Starting phenix.real_space_refine on Fri Feb 6 05:58:26 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9ui5_64184/02_2026/9ui5_64184.cif Found real_map, /net/cci-nas-00/data/ceres_data/9ui5_64184/02_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_64184/02_2026/9ui5_64184.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9ui5_64184/02_2026/9ui5_64184.map" model { file = "/net/cci-nas-00/data/ceres_data/9ui5_64184/02_2026/9ui5_64184.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9ui5_64184/02_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-2.0-5952/lib/python3.9/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: 5.79, 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: 2.01 Conformation dependent library (CDL) restraints added in 985.3 milliseconds 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: 3.05 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: 4.59 Time building geometry restraints manager: 2.59 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=" 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=" N VAL E 38 " pdb=" CA VAL E 38 " ideal model delta sigma weight residual 1.461 1.493 -0.032 1.17e-02 7.31e+03 7.45e+00 bond pdb=" N ASN E 34 " pdb=" CA ASN E 34 " ideal model delta sigma weight residual 1.456 1.489 -0.033 1.23e-02 6.61e+03 6.99e+00 bond pdb=" N ASP E 37 " pdb=" CA ASP E 37 " ideal model delta sigma weight residual 1.459 1.490 -0.031 1.21e-02 6.83e+03 6.40e+00 bond pdb=" N CYS E 31 " pdb=" CA CYS E 31 " ideal model delta sigma weight residual 1.458 1.488 -0.030 1.25e-02 6.40e+03 5.80e+00 ... (remaining 23290 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.58: 31435 3.58 - 7.16: 229 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=" 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 angle pdb=" CA MET H 251 " pdb=" CB MET H 251 " pdb=" CG MET H 251 " ideal model delta sigma weight residual 114.10 124.64 -10.54 2.00e+00 2.50e-01 2.78e+01 angle pdb=" CA LEU F 180 " pdb=" CB LEU F 180 " pdb=" CG LEU F 180 " ideal model delta sigma weight residual 116.30 134.21 -17.91 3.50e+00 8.16e-02 2.62e+01 angle pdb=" N ASN E 36 " pdb=" CA ASN E 36 " pdb=" C ASN E 36 " ideal model delta sigma weight residual 112.38 106.16 6.22 1.22e+00 6.72e-01 2.60e+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: 3044 0.064 - 0.128: 516 0.128 - 0.191: 35 0.191 - 0.255: 1 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=" CA VAL E 38 " pdb=" N VAL E 38 " pdb=" C VAL E 38 " pdb=" CB VAL E 38 " both_signs ideal model delta sigma weight residual False 2.44 2.63 -0.19 2.00e-01 2.50e+01 9.07e-01 ... (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: 4.920 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.330 Check model and map are aligned: 0.060 Set scattering table: 0.060 Process input model: 24.170 Find NCS groups from input model: 0.590 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.120 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 31.320 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6758 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= 0.225 Angle : 0.860 17.909 31697 Z= 0.473 Chirality : 0.046 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 covalent geometry : bond 0.00470 (23295) covalent geometry : angle 0.86009 (31697) hydrogen bonds : bond 0.17747 ( 854) hydrogen bonds : angle 8.19208 ( 2428) Misc. bond : bond 0.00036 ( 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 : 0.790 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: 0.1614 time to fit residues: 79.3942 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 : 0.726 ------------------------------------------------------------------------------- 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: 6.9990 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... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.5046 r_free = 0.5046 target = 0.208773 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.4781 r_free = 0.4781 target = 0.179334 restraints weight = 36937.836| |-----------------------------------------------------------------------------| r_work (start): 0.4725 rms_B_bonded: 3.92 r_work: 0.4360 rms_B_bonded: 4.61 restraints_weight: 0.5000 r_work (final): 0.4360 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6791 moved from start: 0.0752 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.058 23296 Z= 0.207 Angle : 0.713 10.378 31697 Z= 0.368 Chirality : 0.045 0.191 3597 Planarity : 0.005 0.051 3902 Dihedral : 15.908 177.331 4033 Min Nonbonded Distance : 1.783 Molprobity Statistics. All-atom Clashscore : 19.05 Ramachandran Plot: Outliers : 0.11 % Allowed : 8.59 % Favored : 91.30 % Rotamer: Outliers : 7.18 % Allowed : 25.62 % Favored : 67.20 % 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: -0.81 (0.15), residues: 1135 sheet: -2.27 (0.26), residues: 378 loop : -2.54 (0.16), residues: 1268 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG B 310 TYR 0.018 0.002 TYR E 205 PHE 0.024 0.002 PHE I 129 HIS 0.005 0.001 HIS E 47 Details of bonding type rmsd covalent geometry : bond 0.00468 (23295) covalent geometry : angle 0.71350 (31697) hydrogen bonds : bond 0.04838 ( 854) hydrogen bonds : angle 6.15906 ( 2428) Misc. bond : bond 0.00034 ( 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 430 residues out of total 2256 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 162 poor density : 268 time to evaluate : 0.847 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 95 ARG cc_start: 0.6764 (OUTLIER) cc_final: 0.6548 (tpp-160) REVERT: E 229 ARG cc_start: 0.6727 (ttt180) cc_final: 0.6520 (ttt180) REVERT: E 263 VAL cc_start: 0.5178 (OUTLIER) cc_final: 0.4468 (t) REVERT: F 159 TYR cc_start: 0.6370 (OUTLIER) cc_final: 0.6043 (t80) REVERT: F 186 LEU cc_start: 0.6666 (OUTLIER) cc_final: 0.6256 (mt) REVERT: F 279 PHE cc_start: 0.3689 (OUTLIER) cc_final: 0.2360 (p90) REVERT: G 56 PRO cc_start: 0.6250 (Cg_endo) cc_final: 0.5963 (Cg_exo) REVERT: G 163 GLU cc_start: 0.6739 (OUTLIER) cc_final: 0.5758 (pm20) REVERT: G 291 ILE cc_start: 0.6835 (OUTLIER) cc_final: 0.6454 (mp) REVERT: H 118 GLU cc_start: 0.6892 (OUTLIER) cc_final: 0.6566 (pp20) REVERT: H 237 GLU cc_start: 0.3532 (OUTLIER) cc_final: 0.2617 (tp30) REVERT: H 287 ILE cc_start: 0.6232 (OUTLIER) cc_final: 0.5079 (pt) REVERT: H 315 TYR cc_start: 0.5995 (OUTLIER) cc_final: 0.4748 (t80) REVERT: I 49 VAL cc_start: 0.5948 (OUTLIER) cc_final: 0.5512 (p) REVERT: I 81 LEU cc_start: 0.0422 (OUTLIER) cc_final: 0.0143 (tp) REVERT: I 129 PHE cc_start: 0.2978 (OUTLIER) cc_final: 0.2225 (m-80) REVERT: I 158 MET cc_start: 0.1719 (tpt) cc_final: 0.1140 (tpt) REVERT: I 210 MET cc_start: 0.3426 (tpt) cc_final: 0.3181 (tpt) REVERT: I 278 MET cc_start: 0.0809 (OUTLIER) cc_final: -0.0998 (mtm) REVERT: I 306 ARG cc_start: 0.5801 (mmt-90) cc_final: 0.5103 (mmp80) REVERT: A 58 LYS cc_start: 0.5455 (OUTLIER) cc_final: 0.4733 (ttpp) REVERT: A 73 LYS cc_start: 0.8021 (mmmt) cc_final: 0.7573 (tttm) REVERT: A 84 MET cc_start: 0.1826 (OUTLIER) cc_final: -0.2447 (mmt) REVERT: A 124 GLU cc_start: 0.4773 (OUTLIER) cc_final: 0.3852 (tm-30) REVERT: A 215 ARG cc_start: 0.6110 (OUTLIER) cc_final: 0.5361 (mtm180) REVERT: B 122 ILE cc_start: 0.5851 (OUTLIER) cc_final: 0.4728 (mt) REVERT: B 124 GLU cc_start: 0.6417 (OUTLIER) cc_final: 0.5654 (tp30) REVERT: B 210 MET cc_start: 0.6860 (pmm) cc_final: 0.4607 (tmm) REVERT: B 315 TYR cc_start: 0.7002 (OUTLIER) cc_final: 0.5941 (t80) REVERT: C 184 ASP cc_start: 0.6765 (p0) cc_final: 0.6532 (p0) REVERT: C 250 ARG cc_start: 0.7217 (OUTLIER) cc_final: 0.6803 (tmt170) REVERT: D 252 LEU cc_start: 0.8520 (OUTLIER) cc_final: 0.8285 (mp) outliers start: 162 outliers final: 73 residues processed: 400 average time/residue: 0.1592 time to fit residues: 98.8520 Evaluate side-chains 342 residues out of total 2256 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 97 poor density : 245 time to evaluate : 0.750 ------------------------------------------------------------------------------- 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 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 F residue 102 ILE Chi-restraints excluded: chain F residue 146 LEU Chi-restraints excluded: chain F residue 159 TYR 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 230 THR Chi-restraints excluded: chain F residue 273 VAL Chi-restraints excluded: chain F residue 279 PHE Chi-restraints excluded: chain G residue 42 GLU 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 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 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 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 183 SER 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 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 124 GLU 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 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 161 ASP 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 253 LEU Chi-restraints excluded: chain C residue 292 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 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: 0.7980 chunk 246 optimal weight: 0.6980 chunk 24 optimal weight: 1.9990 chunk 96 optimal weight: 20.0000 chunk 204 optimal weight: 9.9990 chunk 215 optimal weight: 0.8980 chunk 47 optimal weight: 0.0270 chunk 46 optimal weight: 9.9990 chunk 277 optimal weight: 1.9990 chunk 131 optimal weight: 30.0000 chunk 20 optimal weight: 0.6980 overall best weight: 0.6238 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.5095 r_free = 0.5095 target = 0.213734 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.4831 r_free = 0.4831 target = 0.184263 restraints weight = 36892.767| |-----------------------------------------------------------------------------| r_work (start): 0.4781 rms_B_bonded: 3.38 r_work: 0.4472 rms_B_bonded: 4.11 restraints_weight: 0.5000 r_work (final): 0.4472 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6611 moved from start: 0.1223 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= 0.126 Angle : 0.616 11.904 31697 Z= 0.319 Chirality : 0.042 0.209 3597 Planarity : 0.004 0.050 3902 Dihedral : 15.261 175.302 3970 Min Nonbonded Distance : 1.862 Molprobity Statistics. All-atom Clashscore : 15.27 Ramachandran Plot: Outliers : 0.07 % Allowed : 6.94 % Favored : 92.99 % Rotamer: Outliers : 5.81 % Allowed : 26.02 % Favored : 68.17 % 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: -2.44 (0.15), residues: 2781 helix: -0.57 (0.15), residues: 1140 sheet: -2.08 (0.25), residues: 409 loop : -2.44 (0.16), residues: 1232 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 310 TYR 0.038 0.001 TYR F 54 PHE 0.019 0.002 PHE G 195 HIS 0.008 0.001 HIS G 93 Details of bonding type rmsd covalent geometry : bond 0.00274 (23295) covalent geometry : angle 0.61629 (31697) hydrogen bonds : bond 0.03886 ( 854) hydrogen bonds : angle 5.59429 ( 2428) Misc. bond : bond 0.00070 ( 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 408 residues out of total 2256 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 131 poor density : 277 time to evaluate : 0.822 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: 0.7385 (pptt) cc_final: 0.6588 (tptt) REVERT: F 210 MET cc_start: 0.6609 (tmt) cc_final: 0.6229 (tmm) REVERT: F 279 PHE cc_start: 0.3472 (OUTLIER) cc_final: 0.2010 (p90) REVERT: G 243 MET cc_start: 0.4837 (mpt) cc_final: 0.4531 (tpt) REVERT: H 118 GLU cc_start: 0.6869 (OUTLIER) cc_final: 0.6450 (pp20) REVERT: H 170 ARG cc_start: 0.7161 (mmp-170) cc_final: 0.6119 (mmp-170) REVERT: H 209 ASP cc_start: 0.8686 (m-30) cc_final: 0.8263 (m-30) REVERT: H 237 GLU cc_start: 0.3143 (OUTLIER) cc_final: 0.2558 (tp30) REVERT: H 248 PHE cc_start: 0.7481 (t80) cc_final: 0.7237 (t80) REVERT: H 251 MET cc_start: 0.8220 (mpt) cc_final: 0.7652 (mmt) REVERT: H 287 ILE cc_start: 0.6194 (OUTLIER) cc_final: 0.5320 (pt) REVERT: H 315 TYR cc_start: 0.5487 (OUTLIER) cc_final: 0.5107 (t80) REVERT: I 49 VAL cc_start: 0.5938 (OUTLIER) cc_final: 0.5487 (p) REVERT: I 81 LEU cc_start: 0.0172 (OUTLIER) cc_final: -0.0055 (tp) REVERT: I 129 PHE cc_start: 0.2863 (OUTLIER) cc_final: 0.2355 (m-80) REVERT: I 278 MET cc_start: 0.0772 (OUTLIER) cc_final: -0.1218 (mtt) REVERT: A 58 LYS cc_start: 0.5335 (OUTLIER) cc_final: 0.4642 (ttpp) REVERT: A 73 LYS cc_start: 0.7958 (mmmt) cc_final: 0.7393 (mtpt) REVERT: A 84 MET cc_start: 0.1478 (OUTLIER) cc_final: -0.2755 (mmt) REVERT: A 124 GLU cc_start: 0.4702 (OUTLIER) cc_final: 0.3814 (tm-30) REVERT: A 215 ARG cc_start: 0.5993 (OUTLIER) cc_final: 0.5095 (mtm180) REVERT: A 311 ILE cc_start: 0.7327 (OUTLIER) cc_final: 0.7021 (tp) REVERT: B 47 HIS cc_start: 0.6566 (OUTLIER) cc_final: 0.6305 (m-70) REVERT: B 210 MET cc_start: 0.6525 (pmm) cc_final: 0.4114 (tmm) REVERT: B 211 MET cc_start: 0.4788 (pmm) cc_final: 0.2954 (pmm) REVERT: B 315 TYR cc_start: 0.6825 (OUTLIER) cc_final: 0.5678 (t80) REVERT: C 250 ARG cc_start: 0.6992 (OUTLIER) cc_final: 0.6608 (tmt170) REVERT: D 252 LEU cc_start: 0.8471 (OUTLIER) cc_final: 0.8115 (mp) outliers start: 131 outliers final: 73 residues processed: 380 average time/residue: 0.1632 time to fit residues: 96.5706 Evaluate side-chains 336 residues out of total 2256 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 91 poor density : 245 time to evaluate : 0.885 ------------------------------------------------------------------------------- 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 219 LEU 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 146 LEU Chi-restraints excluded: chain F residue 180 LEU Chi-restraints excluded: chain F residue 218 LEU Chi-restraints excluded: chain F residue 244 HIS Chi-restraints excluded: chain F residue 253 LEU 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 329 ILE Chi-restraints excluded: chain G residue 75 LEU Chi-restraints excluded: chain G residue 124 GLU Chi-restraints excluded: chain G residue 264 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 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 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 183 SER 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 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 133 LYS Chi-restraints excluded: chain B residue 186 LEU Chi-restraints excluded: chain B residue 251 MET Chi-restraints excluded: chain B residue 261 VAL 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 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 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=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 279 random chunks: chunk 82 optimal weight: 8.9990 chunk 226 optimal weight: 0.9990 chunk 156 optimal weight: 2.9990 chunk 247 optimal weight: 5.9990 chunk 103 optimal weight: 3.9990 chunk 272 optimal weight: 0.3980 chunk 77 optimal weight: 0.7980 chunk 7 optimal weight: 10.0000 chunk 170 optimal weight: 3.9990 chunk 160 optimal weight: 10.0000 chunk 21 optimal weight: 2.9990 overall best weight: 1.6386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 93 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 294 HIS G 93 HIS H 272 GLN I 202 GLN ** 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 ** 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 = 0.5068 r_free = 0.5068 target = 0.210775 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4789 r_free = 0.4789 target = 0.180412 restraints weight = 36614.519| |-----------------------------------------------------------------------------| r_work (start): 0.4736 rms_B_bonded: 3.55 r_work: 0.4404 rms_B_bonded: 4.25 restraints_weight: 0.5000 r_work (final): 0.4404 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6727 moved from start: 0.1313 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= 0.167 Angle : 0.647 12.088 31697 Z= 0.334 Chirality : 0.044 0.284 3597 Planarity : 0.004 0.050 3902 Dihedral : 15.328 176.692 3958 Min Nonbonded Distance : 1.828 Molprobity Statistics. All-atom Clashscore : 16.82 Ramachandran Plot: Outliers : 0.07 % Allowed : 8.05 % Favored : 91.87 % Rotamer: Outliers : 6.87 % Allowed : 25.22 % 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: -2.40 (0.15), residues: 2781 helix: -0.47 (0.15), residues: 1132 sheet: -2.16 (0.24), residues: 406 loop : -2.45 (0.16), residues: 1243 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 310 TYR 0.027 0.002 TYR F 54 PHE 0.022 0.002 PHE I 129 HIS 0.008 0.001 HIS A 199 Details of bonding type rmsd covalent geometry : bond 0.00376 (23295) covalent geometry : angle 0.64673 (31697) hydrogen bonds : bond 0.04130 ( 854) hydrogen bonds : angle 5.46873 ( 2428) Misc. bond : bond 0.00052 ( 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 414 residues out of total 2256 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 155 poor density : 259 time to evaluate : 0.730 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: 0.7392 (pptt) cc_final: 0.6691 (tptt) REVERT: E 138 HIS cc_start: 0.5581 (m90) cc_final: 0.5107 (m90) REVERT: E 250 ARG cc_start: 0.7389 (OUTLIER) cc_final: 0.6190 (ttp-170) REVERT: E 259 PHE cc_start: 0.5675 (t80) cc_final: 0.5285 (t80) REVERT: F 186 LEU cc_start: 0.6624 (OUTLIER) cc_final: 0.6297 (mt) REVERT: F 210 MET cc_start: 0.6564 (tmt) cc_final: 0.6189 (tmm) REVERT: F 279 PHE cc_start: 0.3613 (OUTLIER) cc_final: 0.2245 (p90) REVERT: G 98 GLU cc_start: 0.6069 (pp20) cc_final: 0.4847 (tt0) REVERT: G 163 GLU cc_start: 0.6698 (OUTLIER) cc_final: 0.5534 (pm20) REVERT: H 118 GLU cc_start: 0.6889 (OUTLIER) cc_final: 0.6484 (pp20) REVERT: H 209 ASP cc_start: 0.8768 (m-30) cc_final: 0.8332 (m-30) REVERT: H 237 GLU cc_start: 0.2972 (OUTLIER) cc_final: 0.2657 (tp30) REVERT: H 287 ILE cc_start: 0.6062 (OUTLIER) cc_final: 0.5017 (pt) REVERT: H 315 TYR cc_start: 0.5447 (OUTLIER) cc_final: 0.5026 (t80) REVERT: I 49 VAL cc_start: 0.5996 (OUTLIER) cc_final: 0.5547 (p) REVERT: I 94 GLN cc_start: 0.2954 (OUTLIER) cc_final: 0.2466 (pp30) REVERT: I 129 PHE cc_start: 0.2869 (OUTLIER) cc_final: 0.2257 (m-80) REVERT: I 278 MET cc_start: 0.0570 (OUTLIER) cc_final: -0.1277 (mtt) REVERT: A 58 LYS cc_start: 0.5352 (OUTLIER) cc_final: 0.4582 (ttpp) REVERT: A 73 LYS cc_start: 0.7958 (mmmt) cc_final: 0.7486 (tttm) REVERT: A 84 MET cc_start: 0.1487 (OUTLIER) cc_final: -0.2512 (mmt) REVERT: A 124 GLU cc_start: 0.4776 (OUTLIER) cc_final: 0.3827 (tm-30) REVERT: A 215 ARG cc_start: 0.6000 (OUTLIER) cc_final: 0.5144 (mtm180) REVERT: A 311 ILE cc_start: 0.7436 (OUTLIER) cc_final: 0.7148 (tp) REVERT: B 80 LYS cc_start: 0.8167 (pptt) cc_final: 0.7486 (ptpt) REVERT: B 210 MET cc_start: 0.6672 (pmm) cc_final: 0.4215 (tmm) REVERT: B 211 MET cc_start: 0.5017 (pmm) cc_final: 0.3283 (pmm) REVERT: B 315 TYR cc_start: 0.6885 (OUTLIER) cc_final: 0.5700 (t80) REVERT: C 184 ASP cc_start: 0.6639 (p0) cc_final: 0.6341 (p0) REVERT: C 250 ARG cc_start: 0.7084 (OUTLIER) cc_final: 0.6698 (tmt170) REVERT: D 23 GLN cc_start: 0.6161 (mp10) cc_final: 0.5782 (mp10) REVERT: D 84 MET cc_start: 0.4116 (OUTLIER) cc_final: 0.3901 (mmt) REVERT: D 252 LEU cc_start: 0.8574 (OUTLIER) cc_final: 0.8289 (mp) outliers start: 155 outliers final: 85 residues processed: 385 average time/residue: 0.1594 time to fit residues: 95.2293 Evaluate side-chains 351 residues out of total 2256 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 106 poor density : 245 time to evaluate : 0.793 ------------------------------------------------------------------------------- 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 219 LEU Chi-restraints excluded: chain E residue 250 ARG Chi-restraints excluded: chain E residue 273 VAL Chi-restraints excluded: chain F residue 88 THR Chi-restraints excluded: chain F residue 104 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 186 LEU Chi-restraints excluded: chain F residue 218 LEU 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 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 264 VAL Chi-restraints excluded: chain G residue 282 ASP 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 237 GLU Chi-restraints excluded: chain H residue 238 LEU Chi-restraints excluded: chain H residue 266 THR 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 336 ASP Chi-restraints excluded: chain A residue 30 GLN Chi-restraints excluded: chain A residue 38 VAL 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 183 SER 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 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 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 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 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 171 LEU 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 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 84 MET Chi-restraints excluded: chain D residue 119 THR 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 279 random chunks: chunk 196 optimal weight: 0.5980 chunk 128 optimal weight: 0.9990 chunk 203 optimal weight: 5.9990 chunk 77 optimal weight: 5.9990 chunk 251 optimal weight: 2.9990 chunk 176 optimal weight: 0.7980 chunk 88 optimal weight: 2.9990 chunk 192 optimal weight: 2.9990 chunk 40 optimal weight: 6.9990 chunk 57 optimal weight: 0.0370 chunk 254 optimal weight: 5.9990 overall best weight: 1.0862 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 93 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 93 HIS I 202 GLN ** 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: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5081 r_free = 0.5081 target = 0.212346 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.4813 r_free = 0.4813 target = 0.182111 restraints weight = 36655.114| |-----------------------------------------------------------------------------| r_work (start): 0.4751 rms_B_bonded: 3.52 r_work: 0.4441 rms_B_bonded: 4.15 restraints_weight: 0.5000 r_work (final): 0.4441 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6657 moved from start: 0.1537 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 23296 Z= 0.139 Angle : 0.619 10.348 31697 Z= 0.318 Chirality : 0.043 0.210 3597 Planarity : 0.004 0.049 3902 Dihedral : 15.174 176.074 3954 Min Nonbonded Distance : 1.872 Molprobity Statistics. All-atom Clashscore : 16.16 Ramachandran Plot: Outliers : 0.07 % Allowed : 7.08 % Favored : 92.84 % Rotamer: Outliers : 6.38 % Allowed : 25.98 % Favored : 67.64 % 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: -2.30 (0.15), residues: 2781 helix: -0.36 (0.15), residues: 1141 sheet: -2.14 (0.24), residues: 416 loop : -2.42 (0.16), residues: 1224 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 310 TYR 0.032 0.001 TYR F 54 PHE 0.019 0.002 PHE I 129 HIS 0.008 0.001 HIS G 93 Details of bonding type rmsd covalent geometry : bond 0.00308 (23295) covalent geometry : angle 0.61913 (31697) hydrogen bonds : bond 0.03771 ( 854) hydrogen bonds : angle 5.27089 ( 2428) Misc. bond : bond 0.00053 ( 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 411 residues out of total 2256 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 144 poor density : 267 time to evaluate : 0.784 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 64 LYS cc_start: 0.5681 (mppt) cc_final: 0.5163 (mptt) REVERT: E 80 LYS cc_start: 0.7254 (pptt) cc_final: 0.6581 (tptt) REVERT: E 259 PHE cc_start: 0.5542 (t80) cc_final: 0.5277 (t80) REVERT: F 186 LEU cc_start: 0.6671 (OUTLIER) cc_final: 0.6344 (mt) REVERT: F 210 MET cc_start: 0.6490 (tmt) cc_final: 0.6161 (tmm) REVERT: F 279 PHE cc_start: 0.3546 (OUTLIER) cc_final: 0.2112 (p90) REVERT: G 98 GLU cc_start: 0.5952 (pp20) cc_final: 0.4842 (tt0) REVERT: G 163 GLU cc_start: 0.6653 (OUTLIER) cc_final: 0.5402 (pm20) REVERT: G 243 MET cc_start: 0.5201 (mpt) cc_final: 0.4743 (tpt) REVERT: G 291 ILE cc_start: 0.6783 (OUTLIER) cc_final: 0.6473 (mp) REVERT: H 118 GLU cc_start: 0.6821 (OUTLIER) cc_final: 0.6445 (pp20) REVERT: H 209 ASP cc_start: 0.8686 (m-30) cc_final: 0.8238 (m-30) REVERT: H 237 GLU cc_start: 0.2894 (OUTLIER) cc_final: 0.2474 (tp30) REVERT: H 287 ILE cc_start: 0.6062 (OUTLIER) cc_final: 0.5083 (pt) REVERT: I 49 VAL cc_start: 0.5927 (OUTLIER) cc_final: 0.5495 (p) REVERT: I 94 GLN cc_start: 0.3055 (OUTLIER) cc_final: 0.2517 (pp30) REVERT: I 129 PHE cc_start: 0.2948 (OUTLIER) cc_final: 0.2415 (m-80) REVERT: I 210 MET cc_start: 0.3270 (tpt) cc_final: 0.2992 (tpt) REVERT: I 278 MET cc_start: 0.0693 (OUTLIER) cc_final: -0.1238 (mtt) REVERT: A 58 LYS cc_start: 0.5345 (OUTLIER) cc_final: 0.4613 (ttpp) REVERT: A 73 LYS cc_start: 0.7915 (mmmt) cc_final: 0.7373 (mtpt) REVERT: A 84 MET cc_start: 0.1589 (OUTLIER) cc_final: -0.2550 (mmt) REVERT: A 124 GLU cc_start: 0.4850 (OUTLIER) cc_final: 0.3819 (tm-30) REVERT: A 215 ARG cc_start: 0.5965 (OUTLIER) cc_final: 0.5172 (mtm180) REVERT: A 311 ILE cc_start: 0.7425 (OUTLIER) cc_final: 0.7151 (tp) REVERT: B 80 LYS cc_start: 0.8163 (pptt) cc_final: 0.7488 (ptpt) REVERT: B 94 GLN cc_start: 0.7128 (mm110) cc_final: 0.6529 (pp30) REVERT: B 210 MET cc_start: 0.6706 (pmm) cc_final: 0.4278 (tmm) REVERT: B 211 MET cc_start: 0.4864 (pmm) cc_final: 0.3280 (pmm) REVERT: B 313 LYS cc_start: 0.6178 (OUTLIER) cc_final: 0.5961 (ttpt) REVERT: B 315 TYR cc_start: 0.6822 (OUTLIER) cc_final: 0.5750 (t80) REVERT: C 184 ASP cc_start: 0.6663 (p0) cc_final: 0.6315 (p0) REVERT: C 250 ARG cc_start: 0.7040 (OUTLIER) cc_final: 0.6666 (tmt170) REVERT: D 84 MET cc_start: 0.4108 (OUTLIER) cc_final: 0.3780 (mmt) REVERT: D 252 LEU cc_start: 0.8536 (OUTLIER) cc_final: 0.8319 (mp) outliers start: 144 outliers final: 88 residues processed: 381 average time/residue: 0.1495 time to fit residues: 88.7135 Evaluate side-chains 353 residues out of total 2256 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 109 poor density : 244 time to evaluate : 0.813 ------------------------------------------------------------------------------- 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 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 104 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 244 HIS Chi-restraints excluded: chain F residue 253 LEU 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 G residue 75 LEU Chi-restraints excluded: chain G residue 100 ILE Chi-restraints excluded: chain G residue 109 LEU Chi-restraints excluded: chain G residue 124 GLU 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 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 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 292 ILE Chi-restraints excluded: chain I residue 49 VAL Chi-restraints excluded: chain I residue 91 GLU 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 314 ILE Chi-restraints excluded: chain I residue 336 ASP Chi-restraints excluded: chain A residue 38 VAL 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 183 SER 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 311 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 100 ILE 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 221 VAL 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 310 ARG Chi-restraints excluded: chain B residue 313 LYS 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 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 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 84 MET Chi-restraints excluded: chain D residue 119 THR 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 279 random chunks: chunk 136 optimal weight: 6.9990 chunk 274 optimal weight: 3.9990 chunk 265 optimal weight: 2.9990 chunk 15 optimal weight: 7.9990 chunk 250 optimal weight: 7.9990 chunk 155 optimal weight: 6.9990 chunk 6 optimal weight: 0.0980 chunk 34 optimal weight: 2.9990 chunk 234 optimal weight: 0.8980 chunk 228 optimal weight: 4.9990 chunk 243 optimal weight: 0.9990 overall best weight: 1.5986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 145 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 93 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 93 HIS H 244 HIS I 202 GLN ** 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: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5066 r_free = 0.5066 target = 0.210689 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4797 r_free = 0.4797 target = 0.181151 restraints weight = 36766.957| |-----------------------------------------------------------------------------| r_work (start): 0.4747 rms_B_bonded: 3.75 r_work: 0.4398 rms_B_bonded: 4.42 restraints_weight: 0.5000 r_work (final): 0.4398 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6732 moved from start: 0.1627 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 23296 Z= 0.165 Angle : 0.646 9.631 31697 Z= 0.334 Chirality : 0.043 0.200 3597 Planarity : 0.004 0.049 3902 Dihedral : 15.193 176.331 3950 Min Nonbonded Distance : 1.853 Molprobity Statistics. All-atom Clashscore : 16.86 Ramachandran Plot: Outliers : 0.07 % Allowed : 8.09 % Favored : 91.84 % Rotamer: Outliers : 7.09 % Allowed : 24.91 % Favored : 68.00 % 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: -2.30 (0.15), residues: 2781 helix: -0.34 (0.15), residues: 1130 sheet: -2.16 (0.24), residues: 408 loop : -2.42 (0.16), residues: 1243 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 310 TYR 0.033 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 covalent geometry : bond 0.00371 (23295) covalent geometry : angle 0.64631 (31697) hydrogen bonds : bond 0.03957 ( 854) hydrogen bonds : angle 5.28069 ( 2428) Misc. bond : bond 0.00033 ( 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 417 residues out of total 2256 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 160 poor density : 257 time to evaluate : 0.871 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 64 LYS cc_start: 0.5595 (mppt) cc_final: 0.5081 (mptt) REVERT: E 80 LYS cc_start: 0.7288 (pptt) cc_final: 0.6646 (tptt) REVERT: E 250 ARG cc_start: 0.7378 (OUTLIER) cc_final: 0.6248 (ttp-170) REVERT: E 259 PHE cc_start: 0.5492 (t80) cc_final: 0.5260 (t80) REVERT: F 167 ARG cc_start: 0.4444 (OUTLIER) cc_final: 0.3029 (tpp-160) REVERT: F 178 TYR cc_start: 0.6224 (OUTLIER) cc_final: 0.5153 (m-80) REVERT: F 186 LEU cc_start: 0.6661 (OUTLIER) cc_final: 0.6355 (mt) REVERT: F 210 MET cc_start: 0.6493 (tmt) cc_final: 0.6141 (tmm) REVERT: F 279 PHE cc_start: 0.3524 (OUTLIER) cc_final: 0.2239 (p90) REVERT: F 316 ASP cc_start: 0.4760 (OUTLIER) cc_final: 0.4359 (p0) REVERT: G 98 GLU cc_start: 0.5998 (pp20) cc_final: 0.4862 (tt0) REVERT: G 163 GLU cc_start: 0.6731 (OUTLIER) cc_final: 0.5507 (pm20) REVERT: G 291 ILE cc_start: 0.6775 (OUTLIER) cc_final: 0.6425 (mp) REVERT: H 118 GLU cc_start: 0.6792 (OUTLIER) cc_final: 0.6396 (pp20) REVERT: H 287 ILE cc_start: 0.6035 (OUTLIER) cc_final: 0.4968 (pt) REVERT: I 49 VAL cc_start: 0.5977 (OUTLIER) cc_final: 0.5553 (p) REVERT: I 94 GLN cc_start: 0.3050 (OUTLIER) cc_final: 0.2548 (pp30) REVERT: I 129 PHE cc_start: 0.3019 (OUTLIER) cc_final: 0.2358 (m-80) REVERT: I 210 MET cc_start: 0.3229 (tpt) cc_final: 0.3001 (tpt) REVERT: I 278 MET cc_start: 0.0691 (OUTLIER) cc_final: -0.1194 (mtt) REVERT: I 306 ARG cc_start: 0.5786 (mmt-90) cc_final: 0.5154 (mmp80) REVERT: A 58 LYS cc_start: 0.5346 (OUTLIER) cc_final: 0.4586 (ttpp) REVERT: A 73 LYS cc_start: 0.7939 (mmmt) cc_final: 0.7412 (mtpt) REVERT: A 84 MET cc_start: 0.1366 (OUTLIER) cc_final: -0.2666 (mmt) REVERT: A 124 GLU cc_start: 0.4912 (OUTLIER) cc_final: 0.3988 (tm-30) REVERT: A 311 ILE cc_start: 0.7412 (OUTLIER) cc_final: 0.7117 (tp) REVERT: B 210 MET cc_start: 0.6785 (pmm) cc_final: 0.4359 (tmm) REVERT: B 211 MET cc_start: 0.4932 (pmm) cc_final: 0.3418 (pmm) REVERT: B 313 LYS cc_start: 0.6026 (OUTLIER) cc_final: 0.5762 (ttpt) REVERT: B 315 TYR cc_start: 0.6821 (OUTLIER) cc_final: 0.5633 (t80) REVERT: C 184 ASP cc_start: 0.6680 (p0) cc_final: 0.6313 (p0) REVERT: C 213 GLU cc_start: 0.8237 (OUTLIER) cc_final: 0.7987 (pm20) REVERT: C 241 ARG cc_start: 0.7809 (OUTLIER) cc_final: 0.7444 (ttt-90) REVERT: C 250 ARG cc_start: 0.7150 (OUTLIER) cc_final: 0.6788 (tmt170) REVERT: D 84 MET cc_start: 0.4120 (OUTLIER) cc_final: 0.3819 (mmt) outliers start: 160 outliers final: 105 residues processed: 384 average time/residue: 0.1671 time to fit residues: 98.6452 Evaluate side-chains 374 residues out of total 2256 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 129 poor density : 245 time to evaluate : 0.835 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 107 LYS 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 263 VAL 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 123 THR Chi-restraints excluded: chain F residue 142 VAL Chi-restraints excluded: chain F residue 146 LEU Chi-restraints excluded: chain F residue 167 ARG 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 191 TYR Chi-restraints excluded: chain F residue 218 LEU Chi-restraints excluded: chain F residue 230 THR Chi-restraints excluded: chain F residue 253 LEU 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 100 ILE Chi-restraints excluded: chain G residue 124 GLU Chi-restraints excluded: chain G residue 149 ASP Chi-restraints excluded: chain G residue 161 ASP Chi-restraints excluded: chain G residue 163 GLU Chi-restraints excluded: chain G residue 185 VAL 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 180 LEU Chi-restraints excluded: chain H residue 206 GLN Chi-restraints excluded: chain H residue 254 ARG 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 91 GLU Chi-restraints excluded: chain I residue 94 GLN Chi-restraints excluded: chain I residue 119 THR Chi-restraints excluded: chain I residue 125 MET 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 202 GLN 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 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 183 SER 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 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 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 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 313 LYS Chi-restraints excluded: chain B residue 315 TYR Chi-restraints excluded: chain B residue 326 MET 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 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 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 266 THR 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 84 MET 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 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: 10.0000 chunk 232 optimal weight: 6.9990 chunk 48 optimal weight: 4.9990 chunk 102 optimal weight: 8.9990 chunk 1 optimal weight: 8.9990 chunk 165 optimal weight: 0.6980 chunk 150 optimal weight: 0.4980 chunk 250 optimal weight: 0.7980 chunk 204 optimal weight: 9.9990 chunk 216 optimal weight: 0.9990 chunk 209 optimal weight: 0.8980 overall best weight: 0.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 93 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 93 HIS ** H 23 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 Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5092 r_free = 0.5092 target = 0.213635 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4826 r_free = 0.4826 target = 0.183536 restraints weight = 36854.585| |-----------------------------------------------------------------------------| r_work (start): 0.4767 rms_B_bonded: 3.35 r_work: 0.4464 rms_B_bonded: 4.04 restraints_weight: 0.5000 r_work (final): 0.4464 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6619 moved from start: 0.1846 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 23296 Z= 0.128 Angle : 0.623 10.909 31697 Z= 0.317 Chirality : 0.042 0.213 3597 Planarity : 0.004 0.049 3902 Dihedral : 15.002 177.345 3950 Min Nonbonded Distance : 1.872 Molprobity Statistics. All-atom Clashscore : 15.31 Ramachandran Plot: Outliers : 0.07 % Allowed : 6.65 % Favored : 93.28 % Rotamer: Outliers : 6.38 % Allowed : 26.29 % Favored : 67.33 % 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: -2.20 (0.15), residues: 2781 helix: -0.26 (0.15), residues: 1146 sheet: -2.10 (0.24), residues: 415 loop : -2.38 (0.16), residues: 1220 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 310 TYR 0.029 0.001 TYR F 54 PHE 0.018 0.002 PHE I 129 HIS 0.008 0.001 HIS G 93 Details of bonding type rmsd covalent geometry : bond 0.00281 (23295) covalent geometry : angle 0.62280 (31697) hydrogen bonds : bond 0.03549 ( 854) hydrogen bonds : angle 5.08734 ( 2428) Misc. bond : bond 0.00058 ( 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 398 residues out of total 2256 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 144 poor density : 254 time to evaluate : 0.847 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 64 LYS cc_start: 0.5718 (mppt) cc_final: 0.5186 (mptt) REVERT: E 80 LYS cc_start: 0.7252 (pptt) cc_final: 0.6640 (tptt) REVERT: F 186 LEU cc_start: 0.6708 (OUTLIER) cc_final: 0.6408 (mt) REVERT: F 210 MET cc_start: 0.6444 (tmt) cc_final: 0.6165 (tmm) REVERT: F 279 PHE cc_start: 0.3476 (OUTLIER) cc_final: 0.2041 (p90) REVERT: F 316 ASP cc_start: 0.4672 (OUTLIER) cc_final: 0.4304 (p0) REVERT: G 98 GLU cc_start: 0.5998 (pp20) cc_final: 0.4927 (tt0) REVERT: G 163 GLU cc_start: 0.6615 (OUTLIER) cc_final: 0.5383 (pm20) REVERT: G 243 MET cc_start: 0.5126 (mpt) cc_final: 0.4585 (tpt) REVERT: G 291 ILE cc_start: 0.6808 (OUTLIER) cc_final: 0.6486 (mp) REVERT: H 118 GLU cc_start: 0.6899 (OUTLIER) cc_final: 0.6563 (pp20) REVERT: H 199 HIS cc_start: 0.7874 (t-90) cc_final: 0.7215 (t-90) REVERT: H 287 ILE cc_start: 0.5949 (OUTLIER) cc_final: 0.5058 (pt) REVERT: I 49 VAL cc_start: 0.5979 (OUTLIER) cc_final: 0.5552 (p) REVERT: I 94 GLN cc_start: 0.3026 (OUTLIER) cc_final: 0.2507 (pp30) REVERT: I 129 PHE cc_start: 0.2936 (OUTLIER) cc_final: 0.2469 (m-80) REVERT: I 210 MET cc_start: 0.3002 (tpt) cc_final: 0.2765 (tpt) REVERT: I 278 MET cc_start: 0.0603 (OUTLIER) cc_final: -0.1351 (mtt) REVERT: A 58 LYS cc_start: 0.5340 (OUTLIER) cc_final: 0.4616 (ttpp) REVERT: A 73 LYS cc_start: 0.7895 (mmmt) cc_final: 0.7348 (mtpt) REVERT: A 84 MET cc_start: 0.1522 (OUTLIER) cc_final: -0.2694 (mmt) REVERT: A 124 GLU cc_start: 0.4808 (OUTLIER) cc_final: 0.3704 (tm-30) REVERT: A 215 ARG cc_start: 0.5973 (OUTLIER) cc_final: 0.5108 (mtm180) REVERT: A 311 ILE cc_start: 0.7387 (OUTLIER) cc_final: 0.7114 (tp) REVERT: B 124 GLU cc_start: 0.6281 (OUTLIER) cc_final: 0.5681 (tp30) REVERT: B 210 MET cc_start: 0.6731 (pmm) cc_final: 0.4685 (tmm) REVERT: B 313 LYS cc_start: 0.5771 (OUTLIER) cc_final: 0.5527 (ttpt) REVERT: B 315 TYR cc_start: 0.6603 (OUTLIER) cc_final: 0.5529 (t80) REVERT: C 241 ARG cc_start: 0.7694 (OUTLIER) cc_final: 0.7320 (ttt-90) REVERT: C 243 MET cc_start: 0.6494 (mtt) cc_final: 0.6270 (mtm) REVERT: C 250 ARG cc_start: 0.6991 (OUTLIER) cc_final: 0.6624 (tmt170) REVERT: D 84 MET cc_start: 0.3922 (OUTLIER) cc_final: 0.3578 (mmt) outliers start: 144 outliers final: 98 residues processed: 373 average time/residue: 0.1638 time to fit residues: 94.8504 Evaluate side-chains 363 residues out of total 2256 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 120 poor density : 243 time to evaluate : 0.853 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 107 LYS 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 263 VAL 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 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 244 HIS Chi-restraints excluded: chain F residue 253 LEU 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 100 ILE Chi-restraints excluded: chain G residue 124 GLU Chi-restraints excluded: chain G residue 163 GLU Chi-restraints excluded: chain G residue 211 MET 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 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 254 ARG 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 91 GLU Chi-restraints excluded: chain I residue 94 GLN Chi-restraints excluded: chain I residue 125 MET 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 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 183 SER 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 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 47 HIS Chi-restraints excluded: chain B residue 60 LEU Chi-restraints excluded: chain B residue 67 SER 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 215 ARG Chi-restraints excluded: chain B residue 221 VAL 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 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 313 LYS Chi-restraints excluded: chain B residue 315 TYR Chi-restraints excluded: chain B residue 326 MET Chi-restraints excluded: chain C residue 87 THR Chi-restraints excluded: chain C residue 99 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 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 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 84 MET 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 Chi-restraints excluded: chain D residue 330 ASN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 279 random chunks: chunk 44 optimal weight: 9.9990 chunk 86 optimal weight: 0.0980 chunk 124 optimal weight: 40.0000 chunk 99 optimal weight: 2.9990 chunk 23 optimal weight: 0.8980 chunk 236 optimal weight: 5.9990 chunk 41 optimal weight: 0.9990 chunk 136 optimal weight: 10.0000 chunk 30 optimal weight: 0.6980 chunk 31 optimal weight: 20.0000 chunk 19 optimal weight: 0.0870 overall best weight: 0.5560 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 93 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 294 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 93 HIS ** H 196 ASN ** 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 = 0.5106 r_free = 0.5106 target = 0.215188 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4849 r_free = 0.4849 target = 0.185704 restraints weight = 36606.483| |-----------------------------------------------------------------------------| r_work (start): 0.4788 rms_B_bonded: 3.36 r_work: 0.4488 rms_B_bonded: 4.11 restraints_weight: 0.5000 r_work (final): 0.4488 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6572 moved from start: 0.2109 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 23296 Z= 0.119 Angle : 0.613 14.197 31697 Z= 0.314 Chirality : 0.042 0.235 3597 Planarity : 0.004 0.049 3902 Dihedral : 14.842 179.521 3948 Min Nonbonded Distance : 1.907 Molprobity Statistics. All-atom Clashscore : 14.63 Ramachandran Plot: Outliers : 0.07 % Allowed : 6.58 % Favored : 93.35 % Rotamer: Outliers : 5.50 % Allowed : 27.26 % 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: -2.11 (0.15), residues: 2781 helix: -0.19 (0.15), residues: 1152 sheet: -2.10 (0.23), residues: 412 loop : -2.31 (0.17), residues: 1217 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 310 TYR 0.027 0.001 TYR F 54 PHE 0.016 0.001 PHE I 129 HIS 0.008 0.001 HIS G 93 Details of bonding type rmsd covalent geometry : bond 0.00261 (23295) covalent geometry : angle 0.61309 (31697) hydrogen bonds : bond 0.03347 ( 854) hydrogen bonds : angle 4.96273 ( 2428) Misc. bond : bond 0.00056 ( 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 389 residues out of total 2256 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 124 poor density : 265 time to evaluate : 0.880 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 77 GLU cc_start: 0.6540 (pp20) cc_final: 0.6281 (pp20) REVERT: E 80 LYS cc_start: 0.7223 (pptt) cc_final: 0.6660 (tptt) REVERT: F 178 TYR cc_start: 0.6099 (OUTLIER) cc_final: 0.4974 (m-80) REVERT: F 186 LEU cc_start: 0.6722 (OUTLIER) cc_final: 0.6431 (mt) REVERT: F 279 PHE cc_start: 0.3461 (OUTLIER) cc_final: 0.1929 (p90) REVERT: F 303 ARG cc_start: 0.5381 (ptt-90) cc_final: 0.4862 (ptt-90) REVERT: F 316 ASP cc_start: 0.4615 (OUTLIER) cc_final: 0.4236 (p0) REVERT: G 42 GLU cc_start: 0.5960 (tp30) cc_final: 0.5064 (mm-30) REVERT: G 46 TYR cc_start: 0.6244 (m-80) cc_final: 0.6011 (m-80) REVERT: G 98 GLU cc_start: 0.5976 (pp20) cc_final: 0.4966 (tt0) REVERT: G 163 GLU cc_start: 0.6486 (OUTLIER) cc_final: 0.5327 (pm20) REVERT: G 243 MET cc_start: 0.4956 (mpt) cc_final: 0.4505 (tpt) REVERT: G 291 ILE cc_start: 0.6739 (OUTLIER) cc_final: 0.6433 (mp) REVERT: H 118 GLU cc_start: 0.6882 (OUTLIER) cc_final: 0.6539 (pp20) REVERT: H 209 ASP cc_start: 0.8786 (OUTLIER) cc_final: 0.8244 (m-30) REVERT: H 287 ILE cc_start: 0.6074 (OUTLIER) cc_final: 0.5163 (pt) REVERT: I 49 VAL cc_start: 0.6035 (OUTLIER) cc_final: 0.5608 (p) REVERT: I 94 GLN cc_start: 0.3061 (OUTLIER) cc_final: 0.2531 (pp30) REVERT: I 129 PHE cc_start: 0.3000 (OUTLIER) cc_final: 0.2533 (m-80) REVERT: I 210 MET cc_start: 0.2990 (tpt) cc_final: 0.2789 (tpt) REVERT: I 278 MET cc_start: 0.0607 (OUTLIER) cc_final: -0.1327 (mtt) REVERT: A 58 LYS cc_start: 0.5364 (OUTLIER) cc_final: 0.4648 (ttpp) REVERT: A 73 LYS cc_start: 0.7904 (mmmt) cc_final: 0.7351 (mtpt) REVERT: A 84 MET cc_start: 0.1190 (OUTLIER) cc_final: -0.2915 (mmt) REVERT: A 215 ARG cc_start: 0.5999 (OUTLIER) cc_final: 0.5194 (mtm180) REVERT: A 311 ILE cc_start: 0.7365 (OUTLIER) cc_final: 0.7099 (tp) REVERT: B 124 GLU cc_start: 0.6102 (OUTLIER) cc_final: 0.5861 (tp30) REVERT: B 210 MET cc_start: 0.6553 (pmm) cc_final: 0.4117 (tmm) REVERT: B 313 LYS cc_start: 0.5516 (OUTLIER) cc_final: 0.5294 (ttpt) REVERT: B 315 TYR cc_start: 0.6432 (OUTLIER) cc_final: 0.5516 (t80) REVERT: C 241 ARG cc_start: 0.7502 (OUTLIER) cc_final: 0.7111 (ttt-90) REVERT: C 250 ARG cc_start: 0.6950 (OUTLIER) cc_final: 0.6584 (tmt170) REVERT: D 84 MET cc_start: 0.3833 (OUTLIER) cc_final: 0.3598 (mmt) outliers start: 124 outliers final: 84 residues processed: 366 average time/residue: 0.1726 time to fit residues: 98.9980 Evaluate side-chains 357 residues out of total 2256 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 107 poor density : 250 time to evaluate : 0.779 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 107 LYS Chi-restraints excluded: chain E residue 191 TYR 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 104 THR 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 244 HIS Chi-restraints excluded: chain F residue 253 LEU 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 100 ILE Chi-restraints excluded: chain G residue 124 GLU Chi-restraints excluded: chain G residue 163 GLU Chi-restraints excluded: chain G residue 211 MET 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 112 LEU Chi-restraints excluded: chain H residue 118 GLU Chi-restraints excluded: chain H residue 180 LEU Chi-restraints excluded: chain H residue 209 ASP Chi-restraints excluded: chain H residue 254 ARG Chi-restraints excluded: chain H residue 270 VAL Chi-restraints excluded: chain H residue 287 ILE Chi-restraints excluded: chain I residue 49 VAL Chi-restraints excluded: chain I residue 91 GLU Chi-restraints excluded: chain I residue 94 GLN Chi-restraints excluded: chain I residue 125 MET 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 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 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 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 47 HIS Chi-restraints excluded: chain B residue 60 LEU 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 186 LEU Chi-restraints excluded: chain B residue 215 ARG Chi-restraints excluded: chain B residue 221 VAL Chi-restraints excluded: chain B residue 261 VAL Chi-restraints excluded: chain B residue 266 THR 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 313 LYS Chi-restraints excluded: chain B residue 315 TYR Chi-restraints excluded: chain B residue 326 MET Chi-restraints excluded: chain C residue 87 THR 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 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 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 84 MET Chi-restraints excluded: chain D residue 223 SER Chi-restraints excluded: chain D residue 257 ASP Chi-restraints excluded: chain D residue 297 THR Chi-restraints excluded: chain D residue 330 ASN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 279 random chunks: chunk 67 optimal weight: 8.9990 chunk 272 optimal weight: 0.0870 chunk 195 optimal weight: 4.9990 chunk 153 optimal weight: 20.0000 chunk 162 optimal weight: 1.9990 chunk 171 optimal weight: 6.9990 chunk 176 optimal weight: 7.9990 chunk 123 optimal weight: 8.9990 chunk 41 optimal weight: 0.9990 chunk 248 optimal weight: 0.9980 chunk 25 optimal weight: 0.1980 overall best weight: 0.8562 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 93 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 93 HIS ** H 196 ASN ** 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 = 0.5098 r_free = 0.5098 target = 0.214279 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4841 r_free = 0.4841 target = 0.184845 restraints weight = 36889.225| |-----------------------------------------------------------------------------| r_work (start): 0.4783 rms_B_bonded: 3.63 r_work: 0.4471 rms_B_bonded: 4.20 restraints_weight: 0.5000 r_work (final): 0.4471 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6589 moved from start: 0.2192 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 23296 Z= 0.130 Angle : 0.646 13.916 31697 Z= 0.327 Chirality : 0.044 0.407 3597 Planarity : 0.004 0.048 3902 Dihedral : 14.813 179.501 3940 Min Nonbonded Distance : 1.880 Molprobity Statistics. All-atom Clashscore : 14.87 Ramachandran Plot: Outliers : 0.07 % Allowed : 6.83 % Favored : 93.10 % Rotamer: Outliers : 5.14 % Allowed : 27.75 % Favored : 67.11 % 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: -2.08 (0.15), residues: 2781 helix: -0.20 (0.15), residues: 1158 sheet: -2.00 (0.24), residues: 410 loop : -2.31 (0.17), residues: 1213 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 310 TYR 0.025 0.001 TYR F 54 PHE 0.021 0.002 PHE C 166 HIS 0.015 0.001 HIS A 199 Details of bonding type rmsd covalent geometry : bond 0.00291 (23295) covalent geometry : angle 0.64641 (31697) hydrogen bonds : bond 0.03512 ( 854) hydrogen bonds : angle 4.98232 ( 2428) Misc. bond : bond 0.00044 ( 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 365 residues out of total 2256 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 116 poor density : 249 time to evaluate : 0.864 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 77 GLU cc_start: 0.6521 (pp20) cc_final: 0.6208 (pp20) REVERT: E 80 LYS cc_start: 0.7185 (pptt) cc_final: 0.6636 (tptt) REVERT: F 178 TYR cc_start: 0.6078 (OUTLIER) cc_final: 0.4974 (m-80) REVERT: F 186 LEU cc_start: 0.6763 (OUTLIER) cc_final: 0.6445 (mt) REVERT: F 205 TYR cc_start: 0.6240 (m-10) cc_final: 0.6029 (m-10) REVERT: F 279 PHE cc_start: 0.3536 (OUTLIER) cc_final: 0.2073 (p90) REVERT: F 316 ASP cc_start: 0.4648 (OUTLIER) cc_final: 0.4282 (p0) REVERT: G 56 PRO cc_start: 0.6430 (Cg_endo) cc_final: 0.6217 (Cg_exo) REVERT: G 98 GLU cc_start: 0.5943 (pp20) cc_final: 0.4851 (tt0) REVERT: G 163 GLU cc_start: 0.6438 (OUTLIER) cc_final: 0.5331 (pm20) REVERT: G 243 MET cc_start: 0.5116 (mpt) cc_final: 0.4589 (tpt) REVERT: G 291 ILE cc_start: 0.6782 (OUTLIER) cc_final: 0.6459 (mp) REVERT: H 118 GLU cc_start: 0.6745 (OUTLIER) cc_final: 0.6438 (pp20) REVERT: H 209 ASP cc_start: 0.8652 (OUTLIER) cc_final: 0.8112 (m-30) REVERT: H 248 PHE cc_start: 0.7304 (t80) cc_final: 0.7089 (t80) REVERT: H 287 ILE cc_start: 0.6003 (OUTLIER) cc_final: 0.5116 (pt) REVERT: I 49 VAL cc_start: 0.6137 (OUTLIER) cc_final: 0.5711 (p) REVERT: I 94 GLN cc_start: 0.3059 (OUTLIER) cc_final: 0.2485 (pp30) REVERT: I 129 PHE cc_start: 0.3088 (OUTLIER) cc_final: 0.2590 (m-80) REVERT: I 210 MET cc_start: 0.3093 (tpt) cc_final: 0.2892 (tpt) REVERT: I 278 MET cc_start: 0.0606 (OUTLIER) cc_final: -0.1331 (mtt) REVERT: A 58 LYS cc_start: 0.5426 (OUTLIER) cc_final: 0.4652 (ttpp) REVERT: A 73 LYS cc_start: 0.7923 (mmmt) cc_final: 0.7366 (mtpt) REVERT: A 84 MET cc_start: 0.1143 (OUTLIER) cc_final: -0.2843 (mmt) REVERT: A 215 ARG cc_start: 0.5948 (OUTLIER) cc_final: 0.5148 (mtm180) REVERT: A 311 ILE cc_start: 0.7373 (OUTLIER) cc_final: 0.7091 (tp) REVERT: B 124 GLU cc_start: 0.6056 (OUTLIER) cc_final: 0.5801 (tp30) REVERT: B 210 MET cc_start: 0.6645 (pmm) cc_final: 0.4187 (tmm) REVERT: B 313 LYS cc_start: 0.5483 (OUTLIER) cc_final: 0.5278 (ttpt) REVERT: B 315 TYR cc_start: 0.6517 (OUTLIER) cc_final: 0.5508 (t80) REVERT: C 241 ARG cc_start: 0.7680 (OUTLIER) cc_final: 0.7310 (ttt-90) REVERT: C 243 MET cc_start: 0.6545 (mtp) cc_final: 0.6158 (mmp) REVERT: C 250 ARG cc_start: 0.7019 (OUTLIER) cc_final: 0.6653 (tmt170) REVERT: D 23 GLN cc_start: 0.6411 (mp10) cc_final: 0.5909 (mp10) REVERT: D 84 MET cc_start: 0.3973 (OUTLIER) cc_final: 0.3692 (mmt) REVERT: D 320 LEU cc_start: 0.7166 (OUTLIER) cc_final: 0.6882 (pp) outliers start: 116 outliers final: 85 residues processed: 343 average time/residue: 0.1576 time to fit residues: 84.3700 Evaluate side-chains 351 residues out of total 2256 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 109 poor density : 242 time to evaluate : 0.615 ------------------------------------------------------------------------------- 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 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 104 THR 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 253 LEU 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 100 ILE Chi-restraints excluded: chain G residue 124 GLU Chi-restraints excluded: chain G residue 163 GLU Chi-restraints excluded: chain G residue 211 MET 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 112 LEU Chi-restraints excluded: chain H residue 118 GLU Chi-restraints excluded: chain H residue 180 LEU Chi-restraints excluded: chain H residue 209 ASP Chi-restraints excluded: chain H residue 254 ARG Chi-restraints excluded: chain H residue 270 VAL Chi-restraints excluded: chain H residue 287 ILE Chi-restraints excluded: chain I residue 49 VAL Chi-restraints excluded: chain I residue 91 GLU Chi-restraints excluded: chain I residue 94 GLN Chi-restraints excluded: chain I residue 125 MET 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 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 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 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 47 HIS Chi-restraints excluded: chain B residue 60 LEU 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 186 LEU Chi-restraints excluded: chain B residue 215 ARG Chi-restraints excluded: chain B residue 221 VAL Chi-restraints excluded: chain B residue 261 VAL Chi-restraints excluded: chain B residue 266 THR 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 313 LYS Chi-restraints excluded: chain B residue 315 TYR Chi-restraints excluded: chain B residue 326 MET Chi-restraints excluded: chain C residue 87 THR 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 231 ASP 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 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 84 MET Chi-restraints excluded: chain D residue 119 THR Chi-restraints excluded: chain D residue 223 SER Chi-restraints excluded: chain D residue 257 ASP Chi-restraints excluded: chain D residue 297 THR Chi-restraints excluded: chain D residue 319 CYS Chi-restraints excluded: chain D residue 320 LEU Chi-restraints excluded: chain D residue 330 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 279 random chunks: chunk 25 optimal weight: 0.5980 chunk 159 optimal weight: 20.0000 chunk 113 optimal weight: 0.6980 chunk 195 optimal weight: 2.9990 chunk 163 optimal weight: 0.1980 chunk 152 optimal weight: 3.9990 chunk 164 optimal weight: 8.9990 chunk 71 optimal weight: 0.0270 chunk 2 optimal weight: 2.9990 chunk 69 optimal weight: 3.9990 chunk 255 optimal weight: 6.9990 overall best weight: 0.9040 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 93 HIS ** 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** B 272 GLN ** 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 = 0.5100 r_free = 0.5100 target = 0.214414 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4834 r_free = 0.4834 target = 0.184436 restraints weight = 36804.923| |-----------------------------------------------------------------------------| r_work (start): 0.4784 rms_B_bonded: 3.40 r_work: 0.4479 rms_B_bonded: 4.08 restraints_weight: 0.5000 r_work (final): 0.4479 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6584 moved from start: 0.2267 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.072 23296 Z= 0.134 Angle : 0.660 13.369 31697 Z= 0.333 Chirality : 0.043 0.236 3597 Planarity : 0.004 0.048 3902 Dihedral : 14.819 179.525 3940 Min Nonbonded Distance : 1.881 Molprobity Statistics. All-atom Clashscore : 15.31 Ramachandran Plot: Outliers : 0.07 % Allowed : 6.83 % Favored : 93.10 % Rotamer: Outliers : 5.27 % Allowed : 27.97 % 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: -2.05 (0.15), residues: 2781 helix: -0.17 (0.15), residues: 1154 sheet: -1.99 (0.24), residues: 403 loop : -2.30 (0.17), residues: 1224 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 170 TYR 0.034 0.001 TYR C 54 PHE 0.030 0.002 PHE C 166 HIS 0.014 0.001 HIS A 199 Details of bonding type rmsd covalent geometry : bond 0.00299 (23295) covalent geometry : angle 0.66022 (31697) hydrogen bonds : bond 0.03537 ( 854) hydrogen bonds : angle 4.97858 ( 2428) Misc. bond : bond 0.00040 ( 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 369 residues out of total 2256 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 119 poor density : 250 time to evaluate : 0.767 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 77 GLU cc_start: 0.6570 (pp20) cc_final: 0.6298 (pp20) REVERT: E 80 LYS cc_start: 0.7180 (pptt) cc_final: 0.6646 (tptt) REVERT: E 210 MET cc_start: 0.6850 (ppp) cc_final: 0.6512 (ppp) REVERT: F 178 TYR cc_start: 0.6048 (OUTLIER) cc_final: 0.4954 (m-80) REVERT: F 186 LEU cc_start: 0.6786 (OUTLIER) cc_final: 0.6463 (mt) REVERT: F 279 PHE cc_start: 0.3520 (OUTLIER) cc_final: 0.1968 (p90) REVERT: F 316 ASP cc_start: 0.4657 (OUTLIER) cc_final: 0.4287 (p0) REVERT: G 98 GLU cc_start: 0.5783 (pp20) cc_final: 0.4717 (tt0) REVERT: G 163 GLU cc_start: 0.6436 (OUTLIER) cc_final: 0.5370 (pm20) REVERT: G 243 MET cc_start: 0.5060 (mpt) cc_final: 0.4532 (tpt) REVERT: G 291 ILE cc_start: 0.6769 (OUTLIER) cc_final: 0.6452 (mp) REVERT: H 118 GLU cc_start: 0.6726 (OUTLIER) cc_final: 0.6478 (pp20) REVERT: H 199 HIS cc_start: 0.7867 (t-90) cc_final: 0.7573 (t-90) REVERT: H 209 ASP cc_start: 0.8661 (OUTLIER) cc_final: 0.8124 (m-30) REVERT: H 287 ILE cc_start: 0.5904 (OUTLIER) cc_final: 0.5000 (pt) REVERT: I 49 VAL cc_start: 0.6164 (OUTLIER) cc_final: 0.5744 (p) REVERT: I 94 GLN cc_start: 0.3121 (OUTLIER) cc_final: 0.2549 (pp30) REVERT: I 129 PHE cc_start: 0.3088 (OUTLIER) cc_final: 0.2600 (m-80) REVERT: I 167 ARG cc_start: 0.6195 (mmt180) cc_final: 0.5794 (mmt90) REVERT: I 210 MET cc_start: 0.3158 (tpt) cc_final: 0.2949 (tpt) REVERT: I 278 MET cc_start: 0.0631 (OUTLIER) cc_final: -0.1283 (mtt) REVERT: A 58 LYS cc_start: 0.5433 (OUTLIER) cc_final: 0.4666 (ttpp) REVERT: A 73 LYS cc_start: 0.7922 (mmmt) cc_final: 0.7368 (mtpt) REVERT: A 84 MET cc_start: 0.1171 (OUTLIER) cc_final: -0.2940 (mmt) REVERT: A 215 ARG cc_start: 0.5977 (OUTLIER) cc_final: 0.5159 (mtm180) REVERT: A 311 ILE cc_start: 0.7300 (OUTLIER) cc_final: 0.7010 (tp) REVERT: B 124 GLU cc_start: 0.6028 (OUTLIER) cc_final: 0.5765 (tp30) REVERT: B 210 MET cc_start: 0.6614 (pmm) cc_final: 0.4159 (tmm) REVERT: B 313 LYS cc_start: 0.5414 (OUTLIER) cc_final: 0.5202 (ttpt) REVERT: B 315 TYR cc_start: 0.6466 (OUTLIER) cc_final: 0.5479 (t80) REVERT: C 241 ARG cc_start: 0.7691 (OUTLIER) cc_final: 0.7315 (ttt-90) REVERT: C 243 MET cc_start: 0.6471 (mtp) cc_final: 0.6085 (mmp) REVERT: C 250 ARG cc_start: 0.7026 (OUTLIER) cc_final: 0.6656 (tmt170) REVERT: D 23 GLN cc_start: 0.6421 (mp10) cc_final: 0.5941 (mp10) REVERT: D 84 MET cc_start: 0.3988 (OUTLIER) cc_final: 0.3635 (mmt) REVERT: D 252 LEU cc_start: 0.8492 (OUTLIER) cc_final: 0.8160 (mp) REVERT: D 320 LEU cc_start: 0.7179 (OUTLIER) cc_final: 0.6896 (pp) outliers start: 119 outliers final: 86 residues processed: 346 average time/residue: 0.1581 time to fit residues: 85.4200 Evaluate side-chains 354 residues out of total 2256 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 111 poor density : 243 time to evaluate : 0.823 ------------------------------------------------------------------------------- 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 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 104 THR 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 253 LEU 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 100 ILE Chi-restraints excluded: chain G residue 103 THR Chi-restraints excluded: chain G residue 124 GLU Chi-restraints excluded: chain G residue 163 GLU Chi-restraints excluded: chain G residue 211 MET 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 112 LEU Chi-restraints excluded: chain H residue 118 GLU Chi-restraints excluded: chain H residue 180 LEU Chi-restraints excluded: chain H residue 209 ASP Chi-restraints excluded: chain H residue 254 ARG Chi-restraints excluded: chain H residue 287 ILE Chi-restraints excluded: chain I residue 49 VAL Chi-restraints excluded: chain I residue 91 GLU Chi-restraints excluded: chain I residue 94 GLN Chi-restraints excluded: chain I residue 125 MET 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 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 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 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 47 HIS Chi-restraints excluded: chain B residue 60 LEU 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 186 LEU Chi-restraints excluded: chain B residue 215 ARG Chi-restraints excluded: chain B residue 221 VAL 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 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 313 LYS Chi-restraints excluded: chain B residue 315 TYR Chi-restraints excluded: chain B residue 326 MET Chi-restraints excluded: chain C residue 87 THR 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 231 ASP 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 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 84 MET Chi-restraints excluded: chain D residue 119 THR Chi-restraints excluded: chain D residue 223 SER 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 Chi-restraints excluded: chain D residue 320 LEU Chi-restraints excluded: chain D residue 330 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 279 random chunks: chunk 214 optimal weight: 10.0000 chunk 105 optimal weight: 30.0000 chunk 25 optimal weight: 0.9980 chunk 145 optimal weight: 5.9990 chunk 226 optimal weight: 7.9990 chunk 223 optimal weight: 10.0000 chunk 264 optimal weight: 1.9990 chunk 197 optimal weight: 0.4980 chunk 254 optimal weight: 0.9990 chunk 128 optimal weight: 20.0000 chunk 52 optimal weight: 1.9990 overall best weight: 1.2986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 62 ASN ** F 93 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 93 HIS ** 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: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5086 r_free = 0.5086 target = 0.212854 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.4820 r_free = 0.4820 target = 0.183029 restraints weight = 36744.051| |-----------------------------------------------------------------------------| r_work (start): 0.4765 rms_B_bonded: 3.58 r_work: 0.4437 rms_B_bonded: 4.27 restraints_weight: 0.5000 r_work (final): 0.4437 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6666 moved from start: 0.2248 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 23296 Z= 0.152 Angle : 0.677 14.961 31697 Z= 0.342 Chirality : 0.044 0.267 3597 Planarity : 0.004 0.049 3902 Dihedral : 14.931 178.649 3940 Min Nonbonded Distance : 1.864 Molprobity Statistics. All-atom Clashscore : 15.73 Ramachandran Plot: Outliers : 0.07 % Allowed : 7.59 % Favored : 92.34 % Rotamer: Outliers : 5.01 % Allowed : 28.28 % Favored : 66.71 % 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: -2.09 (0.15), residues: 2781 helix: -0.18 (0.15), residues: 1140 sheet: -2.03 (0.24), residues: 410 loop : -2.30 (0.16), residues: 1231 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG G 250 TYR 0.035 0.001 TYR C 54 PHE 0.028 0.002 PHE C 166 HIS 0.014 0.001 HIS A 199 Details of bonding type rmsd covalent geometry : bond 0.00344 (23295) covalent geometry : angle 0.67653 (31697) hydrogen bonds : bond 0.03697 ( 854) hydrogen bonds : angle 5.04643 ( 2428) Misc. bond : bond 0.00021 ( 1) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7362.20 seconds wall clock time: 126 minutes 33.84 seconds (7593.84 seconds total)