Starting phenix.real_space_refine on Fri Mar 6 02:39:00 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9pqr_71789/03_2026/9pqr_71789.cif Found real_map, /net/cci-nas-00/data/ceres_data/9pqr_71789/03_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/9pqr_71789/03_2026/9pqr_71789.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9pqr_71789/03_2026/9pqr_71789.map" model { file = "/net/cci-nas-00/data/ceres_data/9pqr_71789/03_2026/9pqr_71789.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9pqr_71789/03_2026/9pqr_71789.cif" } 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): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 26754 Number of models: 1 Model: "" Number of chains: 24 Chain: "A" Number of atoms: 2674 Number of conformers: 1 Conformer: "" Number of residues, atoms: 326, 2674 Classifications: {'peptide': 326} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 315} Chain: "B" Number of atoms: 2674 Number of conformers: 1 Conformer: "" Number of residues, atoms: 326, 2674 Classifications: {'peptide': 326} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 315} Chain: "C" Number of atoms: 2674 Number of conformers: 1 Conformer: "" Number of residues, atoms: 326, 2674 Classifications: {'peptide': 326} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 315} Chain: "D" Number of atoms: 2674 Number of conformers: 1 Conformer: "" Number of residues, atoms: 326, 2674 Classifications: {'peptide': 326} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 315} Chain: "E" Number of atoms: 2674 Number of conformers: 1 Conformer: "" Number of residues, atoms: 326, 2674 Classifications: {'peptide': 326} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 315} Chain: "F" Number of atoms: 2674 Number of conformers: 1 Conformer: "" Number of residues, atoms: 326, 2674 Classifications: {'peptide': 326} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 315} Chain: "G" Number of atoms: 1720 Number of conformers: 1 Conformer: "" Number of residues, atoms: 207, 1720 Classifications: {'peptide': 207} Link IDs: {'PCIS': 1, 'PTRANS': 6, 'TRANS': 199} Chain: "H" Number of atoms: 1720 Number of conformers: 1 Conformer: "" Number of residues, atoms: 207, 1720 Classifications: {'peptide': 207} Link IDs: {'PCIS': 1, 'PTRANS': 6, 'TRANS': 199} Chain: "I" Number of atoms: 1720 Number of conformers: 1 Conformer: "" Number of residues, atoms: 207, 1720 Classifications: {'peptide': 207} Link IDs: {'PCIS': 1, 'PTRANS': 6, 'TRANS': 199} Chain: "J" Number of atoms: 1720 Number of conformers: 1 Conformer: "" Number of residues, atoms: 207, 1720 Classifications: {'peptide': 207} Link IDs: {'PCIS': 1, 'PTRANS': 6, 'TRANS': 199} Chain: "K" Number of atoms: 1720 Number of conformers: 1 Conformer: "" Number of residues, atoms: 207, 1720 Classifications: {'peptide': 207} Link IDs: {'PCIS': 1, 'PTRANS': 6, 'TRANS': 199} Chain: "L" Number of atoms: 1720 Number of conformers: 1 Conformer: "" Number of residues, atoms: 207, 1720 Classifications: {'peptide': 207} Link IDs: {'PCIS': 1, 'PTRANS': 6, 'TRANS': 199} Chain: "A" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 33 Unusual residues: {' MG': 2, 'AGS': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "B" Number of atoms: 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: 6.13, per 1000 atoms: 0.23 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: 2.15 Conformation dependent library (CDL) restraints added in 1.1 seconds 6348 Ramachandran restraints generated. 3174 Oldfield, 0 Emsley, 3174 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6000 Finding SS restraints... Secondary structure from input PDB file: 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: 1.02 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: 4.89 Time building geometry restraints manager: 2.95 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=" N ASN F 91 " pdb=" CA ASN F 91 " ideal model delta sigma weight residual 1.457 1.473 -0.015 1.29e-02 6.01e+03 1.44e+00 bond pdb=" CA ASN F 72 " pdb=" CB ASN F 72 " ideal model delta sigma weight residual 1.531 1.567 -0.036 3.12e-02 1.03e+03 1.33e+00 bond pdb=" C ASN K 303 " pdb=" N PHE K 304 " ideal model delta sigma weight residual 1.333 1.363 -0.031 2.74e-02 1.33e+03 1.26e+00 bond pdb=" CA ASN F 91 " pdb=" CB ASN F 91 " ideal model delta sigma weight residual 1.530 1.513 0.017 1.69e-02 3.50e+03 1.05e+00 bond pdb=" CG ARG A 224 " pdb=" CD ARG A 224 " ideal model delta sigma weight residual 1.520 1.490 0.030 3.00e-02 1.11e+03 1.02e+00 ... (remaining 27319 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.08: 36445 2.08 - 4.15: 474 4.15 - 6.23: 43 6.23 - 8.31: 3 8.31 - 10.38: 1 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=" 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 angle pdb=" C PHE J 195 " pdb=" N ASN J 196 " pdb=" CA ASN J 196 " ideal model delta sigma weight residual 121.54 127.59 -6.05 1.91e+00 2.74e-01 1.00e+01 ... (remaining 36961 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 29.90: 15588 29.90 - 59.80: 765 59.80 - 89.69: 88 89.69 - 119.59: 4 119.59 - 149.49: 1 Dihedral angle restraints: 16446 sinusoidal: 7140 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=" O1A AGS L 401 " pdb=" O3A AGS L 401 " pdb=" PA AGS L 401 " pdb=" PB AGS L 401 " ideal model delta sinusoidal sigma weight residual -67.73 81.76 -149.49 1 3.00e+01 1.11e-03 1.99e+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 ... (remaining 16443 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.033: 2506 0.033 - 0.065: 1034 0.065 - 0.098: 244 0.098 - 0.130: 186 0.130 - 0.163: 20 Chirality restraints: 3990 Sorted by residual: chirality pdb=" CB THR G 229 " pdb=" CA THR G 229 " pdb=" OG1 THR G 229 " pdb=" CG2 THR G 229 " both_signs ideal model delta sigma weight residual False 2.55 2.39 0.16 2.00e-01 2.50e+01 6.62e-01 chirality pdb=" CA ILE E 100 " pdb=" N ILE E 100 " pdb=" C ILE E 100 " pdb=" CB ILE E 100 " both_signs ideal model delta sigma weight residual False 2.43 2.59 -0.15 2.00e-01 2.50e+01 5.97e-01 chirality pdb=" CA GLU D 18 " pdb=" N GLU D 18 " pdb=" C GLU D 18 " pdb=" CB GLU D 18 " both_signs ideal model delta sigma weight residual False 2.51 2.36 0.15 2.00e-01 2.50e+01 5.89e-01 ... (remaining 3987 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: 5.550 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: 0.020 Extract box with map and model: 0.420 Check model and map are aligned: 0.070 Set scattering table: 0.080 Process input model: 24.360 Find NCS groups from input model: 0.580 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:6.150 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 37.310 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8866 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 : 0.004 0.039 27324 Z= 0.149 Angle : 0.576 10.381 36966 Z= 0.316 Chirality : 0.042 0.163 3990 Planarity : 0.004 0.052 4632 Dihedral : 16.594 149.488 10446 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 covalent geometry : bond 0.00351 (27324) covalent geometry : angle 0.57576 (36966) hydrogen bonds : bond 0.25146 ( 1016) hydrogen bonds : angle 7.94256 ( 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 : 1.049 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: 0.5799 time to fit residues: 225.7229 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 : 1.049 ------------------------------------------------------------------------------- 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: 4.9990 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: 1.9990 chunk 183 optimal weight: 3.9990 chunk 298 optimal weight: 4.9990 overall best weight: 1.7386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 203 ASN H 156 ASN H 316 ASN I 156 ASN I 203 ASN I 308 ASN J 203 ASN K 156 ASN K 316 ASN L 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 = 0.3240 r_free = 0.3240 target = 0.089695 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2857 r_free = 0.2857 target = 0.067201 restraints weight = 48331.343| |-----------------------------------------------------------------------------| r_work (start): 0.2827 rms_B_bonded: 2.75 r_work: 0.2675 rms_B_bonded: 3.16 restraints_weight: 0.5000 r_work (final): 0.2675 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8580 moved from start: 0.1336 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.043 27324 Z= 0.209 Angle : 0.625 8.656 36966 Z= 0.332 Chirality : 0.046 0.163 3990 Planarity : 0.004 0.046 4632 Dihedral : 11.601 145.956 3714 Min Nonbonded Distance : 1.875 Molprobity Statistics. All-atom Clashscore : 6.53 Ramachandran Plot: Outliers : 0.16 % Allowed : 2.74 % Favored : 97.10 % Rotamer: Outliers : 1.24 % Allowed : 7.49 % Favored : 91.28 % 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: 0.23 (0.15), residues: 3174 helix: 0.61 (0.14), residues: 1224 sheet: -0.26 (0.21), residues: 588 loop : 0.11 (0.18), residues: 1362 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG I 319 TYR 0.026 0.002 TYR C 42 PHE 0.024 0.002 PHE K 304 TRP 0.016 0.001 TRP D 231 HIS 0.006 0.002 HIS A 57 Details of bonding type rmsd covalent geometry : bond 0.00503 (27324) covalent geometry : angle 0.62502 (36966) hydrogen bonds : bond 0.05379 ( 1016) hydrogen bonds : angle 5.50203 ( 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 : 1.044 Fit side-chains REVERT: A 55 THR cc_start: 0.8800 (m) cc_final: 0.8554 (p) REVERT: D 327 MET cc_start: 0.6278 (ppp) cc_final: 0.6058 (pp-130) REVERT: H 241 TYR cc_start: 0.8775 (m-80) cc_final: 0.8548 (m-80) REVERT: H 277 GLU cc_start: 0.8706 (mp0) cc_final: 0.8210 (mp0) REVERT: H 299 GLU cc_start: 0.7239 (pp20) cc_final: 0.6913 (pp20) REVERT: H 327 MET cc_start: 0.7270 (OUTLIER) cc_final: 0.6945 (mpm) REVERT: I 131 ASN cc_start: 0.9056 (m110) cc_final: 0.8761 (m110) REVERT: J 299 GLU cc_start: 0.7467 (pp20) cc_final: 0.7095 (pp20) REVERT: L 131 ASN cc_start: 0.8956 (m110) cc_final: 0.8754 (m110) REVERT: L 133 ASN cc_start: 0.8664 (t0) cc_final: 0.8098 (t0) REVERT: L 137 LEU cc_start: 0.8723 (mt) cc_final: 0.8417 (mp) REVERT: L 299 GLU cc_start: 0.8406 (tt0) cc_final: 0.8029 (tt0) outliers start: 35 outliers final: 14 residues processed: 281 average time/residue: 0.5543 time to fit residues: 185.8313 Evaluate side-chains 252 residues out of total 2832 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 237 time to evaluate : 1.088 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 232 SER Chi-restraints excluded: chain D residue 89 ILE Chi-restraints excluded: chain E residue 140 GLU Chi-restraints excluded: chain E 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 H residue 327 MET Chi-restraints excluded: chain I residue 189 ASP Chi-restraints excluded: chain I residue 226 SER Chi-restraints excluded: chain I residue 320 LYS 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: 0.5980 chunk 184 optimal weight: 0.0770 chunk 97 optimal weight: 1.9990 chunk 89 optimal weight: 0.8980 chunk 94 optimal weight: 4.9990 chunk 292 optimal weight: 10.0000 chunk 250 optimal weight: 6.9990 overall best weight: 0.6540 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 72 ASN E 72 ASN F 246 GLN G 131 ASN G 203 ASN G 316 ASN H 131 ASN H 316 ASN I 316 ASN J 131 ASN J 203 ASN K 316 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 = 0.3271 r_free = 0.3271 target = 0.091596 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2892 r_free = 0.2892 target = 0.069060 restraints weight = 47897.965| |-----------------------------------------------------------------------------| r_work (start): 0.2861 rms_B_bonded: 2.79 r_work: 0.2712 rms_B_bonded: 3.21 restraints_weight: 0.5000 r_work (final): 0.2712 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8535 moved from start: 0.1574 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 27324 Z= 0.115 Angle : 0.521 8.155 36966 Z= 0.275 Chirality : 0.042 0.149 3990 Planarity : 0.004 0.036 4632 Dihedral : 11.189 147.182 3708 Min Nonbonded Distance : 1.940 Molprobity Statistics. All-atom Clashscore : 5.91 Ramachandran Plot: Outliers : 0.13 % Allowed : 2.43 % Favored : 97.45 % Rotamer: Outliers : 1.06 % Allowed : 10.31 % Favored : 88.63 % 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: 0.45 (0.15), residues: 3174 helix: 0.96 (0.15), residues: 1206 sheet: -0.28 (0.21), residues: 570 loop : 0.12 (0.17), residues: 1398 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG E 224 TYR 0.019 0.001 TYR C 42 PHE 0.012 0.001 PHE K 304 TRP 0.018 0.001 TRP A 273 HIS 0.005 0.001 HIS A 57 Details of bonding type rmsd covalent geometry : bond 0.00257 (27324) covalent geometry : angle 0.52070 (36966) hydrogen bonds : bond 0.04212 ( 1016) hydrogen bonds : angle 5.02889 ( 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 279 residues out of total 2832 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 249 time to evaluate : 1.048 Fit side-chains REVERT: A 55 THR cc_start: 0.8820 (m) cc_final: 0.8583 (p) REVERT: A 318 ILE cc_start: 0.8590 (OUTLIER) cc_final: 0.8364 (mp) REVERT: G 308 ASN cc_start: 0.8118 (t0) cc_final: 0.7536 (p0) REVERT: H 139 MET cc_start: 0.8822 (mmt) cc_final: 0.8533 (mmm) REVERT: H 276 LYS cc_start: 0.8724 (mppt) cc_final: 0.8507 (mppt) REVERT: H 277 GLU cc_start: 0.8693 (mp0) cc_final: 0.8190 (mp0) REVERT: H 299 GLU cc_start: 0.7291 (pp20) cc_final: 0.6865 (pp20) REVERT: H 327 MET cc_start: 0.7248 (OUTLIER) cc_final: 0.6914 (mpm) REVERT: I 131 ASN cc_start: 0.9027 (m110) cc_final: 0.8741 (m110) REVERT: J 299 GLU cc_start: 0.7470 (pp20) cc_final: 0.7019 (pp20) REVERT: L 133 ASN cc_start: 0.8671 (t0) cc_final: 0.8137 (t0) REVERT: L 137 LEU cc_start: 0.8702 (mt) cc_final: 0.8393 (mp) REVERT: L 299 GLU cc_start: 0.8408 (tt0) cc_final: 0.8063 (tt0) outliers start: 30 outliers final: 15 residues processed: 275 average time/residue: 0.5073 time to fit residues: 167.6463 Evaluate side-chains 253 residues out of total 2832 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 236 time to evaluate : 1.026 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 318 ILE Chi-restraints excluded: chain B residue 203 ASN Chi-restraints excluded: chain C residue 232 SER Chi-restraints excluded: chain D residue 318 ILE 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 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 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=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 258 optimal weight: 4.9990 chunk 157 optimal weight: 3.9990 chunk 219 optimal weight: 5.9990 chunk 233 optimal weight: 6.9990 chunk 230 optimal weight: 4.9990 chunk 105 optimal weight: 1.9990 chunk 110 optimal weight: 3.9990 chunk 118 optimal weight: 3.9990 chunk 240 optimal weight: 2.9990 chunk 170 optimal weight: 0.4980 chunk 232 optimal weight: 4.9990 overall best weight: 2.6988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 72 ASN C 242 ASN G 131 ASN G 203 ASN G 316 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: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3207 r_free = 0.3207 target = 0.087747 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2811 r_free = 0.2811 target = 0.064904 restraints weight = 48356.558| |-----------------------------------------------------------------------------| r_work (start): 0.2787 rms_B_bonded: 2.83 r_work: 0.2634 rms_B_bonded: 3.21 restraints_weight: 0.5000 r_work (final): 0.2634 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8566 moved from start: 0.1735 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.051 27324 Z= 0.280 Angle : 0.599 8.464 36966 Z= 0.313 Chirality : 0.047 0.166 3990 Planarity : 0.004 0.053 4632 Dihedral : 11.732 150.118 3708 Min Nonbonded Distance : 1.836 Molprobity Statistics. All-atom Clashscore : 6.06 Ramachandran Plot: Outliers : 0.19 % Allowed : 2.96 % Favored : 96.85 % Rotamer: Outliers : 1.94 % Allowed : 11.76 % Favored : 86.30 % 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: 0.34 (0.15), residues: 3174 helix: 0.93 (0.15), residues: 1218 sheet: -0.46 (0.20), residues: 588 loop : 0.07 (0.18), residues: 1368 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG J 224 TYR 0.026 0.002 TYR C 42 PHE 0.025 0.002 PHE K 304 TRP 0.021 0.002 TRP F 273 HIS 0.005 0.002 HIS C 57 Details of bonding type rmsd covalent geometry : bond 0.00689 (27324) covalent geometry : angle 0.59873 (36966) hydrogen bonds : bond 0.04877 ( 1016) hydrogen bonds : angle 5.04905 ( 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 294 residues out of total 2832 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 239 time to evaluate : 1.025 Fit side-chains REVERT: A 121 GLU cc_start: 0.8731 (OUTLIER) cc_final: 0.8425 (pm20) REVERT: A 318 ILE cc_start: 0.8566 (OUTLIER) cc_final: 0.8349 (mp) REVERT: C 69 SER cc_start: 0.9022 (t) cc_final: 0.8445 (p) REVERT: G 241 TYR cc_start: 0.8711 (m-80) cc_final: 0.8331 (m-80) REVERT: H 139 MET cc_start: 0.8790 (mmt) cc_final: 0.8521 (mmm) REVERT: H 276 LYS cc_start: 0.8711 (mppt) cc_final: 0.8464 (mppt) REVERT: H 277 GLU cc_start: 0.8696 (mp0) cc_final: 0.8190 (mp0) REVERT: H 299 GLU cc_start: 0.7309 (pp20) cc_final: 0.6816 (pp20) REVERT: I 131 ASN cc_start: 0.8975 (m110) cc_final: 0.8685 (m110) REVERT: J 299 GLU cc_start: 0.7483 (pp20) cc_final: 0.6980 (pp20) REVERT: L 133 ASN cc_start: 0.8672 (t0) cc_final: 0.8097 (t0) REVERT: L 137 LEU cc_start: 0.8689 (mt) cc_final: 0.8366 (mp) REVERT: L 299 GLU cc_start: 0.8429 (tt0) cc_final: 0.8043 (tt0) outliers start: 55 outliers final: 26 residues processed: 280 average time/residue: 0.4768 time to fit residues: 161.8735 Evaluate side-chains 256 residues out of total 2832 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 228 time to evaluate : 1.017 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 56 VAL Chi-restraints excluded: chain A residue 121 GLU 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 D residue 318 ILE Chi-restraints excluded: chain E residue 25 LEU Chi-restraints excluded: chain E residue 140 GLU 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 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 189 ASP Chi-restraints excluded: chain I residue 203 ASN Chi-restraints excluded: chain I residue 226 SER Chi-restraints excluded: chain J residue 142 VAL 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: 1.9990 chunk 145 optimal weight: 0.9990 chunk 89 optimal weight: 0.6980 chunk 118 optimal weight: 0.6980 chunk 94 optimal weight: 3.9990 chunk 100 optimal weight: 2.9990 chunk 36 optimal weight: 1.9990 chunk 296 optimal weight: 3.9990 chunk 87 optimal weight: 0.5980 chunk 154 optimal weight: 0.9980 chunk 56 optimal weight: 0.5980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 72 ASN G 131 ASN G 316 ASN H 316 ASN I 316 ASN J 133 ASN J 203 ASN K 316 ASN L 131 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3247 r_free = 0.3247 target = 0.090192 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2864 r_free = 0.2864 target = 0.067628 restraints weight = 47780.962| |-----------------------------------------------------------------------------| r_work (start): 0.2835 rms_B_bonded: 2.77 r_work: 0.2684 rms_B_bonded: 3.18 restraints_weight: 0.5000 r_work (final): 0.2684 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8558 moved from start: 0.1852 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 27324 Z= 0.117 Angle : 0.512 9.332 36966 Z= 0.269 Chirality : 0.042 0.152 3990 Planarity : 0.004 0.043 4632 Dihedral : 11.332 148.245 3708 Min Nonbonded Distance : 1.899 Molprobity Statistics. All-atom Clashscore : 5.99 Ramachandran Plot: Outliers : 0.16 % Allowed : 2.49 % Favored : 97.35 % Rotamer: Outliers : 1.66 % Allowed : 12.64 % Favored : 85.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.76 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.51 (0.15), residues: 3174 helix: 1.13 (0.15), residues: 1212 sheet: -0.48 (0.20), residues: 588 loop : 0.18 (0.18), residues: 1374 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG J 224 TYR 0.021 0.001 TYR C 42 PHE 0.010 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 covalent geometry : bond 0.00267 (27324) covalent geometry : angle 0.51249 (36966) hydrogen bonds : bond 0.03778 ( 1016) hydrogen bonds : angle 4.80424 ( 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 280 residues out of total 2832 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 233 time to evaluate : 1.097 Fit side-chains REVERT: A 121 GLU cc_start: 0.8693 (OUTLIER) cc_final: 0.8413 (pm20) REVERT: A 273 TRP cc_start: 0.7242 (p-90) cc_final: 0.7036 (p-90) REVERT: B 88 ARG cc_start: 0.8136 (ppt170) cc_final: 0.7923 (ptm160) REVERT: C 69 SER cc_start: 0.8989 (t) cc_final: 0.8389 (p) REVERT: G 308 ASN cc_start: 0.8067 (t0) cc_final: 0.7519 (p0) REVERT: H 139 MET cc_start: 0.8825 (mmt) cc_final: 0.8572 (mmm) REVERT: H 276 LYS cc_start: 0.8678 (mppt) cc_final: 0.8436 (mppt) REVERT: H 277 GLU cc_start: 0.8719 (mp0) cc_final: 0.8204 (mp0) REVERT: H 299 GLU cc_start: 0.7372 (pp20) cc_final: 0.6843 (pp20) REVERT: I 131 ASN cc_start: 0.8953 (m110) cc_final: 0.8640 (m110) REVERT: I 275 ASN cc_start: 0.8696 (t0) cc_final: 0.8455 (t160) REVERT: I 276 LYS cc_start: 0.8891 (mppt) cc_final: 0.8684 (mppt) REVERT: J 299 GLU cc_start: 0.7536 (pp20) cc_final: 0.6987 (pp20) REVERT: K 139 MET cc_start: 0.8826 (mmt) cc_final: 0.8586 (mmm) REVERT: K 230 GLU cc_start: 0.8110 (tt0) cc_final: 0.7831 (tt0) REVERT: K 241 TYR cc_start: 0.8676 (m-80) cc_final: 0.8459 (m-80) REVERT: K 308 ASN cc_start: 0.8280 (t0) cc_final: 0.7728 (p0) REVERT: L 133 ASN cc_start: 0.8688 (t0) cc_final: 0.8140 (t0) REVERT: L 137 LEU cc_start: 0.8759 (mt) cc_final: 0.8439 (mp) REVERT: L 299 GLU cc_start: 0.8423 (tt0) cc_final: 0.8051 (tt0) outliers start: 47 outliers final: 29 residues processed: 275 average time/residue: 0.4940 time to fit residues: 164.4101 Evaluate side-chains 259 residues out of total 2832 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 229 time to evaluate : 0.892 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 56 VAL Chi-restraints excluded: chain A residue 121 GLU Chi-restraints excluded: chain A residue 318 ILE Chi-restraints excluded: chain B residue 56 VAL 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 D residue 318 ILE Chi-restraints excluded: chain E residue 25 LEU Chi-restraints excluded: chain E residue 56 VAL Chi-restraints excluded: chain E residue 140 GLU Chi-restraints excluded: chain F residue 15 LEU Chi-restraints excluded: chain G residue 147 ASP 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 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 217 VAL Chi-restraints excluded: chain I residue 226 SER Chi-restraints excluded: chain J residue 203 ASN 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 178 optimal weight: 3.9990 chunk 238 optimal weight: 4.9990 chunk 299 optimal weight: 0.7980 chunk 273 optimal weight: 0.9990 chunk 308 optimal weight: 5.9990 chunk 244 optimal weight: 3.9990 chunk 225 optimal weight: 0.9980 chunk 297 optimal weight: 4.9990 chunk 245 optimal weight: 0.7980 chunk 234 optimal weight: 3.9990 chunk 135 optimal weight: 0.4980 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 72 ASN ** C 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 131 ASN G 316 ASN H 316 ASN I 316 ASN J 133 ASN J 203 ASN K 316 ASN L 131 ASN L 316 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3251 r_free = 0.3251 target = 0.090366 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2868 r_free = 0.2868 target = 0.067773 restraints weight = 47990.848| |-----------------------------------------------------------------------------| r_work (start): 0.2839 rms_B_bonded: 2.78 r_work: 0.2689 rms_B_bonded: 3.18 restraints_weight: 0.5000 r_work (final): 0.2689 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8555 moved from start: 0.1945 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 27324 Z= 0.120 Angle : 0.500 9.892 36966 Z= 0.263 Chirality : 0.042 0.153 3990 Planarity : 0.003 0.037 4632 Dihedral : 11.222 148.835 3708 Min Nonbonded Distance : 1.897 Molprobity Statistics. All-atom Clashscore : 5.69 Ramachandran Plot: Outliers : 0.16 % Allowed : 2.61 % Favored : 97.23 % Rotamer: Outliers : 1.55 % Allowed : 13.42 % Favored : 85.03 % 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: 0.54 (0.15), residues: 3174 helix: 1.18 (0.15), residues: 1212 sheet: -0.49 (0.20), residues: 588 loop : 0.17 (0.18), residues: 1374 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG D 71 TYR 0.021 0.001 TYR C 42 PHE 0.009 0.001 PHE K 304 TRP 0.029 0.001 TRP F 273 HIS 0.004 0.001 HIS A 57 Details of bonding type rmsd covalent geometry : bond 0.00279 (27324) covalent geometry : angle 0.50040 (36966) hydrogen bonds : bond 0.03599 ( 1016) hydrogen bonds : angle 4.71044 ( 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 279 residues out of total 2832 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 235 time to evaluate : 0.905 Fit side-chains REVERT: A 121 GLU cc_start: 0.8720 (OUTLIER) cc_final: 0.8431 (pm20) REVERT: C 69 SER cc_start: 0.8986 (t) cc_final: 0.8365 (p) REVERT: E 36 ASP cc_start: 0.8704 (t0) cc_final: 0.8266 (t0) REVERT: G 308 ASN cc_start: 0.8047 (t0) cc_final: 0.7518 (p0) REVERT: H 139 MET cc_start: 0.8794 (mmt) cc_final: 0.8535 (mmm) REVERT: H 276 LYS cc_start: 0.8664 (mppt) cc_final: 0.8425 (mppt) REVERT: H 277 GLU cc_start: 0.8718 (mp0) cc_final: 0.8199 (mp0) REVERT: H 299 GLU cc_start: 0.7374 (pp20) cc_final: 0.6815 (pp20) REVERT: H 327 MET cc_start: 0.7236 (OUTLIER) cc_final: 0.6933 (mpm) REVERT: I 131 ASN cc_start: 0.8952 (m110) cc_final: 0.8633 (m110) REVERT: J 299 GLU cc_start: 0.7541 (pp20) cc_final: 0.6946 (pp20) REVERT: K 139 MET cc_start: 0.8820 (mmt) cc_final: 0.8566 (mmm) REVERT: K 308 ASN cc_start: 0.8177 (t0) cc_final: 0.7638 (p0) REVERT: L 133 ASN cc_start: 0.8694 (t0) cc_final: 0.8164 (t0) REVERT: L 137 LEU cc_start: 0.8757 (mt) cc_final: 0.8434 (mp) REVERT: L 299 GLU cc_start: 0.8425 (tt0) cc_final: 0.8045 (tt0) outliers start: 44 outliers final: 28 residues processed: 273 average time/residue: 0.4775 time to fit residues: 157.3449 Evaluate side-chains 259 residues out of total 2832 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 229 time to evaluate : 1.032 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 56 VAL Chi-restraints excluded: chain A residue 121 GLU Chi-restraints excluded: chain A residue 318 ILE 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 139 MET 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 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 203 ASN Chi-restraints excluded: chain H residue 217 VAL 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 203 ASN Chi-restraints excluded: chain I residue 217 VAL 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 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: 0.9990 chunk 174 optimal weight: 2.9990 chunk 47 optimal weight: 0.6980 chunk 219 optimal weight: 4.9990 chunk 123 optimal weight: 0.9990 chunk 87 optimal weight: 2.9990 chunk 267 optimal weight: 0.8980 chunk 34 optimal weight: 2.9990 chunk 287 optimal weight: 0.8980 chunk 233 optimal weight: 3.9990 chunk 148 optimal weight: 3.9990 overall best weight: 0.8984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 72 ASN ** C 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 72 ASN G 131 ASN G 316 ASN H 316 ASN I 316 ASN J 133 ASN J 203 ASN J 316 ASN K 316 ASN L 131 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 = 0.3253 r_free = 0.3253 target = 0.090525 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.2873 r_free = 0.2873 target = 0.068056 restraints weight = 47686.160| |-----------------------------------------------------------------------------| r_work (start): 0.2842 rms_B_bonded: 2.76 r_work: 0.2692 rms_B_bonded: 3.17 restraints_weight: 0.5000 r_work (final): 0.2692 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8552 moved from start: 0.2008 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 27324 Z= 0.124 Angle : 0.501 10.401 36966 Z= 0.263 Chirality : 0.042 0.153 3990 Planarity : 0.003 0.038 4632 Dihedral : 11.107 149.069 3708 Min Nonbonded Distance : 1.897 Molprobity Statistics. All-atom Clashscore : 5.72 Ramachandran Plot: Outliers : 0.16 % Allowed : 2.65 % Favored : 97.20 % Rotamer: Outliers : 1.80 % Allowed : 13.81 % Favored : 84.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.76 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.64 (0.15), residues: 3174 helix: 1.25 (0.15), residues: 1206 sheet: -0.36 (0.19), residues: 618 loop : 0.22 (0.18), residues: 1350 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG D 71 TYR 0.023 0.001 TYR C 42 PHE 0.010 0.001 PHE K 138 TRP 0.038 0.001 TRP F 273 HIS 0.004 0.001 HIS A 57 Details of bonding type rmsd covalent geometry : bond 0.00294 (27324) covalent geometry : angle 0.50145 (36966) hydrogen bonds : bond 0.03534 ( 1016) hydrogen bonds : angle 4.66078 ( 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 284 residues out of total 2832 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 233 time to evaluate : 1.155 Fit side-chains REVERT: A 121 GLU cc_start: 0.8725 (OUTLIER) cc_final: 0.8460 (pm20) REVERT: C 69 SER cc_start: 0.8981 (t) cc_final: 0.8356 (p) REVERT: E 36 ASP cc_start: 0.8696 (t0) cc_final: 0.8257 (t0) REVERT: G 308 ASN cc_start: 0.8035 (t0) cc_final: 0.7522 (p0) REVERT: H 127 GLU cc_start: 0.8482 (pm20) cc_final: 0.8246 (pm20) REVERT: H 139 MET cc_start: 0.8796 (mmt) cc_final: 0.8551 (mmm) REVERT: H 276 LYS cc_start: 0.8640 (mppt) cc_final: 0.8404 (mppt) REVERT: H 277 GLU cc_start: 0.8703 (mp0) cc_final: 0.8188 (mp0) REVERT: H 299 GLU cc_start: 0.7388 (pp20) cc_final: 0.6809 (pp20) REVERT: H 327 MET cc_start: 0.7221 (OUTLIER) cc_final: 0.6913 (mpm) REVERT: I 131 ASN cc_start: 0.8973 (m110) cc_final: 0.8664 (m110) REVERT: I 275 ASN cc_start: 0.8664 (t0) cc_final: 0.8399 (t0) REVERT: I 276 LYS cc_start: 0.8909 (mppt) cc_final: 0.8679 (mppt) REVERT: J 296 GLU cc_start: 0.8273 (OUTLIER) cc_final: 0.7444 (mp0) REVERT: J 299 GLU cc_start: 0.7547 (pp20) cc_final: 0.6951 (pp20) REVERT: K 139 MET cc_start: 0.8825 (mmt) cc_final: 0.8568 (mmm) REVERT: K 230 GLU cc_start: 0.8092 (tt0) cc_final: 0.7845 (tt0) REVERT: K 241 TYR cc_start: 0.8665 (m-80) cc_final: 0.8418 (m-80) REVERT: K 308 ASN cc_start: 0.8205 (t0) cc_final: 0.7681 (p0) REVERT: L 133 ASN cc_start: 0.8725 (t0) cc_final: 0.8191 (t0) REVERT: L 137 LEU cc_start: 0.8769 (mt) cc_final: 0.8442 (mp) REVERT: L 299 GLU cc_start: 0.8417 (tt0) cc_final: 0.8028 (tt0) outliers start: 51 outliers final: 30 residues processed: 275 average time/residue: 0.5163 time to fit residues: 171.0239 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 : 1.008 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 56 VAL Chi-restraints excluded: chain A residue 121 GLU Chi-restraints excluded: chain A residue 318 ILE 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 139 MET 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 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 203 ASN Chi-restraints excluded: chain H residue 217 VAL 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 203 ASN Chi-restraints excluded: chain I residue 217 VAL Chi-restraints excluded: chain I residue 226 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 25 optimal weight: 0.9990 chunk 240 optimal weight: 0.0170 chunk 165 optimal weight: 0.4980 chunk 293 optimal weight: 6.9990 chunk 202 optimal weight: 3.9990 chunk 194 optimal weight: 0.9990 chunk 307 optimal weight: 1.9990 chunk 215 optimal weight: 1.9990 chunk 102 optimal weight: 0.9990 chunk 265 optimal weight: 0.5980 chunk 110 optimal weight: 0.3980 overall best weight: 0.5020 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 72 ASN ** C 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 72 ASN G 131 ASN G 316 ASN H 316 ASN I 316 ASN J 133 ASN J 203 ASN J 316 ASN K 316 ASN L 131 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 = 0.091526 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2890 r_free = 0.2890 target = 0.068957 restraints weight = 48137.968| |-----------------------------------------------------------------------------| r_work (start): 0.2856 rms_B_bonded: 2.79 r_work: 0.2705 rms_B_bonded: 3.20 restraints_weight: 0.5000 r_work (final): 0.2705 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8534 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 : 0.002 0.076 27324 Z= 0.101 Angle : 0.496 11.751 36966 Z= 0.258 Chirality : 0.041 0.151 3990 Planarity : 0.003 0.042 4632 Dihedral : 10.880 148.441 3708 Min Nonbonded Distance : 1.929 Molprobity Statistics. All-atom Clashscore : 5.74 Ramachandran Plot: Outliers : 0.03 % Allowed : 2.93 % Favored : 97.04 % Rotamer: Outliers : 1.59 % Allowed : 14.34 % Favored : 84.07 % 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: 1.15 (0.15), residues: 1236 sheet: -0.31 (0.20), residues: 600 loop : 0.26 (0.18), residues: 1338 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 0.009 0.001 PHE K 138 TRP 0.042 0.001 TRP A 273 HIS 0.003 0.001 HIS A 57 Details of bonding type rmsd covalent geometry : bond 0.00229 (27324) covalent geometry : angle 0.49612 (36966) hydrogen bonds : bond 0.03255 ( 1016) hydrogen bonds : angle 4.58711 ( 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 276 residues out of total 2832 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 231 time to evaluate : 1.092 Fit side-chains REVERT: A 120 MET cc_start: 0.8158 (tpp) cc_final: 0.7808 (mmm) REVERT: C 69 SER cc_start: 0.8961 (t) cc_final: 0.8332 (p) REVERT: E 36 ASP cc_start: 0.8675 (t0) cc_final: 0.8221 (t0) REVERT: G 308 ASN cc_start: 0.8032 (t0) cc_final: 0.7532 (p0) REVERT: H 139 MET cc_start: 0.8791 (mmt) cc_final: 0.8547 (mmm) REVERT: H 276 LYS cc_start: 0.8607 (mppt) cc_final: 0.8377 (mppt) REVERT: H 277 GLU cc_start: 0.8695 (mp0) cc_final: 0.8173 (mp0) REVERT: H 296 GLU cc_start: 0.8180 (OUTLIER) cc_final: 0.7794 (mp0) REVERT: H 299 GLU cc_start: 0.7389 (pp20) cc_final: 0.6951 (pp20) REVERT: H 327 MET cc_start: 0.7206 (OUTLIER) cc_final: 0.6898 (mpm) REVERT: I 131 ASN cc_start: 0.8984 (m110) cc_final: 0.8673 (m110) REVERT: I 276 LYS cc_start: 0.8896 (mppt) cc_final: 0.8695 (mppt) REVERT: J 296 GLU cc_start: 0.8286 (OUTLIER) cc_final: 0.7443 (mp0) REVERT: J 299 GLU cc_start: 0.7528 (pp20) cc_final: 0.6921 (pp20) REVERT: K 139 MET cc_start: 0.8814 (mmt) cc_final: 0.8544 (mmm) REVERT: K 230 GLU cc_start: 0.8082 (tt0) cc_final: 0.7850 (tt0) REVERT: K 241 TYR cc_start: 0.8641 (m-80) cc_final: 0.8423 (m-80) REVERT: K 308 ASN cc_start: 0.8146 (t0) cc_final: 0.7656 (p0) REVERT: L 133 ASN cc_start: 0.8716 (t0) cc_final: 0.8196 (t0) REVERT: L 137 LEU cc_start: 0.8765 (mt) cc_final: 0.8432 (mp) REVERT: L 299 GLU cc_start: 0.8406 (tt0) cc_final: 0.8001 (tt0) outliers start: 45 outliers final: 28 residues processed: 269 average time/residue: 0.5020 time to fit residues: 162.4411 Evaluate side-chains 254 residues out of total 2832 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 223 time to evaluate : 1.034 ------------------------------------------------------------------------------- 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 72 ASN Chi-restraints excluded: chain B residue 217 VAL 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 D residue 318 ILE Chi-restraints excluded: chain E residue 56 VAL 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 189 ASP 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 H residue 327 MET 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 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 131 ASN Chi-restraints excluded: chain L residue 217 VAL Chi-restraints excluded: chain L residue 226 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 67 optimal weight: 4.9990 chunk 10 optimal weight: 6.9990 chunk 85 optimal weight: 3.9990 chunk 277 optimal weight: 4.9990 chunk 133 optimal weight: 3.9990 chunk 17 optimal weight: 0.8980 chunk 48 optimal weight: 3.9990 chunk 172 optimal weight: 4.9990 chunk 138 optimal weight: 4.9990 chunk 137 optimal weight: 0.9990 chunk 91 optimal weight: 4.9990 overall best weight: 2.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 72 ASN E 72 ASN G 131 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 Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3194 r_free = 0.3194 target = 0.086895 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2797 r_free = 0.2797 target = 0.064118 restraints weight = 48519.126| |-----------------------------------------------------------------------------| r_work (start): 0.2775 rms_B_bonded: 2.82 r_work: 0.2622 rms_B_bonded: 3.19 restraints_weight: 0.5000 r_work (final): 0.2622 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8576 moved from start: 0.2092 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.076 27324 Z= 0.300 Angle : 0.632 9.733 36966 Z= 0.328 Chirality : 0.047 0.164 3990 Planarity : 0.004 0.063 4632 Dihedral : 11.609 152.390 3708 Min Nonbonded Distance : 1.802 Molprobity Statistics. All-atom Clashscore : 6.08 Ramachandran Plot: Outliers : 0.19 % Allowed : 3.12 % Favored : 96.69 % Rotamer: Outliers : 1.62 % Allowed : 14.69 % Favored : 83.69 % 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: 0.33 (0.15), residues: 3174 helix: 0.93 (0.15), residues: 1254 sheet: -0.46 (0.19), residues: 618 loop : 0.04 (0.18), residues: 1302 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG D 71 TYR 0.039 0.002 TYR C 42 PHE 0.023 0.002 PHE K 304 TRP 0.044 0.002 TRP F 273 HIS 0.006 0.002 HIS C 57 Details of bonding type rmsd covalent geometry : bond 0.00735 (27324) covalent geometry : angle 0.63183 (36966) hydrogen bonds : bond 0.04750 ( 1016) hydrogen bonds : angle 4.90382 ( 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 280 residues out of total 2832 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 234 time to evaluate : 0.976 Fit side-chains REVERT: A 318 ILE cc_start: 0.8561 (OUTLIER) cc_final: 0.8359 (mp) REVERT: C 69 SER cc_start: 0.9017 (t) cc_final: 0.8450 (p) REVERT: D 318 ILE cc_start: 0.8518 (OUTLIER) cc_final: 0.8289 (mp) REVERT: E 36 ASP cc_start: 0.8770 (t0) cc_final: 0.8368 (t0) REVERT: G 241 TYR cc_start: 0.8815 (m-80) cc_final: 0.8496 (m-80) REVERT: G 308 ASN cc_start: 0.8072 (t0) cc_final: 0.7523 (p0) REVERT: H 139 MET cc_start: 0.8791 (mmt) cc_final: 0.8527 (mmm) REVERT: H 276 LYS cc_start: 0.8685 (mppt) cc_final: 0.8449 (mppt) REVERT: H 277 GLU cc_start: 0.8689 (mp0) cc_final: 0.8125 (mp0) REVERT: H 299 GLU cc_start: 0.7390 (pp20) cc_final: 0.6857 (pp20) REVERT: I 131 ASN cc_start: 0.8919 (m110) cc_final: 0.8572 (m110) REVERT: I 275 ASN cc_start: 0.8665 (t0) cc_final: 0.8463 (t160) REVERT: J 296 GLU cc_start: 0.8248 (OUTLIER) cc_final: 0.7399 (mp0) REVERT: J 299 GLU cc_start: 0.7507 (pp20) cc_final: 0.6899 (pp20) REVERT: K 308 ASN cc_start: 0.8222 (t0) cc_final: 0.7666 (p0) REVERT: L 133 ASN cc_start: 0.8686 (t0) cc_final: 0.8136 (t0) REVERT: L 137 LEU cc_start: 0.8754 (mt) cc_final: 0.8411 (mp) outliers start: 46 outliers final: 26 residues processed: 272 average time/residue: 0.5067 time to fit residues: 166.3310 Evaluate side-chains 256 residues out of total 2832 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 227 time to evaluate : 1.033 ------------------------------------------------------------------------------- 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 72 ASN Chi-restraints excluded: chain B residue 217 VAL 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 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 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 I residue 310 ASP Chi-restraints excluded: chain J residue 142 VAL 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 131 ASN 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 38 optimal weight: 2.9990 chunk 66 optimal weight: 0.7980 chunk 136 optimal weight: 3.9990 chunk 172 optimal weight: 1.9990 chunk 233 optimal weight: 0.0670 chunk 157 optimal weight: 2.9990 chunk 129 optimal weight: 0.5980 chunk 21 optimal weight: 0.9980 chunk 56 optimal weight: 0.5980 chunk 228 optimal weight: 0.7980 chunk 300 optimal weight: 0.9980 overall best weight: 0.5718 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 72 ASN ** C 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 72 ASN G 131 ASN G 316 ASN H 316 ASN I 133 ASN I 316 ASN J 133 ASN J 203 ASN L 316 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3203 r_free = 0.3203 target = 0.087396 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2811 r_free = 0.2811 target = 0.064837 restraints weight = 48489.261| |-----------------------------------------------------------------------------| r_work (start): 0.2785 rms_B_bonded: 2.73 r_work: 0.2632 rms_B_bonded: 3.13 restraints_weight: 0.5000 r_work: 0.2481 rms_B_bonded: 4.95 restraints_weight: 0.2500 r_work (final): 0.2481 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8705 moved from start: 0.2119 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.138 27324 Z= 0.218 Angle : 0.787 59.190 36966 Z= 0.443 Chirality : 0.044 0.299 3990 Planarity : 0.005 0.127 4632 Dihedral : 11.610 152.202 3708 Min Nonbonded Distance : 1.810 Molprobity Statistics. All-atom Clashscore : 6.62 Ramachandran Plot: Outliers : 0.19 % Allowed : 3.06 % Favored : 96.75 % Rotamer: Outliers : 1.34 % Allowed : 15.15 % Favored : 83.51 % Cbeta Deviations : 0.03 % 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: 0.33 (0.15), residues: 3174 helix: 0.94 (0.15), residues: 1254 sheet: -0.49 (0.19), residues: 618 loop : 0.05 (0.18), residues: 1302 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.027 0.000 ARG J 224 TYR 0.031 0.002 TYR C 42 PHE 0.018 0.001 PHE K 304 TRP 0.040 0.001 TRP F 273 HIS 0.005 0.001 HIS A 57 Details of bonding type rmsd covalent geometry : bond 0.00517 (27324) covalent geometry : angle 0.78696 (36966) hydrogen bonds : bond 0.04567 ( 1016) hydrogen bonds : angle 4.89348 ( 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 265 residues out of total 2832 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 227 time to evaluate : 0.827 Fit side-chains REVERT: A 318 ILE cc_start: 0.8699 (OUTLIER) cc_final: 0.8481 (mp) REVERT: C 69 SER cc_start: 0.9047 (t) cc_final: 0.8485 (p) REVERT: D 318 ILE cc_start: 0.8643 (OUTLIER) cc_final: 0.8393 (mp) REVERT: E 36 ASP cc_start: 0.8861 (t0) cc_final: 0.8441 (t0) REVERT: G 241 TYR cc_start: 0.8917 (m-80) cc_final: 0.8634 (m-80) REVERT: G 308 ASN cc_start: 0.8089 (t0) cc_final: 0.7523 (p0) REVERT: H 139 MET cc_start: 0.8796 (mmt) cc_final: 0.8534 (mmm) REVERT: H 276 LYS cc_start: 0.8685 (mppt) cc_final: 0.8457 (mppt) REVERT: H 277 GLU cc_start: 0.8727 (mp0) cc_final: 0.8200 (mp0) REVERT: H 296 GLU cc_start: 0.8252 (OUTLIER) cc_final: 0.7865 (mp0) REVERT: H 299 GLU cc_start: 0.7552 (pp20) cc_final: 0.7018 (pp20) REVERT: I 131 ASN cc_start: 0.8931 (m110) cc_final: 0.8589 (m110) REVERT: J 296 GLU cc_start: 0.8313 (OUTLIER) cc_final: 0.7455 (mp0) REVERT: J 299 GLU cc_start: 0.7652 (pp20) cc_final: 0.7049 (pp20) REVERT: K 308 ASN cc_start: 0.8232 (t0) cc_final: 0.7661 (p0) REVERT: L 133 ASN cc_start: 0.8688 (t0) cc_final: 0.8131 (t0) REVERT: L 137 LEU cc_start: 0.8769 (mt) cc_final: 0.8426 (mp) outliers start: 38 outliers final: 26 residues processed: 262 average time/residue: 0.5167 time to fit residues: 163.2083 Evaluate side-chains 257 residues out of total 2832 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 227 time to evaluate : 1.053 ------------------------------------------------------------------------------- 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 217 VAL 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 F residue 15 LEU Chi-restraints excluded: chain F residue 139 MET Chi-restraints excluded: chain F residue 239 ASP 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 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 142 VAL 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 131 ASN 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 259 optimal weight: 2.9990 chunk 143 optimal weight: 0.7980 chunk 91 optimal weight: 0.4980 chunk 300 optimal weight: 1.9990 chunk 55 optimal weight: 0.9980 chunk 294 optimal weight: 1.9990 chunk 123 optimal weight: 0.8980 chunk 23 optimal weight: 0.9980 chunk 87 optimal weight: 0.9980 chunk 132 optimal weight: 4.9990 chunk 166 optimal weight: 0.5980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 72 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 72 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 131 ASN G 316 ASN H 316 ASN I 133 ASN I 316 ASN J 133 ASN J 203 ASN L 316 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3204 r_free = 0.3204 target = 0.087402 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2807 r_free = 0.2807 target = 0.064576 restraints weight = 48030.177| |-----------------------------------------------------------------------------| r_work (start): 0.2783 rms_B_bonded: 2.82 r_work: 0.2630 rms_B_bonded: 3.19 restraints_weight: 0.5000 r_work (final): 0.2630 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8564 moved from start: 0.2106 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.138 27324 Z= 0.218 Angle : 0.787 59.190 36966 Z= 0.443 Chirality : 0.044 0.299 3990 Planarity : 0.005 0.127 4632 Dihedral : 11.610 152.202 3708 Min Nonbonded Distance : 1.780 Molprobity Statistics. All-atom Clashscore : 6.96 Ramachandran Plot: Outliers : 0.19 % Allowed : 3.06 % Favored : 96.75 % Rotamer: Outliers : 1.17 % Allowed : 15.29 % Favored : 83.55 % Cbeta Deviations : 0.03 % 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: 0.33 (0.15), residues: 3174 helix: 0.94 (0.15), residues: 1254 sheet: -0.49 (0.19), residues: 618 loop : 0.05 (0.18), residues: 1302 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.027 0.000 ARG J 224 TYR 0.031 0.002 TYR C 42 PHE 0.018 0.001 PHE K 304 TRP 0.040 0.001 TRP F 273 HIS 0.005 0.001 HIS A 57 Details of bonding type rmsd covalent geometry : bond 0.00517 (27324) covalent geometry : angle 0.78696 (36966) hydrogen bonds : bond 0.04567 ( 1016) hydrogen bonds : angle 4.89348 ( 2892) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6435.64 seconds wall clock time: 110 minutes 55.51 seconds (6655.51 seconds total)