Starting phenix.real_space_refine on Mon Aug 25 12:07:52 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8cw9_27024/08_2025/8cw9_27024.cif Found real_map, /net/cci-nas-00/data/ceres_data/8cw9_27024/08_2025/8cw9_27024.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.46 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8cw9_27024/08_2025/8cw9_27024.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8cw9_27024/08_2025/8cw9_27024.map" model { file = "/net/cci-nas-00/data/ceres_data/8cw9_27024/08_2025/8cw9_27024.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8cw9_27024/08_2025/8cw9_27024.cif" } resolution = 3.46 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= 0.002 sd= 1.019 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 9645 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 135 5.16 5 C 12708 2.51 5 N 3420 2.21 5 O 3966 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 4 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 20229 Number of models: 1 Model: "" Number of chains: 18 Chain: "A" Number of atoms: 3260 Number of conformers: 1 Conformer: "" Number of residues, atoms: 430, 3260 Classifications: {'peptide': 430} Link IDs: {'PCIS': 1, 'PTRANS': 13, 'TRANS': 415} Chain breaks: 1 Chain: "B" Number of atoms: 786 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 786 Classifications: {'peptide': 107} Link IDs: {'PTRANS': 7, 'TRANS': 99} Chain: "C" Number of atoms: 963 Number of conformers: 1 Conformer: "B" Number of residues, atoms: 121, 963 Classifications: {'peptide': 121} Link IDs: {'PCIS': 1, 'PTRANS': 4, 'TRANS': 115} Chain: "D" Number of atoms: 797 Number of conformers: 1 Conformer: "" Number of residues, atoms: 106, 797 Classifications: {'peptide': 106} Link IDs: {'PTRANS': 7, 'TRANS': 98} Chain: "E" Number of atoms: 3260 Number of conformers: 1 Conformer: "" Number of residues, atoms: 430, 3260 Classifications: {'peptide': 430} Link IDs: {'PCIS': 1, 'PTRANS': 13, 'TRANS': 415} Chain breaks: 1 Chain: "F" Number of atoms: 3260 Number of conformers: 1 Conformer: "" Number of residues, atoms: 430, 3260 Classifications: {'peptide': 430} Link IDs: {'PCIS': 1, 'PTRANS': 13, 'TRANS': 415} Chain breaks: 1 Chain: "G" Number of atoms: 923 Number of conformers: 1 Conformer: "" Number of residues, atoms: 122, 923 Classifications: {'peptide': 122} Link IDs: {'PTRANS': 3, 'TRANS': 118} Chain: "H" Number of atoms: 963 Number of conformers: 1 Conformer: "B" Number of residues, atoms: 121, 963 Classifications: {'peptide': 121} Link IDs: {'PCIS': 1, 'PTRANS': 4, 'TRANS': 115} Chain: "I" Number of atoms: 963 Number of conformers: 1 Conformer: "B" Number of residues, atoms: 121, 963 Classifications: {'peptide': 121} Link IDs: {'PCIS': 1, 'PTRANS': 4, 'TRANS': 115} Chain: "J" Number of atoms: 923 Number of conformers: 1 Conformer: "" Number of residues, atoms: 122, 923 Classifications: {'peptide': 122} Link IDs: {'PTRANS': 3, 'TRANS': 118} Chain: "K" Number of atoms: 797 Number of conformers: 1 Conformer: "" Number of residues, atoms: 106, 797 Classifications: {'peptide': 106} Link IDs: {'PTRANS': 7, 'TRANS': 98} Chain: "L" Number of atoms: 797 Number of conformers: 1 Conformer: "" Number of residues, atoms: 106, 797 Classifications: {'peptide': 106} Link IDs: {'PTRANS': 7, 'TRANS': 98} Chain: "M" Number of atoms: 786 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 786 Classifications: {'peptide': 107} Link IDs: {'PTRANS': 7, 'TRANS': 99} Chain: "N" Number of atoms: 923 Number of conformers: 1 Conformer: "" Number of residues, atoms: 122, 923 Classifications: {'peptide': 122} Link IDs: {'PTRANS': 3, 'TRANS': 118} Chain: "O" Number of atoms: 786 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 786 Classifications: {'peptide': 107} Link IDs: {'PTRANS': 7, 'TRANS': 99} Chain: "A" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "E" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "F" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 5.48, per 1000 atoms: 0.27 Number of scatterers: 20229 At special positions: 0 Unit cell: (148.989, 144.889, 124.386, 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 135 16.00 O 3966 8.00 N 3420 7.00 C 12708 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=45, symmetry=0 Simple disulfide: pdb=" SG CYS A 28 " - pdb=" SG CYS A 407 " distance=2.03 Simple disulfide: pdb=" SG CYS A 60 " - pdb=" SG CYS A 182 " distance=2.03 Simple disulfide: pdb=" SG CYS A 110 " - pdb=" SG CYS A 322 " distance=2.03 Simple disulfide: pdb=" SG CYS A 127 " - pdb=" SG CYS A 153 " distance=2.03 Simple disulfide: pdb=" SG CYS A 140 " - pdb=" SG CYS A 147 " distance=2.03 Simple disulfide: pdb=" SG CYS A 283 " - pdb=" SG CYS A 311 " distance=2.03 Simple disulfide: pdb=" SG CYS A 292 " - pdb=" SG CYS A 301 " distance=2.03 Simple disulfide: pdb=" SG CYS A 326 " - pdb=" SG CYS A 335 " distance=2.03 Simple disulfide: pdb=" SG CYS A 350 " - pdb=" SG CYS A 361 " distance=2.03 Simple disulfide: pdb=" SG CYS A 365 " - pdb=" SG CYS A 463 " distance=2.03 Simple disulfide: pdb=" SG CYS A 384 " - pdb=" SG CYS A 390 " distance=2.03 Simple disulfide: pdb=" SG CYS B 22 " - pdb=" SG CYS B 90 " distance=2.03 Simple disulfide: pdb=" SG CYS C 22 " - pdb=" SG CYS C 92 " distance=2.03 Simple disulfide: pdb=" SG CYS D 23 " - pdb=" SG CYS D 88 " distance=2.03 Simple disulfide: pdb=" SG CYS E 28 " - pdb=" SG CYS E 407 " distance=2.03 Simple disulfide: pdb=" SG CYS E 60 " - pdb=" SG CYS E 182 " distance=2.03 Simple disulfide: pdb=" SG CYS E 110 " - pdb=" SG CYS E 322 " distance=2.03 Simple disulfide: pdb=" SG CYS E 127 " - pdb=" SG CYS E 153 " distance=2.03 Simple disulfide: pdb=" SG CYS E 140 " - pdb=" SG CYS E 147 " distance=2.03 Simple disulfide: pdb=" SG CYS E 283 " - pdb=" SG CYS E 311 " distance=2.03 Simple disulfide: pdb=" SG CYS E 292 " - pdb=" SG CYS E 301 " distance=2.03 Simple disulfide: pdb=" SG CYS E 326 " - pdb=" SG CYS E 335 " distance=2.03 Simple disulfide: pdb=" SG CYS E 350 " - pdb=" SG CYS E 361 " distance=2.03 Simple disulfide: pdb=" SG CYS E 365 " - pdb=" SG CYS E 463 " distance=2.03 Simple disulfide: pdb=" SG CYS E 384 " - pdb=" SG CYS E 390 " distance=2.03 Simple disulfide: pdb=" SG CYS F 28 " - pdb=" SG CYS F 407 " distance=2.03 Simple disulfide: pdb=" SG CYS F 60 " - pdb=" SG CYS F 182 " distance=2.03 Simple disulfide: pdb=" SG CYS F 110 " - pdb=" SG CYS F 322 " distance=2.03 Simple disulfide: pdb=" SG CYS F 127 " - pdb=" SG CYS F 153 " distance=2.03 Simple disulfide: pdb=" SG CYS F 140 " - pdb=" SG CYS F 147 " distance=2.03 Simple disulfide: pdb=" SG CYS F 283 " - pdb=" SG CYS F 311 " distance=2.03 Simple disulfide: pdb=" SG CYS F 292 " - pdb=" SG CYS F 301 " distance=2.03 Simple disulfide: pdb=" SG CYS F 326 " - pdb=" SG CYS F 335 " distance=2.03 Simple disulfide: pdb=" SG CYS F 350 " - pdb=" SG CYS F 361 " distance=2.03 Simple disulfide: pdb=" SG CYS F 365 " - pdb=" SG CYS F 463 " distance=2.03 Simple disulfide: pdb=" SG CYS F 384 " - pdb=" SG CYS F 390 " distance=2.03 Simple disulfide: pdb=" SG CYS G 22 " - pdb=" SG CYS G 96 " distance=2.03 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 92 " distance=2.03 Simple disulfide: pdb=" SG CYS I 22 " - pdb=" SG CYS I 92 " distance=2.03 Simple disulfide: pdb=" SG CYS J 22 " - pdb=" SG CYS J 96 " distance=2.03 Simple disulfide: pdb=" SG CYS K 23 " - pdb=" SG CYS K 88 " distance=2.03 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 88 " distance=2.03 Simple disulfide: pdb=" SG CYS M 22 " - pdb=" SG CYS M 90 " distance=2.03 Simple disulfide: pdb=" SG CYS N 22 " - pdb=" SG CYS N 96 " distance=2.03 Simple disulfide: pdb=" SG CYS O 22 " - pdb=" SG CYS O 90 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied NAG-ASN " NAG A 601 " - " ASN A 57 " " NAG E 601 " - " ASN E 57 " " NAG F 601 " - " ASN F 57 " Time building additional restraints: 1.87 Conformation dependent library (CDL) restraints added in 1.1 seconds Enol-peptide restraints added in 1.2 microseconds 5244 Ramachandran restraints generated. 2622 Oldfield, 0 Emsley, 2622 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4896 Finding SS restraints... Secondary structure from input PDB file: 58 helices and 54 sheets defined 20.3% alpha, 40.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.25 Creating SS restraints... Processing helix chain 'A' and resid 65 through 84 removed outlier: 3.657A pdb=" N VAL A 84 " --> pdb=" O GLU A 80 " (cutoff:3.500A) Processing helix chain 'A' and resid 104 through 129 removed outlier: 3.915A pdb=" N ILE A 108 " --> pdb=" O VAL A 104 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N ILE A 124 " --> pdb=" O ALA A 120 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N CYS A 127 " --> pdb=" O ALA A 123 " (cutoff:3.500A) Processing helix chain 'A' and resid 130 through 141 Processing helix chain 'A' and resid 163 through 171 Processing helix chain 'A' and resid 171 through 177 Processing helix chain 'A' and resid 178 through 181 Processing helix chain 'A' and resid 186 through 210 removed outlier: 4.025A pdb=" N ALA A 190 " --> pdb=" O ASP A 186 " (cutoff:3.500A) removed outlier: 4.410A pdb=" N ARG A 198 " --> pdb=" O SER A 194 " (cutoff:3.500A) removed outlier: 4.673A pdb=" N ARG A 199 " --> pdb=" O GLN A 195 " (cutoff:3.500A) removed outlier: 4.549A pdb=" N PHE A 200 " --> pdb=" O PHE A 196 " (cutoff:3.500A) Processing helix chain 'A' and resid 223 through 234 Processing helix chain 'A' and resid 237 through 247 Processing helix chain 'A' and resid 247 through 255 removed outlier: 3.515A pdb=" N VAL A 251 " --> pdb=" O ASN A 247 " (cutoff:3.500A) Processing helix chain 'A' and resid 344 through 347 Processing helix chain 'A' and resid 348 through 354 Processing helix chain 'A' and resid 441 through 446 Processing helix chain 'A' and resid 461 through 463 No H-bonds generated for 'chain 'A' and resid 461 through 463' Processing helix chain 'B' and resid 81 through 85 Processing helix chain 'C' and resid 83 through 87 Processing helix chain 'D' and resid 79 through 83 Processing helix chain 'E' and resid 65 through 84 Processing helix chain 'E' and resid 104 through 129 removed outlier: 4.008A pdb=" N ILE E 108 " --> pdb=" O VAL E 104 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N CYS E 127 " --> pdb=" O ALA E 123 " (cutoff:3.500A) Processing helix chain 'E' and resid 130 through 141 Processing helix chain 'E' and resid 163 through 171 Processing helix chain 'E' and resid 171 through 177 removed outlier: 3.601A pdb=" N ARG E 175 " --> pdb=" O LYS E 171 " (cutoff:3.500A) Processing helix chain 'E' and resid 187 through 197 Processing helix chain 'E' and resid 197 through 209 Processing helix chain 'E' and resid 223 through 234 Processing helix chain 'E' and resid 237 through 247 Processing helix chain 'E' and resid 247 through 255 Processing helix chain 'E' and resid 344 through 347 Processing helix chain 'E' and resid 348 through 354 Processing helix chain 'E' and resid 441 through 446 Processing helix chain 'E' and resid 461 through 463 No H-bonds generated for 'chain 'E' and resid 461 through 463' Processing helix chain 'F' and resid 65 through 84 Processing helix chain 'F' and resid 104 through 129 removed outlier: 4.229A pdb=" N ILE F 108 " --> pdb=" O VAL F 104 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N CYS F 127 " --> pdb=" O ALA F 123 " (cutoff:3.500A) Processing helix chain 'F' and resid 130 through 144 removed outlier: 4.275A pdb=" N LYS F 143 " --> pdb=" O ASN F 139 " (cutoff:3.500A) removed outlier: 3.921A pdb=" N THR F 144 " --> pdb=" O CYS F 140 " (cutoff:3.500A) Processing helix chain 'F' and resid 163 through 172 Processing helix chain 'F' and resid 172 through 177 Processing helix chain 'F' and resid 178 through 181 Processing helix chain 'F' and resid 187 through 210 removed outlier: 4.464A pdb=" N ARG F 198 " --> pdb=" O SER F 194 " (cutoff:3.500A) removed outlier: 4.640A pdb=" N ARG F 199 " --> pdb=" O GLN F 195 " (cutoff:3.500A) removed outlier: 4.572A pdb=" N PHE F 200 " --> pdb=" O PHE F 196 " (cutoff:3.500A) Processing helix chain 'F' and resid 223 through 234 Processing helix chain 'F' and resid 237 through 246 Processing helix chain 'F' and resid 247 through 255 Processing helix chain 'F' and resid 344 through 347 Processing helix chain 'F' and resid 348 through 354 removed outlier: 3.512A pdb=" N ILE F 354 " --> pdb=" O CYS F 350 " (cutoff:3.500A) Processing helix chain 'F' and resid 441 through 446 Processing helix chain 'F' and resid 461 through 463 No H-bonds generated for 'chain 'F' and resid 461 through 463' Processing helix chain 'G' and resid 28 through 32 Processing helix chain 'G' and resid 87 through 91 Processing helix chain 'H' and resid 83 through 87 Processing helix chain 'I' and resid 61 through 64 Processing helix chain 'I' and resid 83 through 87 Processing helix chain 'J' and resid 28 through 32 Processing helix chain 'J' and resid 87 through 91 Processing helix chain 'K' and resid 79 through 83 Processing helix chain 'L' and resid 79 through 83 Processing helix chain 'M' and resid 81 through 85 Processing helix chain 'N' and resid 28 through 32 Processing helix chain 'N' and resid 87 through 91 Processing helix chain 'O' and resid 81 through 85 Processing sheet with id=AA1, first strand: chain 'A' and resid 278 through 279 removed outlier: 3.702A pdb=" N VAL A 278 " --> pdb=" O LEU A 39 " (cutoff:3.500A) removed outlier: 3.949A pdb=" N GLY A 34 " --> pdb=" O CYS A 283 " (cutoff:3.500A) removed outlier: 6.112A pdb=" N CYS A 283 " --> pdb=" O GLY A 34 " (cutoff:3.500A) removed outlier: 4.102A pdb=" N TRP A 309 " --> pdb=" O TYR A 320 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 327 through 329 removed outlier: 6.727A pdb=" N GLU A 21 " --> pdb=" O HIS A 435 " (cutoff:3.500A) removed outlier: 7.495A pdb=" N ILE A 437 " --> pdb=" O GLU A 21 " (cutoff:3.500A) removed outlier: 6.551A pdb=" N TYR A 23 " --> pdb=" O ILE A 437 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 146 through 150 removed outlier: 8.303A pdb=" N ARG A 156 " --> pdb=" O TRP A 43 " (cutoff:3.500A) removed outlier: 5.476A pdb=" N THR A 45 " --> pdb=" O ARG A 156 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N LEU A 158 " --> pdb=" O THR A 45 " (cutoff:3.500A) removed outlier: 6.197A pdb=" N MET A 270 " --> pdb=" O LEU A 259 " (cutoff:3.500A) removed outlier: 5.250A pdb=" N LEU A 259 " --> pdb=" O MET A 270 " (cutoff:3.500A) removed outlier: 6.786A pdb=" N GLN A 272 " --> pdb=" O GLY A 257 " (cutoff:3.500A) removed outlier: 5.818A pdb=" N GLY A 257 " --> pdb=" O GLN A 272 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 291 through 293 removed outlier: 7.137A pdb=" N CYS A 365 " --> pdb=" O PHE A 456 " (cutoff:3.500A) removed outlier: 5.248A pdb=" N PHE A 456 " --> pdb=" O CYS A 365 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 372 through 376 Processing sheet with id=AA6, first strand: chain 'A' and resid 398 through 402 removed outlier: 6.798A pdb=" N ILE A 392 " --> pdb=" O ILE A 400 " (cutoff:3.500A) removed outlier: 4.652A pdb=" N GLN A 402 " --> pdb=" O CYS A 390 " (cutoff:3.500A) removed outlier: 7.040A pdb=" N CYS A 390 " --> pdb=" O GLN A 402 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 9 through 11 removed outlier: 6.647A pdb=" N TRP B 37 " --> pdb=" O LEU B 49 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 9 through 11 Processing sheet with id=AA9, first strand: chain 'B' and resid 18 through 22 Processing sheet with id=AB1, first strand: chain 'C' and resid 3 through 6 Processing sheet with id=AB2, first strand: chain 'C' and resid 57 through 59 removed outlier: 6.646A pdb=" N TRP C 36 " --> pdb=" O LEU C 48 " (cutoff:3.500A) removed outlier: 4.869A pdb=" N ARG C 50 " --> pdb=" O VAL C 35A" (cutoff:3.500A) removed outlier: 7.088A pdb=" N VAL C 35A" --> pdb=" O ARG C 50 " (cutoff:3.500A) removed outlier: 5.114A pdb=" N ASP C 52 " --> pdb=" O MET C 34 " (cutoff:3.500A) removed outlier: 7.270A pdb=" N MET C 34 " --> pdb=" O ASP C 52 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N LEU C 102 " --> pdb=" O ARG C 94 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 57 through 59 removed outlier: 6.646A pdb=" N TRP C 36 " --> pdb=" O LEU C 48 " (cutoff:3.500A) removed outlier: 4.869A pdb=" N ARG C 50 " --> pdb=" O VAL C 35A" (cutoff:3.500A) removed outlier: 7.088A pdb=" N VAL C 35A" --> pdb=" O ARG C 50 " (cutoff:3.500A) removed outlier: 5.114A pdb=" N ASP C 52 " --> pdb=" O MET C 34 " (cutoff:3.500A) removed outlier: 7.270A pdb=" N MET C 34 " --> pdb=" O ASP C 52 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'D' and resid 5 through 6 removed outlier: 3.817A pdb=" N THR D 72 " --> pdb=" O PHE D 65 " (cutoff:3.500A) removed outlier: 3.930A pdb=" N PHE D 65 " --> pdb=" O THR D 72 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'D' and resid 9 through 13 removed outlier: 6.451A pdb=" N TRP D 35 " --> pdb=" O LEU D 47 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'D' and resid 9 through 13 Processing sheet with id=AB7, first strand: chain 'E' and resid 278 through 279 removed outlier: 3.907A pdb=" N VAL E 278 " --> pdb=" O LEU E 39 " (cutoff:3.500A) removed outlier: 3.954A pdb=" N GLY E 34 " --> pdb=" O CYS E 283 " (cutoff:3.500A) removed outlier: 6.456A pdb=" N CYS E 283 " --> pdb=" O GLY E 34 " (cutoff:3.500A) removed outlier: 4.088A pdb=" N TRP E 309 " --> pdb=" O TYR E 320 " (cutoff:3.500A) removed outlier: 3.853A pdb=" N THR E 317 " --> pdb=" O VAL E 343 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'E' and resid 327 through 329 removed outlier: 6.823A pdb=" N GLU E 21 " --> pdb=" O HIS E 435 " (cutoff:3.500A) removed outlier: 7.636A pdb=" N ILE E 437 " --> pdb=" O GLU E 21 " (cutoff:3.500A) removed outlier: 6.293A pdb=" N TYR E 23 " --> pdb=" O ILE E 437 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'E' and resid 146 through 150 removed outlier: 8.160A pdb=" N ARG E 156 " --> pdb=" O TRP E 43 " (cutoff:3.500A) removed outlier: 5.203A pdb=" N THR E 45 " --> pdb=" O ARG E 156 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N LEU E 158 " --> pdb=" O THR E 45 " (cutoff:3.500A) removed outlier: 6.248A pdb=" N MET E 270 " --> pdb=" O LEU E 259 " (cutoff:3.500A) removed outlier: 5.259A pdb=" N LEU E 259 " --> pdb=" O MET E 270 " (cutoff:3.500A) removed outlier: 6.842A pdb=" N GLN E 272 " --> pdb=" O GLY E 257 " (cutoff:3.500A) removed outlier: 5.834A pdb=" N GLY E 257 " --> pdb=" O GLN E 272 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'E' and resid 291 through 293 removed outlier: 7.095A pdb=" N CYS E 365 " --> pdb=" O PHE E 456 " (cutoff:3.500A) removed outlier: 5.300A pdb=" N PHE E 456 " --> pdb=" O CYS E 365 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'E' and resid 372 through 376 Processing sheet with id=AC3, first strand: chain 'E' and resid 398 through 402 removed outlier: 6.890A pdb=" N ILE E 392 " --> pdb=" O ILE E 400 " (cutoff:3.500A) removed outlier: 4.740A pdb=" N GLN E 402 " --> pdb=" O CYS E 390 " (cutoff:3.500A) removed outlier: 7.149A pdb=" N CYS E 390 " --> pdb=" O GLN E 402 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'F' and resid 278 through 279 removed outlier: 3.844A pdb=" N VAL F 278 " --> pdb=" O LEU F 39 " (cutoff:3.500A) removed outlier: 4.057A pdb=" N GLY F 34 " --> pdb=" O CYS F 283 " (cutoff:3.500A) removed outlier: 6.133A pdb=" N CYS F 283 " --> pdb=" O GLY F 34 " (cutoff:3.500A) removed outlier: 4.077A pdb=" N TRP F 309 " --> pdb=" O TYR F 320 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'F' and resid 328 through 329 Processing sheet with id=AC6, first strand: chain 'F' and resid 146 through 150 removed outlier: 9.191A pdb=" N TRP F 43 " --> pdb=" O ARG F 156 " (cutoff:3.500A) removed outlier: 9.082A pdb=" N LEU F 158 " --> pdb=" O TRP F 43 " (cutoff:3.500A) removed outlier: 6.909A pdb=" N THR F 45 " --> pdb=" O LEU F 158 " (cutoff:3.500A) removed outlier: 7.716A pdb=" N THR F 160 " --> pdb=" O THR F 45 " (cutoff:3.500A) removed outlier: 6.062A pdb=" N VAL F 47 " --> pdb=" O THR F 160 " (cutoff:3.500A) removed outlier: 7.210A pdb=" N VAL F 162 " --> pdb=" O VAL F 47 " (cutoff:3.500A) removed outlier: 6.475A pdb=" N THR F 49 " --> pdb=" O VAL F 162 " (cutoff:3.500A) removed outlier: 6.267A pdb=" N MET F 270 " --> pdb=" O LEU F 259 " (cutoff:3.500A) removed outlier: 5.306A pdb=" N LEU F 259 " --> pdb=" O MET F 270 " (cutoff:3.500A) removed outlier: 6.766A pdb=" N GLN F 272 " --> pdb=" O GLY F 257 " (cutoff:3.500A) removed outlier: 6.051A pdb=" N GLY F 257 " --> pdb=" O GLN F 272 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'F' and resid 291 through 293 removed outlier: 7.248A pdb=" N CYS F 365 " --> pdb=" O PHE F 456 " (cutoff:3.500A) removed outlier: 5.423A pdb=" N PHE F 456 " --> pdb=" O CYS F 365 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'F' and resid 372 through 375 removed outlier: 3.518A pdb=" N CYS F 384 " --> pdb=" O GLY F 406 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'F' and resid 398 through 402 removed outlier: 6.973A pdb=" N ILE F 392 " --> pdb=" O ILE F 400 " (cutoff:3.500A) removed outlier: 4.814A pdb=" N GLN F 402 " --> pdb=" O CYS F 390 " (cutoff:3.500A) removed outlier: 7.100A pdb=" N CYS F 390 " --> pdb=" O GLN F 402 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'G' and resid 3 through 7 removed outlier: 3.517A pdb=" N GLN G 3 " --> pdb=" O SER G 25 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N SER G 78 " --> pdb=" O ASP G 73 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'G' and resid 10 through 11 removed outlier: 3.623A pdb=" N GLY G 10 " --> pdb=" O LEU G 119 " (cutoff:3.500A) removed outlier: 4.156A pdb=" N THR G 121 " --> pdb=" O GLY G 10 " (cutoff:3.500A) removed outlier: 4.097A pdb=" N SER G 33 " --> pdb=" O ALA G 99 " (cutoff:3.500A) removed outlier: 6.857A pdb=" N MET G 34 " --> pdb=" O SER G 50 " (cutoff:3.500A) removed outlier: 4.608A pdb=" N SER G 50 " --> pdb=" O MET G 34 " (cutoff:3.500A) removed outlier: 6.512A pdb=" N TRP G 36 " --> pdb=" O VAL G 48 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'G' and resid 10 through 11 removed outlier: 3.623A pdb=" N GLY G 10 " --> pdb=" O LEU G 119 " (cutoff:3.500A) removed outlier: 4.156A pdb=" N THR G 121 " --> pdb=" O GLY G 10 " (cutoff:3.500A) removed outlier: 6.983A pdb=" N CYS G 96 " --> pdb=" O TRP G 114 " (cutoff:3.500A) removed outlier: 4.837A pdb=" N TRP G 114 " --> pdb=" O CYS G 96 " (cutoff:3.500A) removed outlier: 6.825A pdb=" N ARG G 98 " --> pdb=" O ASP G 112 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'H' and resid 3 through 6 Processing sheet with id=AD5, first strand: chain 'H' and resid 57 through 59 removed outlier: 6.647A pdb=" N TRP H 36 " --> pdb=" O LEU H 48 " (cutoff:3.500A) removed outlier: 4.658A pdb=" N ARG H 50 " --> pdb=" O VAL H 35A" (cutoff:3.500A) removed outlier: 6.994A pdb=" N VAL H 35A" --> pdb=" O ARG H 50 " (cutoff:3.500A) removed outlier: 5.080A pdb=" N ASP H 52 " --> pdb=" O MET H 34 " (cutoff:3.500A) removed outlier: 7.356A pdb=" N MET H 34 " --> pdb=" O ASP H 52 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'H' and resid 57 through 59 removed outlier: 6.647A pdb=" N TRP H 36 " --> pdb=" O LEU H 48 " (cutoff:3.500A) removed outlier: 4.658A pdb=" N ARG H 50 " --> pdb=" O VAL H 35A" (cutoff:3.500A) removed outlier: 6.994A pdb=" N VAL H 35A" --> pdb=" O ARG H 50 " (cutoff:3.500A) removed outlier: 5.080A pdb=" N ASP H 52 " --> pdb=" O MET H 34 " (cutoff:3.500A) removed outlier: 7.356A pdb=" N MET H 34 " --> pdb=" O ASP H 52 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'I' and resid 5 through 6 removed outlier: 3.533A pdb=" N SER I 70 " --> pdb=" O VAL I 79 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'I' and resid 57 through 59 removed outlier: 6.668A pdb=" N TRP I 36 " --> pdb=" O LEU I 48 " (cutoff:3.500A) removed outlier: 4.775A pdb=" N ARG I 50 " --> pdb=" O VAL I 35A" (cutoff:3.500A) removed outlier: 7.061A pdb=" N VAL I 35A" --> pdb=" O ARG I 50 " (cutoff:3.500A) removed outlier: 5.108A pdb=" N ASP I 52 " --> pdb=" O MET I 34 " (cutoff:3.500A) removed outlier: 7.402A pdb=" N MET I 34 " --> pdb=" O ASP I 52 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N LEU I 102 " --> pdb=" O ARG I 94 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'I' and resid 57 through 59 removed outlier: 6.668A pdb=" N TRP I 36 " --> pdb=" O LEU I 48 " (cutoff:3.500A) removed outlier: 4.775A pdb=" N ARG I 50 " --> pdb=" O VAL I 35A" (cutoff:3.500A) removed outlier: 7.061A pdb=" N VAL I 35A" --> pdb=" O ARG I 50 " (cutoff:3.500A) removed outlier: 5.108A pdb=" N ASP I 52 " --> pdb=" O MET I 34 " (cutoff:3.500A) removed outlier: 7.402A pdb=" N MET I 34 " --> pdb=" O ASP I 52 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'J' and resid 3 through 7 removed outlier: 3.780A pdb=" N ALA J 23 " --> pdb=" O VAL J 5 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N SER J 78 " --> pdb=" O ASP J 73 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'J' and resid 58 through 60 removed outlier: 6.499A pdb=" N TRP J 36 " --> pdb=" O VAL J 48 " (cutoff:3.500A) removed outlier: 4.678A pdb=" N SER J 50 " --> pdb=" O MET J 34 " (cutoff:3.500A) removed outlier: 7.031A pdb=" N MET J 34 " --> pdb=" O SER J 50 " (cutoff:3.500A) removed outlier: 4.010A pdb=" N SER J 33 " --> pdb=" O ALA J 99 " (cutoff:3.500A) removed outlier: 6.914A pdb=" N CYS J 96 " --> pdb=" O TRP J 114 " (cutoff:3.500A) removed outlier: 4.813A pdb=" N TRP J 114 " --> pdb=" O CYS J 96 " (cutoff:3.500A) removed outlier: 6.845A pdb=" N ARG J 98 " --> pdb=" O ASP J 112 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'J' and resid 58 through 60 removed outlier: 6.499A pdb=" N TRP J 36 " --> pdb=" O VAL J 48 " (cutoff:3.500A) removed outlier: 4.678A pdb=" N SER J 50 " --> pdb=" O MET J 34 " (cutoff:3.500A) removed outlier: 7.031A pdb=" N MET J 34 " --> pdb=" O SER J 50 " (cutoff:3.500A) removed outlier: 4.010A pdb=" N SER J 33 " --> pdb=" O ALA J 99 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'K' and resid 5 through 6 removed outlier: 3.689A pdb=" N PHE K 65 " --> pdb=" O THR K 72 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'K' and resid 9 through 13 Processing sheet with id=AE6, first strand: chain 'K' and resid 45 through 48 removed outlier: 6.379A pdb=" N TRP K 35 " --> pdb=" O LEU K 47 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'L' and resid 5 through 6 removed outlier: 5.633A pdb=" N GLN L 17 " --> pdb=" O GLY L 77 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'L' and resid 9 through 13 removed outlier: 6.551A pdb=" N VAL L 11 " --> pdb=" O THR L 105 " (cutoff:3.500A) removed outlier: 6.543A pdb=" N TRP L 35 " --> pdb=" O LEU L 47 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'L' and resid 9 through 13 removed outlier: 6.551A pdb=" N VAL L 11 " --> pdb=" O THR L 105 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'M' and resid 9 through 11 removed outlier: 6.331A pdb=" N TRP M 37 " --> pdb=" O LEU M 49 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'M' and resid 9 through 11 Processing sheet with id=AF3, first strand: chain 'M' and resid 18 through 23 Processing sheet with id=AF4, first strand: chain 'N' and resid 3 through 7 removed outlier: 3.571A pdb=" N SER N 78 " --> pdb=" O ASP N 73 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'N' and resid 58 through 60 removed outlier: 6.477A pdb=" N TRP N 36 " --> pdb=" O VAL N 48 " (cutoff:3.500A) removed outlier: 4.622A pdb=" N SER N 50 " --> pdb=" O MET N 34 " (cutoff:3.500A) removed outlier: 6.992A pdb=" N MET N 34 " --> pdb=" O SER N 50 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N SER N 33 " --> pdb=" O ALA N 99 " (cutoff:3.500A) removed outlier: 6.937A pdb=" N CYS N 96 " --> pdb=" O TRP N 114 " (cutoff:3.500A) removed outlier: 4.842A pdb=" N TRP N 114 " --> pdb=" O CYS N 96 " (cutoff:3.500A) removed outlier: 6.790A pdb=" N ARG N 98 " --> pdb=" O ASP N 112 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'N' and resid 58 through 60 removed outlier: 6.477A pdb=" N TRP N 36 " --> pdb=" O VAL N 48 " (cutoff:3.500A) removed outlier: 4.622A pdb=" N SER N 50 " --> pdb=" O MET N 34 " (cutoff:3.500A) removed outlier: 6.992A pdb=" N MET N 34 " --> pdb=" O SER N 50 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N SER N 33 " --> pdb=" O ALA N 99 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'O' and resid 9 through 11 removed outlier: 6.403A pdb=" N TRP O 37 " --> pdb=" O LEU O 49 " (cutoff:3.500A) Processing sheet with id=AF8, first strand: chain 'O' and resid 9 through 11 Processing sheet with id=AF9, first strand: chain 'O' and resid 18 through 22 removed outlier: 3.639A pdb=" N ALA O 73 " --> pdb=" O CYS O 22 " (cutoff:3.500A) 1010 hydrogen bonds defined for protein. 2550 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: 4.83 Time building geometry restraints manager: 2.50 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 6550 1.34 - 1.46: 4648 1.46 - 1.58: 9235 1.58 - 1.70: 0 1.70 - 1.83: 177 Bond restraints: 20610 Sorted by residual: bond pdb=" N GLY F 366 " pdb=" CA GLY F 366 " ideal model delta sigma weight residual 1.447 1.476 -0.029 9.20e-03 1.18e+04 9.90e+00 bond pdb=" CA ARG F 367 " pdb=" C ARG F 367 " ideal model delta sigma weight residual 1.528 1.504 0.024 1.04e-02 9.25e+03 5.32e+00 bond pdb=" C ARG F 367 " pdb=" N HIS F 368 " ideal model delta sigma weight residual 1.333 1.304 0.029 1.37e-02 5.33e+03 4.61e+00 bond pdb=" C1 NAG F 601 " pdb=" C2 NAG F 601 " ideal model delta sigma weight residual 1.532 1.496 0.036 2.00e-02 2.50e+03 3.29e+00 bond pdb=" C CYS F 365 " pdb=" N GLY F 366 " ideal model delta sigma weight residual 1.325 1.342 -0.017 1.06e-02 8.90e+03 2.58e+00 ... (remaining 20605 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.61: 27070 1.61 - 3.22: 772 3.22 - 4.83: 101 4.83 - 6.44: 24 6.44 - 8.05: 11 Bond angle restraints: 27978 Sorted by residual: angle pdb=" N GLY G 9 " pdb=" CA GLY G 9 " pdb=" C GLY G 9 " ideal model delta sigma weight residual 110.80 117.46 -6.66 1.71e+00 3.42e-01 1.52e+01 angle pdb=" CA GLY F 366 " pdb=" C GLY F 366 " pdb=" O GLY F 366 " ideal model delta sigma weight residual 121.48 117.88 3.60 9.90e-01 1.02e+00 1.32e+01 angle pdb=" N ARG F 367 " pdb=" CA ARG F 367 " pdb=" C ARG F 367 " ideal model delta sigma weight residual 109.71 104.66 5.05 1.41e+00 5.03e-01 1.28e+01 angle pdb=" CA CYS E 140 " pdb=" CB CYS E 140 " pdb=" SG CYS E 140 " ideal model delta sigma weight residual 114.40 122.45 -8.05 2.30e+00 1.89e-01 1.22e+01 angle pdb=" CA CYS F 140 " pdb=" CB CYS F 140 " pdb=" SG CYS F 140 " ideal model delta sigma weight residual 114.40 122.26 -7.86 2.30e+00 1.89e-01 1.17e+01 ... (remaining 27973 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.53: 11448 17.53 - 35.05: 833 35.05 - 52.58: 157 52.58 - 70.10: 51 70.10 - 87.63: 15 Dihedral angle restraints: 12504 sinusoidal: 4863 harmonic: 7641 Sorted by residual: dihedral pdb=" CB CYS F 365 " pdb=" SG CYS F 365 " pdb=" SG CYS F 463 " pdb=" CB CYS F 463 " ideal model delta sinusoidal sigma weight residual 93.00 157.75 -64.75 1 1.00e+01 1.00e-02 5.50e+01 dihedral pdb=" CB CYS A 365 " pdb=" SG CYS A 365 " pdb=" SG CYS A 463 " pdb=" CB CYS A 463 " ideal model delta sinusoidal sigma weight residual 93.00 150.48 -57.48 1 1.00e+01 1.00e-02 4.44e+01 dihedral pdb=" CB CYS E 365 " pdb=" SG CYS E 365 " pdb=" SG CYS E 463 " pdb=" CB CYS E 463 " ideal model delta sinusoidal sigma weight residual 93.00 149.22 -56.22 1 1.00e+01 1.00e-02 4.26e+01 ... (remaining 12501 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.041: 2205 0.041 - 0.082: 728 0.082 - 0.122: 255 0.122 - 0.163: 43 0.163 - 0.204: 6 Chirality restraints: 3237 Sorted by residual: chirality pdb=" CA TRP I 100 " pdb=" N TRP I 100 " pdb=" C TRP I 100 " pdb=" CB TRP I 100 " both_signs ideal model delta sigma weight residual False 2.51 2.31 0.20 2.00e-01 2.50e+01 1.04e+00 chirality pdb=" CA ASP A 280 " pdb=" N ASP A 280 " pdb=" C ASP A 280 " pdb=" CB ASP A 280 " both_signs ideal model delta sigma weight residual False 2.51 2.32 0.19 2.00e-01 2.50e+01 9.29e-01 chirality pdb=" CA ASN M 54 " pdb=" N ASN M 54 " pdb=" C ASN M 54 " pdb=" CB ASN M 54 " both_signs ideal model delta sigma weight residual False 2.51 2.32 0.19 2.00e-01 2.50e+01 8.87e-01 ... (remaining 3234 not shown) Planarity restraints: 3567 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG E 367 " 0.260 9.50e-02 1.11e+02 1.17e-01 1.09e+01 pdb=" NE ARG E 367 " -0.025 2.00e-02 2.50e+03 pdb=" CZ ARG E 367 " 0.025 2.00e-02 2.50e+03 pdb=" NH1 ARG E 367 " -0.012 2.00e-02 2.50e+03 pdb=" NH2 ARG E 367 " 0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG O 56 " -0.253 9.50e-02 1.11e+02 1.14e-01 1.01e+01 pdb=" NE ARG O 56 " 0.024 2.00e-02 2.50e+03 pdb=" CZ ARG O 56 " -0.023 2.00e-02 2.50e+03 pdb=" NH1 ARG O 56 " 0.011 2.00e-02 2.50e+03 pdb=" NH2 ARG O 56 " -0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG M 63 " 0.221 9.50e-02 1.11e+02 1.00e-01 8.25e+00 pdb=" NE ARG M 63 " -0.022 2.00e-02 2.50e+03 pdb=" CZ ARG M 63 " 0.023 2.00e-02 2.50e+03 pdb=" NH1 ARG M 63 " -0.011 2.00e-02 2.50e+03 pdb=" NH2 ARG M 63 " -0.001 2.00e-02 2.50e+03 ... (remaining 3564 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 1300 2.74 - 3.28: 20986 3.28 - 3.82: 33876 3.82 - 4.36: 41780 4.36 - 4.90: 72124 Nonbonded interactions: 170066 Sorted by model distance: nonbonded pdb=" OG SER E 376 " pdb=" O GLY E 379 " model vdw 2.196 3.040 nonbonded pdb=" O PRO F 290 " pdb=" OH TYR F 385 " model vdw 2.207 3.040 nonbonded pdb=" OD1 ASN F 422 " pdb=" NH2 ARG G 100 " model vdw 2.212 3.120 nonbonded pdb=" OD1 ASN A 422 " pdb=" NH2 ARG J 100 " model vdw 2.243 3.120 nonbonded pdb=" O GLN A 307 " pdb=" OH TYR A 319 " model vdw 2.267 3.040 ... (remaining 170061 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.01 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'E' selection = chain 'F' } ncs_group { reference = chain 'B' selection = chain 'M' selection = chain 'O' } ncs_group { reference = chain 'C' selection = chain 'H' selection = chain 'I' } ncs_group { reference = chain 'D' selection = chain 'K' selection = chain 'L' } ncs_group { reference = chain 'G' selection = chain 'J' selection = chain 'N' } 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: 1.360 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: 0.020 Extract box with map and model: 0.320 Check model and map are aligned: 0.060 Set scattering table: 0.060 Process input model: 22.270 Find NCS groups from input model: 0.430 Set up NCS constraints: 0.070 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:1.490 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 26.150 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7021 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 : 0.002 0.036 20658 Z= 0.116 Angle : 0.669 8.050 28077 Z= 0.372 Chirality : 0.046 0.204 3237 Planarity : 0.009 0.117 3564 Dihedral : 13.445 87.628 7473 Min Nonbonded Distance : 2.196 Molprobity Statistics. All-atom Clashscore : 3.46 Ramachandran Plot: Outliers : 0.11 % Allowed : 5.74 % Favored : 94.14 % Rotamer: Outliers : 1.25 % Allowed : 4.99 % Favored : 93.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.23 (0.16), residues: 2622 helix: -1.71 (0.20), residues: 393 sheet: -0.22 (0.18), residues: 774 loop : -0.82 (0.16), residues: 1455 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.028 0.004 ARG E 367 TYR 0.029 0.005 TYR A 44 PHE 0.018 0.002 PHE A 334 TRP 0.020 0.002 TRP E 43 HIS 0.004 0.001 HIS E 435 Details of bonding type rmsd covalent geometry : bond 0.00231 (20610) covalent geometry : angle 0.66528 (27978) SS BOND : bond 0.00248 ( 45) SS BOND : angle 1.41852 ( 90) hydrogen bonds : bond 0.21491 ( 924) hydrogen bonds : angle 9.40359 ( 2550) link_NAG-ASN : bond 0.00180 ( 3) link_NAG-ASN : angle 1.13202 ( 9) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5244 Ramachandran restraints generated. 2622 Oldfield, 0 Emsley, 2622 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5244 Ramachandran restraints generated. 2622 Oldfield, 0 Emsley, 2622 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 764 residues out of total 2244 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 736 time to evaluate : 0.778 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 21 GLU cc_start: 0.6335 (tt0) cc_final: 0.5808 (tt0) REVERT: A 26 GLU cc_start: 0.7466 (pt0) cc_final: 0.7211 (pt0) REVERT: A 35 TYR cc_start: 0.7963 (m-80) cc_final: 0.7418 (m-80) REVERT: A 72 ASP cc_start: 0.6520 (m-30) cc_final: 0.6066 (m-30) REVERT: A 103 PHE cc_start: 0.7830 (m-80) cc_final: 0.7312 (m-10) REVERT: A 110 CYS cc_start: 0.4909 (m) cc_final: 0.3743 (m) REVERT: A 171 LYS cc_start: 0.7589 (mtmt) cc_final: 0.7329 (mtmt) REVERT: A 234 MET cc_start: 0.8091 (ptp) cc_final: 0.7600 (ptm) REVERT: A 269 TYR cc_start: 0.7345 (p90) cc_final: 0.6927 (p90) REVERT: A 299 TYR cc_start: 0.8083 (m-80) cc_final: 0.7523 (m-80) REVERT: A 327 GLU cc_start: 0.7353 (pt0) cc_final: 0.6740 (pt0) REVERT: A 331 ASP cc_start: 0.7875 (t0) cc_final: 0.7432 (t0) REVERT: A 337 THR cc_start: 0.8111 (p) cc_final: 0.7596 (t) REVERT: A 359 TYR cc_start: 0.7307 (t80) cc_final: 0.7086 (t80) REVERT: A 367 ARG cc_start: 0.7573 (ptt-90) cc_final: 0.7352 (ptp90) REVERT: A 409 TYR cc_start: 0.8102 (t80) cc_final: 0.6970 (t80) REVERT: A 410 ILE cc_start: 0.8455 (mm) cc_final: 0.8236 (mm) REVERT: A 428 SER cc_start: 0.7573 (m) cc_final: 0.6997 (p) REVERT: A 433 GLU cc_start: 0.6972 (tt0) cc_final: 0.6767 (tt0) REVERT: A 440 ARG cc_start: 0.7188 (ttm170) cc_final: 0.6843 (ptm-80) REVERT: B 68 LYS cc_start: 0.7737 (tttm) cc_final: 0.7468 (ttpt) REVERT: C 34 MET cc_start: 0.6481 (mmt) cc_final: 0.6240 (mmt) REVERT: C 91 TYR cc_start: 0.6730 (m-80) cc_final: 0.6362 (m-80) REVERT: D 34 HIS cc_start: 0.5611 (m-70) cc_final: 0.4700 (m-70) REVERT: D 79 GLN cc_start: 0.7254 (pp30) cc_final: 0.6613 (pp30) REVERT: E 24 LEU cc_start: 0.8257 (mp) cc_final: 0.7985 (mp) REVERT: E 29 SER cc_start: 0.7822 (t) cc_final: 0.7520 (p) REVERT: E 51 GLU cc_start: 0.7001 (mm-30) cc_final: 0.6707 (mm-30) REVERT: E 85 SER cc_start: 0.7181 (t) cc_final: 0.6800 (m) REVERT: E 129 ARG cc_start: 0.7364 (ptp-110) cc_final: 0.7117 (ttp80) REVERT: E 178 ASN cc_start: 0.7636 (m-40) cc_final: 0.7362 (m-40) REVERT: E 269 TYR cc_start: 0.7303 (p90) cc_final: 0.6791 (p90) REVERT: E 270 MET cc_start: 0.7365 (ptm) cc_final: 0.6958 (ptm) REVERT: E 349 GLU cc_start: 0.6909 (tp30) cc_final: 0.5663 (tp30) REVERT: E 353 ASN cc_start: 0.7219 (m-40) cc_final: 0.6224 (p0) REVERT: E 364 SER cc_start: 0.7042 (t) cc_final: 0.6336 (m) REVERT: E 400 ILE cc_start: 0.7989 (mt) cc_final: 0.7766 (mm) REVERT: E 410 ILE cc_start: 0.8164 (mm) cc_final: 0.7922 (mm) REVERT: E 412 ASN cc_start: 0.6770 (m-40) cc_final: 0.6362 (m-40) REVERT: E 433 GLU cc_start: 0.7096 (tt0) cc_final: 0.6813 (tt0) REVERT: E 438 LYS cc_start: 0.7708 (mttm) cc_final: 0.7464 (mttm) REVERT: E 442 VAL cc_start: 0.8306 (m) cc_final: 0.7914 (t) REVERT: F 27 SER cc_start: 0.8321 (t) cc_final: 0.7929 (p) REVERT: F 35 TYR cc_start: 0.7893 (m-80) cc_final: 0.7257 (m-80) REVERT: F 51 GLU cc_start: 0.7317 (mm-30) cc_final: 0.6945 (mm-30) REVERT: F 56 GLU cc_start: 0.6806 (mt-10) cc_final: 0.6582 (mt-10) REVERT: F 62 ASP cc_start: 0.7435 (t0) cc_final: 0.6984 (t0) REVERT: F 68 LYS cc_start: 0.8465 (tttp) cc_final: 0.7808 (tttm) REVERT: F 72 ASP cc_start: 0.6873 (m-30) cc_final: 0.6592 (m-30) REVERT: F 80 GLU cc_start: 0.6543 (mt-10) cc_final: 0.6177 (mt-10) REVERT: F 85 SER cc_start: 0.7684 (t) cc_final: 0.7406 (m) REVERT: F 126 LYS cc_start: 0.7346 (mmtt) cc_final: 0.7045 (mmtp) REVERT: F 178 ASN cc_start: 0.7995 (m-40) cc_final: 0.7759 (m-40) REVERT: F 188 LYS cc_start: 0.7447 (ttmm) cc_final: 0.7225 (ttmm) REVERT: F 193 PHE cc_start: 0.7502 (t80) cc_final: 0.6872 (t80) REVERT: F 197 ASN cc_start: 0.7562 (p0) cc_final: 0.7201 (p0) REVERT: F 202 ASN cc_start: 0.7121 (m-40) cc_final: 0.6705 (m110) REVERT: F 222 MET cc_start: 0.8018 (ttp) cc_final: 0.7798 (ttm) REVERT: F 234 MET cc_start: 0.8259 (ptp) cc_final: 0.8049 (ptm) REVERT: F 244 MET cc_start: 0.7189 (mtm) cc_final: 0.6967 (mtt) REVERT: F 331 ASP cc_start: 0.7629 (t0) cc_final: 0.7266 (t0) REVERT: F 345 GLU cc_start: 0.6878 (tp30) cc_final: 0.6407 (tp30) REVERT: F 348 LYS cc_start: 0.7544 (ptpt) cc_final: 0.7308 (ptpt) REVERT: F 386 LYS cc_start: 0.7498 (mmtm) cc_final: 0.7194 (mmtm) REVERT: F 412 ASN cc_start: 0.6862 (m-40) cc_final: 0.6294 (m-40) REVERT: F 428 SER cc_start: 0.7426 (m) cc_final: 0.7078 (p) REVERT: F 437 ILE cc_start: 0.8493 (mm) cc_final: 0.8115 (mt) REVERT: F 440 ARG cc_start: 0.7218 (ttm170) cc_final: 0.6922 (ptm160) REVERT: F 462 GLN cc_start: 0.7755 (tt0) cc_final: 0.7517 (tt0) REVERT: G 11 LEU cc_start: 0.7907 (tp) cc_final: 0.7685 (tp) REVERT: G 94 TYR cc_start: 0.7019 (m-80) cc_final: 0.6780 (m-80) REVERT: G 116 GLN cc_start: 0.7749 (mm-40) cc_final: 0.7542 (mm-40) REVERT: H 45 LEU cc_start: 0.8219 (mp) cc_final: 0.7959 (mt) REVERT: H 52 ASP cc_start: 0.7337 (p0) cc_final: 0.7092 (p0) REVERT: H 87 THR cc_start: 0.7510 (m) cc_final: 0.7241 (p) REVERT: H 96 TYR cc_start: 0.8473 (t80) cc_final: 0.8077 (t80) REVERT: I 34 MET cc_start: 0.6484 (mmt) cc_final: 0.6093 (mmt) REVERT: J 5 VAL cc_start: 0.6930 (t) cc_final: 0.6718 (m) REVERT: J 65 LYS cc_start: 0.7841 (tttt) cc_final: 0.7519 (tttt) REVERT: J 108 THR cc_start: 0.7769 (t) cc_final: 0.7467 (t) REVERT: K 34 HIS cc_start: 0.5746 (m-70) cc_final: 0.5190 (m-70) REVERT: K 93 SER cc_start: 0.8687 (t) cc_final: 0.8263 (t) REVERT: L 48 MET cc_start: 0.6808 (mmm) cc_final: 0.6380 (mmm) REVERT: L 75 ILE cc_start: 0.8332 (mt) cc_final: 0.8106 (mt) REVERT: L 76 SER cc_start: 0.8494 (m) cc_final: 0.8193 (p) REVERT: L 87 TYR cc_start: 0.7654 (m-80) cc_final: 0.7428 (m-10) REVERT: M 47 LYS cc_start: 0.7317 (tttt) cc_final: 0.6981 (tttt) REVERT: M 53 ASN cc_start: 0.7063 (m-40) cc_final: 0.6747 (m110) REVERT: M 64 PHE cc_start: 0.6703 (m-80) cc_final: 0.6497 (m-80) REVERT: M 68 LYS cc_start: 0.8244 (tttm) cc_final: 0.7743 (ttpt) REVERT: N 5 VAL cc_start: 0.6424 (t) cc_final: 0.5946 (m) REVERT: N 93 ILE cc_start: 0.8228 (mt) cc_final: 0.7774 (tt) REVERT: N 111 PHE cc_start: 0.7865 (m-10) cc_final: 0.7640 (m-10) REVERT: N 119 LEU cc_start: 0.8017 (tp) cc_final: 0.7749 (tt) REVERT: O 35 VAL cc_start: 0.7822 (t) cc_final: 0.7500 (p) REVERT: O 37 TRP cc_start: 0.8187 (m100) cc_final: 0.7847 (m-90) REVERT: O 53 ASN cc_start: 0.7541 (m-40) cc_final: 0.7212 (m110) outliers start: 28 outliers final: 8 residues processed: 756 average time/residue: 0.1708 time to fit residues: 192.1825 Evaluate side-chains 608 residues out of total 2244 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 600 time to evaluate : 0.754 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 204 VAL Chi-restraints excluded: chain B residue 22 CYS Chi-restraints excluded: chain D residue 107 LEU Chi-restraints excluded: chain E residue 204 VAL Chi-restraints excluded: chain F residue 376 SER Chi-restraints excluded: chain F residue 463 CYS Chi-restraints excluded: chain G residue 108 THR Chi-restraints excluded: chain J residue 59 ASP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 261 random chunks: chunk 197 optimal weight: 1.9990 chunk 215 optimal weight: 5.9990 chunk 20 optimal weight: 0.8980 chunk 132 optimal weight: 0.0980 chunk 248 optimal weight: 2.9990 chunk 207 optimal weight: 0.6980 chunk 155 optimal weight: 0.9980 chunk 244 optimal weight: 0.0980 chunk 183 optimal weight: 0.2980 chunk 111 optimal weight: 3.9990 chunk 258 optimal weight: 6.9990 overall best weight: 0.4180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 247 ASN A 307 GLN A 353 ASN A 455 GLN ** D 34 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 272 GLN E 346 GLN E 353 ASN F 139 ASN F 195 GLN F 353 ASN F 455 GLN H 16 GLN ** K 34 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N 35 ASN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3722 r_free = 0.3722 target = 0.134604 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3486 r_free = 0.3486 target = 0.117483 restraints weight = 31241.740| |-----------------------------------------------------------------------------| r_work (start): 0.3477 rms_B_bonded: 2.13 r_work: 0.3372 rms_B_bonded: 2.43 restraints_weight: 0.5000 r_work: 0.3223 rms_B_bonded: 4.26 restraints_weight: 0.2500 r_work (final): 0.3223 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3223 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3223 r_free = 0.3223 target_work(ls_wunit_k1) = 0.101 | | occupancies: max = 1.00 min = 1.00 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3223 r_free = 0.3223 target_work(ls_wunit_k1) = 0.101 | | occupancies: max = 1.00 min = 0.65 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3223 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7405 moved from start: 0.2165 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 20658 Z= 0.139 Angle : 0.653 8.212 28077 Z= 0.351 Chirality : 0.047 0.240 3237 Planarity : 0.005 0.048 3564 Dihedral : 6.116 47.365 2932 Min Nonbonded Distance : 2.469 Molprobity Statistics. All-atom Clashscore : 7.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.06 % Favored : 96.94 % Rotamer: Outliers : 2.67 % Allowed : 12.12 % Favored : 85.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.13 (0.16), residues: 2622 helix: 0.44 (0.26), residues: 399 sheet: -0.19 (0.18), residues: 786 loop : -0.05 (0.17), residues: 1437 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG I 50 TYR 0.027 0.002 TYR A 385 PHE 0.020 0.002 PHE J 29 TRP 0.016 0.002 TRP J 36 HIS 0.005 0.001 HIS K 34 Details of bonding type rmsd covalent geometry : bond 0.00296 (20610) covalent geometry : angle 0.64433 (27978) SS BOND : bond 0.00384 ( 45) SS BOND : angle 1.93029 ( 90) hydrogen bonds : bond 0.03978 ( 924) hydrogen bonds : angle 6.30673 ( 2550) link_NAG-ASN : bond 0.00303 ( 3) link_NAG-ASN : angle 0.90238 ( 9) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5244 Ramachandran restraints generated. 2622 Oldfield, 0 Emsley, 2622 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5244 Ramachandran restraints generated. 2622 Oldfield, 0 Emsley, 2622 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 690 residues out of total 2244 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 630 time to evaluate : 0.782 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 21 GLU cc_start: 0.6884 (tt0) cc_final: 0.6660 (tt0) REVERT: A 35 TYR cc_start: 0.8104 (m-80) cc_final: 0.7612 (m-80) REVERT: A 62 ASP cc_start: 0.8069 (t0) cc_final: 0.7778 (t0) REVERT: A 72 ASP cc_start: 0.7311 (m-30) cc_final: 0.6838 (m-30) REVERT: A 83 THR cc_start: 0.7490 (m) cc_final: 0.7149 (t) REVERT: A 103 PHE cc_start: 0.8104 (m-80) cc_final: 0.7810 (m-10) REVERT: A 126 LYS cc_start: 0.6976 (mmtt) cc_final: 0.6569 (mmmm) REVERT: A 164 GLU cc_start: 0.7885 (OUTLIER) cc_final: 0.7630 (mp0) REVERT: A 171 LYS cc_start: 0.8037 (mtmt) cc_final: 0.7832 (mtmt) REVERT: A 175 ARG cc_start: 0.7976 (mtm-85) cc_final: 0.7708 (mtm-85) REVERT: A 184 ILE cc_start: 0.8093 (mm) cc_final: 0.7432 (pt) REVERT: A 234 MET cc_start: 0.8264 (ptp) cc_final: 0.7911 (ptm) REVERT: A 307 GLN cc_start: 0.8366 (mt0) cc_final: 0.8067 (mt0) REVERT: A 327 GLU cc_start: 0.8322 (pt0) cc_final: 0.7839 (pt0) REVERT: A 367 ARG cc_start: 0.7968 (ptt-90) cc_final: 0.7496 (ptp90) REVERT: A 376 SER cc_start: 0.8118 (m) cc_final: 0.7797 (p) REVERT: A 385 TYR cc_start: 0.7874 (m-80) cc_final: 0.7504 (m-10) REVERT: A 386 LYS cc_start: 0.8105 (mmmt) cc_final: 0.7869 (mmmt) REVERT: A 392 ILE cc_start: 0.8380 (pt) cc_final: 0.8165 (pt) REVERT: A 402 GLN cc_start: 0.8227 (tt0) cc_final: 0.7887 (tp40) REVERT: A 410 ILE cc_start: 0.8662 (mm) cc_final: 0.8446 (mm) REVERT: A 412 ASN cc_start: 0.7763 (m-40) cc_final: 0.7244 (m110) REVERT: A 413 GLN cc_start: 0.8119 (mp10) cc_final: 0.7847 (mp10) REVERT: A 428 SER cc_start: 0.8008 (m) cc_final: 0.7311 (p) REVERT: A 433 GLU cc_start: 0.7887 (tt0) cc_final: 0.7445 (tt0) REVERT: A 440 ARG cc_start: 0.7642 (ttm170) cc_final: 0.7249 (ptm-80) REVERT: B 37 TRP cc_start: 0.8252 (m100) cc_final: 0.7908 (m-90) REVERT: B 47 LYS cc_start: 0.8052 (tttt) cc_final: 0.7792 (tttt) REVERT: B 51 TYR cc_start: 0.8539 (p90) cc_final: 0.8266 (p90) REVERT: B 68 LYS cc_start: 0.7947 (tttm) cc_final: 0.7668 (ttpt) REVERT: C 34 MET cc_start: 0.6982 (mmt) cc_final: 0.6691 (mmt) REVERT: C 68 THR cc_start: 0.7308 (m) cc_final: 0.6872 (p) REVERT: C 91 TYR cc_start: 0.6867 (m-80) cc_final: 0.6500 (m-80) REVERT: D 34 HIS cc_start: 0.6404 (m-70) cc_final: 0.5385 (m-70) REVERT: E 29 SER cc_start: 0.8070 (t) cc_final: 0.7685 (p) REVERT: E 51 GLU cc_start: 0.7603 (mm-30) cc_final: 0.7180 (mm-30) REVERT: E 68 LYS cc_start: 0.8014 (tttt) cc_final: 0.7786 (tttp) REVERT: E 70 GLU cc_start: 0.6882 (mm-30) cc_final: 0.6632 (mm-30) REVERT: E 85 SER cc_start: 0.7369 (t) cc_final: 0.7003 (m) REVERT: E 143 LYS cc_start: 0.8178 (mtmt) cc_final: 0.7950 (ttmt) REVERT: E 175 ARG cc_start: 0.7704 (mtm-85) cc_final: 0.7001 (mtm-85) REVERT: E 199 ARG cc_start: 0.7641 (ttt-90) cc_final: 0.7321 (ttt-90) REVERT: E 205 ARG cc_start: 0.7758 (mmm-85) cc_final: 0.7186 (mmm-85) REVERT: E 221 LEU cc_start: 0.6447 (mt) cc_final: 0.6094 (mp) REVERT: E 233 ASN cc_start: 0.8590 (OUTLIER) cc_final: 0.8228 (m-40) REVERT: E 245 LEU cc_start: 0.7570 (OUTLIER) cc_final: 0.7215 (mp) REVERT: E 267 VAL cc_start: 0.8744 (OUTLIER) cc_final: 0.8373 (m) REVERT: E 287 LYS cc_start: 0.6943 (ttmm) cc_final: 0.6587 (mmmm) REVERT: E 306 ASP cc_start: 0.7618 (p0) cc_final: 0.7293 (p0) REVERT: E 318 VAL cc_start: 0.8685 (p) cc_final: 0.8276 (m) REVERT: E 335 CYS cc_start: 0.6798 (m) cc_final: 0.6477 (m) REVERT: E 364 SER cc_start: 0.7856 (t) cc_final: 0.7175 (p) REVERT: E 400 ILE cc_start: 0.8064 (mt) cc_final: 0.7798 (mm) REVERT: E 410 ILE cc_start: 0.8394 (mm) cc_final: 0.8168 (mm) REVERT: E 412 ASN cc_start: 0.7164 (m-40) cc_final: 0.6835 (m-40) REVERT: E 433 GLU cc_start: 0.8027 (tt0) cc_final: 0.7754 (tt0) REVERT: E 444 SER cc_start: 0.8600 (m) cc_final: 0.8372 (p) REVERT: F 27 SER cc_start: 0.8621 (t) cc_final: 0.8345 (p) REVERT: F 51 GLU cc_start: 0.8043 (mm-30) cc_final: 0.7551 (mm-30) REVERT: F 62 ASP cc_start: 0.7873 (t0) cc_final: 0.7385 (t0) REVERT: F 68 LYS cc_start: 0.8590 (tttp) cc_final: 0.8114 (tttp) REVERT: F 72 ASP cc_start: 0.7485 (m-30) cc_final: 0.7240 (m-30) REVERT: F 126 LYS cc_start: 0.7546 (mmtt) cc_final: 0.7209 (mmtp) REVERT: F 140 CYS cc_start: 0.5812 (p) cc_final: 0.5592 (p) REVERT: F 183 ASP cc_start: 0.7172 (t70) cc_final: 0.6922 (t70) REVERT: F 198 ARG cc_start: 0.7275 (mmm160) cc_final: 0.6845 (mmm160) REVERT: F 202 ASN cc_start: 0.7460 (m-40) cc_final: 0.6868 (m110) REVERT: F 205 ARG cc_start: 0.7764 (mmm-85) cc_final: 0.7459 (mmm-85) REVERT: F 222 MET cc_start: 0.8340 (ttp) cc_final: 0.8110 (ttm) REVERT: F 386 LYS cc_start: 0.7993 (mmtm) cc_final: 0.7694 (mmtm) REVERT: F 412 ASN cc_start: 0.7561 (m-40) cc_final: 0.7327 (m110) REVERT: F 437 ILE cc_start: 0.8676 (mm) cc_final: 0.8275 (mt) REVERT: G 36 TRP cc_start: 0.7622 (m100) cc_final: 0.7299 (m100) REVERT: G 116 GLN cc_start: 0.8041 (mm-40) cc_final: 0.7821 (mm-40) REVERT: H 34 MET cc_start: 0.6532 (mmt) cc_final: 0.6306 (tpp) REVERT: H 45 LEU cc_start: 0.8437 (mp) cc_final: 0.8150 (mt) REVERT: H 87 THR cc_start: 0.7644 (m) cc_final: 0.7353 (p) REVERT: I 34 MET cc_start: 0.6973 (mmt) cc_final: 0.6610 (mmt) REVERT: I 50 ARG cc_start: 0.8039 (ttp80) cc_final: 0.7321 (ttp-170) REVERT: J 65 LYS cc_start: 0.7949 (tttt) cc_final: 0.7728 (tttt) REVERT: J 119 LEU cc_start: 0.8113 (tp) cc_final: 0.7799 (tt) REVERT: K 93 SER cc_start: 0.8847 (t) cc_final: 0.8470 (p) REVERT: L 12 SER cc_start: 0.8123 (p) cc_final: 0.7881 (t) REVERT: L 39 LYS cc_start: 0.8644 (mttt) cc_final: 0.8254 (mttm) REVERT: L 48 MET cc_start: 0.7225 (mmm) cc_final: 0.6728 (mmm) REVERT: L 52 SER cc_start: 0.8230 (m) cc_final: 0.8018 (p) REVERT: L 75 ILE cc_start: 0.8291 (mt) cc_final: 0.8057 (mt) REVERT: M 36 HIS cc_start: 0.7942 (m-70) cc_final: 0.7153 (m-70) REVERT: M 37 TRP cc_start: 0.8527 (m100) cc_final: 0.7868 (m100) REVERT: M 68 LYS cc_start: 0.8373 (tttm) cc_final: 0.7260 (tttt) REVERT: N 5 VAL cc_start: 0.6843 (t) cc_final: 0.6385 (m) REVERT: N 80 PHE cc_start: 0.7783 (m-80) cc_final: 0.7002 (m-80) REVERT: N 93 ILE cc_start: 0.8313 (mt) cc_final: 0.7786 (tt) REVERT: N 94 TYR cc_start: 0.7792 (m-80) cc_final: 0.7439 (m-80) REVERT: N 119 LEU cc_start: 0.8143 (tp) cc_final: 0.7825 (tt) REVERT: O 10 VAL cc_start: 0.8633 (p) cc_final: 0.8306 (t) REVERT: O 47 LYS cc_start: 0.7890 (tttt) cc_final: 0.7602 (tttt) outliers start: 60 outliers final: 34 residues processed: 660 average time/residue: 0.1655 time to fit residues: 164.1445 Evaluate side-chains 650 residues out of total 2244 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 612 time to evaluate : 0.772 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 164 GLU Chi-restraints excluded: chain A residue 204 VAL Chi-restraints excluded: chain A residue 316 SER Chi-restraints excluded: chain B residue 35 VAL Chi-restraints excluded: chain C residue 12 VAL Chi-restraints excluded: chain C residue 29 LEU Chi-restraints excluded: chain C residue 95 SER Chi-restraints excluded: chain D residue 63 SER Chi-restraints excluded: chain D residue 95 SER Chi-restraints excluded: chain D residue 107 LEU Chi-restraints excluded: chain E residue 108 ILE Chi-restraints excluded: chain E residue 164 GLU Chi-restraints excluded: chain E residue 233 ASN Chi-restraints excluded: chain E residue 234 MET Chi-restraints excluded: chain E residue 245 LEU Chi-restraints excluded: chain E residue 267 VAL Chi-restraints excluded: chain E residue 302 LEU Chi-restraints excluded: chain E residue 394 SER Chi-restraints excluded: chain E residue 401 LYS Chi-restraints excluded: chain F residue 31 ILE Chi-restraints excluded: chain F residue 45 THR Chi-restraints excluded: chain F residue 204 VAL Chi-restraints excluded: chain F residue 227 LEU Chi-restraints excluded: chain G residue 108 THR Chi-restraints excluded: chain H residue 21 THR Chi-restraints excluded: chain H residue 32 SER Chi-restraints excluded: chain H residue 51 ILE Chi-restraints excluded: chain I residue 37 VAL Chi-restraints excluded: chain J residue 69 THR Chi-restraints excluded: chain L residue 79 GLN Chi-restraints excluded: chain L residue 107 LEU Chi-restraints excluded: chain M residue 67 SER Chi-restraints excluded: chain M residue 74 SER Chi-restraints excluded: chain M residue 98 SER Chi-restraints excluded: chain O residue 22 CYS Chi-restraints excluded: chain O residue 65 SER Chi-restraints excluded: chain O residue 74 SER Chi-restraints excluded: chain O residue 98 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 261 random chunks: chunk 56 optimal weight: 6.9990 chunk 141 optimal weight: 2.9990 chunk 78 optimal weight: 0.5980 chunk 142 optimal weight: 0.7980 chunk 83 optimal weight: 4.9990 chunk 174 optimal weight: 5.9990 chunk 126 optimal weight: 3.9990 chunk 230 optimal weight: 2.9990 chunk 130 optimal weight: 2.9990 chunk 53 optimal weight: 5.9990 chunk 150 optimal weight: 0.7980 overall best weight: 1.6384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 172 ASN ** A 178 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 195 GLN A 453 GLN ** A 455 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 36 HIS C 56 ASN ** D 34 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 313 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 346 GLN F 455 GLN H 16 GLN ** K 34 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N 35 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3714 r_free = 0.3714 target = 0.132985 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3487 r_free = 0.3487 target = 0.116755 restraints weight = 31047.058| |-----------------------------------------------------------------------------| r_work (start): 0.3499 rms_B_bonded: 2.01 r_work: 0.3395 rms_B_bonded: 2.31 restraints_weight: 0.5000 r_work: 0.3250 rms_B_bonded: 4.05 restraints_weight: 0.2500 r_work (final): 0.3250 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3146 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3146 r_free = 0.3146 target_work(ls_wunit_k1) = 0.096 | | occupancies: max = 1.00 min = 0.65 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3146 r_free = 0.3146 target_work(ls_wunit_k1) = 0.096 | | occupancies: max = 1.00 min = 0.69 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3146 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7514 moved from start: 0.2828 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.061 20658 Z= 0.286 Angle : 0.703 8.314 28077 Z= 0.380 Chirality : 0.050 0.284 3237 Planarity : 0.005 0.043 3564 Dihedral : 6.057 41.723 2926 Min Nonbonded Distance : 2.469 Molprobity Statistics. All-atom Clashscore : 9.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.06 % Favored : 95.94 % Rotamer: Outliers : 4.06 % Allowed : 14.26 % Favored : 81.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.39 (0.16), residues: 2622 helix: 0.28 (0.25), residues: 399 sheet: -0.29 (0.18), residues: 792 loop : -0.28 (0.17), residues: 1431 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG E 304 TYR 0.030 0.003 TYR F 310 PHE 0.020 0.002 PHE J 29 TRP 0.022 0.003 TRP D 35 HIS 0.009 0.002 HIS L 34 Details of bonding type rmsd covalent geometry : bond 0.00629 (20610) covalent geometry : angle 0.69616 (27978) SS BOND : bond 0.00563 ( 45) SS BOND : angle 1.75256 ( 90) hydrogen bonds : bond 0.04431 ( 924) hydrogen bonds : angle 6.08237 ( 2550) link_NAG-ASN : bond 0.01012 ( 3) link_NAG-ASN : angle 1.57588 ( 9) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5244 Ramachandran restraints generated. 2622 Oldfield, 0 Emsley, 2622 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5244 Ramachandran restraints generated. 2622 Oldfield, 0 Emsley, 2622 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 696 residues out of total 2244 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 91 poor density : 605 time to evaluate : 0.787 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 26 GLU cc_start: 0.7853 (pt0) cc_final: 0.7515 (pt0) REVERT: A 62 ASP cc_start: 0.8122 (t0) cc_final: 0.7795 (t0) REVERT: A 72 ASP cc_start: 0.7223 (m-30) cc_final: 0.6832 (m-30) REVERT: A 126 LYS cc_start: 0.7117 (mmtt) cc_final: 0.6739 (mmmm) REVERT: A 129 ARG cc_start: 0.7439 (ptp-110) cc_final: 0.7155 (ptm160) REVERT: A 142 LYS cc_start: 0.8150 (mmtp) cc_final: 0.7572 (mmtp) REVERT: A 206 GLN cc_start: 0.7535 (mt0) cc_final: 0.7233 (mt0) REVERT: A 250 MET cc_start: 0.6632 (mmm) cc_final: 0.6331 (mmm) REVERT: A 307 GLN cc_start: 0.8192 (mt0) cc_final: 0.7975 (mt0) REVERT: A 327 GLU cc_start: 0.8214 (pt0) cc_final: 0.7908 (pt0) REVERT: A 385 TYR cc_start: 0.7875 (m-80) cc_final: 0.7412 (m-10) REVERT: A 386 LYS cc_start: 0.8152 (mmmt) cc_final: 0.7936 (mmmt) REVERT: A 402 GLN cc_start: 0.8281 (tt0) cc_final: 0.8050 (tt0) REVERT: A 412 ASN cc_start: 0.7596 (m-40) cc_final: 0.7334 (m110) REVERT: A 428 SER cc_start: 0.7964 (m) cc_final: 0.7349 (p) REVERT: A 433 GLU cc_start: 0.8005 (tt0) cc_final: 0.7805 (tt0) REVERT: A 440 ARG cc_start: 0.7662 (ttm170) cc_final: 0.7305 (ptm-80) REVERT: A 453 GLN cc_start: 0.7967 (tt0) cc_final: 0.7623 (tt0) REVERT: C 34 MET cc_start: 0.7130 (mmt) cc_final: 0.6875 (mmt) REVERT: C 91 TYR cc_start: 0.7116 (m-80) cc_final: 0.6641 (m-80) REVERT: D 34 HIS cc_start: 0.6484 (m-70) cc_final: 0.5847 (m-70) REVERT: E 29 SER cc_start: 0.8308 (t) cc_final: 0.7886 (p) REVERT: E 51 GLU cc_start: 0.7577 (mm-30) cc_final: 0.7192 (mm-30) REVERT: E 70 GLU cc_start: 0.6807 (mm-30) cc_final: 0.6585 (mm-30) REVERT: E 72 ASP cc_start: 0.6897 (m-30) cc_final: 0.6521 (m-30) REVERT: E 80 GLU cc_start: 0.7463 (OUTLIER) cc_final: 0.7256 (tt0) REVERT: E 126 LYS cc_start: 0.7411 (mmtt) cc_final: 0.7056 (mmtp) REVERT: E 175 ARG cc_start: 0.7893 (mtm-85) cc_final: 0.7618 (mtm-85) REVERT: E 189 MET cc_start: 0.7161 (tpp) cc_final: 0.6918 (ttm) REVERT: E 233 ASN cc_start: 0.8734 (OUTLIER) cc_final: 0.8247 (m-40) REVERT: E 243 LEU cc_start: 0.7320 (OUTLIER) cc_final: 0.6969 (tp) REVERT: E 267 VAL cc_start: 0.8685 (OUTLIER) cc_final: 0.8349 (m) REVERT: E 287 LYS cc_start: 0.6964 (ttmm) cc_final: 0.6580 (mmmt) REVERT: E 306 ASP cc_start: 0.7686 (p0) cc_final: 0.7485 (p0) REVERT: E 318 VAL cc_start: 0.8745 (p) cc_final: 0.8307 (m) REVERT: E 364 SER cc_start: 0.7958 (t) cc_final: 0.7430 (m) REVERT: E 412 ASN cc_start: 0.7111 (m-40) cc_final: 0.6725 (m-40) REVERT: E 433 GLU cc_start: 0.8146 (tt0) cc_final: 0.7896 (tt0) REVERT: E 444 SER cc_start: 0.8629 (m) cc_final: 0.8286 (p) REVERT: F 27 SER cc_start: 0.8533 (t) cc_final: 0.8311 (p) REVERT: F 47 VAL cc_start: 0.8674 (OUTLIER) cc_final: 0.8400 (m) REVERT: F 51 GLU cc_start: 0.7864 (mm-30) cc_final: 0.7460 (mm-30) REVERT: F 62 ASP cc_start: 0.7824 (t0) cc_final: 0.7264 (t0) REVERT: F 68 LYS cc_start: 0.8591 (tttp) cc_final: 0.8243 (tttp) REVERT: F 126 LYS cc_start: 0.7767 (mmtt) cc_final: 0.7525 (mmtp) REVERT: F 140 CYS cc_start: 0.6015 (p) cc_final: 0.5767 (p) REVERT: F 183 ASP cc_start: 0.7248 (t70) cc_final: 0.6887 (t0) REVERT: F 198 ARG cc_start: 0.7165 (mmm160) cc_final: 0.6930 (mtp85) REVERT: F 294 GLU cc_start: 0.7699 (mt-10) cc_final: 0.7413 (mt-10) REVERT: F 331 ASP cc_start: 0.8164 (t0) cc_final: 0.7533 (t70) REVERT: F 345 GLU cc_start: 0.7865 (tp30) cc_final: 0.7656 (tp30) REVERT: F 412 ASN cc_start: 0.7436 (m-40) cc_final: 0.6878 (m110) REVERT: F 428 SER cc_start: 0.7503 (m) cc_final: 0.7189 (p) REVERT: F 437 ILE cc_start: 0.8696 (mm) cc_final: 0.8321 (mt) REVERT: F 461 ASP cc_start: 0.7853 (t0) cc_final: 0.7635 (t0) REVERT: G 94 TYR cc_start: 0.7474 (m-80) cc_final: 0.7175 (m-80) REVERT: H 34 MET cc_start: 0.6462 (mmt) cc_final: 0.6164 (tpp) REVERT: H 55 ASP cc_start: 0.8423 (t0) cc_final: 0.8067 (t0) REVERT: H 69 ILE cc_start: 0.8385 (pt) cc_final: 0.8046 (mt) REVERT: H 82 MET cc_start: 0.7035 (mmp) cc_final: 0.6561 (mmp) REVERT: H 87 THR cc_start: 0.7778 (m) cc_final: 0.7556 (p) REVERT: I 34 MET cc_start: 0.7003 (mmt) cc_final: 0.6442 (mmt) REVERT: J 65 LYS cc_start: 0.8081 (tttt) cc_final: 0.7859 (tttt) REVERT: J 77 THR cc_start: 0.7764 (OUTLIER) cc_final: 0.7511 (m) REVERT: K 28 LEU cc_start: 0.8590 (mt) cc_final: 0.8317 (mt) REVERT: K 93 SER cc_start: 0.9120 (t) cc_final: 0.8684 (p) REVERT: L 39 LYS cc_start: 0.8721 (mttt) cc_final: 0.8424 (mttm) REVERT: L 48 MET cc_start: 0.7280 (mmm) cc_final: 0.6876 (mmm) REVERT: L 52 SER cc_start: 0.8200 (m) cc_final: 0.7883 (t) REVERT: M 36 HIS cc_start: 0.7963 (m-70) cc_final: 0.7293 (m-70) REVERT: M 37 TRP cc_start: 0.8475 (m100) cc_final: 0.8012 (m100) REVERT: M 64 PHE cc_start: 0.7564 (m-80) cc_final: 0.7363 (m-80) REVERT: N 5 VAL cc_start: 0.6818 (t) cc_final: 0.6327 (m) REVERT: N 35 ASN cc_start: 0.7473 (m-40) cc_final: 0.7228 (m110) REVERT: N 93 ILE cc_start: 0.8371 (mt) cc_final: 0.7900 (tt) REVERT: O 81 GLN cc_start: 0.6798 (mt0) cc_final: 0.6416 (tt0) REVERT: O 83 GLU cc_start: 0.6591 (mp0) cc_final: 0.6201 (mp0) outliers start: 91 outliers final: 59 residues processed: 656 average time/residue: 0.1550 time to fit residues: 155.8039 Evaluate side-chains 633 residues out of total 2244 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 568 time to evaluate : 0.771 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 59 THR Chi-restraints excluded: chain A residue 79 ARG Chi-restraints excluded: chain A residue 83 THR Chi-restraints excluded: chain A residue 147 CYS Chi-restraints excluded: chain A residue 204 VAL Chi-restraints excluded: chain A residue 218 SER Chi-restraints excluded: chain A residue 302 LEU Chi-restraints excluded: chain A residue 316 SER Chi-restraints excluded: chain A residue 442 VAL Chi-restraints excluded: chain B residue 35 VAL Chi-restraints excluded: chain B residue 36 HIS Chi-restraints excluded: chain B residue 65 SER Chi-restraints excluded: chain C residue 12 VAL Chi-restraints excluded: chain C residue 29 LEU Chi-restraints excluded: chain C residue 31 THR Chi-restraints excluded: chain C residue 80 LEU Chi-restraints excluded: chain C residue 95 SER Chi-restraints excluded: chain D residue 63 SER Chi-restraints excluded: chain D residue 107 LEU Chi-restraints excluded: chain E residue 80 GLU Chi-restraints excluded: chain E residue 83 THR Chi-restraints excluded: chain E residue 108 ILE Chi-restraints excluded: chain E residue 164 GLU Chi-restraints excluded: chain E residue 233 ASN Chi-restraints excluded: chain E residue 234 MET Chi-restraints excluded: chain E residue 243 LEU Chi-restraints excluded: chain E residue 267 VAL Chi-restraints excluded: chain E residue 302 LEU Chi-restraints excluded: chain E residue 312 GLN Chi-restraints excluded: chain E residue 389 SER Chi-restraints excluded: chain E residue 394 SER Chi-restraints excluded: chain E residue 401 LYS Chi-restraints excluded: chain E residue 447 ASP Chi-restraints excluded: chain F residue 29 SER Chi-restraints excluded: chain F residue 31 ILE Chi-restraints excluded: chain F residue 45 THR Chi-restraints excluded: chain F residue 47 VAL Chi-restraints excluded: chain F residue 66 LEU Chi-restraints excluded: chain F residue 83 THR Chi-restraints excluded: chain F residue 108 ILE Chi-restraints excluded: chain F residue 204 VAL Chi-restraints excluded: chain F residue 267 VAL Chi-restraints excluded: chain F residue 427 LEU Chi-restraints excluded: chain G residue 50 SER Chi-restraints excluded: chain G residue 108 THR Chi-restraints excluded: chain H residue 20 LEU Chi-restraints excluded: chain H residue 21 THR Chi-restraints excluded: chain H residue 51 ILE Chi-restraints excluded: chain I residue 32 SER Chi-restraints excluded: chain I residue 37 VAL Chi-restraints excluded: chain I residue 102 LEU Chi-restraints excluded: chain J residue 28 THR Chi-restraints excluded: chain J residue 69 THR Chi-restraints excluded: chain J residue 77 THR Chi-restraints excluded: chain L residue 79 GLN Chi-restraints excluded: chain L residue 89 GLN Chi-restraints excluded: chain M residue 65 SER Chi-restraints excluded: chain M residue 67 SER Chi-restraints excluded: chain M residue 74 SER Chi-restraints excluded: chain M residue 98 SER Chi-restraints excluded: chain N residue 3 GLN Chi-restraints excluded: chain O residue 22 CYS Chi-restraints excluded: chain O residue 67 SER Chi-restraints excluded: chain O residue 74 SER Chi-restraints excluded: chain O residue 98 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 261 random chunks: chunk 104 optimal weight: 0.9990 chunk 257 optimal weight: 3.9990 chunk 65 optimal weight: 4.9990 chunk 99 optimal weight: 0.9980 chunk 62 optimal weight: 3.9990 chunk 218 optimal weight: 5.9990 chunk 249 optimal weight: 2.9990 chunk 244 optimal weight: 1.9990 chunk 35 optimal weight: 0.8980 chunk 87 optimal weight: 0.9980 chunk 151 optimal weight: 1.9990 overall best weight: 1.1784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 172 ASN A 272 GLN B 40 GLN ** D 34 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 16 GLN ** K 34 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N 82 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3738 r_free = 0.3738 target = 0.134432 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3513 r_free = 0.3513 target = 0.118396 restraints weight = 30582.217| |-----------------------------------------------------------------------------| r_work (start): 0.3516 rms_B_bonded: 1.99 r_work: 0.3413 rms_B_bonded: 2.28 restraints_weight: 0.5000 r_work: 0.3269 rms_B_bonded: 4.01 restraints_weight: 0.2500 r_work (final): 0.3269 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3182 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3182 r_free = 0.3182 target_work(ls_wunit_k1) = 0.098 | | occupancies: max = 1.00 min = 0.69 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3182 r_free = 0.3182 target_work(ls_wunit_k1) = 0.098 | | occupancies: max = 1.00 min = 0.74 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3182 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7493 moved from start: 0.3117 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.053 20658 Z= 0.219 Angle : 0.654 8.140 28077 Z= 0.350 Chirality : 0.048 0.342 3237 Planarity : 0.004 0.042 3564 Dihedral : 5.740 41.704 2926 Min Nonbonded Distance : 2.504 Molprobity Statistics. All-atom Clashscore : 8.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.13 % Favored : 95.87 % Rotamer: Outliers : 4.68 % Allowed : 16.18 % Favored : 79.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.38 (0.16), residues: 2622 helix: 0.42 (0.25), residues: 399 sheet: -0.32 (0.17), residues: 822 loop : -0.30 (0.17), residues: 1401 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG I 50 TYR 0.029 0.002 TYR F 385 PHE 0.033 0.002 PHE I 27 TRP 0.031 0.002 TRP D 35 HIS 0.017 0.002 HIS B 36 Details of bonding type rmsd covalent geometry : bond 0.00485 (20610) covalent geometry : angle 0.64922 (27978) SS BOND : bond 0.00487 ( 45) SS BOND : angle 1.51693 ( 90) hydrogen bonds : bond 0.03921 ( 924) hydrogen bonds : angle 5.89198 ( 2550) link_NAG-ASN : bond 0.00783 ( 3) link_NAG-ASN : angle 1.46298 ( 9) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5244 Ramachandran restraints generated. 2622 Oldfield, 0 Emsley, 2622 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5244 Ramachandran restraints generated. 2622 Oldfield, 0 Emsley, 2622 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 709 residues out of total 2244 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 105 poor density : 604 time to evaluate : 0.816 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 62 ASP cc_start: 0.8107 (t0) cc_final: 0.7823 (t0) REVERT: A 72 ASP cc_start: 0.7228 (m-30) cc_final: 0.6837 (m-30) REVERT: A 126 LYS cc_start: 0.7081 (mmtt) cc_final: 0.6727 (mmtp) REVERT: A 139 ASN cc_start: 0.8403 (m-40) cc_final: 0.8049 (m-40) REVERT: A 142 LYS cc_start: 0.8160 (mmtp) cc_final: 0.7596 (mmtp) REVERT: A 184 ILE cc_start: 0.8131 (mm) cc_final: 0.7453 (pt) REVERT: A 206 GLN cc_start: 0.7490 (mt0) cc_final: 0.7150 (mt0) REVERT: A 304 ARG cc_start: 0.8306 (mmm-85) cc_final: 0.7969 (mmm-85) REVERT: A 307 GLN cc_start: 0.8240 (mt0) cc_final: 0.8025 (mt0) REVERT: A 385 TYR cc_start: 0.7862 (m-80) cc_final: 0.7430 (m-10) REVERT: A 412 ASN cc_start: 0.7549 (m-40) cc_final: 0.6907 (m110) REVERT: A 428 SER cc_start: 0.7943 (m) cc_final: 0.7310 (p) REVERT: A 440 ARG cc_start: 0.7645 (ttm170) cc_final: 0.7298 (ptm-80) REVERT: A 453 GLN cc_start: 0.7825 (tt0) cc_final: 0.7616 (tt0) REVERT: C 34 MET cc_start: 0.7136 (mmt) cc_final: 0.6862 (mmt) REVERT: C 91 TYR cc_start: 0.7121 (m-80) cc_final: 0.6615 (m-80) REVERT: D 34 HIS cc_start: 0.6460 (m-70) cc_final: 0.6091 (m90) REVERT: E 29 SER cc_start: 0.8306 (t) cc_final: 0.7843 (p) REVERT: E 47 VAL cc_start: 0.8563 (OUTLIER) cc_final: 0.8312 (m) REVERT: E 51 GLU cc_start: 0.7463 (mm-30) cc_final: 0.7138 (mm-30) REVERT: E 70 GLU cc_start: 0.6829 (mm-30) cc_final: 0.6543 (mm-30) REVERT: E 72 ASP cc_start: 0.6946 (m-30) cc_final: 0.6563 (m-30) REVERT: E 80 GLU cc_start: 0.7403 (mt-10) cc_final: 0.7184 (tt0) REVERT: E 126 LYS cc_start: 0.7398 (mmtt) cc_final: 0.7064 (mmtp) REVERT: E 189 MET cc_start: 0.7113 (tpp) cc_final: 0.6901 (mtt) REVERT: E 233 ASN cc_start: 0.8749 (OUTLIER) cc_final: 0.8253 (m-40) REVERT: E 245 LEU cc_start: 0.7582 (OUTLIER) cc_final: 0.7334 (mp) REVERT: E 254 LYS cc_start: 0.7784 (mmtm) cc_final: 0.7573 (mmtm) REVERT: E 267 VAL cc_start: 0.8663 (OUTLIER) cc_final: 0.8303 (m) REVERT: E 287 LYS cc_start: 0.6935 (ttmm) cc_final: 0.6555 (mmmt) REVERT: E 306 ASP cc_start: 0.7556 (p0) cc_final: 0.7323 (p0) REVERT: E 313 ASN cc_start: 0.7453 (OUTLIER) cc_final: 0.7203 (t160) REVERT: E 318 VAL cc_start: 0.8735 (p) cc_final: 0.8325 (m) REVERT: E 331 ASP cc_start: 0.8307 (t0) cc_final: 0.7850 (t0) REVERT: E 364 SER cc_start: 0.7910 (t) cc_final: 0.7623 (p) REVERT: E 409 TYR cc_start: 0.8508 (t80) cc_final: 0.8179 (t80) REVERT: E 412 ASN cc_start: 0.7147 (m-40) cc_final: 0.6763 (m-40) REVERT: E 433 GLU cc_start: 0.8105 (tt0) cc_final: 0.7857 (tt0) REVERT: E 444 SER cc_start: 0.8631 (m) cc_final: 0.8277 (p) REVERT: F 47 VAL cc_start: 0.8630 (OUTLIER) cc_final: 0.8381 (m) REVERT: F 51 GLU cc_start: 0.7900 (mm-30) cc_final: 0.7473 (mm-30) REVERT: F 62 ASP cc_start: 0.7882 (t0) cc_final: 0.7306 (t0) REVERT: F 126 LYS cc_start: 0.7734 (mmtt) cc_final: 0.7501 (mmtp) REVERT: F 183 ASP cc_start: 0.7201 (t70) cc_final: 0.6799 (t0) REVERT: F 198 ARG cc_start: 0.7167 (mmm160) cc_final: 0.6954 (mtp85) REVERT: F 202 ASN cc_start: 0.7328 (m110) cc_final: 0.7087 (m110) REVERT: F 331 ASP cc_start: 0.8116 (t0) cc_final: 0.7597 (t70) REVERT: F 386 LYS cc_start: 0.8173 (mmtm) cc_final: 0.7808 (mmtm) REVERT: F 402 GLN cc_start: 0.8045 (tt0) cc_final: 0.7733 (tp40) REVERT: F 412 ASN cc_start: 0.7409 (m-40) cc_final: 0.7071 (m110) REVERT: F 421 ASP cc_start: 0.7276 (m-30) cc_final: 0.7049 (m-30) REVERT: F 437 ILE cc_start: 0.8666 (mm) cc_final: 0.8291 (mt) REVERT: F 461 ASP cc_start: 0.7750 (t0) cc_final: 0.7451 (t0) REVERT: G 36 TRP cc_start: 0.7589 (m100) cc_final: 0.7380 (m100) REVERT: H 69 ILE cc_start: 0.8185 (pt) cc_final: 0.7859 (mt) REVERT: H 87 THR cc_start: 0.7747 (m) cc_final: 0.7518 (p) REVERT: I 34 MET cc_start: 0.6770 (mmt) cc_final: 0.6283 (mmt) REVERT: J 34 MET cc_start: 0.8119 (mmm) cc_final: 0.7358 (mmm) REVERT: J 65 LYS cc_start: 0.8203 (tttt) cc_final: 0.7979 (tttt) REVERT: J 77 THR cc_start: 0.7521 (OUTLIER) cc_final: 0.7310 (m) REVERT: J 82 GLN cc_start: 0.7368 (tp40) cc_final: 0.6997 (tp40) REVERT: K 28 LEU cc_start: 0.8554 (mt) cc_final: 0.8288 (mt) REVERT: K 31 LYS cc_start: 0.7305 (mmtt) cc_final: 0.7093 (mmtt) REVERT: K 93 SER cc_start: 0.9046 (t) cc_final: 0.8354 (p) REVERT: L 39 LYS cc_start: 0.8727 (mttt) cc_final: 0.8430 (mttm) REVERT: L 48 MET cc_start: 0.7187 (mmm) cc_final: 0.6667 (mmm) REVERT: L 52 SER cc_start: 0.8072 (m) cc_final: 0.7776 (t) REVERT: M 36 HIS cc_start: 0.7869 (m-70) cc_final: 0.7249 (m-70) REVERT: M 37 TRP cc_start: 0.8505 (m100) cc_final: 0.8073 (m100) REVERT: N 5 VAL cc_start: 0.6824 (t) cc_final: 0.6324 (m) REVERT: N 35 ASN cc_start: 0.7355 (m-40) cc_final: 0.6970 (m110) REVERT: N 93 ILE cc_start: 0.8406 (mt) cc_final: 0.7857 (tt) REVERT: O 53 ASN cc_start: 0.8080 (m-40) cc_final: 0.7873 (m-40) REVERT: O 81 GLN cc_start: 0.6756 (mt0) cc_final: 0.6496 (tt0) outliers start: 105 outliers final: 74 residues processed: 660 average time/residue: 0.1632 time to fit residues: 161.8067 Evaluate side-chains 647 residues out of total 2244 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 81 poor density : 566 time to evaluate : 0.823 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 27 SER Chi-restraints excluded: chain A residue 79 ARG Chi-restraints excluded: chain A residue 83 THR Chi-restraints excluded: chain A residue 147 CYS Chi-restraints excluded: chain A residue 204 VAL Chi-restraints excluded: chain A residue 218 SER Chi-restraints excluded: chain A residue 267 VAL Chi-restraints excluded: chain A residue 272 GLN Chi-restraints excluded: chain A residue 302 LEU Chi-restraints excluded: chain A residue 316 SER Chi-restraints excluded: chain A residue 442 VAL Chi-restraints excluded: chain A residue 447 ASP Chi-restraints excluded: chain A residue 455 GLN Chi-restraints excluded: chain B residue 21 SER Chi-restraints excluded: chain B residue 36 HIS Chi-restraints excluded: chain B residue 65 SER Chi-restraints excluded: chain B residue 67 SER Chi-restraints excluded: chain B residue 98 SER Chi-restraints excluded: chain C residue 12 VAL Chi-restraints excluded: chain C residue 29 LEU Chi-restraints excluded: chain C residue 80 LEU Chi-restraints excluded: chain C residue 95 SER Chi-restraints excluded: chain D residue 9 SER Chi-restraints excluded: chain D residue 63 SER Chi-restraints excluded: chain D residue 95 SER Chi-restraints excluded: chain D residue 107 LEU Chi-restraints excluded: chain E residue 47 VAL Chi-restraints excluded: chain E residue 83 THR Chi-restraints excluded: chain E residue 108 ILE Chi-restraints excluded: chain E residue 147 CYS Chi-restraints excluded: chain E residue 164 GLU Chi-restraints excluded: chain E residue 191 VAL Chi-restraints excluded: chain E residue 233 ASN Chi-restraints excluded: chain E residue 234 MET Chi-restraints excluded: chain E residue 245 LEU Chi-restraints excluded: chain E residue 267 VAL Chi-restraints excluded: chain E residue 302 LEU Chi-restraints excluded: chain E residue 312 GLN Chi-restraints excluded: chain E residue 313 ASN Chi-restraints excluded: chain E residue 394 SER Chi-restraints excluded: chain E residue 401 LYS Chi-restraints excluded: chain E residue 447 ASP Chi-restraints excluded: chain F residue 31 ILE Chi-restraints excluded: chain F residue 45 THR Chi-restraints excluded: chain F residue 47 VAL Chi-restraints excluded: chain F residue 66 LEU Chi-restraints excluded: chain F residue 83 THR Chi-restraints excluded: chain F residue 108 ILE Chi-restraints excluded: chain F residue 267 VAL Chi-restraints excluded: chain F residue 302 LEU Chi-restraints excluded: chain F residue 323 GLU Chi-restraints excluded: chain F residue 427 LEU Chi-restraints excluded: chain G residue 50 SER Chi-restraints excluded: chain G residue 77 THR Chi-restraints excluded: chain G residue 108 THR Chi-restraints excluded: chain H residue 20 LEU Chi-restraints excluded: chain H residue 21 THR Chi-restraints excluded: chain H residue 32 SER Chi-restraints excluded: chain H residue 51 ILE Chi-restraints excluded: chain I residue 32 SER Chi-restraints excluded: chain I residue 37 VAL Chi-restraints excluded: chain I residue 70 SER Chi-restraints excluded: chain I residue 102 LEU Chi-restraints excluded: chain J residue 5 VAL Chi-restraints excluded: chain J residue 28 THR Chi-restraints excluded: chain J residue 62 ASP Chi-restraints excluded: chain J residue 69 THR Chi-restraints excluded: chain J residue 77 THR Chi-restraints excluded: chain K residue 9 SER Chi-restraints excluded: chain L residue 79 GLN Chi-restraints excluded: chain L residue 89 GLN Chi-restraints excluded: chain M residue 60 VAL Chi-restraints excluded: chain M residue 65 SER Chi-restraints excluded: chain M residue 74 SER Chi-restraints excluded: chain M residue 98 SER Chi-restraints excluded: chain N residue 3 GLN Chi-restraints excluded: chain N residue 73 ASP Chi-restraints excluded: chain N residue 106 SER Chi-restraints excluded: chain O residue 22 CYS Chi-restraints excluded: chain O residue 74 SER Chi-restraints excluded: chain O residue 98 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 261 random chunks: chunk 7 optimal weight: 1.9990 chunk 248 optimal weight: 4.9990 chunk 231 optimal weight: 1.9990 chunk 51 optimal weight: 2.9990 chunk 94 optimal weight: 2.9990 chunk 135 optimal weight: 1.9990 chunk 23 optimal weight: 6.9990 chunk 122 optimal weight: 3.9990 chunk 5 optimal weight: 0.6980 chunk 31 optimal weight: 0.8980 chunk 171 optimal weight: 1.9990 overall best weight: 1.5186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 240 GLN A 272 GLN ** A 462 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 34 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 346 GLN ** K 34 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 6 GLN ** L 34 HIS ** 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 = 0.3721 r_free = 0.3721 target = 0.133252 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3495 r_free = 0.3495 target = 0.117214 restraints weight = 30601.096| |-----------------------------------------------------------------------------| r_work (start): 0.3497 rms_B_bonded: 1.98 r_work: 0.3394 rms_B_bonded: 2.28 restraints_weight: 0.5000 r_work: 0.3248 rms_B_bonded: 4.02 restraints_weight: 0.2500 r_work (final): 0.3248 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3256 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3256 r_free = 0.3256 target_work(ls_wunit_k1) = 0.102 | | occupancies: max = 1.00 min = 0.74 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3256 r_free = 0.3256 target_work(ls_wunit_k1) = 0.102 | | occupancies: max = 1.00 min = 0.75 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3256 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7512 moved from start: 0.3366 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.083 20658 Z= 0.271 Angle : 0.690 8.654 28077 Z= 0.369 Chirality : 0.050 0.319 3237 Planarity : 0.005 0.046 3564 Dihedral : 5.820 41.554 2926 Min Nonbonded Distance : 2.470 Molprobity Statistics. All-atom Clashscore : 9.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.78 % Favored : 95.22 % Rotamer: Outliers : 5.08 % Allowed : 17.51 % Favored : 77.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.60 (0.16), residues: 2622 helix: 0.23 (0.25), residues: 414 sheet: -0.36 (0.17), residues: 819 loop : -0.53 (0.17), residues: 1389 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG E 199 TYR 0.027 0.003 TYR F 310 PHE 0.027 0.002 PHE I 27 TRP 0.038 0.003 TRP K 35 HIS 0.008 0.002 HIS L 34 Details of bonding type rmsd covalent geometry : bond 0.00601 (20610) covalent geometry : angle 0.68288 (27978) SS BOND : bond 0.00536 ( 45) SS BOND : angle 1.83715 ( 90) hydrogen bonds : bond 0.04132 ( 924) hydrogen bonds : angle 5.93926 ( 2550) link_NAG-ASN : bond 0.00985 ( 3) link_NAG-ASN : angle 1.63741 ( 9) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5244 Ramachandran restraints generated. 2622 Oldfield, 0 Emsley, 2622 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5244 Ramachandran restraints generated. 2622 Oldfield, 0 Emsley, 2622 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 705 residues out of total 2244 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 114 poor density : 591 time to evaluate : 0.748 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 62 ASP cc_start: 0.8171 (t0) cc_final: 0.7834 (t0) REVERT: A 72 ASP cc_start: 0.7184 (m-30) cc_final: 0.6839 (m-30) REVERT: A 126 LYS cc_start: 0.7187 (mmtt) cc_final: 0.6761 (mmtp) REVERT: A 129 ARG cc_start: 0.7490 (ptp-110) cc_final: 0.7186 (ptm160) REVERT: A 139 ASN cc_start: 0.8400 (m-40) cc_final: 0.8179 (m-40) REVERT: A 142 LYS cc_start: 0.8215 (mmtp) cc_final: 0.7803 (mmtp) REVERT: A 184 ILE cc_start: 0.8099 (mm) cc_final: 0.7495 (pt) REVERT: A 324 LYS cc_start: 0.7797 (mtpt) cc_final: 0.7578 (mtpt) REVERT: A 385 TYR cc_start: 0.7842 (m-80) cc_final: 0.7585 (m-10) REVERT: A 400 ILE cc_start: 0.7995 (mt) cc_final: 0.7795 (mp) REVERT: A 402 GLN cc_start: 0.8267 (tt0) cc_final: 0.7877 (tp40) REVERT: A 412 ASN cc_start: 0.7364 (m-40) cc_final: 0.7161 (m110) REVERT: C 34 MET cc_start: 0.7096 (mmt) cc_final: 0.6847 (mmt) REVERT: C 68 THR cc_start: 0.7683 (m) cc_final: 0.7345 (p) REVERT: C 91 TYR cc_start: 0.7172 (m-80) cc_final: 0.6658 (m-80) REVERT: E 29 SER cc_start: 0.8409 (t) cc_final: 0.7985 (p) REVERT: E 47 VAL cc_start: 0.8613 (OUTLIER) cc_final: 0.8333 (m) REVERT: E 51 GLU cc_start: 0.7461 (mm-30) cc_final: 0.7131 (mm-30) REVERT: E 68 LYS cc_start: 0.8071 (tttt) cc_final: 0.7353 (tttp) REVERT: E 70 GLU cc_start: 0.7013 (mm-30) cc_final: 0.6590 (mm-30) REVERT: E 72 ASP cc_start: 0.6997 (m-30) cc_final: 0.6611 (m-30) REVERT: E 126 LYS cc_start: 0.7425 (mmtt) cc_final: 0.7136 (mmtp) REVERT: E 184 ILE cc_start: 0.7790 (tp) cc_final: 0.7412 (pt) REVERT: E 233 ASN cc_start: 0.8766 (OUTLIER) cc_final: 0.8242 (m-40) REVERT: E 243 LEU cc_start: 0.7294 (OUTLIER) cc_final: 0.6875 (tp) REVERT: E 267 VAL cc_start: 0.8655 (OUTLIER) cc_final: 0.8326 (m) REVERT: E 287 LYS cc_start: 0.7023 (ttmm) cc_final: 0.6590 (mmmm) REVERT: E 313 ASN cc_start: 0.7434 (OUTLIER) cc_final: 0.7190 (t160) REVERT: E 318 VAL cc_start: 0.8726 (p) cc_final: 0.8321 (m) REVERT: E 331 ASP cc_start: 0.8372 (t0) cc_final: 0.7935 (t0) REVERT: E 345 GLU cc_start: 0.7729 (tp30) cc_final: 0.7336 (tp30) REVERT: E 364 SER cc_start: 0.7994 (t) cc_final: 0.7620 (p) REVERT: E 385 TYR cc_start: 0.7984 (m-80) cc_final: 0.7668 (m-80) REVERT: E 396 ARG cc_start: 0.7601 (mtm-85) cc_final: 0.7365 (mtm-85) REVERT: E 412 ASN cc_start: 0.7107 (m-40) cc_final: 0.6845 (m-40) REVERT: E 433 GLU cc_start: 0.8147 (tt0) cc_final: 0.7916 (tt0) REVERT: E 462 GLN cc_start: 0.7818 (tt0) cc_final: 0.7226 (tt0) REVERT: F 47 VAL cc_start: 0.8624 (OUTLIER) cc_final: 0.8395 (m) REVERT: F 51 GLU cc_start: 0.7832 (mm-30) cc_final: 0.7464 (mm-30) REVERT: F 62 ASP cc_start: 0.7865 (t0) cc_final: 0.7261 (t0) REVERT: F 70 GLU cc_start: 0.7473 (mm-30) cc_final: 0.7157 (mm-30) REVERT: F 126 LYS cc_start: 0.7838 (mmtt) cc_final: 0.7623 (mmtp) REVERT: F 183 ASP cc_start: 0.7214 (t70) cc_final: 0.6759 (t0) REVERT: F 198 ARG cc_start: 0.7135 (mmm160) cc_final: 0.6914 (mmm160) REVERT: F 331 ASP cc_start: 0.8142 (t0) cc_final: 0.7474 (t70) REVERT: F 386 LYS cc_start: 0.8241 (mmtm) cc_final: 0.7859 (mmtm) REVERT: F 402 GLN cc_start: 0.8061 (tt0) cc_final: 0.7801 (tt0) REVERT: F 409 TYR cc_start: 0.8475 (t80) cc_final: 0.8040 (t80) REVERT: F 412 ASN cc_start: 0.7451 (m-40) cc_final: 0.7224 (m110) REVERT: F 421 ASP cc_start: 0.7314 (m-30) cc_final: 0.7091 (m-30) REVERT: F 437 ILE cc_start: 0.8666 (mm) cc_final: 0.8330 (mt) REVERT: F 461 ASP cc_start: 0.7704 (t0) cc_final: 0.7490 (t0) REVERT: G 36 TRP cc_start: 0.7575 (m100) cc_final: 0.7353 (m100) REVERT: G 82 GLN cc_start: 0.7447 (tp-100) cc_final: 0.7164 (tp-100) REVERT: H 55 ASP cc_start: 0.8354 (t0) cc_final: 0.8042 (t0) REVERT: H 69 ILE cc_start: 0.8141 (pt) cc_final: 0.7833 (mt) REVERT: H 87 THR cc_start: 0.7799 (m) cc_final: 0.7588 (p) REVERT: H 94 ARG cc_start: 0.8746 (OUTLIER) cc_final: 0.8424 (ttp-110) REVERT: I 34 MET cc_start: 0.6796 (mmt) cc_final: 0.6329 (mmt) REVERT: J 34 MET cc_start: 0.8042 (mmm) cc_final: 0.7125 (mmm) REVERT: J 65 LYS cc_start: 0.8156 (tttt) cc_final: 0.7914 (tttt) REVERT: J 77 THR cc_start: 0.7570 (OUTLIER) cc_final: 0.7310 (m) REVERT: J 82 GLN cc_start: 0.7398 (tp40) cc_final: 0.7115 (tp40) REVERT: K 28 LEU cc_start: 0.8605 (mt) cc_final: 0.8364 (mt) REVERT: K 31 LYS cc_start: 0.7321 (mmtt) cc_final: 0.7099 (mmtt) REVERT: K 35 TRP cc_start: 0.7750 (m100) cc_final: 0.7521 (m100) REVERT: K 93 SER cc_start: 0.9048 (t) cc_final: 0.8424 (p) REVERT: L 31 LYS cc_start: 0.7607 (mmmm) cc_final: 0.7256 (mmmm) REVERT: L 39 LYS cc_start: 0.8717 (mttt) cc_final: 0.8457 (mttm) REVERT: L 48 MET cc_start: 0.7152 (mmm) cc_final: 0.6643 (mmm) REVERT: L 52 SER cc_start: 0.8124 (m) cc_final: 0.7837 (t) REVERT: M 36 HIS cc_start: 0.7906 (m-70) cc_final: 0.7617 (m90) REVERT: M 37 TRP cc_start: 0.8464 (m100) cc_final: 0.8233 (m100) REVERT: N 5 VAL cc_start: 0.6822 (t) cc_final: 0.6326 (m) REVERT: N 35 ASN cc_start: 0.7336 (m-40) cc_final: 0.7025 (m110) REVERT: N 36 TRP cc_start: 0.7680 (m100) cc_final: 0.6830 (m100) REVERT: N 93 ILE cc_start: 0.8406 (mt) cc_final: 0.7859 (tt) REVERT: O 81 GLN cc_start: 0.6753 (mt0) cc_final: 0.6497 (tt0) outliers start: 114 outliers final: 83 residues processed: 653 average time/residue: 0.1551 time to fit residues: 154.1674 Evaluate side-chains 663 residues out of total 2244 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 91 poor density : 572 time to evaluate : 0.833 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 27 SER Chi-restraints excluded: chain A residue 59 THR Chi-restraints excluded: chain A residue 79 ARG Chi-restraints excluded: chain A residue 83 THR Chi-restraints excluded: chain A residue 147 CYS Chi-restraints excluded: chain A residue 204 VAL Chi-restraints excluded: chain A residue 218 SER Chi-restraints excluded: chain A residue 267 VAL Chi-restraints excluded: chain A residue 302 LEU Chi-restraints excluded: chain A residue 316 SER Chi-restraints excluded: chain A residue 442 VAL Chi-restraints excluded: chain A residue 447 ASP Chi-restraints excluded: chain A residue 455 GLN Chi-restraints excluded: chain B residue 29 ILE Chi-restraints excluded: chain B residue 65 SER Chi-restraints excluded: chain B residue 67 SER Chi-restraints excluded: chain B residue 109 VAL Chi-restraints excluded: chain C residue 12 VAL Chi-restraints excluded: chain C residue 29 LEU Chi-restraints excluded: chain C residue 31 THR Chi-restraints excluded: chain C residue 45 LEU Chi-restraints excluded: chain C residue 80 LEU Chi-restraints excluded: chain C residue 95 SER Chi-restraints excluded: chain D residue 9 SER Chi-restraints excluded: chain D residue 14 SER Chi-restraints excluded: chain D residue 56 SER Chi-restraints excluded: chain D residue 63 SER Chi-restraints excluded: chain D residue 95 SER Chi-restraints excluded: chain D residue 107 LEU Chi-restraints excluded: chain E residue 47 VAL Chi-restraints excluded: chain E residue 83 THR Chi-restraints excluded: chain E residue 108 ILE Chi-restraints excluded: chain E residue 147 CYS Chi-restraints excluded: chain E residue 164 GLU Chi-restraints excluded: chain E residue 191 VAL Chi-restraints excluded: chain E residue 233 ASN Chi-restraints excluded: chain E residue 234 MET Chi-restraints excluded: chain E residue 243 LEU Chi-restraints excluded: chain E residue 267 VAL Chi-restraints excluded: chain E residue 302 LEU Chi-restraints excluded: chain E residue 312 GLN Chi-restraints excluded: chain E residue 313 ASN Chi-restraints excluded: chain E residue 336 ASP Chi-restraints excluded: chain E residue 394 SER Chi-restraints excluded: chain E residue 401 LYS Chi-restraints excluded: chain E residue 447 ASP Chi-restraints excluded: chain F residue 31 ILE Chi-restraints excluded: chain F residue 45 THR Chi-restraints excluded: chain F residue 47 VAL Chi-restraints excluded: chain F residue 66 LEU Chi-restraints excluded: chain F residue 83 THR Chi-restraints excluded: chain F residue 108 ILE Chi-restraints excluded: chain F residue 130 LEU Chi-restraints excluded: chain F residue 243 LEU Chi-restraints excluded: chain F residue 267 VAL Chi-restraints excluded: chain F residue 427 LEU Chi-restraints excluded: chain G residue 50 SER Chi-restraints excluded: chain G residue 77 THR Chi-restraints excluded: chain G residue 108 THR Chi-restraints excluded: chain H residue 18 LEU Chi-restraints excluded: chain H residue 20 LEU Chi-restraints excluded: chain H residue 21 THR Chi-restraints excluded: chain H residue 51 ILE Chi-restraints excluded: chain H residue 94 ARG Chi-restraints excluded: chain I residue 32 SER Chi-restraints excluded: chain I residue 37 VAL Chi-restraints excluded: chain I residue 51 ILE Chi-restraints excluded: chain I residue 102 LEU Chi-restraints excluded: chain J residue 5 VAL Chi-restraints excluded: chain J residue 28 THR Chi-restraints excluded: chain J residue 69 THR Chi-restraints excluded: chain J residue 77 THR Chi-restraints excluded: chain J residue 95 PHE Chi-restraints excluded: chain K residue 18 THR Chi-restraints excluded: chain L residue 89 GLN Chi-restraints excluded: chain M residue 60 VAL Chi-restraints excluded: chain M residue 65 SER Chi-restraints excluded: chain M residue 67 SER Chi-restraints excluded: chain M residue 74 SER Chi-restraints excluded: chain M residue 98 SER Chi-restraints excluded: chain N residue 65 LYS Chi-restraints excluded: chain N residue 73 ASP Chi-restraints excluded: chain N residue 95 PHE Chi-restraints excluded: chain N residue 106 SER Chi-restraints excluded: chain O residue 22 CYS Chi-restraints excluded: chain O residue 25 SER Chi-restraints excluded: chain O residue 52 ASP Chi-restraints excluded: chain O residue 65 SER Chi-restraints excluded: chain O residue 67 SER Chi-restraints excluded: chain O residue 74 SER Chi-restraints excluded: chain O residue 98 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 261 random chunks: chunk 122 optimal weight: 2.9990 chunk 0 optimal weight: 2.9990 chunk 23 optimal weight: 6.9990 chunk 39 optimal weight: 0.8980 chunk 93 optimal weight: 0.9980 chunk 257 optimal weight: 3.9990 chunk 202 optimal weight: 1.9990 chunk 20 optimal weight: 0.5980 chunk 35 optimal weight: 0.7980 chunk 136 optimal weight: 0.5980 chunk 74 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 462 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 36 HIS ** D 34 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 313 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 202 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 462 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 56 ASN ** K 34 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 6 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3750 r_free = 0.3750 target = 0.135400 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3525 r_free = 0.3525 target = 0.119390 restraints weight = 30447.953| |-----------------------------------------------------------------------------| r_work (start): 0.3527 rms_B_bonded: 2.00 r_work: 0.3427 rms_B_bonded: 2.28 restraints_weight: 0.5000 r_work: 0.3282 rms_B_bonded: 4.03 restraints_weight: 0.2500 r_work (final): 0.3282 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3194 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3194 r_free = 0.3194 target_work(ls_wunit_k1) = 0.099 | | occupancies: max = 1.00 min = 0.75 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3194 r_free = 0.3194 target_work(ls_wunit_k1) = 0.099 | | occupancies: max = 1.00 min = 0.78 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3194 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7471 moved from start: 0.3558 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 20658 Z= 0.164 Angle : 0.631 9.497 28077 Z= 0.335 Chirality : 0.048 0.326 3237 Planarity : 0.004 0.040 3564 Dihedral : 5.446 41.128 2926 Min Nonbonded Distance : 2.436 Molprobity Statistics. All-atom Clashscore : 9.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.13 % Favored : 95.87 % Rotamer: Outliers : 4.14 % Allowed : 19.12 % Favored : 76.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.48 (0.16), residues: 2622 helix: 0.25 (0.25), residues: 432 sheet: -0.22 (0.18), residues: 816 loop : -0.46 (0.17), residues: 1374 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG E 175 TYR 0.021 0.002 TYR H 96 PHE 0.025 0.002 PHE I 27 TRP 0.042 0.002 TRP D 35 HIS 0.006 0.001 HIS L 34 Details of bonding type rmsd covalent geometry : bond 0.00366 (20610) covalent geometry : angle 0.62327 (27978) SS BOND : bond 0.00386 ( 45) SS BOND : angle 1.78359 ( 90) hydrogen bonds : bond 0.03600 ( 924) hydrogen bonds : angle 5.71457 ( 2550) link_NAG-ASN : bond 0.00426 ( 3) link_NAG-ASN : angle 1.27599 ( 9) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5244 Ramachandran restraints generated. 2622 Oldfield, 0 Emsley, 2622 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5244 Ramachandran restraints generated. 2622 Oldfield, 0 Emsley, 2622 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 670 residues out of total 2244 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 93 poor density : 577 time to evaluate : 0.815 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: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 62 ASP cc_start: 0.8156 (t0) cc_final: 0.7715 (t70) REVERT: A 72 ASP cc_start: 0.7207 (m-30) cc_final: 0.6773 (m-30) REVERT: A 126 LYS cc_start: 0.7156 (mmtt) cc_final: 0.6609 (mmtp) REVERT: A 129 ARG cc_start: 0.7518 (ptp-110) cc_final: 0.7186 (ptm160) REVERT: A 139 ASN cc_start: 0.8320 (m-40) cc_final: 0.8030 (m-40) REVERT: A 142 LYS cc_start: 0.8171 (mmtp) cc_final: 0.7770 (mmtp) REVERT: A 184 ILE cc_start: 0.8122 (mm) cc_final: 0.7429 (pt) REVERT: A 324 LYS cc_start: 0.7721 (mtpt) cc_final: 0.7488 (mtpt) REVERT: A 327 GLU cc_start: 0.7938 (pt0) cc_final: 0.7516 (pt0) REVERT: A 402 GLN cc_start: 0.8236 (tt0) cc_final: 0.7845 (tp40) REVERT: A 412 ASN cc_start: 0.7348 (m-40) cc_final: 0.7141 (m110) REVERT: A 461 ASP cc_start: 0.7534 (t0) cc_final: 0.7267 (t0) REVERT: B 37 TRP cc_start: 0.8206 (m100) cc_final: 0.7873 (m-90) REVERT: C 34 MET cc_start: 0.7001 (mmt) cc_final: 0.6763 (mmt) REVERT: C 91 TYR cc_start: 0.7152 (m-80) cc_final: 0.6650 (m-80) REVERT: E 29 SER cc_start: 0.8350 (t) cc_final: 0.7940 (p) REVERT: E 47 VAL cc_start: 0.8568 (OUTLIER) cc_final: 0.8334 (m) REVERT: E 51 GLU cc_start: 0.7473 (mm-30) cc_final: 0.7118 (mm-30) REVERT: E 68 LYS cc_start: 0.8057 (tttt) cc_final: 0.7356 (tttp) REVERT: E 70 GLU cc_start: 0.6957 (mm-30) cc_final: 0.6517 (mm-30) REVERT: E 72 ASP cc_start: 0.6985 (m-30) cc_final: 0.6576 (m-30) REVERT: E 80 GLU cc_start: 0.7497 (tt0) cc_final: 0.7232 (tt0) REVERT: E 126 LYS cc_start: 0.7387 (mmtt) cc_final: 0.7057 (mmtp) REVERT: E 171 LYS cc_start: 0.7761 (mtmt) cc_final: 0.7407 (mtmt) REVERT: E 206 GLN cc_start: 0.7551 (mt0) cc_final: 0.7107 (mt0) REVERT: E 287 LYS cc_start: 0.6966 (ttmm) cc_final: 0.6538 (mmmm) REVERT: E 313 ASN cc_start: 0.7423 (OUTLIER) cc_final: 0.7218 (t160) REVERT: E 318 VAL cc_start: 0.8714 (p) cc_final: 0.8341 (m) REVERT: E 385 TYR cc_start: 0.7987 (m-80) cc_final: 0.7641 (m-80) REVERT: E 412 ASN cc_start: 0.7126 (m-40) cc_final: 0.6663 (m-40) REVERT: E 433 GLU cc_start: 0.8178 (tt0) cc_final: 0.7944 (tt0) REVERT: E 462 GLN cc_start: 0.8004 (tt0) cc_final: 0.7582 (tt0) REVERT: F 47 VAL cc_start: 0.8618 (OUTLIER) cc_final: 0.8277 (t) REVERT: F 51 GLU cc_start: 0.7759 (mm-30) cc_final: 0.7377 (mm-30) REVERT: F 62 ASP cc_start: 0.7806 (t0) cc_final: 0.7174 (t0) REVERT: F 70 GLU cc_start: 0.7395 (mm-30) cc_final: 0.7081 (mm-30) REVERT: F 126 LYS cc_start: 0.7675 (mmtt) cc_final: 0.7440 (mmtp) REVERT: F 229 ARG cc_start: 0.8147 (mmm160) cc_final: 0.7813 (mmm160) REVERT: F 331 ASP cc_start: 0.8076 (t0) cc_final: 0.7360 (t70) REVERT: F 386 LYS cc_start: 0.8165 (mmtm) cc_final: 0.7901 (mmtm) REVERT: F 402 GLN cc_start: 0.7941 (tt0) cc_final: 0.7704 (tt0) REVERT: F 412 ASN cc_start: 0.7430 (m-40) cc_final: 0.7184 (m110) REVERT: F 437 ILE cc_start: 0.8623 (mm) cc_final: 0.8259 (mt) REVERT: F 461 ASP cc_start: 0.7532 (t0) cc_final: 0.7311 (t0) REVERT: G 36 TRP cc_start: 0.7516 (m100) cc_final: 0.7251 (m100) REVERT: H 69 ILE cc_start: 0.8060 (pt) cc_final: 0.7788 (mt) REVERT: H 82 MET cc_start: 0.7032 (mmm) cc_final: 0.6506 (mmp) REVERT: H 87 THR cc_start: 0.7788 (m) cc_final: 0.7560 (p) REVERT: H 94 ARG cc_start: 0.8725 (OUTLIER) cc_final: 0.8433 (ttp-110) REVERT: I 30 THR cc_start: 0.7838 (p) cc_final: 0.7530 (t) REVERT: I 34 MET cc_start: 0.6667 (mmt) cc_final: 0.6193 (mmt) REVERT: J 34 MET cc_start: 0.7930 (mmm) cc_final: 0.7086 (mmm) REVERT: J 65 LYS cc_start: 0.8251 (tttt) cc_final: 0.8034 (tttt) REVERT: J 82 GLN cc_start: 0.7342 (tp40) cc_final: 0.6990 (tp40) REVERT: K 28 LEU cc_start: 0.8580 (mt) cc_final: 0.8335 (mt) REVERT: K 31 LYS cc_start: 0.7443 (mmtt) cc_final: 0.7231 (mmtt) REVERT: K 93 SER cc_start: 0.8999 (t) cc_final: 0.8528 (p) REVERT: L 39 LYS cc_start: 0.8717 (mttt) cc_final: 0.8485 (mttm) REVERT: L 48 MET cc_start: 0.7101 (mmm) cc_final: 0.6564 (mmm) REVERT: L 52 SER cc_start: 0.8041 (m) cc_final: 0.7746 (t) REVERT: M 36 HIS cc_start: 0.7816 (m-70) cc_final: 0.7255 (m-70) REVERT: M 37 TRP cc_start: 0.8475 (m100) cc_final: 0.8231 (m100) REVERT: N 5 VAL cc_start: 0.6861 (t) cc_final: 0.6153 (m) REVERT: N 35 ASN cc_start: 0.7256 (m-40) cc_final: 0.6927 (m110) REVERT: N 93 ILE cc_start: 0.8374 (mt) cc_final: 0.7862 (tt) outliers start: 93 outliers final: 73 residues processed: 627 average time/residue: 0.1589 time to fit residues: 151.1545 Evaluate side-chains 644 residues out of total 2244 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 567 time to evaluate : 0.785 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 27 SER Chi-restraints excluded: chain A residue 83 THR Chi-restraints excluded: chain A residue 147 CYS Chi-restraints excluded: chain A residue 218 SER Chi-restraints excluded: chain A residue 267 VAL Chi-restraints excluded: chain A residue 302 LEU Chi-restraints excluded: chain A residue 447 ASP Chi-restraints excluded: chain A residue 455 GLN Chi-restraints excluded: chain B residue 23 THR Chi-restraints excluded: chain B residue 65 SER Chi-restraints excluded: chain B residue 98 SER Chi-restraints excluded: chain C residue 12 VAL Chi-restraints excluded: chain C residue 29 LEU Chi-restraints excluded: chain C residue 31 THR Chi-restraints excluded: chain C residue 45 LEU Chi-restraints excluded: chain C residue 80 LEU Chi-restraints excluded: chain C residue 95 SER Chi-restraints excluded: chain D residue 9 SER Chi-restraints excluded: chain D residue 56 SER Chi-restraints excluded: chain D residue 63 SER Chi-restraints excluded: chain D residue 107 LEU Chi-restraints excluded: chain E residue 47 VAL Chi-restraints excluded: chain E residue 73 LEU Chi-restraints excluded: chain E residue 108 ILE Chi-restraints excluded: chain E residue 147 CYS Chi-restraints excluded: chain E residue 164 GLU Chi-restraints excluded: chain E residue 191 VAL Chi-restraints excluded: chain E residue 234 MET Chi-restraints excluded: chain E residue 275 ILE Chi-restraints excluded: chain E residue 302 LEU Chi-restraints excluded: chain E residue 312 GLN Chi-restraints excluded: chain E residue 313 ASN Chi-restraints excluded: chain E residue 336 ASP Chi-restraints excluded: chain E residue 401 LYS Chi-restraints excluded: chain E residue 427 LEU Chi-restraints excluded: chain F residue 31 ILE Chi-restraints excluded: chain F residue 45 THR Chi-restraints excluded: chain F residue 47 VAL Chi-restraints excluded: chain F residue 66 LEU Chi-restraints excluded: chain F residue 83 THR Chi-restraints excluded: chain F residue 130 LEU Chi-restraints excluded: chain F residue 243 LEU Chi-restraints excluded: chain F residue 302 LEU Chi-restraints excluded: chain F residue 323 GLU Chi-restraints excluded: chain F residue 427 LEU Chi-restraints excluded: chain G residue 50 SER Chi-restraints excluded: chain G residue 77 THR Chi-restraints excluded: chain G residue 108 THR Chi-restraints excluded: chain H residue 18 LEU Chi-restraints excluded: chain H residue 21 THR Chi-restraints excluded: chain H residue 51 ILE Chi-restraints excluded: chain H residue 94 ARG Chi-restraints excluded: chain I residue 37 VAL Chi-restraints excluded: chain I residue 102 LEU Chi-restraints excluded: chain J residue 3 GLN Chi-restraints excluded: chain J residue 5 VAL Chi-restraints excluded: chain J residue 28 THR Chi-restraints excluded: chain J residue 69 THR Chi-restraints excluded: chain J residue 95 PHE Chi-restraints excluded: chain K residue 18 THR Chi-restraints excluded: chain L residue 89 GLN Chi-restraints excluded: chain L residue 107 LEU Chi-restraints excluded: chain M residue 52 ASP Chi-restraints excluded: chain M residue 60 VAL Chi-restraints excluded: chain M residue 65 SER Chi-restraints excluded: chain M residue 67 SER Chi-restraints excluded: chain M residue 74 SER Chi-restraints excluded: chain M residue 84 ASP Chi-restraints excluded: chain M residue 98 SER Chi-restraints excluded: chain N residue 65 LYS Chi-restraints excluded: chain N residue 73 ASP Chi-restraints excluded: chain N residue 95 PHE Chi-restraints excluded: chain O residue 25 SER Chi-restraints excluded: chain O residue 35 VAL Chi-restraints excluded: chain O residue 65 SER Chi-restraints excluded: chain O residue 74 SER Chi-restraints excluded: chain O residue 98 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/command_line/real_space_refine.py", line 9, in run_program(real_space_refine.Program) File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/iotbx/cli_parser.py", line 999, in run_program task.run() File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/programs/real_space_refine.py", line 206, in run self.rsr_result = rsr_wrappers.run_real_space_refine( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/refinement/rsr/wrappers.py", line 52, in __init__ self._refined = macro_cycle_real_space.run( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/refinement/macro_cycle_real_space.py", line 306, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/refinement/macro_cycle_real_space.py", line 702, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/refinement/macro_cycle_real_space.py", line 755, in minimization_no_ncs ro = mmtbx.refinement.real_space.individual_sites.easy( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 44, in __init__ self.weight = mmtbx.refinement.real_space.weight.run( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/mmtbx/refinement/real_space/weight.py", line 84, in __init__ ro.refine( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 362, in refine real_space_result = refinery( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 233, in __init__ refiner.refine( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 100, in refine self.refined = maptbx.real_space_refinement_simple.lbfgs( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/cctbx/maptbx/real_space_refinement_simple.py", line 168, in __init__ O.minimizer = scitbx.lbfgs.run( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/scitbx/lbfgs/__init__.py", line 270, in run return run_c_plus_plus( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/cctbx/maptbx/real_space_refinement_simple.py", line 243, in compute_functional_and_gradients gr_e = O.geometry_restraints_manager.energies_sites( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/cctbx/geometry_restraints/manager.py", line 1588, in energies_sites pair_proxies = self.pair_proxies( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/cctbx/geometry_restraints/manager.py", line 1491, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/cctbx/geometry_restraints/manager.py", line 1372, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 67.6831 > 50: distance: 18 - 22: 29.036 distance: 22 - 23: 15.546 distance: 22 - 162: 30.145 distance: 23 - 24: 12.299 distance: 23 - 26: 43.641 distance: 24 - 25: 48.945 distance: 24 - 29: 27.576 distance: 26 - 27: 63.142 distance: 26 - 28: 21.878 distance: 29 - 30: 13.647 distance: 30 - 31: 23.416 distance: 30 - 33: 61.641 distance: 31 - 32: 21.275 distance: 31 - 35: 18.421 distance: 33 - 34: 8.404 distance: 35 - 36: 62.814 distance: 35 - 41: 29.770 distance: 36 - 37: 40.651 distance: 36 - 39: 37.644 distance: 37 - 38: 30.802 distance: 37 - 42: 61.812 distance: 39 - 40: 19.247 distance: 40 - 41: 36.905 distance: 42 - 43: 27.578 distance: 43 - 44: 31.111 distance: 44 - 45: 19.688 distance: 44 - 46: 25.492 distance: 46 - 47: 12.162 distance: 47 - 48: 36.874 distance: 47 - 50: 31.450 distance: 48 - 49: 15.416 distance: 48 - 55: 17.916 distance: 50 - 51: 24.410 distance: 51 - 52: 19.127 distance: 52 - 53: 11.840 distance: 52 - 54: 26.890 distance: 55 - 56: 30.134 distance: 56 - 57: 14.037 distance: 56 - 59: 32.366 distance: 57 - 58: 32.846 distance: 57 - 62: 11.584 distance: 59 - 60: 25.173 distance: 59 - 61: 18.888 distance: 62 - 63: 28.814 distance: 62 - 130: 26.159 distance: 63 - 64: 41.309 distance: 63 - 66: 60.087 distance: 64 - 65: 29.340 distance: 64 - 67: 15.740 distance: 65 - 127: 31.705 distance: 67 - 68: 25.080 distance: 68 - 69: 31.439 distance: 68 - 71: 23.095 distance: 69 - 70: 16.203 distance: 69 - 78: 13.992 distance: 71 - 72: 19.841 distance: 72 - 73: 40.587 distance: 73 - 74: 33.905 distance: 74 - 75: 8.196 distance: 75 - 76: 4.396 distance: 75 - 77: 7.437 distance: 78 - 79: 14.141 distance: 78 - 117: 32.908 distance: 79 - 80: 24.696 distance: 79 - 82: 23.573 distance: 80 - 81: 28.388 distance: 80 - 86: 21.538 distance: 81 - 114: 23.105 distance: 82 - 83: 25.727 distance: 82 - 84: 18.487 distance: 83 - 85: 23.754 distance: 86 - 87: 25.319 distance: 86 - 92: 22.388 distance: 87 - 88: 30.157 distance: 87 - 90: 13.209 distance: 88 - 89: 5.738 distance: 88 - 93: 22.939 distance: 90 - 91: 21.739 distance: 91 - 92: 25.784