Starting phenix.real_space_refine on Sat Jul 4 20:56:29 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9ui5_64184/07_2026/9ui5_64184.cif Found real_map, /net/cci-nas-00/data/ceres_data/9ui5_64184/07_2026/9ui5_64184.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.04 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9ui5_64184/07_2026/9ui5_64184.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9ui5_64184/07_2026/9ui5_64184.map" model { file = "/net/cci-nas-00/data/ceres_data/9ui5_64184/07_2026/9ui5_64184.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9ui5_64184/07_2026/9ui5_64184.cif" } resolution = 3.04 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= 0.042 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 76 5.49 5 Mg 9 5.21 5 S 122 5.16 5 C 14063 2.51 5 N 4029 2.21 5 O 4550 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 39 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 22849 Number of models: 1 Model: "" Number of chains: 19 Chain: "E" Number of atoms: 2416 Number of conformers: 1 Conformer: "" Number of residues, atoms: 315, 2416 Classifications: {'peptide': 315} Link IDs: {'PTRANS': 9, 'TRANS': 305} Chain: "F" Number of atoms: 2416 Number of conformers: 1 Conformer: "" Number of residues, atoms: 315, 2416 Classifications: {'peptide': 315} Link IDs: {'PTRANS': 9, 'TRANS': 305} Chain: "G" Number of atoms: 2416 Number of conformers: 1 Conformer: "" Number of residues, atoms: 315, 2416 Classifications: {'peptide': 315} Link IDs: {'PTRANS': 9, 'TRANS': 305} Chain: "H" Number of atoms: 2416 Number of conformers: 1 Conformer: "" Number of residues, atoms: 315, 2416 Classifications: {'peptide': 315} Link IDs: {'PTRANS': 9, 'TRANS': 305} Chain: "I" Number of atoms: 2416 Number of conformers: 1 Conformer: "" Number of residues, atoms: 315, 2416 Classifications: {'peptide': 315} Link IDs: {'PTRANS': 9, 'TRANS': 305} Chain: "L" Number of atoms: 516 Number of conformers: 1 Conformer: "" Number of residues, atoms: 25, 516 Classifications: {'DNA': 25} Link IDs: {'rna3p': 24} Chain: "M" Number of atoms: 489 Number of conformers: 1 Conformer: "" Number of residues, atoms: 24, 489 Classifications: {'DNA': 24} Link IDs: {'rna3p': 23} Chain: "A" Number of atoms: 2369 Number of conformers: 1 Conformer: "" Number of residues, atoms: 308, 2369 Classifications: {'peptide': 308} Link IDs: {'PTRANS': 9, 'TRANS': 298} Chain breaks: 1 Chain: "B" Number of atoms: 2369 Number of conformers: 1 Conformer: "" Number of residues, atoms: 308, 2369 Classifications: {'peptide': 308} Link IDs: {'PTRANS': 9, 'TRANS': 298} Chain breaks: 1 Chain: "C" Number of atoms: 2369 Number of conformers: 1 Conformer: "" Number of residues, atoms: 308, 2369 Classifications: {'peptide': 308} Link IDs: {'PTRANS': 9, 'TRANS': 298} Chain breaks: 1 Chain: "D" Number of atoms: 2369 Number of conformers: 1 Conformer: "" Number of residues, atoms: 308, 2369 Classifications: {'peptide': 308} Link IDs: {'PTRANS': 9, 'TRANS': 298} Chain breaks: 1 Chain: "E" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ANP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "F" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ANP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "G" Number of atoms: 63 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 63 Unusual residues: {' MG': 1, 'ANP': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "H" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 33 Unusual residues: {' MG': 2, 'ANP': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "A" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ANP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ANP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "C" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ANP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "D" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ANP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 5.74, per 1000 atoms: 0.25 Number of scatterers: 22849 At special positions: 0 Unit cell: (117.03, 112.05, 197.54, 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 122 16.00 P 76 15.00 Mg 9 11.99 O 4550 8.00 N 4029 7.00 C 14063 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=1, symmetry=0 Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 1.92 Conformation dependent library (CDL) restraints added in 1.0 seconds 5562 Ramachandran restraints generated. 2781 Oldfield, 0 Emsley, 2781 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5110 Finding SS restraints... Secondary structure from input PDB file: 127 helices and 27 sheets defined 44.2% alpha, 9.2% beta 23 base pairs and 30 stacking pairs defined. Time for finding SS restraints: 2.97 Creating SS restraints... Processing helix chain 'E' and resid 25 through 31 Processing helix chain 'E' and resid 35 through 43 removed outlier: 3.506A pdb=" N LYS E 39 " --> pdb=" O ALA E 35 " (cutoff:3.500A) Processing helix chain 'E' and resid 48 through 54 Processing helix chain 'E' and resid 56 through 61 removed outlier: 3.845A pdb=" N LEU E 60 " --> pdb=" O PRO E 56 " (cutoff:3.500A) removed outlier: 3.928A pdb=" N ILE E 61 " --> pdb=" O LYS E 57 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 56 through 61' Processing helix chain 'E' and resid 68 through 82 removed outlier: 3.925A pdb=" N LYS E 80 " --> pdb=" O THR E 76 " (cutoff:3.500A) Processing helix chain 'E' and resid 88 through 97 removed outlier: 3.824A pdb=" N GLN E 94 " --> pdb=" O THR E 90 " (cutoff:3.500A) Processing helix chain 'E' and resid 109 through 114 Processing helix chain 'E' and resid 132 through 144 Processing helix chain 'E' and resid 169 through 178 Processing helix chain 'E' and resid 181 through 189 Processing helix chain 'E' and resid 196 through 213 removed outlier: 3.512A pdb=" N THR E 201 " --> pdb=" O THR E 197 " (cutoff:3.500A) removed outlier: 4.435A pdb=" N ASP E 209 " --> pdb=" O TYR E 205 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N MET E 210 " --> pdb=" O GLN E 206 " (cutoff:3.500A) Processing helix chain 'E' and resid 227 through 232 removed outlier: 3.595A pdb=" N TYR E 232 " --> pdb=" O TYR E 228 " (cutoff:3.500A) Processing helix chain 'E' and resid 237 through 257 removed outlier: 3.518A pdb=" N ARG E 254 " --> pdb=" O ARG E 250 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N LEU E 255 " --> pdb=" O MET E 251 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N ALA E 256 " --> pdb=" O LEU E 252 " (cutoff:3.500A) Processing helix chain 'E' and resid 288 through 294 Processing helix chain 'F' and resid 34 through 45 removed outlier: 4.173A pdb=" N VAL F 38 " --> pdb=" O ASN F 34 " (cutoff:3.500A) Processing helix chain 'F' and resid 48 through 54 removed outlier: 3.841A pdb=" N VAL F 52 " --> pdb=" O THR F 48 " (cutoff:3.500A) Processing helix chain 'F' and resid 57 through 62 Processing helix chain 'F' and resid 67 through 82 removed outlier: 3.514A pdb=" N VAL F 82 " --> pdb=" O ALA F 78 " (cutoff:3.500A) Processing helix chain 'F' and resid 89 through 97 Processing helix chain 'F' and resid 106 through 111 Processing helix chain 'F' and resid 134 through 143 Processing helix chain 'F' and resid 171 through 175 removed outlier: 3.682A pdb=" N VAL F 174 " --> pdb=" O LEU F 171 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N ALA F 175 " --> pdb=" O LEU F 172 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 171 through 175' Processing helix chain 'F' and resid 196 through 212 removed outlier: 3.827A pdb=" N LEU F 204 " --> pdb=" O GLN F 200 " (cutoff:3.500A) removed outlier: 4.178A pdb=" N TYR F 205 " --> pdb=" O THR F 201 " (cutoff:3.500A) removed outlier: 4.150A pdb=" N GLN F 206 " --> pdb=" O GLN F 202 " (cutoff:3.500A) Processing helix chain 'F' and resid 237 through 260 removed outlier: 3.669A pdb=" N ARG F 241 " --> pdb=" O GLU F 237 " (cutoff:3.500A) Processing helix chain 'F' and resid 289 through 295 removed outlier: 3.642A pdb=" N HIS F 294 " --> pdb=" O ASN F 290 " (cutoff:3.500A) removed outlier: 3.921A pdb=" N ALA F 295 " --> pdb=" O ILE F 291 " (cutoff:3.500A) Processing helix chain 'G' and resid 25 through 30 removed outlier: 3.539A pdb=" N GLN G 30 " --> pdb=" O SER G 26 " (cutoff:3.500A) Processing helix chain 'G' and resid 34 through 45 removed outlier: 3.610A pdb=" N VAL G 38 " --> pdb=" O ASN G 34 " (cutoff:3.500A) Processing helix chain 'G' and resid 48 through 54 Processing helix chain 'G' and resid 56 through 62 Processing helix chain 'G' and resid 65 through 80 removed outlier: 4.237A pdb=" N ALA G 69 " --> pdb=" O GLY G 65 " (cutoff:3.500A) removed outlier: 5.348A pdb=" N ASP G 72 " --> pdb=" O GLU G 68 " (cutoff:3.500A) removed outlier: 5.278A pdb=" N LYS G 73 " --> pdb=" O ALA G 69 " (cutoff:3.500A) removed outlier: 4.237A pdb=" N THR G 76 " --> pdb=" O ASP G 72 " (cutoff:3.500A) Processing helix chain 'G' and resid 88 through 97 Processing helix chain 'G' and resid 106 through 113 Processing helix chain 'G' and resid 132 through 144 Processing helix chain 'G' and resid 145 through 146 No H-bonds generated for 'chain 'G' and resid 145 through 146' Processing helix chain 'G' and resid 147 through 151 Processing helix chain 'G' and resid 167 through 176 removed outlier: 3.629A pdb=" N LEU G 171 " --> pdb=" O ARG G 167 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N GLU G 176 " --> pdb=" O LEU G 172 " (cutoff:3.500A) Processing helix chain 'G' and resid 183 through 188 removed outlier: 4.155A pdb=" N ASP G 187 " --> pdb=" O SER G 183 " (cutoff:3.500A) Processing helix chain 'G' and resid 196 through 211 removed outlier: 3.726A pdb=" N ASP G 209 " --> pdb=" O TYR G 205 " (cutoff:3.500A) Processing helix chain 'G' and resid 225 through 232 Processing helix chain 'G' and resid 240 through 259 Processing helix chain 'G' and resid 290 through 295 Processing helix chain 'H' and resid 34 through 43 Processing helix chain 'H' and resid 48 through 54 Processing helix chain 'H' and resid 56 through 62 Processing helix chain 'H' and resid 73 through 78 removed outlier: 3.533A pdb=" N GLU H 77 " --> pdb=" O LYS H 73 " (cutoff:3.500A) Processing helix chain 'H' and resid 89 through 98 removed outlier: 3.948A pdb=" N GLU H 98 " --> pdb=" O GLN H 94 " (cutoff:3.500A) Processing helix chain 'H' and resid 108 through 113 removed outlier: 3.696A pdb=" N LEU H 113 " --> pdb=" O LEU H 109 " (cutoff:3.500A) Processing helix chain 'H' and resid 129 through 132 removed outlier: 3.749A pdb=" N GLY H 132 " --> pdb=" O PHE H 129 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 129 through 132' Processing helix chain 'H' and resid 134 through 144 Processing helix chain 'H' and resid 167 through 178 removed outlier: 4.068A pdb=" N LEU H 171 " --> pdb=" O ARG H 167 " (cutoff:3.500A) Processing helix chain 'H' and resid 181 through 188 removed outlier: 3.818A pdb=" N VAL H 185 " --> pdb=" O SER H 181 " (cutoff:3.500A) Processing helix chain 'H' and resid 196 through 212 removed outlier: 3.532A pdb=" N GLN H 200 " --> pdb=" O ASN H 196 " (cutoff:3.500A) removed outlier: 3.959A pdb=" N GLU H 208 " --> pdb=" O LEU H 204 " (cutoff:3.500A) removed outlier: 4.322A pdb=" N ASP H 209 " --> pdb=" O TYR H 205 " (cutoff:3.500A) Processing helix chain 'H' and resid 240 through 260 Processing helix chain 'H' and resid 290 through 295 Processing helix chain 'I' and resid 34 through 43 Processing helix chain 'I' and resid 49 through 55 Processing helix chain 'I' and resid 67 through 82 Processing helix chain 'I' and resid 91 through 97 Processing helix chain 'I' and resid 107 through 112 removed outlier: 4.407A pdb=" N LEU I 112 " --> pdb=" O GLU I 108 " (cutoff:3.500A) Processing helix chain 'I' and resid 132 through 145 removed outlier: 3.650A pdb=" N VAL I 142 " --> pdb=" O HIS I 138 " (cutoff:3.500A) removed outlier: 4.034A pdb=" N THR I 143 " --> pdb=" O THR I 139 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N GLN I 145 " --> pdb=" O ALA I 141 " (cutoff:3.500A) Processing helix chain 'I' and resid 147 through 151 Processing helix chain 'I' and resid 167 through 178 removed outlier: 3.676A pdb=" N ARG I 177 " --> pdb=" O ALA I 173 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N TYR I 178 " --> pdb=" O VAL I 174 " (cutoff:3.500A) Processing helix chain 'I' and resid 181 through 187 removed outlier: 4.062A pdb=" N VAL I 185 " --> pdb=" O SER I 181 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N ASP I 187 " --> pdb=" O SER I 183 " (cutoff:3.500A) Processing helix chain 'I' and resid 197 through 202 Processing helix chain 'I' and resid 209 through 213 Processing helix chain 'I' and resid 225 through 232 Processing helix chain 'I' and resid 234 through 236 No H-bonds generated for 'chain 'I' and resid 234 through 236' Processing helix chain 'I' and resid 237 through 259 Processing helix chain 'I' and resid 288 through 294 removed outlier: 3.658A pdb=" N ILE I 292 " --> pdb=" O GLY I 288 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N ALA I 293 " --> pdb=" O GLY I 289 " (cutoff:3.500A) Processing helix chain 'A' and resid 25 through 31 removed outlier: 3.745A pdb=" N CYS A 31 " --> pdb=" O ARG A 27 " (cutoff:3.500A) Processing helix chain 'A' and resid 34 through 45 Processing helix chain 'A' and resid 48 through 54 Processing helix chain 'A' and resid 56 through 62 Processing helix chain 'A' and resid 67 through 79 Processing helix chain 'A' and resid 90 through 97 Processing helix chain 'A' and resid 107 through 113 Processing helix chain 'A' and resid 132 through 144 removed outlier: 3.809A pdb=" N ILE A 136 " --> pdb=" O GLY A 132 " (cutoff:3.500A) removed outlier: 4.261A pdb=" N CYS A 137 " --> pdb=" O LYS A 133 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N VAL A 142 " --> pdb=" O HIS A 138 " (cutoff:3.500A) Processing helix chain 'A' and resid 145 through 146 No H-bonds generated for 'chain 'A' and resid 145 through 146' Processing helix chain 'A' and resid 147 through 151 Processing helix chain 'A' and resid 167 through 178 removed outlier: 4.297A pdb=" N LEU A 171 " --> pdb=" O ARG A 167 " (cutoff:3.500A) Processing helix chain 'A' and resid 182 through 189 removed outlier: 3.729A pdb=" N VAL A 189 " --> pdb=" O VAL A 185 " (cutoff:3.500A) Processing helix chain 'A' and resid 196 through 210 Processing helix chain 'A' and resid 224 through 232 removed outlier: 3.511A pdb=" N TYR A 228 " --> pdb=" O ALA A 224 " (cutoff:3.500A) removed outlier: 3.936A pdb=" N THR A 230 " --> pdb=" O ALA A 226 " (cutoff:3.500A) Processing helix chain 'A' and resid 237 through 260 removed outlier: 3.504A pdb=" N ARG A 241 " --> pdb=" O GLU A 237 " (cutoff:3.500A) Processing helix chain 'A' and resid 289 through 294 Processing helix chain 'B' and resid 34 through 43 Processing helix chain 'B' and resid 48 through 54 Processing helix chain 'B' and resid 56 through 61 Processing helix chain 'B' and resid 69 through 82 Processing helix chain 'B' and resid 89 through 96 Processing helix chain 'B' and resid 97 through 99 No H-bonds generated for 'chain 'B' and resid 97 through 99' Processing helix chain 'B' and resid 132 through 144 Processing helix chain 'B' and resid 167 through 178 removed outlier: 3.667A pdb=" N LEU B 171 " --> pdb=" O ARG B 167 " (cutoff:3.500A) Processing helix chain 'B' and resid 202 through 207 Processing helix chain 'B' and resid 225 through 231 Processing helix chain 'B' and resid 234 through 236 No H-bonds generated for 'chain 'B' and resid 234 through 236' Processing helix chain 'B' and resid 237 through 258 Processing helix chain 'B' and resid 289 through 296 Processing helix chain 'C' and resid 25 through 32 removed outlier: 4.120A pdb=" N GLU C 29 " --> pdb=" O ILE C 25 " (cutoff:3.500A) Processing helix chain 'C' and resid 34 through 43 Processing helix chain 'C' and resid 48 through 55 removed outlier: 3.599A pdb=" N ALA C 55 " --> pdb=" O ALA C 51 " (cutoff:3.500A) Processing helix chain 'C' and resid 56 through 63 removed outlier: 3.744A pdb=" N LEU C 60 " --> pdb=" O PRO C 56 " (cutoff:3.500A) Processing helix chain 'C' and resid 67 through 82 removed outlier: 3.719A pdb=" N LEU C 81 " --> pdb=" O GLU C 77 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N VAL C 82 " --> pdb=" O ALA C 78 " (cutoff:3.500A) Processing helix chain 'C' and resid 89 through 96 Processing helix chain 'C' and resid 108 through 113 Processing helix chain 'C' and resid 132 through 142 removed outlier: 3.787A pdb=" N VAL C 142 " --> pdb=" O HIS C 138 " (cutoff:3.500A) Processing helix chain 'C' and resid 143 through 145 No H-bonds generated for 'chain 'C' and resid 143 through 145' Processing helix chain 'C' and resid 147 through 151 Processing helix chain 'C' and resid 167 through 174 Processing helix chain 'C' and resid 182 through 187 removed outlier: 4.355A pdb=" N LEU C 186 " --> pdb=" O GLY C 182 " (cutoff:3.500A) Processing helix chain 'C' and resid 197 through 212 removed outlier: 4.343A pdb=" N THR C 201 " --> pdb=" O THR C 197 " (cutoff:3.500A) Processing helix chain 'C' and resid 237 through 260 removed outlier: 3.720A pdb=" N ALA C 256 " --> pdb=" O LEU C 252 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N ASP C 257 " --> pdb=" O LEU C 253 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N PHE C 259 " --> pdb=" O LEU C 255 " (cutoff:3.500A) Processing helix chain 'C' and resid 288 through 296 removed outlier: 3.538A pdb=" N ILE C 292 " --> pdb=" O GLY C 288 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N ALA C 293 " --> pdb=" O GLY C 289 " (cutoff:3.500A) removed outlier: 4.078A pdb=" N HIS C 294 " --> pdb=" O ASN C 290 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N SER C 296 " --> pdb=" O ILE C 292 " (cutoff:3.500A) Processing helix chain 'D' and resid 34 through 43 removed outlier: 3.861A pdb=" N GLU D 43 " --> pdb=" O LYS D 39 " (cutoff:3.500A) Processing helix chain 'D' and resid 48 through 55 Processing helix chain 'D' and resid 57 through 62 removed outlier: 4.085A pdb=" N ASN D 62 " --> pdb=" O LYS D 58 " (cutoff:3.500A) Processing helix chain 'D' and resid 67 through 82 Processing helix chain 'D' and resid 89 through 97 Processing helix chain 'D' and resid 106 through 113 removed outlier: 3.720A pdb=" N LYS D 111 " --> pdb=" O LYS D 107 " (cutoff:3.500A) Processing helix chain 'D' and resid 132 through 144 Processing helix chain 'D' and resid 167 through 177 removed outlier: 3.564A pdb=" N VAL D 174 " --> pdb=" O ARG D 170 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N ARG D 177 " --> pdb=" O ALA D 173 " (cutoff:3.500A) Processing helix chain 'D' and resid 178 through 180 No H-bonds generated for 'chain 'D' and resid 178 through 180' Processing helix chain 'D' and resid 183 through 189 removed outlier: 3.649A pdb=" N ASN D 188 " --> pdb=" O ASP D 184 " (cutoff:3.500A) Processing helix chain 'D' and resid 196 through 210 removed outlier: 3.886A pdb=" N LEU D 204 " --> pdb=" O GLN D 200 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N TYR D 205 " --> pdb=" O THR D 201 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N ASP D 209 " --> pdb=" O TYR D 205 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N MET D 210 " --> pdb=" O GLN D 206 " (cutoff:3.500A) Processing helix chain 'D' and resid 225 through 232 Processing helix chain 'D' and resid 237 through 260 Processing helix chain 'D' and resid 288 through 295 removed outlier: 3.949A pdb=" N ILE D 292 " --> pdb=" O GLY D 288 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N HIS D 294 " --> pdb=" O ASN D 290 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'E' and resid 190 through 191 Processing sheet with id=AA2, first strand: chain 'E' and resid 269 through 271 Processing sheet with id=AA3, first strand: chain 'E' and resid 302 through 304 Processing sheet with id=AA4, first strand: chain 'F' and resid 87 through 88 removed outlier: 7.037A pdb=" N ILE G 160 " --> pdb=" O ASP G 222 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'F' and resid 189 through 192 removed outlier: 6.803A pdb=" N ALA F 157 " --> pdb=" O ALA F 190 " (cutoff:3.500A) removed outlier: 8.608A pdb=" N ALA F 192 " --> pdb=" O ALA F 157 " (cutoff:3.500A) removed outlier: 6.788A pdb=" N TYR F 159 " --> pdb=" O ALA F 192 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N MET F 158 " --> pdb=" O LEU F 218 " (cutoff:3.500A) removed outlier: 6.440A pdb=" N LEU F 219 " --> pdb=" O VAL F 264 " (cutoff:3.500A) removed outlier: 8.250A pdb=" N THR F 266 " --> pdb=" O LEU F 219 " (cutoff:3.500A) removed outlier: 7.881A pdb=" N VAL F 221 " --> pdb=" O THR F 266 " (cutoff:3.500A) removed outlier: 6.397A pdb=" N SER F 121 " --> pdb=" O VAL F 263 " (cutoff:3.500A) removed outlier: 8.011A pdb=" N ILE F 265 " --> pdb=" O SER F 121 " (cutoff:3.500A) removed outlier: 5.623A pdb=" N THR F 123 " --> pdb=" O ILE F 265 " (cutoff:3.500A) removed outlier: 6.952A pdb=" N ASN F 267 " --> pdb=" O THR F 123 " (cutoff:3.500A) removed outlier: 6.833A pdb=" N MET F 125 " --> pdb=" O ASN F 267 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N THR F 298 " --> pdb=" O ILE F 122 " (cutoff:3.500A) removed outlier: 6.428A pdb=" N ARG F 299 " --> pdb=" O TYR F 315 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N ARG F 303 " --> pdb=" O ILE F 311 " (cutoff:3.500A) removed outlier: 6.336A pdb=" N THR F 309 " --> pdb=" O GLY F 305 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'F' and resid 269 through 271 Processing sheet with id=AA7, first strand: chain 'F' and resid 328 through 330 removed outlier: 3.617A pdb=" N ALA F 328 " --> pdb=" O GLY F 335 " (cutoff:3.500A) removed outlier: 3.782A pdb=" N GLY F 335 " --> pdb=" O ALA F 328 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N ASN F 330 " --> pdb=" O GLY F 333 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'G' and resid 266 through 267 removed outlier: 6.474A pdb=" N MET G 125 " --> pdb=" O ASN G 267 " (cutoff:3.500A) removed outlier: 6.639A pdb=" N ARG G 299 " --> pdb=" O TYR G 315 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N GLY G 333 " --> pdb=" O ASN G 330 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'G' and resid 218 through 219 Processing sheet with id=AB1, first strand: chain 'G' and resid 269 through 271 Processing sheet with id=AB2, first strand: chain 'H' and resid 87 through 88 removed outlier: 3.540A pdb=" N THR H 87 " --> pdb=" O TYR I 191 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N ALA I 190 " --> pdb=" O ALA I 157 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N ASP I 161 " --> pdb=" O ALA I 192 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'H' and resid 263 through 267 removed outlier: 4.105A pdb=" N GLY H 127 " --> pdb=" O ASN H 267 " (cutoff:3.500A) removed outlier: 6.177A pdb=" N ILE H 122 " --> pdb=" O THR H 298 " (cutoff:3.500A) removed outlier: 7.695A pdb=" N LEU H 300 " --> pdb=" O ILE H 122 " (cutoff:3.500A) removed outlier: 6.618A pdb=" N GLU H 124 " --> pdb=" O LEU H 300 " (cutoff:3.500A) removed outlier: 7.710A pdb=" N LEU H 302 " --> pdb=" O GLU H 124 " (cutoff:3.500A) removed outlier: 6.707A pdb=" N PHE H 126 " --> pdb=" O LEU H 302 " (cutoff:3.500A) removed outlier: 8.217A pdb=" N LYS H 304 " --> pdb=" O PHE H 126 " (cutoff:3.500A) removed outlier: 7.281A pdb=" N ARG H 299 " --> pdb=" O TYR H 315 " (cutoff:3.500A) removed outlier: 3.828A pdb=" N GLY H 305 " --> pdb=" O THR H 309 " (cutoff:3.500A) removed outlier: 5.154A pdb=" N THR H 309 " --> pdb=" O GLY H 305 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N ALA H 325 " --> pdb=" O CYS H 312 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'H' and resid 269 through 270 Processing sheet with id=AB5, first strand: chain 'H' and resid 329 through 330 removed outlier: 3.531A pdb=" N GLY H 333 " --> pdb=" O ASN H 330 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'I' and resid 269 through 270 Processing sheet with id=AB7, first strand: chain 'I' and resid 303 through 304 removed outlier: 3.899A pdb=" N PHE I 327 " --> pdb=" O ARG I 310 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N ILE I 314 " --> pdb=" O ALA I 323 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N ALA I 323 " --> pdb=" O ILE I 314 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'A' and resid 122 through 123 removed outlier: 6.986A pdb=" N LEU A 219 " --> pdb=" O VAL A 264 " (cutoff:3.500A) removed outlier: 7.172A pdb=" N MET A 158 " --> pdb=" O ILE A 220 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'A' and resid 125 through 126 removed outlier: 6.322A pdb=" N PHE A 126 " --> pdb=" O LEU A 302 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N ARG A 303 " --> pdb=" O ILE A 311 " (cutoff:3.500A) removed outlier: 4.016A pdb=" N ILE A 311 " --> pdb=" O ARG A 303 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'A' and resid 270 through 271 removed outlier: 3.776A pdb=" N VAL A 270 " --> pdb=" O LYS A 285 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 158 through 161 removed outlier: 6.284A pdb=" N THR B 123 " --> pdb=" O ILE B 265 " (cutoff:3.500A) removed outlier: 7.907A pdb=" N ASN B 267 " --> pdb=" O THR B 123 " (cutoff:3.500A) removed outlier: 6.476A pdb=" N MET B 125 " --> pdb=" O ASN B 267 " (cutoff:3.500A) removed outlier: 6.991A pdb=" N LEU B 300 " --> pdb=" O ILE B 122 " (cutoff:3.500A) removed outlier: 6.369A pdb=" N GLU B 124 " --> pdb=" O LEU B 300 " (cutoff:3.500A) removed outlier: 7.443A pdb=" N LEU B 302 " --> pdb=" O GLU B 124 " (cutoff:3.500A) removed outlier: 7.756A pdb=" N PHE B 126 " --> pdb=" O LEU B 302 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'C' and resid 87 through 88 Processing sheet with id=AC4, first strand: chain 'C' and resid 221 through 223 removed outlier: 5.922A pdb=" N ASP C 222 " --> pdb=" O THR C 266 " (cutoff:3.500A) removed outlier: 6.019A pdb=" N THR C 123 " --> pdb=" O ILE C 265 " (cutoff:3.500A) removed outlier: 6.339A pdb=" N ARG C 299 " --> pdb=" O TYR C 315 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'C' and resid 269 through 270 removed outlier: 3.607A pdb=" N LYS C 285 " --> pdb=" O VAL C 270 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'C' and resid 328 through 329 Processing sheet with id=AC7, first strand: chain 'D' and resid 101 through 102 Processing sheet with id=AC8, first strand: chain 'D' and resid 156 through 160 removed outlier: 5.986A pdb=" N LYS D 156 " --> pdb=" O TYR D 216 " (cutoff:3.500A) removed outlier: 4.109A pdb=" N LEU D 218 " --> pdb=" O LYS D 156 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N VAL D 264 " --> pdb=" O LEU D 219 " (cutoff:3.500A) removed outlier: 6.107A pdb=" N THR D 123 " --> pdb=" O ILE D 265 " (cutoff:3.500A) removed outlier: 7.330A pdb=" N ASN D 267 " --> pdb=" O THR D 123 " (cutoff:3.500A) removed outlier: 6.276A pdb=" N MET D 125 " --> pdb=" O ASN D 267 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N THR D 298 " --> pdb=" O ILE D 122 " (cutoff:3.500A) removed outlier: 6.423A pdb=" N ARG D 299 " --> pdb=" O TYR D 315 " (cutoff:3.500A) removed outlier: 6.553A pdb=" N THR D 309 " --> pdb=" O GLY D 305 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'D' and resid 269 through 271 795 hydrogen bonds defined for protein. 2310 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 59 hydrogen bonds 118 hydrogen bond angles 0 basepair planarities 23 basepair parallelities 30 stacking parallelities Total time for adding SS restraints: 3.85 Time building geometry restraints manager: 2.54 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 6462 1.33 - 1.45: 4084 1.45 - 1.58: 12409 1.58 - 1.70: 125 1.70 - 1.82: 215 Bond restraints: 23295 Sorted by residual: bond pdb=" C3' DA L 20 " pdb=" O3' DA L 20 " ideal model delta sigma weight residual 1.435 1.384 0.051 1.30e-02 5.92e+03 1.52e+01 bond pdb=" C3' DT L 11 " pdb=" O3' DT L 11 " ideal model delta sigma weight residual 1.435 1.393 0.042 1.30e-02 5.92e+03 1.07e+01 bond pdb=" N ILE E 33 " pdb=" CA ILE E 33 " ideal model delta sigma weight residual 1.459 1.498 -0.039 1.25e-02 6.40e+03 9.56e+00 bond pdb=" C3' DA L 17 " pdb=" O3' DA L 17 " ideal model delta sigma weight residual 1.435 1.395 0.040 1.30e-02 5.92e+03 9.26e+00 bond pdb=" C3' DT M 45 " pdb=" C2' DT M 45 " ideal model delta sigma weight residual 1.516 1.540 -0.024 8.00e-03 1.56e+04 9.13e+00 ... (remaining 23290 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.58: 31429 3.58 - 7.16: 235 7.16 - 10.75: 27 10.75 - 14.33: 5 14.33 - 17.91: 1 Bond angle restraints: 31697 Sorted by residual: angle pdb=" N ILE H 117 " pdb=" CA ILE H 117 " pdb=" C ILE H 117 " ideal model delta sigma weight residual 113.10 104.51 8.59 9.70e-01 1.06e+00 7.84e+01 angle pdb=" O4' DG L 18 " pdb=" C4' DG L 18 " pdb=" C3' DG L 18 " ideal model delta sigma weight residual 106.00 102.18 3.82 6.00e-01 2.78e+00 4.04e+01 angle pdb=" O4' DC L 21 " pdb=" C4' DC L 21 " pdb=" C3' DC L 21 " ideal model delta sigma weight residual 106.00 102.22 3.78 6.00e-01 2.78e+00 3.97e+01 angle pdb=" O4' DT L 15 " pdb=" C4' DT L 15 " pdb=" C3' DT L 15 " ideal model delta sigma weight residual 106.00 102.23 3.77 6.00e-01 2.78e+00 3.95e+01 angle pdb=" CA ASP E 37 " pdb=" CB ASP E 37 " pdb=" CG ASP E 37 " ideal model delta sigma weight residual 112.60 118.84 -6.24 1.00e+00 1.00e+00 3.90e+01 ... (remaining 31692 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.46: 13376 35.46 - 70.91: 724 70.91 - 106.37: 35 106.37 - 141.83: 0 141.83 - 177.29: 2 Dihedral angle restraints: 14137 sinusoidal: 6134 harmonic: 8003 Sorted by residual: dihedral pdb=" CA ILE B 314 " pdb=" C ILE B 314 " pdb=" N TYR B 315 " pdb=" CA TYR B 315 " ideal model delta harmonic sigma weight residual 180.00 154.71 25.29 0 5.00e+00 4.00e-02 2.56e+01 dihedral pdb=" CA SER G 239 " pdb=" C SER G 239 " pdb=" N ALA G 240 " pdb=" CA ALA G 240 " ideal model delta harmonic sigma weight residual 180.00 156.87 23.13 0 5.00e+00 4.00e-02 2.14e+01 dihedral pdb=" CA SER D 296 " pdb=" C SER D 296 " pdb=" N THR D 297 " pdb=" CA THR D 297 " ideal model delta harmonic sigma weight residual -180.00 -158.79 -21.21 0 5.00e+00 4.00e-02 1.80e+01 ... (remaining 14134 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.064: 3009 0.064 - 0.128: 548 0.128 - 0.191: 36 0.191 - 0.255: 3 0.255 - 0.319: 1 Chirality restraints: 3597 Sorted by residual: chirality pdb=" CG LEU E 28 " pdb=" CB LEU E 28 " pdb=" CD1 LEU E 28 " pdb=" CD2 LEU E 28 " both_signs ideal model delta sigma weight residual False -2.59 -2.27 -0.32 2.00e-01 2.50e+01 2.54e+00 chirality pdb=" CG LEU G 252 " pdb=" CB LEU G 252 " pdb=" CD1 LEU G 252 " pdb=" CD2 LEU G 252 " both_signs ideal model delta sigma weight residual False -2.59 -2.37 -0.22 2.00e-01 2.50e+01 1.18e+00 chirality pdb=" C3' DC L 23 " pdb=" C4' DC L 23 " pdb=" O3' DC L 23 " pdb=" C2' DC L 23 " both_signs ideal model delta sigma weight residual False -2.73 -2.53 -0.20 2.00e-01 2.50e+01 1.04e+00 ... (remaining 3594 not shown) Planarity restraints: 3902 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR C 54 " -0.016 2.00e-02 2.50e+03 1.67e-02 5.57e+00 pdb=" CG TYR C 54 " 0.039 2.00e-02 2.50e+03 pdb=" CD1 TYR C 54 " -0.001 2.00e-02 2.50e+03 pdb=" CD2 TYR C 54 " -0.018 2.00e-02 2.50e+03 pdb=" CE1 TYR C 54 " -0.009 2.00e-02 2.50e+03 pdb=" CE2 TYR C 54 " 0.007 2.00e-02 2.50e+03 pdb=" CZ TYR C 54 " -0.001 2.00e-02 2.50e+03 pdb=" OH TYR C 54 " -0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CG GLU H 208 " -0.012 2.00e-02 2.50e+03 2.36e-02 5.55e+00 pdb=" CD GLU H 208 " 0.041 2.00e-02 2.50e+03 pdb=" OE1 GLU H 208 " -0.015 2.00e-02 2.50e+03 pdb=" OE2 GLU H 208 " -0.014 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ARG C 167 " -0.038 5.00e-02 4.00e+02 5.75e-02 5.29e+00 pdb=" N PRO C 168 " 0.099 5.00e-02 4.00e+02 pdb=" CA PRO C 168 " -0.030 5.00e-02 4.00e+02 pdb=" CD PRO C 168 " -0.032 5.00e-02 4.00e+02 ... (remaining 3899 not shown) Histogram of nonbonded interaction distances: 1.81 - 2.43: 36 2.43 - 3.04: 14770 3.04 - 3.66: 37248 3.66 - 4.28: 55277 4.28 - 4.90: 89276 Nonbonded interactions: 196607 Sorted by model distance: nonbonded pdb=" OG1 THR D 134 " pdb="MG MG D 601 " model vdw 1.807 2.170 nonbonded pdb=" O1A ANP B 600 " pdb="MG MG B 601 " model vdw 1.851 2.170 nonbonded pdb=" O3A ANP G 401 " pdb="MG MG G 402 " model vdw 1.856 2.170 nonbonded pdb=" N THR F 134 " pdb="MG MG F 601 " model vdw 1.885 2.250 nonbonded pdb=" O1B ANP B 600 " pdb="MG MG B 601 " model vdw 1.886 2.170 ... (remaining 196602 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and resid 22 through 336) selection = (chain 'B' and resid 22 through 336) selection = (chain 'C' and resid 22 through 336) selection = (chain 'D' and resid 22 through 336) selection = (chain 'E' and (resid 22 through 275 or resid 283 through 336)) selection = (chain 'F' and (resid 22 through 275 or resid 283 through 336)) selection = (chain 'G' and (resid 22 through 275 or resid 283 through 336)) selection = (chain 'H' and (resid 22 through 275 or resid 283 through 336)) selection = (chain 'I' and (resid 22 through 275 or resid 283 through 336)) } 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: 4.740 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.020 Extract box with map and model: 0.460 Check model and map are aligned: 0.060 Set scattering table: 0.040 Process input model: 23.630 Find NCS groups from input model: 0.480 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.010 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 30.490 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6846 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.061 23296 Z= 0.287 Angle : 0.874 17.909 31697 Z= 0.519 Chirality : 0.047 0.319 3597 Planarity : 0.005 0.058 3902 Dihedral : 19.488 177.286 9027 Min Nonbonded Distance : 1.807 Molprobity Statistics. All-atom Clashscore : 18.74 Ramachandran Plot: Outliers : 0.04 % Allowed : 8.34 % Favored : 91.62 % Rotamer: Outliers : 4.12 % Allowed : 29.12 % Favored : 66.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -2.73 (0.15), residues: 2781 helix: -0.85 (0.15), residues: 1104 sheet: -2.20 (0.26), residues: 381 loop : -2.55 (0.15), residues: 1296 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG B 96 TYR 0.039 0.002 TYR C 54 PHE 0.033 0.002 PHE B 92 HIS 0.005 0.001 HIS A 47 Details of bonding type rmsd/Z covalent geometry : bond 0.00485 / 0.29 (23295) covalent geometry : angle 0.87391 / 0.52 (31697) hydrogen bonds : bond 0.17747 / 12.01 ( 854) hydrogen bonds : angle 8.19208 / 5.52 ( 2428) Misc. bond : bond 0.00036 / 0.02 ( 1) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5562 Ramachandran restraints generated. 2781 Oldfield, 0 Emsley, 2781 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5562 Ramachandran restraints generated. 2781 Oldfield, 0 Emsley, 2781 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 333 residues out of total 2256 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 93 poor density : 240 time to evaluate : 0.883 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 28 LEU cc_start: 0.3841 (OUTLIER) cc_final: 0.3534 (tp) REVERT: E 229 ARG cc_start: 0.6786 (ttt180) cc_final: 0.6568 (ttm170) REVERT: F 167 ARG cc_start: 0.4380 (OUTLIER) cc_final: 0.3009 (tpp-160) REVERT: F 178 TYR cc_start: 0.6736 (OUTLIER) cc_final: 0.5619 (m-80) REVERT: F 279 PHE cc_start: 0.3433 (OUTLIER) cc_final: 0.2291 (p90) REVERT: G 91 GLU cc_start: 0.7831 (OUTLIER) cc_final: 0.7303 (tt0) REVERT: G 243 MET cc_start: 0.5545 (mpt) cc_final: 0.4863 (tpt) REVERT: G 291 ILE cc_start: 0.6563 (OUTLIER) cc_final: 0.6159 (mp) REVERT: H 209 ASP cc_start: 0.8744 (t0) cc_final: 0.8285 (m-30) REVERT: H 211 MET cc_start: 0.5816 (mmm) cc_final: 0.5098 (mmm) REVERT: H 287 ILE cc_start: 0.6103 (OUTLIER) cc_final: 0.5249 (pt) REVERT: I 81 LEU cc_start: 0.0612 (OUTLIER) cc_final: 0.0270 (tp) REVERT: I 94 GLN cc_start: 0.2966 (OUTLIER) cc_final: 0.2430 (pp30) REVERT: I 129 PHE cc_start: 0.2660 (OUTLIER) cc_final: 0.2025 (m-80) REVERT: I 158 MET cc_start: 0.1228 (tpt) cc_final: 0.0849 (tpt) REVERT: I 210 MET cc_start: 0.3376 (tpt) cc_final: 0.3106 (tpt) REVERT: I 306 ARG cc_start: 0.5824 (mmt-90) cc_final: 0.5023 (mmp80) REVERT: A 58 LYS cc_start: 0.5391 (OUTLIER) cc_final: 0.4639 (ttpp) REVERT: A 73 LYS cc_start: 0.7908 (mmmt) cc_final: 0.7498 (tttm) REVERT: B 94 GLN cc_start: 0.7799 (mm110) cc_final: 0.6489 (pp30) REVERT: B 210 MET cc_start: 0.7119 (pmm) cc_final: 0.4562 (tmm) REVERT: C 250 ARG cc_start: 0.7127 (OUTLIER) cc_final: 0.6183 (tmt170) outliers start: 93 outliers final: 68 residues processed: 313 average time/residue: 0.1576 time to fit residues: 77.6478 Evaluate side-chains 314 residues out of total 2256 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 80 poor density : 234 time to evaluate : 0.825 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 28 LEU Chi-restraints excluded: chain E residue 191 TYR Chi-restraints excluded: chain E residue 198 ASP Chi-restraints excluded: chain E residue 239 SER Chi-restraints excluded: chain E residue 274 ASP Chi-restraints excluded: chain F residue 88 THR Chi-restraints excluded: chain F residue 123 THR Chi-restraints excluded: chain F residue 146 LEU Chi-restraints excluded: chain F residue 158 MET Chi-restraints excluded: chain F residue 167 ARG Chi-restraints excluded: chain F residue 178 TYR Chi-restraints excluded: chain F residue 201 THR Chi-restraints excluded: chain F residue 218 LEU Chi-restraints excluded: chain F residue 261 VAL Chi-restraints excluded: chain F residue 278 MET Chi-restraints excluded: chain F residue 279 PHE Chi-restraints excluded: chain G residue 91 GLU Chi-restraints excluded: chain G residue 149 ASP Chi-restraints excluded: chain G residue 185 VAL Chi-restraints excluded: chain G residue 189 VAL Chi-restraints excluded: chain G residue 233 SER Chi-restraints excluded: chain G residue 264 VAL Chi-restraints excluded: chain G residue 291 ILE Chi-restraints excluded: chain H residue 52 VAL Chi-restraints excluded: chain H residue 112 LEU Chi-restraints excluded: chain H residue 287 ILE Chi-restraints excluded: chain H residue 315 TYR Chi-restraints excluded: chain I residue 81 LEU Chi-restraints excluded: chain I residue 94 GLN Chi-restraints excluded: chain I residue 119 THR Chi-restraints excluded: chain I residue 129 PHE Chi-restraints excluded: chain I residue 140 LEU Chi-restraints excluded: chain I residue 197 THR Chi-restraints excluded: chain I residue 261 VAL Chi-restraints excluded: chain I residue 266 THR Chi-restraints excluded: chain I residue 296 SER Chi-restraints excluded: chain I residue 310 ARG Chi-restraints excluded: chain I residue 320 LEU Chi-restraints excluded: chain A residue 52 VAL Chi-restraints excluded: chain A residue 58 LYS Chi-restraints excluded: chain A residue 76 THR Chi-restraints excluded: chain A residue 189 VAL Chi-restraints excluded: chain A residue 212 VAL Chi-restraints excluded: chain A residue 213 GLU Chi-restraints excluded: chain A residue 270 VAL Chi-restraints excluded: chain A residue 273 VAL Chi-restraints excluded: chain A residue 291 ILE Chi-restraints excluded: chain A residue 302 LEU Chi-restraints excluded: chain A residue 311 ILE Chi-restraints excluded: chain A residue 319 CYS Chi-restraints excluded: chain B residue 52 VAL Chi-restraints excluded: chain B residue 100 ILE Chi-restraints excluded: chain B residue 117 ILE Chi-restraints excluded: chain B residue 125 MET Chi-restraints excluded: chain B residue 133 LYS Chi-restraints excluded: chain B residue 160 ILE Chi-restraints excluded: chain B residue 186 LEU Chi-restraints excluded: chain B residue 213 GLU Chi-restraints excluded: chain B residue 251 MET Chi-restraints excluded: chain B residue 261 VAL Chi-restraints excluded: chain B residue 266 THR Chi-restraints excluded: chain B residue 269 VAL Chi-restraints excluded: chain B residue 273 VAL Chi-restraints excluded: chain B residue 298 THR Chi-restraints excluded: chain C residue 99 ILE Chi-restraints excluded: chain C residue 161 ASP Chi-restraints excluded: chain C residue 163 GLU Chi-restraints excluded: chain C residue 185 VAL Chi-restraints excluded: chain C residue 195 PHE Chi-restraints excluded: chain C residue 250 ARG Chi-restraints excluded: chain C residue 329 ILE Chi-restraints excluded: chain D residue 38 VAL Chi-restraints excluded: chain D residue 48 THR Chi-restraints excluded: chain D residue 88 THR Chi-restraints excluded: chain D residue 104 THR Chi-restraints excluded: chain D residue 119 THR Chi-restraints excluded: chain D residue 125 MET Chi-restraints excluded: chain D residue 231 ASP Chi-restraints excluded: chain D residue 297 THR Chi-restraints excluded: chain D residue 319 CYS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 279 random chunks: chunk 197 optimal weight: 6.9990 chunk 215 optimal weight: 0.5980 chunk 20 optimal weight: 2.9990 chunk 132 optimal weight: 40.0000 chunk 261 optimal weight: 4.9990 chunk 248 optimal weight: 4.9990 chunk 207 optimal weight: 0.6980 chunk 155 optimal weight: 9.9990 chunk 244 optimal weight: 1.9990 chunk 183 optimal weight: 6.9990 chunk 111 optimal weight: 10.0000 overall best weight: 2.2586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** F 93 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 242 GLN ** F 290 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 93 HIS H 244 HIS ** H 272 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 202 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 268 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 47 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 242 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 330 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 114 GLN ** B 196 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 200 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5051 r_free = 0.5051 target = 0.209340 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.4789 r_free = 0.4789 target = 0.180153 restraints weight = 36881.726| |-----------------------------------------------------------------------------| r_work (start): 0.4728 rms_B_bonded: 3.99 r_work: 0.4354 rms_B_bonded: 4.72 restraints_weight: 0.5000 r_work (final): 0.4354 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6880 moved from start: 0.0558 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.059 23296 Z= 0.204 Angle : 0.732 10.752 31697 Z= 0.381 Chirality : 0.046 0.378 3597 Planarity : 0.005 0.053 3902 Dihedral : 15.907 178.312 4033 Min Nonbonded Distance : 1.776 Molprobity Statistics. All-atom Clashscore : 18.88 Ramachandran Plot: Outliers : 0.11 % Allowed : 8.41 % Favored : 91.48 % Rotamer: Outliers : 6.83 % Allowed : 25.93 % Favored : 67.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -2.76 (0.15), residues: 2781 helix: -0.86 (0.15), residues: 1138 sheet: -2.27 (0.26), residues: 380 loop : -2.59 (0.16), residues: 1263 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG B 96 TYR 0.023 0.002 TYR D 46 PHE 0.023 0.002 PHE I 129 HIS 0.007 0.001 HIS E 138 Details of bonding type rmsd/Z covalent geometry : bond 0.00447 / 0.20 (23295) covalent geometry : angle 0.73228 / 0.38 (31697) hydrogen bonds : bond 0.05372 / 3.51 ( 854) hydrogen bonds : angle 6.46817 / 4.41 ( 2428) Misc. bond : bond 0.00035 / 0.02 ( 1) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5562 Ramachandran restraints generated. 2781 Oldfield, 0 Emsley, 2781 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5562 Ramachandran restraints generated. 2781 Oldfield, 0 Emsley, 2781 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 407 residues out of total 2256 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 154 poor density : 253 time to evaluate : 0.857 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 95 ARG cc_start: 0.6800 (OUTLIER) cc_final: 0.6411 (tpp-160) REVERT: E 229 ARG cc_start: 0.6646 (ttt180) cc_final: 0.6429 (ttt180) REVERT: F 167 ARG cc_start: 0.4446 (OUTLIER) cc_final: 0.3013 (tpp-160) REVERT: F 186 LEU cc_start: 0.6892 (OUTLIER) cc_final: 0.6515 (mt) REVERT: F 198 ASP cc_start: 0.8058 (t0) cc_final: 0.7841 (t0) REVERT: F 279 PHE cc_start: 0.3539 (OUTLIER) cc_final: 0.2319 (p90) REVERT: G 163 GLU cc_start: 0.6698 (OUTLIER) cc_final: 0.5710 (pm20) REVERT: H 118 GLU cc_start: 0.7048 (OUTLIER) cc_final: 0.6743 (pp20) REVERT: H 209 ASP cc_start: 0.8733 (OUTLIER) cc_final: 0.8318 (m-30) REVERT: H 237 GLU cc_start: 0.3556 (OUTLIER) cc_final: 0.2893 (tp30) REVERT: H 287 ILE cc_start: 0.6204 (OUTLIER) cc_final: 0.5095 (pt) REVERT: I 49 VAL cc_start: 0.5934 (OUTLIER) cc_final: 0.5491 (p) REVERT: I 81 LEU cc_start: 0.0504 (OUTLIER) cc_final: 0.0155 (tp) REVERT: I 129 PHE cc_start: 0.2873 (OUTLIER) cc_final: 0.2070 (m-80) REVERT: I 158 MET cc_start: 0.1796 (tpt) cc_final: 0.1318 (tpt) REVERT: I 306 ARG cc_start: 0.5877 (mmt-90) cc_final: 0.5059 (mmp80) REVERT: A 58 LYS cc_start: 0.5520 (OUTLIER) cc_final: 0.4761 (ttpp) REVERT: A 73 LYS cc_start: 0.7983 (mmmt) cc_final: 0.7483 (mtpt) REVERT: A 84 MET cc_start: 0.1850 (OUTLIER) cc_final: -0.2370 (mmt) REVERT: A 124 GLU cc_start: 0.4904 (OUTLIER) cc_final: 0.3960 (tm-30) REVERT: A 215 ARG cc_start: 0.6090 (OUTLIER) cc_final: 0.5372 (mtm180) REVERT: B 122 ILE cc_start: 0.5893 (OUTLIER) cc_final: 0.4781 (mt) REVERT: B 210 MET cc_start: 0.6914 (pmm) cc_final: 0.4402 (tmm) REVERT: B 315 TYR cc_start: 0.7026 (OUTLIER) cc_final: 0.5969 (t80) REVERT: C 184 ASP cc_start: 0.6762 (p0) cc_final: 0.6531 (p0) REVERT: C 250 ARG cc_start: 0.7236 (OUTLIER) cc_final: 0.6807 (tmt170) REVERT: D 252 LEU cc_start: 0.8533 (OUTLIER) cc_final: 0.8217 (mp) outliers start: 154 outliers final: 77 residues processed: 382 average time/residue: 0.1680 time to fit residues: 99.9082 Evaluate side-chains 336 residues out of total 2256 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 97 poor density : 239 time to evaluate : 1.048 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 28 LEU Chi-restraints excluded: chain E residue 52 VAL Chi-restraints excluded: chain E residue 95 ARG Chi-restraints excluded: chain E residue 191 TYR Chi-restraints excluded: chain E residue 198 ASP Chi-restraints excluded: chain E residue 219 LEU Chi-restraints excluded: chain E residue 239 SER Chi-restraints excluded: chain E residue 273 VAL Chi-restraints excluded: chain F residue 102 ILE Chi-restraints excluded: chain F residue 146 LEU Chi-restraints excluded: chain F residue 167 ARG Chi-restraints excluded: chain F residue 185 VAL Chi-restraints excluded: chain F residue 186 LEU Chi-restraints excluded: chain F residue 197 THR Chi-restraints excluded: chain F residue 201 THR Chi-restraints excluded: chain F residue 218 LEU Chi-restraints excluded: chain F residue 273 VAL Chi-restraints excluded: chain F residue 279 PHE Chi-restraints excluded: chain G residue 75 LEU Chi-restraints excluded: chain G residue 124 GLU Chi-restraints excluded: chain G residue 149 ASP Chi-restraints excluded: chain G residue 163 GLU Chi-restraints excluded: chain G residue 189 VAL Chi-restraints excluded: chain G residue 233 SER Chi-restraints excluded: chain G residue 252 LEU Chi-restraints excluded: chain G residue 264 VAL Chi-restraints excluded: chain H residue 52 VAL Chi-restraints excluded: chain H residue 112 LEU Chi-restraints excluded: chain H residue 118 GLU Chi-restraints excluded: chain H residue 206 GLN Chi-restraints excluded: chain H residue 209 ASP Chi-restraints excluded: chain H residue 237 GLU Chi-restraints excluded: chain H residue 287 ILE Chi-restraints excluded: chain H residue 315 TYR Chi-restraints excluded: chain I residue 49 VAL Chi-restraints excluded: chain I residue 81 LEU Chi-restraints excluded: chain I residue 119 THR Chi-restraints excluded: chain I residue 129 PHE Chi-restraints excluded: chain I residue 140 LEU Chi-restraints excluded: chain I residue 197 THR Chi-restraints excluded: chain I residue 220 ILE Chi-restraints excluded: chain I residue 264 VAL Chi-restraints excluded: chain I residue 266 THR Chi-restraints excluded: chain I residue 278 MET Chi-restraints excluded: chain I residue 282 ASP Chi-restraints excluded: chain A residue 30 GLN Chi-restraints excluded: chain A residue 48 THR Chi-restraints excluded: chain A residue 52 VAL Chi-restraints excluded: chain A residue 58 LYS Chi-restraints excluded: chain A residue 61 ILE Chi-restraints excluded: chain A residue 76 THR Chi-restraints excluded: chain A residue 84 MET Chi-restraints excluded: chain A residue 124 GLU Chi-restraints excluded: chain A residue 156 LYS Chi-restraints excluded: chain A residue 189 VAL Chi-restraints excluded: chain A residue 211 MET Chi-restraints excluded: chain A residue 212 VAL Chi-restraints excluded: chain A residue 213 GLU Chi-restraints excluded: chain A residue 215 ARG Chi-restraints excluded: chain A residue 270 VAL Chi-restraints excluded: chain A residue 273 VAL Chi-restraints excluded: chain A residue 291 ILE Chi-restraints excluded: chain A residue 311 ILE Chi-restraints excluded: chain A residue 319 CYS Chi-restraints excluded: chain B residue 25 ILE Chi-restraints excluded: chain B residue 26 SER Chi-restraints excluded: chain B residue 60 LEU Chi-restraints excluded: chain B residue 117 ILE Chi-restraints excluded: chain B residue 122 ILE Chi-restraints excluded: chain B residue 133 LYS Chi-restraints excluded: chain B residue 215 ARG Chi-restraints excluded: chain B residue 251 MET Chi-restraints excluded: chain B residue 261 VAL Chi-restraints excluded: chain B residue 265 ILE Chi-restraints excluded: chain B residue 266 THR Chi-restraints excluded: chain B residue 269 VAL Chi-restraints excluded: chain B residue 273 VAL Chi-restraints excluded: chain B residue 298 THR Chi-restraints excluded: chain B residue 315 TYR Chi-restraints excluded: chain C residue 43 GLU Chi-restraints excluded: chain C residue 99 ILE Chi-restraints excluded: chain C residue 161 ASP Chi-restraints excluded: chain C residue 185 VAL Chi-restraints excluded: chain C residue 195 PHE Chi-restraints excluded: chain C residue 212 VAL Chi-restraints excluded: chain C residue 250 ARG Chi-restraints excluded: chain C residue 253 LEU Chi-restraints excluded: chain C residue 285 LYS Chi-restraints excluded: chain C residue 290 ASN Chi-restraints excluded: chain C residue 292 ILE Chi-restraints excluded: chain D residue 38 VAL Chi-restraints excluded: chain D residue 48 THR Chi-restraints excluded: chain D residue 104 THR Chi-restraints excluded: chain D residue 219 LEU Chi-restraints excluded: chain D residue 231 ASP Chi-restraints excluded: chain D residue 252 LEU Chi-restraints excluded: chain D residue 297 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 279 random chunks: chunk 18 optimal weight: 0.0970 chunk 246 optimal weight: 0.8980 chunk 24 optimal weight: 4.9990 chunk 96 optimal weight: 6.9990 chunk 204 optimal weight: 10.0000 chunk 215 optimal weight: 0.9990 chunk 47 optimal weight: 5.9990 chunk 46 optimal weight: 20.0000 chunk 277 optimal weight: 0.9990 chunk 131 optimal weight: 30.0000 chunk 20 optimal weight: 0.7980 overall best weight: 0.7582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** F 93 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 272 GLN F 294 HIS G 93 HIS ** H 272 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 202 GLN ** I 268 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 47 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 242 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 330 ASN ** B 196 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 200 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5082 r_free = 0.5082 target = 0.212452 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.4813 r_free = 0.4813 target = 0.182548 restraints weight = 36955.846| |-----------------------------------------------------------------------------| r_work (start): 0.4757 rms_B_bonded: 3.53 r_work: 0.4447 rms_B_bonded: 4.18 restraints_weight: 0.5000 r_work (final): 0.4447 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6740 moved from start: 0.0902 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 23296 Z= 0.138 Angle : 0.652 10.044 31697 Z= 0.340 Chirality : 0.044 0.299 3597 Planarity : 0.004 0.052 3902 Dihedral : 15.488 179.400 3977 Min Nonbonded Distance : 1.796 Molprobity Statistics. All-atom Clashscore : 16.71 Ramachandran Plot: Outliers : 0.07 % Allowed : 7.30 % Favored : 92.63 % Rotamer: Outliers : 6.12 % Allowed : 25.98 % Favored : 67.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -2.58 (0.15), residues: 2781 helix: -0.71 (0.15), residues: 1146 sheet: -2.20 (0.24), residues: 398 loop : -2.49 (0.16), residues: 1237 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 310 TYR 0.035 0.001 TYR F 54 PHE 0.018 0.002 PHE I 129 HIS 0.007 0.001 HIS E 138 Details of bonding type rmsd/Z covalent geometry : bond 0.00289 / 0.14 (23295) covalent geometry : angle 0.65225 / 0.34 (31697) hydrogen bonds : bond 0.04491 / 2.93 ( 854) hydrogen bonds : angle 5.95495 / 4.08 ( 2428) Misc. bond : bond 0.00069 / 0.05 ( 1) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5562 Ramachandran restraints generated. 2781 Oldfield, 0 Emsley, 2781 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5562 Ramachandran restraints generated. 2781 Oldfield, 0 Emsley, 2781 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 412 residues out of total 2256 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 138 poor density : 274 time to evaluate : 0.867 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 80 LYS cc_start: 0.7286 (pptt) cc_final: 0.6383 (tptt) REVERT: E 95 ARG cc_start: 0.6800 (OUTLIER) cc_final: 0.6435 (tpp-160) REVERT: F 198 ASP cc_start: 0.8018 (t0) cc_final: 0.7781 (t0) REVERT: F 210 MET cc_start: 0.6517 (tmt) cc_final: 0.6096 (tmm) REVERT: F 279 PHE cc_start: 0.3496 (OUTLIER) cc_final: 0.2190 (p90) REVERT: G 56 PRO cc_start: 0.6251 (Cg_endo) cc_final: 0.5867 (Cg_exo) REVERT: G 163 GLU cc_start: 0.6513 (OUTLIER) cc_final: 0.5506 (pm20) REVERT: G 243 MET cc_start: 0.5194 (mpt) cc_final: 0.4775 (tpt) REVERT: G 291 ILE cc_start: 0.6750 (OUTLIER) cc_final: 0.6460 (mp) REVERT: H 118 GLU cc_start: 0.6942 (OUTLIER) cc_final: 0.6619 (pp20) REVERT: H 170 ARG cc_start: 0.7125 (mmp-170) cc_final: 0.6112 (mmp-170) REVERT: H 237 GLU cc_start: 0.3197 (OUTLIER) cc_final: 0.2652 (tp30) REVERT: H 287 ILE cc_start: 0.6202 (OUTLIER) cc_final: 0.5214 (pt) REVERT: H 315 TYR cc_start: 0.5798 (OUTLIER) cc_final: 0.4938 (t80) REVERT: I 49 VAL cc_start: 0.5957 (OUTLIER) cc_final: 0.5532 (p) REVERT: I 81 LEU cc_start: 0.0322 (OUTLIER) cc_final: -0.0001 (tp) REVERT: I 129 PHE cc_start: 0.2828 (OUTLIER) cc_final: 0.2278 (m-80) REVERT: I 158 MET cc_start: 0.1841 (tpt) cc_final: 0.1284 (tpt) REVERT: I 278 MET cc_start: 0.0759 (OUTLIER) cc_final: -0.1201 (mtt) REVERT: I 306 ARG cc_start: 0.5806 (mmt-90) cc_final: 0.4995 (mmp80) REVERT: A 58 LYS cc_start: 0.5422 (OUTLIER) cc_final: 0.4727 (ttpp) REVERT: A 73 LYS cc_start: 0.7993 (mmmt) cc_final: 0.7428 (mtpt) REVERT: A 84 MET cc_start: 0.1796 (OUTLIER) cc_final: -0.2592 (mmt) REVERT: A 124 GLU cc_start: 0.4795 (OUTLIER) cc_final: 0.3951 (tm-30) REVERT: A 215 ARG cc_start: 0.6093 (OUTLIER) cc_final: 0.5295 (mtm180) REVERT: A 311 ILE cc_start: 0.7235 (OUTLIER) cc_final: 0.6770 (tp) REVERT: B 210 MET cc_start: 0.6623 (pmm) cc_final: 0.4185 (tmm) REVERT: B 211 MET cc_start: 0.4805 (pmm) cc_final: 0.3007 (pmm) REVERT: B 315 TYR cc_start: 0.6912 (OUTLIER) cc_final: 0.5819 (t80) REVERT: C 250 ARG cc_start: 0.7103 (OUTLIER) cc_final: 0.6710 (tmt170) REVERT: D 187 ASP cc_start: 0.6826 (m-30) cc_final: 0.6585 (m-30) REVERT: D 252 LEU cc_start: 0.8417 (OUTLIER) cc_final: 0.8111 (mp) outliers start: 138 outliers final: 68 residues processed: 383 average time/residue: 0.1654 time to fit residues: 98.4214 Evaluate side-chains 334 residues out of total 2256 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 88 poor density : 246 time to evaluate : 0.876 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 52 VAL Chi-restraints excluded: chain E residue 95 ARG Chi-restraints excluded: chain E residue 191 TYR Chi-restraints excluded: chain E residue 198 ASP Chi-restraints excluded: chain E residue 204 LEU Chi-restraints excluded: chain E residue 219 LEU Chi-restraints excluded: chain F residue 88 THR Chi-restraints excluded: chain F residue 104 THR Chi-restraints excluded: chain F residue 146 LEU Chi-restraints excluded: chain F residue 180 LEU Chi-restraints excluded: chain F residue 218 LEU Chi-restraints excluded: chain F residue 278 MET Chi-restraints excluded: chain F residue 279 PHE Chi-restraints excluded: chain F residue 311 ILE Chi-restraints excluded: chain G residue 75 LEU Chi-restraints excluded: chain G residue 124 GLU Chi-restraints excluded: chain G residue 149 ASP Chi-restraints excluded: chain G residue 163 GLU Chi-restraints excluded: chain G residue 252 LEU Chi-restraints excluded: chain G residue 282 ASP Chi-restraints excluded: chain G residue 291 ILE Chi-restraints excluded: chain H residue 52 VAL Chi-restraints excluded: chain H residue 84 MET Chi-restraints excluded: chain H residue 112 LEU Chi-restraints excluded: chain H residue 118 GLU Chi-restraints excluded: chain H residue 206 GLN Chi-restraints excluded: chain H residue 237 GLU Chi-restraints excluded: chain H residue 266 THR Chi-restraints excluded: chain H residue 287 ILE Chi-restraints excluded: chain H residue 315 TYR Chi-restraints excluded: chain I residue 49 VAL Chi-restraints excluded: chain I residue 81 LEU Chi-restraints excluded: chain I residue 119 THR Chi-restraints excluded: chain I residue 129 PHE Chi-restraints excluded: chain I residue 140 LEU Chi-restraints excluded: chain I residue 197 THR Chi-restraints excluded: chain I residue 220 ILE Chi-restraints excluded: chain I residue 264 VAL Chi-restraints excluded: chain I residue 266 THR Chi-restraints excluded: chain I residue 278 MET Chi-restraints excluded: chain I residue 282 ASP Chi-restraints excluded: chain A residue 52 VAL Chi-restraints excluded: chain A residue 58 LYS Chi-restraints excluded: chain A residue 61 ILE Chi-restraints excluded: chain A residue 76 THR Chi-restraints excluded: chain A residue 84 MET Chi-restraints excluded: chain A residue 124 GLU Chi-restraints excluded: chain A residue 156 LYS Chi-restraints excluded: chain A residue 189 VAL Chi-restraints excluded: chain A residue 212 VAL Chi-restraints excluded: chain A residue 213 GLU Chi-restraints excluded: chain A residue 215 ARG Chi-restraints excluded: chain A residue 261 VAL Chi-restraints excluded: chain A residue 270 VAL Chi-restraints excluded: chain A residue 273 VAL Chi-restraints excluded: chain A residue 291 ILE Chi-restraints excluded: chain A residue 311 ILE Chi-restraints excluded: chain A residue 319 CYS Chi-restraints excluded: chain B residue 25 ILE Chi-restraints excluded: chain B residue 26 SER Chi-restraints excluded: chain B residue 60 LEU Chi-restraints excluded: chain B residue 90 THR Chi-restraints excluded: chain B residue 117 ILE Chi-restraints excluded: chain B residue 133 LYS Chi-restraints excluded: chain B residue 186 LEU Chi-restraints excluded: chain B residue 215 ARG Chi-restraints excluded: chain B residue 251 MET Chi-restraints excluded: chain B residue 269 VAL Chi-restraints excluded: chain B residue 273 VAL Chi-restraints excluded: chain B residue 298 THR Chi-restraints excluded: chain B residue 315 TYR Chi-restraints excluded: chain C residue 43 GLU Chi-restraints excluded: chain C residue 161 ASP Chi-restraints excluded: chain C residue 185 VAL Chi-restraints excluded: chain C residue 195 PHE Chi-restraints excluded: chain C residue 231 ASP Chi-restraints excluded: chain C residue 250 ARG Chi-restraints excluded: chain C residue 253 LEU Chi-restraints excluded: chain C residue 292 ILE Chi-restraints excluded: chain C residue 297 THR Chi-restraints excluded: chain D residue 38 VAL Chi-restraints excluded: chain D residue 48 THR Chi-restraints excluded: chain D residue 200 GLN Chi-restraints excluded: chain D residue 219 LEU Chi-restraints excluded: chain D residue 231 ASP Chi-restraints excluded: chain D residue 252 LEU Chi-restraints excluded: chain D residue 297 THR Chi-restraints excluded: chain D residue 319 CYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 279 random chunks: chunk 82 optimal weight: 7.9990 chunk 226 optimal weight: 9.9990 chunk 156 optimal weight: 8.9990 chunk 247 optimal weight: 5.9990 chunk 103 optimal weight: 3.9990 chunk 272 optimal weight: 0.3980 chunk 77 optimal weight: 1.9990 chunk 7 optimal weight: 7.9990 chunk 170 optimal weight: 3.9990 chunk 160 optimal weight: 10.0000 chunk 21 optimal weight: 4.9990 overall best weight: 3.0788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** E 145 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 93 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 290 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 93 HIS H 244 HIS ** H 272 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 202 GLN ** I 268 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 47 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 242 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 196 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 200 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 268 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 47 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 145 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5037 r_free = 0.5037 target = 0.207885 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.4758 r_free = 0.4758 target = 0.177441 restraints weight = 37025.037| |-----------------------------------------------------------------------------| r_work (start): 0.4698 rms_B_bonded: 3.71 r_work: 0.4358 rms_B_bonded: 4.25 restraints_weight: 0.5000 r_work (final): 0.4358 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6876 moved from start: 0.1029 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.068 23296 Z= 0.246 Angle : 0.763 12.270 31697 Z= 0.393 Chirality : 0.048 0.397 3597 Planarity : 0.005 0.051 3902 Dihedral : 15.653 179.501 3961 Min Nonbonded Distance : 1.766 Molprobity Statistics. All-atom Clashscore : 19.36 Ramachandran Plot: Outliers : 0.11 % Allowed : 8.92 % Favored : 90.97 % Rotamer: Outliers : 8.07 % Allowed : 24.65 % Favored : 67.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -2.73 (0.15), residues: 2781 helix: -0.79 (0.15), residues: 1129 sheet: -2.28 (0.25), residues: 379 loop : -2.59 (0.16), residues: 1273 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG B 310 TYR 0.023 0.002 TYR F 315 PHE 0.034 0.003 PHE C 166 HIS 0.008 0.001 HIS G 93 Details of bonding type rmsd/Z covalent geometry : bond 0.00545 / 0.25 (23295) covalent geometry : angle 0.76311 / 0.39 (31697) hydrogen bonds : bond 0.05271 / 3.42 ( 854) hydrogen bonds : angle 6.03025 / 4.12 ( 2428) Misc. bond : bond 0.00005 / 0.00 ( 1) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5562 Ramachandran restraints generated. 2781 Oldfield, 0 Emsley, 2781 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5562 Ramachandran restraints generated. 2781 Oldfield, 0 Emsley, 2781 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 445 residues out of total 2256 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 182 poor density : 263 time to evaluate : 0.711 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 80 LYS cc_start: 0.7245 (pptt) cc_final: 0.6388 (tptt) REVERT: E 95 ARG cc_start: 0.6811 (OUTLIER) cc_final: 0.6513 (tpp-160) REVERT: E 118 GLU cc_start: 0.7324 (OUTLIER) cc_final: 0.7103 (pt0) REVERT: E 158 MET cc_start: 0.2701 (OUTLIER) cc_final: 0.2160 (ppp) REVERT: E 250 ARG cc_start: 0.7463 (OUTLIER) cc_final: 0.6293 (ttp-170) REVERT: F 186 LEU cc_start: 0.6704 (OUTLIER) cc_final: 0.6327 (mt) REVERT: F 198 ASP cc_start: 0.8199 (t70) cc_final: 0.7967 (t0) REVERT: F 279 PHE cc_start: 0.3640 (OUTLIER) cc_final: 0.2480 (p90) REVERT: G 91 GLU cc_start: 0.7888 (OUTLIER) cc_final: 0.7399 (tt0) REVERT: G 163 GLU cc_start: 0.6878 (OUTLIER) cc_final: 0.5413 (pm20) REVERT: G 291 ILE cc_start: 0.6837 (OUTLIER) cc_final: 0.6427 (mp) REVERT: H 118 GLU cc_start: 0.6932 (OUTLIER) cc_final: 0.6607 (pp20) REVERT: H 209 ASP cc_start: 0.8749 (OUTLIER) cc_final: 0.8343 (m-30) REVERT: H 211 MET cc_start: 0.5465 (mmp) cc_final: 0.4979 (mmm) REVERT: H 237 GLU cc_start: 0.3595 (OUTLIER) cc_final: 0.2812 (tp30) REVERT: H 287 ILE cc_start: 0.6073 (OUTLIER) cc_final: 0.4892 (pt) REVERT: H 315 TYR cc_start: 0.5990 (OUTLIER) cc_final: 0.5217 (t80) REVERT: I 49 VAL cc_start: 0.5948 (OUTLIER) cc_final: 0.5531 (p) REVERT: I 81 LEU cc_start: 0.0323 (OUTLIER) cc_final: 0.0040 (tp) REVERT: I 94 GLN cc_start: 0.2992 (OUTLIER) cc_final: 0.2430 (pp30) REVERT: I 129 PHE cc_start: 0.3002 (OUTLIER) cc_final: 0.2284 (m-80) REVERT: I 306 ARG cc_start: 0.5737 (mmt-90) cc_final: 0.5079 (mmp80) REVERT: A 58 LYS cc_start: 0.5484 (OUTLIER) cc_final: 0.4739 (ttpp) REVERT: A 73 LYS cc_start: 0.8011 (mmmt) cc_final: 0.7538 (tttm) REVERT: A 84 MET cc_start: 0.1443 (OUTLIER) cc_final: -0.2358 (mmt) REVERT: A 124 GLU cc_start: 0.4933 (OUTLIER) cc_final: 0.3990 (tm-30) REVERT: A 215 ARG cc_start: 0.6194 (OUTLIER) cc_final: 0.5370 (mtm180) REVERT: A 311 ILE cc_start: 0.7458 (OUTLIER) cc_final: 0.7085 (tp) REVERT: B 47 HIS cc_start: 0.6537 (OUTLIER) cc_final: 0.6244 (m-70) REVERT: B 122 ILE cc_start: 0.5936 (OUTLIER) cc_final: 0.4793 (mt) REVERT: B 124 GLU cc_start: 0.6400 (OUTLIER) cc_final: 0.5499 (tp30) REVERT: B 210 MET cc_start: 0.6778 (pmm) cc_final: 0.4382 (tmm) REVERT: B 211 MET cc_start: 0.4956 (pmm) cc_final: 0.3199 (pmm) REVERT: B 315 TYR cc_start: 0.7013 (OUTLIER) cc_final: 0.5841 (t80) REVERT: C 171 LEU cc_start: 0.3999 (OUTLIER) cc_final: 0.3677 (pt) REVERT: C 184 ASP cc_start: 0.6591 (p0) cc_final: 0.6277 (p0) REVERT: C 250 ARG cc_start: 0.7231 (OUTLIER) cc_final: 0.6805 (tmt170) REVERT: D 252 LEU cc_start: 0.8615 (OUTLIER) cc_final: 0.8338 (mp) REVERT: D 316 ASP cc_start: 0.4203 (t0) cc_final: 0.3948 (t0) outliers start: 182 outliers final: 106 residues processed: 406 average time/residue: 0.1513 time to fit residues: 95.8795 Evaluate side-chains 379 residues out of total 2256 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 136 poor density : 243 time to evaluate : 0.826 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 52 VAL Chi-restraints excluded: chain E residue 95 ARG Chi-restraints excluded: chain E residue 118 GLU Chi-restraints excluded: chain E residue 158 MET Chi-restraints excluded: chain E residue 191 TYR Chi-restraints excluded: chain E residue 198 ASP Chi-restraints excluded: chain E residue 219 LEU Chi-restraints excluded: chain E residue 250 ARG Chi-restraints excluded: chain E residue 273 VAL Chi-restraints excluded: chain E residue 274 ASP Chi-restraints excluded: chain E residue 278 MET Chi-restraints excluded: chain F residue 88 THR Chi-restraints excluded: chain F residue 123 THR Chi-restraints excluded: chain F residue 142 VAL Chi-restraints excluded: chain F residue 146 LEU Chi-restraints excluded: chain F residue 180 LEU Chi-restraints excluded: chain F residue 185 VAL Chi-restraints excluded: chain F residue 186 LEU Chi-restraints excluded: chain F residue 191 TYR Chi-restraints excluded: chain F residue 197 THR Chi-restraints excluded: chain F residue 201 THR Chi-restraints excluded: chain F residue 218 LEU Chi-restraints excluded: chain F residue 255 LEU Chi-restraints excluded: chain F residue 261 VAL Chi-restraints excluded: chain F residue 278 MET Chi-restraints excluded: chain F residue 279 PHE Chi-restraints excluded: chain G residue 42 GLU Chi-restraints excluded: chain G residue 54 TYR Chi-restraints excluded: chain G residue 75 LEU Chi-restraints excluded: chain G residue 91 GLU Chi-restraints excluded: chain G residue 124 GLU Chi-restraints excluded: chain G residue 149 ASP Chi-restraints excluded: chain G residue 163 GLU Chi-restraints excluded: chain G residue 185 VAL Chi-restraints excluded: chain G residue 261 VAL Chi-restraints excluded: chain G residue 264 VAL Chi-restraints excluded: chain G residue 291 ILE Chi-restraints excluded: chain H residue 84 MET Chi-restraints excluded: chain H residue 112 LEU Chi-restraints excluded: chain H residue 118 GLU Chi-restraints excluded: chain H residue 180 LEU Chi-restraints excluded: chain H residue 206 GLN Chi-restraints excluded: chain H residue 209 ASP Chi-restraints excluded: chain H residue 219 LEU Chi-restraints excluded: chain H residue 237 GLU Chi-restraints excluded: chain H residue 238 LEU Chi-restraints excluded: chain H residue 266 THR Chi-restraints excluded: chain H residue 270 VAL Chi-restraints excluded: chain H residue 287 ILE Chi-restraints excluded: chain H residue 292 ILE Chi-restraints excluded: chain H residue 315 TYR Chi-restraints excluded: chain I residue 49 VAL Chi-restraints excluded: chain I residue 81 LEU Chi-restraints excluded: chain I residue 94 GLN Chi-restraints excluded: chain I residue 119 THR Chi-restraints excluded: chain I residue 123 THR Chi-restraints excluded: chain I residue 129 PHE Chi-restraints excluded: chain I residue 140 LEU Chi-restraints excluded: chain I residue 146 LEU Chi-restraints excluded: chain I residue 197 THR Chi-restraints excluded: chain I residue 220 ILE Chi-restraints excluded: chain I residue 264 VAL Chi-restraints excluded: chain I residue 266 THR Chi-restraints excluded: chain I residue 278 MET Chi-restraints excluded: chain I residue 282 ASP Chi-restraints excluded: chain I residue 320 LEU Chi-restraints excluded: chain A residue 30 GLN Chi-restraints excluded: chain A residue 48 THR Chi-restraints excluded: chain A residue 52 VAL Chi-restraints excluded: chain A residue 58 LYS Chi-restraints excluded: chain A residue 61 ILE Chi-restraints excluded: chain A residue 76 THR Chi-restraints excluded: chain A residue 84 MET Chi-restraints excluded: chain A residue 124 GLU Chi-restraints excluded: chain A residue 156 LYS Chi-restraints excluded: chain A residue 189 VAL Chi-restraints excluded: chain A residue 211 MET Chi-restraints excluded: chain A residue 212 VAL Chi-restraints excluded: chain A residue 213 GLU Chi-restraints excluded: chain A residue 215 ARG Chi-restraints excluded: chain A residue 261 VAL Chi-restraints excluded: chain A residue 270 VAL Chi-restraints excluded: chain A residue 273 VAL Chi-restraints excluded: chain A residue 291 ILE Chi-restraints excluded: chain A residue 311 ILE Chi-restraints excluded: chain A residue 319 CYS Chi-restraints excluded: chain B residue 25 ILE Chi-restraints excluded: chain B residue 26 SER Chi-restraints excluded: chain B residue 47 HIS Chi-restraints excluded: chain B residue 60 LEU Chi-restraints excluded: chain B residue 90 THR Chi-restraints excluded: chain B residue 100 ILE Chi-restraints excluded: chain B residue 117 ILE Chi-restraints excluded: chain B residue 122 ILE Chi-restraints excluded: chain B residue 124 GLU Chi-restraints excluded: chain B residue 133 LYS Chi-restraints excluded: chain B residue 160 ILE Chi-restraints excluded: chain B residue 186 LEU Chi-restraints excluded: chain B residue 215 ARG Chi-restraints excluded: chain B residue 251 MET Chi-restraints excluded: chain B residue 261 VAL Chi-restraints excluded: chain B residue 265 ILE Chi-restraints excluded: chain B residue 266 THR Chi-restraints excluded: chain B residue 269 VAL Chi-restraints excluded: chain B residue 273 VAL Chi-restraints excluded: chain B residue 291 ILE Chi-restraints excluded: chain B residue 298 THR Chi-restraints excluded: chain B residue 310 ARG Chi-restraints excluded: chain B residue 315 TYR Chi-restraints excluded: chain C residue 43 GLU Chi-restraints excluded: chain C residue 99 ILE Chi-restraints excluded: chain C residue 117 ILE Chi-restraints excluded: chain C residue 161 ASP Chi-restraints excluded: chain C residue 171 LEU Chi-restraints excluded: chain C residue 185 VAL Chi-restraints excluded: chain C residue 195 PHE Chi-restraints excluded: chain C residue 212 VAL Chi-restraints excluded: chain C residue 231 ASP Chi-restraints excluded: chain C residue 250 ARG Chi-restraints excluded: chain C residue 253 LEU Chi-restraints excluded: chain C residue 285 LYS Chi-restraints excluded: chain C residue 290 ASN Chi-restraints excluded: chain C residue 292 ILE Chi-restraints excluded: chain C residue 297 THR Chi-restraints excluded: chain C residue 329 ILE Chi-restraints excluded: chain D residue 38 VAL Chi-restraints excluded: chain D residue 48 THR Chi-restraints excluded: chain D residue 104 THR Chi-restraints excluded: chain D residue 108 GLU Chi-restraints excluded: chain D residue 119 THR Chi-restraints excluded: chain D residue 133 LYS Chi-restraints excluded: chain D residue 231 ASP Chi-restraints excluded: chain D residue 252 LEU Chi-restraints excluded: chain D residue 257 ASP Chi-restraints excluded: chain D residue 297 THR Chi-restraints excluded: chain D residue 319 CYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 279 random chunks: chunk 196 optimal weight: 2.9990 chunk 128 optimal weight: 30.0000 chunk 203 optimal weight: 4.9990 chunk 77 optimal weight: 6.9990 chunk 251 optimal weight: 0.6980 chunk 176 optimal weight: 9.9990 chunk 88 optimal weight: 0.1980 chunk 192 optimal weight: 4.9990 chunk 40 optimal weight: 7.9990 chunk 57 optimal weight: 0.7980 chunk 254 optimal weight: 5.9990 overall best weight: 1.9384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** E 145 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 93 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 290 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 294 HIS G 93 HIS H 244 HIS ** H 272 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 202 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 268 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 47 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 242 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 196 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 200 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 145 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5055 r_free = 0.5055 target = 0.209633 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.4781 r_free = 0.4781 target = 0.179419 restraints weight = 37031.917| |-----------------------------------------------------------------------------| r_work (start): 0.4723 rms_B_bonded: 3.72 r_work: 0.4384 rms_B_bonded: 4.33 restraints_weight: 0.5000 r_work (final): 0.4384 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6847 moved from start: 0.1129 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 23296 Z= 0.182 Angle : 0.699 11.278 31697 Z= 0.361 Chirality : 0.046 0.365 3597 Planarity : 0.005 0.052 3902 Dihedral : 15.591 178.509 3960 Min Nonbonded Distance : 1.815 Molprobity Statistics. All-atom Clashscore : 18.41 Ramachandran Plot: Outliers : 0.07 % Allowed : 7.84 % Favored : 92.09 % Rotamer: Outliers : 7.23 % Allowed : 25.89 % Favored : 66.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -2.70 (0.15), residues: 2781 helix: -0.71 (0.15), residues: 1142 sheet: -2.38 (0.23), residues: 411 loop : -2.61 (0.16), residues: 1228 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B 310 TYR 0.024 0.002 TYR H 216 PHE 0.024 0.002 PHE C 166 HIS 0.008 0.001 HIS G 93 Details of bonding type rmsd/Z covalent geometry : bond 0.00400 / 0.18 (23295) covalent geometry : angle 0.69934 / 0.36 (31697) hydrogen bonds : bond 0.04628 / 3.00 ( 854) hydrogen bonds : angle 5.80564 / 3.97 ( 2428) Misc. bond : bond 0.00031 / 0.02 ( 1) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5562 Ramachandran restraints generated. 2781 Oldfield, 0 Emsley, 2781 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5562 Ramachandran restraints generated. 2781 Oldfield, 0 Emsley, 2781 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 419 residues out of total 2256 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 163 poor density : 256 time to evaluate : 0.891 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 80 LYS cc_start: 0.7316 (pptt) cc_final: 0.6559 (tptt) REVERT: E 95 ARG cc_start: 0.6768 (OUTLIER) cc_final: 0.6553 (tpp-160) REVERT: E 158 MET cc_start: 0.2709 (OUTLIER) cc_final: 0.2130 (ppp) REVERT: F 186 LEU cc_start: 0.6688 (OUTLIER) cc_final: 0.6313 (mt) REVERT: F 198 ASP cc_start: 0.8183 (t70) cc_final: 0.7954 (t0) REVERT: F 210 MET cc_start: 0.6525 (tmt) cc_final: 0.6151 (tmm) REVERT: F 279 PHE cc_start: 0.3726 (OUTLIER) cc_final: 0.2441 (p90) REVERT: F 316 ASP cc_start: 0.4718 (OUTLIER) cc_final: 0.4348 (p0) REVERT: G 91 GLU cc_start: 0.7885 (OUTLIER) cc_final: 0.7403 (tt0) REVERT: G 163 GLU cc_start: 0.6834 (OUTLIER) cc_final: 0.5553 (pm20) REVERT: G 291 ILE cc_start: 0.6816 (OUTLIER) cc_final: 0.6452 (mp) REVERT: H 118 GLU cc_start: 0.6932 (OUTLIER) cc_final: 0.6569 (pp20) REVERT: H 209 ASP cc_start: 0.8725 (m-30) cc_final: 0.8303 (m-30) REVERT: H 211 MET cc_start: 0.5854 (mmp) cc_final: 0.5337 (mmm) REVERT: H 237 GLU cc_start: 0.3451 (OUTLIER) cc_final: 0.2659 (tp30) REVERT: H 287 ILE cc_start: 0.6114 (OUTLIER) cc_final: 0.4962 (pt) REVERT: H 315 TYR cc_start: 0.5772 (OUTLIER) cc_final: 0.5443 (t80) REVERT: I 49 VAL cc_start: 0.5960 (OUTLIER) cc_final: 0.5541 (p) REVERT: I 81 LEU cc_start: 0.0383 (OUTLIER) cc_final: 0.0116 (tp) REVERT: I 94 GLN cc_start: 0.2969 (OUTLIER) cc_final: 0.2450 (pp30) REVERT: I 129 PHE cc_start: 0.2912 (OUTLIER) cc_final: 0.2259 (m-80) REVERT: I 278 MET cc_start: 0.0777 (OUTLIER) cc_final: -0.1087 (mtm) REVERT: I 306 ARG cc_start: 0.5754 (mmt-90) cc_final: 0.5076 (mmp80) REVERT: A 58 LYS cc_start: 0.5406 (OUTLIER) cc_final: 0.4707 (ttpp) REVERT: A 73 LYS cc_start: 0.7982 (mmmt) cc_final: 0.7485 (tttm) REVERT: A 84 MET cc_start: 0.1460 (OUTLIER) cc_final: -0.2422 (mmt) REVERT: A 124 GLU cc_start: 0.5029 (OUTLIER) cc_final: 0.4067 (tm-30) REVERT: A 215 ARG cc_start: 0.6117 (OUTLIER) cc_final: 0.5248 (mtm180) REVERT: A 311 ILE cc_start: 0.7436 (OUTLIER) cc_final: 0.7104 (tp) REVERT: B 40 LYS cc_start: 0.6092 (ptpt) cc_final: 0.5830 (ptpp) REVERT: B 47 HIS cc_start: 0.6571 (OUTLIER) cc_final: 0.6263 (m-70) REVERT: B 80 LYS cc_start: 0.8190 (pptt) cc_final: 0.7496 (ptpt) REVERT: B 124 GLU cc_start: 0.6477 (OUTLIER) cc_final: 0.5564 (tp30) REVERT: B 210 MET cc_start: 0.6675 (pmm) cc_final: 0.4300 (tmm) REVERT: B 211 MET cc_start: 0.5019 (pmm) cc_final: 0.3362 (pmm) REVERT: B 315 TYR cc_start: 0.7004 (OUTLIER) cc_final: 0.5819 (t80) REVERT: C 184 ASP cc_start: 0.6648 (p0) cc_final: 0.6265 (p0) REVERT: C 250 ARG cc_start: 0.7095 (OUTLIER) cc_final: 0.6702 (tmt170) REVERT: D 252 LEU cc_start: 0.8544 (OUTLIER) cc_final: 0.8298 (mp) outliers start: 163 outliers final: 103 residues processed: 385 average time/residue: 0.1485 time to fit residues: 89.6639 Evaluate side-chains 372 residues out of total 2256 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 130 poor density : 242 time to evaluate : 0.841 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 95 ARG Chi-restraints excluded: chain E residue 158 MET Chi-restraints excluded: chain E residue 191 TYR Chi-restraints excluded: chain E residue 198 ASP Chi-restraints excluded: chain E residue 204 LEU Chi-restraints excluded: chain E residue 219 LEU Chi-restraints excluded: chain E residue 263 VAL Chi-restraints excluded: chain E residue 273 VAL Chi-restraints excluded: chain E residue 274 ASP Chi-restraints excluded: chain E residue 278 MET Chi-restraints excluded: chain F residue 88 THR Chi-restraints excluded: chain F residue 104 THR Chi-restraints excluded: chain F residue 142 VAL Chi-restraints excluded: chain F residue 146 LEU Chi-restraints excluded: chain F residue 180 LEU Chi-restraints excluded: chain F residue 185 VAL Chi-restraints excluded: chain F residue 186 LEU Chi-restraints excluded: chain F residue 218 LEU Chi-restraints excluded: chain F residue 230 THR Chi-restraints excluded: chain F residue 255 LEU Chi-restraints excluded: chain F residue 261 VAL Chi-restraints excluded: chain F residue 278 MET Chi-restraints excluded: chain F residue 279 PHE Chi-restraints excluded: chain F residue 316 ASP Chi-restraints excluded: chain G residue 75 LEU Chi-restraints excluded: chain G residue 91 GLU Chi-restraints excluded: chain G residue 124 GLU Chi-restraints excluded: chain G residue 149 ASP Chi-restraints excluded: chain G residue 163 GLU Chi-restraints excluded: chain G residue 185 VAL Chi-restraints excluded: chain G residue 189 VAL Chi-restraints excluded: chain G residue 243 MET Chi-restraints excluded: chain G residue 253 LEU Chi-restraints excluded: chain G residue 282 ASP Chi-restraints excluded: chain G residue 291 ILE Chi-restraints excluded: chain G residue 313 LYS Chi-restraints excluded: chain H residue 84 MET Chi-restraints excluded: chain H residue 112 LEU Chi-restraints excluded: chain H residue 118 GLU Chi-restraints excluded: chain H residue 180 LEU Chi-restraints excluded: chain H residue 206 GLN Chi-restraints excluded: chain H residue 219 LEU Chi-restraints excluded: chain H residue 237 GLU Chi-restraints excluded: chain H residue 266 THR Chi-restraints excluded: chain H residue 270 VAL Chi-restraints excluded: chain H residue 287 ILE Chi-restraints excluded: chain H residue 292 ILE Chi-restraints excluded: chain H residue 315 TYR Chi-restraints excluded: chain I residue 49 VAL Chi-restraints excluded: chain I residue 81 LEU Chi-restraints excluded: chain I residue 94 GLN Chi-restraints excluded: chain I residue 119 THR Chi-restraints excluded: chain I residue 123 THR Chi-restraints excluded: chain I residue 129 PHE Chi-restraints excluded: chain I residue 140 LEU Chi-restraints excluded: chain I residue 146 LEU Chi-restraints excluded: chain I residue 197 THR Chi-restraints excluded: chain I residue 220 ILE Chi-restraints excluded: chain I residue 264 VAL Chi-restraints excluded: chain I residue 266 THR Chi-restraints excluded: chain I residue 278 MET Chi-restraints excluded: chain I residue 282 ASP Chi-restraints excluded: chain I residue 320 LEU Chi-restraints excluded: chain I residue 336 ASP Chi-restraints excluded: chain A residue 48 THR Chi-restraints excluded: chain A residue 52 VAL Chi-restraints excluded: chain A residue 58 LYS Chi-restraints excluded: chain A residue 61 ILE Chi-restraints excluded: chain A residue 76 THR Chi-restraints excluded: chain A residue 84 MET Chi-restraints excluded: chain A residue 124 GLU Chi-restraints excluded: chain A residue 156 LYS Chi-restraints excluded: chain A residue 189 VAL Chi-restraints excluded: chain A residue 211 MET Chi-restraints excluded: chain A residue 212 VAL Chi-restraints excluded: chain A residue 213 GLU Chi-restraints excluded: chain A residue 215 ARG Chi-restraints excluded: chain A residue 261 VAL Chi-restraints excluded: chain A residue 270 VAL Chi-restraints excluded: chain A residue 273 VAL Chi-restraints excluded: chain A residue 291 ILE Chi-restraints excluded: chain A residue 311 ILE Chi-restraints excluded: chain B residue 25 ILE Chi-restraints excluded: chain B residue 26 SER Chi-restraints excluded: chain B residue 47 HIS Chi-restraints excluded: chain B residue 52 VAL Chi-restraints excluded: chain B residue 60 LEU Chi-restraints excluded: chain B residue 67 SER Chi-restraints excluded: chain B residue 90 THR Chi-restraints excluded: chain B residue 100 ILE Chi-restraints excluded: chain B residue 117 ILE Chi-restraints excluded: chain B residue 124 GLU Chi-restraints excluded: chain B residue 133 LYS Chi-restraints excluded: chain B residue 160 ILE Chi-restraints excluded: chain B residue 186 LEU Chi-restraints excluded: chain B residue 213 GLU Chi-restraints excluded: chain B residue 215 ARG Chi-restraints excluded: chain B residue 251 MET Chi-restraints excluded: chain B residue 265 ILE Chi-restraints excluded: chain B residue 266 THR Chi-restraints excluded: chain B residue 269 VAL Chi-restraints excluded: chain B residue 273 VAL Chi-restraints excluded: chain B residue 291 ILE Chi-restraints excluded: chain B residue 298 THR Chi-restraints excluded: chain B residue 315 TYR Chi-restraints excluded: chain C residue 31 CYS Chi-restraints excluded: chain C residue 43 GLU Chi-restraints excluded: chain C residue 99 ILE Chi-restraints excluded: chain C residue 161 ASP Chi-restraints excluded: chain C residue 185 VAL Chi-restraints excluded: chain C residue 195 PHE Chi-restraints excluded: chain C residue 212 VAL Chi-restraints excluded: chain C residue 250 ARG Chi-restraints excluded: chain C residue 253 LEU Chi-restraints excluded: chain C residue 285 LYS Chi-restraints excluded: chain C residue 292 ILE Chi-restraints excluded: chain C residue 297 THR Chi-restraints excluded: chain C residue 329 ILE Chi-restraints excluded: chain D residue 25 ILE Chi-restraints excluded: chain D residue 38 VAL Chi-restraints excluded: chain D residue 48 THR Chi-restraints excluded: chain D residue 88 THR Chi-restraints excluded: chain D residue 108 GLU Chi-restraints excluded: chain D residue 119 THR Chi-restraints excluded: chain D residue 200 GLN Chi-restraints excluded: chain D residue 231 ASP Chi-restraints excluded: chain D residue 252 LEU Chi-restraints excluded: chain D residue 257 ASP Chi-restraints excluded: chain D residue 297 THR Chi-restraints excluded: chain D residue 319 CYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 279 random chunks: chunk 136 optimal weight: 5.9990 chunk 274 optimal weight: 1.9990 chunk 265 optimal weight: 0.6980 chunk 15 optimal weight: 0.6980 chunk 250 optimal weight: 5.9990 chunk 155 optimal weight: 20.0000 chunk 6 optimal weight: 2.9990 chunk 34 optimal weight: 5.9990 chunk 234 optimal weight: 0.0040 chunk 228 optimal weight: 2.9990 chunk 243 optimal weight: 0.9980 overall best weight: 0.8794 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** E 145 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 93 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 93 HIS H 244 HIS ** H 272 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 202 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 268 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 47 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 242 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 196 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 200 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 145 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5078 r_free = 0.5078 target = 0.211953 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.4808 r_free = 0.4808 target = 0.181826 restraints weight = 36852.783| |-----------------------------------------------------------------------------| r_work (start): 0.4753 rms_B_bonded: 3.42 r_work: 0.4435 rms_B_bonded: 4.17 restraints_weight: 0.5000 r_work (final): 0.4435 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6764 moved from start: 0.1297 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 23296 Z= 0.137 Angle : 0.659 13.693 31697 Z= 0.340 Chirality : 0.045 0.387 3597 Planarity : 0.004 0.051 3902 Dihedral : 15.423 178.856 3959 Min Nonbonded Distance : 1.869 Molprobity Statistics. All-atom Clashscore : 17.11 Ramachandran Plot: Outliers : 0.07 % Allowed : 7.48 % Favored : 92.45 % Rotamer: Outliers : 7.14 % Allowed : 25.89 % Favored : 66.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -2.52 (0.15), residues: 2781 helix: -0.57 (0.15), residues: 1140 sheet: -2.24 (0.24), residues: 405 loop : -2.52 (0.16), residues: 1236 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 310 TYR 0.024 0.001 TYR H 216 PHE 0.028 0.002 PHE C 166 HIS 0.009 0.001 HIS G 93 Details of bonding type rmsd/Z covalent geometry : bond 0.00289 / 0.14 (23295) covalent geometry : angle 0.65875 / 0.34 (31697) hydrogen bonds : bond 0.04109 / 2.66 ( 854) hydrogen bonds : angle 5.54749 / 3.80 ( 2428) Misc. bond : bond 0.00060 / 0.04 ( 1) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5562 Ramachandran restraints generated. 2781 Oldfield, 0 Emsley, 2781 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5562 Ramachandran restraints generated. 2781 Oldfield, 0 Emsley, 2781 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 423 residues out of total 2256 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 161 poor density : 262 time to evaluate : 0.726 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 80 LYS cc_start: 0.7288 (pptt) cc_final: 0.6575 (tptt) REVERT: E 158 MET cc_start: 0.2571 (OUTLIER) cc_final: 0.2095 (ppp) REVERT: F 186 LEU cc_start: 0.6647 (OUTLIER) cc_final: 0.6297 (mt) REVERT: F 198 ASP cc_start: 0.8067 (t70) cc_final: 0.7833 (t0) REVERT: F 279 PHE cc_start: 0.3562 (OUTLIER) cc_final: 0.2226 (p90) REVERT: F 303 ARG cc_start: 0.5221 (ptt-90) cc_final: 0.4701 (ptt-90) REVERT: F 316 ASP cc_start: 0.4637 (OUTLIER) cc_final: 0.4247 (p0) REVERT: G 91 GLU cc_start: 0.7858 (OUTLIER) cc_final: 0.7406 (tt0) REVERT: G 291 ILE cc_start: 0.6733 (OUTLIER) cc_final: 0.6404 (mp) REVERT: H 118 GLU cc_start: 0.6868 (OUTLIER) cc_final: 0.6471 (pp20) REVERT: H 237 GLU cc_start: 0.3179 (OUTLIER) cc_final: 0.2511 (tp30) REVERT: H 287 ILE cc_start: 0.6187 (OUTLIER) cc_final: 0.5177 (pt) REVERT: H 315 TYR cc_start: 0.5518 (OUTLIER) cc_final: 0.5194 (t80) REVERT: I 49 VAL cc_start: 0.5974 (OUTLIER) cc_final: 0.5555 (p) REVERT: I 81 LEU cc_start: 0.0277 (OUTLIER) cc_final: 0.0049 (tp) REVERT: I 94 GLN cc_start: 0.2952 (OUTLIER) cc_final: 0.2428 (pp30) REVERT: I 129 PHE cc_start: 0.2955 (OUTLIER) cc_final: 0.2440 (m-80) REVERT: I 278 MET cc_start: 0.0762 (OUTLIER) cc_final: -0.1092 (mtm) REVERT: I 306 ARG cc_start: 0.5834 (mmt-90) cc_final: 0.5128 (mmp80) REVERT: A 58 LYS cc_start: 0.5347 (OUTLIER) cc_final: 0.4653 (ttpp) REVERT: A 73 LYS cc_start: 0.7988 (mmmt) cc_final: 0.7442 (tttm) REVERT: A 84 MET cc_start: 0.1536 (OUTLIER) cc_final: -0.2478 (mmt) REVERT: A 124 GLU cc_start: 0.5014 (OUTLIER) cc_final: 0.3992 (tm-30) REVERT: A 215 ARG cc_start: 0.6034 (OUTLIER) cc_final: 0.5203 (mtm180) REVERT: A 311 ILE cc_start: 0.7370 (OUTLIER) cc_final: 0.7061 (tp) REVERT: B 47 HIS cc_start: 0.6542 (OUTLIER) cc_final: 0.6216 (m-70) REVERT: B 80 LYS cc_start: 0.8173 (pptt) cc_final: 0.7485 (ptpt) REVERT: B 124 GLU cc_start: 0.6431 (OUTLIER) cc_final: 0.5663 (tp30) REVERT: B 210 MET cc_start: 0.6539 (pmm) cc_final: 0.4157 (tmm) REVERT: B 211 MET cc_start: 0.4960 (pmm) cc_final: 0.3399 (pmm) REVERT: B 315 TYR cc_start: 0.6886 (OUTLIER) cc_final: 0.5824 (t80) REVERT: C 184 ASP cc_start: 0.6681 (p0) cc_final: 0.6324 (p0) REVERT: C 250 ARG cc_start: 0.7039 (OUTLIER) cc_final: 0.6658 (tmt170) REVERT: D 252 LEU cc_start: 0.8494 (OUTLIER) cc_final: 0.8237 (mp) outliers start: 161 outliers final: 92 residues processed: 394 average time/residue: 0.1637 time to fit residues: 99.1768 Evaluate side-chains 362 residues out of total 2256 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 117 poor density : 245 time to evaluate : 0.799 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 158 MET Chi-restraints excluded: chain E residue 191 TYR Chi-restraints excluded: chain E residue 198 ASP Chi-restraints excluded: chain E residue 204 LEU Chi-restraints excluded: chain E residue 219 LEU Chi-restraints excluded: chain E residue 263 VAL Chi-restraints excluded: chain E residue 278 MET Chi-restraints excluded: chain F residue 88 THR Chi-restraints excluded: chain F residue 146 LEU Chi-restraints excluded: chain F residue 180 LEU Chi-restraints excluded: chain F residue 186 LEU Chi-restraints excluded: chain F residue 218 LEU Chi-restraints excluded: chain F residue 230 THR Chi-restraints excluded: chain F residue 278 MET Chi-restraints excluded: chain F residue 279 PHE Chi-restraints excluded: chain F residue 316 ASP Chi-restraints excluded: chain G residue 91 GLU Chi-restraints excluded: chain G residue 124 GLU Chi-restraints excluded: chain G residue 185 VAL Chi-restraints excluded: chain G residue 233 SER Chi-restraints excluded: chain G residue 253 LEU Chi-restraints excluded: chain G residue 264 VAL Chi-restraints excluded: chain G residue 282 ASP Chi-restraints excluded: chain G residue 291 ILE Chi-restraints excluded: chain G residue 313 LYS Chi-restraints excluded: chain H residue 84 MET Chi-restraints excluded: chain H residue 112 LEU Chi-restraints excluded: chain H residue 118 GLU Chi-restraints excluded: chain H residue 206 GLN Chi-restraints excluded: chain H residue 219 LEU Chi-restraints excluded: chain H residue 237 GLU Chi-restraints excluded: chain H residue 266 THR Chi-restraints excluded: chain H residue 270 VAL Chi-restraints excluded: chain H residue 287 ILE Chi-restraints excluded: chain H residue 292 ILE Chi-restraints excluded: chain H residue 315 TYR Chi-restraints excluded: chain I residue 49 VAL Chi-restraints excluded: chain I residue 81 LEU Chi-restraints excluded: chain I residue 94 GLN Chi-restraints excluded: chain I residue 119 THR Chi-restraints excluded: chain I residue 129 PHE Chi-restraints excluded: chain I residue 140 LEU Chi-restraints excluded: chain I residue 146 LEU Chi-restraints excluded: chain I residue 197 THR Chi-restraints excluded: chain I residue 220 ILE Chi-restraints excluded: chain I residue 264 VAL Chi-restraints excluded: chain I residue 266 THR Chi-restraints excluded: chain I residue 278 MET Chi-restraints excluded: chain I residue 282 ASP Chi-restraints excluded: chain I residue 336 ASP Chi-restraints excluded: chain A residue 30 GLN Chi-restraints excluded: chain A residue 48 THR Chi-restraints excluded: chain A residue 52 VAL Chi-restraints excluded: chain A residue 58 LYS Chi-restraints excluded: chain A residue 61 ILE Chi-restraints excluded: chain A residue 84 MET Chi-restraints excluded: chain A residue 124 GLU Chi-restraints excluded: chain A residue 156 LYS Chi-restraints excluded: chain A residue 189 VAL Chi-restraints excluded: chain A residue 211 MET Chi-restraints excluded: chain A residue 212 VAL Chi-restraints excluded: chain A residue 213 GLU Chi-restraints excluded: chain A residue 215 ARG Chi-restraints excluded: chain A residue 261 VAL Chi-restraints excluded: chain A residue 270 VAL Chi-restraints excluded: chain A residue 273 VAL Chi-restraints excluded: chain A residue 291 ILE Chi-restraints excluded: chain A residue 302 LEU Chi-restraints excluded: chain A residue 311 ILE Chi-restraints excluded: chain A residue 314 ILE Chi-restraints excluded: chain B residue 25 ILE Chi-restraints excluded: chain B residue 26 SER Chi-restraints excluded: chain B residue 47 HIS Chi-restraints excluded: chain B residue 60 LEU Chi-restraints excluded: chain B residue 67 SER Chi-restraints excluded: chain B residue 90 THR Chi-restraints excluded: chain B residue 100 ILE Chi-restraints excluded: chain B residue 117 ILE Chi-restraints excluded: chain B residue 124 GLU Chi-restraints excluded: chain B residue 133 LYS Chi-restraints excluded: chain B residue 160 ILE Chi-restraints excluded: chain B residue 177 ARG Chi-restraints excluded: chain B residue 186 LEU Chi-restraints excluded: chain B residue 213 GLU Chi-restraints excluded: chain B residue 215 ARG Chi-restraints excluded: chain B residue 251 MET Chi-restraints excluded: chain B residue 261 VAL Chi-restraints excluded: chain B residue 265 ILE Chi-restraints excluded: chain B residue 266 THR Chi-restraints excluded: chain B residue 269 VAL Chi-restraints excluded: chain B residue 270 VAL Chi-restraints excluded: chain B residue 273 VAL Chi-restraints excluded: chain B residue 298 THR Chi-restraints excluded: chain B residue 310 ARG Chi-restraints excluded: chain B residue 315 TYR Chi-restraints excluded: chain C residue 43 GLU Chi-restraints excluded: chain C residue 99 ILE Chi-restraints excluded: chain C residue 161 ASP Chi-restraints excluded: chain C residue 185 VAL Chi-restraints excluded: chain C residue 195 PHE Chi-restraints excluded: chain C residue 212 VAL Chi-restraints excluded: chain C residue 250 ARG Chi-restraints excluded: chain C residue 253 LEU Chi-restraints excluded: chain C residue 285 LYS Chi-restraints excluded: chain C residue 292 ILE Chi-restraints excluded: chain C residue 297 THR Chi-restraints excluded: chain D residue 25 ILE Chi-restraints excluded: chain D residue 38 VAL Chi-restraints excluded: chain D residue 48 THR Chi-restraints excluded: chain D residue 119 THR Chi-restraints excluded: chain D residue 200 GLN Chi-restraints excluded: chain D residue 223 SER Chi-restraints excluded: chain D residue 231 ASP Chi-restraints excluded: chain D residue 252 LEU Chi-restraints excluded: chain D residue 257 ASP Chi-restraints excluded: chain D residue 297 THR Chi-restraints excluded: chain D residue 319 CYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 279 random chunks: chunk 249 optimal weight: 9.9990 chunk 232 optimal weight: 0.6980 chunk 48 optimal weight: 5.9990 chunk 102 optimal weight: 20.0000 chunk 1 optimal weight: 2.9990 chunk 165 optimal weight: 0.0070 chunk 150 optimal weight: 3.9990 chunk 250 optimal weight: 7.9990 chunk 204 optimal weight: 9.9990 chunk 216 optimal weight: 0.6980 chunk 209 optimal weight: 6.9990 overall best weight: 1.6802 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** E 145 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 93 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 93 HIS ** H 272 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 202 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 268 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 242 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 196 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 200 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 145 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5061 r_free = 0.5061 target = 0.210444 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4784 r_free = 0.4784 target = 0.180099 restraints weight = 37266.300| |-----------------------------------------------------------------------------| r_work (start): 0.4729 rms_B_bonded: 3.51 r_work: 0.4414 rms_B_bonded: 4.08 restraints_weight: 0.5000 r_work (final): 0.4414 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6792 moved from start: 0.1388 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 23296 Z= 0.170 Angle : 0.693 16.551 31697 Z= 0.354 Chirality : 0.045 0.309 3597 Planarity : 0.004 0.052 3902 Dihedral : 15.424 179.743 3956 Min Nonbonded Distance : 1.789 Molprobity Statistics. All-atom Clashscore : 17.68 Ramachandran Plot: Outliers : 0.07 % Allowed : 8.05 % Favored : 91.87 % Rotamer: Outliers : 6.78 % Allowed : 26.64 % Favored : 66.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -2.52 (0.15), residues: 2781 helix: -0.54 (0.15), residues: 1142 sheet: -2.28 (0.24), residues: 413 loop : -2.54 (0.16), residues: 1226 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 310 TYR 0.056 0.002 TYR F 54 PHE 0.024 0.002 PHE C 166 HIS 0.008 0.001 HIS G 93 Details of bonding type rmsd/Z covalent geometry : bond 0.00370 / 0.17 (23295) covalent geometry : angle 0.69296 / 0.35 (31697) hydrogen bonds : bond 0.04309 / 2.79 ( 854) hydrogen bonds : angle 5.55845 / 3.81 ( 2428) Misc. bond : bond 0.00040 / 0.03 ( 1) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5562 Ramachandran restraints generated. 2781 Oldfield, 0 Emsley, 2781 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5562 Ramachandran restraints generated. 2781 Oldfield, 0 Emsley, 2781 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 404 residues out of total 2256 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 153 poor density : 251 time to evaluate : 0.765 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 80 LYS cc_start: 0.7221 (pptt) cc_final: 0.6512 (tptt) REVERT: F 186 LEU cc_start: 0.6707 (OUTLIER) cc_final: 0.6348 (mt) REVERT: F 198 ASP cc_start: 0.8122 (t70) cc_final: 0.7874 (t0) REVERT: F 210 MET cc_start: 0.6490 (tmt) cc_final: 0.6178 (tmm) REVERT: F 279 PHE cc_start: 0.3560 (OUTLIER) cc_final: 0.2226 (p90) REVERT: F 303 ARG cc_start: 0.5280 (ptt-90) cc_final: 0.4728 (ptt-90) REVERT: F 316 ASP cc_start: 0.4707 (OUTLIER) cc_final: 0.4289 (p0) REVERT: G 91 GLU cc_start: 0.7944 (OUTLIER) cc_final: 0.7483 (tt0) REVERT: G 163 GLU cc_start: 0.6750 (OUTLIER) cc_final: 0.5512 (pm20) REVERT: G 193 ARG cc_start: 0.3412 (mmm-85) cc_final: 0.3123 (mmm-85) REVERT: G 291 ILE cc_start: 0.6771 (OUTLIER) cc_final: 0.6401 (mp) REVERT: H 118 GLU cc_start: 0.6811 (OUTLIER) cc_final: 0.6427 (pp20) REVERT: H 211 MET cc_start: 0.6862 (mmm) cc_final: 0.6597 (mmm) REVERT: H 237 GLU cc_start: 0.3131 (OUTLIER) cc_final: 0.2515 (tp30) REVERT: H 287 ILE cc_start: 0.6073 (OUTLIER) cc_final: 0.5021 (pt) REVERT: H 315 TYR cc_start: 0.5511 (OUTLIER) cc_final: 0.5143 (t80) REVERT: I 49 VAL cc_start: 0.5997 (OUTLIER) cc_final: 0.5557 (p) REVERT: I 81 LEU cc_start: 0.0200 (OUTLIER) cc_final: -0.0004 (tp) REVERT: I 94 GLN cc_start: 0.3013 (OUTLIER) cc_final: 0.2478 (pp30) REVERT: I 129 PHE cc_start: 0.3004 (OUTLIER) cc_final: 0.2421 (m-80) REVERT: I 278 MET cc_start: 0.0732 (OUTLIER) cc_final: -0.1168 (mtm) REVERT: I 306 ARG cc_start: 0.5790 (mmt-90) cc_final: 0.5118 (mmp80) REVERT: A 58 LYS cc_start: 0.5390 (OUTLIER) cc_final: 0.4675 (ttpp) REVERT: A 73 LYS cc_start: 0.8010 (mmmt) cc_final: 0.7447 (tttm) REVERT: A 84 MET cc_start: 0.1525 (OUTLIER) cc_final: -0.2431 (mmt) REVERT: A 124 GLU cc_start: 0.5076 (OUTLIER) cc_final: 0.4114 (tm-30) REVERT: A 311 ILE cc_start: 0.7403 (OUTLIER) cc_final: 0.6913 (tp) REVERT: B 47 HIS cc_start: 0.6558 (OUTLIER) cc_final: 0.6215 (m-70) REVERT: B 80 LYS cc_start: 0.8192 (pptt) cc_final: 0.7490 (ptpt) REVERT: B 94 GLN cc_start: 0.7226 (mm110) cc_final: 0.6490 (pp30) REVERT: B 210 MET cc_start: 0.6505 (pmm) cc_final: 0.4159 (tmm) REVERT: B 211 MET cc_start: 0.4925 (pmm) cc_final: 0.3435 (pmm) REVERT: B 315 TYR cc_start: 0.6882 (OUTLIER) cc_final: 0.5854 (t80) REVERT: C 184 ASP cc_start: 0.6619 (p0) cc_final: 0.6242 (p0) REVERT: C 213 GLU cc_start: 0.8153 (OUTLIER) cc_final: 0.7940 (pm20) REVERT: C 250 ARG cc_start: 0.7072 (OUTLIER) cc_final: 0.6695 (tmt170) REVERT: D 252 LEU cc_start: 0.8551 (OUTLIER) cc_final: 0.8314 (mp) outliers start: 153 outliers final: 108 residues processed: 377 average time/residue: 0.1665 time to fit residues: 96.9704 Evaluate side-chains 374 residues out of total 2256 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 132 poor density : 242 time to evaluate : 0.893 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 187 ASP Chi-restraints excluded: chain E residue 191 TYR Chi-restraints excluded: chain E residue 198 ASP Chi-restraints excluded: chain E residue 204 LEU Chi-restraints excluded: chain E residue 219 LEU Chi-restraints excluded: chain E residue 263 VAL Chi-restraints excluded: chain E residue 274 ASP Chi-restraints excluded: chain E residue 278 MET Chi-restraints excluded: chain F residue 88 THR Chi-restraints excluded: chain F residue 104 THR Chi-restraints excluded: chain F residue 142 VAL Chi-restraints excluded: chain F residue 146 LEU Chi-restraints excluded: chain F residue 180 LEU Chi-restraints excluded: chain F residue 185 VAL Chi-restraints excluded: chain F residue 186 LEU Chi-restraints excluded: chain F residue 201 THR Chi-restraints excluded: chain F residue 218 LEU Chi-restraints excluded: chain F residue 230 THR Chi-restraints excluded: chain F residue 278 MET Chi-restraints excluded: chain F residue 279 PHE Chi-restraints excluded: chain F residue 316 ASP Chi-restraints excluded: chain G residue 75 LEU Chi-restraints excluded: chain G residue 91 GLU Chi-restraints excluded: chain G residue 109 LEU Chi-restraints excluded: chain G residue 124 GLU Chi-restraints excluded: chain G residue 149 ASP Chi-restraints excluded: chain G residue 163 GLU Chi-restraints excluded: chain G residue 185 VAL Chi-restraints excluded: chain G residue 233 SER Chi-restraints excluded: chain G residue 253 LEU Chi-restraints excluded: chain G residue 264 VAL Chi-restraints excluded: chain G residue 282 ASP Chi-restraints excluded: chain G residue 291 ILE Chi-restraints excluded: chain G residue 313 LYS Chi-restraints excluded: chain H residue 84 MET Chi-restraints excluded: chain H residue 112 LEU Chi-restraints excluded: chain H residue 118 GLU Chi-restraints excluded: chain H residue 124 GLU Chi-restraints excluded: chain H residue 180 LEU Chi-restraints excluded: chain H residue 206 GLN Chi-restraints excluded: chain H residue 237 GLU Chi-restraints excluded: chain H residue 266 THR Chi-restraints excluded: chain H residue 270 VAL Chi-restraints excluded: chain H residue 287 ILE Chi-restraints excluded: chain H residue 292 ILE Chi-restraints excluded: chain H residue 315 TYR Chi-restraints excluded: chain I residue 49 VAL Chi-restraints excluded: chain I residue 81 LEU Chi-restraints excluded: chain I residue 94 GLN Chi-restraints excluded: chain I residue 119 THR Chi-restraints excluded: chain I residue 123 THR Chi-restraints excluded: chain I residue 129 PHE Chi-restraints excluded: chain I residue 140 LEU Chi-restraints excluded: chain I residue 146 LEU Chi-restraints excluded: chain I residue 197 THR Chi-restraints excluded: chain I residue 264 VAL Chi-restraints excluded: chain I residue 266 THR Chi-restraints excluded: chain I residue 278 MET Chi-restraints excluded: chain I residue 282 ASP Chi-restraints excluded: chain I residue 314 ILE Chi-restraints excluded: chain I residue 320 LEU Chi-restraints excluded: chain I residue 336 ASP Chi-restraints excluded: chain A residue 25 ILE Chi-restraints excluded: chain A residue 30 GLN Chi-restraints excluded: chain A residue 48 THR Chi-restraints excluded: chain A residue 52 VAL Chi-restraints excluded: chain A residue 58 LYS Chi-restraints excluded: chain A residue 61 ILE Chi-restraints excluded: chain A residue 76 THR Chi-restraints excluded: chain A residue 84 MET Chi-restraints excluded: chain A residue 124 GLU Chi-restraints excluded: chain A residue 156 LYS Chi-restraints excluded: chain A residue 189 VAL Chi-restraints excluded: chain A residue 212 VAL Chi-restraints excluded: chain A residue 213 GLU Chi-restraints excluded: chain A residue 261 VAL Chi-restraints excluded: chain A residue 270 VAL Chi-restraints excluded: chain A residue 273 VAL Chi-restraints excluded: chain A residue 291 ILE Chi-restraints excluded: chain A residue 302 LEU Chi-restraints excluded: chain A residue 311 ILE Chi-restraints excluded: chain A residue 314 ILE Chi-restraints excluded: chain B residue 25 ILE Chi-restraints excluded: chain B residue 26 SER Chi-restraints excluded: chain B residue 47 HIS Chi-restraints excluded: chain B residue 60 LEU Chi-restraints excluded: chain B residue 67 SER Chi-restraints excluded: chain B residue 90 THR Chi-restraints excluded: chain B residue 100 ILE Chi-restraints excluded: chain B residue 117 ILE Chi-restraints excluded: chain B residue 124 GLU Chi-restraints excluded: chain B residue 133 LYS Chi-restraints excluded: chain B residue 160 ILE Chi-restraints excluded: chain B residue 177 ARG Chi-restraints excluded: chain B residue 186 LEU Chi-restraints excluded: chain B residue 213 GLU Chi-restraints excluded: chain B residue 215 ARG Chi-restraints excluded: chain B residue 251 MET Chi-restraints excluded: chain B residue 261 VAL Chi-restraints excluded: chain B residue 265 ILE Chi-restraints excluded: chain B residue 266 THR Chi-restraints excluded: chain B residue 269 VAL Chi-restraints excluded: chain B residue 273 VAL Chi-restraints excluded: chain B residue 298 THR Chi-restraints excluded: chain B residue 309 THR Chi-restraints excluded: chain B residue 310 ARG Chi-restraints excluded: chain B residue 315 TYR Chi-restraints excluded: chain B residue 326 MET Chi-restraints excluded: chain C residue 31 CYS Chi-restraints excluded: chain C residue 43 GLU Chi-restraints excluded: chain C residue 99 ILE Chi-restraints excluded: chain C residue 161 ASP Chi-restraints excluded: chain C residue 185 VAL Chi-restraints excluded: chain C residue 195 PHE Chi-restraints excluded: chain C residue 212 VAL Chi-restraints excluded: chain C residue 213 GLU Chi-restraints excluded: chain C residue 250 ARG Chi-restraints excluded: chain C residue 253 LEU Chi-restraints excluded: chain C residue 285 LYS Chi-restraints excluded: chain C residue 292 ILE Chi-restraints excluded: chain C residue 297 THR Chi-restraints excluded: chain C residue 329 ILE Chi-restraints excluded: chain D residue 25 ILE Chi-restraints excluded: chain D residue 38 VAL Chi-restraints excluded: chain D residue 48 THR Chi-restraints excluded: chain D residue 119 THR Chi-restraints excluded: chain D residue 223 SER Chi-restraints excluded: chain D residue 231 ASP Chi-restraints excluded: chain D residue 252 LEU Chi-restraints excluded: chain D residue 257 ASP Chi-restraints excluded: chain D residue 297 THR Chi-restraints excluded: chain D residue 319 CYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 279 random chunks: chunk 44 optimal weight: 10.0000 chunk 86 optimal weight: 0.0050 chunk 124 optimal weight: 50.0000 chunk 99 optimal weight: 0.6980 chunk 23 optimal weight: 2.9990 chunk 236 optimal weight: 4.9990 chunk 41 optimal weight: 0.9990 chunk 136 optimal weight: 10.0000 chunk 30 optimal weight: 4.9990 chunk 31 optimal weight: 20.0000 chunk 19 optimal weight: 2.9990 overall best weight: 1.5400 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** E 145 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 93 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 93 HIS ** H 272 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 202 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 268 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 242 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 244 HIS ** B 196 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 200 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 145 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5066 r_free = 0.5066 target = 0.210622 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.4793 r_free = 0.4793 target = 0.180206 restraints weight = 36305.959| |-----------------------------------------------------------------------------| r_work (start): 0.4731 rms_B_bonded: 3.50 r_work: 0.4412 rms_B_bonded: 4.19 restraints_weight: 0.5000 r_work (final): 0.4412 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6789 moved from start: 0.1483 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 23296 Z= 0.160 Angle : 0.681 15.364 31697 Z= 0.348 Chirality : 0.045 0.301 3597 Planarity : 0.004 0.053 3902 Dihedral : 15.408 179.061 3956 Min Nonbonded Distance : 1.849 Molprobity Statistics. All-atom Clashscore : 17.64 Ramachandran Plot: Outliers : 0.07 % Allowed : 7.98 % Favored : 91.95 % Rotamer: Outliers : 6.87 % Allowed : 26.46 % Favored : 66.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -2.48 (0.15), residues: 2781 helix: -0.50 (0.15), residues: 1143 sheet: -2.19 (0.24), residues: 397 loop : -2.54 (0.16), residues: 1241 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 310 TYR 0.020 0.002 TYR F 54 PHE 0.021 0.002 PHE I 129 HIS 0.008 0.001 HIS G 93 Details of bonding type rmsd/Z covalent geometry : bond 0.00348 / 0.16 (23295) covalent geometry : angle 0.68108 / 0.35 (31697) hydrogen bonds : bond 0.04146 / 2.68 ( 854) hydrogen bonds : angle 5.48996 / 3.77 ( 2428) Misc. bond : bond 0.00040 / 0.03 ( 1) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5562 Ramachandran restraints generated. 2781 Oldfield, 0 Emsley, 2781 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5562 Ramachandran restraints generated. 2781 Oldfield, 0 Emsley, 2781 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 407 residues out of total 2256 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 155 poor density : 252 time to evaluate : 0.847 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 80 LYS cc_start: 0.7327 (pptt) cc_final: 0.6618 (tptt) REVERT: F 178 TYR cc_start: 0.6368 (OUTLIER) cc_final: 0.5341 (m-80) REVERT: F 186 LEU cc_start: 0.6638 (OUTLIER) cc_final: 0.6307 (mt) REVERT: F 198 ASP cc_start: 0.8085 (t70) cc_final: 0.7850 (t0) REVERT: F 205 TYR cc_start: 0.6528 (m-10) cc_final: 0.6302 (m-10) REVERT: F 210 MET cc_start: 0.6468 (tmt) cc_final: 0.6170 (tmm) REVERT: F 279 PHE cc_start: 0.3597 (OUTLIER) cc_final: 0.2291 (p90) REVERT: F 303 ARG cc_start: 0.5303 (ptt-90) cc_final: 0.4790 (ptt-90) REVERT: F 316 ASP cc_start: 0.4698 (OUTLIER) cc_final: 0.4277 (p0) REVERT: G 91 GLU cc_start: 0.7951 (OUTLIER) cc_final: 0.7456 (tt0) REVERT: G 98 GLU cc_start: 0.6187 (pp20) cc_final: 0.4869 (tt0) REVERT: G 163 GLU cc_start: 0.6602 (OUTLIER) cc_final: 0.5448 (pm20) REVERT: G 291 ILE cc_start: 0.6812 (OUTLIER) cc_final: 0.6456 (mp) REVERT: H 118 GLU cc_start: 0.6809 (OUTLIER) cc_final: 0.6430 (pp20) REVERT: H 209 ASP cc_start: 0.8684 (m-30) cc_final: 0.8207 (m-30) REVERT: H 237 GLU cc_start: 0.3073 (OUTLIER) cc_final: 0.2508 (tp30) REVERT: H 254 ARG cc_start: 0.7686 (ppp80) cc_final: 0.7481 (ppp80) REVERT: H 287 ILE cc_start: 0.6067 (OUTLIER) cc_final: 0.5043 (pt) REVERT: H 315 TYR cc_start: 0.5488 (OUTLIER) cc_final: 0.5068 (t80) REVERT: I 49 VAL cc_start: 0.6004 (OUTLIER) cc_final: 0.5565 (p) REVERT: I 94 GLN cc_start: 0.3061 (OUTLIER) cc_final: 0.2485 (pp30) REVERT: I 129 PHE cc_start: 0.3060 (OUTLIER) cc_final: 0.2490 (m-80) REVERT: I 278 MET cc_start: 0.0720 (OUTLIER) cc_final: -0.1292 (mtt) REVERT: I 306 ARG cc_start: 0.5805 (mmt-90) cc_final: 0.5171 (mmp80) REVERT: A 58 LYS cc_start: 0.5328 (OUTLIER) cc_final: 0.4602 (ttpp) REVERT: A 73 LYS cc_start: 0.7991 (mmmt) cc_final: 0.7402 (mtpt) REVERT: A 84 MET cc_start: 0.1531 (OUTLIER) cc_final: -0.2561 (mmt) REVERT: A 124 GLU cc_start: 0.5046 (OUTLIER) cc_final: 0.4079 (tm-30) REVERT: A 215 ARG cc_start: 0.6057 (OUTLIER) cc_final: 0.5146 (mmp-170) REVERT: A 311 ILE cc_start: 0.7404 (OUTLIER) cc_final: 0.6939 (tp) REVERT: B 80 LYS cc_start: 0.8214 (pptt) cc_final: 0.7521 (ptpt) REVERT: B 94 GLN cc_start: 0.7265 (mm110) cc_final: 0.6494 (pp30) REVERT: B 210 MET cc_start: 0.6547 (pmm) cc_final: 0.4184 (tmm) REVERT: B 211 MET cc_start: 0.4922 (pmm) cc_final: 0.3437 (pmm) REVERT: B 315 TYR cc_start: 0.6902 (OUTLIER) cc_final: 0.5728 (t80) REVERT: C 213 GLU cc_start: 0.8191 (OUTLIER) cc_final: 0.7943 (pm20) REVERT: C 250 ARG cc_start: 0.7063 (OUTLIER) cc_final: 0.6694 (tmt170) REVERT: D 252 LEU cc_start: 0.8553 (OUTLIER) cc_final: 0.8337 (mp) outliers start: 155 outliers final: 105 residues processed: 381 average time/residue: 0.1562 time to fit residues: 92.0464 Evaluate side-chains 373 residues out of total 2256 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 129 poor density : 244 time to evaluate : 0.620 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 191 TYR Chi-restraints excluded: chain E residue 198 ASP Chi-restraints excluded: chain E residue 204 LEU Chi-restraints excluded: chain E residue 219 LEU Chi-restraints excluded: chain E residue 263 VAL Chi-restraints excluded: chain E residue 273 VAL Chi-restraints excluded: chain E residue 274 ASP Chi-restraints excluded: chain E residue 278 MET Chi-restraints excluded: chain F residue 88 THR Chi-restraints excluded: chain F residue 104 THR Chi-restraints excluded: chain F residue 142 VAL Chi-restraints excluded: chain F residue 146 LEU Chi-restraints excluded: chain F residue 178 TYR Chi-restraints excluded: chain F residue 180 LEU Chi-restraints excluded: chain F residue 186 LEU Chi-restraints excluded: chain F residue 218 LEU Chi-restraints excluded: chain F residue 230 THR Chi-restraints excluded: chain F residue 261 VAL Chi-restraints excluded: chain F residue 273 VAL Chi-restraints excluded: chain F residue 278 MET Chi-restraints excluded: chain F residue 279 PHE Chi-restraints excluded: chain F residue 315 TYR Chi-restraints excluded: chain F residue 316 ASP Chi-restraints excluded: chain G residue 75 LEU Chi-restraints excluded: chain G residue 91 GLU Chi-restraints excluded: chain G residue 100 ILE Chi-restraints excluded: chain G residue 124 GLU Chi-restraints excluded: chain G residue 149 ASP Chi-restraints excluded: chain G residue 163 GLU Chi-restraints excluded: chain G residue 185 VAL Chi-restraints excluded: chain G residue 233 SER Chi-restraints excluded: chain G residue 253 LEU Chi-restraints excluded: chain G residue 261 VAL Chi-restraints excluded: chain G residue 264 VAL Chi-restraints excluded: chain G residue 282 ASP Chi-restraints excluded: chain G residue 291 ILE Chi-restraints excluded: chain H residue 84 MET Chi-restraints excluded: chain H residue 112 LEU Chi-restraints excluded: chain H residue 118 GLU Chi-restraints excluded: chain H residue 124 GLU Chi-restraints excluded: chain H residue 180 LEU Chi-restraints excluded: chain H residue 206 GLN Chi-restraints excluded: chain H residue 237 GLU Chi-restraints excluded: chain H residue 266 THR Chi-restraints excluded: chain H residue 270 VAL Chi-restraints excluded: chain H residue 287 ILE Chi-restraints excluded: chain H residue 292 ILE Chi-restraints excluded: chain H residue 315 TYR Chi-restraints excluded: chain I residue 49 VAL Chi-restraints excluded: chain I residue 94 GLN Chi-restraints excluded: chain I residue 119 THR Chi-restraints excluded: chain I residue 129 PHE Chi-restraints excluded: chain I residue 140 LEU Chi-restraints excluded: chain I residue 146 LEU Chi-restraints excluded: chain I residue 197 THR Chi-restraints excluded: chain I residue 264 VAL Chi-restraints excluded: chain I residue 266 THR Chi-restraints excluded: chain I residue 278 MET Chi-restraints excluded: chain I residue 282 ASP Chi-restraints excluded: chain I residue 320 LEU Chi-restraints excluded: chain I residue 336 ASP Chi-restraints excluded: chain A residue 25 ILE Chi-restraints excluded: chain A residue 30 GLN Chi-restraints excluded: chain A residue 48 THR Chi-restraints excluded: chain A residue 52 VAL Chi-restraints excluded: chain A residue 58 LYS Chi-restraints excluded: chain A residue 61 ILE Chi-restraints excluded: chain A residue 76 THR Chi-restraints excluded: chain A residue 84 MET Chi-restraints excluded: chain A residue 124 GLU Chi-restraints excluded: chain A residue 156 LYS Chi-restraints excluded: chain A residue 189 VAL Chi-restraints excluded: chain A residue 212 VAL Chi-restraints excluded: chain A residue 213 GLU Chi-restraints excluded: chain A residue 215 ARG Chi-restraints excluded: chain A residue 261 VAL Chi-restraints excluded: chain A residue 270 VAL Chi-restraints excluded: chain A residue 273 VAL Chi-restraints excluded: chain A residue 291 ILE Chi-restraints excluded: chain A residue 302 LEU Chi-restraints excluded: chain A residue 311 ILE Chi-restraints excluded: chain A residue 314 ILE Chi-restraints excluded: chain B residue 25 ILE Chi-restraints excluded: chain B residue 26 SER Chi-restraints excluded: chain B residue 60 LEU Chi-restraints excluded: chain B residue 67 SER Chi-restraints excluded: chain B residue 90 THR Chi-restraints excluded: chain B residue 100 ILE Chi-restraints excluded: chain B residue 117 ILE Chi-restraints excluded: chain B residue 124 GLU Chi-restraints excluded: chain B residue 133 LYS Chi-restraints excluded: chain B residue 160 ILE Chi-restraints excluded: chain B residue 177 ARG Chi-restraints excluded: chain B residue 186 LEU Chi-restraints excluded: chain B residue 213 GLU Chi-restraints excluded: chain B residue 215 ARG Chi-restraints excluded: chain B residue 251 MET Chi-restraints excluded: chain B residue 261 VAL Chi-restraints excluded: chain B residue 265 ILE Chi-restraints excluded: chain B residue 266 THR Chi-restraints excluded: chain B residue 269 VAL Chi-restraints excluded: chain B residue 273 VAL Chi-restraints excluded: chain B residue 291 ILE Chi-restraints excluded: chain B residue 298 THR Chi-restraints excluded: chain B residue 310 ARG Chi-restraints excluded: chain B residue 315 TYR Chi-restraints excluded: chain C residue 31 CYS Chi-restraints excluded: chain C residue 43 GLU Chi-restraints excluded: chain C residue 99 ILE Chi-restraints excluded: chain C residue 161 ASP Chi-restraints excluded: chain C residue 185 VAL Chi-restraints excluded: chain C residue 195 PHE Chi-restraints excluded: chain C residue 212 VAL Chi-restraints excluded: chain C residue 213 GLU Chi-restraints excluded: chain C residue 250 ARG Chi-restraints excluded: chain C residue 253 LEU Chi-restraints excluded: chain C residue 285 LYS Chi-restraints excluded: chain C residue 292 ILE Chi-restraints excluded: chain C residue 297 THR Chi-restraints excluded: chain D residue 25 ILE Chi-restraints excluded: chain D residue 38 VAL Chi-restraints excluded: chain D residue 48 THR Chi-restraints excluded: chain D residue 119 THR Chi-restraints excluded: chain D residue 223 SER Chi-restraints excluded: chain D residue 231 ASP Chi-restraints excluded: chain D residue 252 LEU Chi-restraints excluded: chain D residue 257 ASP Chi-restraints excluded: chain D residue 297 THR Chi-restraints excluded: chain D residue 319 CYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 279 random chunks: chunk 67 optimal weight: 7.9990 chunk 272 optimal weight: 0.7980 chunk 195 optimal weight: 7.9990 chunk 153 optimal weight: 10.0000 chunk 162 optimal weight: 3.9990 chunk 171 optimal weight: 2.9990 chunk 176 optimal weight: 1.9990 chunk 123 optimal weight: 5.9990 chunk 41 optimal weight: 0.9990 chunk 248 optimal weight: 2.9990 chunk 25 optimal weight: 0.9990 overall best weight: 1.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** E 145 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 93 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 93 HIS ** H 196 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 272 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 202 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 268 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 242 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 196 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 200 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 145 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5065 r_free = 0.5065 target = 0.210555 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4791 r_free = 0.4791 target = 0.180178 restraints weight = 36621.759| |-----------------------------------------------------------------------------| r_work (start): 0.4732 rms_B_bonded: 3.54 r_work: 0.4410 rms_B_bonded: 4.18 restraints_weight: 0.5000 r_work (final): 0.4410 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6794 moved from start: 0.1568 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 23296 Z= 0.162 Angle : 0.690 15.073 31697 Z= 0.352 Chirality : 0.045 0.289 3597 Planarity : 0.004 0.054 3902 Dihedral : 15.386 179.056 3954 Min Nonbonded Distance : 1.831 Molprobity Statistics. All-atom Clashscore : 17.28 Ramachandran Plot: Outliers : 0.07 % Allowed : 7.84 % Favored : 92.09 % Rotamer: Outliers : 6.52 % Allowed : 26.82 % Favored : 66.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -2.46 (0.15), residues: 2781 helix: -0.51 (0.15), residues: 1145 sheet: -2.22 (0.24), residues: 393 loop : -2.50 (0.16), residues: 1243 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 310 TYR 0.028 0.002 TYR F 54 PHE 0.021 0.002 PHE I 129 HIS 0.008 0.001 HIS G 93 Details of bonding type rmsd/Z covalent geometry : bond 0.00354 / 0.16 (23295) covalent geometry : angle 0.68975 / 0.35 (31697) hydrogen bonds : bond 0.04158 / 2.69 ( 854) hydrogen bonds : angle 5.46429 / 3.76 ( 2428) Misc. bond : bond 0.00038 / 0.03 ( 1) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5562 Ramachandran restraints generated. 2781 Oldfield, 0 Emsley, 2781 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5562 Ramachandran restraints generated. 2781 Oldfield, 0 Emsley, 2781 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 397 residues out of total 2256 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 147 poor density : 250 time to evaluate : 0.605 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 80 LYS cc_start: 0.7299 (pptt) cc_final: 0.6600 (tptt) REVERT: E 259 PHE cc_start: 0.5571 (t80) cc_final: 0.5162 (t80) REVERT: F 136 ILE cc_start: 0.6533 (OUTLIER) cc_final: 0.6267 (mt) REVERT: F 178 TYR cc_start: 0.6309 (OUTLIER) cc_final: 0.5183 (m-80) REVERT: F 186 LEU cc_start: 0.6725 (OUTLIER) cc_final: 0.6459 (tp) REVERT: F 198 ASP cc_start: 0.8062 (t70) cc_final: 0.7821 (t0) REVERT: F 210 MET cc_start: 0.6456 (tmt) cc_final: 0.6160 (tmm) REVERT: F 279 PHE cc_start: 0.3531 (OUTLIER) cc_final: 0.2239 (p90) REVERT: F 303 ARG cc_start: 0.5355 (ptt-90) cc_final: 0.4813 (ptt-90) REVERT: F 316 ASP cc_start: 0.4698 (OUTLIER) cc_final: 0.4285 (p0) REVERT: G 91 GLU cc_start: 0.7935 (OUTLIER) cc_final: 0.7478 (tt0) REVERT: G 98 GLU cc_start: 0.6084 (pp20) cc_final: 0.4800 (tt0) REVERT: G 163 GLU cc_start: 0.6552 (OUTLIER) cc_final: 0.5557 (pm20) REVERT: G 291 ILE cc_start: 0.6803 (OUTLIER) cc_final: 0.6443 (mp) REVERT: H 118 GLU cc_start: 0.6781 (OUTLIER) cc_final: 0.6407 (pp20) REVERT: H 211 MET cc_start: 0.5868 (mmp) cc_final: 0.5048 (mmm) REVERT: H 237 GLU cc_start: 0.3029 (OUTLIER) cc_final: 0.2462 (tp30) REVERT: H 254 ARG cc_start: 0.7733 (ppp80) cc_final: 0.7494 (ppp80) REVERT: H 287 ILE cc_start: 0.6049 (OUTLIER) cc_final: 0.5019 (pt) REVERT: H 315 TYR cc_start: 0.5515 (OUTLIER) cc_final: 0.5020 (t80) REVERT: I 49 VAL cc_start: 0.6007 (OUTLIER) cc_final: 0.5577 (p) REVERT: I 94 GLN cc_start: 0.3108 (OUTLIER) cc_final: 0.2588 (pp30) REVERT: I 129 PHE cc_start: 0.3016 (OUTLIER) cc_final: 0.2447 (m-80) REVERT: I 278 MET cc_start: 0.0626 (OUTLIER) cc_final: -0.1346 (mtt) REVERT: I 306 ARG cc_start: 0.5791 (mmt-90) cc_final: 0.5142 (mmp80) REVERT: A 58 LYS cc_start: 0.5359 (OUTLIER) cc_final: 0.4626 (ttpp) REVERT: A 73 LYS cc_start: 0.8009 (mmmt) cc_final: 0.7405 (mtpt) REVERT: A 84 MET cc_start: 0.1410 (OUTLIER) cc_final: -0.2611 (mmt) REVERT: A 124 GLU cc_start: 0.5020 (OUTLIER) cc_final: 0.4078 (tm-30) REVERT: A 215 ARG cc_start: 0.5993 (OUTLIER) cc_final: 0.5152 (mmp-170) REVERT: A 311 ILE cc_start: 0.7412 (OUTLIER) cc_final: 0.7090 (tp) REVERT: B 80 LYS cc_start: 0.8137 (pptt) cc_final: 0.7461 (ptpt) REVERT: B 94 GLN cc_start: 0.7122 (mm110) cc_final: 0.6450 (pp30) REVERT: B 210 MET cc_start: 0.6568 (pmm) cc_final: 0.4229 (tmm) REVERT: B 211 MET cc_start: 0.4911 (pmm) cc_final: 0.3500 (pmm) REVERT: B 315 TYR cc_start: 0.6851 (OUTLIER) cc_final: 0.5660 (t80) REVERT: C 213 GLU cc_start: 0.8215 (OUTLIER) cc_final: 0.7974 (pm20) REVERT: C 250 ARG cc_start: 0.7082 (OUTLIER) cc_final: 0.6716 (tmt170) REVERT: D 252 LEU cc_start: 0.8566 (OUTLIER) cc_final: 0.8362 (mp) outliers start: 147 outliers final: 109 residues processed: 374 average time/residue: 0.1613 time to fit residues: 93.5981 Evaluate side-chains 378 residues out of total 2256 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 134 poor density : 244 time to evaluate : 0.665 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 187 ASP Chi-restraints excluded: chain E residue 191 TYR Chi-restraints excluded: chain E residue 198 ASP Chi-restraints excluded: chain E residue 204 LEU Chi-restraints excluded: chain E residue 219 LEU Chi-restraints excluded: chain E residue 239 SER Chi-restraints excluded: chain E residue 263 VAL Chi-restraints excluded: chain E residue 273 VAL Chi-restraints excluded: chain E residue 274 ASP Chi-restraints excluded: chain E residue 278 MET Chi-restraints excluded: chain F residue 88 THR Chi-restraints excluded: chain F residue 104 THR Chi-restraints excluded: chain F residue 136 ILE Chi-restraints excluded: chain F residue 142 VAL Chi-restraints excluded: chain F residue 146 LEU Chi-restraints excluded: chain F residue 178 TYR Chi-restraints excluded: chain F residue 180 LEU Chi-restraints excluded: chain F residue 185 VAL Chi-restraints excluded: chain F residue 186 LEU Chi-restraints excluded: chain F residue 201 THR Chi-restraints excluded: chain F residue 218 LEU Chi-restraints excluded: chain F residue 230 THR Chi-restraints excluded: chain F residue 261 VAL Chi-restraints excluded: chain F residue 273 VAL Chi-restraints excluded: chain F residue 278 MET Chi-restraints excluded: chain F residue 279 PHE Chi-restraints excluded: chain F residue 315 TYR Chi-restraints excluded: chain F residue 316 ASP Chi-restraints excluded: chain G residue 75 LEU Chi-restraints excluded: chain G residue 91 GLU Chi-restraints excluded: chain G residue 100 ILE Chi-restraints excluded: chain G residue 124 GLU Chi-restraints excluded: chain G residue 149 ASP Chi-restraints excluded: chain G residue 163 GLU Chi-restraints excluded: chain G residue 185 VAL Chi-restraints excluded: chain G residue 233 SER Chi-restraints excluded: chain G residue 253 LEU Chi-restraints excluded: chain G residue 261 VAL Chi-restraints excluded: chain G residue 264 VAL Chi-restraints excluded: chain G residue 282 ASP Chi-restraints excluded: chain G residue 291 ILE Chi-restraints excluded: chain H residue 84 MET Chi-restraints excluded: chain H residue 112 LEU Chi-restraints excluded: chain H residue 118 GLU Chi-restraints excluded: chain H residue 124 GLU Chi-restraints excluded: chain H residue 180 LEU Chi-restraints excluded: chain H residue 206 GLN Chi-restraints excluded: chain H residue 237 GLU Chi-restraints excluded: chain H residue 266 THR Chi-restraints excluded: chain H residue 270 VAL Chi-restraints excluded: chain H residue 287 ILE Chi-restraints excluded: chain H residue 292 ILE Chi-restraints excluded: chain H residue 315 TYR Chi-restraints excluded: chain I residue 49 VAL Chi-restraints excluded: chain I residue 94 GLN Chi-restraints excluded: chain I residue 119 THR Chi-restraints excluded: chain I residue 129 PHE Chi-restraints excluded: chain I residue 140 LEU Chi-restraints excluded: chain I residue 146 LEU Chi-restraints excluded: chain I residue 197 THR Chi-restraints excluded: chain I residue 264 VAL Chi-restraints excluded: chain I residue 266 THR Chi-restraints excluded: chain I residue 278 MET Chi-restraints excluded: chain I residue 282 ASP Chi-restraints excluded: chain I residue 320 LEU Chi-restraints excluded: chain I residue 336 ASP Chi-restraints excluded: chain A residue 25 ILE Chi-restraints excluded: chain A residue 30 GLN Chi-restraints excluded: chain A residue 48 THR Chi-restraints excluded: chain A residue 52 VAL Chi-restraints excluded: chain A residue 58 LYS Chi-restraints excluded: chain A residue 61 ILE Chi-restraints excluded: chain A residue 76 THR Chi-restraints excluded: chain A residue 84 MET Chi-restraints excluded: chain A residue 124 GLU Chi-restraints excluded: chain A residue 156 LYS Chi-restraints excluded: chain A residue 189 VAL Chi-restraints excluded: chain A residue 212 VAL Chi-restraints excluded: chain A residue 213 GLU Chi-restraints excluded: chain A residue 215 ARG Chi-restraints excluded: chain A residue 261 VAL Chi-restraints excluded: chain A residue 270 VAL Chi-restraints excluded: chain A residue 273 VAL Chi-restraints excluded: chain A residue 291 ILE Chi-restraints excluded: chain A residue 302 LEU Chi-restraints excluded: chain A residue 311 ILE Chi-restraints excluded: chain A residue 314 ILE Chi-restraints excluded: chain B residue 25 ILE Chi-restraints excluded: chain B residue 26 SER Chi-restraints excluded: chain B residue 60 LEU Chi-restraints excluded: chain B residue 67 SER Chi-restraints excluded: chain B residue 90 THR Chi-restraints excluded: chain B residue 100 ILE Chi-restraints excluded: chain B residue 117 ILE Chi-restraints excluded: chain B residue 124 GLU Chi-restraints excluded: chain B residue 133 LYS Chi-restraints excluded: chain B residue 160 ILE Chi-restraints excluded: chain B residue 177 ARG Chi-restraints excluded: chain B residue 186 LEU Chi-restraints excluded: chain B residue 213 GLU Chi-restraints excluded: chain B residue 215 ARG Chi-restraints excluded: chain B residue 251 MET Chi-restraints excluded: chain B residue 261 VAL Chi-restraints excluded: chain B residue 265 ILE Chi-restraints excluded: chain B residue 266 THR Chi-restraints excluded: chain B residue 269 VAL Chi-restraints excluded: chain B residue 273 VAL Chi-restraints excluded: chain B residue 291 ILE Chi-restraints excluded: chain B residue 298 THR Chi-restraints excluded: chain B residue 310 ARG Chi-restraints excluded: chain B residue 315 TYR Chi-restraints excluded: chain C residue 31 CYS Chi-restraints excluded: chain C residue 43 GLU Chi-restraints excluded: chain C residue 99 ILE Chi-restraints excluded: chain C residue 161 ASP Chi-restraints excluded: chain C residue 195 PHE Chi-restraints excluded: chain C residue 212 VAL Chi-restraints excluded: chain C residue 213 GLU Chi-restraints excluded: chain C residue 250 ARG Chi-restraints excluded: chain C residue 253 LEU Chi-restraints excluded: chain C residue 285 LYS Chi-restraints excluded: chain C residue 292 ILE Chi-restraints excluded: chain C residue 297 THR Chi-restraints excluded: chain D residue 25 ILE Chi-restraints excluded: chain D residue 38 VAL Chi-restraints excluded: chain D residue 48 THR Chi-restraints excluded: chain D residue 88 THR Chi-restraints excluded: chain D residue 119 THR Chi-restraints excluded: chain D residue 223 SER Chi-restraints excluded: chain D residue 231 ASP Chi-restraints excluded: chain D residue 252 LEU Chi-restraints excluded: chain D residue 257 ASP Chi-restraints excluded: chain D residue 297 THR Chi-restraints excluded: chain D residue 319 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 279 random chunks: chunk 25 optimal weight: 0.7980 chunk 159 optimal weight: 20.0000 chunk 113 optimal weight: 9.9990 chunk 195 optimal weight: 1.9990 chunk 163 optimal weight: 3.9990 chunk 152 optimal weight: 4.9990 chunk 164 optimal weight: 20.0000 chunk 71 optimal weight: 0.0000 chunk 2 optimal weight: 0.7980 chunk 69 optimal weight: 3.9990 chunk 255 optimal weight: 9.9990 overall best weight: 1.5188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** F 93 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 93 HIS ** H 196 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 272 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 202 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 268 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 242 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 196 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 200 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 145 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5066 r_free = 0.5066 target = 0.210726 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4791 r_free = 0.4791 target = 0.180153 restraints weight = 36861.741| |-----------------------------------------------------------------------------| r_work (start): 0.4730 rms_B_bonded: 3.54 r_work: 0.4413 rms_B_bonded: 4.17 restraints_weight: 0.5000 r_work (final): 0.4413 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6800 moved from start: 0.1620 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 23296 Z= 0.161 Angle : 0.693 14.806 31697 Z= 0.354 Chirality : 0.045 0.277 3597 Planarity : 0.004 0.055 3902 Dihedral : 15.375 178.685 3953 Min Nonbonded Distance : 1.803 Molprobity Statistics. All-atom Clashscore : 17.06 Ramachandran Plot: Outliers : 0.07 % Allowed : 7.87 % Favored : 92.05 % Rotamer: Outliers : 6.16 % Allowed : 27.39 % Favored : 66.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -2.46 (0.15), residues: 2781 helix: -0.51 (0.15), residues: 1143 sheet: -2.26 (0.24), residues: 386 loop : -2.48 (0.16), residues: 1252 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 310 TYR 0.026 0.002 TYR H 216 PHE 0.021 0.002 PHE I 129 HIS 0.008 0.001 HIS G 93 Details of bonding type rmsd/Z covalent geometry : bond 0.00351 / 0.16 (23295) covalent geometry : angle 0.69321 / 0.35 (31697) hydrogen bonds : bond 0.04113 / 2.66 ( 854) hydrogen bonds : angle 5.45300 / 3.76 ( 2428) Misc. bond : bond 0.00036 / 0.02 ( 1) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5562 Ramachandran restraints generated. 2781 Oldfield, 0 Emsley, 2781 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5562 Ramachandran restraints generated. 2781 Oldfield, 0 Emsley, 2781 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 388 residues out of total 2256 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 139 poor density : 249 time to evaluate : 0.690 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 80 LYS cc_start: 0.7300 (pptt) cc_final: 0.6632 (tptt) REVERT: E 210 MET cc_start: 0.6880 (ppp) cc_final: 0.6498 (ppp) REVERT: E 259 PHE cc_start: 0.5576 (t80) cc_final: 0.5223 (t80) REVERT: F 136 ILE cc_start: 0.6570 (OUTLIER) cc_final: 0.6299 (mt) REVERT: F 178 TYR cc_start: 0.6321 (OUTLIER) cc_final: 0.5191 (m-80) REVERT: F 186 LEU cc_start: 0.6713 (OUTLIER) cc_final: 0.6435 (tp) REVERT: F 198 ASP cc_start: 0.8033 (t70) cc_final: 0.7792 (t0) REVERT: F 205 TYR cc_start: 0.6497 (m-10) cc_final: 0.6281 (m-10) REVERT: F 210 MET cc_start: 0.6515 (tmt) cc_final: 0.6251 (tmm) REVERT: F 279 PHE cc_start: 0.3554 (OUTLIER) cc_final: 0.2299 (p90) REVERT: F 303 ARG cc_start: 0.5385 (ptt-90) cc_final: 0.4832 (ptt-90) REVERT: F 316 ASP cc_start: 0.4687 (OUTLIER) cc_final: 0.4278 (p0) REVERT: G 91 GLU cc_start: 0.7932 (OUTLIER) cc_final: 0.7456 (tt0) REVERT: G 98 GLU cc_start: 0.6051 (pp20) cc_final: 0.4802 (tt0) REVERT: G 163 GLU cc_start: 0.6567 (OUTLIER) cc_final: 0.5566 (pm20) REVERT: G 291 ILE cc_start: 0.6821 (OUTLIER) cc_final: 0.6460 (mp) REVERT: H 118 GLU cc_start: 0.6859 (OUTLIER) cc_final: 0.6468 (pp20) REVERT: H 209 ASP cc_start: 0.8719 (m-30) cc_final: 0.8254 (m-30) REVERT: H 211 MET cc_start: 0.6171 (mmp) cc_final: 0.5276 (mmm) REVERT: H 237 GLU cc_start: 0.2960 (OUTLIER) cc_final: 0.2454 (tp30) REVERT: H 287 ILE cc_start: 0.6015 (OUTLIER) cc_final: 0.4996 (pt) REVERT: I 49 VAL cc_start: 0.6020 (OUTLIER) cc_final: 0.5589 (p) REVERT: I 94 GLN cc_start: 0.3091 (OUTLIER) cc_final: 0.2594 (pp30) REVERT: I 129 PHE cc_start: 0.2984 (OUTLIER) cc_final: 0.2410 (m-80) REVERT: I 210 MET cc_start: 0.3228 (tpt) cc_final: 0.2872 (tpt) REVERT: I 278 MET cc_start: 0.0706 (OUTLIER) cc_final: -0.1242 (mtt) REVERT: I 306 ARG cc_start: 0.5815 (mmt-90) cc_final: 0.5154 (mmp80) REVERT: A 58 LYS cc_start: 0.5362 (OUTLIER) cc_final: 0.4628 (ttpp) REVERT: A 73 LYS cc_start: 0.7987 (mmmt) cc_final: 0.7399 (mtpt) REVERT: A 84 MET cc_start: 0.1431 (OUTLIER) cc_final: -0.2487 (mmt) REVERT: A 124 GLU cc_start: 0.5012 (OUTLIER) cc_final: 0.4073 (tm-30) REVERT: A 215 ARG cc_start: 0.5982 (OUTLIER) cc_final: 0.5106 (mmp-170) REVERT: A 311 ILE cc_start: 0.7402 (OUTLIER) cc_final: 0.7086 (tp) REVERT: B 80 LYS cc_start: 0.8161 (pptt) cc_final: 0.7486 (ptpt) REVERT: B 94 GLN cc_start: 0.7161 (mm110) cc_final: 0.6496 (pp30) REVERT: B 210 MET cc_start: 0.6608 (pmm) cc_final: 0.4602 (tmm) REVERT: B 315 TYR cc_start: 0.6852 (OUTLIER) cc_final: 0.5670 (t80) REVERT: C 213 GLU cc_start: 0.8205 (OUTLIER) cc_final: 0.7969 (pm20) REVERT: C 241 ARG cc_start: 0.7781 (OUTLIER) cc_final: 0.7401 (ttt-90) REVERT: C 250 ARG cc_start: 0.7075 (OUTLIER) cc_final: 0.6711 (tmt170) outliers start: 139 outliers final: 107 residues processed: 366 average time/residue: 0.1576 time to fit residues: 89.3818 Evaluate side-chains 374 residues out of total 2256 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 131 poor density : 243 time to evaluate : 0.510 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 191 TYR Chi-restraints excluded: chain E residue 198 ASP Chi-restraints excluded: chain E residue 204 LEU Chi-restraints excluded: chain E residue 219 LEU Chi-restraints excluded: chain E residue 239 SER Chi-restraints excluded: chain E residue 263 VAL Chi-restraints excluded: chain E residue 273 VAL Chi-restraints excluded: chain E residue 274 ASP Chi-restraints excluded: chain E residue 278 MET Chi-restraints excluded: chain F residue 88 THR Chi-restraints excluded: chain F residue 104 THR Chi-restraints excluded: chain F residue 136 ILE Chi-restraints excluded: chain F residue 142 VAL Chi-restraints excluded: chain F residue 146 LEU Chi-restraints excluded: chain F residue 178 TYR Chi-restraints excluded: chain F residue 180 LEU Chi-restraints excluded: chain F residue 185 VAL Chi-restraints excluded: chain F residue 186 LEU Chi-restraints excluded: chain F residue 201 THR Chi-restraints excluded: chain F residue 218 LEU Chi-restraints excluded: chain F residue 230 THR Chi-restraints excluded: chain F residue 261 VAL Chi-restraints excluded: chain F residue 273 VAL Chi-restraints excluded: chain F residue 278 MET Chi-restraints excluded: chain F residue 279 PHE Chi-restraints excluded: chain F residue 315 TYR Chi-restraints excluded: chain F residue 316 ASP Chi-restraints excluded: chain G residue 75 LEU Chi-restraints excluded: chain G residue 91 GLU Chi-restraints excluded: chain G residue 100 ILE Chi-restraints excluded: chain G residue 124 GLU Chi-restraints excluded: chain G residue 149 ASP Chi-restraints excluded: chain G residue 163 GLU Chi-restraints excluded: chain G residue 185 VAL Chi-restraints excluded: chain G residue 233 SER Chi-restraints excluded: chain G residue 253 LEU Chi-restraints excluded: chain G residue 261 VAL Chi-restraints excluded: chain G residue 264 VAL Chi-restraints excluded: chain G residue 282 ASP Chi-restraints excluded: chain G residue 291 ILE Chi-restraints excluded: chain H residue 84 MET Chi-restraints excluded: chain H residue 112 LEU Chi-restraints excluded: chain H residue 118 GLU Chi-restraints excluded: chain H residue 124 GLU Chi-restraints excluded: chain H residue 206 GLN Chi-restraints excluded: chain H residue 237 GLU Chi-restraints excluded: chain H residue 266 THR Chi-restraints excluded: chain H residue 270 VAL Chi-restraints excluded: chain H residue 287 ILE Chi-restraints excluded: chain H residue 292 ILE Chi-restraints excluded: chain I residue 49 VAL Chi-restraints excluded: chain I residue 94 GLN Chi-restraints excluded: chain I residue 119 THR Chi-restraints excluded: chain I residue 129 PHE Chi-restraints excluded: chain I residue 140 LEU Chi-restraints excluded: chain I residue 146 LEU Chi-restraints excluded: chain I residue 197 THR Chi-restraints excluded: chain I residue 264 VAL Chi-restraints excluded: chain I residue 266 THR Chi-restraints excluded: chain I residue 278 MET Chi-restraints excluded: chain I residue 282 ASP Chi-restraints excluded: chain I residue 320 LEU Chi-restraints excluded: chain I residue 336 ASP Chi-restraints excluded: chain A residue 25 ILE Chi-restraints excluded: chain A residue 30 GLN Chi-restraints excluded: chain A residue 48 THR Chi-restraints excluded: chain A residue 52 VAL Chi-restraints excluded: chain A residue 58 LYS Chi-restraints excluded: chain A residue 61 ILE Chi-restraints excluded: chain A residue 76 THR Chi-restraints excluded: chain A residue 84 MET Chi-restraints excluded: chain A residue 124 GLU Chi-restraints excluded: chain A residue 156 LYS Chi-restraints excluded: chain A residue 189 VAL Chi-restraints excluded: chain A residue 212 VAL Chi-restraints excluded: chain A residue 213 GLU Chi-restraints excluded: chain A residue 215 ARG Chi-restraints excluded: chain A residue 261 VAL Chi-restraints excluded: chain A residue 270 VAL Chi-restraints excluded: chain A residue 273 VAL Chi-restraints excluded: chain A residue 291 ILE Chi-restraints excluded: chain A residue 302 LEU Chi-restraints excluded: chain A residue 311 ILE Chi-restraints excluded: chain A residue 314 ILE Chi-restraints excluded: chain A residue 319 CYS Chi-restraints excluded: chain B residue 25 ILE Chi-restraints excluded: chain B residue 26 SER Chi-restraints excluded: chain B residue 60 LEU Chi-restraints excluded: chain B residue 67 SER Chi-restraints excluded: chain B residue 90 THR Chi-restraints excluded: chain B residue 100 ILE Chi-restraints excluded: chain B residue 117 ILE Chi-restraints excluded: chain B residue 124 GLU Chi-restraints excluded: chain B residue 133 LYS Chi-restraints excluded: chain B residue 160 ILE Chi-restraints excluded: chain B residue 177 ARG Chi-restraints excluded: chain B residue 186 LEU Chi-restraints excluded: chain B residue 215 ARG Chi-restraints excluded: chain B residue 251 MET Chi-restraints excluded: chain B residue 261 VAL Chi-restraints excluded: chain B residue 265 ILE Chi-restraints excluded: chain B residue 266 THR Chi-restraints excluded: chain B residue 269 VAL Chi-restraints excluded: chain B residue 273 VAL Chi-restraints excluded: chain B residue 291 ILE Chi-restraints excluded: chain B residue 298 THR Chi-restraints excluded: chain B residue 310 ARG Chi-restraints excluded: chain B residue 315 TYR Chi-restraints excluded: chain C residue 31 CYS Chi-restraints excluded: chain C residue 43 GLU Chi-restraints excluded: chain C residue 99 ILE Chi-restraints excluded: chain C residue 161 ASP Chi-restraints excluded: chain C residue 195 PHE Chi-restraints excluded: chain C residue 212 VAL Chi-restraints excluded: chain C residue 213 GLU Chi-restraints excluded: chain C residue 241 ARG Chi-restraints excluded: chain C residue 250 ARG Chi-restraints excluded: chain C residue 253 LEU Chi-restraints excluded: chain C residue 285 LYS Chi-restraints excluded: chain C residue 292 ILE Chi-restraints excluded: chain C residue 297 THR Chi-restraints excluded: chain D residue 25 ILE Chi-restraints excluded: chain D residue 38 VAL Chi-restraints excluded: chain D residue 48 THR Chi-restraints excluded: chain D residue 88 THR Chi-restraints excluded: chain D residue 119 THR Chi-restraints excluded: chain D residue 223 SER Chi-restraints excluded: chain D residue 231 ASP Chi-restraints excluded: chain D residue 257 ASP Chi-restraints excluded: chain D residue 297 THR Chi-restraints excluded: chain D residue 319 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 279 random chunks: chunk 214 optimal weight: 0.1980 chunk 105 optimal weight: 5.9990 chunk 25 optimal weight: 0.8980 chunk 145 optimal weight: 6.9990 chunk 226 optimal weight: 3.9990 chunk 223 optimal weight: 5.9990 chunk 264 optimal weight: 2.9990 chunk 197 optimal weight: 0.3980 chunk 254 optimal weight: 1.9990 chunk 128 optimal weight: 8.9990 chunk 52 optimal weight: 0.2980 overall best weight: 0.7582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** F 93 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 93 HIS ** H 196 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 272 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 202 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 268 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 242 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 196 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 200 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 145 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5087 r_free = 0.5087 target = 0.212921 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4821 r_free = 0.4821 target = 0.182472 restraints weight = 36760.456| |-----------------------------------------------------------------------------| r_work (start): 0.4757 rms_B_bonded: 3.46 r_work: 0.4467 rms_B_bonded: 3.98 restraints_weight: 0.5000 r_work (final): 0.4467 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6696 moved from start: 0.1751 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 23296 Z= 0.132 Angle : 0.671 14.545 31697 Z= 0.342 Chirality : 0.044 0.254 3597 Planarity : 0.004 0.052 3902 Dihedral : 15.248 178.298 3951 Min Nonbonded Distance : 1.844 Molprobity Statistics. All-atom Clashscore : 16.49 Ramachandran Plot: Outliers : 0.07 % Allowed : 6.90 % Favored : 93.02 % Rotamer: Outliers : 5.90 % Allowed : 27.35 % Favored : 66.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -2.33 (0.15), residues: 2781 helix: -0.43 (0.15), residues: 1150 sheet: -2.04 (0.24), residues: 398 loop : -2.44 (0.16), residues: 1233 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG G 193 TYR 0.022 0.001 TYR H 216 PHE 0.028 0.002 PHE G 195 HIS 0.009 0.001 HIS G 93 Details of bonding type rmsd/Z covalent geometry : bond 0.00280 / 0.13 (23295) covalent geometry : angle 0.67089 / 0.34 (31697) hydrogen bonds : bond 0.03763 / 2.43 ( 854) hydrogen bonds : angle 5.28767 / 3.66 ( 2428) Misc. bond : bond 0.00069 / 0.05 ( 1) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6814.00 seconds wall clock time: 117 minutes 13.48 seconds (7033.48 seconds total)