Starting phenix.real_space_refine on Thu Mar 5 19:20:49 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6v4o_21043/03_2026/6v4o_21043_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/6v4o_21043/03_2026/6v4o_21043.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/6v4o_21043/03_2026/6v4o_21043.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6v4o_21043/03_2026/6v4o_21043.map" model { file = "/net/cci-nas-00/data/ceres_data/6v4o_21043/03_2026/6v4o_21043_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6v4o_21043/03_2026/6v4o_21043_neut.cif" } resolution = 2.8 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.004 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians Ca 4 9.91 5 S 152 5.16 5 C 15628 2.51 5 N 4220 2.21 5 O 4792 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 20 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 24796 Number of models: 1 Model: "" Number of chains: 5 Chain: "I" Number of atoms: 2830 Number of conformers: 1 Conformer: "" Number of residues, atoms: 364, 2830 Classifications: {'peptide': 364} Link IDs: {'PCIS': 1, 'PTRANS': 17, 'TRANS': 345} Chain breaks: 3 Chain: "A" Number of atoms: 1695 Number of conformers: 1 Conformer: "" Number of residues, atoms: 223, 1695 Classifications: {'peptide': 223} Link IDs: {'PCIS': 2, 'PTRANS': 11, 'TRANS': 209} Chain breaks: 1 Chain: "B" Number of atoms: 1634 Number of conformers: 1 Conformer: "" Number of residues, atoms: 214, 1634 Classifications: {'peptide': 214} Link IDs: {'PCIS': 2, 'PTRANS': 10, 'TRANS': 201} Chain: "F" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "I" Number of atoms: 12 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 12 Unusual residues: {' CA': 1, 'BMA': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Restraints were copied for chains: M, N, W, C, D, H, E, G, L, J, K, O Time building chain proxies: 4.14, per 1000 atoms: 0.17 Number of scatterers: 24796 At special positions: 0 Unit cell: (174.9, 174.9, 123.2, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) Ca 4 19.99 S 152 16.00 O 4792 8.00 N 4220 7.00 C 15628 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=36, symmetry=0 Simple disulfide: pdb=" SG CYS I 87 " - pdb=" SG CYS I 420 " distance=2.03 Simple disulfide: pdb=" SG CYS I 122 " - pdb=" SG CYS I 127 " distance=2.03 Simple disulfide: pdb=" SG CYS I 182 " - pdb=" SG CYS I 229 " distance=2.03 Simple disulfide: pdb=" SG CYS I 231 " - pdb=" SG CYS I 236 " distance=2.03 Simple disulfide: pdb=" SG CYS I 277 " - pdb=" SG CYS I 291 " distance=2.02 Simple disulfide: pdb=" SG CYS I 279 " - pdb=" SG CYS I 289 " distance=2.02 Simple disulfide: pdb=" SG CYS I 318 " - pdb=" SG CYS I 337 " distance=2.03 Simple disulfide: pdb=" SG CYS I 424 " - pdb=" SG CYS I 447 " distance=2.03 Simple disulfide: pdb=" SG CYS M 231 " - pdb=" SG CYS M 231 " distance=0.00 Simple disulfide: pdb=" SG CYS M 231 " - pdb=" SG CYS M 236 " distance=2.03 Simple disulfide: pdb=" SG CYS N 127 " - pdb=" SG CYS N 122 " distance=2.03 Simple disulfide: pdb=" SG CYS N 127 " - pdb=" SG CYS N 127 " distance=0.00 Simple disulfide: pdb=" SG CYS M 87 " - pdb=" SG CYS M 420 " distance=2.03 Simple disulfide: pdb=" SG CYS N 87 " - pdb=" SG CYS N 420 " distance=2.03 Simple disulfide: pdb=" SG CYS W 87 " - pdb=" SG CYS W 420 " distance=2.03 Simple disulfide: pdb=" SG CYS M 122 " - pdb=" SG CYS M 127 " distance=2.03 Simple disulfide: pdb=" SG CYS N 122 " - pdb=" SG CYS N 127 " distance=2.03 Simple disulfide: pdb=" SG CYS W 122 " - pdb=" SG CYS W 127 " distance=2.03 Simple disulfide: pdb=" SG CYS M 182 " - pdb=" SG CYS M 229 " distance=2.03 Simple disulfide: pdb=" SG CYS N 182 " - pdb=" SG CYS N 229 " distance=2.03 Simple disulfide: pdb=" SG CYS W 182 " - pdb=" SG CYS W 229 " distance=2.03 Simple disulfide: pdb=" SG CYS M 231 " - pdb=" SG CYS M 236 " distance=2.03 Simple disulfide: pdb=" SG CYS N 231 " - pdb=" SG CYS N 236 " distance=2.03 Simple disulfide: pdb=" SG CYS W 231 " - pdb=" SG CYS W 236 " distance=2.03 Simple disulfide: pdb=" SG CYS M 277 " - pdb=" SG CYS M 291 " distance=2.02 Simple disulfide: pdb=" SG CYS N 277 " - pdb=" SG CYS N 291 " distance=2.02 Simple disulfide: pdb=" SG CYS W 277 " - pdb=" SG CYS W 291 " distance=2.02 Simple disulfide: pdb=" SG CYS M 279 " - pdb=" SG CYS M 289 " distance=2.03 Simple disulfide: pdb=" SG CYS N 279 " - pdb=" SG CYS N 289 " distance=2.02 Simple disulfide: pdb=" SG CYS W 279 " - pdb=" SG CYS W 289 " distance=2.03 Simple disulfide: pdb=" SG CYS M 318 " - pdb=" SG CYS M 337 " distance=2.03 Simple disulfide: pdb=" SG CYS N 318 " - pdb=" SG CYS N 337 " distance=2.03 Simple disulfide: pdb=" SG CYS W 318 " - pdb=" SG CYS W 337 " distance=2.03 Simple disulfide: pdb=" SG CYS M 424 " - pdb=" SG CYS M 447 " distance=2.03 Simple disulfide: pdb=" SG CYS N 424 " - pdb=" SG CYS N 447 " distance=2.03 Simple disulfide: pdb=" SG CYS W 424 " - pdb=" SG CYS W 447 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied BETA1-4 " NAG F 1 " - " NAG F 2 " " NAG F 2 " - " BMA I 503 " " NAG J 1 " - " NAG J 2 " " NAG J 2 " - " BMA M 503 " " NAG K 1 " - " NAG K 2 " " NAG K 2 " - " BMA N 503 " " NAG O 1 " - " NAG O 2 " " NAG O 2 " - " BMA W 503 " NAG-ASN " NAG F 1 " - " ASN I 284 " " NAG J 1 " - " ASN M 284 " " NAG K 1 " - " ASN N 284 " " NAG O 1 " - " ASN W 284 " Time building additional restraints: 1.84 Conformation dependent library (CDL) restraints added in 1.1 seconds 6296 Ramachandran restraints generated. 3148 Oldfield, 0 Emsley, 3148 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5856 Finding SS restraints... Secondary structure from input PDB file: 32 helices and 68 sheets defined 5.2% alpha, 40.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.78 Creating SS restraints... Processing helix chain 'I' and resid 99 through 104 removed outlier: 3.594A pdb=" N GLY I 104 " --> pdb=" O HIS I 101 " (cutoff:3.500A) Processing helix chain 'I' and resid 386 through 390 removed outlier: 4.208A pdb=" N ASP I 390 " --> pdb=" O PRO I 387 " (cutoff:3.500A) Processing helix chain 'M' and resid 99 through 104 removed outlier: 3.595A pdb=" N GLY M 104 " --> pdb=" O HIS M 101 " (cutoff:3.500A) Processing helix chain 'M' and resid 386 through 390 removed outlier: 4.209A pdb=" N ASP M 390 " --> pdb=" O PRO M 387 " (cutoff:3.500A) Processing helix chain 'N' and resid 99 through 104 removed outlier: 3.594A pdb=" N GLY N 104 " --> pdb=" O HIS N 101 " (cutoff:3.500A) Processing helix chain 'N' and resid 386 through 390 removed outlier: 4.208A pdb=" N ASP N 390 " --> pdb=" O PRO N 387 " (cutoff:3.500A) Processing helix chain 'W' and resid 99 through 104 removed outlier: 3.594A pdb=" N GLY W 104 " --> pdb=" O HIS W 101 " (cutoff:3.500A) Processing helix chain 'W' and resid 386 through 390 removed outlier: 4.208A pdb=" N ASP W 390 " --> pdb=" O PRO W 387 " (cutoff:3.500A) Processing helix chain 'A' and resid 28 through 32 removed outlier: 3.726A pdb=" N HIS A 32 " --> pdb=" O PHE A 29 " (cutoff:3.500A) Processing helix chain 'A' and resid 185 through 189 removed outlier: 3.673A pdb=" N LEU A 189 " --> pdb=" O SER A 186 " (cutoff:3.500A) Processing helix chain 'A' and resid 200 through 204 Processing helix chain 'C' and resid 28 through 32 removed outlier: 3.725A pdb=" N HIS C 32 " --> pdb=" O PHE C 29 " (cutoff:3.500A) Processing helix chain 'C' and resid 185 through 189 removed outlier: 3.672A pdb=" N LEU C 189 " --> pdb=" O SER C 186 " (cutoff:3.500A) Processing helix chain 'C' and resid 200 through 204 Processing helix chain 'D' and resid 28 through 32 removed outlier: 3.725A pdb=" N HIS D 32 " --> pdb=" O PHE D 29 " (cutoff:3.500A) Processing helix chain 'D' and resid 185 through 189 removed outlier: 3.672A pdb=" N LEU D 189 " --> pdb=" O SER D 186 " (cutoff:3.500A) Processing helix chain 'D' and resid 200 through 204 Processing helix chain 'H' and resid 28 through 32 removed outlier: 3.725A pdb=" N HIS H 32 " --> pdb=" O PHE H 29 " (cutoff:3.500A) Processing helix chain 'H' and resid 185 through 189 removed outlier: 3.674A pdb=" N LEU H 189 " --> pdb=" O SER H 186 " (cutoff:3.500A) Processing helix chain 'H' and resid 200 through 204 Processing helix chain 'B' and resid 79 through 83 removed outlier: 4.244A pdb=" N PHE B 83 " --> pdb=" O PRO B 80 " (cutoff:3.500A) Processing helix chain 'B' and resid 121 through 128 removed outlier: 3.883A pdb=" N GLY B 128 " --> pdb=" O GLN B 124 " (cutoff:3.500A) Processing helix chain 'B' and resid 184 through 186 No H-bonds generated for 'chain 'B' and resid 184 through 186' Processing helix chain 'E' and resid 79 through 83 removed outlier: 4.243A pdb=" N PHE E 83 " --> pdb=" O PRO E 80 " (cutoff:3.500A) Processing helix chain 'E' and resid 121 through 128 removed outlier: 3.883A pdb=" N GLY E 128 " --> pdb=" O GLN E 124 " (cutoff:3.500A) Processing helix chain 'E' and resid 184 through 186 No H-bonds generated for 'chain 'E' and resid 184 through 186' Processing helix chain 'G' and resid 79 through 83 removed outlier: 4.243A pdb=" N PHE G 83 " --> pdb=" O PRO G 80 " (cutoff:3.500A) Processing helix chain 'G' and resid 121 through 128 removed outlier: 3.883A pdb=" N GLY G 128 " --> pdb=" O GLN G 124 " (cutoff:3.500A) Processing helix chain 'G' and resid 184 through 186 No H-bonds generated for 'chain 'G' and resid 184 through 186' Processing helix chain 'L' and resid 79 through 83 removed outlier: 4.244A pdb=" N PHE L 83 " --> pdb=" O PRO L 80 " (cutoff:3.500A) Processing helix chain 'L' and resid 121 through 128 removed outlier: 3.882A pdb=" N GLY L 128 " --> pdb=" O GLN L 124 " (cutoff:3.500A) Processing helix chain 'L' and resid 184 through 186 No H-bonds generated for 'chain 'L' and resid 184 through 186' Processing sheet with id=AA1, first strand: chain 'I' and resid 92 through 98 removed outlier: 5.551A pdb=" N LYS I 94 " --> pdb=" O CYS I 447 " (cutoff:3.500A) removed outlier: 6.130A pdb=" N CYS I 447 " --> pdb=" O LYS I 94 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'I' and resid 119 through 122 removed outlier: 3.929A pdb=" N MET I 174 " --> pdb=" O LEU I 156 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'I' and resid 178 through 183 removed outlier: 3.825A pdb=" N SER I 178 " --> pdb=" O VAL I 193 " (cutoff:3.500A) removed outlier: 4.181A pdb=" N ASP I 212 " --> pdb=" O ILE I 204 " (cutoff:3.500A) removed outlier: 6.556A pdb=" N TYR I 206 " --> pdb=" O TYR I 210 " (cutoff:3.500A) removed outlier: 5.887A pdb=" N TYR I 210 " --> pdb=" O TYR I 206 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'I' and resid 222 through 224 removed outlier: 3.583A pdb=" N ASN I 230 " --> pdb=" O TYR I 237 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'I' and resid 222 through 224 removed outlier: 3.646A pdb=" N ASP I 242 " --> pdb=" O GLU I 250 " (cutoff:3.500A) removed outlier: 4.033A pdb=" N GLU I 250 " --> pdb=" O ASP I 242 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N LYS I 263 " --> pdb=" O LYS I 255 " (cutoff:3.500A) removed outlier: 6.316A pdb=" N ARG I 257 " --> pdb=" O ILE I 261 " (cutoff:3.500A) removed outlier: 5.258A pdb=" N ILE I 261 " --> pdb=" O ARG I 257 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'I' and resid 268 through 269 removed outlier: 6.558A pdb=" N THR I 268 " --> pdb=" O ILE I 314 " (cutoff:3.500A) removed outlier: 8.880A pdb=" N LEU I 316 " --> pdb=" O THR I 268 " (cutoff:3.500A) removed outlier: 6.198A pdb=" N THR I 286 " --> pdb=" O ALA I 282 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'I' and resid 352 through 356 removed outlier: 8.173A pdb=" N MET I 375 " --> pdb=" O VAL I 401 " (cutoff:3.500A) removed outlier: 8.122A pdb=" N VAL I 401 " --> pdb=" O MET I 375 " (cutoff:3.500A) removed outlier: 7.116A pdb=" N MET I 377 " --> pdb=" O VAL I 399 " (cutoff:3.500A) removed outlier: 5.128A pdb=" N VAL I 399 " --> pdb=" O MET I 377 " (cutoff:3.500A) removed outlier: 7.126A pdb=" N LEU I 379 " --> pdb=" O SER I 397 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'M' and resid 92 through 98 removed outlier: 5.552A pdb=" N LYS M 94 " --> pdb=" O CYS M 447 " (cutoff:3.500A) removed outlier: 6.129A pdb=" N CYS M 447 " --> pdb=" O LYS M 94 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'M' and resid 119 through 122 removed outlier: 3.928A pdb=" N MET M 174 " --> pdb=" O LEU M 156 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'M' and resid 178 through 183 removed outlier: 3.825A pdb=" N SER M 178 " --> pdb=" O VAL M 193 " (cutoff:3.500A) removed outlier: 4.181A pdb=" N ASP M 212 " --> pdb=" O ILE M 204 " (cutoff:3.500A) removed outlier: 6.556A pdb=" N TYR M 206 " --> pdb=" O TYR M 210 " (cutoff:3.500A) removed outlier: 5.887A pdb=" N TYR M 210 " --> pdb=" O TYR M 206 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'M' and resid 222 through 224 removed outlier: 3.582A pdb=" N ASN M 230 " --> pdb=" O TYR M 237 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'M' and resid 222 through 224 removed outlier: 3.646A pdb=" N ASP M 242 " --> pdb=" O GLU M 250 " (cutoff:3.500A) removed outlier: 4.033A pdb=" N GLU M 250 " --> pdb=" O ASP M 242 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N LYS M 263 " --> pdb=" O LYS M 255 " (cutoff:3.500A) removed outlier: 6.316A pdb=" N ARG M 257 " --> pdb=" O ILE M 261 " (cutoff:3.500A) removed outlier: 5.259A pdb=" N ILE M 261 " --> pdb=" O ARG M 257 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'M' and resid 268 through 269 removed outlier: 6.558A pdb=" N THR M 268 " --> pdb=" O ILE M 314 " (cutoff:3.500A) removed outlier: 8.880A pdb=" N LEU M 316 " --> pdb=" O THR M 268 " (cutoff:3.500A) removed outlier: 6.198A pdb=" N THR M 286 " --> pdb=" O ALA M 282 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'M' and resid 352 through 356 removed outlier: 8.172A pdb=" N MET M 375 " --> pdb=" O VAL M 401 " (cutoff:3.500A) removed outlier: 8.122A pdb=" N VAL M 401 " --> pdb=" O MET M 375 " (cutoff:3.500A) removed outlier: 7.115A pdb=" N MET M 377 " --> pdb=" O VAL M 399 " (cutoff:3.500A) removed outlier: 5.128A pdb=" N VAL M 399 " --> pdb=" O MET M 377 " (cutoff:3.500A) removed outlier: 7.127A pdb=" N LEU M 379 " --> pdb=" O SER M 397 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'N' and resid 92 through 98 removed outlier: 5.553A pdb=" N LYS N 94 " --> pdb=" O CYS N 447 " (cutoff:3.500A) removed outlier: 6.130A pdb=" N CYS N 447 " --> pdb=" O LYS N 94 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'N' and resid 119 through 122 removed outlier: 3.928A pdb=" N MET N 174 " --> pdb=" O LEU N 156 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'N' and resid 178 through 183 removed outlier: 3.825A pdb=" N SER N 178 " --> pdb=" O VAL N 193 " (cutoff:3.500A) removed outlier: 4.181A pdb=" N ASP N 212 " --> pdb=" O ILE N 204 " (cutoff:3.500A) removed outlier: 6.557A pdb=" N TYR N 206 " --> pdb=" O TYR N 210 " (cutoff:3.500A) removed outlier: 5.886A pdb=" N TYR N 210 " --> pdb=" O TYR N 206 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'N' and resid 222 through 224 removed outlier: 3.582A pdb=" N ASN N 230 " --> pdb=" O TYR N 237 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'N' and resid 222 through 224 removed outlier: 3.647A pdb=" N ASP N 242 " --> pdb=" O GLU N 250 " (cutoff:3.500A) removed outlier: 4.033A pdb=" N GLU N 250 " --> pdb=" O ASP N 242 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N LYS N 263 " --> pdb=" O LYS N 255 " (cutoff:3.500A) removed outlier: 6.316A pdb=" N ARG N 257 " --> pdb=" O ILE N 261 " (cutoff:3.500A) removed outlier: 5.259A pdb=" N ILE N 261 " --> pdb=" O ARG N 257 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'N' and resid 268 through 269 removed outlier: 6.559A pdb=" N THR N 268 " --> pdb=" O ILE N 314 " (cutoff:3.500A) removed outlier: 8.880A pdb=" N LEU N 316 " --> pdb=" O THR N 268 " (cutoff:3.500A) removed outlier: 6.198A pdb=" N THR N 286 " --> pdb=" O ALA N 282 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'N' and resid 352 through 356 removed outlier: 8.172A pdb=" N MET N 375 " --> pdb=" O VAL N 401 " (cutoff:3.500A) removed outlier: 8.122A pdb=" N VAL N 401 " --> pdb=" O MET N 375 " (cutoff:3.500A) removed outlier: 7.115A pdb=" N MET N 377 " --> pdb=" O VAL N 399 " (cutoff:3.500A) removed outlier: 5.127A pdb=" N VAL N 399 " --> pdb=" O MET N 377 " (cutoff:3.500A) removed outlier: 7.127A pdb=" N LEU N 379 " --> pdb=" O SER N 397 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'W' and resid 92 through 98 removed outlier: 5.552A pdb=" N LYS W 94 " --> pdb=" O CYS W 447 " (cutoff:3.500A) removed outlier: 6.130A pdb=" N CYS W 447 " --> pdb=" O LYS W 94 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'W' and resid 119 through 122 removed outlier: 3.928A pdb=" N MET W 174 " --> pdb=" O LEU W 156 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'W' and resid 178 through 183 removed outlier: 3.824A pdb=" N SER W 178 " --> pdb=" O VAL W 193 " (cutoff:3.500A) removed outlier: 4.180A pdb=" N ASP W 212 " --> pdb=" O ILE W 204 " (cutoff:3.500A) removed outlier: 6.556A pdb=" N TYR W 206 " --> pdb=" O TYR W 210 " (cutoff:3.500A) removed outlier: 5.887A pdb=" N TYR W 210 " --> pdb=" O TYR W 206 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'W' and resid 222 through 224 removed outlier: 3.583A pdb=" N ASN W 230 " --> pdb=" O TYR W 237 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'W' and resid 222 through 224 removed outlier: 3.646A pdb=" N ASP W 242 " --> pdb=" O GLU W 250 " (cutoff:3.500A) removed outlier: 4.032A pdb=" N GLU W 250 " --> pdb=" O ASP W 242 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N LYS W 263 " --> pdb=" O LYS W 255 " (cutoff:3.500A) removed outlier: 6.316A pdb=" N ARG W 257 " --> pdb=" O ILE W 261 " (cutoff:3.500A) removed outlier: 5.259A pdb=" N ILE W 261 " --> pdb=" O ARG W 257 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'W' and resid 268 through 269 removed outlier: 6.559A pdb=" N THR W 268 " --> pdb=" O ILE W 314 " (cutoff:3.500A) removed outlier: 8.880A pdb=" N LEU W 316 " --> pdb=" O THR W 268 " (cutoff:3.500A) removed outlier: 6.197A pdb=" N THR W 286 " --> pdb=" O ALA W 282 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'W' and resid 352 through 356 removed outlier: 8.172A pdb=" N MET W 375 " --> pdb=" O VAL W 401 " (cutoff:3.500A) removed outlier: 8.122A pdb=" N VAL W 401 " --> pdb=" O MET W 375 " (cutoff:3.500A) removed outlier: 7.115A pdb=" N MET W 377 " --> pdb=" O VAL W 399 " (cutoff:3.500A) removed outlier: 5.127A pdb=" N VAL W 399 " --> pdb=" O MET W 377 " (cutoff:3.500A) removed outlier: 7.127A pdb=" N LEU W 379 " --> pdb=" O SER W 397 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'A' and resid 3 through 6 Processing sheet with id=AD3, first strand: chain 'A' and resid 58 through 59 removed outlier: 6.775A pdb=" N TRP A 36 " --> pdb=" O VAL A 48 " (cutoff:3.500A) removed outlier: 4.441A pdb=" N GLY A 50 " --> pdb=" O LEU A 34 " (cutoff:3.500A) removed outlier: 6.593A pdb=" N LEU A 34 " --> pdb=" O GLY A 50 " (cutoff:3.500A) removed outlier: 4.054A pdb=" N VAL A 102 " --> pdb=" O ARG A 94 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'A' and resid 58 through 59 removed outlier: 6.775A pdb=" N TRP A 36 " --> pdb=" O VAL A 48 " (cutoff:3.500A) removed outlier: 4.441A pdb=" N GLY A 50 " --> pdb=" O LEU A 34 " (cutoff:3.500A) removed outlier: 6.593A pdb=" N LEU A 34 " --> pdb=" O GLY A 50 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'A' and resid 120 through 124 removed outlier: 3.888A pdb=" N GLY A 139 " --> pdb=" O LEU A 124 " (cutoff:3.500A) removed outlier: 4.159A pdb=" N GLY A 139 " --> pdb=" O VAL A 182 " (cutoff:3.500A) removed outlier: 6.521A pdb=" N VAL A 182 " --> pdb=" O GLY A 139 " (cutoff:3.500A) removed outlier: 4.657A pdb=" N LEU A 141 " --> pdb=" O SER A 180 " (cutoff:3.500A) removed outlier: 6.800A pdb=" N SER A 180 " --> pdb=" O LEU A 141 " (cutoff:3.500A) removed outlier: 4.931A pdb=" N LYS A 143 " --> pdb=" O LEU A 178 " (cutoff:3.500A) removed outlier: 6.596A pdb=" N LEU A 178 " --> pdb=" O LYS A 143 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N LEU A 175 " --> pdb=" O GLN A 171 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N VAL A 169 " --> pdb=" O SER A 177 " (cutoff:3.500A) removed outlier: 4.969A pdb=" N SER A 179 " --> pdb=" O PRO A 167 " (cutoff:3.500A) removed outlier: 7.136A pdb=" N VAL A 181 " --> pdb=" O THR A 165 " (cutoff:3.500A) removed outlier: 5.103A pdb=" N THR A 165 " --> pdb=" O VAL A 181 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'C' and resid 3 through 6 Processing sheet with id=AD7, first strand: chain 'C' and resid 58 through 59 removed outlier: 6.775A pdb=" N TRP C 36 " --> pdb=" O VAL C 48 " (cutoff:3.500A) removed outlier: 4.440A pdb=" N GLY C 50 " --> pdb=" O LEU C 34 " (cutoff:3.500A) removed outlier: 6.593A pdb=" N LEU C 34 " --> pdb=" O GLY C 50 " (cutoff:3.500A) removed outlier: 4.055A pdb=" N VAL C 102 " --> pdb=" O ARG C 94 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'C' and resid 58 through 59 removed outlier: 6.775A pdb=" N TRP C 36 " --> pdb=" O VAL C 48 " (cutoff:3.500A) removed outlier: 4.440A pdb=" N GLY C 50 " --> pdb=" O LEU C 34 " (cutoff:3.500A) removed outlier: 6.593A pdb=" N LEU C 34 " --> pdb=" O GLY C 50 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'C' and resid 120 through 124 removed outlier: 3.888A pdb=" N GLY C 139 " --> pdb=" O LEU C 124 " (cutoff:3.500A) removed outlier: 4.158A pdb=" N GLY C 139 " --> pdb=" O VAL C 182 " (cutoff:3.500A) removed outlier: 6.520A pdb=" N VAL C 182 " --> pdb=" O GLY C 139 " (cutoff:3.500A) removed outlier: 4.656A pdb=" N LEU C 141 " --> pdb=" O SER C 180 " (cutoff:3.500A) removed outlier: 6.799A pdb=" N SER C 180 " --> pdb=" O LEU C 141 " (cutoff:3.500A) removed outlier: 4.931A pdb=" N LYS C 143 " --> pdb=" O LEU C 178 " (cutoff:3.500A) removed outlier: 6.596A pdb=" N LEU C 178 " --> pdb=" O LYS C 143 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N LEU C 175 " --> pdb=" O GLN C 171 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N VAL C 169 " --> pdb=" O SER C 177 " (cutoff:3.500A) removed outlier: 4.969A pdb=" N SER C 179 " --> pdb=" O PRO C 167 " (cutoff:3.500A) removed outlier: 7.136A pdb=" N VAL C 181 " --> pdb=" O THR C 165 " (cutoff:3.500A) removed outlier: 5.103A pdb=" N THR C 165 " --> pdb=" O VAL C 181 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'D' and resid 3 through 6 Processing sheet with id=AE2, first strand: chain 'D' and resid 58 through 59 removed outlier: 6.775A pdb=" N TRP D 36 " --> pdb=" O VAL D 48 " (cutoff:3.500A) removed outlier: 4.440A pdb=" N GLY D 50 " --> pdb=" O LEU D 34 " (cutoff:3.500A) removed outlier: 6.594A pdb=" N LEU D 34 " --> pdb=" O GLY D 50 " (cutoff:3.500A) removed outlier: 4.054A pdb=" N VAL D 102 " --> pdb=" O ARG D 94 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'D' and resid 58 through 59 removed outlier: 6.775A pdb=" N TRP D 36 " --> pdb=" O VAL D 48 " (cutoff:3.500A) removed outlier: 4.440A pdb=" N GLY D 50 " --> pdb=" O LEU D 34 " (cutoff:3.500A) removed outlier: 6.594A pdb=" N LEU D 34 " --> pdb=" O GLY D 50 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'D' and resid 120 through 124 removed outlier: 3.888A pdb=" N GLY D 139 " --> pdb=" O LEU D 124 " (cutoff:3.500A) removed outlier: 4.159A pdb=" N GLY D 139 " --> pdb=" O VAL D 182 " (cutoff:3.500A) removed outlier: 6.520A pdb=" N VAL D 182 " --> pdb=" O GLY D 139 " (cutoff:3.500A) removed outlier: 4.657A pdb=" N LEU D 141 " --> pdb=" O SER D 180 " (cutoff:3.500A) removed outlier: 6.800A pdb=" N SER D 180 " --> pdb=" O LEU D 141 " (cutoff:3.500A) removed outlier: 4.931A pdb=" N LYS D 143 " --> pdb=" O LEU D 178 " (cutoff:3.500A) removed outlier: 6.596A pdb=" N LEU D 178 " --> pdb=" O LYS D 143 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N LEU D 175 " --> pdb=" O GLN D 171 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N VAL D 169 " --> pdb=" O SER D 177 " (cutoff:3.500A) removed outlier: 4.969A pdb=" N SER D 179 " --> pdb=" O PRO D 167 " (cutoff:3.500A) removed outlier: 7.135A pdb=" N VAL D 181 " --> pdb=" O THR D 165 " (cutoff:3.500A) removed outlier: 5.103A pdb=" N THR D 165 " --> pdb=" O VAL D 181 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'H' and resid 3 through 6 Processing sheet with id=AE6, first strand: chain 'H' and resid 58 through 59 removed outlier: 6.775A pdb=" N TRP H 36 " --> pdb=" O VAL H 48 " (cutoff:3.500A) removed outlier: 4.441A pdb=" N GLY H 50 " --> pdb=" O LEU H 34 " (cutoff:3.500A) removed outlier: 6.594A pdb=" N LEU H 34 " --> pdb=" O GLY H 50 " (cutoff:3.500A) removed outlier: 4.055A pdb=" N VAL H 102 " --> pdb=" O ARG H 94 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'H' and resid 58 through 59 removed outlier: 6.775A pdb=" N TRP H 36 " --> pdb=" O VAL H 48 " (cutoff:3.500A) removed outlier: 4.441A pdb=" N GLY H 50 " --> pdb=" O LEU H 34 " (cutoff:3.500A) removed outlier: 6.594A pdb=" N LEU H 34 " --> pdb=" O GLY H 50 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'H' and resid 120 through 124 removed outlier: 3.888A pdb=" N GLY H 139 " --> pdb=" O LEU H 124 " (cutoff:3.500A) removed outlier: 4.158A pdb=" N GLY H 139 " --> pdb=" O VAL H 182 " (cutoff:3.500A) removed outlier: 6.521A pdb=" N VAL H 182 " --> pdb=" O GLY H 139 " (cutoff:3.500A) removed outlier: 4.656A pdb=" N LEU H 141 " --> pdb=" O SER H 180 " (cutoff:3.500A) removed outlier: 6.799A pdb=" N SER H 180 " --> pdb=" O LEU H 141 " (cutoff:3.500A) removed outlier: 4.930A pdb=" N LYS H 143 " --> pdb=" O LEU H 178 " (cutoff:3.500A) removed outlier: 6.596A pdb=" N LEU H 178 " --> pdb=" O LYS H 143 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N LEU H 175 " --> pdb=" O GLN H 171 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N VAL H 169 " --> pdb=" O SER H 177 " (cutoff:3.500A) removed outlier: 4.969A pdb=" N SER H 179 " --> pdb=" O PRO H 167 " (cutoff:3.500A) removed outlier: 7.136A pdb=" N VAL H 181 " --> pdb=" O THR H 165 " (cutoff:3.500A) removed outlier: 5.103A pdb=" N THR H 165 " --> pdb=" O VAL H 181 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'B' and resid 5 through 7 removed outlier: 3.516A pdb=" N ARG B 24 " --> pdb=" O THR B 5 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'B' and resid 10 through 13 removed outlier: 6.545A pdb=" N LEU B 11 " --> pdb=" O GLU B 105 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N VAL B 85 " --> pdb=" O HIS B 38 " (cutoff:3.500A) removed outlier: 6.351A pdb=" N LEU B 33 " --> pdb=" O ASN B 49 " (cutoff:3.500A) removed outlier: 4.654A pdb=" N ASN B 49 " --> pdb=" O LEU B 33 " (cutoff:3.500A) removed outlier: 6.520A pdb=" N TRP B 35 " --> pdb=" O LEU B 47 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'B' and resid 10 through 13 removed outlier: 6.545A pdb=" N LEU B 11 " --> pdb=" O GLU B 105 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N ARG B 90 " --> pdb=" O THR B 97 " (cutoff:3.500A) removed outlier: 4.077A pdb=" N THR B 97 " --> pdb=" O ARG B 90 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'B' and resid 116 through 118 removed outlier: 4.049A pdb=" N THR B 178 " --> pdb=" O GLN B 160 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'B' and resid 116 through 118 removed outlier: 5.944A pdb=" N TYR B 173 " --> pdb=" O ASN B 138 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'B' and resid 145 through 149 removed outlier: 3.794A pdb=" N ALA B 193 " --> pdb=" O LYS B 149 " (cutoff:3.500A) removed outlier: 3.870A pdb=" N VAL B 196 " --> pdb=" O VAL B 205 " (cutoff:3.500A) removed outlier: 4.115A pdb=" N VAL B 205 " --> pdb=" O VAL B 196 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'E' and resid 5 through 7 removed outlier: 3.516A pdb=" N ARG E 24 " --> pdb=" O THR E 5 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'E' and resid 10 through 13 removed outlier: 6.545A pdb=" N LEU E 11 " --> pdb=" O GLU E 105 " (cutoff:3.500A) removed outlier: 6.352A pdb=" N LEU E 33 " --> pdb=" O ASN E 49 " (cutoff:3.500A) removed outlier: 4.654A pdb=" N ASN E 49 " --> pdb=" O LEU E 33 " (cutoff:3.500A) removed outlier: 6.521A pdb=" N TRP E 35 " --> pdb=" O LEU E 47 " (cutoff:3.500A) Processing sheet with id=AF8, first strand: chain 'E' and resid 10 through 13 removed outlier: 6.545A pdb=" N LEU E 11 " --> pdb=" O GLU E 105 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N ARG E 90 " --> pdb=" O THR E 97 " (cutoff:3.500A) removed outlier: 4.078A pdb=" N THR E 97 " --> pdb=" O ARG E 90 " (cutoff:3.500A) Processing sheet with id=AF9, first strand: chain 'E' and resid 116 through 118 removed outlier: 4.049A pdb=" N THR E 178 " --> pdb=" O GLN E 160 " (cutoff:3.500A) Processing sheet with id=AG1, first strand: chain 'E' and resid 116 through 118 removed outlier: 5.944A pdb=" N TYR E 173 " --> pdb=" O ASN E 138 " (cutoff:3.500A) Processing sheet with id=AG2, first strand: chain 'E' and resid 145 through 149 removed outlier: 3.794A pdb=" N ALA E 193 " --> pdb=" O LYS E 149 " (cutoff:3.500A) removed outlier: 3.870A pdb=" N VAL E 196 " --> pdb=" O VAL E 205 " (cutoff:3.500A) removed outlier: 4.115A pdb=" N VAL E 205 " --> pdb=" O VAL E 196 " (cutoff:3.500A) Processing sheet with id=AG3, first strand: chain 'G' and resid 5 through 7 removed outlier: 3.517A pdb=" N ARG G 24 " --> pdb=" O THR G 5 " (cutoff:3.500A) Processing sheet with id=AG4, first strand: chain 'G' and resid 10 through 13 removed outlier: 6.545A pdb=" N LEU G 11 " --> pdb=" O GLU G 105 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N VAL G 85 " --> pdb=" O HIS G 38 " (cutoff:3.500A) removed outlier: 6.352A pdb=" N LEU G 33 " --> pdb=" O ASN G 49 " (cutoff:3.500A) removed outlier: 4.654A pdb=" N ASN G 49 " --> pdb=" O LEU G 33 " (cutoff:3.500A) removed outlier: 6.520A pdb=" N TRP G 35 " --> pdb=" O LEU G 47 " (cutoff:3.500A) Processing sheet with id=AG5, first strand: chain 'G' and resid 10 through 13 removed outlier: 6.545A pdb=" N LEU G 11 " --> pdb=" O GLU G 105 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N ARG G 90 " --> pdb=" O THR G 97 " (cutoff:3.500A) removed outlier: 4.077A pdb=" N THR G 97 " --> pdb=" O ARG G 90 " (cutoff:3.500A) Processing sheet with id=AG6, first strand: chain 'G' and resid 116 through 118 removed outlier: 4.049A pdb=" N THR G 178 " --> pdb=" O GLN G 160 " (cutoff:3.500A) Processing sheet with id=AG7, first strand: chain 'G' and resid 116 through 118 removed outlier: 5.944A pdb=" N TYR G 173 " --> pdb=" O ASN G 138 " (cutoff:3.500A) Processing sheet with id=AG8, first strand: chain 'G' and resid 145 through 149 removed outlier: 3.795A pdb=" N ALA G 193 " --> pdb=" O LYS G 149 " (cutoff:3.500A) removed outlier: 3.870A pdb=" N VAL G 196 " --> pdb=" O VAL G 205 " (cutoff:3.500A) removed outlier: 4.114A pdb=" N VAL G 205 " --> pdb=" O VAL G 196 " (cutoff:3.500A) Processing sheet with id=AG9, first strand: chain 'L' and resid 5 through 7 removed outlier: 3.516A pdb=" N ARG L 24 " --> pdb=" O THR L 5 " (cutoff:3.500A) Processing sheet with id=AH1, first strand: chain 'L' and resid 10 through 13 removed outlier: 6.545A pdb=" N LEU L 11 " --> pdb=" O GLU L 105 " (cutoff:3.500A) removed outlier: 6.350A pdb=" N LEU L 33 " --> pdb=" O ASN L 49 " (cutoff:3.500A) removed outlier: 4.655A pdb=" N ASN L 49 " --> pdb=" O LEU L 33 " (cutoff:3.500A) removed outlier: 6.520A pdb=" N TRP L 35 " --> pdb=" O LEU L 47 " (cutoff:3.500A) Processing sheet with id=AH2, first strand: chain 'L' and resid 10 through 13 removed outlier: 6.545A pdb=" N LEU L 11 " --> pdb=" O GLU L 105 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N ARG L 90 " --> pdb=" O THR L 97 " (cutoff:3.500A) removed outlier: 4.077A pdb=" N THR L 97 " --> pdb=" O ARG L 90 " (cutoff:3.500A) Processing sheet with id=AH3, first strand: chain 'L' and resid 116 through 118 removed outlier: 4.049A pdb=" N THR L 178 " --> pdb=" O GLN L 160 " (cutoff:3.500A) Processing sheet with id=AH4, first strand: chain 'L' and resid 116 through 118 removed outlier: 5.943A pdb=" N TYR L 173 " --> pdb=" O ASN L 138 " (cutoff:3.500A) Processing sheet with id=AH5, first strand: chain 'L' and resid 145 through 149 removed outlier: 3.794A pdb=" N ALA L 193 " --> pdb=" O LYS L 149 " (cutoff:3.500A) removed outlier: 3.870A pdb=" N VAL L 196 " --> pdb=" O VAL L 205 " (cutoff:3.500A) removed outlier: 4.115A pdb=" N VAL L 205 " --> pdb=" O VAL L 196 " (cutoff:3.500A) 782 hydrogen bonds defined for protein. 1932 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: 5.27 Time building geometry restraints manager: 2.51 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: 7952 1.34 - 1.46: 6422 1.46 - 1.58: 10798 1.58 - 1.70: 0 1.70 - 1.82: 204 Bond restraints: 25376 Sorted by residual: bond pdb=" CA LYS I 255 " pdb=" CB LYS I 255 " ideal model delta sigma weight residual 1.526 1.446 0.080 1.53e-02 4.27e+03 2.76e+01 bond pdb=" CA LYS M 255 " pdb=" CB LYS M 255 " ideal model delta sigma weight residual 1.526 1.446 0.080 1.53e-02 4.27e+03 2.75e+01 bond pdb=" CA LYS W 255 " pdb=" CB LYS W 255 " ideal model delta sigma weight residual 1.526 1.446 0.080 1.53e-02 4.27e+03 2.75e+01 bond pdb=" CA LYS N 255 " pdb=" CB LYS N 255 " ideal model delta sigma weight residual 1.526 1.446 0.080 1.53e-02 4.27e+03 2.75e+01 bond pdb=" C GLU I 404 " pdb=" N GLU I 405 " ideal model delta sigma weight residual 1.327 1.274 0.053 1.71e-02 3.42e+03 9.51e+00 ... (remaining 25371 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.76: 33957 2.76 - 5.51: 399 5.51 - 8.27: 20 8.27 - 11.03: 0 11.03 - 13.79: 8 Bond angle restraints: 34384 Sorted by residual: angle pdb=" C GLY I 145 " pdb=" N THR I 146 " pdb=" CA THR I 146 " ideal model delta sigma weight residual 120.95 134.29 -13.34 1.78e+00 3.16e-01 5.61e+01 angle pdb=" C GLY M 145 " pdb=" N THR M 146 " pdb=" CA THR M 146 " ideal model delta sigma weight residual 120.95 134.25 -13.30 1.78e+00 3.16e-01 5.58e+01 angle pdb=" C GLY W 145 " pdb=" N THR W 146 " pdb=" CA THR W 146 " ideal model delta sigma weight residual 120.95 134.21 -13.26 1.78e+00 3.16e-01 5.55e+01 angle pdb=" C GLY N 145 " pdb=" N THR N 146 " pdb=" CA THR N 146 " ideal model delta sigma weight residual 120.95 134.21 -13.26 1.78e+00 3.16e-01 5.55e+01 angle pdb=" C TRP I 408 " pdb=" N TYR I 409 " pdb=" CA TYR I 409 " ideal model delta sigma weight residual 121.54 135.33 -13.79 1.91e+00 2.74e-01 5.21e+01 ... (remaining 34379 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 21.54: 14169 21.54 - 43.08: 935 43.08 - 64.63: 196 64.63 - 86.17: 40 86.17 - 107.71: 20 Dihedral angle restraints: 15360 sinusoidal: 6192 harmonic: 9168 Sorted by residual: dihedral pdb=" CA THR C 183 " pdb=" C THR C 183 " pdb=" N VAL C 184 " pdb=" CA VAL C 184 " ideal model delta harmonic sigma weight residual 180.00 -145.98 -34.02 0 5.00e+00 4.00e-02 4.63e+01 dihedral pdb=" CA THR A 183 " pdb=" C THR A 183 " pdb=" N VAL A 184 " pdb=" CA VAL A 184 " ideal model delta harmonic sigma weight residual 180.00 -145.99 -34.01 0 5.00e+00 4.00e-02 4.63e+01 dihedral pdb=" CA THR H 183 " pdb=" C THR H 183 " pdb=" N VAL H 184 " pdb=" CA VAL H 184 " ideal model delta harmonic sigma weight residual -180.00 -146.00 -34.00 0 5.00e+00 4.00e-02 4.62e+01 ... (remaining 15357 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.336: 3804 0.336 - 0.671: 0 0.671 - 1.007: 0 1.007 - 1.343: 0 1.343 - 1.679: 4 Chirality restraints: 3808 Sorted by residual: chirality pdb=" C1 BMA W 503 " pdb=" O4 NAG O 2 " pdb=" C2 BMA W 503 " pdb=" O5 BMA W 503 " both_signs ideal model delta sigma weight residual False -2.40 -0.72 -1.68 2.00e-02 2.50e+03 7.04e+03 chirality pdb=" C1 BMA N 503 " pdb=" O4 NAG K 2 " pdb=" C2 BMA N 503 " pdb=" O5 BMA N 503 " both_signs ideal model delta sigma weight residual False -2.40 -0.72 -1.68 2.00e-02 2.50e+03 7.04e+03 chirality pdb=" C1 BMA I 503 " pdb=" O4 NAG F 2 " pdb=" C2 BMA I 503 " pdb=" O5 BMA I 503 " both_signs ideal model delta sigma weight residual False -2.40 -0.72 -1.68 2.00e-02 2.50e+03 7.03e+03 ... (remaining 3805 not shown) Planarity restraints: 4384 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB PHE D 100C" -0.024 2.00e-02 2.50e+03 1.68e-02 4.92e+00 pdb=" CG PHE D 100C" 0.035 2.00e-02 2.50e+03 pdb=" CD1 PHE D 100C" 0.003 2.00e-02 2.50e+03 pdb=" CD2 PHE D 100C" 0.003 2.00e-02 2.50e+03 pdb=" CE1 PHE D 100C" -0.004 2.00e-02 2.50e+03 pdb=" CE2 PHE D 100C" -0.004 2.00e-02 2.50e+03 pdb=" CZ PHE D 100C" -0.009 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE H 100C" -0.024 2.00e-02 2.50e+03 1.67e-02 4.86e+00 pdb=" CG PHE H 100C" 0.035 2.00e-02 2.50e+03 pdb=" CD1 PHE H 100C" 0.004 2.00e-02 2.50e+03 pdb=" CD2 PHE H 100C" 0.002 2.00e-02 2.50e+03 pdb=" CE1 PHE H 100C" -0.004 2.00e-02 2.50e+03 pdb=" CE2 PHE H 100C" -0.003 2.00e-02 2.50e+03 pdb=" CZ PHE H 100C" -0.009 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE A 100C" 0.024 2.00e-02 2.50e+03 1.66e-02 4.85e+00 pdb=" CG PHE A 100C" -0.035 2.00e-02 2.50e+03 pdb=" CD1 PHE A 100C" -0.004 2.00e-02 2.50e+03 pdb=" CD2 PHE A 100C" -0.003 2.00e-02 2.50e+03 pdb=" CE1 PHE A 100C" 0.004 2.00e-02 2.50e+03 pdb=" CE2 PHE A 100C" 0.003 2.00e-02 2.50e+03 pdb=" CZ PHE A 100C" 0.009 2.00e-02 2.50e+03 ... (remaining 4381 not shown) Histogram of nonbonded interaction distances: 1.60 - 2.26: 61 2.26 - 2.92: 11380 2.92 - 3.58: 32148 3.58 - 4.24: 58633 4.24 - 4.90: 99748 Nonbonded interactions: 201970 Sorted by model distance: nonbonded pdb=" OG1 THR H 135 " pdb=" O VAL H 184 " model vdw 1.602 3.040 nonbonded pdb=" OG1 THR C 135 " pdb=" O VAL C 184 " model vdw 1.602 3.040 nonbonded pdb=" OG1 THR A 135 " pdb=" O VAL A 184 " model vdw 1.603 3.040 nonbonded pdb=" OG1 THR D 135 " pdb=" O VAL D 184 " model vdw 1.603 3.040 nonbonded pdb=" O GLN B 124 " pdb=" OG SER B 127 " model vdw 2.002 3.040 ... (remaining 201965 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: 0.07 Found NCS groups: ncs_group { reference = chain 'I' selection = chain 'M' selection = chain 'N' selection = chain 'W' } ncs_group { reference = chain 'A' selection = chain 'C' selection = chain 'D' selection = chain 'H' } ncs_group { reference = chain 'B' selection = chain 'E' selection = chain 'G' selection = chain 'L' } ncs_group { reference = chain 'F' selection = chain 'J' selection = chain 'K' selection = chain 'O' } 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=0.05 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: 1.290 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.320 Check model and map are aligned: 0.060 Set scattering table: 0.030 Process input model: 20.990 Find NCS groups from input model: 0.210 Set up NCS constraints: 0.040 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:9.280 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 32.240 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8127 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.011 0.162 25420 Z= 0.463 Angle : 0.917 29.051 34486 Z= 0.484 Chirality : 0.075 1.679 3808 Planarity : 0.005 0.047 4380 Dihedral : 15.492 107.711 9404 Min Nonbonded Distance : 1.602 Molprobity Statistics. All-atom Clashscore : 7.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.88 % Favored : 90.12 % Rotamer: Outliers : 2.95 % Allowed : 13.44 % Favored : 83.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.63 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.13 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -4.27 (0.12), residues: 3148 helix: -5.17 (0.18), residues: 28 sheet: -1.94 (0.13), residues: 1240 loop : -3.61 (0.10), residues: 1880 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG N 154 TYR 0.012 0.001 TYR N 383 PHE 0.035 0.002 PHE D 100C TRP 0.011 0.001 TRP D 154 HIS 0.006 0.001 HIS N 183 Details of bonding type rmsd covalent geometry : bond 0.01096 (25376) covalent geometry : angle 0.81251 (34384) SS BOND : bond 0.00452 ( 32) SS BOND : angle 2.08091 ( 66) hydrogen bonds : bond 0.19004 ( 706) hydrogen bonds : angle 8.43617 ( 1932) link_BETA1-4 : bond 0.12290 ( 8) link_BETA1-4 : angle 15.76358 ( 24) link_NAG-ASN : bond 0.00876 ( 4) link_NAG-ASN : angle 2.06429 ( 12) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6296 Ramachandran restraints generated. 3148 Oldfield, 0 Emsley, 3148 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6296 Ramachandran restraints generated. 3148 Oldfield, 0 Emsley, 3148 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 506 residues out of total 2708 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 80 poor density : 426 time to evaluate : 0.971 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 72 ASP cc_start: 0.7668 (t70) cc_final: 0.7252 (t70) REVERT: A 100 TYR cc_start: 0.8902 (m-80) cc_final: 0.8688 (m-80) REVERT: A 145 TYR cc_start: 0.7152 (p90) cc_final: 0.6675 (p90) REVERT: A 176 TYR cc_start: 0.7568 (m-80) cc_final: 0.7269 (m-80) REVERT: C 72 ASP cc_start: 0.7394 (t70) cc_final: 0.6976 (t70) REVERT: C 100 TYR cc_start: 0.9134 (m-80) cc_final: 0.8930 (m-80) REVERT: D 72 ASP cc_start: 0.7472 (t70) cc_final: 0.7025 (t70) REVERT: D 100 TYR cc_start: 0.9096 (m-80) cc_final: 0.8811 (m-80) REVERT: D 145 TYR cc_start: 0.7000 (p90) cc_final: 0.6583 (p90) REVERT: D 176 TYR cc_start: 0.7769 (m-80) cc_final: 0.7160 (m-10) REVERT: H 72 ASP cc_start: 0.7403 (t70) cc_final: 0.6983 (t70) REVERT: H 100 TYR cc_start: 0.9104 (m-80) cc_final: 0.8902 (m-80) REVERT: H 145 TYR cc_start: 0.6776 (p90) cc_final: 0.6268 (p90) REVERT: H 176 TYR cc_start: 0.7588 (m-80) cc_final: 0.7346 (m-80) REVERT: B 143 GLU cc_start: 0.7814 (OUTLIER) cc_final: 0.7334 (tm-30) REVERT: B 190 LYS cc_start: 0.8145 (mmmt) cc_final: 0.7677 (tptt) REVERT: E 143 GLU cc_start: 0.7748 (OUTLIER) cc_final: 0.7388 (tm-30) REVERT: E 190 LYS cc_start: 0.8123 (mmmt) cc_final: 0.7810 (tttp) REVERT: G 143 GLU cc_start: 0.7895 (OUTLIER) cc_final: 0.7381 (tm-30) REVERT: L 143 GLU cc_start: 0.7830 (OUTLIER) cc_final: 0.7313 (tm-30) outliers start: 80 outliers final: 30 residues processed: 490 average time/residue: 0.7373 time to fit residues: 407.2482 Evaluate side-chains 361 residues out of total 2708 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 327 time to evaluate : 0.909 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain I residue 87 CYS Chi-restraints excluded: chain I residue 182 CYS Chi-restraints excluded: chain I residue 229 CYS Chi-restraints excluded: chain I residue 366 SER Chi-restraints excluded: chain I residue 420 CYS Chi-restraints excluded: chain M residue 87 CYS Chi-restraints excluded: chain M residue 182 CYS Chi-restraints excluded: chain M residue 229 CYS Chi-restraints excluded: chain M residue 366 SER Chi-restraints excluded: chain M residue 420 CYS Chi-restraints excluded: chain N residue 87 CYS Chi-restraints excluded: chain N residue 182 CYS Chi-restraints excluded: chain N residue 229 CYS Chi-restraints excluded: chain N residue 366 SER Chi-restraints excluded: chain N residue 420 CYS Chi-restraints excluded: chain W residue 87 CYS Chi-restraints excluded: chain W residue 182 CYS Chi-restraints excluded: chain W residue 229 CYS Chi-restraints excluded: chain W residue 366 SER Chi-restraints excluded: chain W residue 420 CYS Chi-restraints excluded: chain C residue 81 ASP Chi-restraints excluded: chain C residue 173 SER Chi-restraints excluded: chain D residue 81 ASP Chi-restraints excluded: chain D residue 173 SER Chi-restraints excluded: chain H residue 81 ASP Chi-restraints excluded: chain H residue 173 SER Chi-restraints excluded: chain B residue 33 LEU Chi-restraints excluded: chain B residue 49 ASN Chi-restraints excluded: chain B residue 143 GLU Chi-restraints excluded: chain E residue 33 LEU Chi-restraints excluded: chain E residue 143 GLU Chi-restraints excluded: chain G residue 32 SER Chi-restraints excluded: chain G residue 143 GLU Chi-restraints excluded: chain L residue 143 GLU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 316 random chunks: chunk 197 optimal weight: 5.9990 chunk 215 optimal weight: 3.9990 chunk 20 optimal weight: 1.9990 chunk 132 optimal weight: 1.9990 chunk 261 optimal weight: 0.8980 chunk 248 optimal weight: 8.9990 chunk 207 optimal weight: 5.9990 chunk 155 optimal weight: 2.9990 chunk 244 optimal weight: 0.9980 chunk 183 optimal weight: 9.9990 chunk 298 optimal weight: 0.9980 overall best weight: 1.3784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: I 431 HIS M 329 ASN M 431 HIS N 329 ASN N 431 HIS W 431 HIS A 39 GLN A 204 ASN ** C 164 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 204 ASN D 204 ASN H 155 ASN ** H 164 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 204 ASN ** B 147 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 166 GLN ** B 198 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 199 GLN ** E 198 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 166 GLN ** G 198 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 6 GLN L 166 GLN ** L 198 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3951 r_free = 0.3951 target = 0.147117 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3172 r_free = 0.3172 target = 0.087799 restraints weight = 36671.650| |-----------------------------------------------------------------------------| r_work (start): 0.3081 rms_B_bonded: 2.40 r_work: 0.2957 rms_B_bonded: 2.50 restraints_weight: 0.5000 r_work: 0.2821 rms_B_bonded: 3.94 restraints_weight: 0.2500 r_work (final): 0.2821 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2798 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2798 r_free = 0.2798 target_work(ls_wunit_k1) = 0.066 | | occupancies: max = 1.00 min = 0.05 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2798 r_free = 0.2798 target_work(ls_wunit_k1) = 0.066 | | occupancies: max = 1.00 min = 0.01 number of occupancies < 0.1: 7 | |-----------------------------------------------------------------------------| r_final: 0.2798 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8328 moved from start: 0.1957 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 25420 Z= 0.153 Angle : 0.683 7.165 34486 Z= 0.359 Chirality : 0.048 0.258 3808 Planarity : 0.006 0.051 4380 Dihedral : 8.474 56.344 3748 Min Nonbonded Distance : 2.344 Molprobity Statistics. All-atom Clashscore : 6.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.50 % Favored : 94.50 % Rotamer: Outliers : 4.80 % Allowed : 17.69 % Favored : 77.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.63 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.02 (0.13), residues: 3148 helix: -4.58 (0.16), residues: 32 sheet: -1.38 (0.14), residues: 1264 loop : -2.49 (0.12), residues: 1852 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG C 83 TYR 0.021 0.002 TYR G 186 PHE 0.020 0.002 PHE D 100C TRP 0.011 0.001 TRP I 408 HIS 0.012 0.001 HIS A 164 Details of bonding type rmsd covalent geometry : bond 0.00340 (25376) covalent geometry : angle 0.67933 (34384) SS BOND : bond 0.00189 ( 32) SS BOND : angle 0.91431 ( 66) hydrogen bonds : bond 0.03843 ( 706) hydrogen bonds : angle 6.08510 ( 1932) link_BETA1-4 : bond 0.00723 ( 8) link_BETA1-4 : angle 2.36156 ( 24) link_NAG-ASN : bond 0.00205 ( 4) link_NAG-ASN : angle 1.12403 ( 12) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6296 Ramachandran restraints generated. 3148 Oldfield, 0 Emsley, 3148 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6296 Ramachandran restraints generated. 3148 Oldfield, 0 Emsley, 3148 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 485 residues out of total 2708 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 130 poor density : 355 time to evaluate : 0.880 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: I 375 MET cc_start: 0.9311 (mmm) cc_final: 0.8906 (mmt) REVERT: I 390 ASP cc_start: 0.7325 (OUTLIER) cc_final: 0.6691 (m-30) REVERT: M 375 MET cc_start: 0.9248 (mmm) cc_final: 0.9004 (mmt) REVERT: M 390 ASP cc_start: 0.7317 (OUTLIER) cc_final: 0.6694 (m-30) REVERT: N 375 MET cc_start: 0.9300 (mmm) cc_final: 0.9062 (mmm) REVERT: N 384 ASP cc_start: 0.8498 (m-30) cc_final: 0.8213 (m-30) REVERT: N 390 ASP cc_start: 0.7301 (OUTLIER) cc_final: 0.6656 (m-30) REVERT: W 384 ASP cc_start: 0.8392 (m-30) cc_final: 0.8106 (m-30) REVERT: W 390 ASP cc_start: 0.7262 (OUTLIER) cc_final: 0.6608 (m-30) REVERT: A 72 ASP cc_start: 0.8066 (t70) cc_final: 0.7293 (t70) REVERT: A 145 TYR cc_start: 0.6975 (p90) cc_final: 0.6496 (p90) REVERT: A 176 TYR cc_start: 0.7185 (m-80) cc_final: 0.6965 (m-80) REVERT: C 30 ILE cc_start: 0.9034 (tt) cc_final: 0.8742 (tp) REVERT: C 72 ASP cc_start: 0.7765 (t70) cc_final: 0.7034 (t70) REVERT: C 176 TYR cc_start: 0.7059 (m-80) cc_final: 0.6823 (m-80) REVERT: D 30 ILE cc_start: 0.9114 (tt) cc_final: 0.8804 (tp) REVERT: D 72 ASP cc_start: 0.7794 (t70) cc_final: 0.7038 (t70) REVERT: D 100 TYR cc_start: 0.9101 (m-80) cc_final: 0.8825 (m-80) REVERT: D 145 TYR cc_start: 0.6885 (p90) cc_final: 0.6358 (p90) REVERT: D 176 TYR cc_start: 0.7350 (m-80) cc_final: 0.6880 (m-10) REVERT: H 30 ILE cc_start: 0.8989 (tt) cc_final: 0.8688 (tp) REVERT: H 72 ASP cc_start: 0.7819 (t70) cc_final: 0.7091 (t70) REVERT: H 81 ASP cc_start: 0.8006 (t70) cc_final: 0.7777 (t0) REVERT: H 100 TYR cc_start: 0.9117 (m-80) cc_final: 0.8837 (m-80) REVERT: H 145 TYR cc_start: 0.6648 (p90) cc_final: 0.6062 (p90) REVERT: H 176 TYR cc_start: 0.7341 (m-80) cc_final: 0.6847 (m-10) REVERT: B 24 ARG cc_start: 0.7974 (OUTLIER) cc_final: 0.7750 (ttt-90) REVERT: B 143 GLU cc_start: 0.8317 (OUTLIER) cc_final: 0.7955 (tm-30) REVERT: E 143 GLU cc_start: 0.8461 (OUTLIER) cc_final: 0.8197 (tm-30) REVERT: E 160 GLN cc_start: 0.5852 (mt0) cc_final: 0.5636 (mt0) REVERT: E 190 LYS cc_start: 0.8088 (mmmt) cc_final: 0.7637 (tptt) REVERT: G 108 ARG cc_start: 0.7750 (ptm160) cc_final: 0.7434 (ptm-80) REVERT: G 143 GLU cc_start: 0.8406 (OUTLIER) cc_final: 0.8150 (tm-30) REVERT: L 6 GLN cc_start: 0.8175 (OUTLIER) cc_final: 0.7378 (mt0) REVERT: L 18 ARG cc_start: 0.8429 (OUTLIER) cc_final: 0.7415 (ttm110) outliers start: 130 outliers final: 70 residues processed: 461 average time/residue: 0.6236 time to fit residues: 330.7311 Evaluate side-chains 398 residues out of total 2708 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 80 poor density : 318 time to evaluate : 0.992 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain I residue 182 CYS Chi-restraints excluded: chain I residue 198 SER Chi-restraints excluded: chain I residue 229 CYS Chi-restraints excluded: chain I residue 307 VAL Chi-restraints excluded: chain I residue 337 CYS Chi-restraints excluded: chain I residue 366 SER Chi-restraints excluded: chain I residue 390 ASP Chi-restraints excluded: chain I residue 410 SER Chi-restraints excluded: chain M residue 182 CYS Chi-restraints excluded: chain M residue 198 SER Chi-restraints excluded: chain M residue 229 CYS Chi-restraints excluded: chain M residue 307 VAL Chi-restraints excluded: chain M residue 337 CYS Chi-restraints excluded: chain M residue 357 MET Chi-restraints excluded: chain M residue 359 SER Chi-restraints excluded: chain M residue 366 SER Chi-restraints excluded: chain M residue 390 ASP Chi-restraints excluded: chain M residue 410 SER Chi-restraints excluded: chain N residue 182 CYS Chi-restraints excluded: chain N residue 198 SER Chi-restraints excluded: chain N residue 229 CYS Chi-restraints excluded: chain N residue 307 VAL Chi-restraints excluded: chain N residue 337 CYS Chi-restraints excluded: chain N residue 357 MET Chi-restraints excluded: chain N residue 366 SER Chi-restraints excluded: chain N residue 390 ASP Chi-restraints excluded: chain N residue 410 SER Chi-restraints excluded: chain W residue 182 CYS Chi-restraints excluded: chain W residue 198 SER Chi-restraints excluded: chain W residue 229 CYS Chi-restraints excluded: chain W residue 307 VAL Chi-restraints excluded: chain W residue 337 CYS Chi-restraints excluded: chain W residue 357 MET Chi-restraints excluded: chain W residue 366 SER Chi-restraints excluded: chain W residue 390 ASP Chi-restraints excluded: chain W residue 410 SER Chi-restraints excluded: chain A residue 17 SER Chi-restraints excluded: chain A residue 28 THR Chi-restraints excluded: chain A residue 87 THR Chi-restraints excluded: chain A residue 184 VAL Chi-restraints excluded: chain C residue 17 SER Chi-restraints excluded: chain C residue 87 THR Chi-restraints excluded: chain C residue 100 ASP Chi-restraints excluded: chain C residue 184 VAL Chi-restraints excluded: chain C residue 193 THR Chi-restraints excluded: chain D residue 17 SER Chi-restraints excluded: chain D residue 87 THR Chi-restraints excluded: chain D residue 100 ASP Chi-restraints excluded: chain D residue 184 VAL Chi-restraints excluded: chain H residue 17 SER Chi-restraints excluded: chain H residue 87 THR Chi-restraints excluded: chain H residue 100 ASP Chi-restraints excluded: chain H residue 184 VAL Chi-restraints excluded: chain B residue 24 ARG Chi-restraints excluded: chain B residue 30 SER Chi-restraints excluded: chain B residue 33 LEU Chi-restraints excluded: chain B residue 76 SER Chi-restraints excluded: chain B residue 143 GLU Chi-restraints excluded: chain B residue 182 SER Chi-restraints excluded: chain B residue 206 THR Chi-restraints excluded: chain E residue 30 SER Chi-restraints excluded: chain E residue 33 LEU Chi-restraints excluded: chain E residue 49 ASN Chi-restraints excluded: chain E residue 76 SER Chi-restraints excluded: chain E residue 143 GLU Chi-restraints excluded: chain E residue 150 VAL Chi-restraints excluded: chain E residue 174 SER Chi-restraints excluded: chain G residue 30 SER Chi-restraints excluded: chain G residue 76 SER Chi-restraints excluded: chain G residue 143 GLU Chi-restraints excluded: chain G residue 182 SER Chi-restraints excluded: chain G residue 206 THR Chi-restraints excluded: chain L residue 6 GLN Chi-restraints excluded: chain L residue 18 ARG Chi-restraints excluded: chain L residue 30 SER Chi-restraints excluded: chain L residue 33 LEU Chi-restraints excluded: chain L residue 76 SER Chi-restraints excluded: chain L residue 150 VAL Chi-restraints excluded: chain L residue 182 SER Chi-restraints excluded: chain L residue 206 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 316 random chunks: chunk 49 optimal weight: 4.9990 chunk 58 optimal weight: 5.9990 chunk 57 optimal weight: 3.9990 chunk 310 optimal weight: 10.0000 chunk 151 optimal weight: 5.9990 chunk 95 optimal weight: 4.9990 chunk 199 optimal weight: 7.9990 chunk 280 optimal weight: 9.9990 chunk 0 optimal weight: 8.9990 chunk 110 optimal weight: 5.9990 chunk 70 optimal weight: 1.9990 overall best weight: 4.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: I 183 HIS I 225 GLN I 273 HIS M 183 HIS M 225 GLN M 273 HIS N 183 HIS N 225 GLN N 273 HIS W 183 HIS W 225 GLN W 273 HIS ** B 147 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 166 GLN E 27 GLN ** G 155 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 166 GLN L 166 GLN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3886 r_free = 0.3886 target = 0.142204 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 68)----------------| | r_work = 0.3061 r_free = 0.3061 target = 0.081423 restraints weight = 36889.529| |-----------------------------------------------------------------------------| r_work (start): 0.2960 rms_B_bonded: 2.38 r_work: 0.2831 rms_B_bonded: 2.45 restraints_weight: 0.5000 r_work: 0.2695 rms_B_bonded: 3.81 restraints_weight: 0.2500 r_work (final): 0.2695 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2684 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2684 r_free = 0.2684 target_work(ls_wunit_k1) = 0.061 | | occupancies: max = 1.00 min = 0.01 number of occupancies < 0.1: 7 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2684 r_free = 0.2684 target_work(ls_wunit_k1) = 0.061 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| r_final: 0.2684 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8414 moved from start: 0.2615 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.053 25420 Z= 0.317 Angle : 0.717 7.597 34486 Z= 0.377 Chirality : 0.049 0.197 3808 Planarity : 0.006 0.063 4380 Dihedral : 7.220 59.957 3725 Min Nonbonded Distance : 2.255 Molprobity Statistics. All-atom Clashscore : 7.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.53 % Favored : 94.47 % Rotamer: Outliers : 5.69 % Allowed : 18.98 % Favored : 75.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.63 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.40 (0.13), residues: 3148 helix: -4.44 (0.16), residues: 32 sheet: -0.91 (0.14), residues: 1264 loop : -2.10 (0.12), residues: 1852 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG G 142 TYR 0.022 0.002 TYR L 173 PHE 0.040 0.003 PHE C 100C TRP 0.016 0.002 TRP G 148 HIS 0.006 0.001 HIS E 198 Details of bonding type rmsd covalent geometry : bond 0.00748 (25376) covalent geometry : angle 0.71124 (34384) SS BOND : bond 0.00404 ( 32) SS BOND : angle 1.77625 ( 66) hydrogen bonds : bond 0.04267 ( 706) hydrogen bonds : angle 5.71276 ( 1932) link_BETA1-4 : bond 0.00395 ( 8) link_BETA1-4 : angle 2.15883 ( 24) link_NAG-ASN : bond 0.00449 ( 4) link_NAG-ASN : angle 1.17757 ( 12) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6296 Ramachandran restraints generated. 3148 Oldfield, 0 Emsley, 3148 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6296 Ramachandran restraints generated. 3148 Oldfield, 0 Emsley, 3148 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 469 residues out of total 2708 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 154 poor density : 315 time to evaluate : 0.792 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: I 116 ARG cc_start: 0.8273 (OUTLIER) cc_final: 0.6231 (tmm160) REVERT: I 338 GLU cc_start: 0.8407 (OUTLIER) cc_final: 0.8118 (mp0) REVERT: I 390 ASP cc_start: 0.7757 (OUTLIER) cc_final: 0.7298 (m-30) REVERT: M 116 ARG cc_start: 0.8209 (OUTLIER) cc_final: 0.6147 (tmm160) REVERT: M 419 LYS cc_start: 0.9252 (OUTLIER) cc_final: 0.8990 (mttm) REVERT: N 116 ARG cc_start: 0.8178 (OUTLIER) cc_final: 0.6146 (tmm160) REVERT: N 338 GLU cc_start: 0.8401 (OUTLIER) cc_final: 0.8114 (mp0) REVERT: N 429 MET cc_start: 0.9419 (mtp) cc_final: 0.9218 (mtm) REVERT: W 116 ARG cc_start: 0.8197 (OUTLIER) cc_final: 0.6172 (tmm160) REVERT: W 338 GLU cc_start: 0.8412 (OUTLIER) cc_final: 0.8114 (mp0) REVERT: W 419 LYS cc_start: 0.9277 (OUTLIER) cc_final: 0.9019 (mttm) REVERT: W 429 MET cc_start: 0.9423 (mtp) cc_final: 0.9221 (mtm) REVERT: A 72 ASP cc_start: 0.8272 (t70) cc_final: 0.7519 (t70) REVERT: A 145 TYR cc_start: 0.7084 (p90) cc_final: 0.6513 (p90) REVERT: A 176 TYR cc_start: 0.7277 (m-80) cc_final: 0.6964 (m-80) REVERT: C 30 ILE cc_start: 0.9076 (tt) cc_final: 0.8780 (tp) REVERT: C 72 ASP cc_start: 0.8068 (t70) cc_final: 0.7303 (t70) REVERT: D 72 ASP cc_start: 0.8123 (t70) cc_final: 0.7342 (t70) REVERT: D 145 TYR cc_start: 0.7138 (p90) cc_final: 0.6548 (p90) REVERT: D 176 TYR cc_start: 0.7329 (m-80) cc_final: 0.7051 (m-80) REVERT: H 30 ILE cc_start: 0.9074 (tt) cc_final: 0.8772 (tp) REVERT: H 72 ASP cc_start: 0.8106 (t70) cc_final: 0.7331 (t70) REVERT: H 81 ASP cc_start: 0.8096 (t70) cc_final: 0.7885 (t0) REVERT: H 145 TYR cc_start: 0.7131 (p90) cc_final: 0.6567 (p90) REVERT: H 176 TYR cc_start: 0.7498 (m-80) cc_final: 0.6969 (m-10) REVERT: B 143 GLU cc_start: 0.8358 (OUTLIER) cc_final: 0.8107 (tm-30) REVERT: B 165 GLU cc_start: 0.8295 (tp30) cc_final: 0.7793 (tp30) REVERT: B 166 GLN cc_start: 0.8936 (OUTLIER) cc_final: 0.8454 (tt0) REVERT: E 42 GLN cc_start: 0.7622 (mp10) cc_final: 0.7418 (mp10) REVERT: E 190 LYS cc_start: 0.8181 (mmmt) cc_final: 0.7823 (tptt) REVERT: G 108 ARG cc_start: 0.7862 (ptm160) cc_final: 0.7587 (ptm-80) REVERT: G 142 ARG cc_start: 0.8642 (ttp80) cc_final: 0.8411 (ttp80) REVERT: G 165 GLU cc_start: 0.8355 (tp30) cc_final: 0.7852 (tp30) REVERT: G 166 GLN cc_start: 0.8829 (OUTLIER) cc_final: 0.8386 (tt0) REVERT: G 173 TYR cc_start: 0.8098 (m-10) cc_final: 0.7801 (m-10) outliers start: 154 outliers final: 85 residues processed: 433 average time/residue: 0.6494 time to fit residues: 321.0039 Evaluate side-chains 378 residues out of total 2708 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 98 poor density : 280 time to evaluate : 0.995 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain I residue 116 ARG Chi-restraints excluded: chain I residue 146 THR Chi-restraints excluded: chain I residue 182 CYS Chi-restraints excluded: chain I residue 198 SER Chi-restraints excluded: chain I residue 229 CYS Chi-restraints excluded: chain I residue 307 VAL Chi-restraints excluded: chain I residue 337 CYS Chi-restraints excluded: chain I residue 338 GLU Chi-restraints excluded: chain I residue 359 SER Chi-restraints excluded: chain I residue 366 SER Chi-restraints excluded: chain I residue 390 ASP Chi-restraints excluded: chain M residue 116 ARG Chi-restraints excluded: chain M residue 146 THR Chi-restraints excluded: chain M residue 182 CYS Chi-restraints excluded: chain M residue 198 SER Chi-restraints excluded: chain M residue 229 CYS Chi-restraints excluded: chain M residue 307 VAL Chi-restraints excluded: chain M residue 337 CYS Chi-restraints excluded: chain M residue 359 SER Chi-restraints excluded: chain M residue 366 SER Chi-restraints excluded: chain M residue 419 LYS Chi-restraints excluded: chain N residue 116 ARG Chi-restraints excluded: chain N residue 146 THR Chi-restraints excluded: chain N residue 182 CYS Chi-restraints excluded: chain N residue 198 SER Chi-restraints excluded: chain N residue 229 CYS Chi-restraints excluded: chain N residue 307 VAL Chi-restraints excluded: chain N residue 337 CYS Chi-restraints excluded: chain N residue 338 GLU Chi-restraints excluded: chain N residue 359 SER Chi-restraints excluded: chain N residue 366 SER Chi-restraints excluded: chain W residue 116 ARG Chi-restraints excluded: chain W residue 146 THR Chi-restraints excluded: chain W residue 182 CYS Chi-restraints excluded: chain W residue 198 SER Chi-restraints excluded: chain W residue 229 CYS Chi-restraints excluded: chain W residue 307 VAL Chi-restraints excluded: chain W residue 337 CYS Chi-restraints excluded: chain W residue 338 GLU Chi-restraints excluded: chain W residue 359 SER Chi-restraints excluded: chain W residue 366 SER Chi-restraints excluded: chain W residue 419 LYS Chi-restraints excluded: chain A residue 11 VAL Chi-restraints excluded: chain A residue 17 SER Chi-restraints excluded: chain A residue 87 THR Chi-restraints excluded: chain A residue 100 ASP Chi-restraints excluded: chain A residue 159 LEU Chi-restraints excluded: chain A residue 184 VAL Chi-restraints excluded: chain C residue 11 VAL Chi-restraints excluded: chain C residue 17 SER Chi-restraints excluded: chain C residue 84 SER Chi-restraints excluded: chain C residue 87 THR Chi-restraints excluded: chain C residue 100 ASP Chi-restraints excluded: chain C residue 100 SER Chi-restraints excluded: chain C residue 184 VAL Chi-restraints excluded: chain D residue 11 VAL Chi-restraints excluded: chain D residue 17 SER Chi-restraints excluded: chain D residue 84 SER Chi-restraints excluded: chain D residue 87 THR Chi-restraints excluded: chain D residue 100 ASP Chi-restraints excluded: chain D residue 100 SER Chi-restraints excluded: chain H residue 11 VAL Chi-restraints excluded: chain H residue 17 SER Chi-restraints excluded: chain H residue 87 THR Chi-restraints excluded: chain H residue 100 ASP Chi-restraints excluded: chain H residue 100 SER Chi-restraints excluded: chain H residue 184 VAL Chi-restraints excluded: chain B residue 30 SER Chi-restraints excluded: chain B residue 33 LEU Chi-restraints excluded: chain B residue 76 SER Chi-restraints excluded: chain B residue 79 GLU Chi-restraints excluded: chain B residue 143 GLU Chi-restraints excluded: chain B residue 166 GLN Chi-restraints excluded: chain B residue 182 SER Chi-restraints excluded: chain B residue 202 SER Chi-restraints excluded: chain B residue 206 THR Chi-restraints excluded: chain E residue 30 SER Chi-restraints excluded: chain E residue 33 LEU Chi-restraints excluded: chain E residue 49 ASN Chi-restraints excluded: chain E residue 76 SER Chi-restraints excluded: chain E residue 150 VAL Chi-restraints excluded: chain E residue 182 SER Chi-restraints excluded: chain G residue 30 SER Chi-restraints excluded: chain G residue 58 ILE Chi-restraints excluded: chain G residue 76 SER Chi-restraints excluded: chain G residue 79 GLU Chi-restraints excluded: chain G residue 166 GLN Chi-restraints excluded: chain G residue 174 SER Chi-restraints excluded: chain G residue 202 SER Chi-restraints excluded: chain G residue 206 THR Chi-restraints excluded: chain L residue 30 SER Chi-restraints excluded: chain L residue 76 SER Chi-restraints excluded: chain L residue 79 GLU Chi-restraints excluded: chain L residue 150 VAL Chi-restraints excluded: chain L residue 174 SER Chi-restraints excluded: chain L residue 182 SER Chi-restraints excluded: chain L residue 202 SER Chi-restraints excluded: chain L residue 206 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 316 random chunks: chunk 294 optimal weight: 0.9990 chunk 254 optimal weight: 9.9990 chunk 46 optimal weight: 0.8980 chunk 121 optimal weight: 1.9990 chunk 47 optimal weight: 2.9990 chunk 58 optimal weight: 0.0980 chunk 2 optimal weight: 0.9990 chunk 278 optimal weight: 4.9990 chunk 264 optimal weight: 50.0000 chunk 191 optimal weight: 7.9990 chunk 43 optimal weight: 2.9990 overall best weight: 0.9986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: I 329 ASN E 27 GLN E 166 GLN G 27 GLN ** G 155 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 166 GLN L 6 GLN L 166 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3923 r_free = 0.3923 target = 0.145123 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3125 r_free = 0.3125 target = 0.085012 restraints weight = 36479.937| |-----------------------------------------------------------------------------| r_work (start): 0.3030 rms_B_bonded: 2.35 r_work: 0.2901 rms_B_bonded: 2.45 restraints_weight: 0.5000 r_work: 0.2767 rms_B_bonded: 3.81 restraints_weight: 0.2500 r_work (final): 0.2767 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2756 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2756 r_free = 0.2756 target_work(ls_wunit_k1) = 0.064 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2756 r_free = 0.2756 target_work(ls_wunit_k1) = 0.064 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| r_final: 0.2756 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8351 moved from start: 0.2857 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 25420 Z= 0.117 Angle : 0.584 8.446 34486 Z= 0.304 Chirality : 0.044 0.151 3808 Planarity : 0.005 0.054 4380 Dihedral : 6.028 55.783 3719 Min Nonbonded Distance : 2.344 Molprobity Statistics. All-atom Clashscore : 6.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.08 % Favored : 94.92 % Rotamer: Outliers : 2.95 % Allowed : 22.64 % Favored : 74.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.63 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.05 (0.14), residues: 3148 helix: -4.39 (0.17), residues: 32 sheet: -0.72 (0.14), residues: 1276 loop : -1.82 (0.13), residues: 1840 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG L 142 TYR 0.024 0.001 TYR B 140 PHE 0.020 0.002 PHE D 100C TRP 0.008 0.001 TRP I 80 HIS 0.003 0.001 HIS B 198 Details of bonding type rmsd covalent geometry : bond 0.00268 (25376) covalent geometry : angle 0.58146 (34384) SS BOND : bond 0.00129 ( 32) SS BOND : angle 0.91771 ( 66) hydrogen bonds : bond 0.03200 ( 706) hydrogen bonds : angle 5.21992 ( 1932) link_BETA1-4 : bond 0.00461 ( 8) link_BETA1-4 : angle 1.74859 ( 24) link_NAG-ASN : bond 0.00036 ( 4) link_NAG-ASN : angle 0.93610 ( 12) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6296 Ramachandran restraints generated. 3148 Oldfield, 0 Emsley, 3148 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6296 Ramachandran restraints generated. 3148 Oldfield, 0 Emsley, 3148 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 407 residues out of total 2708 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 80 poor density : 327 time to evaluate : 1.071 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: I 390 ASP cc_start: 0.7569 (OUTLIER) cc_final: 0.7302 (m-30) REVERT: I 419 LYS cc_start: 0.9305 (mttt) cc_final: 0.9023 (mttm) REVERT: I 429 MET cc_start: 0.9410 (mtp) cc_final: 0.9204 (mtm) REVERT: M 338 GLU cc_start: 0.8389 (OUTLIER) cc_final: 0.8114 (mp0) REVERT: M 419 LYS cc_start: 0.9272 (mttt) cc_final: 0.8958 (mttm) REVERT: M 429 MET cc_start: 0.9403 (mtp) cc_final: 0.9197 (mtm) REVERT: N 371 LYS cc_start: 0.9190 (OUTLIER) cc_final: 0.8882 (ptpp) REVERT: N 419 LYS cc_start: 0.9282 (mttt) cc_final: 0.8980 (mttm) REVERT: N 429 MET cc_start: 0.9381 (mtp) cc_final: 0.9170 (mtm) REVERT: W 371 LYS cc_start: 0.9197 (OUTLIER) cc_final: 0.8842 (ptpp) REVERT: W 419 LYS cc_start: 0.9275 (mttt) cc_final: 0.8966 (mttm) REVERT: W 429 MET cc_start: 0.9385 (mtp) cc_final: 0.9173 (mtm) REVERT: A 72 ASP cc_start: 0.8252 (t70) cc_final: 0.7514 (t70) REVERT: A 100 PHE cc_start: 0.7684 (OUTLIER) cc_final: 0.7257 (p90) REVERT: A 138 LEU cc_start: 0.6471 (pp) cc_final: 0.6156 (pt) REVERT: A 145 TYR cc_start: 0.6945 (p90) cc_final: 0.6389 (p90) REVERT: A 176 TYR cc_start: 0.7197 (m-80) cc_final: 0.6946 (m-80) REVERT: A 184 VAL cc_start: 0.8480 (OUTLIER) cc_final: 0.8239 (p) REVERT: C 30 ILE cc_start: 0.9045 (tt) cc_final: 0.8759 (tp) REVERT: C 72 ASP cc_start: 0.8016 (t70) cc_final: 0.7240 (t70) REVERT: D 30 ILE cc_start: 0.9044 (tt) cc_final: 0.8772 (tp) REVERT: D 72 ASP cc_start: 0.8049 (t70) cc_final: 0.7279 (t70) REVERT: D 145 TYR cc_start: 0.7024 (p90) cc_final: 0.6372 (p90) REVERT: D 176 TYR cc_start: 0.7219 (m-80) cc_final: 0.6960 (m-80) REVERT: H 30 ILE cc_start: 0.9039 (tt) cc_final: 0.8750 (tp) REVERT: H 72 ASP cc_start: 0.8045 (t70) cc_final: 0.7266 (t70) REVERT: H 81 ASP cc_start: 0.8104 (t70) cc_final: 0.7897 (t0) REVERT: H 145 TYR cc_start: 0.6962 (p90) cc_final: 0.6302 (p90) REVERT: H 169 VAL cc_start: 0.7695 (OUTLIER) cc_final: 0.7492 (p) REVERT: H 176 TYR cc_start: 0.7381 (m-80) cc_final: 0.7138 (m-80) REVERT: B 143 GLU cc_start: 0.8421 (OUTLIER) cc_final: 0.8157 (tm-30) REVERT: E 42 GLN cc_start: 0.7471 (mp10) cc_final: 0.7197 (mp10) REVERT: E 108 ARG cc_start: 0.8037 (ptm160) cc_final: 0.7812 (ptt90) REVERT: E 190 LYS cc_start: 0.8184 (mmmt) cc_final: 0.7809 (tptt) REVERT: G 108 ARG cc_start: 0.7764 (ptm160) cc_final: 0.7413 (ptm-80) REVERT: G 166 GLN cc_start: 0.8862 (OUTLIER) cc_final: 0.8486 (tt0) REVERT: G 173 TYR cc_start: 0.8177 (m-80) cc_final: 0.7769 (m-10) REVERT: L 108 ARG cc_start: 0.7709 (ptm160) cc_final: 0.7046 (ptm-80) outliers start: 80 outliers final: 40 residues processed: 395 average time/residue: 0.6618 time to fit residues: 298.2912 Evaluate side-chains 342 residues out of total 2708 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 293 time to evaluate : 0.924 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain I residue 182 CYS Chi-restraints excluded: chain I residue 198 SER Chi-restraints excluded: chain I residue 229 CYS Chi-restraints excluded: chain I residue 337 CYS Chi-restraints excluded: chain I residue 390 ASP Chi-restraints excluded: chain M residue 182 CYS Chi-restraints excluded: chain M residue 198 SER Chi-restraints excluded: chain M residue 229 CYS Chi-restraints excluded: chain M residue 337 CYS Chi-restraints excluded: chain M residue 338 GLU Chi-restraints excluded: chain N residue 182 CYS Chi-restraints excluded: chain N residue 198 SER Chi-restraints excluded: chain N residue 229 CYS Chi-restraints excluded: chain N residue 337 CYS Chi-restraints excluded: chain N residue 359 SER Chi-restraints excluded: chain N residue 371 LYS Chi-restraints excluded: chain W residue 182 CYS Chi-restraints excluded: chain W residue 198 SER Chi-restraints excluded: chain W residue 229 CYS Chi-restraints excluded: chain W residue 337 CYS Chi-restraints excluded: chain W residue 371 LYS Chi-restraints excluded: chain A residue 87 THR Chi-restraints excluded: chain A residue 100 PHE Chi-restraints excluded: chain A residue 100 ASP Chi-restraints excluded: chain A residue 100 SER Chi-restraints excluded: chain A residue 184 VAL Chi-restraints excluded: chain C residue 87 THR Chi-restraints excluded: chain D residue 87 THR Chi-restraints excluded: chain D residue 100 ASP Chi-restraints excluded: chain D residue 184 VAL Chi-restraints excluded: chain H residue 87 THR Chi-restraints excluded: chain H residue 169 VAL Chi-restraints excluded: chain H residue 184 VAL Chi-restraints excluded: chain B residue 30 SER Chi-restraints excluded: chain B residue 143 GLU Chi-restraints excluded: chain B residue 174 SER Chi-restraints excluded: chain B residue 202 SER Chi-restraints excluded: chain B residue 206 THR Chi-restraints excluded: chain E residue 27 GLN Chi-restraints excluded: chain E residue 49 ASN Chi-restraints excluded: chain E residue 182 SER Chi-restraints excluded: chain E residue 202 SER Chi-restraints excluded: chain G residue 30 SER Chi-restraints excluded: chain G residue 33 LEU Chi-restraints excluded: chain G residue 79 GLU Chi-restraints excluded: chain G residue 166 GLN Chi-restraints excluded: chain G residue 202 SER Chi-restraints excluded: chain L residue 30 SER Chi-restraints excluded: chain L residue 33 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 316 random chunks: chunk 1 optimal weight: 6.9990 chunk 103 optimal weight: 4.9990 chunk 301 optimal weight: 10.0000 chunk 229 optimal weight: 0.4980 chunk 204 optimal weight: 6.9990 chunk 61 optimal weight: 9.9990 chunk 210 optimal weight: 5.9990 chunk 82 optimal weight: 4.9990 chunk 81 optimal weight: 1.9990 chunk 307 optimal weight: 0.0050 chunk 37 optimal weight: 6.9990 overall best weight: 2.5000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: W 329 ASN B 6 GLN B 27 GLN B 42 GLN E 6 GLN E 27 GLN E 166 GLN G 27 GLN G 42 GLN ** G 155 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 166 GLN L 6 GLN L 27 GLN L 42 GLN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3903 r_free = 0.3903 target = 0.143649 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3094 r_free = 0.3094 target = 0.083220 restraints weight = 36591.138| |-----------------------------------------------------------------------------| r_work (start): 0.3000 rms_B_bonded: 2.34 r_work: 0.2870 rms_B_bonded: 2.44 restraints_weight: 0.5000 r_work: 0.2737 rms_B_bonded: 3.79 restraints_weight: 0.2500 r_work (final): 0.2737 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2728 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2728 r_free = 0.2728 target_work(ls_wunit_k1) = 0.063 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2728 r_free = 0.2728 target_work(ls_wunit_k1) = 0.063 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| r_final: 0.2728 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8383 moved from start: 0.3053 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.057 25420 Z= 0.195 Angle : 0.617 7.741 34486 Z= 0.320 Chirality : 0.045 0.135 3808 Planarity : 0.005 0.053 4380 Dihedral : 5.733 43.399 3711 Min Nonbonded Distance : 2.292 Molprobity Statistics. All-atom Clashscore : 6.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.73 % Favored : 95.27 % Rotamer: Outliers : 4.39 % Allowed : 22.42 % Favored : 73.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.63 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.99 (0.14), residues: 3148 helix: -4.33 (0.18), residues: 32 sheet: -0.58 (0.14), residues: 1280 loop : -1.86 (0.13), residues: 1836 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 24 TYR 0.024 0.002 TYR B 140 PHE 0.028 0.002 PHE D 100C TRP 0.007 0.001 TRP D 103 HIS 0.004 0.001 HIS N 129 Details of bonding type rmsd covalent geometry : bond 0.00463 (25376) covalent geometry : angle 0.60924 (34384) SS BOND : bond 0.00403 ( 32) SS BOND : angle 2.05998 ( 66) hydrogen bonds : bond 0.03397 ( 706) hydrogen bonds : angle 5.11003 ( 1932) link_BETA1-4 : bond 0.00379 ( 8) link_BETA1-4 : angle 1.66133 ( 24) link_NAG-ASN : bond 0.00196 ( 4) link_NAG-ASN : angle 1.01856 ( 12) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6296 Ramachandran restraints generated. 3148 Oldfield, 0 Emsley, 3148 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6296 Ramachandran restraints generated. 3148 Oldfield, 0 Emsley, 3148 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 416 residues out of total 2708 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 119 poor density : 297 time to evaluate : 0.863 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: I 338 GLU cc_start: 0.8367 (OUTLIER) cc_final: 0.8068 (mp0) REVERT: I 419 LYS cc_start: 0.9206 (mttt) cc_final: 0.9000 (mttm) REVERT: M 338 GLU cc_start: 0.8345 (OUTLIER) cc_final: 0.8097 (mp0) REVERT: M 419 LYS cc_start: 0.9181 (mttt) cc_final: 0.8939 (mttm) REVERT: N 338 GLU cc_start: 0.8372 (OUTLIER) cc_final: 0.8073 (mp0) REVERT: N 371 LYS cc_start: 0.9218 (OUTLIER) cc_final: 0.8865 (ptpp) REVERT: N 419 LYS cc_start: 0.9235 (mttt) cc_final: 0.9021 (mttm) REVERT: N 429 MET cc_start: 0.9414 (mtp) cc_final: 0.9186 (mtm) REVERT: W 338 GLU cc_start: 0.8366 (OUTLIER) cc_final: 0.8073 (mp0) REVERT: W 371 LYS cc_start: 0.9221 (OUTLIER) cc_final: 0.8892 (ptpp) REVERT: W 419 LYS cc_start: 0.9199 (mttt) cc_final: 0.8965 (mttm) REVERT: W 429 MET cc_start: 0.9415 (mtp) cc_final: 0.9187 (mtm) REVERT: A 72 ASP cc_start: 0.8301 (t70) cc_final: 0.7595 (t70) REVERT: A 100 PHE cc_start: 0.7968 (OUTLIER) cc_final: 0.7209 (p90) REVERT: A 138 LEU cc_start: 0.6601 (pp) cc_final: 0.6239 (pt) REVERT: A 145 TYR cc_start: 0.7004 (p90) cc_final: 0.6372 (p90) REVERT: A 176 TYR cc_start: 0.7166 (m-80) cc_final: 0.6904 (m-80) REVERT: A 184 VAL cc_start: 0.8418 (OUTLIER) cc_final: 0.8170 (p) REVERT: C 30 ILE cc_start: 0.9067 (tt) cc_final: 0.8773 (tp) REVERT: C 72 ASP cc_start: 0.8226 (t70) cc_final: 0.7489 (t70) REVERT: C 100 PHE cc_start: 0.7786 (OUTLIER) cc_final: 0.7381 (p90) REVERT: D 30 ILE cc_start: 0.9050 (tt) cc_final: 0.8771 (tp) REVERT: D 72 ASP cc_start: 0.8228 (t70) cc_final: 0.7489 (t70) REVERT: D 100 PHE cc_start: 0.7760 (OUTLIER) cc_final: 0.7362 (p90) REVERT: D 145 TYR cc_start: 0.7117 (p90) cc_final: 0.6499 (p90) REVERT: H 30 ILE cc_start: 0.9063 (tt) cc_final: 0.8766 (tp) REVERT: H 72 ASP cc_start: 0.8216 (t70) cc_final: 0.7484 (t70) REVERT: H 100 PHE cc_start: 0.7775 (OUTLIER) cc_final: 0.7369 (p90) REVERT: H 184 VAL cc_start: 0.8500 (OUTLIER) cc_final: 0.8300 (p) REVERT: B 108 ARG cc_start: 0.7836 (ptm160) cc_final: 0.7581 (ptt90) REVERT: E 27 GLN cc_start: 0.8884 (OUTLIER) cc_final: 0.8554 (pm20) REVERT: E 42 GLN cc_start: 0.7456 (mp10) cc_final: 0.7159 (mp10) REVERT: E 108 ARG cc_start: 0.8090 (ptm160) cc_final: 0.7882 (ptt90) REVERT: E 190 LYS cc_start: 0.8323 (mmmt) cc_final: 0.7966 (tptt) REVERT: E 201 LEU cc_start: 0.6611 (OUTLIER) cc_final: 0.6404 (pp) REVERT: G 108 ARG cc_start: 0.7776 (ptm160) cc_final: 0.7568 (ptm-80) REVERT: G 173 TYR cc_start: 0.8189 (m-80) cc_final: 0.7902 (m-10) outliers start: 119 outliers final: 73 residues processed: 399 average time/residue: 0.6157 time to fit residues: 282.8399 Evaluate side-chains 371 residues out of total 2708 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 87 poor density : 284 time to evaluate : 0.916 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain I residue 102 ARG Chi-restraints excluded: chain I residue 146 THR Chi-restraints excluded: chain I residue 182 CYS Chi-restraints excluded: chain I residue 198 SER Chi-restraints excluded: chain I residue 229 CYS Chi-restraints excluded: chain I residue 307 VAL Chi-restraints excluded: chain I residue 337 CYS Chi-restraints excluded: chain I residue 338 GLU Chi-restraints excluded: chain I residue 359 SER Chi-restraints excluded: chain M residue 87 CYS Chi-restraints excluded: chain M residue 102 ARG Chi-restraints excluded: chain M residue 146 THR Chi-restraints excluded: chain M residue 182 CYS Chi-restraints excluded: chain M residue 198 SER Chi-restraints excluded: chain M residue 229 CYS Chi-restraints excluded: chain M residue 307 VAL Chi-restraints excluded: chain M residue 337 CYS Chi-restraints excluded: chain M residue 338 GLU Chi-restraints excluded: chain M residue 361 ILE Chi-restraints excluded: chain N residue 87 CYS Chi-restraints excluded: chain N residue 146 THR Chi-restraints excluded: chain N residue 182 CYS Chi-restraints excluded: chain N residue 198 SER Chi-restraints excluded: chain N residue 229 CYS Chi-restraints excluded: chain N residue 307 VAL Chi-restraints excluded: chain N residue 337 CYS Chi-restraints excluded: chain N residue 338 GLU Chi-restraints excluded: chain N residue 359 SER Chi-restraints excluded: chain N residue 371 LYS Chi-restraints excluded: chain W residue 87 CYS Chi-restraints excluded: chain W residue 146 THR Chi-restraints excluded: chain W residue 182 CYS Chi-restraints excluded: chain W residue 198 SER Chi-restraints excluded: chain W residue 229 CYS Chi-restraints excluded: chain W residue 307 VAL Chi-restraints excluded: chain W residue 337 CYS Chi-restraints excluded: chain W residue 338 GLU Chi-restraints excluded: chain W residue 371 LYS Chi-restraints excluded: chain A residue 17 SER Chi-restraints excluded: chain A residue 87 THR Chi-restraints excluded: chain A residue 100 PHE Chi-restraints excluded: chain A residue 100 ASP Chi-restraints excluded: chain A residue 100 SER Chi-restraints excluded: chain A residue 184 VAL Chi-restraints excluded: chain C residue 11 VAL Chi-restraints excluded: chain C residue 17 SER Chi-restraints excluded: chain C residue 25 SER Chi-restraints excluded: chain C residue 87 THR Chi-restraints excluded: chain C residue 100 PHE Chi-restraints excluded: chain C residue 100 ASP Chi-restraints excluded: chain C residue 184 VAL Chi-restraints excluded: chain D residue 17 SER Chi-restraints excluded: chain D residue 25 SER Chi-restraints excluded: chain D residue 87 THR Chi-restraints excluded: chain D residue 100 PHE Chi-restraints excluded: chain D residue 100 ASP Chi-restraints excluded: chain H residue 11 VAL Chi-restraints excluded: chain H residue 17 SER Chi-restraints excluded: chain H residue 25 SER Chi-restraints excluded: chain H residue 87 THR Chi-restraints excluded: chain H residue 100 PHE Chi-restraints excluded: chain H residue 100 ASP Chi-restraints excluded: chain H residue 184 VAL Chi-restraints excluded: chain B residue 27 GLN Chi-restraints excluded: chain B residue 30 SER Chi-restraints excluded: chain B residue 76 SER Chi-restraints excluded: chain B residue 79 GLU Chi-restraints excluded: chain B residue 174 SER Chi-restraints excluded: chain B residue 182 SER Chi-restraints excluded: chain B residue 202 SER Chi-restraints excluded: chain B residue 206 THR Chi-restraints excluded: chain E residue 27 GLN Chi-restraints excluded: chain E residue 30 SER Chi-restraints excluded: chain E residue 49 ASN Chi-restraints excluded: chain E residue 76 SER Chi-restraints excluded: chain E residue 182 SER Chi-restraints excluded: chain E residue 201 LEU Chi-restraints excluded: chain E residue 202 SER Chi-restraints excluded: chain G residue 27 GLN Chi-restraints excluded: chain G residue 30 SER Chi-restraints excluded: chain G residue 76 SER Chi-restraints excluded: chain G residue 79 GLU Chi-restraints excluded: chain G residue 202 SER Chi-restraints excluded: chain L residue 27 GLN Chi-restraints excluded: chain L residue 30 SER Chi-restraints excluded: chain L residue 76 SER Chi-restraints excluded: chain L residue 202 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 316 random chunks: chunk 204 optimal weight: 20.0000 chunk 40 optimal weight: 3.9990 chunk 57 optimal weight: 0.0270 chunk 102 optimal weight: 1.9990 chunk 51 optimal weight: 4.9990 chunk 270 optimal weight: 6.9990 chunk 263 optimal weight: 6.9990 chunk 33 optimal weight: 0.9980 chunk 221 optimal weight: 6.9990 chunk 247 optimal weight: 0.0370 chunk 224 optimal weight: 50.0000 overall best weight: 1.4120 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: I 101 HIS I 329 ASN B 6 GLN E 6 GLN E 27 GLN E 166 GLN ** G 155 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 160 GLN G 166 GLN L 6 GLN L 160 GLN L 198 HIS Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3915 r_free = 0.3915 target = 0.144618 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 71)----------------| | r_work = 0.3115 r_free = 0.3115 target = 0.084291 restraints weight = 36544.267| |-----------------------------------------------------------------------------| r_work (start): 0.3021 rms_B_bonded: 2.41 r_work: 0.2893 rms_B_bonded: 2.48 restraints_weight: 0.5000 r_work: 0.2758 rms_B_bonded: 3.88 restraints_weight: 0.2500 r_work (final): 0.2758 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2747 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2747 r_free = 0.2747 target_work(ls_wunit_k1) = 0.064 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2747 r_free = 0.2747 target_work(ls_wunit_k1) = 0.064 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| r_final: 0.2747 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8366 moved from start: 0.3201 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 25420 Z= 0.133 Angle : 0.583 7.584 34486 Z= 0.302 Chirality : 0.044 0.181 3808 Planarity : 0.004 0.051 4380 Dihedral : 5.382 37.739 3708 Min Nonbonded Distance : 2.323 Molprobity Statistics. All-atom Clashscore : 6.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.64 % Favored : 95.36 % Rotamer: Outliers : 3.84 % Allowed : 23.56 % Favored : 72.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.63 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.85 (0.14), residues: 3148 helix: -4.32 (0.18), residues: 32 sheet: -0.52 (0.14), residues: 1296 loop : -1.75 (0.13), residues: 1820 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG L 108 TYR 0.028 0.001 TYR L 140 PHE 0.023 0.002 PHE D 100C TRP 0.006 0.001 TRP I 80 HIS 0.008 0.001 HIS I 101 Details of bonding type rmsd covalent geometry : bond 0.00314 (25376) covalent geometry : angle 0.57875 (34384) SS BOND : bond 0.00200 ( 32) SS BOND : angle 1.47627 ( 66) hydrogen bonds : bond 0.03076 ( 706) hydrogen bonds : angle 4.94287 ( 1932) link_BETA1-4 : bond 0.00432 ( 8) link_BETA1-4 : angle 1.52390 ( 24) link_NAG-ASN : bond 0.00093 ( 4) link_NAG-ASN : angle 0.93385 ( 12) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6296 Ramachandran restraints generated. 3148 Oldfield, 0 Emsley, 3148 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6296 Ramachandran restraints generated. 3148 Oldfield, 0 Emsley, 3148 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 401 residues out of total 2708 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 104 poor density : 297 time to evaluate : 1.012 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: I 338 GLU cc_start: 0.8328 (OUTLIER) cc_final: 0.8060 (mp0) REVERT: I 419 LYS cc_start: 0.9179 (mttt) cc_final: 0.8968 (mttm) REVERT: I 429 MET cc_start: 0.9417 (mtp) cc_final: 0.9200 (mtm) REVERT: M 338 GLU cc_start: 0.8308 (OUTLIER) cc_final: 0.8081 (mp0) REVERT: M 419 LYS cc_start: 0.9189 (mttt) cc_final: 0.8962 (mttm) REVERT: M 429 MET cc_start: 0.9414 (mtp) cc_final: 0.9200 (mtm) REVERT: N 338 GLU cc_start: 0.8347 (OUTLIER) cc_final: 0.8066 (mp0) REVERT: N 371 LYS cc_start: 0.9219 (OUTLIER) cc_final: 0.8912 (ptpp) REVERT: N 419 LYS cc_start: 0.9187 (mttt) cc_final: 0.8941 (mttm) REVERT: N 429 MET cc_start: 0.9392 (mtp) cc_final: 0.9160 (mtm) REVERT: W 338 GLU cc_start: 0.8340 (OUTLIER) cc_final: 0.8057 (mp0) REVERT: W 371 LYS cc_start: 0.9221 (OUTLIER) cc_final: 0.8873 (ptpp) REVERT: W 419 LYS cc_start: 0.9185 (mttt) cc_final: 0.8958 (mttm) REVERT: W 429 MET cc_start: 0.9393 (mtp) cc_final: 0.9160 (mtm) REVERT: A 72 ASP cc_start: 0.8288 (t70) cc_final: 0.7608 (t70) REVERT: A 100 PHE cc_start: 0.7839 (OUTLIER) cc_final: 0.7340 (p90) REVERT: A 145 TYR cc_start: 0.6989 (p90) cc_final: 0.6356 (p90) REVERT: A 176 TYR cc_start: 0.7128 (m-80) cc_final: 0.6888 (m-80) REVERT: C 30 ILE cc_start: 0.9063 (tt) cc_final: 0.8770 (tp) REVERT: C 72 ASP cc_start: 0.8204 (t70) cc_final: 0.7465 (t70) REVERT: C 100 PHE cc_start: 0.7884 (OUTLIER) cc_final: 0.7519 (p90) REVERT: D 30 ILE cc_start: 0.9045 (tt) cc_final: 0.8769 (tp) REVERT: D 72 ASP cc_start: 0.8221 (t70) cc_final: 0.7481 (t70) REVERT: D 100 PHE cc_start: 0.7858 (OUTLIER) cc_final: 0.7474 (p90) REVERT: D 145 TYR cc_start: 0.6958 (p90) cc_final: 0.6255 (p90) REVERT: H 30 ILE cc_start: 0.9060 (tt) cc_final: 0.8768 (tp) REVERT: H 72 ASP cc_start: 0.8228 (t70) cc_final: 0.7474 (t70) REVERT: H 100 PHE cc_start: 0.8027 (OUTLIER) cc_final: 0.7658 (p90) REVERT: B 108 ARG cc_start: 0.7832 (ptm160) cc_final: 0.7539 (ptt90) REVERT: E 27 GLN cc_start: 0.8810 (OUTLIER) cc_final: 0.8515 (pm20) REVERT: E 42 GLN cc_start: 0.7441 (mp10) cc_final: 0.7183 (mp10) REVERT: E 108 ARG cc_start: 0.8079 (ptm160) cc_final: 0.7872 (ptt90) REVERT: E 165 GLU cc_start: 0.8452 (mm-30) cc_final: 0.7952 (tp30) REVERT: G 108 ARG cc_start: 0.7897 (ptm160) cc_final: 0.7600 (ptt90) REVERT: G 140 TYR cc_start: 0.6844 (t80) cc_final: 0.6635 (t80) REVERT: L 140 TYR cc_start: 0.6877 (OUTLIER) cc_final: 0.6527 (t80) outliers start: 104 outliers final: 67 residues processed: 385 average time/residue: 0.6796 time to fit residues: 297.5295 Evaluate side-chains 366 residues out of total 2708 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 79 poor density : 287 time to evaluate : 0.967 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain I residue 102 ARG Chi-restraints excluded: chain I residue 146 THR Chi-restraints excluded: chain I residue 182 CYS Chi-restraints excluded: chain I residue 198 SER Chi-restraints excluded: chain I residue 229 CYS Chi-restraints excluded: chain I residue 337 CYS Chi-restraints excluded: chain I residue 338 GLU Chi-restraints excluded: chain I residue 357 MET Chi-restraints excluded: chain I residue 359 SER Chi-restraints excluded: chain I residue 361 ILE Chi-restraints excluded: chain M residue 87 CYS Chi-restraints excluded: chain M residue 102 ARG Chi-restraints excluded: chain M residue 182 CYS Chi-restraints excluded: chain M residue 198 SER Chi-restraints excluded: chain M residue 229 CYS Chi-restraints excluded: chain M residue 337 CYS Chi-restraints excluded: chain M residue 338 GLU Chi-restraints excluded: chain M residue 357 MET Chi-restraints excluded: chain M residue 359 SER Chi-restraints excluded: chain M residue 361 ILE Chi-restraints excluded: chain N residue 87 CYS Chi-restraints excluded: chain N residue 146 THR Chi-restraints excluded: chain N residue 182 CYS Chi-restraints excluded: chain N residue 198 SER Chi-restraints excluded: chain N residue 229 CYS Chi-restraints excluded: chain N residue 337 CYS Chi-restraints excluded: chain N residue 338 GLU Chi-restraints excluded: chain N residue 357 MET Chi-restraints excluded: chain N residue 359 SER Chi-restraints excluded: chain N residue 361 ILE Chi-restraints excluded: chain N residue 371 LYS Chi-restraints excluded: chain W residue 87 CYS Chi-restraints excluded: chain W residue 146 THR Chi-restraints excluded: chain W residue 182 CYS Chi-restraints excluded: chain W residue 198 SER Chi-restraints excluded: chain W residue 229 CYS Chi-restraints excluded: chain W residue 337 CYS Chi-restraints excluded: chain W residue 338 GLU Chi-restraints excluded: chain W residue 357 MET Chi-restraints excluded: chain W residue 359 SER Chi-restraints excluded: chain W residue 361 ILE Chi-restraints excluded: chain W residue 371 LYS Chi-restraints excluded: chain A residue 11 VAL Chi-restraints excluded: chain A residue 17 SER Chi-restraints excluded: chain A residue 87 THR Chi-restraints excluded: chain A residue 100 PHE Chi-restraints excluded: chain A residue 100 ASP Chi-restraints excluded: chain A residue 100 SER Chi-restraints excluded: chain C residue 25 SER Chi-restraints excluded: chain C residue 87 THR Chi-restraints excluded: chain C residue 100 PHE Chi-restraints excluded: chain C residue 100 ASP Chi-restraints excluded: chain C residue 184 VAL Chi-restraints excluded: chain D residue 11 VAL Chi-restraints excluded: chain D residue 25 SER Chi-restraints excluded: chain D residue 87 THR Chi-restraints excluded: chain D residue 100 PHE Chi-restraints excluded: chain D residue 100 ASP Chi-restraints excluded: chain H residue 17 SER Chi-restraints excluded: chain H residue 25 SER Chi-restraints excluded: chain H residue 87 THR Chi-restraints excluded: chain H residue 100 PHE Chi-restraints excluded: chain H residue 100 ASP Chi-restraints excluded: chain H residue 100 SER Chi-restraints excluded: chain B residue 30 SER Chi-restraints excluded: chain B residue 33 LEU Chi-restraints excluded: chain B residue 202 SER Chi-restraints excluded: chain B residue 206 THR Chi-restraints excluded: chain E residue 27 GLN Chi-restraints excluded: chain E residue 30 SER Chi-restraints excluded: chain E residue 174 SER Chi-restraints excluded: chain E residue 182 SER Chi-restraints excluded: chain E residue 202 SER Chi-restraints excluded: chain G residue 30 SER Chi-restraints excluded: chain G residue 202 SER Chi-restraints excluded: chain L residue 30 SER Chi-restraints excluded: chain L residue 76 SER Chi-restraints excluded: chain L residue 140 TYR Chi-restraints excluded: chain L residue 202 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 316 random chunks: chunk 43 optimal weight: 4.9990 chunk 24 optimal weight: 1.9990 chunk 20 optimal weight: 6.9990 chunk 259 optimal weight: 8.9990 chunk 47 optimal weight: 6.9990 chunk 199 optimal weight: 7.9990 chunk 108 optimal weight: 7.9990 chunk 1 optimal weight: 4.9990 chunk 211 optimal weight: 3.9990 chunk 87 optimal weight: 6.9990 chunk 214 optimal weight: 9.9990 overall best weight: 4.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: I 101 HIS ** I 354 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 101 HIS ** M 354 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 354 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 354 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 6 GLN E 6 GLN E 27 GLN ** E 124 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 166 GLN ** G 155 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 6 GLN ** L 198 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3878 r_free = 0.3878 target = 0.141607 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3055 r_free = 0.3055 target = 0.080918 restraints weight = 36707.553| |-----------------------------------------------------------------------------| r_work (start): 0.2956 rms_B_bonded: 2.35 r_work: 0.2829 rms_B_bonded: 2.42 restraints_weight: 0.5000 r_work: 0.2695 rms_B_bonded: 3.75 restraints_weight: 0.2500 r_work (final): 0.2695 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2680 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2680 r_free = 0.2680 target_work(ls_wunit_k1) = 0.060 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2680 r_free = 0.2680 target_work(ls_wunit_k1) = 0.060 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| r_final: 0.2680 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8418 moved from start: 0.3342 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.086 25420 Z= 0.323 Angle : 0.699 8.024 34486 Z= 0.363 Chirality : 0.048 0.168 3808 Planarity : 0.005 0.045 4380 Dihedral : 5.758 35.580 3708 Min Nonbonded Distance : 2.254 Molprobity Statistics. All-atom Clashscore : 6.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.30 % Favored : 94.70 % Rotamer: Outliers : 4.76 % Allowed : 23.01 % Favored : 72.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.63 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.89 (0.14), residues: 3148 helix: -4.47 (0.19), residues: 56 sheet: -0.43 (0.14), residues: 1312 loop : -1.84 (0.13), residues: 1780 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG B 24 TYR 0.021 0.002 TYR E 140 PHE 0.038 0.003 PHE D 100C TRP 0.011 0.002 TRP D 47 HIS 0.009 0.001 HIS I 101 Details of bonding type rmsd covalent geometry : bond 0.00773 (25376) covalent geometry : angle 0.68869 (34384) SS BOND : bond 0.00465 ( 32) SS BOND : angle 2.62611 ( 66) hydrogen bonds : bond 0.03787 ( 706) hydrogen bonds : angle 5.16418 ( 1932) link_BETA1-4 : bond 0.00318 ( 8) link_BETA1-4 : angle 1.67826 ( 24) link_NAG-ASN : bond 0.00427 ( 4) link_NAG-ASN : angle 1.20703 ( 12) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6296 Ramachandran restraints generated. 3148 Oldfield, 0 Emsley, 3148 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6296 Ramachandran restraints generated. 3148 Oldfield, 0 Emsley, 3148 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 406 residues out of total 2708 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 129 poor density : 277 time to evaluate : 0.874 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: I 116 ARG cc_start: 0.8242 (OUTLIER) cc_final: 0.6108 (tmm160) REVERT: I 338 GLU cc_start: 0.8393 (OUTLIER) cc_final: 0.8096 (mp0) REVERT: I 419 LYS cc_start: 0.9210 (mttt) cc_final: 0.8966 (mttm) REVERT: M 116 ARG cc_start: 0.8225 (OUTLIER) cc_final: 0.6113 (tmm160) REVERT: M 338 GLU cc_start: 0.8401 (OUTLIER) cc_final: 0.8130 (mp0) REVERT: M 419 LYS cc_start: 0.9214 (mttt) cc_final: 0.8965 (mttm) REVERT: N 338 GLU cc_start: 0.8396 (OUTLIER) cc_final: 0.8093 (mp0) REVERT: N 371 LYS cc_start: 0.9280 (OUTLIER) cc_final: 0.8927 (ptpp) REVERT: N 419 LYS cc_start: 0.9213 (mttt) cc_final: 0.8968 (mttm) REVERT: N 429 MET cc_start: 0.9432 (mtp) cc_final: 0.9179 (mtm) REVERT: W 338 GLU cc_start: 0.8399 (OUTLIER) cc_final: 0.8090 (mp0) REVERT: W 371 LYS cc_start: 0.9284 (OUTLIER) cc_final: 0.8880 (ptpp) REVERT: W 419 LYS cc_start: 0.9205 (mttt) cc_final: 0.8957 (mttm) REVERT: W 429 MET cc_start: 0.9431 (mtp) cc_final: 0.9177 (mtm) REVERT: A 72 ASP cc_start: 0.8379 (t70) cc_final: 0.7695 (t70) REVERT: A 100 ASP cc_start: 0.8384 (OUTLIER) cc_final: 0.7767 (m-30) REVERT: A 100 PHE cc_start: 0.7918 (OUTLIER) cc_final: 0.7147 (p90) REVERT: A 123 PRO cc_start: 0.3764 (Cg_endo) cc_final: 0.3562 (Cg_exo) REVERT: C 30 ILE cc_start: 0.9098 (tt) cc_final: 0.8802 (tp) REVERT: C 46 GLU cc_start: 0.8493 (tt0) cc_final: 0.8291 (tt0) REVERT: C 72 ASP cc_start: 0.8322 (t70) cc_final: 0.7645 (t70) REVERT: D 72 ASP cc_start: 0.8340 (t70) cc_final: 0.7662 (t70) REVERT: D 145 TYR cc_start: 0.7128 (p90) cc_final: 0.6514 (p90) REVERT: H 30 ILE cc_start: 0.9099 (tt) cc_final: 0.8803 (tp) REVERT: H 72 ASP cc_start: 0.8348 (t70) cc_final: 0.7656 (t70) REVERT: E 42 GLN cc_start: 0.7556 (mp10) cc_final: 0.7273 (mp10) REVERT: E 108 ARG cc_start: 0.8168 (ptm160) cc_final: 0.7915 (ptt90) REVERT: G 108 ARG cc_start: 0.7905 (ptm160) cc_final: 0.7633 (ptt90) REVERT: L 108 ARG cc_start: 0.7796 (ptt90) cc_final: 0.7558 (ptt90) REVERT: L 140 TYR cc_start: 0.6889 (OUTLIER) cc_final: 0.6656 (t80) REVERT: L 199 GLN cc_start: 0.8383 (OUTLIER) cc_final: 0.7331 (pm20) outliers start: 129 outliers final: 79 residues processed: 384 average time/residue: 0.6522 time to fit residues: 286.0437 Evaluate side-chains 360 residues out of total 2708 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 91 poor density : 269 time to evaluate : 0.938 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain I residue 87 CYS Chi-restraints excluded: chain I residue 116 ARG Chi-restraints excluded: chain I residue 146 THR Chi-restraints excluded: chain I residue 182 CYS Chi-restraints excluded: chain I residue 198 SER Chi-restraints excluded: chain I residue 229 CYS Chi-restraints excluded: chain I residue 307 VAL Chi-restraints excluded: chain I residue 337 CYS Chi-restraints excluded: chain I residue 338 GLU Chi-restraints excluded: chain I residue 359 SER Chi-restraints excluded: chain I residue 361 ILE Chi-restraints excluded: chain M residue 87 CYS Chi-restraints excluded: chain M residue 116 ARG Chi-restraints excluded: chain M residue 146 THR Chi-restraints excluded: chain M residue 182 CYS Chi-restraints excluded: chain M residue 198 SER Chi-restraints excluded: chain M residue 229 CYS Chi-restraints excluded: chain M residue 307 VAL Chi-restraints excluded: chain M residue 337 CYS Chi-restraints excluded: chain M residue 338 GLU Chi-restraints excluded: chain M residue 359 SER Chi-restraints excluded: chain M residue 361 ILE Chi-restraints excluded: chain N residue 87 CYS Chi-restraints excluded: chain N residue 146 THR Chi-restraints excluded: chain N residue 182 CYS Chi-restraints excluded: chain N residue 198 SER Chi-restraints excluded: chain N residue 229 CYS Chi-restraints excluded: chain N residue 307 VAL Chi-restraints excluded: chain N residue 337 CYS Chi-restraints excluded: chain N residue 338 GLU Chi-restraints excluded: chain N residue 359 SER Chi-restraints excluded: chain N residue 361 ILE Chi-restraints excluded: chain N residue 371 LYS Chi-restraints excluded: chain W residue 87 CYS Chi-restraints excluded: chain W residue 146 THR Chi-restraints excluded: chain W residue 182 CYS Chi-restraints excluded: chain W residue 198 SER Chi-restraints excluded: chain W residue 229 CYS Chi-restraints excluded: chain W residue 307 VAL Chi-restraints excluded: chain W residue 337 CYS Chi-restraints excluded: chain W residue 338 GLU Chi-restraints excluded: chain W residue 359 SER Chi-restraints excluded: chain W residue 361 ILE Chi-restraints excluded: chain W residue 371 LYS Chi-restraints excluded: chain A residue 11 VAL Chi-restraints excluded: chain A residue 17 SER Chi-restraints excluded: chain A residue 87 THR Chi-restraints excluded: chain A residue 100 ASP Chi-restraints excluded: chain A residue 100 PHE Chi-restraints excluded: chain A residue 100 ASP Chi-restraints excluded: chain A residue 100 SER Chi-restraints excluded: chain A residue 159 LEU Chi-restraints excluded: chain A residue 184 VAL Chi-restraints excluded: chain C residue 11 VAL Chi-restraints excluded: chain C residue 17 SER Chi-restraints excluded: chain C residue 25 SER Chi-restraints excluded: chain C residue 87 THR Chi-restraints excluded: chain C residue 100 ASP Chi-restraints excluded: chain C residue 100 SER Chi-restraints excluded: chain C residue 184 VAL Chi-restraints excluded: chain D residue 11 VAL Chi-restraints excluded: chain D residue 17 SER Chi-restraints excluded: chain D residue 87 THR Chi-restraints excluded: chain D residue 100 ASP Chi-restraints excluded: chain D residue 100 SER Chi-restraints excluded: chain H residue 11 VAL Chi-restraints excluded: chain H residue 17 SER Chi-restraints excluded: chain H residue 87 THR Chi-restraints excluded: chain H residue 100 ASP Chi-restraints excluded: chain H residue 100 SER Chi-restraints excluded: chain H residue 184 VAL Chi-restraints excluded: chain B residue 30 SER Chi-restraints excluded: chain B residue 76 SER Chi-restraints excluded: chain B residue 79 GLU Chi-restraints excluded: chain B residue 174 SER Chi-restraints excluded: chain B residue 182 SER Chi-restraints excluded: chain B residue 202 SER Chi-restraints excluded: chain B residue 206 THR Chi-restraints excluded: chain E residue 30 SER Chi-restraints excluded: chain E residue 76 SER Chi-restraints excluded: chain E residue 174 SER Chi-restraints excluded: chain E residue 182 SER Chi-restraints excluded: chain E residue 202 SER Chi-restraints excluded: chain G residue 30 SER Chi-restraints excluded: chain G residue 76 SER Chi-restraints excluded: chain G residue 202 SER Chi-restraints excluded: chain L residue 30 SER Chi-restraints excluded: chain L residue 76 SER Chi-restraints excluded: chain L residue 140 TYR Chi-restraints excluded: chain L residue 199 GLN Chi-restraints excluded: chain L residue 202 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 316 random chunks: chunk 121 optimal weight: 0.9980 chunk 60 optimal weight: 2.9990 chunk 176 optimal weight: 0.9980 chunk 197 optimal weight: 6.9990 chunk 257 optimal weight: 3.9990 chunk 296 optimal weight: 6.9990 chunk 290 optimal weight: 20.0000 chunk 34 optimal weight: 0.9980 chunk 235 optimal weight: 4.9990 chunk 48 optimal weight: 0.9980 chunk 183 optimal weight: 10.0000 overall best weight: 1.3982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: I 101 HIS M 101 HIS W 101 HIS ** B 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 198 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 27 GLN ** E 124 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 155 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 166 GLN ** G 155 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3912 r_free = 0.3912 target = 0.144374 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3116 r_free = 0.3116 target = 0.084328 restraints weight = 36462.583| |-----------------------------------------------------------------------------| r_work (start): 0.3020 rms_B_bonded: 2.35 r_work: 0.2891 rms_B_bonded: 2.45 restraints_weight: 0.5000 r_work: 0.2758 rms_B_bonded: 3.81 restraints_weight: 0.2500 r_work (final): 0.2758 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2748 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2748 r_free = 0.2748 target_work(ls_wunit_k1) = 0.064 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2748 r_free = 0.2748 target_work(ls_wunit_k1) = 0.064 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| r_final: 0.2748 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8361 moved from start: 0.3476 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 25420 Z= 0.132 Angle : 0.597 13.111 34486 Z= 0.308 Chirality : 0.044 0.182 3808 Planarity : 0.004 0.049 4380 Dihedral : 5.287 38.198 3708 Min Nonbonded Distance : 2.334 Molprobity Statistics. All-atom Clashscore : 6.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.10 % Favored : 95.90 % Rotamer: Outliers : 3.47 % Allowed : 24.52 % Favored : 72.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.63 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.72 (0.14), residues: 3148 helix: -4.40 (0.19), residues: 56 sheet: -0.33 (0.14), residues: 1296 loop : -1.70 (0.13), residues: 1796 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG B 108 TYR 0.024 0.002 TYR G 173 PHE 0.030 0.002 PHE D 100C TRP 0.019 0.001 TRP E 148 HIS 0.009 0.001 HIS W 101 Details of bonding type rmsd covalent geometry : bond 0.00310 (25376) covalent geometry : angle 0.59399 (34384) SS BOND : bond 0.00386 ( 32) SS BOND : angle 1.25853 ( 66) hydrogen bonds : bond 0.03009 ( 706) hydrogen bonds : angle 4.88768 ( 1932) link_BETA1-4 : bond 0.00436 ( 8) link_BETA1-4 : angle 1.44223 ( 24) link_NAG-ASN : bond 0.00061 ( 4) link_NAG-ASN : angle 0.94768 ( 12) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6296 Ramachandran restraints generated. 3148 Oldfield, 0 Emsley, 3148 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6296 Ramachandran restraints generated. 3148 Oldfield, 0 Emsley, 3148 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 382 residues out of total 2708 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 94 poor density : 288 time to evaluate : 0.698 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: I 338 GLU cc_start: 0.8328 (OUTLIER) cc_final: 0.8050 (mp0) REVERT: I 419 LYS cc_start: 0.9141 (mttt) cc_final: 0.8912 (mttm) REVERT: M 338 GLU cc_start: 0.8328 (OUTLIER) cc_final: 0.8070 (mp0) REVERT: M 419 LYS cc_start: 0.9142 (mttt) cc_final: 0.8912 (mttm) REVERT: M 429 MET cc_start: 0.9410 (mtp) cc_final: 0.9193 (mtm) REVERT: N 338 GLU cc_start: 0.8332 (OUTLIER) cc_final: 0.8040 (mp0) REVERT: N 371 LYS cc_start: 0.9247 (OUTLIER) cc_final: 0.8822 (ptpp) REVERT: N 419 LYS cc_start: 0.9154 (mttt) cc_final: 0.8930 (mttm) REVERT: W 338 GLU cc_start: 0.8350 (OUTLIER) cc_final: 0.8047 (mp0) REVERT: W 371 LYS cc_start: 0.9236 (OUTLIER) cc_final: 0.8853 (ptpp) REVERT: W 419 LYS cc_start: 0.9140 (mttt) cc_final: 0.8910 (mttm) REVERT: W 429 MET cc_start: 0.9382 (mtp) cc_final: 0.9125 (mtm) REVERT: A 72 ASP cc_start: 0.8322 (t70) cc_final: 0.7632 (t70) REVERT: A 100 PHE cc_start: 0.7785 (OUTLIER) cc_final: 0.7386 (p90) REVERT: A 123 PRO cc_start: 0.3671 (Cg_endo) cc_final: 0.3462 (Cg_exo) REVERT: C 30 ILE cc_start: 0.9027 (tt) cc_final: 0.8739 (tp) REVERT: C 72 ASP cc_start: 0.8250 (t70) cc_final: 0.7580 (t70) REVERT: D 72 ASP cc_start: 0.8276 (t70) cc_final: 0.7606 (t70) REVERT: D 145 TYR cc_start: 0.6991 (p90) cc_final: 0.6281 (p90) REVERT: H 30 ILE cc_start: 0.9037 (tt) cc_final: 0.8749 (tp) REVERT: H 72 ASP cc_start: 0.8290 (t70) cc_final: 0.7608 (t70) REVERT: H 80 MET cc_start: 0.8326 (OUTLIER) cc_final: 0.8080 (ttp) REVERT: B 142 ARG cc_start: 0.8436 (tpp80) cc_final: 0.8149 (tpp80) REVERT: E 42 GLN cc_start: 0.7564 (mp10) cc_final: 0.7284 (mp10) REVERT: G 108 ARG cc_start: 0.7851 (ptm160) cc_final: 0.7647 (ptt90) REVERT: L 108 ARG cc_start: 0.7793 (ptt90) cc_final: 0.7557 (ptt90) REVERT: L 201 LEU cc_start: 0.6498 (OUTLIER) cc_final: 0.6263 (pp) outliers start: 94 outliers final: 63 residues processed: 374 average time/residue: 0.6485 time to fit residues: 277.6236 Evaluate side-chains 353 residues out of total 2708 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 281 time to evaluate : 0.749 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain I residue 87 CYS Chi-restraints excluded: chain I residue 182 CYS Chi-restraints excluded: chain I residue 198 SER Chi-restraints excluded: chain I residue 229 CYS Chi-restraints excluded: chain I residue 338 GLU Chi-restraints excluded: chain I residue 359 SER Chi-restraints excluded: chain M residue 87 CYS Chi-restraints excluded: chain M residue 146 THR Chi-restraints excluded: chain M residue 182 CYS Chi-restraints excluded: chain M residue 198 SER Chi-restraints excluded: chain M residue 229 CYS Chi-restraints excluded: chain M residue 337 CYS Chi-restraints excluded: chain M residue 338 GLU Chi-restraints excluded: chain M residue 359 SER Chi-restraints excluded: chain N residue 87 CYS Chi-restraints excluded: chain N residue 182 CYS Chi-restraints excluded: chain N residue 198 SER Chi-restraints excluded: chain N residue 229 CYS Chi-restraints excluded: chain N residue 337 CYS Chi-restraints excluded: chain N residue 338 GLU Chi-restraints excluded: chain N residue 359 SER Chi-restraints excluded: chain N residue 371 LYS Chi-restraints excluded: chain W residue 87 CYS Chi-restraints excluded: chain W residue 182 CYS Chi-restraints excluded: chain W residue 198 SER Chi-restraints excluded: chain W residue 229 CYS Chi-restraints excluded: chain W residue 337 CYS Chi-restraints excluded: chain W residue 338 GLU Chi-restraints excluded: chain W residue 359 SER Chi-restraints excluded: chain W residue 371 LYS Chi-restraints excluded: chain A residue 11 VAL Chi-restraints excluded: chain A residue 17 SER Chi-restraints excluded: chain A residue 87 THR Chi-restraints excluded: chain A residue 100 PHE Chi-restraints excluded: chain A residue 100 ASP Chi-restraints excluded: chain A residue 100 SER Chi-restraints excluded: chain C residue 17 SER Chi-restraints excluded: chain C residue 25 SER Chi-restraints excluded: chain C residue 87 THR Chi-restraints excluded: chain C residue 100 ASP Chi-restraints excluded: chain C residue 100 SER Chi-restraints excluded: chain D residue 17 SER Chi-restraints excluded: chain D residue 87 THR Chi-restraints excluded: chain D residue 100 ASP Chi-restraints excluded: chain D residue 100 SER Chi-restraints excluded: chain D residue 100 SER Chi-restraints excluded: chain H residue 17 SER Chi-restraints excluded: chain H residue 80 MET Chi-restraints excluded: chain H residue 87 THR Chi-restraints excluded: chain H residue 100 ASP Chi-restraints excluded: chain H residue 100 SER Chi-restraints excluded: chain H residue 100 SER Chi-restraints excluded: chain H residue 184 VAL Chi-restraints excluded: chain B residue 30 SER Chi-restraints excluded: chain B residue 76 SER Chi-restraints excluded: chain B residue 174 SER Chi-restraints excluded: chain B residue 202 SER Chi-restraints excluded: chain B residue 206 THR Chi-restraints excluded: chain E residue 27 GLN Chi-restraints excluded: chain E residue 30 SER Chi-restraints excluded: chain E residue 76 SER Chi-restraints excluded: chain E residue 174 SER Chi-restraints excluded: chain E residue 182 SER Chi-restraints excluded: chain E residue 198 HIS Chi-restraints excluded: chain E residue 202 SER Chi-restraints excluded: chain G residue 30 SER Chi-restraints excluded: chain G residue 201 LEU Chi-restraints excluded: chain G residue 202 SER Chi-restraints excluded: chain L residue 30 SER Chi-restraints excluded: chain L residue 76 SER Chi-restraints excluded: chain L residue 201 LEU Chi-restraints excluded: chain L residue 202 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 316 random chunks: chunk 190 optimal weight: 8.9990 chunk 26 optimal weight: 4.9990 chunk 235 optimal weight: 0.9980 chunk 91 optimal weight: 3.9990 chunk 121 optimal weight: 4.9990 chunk 139 optimal weight: 6.9990 chunk 94 optimal weight: 1.9990 chunk 294 optimal weight: 7.9990 chunk 137 optimal weight: 2.9990 chunk 43 optimal weight: 1.9990 chunk 175 optimal weight: 5.9990 overall best weight: 2.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: I 101 HIS M 101 HIS N 101 HIS W 101 HIS B 6 GLN E 6 GLN E 27 GLN ** E 124 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 155 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 166 GLN ** G 155 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 6 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3899 r_free = 0.3899 target = 0.143316 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3085 r_free = 0.3085 target = 0.082521 restraints weight = 36578.157| |-----------------------------------------------------------------------------| r_work (start): 0.2997 rms_B_bonded: 2.36 r_work: 0.2869 rms_B_bonded: 2.45 restraints_weight: 0.5000 r_work: 0.2735 rms_B_bonded: 3.80 restraints_weight: 0.2500 r_work (final): 0.2735 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2725 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2725 r_free = 0.2725 target_work(ls_wunit_k1) = 0.062 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2725 r_free = 0.2725 target_work(ls_wunit_k1) = 0.062 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| r_final: 0.2725 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8386 moved from start: 0.3555 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.057 25420 Z= 0.190 Angle : 0.625 10.628 34486 Z= 0.322 Chirality : 0.044 0.184 3808 Planarity : 0.005 0.080 4380 Dihedral : 5.312 36.874 3708 Min Nonbonded Distance : 2.289 Molprobity Statistics. All-atom Clashscore : 7.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.80 % Favored : 95.20 % Rotamer: Outliers : 3.58 % Allowed : 25.26 % Favored : 71.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.63 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.65 (0.14), residues: 3148 helix: -4.18 (0.26), residues: 56 sheet: -0.23 (0.14), residues: 1280 loop : -1.68 (0.13), residues: 1812 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG E 24 TYR 0.021 0.002 TYR E 140 PHE 0.027 0.002 PHE C 100C TRP 0.009 0.001 TRP C 47 HIS 0.009 0.001 HIS N 101 Details of bonding type rmsd covalent geometry : bond 0.00452 (25376) covalent geometry : angle 0.62038 (34384) SS BOND : bond 0.00285 ( 32) SS BOND : angle 1.69764 ( 66) hydrogen bonds : bond 0.03203 ( 706) hydrogen bonds : angle 4.90641 ( 1932) link_BETA1-4 : bond 0.00396 ( 8) link_BETA1-4 : angle 1.51186 ( 24) link_NAG-ASN : bond 0.00228 ( 4) link_NAG-ASN : angle 1.05335 ( 12) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6296 Ramachandran restraints generated. 3148 Oldfield, 0 Emsley, 3148 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6296 Ramachandran restraints generated. 3148 Oldfield, 0 Emsley, 3148 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 383 residues out of total 2708 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 97 poor density : 286 time to evaluate : 0.897 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: I 338 GLU cc_start: 0.8353 (OUTLIER) cc_final: 0.8063 (mp0) REVERT: I 419 LYS cc_start: 0.9071 (OUTLIER) cc_final: 0.8830 (mttm) REVERT: M 338 GLU cc_start: 0.8360 (OUTLIER) cc_final: 0.8100 (mp0) REVERT: M 419 LYS cc_start: 0.9075 (mttt) cc_final: 0.8829 (mttm) REVERT: N 102 ARG cc_start: 0.6593 (ttm170) cc_final: 0.6378 (ttp-110) REVERT: N 338 GLU cc_start: 0.8350 (OUTLIER) cc_final: 0.8058 (mp0) REVERT: N 371 LYS cc_start: 0.9270 (OUTLIER) cc_final: 0.8838 (ptpp) REVERT: N 419 LYS cc_start: 0.9085 (mttt) cc_final: 0.8854 (mttm) REVERT: W 102 ARG cc_start: 0.6518 (ttm170) cc_final: 0.6302 (ttp-110) REVERT: W 338 GLU cc_start: 0.8361 (OUTLIER) cc_final: 0.8068 (mp0) REVERT: W 371 LYS cc_start: 0.9274 (OUTLIER) cc_final: 0.8877 (ptpp) REVERT: W 419 LYS cc_start: 0.9078 (mttt) cc_final: 0.8834 (mttm) REVERT: W 429 MET cc_start: 0.9408 (mtp) cc_final: 0.9154 (mtm) REVERT: A 72 ASP cc_start: 0.8359 (t70) cc_final: 0.7681 (t70) REVERT: A 82 ARG cc_start: 0.7190 (mtm-85) cc_final: 0.6987 (mtm180) REVERT: A 100 PHE cc_start: 0.7946 (OUTLIER) cc_final: 0.7483 (p90) REVERT: C 30 ILE cc_start: 0.9033 (tt) cc_final: 0.8731 (tp) REVERT: C 72 ASP cc_start: 0.8324 (t70) cc_final: 0.7640 (t70) REVERT: C 100 PHE cc_start: 0.7782 (OUTLIER) cc_final: 0.7503 (p90) REVERT: D 72 ASP cc_start: 0.8340 (t70) cc_final: 0.7652 (t70) REVERT: D 100 PHE cc_start: 0.7771 (OUTLIER) cc_final: 0.7418 (p90) REVERT: H 30 ILE cc_start: 0.9041 (tt) cc_final: 0.8742 (tp) REVERT: H 72 ASP cc_start: 0.8355 (t70) cc_final: 0.7661 (t70) REVERT: H 100 PHE cc_start: 0.7778 (OUTLIER) cc_final: 0.7493 (p90) REVERT: B 142 ARG cc_start: 0.8402 (tpp80) cc_final: 0.8066 (tpp80) REVERT: E 42 GLN cc_start: 0.7515 (mp10) cc_final: 0.7232 (mp10) REVERT: E 108 ARG cc_start: 0.7989 (ptt90) cc_final: 0.7746 (ptt90) REVERT: E 116 PHE cc_start: 0.5951 (m-80) cc_final: 0.5366 (m-10) REVERT: L 201 LEU cc_start: 0.6495 (OUTLIER) cc_final: 0.6258 (pp) outliers start: 97 outliers final: 71 residues processed: 372 average time/residue: 0.6326 time to fit residues: 270.0257 Evaluate side-chains 361 residues out of total 2708 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 83 poor density : 278 time to evaluate : 0.956 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain I residue 87 CYS Chi-restraints excluded: chain I residue 102 ARG Chi-restraints excluded: chain I residue 182 CYS Chi-restraints excluded: chain I residue 198 SER Chi-restraints excluded: chain I residue 229 CYS Chi-restraints excluded: chain I residue 337 CYS Chi-restraints excluded: chain I residue 338 GLU Chi-restraints excluded: chain I residue 359 SER Chi-restraints excluded: chain I residue 361 ILE Chi-restraints excluded: chain I residue 419 LYS Chi-restraints excluded: chain M residue 87 CYS Chi-restraints excluded: chain M residue 102 ARG Chi-restraints excluded: chain M residue 146 THR Chi-restraints excluded: chain M residue 182 CYS Chi-restraints excluded: chain M residue 198 SER Chi-restraints excluded: chain M residue 229 CYS Chi-restraints excluded: chain M residue 337 CYS Chi-restraints excluded: chain M residue 338 GLU Chi-restraints excluded: chain M residue 359 SER Chi-restraints excluded: chain M residue 361 ILE Chi-restraints excluded: chain N residue 87 CYS Chi-restraints excluded: chain N residue 182 CYS Chi-restraints excluded: chain N residue 198 SER Chi-restraints excluded: chain N residue 229 CYS Chi-restraints excluded: chain N residue 337 CYS Chi-restraints excluded: chain N residue 338 GLU Chi-restraints excluded: chain N residue 359 SER Chi-restraints excluded: chain N residue 361 ILE Chi-restraints excluded: chain N residue 371 LYS Chi-restraints excluded: chain W residue 87 CYS Chi-restraints excluded: chain W residue 182 CYS Chi-restraints excluded: chain W residue 198 SER Chi-restraints excluded: chain W residue 229 CYS Chi-restraints excluded: chain W residue 337 CYS Chi-restraints excluded: chain W residue 338 GLU Chi-restraints excluded: chain W residue 359 SER Chi-restraints excluded: chain W residue 361 ILE Chi-restraints excluded: chain W residue 371 LYS Chi-restraints excluded: chain A residue 11 VAL Chi-restraints excluded: chain A residue 17 SER Chi-restraints excluded: chain A residue 87 THR Chi-restraints excluded: chain A residue 100 PHE Chi-restraints excluded: chain A residue 100 ASP Chi-restraints excluded: chain A residue 100 SER Chi-restraints excluded: chain C residue 11 VAL Chi-restraints excluded: chain C residue 17 SER Chi-restraints excluded: chain C residue 87 THR Chi-restraints excluded: chain C residue 100 PHE Chi-restraints excluded: chain C residue 100 ASP Chi-restraints excluded: chain C residue 100 SER Chi-restraints excluded: chain D residue 11 VAL Chi-restraints excluded: chain D residue 17 SER Chi-restraints excluded: chain D residue 84 SER Chi-restraints excluded: chain D residue 87 THR Chi-restraints excluded: chain D residue 100 PHE Chi-restraints excluded: chain D residue 100 ASP Chi-restraints excluded: chain D residue 100 SER Chi-restraints excluded: chain D residue 100 SER Chi-restraints excluded: chain H residue 17 SER Chi-restraints excluded: chain H residue 87 THR Chi-restraints excluded: chain H residue 100 PHE Chi-restraints excluded: chain H residue 100 ASP Chi-restraints excluded: chain H residue 100 SER Chi-restraints excluded: chain H residue 100 SER Chi-restraints excluded: chain B residue 30 SER Chi-restraints excluded: chain B residue 76 SER Chi-restraints excluded: chain B residue 174 SER Chi-restraints excluded: chain B residue 182 SER Chi-restraints excluded: chain B residue 202 SER Chi-restraints excluded: chain B residue 206 THR Chi-restraints excluded: chain E residue 30 SER Chi-restraints excluded: chain E residue 76 SER Chi-restraints excluded: chain E residue 174 SER Chi-restraints excluded: chain E residue 182 SER Chi-restraints excluded: chain E residue 202 SER Chi-restraints excluded: chain G residue 30 SER Chi-restraints excluded: chain G residue 76 SER Chi-restraints excluded: chain G residue 201 LEU Chi-restraints excluded: chain G residue 202 SER Chi-restraints excluded: chain L residue 30 SER Chi-restraints excluded: chain L residue 76 SER Chi-restraints excluded: chain L residue 201 LEU Chi-restraints excluded: chain L residue 202 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 316 random chunks: chunk 24 optimal weight: 3.9990 chunk 147 optimal weight: 8.9990 chunk 98 optimal weight: 1.9990 chunk 53 optimal weight: 4.9990 chunk 51 optimal weight: 0.7980 chunk 22 optimal weight: 4.9990 chunk 65 optimal weight: 5.9990 chunk 290 optimal weight: 4.9990 chunk 226 optimal weight: 5.9990 chunk 300 optimal weight: 0.8980 chunk 294 optimal weight: 7.9990 overall best weight: 2.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: I 101 HIS M 101 HIS N 101 HIS W 101 HIS E 27 GLN ** E 124 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 155 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 155 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3916 r_free = 0.3916 target = 0.143968 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 76)----------------| | r_work = 0.3118 r_free = 0.3118 target = 0.083630 restraints weight = 35923.863| |-----------------------------------------------------------------------------| r_work (start): 0.3019 rms_B_bonded: 2.31 r_work: 0.2880 rms_B_bonded: 2.41 restraints_weight: 0.5000 r_work: 0.2745 rms_B_bonded: 3.73 restraints_weight: 0.2500 r_work (final): 0.2745 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2745 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2745 r_free = 0.2745 target_work(ls_wunit_k1) = 0.063 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2745 r_free = 0.2745 target_work(ls_wunit_k1) = 0.063 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| r_final: 0.2745 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8443 moved from start: 0.3642 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.057 25420 Z= 0.195 Angle : 0.626 10.595 34486 Z= 0.322 Chirality : 0.045 0.175 3808 Planarity : 0.005 0.079 4380 Dihedral : 5.314 36.753 3708 Min Nonbonded Distance : 2.296 Molprobity Statistics. All-atom Clashscore : 7.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.61 % Favored : 95.39 % Rotamer: Outliers : 3.32 % Allowed : 25.30 % Favored : 71.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.63 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.61 (0.14), residues: 3148 helix: -4.01 (0.32), residues: 56 sheet: -0.23 (0.14), residues: 1296 loop : -1.65 (0.13), residues: 1796 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG L 142 TYR 0.018 0.002 TYR G 186 PHE 0.029 0.002 PHE H 100C TRP 0.008 0.001 TRP D 47 HIS 0.009 0.001 HIS N 101 Details of bonding type rmsd covalent geometry : bond 0.00467 (25376) covalent geometry : angle 0.62089 (34384) SS BOND : bond 0.00307 ( 32) SS BOND : angle 1.69380 ( 66) hydrogen bonds : bond 0.03189 ( 706) hydrogen bonds : angle 4.87760 ( 1932) link_BETA1-4 : bond 0.00420 ( 8) link_BETA1-4 : angle 1.48418 ( 24) link_NAG-ASN : bond 0.00216 ( 4) link_NAG-ASN : angle 1.03526 ( 12) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6296 Ramachandran restraints generated. 3148 Oldfield, 0 Emsley, 3148 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6296 Ramachandran restraints generated. 3148 Oldfield, 0 Emsley, 3148 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 372 residues out of total 2708 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 90 poor density : 282 time to evaluate : 0.890 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: I 338 GLU cc_start: 0.8354 (OUTLIER) cc_final: 0.7993 (mp0) REVERT: I 419 LYS cc_start: 0.9187 (OUTLIER) cc_final: 0.8955 (mttm) REVERT: M 338 GLU cc_start: 0.8388 (OUTLIER) cc_final: 0.8117 (mp0) REVERT: M 419 LYS cc_start: 0.9179 (mttt) cc_final: 0.8943 (mttm) REVERT: N 338 GLU cc_start: 0.8369 (OUTLIER) cc_final: 0.8077 (mp0) REVERT: N 371 LYS cc_start: 0.9267 (OUTLIER) cc_final: 0.8803 (ptpp) REVERT: N 419 LYS cc_start: 0.9184 (mttt) cc_final: 0.8958 (mttm) REVERT: W 102 ARG cc_start: 0.6633 (ttm170) cc_final: 0.6403 (ttp-110) REVERT: W 338 GLU cc_start: 0.8391 (OUTLIER) cc_final: 0.8098 (mp0) REVERT: W 371 LYS cc_start: 0.9267 (OUTLIER) cc_final: 0.8829 (ptpp) REVERT: W 419 LYS cc_start: 0.9168 (mttt) cc_final: 0.8931 (mttm) REVERT: W 429 MET cc_start: 0.9398 (mtp) cc_final: 0.9149 (mtm) REVERT: A 72 ASP cc_start: 0.8424 (t70) cc_final: 0.7760 (t70) REVERT: A 100 PHE cc_start: 0.7949 (OUTLIER) cc_final: 0.7658 (p90) REVERT: C 30 ILE cc_start: 0.9044 (tt) cc_final: 0.8751 (tp) REVERT: C 72 ASP cc_start: 0.8397 (t70) cc_final: 0.7714 (t70) REVERT: C 100 PHE cc_start: 0.7791 (OUTLIER) cc_final: 0.7526 (p90) REVERT: D 72 ASP cc_start: 0.8396 (t70) cc_final: 0.7744 (t70) REVERT: D 100 PHE cc_start: 0.7788 (OUTLIER) cc_final: 0.7524 (p90) REVERT: D 123 PRO cc_start: 0.3213 (Cg_endo) cc_final: 0.3002 (Cg_exo) REVERT: H 30 ILE cc_start: 0.9053 (tt) cc_final: 0.8767 (tp) REVERT: H 72 ASP cc_start: 0.8420 (t70) cc_final: 0.7759 (t70) REVERT: H 100 PHE cc_start: 0.7789 (OUTLIER) cc_final: 0.7520 (p90) REVERT: B 142 ARG cc_start: 0.8384 (tpp80) cc_final: 0.8106 (tpp80) REVERT: B 201 LEU cc_start: 0.6554 (OUTLIER) cc_final: 0.6255 (pp) REVERT: E 42 GLN cc_start: 0.7567 (mp10) cc_final: 0.7271 (mp10) REVERT: E 108 ARG cc_start: 0.7915 (ptt90) cc_final: 0.7702 (ptt90) REVERT: L 201 LEU cc_start: 0.6514 (OUTLIER) cc_final: 0.6261 (pp) outliers start: 90 outliers final: 67 residues processed: 361 average time/residue: 0.6442 time to fit residues: 266.6854 Evaluate side-chains 362 residues out of total 2708 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 80 poor density : 282 time to evaluate : 0.914 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain I residue 87 CYS Chi-restraints excluded: chain I residue 182 CYS Chi-restraints excluded: chain I residue 198 SER Chi-restraints excluded: chain I residue 229 CYS Chi-restraints excluded: chain I residue 338 GLU Chi-restraints excluded: chain I residue 359 SER Chi-restraints excluded: chain I residue 361 ILE Chi-restraints excluded: chain I residue 419 LYS Chi-restraints excluded: chain M residue 87 CYS Chi-restraints excluded: chain M residue 146 THR Chi-restraints excluded: chain M residue 182 CYS Chi-restraints excluded: chain M residue 198 SER Chi-restraints excluded: chain M residue 229 CYS Chi-restraints excluded: chain M residue 338 GLU Chi-restraints excluded: chain M residue 359 SER Chi-restraints excluded: chain M residue 361 ILE Chi-restraints excluded: chain N residue 87 CYS Chi-restraints excluded: chain N residue 182 CYS Chi-restraints excluded: chain N residue 198 SER Chi-restraints excluded: chain N residue 229 CYS Chi-restraints excluded: chain N residue 337 CYS Chi-restraints excluded: chain N residue 338 GLU Chi-restraints excluded: chain N residue 359 SER Chi-restraints excluded: chain N residue 361 ILE Chi-restraints excluded: chain N residue 371 LYS Chi-restraints excluded: chain W residue 87 CYS Chi-restraints excluded: chain W residue 182 CYS Chi-restraints excluded: chain W residue 198 SER Chi-restraints excluded: chain W residue 229 CYS Chi-restraints excluded: chain W residue 337 CYS Chi-restraints excluded: chain W residue 338 GLU Chi-restraints excluded: chain W residue 359 SER Chi-restraints excluded: chain W residue 361 ILE Chi-restraints excluded: chain W residue 371 LYS Chi-restraints excluded: chain A residue 11 VAL Chi-restraints excluded: chain A residue 17 SER Chi-restraints excluded: chain A residue 87 THR Chi-restraints excluded: chain A residue 100 PHE Chi-restraints excluded: chain A residue 100 ASP Chi-restraints excluded: chain A residue 100 SER Chi-restraints excluded: chain C residue 11 VAL Chi-restraints excluded: chain C residue 17 SER Chi-restraints excluded: chain C residue 84 SER Chi-restraints excluded: chain C residue 87 THR Chi-restraints excluded: chain C residue 100 PHE Chi-restraints excluded: chain C residue 100 ASP Chi-restraints excluded: chain C residue 100 SER Chi-restraints excluded: chain D residue 11 VAL Chi-restraints excluded: chain D residue 17 SER Chi-restraints excluded: chain D residue 84 SER Chi-restraints excluded: chain D residue 87 THR Chi-restraints excluded: chain D residue 100 PHE Chi-restraints excluded: chain D residue 100 ASP Chi-restraints excluded: chain D residue 100 SER Chi-restraints excluded: chain D residue 100 SER Chi-restraints excluded: chain H residue 17 SER Chi-restraints excluded: chain H residue 87 THR Chi-restraints excluded: chain H residue 100 PHE Chi-restraints excluded: chain H residue 100 ASP Chi-restraints excluded: chain H residue 100 SER Chi-restraints excluded: chain H residue 100 SER Chi-restraints excluded: chain B residue 30 SER Chi-restraints excluded: chain B residue 76 SER Chi-restraints excluded: chain B residue 174 SER Chi-restraints excluded: chain B residue 201 LEU Chi-restraints excluded: chain B residue 202 SER Chi-restraints excluded: chain B residue 206 THR Chi-restraints excluded: chain E residue 27 GLN Chi-restraints excluded: chain E residue 30 SER Chi-restraints excluded: chain E residue 76 SER Chi-restraints excluded: chain E residue 174 SER Chi-restraints excluded: chain E residue 182 SER Chi-restraints excluded: chain E residue 202 SER Chi-restraints excluded: chain G residue 30 SER Chi-restraints excluded: chain G residue 76 SER Chi-restraints excluded: chain G residue 202 SER Chi-restraints excluded: chain L residue 30 SER Chi-restraints excluded: chain L residue 76 SER Chi-restraints excluded: chain L residue 201 LEU Chi-restraints excluded: chain L residue 202 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 316 random chunks: chunk 208 optimal weight: 50.0000 chunk 163 optimal weight: 20.0000 chunk 292 optimal weight: 4.9990 chunk 224 optimal weight: 30.0000 chunk 17 optimal weight: 2.9990 chunk 186 optimal weight: 30.0000 chunk 211 optimal weight: 0.9990 chunk 104 optimal weight: 0.9990 chunk 204 optimal weight: 0.1980 chunk 306 optimal weight: 10.0000 chunk 184 optimal weight: 8.9990 overall best weight: 2.0388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: N 101 HIS W 101 HIS E 27 GLN ** E 124 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 155 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 155 GLN ** 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 = 0.3904 r_free = 0.3904 target = 0.143723 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.3101 r_free = 0.3101 target = 0.083210 restraints weight = 36193.102| |-----------------------------------------------------------------------------| r_work (start): 0.3002 rms_B_bonded: 2.35 r_work: 0.2869 rms_B_bonded: 2.44 restraints_weight: 0.5000 r_work: 0.2737 rms_B_bonded: 3.78 restraints_weight: 0.2500 r_work (final): 0.2737 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2731 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2731 r_free = 0.2731 target_work(ls_wunit_k1) = 0.063 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2731 r_free = 0.2731 target_work(ls_wunit_k1) = 0.063 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| r_final: 0.2731 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8410 moved from start: 0.3707 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 25420 Z= 0.167 Angle : 0.622 14.097 34486 Z= 0.319 Chirality : 0.044 0.173 3808 Planarity : 0.005 0.072 4380 Dihedral : 5.230 37.289 3708 Min Nonbonded Distance : 2.306 Molprobity Statistics. All-atom Clashscore : 7.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.35 % Favored : 95.65 % Rotamer: Outliers : 3.43 % Allowed : 25.30 % Favored : 71.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.63 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.55 (0.14), residues: 3148 helix: -3.95 (0.33), residues: 56 sheet: -0.13 (0.14), residues: 1288 loop : -1.66 (0.13), residues: 1804 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG L 142 TYR 0.024 0.001 TYR E 140 PHE 0.028 0.002 PHE G 116 TRP 0.008 0.001 TRP D 47 HIS 0.009 0.001 HIS N 101 Details of bonding type rmsd covalent geometry : bond 0.00399 (25376) covalent geometry : angle 0.61739 (34384) SS BOND : bond 0.00233 ( 32) SS BOND : angle 1.55530 ( 66) hydrogen bonds : bond 0.03059 ( 706) hydrogen bonds : angle 4.83176 ( 1932) link_BETA1-4 : bond 0.00434 ( 8) link_BETA1-4 : angle 1.45608 ( 24) link_NAG-ASN : bond 0.00173 ( 4) link_NAG-ASN : angle 1.01822 ( 12) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 13015.86 seconds wall clock time: 221 minutes 5.38 seconds (13265.38 seconds total)