Starting phenix.real_space_refine on Fri Mar 6 07:26:55 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7luc_23520/03_2026/7luc_23520.cif Found real_map, /net/cci-nas-00/data/ceres_data/7luc_23520/03_2026/7luc_23520.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.21 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7luc_23520/03_2026/7luc_23520.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7luc_23520/03_2026/7luc_23520.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7luc_23520/03_2026/7luc_23520.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7luc_23520/03_2026/7luc_23520.map" } resolution = 3.21 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.024 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 10401 atoms to isotropic. 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 111 5.16 5 C 13473 2.51 5 N 3561 2.21 5 O 4143 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 59 residue(s): 0.02s 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: 21288 Number of models: 1 Model: "" Number of chains: 15 Chain: "A" Number of atoms: 3477 Number of conformers: 1 Conformer: "" Number of residues, atoms: 449, 3477 Classifications: {'peptide': 449} Link IDs: {'PCIS': 1, 'PTRANS': 12, 'TRANS': 435} Chain breaks: 1 Chain: "B" Number of atoms: 3477 Number of conformers: 1 Conformer: "" Number of residues, atoms: 449, 3477 Classifications: {'peptide': 449} Link IDs: {'PCIS': 1, 'PTRANS': 12, 'TRANS': 435} Chain breaks: 1 Chain: "C" Number of atoms: 3477 Number of conformers: 1 Conformer: "" Number of residues, atoms: 449, 3477 Classifications: {'peptide': 449} Link IDs: {'PCIS': 1, 'PTRANS': 12, 'TRANS': 435} Chain breaks: 1 Chain: "D" Number of atoms: 925 Number of conformers: 1 Conformer: "" Number of residues, atoms: 121, 925 Classifications: {'peptide': 121} Link IDs: {'PTRANS': 5, 'TRANS': 115} Chain: "E" Number of atoms: 879 Number of conformers: 1 Conformer: "" Number of residues, atoms: 112, 879 Classifications: {'peptide': 112} Link IDs: {'PCIS': 2, 'PTRANS': 5, 'TRANS': 104} Chain: "F" Number of atoms: 925 Number of conformers: 1 Conformer: "" Number of residues, atoms: 121, 925 Classifications: {'peptide': 121} Link IDs: {'PTRANS': 5, 'TRANS': 115} Chain: "G" Number of atoms: 879 Number of conformers: 1 Conformer: "" Number of residues, atoms: 112, 879 Classifications: {'peptide': 112} Link IDs: {'PCIS': 2, 'PTRANS': 5, 'TRANS': 104} Chain: "H" Number of atoms: 925 Number of conformers: 1 Conformer: "" Number of residues, atoms: 121, 925 Classifications: {'peptide': 121} Link IDs: {'PTRANS': 5, 'TRANS': 115} Chain: "I" Number of atoms: 879 Number of conformers: 1 Conformer: "" Number of residues, atoms: 112, 879 Classifications: {'peptide': 112} Link IDs: {'PCIS': 2, 'PTRANS': 5, 'TRANS': 104} Chain: "J" Number of atoms: 995 Number of conformers: 1 Conformer: "" Number of residues, atoms: 129, 995 Classifications: {'peptide': 129} Link IDs: {'PCIS': 2, 'PTRANS': 5, 'TRANS': 121} Chain: "K" Number of atoms: 820 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 107, 818 Classifications: {'peptide': 107} Link IDs: {'PCIS': 2, 'PTRANS': 5, 'TRANS': 99} Unresolved chain link angles: 2 Unresolved chain link dihedrals: 4 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Conformer: "B" Number of residues, atoms: 107, 818 Classifications: {'peptide': 107} Link IDs: {'PCIS': 2, 'PTRANS': 5, 'TRANS': 99} Unresolved chain link angles: 2 Unresolved chain link dihedrals: 4 Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 2 bond proxies already assigned to first conformer: 830 Chain: "L" Number of atoms: 995 Number of conformers: 1 Conformer: "" Number of residues, atoms: 129, 995 Classifications: {'peptide': 129} Link IDs: {'PCIS': 2, 'PTRANS': 5, 'TRANS': 121} Chain: "M" Number of atoms: 820 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 107, 818 Classifications: {'peptide': 107} Link IDs: {'PCIS': 2, 'PTRANS': 5, 'TRANS': 99} Unresolved chain link angles: 2 Unresolved chain link dihedrals: 4 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Conformer: "B" Number of residues, atoms: 107, 818 Classifications: {'peptide': 107} Link IDs: {'PCIS': 2, 'PTRANS': 5, 'TRANS': 99} Unresolved chain link angles: 2 Unresolved chain link dihedrals: 4 Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 2 bond proxies already assigned to first conformer: 830 Chain: "N" Number of atoms: 995 Number of conformers: 1 Conformer: "" Number of residues, atoms: 129, 995 Classifications: {'peptide': 129} Link IDs: {'PCIS': 2, 'PTRANS': 5, 'TRANS': 121} Chain: "O" Number of atoms: 820 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 107, 818 Classifications: {'peptide': 107} Link IDs: {'PCIS': 2, 'PTRANS': 5, 'TRANS': 99} Unresolved chain link angles: 2 Unresolved chain link dihedrals: 4 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Conformer: "B" Number of residues, atoms: 107, 818 Classifications: {'peptide': 107} Link IDs: {'PCIS': 2, 'PTRANS': 5, 'TRANS': 99} Unresolved chain link angles: 2 Unresolved chain link dihedrals: 4 Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 2 bond proxies already assigned to first conformer: 830 Time building chain proxies: 5.39, per 1000 atoms: 0.25 Number of scatterers: 21288 At special positions: 0 Unit cell: (140.563, 137.344, 152.366, 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 111 16.00 O 4143 8.00 N 3561 7.00 C 13473 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=33, symmetry=0 Simple disulfide: pdb=" SG CYS A 37 " - pdb=" SG CYS A 439 " distance=2.03 Simple disulfide: pdb=" SG CYS A 69 " - pdb=" SG CYS A 212 " distance=2.03 Simple disulfide: pdb=" SG CYS A 313 " - pdb=" SG CYS A 343 " distance=2.03 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 B 37 " - pdb=" SG CYS B 439 " distance=2.03 Simple disulfide: pdb=" SG CYS B 69 " - pdb=" SG CYS B 212 " distance=2.03 Simple disulfide: pdb=" SG CYS B 313 " - pdb=" SG CYS B 343 " distance=2.03 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 C 37 " - pdb=" SG CYS C 439 " distance=2.03 Simple disulfide: pdb=" SG CYS C 69 " - pdb=" SG CYS C 212 " distance=2.03 Simple disulfide: pdb=" SG CYS C 313 " - pdb=" SG CYS C 343 " distance=2.03 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=2.03 Simple disulfide: pdb=" SG CYS E 23 " - pdb=" SG CYS E 88 " distance=2.03 Simple disulfide: pdb=" SG CYS F 22 " - pdb=" SG CYS F 92 " distance=2.03 Simple disulfide: pdb=" SG CYS G 23 " - pdb=" SG CYS G 88 " distance=2.03 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 92 " distance=2.03 Simple disulfide: pdb=" SG CYS I 23 " - pdb=" SG CYS I 88 " distance=2.03 Simple disulfide: pdb=" SG CYS J 22 " - pdb=" SG CYS J 92 " distance=2.03 Simple disulfide: pdb=" SG CYS K 23 " - pdb=" SG CYS K 88 " distance=2.04 Simple disulfide: pdb=" SG CYS L 22 " - pdb=" SG CYS L 92 " distance=2.03 Simple disulfide: pdb=" SG CYS M 23 " - pdb=" SG CYS M 88 " distance=2.04 Simple disulfide: pdb=" SG CYS N 22 " - pdb=" SG CYS N 92 " distance=2.03 Simple disulfide: pdb=" SG CYS O 23 " - pdb=" SG CYS O 88 " distance=2.04 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 Time building additional restraints: 1.41 Conformation dependent library (CDL) restraints added in 1.1 seconds 5436 Ramachandran restraints generated. 2718 Oldfield, 0 Emsley, 2718 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5112 Finding SS restraints... Secondary structure from input PDB file: 61 helices and 46 sheets defined 20.7% alpha, 31.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.95 Creating SS restraints... Processing helix chain 'A' and resid 73 through 96 Processing helix chain 'A' and resid 138 through 142 Processing helix chain 'A' and resid 148 through 159 Processing helix chain 'A' and resid 162 through 171 removed outlier: 3.557A pdb=" N LEU A 171 " --> pdb=" O ILE A 167 " (cutoff:3.500A) Processing helix chain 'A' and resid 194 through 202 Processing helix chain 'A' and resid 203 through 210 Processing helix chain 'A' and resid 216 through 240 removed outlier: 4.397A pdb=" N VAL A 220 " --> pdb=" O ASN A 216 " (cutoff:3.500A) removed outlier: 4.369A pdb=" N ARG A 229 " --> pdb=" O GLN A 225 " (cutoff:3.500A) removed outlier: 4.315A pdb=" N LEU A 230 " --> pdb=" O LYS A 226 " (cutoff:3.500A) Processing helix chain 'A' and resid 253 through 263 Processing helix chain 'A' and resid 267 through 277 removed outlier: 3.553A pdb=" N LYS A 271 " --> pdb=" O THR A 267 " (cutoff:3.500A) Processing helix chain 'A' and resid 277 through 284 Processing helix chain 'A' and resid 354 through 358 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 376 through 384 Processing helix chain 'A' and resid 473 through 478 removed outlier: 3.662A pdb=" N ASN A 476 " --> pdb=" O PRO A 473 " (cutoff:3.500A) Processing helix chain 'A' and resid 491 through 509 Processing helix chain 'B' and resid 73 through 96 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 removed outlier: 3.558A pdb=" N LEU B 171 " --> pdb=" O ILE B 167 " (cutoff:3.500A) Processing helix chain 'B' and resid 194 through 202 Processing helix chain 'B' and resid 203 through 210 Processing helix chain 'B' and resid 216 through 240 removed outlier: 4.397A pdb=" N VAL B 220 " --> pdb=" O ASN B 216 " (cutoff:3.500A) removed outlier: 4.369A pdb=" N ARG B 229 " --> pdb=" O GLN B 225 " (cutoff:3.500A) removed outlier: 4.315A 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 277 removed outlier: 3.552A pdb=" N LYS B 271 " --> pdb=" O THR B 267 " (cutoff:3.500A) Processing helix chain 'B' and resid 277 through 284 Processing helix chain 'B' and resid 354 through 358 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 384 Processing helix chain 'B' and resid 473 through 478 removed outlier: 3.661A pdb=" N ASN B 476 " --> pdb=" O PRO B 473 " (cutoff:3.500A) Processing helix chain 'B' and resid 491 through 509 Processing helix chain 'C' and resid 73 through 96 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 removed outlier: 3.558A pdb=" N LEU C 171 " --> pdb=" O ILE C 167 " (cutoff:3.500A) Processing helix chain 'C' and resid 194 through 202 Processing helix chain 'C' and resid 203 through 210 Processing helix chain 'C' and resid 216 through 240 removed outlier: 4.396A pdb=" N VAL C 220 " --> pdb=" O ASN C 216 " (cutoff:3.500A) removed outlier: 4.369A pdb=" N ARG C 229 " --> pdb=" O GLN C 225 " (cutoff:3.500A) removed outlier: 4.315A 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 277 removed outlier: 3.553A pdb=" N LYS C 271 " --> pdb=" O THR C 267 " (cutoff:3.500A) Processing helix chain 'C' and resid 277 through 284 Processing helix chain 'C' and resid 354 through 358 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 384 Processing helix chain 'C' and resid 473 through 478 removed outlier: 3.662A pdb=" N ASN C 476 " --> pdb=" O PRO C 473 " (cutoff:3.500A) Processing helix chain 'C' and resid 491 through 509 Processing helix chain 'D' and resid 28 through 31 Processing helix chain 'D' and resid 61 through 64 Processing helix chain 'D' and resid 83 through 87 removed outlier: 3.651A pdb=" N THR D 87 " --> pdb=" O SER D 84 " (cutoff:3.500A) Processing helix chain 'F' and resid 28 through 31 Processing helix chain 'F' and resid 61 through 64 Processing helix chain 'F' and resid 83 through 87 removed outlier: 3.651A pdb=" N THR F 87 " --> pdb=" O SER F 84 " (cutoff:3.500A) Processing helix chain 'H' and resid 28 through 31 Processing helix chain 'H' and resid 61 through 64 Processing helix chain 'H' and resid 83 through 87 removed outlier: 3.651A pdb=" N THR H 87 " --> pdb=" O SER H 84 " (cutoff:3.500A) Processing helix chain 'J' and resid 27 through 31 removed outlier: 3.831A pdb=" N THR J 30 " --> pdb=" O ASP J 27 " (cutoff:3.500A) Processing helix chain 'J' and resid 83 through 87 removed outlier: 3.656A pdb=" N THR J 87 " --> pdb=" O ALA J 84 " (cutoff:3.500A) Processing helix chain 'L' and resid 27 through 31 removed outlier: 3.832A pdb=" N THR L 30 " --> pdb=" O ASP L 27 " (cutoff:3.500A) Processing helix chain 'L' and resid 83 through 87 removed outlier: 3.657A pdb=" N THR L 87 " --> pdb=" O ALA L 84 " (cutoff:3.500A) Processing helix chain 'N' and resid 27 through 31 removed outlier: 3.831A pdb=" N THR N 30 " --> pdb=" O ASP N 27 " (cutoff:3.500A) Processing helix chain 'N' and resid 83 through 87 removed outlier: 3.657A pdb=" N THR N 87 " --> pdb=" O ALA N 84 " (cutoff:3.500A) Processing helix chain 'O' and resid 79 through 83 removed outlier: 3.690A pdb=" N PHE O 83 " --> pdb=" O PRO O 80 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 373 through 374 removed outlier: 3.599A pdb=" N SER A 348 " --> pdb=" O ASN A 345 " (cutoff:3.500A) removed outlier: 4.042A pdb=" N ASN A 345 " --> pdb=" O SER A 348 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 308 through 309 removed outlier: 4.178A pdb=" N VAL A 308 " --> pdb=" O LEU A 48 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N LEU A 48 " --> pdb=" O VAL A 308 " (cutoff:3.500A) removed outlier: 6.218A pdb=" N LEU A 45 " --> pdb=" O VAL A 365 " (cutoff:3.500A) removed outlier: 7.575A pdb=" N CYS A 367 " --> pdb=" O LEU A 45 " (cutoff:3.500A) removed outlier: 6.099A 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: 11.429A pdb=" N SER A 186 " --> pdb=" O TRP A 52 " (cutoff:3.500A) removed outlier: 8.026A pdb=" N THR A 54 " --> pdb=" O SER A 186 " (cutoff:3.500A) removed outlier: 4.663A pdb=" N LEU A 188 " --> pdb=" O THR A 54 " (cutoff:3.500A) removed outlier: 5.168A pdb=" N ALA A 298 " --> pdb=" O SER A 290 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 321 through 322 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: 5.095A pdb=" N ILE A 431 " --> pdb=" O ASN A 426 " (cutoff:3.500A) removed outlier: 6.664A pdb=" N ASN A 426 " --> pdb=" O ILE A 431 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 373 through 374 Processing sheet with id=AA8, first strand: chain 'B' and resid 308 through 309 removed outlier: 4.178A pdb=" N VAL B 308 " --> pdb=" O LEU B 48 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N LEU B 48 " --> pdb=" O VAL B 308 " (cutoff:3.500A) removed outlier: 6.218A pdb=" N LEU B 45 " --> pdb=" O VAL B 365 " (cutoff:3.500A) removed outlier: 7.576A pdb=" N CYS B 367 " --> pdb=" O LEU B 45 " (cutoff:3.500A) removed outlier: 6.099A pdb=" N ALA B 47 " --> pdb=" O CYS B 367 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 176 through 180 removed outlier: 11.429A pdb=" N SER B 186 " --> pdb=" O TRP B 52 " (cutoff:3.500A) removed outlier: 8.026A pdb=" N THR B 54 " --> pdb=" O SER B 186 " (cutoff:3.500A) removed outlier: 4.664A pdb=" N LEU B 188 " --> pdb=" O THR B 54 " (cutoff:3.500A) removed outlier: 5.169A pdb=" N ALA B 298 " --> pdb=" O SER B 290 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 321 through 322 Processing sheet with id=AB2, first strand: chain 'B' and resid 404 through 407 Processing sheet with id=AB3, first strand: chain 'B' and resid 430 through 434 removed outlier: 5.095A pdb=" N ILE B 431 " --> pdb=" O ASN B 426 " (cutoff:3.500A) removed outlier: 6.664A pdb=" N ASN B 426 " --> pdb=" O ILE B 431 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 373 through 374 removed outlier: 3.619A pdb=" N SER C 348 " --> pdb=" O ASN C 345 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N ASN C 345 " --> pdb=" O SER C 348 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'C' and resid 308 through 309 removed outlier: 4.179A pdb=" N VAL C 308 " --> pdb=" O LEU C 48 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N LEU C 48 " --> pdb=" O VAL C 308 " (cutoff:3.500A) removed outlier: 6.218A pdb=" N LEU C 45 " --> pdb=" O VAL C 365 " (cutoff:3.500A) removed outlier: 7.576A pdb=" N CYS C 367 " --> pdb=" O LEU C 45 " (cutoff:3.500A) removed outlier: 6.099A pdb=" N ALA C 47 " --> pdb=" O CYS C 367 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'C' and resid 176 through 180 removed outlier: 11.430A pdb=" N SER C 186 " --> pdb=" O TRP C 52 " (cutoff:3.500A) removed outlier: 8.026A pdb=" N THR C 54 " --> pdb=" O SER C 186 " (cutoff:3.500A) removed outlier: 4.663A pdb=" N LEU C 188 " --> pdb=" O THR C 54 " (cutoff:3.500A) removed outlier: 5.169A pdb=" N ALA C 298 " --> pdb=" O SER C 290 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'C' and resid 66 through 67 removed outlier: 4.256A pdb=" N GLU C 66 " --> pdb=" O VAL N 100A" (cutoff:3.500A) removed outlier: 4.266A pdb=" N VAL N 100A" --> pdb=" O GLU C 66 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB7 Processing sheet with id=AB8, first strand: chain 'C' and resid 321 through 322 Processing sheet with id=AB9, first strand: chain 'C' and resid 404 through 407 Processing sheet with id=AC1, first strand: chain 'C' and resid 430 through 434 removed outlier: 5.096A pdb=" N ILE C 431 " --> pdb=" O ASN C 426 " (cutoff:3.500A) removed outlier: 6.664A pdb=" N ASN C 426 " --> pdb=" O ILE C 431 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'D' and resid 3 through 6 Processing sheet with id=AC3, first strand: chain 'D' and resid 10 through 12 removed outlier: 3.589A pdb=" N GLY D 49 " --> pdb=" O TRP D 36 " (cutoff:3.500A) removed outlier: 7.020A pdb=" N ARG D 38 " --> pdb=" O TRP D 47 " (cutoff:3.500A) removed outlier: 6.070A pdb=" N TRP D 47 " --> pdb=" O ARG D 38 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'E' and resid 5 through 7 Processing sheet with id=AC5, first strand: chain 'E' and resid 10 through 13 removed outlier: 4.796A pdb=" N LEU E 33 " --> pdb=" O TYR E 49 " (cutoff:3.500A) removed outlier: 5.263A pdb=" N TYR E 49 " --> pdb=" O LEU E 33 " (cutoff:3.500A) removed outlier: 6.430A pdb=" N TRP E 35 " --> pdb=" O LEU E 47 " (cutoff:3.500A) removed outlier: 4.282A pdb=" N ARG E 50 " --> pdb=" O HIS E 53 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'F' and resid 3 through 6 Processing sheet with id=AC7, first strand: chain 'F' and resid 10 through 12 removed outlier: 3.590A pdb=" N GLY F 49 " --> pdb=" O TRP F 36 " (cutoff:3.500A) removed outlier: 7.021A pdb=" N ARG F 38 " --> pdb=" O TRP F 47 " (cutoff:3.500A) removed outlier: 6.069A pdb=" N TRP F 47 " --> pdb=" O ARG F 38 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'G' and resid 5 through 7 Processing sheet with id=AC9, first strand: chain 'G' and resid 10 through 13 removed outlier: 4.796A pdb=" N LEU G 33 " --> pdb=" O TYR G 49 " (cutoff:3.500A) removed outlier: 5.262A pdb=" N TYR G 49 " --> pdb=" O LEU G 33 " (cutoff:3.500A) removed outlier: 6.432A pdb=" N TRP G 35 " --> pdb=" O LEU G 47 " (cutoff:3.500A) removed outlier: 4.281A pdb=" N ARG G 50 " --> pdb=" O HIS G 53 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'H' and resid 3 through 6 Processing sheet with id=AD2, first strand: chain 'H' and resid 10 through 12 removed outlier: 3.590A pdb=" N GLY H 49 " --> pdb=" O TRP H 36 " (cutoff:3.500A) removed outlier: 7.020A pdb=" N ARG H 38 " --> pdb=" O TRP H 47 " (cutoff:3.500A) removed outlier: 6.070A pdb=" N TRP H 47 " --> pdb=" O ARG H 38 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'I' and resid 5 through 7 Processing sheet with id=AD4, first strand: chain 'I' and resid 10 through 13 removed outlier: 6.431A pdb=" N TRP I 35 " --> pdb=" O LEU I 47 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'J' and resid 5 through 6 removed outlier: 3.928A pdb=" N LEU J 18 " --> pdb=" O TRP J 82 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'J' and resid 10 through 12 removed outlier: 6.689A pdb=" N ILE J 34 " --> pdb=" O MET J 50 " (cutoff:3.500A) removed outlier: 4.560A pdb=" N MET J 50 " --> pdb=" O ILE J 34 " (cutoff:3.500A) removed outlier: 6.593A pdb=" N TRP J 36 " --> pdb=" O MET J 48 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'J' and resid 10 through 12 removed outlier: 4.216A pdb=" N ALA J 102 " --> pdb=" O ARG J 94 " (cutoff:3.500A) removed outlier: 7.577A pdb=" N VAL J 96 " --> pdb=" O MET J 100L" (cutoff:3.500A) removed outlier: 6.194A pdb=" N MET J 100L" --> pdb=" O VAL J 96 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'K' and resid 4 through 7 Processing sheet with id=AD9, first strand: chain 'K' and resid 10 through 13 removed outlier: 6.448A pdb=" N LEU K 11 " --> pdb=" O GLU K 105 " (cutoff:3.500A) removed outlier: 6.475A pdb=" N GLN K 37 " --> pdb=" O LEU K 46 " (cutoff:3.500A) removed outlier: 5.498A pdb=" N LEU K 46 " --> pdb=" O GLN K 37 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'L' and resid 5 through 6 removed outlier: 3.928A pdb=" N LEU L 18 " --> pdb=" O TRP L 82 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'L' and resid 10 through 12 removed outlier: 6.688A pdb=" N ILE L 34 " --> pdb=" O MET L 50 " (cutoff:3.500A) removed outlier: 4.560A pdb=" N MET L 50 " --> pdb=" O ILE L 34 " (cutoff:3.500A) removed outlier: 6.593A pdb=" N TRP L 36 " --> pdb=" O MET L 48 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'L' and resid 10 through 12 removed outlier: 4.216A pdb=" N ALA L 102 " --> pdb=" O ARG L 94 " (cutoff:3.500A) removed outlier: 7.577A pdb=" N VAL L 96 " --> pdb=" O MET L 100L" (cutoff:3.500A) removed outlier: 6.194A pdb=" N MET L 100L" --> pdb=" O VAL L 96 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'M' and resid 4 through 7 Processing sheet with id=AE5, first strand: chain 'M' and resid 10 through 13 removed outlier: 3.532A pdb=" N LEU M 11 " --> pdb=" O LYS M 103 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N THR M 102 " --> pdb=" O TYR M 86 " (cutoff:3.500A) removed outlier: 6.731A pdb=" N LEU M 33 " --> pdb=" O PHE M 49 " (cutoff:3.500A) removed outlier: 4.867A pdb=" N PHE M 49 " --> pdb=" O LEU M 33 " (cutoff:3.500A) removed outlier: 6.607A pdb=" N TRP M 35 " --> pdb=" O LEU M 47 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'N' and resid 5 through 6 removed outlier: 3.929A pdb=" N LEU N 18 " --> pdb=" O TRP N 82 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'N' and resid 10 through 12 removed outlier: 6.689A pdb=" N ILE N 34 " --> pdb=" O MET N 50 " (cutoff:3.500A) removed outlier: 4.560A pdb=" N MET N 50 " --> pdb=" O ILE N 34 " (cutoff:3.500A) removed outlier: 6.594A pdb=" N TRP N 36 " --> pdb=" O MET N 48 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'N' and resid 10 through 12 removed outlier: 4.216A pdb=" N ALA N 102 " --> pdb=" O ARG N 94 " (cutoff:3.500A) removed outlier: 7.577A pdb=" N VAL N 96 " --> pdb=" O MET N 100L" (cutoff:3.500A) removed outlier: 6.194A pdb=" N MET N 100L" --> pdb=" O VAL N 96 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'O' and resid 4 through 7 Processing sheet with id=AF1, first strand: chain 'O' and resid 10 through 13 removed outlier: 6.264A pdb=" N LEU O 11 " --> pdb=" O GLU O 105 " (cutoff:3.500A) removed outlier: 6.631A pdb=" N GLN O 37 " --> pdb=" O LEU O 46 " (cutoff:3.500A) removed outlier: 5.540A pdb=" N LEU O 46 " --> pdb=" O GLN O 37 " (cutoff:3.500A) 968 hydrogen bonds defined for protein. 2367 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: 4.33 Time building geometry restraints manager: 2.11 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.13 - 1.26: 3496 1.26 - 1.40: 5153 1.40 - 1.54: 12807 1.54 - 1.68: 102 1.68 - 1.82: 156 Bond restraints: 21714 Sorted by residual: bond pdb=" C ASN C 345 " pdb=" O ASN C 345 " ideal model delta sigma weight residual 1.235 1.125 0.110 1.12e-02 7.97e+03 9.66e+01 bond pdb=" CA SER A 350 " pdb=" C SER A 350 " ideal model delta sigma weight residual 1.526 1.638 -0.112 1.37e-02 5.33e+03 6.63e+01 bond pdb=" C ALA C 346 " pdb=" O ALA C 346 " ideal model delta sigma weight residual 1.239 1.162 0.077 9.60e-03 1.09e+04 6.41e+01 bond pdb=" CA SER C 350 " pdb=" C SER C 350 " ideal model delta sigma weight residual 1.526 1.634 -0.108 1.37e-02 5.33e+03 6.18e+01 bond pdb=" CA SER A 350 " pdb=" CB SER A 350 " ideal model delta sigma weight residual 1.529 1.418 0.111 1.66e-02 3.63e+03 4.46e+01 ... (remaining 21709 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.77: 29164 2.77 - 5.54: 238 5.54 - 8.31: 43 8.31 - 11.08: 8 11.08 - 13.85: 13 Bond angle restraints: 29466 Sorted by residual: angle pdb=" N ALA C 346 " pdb=" CA ALA C 346 " pdb=" C ALA C 346 " ideal model delta sigma weight residual 108.31 122.16 -13.85 1.52e+00 4.33e-01 8.31e+01 angle pdb=" CA PRO B 215 " pdb=" N PRO B 215 " pdb=" CD PRO B 215 " ideal model delta sigma weight residual 112.00 99.34 12.66 1.40e+00 5.10e-01 8.18e+01 angle pdb=" CA PRO C 215 " pdb=" N PRO C 215 " pdb=" CD PRO C 215 " ideal model delta sigma weight residual 112.00 99.34 12.66 1.40e+00 5.10e-01 8.17e+01 angle pdb=" CA PRO A 215 " pdb=" N PRO A 215 " pdb=" CD PRO A 215 " ideal model delta sigma weight residual 112.00 99.37 12.63 1.40e+00 5.10e-01 8.14e+01 angle pdb=" N GLY C 347 " pdb=" CA GLY C 347 " pdb=" C GLY C 347 " ideal model delta sigma weight residual 113.24 122.70 -9.46 1.31e+00 5.83e-01 5.22e+01 ... (remaining 29461 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.12: 11524 17.12 - 34.24: 1151 34.24 - 51.37: 314 51.37 - 68.49: 92 68.49 - 85.61: 32 Dihedral angle restraints: 13113 sinusoidal: 5148 harmonic: 7965 Sorted by residual: dihedral pdb=" CB CYS B 382 " pdb=" SG CYS B 382 " pdb=" SG CYS B 393 " pdb=" CB CYS B 393 " ideal model delta sinusoidal sigma weight residual 93.00 165.50 -72.50 1 1.00e+01 1.00e-02 6.71e+01 dihedral pdb=" CB CYS A 382 " pdb=" SG CYS A 382 " pdb=" SG CYS A 393 " pdb=" CB CYS A 393 " ideal model delta sinusoidal sigma weight residual 93.00 165.48 -72.48 1 1.00e+01 1.00e-02 6.71e+01 dihedral pdb=" CB CYS C 382 " pdb=" SG CYS C 382 " pdb=" SG CYS C 393 " pdb=" CB CYS C 393 " ideal model delta sinusoidal sigma weight residual 93.00 165.46 -72.46 1 1.00e+01 1.00e-02 6.71e+01 ... (remaining 13110 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.116: 3320 0.116 - 0.232: 60 0.232 - 0.349: 6 0.349 - 0.465: 0 0.465 - 0.581: 1 Chirality restraints: 3387 Sorted by residual: chirality pdb=" CA ALA C 346 " pdb=" N ALA C 346 " pdb=" C ALA C 346 " pdb=" CB ALA C 346 " both_signs ideal model delta sigma weight residual False 2.48 1.90 0.58 2.00e-01 2.50e+01 8.44e+00 chirality pdb=" CA SER A 350 " pdb=" N SER A 350 " pdb=" C SER A 350 " pdb=" CB SER A 350 " both_signs ideal model delta sigma weight residual False 2.51 2.20 0.31 2.00e-01 2.50e+01 2.47e+00 chirality pdb=" CA ASN C 345 " pdb=" N ASN C 345 " pdb=" C ASN C 345 " pdb=" CB ASN C 345 " both_signs ideal model delta sigma weight residual False 2.51 2.82 -0.31 2.00e-01 2.50e+01 2.35e+00 ... (remaining 3384 not shown) Planarity restraints: 3732 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASP C 344 " 0.020 2.00e-02 2.50e+03 3.95e-02 1.56e+01 pdb=" CG ASP C 344 " -0.068 2.00e-02 2.50e+03 pdb=" OD1 ASP C 344 " 0.024 2.00e-02 2.50e+03 pdb=" OD2 ASP C 344 " 0.025 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ILE B 214 " -0.064 5.00e-02 4.00e+02 8.78e-02 1.23e+01 pdb=" N PRO B 215 " 0.151 5.00e-02 4.00e+02 pdb=" CA PRO B 215 " -0.040 5.00e-02 4.00e+02 pdb=" CD PRO B 215 " -0.048 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ILE A 214 " 0.064 5.00e-02 4.00e+02 8.77e-02 1.23e+01 pdb=" N PRO A 215 " -0.151 5.00e-02 4.00e+02 pdb=" CA PRO A 215 " 0.040 5.00e-02 4.00e+02 pdb=" CD PRO A 215 " 0.048 5.00e-02 4.00e+02 ... (remaining 3729 not shown) Histogram of nonbonded interaction distances: 1.94 - 2.53: 194 2.53 - 3.12: 15620 3.12 - 3.71: 32616 3.71 - 4.31: 45981 4.31 - 4.90: 77413 Nonbonded interactions: 171824 Sorted by model distance: nonbonded pdb=" CB SER B 348 " pdb=" O LEU B 375 " model vdw 1.937 3.440 nonbonded pdb=" NZ LYS B 209 " pdb=" OD2 ASP M 50 " model vdw 1.942 3.120 nonbonded pdb=" OG1 THR C 311 " pdb=" O ASP C 344 " model vdw 1.960 3.040 nonbonded pdb=" CB SER A 348 " pdb=" O LEU A 375 " model vdw 1.998 3.440 nonbonded pdb=" NZ LYS C 209 " pdb=" OD2 ASP O 50 " model vdw 2.012 3.120 ... (remaining 171819 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: 0.06 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 'I' } ncs_group { reference = chain 'J' selection = chain 'L' selection = chain 'N' } ncs_group { reference = (chain 'K' and (resid 1 through 71 or resid 73 through 75 or resid 77 through 10 \ 7)) selection = (chain 'M' and (resid 1 through 71 or resid 73 through 75 or resid 77 through 10 \ 7)) selection = (chain 'O' and (resid 1 through 71 or resid 73 through 75 or resid 77 through 10 \ 7)) } 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: 2.720 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.070 Construct map_model_manager: 0.030 Extract box with map and model: 0.350 Check model and map are aligned: 0.070 Set scattering table: 0.050 Process input model: 21.080 Find NCS groups from input model: 0.420 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.500 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 26.350 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5908 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 0.112 21747 Z= 0.234 Angle : 0.765 39.248 29532 Z= 0.421 Chirality : 0.046 0.581 3387 Planarity : 0.005 0.088 3732 Dihedral : 15.744 85.612 7902 Min Nonbonded Distance : 1.937 Molprobity Statistics. All-atom Clashscore : 16.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.54 % Favored : 96.46 % Rotamer: Outliers : 3.51 % Allowed : 14.37 % Favored : 82.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 17.95 % 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: -1.82 (0.15), residues: 2718 helix: -0.68 (0.22), residues: 426 sheet: -0.75 (0.15), residues: 1026 loop : -1.71 (0.16), residues: 1266 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG B 429 TYR 0.011 0.001 TYR I 49 PHE 0.010 0.001 PHE C 32 TRP 0.009 0.001 TRP L 36 HIS 0.002 0.001 HIS L 32 Details of bonding type rmsd covalent geometry : bond 0.00397 (21714) covalent geometry : angle 0.72975 (29466) SS BOND : bond 0.00327 ( 33) SS BOND : angle 4.93039 ( 66) hydrogen bonds : bond 0.16815 ( 947) hydrogen bonds : angle 7.46825 ( 2367) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5436 Ramachandran restraints generated. 2718 Oldfield, 0 Emsley, 2718 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5436 Ramachandran restraints generated. 2718 Oldfield, 0 Emsley, 2718 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 548 residues out of total 2421 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 85 poor density : 463 time to evaluate : 0.786 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 163 GLU cc_start: 0.5781 (OUTLIER) cc_final: 0.5554 (mm-30) REVERT: A 191 LYS cc_start: 0.6661 (mtpt) cc_final: 0.6452 (mtmt) REVERT: A 234 THR cc_start: 0.7902 (m) cc_final: 0.7415 (p) REVERT: B 198 TYR cc_start: 0.8082 (t80) cc_final: 0.7840 (t80) REVERT: C 191 LYS cc_start: 0.6642 (mtpt) cc_final: 0.6337 (mtmt) REVERT: D 59 TYR cc_start: 0.6525 (m-10) cc_final: 0.6255 (m-80) REVERT: F 59 TYR cc_start: 0.6535 (m-10) cc_final: 0.6183 (m-80) REVERT: F 95 ASP cc_start: 0.7269 (OUTLIER) cc_final: 0.6779 (t0) REVERT: H 59 TYR cc_start: 0.6558 (m-10) cc_final: 0.6239 (m-80) REVERT: H 103 TRP cc_start: 0.6988 (m-10) cc_final: 0.6660 (m-10) outliers start: 85 outliers final: 42 residues processed: 530 average time/residue: 0.1456 time to fit residues: 120.7501 Evaluate side-chains 476 residues out of total 2421 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 432 time to evaluate : 0.515 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 CYS Chi-restraints excluded: chain A residue 163 GLU Chi-restraints excluded: chain A residue 174 THR Chi-restraints excluded: chain A residue 245 THR Chi-restraints excluded: chain A residue 273 LEU Chi-restraints excluded: chain A residue 292 ILE Chi-restraints excluded: chain A residue 337 THR Chi-restraints excluded: chain A residue 344 ASP Chi-restraints excluded: chain A residue 350 SER Chi-restraints excluded: chain B residue 37 CYS Chi-restraints excluded: chain B residue 174 THR Chi-restraints excluded: chain B residue 245 THR Chi-restraints excluded: chain B residue 292 ILE Chi-restraints excluded: chain B residue 323 THR Chi-restraints excluded: chain B residue 337 THR Chi-restraints excluded: chain B residue 344 ASP Chi-restraints excluded: chain B residue 350 SER Chi-restraints excluded: chain B residue 369 THR Chi-restraints excluded: chain B residue 402 VAL Chi-restraints excluded: chain C residue 37 CYS Chi-restraints excluded: chain C residue 174 THR Chi-restraints excluded: chain C residue 245 THR Chi-restraints excluded: chain C residue 292 ILE Chi-restraints excluded: chain C residue 344 ASP Chi-restraints excluded: chain C residue 350 SER Chi-restraints excluded: chain C residue 369 THR Chi-restraints excluded: chain D residue 70 THR Chi-restraints excluded: chain D residue 101 ASP Chi-restraints excluded: chain E residue 104 VAL Chi-restraints excluded: chain F residue 70 THR Chi-restraints excluded: chain F residue 95 ASP Chi-restraints excluded: chain F residue 101 ASP Chi-restraints excluded: chain G residue 104 VAL Chi-restraints excluded: chain H residue 70 THR Chi-restraints excluded: chain H residue 95 ASP Chi-restraints excluded: chain H residue 101 ASP Chi-restraints excluded: chain I residue 104 VAL Chi-restraints excluded: chain J residue 23 LYS Chi-restraints excluded: chain J residue 40 THR Chi-restraints excluded: chain L residue 23 LYS Chi-restraints excluded: chain L residue 40 THR Chi-restraints excluded: chain N residue 23 LYS Chi-restraints excluded: chain N residue 40 THR Chi-restraints excluded: chain O residue 47 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 267 random chunks: chunk 197 optimal weight: 2.9990 chunk 215 optimal weight: 3.9990 chunk 20 optimal weight: 0.9980 chunk 132 optimal weight: 5.9990 chunk 261 optimal weight: 0.8980 chunk 248 optimal weight: 3.9990 chunk 207 optimal weight: 0.5980 chunk 155 optimal weight: 5.9990 chunk 244 optimal weight: 0.0010 chunk 183 optimal weight: 0.9990 chunk 111 optimal weight: 0.7980 overall best weight: 0.6586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 197 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 224 GLN A 283 GLN A 325 ASN A 331 ASN ** A 383 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 494 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 501 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 183 ASN B 197 ASN B 283 GLN B 325 ASN B 331 ASN B 383 ASN B 454 ASN B 494 GLN C 183 ASN C 225 GLN ** C 279 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 325 ASN C 331 ASN ** C 383 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 444 ASN ** C 494 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 6 GLN G 6 GLN I 6 GLN ** J 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 81 GLN K 70 HIS ** K 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 81 GLN L 95 GLN M 34 ASN ** M 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 81 GLN O 37 GLN ** O 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 27 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4165 r_free = 0.4165 target = 0.175614 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3969 r_free = 0.3969 target = 0.158423 restraints weight = 33098.054| |-----------------------------------------------------------------------------| r_work (start): 0.3969 rms_B_bonded: 2.39 r_work: 0.3875 rms_B_bonded: 2.74 restraints_weight: 0.5000 r_work: 0.3727 rms_B_bonded: 4.89 restraints_weight: 0.2500 r_work (final): 0.3727 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3729 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3729 r_free = 0.3729 target_work(ls_wunit_k1) = 0.135 | | occupancies: max = 1.00 min = 1.00 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3729 r_free = 0.3729 target_work(ls_wunit_k1) = 0.135 | | occupancies: max = 1.00 min = 0.33 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3729 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6838 moved from start: 0.1532 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 21747 Z= 0.170 Angle : 0.638 10.905 29532 Z= 0.331 Chirality : 0.045 0.235 3387 Planarity : 0.005 0.064 3732 Dihedral : 6.626 67.600 3008 Min Nonbonded Distance : 2.350 Molprobity Statistics. All-atom Clashscore : 11.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.17 % Favored : 96.83 % Rotamer: Outliers : 4.30 % Allowed : 18.22 % Favored : 77.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 17.95 % 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: -0.89 (0.16), residues: 2718 helix: 0.29 (0.23), residues: 429 sheet: -0.23 (0.16), residues: 990 loop : -1.12 (0.17), residues: 1299 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG J 38 TYR 0.021 0.002 TYR E 87 PHE 0.040 0.002 PHE A 505 TRP 0.021 0.002 TRP C 341 HIS 0.005 0.001 HIS C 317 Details of bonding type rmsd covalent geometry : bond 0.00382 (21714) covalent geometry : angle 0.63515 (29466) SS BOND : bond 0.00521 ( 33) SS BOND : angle 1.37635 ( 66) hydrogen bonds : bond 0.03923 ( 947) hydrogen bonds : angle 6.09406 ( 2367) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5436 Ramachandran restraints generated. 2718 Oldfield, 0 Emsley, 2718 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5436 Ramachandran restraints generated. 2718 Oldfield, 0 Emsley, 2718 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 554 residues out of total 2421 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 104 poor density : 450 time to evaluate : 0.766 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 30 GLU cc_start: 0.7108 (tt0) cc_final: 0.6644 (mt-10) REVERT: A 191 LYS cc_start: 0.7802 (mtpt) cc_final: 0.7584 (mtmt) REVERT: A 289 MET cc_start: 0.7869 (tpt) cc_final: 0.7221 (tpt) REVERT: A 331 ASN cc_start: 0.4163 (OUTLIER) cc_final: 0.3493 (p0) REVERT: A 361 GLN cc_start: 0.7336 (tm-30) cc_final: 0.6771 (tm-30) REVERT: A 365 VAL cc_start: 0.5523 (OUTLIER) cc_final: 0.5206 (t) REVERT: B 92 GLU cc_start: 0.6885 (tp30) cc_final: 0.6665 (tp30) REVERT: B 163 GLU cc_start: 0.7507 (mm-30) cc_final: 0.7297 (mm-30) REVERT: B 224 GLN cc_start: 0.7948 (mt0) cc_final: 0.7660 (mm-40) REVERT: B 331 ASN cc_start: 0.4064 (OUTLIER) cc_final: 0.3583 (p0) REVERT: B 361 GLN cc_start: 0.7248 (tm-30) cc_final: 0.6659 (tm-30) REVERT: B 365 VAL cc_start: 0.5012 (OUTLIER) cc_final: 0.3940 (p) REVERT: B 508 LYS cc_start: 0.8474 (pttp) cc_final: 0.8205 (pttp) REVERT: C 68 LYS cc_start: 0.7187 (ttpp) cc_final: 0.6960 (ttpp) REVERT: C 191 LYS cc_start: 0.7587 (mtpt) cc_final: 0.7098 (mtpt) REVERT: C 224 GLN cc_start: 0.8271 (mt0) cc_final: 0.7852 (mm-40) REVERT: C 343 CYS cc_start: 0.5709 (OUTLIER) cc_final: 0.5396 (m) REVERT: D 29 PHE cc_start: 0.6960 (t80) cc_final: 0.6633 (t80) REVERT: D 59 TYR cc_start: 0.7837 (m-10) cc_final: 0.7527 (m-80) REVERT: F 59 TYR cc_start: 0.7899 (m-10) cc_final: 0.7632 (m-80) REVERT: F 99 VAL cc_start: 0.8156 (OUTLIER) cc_final: 0.7934 (m) REVERT: H 59 TYR cc_start: 0.7749 (m-10) cc_final: 0.7403 (m-80) REVERT: H 103 TRP cc_start: 0.7953 (m-10) cc_final: 0.7548 (m-10) REVERT: I 81 GLU cc_start: 0.7238 (tp30) cc_final: 0.6996 (tp30) REVERT: J 38 ARG cc_start: 0.7310 (OUTLIER) cc_final: 0.7021 (ttp80) REVERT: K 11 LEU cc_start: 0.7249 (tt) cc_final: 0.6506 (mp) REVERT: L 100 GLU cc_start: 0.7280 (mm-30) cc_final: 0.7035 (mm-30) REVERT: M 11 LEU cc_start: 0.6757 (tt) cc_final: 0.6485 (mp) REVERT: N 38 ARG cc_start: 0.7472 (OUTLIER) cc_final: 0.7251 (ttt-90) outliers start: 104 outliers final: 62 residues processed: 509 average time/residue: 0.1430 time to fit residues: 113.2303 Evaluate side-chains 500 residues out of total 2421 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 430 time to evaluate : 0.738 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 163 GLU Chi-restraints excluded: chain A residue 174 THR Chi-restraints excluded: chain A residue 180 SER Chi-restraints excluded: chain A residue 222 GLU Chi-restraints excluded: chain A residue 245 THR Chi-restraints excluded: chain A residue 292 ILE Chi-restraints excluded: chain A residue 324 THR Chi-restraints excluded: chain A residue 331 ASN Chi-restraints excluded: chain A residue 343 CYS Chi-restraints excluded: chain A residue 344 ASP Chi-restraints excluded: chain A residue 365 VAL Chi-restraints excluded: chain A residue 369 THR Chi-restraints excluded: chain B residue 174 THR Chi-restraints excluded: chain B residue 183 ASN Chi-restraints excluded: chain B residue 201 LYS Chi-restraints excluded: chain B residue 222 GLU Chi-restraints excluded: chain B residue 245 THR Chi-restraints excluded: chain B residue 248 SER Chi-restraints excluded: chain B residue 296 VAL Chi-restraints excluded: chain B residue 324 THR Chi-restraints excluded: chain B residue 331 ASN Chi-restraints excluded: chain B residue 344 ASP Chi-restraints excluded: chain B residue 349 VAL Chi-restraints excluded: chain B residue 350 SER Chi-restraints excluded: chain B residue 365 VAL Chi-restraints excluded: chain B residue 369 THR Chi-restraints excluded: chain B residue 381 LEU Chi-restraints excluded: chain C residue 174 THR Chi-restraints excluded: chain C residue 183 ASN Chi-restraints excluded: chain C residue 245 THR Chi-restraints excluded: chain C residue 292 ILE Chi-restraints excluded: chain C residue 324 THR Chi-restraints excluded: chain C residue 331 ASN Chi-restraints excluded: chain C residue 343 CYS Chi-restraints excluded: chain C residue 344 ASP Chi-restraints excluded: chain C residue 365 VAL Chi-restraints excluded: chain C residue 369 THR Chi-restraints excluded: chain C residue 423 THR Chi-restraints excluded: chain D residue 11 VAL Chi-restraints excluded: chain D residue 45 LEU Chi-restraints excluded: chain E residue 2 VAL Chi-restraints excluded: chain E residue 14 THR Chi-restraints excluded: chain E residue 69 THR Chi-restraints excluded: chain E residue 104 VAL Chi-restraints excluded: chain F residue 11 VAL Chi-restraints excluded: chain F residue 66 ARG Chi-restraints excluded: chain F residue 70 THR Chi-restraints excluded: chain F residue 99 VAL Chi-restraints excluded: chain F residue 101 ASP Chi-restraints excluded: chain G residue 2 VAL Chi-restraints excluded: chain G residue 14 THR Chi-restraints excluded: chain G residue 83 VAL Chi-restraints excluded: chain G residue 104 VAL Chi-restraints excluded: chain H residue 11 VAL Chi-restraints excluded: chain I residue 7 SER Chi-restraints excluded: chain I residue 14 THR Chi-restraints excluded: chain I residue 27 LEU Chi-restraints excluded: chain I residue 33 LEU Chi-restraints excluded: chain I residue 69 THR Chi-restraints excluded: chain I residue 104 VAL Chi-restraints excluded: chain J residue 23 LYS Chi-restraints excluded: chain J residue 38 ARG Chi-restraints excluded: chain K residue 5 THR Chi-restraints excluded: chain K residue 54 LEU Chi-restraints excluded: chain L residue 23 LYS Chi-restraints excluded: chain L residue 38 ARG Chi-restraints excluded: chain M residue 73 LEU Chi-restraints excluded: chain N residue 23 LYS Chi-restraints excluded: chain N residue 38 ARG Chi-restraints excluded: chain O residue 53 LYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 267 random chunks: chunk 164 optimal weight: 0.9990 chunk 123 optimal weight: 2.9990 chunk 181 optimal weight: 1.9990 chunk 14 optimal weight: 0.8980 chunk 256 optimal weight: 2.9990 chunk 244 optimal weight: 0.8980 chunk 1 optimal weight: 0.7980 chunk 182 optimal weight: 1.9990 chunk 144 optimal weight: 0.5980 chunk 105 optimal weight: 2.9990 chunk 82 optimal weight: 3.9990 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 331 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 383 ASN ** A 494 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 501 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 279 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 283 GLN ** B 494 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 225 GLN ** C 279 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 383 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 30 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 34 ASN ** M 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4146 r_free = 0.4146 target = 0.172398 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3940 r_free = 0.3940 target = 0.154450 restraints weight = 32743.493| |-----------------------------------------------------------------------------| r_work (start): 0.3935 rms_B_bonded: 2.61 r_work: 0.3830 rms_B_bonded: 2.89 restraints_weight: 0.5000 r_work (final): 0.3830 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3841 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3841 r_free = 0.3841 target_work(ls_wunit_k1) = 0.144 | | occupancies: max = 1.00 min = 0.33 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3841 r_free = 0.3841 target_work(ls_wunit_k1) = 0.144 | | occupancies: max = 1.00 min = 1.00 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3841 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6717 moved from start: 0.1993 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 21747 Z= 0.182 Angle : 0.627 10.300 29532 Z= 0.325 Chirality : 0.045 0.210 3387 Planarity : 0.004 0.064 3732 Dihedral : 5.789 57.770 2980 Min Nonbonded Distance : 2.478 Molprobity Statistics. All-atom Clashscore : 12.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.09 % Favored : 95.91 % Rotamer: Outliers : 4.71 % Allowed : 20.74 % Favored : 74.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 17.95 % 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: -0.67 (0.16), residues: 2718 helix: 0.62 (0.24), residues: 429 sheet: -0.19 (0.16), residues: 1026 loop : -0.97 (0.18), residues: 1263 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 282 TYR 0.019 0.002 TYR E 49 PHE 0.033 0.002 PHE A 505 TRP 0.020 0.002 TRP C 341 HIS 0.004 0.001 HIS E 53 Details of bonding type rmsd covalent geometry : bond 0.00414 (21714) covalent geometry : angle 0.62381 (29466) SS BOND : bond 0.00462 ( 33) SS BOND : angle 1.47835 ( 66) hydrogen bonds : bond 0.04087 ( 947) hydrogen bonds : angle 5.90008 ( 2367) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5436 Ramachandran restraints generated. 2718 Oldfield, 0 Emsley, 2718 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5436 Ramachandran restraints generated. 2718 Oldfield, 0 Emsley, 2718 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 553 residues out of total 2421 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 114 poor density : 439 time to evaluate : 0.729 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 78 LEU cc_start: 0.8158 (OUTLIER) cc_final: 0.7913 (mp) REVERT: A 163 GLU cc_start: 0.7121 (OUTLIER) cc_final: 0.6892 (mm-30) REVERT: A 191 LYS cc_start: 0.7712 (mtpt) cc_final: 0.7294 (mtpt) REVERT: A 264 MET cc_start: 0.7434 (mtp) cc_final: 0.7207 (mtt) REVERT: A 289 MET cc_start: 0.7650 (tpt) cc_final: 0.6913 (tpt) REVERT: A 361 GLN cc_start: 0.7064 (tm-30) cc_final: 0.6547 (tm-30) REVERT: B 30 GLU cc_start: 0.7007 (tm-30) cc_final: 0.6669 (tm-30) REVERT: B 82 GLU cc_start: 0.6674 (OUTLIER) cc_final: 0.6079 (mm-30) REVERT: B 163 GLU cc_start: 0.7316 (mm-30) cc_final: 0.7070 (mm-30) REVERT: B 224 GLN cc_start: 0.7971 (mt0) cc_final: 0.7695 (mm-40) REVERT: B 361 GLN cc_start: 0.7113 (tm-30) cc_final: 0.6422 (tm-30) REVERT: C 84 ASP cc_start: 0.7749 (t0) cc_final: 0.7304 (t0) REVERT: C 191 LYS cc_start: 0.7563 (mtpt) cc_final: 0.7180 (mtpt) REVERT: C 361 GLN cc_start: 0.7326 (tm-30) cc_final: 0.6937 (tm-30) REVERT: D 29 PHE cc_start: 0.6962 (t80) cc_final: 0.6638 (t80) REVERT: D 59 TYR cc_start: 0.7682 (m-10) cc_final: 0.7361 (m-80) REVERT: F 59 TYR cc_start: 0.7686 (m-10) cc_final: 0.7413 (m-80) REVERT: G 17 GLN cc_start: 0.6520 (mm110) cc_final: 0.6201 (mp10) REVERT: H 59 TYR cc_start: 0.7566 (m-10) cc_final: 0.7202 (m-80) REVERT: H 103 TRP cc_start: 0.7892 (m-10) cc_final: 0.7570 (m-10) REVERT: I 81 GLU cc_start: 0.6830 (tp30) cc_final: 0.6597 (tp30) REVERT: I 100 GLN cc_start: 0.7424 (mp10) cc_final: 0.6937 (mp10) REVERT: J 38 ARG cc_start: 0.7163 (OUTLIER) cc_final: 0.6908 (ttp80) REVERT: K 11 LEU cc_start: 0.7210 (tt) cc_final: 0.6496 (mp) REVERT: K 39 ARG cc_start: 0.6731 (mpt-90) cc_final: 0.6329 (mpt-90) REVERT: L 38 ARG cc_start: 0.7349 (OUTLIER) cc_final: 0.7122 (ptm160) REVERT: M 11 LEU cc_start: 0.6866 (tt) cc_final: 0.6543 (mp) REVERT: N 38 ARG cc_start: 0.7464 (OUTLIER) cc_final: 0.7232 (ttt-90) outliers start: 114 outliers final: 81 residues processed: 512 average time/residue: 0.1441 time to fit residues: 115.8089 Evaluate side-chains 507 residues out of total 2421 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 87 poor density : 420 time to evaluate : 0.756 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 40 VAL Chi-restraints excluded: chain A residue 61 LEU Chi-restraints excluded: chain A residue 72 THR Chi-restraints excluded: chain A residue 78 LEU Chi-restraints excluded: chain A residue 163 GLU Chi-restraints excluded: chain A residue 174 THR Chi-restraints excluded: chain A residue 180 SER Chi-restraints excluded: chain A residue 222 GLU Chi-restraints excluded: chain A residue 245 THR Chi-restraints excluded: chain A residue 292 ILE Chi-restraints excluded: chain A residue 305 LEU Chi-restraints excluded: chain A residue 324 THR Chi-restraints excluded: chain A residue 334 LEU Chi-restraints excluded: chain A residue 344 ASP Chi-restraints excluded: chain A residue 369 THR Chi-restraints excluded: chain A residue 381 LEU Chi-restraints excluded: chain A residue 467 LEU Chi-restraints excluded: chain A residue 482 VAL Chi-restraints excluded: chain B residue 40 VAL Chi-restraints excluded: chain B residue 72 THR Chi-restraints excluded: chain B residue 82 GLU Chi-restraints excluded: chain B residue 174 THR Chi-restraints excluded: chain B residue 201 LYS Chi-restraints excluded: chain B residue 222 GLU Chi-restraints excluded: chain B residue 245 THR Chi-restraints excluded: chain B residue 273 LEU Chi-restraints excluded: chain B residue 296 VAL Chi-restraints excluded: chain B residue 344 ASP Chi-restraints excluded: chain B residue 349 VAL Chi-restraints excluded: chain B residue 365 VAL Chi-restraints excluded: chain B residue 369 THR Chi-restraints excluded: chain B residue 381 LEU Chi-restraints excluded: chain B residue 466 SER Chi-restraints excluded: chain B residue 482 VAL Chi-restraints excluded: chain C residue 72 THR Chi-restraints excluded: chain C residue 174 THR Chi-restraints excluded: chain C residue 201 LYS Chi-restraints excluded: chain C residue 245 THR Chi-restraints excluded: chain C residue 292 ILE Chi-restraints excluded: chain C residue 324 THR Chi-restraints excluded: chain C residue 344 ASP Chi-restraints excluded: chain C residue 365 VAL Chi-restraints excluded: chain C residue 381 LEU Chi-restraints excluded: chain C residue 423 THR Chi-restraints excluded: chain C residue 482 VAL Chi-restraints excluded: chain D residue 11 VAL Chi-restraints excluded: chain D residue 45 LEU Chi-restraints excluded: chain D residue 66 ARG Chi-restraints excluded: chain D residue 70 THR Chi-restraints excluded: chain D residue 101 ASP Chi-restraints excluded: chain E residue 2 VAL Chi-restraints excluded: chain E residue 14 THR Chi-restraints excluded: chain E residue 69 THR Chi-restraints excluded: chain E residue 104 VAL Chi-restraints excluded: chain F residue 11 VAL Chi-restraints excluded: chain F residue 45 LEU Chi-restraints excluded: chain F residue 66 ARG Chi-restraints excluded: chain F residue 70 THR Chi-restraints excluded: chain F residue 95 ASP Chi-restraints excluded: chain F residue 101 ASP Chi-restraints excluded: chain G residue 2 VAL Chi-restraints excluded: chain G residue 14 THR Chi-restraints excluded: chain G residue 28 ASP Chi-restraints excluded: chain G residue 104 VAL Chi-restraints excluded: chain H residue 11 VAL Chi-restraints excluded: chain H residue 70 THR Chi-restraints excluded: chain H residue 101 ASP Chi-restraints excluded: chain I residue 14 THR Chi-restraints excluded: chain I residue 27 LEU Chi-restraints excluded: chain I residue 47 LEU Chi-restraints excluded: chain I residue 69 THR Chi-restraints excluded: chain I residue 104 VAL Chi-restraints excluded: chain J residue 23 LYS Chi-restraints excluded: chain J residue 38 ARG Chi-restraints excluded: chain J residue 40 THR Chi-restraints excluded: chain J residue 75 VAL Chi-restraints excluded: chain K residue 54 LEU Chi-restraints excluded: chain K residue 63 SER Chi-restraints excluded: chain L residue 23 LYS Chi-restraints excluded: chain L residue 38 ARG Chi-restraints excluded: chain L residue 40 THR Chi-restraints excluded: chain M residue 73 LEU Chi-restraints excluded: chain N residue 38 ARG Chi-restraints excluded: chain N residue 40 THR Chi-restraints excluded: chain N residue 67 VAL Chi-restraints excluded: chain O residue 47 LEU Chi-restraints excluded: chain O residue 73 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 267 random chunks: chunk 187 optimal weight: 0.6980 chunk 152 optimal weight: 3.9990 chunk 25 optimal weight: 0.6980 chunk 175 optimal weight: 0.3980 chunk 200 optimal weight: 3.9990 chunk 11 optimal weight: 0.8980 chunk 195 optimal weight: 0.9990 chunk 88 optimal weight: 2.9990 chunk 44 optimal weight: 2.9990 chunk 67 optimal weight: 3.9990 chunk 140 optimal weight: 3.9990 overall best weight: 0.7382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 224 GLN A 225 GLN ** A 331 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 494 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 279 GLN B 494 GLN ** B 501 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 183 ASN C 225 GLN ** C 331 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 383 ASN ** D 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 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 = 0.4123 r_free = 0.4123 target = 0.163986 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3924 r_free = 0.3924 target = 0.147266 restraints weight = 33383.000| |-----------------------------------------------------------------------------| r_work (start): 0.3946 rms_B_bonded: 2.31 r_work: 0.3850 rms_B_bonded: 2.70 restraints_weight: 0.5000 r_work: 0.3702 rms_B_bonded: 4.81 restraints_weight: 0.2500 r_work (final): 0.3702 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3695 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3695 r_free = 0.3695 target_work(ls_wunit_k1) = 0.131 | | occupancies: max = 1.00 min = 1.00 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3695 r_free = 0.3695 target_work(ls_wunit_k1) = 0.131 | | occupancies: max = 1.00 min = 1.00 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3695 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6884 moved from start: 0.2361 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.060 21747 Z= 0.165 Angle : 0.615 9.973 29532 Z= 0.317 Chirality : 0.045 0.178 3387 Planarity : 0.004 0.061 3732 Dihedral : 5.325 51.554 2974 Min Nonbonded Distance : 2.398 Molprobity Statistics. All-atom Clashscore : 11.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.16 % Favored : 95.84 % Rotamer: Outliers : 5.08 % Allowed : 21.07 % Favored : 73.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 17.95 % 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: -0.42 (0.16), residues: 2718 helix: 0.94 (0.25), residues: 420 sheet: 0.06 (0.17), residues: 993 loop : -0.90 (0.18), residues: 1305 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 507 TYR 0.020 0.002 TYR G 49 PHE 0.043 0.002 PHE A 505 TRP 0.021 0.002 TRP C 341 HIS 0.004 0.001 HIS E 53 Details of bonding type rmsd covalent geometry : bond 0.00374 (21714) covalent geometry : angle 0.61156 (29466) SS BOND : bond 0.00717 ( 33) SS BOND : angle 1.42095 ( 66) hydrogen bonds : bond 0.03844 ( 947) hydrogen bonds : angle 5.77633 ( 2367) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5436 Ramachandran restraints generated. 2718 Oldfield, 0 Emsley, 2718 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5436 Ramachandran restraints generated. 2718 Oldfield, 0 Emsley, 2718 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 558 residues out of total 2421 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 123 poor density : 435 time to evaluate : 0.589 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 78 LEU cc_start: 0.8189 (OUTLIER) cc_final: 0.7976 (mp) REVERT: A 191 LYS cc_start: 0.7817 (mtpt) cc_final: 0.7412 (mtpt) REVERT: A 201 LYS cc_start: 0.7611 (OUTLIER) cc_final: 0.7309 (pttt) REVERT: A 227 ASN cc_start: 0.8260 (t0) cc_final: 0.8027 (t0) REVERT: A 361 GLN cc_start: 0.7367 (tm-30) cc_final: 0.6845 (tm-30) REVERT: B 82 GLU cc_start: 0.6971 (OUTLIER) cc_final: 0.6388 (mm-30) REVERT: B 191 LYS cc_start: 0.7876 (mtpt) cc_final: 0.7471 (mtmt) REVERT: B 224 GLN cc_start: 0.8136 (mt0) cc_final: 0.7842 (mm-40) REVERT: B 354 GLN cc_start: 0.7844 (OUTLIER) cc_final: 0.7586 (mm-40) REVERT: B 361 GLN cc_start: 0.7477 (tm-30) cc_final: 0.6685 (tm-30) REVERT: C 68 LYS cc_start: 0.7351 (ttpp) cc_final: 0.7131 (ttpp) REVERT: C 84 ASP cc_start: 0.8043 (t0) cc_final: 0.7555 (t0) REVERT: C 191 LYS cc_start: 0.7683 (mtpt) cc_final: 0.7259 (mtpt) REVERT: C 224 GLN cc_start: 0.8301 (mt0) cc_final: 0.7984 (mm-40) REVERT: C 354 GLN cc_start: 0.7888 (OUTLIER) cc_final: 0.7518 (mm110) REVERT: C 361 GLN cc_start: 0.7585 (tm-30) cc_final: 0.7128 (tm-30) REVERT: D 29 PHE cc_start: 0.7066 (t80) cc_final: 0.6696 (t80) REVERT: D 59 TYR cc_start: 0.7888 (m-10) cc_final: 0.7576 (m-80) REVERT: E 27 LEU cc_start: 0.8548 (OUTLIER) cc_final: 0.8256 (tt) REVERT: F 59 TYR cc_start: 0.7918 (m-10) cc_final: 0.7660 (m-80) REVERT: H 36 TRP cc_start: 0.7329 (m100) cc_final: 0.7097 (m100) REVERT: H 59 TYR cc_start: 0.7785 (m-10) cc_final: 0.7428 (m-80) REVERT: H 103 TRP cc_start: 0.7943 (m-10) cc_final: 0.7622 (m-10) REVERT: I 100 GLN cc_start: 0.7444 (mp10) cc_final: 0.6961 (mp10) REVERT: K 11 LEU cc_start: 0.7215 (tt) cc_final: 0.6542 (mp) REVERT: L 38 ARG cc_start: 0.7541 (OUTLIER) cc_final: 0.7293 (ptm160) REVERT: M 11 LEU cc_start: 0.6785 (tt) cc_final: 0.6415 (mp) REVERT: N 38 ARG cc_start: 0.7532 (OUTLIER) cc_final: 0.7228 (ttp80) REVERT: N 86 ASP cc_start: 0.6988 (OUTLIER) cc_final: 0.6735 (t0) REVERT: O 89 GLN cc_start: 0.6704 (OUTLIER) cc_final: 0.6186 (tp40) outliers start: 123 outliers final: 80 residues processed: 515 average time/residue: 0.1358 time to fit residues: 110.7828 Evaluate side-chains 507 residues out of total 2421 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 90 poor density : 417 time to evaluate : 0.723 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 40 VAL Chi-restraints excluded: chain A residue 61 LEU Chi-restraints excluded: chain A residue 72 THR Chi-restraints excluded: chain A residue 78 LEU Chi-restraints excluded: chain A residue 174 THR Chi-restraints excluded: chain A residue 180 SER Chi-restraints excluded: chain A residue 201 LYS Chi-restraints excluded: chain A residue 222 GLU Chi-restraints excluded: chain A residue 296 VAL Chi-restraints excluded: chain A residue 324 THR Chi-restraints excluded: chain A residue 334 LEU Chi-restraints excluded: chain A residue 344 ASP Chi-restraints excluded: chain A residue 369 THR Chi-restraints excluded: chain A residue 467 LEU Chi-restraints excluded: chain A residue 482 VAL Chi-restraints excluded: chain B residue 40 VAL Chi-restraints excluded: chain B residue 72 THR Chi-restraints excluded: chain B residue 82 GLU Chi-restraints excluded: chain B residue 222 GLU Chi-restraints excluded: chain B residue 245 THR Chi-restraints excluded: chain B residue 273 LEU Chi-restraints excluded: chain B residue 296 VAL Chi-restraints excluded: chain B residue 324 THR Chi-restraints excluded: chain B residue 337 THR Chi-restraints excluded: chain B residue 344 ASP Chi-restraints excluded: chain B residue 349 VAL Chi-restraints excluded: chain B residue 354 GLN Chi-restraints excluded: chain B residue 365 VAL Chi-restraints excluded: chain B residue 369 THR Chi-restraints excluded: chain B residue 379 VAL Chi-restraints excluded: chain B residue 381 LEU Chi-restraints excluded: chain B residue 466 SER Chi-restraints excluded: chain B residue 467 LEU Chi-restraints excluded: chain B residue 482 VAL Chi-restraints excluded: chain C residue 72 THR Chi-restraints excluded: chain C residue 245 THR Chi-restraints excluded: chain C residue 273 LEU Chi-restraints excluded: chain C residue 292 ILE Chi-restraints excluded: chain C residue 317 HIS Chi-restraints excluded: chain C residue 324 THR Chi-restraints excluded: chain C residue 344 ASP Chi-restraints excluded: chain C residue 354 GLN Chi-restraints excluded: chain C residue 365 VAL Chi-restraints excluded: chain C residue 381 LEU Chi-restraints excluded: chain C residue 423 THR Chi-restraints excluded: chain C residue 482 VAL Chi-restraints excluded: chain D residue 11 VAL Chi-restraints excluded: chain D residue 45 LEU Chi-restraints excluded: chain D residue 70 THR Chi-restraints excluded: chain D residue 101 ASP Chi-restraints excluded: chain E residue 2 VAL Chi-restraints excluded: chain E residue 14 THR Chi-restraints excluded: chain E residue 27 LEU Chi-restraints excluded: chain E residue 69 THR Chi-restraints excluded: chain E residue 104 VAL Chi-restraints excluded: chain F residue 11 VAL Chi-restraints excluded: chain F residue 45 LEU Chi-restraints excluded: chain F residue 95 ASP Chi-restraints excluded: chain F residue 101 ASP Chi-restraints excluded: chain G residue 2 VAL Chi-restraints excluded: chain G residue 14 THR Chi-restraints excluded: chain G residue 28 ASP Chi-restraints excluded: chain G residue 104 VAL Chi-restraints excluded: chain H residue 11 VAL Chi-restraints excluded: chain H residue 70 THR Chi-restraints excluded: chain H residue 101 ASP Chi-restraints excluded: chain I residue 14 THR Chi-restraints excluded: chain I residue 27 LEU Chi-restraints excluded: chain I residue 33 LEU Chi-restraints excluded: chain I residue 47 LEU Chi-restraints excluded: chain I residue 69 THR Chi-restraints excluded: chain I residue 104 VAL Chi-restraints excluded: chain J residue 40 THR Chi-restraints excluded: chain J residue 100 VAL Chi-restraints excluded: chain K residue 23 CYS Chi-restraints excluded: chain K residue 54 LEU Chi-restraints excluded: chain L residue 38 ARG Chi-restraints excluded: chain L residue 40 THR Chi-restraints excluded: chain L residue 75 VAL Chi-restraints excluded: chain M residue 73 LEU Chi-restraints excluded: chain N residue 38 ARG Chi-restraints excluded: chain N residue 40 THR Chi-restraints excluded: chain N residue 67 VAL Chi-restraints excluded: chain N residue 75 VAL Chi-restraints excluded: chain N residue 86 ASP Chi-restraints excluded: chain O residue 23 CYS Chi-restraints excluded: chain O residue 47 LEU Chi-restraints excluded: chain O residue 53 LYS Chi-restraints excluded: chain O residue 73 LEU Chi-restraints excluded: chain O residue 89 GLN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 267 random chunks: chunk 79 optimal weight: 4.9990 chunk 43 optimal weight: 0.9980 chunk 240 optimal weight: 4.9990 chunk 155 optimal weight: 4.9990 chunk 249 optimal weight: 0.5980 chunk 70 optimal weight: 1.9990 chunk 244 optimal weight: 0.5980 chunk 52 optimal weight: 4.9990 chunk 33 optimal weight: 2.9990 chunk 177 optimal weight: 0.6980 chunk 184 optimal weight: 0.8980 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 224 GLN A 225 GLN A 277 ASN A 302 GLN ** A 331 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 494 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 494 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 501 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 225 GLN C 331 ASN ** D 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 42 HIS ** K 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 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 = 0.4115 r_free = 0.4115 target = 0.163353 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3913 r_free = 0.3913 target = 0.146580 restraints weight = 33146.668| |-----------------------------------------------------------------------------| r_work (start): 0.3940 rms_B_bonded: 2.31 r_work: 0.3846 rms_B_bonded: 2.67 restraints_weight: 0.5000 r_work: 0.3697 rms_B_bonded: 4.77 restraints_weight: 0.2500 r_work (final): 0.3697 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3686 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3686 r_free = 0.3686 target_work(ls_wunit_k1) = 0.131 | | occupancies: max = 1.00 min = 1.00 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3686 r_free = 0.3686 target_work(ls_wunit_k1) = 0.131 | | occupancies: max = 1.00 min = 1.00 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3686 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6889 moved from start: 0.2617 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.058 21747 Z= 0.168 Angle : 0.620 9.536 29532 Z= 0.320 Chirality : 0.045 0.262 3387 Planarity : 0.004 0.059 3732 Dihedral : 4.966 40.729 2957 Min Nonbonded Distance : 2.471 Molprobity Statistics. All-atom Clashscore : 11.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.53 % Favored : 95.47 % Rotamer: Outliers : 5.41 % Allowed : 21.48 % Favored : 73.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 17.95 % 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: -0.36 (0.17), residues: 2718 helix: 1.03 (0.25), residues: 426 sheet: -0.04 (0.16), residues: 1068 loop : -0.80 (0.19), residues: 1224 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG M 18 TYR 0.021 0.002 TYR G 49 PHE 0.039 0.002 PHE A 505 TRP 0.021 0.002 TRP C 341 HIS 0.004 0.001 HIS E 53 Details of bonding type rmsd covalent geometry : bond 0.00382 (21714) covalent geometry : angle 0.61507 (29466) SS BOND : bond 0.00472 ( 33) SS BOND : angle 1.70323 ( 66) hydrogen bonds : bond 0.03900 ( 947) hydrogen bonds : angle 5.75588 ( 2367) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5436 Ramachandran restraints generated. 2718 Oldfield, 0 Emsley, 2718 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5436 Ramachandran restraints generated. 2718 Oldfield, 0 Emsley, 2718 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 555 residues out of total 2421 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 131 poor density : 424 time to evaluate : 0.759 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 78 LEU cc_start: 0.8171 (OUTLIER) cc_final: 0.7969 (mp) REVERT: A 191 LYS cc_start: 0.7806 (mtpt) cc_final: 0.7373 (mtmt) REVERT: A 201 LYS cc_start: 0.7532 (OUTLIER) cc_final: 0.7223 (pttt) REVERT: A 227 ASN cc_start: 0.8222 (t0) cc_final: 0.7937 (t0) REVERT: A 301 VAL cc_start: 0.8208 (m) cc_final: 0.6963 (p) REVERT: A 361 GLN cc_start: 0.7462 (tm-30) cc_final: 0.6777 (tm-30) REVERT: B 82 GLU cc_start: 0.6931 (OUTLIER) cc_final: 0.6272 (mm-30) REVERT: B 191 LYS cc_start: 0.7879 (mtpt) cc_final: 0.7457 (mtmt) REVERT: B 224 GLN cc_start: 0.8212 (mt0) cc_final: 0.7861 (mm-40) REVERT: B 268 ASN cc_start: 0.7414 (t0) cc_final: 0.7213 (t0) REVERT: B 354 GLN cc_start: 0.7877 (OUTLIER) cc_final: 0.7480 (mm-40) REVERT: B 361 GLN cc_start: 0.7483 (tm-30) cc_final: 0.6679 (tm-30) REVERT: B 417 TYR cc_start: 0.6375 (m-80) cc_final: 0.6008 (m-80) REVERT: C 80 LYS cc_start: 0.8291 (ttpt) cc_final: 0.8024 (ttmt) REVERT: C 191 LYS cc_start: 0.7691 (mtpt) cc_final: 0.7374 (mtmt) REVERT: C 218 GLU cc_start: 0.8217 (mp0) cc_final: 0.8005 (mp0) REVERT: C 222 GLU cc_start: 0.7718 (pt0) cc_final: 0.7507 (pt0) REVERT: C 224 GLN cc_start: 0.8329 (mt0) cc_final: 0.8056 (mm-40) REVERT: C 295 GLU cc_start: 0.7524 (mt-10) cc_final: 0.7278 (mt-10) REVERT: C 354 GLN cc_start: 0.7894 (OUTLIER) cc_final: 0.7522 (mm110) REVERT: C 361 GLN cc_start: 0.7646 (tm-30) cc_final: 0.7067 (tm-30) REVERT: D 29 PHE cc_start: 0.7051 (t80) cc_final: 0.6650 (t80) REVERT: D 59 TYR cc_start: 0.7879 (m-10) cc_final: 0.7574 (m-80) REVERT: E 27 LEU cc_start: 0.8539 (OUTLIER) cc_final: 0.8256 (tt) REVERT: F 59 TYR cc_start: 0.7893 (m-10) cc_final: 0.7617 (m-80) REVERT: G 17 GLN cc_start: 0.6616 (mm110) cc_final: 0.6277 (mm-40) REVERT: H 36 TRP cc_start: 0.7353 (m100) cc_final: 0.7051 (m100) REVERT: H 59 TYR cc_start: 0.7784 (m-10) cc_final: 0.7429 (m-80) REVERT: H 103 TRP cc_start: 0.7984 (m-10) cc_final: 0.7650 (m-10) REVERT: I 81 GLU cc_start: 0.7119 (tp30) cc_final: 0.6891 (tp30) REVERT: I 100 GLN cc_start: 0.7416 (mp10) cc_final: 0.6888 (mp10) REVERT: J 38 ARG cc_start: 0.7339 (OUTLIER) cc_final: 0.7109 (ttp80) REVERT: K 11 LEU cc_start: 0.7236 (tt) cc_final: 0.6500 (mp) REVERT: K 39 ARG cc_start: 0.6960 (mpt-90) cc_final: 0.6576 (mpt-90) REVERT: L 38 ARG cc_start: 0.7524 (OUTLIER) cc_final: 0.7261 (ptm160) REVERT: N 38 ARG cc_start: 0.7519 (OUTLIER) cc_final: 0.7168 (ttp80) REVERT: N 86 ASP cc_start: 0.6973 (OUTLIER) cc_final: 0.6707 (t0) outliers start: 131 outliers final: 94 residues processed: 510 average time/residue: 0.1398 time to fit residues: 111.8361 Evaluate side-chains 515 residues out of total 2421 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 104 poor density : 411 time to evaluate : 0.612 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 40 VAL Chi-restraints excluded: chain A residue 61 LEU Chi-restraints excluded: chain A residue 72 THR Chi-restraints excluded: chain A residue 78 LEU Chi-restraints excluded: chain A residue 201 LYS Chi-restraints excluded: chain A residue 222 GLU Chi-restraints excluded: chain A residue 245 THR Chi-restraints excluded: chain A residue 292 ILE Chi-restraints excluded: chain A residue 296 VAL Chi-restraints excluded: chain A residue 324 THR Chi-restraints excluded: chain A residue 334 LEU Chi-restraints excluded: chain A residue 344 ASP Chi-restraints excluded: chain A residue 369 THR Chi-restraints excluded: chain A residue 381 LEU Chi-restraints excluded: chain A residue 467 LEU Chi-restraints excluded: chain A residue 482 VAL Chi-restraints excluded: chain B residue 40 VAL Chi-restraints excluded: chain B residue 42 LYS Chi-restraints excluded: chain B residue 72 THR Chi-restraints excluded: chain B residue 82 GLU Chi-restraints excluded: chain B residue 180 SER Chi-restraints excluded: chain B residue 201 LYS Chi-restraints excluded: chain B residue 222 GLU Chi-restraints excluded: chain B residue 245 THR Chi-restraints excluded: chain B residue 273 LEU Chi-restraints excluded: chain B residue 296 VAL Chi-restraints excluded: chain B residue 308 VAL Chi-restraints excluded: chain B residue 311 THR Chi-restraints excluded: chain B residue 324 THR Chi-restraints excluded: chain B residue 337 THR Chi-restraints excluded: chain B residue 344 ASP Chi-restraints excluded: chain B residue 349 VAL Chi-restraints excluded: chain B residue 354 GLN Chi-restraints excluded: chain B residue 365 VAL Chi-restraints excluded: chain B residue 369 THR Chi-restraints excluded: chain B residue 379 VAL Chi-restraints excluded: chain B residue 381 LEU Chi-restraints excluded: chain B residue 467 LEU Chi-restraints excluded: chain B residue 482 VAL Chi-restraints excluded: chain C residue 72 THR Chi-restraints excluded: chain C residue 187 VAL Chi-restraints excluded: chain C residue 245 THR Chi-restraints excluded: chain C residue 273 LEU Chi-restraints excluded: chain C residue 292 ILE Chi-restraints excluded: chain C residue 324 THR Chi-restraints excluded: chain C residue 331 ASN Chi-restraints excluded: chain C residue 337 THR Chi-restraints excluded: chain C residue 344 ASP Chi-restraints excluded: chain C residue 354 GLN Chi-restraints excluded: chain C residue 365 VAL Chi-restraints excluded: chain C residue 381 LEU Chi-restraints excluded: chain C residue 406 VAL Chi-restraints excluded: chain C residue 423 THR Chi-restraints excluded: chain C residue 456 LEU Chi-restraints excluded: chain C residue 482 VAL Chi-restraints excluded: chain D residue 11 VAL Chi-restraints excluded: chain D residue 45 LEU Chi-restraints excluded: chain D residue 70 THR Chi-restraints excluded: chain D residue 101 ASP Chi-restraints excluded: chain E residue 2 VAL Chi-restraints excluded: chain E residue 14 THR Chi-restraints excluded: chain E residue 27 LEU Chi-restraints excluded: chain E residue 47 LEU Chi-restraints excluded: chain E residue 69 THR Chi-restraints excluded: chain E residue 104 VAL Chi-restraints excluded: chain F residue 11 VAL Chi-restraints excluded: chain F residue 45 LEU Chi-restraints excluded: chain F residue 70 THR Chi-restraints excluded: chain F residue 95 ASP Chi-restraints excluded: chain F residue 101 ASP Chi-restraints excluded: chain G residue 2 VAL Chi-restraints excluded: chain G residue 14 THR Chi-restraints excluded: chain G residue 28 ASP Chi-restraints excluded: chain G residue 104 VAL Chi-restraints excluded: chain H residue 11 VAL Chi-restraints excluded: chain H residue 70 THR Chi-restraints excluded: chain H residue 99 VAL Chi-restraints excluded: chain H residue 101 ASP Chi-restraints excluded: chain I residue 14 THR Chi-restraints excluded: chain I residue 27 LEU Chi-restraints excluded: chain I residue 33 LEU Chi-restraints excluded: chain I residue 69 THR Chi-restraints excluded: chain I residue 104 VAL Chi-restraints excluded: chain J residue 38 ARG Chi-restraints excluded: chain J residue 40 THR Chi-restraints excluded: chain J residue 75 VAL Chi-restraints excluded: chain K residue 23 CYS Chi-restraints excluded: chain K residue 54 LEU Chi-restraints excluded: chain K residue 63 SER Chi-restraints excluded: chain K residue 73 LEU Chi-restraints excluded: chain L residue 38 ARG Chi-restraints excluded: chain L residue 40 THR Chi-restraints excluded: chain L residue 75 VAL Chi-restraints excluded: chain L residue 107 THR Chi-restraints excluded: chain M residue 23 CYS Chi-restraints excluded: chain M residue 73 LEU Chi-restraints excluded: chain N residue 38 ARG Chi-restraints excluded: chain N residue 40 THR Chi-restraints excluded: chain N residue 67 VAL Chi-restraints excluded: chain N residue 75 VAL Chi-restraints excluded: chain N residue 86 ASP Chi-restraints excluded: chain O residue 23 CYS Chi-restraints excluded: chain O residue 47 LEU Chi-restraints excluded: chain O residue 73 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 267 random chunks: chunk 215 optimal weight: 2.9990 chunk 246 optimal weight: 0.0870 chunk 102 optimal weight: 0.7980 chunk 30 optimal weight: 0.5980 chunk 142 optimal weight: 0.5980 chunk 121 optimal weight: 0.9990 chunk 197 optimal weight: 1.9990 chunk 188 optimal weight: 2.9990 chunk 75 optimal weight: 0.3980 chunk 238 optimal weight: 1.9990 chunk 72 optimal weight: 0.6980 overall best weight: 0.4758 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 224 GLN A 225 GLN A 302 GLN A 331 ASN ** A 494 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 494 GLN ** B 501 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 94 GLN C 225 GLN ** D 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 42 HIS ** J 95 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 95 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 89 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4133 r_free = 0.4133 target = 0.164802 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3936 r_free = 0.3936 target = 0.148140 restraints weight = 33237.589| |-----------------------------------------------------------------------------| r_work (start): 0.3954 rms_B_bonded: 2.29 r_work: 0.3859 rms_B_bonded: 2.69 restraints_weight: 0.5000 r_work: 0.3707 rms_B_bonded: 4.86 restraints_weight: 0.2500 r_work (final): 0.3707 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3703 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3703 r_free = 0.3703 target_work(ls_wunit_k1) = 0.132 | | occupancies: max = 1.00 min = 1.00 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3703 r_free = 0.3703 target_work(ls_wunit_k1) = 0.132 | | occupancies: max = 1.00 min = 1.00 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3703 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6871 moved from start: 0.2736 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 21747 Z= 0.133 Angle : 0.601 9.598 29532 Z= 0.308 Chirality : 0.044 0.166 3387 Planarity : 0.004 0.058 3732 Dihedral : 4.841 40.023 2956 Min Nonbonded Distance : 2.466 Molprobity Statistics. All-atom Clashscore : 10.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.16 % Favored : 95.84 % Rotamer: Outliers : 5.41 % Allowed : 22.35 % Favored : 72.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 17.95 % 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: -0.22 (0.17), residues: 2718 helix: 1.15 (0.25), residues: 426 sheet: 0.13 (0.17), residues: 999 loop : -0.76 (0.18), residues: 1293 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG F 66 TYR 0.018 0.001 TYR E 49 PHE 0.043 0.002 PHE A 505 TRP 0.022 0.001 TRP C 341 HIS 0.003 0.001 HIS E 53 Details of bonding type rmsd covalent geometry : bond 0.00303 (21714) covalent geometry : angle 0.59697 (29466) SS BOND : bond 0.00440 ( 33) SS BOND : angle 1.50872 ( 66) hydrogen bonds : bond 0.03625 ( 947) hydrogen bonds : angle 5.64996 ( 2367) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5436 Ramachandran restraints generated. 2718 Oldfield, 0 Emsley, 2718 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5436 Ramachandran restraints generated. 2718 Oldfield, 0 Emsley, 2718 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 552 residues out of total 2421 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 131 poor density : 421 time to evaluate : 0.790 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 165 ASN cc_start: 0.7483 (m110) cc_final: 0.7224 (m110) REVERT: A 191 LYS cc_start: 0.7761 (mtpt) cc_final: 0.7370 (mtpt) REVERT: A 197 ASN cc_start: 0.8165 (t0) cc_final: 0.7899 (t0) REVERT: A 201 LYS cc_start: 0.7529 (OUTLIER) cc_final: 0.7063 (pttt) REVERT: A 227 ASN cc_start: 0.8169 (t0) cc_final: 0.7864 (t0) REVERT: A 331 ASN cc_start: 0.4545 (OUTLIER) cc_final: 0.3852 (p0) REVERT: A 361 GLN cc_start: 0.7432 (tm-30) cc_final: 0.6757 (tm-30) REVERT: A 365 VAL cc_start: 0.5611 (OUTLIER) cc_final: 0.5172 (t) REVERT: A 379 VAL cc_start: 0.4384 (OUTLIER) cc_final: 0.4142 (p) REVERT: A 501 GLN cc_start: 0.6555 (OUTLIER) cc_final: 0.5938 (pp30) REVERT: B 191 LYS cc_start: 0.7826 (mtpt) cc_final: 0.7568 (mtpt) REVERT: B 201 LYS cc_start: 0.7418 (OUTLIER) cc_final: 0.7135 (pttt) REVERT: B 224 GLN cc_start: 0.8121 (mt0) cc_final: 0.7675 (mm-40) REVERT: B 354 GLN cc_start: 0.7833 (OUTLIER) cc_final: 0.7443 (mm-40) REVERT: B 361 GLN cc_start: 0.7429 (tm-30) cc_final: 0.6641 (tm-30) REVERT: B 417 TYR cc_start: 0.6297 (m-80) cc_final: 0.5942 (m-80) REVERT: B 487 GLU cc_start: 0.6710 (OUTLIER) cc_final: 0.6142 (mm-30) REVERT: C 68 LYS cc_start: 0.7209 (OUTLIER) cc_final: 0.6968 (ttpp) REVERT: C 80 LYS cc_start: 0.8253 (ttpt) cc_final: 0.7975 (ttmt) REVERT: C 84 ASP cc_start: 0.8116 (t0) cc_final: 0.7580 (t0) REVERT: C 191 LYS cc_start: 0.7656 (mtpt) cc_final: 0.7370 (mtmt) REVERT: C 224 GLN cc_start: 0.8243 (mt0) cc_final: 0.7949 (mm-40) REVERT: C 274 MET cc_start: 0.7272 (mtt) cc_final: 0.7027 (tpp) REVERT: C 295 GLU cc_start: 0.7579 (mt-10) cc_final: 0.7355 (mt-10) REVERT: C 354 GLN cc_start: 0.7863 (OUTLIER) cc_final: 0.7519 (mm110) REVERT: C 361 GLN cc_start: 0.7606 (tm-30) cc_final: 0.7027 (tm-30) REVERT: D 29 PHE cc_start: 0.6930 (t80) cc_final: 0.6539 (t80) REVERT: D 59 TYR cc_start: 0.7876 (m-10) cc_final: 0.7561 (m-80) REVERT: D 86 ASP cc_start: 0.4432 (OUTLIER) cc_final: 0.4146 (t0) REVERT: F 59 TYR cc_start: 0.7846 (m-10) cc_final: 0.7550 (m-80) REVERT: G 17 GLN cc_start: 0.6528 (mm110) cc_final: 0.6200 (mm-40) REVERT: H 36 TRP cc_start: 0.7315 (m100) cc_final: 0.6974 (m100) REVERT: H 59 TYR cc_start: 0.7777 (m-10) cc_final: 0.7425 (m-80) REVERT: H 103 TRP cc_start: 0.7976 (m-10) cc_final: 0.7629 (m-10) REVERT: I 100 GLN cc_start: 0.7409 (mp10) cc_final: 0.6882 (mp10) REVERT: J 38 ARG cc_start: 0.7277 (OUTLIER) cc_final: 0.7025 (ttp80) REVERT: K 11 LEU cc_start: 0.7221 (tt) cc_final: 0.6492 (mp) REVERT: K 39 ARG cc_start: 0.6909 (mpt-90) cc_final: 0.6508 (mpt-90) REVERT: N 86 ASP cc_start: 0.6895 (OUTLIER) cc_final: 0.6638 (t0) outliers start: 131 outliers final: 97 residues processed: 506 average time/residue: 0.1391 time to fit residues: 111.1349 Evaluate side-chains 520 residues out of total 2421 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 110 poor density : 410 time to evaluate : 0.743 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 40 VAL Chi-restraints excluded: chain A residue 61 LEU Chi-restraints excluded: chain A residue 67 ILE Chi-restraints excluded: chain A residue 72 THR Chi-restraints excluded: chain A residue 201 LYS Chi-restraints excluded: chain A residue 222 GLU Chi-restraints excluded: chain A residue 224 GLN Chi-restraints excluded: chain A residue 245 THR Chi-restraints excluded: chain A residue 296 VAL Chi-restraints excluded: chain A residue 300 VAL Chi-restraints excluded: chain A residue 331 ASN Chi-restraints excluded: chain A residue 334 LEU Chi-restraints excluded: chain A residue 344 ASP Chi-restraints excluded: chain A residue 365 VAL Chi-restraints excluded: chain A residue 369 THR Chi-restraints excluded: chain A residue 379 VAL Chi-restraints excluded: chain A residue 381 LEU Chi-restraints excluded: chain A residue 467 LEU Chi-restraints excluded: chain A residue 482 VAL Chi-restraints excluded: chain A residue 501 GLN Chi-restraints excluded: chain B residue 40 VAL Chi-restraints excluded: chain B residue 42 LYS Chi-restraints excluded: chain B residue 72 THR Chi-restraints excluded: chain B residue 180 SER Chi-restraints excluded: chain B residue 201 LYS Chi-restraints excluded: chain B residue 222 GLU Chi-restraints excluded: chain B residue 245 THR Chi-restraints excluded: chain B residue 248 SER Chi-restraints excluded: chain B residue 273 LEU Chi-restraints excluded: chain B residue 296 VAL Chi-restraints excluded: chain B residue 308 VAL Chi-restraints excluded: chain B residue 311 THR Chi-restraints excluded: chain B residue 324 THR Chi-restraints excluded: chain B residue 337 THR Chi-restraints excluded: chain B residue 344 ASP Chi-restraints excluded: chain B residue 349 VAL Chi-restraints excluded: chain B residue 354 GLN Chi-restraints excluded: chain B residue 365 VAL Chi-restraints excluded: chain B residue 369 THR Chi-restraints excluded: chain B residue 379 VAL Chi-restraints excluded: chain B residue 381 LEU Chi-restraints excluded: chain B residue 467 LEU Chi-restraints excluded: chain B residue 482 VAL Chi-restraints excluded: chain B residue 487 GLU Chi-restraints excluded: chain C residue 67 ILE Chi-restraints excluded: chain C residue 68 LYS Chi-restraints excluded: chain C residue 72 THR Chi-restraints excluded: chain C residue 187 VAL Chi-restraints excluded: chain C residue 273 LEU Chi-restraints excluded: chain C residue 292 ILE Chi-restraints excluded: chain C residue 317 HIS Chi-restraints excluded: chain C residue 324 THR Chi-restraints excluded: chain C residue 337 THR Chi-restraints excluded: chain C residue 339 ARG Chi-restraints excluded: chain C residue 344 ASP Chi-restraints excluded: chain C residue 354 GLN Chi-restraints excluded: chain C residue 365 VAL Chi-restraints excluded: chain C residue 381 LEU Chi-restraints excluded: chain C residue 423 THR Chi-restraints excluded: chain C residue 456 LEU Chi-restraints excluded: chain C residue 482 VAL Chi-restraints excluded: chain D residue 11 VAL Chi-restraints excluded: chain D residue 45 LEU Chi-restraints excluded: chain D residue 70 THR Chi-restraints excluded: chain D residue 86 ASP Chi-restraints excluded: chain E residue 2 VAL Chi-restraints excluded: chain E residue 11 LEU Chi-restraints excluded: chain E residue 14 THR Chi-restraints excluded: chain E residue 27 LEU Chi-restraints excluded: chain E residue 69 THR Chi-restraints excluded: chain E residue 76 SER Chi-restraints excluded: chain F residue 11 VAL Chi-restraints excluded: chain F residue 45 LEU Chi-restraints excluded: chain F residue 95 ASP Chi-restraints excluded: chain F residue 101 ASP Chi-restraints excluded: chain G residue 2 VAL Chi-restraints excluded: chain G residue 14 THR Chi-restraints excluded: chain G residue 28 ASP Chi-restraints excluded: chain G residue 33 LEU Chi-restraints excluded: chain G residue 104 VAL Chi-restraints excluded: chain H residue 11 VAL Chi-restraints excluded: chain H residue 99 VAL Chi-restraints excluded: chain H residue 101 ASP Chi-restraints excluded: chain I residue 3 VAL Chi-restraints excluded: chain I residue 14 THR Chi-restraints excluded: chain I residue 27 LEU Chi-restraints excluded: chain I residue 33 LEU Chi-restraints excluded: chain I residue 69 THR Chi-restraints excluded: chain I residue 104 VAL Chi-restraints excluded: chain J residue 38 ARG Chi-restraints excluded: chain J residue 40 THR Chi-restraints excluded: chain J residue 75 VAL Chi-restraints excluded: chain K residue 23 CYS Chi-restraints excluded: chain K residue 54 LEU Chi-restraints excluded: chain K residue 63 SER Chi-restraints excluded: chain K residue 73 LEU Chi-restraints excluded: chain L residue 38 ARG Chi-restraints excluded: chain L residue 40 THR Chi-restraints excluded: chain L residue 75 VAL Chi-restraints excluded: chain L residue 107 THR Chi-restraints excluded: chain M residue 23 CYS Chi-restraints excluded: chain M residue 73 LEU Chi-restraints excluded: chain N residue 38 ARG Chi-restraints excluded: chain N residue 40 THR Chi-restraints excluded: chain N residue 67 VAL Chi-restraints excluded: chain N residue 75 VAL Chi-restraints excluded: chain N residue 86 ASP Chi-restraints excluded: chain O residue 47 LEU Chi-restraints excluded: chain O residue 53 LYS Chi-restraints excluded: chain O residue 73 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 267 random chunks: chunk 227 optimal weight: 3.9990 chunk 189 optimal weight: 0.7980 chunk 167 optimal weight: 2.9990 chunk 98 optimal weight: 0.9980 chunk 135 optimal weight: 2.9990 chunk 203 optimal weight: 0.8980 chunk 188 optimal weight: 1.9990 chunk 94 optimal weight: 0.6980 chunk 101 optimal weight: 0.7980 chunk 176 optimal weight: 0.6980 chunk 194 optimal weight: 0.0270 overall best weight: 0.6038 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 224 GLN A 225 GLN ** A 494 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 283 GLN B 494 GLN ** B 501 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 94 GLN C 225 GLN ** C 331 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 494 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 42 HIS ** K 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 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 = 0.4128 r_free = 0.4128 target = 0.164763 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3931 r_free = 0.3931 target = 0.148173 restraints weight = 33107.470| |-----------------------------------------------------------------------------| r_work (start): 0.3943 rms_B_bonded: 2.29 r_work: 0.3847 rms_B_bonded: 2.69 restraints_weight: 0.5000 r_work: 0.3696 rms_B_bonded: 4.82 restraints_weight: 0.2500 r_work (final): 0.3696 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3698 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3698 r_free = 0.3698 target_work(ls_wunit_k1) = 0.131 | | occupancies: max = 1.00 min = 1.00 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3698 r_free = 0.3698 target_work(ls_wunit_k1) = 0.131 | | occupancies: max = 1.00 min = 1.00 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3698 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6881 moved from start: 0.2832 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 21747 Z= 0.146 Angle : 0.601 9.374 29532 Z= 0.309 Chirality : 0.044 0.163 3387 Planarity : 0.004 0.058 3732 Dihedral : 4.795 35.776 2954 Min Nonbonded Distance : 2.477 Molprobity Statistics. All-atom Clashscore : 10.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.35 % Favored : 95.65 % Rotamer: Outliers : 5.53 % Allowed : 22.39 % Favored : 72.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 17.95 % 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: -0.11 (0.17), residues: 2718 helix: 1.47 (0.26), residues: 408 sheet: 0.15 (0.17), residues: 999 loop : -0.69 (0.18), residues: 1311 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG F 66 TYR 0.019 0.002 TYR E 49 PHE 0.042 0.002 PHE A 505 TRP 0.015 0.001 TRP C 341 HIS 0.003 0.001 HIS E 53 Details of bonding type rmsd covalent geometry : bond 0.00332 (21714) covalent geometry : angle 0.59754 (29466) SS BOND : bond 0.00428 ( 33) SS BOND : angle 1.49401 ( 66) hydrogen bonds : bond 0.03662 ( 947) hydrogen bonds : angle 5.61418 ( 2367) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5436 Ramachandran restraints generated. 2718 Oldfield, 0 Emsley, 2718 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5436 Ramachandran restraints generated. 2718 Oldfield, 0 Emsley, 2718 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 555 residues out of total 2421 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 134 poor density : 421 time to evaluate : 0.657 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 97 MET cc_start: 0.6964 (mtm) cc_final: 0.6761 (mtm) REVERT: A 165 ASN cc_start: 0.7517 (m110) cc_final: 0.7283 (m110) REVERT: A 191 LYS cc_start: 0.7768 (mtpt) cc_final: 0.7319 (mtmm) REVERT: A 197 ASN cc_start: 0.8158 (t0) cc_final: 0.7903 (t0) REVERT: A 201 LYS cc_start: 0.7485 (OUTLIER) cc_final: 0.7062 (pttt) REVERT: A 225 GLN cc_start: 0.8365 (OUTLIER) cc_final: 0.7953 (mm110) REVERT: A 227 ASN cc_start: 0.8124 (t0) cc_final: 0.7809 (t0) REVERT: A 354 GLN cc_start: 0.7620 (OUTLIER) cc_final: 0.6939 (mt0) REVERT: A 361 GLN cc_start: 0.7441 (tm-30) cc_final: 0.6763 (tm-30) REVERT: A 365 VAL cc_start: 0.5505 (OUTLIER) cc_final: 0.5075 (t) REVERT: A 379 VAL cc_start: 0.4461 (OUTLIER) cc_final: 0.4184 (p) REVERT: A 501 GLN cc_start: 0.6578 (OUTLIER) cc_final: 0.5985 (pp30) REVERT: B 148 ILE cc_start: 0.7627 (pt) cc_final: 0.7361 (mm) REVERT: B 191 LYS cc_start: 0.7867 (mtpt) cc_final: 0.7561 (mtpt) REVERT: B 201 LYS cc_start: 0.7351 (OUTLIER) cc_final: 0.7080 (pttt) REVERT: B 224 GLN cc_start: 0.8125 (mt0) cc_final: 0.7667 (mm-40) REVERT: B 264 MET cc_start: 0.7702 (mtp) cc_final: 0.7364 (mtt) REVERT: B 289 MET cc_start: 0.8276 (tpt) cc_final: 0.8002 (tpt) REVERT: B 354 GLN cc_start: 0.7891 (OUTLIER) cc_final: 0.7469 (mm-40) REVERT: B 361 GLN cc_start: 0.7446 (tm-30) cc_final: 0.6686 (tm-30) REVERT: B 487 GLU cc_start: 0.6752 (OUTLIER) cc_final: 0.5408 (mp0) REVERT: C 68 LYS cc_start: 0.7258 (OUTLIER) cc_final: 0.7007 (ttpp) REVERT: C 80 LYS cc_start: 0.8302 (ttpt) cc_final: 0.8070 (ttmt) REVERT: C 84 ASP cc_start: 0.8177 (t0) cc_final: 0.7965 (t0) REVERT: C 191 LYS cc_start: 0.7683 (mtpt) cc_final: 0.7391 (mtpt) REVERT: C 218 GLU cc_start: 0.8198 (mp0) cc_final: 0.7747 (mp0) REVERT: C 354 GLN cc_start: 0.7860 (OUTLIER) cc_final: 0.7489 (mm110) REVERT: C 361 GLN cc_start: 0.7642 (tm-30) cc_final: 0.7076 (tm-30) REVERT: D 29 PHE cc_start: 0.6976 (t80) cc_final: 0.6645 (t80) REVERT: D 59 TYR cc_start: 0.7921 (m-10) cc_final: 0.7605 (m-80) REVERT: D 86 ASP cc_start: 0.4477 (OUTLIER) cc_final: 0.4192 (t0) REVERT: F 59 TYR cc_start: 0.7859 (m-10) cc_final: 0.7565 (m-80) REVERT: G 17 GLN cc_start: 0.6538 (mm110) cc_final: 0.6238 (mm-40) REVERT: H 36 TRP cc_start: 0.7241 (m100) cc_final: 0.6870 (m100) REVERT: H 59 TYR cc_start: 0.7872 (m-10) cc_final: 0.7497 (m-80) REVERT: H 103 TRP cc_start: 0.8003 (m-10) cc_final: 0.7662 (m-10) REVERT: I 100 GLN cc_start: 0.7444 (mp10) cc_final: 0.6922 (mp10) REVERT: J 38 ARG cc_start: 0.7286 (OUTLIER) cc_final: 0.7040 (ttp80) REVERT: K 11 LEU cc_start: 0.7217 (tt) cc_final: 0.6503 (mp) REVERT: K 39 ARG cc_start: 0.6930 (mpt-90) cc_final: 0.6533 (mpt-90) REVERT: L 38 ARG cc_start: 0.7490 (OUTLIER) cc_final: 0.7245 (ptm160) outliers start: 134 outliers final: 104 residues processed: 505 average time/residue: 0.1395 time to fit residues: 111.4804 Evaluate side-chains 535 residues out of total 2421 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 118 poor density : 417 time to evaluate : 0.728 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 40 VAL Chi-restraints excluded: chain A residue 61 LEU Chi-restraints excluded: chain A residue 72 THR Chi-restraints excluded: chain A residue 201 LYS Chi-restraints excluded: chain A residue 222 GLU Chi-restraints excluded: chain A residue 225 GLN Chi-restraints excluded: chain A residue 245 THR Chi-restraints excluded: chain A residue 292 ILE Chi-restraints excluded: chain A residue 296 VAL Chi-restraints excluded: chain A residue 300 VAL Chi-restraints excluded: chain A residue 311 THR Chi-restraints excluded: chain A residue 334 LEU Chi-restraints excluded: chain A residue 344 ASP Chi-restraints excluded: chain A residue 354 GLN Chi-restraints excluded: chain A residue 365 VAL Chi-restraints excluded: chain A residue 369 THR Chi-restraints excluded: chain A residue 379 VAL Chi-restraints excluded: chain A residue 381 LEU Chi-restraints excluded: chain A residue 467 LEU Chi-restraints excluded: chain A residue 482 VAL Chi-restraints excluded: chain A residue 501 GLN Chi-restraints excluded: chain B residue 40 VAL Chi-restraints excluded: chain B residue 42 LYS Chi-restraints excluded: chain B residue 72 THR Chi-restraints excluded: chain B residue 180 SER Chi-restraints excluded: chain B residue 201 LYS Chi-restraints excluded: chain B residue 222 GLU Chi-restraints excluded: chain B residue 245 THR Chi-restraints excluded: chain B residue 248 SER Chi-restraints excluded: chain B residue 273 LEU Chi-restraints excluded: chain B residue 296 VAL Chi-restraints excluded: chain B residue 308 VAL Chi-restraints excluded: chain B residue 311 THR Chi-restraints excluded: chain B residue 337 THR Chi-restraints excluded: chain B residue 344 ASP Chi-restraints excluded: chain B residue 349 VAL Chi-restraints excluded: chain B residue 354 GLN Chi-restraints excluded: chain B residue 365 VAL Chi-restraints excluded: chain B residue 369 THR Chi-restraints excluded: chain B residue 379 VAL Chi-restraints excluded: chain B residue 381 LEU Chi-restraints excluded: chain B residue 386 ILE Chi-restraints excluded: chain B residue 467 LEU Chi-restraints excluded: chain B residue 482 VAL Chi-restraints excluded: chain B residue 487 GLU Chi-restraints excluded: chain C residue 67 ILE Chi-restraints excluded: chain C residue 68 LYS Chi-restraints excluded: chain C residue 72 THR Chi-restraints excluded: chain C residue 187 VAL Chi-restraints excluded: chain C residue 201 LYS Chi-restraints excluded: chain C residue 245 THR Chi-restraints excluded: chain C residue 273 LEU Chi-restraints excluded: chain C residue 311 THR Chi-restraints excluded: chain C residue 317 HIS Chi-restraints excluded: chain C residue 324 THR Chi-restraints excluded: chain C residue 337 THR Chi-restraints excluded: chain C residue 339 ARG Chi-restraints excluded: chain C residue 344 ASP Chi-restraints excluded: chain C residue 354 GLN Chi-restraints excluded: chain C residue 365 VAL Chi-restraints excluded: chain C residue 369 THR Chi-restraints excluded: chain C residue 381 LEU Chi-restraints excluded: chain C residue 406 VAL Chi-restraints excluded: chain C residue 423 THR Chi-restraints excluded: chain C residue 456 LEU Chi-restraints excluded: chain C residue 482 VAL Chi-restraints excluded: chain D residue 11 VAL Chi-restraints excluded: chain D residue 45 LEU Chi-restraints excluded: chain D residue 66 ARG Chi-restraints excluded: chain D residue 70 THR Chi-restraints excluded: chain D residue 86 ASP Chi-restraints excluded: chain D residue 101 ASP Chi-restraints excluded: chain E residue 2 VAL Chi-restraints excluded: chain E residue 11 LEU Chi-restraints excluded: chain E residue 14 THR Chi-restraints excluded: chain E residue 27 LEU Chi-restraints excluded: chain E residue 69 THR Chi-restraints excluded: chain E residue 76 SER Chi-restraints excluded: chain E residue 104 VAL Chi-restraints excluded: chain F residue 11 VAL Chi-restraints excluded: chain F residue 45 LEU Chi-restraints excluded: chain F residue 70 THR Chi-restraints excluded: chain F residue 95 ASP Chi-restraints excluded: chain F residue 101 ASP Chi-restraints excluded: chain G residue 2 VAL Chi-restraints excluded: chain G residue 14 THR Chi-restraints excluded: chain G residue 28 ASP Chi-restraints excluded: chain G residue 33 LEU Chi-restraints excluded: chain G residue 104 VAL Chi-restraints excluded: chain H residue 11 VAL Chi-restraints excluded: chain H residue 70 THR Chi-restraints excluded: chain H residue 99 VAL Chi-restraints excluded: chain H residue 101 ASP Chi-restraints excluded: chain I residue 3 VAL Chi-restraints excluded: chain I residue 14 THR Chi-restraints excluded: chain I residue 27 LEU Chi-restraints excluded: chain I residue 33 LEU Chi-restraints excluded: chain I residue 69 THR Chi-restraints excluded: chain I residue 104 VAL Chi-restraints excluded: chain J residue 38 ARG Chi-restraints excluded: chain J residue 40 THR Chi-restraints excluded: chain J residue 75 VAL Chi-restraints excluded: chain K residue 23 CYS Chi-restraints excluded: chain K residue 54 LEU Chi-restraints excluded: chain K residue 63 SER Chi-restraints excluded: chain K residue 73 LEU Chi-restraints excluded: chain L residue 38 ARG Chi-restraints excluded: chain L residue 40 THR Chi-restraints excluded: chain L residue 75 VAL Chi-restraints excluded: chain L residue 107 THR Chi-restraints excluded: chain M residue 23 CYS Chi-restraints excluded: chain M residue 73 LEU Chi-restraints excluded: chain N residue 38 ARG Chi-restraints excluded: chain N residue 40 THR Chi-restraints excluded: chain N residue 75 VAL Chi-restraints excluded: chain O residue 23 CYS Chi-restraints excluded: chain O residue 47 LEU Chi-restraints excluded: chain O residue 73 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 267 random chunks: chunk 83 optimal weight: 1.9990 chunk 41 optimal weight: 0.6980 chunk 126 optimal weight: 2.9990 chunk 29 optimal weight: 0.9980 chunk 176 optimal weight: 0.7980 chunk 148 optimal weight: 0.8980 chunk 169 optimal weight: 0.7980 chunk 203 optimal weight: 0.8980 chunk 151 optimal weight: 1.9990 chunk 207 optimal weight: 1.9990 chunk 168 optimal weight: 0.8980 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 94 GLN A 224 GLN ** A 331 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 494 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 494 GLN ** B 501 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 94 GLN C 225 GLN C 331 ASN ** D 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 42 HIS I 42 HIS ** K 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4115 r_free = 0.4115 target = 0.163433 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3915 r_free = 0.3915 target = 0.146690 restraints weight = 33166.921| |-----------------------------------------------------------------------------| r_work (start): 0.3929 rms_B_bonded: 2.30 r_work: 0.3835 rms_B_bonded: 2.66 restraints_weight: 0.5000 r_work: 0.3682 rms_B_bonded: 4.80 restraints_weight: 0.2500 r_work (final): 0.3682 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3683 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3683 r_free = 0.3683 target_work(ls_wunit_k1) = 0.130 | | occupancies: max = 1.00 min = 1.00 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3683 r_free = 0.3683 target_work(ls_wunit_k1) = 0.130 | | occupancies: max = 1.00 min = 1.00 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3683 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6903 moved from start: 0.3005 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 21747 Z= 0.178 Angle : 0.627 8.946 29532 Z= 0.324 Chirality : 0.045 0.172 3387 Planarity : 0.004 0.058 3732 Dihedral : 4.899 34.544 2952 Min Nonbonded Distance : 2.484 Molprobity Statistics. All-atom Clashscore : 11.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.60 % Favored : 95.40 % Rotamer: Outliers : 5.66 % Allowed : 22.14 % Favored : 72.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 17.95 % 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: -0.23 (0.17), residues: 2718 helix: 1.15 (0.25), residues: 426 sheet: 0.13 (0.16), residues: 1026 loop : -0.78 (0.18), residues: 1266 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG F 66 TYR 0.022 0.002 TYR E 49 PHE 0.039 0.002 PHE A 505 TRP 0.029 0.002 TRP C 341 HIS 0.005 0.001 HIS E 53 Details of bonding type rmsd covalent geometry : bond 0.00404 (21714) covalent geometry : angle 0.62300 (29466) SS BOND : bond 0.00482 ( 33) SS BOND : angle 1.67317 ( 66) hydrogen bonds : bond 0.03881 ( 947) hydrogen bonds : angle 5.69325 ( 2367) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5436 Ramachandran restraints generated. 2718 Oldfield, 0 Emsley, 2718 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5436 Ramachandran restraints generated. 2718 Oldfield, 0 Emsley, 2718 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 575 residues out of total 2421 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 137 poor density : 438 time to evaluate : 0.853 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 97 MET cc_start: 0.7002 (mtm) cc_final: 0.6773 (mtm) REVERT: A 165 ASN cc_start: 0.7642 (m110) cc_final: 0.7399 (m110) REVERT: A 191 LYS cc_start: 0.7788 (mtpt) cc_final: 0.7362 (mtmt) REVERT: A 197 ASN cc_start: 0.8150 (t0) cc_final: 0.7875 (t0) REVERT: A 201 LYS cc_start: 0.7491 (OUTLIER) cc_final: 0.7069 (pttt) REVERT: A 204 LEU cc_start: 0.8421 (OUTLIER) cc_final: 0.8208 (mt) REVERT: A 227 ASN cc_start: 0.8081 (t0) cc_final: 0.7748 (t0) REVERT: A 251 MET cc_start: 0.7346 (ttm) cc_final: 0.6887 (ttm) REVERT: A 282 ARG cc_start: 0.7937 (OUTLIER) cc_final: 0.6934 (ttm-80) REVERT: A 301 VAL cc_start: 0.8314 (m) cc_final: 0.7136 (p) REVERT: A 354 GLN cc_start: 0.7642 (OUTLIER) cc_final: 0.6955 (mt0) REVERT: A 361 GLN cc_start: 0.7460 (tm-30) cc_final: 0.6803 (tm-30) REVERT: A 379 VAL cc_start: 0.4219 (OUTLIER) cc_final: 0.3977 (p) REVERT: A 457 TYR cc_start: 0.7155 (m-80) cc_final: 0.6779 (m-80) REVERT: A 501 GLN cc_start: 0.6641 (OUTLIER) cc_final: 0.6032 (pp30) REVERT: B 148 ILE cc_start: 0.7677 (pt) cc_final: 0.7423 (mm) REVERT: B 191 LYS cc_start: 0.7909 (mtpt) cc_final: 0.7590 (mtpt) REVERT: B 201 LYS cc_start: 0.7345 (OUTLIER) cc_final: 0.7079 (pttt) REVERT: B 224 GLN cc_start: 0.8234 (mt0) cc_final: 0.8028 (mt0) REVERT: B 264 MET cc_start: 0.7764 (mtp) cc_final: 0.7443 (mtt) REVERT: B 289 MET cc_start: 0.8331 (tpt) cc_final: 0.8046 (tpt) REVERT: B 354 GLN cc_start: 0.7842 (OUTLIER) cc_final: 0.7535 (mm-40) REVERT: B 361 GLN cc_start: 0.7495 (tm-30) cc_final: 0.6715 (tm-30) REVERT: B 417 TYR cc_start: 0.6461 (m-80) cc_final: 0.6227 (m-80) REVERT: B 487 GLU cc_start: 0.6817 (OUTLIER) cc_final: 0.5699 (mp0) REVERT: C 68 LYS cc_start: 0.7259 (OUTLIER) cc_final: 0.7016 (ttpp) REVERT: C 80 LYS cc_start: 0.8304 (ttpt) cc_final: 0.8070 (ttmt) REVERT: C 191 LYS cc_start: 0.7762 (mtpt) cc_final: 0.7412 (mtmt) REVERT: C 218 GLU cc_start: 0.8256 (mp0) cc_final: 0.7794 (mp0) REVERT: C 274 MET cc_start: 0.7311 (mtt) cc_final: 0.7103 (tpp) REVERT: C 354 GLN cc_start: 0.7906 (OUTLIER) cc_final: 0.7596 (mm-40) REVERT: C 361 GLN cc_start: 0.7651 (tm-30) cc_final: 0.7084 (tm-30) REVERT: D 59 TYR cc_start: 0.7882 (m-10) cc_final: 0.7576 (m-80) REVERT: D 86 ASP cc_start: 0.4563 (OUTLIER) cc_final: 0.4262 (t70) REVERT: F 59 TYR cc_start: 0.7808 (m-10) cc_final: 0.7541 (m-80) REVERT: G 17 GLN cc_start: 0.6589 (mm110) cc_final: 0.6327 (mm-40) REVERT: H 36 TRP cc_start: 0.7278 (m100) cc_final: 0.6889 (m100) REVERT: H 59 TYR cc_start: 0.7884 (m-10) cc_final: 0.7547 (m-80) REVERT: H 103 TRP cc_start: 0.8038 (m-10) cc_final: 0.7731 (m-10) REVERT: I 100 GLN cc_start: 0.7451 (mp10) cc_final: 0.6886 (mp10) REVERT: J 38 ARG cc_start: 0.7305 (OUTLIER) cc_final: 0.7056 (ttp80) REVERT: K 11 LEU cc_start: 0.7237 (tt) cc_final: 0.6524 (mp) REVERT: K 39 ARG cc_start: 0.6919 (mpt-90) cc_final: 0.6520 (mpt-90) REVERT: N 38 ARG cc_start: 0.7564 (OUTLIER) cc_final: 0.7219 (ttp80) REVERT: N 86 ASP cc_start: 0.6986 (OUTLIER) cc_final: 0.6700 (t0) outliers start: 137 outliers final: 110 residues processed: 524 average time/residue: 0.1324 time to fit residues: 110.0110 Evaluate side-chains 553 residues out of total 2421 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 125 poor density : 428 time to evaluate : 0.741 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 40 VAL Chi-restraints excluded: chain A residue 61 LEU Chi-restraints excluded: chain A residue 72 THR Chi-restraints excluded: chain A residue 78 LEU Chi-restraints excluded: chain A residue 201 LYS Chi-restraints excluded: chain A residue 204 LEU Chi-restraints excluded: chain A residue 224 GLN Chi-restraints excluded: chain A residue 245 THR Chi-restraints excluded: chain A residue 282 ARG Chi-restraints excluded: chain A residue 292 ILE Chi-restraints excluded: chain A residue 296 VAL Chi-restraints excluded: chain A residue 300 VAL Chi-restraints excluded: chain A residue 311 THR Chi-restraints excluded: chain A residue 334 LEU Chi-restraints excluded: chain A residue 344 ASP Chi-restraints excluded: chain A residue 354 GLN Chi-restraints excluded: chain A residue 369 THR Chi-restraints excluded: chain A residue 379 VAL Chi-restraints excluded: chain A residue 381 LEU Chi-restraints excluded: chain A residue 414 VAL Chi-restraints excluded: chain A residue 482 VAL Chi-restraints excluded: chain A residue 501 GLN Chi-restraints excluded: chain B residue 40 VAL Chi-restraints excluded: chain B residue 42 LYS Chi-restraints excluded: chain B residue 72 THR Chi-restraints excluded: chain B residue 152 VAL Chi-restraints excluded: chain B residue 180 SER Chi-restraints excluded: chain B residue 201 LYS Chi-restraints excluded: chain B residue 222 GLU Chi-restraints excluded: chain B residue 245 THR Chi-restraints excluded: chain B residue 273 LEU Chi-restraints excluded: chain B residue 296 VAL Chi-restraints excluded: chain B residue 308 VAL Chi-restraints excluded: chain B residue 311 THR Chi-restraints excluded: chain B residue 323 THR Chi-restraints excluded: chain B residue 337 THR Chi-restraints excluded: chain B residue 344 ASP Chi-restraints excluded: chain B residue 349 VAL Chi-restraints excluded: chain B residue 354 GLN Chi-restraints excluded: chain B residue 365 VAL Chi-restraints excluded: chain B residue 369 THR Chi-restraints excluded: chain B residue 379 VAL Chi-restraints excluded: chain B residue 381 LEU Chi-restraints excluded: chain B residue 386 ILE Chi-restraints excluded: chain B residue 396 MET Chi-restraints excluded: chain B residue 431 ILE Chi-restraints excluded: chain B residue 467 LEU Chi-restraints excluded: chain B residue 482 VAL Chi-restraints excluded: chain B residue 487 GLU Chi-restraints excluded: chain C residue 40 VAL Chi-restraints excluded: chain C residue 67 ILE Chi-restraints excluded: chain C residue 68 LYS Chi-restraints excluded: chain C residue 72 THR Chi-restraints excluded: chain C residue 187 VAL Chi-restraints excluded: chain C residue 245 THR Chi-restraints excluded: chain C residue 273 LEU Chi-restraints excluded: chain C residue 311 THR Chi-restraints excluded: chain C residue 317 HIS Chi-restraints excluded: chain C residue 324 THR Chi-restraints excluded: chain C residue 331 ASN Chi-restraints excluded: chain C residue 337 THR Chi-restraints excluded: chain C residue 339 ARG Chi-restraints excluded: chain C residue 344 ASP Chi-restraints excluded: chain C residue 354 GLN Chi-restraints excluded: chain C residue 365 VAL Chi-restraints excluded: chain C residue 406 VAL Chi-restraints excluded: chain C residue 423 THR Chi-restraints excluded: chain C residue 456 LEU Chi-restraints excluded: chain C residue 482 VAL Chi-restraints excluded: chain D residue 11 VAL Chi-restraints excluded: chain D residue 45 LEU Chi-restraints excluded: chain D residue 70 THR Chi-restraints excluded: chain D residue 86 ASP Chi-restraints excluded: chain D residue 101 ASP Chi-restraints excluded: chain E residue 2 VAL Chi-restraints excluded: chain E residue 11 LEU Chi-restraints excluded: chain E residue 14 THR Chi-restraints excluded: chain E residue 27 LEU Chi-restraints excluded: chain E residue 51 ILE Chi-restraints excluded: chain E residue 69 THR Chi-restraints excluded: chain E residue 76 SER Chi-restraints excluded: chain E residue 104 VAL Chi-restraints excluded: chain F residue 11 VAL Chi-restraints excluded: chain F residue 45 LEU Chi-restraints excluded: chain F residue 70 THR Chi-restraints excluded: chain F residue 95 ASP Chi-restraints excluded: chain F residue 101 ASP Chi-restraints excluded: chain F residue 105 GLN Chi-restraints excluded: chain G residue 2 VAL Chi-restraints excluded: chain G residue 14 THR Chi-restraints excluded: chain G residue 28 ASP Chi-restraints excluded: chain G residue 33 LEU Chi-restraints excluded: chain G residue 104 VAL Chi-restraints excluded: chain H residue 11 VAL Chi-restraints excluded: chain H residue 70 THR Chi-restraints excluded: chain H residue 99 VAL Chi-restraints excluded: chain H residue 101 ASP Chi-restraints excluded: chain I residue 3 VAL Chi-restraints excluded: chain I residue 7 SER Chi-restraints excluded: chain I residue 14 THR Chi-restraints excluded: chain I residue 27 LEU Chi-restraints excluded: chain I residue 33 LEU Chi-restraints excluded: chain I residue 104 VAL Chi-restraints excluded: chain J residue 7 SER Chi-restraints excluded: chain J residue 38 ARG Chi-restraints excluded: chain J residue 40 THR Chi-restraints excluded: chain J residue 75 VAL Chi-restraints excluded: chain K residue 23 CYS Chi-restraints excluded: chain K residue 54 LEU Chi-restraints excluded: chain K residue 63 SER Chi-restraints excluded: chain K residue 73 LEU Chi-restraints excluded: chain L residue 7 SER Chi-restraints excluded: chain L residue 40 THR Chi-restraints excluded: chain L residue 75 VAL Chi-restraints excluded: chain L residue 100 VAL Chi-restraints excluded: chain L residue 107 THR Chi-restraints excluded: chain M residue 73 LEU Chi-restraints excluded: chain N residue 38 ARG Chi-restraints excluded: chain N residue 40 THR Chi-restraints excluded: chain N residue 67 VAL Chi-restraints excluded: chain N residue 75 VAL Chi-restraints excluded: chain N residue 86 ASP Chi-restraints excluded: chain O residue 23 CYS Chi-restraints excluded: chain O residue 47 LEU Chi-restraints excluded: chain O residue 73 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 267 random chunks: chunk 99 optimal weight: 4.9990 chunk 181 optimal weight: 4.9990 chunk 224 optimal weight: 0.7980 chunk 240 optimal weight: 0.0670 chunk 24 optimal weight: 0.8980 chunk 49 optimal weight: 2.9990 chunk 36 optimal weight: 3.9990 chunk 50 optimal weight: 0.7980 chunk 1 optimal weight: 1.9990 chunk 34 optimal weight: 2.9990 chunk 203 optimal weight: 1.9990 overall best weight: 0.9120 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 94 GLN A 224 GLN ** A 331 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 494 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 283 GLN B 454 ASN B 494 GLN ** B 501 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 94 GLN C 225 GLN C 331 ASN ** C 363 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 462 GLN ** D 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 42 HIS I 42 HIS ** K 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4111 r_free = 0.4111 target = 0.162997 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3910 r_free = 0.3910 target = 0.146200 restraints weight = 33073.879| |-----------------------------------------------------------------------------| r_work (start): 0.3925 rms_B_bonded: 2.29 r_work: 0.3831 rms_B_bonded: 2.66 restraints_weight: 0.5000 r_work: 0.3678 rms_B_bonded: 4.79 restraints_weight: 0.2500 r_work (final): 0.3678 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3679 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3679 r_free = 0.3679 target_work(ls_wunit_k1) = 0.130 | | occupancies: max = 1.00 min = 1.00 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3679 r_free = 0.3679 target_work(ls_wunit_k1) = 0.130 | | occupancies: max = 1.00 min = 1.00 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3679 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6911 moved from start: 0.3113 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 21747 Z= 0.190 Angle : 0.643 9.677 29532 Z= 0.334 Chirality : 0.046 0.175 3387 Planarity : 0.004 0.058 3732 Dihedral : 4.970 34.533 2952 Min Nonbonded Distance : 2.317 Molprobity Statistics. All-atom Clashscore : 12.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.57 % Favored : 95.43 % Rotamer: Outliers : 5.58 % Allowed : 22.76 % Favored : 71.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 17.95 % 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: -0.25 (0.16), residues: 2718 helix: 1.18 (0.25), residues: 423 sheet: 0.11 (0.16), residues: 1026 loop : -0.80 (0.18), residues: 1269 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG F 66 TYR 0.024 0.002 TYR E 49 PHE 0.037 0.002 PHE A 505 TRP 0.024 0.002 TRP C 341 HIS 0.005 0.001 HIS E 53 Details of bonding type rmsd covalent geometry : bond 0.00433 (21714) covalent geometry : angle 0.63877 (29466) SS BOND : bond 0.00491 ( 33) SS BOND : angle 1.68558 ( 66) hydrogen bonds : bond 0.03985 ( 947) hydrogen bonds : angle 5.74615 ( 2367) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5436 Ramachandran restraints generated. 2718 Oldfield, 0 Emsley, 2718 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5436 Ramachandran restraints generated. 2718 Oldfield, 0 Emsley, 2718 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 572 residues out of total 2421 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 135 poor density : 437 time to evaluate : 0.761 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 97 MET cc_start: 0.7079 (mtm) cc_final: 0.6845 (mtm) REVERT: A 165 ASN cc_start: 0.7542 (m110) cc_final: 0.7261 (m110) REVERT: A 191 LYS cc_start: 0.7788 (mtpt) cc_final: 0.7378 (mtmt) REVERT: A 197 ASN cc_start: 0.8135 (t0) cc_final: 0.7877 (t0) REVERT: A 201 LYS cc_start: 0.7486 (OUTLIER) cc_final: 0.7067 (pttt) REVERT: A 204 LEU cc_start: 0.8398 (OUTLIER) cc_final: 0.8181 (mt) REVERT: A 224 GLN cc_start: 0.8244 (OUTLIER) cc_final: 0.7938 (mm-40) REVERT: A 225 GLN cc_start: 0.8483 (mm-40) cc_final: 0.8278 (mm-40) REVERT: A 227 ASN cc_start: 0.8149 (t0) cc_final: 0.7830 (t0) REVERT: A 251 MET cc_start: 0.7502 (ttm) cc_final: 0.7174 (ttm) REVERT: A 282 ARG cc_start: 0.7937 (OUTLIER) cc_final: 0.6913 (ttm-80) REVERT: A 289 MET cc_start: 0.7989 (tpt) cc_final: 0.7531 (tpt) REVERT: A 301 VAL cc_start: 0.8339 (m) cc_final: 0.7154 (p) REVERT: A 354 GLN cc_start: 0.7664 (OUTLIER) cc_final: 0.6989 (mt0) REVERT: A 361 GLN cc_start: 0.7488 (tm-30) cc_final: 0.6781 (tm-30) REVERT: A 501 GLN cc_start: 0.6601 (OUTLIER) cc_final: 0.5960 (pp30) REVERT: B 148 ILE cc_start: 0.7730 (pt) cc_final: 0.7487 (mm) REVERT: B 191 LYS cc_start: 0.7909 (mtpt) cc_final: 0.7548 (mtmt) REVERT: B 201 LYS cc_start: 0.7367 (OUTLIER) cc_final: 0.7040 (pttt) REVERT: B 224 GLN cc_start: 0.8368 (mt0) cc_final: 0.8110 (mt0) REVERT: B 262 ASN cc_start: 0.6619 (t0) cc_final: 0.6404 (t0) REVERT: B 264 MET cc_start: 0.7860 (mtp) cc_final: 0.7547 (mtt) REVERT: B 354 GLN cc_start: 0.7860 (OUTLIER) cc_final: 0.7531 (mm-40) REVERT: B 361 GLN cc_start: 0.7528 (tm-30) cc_final: 0.6798 (tm-30) REVERT: B 417 TYR cc_start: 0.6433 (m-80) cc_final: 0.6206 (m-80) REVERT: B 487 GLU cc_start: 0.6844 (OUTLIER) cc_final: 0.5953 (mp0) REVERT: C 68 LYS cc_start: 0.7041 (OUTLIER) cc_final: 0.6784 (tttm) REVERT: C 80 LYS cc_start: 0.8325 (ttpt) cc_final: 0.8079 (ttmt) REVERT: C 148 ILE cc_start: 0.8087 (pt) cc_final: 0.7840 (mm) REVERT: C 191 LYS cc_start: 0.7777 (mtpt) cc_final: 0.7315 (mtmt) REVERT: C 218 GLU cc_start: 0.8240 (mp0) cc_final: 0.7577 (mp0) REVERT: C 222 GLU cc_start: 0.7705 (pt0) cc_final: 0.7501 (pt0) REVERT: C 274 MET cc_start: 0.7315 (mtt) cc_final: 0.7085 (tpp) REVERT: C 354 GLN cc_start: 0.7928 (OUTLIER) cc_final: 0.7615 (mm-40) REVERT: C 361 GLN cc_start: 0.7663 (tm-30) cc_final: 0.7092 (tm-30) REVERT: D 59 TYR cc_start: 0.7874 (m-10) cc_final: 0.7570 (m-80) REVERT: D 86 ASP cc_start: 0.4584 (OUTLIER) cc_final: 0.4212 (t0) REVERT: F 47 TRP cc_start: 0.7671 (t60) cc_final: 0.7400 (t60) REVERT: F 59 TYR cc_start: 0.7810 (m-10) cc_final: 0.7520 (m-80) REVERT: G 17 GLN cc_start: 0.6608 (mm110) cc_final: 0.6195 (mp10) REVERT: H 36 TRP cc_start: 0.7293 (m100) cc_final: 0.6868 (m100) REVERT: H 59 TYR cc_start: 0.7899 (m-10) cc_final: 0.7555 (m-80) REVERT: H 103 TRP cc_start: 0.8051 (m-10) cc_final: 0.7721 (m-10) REVERT: I 100 GLN cc_start: 0.7507 (mp10) cc_final: 0.6987 (mp10) REVERT: J 38 ARG cc_start: 0.7298 (OUTLIER) cc_final: 0.7056 (ttp80) REVERT: K 11 LEU cc_start: 0.7246 (tt) cc_final: 0.6519 (mp) REVERT: K 39 ARG cc_start: 0.6918 (mpt-90) cc_final: 0.6512 (mpt-90) REVERT: M 89 GLN cc_start: 0.7233 (OUTLIER) cc_final: 0.6398 (tp-100) REVERT: N 38 ARG cc_start: 0.7571 (OUTLIER) cc_final: 0.7227 (ttp80) REVERT: N 86 ASP cc_start: 0.6982 (OUTLIER) cc_final: 0.6681 (t0) outliers start: 135 outliers final: 106 residues processed: 523 average time/residue: 0.1317 time to fit residues: 109.5304 Evaluate side-chains 557 residues out of total 2421 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 122 poor density : 435 time to evaluate : 0.723 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 40 VAL Chi-restraints excluded: chain A residue 61 LEU Chi-restraints excluded: chain A residue 72 THR Chi-restraints excluded: chain A residue 78 LEU Chi-restraints excluded: chain A residue 201 LYS Chi-restraints excluded: chain A residue 204 LEU Chi-restraints excluded: chain A residue 222 GLU Chi-restraints excluded: chain A residue 224 GLN Chi-restraints excluded: chain A residue 245 THR Chi-restraints excluded: chain A residue 282 ARG Chi-restraints excluded: chain A residue 292 ILE Chi-restraints excluded: chain A residue 296 VAL Chi-restraints excluded: chain A residue 311 THR Chi-restraints excluded: chain A residue 334 LEU Chi-restraints excluded: chain A residue 344 ASP Chi-restraints excluded: chain A residue 354 GLN Chi-restraints excluded: chain A residue 369 THR Chi-restraints excluded: chain A residue 381 LEU Chi-restraints excluded: chain A residue 414 VAL Chi-restraints excluded: chain A residue 482 VAL Chi-restraints excluded: chain A residue 501 GLN Chi-restraints excluded: chain B residue 40 VAL Chi-restraints excluded: chain B residue 42 LYS Chi-restraints excluded: chain B residue 72 THR Chi-restraints excluded: chain B residue 152 VAL Chi-restraints excluded: chain B residue 180 SER Chi-restraints excluded: chain B residue 201 LYS Chi-restraints excluded: chain B residue 222 GLU Chi-restraints excluded: chain B residue 245 THR Chi-restraints excluded: chain B residue 273 LEU Chi-restraints excluded: chain B residue 296 VAL Chi-restraints excluded: chain B residue 308 VAL Chi-restraints excluded: chain B residue 311 THR Chi-restraints excluded: chain B residue 323 THR Chi-restraints excluded: chain B residue 337 THR Chi-restraints excluded: chain B residue 344 ASP Chi-restraints excluded: chain B residue 349 VAL Chi-restraints excluded: chain B residue 354 GLN Chi-restraints excluded: chain B residue 365 VAL Chi-restraints excluded: chain B residue 369 THR Chi-restraints excluded: chain B residue 379 VAL Chi-restraints excluded: chain B residue 381 LEU Chi-restraints excluded: chain B residue 386 ILE Chi-restraints excluded: chain B residue 406 VAL Chi-restraints excluded: chain B residue 431 ILE Chi-restraints excluded: chain B residue 467 LEU Chi-restraints excluded: chain B residue 482 VAL Chi-restraints excluded: chain B residue 487 GLU Chi-restraints excluded: chain C residue 40 VAL Chi-restraints excluded: chain C residue 67 ILE Chi-restraints excluded: chain C residue 68 LYS Chi-restraints excluded: chain C residue 72 THR Chi-restraints excluded: chain C residue 187 VAL Chi-restraints excluded: chain C residue 245 THR Chi-restraints excluded: chain C residue 273 LEU Chi-restraints excluded: chain C residue 311 THR Chi-restraints excluded: chain C residue 317 HIS Chi-restraints excluded: chain C residue 324 THR Chi-restraints excluded: chain C residue 331 ASN Chi-restraints excluded: chain C residue 337 THR Chi-restraints excluded: chain C residue 344 ASP Chi-restraints excluded: chain C residue 354 GLN Chi-restraints excluded: chain C residue 365 VAL Chi-restraints excluded: chain C residue 406 VAL Chi-restraints excluded: chain C residue 423 THR Chi-restraints excluded: chain C residue 456 LEU Chi-restraints excluded: chain C residue 482 VAL Chi-restraints excluded: chain D residue 11 VAL Chi-restraints excluded: chain D residue 45 LEU Chi-restraints excluded: chain D residue 70 THR Chi-restraints excluded: chain D residue 86 ASP Chi-restraints excluded: chain D residue 101 ASP Chi-restraints excluded: chain E residue 2 VAL Chi-restraints excluded: chain E residue 11 LEU Chi-restraints excluded: chain E residue 14 THR Chi-restraints excluded: chain E residue 27 LEU Chi-restraints excluded: chain E residue 69 THR Chi-restraints excluded: chain E residue 104 VAL Chi-restraints excluded: chain F residue 11 VAL Chi-restraints excluded: chain F residue 45 LEU Chi-restraints excluded: chain F residue 70 THR Chi-restraints excluded: chain F residue 95 ASP Chi-restraints excluded: chain F residue 101 ASP Chi-restraints excluded: chain F residue 105 GLN Chi-restraints excluded: chain G residue 2 VAL Chi-restraints excluded: chain G residue 14 THR Chi-restraints excluded: chain G residue 28 ASP Chi-restraints excluded: chain G residue 33 LEU Chi-restraints excluded: chain G residue 104 VAL Chi-restraints excluded: chain H residue 11 VAL Chi-restraints excluded: chain H residue 70 THR Chi-restraints excluded: chain H residue 99 VAL Chi-restraints excluded: chain H residue 101 ASP Chi-restraints excluded: chain I residue 3 VAL Chi-restraints excluded: chain I residue 14 THR Chi-restraints excluded: chain I residue 27 LEU Chi-restraints excluded: chain I residue 33 LEU Chi-restraints excluded: chain I residue 104 VAL Chi-restraints excluded: chain I residue 107 LYS Chi-restraints excluded: chain J residue 7 SER Chi-restraints excluded: chain J residue 38 ARG Chi-restraints excluded: chain J residue 40 THR Chi-restraints excluded: chain J residue 75 VAL Chi-restraints excluded: chain K residue 23 CYS Chi-restraints excluded: chain K residue 54 LEU Chi-restraints excluded: chain K residue 63 SER Chi-restraints excluded: chain K residue 73 LEU Chi-restraints excluded: chain L residue 7 SER Chi-restraints excluded: chain L residue 40 THR Chi-restraints excluded: chain L residue 75 VAL Chi-restraints excluded: chain L residue 100 VAL Chi-restraints excluded: chain L residue 107 THR Chi-restraints excluded: chain M residue 73 LEU Chi-restraints excluded: chain M residue 89 GLN Chi-restraints excluded: chain N residue 38 ARG Chi-restraints excluded: chain N residue 40 THR Chi-restraints excluded: chain N residue 67 VAL Chi-restraints excluded: chain N residue 75 VAL Chi-restraints excluded: chain N residue 86 ASP Chi-restraints excluded: chain O residue 23 CYS Chi-restraints excluded: chain O residue 47 LEU Chi-restraints excluded: chain O residue 73 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 267 random chunks: chunk 108 optimal weight: 0.8980 chunk 99 optimal weight: 4.9990 chunk 146 optimal weight: 4.9990 chunk 76 optimal weight: 0.9990 chunk 7 optimal weight: 0.7980 chunk 263 optimal weight: 1.9990 chunk 179 optimal weight: 0.5980 chunk 27 optimal weight: 0.5980 chunk 251 optimal weight: 0.0170 chunk 71 optimal weight: 0.9990 chunk 152 optimal weight: 2.9990 overall best weight: 0.5818 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 94 GLN A 224 GLN ** A 494 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 283 GLN B 494 GLN ** B 501 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 94 GLN C 225 GLN ** C 363 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 42 HIS I 42 HIS ** K 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4124 r_free = 0.4124 target = 0.164038 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3925 r_free = 0.3925 target = 0.147371 restraints weight = 33075.656| |-----------------------------------------------------------------------------| r_work (start): 0.3937 rms_B_bonded: 2.28 r_work: 0.3843 rms_B_bonded: 2.66 restraints_weight: 0.5000 r_work: 0.3692 rms_B_bonded: 4.78 restraints_weight: 0.2500 r_work (final): 0.3692 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3694 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3694 r_free = 0.3694 target_work(ls_wunit_k1) = 0.131 | | occupancies: max = 1.00 min = 1.00 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3694 r_free = 0.3694 target_work(ls_wunit_k1) = 0.131 | | occupancies: max = 1.00 min = 1.00 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3694 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6887 moved from start: 0.3169 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 21747 Z= 0.148 Angle : 0.624 8.680 29532 Z= 0.322 Chirality : 0.045 0.166 3387 Planarity : 0.004 0.057 3732 Dihedral : 4.884 34.210 2952 Min Nonbonded Distance : 2.335 Molprobity Statistics. All-atom Clashscore : 11.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.24 % Favored : 95.76 % Rotamer: Outliers : 5.08 % Allowed : 23.42 % Favored : 71.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 17.95 % 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: -0.24 (0.17), residues: 2718 helix: 1.21 (0.25), residues: 423 sheet: 0.03 (0.16), residues: 1047 loop : -0.73 (0.18), residues: 1248 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG M 18 TYR 0.021 0.002 TYR E 49 PHE 0.037 0.002 PHE A 505 TRP 0.021 0.002 TRP C 341 HIS 0.005 0.001 HIS E 42 Details of bonding type rmsd covalent geometry : bond 0.00340 (21714) covalent geometry : angle 0.62016 (29466) SS BOND : bond 0.00459 ( 33) SS BOND : angle 1.56377 ( 66) hydrogen bonds : bond 0.03727 ( 947) hydrogen bonds : angle 5.68831 ( 2367) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5436 Ramachandran restraints generated. 2718 Oldfield, 0 Emsley, 2718 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5436 Ramachandran restraints generated. 2718 Oldfield, 0 Emsley, 2718 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 552 residues out of total 2421 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 123 poor density : 429 time to evaluate : 0.859 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 97 MET cc_start: 0.7049 (mtm) cc_final: 0.6817 (mtm) REVERT: A 165 ASN cc_start: 0.7606 (m110) cc_final: 0.7348 (m110) REVERT: A 191 LYS cc_start: 0.7762 (mtpt) cc_final: 0.7382 (mtpt) REVERT: A 197 ASN cc_start: 0.8101 (t0) cc_final: 0.7811 (t0) REVERT: A 201 LYS cc_start: 0.7417 (OUTLIER) cc_final: 0.6996 (pttt) REVERT: A 204 LEU cc_start: 0.8378 (OUTLIER) cc_final: 0.8171 (mt) REVERT: A 227 ASN cc_start: 0.8136 (t0) cc_final: 0.7829 (t0) REVERT: A 251 MET cc_start: 0.7516 (ttm) cc_final: 0.7162 (ttm) REVERT: A 282 ARG cc_start: 0.7933 (OUTLIER) cc_final: 0.6933 (ttm-80) REVERT: A 289 MET cc_start: 0.7990 (tpt) cc_final: 0.7532 (tpt) REVERT: A 301 VAL cc_start: 0.8345 (m) cc_final: 0.7167 (p) REVERT: A 354 GLN cc_start: 0.7640 (OUTLIER) cc_final: 0.6952 (mt0) REVERT: A 361 GLN cc_start: 0.7448 (tm-30) cc_final: 0.6763 (tm-30) REVERT: A 457 TYR cc_start: 0.7128 (m-80) cc_final: 0.6801 (m-80) REVERT: A 501 GLN cc_start: 0.6621 (OUTLIER) cc_final: 0.5972 (pp30) REVERT: B 148 ILE cc_start: 0.7695 (pt) cc_final: 0.7459 (mm) REVERT: B 191 LYS cc_start: 0.7871 (mtpt) cc_final: 0.7493 (mtmt) REVERT: B 201 LYS cc_start: 0.7324 (OUTLIER) cc_final: 0.7022 (pttt) REVERT: B 224 GLN cc_start: 0.8351 (mt0) cc_final: 0.8094 (mt0) REVERT: B 264 MET cc_start: 0.7809 (mtp) cc_final: 0.7518 (mtt) REVERT: B 323 THR cc_start: 0.7348 (OUTLIER) cc_final: 0.7141 (t) REVERT: B 354 GLN cc_start: 0.7822 (OUTLIER) cc_final: 0.7490 (mm-40) REVERT: B 361 GLN cc_start: 0.7495 (tm-30) cc_final: 0.6741 (tm-30) REVERT: B 487 GLU cc_start: 0.6802 (OUTLIER) cc_final: 0.5765 (mp0) REVERT: C 68 LYS cc_start: 0.7019 (OUTLIER) cc_final: 0.6806 (tttm) REVERT: C 80 LYS cc_start: 0.8328 (ttpt) cc_final: 0.8091 (ttmt) REVERT: C 148 ILE cc_start: 0.8069 (pt) cc_final: 0.7828 (mm) REVERT: C 191 LYS cc_start: 0.7699 (mtpt) cc_final: 0.7392 (mtmt) REVERT: C 218 GLU cc_start: 0.8242 (mp0) cc_final: 0.7571 (mp0) REVERT: C 222 GLU cc_start: 0.7724 (pt0) cc_final: 0.7517 (pt0) REVERT: C 354 GLN cc_start: 0.7920 (OUTLIER) cc_final: 0.7596 (mm-40) REVERT: C 361 GLN cc_start: 0.7619 (tm-30) cc_final: 0.7014 (tm-30) REVERT: D 59 TYR cc_start: 0.7868 (m-10) cc_final: 0.7569 (m-80) REVERT: D 86 ASP cc_start: 0.4599 (OUTLIER) cc_final: 0.4235 (t0) REVERT: F 59 TYR cc_start: 0.7801 (m-10) cc_final: 0.7526 (m-80) REVERT: F 101 ASP cc_start: 0.6661 (OUTLIER) cc_final: 0.6005 (p0) REVERT: G 17 GLN cc_start: 0.6598 (mm110) cc_final: 0.6336 (mm-40) REVERT: H 36 TRP cc_start: 0.7274 (m100) cc_final: 0.6850 (m100) REVERT: H 59 TYR cc_start: 0.7881 (m-10) cc_final: 0.7529 (m-80) REVERT: H 103 TRP cc_start: 0.8031 (m-10) cc_final: 0.7675 (m-10) REVERT: I 81 GLU cc_start: 0.7078 (OUTLIER) cc_final: 0.6566 (mp0) REVERT: I 100 GLN cc_start: 0.7436 (mp10) cc_final: 0.6938 (mp10) REVERT: J 38 ARG cc_start: 0.7300 (OUTLIER) cc_final: 0.7046 (ttp80) REVERT: K 11 LEU cc_start: 0.7210 (tt) cc_final: 0.6485 (mp) REVERT: K 39 ARG cc_start: 0.6869 (mpt-90) cc_final: 0.6510 (mpt-90) REVERT: M 89 GLN cc_start: 0.7218 (OUTLIER) cc_final: 0.6427 (tp40) REVERT: N 86 ASP cc_start: 0.6963 (OUTLIER) cc_final: 0.6660 (t0) outliers start: 123 outliers final: 98 residues processed: 502 average time/residue: 0.1417 time to fit residues: 112.1824 Evaluate side-chains 542 residues out of total 2421 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 115 poor density : 427 time to evaluate : 0.737 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 61 LEU Chi-restraints excluded: chain A residue 67 ILE Chi-restraints excluded: chain A residue 72 THR Chi-restraints excluded: chain A residue 78 LEU Chi-restraints excluded: chain A residue 201 LYS Chi-restraints excluded: chain A residue 204 LEU Chi-restraints excluded: chain A residue 222 GLU Chi-restraints excluded: chain A residue 245 THR Chi-restraints excluded: chain A residue 282 ARG Chi-restraints excluded: chain A residue 292 ILE Chi-restraints excluded: chain A residue 296 VAL Chi-restraints excluded: chain A residue 311 THR Chi-restraints excluded: chain A residue 334 LEU Chi-restraints excluded: chain A residue 344 ASP Chi-restraints excluded: chain A residue 354 GLN Chi-restraints excluded: chain A residue 369 THR Chi-restraints excluded: chain A residue 381 LEU Chi-restraints excluded: chain A residue 414 VAL Chi-restraints excluded: chain A residue 482 VAL Chi-restraints excluded: chain A residue 501 GLN Chi-restraints excluded: chain B residue 40 VAL Chi-restraints excluded: chain B residue 42 LYS Chi-restraints excluded: chain B residue 72 THR Chi-restraints excluded: chain B residue 180 SER Chi-restraints excluded: chain B residue 201 LYS Chi-restraints excluded: chain B residue 222 GLU Chi-restraints excluded: chain B residue 245 THR Chi-restraints excluded: chain B residue 248 SER Chi-restraints excluded: chain B residue 273 LEU Chi-restraints excluded: chain B residue 283 GLN Chi-restraints excluded: chain B residue 296 VAL Chi-restraints excluded: chain B residue 308 VAL Chi-restraints excluded: chain B residue 311 THR Chi-restraints excluded: chain B residue 323 THR Chi-restraints excluded: chain B residue 337 THR Chi-restraints excluded: chain B residue 344 ASP Chi-restraints excluded: chain B residue 349 VAL Chi-restraints excluded: chain B residue 354 GLN Chi-restraints excluded: chain B residue 365 VAL Chi-restraints excluded: chain B residue 369 THR Chi-restraints excluded: chain B residue 379 VAL Chi-restraints excluded: chain B residue 381 LEU Chi-restraints excluded: chain B residue 431 ILE Chi-restraints excluded: chain B residue 467 LEU Chi-restraints excluded: chain B residue 487 GLU Chi-restraints excluded: chain C residue 67 ILE Chi-restraints excluded: chain C residue 68 LYS Chi-restraints excluded: chain C residue 72 THR Chi-restraints excluded: chain C residue 187 VAL Chi-restraints excluded: chain C residue 245 THR Chi-restraints excluded: chain C residue 273 LEU Chi-restraints excluded: chain C residue 292 ILE Chi-restraints excluded: chain C residue 311 THR Chi-restraints excluded: chain C residue 317 HIS Chi-restraints excluded: chain C residue 324 THR Chi-restraints excluded: chain C residue 337 THR Chi-restraints excluded: chain C residue 339 ARG Chi-restraints excluded: chain C residue 344 ASP Chi-restraints excluded: chain C residue 354 GLN Chi-restraints excluded: chain C residue 365 VAL Chi-restraints excluded: chain C residue 406 VAL Chi-restraints excluded: chain C residue 423 THR Chi-restraints excluded: chain C residue 482 VAL Chi-restraints excluded: chain D residue 11 VAL Chi-restraints excluded: chain D residue 45 LEU Chi-restraints excluded: chain D residue 70 THR Chi-restraints excluded: chain D residue 86 ASP Chi-restraints excluded: chain E residue 2 VAL Chi-restraints excluded: chain E residue 11 LEU Chi-restraints excluded: chain E residue 14 THR Chi-restraints excluded: chain E residue 27 LEU Chi-restraints excluded: chain E residue 69 THR Chi-restraints excluded: chain E residue 104 VAL Chi-restraints excluded: chain F residue 45 LEU Chi-restraints excluded: chain F residue 70 THR Chi-restraints excluded: chain F residue 95 ASP Chi-restraints excluded: chain F residue 101 ASP Chi-restraints excluded: chain F residue 105 GLN Chi-restraints excluded: chain G residue 2 VAL Chi-restraints excluded: chain G residue 14 THR Chi-restraints excluded: chain G residue 28 ASP Chi-restraints excluded: chain G residue 33 LEU Chi-restraints excluded: chain G residue 104 VAL Chi-restraints excluded: chain H residue 11 VAL Chi-restraints excluded: chain H residue 70 THR Chi-restraints excluded: chain H residue 99 VAL Chi-restraints excluded: chain H residue 101 ASP Chi-restraints excluded: chain I residue 3 VAL Chi-restraints excluded: chain I residue 7 SER Chi-restraints excluded: chain I residue 14 THR Chi-restraints excluded: chain I residue 27 LEU Chi-restraints excluded: chain I residue 33 LEU Chi-restraints excluded: chain I residue 81 GLU Chi-restraints excluded: chain J residue 38 ARG Chi-restraints excluded: chain J residue 40 THR Chi-restraints excluded: chain J residue 75 VAL Chi-restraints excluded: chain K residue 23 CYS Chi-restraints excluded: chain K residue 54 LEU Chi-restraints excluded: chain K residue 63 SER Chi-restraints excluded: chain K residue 73 LEU Chi-restraints excluded: chain L residue 40 THR Chi-restraints excluded: chain L residue 75 VAL Chi-restraints excluded: chain L residue 100 VAL Chi-restraints excluded: chain L residue 107 THR Chi-restraints excluded: chain M residue 23 CYS Chi-restraints excluded: chain M residue 73 LEU Chi-restraints excluded: chain M residue 89 GLN Chi-restraints excluded: chain N residue 38 ARG Chi-restraints excluded: chain N residue 40 THR Chi-restraints excluded: chain N residue 67 VAL Chi-restraints excluded: chain N residue 75 VAL Chi-restraints excluded: chain N residue 86 ASP Chi-restraints excluded: chain O residue 23 CYS Chi-restraints excluded: chain O residue 47 LEU Chi-restraints excluded: chain O residue 73 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 267 random chunks: chunk 175 optimal weight: 0.0270 chunk 134 optimal weight: 2.9990 chunk 26 optimal weight: 0.9990 chunk 166 optimal weight: 1.9990 chunk 226 optimal weight: 1.9990 chunk 260 optimal weight: 0.9990 chunk 163 optimal weight: 2.9990 chunk 47 optimal weight: 0.7980 chunk 142 optimal weight: 0.3980 chunk 236 optimal weight: 0.9980 chunk 227 optimal weight: 0.6980 overall best weight: 0.5838 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 94 GLN ** A 363 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 494 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 283 GLN B 494 GLN ** B 501 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 225 GLN C 331 ASN ** C 363 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 42 HIS I 42 HIS ** K 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 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 = 0.4125 r_free = 0.4125 target = 0.164143 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3927 r_free = 0.3927 target = 0.147474 restraints weight = 33119.027| |-----------------------------------------------------------------------------| r_work (start): 0.3940 rms_B_bonded: 2.29 r_work: 0.3846 rms_B_bonded: 2.67 restraints_weight: 0.5000 r_work: 0.3695 rms_B_bonded: 4.78 restraints_weight: 0.2500 r_work (final): 0.3695 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3697 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3697 r_free = 0.3697 target_work(ls_wunit_k1) = 0.131 | | occupancies: max = 1.00 min = 1.00 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3697 r_free = 0.3697 target_work(ls_wunit_k1) = 0.131 | | occupancies: max = 1.00 min = 1.00 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3697 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6883 moved from start: 0.3238 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 21747 Z= 0.147 Angle : 0.622 9.106 29532 Z= 0.321 Chirality : 0.045 0.166 3387 Planarity : 0.004 0.057 3732 Dihedral : 4.845 33.649 2951 Min Nonbonded Distance : 2.303 Molprobity Statistics. All-atom Clashscore : 11.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.60 % Favored : 95.40 % Rotamer: Outliers : 5.37 % Allowed : 23.09 % Favored : 71.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 17.95 % 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 (0.17), residues: 2718 helix: 1.51 (0.25), residues: 405 sheet: 0.03 (0.16), residues: 1047 loop : -0.67 (0.18), residues: 1266 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG M 18 TYR 0.021 0.002 TYR E 49 PHE 0.037 0.002 PHE A 505 TRP 0.020 0.002 TRP C 341 HIS 0.005 0.001 HIS E 42 Details of bonding type rmsd covalent geometry : bond 0.00338 (21714) covalent geometry : angle 0.61826 (29466) SS BOND : bond 0.00428 ( 33) SS BOND : angle 1.52392 ( 66) hydrogen bonds : bond 0.03670 ( 947) hydrogen bonds : angle 5.65524 ( 2367) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5597.40 seconds wall clock time: 96 minutes 34.34 seconds (5794.34 seconds total)