Starting phenix.real_space_refine on Sat Jun 21 12:14:05 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6v4o_21043/06_2025/6v4o_21043_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/6v4o_21043/06_2025/6v4o_21043.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/6v4o_21043/06_2025/6v4o_21043.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6v4o_21043/06_2025/6v4o_21043.map" model { file = "/net/cci-nas-00/data/ceres_data/6v4o_21043/06_2025/6v4o_21043_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6v4o_21043/06_2025/6v4o_21043_neut.cif" } resolution = 2.8 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 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): 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib" Total number of atoms: 24796 Number of models: 1 Model: "" Number of chains: 5 Chain: "I" Number of atoms: 2830 Number of conformers: 1 Conformer: "" Number of residues, atoms: 364, 2830 Classifications: {'peptide': 364} Link IDs: {'PCIS': 1, 'PTRANS': 17, 'TRANS': 345} Chain breaks: 3 Chain: "A" Number of atoms: 1695 Number of conformers: 1 Conformer: "" Number of residues, atoms: 223, 1695 Classifications: {'peptide': 223} Link IDs: {'PCIS': 2, 'PTRANS': 11, 'TRANS': 209} Chain breaks: 1 Chain: "B" Number of atoms: 1634 Number of conformers: 1 Conformer: "" Number of residues, atoms: 214, 1634 Classifications: {'peptide': 214} Link IDs: {'PCIS': 2, 'PTRANS': 10, 'TRANS': 201} Chain: "F" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "I" Number of atoms: 12 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 12 Unusual residues: {' CA': 1, 'BMA': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Restraints were copied for chains: E, G, L, K, J, O, M, N, W, C, D, H Time building chain proxies: 14.13, per 1000 atoms: 0.57 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: 7.70 Conformation dependent library (CDL) restraints added in 3.3 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: 5.75 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: 18.16 Time building geometry restraints manager: 8.90 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: 0.15 Found NCS groups: ncs_group { reference = chain 'B' selection = chain 'E' selection = chain 'G' selection = chain 'L' } ncs_group { reference = chain 'F' selection = chain 'K' selection = chain 'J' selection = chain 'O' } 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' } 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: 60.490 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.040 Extract box with map and model: 0.940 Check model and map are aligned: 0.170 Set scattering table: 0.220 Process input model: 72.970 Find NCS groups from input model: 0.470 Set up NCS constraints: 0.100 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:89.570 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 224.980 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8127 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.011 0.162 25420 Z= 0.463 Angle : 0.917 29.051 34486 Z= 0.484 Chirality : 0.075 1.679 3808 Planarity : 0.005 0.047 4380 Dihedral : 15.492 107.711 9404 Min Nonbonded Distance : 1.602 Molprobity Statistics. All-atom Clashscore : 7.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.88 % Favored : 90.12 % Rotamer: Outliers : 2.95 % Allowed : 13.44 % Favored : 83.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.63 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.13 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -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 TRP 0.011 0.001 TRP D 154 HIS 0.006 0.001 HIS N 183 PHE 0.035 0.002 PHE D 100C TYR 0.012 0.001 TYR N 383 ARG 0.003 0.001 ARG N 154 Details of bonding type rmsd link_NAG-ASN : bond 0.00876 ( 4) link_NAG-ASN : angle 2.06429 ( 12) link_BETA1-4 : bond 0.12290 ( 8) link_BETA1-4 : angle 15.76358 ( 24) hydrogen bonds : bond 0.19004 ( 706) hydrogen bonds : angle 8.43617 ( 1932) SS BOND : bond 0.00452 ( 32) SS BOND : angle 2.08091 ( 66) covalent geometry : bond 0.01096 (25376) covalent geometry : angle 0.81251 (34384) *********************** 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 : 2.683 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 116 PHE cc_start: 0.5661 (m-10) cc_final: 0.5444 (m-10) 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: 0.7312 (tm-30) outliers start: 80 outliers final: 30 residues processed: 490 average time/residue: 1.6211 time to fit residues: 901.5036 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 : 2.660 ------------------------------------------------------------------------------- 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 266 optimal weight: 40.0000 chunk 239 optimal weight: 7.9990 chunk 132 optimal weight: 0.9980 chunk 81 optimal weight: 0.8980 chunk 161 optimal weight: 6.9990 chunk 127 optimal weight: 4.9990 chunk 247 optimal weight: 0.9980 chunk 95 optimal weight: 0.8980 chunk 150 optimal weight: 2.9990 chunk 184 optimal weight: 20.0000 chunk 286 optimal weight: 0.0030 overall best weight: 0.7590 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: I 431 HIS M 329 ASN M 431 HIS N 329 ASN N 431 HIS W 431 HIS A 39 GLN A 204 ASN ** C 164 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 204 ASN D 204 ASN H 155 ASN ** H 164 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 204 ASN ** B 147 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 166 GLN ** B 198 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 199 GLN 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 = 0.3969 r_free = 0.3969 target = 0.148540 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3210 r_free = 0.3210 target = 0.089967 restraints weight = 36713.474| |-----------------------------------------------------------------------------| r_work (start): 0.3116 rms_B_bonded: 2.34 r_work: 0.2989 rms_B_bonded: 2.48 restraints_weight: 0.5000 r_work: 0.2855 rms_B_bonded: 3.89 restraints_weight: 0.2500 r_work (final): 0.2855 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2849 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2849 r_free = 0.2849 target_work(ls_wunit_k1) = 0.069 | | occupancies: max = 1.00 min = 0.05 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2849 r_free = 0.2849 target_work(ls_wunit_k1) = 0.069 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 7 | |-----------------------------------------------------------------------------| r_final: 0.2849 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8295 moved from start: 0.2004 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 25420 Z= 0.131 Angle : 0.672 7.212 34486 Z= 0.352 Chirality : 0.048 0.258 3808 Planarity : 0.005 0.050 4380 Dihedral : 8.363 55.369 3748 Min Nonbonded Distance : 2.377 Molprobity Statistics. All-atom Clashscore : 6.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.46 % Favored : 94.54 % Rotamer: Outliers : 4.54 % Allowed : 17.98 % Favored : 77.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.63 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.97 (0.13), residues: 3148 helix: -4.55 (0.15), residues: 32 sheet: -1.36 (0.14), residues: 1264 loop : -2.44 (0.12), residues: 1852 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP I 408 HIS 0.013 0.001 HIS A 164 PHE 0.017 0.002 PHE B 209 TYR 0.021 0.002 TYR G 186 ARG 0.007 0.001 ARG C 83 Details of bonding type rmsd link_NAG-ASN : bond 0.00315 ( 4) link_NAG-ASN : angle 1.02956 ( 12) link_BETA1-4 : bond 0.00524 ( 8) link_BETA1-4 : angle 2.26263 ( 24) hydrogen bonds : bond 0.03668 ( 706) hydrogen bonds : angle 6.05190 ( 1932) SS BOND : bond 0.00126 ( 32) SS BOND : angle 0.74443 ( 66) covalent geometry : bond 0.00283 (25376) covalent geometry : angle 0.66909 (34384) *********************** 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 473 residues out of total 2708 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 123 poor density : 350 time to evaluate : 3.010 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: I 375 MET cc_start: 0.9319 (mmm) cc_final: 0.8908 (mmt) REVERT: I 390 ASP cc_start: 0.7290 (OUTLIER) cc_final: 0.6656 (m-30) REVERT: M 375 MET cc_start: 0.9248 (mmm) cc_final: 0.8932 (mmt) REVERT: M 384 ASP cc_start: 0.8465 (m-30) cc_final: 0.8186 (m-30) REVERT: M 390 ASP cc_start: 0.7246 (OUTLIER) cc_final: 0.6607 (m-30) REVERT: N 375 MET cc_start: 0.9300 (mmm) cc_final: 0.9061 (mmm) REVERT: N 384 ASP cc_start: 0.8361 (m-30) cc_final: 0.8102 (m-30) REVERT: N 390 ASP cc_start: 0.7262 (OUTLIER) cc_final: 0.6611 (m-30) REVERT: W 384 ASP cc_start: 0.8337 (m-30) cc_final: 0.8079 (m-30) REVERT: W 390 ASP cc_start: 0.7212 (OUTLIER) cc_final: 0.6601 (m-30) REVERT: W 429 MET cc_start: 0.9304 (mtp) cc_final: 0.9088 (mtp) REVERT: A 72 ASP cc_start: 0.8048 (t70) cc_final: 0.7270 (t70) REVERT: A 145 TYR cc_start: 0.6921 (p90) cc_final: 0.6448 (p90) REVERT: A 176 TYR cc_start: 0.7165 (m-80) cc_final: 0.6941 (m-80) REVERT: C 30 ILE cc_start: 0.8992 (tt) cc_final: 0.8699 (tp) REVERT: C 72 ASP cc_start: 0.7730 (t70) cc_final: 0.6981 (t70) REVERT: D 30 ILE cc_start: 0.9103 (tt) cc_final: 0.8796 (tp) REVERT: D 72 ASP cc_start: 0.7765 (t70) cc_final: 0.7014 (t70) REVERT: D 100 TYR cc_start: 0.9073 (m-80) cc_final: 0.8714 (m-80) REVERT: D 145 TYR cc_start: 0.6858 (p90) cc_final: 0.6392 (p90) REVERT: D 176 TYR cc_start: 0.7263 (m-80) cc_final: 0.6811 (m-10) REVERT: H 30 ILE cc_start: 0.8995 (tt) cc_final: 0.8685 (tp) REVERT: H 72 ASP cc_start: 0.7778 (t70) cc_final: 0.7052 (t70) REVERT: H 81 ASP cc_start: 0.7985 (t70) cc_final: 0.7749 (t0) REVERT: H 100 TYR cc_start: 0.9089 (m-80) cc_final: 0.8795 (m-80) REVERT: H 145 TYR cc_start: 0.6619 (p90) cc_final: 0.6056 (p90) REVERT: H 176 TYR cc_start: 0.7254 (m-80) cc_final: 0.6801 (m-10) REVERT: B 24 ARG cc_start: 0.7956 (OUTLIER) cc_final: 0.7740 (ttt-90) REVERT: B 42 GLN cc_start: 0.7313 (mp10) cc_final: 0.7104 (mp10) REVERT: B 143 GLU cc_start: 0.8317 (OUTLIER) cc_final: 0.8092 (tm-30) REVERT: E 143 GLU cc_start: 0.8461 (OUTLIER) cc_final: 0.8198 (tm-30) REVERT: E 160 GLN cc_start: 0.5806 (mt0) cc_final: 0.5579 (mt0) REVERT: E 165 GLU cc_start: 0.8227 (tp30) cc_final: 0.7785 (mp0) REVERT: E 190 LYS cc_start: 0.8057 (mmmt) cc_final: 0.7632 (tptt) REVERT: G 108 ARG cc_start: 0.7729 (ptm160) cc_final: 0.6866 (ptm-80) REVERT: G 143 GLU cc_start: 0.8405 (OUTLIER) cc_final: 0.8200 (tm-30) REVERT: L 6 GLN cc_start: 0.8131 (OUTLIER) cc_final: 0.7321 (mt0) REVERT: L 18 ARG cc_start: 0.8420 (OUTLIER) cc_final: 0.7389 (ttm110) outliers start: 123 outliers final: 65 residues processed: 448 average time/residue: 1.3161 time to fit residues: 681.3867 Evaluate side-chains 391 residues out of total 2708 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 316 time to evaluate : 2.931 ------------------------------------------------------------------------------- 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 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 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 82 SER Chi-restraints excluded: chain C residue 87 THR Chi-restraints excluded: chain C residue 100 ASP Chi-restraints excluded: chain C residue 184 VAL Chi-restraints excluded: chain C residue 193 THR Chi-restraints excluded: chain D residue 17 SER Chi-restraints excluded: chain D residue 87 THR Chi-restraints excluded: chain D residue 100 ASP Chi-restraints excluded: chain D residue 184 VAL Chi-restraints excluded: chain H residue 17 SER Chi-restraints excluded: chain H residue 87 THR Chi-restraints excluded: chain H residue 100 ASP Chi-restraints excluded: chain H residue 184 VAL Chi-restraints excluded: chain B residue 24 ARG Chi-restraints excluded: chain B residue 30 SER Chi-restraints excluded: chain B residue 33 LEU Chi-restraints excluded: chain B residue 76 SER Chi-restraints excluded: chain B residue 143 GLU Chi-restraints excluded: chain B residue 182 SER Chi-restraints excluded: chain B residue 206 THR Chi-restraints excluded: chain E residue 30 SER Chi-restraints excluded: chain E residue 33 LEU Chi-restraints excluded: chain E residue 49 ASN Chi-restraints excluded: chain E residue 76 SER Chi-restraints excluded: chain E residue 143 GLU Chi-restraints excluded: chain E residue 150 VAL Chi-restraints excluded: chain 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 182 SER Chi-restraints excluded: chain L residue 206 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 316 random chunks: chunk 163 optimal weight: 5.9990 chunk 171 optimal weight: 6.9990 chunk 145 optimal weight: 6.9990 chunk 160 optimal weight: 9.9990 chunk 293 optimal weight: 40.0000 chunk 291 optimal weight: 30.0000 chunk 136 optimal weight: 8.9990 chunk 301 optimal weight: 9.9990 chunk 244 optimal weight: 8.9990 chunk 106 optimal weight: 7.9990 chunk 110 optimal weight: 4.9990 overall best weight: 6.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: I 183 HIS I 273 HIS M 183 HIS M 225 GLN M 273 HIS N 183 HIS N 225 GLN N 273 HIS W 183 HIS W 273 HIS B 27 GLN ** B 147 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 166 GLN E 27 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: 17 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3871 r_free = 0.3871 target = 0.140942 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3043 r_free = 0.3043 target = 0.080254 restraints weight = 36759.421| |-----------------------------------------------------------------------------| r_work (start): 0.2943 rms_B_bonded: 2.35 r_work: 0.2815 rms_B_bonded: 2.42 restraints_weight: 0.5000 r_work: 0.2680 rms_B_bonded: 3.74 restraints_weight: 0.2500 r_work (final): 0.2680 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2664 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2664 r_free = 0.2664 target_work(ls_wunit_k1) = 0.060 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 7 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2664 r_free = 0.2664 target_work(ls_wunit_k1) = 0.060 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| r_final: 0.2664 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8441 moved from start: 0.2633 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.011 0.078 25420 Z= 0.447 Angle : 0.788 8.480 34486 Z= 0.415 Chirality : 0.052 0.194 3808 Planarity : 0.006 0.062 4380 Dihedral : 7.512 59.772 3725 Min Nonbonded Distance : 2.250 Molprobity Statistics. All-atom Clashscore : 7.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.91 % Favored : 94.09 % Rotamer: Outliers : 5.72 % Allowed : 19.09 % Favored : 75.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.63 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.55 (0.13), residues: 3148 helix: -4.42 (0.16), residues: 32 sheet: -1.00 (0.14), residues: 1284 loop : -2.24 (0.12), residues: 1832 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP L 148 HIS 0.006 0.002 HIS E 198 PHE 0.047 0.003 PHE D 100C TYR 0.021 0.002 TYR L 173 ARG 0.005 0.001 ARG M 374 Details of bonding type rmsd link_NAG-ASN : bond 0.00476 ( 4) link_NAG-ASN : angle 1.06546 ( 12) link_BETA1-4 : bond 0.00590 ( 8) link_BETA1-4 : angle 2.30098 ( 24) hydrogen bonds : bond 0.04594 ( 706) hydrogen bonds : angle 5.86355 ( 1932) SS BOND : bond 0.00667 ( 32) SS BOND : angle 2.22461 ( 66) covalent geometry : bond 0.01059 (25376) covalent geometry : angle 0.78063 (34384) *********************** 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 458 residues out of total 2708 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 155 poor density : 303 time to evaluate : 2.675 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: I 116 ARG cc_start: 0.8337 (OUTLIER) cc_final: 0.6272 (tmm160) REVERT: M 116 ARG cc_start: 0.8306 (OUTLIER) cc_final: 0.6311 (tmm160) REVERT: N 116 ARG cc_start: 0.8297 (OUTLIER) cc_final: 0.6295 (tmm160) REVERT: N 429 MET cc_start: 0.9440 (mtp) cc_final: 0.9224 (mtm) REVERT: W 116 ARG cc_start: 0.8309 (OUTLIER) cc_final: 0.6294 (tmm160) REVERT: A 72 ASP cc_start: 0.8305 (t70) cc_final: 0.7543 (t70) REVERT: A 100 PHE cc_start: 0.7980 (OUTLIER) cc_final: 0.7499 (p90) REVERT: A 145 TYR cc_start: 0.7166 (p90) cc_final: 0.6658 (p90) REVERT: A 176 TYR cc_start: 0.7329 (m-80) cc_final: 0.7010 (m-80) REVERT: C 30 ILE cc_start: 0.9089 (tt) cc_final: 0.8789 (tp) REVERT: C 72 ASP cc_start: 0.8187 (t70) cc_final: 0.7456 (t70) REVERT: D 72 ASP cc_start: 0.8197 (t70) cc_final: 0.7458 (t70) REVERT: D 145 TYR cc_start: 0.7191 (p90) cc_final: 0.6605 (p90) REVERT: D 176 TYR cc_start: 0.7343 (m-80) cc_final: 0.7054 (m-80) REVERT: H 30 ILE cc_start: 0.9084 (tt) cc_final: 0.8779 (tp) REVERT: H 72 ASP cc_start: 0.8184 (t70) cc_final: 0.7443 (t70) REVERT: H 81 ASP cc_start: 0.8132 (t70) cc_final: 0.7915 (t0) REVERT: H 145 TYR cc_start: 0.7059 (p90) cc_final: 0.6376 (p90) REVERT: H 176 TYR cc_start: 0.7435 (m-80) cc_final: 0.7100 (m-80) REVERT: B 42 GLN cc_start: 0.7493 (mp10) cc_final: 0.7255 (mp10) REVERT: B 143 GLU cc_start: 0.8385 (OUTLIER) cc_final: 0.8099 (tm-30) REVERT: B 165 GLU cc_start: 0.8266 (tp30) cc_final: 0.7728 (tp30) REVERT: B 166 GLN cc_start: 0.8985 (OUTLIER) cc_final: 0.8507 (tt0) REVERT: E 108 ARG cc_start: 0.8020 (ptm160) cc_final: 0.7477 (ptt90) REVERT: E 190 LYS cc_start: 0.8194 (mmmt) cc_final: 0.7826 (tptt) REVERT: G 108 ARG cc_start: 0.7899 (ptm160) cc_final: 0.7060 (ptm-80) REVERT: G 142 ARG cc_start: 0.8583 (ttp80) cc_final: 0.8286 (ttp80) REVERT: G 165 GLU cc_start: 0.8304 (tp30) cc_final: 0.7838 (tp30) REVERT: G 166 GLN cc_start: 0.8974 (OUTLIER) cc_final: 0.8507 (tt0) REVERT: L 108 ARG cc_start: 0.7612 (ptm160) cc_final: 0.7406 (ptm-80) REVERT: L 143 GLU cc_start: 0.8110 (OUTLIER) cc_final: 0.7837 (tm-30) outliers start: 155 outliers final: 83 residues processed: 423 average time/residue: 1.4617 time to fit residues: 719.3545 Evaluate side-chains 367 residues out of total 2708 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 92 poor density : 275 time to evaluate : 2.880 ------------------------------------------------------------------------------- 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 359 SER Chi-restraints excluded: chain I residue 366 SER Chi-restraints excluded: chain M residue 116 ARG Chi-restraints excluded: chain M residue 146 THR Chi-restraints excluded: chain M residue 182 CYS Chi-restraints excluded: chain M residue 198 SER Chi-restraints excluded: chain M residue 229 CYS Chi-restraints excluded: chain M residue 307 VAL Chi-restraints excluded: chain M residue 337 CYS Chi-restraints excluded: chain M residue 359 SER Chi-restraints excluded: chain M residue 366 SER Chi-restraints excluded: chain N residue 116 ARG Chi-restraints excluded: chain N residue 146 THR Chi-restraints excluded: chain N residue 182 CYS Chi-restraints excluded: chain N residue 198 SER Chi-restraints excluded: chain N residue 229 CYS Chi-restraints excluded: chain N residue 307 VAL Chi-restraints excluded: chain N residue 337 CYS Chi-restraints excluded: chain N residue 359 SER Chi-restraints excluded: chain N residue 366 SER Chi-restraints excluded: chain W residue 116 ARG Chi-restraints excluded: chain W residue 146 THR Chi-restraints excluded: chain W residue 182 CYS Chi-restraints excluded: chain W residue 198 SER Chi-restraints excluded: chain W residue 229 CYS Chi-restraints excluded: chain W residue 307 VAL Chi-restraints excluded: chain W residue 337 CYS Chi-restraints excluded: chain W residue 359 SER Chi-restraints excluded: chain W residue 366 SER Chi-restraints excluded: chain A residue 11 VAL Chi-restraints excluded: chain A residue 17 SER Chi-restraints excluded: chain A residue 87 THR Chi-restraints excluded: chain A residue 100 PHE Chi-restraints excluded: chain A residue 100 ASP Chi-restraints excluded: chain A residue 100 SER Chi-restraints excluded: chain A residue 159 LEU Chi-restraints excluded: chain A residue 184 VAL Chi-restraints excluded: chain C residue 11 VAL Chi-restraints excluded: chain C residue 17 SER Chi-restraints excluded: chain C residue 87 THR Chi-restraints excluded: chain C residue 100 ASP Chi-restraints excluded: chain C residue 100 SER Chi-restraints excluded: chain C residue 184 VAL Chi-restraints excluded: chain D residue 11 VAL Chi-restraints excluded: chain D residue 17 SER Chi-restraints excluded: chain D residue 84 SER Chi-restraints excluded: chain D residue 87 THR Chi-restraints excluded: chain D residue 100 ASP Chi-restraints excluded: chain D residue 100 SER Chi-restraints excluded: chain H residue 11 VAL Chi-restraints excluded: chain H residue 17 SER Chi-restraints excluded: chain H residue 87 THR Chi-restraints excluded: chain H residue 100 ASP Chi-restraints excluded: chain H residue 100 SER Chi-restraints excluded: chain H residue 184 VAL Chi-restraints excluded: chain B residue 30 SER Chi-restraints excluded: chain B residue 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 174 SER Chi-restraints excluded: chain B residue 182 SER Chi-restraints excluded: chain B residue 202 SER Chi-restraints excluded: chain B residue 206 THR Chi-restraints excluded: chain E residue 30 SER Chi-restraints excluded: chain E residue 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 E residue 202 SER Chi-restraints excluded: chain G residue 76 SER Chi-restraints excluded: chain G residue 79 GLU Chi-restraints excluded: chain G residue 166 GLN Chi-restraints excluded: chain G residue 174 SER Chi-restraints excluded: chain G residue 202 SER Chi-restraints excluded: chain G residue 206 THR Chi-restraints excluded: chain L residue 30 SER Chi-restraints excluded: chain L residue 76 SER Chi-restraints excluded: chain L residue 79 GLU Chi-restraints excluded: chain L residue 143 GLU Chi-restraints excluded: chain L residue 150 VAL Chi-restraints excluded: chain L residue 174 SER Chi-restraints excluded: chain L residue 182 SER Chi-restraints excluded: chain L residue 202 SER Chi-restraints excluded: chain L residue 206 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 316 random chunks: chunk 217 optimal weight: 7.9990 chunk 63 optimal weight: 0.7980 chunk 66 optimal weight: 2.9990 chunk 214 optimal weight: 3.9990 chunk 101 optimal weight: 0.8980 chunk 191 optimal weight: 2.9990 chunk 103 optimal weight: 3.9990 chunk 114 optimal weight: 3.9990 chunk 36 optimal weight: 3.9990 chunk 8 optimal weight: 2.9990 chunk 123 optimal weight: 0.6980 overall best weight: 1.6784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: I 225 GLN I 329 ASN W 225 GLN B 166 GLN E 27 GLN E 166 GLN ** G 155 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 6 GLN ** L 155 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 166 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3909 r_free = 0.3909 target = 0.143902 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3097 r_free = 0.3097 target = 0.083439 restraints weight = 36721.599| |-----------------------------------------------------------------------------| r_work (start): 0.3005 rms_B_bonded: 2.40 r_work: 0.2879 rms_B_bonded: 2.46 restraints_weight: 0.5000 r_work: 0.2744 rms_B_bonded: 3.84 restraints_weight: 0.2500 r_work (final): 0.2744 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2733 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2733 r_free = 0.2733 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 = 0.2733 r_free = 0.2733 target_work(ls_wunit_k1) = 0.063 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| r_final: 0.2733 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8374 moved from start: 0.2855 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 25420 Z= 0.148 Angle : 0.605 7.673 34486 Z= 0.317 Chirality : 0.044 0.161 3808 Planarity : 0.005 0.056 4380 Dihedral : 6.163 41.939 3715 Min Nonbonded Distance : 2.324 Molprobity Statistics. All-atom Clashscore : 6.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.99 % Favored : 95.01 % Rotamer: Outliers : 3.25 % Allowed : 21.97 % Favored : 74.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.63 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.18 (0.14), residues: 3148 helix: -4.33 (0.17), residues: 32 sheet: -0.78 (0.14), residues: 1292 loop : -1.94 (0.13), residues: 1824 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP G 148 HIS 0.003 0.001 HIS L 198 PHE 0.025 0.002 PHE H 100C TYR 0.024 0.002 TYR B 140 ARG 0.003 0.000 ARG I 116 Details of bonding type rmsd link_NAG-ASN : bond 0.00127 ( 4) link_NAG-ASN : angle 1.01782 ( 12) link_BETA1-4 : bond 0.00412 ( 8) link_BETA1-4 : angle 1.74662 ( 24) hydrogen bonds : bond 0.03411 ( 706) hydrogen bonds : angle 5.31370 ( 1932) SS BOND : bond 0.00247 ( 32) SS BOND : angle 1.03213 ( 66) covalent geometry : bond 0.00342 (25376) covalent geometry : angle 0.60233 (34384) *********************** 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 420 residues out of total 2708 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 88 poor density : 332 time to evaluate : 2.581 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: I 338 GLU cc_start: 0.8335 (OUTLIER) cc_final: 0.8075 (mp0) REVERT: I 419 LYS cc_start: 0.9291 (mttt) cc_final: 0.9010 (mttm) REVERT: I 429 MET cc_start: 0.9426 (mtp) cc_final: 0.9205 (mtm) REVERT: M 338 GLU cc_start: 0.8338 (OUTLIER) cc_final: 0.8061 (mp0) REVERT: M 419 LYS cc_start: 0.9283 (mttt) cc_final: 0.9005 (mttm) REVERT: M 429 MET cc_start: 0.9422 (mtp) cc_final: 0.9204 (mtm) REVERT: N 338 GLU cc_start: 0.8362 (OUTLIER) cc_final: 0.8069 (mp0) REVERT: N 371 LYS cc_start: 0.9213 (OUTLIER) cc_final: 0.8866 (ptpp) REVERT: N 419 LYS cc_start: 0.9289 (mttt) cc_final: 0.8999 (mttm) REVERT: N 429 MET cc_start: 0.9407 (mtp) cc_final: 0.9181 (mtm) REVERT: W 338 GLU cc_start: 0.8359 (OUTLIER) cc_final: 0.8064 (mp0) REVERT: W 371 LYS cc_start: 0.9218 (OUTLIER) cc_final: 0.8817 (ptpp) REVERT: W 390 ASP cc_start: 0.8181 (OUTLIER) cc_final: 0.7852 (m-30) REVERT: W 419 LYS cc_start: 0.9286 (mttt) cc_final: 0.9008 (mttm) REVERT: A 72 ASP cc_start: 0.8261 (t70) cc_final: 0.7490 (t70) REVERT: A 145 TYR cc_start: 0.7026 (p90) cc_final: 0.6433 (p90) REVERT: A 176 TYR cc_start: 0.7101 (m-80) cc_final: 0.6832 (m-80) REVERT: C 30 ILE cc_start: 0.9053 (tt) cc_final: 0.8761 (tp) REVERT: C 72 ASP cc_start: 0.8130 (t70) cc_final: 0.7387 (t70) REVERT: C 100 PHE cc_start: 0.7930 (OUTLIER) cc_final: 0.7575 (p90) REVERT: D 30 ILE cc_start: 0.9006 (tt) cc_final: 0.8728 (tp) REVERT: D 72 ASP cc_start: 0.8178 (t70) cc_final: 0.7424 (t70) REVERT: D 100 PHE cc_start: 0.7916 (OUTLIER) cc_final: 0.7563 (p90) REVERT: D 145 TYR cc_start: 0.7121 (p90) cc_final: 0.6534 (p90) REVERT: D 176 TYR cc_start: 0.7249 (m-80) cc_final: 0.7032 (m-80) REVERT: H 30 ILE cc_start: 0.9049 (tt) cc_final: 0.8755 (tp) REVERT: H 72 ASP cc_start: 0.8129 (t70) cc_final: 0.7365 (t70) REVERT: H 100 PHE cc_start: 0.7932 (OUTLIER) cc_final: 0.7577 (p90) REVERT: H 145 TYR cc_start: 0.7017 (p90) cc_final: 0.6363 (p90) REVERT: H 169 VAL cc_start: 0.7533 (OUTLIER) cc_final: 0.7302 (p) REVERT: B 42 GLN cc_start: 0.7358 (mp10) cc_final: 0.7088 (mp10) REVERT: B 108 ARG cc_start: 0.7801 (ptm160) cc_final: 0.7025 (ptm-80) REVERT: E 108 ARG cc_start: 0.8023 (ptm160) cc_final: 0.7364 (ptm-80) REVERT: E 190 LYS cc_start: 0.8254 (mmmt) cc_final: 0.7890 (tptt) REVERT: G 108 ARG cc_start: 0.7862 (ptm160) cc_final: 0.7012 (ptm-80) REVERT: L 108 ARG cc_start: 0.7787 (ptm160) cc_final: 0.6968 (ptm-80) REVERT: L 142 ARG cc_start: 0.8740 (ttp-170) cc_final: 0.8481 (ttp80) outliers start: 88 outliers final: 45 residues processed: 408 average time/residue: 1.3401 time to fit residues: 629.5885 Evaluate side-chains 344 residues out of total 2708 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 288 time to evaluate : 2.601 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain I residue 182 CYS Chi-restraints excluded: chain I residue 198 SER Chi-restraints excluded: chain I residue 229 CYS Chi-restraints excluded: chain I residue 337 CYS Chi-restraints excluded: chain I residue 338 GLU Chi-restraints excluded: chain M residue 182 CYS Chi-restraints excluded: chain M residue 198 SER Chi-restraints excluded: chain M residue 229 CYS Chi-restraints excluded: chain M residue 337 CYS Chi-restraints excluded: chain M residue 338 GLU Chi-restraints excluded: chain M residue 359 SER Chi-restraints excluded: chain N residue 182 CYS Chi-restraints excluded: chain N residue 198 SER Chi-restraints excluded: chain N residue 229 CYS Chi-restraints excluded: chain N residue 337 CYS Chi-restraints excluded: chain N residue 338 GLU Chi-restraints excluded: chain N residue 371 LYS Chi-restraints excluded: chain W residue 182 CYS Chi-restraints excluded: chain W residue 198 SER Chi-restraints excluded: chain W residue 229 CYS Chi-restraints excluded: chain W residue 337 CYS Chi-restraints excluded: chain W residue 338 GLU Chi-restraints excluded: chain W residue 359 SER Chi-restraints excluded: chain W residue 371 LYS Chi-restraints excluded: chain W residue 390 ASP 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 184 VAL Chi-restraints excluded: chain C residue 87 THR Chi-restraints excluded: chain C residue 100 PHE Chi-restraints excluded: chain C residue 100 ASP Chi-restraints excluded: chain C residue 184 VAL 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 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 PHE Chi-restraints excluded: chain H residue 100 ASP Chi-restraints excluded: chain H residue 169 VAL Chi-restraints excluded: chain H residue 184 VAL Chi-restraints excluded: chain B residue 30 SER Chi-restraints excluded: chain B residue 202 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 182 SER Chi-restraints excluded: chain E residue 202 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 33 LEU Chi-restraints excluded: chain L residue 76 SER 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 62 optimal weight: 1.9990 chunk 17 optimal weight: 5.9990 chunk 129 optimal weight: 4.9990 chunk 71 optimal weight: 4.9990 chunk 55 optimal weight: 0.5980 chunk 122 optimal weight: 6.9990 chunk 298 optimal weight: 5.9990 chunk 243 optimal weight: 7.9990 chunk 254 optimal weight: 9.9990 chunk 50 optimal weight: 0.9990 chunk 15 optimal weight: 0.8980 overall best weight: 1.8986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: W 329 ASN B 27 GLN B 166 GLN E 6 GLN E 27 GLN E 166 GLN G 27 GLN ** G 155 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 6 GLN ** L 155 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3909 r_free = 0.3909 target = 0.143953 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3101 r_free = 0.3101 target = 0.083504 restraints weight = 36521.314| |-----------------------------------------------------------------------------| r_work (start): 0.3007 rms_B_bonded: 2.38 r_work: 0.2878 rms_B_bonded: 2.47 restraints_weight: 0.5000 r_work: 0.2744 rms_B_bonded: 3.84 restraints_weight: 0.2500 r_work (final): 0.2744 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2734 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2734 r_free = 0.2734 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 = 0.2734 r_free = 0.2734 target_work(ls_wunit_k1) = 0.063 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| r_final: 0.2734 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8376 moved from start: 0.3077 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 25420 Z= 0.161 Angle : 0.604 7.623 34486 Z= 0.315 Chirality : 0.044 0.133 3808 Planarity : 0.005 0.053 4380 Dihedral : 5.754 37.201 3708 Min Nonbonded Distance : 2.304 Molprobity Statistics. All-atom Clashscore : 6.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.67 % Favored : 95.33 % Rotamer: Outliers : 4.14 % Allowed : 22.38 % Favored : 73.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.63 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.00 (0.14), residues: 3148 helix: -4.25 (0.19), residues: 32 sheet: -0.63 (0.14), residues: 1292 loop : -1.85 (0.13), residues: 1824 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP C 103 HIS 0.003 0.001 HIS G 198 PHE 0.026 0.002 PHE H 100C TYR 0.025 0.002 TYR E 140 ARG 0.002 0.000 ARG M 374 Details of bonding type rmsd link_NAG-ASN : bond 0.00151 ( 4) link_NAG-ASN : angle 0.99159 ( 12) link_BETA1-4 : bond 0.00423 ( 8) link_BETA1-4 : angle 1.62497 ( 24) hydrogen bonds : bond 0.03301 ( 706) hydrogen bonds : angle 5.10640 ( 1932) SS BOND : bond 0.00312 ( 32) SS BOND : angle 1.55644 ( 66) covalent geometry : bond 0.00381 (25376) covalent geometry : angle 0.59911 (34384) *********************** 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 406 residues out of total 2708 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 112 poor density : 294 time to evaluate : 2.584 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: 0.8373 (OUTLIER) cc_final: 0.7999 (mp0) REVERT: M 338 GLU cc_start: 0.8328 (OUTLIER) cc_final: 0.7996 (mp0) REVERT: M 419 LYS cc_start: 0.9182 (mttt) cc_final: 0.8978 (mttm) REVERT: N 338 GLU cc_start: 0.8393 (OUTLIER) cc_final: 0.8009 (mp0) REVERT: N 371 LYS cc_start: 0.9229 (OUTLIER) cc_final: 0.8821 (ptpp) REVERT: N 390 ASP cc_start: 0.8333 (OUTLIER) cc_final: 0.8043 (m-30) REVERT: N 419 LYS cc_start: 0.9193 (mttt) cc_final: 0.8992 (mttm) REVERT: N 429 MET cc_start: 0.9418 (mtp) cc_final: 0.9179 (mtm) REVERT: W 338 GLU cc_start: 0.8376 (OUTLIER) cc_final: 0.7997 (mp0) REVERT: W 371 LYS cc_start: 0.9227 (OUTLIER) cc_final: 0.8852 (ptpp) REVERT: W 390 ASP cc_start: 0.8205 (OUTLIER) cc_final: 0.7932 (m-30) REVERT: W 419 LYS cc_start: 0.9190 (mttt) cc_final: 0.8989 (mttm) REVERT: A 72 ASP cc_start: 0.8305 (t70) cc_final: 0.7599 (t70) REVERT: A 100 PHE cc_start: 0.7967 (OUTLIER) cc_final: 0.7557 (p90) REVERT: A 145 TYR cc_start: 0.6995 (p90) cc_final: 0.6353 (p90) REVERT: A 176 TYR cc_start: 0.7161 (m-80) cc_final: 0.6956 (m-80) REVERT: A 184 VAL cc_start: 0.8583 (OUTLIER) cc_final: 0.8369 (p) REVERT: C 30 ILE cc_start: 0.9066 (tt) cc_final: 0.8771 (tp) REVERT: C 72 ASP cc_start: 0.8231 (t70) cc_final: 0.7496 (t70) REVERT: C 100 PHE cc_start: 0.7877 (OUTLIER) cc_final: 0.7542 (p90) REVERT: D 72 ASP cc_start: 0.8237 (t70) cc_final: 0.7494 (t70) REVERT: D 100 PHE cc_start: 0.7914 (OUTLIER) cc_final: 0.7603 (p90) REVERT: D 145 TYR cc_start: 0.7177 (p90) cc_final: 0.6565 (p90) REVERT: D 176 TYR cc_start: 0.7283 (m-80) cc_final: 0.7074 (m-80) REVERT: H 30 ILE cc_start: 0.9053 (tt) cc_final: 0.8752 (tp) REVERT: H 72 ASP cc_start: 0.8236 (t70) cc_final: 0.7499 (t70) REVERT: H 100 PHE cc_start: 0.7879 (OUTLIER) cc_final: 0.7545 (p90) REVERT: H 169 VAL cc_start: 0.7767 (OUTLIER) cc_final: 0.7553 (p) REVERT: H 184 VAL cc_start: 0.8510 (OUTLIER) cc_final: 0.8309 (p) REVERT: B 42 GLN cc_start: 0.7375 (mp10) cc_final: 0.7080 (mp10) REVERT: B 108 ARG cc_start: 0.7889 (ptm160) cc_final: 0.7579 (ptm-80) REVERT: E 49 ASN cc_start: 0.8025 (OUTLIER) cc_final: 0.7772 (p0) REVERT: E 108 ARG cc_start: 0.8019 (ptm160) cc_final: 0.7419 (ptm-80) REVERT: E 190 LYS cc_start: 0.8348 (mmmt) cc_final: 0.8010 (tptt) REVERT: G 108 ARG cc_start: 0.7810 (ptm160) cc_final: 0.7139 (ptm-80) REVERT: L 108 ARG cc_start: 0.7775 (ptm160) cc_final: 0.7079 (ptm-80) outliers start: 112 outliers final: 69 residues processed: 394 average time/residue: 1.3067 time to fit residues: 595.6034 Evaluate side-chains 372 residues out of total 2708 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 85 poor density : 287 time to evaluate : 2.856 ------------------------------------------------------------------------------- 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 359 SER Chi-restraints excluded: chain I residue 361 ILE Chi-restraints excluded: chain I residue 390 ASP Chi-restraints excluded: chain M residue 102 ARG Chi-restraints excluded: chain M residue 146 THR Chi-restraints excluded: chain M residue 182 CYS Chi-restraints excluded: chain M residue 198 SER Chi-restraints excluded: chain M residue 229 CYS Chi-restraints excluded: chain M residue 307 VAL Chi-restraints excluded: chain M residue 337 CYS Chi-restraints excluded: chain M residue 338 GLU Chi-restraints excluded: chain M residue 359 SER Chi-restraints excluded: chain M residue 361 ILE Chi-restraints excluded: chain M residue 390 ASP Chi-restraints excluded: chain N residue 146 THR Chi-restraints excluded: chain N residue 182 CYS Chi-restraints excluded: chain N residue 198 SER Chi-restraints excluded: chain N residue 229 CYS Chi-restraints excluded: chain N residue 307 VAL Chi-restraints excluded: chain N residue 337 CYS Chi-restraints excluded: chain N residue 338 GLU Chi-restraints excluded: chain N residue 359 SER Chi-restraints excluded: chain N residue 361 ILE Chi-restraints excluded: chain N residue 371 LYS Chi-restraints excluded: chain N residue 390 ASP Chi-restraints excluded: chain W residue 146 THR Chi-restraints excluded: chain W residue 182 CYS Chi-restraints excluded: chain W residue 198 SER Chi-restraints excluded: chain W residue 229 CYS Chi-restraints excluded: chain W residue 307 VAL Chi-restraints excluded: chain W residue 337 CYS Chi-restraints excluded: chain W residue 338 GLU Chi-restraints excluded: chain W residue 359 SER Chi-restraints excluded: chain W residue 361 ILE Chi-restraints excluded: chain W residue 371 LYS Chi-restraints excluded: chain W residue 390 ASP 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 184 VAL Chi-restraints excluded: chain C residue 11 VAL Chi-restraints excluded: chain C residue 17 SER Chi-restraints excluded: chain C residue 25 SER Chi-restraints excluded: chain C residue 84 SER Chi-restraints excluded: chain C residue 87 THR Chi-restraints excluded: chain C residue 100 PHE Chi-restraints excluded: chain C residue 100 ASP Chi-restraints excluded: chain 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 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 PHE Chi-restraints excluded: chain H residue 100 ASP Chi-restraints excluded: chain H residue 169 VAL Chi-restraints excluded: chain H residue 184 VAL Chi-restraints excluded: chain B residue 27 GLN Chi-restraints excluded: chain B residue 30 SER Chi-restraints excluded: chain B residue 33 LEU Chi-restraints excluded: chain B residue 76 SER Chi-restraints excluded: chain B residue 79 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 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 G residue 27 GLN Chi-restraints excluded: chain G residue 76 SER Chi-restraints excluded: chain G residue 202 SER Chi-restraints excluded: chain L residue 30 SER Chi-restraints excluded: chain L residue 76 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 316 random chunks: chunk 116 optimal weight: 0.7980 chunk 137 optimal weight: 6.9990 chunk 238 optimal weight: 10.0000 chunk 299 optimal weight: 2.9990 chunk 274 optimal weight: 7.9990 chunk 213 optimal weight: 6.9990 chunk 132 optimal weight: 0.9980 chunk 186 optimal weight: 30.0000 chunk 78 optimal weight: 0.0470 chunk 105 optimal weight: 3.9990 chunk 80 optimal weight: 3.9990 overall best weight: 1.7682 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: I 101 HIS B 166 GLN E 6 GLN E 27 GLN ** E 124 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 166 GLN ** G 155 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 155 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 198 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3912 r_free = 0.3912 target = 0.144168 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.3108 r_free = 0.3108 target = 0.083873 restraints weight = 36495.166| |-----------------------------------------------------------------------------| r_work (start): 0.3013 rms_B_bonded: 2.36 r_work: 0.2884 rms_B_bonded: 2.46 restraints_weight: 0.5000 r_work: 0.2750 rms_B_bonded: 3.82 restraints_weight: 0.2500 r_work (final): 0.2750 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2742 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2742 r_free = 0.2742 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 = 0.2742 r_free = 0.2742 target_work(ls_wunit_k1) = 0.063 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| r_final: 0.2742 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8370 moved from start: 0.3200 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 25420 Z= 0.152 Angle : 0.591 7.611 34486 Z= 0.308 Chirality : 0.044 0.181 3808 Planarity : 0.004 0.054 4380 Dihedral : 5.519 37.438 3708 Min Nonbonded Distance : 2.315 Molprobity Statistics. All-atom Clashscore : 6.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.70 % Favored : 95.30 % Rotamer: Outliers : 4.14 % Allowed : 22.75 % Favored : 73.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.63 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.88 (0.14), residues: 3148 helix: -4.15 (0.21), residues: 32 sheet: -0.53 (0.14), residues: 1296 loop : -1.78 (0.13), residues: 1820 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP D 103 HIS 0.008 0.001 HIS I 101 PHE 0.025 0.002 PHE C 100C TYR 0.023 0.002 TYR B 140 ARG 0.005 0.000 ARG B 24 Details of bonding type rmsd link_NAG-ASN : bond 0.00130 ( 4) link_NAG-ASN : angle 0.97129 ( 12) link_BETA1-4 : bond 0.00439 ( 8) link_BETA1-4 : angle 1.55132 ( 24) hydrogen bonds : bond 0.03159 ( 706) hydrogen bonds : angle 5.01066 ( 1932) SS BOND : bond 0.00239 ( 32) SS BOND : angle 1.58750 ( 66) covalent geometry : bond 0.00361 (25376) covalent geometry : angle 0.58632 (34384) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6296 Ramachandran restraints generated. 3148 Oldfield, 0 Emsley, 3148 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6296 Ramachandran restraints generated. 3148 Oldfield, 0 Emsley, 3148 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 407 residues out of total 2708 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 112 poor density : 295 time to evaluate : 2.820 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: I 338 GLU cc_start: 0.8355 (OUTLIER) cc_final: 0.8006 (mp0) REVERT: M 338 GLU cc_start: 0.8343 (OUTLIER) cc_final: 0.8008 (mp0) REVERT: M 419 LYS cc_start: 0.9187 (OUTLIER) cc_final: 0.8985 (mttm) REVERT: N 338 GLU cc_start: 0.8372 (OUTLIER) cc_final: 0.7992 (mp0) REVERT: N 371 LYS cc_start: 0.9237 (OUTLIER) cc_final: 0.8876 (ptpp) REVERT: N 390 ASP cc_start: 0.8265 (OUTLIER) cc_final: 0.8001 (m-30) REVERT: N 429 MET cc_start: 0.9406 (mtp) cc_final: 0.9159 (mtm) REVERT: W 338 GLU cc_start: 0.8366 (OUTLIER) cc_final: 0.7986 (mp0) REVERT: W 371 LYS cc_start: 0.9236 (OUTLIER) cc_final: 0.8810 (ptpp) REVERT: W 390 ASP cc_start: 0.8159 (OUTLIER) cc_final: 0.7913 (m-30) REVERT: W 419 LYS cc_start: 0.9186 (OUTLIER) cc_final: 0.8983 (mttm) REVERT: A 72 ASP cc_start: 0.8298 (t70) cc_final: 0.7605 (t70) REVERT: A 100 PHE cc_start: 0.7917 (OUTLIER) cc_final: 0.7443 (p90) REVERT: A 145 TYR cc_start: 0.7003 (p90) cc_final: 0.6380 (p90) REVERT: A 176 TYR cc_start: 0.7127 (m-80) cc_final: 0.6916 (m-80) REVERT: C 30 ILE cc_start: 0.9071 (tt) cc_final: 0.8769 (tp) REVERT: C 72 ASP cc_start: 0.8222 (t70) cc_final: 0.7484 (t70) REVERT: C 100 PHE cc_start: 0.7874 (OUTLIER) cc_final: 0.7571 (p90) REVERT: D 72 ASP cc_start: 0.8241 (t70) cc_final: 0.7496 (t70) REVERT: D 100 PHE cc_start: 0.7853 (OUTLIER) cc_final: 0.7551 (p90) REVERT: D 145 TYR cc_start: 0.6956 (p90) cc_final: 0.6221 (p90) REVERT: D 176 TYR cc_start: 0.7251 (m-80) cc_final: 0.7037 (m-80) REVERT: H 30 ILE cc_start: 0.9070 (tt) cc_final: 0.8767 (tp) REVERT: H 72 ASP cc_start: 0.8263 (t70) cc_final: 0.7512 (t70) REVERT: H 100 PHE cc_start: 0.7874 (OUTLIER) cc_final: 0.7570 (p90) REVERT: H 169 VAL cc_start: 0.7598 (OUTLIER) cc_final: 0.7398 (p) REVERT: B 27 GLN cc_start: 0.8857 (OUTLIER) cc_final: 0.8482 (pm20) REVERT: B 42 GLN cc_start: 0.7370 (mp10) cc_final: 0.7078 (mp10) REVERT: B 108 ARG cc_start: 0.7885 (ptm160) cc_final: 0.7549 (ptm-80) REVERT: B 116 PHE cc_start: 0.5714 (m-10) cc_final: 0.5475 (m-10) REVERT: E 108 ARG cc_start: 0.8059 (ptm160) cc_final: 0.7508 (ptm-80) REVERT: G 27 GLN cc_start: 0.8869 (OUTLIER) cc_final: 0.8493 (pm20) REVERT: G 108 ARG cc_start: 0.7906 (ptm160) cc_final: 0.7635 (ptt90) REVERT: L 108 ARG cc_start: 0.7684 (ptm160) cc_final: 0.7457 (ptt90) outliers start: 112 outliers final: 71 residues processed: 392 average time/residue: 1.3561 time to fit residues: 611.6513 Evaluate side-chains 366 residues out of total 2708 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 88 poor density : 278 time to evaluate : 2.635 ------------------------------------------------------------------------------- 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 359 SER Chi-restraints excluded: chain I residue 361 ILE Chi-restraints excluded: chain M residue 102 ARG Chi-restraints excluded: chain M residue 146 THR Chi-restraints excluded: chain M residue 182 CYS Chi-restraints excluded: chain M residue 198 SER Chi-restraints excluded: chain M residue 229 CYS Chi-restraints excluded: chain M residue 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 361 ILE Chi-restraints excluded: chain M residue 419 LYS Chi-restraints excluded: chain N residue 146 THR Chi-restraints excluded: chain N residue 182 CYS Chi-restraints excluded: chain N residue 198 SER Chi-restraints excluded: chain N residue 229 CYS Chi-restraints excluded: chain N residue 307 VAL Chi-restraints excluded: chain N residue 337 CYS Chi-restraints excluded: chain N residue 338 GLU Chi-restraints excluded: chain N residue 357 MET Chi-restraints excluded: chain N residue 359 SER Chi-restraints excluded: chain N residue 361 ILE Chi-restraints excluded: chain N residue 371 LYS Chi-restraints excluded: chain N residue 390 ASP 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 361 ILE Chi-restraints excluded: chain W residue 371 LYS Chi-restraints excluded: chain W residue 390 ASP Chi-restraints excluded: chain W residue 419 LYS Chi-restraints excluded: chain A residue 11 VAL Chi-restraints excluded: chain A residue 17 SER Chi-restraints excluded: chain A residue 87 THR Chi-restraints excluded: chain A residue 100 PHE Chi-restraints excluded: chain A residue 100 ASP Chi-restraints excluded: chain C residue 17 SER Chi-restraints excluded: chain C residue 25 SER Chi-restraints excluded: chain C residue 84 SER Chi-restraints excluded: chain C residue 87 THR Chi-restraints excluded: chain C residue 100 PHE Chi-restraints excluded: chain C residue 100 ASP Chi-restraints excluded: chain C residue 184 VAL Chi-restraints excluded: chain D residue 17 SER Chi-restraints excluded: chain D residue 87 THR Chi-restraints excluded: chain D residue 100 PHE Chi-restraints excluded: chain D residue 100 ASP Chi-restraints excluded: chain D residue 184 VAL Chi-restraints excluded: chain H residue 11 VAL Chi-restraints excluded: chain H residue 17 SER Chi-restraints excluded: chain H residue 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 169 VAL Chi-restraints excluded: chain B residue 27 GLN Chi-restraints excluded: chain B residue 30 SER Chi-restraints excluded: chain B residue 33 LEU Chi-restraints excluded: chain B residue 76 SER Chi-restraints excluded: chain B residue 182 SER Chi-restraints excluded: chain B residue 202 SER Chi-restraints excluded: chain B residue 206 THR Chi-restraints excluded: chain E residue 27 GLN Chi-restraints excluded: chain E residue 30 SER Chi-restraints excluded: chain E residue 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 76 SER Chi-restraints excluded: chain G residue 202 SER Chi-restraints excluded: chain L residue 30 SER Chi-restraints excluded: chain L residue 76 SER Chi-restraints excluded: chain L residue 202 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 316 random chunks: chunk 82 optimal weight: 5.9990 chunk 102 optimal weight: 5.9990 chunk 280 optimal weight: 10.0000 chunk 291 optimal weight: 20.0000 chunk 300 optimal weight: 0.4980 chunk 215 optimal weight: 1.9990 chunk 195 optimal weight: 4.9990 chunk 138 optimal weight: 0.9990 chunk 11 optimal weight: 1.9990 chunk 137 optimal weight: 6.9990 chunk 167 optimal weight: 10.0000 overall best weight: 2.0988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: I 101 HIS M 101 HIS W 101 HIS ** E 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 124 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 166 GLN ** G 155 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 160 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 6 GLN ** L 155 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3908 r_free = 0.3908 target = 0.143850 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3101 r_free = 0.3101 target = 0.083429 restraints weight = 36645.966| |-----------------------------------------------------------------------------| r_work (start): 0.3004 rms_B_bonded: 2.40 r_work: 0.2875 rms_B_bonded: 2.48 restraints_weight: 0.5000 r_work: 0.2741 rms_B_bonded: 3.86 restraints_weight: 0.2500 r_work (final): 0.2741 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2729 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2729 r_free = 0.2729 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 = 0.2729 r_free = 0.2729 target_work(ls_wunit_k1) = 0.063 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| r_final: 0.2729 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8379 moved from start: 0.3333 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 25420 Z= 0.169 Angle : 0.594 7.569 34486 Z= 0.309 Chirality : 0.044 0.185 3808 Planarity : 0.004 0.043 4380 Dihedral : 5.373 37.273 3708 Min Nonbonded Distance : 2.306 Molprobity Statistics. All-atom Clashscore : 6.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.48 % Favored : 95.52 % Rotamer: Outliers : 3.99 % Allowed : 23.30 % Favored : 72.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.63 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.76 (0.14), residues: 3148 helix: -4.13 (0.23), residues: 32 sheet: -0.42 (0.14), residues: 1296 loop : -1.72 (0.13), residues: 1820 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP H 47 HIS 0.008 0.001 HIS W 101 PHE 0.027 0.002 PHE C 100C TYR 0.023 0.002 TYR E 140 ARG 0.004 0.000 ARG B 24 Details of bonding type rmsd link_NAG-ASN : bond 0.00175 ( 4) link_NAG-ASN : angle 1.00475 ( 12) link_BETA1-4 : bond 0.00361 ( 8) link_BETA1-4 : angle 1.51381 ( 24) hydrogen bonds : bond 0.03171 ( 706) hydrogen bonds : angle 4.93168 ( 1932) SS BOND : bond 0.00276 ( 32) SS BOND : angle 1.59323 ( 66) covalent geometry : bond 0.00403 (25376) covalent geometry : angle 0.58882 (34384) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6296 Ramachandran restraints generated. 3148 Oldfield, 0 Emsley, 3148 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6296 Ramachandran restraints generated. 3148 Oldfield, 0 Emsley, 3148 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 395 residues out of total 2708 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 108 poor density : 287 time to evaluate : 2.633 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: I 338 GLU cc_start: 0.8344 (OUTLIER) cc_final: 0.7991 (mp0) REVERT: M 338 GLU cc_start: 0.8352 (OUTLIER) cc_final: 0.7989 (mp0) REVERT: M 419 LYS cc_start: 0.9179 (OUTLIER) cc_final: 0.8953 (mttm) REVERT: N 338 GLU cc_start: 0.8340 (OUTLIER) cc_final: 0.7954 (mp0) REVERT: N 371 LYS cc_start: 0.9262 (OUTLIER) cc_final: 0.8864 (ptpp) REVERT: N 390 ASP cc_start: 0.8294 (OUTLIER) cc_final: 0.8066 (m-30) REVERT: N 429 MET cc_start: 0.9412 (mtp) cc_final: 0.9150 (mtm) REVERT: W 338 GLU cc_start: 0.8324 (OUTLIER) cc_final: 0.7947 (mp0) REVERT: W 371 LYS cc_start: 0.9259 (OUTLIER) cc_final: 0.8817 (ptpp) REVERT: W 390 ASP cc_start: 0.8304 (OUTLIER) cc_final: 0.8050 (m-30) REVERT: W 419 LYS cc_start: 0.9182 (OUTLIER) cc_final: 0.8954 (mttm) REVERT: A 72 ASP cc_start: 0.8341 (t70) cc_final: 0.7653 (t70) REVERT: A 100 PHE cc_start: 0.7967 (OUTLIER) cc_final: 0.7492 (p90) REVERT: C 30 ILE cc_start: 0.9035 (tt) cc_final: 0.8730 (tp) REVERT: C 72 ASP cc_start: 0.8266 (t70) cc_final: 0.7587 (t70) REVERT: C 100 PHE cc_start: 0.7869 (OUTLIER) cc_final: 0.7560 (p90) REVERT: D 72 ASP cc_start: 0.8289 (t70) cc_final: 0.7595 (t70) REVERT: D 100 PHE cc_start: 0.7894 (OUTLIER) cc_final: 0.7596 (p90) REVERT: D 145 TYR cc_start: 0.7041 (p90) cc_final: 0.6342 (p90) REVERT: H 30 ILE cc_start: 0.9033 (tt) cc_final: 0.8729 (tp) REVERT: H 72 ASP cc_start: 0.8289 (t70) cc_final: 0.7604 (t70) REVERT: H 100 PHE cc_start: 0.7869 (OUTLIER) cc_final: 0.7549 (p90) REVERT: H 169 VAL cc_start: 0.7501 (OUTLIER) cc_final: 0.7279 (p) REVERT: B 42 GLN cc_start: 0.7386 (mp10) cc_final: 0.7090 (mp10) REVERT: B 108 ARG cc_start: 0.7895 (ptm160) cc_final: 0.7574 (ptm-80) REVERT: E 108 ARG cc_start: 0.8076 (ptm160) cc_final: 0.7541 (ptm-80) REVERT: G 108 ARG cc_start: 0.7842 (ptm160) cc_final: 0.7620 (ptt90) REVERT: G 116 PHE cc_start: 0.5540 (m-10) cc_final: 0.5334 (m-10) outliers start: 108 outliers final: 74 residues processed: 382 average time/residue: 1.3213 time to fit residues: 584.4372 Evaluate side-chains 367 residues out of total 2708 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 89 poor density : 278 time to evaluate : 2.874 ------------------------------------------------------------------------------- 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 359 SER Chi-restraints excluded: chain I residue 361 ILE Chi-restraints excluded: chain M residue 102 ARG Chi-restraints excluded: chain M residue 146 THR Chi-restraints excluded: chain M residue 182 CYS Chi-restraints excluded: chain M residue 198 SER Chi-restraints excluded: chain M residue 229 CYS Chi-restraints excluded: chain M residue 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 M residue 419 LYS Chi-restraints excluded: chain N residue 146 THR Chi-restraints excluded: chain N residue 182 CYS Chi-restraints excluded: chain N residue 198 SER Chi-restraints excluded: chain N residue 229 CYS Chi-restraints excluded: chain N residue 307 VAL Chi-restraints excluded: chain N residue 337 CYS Chi-restraints excluded: chain N residue 338 GLU Chi-restraints excluded: chain N residue 359 SER Chi-restraints excluded: chain N residue 361 ILE Chi-restraints excluded: chain N residue 371 LYS Chi-restraints excluded: chain N residue 390 ASP 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 338 GLU Chi-restraints excluded: chain W residue 359 SER Chi-restraints excluded: chain W residue 361 ILE Chi-restraints excluded: chain W residue 371 LYS Chi-restraints excluded: chain W residue 390 ASP Chi-restraints excluded: chain W residue 419 LYS Chi-restraints excluded: chain A residue 11 VAL Chi-restraints excluded: chain A residue 17 SER Chi-restraints excluded: chain A residue 87 THR Chi-restraints excluded: chain A residue 100 PHE Chi-restraints excluded: chain A residue 100 ASP Chi-restraints excluded: chain A residue 138 LEU Chi-restraints excluded: chain A residue 184 VAL Chi-restraints excluded: chain C residue 11 VAL Chi-restraints excluded: chain C residue 17 SER Chi-restraints excluded: chain C residue 84 SER Chi-restraints excluded: chain C residue 87 THR Chi-restraints excluded: chain C residue 100 PHE Chi-restraints excluded: chain C residue 100 ASP Chi-restraints excluded: chain C residue 184 VAL Chi-restraints excluded: chain D residue 11 VAL Chi-restraints excluded: chain D residue 17 SER Chi-restraints excluded: chain D residue 87 THR Chi-restraints excluded: chain D residue 100 PHE 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 PHE Chi-restraints excluded: chain H residue 100 ASP Chi-restraints excluded: chain H residue 169 VAL Chi-restraints excluded: chain H residue 184 VAL Chi-restraints excluded: chain B residue 30 SER Chi-restraints excluded: chain B residue 33 LEU Chi-restraints excluded: chain B residue 76 SER Chi-restraints excluded: chain B residue 182 SER Chi-restraints excluded: chain B residue 202 SER Chi-restraints excluded: chain B residue 206 THR Chi-restraints excluded: chain E residue 30 SER Chi-restraints excluded: chain E residue 33 LEU 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 76 SER Chi-restraints excluded: chain G residue 202 SER Chi-restraints excluded: chain L residue 30 SER Chi-restraints excluded: chain L residue 76 SER Chi-restraints excluded: chain L residue 150 VAL Chi-restraints excluded: chain L residue 202 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 316 random chunks: chunk 155 optimal weight: 5.9990 chunk 7 optimal weight: 4.9990 chunk 204 optimal weight: 4.9990 chunk 10 optimal weight: 3.9990 chunk 276 optimal weight: 10.0000 chunk 135 optimal weight: 0.9990 chunk 221 optimal weight: 6.9990 chunk 14 optimal weight: 3.9990 chunk 302 optimal weight: 10.0000 chunk 305 optimal weight: 5.9990 chunk 277 optimal weight: 6.9990 overall best weight: 3.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** I 354 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 101 HIS ** M 354 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 354 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** W 101 HIS ** W 354 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 6 GLN ** E 124 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 166 GLN ** G 155 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 155 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3882 r_free = 0.3882 target = 0.141930 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3057 r_free = 0.3057 target = 0.080943 restraints weight = 36614.712| |-----------------------------------------------------------------------------| r_work (start): 0.2963 rms_B_bonded: 2.40 r_work: 0.2831 rms_B_bonded: 2.47 restraints_weight: 0.5000 r_work: 0.2697 rms_B_bonded: 3.82 restraints_weight: 0.2500 r_work (final): 0.2697 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2690 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2690 r_free = 0.2690 target_work(ls_wunit_k1) = 0.061 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2690 r_free = 0.2690 target_work(ls_wunit_k1) = 0.061 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| r_final: 0.2690 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8419 moved from start: 0.3448 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.077 25420 Z= 0.279 Angle : 0.683 8.336 34486 Z= 0.354 Chirality : 0.047 0.186 3808 Planarity : 0.005 0.077 4380 Dihedral : 5.669 35.887 3708 Min Nonbonded Distance : 2.262 Molprobity Statistics. All-atom Clashscore : 6.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.18 % Favored : 94.82 % Rotamer: Outliers : 4.06 % Allowed : 23.34 % Favored : 72.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.63 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.76 (0.14), residues: 3148 helix: -4.36 (0.22), residues: 56 sheet: -0.28 (0.14), residues: 1300 loop : -1.80 (0.13), residues: 1792 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP C 47 HIS 0.008 0.001 HIS M 101 PHE 0.037 0.002 PHE D 100C TYR 0.022 0.002 TYR L 173 ARG 0.006 0.001 ARG L 108 Details of bonding type rmsd link_NAG-ASN : bond 0.00365 ( 4) link_NAG-ASN : angle 1.17242 ( 12) link_BETA1-4 : bond 0.00367 ( 8) link_BETA1-4 : angle 1.59554 ( 24) hydrogen bonds : bond 0.03626 ( 706) hydrogen bonds : angle 5.07295 ( 1932) SS BOND : bond 0.00438 ( 32) SS BOND : angle 2.37719 ( 66) covalent geometry : bond 0.00667 (25376) covalent geometry : angle 0.67390 (34384) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6296 Ramachandran restraints generated. 3148 Oldfield, 0 Emsley, 3148 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6296 Ramachandran restraints generated. 3148 Oldfield, 0 Emsley, 3148 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 389 residues out of total 2708 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 110 poor density : 279 time to evaluate : 2.865 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: I 338 GLU cc_start: 0.8418 (OUTLIER) cc_final: 0.8008 (mp0) REVERT: M 338 GLU cc_start: 0.8444 (OUTLIER) cc_final: 0.8202 (pm20) REVERT: M 419 LYS cc_start: 0.9212 (OUTLIER) cc_final: 0.8966 (mttm) REVERT: N 338 GLU cc_start: 0.8450 (OUTLIER) cc_final: 0.7996 (mp0) REVERT: N 371 LYS cc_start: 0.9289 (OUTLIER) cc_final: 0.8858 (ptpp) REVERT: N 429 MET cc_start: 0.9433 (mtp) cc_final: 0.9177 (mtm) REVERT: W 338 GLU cc_start: 0.8429 (OUTLIER) cc_final: 0.8023 (mp0) REVERT: W 371 LYS cc_start: 0.9284 (OUTLIER) cc_final: 0.8878 (ptpp) REVERT: W 419 LYS cc_start: 0.9196 (OUTLIER) cc_final: 0.8953 (mttm) REVERT: A 72 ASP cc_start: 0.8405 (t70) cc_final: 0.7708 (t70) REVERT: C 30 ILE cc_start: 0.9065 (tt) cc_final: 0.8759 (tp) REVERT: C 72 ASP cc_start: 0.8334 (t70) cc_final: 0.7664 (t70) REVERT: C 100 PHE cc_start: 0.7965 (OUTLIER) cc_final: 0.7694 (p90) REVERT: D 72 ASP cc_start: 0.8361 (t70) cc_final: 0.7679 (t70) REVERT: D 100 PHE cc_start: 0.7961 (OUTLIER) cc_final: 0.7545 (p90) REVERT: D 123 PRO cc_start: 0.3379 (Cg_endo) cc_final: 0.3171 (Cg_exo) REVERT: D 145 TYR cc_start: 0.7169 (p90) cc_final: 0.6555 (p90) REVERT: D 176 TYR cc_start: 0.7322 (m-80) cc_final: 0.7094 (m-80) REVERT: H 30 ILE cc_start: 0.9061 (tt) cc_final: 0.8753 (tp) REVERT: H 72 ASP cc_start: 0.8363 (t70) cc_final: 0.7689 (t70) REVERT: H 169 VAL cc_start: 0.7461 (OUTLIER) cc_final: 0.7223 (p) REVERT: B 42 GLN cc_start: 0.7464 (mp10) cc_final: 0.7151 (mp10) REVERT: B 108 ARG cc_start: 0.7932 (ptm160) cc_final: 0.7655 (ptt90) REVERT: E 90 ARG cc_start: 0.8940 (OUTLIER) cc_final: 0.8089 (mmm-85) REVERT: E 108 ARG cc_start: 0.8044 (ptm160) cc_final: 0.7478 (ptm-80) REVERT: L 201 LEU cc_start: 0.6608 (OUTLIER) cc_final: 0.6349 (pp) outliers start: 110 outliers final: 67 residues processed: 373 average time/residue: 1.3888 time to fit residues: 600.8619 Evaluate side-chains 356 residues out of total 2708 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 80 poor density : 276 time to evaluate : 2.646 ------------------------------------------------------------------------------- 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 338 GLU Chi-restraints excluded: chain I residue 359 SER Chi-restraints excluded: chain I residue 361 ILE Chi-restraints excluded: chain M residue 146 THR Chi-restraints excluded: chain M residue 182 CYS Chi-restraints excluded: chain M residue 198 SER Chi-restraints excluded: chain M residue 229 CYS Chi-restraints excluded: chain M residue 307 VAL Chi-restraints excluded: chain M residue 338 GLU Chi-restraints excluded: chain M residue 359 SER Chi-restraints excluded: chain M residue 419 LYS Chi-restraints excluded: chain N residue 146 THR Chi-restraints excluded: chain N residue 182 CYS Chi-restraints excluded: chain N residue 198 SER Chi-restraints excluded: chain N residue 229 CYS Chi-restraints excluded: chain N residue 307 VAL Chi-restraints excluded: chain N residue 338 GLU Chi-restraints excluded: chain N residue 359 SER Chi-restraints excluded: chain N residue 371 LYS Chi-restraints excluded: chain W residue 146 THR Chi-restraints excluded: chain W residue 182 CYS Chi-restraints excluded: chain W residue 198 SER Chi-restraints excluded: chain W residue 229 CYS Chi-restraints excluded: chain W residue 307 VAL Chi-restraints excluded: chain W residue 338 GLU Chi-restraints excluded: chain W residue 359 SER Chi-restraints excluded: chain W residue 361 ILE Chi-restraints excluded: chain W residue 371 LYS Chi-restraints excluded: chain W residue 419 LYS Chi-restraints excluded: chain A residue 11 VAL Chi-restraints excluded: chain A residue 17 SER Chi-restraints excluded: chain A residue 87 THR Chi-restraints excluded: chain A residue 100 ASP Chi-restraints excluded: chain C residue 11 VAL Chi-restraints excluded: chain C residue 17 SER Chi-restraints excluded: chain C residue 84 SER Chi-restraints excluded: chain C residue 87 THR Chi-restraints excluded: chain C residue 100 PHE Chi-restraints excluded: chain C residue 100 ASP Chi-restraints excluded: chain C residue 100 SER Chi-restraints excluded: chain C residue 179 SER Chi-restraints excluded: chain C residue 184 VAL Chi-restraints excluded: chain D residue 11 VAL Chi-restraints excluded: chain D residue 17 SER Chi-restraints excluded: chain D residue 84 SER Chi-restraints excluded: chain D residue 87 THR Chi-restraints excluded: chain D residue 100 PHE 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 169 VAL Chi-restraints excluded: chain B residue 30 SER Chi-restraints excluded: chain B residue 76 SER Chi-restraints excluded: chain B residue 182 SER Chi-restraints excluded: chain B residue 202 SER Chi-restraints excluded: chain B residue 206 THR Chi-restraints excluded: chain E residue 30 SER Chi-restraints excluded: chain E residue 76 SER Chi-restraints excluded: chain E residue 90 ARG Chi-restraints excluded: chain E residue 182 SER Chi-restraints excluded: chain E residue 202 SER Chi-restraints excluded: chain G residue 76 SER Chi-restraints excluded: chain G residue 201 LEU Chi-restraints excluded: chain G residue 202 SER Chi-restraints excluded: chain L residue 30 SER Chi-restraints excluded: chain L residue 76 SER Chi-restraints excluded: chain L residue 150 VAL Chi-restraints excluded: chain L residue 201 LEU Chi-restraints excluded: chain L residue 202 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 316 random chunks: chunk 120 optimal weight: 2.9990 chunk 237 optimal weight: 6.9990 chunk 227 optimal weight: 8.9990 chunk 31 optimal weight: 0.3980 chunk 81 optimal weight: 2.9990 chunk 32 optimal weight: 6.9990 chunk 103 optimal weight: 0.7980 chunk 193 optimal weight: 2.9990 chunk 273 optimal weight: 4.9990 chunk 61 optimal weight: 1.9990 chunk 218 optimal weight: 8.9990 overall best weight: 1.8386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: I 101 HIS M 101 HIS W 101 HIS ** E 124 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 155 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 166 GLN ** G 155 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 160 GLN ** L 155 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3905 r_free = 0.3905 target = 0.143718 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.3099 r_free = 0.3099 target = 0.083257 restraints weight = 36534.586| |-----------------------------------------------------------------------------| r_work (start): 0.3004 rms_B_bonded: 2.39 r_work: 0.2875 rms_B_bonded: 2.47 restraints_weight: 0.5000 r_work: 0.2743 rms_B_bonded: 3.83 restraints_weight: 0.2500 r_work (final): 0.2743 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2732 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2732 r_free = 0.2732 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 = 0.2732 r_free = 0.2732 target_work(ls_wunit_k1) = 0.063 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| r_final: 0.2732 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8378 moved from start: 0.3543 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 25420 Z= 0.158 Angle : 0.607 7.582 34486 Z= 0.316 Chirality : 0.044 0.184 3808 Planarity : 0.005 0.085 4380 Dihedral : 5.342 37.332 3708 Min Nonbonded Distance : 2.310 Molprobity Statistics. All-atom Clashscore : 7.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.97 % Favored : 96.03 % Rotamer: Outliers : 3.40 % Allowed : 24.41 % Favored : 72.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.63 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.68 (0.14), residues: 3148 helix: -4.35 (0.21), residues: 56 sheet: -0.28 (0.14), residues: 1296 loop : -1.69 (0.13), residues: 1796 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP E 148 HIS 0.009 0.001 HIS I 101 PHE 0.033 0.002 PHE H 100C TYR 0.024 0.002 TYR E 140 ARG 0.007 0.000 ARG G 108 Details of bonding type rmsd link_NAG-ASN : bond 0.00143 ( 4) link_NAG-ASN : angle 1.05842 ( 12) link_BETA1-4 : bond 0.00421 ( 8) link_BETA1-4 : angle 1.45234 ( 24) hydrogen bonds : bond 0.03099 ( 706) hydrogen bonds : angle 4.89043 ( 1932) SS BOND : bond 0.00188 ( 32) SS BOND : angle 1.52575 ( 66) covalent geometry : bond 0.00378 (25376) covalent geometry : angle 0.60285 (34384) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6296 Ramachandran restraints generated. 3148 Oldfield, 0 Emsley, 3148 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6296 Ramachandran restraints generated. 3148 Oldfield, 0 Emsley, 3148 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 378 residues out of total 2708 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 92 poor density : 286 time to evaluate : 2.670 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: I 338 GLU cc_start: 0.8382 (OUTLIER) cc_final: 0.8160 (pm20) REVERT: M 338 GLU cc_start: 0.8384 (OUTLIER) cc_final: 0.8140 (pm20) REVERT: M 419 LYS cc_start: 0.9154 (OUTLIER) cc_final: 0.8912 (mttm) REVERT: N 338 GLU cc_start: 0.8391 (OUTLIER) cc_final: 0.8141 (pm20) REVERT: N 371 LYS cc_start: 0.9259 (OUTLIER) cc_final: 0.8847 (ptpp) REVERT: W 338 GLU cc_start: 0.8378 (OUTLIER) cc_final: 0.8146 (pm20) REVERT: W 371 LYS cc_start: 0.9257 (OUTLIER) cc_final: 0.8804 (ptpp) REVERT: W 419 LYS cc_start: 0.9160 (OUTLIER) cc_final: 0.8920 (mttm) REVERT: A 72 ASP cc_start: 0.8375 (t70) cc_final: 0.7701 (t70) REVERT: A 82 ARG cc_start: 0.7187 (mtm-85) cc_final: 0.6952 (mtm180) REVERT: C 30 ILE cc_start: 0.9040 (tt) cc_final: 0.8733 (tp) REVERT: C 72 ASP cc_start: 0.8319 (t70) cc_final: 0.7645 (t70) REVERT: D 30 ILE cc_start: 0.9024 (tt) cc_final: 0.8740 (tp) REVERT: D 72 ASP cc_start: 0.8332 (t70) cc_final: 0.7650 (t70) REVERT: D 100 PHE cc_start: 0.7814 (OUTLIER) cc_final: 0.7554 (p90) REVERT: H 30 ILE cc_start: 0.9036 (tt) cc_final: 0.8728 (tp) REVERT: H 72 ASP cc_start: 0.8328 (t70) cc_final: 0.7654 (t70) REVERT: H 169 VAL cc_start: 0.7444 (OUTLIER) cc_final: 0.7209 (p) REVERT: B 42 GLN cc_start: 0.7436 (mp10) cc_final: 0.7123 (mp10) REVERT: E 108 ARG cc_start: 0.8020 (ptm160) cc_final: 0.7435 (ptm-80) REVERT: L 201 LEU cc_start: 0.6550 (OUTLIER) cc_final: 0.6322 (pp) outliers start: 92 outliers final: 64 residues processed: 367 average time/residue: 1.3422 time to fit residues: 568.9839 Evaluate side-chains 354 residues out of total 2708 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 279 time to evaluate : 2.626 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain I residue 102 ARG Chi-restraints excluded: chain I residue 182 CYS Chi-restraints excluded: chain I residue 198 SER Chi-restraints excluded: chain I residue 229 CYS Chi-restraints excluded: chain I residue 307 VAL Chi-restraints excluded: chain I residue 338 GLU Chi-restraints excluded: chain I residue 359 SER Chi-restraints excluded: chain M residue 102 ARG Chi-restraints excluded: chain M residue 182 CYS Chi-restraints excluded: chain M residue 198 SER Chi-restraints excluded: chain M residue 229 CYS Chi-restraints excluded: chain M residue 307 VAL Chi-restraints excluded: chain M residue 338 GLU Chi-restraints excluded: chain M residue 359 SER Chi-restraints excluded: chain M residue 419 LYS 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 338 GLU Chi-restraints excluded: chain N residue 359 SER Chi-restraints excluded: chain N residue 371 LYS Chi-restraints excluded: chain W residue 182 CYS Chi-restraints excluded: chain W residue 198 SER Chi-restraints excluded: chain W residue 229 CYS Chi-restraints excluded: chain W residue 307 VAL Chi-restraints excluded: chain W residue 338 GLU Chi-restraints excluded: chain W residue 359 SER Chi-restraints excluded: chain W residue 371 LYS Chi-restraints excluded: chain W residue 419 LYS Chi-restraints excluded: chain A residue 11 VAL Chi-restraints excluded: chain A residue 17 SER Chi-restraints excluded: chain A residue 87 THR Chi-restraints excluded: chain A residue 100 ASP Chi-restraints excluded: chain C residue 11 VAL Chi-restraints excluded: chain C residue 17 SER Chi-restraints excluded: chain C residue 84 SER Chi-restraints excluded: chain C residue 87 THR Chi-restraints excluded: chain C residue 100 ASP Chi-restraints excluded: chain C residue 100 SER Chi-restraints excluded: chain C residue 179 SER Chi-restraints excluded: chain D residue 11 VAL Chi-restraints excluded: chain D residue 17 SER Chi-restraints excluded: chain D residue 84 SER Chi-restraints excluded: chain D residue 87 THR Chi-restraints excluded: chain D residue 100 PHE Chi-restraints excluded: chain D residue 100 ASP Chi-restraints excluded: chain D residue 100 SER Chi-restraints excluded: chain D residue 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 169 VAL Chi-restraints excluded: chain H residue 184 VAL Chi-restraints excluded: chain B residue 30 SER Chi-restraints excluded: chain B residue 76 SER Chi-restraints excluded: chain B residue 182 SER Chi-restraints excluded: chain B residue 202 SER Chi-restraints excluded: chain B residue 206 THR Chi-restraints excluded: chain E residue 30 SER Chi-restraints excluded: chain E residue 76 SER Chi-restraints excluded: chain E residue 124 GLN Chi-restraints excluded: chain E residue 182 SER Chi-restraints excluded: chain E residue 202 SER Chi-restraints excluded: chain G residue 76 SER Chi-restraints excluded: chain G residue 201 LEU Chi-restraints excluded: chain G residue 202 SER Chi-restraints excluded: chain L residue 30 SER Chi-restraints excluded: chain L residue 76 SER Chi-restraints excluded: chain L residue 150 VAL Chi-restraints excluded: chain L residue 201 LEU Chi-restraints excluded: chain L residue 202 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 316 random chunks: chunk 200 optimal weight: 10.0000 chunk 238 optimal weight: 9.9990 chunk 222 optimal weight: 10.0000 chunk 92 optimal weight: 0.9980 chunk 108 optimal weight: 7.9990 chunk 9 optimal weight: 5.9990 chunk 206 optimal weight: 20.0000 chunk 314 optimal weight: 0.2980 chunk 268 optimal weight: 0.0010 chunk 146 optimal weight: 6.9990 chunk 230 optimal weight: 8.9990 overall best weight: 2.8590 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: I 101 HIS M 101 HIS ** M 354 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N 101 HIS ** N 354 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 124 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 155 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 155 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 155 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3911 r_free = 0.3911 target = 0.143511 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3110 r_free = 0.3110 target = 0.083368 restraints weight = 36048.209| |-----------------------------------------------------------------------------| r_work (start): 0.3001 rms_B_bonded: 2.67 r_work: 0.2844 rms_B_bonded: 2.60 restraints_weight: 0.5000 r_work: 0.2708 rms_B_bonded: 4.01 restraints_weight: 0.2500 r_work (final): 0.2708 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2723 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2723 r_free = 0.2723 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 = 0.2723 r_free = 0.2723 target_work(ls_wunit_k1) = 0.062 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| r_final: 0.2723 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8459 moved from start: 0.3627 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.062 25420 Z= 0.218 Angle : 0.638 7.492 34486 Z= 0.331 Chirality : 0.045 0.173 3808 Planarity : 0.005 0.073 4380 Dihedral : 5.409 36.481 3708 Min Nonbonded Distance : 2.281 Molprobity Statistics. All-atom Clashscore : 7.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.21 % Favored : 94.79 % Rotamer: Outliers : 3.36 % Allowed : 24.52 % Favored : 72.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.63 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.62 (0.14), residues: 3148 helix: -4.24 (0.24), residues: 56 sheet: -0.22 (0.14), residues: 1316 loop : -1.68 (0.13), residues: 1776 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C 47 HIS 0.009 0.001 HIS N 101 PHE 0.041 0.002 PHE C 100C TYR 0.018 0.002 TYR L 186 ARG 0.007 0.001 ARG B 108 Details of bonding type rmsd link_NAG-ASN : bond 0.00274 ( 4) link_NAG-ASN : angle 1.10541 ( 12) link_BETA1-4 : bond 0.00338 ( 8) link_BETA1-4 : angle 1.50146 ( 24) hydrogen bonds : bond 0.03301 ( 706) hydrogen bonds : angle 4.93368 ( 1932) SS BOND : bond 0.00326 ( 32) SS BOND : angle 1.89370 ( 66) covalent geometry : bond 0.00522 (25376) covalent geometry : angle 0.63209 (34384) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6296 Ramachandran restraints generated. 3148 Oldfield, 0 Emsley, 3148 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6296 Ramachandran restraints generated. 3148 Oldfield, 0 Emsley, 3148 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 373 residues out of total 2708 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 91 poor density : 282 time to evaluate : 2.609 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: I 338 GLU cc_start: 0.8440 (OUTLIER) cc_final: 0.8209 (pm20) REVERT: M 338 GLU cc_start: 0.8467 (OUTLIER) cc_final: 0.8201 (pm20) REVERT: M 419 LYS cc_start: 0.9187 (OUTLIER) cc_final: 0.8940 (mttm) REVERT: N 338 GLU cc_start: 0.8447 (OUTLIER) cc_final: 0.8182 (pm20) REVERT: N 371 LYS cc_start: 0.9306 (OUTLIER) cc_final: 0.8855 (ptpp) REVERT: W 338 GLU cc_start: 0.8432 (OUTLIER) cc_final: 0.8210 (pm20) REVERT: W 371 LYS cc_start: 0.9300 (OUTLIER) cc_final: 0.8822 (ptpp) REVERT: W 419 LYS cc_start: 0.9184 (OUTLIER) cc_final: 0.8934 (mttm) REVERT: A 72 ASP cc_start: 0.8453 (t70) cc_final: 0.7791 (t70) REVERT: A 100 PHE cc_start: 0.7788 (OUTLIER) cc_final: 0.7517 (p90) REVERT: C 30 ILE cc_start: 0.9062 (tt) cc_final: 0.8761 (tp) REVERT: C 72 ASP cc_start: 0.8413 (t70) cc_final: 0.7739 (t70) REVERT: D 30 ILE cc_start: 0.9049 (tt) cc_final: 0.8776 (tp) REVERT: D 72 ASP cc_start: 0.8435 (t70) cc_final: 0.7764 (t70) REVERT: D 100 PHE cc_start: 0.7863 (OUTLIER) cc_final: 0.7558 (p90) REVERT: D 123 PRO cc_start: 0.3300 (Cg_endo) cc_final: 0.3092 (Cg_exo) REVERT: H 30 ILE cc_start: 0.9060 (tt) cc_final: 0.8761 (tp) REVERT: H 72 ASP cc_start: 0.8438 (t70) cc_final: 0.7775 (t70) REVERT: H 169 VAL cc_start: 0.7449 (OUTLIER) cc_final: 0.7210 (p) REVERT: B 190 LYS cc_start: 0.8556 (mmmt) cc_final: 0.8126 (tptt) REVERT: E 108 ARG cc_start: 0.8039 (ptm160) cc_final: 0.7540 (ttm110) REVERT: E 116 PHE cc_start: 0.5876 (m-80) cc_final: 0.5454 (m-10) REVERT: L 142 ARG cc_start: 0.8233 (tpp80) cc_final: 0.7406 (ttm170) REVERT: L 201 LEU cc_start: 0.6522 (OUTLIER) cc_final: 0.6259 (pp) outliers start: 91 outliers final: 68 residues processed: 362 average time/residue: 1.3151 time to fit residues: 549.3249 Evaluate side-chains 356 residues out of total 2708 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 80 poor density : 276 time to evaluate : 2.726 ------------------------------------------------------------------------------- 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 338 GLU Chi-restraints excluded: chain I residue 359 SER Chi-restraints excluded: chain I residue 361 ILE Chi-restraints excluded: chain M residue 146 THR Chi-restraints excluded: chain M residue 182 CYS Chi-restraints excluded: chain M residue 198 SER Chi-restraints excluded: chain M residue 229 CYS Chi-restraints excluded: chain M residue 307 VAL Chi-restraints excluded: chain M residue 338 GLU Chi-restraints excluded: chain M residue 359 SER Chi-restraints excluded: chain M residue 419 LYS Chi-restraints excluded: chain N residue 146 THR Chi-restraints excluded: chain N residue 182 CYS Chi-restraints excluded: chain N residue 198 SER Chi-restraints excluded: chain N residue 229 CYS Chi-restraints excluded: chain N residue 307 VAL Chi-restraints excluded: chain N residue 338 GLU Chi-restraints excluded: chain N residue 359 SER Chi-restraints excluded: chain N residue 371 LYS Chi-restraints excluded: chain W residue 146 THR Chi-restraints excluded: chain W residue 182 CYS Chi-restraints excluded: chain W residue 198 SER Chi-restraints excluded: chain W residue 229 CYS Chi-restraints excluded: chain W residue 307 VAL Chi-restraints excluded: chain W residue 338 GLU Chi-restraints excluded: chain W residue 359 SER Chi-restraints excluded: chain W residue 361 ILE Chi-restraints excluded: chain W residue 371 LYS Chi-restraints excluded: chain W residue 419 LYS Chi-restraints excluded: chain A residue 11 VAL Chi-restraints excluded: chain A residue 17 SER Chi-restraints excluded: chain A residue 87 THR Chi-restraints excluded: chain A residue 100 PHE Chi-restraints excluded: chain A residue 100 ASP Chi-restraints excluded: chain A residue 138 LEU Chi-restraints excluded: chain C residue 11 VAL Chi-restraints excluded: chain C residue 17 SER Chi-restraints excluded: chain C residue 84 SER Chi-restraints excluded: chain C residue 87 THR Chi-restraints excluded: chain C residue 100 ASP Chi-restraints excluded: chain C residue 100 SER Chi-restraints excluded: chain C residue 179 SER Chi-restraints excluded: chain D residue 11 VAL Chi-restraints excluded: chain D residue 17 SER Chi-restraints excluded: chain D residue 84 SER Chi-restraints excluded: chain D residue 87 THR Chi-restraints excluded: chain D residue 100 PHE Chi-restraints excluded: chain D residue 100 ASP Chi-restraints excluded: chain D residue 100 SER Chi-restraints excluded: chain D residue 184 VAL Chi-restraints excluded: chain H residue 11 VAL Chi-restraints excluded: chain H residue 17 SER Chi-restraints excluded: chain H residue 87 THR Chi-restraints excluded: chain H residue 100 ASP Chi-restraints excluded: chain H residue 100 SER Chi-restraints excluded: chain H residue 169 VAL Chi-restraints excluded: chain H residue 184 VAL Chi-restraints excluded: chain B residue 30 SER Chi-restraints excluded: chain B residue 76 SER Chi-restraints excluded: chain B residue 182 SER Chi-restraints excluded: chain B residue 202 SER Chi-restraints excluded: chain B residue 206 THR Chi-restraints excluded: chain E residue 30 SER Chi-restraints excluded: chain E residue 76 SER Chi-restraints excluded: chain E residue 124 GLN Chi-restraints excluded: chain E residue 182 SER Chi-restraints excluded: chain E residue 202 SER Chi-restraints excluded: chain G residue 76 SER Chi-restraints excluded: chain G residue 201 LEU Chi-restraints excluded: chain G residue 202 SER Chi-restraints excluded: chain L residue 30 SER Chi-restraints excluded: chain L residue 76 SER Chi-restraints excluded: chain L residue 150 VAL Chi-restraints excluded: chain L residue 201 LEU Chi-restraints excluded: chain L residue 202 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 316 random chunks: chunk 77 optimal weight: 0.8980 chunk 252 optimal weight: 0.9980 chunk 154 optimal weight: 0.4980 chunk 28 optimal weight: 0.7980 chunk 299 optimal weight: 3.9990 chunk 266 optimal weight: 40.0000 chunk 230 optimal weight: 9.9990 chunk 265 optimal weight: 3.9990 chunk 144 optimal weight: 0.7980 chunk 164 optimal weight: 50.0000 chunk 296 optimal weight: 0.2980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: I 101 HIS N 101 HIS ** E 124 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 155 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 155 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 155 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3930 r_free = 0.3930 target = 0.145678 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3152 r_free = 0.3152 target = 0.086499 restraints weight = 36058.799| |-----------------------------------------------------------------------------| r_work (start): 0.3063 rms_B_bonded: 2.77 r_work: 0.2900 rms_B_bonded: 2.71 restraints_weight: 0.5000 r_work: 0.2766 rms_B_bonded: 4.21 restraints_weight: 0.2500 r_work (final): 0.2766 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2743 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2743 r_free = 0.2743 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 = 0.2743 r_free = 0.2743 target_work(ls_wunit_k1) = 0.063 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| r_final: 0.2743 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8366 moved from start: 0.3738 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.043 25420 Z= 0.106 Angle : 0.588 7.719 34486 Z= 0.306 Chirality : 0.043 0.171 3808 Planarity : 0.004 0.070 4380 Dihedral : 4.985 38.405 3708 Min Nonbonded Distance : 2.356 Molprobity Statistics. All-atom Clashscore : 7.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.84 % Favored : 96.16 % Rotamer: Outliers : 2.47 % Allowed : 25.66 % Favored : 71.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.63 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.43 (0.14), residues: 3148 helix: -4.09 (0.28), residues: 56 sheet: -0.04 (0.14), residues: 1272 loop : -1.57 (0.13), residues: 1820 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP I 408 HIS 0.010 0.001 HIS I 101 PHE 0.031 0.001 PHE L 116 TYR 0.026 0.001 TYR E 140 ARG 0.006 0.000 ARG B 142 Details of bonding type rmsd link_NAG-ASN : bond 0.00050 ( 4) link_NAG-ASN : angle 0.87148 ( 12) link_BETA1-4 : bond 0.00491 ( 8) link_BETA1-4 : angle 1.43419 ( 24) hydrogen bonds : bond 0.02758 ( 706) hydrogen bonds : angle 4.70725 ( 1932) SS BOND : bond 0.00123 ( 32) SS BOND : angle 0.97750 ( 66) covalent geometry : bond 0.00247 (25376) covalent geometry : angle 0.58634 (34384) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 27402.49 seconds wall clock time: 466 minutes 21.72 seconds (27981.72 seconds total)