Starting phenix.real_space_refine on Fri Mar 6 02:33:00 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9pqq_71788/03_2026/9pqq_71788.cif Found real_map, /net/cci-nas-00/data/ceres_data/9pqq_71788/03_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_71788/03_2026/9pqq_71788.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9pqq_71788/03_2026/9pqq_71788.map" model { file = "/net/cci-nas-00/data/ceres_data/9pqq_71788/03_2026/9pqq_71788.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9pqq_71788/03_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-5986/lib/python3.9/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: 6.23, per 1000 atoms: 0.23 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: 2.19 Conformation dependent library (CDL) restraints added in 965.6 milliseconds 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: 0.96 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: 5.19 Time building geometry restraints manager: 2.93 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=" N ARG H 224 " pdb=" CA ARG H 224 " ideal model delta sigma weight residual 1.455 1.490 -0.034 1.23e-02 6.61e+03 7.78e+00 bond pdb=" N ILE D 21 " pdb=" CA ILE D 21 " ideal model delta sigma weight residual 1.458 1.489 -0.031 1.24e-02 6.50e+03 6.22e+00 bond pdb=" N PHE K 223 " pdb=" CA PHE K 223 " ideal model delta sigma weight residual 1.457 1.488 -0.031 1.31e-02 5.83e+03 5.59e+00 bond pdb=" CA GLN B 90 " pdb=" CB GLN B 90 " ideal model delta sigma weight residual 1.531 1.604 -0.073 3.28e-02 9.30e+02 5.00e+00 bond pdb=" N ARG D 20 " pdb=" CA ARG D 20 " ideal model delta sigma weight residual 1.454 1.484 -0.030 1.42e-02 4.96e+03 4.56e+00 ... (remaining 27319 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.84: 36143 1.84 - 3.68: 717 3.68 - 5.52: 87 5.52 - 7.37: 15 7.37 - 9.21: 4 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 - 29.43: 15522 29.43 - 58.86: 837 58.86 - 88.29: 77 88.29 - 117.72: 9 117.72 - 147.15: 1 Dihedral angle restraints: 16446 sinusoidal: 7140 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=" O1A AGS L 401 " pdb=" O3A AGS L 401 " pdb=" PA AGS L 401 " pdb=" PB AGS L 401 " ideal model delta sinusoidal sigma weight residual -67.73 79.42 -147.15 1 3.00e+01 1.11e-03 1.96e+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 ... (remaining 16443 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.059: 3434 0.059 - 0.118: 510 0.118 - 0.176: 42 0.176 - 0.235: 3 0.235 - 0.294: 1 Chirality restraints: 3990 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=" CG LEU C 314 " pdb=" CB LEU C 314 " pdb=" CD1 LEU C 314 " pdb=" CD2 LEU C 314 " both_signs ideal model delta sigma weight residual False -2.59 -2.80 0.21 2.00e-01 2.50e+01 1.13e+00 chirality pdb=" CA ARG K 224 " pdb=" N ARG K 224 " pdb=" C ARG K 224 " pdb=" CB ARG K 224 " both_signs ideal model delta sigma weight residual False 2.51 2.72 -0.21 2.00e-01 2.50e+01 1.08e+00 ... (remaining 3987 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: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 5.780 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.470 Check model and map are aligned: 0.080 Set scattering table: 0.080 Process input model: 24.370 Find NCS groups from input model: 0.650 Set up NCS constraints: 0.050 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:1.310 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 32.810 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8565 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 : 0.003 0.073 27324 Z= 0.135 Angle : 0.615 9.207 36966 Z= 0.333 Chirality : 0.043 0.294 3990 Planarity : 0.005 0.126 4632 Dihedral : 16.656 147.147 10446 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 covalent geometry : bond 0.00288 (27324) covalent geometry : angle 0.61460 (36966) hydrogen bonds : bond 0.26596 ( 973) hydrogen bonds : angle 8.43478 ( 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 : 1.070 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: 0.1759 time to fit residues: 119.3931 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 : 1.033 ------------------------------------------------------------------------------- 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: 4.9990 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: 0.8980 chunk 207 optimal weight: 0.9980 chunk 155 optimal weight: 5.9990 chunk 244 optimal weight: 4.9990 chunk 183 optimal weight: 0.3980 chunk 298 optimal weight: 5.9990 overall best weight: 0.7182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 91 ASN B 92 ASN ** C 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 272 GLN ** 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 = 0.3320 r_free = 0.3320 target = 0.095057 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3031 r_free = 0.3031 target = 0.077450 restraints weight = 49820.034| |-----------------------------------------------------------------------------| r_work (start): 0.3032 rms_B_bonded: 2.60 r_work: 0.2904 rms_B_bonded: 3.12 restraints_weight: 0.5000 r_work (final): 0.2904 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8539 moved from start: 0.1251 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= 0.133 Angle : 0.591 9.295 36966 Z= 0.315 Chirality : 0.044 0.156 3990 Planarity : 0.004 0.046 4632 Dihedral : 10.379 144.676 3710 Min Nonbonded Distance : 1.914 Molprobity Statistics. All-atom Clashscore : 7.41 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.65 % Favored : 96.31 % Rotamer: Outliers : 1.20 % Allowed : 7.63 % Favored : 91.17 % 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: -0.22 (0.14), residues: 3174 helix: 0.09 (0.14), residues: 1176 sheet: 0.81 (0.23), residues: 510 loop : -0.58 (0.15), residues: 1488 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG D 123 TYR 0.021 0.001 TYR C 295 PHE 0.016 0.001 PHE K 195 TRP 0.019 0.001 TRP C 273 HIS 0.005 0.001 HIS C 85 Details of bonding type rmsd covalent geometry : bond 0.00286 (27324) covalent geometry : angle 0.59090 (36966) hydrogen bonds : bond 0.05177 ( 973) hydrogen bonds : angle 5.68785 ( 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 342 residues out of total 2832 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 308 time to evaluate : 1.043 Fit side-chains REVERT: A 297 ASP cc_start: 0.7932 (m-30) cc_final: 0.7282 (t0) REVERT: B 286 GLN cc_start: 0.8428 (tp40) cc_final: 0.8076 (tp40) REVERT: C 81 ASN cc_start: 0.8440 (t0) cc_final: 0.7931 (t0) REVERT: C 327 MET cc_start: 0.6197 (mtm) cc_final: 0.4737 (tpt) REVERT: D 30 GLU cc_start: 0.8144 (OUTLIER) cc_final: 0.7471 (mp0) REVERT: E 127 GLU cc_start: 0.8092 (OUTLIER) cc_final: 0.7408 (mp0) REVERT: H 201 MET cc_start: 0.8014 (ttt) cc_final: 0.7796 (ttt) REVERT: H 213 ARG cc_start: 0.8465 (mtp180) cc_final: 0.8003 (mtm-85) outliers start: 34 outliers final: 20 residues processed: 334 average time/residue: 0.1736 time to fit residues: 94.2356 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 : 1.086 ------------------------------------------------------------------------------- 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 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 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 232 SER Chi-restraints excluded: chain G residue 247 VAL Chi-restraints excluded: chain I residue 142 VAL Chi-restraints excluded: chain I residue 312 LEU Chi-restraints excluded: chain J residue 205 THR Chi-restraints excluded: chain J residue 226 SER Chi-restraints excluded: chain J residue 276 LYS Chi-restraints excluded: chain K residue 280 ILE Chi-restraints excluded: chain L residue 122 LYS Chi-restraints excluded: chain L residue 275 ASN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 196 optimal weight: 6.9990 chunk 67 optimal weight: 8.9990 chunk 187 optimal weight: 4.9990 chunk 153 optimal weight: 2.9990 chunk 142 optimal weight: 6.9990 chunk 184 optimal weight: 0.2980 chunk 97 optimal weight: 6.9990 chunk 89 optimal weight: 0.4980 chunk 94 optimal weight: 7.9990 chunk 292 optimal weight: 9.9990 chunk 250 optimal weight: 2.9990 overall best weight: 2.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 90 GLN B 91 ASN B 98 ASN B 246 GLN B 303 ASN C 203 ASN D 131 ASN F 316 ASN G 131 ASN G 303 ASN J 272 GLN K 131 ASN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3260 r_free = 0.3260 target = 0.091286 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2963 r_free = 0.2963 target = 0.073530 restraints weight = 50249.747| |-----------------------------------------------------------------------------| r_work (start): 0.2962 rms_B_bonded: 2.70 r_work: 0.2829 rms_B_bonded: 3.21 restraints_weight: 0.5000 r_work (final): 0.2829 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8594 moved from start: 0.1670 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.045 27324 Z= 0.209 Angle : 0.589 7.135 36966 Z= 0.309 Chirality : 0.045 0.161 3990 Planarity : 0.004 0.037 4632 Dihedral : 10.606 146.350 3708 Min Nonbonded Distance : 1.859 Molprobity Statistics. All-atom Clashscore : 7.59 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.69 % Favored : 96.28 % Rotamer: Outliers : 1.69 % Allowed : 10.17 % Favored : 88.14 % 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: -0.22 (0.14), residues: 3174 helix: 0.32 (0.15), residues: 1152 sheet: 0.32 (0.21), residues: 570 loop : -0.62 (0.16), residues: 1452 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG K 213 TYR 0.018 0.002 TYR E 42 PHE 0.026 0.001 PHE A 106 TRP 0.023 0.001 TRP C 273 HIS 0.005 0.001 HIS B 57 Details of bonding type rmsd covalent geometry : bond 0.00504 (27324) covalent geometry : angle 0.58879 (36966) hydrogen bonds : bond 0.04881 ( 973) hydrogen bonds : angle 5.33211 ( 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 328 residues out of total 2832 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 280 time to evaluate : 1.063 Fit side-chains revert: symmetry clash REVERT: A 297 ASP cc_start: 0.7903 (m-30) cc_final: 0.7317 (t0) REVERT: B 120 MET cc_start: 0.8414 (mpp) cc_final: 0.7950 (mmm) REVERT: B 286 GLN cc_start: 0.8569 (tp40) cc_final: 0.8210 (tp40) REVERT: B 297 ASP cc_start: 0.7883 (t0) cc_final: 0.7576 (t0) REVERT: E 127 GLU cc_start: 0.8155 (OUTLIER) cc_final: 0.7457 (mp0) REVERT: F 227 MET cc_start: 0.9156 (mtt) cc_final: 0.8873 (mtt) REVERT: H 273 TRP cc_start: 0.7226 (t60) cc_final: 0.6933 (t-100) REVERT: I 327 MET cc_start: 0.6887 (tpp) cc_final: 0.6174 (ttp) REVERT: J 139 MET cc_start: 0.8709 (mmm) cc_final: 0.8465 (mmm) outliers start: 48 outliers final: 31 residues processed: 314 average time/residue: 0.1591 time to fit residues: 82.6887 Evaluate side-chains 290 residues out of total 2832 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 258 time to evaluate : 1.039 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 56 VAL Chi-restraints excluded: chain A residue 239 ASP Chi-restraints excluded: chain A residue 282 GLU Chi-restraints excluded: chain B residue 46 CYS Chi-restraints excluded: chain B residue 70 THR Chi-restraints excluded: chain B residue 280 ILE Chi-restraints excluded: chain B residue 318 ILE Chi-restraints excluded: chain C residue 201 MET Chi-restraints excluded: chain C residue 203 ASN Chi-restraints excluded: chain D residue 30 GLU Chi-restraints excluded: chain D residue 312 LEU Chi-restraints excluded: chain D residue 327 MET 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 232 SER 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 226 SER 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 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: 1.9990 chunk 219 optimal weight: 0.9990 chunk 233 optimal weight: 8.9990 chunk 230 optimal weight: 0.6980 chunk 105 optimal weight: 2.9990 chunk 110 optimal weight: 0.6980 chunk 118 optimal weight: 1.9990 chunk 240 optimal weight: 0.9980 chunk 170 optimal weight: 7.9990 chunk 232 optimal weight: 10.0000 overall best weight: 1.0784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 90 GLN B 91 ASN B 303 ASN C 203 ASN D 255 GLN ** E 242 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 272 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 131 ASN G 303 ASN 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 = 0.3285 r_free = 0.3285 target = 0.092860 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2991 r_free = 0.2991 target = 0.075084 restraints weight = 49834.138| |-----------------------------------------------------------------------------| r_work (start): 0.2992 rms_B_bonded: 2.71 r_work: 0.2858 rms_B_bonded: 3.23 restraints_weight: 0.5000 r_work (final): 0.2858 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8559 moved from start: 0.1833 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 27324 Z= 0.123 Angle : 0.522 8.654 36966 Z= 0.274 Chirality : 0.043 0.177 3990 Planarity : 0.003 0.040 4632 Dihedral : 10.250 145.924 3708 Min Nonbonded Distance : 1.892 Molprobity Statistics. All-atom Clashscore : 6.64 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.56 % Favored : 96.41 % Rotamer: Outliers : 1.91 % Allowed : 11.55 % Favored : 86.55 % 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: -0.04 (0.15), residues: 3174 helix: 0.54 (0.15), residues: 1158 sheet: 0.27 (0.21), residues: 570 loop : -0.52 (0.16), residues: 1446 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG K 213 TYR 0.016 0.001 TYR E 42 PHE 0.019 0.001 PHE A 106 TRP 0.015 0.001 TRP I 273 HIS 0.005 0.001 HIS B 57 Details of bonding type rmsd covalent geometry : bond 0.00281 (27324) covalent geometry : angle 0.52208 (36966) hydrogen bonds : bond 0.03896 ( 973) hydrogen bonds : angle 5.04758 ( 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 337 residues out of total 2832 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 283 time to evaluate : 0.929 Fit side-chains revert: symmetry clash REVERT: A 297 ASP cc_start: 0.7905 (m-30) cc_final: 0.7299 (t0) REVERT: B 120 MET cc_start: 0.8414 (mpp) cc_final: 0.8053 (mmp) REVERT: B 286 GLN cc_start: 0.8473 (tp40) cc_final: 0.8175 (tp40) REVERT: B 297 ASP cc_start: 0.7911 (t0) cc_final: 0.7583 (t0) REVERT: C 327 MET cc_start: 0.6271 (mtm) cc_final: 0.4843 (tpt) REVERT: E 127 GLU cc_start: 0.8105 (OUTLIER) cc_final: 0.7412 (mp0) REVERT: E 139 MET cc_start: 0.9027 (mmt) cc_final: 0.8766 (mmm) REVERT: H 201 MET cc_start: 0.7946 (ttt) cc_final: 0.7725 (ttt) REVERT: J 275 ASN cc_start: 0.8597 (t0) cc_final: 0.8292 (t0) outliers start: 54 outliers final: 26 residues processed: 324 average time/residue: 0.1669 time to fit residues: 87.9947 Evaluate side-chains 286 residues out of total 2832 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 259 time to evaluate : 1.028 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 56 VAL 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 33 GLU Chi-restraints excluded: chain C residue 201 MET Chi-restraints excluded: chain C residue 324 LEU 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 I residue 131 ASN Chi-restraints excluded: chain I residue 142 VAL Chi-restraints excluded: chain I residue 312 LEU Chi-restraints excluded: chain J residue 226 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 234 optimal weight: 10.0000 chunk 145 optimal weight: 4.9990 chunk 89 optimal weight: 4.9990 chunk 118 optimal weight: 0.9990 chunk 94 optimal weight: 2.9990 chunk 100 optimal weight: 4.9990 chunk 36 optimal weight: 2.9990 chunk 296 optimal weight: 3.9990 chunk 87 optimal weight: 2.9990 chunk 154 optimal weight: 0.8980 chunk 56 optimal weight: 5.9990 overall best weight: 2.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 90 GLN B 303 ASN D 246 GLN E 81 ASN ** E 242 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 272 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 303 ASN K 131 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3255 r_free = 0.3255 target = 0.091045 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2958 r_free = 0.2958 target = 0.073309 restraints weight = 50172.159| |-----------------------------------------------------------------------------| r_work (start): 0.2956 rms_B_bonded: 2.70 r_work: 0.2825 rms_B_bonded: 3.18 restraints_weight: 0.5000 r_work (final): 0.2825 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8575 moved from start: 0.1988 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.043 27324 Z= 0.191 Angle : 0.551 9.436 36966 Z= 0.287 Chirality : 0.044 0.160 3990 Planarity : 0.004 0.035 4632 Dihedral : 10.413 146.760 3708 Min Nonbonded Distance : 1.874 Molprobity Statistics. All-atom Clashscore : 6.79 Ramachandran Plot: Outliers : 0.06 % Allowed : 4.00 % Favored : 95.94 % Rotamer: Outliers : 2.01 % Allowed : 12.64 % Favored : 85.35 % 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: 0.55 (0.15), residues: 1158 sheet: 0.17 (0.21), residues: 570 loop : -0.56 (0.16), residues: 1446 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG K 213 TYR 0.018 0.002 TYR E 42 PHE 0.014 0.001 PHE A 106 TRP 0.028 0.001 TRP H 208 HIS 0.005 0.001 HIS B 57 Details of bonding type rmsd covalent geometry : bond 0.00459 (27324) covalent geometry : angle 0.55109 (36966) hydrogen bonds : bond 0.04135 ( 973) hydrogen bonds : angle 5.02513 ( 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 329 residues out of total 2832 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 272 time to evaluate : 1.061 Fit side-chains revert: symmetry clash REVERT: A 297 ASP cc_start: 0.7884 (m-30) cc_final: 0.7309 (t0) REVERT: A 315 GLU cc_start: 0.8581 (mm-30) cc_final: 0.8043 (mp0) REVERT: B 120 MET cc_start: 0.8446 (mpp) cc_final: 0.7973 (mmm) REVERT: B 286 GLN cc_start: 0.8548 (tp40) cc_final: 0.8246 (tp40) REVERT: B 297 ASP cc_start: 0.7965 (t0) cc_final: 0.7633 (t0) REVERT: C 327 MET cc_start: 0.6409 (mtm) cc_final: 0.4971 (tpt) REVERT: D 83 MET cc_start: 0.8742 (tpt) cc_final: 0.8542 (tpt) REVERT: D 224 ARG cc_start: 0.7939 (OUTLIER) cc_final: 0.7059 (ptt90) REVERT: E 127 GLU cc_start: 0.8132 (OUTLIER) cc_final: 0.7448 (mp0) REVERT: E 139 MET cc_start: 0.9035 (mmt) cc_final: 0.8773 (mmm) REVERT: H 201 MET cc_start: 0.8079 (ttt) cc_final: 0.7846 (ttt) REVERT: H 273 TRP cc_start: 0.7070 (t60) cc_final: 0.6860 (t60) REVERT: I 327 MET cc_start: 0.6947 (tpp) cc_final: 0.6334 (ttp) REVERT: J 275 ASN cc_start: 0.8601 (t0) cc_final: 0.8259 (t0) outliers start: 57 outliers final: 39 residues processed: 312 average time/residue: 0.1562 time to fit residues: 80.9164 Evaluate side-chains 298 residues out of total 2832 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 257 time to evaluate : 1.017 ------------------------------------------------------------------------------- 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 70 THR 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 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 246 GLN Chi-restraints excluded: chain D residue 312 LEU Chi-restraints excluded: chain D residue 327 MET 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 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 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 J residue 146 ILE Chi-restraints excluded: chain J residue 226 SER 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 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: 2.9990 chunk 238 optimal weight: 4.9990 chunk 299 optimal weight: 3.9990 chunk 273 optimal weight: 3.9990 chunk 308 optimal weight: 5.9990 chunk 244 optimal weight: 3.9990 chunk 225 optimal weight: 0.7980 chunk 297 optimal weight: 0.8980 chunk 245 optimal weight: 0.7980 chunk 234 optimal weight: 7.9990 chunk 135 optimal weight: 8.9990 overall best weight: 1.8984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 90 GLN B 303 ASN ** E 242 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 272 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 131 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3254 r_free = 0.3254 target = 0.091072 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2957 r_free = 0.2957 target = 0.073299 restraints weight = 50228.659| |-----------------------------------------------------------------------------| r_work (start): 0.2959 rms_B_bonded: 2.71 r_work: 0.2826 rms_B_bonded: 3.20 restraints_weight: 0.5000 r_work (final): 0.2826 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8573 moved from start: 0.2066 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 27324 Z= 0.172 Angle : 0.531 9.953 36966 Z= 0.278 Chirality : 0.043 0.161 3990 Planarity : 0.004 0.038 4632 Dihedral : 10.311 146.341 3708 Min Nonbonded Distance : 1.880 Molprobity Statistics. All-atom Clashscore : 6.66 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.72 % Favored : 96.22 % Rotamer: Outliers : 2.33 % Allowed : 13.38 % Favored : 84.29 % 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: -0.01 (0.15), residues: 3174 helix: 0.66 (0.15), residues: 1122 sheet: 0.14 (0.21), residues: 570 loop : -0.48 (0.16), residues: 1482 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG K 213 TYR 0.019 0.001 TYR E 42 PHE 0.013 0.001 PHE A 106 TRP 0.016 0.001 TRP H 208 HIS 0.005 0.001 HIS B 57 Details of bonding type rmsd covalent geometry : bond 0.00411 (27324) covalent geometry : angle 0.53133 (36966) hydrogen bonds : bond 0.03920 ( 973) hydrogen bonds : angle 4.94563 ( 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 339 residues out of total 2832 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 273 time to evaluate : 1.093 Fit side-chains revert: symmetry clash REVERT: A 297 ASP cc_start: 0.7945 (m-30) cc_final: 0.7327 (t0) REVERT: A 315 GLU cc_start: 0.8589 (mm-30) cc_final: 0.8043 (mp0) REVERT: B 120 MET cc_start: 0.8466 (mpp) cc_final: 0.8104 (mmp) REVERT: B 286 GLN cc_start: 0.8531 (tp40) cc_final: 0.8242 (tp40) REVERT: B 297 ASP cc_start: 0.7967 (t0) cc_final: 0.7611 (t0) REVERT: D 224 ARG cc_start: 0.7926 (OUTLIER) cc_final: 0.7067 (ptt90) REVERT: E 127 GLU cc_start: 0.8114 (OUTLIER) cc_final: 0.7426 (mp0) REVERT: E 139 MET cc_start: 0.9031 (mmt) cc_final: 0.8752 (mmm) REVERT: E 314 LEU cc_start: 0.8421 (mt) cc_final: 0.8152 (mp) REVERT: H 178 GLU cc_start: 0.7809 (pm20) cc_final: 0.7583 (pm20) REVERT: H 201 MET cc_start: 0.8032 (ttt) cc_final: 0.7830 (ttt) REVERT: H 310 ASP cc_start: 0.8062 (OUTLIER) cc_final: 0.7840 (t0) REVERT: J 275 ASN cc_start: 0.8616 (t0) cc_final: 0.8263 (t0) outliers start: 66 outliers final: 41 residues processed: 322 average time/residue: 0.1672 time to fit residues: 88.5719 Evaluate side-chains 303 residues out of total 2832 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 259 time to evaluate : 1.023 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 56 VAL Chi-restraints excluded: chain A residue 225 LYS 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 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 D residue 327 MET 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 E residue 183 LYS 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 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 229 THR Chi-restraints excluded: chain H residue 310 ASP 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 J residue 226 SER 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: 0.9990 chunk 174 optimal weight: 3.9990 chunk 47 optimal weight: 0.9980 chunk 219 optimal weight: 3.9990 chunk 123 optimal weight: 8.9990 chunk 87 optimal weight: 2.9990 chunk 267 optimal weight: 6.9990 chunk 34 optimal weight: 2.9990 chunk 287 optimal weight: 5.9990 chunk 233 optimal weight: 6.9990 chunk 148 optimal weight: 4.9990 overall best weight: 2.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 90 GLN B 303 ASN ** E 242 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 272 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 131 ASN K 133 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3304 r_free = 0.3304 target = 0.093758 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3031 r_free = 0.3031 target = 0.077544 restraints weight = 49258.555| |-----------------------------------------------------------------------------| r_work (start): 0.3024 rms_B_bonded: 2.24 r_work: 0.2913 rms_B_bonded: 2.69 restraints_weight: 0.5000 r_work: 0.2774 rms_B_bonded: 4.48 restraints_weight: 0.2500 r_work (final): 0.2774 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8760 moved from start: 0.2168 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.046 27324 Z= 0.208 Angle : 0.558 8.994 36966 Z= 0.292 Chirality : 0.044 0.162 3990 Planarity : 0.004 0.041 4632 Dihedral : 10.401 146.676 3708 Min Nonbonded Distance : 1.878 Molprobity Statistics. All-atom Clashscore : 6.83 Ramachandran Plot: Outliers : 0.06 % Allowed : 4.32 % Favored : 95.62 % Rotamer: Outliers : 1.98 % Allowed : 14.62 % Favored : 83.40 % 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: -0.10 (0.14), residues: 3174 helix: 0.59 (0.15), residues: 1122 sheet: 0.05 (0.21), residues: 570 loop : -0.53 (0.16), residues: 1482 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG K 213 TYR 0.020 0.002 TYR E 42 PHE 0.012 0.001 PHE A 106 TRP 0.028 0.001 TRP H 208 HIS 0.005 0.001 HIS C 57 Details of bonding type rmsd covalent geometry : bond 0.00501 (27324) covalent geometry : angle 0.55756 (36966) hydrogen bonds : bond 0.04076 ( 973) hydrogen bonds : angle 4.97890 ( 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 322 residues out of total 2832 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 266 time to evaluate : 1.434 Fit side-chains revert: symmetry clash REVERT: A 297 ASP cc_start: 0.8081 (m-30) cc_final: 0.7483 (t0) REVERT: A 315 GLU cc_start: 0.8594 (mm-30) cc_final: 0.8142 (mp0) REVERT: B 120 MET cc_start: 0.8513 (mpp) cc_final: 0.8211 (mmp) REVERT: B 286 GLN cc_start: 0.8563 (tp40) cc_final: 0.8310 (tp40) REVERT: B 297 ASP cc_start: 0.8079 (t0) cc_final: 0.7720 (t0) REVERT: C 327 MET cc_start: 0.6324 (mtm) cc_final: 0.4890 (tpt) REVERT: D 224 ARG cc_start: 0.8086 (OUTLIER) cc_final: 0.7159 (ptt90) REVERT: E 127 GLU cc_start: 0.8163 (OUTLIER) cc_final: 0.7549 (mp0) REVERT: E 314 LEU cc_start: 0.8676 (mt) cc_final: 0.8407 (mp) REVERT: H 310 ASP cc_start: 0.8110 (OUTLIER) cc_final: 0.7905 (t0) REVERT: I 165 ASP cc_start: 0.7460 (m-30) cc_final: 0.7222 (m-30) REVERT: J 275 ASN cc_start: 0.8626 (t0) cc_final: 0.8332 (t0) REVERT: K 327 MET cc_start: 0.6854 (mtm) cc_final: 0.6154 (tmm) outliers start: 56 outliers final: 43 residues processed: 307 average time/residue: 0.1580 time to fit residues: 80.7396 Evaluate side-chains 303 residues out of total 2832 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 257 time to evaluate : 0.987 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 56 VAL Chi-restraints excluded: chain B residue 5 LEU 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 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 D residue 327 MET 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 E residue 183 LYS 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 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 H residue 229 THR Chi-restraints excluded: chain H residue 310 ASP 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 310 ASP 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: 1.9990 chunk 240 optimal weight: 0.9980 chunk 165 optimal weight: 4.9990 chunk 293 optimal weight: 4.9990 chunk 202 optimal weight: 3.9990 chunk 194 optimal weight: 4.9990 chunk 307 optimal weight: 0.9990 chunk 215 optimal weight: 0.7980 chunk 102 optimal weight: 1.9990 chunk 265 optimal weight: 2.9990 chunk 110 optimal weight: 1.9990 overall best weight: 1.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 90 GLN B 303 ASN D 246 GLN ** E 242 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 272 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3328 r_free = 0.3328 target = 0.095296 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3058 r_free = 0.3058 target = 0.079105 restraints weight = 49456.117| |-----------------------------------------------------------------------------| r_work (start): 0.3049 rms_B_bonded: 2.25 r_work: 0.2938 rms_B_bonded: 2.71 restraints_weight: 0.5000 r_work: 0.2799 rms_B_bonded: 4.51 restraints_weight: 0.2500 r_work (final): 0.2799 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8733 moved from start: 0.2227 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= 0.136 Angle : 0.515 8.993 36966 Z= 0.271 Chirality : 0.043 0.161 3990 Planarity : 0.004 0.039 4632 Dihedral : 10.167 146.672 3708 Min Nonbonded Distance : 1.907 Molprobity Statistics. All-atom Clashscore : 6.49 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.75 % Favored : 96.19 % Rotamer: Outliers : 1.87 % Allowed : 14.87 % Favored : 83.26 % 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: 0.06 (0.15), residues: 3174 helix: 0.75 (0.15), residues: 1116 sheet: 0.04 (0.21), residues: 570 loop : -0.42 (0.16), residues: 1488 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG K 213 TYR 0.017 0.001 TYR E 42 PHE 0.012 0.001 PHE A 106 TRP 0.023 0.001 TRP H 208 HIS 0.004 0.001 HIS C 57 Details of bonding type rmsd covalent geometry : bond 0.00322 (27324) covalent geometry : angle 0.51512 (36966) hydrogen bonds : bond 0.03623 ( 973) hydrogen bonds : angle 4.82738 ( 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 334 residues out of total 2832 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 281 time to evaluate : 0.957 Fit side-chains revert: symmetry clash REVERT: A 297 ASP cc_start: 0.8074 (m-30) cc_final: 0.7474 (t0) REVERT: A 315 GLU cc_start: 0.8578 (mm-30) cc_final: 0.8141 (mp0) REVERT: B 120 MET cc_start: 0.8506 (mpp) cc_final: 0.8195 (mmp) REVERT: B 286 GLN cc_start: 0.8483 (tp40) cc_final: 0.8274 (tp40) REVERT: B 297 ASP cc_start: 0.8084 (t0) cc_final: 0.7734 (t0) REVERT: C 327 MET cc_start: 0.6381 (mtm) cc_final: 0.4824 (tpt) REVERT: D 224 ARG cc_start: 0.8036 (OUTLIER) cc_final: 0.7131 (ptt90) REVERT: E 127 GLU cc_start: 0.8141 (OUTLIER) cc_final: 0.7554 (mp0) REVERT: E 139 MET cc_start: 0.9139 (mmt) cc_final: 0.8873 (mmm) REVERT: E 314 LEU cc_start: 0.8690 (mt) cc_final: 0.8314 (mp) REVERT: E 320 LYS cc_start: 0.8849 (ttmt) cc_final: 0.8649 (tttp) REVERT: G 248 LYS cc_start: 0.7801 (tppt) cc_final: 0.7015 (tptm) REVERT: H 310 ASP cc_start: 0.8077 (OUTLIER) cc_final: 0.7826 (t0) REVERT: I 165 ASP cc_start: 0.7459 (m-30) cc_final: 0.7232 (m-30) REVERT: J 275 ASN cc_start: 0.8622 (t0) cc_final: 0.8336 (t0) REVERT: K 327 MET cc_start: 0.6737 (mtm) cc_final: 0.6040 (tmm) outliers start: 53 outliers final: 40 residues processed: 318 average time/residue: 0.1671 time to fit residues: 87.4873 Evaluate side-chains 309 residues out of total 2832 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 266 time to evaluate : 1.093 ------------------------------------------------------------------------------- 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 83 MET 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 D residue 327 MET Chi-restraints excluded: chain E residue 46 CYS Chi-restraints excluded: chain E residue 127 GLU Chi-restraints excluded: chain E residue 183 LYS Chi-restraints excluded: chain F residue 9 ASN Chi-restraints excluded: chain F residue 46 CYS Chi-restraints excluded: chain F residue 56 VAL 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 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 H residue 229 THR Chi-restraints excluded: chain H residue 310 ASP 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 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 268 SER Chi-restraints excluded: chain L residue 275 ASN Chi-restraints excluded: chain L residue 317 THR 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: 8.9990 chunk 85 optimal weight: 0.9990 chunk 277 optimal weight: 0.7980 chunk 133 optimal weight: 5.9990 chunk 17 optimal weight: 5.9990 chunk 48 optimal weight: 2.9990 chunk 172 optimal weight: 0.9980 chunk 138 optimal weight: 6.9990 chunk 137 optimal weight: 0.9990 chunk 91 optimal weight: 4.9990 overall best weight: 1.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 242 ASN B 90 GLN B 303 ASN ** E 242 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 272 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 131 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3329 r_free = 0.3329 target = 0.095285 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3060 r_free = 0.3060 target = 0.079102 restraints weight = 49195.345| |-----------------------------------------------------------------------------| r_work (start): 0.3053 rms_B_bonded: 2.25 r_work: 0.2942 rms_B_bonded: 2.70 restraints_weight: 0.5000 r_work: 0.2804 rms_B_bonded: 4.49 restraints_weight: 0.2500 r_work (final): 0.2804 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8729 moved from start: 0.2285 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= 0.138 Angle : 0.517 8.970 36966 Z= 0.272 Chirality : 0.042 0.161 3990 Planarity : 0.004 0.046 4632 Dihedral : 10.114 147.236 3708 Min Nonbonded Distance : 1.911 Molprobity Statistics. All-atom Clashscore : 6.42 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.03 % Favored : 95.87 % Rotamer: Outliers : 1.77 % Allowed : 15.25 % Favored : 82.98 % 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: 0.77 (0.16), residues: 1122 sheet: 0.04 (0.21), residues: 570 loop : -0.39 (0.16), residues: 1482 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG K 213 TYR 0.017 0.001 TYR E 42 PHE 0.011 0.001 PHE A 106 TRP 0.019 0.001 TRP H 208 HIS 0.004 0.001 HIS C 57 Details of bonding type rmsd covalent geometry : bond 0.00326 (27324) covalent geometry : angle 0.51697 (36966) hydrogen bonds : bond 0.03555 ( 973) hydrogen bonds : angle 4.79176 ( 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: 50 poor density : 279 time to evaluate : 1.190 Fit side-chains revert: symmetry clash REVERT: A 297 ASP cc_start: 0.8088 (m-30) cc_final: 0.7480 (t0) REVERT: A 315 GLU cc_start: 0.8560 (mm-30) cc_final: 0.8130 (mp0) REVERT: B 120 MET cc_start: 0.8530 (mpp) cc_final: 0.8201 (mmp) REVERT: B 286 GLN cc_start: 0.8495 (tp40) cc_final: 0.8285 (tp40) REVERT: B 297 ASP cc_start: 0.8036 (t0) cc_final: 0.7664 (t0) REVERT: C 327 MET cc_start: 0.6365 (mtm) cc_final: 0.6140 (mtm) REVERT: D 224 ARG cc_start: 0.8023 (OUTLIER) cc_final: 0.7120 (ptt90) REVERT: E 127 GLU cc_start: 0.8106 (OUTLIER) cc_final: 0.7547 (mp0) REVERT: E 139 MET cc_start: 0.9139 (mmt) cc_final: 0.8876 (mmm) REVERT: E 314 LEU cc_start: 0.8707 (mt) cc_final: 0.8365 (mp) REVERT: G 248 LYS cc_start: 0.7818 (tppt) cc_final: 0.7025 (tptm) REVERT: H 310 ASP cc_start: 0.8070 (OUTLIER) cc_final: 0.7828 (t0) REVERT: I 165 ASP cc_start: 0.7471 (m-30) cc_final: 0.7241 (m-30) REVERT: J 275 ASN cc_start: 0.8615 (t0) cc_final: 0.8328 (t0) REVERT: K 327 MET cc_start: 0.6740 (mtm) cc_final: 0.6025 (tmm) outliers start: 50 outliers final: 40 residues processed: 313 average time/residue: 0.1630 time to fit residues: 85.1752 Evaluate side-chains 311 residues out of total 2832 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 268 time to evaluate : 1.112 ------------------------------------------------------------------------------- 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 83 MET 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 D residue 327 MET Chi-restraints excluded: chain E residue 46 CYS Chi-restraints excluded: chain E residue 127 GLU Chi-restraints excluded: chain E residue 183 LYS Chi-restraints excluded: chain F residue 9 ASN Chi-restraints excluded: chain F residue 46 CYS Chi-restraints excluded: chain F residue 56 VAL 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 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 H residue 229 THR Chi-restraints excluded: chain H residue 310 ASP 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 312 LEU Chi-restraints excluded: chain J residue 226 SER 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 38 optimal weight: 7.9990 chunk 66 optimal weight: 4.9990 chunk 136 optimal weight: 5.9990 chunk 172 optimal weight: 1.9990 chunk 233 optimal weight: 7.9990 chunk 157 optimal weight: 3.9990 chunk 129 optimal weight: 2.9990 chunk 21 optimal weight: 0.2980 chunk 56 optimal weight: 1.9990 chunk 228 optimal weight: 5.9990 chunk 300 optimal weight: 0.0980 overall best weight: 1.4786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 90 GLN B 303 ASN ** E 242 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 272 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 131 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3322 r_free = 0.3322 target = 0.094876 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3055 r_free = 0.3055 target = 0.078742 restraints weight = 49279.252| |-----------------------------------------------------------------------------| r_work (start): 0.3054 rms_B_bonded: 2.24 r_work: 0.2943 rms_B_bonded: 2.69 restraints_weight: 0.5000 r_work: 0.2805 rms_B_bonded: 4.48 restraints_weight: 0.2500 r_work (final): 0.2805 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8730 moved from start: 0.2322 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 27324 Z= 0.144 Angle : 0.522 9.284 36966 Z= 0.275 Chirality : 0.043 0.161 3990 Planarity : 0.004 0.049 4632 Dihedral : 10.095 147.302 3708 Min Nonbonded Distance : 1.908 Molprobity Statistics. All-atom Clashscore : 6.43 Ramachandran Plot: Outliers : 0.09 % Allowed : 3.94 % Favored : 95.97 % Rotamer: Outliers : 1.77 % Allowed : 15.57 % Favored : 82.66 % 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: 0.08 (0.15), residues: 3174 helix: 0.77 (0.16), residues: 1122 sheet: 0.01 (0.21), residues: 570 loop : -0.39 (0.16), residues: 1482 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG K 213 TYR 0.017 0.001 TYR E 42 PHE 0.012 0.001 PHE D 22 TRP 0.020 0.001 TRP H 208 HIS 0.005 0.001 HIS C 57 Details of bonding type rmsd covalent geometry : bond 0.00343 (27324) covalent geometry : angle 0.52249 (36966) hydrogen bonds : bond 0.03551 ( 973) hydrogen bonds : angle 4.78635 ( 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 322 residues out of total 2832 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 272 time to evaluate : 1.081 Fit side-chains revert: symmetry clash REVERT: A 297 ASP cc_start: 0.8103 (m-30) cc_final: 0.7479 (t0) REVERT: A 315 GLU cc_start: 0.8540 (mm-30) cc_final: 0.8118 (mp0) REVERT: B 120 MET cc_start: 0.8538 (mpp) cc_final: 0.8205 (mmp) REVERT: B 297 ASP cc_start: 0.8025 (t0) cc_final: 0.7668 (t0) REVERT: C 327 MET cc_start: 0.6380 (mtm) cc_final: 0.6161 (mtm) REVERT: D 224 ARG cc_start: 0.8031 (OUTLIER) cc_final: 0.7134 (ptt90) REVERT: E 127 GLU cc_start: 0.8081 (OUTLIER) cc_final: 0.7521 (mp0) REVERT: E 139 MET cc_start: 0.9137 (mmt) cc_final: 0.8879 (mmm) REVERT: E 314 LEU cc_start: 0.8734 (mt) cc_final: 0.8419 (mp) REVERT: F 140 GLU cc_start: 0.8021 (mt-10) cc_final: 0.7603 (mp0) REVERT: G 248 LYS cc_start: 0.7847 (tppt) cc_final: 0.7054 (tptm) REVERT: H 310 ASP cc_start: 0.8065 (OUTLIER) cc_final: 0.7844 (t0) REVERT: I 165 ASP cc_start: 0.7458 (m-30) cc_final: 0.7235 (m-30) REVERT: J 275 ASN cc_start: 0.8629 (t0) cc_final: 0.8350 (t0) REVERT: K 327 MET cc_start: 0.6709 (mtm) cc_final: 0.6044 (tmm) outliers start: 50 outliers final: 39 residues processed: 304 average time/residue: 0.1609 time to fit residues: 81.8123 Evaluate side-chains 311 residues out of total 2832 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 269 time to evaluate : 1.072 ------------------------------------------------------------------------------- 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 D residue 327 MET Chi-restraints excluded: chain E residue 46 CYS Chi-restraints excluded: chain E residue 127 GLU Chi-restraints excluded: chain E residue 183 LYS Chi-restraints excluded: chain F residue 9 ASN Chi-restraints excluded: chain F residue 46 CYS Chi-restraints excluded: chain F residue 56 VAL 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 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 H residue 229 THR Chi-restraints excluded: chain H residue 310 ASP 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 226 SER 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: 3.9990 chunk 91 optimal weight: 0.9990 chunk 300 optimal weight: 3.9990 chunk 55 optimal weight: 0.6980 chunk 294 optimal weight: 0.9980 chunk 123 optimal weight: 0.0170 chunk 23 optimal weight: 4.9990 chunk 87 optimal weight: 2.9990 chunk 132 optimal weight: 1.9990 chunk 166 optimal weight: 1.9990 overall best weight: 0.9422 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 90 GLN B 303 ASN D 6 GLN ** E 242 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 272 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 131 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 = 0.3347 r_free = 0.3347 target = 0.096424 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3080 r_free = 0.3080 target = 0.080207 restraints weight = 48679.867| |-----------------------------------------------------------------------------| r_work (start): 0.3073 rms_B_bonded: 2.24 r_work: 0.2962 rms_B_bonded: 2.70 restraints_weight: 0.5000 r_work: 0.2822 rms_B_bonded: 4.52 restraints_weight: 0.2500 r_work (final): 0.2822 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8712 moved from start: 0.2379 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 27324 Z= 0.113 Angle : 0.502 9.583 36966 Z= 0.264 Chirality : 0.042 0.162 3990 Planarity : 0.003 0.044 4632 Dihedral : 9.958 147.121 3708 Min Nonbonded Distance : 1.928 Molprobity Statistics. All-atom Clashscore : 6.30 Ramachandran Plot: Outliers : 0.09 % Allowed : 3.62 % Favored : 96.28 % Rotamer: Outliers : 1.59 % Allowed : 15.61 % Favored : 82.80 % 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: 0.12 (0.15), residues: 3174 helix: 0.81 (0.16), residues: 1134 sheet: 0.03 (0.21), residues: 570 loop : -0.37 (0.16), residues: 1470 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 0.012 0.001 PHE A 106 TRP 0.021 0.001 TRP H 208 HIS 0.004 0.001 HIS C 57 Details of bonding type rmsd covalent geometry : bond 0.00261 (27324) covalent geometry : angle 0.50193 (36966) hydrogen bonds : bond 0.03299 ( 973) hydrogen bonds : angle 4.70457 ( 2769) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5403.95 seconds wall clock time: 93 minutes 45.07 seconds (5625.07 seconds total)