 239 VAL Chi-restraints excluded: chain C residue 384 VAL Chi-restraints excluded: chain C residue 402 VAL Chi-restraints excluded: chain C residue 465 LYS Chi-restraints excluded: chain D residue 21 SER Chi-restraints excluded: chain D residue 68 THR Chi-restraints excluded: chain E residue 20 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 198 random chunks: chunk 149 optimal weight: 0.7980 chunk 171 optimal weight: 2.9990 chunk 40 optimal weight: 2.9990 chunk 58 optimal weight: 5.9990 chunk 8 optimal weight: 0.8980 chunk 30 optimal weight: 0.8980 chunk 32 optimal weight: 1.9990 chunk 195 optimal weight: 5.9990 chunk 180 optimal weight: 0.7980 chunk 158 optimal weight: 0.9980 chunk 106 optimal weight: 0.9980 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 268 ASN F 81 GLN G 38 GLN C 197 ASN C 325 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3668 r_free = 0.3668 target = 0.149747 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3295 r_free = 0.3295 target = 0.119075 restraints weight = 13676.225| |-----------------------------------------------------------------------------| r_work (start): 0.3301 rms_B_bonded: 1.23 r_work: 0.3200 rms_B_bonded: 1.59 restraints_weight: 0.5000 r_work: 0.3097 rms_B_bonded: 2.58 restraints_weight: 0.2500 r_work (final): 0.3097 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8253 moved from start: 0.1578 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.068 15738 Z= 0.135 Angle : 0.589 17.237 21348 Z= 0.305 Chirality : 0.046 0.558 2508 Planarity : 0.004 0.046 2685 Dihedral : 5.287 54.245 2258 Min Nonbonded Distance : 2.521 Molprobity Statistics. All-atom Clashscore : 3.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.59 % Favored : 97.41 % Rotamer: Outliers : 3.13 % Allowed : 19.72 % Favored : 77.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.34 (0.18), residues: 1971 helix: 2.17 (0.25), residues: 414 sheet: 0.11 (0.20), residues: 597 loop : -0.53 (0.19), residues: 960 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG L 54 TYR 0.018 0.002 TYR B 457 PHE 0.011 0.002 PHE F 29 TRP 0.008 0.002 TRP D 103 HIS 0.003 0.001 HIS C 317 Details of bonding type rmsd covalent geometry : bond 0.00295 (15708) covalent geometry : angle 0.56651 (21282) SS BOND : bond 0.00383 ( 24) SS BOND : angle 0.63850 ( 48) hydrogen bonds : bond 0.03917 ( 728) hydrogen bonds : angle 5.27645 ( 1917) link_NAG-ASN : bond 0.01292 ( 6) link_NAG-ASN : angle 5.56493 ( 18) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3942 Ramachandran restraints generated. 1971 Oldfield, 0 Emsley, 1971 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3942 Ramachandran restraints generated. 1971 Oldfield, 0 Emsley, 1971 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 266 residues out of total 1758 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 211 time to evaluate : 0.531 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 75 LYS cc_start: 0.8250 (mtmm) cc_final: 0.8010 (mppt) REVERT: A 196 LYS cc_start: 0.8565 (tttp) cc_final: 0.8070 (ttmt) REVERT: A 472 GLU cc_start: 0.8243 (OUTLIER) cc_final: 0.7883 (tt0) REVERT: H 107 ILE cc_start: 0.8477 (OUTLIER) cc_final: 0.8192 (tt) REVERT: B 176 LYS cc_start: 0.8552 (ttpp) cc_final: 0.8145 (tttp) REVERT: B 222 GLU cc_start: 0.7934 (tt0) cc_final: 0.7682 (tt0) REVERT: B 295 GLU cc_start: 0.7654 (mt-10) cc_final: 0.7195 (mp0) REVERT: B 512 LEU cc_start: 0.3959 (OUTLIER) cc_final: 0.3745 (tt) REVERT: C 272 LYS cc_start: 0.8161 (mttt) cc_final: 0.7942 (mttp) REVERT: C 489 ASP cc_start: 0.7991 (t70) cc_final: 0.7751 (t0) outliers start: 55 outliers final: 36 residues processed: 246 average time/residue: 0.5669 time to fit residues: 154.2290 Evaluate side-chains 240 residues out of total 1758 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 201 time to evaluate : 0.580 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 THR Chi-restraints excluded: chain A residue 64 ILE Chi-restraints excluded: chain A residue 217 ILE Chi-restraints excluded: chain A residue 239 VAL Chi-restraints excluded: chain A residue 255 SER Chi-restraints excluded: chain A residue 296 VAL Chi-restraints excluded: chain A residue 319 SER Chi-restraints excluded: chain A residue 371 ASN Chi-restraints excluded: chain A residue 384 VAL Chi-restraints excluded: chain A residue 386 ILE Chi-restraints excluded: chain A residue 455 THR Chi-restraints excluded: chain A residue 472 GLU Chi-restraints excluded: chain H residue 4 VAL Chi-restraints excluded: chain H residue 68 THR Chi-restraints excluded: chain H residue 101 GLU Chi-restraints excluded: chain H residue 107 ILE Chi-restraints excluded: chain L residue 2 SER Chi-restraints excluded: chain L residue 20 THR Chi-restraints excluded: chain B residue 180 SER Chi-restraints excluded: chain B residue 296 VAL Chi-restraints excluded: chain B residue 319 SER Chi-restraints excluded: chain B residue 348 SER Chi-restraints excluded: chain B residue 371 ASN Chi-restraints excluded: chain B residue 384 VAL Chi-restraints excluded: chain B residue 402 VAL Chi-restraints excluded: chain B residue 465 LYS Chi-restraints excluded: chain B residue 512 LEU Chi-restraints excluded: chain C residue 41 SER Chi-restraints excluded: chain C residue 239 VAL Chi-restraints excluded: chain C residue 254 ASN Chi-restraints excluded: chain C residue 384 VAL Chi-restraints excluded: chain C residue 402 VAL Chi-restraints excluded: chain C residue 442 VAL Chi-restraints excluded: chain D residue 12 VAL Chi-restraints excluded: chain D residue 21 SER Chi-restraints excluded: chain D residue 68 THR Chi-restraints excluded: chain D residue 85 ASP Chi-restraints excluded: chain E residue 12 SER Chi-restraints excluded: chain E residue 52 ASN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 198 random chunks: chunk 79 optimal weight: 6.9990 chunk 55 optimal weight: 1.9990 chunk 164 optimal weight: 3.9990 chunk 49 optimal weight: 3.9990 chunk 47 optimal weight: 2.9990 chunk 103 optimal weight: 4.9990 chunk 139 optimal weight: 2.9990 chunk 137 optimal weight: 5.9990 chunk 177 optimal weight: 5.9990 chunk 52 optimal weight: 2.9990 chunk 127 optimal weight: 0.0370 overall best weight: 2.2066 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 76 ASN F 81 GLN C 197 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3639 r_free = 0.3639 target = 0.146894 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3256 r_free = 0.3256 target = 0.115903 restraints weight = 13627.394| |-----------------------------------------------------------------------------| r_work (start): 0.3260 rms_B_bonded: 1.23 r_work: 0.3161 rms_B_bonded: 1.57 restraints_weight: 0.5000 r_work: 0.3057 rms_B_bonded: 2.53 restraints_weight: 0.2500 r_work (final): 0.3057 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8287 moved from start: 0.1686 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.115 15738 Z= 0.252 Angle : 0.746 17.543 21348 Z= 0.390 Chirality : 0.051 0.554 2508 Planarity : 0.005 0.048 2685 Dihedral : 5.866 53.119 2258 Min Nonbonded Distance : 2.480 Molprobity Statistics. All-atom Clashscore : 3.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.45 % Favored : 96.55 % Rotamer: Outliers : 3.76 % Allowed : 18.35 % Favored : 77.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.15 (0.18), residues: 1971 helix: 1.85 (0.24), residues: 414 sheet: 0.18 (0.21), residues: 558 loop : -0.67 (0.18), residues: 999 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG H 98 TYR 0.024 0.003 TYR B 457 PHE 0.016 0.002 PHE F 91 TRP 0.011 0.003 TRP D 103 HIS 0.006 0.003 HIS A 317 Details of bonding type rmsd covalent geometry : bond 0.00571 (15708) covalent geometry : angle 0.72573 (21282) SS BOND : bond 0.00785 ( 24) SS BOND : angle 1.02230 ( 48) hydrogen bonds : bond 0.05216 ( 728) hydrogen bonds : angle 5.70968 ( 1917) link_NAG-ASN : bond 0.01411 ( 6) link_NAG-ASN : angle 5.84033 ( 18) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3942 Ramachandran restraints generated. 1971 Oldfield, 0 Emsley, 1971 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3942 Ramachandran restraints generated. 1971 Oldfield, 0 Emsley, 1971 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 284 residues out of total 1758 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 218 time to evaluate : 0.737 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 196 LYS cc_start: 0.8566 (tttp) cc_final: 0.8103 (ttmt) REVERT: A 472 GLU cc_start: 0.8351 (OUTLIER) cc_final: 0.7985 (tt0) REVERT: H 107 ILE cc_start: 0.8555 (OUTLIER) cc_final: 0.8245 (tt) REVERT: L 50 ASP cc_start: 0.8688 (m-30) cc_final: 0.8479 (m-30) REVERT: B 176 LYS cc_start: 0.8585 (ttpp) cc_final: 0.8186 (tttp) REVERT: B 254 ASN cc_start: 0.9295 (OUTLIER) cc_final: 0.9079 (t0) REVERT: B 512 LEU cc_start: 0.4129 (OUTLIER) cc_final: 0.3898 (tt) REVERT: G 50 ASP cc_start: 0.8664 (m-30) cc_final: 0.8405 (m-30) REVERT: C 204 LEU cc_start: 0.6639 (OUTLIER) cc_final: 0.6397 (tp) REVERT: C 432 ILE cc_start: 0.8863 (OUTLIER) cc_final: 0.8535 (pp) REVERT: C 489 ASP cc_start: 0.8025 (t70) cc_final: 0.7784 (t0) REVERT: D 43 LYS cc_start: 0.8134 (mptt) cc_final: 0.6798 (pptt) outliers start: 66 outliers final: 46 residues processed: 256 average time/residue: 0.5647 time to fit residues: 160.0931 Evaluate side-chains 255 residues out of total 1758 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 203 time to evaluate : 0.562 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 THR Chi-restraints excluded: chain A residue 76 VAL Chi-restraints excluded: chain A residue 165 ASN Chi-restraints excluded: chain A residue 180 SER Chi-restraints excluded: chain A residue 217 ILE Chi-restraints excluded: chain A residue 239 VAL Chi-restraints excluded: chain A residue 255 SER Chi-restraints excluded: chain A residue 296 VAL Chi-restraints excluded: chain A residue 319 SER Chi-restraints excluded: chain A residue 384 VAL Chi-restraints excluded: chain A residue 386 ILE Chi-restraints excluded: chain A residue 450 VAL Chi-restraints excluded: chain A residue 455 THR Chi-restraints excluded: chain A residue 472 GLU Chi-restraints excluded: chain H residue 4 VAL Chi-restraints excluded: chain H residue 68 THR Chi-restraints excluded: chain H residue 101 GLU Chi-restraints excluded: chain H residue 107 ILE Chi-restraints excluded: chain L residue 20 THR Chi-restraints excluded: chain B residue 76 VAL Chi-restraints excluded: chain B residue 180 SER Chi-restraints excluded: chain B residue 196 LYS Chi-restraints excluded: chain B residue 217 ILE Chi-restraints excluded: chain B residue 254 ASN Chi-restraints excluded: chain B residue 296 VAL Chi-restraints excluded: chain B residue 319 SER Chi-restraints excluded: chain B residue 348 SER Chi-restraints excluded: chain B residue 371 ASN Chi-restraints excluded: chain B residue 384 VAL Chi-restraints excluded: chain B residue 402 VAL Chi-restraints excluded: chain B residue 465 LYS Chi-restraints excluded: chain B residue 500 ASN Chi-restraints excluded: chain B residue 512 LEU Chi-restraints excluded: chain F residue 12 VAL Chi-restraints excluded: chain F residue 111 VAL Chi-restraints excluded: chain C residue 180 SER Chi-restraints excluded: chain C residue 204 LEU Chi-restraints excluded: chain C residue 239 VAL Chi-restraints excluded: chain C residue 283 GLN Chi-restraints excluded: chain C residue 319 SER Chi-restraints excluded: chain C residue 371 ASN Chi-restraints excluded: chain C residue 384 VAL Chi-restraints excluded: chain C residue 402 VAL Chi-restraints excluded: chain C residue 432 ILE Chi-restraints excluded: chain C residue 442 VAL Chi-restraints excluded: chain C residue 465 LYS Chi-restraints excluded: chain D residue 12 VAL Chi-restraints excluded: chain D residue 21 SER Chi-restraints excluded: chain D residue 68 THR Chi-restraints excluded: chain D residue 85 ASP Chi-restraints excluded: chain E residue 12 SER Chi-restraints excluded: chain E residue 20 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 198 random chunks: chunk 52 optimal weight: 2.9990 chunk 129 optimal weight: 2.9990 chunk 85 optimal weight: 0.7980 chunk 86 optimal weight: 0.2980 chunk 47 optimal weight: 2.9990 chunk 142 optimal weight: 0.9980 chunk 2 optimal weight: 0.8980 chunk 106 optimal weight: 0.7980 chunk 4 optimal weight: 8.9990 chunk 141 optimal weight: 1.9990 chunk 113 optimal weight: 2.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 462 GLN L 27BASN C 197 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3676 r_free = 0.3676 target = 0.150302 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3306 r_free = 0.3306 target = 0.119758 restraints weight = 13579.341| |-----------------------------------------------------------------------------| r_work (start): 0.3311 rms_B_bonded: 1.22 r_work: 0.3213 rms_B_bonded: 1.57 restraints_weight: 0.5000 r_work: 0.3111 rms_B_bonded: 2.55 restraints_weight: 0.2500 r_work (final): 0.3111 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8234 moved from start: 0.1776 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.063 15738 Z= 0.126 Angle : 0.582 16.741 21348 Z= 0.302 Chirality : 0.045 0.536 2508 Planarity : 0.004 0.043 2685 Dihedral : 5.248 54.195 2258 Min Nonbonded Distance : 2.506 Molprobity Statistics. All-atom Clashscore : 3.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.33 % Favored : 97.67 % Rotamer: Outliers : 2.74 % Allowed : 19.26 % Favored : 78.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.35 (0.18), residues: 1971 helix: 2.23 (0.25), residues: 414 sheet: 0.21 (0.21), residues: 537 loop : -0.58 (0.18), residues: 1020 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG L 54 TYR 0.018 0.002 TYR B 457 PHE 0.014 0.002 PHE C 190 TRP 0.008 0.001 TRP D 103 HIS 0.003 0.001 HIS A 317 Details of bonding type rmsd covalent geometry : bond 0.00273 (15708) covalent geometry : angle 0.55967 (21282) SS BOND : bond 0.00356 ( 24) SS BOND : angle 0.61875 ( 48) hydrogen bonds : bond 0.03774 ( 728) hydrogen bonds : angle 5.23262 ( 1917) link_NAG-ASN : bond 0.01179 ( 6) link_NAG-ASN : angle 5.51389 ( 18) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3942 Ramachandran restraints generated. 1971 Oldfield, 0 Emsley, 1971 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3942 Ramachandran restraints generated. 1971 Oldfield, 0 Emsley, 1971 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 260 residues out of total 1758 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 212 time to evaluate : 0.613 Fit side-chains revert: symmetry clash REVERT: A 75 LYS cc_start: 0.8118 (mtmm) cc_final: 0.7905 (mppt) REVERT: A 272 LYS cc_start: 0.8593 (mttp) cc_final: 0.8376 (mtpm) REVERT: A 472 GLU cc_start: 0.8213 (OUTLIER) cc_final: 0.7855 (tt0) REVERT: H 107 ILE cc_start: 0.8487 (OUTLIER) cc_final: 0.8228 (tt) REVERT: L 27 ASN cc_start: 0.8046 (m-40) cc_final: 0.7512 (p0) REVERT: B 176 LYS cc_start: 0.8567 (ttpp) cc_final: 0.8151 (tttp) REVERT: B 222 GLU cc_start: 0.7924 (tt0) cc_final: 0.7609 (tt0) REVERT: B 295 GLU cc_start: 0.7667 (mt-10) cc_final: 0.7223 (mp0) REVERT: B 512 LEU cc_start: 0.4061 (OUTLIER) cc_final: 0.3826 (tt) REVERT: C 204 LEU cc_start: 0.6504 (OUTLIER) cc_final: 0.6300 (tp) REVERT: C 489 ASP cc_start: 0.7832 (t70) cc_final: 0.7598 (t0) outliers start: 48 outliers final: 36 residues processed: 243 average time/residue: 0.5749 time to fit residues: 154.2855 Evaluate side-chains 243 residues out of total 1758 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 203 time to evaluate : 0.565 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 239 VAL Chi-restraints excluded: chain A residue 255 SER Chi-restraints excluded: chain A residue 296 VAL Chi-restraints excluded: chain A residue 319 SER Chi-restraints excluded: chain A residue 384 VAL Chi-restraints excluded: chain A residue 455 THR Chi-restraints excluded: chain A residue 472 GLU Chi-restraints excluded: chain H residue 4 VAL Chi-restraints excluded: chain H residue 68 THR Chi-restraints excluded: chain H residue 101 GLU Chi-restraints excluded: chain H residue 107 ILE Chi-restraints excluded: chain L residue 20 THR Chi-restraints excluded: chain B residue 76 VAL Chi-restraints excluded: chain B residue 180 SER Chi-restraints excluded: chain B residue 196 LYS Chi-restraints excluded: chain B residue 204 LEU Chi-restraints excluded: chain B residue 217 ILE Chi-restraints excluded: chain B residue 296 VAL Chi-restraints excluded: chain B residue 319 SER Chi-restraints excluded: chain B residue 348 SER Chi-restraints excluded: chain B residue 356 GLU Chi-restraints excluded: chain B residue 371 ASN Chi-restraints excluded: chain B residue 384 VAL Chi-restraints excluded: chain B residue 402 VAL Chi-restraints excluded: chain B residue 465 LYS Chi-restraints excluded: chain B residue 500 ASN Chi-restraints excluded: chain B residue 512 LEU Chi-restraints excluded: chain C residue 204 LEU Chi-restraints excluded: chain C residue 239 VAL Chi-restraints excluded: chain C residue 319 SER Chi-restraints excluded: chain C residue 371 ASN Chi-restraints excluded: chain C residue 384 VAL Chi-restraints excluded: chain C residue 402 VAL Chi-restraints excluded: chain C residue 442 VAL Chi-restraints excluded: chain C residue 465 LYS Chi-restraints excluded: chain D residue 12 VAL Chi-restraints excluded: chain D residue 68 THR Chi-restraints excluded: chain D residue 85 ASP Chi-restraints excluded: chain E residue 12 SER Chi-restraints excluded: chain E residue 52 ASN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 198 random chunks: chunk 119 optimal weight: 0.8980 chunk 65 optimal weight: 5.9990 chunk 114 optimal weight: 4.9990 chunk 125 optimal weight: 2.9990 chunk 46 optimal weight: 4.9990 chunk 116 optimal weight: 1.9990 chunk 41 optimal weight: 0.0970 chunk 23 optimal weight: 3.9990 chunk 78 optimal weight: 2.9990 chunk 105 optimal weight: 0.9990 chunk 57 optimal weight: 2.9990 overall best weight: 1.3984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 363 ASN F 76 ASN C 197 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3668 r_free = 0.3668 target = 0.149539 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3296 r_free = 0.3296 target = 0.119014 restraints weight = 13633.364| |-----------------------------------------------------------------------------| r_work (start): 0.3302 rms_B_bonded: 1.22 r_work: 0.3204 rms_B_bonded: 1.57 restraints_weight: 0.5000 r_work: 0.3101 rms_B_bonded: 2.54 restraints_weight: 0.2500 r_work (final): 0.3101 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8247 moved from start: 0.1796 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.079 15738 Z= 0.173 Angle : 0.841 59.199 21348 Z= 0.448 Chirality : 0.047 0.497 2508 Planarity : 0.004 0.041 2685 Dihedral : 5.396 53.962 2258 Min Nonbonded Distance : 2.495 Molprobity Statistics. All-atom Clashscore : 4.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.44 % Favored : 97.56 % Rotamer: Outliers : 2.62 % Allowed : 19.49 % Favored : 77.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.35 (0.18), residues: 1971 helix: 2.22 (0.25), residues: 414 sheet: 0.23 (0.21), residues: 537 loop : -0.58 (0.18), residues: 1020 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG E 61 TYR 0.019 0.002 TYR B 457 PHE 0.016 0.002 PHE C 190 TRP 0.009 0.002 TRP D 103 HIS 0.004 0.002 HIS C 317 Details of bonding type rmsd covalent geometry : bond 0.00385 (15708) covalent geometry : angle 0.80081 (21282) SS BOND : bond 0.00480 ( 24) SS BOND : angle 0.68188 ( 48) hydrogen bonds : bond 0.04002 ( 728) hydrogen bonds : angle 5.27699 ( 1917) link_NAG-ASN : bond 0.01050 ( 6) link_NAG-ASN : angle 8.91520 ( 18) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3942 Ramachandran restraints generated. 1971 Oldfield, 0 Emsley, 1971 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3942 Ramachandran restraints generated. 1971 Oldfield, 0 Emsley, 1971 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 249 residues out of total 1758 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 203 time to evaluate : 0.633 Fit side-chains revert: symmetry clash REVERT: A 75 LYS cc_start: 0.8132 (mtmm) cc_final: 0.7929 (mppt) REVERT: A 196 LYS cc_start: 0.8579 (tttp) cc_final: 0.8064 (ttmt) REVERT: A 472 GLU cc_start: 0.8214 (OUTLIER) cc_final: 0.7857 (tt0) REVERT: H 107 ILE cc_start: 0.8498 (OUTLIER) cc_final: 0.8233 (tt) REVERT: L 27 ASN cc_start: 0.8067 (m-40) cc_final: 0.7522 (p0) REVERT: B 176 LYS cc_start: 0.8571 (ttpp) cc_final: 0.8131 (tttp) REVERT: B 222 GLU cc_start: 0.7982 (tt0) cc_final: 0.7626 (tt0) REVERT: B 295 GLU cc_start: 0.7676 (mt-10) cc_final: 0.7231 (mp0) REVERT: B 512 LEU cc_start: 0.4073 (OUTLIER) cc_final: 0.3836 (tt) REVERT: C 204 LEU cc_start: 0.6534 (OUTLIER) cc_final: 0.6330 (tp) REVERT: C 489 ASP cc_start: 0.7811 (t70) cc_final: 0.7589 (t0) outliers start: 46 outliers final: 37 residues processed: 233 average time/residue: 0.5967 time to fit residues: 153.2324 Evaluate side-chains 243 residues out of total 1758 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 202 time to evaluate : 0.569 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 217 ILE Chi-restraints excluded: chain A residue 239 VAL Chi-restraints excluded: chain A residue 296 VAL Chi-restraints excluded: chain A residue 319 SER Chi-restraints excluded: chain A residue 384 VAL Chi-restraints excluded: chain A residue 455 THR Chi-restraints excluded: chain A residue 472 GLU Chi-restraints excluded: chain H residue 4 VAL Chi-restraints excluded: chain H residue 68 THR Chi-restraints excluded: chain H residue 101 GLU Chi-restraints excluded: chain H residue 107 ILE Chi-restraints excluded: chain L residue 20 THR Chi-restraints excluded: chain B residue 76 VAL Chi-restraints excluded: chain B residue 180 SER Chi-restraints excluded: chain B residue 196 LYS Chi-restraints excluded: chain B residue 204 LEU Chi-restraints excluded: chain B residue 217 ILE Chi-restraints excluded: chain B residue 296 VAL Chi-restraints excluded: chain B residue 319 SER Chi-restraints excluded: chain B residue 348 SER Chi-restraints excluded: chain B residue 356 GLU Chi-restraints excluded: chain B residue 371 ASN Chi-restraints excluded: chain B residue 384 VAL Chi-restraints excluded: chain B residue 402 VAL Chi-restraints excluded: chain B residue 465 LYS Chi-restraints excluded: chain B residue 500 ASN Chi-restraints excluded: chain B residue 512 LEU Chi-restraints excluded: chain C residue 204 LEU Chi-restraints excluded: chain C residue 239 VAL Chi-restraints excluded: chain C residue 254 ASN Chi-restraints excluded: chain C residue 319 SER Chi-restraints excluded: chain C residue 371 ASN Chi-restraints excluded: chain C residue 384 VAL Chi-restraints excluded: chain C residue 402 VAL Chi-restraints excluded: chain C residue 442 VAL Chi-restraints excluded: chain C residue 465 LYS Chi-restraints excluded: chain D residue 12 VAL Chi-restraints excluded: chain D residue 21 SER Chi-restraints excluded: chain D residue 68 THR Chi-restraints excluded: chain D residue 85 ASP Chi-restraints excluded: chain E residue 12 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 198 random chunks: chunk 84 optimal weight: 0.9990 chunk 56 optimal weight: 4.9990 chunk 67 optimal weight: 4.9990 chunk 116 optimal weight: 0.0170 chunk 101 optimal weight: 0.8980 chunk 72 optimal weight: 3.9990 chunk 154 optimal weight: 3.9990 chunk 113 optimal weight: 7.9990 chunk 62 optimal weight: 1.9990 chunk 14 optimal weight: 0.9980 chunk 9 optimal weight: 1.9990 overall best weight: 0.9822 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 197 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3668 r_free = 0.3668 target = 0.149545 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3296 r_free = 0.3296 target = 0.118941 restraints weight = 13737.405| |-----------------------------------------------------------------------------| r_work (start): 0.3298 rms_B_bonded: 1.22 r_work: 0.3201 rms_B_bonded: 1.57 restraints_weight: 0.5000 r_work: 0.3097 rms_B_bonded: 2.54 restraints_weight: 0.2500 r_work (final): 0.3097 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8249 moved from start: 0.1798 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.079 15738 Z= 0.173 Angle : 0.841 59.199 21348 Z= 0.448 Chirality : 0.047 0.497 2508 Planarity : 0.004 0.041 2685 Dihedral : 5.396 53.962 2258 Min Nonbonded Distance : 2.495 Molprobity Statistics. All-atom Clashscore : 4.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.44 % Favored : 97.56 % Rotamer: Outliers : 2.34 % Allowed : 19.66 % Favored : 78.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.35 (0.18), residues: 1971 helix: 2.22 (0.25), residues: 414 sheet: 0.23 (0.21), residues: 537 loop : -0.58 (0.18), residues: 1020 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG E 61 TYR 0.019 0.002 TYR B 457 PHE 0.016 0.002 PHE C 190 TRP 0.009 0.002 TRP D 103 HIS 0.004 0.002 HIS C 317 Details of bonding type rmsd covalent geometry : bond 0.00385 (15708) covalent geometry : angle 0.80081 (21282) SS BOND : bond 0.00480 ( 24) SS BOND : angle 0.68188 ( 48) hydrogen bonds : bond 0.04002 ( 728) hydrogen bonds : angle 5.27699 ( 1917) link_NAG-ASN : bond 0.01050 ( 6) link_NAG-ASN : angle 8.91520 ( 18) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3942 Ramachandran restraints generated. 1971 Oldfield, 0 Emsley, 1971 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3942 Ramachandran restraints generated. 1971 Oldfield, 0 Emsley, 1971 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 243 residues out of total 1758 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 202 time to evaluate : 0.638 Fit side-chains revert: symmetry clash REVERT: A 75 LYS cc_start: 0.8123 (mtmm) cc_final: 0.7918 (mppt) REVERT: A 196 LYS cc_start: 0.8578 (tttp) cc_final: 0.8062 (ttmt) REVERT: A 472 GLU cc_start: 0.8222 (OUTLIER) cc_final: 0.7866 (tt0) REVERT: H 107 ILE cc_start: 0.8498 (OUTLIER) cc_final: 0.8230 (tt) REVERT: L 27 ASN cc_start: 0.8069 (m-40) cc_final: 0.7523 (p0) REVERT: B 176 LYS cc_start: 0.8576 (ttpp) cc_final: 0.8185 (tttm) REVERT: B 222 GLU cc_start: 0.7982 (tt0) cc_final: 0.7623 (tt0) REVERT: B 295 GLU cc_start: 0.7684 (mt-10) cc_final: 0.7240 (mp0) REVERT: B 512 LEU cc_start: 0.4056 (OUTLIER) cc_final: 0.3823 (tt) REVERT: C 204 LEU cc_start: 0.6524 (OUTLIER) cc_final: 0.6318 (tp) REVERT: C 489 ASP cc_start: 0.7811 (t70) cc_final: 0.7589 (t0) outliers start: 41 outliers final: 37 residues processed: 229 average time/residue: 0.5900 time to fit residues: 148.7858 Evaluate side-chains 242 residues out of total 1758 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 201 time to evaluate : 0.596 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 217 ILE Chi-restraints excluded: chain A residue 239 VAL Chi-restraints excluded: chain A residue 296 VAL Chi-restraints excluded: chain A residue 319 SER Chi-restraints excluded: chain A residue 384 VAL Chi-restraints excluded: chain A residue 455 THR Chi-restraints excluded: chain A residue 472 GLU Chi-restraints excluded: chain H residue 4 VAL Chi-restraints excluded: chain H residue 68 THR Chi-restraints excluded: chain H residue 101 GLU Chi-restraints excluded: chain H residue 107 ILE Chi-restraints excluded: chain L residue 20 THR Chi-restraints excluded: chain B residue 76 VAL Chi-restraints excluded: chain B residue 180 SER Chi-restraints excluded: chain B residue 196 LYS Chi-restraints excluded: chain B residue 204 LEU Chi-restraints excluded: chain B residue 217 ILE Chi-restraints excluded: chain B residue 296 VAL Chi-restraints excluded: chain B residue 319 SER Chi-restraints excluded: chain B residue 348 SER Chi-restraints excluded: chain B residue 356 GLU Chi-restraints excluded: chain B residue 371 ASN Chi-restraints excluded: chain B residue 384 VAL Chi-restraints excluded: chain B residue 402 VAL Chi-restraints excluded: chain B residue 465 LYS Chi-restraints excluded: chain B residue 500 ASN Chi-restraints excluded: chain B residue 512 LEU Chi-restraints excluded: chain C residue 204 LEU Chi-restraints excluded: chain C residue 239 VAL Chi-restraints excluded: chain C residue 254 ASN Chi-restraints excluded: chain C residue 319 SER Chi-restraints excluded: chain C residue 371 ASN Chi-restraints excluded: chain C residue 384 VAL Chi-restraints excluded: chain C residue 402 VAL Chi-restraints excluded: chain C residue 442 VAL Chi-restraints excluded: chain C residue 465 LYS Chi-restraints excluded: chain D residue 12 VAL Chi-restraints excluded: chain D residue 21 SER Chi-restraints excluded: chain D residue 68 THR Chi-restraints excluded: chain D residue 85 ASP Chi-restraints excluded: chain E residue 12 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 198 random chunks: chunk 17 optimal weight: 0.1980 chunk 96 optimal weight: 3.9990 chunk 47 optimal weight: 0.2980 chunk 58 optimal weight: 2.9990 chunk 43 optimal weight: 9.9990 chunk 165 optimal weight: 0.9980 chunk 76 optimal weight: 3.9990 chunk 133 optimal weight: 2.9990 chunk 44 optimal weight: 0.4980 chunk 5 optimal weight: 1.9990 chunk 91 optimal weight: 3.9990 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 197 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3668 r_free = 0.3668 target = 0.149541 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3296 r_free = 0.3296 target = 0.118960 restraints weight = 13647.493| |-----------------------------------------------------------------------------| r_work (start): 0.3298 rms_B_bonded: 1.22 r_work: 0.3201 rms_B_bonded: 1.56 restraints_weight: 0.5000 r_work: 0.3098 rms_B_bonded: 2.54 restraints_weight: 0.2500 r_work (final): 0.3098 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8247 moved from start: 0.1796 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.079 15738 Z= 0.173 Angle : 0.841 59.199 21348 Z= 0.448 Chirality : 0.047 0.497 2508 Planarity : 0.004 0.041 2685 Dihedral : 5.396 53.962 2258 Min Nonbonded Distance : 2.304 Molprobity Statistics. All-atom Clashscore : 4.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.44 % Favored : 97.56 % Rotamer: Outliers : 2.34 % Allowed : 19.72 % Favored : 77.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.35 (0.18), residues: 1971 helix: 2.22 (0.25), residues: 414 sheet: 0.23 (0.21), residues: 537 loop : -0.58 (0.18), residues: 1020 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG E 61 TYR 0.019 0.002 TYR B 457 PHE 0.016 0.002 PHE C 190 TRP 0.009 0.002 TRP D 103 HIS 0.004 0.002 HIS C 317 Details of bonding type rmsd covalent geometry : bond 0.00385 (15708) covalent geometry : angle 0.80081 (21282) SS BOND : bond 0.00480 ( 24) SS BOND : angle 0.68188 ( 48) hydrogen bonds : bond 0.04002 ( 728) hydrogen bonds : angle 5.27699 ( 1917) link_NAG-ASN : bond 0.01050 ( 6) link_NAG-ASN : angle 8.91520 ( 18) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3942 Ramachandran restraints generated. 1971 Oldfield, 0 Emsley, 1971 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3942 Ramachandran restraints generated. 1971 Oldfield, 0 Emsley, 1971 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 242 residues out of total 1758 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 201 time to evaluate : 0.640 Fit side-chains revert: symmetry clash REVERT: A 75 LYS cc_start: 0.8134 (mtmm) cc_final: 0.7931 (mppt) REVERT: A 196 LYS cc_start: 0.8582 (tttp) cc_final: 0.8066 (ttmt) REVERT: A 472 GLU cc_start: 0.8212 (OUTLIER) cc_final: 0.7855 (tt0) REVERT: H 107 ILE cc_start: 0.8498 (OUTLIER) cc_final: 0.8231 (tt) REVERT: L 27 ASN cc_start: 0.8066 (m-40) cc_final: 0.7521 (p0) REVERT: B 176 LYS cc_start: 0.8572 (ttpp) cc_final: 0.8181 (tttm) REVERT: B 222 GLU cc_start: 0.7984 (tt0) cc_final: 0.7629 (tt0) REVERT: B 295 GLU cc_start: 0.7676 (mt-10) cc_final: 0.7231 (mp0) REVERT: B 512 LEU cc_start: 0.4080 (OUTLIER) cc_final: 0.3842 (tt) REVERT: C 204 LEU cc_start: 0.6535 (OUTLIER) cc_final: 0.6330 (tp) REVERT: C 489 ASP cc_start: 0.7809 (t70) cc_final: 0.7588 (t0) outliers start: 41 outliers final: 37 residues processed: 228 average time/residue: 0.6000 time to fit residues: 150.7050 Evaluate side-chains 242 residues out of total 1758 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 201 time to evaluate : 0.451 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 217 ILE Chi-restraints excluded: chain A residue 239 VAL Chi-restraints excluded: chain A residue 296 VAL Chi-restraints excluded: chain A residue 319 SER Chi-restraints excluded: chain A residue 384 VAL Chi-restraints excluded: chain A residue 455 THR Chi-restraints excluded: chain A residue 472 GLU Chi-restraints excluded: chain H residue 4 VAL Chi-restraints excluded: chain H residue 68 THR Chi-restraints excluded: chain H residue 101 GLU Chi-restraints excluded: chain H residue 107 ILE Chi-restraints excluded: chain L residue 20 THR Chi-restraints excluded: chain B residue 76 VAL Chi-restraints excluded: chain B residue 180 SER Chi-restraints excluded: chain B residue 196 LYS Chi-restraints excluded: chain B residue 204 LEU Chi-restraints excluded: chain B residue 217 ILE Chi-restraints excluded: chain B residue 296 VAL Chi-restraints excluded: chain B residue 319 SER Chi-restraints excluded: chain B residue 348 SER Chi-restraints excluded: chain B residue 356 GLU Chi-restraints excluded: chain B residue 371 ASN Chi-restraints excluded: chain B residue 384 VAL Chi-restraints excluded: chain B residue 402 VAL Chi-restraints excluded: chain B residue 465 LYS Chi-restraints excluded: chain B residue 500 ASN Chi-restraints excluded: chain B residue 512 LEU Chi-restraints excluded: chain C residue 204 LEU Chi-restraints excluded: chain C residue 239 VAL Chi-restraints excluded: chain C residue 254 ASN Chi-restraints excluded: chain C residue 319 SER Chi-restraints excluded: chain C residue 371 ASN Chi-restraints excluded: chain C residue 384 VAL Chi-restraints excluded: chain C residue 402 VAL Chi-restraints excluded: chain C residue 442 VAL Chi-restraints excluded: chain C residue 465 LYS Chi-restraints excluded: chain D residue 12 VAL Chi-restraints excluded: chain D residue 21 SER Chi-restraints excluded: chain D residue 68 THR Chi-restraints excluded: chain D residue 85 ASP Chi-restraints excluded: chain E residue 12 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 198 random chunks: chunk 129 optimal weight: 2.9990 chunk 117 optimal weight: 1.9990 chunk 105 optimal weight: 0.4980 chunk 5 optimal weight: 0.9990 chunk 35 optimal weight: 0.4980 chunk 134 optimal weight: 3.9990 chunk 185 optimal weight: 2.9990 chunk 118 optimal weight: 1.9990 chunk 95 optimal weight: 2.9990 chunk 154 optimal weight: 2.9990 chunk 36 optimal weight: 0.9990 overall best weight: 0.9986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 197 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3668 r_free = 0.3668 target = 0.149541 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3295 r_free = 0.3295 target = 0.118939 restraints weight = 13697.976| |-----------------------------------------------------------------------------| r_work (start): 0.3298 rms_B_bonded: 1.22 r_work: 0.3200 rms_B_bonded: 1.57 restraints_weight: 0.5000 r_work: 0.3097 rms_B_bonded: 2.55 restraints_weight: 0.2500 r_work (final): 0.3097 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8248 moved from start: 0.1796 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.079 15738 Z= 0.173 Angle : 0.841 59.199 21348 Z= 0.448 Chirality : 0.047 0.497 2508 Planarity : 0.004 0.041 2685 Dihedral : 5.396 53.962 2258 Min Nonbonded Distance : 2.304 Molprobity Statistics. All-atom Clashscore : 4.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.44 % Favored : 97.56 % Rotamer: Outliers : 2.34 % Allowed : 19.72 % Favored : 77.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.35 (0.18), residues: 1971 helix: 2.22 (0.25), residues: 414 sheet: 0.23 (0.21), residues: 537 loop : -0.58 (0.18), residues: 1020 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG E 61 TYR 0.019 0.002 TYR B 457 PHE 0.016 0.002 PHE C 190 TRP 0.009 0.002 TRP D 103 HIS 0.004 0.002 HIS C 317 Details of bonding type rmsd covalent geometry : bond 0.00385 (15708) covalent geometry : angle 0.80081 (21282) SS BOND : bond 0.00480 ( 24) SS BOND : angle 0.68188 ( 48) hydrogen bonds : bond 0.04002 ( 728) hydrogen bonds : angle 5.27699 ( 1917) link_NAG-ASN : bond 0.01050 ( 6) link_NAG-ASN : angle 8.91520 ( 18) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3942 Ramachandran restraints generated. 1971 Oldfield, 0 Emsley, 1971 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3942 Ramachandran restraints generated. 1971 Oldfield, 0 Emsley, 1971 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 242 residues out of total 1758 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 201 time to evaluate : 0.569 Fit side-chains revert: symmetry clash REVERT: A 75 LYS cc_start: 0.8122 (mtmm) cc_final: 0.7916 (mppt) REVERT: A 196 LYS cc_start: 0.8578 (tttp) cc_final: 0.8062 (ttmt) REVERT: A 472 GLU cc_start: 0.8218 (OUTLIER) cc_final: 0.7862 (tt0) REVERT: H 107 ILE cc_start: 0.8498 (OUTLIER) cc_final: 0.8230 (tt) REVERT: L 27 ASN cc_start: 0.8067 (m-40) cc_final: 0.7522 (p0) REVERT: B 176 LYS cc_start: 0.8578 (ttpp) cc_final: 0.8185 (tttm) REVERT: B 222 GLU cc_start: 0.7981 (tt0) cc_final: 0.7621 (tt0) REVERT: B 295 GLU cc_start: 0.7682 (mt-10) cc_final: 0.7238 (mp0) REVERT: B 512 LEU cc_start: 0.4051 (OUTLIER) cc_final: 0.3819 (tt) REVERT: C 204 LEU cc_start: 0.6520 (OUTLIER) cc_final: 0.6315 (tp) REVERT: C 489 ASP cc_start: 0.7813 (t70) cc_final: 0.7591 (t0) outliers start: 41 outliers final: 37 residues processed: 228 average time/residue: 0.5917 time to fit residues: 148.4805 Evaluate side-chains 242 residues out of total 1758 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 201 time to evaluate : 0.583 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 217 ILE Chi-restraints excluded: chain A residue 239 VAL Chi-restraints excluded: chain A residue 296 VAL Chi-restraints excluded: chain A residue 319 SER Chi-restraints excluded: chain A residue 384 VAL Chi-restraints excluded: chain A residue 455 THR Chi-restraints excluded: chain A residue 472 GLU Chi-restraints excluded: chain H residue 4 VAL Chi-restraints excluded: chain H residue 68 THR Chi-restraints excluded: chain H residue 101 GLU Chi-restraints excluded: chain H residue 107 ILE Chi-restraints excluded: chain L residue 20 THR Chi-restraints excluded: chain B residue 76 VAL Chi-restraints excluded: chain B residue 180 SER Chi-restraints excluded: chain B residue 196 LYS Chi-restraints excluded: chain B residue 204 LEU Chi-restraints excluded: chain B residue 217 ILE Chi-restraints excluded: chain B residue 296 VAL Chi-restraints excluded: chain B residue 319 SER Chi-restraints excluded: chain B residue 348 SER Chi-restraints excluded: chain B residue 356 GLU Chi-restraints excluded: chain B residue 371 ASN Chi-restraints excluded: chain B residue 384 VAL Chi-restraints excluded: chain B residue 402 VAL Chi-restraints excluded: chain B residue 465 LYS Chi-restraints excluded: chain B residue 500 ASN Chi-restraints excluded: chain B residue 512 LEU Chi-restraints excluded: chain C residue 204 LEU Chi-restraints excluded: chain C residue 239 VAL Chi-restraints excluded: chain C residue 254 ASN Chi-restraints excluded: chain C residue 319 SER Chi-restraints excluded: chain C residue 371 ASN Chi-restraints excluded: chain C residue 384 VAL Chi-restraints excluded: chain C residue 402 VAL Chi-restraints excluded: chain C residue 442 VAL Chi-restraints excluded: chain C residue 465 LYS Chi-restraints excluded: chain D residue 12 VAL Chi-restraints excluded: chain D residue 21 SER Chi-restraints excluded: chain D residue 68 THR Chi-restraints excluded: chain D residue 85 ASP Chi-restraints excluded: chain E residue 12 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 198 random chunks: chunk 131 optimal weight: 1.9990 chunk 28 optimal weight: 0.9980 chunk 193 optimal weight: 6.9990 chunk 163 optimal weight: 4.9990 chunk 36 optimal weight: 2.9990 chunk 85 optimal weight: 2.9990 chunk 68 optimal weight: 4.9990 chunk 67 optimal weight: 3.9990 chunk 133 optimal weight: 2.9990 chunk 149 optimal weight: 0.2980 chunk 62 optimal weight: 9.9990 overall best weight: 1.8586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 197 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3668 r_free = 0.3668 target = 0.149542 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3296 r_free = 0.3296 target = 0.118975 restraints weight = 13597.477| |-----------------------------------------------------------------------------| r_work (start): 0.3300 rms_B_bonded: 1.22 r_work: 0.3201 rms_B_bonded: 1.57 restraints_weight: 0.5000 r_work: 0.3099 rms_B_bonded: 2.55 restraints_weight: 0.2500 r_work (final): 0.3099 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8246 moved from start: 0.1796 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.079 15738 Z= 0.173 Angle : 0.841 59.199 21348 Z= 0.448 Chirality : 0.047 0.497 2508 Planarity : 0.004 0.041 2685 Dihedral : 5.396 53.962 2258 Min Nonbonded Distance : 2.304 Molprobity Statistics. All-atom Clashscore : 4.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.44 % Favored : 97.56 % Rotamer: Outliers : 2.34 % Allowed : 19.72 % Favored : 77.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.35 (0.18), residues: 1971 helix: 2.22 (0.25), residues: 414 sheet: 0.23 (0.21), residues: 537 loop : -0.58 (0.18), residues: 1020 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG E 61 TYR 0.019 0.002 TYR B 457 PHE 0.016 0.002 PHE C 190 TRP 0.009 0.002 TRP D 103 HIS 0.004 0.002 HIS C 317 Details of bonding type rmsd covalent geometry : bond 0.00385 (15708) covalent geometry : angle 0.80081 (21282) SS BOND : bond 0.00480 ( 24) SS BOND : angle 0.68188 ( 48) hydrogen bonds : bond 0.04002 ( 728) hydrogen bonds : angle 5.27699 ( 1917) link_NAG-ASN : bond 0.01050 ( 6) link_NAG-ASN : angle 8.91520 ( 18) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7555.92 seconds wall clock time: 128 minutes 55.41 seconds (7735.41 seconds total)