Starting phenix.real_space_refine on Sun Jul 5 10:57:53 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9pqr_71789/07_2026/9pqr_71789.cif Found real_map, /net/cci-nas-00/data/ceres_data/9pqr_71789/07_2026/9pqr_71789.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.95 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9pqr_71789/07_2026/9pqr_71789.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9pqr_71789/07_2026/9pqr_71789.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9pqr_71789/07_2026/9pqr_71789.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9pqr_71789/07_2026/9pqr_71789.map" } resolution = 2.95 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 97 residue(s): 0.04s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 26754 Number of models: 1 Model: "" Number of chains: 24 Chain: "A" Number of atoms: 2674 Number of conformers: 1 Conformer: "" Number of residues, atoms: 326, 2674 Classifications: {'peptide': 326} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 315} Chain: "B" Number of atoms: 2674 Number of conformers: 1 Conformer: "" Number of residues, atoms: 326, 2674 Classifications: {'peptide': 326} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 315} Chain: "C" Number of atoms: 2674 Number of conformers: 1 Conformer: "" Number of residues, atoms: 326, 2674 Classifications: {'peptide': 326} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 315} Chain: "D" Number of atoms: 2674 Number of conformers: 1 Conformer: "" Number of residues, atoms: 326, 2674 Classifications: {'peptide': 326} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 315} Chain: "E" Number of atoms: 2674 Number of conformers: 1 Conformer: "" Number of residues, atoms: 326, 2674 Classifications: {'peptide': 326} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 315} Chain: "F" Number of atoms: 2674 Number of conformers: 1 Conformer: "" Number of residues, atoms: 326, 2674 Classifications: {'peptide': 326} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 315} Chain: "G" Number of atoms: 1720 Number of conformers: 1 Conformer: "" Number of residues, atoms: 207, 1720 Classifications: {'peptide': 207} Link IDs: {'PCIS': 1, 'PTRANS': 6, 'TRANS': 199} Chain: "H" Number of atoms: 1720 Number of conformers: 1 Conformer: "" Number of residues, atoms: 207, 1720 Classifications: {'peptide': 207} Link IDs: {'PCIS': 1, 'PTRANS': 6, 'TRANS': 199} Chain: "I" Number of atoms: 1720 Number of conformers: 1 Conformer: "" Number of residues, atoms: 207, 1720 Classifications: {'peptide': 207} Link IDs: {'PCIS': 1, 'PTRANS': 6, 'TRANS': 199} Chain: "J" Number of atoms: 1720 Number of conformers: 1 Conformer: "" Number of residues, atoms: 207, 1720 Classifications: {'peptide': 207} Link IDs: {'PCIS': 1, 'PTRANS': 6, 'TRANS': 199} Chain: "K" Number of atoms: 1720 Number of conformers: 1 Conformer: "" Number of residues, atoms: 207, 1720 Classifications: {'peptide': 207} Link IDs: {'PCIS': 1, 'PTRANS': 6, 'TRANS': 199} Chain: "L" Number of atoms: 1720 Number of conformers: 1 Conformer: "" Number of residues, atoms: 207, 1720 Classifications: {'peptide': 207} Link IDs: {'PCIS': 1, 'PTRANS': 6, 'TRANS': 199} Chain: "A" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 33 Unusual residues: {' MG': 2, 'AGS': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "B" Number of atoms: 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: "C" 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: "D" 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: "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: 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: "G" 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: "H" 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: "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: 6.50, per 1000 atoms: 0.24 Number of scatterers: 26754 At special positions: 0 Unit cell: (118.44, 113.4, 180.6, 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: 2.20 Conformation dependent library (CDL) restraints added in 1.3 seconds 6348 Ramachandran restraints generated. 3174 Oldfield, 0 Emsley, 3174 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6000 Finding SS restraints... Secondary structure from input PDB file: 134 helices and 49 sheets defined 43.4% alpha, 16.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.61 Creating SS restraints... Processing helix chain 'A' and resid 23 through 30 Processing helix chain 'A' and resid 33 through 38 removed outlier: 4.302A pdb=" N LYS A 37 " --> pdb=" O ARG A 34 " (cutoff:3.500A) 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 122 through 132 Processing helix chain 'A' and resid 133 through 140 Processing helix chain 'A' and resid 144 through 162 removed outlier: 3.691A pdb=" N VAL A 160 " --> pdb=" O ASN A 156 " (cutoff:3.500A) Processing helix chain 'A' and resid 182 through 196 removed outlier: 3.505A pdb=" N ALA A 191 " --> pdb=" O ALA A 187 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N ASN A 196 " --> pdb=" O GLU A 192 " (cutoff:3.500A) Processing helix chain 'A' and resid 224 through 228 Processing helix chain 'A' and resid 232 through 239 removed outlier: 3.576A pdb=" N ARG A 236 " --> pdb=" O SER A 232 " (cutoff:3.500A) Processing helix chain 'A' and resid 266 through 271 removed outlier: 3.665A pdb=" N PHE A 271 " --> pdb=" O PRO A 267 " (cutoff:3.500A) Processing helix chain 'A' and resid 285 through 294 removed outlier: 3.531A pdb=" N ARG A 292 " --> pdb=" O GLN A 288 " (cutoff:3.500A) Processing helix chain 'A' and resid 307 through 323 removed outlier: 3.512A pdb=" N ILE A 318 " --> pdb=" O LEU A 314 " (cutoff:3.500A) 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 72 through 78 removed outlier: 4.069A pdb=" N LEU B 76 " --> pdb=" O ASN B 72 " (cutoff:3.500A) Processing helix chain 'B' and resid 92 through 100 Processing helix chain 'B' and resid 110 through 114 Processing helix chain 'B' and resid 118 through 132 removed outlier: 3.850A pdb=" N GLU B 124 " --> pdb=" O MET B 120 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N LYS B 125 " --> pdb=" O GLU B 121 " (cutoff:3.500A) Processing helix chain 'B' and resid 133 through 140 Processing helix chain 'B' and resid 144 through 162 removed outlier: 3.724A pdb=" N VAL B 160 " --> pdb=" O ASN B 156 " (cutoff:3.500A) Processing helix chain 'B' and resid 182 through 195 Processing helix chain 'B' and resid 224 through 228 Processing helix chain 'B' and resid 232 through 239 Processing helix chain 'B' and resid 266 through 271 removed outlier: 3.720A pdb=" N PHE B 271 " --> pdb=" O PRO B 267 " (cutoff:3.500A) Processing helix chain 'B' and resid 285 through 294 removed outlier: 3.543A pdb=" N ARG B 292 " --> pdb=" O GLN B 288 " (cutoff:3.500A) Processing helix chain 'B' and resid 307 through 323 removed outlier: 3.686A pdb=" N ILE B 318 " --> pdb=" O LEU B 314 " (cutoff:3.500A) 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 118 through 132 removed outlier: 3.962A pdb=" N GLU C 124 " --> pdb=" O MET C 120 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N LYS C 125 " --> pdb=" O GLU C 121 " (cutoff:3.500A) Processing helix chain 'C' and resid 133 through 140 Processing helix chain 'C' and resid 144 through 162 removed outlier: 3.858A pdb=" N VAL C 160 " --> pdb=" O ASN C 156 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N GLN C 161 " --> pdb=" O ILE C 157 " (cutoff:3.500A) Processing helix chain 'C' and resid 182 through 195 removed outlier: 3.509A pdb=" N ALA C 191 " --> pdb=" O ALA C 187 " (cutoff:3.500A) Processing helix chain 'C' and resid 224 through 228 removed outlier: 3.797A pdb=" N LEU C 228 " --> pdb=" O LYS C 225 " (cutoff:3.500A) Processing helix chain 'C' and resid 231 through 239 removed outlier: 4.312A pdb=" N LEU C 235 " --> pdb=" O TRP C 231 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N ARG C 236 " --> pdb=" O SER C 232 " (cutoff:3.500A) Processing helix chain 'C' and resid 266 through 271 removed outlier: 3.789A pdb=" N PHE C 271 " --> pdb=" O PRO C 267 " (cutoff:3.500A) Processing helix chain 'C' and resid 285 through 293 Processing helix chain 'C' and resid 307 through 323 removed outlier: 3.692A pdb=" N ILE C 318 " --> pdb=" O LEU C 314 " (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 73 through 78 Processing helix chain 'D' and resid 92 through 100 Processing helix chain 'D' and resid 118 through 132 removed outlier: 3.919A pdb=" N GLU D 124 " --> pdb=" O MET D 120 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N LYS D 125 " --> pdb=" O GLU D 121 " (cutoff:3.500A) Processing helix chain 'D' and resid 133 through 140 Processing helix chain 'D' and resid 144 through 162 removed outlier: 3.713A pdb=" N VAL D 160 " --> pdb=" O ASN D 156 " (cutoff:3.500A) Processing helix chain 'D' and resid 182 through 195 Processing helix chain 'D' and resid 224 through 228 Processing helix chain 'D' and resid 232 through 239 removed outlier: 3.637A pdb=" N ARG D 236 " --> pdb=" O SER D 232 " (cutoff:3.500A) Processing helix chain 'D' and resid 266 through 271 removed outlier: 3.705A pdb=" N PHE D 271 " --> pdb=" O PRO D 267 " (cutoff:3.500A) Processing helix chain 'D' and resid 285 through 294 removed outlier: 3.561A pdb=" N ARG D 292 " --> pdb=" O GLN D 288 " (cutoff:3.500A) Processing helix chain 'D' and resid 307 through 323 removed outlier: 3.525A pdb=" N ILE D 318 " --> pdb=" O LEU D 314 " (cutoff:3.500A) Processing helix chain 'E' and resid 23 through 33 Processing helix chain 'E' and resid 72 through 78 removed outlier: 4.063A pdb=" N LEU E 76 " --> pdb=" O ASN E 72 " (cutoff:3.500A) Processing helix chain 'E' and resid 92 through 100 Processing helix chain 'E' and resid 110 through 114 removed outlier: 3.536A pdb=" N ALA E 114 " --> pdb=" O LYS E 111 " (cutoff:3.500A) Processing helix chain 'E' and resid 118 through 132 removed outlier: 4.106A pdb=" N GLU E 124 " --> pdb=" O MET E 120 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N LYS E 125 " --> pdb=" O GLU E 121 " (cutoff:3.500A) Processing helix chain 'E' and resid 133 through 140 Processing helix chain 'E' and resid 144 through 162 removed outlier: 3.501A pdb=" N LYS E 153 " --> pdb=" O ILE E 149 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N VAL E 160 " --> pdb=" O ASN E 156 " (cutoff:3.500A) Processing helix chain 'E' and resid 182 through 195 removed outlier: 3.527A pdb=" N ALA E 191 " --> pdb=" O ALA E 187 " (cutoff:3.500A) Processing helix chain 'E' and resid 224 through 228 Processing helix chain 'E' and resid 232 through 239 removed outlier: 3.656A pdb=" N ARG E 236 " --> pdb=" O SER E 232 " (cutoff:3.500A) Processing helix chain 'E' and resid 266 through 271 removed outlier: 3.735A pdb=" N PHE E 271 " --> pdb=" O PRO E 267 " (cutoff:3.500A) Processing helix chain 'E' and resid 285 through 294 removed outlier: 3.560A pdb=" N ARG E 292 " --> pdb=" O GLN E 288 " (cutoff:3.500A) Processing helix chain 'E' and resid 307 through 323 removed outlier: 3.646A pdb=" N ILE E 318 " --> pdb=" O LEU E 314 " (cutoff:3.500A) Processing helix chain 'F' and resid 23 through 35 Processing helix chain 'F' and resid 72 through 78 removed outlier: 3.579A pdb=" N LEU F 76 " --> pdb=" O ASN F 72 " (cutoff:3.500A) Processing helix chain 'F' and resid 92 through 100 Processing helix chain 'F' and resid 118 through 132 removed outlier: 3.851A pdb=" N GLU F 124 " --> pdb=" O MET F 120 " (cutoff:3.500A) Processing helix chain 'F' and resid 133 through 140 removed outlier: 3.708A pdb=" N MET F 139 " --> pdb=" O ARG F 135 " (cutoff:3.500A) Processing helix chain 'F' and resid 144 through 161 removed outlier: 3.831A pdb=" N VAL F 160 " --> pdb=" O ASN F 156 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N GLN F 161 " --> pdb=" O ILE F 157 " (cutoff:3.500A) Processing helix chain 'F' and resid 182 through 195 removed outlier: 3.558A pdb=" N ALA F 191 " --> pdb=" O ALA F 187 " (cutoff:3.500A) Processing helix chain 'F' and resid 224 through 228 Processing helix chain 'F' and resid 232 through 239 removed outlier: 3.718A pdb=" N ARG F 236 " --> pdb=" O SER F 232 " (cutoff:3.500A) Processing helix chain 'F' and resid 266 through 271 removed outlier: 3.874A pdb=" N PHE F 271 " --> pdb=" O PRO F 267 " (cutoff:3.500A) Processing helix chain 'F' and resid 285 through 293 Processing helix chain 'F' and resid 307 through 323 removed outlier: 3.713A pdb=" N ILE F 318 " --> pdb=" O LEU F 314 " (cutoff:3.500A) Processing helix chain 'G' and resid 122 through 132 removed outlier: 3.538A pdb=" N ALA G 126 " --> pdb=" O LYS G 122 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N GLU G 127 " --> pdb=" O ARG G 123 " (cutoff:3.500A) Processing helix chain 'G' and resid 133 through 140 Processing helix chain 'G' and resid 144 through 162 removed outlier: 3.775A pdb=" N VAL G 160 " --> pdb=" O ASN G 156 " (cutoff:3.500A) Processing helix chain 'G' and resid 182 through 195 Processing helix chain 'G' and resid 224 through 228 Processing helix chain 'G' and resid 232 through 238 removed outlier: 3.835A pdb=" N ARG G 236 " --> pdb=" O SER G 232 " (cutoff:3.500A) Processing helix chain 'G' and resid 266 through 272 removed outlier: 3.851A 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: 3.581A pdb=" N LEU G 314 " --> pdb=" O ASP G 310 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N GLU G 315 " --> pdb=" O GLN G 311 " (cutoff:3.500A) Processing helix chain 'H' and resid 122 through 132 removed outlier: 3.553A pdb=" N ALA H 126 " --> pdb=" O LYS H 122 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N GLU H 127 " --> pdb=" O ARG H 123 " (cutoff:3.500A) Processing helix chain 'H' and resid 133 through 141 removed outlier: 3.537A pdb=" N GLU H 140 " --> pdb=" O GLU H 136 " (cutoff:3.500A) Processing helix chain 'H' and resid 144 through 162 removed outlier: 3.738A pdb=" N VAL H 160 " --> pdb=" O ASN H 156 " (cutoff:3.500A) Processing helix chain 'H' and resid 182 through 195 removed outlier: 3.544A 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: 3.769A pdb=" N ARG H 236 " --> pdb=" O SER H 232 " (cutoff:3.500A) Processing helix chain 'H' and resid 266 through 272 removed outlier: 3.857A pdb=" N PHE H 271 " --> pdb=" O PRO H 267 " (cutoff:3.500A) Processing helix chain 'H' and resid 285 through 293 Processing helix chain 'H' and resid 307 through 323 removed outlier: 3.813A pdb=" N ILE H 318 " --> pdb=" O LEU H 314 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N ARG H 319 " --> pdb=" O GLU H 315 " (cutoff:3.500A) Processing helix chain 'I' and resid 122 through 132 removed outlier: 3.562A pdb=" N ALA I 126 " --> pdb=" O LYS I 122 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N GLU I 127 " --> pdb=" O ARG I 123 " (cutoff:3.500A) Processing helix chain 'I' and resid 133 through 140 Processing helix chain 'I' and resid 144 through 162 removed outlier: 3.738A pdb=" N VAL I 160 " --> pdb=" O ASN I 156 " (cutoff:3.500A) Processing helix chain 'I' and resid 182 through 194 removed outlier: 3.502A pdb=" N ALA I 191 " --> pdb=" O ALA I 187 " (cutoff:3.500A) Processing helix chain 'I' and resid 224 through 228 Processing helix chain 'I' and resid 232 through 238 removed outlier: 3.743A pdb=" N ARG I 236 " --> pdb=" O SER I 232 " (cutoff:3.500A) Processing helix chain 'I' and resid 266 through 272 removed outlier: 3.667A pdb=" N PHE I 271 " --> pdb=" O PRO I 267 " (cutoff:3.500A) Processing helix chain 'I' and resid 285 through 293 Processing helix chain 'I' and resid 307 through 323 removed outlier: 3.729A pdb=" N ILE I 318 " --> pdb=" O LEU I 314 " (cutoff:3.500A) Processing helix chain 'J' and resid 122 through 132 removed outlier: 3.620A pdb=" N ALA J 126 " --> pdb=" O LYS J 122 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N GLU J 127 " --> pdb=" O ARG J 123 " (cutoff:3.500A) Processing helix chain 'J' and resid 133 through 140 Processing helix chain 'J' and resid 144 through 162 removed outlier: 3.521A pdb=" N ILE J 149 " --> pdb=" O ALA J 145 " (cutoff:3.500A) removed outlier: 3.698A 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 224 through 228 Processing helix chain 'J' and resid 232 through 238 removed outlier: 3.733A pdb=" N ARG J 236 " --> pdb=" O SER J 232 " (cutoff:3.500A) Processing helix chain 'J' and resid 266 through 272 removed outlier: 3.835A pdb=" N PHE J 271 " --> pdb=" O PRO J 267 " (cutoff:3.500A) Processing helix chain 'J' and resid 285 through 293 Processing helix chain 'J' and resid 307 through 323 Processing helix chain 'K' and resid 122 through 132 removed outlier: 3.669A pdb=" N ALA K 126 " --> pdb=" O LYS K 122 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N GLU K 127 " --> pdb=" O ARG K 123 " (cutoff:3.500A) Processing helix chain 'K' and resid 133 through 140 Processing helix chain 'K' and resid 144 through 162 removed outlier: 3.773A pdb=" N VAL K 160 " --> pdb=" O ASN K 156 " (cutoff:3.500A) Processing helix chain 'K' and resid 182 through 196 removed outlier: 3.532A pdb=" N ALA K 187 " --> pdb=" O LYS K 183 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N ALA K 191 " --> pdb=" O ALA K 187 " (cutoff:3.500A) removed outlier: 3.846A pdb=" N ASN K 196 " --> pdb=" O GLU K 192 " (cutoff:3.500A) Processing helix chain 'K' and resid 224 through 228 Processing helix chain 'K' and resid 232 through 238 removed outlier: 3.555A pdb=" N ARG K 236 " --> pdb=" O SER K 232 " (cutoff:3.500A) Processing helix chain 'K' and resid 266 through 271 removed outlier: 3.632A pdb=" N PHE K 271 " --> pdb=" O PRO K 267 " (cutoff:3.500A) Processing helix chain 'K' and resid 285 through 293 Processing helix chain 'K' and resid 307 through 323 removed outlier: 3.627A pdb=" N LEU K 314 " --> pdb=" O ASP K 310 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N GLU K 315 " --> pdb=" O GLN K 311 " (cutoff:3.500A) Processing helix chain 'L' and resid 122 through 132 removed outlier: 3.708A pdb=" N ALA L 126 " --> pdb=" O LYS L 122 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N GLU L 127 " --> pdb=" O ARG L 123 " (cutoff:3.500A) Processing helix chain 'L' and resid 133 through 140 Processing helix chain 'L' and resid 144 through 162 removed outlier: 3.765A pdb=" N VAL L 160 " --> pdb=" O ASN L 156 " (cutoff:3.500A) Processing helix chain 'L' and resid 182 through 194 removed outlier: 3.540A pdb=" N ALA L 191 " --> pdb=" O ALA L 187 " (cutoff:3.500A) Processing helix chain 'L' and resid 224 through 228 removed outlier: 3.571A pdb=" N LEU L 228 " --> pdb=" O LYS L 225 " (cutoff:3.500A) Processing helix chain 'L' and resid 232 through 238 removed outlier: 3.726A pdb=" N ARG L 236 " --> pdb=" O SER L 232 " (cutoff:3.500A) Processing helix chain 'L' and resid 266 through 272 removed outlier: 3.763A pdb=" N PHE L 271 " --> pdb=" O PRO L 267 " (cutoff:3.500A) Processing helix chain 'L' and resid 285 through 294 Processing helix chain 'L' and resid 307 through 323 removed outlier: 3.518A 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: 9.708A pdb=" N GLN A 6 " --> pdb=" O ASN A 66 " (cutoff:3.500A) removed outlier: 11.684A pdb=" N ASN A 66 " --> pdb=" O GLN A 6 " (cutoff:3.500A) removed outlier: 6.227A pdb=" N LYS A 8 " --> pdb=" O CYS A 64 " (cutoff:3.500A) removed outlier: 6.871A pdb=" N HIS A 57 " --> pdb=" O LYS A 47 " (cutoff:3.500A) removed outlier: 4.869A pdb=" N LYS A 47 " --> pdb=" O HIS A 57 " (cutoff:3.500A) removed outlier: 6.670A pdb=" N HIS A 59 " --> pdb=" O ALA A 45 " (cutoff:3.500A) removed outlier: 4.299A pdb=" N ALA A 45 " --> pdb=" O HIS A 59 " (cutoff:3.500A) removed outlier: 6.620A pdb=" N LEU A 61 " --> pdb=" O ALA A 43 " (cutoff:3.500A) removed outlier: 4.300A pdb=" N ALA A 43 " --> pdb=" O LEU A 61 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N CYS A 63 " --> pdb=" O LYS A 41 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 199 through 201 removed outlier: 6.417A pdb=" N TRP A 200 " --> pdb=" O ILE A 219 " (cutoff:3.500A) removed outlier: 7.294A pdb=" N ASP A 221 " --> pdb=" O TRP A 200 " (cutoff:3.500A) removed outlier: 6.261A pdb=" N LEU A 171 " --> pdb=" O ILE A 259 " (cutoff:3.500A) removed outlier: 7.611A pdb=" N VAL A 261 " --> pdb=" O LEU A 171 " (cutoff:3.500A) removed outlier: 6.486A pdb=" N LEU A 173 " --> pdb=" O VAL A 261 " (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: 9.686A pdb=" N GLN B 6 " --> pdb=" O ASN B 66 " (cutoff:3.500A) removed outlier: 11.759A pdb=" N ASN B 66 " --> pdb=" O GLN B 6 " (cutoff:3.500A) removed outlier: 6.204A pdb=" N LYS B 8 " --> pdb=" O CYS B 64 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N CYS B 64 " --> pdb=" O LYS B 8 " (cutoff:3.500A) removed outlier: 6.685A pdb=" N HIS B 57 " --> pdb=" O LYS B 47 " (cutoff:3.500A) removed outlier: 4.732A pdb=" N LYS B 47 " --> pdb=" O HIS B 57 " (cutoff:3.500A) removed outlier: 6.580A pdb=" N HIS B 59 " --> pdb=" O ALA B 45 " (cutoff:3.500A) removed outlier: 4.216A pdb=" N ALA B 45 " --> pdb=" O HIS B 59 " (cutoff:3.500A) removed outlier: 6.633A pdb=" N LEU B 61 " --> pdb=" O ALA B 43 " (cutoff:3.500A) removed outlier: 4.131A pdb=" N ALA B 43 " --> pdb=" O LEU B 61 " (cutoff:3.500A) removed outlier: 6.745A pdb=" N CYS B 63 " --> pdb=" O LYS B 41 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 199 through 201 removed outlier: 6.425A pdb=" N TRP B 200 " --> pdb=" O ILE B 219 " (cutoff:3.500A) removed outlier: 7.283A pdb=" N ASP B 221 " --> pdb=" O TRP B 200 " (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 Processing sheet with id=AA9, first strand: chain 'C' and resid 6 through 14 removed outlier: 9.729A pdb=" N GLN C 6 " --> pdb=" O ASN C 66 " (cutoff:3.500A) removed outlier: 11.689A pdb=" N ASN C 66 " --> pdb=" O GLN C 6 " (cutoff:3.500A) removed outlier: 5.864A pdb=" N LYS C 8 " --> pdb=" O CYS C 64 " (cutoff:3.500A) removed outlier: 6.682A pdb=" N HIS C 57 " --> pdb=" O LYS C 47 " (cutoff:3.500A) removed outlier: 4.780A pdb=" N LYS C 47 " --> pdb=" O HIS C 57 " (cutoff:3.500A) removed outlier: 6.596A pdb=" N HIS C 59 " --> pdb=" O ALA C 45 " (cutoff:3.500A) removed outlier: 4.264A pdb=" N ALA C 45 " --> pdb=" O HIS C 59 " (cutoff:3.500A) removed outlier: 6.597A pdb=" N LEU C 61 " --> pdb=" O ALA C 43 " (cutoff:3.500A) removed outlier: 4.269A pdb=" N ALA C 43 " --> pdb=" O LEU C 61 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N CYS C 63 " --> pdb=" O LYS C 41 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 199 through 201 removed outlier: 6.342A pdb=" N TRP C 200 " --> pdb=" O ILE C 219 " (cutoff:3.500A) removed outlier: 7.051A pdb=" N ASP C 221 " --> pdb=" O TRP C 200 " (cutoff:3.500A) removed outlier: 8.227A pdb=" N TYR C 302 " --> pdb=" O ILE C 172 " (cutoff:3.500A) removed outlier: 6.709A pdb=" N TRP C 174 " --> pdb=" O TYR C 302 " (cutoff:3.500A) removed outlier: 7.599A pdb=" N PHE C 304 " --> pdb=" O TRP C 174 " (cutoff:3.500A) removed outlier: 6.873A pdb=" N LYS C 176 " --> pdb=" O PHE C 304 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 244 through 247 removed outlier: 3.513A pdb=" N GLY C 250 " --> pdb=" O VAL C 247 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 273 through 274 Processing sheet with id=AB4, first strand: chain 'C' and resid 294 through 295 removed outlier: 3.525A pdb=" N GLU C 298 " --> pdb=" O TYR C 295 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'D' and resid 6 through 14 removed outlier: 9.761A pdb=" N GLN D 6 " --> pdb=" O ASN D 66 " (cutoff:3.500A) removed outlier: 11.758A pdb=" N ASN D 66 " --> pdb=" O GLN D 6 " (cutoff:3.500A) removed outlier: 6.428A pdb=" N LYS D 8 " --> pdb=" O CYS D 64 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N CYS D 64 " --> pdb=" O LYS D 8 " (cutoff:3.500A) removed outlier: 6.119A pdb=" N GLU D 65 " --> pdb=" O VAL D 40 " (cutoff:3.500A) removed outlier: 8.319A pdb=" N VAL D 40 " --> pdb=" O GLU D 65 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'D' and resid 199 through 201 removed outlier: 6.467A pdb=" N TRP D 200 " --> pdb=" O ILE D 219 " (cutoff:3.500A) removed outlier: 7.356A pdb=" N ASP D 221 " --> pdb=" O TRP D 200 " (cutoff:3.500A) removed outlier: 6.227A pdb=" N LEU D 171 " --> pdb=" O ILE D 259 " (cutoff:3.500A) removed outlier: 7.481A pdb=" N VAL D 261 " --> pdb=" O LEU D 171 " (cutoff:3.500A) removed outlier: 6.464A pdb=" N LEU D 173 " --> pdb=" O VAL D 261 " (cutoff:3.500A) removed outlier: 8.264A pdb=" N TYR D 302 " --> pdb=" O ILE D 172 " (cutoff:3.500A) removed outlier: 6.724A pdb=" N TRP D 174 " --> pdb=" O TYR D 302 " (cutoff:3.500A) removed outlier: 7.614A pdb=" N PHE D 304 " --> pdb=" O TRP D 174 " (cutoff:3.500A) removed outlier: 6.989A pdb=" N LYS D 176 " --> pdb=" O PHE D 304 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'D' and resid 244 through 247 Processing sheet with id=AB8, first strand: chain 'D' and resid 273 through 274 Processing sheet with id=AB9, first strand: chain 'E' and resid 6 through 14 removed outlier: 9.635A pdb=" N GLN E 6 " --> pdb=" O ASN E 66 " (cutoff:3.500A) removed outlier: 11.693A pdb=" N ASN E 66 " --> pdb=" O GLN E 6 " (cutoff:3.500A) removed outlier: 5.985A pdb=" N LYS E 8 " --> pdb=" O CYS E 64 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N CYS E 63 " --> pdb=" O TYR E 42 " (cutoff:3.500A) removed outlier: 4.724A pdb=" N TYR E 42 " --> pdb=" O CYS E 63 " (cutoff:3.500A) removed outlier: 6.160A pdb=" N GLU E 65 " --> pdb=" O VAL E 40 " (cutoff:3.500A) removed outlier: 7.746A pdb=" N VAL E 40 " --> pdb=" O GLU E 65 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'E' and resid 199 through 201 removed outlier: 6.499A pdb=" N TRP E 200 " --> pdb=" O ILE E 219 " (cutoff:3.500A) removed outlier: 7.403A pdb=" N ASP E 221 " --> pdb=" O TRP E 200 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'E' and resid 244 through 247 removed outlier: 3.543A pdb=" N GLY E 250 " --> pdb=" O VAL E 247 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'E' and resid 273 through 274 Processing sheet with id=AC4, first strand: chain 'F' and resid 7 through 16 removed outlier: 5.579A pdb=" N LYS F 8 " --> pdb=" O CYS F 64 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N ASP F 16 " --> pdb=" O VAL F 56 " (cutoff:3.500A) removed outlier: 4.395A pdb=" N VAL F 56 " --> pdb=" O ASP F 16 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N TYR F 42 " --> pdb=" O CYS F 63 " (cutoff:3.500A) removed outlier: 6.624A pdb=" N GLU F 65 " --> pdb=" O VAL F 40 " (cutoff:3.500A) removed outlier: 8.699A pdb=" N VAL F 40 " --> pdb=" O GLU F 65 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'F' and resid 199 through 201 removed outlier: 6.481A pdb=" N TRP F 200 " --> pdb=" O ILE F 219 " (cutoff:3.500A) removed outlier: 7.098A pdb=" N ASP F 221 " --> pdb=" O TRP F 200 " (cutoff:3.500A) removed outlier: 8.149A pdb=" N TYR F 302 " --> pdb=" O ILE F 172 " (cutoff:3.500A) removed outlier: 6.560A pdb=" N TRP F 174 " --> pdb=" O TYR F 302 " (cutoff:3.500A) removed outlier: 7.509A pdb=" N PHE F 304 " --> pdb=" O TRP F 174 " (cutoff:3.500A) removed outlier: 6.729A pdb=" N LYS F 176 " --> pdb=" O PHE F 304 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'F' and resid 244 through 247 Processing sheet with id=AC7, first strand: chain 'F' and resid 273 through 274 Processing sheet with id=AC8, first strand: chain 'F' and resid 294 through 295 removed outlier: 3.672A pdb=" N GLU F 298 " --> pdb=" O TYR F 295 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'G' and resid 199 through 201 removed outlier: 6.269A pdb=" N TRP G 200 " --> pdb=" O ILE G 219 " (cutoff:3.500A) removed outlier: 7.092A pdb=" N ASP G 221 " --> pdb=" O TRP G 200 " (cutoff:3.500A) removed outlier: 6.504A pdb=" N LEU G 171 " --> pdb=" O ILE G 259 " (cutoff:3.500A) removed outlier: 7.867A pdb=" N VAL G 261 " --> pdb=" O LEU G 171 " (cutoff:3.500A) removed outlier: 6.448A pdb=" N LEU G 173 " --> pdb=" O VAL G 261 " (cutoff:3.500A) removed outlier: 8.326A pdb=" N TYR G 302 " --> pdb=" O ILE G 172 " (cutoff:3.500A) removed outlier: 6.411A pdb=" N TRP G 174 " --> pdb=" O TYR G 302 " (cutoff:3.500A) removed outlier: 7.456A pdb=" N PHE G 304 " --> pdb=" O TRP G 174 " (cutoff:3.500A) removed outlier: 6.704A pdb=" N LYS G 176 " --> pdb=" O PHE G 304 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'G' and resid 244 through 247 Processing sheet with id=AD2, first strand: chain 'G' and resid 273 through 274 Processing sheet with id=AD3, first strand: chain 'G' and resid 294 through 295 removed outlier: 3.616A pdb=" N GLU G 298 " --> pdb=" O TYR G 295 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'H' and resid 199 through 201 removed outlier: 6.278A pdb=" N TRP H 200 " --> pdb=" O ILE H 219 " (cutoff:3.500A) removed outlier: 7.184A pdb=" N ASP H 221 " --> pdb=" O TRP H 200 " (cutoff:3.500A) removed outlier: 8.276A pdb=" N TYR H 302 " --> pdb=" O ILE H 172 " (cutoff:3.500A) removed outlier: 6.420A pdb=" N TRP H 174 " --> pdb=" O TYR H 302 " (cutoff:3.500A) removed outlier: 7.417A pdb=" N PHE H 304 " --> pdb=" O TRP H 174 " (cutoff:3.500A) removed outlier: 6.630A pdb=" N LYS H 176 " --> pdb=" O PHE H 304 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'H' and resid 244 through 247 Processing sheet with id=AD6, first strand: chain 'H' and resid 273 through 274 Processing sheet with id=AD7, first strand: chain 'H' and resid 294 through 295 removed outlier: 3.587A pdb=" N GLU H 298 " --> pdb=" O TYR H 295 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'I' and resid 199 through 201 removed outlier: 6.259A pdb=" N TRP I 200 " --> pdb=" O ILE I 219 " (cutoff:3.500A) removed outlier: 7.024A pdb=" N ASP I 221 " --> pdb=" O TRP I 200 " (cutoff:3.500A) removed outlier: 6.549A pdb=" N LEU I 171 " --> pdb=" O ILE I 259 " (cutoff:3.500A) removed outlier: 7.898A pdb=" N VAL I 261 " --> pdb=" O LEU I 171 " (cutoff:3.500A) removed outlier: 6.504A pdb=" N LEU I 173 " --> pdb=" O VAL I 261 " (cutoff:3.500A) removed outlier: 8.270A pdb=" N TYR I 302 " --> pdb=" O ILE I 172 " (cutoff:3.500A) removed outlier: 6.431A pdb=" N TRP I 174 " --> pdb=" O TYR I 302 " (cutoff:3.500A) removed outlier: 7.442A pdb=" N PHE I 304 " --> pdb=" O TRP I 174 " (cutoff:3.500A) removed outlier: 6.730A pdb=" N LYS I 176 " --> pdb=" O PHE I 304 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'I' and resid 244 through 247 removed outlier: 3.509A pdb=" N VAL I 247 " --> pdb=" O GLY I 250 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N GLY I 250 " --> pdb=" O VAL I 247 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'I' and resid 273 through 274 Processing sheet with id=AE2, first strand: chain 'I' and resid 294 through 295 removed outlier: 3.784A pdb=" N GLU I 298 " --> pdb=" O TYR I 295 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'J' and resid 199 through 201 removed outlier: 6.296A pdb=" N TRP J 200 " --> pdb=" O ILE J 219 " (cutoff:3.500A) removed outlier: 7.088A pdb=" N ASP J 221 " --> pdb=" O TRP J 200 " (cutoff:3.500A) removed outlier: 8.288A pdb=" N TYR J 302 " --> pdb=" O ILE J 172 " (cutoff:3.500A) removed outlier: 6.410A pdb=" N TRP J 174 " --> pdb=" O TYR J 302 " (cutoff:3.500A) removed outlier: 7.425A pdb=" N PHE J 304 " --> pdb=" O TRP J 174 " (cutoff:3.500A) removed outlier: 6.649A pdb=" N LYS J 176 " --> pdb=" O PHE J 304 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'J' and resid 244 through 247 Processing sheet with id=AE5, first strand: chain 'J' and resid 273 through 274 Processing sheet with id=AE6, first strand: chain 'J' and resid 294 through 295 removed outlier: 3.543A pdb=" N GLU J 298 " --> pdb=" O TYR J 295 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'K' and resid 199 through 201 removed outlier: 6.344A pdb=" N TRP K 200 " --> pdb=" O ILE K 219 " (cutoff:3.500A) removed outlier: 7.191A pdb=" N ASP K 221 " --> pdb=" O TRP K 200 " (cutoff:3.500A) removed outlier: 8.248A pdb=" N TYR K 302 " --> pdb=" O ILE K 172 " (cutoff:3.500A) removed outlier: 6.412A pdb=" N TRP K 174 " --> pdb=" O TYR K 302 " (cutoff:3.500A) removed outlier: 7.423A pdb=" N PHE K 304 " --> pdb=" O TRP K 174 " (cutoff:3.500A) removed outlier: 6.822A pdb=" N LYS K 176 " --> pdb=" O PHE K 304 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'K' and resid 244 through 247 Processing sheet with id=AE9, first strand: chain 'K' and resid 273 through 274 Processing sheet with id=AF1, first strand: chain 'K' and resid 294 through 295 removed outlier: 3.676A pdb=" N GLU K 298 " --> pdb=" O TYR K 295 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'L' and resid 199 through 201 removed outlier: 6.345A pdb=" N TRP L 200 " --> pdb=" O ILE L 219 " (cutoff:3.500A) removed outlier: 7.031A pdb=" N ASP L 221 " --> pdb=" O TRP L 200 " (cutoff:3.500A) removed outlier: 8.290A pdb=" N TYR L 302 " --> pdb=" O ILE L 172 " (cutoff:3.500A) removed outlier: 6.510A pdb=" N TRP L 174 " --> pdb=" O TYR L 302 " (cutoff:3.500A) removed outlier: 7.519A pdb=" N PHE L 304 " --> pdb=" O TRP L 174 " (cutoff:3.500A) removed outlier: 6.830A pdb=" N LYS L 176 " --> pdb=" O PHE L 304 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'L' and resid 244 through 247 Processing sheet with id=AF4, first strand: chain 'L' and resid 273 through 274 1016 hydrogen bonds defined for protein. 2892 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: 5.07 Time building geometry restraints manager: 2.97 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: 8791 1.37 - 1.51: 8336 1.51 - 1.66: 10017 1.66 - 1.80: 130 1.80 - 1.95: 50 Bond restraints: 27324 Sorted by residual: bond pdb=" O3B AGS B 401 " pdb=" PB AGS B 401 " ideal model delta sigma weight residual 1.673 1.578 0.095 2.00e-02 2.50e+03 2.26e+01 bond pdb=" O3B AGS E 401 " pdb=" PB AGS E 401 " ideal model delta sigma weight residual 1.673 1.578 0.095 2.00e-02 2.50e+03 2.25e+01 bond pdb=" O3B AGS F 401 " pdb=" PB AGS F 401 " ideal model delta sigma weight residual 1.673 1.578 0.095 2.00e-02 2.50e+03 2.25e+01 bond pdb=" O3B AGS C 401 " pdb=" PB AGS C 401 " ideal model delta sigma weight residual 1.673 1.579 0.094 2.00e-02 2.50e+03 2.21e+01 bond pdb=" O3B AGS A 401 " pdb=" PB AGS A 401 " ideal model delta sigma weight residual 1.673 1.580 0.093 2.00e-02 2.50e+03 2.18e+01 ... (remaining 27319 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.08: 36175 2.08 - 4.15: 617 4.15 - 6.23: 92 6.23 - 8.31: 34 8.31 - 10.38: 48 Bond angle restraints: 36966 Sorted by residual: angle pdb=" N GLY F 240 " pdb=" CA GLY F 240 " pdb=" C GLY F 240 " ideal model delta sigma weight residual 113.86 118.83 -4.97 1.50e+00 4.44e-01 1.10e+01 angle pdb=" C PHE H 195 " pdb=" N ASN H 196 " pdb=" CA ASN H 196 " ideal model delta sigma weight residual 121.54 127.82 -6.28 1.91e+00 2.74e-01 1.08e+01 angle pdb=" C PHE I 195 " pdb=" N ASN I 196 " pdb=" CA ASN I 196 " ideal model delta sigma weight residual 121.54 127.73 -6.19 1.91e+00 2.74e-01 1.05e+01 angle pdb=" O3A AGS L 401 " pdb=" PB AGS L 401 " pdb=" O3B AGS L 401 " ideal model delta sigma weight residual 100.38 110.09 -9.71 3.00e+00 1.11e-01 1.05e+01 angle pdb=" C PHE L 195 " pdb=" N ASN L 196 " pdb=" CA ASN L 196 " ideal model delta sigma weight residual 121.54 127.70 -6.16 1.91e+00 2.74e-01 1.04e+01 ... (remaining 36961 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 19.03: 14464 19.03 - 38.06: 1646 38.06 - 57.09: 285 57.09 - 76.11: 189 76.11 - 95.14: 78 Dihedral angle restraints: 16662 sinusoidal: 7356 harmonic: 9306 Sorted by residual: dihedral pdb=" CA GLU B 18 " pdb=" C GLU B 18 " pdb=" N GLU B 19 " pdb=" CA GLU B 19 " ideal model delta harmonic sigma weight residual 180.00 156.19 23.81 0 5.00e+00 4.00e-02 2.27e+01 dihedral pdb=" CA THR G 229 " pdb=" C THR G 229 " pdb=" N GLU G 230 " pdb=" CA GLU G 230 " ideal model delta harmonic sigma weight residual 180.00 158.53 21.47 0 5.00e+00 4.00e-02 1.84e+01 dihedral pdb=" CA GLU D 18 " pdb=" C GLU D 18 " pdb=" N GLU D 19 " pdb=" CA GLU D 19 " ideal model delta harmonic sigma weight residual 180.00 158.57 21.43 0 5.00e+00 4.00e-02 1.84e+01 ... (remaining 16659 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.054: 3284 0.054 - 0.109: 557 0.109 - 0.163: 113 0.163 - 0.217: 0 0.217 - 0.272: 12 Chirality restraints: 3966 Sorted by residual: chirality pdb=" C3' AGS E 401 " pdb=" C2' AGS E 401 " pdb=" C4' AGS E 401 " pdb=" O3' AGS E 401 " both_signs ideal model delta sigma weight residual False -2.37 -2.64 0.27 2.00e-01 2.50e+01 1.85e+00 chirality pdb=" C3' AGS B 401 " pdb=" C2' AGS B 401 " pdb=" C4' AGS B 401 " pdb=" O3' AGS B 401 " both_signs ideal model delta sigma weight residual False -2.37 -2.64 0.27 2.00e-01 2.50e+01 1.78e+00 chirality pdb=" C3' AGS F 401 " pdb=" C2' AGS F 401 " pdb=" C4' AGS F 401 " pdb=" O3' AGS F 401 " both_signs ideal model delta sigma weight residual False -2.37 -2.64 0.26 2.00e-01 2.50e+01 1.75e+00 ... (remaining 3963 not shown) Planarity restraints: 4632 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB PHE F 251 " -0.014 2.00e-02 2.50e+03 1.59e-02 4.43e+00 pdb=" CG PHE F 251 " 0.035 2.00e-02 2.50e+03 pdb=" CD1 PHE F 251 " -0.015 2.00e-02 2.50e+03 pdb=" CD2 PHE F 251 " 0.001 2.00e-02 2.50e+03 pdb=" CE1 PHE F 251 " 0.004 2.00e-02 2.50e+03 pdb=" CE2 PHE F 251 " -0.011 2.00e-02 2.50e+03 pdb=" CZ PHE F 251 " 0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C GLN B 255 " -0.034 5.00e-02 4.00e+02 5.20e-02 4.32e+00 pdb=" N PRO B 256 " 0.090 5.00e-02 4.00e+02 pdb=" CA PRO B 256 " -0.026 5.00e-02 4.00e+02 pdb=" CD PRO B 256 " -0.029 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB PHE D 251 " 0.014 2.00e-02 2.50e+03 1.54e-02 4.17e+00 pdb=" CG PHE D 251 " -0.033 2.00e-02 2.50e+03 pdb=" CD1 PHE D 251 " 0.014 2.00e-02 2.50e+03 pdb=" CD2 PHE D 251 " -0.001 2.00e-02 2.50e+03 pdb=" CE1 PHE D 251 " -0.004 2.00e-02 2.50e+03 pdb=" CE2 PHE D 251 " 0.011 2.00e-02 2.50e+03 pdb=" CZ PHE D 251 " -0.002 2.00e-02 2.50e+03 ... (remaining 4629 not shown) Histogram of nonbonded interaction distances: 1.92 - 2.52: 230 2.52 - 3.11: 19878 3.11 - 3.71: 38928 3.71 - 4.30: 58797 4.30 - 4.90: 98422 Nonbonded interactions: 216255 Sorted by model distance: nonbonded pdb=" OE2 GLU J 279 " pdb="MG MG E 403 " model vdw 1.923 2.170 nonbonded pdb=" OE2 GLU G 279 " pdb="MG MG B 403 " model vdw 1.930 2.170 nonbonded pdb=" OE1 GLU I 279 " pdb="MG MG D 403 " model vdw 1.970 2.170 nonbonded pdb=" OG1 THR I 184 " pdb="MG MG I 402 " model vdw 1.982 2.170 nonbonded pdb=" O2B AGS I 401 " pdb="MG MG I 402 " model vdw 1.995 2.170 ... (remaining 216250 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: 0.01 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' } ncs_group { reference = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'J' selection = chain 'K' selection = chain 'L' } 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: 7.550 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: 0.060 Extract box with map and model: 0.590 Check model and map are aligned: 0.130 Set scattering table: 0.050 Process input model: 24.540 Find NCS groups from input model: 0.640 Set up NCS constraints: 0.080 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:7.620 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 41.260 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9065 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.095 27324 Z= 0.238 Angle : 0.740 10.381 36966 Z= 0.352 Chirality : 0.045 0.272 3966 Planarity : 0.004 0.052 4632 Dihedral : 18.492 95.143 10662 Min Nonbonded Distance : 1.923 Molprobity Statistics. All-atom Clashscore : 7.86 Ramachandran Plot: Outliers : 0.13 % Allowed : 2.49 % Favored : 97.39 % Rotamer: Outliers : 0.46 % Allowed : 0.71 % Favored : 98.83 % 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: 0.35 (0.15), residues: 3174 helix: 0.58 (0.16), residues: 1074 sheet: 0.17 (0.21), residues: 582 loop : 0.17 (0.17), residues: 1518 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG I 319 TYR 0.027 0.002 TYR I 295 PHE 0.035 0.002 PHE F 251 TRP 0.018 0.001 TRP K 208 HIS 0.007 0.001 HIS C 57 Details of bonding type rmsd/Z covalent geometry : bond 0.00512 / 0.24 (27324) covalent geometry : angle 0.74045 / 0.35 (36966) hydrogen bonds : bond 0.25146 / 16.87 ( 1016) hydrogen bonds : angle 7.94256 / 5.53 ( 2892) *********************** 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 329 residues out of total 2832 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 316 time to evaluate : 1.009 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: H 277 GLU cc_start: 0.8692 (mp0) cc_final: 0.8393 (mp0) REVERT: I 131 ASN cc_start: 0.9150 (m110) cc_final: 0.8854 (m110) REVERT: J 275 ASN cc_start: 0.8317 (t0) cc_final: 0.8004 (t0) REVERT: J 299 GLU cc_start: 0.7994 (pp20) cc_final: 0.7697 (pp20) REVERT: J 308 ASN cc_start: 0.8371 (t0) cc_final: 0.7823 (p0) REVERT: L 131 ASN cc_start: 0.9134 (m110) cc_final: 0.8863 (m110) REVERT: L 133 ASN cc_start: 0.8816 (t0) cc_final: 0.8497 (t0) REVERT: L 137 LEU cc_start: 0.8803 (mt) cc_final: 0.8479 (mp) REVERT: L 299 GLU cc_start: 0.8257 (tt0) cc_final: 0.8047 (tt0) REVERT: L 308 ASN cc_start: 0.8195 (t0) cc_final: 0.7970 (p0) outliers start: 13 outliers final: 3 residues processed: 329 average time/residue: 0.5469 time to fit residues: 214.8006 Evaluate side-chains 247 residues out of total 2832 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 244 time to evaluate : 0.923 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 ASP Chi-restraints excluded: chain B residue 72 ASN Chi-restraints excluded: chain E residue 72 ASN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 197 optimal weight: 1.9990 chunk 215 optimal weight: 1.9990 chunk 20 optimal weight: 2.9990 chunk 132 optimal weight: 5.9990 chunk 261 optimal weight: 4.9990 chunk 248 optimal weight: 0.8980 chunk 207 optimal weight: 0.7980 chunk 155 optimal weight: 7.9990 chunk 244 optimal weight: 0.5980 chunk 183 optimal weight: 3.9990 chunk 298 optimal weight: 0.9980 overall best weight: 1.0582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... F 246 GLN G 203 ASN H 156 ASN H 316 ASN I 156 ASN I 203 ASN I 308 ASN J 131 ASN J 203 ASN K 156 ASN K 316 ASN L 203 ASN L 316 ASN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3270 r_free = 0.3270 target = 0.091522 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2893 r_free = 0.2893 target = 0.069047 restraints weight = 48038.328| |-----------------------------------------------------------------------------| r_work (start): 0.2860 rms_B_bonded: 2.79 r_work: 0.2707 rms_B_bonded: 3.21 restraints_weight: 0.5000 r_work (final): 0.2707 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8794 moved from start: 0.1495 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 27324 Z= 0.151 Angle : 0.577 7.670 36966 Z= 0.304 Chirality : 0.044 0.159 3966 Planarity : 0.004 0.047 4632 Dihedral : 10.363 59.955 3930 Min Nonbonded Distance : 1.905 Molprobity Statistics. All-atom Clashscore : 6.64 Ramachandran Plot: Outliers : 0.13 % Allowed : 2.71 % Favored : 97.16 % Rotamer: Outliers : 1.24 % Allowed : 6.85 % Favored : 91.91 % 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: 0.42 (0.15), residues: 3174 helix: 0.81 (0.14), residues: 1206 sheet: -0.17 (0.21), residues: 570 loop : 0.17 (0.18), residues: 1398 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG D 135 TYR 0.020 0.001 TYR C 42 PHE 0.021 0.001 PHE K 304 TRP 0.014 0.001 TRP D 231 HIS 0.006 0.001 HIS A 57 Details of bonding type rmsd/Z covalent geometry : bond 0.00355 / 0.15 (27324) covalent geometry : angle 0.57703 / 0.30 (36966) hydrogen bonds : bond 0.04498 / 3.00 ( 1016) hydrogen bonds : angle 5.33892 / 3.70 ( 2892) *********************** 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 287 residues out of total 2832 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 252 time to evaluate : 1.109 Fit side-chains revert: symmetry clash REVERT: A 55 THR cc_start: 0.8794 (m) cc_final: 0.8550 (p) REVERT: H 241 TYR cc_start: 0.8715 (m-80) cc_final: 0.8363 (m-80) REVERT: H 277 GLU cc_start: 0.8734 (mp0) cc_final: 0.8276 (mp0) REVERT: H 327 MET cc_start: 0.7257 (OUTLIER) cc_final: 0.6925 (mpm) REVERT: I 131 ASN cc_start: 0.9038 (m110) cc_final: 0.8741 (m110) REVERT: I 241 TYR cc_start: 0.8685 (m-80) cc_final: 0.8406 (m-80) REVERT: J 299 GLU cc_start: 0.7456 (pp20) cc_final: 0.7063 (pp20) REVERT: L 133 ASN cc_start: 0.8634 (t0) cc_final: 0.8108 (t0) REVERT: L 137 LEU cc_start: 0.8687 (mt) cc_final: 0.8388 (mp) REVERT: L 299 GLU cc_start: 0.8388 (tt0) cc_final: 0.8004 (tt0) outliers start: 35 outliers final: 15 residues processed: 278 average time/residue: 0.5313 time to fit residues: 177.2839 Evaluate side-chains 251 residues out of total 2832 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 235 time to evaluate : 1.029 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 139 MET Chi-restraints excluded: chain C residue 232 SER Chi-restraints excluded: chain E residue 140 GLU Chi-restraints excluded: chain G residue 226 SER Chi-restraints excluded: chain G residue 312 LEU Chi-restraints excluded: chain H residue 189 ASP Chi-restraints excluded: chain H residue 203 ASN Chi-restraints excluded: chain H residue 226 SER Chi-restraints excluded: chain H residue 327 MET Chi-restraints excluded: chain I residue 189 ASP Chi-restraints excluded: chain I residue 226 SER Chi-restraints excluded: chain K residue 189 ASP Chi-restraints excluded: chain K residue 196 ASN Chi-restraints excluded: chain K residue 203 ASN Chi-restraints excluded: chain K residue 226 SER Chi-restraints excluded: chain L residue 226 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 196 optimal weight: 5.9990 chunk 67 optimal weight: 4.9990 chunk 187 optimal weight: 0.6980 chunk 153 optimal weight: 0.9990 chunk 142 optimal weight: 0.9990 chunk 184 optimal weight: 0.9990 chunk 97 optimal weight: 0.0970 chunk 89 optimal weight: 1.9990 chunk 94 optimal weight: 0.1980 chunk 292 optimal weight: 8.9990 chunk 250 optimal weight: 6.9990 overall best weight: 0.5982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 113 ASN B 72 ASN ** C 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 72 ASN G 203 ASN G 316 ASN H 131 ASN H 196 ASN H 316 ASN I 316 ASN J 203 ASN J 316 ASN K 316 ASN L 131 ASN L 316 ASN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3295 r_free = 0.3295 target = 0.093045 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.2923 r_free = 0.2923 target = 0.070612 restraints weight = 47802.787| |-----------------------------------------------------------------------------| r_work (start): 0.2886 rms_B_bonded: 2.79 r_work: 0.2733 rms_B_bonded: 3.23 restraints_weight: 0.5000 r_work (final): 0.2733 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8764 moved from start: 0.1847 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 27324 Z= 0.106 Angle : 0.492 7.389 36966 Z= 0.260 Chirality : 0.042 0.154 3966 Planarity : 0.003 0.033 4632 Dihedral : 7.261 57.979 3924 Min Nonbonded Distance : 1.947 Molprobity Statistics. All-atom Clashscore : 5.72 Ramachandran Plot: Outliers : 0.06 % Allowed : 2.49 % Favored : 97.45 % Rotamer: Outliers : 1.45 % Allowed : 9.71 % Favored : 88.84 % 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: 0.64 (0.15), residues: 3174 helix: 1.13 (0.15), residues: 1206 sheet: -0.12 (0.20), residues: 600 loop : 0.21 (0.18), residues: 1368 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG J 224 TYR 0.016 0.001 TYR C 42 PHE 0.013 0.001 PHE K 304 TRP 0.019 0.001 TRP A 273 HIS 0.005 0.001 HIS A 57 Details of bonding type rmsd/Z covalent geometry : bond 0.00241 / 0.11 (27324) covalent geometry : angle 0.49155 / 0.26 (36966) hydrogen bonds : bond 0.03548 / 2.36 ( 1016) hydrogen bonds : angle 4.86631 / 3.38 ( 2892) *********************** 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 293 residues out of total 2832 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 252 time to evaluate : 1.185 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 55 THR cc_start: 0.8857 (m) cc_final: 0.8610 (p) REVERT: A 120 MET cc_start: 0.8111 (tpp) cc_final: 0.7788 (mmm) REVERT: B 83 MET cc_start: 0.9033 (tpt) cc_final: 0.8749 (tpt) REVERT: E 36 ASP cc_start: 0.8686 (t0) cc_final: 0.8240 (t0) REVERT: F 88 ARG cc_start: 0.8731 (OUTLIER) cc_final: 0.8473 (ptp90) REVERT: G 308 ASN cc_start: 0.8067 (t0) cc_final: 0.7543 (p0) REVERT: H 139 MET cc_start: 0.8858 (mmt) cc_final: 0.8589 (mmm) REVERT: H 241 TYR cc_start: 0.8685 (m-80) cc_final: 0.8331 (m-80) REVERT: H 277 GLU cc_start: 0.8690 (mp0) cc_final: 0.8163 (mp0) REVERT: I 131 ASN cc_start: 0.8992 (m110) cc_final: 0.8686 (m110) REVERT: I 226 SER cc_start: 0.9265 (OUTLIER) cc_final: 0.8878 (p) REVERT: I 276 LYS cc_start: 0.8863 (mppt) cc_final: 0.8653 (mppt) REVERT: J 299 GLU cc_start: 0.7478 (pp20) cc_final: 0.6991 (pp20) REVERT: K 139 MET cc_start: 0.8860 (OUTLIER) cc_final: 0.8587 (mmm) REVERT: L 133 ASN cc_start: 0.8654 (t0) cc_final: 0.8134 (t0) REVERT: L 137 LEU cc_start: 0.8697 (mt) cc_final: 0.8371 (mp) REVERT: L 299 GLU cc_start: 0.8392 (tt0) cc_final: 0.7992 (tt0) outliers start: 41 outliers final: 14 residues processed: 283 average time/residue: 0.5237 time to fit residues: 178.8614 Evaluate side-chains 250 residues out of total 2832 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 233 time to evaluate : 1.331 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 318 ILE Chi-restraints excluded: chain C residue 139 MET Chi-restraints excluded: chain C residue 232 SER Chi-restraints excluded: chain E residue 140 GLU Chi-restraints excluded: chain F residue 15 LEU Chi-restraints excluded: chain F residue 88 ARG Chi-restraints excluded: chain G residue 203 ASN Chi-restraints excluded: chain G residue 226 SER Chi-restraints excluded: chain G residue 312 LEU Chi-restraints excluded: chain H residue 203 ASN Chi-restraints excluded: chain H residue 226 SER Chi-restraints excluded: chain I residue 203 ASN Chi-restraints excluded: chain I residue 226 SER Chi-restraints excluded: chain K residue 139 MET Chi-restraints excluded: chain K residue 203 ASN Chi-restraints excluded: chain K residue 226 SER Chi-restraints excluded: chain L residue 226 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 258 optimal weight: 5.9990 chunk 157 optimal weight: 3.9990 chunk 219 optimal weight: 4.9990 chunk 233 optimal weight: 2.9990 chunk 230 optimal weight: 0.0030 chunk 105 optimal weight: 0.3980 chunk 110 optimal weight: 0.9990 chunk 118 optimal weight: 3.9990 chunk 240 optimal weight: 2.9990 chunk 170 optimal weight: 5.9990 chunk 232 optimal weight: 0.9990 overall best weight: 1.0796 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 72 ASN A 113 ASN B 72 ASN E 72 ASN G 203 ASN G 316 ASN H 316 ASN I 316 ASN J 203 ASN J 316 ASN K 316 ASN L 316 ASN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3266 r_free = 0.3266 target = 0.091199 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2887 r_free = 0.2887 target = 0.068663 restraints weight = 47957.961| |-----------------------------------------------------------------------------| r_work (start): 0.2852 rms_B_bonded: 2.78 r_work: 0.2700 rms_B_bonded: 3.21 restraints_weight: 0.5000 r_work (final): 0.2700 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8799 moved from start: 0.1967 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= 0.140 Angle : 0.508 9.641 36966 Z= 0.267 Chirality : 0.043 0.153 3966 Planarity : 0.003 0.045 4632 Dihedral : 6.641 45.687 3924 Min Nonbonded Distance : 1.892 Molprobity Statistics. All-atom Clashscore : 5.72 Ramachandran Plot: Outliers : 0.03 % Allowed : 2.65 % Favored : 97.32 % Rotamer: Outliers : 1.62 % Allowed : 11.37 % Favored : 87.01 % 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: 0.65 (0.15), residues: 3174 helix: 1.24 (0.15), residues: 1212 sheet: -0.27 (0.21), residues: 570 loop : 0.17 (0.18), residues: 1392 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG J 224 TYR 0.020 0.001 TYR C 42 PHE 0.017 0.001 PHE K 304 TRP 0.022 0.001 TRP A 273 HIS 0.005 0.001 HIS A 57 Details of bonding type rmsd/Z covalent geometry : bond 0.00332 / 0.14 (27324) covalent geometry : angle 0.50772 / 0.27 (36966) hydrogen bonds : bond 0.03716 / 2.48 ( 1016) hydrogen bonds : angle 4.75769 / 3.30 ( 2892) *********************** 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 286 residues out of total 2832 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 240 time to evaluate : 1.142 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: E 36 ASP cc_start: 0.8677 (t0) cc_final: 0.8233 (t0) REVERT: G 308 ASN cc_start: 0.8051 (t0) cc_final: 0.7541 (p0) REVERT: H 139 MET cc_start: 0.8821 (OUTLIER) cc_final: 0.8561 (mmm) REVERT: H 241 TYR cc_start: 0.8724 (m-80) cc_final: 0.8373 (m-80) REVERT: H 277 GLU cc_start: 0.8699 (mp0) cc_final: 0.8167 (mp0) REVERT: I 131 ASN cc_start: 0.8993 (m110) cc_final: 0.8682 (m110) REVERT: J 299 GLU cc_start: 0.7490 (pp20) cc_final: 0.6949 (pp20) REVERT: K 139 MET cc_start: 0.8844 (mmt) cc_final: 0.8566 (mmm) REVERT: K 241 TYR cc_start: 0.8547 (m-80) cc_final: 0.8193 (m-80) REVERT: K 308 ASN cc_start: 0.8277 (t0) cc_final: 0.7771 (p0) REVERT: L 133 ASN cc_start: 0.8673 (t0) cc_final: 0.8127 (t0) REVERT: L 137 LEU cc_start: 0.8727 (mt) cc_final: 0.8407 (mp) REVERT: L 299 GLU cc_start: 0.8357 (tt0) cc_final: 0.7961 (tt0) outliers start: 46 outliers final: 22 residues processed: 275 average time/residue: 0.5061 time to fit residues: 168.5639 Evaluate side-chains 253 residues out of total 2832 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 230 time to evaluate : 1.087 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 56 VAL Chi-restraints excluded: chain A residue 318 ILE Chi-restraints excluded: chain B residue 56 VAL Chi-restraints excluded: chain B residue 203 ASN Chi-restraints excluded: chain B residue 217 VAL Chi-restraints excluded: chain C residue 139 MET Chi-restraints excluded: chain C residue 232 SER Chi-restraints excluded: chain D residue 56 VAL Chi-restraints excluded: chain E residue 140 GLU Chi-restraints excluded: chain E residue 203 ASN Chi-restraints excluded: chain F residue 15 LEU Chi-restraints excluded: chain F residue 93 LEU Chi-restraints excluded: chain G residue 226 SER Chi-restraints excluded: chain G residue 312 LEU Chi-restraints excluded: chain H residue 139 MET Chi-restraints excluded: chain H residue 203 ASN Chi-restraints excluded: chain H residue 226 SER Chi-restraints excluded: chain I residue 203 ASN Chi-restraints excluded: chain I residue 226 SER Chi-restraints excluded: chain K residue 203 ASN Chi-restraints excluded: chain K residue 226 SER Chi-restraints excluded: chain L residue 203 ASN Chi-restraints excluded: chain L residue 226 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 234 optimal weight: 0.9980 chunk 145 optimal weight: 2.9990 chunk 89 optimal weight: 0.9990 chunk 118 optimal weight: 0.2980 chunk 94 optimal weight: 1.9990 chunk 100 optimal weight: 4.9990 chunk 36 optimal weight: 4.9990 chunk 296 optimal weight: 4.9990 chunk 87 optimal weight: 2.9990 chunk 154 optimal weight: 0.8980 chunk 56 optimal weight: 0.9980 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 72 ASN C 242 ASN E 72 ASN G 203 ASN G 316 ASN H 316 ASN I 316 ASN J 203 ASN J 316 ASN K 316 ASN L 316 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3275 r_free = 0.3275 target = 0.091727 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2896 r_free = 0.2896 target = 0.069179 restraints weight = 47726.064| |-----------------------------------------------------------------------------| r_work (start): 0.2864 rms_B_bonded: 2.79 r_work: 0.2713 rms_B_bonded: 3.21 restraints_weight: 0.5000 r_work (final): 0.2713 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8787 moved from start: 0.2102 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= 0.118 Angle : 0.483 8.453 36966 Z= 0.255 Chirality : 0.042 0.151 3966 Planarity : 0.003 0.032 4632 Dihedral : 6.279 39.788 3924 Min Nonbonded Distance : 1.907 Molprobity Statistics. All-atom Clashscore : 5.48 Ramachandran Plot: Outliers : 0.03 % Allowed : 2.49 % Favored : 97.48 % Rotamer: Outliers : 1.59 % Allowed : 12.89 % Favored : 85.52 % 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: 0.69 (0.15), residues: 3174 helix: 1.18 (0.15), residues: 1236 sheet: -0.31 (0.20), residues: 570 loop : 0.30 (0.18), residues: 1368 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG D 71 TYR 0.020 0.001 TYR C 42 PHE 0.013 0.001 PHE K 304 TRP 0.027 0.001 TRP A 273 HIS 0.004 0.001 HIS A 57 Details of bonding type rmsd/Z covalent geometry : bond 0.00276 / 0.12 (27324) covalent geometry : angle 0.48285 / 0.25 (36966) hydrogen bonds : bond 0.03372 / 2.25 ( 1016) hydrogen bonds : angle 4.62107 / 3.20 ( 2892) *********************** 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 282 residues out of total 2832 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 237 time to evaluate : 0.813 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 88 ARG cc_start: 0.8901 (OUTLIER) cc_final: 0.8527 (ptp90) REVERT: A 318 ILE cc_start: 0.8597 (OUTLIER) cc_final: 0.8387 (mp) REVERT: B 230 GLU cc_start: 0.6829 (tp30) cc_final: 0.6591 (tm-30) REVERT: E 36 ASP cc_start: 0.8668 (t0) cc_final: 0.8211 (t0) REVERT: F 221 ASP cc_start: 0.8650 (t70) cc_final: 0.8279 (m-30) REVERT: G 308 ASN cc_start: 0.8060 (t0) cc_final: 0.7581 (p0) REVERT: H 136 GLU cc_start: 0.8408 (tm-30) cc_final: 0.8206 (tm-30) REVERT: H 139 MET cc_start: 0.8833 (OUTLIER) cc_final: 0.8563 (mmm) REVERT: H 241 TYR cc_start: 0.8690 (m-80) cc_final: 0.8306 (m-80) REVERT: H 277 GLU cc_start: 0.8694 (mp0) cc_final: 0.8160 (mp0) REVERT: H 308 ASN cc_start: 0.8022 (t0) cc_final: 0.7496 (OUTLIER) REVERT: I 131 ASN cc_start: 0.8979 (m110) cc_final: 0.8661 (m110) REVERT: I 226 SER cc_start: 0.9253 (OUTLIER) cc_final: 0.8890 (p) REVERT: J 299 GLU cc_start: 0.7476 (pp20) cc_final: 0.6995 (pp20) REVERT: K 139 MET cc_start: 0.8866 (mmt) cc_final: 0.8602 (mmm) REVERT: K 241 TYR cc_start: 0.8554 (m-80) cc_final: 0.8193 (m-80) REVERT: K 308 ASN cc_start: 0.8240 (t0) cc_final: 0.7778 (p0) REVERT: L 133 ASN cc_start: 0.8700 (t0) cc_final: 0.8144 (t0) REVERT: L 137 LEU cc_start: 0.8742 (mt) cc_final: 0.8417 (mp) REVERT: L 299 GLU cc_start: 0.8391 (tt0) cc_final: 0.8012 (tt0) outliers start: 45 outliers final: 24 residues processed: 273 average time/residue: 0.4849 time to fit residues: 160.3340 Evaluate side-chains 256 residues out of total 2832 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 229 time to evaluate : 0.972 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 56 VAL Chi-restraints excluded: chain A residue 88 ARG Chi-restraints excluded: chain A residue 318 ILE Chi-restraints excluded: chain B residue 56 VAL Chi-restraints excluded: chain B residue 203 ASN Chi-restraints excluded: chain C residue 56 VAL Chi-restraints excluded: chain C residue 139 MET Chi-restraints excluded: chain C residue 232 SER Chi-restraints excluded: chain D residue 56 VAL Chi-restraints excluded: chain E residue 140 GLU Chi-restraints excluded: chain F residue 15 LEU Chi-restraints excluded: chain F residue 93 LEU Chi-restraints excluded: chain G residue 226 SER Chi-restraints excluded: chain G residue 229 THR Chi-restraints excluded: chain G residue 312 LEU Chi-restraints excluded: chain H residue 139 MET Chi-restraints excluded: chain H residue 203 ASN Chi-restraints excluded: chain H residue 217 VAL Chi-restraints excluded: chain H residue 226 SER Chi-restraints excluded: chain I residue 189 ASP Chi-restraints excluded: chain I residue 203 ASN Chi-restraints excluded: chain I residue 226 SER Chi-restraints excluded: chain K residue 203 ASN Chi-restraints excluded: chain K residue 217 VAL Chi-restraints excluded: chain K residue 226 SER Chi-restraints excluded: chain L residue 203 ASN Chi-restraints excluded: chain L residue 226 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 178 optimal weight: 4.9990 chunk 238 optimal weight: 4.9990 chunk 299 optimal weight: 1.9990 chunk 273 optimal weight: 4.9990 chunk 308 optimal weight: 1.9990 chunk 244 optimal weight: 2.9990 chunk 225 optimal weight: 2.9990 chunk 297 optimal weight: 4.9990 chunk 245 optimal weight: 0.8980 chunk 234 optimal weight: 0.9980 chunk 135 optimal weight: 3.9990 overall best weight: 1.7786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 72 ASN E 72 ASN G 203 ASN G 316 ASN H 316 ASN I 316 ASN J 203 ASN J 316 ASN K 133 ASN K 316 ASN L 316 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3228 r_free = 0.3228 target = 0.088811 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2842 r_free = 0.2842 target = 0.066361 restraints weight = 48077.836| |-----------------------------------------------------------------------------| r_work (start): 0.2813 rms_B_bonded: 2.73 r_work: 0.2662 rms_B_bonded: 3.14 restraints_weight: 0.5000 r_work: 0.2511 rms_B_bonded: 4.98 restraints_weight: 0.2500 r_work (final): 0.2511 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8913 moved from start: 0.2120 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.047 27324 Z= 0.200 Angle : 0.553 11.619 36966 Z= 0.287 Chirality : 0.044 0.167 3966 Planarity : 0.004 0.049 4632 Dihedral : 6.618 39.632 3924 Min Nonbonded Distance : 1.844 Molprobity Statistics. All-atom Clashscore : 6.00 Ramachandran Plot: Outliers : 0.13 % Allowed : 2.77 % Favored : 97.10 % Rotamer: Outliers : 2.30 % Allowed : 12.85 % Favored : 84.85 % 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: 0.63 (0.15), residues: 3174 helix: 1.28 (0.15), residues: 1218 sheet: -0.40 (0.20), residues: 588 loop : 0.17 (0.18), residues: 1368 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG D 88 TYR 0.027 0.001 TYR C 42 PHE 0.020 0.001 PHE K 304 TRP 0.034 0.001 TRP A 273 HIS 0.005 0.001 HIS C 57 Details of bonding type rmsd/Z covalent geometry : bond 0.00486 / 0.20 (27324) covalent geometry : angle 0.55264 / 0.29 (36966) hydrogen bonds : bond 0.04219 / 2.82 ( 1016) hydrogen bonds : angle 4.76710 / 3.30 ( 2892) *********************** 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 302 residues out of total 2832 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 237 time to evaluate : 0.897 Fit side-chains REVERT: A 83 MET cc_start: 0.9117 (tpt) cc_final: 0.8908 (tpp) REVERT: A 318 ILE cc_start: 0.8702 (OUTLIER) cc_final: 0.8499 (mp) REVERT: C 69 SER cc_start: 0.9041 (t) cc_final: 0.8457 (p) REVERT: D 318 ILE cc_start: 0.8644 (OUTLIER) cc_final: 0.8382 (mt) REVERT: E 36 ASP cc_start: 0.8858 (t0) cc_final: 0.8423 (t0) REVERT: F 221 ASP cc_start: 0.8902 (t70) cc_final: 0.8510 (m-30) REVERT: G 308 ASN cc_start: 0.8106 (t0) cc_final: 0.7579 (p0) REVERT: H 136 GLU cc_start: 0.8514 (tm-30) cc_final: 0.8286 (tm-30) REVERT: H 139 MET cc_start: 0.8795 (OUTLIER) cc_final: 0.8530 (mmm) REVERT: H 277 GLU cc_start: 0.8724 (mp0) cc_final: 0.8279 (mp0) REVERT: I 131 ASN cc_start: 0.8908 (m110) cc_final: 0.8588 (m110) REVERT: J 296 GLU cc_start: 0.8325 (OUTLIER) cc_final: 0.7425 (mp0) REVERT: J 299 GLU cc_start: 0.7635 (pp20) cc_final: 0.7035 (pp20) REVERT: K 133 ASN cc_start: 0.8509 (t0) cc_final: 0.8145 (p0) REVERT: K 139 MET cc_start: 0.8809 (mmt) cc_final: 0.8541 (mmm) REVERT: K 241 TYR cc_start: 0.8829 (m-80) cc_final: 0.8493 (m-80) REVERT: K 308 ASN cc_start: 0.8206 (t0) cc_final: 0.7694 (p0) REVERT: L 133 ASN cc_start: 0.8690 (t0) cc_final: 0.8107 (t0) REVERT: L 137 LEU cc_start: 0.8756 (mt) cc_final: 0.8404 (mp) outliers start: 65 outliers final: 31 residues processed: 287 average time/residue: 0.4950 time to fit residues: 172.8130 Evaluate side-chains 262 residues out of total 2832 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 227 time to evaluate : 1.083 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 56 VAL Chi-restraints excluded: chain A residue 318 ILE Chi-restraints excluded: chain B residue 3 LEU Chi-restraints excluded: chain B residue 56 VAL Chi-restraints excluded: chain B residue 217 VAL Chi-restraints excluded: chain C residue 56 VAL Chi-restraints excluded: chain C residue 232 SER Chi-restraints excluded: chain D residue 56 VAL Chi-restraints excluded: chain D residue 89 ILE Chi-restraints excluded: chain D residue 242 ASN Chi-restraints excluded: chain D residue 318 ILE Chi-restraints excluded: chain E residue 56 VAL Chi-restraints excluded: chain E residue 103 ASP Chi-restraints excluded: chain E residue 203 ASN Chi-restraints excluded: chain E residue 312 LEU Chi-restraints excluded: chain F residue 15 LEU Chi-restraints excluded: chain F residue 93 LEU Chi-restraints excluded: chain F residue 139 MET Chi-restraints excluded: chain G residue 226 SER Chi-restraints excluded: chain G residue 312 LEU Chi-restraints excluded: chain H residue 139 MET Chi-restraints excluded: chain H residue 203 ASN Chi-restraints excluded: chain H residue 217 VAL Chi-restraints excluded: chain H residue 226 SER Chi-restraints excluded: chain I residue 203 ASN Chi-restraints excluded: chain I residue 217 VAL Chi-restraints excluded: chain I residue 226 SER Chi-restraints excluded: chain J residue 263 SER Chi-restraints excluded: chain J residue 296 GLU Chi-restraints excluded: chain K residue 203 ASN Chi-restraints excluded: chain K residue 217 VAL Chi-restraints excluded: chain K residue 226 SER Chi-restraints excluded: chain L residue 203 ASN Chi-restraints excluded: chain L residue 217 VAL Chi-restraints excluded: chain L residue 226 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 62 optimal weight: 0.8980 chunk 174 optimal weight: 2.9990 chunk 47 optimal weight: 0.7980 chunk 219 optimal weight: 3.9990 chunk 123 optimal weight: 0.9990 chunk 87 optimal weight: 0.9980 chunk 267 optimal weight: 0.4980 chunk 34 optimal weight: 0.3980 chunk 287 optimal weight: 2.9990 chunk 233 optimal weight: 1.9990 chunk 148 optimal weight: 1.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 72 ASN E 72 ASN G 203 ASN G 316 ASN H 316 ASN I 133 ASN I 316 ASN J 133 ASN J 203 ASN J 316 ASN K 316 ASN L 316 ASN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3270 r_free = 0.3270 target = 0.091380 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2890 r_free = 0.2890 target = 0.068820 restraints weight = 47375.326| |-----------------------------------------------------------------------------| r_work (start): 0.2862 rms_B_bonded: 2.77 r_work: 0.2711 rms_B_bonded: 3.19 restraints_weight: 0.5000 r_work (final): 0.2711 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8788 moved from start: 0.2247 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 27324 Z= 0.111 Angle : 0.493 9.453 36966 Z= 0.258 Chirality : 0.042 0.159 3966 Planarity : 0.003 0.043 4632 Dihedral : 6.139 35.672 3924 Min Nonbonded Distance : 1.907 Molprobity Statistics. All-atom Clashscore : 5.56 Ramachandran Plot: Outliers : 0.06 % Allowed : 2.58 % Favored : 97.35 % Rotamer: Outliers : 1.66 % Allowed : 13.91 % Favored : 84.43 % 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: 0.69 (0.15), residues: 3174 helix: 1.20 (0.15), residues: 1236 sheet: -0.24 (0.20), residues: 600 loop : 0.27 (0.18), residues: 1338 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG D 88 TYR 0.021 0.001 TYR C 42 PHE 0.009 0.001 PHE K 304 TRP 0.036 0.001 TRP A 273 HIS 0.004 0.001 HIS A 57 Details of bonding type rmsd/Z covalent geometry : bond 0.00262 / 0.11 (27324) covalent geometry : angle 0.49263 / 0.26 (36966) hydrogen bonds : bond 0.03221 / 2.15 ( 1016) hydrogen bonds : angle 4.54785 / 3.15 ( 2892) *********************** 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 282 residues out of total 2832 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 235 time to evaluate : 1.168 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 69 SER cc_start: 0.8975 (t) cc_final: 0.8352 (p) REVERT: C 222 ASP cc_start: 0.8588 (OUTLIER) cc_final: 0.8269 (t0) REVERT: D 90 GLN cc_start: 0.7170 (mt0) cc_final: 0.6935 (mp10) REVERT: E 36 ASP cc_start: 0.8657 (t0) cc_final: 0.8202 (t0) REVERT: E 140 GLU cc_start: 0.8344 (OUTLIER) cc_final: 0.7963 (pm20) REVERT: F 221 ASP cc_start: 0.8623 (t70) cc_final: 0.8247 (m-30) REVERT: G 308 ASN cc_start: 0.8045 (t0) cc_final: 0.7580 (p0) REVERT: H 136 GLU cc_start: 0.8432 (tm-30) cc_final: 0.8187 (tm-30) REVERT: H 139 MET cc_start: 0.8823 (OUTLIER) cc_final: 0.8561 (mmm) REVERT: H 241 TYR cc_start: 0.8736 (m-80) cc_final: 0.8307 (m-80) REVERT: H 277 GLU cc_start: 0.8688 (mp0) cc_final: 0.8158 (mp0) REVERT: H 296 GLU cc_start: 0.8157 (OUTLIER) cc_final: 0.7761 (mp0) REVERT: H 308 ASN cc_start: 0.8048 (t0) cc_final: 0.7514 (p0) REVERT: H 327 MET cc_start: 0.7294 (mpm) cc_final: 0.6986 (mpm) REVERT: I 131 ASN cc_start: 0.8857 (m110) cc_final: 0.8535 (m110) REVERT: I 226 SER cc_start: 0.9262 (OUTLIER) cc_final: 0.8922 (p) REVERT: I 308 ASN cc_start: 0.7868 (t0) cc_final: 0.7492 (p0) REVERT: J 296 GLU cc_start: 0.8253 (OUTLIER) cc_final: 0.7375 (mp0) REVERT: K 139 MET cc_start: 0.8859 (OUTLIER) cc_final: 0.8572 (mmm) REVERT: K 241 TYR cc_start: 0.8658 (m-80) cc_final: 0.8259 (m-80) REVERT: K 308 ASN cc_start: 0.8191 (t0) cc_final: 0.7743 (p0) REVERT: L 133 ASN cc_start: 0.8680 (t0) cc_final: 0.8308 (t0) REVERT: L 299 GLU cc_start: 0.8357 (tt0) cc_final: 0.7986 (tt0) outliers start: 47 outliers final: 26 residues processed: 276 average time/residue: 0.5278 time to fit residues: 175.8801 Evaluate side-chains 259 residues out of total 2832 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 226 time to evaluate : 1.128 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 56 VAL Chi-restraints excluded: chain A residue 121 GLU Chi-restraints excluded: chain B residue 56 VAL Chi-restraints excluded: chain B residue 72 ASN Chi-restraints excluded: chain B residue 217 VAL Chi-restraints excluded: chain C residue 56 VAL Chi-restraints excluded: chain C residue 222 ASP Chi-restraints excluded: chain C residue 232 SER Chi-restraints excluded: chain D residue 56 VAL Chi-restraints excluded: chain E residue 56 VAL Chi-restraints excluded: chain E residue 72 ASN Chi-restraints excluded: chain E residue 103 ASP Chi-restraints excluded: chain E residue 140 GLU Chi-restraints excluded: chain F residue 15 LEU Chi-restraints excluded: chain G residue 226 SER Chi-restraints excluded: chain G residue 312 LEU Chi-restraints excluded: chain H residue 139 MET Chi-restraints excluded: chain H residue 203 ASN Chi-restraints excluded: chain H residue 217 VAL Chi-restraints excluded: chain H residue 226 SER Chi-restraints excluded: chain H residue 296 GLU Chi-restraints excluded: chain I residue 203 ASN Chi-restraints excluded: chain I residue 217 VAL Chi-restraints excluded: chain I residue 226 SER Chi-restraints excluded: chain I residue 310 ASP Chi-restraints excluded: chain J residue 296 GLU Chi-restraints excluded: chain K residue 139 MET Chi-restraints excluded: chain K residue 203 ASN Chi-restraints excluded: chain K residue 217 VAL Chi-restraints excluded: chain K residue 226 SER Chi-restraints excluded: chain L residue 203 ASN Chi-restraints excluded: chain L residue 217 VAL Chi-restraints excluded: chain L residue 226 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 25 optimal weight: 0.3980 chunk 240 optimal weight: 0.5980 chunk 165 optimal weight: 0.5980 chunk 293 optimal weight: 7.9990 chunk 202 optimal weight: 4.9990 chunk 194 optimal weight: 0.9980 chunk 307 optimal weight: 0.0470 chunk 215 optimal weight: 1.9990 chunk 102 optimal weight: 0.9990 chunk 265 optimal weight: 0.6980 chunk 110 optimal weight: 3.9990 overall best weight: 0.4678 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 72 ASN D 246 GLN E 72 ASN G 196 ASN G 203 ASN G 316 ASN H 133 ASN H 316 ASN I 133 ASN I 316 ASN J 133 ASN J 196 ASN J 203 ASN J 316 ASN K 133 ASN K 203 ASN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3293 r_free = 0.3293 target = 0.092826 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2920 r_free = 0.2920 target = 0.070368 restraints weight = 47906.111| |-----------------------------------------------------------------------------| r_work (start): 0.2890 rms_B_bonded: 2.79 r_work: 0.2739 rms_B_bonded: 3.22 restraints_weight: 0.5000 r_work (final): 0.2739 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8765 moved from start: 0.2403 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.046 27324 Z= 0.096 Angle : 0.486 12.462 36966 Z= 0.252 Chirality : 0.041 0.152 3966 Planarity : 0.003 0.048 4632 Dihedral : 5.785 30.899 3924 Min Nonbonded Distance : 1.947 Molprobity Statistics. All-atom Clashscore : 5.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.99 % Favored : 97.01 % Rotamer: Outliers : 1.80 % Allowed : 14.09 % Favored : 84.11 % 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: 0.99 (0.15), residues: 3174 helix: 1.25 (0.15), residues: 1242 sheet: 0.66 (0.21), residues: 480 loop : 0.28 (0.18), residues: 1452 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG D 88 TYR 0.014 0.001 TYR C 42 PHE 0.007 0.001 PHE B 251 TRP 0.039 0.001 TRP F 273 HIS 0.003 0.001 HIS A 57 Details of bonding type rmsd/Z covalent geometry : bond 0.00217 / 0.10 (27324) covalent geometry : angle 0.48587 / 0.25 (36966) hydrogen bonds : bond 0.02945 / 1.97 ( 1016) hydrogen bonds : angle 4.44054 / 3.08 ( 2892) *********************** 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 286 residues out of total 2832 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 235 time to evaluate : 1.125 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 222 ASP cc_start: 0.8509 (OUTLIER) cc_final: 0.8210 (t0) REVERT: D 318 ILE cc_start: 0.8526 (OUTLIER) cc_final: 0.8284 (mt) REVERT: E 140 GLU cc_start: 0.8314 (OUTLIER) cc_final: 0.7789 (pm20) REVERT: F 221 ASP cc_start: 0.8598 (t70) cc_final: 0.8223 (m-30) REVERT: F 239 ASP cc_start: 0.8593 (OUTLIER) cc_final: 0.8336 (m-30) REVERT: G 296 GLU cc_start: 0.8179 (OUTLIER) cc_final: 0.7376 (mp0) REVERT: G 308 ASN cc_start: 0.8079 (t0) cc_final: 0.7610 (p0) REVERT: H 139 MET cc_start: 0.8814 (OUTLIER) cc_final: 0.8550 (mmm) REVERT: H 277 GLU cc_start: 0.8639 (mp0) cc_final: 0.8130 (mp0) REVERT: H 296 GLU cc_start: 0.8112 (OUTLIER) cc_final: 0.7718 (mp0) REVERT: H 308 ASN cc_start: 0.8074 (t0) cc_final: 0.7541 (p0) REVERT: H 327 MET cc_start: 0.7304 (mpm) cc_final: 0.7016 (mpm) REVERT: I 131 ASN cc_start: 0.8851 (m110) cc_final: 0.8554 (m110) REVERT: I 226 SER cc_start: 0.9269 (OUTLIER) cc_final: 0.8944 (p) REVERT: I 308 ASN cc_start: 0.7898 (t0) cc_final: 0.7539 (p0) REVERT: J 296 GLU cc_start: 0.8208 (OUTLIER) cc_final: 0.7326 (mp0) REVERT: J 299 GLU cc_start: 0.7405 (OUTLIER) cc_final: 0.6886 (pp20) REVERT: K 137 LEU cc_start: 0.8522 (mt) cc_final: 0.8110 (mt) REVERT: K 139 MET cc_start: 0.8824 (OUTLIER) cc_final: 0.8539 (mmm) REVERT: K 241 TYR cc_start: 0.8636 (m-80) cc_final: 0.8283 (m-80) REVERT: K 296 GLU cc_start: 0.8156 (OUTLIER) cc_final: 0.7752 (mp0) REVERT: K 308 ASN cc_start: 0.8144 (t0) cc_final: 0.7739 (p0) REVERT: L 133 ASN cc_start: 0.8654 (t0) cc_final: 0.8277 (t0) REVERT: L 226 SER cc_start: 0.9259 (m) cc_final: 0.9028 (p) REVERT: L 290 THR cc_start: 0.8738 (m) cc_final: 0.8435 (p) REVERT: L 299 GLU cc_start: 0.8377 (tt0) cc_final: 0.8043 (tt0) outliers start: 51 outliers final: 23 residues processed: 278 average time/residue: 0.4937 time to fit residues: 166.4422 Evaluate side-chains 260 residues out of total 2832 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 225 time to evaluate : 1.063 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 56 VAL Chi-restraints excluded: chain A residue 121 GLU Chi-restraints excluded: chain B residue 56 VAL Chi-restraints excluded: chain B residue 72 ASN Chi-restraints excluded: chain B residue 217 VAL Chi-restraints excluded: chain C residue 56 VAL Chi-restraints excluded: chain C residue 222 ASP Chi-restraints excluded: chain C residue 232 SER Chi-restraints excluded: chain D residue 56 VAL Chi-restraints excluded: chain D residue 318 ILE Chi-restraints excluded: chain E residue 56 VAL Chi-restraints excluded: chain E residue 72 ASN Chi-restraints excluded: chain E residue 103 ASP Chi-restraints excluded: chain E residue 140 GLU Chi-restraints excluded: chain F residue 15 LEU Chi-restraints excluded: chain F residue 239 ASP Chi-restraints excluded: chain G residue 226 SER Chi-restraints excluded: chain G residue 296 GLU Chi-restraints excluded: chain G residue 312 LEU Chi-restraints excluded: chain H residue 139 MET Chi-restraints excluded: chain H residue 203 ASN Chi-restraints excluded: chain H residue 217 VAL Chi-restraints excluded: chain H residue 226 SER Chi-restraints excluded: chain H residue 296 GLU Chi-restraints excluded: chain I residue 203 ASN Chi-restraints excluded: chain I residue 217 VAL Chi-restraints excluded: chain I residue 226 SER Chi-restraints excluded: chain I residue 310 ASP Chi-restraints excluded: chain J residue 296 GLU Chi-restraints excluded: chain J residue 299 GLU Chi-restraints excluded: chain K residue 139 MET Chi-restraints excluded: chain K residue 217 VAL Chi-restraints excluded: chain K residue 226 SER Chi-restraints excluded: chain K residue 296 GLU Chi-restraints excluded: chain L residue 217 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 67 optimal weight: 1.9990 chunk 10 optimal weight: 6.9990 chunk 85 optimal weight: 2.9990 chunk 277 optimal weight: 4.9990 chunk 133 optimal weight: 6.9990 chunk 17 optimal weight: 0.8980 chunk 48 optimal weight: 0.0070 chunk 172 optimal weight: 4.9990 chunk 138 optimal weight: 2.9990 chunk 137 optimal weight: 1.9990 chunk 91 optimal weight: 3.9990 overall best weight: 1.5804 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 72 ASN E 72 ASN G 203 ASN G 316 ASN H 316 ASN I 316 ASN J 203 ASN J 316 ASN K 196 ASN K 203 ASN L 316 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3237 r_free = 0.3237 target = 0.089343 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2855 r_free = 0.2855 target = 0.066913 restraints weight = 47975.434| |-----------------------------------------------------------------------------| r_work (start): 0.2826 rms_B_bonded: 2.73 r_work: 0.2673 rms_B_bonded: 3.15 restraints_weight: 0.5000 r_work: 0.2522 rms_B_bonded: 5.00 restraints_weight: 0.2500 r_work (final): 0.2522 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8902 moved from start: 0.2316 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 27324 Z= 0.185 Angle : 0.562 11.399 36966 Z= 0.290 Chirality : 0.044 0.188 3966 Planarity : 0.004 0.053 4632 Dihedral : 6.202 35.600 3924 Min Nonbonded Distance : 1.866 Molprobity Statistics. All-atom Clashscore : 5.89 Ramachandran Plot: Outliers : 0.09 % Allowed : 2.61 % Favored : 97.29 % Rotamer: Outliers : 1.52 % Allowed : 14.76 % Favored : 83.72 % 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: 0.66 (0.15), residues: 3174 helix: 1.13 (0.15), residues: 1248 sheet: -0.15 (0.21), residues: 558 loop : 0.22 (0.18), residues: 1368 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG D 71 TYR 0.028 0.001 TYR C 42 PHE 0.016 0.001 PHE K 304 TRP 0.041 0.001 TRP F 273 HIS 0.004 0.001 HIS A 57 Details of bonding type rmsd/Z covalent geometry : bond 0.00447 / 0.18 (27324) covalent geometry : angle 0.56155 / 0.29 (36966) hydrogen bonds : bond 0.03997 / 2.69 ( 1016) hydrogen bonds : angle 4.62617 / 3.21 ( 2892) *********************** 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 270 residues out of total 2832 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 227 time to evaluate : 0.963 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 222 ASP cc_start: 0.8686 (OUTLIER) cc_final: 0.8386 (t0) REVERT: D 90 GLN cc_start: 0.7234 (mt0) cc_final: 0.6994 (mp10) REVERT: E 140 GLU cc_start: 0.8553 (OUTLIER) cc_final: 0.8288 (pm20) REVERT: F 221 ASP cc_start: 0.8865 (t70) cc_final: 0.8486 (m-30) REVERT: G 296 GLU cc_start: 0.8278 (OUTLIER) cc_final: 0.7434 (mp0) REVERT: G 308 ASN cc_start: 0.8075 (t0) cc_final: 0.7577 (p0) REVERT: H 139 MET cc_start: 0.8792 (mmt) cc_final: 0.8526 (mmm) REVERT: H 277 GLU cc_start: 0.8674 (mp0) cc_final: 0.8168 (mp0) REVERT: H 296 GLU cc_start: 0.8225 (OUTLIER) cc_final: 0.7824 (mp0) REVERT: H 308 ASN cc_start: 0.8044 (t0) cc_final: 0.7488 (p0) REVERT: H 327 MET cc_start: 0.7282 (mpm) cc_final: 0.6994 (mpm) REVERT: I 131 ASN cc_start: 0.8863 (m110) cc_final: 0.8566 (m110) REVERT: I 133 ASN cc_start: 0.8476 (p0) cc_final: 0.7608 (p0) REVERT: I 308 ASN cc_start: 0.7857 (t0) cc_final: 0.7479 (p0) REVERT: J 296 GLU cc_start: 0.8279 (OUTLIER) cc_final: 0.7374 (mp0) REVERT: K 139 MET cc_start: 0.8773 (OUTLIER) cc_final: 0.8536 (mmm) REVERT: K 241 TYR cc_start: 0.8859 (m-80) cc_final: 0.8550 (m-80) REVERT: K 296 GLU cc_start: 0.8234 (OUTLIER) cc_final: 0.7815 (mp0) REVERT: K 308 ASN cc_start: 0.8204 (t0) cc_final: 0.7736 (p0) REVERT: L 133 ASN cc_start: 0.8685 (t0) cc_final: 0.8286 (t0) outliers start: 43 outliers final: 25 residues processed: 264 average time/residue: 0.4935 time to fit residues: 158.4890 Evaluate side-chains 249 residues out of total 2832 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 217 time to evaluate : 1.068 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 56 VAL Chi-restraints excluded: chain A residue 121 GLU Chi-restraints excluded: chain B residue 56 VAL Chi-restraints excluded: chain B residue 72 ASN Chi-restraints excluded: chain B residue 217 VAL Chi-restraints excluded: chain C residue 56 VAL Chi-restraints excluded: chain C residue 222 ASP Chi-restraints excluded: chain C residue 232 SER Chi-restraints excluded: chain D residue 56 VAL Chi-restraints excluded: chain E residue 56 VAL Chi-restraints excluded: chain E residue 72 ASN Chi-restraints excluded: chain E residue 103 ASP Chi-restraints excluded: chain E residue 140 GLU Chi-restraints excluded: chain F residue 15 LEU Chi-restraints excluded: chain G residue 226 SER Chi-restraints excluded: chain G residue 296 GLU Chi-restraints excluded: chain G residue 312 LEU Chi-restraints excluded: chain H residue 203 ASN Chi-restraints excluded: chain H residue 217 VAL Chi-restraints excluded: chain H residue 226 SER Chi-restraints excluded: chain H residue 296 GLU Chi-restraints excluded: chain I residue 203 ASN Chi-restraints excluded: chain I residue 217 VAL Chi-restraints excluded: chain I residue 226 SER Chi-restraints excluded: chain I residue 310 ASP Chi-restraints excluded: chain J residue 296 GLU Chi-restraints excluded: chain K residue 139 MET Chi-restraints excluded: chain K residue 217 VAL Chi-restraints excluded: chain K residue 226 SER Chi-restraints excluded: chain K residue 296 GLU Chi-restraints excluded: chain L residue 203 ASN Chi-restraints excluded: chain L residue 217 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 38 optimal weight: 3.9990 chunk 66 optimal weight: 0.9980 chunk 136 optimal weight: 0.0050 chunk 172 optimal weight: 4.9990 chunk 233 optimal weight: 0.0030 chunk 157 optimal weight: 0.0370 chunk 129 optimal weight: 0.9990 chunk 21 optimal weight: 0.9990 chunk 56 optimal weight: 0.7980 chunk 228 optimal weight: 2.9990 chunk 300 optimal weight: 1.9990 overall best weight: 0.3682 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 246 GLN B 72 ASN E 72 ASN E 246 GLN G 203 ASN G 316 ASN H 316 ASN I 316 ASN J 203 ASN K 196 ASN K 316 ASN L 316 ASN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3294 r_free = 0.3294 target = 0.092925 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2921 r_free = 0.2921 target = 0.070369 restraints weight = 47630.766| |-----------------------------------------------------------------------------| r_work (start): 0.2890 rms_B_bonded: 2.79 r_work: 0.2737 rms_B_bonded: 3.24 restraints_weight: 0.5000 r_work (final): 0.2737 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8760 moved from start: 0.2499 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.042 27324 Z= 0.095 Angle : 0.504 10.670 36966 Z= 0.261 Chirality : 0.041 0.176 3966 Planarity : 0.003 0.050 4632 Dihedral : 5.838 31.950 3924 Min Nonbonded Distance : 1.953 Molprobity Statistics. All-atom Clashscore : 5.41 Ramachandran Plot: Outliers : 0.03 % Allowed : 2.77 % Favored : 97.20 % Rotamer: Outliers : 1.17 % Allowed : 15.25 % Favored : 83.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.76 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.93 (0.15), residues: 3174 helix: 1.16 (0.15), residues: 1242 sheet: 0.61 (0.21), residues: 480 loop : 0.29 (0.17), residues: 1452 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG B 71 TYR 0.017 0.001 TYR A 42 PHE 0.010 0.001 PHE F 22 TRP 0.041 0.001 TRP F 273 HIS 0.003 0.001 HIS A 57 Details of bonding type rmsd/Z covalent geometry : bond 0.00212 / 0.10 (27324) covalent geometry : angle 0.50394 / 0.26 (36966) hydrogen bonds : bond 0.02910 / 1.95 ( 1016) hydrogen bonds : angle 4.44730 / 3.08 ( 2892) ********************** 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 262 residues out of total 2832 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 229 time to evaluate : 1.112 Fit side-chains revert: symmetry clash REVERT: C 222 ASP cc_start: 0.8514 (OUTLIER) cc_final: 0.8222 (t0) REVERT: D 90 GLN cc_start: 0.7154 (mt0) cc_final: 0.6938 (mp10) REVERT: E 140 GLU cc_start: 0.8309 (OUTLIER) cc_final: 0.7853 (pm20) REVERT: F 221 ASP cc_start: 0.8516 (t70) cc_final: 0.8156 (m-30) REVERT: G 296 GLU cc_start: 0.8188 (OUTLIER) cc_final: 0.7384 (mp0) REVERT: G 308 ASN cc_start: 0.8049 (t0) cc_final: 0.7592 (p0) REVERT: H 139 MET cc_start: 0.8808 (mmt) cc_final: 0.8522 (mmm) REVERT: H 241 TYR cc_start: 0.8702 (m-80) cc_final: 0.8214 (m-80) REVERT: H 277 GLU cc_start: 0.8640 (mp0) cc_final: 0.8121 (mp0) REVERT: H 296 GLU cc_start: 0.8100 (OUTLIER) cc_final: 0.7701 (mp0) REVERT: H 308 ASN cc_start: 0.8058 (t0) cc_final: 0.7539 (p0) REVERT: H 327 MET cc_start: 0.7274 (mpm) cc_final: 0.6976 (mpm) REVERT: I 131 ASN cc_start: 0.8926 (m110) cc_final: 0.8641 (m-40) REVERT: I 226 SER cc_start: 0.9268 (m) cc_final: 0.8945 (p) REVERT: I 308 ASN cc_start: 0.7892 (t0) cc_final: 0.7519 (p0) REVERT: J 296 GLU cc_start: 0.8210 (OUTLIER) cc_final: 0.7379 (mp0) REVERT: J 299 GLU cc_start: 0.7401 (OUTLIER) cc_final: 0.6971 (pp20) REVERT: K 131 ASN cc_start: 0.8911 (m-40) cc_final: 0.8627 (m110) REVERT: K 139 MET cc_start: 0.8805 (OUTLIER) cc_final: 0.8532 (mmm) REVERT: K 241 TYR cc_start: 0.8649 (m-80) cc_final: 0.8325 (m-80) REVERT: K 296 GLU cc_start: 0.8131 (OUTLIER) cc_final: 0.7739 (mp0) REVERT: K 308 ASN cc_start: 0.8060 (t0) cc_final: 0.7674 (p0) REVERT: L 133 ASN cc_start: 0.8651 (t0) cc_final: 0.8277 (t0) REVERT: L 290 THR cc_start: 0.8725 (m) cc_final: 0.8432 (p) REVERT: L 299 GLU cc_start: 0.8371 (tt0) cc_final: 0.8021 (tt0) outliers start: 33 outliers final: 20 residues processed: 259 average time/residue: 0.4998 time to fit residues: 156.7084 Evaluate side-chains 251 residues out of total 2832 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 223 time to evaluate : 1.066 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 56 VAL Chi-restraints excluded: chain A residue 121 GLU Chi-restraints excluded: chain B residue 56 VAL Chi-restraints excluded: chain B residue 72 ASN Chi-restraints excluded: chain B residue 217 VAL Chi-restraints excluded: chain C residue 56 VAL Chi-restraints excluded: chain C residue 222 ASP Chi-restraints excluded: chain E residue 56 VAL Chi-restraints excluded: chain E residue 103 ASP Chi-restraints excluded: chain E residue 140 GLU Chi-restraints excluded: chain F residue 15 LEU Chi-restraints excluded: chain G residue 296 GLU Chi-restraints excluded: chain G residue 312 LEU Chi-restraints excluded: chain H residue 203 ASN Chi-restraints excluded: chain H residue 217 VAL Chi-restraints excluded: chain H residue 226 SER Chi-restraints excluded: chain H residue 296 GLU Chi-restraints excluded: chain I residue 203 ASN Chi-restraints excluded: chain I residue 217 VAL Chi-restraints excluded: chain I residue 310 ASP Chi-restraints excluded: chain J residue 296 GLU Chi-restraints excluded: chain J residue 299 GLU Chi-restraints excluded: chain K residue 139 MET Chi-restraints excluded: chain K residue 201 MET Chi-restraints excluded: chain K residue 217 VAL Chi-restraints excluded: chain K residue 226 SER Chi-restraints excluded: chain K residue 296 GLU Chi-restraints excluded: chain L residue 217 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 259 optimal weight: 3.9990 chunk 143 optimal weight: 3.9990 chunk 91 optimal weight: 2.9990 chunk 300 optimal weight: 2.9990 chunk 55 optimal weight: 1.9990 chunk 294 optimal weight: 0.4980 chunk 123 optimal weight: 0.0060 chunk 23 optimal weight: 1.9990 chunk 87 optimal weight: 0.6980 chunk 132 optimal weight: 3.9990 chunk 166 optimal weight: 0.9990 overall best weight: 0.8400 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 72 ASN G 203 ASN G 316 ASN H 316 ASN I 316 ASN J 203 ASN K 196 ASN K 316 ASN L 316 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3274 r_free = 0.3274 target = 0.091618 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2896 r_free = 0.2896 target = 0.069048 restraints weight = 47381.997| |-----------------------------------------------------------------------------| r_work (start): 0.2870 rms_B_bonded: 2.78 r_work: 0.2720 rms_B_bonded: 3.21 restraints_weight: 0.5000 r_work (final): 0.2720 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8782 moved from start: 0.2466 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.080 27324 Z= 0.121 Angle : 0.520 12.377 36966 Z= 0.267 Chirality : 0.042 0.153 3966 Planarity : 0.003 0.051 4632 Dihedral : 5.827 32.073 3924 Min Nonbonded Distance : 1.917 Molprobity Statistics. All-atom Clashscore : 5.57 Ramachandran Plot: Outliers : 0.03 % Allowed : 2.77 % Favored : 97.20 % Rotamer: Outliers : 1.34 % Allowed : 15.25 % 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: 0.77 (0.15), residues: 3174 helix: 1.19 (0.15), residues: 1242 sheet: -0.05 (0.21), residues: 540 loop : 0.29 (0.18), residues: 1392 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG D 71 TYR 0.020 0.001 TYR C 42 PHE 0.010 0.001 PHE K 304 TRP 0.041 0.001 TRP F 273 HIS 0.004 0.001 HIS A 57 Details of bonding type rmsd/Z covalent geometry : bond 0.00290 / 0.12 (27324) covalent geometry : angle 0.52010 / 0.27 (36966) hydrogen bonds : bond 0.03270 / 2.20 ( 1016) hydrogen bonds : angle 4.49330 / 3.11 ( 2892) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6673.38 seconds wall clock time: 115 minutes 6.12 seconds (6906.12 seconds total)