Starting phenix.real_space_refine on Tue Jun 24 01:12:11 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8cw9_27024/06_2025/8cw9_27024.cif Found real_map, /net/cci-nas-00/data/ceres_data/8cw9_27024/06_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_27024/06_2025/8cw9_27024.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8cw9_27024/06_2025/8cw9_27024.map" model { file = "/net/cci-nas-00/data/ceres_data/8cw9_27024/06_2025/8cw9_27024.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8cw9_27024/06_2025/8cw9_27024.cif" } resolution = 3.46 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } 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): 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/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: 10.95, per 1000 atoms: 0.54 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: 4.32 Conformation dependent library (CDL) restraints added in 2.5 seconds 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: 3.27 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: 7.67 Time building geometry restraints manager: 5.22 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: 0.03 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: 1.060 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.160 Construct map_model_manager: 0.010 Extract box with map and model: 0.670 Check model and map are aligned: 0.130 Set scattering table: 0.180 Process input model: 44.950 Find NCS groups from input model: 0.860 Set up NCS constraints: 0.100 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: 0.010 Load rotamer database and sin/cos tables:2.680 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 50.810 ------------------------------------------------------------------------------- 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. 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 TRP 0.020 0.002 TRP E 43 HIS 0.004 0.001 HIS E 435 PHE 0.018 0.002 PHE A 334 TYR 0.029 0.005 TYR A 44 ARG 0.028 0.004 ARG E 367 Details of bonding type rmsd link_NAG-ASN : bond 0.00180 ( 3) link_NAG-ASN : angle 1.13202 ( 9) hydrogen bonds : bond 0.21491 ( 924) hydrogen bonds : angle 9.40359 ( 2550) SS BOND : bond 0.00248 ( 45) SS BOND : angle 1.41852 ( 90) covalent geometry : bond 0.00231 (20610) covalent geometry : angle 0.66528 (27978) *********************** 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 : 2.022 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: 0.3531 time to fit residues: 396.5833 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 : 2.042 ------------------------------------------------------------------------------- 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 220 optimal weight: 0.7980 chunk 197 optimal weight: 1.9990 chunk 109 optimal weight: 2.9990 chunk 67 optimal weight: 0.2980 chunk 133 optimal weight: 1.9990 chunk 105 optimal weight: 0.9990 chunk 204 optimal weight: 0.0570 chunk 79 optimal weight: 0.7980 chunk 124 optimal weight: 0.8980 chunk 152 optimal weight: 3.9990 chunk 237 optimal weight: 2.9990 overall best weight: 0.5698 ------------------------------------------------------------------------------- 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 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: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3772 r_free = 0.3772 target = 0.137456 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3553 r_free = 0.3553 target = 0.121324 restraints weight = 30834.307| |-----------------------------------------------------------------------------| r_work (start): 0.3562 rms_B_bonded: 2.02 r_work: 0.3458 rms_B_bonded: 2.34 restraints_weight: 0.5000 r_work: 0.3313 rms_B_bonded: 4.10 restraints_weight: 0.2500 r_work (final): 0.3313 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3321 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3321 r_free = 0.3321 target_work(ls_wunit_k1) = 0.106 | | occupancies: max = 1.00 min = 1.00 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3321 r_free = 0.3321 target_work(ls_wunit_k1) = 0.106 | | occupancies: max = 1.00 min = 0.65 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3321 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7438 moved from start: 0.2225 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 20658 Z= 0.149 Angle : 0.655 8.196 28077 Z= 0.352 Chirality : 0.047 0.231 3237 Planarity : 0.005 0.049 3564 Dihedral : 6.124 46.739 2932 Min Nonbonded Distance : 2.471 Molprobity Statistics. All-atom Clashscore : 7.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.10 % Favored : 96.90 % Rotamer: Outliers : 2.99 % Allowed : 12.08 % Favored : 84.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.20 (0.16), residues: 2622 helix: 0.29 (0.25), residues: 417 sheet: -0.22 (0.18), residues: 795 loop : -0.08 (0.17), residues: 1410 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP J 36 HIS 0.005 0.002 HIS K 34 PHE 0.020 0.002 PHE J 29 TYR 0.027 0.002 TYR A 385 ARG 0.007 0.001 ARG E 304 Details of bonding type rmsd link_NAG-ASN : bond 0.00398 ( 3) link_NAG-ASN : angle 0.92194 ( 9) hydrogen bonds : bond 0.03999 ( 924) hydrogen bonds : angle 6.25656 ( 2550) SS BOND : bond 0.00372 ( 45) SS BOND : angle 2.06532 ( 90) covalent geometry : bond 0.00324 (20610) covalent geometry : angle 0.64555 (27978) *********************** 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 707 residues out of total 2244 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 640 time to evaluate : 2.248 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 35 TYR cc_start: 0.8178 (m-80) cc_final: 0.7655 (m-80) REVERT: A 62 ASP cc_start: 0.7962 (t0) cc_final: 0.7672 (t0) REVERT: A 72 ASP cc_start: 0.7133 (m-30) cc_final: 0.6705 (m-30) REVERT: A 83 THR cc_start: 0.7520 (OUTLIER) cc_final: 0.7201 (t) REVERT: A 126 LYS cc_start: 0.6985 (mmtt) cc_final: 0.6589 (mmmm) REVERT: A 164 GLU cc_start: 0.7862 (OUTLIER) cc_final: 0.7651 (mp0) REVERT: A 184 ILE cc_start: 0.8073 (mm) cc_final: 0.7418 (pt) REVERT: A 234 MET cc_start: 0.8311 (ptp) cc_final: 0.7984 (ptm) REVERT: A 307 GLN cc_start: 0.8298 (mt0) cc_final: 0.8001 (mt0) REVERT: A 327 GLU cc_start: 0.8257 (pt0) cc_final: 0.7786 (pt0) REVERT: A 367 ARG cc_start: 0.8101 (ptt-90) cc_final: 0.7648 (ptp90) REVERT: A 376 SER cc_start: 0.8119 (m) cc_final: 0.7886 (p) REVERT: A 385 TYR cc_start: 0.7888 (m-80) cc_final: 0.7505 (m-10) REVERT: A 386 LYS cc_start: 0.8051 (mmmt) cc_final: 0.7830 (mmmt) REVERT: A 402 GLN cc_start: 0.8288 (tt0) cc_final: 0.7977 (tp40) REVERT: A 412 ASN cc_start: 0.7602 (m-40) cc_final: 0.7125 (m110) REVERT: A 428 SER cc_start: 0.7950 (m) cc_final: 0.7367 (p) REVERT: A 433 GLU cc_start: 0.8020 (tt0) cc_final: 0.7799 (tt0) REVERT: A 440 ARG cc_start: 0.7625 (ttm170) cc_final: 0.7286 (ptm-80) REVERT: B 37 TRP cc_start: 0.8299 (m100) cc_final: 0.7960 (m-90) REVERT: B 47 LYS cc_start: 0.8088 (tttt) cc_final: 0.7856 (tttt) REVERT: B 51 TYR cc_start: 0.8579 (p90) cc_final: 0.8301 (p90) REVERT: B 68 LYS cc_start: 0.7964 (tttm) cc_final: 0.7633 (ttpt) REVERT: C 34 MET cc_start: 0.6950 (mmt) cc_final: 0.6722 (mmt) REVERT: C 68 THR cc_start: 0.7346 (m) cc_final: 0.6982 (p) REVERT: C 91 TYR cc_start: 0.6925 (m-80) cc_final: 0.6543 (m-80) REVERT: D 34 HIS cc_start: 0.6391 (m-70) cc_final: 0.5654 (m90) REVERT: D 89 GLN cc_start: 0.7910 (pp30) cc_final: 0.7188 (pp30) REVERT: E 29 SER cc_start: 0.8124 (t) cc_final: 0.7810 (p) REVERT: E 51 GLU cc_start: 0.7501 (mm-30) cc_final: 0.7105 (mm-30) REVERT: E 68 LYS cc_start: 0.7922 (tttt) cc_final: 0.7712 (tttp) REVERT: E 70 GLU cc_start: 0.6778 (mm-30) cc_final: 0.6556 (mm-30) REVERT: E 126 LYS cc_start: 0.7257 (mmtt) cc_final: 0.7010 (mmtp) REVERT: E 143 LYS cc_start: 0.8166 (mtmt) cc_final: 0.7961 (ttmt) REVERT: E 175 ARG cc_start: 0.7698 (mtm-85) cc_final: 0.7441 (mtm-85) REVERT: E 205 ARG cc_start: 0.7690 (mmm-85) cc_final: 0.7172 (mmm-85) REVERT: E 233 ASN cc_start: 0.8685 (OUTLIER) cc_final: 0.8237 (m-40) REVERT: E 245 LEU cc_start: 0.7615 (OUTLIER) cc_final: 0.7245 (mp) REVERT: E 267 VAL cc_start: 0.8716 (OUTLIER) cc_final: 0.8367 (m) REVERT: E 287 LYS cc_start: 0.6891 (ttmm) cc_final: 0.6526 (mmmm) REVERT: E 306 ASP cc_start: 0.7629 (p0) cc_final: 0.7290 (p0) REVERT: E 318 VAL cc_start: 0.8731 (p) cc_final: 0.8317 (m) REVERT: E 335 CYS cc_start: 0.6664 (m) cc_final: 0.6363 (m) REVERT: E 364 SER cc_start: 0.7692 (t) cc_final: 0.7160 (p) REVERT: E 400 ILE cc_start: 0.8072 (mt) cc_final: 0.7763 (mm) REVERT: E 410 ILE cc_start: 0.8393 (mm) cc_final: 0.8189 (mm) REVERT: E 412 ASN cc_start: 0.7057 (m-40) cc_final: 0.6729 (m-40) REVERT: E 433 GLU cc_start: 0.7980 (tt0) cc_final: 0.7721 (tt0) REVERT: F 27 SER cc_start: 0.8649 (t) cc_final: 0.8393 (p) REVERT: F 51 GLU cc_start: 0.7932 (mm-30) cc_final: 0.7503 (mm-30) REVERT: F 62 ASP cc_start: 0.7782 (t0) cc_final: 0.7315 (t0) REVERT: F 68 LYS cc_start: 0.8485 (tttp) cc_final: 0.8046 (tttp) REVERT: F 72 ASP cc_start: 0.7244 (m-30) cc_final: 0.7026 (m-30) REVERT: F 126 LYS cc_start: 0.7494 (mmtt) cc_final: 0.7201 (mmtp) REVERT: F 140 CYS cc_start: 0.5926 (p) cc_final: 0.5695 (p) REVERT: F 198 ARG cc_start: 0.7209 (mmm160) cc_final: 0.6818 (mmm160) REVERT: F 202 ASN cc_start: 0.7501 (m-40) cc_final: 0.6974 (m110) REVERT: F 205 ARG cc_start: 0.7816 (mmm-85) cc_final: 0.7580 (mmm-85) REVERT: F 222 MET cc_start: 0.8389 (ttp) cc_final: 0.8174 (ttm) REVERT: F 331 ASP cc_start: 0.7896 (t0) cc_final: 0.7378 (t70) REVERT: F 386 LYS cc_start: 0.7972 (mmtm) cc_final: 0.7744 (mmtm) REVERT: F 412 ASN cc_start: 0.7476 (m-40) cc_final: 0.7259 (m110) REVERT: F 437 ILE cc_start: 0.8682 (mm) cc_final: 0.8303 (mt) REVERT: G 36 TRP cc_start: 0.7623 (m100) cc_final: 0.7334 (m100) REVERT: G 116 GLN cc_start: 0.7993 (mm-40) cc_final: 0.7779 (mm-40) REVERT: H 34 MET cc_start: 0.6365 (mmt) cc_final: 0.6163 (tpp) REVERT: H 45 LEU cc_start: 0.8460 (mp) cc_final: 0.8164 (mt) REVERT: H 87 THR cc_start: 0.7617 (m) cc_final: 0.7357 (p) REVERT: I 34 MET cc_start: 0.6867 (mmt) cc_final: 0.6568 (mmt) REVERT: I 50 ARG cc_start: 0.8084 (ttp80) cc_final: 0.7374 (ttp-170) REVERT: J 34 MET cc_start: 0.8221 (mmm) cc_final: 0.7733 (mmm) REVERT: J 65 LYS cc_start: 0.7981 (tttt) cc_final: 0.7759 (tttt) REVERT: K 93 SER cc_start: 0.8957 (t) cc_final: 0.8551 (p) REVERT: L 12 SER cc_start: 0.8086 (p) cc_final: 0.7856 (t) REVERT: L 35 TRP cc_start: 0.8259 (m100) cc_final: 0.8038 (m100) REVERT: L 39 LYS cc_start: 0.8718 (mttt) cc_final: 0.8355 (mttm) REVERT: L 48 MET cc_start: 0.7114 (mmm) cc_final: 0.6743 (mmm) REVERT: L 52 SER cc_start: 0.8168 (m) cc_final: 0.7930 (p) REVERT: L 75 ILE cc_start: 0.8368 (mt) cc_final: 0.8091 (mt) REVERT: L 87 TYR cc_start: 0.7754 (m-80) cc_final: 0.7497 (m-10) REVERT: M 36 HIS cc_start: 0.7851 (m-70) cc_final: 0.7200 (m-70) REVERT: M 37 TRP cc_start: 0.8522 (m100) cc_final: 0.7920 (m100) REVERT: M 67 SER cc_start: 0.8135 (OUTLIER) cc_final: 0.7931 (m) REVERT: M 68 LYS cc_start: 0.8372 (tttm) cc_final: 0.7302 (tttt) REVERT: N 5 VAL cc_start: 0.6837 (t) cc_final: 0.6389 (m) REVERT: N 80 PHE cc_start: 0.7854 (m-80) cc_final: 0.7081 (m-80) REVERT: N 93 ILE cc_start: 0.8510 (mt) cc_final: 0.7955 (tt) REVERT: N 94 TYR cc_start: 0.7889 (m-80) cc_final: 0.7520 (m-80) REVERT: N 119 LEU cc_start: 0.8303 (tp) cc_final: 0.7956 (tt) REVERT: O 10 VAL cc_start: 0.8724 (p) cc_final: 0.8374 (t) REVERT: O 47 LYS cc_start: 0.7923 (tttt) cc_final: 0.7664 (tttt) outliers start: 67 outliers final: 39 residues processed: 670 average time/residue: 0.3345 time to fit residues: 335.9132 Evaluate side-chains 662 residues out of total 2244 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 617 time to evaluate : 2.359 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 83 THR 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 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 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 73 LEU 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 I residue 70 SER Chi-restraints excluded: chain J residue 69 THR Chi-restraints excluded: chain L residue 79 GLN Chi-restraints excluded: chain L residue 89 GLN Chi-restraints excluded: chain L residue 107 LEU Chi-restraints excluded: chain M residue 21 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 O residue 22 CYS 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=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 261 random chunks: chunk 46 optimal weight: 0.7980 chunk 185 optimal weight: 4.9990 chunk 232 optimal weight: 0.9980 chunk 180 optimal weight: 4.9990 chunk 69 optimal weight: 6.9990 chunk 238 optimal weight: 1.9990 chunk 62 optimal weight: 4.9990 chunk 25 optimal weight: 0.7980 chunk 172 optimal weight: 0.7980 chunk 55 optimal weight: 0.6980 chunk 197 optimal weight: 0.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 172 ASN ** A 178 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 195 GLN A 453 GLN A 455 GLN 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 E 353 ASN F 455 GLN H 16 GLN ** K 34 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N 35 ASN ** O 53 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3753 r_free = 0.3753 target = 0.135922 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3532 r_free = 0.3532 target = 0.119781 restraints weight = 30585.769| |-----------------------------------------------------------------------------| r_work (start): 0.3542 rms_B_bonded: 2.00 r_work: 0.3439 rms_B_bonded: 2.31 restraints_weight: 0.5000 r_work: 0.3294 rms_B_bonded: 4.06 restraints_weight: 0.2500 r_work (final): 0.3294 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3273 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3273 r_free = 0.3273 target_work(ls_wunit_k1) = 0.103 | | occupancies: max = 1.00 min = 0.65 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3273 r_free = 0.3273 target_work(ls_wunit_k1) = 0.103 | | occupancies: max = 1.00 min = 0.68 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3273 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7458 moved from start: 0.2846 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 20658 Z= 0.168 Angle : 0.621 7.945 28077 Z= 0.333 Chirality : 0.047 0.280 3237 Planarity : 0.004 0.043 3564 Dihedral : 5.539 42.030 2926 Min Nonbonded Distance : 2.496 Molprobity Statistics. All-atom Clashscore : 7.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.52 % Favored : 96.48 % Rotamer: Outliers : 3.79 % Allowed : 14.35 % Favored : 81.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.10 (0.16), residues: 2622 helix: 0.56 (0.25), residues: 417 sheet: -0.29 (0.18), residues: 798 loop : 0.02 (0.17), residues: 1407 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.002 TRP D 35 HIS 0.006 0.002 HIS L 34 PHE 0.015 0.002 PHE J 29 TYR 0.023 0.002 TYR F 385 ARG 0.006 0.001 ARG E 304 Details of bonding type rmsd link_NAG-ASN : bond 0.00523 ( 3) link_NAG-ASN : angle 1.13611 ( 9) hydrogen bonds : bond 0.03764 ( 924) hydrogen bonds : angle 5.79465 ( 2550) SS BOND : bond 0.00434 ( 45) SS BOND : angle 1.53662 ( 90) covalent geometry : bond 0.00370 (20610) covalent geometry : angle 0.61536 (27978) *********************** 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 703 residues out of total 2244 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 85 poor density : 618 time to evaluate : 2.095 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 26 GLU cc_start: 0.7882 (pt0) cc_final: 0.7562 (pt0) REVERT: A 62 ASP cc_start: 0.8078 (t0) cc_final: 0.7798 (t0) REVERT: A 72 ASP cc_start: 0.7131 (m-30) cc_final: 0.6667 (m-30) REVERT: A 126 LYS cc_start: 0.6975 (mmtt) cc_final: 0.6670 (mmmm) REVERT: A 133 GLU cc_start: 0.7409 (mm-30) cc_final: 0.7183 (mm-30) REVERT: A 164 GLU cc_start: 0.7828 (OUTLIER) cc_final: 0.7606 (mp0) REVERT: A 250 MET cc_start: 0.6759 (mmm) cc_final: 0.6322 (mmm) REVERT: A 327 GLU cc_start: 0.8149 (pt0) cc_final: 0.7628 (pt0) REVERT: A 385 TYR cc_start: 0.7833 (m-80) cc_final: 0.7445 (m-10) REVERT: A 402 GLN cc_start: 0.8256 (tt0) cc_final: 0.7920 (tp40) REVERT: A 428 SER cc_start: 0.7990 (m) cc_final: 0.7428 (p) REVERT: A 433 GLU cc_start: 0.8008 (tt0) cc_final: 0.7734 (tt0) REVERT: B 37 TRP cc_start: 0.8308 (m100) cc_final: 0.7950 (m-90) REVERT: C 34 MET cc_start: 0.7004 (mmt) cc_final: 0.6760 (mmt) REVERT: C 68 THR cc_start: 0.7533 (m) cc_final: 0.7212 (p) REVERT: C 91 TYR cc_start: 0.6996 (m-80) cc_final: 0.6563 (m-80) REVERT: D 34 HIS cc_start: 0.6467 (m-70) cc_final: 0.5840 (m90) REVERT: E 29 SER cc_start: 0.8225 (t) cc_final: 0.7805 (p) REVERT: E 51 GLU cc_start: 0.7530 (mm-30) cc_final: 0.7143 (mm-30) REVERT: E 68 LYS cc_start: 0.7935 (tttt) cc_final: 0.7731 (tttp) REVERT: E 70 GLU cc_start: 0.6826 (mm-30) cc_final: 0.6586 (mm-30) REVERT: E 126 LYS cc_start: 0.7282 (mmtt) cc_final: 0.6995 (mmtp) REVERT: E 143 LYS cc_start: 0.8214 (mtmt) cc_final: 0.8010 (ttmt) REVERT: E 175 ARG cc_start: 0.7850 (mtm-85) cc_final: 0.7644 (mtm-85) REVERT: E 181 LYS cc_start: 0.8657 (mtmm) cc_final: 0.8211 (mtmm) REVERT: E 233 ASN cc_start: 0.8660 (OUTLIER) cc_final: 0.8226 (m-40) REVERT: E 245 LEU cc_start: 0.7598 (OUTLIER) cc_final: 0.7333 (mp) REVERT: E 267 VAL cc_start: 0.8679 (OUTLIER) cc_final: 0.8345 (m) REVERT: E 318 VAL cc_start: 0.8747 (p) cc_final: 0.8320 (m) REVERT: E 327 GLU cc_start: 0.7364 (pt0) cc_final: 0.7101 (pt0) REVERT: E 412 ASN cc_start: 0.7145 (m-40) cc_final: 0.6786 (m-40) REVERT: F 27 SER cc_start: 0.8571 (t) cc_final: 0.8332 (p) REVERT: F 47 VAL cc_start: 0.8599 (OUTLIER) cc_final: 0.8386 (m) REVERT: F 51 GLU cc_start: 0.7938 (mm-30) cc_final: 0.7490 (mm-30) REVERT: F 62 ASP cc_start: 0.7813 (t0) cc_final: 0.7276 (t0) REVERT: F 68 LYS cc_start: 0.8403 (tttp) cc_final: 0.8037 (tttp) REVERT: F 72 ASP cc_start: 0.7300 (m-30) cc_final: 0.7100 (m-30) REVERT: F 126 LYS cc_start: 0.7575 (mmtt) cc_final: 0.7347 (mmtp) REVERT: F 183 ASP cc_start: 0.7192 (t0) cc_final: 0.6907 (t0) REVERT: F 205 ARG cc_start: 0.7825 (mmm-85) cc_final: 0.7535 (mmm-85) REVERT: F 226 GLU cc_start: 0.8112 (mt-10) cc_final: 0.7766 (mt-10) REVERT: F 331 ASP cc_start: 0.7988 (t0) cc_final: 0.7438 (t70) REVERT: F 345 GLU cc_start: 0.7833 (tp30) cc_final: 0.7629 (tp30) REVERT: F 412 ASN cc_start: 0.7458 (m-40) cc_final: 0.7215 (m110) REVERT: F 437 ILE cc_start: 0.8662 (mm) cc_final: 0.8288 (mt) REVERT: F 461 ASP cc_start: 0.7764 (t0) cc_final: 0.7521 (t0) REVERT: G 36 TRP cc_start: 0.7578 (m100) cc_final: 0.7325 (m100) REVERT: G 94 TYR cc_start: 0.7389 (m-80) cc_final: 0.6975 (m-80) REVERT: H 69 ILE cc_start: 0.8394 (pt) cc_final: 0.8009 (mt) REVERT: H 82 MET cc_start: 0.6675 (mmp) cc_final: 0.6464 (mmp) REVERT: H 87 THR cc_start: 0.7651 (m) cc_final: 0.7410 (p) REVERT: I 34 MET cc_start: 0.6936 (mmt) cc_final: 0.6436 (mmt) REVERT: I 50 ARG cc_start: 0.8060 (ttp80) cc_final: 0.7375 (ttp-170) REVERT: J 34 MET cc_start: 0.7938 (mmm) cc_final: 0.7273 (mmm) REVERT: J 100 ARG cc_start: 0.8461 (mtp85) cc_final: 0.8232 (mtp-110) REVERT: K 93 SER cc_start: 0.9037 (t) cc_final: 0.8607 (p) REVERT: L 12 SER cc_start: 0.8045 (p) cc_final: 0.7827 (t) REVERT: L 39 LYS cc_start: 0.8659 (mttt) cc_final: 0.8348 (mttm) REVERT: L 48 MET cc_start: 0.7193 (mmm) cc_final: 0.6774 (mmm) REVERT: L 52 SER cc_start: 0.8157 (m) cc_final: 0.7818 (t) REVERT: M 28 ASN cc_start: 0.7782 (m-40) cc_final: 0.7453 (m-40) REVERT: M 36 HIS cc_start: 0.7838 (m-70) cc_final: 0.7074 (m-70) REVERT: M 37 TRP cc_start: 0.8514 (m100) cc_final: 0.7923 (m100) REVERT: M 64 PHE cc_start: 0.7404 (m-80) cc_final: 0.7164 (m-80) REVERT: N 5 VAL cc_start: 0.6825 (t) cc_final: 0.6384 (m) REVERT: N 32 TYR cc_start: 0.7948 (m-80) cc_final: 0.7727 (m-80) REVERT: N 35 ASN cc_start: 0.7414 (m-40) cc_final: 0.7119 (m110) REVERT: N 93 ILE cc_start: 0.8437 (mt) cc_final: 0.7909 (tt) REVERT: N 94 TYR cc_start: 0.7849 (m-80) cc_final: 0.7584 (m-80) REVERT: O 10 VAL cc_start: 0.8691 (p) cc_final: 0.8407 (t) outliers start: 85 outliers final: 51 residues processed: 662 average time/residue: 0.3366 time to fit residues: 334.7336 Evaluate side-chains 618 residues out of total 2244 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 562 time to evaluate : 2.040 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 83 THR Chi-restraints excluded: chain A residue 147 CYS Chi-restraints excluded: chain A residue 164 GLU Chi-restraints excluded: chain A residue 302 LEU Chi-restraints excluded: chain A residue 316 SER 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 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 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 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 73 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 J residue 28 THR Chi-restraints excluded: chain J residue 69 THR Chi-restraints excluded: chain L residue 79 GLN Chi-restraints excluded: chain L residue 89 GLN Chi-restraints excluded: chain L residue 107 LEU 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 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 10 optimal weight: 0.4980 chunk 100 optimal weight: 0.7980 chunk 97 optimal weight: 0.8980 chunk 56 optimal weight: 3.9990 chunk 139 optimal weight: 0.8980 chunk 191 optimal weight: 6.9990 chunk 123 optimal weight: 1.9990 chunk 108 optimal weight: 0.0770 chunk 60 optimal weight: 5.9990 chunk 78 optimal weight: 0.7980 chunk 150 optimal weight: 0.9980 overall best weight: 0.6138 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 178 ASN B 36 HIS ** D 34 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 313 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 455 GLN H 16 GLN H 56 ASN ** O 53 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 81 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3764 r_free = 0.3764 target = 0.136695 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3539 r_free = 0.3539 target = 0.120328 restraints weight = 31044.030| |-----------------------------------------------------------------------------| r_work (start): 0.3548 rms_B_bonded: 2.08 r_work: 0.3444 rms_B_bonded: 2.37 restraints_weight: 0.5000 r_work: 0.3296 rms_B_bonded: 4.17 restraints_weight: 0.2500 r_work (final): 0.3296 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3288 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3288 r_free = 0.3288 target_work(ls_wunit_k1) = 0.104 | | occupancies: max = 1.00 min = 0.68 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3288 r_free = 0.3288 target_work(ls_wunit_k1) = 0.104 | | occupancies: max = 1.00 min = 0.70 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3288 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7454 moved from start: 0.3164 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 20658 Z= 0.145 Angle : 0.604 9.021 28077 Z= 0.320 Chirality : 0.046 0.303 3237 Planarity : 0.004 0.041 3564 Dihedral : 5.302 41.386 2925 Min Nonbonded Distance : 2.499 Molprobity Statistics. All-atom Clashscore : 8.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.44 % Favored : 96.56 % Rotamer: Outliers : 4.10 % Allowed : 16.53 % Favored : 79.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.08 (0.16), residues: 2622 helix: 0.44 (0.25), residues: 432 sheet: -0.09 (0.18), residues: 792 loop : -0.06 (0.17), residues: 1398 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.002 TRP D 35 HIS 0.016 0.002 HIS B 36 PHE 0.030 0.002 PHE I 27 TYR 0.020 0.002 TYR A 385 ARG 0.005 0.001 ARG A 175 Details of bonding type rmsd link_NAG-ASN : bond 0.00321 ( 3) link_NAG-ASN : angle 1.06592 ( 9) hydrogen bonds : bond 0.03420 ( 924) hydrogen bonds : angle 5.59122 ( 2550) SS BOND : bond 0.00363 ( 45) SS BOND : angle 1.48538 ( 90) covalent geometry : bond 0.00322 (20610) covalent geometry : angle 0.59878 (27978) *********************** 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 681 residues out of total 2244 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 92 poor density : 589 time to evaluate : 2.080 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: 0.6883 (tt0) cc_final: 0.6648 (tt0) REVERT: A 32 THR cc_start: 0.8115 (m) cc_final: 0.7838 (m) REVERT: A 62 ASP cc_start: 0.8031 (t0) cc_final: 0.7735 (t0) REVERT: A 66 LEU cc_start: 0.7199 (mt) cc_final: 0.6695 (mt) REVERT: A 72 ASP cc_start: 0.7252 (m-30) cc_final: 0.6757 (m-30) REVERT: A 83 THR cc_start: 0.7684 (m) cc_final: 0.7372 (t) REVERT: A 126 LYS cc_start: 0.7008 (mmtt) cc_final: 0.6587 (mmtp) REVERT: A 129 ARG cc_start: 0.7482 (ptp-110) cc_final: 0.7169 (ptm160) REVERT: A 133 GLU cc_start: 0.7393 (mm-30) cc_final: 0.7157 (mm-30) REVERT: A 327 GLU cc_start: 0.8247 (pt0) cc_final: 0.7907 (pt0) REVERT: A 385 TYR cc_start: 0.7875 (m-80) cc_final: 0.7605 (m-10) REVERT: A 386 LYS cc_start: 0.7983 (mmmt) cc_final: 0.7734 (mmmt) REVERT: A 402 GLN cc_start: 0.8299 (tt0) cc_final: 0.7969 (tp40) REVERT: A 412 ASN cc_start: 0.7459 (m110) cc_final: 0.6879 (t0) REVERT: A 433 GLU cc_start: 0.8012 (tt0) cc_final: 0.7782 (tt0) REVERT: B 37 TRP cc_start: 0.8259 (m100) cc_final: 0.7960 (m-90) REVERT: C 34 MET cc_start: 0.6749 (mmt) cc_final: 0.6544 (mmt) REVERT: C 68 THR cc_start: 0.7663 (m) cc_final: 0.7352 (p) REVERT: C 91 TYR cc_start: 0.6985 (m-80) cc_final: 0.6543 (m-80) REVERT: D 34 HIS cc_start: 0.6479 (m-70) cc_final: 0.5772 (m-70) REVERT: E 29 SER cc_start: 0.8153 (t) cc_final: 0.7741 (p) REVERT: E 33 GLU cc_start: 0.7742 (mt-10) cc_final: 0.7507 (mt-10) REVERT: E 47 VAL cc_start: 0.8519 (OUTLIER) cc_final: 0.8238 (m) REVERT: E 51 GLU cc_start: 0.7496 (mm-30) cc_final: 0.7095 (mm-30) REVERT: E 66 LEU cc_start: 0.7613 (mt) cc_final: 0.7321 (mt) REVERT: E 70 GLU cc_start: 0.6828 (mm-30) cc_final: 0.6479 (mm-30) REVERT: E 80 GLU cc_start: 0.7588 (tt0) cc_final: 0.7318 (tt0) REVERT: E 126 LYS cc_start: 0.7255 (mmtt) cc_final: 0.6986 (mmtp) REVERT: E 129 ARG cc_start: 0.7676 (ptp-110) cc_final: 0.7348 (ttp80) REVERT: E 206 GLN cc_start: 0.7618 (mt0) cc_final: 0.7140 (mt0) REVERT: E 233 ASN cc_start: 0.8684 (OUTLIER) cc_final: 0.8226 (m-40) REVERT: E 245 LEU cc_start: 0.7560 (OUTLIER) cc_final: 0.7301 (mp) REVERT: E 267 VAL cc_start: 0.8675 (OUTLIER) cc_final: 0.8338 (m) REVERT: E 313 ASN cc_start: 0.7370 (OUTLIER) cc_final: 0.7164 (t160) REVERT: E 318 VAL cc_start: 0.8748 (p) cc_final: 0.8362 (m) REVERT: E 388 VAL cc_start: 0.7649 (t) cc_final: 0.7103 (p) REVERT: E 412 ASN cc_start: 0.7169 (m-40) cc_final: 0.6804 (m-40) REVERT: E 462 GLN cc_start: 0.8335 (tt0) cc_final: 0.7983 (tt0) REVERT: F 27 SER cc_start: 0.8567 (t) cc_final: 0.8336 (p) REVERT: F 47 VAL cc_start: 0.8597 (OUTLIER) cc_final: 0.8374 (m) REVERT: F 51 GLU cc_start: 0.7797 (mm-30) cc_final: 0.7569 (mm-30) REVERT: F 62 ASP cc_start: 0.7862 (t0) cc_final: 0.7313 (t0) REVERT: F 68 LYS cc_start: 0.8409 (tttp) cc_final: 0.8006 (tttp) REVERT: F 70 GLU cc_start: 0.7378 (mm-30) cc_final: 0.7109 (mm-30) REVERT: F 126 LYS cc_start: 0.7552 (mmtt) cc_final: 0.7334 (mmtp) REVERT: F 183 ASP cc_start: 0.7175 (t0) cc_final: 0.6861 (t0) REVERT: F 205 ARG cc_start: 0.7796 (mmm-85) cc_final: 0.7560 (mmm-85) REVERT: F 306 ASP cc_start: 0.7905 (p0) cc_final: 0.7651 (p0) REVERT: F 331 ASP cc_start: 0.8030 (t0) cc_final: 0.7357 (t0) REVERT: F 402 GLN cc_start: 0.7992 (tt0) cc_final: 0.7709 (tp40) REVERT: F 412 ASN cc_start: 0.7463 (m-40) cc_final: 0.7216 (m110) REVERT: F 437 ILE cc_start: 0.8637 (mm) cc_final: 0.8268 (mt) REVERT: F 461 ASP cc_start: 0.7725 (t0) cc_final: 0.7411 (t0) REVERT: G 36 TRP cc_start: 0.7457 (m100) cc_final: 0.7163 (m100) REVERT: G 94 TYR cc_start: 0.7393 (m-80) cc_final: 0.7127 (m-80) REVERT: H 69 ILE cc_start: 0.8254 (pt) cc_final: 0.7924 (mt) REVERT: H 87 THR cc_start: 0.7626 (m) cc_final: 0.7400 (p) REVERT: I 34 MET cc_start: 0.6642 (mmt) cc_final: 0.6249 (mmt) REVERT: I 50 ARG cc_start: 0.8039 (ttp80) cc_final: 0.7361 (ttp-170) REVERT: J 34 MET cc_start: 0.7896 (mmm) cc_final: 0.7271 (mmm) REVERT: K 28 LEU cc_start: 0.8528 (mt) cc_final: 0.8252 (mt) REVERT: K 93 SER cc_start: 0.9023 (t) cc_final: 0.8610 (p) REVERT: K 98 PHE cc_start: 0.8362 (m-80) cc_final: 0.7943 (m-80) REVERT: L 12 SER cc_start: 0.8036 (p) cc_final: 0.7799 (t) REVERT: L 37 GLN cc_start: 0.8245 (tt0) cc_final: 0.7772 (tt0) REVERT: L 39 LYS cc_start: 0.8641 (mttt) cc_final: 0.8427 (mttm) REVERT: L 52 SER cc_start: 0.8080 (m) cc_final: 0.7727 (t) REVERT: M 36 HIS cc_start: 0.7872 (m-70) cc_final: 0.7181 (m-70) REVERT: M 37 TRP cc_start: 0.8527 (m100) cc_final: 0.7908 (m100) REVERT: N 32 TYR cc_start: 0.7944 (m-80) cc_final: 0.7700 (m-80) REVERT: N 35 ASN cc_start: 0.7330 (m-40) cc_final: 0.6963 (m110) REVERT: N 93 ILE cc_start: 0.8391 (mt) cc_final: 0.7883 (tt) REVERT: O 10 VAL cc_start: 0.8685 (p) cc_final: 0.8405 (t) outliers start: 92 outliers final: 61 residues processed: 633 average time/residue: 0.3456 time to fit residues: 335.7011 Evaluate side-chains 637 residues out of total 2244 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 570 time to evaluate : 2.658 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 147 CYS Chi-restraints excluded: chain A residue 187 LEU Chi-restraints excluded: chain A residue 267 VAL Chi-restraints excluded: chain A residue 302 LEU Chi-restraints excluded: chain A residue 442 VAL Chi-restraints excluded: chain A residue 455 GLN Chi-restraints excluded: chain B residue 35 VAL 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 63 SER Chi-restraints excluded: chain D residue 107 LEU Chi-restraints excluded: chain E residue 47 VAL 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 273 LEU 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 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 73 LEU Chi-restraints excluded: chain F residue 83 THR Chi-restraints excluded: chain F residue 130 LEU Chi-restraints excluded: chain F residue 227 LEU Chi-restraints excluded: chain F residue 267 VAL Chi-restraints excluded: chain F residue 302 LEU 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 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 K residue 107 LEU Chi-restraints excluded: chain L residue 79 GLN Chi-restraints excluded: chain L residue 89 GLN Chi-restraints excluded: chain L residue 107 LEU Chi-restraints excluded: chain M residue 65 SER Chi-restraints excluded: chain M residue 67 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 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 52 optimal weight: 0.6980 chunk 228 optimal weight: 0.8980 chunk 168 optimal weight: 4.9990 chunk 16 optimal weight: 2.9990 chunk 229 optimal weight: 0.8980 chunk 148 optimal weight: 0.5980 chunk 155 optimal weight: 2.9990 chunk 260 optimal weight: 1.9990 chunk 204 optimal weight: 5.9990 chunk 252 optimal weight: 2.9990 chunk 87 optimal weight: 3.9990 overall best weight: 1.0182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 172 ASN A 240 GLN A 272 GLN ** A 412 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 455 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 34 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 313 ASN E 346 GLN H 16 GLN ** K 34 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 6 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3756 r_free = 0.3756 target = 0.135932 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3533 r_free = 0.3533 target = 0.119825 restraints weight = 30676.332| |-----------------------------------------------------------------------------| r_work (start): 0.3526 rms_B_bonded: 2.00 r_work: 0.3424 rms_B_bonded: 2.29 restraints_weight: 0.5000 r_work: 0.3278 rms_B_bonded: 4.03 restraints_weight: 0.2500 r_work (final): 0.3278 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3230 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3230 r_free = 0.3230 target_work(ls_wunit_k1) = 0.101 | | occupancies: max = 1.00 min = 0.70 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3230 r_free = 0.3230 target_work(ls_wunit_k1) = 0.101 | | occupancies: max = 1.00 min = 0.74 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3230 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7474 moved from start: 0.3375 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.072 20658 Z= 0.196 Angle : 0.622 8.253 28077 Z= 0.332 Chirality : 0.047 0.306 3237 Planarity : 0.004 0.043 3564 Dihedral : 5.345 40.011 2925 Min Nonbonded Distance : 2.468 Molprobity Statistics. All-atom Clashscore : 8.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.02 % Favored : 95.98 % Rotamer: Outliers : 4.55 % Allowed : 17.47 % Favored : 77.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.24 (0.16), residues: 2622 helix: 0.19 (0.25), residues: 450 sheet: -0.08 (0.18), residues: 780 loop : -0.20 (0.17), residues: 1392 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.037 0.002 TRP K 35 HIS 0.006 0.001 HIS L 34 PHE 0.027 0.002 PHE I 27 TYR 0.021 0.002 TYR F 310 ARG 0.004 0.001 ARG A 156 Details of bonding type rmsd link_NAG-ASN : bond 0.00612 ( 3) link_NAG-ASN : angle 1.28092 ( 9) hydrogen bonds : bond 0.03628 ( 924) hydrogen bonds : angle 5.61106 ( 2550) SS BOND : bond 0.00411 ( 45) SS BOND : angle 1.69449 ( 90) covalent geometry : bond 0.00437 (20610) covalent geometry : angle 0.61484 (27978) *********************** 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 696 residues out of total 2244 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 102 poor density : 594 time to evaluate : 2.148 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 21 GLU cc_start: 0.7076 (tt0) cc_final: 0.6791 (tt0) REVERT: A 32 THR cc_start: 0.8082 (m) cc_final: 0.7822 (m) REVERT: A 62 ASP cc_start: 0.8124 (t0) cc_final: 0.7787 (t0) REVERT: A 72 ASP cc_start: 0.7281 (m-30) cc_final: 0.6736 (m-30) REVERT: A 126 LYS cc_start: 0.7049 (mmtt) cc_final: 0.6600 (mmtp) REVERT: A 129 ARG cc_start: 0.7488 (ptp-110) cc_final: 0.7093 (ptm160) REVERT: A 133 GLU cc_start: 0.7383 (mm-30) cc_final: 0.7167 (mm-30) REVERT: A 184 ILE cc_start: 0.8036 (mm) cc_final: 0.7391 (pt) REVERT: A 248 ARG cc_start: 0.7468 (mtp85) cc_final: 0.7220 (mtp85) REVERT: A 305 GLU cc_start: 0.6947 (mm-30) cc_final: 0.6717 (mm-30) REVERT: A 324 LYS cc_start: 0.7655 (mtpt) cc_final: 0.7433 (mtpt) REVERT: A 327 GLU cc_start: 0.8156 (pt0) cc_final: 0.7886 (pt0) REVERT: A 349 GLU cc_start: 0.7627 (mt-10) cc_final: 0.7215 (mt-10) REVERT: A 385 TYR cc_start: 0.7841 (m-80) cc_final: 0.7423 (m-10) REVERT: A 386 LYS cc_start: 0.8052 (mmmt) cc_final: 0.7825 (mmmt) REVERT: A 402 GLN cc_start: 0.8269 (tt0) cc_final: 0.7899 (tp40) REVERT: A 433 GLU cc_start: 0.8040 (tt0) cc_final: 0.7814 (tt0) REVERT: A 440 ARG cc_start: 0.7650 (ttp-170) cc_final: 0.7333 (ptm-80) REVERT: A 462 GLN cc_start: 0.8285 (tm-30) cc_final: 0.7602 (tm-30) REVERT: B 36 HIS cc_start: 0.7584 (m90) cc_final: 0.7032 (m90) REVERT: B 37 TRP cc_start: 0.8292 (m100) cc_final: 0.7877 (m-90) REVERT: C 34 MET cc_start: 0.6964 (mmt) cc_final: 0.6727 (mmt) REVERT: C 68 THR cc_start: 0.7721 (m) cc_final: 0.7400 (p) REVERT: C 91 TYR cc_start: 0.7097 (m-80) cc_final: 0.6606 (m-80) REVERT: D 28 LEU cc_start: 0.8021 (mt) cc_final: 0.7809 (mt) REVERT: D 34 HIS cc_start: 0.6517 (m-70) cc_final: 0.6010 (m-70) REVERT: E 29 SER cc_start: 0.8226 (t) cc_final: 0.7853 (p) REVERT: E 47 VAL cc_start: 0.8538 (OUTLIER) cc_final: 0.8313 (m) REVERT: E 51 GLU cc_start: 0.7445 (mm-30) cc_final: 0.7078 (mm-30) REVERT: E 70 GLU cc_start: 0.6984 (mm-30) cc_final: 0.6574 (mm-30) REVERT: E 80 GLU cc_start: 0.7520 (tt0) cc_final: 0.7281 (tt0) REVERT: E 126 LYS cc_start: 0.7345 (mmtt) cc_final: 0.7081 (mmtp) REVERT: E 129 ARG cc_start: 0.7827 (ptp-110) cc_final: 0.7322 (ttp80) REVERT: E 171 LYS cc_start: 0.7729 (mtmt) cc_final: 0.7314 (mtmm) REVERT: E 184 ILE cc_start: 0.7788 (tp) cc_final: 0.7426 (pt) REVERT: E 206 GLN cc_start: 0.7578 (mt0) cc_final: 0.7093 (mt0) REVERT: E 233 ASN cc_start: 0.8715 (OUTLIER) cc_final: 0.8219 (m-40) REVERT: E 318 VAL cc_start: 0.8759 (p) cc_final: 0.8347 (m) REVERT: E 412 ASN cc_start: 0.7143 (m-40) cc_final: 0.6754 (m-40) REVERT: F 47 VAL cc_start: 0.8656 (OUTLIER) cc_final: 0.8425 (m) REVERT: F 51 GLU cc_start: 0.7799 (mm-30) cc_final: 0.7381 (mm-30) REVERT: F 62 ASP cc_start: 0.7819 (t0) cc_final: 0.7233 (t0) REVERT: F 70 GLU cc_start: 0.7431 (mm-30) cc_final: 0.7143 (mm-30) REVERT: F 126 LYS cc_start: 0.7696 (mmtt) cc_final: 0.7486 (mmtp) REVERT: F 183 ASP cc_start: 0.7160 (t0) cc_final: 0.6797 (t0) REVERT: F 205 ARG cc_start: 0.7809 (mmm-85) cc_final: 0.7558 (mmm-85) REVERT: F 226 GLU cc_start: 0.8092 (mt-10) cc_final: 0.7790 (mt-10) REVERT: F 331 ASP cc_start: 0.8057 (t0) cc_final: 0.7396 (t0) REVERT: F 386 LYS cc_start: 0.8079 (OUTLIER) cc_final: 0.7725 (mmtm) REVERT: F 402 GLN cc_start: 0.7983 (tt0) cc_final: 0.7745 (tt0) REVERT: F 412 ASN cc_start: 0.7445 (m-40) cc_final: 0.7190 (m110) REVERT: F 461 ASP cc_start: 0.7677 (t0) cc_final: 0.7427 (t0) REVERT: G 94 TYR cc_start: 0.7378 (m-80) cc_final: 0.7106 (m-80) REVERT: H 69 ILE cc_start: 0.8107 (pt) cc_final: 0.7813 (mt) REVERT: H 87 THR cc_start: 0.7732 (m) cc_final: 0.7494 (p) REVERT: I 30 THR cc_start: 0.7994 (p) cc_final: 0.7739 (t) REVERT: I 34 MET cc_start: 0.6681 (mmt) cc_final: 0.6292 (mmt) REVERT: I 50 ARG cc_start: 0.8084 (ttp80) cc_final: 0.7394 (ttp-170) REVERT: J 34 MET cc_start: 0.7833 (mmm) cc_final: 0.7197 (mmm) REVERT: K 28 LEU cc_start: 0.8576 (mt) cc_final: 0.8299 (mt) REVERT: K 30 LYS cc_start: 0.7979 (mttt) cc_final: 0.7729 (mtpt) REVERT: K 31 LYS cc_start: 0.7491 (mmtt) cc_final: 0.7232 (mmtt) REVERT: K 93 SER cc_start: 0.9023 (t) cc_final: 0.8535 (p) REVERT: K 98 PHE cc_start: 0.8342 (m-80) cc_final: 0.7935 (m-80) REVERT: L 37 GLN cc_start: 0.8259 (tt0) cc_final: 0.7822 (tt0) REVERT: L 39 LYS cc_start: 0.8699 (mttt) cc_final: 0.8494 (mttm) REVERT: L 52 SER cc_start: 0.8116 (m) cc_final: 0.7807 (t) REVERT: M 36 HIS cc_start: 0.7906 (m-70) cc_final: 0.7286 (m-70) REVERT: M 37 TRP cc_start: 0.8542 (m100) cc_final: 0.7917 (m100) REVERT: N 5 VAL cc_start: 0.6818 (t) cc_final: 0.6359 (m) REVERT: N 32 TYR cc_start: 0.7962 (m-80) cc_final: 0.7685 (m-80) REVERT: N 35 ASN cc_start: 0.7349 (m-40) cc_final: 0.7028 (m110) REVERT: N 36 TRP cc_start: 0.7665 (m100) cc_final: 0.6885 (m100) REVERT: N 81 LEU cc_start: 0.7568 (tp) cc_final: 0.7264 (tt) REVERT: N 93 ILE cc_start: 0.8365 (mt) cc_final: 0.7866 (tt) outliers start: 102 outliers final: 77 residues processed: 648 average time/residue: 0.3532 time to fit residues: 353.6089 Evaluate side-chains 646 residues out of total 2244 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 81 poor density : 565 time to evaluate : 2.085 ------------------------------------------------------------------------------- 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 142 LYS Chi-restraints excluded: chain A residue 147 CYS Chi-restraints excluded: chain A residue 183 ASP Chi-restraints excluded: chain A residue 187 LEU 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 323 GLU Chi-restraints excluded: chain A residue 442 VAL Chi-restraints excluded: chain B residue 35 VAL 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 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 47 VAL Chi-restraints excluded: chain E residue 73 LEU 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 273 LEU Chi-restraints excluded: chain E residue 302 LEU Chi-restraints excluded: chain E residue 312 GLN 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 417 THR Chi-restraints excluded: chain E residue 447 ASP Chi-restraints excluded: chain F residue 31 ILE Chi-restraints excluded: chain F residue 33 GLU 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 73 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 204 VAL Chi-restraints excluded: chain F residue 243 LEU Chi-restraints excluded: chain F residue 267 VAL Chi-restraints excluded: chain F residue 386 LYS 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 G residue 113 ILE 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 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 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 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 65 SER Chi-restraints excluded: chain M residue 67 SER Chi-restraints excluded: chain M residue 98 SER Chi-restraints excluded: chain N residue 3 GLN Chi-restraints excluded: chain N residue 65 LYS Chi-restraints excluded: chain N residue 106 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 177 optimal weight: 0.9990 chunk 183 optimal weight: 0.9990 chunk 32 optimal weight: 3.9990 chunk 65 optimal weight: 4.9990 chunk 95 optimal weight: 1.9990 chunk 131 optimal weight: 1.9990 chunk 58 optimal weight: 5.9990 chunk 223 optimal weight: 0.9980 chunk 250 optimal weight: 0.7980 chunk 34 optimal weight: 0.9990 chunk 61 optimal weight: 7.9990 overall best weight: 0.9586 ------------------------------------------------------------------------------- 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 ** A 412 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 455 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 34 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 346 GLN H 16 GLN ** K 34 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 6 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3740 r_free = 0.3740 target = 0.134891 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3514 r_free = 0.3514 target = 0.118560 restraints weight = 30799.870| |-----------------------------------------------------------------------------| r_work (start): 0.3525 rms_B_bonded: 2.04 r_work: 0.3422 rms_B_bonded: 2.32 restraints_weight: 0.5000 r_work: 0.3275 rms_B_bonded: 4.09 restraints_weight: 0.2500 r_work (final): 0.3275 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3212 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3212 r_free = 0.3212 target_work(ls_wunit_k1) = 0.100 | | occupancies: max = 1.00 min = 0.74 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3212 r_free = 0.3212 target_work(ls_wunit_k1) = 0.100 | | occupancies: max = 1.00 min = 0.76 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3212 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7475 moved from start: 0.3527 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.060 20658 Z= 0.189 Angle : 0.630 13.415 28077 Z= 0.335 Chirality : 0.048 0.328 3237 Planarity : 0.004 0.041 3564 Dihedral : 5.300 37.630 2925 Min Nonbonded Distance : 2.429 Molprobity Statistics. All-atom Clashscore : 9.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.02 % Favored : 95.98 % Rotamer: Outliers : 4.50 % Allowed : 18.05 % Favored : 77.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.34 (0.16), residues: 2622 helix: 0.17 (0.24), residues: 450 sheet: -0.24 (0.18), residues: 813 loop : -0.23 (0.17), residues: 1359 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.035 0.002 TRP K 35 HIS 0.006 0.001 HIS L 34 PHE 0.026 0.002 PHE I 27 TYR 0.029 0.002 TYR F 385 ARG 0.004 0.001 ARG E 175 Details of bonding type rmsd link_NAG-ASN : bond 0.00594 ( 3) link_NAG-ASN : angle 1.28795 ( 9) hydrogen bonds : bond 0.03609 ( 924) hydrogen bonds : angle 5.60042 ( 2550) SS BOND : bond 0.00379 ( 45) SS BOND : angle 2.26105 ( 90) covalent geometry : bond 0.00422 (20610) covalent geometry : angle 0.61739 (27978) *********************** 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 667 residues out of total 2244 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 101 poor density : 566 time to evaluate : 1.970 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 21 GLU cc_start: 0.7092 (tt0) cc_final: 0.6853 (tt0) REVERT: A 32 THR cc_start: 0.8090 (m) cc_final: 0.7820 (m) REVERT: A 62 ASP cc_start: 0.8139 (t0) cc_final: 0.7845 (t0) REVERT: A 72 ASP cc_start: 0.7281 (m-30) cc_final: 0.6750 (m-30) REVERT: A 80 GLU cc_start: 0.7437 (mt-10) cc_final: 0.7227 (mt-10) REVERT: A 126 LYS cc_start: 0.7097 (mmtt) cc_final: 0.6666 (mmtp) REVERT: A 129 ARG cc_start: 0.7532 (ptp-110) cc_final: 0.7185 (ptm160) REVERT: A 184 ILE cc_start: 0.7975 (mm) cc_final: 0.7306 (pt) REVERT: A 327 GLU cc_start: 0.8142 (pt0) cc_final: 0.7834 (pt0) REVERT: A 349 GLU cc_start: 0.7624 (mt-10) cc_final: 0.7223 (mt-10) REVERT: A 385 TYR cc_start: 0.7848 (m-80) cc_final: 0.7452 (m-10) REVERT: A 386 LYS cc_start: 0.8062 (mmmt) cc_final: 0.7840 (mmmt) REVERT: A 402 GLN cc_start: 0.8270 (tt0) cc_final: 0.7899 (tp40) REVERT: A 412 ASN cc_start: 0.7509 (m110) cc_final: 0.6919 (t0) REVERT: A 433 GLU cc_start: 0.7927 (tt0) cc_final: 0.7692 (tt0) REVERT: A 440 ARG cc_start: 0.7659 (ttp-170) cc_final: 0.7347 (ptm-80) REVERT: A 461 ASP cc_start: 0.7659 (t0) cc_final: 0.7438 (t0) REVERT: A 462 GLN cc_start: 0.8308 (tm-30) cc_final: 0.7684 (tm-30) REVERT: B 36 HIS cc_start: 0.7532 (m90) cc_final: 0.6999 (m90) REVERT: B 37 TRP cc_start: 0.8316 (m100) cc_final: 0.7869 (m-90) REVERT: C 34 MET cc_start: 0.6931 (mmt) cc_final: 0.6700 (mmt) REVERT: C 68 THR cc_start: 0.7743 (m) cc_final: 0.7422 (p) REVERT: C 91 TYR cc_start: 0.7133 (m-80) cc_final: 0.6626 (m-80) REVERT: D 34 HIS cc_start: 0.6583 (m-70) cc_final: 0.6139 (m-70) REVERT: E 29 SER cc_start: 0.8278 (t) cc_final: 0.7884 (p) REVERT: E 47 VAL cc_start: 0.8575 (OUTLIER) cc_final: 0.8324 (m) REVERT: E 51 GLU cc_start: 0.7475 (mm-30) cc_final: 0.7121 (mm-30) REVERT: E 70 GLU cc_start: 0.7024 (mm-30) cc_final: 0.6573 (mm-30) REVERT: E 80 GLU cc_start: 0.7538 (tt0) cc_final: 0.7297 (tt0) REVERT: E 126 LYS cc_start: 0.7309 (mmtt) cc_final: 0.7076 (mmtp) REVERT: E 129 ARG cc_start: 0.7763 (ptp-110) cc_final: 0.7307 (ttp80) REVERT: E 171 LYS cc_start: 0.7738 (mtmt) cc_final: 0.7102 (mtmt) REVERT: E 175 ARG cc_start: 0.7716 (mtm-85) cc_final: 0.7134 (mtm-85) REVERT: E 184 ILE cc_start: 0.7761 (tp) cc_final: 0.7422 (pt) REVERT: E 206 GLN cc_start: 0.7589 (mt0) cc_final: 0.7103 (mt0) REVERT: E 233 ASN cc_start: 0.8737 (OUTLIER) cc_final: 0.8248 (m-40) REVERT: E 267 VAL cc_start: 0.8709 (OUTLIER) cc_final: 0.8340 (m) REVERT: E 318 VAL cc_start: 0.8747 (p) cc_final: 0.8353 (m) REVERT: E 331 ASP cc_start: 0.8346 (t0) cc_final: 0.7982 (t0) REVERT: E 367 ARG cc_start: 0.8013 (ptp-170) cc_final: 0.7782 (ptp90) REVERT: E 412 ASN cc_start: 0.7117 (m-40) cc_final: 0.6719 (m-40) REVERT: E 462 GLN cc_start: 0.8146 (tt0) cc_final: 0.7498 (tt0) REVERT: F 47 VAL cc_start: 0.8662 (OUTLIER) cc_final: 0.8425 (m) REVERT: F 51 GLU cc_start: 0.7820 (mm-30) cc_final: 0.7387 (mm-30) REVERT: F 62 ASP cc_start: 0.7798 (t0) cc_final: 0.7161 (t0) REVERT: F 205 ARG cc_start: 0.7802 (mmm-85) cc_final: 0.7562 (mmm-85) REVERT: F 263 TYR cc_start: 0.8216 (m-80) cc_final: 0.7497 (m-80) REVERT: F 331 ASP cc_start: 0.8034 (t0) cc_final: 0.7662 (t0) REVERT: F 386 LYS cc_start: 0.8037 (OUTLIER) cc_final: 0.7576 (mmtm) REVERT: F 402 GLN cc_start: 0.7988 (tt0) cc_final: 0.7747 (tt0) REVERT: F 412 ASN cc_start: 0.7416 (m-40) cc_final: 0.7172 (m110) REVERT: F 461 ASP cc_start: 0.7676 (t0) cc_final: 0.7471 (t0) REVERT: G 36 TRP cc_start: 0.7496 (m100) cc_final: 0.7251 (m100) REVERT: H 69 ILE cc_start: 0.8047 (pt) cc_final: 0.7767 (mt) REVERT: H 87 THR cc_start: 0.7722 (m) cc_final: 0.7492 (p) REVERT: I 30 THR cc_start: 0.8015 (p) cc_final: 0.7748 (t) REVERT: I 34 MET cc_start: 0.6673 (mmt) cc_final: 0.6253 (mmt) REVERT: J 34 MET cc_start: 0.7817 (mmm) cc_final: 0.7171 (mmm) REVERT: J 82 GLN cc_start: 0.7252 (tp40) cc_final: 0.6845 (tp40) REVERT: K 28 LEU cc_start: 0.8597 (mt) cc_final: 0.8324 (mt) REVERT: K 30 LYS cc_start: 0.8029 (mttt) cc_final: 0.7742 (mtpt) REVERT: K 31 LYS cc_start: 0.7477 (mmtt) cc_final: 0.7247 (mmtt) REVERT: K 93 SER cc_start: 0.8965 (t) cc_final: 0.8518 (p) REVERT: K 98 PHE cc_start: 0.8350 (m-80) cc_final: 0.7925 (m-80) REVERT: L 37 GLN cc_start: 0.8285 (tt0) cc_final: 0.7830 (tt0) REVERT: L 39 LYS cc_start: 0.8697 (mttt) cc_final: 0.8495 (mttm) REVERT: L 52 SER cc_start: 0.8097 (m) cc_final: 0.7830 (t) REVERT: M 37 TRP cc_start: 0.8546 (m100) cc_final: 0.7959 (m100) REVERT: N 5 VAL cc_start: 0.6817 (t) cc_final: 0.6337 (m) REVERT: N 35 ASN cc_start: 0.7274 (m-40) cc_final: 0.6900 (m110) REVERT: N 36 TRP cc_start: 0.7657 (m100) cc_final: 0.6797 (m100) REVERT: N 81 LEU cc_start: 0.7597 (tp) cc_final: 0.7287 (tt) REVERT: N 93 ILE cc_start: 0.8362 (mt) cc_final: 0.7850 (tt) outliers start: 101 outliers final: 80 residues processed: 621 average time/residue: 0.3188 time to fit residues: 302.0352 Evaluate side-chains 638 residues out of total 2244 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 85 poor density : 553 time to evaluate : 2.154 ------------------------------------------------------------------------------- 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 66 LEU 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 316 SER Chi-restraints excluded: chain A residue 323 GLU Chi-restraints excluded: chain A residue 442 VAL Chi-restraints excluded: chain B residue 35 VAL 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 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 143 LYS 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 267 VAL Chi-restraints excluded: chain E residue 273 LEU Chi-restraints excluded: chain E residue 302 LEU Chi-restraints excluded: chain E residue 312 GLN 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 417 THR 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 59 THR Chi-restraints excluded: chain F residue 66 LEU Chi-restraints excluded: chain F residue 73 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 204 VAL Chi-restraints excluded: chain F residue 227 LEU Chi-restraints excluded: chain F residue 243 LEU 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 386 LYS 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 G residue 113 ILE 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 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 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 K residue 18 THR Chi-restraints excluded: chain K residue 107 LEU 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 84 ASP Chi-restraints excluded: chain M residue 98 SER Chi-restraints excluded: chain N residue 3 GLN Chi-restraints excluded: chain N residue 65 LYS Chi-restraints excluded: chain N residue 95 PHE Chi-restraints excluded: chain O residue 5 THR Chi-restraints excluded: chain O residue 25 SER Chi-restraints excluded: chain O residue 67 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 261 random chunks: chunk 77 optimal weight: 1.9990 chunk 65 optimal weight: 4.9990 chunk 169 optimal weight: 1.9990 chunk 165 optimal weight: 2.9990 chunk 229 optimal weight: 0.6980 chunk 35 optimal weight: 2.9990 chunk 185 optimal weight: 5.9990 chunk 220 optimal weight: 0.9990 chunk 241 optimal weight: 0.6980 chunk 1 optimal weight: 0.6980 chunk 94 optimal weight: 1.9990 overall best weight: 1.0184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 172 ASN A 412 ASN ** A 455 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 34 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 202 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 462 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 35 ASN ** K 34 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 34 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3736 r_free = 0.3736 target = 0.134617 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3510 r_free = 0.3510 target = 0.118335 restraints weight = 30667.397| |-----------------------------------------------------------------------------| r_work (start): 0.3520 rms_B_bonded: 2.02 r_work: 0.3418 rms_B_bonded: 2.31 restraints_weight: 0.5000 r_work: 0.3277 rms_B_bonded: 4.02 restraints_weight: 0.2500 r_work (final): 0.3277 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3228 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3228 r_free = 0.3228 target_work(ls_wunit_k1) = 0.101 | | occupancies: max = 1.00 min = 0.76 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3228 r_free = 0.3228 target_work(ls_wunit_k1) = 0.101 | | occupancies: max = 1.00 min = 0.80 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3228 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7475 moved from start: 0.3695 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 20658 Z= 0.196 Angle : 0.633 9.519 28077 Z= 0.336 Chirality : 0.048 0.336 3237 Planarity : 0.004 0.041 3564 Dihedral : 5.299 33.068 2925 Min Nonbonded Distance : 2.450 Molprobity Statistics. All-atom Clashscore : 9.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.52 % Favored : 95.48 % Rotamer: Outliers : 4.28 % Allowed : 18.98 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.34 (0.16), residues: 2622 helix: 0.15 (0.24), residues: 450 sheet: -0.10 (0.17), residues: 816 loop : -0.32 (0.17), residues: 1356 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.036 0.002 TRP D 35 HIS 0.006 0.001 HIS L 34 PHE 0.027 0.002 PHE I 27 TYR 0.029 0.002 TYR F 385 ARG 0.007 0.000 ARG I 50 Details of bonding type rmsd link_NAG-ASN : bond 0.00628 ( 3) link_NAG-ASN : angle 1.34831 ( 9) hydrogen bonds : bond 0.03637 ( 924) hydrogen bonds : angle 5.57155 ( 2550) SS BOND : bond 0.00386 ( 45) SS BOND : angle 1.85940 ( 90) covalent geometry : bond 0.00438 (20610) covalent geometry : angle 0.62460 (27978) *********************** REFINEMENT MACRO_CYCLE 7 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 660 residues out of total 2244 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 96 poor density : 564 time to evaluate : 2.439 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: A 62 ASP cc_start: 0.8199 (t0) cc_final: 0.7703 (t70) REVERT: A 72 ASP cc_start: 0.7263 (m-30) cc_final: 0.6719 (m-30) REVERT: A 80 GLU cc_start: 0.7430 (mt-10) cc_final: 0.7223 (tt0) REVERT: A 81 LEU cc_start: 0.8067 (tt) cc_final: 0.7729 (tp) REVERT: A 126 LYS cc_start: 0.7175 (mmtt) cc_final: 0.6638 (mmtp) REVERT: A 129 ARG cc_start: 0.7511 (ptp-110) cc_final: 0.7222 (ptm160) REVERT: A 171 LYS cc_start: 0.8193 (mttp) cc_final: 0.7854 (mttp) REVERT: A 175 ARG cc_start: 0.7928 (mtt-85) cc_final: 0.7649 (mtm-85) REVERT: A 184 ILE cc_start: 0.7888 (mm) cc_final: 0.7242 (pt) REVERT: A 324 LYS cc_start: 0.7574 (mtpt) cc_final: 0.7356 (mtpt) REVERT: A 327 GLU cc_start: 0.8126 (pt0) cc_final: 0.7873 (pt0) REVERT: A 385 TYR cc_start: 0.7809 (m-80) cc_final: 0.7443 (m-10) REVERT: A 386 LYS cc_start: 0.8080 (mmmt) cc_final: 0.7859 (mmmt) REVERT: A 402 GLN cc_start: 0.8230 (tt0) cc_final: 0.7853 (tp40) REVERT: A 412 ASN cc_start: 0.7551 (m-40) cc_final: 0.6995 (t0) REVERT: A 433 GLU cc_start: 0.7952 (tt0) cc_final: 0.7746 (tt0) REVERT: A 440 ARG cc_start: 0.7645 (ttp-170) cc_final: 0.7338 (ptm-80) REVERT: A 461 ASP cc_start: 0.7736 (t0) cc_final: 0.7490 (t0) REVERT: A 462 GLN cc_start: 0.8297 (tm-30) cc_final: 0.7749 (tm-30) REVERT: B 36 HIS cc_start: 0.7518 (m90) cc_final: 0.7083 (m90) REVERT: C 34 MET cc_start: 0.6997 (mmt) cc_final: 0.6748 (mmt) REVERT: C 68 THR cc_start: 0.7750 (m) cc_final: 0.7414 (p) REVERT: C 91 TYR cc_start: 0.7144 (m-80) cc_final: 0.6639 (m-80) REVERT: D 34 HIS cc_start: 0.6542 (m-70) cc_final: 0.6081 (m-70) REVERT: E 29 SER cc_start: 0.8314 (t) cc_final: 0.7932 (p) REVERT: E 47 VAL cc_start: 0.8604 (OUTLIER) cc_final: 0.8344 (m) REVERT: E 51 GLU cc_start: 0.7473 (mm-30) cc_final: 0.7143 (mm-30) REVERT: E 66 LEU cc_start: 0.7304 (mt) cc_final: 0.7083 (mt) REVERT: E 70 GLU cc_start: 0.7066 (mm-30) cc_final: 0.6562 (mm-30) REVERT: E 72 ASP cc_start: 0.6988 (m-30) cc_final: 0.6589 (m-30) REVERT: E 80 GLU cc_start: 0.7540 (tt0) cc_final: 0.7302 (tt0) REVERT: E 126 LYS cc_start: 0.7351 (mmtt) cc_final: 0.7114 (mmtp) REVERT: E 129 ARG cc_start: 0.7723 (ptp-110) cc_final: 0.7247 (ttp80) REVERT: E 142 LYS cc_start: 0.7957 (mmtp) cc_final: 0.7738 (mmtp) REVERT: E 171 LYS cc_start: 0.7779 (mtmt) cc_final: 0.7466 (mtmt) REVERT: E 175 ARG cc_start: 0.7737 (mtm-85) cc_final: 0.7440 (mtm-85) REVERT: E 184 ILE cc_start: 0.7825 (tp) cc_final: 0.7484 (pt) REVERT: E 206 GLN cc_start: 0.7563 (mt0) cc_final: 0.7098 (mt0) REVERT: E 267 VAL cc_start: 0.8720 (OUTLIER) cc_final: 0.8350 (m) REVERT: E 318 VAL cc_start: 0.8729 (p) cc_final: 0.8344 (m) REVERT: E 345 GLU cc_start: 0.7753 (tp30) cc_final: 0.7434 (tp30) REVERT: E 349 GLU cc_start: 0.7636 (tp30) cc_final: 0.7122 (tp30) REVERT: E 412 ASN cc_start: 0.7073 (m-40) cc_final: 0.6748 (m-40) REVERT: E 462 GLN cc_start: 0.8109 (tt0) cc_final: 0.7563 (tt0) REVERT: F 47 VAL cc_start: 0.8671 (OUTLIER) cc_final: 0.8433 (m) REVERT: F 51 GLU cc_start: 0.7770 (mm-30) cc_final: 0.7375 (mm-30) REVERT: F 62 ASP cc_start: 0.7748 (t0) cc_final: 0.7136 (t0) REVERT: F 205 ARG cc_start: 0.7785 (mmm-85) cc_final: 0.7581 (mmm-85) REVERT: F 263 TYR cc_start: 0.8309 (m-80) cc_final: 0.7599 (m-80) REVERT: F 331 ASP cc_start: 0.8041 (t0) cc_final: 0.7650 (t0) REVERT: F 386 LYS cc_start: 0.8038 (mmtm) cc_final: 0.7566 (mmtm) REVERT: F 412 ASN cc_start: 0.7401 (m-40) cc_final: 0.7159 (m110) REVERT: F 421 ASP cc_start: 0.6886 (m-30) cc_final: 0.6654 (m-30) REVERT: G 36 TRP cc_start: 0.7485 (m100) cc_final: 0.7202 (m100) REVERT: H 69 ILE cc_start: 0.8013 (pt) cc_final: 0.7772 (mt) REVERT: H 87 THR cc_start: 0.7730 (m) cc_final: 0.7499 (p) REVERT: H 94 ARG cc_start: 0.8739 (OUTLIER) cc_final: 0.8313 (ttp80) REVERT: I 30 THR cc_start: 0.7990 (p) cc_final: 0.7726 (t) REVERT: I 34 MET cc_start: 0.6704 (mmt) cc_final: 0.6245 (mmt) REVERT: J 34 MET cc_start: 0.7795 (mmm) cc_final: 0.7174 (mmm) REVERT: J 82 GLN cc_start: 0.7177 (tp40) cc_final: 0.6784 (tp40) REVERT: K 28 LEU cc_start: 0.8622 (mt) cc_final: 0.8357 (mt) REVERT: K 31 LYS cc_start: 0.7456 (mmtt) cc_final: 0.7214 (mmtt) REVERT: K 93 SER cc_start: 0.8971 (t) cc_final: 0.8507 (p) REVERT: K 98 PHE cc_start: 0.8333 (m-80) cc_final: 0.7934 (m-80) REVERT: L 37 GLN cc_start: 0.8213 (tt0) cc_final: 0.7773 (tt0) REVERT: L 52 SER cc_start: 0.8129 (m) cc_final: 0.7797 (t) REVERT: M 37 TRP cc_start: 0.8547 (m100) cc_final: 0.8079 (m100) REVERT: N 5 VAL cc_start: 0.6833 (t) cc_final: 0.6355 (m) REVERT: N 35 ASN cc_start: 0.7229 (m-40) cc_final: 0.6898 (m110) REVERT: N 36 TRP cc_start: 0.7622 (m100) cc_final: 0.6694 (m100) REVERT: N 80 PHE cc_start: 0.7935 (m-80) cc_final: 0.7086 (m-80) REVERT: N 81 LEU cc_start: 0.7748 (tp) cc_final: 0.7421 (tt) REVERT: N 93 ILE cc_start: 0.8363 (mt) cc_final: 0.7864 (tt) outliers start: 96 outliers final: 79 residues processed: 621 average time/residue: 0.3345 time to fit residues: 315.9671 Evaluate side-chains 630 residues out of total 2244 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 83 poor density : 547 time to evaluate : 2.136 ------------------------------------------------------------------------------- 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 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 323 GLU Chi-restraints excluded: chain A residue 442 VAL Chi-restraints excluded: chain B residue 35 VAL 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 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 267 VAL Chi-restraints excluded: chain E residue 273 LEU Chi-restraints excluded: chain E residue 302 LEU Chi-restraints excluded: chain E residue 312 GLN Chi-restraints excluded: chain E residue 394 SER Chi-restraints excluded: chain E residue 401 LYS Chi-restraints excluded: chain E residue 417 THR Chi-restraints excluded: chain F residue 31 ILE Chi-restraints excluded: chain F residue 33 GLU Chi-restraints excluded: chain F residue 45 THR Chi-restraints excluded: chain F residue 47 VAL Chi-restraints excluded: chain F residue 59 THR Chi-restraints excluded: chain F residue 66 LEU Chi-restraints excluded: chain F residue 73 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 302 LEU 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 32 SER 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 78 VAL 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 K residue 107 LEU Chi-restraints excluded: chain L residue 89 GLN Chi-restraints excluded: chain L residue 107 LEU Chi-restraints excluded: chain M residue 35 VAL 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 3 GLN 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 25 SER Chi-restraints excluded: chain O residue 67 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 261 random chunks: chunk 237 optimal weight: 2.9990 chunk 223 optimal weight: 2.9990 chunk 96 optimal weight: 0.1980 chunk 38 optimal weight: 3.9990 chunk 111 optimal weight: 0.3980 chunk 202 optimal weight: 0.9990 chunk 214 optimal weight: 0.8980 chunk 25 optimal weight: 0.9980 chunk 168 optimal weight: 3.9990 chunk 153 optimal weight: 0.8980 chunk 228 optimal weight: 0.0070 overall best weight: 0.4798 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 172 ASN ** A 455 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 34 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 202 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 34 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3761 r_free = 0.3761 target = 0.136615 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3540 r_free = 0.3540 target = 0.120393 restraints weight = 30775.554| |-----------------------------------------------------------------------------| r_work (start): 0.3550 rms_B_bonded: 2.04 r_work: 0.3449 rms_B_bonded: 2.33 restraints_weight: 0.5000 r_work: 0.3302 rms_B_bonded: 4.12 restraints_weight: 0.2500 r_work (final): 0.3302 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3215 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3215 r_free = 0.3215 target_work(ls_wunit_k1) = 0.100 | | occupancies: max = 1.00 min = 0.80 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3215 r_free = 0.3215 target_work(ls_wunit_k1) = 0.100 | | occupancies: max = 1.00 min = 0.81 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3215 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7443 moved from start: 0.3886 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.061 20658 Z= 0.131 Angle : 0.609 11.953 28077 Z= 0.321 Chirality : 0.047 0.321 3237 Planarity : 0.004 0.039 3564 Dihedral : 5.020 30.474 2925 Min Nonbonded Distance : 2.470 Molprobity Statistics. All-atom Clashscore : 9.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.79 % Favored : 96.21 % Rotamer: Outliers : 3.21 % Allowed : 20.45 % Favored : 76.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.17 (0.16), residues: 2622 helix: 0.35 (0.25), residues: 444 sheet: 0.06 (0.17), residues: 825 loop : -0.27 (0.17), residues: 1353 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.047 0.002 TRP K 35 HIS 0.005 0.001 HIS M 36 PHE 0.024 0.001 PHE I 27 TYR 0.026 0.002 TYR F 385 ARG 0.007 0.000 ARG I 50 Details of bonding type rmsd link_NAG-ASN : bond 0.00245 ( 3) link_NAG-ASN : angle 1.06377 ( 9) hydrogen bonds : bond 0.03270 ( 924) hydrogen bonds : angle 5.42346 ( 2550) SS BOND : bond 0.00324 ( 45) SS BOND : angle 2.02608 ( 90) covalent geometry : bond 0.00293 (20610) covalent geometry : angle 0.59924 (27978) *********************** REFINEMENT MACRO_CYCLE 8 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 627 residues out of total 2244 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 555 time to evaluate : 2.213 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 24 LEU cc_start: 0.8070 (mm) cc_final: 0.7758 (mp) REVERT: A 62 ASP cc_start: 0.8211 (t0) cc_final: 0.7728 (t70) REVERT: A 70 GLU cc_start: 0.6524 (mm-30) cc_final: 0.6242 (mm-30) REVERT: A 81 LEU cc_start: 0.7972 (tt) cc_final: 0.7749 (tp) REVERT: A 84 VAL cc_start: 0.8323 (p) cc_final: 0.8050 (m) REVERT: A 126 LYS cc_start: 0.7164 (mmtt) cc_final: 0.6658 (mmtp) REVERT: A 129 ARG cc_start: 0.7569 (ptp-110) cc_final: 0.7215 (ptm160) REVERT: A 171 LYS cc_start: 0.8216 (mttp) cc_final: 0.7892 (mttp) REVERT: A 175 ARG cc_start: 0.7963 (mtt-85) cc_final: 0.7653 (mtm-85) REVERT: A 184 ILE cc_start: 0.7851 (mm) cc_final: 0.7199 (pt) REVERT: A 206 GLN cc_start: 0.7369 (mt0) cc_final: 0.6933 (mt0) REVERT: A 327 GLU cc_start: 0.8095 (pt0) cc_final: 0.7783 (pt0) REVERT: A 349 GLU cc_start: 0.7591 (mt-10) cc_final: 0.7202 (mt-10) REVERT: A 385 TYR cc_start: 0.7756 (m-80) cc_final: 0.7456 (m-10) REVERT: A 386 LYS cc_start: 0.8061 (mmmt) cc_final: 0.7740 (mmtm) REVERT: A 402 GLN cc_start: 0.8222 (tt0) cc_final: 0.8001 (tt0) REVERT: A 421 ASP cc_start: 0.6952 (t0) cc_final: 0.6572 (t0) REVERT: A 433 GLU cc_start: 0.7911 (tt0) cc_final: 0.7703 (tt0) REVERT: A 440 ARG cc_start: 0.7549 (ttp-170) cc_final: 0.7230 (ptm-80) REVERT: A 461 ASP cc_start: 0.7665 (t0) cc_final: 0.7439 (t0) REVERT: A 462 GLN cc_start: 0.8289 (tm-30) cc_final: 0.7776 (tm-30) REVERT: B 37 TRP cc_start: 0.8300 (m100) cc_final: 0.7906 (m-90) REVERT: C 68 THR cc_start: 0.7823 (m) cc_final: 0.7412 (p) REVERT: C 91 TYR cc_start: 0.7112 (m-80) cc_final: 0.6620 (m-80) REVERT: E 29 SER cc_start: 0.8308 (t) cc_final: 0.7879 (p) REVERT: E 47 VAL cc_start: 0.8574 (OUTLIER) cc_final: 0.8319 (m) REVERT: E 51 GLU cc_start: 0.7451 (mm-30) cc_final: 0.7106 (mm-30) REVERT: E 70 GLU cc_start: 0.7033 (mm-30) cc_final: 0.6518 (mm-30) REVERT: E 80 GLU cc_start: 0.7486 (tt0) cc_final: 0.7205 (tt0) REVERT: E 126 LYS cc_start: 0.7239 (mmtt) cc_final: 0.7003 (mmtp) REVERT: E 129 ARG cc_start: 0.7626 (ptp-110) cc_final: 0.7223 (ttp80) REVERT: E 171 LYS cc_start: 0.7762 (mtmt) cc_final: 0.7391 (mtmt) REVERT: E 184 ILE cc_start: 0.7780 (tp) cc_final: 0.7519 (pt) REVERT: E 206 GLN cc_start: 0.7550 (mt0) cc_final: 0.7118 (mt0) REVERT: E 233 ASN cc_start: 0.8686 (OUTLIER) cc_final: 0.8079 (m-40) REVERT: E 267 VAL cc_start: 0.8709 (OUTLIER) cc_final: 0.8350 (m) REVERT: E 345 GLU cc_start: 0.7709 (tp30) cc_final: 0.7376 (tp30) REVERT: E 349 GLU cc_start: 0.7613 (tp30) cc_final: 0.7105 (tp30) REVERT: E 412 ASN cc_start: 0.7111 (m-40) cc_final: 0.6751 (m-40) REVERT: E 416 ASP cc_start: 0.7737 (m-30) cc_final: 0.7409 (m-30) REVERT: E 462 GLN cc_start: 0.8074 (tt0) cc_final: 0.7569 (tt0) REVERT: F 47 VAL cc_start: 0.8657 (OUTLIER) cc_final: 0.8429 (m) REVERT: F 51 GLU cc_start: 0.7739 (mm-30) cc_final: 0.7328 (mm-30) REVERT: F 62 ASP cc_start: 0.7697 (t0) cc_final: 0.7035 (t0) REVERT: F 205 ARG cc_start: 0.7757 (mmm-85) cc_final: 0.7549 (mmm-85) REVERT: F 263 TYR cc_start: 0.8250 (m-80) cc_final: 0.7283 (m-80) REVERT: F 386 LYS cc_start: 0.8004 (mmtm) cc_final: 0.7488 (mmtm) REVERT: F 412 ASN cc_start: 0.7380 (m-40) cc_final: 0.7166 (m110) REVERT: F 421 ASP cc_start: 0.6852 (m-30) cc_final: 0.6617 (m-30) REVERT: G 3 GLN cc_start: 0.6678 (pp30) cc_final: 0.6438 (tm-30) REVERT: H 66 ARG cc_start: 0.7530 (ttm170) cc_final: 0.7088 (ttm110) REVERT: H 87 THR cc_start: 0.7670 (m) cc_final: 0.7447 (p) REVERT: H 94 ARG cc_start: 0.8703 (OUTLIER) cc_final: 0.8283 (ttp-110) REVERT: I 30 THR cc_start: 0.7928 (p) cc_final: 0.7649 (t) REVERT: I 34 MET cc_start: 0.6617 (mmt) cc_final: 0.6192 (mmt) REVERT: I 47 TRP cc_start: 0.8290 (t60) cc_final: 0.7612 (t60) REVERT: J 34 MET cc_start: 0.7726 (mmm) cc_final: 0.7195 (mmm) REVERT: J 81 LEU cc_start: 0.7634 (tp) cc_final: 0.7403 (mt) REVERT: J 82 GLN cc_start: 0.7130 (tp40) cc_final: 0.6807 (tp40) REVERT: J 84 ASN cc_start: 0.8004 (m-40) cc_final: 0.7458 (p0) REVERT: K 28 LEU cc_start: 0.8595 (mt) cc_final: 0.8329 (mt) REVERT: K 30 LYS cc_start: 0.7941 (mtpt) cc_final: 0.7626 (mtpt) REVERT: K 93 SER cc_start: 0.8935 (t) cc_final: 0.8508 (p) REVERT: K 98 PHE cc_start: 0.8198 (m-80) cc_final: 0.7779 (m-80) REVERT: L 37 GLN cc_start: 0.8205 (tt0) cc_final: 0.7791 (tt0) REVERT: L 52 SER cc_start: 0.8021 (m) cc_final: 0.7689 (t) REVERT: M 37 TRP cc_start: 0.8494 (m100) cc_final: 0.7897 (m100) REVERT: N 35 ASN cc_start: 0.7229 (m-40) cc_final: 0.6909 (m110) REVERT: N 36 TRP cc_start: 0.7273 (m100) cc_final: 0.6346 (m100) REVERT: N 80 PHE cc_start: 0.7952 (m-80) cc_final: 0.7674 (m-80) REVERT: N 93 ILE cc_start: 0.8336 (mt) cc_final: 0.7834 (tt) outliers start: 72 outliers final: 54 residues processed: 597 average time/residue: 0.3378 time to fit residues: 307.9351 Evaluate side-chains 601 residues out of total 2244 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 542 time to evaluate : 2.131 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 59 THR Chi-restraints excluded: chain A residue 147 CYS Chi-restraints excluded: chain A residue 267 VAL Chi-restraints excluded: chain A residue 316 SER Chi-restraints excluded: chain A residue 323 GLU Chi-restraints excluded: chain B residue 35 VAL 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 45 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 47 VAL 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 267 VAL Chi-restraints excluded: chain E residue 273 LEU Chi-restraints excluded: chain E residue 401 LYS Chi-restraints excluded: chain E residue 417 THR Chi-restraints excluded: chain F residue 33 GLU 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 73 LEU Chi-restraints excluded: chain F residue 83 THR Chi-restraints excluded: chain F residue 108 ILE Chi-restraints excluded: chain F residue 227 LEU Chi-restraints excluded: chain F residue 243 LEU Chi-restraints excluded: chain F residue 267 VAL Chi-restraints excluded: chain F residue 302 LEU Chi-restraints excluded: chain F residue 427 LEU Chi-restraints excluded: chain G residue 77 THR Chi-restraints excluded: chain G residue 108 THR Chi-restraints excluded: chain H residue 32 SER 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 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 K residue 107 LEU Chi-restraints excluded: chain L residue 89 GLN Chi-restraints excluded: chain L residue 107 LEU 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 65 LYS Chi-restraints excluded: chain N residue 95 PHE Chi-restraints excluded: chain N residue 106 SER Chi-restraints excluded: chain O residue 35 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 261 random chunks: chunk 248 optimal weight: 2.9990 chunk 194 optimal weight: 5.9990 chunk 59 optimal weight: 4.9990 chunk 203 optimal weight: 0.0970 chunk 49 optimal weight: 0.0970 chunk 140 optimal weight: 0.7980 chunk 125 optimal weight: 0.9980 chunk 145 optimal weight: 2.9990 chunk 43 optimal weight: 0.7980 chunk 2 optimal weight: 0.6980 chunk 221 optimal weight: 0.9980 overall best weight: 0.4976 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 172 ASN A 307 GLN ** A 455 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 202 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 35 ASN H 16 GLN ** K 34 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 34 HIS N 39 GLN O 40 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3767 r_free = 0.3767 target = 0.137024 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3547 r_free = 0.3547 target = 0.120844 restraints weight = 30828.807| |-----------------------------------------------------------------------------| r_work (start): 0.3540 rms_B_bonded: 2.04 r_work: 0.3439 rms_B_bonded: 2.34 restraints_weight: 0.5000 r_work: 0.3295 rms_B_bonded: 4.09 restraints_weight: 0.2500 r_work (final): 0.3295 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3224 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3224 r_free = 0.3224 target_work(ls_wunit_k1) = 0.101 | | occupancies: max = 1.00 min = 0.81 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3224 r_free = 0.3224 target_work(ls_wunit_k1) = 0.101 | | occupancies: max = 1.00 min = 0.81 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3224 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7436 moved from start: 0.4011 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 20658 Z= 0.133 Angle : 0.614 10.365 28077 Z= 0.321 Chirality : 0.047 0.346 3237 Planarity : 0.004 0.040 3564 Dihedral : 4.921 30.129 2925 Min Nonbonded Distance : 2.407 Molprobity Statistics. All-atom Clashscore : 9.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.06 % Favored : 95.94 % Rotamer: Outliers : 3.16 % Allowed : 21.03 % Favored : 75.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.13 (0.16), residues: 2622 helix: 0.35 (0.25), residues: 447 sheet: 0.20 (0.18), residues: 789 loop : -0.31 (0.17), residues: 1386 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.040 0.002 TRP K 35 HIS 0.011 0.002 HIS B 36 PHE 0.028 0.001 PHE I 27 TYR 0.023 0.002 TYR F 385 ARG 0.007 0.001 ARG I 50 Details of bonding type rmsd link_NAG-ASN : bond 0.00255 ( 3) link_NAG-ASN : angle 1.03923 ( 9) hydrogen bonds : bond 0.03263 ( 924) hydrogen bonds : angle 5.36916 ( 2550) SS BOND : bond 0.00324 ( 45) SS BOND : angle 1.85507 ( 90) covalent geometry : bond 0.00295 (20610) covalent geometry : angle 0.60587 (27978) *********************** REFINEMENT MACRO_CYCLE 9 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 619 residues out of total 2244 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 548 time to evaluate : 2.210 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 24 LEU cc_start: 0.8234 (mm) cc_final: 0.7839 (mp) REVERT: A 62 ASP cc_start: 0.8189 (t0) cc_final: 0.7699 (t70) REVERT: A 84 VAL cc_start: 0.8275 (p) cc_final: 0.8009 (m) REVERT: A 126 LYS cc_start: 0.7185 (mmtt) cc_final: 0.6678 (mmtp) REVERT: A 129 ARG cc_start: 0.7580 (ptp-110) cc_final: 0.7231 (ptm160) REVERT: A 171 LYS cc_start: 0.8234 (mttp) cc_final: 0.7915 (mttp) REVERT: A 175 ARG cc_start: 0.7966 (mtt-85) cc_final: 0.7652 (mtm-85) REVERT: A 327 GLU cc_start: 0.8074 (pt0) cc_final: 0.7759 (pt0) REVERT: A 349 GLU cc_start: 0.7612 (mt-10) cc_final: 0.7229 (mt-10) REVERT: A 367 ARG cc_start: 0.8080 (ptt-90) cc_final: 0.7793 (ptt-90) REVERT: A 385 TYR cc_start: 0.7737 (m-80) cc_final: 0.7522 (m-10) REVERT: A 402 GLN cc_start: 0.8226 (tt0) cc_final: 0.7867 (tp40) REVERT: A 421 ASP cc_start: 0.6922 (t0) cc_final: 0.6515 (t0) REVERT: A 433 GLU cc_start: 0.7927 (tt0) cc_final: 0.7706 (tt0) REVERT: A 440 ARG cc_start: 0.7531 (ttp-170) cc_final: 0.7221 (ptm-80) REVERT: A 461 ASP cc_start: 0.7655 (t0) cc_final: 0.7425 (t0) REVERT: A 462 GLN cc_start: 0.8288 (tm-30) cc_final: 0.7569 (tm-30) REVERT: B 36 HIS cc_start: 0.7380 (m90) cc_final: 0.6820 (m90) REVERT: B 37 TRP cc_start: 0.8338 (m100) cc_final: 0.8014 (m-90) REVERT: C 34 MET cc_start: 0.6616 (mmt) cc_final: 0.6324 (tpp) REVERT: C 68 THR cc_start: 0.7809 (m) cc_final: 0.7395 (p) REVERT: C 91 TYR cc_start: 0.7101 (m-80) cc_final: 0.6606 (m-80) REVERT: E 24 LEU cc_start: 0.8142 (OUTLIER) cc_final: 0.7847 (mp) REVERT: E 29 SER cc_start: 0.8328 (t) cc_final: 0.7969 (p) REVERT: E 47 VAL cc_start: 0.8555 (OUTLIER) cc_final: 0.8299 (m) REVERT: E 51 GLU cc_start: 0.7440 (mm-30) cc_final: 0.7109 (mm-30) REVERT: E 80 GLU cc_start: 0.7475 (tt0) cc_final: 0.7194 (tt0) REVERT: E 126 LYS cc_start: 0.7214 (mmtt) cc_final: 0.6941 (mmtp) REVERT: E 129 ARG cc_start: 0.7656 (ptp-110) cc_final: 0.7241 (ttp80) REVERT: E 171 LYS cc_start: 0.7739 (mtmt) cc_final: 0.7380 (mtmt) REVERT: E 184 ILE cc_start: 0.7763 (tp) cc_final: 0.7499 (pt) REVERT: E 206 GLN cc_start: 0.7516 (mt0) cc_final: 0.7078 (mt0) REVERT: E 233 ASN cc_start: 0.8659 (OUTLIER) cc_final: 0.8256 (m-40) REVERT: E 267 VAL cc_start: 0.8746 (OUTLIER) cc_final: 0.8367 (m) REVERT: E 345 GLU cc_start: 0.7713 (tp30) cc_final: 0.7363 (tp30) REVERT: E 349 GLU cc_start: 0.7637 (tp30) cc_final: 0.7134 (tp30) REVERT: E 412 ASN cc_start: 0.7101 (m-40) cc_final: 0.6779 (m-40) REVERT: E 462 GLN cc_start: 0.8072 (tt0) cc_final: 0.7607 (tt0) REVERT: F 47 VAL cc_start: 0.8642 (OUTLIER) cc_final: 0.8433 (m) REVERT: F 51 GLU cc_start: 0.7675 (mm-30) cc_final: 0.7271 (mm-30) REVERT: F 62 ASP cc_start: 0.7664 (t0) cc_final: 0.7027 (t0) REVERT: F 205 ARG cc_start: 0.7723 (mmm-85) cc_final: 0.7493 (mmm-85) REVERT: F 222 MET cc_start: 0.7963 (ttp) cc_final: 0.7695 (ttm) REVERT: F 263 TYR cc_start: 0.8227 (m-80) cc_final: 0.7771 (m-10) REVERT: F 386 LYS cc_start: 0.7931 (mmtm) cc_final: 0.7441 (mmtm) REVERT: F 412 ASN cc_start: 0.7422 (m-40) cc_final: 0.7207 (m110) REVERT: G 3 GLN cc_start: 0.6430 (pp30) cc_final: 0.6174 (tm-30) REVERT: G 36 TRP cc_start: 0.7458 (m100) cc_final: 0.7188 (m100) REVERT: G 55 SER cc_start: 0.8304 (t) cc_final: 0.8019 (p) REVERT: G 82 GLN cc_start: 0.7428 (tp-100) cc_final: 0.7194 (tp-100) REVERT: H 66 ARG cc_start: 0.7531 (ttm170) cc_final: 0.7279 (ttm110) REVERT: H 87 THR cc_start: 0.7565 (m) cc_final: 0.7346 (p) REVERT: H 94 ARG cc_start: 0.8702 (OUTLIER) cc_final: 0.8295 (ttp-110) REVERT: I 30 THR cc_start: 0.7921 (p) cc_final: 0.7624 (t) REVERT: I 34 MET cc_start: 0.6631 (mmt) cc_final: 0.6196 (mmt) REVERT: I 47 TRP cc_start: 0.8269 (t60) cc_final: 0.7573 (t60) REVERT: J 34 MET cc_start: 0.7680 (mmm) cc_final: 0.7261 (mmm) REVERT: J 81 LEU cc_start: 0.7667 (tp) cc_final: 0.7453 (mt) REVERT: J 82 GLN cc_start: 0.7099 (tp40) cc_final: 0.6795 (tp40) REVERT: J 83 MET cc_start: 0.7796 (mtt) cc_final: 0.7585 (mtt) REVERT: J 84 ASN cc_start: 0.8020 (m-40) cc_final: 0.7488 (p0) REVERT: K 28 LEU cc_start: 0.8596 (mt) cc_final: 0.8321 (mt) REVERT: K 30 LYS cc_start: 0.8004 (mtpt) cc_final: 0.7710 (mtpt) REVERT: K 93 SER cc_start: 0.8827 (t) cc_final: 0.8385 (p) REVERT: K 98 PHE cc_start: 0.8185 (m-80) cc_final: 0.7772 (m-80) REVERT: L 37 GLN cc_start: 0.8196 (tt0) cc_final: 0.7801 (tt0) REVERT: L 52 SER cc_start: 0.7935 (m) cc_final: 0.7608 (t) REVERT: M 37 TRP cc_start: 0.8497 (m100) cc_final: 0.7891 (m100) REVERT: N 35 ASN cc_start: 0.7204 (m-40) cc_final: 0.6851 (m110) REVERT: N 36 TRP cc_start: 0.7270 (m100) cc_final: 0.6338 (m100) REVERT: N 80 PHE cc_start: 0.7950 (m-80) cc_final: 0.7613 (m-80) REVERT: N 84 ASN cc_start: 0.8191 (m-40) cc_final: 0.7972 (p0) REVERT: N 93 ILE cc_start: 0.8316 (mt) cc_final: 0.7832 (tt) outliers start: 71 outliers final: 60 residues processed: 586 average time/residue: 0.3873 time to fit residues: 344.5328 Evaluate side-chains 601 residues out of total 2244 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 535 time to evaluate : 2.136 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 59 THR Chi-restraints excluded: chain A residue 142 LYS Chi-restraints excluded: chain A residue 147 CYS 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 B residue 35 VAL 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 95 SER Chi-restraints excluded: chain D residue 63 SER Chi-restraints excluded: chain D residue 107 LEU Chi-restraints excluded: chain E residue 24 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 233 ASN Chi-restraints excluded: chain E residue 234 MET Chi-restraints excluded: chain E residue 267 VAL Chi-restraints excluded: chain E residue 273 LEU Chi-restraints excluded: chain E residue 302 LEU Chi-restraints excluded: chain E residue 401 LYS Chi-restraints excluded: chain E residue 417 THR Chi-restraints excluded: chain E residue 454 ASP Chi-restraints excluded: chain F residue 33 GLU 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 73 LEU Chi-restraints excluded: chain F residue 83 THR Chi-restraints excluded: chain F residue 108 ILE Chi-restraints excluded: chain F residue 227 LEU Chi-restraints excluded: chain F residue 243 LEU Chi-restraints excluded: chain F residue 267 VAL Chi-restraints excluded: chain F residue 302 LEU 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 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 78 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 K residue 107 LEU Chi-restraints excluded: chain L residue 89 GLN Chi-restraints excluded: chain L residue 107 LEU 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 65 LYS Chi-restraints excluded: chain N residue 95 PHE Chi-restraints excluded: chain N residue 106 SER Chi-restraints excluded: chain O residue 35 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 261 random chunks: chunk 259 optimal weight: 0.7980 chunk 123 optimal weight: 0.7980 chunk 49 optimal weight: 0.0020 chunk 89 optimal weight: 0.9980 chunk 74 optimal weight: 4.9990 chunk 214 optimal weight: 0.6980 chunk 66 optimal weight: 5.9990 chunk 154 optimal weight: 0.5980 chunk 188 optimal weight: 4.9990 chunk 60 optimal weight: 0.9980 chunk 180 optimal weight: 0.9980 overall best weight: 0.5788 ------------------------------------------------------------------------------- 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 ** A 455 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 272 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 195 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 202 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 16 GLN ** K 34 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 17 GLN O 40 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3764 r_free = 0.3764 target = 0.136791 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3543 r_free = 0.3543 target = 0.120548 restraints weight = 30664.217| |-----------------------------------------------------------------------------| r_work (start): 0.3552 rms_B_bonded: 2.05 r_work: 0.3450 rms_B_bonded: 2.34 restraints_weight: 0.5000 r_work: 0.3304 rms_B_bonded: 4.13 restraints_weight: 0.2500 r_work (final): 0.3304 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3242 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3242 r_free = 0.3242 target_work(ls_wunit_k1) = 0.102 | | occupancies: max = 1.00 min = 0.81 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3242 r_free = 0.3242 target_work(ls_wunit_k1) = 0.102 | | occupancies: max = 1.00 min = 0.82 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3242 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7438 moved from start: 0.4113 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 20658 Z= 0.141 Angle : 0.626 12.241 28077 Z= 0.327 Chirality : 0.047 0.329 3237 Planarity : 0.004 0.039 3564 Dihedral : 4.895 29.915 2925 Min Nonbonded Distance : 2.324 Molprobity Statistics. All-atom Clashscore : 9.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.87 % Favored : 96.13 % Rotamer: Outliers : 3.21 % Allowed : 21.17 % Favored : 75.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.14 (0.16), residues: 2622 helix: 0.34 (0.25), residues: 447 sheet: 0.25 (0.18), residues: 774 loop : -0.35 (0.17), residues: 1401 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.043 0.002 TRP K 35 HIS 0.011 0.002 HIS B 36 PHE 0.027 0.001 PHE I 27 TYR 0.023 0.002 TYR F 385 ARG 0.008 0.001 ARG E 175 Details of bonding type rmsd link_NAG-ASN : bond 0.00342 ( 3) link_NAG-ASN : angle 1.11262 ( 9) hydrogen bonds : bond 0.03289 ( 924) hydrogen bonds : angle 5.33339 ( 2550) SS BOND : bond 0.00322 ( 45) SS BOND : angle 1.76546 ( 90) covalent geometry : bond 0.00315 (20610) covalent geometry : angle 0.61921 (27978) ********************** REFINEMENT MACRO_CYCLE 10 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 618 residues out of total 2244 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 546 time to evaluate : 2.222 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: A 24 LEU cc_start: 0.8224 (mm) cc_final: 0.8019 (mt) REVERT: A 62 ASP cc_start: 0.8167 (t0) cc_final: 0.7755 (t0) REVERT: A 126 LYS cc_start: 0.7219 (mmtt) cc_final: 0.6719 (mmtp) REVERT: A 129 ARG cc_start: 0.7587 (ptp-110) cc_final: 0.7239 (ptm160) REVERT: A 171 LYS cc_start: 0.8235 (mttp) cc_final: 0.7794 (mttp) REVERT: A 175 ARG cc_start: 0.7940 (mtt-85) cc_final: 0.7624 (mtm-85) REVERT: A 178 ASN cc_start: 0.8037 (t0) cc_final: 0.7831 (t0) REVERT: A 258 ILE cc_start: 0.8198 (OUTLIER) cc_final: 0.7969 (mt) REVERT: A 327 GLU cc_start: 0.8072 (pt0) cc_final: 0.7857 (pt0) REVERT: A 349 GLU cc_start: 0.7664 (mt-10) cc_final: 0.7269 (mt-10) REVERT: A 385 TYR cc_start: 0.7754 (m-80) cc_final: 0.7527 (m-10) REVERT: A 386 LYS cc_start: 0.8062 (mmmt) cc_final: 0.7703 (mmtm) REVERT: A 402 GLN cc_start: 0.8215 (tt0) cc_final: 0.7855 (tp40) REVERT: A 421 ASP cc_start: 0.6915 (t0) cc_final: 0.6525 (t0) REVERT: A 433 GLU cc_start: 0.7931 (tt0) cc_final: 0.7707 (tt0) REVERT: A 440 ARG cc_start: 0.7533 (ttp-170) cc_final: 0.7228 (ptm-80) REVERT: A 461 ASP cc_start: 0.7690 (t0) cc_final: 0.7474 (t0) REVERT: A 462 GLN cc_start: 0.8308 (tm-30) cc_final: 0.7569 (tm-30) REVERT: B 36 HIS cc_start: 0.7424 (m90) cc_final: 0.6887 (m90) REVERT: B 37 TRP cc_start: 0.8334 (m100) cc_final: 0.8054 (m-90) REVERT: C 34 MET cc_start: 0.6589 (mmt) cc_final: 0.6194 (tpp) REVERT: C 68 THR cc_start: 0.7811 (m) cc_final: 0.7384 (p) REVERT: C 91 TYR cc_start: 0.7113 (m-80) cc_final: 0.6613 (m-80) REVERT: E 24 LEU cc_start: 0.8245 (mm) cc_final: 0.7988 (mt) REVERT: E 29 SER cc_start: 0.8336 (t) cc_final: 0.7917 (p) REVERT: E 47 VAL cc_start: 0.8551 (OUTLIER) cc_final: 0.8306 (m) REVERT: E 51 GLU cc_start: 0.7446 (mm-30) cc_final: 0.7143 (mm-30) REVERT: E 80 GLU cc_start: 0.7486 (tt0) cc_final: 0.7203 (tt0) REVERT: E 129 ARG cc_start: 0.7687 (ptp-110) cc_final: 0.7199 (ttp80) REVERT: E 139 ASN cc_start: 0.8339 (m-40) cc_final: 0.7866 (m-40) REVERT: E 142 LYS cc_start: 0.7827 (mmtp) cc_final: 0.7495 (mttt) REVERT: E 171 LYS cc_start: 0.7711 (mtmt) cc_final: 0.7312 (mtmt) REVERT: E 184 ILE cc_start: 0.7776 (tp) cc_final: 0.7523 (pt) REVERT: E 206 GLN cc_start: 0.7542 (mt0) cc_final: 0.7110 (mt0) REVERT: E 233 ASN cc_start: 0.8676 (OUTLIER) cc_final: 0.8169 (t0) REVERT: E 267 VAL cc_start: 0.8766 (OUTLIER) cc_final: 0.8388 (m) REVERT: E 345 GLU cc_start: 0.7708 (tp30) cc_final: 0.7359 (tp30) REVERT: E 349 GLU cc_start: 0.7634 (tp30) cc_final: 0.7129 (tp30) REVERT: E 412 ASN cc_start: 0.7073 (m-40) cc_final: 0.6763 (m-40) REVERT: E 462 GLN cc_start: 0.8100 (tt0) cc_final: 0.7823 (tt0) REVERT: F 47 VAL cc_start: 0.8655 (OUTLIER) cc_final: 0.8337 (t) REVERT: F 51 GLU cc_start: 0.7682 (mm-30) cc_final: 0.7287 (mm-30) REVERT: F 62 ASP cc_start: 0.7681 (t0) cc_final: 0.7038 (t0) REVERT: F 188 LYS cc_start: 0.7668 (ttmm) cc_final: 0.7397 (ttpp) REVERT: F 205 ARG cc_start: 0.7753 (mmm-85) cc_final: 0.7506 (mmm-85) REVERT: F 222 MET cc_start: 0.7966 (ttp) cc_final: 0.7694 (ttm) REVERT: F 263 TYR cc_start: 0.8211 (m-80) cc_final: 0.7777 (m-10) REVERT: F 280 ASP cc_start: 0.7376 (p0) cc_final: 0.6958 (p0) REVERT: F 331 ASP cc_start: 0.8006 (t0) cc_final: 0.7361 (t0) REVERT: F 386 LYS cc_start: 0.7910 (mmtm) cc_final: 0.7405 (mmtm) REVERT: F 412 ASN cc_start: 0.7410 (m-40) cc_final: 0.7196 (m110) REVERT: F 450 LYS cc_start: 0.8254 (mtmm) cc_final: 0.8049 (mppt) REVERT: G 3 GLN cc_start: 0.6377 (pp30) cc_final: 0.6177 (tm-30) REVERT: G 35 ASN cc_start: 0.7155 (m-40) cc_final: 0.6929 (m110) REVERT: G 36 TRP cc_start: 0.7389 (m100) cc_final: 0.7136 (m100) REVERT: G 55 SER cc_start: 0.8282 (t) cc_final: 0.7993 (p) REVERT: G 82 GLN cc_start: 0.7427 (tp-100) cc_final: 0.7216 (tp-100) REVERT: H 50 ARG cc_start: 0.8465 (ttp-110) cc_final: 0.8259 (ttp-110) REVERT: H 87 THR cc_start: 0.7596 (m) cc_final: 0.7366 (p) REVERT: H 94 ARG cc_start: 0.8712 (OUTLIER) cc_final: 0.8309 (ttp-110) REVERT: I 30 THR cc_start: 0.7935 (p) cc_final: 0.7633 (t) REVERT: I 34 MET cc_start: 0.6677 (mmt) cc_final: 0.6215 (mmt) REVERT: I 47 TRP cc_start: 0.8245 (t60) cc_final: 0.7583 (t60) REVERT: J 34 MET cc_start: 0.7663 (mmm) cc_final: 0.7277 (mmm) REVERT: J 81 LEU cc_start: 0.7626 (tp) cc_final: 0.7381 (mt) REVERT: J 82 GLN cc_start: 0.7059 (tp40) cc_final: 0.6767 (tp40) REVERT: J 83 MET cc_start: 0.7820 (mtt) cc_final: 0.7580 (mtt) REVERT: J 84 ASN cc_start: 0.8031 (m-40) cc_final: 0.7500 (p0) REVERT: K 28 LEU cc_start: 0.8589 (mt) cc_final: 0.8315 (mt) REVERT: K 35 TRP cc_start: 0.7674 (m100) cc_final: 0.7458 (m100) REVERT: K 93 SER cc_start: 0.8781 (t) cc_final: 0.8460 (p) REVERT: L 37 GLN cc_start: 0.8217 (tt0) cc_final: 0.7810 (tt0) REVERT: L 52 SER cc_start: 0.7975 (m) cc_final: 0.7699 (t) REVERT: M 37 TRP cc_start: 0.8526 (m100) cc_final: 0.7929 (m100) REVERT: N 35 ASN cc_start: 0.7172 (m-40) cc_final: 0.6798 (m110) REVERT: N 36 TRP cc_start: 0.7279 (m100) cc_final: 0.6403 (m100) REVERT: N 80 PHE cc_start: 0.7967 (m-80) cc_final: 0.7599 (m-80) REVERT: N 81 LEU cc_start: 0.7779 (tp) cc_final: 0.7460 (tt) REVERT: N 84 ASN cc_start: 0.8179 (m-40) cc_final: 0.7943 (p0) REVERT: N 93 ILE cc_start: 0.8295 (mt) cc_final: 0.7825 (tt) outliers start: 72 outliers final: 60 residues processed: 588 average time/residue: 0.3325 time to fit residues: 296.6615 Evaluate side-chains 602 residues out of total 2244 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 536 time to evaluate : 2.005 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 147 CYS Chi-restraints excluded: chain A residue 258 ILE 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 323 GLU Chi-restraints excluded: chain A residue 455 GLN Chi-restraints excluded: chain B residue 35 VAL 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 45 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 47 VAL 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 174 THR 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 267 VAL Chi-restraints excluded: chain E residue 273 LEU Chi-restraints excluded: chain E residue 302 LEU Chi-restraints excluded: chain E residue 401 LYS Chi-restraints excluded: chain E residue 417 THR Chi-restraints excluded: chain E residue 454 ASP Chi-restraints excluded: chain F residue 31 ILE Chi-restraints excluded: chain F residue 33 GLU 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 73 LEU Chi-restraints excluded: chain F residue 83 THR Chi-restraints excluded: chain F residue 108 ILE Chi-restraints excluded: chain F residue 227 LEU Chi-restraints excluded: chain F residue 243 LEU Chi-restraints excluded: chain F residue 267 VAL Chi-restraints excluded: chain F residue 302 LEU 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 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 78 VAL 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 K residue 107 LEU Chi-restraints excluded: chain L residue 89 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 N residue 3 GLN Chi-restraints excluded: chain N residue 95 PHE Chi-restraints excluded: chain N residue 106 SER Chi-restraints excluded: chain O residue 35 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 261 random chunks: chunk 226 optimal weight: 0.9990 chunk 79 optimal weight: 0.7980 chunk 205 optimal weight: 3.9990 chunk 51 optimal weight: 0.0970 chunk 236 optimal weight: 6.9990 chunk 3 optimal weight: 3.9990 chunk 55 optimal weight: 0.7980 chunk 136 optimal weight: 0.9980 chunk 62 optimal weight: 4.9990 chunk 128 optimal weight: 1.9990 chunk 54 optimal weight: 10.0000 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 172 ASN A 178 ASN ** A 455 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 272 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 195 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 202 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 16 GLN ** K 34 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** O 40 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3755 r_free = 0.3755 target = 0.136034 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3529 r_free = 0.3529 target = 0.119643 restraints weight = 30978.149| |-----------------------------------------------------------------------------| r_work (start): 0.3539 rms_B_bonded: 2.05 r_work: 0.3436 rms_B_bonded: 2.35 restraints_weight: 0.5000 r_work: 0.3292 rms_B_bonded: 4.11 restraints_weight: 0.2500 r_work (final): 0.3292 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3244 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3244 r_free = 0.3244 target_work(ls_wunit_k1) = 0.102 | | occupancies: max = 1.00 min = 0.82 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3244 r_free = 0.3244 target_work(ls_wunit_k1) = 0.102 | | occupancies: max = 1.00 min = 0.85 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3244 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7452 moved from start: 0.4144 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 20658 Z= 0.160 Angle : 0.638 12.844 28077 Z= 0.334 Chirality : 0.047 0.325 3237 Planarity : 0.004 0.039 3564 Dihedral : 4.966 30.039 2925 Min Nonbonded Distance : 2.390 Molprobity Statistics. All-atom Clashscore : 9.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.09 % Favored : 95.91 % Rotamer: Outliers : 3.30 % Allowed : 21.75 % Favored : 74.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.18 (0.16), residues: 2622 helix: 0.34 (0.25), residues: 447 sheet: 0.30 (0.18), residues: 759 loop : -0.44 (0.17), residues: 1416 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.037 0.002 TRP K 35 HIS 0.010 0.002 HIS B 36 PHE 0.026 0.001 PHE I 27 TYR 0.023 0.002 TYR F 385 ARG 0.007 0.001 ARG I 50 Details of bonding type rmsd link_NAG-ASN : bond 0.00406 ( 3) link_NAG-ASN : angle 1.14988 ( 9) hydrogen bonds : bond 0.03407 ( 924) hydrogen bonds : angle 5.36410 ( 2550) SS BOND : bond 0.00353 ( 45) SS BOND : angle 1.78955 ( 90) covalent geometry : bond 0.00359 (20610) covalent geometry : angle 0.63063 (27978) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 12424.31 seconds wall clock time: 215 minutes 37.93 seconds (12937.93 seconds total)