Starting phenix.real_space_refine on Sun Jul 5 01:42:41 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6v4o_21043/07_2026/6v4o_21043_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/6v4o_21043/07_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_21043/07_2026/6v4o_21043_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6v4o_21043/07_2026/6v4o_21043_neut.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/6v4o_21043/07_2026/6v4o_21043.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6v4o_21043/07_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): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/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, 11 Ad-hoc single atom residues: {' CA': 1} Unusual residues: {'BMA': 1} Classifications: {'undetermined': 1} Chain breaks: 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: 5.04, 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=36, symmetry=0 Simple disulfide: pdb=" SG CYS I 87 " - pdb=" SG CYS I 420 " distance=2.03 Simple disulfide: pdb=" SG CYS I 122 " - pdb=" SG CYS I 127 " distance=2.03 Simple disulfide: pdb=" SG CYS I 182 " - pdb=" SG CYS I 229 " distance=2.03 Simple disulfide: pdb=" SG CYS I 231 " - pdb=" SG CYS I 236 " distance=2.03 Simple disulfide: pdb=" SG CYS I 277 " - pdb=" SG CYS I 291 " distance=2.02 Simple disulfide: pdb=" SG CYS I 279 " - pdb=" SG CYS I 289 " distance=2.02 Simple disulfide: pdb=" SG CYS I 318 " - pdb=" SG CYS I 337 " distance=2.03 Simple disulfide: pdb=" SG CYS I 424 " - pdb=" SG CYS I 447 " distance=2.03 Simple disulfide: pdb=" SG CYS M 231 " - pdb=" SG CYS M 231 " distance=0.00 Simple disulfide: pdb=" SG CYS M 231 " - pdb=" SG CYS M 236 " distance=2.03 Simple disulfide: pdb=" SG CYS N 127 " - pdb=" SG CYS N 122 " distance=2.03 Simple disulfide: pdb=" SG CYS N 127 " - pdb=" SG CYS N 127 " distance=0.00 Simple disulfide: pdb=" SG CYS M 87 " - pdb=" SG CYS M 420 " distance=2.03 Simple disulfide: pdb=" SG CYS N 87 " - pdb=" SG CYS N 420 " distance=2.03 Simple disulfide: pdb=" SG CYS W 87 " - pdb=" SG CYS W 420 " distance=2.03 Simple disulfide: pdb=" SG CYS M 122 " - pdb=" SG CYS M 127 " distance=2.03 Simple disulfide: pdb=" SG CYS N 122 " - pdb=" SG CYS N 127 " distance=2.03 Simple disulfide: pdb=" SG CYS W 122 " - pdb=" SG CYS W 127 " distance=2.03 Simple disulfide: pdb=" SG CYS M 182 " - pdb=" SG CYS M 229 " distance=2.03 Simple disulfide: pdb=" SG CYS N 182 " - pdb=" SG CYS N 229 " distance=2.03 Simple disulfide: pdb=" SG CYS W 182 " - pdb=" SG CYS W 229 " distance=2.03 Simple disulfide: pdb=" SG CYS M 231 " - pdb=" SG CYS M 236 " distance=2.03 Simple disulfide: pdb=" SG CYS N 231 " - pdb=" SG CYS N 236 " distance=2.03 Simple disulfide: pdb=" SG CYS W 231 " - pdb=" SG CYS W 236 " distance=2.03 Simple disulfide: pdb=" SG CYS M 277 " - pdb=" SG CYS M 291 " distance=2.02 Simple disulfide: pdb=" SG CYS N 277 " - pdb=" SG CYS N 291 " distance=2.02 Simple disulfide: pdb=" SG CYS W 277 " - pdb=" SG CYS W 291 " distance=2.02 Simple disulfide: pdb=" SG CYS M 279 " - pdb=" SG CYS M 289 " distance=2.03 Simple disulfide: pdb=" SG CYS N 279 " - pdb=" SG CYS N 289 " distance=2.02 Simple disulfide: pdb=" SG CYS W 279 " - pdb=" SG CYS W 289 " distance=2.03 Simple disulfide: pdb=" SG CYS M 318 " - pdb=" SG CYS M 337 " distance=2.03 Simple disulfide: pdb=" SG CYS N 318 " - pdb=" SG CYS N 337 " distance=2.03 Simple disulfide: pdb=" SG CYS W 318 " - pdb=" SG CYS W 337 " distance=2.03 Simple disulfide: pdb=" SG CYS M 424 " - pdb=" SG CYS M 447 " distance=2.03 Simple disulfide: pdb=" SG CYS N 424 " - pdb=" SG CYS N 447 " distance=2.03 Simple disulfide: pdb=" SG CYS W 424 " - pdb=" SG CYS W 447 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied BETA1-4 " NAG F 1 " - " NAG F 2 " " NAG F 2 " - " BMA I 503 " " NAG J 1 " - " NAG J 2 " " NAG J 2 " - " BMA M 503 " " NAG K 1 " - " NAG K 2 " " NAG K 2 " - " BMA N 503 " " NAG O 1 " - " NAG O 2 " " NAG O 2 " - " BMA W 503 " NAG-ASN " NAG F 1 " - " ASN I 284 " " NAG J 1 " - " ASN M 284 " " NAG K 1 " - " ASN N 284 " " NAG O 1 " - " ASN W 284 " Time building additional restraints: 2.23 Conformation dependent library (CDL) restraints added in 1.1 seconds 6296 Ramachandran restraints generated. 3148 Oldfield, 0 Emsley, 3148 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5856 Finding SS restraints... Secondary structure from input PDB file: 32 helices and 68 sheets defined 5.2% alpha, 40.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.17 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: 5.78 Time building geometry restraints manager: 2.96 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 7952 1.34 - 1.46: 6422 1.46 - 1.58: 10798 1.58 - 1.70: 0 1.70 - 1.82: 204 Bond restraints: 25376 Sorted by residual: bond pdb=" CA LYS I 255 " pdb=" CB LYS I 255 " ideal model delta sigma weight residual 1.526 1.446 0.080 1.53e-02 4.27e+03 2.76e+01 bond pdb=" CA LYS M 255 " pdb=" CB LYS M 255 " ideal model delta sigma weight residual 1.526 1.446 0.080 1.53e-02 4.27e+03 2.75e+01 bond pdb=" CA LYS W 255 " pdb=" CB LYS W 255 " ideal model delta sigma weight residual 1.526 1.446 0.080 1.53e-02 4.27e+03 2.75e+01 bond pdb=" CA LYS N 255 " pdb=" CB LYS N 255 " ideal model delta sigma weight residual 1.526 1.446 0.080 1.53e-02 4.27e+03 2.75e+01 bond pdb=" C GLU I 404 " pdb=" N GLU I 405 " ideal model delta sigma weight residual 1.327 1.274 0.053 1.71e-02 3.42e+03 9.51e+00 ... (remaining 25371 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.76: 33957 2.76 - 5.51: 399 5.51 - 8.27: 20 8.27 - 11.03: 0 11.03 - 13.79: 8 Bond angle restraints: 34384 Sorted by residual: angle pdb=" C GLY I 145 " pdb=" N THR I 146 " pdb=" CA THR I 146 " ideal model delta sigma weight residual 120.95 134.29 -13.34 1.78e+00 3.16e-01 5.61e+01 angle pdb=" C GLY M 145 " pdb=" N THR M 146 " pdb=" CA THR M 146 " ideal model delta sigma weight residual 120.95 134.25 -13.30 1.78e+00 3.16e-01 5.58e+01 angle pdb=" C GLY W 145 " pdb=" N THR W 146 " pdb=" CA THR W 146 " ideal model delta sigma weight residual 120.95 134.21 -13.26 1.78e+00 3.16e-01 5.55e+01 angle pdb=" C GLY N 145 " pdb=" N THR N 146 " pdb=" CA THR N 146 " ideal model delta sigma weight residual 120.95 134.21 -13.26 1.78e+00 3.16e-01 5.55e+01 angle pdb=" C TRP I 408 " pdb=" N TYR I 409 " pdb=" CA TYR I 409 " ideal model delta sigma weight residual 121.54 135.33 -13.79 1.91e+00 2.74e-01 5.21e+01 ... (remaining 34379 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 21.54: 14169 21.54 - 43.08: 935 43.08 - 64.63: 196 64.63 - 86.17: 40 86.17 - 107.71: 20 Dihedral angle restraints: 15360 sinusoidal: 6192 harmonic: 9168 Sorted by residual: dihedral pdb=" CA THR C 183 " pdb=" C THR C 183 " pdb=" N VAL C 184 " pdb=" CA VAL C 184 " ideal model delta harmonic sigma weight residual 180.00 -145.98 -34.02 0 5.00e+00 4.00e-02 4.63e+01 dihedral pdb=" CA THR A 183 " pdb=" C THR A 183 " pdb=" N VAL A 184 " pdb=" CA VAL A 184 " ideal model delta harmonic sigma weight residual 180.00 -145.99 -34.01 0 5.00e+00 4.00e-02 4.63e+01 dihedral pdb=" CA THR H 183 " pdb=" C THR H 183 " pdb=" N VAL H 184 " pdb=" CA VAL H 184 " ideal model delta harmonic sigma weight residual -180.00 -146.00 -34.00 0 5.00e+00 4.00e-02 4.62e+01 ... (remaining 15357 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.336: 3804 0.336 - 0.671: 0 0.671 - 1.007: 0 1.007 - 1.343: 0 1.343 - 1.679: 4 Chirality restraints: 3808 Sorted by residual: chirality pdb=" C1 BMA W 503 " pdb=" O4 NAG O 2 " pdb=" C2 BMA W 503 " pdb=" O5 BMA W 503 " both_signs ideal model delta sigma weight residual False -2.40 -0.72 -1.68 2.00e-02 2.50e+03 7.04e+03 chirality pdb=" C1 BMA N 503 " pdb=" O4 NAG K 2 " pdb=" C2 BMA N 503 " pdb=" O5 BMA N 503 " both_signs ideal model delta sigma weight residual False -2.40 -0.72 -1.68 2.00e-02 2.50e+03 7.04e+03 chirality pdb=" C1 BMA I 503 " pdb=" O4 NAG F 2 " pdb=" C2 BMA I 503 " pdb=" O5 BMA I 503 " both_signs ideal model delta sigma weight residual False -2.40 -0.72 -1.68 2.00e-02 2.50e+03 7.03e+03 ... (remaining 3805 not shown) Planarity restraints: 4384 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB PHE D 100C" -0.024 2.00e-02 2.50e+03 1.68e-02 4.92e+00 pdb=" CG PHE D 100C" 0.035 2.00e-02 2.50e+03 pdb=" CD1 PHE D 100C" 0.003 2.00e-02 2.50e+03 pdb=" CD2 PHE D 100C" 0.003 2.00e-02 2.50e+03 pdb=" CE1 PHE D 100C" -0.004 2.00e-02 2.50e+03 pdb=" CE2 PHE D 100C" -0.004 2.00e-02 2.50e+03 pdb=" CZ PHE D 100C" -0.009 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE H 100C" -0.024 2.00e-02 2.50e+03 1.67e-02 4.86e+00 pdb=" CG PHE H 100C" 0.035 2.00e-02 2.50e+03 pdb=" CD1 PHE H 100C" 0.004 2.00e-02 2.50e+03 pdb=" CD2 PHE H 100C" 0.002 2.00e-02 2.50e+03 pdb=" CE1 PHE H 100C" -0.004 2.00e-02 2.50e+03 pdb=" CE2 PHE H 100C" -0.003 2.00e-02 2.50e+03 pdb=" CZ PHE H 100C" -0.009 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE A 100C" 0.024 2.00e-02 2.50e+03 1.66e-02 4.85e+00 pdb=" CG PHE A 100C" -0.035 2.00e-02 2.50e+03 pdb=" CD1 PHE A 100C" -0.004 2.00e-02 2.50e+03 pdb=" CD2 PHE A 100C" -0.003 2.00e-02 2.50e+03 pdb=" CE1 PHE A 100C" 0.004 2.00e-02 2.50e+03 pdb=" CE2 PHE A 100C" 0.003 2.00e-02 2.50e+03 pdb=" CZ PHE A 100C" 0.009 2.00e-02 2.50e+03 ... (remaining 4381 not shown) Histogram of nonbonded interaction distances: 1.60 - 2.26: 61 2.26 - 2.92: 11380 2.92 - 3.58: 32148 3.58 - 4.24: 58633 4.24 - 4.90: 99748 Nonbonded interactions: 201970 Sorted by model distance: nonbonded pdb=" OG1 THR H 135 " pdb=" O VAL H 184 " model vdw 1.602 3.040 nonbonded pdb=" OG1 THR C 135 " pdb=" O VAL C 184 " model vdw 1.602 3.040 nonbonded pdb=" OG1 THR A 135 " pdb=" O VAL A 184 " model vdw 1.603 3.040 nonbonded pdb=" OG1 THR D 135 " pdb=" O VAL D 184 " model vdw 1.603 3.040 nonbonded pdb=" O GLN B 124 " pdb=" OG SER B 127 " model vdw 2.002 3.040 ... (remaining 201965 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.08 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: 1.610 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: 0.460 Check model and map are aligned: 0.080 Set scattering table: 0.060 Process input model: 24.600 Find NCS groups from input model: 0.230 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:6.680 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 33.810 ------------------------------------------------------------------------------- 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 25420 Z= 0.463 Angle : 0.917 29.051 34486 Z= 0.484 Chirality : 0.075 1.679 3808 Planarity : 0.005 0.047 4380 Dihedral : 15.492 107.711 9404 Min Nonbonded Distance : 1.602 Molprobity Statistics. All-atom Clashscore : 7.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.88 % Favored : 90.12 % Rotamer: Outliers : 2.95 % Allowed : 13.44 % Favored : 83.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.63 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.13 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -4.27 (0.12), residues: 3148 helix: -5.17 (0.18), residues: 28 sheet: -1.94 (0.13), residues: 1240 loop : -3.61 (0.10), residues: 1880 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG N 154 TYR 0.012 0.001 TYR N 383 PHE 0.035 0.002 PHE D 100C TRP 0.011 0.001 TRP D 154 HIS 0.006 0.001 HIS N 183 Details of bonding type rmsd/Z covalent geometry : bond 0.01096 / 0.45 (25376) covalent geometry : angle 0.81251 / 0.46 (34384) SS BOND : bond 0.00452 / 0.28 ( 32) SS BOND : angle 2.08091 / 1.53 ( 66) 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 : 0.974 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: 0.7304 time to fit residues: 405.8660 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 : 1.164 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain I residue 87 CYS Chi-restraints excluded: chain I residue 182 CYS Chi-restraints excluded: chain I residue 229 CYS Chi-restraints excluded: chain I residue 366 SER Chi-restraints excluded: chain I residue 420 CYS Chi-restraints excluded: chain M residue 87 CYS Chi-restraints excluded: chain M residue 182 CYS Chi-restraints excluded: chain M residue 229 CYS Chi-restraints excluded: chain M residue 366 SER Chi-restraints excluded: chain M residue 420 CYS Chi-restraints excluded: chain N residue 87 CYS Chi-restraints excluded: chain N residue 182 CYS Chi-restraints excluded: chain N residue 229 CYS Chi-restraints excluded: chain N residue 366 SER Chi-restraints excluded: chain N residue 420 CYS Chi-restraints excluded: chain W residue 87 CYS Chi-restraints excluded: chain W residue 182 CYS Chi-restraints excluded: chain W residue 229 CYS Chi-restraints excluded: chain W residue 366 SER Chi-restraints excluded: chain W residue 420 CYS Chi-restraints excluded: chain C residue 81 ASP Chi-restraints excluded: chain C residue 173 SER Chi-restraints excluded: chain D residue 81 ASP Chi-restraints excluded: chain D residue 173 SER Chi-restraints excluded: chain H residue 81 ASP Chi-restraints excluded: chain H residue 173 SER Chi-restraints excluded: chain B residue 33 LEU Chi-restraints excluded: chain B residue 49 ASN Chi-restraints excluded: chain B residue 143 GLU Chi-restraints excluded: chain E residue 33 LEU Chi-restraints excluded: chain E residue 143 GLU Chi-restraints excluded: chain G residue 32 SER Chi-restraints excluded: chain G residue 143 GLU Chi-restraints excluded: chain L residue 143 GLU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 316 random chunks: chunk 197 optimal weight: 5.9990 chunk 215 optimal weight: 3.9990 chunk 20 optimal weight: 0.9980 chunk 132 optimal weight: 1.9990 chunk 261 optimal weight: 0.8980 chunk 248 optimal weight: 8.9990 chunk 207 optimal weight: 5.9990 chunk 155 optimal weight: 2.9990 chunk 244 optimal weight: 0.9980 chunk 183 optimal weight: 9.9990 chunk 298 optimal weight: 0.9980 overall best weight: 1.1782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... I 431 HIS M 329 ASN M 431 HIS N 329 ASN N 431 HIS W 431 HIS A 39 GLN A 204 ASN ** C 164 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 204 ASN D 204 ASN H 155 ASN ** H 164 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 204 ASN ** B 147 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 166 GLN ** B 198 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 199 GLN ** E 198 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 166 GLN ** G 198 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 6 GLN L 166 GLN ** L 198 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3962 r_free = 0.3962 target = 0.147927 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3188 r_free = 0.3188 target = 0.088881 restraints weight = 36690.111| |-----------------------------------------------------------------------------| r_work (start): 0.3093 rms_B_bonded: 2.38 r_work: 0.2966 rms_B_bonded: 2.49 restraints_weight: 0.5000 r_work: 0.2831 rms_B_bonded: 3.91 restraints_weight: 0.2500 r_work (final): 0.2831 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2822 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2822 r_free = 0.2822 target_work(ls_wunit_k1) = 0.068 | | occupancies: max = 1.00 min = 0.05 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2822 r_free = 0.2822 target_work(ls_wunit_k1) = 0.068 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 7 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (6 function evaluations) r_final: 0.2822 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8560 moved from start: 0.1965 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 25420 Z= 0.143 Angle : 0.676 7.292 34486 Z= 0.354 Chirality : 0.048 0.259 3808 Planarity : 0.005 0.050 4380 Dihedral : 8.466 55.950 3748 Min Nonbonded Distance : 2.455 Molprobity Statistics. All-atom Clashscore : 6.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.53 % Favored : 94.47 % Rotamer: Outliers : 4.69 % Allowed : 17.87 % Favored : 77.44 % 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: -3.01 (0.13), residues: 3148 helix: -4.59 (0.16), residues: 32 sheet: -1.38 (0.14), residues: 1264 loop : -2.48 (0.12), residues: 1852 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG C 83 TYR 0.020 0.002 TYR G 186 PHE 0.017 0.002 PHE D 100C TRP 0.012 0.001 TRP N 408 HIS 0.012 0.001 HIS A 164 Details of bonding type rmsd/Z covalent geometry : bond 0.00317 / 0.14 (25376) covalent geometry : angle 0.67287 / 0.35 (34384) SS BOND : bond 0.00115 / 0.07 ( 32) SS BOND : angle 0.86704 / 0.56 ( 66) hydrogen bonds : bond 0.03798 / 2.49 ( 706) hydrogen bonds : angle 6.07466 / 4.12 ( 1932) link_BETA1-4 : bond 0.00880 / 0.46 ( 8) link_BETA1-4 : angle 2.29543 / 1.47 ( 24) link_NAG-ASN : bond 0.00144 / 0.09 ( 4) link_NAG-ASN : angle 1.10308 / 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 483 residues out of total 2708 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 127 poor density : 356 time to evaluate : 0.998 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: 0.9303 (mmm) cc_final: 0.8883 (mmt) REVERT: I 390 ASP cc_start: 0.7323 (OUTLIER) cc_final: 0.6663 (m-30) REVERT: M 375 MET cc_start: 0.9237 (mmm) cc_final: 0.8986 (mmt) REVERT: M 384 ASP cc_start: 0.8491 (m-30) cc_final: 0.8186 (m-30) REVERT: M 390 ASP cc_start: 0.7296 (OUTLIER) cc_final: 0.6644 (m-30) REVERT: N 375 MET cc_start: 0.9289 (mmm) cc_final: 0.9043 (mmm) REVERT: N 384 ASP cc_start: 0.8477 (m-30) cc_final: 0.8188 (m-30) REVERT: N 390 ASP cc_start: 0.7290 (OUTLIER) cc_final: 0.6667 (m-30) REVERT: W 384 ASP cc_start: 0.8374 (m-30) cc_final: 0.8089 (m-30) REVERT: W 390 ASP cc_start: 0.7238 (OUTLIER) cc_final: 0.6583 (m-30) REVERT: W 429 MET cc_start: 0.9343 (mtp) cc_final: 0.9133 (mtp) REVERT: A 72 ASP cc_start: 0.8055 (t70) cc_final: 0.7282 (t70) REVERT: A 145 TYR cc_start: 0.6953 (p90) cc_final: 0.6471 (p90) REVERT: A 176 TYR cc_start: 0.7169 (m-80) cc_final: 0.6949 (m-80) REVERT: C 30 ILE cc_start: 0.9002 (tt) cc_final: 0.8709 (tp) REVERT: C 72 ASP cc_start: 0.7749 (t70) cc_final: 0.7004 (t70) REVERT: C 176 TYR cc_start: 0.6994 (m-80) cc_final: 0.6755 (m-80) REVERT: D 30 ILE cc_start: 0.9116 (tt) cc_final: 0.8807 (tp) REVERT: D 72 ASP cc_start: 0.7778 (t70) cc_final: 0.7019 (t70) REVERT: D 100 TYR cc_start: 0.9079 (m-80) cc_final: 0.8729 (m-80) REVERT: D 145 TYR cc_start: 0.6859 (p90) cc_final: 0.6380 (p90) REVERT: D 176 TYR cc_start: 0.7333 (m-80) cc_final: 0.6883 (m-10) REVERT: H 30 ILE cc_start: 0.8987 (tt) cc_final: 0.8688 (tp) REVERT: H 72 ASP cc_start: 0.7801 (t70) cc_final: 0.7069 (t70) REVERT: H 81 ASP cc_start: 0.7992 (t70) cc_final: 0.7761 (t0) REVERT: H 100 TYR cc_start: 0.9104 (m-80) cc_final: 0.8821 (m-80) REVERT: H 145 TYR cc_start: 0.6616 (p90) cc_final: 0.6033 (p90) REVERT: H 176 TYR cc_start: 0.7322 (m-80) cc_final: 0.6839 (m-10) REVERT: B 24 ARG cc_start: 0.7963 (OUTLIER) cc_final: 0.7741 (ttt-90) REVERT: B 143 GLU cc_start: 0.8310 (OUTLIER) cc_final: 0.7966 (tm-30) REVERT: E 143 GLU cc_start: 0.8454 (OUTLIER) cc_final: 0.8191 (tm-30) REVERT: E 160 GLN cc_start: 0.5859 (mt0) cc_final: 0.5633 (mt0) REVERT: E 165 GLU cc_start: 0.8234 (tp30) cc_final: 0.7800 (mp0) REVERT: E 190 LYS cc_start: 0.8053 (mmmt) cc_final: 0.7636 (tptt) REVERT: G 24 ARG cc_start: 0.7940 (OUTLIER) cc_final: 0.7740 (ttt-90) REVERT: G 108 ARG cc_start: 0.7746 (ptm160) cc_final: 0.6868 (ptm-80) REVERT: G 143 GLU cc_start: 0.8413 (OUTLIER) cc_final: 0.8204 (tm-30) REVERT: L 6 GLN cc_start: 0.8142 (OUTLIER) cc_final: 0.7332 (mt0) REVERT: L 18 ARG cc_start: 0.8435 (OUTLIER) cc_final: 0.7421 (ttm110) outliers start: 127 outliers final: 67 residues processed: 459 average time/residue: 0.6347 time to fit residues: 337.2522 Evaluate side-chains 395 residues out of total 2708 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 317 time to evaluate : 0.965 ------------------------------------------------------------------------------- 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 366 SER Chi-restraints excluded: chain M residue 390 ASP Chi-restraints excluded: chain M residue 410 SER Chi-restraints excluded: chain N residue 182 CYS Chi-restraints excluded: chain N residue 198 SER Chi-restraints excluded: chain N residue 229 CYS Chi-restraints excluded: chain N residue 307 VAL Chi-restraints excluded: chain N residue 337 CYS Chi-restraints excluded: chain N residue 366 SER Chi-restraints excluded: chain N residue 390 ASP Chi-restraints excluded: chain N residue 410 SER Chi-restraints excluded: chain W residue 182 CYS Chi-restraints excluded: chain W residue 198 SER Chi-restraints excluded: chain W residue 229 CYS Chi-restraints excluded: chain W residue 307 VAL Chi-restraints excluded: chain W residue 337 CYS Chi-restraints excluded: chain W residue 366 SER Chi-restraints excluded: chain W residue 390 ASP Chi-restraints excluded: chain W residue 410 SER Chi-restraints excluded: chain A residue 17 SER Chi-restraints excluded: chain A residue 28 THR Chi-restraints excluded: chain A residue 87 THR Chi-restraints excluded: chain A residue 184 VAL Chi-restraints excluded: chain C residue 17 SER Chi-restraints excluded: chain C residue 87 THR Chi-restraints excluded: chain C residue 100 ASP Chi-restraints excluded: chain C residue 184 VAL Chi-restraints excluded: chain C residue 193 THR Chi-restraints excluded: chain D residue 17 SER Chi-restraints excluded: chain D residue 87 THR Chi-restraints excluded: chain D residue 100 ASP Chi-restraints excluded: chain D residue 184 VAL Chi-restraints excluded: chain H residue 17 SER Chi-restraints excluded: chain H residue 87 THR Chi-restraints excluded: chain H residue 100 ASP Chi-restraints excluded: chain H residue 184 VAL Chi-restraints excluded: chain B residue 24 ARG Chi-restraints excluded: chain B residue 30 SER Chi-restraints excluded: chain B residue 33 LEU Chi-restraints excluded: chain B residue 76 SER Chi-restraints excluded: chain B residue 143 GLU Chi-restraints excluded: chain B residue 182 SER Chi-restraints excluded: chain B residue 202 SER Chi-restraints excluded: chain B residue 206 THR Chi-restraints excluded: chain E residue 30 SER Chi-restraints excluded: chain E residue 33 LEU Chi-restraints excluded: chain E residue 49 ASN Chi-restraints excluded: chain E residue 76 SER Chi-restraints excluded: chain E residue 143 GLU Chi-restraints excluded: chain E residue 150 VAL Chi-restraints excluded: chain G residue 24 ARG Chi-restraints excluded: chain G residue 30 SER Chi-restraints excluded: chain G residue 33 LEU Chi-restraints excluded: chain G residue 76 SER Chi-restraints excluded: chain G residue 143 GLU Chi-restraints excluded: chain G residue 160 GLN Chi-restraints excluded: chain G residue 182 SER Chi-restraints excluded: chain G residue 206 THR Chi-restraints excluded: chain L residue 6 GLN Chi-restraints excluded: chain L residue 18 ARG Chi-restraints excluded: chain L residue 30 SER Chi-restraints excluded: chain L residue 33 LEU Chi-restraints excluded: chain L residue 76 SER Chi-restraints excluded: chain L residue 150 VAL Chi-restraints excluded: chain L residue 206 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 316 random chunks: chunk 49 optimal weight: 4.9990 chunk 58 optimal weight: 6.9990 chunk 57 optimal weight: 0.5980 chunk 310 optimal weight: 0.9990 chunk 151 optimal weight: 4.9990 chunk 95 optimal weight: 5.9990 chunk 199 optimal weight: 7.9990 chunk 280 optimal weight: 8.9990 chunk 0 optimal weight: 8.9990 chunk 110 optimal weight: 2.9990 chunk 70 optimal weight: 4.9990 overall best weight: 2.9188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... I 183 HIS I 225 GLN M 183 HIS M 225 GLN N 183 HIS N 225 GLN W 183 HIS W 225 GLN ** B 147 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 166 GLN E 27 GLN ** G 155 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 166 GLN L 27 GLN ** L 155 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 166 GLN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3911 r_free = 0.3911 target = 0.144006 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3100 r_free = 0.3100 target = 0.083607 restraints weight = 36756.717| |-----------------------------------------------------------------------------| r_work (start): 0.3005 rms_B_bonded: 2.34 r_work: 0.2878 rms_B_bonded: 2.43 restraints_weight: 0.5000 r_work: 0.2743 rms_B_bonded: 3.79 restraints_weight: 0.2500 r_work (final): 0.2743 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2722 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2722 r_free = 0.2722 target_work(ls_wunit_k1) = 0.063 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 7 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2722 r_free = 0.2722 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 (8 function evaluations) r_final: 0.2722 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8618 moved from start: 0.2534 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.042 25420 Z= 0.228 Angle : 0.655 7.591 34486 Z= 0.344 Chirality : 0.047 0.192 3808 Planarity : 0.005 0.060 4380 Dihedral : 6.896 55.990 3725 Min Nonbonded Distance : 2.506 Molprobity Statistics. All-atom Clashscore : 6.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.11 % Favored : 94.89 % Rotamer: Outliers : 4.87 % Allowed : 19.53 % Favored : 75.59 % 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: -2.38 (0.13), residues: 3148 helix: -4.44 (0.15), residues: 32 sheet: -0.91 (0.14), residues: 1264 loop : -2.07 (0.13), residues: 1852 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG N 79 TYR 0.022 0.002 TYR B 173 PHE 0.032 0.002 PHE H 100C TRP 0.016 0.001 TRP G 148 HIS 0.004 0.001 HIS W 215 Details of bonding type rmsd/Z covalent geometry : bond 0.00536 / 0.23 (25376) covalent geometry : angle 0.65030 / 0.34 (34384) SS BOND : bond 0.00355 / 0.24 ( 32) SS BOND : angle 1.43577 / 0.99 ( 66) hydrogen bonds : bond 0.03890 / 2.54 ( 706) hydrogen bonds : angle 5.58840 / 3.81 ( 1932) link_BETA1-4 : bond 0.00476 / 0.28 ( 8) link_BETA1-4 : angle 2.10807 / 1.37 ( 24) link_NAG-ASN : bond 0.00309 / 0.18 ( 4) link_NAG-ASN : angle 1.09172 / 0.60 ( 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 461 residues out of total 2708 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 132 poor density : 329 time to evaluate : 0.994 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: 0.7657 (OUTLIER) cc_final: 0.7266 (m-30) REVERT: M 419 LYS cc_start: 0.9193 (mttt) cc_final: 0.8940 (mttm) REVERT: A 72 ASP cc_start: 0.8242 (t70) cc_final: 0.7478 (t70) REVERT: A 138 LEU cc_start: 0.6581 (pp) cc_final: 0.6309 (pt) REVERT: A 145 TYR cc_start: 0.7008 (p90) cc_final: 0.6491 (p90) REVERT: A 176 TYR cc_start: 0.7310 (m-80) cc_final: 0.7060 (m-80) REVERT: C 30 ILE cc_start: 0.9062 (tt) cc_final: 0.8770 (tp) REVERT: C 72 ASP cc_start: 0.8035 (t70) cc_final: 0.7268 (t70) REVERT: C 145 TYR cc_start: 0.6330 (p90) cc_final: 0.5910 (p90) REVERT: D 30 ILE cc_start: 0.9070 (tt) cc_final: 0.8808 (tp) REVERT: D 72 ASP cc_start: 0.8042 (t70) cc_final: 0.7248 (t70) REVERT: D 145 TYR cc_start: 0.7078 (p90) cc_final: 0.6583 (p90) REVERT: D 176 TYR cc_start: 0.7354 (m-80) cc_final: 0.6832 (m-10) REVERT: H 30 ILE cc_start: 0.9053 (tt) cc_final: 0.8754 (tp) REVERT: H 72 ASP cc_start: 0.8022 (t70) cc_final: 0.7239 (t70) REVERT: H 81 ASP cc_start: 0.8111 (t70) cc_final: 0.7896 (t0) REVERT: H 145 TYR cc_start: 0.7040 (p90) cc_final: 0.6433 (p90) REVERT: H 176 TYR cc_start: 0.7553 (m-80) cc_final: 0.7092 (m-10) REVERT: B 143 GLU cc_start: 0.8349 (OUTLIER) cc_final: 0.8100 (tm-30) REVERT: B 165 GLU cc_start: 0.8308 (tp30) cc_final: 0.7782 (tp30) REVERT: B 166 GLN cc_start: 0.8830 (OUTLIER) cc_final: 0.8319 (tt0) REVERT: E 42 GLN cc_start: 0.7611 (mp10) cc_final: 0.7394 (mp10) REVERT: E 108 ARG cc_start: 0.8014 (ptm160) cc_final: 0.7616 (ptm-80) REVERT: E 190 LYS cc_start: 0.8021 (mmmt) cc_final: 0.7736 (tptt) REVERT: G 108 ARG cc_start: 0.7767 (ptm160) cc_final: 0.7491 (ptm-80) REVERT: G 143 GLU cc_start: 0.8370 (OUTLIER) cc_final: 0.8137 (tm-30) REVERT: G 165 GLU cc_start: 0.8055 (tp30) cc_final: 0.7423 (tp30) REVERT: G 166 GLN cc_start: 0.8785 (OUTLIER) cc_final: 0.8367 (tt0) REVERT: G 173 TYR cc_start: 0.8135 (m-80) cc_final: 0.7860 (m-10) REVERT: L 108 ARG cc_start: 0.7636 (ptm160) cc_final: 0.6901 (ptm-80) REVERT: L 143 GLU cc_start: 0.8090 (OUTLIER) cc_final: 0.7868 (tm-30) REVERT: L 173 TYR cc_start: 0.8081 (m-10) cc_final: 0.7816 (m-10) outliers start: 132 outliers final: 83 residues processed: 432 average time/residue: 0.6195 time to fit residues: 310.2578 Evaluate side-chains 381 residues out of total 2708 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 89 poor density : 292 time to evaluate : 0.994 ------------------------------------------------------------------------------- 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 357 MET Chi-restraints excluded: chain I residue 359 SER Chi-restraints excluded: chain I residue 366 SER Chi-restraints excluded: chain I residue 390 ASP Chi-restraints excluded: chain M residue 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 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 357 MET Chi-restraints excluded: chain N residue 359 SER Chi-restraints excluded: chain N residue 366 SER 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 357 MET Chi-restraints excluded: chain W residue 359 SER Chi-restraints excluded: chain W residue 366 SER Chi-restraints excluded: chain A residue 17 SER Chi-restraints excluded: chain A residue 87 THR Chi-restraints excluded: chain A residue 100 ASP Chi-restraints excluded: chain A residue 159 LEU Chi-restraints excluded: chain A residue 184 VAL Chi-restraints excluded: chain C residue 11 VAL Chi-restraints excluded: chain C residue 17 SER Chi-restraints excluded: chain C residue 84 SER Chi-restraints excluded: chain C residue 87 THR Chi-restraints excluded: chain C residue 100 ASP Chi-restraints excluded: chain C residue 138 LEU Chi-restraints excluded: chain C residue 184 VAL Chi-restraints excluded: chain D residue 11 VAL Chi-restraints excluded: chain D residue 17 SER Chi-restraints excluded: chain D residue 84 SER Chi-restraints excluded: chain D residue 87 THR Chi-restraints excluded: chain D residue 100 ASP Chi-restraints excluded: chain 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 138 LEU Chi-restraints excluded: chain H residue 184 VAL Chi-restraints excluded: chain B residue 30 SER Chi-restraints excluded: chain B residue 33 LEU Chi-restraints excluded: chain B residue 76 SER Chi-restraints excluded: chain B residue 79 GLU Chi-restraints excluded: chain B residue 143 GLU Chi-restraints excluded: chain B residue 166 GLN Chi-restraints excluded: chain B residue 182 SER Chi-restraints excluded: chain B residue 206 THR Chi-restraints excluded: chain E residue 30 SER Chi-restraints excluded: chain E residue 49 ASN Chi-restraints excluded: chain E residue 76 SER Chi-restraints excluded: chain E residue 150 VAL Chi-restraints excluded: chain E residue 182 SER 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 174 SER Chi-restraints excluded: chain G residue 202 SER Chi-restraints excluded: chain G residue 206 THR Chi-restraints excluded: chain L residue 30 SER Chi-restraints excluded: chain L residue 76 SER Chi-restraints excluded: chain L residue 79 GLU Chi-restraints excluded: chain L residue 143 GLU Chi-restraints excluded: chain L residue 174 SER Chi-restraints excluded: chain L residue 182 SER Chi-restraints excluded: chain L residue 202 SER Chi-restraints excluded: chain L residue 206 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 316 random chunks: chunk 294 optimal weight: 3.9990 chunk 254 optimal weight: 8.9990 chunk 46 optimal weight: 4.9990 chunk 121 optimal weight: 4.9990 chunk 47 optimal weight: 0.7980 chunk 58 optimal weight: 5.9990 chunk 2 optimal weight: 3.9990 chunk 278 optimal weight: 6.9990 chunk 264 optimal weight: 30.0000 chunk 191 optimal weight: 3.9990 chunk 43 optimal weight: 2.9990 overall best weight: 3.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... I 329 ASN ** I 354 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 354 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** W 329 ASN B 27 GLN B 166 GLN E 27 GLN E 166 GLN G 27 GLN ** G 155 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 166 GLN L 27 GLN ** L 155 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 166 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3899 r_free = 0.3899 target = 0.143182 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3078 r_free = 0.3078 target = 0.082478 restraints weight = 36586.574| |-----------------------------------------------------------------------------| r_work (start): 0.2987 rms_B_bonded: 2.35 r_work: 0.2860 rms_B_bonded: 2.43 restraints_weight: 0.5000 r_work: 0.2724 rms_B_bonded: 3.78 restraints_weight: 0.2500 r_work (final): 0.2724 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2714 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2714 r_free = 0.2714 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 = 0.2714 r_free = 0.2714 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: 0.2714 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8623 moved from start: 0.2834 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.041 25420 Z= 0.232 Angle : 0.633 7.606 34486 Z= 0.331 Chirality : 0.046 0.150 3808 Planarity : 0.005 0.055 4380 Dihedral : 6.208 55.841 3720 Min Nonbonded Distance : 2.531 Molprobity Statistics. All-atom Clashscore : 6.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.89 % Favored : 95.11 % Rotamer: Outliers : 4.73 % Allowed : 20.97 % Favored : 74.30 % 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: -2.12 (0.14), residues: 3148 helix: -4.36 (0.17), residues: 32 sheet: -0.69 (0.14), residues: 1296 loop : -1.95 (0.13), residues: 1820 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG E 18 TYR 0.025 0.002 TYR B 140 PHE 0.031 0.002 PHE D 100C TRP 0.008 0.001 TRP G 148 HIS 0.004 0.001 HIS L 198 Details of bonding type rmsd/Z covalent geometry : bond 0.00550 / 0.23 (25376) covalent geometry : angle 0.62925 / 0.33 (34384) SS BOND : bond 0.00258 / 0.16 ( 32) SS BOND : angle 1.42990 / 0.99 ( 66) hydrogen bonds : bond 0.03640 / 2.38 ( 706) hydrogen bonds : angle 5.30663 / 3.62 ( 1932) link_BETA1-4 : bond 0.00254 / 0.14 ( 8) link_BETA1-4 : angle 1.78578 / 1.16 ( 24) link_NAG-ASN : bond 0.00217 / 0.13 ( 4) link_NAG-ASN : angle 1.06718 / 0.57 ( 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 428 residues out of total 2708 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 128 poor density : 300 time to evaluate : 0.925 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: 0.8087 (OUTLIER) cc_final: 0.5951 (tmm160) REVERT: I 338 GLU cc_start: 0.8353 (OUTLIER) cc_final: 0.8062 (mp0) REVERT: I 390 ASP cc_start: 0.7733 (OUTLIER) cc_final: 0.7390 (m-30) REVERT: I 419 LYS cc_start: 0.9307 (OUTLIER) cc_final: 0.9048 (mttm) REVERT: M 116 ARG cc_start: 0.8057 (OUTLIER) cc_final: 0.5892 (tmm160) REVERT: M 338 GLU cc_start: 0.8453 (OUTLIER) cc_final: 0.8165 (mp0) REVERT: M 419 LYS cc_start: 0.9277 (OUTLIER) cc_final: 0.9006 (mttm) REVERT: N 116 ARG cc_start: 0.8046 (OUTLIER) cc_final: 0.5885 (tmm160) REVERT: N 338 GLU cc_start: 0.8351 (OUTLIER) cc_final: 0.8079 (mp0) REVERT: N 371 LYS cc_start: 0.9250 (OUTLIER) cc_final: 0.8927 (ptpp) REVERT: N 419 LYS cc_start: 0.9292 (OUTLIER) cc_final: 0.9029 (mttm) REVERT: W 116 ARG cc_start: 0.8064 (OUTLIER) cc_final: 0.5904 (tmm160) REVERT: W 338 GLU cc_start: 0.8338 (OUTLIER) cc_final: 0.8069 (mp0) REVERT: W 371 LYS cc_start: 0.9221 (OUTLIER) cc_final: 0.8866 (ptpp) REVERT: W 419 LYS cc_start: 0.9265 (OUTLIER) cc_final: 0.8996 (mttm) REVERT: A 72 ASP cc_start: 0.8272 (t70) cc_final: 0.7515 (t70) REVERT: A 100 PHE cc_start: 0.7835 (OUTLIER) cc_final: 0.7134 (p90) REVERT: A 145 TYR cc_start: 0.7051 (p90) cc_final: 0.6485 (p90) REVERT: A 176 TYR cc_start: 0.7138 (m-80) cc_final: 0.6886 (m-80) REVERT: C 30 ILE cc_start: 0.9068 (tt) cc_final: 0.8777 (tp) REVERT: C 72 ASP cc_start: 0.8150 (t70) cc_final: 0.7394 (t70) REVERT: D 30 ILE cc_start: 0.9068 (tt) cc_final: 0.8795 (tp) REVERT: D 72 ASP cc_start: 0.8161 (t70) cc_final: 0.7386 (t70) REVERT: D 145 TYR cc_start: 0.7150 (p90) cc_final: 0.6569 (p90) REVERT: D 176 TYR cc_start: 0.7299 (m-80) cc_final: 0.7094 (m-80) REVERT: H 30 ILE cc_start: 0.9062 (tt) cc_final: 0.8767 (tp) REVERT: H 72 ASP cc_start: 0.8135 (t70) cc_final: 0.7372 (t70) REVERT: H 145 TYR cc_start: 0.7058 (p90) cc_final: 0.6450 (p90) REVERT: H 176 TYR cc_start: 0.7448 (m-80) cc_final: 0.7218 (m-80) REVERT: B 108 ARG cc_start: 0.7829 (ptm160) cc_final: 0.7614 (ptt90) REVERT: B 142 ARG cc_start: 0.8713 (OUTLIER) cc_final: 0.8473 (ttp80) REVERT: E 42 GLN cc_start: 0.7521 (mp10) cc_final: 0.7218 (mp10) REVERT: E 108 ARG cc_start: 0.8035 (ptm160) cc_final: 0.7391 (ptm-80) REVERT: E 190 LYS cc_start: 0.8254 (mmmt) cc_final: 0.7878 (tptt) REVERT: G 108 ARG cc_start: 0.7860 (ptm160) cc_final: 0.7586 (ptm-80) REVERT: G 173 TYR cc_start: 0.8197 (m-80) cc_final: 0.7954 (m-10) REVERT: L 108 ARG cc_start: 0.7709 (ptm160) cc_final: 0.7392 (ptm-80) REVERT: L 142 ARG cc_start: 0.8740 (ttp-170) cc_final: 0.8465 (ttp80) REVERT: L 173 TYR cc_start: 0.8219 (m-80) cc_final: 0.7733 (m-10) outliers start: 128 outliers final: 78 residues processed: 406 average time/residue: 0.6504 time to fit residues: 304.1785 Evaluate side-chains 380 residues out of total 2708 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 95 poor density : 285 time to evaluate : 0.796 ------------------------------------------------------------------------------- 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 I residue 419 LYS 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 357 MET Chi-restraints excluded: chain M residue 359 SER Chi-restraints excluded: chain M residue 419 LYS Chi-restraints excluded: chain N residue 116 ARG Chi-restraints excluded: chain N residue 146 THR Chi-restraints excluded: chain N residue 182 CYS Chi-restraints excluded: chain N residue 198 SER Chi-restraints excluded: chain N residue 229 CYS Chi-restraints excluded: chain N residue 307 VAL Chi-restraints excluded: chain N residue 337 CYS Chi-restraints excluded: chain N residue 338 GLU Chi-restraints excluded: chain N residue 357 MET Chi-restraints excluded: chain N residue 359 SER Chi-restraints excluded: chain N residue 371 LYS Chi-restraints excluded: chain N residue 419 LYS Chi-restraints excluded: chain W residue 116 ARG Chi-restraints excluded: chain W residue 146 THR Chi-restraints excluded: chain W residue 182 CYS Chi-restraints excluded: chain W residue 198 SER Chi-restraints excluded: chain W residue 229 CYS Chi-restraints excluded: chain W residue 307 VAL Chi-restraints excluded: chain W residue 337 CYS Chi-restraints excluded: chain W residue 338 GLU Chi-restraints excluded: chain W residue 357 MET Chi-restraints excluded: chain W residue 359 SER Chi-restraints excluded: chain W residue 371 LYS Chi-restraints excluded: chain W residue 419 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 159 LEU 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 84 SER Chi-restraints excluded: chain D residue 87 THR Chi-restraints excluded: chain D residue 100 ASP Chi-restraints excluded: chain D residue 100 SER Chi-restraints excluded: chain 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 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 142 ARG Chi-restraints excluded: chain B residue 182 SER Chi-restraints excluded: chain B residue 206 THR Chi-restraints excluded: chain E residue 27 GLN Chi-restraints excluded: chain E residue 30 SER Chi-restraints excluded: chain E residue 49 ASN Chi-restraints excluded: chain E residue 76 SER Chi-restraints excluded: chain E residue 182 SER Chi-restraints excluded: chain E residue 202 SER Chi-restraints excluded: chain G residue 27 GLN Chi-restraints excluded: chain G residue 30 SER Chi-restraints excluded: chain G residue 76 SER Chi-restraints excluded: chain G residue 202 SER 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 202 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 316 random chunks: chunk 1 optimal weight: 0.9990 chunk 103 optimal weight: 1.9990 chunk 301 optimal weight: 10.0000 chunk 229 optimal weight: 10.0000 chunk 204 optimal weight: 0.6980 chunk 61 optimal weight: 7.9990 chunk 210 optimal weight: 2.9990 chunk 82 optimal weight: 4.9990 chunk 81 optimal weight: 0.8980 chunk 307 optimal weight: 30.0000 chunk 37 optimal weight: 3.9990 overall best weight: 1.5186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 6 GLN B 27 GLN B 166 GLN E 6 GLN E 27 GLN E 166 GLN G 42 GLN ** G 155 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 166 GLN L 6 GLN ** L 155 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3914 r_free = 0.3914 target = 0.144446 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3110 r_free = 0.3110 target = 0.084179 restraints weight = 36552.169| |-----------------------------------------------------------------------------| r_work (start): 0.3019 rms_B_bonded: 2.32 r_work: 0.2892 rms_B_bonded: 2.42 restraints_weight: 0.5000 r_work: 0.2759 rms_B_bonded: 3.77 restraints_weight: 0.2500 r_work (final): 0.2759 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2736 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2736 r_free = 0.2736 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 = 0.2736 r_free = 0.2736 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: 0.2736 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8594 moved from start: 0.3039 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 25420 Z= 0.136 Angle : 0.570 7.570 34486 Z= 0.298 Chirality : 0.044 0.131 3808 Planarity : 0.004 0.053 4380 Dihedral : 5.546 52.962 3710 Min Nonbonded Distance : 2.487 Molprobity Statistics. All-atom Clashscore : 5.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.48 % Favored : 95.52 % Rotamer: Outliers : 4.54 % Allowed : 22.08 % Favored : 73.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.63 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.94 (0.14), residues: 3148 helix: -4.35 (0.18), residues: 32 sheet: -0.57 (0.14), residues: 1284 loop : -1.81 (0.13), residues: 1832 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG E 18 TYR 0.025 0.001 TYR B 140 PHE 0.024 0.002 PHE H 100C TRP 0.007 0.001 TRP N 80 HIS 0.003 0.001 HIS L 198 Details of bonding type rmsd/Z covalent geometry : bond 0.00318 / 0.14 (25376) covalent geometry : angle 0.56706 / 0.30 (34384) SS BOND : bond 0.00419 / 0.29 ( 32) SS BOND : angle 0.96937 / 0.67 ( 66) hydrogen bonds : bond 0.03169 / 2.07 ( 706) hydrogen bonds : angle 5.04630 / 3.44 ( 1932) link_BETA1-4 : bond 0.00452 / 0.24 ( 8) link_BETA1-4 : angle 1.57743 / 1.02 ( 24) link_NAG-ASN : bond 0.00116 / 0.07 ( 4) link_NAG-ASN : angle 0.97970 / 0.53 ( 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 432 residues out of total 2708 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 123 poor density : 309 time to evaluate : 1.002 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: I 338 GLU cc_start: 0.8327 (OUTLIER) cc_final: 0.7979 (mp0) REVERT: I 390 ASP cc_start: 0.7597 (OUTLIER) cc_final: 0.7369 (m-30) REVERT: I 419 LYS cc_start: 0.9300 (OUTLIER) cc_final: 0.9028 (mttm) REVERT: M 338 GLU cc_start: 0.8354 (OUTLIER) cc_final: 0.8105 (mp0) REVERT: M 419 LYS cc_start: 0.9262 (mttt) cc_final: 0.8970 (mttm) REVERT: M 429 MET cc_start: 0.9417 (mtp) cc_final: 0.9195 (mtm) REVERT: N 338 GLU cc_start: 0.8330 (OUTLIER) cc_final: 0.8048 (mp0) REVERT: N 419 LYS cc_start: 0.9281 (mttt) cc_final: 0.8997 (mttm) REVERT: W 338 GLU cc_start: 0.8338 (OUTLIER) cc_final: 0.7981 (mp0) REVERT: W 419 LYS cc_start: 0.9255 (mttt) cc_final: 0.8942 (mttm) REVERT: A 72 ASP cc_start: 0.8293 (t70) cc_final: 0.7608 (t70) REVERT: A 100 PHE cc_start: 0.7966 (OUTLIER) cc_final: 0.7476 (p90) REVERT: A 145 TYR cc_start: 0.6950 (p90) cc_final: 0.6335 (p90) REVERT: A 176 TYR cc_start: 0.7115 (m-80) cc_final: 0.6894 (m-80) REVERT: C 30 ILE cc_start: 0.9049 (tt) cc_final: 0.8756 (tp) REVERT: C 72 ASP cc_start: 0.8219 (t70) cc_final: 0.7490 (t70) REVERT: C 82 ARG cc_start: 0.7032 (mtm-85) cc_final: 0.6758 (mtm-85) REVERT: C 100 PHE cc_start: 0.7917 (OUTLIER) cc_final: 0.7506 (p90) REVERT: D 30 ILE cc_start: 0.9034 (tt) cc_final: 0.8762 (tp) REVERT: D 72 ASP cc_start: 0.8211 (t70) cc_final: 0.7468 (t70) REVERT: D 100 PHE cc_start: 0.7907 (OUTLIER) cc_final: 0.7503 (p90) REVERT: D 145 TYR cc_start: 0.7083 (p90) cc_final: 0.6434 (p90) REVERT: D 176 TYR cc_start: 0.7302 (m-80) cc_final: 0.7075 (m-80) REVERT: H 30 ILE cc_start: 0.9043 (tt) cc_final: 0.8749 (tp) REVERT: H 72 ASP cc_start: 0.8202 (t70) cc_final: 0.7465 (t70) REVERT: H 82 ARG cc_start: 0.7039 (mtm-85) cc_final: 0.6767 (mtm-85) REVERT: H 100 PHE cc_start: 0.7914 (OUTLIER) cc_final: 0.7555 (p90) REVERT: E 42 GLN cc_start: 0.7451 (mp10) cc_final: 0.7144 (mp10) REVERT: E 108 ARG cc_start: 0.8029 (ptm160) cc_final: 0.7379 (ptm-80) REVERT: E 190 LYS cc_start: 0.8314 (mmmt) cc_final: 0.7962 (tptt) REVERT: G 27 GLN cc_start: 0.8842 (OUTLIER) cc_final: 0.8490 (pm20) REVERT: G 108 ARG cc_start: 0.7839 (ptm160) cc_final: 0.7151 (ptm-80) REVERT: L 108 ARG cc_start: 0.7815 (ptm160) cc_final: 0.7452 (ptm-80) outliers start: 123 outliers final: 73 residues processed: 415 average time/residue: 0.6075 time to fit residues: 292.5265 Evaluate side-chains 372 residues out of total 2708 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 84 poor density : 288 time to evaluate : 0.998 ------------------------------------------------------------------------------- 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 338 GLU Chi-restraints excluded: chain I residue 357 MET Chi-restraints excluded: chain I residue 361 ILE 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 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 359 SER Chi-restraints excluded: chain N residue 361 ILE Chi-restraints excluded: chain W residue 146 THR Chi-restraints excluded: chain W residue 182 CYS Chi-restraints excluded: chain W residue 198 SER Chi-restraints excluded: chain W residue 229 CYS Chi-restraints excluded: chain W residue 307 VAL Chi-restraints excluded: chain W residue 337 CYS Chi-restraints excluded: chain W residue 338 GLU Chi-restraints excluded: chain W residue 359 SER Chi-restraints excluded: chain W residue 361 ILE Chi-restraints excluded: chain 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 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 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 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 17 SER Chi-restraints excluded: chain H residue 25 SER Chi-restraints excluded: chain H residue 87 THR Chi-restraints excluded: chain H residue 100 PHE Chi-restraints excluded: chain H residue 100 ASP Chi-restraints excluded: chain H residue 100 SER Chi-restraints excluded: chain B residue 27 GLN Chi-restraints excluded: chain B residue 30 SER Chi-restraints excluded: chain B residue 76 SER Chi-restraints excluded: chain B residue 206 THR Chi-restraints excluded: chain E residue 27 GLN Chi-restraints excluded: chain E residue 30 SER Chi-restraints excluded: chain E residue 49 ASN Chi-restraints excluded: chain E residue 76 SER Chi-restraints excluded: chain E residue 182 SER Chi-restraints excluded: chain E residue 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 76 SER Chi-restraints excluded: chain G residue 125 LEU Chi-restraints excluded: chain G residue 202 SER 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 202 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/phenix/command_line/real_space_refine.py", line 9, in run_program(real_space_refine.Program) File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/iotbx/cli_parser.py", line 987, in run_program task.run() File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/phenix/programs/real_space_refine.py", line 206, in run self.rsr_result = rsr_wrappers.run_real_space_refine( ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/phenix/refinement/rsr/wrappers.py", line 52, in __init__ self._refined = macro_cycle_real_space.run( ^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/phenix/refinement/macro_cycle_real_space.py", line 306, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/phenix/refinement/macro_cycle_real_space.py", line 702, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/phenix/refinement/macro_cycle_real_space.py", line 755, in minimization_no_ncs ro = mmtbx.refinement.real_space.individual_sites.easy( ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 44, in __init__ self.weight = mmtbx.refinement.real_space.weight.run( ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/mmtbx/refinement/real_space/weight.py", line 84, in __init__ ro.refine( File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 362, in refine real_space_result = refinery( ^^^^^^^^^ File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 233, in __init__ refiner.refine( File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 100, in refine self.refined = maptbx.real_space_refinement_simple.lbfgs( ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/cctbx/maptbx/real_space_refinement_simple.py", line 168, in __init__ O.minimizer = scitbx.lbfgs.run( ^^^^^^^^^^^^^^^^^ File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/scitbx/lbfgs/__init__.py", line 270, in run return run_c_plus_plus( ^^^^^^^^^^^^^^^^ File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/cctbx/maptbx/real_space_refinement_simple.py", line 243, in compute_functional_and_gradients gr_e = O.geometry_restraints_manager.energies_sites( ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/cctbx/geometry_restraints/manager.py", line 1602, in energies_sites pair_proxies = self.pair_proxies( ^^^^^^^^^^^^^^^^^^ File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/cctbx/geometry_restraints/manager.py", line 1505, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/cctbx/geometry_restraints/manager.py", line 1386, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 58.3351 > 50: distance: 4 - 9: 9.574 distance: 9 - 10: 11.004 distance: 9 - 15: 7.196 distance: 10 - 11: 7.531 distance: 10 - 13: 7.424 distance: 11 - 12: 8.980 distance: 11 - 16: 6.024 distance: 13 - 14: 5.627 distance: 14 - 15: 16.231 distance: 16 - 17: 14.051 distance: 16 - 68: 44.806 distance: 17 - 18: 15.430 distance: 17 - 20: 15.166 distance: 18 - 19: 11.257 distance: 18 - 24: 4.338 distance: 20 - 21: 31.100 distance: 21 - 22: 11.076 distance: 21 - 23: 13.769 distance: 24 - 25: 6.832 distance: 25 - 26: 27.362 distance: 25 - 28: 23.534 distance: 26 - 29: 19.794 distance: 29 - 30: 15.140 distance: 29 - 35: 14.949 distance: 30 - 31: 39.788 distance: 30 - 33: 24.284 distance: 31 - 32: 18.118 distance: 33 - 34: 10.125 distance: 34 - 35: 8.308 distance: 36 - 37: 14.791 distance: 37 - 38: 6.104 distance: 38 - 39: 13.373 distance: 38 - 40: 7.309 distance: 40 - 41: 10.972 distance: 41 - 42: 5.439 distance: 41 - 44: 7.111 distance: 42 - 43: 18.334 distance: 42 - 47: 12.270 distance: 44 - 45: 14.640 distance: 44 - 46: 12.189 distance: 47 - 48: 11.809 distance: 48 - 49: 17.034 distance: 48 - 51: 11.787 distance: 49 - 50: 28.145 distance: 49 - 52: 7.648 distance: 52 - 53: 29.988 distance: 53 - 54: 19.522 distance: 53 - 56: 21.793 distance: 54 - 55: 20.352 distance: 54 - 57: 15.205 distance: 58 - 59: 3.367 distance: 58 - 61: 12.996 distance: 59 - 60: 16.855 distance: 59 - 65: 24.955 distance: 61 - 62: 20.201 distance: 62 - 63: 29.639 distance: 62 - 64: 16.105 distance: 65 - 66: 18.241 distance: 66 - 67: 27.016 distance: 67 - 68: 32.768 distance: 67 - 69: 11.415