Starting phenix.real_space_refine on Sun Jul 5 10:51:35 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9pqq_71788/07_2026/9pqq_71788.cif Found real_map, /net/cci-nas-00/data/ceres_data/9pqq_71788/07_2026/9pqq_71788.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.32 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9pqq_71788/07_2026/9pqq_71788.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9pqq_71788/07_2026/9pqq_71788.map" model { file = "/net/cci-nas-00/data/ceres_data/9pqq_71788/07_2026/9pqq_71788.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9pqq_71788/07_2026/9pqq_71788.cif" } resolution = 3.32 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 1.000 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: 6 Type Number sf(0) Gaussians P 36 5.49 5 Mg 18 5.21 5 S 108 5.16 5 C 17136 2.51 5 N 4500 2.21 5 O 4956 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 113 residue(s): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 26754 Number of models: 1 Model: "" Number of chains: 24 Chain: "A" Number of atoms: 2674 Number of conformers: 1 Conformer: "" Number of residues, atoms: 326, 2674 Classifications: {'peptide': 326} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 315} Chain: "B" Number of atoms: 2674 Number of conformers: 1 Conformer: "" Number of residues, atoms: 326, 2674 Classifications: {'peptide': 326} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 315} Chain: "C" Number of atoms: 2674 Number of conformers: 1 Conformer: "" Number of residues, atoms: 326, 2674 Classifications: {'peptide': 326} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 315} Chain: "D" Number of atoms: 2674 Number of conformers: 1 Conformer: "" Number of residues, atoms: 326, 2674 Classifications: {'peptide': 326} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 315} Chain: "E" Number of atoms: 2674 Number of conformers: 1 Conformer: "" Number of residues, atoms: 326, 2674 Classifications: {'peptide': 326} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 315} Chain: "F" Number of atoms: 2674 Number of conformers: 1 Conformer: "" Number of residues, atoms: 326, 2674 Classifications: {'peptide': 326} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 315} Chain: "G" Number of atoms: 1720 Number of conformers: 1 Conformer: "" Number of residues, atoms: 207, 1720 Classifications: {'peptide': 207} Link IDs: {'PCIS': 1, 'PTRANS': 6, 'TRANS': 199} Chain: "H" Number of atoms: 1720 Number of conformers: 1 Conformer: "" Number of residues, atoms: 207, 1720 Classifications: {'peptide': 207} Link IDs: {'PCIS': 1, 'PTRANS': 6, 'TRANS': 199} Chain: "I" Number of atoms: 1720 Number of conformers: 1 Conformer: "" Number of residues, atoms: 207, 1720 Classifications: {'peptide': 207} Link IDs: {'PCIS': 1, 'PTRANS': 6, 'TRANS': 199} Chain: "J" Number of atoms: 1720 Number of conformers: 1 Conformer: "" Number of residues, atoms: 207, 1720 Classifications: {'peptide': 207} Link IDs: {'PCIS': 1, 'PTRANS': 6, 'TRANS': 199} Chain: "K" Number of atoms: 1720 Number of conformers: 1 Conformer: "" Number of residues, atoms: 207, 1720 Classifications: {'peptide': 207} Link IDs: {'PCIS': 1, 'PTRANS': 6, 'TRANS': 199} Chain: "L" Number of atoms: 1720 Number of conformers: 1 Conformer: "" Number of residues, atoms: 207, 1720 Classifications: {'peptide': 207} Link IDs: {'PCIS': 1, 'PTRANS': 6, 'TRANS': 199} Chain: "A" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 33 Unusual residues: {' MG': 2, 'AGS': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "B" Number of atoms: 64 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 64 Unusual residues: {' MG': 2, 'AGS': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "C" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' MG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "D" Number of atoms: 64 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 64 Unusual residues: {' MG': 2, 'AGS': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "E" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 33 Unusual residues: {' MG': 2, 'AGS': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "F" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' MG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "G" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "H" Number of atoms: 63 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 63 Unusual residues: {' MG': 1, 'AGS': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "I" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'AGS': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "J" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'AGS': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "K" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'AGS': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "L" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'AGS': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 5.82, per 1000 atoms: 0.22 Number of scatterers: 26754 At special positions: 0 Unit cell: (120.12, 114.24, 183.96, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 108 16.00 P 36 15.00 Mg 18 11.99 O 4956 8.00 N 4500 7.00 C 17136 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 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 Time building additional restraints: 2.04 Conformation dependent library (CDL) restraints added in 1.1 seconds 6348 Ramachandran restraints generated. 3174 Oldfield, 0 Emsley, 3174 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6000 Finding SS restraints... Secondary structure from input PDB file: 128 helices and 51 sheets defined 41.7% alpha, 16.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.77 Creating SS restraints... Processing helix chain 'A' and resid 23 through 30 removed outlier: 3.611A pdb=" N GLU A 30 " --> pdb=" O ILE A 26 " (cutoff:3.500A) Processing helix chain 'A' and resid 35 through 38 Processing helix chain 'A' and resid 73 through 78 Processing helix chain 'A' and resid 92 through 100 Processing helix chain 'A' and resid 110 through 114 Processing helix chain 'A' and resid 120 through 132 removed outlier: 4.477A pdb=" N GLU A 124 " --> pdb=" O MET A 120 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N LYS A 125 " --> pdb=" O GLU A 121 " (cutoff:3.500A) Processing helix chain 'A' and resid 133 through 140 removed outlier: 3.637A pdb=" N MET A 139 " --> pdb=" O ARG A 135 " (cutoff:3.500A) Processing helix chain 'A' and resid 144 through 162 removed outlier: 3.530A pdb=" N ILE A 148 " --> pdb=" O GLY A 144 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N ILE A 149 " --> pdb=" O ALA A 145 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N VAL A 160 " --> pdb=" O ASN A 156 " (cutoff:3.500A) Processing helix chain 'A' and resid 182 through 195 Processing helix chain 'A' and resid 224 through 228 Processing helix chain 'A' and resid 232 through 239 removed outlier: 3.557A pdb=" N ARG A 236 " --> pdb=" O SER A 232 " (cutoff:3.500A) Processing helix chain 'A' and resid 266 through 271 removed outlier: 3.685A pdb=" N PHE A 271 " --> pdb=" O PRO A 267 " (cutoff:3.500A) Processing helix chain 'A' and resid 285 through 294 removed outlier: 3.579A pdb=" N LEU A 289 " --> pdb=" O LYS A 285 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N ARG A 292 " --> pdb=" O GLN A 288 " (cutoff:3.500A) Processing helix chain 'A' and resid 307 through 323 Processing helix chain 'B' and resid 23 through 35 Processing helix chain 'B' and resid 36 through 38 No H-bonds generated for 'chain 'B' and resid 36 through 38' Processing helix chain 'B' and resid 73 through 78 removed outlier: 3.599A pdb=" N THR B 78 " --> pdb=" O LYS B 74 " (cutoff:3.500A) Processing helix chain 'B' and resid 93 through 100 Processing helix chain 'B' and resid 110 through 114 removed outlier: 3.646A pdb=" N ALA B 114 " --> pdb=" O LYS B 111 " (cutoff:3.500A) Processing helix chain 'B' and resid 119 through 132 Processing helix chain 'B' and resid 133 through 140 removed outlier: 3.745A pdb=" N MET B 139 " --> pdb=" O ARG B 135 " (cutoff:3.500A) Processing helix chain 'B' and resid 144 through 161 removed outlier: 3.512A pdb=" N ILE B 149 " --> pdb=" O ALA B 145 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N VAL B 160 " --> pdb=" O ASN B 156 " (cutoff:3.500A) Processing helix chain 'B' and resid 182 through 194 Processing helix chain 'B' and resid 224 through 228 removed outlier: 3.509A pdb=" N MET B 227 " --> pdb=" O ARG B 224 " (cutoff:3.500A) removed outlier: 4.092A pdb=" N LEU B 228 " --> pdb=" O LYS B 225 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 224 through 228' Processing helix chain 'B' and resid 232 through 239 removed outlier: 3.521A pdb=" N ARG B 236 " --> pdb=" O SER B 232 " (cutoff:3.500A) Processing helix chain 'B' and resid 266 through 271 removed outlier: 3.830A pdb=" N PHE B 271 " --> pdb=" O PRO B 267 " (cutoff:3.500A) Processing helix chain 'B' and resid 285 through 293 removed outlier: 3.511A pdb=" N LEU B 289 " --> pdb=" O LYS B 285 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N ARG B 292 " --> pdb=" O GLN B 288 " (cutoff:3.500A) Processing helix chain 'B' and resid 307 through 323 Processing helix chain 'C' and resid 23 through 35 Processing helix chain 'C' and resid 36 through 38 No H-bonds generated for 'chain 'C' and resid 36 through 38' Processing helix chain 'C' and resid 73 through 78 Processing helix chain 'C' and resid 92 through 100 Processing helix chain 'C' and resid 110 through 114 Processing helix chain 'C' and resid 120 through 132 removed outlier: 3.578A pdb=" N GLU C 124 " --> pdb=" O MET C 120 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N LYS C 125 " --> pdb=" O GLU C 121 " (cutoff:3.500A) Processing helix chain 'C' and resid 133 through 140 removed outlier: 3.660A pdb=" N MET C 139 " --> pdb=" O ARG C 135 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N GLU C 140 " --> pdb=" O GLU C 136 " (cutoff:3.500A) Processing helix chain 'C' and resid 144 through 162 removed outlier: 3.588A pdb=" N ILE C 148 " --> pdb=" O GLY C 144 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N VAL C 160 " --> pdb=" O ASN C 156 " (cutoff:3.500A) Processing helix chain 'C' and resid 182 through 194 Processing helix chain 'C' and resid 224 through 228 removed outlier: 4.053A pdb=" N LEU C 228 " --> pdb=" O LYS C 225 " (cutoff:3.500A) Processing helix chain 'C' and resid 232 through 238 removed outlier: 3.749A pdb=" N ARG C 236 " --> pdb=" O SER C 232 " (cutoff:3.500A) Processing helix chain 'C' and resid 266 through 271 removed outlier: 3.578A pdb=" N PHE C 271 " --> pdb=" O PRO C 267 " (cutoff:3.500A) Processing helix chain 'C' and resid 285 through 293 removed outlier: 3.616A pdb=" N LEU C 289 " --> pdb=" O LYS C 285 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N ARG C 292 " --> pdb=" O GLN C 288 " (cutoff:3.500A) Processing helix chain 'C' and resid 307 through 323 removed outlier: 3.566A pdb=" N LEU C 312 " --> pdb=" O ASN C 308 " (cutoff:3.500A) Processing helix chain 'D' and resid 23 through 35 Processing helix chain 'D' and resid 36 through 38 No H-bonds generated for 'chain 'D' and resid 36 through 38' Processing helix chain 'D' and resid 72 through 78 removed outlier: 4.114A pdb=" N LEU D 76 " --> pdb=" O ASN D 72 " (cutoff:3.500A) Processing helix chain 'D' and resid 93 through 100 Processing helix chain 'D' and resid 110 through 114 Processing helix chain 'D' and resid 120 through 132 removed outlier: 3.514A pdb=" N ILE D 130 " --> pdb=" O ALA D 126 " (cutoff:3.500A) Processing helix chain 'D' and resid 133 through 140 removed outlier: 3.852A pdb=" N MET D 139 " --> pdb=" O ARG D 135 " (cutoff:3.500A) Processing helix chain 'D' and resid 144 through 162 removed outlier: 3.506A pdb=" N ILE D 148 " --> pdb=" O GLY D 144 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N ILE D 149 " --> pdb=" O ALA D 145 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N VAL D 160 " --> pdb=" O ASN D 156 " (cutoff:3.500A) Processing helix chain 'D' and resid 182 through 195 removed outlier: 3.766A pdb=" N ALA D 191 " --> pdb=" O ALA D 187 " (cutoff:3.500A) Processing helix chain 'D' and resid 224 through 228 Processing helix chain 'D' and resid 232 through 238 removed outlier: 3.850A pdb=" N ARG D 236 " --> pdb=" O SER D 232 " (cutoff:3.500A) Processing helix chain 'D' and resid 266 through 271 removed outlier: 3.852A pdb=" N PHE D 271 " --> pdb=" O PRO D 267 " (cutoff:3.500A) Processing helix chain 'D' and resid 285 through 293 removed outlier: 3.673A pdb=" N LEU D 289 " --> pdb=" O LYS D 285 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N ARG D 292 " --> pdb=" O GLN D 288 " (cutoff:3.500A) Processing helix chain 'D' and resid 307 through 323 removed outlier: 3.710A pdb=" N ILE D 318 " --> pdb=" O LEU D 314 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N ARG D 319 " --> pdb=" O GLU D 315 " (cutoff:3.500A) Processing helix chain 'E' and resid 23 through 33 Processing helix chain 'E' and resid 73 through 78 Processing helix chain 'E' and resid 92 through 100 Processing helix chain 'E' and resid 110 through 114 Processing helix chain 'E' and resid 119 through 132 removed outlier: 3.633A pdb=" N LEU E 128 " --> pdb=" O GLU E 124 " (cutoff:3.500A) Processing helix chain 'E' and resid 133 through 140 Processing helix chain 'E' and resid 144 through 162 removed outlier: 3.582A pdb=" N ILE E 148 " --> pdb=" O GLY E 144 " (cutoff:3.500A) removed outlier: 3.834A pdb=" N ILE E 149 " --> pdb=" O ALA E 145 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N VAL E 160 " --> pdb=" O ASN E 156 " (cutoff:3.500A) Processing helix chain 'E' and resid 182 through 195 Processing helix chain 'E' and resid 232 through 238 removed outlier: 3.647A pdb=" N ARG E 236 " --> pdb=" O SER E 232 " (cutoff:3.500A) Processing helix chain 'E' and resid 266 through 271 Processing helix chain 'E' and resid 285 through 293 removed outlier: 3.643A pdb=" N ARG E 292 " --> pdb=" O GLN E 288 " (cutoff:3.500A) Processing helix chain 'E' and resid 309 through 323 removed outlier: 3.568A pdb=" N GLU E 315 " --> pdb=" O GLN E 311 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N THR E 317 " --> pdb=" O LYS E 313 " (cutoff:3.500A) Processing helix chain 'F' and resid 23 through 35 Processing helix chain 'F' and resid 73 through 78 removed outlier: 3.715A pdb=" N THR F 78 " --> pdb=" O LYS F 74 " (cutoff:3.500A) Processing helix chain 'F' and resid 92 through 100 removed outlier: 4.169A pdb=" N ILE F 96 " --> pdb=" O ASN F 92 " (cutoff:3.500A) Processing helix chain 'F' and resid 118 through 132 removed outlier: 3.569A pdb=" N GLU F 127 " --> pdb=" O ARG F 123 " (cutoff:3.500A) Processing helix chain 'F' and resid 133 through 141 Processing helix chain 'F' and resid 144 through 162 removed outlier: 3.786A pdb=" N VAL F 160 " --> pdb=" O ASN F 156 " (cutoff:3.500A) Processing helix chain 'F' and resid 182 through 194 Processing helix chain 'F' and resid 232 through 239 removed outlier: 3.635A pdb=" N ARG F 236 " --> pdb=" O SER F 232 " (cutoff:3.500A) Processing helix chain 'F' and resid 268 through 272 removed outlier: 3.546A pdb=" N PHE F 271 " --> pdb=" O SER F 268 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N GLN F 272 " --> pdb=" O GLU F 269 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 268 through 272' Processing helix chain 'F' and resid 285 through 294 removed outlier: 3.693A pdb=" N LEU F 289 " --> pdb=" O LYS F 285 " (cutoff:3.500A) Processing helix chain 'F' and resid 307 through 323 removed outlier: 3.517A pdb=" N LEU F 312 " --> pdb=" O ASN F 308 " (cutoff:3.500A) Processing helix chain 'G' and resid 122 through 132 Processing helix chain 'G' and resid 133 through 141 Processing helix chain 'G' and resid 144 through 162 removed outlier: 3.608A pdb=" N ILE G 149 " --> pdb=" O ALA G 145 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N VAL G 160 " --> pdb=" O ASN G 156 " (cutoff:3.500A) Processing helix chain 'G' and resid 182 through 194 Processing helix chain 'G' and resid 224 through 228 removed outlier: 3.550A pdb=" N LEU G 228 " --> pdb=" O LYS G 225 " (cutoff:3.500A) Processing helix chain 'G' and resid 232 through 238 removed outlier: 3.604A pdb=" N ARG G 236 " --> pdb=" O SER G 232 " (cutoff:3.500A) Processing helix chain 'G' and resid 266 through 272 removed outlier: 3.975A pdb=" N PHE G 271 " --> pdb=" O PRO G 267 " (cutoff:3.500A) Processing helix chain 'G' and resid 285 through 293 Processing helix chain 'G' and resid 307 through 323 removed outlier: 3.683A pdb=" N LEU G 312 " --> pdb=" O ASN G 308 " (cutoff:3.500A) removed outlier: 3.997A pdb=" N GLU G 315 " --> pdb=" O GLN G 311 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N ILE G 318 " --> pdb=" O LEU G 314 " (cutoff:3.500A) Processing helix chain 'H' and resid 122 through 132 removed outlier: 3.795A pdb=" N GLU H 127 " --> pdb=" O ARG H 123 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N ILE H 130 " --> pdb=" O ALA H 126 " (cutoff:3.500A) Processing helix chain 'H' and resid 133 through 140 removed outlier: 3.579A pdb=" N MET H 139 " --> pdb=" O ARG H 135 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N GLU H 140 " --> pdb=" O GLU H 136 " (cutoff:3.500A) Processing helix chain 'H' and resid 144 through 161 removed outlier: 3.520A pdb=" N ILE H 148 " --> pdb=" O GLY H 144 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N ILE H 149 " --> pdb=" O ALA H 145 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N VAL H 160 " --> pdb=" O ASN H 156 " (cutoff:3.500A) Processing helix chain 'H' and resid 182 through 194 removed outlier: 3.505A pdb=" N ALA H 191 " --> pdb=" O ALA H 187 " (cutoff:3.500A) Processing helix chain 'H' and resid 224 through 228 Processing helix chain 'H' and resid 232 through 239 removed outlier: 3.592A pdb=" N ARG H 236 " --> pdb=" O SER H 232 " (cutoff:3.500A) Processing helix chain 'H' and resid 285 through 293 Processing helix chain 'H' and resid 307 through 323 removed outlier: 3.644A pdb=" N ILE H 318 " --> pdb=" O LEU H 314 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N ARG H 319 " --> pdb=" O GLU H 315 " (cutoff:3.500A) Processing helix chain 'I' and resid 122 through 132 Processing helix chain 'I' and resid 133 through 140 removed outlier: 3.757A pdb=" N MET I 139 " --> pdb=" O ARG I 135 " (cutoff:3.500A) Processing helix chain 'I' and resid 144 through 162 removed outlier: 3.656A pdb=" N ILE I 149 " --> pdb=" O ALA I 145 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N LYS I 153 " --> pdb=" O ILE I 149 " (cutoff:3.500A) Processing helix chain 'I' and resid 182 through 194 Processing helix chain 'I' and resid 232 through 239 removed outlier: 3.676A pdb=" N ARG I 236 " --> pdb=" O SER I 232 " (cutoff:3.500A) Processing helix chain 'I' and resid 285 through 293 Processing helix chain 'I' and resid 307 through 323 removed outlier: 3.880A pdb=" N LEU I 312 " --> pdb=" O ASN I 308 " (cutoff:3.500A) Processing helix chain 'J' and resid 122 through 132 removed outlier: 3.900A pdb=" N ILE J 130 " --> pdb=" O ALA J 126 " (cutoff:3.500A) Processing helix chain 'J' and resid 133 through 140 removed outlier: 4.256A pdb=" N MET J 139 " --> pdb=" O ARG J 135 " (cutoff:3.500A) removed outlier: 3.889A pdb=" N GLU J 140 " --> pdb=" O GLU J 136 " (cutoff:3.500A) Processing helix chain 'J' and resid 144 through 162 removed outlier: 3.600A pdb=" N ILE J 148 " --> pdb=" O GLY J 144 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N ILE J 149 " --> pdb=" O ALA J 145 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N VAL J 160 " --> pdb=" O ASN J 156 " (cutoff:3.500A) Processing helix chain 'J' and resid 182 through 195 Processing helix chain 'J' and resid 232 through 239 removed outlier: 3.637A pdb=" N ARG J 236 " --> pdb=" O SER J 232 " (cutoff:3.500A) Processing helix chain 'J' and resid 266 through 271 removed outlier: 4.173A pdb=" N PHE J 271 " --> pdb=" O PRO J 267 " (cutoff:3.500A) Processing helix chain 'J' and resid 285 through 294 removed outlier: 3.849A pdb=" N LEU J 289 " --> pdb=" O LYS J 285 " (cutoff:3.500A) Processing helix chain 'J' and resid 307 through 323 removed outlier: 3.835A pdb=" N TYR J 321 " --> pdb=" O THR J 317 " (cutoff:3.500A) Processing helix chain 'K' and resid 122 through 132 Processing helix chain 'K' and resid 133 through 140 removed outlier: 4.061A pdb=" N LEU K 137 " --> pdb=" O ASN K 133 " (cutoff:3.500A) Processing helix chain 'K' and resid 144 through 162 removed outlier: 3.691A pdb=" N LYS K 153 " --> pdb=" O ILE K 149 " (cutoff:3.500A) removed outlier: 3.901A pdb=" N VAL K 160 " --> pdb=" O ASN K 156 " (cutoff:3.500A) Processing helix chain 'K' and resid 182 through 196 Processing helix chain 'K' and resid 224 through 228 Processing helix chain 'K' and resid 232 through 238 Processing helix chain 'K' and resid 266 through 272 removed outlier: 3.995A pdb=" N PHE K 271 " --> pdb=" O PRO K 267 " (cutoff:3.500A) removed outlier: 4.029A pdb=" N GLN K 272 " --> pdb=" O SER K 268 " (cutoff:3.500A) Processing helix chain 'K' and resid 285 through 293 removed outlier: 3.522A pdb=" N ARG K 292 " --> pdb=" O GLN K 288 " (cutoff:3.500A) Processing helix chain 'K' and resid 307 through 323 removed outlier: 3.603A pdb=" N GLU K 315 " --> pdb=" O GLN K 311 " (cutoff:3.500A) Processing helix chain 'L' and resid 122 through 132 Processing helix chain 'L' and resid 133 through 140 Processing helix chain 'L' and resid 144 through 162 removed outlier: 3.652A pdb=" N ALA L 151 " --> pdb=" O ASP L 147 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N VAL L 160 " --> pdb=" O ASN L 156 " (cutoff:3.500A) Processing helix chain 'L' and resid 182 through 194 Processing helix chain 'L' and resid 232 through 238 removed outlier: 3.627A pdb=" N ARG L 236 " --> pdb=" O SER L 232 " (cutoff:3.500A) Processing helix chain 'L' and resid 266 through 272 removed outlier: 3.788A pdb=" N PHE L 271 " --> pdb=" O PRO L 267 " (cutoff:3.500A) Processing helix chain 'L' and resid 285 through 293 removed outlier: 3.512A pdb=" N ARG L 292 " --> pdb=" O GLN L 288 " (cutoff:3.500A) Processing helix chain 'L' and resid 307 through 323 removed outlier: 3.708A pdb=" N ILE L 318 " --> pdb=" O LEU L 314 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 6 through 14 removed outlier: 9.841A pdb=" N GLN A 6 " --> pdb=" O ASN A 66 " (cutoff:3.500A) removed outlier: 11.984A pdb=" N ASN A 66 " --> pdb=" O GLN A 6 " (cutoff:3.500A) removed outlier: 6.640A pdb=" N LYS A 8 " --> pdb=" O CYS A 64 " (cutoff:3.500A) removed outlier: 6.806A pdb=" N HIS A 57 " --> pdb=" O LYS A 47 " (cutoff:3.500A) removed outlier: 4.844A pdb=" N LYS A 47 " --> pdb=" O HIS A 57 " (cutoff:3.500A) removed outlier: 6.659A pdb=" N HIS A 59 " --> pdb=" O ALA A 45 " (cutoff:3.500A) removed outlier: 4.263A pdb=" N ALA A 45 " --> pdb=" O HIS A 59 " (cutoff:3.500A) removed outlier: 6.571A pdb=" N LEU A 61 " --> pdb=" O ALA A 43 " (cutoff:3.500A) removed outlier: 4.263A pdb=" N ALA A 43 " --> pdb=" O LEU A 61 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N CYS A 63 " --> pdb=" O LYS A 41 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 200 through 201 removed outlier: 6.311A pdb=" N TRP A 200 " --> pdb=" O ILE A 219 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N GLY A 177 " --> pdb=" O SER A 263 " (cutoff:3.500A) removed outlier: 8.156A pdb=" N TYR A 302 " --> pdb=" O ILE A 172 " (cutoff:3.500A) removed outlier: 6.415A pdb=" N TRP A 174 " --> pdb=" O TYR A 302 " (cutoff:3.500A) removed outlier: 7.413A pdb=" N PHE A 304 " --> pdb=" O TRP A 174 " (cutoff:3.500A) removed outlier: 6.699A pdb=" N LYS A 176 " --> pdb=" O PHE A 304 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 244 through 247 Processing sheet with id=AA4, first strand: chain 'A' and resid 273 through 274 Processing sheet with id=AA5, first strand: chain 'B' and resid 6 through 14 removed outlier: 9.749A pdb=" N GLN B 6 " --> pdb=" O ASN B 66 " (cutoff:3.500A) removed outlier: 11.680A pdb=" N ASN B 66 " --> pdb=" O GLN B 6 " (cutoff:3.500A) removed outlier: 6.181A pdb=" N LYS B 8 " --> pdb=" O CYS B 64 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N CYS B 64 " --> pdb=" O LYS B 8 " (cutoff:3.500A) removed outlier: 6.365A pdb=" N GLU B 65 " --> pdb=" O VAL B 40 " (cutoff:3.500A) removed outlier: 8.268A pdb=" N VAL B 40 " --> pdb=" O GLU B 65 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 200 through 201 removed outlier: 6.178A pdb=" N TRP B 200 " --> pdb=" O ILE B 219 " (cutoff:3.500A) removed outlier: 6.952A pdb=" N ASP B 221 " --> pdb=" O TRP B 200 " (cutoff:3.500A) removed outlier: 6.323A pdb=" N LEU B 171 " --> pdb=" O ILE B 259 " (cutoff:3.500A) removed outlier: 7.586A pdb=" N VAL B 261 " --> pdb=" O LEU B 171 " (cutoff:3.500A) removed outlier: 6.378A pdb=" N LEU B 173 " --> pdb=" O VAL B 261 " (cutoff:3.500A) removed outlier: 8.163A pdb=" N TYR B 302 " --> pdb=" O ILE B 172 " (cutoff:3.500A) removed outlier: 6.425A pdb=" N TRP B 174 " --> pdb=" O TYR B 302 " (cutoff:3.500A) removed outlier: 7.360A pdb=" N PHE B 304 " --> pdb=" O TRP B 174 " (cutoff:3.500A) removed outlier: 6.677A pdb=" N LYS B 176 " --> pdb=" O PHE B 304 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 244 through 247 Processing sheet with id=AA8, first strand: chain 'B' and resid 273 through 274 removed outlier: 3.919A pdb=" N TRP B 273 " --> pdb=" O ILE B 281 " (cutoff:3.500A) removed outlier: 3.982A pdb=" N ILE B 281 " --> pdb=" O TRP B 273 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA8 Processing sheet with id=AA9, first strand: chain 'B' and resid 294 through 295 Processing sheet with id=AB1, first strand: chain 'C' and resid 7 through 14 removed outlier: 6.177A pdb=" N LYS C 8 " --> pdb=" O CYS C 64 " (cutoff:3.500A) removed outlier: 7.134A pdb=" N HIS C 57 " --> pdb=" O LYS C 47 " (cutoff:3.500A) removed outlier: 5.234A pdb=" N LYS C 47 " --> pdb=" O HIS C 57 " (cutoff:3.500A) removed outlier: 6.530A pdb=" N HIS C 59 " --> pdb=" O ALA C 45 " (cutoff:3.500A) removed outlier: 4.211A pdb=" N ALA C 45 " --> pdb=" O HIS C 59 " (cutoff:3.500A) removed outlier: 6.683A pdb=" N LEU C 61 " --> pdb=" O ALA C 43 " (cutoff:3.500A) removed outlier: 4.300A pdb=" N ALA C 43 " --> pdb=" O LEU C 61 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N CYS C 63 " --> pdb=" O LYS C 41 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 199 through 201 removed outlier: 6.450A pdb=" N TRP C 200 " --> pdb=" O ILE C 219 " (cutoff:3.500A) removed outlier: 8.338A pdb=" N TYR C 302 " --> pdb=" O ILE C 172 " (cutoff:3.500A) removed outlier: 6.692A pdb=" N TRP C 174 " --> pdb=" O TYR C 302 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 244 through 247 removed outlier: 3.746A pdb=" N GLY C 250 " --> pdb=" O VAL C 247 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 273 through 274 removed outlier: 3.699A pdb=" N TRP C 273 " --> pdb=" O ILE C 281 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N ILE C 281 " --> pdb=" O TRP C 273 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB4 Processing sheet with id=AB5, first strand: chain 'C' and resid 294 through 295 Processing sheet with id=AB6, first strand: chain 'D' and resid 6 through 14 removed outlier: 9.760A pdb=" N GLN D 6 " --> pdb=" O ASN D 66 " (cutoff:3.500A) removed outlier: 11.868A pdb=" N ASN D 66 " --> pdb=" O GLN D 6 " (cutoff:3.500A) removed outlier: 6.693A pdb=" N LYS D 8 " --> pdb=" O CYS D 64 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N CYS D 64 " --> pdb=" O LYS D 8 " (cutoff:3.500A) removed outlier: 6.525A pdb=" N HIS D 57 " --> pdb=" O LYS D 47 " (cutoff:3.500A) removed outlier: 4.699A pdb=" N LYS D 47 " --> pdb=" O HIS D 57 " (cutoff:3.500A) removed outlier: 6.611A pdb=" N HIS D 59 " --> pdb=" O ALA D 45 " (cutoff:3.500A) removed outlier: 4.219A pdb=" N ALA D 45 " --> pdb=" O HIS D 59 " (cutoff:3.500A) removed outlier: 6.634A pdb=" N LEU D 61 " --> pdb=" O ALA D 43 " (cutoff:3.500A) removed outlier: 4.057A pdb=" N ALA D 43 " --> pdb=" O LEU D 61 " (cutoff:3.500A) removed outlier: 6.609A pdb=" N CYS D 63 " --> pdb=" O LYS D 41 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'D' and resid 199 through 201 removed outlier: 6.094A pdb=" N TRP D 200 " --> pdb=" O ILE D 219 " (cutoff:3.500A) removed outlier: 6.306A pdb=" N LEU D 171 " --> pdb=" O ILE D 259 " (cutoff:3.500A) removed outlier: 7.584A pdb=" N VAL D 261 " --> pdb=" O LEU D 171 " (cutoff:3.500A) removed outlier: 6.375A pdb=" N LEU D 173 " --> pdb=" O VAL D 261 " (cutoff:3.500A) removed outlier: 7.852A pdb=" N TYR D 302 " --> pdb=" O ILE D 172 " (cutoff:3.500A) removed outlier: 6.355A pdb=" N TRP D 174 " --> pdb=" O TYR D 302 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'D' and resid 244 through 247 Processing sheet with id=AB9, first strand: chain 'D' and resid 273 through 274 Processing sheet with id=AC1, first strand: chain 'D' and resid 294 through 295 Processing sheet with id=AC2, first strand: chain 'E' and resid 85 through 86 removed outlier: 9.572A pdb=" N GLN E 6 " --> pdb=" O ASN E 66 " (cutoff:3.500A) removed outlier: 11.539A pdb=" N ASN E 66 " --> pdb=" O GLN E 6 " (cutoff:3.500A) removed outlier: 5.818A pdb=" N LYS E 8 " --> pdb=" O CYS E 64 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N CYS E 63 " --> pdb=" O TYR E 42 " (cutoff:3.500A) removed outlier: 4.847A pdb=" N TYR E 42 " --> pdb=" O CYS E 63 " (cutoff:3.500A) removed outlier: 6.526A pdb=" N GLU E 65 " --> pdb=" O VAL E 40 " (cutoff:3.500A) removed outlier: 7.957A pdb=" N VAL E 40 " --> pdb=" O GLU E 65 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'E' and resid 199 through 201 removed outlier: 6.146A pdb=" N TRP E 200 " --> pdb=" O ILE E 219 " (cutoff:3.500A) removed outlier: 6.622A pdb=" N ASP E 221 " --> pdb=" O TRP E 200 " (cutoff:3.500A) removed outlier: 6.475A pdb=" N LEU E 171 " --> pdb=" O ILE E 259 " (cutoff:3.500A) removed outlier: 7.697A pdb=" N VAL E 261 " --> pdb=" O LEU E 171 " (cutoff:3.500A) removed outlier: 6.485A pdb=" N LEU E 173 " --> pdb=" O VAL E 261 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'E' and resid 244 through 247 removed outlier: 3.602A pdb=" N GLY E 250 " --> pdb=" O VAL E 247 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'E' and resid 273 through 274 Processing sheet with id=AC6, first strand: chain 'E' and resid 294 through 295 Processing sheet with id=AC7, first strand: chain 'F' and resid 7 through 16 removed outlier: 6.120A pdb=" N LYS F 8 " --> pdb=" O CYS F 64 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N VAL F 56 " --> pdb=" O ASP F 16 " (cutoff:3.500A) removed outlier: 6.681A pdb=" N GLU F 65 " --> pdb=" O VAL F 40 " (cutoff:3.500A) removed outlier: 8.566A pdb=" N VAL F 40 " --> pdb=" O GLU F 65 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'F' and resid 199 through 201 removed outlier: 6.240A pdb=" N LEU F 171 " --> pdb=" O ILE F 259 " (cutoff:3.500A) removed outlier: 7.609A pdb=" N VAL F 261 " --> pdb=" O LEU F 171 " (cutoff:3.500A) removed outlier: 6.258A pdb=" N LEU F 173 " --> pdb=" O VAL F 261 " (cutoff:3.500A) removed outlier: 8.346A pdb=" N TYR F 302 " --> pdb=" O ILE F 172 " (cutoff:3.500A) removed outlier: 6.723A pdb=" N TRP F 174 " --> pdb=" O TYR F 302 " (cutoff:3.500A) removed outlier: 7.539A pdb=" N PHE F 304 " --> pdb=" O TRP F 174 " (cutoff:3.500A) removed outlier: 7.156A pdb=" N LYS F 176 " --> pdb=" O PHE F 304 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'F' and resid 244 through 247 Processing sheet with id=AD1, first strand: chain 'F' and resid 273 through 274 Processing sheet with id=AD2, first strand: chain 'G' and resid 199 through 201 removed outlier: 6.046A pdb=" N TRP G 200 " --> pdb=" O ILE G 219 " (cutoff:3.500A) removed outlier: 6.855A pdb=" N ASP G 221 " --> pdb=" O TRP G 200 " (cutoff:3.500A) removed outlier: 8.605A pdb=" N TYR G 302 " --> pdb=" O ILE G 172 " (cutoff:3.500A) removed outlier: 6.637A pdb=" N TRP G 174 " --> pdb=" O TYR G 302 " (cutoff:3.500A) removed outlier: 7.545A pdb=" N PHE G 304 " --> pdb=" O TRP G 174 " (cutoff:3.500A) removed outlier: 6.920A pdb=" N LYS G 176 " --> pdb=" O PHE G 304 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'G' and resid 244 through 247 removed outlier: 3.500A pdb=" N VAL G 247 " --> pdb=" O GLY G 250 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'G' and resid 273 through 274 Processing sheet with id=AD5, first strand: chain 'G' and resid 294 through 295 Processing sheet with id=AD6, first strand: chain 'H' and resid 199 through 201 removed outlier: 6.474A pdb=" N TRP H 200 " --> pdb=" O ILE H 219 " (cutoff:3.500A) removed outlier: 7.238A pdb=" N ASP H 221 " --> pdb=" O TRP H 200 " (cutoff:3.500A) removed outlier: 6.235A pdb=" N LEU H 171 " --> pdb=" O ILE H 259 " (cutoff:3.500A) removed outlier: 7.556A pdb=" N VAL H 261 " --> pdb=" O LEU H 171 " (cutoff:3.500A) removed outlier: 6.344A pdb=" N LEU H 173 " --> pdb=" O VAL H 261 " (cutoff:3.500A) removed outlier: 8.227A pdb=" N TYR H 302 " --> pdb=" O ILE H 172 " (cutoff:3.500A) removed outlier: 6.433A pdb=" N TRP H 174 " --> pdb=" O TYR H 302 " (cutoff:3.500A) removed outlier: 7.545A pdb=" N PHE H 304 " --> pdb=" O TRP H 174 " (cutoff:3.500A) removed outlier: 6.816A pdb=" N LYS H 176 " --> pdb=" O PHE H 304 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'H' and resid 244 through 247 Processing sheet with id=AD8, first strand: chain 'H' and resid 273 through 274 Processing sheet with id=AD9, first strand: chain 'H' and resid 294 through 295 Processing sheet with id=AE1, first strand: chain 'I' and resid 199 through 201 removed outlier: 6.163A pdb=" N TRP I 200 " --> pdb=" O ILE I 219 " (cutoff:3.500A) removed outlier: 7.194A pdb=" N ASP I 221 " --> pdb=" O TRP I 200 " (cutoff:3.500A) removed outlier: 6.393A pdb=" N LEU I 171 " --> pdb=" O ILE I 259 " (cutoff:3.500A) removed outlier: 7.687A pdb=" N VAL I 261 " --> pdb=" O LEU I 171 " (cutoff:3.500A) removed outlier: 6.563A pdb=" N LEU I 173 " --> pdb=" O VAL I 261 " (cutoff:3.500A) removed outlier: 8.070A pdb=" N TYR I 302 " --> pdb=" O ILE I 172 " (cutoff:3.500A) removed outlier: 6.362A pdb=" N TRP I 174 " --> pdb=" O TYR I 302 " (cutoff:3.500A) removed outlier: 7.464A pdb=" N PHE I 304 " --> pdb=" O TRP I 174 " (cutoff:3.500A) removed outlier: 6.936A pdb=" N LYS I 176 " --> pdb=" O PHE I 304 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'I' and resid 244 through 247 Processing sheet with id=AE3, first strand: chain 'I' and resid 273 through 274 Processing sheet with id=AE4, first strand: chain 'I' and resid 294 through 295 Processing sheet with id=AE5, first strand: chain 'J' and resid 199 through 201 Processing sheet with id=AE6, first strand: chain 'J' and resid 244 through 247 Processing sheet with id=AE7, first strand: chain 'J' and resid 273 through 274 removed outlier: 3.808A pdb=" N TRP J 273 " --> pdb=" O ILE J 281 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'K' and resid 199 through 201 removed outlier: 6.373A pdb=" N TRP K 200 " --> pdb=" O ILE K 219 " (cutoff:3.500A) removed outlier: 7.252A pdb=" N ASP K 221 " --> pdb=" O TRP K 200 " (cutoff:3.500A) removed outlier: 8.351A pdb=" N TYR K 302 " --> pdb=" O ILE K 172 " (cutoff:3.500A) removed outlier: 6.379A pdb=" N TRP K 174 " --> pdb=" O TYR K 302 " (cutoff:3.500A) removed outlier: 7.372A pdb=" N PHE K 304 " --> pdb=" O TRP K 174 " (cutoff:3.500A) removed outlier: 6.658A pdb=" N LYS K 176 " --> pdb=" O PHE K 304 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'K' and resid 244 through 247 Processing sheet with id=AF1, first strand: chain 'K' and resid 273 through 274 Processing sheet with id=AF2, first strand: chain 'K' and resid 294 through 295 Processing sheet with id=AF3, first strand: chain 'L' and resid 199 through 201 removed outlier: 6.272A pdb=" N TRP L 200 " --> pdb=" O ILE L 219 " (cutoff:3.500A) removed outlier: 7.110A pdb=" N ASP L 221 " --> pdb=" O TRP L 200 " (cutoff:3.500A) removed outlier: 8.446A pdb=" N TYR L 302 " --> pdb=" O ILE L 172 " (cutoff:3.500A) removed outlier: 6.524A pdb=" N TRP L 174 " --> pdb=" O TYR L 302 " (cutoff:3.500A) removed outlier: 7.569A pdb=" N PHE L 304 " --> pdb=" O TRP L 174 " (cutoff:3.500A) removed outlier: 6.821A pdb=" N LYS L 176 " --> pdb=" O PHE L 304 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'L' and resid 244 through 247 Processing sheet with id=AF5, first strand: chain 'L' and resid 273 through 274 Processing sheet with id=AF6, first strand: chain 'L' and resid 294 through 295 973 hydrogen bonds defined for protein. 2769 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: 4.55 Time building geometry restraints manager: 2.76 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.37: 8774 1.37 - 1.51: 7916 1.51 - 1.66: 10454 1.66 - 1.80: 125 1.80 - 1.95: 55 Bond restraints: 27324 Sorted by residual: bond pdb=" O3B AGS H 402 " pdb=" PB AGS H 402 " ideal model delta sigma weight residual 1.673 1.582 0.091 2.00e-02 2.50e+03 2.07e+01 bond pdb=" O3B AGS A 403 " pdb=" PB AGS A 403 " ideal model delta sigma weight residual 1.673 1.583 0.090 2.00e-02 2.50e+03 2.04e+01 bond pdb=" O3B AGS J 401 " pdb=" PB AGS J 401 " ideal model delta sigma weight residual 1.673 1.583 0.090 2.00e-02 2.50e+03 2.03e+01 bond pdb=" O3B AGS I 401 " pdb=" PB AGS I 401 " ideal model delta sigma weight residual 1.673 1.584 0.089 2.00e-02 2.50e+03 1.97e+01 bond pdb=" O3B AGS H 401 " pdb=" PB AGS H 401 " ideal model delta sigma weight residual 1.673 1.585 0.088 2.00e-02 2.50e+03 1.95e+01 ... (remaining 27319 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.86: 35890 1.86 - 3.71: 820 3.71 - 5.57: 151 5.57 - 7.42: 32 7.42 - 9.28: 73 Bond angle restraints: 36966 Sorted by residual: angle pdb=" N ARG D 20 " pdb=" CA ARG D 20 " pdb=" C ARG D 20 " ideal model delta sigma weight residual 114.12 108.75 5.37 1.39e+00 5.18e-01 1.49e+01 angle pdb=" C GLU C 204 " pdb=" CA GLU C 204 " pdb=" CB GLU C 204 " ideal model delta sigma weight residual 110.42 117.39 -6.97 1.99e+00 2.53e-01 1.23e+01 angle pdb=" CA GLU D 18 " pdb=" C GLU D 18 " pdb=" N GLU D 19 " ideal model delta sigma weight residual 118.82 114.44 4.38 1.26e+00 6.30e-01 1.21e+01 angle pdb=" C GLU G 204 " pdb=" CA GLU G 204 " pdb=" CB GLU G 204 " ideal model delta sigma weight residual 110.42 117.19 -6.77 1.99e+00 2.53e-01 1.16e+01 angle pdb=" C PHE L 195 " pdb=" N ASN L 196 " pdb=" CA ASN L 196 " ideal model delta sigma weight residual 121.54 127.74 -6.20 1.91e+00 2.74e-01 1.05e+01 ... (remaining 36961 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 22.09: 14813 22.09 - 44.19: 1470 44.19 - 66.28: 222 66.28 - 88.37: 141 88.37 - 110.47: 16 Dihedral angle restraints: 16662 sinusoidal: 7356 harmonic: 9306 Sorted by residual: dihedral pdb=" CA TYR C 295 " pdb=" C TYR C 295 " pdb=" N GLU C 296 " pdb=" CA GLU C 296 " ideal model delta harmonic sigma weight residual -180.00 -154.29 -25.71 0 5.00e+00 4.00e-02 2.64e+01 dihedral pdb=" CA GLU E 119 " pdb=" C GLU E 119 " pdb=" N MET E 120 " pdb=" CA MET E 120 " ideal model delta harmonic sigma weight residual -180.00 -158.48 -21.52 0 5.00e+00 4.00e-02 1.85e+01 dihedral pdb=" CA ARG B 4 " pdb=" C ARG B 4 " pdb=" N LEU B 5 " pdb=" CA LEU B 5 " ideal model delta harmonic sigma weight residual 180.00 159.06 20.94 0 5.00e+00 4.00e-02 1.75e+01 ... (remaining 16659 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.059: 3398 0.059 - 0.118: 510 0.118 - 0.176: 42 0.176 - 0.235: 3 0.235 - 0.294: 13 Chirality restraints: 3966 Sorted by residual: chirality pdb=" CA ARG H 224 " pdb=" N ARG H 224 " pdb=" C ARG H 224 " pdb=" CB ARG H 224 " both_signs ideal model delta sigma weight residual False 2.51 2.80 -0.29 2.00e-01 2.50e+01 2.16e+00 chirality pdb=" C3' AGS I 401 " pdb=" C2' AGS I 401 " pdb=" C4' AGS I 401 " pdb=" O3' AGS I 401 " both_signs ideal model delta sigma weight residual False -2.37 -2.63 0.26 2.00e-01 2.50e+01 1.70e+00 chirality pdb=" C3' AGS D 402 " pdb=" C2' AGS D 402 " pdb=" C4' AGS D 402 " pdb=" O3' AGS D 402 " both_signs ideal model delta sigma weight residual False -2.37 -2.63 0.26 2.00e-01 2.50e+01 1.68e+00 ... (remaining 3963 not shown) Planarity restraints: 4632 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA PHE H 223 " -0.018 2.00e-02 2.50e+03 3.67e-02 1.35e+01 pdb=" C PHE H 223 " 0.064 2.00e-02 2.50e+03 pdb=" O PHE H 223 " -0.024 2.00e-02 2.50e+03 pdb=" N ARG H 224 " -0.021 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG K 224 " -0.282 9.50e-02 1.11e+02 1.26e-01 9.83e+00 pdb=" NE ARG K 224 " 0.018 2.00e-02 2.50e+03 pdb=" CZ ARG K 224 " 0.000 2.00e-02 2.50e+03 pdb=" NH1 ARG K 224 " 0.004 2.00e-02 2.50e+03 pdb=" NH2 ARG K 224 " -0.009 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG D 20 " 0.257 9.50e-02 1.11e+02 1.15e-01 8.14e+00 pdb=" NE ARG D 20 " -0.016 2.00e-02 2.50e+03 pdb=" CZ ARG D 20 " -0.002 2.00e-02 2.50e+03 pdb=" NH1 ARG D 20 " -0.003 2.00e-02 2.50e+03 pdb=" NH2 ARG D 20 " 0.009 2.00e-02 2.50e+03 ... (remaining 4629 not shown) Histogram of nonbonded interaction distances: 1.94 - 2.53: 243 2.53 - 3.12: 20315 3.12 - 3.72: 38992 3.72 - 4.31: 56671 4.31 - 4.90: 95011 Nonbonded interactions: 211232 Sorted by model distance: nonbonded pdb=" OE2 GLU B 48 " pdb="MG MG B 404 " model vdw 1.938 2.170 nonbonded pdb=" OE1 GLU F 48 " pdb="MG MG F 402 " model vdw 1.971 2.170 nonbonded pdb=" NE2 HIS E 57 " pdb="MG MG E 403 " model vdw 1.983 2.250 nonbonded pdb=" OE1 GLU G 279 " pdb="MG MG B 404 " model vdw 1.995 2.170 nonbonded pdb=" OG1 THR D 184 " pdb="MG MG D 403 " model vdw 1.999 2.170 ... (remaining 211227 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: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and resid 2 through 327) selection = (chain 'B' and resid 2 through 327) selection = (chain 'C' and resid 2 through 327) selection = (chain 'D' and resid 2 through 327) selection = (chain 'E' and resid 2 through 327) selection = (chain 'F' and resid 2 through 327) } ncs_group { reference = (chain 'G' and resid 121 through 327) selection = (chain 'H' and resid 121 through 327) selection = (chain 'I' and resid 121 through 327) selection = (chain 'J' and resid 121 through 327) selection = (chain 'K' and resid 121 through 327) selection = (chain 'L' and resid 121 through 327) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.010 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 5.460 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.020 Extract box with map and model: 0.500 Check model and map are aligned: 0.070 Set scattering table: 0.070 Process input model: 23.220 Find NCS groups from input model: 0.600 Set up NCS constraints: 0.060 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: 0.000 Load rotamer database and sin/cos tables:1.250 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 31.270 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8719 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 : 0.005 0.091 27324 Z= 0.224 Angle : 0.770 9.279 36966 Z= 0.366 Chirality : 0.045 0.294 3966 Planarity : 0.005 0.126 4632 Dihedral : 18.602 110.466 10662 Min Nonbonded Distance : 1.938 Molprobity Statistics. All-atom Clashscore : 10.36 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.75 % Favored : 96.22 % Rotamer: Outliers : 0.21 % Allowed : 1.06 % Favored : 98.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.76 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.51 (0.14), residues: 3174 helix: -0.49 (0.15), residues: 1092 sheet: 1.01 (0.24), residues: 486 loop : -0.56 (0.15), residues: 1596 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG F 224 TYR 0.024 0.002 TYR C 302 PHE 0.028 0.001 PHE E 106 TRP 0.026 0.001 TRP H 208 HIS 0.004 0.001 HIS B 57 Details of bonding type rmsd/Z covalent geometry : bond 0.00460 / 0.22 (27324) covalent geometry : angle 0.77015 / 0.37 (36966) hydrogen bonds : bond 0.26596 / 17.84 ( 973) hydrogen bonds : angle 8.43478 / 5.91 ( 2769) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6348 Ramachandran restraints generated. 3174 Oldfield, 0 Emsley, 3174 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6348 Ramachandran restraints generated. 3174 Oldfield, 0 Emsley, 3174 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 422 residues out of total 2832 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 416 time to evaluate : 1.025 Fit side-chains revert: symmetry clash REVERT: A 297 ASP cc_start: 0.7859 (m-30) cc_final: 0.7527 (t0) REVERT: B 286 GLN cc_start: 0.8357 (tp40) cc_final: 0.8101 (tp40) REVERT: C 81 ASN cc_start: 0.7621 (t0) cc_final: 0.7279 (t0) REVERT: C 327 MET cc_start: 0.5921 (mtm) cc_final: 0.4655 (tpt) REVERT: I 273 TRP cc_start: 0.8763 (p-90) cc_final: 0.8543 (p-90) outliers start: 6 outliers final: 1 residues processed: 421 average time/residue: 0.1651 time to fit residues: 112.9049 Evaluate side-chains 296 residues out of total 2832 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 295 time to evaluate : 1.305 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 303 ASN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 197 optimal weight: 0.9990 chunk 215 optimal weight: 0.9990 chunk 20 optimal weight: 0.2980 chunk 132 optimal weight: 8.9990 chunk 261 optimal weight: 5.9990 chunk 248 optimal weight: 0.7980 chunk 207 optimal weight: 2.9990 chunk 155 optimal weight: 5.9990 chunk 244 optimal weight: 3.9990 chunk 183 optimal weight: 0.3980 chunk 298 optimal weight: 0.9990 overall best weight: 0.6984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 91 ASN B 98 ASN B 246 GLN ** C 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 246 GLN G 131 ASN G 303 ASN ** K 300 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3333 r_free = 0.3333 target = 0.095831 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3044 r_free = 0.3044 target = 0.078167 restraints weight = 49594.210| |-----------------------------------------------------------------------------| r_work (start): 0.3044 rms_B_bonded: 2.61 r_work: 0.2917 rms_B_bonded: 3.12 restraints_weight: 0.5000 r_work (final): 0.2917 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8727 moved from start: 0.1524 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 27324 Z= 0.120 Angle : 0.567 7.819 36966 Z= 0.299 Chirality : 0.044 0.170 3966 Planarity : 0.004 0.041 4632 Dihedral : 10.689 90.474 3926 Min Nonbonded Distance : 1.867 Molprobity Statistics. All-atom Clashscore : 7.33 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.53 % Favored : 96.44 % Rotamer: Outliers : 0.95 % Allowed : 8.12 % Favored : 90.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.76 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.15 (0.14), residues: 3174 helix: 0.09 (0.14), residues: 1164 sheet: 0.86 (0.23), residues: 510 loop : -0.49 (0.16), residues: 1500 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG F 319 TYR 0.020 0.001 TYR C 295 PHE 0.011 0.001 PHE K 195 TRP 0.019 0.001 TRP C 273 HIS 0.005 0.001 HIS B 57 Details of bonding type rmsd/Z covalent geometry : bond 0.00265 / 0.12 (27324) covalent geometry : angle 0.56685 / 0.30 (36966) hydrogen bonds : bond 0.04345 / 2.89 ( 973) hydrogen bonds : angle 5.46257 / 3.82 ( 2769) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6348 Ramachandran restraints generated. 3174 Oldfield, 0 Emsley, 3174 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6348 Ramachandran restraints generated. 3174 Oldfield, 0 Emsley, 3174 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 345 residues out of total 2832 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 318 time to evaluate : 0.992 Fit side-chains revert: symmetry clash REVERT: A 297 ASP cc_start: 0.7955 (m-30) cc_final: 0.7252 (t0) REVERT: B 120 MET cc_start: 0.8415 (mpp) cc_final: 0.8072 (mmp) REVERT: B 286 GLN cc_start: 0.8455 (tp40) cc_final: 0.8111 (tp40) REVERT: C 81 ASN cc_start: 0.8388 (t0) cc_final: 0.7871 (t0) REVERT: E 127 GLU cc_start: 0.8033 (OUTLIER) cc_final: 0.7397 (mp0) REVERT: H 213 ARG cc_start: 0.8486 (mtp180) cc_final: 0.8021 (mtm-85) outliers start: 27 outliers final: 21 residues processed: 337 average time/residue: 0.1580 time to fit residues: 86.2014 Evaluate side-chains 295 residues out of total 2832 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 273 time to evaluate : 1.072 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 56 VAL Chi-restraints excluded: chain A residue 225 LYS Chi-restraints excluded: chain A residue 282 GLU Chi-restraints excluded: chain B residue 318 ILE Chi-restraints excluded: chain C residue 201 MET Chi-restraints excluded: chain D residue 30 GLU Chi-restraints excluded: chain D residue 312 LEU Chi-restraints excluded: chain E residue 127 GLU Chi-restraints excluded: chain F residue 203 ASN Chi-restraints excluded: chain F residue 324 LEU Chi-restraints excluded: chain G residue 160 VAL Chi-restraints excluded: chain G residue 203 ASN Chi-restraints excluded: chain G residue 247 VAL Chi-restraints excluded: chain I residue 142 VAL Chi-restraints excluded: chain I residue 226 SER Chi-restraints excluded: chain I residue 312 LEU Chi-restraints excluded: chain J residue 276 LYS Chi-restraints excluded: chain K residue 263 SER Chi-restraints excluded: chain K residue 280 ILE Chi-restraints excluded: chain L residue 122 LYS Chi-restraints excluded: chain L residue 275 ASN Chi-restraints excluded: chain L residue 317 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 196 optimal weight: 7.9990 chunk 67 optimal weight: 8.9990 chunk 187 optimal weight: 6.9990 chunk 153 optimal weight: 0.8980 chunk 142 optimal weight: 5.9990 chunk 184 optimal weight: 4.9990 chunk 97 optimal weight: 0.8980 chunk 89 optimal weight: 0.5980 chunk 94 optimal weight: 4.9990 chunk 292 optimal weight: 9.9990 chunk 250 optimal weight: 0.6980 overall best weight: 1.6182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 90 GLN B 91 ASN ** B 272 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 131 ASN ** E 242 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 131 ASN G 303 ASN I 131 ASN J 272 GLN K 131 ASN ** K 300 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 = 0.3357 r_free = 0.3357 target = 0.096948 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3092 r_free = 0.3092 target = 0.080774 restraints weight = 48911.847| |-----------------------------------------------------------------------------| r_work (start): 0.3080 rms_B_bonded: 2.24 r_work: 0.2969 rms_B_bonded: 2.70 restraints_weight: 0.5000 r_work: 0.2831 rms_B_bonded: 4.50 restraints_weight: 0.2500 r_work (final): 0.2831 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8870 moved from start: 0.1843 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 27324 Z= 0.156 Angle : 0.538 7.163 36966 Z= 0.283 Chirality : 0.044 0.159 3966 Planarity : 0.004 0.037 4632 Dihedral : 8.429 75.009 3924 Min Nonbonded Distance : 1.877 Molprobity Statistics. All-atom Clashscore : 7.26 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.81 % Favored : 96.16 % Rotamer: Outliers : 1.84 % Allowed : 9.85 % Favored : 88.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.76 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.03 (0.15), residues: 3174 helix: 0.43 (0.15), residues: 1158 sheet: 0.45 (0.21), residues: 570 loop : -0.49 (0.16), residues: 1446 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG L 213 TYR 0.015 0.001 TYR A 99 PHE 0.029 0.001 PHE A 106 TRP 0.021 0.001 TRP C 273 HIS 0.005 0.001 HIS B 57 Details of bonding type rmsd/Z covalent geometry : bond 0.00370 / 0.16 (27324) covalent geometry : angle 0.53821 / 0.28 (36966) hydrogen bonds : bond 0.04195 / 2.78 ( 973) hydrogen bonds : angle 5.10152 / 3.58 ( 2769) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6348 Ramachandran restraints generated. 3174 Oldfield, 0 Emsley, 3174 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6348 Ramachandran restraints generated. 3174 Oldfield, 0 Emsley, 3174 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 345 residues out of total 2832 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 293 time to evaluate : 0.981 Fit side-chains revert: symmetry clash REVERT: A 297 ASP cc_start: 0.8075 (m-30) cc_final: 0.7460 (t0) REVERT: A 315 GLU cc_start: 0.8575 (mm-30) cc_final: 0.8125 (mp0) REVERT: B 120 MET cc_start: 0.8516 (mpp) cc_final: 0.8171 (mmp) REVERT: B 286 GLN cc_start: 0.8466 (tp40) cc_final: 0.8169 (tp40) REVERT: C 327 MET cc_start: 0.6161 (mtm) cc_final: 0.4625 (tpt) REVERT: E 127 GLU cc_start: 0.8131 (OUTLIER) cc_final: 0.7548 (mp0) REVERT: G 315 GLU cc_start: 0.8224 (OUTLIER) cc_final: 0.8020 (pm20) REVERT: H 273 TRP cc_start: 0.7320 (t60) cc_final: 0.6995 (t-100) outliers start: 52 outliers final: 26 residues processed: 330 average time/residue: 0.1631 time to fit residues: 88.4692 Evaluate side-chains 293 residues out of total 2832 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 265 time to evaluate : 1.062 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 56 VAL Chi-restraints excluded: chain B residue 46 CYS Chi-restraints excluded: chain B residue 280 ILE Chi-restraints excluded: chain B residue 318 ILE Chi-restraints excluded: chain C residue 26 ILE Chi-restraints excluded: chain C residue 33 GLU Chi-restraints excluded: chain C residue 201 MET Chi-restraints excluded: chain D residue 30 GLU Chi-restraints excluded: chain D residue 312 LEU Chi-restraints excluded: chain E residue 46 CYS Chi-restraints excluded: chain E residue 127 GLU Chi-restraints excluded: chain F residue 46 CYS Chi-restraints excluded: chain F residue 203 ASN Chi-restraints excluded: chain F residue 324 LEU Chi-restraints excluded: chain G residue 160 VAL Chi-restraints excluded: chain G residue 203 ASN Chi-restraints excluded: chain G residue 247 VAL Chi-restraints excluded: chain G residue 315 GLU Chi-restraints excluded: chain I residue 142 VAL Chi-restraints excluded: chain I residue 226 SER Chi-restraints excluded: chain I residue 312 LEU Chi-restraints excluded: chain K residue 263 SER Chi-restraints excluded: chain K residue 280 ILE Chi-restraints excluded: chain L residue 122 LYS Chi-restraints excluded: chain L residue 202 SER Chi-restraints excluded: chain L residue 268 SER Chi-restraints excluded: chain L residue 275 ASN Chi-restraints excluded: chain L residue 317 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 258 optimal weight: 1.9990 chunk 157 optimal weight: 2.9990 chunk 219 optimal weight: 1.9990 chunk 233 optimal weight: 7.9990 chunk 230 optimal weight: 0.9980 chunk 105 optimal weight: 0.1980 chunk 110 optimal weight: 0.9990 chunk 118 optimal weight: 1.9990 chunk 240 optimal weight: 2.9990 chunk 170 optimal weight: 5.9990 chunk 232 optimal weight: 8.9990 overall best weight: 1.2386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 90 GLN B 91 ASN ** B 272 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 255 GLN E 81 ASN ** E 242 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 131 ASN G 303 ASN K 131 ASN K 133 ASN ** K 300 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 = 0.3360 r_free = 0.3360 target = 0.097223 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3092 r_free = 0.3092 target = 0.080707 restraints weight = 48780.907| |-----------------------------------------------------------------------------| r_work (start): 0.3086 rms_B_bonded: 2.31 r_work: 0.2973 rms_B_bonded: 2.78 restraints_weight: 0.5000 r_work: 0.2833 rms_B_bonded: 4.63 restraints_weight: 0.2500 r_work (final): 0.2833 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8864 moved from start: 0.2051 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 27324 Z= 0.128 Angle : 0.506 8.697 36966 Z= 0.266 Chirality : 0.043 0.165 3966 Planarity : 0.003 0.038 4632 Dihedral : 7.670 64.539 3924 Min Nonbonded Distance : 1.890 Molprobity Statistics. All-atom Clashscore : 6.21 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.78 % Favored : 96.19 % Rotamer: Outliers : 2.01 % Allowed : 11.09 % Favored : 86.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.76 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.07 (0.15), residues: 3174 helix: 0.61 (0.15), residues: 1158 sheet: 0.36 (0.21), residues: 570 loop : -0.45 (0.16), residues: 1446 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG K 213 TYR 0.020 0.001 TYR E 302 PHE 0.019 0.001 PHE A 106 TRP 0.024 0.001 TRP H 208 HIS 0.004 0.001 HIS B 57 Details of bonding type rmsd/Z covalent geometry : bond 0.00298 / 0.13 (27324) covalent geometry : angle 0.50644 / 0.27 (36966) hydrogen bonds : bond 0.03620 / 2.39 ( 973) hydrogen bonds : angle 4.85731 / 3.40 ( 2769) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6348 Ramachandran restraints generated. 3174 Oldfield, 0 Emsley, 3174 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6348 Ramachandran restraints generated. 3174 Oldfield, 0 Emsley, 3174 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 347 residues out of total 2832 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 290 time to evaluate : 1.143 Fit side-chains revert: symmetry clash REVERT: A 297 ASP cc_start: 0.8084 (m-30) cc_final: 0.7468 (t0) REVERT: A 315 GLU cc_start: 0.8532 (mm-30) cc_final: 0.8102 (mp0) REVERT: B 120 MET cc_start: 0.8439 (mpp) cc_final: 0.8134 (mmp) REVERT: B 286 GLN cc_start: 0.8451 (tp40) cc_final: 0.8202 (tp40) REVERT: C 327 MET cc_start: 0.6322 (mtm) cc_final: 0.4644 (tpt) REVERT: E 127 GLU cc_start: 0.8085 (OUTLIER) cc_final: 0.7557 (mp0) REVERT: J 275 ASN cc_start: 0.8568 (t0) cc_final: 0.8328 (t0) REVERT: K 133 ASN cc_start: 0.7732 (OUTLIER) cc_final: 0.7525 (p0) outliers start: 57 outliers final: 34 residues processed: 333 average time/residue: 0.1644 time to fit residues: 89.1007 Evaluate side-chains 302 residues out of total 2832 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 266 time to evaluate : 1.009 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 56 VAL Chi-restraints excluded: chain B residue 46 CYS Chi-restraints excluded: chain B residue 225 LYS Chi-restraints excluded: chain B residue 280 ILE Chi-restraints excluded: chain B residue 318 ILE Chi-restraints excluded: chain C residue 5 LEU Chi-restraints excluded: chain C residue 26 ILE Chi-restraints excluded: chain C residue 33 GLU Chi-restraints excluded: chain C residue 201 MET Chi-restraints excluded: chain D residue 30 GLU Chi-restraints excluded: chain D residue 312 LEU Chi-restraints excluded: chain E residue 46 CYS Chi-restraints excluded: chain E residue 127 GLU Chi-restraints excluded: chain F residue 15 LEU Chi-restraints excluded: chain F residue 46 CYS Chi-restraints excluded: chain F residue 112 GLU Chi-restraints excluded: chain F residue 203 ASN Chi-restraints excluded: chain F residue 324 LEU Chi-restraints excluded: chain G residue 160 VAL Chi-restraints excluded: chain G residue 203 ASN Chi-restraints excluded: chain G residue 247 VAL Chi-restraints excluded: chain G residue 274 VAL Chi-restraints excluded: chain I residue 142 VAL Chi-restraints excluded: chain I residue 221 ASP Chi-restraints excluded: chain I residue 226 SER Chi-restraints excluded: chain I residue 312 LEU Chi-restraints excluded: chain J residue 146 ILE Chi-restraints excluded: chain K residue 133 ASN Chi-restraints excluded: chain K residue 154 LEU Chi-restraints excluded: chain K residue 263 SER Chi-restraints excluded: chain K residue 280 ILE Chi-restraints excluded: chain L residue 122 LYS Chi-restraints excluded: chain L residue 202 SER Chi-restraints excluded: chain L residue 268 SER Chi-restraints excluded: chain L residue 275 ASN Chi-restraints excluded: chain L residue 317 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 234 optimal weight: 0.7980 chunk 145 optimal weight: 3.9990 chunk 89 optimal weight: 0.7980 chunk 118 optimal weight: 0.9990 chunk 94 optimal weight: 3.9990 chunk 100 optimal weight: 3.9990 chunk 36 optimal weight: 3.9990 chunk 296 optimal weight: 7.9990 chunk 87 optimal weight: 3.9990 chunk 154 optimal weight: 2.9990 chunk 56 optimal weight: 5.9990 overall best weight: 1.9186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 90 GLN ** B 272 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 242 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 316 ASN G 131 ASN G 303 ASN I 131 ASN K 131 ASN ** K 300 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3262 r_free = 0.3262 target = 0.091621 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2968 r_free = 0.2968 target = 0.073897 restraints weight = 49885.965| |-----------------------------------------------------------------------------| r_work (start): 0.2966 rms_B_bonded: 2.70 r_work: 0.2834 rms_B_bonded: 3.20 restraints_weight: 0.5000 r_work (final): 0.2834 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8785 moved from start: 0.2196 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 27324 Z= 0.172 Angle : 0.531 7.665 36966 Z= 0.278 Chirality : 0.043 0.168 3966 Planarity : 0.003 0.035 4632 Dihedral : 7.523 59.846 3924 Min Nonbonded Distance : 1.882 Molprobity Statistics. All-atom Clashscore : 6.64 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.81 % Favored : 96.12 % Rotamer: Outliers : 2.05 % Allowed : 12.50 % Favored : 85.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.76 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.07 (0.15), residues: 3174 helix: 0.68 (0.15), residues: 1122 sheet: 0.25 (0.21), residues: 570 loop : -0.43 (0.16), residues: 1482 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG L 213 TYR 0.018 0.001 TYR E 42 PHE 0.015 0.001 PHE A 106 TRP 0.014 0.001 TRP F 254 HIS 0.005 0.001 HIS B 57 Details of bonding type rmsd/Z covalent geometry : bond 0.00413 / 0.17 (27324) covalent geometry : angle 0.53145 / 0.28 (36966) hydrogen bonds : bond 0.03874 / 2.56 ( 973) hydrogen bonds : angle 4.86877 / 3.42 ( 2769) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6348 Ramachandran restraints generated. 3174 Oldfield, 0 Emsley, 3174 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6348 Ramachandran restraints generated. 3174 Oldfield, 0 Emsley, 3174 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 334 residues out of total 2832 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 276 time to evaluate : 1.062 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 297 ASP cc_start: 0.7897 (m-30) cc_final: 0.7332 (t0) REVERT: A 315 GLU cc_start: 0.8561 (mm-30) cc_final: 0.8042 (mp0) REVERT: B 120 MET cc_start: 0.8496 (mpp) cc_final: 0.8144 (mmp) REVERT: B 286 GLN cc_start: 0.8496 (tp40) cc_final: 0.8195 (tp40) REVERT: C 327 MET cc_start: 0.6361 (mtm) cc_final: 0.4748 (tpt) REVERT: D 83 MET cc_start: 0.8764 (tpt) cc_final: 0.8545 (tpt) REVERT: D 224 ARG cc_start: 0.7940 (OUTLIER) cc_final: 0.7128 (ptt90) REVERT: E 127 GLU cc_start: 0.8061 (OUTLIER) cc_final: 0.7461 (mp0) REVERT: E 139 MET cc_start: 0.9064 (mmt) cc_final: 0.8835 (mmm) REVERT: J 275 ASN cc_start: 0.8578 (t0) cc_final: 0.8264 (t0) outliers start: 58 outliers final: 36 residues processed: 320 average time/residue: 0.1626 time to fit residues: 84.9317 Evaluate side-chains 295 residues out of total 2832 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 257 time to evaluate : 0.918 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 56 VAL Chi-restraints excluded: chain B residue 46 CYS Chi-restraints excluded: chain B residue 225 LYS Chi-restraints excluded: chain B residue 280 ILE Chi-restraints excluded: chain C residue 5 LEU Chi-restraints excluded: chain C residue 26 ILE Chi-restraints excluded: chain C residue 33 GLU Chi-restraints excluded: chain C residue 103 ASP Chi-restraints excluded: chain C residue 201 MET Chi-restraints excluded: chain C residue 324 LEU Chi-restraints excluded: chain D residue 15 LEU Chi-restraints excluded: chain D residue 30 GLU Chi-restraints excluded: chain D residue 56 VAL Chi-restraints excluded: chain D residue 224 ARG Chi-restraints excluded: chain D residue 312 LEU Chi-restraints excluded: chain E residue 17 THR Chi-restraints excluded: chain E residue 46 CYS Chi-restraints excluded: chain E residue 127 GLU Chi-restraints excluded: chain F residue 46 CYS Chi-restraints excluded: chain F residue 82 ILE Chi-restraints excluded: chain F residue 112 GLU Chi-restraints excluded: chain F residue 203 ASN Chi-restraints excluded: chain F residue 324 LEU Chi-restraints excluded: chain G residue 160 VAL Chi-restraints excluded: chain G residue 203 ASN Chi-restraints excluded: chain G residue 247 VAL Chi-restraints excluded: chain G residue 274 VAL Chi-restraints excluded: chain H residue 226 SER Chi-restraints excluded: chain I residue 142 VAL Chi-restraints excluded: chain I residue 226 SER Chi-restraints excluded: chain I residue 312 LEU Chi-restraints excluded: chain K residue 154 LEU Chi-restraints excluded: chain K residue 263 SER Chi-restraints excluded: chain K residue 280 ILE Chi-restraints excluded: chain L residue 122 LYS Chi-restraints excluded: chain L residue 268 SER Chi-restraints excluded: chain L residue 275 ASN Chi-restraints excluded: chain L residue 317 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 178 optimal weight: 1.9990 chunk 238 optimal weight: 4.9990 chunk 299 optimal weight: 3.9990 chunk 273 optimal weight: 6.9990 chunk 308 optimal weight: 0.6980 chunk 244 optimal weight: 6.9990 chunk 225 optimal weight: 0.9980 chunk 297 optimal weight: 0.7980 chunk 245 optimal weight: 1.9990 chunk 234 optimal weight: 3.9990 chunk 135 optimal weight: 7.9990 overall best weight: 1.2984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 90 GLN ** B 272 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 242 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 272 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 303 ASN ** K 300 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 = 0.3351 r_free = 0.3351 target = 0.096825 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3087 r_free = 0.3087 target = 0.080723 restraints weight = 48864.530| |-----------------------------------------------------------------------------| r_work (start): 0.3074 rms_B_bonded: 2.24 r_work: 0.2962 rms_B_bonded: 2.70 restraints_weight: 0.5000 r_work: 0.2823 rms_B_bonded: 4.50 restraints_weight: 0.2500 r_work (final): 0.2823 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8873 moved from start: 0.2323 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 27324 Z= 0.129 Angle : 0.496 7.997 36966 Z= 0.261 Chirality : 0.042 0.158 3966 Planarity : 0.003 0.038 4632 Dihedral : 7.297 59.824 3924 Min Nonbonded Distance : 1.907 Molprobity Statistics. All-atom Clashscore : 6.14 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.65 % Favored : 96.28 % Rotamer: Outliers : 1.80 % Allowed : 13.81 % Favored : 84.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.76 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.17 (0.15), residues: 3174 helix: 0.82 (0.16), residues: 1122 sheet: 0.21 (0.21), residues: 570 loop : -0.39 (0.16), residues: 1482 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG K 213 TYR 0.016 0.001 TYR E 42 PHE 0.014 0.001 PHE A 106 TRP 0.018 0.001 TRP H 208 HIS 0.004 0.001 HIS C 57 Details of bonding type rmsd/Z covalent geometry : bond 0.00303 / 0.13 (27324) covalent geometry : angle 0.49621 / 0.26 (36966) hydrogen bonds : bond 0.03429 / 2.27 ( 973) hydrogen bonds : angle 4.74666 / 3.33 ( 2769) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6348 Ramachandran restraints generated. 3174 Oldfield, 0 Emsley, 3174 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6348 Ramachandran restraints generated. 3174 Oldfield, 0 Emsley, 3174 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 335 residues out of total 2832 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 284 time to evaluate : 1.017 Fit side-chains revert: symmetry clash REVERT: A 297 ASP cc_start: 0.8058 (m-30) cc_final: 0.7465 (t0) REVERT: A 315 GLU cc_start: 0.8524 (mm-30) cc_final: 0.8213 (mp0) REVERT: B 120 MET cc_start: 0.8554 (mpp) cc_final: 0.8233 (mmp) REVERT: B 166 LYS cc_start: 0.8766 (mmmt) cc_final: 0.8546 (mmmt) REVERT: B 286 GLN cc_start: 0.8438 (tp40) cc_final: 0.8200 (tp40) REVERT: C 327 MET cc_start: 0.6411 (mtm) cc_final: 0.4767 (tpt) REVERT: D 224 ARG cc_start: 0.8040 (OUTLIER) cc_final: 0.7182 (ptt90) REVERT: E 127 GLU cc_start: 0.8075 (OUTLIER) cc_final: 0.7572 (mp0) REVERT: E 139 MET cc_start: 0.9120 (mmt) cc_final: 0.8873 (mmm) REVERT: E 314 LEU cc_start: 0.8678 (mt) cc_final: 0.8445 (mp) REVERT: G 284 ASP cc_start: 0.8774 (p0) cc_final: 0.8492 (p0) REVERT: J 275 ASN cc_start: 0.8595 (t0) cc_final: 0.8352 (t0) REVERT: K 196 ASN cc_start: 0.8569 (m-40) cc_final: 0.8352 (m-40) outliers start: 51 outliers final: 35 residues processed: 321 average time/residue: 0.1620 time to fit residues: 85.8232 Evaluate side-chains 298 residues out of total 2832 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 261 time to evaluate : 1.119 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 56 VAL Chi-restraints excluded: chain B residue 46 CYS Chi-restraints excluded: chain B residue 225 LYS Chi-restraints excluded: chain B residue 280 ILE Chi-restraints excluded: chain B residue 318 ILE Chi-restraints excluded: chain C residue 26 ILE Chi-restraints excluded: chain C residue 33 GLU Chi-restraints excluded: chain C residue 83 MET Chi-restraints excluded: chain C residue 103 ASP Chi-restraints excluded: chain C residue 201 MET Chi-restraints excluded: chain D residue 15 LEU Chi-restraints excluded: chain D residue 30 GLU Chi-restraints excluded: chain D residue 56 VAL Chi-restraints excluded: chain D residue 224 ARG Chi-restraints excluded: chain D residue 312 LEU Chi-restraints excluded: chain E residue 46 CYS Chi-restraints excluded: chain E residue 127 GLU Chi-restraints excluded: chain F residue 46 CYS Chi-restraints excluded: chain F residue 82 ILE Chi-restraints excluded: chain F residue 112 GLU Chi-restraints excluded: chain F residue 203 ASN Chi-restraints excluded: chain F residue 324 LEU Chi-restraints excluded: chain G residue 160 VAL Chi-restraints excluded: chain G residue 203 ASN Chi-restraints excluded: chain G residue 247 VAL Chi-restraints excluded: chain G residue 274 VAL Chi-restraints excluded: chain I residue 142 VAL Chi-restraints excluded: chain I residue 221 ASP Chi-restraints excluded: chain I residue 226 SER Chi-restraints excluded: chain I residue 312 LEU Chi-restraints excluded: chain K residue 154 LEU Chi-restraints excluded: chain K residue 263 SER Chi-restraints excluded: chain K residue 280 ILE Chi-restraints excluded: chain L residue 122 LYS Chi-restraints excluded: chain L residue 268 SER Chi-restraints excluded: chain L residue 275 ASN Chi-restraints excluded: chain L residue 317 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 62 optimal weight: 0.0270 chunk 174 optimal weight: 2.9990 chunk 47 optimal weight: 0.9990 chunk 219 optimal weight: 2.9990 chunk 123 optimal weight: 5.9990 chunk 87 optimal weight: 3.9990 chunk 267 optimal weight: 10.0000 chunk 34 optimal weight: 3.9990 chunk 287 optimal weight: 0.5980 chunk 233 optimal weight: 6.9990 chunk 148 optimal weight: 5.9990 overall best weight: 1.5244 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 90 GLN ** B 272 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 246 GLN E 81 ASN ** E 242 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 303 ASN ** K 300 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 = 0.3340 r_free = 0.3340 target = 0.096092 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3072 r_free = 0.3072 target = 0.079879 restraints weight = 48675.881| |-----------------------------------------------------------------------------| r_work (start): 0.3063 rms_B_bonded: 2.24 r_work: 0.2951 rms_B_bonded: 2.71 restraints_weight: 0.5000 r_work: 0.2812 rms_B_bonded: 4.52 restraints_weight: 0.2500 r_work (final): 0.2812 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8885 moved from start: 0.2382 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 27324 Z= 0.145 Angle : 0.510 8.977 36966 Z= 0.266 Chirality : 0.043 0.160 3966 Planarity : 0.003 0.039 4632 Dihedral : 7.231 59.764 3924 Min Nonbonded Distance : 1.897 Molprobity Statistics. All-atom Clashscore : 6.19 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.88 % Favored : 96.06 % Rotamer: Outliers : 1.94 % Allowed : 14.12 % Favored : 83.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.76 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.16 (0.15), residues: 3174 helix: 0.84 (0.15), residues: 1122 sheet: 0.18 (0.21), residues: 570 loop : -0.39 (0.16), residues: 1482 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG K 213 TYR 0.016 0.001 TYR E 42 PHE 0.012 0.001 PHE A 106 TRP 0.017 0.001 TRP H 208 HIS 0.004 0.001 HIS C 57 Details of bonding type rmsd/Z covalent geometry : bond 0.00345 / 0.15 (27324) covalent geometry : angle 0.50987 / 0.27 (36966) hydrogen bonds : bond 0.03530 / 2.33 ( 973) hydrogen bonds : angle 4.73986 / 3.33 ( 2769) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6348 Ramachandran restraints generated. 3174 Oldfield, 0 Emsley, 3174 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6348 Ramachandran restraints generated. 3174 Oldfield, 0 Emsley, 3174 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 332 residues out of total 2832 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 277 time to evaluate : 1.013 Fit side-chains revert: symmetry clash REVERT: A 297 ASP cc_start: 0.8057 (m-30) cc_final: 0.7456 (t0) REVERT: B 120 MET cc_start: 0.8583 (mpp) cc_final: 0.8247 (mmp) REVERT: B 286 GLN cc_start: 0.8479 (tp40) cc_final: 0.8236 (tp40) REVERT: C 327 MET cc_start: 0.6438 (mtm) cc_final: 0.4817 (tpt) REVERT: D 224 ARG cc_start: 0.8066 (OUTLIER) cc_final: 0.7208 (ptt90) REVERT: E 127 GLU cc_start: 0.8070 (OUTLIER) cc_final: 0.7594 (mp0) REVERT: E 139 MET cc_start: 0.9139 (mmt) cc_final: 0.8898 (mmm) REVERT: E 314 LEU cc_start: 0.8709 (mt) cc_final: 0.8352 (mp) REVERT: G 284 ASP cc_start: 0.8769 (p0) cc_final: 0.8496 (p0) REVERT: H 213 ARG cc_start: 0.8346 (mtp180) cc_final: 0.7774 (mtm-85) REVERT: J 239 ASP cc_start: 0.8380 (t0) cc_final: 0.8116 (m-30) REVERT: J 275 ASN cc_start: 0.8607 (t0) cc_final: 0.8346 (t0) REVERT: K 196 ASN cc_start: 0.8570 (m-40) cc_final: 0.8367 (m-40) outliers start: 55 outliers final: 36 residues processed: 317 average time/residue: 0.1662 time to fit residues: 86.8469 Evaluate side-chains 306 residues out of total 2832 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 268 time to evaluate : 1.035 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 56 VAL Chi-restraints excluded: chain B residue 46 CYS Chi-restraints excluded: chain B residue 280 ILE Chi-restraints excluded: chain C residue 26 ILE Chi-restraints excluded: chain C residue 33 GLU Chi-restraints excluded: chain C residue 103 ASP Chi-restraints excluded: chain C residue 201 MET Chi-restraints excluded: chain C residue 324 LEU Chi-restraints excluded: chain D residue 15 LEU Chi-restraints excluded: chain D residue 30 GLU Chi-restraints excluded: chain D residue 56 VAL Chi-restraints excluded: chain D residue 224 ARG Chi-restraints excluded: chain D residue 312 LEU Chi-restraints excluded: chain E residue 17 THR Chi-restraints excluded: chain E residue 46 CYS Chi-restraints excluded: chain E residue 127 GLU Chi-restraints excluded: chain F residue 46 CYS Chi-restraints excluded: chain F residue 82 ILE Chi-restraints excluded: chain F residue 112 GLU Chi-restraints excluded: chain F residue 203 ASN Chi-restraints excluded: chain F residue 324 LEU Chi-restraints excluded: chain G residue 160 VAL Chi-restraints excluded: chain G residue 179 THR Chi-restraints excluded: chain G residue 203 ASN Chi-restraints excluded: chain G residue 247 VAL Chi-restraints excluded: chain G residue 274 VAL Chi-restraints excluded: chain I residue 131 ASN Chi-restraints excluded: chain I residue 142 VAL Chi-restraints excluded: chain I residue 221 ASP Chi-restraints excluded: chain I residue 226 SER Chi-restraints excluded: chain I residue 312 LEU Chi-restraints excluded: chain K residue 154 LEU Chi-restraints excluded: chain K residue 263 SER Chi-restraints excluded: chain K residue 280 ILE Chi-restraints excluded: chain L residue 122 LYS Chi-restraints excluded: chain L residue 268 SER Chi-restraints excluded: chain L residue 275 ASN Chi-restraints excluded: chain L residue 317 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 25 optimal weight: 0.9990 chunk 240 optimal weight: 0.8980 chunk 165 optimal weight: 0.7980 chunk 293 optimal weight: 6.9990 chunk 202 optimal weight: 1.9990 chunk 194 optimal weight: 0.9980 chunk 307 optimal weight: 0.7980 chunk 215 optimal weight: 0.7980 chunk 102 optimal weight: 0.9980 chunk 265 optimal weight: 1.9990 chunk 110 optimal weight: 0.9990 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 242 ASN B 90 GLN B 91 ASN ** B 272 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 6 GLN E 81 ASN ** E 242 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 131 ASN G 303 ASN ** K 300 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3536 r_free = 0.3536 target = 0.101904 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3243 r_free = 0.3243 target = 0.084126 restraints weight = 49351.297| |-----------------------------------------------------------------------------| r_work (start): 0.3250 rms_B_bonded: 2.54 r_work: 0.3117 rms_B_bonded: 3.07 restraints_weight: 0.5000 r_work (final): 0.3117 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8788 moved from start: 0.2492 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 27324 Z= 0.105 Angle : 0.483 8.192 36966 Z= 0.253 Chirality : 0.042 0.160 3966 Planarity : 0.003 0.039 4632 Dihedral : 6.929 56.472 3924 Min Nonbonded Distance : 1.923 Molprobity Statistics. All-atom Clashscore : 6.21 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.40 % Favored : 96.53 % Rotamer: Outliers : 1.66 % Allowed : 14.55 % Favored : 83.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.76 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.29 (0.15), residues: 3174 helix: 0.93 (0.16), residues: 1122 sheet: 0.20 (0.21), residues: 570 loop : -0.29 (0.16), residues: 1482 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG K 213 TYR 0.013 0.001 TYR E 42 PHE 0.012 0.001 PHE D 22 TRP 0.022 0.001 TRP H 208 HIS 0.004 0.001 HIS C 57 Details of bonding type rmsd/Z covalent geometry : bond 0.00242 / 0.11 (27324) covalent geometry : angle 0.48293 / 0.25 (36966) hydrogen bonds : bond 0.03141 / 2.08 ( 973) hydrogen bonds : angle 4.60875 / 3.23 ( 2769) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6348 Ramachandran restraints generated. 3174 Oldfield, 0 Emsley, 3174 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6348 Ramachandran restraints generated. 3174 Oldfield, 0 Emsley, 3174 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 341 residues out of total 2832 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 294 time to evaluate : 1.143 Fit side-chains revert: symmetry clash REVERT: A 297 ASP cc_start: 0.7915 (m-30) cc_final: 0.7358 (t0) REVERT: B 120 MET cc_start: 0.8364 (mpp) cc_final: 0.8118 (mmp) REVERT: B 273 TRP cc_start: 0.8001 (t60) cc_final: 0.7726 (p-90) REVERT: B 286 GLN cc_start: 0.8400 (tp40) cc_final: 0.8173 (tp40) REVERT: D 224 ARG cc_start: 0.7907 (OUTLIER) cc_final: 0.7042 (ptt90) REVERT: E 127 GLU cc_start: 0.7918 (OUTLIER) cc_final: 0.7502 (mp0) REVERT: E 139 MET cc_start: 0.9029 (mmt) cc_final: 0.8772 (mmm) REVERT: E 314 LEU cc_start: 0.8618 (mt) cc_final: 0.8353 (mp) REVERT: G 284 ASP cc_start: 0.8600 (p0) cc_final: 0.8327 (p0) REVERT: J 239 ASP cc_start: 0.8192 (t0) cc_final: 0.7900 (m-30) REVERT: J 275 ASN cc_start: 0.8535 (t0) cc_final: 0.8311 (t0) REVERT: K 327 MET cc_start: 0.6360 (mtm) cc_final: 0.5632 (tmm) REVERT: L 221 ASP cc_start: 0.8826 (t0) cc_final: 0.8612 (m-30) REVERT: L 299 GLU cc_start: 0.7542 (tt0) cc_final: 0.7334 (tp30) outliers start: 47 outliers final: 34 residues processed: 326 average time/residue: 0.1677 time to fit residues: 89.9476 Evaluate side-chains 307 residues out of total 2832 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 271 time to evaluate : 0.935 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 56 VAL Chi-restraints excluded: chain B residue 46 CYS Chi-restraints excluded: chain B residue 280 ILE Chi-restraints excluded: chain C residue 5 LEU Chi-restraints excluded: chain C residue 33 GLU Chi-restraints excluded: chain C residue 103 ASP Chi-restraints excluded: chain C residue 201 MET Chi-restraints excluded: chain D residue 15 LEU Chi-restraints excluded: chain D residue 30 GLU Chi-restraints excluded: chain D residue 56 VAL Chi-restraints excluded: chain D residue 224 ARG Chi-restraints excluded: chain D residue 312 LEU Chi-restraints excluded: chain E residue 17 THR Chi-restraints excluded: chain E residue 46 CYS Chi-restraints excluded: chain E residue 127 GLU Chi-restraints excluded: chain F residue 46 CYS Chi-restraints excluded: chain F residue 82 ILE Chi-restraints excluded: chain F residue 112 GLU Chi-restraints excluded: chain F residue 160 VAL Chi-restraints excluded: chain F residue 203 ASN Chi-restraints excluded: chain F residue 324 LEU Chi-restraints excluded: chain G residue 179 THR Chi-restraints excluded: chain G residue 203 ASN Chi-restraints excluded: chain G residue 247 VAL Chi-restraints excluded: chain G residue 274 VAL Chi-restraints excluded: chain I residue 131 ASN Chi-restraints excluded: chain I residue 142 VAL Chi-restraints excluded: chain I residue 221 ASP Chi-restraints excluded: chain I residue 226 SER Chi-restraints excluded: chain I residue 312 LEU Chi-restraints excluded: chain K residue 154 LEU Chi-restraints excluded: chain K residue 263 SER Chi-restraints excluded: chain K residue 280 ILE Chi-restraints excluded: chain L residue 122 LYS Chi-restraints excluded: chain L residue 275 ASN Chi-restraints excluded: chain L residue 310 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 67 optimal weight: 8.9990 chunk 10 optimal weight: 0.9980 chunk 85 optimal weight: 2.9990 chunk 277 optimal weight: 2.9990 chunk 133 optimal weight: 0.9980 chunk 17 optimal weight: 5.9990 chunk 48 optimal weight: 5.9990 chunk 172 optimal weight: 3.9990 chunk 138 optimal weight: 6.9990 chunk 137 optimal weight: 0.8980 chunk 91 optimal weight: 0.1980 overall best weight: 1.2182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 90 GLN ** B 272 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 81 ASN ** E 242 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 131 ASN G 303 ASN ** K 300 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 = 0.3356 r_free = 0.3356 target = 0.097123 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3090 r_free = 0.3090 target = 0.080882 restraints weight = 48829.920| |-----------------------------------------------------------------------------| r_work (start): 0.3080 rms_B_bonded: 2.25 r_work: 0.2968 rms_B_bonded: 2.71 restraints_weight: 0.5000 r_work: 0.2829 rms_B_bonded: 4.53 restraints_weight: 0.2500 r_work (final): 0.2829 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8867 moved from start: 0.2520 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 27324 Z= 0.126 Angle : 0.505 9.508 36966 Z= 0.262 Chirality : 0.042 0.160 3966 Planarity : 0.003 0.046 4632 Dihedral : 6.847 54.524 3924 Min Nonbonded Distance : 1.911 Molprobity Statistics. All-atom Clashscore : 6.19 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.65 % Favored : 96.28 % Rotamer: Outliers : 1.66 % Allowed : 14.69 % Favored : 83.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.76 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.28 (0.15), residues: 3174 helix: 0.93 (0.16), residues: 1122 sheet: 0.19 (0.21), residues: 570 loop : -0.30 (0.16), residues: 1482 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG K 213 TYR 0.015 0.001 TYR E 42 PHE 0.021 0.001 PHE E 22 TRP 0.019 0.001 TRP H 208 HIS 0.004 0.001 HIS C 57 Details of bonding type rmsd/Z covalent geometry : bond 0.00297 / 0.13 (27324) covalent geometry : angle 0.50489 / 0.26 (36966) hydrogen bonds : bond 0.03283 / 2.16 ( 973) hydrogen bonds : angle 4.62787 / 3.25 ( 2769) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6348 Ramachandran restraints generated. 3174 Oldfield, 0 Emsley, 3174 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6348 Ramachandran restraints generated. 3174 Oldfield, 0 Emsley, 3174 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 329 residues out of total 2832 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 282 time to evaluate : 1.078 Fit side-chains revert: symmetry clash REVERT: A 297 ASP cc_start: 0.8074 (m-30) cc_final: 0.7429 (t0) REVERT: B 120 MET cc_start: 0.8516 (mpp) cc_final: 0.8184 (mmp) REVERT: B 273 TRP cc_start: 0.8075 (t60) cc_final: 0.7786 (p-90) REVERT: B 286 GLN cc_start: 0.8448 (tp40) cc_final: 0.8242 (tp40) REVERT: C 327 MET cc_start: 0.6175 (mtm) cc_final: 0.4517 (tpt) REVERT: D 224 ARG cc_start: 0.8019 (OUTLIER) cc_final: 0.7137 (ptt90) REVERT: E 127 GLU cc_start: 0.8015 (OUTLIER) cc_final: 0.7617 (mp0) REVERT: E 139 MET cc_start: 0.9139 (mmt) cc_final: 0.8893 (mmm) REVERT: E 314 LEU cc_start: 0.8673 (mt) cc_final: 0.8456 (mp) REVERT: F 22 PHE cc_start: 0.8842 (t80) cc_final: 0.8574 (t80) REVERT: G 123 ARG cc_start: 0.8583 (mtp-110) cc_final: 0.8231 (ttm110) REVERT: G 284 ASP cc_start: 0.8731 (p0) cc_final: 0.8456 (p0) REVERT: H 213 ARG cc_start: 0.8309 (mtp180) cc_final: 0.7775 (mtm-85) REVERT: J 239 ASP cc_start: 0.8364 (t0) cc_final: 0.8094 (m-30) REVERT: J 275 ASN cc_start: 0.8576 (t0) cc_final: 0.8327 (t0) REVERT: K 327 MET cc_start: 0.6748 (mtm) cc_final: 0.5828 (tmm) REVERT: L 299 GLU cc_start: 0.7659 (tt0) cc_final: 0.7435 (tp30) outliers start: 47 outliers final: 37 residues processed: 317 average time/residue: 0.1649 time to fit residues: 86.5445 Evaluate side-chains 311 residues out of total 2832 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 272 time to evaluate : 1.071 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 56 VAL Chi-restraints excluded: chain B residue 46 CYS Chi-restraints excluded: chain B residue 280 ILE Chi-restraints excluded: chain C residue 5 LEU Chi-restraints excluded: chain C residue 26 ILE Chi-restraints excluded: chain C residue 33 GLU Chi-restraints excluded: chain C residue 103 ASP Chi-restraints excluded: chain C residue 201 MET Chi-restraints excluded: chain C residue 314 LEU Chi-restraints excluded: chain C residue 324 LEU Chi-restraints excluded: chain D residue 15 LEU Chi-restraints excluded: chain D residue 30 GLU Chi-restraints excluded: chain D residue 56 VAL Chi-restraints excluded: chain D residue 224 ARG Chi-restraints excluded: chain D residue 312 LEU Chi-restraints excluded: chain E residue 17 THR Chi-restraints excluded: chain E residue 46 CYS Chi-restraints excluded: chain E residue 127 GLU Chi-restraints excluded: chain F residue 46 CYS Chi-restraints excluded: chain F residue 82 ILE Chi-restraints excluded: chain F residue 112 GLU Chi-restraints excluded: chain F residue 160 VAL Chi-restraints excluded: chain F residue 203 ASN Chi-restraints excluded: chain F residue 324 LEU Chi-restraints excluded: chain G residue 179 THR Chi-restraints excluded: chain G residue 203 ASN Chi-restraints excluded: chain G residue 247 VAL Chi-restraints excluded: chain G residue 274 VAL Chi-restraints excluded: chain G residue 303 ASN Chi-restraints excluded: chain I residue 142 VAL Chi-restraints excluded: chain I residue 221 ASP Chi-restraints excluded: chain I residue 226 SER Chi-restraints excluded: chain I residue 312 LEU Chi-restraints excluded: chain K residue 154 LEU Chi-restraints excluded: chain K residue 263 SER Chi-restraints excluded: chain K residue 280 ILE Chi-restraints excluded: chain L residue 122 LYS Chi-restraints excluded: chain L residue 275 ASN Chi-restraints excluded: chain L residue 310 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 38 optimal weight: 7.9990 chunk 66 optimal weight: 4.9990 chunk 136 optimal weight: 3.9990 chunk 172 optimal weight: 3.9990 chunk 233 optimal weight: 7.9990 chunk 157 optimal weight: 4.9990 chunk 129 optimal weight: 3.9990 chunk 21 optimal weight: 3.9990 chunk 56 optimal weight: 1.9990 chunk 228 optimal weight: 4.9990 chunk 300 optimal weight: 2.9990 overall best weight: 3.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 90 GLN ** B 272 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 85 HIS E 81 ASN ** E 242 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 131 ASN K 133 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3291 r_free = 0.3291 target = 0.093023 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3015 r_free = 0.3015 target = 0.076715 restraints weight = 49918.222| |-----------------------------------------------------------------------------| r_work (start): 0.3014 rms_B_bonded: 2.26 r_work: 0.2901 rms_B_bonded: 2.70 restraints_weight: 0.5000 r_work: 0.2762 rms_B_bonded: 4.48 restraints_weight: 0.2500 r_work (final): 0.2762 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8937 moved from start: 0.2529 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.061 27324 Z= 0.282 Angle : 0.628 10.853 36966 Z= 0.323 Chirality : 0.047 0.202 3966 Planarity : 0.004 0.041 4632 Dihedral : 7.584 57.915 3924 Min Nonbonded Distance : 1.840 Molprobity Statistics. All-atom Clashscore : 7.28 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.57 % Favored : 95.34 % Rotamer: Outliers : 1.62 % Allowed : 14.80 % Favored : 83.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.76 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.09 (0.15), residues: 3174 helix: 0.60 (0.15), residues: 1116 sheet: -0.02 (0.21), residues: 588 loop : -0.49 (0.16), residues: 1470 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG F 71 TYR 0.024 0.002 TYR E 42 PHE 0.030 0.002 PHE G 304 TRP 0.017 0.002 TRP E 254 HIS 0.006 0.002 HIS C 57 Details of bonding type rmsd/Z covalent geometry : bond 0.00680 / 0.28 (27324) covalent geometry : angle 0.62809 / 0.32 (36966) hydrogen bonds : bond 0.04431 / 2.91 ( 973) hydrogen bonds : angle 5.00562 / 3.53 ( 2769) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6348 Ramachandran restraints generated. 3174 Oldfield, 0 Emsley, 3174 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6348 Ramachandran restraints generated. 3174 Oldfield, 0 Emsley, 3174 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 318 residues out of total 2832 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 272 time to evaluate : 1.032 Fit side-chains revert: symmetry clash REVERT: A 297 ASP cc_start: 0.8070 (m-30) cc_final: 0.7496 (t0) REVERT: B 120 MET cc_start: 0.8551 (mpp) cc_final: 0.8242 (mmp) REVERT: B 273 TRP cc_start: 0.8105 (t60) cc_final: 0.7801 (p-90) REVERT: B 286 GLN cc_start: 0.8588 (tp40) cc_final: 0.8325 (tp40) REVERT: C 327 MET cc_start: 0.6221 (mtm) cc_final: 0.4626 (tpt) REVERT: D 224 ARG cc_start: 0.8145 (OUTLIER) cc_final: 0.7201 (ptt90) REVERT: E 127 GLU cc_start: 0.8146 (OUTLIER) cc_final: 0.7575 (mp0) REVERT: E 314 LEU cc_start: 0.8704 (mt) cc_final: 0.8443 (mp) REVERT: G 123 ARG cc_start: 0.8573 (mtp-110) cc_final: 0.8213 (ttm110) REVERT: G 284 ASP cc_start: 0.8804 (p0) cc_final: 0.8554 (p0) REVERT: J 275 ASN cc_start: 0.8662 (t0) cc_final: 0.8326 (t0) REVERT: K 327 MET cc_start: 0.6736 (mtm) cc_final: 0.5937 (tmm) outliers start: 46 outliers final: 36 residues processed: 303 average time/residue: 0.1543 time to fit residues: 77.2735 Evaluate side-chains 302 residues out of total 2832 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 264 time to evaluate : 1.032 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 56 VAL Chi-restraints excluded: chain B residue 46 CYS Chi-restraints excluded: chain B residue 280 ILE Chi-restraints excluded: chain C residue 5 LEU Chi-restraints excluded: chain C residue 26 ILE Chi-restraints excluded: chain C residue 33 GLU Chi-restraints excluded: chain C residue 201 MET Chi-restraints excluded: chain C residue 324 LEU Chi-restraints excluded: chain D residue 15 LEU Chi-restraints excluded: chain D residue 30 GLU Chi-restraints excluded: chain D residue 56 VAL Chi-restraints excluded: chain D residue 82 ILE Chi-restraints excluded: chain D residue 224 ARG Chi-restraints excluded: chain D residue 312 LEU Chi-restraints excluded: chain E residue 17 THR Chi-restraints excluded: chain E residue 46 CYS Chi-restraints excluded: chain E residue 127 GLU Chi-restraints excluded: chain F residue 46 CYS Chi-restraints excluded: chain F residue 82 ILE Chi-restraints excluded: chain F residue 112 GLU Chi-restraints excluded: chain F residue 160 VAL Chi-restraints excluded: chain F residue 324 LEU Chi-restraints excluded: chain G residue 179 THR Chi-restraints excluded: chain G residue 203 ASN Chi-restraints excluded: chain G residue 247 VAL Chi-restraints excluded: chain G residue 274 VAL Chi-restraints excluded: chain I residue 131 ASN Chi-restraints excluded: chain I residue 142 VAL Chi-restraints excluded: chain I residue 226 SER Chi-restraints excluded: chain I residue 312 LEU Chi-restraints excluded: chain K residue 133 ASN Chi-restraints excluded: chain K residue 154 LEU Chi-restraints excluded: chain K residue 263 SER Chi-restraints excluded: chain K residue 280 ILE Chi-restraints excluded: chain L residue 122 LYS Chi-restraints excluded: chain L residue 268 SER Chi-restraints excluded: chain L residue 275 ASN Chi-restraints excluded: chain L residue 317 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 259 optimal weight: 1.9990 chunk 143 optimal weight: 1.9990 chunk 91 optimal weight: 2.9990 chunk 300 optimal weight: 0.8980 chunk 55 optimal weight: 1.9990 chunk 294 optimal weight: 0.3980 chunk 123 optimal weight: 0.0570 chunk 23 optimal weight: 1.9990 chunk 87 optimal weight: 0.6980 chunk 132 optimal weight: 0.0870 chunk 166 optimal weight: 4.9990 overall best weight: 0.4276 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 90 GLN ** B 272 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 85 HIS E 81 ASN ** E 242 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 303 ASN ** K 300 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 = 0.3330 r_free = 0.3330 target = 0.095368 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3063 r_free = 0.3063 target = 0.079144 restraints weight = 48457.855| |-----------------------------------------------------------------------------| r_work (start): 0.3060 rms_B_bonded: 2.23 r_work: 0.2949 rms_B_bonded: 2.69 restraints_weight: 0.5000 r_work: 0.2811 rms_B_bonded: 4.47 restraints_weight: 0.2500 r_work (final): 0.2811 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8889 moved from start: 0.2529 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.044 27324 Z= 0.109 Angle : 0.529 9.522 36966 Z= 0.278 Chirality : 0.043 0.368 3966 Planarity : 0.004 0.063 4632 Dihedral : 7.407 56.945 3924 Min Nonbonded Distance : 1.932 Molprobity Statistics. All-atom Clashscore : 6.73 Ramachandran Plot: Outliers : 0.09 % Allowed : 3.75 % Favored : 96.16 % Rotamer: Outliers : 1.34 % Allowed : 15.15 % Favored : 83.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.76 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.07 (0.15), residues: 3174 helix: 0.78 (0.16), residues: 1116 sheet: -0.00 (0.21), residues: 570 loop : -0.40 (0.16), residues: 1488 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG K 135 TYR 0.022 0.001 TYR A 42 PHE 0.013 0.001 PHE A 106 TRP 0.023 0.001 TRP H 208 HIS 0.005 0.001 HIS C 57 Details of bonding type rmsd/Z covalent geometry : bond 0.00241 / 0.11 (27324) covalent geometry : angle 0.52950 / 0.28 (36966) hydrogen bonds : bond 0.03642 / 2.41 ( 973) hydrogen bonds : angle 4.80369 / 3.38 ( 2769) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5716.44 seconds wall clock time: 98 minutes 59.13 seconds (5939.13 seconds total)