Starting phenix.real_space_refine on Wed Apr 8 04:53:26 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9q29_72153/04_2026/9q29_72153_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/9q29_72153/04_2026/9q29_72153.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.61 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9q29_72153/04_2026/9q29_72153.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9q29_72153/04_2026/9q29_72153.map" model { file = "/net/cci-nas-00/data/ceres_data/9q29_72153/04_2026/9q29_72153_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9q29_72153/04_2026/9q29_72153_trim.cif" } resolution = 2.61 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= 0.006 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: 7 Type Number sf(0) Gaussians Ca 13 9.91 5 P 49 5.49 5 S 118 5.16 5 C 13559 2.51 5 N 3793 2.21 5 O 4229 1.98 5 H 11627 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 2 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.1rc1-6017/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 33388 Number of models: 1 Model: "" Number of chains: 19 Chain: "C" Number of atoms: 5164 Number of conformers: 1 Conformer: "" Number of residues, atoms: 325, 5164 Classifications: {'peptide': 325} Link IDs: {'CIS': 1, 'PTRANS': 11, 'TRANS': 312} Chain breaks: 1 Chain: "D" Number of atoms: 4685 Number of conformers: 1 Conformer: "" Number of residues, atoms: 305, 4685 Classifications: {'peptide': 305} Link IDs: {'CIS': 1, 'PTRANS': 7, 'TRANS': 296} Chain breaks: 1 Chain: "G" Number of atoms: 2372 Number of conformers: 1 Conformer: "" Number of residues, atoms: 309, 2372 Classifications: {'peptide': 309} Modifications used: {'COO': 1} Link IDs: {'CIS': 1, 'PTRANS': 9, 'TRANS': 298} Chain breaks: 1 Chain: "H" Number of atoms: 520 Number of conformers: 1 Conformer: "" Number of residues, atoms: 26, 520 Classifications: {'DNA': 26} Link IDs: {'rna3p': 25} Chain: "I" Number of atoms: 4502 Number of conformers: 1 Conformer: "" Number of residues, atoms: 300, 4502 Classifications: {'peptide': 300} Link IDs: {'CIS': 1, 'PTRANS': 9, 'TRANS': 289} Chain breaks: 2 Chain: "J" Number of atoms: 2371 Number of conformers: 1 Conformer: "" Number of residues, atoms: 309, 2371 Classifications: {'peptide': 309} Link IDs: {'CIS': 2, 'PTRANS': 9, 'TRANS': 297} Chain breaks: 1 Chain: "K" Number of atoms: 2363 Number of conformers: 1 Conformer: "" Number of residues, atoms: 308, 2363 Classifications: {'peptide': 308} Link IDs: {'CIS': 2, 'PTRANS': 9, 'TRANS': 296} Chain breaks: 1 Chain: "L" Number of atoms: 2356 Number of conformers: 1 Conformer: "" Number of residues, atoms: 307, 2356 Classifications: {'peptide': 307} Link IDs: {'CIS': 2, 'PTRANS': 9, 'TRANS': 295} Chain breaks: 1 Chain: "R" Number of atoms: 5033 Number of conformers: 1 Conformer: "" Number of residues, atoms: 321, 5033 Classifications: {'peptide': 321} Modifications used: {'COO': 1} Link IDs: {'CIS': 1, 'PTRANS': 19, 'TRANS': 300} Chain breaks: 2 Chain: "X" Number of atoms: 3765 Number of conformers: 1 Conformer: "" Number of residues, atoms: 233, 3765 Classifications: {'peptide': 233} Modifications used: {'COO': 1} Link IDs: {'CIS': 1, 'PTRANS': 5, 'TRANS': 226} Chain breaks: 3 Chain: "C" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' CA': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "D" Number of atoms: 63 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 63 Unusual residues: {' CA': 1, 'ATP': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "G" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 33 Unusual residues: {' CA': 2, 'ATP': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "I" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' CA': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "J" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 33 Unusual residues: {' CA': 2, 'ATP': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "K" Number of atoms: 64 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 64 Unusual residues: {' CA': 2, 'ATP': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "L" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' CA': 1} Classifications: {'undetermined': 1} Chain: "R" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' CA': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "X" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' CA': 1} Classifications: {'undetermined': 1} Time building chain proxies: 7.43, per 1000 atoms: 0.22 Number of scatterers: 33388 At special positions: 0 Unit cell: (134.56, 120.64, 203.232, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Ca 13 19.99 S 118 16.00 P 49 15.00 O 4229 8.00 N 3793 7.00 C 13559 6.00 H 11627 1.00 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=4, symmetry=0 Number of additional bonds: simple=4, symmetry=0 Coordination: Other bonds: Time building additional restraints: 3.46 Conformation dependent library (CDL) restraints added in 1.2 seconds 5346 Ramachandran restraints generated. 2673 Oldfield, 0 Emsley, 2673 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5024 Finding SS restraints... Secondary structure from input PDB file: 136 helices and 20 sheets defined 53.3% alpha, 16.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.17 Creating SS restraints... Processing helix chain 'C' and resid 13 through 17 Processing helix chain 'C' and resid 20 through 30 Processing helix chain 'C' and resid 34 through 38 Processing helix chain 'C' and resid 42 through 51 Processing helix chain 'C' and resid 53 through 68 Processing helix chain 'C' and resid 87 through 97 Processing helix chain 'C' and resid 104 through 112 Processing helix chain 'C' and resid 130 through 142 Processing helix chain 'C' and resid 143 through 144 No H-bonds generated for 'chain 'C' and resid 143 through 144' Processing helix chain 'C' and resid 145 through 149 Processing helix chain 'C' and resid 165 through 188 Processing helix chain 'C' and resid 189 through 197 removed outlier: 3.563A pdb=" N GLU C 197 " --> pdb=" O ARG C 193 " (cutoff:3.500A) Processing helix chain 'C' and resid 200 through 207 Processing helix chain 'C' and resid 215 through 233 Proline residue: C 227 - end of helix Processing helix chain 'C' and resid 246 through 250 removed outlier: 4.283A pdb=" N HIS C 250 " --> pdb=" O PRO C 247 " (cutoff:3.500A) Processing helix chain 'C' and resid 254 through 276 Processing helix chain 'C' and resid 303 through 308 Processing helix chain 'D' and resid 13 through 23 Processing helix chain 'D' and resid 27 through 34 Processing helix chain 'D' and resid 35 through 44 Processing helix chain 'D' and resid 46 through 61 Processing helix chain 'D' and resid 68 through 79 Processing helix chain 'D' and resid 86 through 93 Processing helix chain 'D' and resid 112 through 127 Processing helix chain 'D' and resid 142 through 152 Processing helix chain 'D' and resid 156 through 166 Processing helix chain 'D' and resid 174 through 193 Processing helix chain 'D' and resid 207 through 213 removed outlier: 3.987A pdb=" N VAL D 211 " --> pdb=" O SER D 207 " (cutoff:3.500A) Processing helix chain 'D' and resid 220 through 240 removed outlier: 4.029A pdb=" N LEU D 224 " --> pdb=" O GLN D 220 " (cutoff:3.500A) Processing helix chain 'D' and resid 265 through 270 removed outlier: 3.668A pdb=" N PHE D 270 " --> pdb=" O ARG D 266 " (cutoff:3.500A) Processing helix chain 'G' and resid 24 through 32 Processing helix chain 'G' and resid 34 through 44 Processing helix chain 'G' and resid 48 through 54 Processing helix chain 'G' and resid 56 through 61 removed outlier: 3.517A pdb=" N ILE G 61 " --> pdb=" O LYS G 57 " (cutoff:3.500A) Processing helix chain 'G' and resid 67 through 81 Processing helix chain 'G' and resid 89 through 96 Processing helix chain 'G' and resid 106 through 114 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 179 removed outlier: 3.577A pdb=" N LEU G 171 " --> pdb=" O ARG G 167 " (cutoff:3.500A) Processing helix chain 'G' and resid 181 through 188 Processing helix chain 'G' and resid 196 through 214 Processing helix chain 'G' and resid 227 through 232 Processing helix chain 'G' and resid 234 through 236 No H-bonds generated for 'chain 'G' and resid 234 through 236' Processing helix chain 'G' and resid 237 through 260 Processing helix chain 'G' and resid 288 through 296 removed outlier: 3.912A pdb=" N ILE G 292 " --> pdb=" O GLY G 288 " (cutoff:3.500A) Processing helix chain 'I' and resid 26 through 31 removed outlier: 3.698A pdb=" N GLN I 30 " --> pdb=" O SER I 26 " (cutoff:3.500A) Processing helix chain 'I' and resid 34 through 44 Processing helix chain 'I' and resid 48 through 55 Processing helix chain 'I' and resid 56 through 62 removed outlier: 3.512A pdb=" N LEU I 60 " --> pdb=" O PRO I 56 " (cutoff:3.500A) Processing helix chain 'I' and resid 67 through 82 Processing helix chain 'I' and resid 89 through 98 Processing helix chain 'I' and resid 106 through 114 Processing helix chain 'I' and resid 132 through 144 Processing helix chain 'I' and resid 145 through 146 No H-bonds generated for 'chain 'I' and resid 145 through 146' Processing helix chain 'I' and resid 147 through 151 Processing helix chain 'I' and resid 167 through 179 removed outlier: 3.718A pdb=" N LEU I 171 " --> pdb=" O ARG I 167 " (cutoff:3.500A) Processing helix chain 'I' and resid 181 through 188 Processing helix chain 'I' and resid 196 through 214 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 260 Processing helix chain 'I' and resid 288 through 296 removed outlier: 3.851A pdb=" N ILE I 292 " --> pdb=" O GLY I 288 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N ALA I 293 " --> pdb=" O GLY I 289 " (cutoff:3.500A) Processing helix chain 'J' and resid 24 through 31 Processing helix chain 'J' and resid 34 through 45 Processing helix chain 'J' and resid 48 through 55 Processing helix chain 'J' and resid 56 through 62 Processing helix chain 'J' and resid 67 through 82 Processing helix chain 'J' and resid 89 through 98 Processing helix chain 'J' and resid 106 through 114 Processing helix chain 'J' and resid 132 through 144 removed outlier: 3.695A pdb=" N CYS J 137 " --> pdb=" O LYS J 133 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N VAL J 142 " --> pdb=" O HIS J 138 " (cutoff:3.500A) Processing helix chain 'J' and resid 147 through 151 Processing helix chain 'J' and resid 167 through 179 removed outlier: 3.763A pdb=" N LEU J 171 " --> pdb=" O ARG J 167 " (cutoff:3.500A) Processing helix chain 'J' and resid 181 through 187 removed outlier: 3.528A pdb=" N ASP J 187 " --> pdb=" O SER J 183 " (cutoff:3.500A) Processing helix chain 'J' and resid 196 through 214 removed outlier: 3.534A pdb=" N THR J 201 " --> pdb=" O THR J 197 " (cutoff:3.500A) Processing helix chain 'J' and resid 227 through 232 removed outlier: 3.504A pdb=" N TYR J 232 " --> pdb=" O TYR J 228 " (cutoff:3.500A) Processing helix chain 'J' and resid 237 through 260 Processing helix chain 'J' and resid 289 through 296 Processing helix chain 'K' and resid 24 through 31 removed outlier: 3.610A pdb=" N LEU K 28 " --> pdb=" O ILE K 25 " (cutoff:3.500A) Processing helix chain 'K' and resid 34 through 45 Processing helix chain 'K' and resid 48 through 54 Processing helix chain 'K' and resid 56 through 62 Processing helix chain 'K' and resid 67 through 82 Processing helix chain 'K' and resid 89 through 98 Processing helix chain 'K' and resid 106 through 114 Processing helix chain 'K' and resid 132 through 144 removed outlier: 3.750A pdb=" N CYS K 137 " --> pdb=" O LYS K 133 " (cutoff:3.500A) Processing helix chain 'K' and resid 145 through 146 No H-bonds generated for 'chain 'K' and resid 145 through 146' Processing helix chain 'K' and resid 147 through 151 Processing helix chain 'K' and resid 167 through 179 removed outlier: 3.808A pdb=" N LEU K 171 " --> pdb=" O ARG K 167 " (cutoff:3.500A) Processing helix chain 'K' and resid 181 through 187 Processing helix chain 'K' and resid 196 through 214 Processing helix chain 'K' and resid 227 through 232 removed outlier: 3.583A pdb=" N TYR K 232 " --> pdb=" O TYR K 228 " (cutoff:3.500A) Processing helix chain 'K' and resid 237 through 260 Processing helix chain 'K' and resid 289 through 296 Processing helix chain 'L' and resid 27 through 31 removed outlier: 3.534A pdb=" N GLN L 30 " --> pdb=" O ARG L 27 " (cutoff:3.500A) Processing helix chain 'L' and resid 34 through 45 Processing helix chain 'L' and resid 48 through 54 removed outlier: 3.513A pdb=" N VAL L 52 " --> pdb=" O THR L 48 " (cutoff:3.500A) Processing helix chain 'L' and resid 56 through 62 Processing helix chain 'L' and resid 67 through 82 Processing helix chain 'L' and resid 89 through 98 Processing helix chain 'L' and resid 106 through 114 Processing helix chain 'L' and resid 132 through 144 removed outlier: 3.616A pdb=" N VAL L 142 " --> pdb=" O HIS L 138 " (cutoff:3.500A) Processing helix chain 'L' and resid 147 through 151 Processing helix chain 'L' and resid 167 through 179 removed outlier: 3.812A pdb=" N LEU L 171 " --> pdb=" O ARG L 167 " (cutoff:3.500A) Processing helix chain 'L' and resid 181 through 187 Processing helix chain 'L' and resid 196 through 214 removed outlier: 3.875A pdb=" N THR L 201 " --> pdb=" O THR L 197 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N GLN L 202 " --> pdb=" O ASP L 198 " (cutoff:3.500A) Processing helix chain 'L' and resid 225 through 232 removed outlier: 3.933A pdb=" N THR L 230 " --> pdb=" O ALA L 226 " (cutoff:3.500A) Processing helix chain 'L' and resid 237 through 260 Processing helix chain 'L' and resid 289 through 296 Processing helix chain 'R' and resid 2 through 6 Processing helix chain 'R' and resid 9 through 19 Processing helix chain 'R' and resid 23 through 30 removed outlier: 3.734A pdb=" N PHE R 30 " --> pdb=" O GLU R 26 " (cutoff:3.500A) Processing helix chain 'R' and resid 31 through 40 Processing helix chain 'R' and resid 42 through 59 Processing helix chain 'R' and resid 65 through 71 Processing helix chain 'R' and resid 75 through 80 removed outlier: 3.629A pdb=" N HIS R 79 " --> pdb=" O PHE R 75 " (cutoff:3.500A) Processing helix chain 'R' and resid 86 through 94 Processing helix chain 'R' and resid 112 through 124 Processing helix chain 'R' and resid 125 through 126 No H-bonds generated for 'chain 'R' and resid 125 through 126' Processing helix chain 'R' and resid 127 through 131 Processing helix chain 'R' and resid 147 through 162 Proline residue: R 159 - end of helix Processing helix chain 'R' and resid 166 through 172 Processing helix chain 'R' and resid 174 through 178 Processing helix chain 'R' and resid 186 through 204 removed outlier: 4.460A pdb=" N VAL R 198 " --> pdb=" O VAL R 194 " (cutoff:3.500A) Proline residue: R 199 - end of helix Processing helix chain 'R' and resid 215 through 223 removed outlier: 4.043A pdb=" N PHE R 219 " --> pdb=" O VAL R 215 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N CYS R 221 " --> pdb=" O ALA R 217 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N GLU R 222 " --> pdb=" O PRO R 218 " (cutoff:3.500A) Processing helix chain 'R' and resid 227 through 250 Processing helix chain 'R' and resid 284 through 290 removed outlier: 3.789A pdb=" N TRP R 288 " --> pdb=" O LEU R 284 " (cutoff:3.500A) Processing helix chain 'X' and resid 53 through 67 Processing helix chain 'X' and resid 68 through 72 Processing helix chain 'X' and resid 88 through 99 Processing helix chain 'X' and resid 104 through 113 Processing helix chain 'X' and resid 122 through 140 removed outlier: 3.994A pdb=" N GLU X 134 " --> pdb=" O LEU X 130 " (cutoff:3.500A) removed outlier: 5.221A pdb=" N SER X 135 " --> pdb=" O TYR X 131 " (cutoff:3.500A) removed outlier: 4.204A pdb=" N MET X 136 " --> pdb=" O SER X 132 " (cutoff:3.500A) Processing helix chain 'X' and resid 150 through 153 Processing helix chain 'X' and resid 154 through 162 Processing helix chain 'X' and resid 165 through 188 removed outlier: 4.792A pdb=" N THR X 172 " --> pdb=" O LEU X 168 " (cutoff:3.500A) removed outlier: 5.102A pdb=" N LEU X 173 " --> pdb=" O GLN X 169 " (cutoff:3.500A) Processing helix chain 'X' and resid 228 through 235 removed outlier: 3.719A pdb=" N LEU X 234 " --> pdb=" O ALA X 230 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'C' and resid 85 through 86 removed outlier: 3.698A pdb=" N CYS C 85 " --> pdb=" O VAL D 169 " (cutoff:3.500A) removed outlier: 6.361A pdb=" N VAL D 132 " --> pdb=" O GLN D 168 " (cutoff:3.500A) removed outlier: 7.785A pdb=" N VAL D 170 " --> pdb=" O VAL D 132 " (cutoff:3.500A) removed outlier: 6.326A pdb=" N TYR D 134 " --> pdb=" O VAL D 170 " (cutoff:3.500A) removed outlier: 6.559A pdb=" N ASN D 131 " --> pdb=" O VAL D 200 " (cutoff:3.500A) removed outlier: 3.842A pdb=" N VAL D 202 " --> pdb=" O ASN D 131 " (cutoff:3.500A) removed outlier: 7.035A pdb=" N LYS D 201 " --> pdb=" O ALA D 244 " (cutoff:3.500A) removed outlier: 7.902A pdb=" N VAL D 246 " --> pdb=" O LYS D 201 " (cutoff:3.500A) removed outlier: 6.135A pdb=" N VAL D 203 " --> pdb=" O VAL D 246 " (cutoff:3.500A) removed outlier: 7.799A pdb=" N THR D 248 " --> pdb=" O VAL D 203 " (cutoff:3.500A) removed outlier: 6.900A pdb=" N VAL D 205 " --> pdb=" O THR D 248 " (cutoff:3.500A) removed outlier: 6.462A pdb=" N THR D 103 " --> pdb=" O VAL D 247 " (cutoff:3.500A) removed outlier: 7.671A pdb=" N ASN D 249 " --> pdb=" O THR D 103 " (cutoff:3.500A) removed outlier: 6.055A pdb=" N ILE D 105 " --> pdb=" O ASN D 249 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'C' and resid 99 through 100 Processing sheet with id=AA3, first strand: chain 'C' and resid 294 through 299 removed outlier: 3.687A pdb=" N LEU C 296 " --> pdb=" O LYS C 289 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N GLY C 125 " --> pdb=" O ASN C 284 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N MET C 286 " --> pdb=" O GLY C 125 " (cutoff:3.500A) removed outlier: 6.432A pdb=" N THR C 120 " --> pdb=" O ILE C 311 " (cutoff:3.500A) removed outlier: 7.883A pdb=" N LEU C 313 " --> pdb=" O THR C 120 " (cutoff:3.500A) removed outlier: 6.223A pdb=" N GLU C 122 " --> pdb=" O LEU C 313 " (cutoff:3.500A) removed outlier: 7.594A pdb=" N PHE C 315 " --> pdb=" O GLU C 122 " (cutoff:3.500A) removed outlier: 6.527A pdb=" N CYS C 124 " --> pdb=" O PHE C 315 " (cutoff:3.500A) removed outlier: 8.793A pdb=" N TRP C 317 " --> pdb=" O CYS C 124 " (cutoff:3.500A) removed outlier: 6.667A pdb=" N ARG C 312 " --> pdb=" O TYR C 327 " (cutoff:3.500A) removed outlier: 4.091A pdb=" N ARG C 322 " --> pdb=" O PHE C 339 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'C' and resid 294 through 299 removed outlier: 3.687A pdb=" N LEU C 296 " --> pdb=" O LYS C 289 " (cutoff:3.500A) removed outlier: 6.703A pdb=" N ARG C 237 " --> pdb=" O ALA C 279 " (cutoff:3.500A) removed outlier: 7.906A pdb=" N ILE C 281 " --> pdb=" O ARG C 237 " (cutoff:3.500A) removed outlier: 6.345A pdb=" N VAL C 239 " --> pdb=" O ILE C 281 " (cutoff:3.500A) removed outlier: 7.975A pdb=" N THR C 283 " --> pdb=" O VAL C 239 " (cutoff:3.500A) removed outlier: 7.115A pdb=" N VAL C 241 " --> pdb=" O THR C 283 " (cutoff:3.500A) removed outlier: 8.785A pdb=" N GLN C 285 " --> pdb=" O VAL C 241 " (cutoff:3.500A) removed outlier: 6.693A pdb=" N GLU C 154 " --> pdb=" O LEU C 238 " (cutoff:3.500A) removed outlier: 8.205A pdb=" N ILE C 240 " --> pdb=" O GLU C 154 " (cutoff:3.500A) removed outlier: 6.589A pdb=" N VAL C 156 " --> pdb=" O ILE C 240 " (cutoff:3.500A) removed outlier: 7.696A pdb=" N ASP C 242 " --> pdb=" O VAL C 156 " (cutoff:3.500A) removed outlier: 6.661A pdb=" N ILE C 158 " --> pdb=" O ASP C 242 " (cutoff:3.500A) removed outlier: 4.481A pdb=" N LEU R 63 " --> pdb=" O TYR C 210 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'D' and resid 66 through 67 removed outlier: 3.660A pdb=" N VAL D 66 " --> pdb=" O LEU X 117 " (cutoff:3.500A) removed outlier: 4.027A pdb=" N LEU X 117 " --> pdb=" O VAL D 66 " (cutoff:3.500A) removed outlier: 6.538A pdb=" N VAL X 78 " --> pdb=" O PHE X 116 " (cutoff:3.500A) removed outlier: 8.109A pdb=" N VAL X 118 " --> pdb=" O VAL X 78 " (cutoff:3.500A) removed outlier: 6.443A pdb=" N PHE X 80 " --> pdb=" O VAL X 118 " (cutoff:3.500A) removed outlier: 6.581A pdb=" N GLU X 77 " --> pdb=" O LEU X 143 " (cutoff:3.500A) removed outlier: 3.833A pdb=" N LEU X 145 " --> pdb=" O GLU X 77 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N HIS X 237 " --> pdb=" O ILE X 43 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'D' and resid 81 through 82 Processing sheet with id=AA7, first strand: chain 'D' and resid 251 through 253 Processing sheet with id=AA8, first strand: chain 'D' and resid 291 through 294 removed outlier: 3.632A pdb=" N ALA D 293 " --> pdb=" O GLU D 307 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'G' and resid 87 through 88 removed outlier: 4.327A pdb=" N THR G 87 " --> pdb=" O ILE R 181 " (cutoff:3.500A) removed outlier: 6.614A pdb=" N ALA R 137 " --> pdb=" O PHE R 180 " (cutoff:3.500A) removed outlier: 7.802A pdb=" N GLU R 182 " --> pdb=" O ALA R 137 " (cutoff:3.500A) removed outlier: 6.230A pdb=" N TYR R 139 " --> pdb=" O GLU R 182 " (cutoff:3.500A) removed outlier: 5.562A pdb=" N GLY R 136 " --> pdb=" O ALA R 207 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N LEU R 209 " --> pdb=" O GLY R 136 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N GLY R 107 " --> pdb=" O ASN R 257 " (cutoff:3.500A) removed outlier: 6.277A pdb=" N ILE R 102 " --> pdb=" O VAL R 294 " (cutoff:3.500A) removed outlier: 7.767A pdb=" N LEU R 296 " --> pdb=" O ILE R 102 " (cutoff:3.500A) removed outlier: 6.329A pdb=" N GLU R 104 " --> pdb=" O LEU R 296 " (cutoff:3.500A) removed outlier: 7.492A pdb=" N ALA R 298 " --> pdb=" O GLU R 104 " (cutoff:3.500A) removed outlier: 6.716A pdb=" N ALA R 106 " --> pdb=" O ALA R 298 " (cutoff:3.500A) removed outlier: 6.798A pdb=" N ARG R 295 " --> pdb=" O LEU R 318 " (cutoff:3.500A) removed outlier: 4.072A pdb=" N ARG R 313 " --> pdb=" O TYR R 330 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'G' and resid 333 through 336 removed outlier: 5.359A pdb=" N CYS G 312 " --> pdb=" O ARG G 303 " (cutoff:3.500A) removed outlier: 7.192A pdb=" N ARG G 303 " --> pdb=" O CYS G 312 " (cutoff:3.500A) removed outlier: 5.543A pdb=" N ILE G 314 " --> pdb=" O TYR G 301 " (cutoff:3.500A) removed outlier: 6.388A pdb=" N TYR G 301 " --> pdb=" O ILE G 314 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N GLY G 127 " --> pdb=" O ASN G 267 " (cutoff:3.500A) removed outlier: 5.371A pdb=" N LYS G 156 " --> pdb=" O TYR G 216 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'G' and resid 269 through 271 Processing sheet with id=AB3, first strand: chain 'I' and resid 101 through 102 Processing sheet with id=AB4, first strand: chain 'I' and resid 324 through 326 removed outlier: 6.147A pdb=" N ARG I 299 " --> pdb=" O TYR I 315 " (cutoff:3.500A) removed outlier: 6.189A pdb=" N THR I 123 " --> pdb=" O ILE I 265 " (cutoff:3.500A) removed outlier: 7.469A pdb=" N ASN I 267 " --> pdb=" O THR I 123 " (cutoff:3.500A) removed outlier: 6.215A pdb=" N MET I 125 " --> pdb=" O ASN I 267 " (cutoff:3.500A) removed outlier: 6.624A pdb=" N LYS I 156 " --> pdb=" O LEU I 218 " (cutoff:3.500A) removed outlier: 8.130A pdb=" N ILE I 220 " --> pdb=" O LYS I 156 " (cutoff:3.500A) removed outlier: 6.288A pdb=" N MET I 158 " --> pdb=" O ILE I 220 " (cutoff:3.500A) removed outlier: 7.401A pdb=" N ASP I 222 " --> pdb=" O MET I 158 " (cutoff:3.500A) removed outlier: 6.492A pdb=" N ILE I 160 " --> pdb=" O ASP I 222 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'I' and resid 269 through 271 Processing sheet with id=AB6, first strand: chain 'I' and resid 328 through 330 Processing sheet with id=AB7, first strand: chain 'J' and resid 333 through 335 removed outlier: 3.505A pdb=" N GLY J 333 " --> pdb=" O ASN J 330 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N GLY J 127 " --> pdb=" O ASN J 267 " (cutoff:3.500A) removed outlier: 7.199A pdb=" N LYS J 156 " --> pdb=" O ALA J 217 " (cutoff:3.500A) removed outlier: 6.149A pdb=" N LEU J 219 " --> pdb=" O LYS J 156 " (cutoff:3.500A) removed outlier: 6.698A pdb=" N MET J 158 " --> pdb=" O LEU J 219 " (cutoff:3.500A) removed outlier: 5.513A pdb=" N VAL J 221 " --> pdb=" O MET J 158 " (cutoff:3.500A) removed outlier: 6.792A pdb=" N ILE J 160 " --> pdb=" O VAL J 221 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'K' and resid 333 through 335 removed outlier: 3.741A pdb=" N ALA K 328 " --> pdb=" O GLY K 335 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N ILE K 311 " --> pdb=" O ARG K 303 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N GLY K 127 " --> pdb=" O ASN K 267 " (cutoff:3.500A) removed outlier: 7.070A pdb=" N ALA K 217 " --> pdb=" O ALA K 262 " (cutoff:3.500A) removed outlier: 7.965A pdb=" N VAL K 264 " --> pdb=" O ALA K 217 " (cutoff:3.500A) removed outlier: 6.213A pdb=" N LEU K 219 " --> pdb=" O VAL K 264 " (cutoff:3.500A) removed outlier: 7.983A pdb=" N THR K 266 " --> pdb=" O LEU K 219 " (cutoff:3.500A) removed outlier: 7.201A pdb=" N VAL K 221 " --> pdb=" O THR K 266 " (cutoff:3.500A) removed outlier: 7.114A pdb=" N LYS K 156 " --> pdb=" O ALA K 217 " (cutoff:3.500A) removed outlier: 6.130A pdb=" N LEU K 219 " --> pdb=" O LYS K 156 " (cutoff:3.500A) removed outlier: 6.742A pdb=" N MET K 158 " --> pdb=" O LEU K 219 " (cutoff:3.500A) removed outlier: 5.530A pdb=" N VAL K 221 " --> pdb=" O MET K 158 " (cutoff:3.500A) removed outlier: 6.785A pdb=" N ILE K 160 " --> pdb=" O VAL K 221 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'L' and resid 190 through 193 removed outlier: 6.835A pdb=" N ALA L 157 " --> pdb=" O ALA L 190 " (cutoff:3.500A) removed outlier: 8.231A pdb=" N ALA L 192 " --> pdb=" O ALA L 157 " (cutoff:3.500A) removed outlier: 6.319A pdb=" N TYR L 159 " --> pdb=" O ALA L 192 " (cutoff:3.500A) removed outlier: 7.051A pdb=" N LYS L 156 " --> pdb=" O ALA L 217 " (cutoff:3.500A) removed outlier: 5.987A pdb=" N LEU L 219 " --> pdb=" O LYS L 156 " (cutoff:3.500A) removed outlier: 6.683A pdb=" N MET L 158 " --> pdb=" O LEU L 219 " (cutoff:3.500A) removed outlier: 5.549A pdb=" N VAL L 221 " --> pdb=" O MET L 158 " (cutoff:3.500A) removed outlier: 6.815A pdb=" N ILE L 160 " --> pdb=" O VAL L 221 " (cutoff:3.500A) removed outlier: 7.188A pdb=" N ALA L 217 " --> pdb=" O ALA L 262 " (cutoff:3.500A) removed outlier: 8.199A pdb=" N VAL L 264 " --> pdb=" O ALA L 217 " (cutoff:3.500A) removed outlier: 6.364A pdb=" N LEU L 219 " --> pdb=" O VAL L 264 " (cutoff:3.500A) removed outlier: 7.986A pdb=" N THR L 266 " --> pdb=" O LEU L 219 " (cutoff:3.500A) removed outlier: 7.035A pdb=" N VAL L 221 " --> pdb=" O THR L 266 " (cutoff:3.500A) removed outlier: 6.249A pdb=" N THR L 123 " --> pdb=" O ILE L 265 " (cutoff:3.500A) removed outlier: 7.492A pdb=" N ASN L 267 " --> pdb=" O THR L 123 " (cutoff:3.500A) removed outlier: 5.989A pdb=" N MET L 125 " --> pdb=" O ASN L 267 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'R' and resid 81 through 82 Processing sheet with id=AC2, first strand: chain 'R' and resid 259 through 261 1135 hydrogen bonds defined for protein. 3189 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 8.09 Time building geometry restraints manager: 4.59 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.03: 11591 1.03 - 1.23: 86 1.23 - 1.42: 8867 1.42 - 1.62: 13032 1.62 - 1.81: 180 Bond restraints: 33756 Sorted by residual: bond pdb=" C4 ADP C 401 " pdb=" C5 ADP C 401 " ideal model delta sigma weight residual 1.490 1.463 0.027 2.00e-02 2.50e+03 1.83e+00 bond pdb=" C4' DT H 19 " pdb=" O4' DT H 19 " ideal model delta sigma weight residual 1.450 1.430 0.020 2.00e-02 2.50e+03 9.82e-01 bond pdb=" CB ARG G 130 " pdb=" CG ARG G 130 " ideal model delta sigma weight residual 1.520 1.492 0.028 3.00e-02 1.11e+03 8.99e-01 bond pdb=" C2' ATP J 401 " pdb=" C3' ATP J 401 " ideal model delta sigma weight residual 1.531 1.520 0.011 1.20e-02 6.94e+03 8.21e-01 bond pdb=" C2' ATP K 401 " pdb=" C3' ATP K 401 " ideal model delta sigma weight residual 1.531 1.520 0.011 1.20e-02 6.94e+03 8.14e-01 ... (remaining 33751 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.55: 55693 1.55 - 3.09: 575 3.09 - 4.64: 89 4.64 - 6.19: 27 6.19 - 7.73: 15 Bond angle restraints: 56399 Sorted by residual: angle pdb=" C ASP I 222 " pdb=" N SER I 223 " pdb=" CA SER I 223 " ideal model delta sigma weight residual 121.70 129.43 -7.73 1.80e+00 3.09e-01 1.85e+01 angle pdb=" C ASP X 149 " pdb=" N SER X 150 " pdb=" CA SER X 150 " ideal model delta sigma weight residual 121.70 129.33 -7.63 1.80e+00 3.09e-01 1.80e+01 angle pdb=" C ASP R 213 " pdb=" N SER R 214 " pdb=" CA SER R 214 " ideal model delta sigma weight residual 121.70 128.94 -7.24 1.80e+00 3.09e-01 1.62e+01 angle pdb=" C ASP D 206 " pdb=" N SER D 207 " pdb=" CA SER D 207 " ideal model delta sigma weight residual 121.70 127.93 -6.23 1.80e+00 3.09e-01 1.20e+01 angle pdb=" C ASP C 242 " pdb=" N GLY C 243 " pdb=" CA GLY C 243 " ideal model delta sigma weight residual 121.70 127.70 -6.00 1.80e+00 3.09e-01 1.11e+01 ... (remaining 56394 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 27.46: 16619 27.46 - 54.92: 522 54.92 - 82.39: 96 82.39 - 109.85: 6 109.85 - 137.31: 2 Dihedral angle restraints: 17245 sinusoidal: 8897 harmonic: 8348 Sorted by residual: dihedral pdb=" C5' ADP C 401 " pdb=" O5' ADP C 401 " pdb=" PA ADP C 401 " pdb=" O2A ADP C 401 " ideal model delta sinusoidal sigma weight residual -60.00 -169.96 109.97 1 2.00e+01 2.50e-03 3.22e+01 dihedral pdb=" CA ALA J 337 " pdb=" C ALA J 337 " pdb=" N LYS J 338 " pdb=" CA LYS J 338 " ideal model delta harmonic sigma weight residual 0.00 21.23 -21.23 0 5.00e+00 4.00e-02 1.80e+01 dihedral pdb=" CA ALA K 337 " pdb=" C ALA K 337 " pdb=" N LYS K 338 " pdb=" CA LYS K 338 " ideal model delta harmonic sigma weight residual 0.00 20.91 -20.91 0 5.00e+00 4.00e-02 1.75e+01 ... (remaining 17242 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.060: 3054 0.060 - 0.119: 374 0.119 - 0.179: 30 0.179 - 0.238: 1 0.238 - 0.298: 20 Chirality restraints: 3479 Sorted by residual: chirality pdb=" C2' ATP D 402 " pdb=" C1' ATP D 402 " pdb=" C3' ATP D 402 " pdb=" O2' ATP D 402 " both_signs ideal model delta sigma weight residual False -2.68 -2.98 0.30 2.00e-01 2.50e+01 2.21e+00 chirality pdb=" C2' ATP D 401 " pdb=" C1' ATP D 401 " pdb=" C3' ATP D 401 " pdb=" O2' ATP D 401 " both_signs ideal model delta sigma weight residual False -2.68 -2.98 0.30 2.00e-01 2.50e+01 2.20e+00 chirality pdb=" C3' ATP G 401 " pdb=" C2' ATP G 401 " pdb=" C4' ATP G 401 " pdb=" O3' ATP G 401 " both_signs ideal model delta sigma weight residual False -2.63 -2.92 0.28 2.00e-01 2.50e+01 2.03e+00 ... (remaining 3476 not shown) Planarity restraints: 5136 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LYS K 285 " -0.036 5.00e-02 4.00e+02 5.49e-02 4.83e+00 pdb=" N PRO K 286 " 0.095 5.00e-02 4.00e+02 pdb=" CA PRO K 286 " -0.028 5.00e-02 4.00e+02 pdb=" CD PRO K 286 " -0.030 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LYS J 285 " -0.034 5.00e-02 4.00e+02 5.20e-02 4.32e+00 pdb=" N PRO J 286 " 0.090 5.00e-02 4.00e+02 pdb=" CA PRO J 286 " -0.027 5.00e-02 4.00e+02 pdb=" CD PRO J 286 " -0.029 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C VAL G 82 " -0.025 5.00e-02 4.00e+02 3.77e-02 2.27e+00 pdb=" N PRO G 83 " 0.065 5.00e-02 4.00e+02 pdb=" CA PRO G 83 " -0.019 5.00e-02 4.00e+02 pdb=" CD PRO G 83 " -0.021 5.00e-02 4.00e+02 ... (remaining 5133 not shown) Histogram of nonbonded interaction distances: 1.51 - 2.13: 522 2.13 - 2.75: 45608 2.75 - 3.36: 78227 3.36 - 3.98: 107034 3.98 - 4.60: 169829 Nonbonded interactions: 401220 Sorted by model distance: nonbonded pdb=" CE LYS K 313 " pdb=" OE1 GLU K 324 " model vdw 1.511 3.100 nonbonded pdb=" HG1 THR D 84 " pdb=" OD1 ASP D 90 " model vdw 1.572 2.450 nonbonded pdb=" OG SER G 233 " pdb="HH22 ARG I 247 " model vdw 1.579 2.450 nonbonded pdb=" HG SER C 47 " pdb=" O ILE C 52 " model vdw 1.582 2.450 nonbonded pdb=" OE1 GLU D 104 " pdb=" HE ARG D 275 " model vdw 1.600 2.450 ... (remaining 401215 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 'G' and (resid 23 through 272 or resid 283 through 303 or resid 310 throu \ gh 336 or resid 403)) selection = (chain 'I' and ((resid 23 and (name N or name CA or name C or name O or name CB \ or name CG or name CD or name OE1 or name NE2)) or (resid 24 and (name N or name \ CA or name C or name O or name CB or name CG or name CD )) or (resid 25 and (na \ me N or name CA or name C or name O or name CB or name CG1 or name CG2 or name C \ D1)) or (resid 26 and (name N or name CA or name C or name O or name CB or name \ OG )) or (resid 27 and (name N or name CA or name C or name O or name CB or name \ CG or name CD or name NE or name CZ or name NH1 or name NH2)) or (resid 28 and \ (name N or name CA or name C or name O or name CB or name CG or name CD1 or name \ CD2)) or (resid 29 and (name N or name CA or name C or name O or name CB or nam \ e CG or name CD or name OE1 or name OE2)) or (resid 30 and (name N or name CA or \ name C or name O or name CB or name CG or name CD or name OE1 or name NE2)) or \ (resid 31 and (name N or name CA or name C or name O or name CB or name SG )) or \ (resid 32 and (name N or name CA or name C or name O )) or (resid 33 and (name \ N or name CA or name C or name O or name CB or name CG1 or name CG2 or name CD1) \ ) or (resid 34 and (name N or name CA or name C or name O or name CB or name CG \ or name OD1 or name ND2)) or (resid 35 and (name N or name CA or name C or name \ O or name CB )) or (resid 36 and (name N or name CA or name C or name O or name \ CB or name CG or name OD1 or name ND2)) or (resid 37 and (name N or name CA or n \ ame C or name O or name CB or name CG or name OD1 or name OD2)) or (resid 38 and \ (name N or name CA or name C or name O or name CB or name CG1 or name CG2)) or \ (resid 39 through 40 and (name N or name CA or name C or name O or name CB or na \ me CG or name CD or name CE or name NZ )) or (resid 41 and (name N or name CA or \ name C or name O or name CB or name CG or name CD1 or name CD2)) or (resid 42 t \ hrough 43 and (name N or name CA or name C or name O or name CB or name CG or na \ me CD or name OE1 or name OE2)) or (resid 44 and (name N or name CA or name C or \ name O or name CB )) or (resid 45 and (name N or name CA or name C or name O )) \ or (resid 46 and (name N or name CA or name C or name O or name CB or name CG o \ r name CD1 or name CD2 or name CE1 or name CE2 or name CZ )) or (resid 47 and (n \ ame N or name CA or name C or name O or name CB or name CG or name ND1 or name C \ D2 or name CE1 or name NE2)) or (resid 48 and (name N or name CA or name C or na \ me O or name CB or name OG1 or name CG2)) or (resid 49 and (name N or name CA or \ name C or name O or name CB or name CG1 or name CG2)) or (resid 50 and (name N \ or name CA or name C or name O or name CB or name CG or name CD or name OE1 or n \ ame OE2)) or (resid 51 and (name N or name CA or name C or name O or name CB )) \ or (resid 52 and (name N or name CA or name C or name O or name CB or name CG1 o \ r name CG2)) or (resid 53 and (name N or name CA or name C or name O or name CB \ )) or (resid 54 and (name N or name CA or name C or name O or name CB or name CG \ or name CD1 or name CD2 or name CE1 or name CE2 or name CZ or name OH )) or (re \ sid 55 and (name N or name CA or name C or name O or name CB )) or (resid 56 and \ (name N or name CA or name C or name O or name CB or name CG or name CD )) or ( \ resid 57 through 58 and (name N or name CA or name C or name O or name CB or nam \ e CG or name CD or name CE or name NZ )) or (resid 59 and (name N or name CA or \ name C or name O or name CB or name CG or name CD or name OE1 or name OE2)) or ( \ resid 60 and (name N or name CA or name C or name O or name CB or name CG or nam \ e CD1 or name CD2)) or (resid 61 and (name N or name CA or name C or name O or n \ ame CB or name CG1 or name CG2 or name CD1)) or (resid 62 and (name N or name CA \ or name C or name O or name CB or name CG or name OD1 or name ND2)) or (resid 6 \ 3 and (name N or name CA or name C or name O or name CB or name CG1 or name CG2 \ or name CD1)) or (resid 64 and (name N or name CA or name C or name O or name CB \ or name CG or name CD or name CE or name NZ )) or (resid 65 and (name N or name \ CA or name C or name O )) or (resid 66 and (name N or name CA or name C or name \ O or name CB or name CG1 or name CG2 or name CD1)) or (resid 67 and (name N or \ name CA or name C or name O or name CB or name OG )) or (resid 68 and (name N or \ name CA or name C or name O or name CB or name CG or name CD or name OE1 or nam \ e OE2)) or (resid 69 and (name N or name CA or name C or name O or name CB )) or \ (resid 70 and (name N or name CA or name C or name O or name CB or name CG or n \ ame CD or name CE or name NZ )) or (resid 71 and (name N or name CA or name C or \ name O or name CB )) or (resid 72 and (name N or name CA or name C or name O or \ name CB or name CG or name OD1 or name OD2)) or (resid 73 and (name N or name C \ A or name C or name O or name CB or name CG or name CD or name CE or name NZ )) \ or (resid 74 and (name N or name CA or name C or name O or name CB or name CG1 o \ r name CG2 or name CD1)) or (resid 75 and (name N or name CA or name C or name O \ or name CB or name CG or name CD1 or name CD2)) or (resid 76 and (name N or nam \ e CA or name C or name O or name CB )) or (resid 77 and (name N or name CA or na \ me C or name O or name CB or name CG or name CD or name OE1 or name OE2)) or (re \ sid 78 through 79 and (name N or name CA or name C or name O or name CB )) or (r \ esid 80 and (name N or name CA or name C or name O or name CB or name CG or name \ CD or name CE or name NZ )) or (resid 81 and (name N or name CA or name C or na \ me O or name CB or name CG or name CD1 or name CD2)) or (resid 82 and (name N or \ name CA or name C or name O or name CB or name CG1 or name CG2)) or (resid 83 a \ nd (name N or name CA or name C or name O or name CB or name CG or name CD )) or \ (resid 84 and (name N or name CA or name C or name O or name CB or name CG or n \ ame SD or name CE )) or (resid 85 and (name N or name CA or name C or name O )) \ or (resid 86 and (name N or name CA or name C or name O or name CB or name CG or \ name CD1 or name CD2 or name CE1 or name CE2 or name CZ )) or (resid 87 through \ 88 and (name N or name CA or name C or name O or name CB or name OG1 or name CG \ 2)) or (resid 89 and (name N or name CA or name C or name O or name CB )) or (re \ sid 90 and (name N or name CA or name C or name O or name CB or name OG1 or name \ CG2)) or (resid 91 and (name N or name CA or name C or name O or name CB or nam \ e CG or name CD or name OE1 or name OE2)) or (resid 92 and (name N or name CA or \ name C or name O or name CB or name CG or name CD1 or name CD2 or name CE1 or n \ ame CE2 or name CZ )) or (resid 93 and (name N or name CA or name C or name O or \ name CB or name CG or name ND1 or name CD2 or name CE1 or name NE2)) or (resid \ 94 and (name N or name CA or name C or name O or name CB or name CG or name CD o \ r name OE1 or name NE2)) or (resid 95 through 96 and (name N or name CA or name \ C or name O or name CB or name CG or name CD or name NE or name CZ or name NH1 o \ r name NH2)) or (resid 97 and (name N or name CA or name C or name O or name CB \ or name OG )) or (resid 98 and (name N or name CA or name C or name O or name CB \ or name CG or name CD or name OE1 or name OE2)) or (resid 99 through 100 and (n \ ame N or name CA or name C or name O or name CB or name CG1 or name CG2 or name \ CD1)) or (resid 101 and (name N or name CA or name C or name O or name CB or nam \ e CG or name CD or name OE1 or name NE2)) or (resid 102 and (name N or name CA o \ r name C or name O or name CB or name CG1 or name CG2 or name CD1)) or (resid 10 \ 3 through 104 and (name N or name CA or name C or name O or name CB or name OG1 \ or name CG2)) or (resid 105 and (name N or name CA or name C or name O )) or (re \ sid 106 and (name N or name CA or name C or name O or name CB or name OG )) or ( \ resid 107 and (name N or name CA or name C or name O or name CB or name CG or na \ me CD or name CE or name NZ )) or (resid 108 and (name N or name CA or name C or \ name O or name CB or name CG or name CD or name OE1 or name OE2)) or (resid 109 \ and (name N or name CA or name C or name O or name CB or name CG or name CD1 or \ name CD2)) or (resid 110 and (name N or name CA or name C or name O or name CB \ or name CG or name OD1 or name OD2)) or (resid 111 and (name N or name CA or nam \ e C or name O or name CB or name CG or name CD or name CE or name NZ )) or (resi \ d 112 through 113 and (name N or name CA or name C or name O or name CB or name \ CG or name CD1 or name CD2)) or (resid 114 and (name N or name CA or name C or n \ ame O or name CB or name CG or name CD or name OE1 or name NE2)) or (resid 115 t \ hrough 116 and (name N or name CA or name C or name O )) or (resid 117 and (name \ N or name CA or name C or name O or name CB or name CG1 or name CG2 or name CD1 \ )) or (resid 118 and (name N or name CA or name C or name O or name CB or name C \ G or name CD or name OE1 or name OE2)) or (resid 119 and (name N or name CA or n \ ame C or name O or name CB or name OG1 or name CG2)) or (resid 120 and (name N o \ r name CA or name C or name O )) or (resid 121 and (name N or name CA or name C \ or name O or name CB or name OG )) or (resid 122 and (name N or name CA or name \ C or name O or name CB or name CG1 or name CG2 or name CD1)) or (resid 123 and ( \ name N or name CA or name C or name O or name CB or name OG1 or name CG2)) or (r \ esid 124 and (name N or name CA or name C or name O or name CB or name CG or nam \ e CD or name OE1 or name OE2)) or (resid 125 and (name N or name CA or name C or \ name O or name CB or name CG or name SD or name CE )) or (resid 126 and (name N \ or name CA or name C or name O or name CB or name CG or name CD1 or name CD2 or \ name CE1 or name CE2 or name CZ )) or (resid 127 and (name N or name CA or name \ C or name O )) or (resid 128 and (name N or name CA or name C or name O or name \ CB or name CG or name CD or name OE1 or name OE2)) or (resid 129 and (name N or \ name CA or name C or name O or name CB or name CG or name CD1 or name CD2 or na \ me CE1 or name CE2 or name CZ )) or (resid 130 and (name N or name CA or name C \ or name O or name CB or name CG or name CD or name NE or name CZ or name NH1 or \ name NH2)) or (resid 131 and (name N or name CA or name C or name O or name CB o \ r name OG1 or name CG2)) or (resid 132 and (name N or name CA or name C or name \ O )) or (resid 133 and (name N or name CA or name C or name O or name CB or name \ CG or name CD or name CE or name NZ )) or (resid 134 and (name N or name CA or \ name C or name O or name CB or name OG1 or name CG2)) or (resid 135 and (name N \ or name CA or name C or name O or name CB or name CG or name CD or name OE1 or n \ ame NE2)) or (resid 136 and (name N or name CA or name C or name O or name CB or \ name CG1 or name CG2 or name CD1)) or (resid 137 and (name N or name CA or name \ C or name O or name CB or name SG )) or (resid 138 and (name N or name CA or na \ me C or name O or name CB or name CG or name ND1 or name CD2 or name CE1 or name \ NE2)) or (resid 139 and (name N or name CA or name C or name O or name CB or na \ me OG1 or name CG2)) or (resid 140 and (name N or name CA or name C or name O or \ name CB or name CG or name CD1 or name CD2)) or (resid 141 and (name N or name \ CA or name C or name O or name CB )) or (resid 142 and (name N or name CA or nam \ e C or name O or name CB or name CG1 or name CG2)) or (resid 143 and (name N or \ name CA or name C or name O or name CB or name OG1 or name CG2)) or (resid 144 a \ nd (name N or name CA or name C or name O or name CB or name SG )) or (resid 145 \ and (name N or name CA or name C or name O or name CB or name CG or name CD or \ name OE1 or name NE2)) or (resid 146 and (name N or name CA or name C or name O \ or name CB or name CG or name CD1 or name CD2)) or (resid 147 and (name N or nam \ e CA or name C or name O or name CB or name CG or name CD )) or (resid 148 and ( \ name N or name CA or name C or name O or name CB or name CG1 or name CG2 or name \ CD1)) or (resid 149 and (name N or name CA or name C or name O or name CB or na \ me CG or name OD1 or name OD2)) or (resid 150 and (name N or name CA or name C o \ r name O or name CB or name CG or name CD or name NE or name CZ or name NH1 or n \ ame NH2)) or (resid 151 through 153 and (name N or name CA or name C or name O ) \ ) or (resid 154 and (name N or name CA or name C or name O or name CB or name CG \ or name CD or name OE1 or name OE2)) or (resid 155 and (name N or name CA or na \ me C or name O )) or (resid 156 and (name N or name CA or name C or name O or na \ me CB or name CG or name CD or name CE or name NZ )) or (resid 157 and (name N o \ r name CA or name C or name O or name CB )) or (resid 158 and (name N or name CA \ or name C or name O or name CB or name CG or name SD or name CE )) or (resid 15 \ 9 and (name N or name CA or name C or name O or name CB or name CG or name CD1 o \ r name CD2 or name CE1 or name CE2 or name CZ or name OH )) or (resid 160 and (n \ ame N or name CA or name C or name O or name CB or name CG1 or name CG2 or name \ CD1)) or (resid 161 and (name N or name CA or name C or name O or name CB or nam \ e CG or name OD1 or name OD2)) or (resid 162 and (name N or name CA or name C or \ name O or name CB or name OG1 or name CG2)) or (resid 163 and (name N or name C \ A or name C or name O or name CB or name CG or name CD or name OE1 or name OE2)) \ or (resid 164 and (name N or name CA or name C or name O )) or (resid 165 and ( \ name N or name CA or name C or name O or name CB or name OG1 or name CG2)) or (r \ esid 166 and (name N or name CA or name C or name O or name CB or name CG or nam \ e CD1 or name CD2 or name CE1 or name CE2 or name CZ )) or (resid 167 and (name \ N or name CA or name C or name O or name CB or name CG or name CD or name NE or \ name CZ or name NH1 or name NH2)) or (resid 168 and (name N or name CA or name C \ or name O or name CB or name CG or name CD )) or (resid 169 and (name N or name \ CA or name C or name O or name CB or name CG or name CD or name OE1 or name OE2 \ )) or (resid 170 and (name N or name CA or name C or name O or name CB or name C \ G or name CD or name NE or name CZ or name NH1 or name NH2)) or (resid 171 throu \ gh 172 and (name N or name CA or name C or name O or name CB or name CG or name \ CD1 or name CD2)) or (resid 173 and (name N or name CA or name C or name O or na \ me CB )) or (resid 174 and (name N or name CA or name C or name O or name CB or \ name CG1 or name CG2)) or (resid 175 and (name N or name CA or name C or name O \ or name CB )) or (resid 176 and (name N or name CA or name C or name O or name C \ B or name CG or name CD or name OE1 or name OE2)) or (resid 177 and (name N or n \ ame CA or name C or name O or name CB or name CG or name CD or name NE or name C \ Z or name NH1 or name NH2)) or (resid 178 and (name N or name CA or name C or na \ me O or name CB or name CG or name CD1 or name CD2 or name CE1 or name CE2 or na \ me CZ or name OH )) or (resid 179 and (name N or name CA or name C or name O )) \ or (resid 180 and (name N or name CA or name C or name O or name CB or name CG o \ r name CD1 or name CD2)) or (resid 181 and (name N or name CA or name C or name \ O or name CB or name OG )) or (resid 182 and (name N or name CA or name C or nam \ e O )) or (resid 183 and (name N or name CA or name C or name O or name CB or na \ me OG )) or (resid 184 and (name N or name CA or name C or name O or name CB or \ name CG or name OD1 or name OD2)) or (resid 185 and (name N or name CA or name C \ or name O or name CB or name CG1 or name CG2)) or (resid 186 and (name N or nam \ e CA or name C or name O or name CB or name CG or name CD1 or name CD2)) or (res \ id 187 and (name N or name CA or name C or name O or name CB or name CG or name \ OD1 or name OD2)) or (resid 188 and (name N or name CA or name C or name O or na \ me CB or name CG or name OD1 or name ND2)) or (resid 189 and (name N or name CA \ or name C or name O or name CB or name CG1 or name CG2)) or (resid 190 and (name \ N or name CA or name C or name O or name CB )) or (resid 191 and (name N or nam \ e CA or name C or name O or name CB or name CG or name CD1 or name CD2 or name C \ E1 or name CE2 or name CZ or name OH )) or (resid 192 and (name N or name CA or \ name C or name O or name CB )) or (resid 193 and (name N or name CA or name C or \ name O or name CB or name CG or name CD or name NE or name CZ or name NH1 or na \ me NH2)) or (resid 194 and (name N or name CA or name C or name O or name CB )) \ or (resid 195 and (name N or name CA or name C or name O or name CB or name CG o \ r name CD1 or name CD2 or name CE1 or name CE2 or name CZ )) or (resid 196 and ( \ name N or name CA or name C or name O or name CB or name CG or name OD1 or name \ ND2)) or (resid 197 and (name N or name CA or name C or name O or name CB or nam \ e OG1 or name CG2)) or (resid 198 and (name N or name CA or name C or name O or \ name CB or name CG or name OD1 or name OD2)) or (resid 199 and (name N or name C \ A or name C or name O or name CB or name CG or name ND1 or name CD2 or name CE1 \ or name NE2)) or (resid 200 and (name N or name CA or name C or name O or name C \ B or name CG or name CD or name OE1 or name NE2)) or (resid 201 and (name N or n \ ame CA or name C or name O or name CB or name OG1 or name CG2)) or (resid 202 an \ d (name N or name CA or name C or name O or name CB or name CG or name CD or nam \ e OE1 or name NE2)) or (resid 203 through 204 and (name N or name CA or name C o \ r name O or name CB or name CG or name CD1 or name CD2)) or (resid 205 and (name \ N or name CA or name C or name O or name CB or name CG or name CD1 or name CD2 \ or name CE1 or name CE2 or name CZ or name OH )) or (resid 206 and (name N or na \ me CA or name C or name O or name CB or name CG or name CD or name OE1 or name N \ E2)) or (resid 207 and (name N or name CA or name C or name O or name CB )) or ( \ resid 208 and (name N or name CA or name C or name O or name CB or name OG )) or \ (resid 209 and (name N or name CA or name C or name O or name CB )) or (resid 2 \ 10 through 211 and (name N or name CA or name C or name O or name CB or name CG \ or name SD or name CE )) or (resid 212 and (name N or name CA or name C or name \ O or name CB or name CG1 or name CG2)) or (resid 213 and (name N or name CA or n \ ame C or name O or name CB or name CG or name CD or name OE1 or name OE2)) or (r \ esid 214 and (name N or name CA or name C or name O or name CB or name OG )) or \ (resid 215 and (name N or name CA or name C or name O or name CB or name CG or n \ ame CD or name NE or name CZ or name NH1 or name NH2)) or (resid 216 and (name N \ or name CA or name C or name O or name CB or name CG or name CD1 or name CD2 or \ name CE1 or name CE2 or name CZ or name OH )) or (resid 217 and (name N or name \ CA or name C or name O or name CB )) or (resid 218 through 219 and (name N or n \ ame CA or name C or name O or name CB or name CG or name CD1 or name CD2)) or (r \ esid 220 and (name N or name CA or name C or name O or name CB or name CG1 or na \ me CG2 or name CD1)) or (resid 221 and (name N or name CA or name C or name O or \ name CB or name CG1 or name CG2)) or (resid 222 and (name N or name CA or name \ C or name O or name CB or name CG or name OD1 or name OD2)) or (resid 223 and (n \ ame N or name CA or name C or name O or name CB or name OG )) or (resid 224 and \ (name N or name CA or name C or name O or name CB )) or (resid 225 and (name N o \ r name CA or name C or name O or name CB or name OG1 or name CG2)) or (resid 226 \ and (name N or name CA or name C or name O or name CB )) or (resid 227 and (nam \ e N or name CA or name C or name O or name CB or name CG or name CD1 or name CD2 \ )) or (resid 228 and (name N or name CA or name C or name O or name CB or name C \ G or name CD1 or name CD2 or name CE1 or name CE2 or name CZ or name OH )) or (r \ esid 229 and (name N or name CA or name C or name O or name CB or name CG or nam \ e CD or name NE or name CZ or name NH1 or name NH2)) or resid 230 through 237 or \ (resid 238 and (name N or name CA or name C or name O or name CB or name CG or \ name CD1 or name CD2)) or (resid 239 and (name N or name CA or name C or name O \ or name CB or name OG )) or (resid 240 and (name N or name CA or name C or name \ O or name CB )) or (resid 241 and (name N or name CA or name C or name O or name \ CB or name CG or name CD or name NE or name CZ or name NH1 or name NH2)) or (re \ sid 242 and (name N or name CA or name C or name O or name CB or name CG or name \ CD or name OE1 or name NE2)) or (resid 243 and (name N or name CA or name C or \ name O or name CB or name CG or name SD or name CE )) or (resid 244 and (name N \ or name CA or name C or name O or name CB or name CG or name ND1 or name CD2 or \ name CE1 or name NE2)) or (resid 245 and (name N or name CA or name C or name O \ or name CB or name CG or name CD1 or name CD2)) or (resid 246 and (name N or nam \ e CA or name C or name O or name CB )) or (resid 247 and (name N or name CA or n \ ame C or name O or name CB or name CG or name CD or name NE or name CZ or name N \ H1 or name NH2)) or (resid 248 and (name N or name CA or name C or name O or nam \ e CB or name CG or name CD1 or name CD2 or name CE1 or name CE2 or name CZ )) or \ (resid 249 and (name N or name CA or name C or name O or name CB or name CG or \ name CD1 or name CD2)) or (resid 250 and (name N or name CA or name C or name O \ or name CB or name CG or name CD or name NE or name CZ or name NH1 or name NH2)) \ or (resid 251 and (name N or name CA or name C or name O or name CB or name CG \ or name SD or name CE )) or (resid 252 through 253 and (name N or name CA or nam \ e C or name O or name CB or name CG or name CD1 or name CD2)) or (resid 254 and \ (name N or name CA or name C or name O or name CB or name CG or name CD or name \ NE or name CZ or name NH1 or name NH2)) or (resid 255 and (name N or name CA or \ name C or name O or name CB or name CG or name CD1 or name CD2)) or (resid 256 a \ nd (name N or name CA or name C or name O or name CB )) or (resid 257 and (name \ N or name CA or name C or name O or name CB or name CG or name OD1 or name OD2)) \ or (resid 258 and (name N or name CA or name C or name O or name CB or name CG \ or name CD or name OE1 or name OE2)) or (resid 259 and (name N or name CA or nam \ e C or name O or name CB or name CG or name CD1 or name CD2 or name CE1 or name \ CE2 or name CZ )) or (resid 260 and (name N or name CA or name C or name O )) or \ (resid 261 and (name N or name CA or name C or name O or name CB or name CG1 or \ name CG2)) or (resid 262 and (name N or name CA or name C or name O or name CB \ )) or (resid 263 through 264 and (name N or name CA or name C or name O or name \ CB or name CG1 or name CG2)) or (resid 265 and (name N or name CA or name C or n \ ame O or name CB or name CG1 or name CG2 or name CD1)) or (resid 266 and (name N \ or name CA or name C or name O or name CB or name OG1 or name CG2)) or (resid 2 \ 67 and (name N or name CA or name C or name O or name CB or name CG or name OD1 \ or name ND2)) or (resid 268 and (name N or name CA or name C or name O or name C \ B or name CG or name CD or name OE1 or name NE2)) or resid 269 through 272 or re \ sid 283 through 286 or (resid 287 and (name N or name CA or name C or name O or \ name CB or name CG1 or name CG2 or name CD1)) or (resid 288 through 289 and (nam \ e N or name CA or name C or name O )) or (resid 290 and (name N or name CA or na \ me C or name O or name CB or name CG or name OD1 or name ND2)) or (resid 291 thr \ ough 292 and (name N or name CA or name C or name O or name CB or name CG1 or na \ me CG2 or name CD1)) or (resid 293 and (name N or name CA or name C or name O or \ name CB )) or (resid 294 and (name N or name CA or name C or name O or name CB \ or name CG or name ND1 or name CD2 or name CE1 or name NE2)) or (resid 295 and ( \ name N or name CA or name C or name O or name CB )) or (resid 296 and (name N or \ name CA or name C or name O or name CB or name OG )) or (resid 297 through 298 \ and (name N or name CA or name C or name O or name CB or name OG1 or name CG2)) \ or (resid 299 and (name N or name CA or name C or name O or name CB or name CG o \ r name CD or name NE or name CZ or name NH1 or name NH2)) or (resid 300 and (nam \ e N or name CA or name C or name O or name CB or name CG or name CD1 or name CD2 \ )) or (resid 301 and (name N or name CA or name C or name O or name CB or name C \ G or name CD1 or name CD2 or name CE1 or name CE2 or name CZ or name OH )) or (r \ esid 302 and (name N or name CA or name C or name O or name CB or name CG or nam \ e CD1 or name CD2)) or (resid 303 through 310 and (name N or name CA or name C o \ r name O or name CB or name CG or name CD or name NE or name CZ or name NH1 or n \ ame NH2)) or (resid 311 and (name N or name CA or name C or name O or name CB or \ name CG1 or name CG2 or name CD1)) or (resid 312 and (name N or name CA or name \ C or name O or name CB or name SG )) or (resid 313 and (name N or name CA or na \ me C or name O or name CB or name CG or name CD or name CE or name NZ )) or (res \ id 314 and (name N or name CA or name C or name O or name CB or name CG1 or name \ CG2 or name CD1)) or (resid 315 and (name N or name CA or name C or name O or n \ ame CB or name CG or name CD1 or name CD2 or name CE1 or name CE2 or name CZ or \ name OH )) or (resid 316 and (name N or name CA or name C or name O or name CB o \ r name CG or name OD1 or name OD2)) or (resid 317 and (name N or name CA or name \ C or name O or name CB or name OG )) or (resid 318 and (name N or name CA or na \ me C or name O or name CB or name CG or name CD )) or (resid 319 and (name N or \ name CA or name C or name O or name CB or name SG )) or (resid 320 and (name N o \ r name CA or name C or name O or name CB or name CG or name CD1 or name CD2)) or \ (resid 321 and (name N or name CA or name C or name O or name CB or name CG or \ name CD )) or (resid 322 and (name N or name CA or name C or name O or name CB o \ r name CG or name CD or name OE1 or name OE2)) or (resid 323 and (name N or name \ CA or name C or name O or name CB )) or (resid 324 and (name N or name CA or na \ me C or name O or name CB or name CG or name CD or name OE1 or name OE2)) or (re \ sid 325 and (name N or name CA or name C or name O or name CB )) or (resid 326 a \ nd (name N or name CA or name C or name O or name CB or name CG or name SD or na \ me CE )) or (resid 327 and (name N or name CA or name C or name O or name CB or \ name CG or name CD1 or name CD2 or name CE1 or name CE2 or name CZ )) or (resid \ 328 and (name N or name CA or name C or name O or name CB )) or (resid 329 and ( \ name N or name CA or name C or name O or name CB or name CG1 or name CG2 or name \ CD1)) or (resid 330 and (name N or name CA or name C or name O or name CB or na \ me CG or name OD1 or name ND2)) or (resid 331 and (name N or name CA or name C o \ r name O or name CB )) or (resid 332 and (name N or name CA or name C or name O \ or name CB or name CG or name OD1 or name OD2)) or (resid 333 and (name N or nam \ e CA or name C or name O )) or (resid 334 and (name N or name CA or name C or na \ me O or name CB or name CG1 or name CG2)) or (resid 335 and (name N or name CA o \ r name C or name O )) or (resid 336 and (name N or name CA or name C or name O o \ r name CB or name CG or name OD1 or name OD2)) or resid 402)) selection = (chain 'J' and (resid 23 through 272 or resid 283 through 303 or resid 310 throu \ gh 336 or resid 403)) selection = (chain 'K' and (resid 23 through 272 or resid 283 through 303 or resid 310 throu \ gh 336 or resid 404)) selection = (chain 'L' and (resid 23 through 303 or resid 310 through 336 or resid 401)) } 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: 8.960 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: 0.250 Extract box with map and model: 0.510 Check model and map are aligned: 0.110 Set scattering table: 0.090 Process input model: 33.960 Find NCS groups from input model: 0.560 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:8.210 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 52.710 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8072 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.145 22133 Z= 0.199 Angle : 0.519 7.733 30029 Z= 0.281 Chirality : 0.044 0.298 3479 Planarity : 0.003 0.055 3733 Dihedral : 12.445 137.312 8475 Min Nonbonded Distance : 1.511 Molprobity Statistics. All-atom Clashscore : 17.66 Ramachandran Plot: Outliers : 0.11 % Allowed : 2.92 % Favored : 96.97 % Rotamer: Outliers : 1.11 % Allowed : 3.64 % Favored : 95.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.46 % 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: 1.34 (0.17), residues: 2673 helix: 2.12 (0.15), residues: 1265 sheet: -0.14 (0.24), residues: 470 loop : -0.19 (0.21), residues: 938 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG G 130 TYR 0.016 0.001 TYR K 315 PHE 0.014 0.001 PHE G 129 TRP 0.004 0.001 TRP X 231 HIS 0.003 0.001 HIS R 79 Details of bonding type rmsd covalent geometry : bond 0.00336 (22129) covalent geometry : angle 0.51872 (30029) hydrogen bonds : bond 0.13905 ( 1130) hydrogen bonds : angle 5.86005 ( 3189) Misc. bond : bond 0.08669 ( 4) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5346 Ramachandran restraints generated. 2673 Oldfield, 0 Emsley, 2673 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5346 Ramachandran restraints generated. 2673 Oldfield, 0 Emsley, 2673 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 447 residues out of total 2251 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 422 time to evaluate : 1.049 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 95 HIS cc_start: 0.8044 (m-70) cc_final: 0.7778 (m90) REVERT: C 165 MET cc_start: 0.9054 (mmt) cc_final: 0.8424 (mmt) REVERT: C 321 GLN cc_start: 0.8490 (mt0) cc_final: 0.8271 (mm110) REVERT: D 15 GLU cc_start: 0.8643 (mt-10) cc_final: 0.8351 (pm20) REVERT: D 21 ARG cc_start: 0.8125 (mtt180) cc_final: 0.7819 (tpm170) REVERT: D 24 ARG cc_start: 0.7856 (mtt180) cc_final: 0.7511 (mtt90) REVERT: D 26 LYS cc_start: 0.8514 (mttt) cc_final: 0.7957 (mmmm) REVERT: D 98 TYR cc_start: 0.7492 (m-80) cc_final: 0.7157 (m-80) REVERT: D 279 ASP cc_start: 0.7584 (t0) cc_final: 0.7204 (p0) REVERT: D 308 MET cc_start: 0.5136 (mtm) cc_final: 0.4733 (ptp) REVERT: I 62 ASN cc_start: 0.8179 (m-40) cc_final: 0.7951 (t0) REVERT: I 72 ASP cc_start: 0.8323 (m-30) cc_final: 0.8113 (m-30) REVERT: J 243 MET cc_start: 0.8906 (mtt) cc_final: 0.8558 (mmm) REVERT: J 315 TYR cc_start: 0.7618 (OUTLIER) cc_final: 0.5669 (m-80) REVERT: L 147 PRO cc_start: 0.8827 (Cg_exo) cc_final: 0.8627 (Cg_endo) REVERT: L 202 GLN cc_start: 0.8146 (mt0) cc_final: 0.7912 (mm110) REVERT: L 210 MET cc_start: 0.7821 (mtp) cc_final: 0.7524 (mtt) REVERT: L 315 TYR cc_start: 0.6900 (OUTLIER) cc_final: 0.6004 (m-80) REVERT: R 25 LYS cc_start: 0.7860 (mttt) cc_final: 0.7588 (tmtt) REVERT: R 41 LEU cc_start: 0.8380 (mt) cc_final: 0.8142 (mt) REVERT: R 44 PRO cc_start: 0.8052 (Cg_exo) cc_final: 0.7787 (Cg_endo) REVERT: R 182 GLU cc_start: 0.7776 (tp30) cc_final: 0.7548 (mp0) REVERT: R 263 MET cc_start: 0.7465 (mmm) cc_final: 0.6848 (ttt) REVERT: X 156 TRP cc_start: 0.6877 (m100) cc_final: 0.5960 (m100) outliers start: 25 outliers final: 7 residues processed: 439 average time/residue: 1.5516 time to fit residues: 748.9854 Evaluate side-chains 244 residues out of total 2251 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 235 time to evaluate : 1.104 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 228 ASP Chi-restraints excluded: chain C residue 251 ASP Chi-restraints excluded: chain G residue 287 ILE Chi-restraints excluded: chain I residue 269 VAL Chi-restraints excluded: chain I residue 287 ILE Chi-restraints excluded: chain J residue 315 TYR Chi-restraints excluded: chain L residue 142 VAL Chi-restraints excluded: chain L residue 187 ASP Chi-restraints excluded: chain L residue 315 TYR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 269 random chunks: chunk 197 optimal weight: 6.9990 chunk 215 optimal weight: 0.0370 chunk 20 optimal weight: 0.4980 chunk 132 optimal weight: 2.9990 chunk 261 optimal weight: 9.9990 chunk 248 optimal weight: 0.9990 chunk 207 optimal weight: 0.7980 chunk 155 optimal weight: 0.3980 chunk 244 optimal weight: 1.9990 chunk 183 optimal weight: 1.9990 chunk 111 optimal weight: 0.8980 overall best weight: 0.5258 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 181 GLN C 233 HIS C 267 GLN D 123 ASN G 62 ASN G 94 GLN G 244 HIS ** G 272 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 290 ASN J 30 GLN J 62 ASN J 138 HIS J 200 GLN K 93 HIS K 94 GLN K 138 HIS K 200 GLN K 206 GLN L 30 GLN L 138 HIS ** L 145 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 200 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 158 GLN R 195 ASN ** X 47 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** X 251 ASN Total number of N/Q/H flips: 22 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3961 r_free = 0.3961 target = 0.130881 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 69)----------------| | r_work = 0.3311 r_free = 0.3311 target = 0.083125 restraints weight = 82347.481| |-----------------------------------------------------------------------------| r_work (start): 0.3201 rms_B_bonded: 2.80 r_work: 0.3061 rms_B_bonded: 2.98 restraints_weight: 0.5000 r_work: 0.2941 rms_B_bonded: 4.72 restraints_weight: 0.2500 r_work (final): 0.2941 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7907 moved from start: 0.2351 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 22133 Z= 0.119 Angle : 0.480 5.989 30029 Z= 0.258 Chirality : 0.039 0.147 3479 Planarity : 0.004 0.103 3733 Dihedral : 12.876 138.139 3462 Min Nonbonded Distance : 2.108 Molprobity Statistics. All-atom Clashscore : 15.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.03 % Favored : 96.97 % Rotamer: Outliers : 1.51 % Allowed : 11.51 % Favored : 86.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.46 % 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: 1.29 (0.17), residues: 2673 helix: 2.05 (0.15), residues: 1309 sheet: -0.27 (0.24), residues: 458 loop : -0.22 (0.22), residues: 906 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.018 0.000 ARG G 170 TYR 0.011 0.001 TYR K 315 PHE 0.012 0.001 PHE X 270 TRP 0.006 0.001 TRP D 268 HIS 0.007 0.001 HIS C 187 Details of bonding type rmsd covalent geometry : bond 0.00251 (22129) covalent geometry : angle 0.47980 (30029) hydrogen bonds : bond 0.03705 ( 1130) hydrogen bonds : angle 4.70031 ( 3189) Misc. bond : bond 0.00727 ( 4) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5346 Ramachandran restraints generated. 2673 Oldfield, 0 Emsley, 2673 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5346 Ramachandran restraints generated. 2673 Oldfield, 0 Emsley, 2673 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 287 residues out of total 2251 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 253 time to evaluate : 1.027 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 95 HIS cc_start: 0.8331 (m-70) cc_final: 0.8008 (m90) REVERT: C 321 GLN cc_start: 0.8415 (mt0) cc_final: 0.7946 (mm110) REVERT: D 15 GLU cc_start: 0.8848 (mt-10) cc_final: 0.8413 (pm20) REVERT: D 26 LYS cc_start: 0.8452 (mttt) cc_final: 0.8220 (mttp) REVERT: D 98 TYR cc_start: 0.7552 (m-80) cc_final: 0.7187 (m-80) REVERT: D 279 ASP cc_start: 0.7827 (t0) cc_final: 0.7040 (p0) REVERT: D 308 MET cc_start: 0.5099 (mtm) cc_final: 0.4638 (ptp) REVERT: G 130 ARG cc_start: 0.8318 (OUTLIER) cc_final: 0.7640 (ptt180) REVERT: J 30 GLN cc_start: 0.8519 (mt0) cc_final: 0.8117 (pp30) REVERT: J 243 MET cc_start: 0.8928 (mtt) cc_final: 0.8364 (mmm) REVERT: J 315 TYR cc_start: 0.7620 (OUTLIER) cc_final: 0.5581 (m-80) REVERT: K 315 TYR cc_start: 0.7105 (OUTLIER) cc_final: 0.6229 (m-80) REVERT: L 147 PRO cc_start: 0.8685 (Cg_exo) cc_final: 0.8471 (Cg_endo) REVERT: L 315 TYR cc_start: 0.7021 (OUTLIER) cc_final: 0.6300 (m-80) REVERT: R 25 LYS cc_start: 0.7598 (mttt) cc_final: 0.7294 (tmtt) REVERT: R 182 GLU cc_start: 0.8082 (tp30) cc_final: 0.7335 (mp0) REVERT: R 197 LYS cc_start: 0.8411 (mttt) cc_final: 0.8021 (mmmt) REVERT: R 263 MET cc_start: 0.7374 (mmm) cc_final: 0.7035 (ttm) outliers start: 34 outliers final: 11 residues processed: 272 average time/residue: 1.2150 time to fit residues: 373.1094 Evaluate side-chains 223 residues out of total 2251 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 208 time to evaluate : 1.056 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 124 CYS Chi-restraints excluded: chain G residue 87 THR Chi-restraints excluded: chain G residue 99 ILE Chi-restraints excluded: chain G residue 130 ARG Chi-restraints excluded: chain G residue 287 ILE Chi-restraints excluded: chain I residue 269 VAL Chi-restraints excluded: chain I residue 287 ILE Chi-restraints excluded: chain J residue 223 SER Chi-restraints excluded: chain J residue 315 TYR Chi-restraints excluded: chain K residue 315 TYR Chi-restraints excluded: chain K residue 326 MET Chi-restraints excluded: chain L residue 218 LEU Chi-restraints excluded: chain L residue 223 SER Chi-restraints excluded: chain L residue 315 TYR Chi-restraints excluded: chain R residue 27 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 269 random chunks: chunk 230 optimal weight: 3.9990 chunk 257 optimal weight: 7.9990 chunk 167 optimal weight: 3.9990 chunk 176 optimal weight: 3.9990 chunk 231 optimal weight: 1.9990 chunk 117 optimal weight: 0.9980 chunk 227 optimal weight: 1.9990 chunk 118 optimal weight: 0.5980 chunk 179 optimal weight: 2.9990 chunk 21 optimal weight: 2.9990 chunk 139 optimal weight: 3.9990 overall best weight: 1.7186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 340 GLN G 94 GLN ** G 272 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 62 ASN J 200 GLN K 206 GLN L 93 HIS ** L 200 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 202 GLN L 268 GLN ** X 251 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3904 r_free = 0.3904 target = 0.126714 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3224 r_free = 0.3224 target = 0.078418 restraints weight = 82204.318| |-----------------------------------------------------------------------------| r_work (start): 0.3112 rms_B_bonded: 2.77 r_work: 0.2970 rms_B_bonded: 2.94 restraints_weight: 0.5000 r_work: 0.2851 rms_B_bonded: 4.63 restraints_weight: 0.2500 r_work (final): 0.2851 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7995 moved from start: 0.2960 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.044 22133 Z= 0.235 Angle : 0.544 6.550 30029 Z= 0.290 Chirality : 0.041 0.155 3479 Planarity : 0.004 0.091 3733 Dihedral : 12.766 138.267 3455 Min Nonbonded Distance : 2.035 Molprobity Statistics. All-atom Clashscore : 14.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.59 % Favored : 96.41 % Rotamer: Outliers : 2.44 % Allowed : 11.73 % Favored : 85.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.46 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.98 (0.17), residues: 2673 helix: 1.83 (0.15), residues: 1309 sheet: -0.31 (0.23), residues: 452 loop : -0.51 (0.21), residues: 912 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.017 0.001 ARG G 170 TYR 0.017 0.002 TYR K 315 PHE 0.011 0.001 PHE L 248 TRP 0.014 0.002 TRP X 231 HIS 0.008 0.001 HIS C 187 Details of bonding type rmsd covalent geometry : bond 0.00530 (22129) covalent geometry : angle 0.54370 (30029) hydrogen bonds : bond 0.04200 ( 1130) hydrogen bonds : angle 4.77844 ( 3189) Misc. bond : bond 0.00434 ( 4) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5346 Ramachandran restraints generated. 2673 Oldfield, 0 Emsley, 2673 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5346 Ramachandran restraints generated. 2673 Oldfield, 0 Emsley, 2673 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 268 residues out of total 2251 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 213 time to evaluate : 1.072 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 95 HIS cc_start: 0.8364 (m-70) cc_final: 0.8063 (m90) REVERT: C 303 GLU cc_start: 0.8530 (mm-30) cc_final: 0.8025 (pt0) REVERT: C 321 GLN cc_start: 0.8398 (mt0) cc_final: 0.7885 (mm110) REVERT: D 15 GLU cc_start: 0.8854 (mt-10) cc_final: 0.8442 (pm20) REVERT: D 251 ILE cc_start: 0.8647 (tp) cc_final: 0.8399 (tp) REVERT: D 279 ASP cc_start: 0.7939 (t0) cc_final: 0.7616 (t0) REVERT: D 308 MET cc_start: 0.5496 (mtm) cc_final: 0.5222 (ptp) REVERT: G 130 ARG cc_start: 0.8632 (OUTLIER) cc_final: 0.7872 (ptt180) REVERT: J 30 GLN cc_start: 0.8473 (mt0) cc_final: 0.8028 (pp30) REVERT: J 91 GLU cc_start: 0.8627 (OUTLIER) cc_final: 0.8329 (mt-10) REVERT: J 163 GLU cc_start: 0.8872 (mt-10) cc_final: 0.8663 (mt-10) REVERT: J 210 MET cc_start: 0.8882 (mtm) cc_final: 0.8418 (mtp) REVERT: J 213 GLU cc_start: 0.8346 (tm-30) cc_final: 0.8107 (pp20) REVERT: J 243 MET cc_start: 0.8893 (mtt) cc_final: 0.8384 (mmm) REVERT: J 315 TYR cc_start: 0.7913 (OUTLIER) cc_final: 0.5386 (m-80) REVERT: L 111 LYS cc_start: 0.8847 (OUTLIER) cc_final: 0.8560 (ttpt) REVERT: L 284 LYS cc_start: 0.5953 (OUTLIER) cc_final: 0.5247 (pmmt) REVERT: L 315 TYR cc_start: 0.7211 (OUTLIER) cc_final: 0.6281 (m-80) REVERT: R 25 LYS cc_start: 0.7548 (mttt) cc_final: 0.7191 (tmtt) REVERT: R 182 GLU cc_start: 0.7962 (tp30) cc_final: 0.7262 (mp0) REVERT: R 197 LYS cc_start: 0.8578 (mttt) cc_final: 0.8120 (mmmt) REVERT: R 263 MET cc_start: 0.7465 (mmm) cc_final: 0.6537 (ttt) REVERT: X 84 ASP cc_start: 0.7219 (t70) cc_final: 0.6778 (t70) outliers start: 55 outliers final: 23 residues processed: 253 average time/residue: 1.1128 time to fit residues: 320.1266 Evaluate side-chains 224 residues out of total 2251 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 195 time to evaluate : 0.924 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 124 CYS Chi-restraints excluded: chain C residue 296 LEU Chi-restraints excluded: chain D residue 81 ILE Chi-restraints excluded: chain D residue 91 LYS Chi-restraints excluded: chain G residue 87 THR Chi-restraints excluded: chain G residue 99 ILE Chi-restraints excluded: chain G residue 130 ARG Chi-restraints excluded: chain G residue 287 ILE Chi-restraints excluded: chain I residue 269 VAL Chi-restraints excluded: chain I residue 287 ILE Chi-restraints excluded: chain J residue 91 GLU Chi-restraints excluded: chain J residue 125 MET Chi-restraints excluded: chain J residue 158 MET Chi-restraints excluded: chain J residue 196 ASN Chi-restraints excluded: chain J residue 223 SER Chi-restraints excluded: chain J residue 315 TYR Chi-restraints excluded: chain K residue 104 THR Chi-restraints excluded: chain K residue 158 MET Chi-restraints excluded: chain L residue 67 SER Chi-restraints excluded: chain L residue 111 LYS Chi-restraints excluded: chain L residue 142 VAL Chi-restraints excluded: chain L residue 185 VAL Chi-restraints excluded: chain L residue 218 LEU Chi-restraints excluded: chain L residue 284 LYS Chi-restraints excluded: chain L residue 315 TYR Chi-restraints excluded: chain R residue 331 THR Chi-restraints excluded: chain X residue 30 ASN Chi-restraints excluded: chain X residue 50 GLU Chi-restraints excluded: chain X residue 86 HIS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 269 random chunks: chunk 209 optimal weight: 4.9990 chunk 5 optimal weight: 7.9990 chunk 261 optimal weight: 5.9990 chunk 123 optimal weight: 0.9990 chunk 98 optimal weight: 0.9990 chunk 246 optimal weight: 7.9990 chunk 130 optimal weight: 3.9990 chunk 218 optimal weight: 1.9990 chunk 43 optimal weight: 3.9990 chunk 186 optimal weight: 4.9990 chunk 242 optimal weight: 1.9990 overall best weight: 1.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 94 GLN ** G 272 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 62 ASN J 62 ASN ** J 242 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 290 ASN K 200 GLN L 62 ASN ** L 200 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 344 GLN X 167 ASN ** X 244 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3880 r_free = 0.3880 target = 0.125048 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 70)----------------| | r_work = 0.3198 r_free = 0.3198 target = 0.077116 restraints weight = 81941.662| |-----------------------------------------------------------------------------| r_work (start): 0.3092 rms_B_bonded: 2.73 r_work: 0.2950 rms_B_bonded: 2.89 restraints_weight: 0.5000 r_work: 0.2832 rms_B_bonded: 4.55 restraints_weight: 0.2500 r_work (final): 0.2832 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7996 moved from start: 0.3466 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.046 22133 Z= 0.254 Angle : 0.551 6.655 30029 Z= 0.294 Chirality : 0.041 0.150 3479 Planarity : 0.004 0.066 3733 Dihedral : 12.600 138.329 3455 Min Nonbonded Distance : 2.020 Molprobity Statistics. All-atom Clashscore : 14.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.70 % Favored : 96.30 % Rotamer: Outliers : 2.71 % Allowed : 12.22 % Favored : 85.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.46 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.74 (0.17), residues: 2673 helix: 1.67 (0.15), residues: 1314 sheet: -0.34 (0.24), residues: 451 loop : -0.76 (0.21), residues: 908 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG G 170 TYR 0.019 0.002 TYR J 315 PHE 0.011 0.001 PHE L 248 TRP 0.006 0.001 TRP R 288 HIS 0.011 0.001 HIS C 187 Details of bonding type rmsd covalent geometry : bond 0.00577 (22129) covalent geometry : angle 0.55079 (30029) hydrogen bonds : bond 0.04176 ( 1130) hydrogen bonds : angle 4.78972 ( 3189) Misc. bond : bond 0.00398 ( 4) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5346 Ramachandran restraints generated. 2673 Oldfield, 0 Emsley, 2673 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5346 Ramachandran restraints generated. 2673 Oldfield, 0 Emsley, 2673 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 270 residues out of total 2251 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 209 time to evaluate : 1.012 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 95 HIS cc_start: 0.8268 (m-70) cc_final: 0.7974 (m90) REVERT: C 165 MET cc_start: 0.8744 (mmt) cc_final: 0.8210 (mmt) REVERT: C 303 GLU cc_start: 0.8534 (mm-30) cc_final: 0.8002 (pt0) REVERT: C 321 GLN cc_start: 0.8399 (mt0) cc_final: 0.7905 (mm110) REVERT: D 15 GLU cc_start: 0.8886 (mt-10) cc_final: 0.8482 (pm20) REVERT: D 251 ILE cc_start: 0.8760 (tp) cc_final: 0.8505 (tp) REVERT: D 279 ASP cc_start: 0.8052 (t0) cc_final: 0.7709 (t0) REVERT: D 308 MET cc_start: 0.5661 (mtm) cc_final: 0.5418 (ptp) REVERT: G 130 ARG cc_start: 0.8628 (OUTLIER) cc_final: 0.7855 (ptt180) REVERT: I 235 ARG cc_start: 0.8667 (OUTLIER) cc_final: 0.8303 (ttm170) REVERT: J 30 GLN cc_start: 0.8641 (mt0) cc_final: 0.7956 (pp30) REVERT: J 91 GLU cc_start: 0.8592 (OUTLIER) cc_final: 0.8352 (mt-10) REVERT: J 163 GLU cc_start: 0.8860 (mt-10) cc_final: 0.8660 (mt-10) REVERT: J 210 MET cc_start: 0.8851 (mtm) cc_final: 0.8628 (mtp) REVERT: J 243 MET cc_start: 0.8886 (mtt) cc_final: 0.8368 (mmm) REVERT: J 315 TYR cc_start: 0.7985 (OUTLIER) cc_final: 0.5783 (m-80) REVERT: L 111 LYS cc_start: 0.8862 (OUTLIER) cc_final: 0.8552 (ttpt) REVERT: L 284 LYS cc_start: 0.5729 (OUTLIER) cc_final: 0.5216 (pmmt) REVERT: L 315 TYR cc_start: 0.7298 (OUTLIER) cc_final: 0.6480 (m-80) REVERT: R 25 LYS cc_start: 0.7632 (mttt) cc_final: 0.7166 (tmtt) REVERT: R 182 GLU cc_start: 0.7929 (tp30) cc_final: 0.7225 (mp0) REVERT: R 197 LYS cc_start: 0.8641 (mttt) cc_final: 0.8071 (mmmm) REVERT: X 47 HIS cc_start: 0.6830 (t-90) cc_final: 0.6281 (t70) outliers start: 61 outliers final: 28 residues processed: 252 average time/residue: 1.1915 time to fit residues: 340.1700 Evaluate side-chains 227 residues out of total 2251 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 192 time to evaluate : 1.042 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 274 ASN Chi-restraints excluded: chain C residue 296 LEU Chi-restraints excluded: chain D residue 81 ILE Chi-restraints excluded: chain G residue 87 THR Chi-restraints excluded: chain G residue 99 ILE Chi-restraints excluded: chain G residue 130 ARG Chi-restraints excluded: chain G residue 287 ILE Chi-restraints excluded: chain I residue 235 ARG Chi-restraints excluded: chain I residue 269 VAL Chi-restraints excluded: chain I residue 287 ILE Chi-restraints excluded: chain J residue 91 GLU Chi-restraints excluded: chain J residue 100 ILE Chi-restraints excluded: chain J residue 125 MET Chi-restraints excluded: chain J residue 130 ARG Chi-restraints excluded: chain J residue 158 MET Chi-restraints excluded: chain J residue 196 ASN Chi-restraints excluded: chain J residue 223 SER Chi-restraints excluded: chain J residue 315 TYR Chi-restraints excluded: chain K residue 88 THR Chi-restraints excluded: chain K residue 104 THR Chi-restraints excluded: chain K residue 158 MET Chi-restraints excluded: chain L residue 67 SER Chi-restraints excluded: chain L residue 111 LYS Chi-restraints excluded: chain L residue 142 VAL Chi-restraints excluded: chain L residue 185 VAL Chi-restraints excluded: chain L residue 218 LEU Chi-restraints excluded: chain L residue 223 SER Chi-restraints excluded: chain L residue 284 LYS Chi-restraints excluded: chain L residue 315 TYR Chi-restraints excluded: chain R residue 29 HIS Chi-restraints excluded: chain R residue 331 THR Chi-restraints excluded: chain X residue 30 ASN Chi-restraints excluded: chain X residue 50 GLU Chi-restraints excluded: chain X residue 109 LYS Chi-restraints excluded: chain X residue 154 PHE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 269 random chunks: chunk 83 optimal weight: 3.9990 chunk 3 optimal weight: 0.5980 chunk 131 optimal weight: 0.9980 chunk 182 optimal weight: 0.9980 chunk 87 optimal weight: 0.9980 chunk 250 optimal weight: 0.0070 chunk 18 optimal weight: 2.9990 chunk 67 optimal weight: 2.9990 chunk 44 optimal weight: 6.9990 chunk 231 optimal weight: 1.9990 chunk 214 optimal weight: 7.9990 overall best weight: 0.7198 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 274 ASN G 94 GLN G 202 GLN ** G 272 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 62 ASN K 200 GLN ** L 200 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 47 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** X 161 ASN X 232 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3900 r_free = 0.3900 target = 0.127334 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 68)----------------| | r_work = 0.3212 r_free = 0.3212 target = 0.079011 restraints weight = 81623.149| |-----------------------------------------------------------------------------| r_work (start): 0.3130 rms_B_bonded: 2.86 r_work: 0.2985 rms_B_bonded: 3.02 restraints_weight: 0.5000 r_work: 0.2859 rms_B_bonded: 4.76 restraints_weight: 0.2500 r_work (final): 0.2859 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7914 moved from start: 0.3609 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 22133 Z= 0.126 Angle : 0.467 7.010 30029 Z= 0.250 Chirality : 0.038 0.133 3479 Planarity : 0.003 0.048 3733 Dihedral : 12.045 138.873 3455 Min Nonbonded Distance : 2.095 Molprobity Statistics. All-atom Clashscore : 15.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.44 % Favored : 96.56 % Rotamer: Outliers : 2.22 % Allowed : 13.51 % Favored : 84.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.46 % 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: 1.00 (0.17), residues: 2673 helix: 1.94 (0.15), residues: 1319 sheet: -0.45 (0.24), residues: 454 loop : -0.60 (0.21), residues: 900 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG X 174 TYR 0.012 0.001 TYR J 315 PHE 0.008 0.001 PHE J 92 TRP 0.006 0.001 TRP R 47 HIS 0.011 0.001 HIS C 187 Details of bonding type rmsd covalent geometry : bond 0.00274 (22129) covalent geometry : angle 0.46742 (30029) hydrogen bonds : bond 0.03243 ( 1130) hydrogen bonds : angle 4.43646 ( 3189) Misc. bond : bond 0.00182 ( 4) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5346 Ramachandran restraints generated. 2673 Oldfield, 0 Emsley, 2673 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5346 Ramachandran restraints generated. 2673 Oldfield, 0 Emsley, 2673 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 256 residues out of total 2251 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 206 time to evaluate : 1.290 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 42 LYS cc_start: 0.7592 (mmmm) cc_final: 0.7338 (ptpp) REVERT: C 95 HIS cc_start: 0.8265 (m-70) cc_final: 0.7907 (m90) REVERT: C 165 MET cc_start: 0.8659 (mmt) cc_final: 0.8143 (mmt) REVERT: C 303 GLU cc_start: 0.8538 (mm-30) cc_final: 0.7985 (pt0) REVERT: C 321 GLN cc_start: 0.8351 (mt0) cc_final: 0.7878 (mm110) REVERT: D 15 GLU cc_start: 0.8878 (mt-10) cc_final: 0.8515 (pm20) REVERT: D 251 ILE cc_start: 0.8789 (tp) cc_final: 0.8494 (tp) REVERT: D 279 ASP cc_start: 0.8117 (t0) cc_final: 0.7695 (t0) REVERT: D 308 MET cc_start: 0.5667 (mtm) cc_final: 0.5407 (ptp) REVERT: G 130 ARG cc_start: 0.8498 (OUTLIER) cc_final: 0.7696 (ptt180) REVERT: I 235 ARG cc_start: 0.8606 (OUTLIER) cc_final: 0.8193 (ttm170) REVERT: J 30 GLN cc_start: 0.8630 (mt0) cc_final: 0.8011 (pp30) REVERT: J 219 LEU cc_start: 0.9193 (OUTLIER) cc_final: 0.8787 (tp) REVERT: J 243 MET cc_start: 0.8795 (mtt) cc_final: 0.8299 (mmm) REVERT: J 315 TYR cc_start: 0.7725 (OUTLIER) cc_final: 0.5674 (m-80) REVERT: K 306 ARG cc_start: 0.7223 (OUTLIER) cc_final: 0.6418 (mmp-170) REVERT: L 111 LYS cc_start: 0.8840 (OUTLIER) cc_final: 0.8532 (ttpt) REVERT: L 284 LYS cc_start: 0.5759 (OUTLIER) cc_final: 0.5348 (pmmt) REVERT: L 315 TYR cc_start: 0.7183 (OUTLIER) cc_final: 0.6548 (m-80) REVERT: R 25 LYS cc_start: 0.7599 (mttt) cc_final: 0.7147 (tmtt) REVERT: R 182 GLU cc_start: 0.7912 (tp30) cc_final: 0.7198 (mp0) REVERT: R 197 LYS cc_start: 0.8571 (mttt) cc_final: 0.8046 (mmmt) REVERT: X 47 HIS cc_start: 0.6699 (t-90) cc_final: 0.6109 (t70) outliers start: 50 outliers final: 22 residues processed: 236 average time/residue: 1.2189 time to fit residues: 325.7947 Evaluate side-chains 228 residues out of total 2251 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 198 time to evaluate : 1.244 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 124 CYS Chi-restraints excluded: chain C residue 296 LEU Chi-restraints excluded: chain D residue 36 LEU Chi-restraints excluded: chain D residue 81 ILE Chi-restraints excluded: chain G residue 87 THR Chi-restraints excluded: chain G residue 99 ILE Chi-restraints excluded: chain G residue 130 ARG Chi-restraints excluded: chain G residue 287 ILE Chi-restraints excluded: chain I residue 235 ARG Chi-restraints excluded: chain I residue 269 VAL Chi-restraints excluded: chain I residue 287 ILE Chi-restraints excluded: chain J residue 125 MET Chi-restraints excluded: chain J residue 176 GLU Chi-restraints excluded: chain J residue 196 ASN Chi-restraints excluded: chain J residue 219 LEU Chi-restraints excluded: chain J residue 223 SER Chi-restraints excluded: chain J residue 315 TYR Chi-restraints excluded: chain K residue 158 MET Chi-restraints excluded: chain K residue 306 ARG Chi-restraints excluded: chain L residue 111 LYS Chi-restraints excluded: chain L residue 142 VAL Chi-restraints excluded: chain L residue 185 VAL Chi-restraints excluded: chain L residue 218 LEU Chi-restraints excluded: chain L residue 223 SER Chi-restraints excluded: chain L residue 284 LYS Chi-restraints excluded: chain L residue 315 TYR Chi-restraints excluded: chain R residue 29 HIS Chi-restraints excluded: chain R residue 36 LYS Chi-restraints excluded: chain R residue 331 THR Chi-restraints excluded: chain X residue 30 ASN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 269 random chunks: chunk 13 optimal weight: 2.9990 chunk 16 optimal weight: 0.9980 chunk 77 optimal weight: 1.9990 chunk 207 optimal weight: 3.9990 chunk 141 optimal weight: 3.9990 chunk 152 optimal weight: 3.9990 chunk 69 optimal weight: 0.2980 chunk 163 optimal weight: 4.9990 chunk 9 optimal weight: 4.9990 chunk 74 optimal weight: 0.9990 chunk 136 optimal weight: 0.9990 overall best weight: 1.0586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 274 ASN G 94 GLN ** G 272 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 62 ASN J 62 ASN L 62 ASN ** L 200 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 47 HIS ** 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 = 0.3885 r_free = 0.3885 target = 0.126556 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 75)----------------| | r_work = 0.3189 r_free = 0.3189 target = 0.078119 restraints weight = 81428.840| |-----------------------------------------------------------------------------| r_work (start): 0.3111 rms_B_bonded: 2.79 r_work: 0.2968 rms_B_bonded: 2.96 restraints_weight: 0.5000 r_work: 0.2843 rms_B_bonded: 4.66 restraints_weight: 0.2500 r_work (final): 0.2843 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7932 moved from start: 0.3759 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 22133 Z= 0.158 Angle : 0.482 6.865 30029 Z= 0.257 Chirality : 0.039 0.133 3479 Planarity : 0.003 0.050 3733 Dihedral : 11.953 139.160 3455 Min Nonbonded Distance : 2.092 Molprobity Statistics. All-atom Clashscore : 15.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.59 % Favored : 96.41 % Rotamer: Outliers : 2.40 % Allowed : 13.68 % Favored : 83.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.46 % 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: 1.06 (0.17), residues: 2673 helix: 2.01 (0.15), residues: 1310 sheet: -0.46 (0.24), residues: 455 loop : -0.55 (0.21), residues: 908 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG X 174 TYR 0.016 0.001 TYR J 315 PHE 0.010 0.001 PHE J 92 TRP 0.005 0.001 TRP C 317 HIS 0.012 0.001 HIS C 187 Details of bonding type rmsd covalent geometry : bond 0.00352 (22129) covalent geometry : angle 0.48197 (30029) hydrogen bonds : bond 0.03410 ( 1130) hydrogen bonds : angle 4.43712 ( 3189) Misc. bond : bond 0.00264 ( 4) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5346 Ramachandran restraints generated. 2673 Oldfield, 0 Emsley, 2673 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5346 Ramachandran restraints generated. 2673 Oldfield, 0 Emsley, 2673 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 247 residues out of total 2251 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 193 time to evaluate : 1.081 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 42 LYS cc_start: 0.7637 (mmmm) cc_final: 0.7384 (ptpp) REVERT: C 95 HIS cc_start: 0.8202 (m-70) cc_final: 0.7854 (m90) REVERT: C 165 MET cc_start: 0.8678 (mmt) cc_final: 0.8115 (mmt) REVERT: C 303 GLU cc_start: 0.8538 (mm-30) cc_final: 0.8014 (pt0) REVERT: D 15 GLU cc_start: 0.8875 (mt-10) cc_final: 0.8480 (pm20) REVERT: D 251 ILE cc_start: 0.8812 (tp) cc_final: 0.8501 (tp) REVERT: D 279 ASP cc_start: 0.8132 (t0) cc_final: 0.7759 (t0) REVERT: D 308 MET cc_start: 0.5746 (mtm) cc_final: 0.5528 (ptp) REVERT: G 130 ARG cc_start: 0.8598 (OUTLIER) cc_final: 0.7833 (ptt180) REVERT: I 235 ARG cc_start: 0.8628 (OUTLIER) cc_final: 0.8266 (ttm170) REVERT: J 30 GLN cc_start: 0.8627 (mt0) cc_final: 0.8053 (pp30) REVERT: J 91 GLU cc_start: 0.8589 (OUTLIER) cc_final: 0.8112 (mt-10) REVERT: J 219 LEU cc_start: 0.9214 (OUTLIER) cc_final: 0.8783 (tp) REVERT: J 243 MET cc_start: 0.8768 (mtt) cc_final: 0.8298 (mmm) REVERT: J 315 TYR cc_start: 0.7858 (OUTLIER) cc_final: 0.5710 (m-80) REVERT: K 306 ARG cc_start: 0.7227 (OUTLIER) cc_final: 0.6435 (mmp-170) REVERT: L 111 LYS cc_start: 0.8857 (OUTLIER) cc_final: 0.8593 (ttpt) REVERT: L 284 LYS cc_start: 0.5732 (OUTLIER) cc_final: 0.5251 (pmmt) REVERT: L 315 TYR cc_start: 0.7209 (OUTLIER) cc_final: 0.6496 (m-80) REVERT: R 25 LYS cc_start: 0.7562 (mttt) cc_final: 0.7092 (tmtt) REVERT: R 182 GLU cc_start: 0.7921 (tp30) cc_final: 0.7192 (mp0) REVERT: R 197 LYS cc_start: 0.8544 (mttt) cc_final: 0.7977 (mtpp) REVERT: X 47 HIS cc_start: 0.6670 (t-90) cc_final: 0.6073 (t70) outliers start: 54 outliers final: 28 residues processed: 226 average time/residue: 1.1929 time to fit residues: 305.9355 Evaluate side-chains 227 residues out of total 2251 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 190 time to evaluate : 1.236 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 124 CYS Chi-restraints excluded: chain C residue 296 LEU Chi-restraints excluded: chain D residue 36 LEU Chi-restraints excluded: chain D residue 81 ILE Chi-restraints excluded: chain G residue 87 THR Chi-restraints excluded: chain G residue 99 ILE Chi-restraints excluded: chain G residue 130 ARG Chi-restraints excluded: chain G residue 287 ILE Chi-restraints excluded: chain I residue 235 ARG Chi-restraints excluded: chain I residue 269 VAL Chi-restraints excluded: chain I residue 287 ILE Chi-restraints excluded: chain J residue 61 ILE Chi-restraints excluded: chain J residue 91 GLU Chi-restraints excluded: chain J residue 125 MET Chi-restraints excluded: chain J residue 158 MET Chi-restraints excluded: chain J residue 176 GLU Chi-restraints excluded: chain J residue 196 ASN Chi-restraints excluded: chain J residue 219 LEU Chi-restraints excluded: chain J residue 223 SER Chi-restraints excluded: chain J residue 315 TYR Chi-restraints excluded: chain J residue 319 CYS Chi-restraints excluded: chain K residue 158 MET Chi-restraints excluded: chain K residue 306 ARG Chi-restraints excluded: chain L residue 111 LYS Chi-restraints excluded: chain L residue 142 VAL Chi-restraints excluded: chain L residue 185 VAL Chi-restraints excluded: chain L residue 218 LEU Chi-restraints excluded: chain L residue 223 SER Chi-restraints excluded: chain L residue 284 LYS Chi-restraints excluded: chain L residue 315 TYR Chi-restraints excluded: chain R residue 29 HIS Chi-restraints excluded: chain R residue 36 LYS Chi-restraints excluded: chain R residue 263 MET Chi-restraints excluded: chain R residue 331 THR Chi-restraints excluded: chain X residue 30 ASN Chi-restraints excluded: chain X residue 136 MET Chi-restraints excluded: chain X residue 154 PHE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 269 random chunks: chunk 229 optimal weight: 2.9990 chunk 154 optimal weight: 0.7980 chunk 236 optimal weight: 1.9990 chunk 132 optimal weight: 2.9990 chunk 23 optimal weight: 2.9990 chunk 37 optimal weight: 10.0000 chunk 39 optimal weight: 3.9990 chunk 2 optimal weight: 10.0000 chunk 170 optimal weight: 0.5980 chunk 209 optimal weight: 8.9990 chunk 152 optimal weight: 1.9990 overall best weight: 1.6786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 274 ASN G 94 GLN ** G 272 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 62 ASN J 330 ASN ** L 200 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 47 HIS ** 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 = 0.3861 r_free = 0.3861 target = 0.124759 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 72)----------------| | r_work = 0.3162 r_free = 0.3162 target = 0.076640 restraints weight = 81488.172| |-----------------------------------------------------------------------------| r_work (start): 0.3085 rms_B_bonded: 2.75 r_work: 0.2939 rms_B_bonded: 2.93 restraints_weight: 0.5000 r_work: 0.2814 rms_B_bonded: 4.61 restraints_weight: 0.2500 r_work (final): 0.2814 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7958 moved from start: 0.3966 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.044 22133 Z= 0.222 Angle : 0.530 8.448 30029 Z= 0.282 Chirality : 0.040 0.151 3479 Planarity : 0.004 0.070 3733 Dihedral : 12.103 138.434 3455 Min Nonbonded Distance : 2.043 Molprobity Statistics. All-atom Clashscore : 14.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.15 % Favored : 95.85 % Rotamer: Outliers : 2.22 % Allowed : 14.22 % Favored : 83.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.46 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.88 (0.17), residues: 2673 helix: 1.84 (0.15), residues: 1314 sheet: -0.52 (0.24), residues: 447 loop : -0.64 (0.21), residues: 912 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG X 174 TYR 0.019 0.001 TYR J 315 PHE 0.010 0.001 PHE J 92 TRP 0.006 0.001 TRP C 317 HIS 0.015 0.001 HIS C 187 Details of bonding type rmsd covalent geometry : bond 0.00501 (22129) covalent geometry : angle 0.53048 (30029) hydrogen bonds : bond 0.03908 ( 1130) hydrogen bonds : angle 4.62020 ( 3189) Misc. bond : bond 0.00391 ( 4) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5346 Ramachandran restraints generated. 2673 Oldfield, 0 Emsley, 2673 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5346 Ramachandran restraints generated. 2673 Oldfield, 0 Emsley, 2673 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 240 residues out of total 2251 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 190 time to evaluate : 1.123 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 42 LYS cc_start: 0.7756 (mmmm) cc_final: 0.7464 (ptpp) REVERT: C 95 HIS cc_start: 0.8214 (m-70) cc_final: 0.7860 (m90) REVERT: C 165 MET cc_start: 0.8733 (mmt) cc_final: 0.8170 (mmt) REVERT: C 303 GLU cc_start: 0.8563 (mm-30) cc_final: 0.8016 (pt0) REVERT: D 15 GLU cc_start: 0.8886 (mt-10) cc_final: 0.8497 (pm20) REVERT: D 251 ILE cc_start: 0.8789 (tp) cc_final: 0.8491 (tp) REVERT: D 279 ASP cc_start: 0.8213 (t0) cc_final: 0.7797 (t0) REVERT: G 130 ARG cc_start: 0.8630 (OUTLIER) cc_final: 0.7846 (ptt180) REVERT: I 235 ARG cc_start: 0.8672 (OUTLIER) cc_final: 0.8306 (ttm170) REVERT: J 30 GLN cc_start: 0.8557 (mt0) cc_final: 0.7997 (pp30) REVERT: J 91 GLU cc_start: 0.8581 (OUTLIER) cc_final: 0.8321 (mt-10) REVERT: J 163 GLU cc_start: 0.8818 (mt-10) cc_final: 0.8614 (mt-10) REVERT: J 243 MET cc_start: 0.8801 (mtt) cc_final: 0.8308 (mmm) REVERT: J 315 TYR cc_start: 0.7971 (OUTLIER) cc_final: 0.5882 (m-80) REVERT: L 111 LYS cc_start: 0.8877 (OUTLIER) cc_final: 0.8636 (ttpt) REVERT: L 284 LYS cc_start: 0.5771 (OUTLIER) cc_final: 0.5429 (pmmt) REVERT: L 315 TYR cc_start: 0.7326 (OUTLIER) cc_final: 0.6454 (m-80) REVERT: R 25 LYS cc_start: 0.7644 (mttt) cc_final: 0.7106 (tmtt) REVERT: R 182 GLU cc_start: 0.7940 (tp30) cc_final: 0.7209 (mp0) REVERT: R 197 LYS cc_start: 0.8601 (mttt) cc_final: 0.8012 (mtpp) REVERT: R 263 MET cc_start: 0.7400 (mtt) cc_final: 0.6832 (ttm) REVERT: X 47 HIS cc_start: 0.6638 (t-90) cc_final: 0.6123 (t70) REVERT: X 64 ARG cc_start: 0.5126 (ttt180) cc_final: 0.4206 (tpt170) outliers start: 50 outliers final: 30 residues processed: 222 average time/residue: 1.2552 time to fit residues: 313.9837 Evaluate side-chains 224 residues out of total 2251 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 187 time to evaluate : 1.139 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 124 CYS Chi-restraints excluded: chain C residue 296 LEU Chi-restraints excluded: chain D residue 31 LEU Chi-restraints excluded: chain D residue 36 LEU Chi-restraints excluded: chain G residue 87 THR Chi-restraints excluded: chain G residue 99 ILE Chi-restraints excluded: chain G residue 130 ARG Chi-restraints excluded: chain G residue 287 ILE Chi-restraints excluded: chain I residue 235 ARG Chi-restraints excluded: chain I residue 269 VAL Chi-restraints excluded: chain I residue 287 ILE Chi-restraints excluded: chain J residue 61 ILE Chi-restraints excluded: chain J residue 91 GLU Chi-restraints excluded: chain J residue 125 MET Chi-restraints excluded: chain J residue 176 GLU Chi-restraints excluded: chain J residue 196 ASN Chi-restraints excluded: chain J residue 223 SER Chi-restraints excluded: chain J residue 315 TYR Chi-restraints excluded: chain J residue 319 CYS Chi-restraints excluded: chain K residue 158 MET Chi-restraints excluded: chain L residue 111 LYS Chi-restraints excluded: chain L residue 142 VAL Chi-restraints excluded: chain L residue 158 MET Chi-restraints excluded: chain L residue 185 VAL Chi-restraints excluded: chain L residue 218 LEU Chi-restraints excluded: chain L residue 223 SER Chi-restraints excluded: chain L residue 284 LYS Chi-restraints excluded: chain L residue 315 TYR Chi-restraints excluded: chain R residue 29 HIS Chi-restraints excluded: chain R residue 36 LYS Chi-restraints excluded: chain R residue 331 THR Chi-restraints excluded: chain X residue 30 ASN Chi-restraints excluded: chain X residue 84 ASP Chi-restraints excluded: chain X residue 109 LYS Chi-restraints excluded: chain X residue 111 CYS Chi-restraints excluded: chain X residue 136 MET Chi-restraints excluded: chain X residue 154 PHE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 269 random chunks: chunk 62 optimal weight: 4.9990 chunk 236 optimal weight: 0.5980 chunk 37 optimal weight: 10.0000 chunk 80 optimal weight: 0.8980 chunk 157 optimal weight: 1.9990 chunk 237 optimal weight: 0.6980 chunk 124 optimal weight: 0.0980 chunk 265 optimal weight: 9.9990 chunk 137 optimal weight: 0.6980 chunk 134 optimal weight: 0.5980 chunk 191 optimal weight: 2.9990 overall best weight: 0.5380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 274 ASN G 94 GLN G 202 GLN ** G 272 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 62 ASN J 62 ASN L 62 ASN ** L 200 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 47 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3895 r_free = 0.3895 target = 0.127249 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 71)----------------| | r_work = 0.3207 r_free = 0.3207 target = 0.078951 restraints weight = 80725.411| |-----------------------------------------------------------------------------| r_work (start): 0.3129 rms_B_bonded: 2.86 r_work: 0.2989 rms_B_bonded: 3.00 restraints_weight: 0.5000 r_work: 0.2864 rms_B_bonded: 4.76 restraints_weight: 0.2500 r_work (final): 0.2864 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7900 moved from start: 0.4056 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.043 22133 Z= 0.112 Angle : 0.468 7.895 30029 Z= 0.248 Chirality : 0.038 0.133 3479 Planarity : 0.003 0.047 3733 Dihedral : 11.758 138.237 3455 Min Nonbonded Distance : 2.130 Molprobity Statistics. All-atom Clashscore : 16.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.29 % Favored : 96.71 % Rotamer: Outliers : 1.95 % Allowed : 14.75 % Favored : 83.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.46 % 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: 1.16 (0.17), residues: 2673 helix: 2.17 (0.15), residues: 1300 sheet: -0.53 (0.24), residues: 434 loop : -0.54 (0.21), residues: 939 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG X 174 TYR 0.012 0.001 TYR J 315 PHE 0.007 0.001 PHE J 92 TRP 0.006 0.001 TRP C 317 HIS 0.014 0.001 HIS C 187 Details of bonding type rmsd covalent geometry : bond 0.00245 (22129) covalent geometry : angle 0.46773 (30029) hydrogen bonds : bond 0.03065 ( 1130) hydrogen bonds : angle 4.32974 ( 3189) Misc. bond : bond 0.00146 ( 4) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5346 Ramachandran restraints generated. 2673 Oldfield, 0 Emsley, 2673 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5346 Ramachandran restraints generated. 2673 Oldfield, 0 Emsley, 2673 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 242 residues out of total 2251 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 198 time to evaluate : 1.072 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 42 LYS cc_start: 0.7736 (mmmm) cc_final: 0.7454 (ptpp) REVERT: C 95 HIS cc_start: 0.8224 (m-70) cc_final: 0.7871 (m90) REVERT: C 165 MET cc_start: 0.8650 (mmt) cc_final: 0.8099 (mmt) REVERT: C 303 GLU cc_start: 0.8495 (mm-30) cc_final: 0.7961 (pt0) REVERT: D 15 GLU cc_start: 0.8903 (mt-10) cc_final: 0.8500 (pm20) REVERT: D 251 ILE cc_start: 0.8811 (tp) cc_final: 0.8463 (tp) REVERT: D 279 ASP cc_start: 0.8124 (t0) cc_final: 0.7698 (t0) REVERT: G 130 ARG cc_start: 0.8480 (OUTLIER) cc_final: 0.7699 (ptt180) REVERT: I 235 ARG cc_start: 0.8583 (OUTLIER) cc_final: 0.8167 (ttm170) REVERT: J 30 GLN cc_start: 0.8637 (mt0) cc_final: 0.7975 (pp30) REVERT: J 91 GLU cc_start: 0.8579 (OUTLIER) cc_final: 0.8182 (mt-10) REVERT: J 243 MET cc_start: 0.8769 (mtt) cc_final: 0.8285 (mmm) REVERT: J 315 TYR cc_start: 0.7713 (OUTLIER) cc_final: 0.5806 (m-80) REVERT: L 284 LYS cc_start: 0.5735 (OUTLIER) cc_final: 0.5299 (pmmt) REVERT: L 315 TYR cc_start: 0.7192 (OUTLIER) cc_final: 0.6464 (m-80) REVERT: R 25 LYS cc_start: 0.7627 (mttt) cc_final: 0.7100 (tmtt) REVERT: R 182 GLU cc_start: 0.7926 (tp30) cc_final: 0.7200 (mp0) REVERT: R 197 LYS cc_start: 0.8585 (mttt) cc_final: 0.7989 (mtpp) REVERT: R 263 MET cc_start: 0.7563 (mtt) cc_final: 0.6951 (ttm) REVERT: X 47 HIS cc_start: 0.6670 (t-90) cc_final: 0.6049 (t70) REVERT: X 64 ARG cc_start: 0.5065 (ttt180) cc_final: 0.4103 (tpt170) outliers start: 44 outliers final: 23 residues processed: 226 average time/residue: 1.2221 time to fit residues: 311.5898 Evaluate side-chains 218 residues out of total 2251 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 189 time to evaluate : 1.058 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 296 LEU Chi-restraints excluded: chain D residue 31 LEU Chi-restraints excluded: chain D residue 36 LEU Chi-restraints excluded: chain G residue 87 THR Chi-restraints excluded: chain G residue 99 ILE Chi-restraints excluded: chain G residue 130 ARG Chi-restraints excluded: chain G residue 230 THR Chi-restraints excluded: chain G residue 287 ILE Chi-restraints excluded: chain I residue 230 THR Chi-restraints excluded: chain I residue 235 ARG Chi-restraints excluded: chain I residue 269 VAL Chi-restraints excluded: chain I residue 287 ILE Chi-restraints excluded: chain J residue 91 GLU Chi-restraints excluded: chain J residue 125 MET Chi-restraints excluded: chain J residue 176 GLU Chi-restraints excluded: chain J residue 196 ASN Chi-restraints excluded: chain J residue 223 SER Chi-restraints excluded: chain J residue 315 TYR Chi-restraints excluded: chain L residue 67 SER Chi-restraints excluded: chain L residue 218 LEU Chi-restraints excluded: chain L residue 223 SER Chi-restraints excluded: chain L residue 284 LYS Chi-restraints excluded: chain L residue 315 TYR Chi-restraints excluded: chain R residue 29 HIS Chi-restraints excluded: chain R residue 331 THR Chi-restraints excluded: chain X residue 30 ASN Chi-restraints excluded: chain X residue 109 LYS Chi-restraints excluded: chain X residue 136 MET Chi-restraints excluded: chain X residue 154 PHE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 269 random chunks: chunk 18 optimal weight: 2.9990 chunk 71 optimal weight: 0.0570 chunk 116 optimal weight: 1.9990 chunk 202 optimal weight: 6.9990 chunk 163 optimal weight: 4.9990 chunk 117 optimal weight: 0.5980 chunk 180 optimal weight: 1.9990 chunk 222 optimal weight: 0.9990 chunk 42 optimal weight: 3.9990 chunk 165 optimal weight: 0.9980 chunk 140 optimal weight: 3.9990 overall best weight: 0.9302 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 274 ASN G 94 GLN ** G 272 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 62 ASN ** L 200 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 47 HIS ** 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 = 0.3885 r_free = 0.3885 target = 0.126543 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 70)----------------| | r_work = 0.3193 r_free = 0.3193 target = 0.078221 restraints weight = 81241.460| |-----------------------------------------------------------------------------| r_work (start): 0.3115 rms_B_bonded: 2.80 r_work: 0.2971 rms_B_bonded: 2.97 restraints_weight: 0.5000 r_work: 0.2846 rms_B_bonded: 4.69 restraints_weight: 0.2500 r_work (final): 0.2846 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7932 moved from start: 0.4121 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 22133 Z= 0.144 Angle : 0.484 9.571 30029 Z= 0.255 Chirality : 0.038 0.133 3479 Planarity : 0.003 0.097 3733 Dihedral : 11.768 138.643 3455 Min Nonbonded Distance : 2.102 Molprobity Statistics. All-atom Clashscore : 15.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.67 % Favored : 96.33 % Rotamer: Outliers : 1.69 % Allowed : 15.28 % Favored : 83.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.46 % 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: 1.17 (0.17), residues: 2673 helix: 2.19 (0.15), residues: 1300 sheet: -0.56 (0.24), residues: 436 loop : -0.53 (0.21), residues: 937 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.000 ARG X 174 TYR 0.015 0.001 TYR J 315 PHE 0.009 0.001 PHE J 92 TRP 0.006 0.001 TRP C 317 HIS 0.014 0.001 HIS C 187 Details of bonding type rmsd covalent geometry : bond 0.00322 (22129) covalent geometry : angle 0.48357 (30029) hydrogen bonds : bond 0.03218 ( 1130) hydrogen bonds : angle 4.33445 ( 3189) Misc. bond : bond 0.00241 ( 4) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5346 Ramachandran restraints generated. 2673 Oldfield, 0 Emsley, 2673 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5346 Ramachandran restraints generated. 2673 Oldfield, 0 Emsley, 2673 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 224 residues out of total 2251 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 186 time to evaluate : 0.967 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 42 LYS cc_start: 0.7790 (mmmm) cc_final: 0.7490 (ptpp) REVERT: C 95 HIS cc_start: 0.8236 (m-70) cc_final: 0.7883 (m90) REVERT: C 165 MET cc_start: 0.8685 (mmt) cc_final: 0.8128 (mmt) REVERT: C 303 GLU cc_start: 0.8507 (mm-30) cc_final: 0.7965 (pt0) REVERT: D 15 GLU cc_start: 0.8905 (mt-10) cc_final: 0.8489 (pm20) REVERT: D 251 ILE cc_start: 0.8799 (tp) cc_final: 0.8503 (tp) REVERT: D 279 ASP cc_start: 0.8141 (t0) cc_final: 0.7714 (t0) REVERT: G 130 ARG cc_start: 0.8566 (OUTLIER) cc_final: 0.7792 (ptt180) REVERT: I 62 ASN cc_start: 0.8605 (t0) cc_final: 0.8399 (t160) REVERT: I 235 ARG cc_start: 0.8605 (OUTLIER) cc_final: 0.8194 (ttm170) REVERT: J 30 GLN cc_start: 0.8618 (mt0) cc_final: 0.7920 (pp30) REVERT: J 91 GLU cc_start: 0.8582 (OUTLIER) cc_final: 0.8132 (mt-10) REVERT: J 163 GLU cc_start: 0.8823 (mt-10) cc_final: 0.8617 (mt-10) REVERT: J 219 LEU cc_start: 0.9181 (OUTLIER) cc_final: 0.8757 (tp) REVERT: J 243 MET cc_start: 0.8779 (mtt) cc_final: 0.8318 (mmm) REVERT: J 315 TYR cc_start: 0.7819 (OUTLIER) cc_final: 0.5695 (m-80) REVERT: L 284 LYS cc_start: 0.5749 (OUTLIER) cc_final: 0.5260 (pmmt) REVERT: L 315 TYR cc_start: 0.7249 (OUTLIER) cc_final: 0.6449 (m-80) REVERT: R 25 LYS cc_start: 0.7620 (mttt) cc_final: 0.7080 (tmtt) REVERT: R 172 LYS cc_start: 0.8800 (tppp) cc_final: 0.8590 (tppt) REVERT: R 182 GLU cc_start: 0.7964 (tp30) cc_final: 0.7197 (mp0) REVERT: R 197 LYS cc_start: 0.8597 (mttt) cc_final: 0.8001 (mtpp) REVERT: R 263 MET cc_start: 0.7623 (mtt) cc_final: 0.7054 (ttm) REVERT: X 47 HIS cc_start: 0.6647 (t-90) cc_final: 0.6044 (t70) outliers start: 38 outliers final: 27 residues processed: 211 average time/residue: 1.2296 time to fit residues: 292.6465 Evaluate side-chains 220 residues out of total 2251 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 186 time to evaluate : 0.924 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 296 LEU Chi-restraints excluded: chain D residue 31 LEU Chi-restraints excluded: chain D residue 36 LEU Chi-restraints excluded: chain G residue 87 THR Chi-restraints excluded: chain G residue 99 ILE Chi-restraints excluded: chain G residue 130 ARG Chi-restraints excluded: chain G residue 230 THR Chi-restraints excluded: chain G residue 287 ILE Chi-restraints excluded: chain I residue 230 THR Chi-restraints excluded: chain I residue 235 ARG Chi-restraints excluded: chain I residue 269 VAL Chi-restraints excluded: chain I residue 287 ILE Chi-restraints excluded: chain J residue 91 GLU Chi-restraints excluded: chain J residue 125 MET Chi-restraints excluded: chain J residue 176 GLU Chi-restraints excluded: chain J residue 196 ASN Chi-restraints excluded: chain J residue 219 LEU Chi-restraints excluded: chain J residue 223 SER Chi-restraints excluded: chain J residue 315 TYR Chi-restraints excluded: chain J residue 319 CYS Chi-restraints excluded: chain L residue 142 VAL Chi-restraints excluded: chain L residue 158 MET Chi-restraints excluded: chain L residue 185 VAL Chi-restraints excluded: chain L residue 218 LEU Chi-restraints excluded: chain L residue 223 SER Chi-restraints excluded: chain L residue 284 LYS Chi-restraints excluded: chain L residue 315 TYR Chi-restraints excluded: chain R residue 29 HIS Chi-restraints excluded: chain R residue 331 THR Chi-restraints excluded: chain X residue 30 ASN Chi-restraints excluded: chain X residue 84 ASP Chi-restraints excluded: chain X residue 109 LYS Chi-restraints excluded: chain X residue 111 CYS Chi-restraints excluded: chain X residue 154 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 269 random chunks: chunk 103 optimal weight: 1.9990 chunk 119 optimal weight: 1.9990 chunk 94 optimal weight: 1.9990 chunk 46 optimal weight: 2.9990 chunk 222 optimal weight: 0.7980 chunk 252 optimal weight: 8.9990 chunk 39 optimal weight: 4.9990 chunk 114 optimal weight: 0.9980 chunk 155 optimal weight: 5.9990 chunk 179 optimal weight: 0.3980 chunk 189 optimal weight: 2.9990 overall best weight: 1.2384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 94 GLN ** G 272 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 62 ASN ** L 200 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 47 HIS ** 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 = 0.3875 r_free = 0.3875 target = 0.125764 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3180 r_free = 0.3180 target = 0.077515 restraints weight = 81711.580| |-----------------------------------------------------------------------------| r_work (start): 0.3102 rms_B_bonded: 2.79 r_work: 0.2958 rms_B_bonded: 2.96 restraints_weight: 0.5000 r_work: 0.2832 rms_B_bonded: 4.67 restraints_weight: 0.2500 r_work (final): 0.2832 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7946 moved from start: 0.4216 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 22133 Z= 0.174 Angle : 0.504 10.848 30029 Z= 0.266 Chirality : 0.039 0.133 3479 Planarity : 0.003 0.053 3733 Dihedral : 11.866 138.323 3455 Min Nonbonded Distance : 2.064 Molprobity Statistics. All-atom Clashscore : 15.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.93 % Favored : 96.07 % Rotamer: Outliers : 1.73 % Allowed : 15.37 % Favored : 82.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.46 % 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: 1.11 (0.17), residues: 2673 helix: 2.13 (0.15), residues: 1299 sheet: -0.62 (0.24), residues: 438 loop : -0.52 (0.21), residues: 936 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG X 174 TYR 0.016 0.001 TYR J 315 PHE 0.010 0.001 PHE J 92 TRP 0.005 0.001 TRP C 317 HIS 0.015 0.001 HIS C 187 Details of bonding type rmsd covalent geometry : bond 0.00391 (22129) covalent geometry : angle 0.50383 (30029) hydrogen bonds : bond 0.03436 ( 1130) hydrogen bonds : angle 4.41619 ( 3189) Misc. bond : bond 0.00280 ( 4) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5346 Ramachandran restraints generated. 2673 Oldfield, 0 Emsley, 2673 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5346 Ramachandran restraints generated. 2673 Oldfield, 0 Emsley, 2673 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 225 residues out of total 2251 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 186 time to evaluate : 1.116 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 42 LYS cc_start: 0.7810 (mmmm) cc_final: 0.7509 (ptpp) REVERT: C 95 HIS cc_start: 0.8224 (m-70) cc_final: 0.7865 (m90) REVERT: C 165 MET cc_start: 0.8702 (mmt) cc_final: 0.8165 (mmt) REVERT: C 303 GLU cc_start: 0.8510 (mm-30) cc_final: 0.7979 (pt0) REVERT: D 15 GLU cc_start: 0.8908 (mt-10) cc_final: 0.8511 (pm20) REVERT: D 251 ILE cc_start: 0.8813 (tp) cc_final: 0.8501 (tp) REVERT: D 279 ASP cc_start: 0.8172 (t0) cc_final: 0.7743 (t0) REVERT: G 130 ARG cc_start: 0.8608 (OUTLIER) cc_final: 0.7839 (ptt180) REVERT: I 62 ASN cc_start: 0.8494 (t0) cc_final: 0.8280 (t0) REVERT: I 235 ARG cc_start: 0.8635 (OUTLIER) cc_final: 0.8273 (ttm170) REVERT: J 30 GLN cc_start: 0.8447 (mt0) cc_final: 0.7799 (pp30) REVERT: J 91 GLU cc_start: 0.8598 (OUTLIER) cc_final: 0.8121 (mt-10) REVERT: J 158 MET cc_start: 0.9090 (OUTLIER) cc_final: 0.8772 (ptp) REVERT: J 163 GLU cc_start: 0.8821 (mt-10) cc_final: 0.8607 (mt-10) REVERT: J 243 MET cc_start: 0.8790 (mtt) cc_final: 0.8324 (mmm) REVERT: J 315 TYR cc_start: 0.7873 (OUTLIER) cc_final: 0.5768 (m-80) REVERT: L 284 LYS cc_start: 0.5751 (OUTLIER) cc_final: 0.5201 (pmmt) REVERT: L 315 TYR cc_start: 0.7271 (OUTLIER) cc_final: 0.6418 (m-80) REVERT: R 25 LYS cc_start: 0.7659 (mttt) cc_final: 0.7093 (tmtt) REVERT: R 172 LYS cc_start: 0.8808 (tppp) cc_final: 0.8596 (tppt) REVERT: R 182 GLU cc_start: 0.7954 (tp30) cc_final: 0.7210 (mp0) REVERT: R 197 LYS cc_start: 0.8625 (mttt) cc_final: 0.8024 (mtpp) REVERT: R 263 MET cc_start: 0.7495 (mtt) cc_final: 0.6867 (ttm) REVERT: X 47 HIS cc_start: 0.6655 (t-90) cc_final: 0.6060 (t70) outliers start: 39 outliers final: 28 residues processed: 211 average time/residue: 1.2159 time to fit residues: 288.8250 Evaluate side-chains 219 residues out of total 2251 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 184 time to evaluate : 0.890 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 31 LEU Chi-restraints excluded: chain D residue 36 LEU Chi-restraints excluded: chain G residue 87 THR Chi-restraints excluded: chain G residue 99 ILE Chi-restraints excluded: chain G residue 130 ARG Chi-restraints excluded: chain G residue 230 THR Chi-restraints excluded: chain G residue 287 ILE Chi-restraints excluded: chain I residue 128 GLU Chi-restraints excluded: chain I residue 230 THR Chi-restraints excluded: chain I residue 235 ARG Chi-restraints excluded: chain I residue 269 VAL Chi-restraints excluded: chain I residue 287 ILE Chi-restraints excluded: chain J residue 91 GLU Chi-restraints excluded: chain J residue 125 MET Chi-restraints excluded: chain J residue 158 MET Chi-restraints excluded: chain J residue 176 GLU Chi-restraints excluded: chain J residue 196 ASN Chi-restraints excluded: chain J residue 223 SER Chi-restraints excluded: chain J residue 315 TYR Chi-restraints excluded: chain J residue 319 CYS Chi-restraints excluded: chain K residue 72 ASP Chi-restraints excluded: chain L residue 142 VAL Chi-restraints excluded: chain L residue 149 ASP Chi-restraints excluded: chain L residue 158 MET Chi-restraints excluded: chain L residue 185 VAL Chi-restraints excluded: chain L residue 218 LEU Chi-restraints excluded: chain L residue 223 SER Chi-restraints excluded: chain L residue 284 LYS Chi-restraints excluded: chain L residue 315 TYR Chi-restraints excluded: chain R residue 29 HIS Chi-restraints excluded: chain R residue 331 THR Chi-restraints excluded: chain X residue 30 ASN Chi-restraints excluded: chain X residue 84 ASP Chi-restraints excluded: chain X residue 109 LYS Chi-restraints excluded: chain X residue 111 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 269 random chunks: chunk 69 optimal weight: 5.9990 chunk 109 optimal weight: 0.9990 chunk 79 optimal weight: 2.9990 chunk 267 optimal weight: 10.0000 chunk 245 optimal weight: 2.9990 chunk 129 optimal weight: 2.9990 chunk 146 optimal weight: 1.9990 chunk 167 optimal weight: 2.9990 chunk 266 optimal weight: 5.9990 chunk 250 optimal weight: 5.9990 chunk 68 optimal weight: 0.6980 overall best weight: 1.9388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 94 GLN ** G 272 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 62 ASN ** L 200 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 47 HIS ** 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 = 0.3860 r_free = 0.3860 target = 0.124699 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.3155 r_free = 0.3155 target = 0.076261 restraints weight = 81297.183| |-----------------------------------------------------------------------------| r_work (start): 0.3081 rms_B_bonded: 2.77 r_work: 0.2937 rms_B_bonded: 2.94 restraints_weight: 0.5000 r_work: 0.2811 rms_B_bonded: 4.62 restraints_weight: 0.2500 r_work (final): 0.2811 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7962 moved from start: 0.4286 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.050 22133 Z= 0.246 Angle : 0.543 10.631 30029 Z= 0.286 Chirality : 0.041 0.144 3479 Planarity : 0.004 0.073 3733 Dihedral : 12.013 137.847 3455 Min Nonbonded Distance : 2.039 Molprobity Statistics. All-atom Clashscore : 15.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.08 % Favored : 95.92 % Rotamer: Outliers : 1.64 % Allowed : 15.55 % Favored : 82.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.46 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.95 (0.17), residues: 2673 helix: 1.99 (0.15), residues: 1305 sheet: -0.60 (0.24), residues: 436 loop : -0.68 (0.21), residues: 932 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG X 174 TYR 0.018 0.001 TYR J 315 PHE 0.010 0.001 PHE J 92 TRP 0.005 0.001 TRP C 317 HIS 0.014 0.001 HIS C 187 Details of bonding type rmsd covalent geometry : bond 0.00561 (22129) covalent geometry : angle 0.54273 (30029) hydrogen bonds : bond 0.03788 ( 1130) hydrogen bonds : angle 4.55738 ( 3189) Misc. bond : bond 0.00424 ( 4) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 17897.62 seconds wall clock time: 302 minutes 43.20 seconds (18163.20 seconds total)