Starting phenix.real_space_refine on Tue Oct 27 11:52:21 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6v4o_21043/10_2026/6v4o_21043_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/6v4o_21043/10_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 { model { file = "/net/cci-nas-00/data/ceres_data/6v4o_21043/10_2026/6v4o_21043_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6v4o_21043/10_2026/6v4o_21043_neut.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/6v4o_21043/10_2026/6v4o_21043.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6v4o_21043/10_2026/6v4o_21043.map" } 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-2.3rc1-6221/lib/python3.11/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: 4.99, per 1000 atoms: 0.20 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=48, 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 87 " - pdb=" SG CYS M 420 " distance=2.03 Simple disulfide: pdb=" SG CYS M 122 " - pdb=" SG CYS M 127 " distance=2.03 Simple disulfide: pdb=" SG CYS M 182 " - pdb=" SG CYS M 229 " distance=2.03 Simple disulfide: pdb=" SG CYS M 231 " - pdb=" SG CYS M 236 " distance=2.03 Simple disulfide: pdb=" SG CYS M 277 " - pdb=" SG CYS M 291 " distance=2.02 Simple disulfide: pdb=" SG CYS M 279 " - pdb=" SG CYS M 289 " distance=2.03 Simple disulfide: pdb=" SG CYS M 318 " - pdb=" SG CYS M 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 87 " - pdb=" SG CYS N 420 " distance=2.03 Simple disulfide: pdb=" SG CYS N 122 " - pdb=" SG CYS N 127 " distance=2.03 Simple disulfide: pdb=" SG CYS N 182 " - pdb=" SG CYS N 229 " distance=2.03 Simple disulfide: pdb=" SG CYS N 231 " - pdb=" SG CYS N 236 " distance=2.03 Simple disulfide: pdb=" SG CYS N 277 " - pdb=" SG CYS N 291 " distance=2.02 Simple disulfide: pdb=" SG CYS N 279 " - pdb=" SG CYS N 289 " distance=2.02 Simple disulfide: pdb=" SG CYS N 318 " - pdb=" SG CYS N 337 " distance=2.03 Simple disulfide: pdb=" SG CYS N 424 " - pdb=" SG CYS N 447 " distance=2.03 Simple disulfide: pdb=" SG CYS W 87 " - pdb=" SG CYS W 420 " distance=2.03 Simple disulfide: pdb=" SG CYS W 122 " - pdb=" SG CYS W 127 " distance=2.03 Simple disulfide: pdb=" SG CYS W 182 " - pdb=" SG CYS W 229 " distance=2.03 Simple disulfide: pdb=" SG CYS W 231 " - pdb=" SG CYS W 236 " distance=2.03 Simple disulfide: pdb=" SG CYS W 277 " - pdb=" SG CYS W 291 " distance=2.02 Simple disulfide: pdb=" SG CYS W 279 " - pdb=" SG CYS W 289 " distance=2.03 Simple disulfide: pdb=" SG CYS W 318 " - pdb=" SG CYS W 337 " distance=2.03 Simple disulfide: pdb=" SG CYS W 424 " - pdb=" SG CYS W 447 " distance=2.03 Simple disulfide: pdb=" SG CYS A 22 " - pdb=" SG CYS A 92 " distance=2.04 Simple disulfide: pdb=" SG CYS A 140 " - pdb=" SG CYS A 196 " distance=2.03 Simple disulfide: pdb=" SG CYS C 22 " - pdb=" SG CYS C 92 " distance=2.04 Simple disulfide: pdb=" SG CYS C 140 " - pdb=" SG CYS C 196 " distance=2.03 Simple disulfide: pdb=" SG CYS D 22 " - pdb=" SG CYS D 92 " distance=2.04 Simple disulfide: pdb=" SG CYS D 140 " - pdb=" SG CYS D 196 " distance=2.03 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 92 " distance=2.04 Simple disulfide: pdb=" SG CYS H 140 " - pdb=" SG CYS H 196 " distance=2.03 Simple disulfide: pdb=" SG CYS B 23 " - pdb=" SG CYS B 88 " distance=2.03 Simple disulfide: pdb=" SG CYS B 134 " - pdb=" SG CYS B 194 " distance=2.03 Simple disulfide: pdb=" SG CYS E 23 " - pdb=" SG CYS E 88 " distance=2.03 Simple disulfide: pdb=" SG CYS E 134 " - pdb=" SG CYS E 194 " distance=2.03 Simple disulfide: pdb=" SG CYS G 23 " - pdb=" SG CYS G 88 " distance=2.03 Simple disulfide: pdb=" SG CYS G 134 " - pdb=" SG CYS G 194 " distance=2.03 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 88 " distance=2.03 Simple disulfide: pdb=" SG CYS L 134 " - pdb=" SG CYS L 194 " 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: 2.56 Conformation dependent library (CDL) restraints added in 1.0 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: 0.77 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: 5.13 Time building geometry restraints manager: 3.28 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: 14177 21.54 - 43.08: 951 43.08 - 64.63: 216 64.63 - 86.17: 40 86.17 - 107.71: 20 Dihedral angle restraints: 15404 sinusoidal: 6236 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 15401 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: 45 2.26 - 2.92: 11380 2.92 - 3.58: 32116 3.58 - 4.24: 58633 4.24 - 4.90: 99748 Nonbonded interactions: 201922 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 201917 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: 0.04 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: 1.330 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.030 Extract box with map and model: 0.480 Check model and map are aligned: 0.070 Set scattering table: 0.060 Process input model: 22.870 Find NCS groups from input model: 0.140 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:5.840 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 30.880 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8448 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 25436 Z= 0.463 Angle : 0.918 29.051 34516 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/Z covalent geometry : bond 0.01096 / 0.45 (25376) covalent geometry : angle 0.81251 / 0.46 (34384) SS BOND : bond 0.00411 / 0.26 ( 48) SS BOND : angle 1.92339 / 1.28 ( 96) hydrogen bonds : bond 0.19004 / 12.57 ( 706) hydrogen bonds : angle 8.43617 / 5.69 ( 1932) link_BETA1-4 : bond 0.12290 / 7.04 ( 8) link_BETA1-4 : angle 15.76358 / 10.18 ( 24) link_NAG-ASN : bond 0.00876 / 0.52 ( 4) link_NAG-ASN : angle 2.06429 / 0.88 ( 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 : 0.957 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: 0.7030 time to fit residues: 392.0812 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 : 1.052 ------------------------------------------------------------------------------- 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: [197, 215, 20, 132, 261, 248, 207, 155, 244, 183, 298] chunk 197 optimal weight: 1.9990 chunk 215 optimal weight: 3.9990 chunk 20 optimal weight: 1.9990 chunk 132 optimal weight: 1.9990 chunk 261 optimal weight: 3.9990 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: 1.5986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... I 329 ASN I 431 HIS 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 ** both conformations clash, **PLEASE CHECK MANUALLY** L 166 GLN ** L 198 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3948 r_free = 0.3948 target = 0.146921 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 67)----------------| | r_work = 0.3168 r_free = 0.3168 target = 0.087582 restraints weight = 36499.797| |-----------------------------------------------------------------------------| r_work (start): 0.3073 rms_B_bonded: 2.37 r_work: 0.2948 rms_B_bonded: 2.46 restraints_weight: 0.5000 r_work: 0.2812 rms_B_bonded: 3.86 restraints_weight: 0.2500 r_work (final): 0.2812 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2801 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2801 r_free = 0.2801 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 = 0.2800 r_free = 0.2800 target_work(ls_wunit_k1) = 0.066 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (6 function evaluations) r_final: 0.2800 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8581 moved from start: 0.1915 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 25436 Z= 0.166 Angle : 0.681 7.086 34516 Z= 0.356 Chirality : 0.048 0.259 3808 Planarity : 0.006 0.052 4380 Dihedral : 8.492 57.359 3748 Min Nonbonded Distance : 2.333 Molprobity Statistics. All-atom Clashscore : 6.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.46 % Favored : 94.54 % Rotamer: Outliers : 4.80 % Allowed : 17.65 % Favored : 77.55 % 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: -3.07 (0.13), residues: 3148 helix: -4.59 (0.17), residues: 32 sheet: -1.44 (0.14), residues: 1264 loop : -2.51 (0.12), residues: 1852 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG C 83 TYR 0.021 0.002 TYR G 186 PHE 0.021 0.002 PHE D 100C TRP 0.011 0.001 TRP N 408 HIS 0.012 0.001 HIS A 164 Details of bonding type rmsd/Z covalent geometry : bond 0.00377 / 0.17 (25376) covalent geometry : angle 0.67683 / 0.35 (34384) SS BOND : bond 0.00478 / 0.30 ( 48) SS BOND : angle 1.24118 / 0.89 ( 96) hydrogen bonds : bond 0.04057 / 2.68 ( 706) hydrogen bonds : angle 6.11899 / 4.15 ( 1932) link_BETA1-4 : bond 0.00579 / 0.33 ( 8) link_BETA1-4 : angle 2.08584 / 1.34 ( 24) link_NAG-ASN : bond 0.00154 / 0.09 ( 4) link_NAG-ASN : angle 1.09529 / 0.47 ( 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 469 residues out of total 2708 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 130 poor density : 339 time to evaluate : 1.011 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: 0.9308 (mmm) cc_final: 0.8896 (mmt) REVERT: I 390 ASP cc_start: 0.7340 (OUTLIER) cc_final: 0.6705 (m-30) REVERT: M 390 ASP cc_start: 0.7337 (OUTLIER) cc_final: 0.6703 (m-30) REVERT: N 384 ASP cc_start: 0.8498 (m-30) cc_final: 0.8216 (m-30) REVERT: N 390 ASP cc_start: 0.7314 (OUTLIER) cc_final: 0.6616 (m-30) REVERT: W 384 ASP cc_start: 0.8390 (m-30) cc_final: 0.8111 (m-30) REVERT: W 390 ASP cc_start: 0.7276 (OUTLIER) cc_final: 0.6612 (m-30) REVERT: A 72 ASP cc_start: 0.8057 (t70) cc_final: 0.7281 (t70) REVERT: A 100 TYR cc_start: 0.9033 (m-80) cc_final: 0.8772 (m-80) REVERT: A 145 TYR cc_start: 0.6978 (p90) cc_final: 0.6480 (p90) REVERT: A 176 TYR cc_start: 0.7190 (m-80) cc_final: 0.6963 (m-80) REVERT: C 30 ILE cc_start: 0.9035 (tt) cc_final: 0.8739 (tp) REVERT: C 72 ASP cc_start: 0.7664 (t70) cc_final: 0.6934 (t70) REVERT: C 176 TYR cc_start: 0.7085 (m-80) cc_final: 0.6841 (m-80) REVERT: D 30 ILE cc_start: 0.9116 (tt) cc_final: 0.8827 (tp) REVERT: D 72 ASP cc_start: 0.7777 (t70) cc_final: 0.7020 (t70) REVERT: D 100 TYR cc_start: 0.9104 (m-80) cc_final: 0.8826 (m-80) REVERT: D 145 TYR cc_start: 0.6894 (p90) cc_final: 0.6358 (p90) REVERT: D 176 TYR cc_start: 0.7363 (m-80) cc_final: 0.6895 (m-10) REVERT: H 30 ILE cc_start: 0.9021 (tt) cc_final: 0.8721 (tp) REVERT: H 72 ASP cc_start: 0.7771 (t70) cc_final: 0.7041 (t70) REVERT: H 81 ASP cc_start: 0.7985 (t70) cc_final: 0.7743 (t0) REVERT: H 100 TYR cc_start: 0.9122 (m-80) cc_final: 0.8846 (m-80) REVERT: H 145 TYR cc_start: 0.6647 (p90) cc_final: 0.6053 (p90) REVERT: H 176 TYR cc_start: 0.7339 (m-80) cc_final: 0.6848 (m-10) REVERT: B 108 ARG cc_start: 0.7541 (ptm160) cc_final: 0.7231 (ptm-80) REVERT: B 143 GLU cc_start: 0.8332 (OUTLIER) cc_final: 0.7995 (tm-30) REVERT: E 143 GLU cc_start: 0.8459 (OUTLIER) cc_final: 0.8233 (tm-30) REVERT: E 165 GLU cc_start: 0.8248 (tp30) cc_final: 0.7798 (mp0) REVERT: E 190 LYS cc_start: 0.8093 (mmmt) cc_final: 0.7714 (tptt) REVERT: E 201 LEU cc_start: 0.6439 (mm) cc_final: 0.6203 (pp) REVERT: G 108 ARG cc_start: 0.7758 (ptm160) cc_final: 0.6883 (ptm-80) REVERT: G 143 GLU cc_start: 0.8408 (OUTLIER) cc_final: 0.8159 (tm-30) REVERT: L 18 ARG cc_start: 0.8433 (OUTLIER) cc_final: 0.7421 (ttm110) REVERT: L 108 ARG cc_start: 0.7547 (ptm160) cc_final: 0.7219 (ptm-80) outliers start: 130 outliers final: 74 residues processed: 444 average time/residue: 0.5919 time to fit residues: 305.6091 Evaluate side-chains 400 residues out of total 2708 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 82 poor density : 318 time to evaluate : 0.946 ------------------------------------------------------------------------------- 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 318 CYS Chi-restraints excluded: chain N residue 337 CYS Chi-restraints excluded: chain N residue 357 MET Chi-restraints excluded: chain N residue 359 SER 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 318 CYS Chi-restraints excluded: chain W residue 337 CYS Chi-restraints excluded: chain W residue 357 MET Chi-restraints excluded: chain W residue 359 SER 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 100 ASP Chi-restraints excluded: chain A residue 138 LEU 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 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 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 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 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: [49, 58, 57, 310, 151, 95, 199, 280, 0, 110, 70] chunk 49 optimal weight: 4.9990 chunk 58 optimal weight: 6.9990 chunk 57 optimal weight: 2.9990 chunk 310 optimal weight: 1.9990 chunk 151 optimal weight: 10.0000 chunk 95 optimal weight: 2.9990 chunk 199 optimal weight: 7.9990 chunk 280 optimal weight: 8.9990 chunk 0 optimal weight: 8.9990 chunk 110 optimal weight: 4.9990 chunk 70 optimal weight: 2.9990 overall best weight: 3.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... I 183 HIS I 225 GLN M 183 HIS M 225 GLN M 329 ASN N 183 HIS N 225 GLN W 183 HIS W 225 GLN B 166 GLN ** G 155 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 166 GLN ** L 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 155 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 166 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3904 r_free = 0.3904 target = 0.143534 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3090 r_free = 0.3090 target = 0.083026 restraints weight = 36588.465| |-----------------------------------------------------------------------------| r_work (start): 0.2993 rms_B_bonded: 2.36 r_work: 0.2864 rms_B_bonded: 2.45 restraints_weight: 0.5000 r_work: 0.2728 rms_B_bonded: 3.83 restraints_weight: 0.2500 r_work (final): 0.2728 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2719 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2719 r_free = 0.2719 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 = 0.2718 r_free = 0.2718 target_work(ls_wunit_k1) = 0.062 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.2718 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8631 moved from start: 0.2485 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.043 25436 Z= 0.242 Angle : 0.661 7.505 34516 Z= 0.346 Chirality : 0.047 0.192 3808 Planarity : 0.005 0.062 4380 Dihedral : 7.004 58.002 3725 Min Nonbonded Distance : 2.277 Molprobity Statistics. All-atom Clashscore : 6.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.18 % Favored : 94.82 % Rotamer: Outliers : 4.80 % Allowed : 19.35 % Favored : 75.85 % 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: -2.43 (0.13), residues: 3148 helix: -4.45 (0.16), residues: 32 sheet: -0.98 (0.14), residues: 1272 loop : -2.08 (0.13), residues: 1844 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG L 142 TYR 0.024 0.002 TYR L 173 PHE 0.033 0.002 PHE H 100C TRP 0.017 0.001 TRP G 148 HIS 0.008 0.001 HIS E 198 Details of bonding type rmsd/Z covalent geometry : bond 0.00570 / 0.24 (25376) covalent geometry : angle 0.65561 / 0.34 (34384) SS BOND : bond 0.00404 / 0.27 ( 48) SS BOND : angle 1.37779 / 0.99 ( 96) hydrogen bonds : bond 0.03915 / 2.55 ( 706) hydrogen bonds : angle 5.58423 / 3.80 ( 1932) link_BETA1-4 : bond 0.00474 / 0.28 ( 8) link_BETA1-4 : angle 2.11783 / 1.38 ( 24) link_NAG-ASN : bond 0.00264 / 0.16 ( 4) link_NAG-ASN : angle 1.07960 / 0.59 ( 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 450 residues out of total 2708 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 130 poor density : 320 time to evaluate : 0.901 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 390 ASP cc_start: 0.7683 (OUTLIER) cc_final: 0.7217 (m-30) REVERT: I 429 MET cc_start: 0.9431 (mtp) cc_final: 0.9223 (mtm) REVERT: M 419 LYS cc_start: 0.9242 (OUTLIER) cc_final: 0.8968 (mttm) REVERT: N 338 GLU cc_start: 0.8351 (OUTLIER) cc_final: 0.8098 (mp0) REVERT: N 390 ASP cc_start: 0.7609 (OUTLIER) cc_final: 0.7117 (m-30) REVERT: W 338 GLU cc_start: 0.8363 (OUTLIER) cc_final: 0.8101 (mp0) REVERT: W 419 LYS cc_start: 0.9223 (OUTLIER) cc_final: 0.8966 (mttm) REVERT: A 72 ASP cc_start: 0.8216 (t70) cc_final: 0.7444 (t70) REVERT: A 100 TYR cc_start: 0.9090 (m-80) cc_final: 0.8763 (m-80) REVERT: A 145 TYR cc_start: 0.7046 (p90) cc_final: 0.6502 (p90) REVERT: A 176 TYR cc_start: 0.7398 (m-80) cc_final: 0.7107 (m-80) REVERT: C 30 ILE cc_start: 0.9068 (tt) cc_final: 0.8774 (tp) REVERT: C 72 ASP cc_start: 0.8021 (t70) cc_final: 0.7245 (t70) REVERT: C 145 TYR cc_start: 0.6291 (p90) cc_final: 0.5894 (p90) REVERT: D 30 ILE cc_start: 0.9074 (tt) cc_final: 0.8810 (tp) REVERT: D 72 ASP cc_start: 0.8034 (t70) cc_final: 0.7247 (t70) REVERT: D 145 TYR cc_start: 0.6996 (p90) cc_final: 0.6492 (p90) REVERT: D 176 TYR cc_start: 0.7302 (m-80) cc_final: 0.6826 (m-10) REVERT: H 30 ILE cc_start: 0.9058 (tt) cc_final: 0.8757 (tp) REVERT: H 72 ASP cc_start: 0.8015 (t70) cc_final: 0.7252 (t70) REVERT: H 81 ASP cc_start: 0.8126 (t70) cc_final: 0.7913 (t0) REVERT: H 145 TYR cc_start: 0.7023 (p90) cc_final: 0.6434 (p90) REVERT: H 176 TYR cc_start: 0.7611 (m-80) cc_final: 0.7110 (m-10) REVERT: B 143 GLU cc_start: 0.8345 (OUTLIER) cc_final: 0.8023 (tm-30) REVERT: E 42 GLN cc_start: 0.7713 (mp10) cc_final: 0.7503 (mp10) REVERT: E 143 GLU cc_start: 0.8551 (OUTLIER) cc_final: 0.8337 (tm-30) REVERT: E 190 LYS cc_start: 0.8174 (mmmt) cc_final: 0.7839 (tptt) REVERT: E 191 VAL cc_start: 0.5089 (OUTLIER) cc_final: 0.4835 (t) REVERT: G 108 ARG cc_start: 0.7797 (ptm160) cc_final: 0.7521 (ptm-80) REVERT: G 143 GLU cc_start: 0.8425 (OUTLIER) cc_final: 0.8157 (tm-30) REVERT: G 165 GLU cc_start: 0.8074 (tp30) cc_final: 0.7435 (tp30) REVERT: G 166 GLN cc_start: 0.8771 (OUTLIER) cc_final: 0.8349 (tt0) REVERT: G 173 TYR cc_start: 0.8120 (m-80) cc_final: 0.7906 (m-10) REVERT: L 108 ARG cc_start: 0.7651 (ptm160) cc_final: 0.6889 (ptm-80) REVERT: L 143 GLU cc_start: 0.8095 (OUTLIER) cc_final: 0.7842 (tm-30) REVERT: L 165 GLU cc_start: 0.8009 (tp30) cc_final: 0.7488 (tp30) REVERT: L 173 TYR cc_start: 0.8096 (m-10) cc_final: 0.7806 (m-10) outliers start: 130 outliers final: 82 residues processed: 424 average time/residue: 0.5959 time to fit residues: 292.7570 Evaluate side-chains 385 residues out of total 2708 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 94 poor density : 291 time to evaluate : 0.925 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 359 SER Chi-restraints excluded: chain I residue 366 SER Chi-restraints excluded: chain I residue 390 ASP Chi-restraints excluded: chain I residue 419 LYS 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 357 MET 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 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 357 MET Chi-restraints excluded: chain N residue 359 SER Chi-restraints excluded: chain N residue 366 SER Chi-restraints excluded: chain N residue 390 ASP Chi-restraints excluded: chain N residue 419 LYS 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 357 MET 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 138 LEU 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 87 THR 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 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 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 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 182 SER Chi-restraints excluded: chain B residue 202 SER Chi-restraints excluded: chain B residue 206 THR Chi-restraints excluded: chain E residue 33 LEU 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 182 SER Chi-restraints excluded: chain E residue 191 VAL 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 143 GLU Chi-restraints excluded: chain G residue 166 GLN 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 143 GLU Chi-restraints excluded: chain L residue 150 VAL Chi-restraints excluded: chain L residue 174 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: [294, 254, 46, 121, 47, 58, 2, 278, 264, 191, 43] chunk 294 optimal weight: 0.0060 chunk 254 optimal weight: 9.9990 chunk 46 optimal weight: 3.9990 chunk 121 optimal weight: 3.9990 chunk 47 optimal weight: 3.9990 chunk 58 optimal weight: 2.9990 chunk 2 optimal weight: 3.9990 chunk 278 optimal weight: 3.9990 chunk 264 optimal weight: 50.0000 chunk 191 optimal weight: 4.9990 chunk 43 optimal weight: 2.9990 overall best weight: 2.8004 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** I 354 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 354 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 354 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** W 329 ASN B 166 GLN ** E 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 166 GLN G 27 GLN ** G 155 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 166 GLN ** L 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 27 GLN ** L 155 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3902 r_free = 0.3902 target = 0.143496 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.3086 r_free = 0.3086 target = 0.082867 restraints weight = 36357.528| |-----------------------------------------------------------------------------| r_work (start): 0.2992 rms_B_bonded: 2.37 r_work: 0.2865 rms_B_bonded: 2.45 restraints_weight: 0.5000 r_work: 0.2731 rms_B_bonded: 3.81 restraints_weight: 0.2500 r_work (final): 0.2731 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2719 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2719 r_free = 0.2719 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 = 0.2719 r_free = 0.2719 target_work(ls_wunit_k1) = 0.062 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.2719 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8624 moved from start: 0.2809 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.039 25436 Z= 0.208 Angle : 0.629 12.384 34516 Z= 0.325 Chirality : 0.046 0.167 3808 Planarity : 0.005 0.057 4380 Dihedral : 6.275 59.628 3725 Min Nonbonded Distance : 2.297 Molprobity Statistics. All-atom Clashscore : 6.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.34 % Favored : 94.66 % Rotamer: Outliers : 4.65 % Allowed : 20.86 % Favored : 74.48 % 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: -2.09 (0.14), residues: 3148 helix: -4.34 (0.17), residues: 32 sheet: -0.68 (0.14), residues: 1260 loop : -1.90 (0.13), residues: 1856 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG E 18 TYR 0.023 0.002 TYR B 140 PHE 0.029 0.002 PHE H 100C TRP 0.009 0.001 TRP L 148 HIS 0.005 0.001 HIS E 198 Details of bonding type rmsd/Z covalent geometry : bond 0.00493 / 0.21 (25376) covalent geometry : angle 0.62461 / 0.32 (34384) SS BOND : bond 0.00237 / 0.15 ( 48) SS BOND : angle 1.20383 / 0.88 ( 96) hydrogen bonds : bond 0.03543 / 2.32 ( 706) hydrogen bonds : angle 5.21407 / 3.55 ( 1932) link_BETA1-4 : bond 0.00379 / 0.21 ( 8) link_BETA1-4 : angle 1.73579 / 1.13 ( 24) link_NAG-ASN : bond 0.00227 / 0.14 ( 4) link_NAG-ASN : angle 1.07614 / 0.56 ( 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 432 residues out of total 2708 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 126 poor density : 306 time to evaluate : 0.952 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 116 ARG cc_start: 0.8061 (OUTLIER) cc_final: 0.5896 (tmm160) REVERT: I 338 GLU cc_start: 0.8424 (OUTLIER) cc_final: 0.8158 (mp0) REVERT: I 390 ASP cc_start: 0.7710 (OUTLIER) cc_final: 0.7443 (m-30) REVERT: I 419 LYS cc_start: 0.9278 (mttt) cc_final: 0.9001 (mttm) REVERT: M 116 ARG cc_start: 0.8041 (OUTLIER) cc_final: 0.5951 (tmm160) REVERT: M 338 GLU cc_start: 0.8427 (OUTLIER) cc_final: 0.8163 (mp0) REVERT: M 419 LYS cc_start: 0.9290 (mttt) cc_final: 0.9010 (mttm) REVERT: N 116 ARG cc_start: 0.8026 (OUTLIER) cc_final: 0.5897 (tmm160) REVERT: N 371 LYS cc_start: 0.9233 (OUTLIER) cc_final: 0.8936 (ptpp) REVERT: N 390 ASP cc_start: 0.7747 (OUTLIER) cc_final: 0.7443 (m-30) REVERT: N 419 LYS cc_start: 0.9283 (mttt) cc_final: 0.9005 (mttm) REVERT: W 116 ARG cc_start: 0.8035 (OUTLIER) cc_final: 0.5907 (tmm160) REVERT: W 371 LYS cc_start: 0.9233 (OUTLIER) cc_final: 0.8894 (ptpp) REVERT: W 419 LYS cc_start: 0.9291 (mttt) cc_final: 0.9014 (mttm) REVERT: A 72 ASP cc_start: 0.8242 (t70) cc_final: 0.7476 (t70) REVERT: A 100 PHE cc_start: 0.7920 (OUTLIER) cc_final: 0.7132 (p90) REVERT: A 145 TYR cc_start: 0.7054 (p90) cc_final: 0.6498 (p90) REVERT: A 176 TYR cc_start: 0.7109 (m-80) cc_final: 0.6801 (m-80) REVERT: C 30 ILE cc_start: 0.9069 (tt) cc_final: 0.8775 (tp) REVERT: C 46 GLU cc_start: 0.8511 (tt0) cc_final: 0.8274 (tt0) REVERT: C 72 ASP cc_start: 0.8052 (t70) cc_final: 0.7272 (t70) REVERT: D 30 ILE cc_start: 0.9058 (tt) cc_final: 0.8780 (tp) REVERT: D 72 ASP cc_start: 0.8095 (t70) cc_final: 0.7340 (t70) REVERT: D 100 PHE cc_start: 0.7761 (OUTLIER) cc_final: 0.7320 (p90) REVERT: D 145 TYR cc_start: 0.7143 (p90) cc_final: 0.6541 (p90) REVERT: D 176 TYR cc_start: 0.7293 (m-80) cc_final: 0.7089 (m-80) REVERT: H 30 ILE cc_start: 0.9066 (tt) cc_final: 0.8770 (tp) REVERT: H 72 ASP cc_start: 0.8089 (t70) cc_final: 0.7322 (t70) REVERT: H 145 TYR cc_start: 0.7050 (p90) cc_final: 0.6401 (p90) REVERT: H 176 TYR cc_start: 0.7441 (m-80) cc_final: 0.7189 (m-80) REVERT: B 108 ARG cc_start: 0.7758 (ptm160) cc_final: 0.7020 (ptm-80) REVERT: B 143 GLU cc_start: 0.8363 (OUTLIER) cc_final: 0.8163 (tm-30) REVERT: E 42 GLN cc_start: 0.7528 (mp10) cc_final: 0.7225 (mp10) REVERT: E 108 ARG cc_start: 0.8103 (ptm160) cc_final: 0.7881 (ptt90) REVERT: E 190 LYS cc_start: 0.8270 (mmmt) cc_final: 0.7914 (tptt) REVERT: G 108 ARG cc_start: 0.7870 (ptm160) cc_final: 0.7604 (ptm-80) REVERT: G 166 GLN cc_start: 0.8662 (OUTLIER) cc_final: 0.8376 (tt0) REVERT: G 173 TYR cc_start: 0.8110 (m-80) cc_final: 0.7740 (m-10) REVERT: L 108 ARG cc_start: 0.7697 (ptm160) cc_final: 0.7196 (ptm-80) REVERT: L 142 ARG cc_start: 0.8686 (ttp-170) cc_final: 0.8416 (ttp80) outliers start: 126 outliers final: 76 residues processed: 417 average time/residue: 0.5828 time to fit residues: 281.4610 Evaluate side-chains 374 residues out of total 2708 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 90 poor density : 284 time to evaluate : 0.917 ------------------------------------------------------------------------------- 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 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 338 GLU Chi-restraints excluded: chain M residue 359 SER 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 359 SER Chi-restraints excluded: chain N residue 371 LYS Chi-restraints excluded: chain N residue 390 ASP 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 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 A residue 138 LEU 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 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 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 25 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 174 SER Chi-restraints excluded: chain B residue 176 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 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 166 GLN 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 150 VAL Chi-restraints excluded: chain L residue 202 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 316 random chunks: [1, 103, 301, 229, 204, 61, 210, 82, 81, 307, 37] chunk 1 optimal weight: 3.9990 chunk 103 optimal weight: 0.0170 chunk 301 optimal weight: 10.0000 chunk 229 optimal weight: 30.0000 chunk 204 optimal weight: 4.9990 chunk 61 optimal weight: 6.9990 chunk 210 optimal weight: 2.9990 chunk 82 optimal weight: 4.9990 chunk 81 optimal weight: 0.6980 chunk 307 optimal weight: 0.0370 chunk 37 optimal weight: 0.9980 overall best weight: 0.9498 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 166 GLN ** G 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 27 GLN G 42 GLN ** G 155 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 166 GLN ** L 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 27 GLN ** L 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 = 0.3925 r_free = 0.3925 target = 0.145428 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3131 r_free = 0.3131 target = 0.085371 restraints weight = 36271.290| |-----------------------------------------------------------------------------| r_work (start): 0.3035 rms_B_bonded: 2.34 r_work: 0.2912 rms_B_bonded: 2.43 restraints_weight: 0.5000 r_work: 0.2778 rms_B_bonded: 3.79 restraints_weight: 0.2500 r_work (final): 0.2778 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2767 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2767 r_free = 0.2767 target_work(ls_wunit_k1) = 0.065 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2767 r_free = 0.2767 target_work(ls_wunit_k1) = 0.065 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.2767 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8576 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 : 0.002 0.032 25436 Z= 0.107 Angle : 0.559 9.219 34516 Z= 0.289 Chirality : 0.043 0.135 3808 Planarity : 0.005 0.052 4380 Dihedral : 5.418 52.830 3713 Min Nonbonded Distance : 2.349 Molprobity Statistics. All-atom Clashscore : 6.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.64 % Favored : 95.36 % Rotamer: Outliers : 3.25 % Allowed : 23.49 % Favored : 73.26 % 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: -1.91 (0.14), residues: 3148 helix: -4.32 (0.18), residues: 32 sheet: -0.57 (0.14), residues: 1312 loop : -1.79 (0.13), residues: 1804 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG E 18 TYR 0.026 0.001 TYR B 140 PHE 0.019 0.002 PHE H 100C TRP 0.008 0.001 TRP G 148 HIS 0.003 0.001 HIS E 198 Details of bonding type rmsd/Z covalent geometry : bond 0.00247 / 0.11 (25376) covalent geometry : angle 0.55735 / 0.29 (34384) SS BOND : bond 0.00269 / 0.19 ( 48) SS BOND : angle 0.72929 / 0.53 ( 96) hydrogen bonds : bond 0.02939 / 1.92 ( 706) hydrogen bonds : angle 4.85600 / 3.30 ( 1932) link_BETA1-4 : bond 0.00456 / 0.26 ( 8) link_BETA1-4 : angle 1.53618 / 0.99 ( 24) link_NAG-ASN : bond 0.00020 / 0.01 ( 4) link_NAG-ASN : angle 0.89341 / 0.47 ( 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 393 residues out of total 2708 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 88 poor density : 305 time to evaluate : 0.785 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: 0.8321 (OUTLIER) cc_final: 0.8102 (mp0) REVERT: I 419 LYS cc_start: 0.9256 (mttt) cc_final: 0.8971 (mttm) REVERT: I 429 MET cc_start: 0.9397 (mtp) cc_final: 0.9194 (mtm) REVERT: M 338 GLU cc_start: 0.8316 (OUTLIER) cc_final: 0.8096 (mp0) REVERT: M 419 LYS cc_start: 0.9253 (mttt) cc_final: 0.8957 (mttm) REVERT: N 338 GLU cc_start: 0.8326 (OUTLIER) cc_final: 0.8051 (mp0) REVERT: N 419 LYS cc_start: 0.9257 (mttt) cc_final: 0.8973 (mttm) REVERT: W 338 GLU cc_start: 0.8320 (OUTLIER) cc_final: 0.8046 (mp0) REVERT: W 419 LYS cc_start: 0.9262 (mttt) cc_final: 0.8968 (mttm) REVERT: A 72 ASP cc_start: 0.8231 (t70) cc_final: 0.7486 (t70) REVERT: A 100 PHE cc_start: 0.7814 (OUTLIER) cc_final: 0.7367 (p90) REVERT: A 145 TYR cc_start: 0.6965 (p90) cc_final: 0.6351 (p90) REVERT: A 176 TYR cc_start: 0.7105 (m-80) cc_final: 0.6835 (m-80) REVERT: C 30 ILE cc_start: 0.9046 (tt) cc_final: 0.8754 (tp) REVERT: C 72 ASP cc_start: 0.8037 (t70) cc_final: 0.7273 (t70) REVERT: C 100 PHE cc_start: 0.7912 (OUTLIER) cc_final: 0.7474 (p90) REVERT: D 30 ILE cc_start: 0.9014 (tt) cc_final: 0.8731 (tp) REVERT: D 72 ASP cc_start: 0.8091 (t70) cc_final: 0.7330 (t70) REVERT: D 145 TYR cc_start: 0.7062 (p90) cc_final: 0.6346 (p90) REVERT: D 176 TYR cc_start: 0.7310 (m-80) cc_final: 0.7094 (m-80) REVERT: H 30 ILE cc_start: 0.9040 (tt) cc_final: 0.8748 (tp) REVERT: H 72 ASP cc_start: 0.8083 (t70) cc_final: 0.7313 (t70) REVERT: H 100 PHE cc_start: 0.7922 (OUTLIER) cc_final: 0.7539 (p90) REVERT: B 108 ARG cc_start: 0.7810 (ptm160) cc_final: 0.7532 (ptm-80) REVERT: B 116 PHE cc_start: 0.5801 (m-10) cc_final: 0.5574 (m-10) REVERT: E 42 GLN cc_start: 0.7409 (mp10) cc_final: 0.7104 (mp10) REVERT: E 108 ARG cc_start: 0.8114 (ptm160) cc_final: 0.7885 (ptt90) REVERT: E 190 LYS cc_start: 0.8265 (mmmt) cc_final: 0.7918 (tptt) REVERT: G 108 ARG cc_start: 0.7844 (ptm160) cc_final: 0.7116 (ptm-80) REVERT: G 116 PHE cc_start: 0.5683 (m-10) cc_final: 0.5456 (m-10) REVERT: L 108 ARG cc_start: 0.7722 (ptm160) cc_final: 0.6954 (ptm-80) outliers start: 88 outliers final: 47 residues processed: 384 average time/residue: 0.5697 time to fit residues: 254.3290 Evaluate side-chains 331 residues out of total 2708 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 277 time to evaluate : 0.875 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain I residue 146 THR Chi-restraints excluded: chain I residue 182 CYS 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 361 ILE Chi-restraints excluded: chain M residue 146 THR Chi-restraints excluded: chain M residue 182 CYS 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 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 W residue 146 THR Chi-restraints excluded: chain W residue 182 CYS 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 A residue 25 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 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 100 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 138 LEU Chi-restraints excluded: chain D residue 184 VAL 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 174 SER Chi-restraints excluded: chain B residue 202 SER Chi-restraints excluded: chain E residue 30 SER Chi-restraints excluded: chain E residue 182 SER 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 33 LEU Chi-restraints excluded: chain L residue 27 GLN Chi-restraints excluded: chain L residue 30 SER Chi-restraints excluded: chain L residue 33 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 316 random chunks: [204, 40, 57, 102, 51, 270, 263, 33, 221, 247, 224] chunk 204 optimal weight: 9.9990 chunk 40 optimal weight: 5.9990 chunk 57 optimal weight: 4.9990 chunk 102 optimal weight: 4.9990 chunk 51 optimal weight: 7.9990 chunk 270 optimal weight: 0.9990 chunk 263 optimal weight: 0.9980 chunk 33 optimal weight: 0.3980 chunk 221 optimal weight: 6.9990 chunk 247 optimal weight: 0.0370 chunk 224 optimal weight: 30.0000 overall best weight: 1.4862 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... I 101 HIS ** B 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 27 GLN B 42 GLN B 166 GLN ** E 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 27 GLN E 166 GLN ** G 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 155 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 166 GLN ** L 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 155 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3923 r_free = 0.3923 target = 0.145163 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3122 r_free = 0.3122 target = 0.084742 restraints weight = 36362.720| |-----------------------------------------------------------------------------| r_work (start): 0.3030 rms_B_bonded: 2.35 r_work: 0.2903 rms_B_bonded: 2.45 restraints_weight: 0.5000 r_work: 0.2768 rms_B_bonded: 3.82 restraints_weight: 0.2500 r_work (final): 0.2768 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2758 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2758 r_free = 0.2758 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 = 0.2758 r_free = 0.2758 target_work(ls_wunit_k1) = 0.064 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.2758 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8589 moved from start: 0.3174 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 25436 Z= 0.136 Angle : 0.588 9.010 34516 Z= 0.302 Chirality : 0.044 0.188 3808 Planarity : 0.004 0.043 4380 Dihedral : 5.223 37.858 3708 Min Nonbonded Distance : 2.324 Molprobity Statistics. All-atom Clashscore : 6.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.51 % Favored : 95.49 % Rotamer: Outliers : 3.43 % Allowed : 23.78 % Favored : 72.78 % 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: -1.80 (0.14), residues: 3148 helix: -4.32 (0.18), residues: 32 sheet: -0.42 (0.14), residues: 1308 loop : -1.78 (0.13), residues: 1808 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG G 142 TYR 0.026 0.001 TYR B 140 PHE 0.023 0.002 PHE L 116 TRP 0.006 0.001 TRP I 177 HIS 0.008 0.001 HIS I 101 Details of bonding type rmsd/Z covalent geometry : bond 0.00323 / 0.14 (25376) covalent geometry : angle 0.58196 / 0.30 (34384) SS BOND : bond 0.00309 / 0.21 ( 48) SS BOND : angle 1.55288 / 1.03 ( 96) hydrogen bonds : bond 0.02987 / 1.96 ( 706) hydrogen bonds : angle 4.80717 / 3.27 ( 1932) link_BETA1-4 : bond 0.00466 / 0.27 ( 8) link_BETA1-4 : angle 1.51684 / 0.97 ( 24) link_NAG-ASN : bond 0.00070 / 0.04 ( 4) link_NAG-ASN : angle 0.90685 / 0.51 ( 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 385 residues out of total 2708 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 93 poor density : 292 time to evaluate : 0.662 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: 0.8299 (OUTLIER) cc_final: 0.8096 (mp0) REVERT: I 419 LYS cc_start: 0.9172 (mttt) cc_final: 0.8970 (mttm) REVERT: I 429 MET cc_start: 0.9418 (mtp) cc_final: 0.9199 (mtm) REVERT: M 338 GLU cc_start: 0.8299 (OUTLIER) cc_final: 0.8088 (mp0) REVERT: M 419 LYS cc_start: 0.9144 (mttt) cc_final: 0.8936 (mttm) REVERT: N 338 GLU cc_start: 0.8288 (OUTLIER) cc_final: 0.8036 (mp0) REVERT: N 371 LYS cc_start: 0.9222 (OUTLIER) cc_final: 0.8938 (ptpp) REVERT: N 419 LYS cc_start: 0.9176 (mttt) cc_final: 0.8974 (mttm) REVERT: W 338 GLU cc_start: 0.8291 (OUTLIER) cc_final: 0.8040 (mp0) REVERT: W 419 LYS cc_start: 0.9148 (mttt) cc_final: 0.8942 (mttm) REVERT: A 72 ASP cc_start: 0.8257 (t70) cc_final: 0.7545 (t70) REVERT: A 100 PHE cc_start: 0.7948 (OUTLIER) cc_final: 0.7508 (p90) REVERT: A 145 TYR cc_start: 0.7001 (p90) cc_final: 0.6391 (p90) REVERT: A 176 TYR cc_start: 0.7162 (m-80) cc_final: 0.6953 (m-80) REVERT: C 30 ILE cc_start: 0.9058 (tt) cc_final: 0.8761 (tp) REVERT: C 72 ASP cc_start: 0.8132 (t70) cc_final: 0.7369 (t70) REVERT: C 100 PHE cc_start: 0.7873 (OUTLIER) cc_final: 0.7450 (p90) REVERT: D 30 ILE cc_start: 0.9023 (tt) cc_final: 0.8733 (tp) REVERT: D 72 ASP cc_start: 0.8150 (t70) cc_final: 0.7392 (t70) REVERT: D 145 TYR cc_start: 0.6949 (p90) cc_final: 0.6210 (p90) REVERT: D 176 TYR cc_start: 0.7337 (m-80) cc_final: 0.7128 (m-80) REVERT: H 30 ILE cc_start: 0.9053 (tt) cc_final: 0.8756 (tp) REVERT: H 72 ASP cc_start: 0.8152 (t70) cc_final: 0.7408 (t70) REVERT: H 100 PHE cc_start: 0.7885 (OUTLIER) cc_final: 0.7400 (p90) REVERT: B 108 ARG cc_start: 0.7826 (ptm160) cc_final: 0.7555 (ptm-80) REVERT: B 116 PHE cc_start: 0.5938 (m-10) cc_final: 0.5700 (m-10) REVERT: E 42 GLN cc_start: 0.7425 (mp10) cc_final: 0.7158 (mp10) REVERT: E 108 ARG cc_start: 0.8157 (ptm160) cc_final: 0.7943 (ptt90) REVERT: G 108 ARG cc_start: 0.7859 (ptm160) cc_final: 0.7514 (ptt90) REVERT: G 140 TYR cc_start: 0.6996 (OUTLIER) cc_final: 0.6440 (t80) REVERT: L 108 ARG cc_start: 0.7765 (ptm160) cc_final: 0.7090 (ptm-80) outliers start: 93 outliers final: 66 residues processed: 368 average time/residue: 0.5733 time to fit residues: 244.5292 Evaluate side-chains 355 residues out of total 2708 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 280 time to evaluate : 0.844 ------------------------------------------------------------------------------- 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 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 357 MET Chi-restraints excluded: chain M residue 361 ILE 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 361 ILE Chi-restraints excluded: chain N residue 371 LYS Chi-restraints excluded: chain W residue 102 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 337 CYS Chi-restraints excluded: chain W residue 338 GLU Chi-restraints excluded: chain W residue 357 MET Chi-restraints excluded: chain W residue 361 ILE 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 C residue 100 PHE 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 25 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 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 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 33 LEU Chi-restraints excluded: chain B residue 79 GLU Chi-restraints excluded: chain B residue 174 SER Chi-restraints excluded: chain B residue 202 SER 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 182 SER 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 33 LEU Chi-restraints excluded: chain G residue 140 TYR Chi-restraints excluded: chain G residue 202 SER Chi-restraints excluded: chain L residue 27 GLN Chi-restraints excluded: chain L residue 30 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 316 random chunks: [43, 24, 20, 259, 47, 199, 108, 1, 211, 87, 214] chunk 43 optimal weight: 2.9990 chunk 24 optimal weight: 1.9990 chunk 20 optimal weight: 6.9990 chunk 259 optimal weight: 10.0000 chunk 47 optimal weight: 3.9990 chunk 199 optimal weight: 5.9990 chunk 108 optimal weight: 7.9990 chunk 1 optimal weight: 4.9990 chunk 211 optimal weight: 0.2980 chunk 87 optimal weight: 6.9990 chunk 214 optimal weight: 10.0000 overall best weight: 2.8588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... I 101 HIS M 101 HIS W 101 HIS ** B 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 166 GLN E 166 GLN ** G 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 155 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 155 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 198 HIS ** 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 = 0.3905 r_free = 0.3905 target = 0.143689 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3100 r_free = 0.3100 target = 0.083430 restraints weight = 36416.090| |-----------------------------------------------------------------------------| r_work (start): 0.2990 rms_B_bonded: 2.31 r_work: 0.2850 rms_B_bonded: 2.46 restraints_weight: 0.5000 r_work: 0.2713 rms_B_bonded: 3.81 restraints_weight: 0.2500 r_work (final): 0.2713 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2712 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2712 r_free = 0.2712 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 = 0.2712 r_free = 0.2712 target_work(ls_wunit_k1) = 0.062 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.2712 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8623 moved from start: 0.3274 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.060 25436 Z= 0.212 Angle : 0.618 8.870 34516 Z= 0.319 Chirality : 0.045 0.194 3808 Planarity : 0.005 0.082 4380 Dihedral : 5.354 36.627 3708 Min Nonbonded Distance : 2.292 Molprobity Statistics. All-atom Clashscore : 6.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.64 % Favored : 95.36 % Rotamer: Outliers : 3.80 % Allowed : 23.38 % Favored : 72.82 % 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: -4.30 (0.19), residues: 32 sheet: -0.24 (0.14), residues: 1300 loop : -1.74 (0.13), residues: 1816 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG L 24 TYR 0.024 0.002 TYR B 140 PHE 0.030 0.002 PHE C 100C TRP 0.009 0.001 TRP C 47 HIS 0.008 0.001 HIS I 101 Details of bonding type rmsd/Z covalent geometry : bond 0.00507 / 0.21 (25376) covalent geometry : angle 0.61158 / 0.32 (34384) SS BOND : bond 0.00371 / 0.26 ( 48) SS BOND : angle 1.55134 / 1.06 ( 96) hydrogen bonds : bond 0.03258 / 2.14 ( 706) hydrogen bonds : angle 4.86351 / 3.31 ( 1932) link_BETA1-4 : bond 0.00382 / 0.22 ( 8) link_BETA1-4 : angle 1.53833 / 0.98 ( 24) link_NAG-ASN : bond 0.00248 / 0.15 ( 4) link_NAG-ASN : angle 1.05999 / 0.62 ( 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 392 residues out of total 2708 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 103 poor density : 289 time to evaluate : 0.843 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: M 338 GLU cc_start: 0.8322 (OUTLIER) cc_final: 0.8103 (mp0) REVERT: M 419 LYS cc_start: 0.9161 (mttt) cc_final: 0.8933 (mttm) REVERT: N 338 GLU cc_start: 0.8326 (OUTLIER) cc_final: 0.8071 (mp0) REVERT: N 371 LYS cc_start: 0.9261 (OUTLIER) cc_final: 0.8969 (ptpp) REVERT: W 338 GLU cc_start: 0.8324 (OUTLIER) cc_final: 0.8074 (mp0) REVERT: W 371 LYS cc_start: 0.9269 (OUTLIER) cc_final: 0.8975 (ptpp) REVERT: W 419 LYS cc_start: 0.9159 (mttt) cc_final: 0.8932 (mttm) REVERT: A 72 ASP cc_start: 0.8310 (t70) cc_final: 0.7611 (t70) REVERT: A 100 PHE cc_start: 0.7765 (OUTLIER) cc_final: 0.7379 (p90) REVERT: A 145 TYR cc_start: 0.6939 (p90) cc_final: 0.6267 (p90) REVERT: A 176 TYR cc_start: 0.7144 (m-80) cc_final: 0.6894 (m-80) REVERT: C 30 ILE cc_start: 0.9082 (tt) cc_final: 0.8785 (tp) REVERT: C 72 ASP cc_start: 0.8219 (t70) cc_final: 0.7545 (t70) REVERT: C 100 PHE cc_start: 0.7814 (OUTLIER) cc_final: 0.7418 (p90) REVERT: D 72 ASP cc_start: 0.8245 (t70) cc_final: 0.7572 (t70) REVERT: D 100 PHE cc_start: 0.7798 (OUTLIER) cc_final: 0.7383 (p90) REVERT: D 145 TYR cc_start: 0.6995 (p90) cc_final: 0.6291 (p90) REVERT: H 30 ILE cc_start: 0.9076 (tt) cc_final: 0.8780 (tp) REVERT: H 38 ARG cc_start: 0.8139 (OUTLIER) cc_final: 0.7388 (ptm-80) REVERT: H 72 ASP cc_start: 0.8244 (t70) cc_final: 0.7567 (t70) REVERT: H 100 PHE cc_start: 0.7801 (OUTLIER) cc_final: 0.7478 (p90) REVERT: B 108 ARG cc_start: 0.7885 (ptm160) cc_final: 0.7578 (ptm-80) REVERT: B 116 PHE cc_start: 0.5905 (m-10) cc_final: 0.5653 (m-10) REVERT: B 201 LEU cc_start: 0.6596 (OUTLIER) cc_final: 0.6281 (pp) REVERT: E 42 GLN cc_start: 0.7545 (mp10) cc_final: 0.7265 (mp10) REVERT: E 108 ARG cc_start: 0.8175 (ptm160) cc_final: 0.7928 (ptt90) REVERT: E 142 ARG cc_start: 0.8560 (ttp80) cc_final: 0.8277 (tpp80) REVERT: G 108 ARG cc_start: 0.7940 (ptm160) cc_final: 0.7690 (ptt90) REVERT: G 140 TYR cc_start: 0.6877 (OUTLIER) cc_final: 0.6426 (t80) REVERT: L 108 ARG cc_start: 0.7816 (ptm160) cc_final: 0.7487 (ptm-80) REVERT: L 116 PHE cc_start: 0.5468 (m-10) cc_final: 0.5252 (m-10) outliers start: 103 outliers final: 73 residues processed: 381 average time/residue: 0.5459 time to fit residues: 242.5840 Evaluate side-chains 366 residues out of total 2708 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 85 poor density : 281 time to evaluate : 0.892 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 359 SER Chi-restraints excluded: chain I residue 361 ILE 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 357 MET Chi-restraints excluded: chain M residue 361 ILE 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 361 ILE Chi-restraints excluded: chain N residue 371 LYS 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 357 MET 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 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 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 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 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 D residue 100 SER 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 38 ARG 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 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 201 LEU Chi-restraints excluded: chain B residue 202 SER Chi-restraints excluded: chain E residue 30 SER Chi-restraints excluded: chain E residue 76 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 140 TYR Chi-restraints excluded: chain G residue 176 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 174 SER Chi-restraints excluded: chain L residue 176 SER 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: [121, 60, 176, 197, 257, 296, 290, 34, 235, 48, 183] chunk 121 optimal weight: 3.9990 chunk 60 optimal weight: 2.9990 chunk 176 optimal weight: 0.8980 chunk 197 optimal weight: 4.9990 chunk 257 optimal weight: 4.9990 chunk 296 optimal weight: 9.9990 chunk 290 optimal weight: 9.9990 chunk 34 optimal weight: 5.9990 chunk 235 optimal weight: 7.9990 chunk 48 optimal weight: 4.9990 chunk 183 optimal weight: 8.9990 overall best weight: 3.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 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 101 HIS ** W 354 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 166 GLN E 166 GLN ** G 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 155 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 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 = 0.3891 r_free = 0.3891 target = 0.142715 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 73)----------------| | r_work = 0.3066 r_free = 0.3066 target = 0.081497 restraints weight = 36393.632| |-----------------------------------------------------------------------------| r_work (start): 0.2972 rms_B_bonded: 2.40 r_work: 0.2844 rms_B_bonded: 2.46 restraints_weight: 0.5000 r_work: 0.2711 rms_B_bonded: 3.80 restraints_weight: 0.2500 r_work (final): 0.2711 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2691 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2691 r_free = 0.2691 target_work(ls_wunit_k1) = 0.061 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2691 r_free = 0.2691 target_work(ls_wunit_k1) = 0.061 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.2691 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8634 moved from start: 0.3414 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.071 25436 Z= 0.259 Angle : 0.662 9.159 34516 Z= 0.342 Chirality : 0.046 0.189 3808 Planarity : 0.005 0.079 4380 Dihedral : 5.565 35.941 3708 Min Nonbonded Distance : 2.272 Molprobity Statistics. All-atom Clashscore : 7.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.86 % Favored : 95.14 % Rotamer: Outliers : 3.95 % Allowed : 23.41 % Favored : 72.64 % 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: -1.69 (0.14), residues: 3148 helix: -4.41 (0.21), residues: 56 sheet: -0.18 (0.14), residues: 1300 loop : -1.79 (0.13), residues: 1792 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG G 24 TYR 0.020 0.002 TYR G 173 PHE 0.035 0.002 PHE D 100C TRP 0.010 0.001 TRP C 47 HIS 0.008 0.001 HIS I 101 Details of bonding type rmsd/Z covalent geometry : bond 0.00620 / 0.26 (25376) covalent geometry : angle 0.65484 / 0.34 (34384) SS BOND : bond 0.00402 / 0.28 ( 48) SS BOND : angle 1.78364 / 1.22 ( 96) hydrogen bonds : bond 0.03488 / 2.28 ( 706) hydrogen bonds : angle 4.92625 / 3.35 ( 1932) link_BETA1-4 : bond 0.00333 / 0.18 ( 8) link_BETA1-4 : angle 1.53466 / 0.97 ( 24) link_NAG-ASN : bond 0.00326 / 0.19 ( 4) link_NAG-ASN : angle 1.17582 / 0.70 ( 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 380 residues out of total 2708 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 107 poor density : 273 time to evaluate : 0.816 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: M 338 GLU cc_start: 0.8362 (OUTLIER) cc_final: 0.8106 (mp0) REVERT: N 338 GLU cc_start: 0.8368 (OUTLIER) cc_final: 0.8081 (mp0) REVERT: N 371 LYS cc_start: 0.9278 (OUTLIER) cc_final: 0.8916 (ptpp) REVERT: W 338 GLU cc_start: 0.8360 (OUTLIER) cc_final: 0.8079 (mp0) REVERT: W 371 LYS cc_start: 0.9280 (OUTLIER) cc_final: 0.8921 (ptpp) REVERT: A 72 ASP cc_start: 0.8434 (t70) cc_final: 0.7758 (t70) REVERT: A 100 PHE cc_start: 0.7886 (OUTLIER) cc_final: 0.7470 (p90) REVERT: C 30 ILE cc_start: 0.9091 (tt) cc_final: 0.8794 (tp) REVERT: C 72 ASP cc_start: 0.8306 (t70) cc_final: 0.7622 (t70) REVERT: D 46 GLU cc_start: 0.8563 (tt0) cc_final: 0.8295 (tt0) REVERT: D 72 ASP cc_start: 0.8327 (t70) cc_final: 0.7643 (t70) REVERT: D 145 TYR cc_start: 0.7206 (p90) cc_final: 0.6589 (p90) REVERT: H 30 ILE cc_start: 0.9088 (tt) cc_final: 0.8792 (tp) REVERT: H 38 ARG cc_start: 0.8259 (OUTLIER) cc_final: 0.7517 (ptm-80) REVERT: H 72 ASP cc_start: 0.8313 (t70) cc_final: 0.7654 (t70) REVERT: B 116 PHE cc_start: 0.5786 (m-10) cc_final: 0.5569 (m-10) REVERT: B 140 TYR cc_start: 0.7445 (t80) cc_final: 0.7210 (t80) REVERT: B 201 LEU cc_start: 0.6592 (OUTLIER) cc_final: 0.6281 (pp) REVERT: E 42 GLN cc_start: 0.7589 (mp10) cc_final: 0.7285 (mp10) REVERT: E 142 ARG cc_start: 0.8578 (ttp80) cc_final: 0.8296 (tpp80) REVERT: G 108 ARG cc_start: 0.7930 (ptm160) cc_final: 0.7716 (ptt90) REVERT: G 140 TYR cc_start: 0.6880 (t80) cc_final: 0.6542 (t80) REVERT: G 201 LEU cc_start: 0.6292 (OUTLIER) cc_final: 0.6075 (pp) REVERT: L 108 ARG cc_start: 0.7898 (ptm160) cc_final: 0.7629 (ptt90) REVERT: L 116 PHE cc_start: 0.5627 (m-10) cc_final: 0.5412 (m-10) outliers start: 107 outliers final: 74 residues processed: 366 average time/residue: 0.5541 time to fit residues: 236.0886 Evaluate side-chains 354 residues out of total 2708 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 83 poor density : 271 time to evaluate : 0.915 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 359 SER Chi-restraints excluded: chain I residue 361 ILE 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 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 361 ILE Chi-restraints excluded: chain N residue 371 LYS 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 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 25 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 ASP Chi-restraints excluded: chain C residue 100 SER 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 25 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 11 VAL Chi-restraints excluded: chain H residue 17 SER Chi-restraints excluded: chain H residue 38 ARG 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 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 201 LEU Chi-restraints excluded: chain B residue 202 SER Chi-restraints excluded: chain E residue 30 SER Chi-restraints excluded: chain E residue 76 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 150 VAL Chi-restraints excluded: chain L residue 174 SER Chi-restraints excluded: chain L residue 176 SER 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: [190, 26, 235, 91, 121, 139, 94, 294, 137, 43, 175] chunk 190 optimal weight: 3.9990 chunk 26 optimal weight: 3.9990 chunk 235 optimal weight: 6.9990 chunk 91 optimal weight: 1.9990 chunk 121 optimal weight: 0.7980 chunk 139 optimal weight: 3.9990 chunk 94 optimal weight: 1.9990 chunk 294 optimal weight: 0.0870 chunk 137 optimal weight: 3.9990 chunk 43 optimal weight: 0.8980 chunk 175 optimal weight: 5.9990 overall best weight: 1.1562 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... I 101 HIS M 101 HIS N 101 HIS W 101 HIS ** B 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 166 GLN ** G 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 155 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 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 = 0.3931 r_free = 0.3931 target = 0.145687 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3140 r_free = 0.3140 target = 0.085379 restraints weight = 36042.316| |-----------------------------------------------------------------------------| r_work (start): 0.3042 rms_B_bonded: 2.31 r_work: 0.2911 rms_B_bonded: 2.42 restraints_weight: 0.5000 r_work: 0.2780 rms_B_bonded: 3.76 restraints_weight: 0.2500 r_work (final): 0.2780 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2765 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2765 r_free = 0.2765 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 = 0.2765 r_free = 0.2765 target_work(ls_wunit_k1) = 0.064 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.2765 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8588 moved from start: 0.3531 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 25436 Z= 0.121 Angle : 0.581 8.852 34516 Z= 0.299 Chirality : 0.043 0.177 3808 Planarity : 0.005 0.075 4380 Dihedral : 5.113 38.280 3708 Min Nonbonded Distance : 2.345 Molprobity Statistics. All-atom Clashscore : 6.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.10 % Favored : 95.90 % Rotamer: Outliers : 3.03 % Allowed : 24.89 % Favored : 72.08 % 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: -4.29 (0.24), residues: 56 sheet: -0.14 (0.14), residues: 1288 loop : -1.64 (0.13), residues: 1804 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG E 108 TYR 0.023 0.001 TYR E 140 PHE 0.029 0.001 PHE D 100C TRP 0.008 0.001 TRP C 47 HIS 0.009 0.001 HIS N 101 Details of bonding type rmsd/Z covalent geometry : bond 0.00286 / 0.12 (25376) covalent geometry : angle 0.57794 / 0.30 (34384) SS BOND : bond 0.00177 / 0.12 ( 48) SS BOND : angle 0.95422 / 0.64 ( 96) hydrogen bonds : bond 0.02857 / 1.88 ( 706) hydrogen bonds : angle 4.69152 / 3.19 ( 1932) link_BETA1-4 : bond 0.00438 / 0.26 ( 8) link_BETA1-4 : angle 1.41896 / 0.90 ( 24) link_NAG-ASN : bond 0.00035 / 0.02 ( 4) link_NAG-ASN : angle 0.95549 / 0.49 ( 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 369 residues out of total 2708 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 82 poor density : 287 time to evaluate : 0.805 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 419 LYS cc_start: 0.9113 (OUTLIER) cc_final: 0.8903 (mttm) REVERT: I 429 MET cc_start: 0.9417 (mtp) cc_final: 0.9196 (mtm) REVERT: M 102 ARG cc_start: 0.6647 (ttm170) cc_final: 0.6426 (ttp-110) REVERT: M 338 GLU cc_start: 0.8330 (OUTLIER) cc_final: 0.8094 (mp0) REVERT: N 338 GLU cc_start: 0.8341 (OUTLIER) cc_final: 0.8056 (mp0) REVERT: N 371 LYS cc_start: 0.9223 (OUTLIER) cc_final: 0.8828 (ptpp) REVERT: W 102 ARG cc_start: 0.6673 (ttm170) cc_final: 0.6446 (ttp-110) REVERT: W 338 GLU cc_start: 0.8317 (OUTLIER) cc_final: 0.8048 (mp0) REVERT: W 371 LYS cc_start: 0.9230 (OUTLIER) cc_final: 0.8815 (ptpp) REVERT: A 72 ASP cc_start: 0.8370 (t70) cc_final: 0.7695 (t70) REVERT: A 100 PHE cc_start: 0.7853 (OUTLIER) cc_final: 0.7518 (p90) REVERT: C 30 ILE cc_start: 0.9034 (tt) cc_final: 0.8736 (tp) REVERT: C 72 ASP cc_start: 0.8324 (t70) cc_final: 0.7636 (t70) REVERT: D 30 ILE cc_start: 0.9026 (tt) cc_final: 0.8744 (tp) REVERT: D 72 ASP cc_start: 0.8336 (t70) cc_final: 0.7666 (t70) REVERT: D 145 TYR cc_start: 0.6992 (p90) cc_final: 0.6320 (p90) REVERT: H 30 ILE cc_start: 0.9033 (tt) cc_final: 0.8734 (tp) REVERT: H 38 ARG cc_start: 0.8121 (OUTLIER) cc_final: 0.7286 (ptm-80) REVERT: H 72 ASP cc_start: 0.8340 (t70) cc_final: 0.7672 (t70) REVERT: B 116 PHE cc_start: 0.5878 (m-10) cc_final: 0.5665 (m-10) REVERT: E 42 GLN cc_start: 0.7516 (mp10) cc_final: 0.7226 (mp10) REVERT: E 116 PHE cc_start: 0.5770 (m-80) cc_final: 0.5350 (m-10) REVERT: E 142 ARG cc_start: 0.8605 (ttp80) cc_final: 0.8322 (tpp80) REVERT: G 108 ARG cc_start: 0.7894 (ptm160) cc_final: 0.7643 (ptt90) REVERT: G 140 TYR cc_start: 0.6961 (OUTLIER) cc_final: 0.6706 (t80) REVERT: G 201 LEU cc_start: 0.6246 (OUTLIER) cc_final: 0.5945 (pp) REVERT: L 108 ARG cc_start: 0.7821 (ptm160) cc_final: 0.7617 (ptt90) REVERT: L 116 PHE cc_start: 0.5580 (m-10) cc_final: 0.5331 (m-10) outliers start: 82 outliers final: 58 residues processed: 358 average time/residue: 0.5885 time to fit residues: 243.9009 Evaluate side-chains 344 residues out of total 2708 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 276 time to evaluate : 0.832 ------------------------------------------------------------------------------- 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 359 SER Chi-restraints excluded: chain I residue 361 ILE Chi-restraints excluded: chain I residue 419 LYS 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 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 371 LYS 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 359 SER Chi-restraints excluded: chain W residue 371 LYS Chi-restraints excluded: chain A residue 17 SER Chi-restraints excluded: chain A residue 25 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 ASP Chi-restraints excluded: chain C residue 100 SER Chi-restraints excluded: chain C residue 100 SER 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 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 38 ARG 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 B residue 30 SER Chi-restraints excluded: chain B residue 174 SER Chi-restraints excluded: chain B residue 202 SER Chi-restraints excluded: chain E residue 30 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 140 TYR Chi-restraints excluded: chain G residue 176 SER Chi-restraints excluded: chain G residue 201 LEU Chi-restraints excluded: chain L residue 30 SER Chi-restraints excluded: chain L residue 76 SER Chi-restraints excluded: chain L residue 150 VAL 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: [24, 147, 98, 53, 51, 22, 65, 290, 226, 300, 294] chunk 24 skipped: trial refinement blew up (Bond distance > max_reasonable_bond_distance: 51.9485 > 50:) chunk 147 optimal weight: 10.0000 chunk 98 optimal weight: 2.9990 chunk 53 optimal weight: 3.9990 chunk 51 optimal weight: 0.8980 chunk 22 optimal weight: 1.9990 chunk 65 optimal weight: 1.9990 chunk 290 optimal weight: 30.0000 chunk 226 optimal weight: 10.0000 chunk 300 optimal weight: 9.9990 chunk 294 optimal weight: 5.9990 overall best weight: 2.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... I 101 HIS M 101 HIS N 101 HIS W 101 HIS D 171 GLN ** B 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 160 GLN ** G 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 155 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 155 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3913 r_free = 0.3913 target = 0.144257 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3106 r_free = 0.3106 target = 0.083534 restraints weight = 35990.078| |-----------------------------------------------------------------------------| r_work (start): 0.3005 rms_B_bonded: 2.33 r_work: 0.2872 rms_B_bonded: 2.43 restraints_weight: 0.5000 r_work: 0.2739 rms_B_bonded: 3.76 restraints_weight: 0.2500 r_work (final): 0.2739 ------------------------------------------------------------------------------- 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 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.2731 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8636 moved from start: 0.3590 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 25436 Z= 0.186 Angle : 0.618 9.083 34516 Z= 0.317 Chirality : 0.045 0.214 3808 Planarity : 0.005 0.074 4380 Dihedral : 5.205 37.158 3708 Min Nonbonded Distance : 2.296 Molprobity Statistics. All-atom Clashscore : 7.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.92 % Favored : 95.08 % Rotamer: Outliers : 3.43 % Allowed : 24.63 % Favored : 71.94 % 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: -1.52 (0.14), residues: 3148 helix: -4.11 (0.29), residues: 56 sheet: -0.08 (0.14), residues: 1272 loop : -1.65 (0.13), residues: 1820 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG E 108 TYR 0.018 0.002 TYR B 173 PHE 0.036 0.002 PHE D 100C TRP 0.008 0.001 TRP C 47 HIS 0.009 0.001 HIS N 101 Details of bonding type rmsd/Z covalent geometry : bond 0.00447 / 0.19 (25376) covalent geometry : angle 0.61328 / 0.32 (34384) SS BOND : bond 0.00294 / 0.20 ( 48) SS BOND : angle 1.31501 / 0.89 ( 96) hydrogen bonds : bond 0.03106 / 2.05 ( 706) hydrogen bonds : angle 4.74628 / 3.22 ( 1932) link_BETA1-4 : bond 0.00408 / 0.23 ( 8) link_BETA1-4 : angle 1.46574 / 0.92 ( 24) link_NAG-ASN : bond 0.00210 / 0.13 ( 4) link_NAG-ASN : angle 1.02113 / 0.59 ( 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 368 residues out of total 2708 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 93 poor density : 275 time to evaluate : 0.865 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: M 102 ARG cc_start: 0.6584 (ttm170) cc_final: 0.6368 (ttp-110) REVERT: M 338 GLU cc_start: 0.8353 (OUTLIER) cc_final: 0.8116 (mp0) REVERT: N 338 GLU cc_start: 0.8343 (OUTLIER) cc_final: 0.8063 (mp0) REVERT: N 371 LYS cc_start: 0.9256 (OUTLIER) cc_final: 0.8846 (ptpp) REVERT: N 419 LYS cc_start: 0.9135 (mttt) cc_final: 0.8896 (mttm) REVERT: W 338 GLU cc_start: 0.8357 (OUTLIER) cc_final: 0.8077 (mp0) REVERT: W 371 LYS cc_start: 0.9262 (OUTLIER) cc_final: 0.8845 (ptpp) REVERT: A 72 ASP cc_start: 0.8424 (t70) cc_final: 0.7789 (t70) REVERT: A 100 PHE cc_start: 0.7849 (OUTLIER) cc_final: 0.7560 (p90) REVERT: C 30 ILE cc_start: 0.9070 (tt) cc_final: 0.8769 (tp) REVERT: C 72 ASP cc_start: 0.8385 (t70) cc_final: 0.7711 (t70) REVERT: D 30 ILE cc_start: 0.9058 (tt) cc_final: 0.8777 (tp) REVERT: D 72 ASP cc_start: 0.8382 (t70) cc_final: 0.7702 (t70) REVERT: D 145 TYR cc_start: 0.7056 (p90) cc_final: 0.6475 (p90) REVERT: H 30 ILE cc_start: 0.9060 (tt) cc_final: 0.8757 (tp) REVERT: H 38 ARG cc_start: 0.8173 (OUTLIER) cc_final: 0.7438 (ptm-80) REVERT: H 72 ASP cc_start: 0.8381 (t70) cc_final: 0.7720 (t70) REVERT: B 116 PHE cc_start: 0.5868 (m-10) cc_final: 0.5559 (m-10) REVERT: B 142 ARG cc_start: 0.8492 (tpp80) cc_final: 0.7872 (ttm170) REVERT: B 201 LEU cc_start: 0.6533 (OUTLIER) cc_final: 0.6214 (pp) REVERT: E 42 GLN cc_start: 0.7529 (mp10) cc_final: 0.7227 (mp10) REVERT: E 116 PHE cc_start: 0.5799 (m-80) cc_final: 0.5362 (m-10) REVERT: E 142 ARG cc_start: 0.8622 (ttp80) cc_final: 0.8406 (tpp80) REVERT: G 108 ARG cc_start: 0.7943 (ptm160) cc_final: 0.7694 (ptt90) REVERT: G 140 TYR cc_start: 0.6985 (t80) cc_final: 0.6712 (t80) REVERT: G 201 LEU cc_start: 0.6095 (OUTLIER) cc_final: 0.5834 (pp) REVERT: L 108 ARG cc_start: 0.7878 (ptm160) cc_final: 0.7664 (ptt90) REVERT: L 116 PHE cc_start: 0.5624 (m-10) cc_final: 0.5374 (m-10) outliers start: 93 outliers final: 63 residues processed: 352 average time/residue: 0.5632 time to fit residues: 230.5960 Evaluate side-chains 340 residues out of total 2708 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 268 time to evaluate : 0.931 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 359 SER Chi-restraints excluded: chain I residue 361 ILE 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 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 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 359 SER Chi-restraints excluded: chain W residue 361 ILE 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 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 ASP Chi-restraints excluded: chain C residue 100 SER Chi-restraints excluded: chain C residue 100 SER 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 ASP Chi-restraints excluded: chain D residue 100 SER Chi-restraints excluded: chain H residue 17 SER Chi-restraints excluded: chain H residue 38 ARG 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 B residue 30 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 E residue 30 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 176 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 150 VAL Chi-restraints excluded: chain L residue 176 SER 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: [208, 163, 292, 224, 17, 186, 211, 104, 204, 306, 184] chunk 208 optimal weight: 40.0000 chunk 163 optimal weight: 30.0000 chunk 292 optimal weight: 0.9990 chunk 224 optimal weight: 2.9990 chunk 17 optimal weight: 3.9990 chunk 186 optimal weight: 40.0000 chunk 211 optimal weight: 0.0980 chunk 104 optimal weight: 0.6980 chunk 204 optimal weight: 7.9990 chunk 306 optimal weight: 30.0000 chunk 184 optimal weight: 9.9990 overall best weight: 1.7586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... I 101 HIS M 101 HIS N 101 HIS ** B 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 160 GLN ** G 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 155 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 155 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3920 r_free = 0.3920 target = 0.144850 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3119 r_free = 0.3119 target = 0.084315 restraints weight = 35996.842| |-----------------------------------------------------------------------------| r_work (start): 0.3023 rms_B_bonded: 2.69 r_work: 0.2872 rms_B_bonded: 2.64 restraints_weight: 0.5000 r_work: 0.2738 rms_B_bonded: 4.07 restraints_weight: 0.2500 r_work (final): 0.2738 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2722 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2722 r_free = 0.2722 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 = 0.2722 r_free = 0.2722 target_work(ls_wunit_k1) = 0.062 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.2722 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8606 moved from start: 0.3687 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 25436 Z= 0.149 Angle : 0.599 8.995 34516 Z= 0.308 Chirality : 0.044 0.180 3808 Planarity : 0.005 0.069 4380 Dihedral : 5.097 37.603 3708 Min Nonbonded Distance : 2.317 Molprobity Statistics. All-atom Clashscore : 7.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.26 % Favored : 95.74 % Rotamer: Outliers : 2.92 % Allowed : 25.00 % Favored : 72.08 % 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: -1.41 (0.14), residues: 3148 helix: -3.97 (0.33), residues: 56 sheet: 0.02 (0.14), residues: 1272 loop : -1.60 (0.13), residues: 1820 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG B 108 TYR 0.026 0.001 TYR E 140 PHE 0.027 0.002 PHE H 100C TRP 0.009 0.001 TRP C 47 HIS 0.009 0.001 HIS N 101 Details of bonding type rmsd/Z covalent geometry : bond 0.00353 / 0.15 (25376) covalent geometry : angle 0.59617 / 0.31 (34384) SS BOND : bond 0.00241 / 0.16 ( 48) SS BOND : angle 1.13948 / 0.77 ( 96) hydrogen bonds : bond 0.02947 / 1.94 ( 706) hydrogen bonds : angle 4.67044 / 3.17 ( 1932) link_BETA1-4 : bond 0.00422 / 0.23 ( 8) link_BETA1-4 : angle 1.42358 / 0.90 ( 24) link_NAG-ASN : bond 0.00124 / 0.07 ( 4) link_NAG-ASN : angle 0.95463 / 0.53 ( 12) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 12288.64 seconds wall clock time: 209 minutes 2.26 seconds (12542.26 seconds total)