Starting phenix.real_space_refine on Thu Aug 6 13:40:56 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/8ouf_17191/08_2026/8ouf_17191.cif Found real_map, /net/cci-nas-00/data/ceres_data/8ouf_17191/08_2026/8ouf_17191.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8ouf_17191/08_2026/8ouf_17191.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8ouf_17191/08_2026/8ouf_17191.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8ouf_17191/08_2026/8ouf_17191.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8ouf_17191/08_2026/8ouf_17191.map" restraint_files = "/net/cci-nas-00/data/ceres_data/8ouf_17191/08_2026/8ouf_17191.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/8ouf_17191/08_2026/8ouf_17191.cif" } resolution = 3.1 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= 0.005 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: 5 Type Number sf(0) Gaussians P 86 5.49 5 S 86 5.16 5 C 9354 2.51 5 N 2681 2.21 5 O 3023 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 1 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 15230 Number of models: 1 Model: "" Number of chains: 10 Chain: "B" Number of atoms: 1849 Number of conformers: 1 Conformer: "" Number of residues, atoms: 86, 1849 Classifications: {'RNAv2': 86} Modifications used: {'rna2p_pur': 11, 'rna2p_pyr': 5, 'rna3p_pur': 37, 'rna3p_pyr': 33} Link IDs: {'rna2p': 15, 'rna3p': 70} Chain breaks: 6 Chain: "C" Number of atoms: 3129 Number of conformers: 1 Conformer: "" Number of residues, atoms: 394, 3129 Classifications: {'peptide': 394} Link IDs: {'PTRANS': 16, 'TRANS': 377} Chain breaks: 1 Chain: "D" Number of atoms: 780 Number of conformers: 1 Conformer: "" Number of residues, atoms: 94, 780 Classifications: {'peptide': 94} Link IDs: {'PTRANS': 7, 'TRANS': 86} Chain: "E" Number of atoms: 1035 Number of conformers: 1 Conformer: "" Number of residues, atoms: 130, 1035 Classifications: {'peptide': 130} Link IDs: {'PCIS': 2, 'PTRANS': 8, 'TRANS': 119} Chain: "F" Number of atoms: 542 Number of conformers: 1 Conformer: "" Number of residues, atoms: 64, 542 Classifications: {'peptide': 64} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 58} Chain: "G" Number of atoms: 2792 Number of conformers: 1 Conformer: "" Number of residues, atoms: 353, 2792 Classifications: {'peptide': 353} Link IDs: {'PTRANS': 13, 'TRANS': 339} Chain: "H" Number of atoms: 802 Number of conformers: 1 Conformer: "" Number of residues, atoms: 97, 802 Classifications: {'peptide': 97} Link IDs: {'PTRANS': 9, 'TRANS': 87} Chain: "I" Number of atoms: 1035 Number of conformers: 1 Conformer: "" Number of residues, atoms: 130, 1035 Classifications: {'peptide': 130} Link IDs: {'PCIS': 2, 'PTRANS': 8, 'TRANS': 119} Chain: "J" Number of atoms: 542 Number of conformers: 1 Conformer: "" Number of residues, atoms: 64, 542 Classifications: {'peptide': 64} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 58} Chain: "K" Number of atoms: 2724 Number of conformers: 1 Conformer: "" Number of residues, atoms: 348, 2724 Classifications: {'peptide': 348} Link IDs: {'PTRANS': 23, 'TRANS': 324} Chain breaks: 3 Time building chain proxies: 2.68, per 1000 atoms: 0.18 Number of scatterers: 15230 At special positions: 0 Unit cell: (159.909, 110.136, 117.549, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 86 16.00 P 86 15.00 O 3023 8.00 N 2681 7.00 C 9354 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.15 Conformation dependent library (CDL) restraints added in 495.2 milliseconds 3296 Ramachandran restraints generated. 1648 Oldfield, 0 Emsley, 1648 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3138 Finding SS restraints... Secondary structure from input PDB file: 59 helices and 19 sheets defined 30.8% alpha, 21.7% beta 30 base pairs and 46 stacking pairs defined. Time for finding SS restraints: 1.54 Creating SS restraints... Processing helix chain 'C' and resid 23 through 34 Processing helix chain 'C' and resid 53 through 57 Processing helix chain 'C' and resid 58 through 62 removed outlier: 3.689A pdb=" N LEU C 62 " --> pdb=" O PHE C 59 " (cutoff:3.500A) Processing helix chain 'C' and resid 82 through 89 Processing helix chain 'C' and resid 101 through 114 Processing helix chain 'C' and resid 138 through 141 Processing helix chain 'C' and resid 142 through 148 Processing helix chain 'C' and resid 165 through 176 removed outlier: 3.685A pdb=" N LEU C 169 " --> pdb=" O GLY C 165 " (cutoff:3.500A) Processing helix chain 'C' and resid 225 through 238 Processing helix chain 'C' and resid 263 through 277 Processing helix chain 'C' and resid 279 through 285 Processing helix chain 'C' and resid 290 through 296 removed outlier: 3.518A pdb=" N THR C 294 " --> pdb=" O LYS C 291 " (cutoff:3.500A) removed outlier: 4.498A pdb=" N SER C 295 " --> pdb=" O LEU C 292 " (cutoff:3.500A) Processing helix chain 'C' and resid 302 through 312 removed outlier: 3.554A pdb=" N VAL C 306 " --> pdb=" O LYS C 302 " (cutoff:3.500A) removed outlier: 4.562A pdb=" N ASN C 307 " --> pdb=" O ASP C 303 " (cutoff:3.500A) removed outlier: 4.644A pdb=" N ALA C 308 " --> pdb=" O SER C 304 " (cutoff:3.500A) Processing helix chain 'C' and resid 351 through 358 Processing helix chain 'C' and resid 383 through 395 removed outlier: 3.652A pdb=" N LYS C 394 " --> pdb=" O LYS C 390 " (cutoff:3.500A) Processing helix chain 'C' and resid 409 through 416 Processing helix chain 'D' and resid 90 through 94 removed outlier: 3.593A pdb=" N LYS D 94 " --> pdb=" O ASP D 91 " (cutoff:3.500A) Processing helix chain 'D' and resid 134 through 138 Processing helix chain 'D' and resid 147 through 151 Processing helix chain 'D' and resid 153 through 157 Processing helix chain 'E' and resid 24 through 28 Processing helix chain 'E' and resid 40 through 57 removed outlier: 3.890A pdb=" N LYS E 56 " --> pdb=" O LYS E 52 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N GLN E 57 " --> pdb=" O LYS E 53 " (cutoff:3.500A) Processing helix chain 'E' and resid 63 through 74 Processing helix chain 'E' and resid 88 through 102 removed outlier: 4.604A pdb=" N HIS E 93 " --> pdb=" O GLU E 89 " (cutoff:3.500A) removed outlier: 5.518A pdb=" N LEU E 94 " --> pdb=" O VAL E 90 " (cutoff:3.500A) Proline residue: E 95 - end of helix Processing helix chain 'E' and resid 110 through 119 removed outlier: 3.981A pdb=" N LEU E 114 " --> pdb=" O SER E 110 " (cutoff:3.500A) Processing helix chain 'E' and resid 135 through 148 Processing helix chain 'F' and resid 41 through 52 Processing helix chain 'G' and resid 43 through 47 Processing helix chain 'G' and resid 48 through 52 Processing helix chain 'G' and resid 53 through 57 Processing helix chain 'G' and resid 58 through 62 Processing helix chain 'G' and resid 77 through 81 removed outlier: 3.608A pdb=" N ARG G 81 " --> pdb=" O PRO G 78 " (cutoff:3.500A) Processing helix chain 'G' and resid 82 through 89 Processing helix chain 'G' and resid 101 through 113 Processing helix chain 'G' and resid 138 through 141 Processing helix chain 'G' and resid 142 through 149 removed outlier: 3.543A pdb=" N ALA G 149 " --> pdb=" O SER G 145 " (cutoff:3.500A) Processing helix chain 'G' and resid 165 through 176 removed outlier: 3.845A pdb=" N LEU G 169 " --> pdb=" O GLY G 165 " (cutoff:3.500A) Processing helix chain 'G' and resid 225 through 238 Processing helix chain 'G' and resid 263 through 277 Processing helix chain 'G' and resid 279 through 286 Processing helix chain 'G' and resid 290 through 292 No H-bonds generated for 'chain 'G' and resid 290 through 292' Processing helix chain 'G' and resid 304 through 311 removed outlier: 4.413A pdb=" N ALA G 308 " --> pdb=" O SER G 304 " (cutoff:3.500A) Processing helix chain 'G' and resid 351 through 358 Processing helix chain 'G' and resid 383 through 395 Processing helix chain 'H' and resid 134 through 138 removed outlier: 3.586A pdb=" N PHE H 138 " --> pdb=" O ALA H 135 " (cutoff:3.500A) Processing helix chain 'H' and resid 147 through 149 No H-bonds generated for 'chain 'H' and resid 147 through 149' Processing helix chain 'H' and resid 153 through 158 Processing helix chain 'I' and resid 24 through 30 removed outlier: 3.767A pdb=" N ASN I 30 " --> pdb=" O GLU I 26 " (cutoff:3.500A) Processing helix chain 'I' and resid 40 through 57 Processing helix chain 'I' and resid 63 through 73 Processing helix chain 'I' and resid 87 through 91 Processing helix chain 'I' and resid 93 through 102 removed outlier: 3.536A pdb=" N ARG I 101 " --> pdb=" O MET I 97 " (cutoff:3.500A) Processing helix chain 'I' and resid 110 through 118 removed outlier: 3.629A pdb=" N ALA I 118 " --> pdb=" O LEU I 114 " (cutoff:3.500A) Processing helix chain 'I' and resid 135 through 149 Processing helix chain 'J' and resid 41 through 52 Processing helix chain 'J' and resid 55 through 59 Processing helix chain 'K' and resid 163 through 167 Processing helix chain 'K' and resid 199 through 203 Processing helix chain 'K' and resid 239 through 242 removed outlier: 3.612A pdb=" N THR K 242 " --> pdb=" O GLN K 239 " (cutoff:3.500A) No H-bonds generated for 'chain 'K' and resid 239 through 242' Processing sheet with id=AA1, first strand: chain 'C' and resid 63 through 64 removed outlier: 6.539A pdb=" N VAL C 300 " --> pdb=" O LEU C 321 " (cutoff:3.500A) removed outlier: 4.661A pdb=" N TYR C 323 " --> pdb=" O ARG C 298 " (cutoff:3.500A) removed outlier: 7.151A pdb=" N ARG C 298 " --> pdb=" O TYR C 323 " (cutoff:3.500A) removed outlier: 6.106A pdb=" N LYS C 297 " --> pdb=" O VAL C 334 " (cutoff:3.500A) removed outlier: 7.135A pdb=" N ILE C 336 " --> pdb=" O LYS C 297 " (cutoff:3.500A) removed outlier: 5.893A pdb=" N LEU C 299 " --> pdb=" O ILE C 336 " (cutoff:3.500A) removed outlier: 6.694A pdb=" N ILE C 333 " --> pdb=" O MET C 345 " (cutoff:3.500A) removed outlier: 4.837A pdb=" N MET C 345 " --> pdb=" O ILE C 333 " (cutoff:3.500A) removed outlier: 6.915A pdb=" N VAL C 335 " --> pdb=" O ILE C 343 " (cutoff:3.500A) removed outlier: 8.083A pdb=" N ILE C 343 " --> pdb=" O VAL C 369 " (cutoff:3.500A) removed outlier: 5.178A pdb=" N VAL C 369 " --> pdb=" O ILE C 343 " (cutoff:3.500A) removed outlier: 6.525A pdb=" N MET C 345 " --> pdb=" O LYS C 367 " (cutoff:3.500A) removed outlier: 7.256A pdb=" N ILE C 315 " --> pdb=" O VAL C 363 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'C' and resid 90 through 96 WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 90 through 96 current: chain 'C' and resid 129 through 136 WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 129 through 136 current: chain 'C' and resid 195 through 207 removed outlier: 3.841A pdb=" N GLU C 201 " --> pdb=" O SER C 219 " (cutoff:3.500A) removed outlier: 6.995A pdb=" N ILE C 215 " --> pdb=" O ILE C 205 " (cutoff:3.500A) removed outlier: 4.964A pdb=" N TYR C 207 " --> pdb=" O LEU C 213 " (cutoff:3.500A) removed outlier: 7.183A pdb=" N LEU C 213 " --> pdb=" O TYR C 207 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 213 through 220 current: chain 'C' and resid 254 through 255 Processing sheet with id=AA3, first strand: chain 'D' and resid 71 through 80 removed outlier: 5.374A pdb=" N PHE D 76 " --> pdb=" O LYS D 87 " (cutoff:3.500A) removed outlier: 5.161A pdb=" N LYS D 87 " --> pdb=" O PHE D 76 " (cutoff:3.500A) removed outlier: 4.091A pdb=" N HIS D 78 " --> pdb=" O VAL D 85 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N VAL D 85 " --> pdb=" O HIS D 78 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N ILE D 84 " --> pdb=" O VAL D 127 " (cutoff:3.500A) removed outlier: 6.938A pdb=" N TYR D 124 " --> pdb=" O ILE D 116 " (cutoff:3.500A) removed outlier: 4.960A pdb=" N ILE D 116 " --> pdb=" O TYR D 124 " (cutoff:3.500A) removed outlier: 6.771A pdb=" N SER D 126 " --> pdb=" O ASP D 114 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N GLY D 111 " --> pdb=" O VAL D 102 " (cutoff:3.500A) removed outlier: 6.585A pdb=" N PHE D 144 " --> pdb=" O LEU D 73 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'E' and resid 60 through 62 Processing sheet with id=AA5, first strand: chain 'F' and resid 13 through 16 Processing sheet with id=AA6, first strand: chain 'G' and resid 63 through 64 removed outlier: 6.607A pdb=" N VAL G 300 " --> pdb=" O LEU G 321 " (cutoff:3.500A) removed outlier: 4.789A pdb=" N TYR G 323 " --> pdb=" O ARG G 298 " (cutoff:3.500A) removed outlier: 7.165A pdb=" N ARG G 298 " --> pdb=" O TYR G 323 " (cutoff:3.500A) removed outlier: 6.263A pdb=" N LEU G 299 " --> pdb=" O ILE G 336 " (cutoff:3.500A) removed outlier: 5.360A pdb=" N ILE G 347 " --> pdb=" O ILE G 366 " (cutoff:3.500A) removed outlier: 5.594A pdb=" N ILE G 366 " --> pdb=" O ILE G 347 " (cutoff:3.500A) removed outlier: 6.700A pdb=" N ILE G 315 " --> pdb=" O VAL G 363 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'G' and resid 90 through 96 WARNING: can't find start of bonding for strands! previous: chain 'G' and resid 90 through 96 current: chain 'G' and resid 129 through 136 WARNING: can't find start of bonding for strands! previous: chain 'G' and resid 129 through 136 current: chain 'G' and resid 195 through 208 removed outlier: 5.355A pdb=" N SER G 202 " --> pdb=" O SER G 219 " (cutoff:3.500A) removed outlier: 6.882A pdb=" N SER G 219 " --> pdb=" O SER G 202 " (cutoff:3.500A) removed outlier: 5.355A pdb=" N MET G 204 " --> pdb=" O TRP G 217 " (cutoff:3.500A) removed outlier: 6.496A pdb=" N TRP G 217 " --> pdb=" O MET G 204 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N GLU G 206 " --> pdb=" O ILE G 215 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'G' and resid 213 through 220 current: chain 'G' and resid 254 through 255 Processing sheet with id=AA8, first strand: chain 'H' and resid 71 through 79 removed outlier: 4.311A pdb=" N VAL H 85 " --> pdb=" O LEU H 77 " (cutoff:3.500A) removed outlier: 5.187A pdb=" N PHE H 123 " --> pdb=" O CYS H 88 " (cutoff:3.500A) removed outlier: 6.815A pdb=" N TYR H 124 " --> pdb=" O ILE H 116 " (cutoff:3.500A) removed outlier: 4.881A pdb=" N ILE H 116 " --> pdb=" O TYR H 124 " (cutoff:3.500A) removed outlier: 6.409A pdb=" N SER H 126 " --> pdb=" O ASP H 114 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N GLY H 111 " --> pdb=" O VAL H 102 " (cutoff:3.500A) removed outlier: 6.458A pdb=" N PHE H 144 " --> pdb=" O LEU H 73 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'H' and resid 95 through 96 Processing sheet with id=AB1, first strand: chain 'I' and resid 60 through 62 removed outlier: 6.485A pdb=" N MET I 79 " --> pdb=" O VAL I 106 " (cutoff:3.500A) removed outlier: 7.598A pdb=" N ILE I 108 " --> pdb=" O MET I 79 " (cutoff:3.500A) removed outlier: 6.330A pdb=" N LEU I 81 " --> pdb=" O ILE I 108 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'J' and resid 13 through 16 Processing sheet with id=AB3, first strand: chain 'K' and resid 155 through 160 removed outlier: 4.247A pdb=" N GLY K 159 " --> pdb=" O LEU K 514 " (cutoff:3.500A) removed outlier: 6.665A pdb=" N LEU K 514 " --> pdb=" O GLY K 159 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'K' and resid 172 through 177 removed outlier: 4.013A pdb=" N GLY K 174 " --> pdb=" O ASN K 187 " (cutoff:3.500A) removed outlier: 4.107A pdb=" N SER K 188 " --> pdb=" O ILE K 192 " (cutoff:3.500A) removed outlier: 4.290A pdb=" N ILE K 192 " --> pdb=" O SER K 188 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N ILE K 195 " --> pdb=" O LEU K 218 " (cutoff:3.500A) removed outlier: 4.057A pdb=" N LEU K 218 " --> pdb=" O ILE K 195 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'K' and resid 226 through 231 removed outlier: 3.649A pdb=" N ASP K 228 " --> pdb=" O SER K 248 " (cutoff:3.500A) removed outlier: 6.256A pdb=" N ILE K 254 " --> pdb=" O SER K 267 " (cutoff:3.500A) removed outlier: 4.398A pdb=" N SER K 267 " --> pdb=" O ILE K 254 " (cutoff:3.500A) removed outlier: 6.557A pdb=" N ILE K 256 " --> pdb=" O ARG K 265 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'K' and resid 282 through 285 removed outlier: 3.889A pdb=" N SER K 282 " --> pdb=" O GLY K 295 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'K' and resid 318 through 319 Processing sheet with id=AB8, first strand: chain 'K' and resid 328 through 333 removed outlier: 3.556A pdb=" N CYS K 330 " --> pdb=" O GLY K 343 " (cutoff:3.500A) removed outlier: 4.088A pdb=" N SER K 348 " --> pdb=" O SER K 344 " (cutoff:3.500A) removed outlier: 6.596A pdb=" N LEU K 349 " --> pdb=" O LEU K 362 " (cutoff:3.500A) removed outlier: 4.541A pdb=" N LEU K 362 " --> pdb=" O LEU K 349 " (cutoff:3.500A) removed outlier: 6.511A pdb=" N LEU K 351 " --> pdb=" O LEU K 360 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'K' and resid 370 through 375 removed outlier: 3.561A pdb=" N HIS K 372 " --> pdb=" O GLY K 385 " (cutoff:3.500A) removed outlier: 4.748A pdb=" N ALA K 386 " --> pdb=" O GLU K 391 " (cutoff:3.500A) removed outlier: 6.903A pdb=" N GLU K 391 " --> pdb=" O ALA K 386 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N TRP K 405 " --> pdb=" O CYS K 394 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'K' and resid 419 through 421 removed outlier: 6.612A pdb=" N VAL K 437 " --> pdb=" O SER K 456 " (cutoff:3.500A) removed outlier: 4.272A pdb=" N SER K 456 " --> pdb=" O VAL K 437 " (cutoff:3.500A) removed outlier: 6.629A pdb=" N VAL K 439 " --> pdb=" O VAL K 454 " (cutoff:3.500A) 433 hydrogen bonds defined for protein. 1137 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 82 hydrogen bonds 156 hydrogen bond angles 0 basepair planarities 30 basepair parallelities 46 stacking parallelities Total time for adding SS restraints: 2.26 Time building geometry restraints manager: 1.52 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 4163 1.33 - 1.46: 3172 1.46 - 1.58: 8115 1.58 - 1.70: 165 1.70 - 1.82: 125 Bond restraints: 15740 Sorted by residual: bond pdb=" CA PRO H 66 " pdb=" C PRO H 66 " ideal model delta sigma weight residual 1.514 1.530 -0.016 5.50e-03 3.31e+04 8.08e+00 bond pdb=" CA PRO G 184 " pdb=" C PRO G 184 " ideal model delta sigma weight residual 1.514 1.529 -0.014 5.50e-03 3.31e+04 6.89e+00 bond pdb=" N GLY H 65 " pdb=" CA GLY H 65 " ideal model delta sigma weight residual 1.451 1.489 -0.038 1.60e-02 3.91e+03 5.50e+00 bond pdb=" C LEU G 317 " pdb=" O LEU G 317 " ideal model delta sigma weight residual 1.243 1.222 0.022 9.50e-03 1.11e+04 5.22e+00 bond pdb=" C ARG C 284 " pdb=" O ARG C 284 " ideal model delta sigma weight residual 1.237 1.211 0.025 1.19e-02 7.06e+03 4.49e+00 ... (remaining 15735 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.64: 19689 1.64 - 3.27: 1619 3.27 - 4.91: 333 4.91 - 6.55: 45 6.55 - 8.19: 11 Bond angle restraints: 21697 Sorted by residual: angle pdb=" N GLY G 130 " pdb=" CA GLY G 130 " pdb=" C GLY G 130 " ideal model delta sigma weight residual 111.56 117.55 -5.99 1.01e+00 9.80e-01 3.52e+01 angle pdb=" N PRO C 404 " pdb=" CA PRO C 404 " pdb=" C PRO C 404 " ideal model delta sigma weight residual 111.33 117.36 -6.03 1.43e+00 4.89e-01 1.78e+01 angle pdb=" N LEU D 120 " pdb=" CA LEU D 120 " pdb=" C LEU D 120 " ideal model delta sigma weight residual 111.07 115.30 -4.23 1.07e+00 8.73e-01 1.56e+01 angle pdb=" N ALA I 35 " pdb=" CA ALA I 35 " pdb=" C ALA I 35 " ideal model delta sigma weight residual 112.38 117.15 -4.77 1.22e+00 6.72e-01 1.53e+01 angle pdb=" C LEU G 54 " pdb=" CA LEU G 54 " pdb=" CB LEU G 54 " ideal model delta sigma weight residual 116.63 112.19 4.44 1.16e+00 7.43e-01 1.47e+01 ... (remaining 21692 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.69: 8476 17.69 - 35.38: 772 35.38 - 53.07: 212 53.07 - 70.76: 191 70.76 - 88.45: 61 Dihedral angle restraints: 9712 sinusoidal: 4841 harmonic: 4871 Sorted by residual: dihedral pdb=" C4' G B 380 " pdb=" C3' G B 380 " pdb=" C2' G B 380 " pdb=" C1' G B 380 " ideal model delta sinusoidal sigma weight residual 36.34 -41.91 78.25 1 3.10e+00 1.04e-01 7.96e+02 dihedral pdb=" C4' A B 378 " pdb=" C3' A B 378 " pdb=" C2' A B 378 " pdb=" C1' A B 378 " ideal model delta sinusoidal sigma weight residual 36.34 -40.57 76.92 1 3.10e+00 1.04e-01 7.73e+02 dihedral pdb=" C4' A B 374 " pdb=" C3' A B 374 " pdb=" C2' A B 374 " pdb=" C1' A B 374 " ideal model delta sinusoidal sigma weight residual 36.34 -38.86 75.20 1 3.10e+00 1.04e-01 7.44e+02 ... (remaining 9709 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.066: 1612 0.066 - 0.132: 540 0.132 - 0.198: 151 0.198 - 0.264: 160 0.264 - 0.329: 9 Chirality restraints: 2472 Sorted by residual: chirality pdb=" C2' U B 416 " pdb=" C3' U B 416 " pdb=" O2' U B 416 " pdb=" C1' U B 416 " both_signs ideal model delta sigma weight residual False -2.79 -2.46 -0.33 2.00e-01 2.50e+01 2.71e+00 chirality pdb=" C3' A B 374 " pdb=" C4' A B 374 " pdb=" O3' A B 374 " pdb=" C2' A B 374 " both_signs ideal model delta sigma weight residual False -2.50 -2.81 0.31 2.00e-01 2.50e+01 2.44e+00 chirality pdb=" C2' C B 436 " pdb=" C3' C B 436 " pdb=" O2' C B 436 " pdb=" C1' C B 436 " both_signs ideal model delta sigma weight residual False -2.79 -2.51 -0.28 2.00e-01 2.50e+01 2.02e+00 ... (remaining 2469 not shown) Planarity restraints: 2448 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG G 88 " 0.164 9.50e-02 1.11e+02 7.43e-02 4.51e+00 pdb=" NE ARG G 88 " -0.016 2.00e-02 2.50e+03 pdb=" CZ ARG G 88 " 0.017 2.00e-02 2.50e+03 pdb=" NH1 ARG G 88 " -0.008 2.00e-02 2.50e+03 pdb=" NH2 ARG G 88 " -0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' U B 416 " 0.021 2.00e-02 2.50e+03 1.27e-02 3.62e+00 pdb=" N1 U B 416 " -0.032 2.00e-02 2.50e+03 pdb=" C2 U B 416 " -0.000 2.00e-02 2.50e+03 pdb=" O2 U B 416 " 0.001 2.00e-02 2.50e+03 pdb=" N3 U B 416 " 0.001 2.00e-02 2.50e+03 pdb=" C4 U B 416 " 0.004 2.00e-02 2.50e+03 pdb=" O4 U B 416 " 0.004 2.00e-02 2.50e+03 pdb=" C5 U B 416 " 0.001 2.00e-02 2.50e+03 pdb=" C6 U B 416 " 0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C LYS G 96 " -0.030 5.00e-02 4.00e+02 4.59e-02 3.36e+00 pdb=" N PRO G 97 " 0.079 5.00e-02 4.00e+02 pdb=" CA PRO G 97 " -0.023 5.00e-02 4.00e+02 pdb=" CD PRO G 97 " -0.026 5.00e-02 4.00e+02 ... (remaining 2445 not shown) Histogram of nonbonded interaction distances: 2.21 - 2.75: 1209 2.75 - 3.29: 14763 3.29 - 3.83: 25550 3.83 - 4.36: 32610 4.36 - 4.90: 53093 Nonbonded interactions: 127225 Sorted by model distance: nonbonded pdb=" O LYS E 130 " pdb=" OH TYR E 135 " model vdw 2.213 3.040 nonbonded pdb=" OE2 GLU K 163 " pdb=" OH TYR K 196 " model vdw 2.277 3.040 nonbonded pdb=" OG SER K 329 " pdb=" O ILE K 370 " model vdw 2.319 3.040 nonbonded pdb=" O LYS I 130 " pdb=" OH TYR I 135 " model vdw 2.359 3.040 nonbonded pdb=" O GLU G 137 " pdb=" OG1 THR G 140 " model vdw 2.420 3.040 ... (remaining 127220 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 'C' and resid 43 through 395) selection = (chain 'G' and (resid 43 through 186 or resid 192 through 395)) } ncs_group { reference = chain 'D' selection = (chain 'H' and resid 66 through 159) } ncs_group { reference = chain 'E' selection = chain 'I' } ncs_group { reference = chain 'F' selection = chain 'J' } 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: 1.540 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: 0.000 Extract box with map and model: 0.240 Check model and map are aligned: 0.030 Set scattering table: 0.050 Process input model: 14.010 Find NCS groups from input model: 0.140 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.050 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 17.090 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7588 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 : 0.006 0.038 15740 Z= 0.407 Angle : 1.041 8.185 21697 Z= 0.592 Chirality : 0.088 0.329 2472 Planarity : 0.006 0.074 2448 Dihedral : 18.518 88.452 6574 Min Nonbonded Distance : 2.213 Molprobity Statistics. All-atom Clashscore : 1.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.91 % Favored : 99.09 % Rotamer: Outliers : 0.14 % Allowed : 0.34 % Favored : 99.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.08 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.59 (0.20), residues: 1648 helix: -0.36 (0.24), residues: 385 sheet: -1.44 (0.25), residues: 360 loop : 0.26 (0.21), residues: 903 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.022 0.002 ARG G 197 TYR 0.024 0.004 TYR E 91 PHE 0.015 0.003 PHE K 382 TRP 0.025 0.003 TRP G 380 HIS 0.012 0.002 HIS H 78 Details of bonding type rmsd/Z covalent geometry : bond 0.00615 / 0.41 (15740) covalent geometry : angle 1.04068 / 0.59 (21697) hydrogen bonds : bond 0.17897 / 9.17 ( 515) hydrogen bonds : angle 7.46710 / 3.05 ( 1293) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3296 Ramachandran restraints generated. 1648 Oldfield, 0 Emsley, 1648 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3296 Ramachandran restraints generated. 1648 Oldfield, 0 Emsley, 1648 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 296 residues out of total 1478 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 294 time to evaluate : 0.519 Fit side-chains revert: symmetry clash REVERT: C 144 LYS cc_start: 0.7653 (tttt) cc_final: 0.7229 (mmmt) REVERT: C 164 GLU cc_start: 0.7602 (tt0) cc_final: 0.7095 (mm-30) REVERT: C 183 ARG cc_start: 0.7634 (mtp180) cc_final: 0.7309 (mtp180) REVERT: C 195 ARG cc_start: 0.6750 (mtp180) cc_final: 0.6403 (mtm180) REVERT: C 203 LYS cc_start: 0.7635 (mtmt) cc_final: 0.6747 (mmtm) REVERT: C 258 ASP cc_start: 0.6441 (t0) cc_final: 0.5977 (t0) REVERT: C 280 SER cc_start: 0.7658 (t) cc_final: 0.7423 (p) REVERT: C 284 ARG cc_start: 0.7457 (mmt-90) cc_final: 0.7006 (mmm-85) REVERT: C 372 GLU cc_start: 0.8051 (tt0) cc_final: 0.7520 (tp30) REVERT: C 414 GLN cc_start: 0.8166 (tp40) cc_final: 0.7810 (tm-30) REVERT: D 97 TYR cc_start: 0.7201 (m-10) cc_final: 0.6712 (m-80) REVERT: D 108 GLU cc_start: 0.7881 (tt0) cc_final: 0.7505 (pt0) REVERT: D 144 PHE cc_start: 0.7386 (m-80) cc_final: 0.7106 (m-80) REVERT: D 150 LYS cc_start: 0.6916 (mttp) cc_final: 0.6526 (mttp) REVERT: E 36 GLN cc_start: 0.7203 (mt0) cc_final: 0.6862 (mm-40) REVERT: E 62 ARG cc_start: 0.6387 (ptt90) cc_final: 0.5969 (ttp-170) REVERT: E 66 GLU cc_start: 0.7615 (tt0) cc_final: 0.7297 (tt0) REVERT: E 101 ARG cc_start: 0.5883 (mtt-85) cc_final: 0.5623 (mmm-85) REVERT: E 144 GLU cc_start: 0.7130 (tt0) cc_final: 0.6588 (tm-30) REVERT: F 21 ASP cc_start: 0.5405 (p0) cc_final: 0.4858 (p0) REVERT: F 25 GLN cc_start: 0.7341 (pt0) cc_final: 0.6458 (pm20) REVERT: F 36 SER cc_start: 0.8105 (p) cc_final: 0.7859 (p) REVERT: G 81 ARG cc_start: 0.8457 (mtt180) cc_final: 0.8252 (mtt180) REVERT: G 144 LYS cc_start: 0.8094 (tttm) cc_final: 0.7788 (mptt) REVERT: G 161 ASN cc_start: 0.8646 (t0) cc_final: 0.8443 (t0) REVERT: G 164 GLU cc_start: 0.7749 (mt-10) cc_final: 0.7222 (tm-30) REVERT: G 316 MET cc_start: 0.8854 (mmt) cc_final: 0.8215 (mmt) REVERT: G 328 GLU cc_start: 0.8321 (mm-30) cc_final: 0.8083 (mm-30) REVERT: G 372 GLU cc_start: 0.7735 (mt-10) cc_final: 0.7428 (tp30) REVERT: H 108 GLU cc_start: 0.7624 (tt0) cc_final: 0.7274 (tt0) REVERT: H 130 SER cc_start: 0.8125 (m) cc_final: 0.7619 (m) REVERT: H 133 MET cc_start: 0.7506 (mmt) cc_final: 0.7086 (mmm) REVERT: H 139 LYS cc_start: 0.6997 (mtpt) cc_final: 0.6322 (pttm) REVERT: I 36 GLN cc_start: 0.6576 (mt0) cc_final: 0.6338 (mp10) REVERT: I 41 ARG cc_start: 0.6720 (ttt-90) cc_final: 0.6384 (ttt180) REVERT: I 52 LYS cc_start: 0.7895 (tttt) cc_final: 0.7537 (mmtt) REVERT: I 89 GLU cc_start: 0.8230 (mt-10) cc_final: 0.7962 (mp0) REVERT: I 113 ASP cc_start: 0.8476 (m-30) cc_final: 0.8219 (m-30) REVERT: I 145 GLU cc_start: 0.7589 (tt0) cc_final: 0.7272 (tp30) REVERT: J 40 LYS cc_start: 0.8684 (mttt) cc_final: 0.8412 (mmmt) REVERT: J 53 LYS cc_start: 0.8640 (mmtt) cc_final: 0.8351 (mmtm) REVERT: K 147 ASN cc_start: 0.5952 (t0) cc_final: 0.5686 (t0) REVERT: K 182 SER cc_start: 0.8772 (t) cc_final: 0.8331 (m) REVERT: K 273 HIS cc_start: 0.8686 (p-80) cc_final: 0.8387 (p90) REVERT: K 274 LEU cc_start: 0.8845 (mt) cc_final: 0.8587 (mt) REVERT: K 307 ARG cc_start: 0.7778 (ttp-170) cc_final: 0.7233 (tpt170) outliers start: 2 outliers final: 2 residues processed: 295 average time/residue: 0.1346 time to fit residues: 55.7145 Evaluate side-chains 224 residues out of total 1478 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 222 time to evaluate : 0.405 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 91 TYR Chi-restraints excluded: chain I residue 91 TYR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 172 random chunks: chunk 98 optimal weight: 0.7980 chunk 107 optimal weight: 3.9990 chunk 10 optimal weight: 6.9990 chunk 66 optimal weight: 9.9990 chunk 130 optimal weight: 6.9990 chunk 124 optimal weight: 3.9990 chunk 103 optimal weight: 2.9990 chunk 77 optimal weight: 0.6980 chunk 122 optimal weight: 5.9990 chunk 91 optimal weight: 1.9990 chunk 149 optimal weight: 2.9990 overall best weight: 1.8986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 99 ASN E 68 GLN F 10 GLN F 44 HIS G 160 HIS G 168 GLN G 259 HIS G 296 HIS G 395 GLN I 30 ASN ** I 57 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 147 GLN J 31 HIS J 44 HIS J 58 GLN K 197 ASN K 366 HIS K 515 GLN Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3703 r_free = 0.3703 target = 0.133823 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3275 r_free = 0.3275 target = 0.101634 restraints weight = 21600.742| |-----------------------------------------------------------------------------| r_work (start): 0.3250 rms_B_bonded: 1.60 r_work: 0.3076 rms_B_bonded: 2.47 restraints_weight: 0.5000 r_work: 0.2955 rms_B_bonded: 3.89 restraints_weight: 0.2500 r_work (final): 0.2955 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8453 moved from start: 0.1569 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.068 15740 Z= 0.222 Angle : 0.977 20.145 21697 Z= 0.455 Chirality : 0.091 1.624 2472 Planarity : 0.005 0.047 2448 Dihedral : 18.625 144.436 3206 Min Nonbonded Distance : 2.228 Molprobity Statistics. All-atom Clashscore : 4.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.52 % Favored : 98.48 % Rotamer: Outliers : 1.15 % Allowed : 6.36 % Favored : 92.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.08 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.33 (0.20), residues: 1648 helix: 0.46 (0.26), residues: 387 sheet: -1.44 (0.24), residues: 376 loop : 0.22 (0.21), residues: 885 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG I 42 TYR 0.028 0.002 TYR C 281 PHE 0.018 0.002 PHE K 382 TRP 0.025 0.002 TRP G 380 HIS 0.009 0.001 HIS E 132 Details of bonding type rmsd/Z covalent geometry : bond 0.00510 / 0.22 (15740) covalent geometry : angle 0.97716 / 0.46 (21697) hydrogen bonds : bond 0.05339 / 2.75 ( 515) hydrogen bonds : angle 5.74254 / 2.33 ( 1293) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3296 Ramachandran restraints generated. 1648 Oldfield, 0 Emsley, 1648 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3296 Ramachandran restraints generated. 1648 Oldfield, 0 Emsley, 1648 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 247 residues out of total 1478 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 230 time to evaluate : 0.520 Fit side-chains revert: symmetry clash REVERT: C 164 GLU cc_start: 0.7567 (tt0) cc_final: 0.7335 (mm-30) REVERT: C 203 LYS cc_start: 0.7903 (mtmt) cc_final: 0.7416 (mttp) REVERT: C 284 ARG cc_start: 0.8052 (mmt-90) cc_final: 0.7817 (mmt180) REVERT: E 44 THR cc_start: 0.8354 (m) cc_final: 0.8095 (p) REVERT: F 21 ASP cc_start: 0.6660 (p0) cc_final: 0.6429 (p0) REVERT: F 25 GLN cc_start: 0.7909 (pt0) cc_final: 0.7454 (pm20) REVERT: F 36 SER cc_start: 0.8931 (p) cc_final: 0.8666 (t) REVERT: G 316 MET cc_start: 0.8632 (mmt) cc_final: 0.8250 (mmt) REVERT: H 130 SER cc_start: 0.8313 (m) cc_final: 0.8081 (m) REVERT: I 113 ASP cc_start: 0.9036 (m-30) cc_final: 0.8771 (m-30) REVERT: K 265 ARG cc_start: 0.8493 (ttt180) cc_final: 0.7694 (ttp80) REVERT: K 274 LEU cc_start: 0.9196 (mt) cc_final: 0.8796 (mt) outliers start: 17 outliers final: 11 residues processed: 239 average time/residue: 0.1283 time to fit residues: 42.9903 Evaluate side-chains 212 residues out of total 1478 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 201 time to evaluate : 0.360 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 393 ILE Chi-restraints excluded: chain D residue 71 VAL Chi-restraints excluded: chain E residue 40 SER Chi-restraints excluded: chain E residue 91 TYR Chi-restraints excluded: chain G residue 66 THR Chi-restraints excluded: chain G residue 67 THR Chi-restraints excluded: chain I residue 78 ILE Chi-restraints excluded: chain I residue 91 TYR Chi-restraints excluded: chain I residue 148 SER Chi-restraints excluded: chain K residue 218 LEU Chi-restraints excluded: chain K residue 235 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 172 random chunks: chunk 142 optimal weight: 3.9990 chunk 154 optimal weight: 1.9990 chunk 164 optimal weight: 2.9990 chunk 7 optimal weight: 8.9990 chunk 47 optimal weight: 7.9990 chunk 28 optimal weight: 3.9990 chunk 52 optimal weight: 1.9990 chunk 117 optimal weight: 3.9990 chunk 49 optimal weight: 2.9990 chunk 32 optimal weight: 4.9990 chunk 79 optimal weight: 1.9990 overall best weight: 2.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 99 ASN C 168 GLN ** I 57 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3710 r_free = 0.3710 target = 0.134174 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3279 r_free = 0.3279 target = 0.101768 restraints weight = 21785.991| |-----------------------------------------------------------------------------| r_work (start): 0.3265 rms_B_bonded: 1.73 r_work: 0.3051 rms_B_bonded: 2.86 restraints_weight: 0.5000 r_work: 0.2924 rms_B_bonded: 4.56 restraints_weight: 0.2500 r_work (final): 0.2924 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8501 moved from start: 0.2210 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.091 15740 Z= 0.236 Angle : 0.851 15.357 21697 Z= 0.403 Chirality : 0.080 2.043 2472 Planarity : 0.005 0.047 2448 Dihedral : 18.813 159.545 3206 Min Nonbonded Distance : 2.203 Molprobity Statistics. All-atom Clashscore : 4.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.70 % Favored : 98.30 % Rotamer: Outliers : 1.89 % Allowed : 9.27 % Favored : 88.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.08 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.42 (0.20), residues: 1648 helix: 0.54 (0.26), residues: 387 sheet: -1.54 (0.24), residues: 392 loop : 0.14 (0.21), residues: 869 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG I 62 TYR 0.020 0.002 TYR C 281 PHE 0.015 0.002 PHE K 382 TRP 0.021 0.002 TRP G 380 HIS 0.006 0.001 HIS C 259 Details of bonding type rmsd/Z covalent geometry : bond 0.00558 / 0.24 (15740) covalent geometry : angle 0.85149 / 0.40 (21697) hydrogen bonds : bond 0.04894 / 2.53 ( 515) hydrogen bonds : angle 5.41295 / 2.19 ( 1293) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3296 Ramachandran restraints generated. 1648 Oldfield, 0 Emsley, 1648 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3296 Ramachandran restraints generated. 1648 Oldfield, 0 Emsley, 1648 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 232 residues out of total 1478 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 204 time to evaluate : 0.549 Fit side-chains REVERT: C 164 GLU cc_start: 0.7748 (tt0) cc_final: 0.7442 (mm-30) REVERT: C 203 LYS cc_start: 0.7987 (mtmt) cc_final: 0.7403 (mttp) REVERT: C 284 ARG cc_start: 0.8185 (mmt-90) cc_final: 0.7913 (mmt180) REVERT: D 143 LYS cc_start: 0.7595 (mtmt) cc_final: 0.6732 (mmmm) REVERT: E 44 THR cc_start: 0.8303 (m) cc_final: 0.8082 (p) REVERT: E 57 GLN cc_start: 0.7688 (mm-40) cc_final: 0.7409 (mm-40) REVERT: F 21 ASP cc_start: 0.6657 (p0) cc_final: 0.6323 (p0) REVERT: F 25 GLN cc_start: 0.8107 (pt0) cc_final: 0.7539 (pm20) REVERT: F 36 SER cc_start: 0.9021 (p) cc_final: 0.8805 (t) REVERT: I 113 ASP cc_start: 0.9051 (m-30) cc_final: 0.8777 (m-30) REVERT: J 58 GLN cc_start: 0.8797 (OUTLIER) cc_final: 0.8571 (mt0) REVERT: K 211 TYR cc_start: 0.7147 (m-80) cc_final: 0.6581 (m-80) REVERT: K 265 ARG cc_start: 0.8637 (ttt180) cc_final: 0.7845 (ttp80) REVERT: K 321 LYS cc_start: 0.7755 (pttt) cc_final: 0.6951 (mttt) outliers start: 28 outliers final: 15 residues processed: 223 average time/residue: 0.1187 time to fit residues: 38.0138 Evaluate side-chains 207 residues out of total 1478 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 191 time to evaluate : 0.527 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 230 CYS Chi-restraints excluded: chain C residue 393 ILE Chi-restraints excluded: chain D residue 71 VAL Chi-restraints excluded: chain D residue 73 LEU Chi-restraints excluded: chain D residue 90 THR Chi-restraints excluded: chain E residue 40 SER Chi-restraints excluded: chain E residue 91 TYR Chi-restraints excluded: chain E residue 129 VAL Chi-restraints excluded: chain G residue 66 THR Chi-restraints excluded: chain G residue 67 THR Chi-restraints excluded: chain H residue 71 VAL Chi-restraints excluded: chain I residue 78 ILE Chi-restraints excluded: chain I residue 91 TYR Chi-restraints excluded: chain J residue 58 GLN Chi-restraints excluded: chain K residue 182 SER Chi-restraints excluded: chain K residue 218 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 172 random chunks: chunk 43 optimal weight: 3.9990 chunk 83 optimal weight: 0.7980 chunk 108 optimal weight: 2.9990 chunk 11 optimal weight: 0.9990 chunk 122 optimal weight: 5.9990 chunk 127 optimal weight: 0.0980 chunk 155 optimal weight: 8.9990 chunk 40 optimal weight: 7.9990 chunk 170 optimal weight: 6.9990 chunk 152 optimal weight: 1.9990 chunk 87 optimal weight: 3.9990 overall best weight: 1.3786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 99 ASN C 360 HIS I 57 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3729 r_free = 0.3729 target = 0.135745 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3307 r_free = 0.3307 target = 0.103507 restraints weight = 21593.427| |-----------------------------------------------------------------------------| r_work (start): 0.3295 rms_B_bonded: 1.76 r_work: 0.3084 rms_B_bonded: 2.95 restraints_weight: 0.5000 r_work: 0.2955 rms_B_bonded: 4.72 restraints_weight: 0.2500 r_work (final): 0.2955 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8466 moved from start: 0.2507 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 15740 Z= 0.162 Angle : 0.761 11.812 21697 Z= 0.356 Chirality : 0.070 1.642 2472 Planarity : 0.004 0.047 2448 Dihedral : 18.760 175.121 3206 Min Nonbonded Distance : 2.296 Molprobity Statistics. All-atom Clashscore : 5.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.88 % Favored : 98.12 % Rotamer: Outliers : 1.96 % Allowed : 10.35 % Favored : 87.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.08 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.29 (0.21), residues: 1648 helix: 0.78 (0.27), residues: 391 sheet: -1.56 (0.24), residues: 403 loop : 0.24 (0.21), residues: 854 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG E 62 TYR 0.017 0.001 TYR G 281 PHE 0.013 0.001 PHE K 382 TRP 0.018 0.001 TRP G 380 HIS 0.004 0.001 HIS J 44 Details of bonding type rmsd/Z covalent geometry : bond 0.00377 / 0.16 (15740) covalent geometry : angle 0.76147 / 0.36 (21697) hydrogen bonds : bond 0.04115 / 2.13 ( 515) hydrogen bonds : angle 5.10809 / 2.07 ( 1293) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3296 Ramachandran restraints generated. 1648 Oldfield, 0 Emsley, 1648 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3296 Ramachandran restraints generated. 1648 Oldfield, 0 Emsley, 1648 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 229 residues out of total 1478 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 200 time to evaluate : 0.530 Fit side-chains REVERT: C 164 GLU cc_start: 0.7650 (tt0) cc_final: 0.7369 (mm-30) REVERT: C 203 LYS cc_start: 0.7932 (mtmt) cc_final: 0.7372 (mttp) REVERT: C 284 ARG cc_start: 0.8108 (mmt-90) cc_final: 0.7827 (mmt180) REVERT: C 421 GLU cc_start: 0.4342 (mm-30) cc_final: 0.3513 (pt0) REVERT: E 44 THR cc_start: 0.8233 (m) cc_final: 0.8010 (p) REVERT: E 57 GLN cc_start: 0.7555 (mm-40) cc_final: 0.7266 (mm-40) REVERT: F 21 ASP cc_start: 0.6609 (p0) cc_final: 0.6239 (p0) REVERT: F 25 GLN cc_start: 0.8043 (pt0) cc_final: 0.7430 (pm20) REVERT: F 59 GLN cc_start: 0.5753 (mt0) cc_final: 0.5268 (mt0) REVERT: G 66 THR cc_start: 0.8194 (OUTLIER) cc_final: 0.7894 (t) REVERT: H 115 GLU cc_start: 0.8147 (mm-30) cc_final: 0.7898 (mm-30) REVERT: I 145 GLU cc_start: 0.8192 (tp30) cc_final: 0.7838 (tp30) REVERT: J 58 GLN cc_start: 0.8785 (OUTLIER) cc_final: 0.8573 (mt0) REVERT: K 265 ARG cc_start: 0.8643 (ttt180) cc_final: 0.7893 (ttp80) REVERT: K 321 LYS cc_start: 0.7703 (pttt) cc_final: 0.6961 (mttt) REVERT: K 391 GLU cc_start: 0.8226 (pt0) cc_final: 0.7986 (pt0) outliers start: 29 outliers final: 19 residues processed: 222 average time/residue: 0.1357 time to fit residues: 42.8371 Evaluate side-chains 211 residues out of total 1478 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 190 time to evaluate : 0.553 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 261 VAL Chi-restraints excluded: chain C residue 351 THR Chi-restraints excluded: chain D residue 71 VAL Chi-restraints excluded: chain D residue 73 LEU Chi-restraints excluded: chain D residue 84 ILE Chi-restraints excluded: chain D residue 110 ILE Chi-restraints excluded: chain E residue 40 SER Chi-restraints excluded: chain E residue 78 ILE Chi-restraints excluded: chain E residue 91 TYR Chi-restraints excluded: chain F residue 54 VAL Chi-restraints excluded: chain G residue 66 THR Chi-restraints excluded: chain G residue 67 THR Chi-restraints excluded: chain G residue 118 THR Chi-restraints excluded: chain G residue 167 THR Chi-restraints excluded: chain H residue 71 VAL Chi-restraints excluded: chain I residue 91 TYR Chi-restraints excluded: chain I residue 134 GLU Chi-restraints excluded: chain J residue 58 GLN Chi-restraints excluded: chain K residue 182 SER Chi-restraints excluded: chain K residue 218 LEU Chi-restraints excluded: chain K residue 363 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 172 random chunks: chunk 123 optimal weight: 3.9990 chunk 170 optimal weight: 4.9990 chunk 51 optimal weight: 6.9990 chunk 136 optimal weight: 0.6980 chunk 38 optimal weight: 3.9990 chunk 3 optimal weight: 8.9990 chunk 85 optimal weight: 2.9990 chunk 80 optimal weight: 1.9990 chunk 10 optimal weight: 7.9990 chunk 117 optimal weight: 0.3980 chunk 144 optimal weight: 0.0040 overall best weight: 1.2196 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 99 ASN G 270 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3731 r_free = 0.3731 target = 0.135955 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3313 r_free = 0.3313 target = 0.104061 restraints weight = 21678.549| |-----------------------------------------------------------------------------| r_work (start): 0.3303 rms_B_bonded: 1.67 r_work: 0.3107 rms_B_bonded: 2.67 restraints_weight: 0.5000 r_work: 0.2981 rms_B_bonded: 4.28 restraints_weight: 0.2500 r_work (final): 0.2981 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8425 moved from start: 0.2763 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 15740 Z= 0.149 Angle : 0.721 11.659 21697 Z= 0.337 Chirality : 0.063 1.062 2472 Planarity : 0.004 0.045 2448 Dihedral : 18.777 177.279 3206 Min Nonbonded Distance : 2.306 Molprobity Statistics. All-atom Clashscore : 5.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.76 % Favored : 98.24 % Rotamer: Outliers : 2.23 % Allowed : 11.57 % Favored : 86.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.08 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.19 (0.21), residues: 1648 helix: 0.90 (0.27), residues: 391 sheet: -1.53 (0.24), residues: 396 loop : 0.28 (0.22), residues: 861 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG I 41 TYR 0.014 0.001 TYR E 135 PHE 0.012 0.001 PHE K 382 TRP 0.017 0.001 TRP G 380 HIS 0.006 0.001 HIS K 376 Details of bonding type rmsd/Z covalent geometry : bond 0.00348 / 0.15 (15740) covalent geometry : angle 0.72100 / 0.34 (21697) hydrogen bonds : bond 0.03841 / 1.99 ( 515) hydrogen bonds : angle 4.96625 / 2.01 ( 1293) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3296 Ramachandran restraints generated. 1648 Oldfield, 0 Emsley, 1648 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3296 Ramachandran restraints generated. 1648 Oldfield, 0 Emsley, 1648 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 234 residues out of total 1478 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 201 time to evaluate : 0.567 Fit side-chains REVERT: C 164 GLU cc_start: 0.7720 (tt0) cc_final: 0.7408 (mm-30) REVERT: C 203 LYS cc_start: 0.7982 (mtmt) cc_final: 0.7381 (mttp) REVERT: C 284 ARG cc_start: 0.8096 (mmt-90) cc_final: 0.7817 (mmt180) REVERT: C 421 GLU cc_start: 0.4541 (mm-30) cc_final: 0.3697 (pt0) REVERT: E 57 GLN cc_start: 0.7537 (mm-40) cc_final: 0.7249 (mm-40) REVERT: F 21 ASP cc_start: 0.6529 (p0) cc_final: 0.6176 (p0) REVERT: F 25 GLN cc_start: 0.7827 (pt0) cc_final: 0.7314 (pm20) REVERT: F 59 GLN cc_start: 0.5675 (mt0) cc_final: 0.5357 (mm-40) REVERT: G 66 THR cc_start: 0.8202 (OUTLIER) cc_final: 0.7899 (t) REVERT: H 115 GLU cc_start: 0.8119 (mm-30) cc_final: 0.7870 (mm-30) REVERT: I 145 GLU cc_start: 0.8206 (tp30) cc_final: 0.7817 (tp30) REVERT: J 58 GLN cc_start: 0.8755 (OUTLIER) cc_final: 0.8544 (mt0) REVERT: K 265 ARG cc_start: 0.8679 (ttt180) cc_final: 0.7946 (ttp80) REVERT: K 321 LYS cc_start: 0.7619 (pttt) cc_final: 0.6911 (mttt) REVERT: K 391 GLU cc_start: 0.8100 (pt0) cc_final: 0.7849 (pt0) outliers start: 33 outliers final: 23 residues processed: 227 average time/residue: 0.1245 time to fit residues: 40.4539 Evaluate side-chains 211 residues out of total 1478 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 186 time to evaluate : 0.354 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 215 ILE Chi-restraints excluded: chain C residue 261 VAL Chi-restraints excluded: chain C residue 351 THR Chi-restraints excluded: chain D residue 71 VAL Chi-restraints excluded: chain D residue 84 ILE Chi-restraints excluded: chain D residue 110 ILE Chi-restraints excluded: chain D residue 122 ASP Chi-restraints excluded: chain E residue 40 SER Chi-restraints excluded: chain E residue 78 ILE Chi-restraints excluded: chain E residue 91 TYR Chi-restraints excluded: chain E residue 110 SER Chi-restraints excluded: chain E residue 129 VAL Chi-restraints excluded: chain E residue 149 LEU Chi-restraints excluded: chain G residue 66 THR Chi-restraints excluded: chain G residue 67 THR Chi-restraints excluded: chain G residue 118 THR Chi-restraints excluded: chain G residue 167 THR Chi-restraints excluded: chain H residue 71 VAL Chi-restraints excluded: chain I residue 40 SER Chi-restraints excluded: chain I residue 80 VAL Chi-restraints excluded: chain I residue 91 TYR Chi-restraints excluded: chain I residue 134 GLU Chi-restraints excluded: chain J residue 58 GLN Chi-restraints excluded: chain K residue 182 SER Chi-restraints excluded: chain K residue 218 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 172 random chunks: chunk 111 optimal weight: 0.9990 chunk 155 optimal weight: 8.9990 chunk 142 optimal weight: 3.9990 chunk 143 optimal weight: 0.7980 chunk 73 optimal weight: 7.9990 chunk 50 optimal weight: 8.9990 chunk 20 optimal weight: 0.8980 chunk 18 optimal weight: 5.9990 chunk 16 optimal weight: 0.7980 chunk 65 optimal weight: 0.1980 chunk 105 optimal weight: 3.9990 overall best weight: 0.7382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** F 8 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 106 ASN I 147 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3760 r_free = 0.3760 target = 0.138161 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3352 r_free = 0.3352 target = 0.106676 restraints weight = 21589.436| |-----------------------------------------------------------------------------| r_work (start): 0.3342 rms_B_bonded: 1.70 r_work: 0.3145 rms_B_bonded: 2.70 restraints_weight: 0.5000 r_work: 0.3018 rms_B_bonded: 4.34 restraints_weight: 0.2500 r_work (final): 0.3018 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8389 moved from start: 0.3038 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 15740 Z= 0.120 Angle : 0.675 10.997 21697 Z= 0.315 Chirality : 0.056 0.558 2472 Planarity : 0.004 0.044 2448 Dihedral : 18.727 178.503 3206 Min Nonbonded Distance : 2.270 Molprobity Statistics. All-atom Clashscore : 5.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.40 % Favored : 98.60 % Rotamer: Outliers : 1.89 % Allowed : 12.65 % Favored : 85.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.08 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.02 (0.21), residues: 1648 helix: 1.07 (0.27), residues: 391 sheet: -1.40 (0.25), residues: 377 loop : 0.30 (0.21), residues: 880 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG I 41 TYR 0.013 0.001 TYR E 135 PHE 0.011 0.001 PHE K 382 TRP 0.015 0.001 TRP G 380 HIS 0.003 0.001 HIS J 44 Details of bonding type rmsd/Z covalent geometry : bond 0.00273 / 0.12 (15740) covalent geometry : angle 0.67506 / 0.31 (21697) hydrogen bonds : bond 0.03472 / 1.79 ( 515) hydrogen bonds : angle 4.78374 / 1.94 ( 1293) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3296 Ramachandran restraints generated. 1648 Oldfield, 0 Emsley, 1648 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3296 Ramachandran restraints generated. 1648 Oldfield, 0 Emsley, 1648 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 237 residues out of total 1478 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 209 time to evaluate : 0.562 Fit side-chains REVERT: C 164 GLU cc_start: 0.7615 (tt0) cc_final: 0.7329 (mm-30) REVERT: C 203 LYS cc_start: 0.7954 (mtmt) cc_final: 0.7343 (mttp) REVERT: C 284 ARG cc_start: 0.8048 (mmt-90) cc_final: 0.7780 (mmt180) REVERT: C 421 GLU cc_start: 0.4646 (mm-30) cc_final: 0.3744 (pt0) REVERT: D 133 MET cc_start: 0.7553 (tpp) cc_final: 0.7194 (tpt) REVERT: D 150 LYS cc_start: 0.7190 (mtmm) cc_final: 0.6982 (mtmt) REVERT: F 2 PHE cc_start: 0.8225 (m-80) cc_final: 0.7965 (m-80) REVERT: F 21 ASP cc_start: 0.6416 (p0) cc_final: 0.6094 (p0) REVERT: F 25 GLN cc_start: 0.7797 (pt0) cc_final: 0.7451 (pm20) REVERT: F 59 GLN cc_start: 0.5567 (mt0) cc_final: 0.5173 (mm-40) REVERT: G 66 THR cc_start: 0.8169 (OUTLIER) cc_final: 0.7903 (t) REVERT: H 115 GLU cc_start: 0.8110 (mm-30) cc_final: 0.7873 (mm-30) REVERT: I 145 GLU cc_start: 0.8212 (tp30) cc_final: 0.7817 (tp30) REVERT: K 265 ARG cc_start: 0.8547 (ttt180) cc_final: 0.7937 (ttp80) REVERT: K 321 LYS cc_start: 0.7512 (pttt) cc_final: 0.6819 (mttt) REVERT: K 360 LEU cc_start: 0.8530 (mt) cc_final: 0.8322 (mt) REVERT: K 391 GLU cc_start: 0.8001 (pt0) cc_final: 0.7739 (pt0) outliers start: 28 outliers final: 22 residues processed: 231 average time/residue: 0.1272 time to fit residues: 42.1640 Evaluate side-chains 213 residues out of total 1478 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 190 time to evaluate : 0.334 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 27 VAL Chi-restraints excluded: chain C residue 215 ILE Chi-restraints excluded: chain C residue 351 THR Chi-restraints excluded: chain D residue 71 VAL Chi-restraints excluded: chain D residue 73 LEU Chi-restraints excluded: chain D residue 84 ILE Chi-restraints excluded: chain D residue 110 ILE Chi-restraints excluded: chain D residue 122 ASP Chi-restraints excluded: chain E residue 40 SER Chi-restraints excluded: chain E residue 78 ILE Chi-restraints excluded: chain E residue 91 TYR Chi-restraints excluded: chain E residue 110 SER Chi-restraints excluded: chain F residue 54 VAL Chi-restraints excluded: chain G residue 44 VAL Chi-restraints excluded: chain G residue 66 THR Chi-restraints excluded: chain G residue 67 THR Chi-restraints excluded: chain G residue 118 THR Chi-restraints excluded: chain H residue 71 VAL Chi-restraints excluded: chain I residue 80 VAL Chi-restraints excluded: chain I residue 91 TYR Chi-restraints excluded: chain K residue 218 LEU Chi-restraints excluded: chain K residue 241 ASP Chi-restraints excluded: chain K residue 347 ARG Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 172 random chunks: chunk 137 optimal weight: 1.9990 chunk 13 optimal weight: 0.9980 chunk 71 optimal weight: 8.9990 chunk 1 optimal weight: 7.9990 chunk 8 optimal weight: 6.9990 chunk 102 optimal weight: 0.9990 chunk 132 optimal weight: 2.9990 chunk 2 optimal weight: 4.9990 chunk 25 optimal weight: 9.9990 chunk 144 optimal weight: 0.0040 chunk 42 optimal weight: 0.7980 overall best weight: 0.9596 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 99 ASN H 106 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3766 r_free = 0.3766 target = 0.138601 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3352 r_free = 0.3352 target = 0.106737 restraints weight = 21553.224| |-----------------------------------------------------------------------------| r_work (start): 0.3333 rms_B_bonded: 1.76 r_work: 0.3124 rms_B_bonded: 2.88 restraints_weight: 0.5000 r_work: 0.2997 rms_B_bonded: 4.62 restraints_weight: 0.2500 r_work (final): 0.2997 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8418 moved from start: 0.3117 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 15740 Z= 0.131 Angle : 0.678 10.965 21697 Z= 0.317 Chirality : 0.056 0.555 2472 Planarity : 0.004 0.046 2448 Dihedral : 18.681 179.409 3206 Min Nonbonded Distance : 2.346 Molprobity Statistics. All-atom Clashscore : 5.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.64 % Favored : 98.36 % Rotamer: Outliers : 2.23 % Allowed : 13.53 % Favored : 84.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.08 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.00 (0.21), residues: 1648 helix: 1.11 (0.27), residues: 391 sheet: -1.38 (0.25), residues: 383 loop : 0.32 (0.21), residues: 874 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG I 41 TYR 0.015 0.001 TYR F 41 PHE 0.011 0.001 PHE K 382 TRP 0.013 0.001 TRP G 380 HIS 0.004 0.001 HIS C 259 Details of bonding type rmsd/Z covalent geometry : bond 0.00305 / 0.13 (15740) covalent geometry : angle 0.67766 / 0.32 (21697) hydrogen bonds : bond 0.03522 / 1.82 ( 515) hydrogen bonds : angle 4.76977 / 1.94 ( 1293) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3296 Ramachandran restraints generated. 1648 Oldfield, 0 Emsley, 1648 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3296 Ramachandran restraints generated. 1648 Oldfield, 0 Emsley, 1648 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 231 residues out of total 1478 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 198 time to evaluate : 0.585 Fit side-chains REVERT: C 60 ASP cc_start: 0.8700 (OUTLIER) cc_final: 0.8498 (p0) REVERT: C 164 GLU cc_start: 0.7724 (tt0) cc_final: 0.7446 (mm-30) REVERT: C 203 LYS cc_start: 0.7950 (mtmt) cc_final: 0.7354 (mttp) REVERT: C 284 ARG cc_start: 0.8063 (mmt-90) cc_final: 0.7807 (mmt180) REVERT: D 133 MET cc_start: 0.7541 (tpp) cc_final: 0.7228 (tpt) REVERT: F 2 PHE cc_start: 0.8239 (m-80) cc_final: 0.7979 (m-80) REVERT: F 21 ASP cc_start: 0.6404 (p0) cc_final: 0.6092 (p0) REVERT: F 25 GLN cc_start: 0.7764 (pt0) cc_final: 0.7454 (pm20) REVERT: F 59 GLN cc_start: 0.5589 (mt0) cc_final: 0.5253 (mm-40) REVERT: G 66 THR cc_start: 0.8199 (OUTLIER) cc_final: 0.7912 (t) REVERT: G 243 MET cc_start: 0.8542 (ttp) cc_final: 0.8047 (ttp) REVERT: H 115 GLU cc_start: 0.8141 (mm-30) cc_final: 0.7921 (mm-30) REVERT: I 145 GLU cc_start: 0.8204 (tp30) cc_final: 0.7838 (tp30) REVERT: K 265 ARG cc_start: 0.8599 (ttt180) cc_final: 0.8010 (ttp80) REVERT: K 321 LYS cc_start: 0.7519 (pttt) cc_final: 0.6836 (mttt) REVERT: K 391 GLU cc_start: 0.8026 (pt0) cc_final: 0.7803 (pt0) outliers start: 33 outliers final: 27 residues processed: 225 average time/residue: 0.1493 time to fit residues: 47.7665 Evaluate side-chains 219 residues out of total 1478 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 190 time to evaluate : 0.520 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 27 VAL Chi-restraints excluded: chain C residue 60 ASP Chi-restraints excluded: chain C residue 215 ILE Chi-restraints excluded: chain C residue 261 VAL Chi-restraints excluded: chain C residue 281 TYR Chi-restraints excluded: chain C residue 351 THR Chi-restraints excluded: chain D residue 71 VAL Chi-restraints excluded: chain D residue 73 LEU Chi-restraints excluded: chain D residue 84 ILE Chi-restraints excluded: chain D residue 110 ILE Chi-restraints excluded: chain D residue 122 ASP Chi-restraints excluded: chain E residue 40 SER Chi-restraints excluded: chain E residue 78 ILE Chi-restraints excluded: chain E residue 91 TYR Chi-restraints excluded: chain E residue 110 SER Chi-restraints excluded: chain F residue 54 VAL Chi-restraints excluded: chain G residue 44 VAL Chi-restraints excluded: chain G residue 66 THR Chi-restraints excluded: chain G residue 67 THR Chi-restraints excluded: chain G residue 118 THR Chi-restraints excluded: chain G residue 167 THR Chi-restraints excluded: chain H residue 71 VAL Chi-restraints excluded: chain I residue 40 SER Chi-restraints excluded: chain I residue 80 VAL Chi-restraints excluded: chain I residue 91 TYR Chi-restraints excluded: chain K residue 182 SER Chi-restraints excluded: chain K residue 218 LEU Chi-restraints excluded: chain K residue 241 ASP Chi-restraints excluded: chain K residue 347 ARG Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 172 random chunks: chunk 132 optimal weight: 3.9990 chunk 7 optimal weight: 10.0000 chunk 125 optimal weight: 2.9990 chunk 77 optimal weight: 5.9990 chunk 144 optimal weight: 2.9990 chunk 3 optimal weight: 6.9990 chunk 17 optimal weight: 0.0050 chunk 117 optimal weight: 5.9990 chunk 114 optimal weight: 2.9990 chunk 121 optimal weight: 1.9990 chunk 29 optimal weight: 1.9990 overall best weight: 2.0002 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 99 ASN C 120 HIS C 161 ASN E 132 HIS H 106 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3735 r_free = 0.3735 target = 0.135925 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3307 r_free = 0.3307 target = 0.103429 restraints weight = 21734.437| |-----------------------------------------------------------------------------| r_work (start): 0.3289 rms_B_bonded: 1.76 r_work: 0.3097 rms_B_bonded: 2.67 restraints_weight: 0.5000 r_work: 0.2973 rms_B_bonded: 4.24 restraints_weight: 0.2500 r_work (final): 0.2973 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8437 moved from start: 0.3072 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.084 15740 Z= 0.194 Angle : 0.734 12.484 21697 Z= 0.345 Chirality : 0.060 0.666 2472 Planarity : 0.005 0.047 2448 Dihedral : 18.721 179.315 3206 Min Nonbonded Distance : 2.226 Molprobity Statistics. All-atom Clashscore : 5.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.70 % Favored : 98.30 % Rotamer: Outliers : 2.37 % Allowed : 13.60 % Favored : 84.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.08 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.06 (0.21), residues: 1648 helix: 1.02 (0.27), residues: 393 sheet: -1.33 (0.25), residues: 369 loop : 0.22 (0.21), residues: 886 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG I 41 TYR 0.022 0.001 TYR F 41 PHE 0.014 0.002 PHE K 382 TRP 0.014 0.001 TRP G 380 HIS 0.007 0.001 HIS E 132 Details of bonding type rmsd/Z covalent geometry : bond 0.00462 / 0.19 (15740) covalent geometry : angle 0.73370 / 0.34 (21697) hydrogen bonds : bond 0.03962 / 2.04 ( 515) hydrogen bonds : angle 4.89792 / 2.00 ( 1293) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3296 Ramachandran restraints generated. 1648 Oldfield, 0 Emsley, 1648 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3296 Ramachandran restraints generated. 1648 Oldfield, 0 Emsley, 1648 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 230 residues out of total 1478 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 195 time to evaluate : 0.561 Fit side-chains REVERT: C 164 GLU cc_start: 0.7585 (tt0) cc_final: 0.7377 (mm-30) REVERT: C 203 LYS cc_start: 0.7989 (mtmt) cc_final: 0.7378 (mttp) REVERT: C 284 ARG cc_start: 0.8128 (mmt-90) cc_final: 0.7780 (mmt180) REVERT: C 421 GLU cc_start: 0.5071 (mm-30) cc_final: 0.3942 (pt0) REVERT: D 97 TYR cc_start: 0.7086 (m-80) cc_final: 0.6871 (m-80) REVERT: D 133 MET cc_start: 0.7491 (tpp) cc_final: 0.7177 (tpt) REVERT: F 21 ASP cc_start: 0.6459 (p0) cc_final: 0.6163 (p0) REVERT: F 25 GLN cc_start: 0.7834 (pt0) cc_final: 0.7494 (pm20) REVERT: F 59 GLN cc_start: 0.5658 (mt0) cc_final: 0.5305 (mm-40) REVERT: G 243 MET cc_start: 0.8749 (ttp) cc_final: 0.8248 (ttp) REVERT: H 115 GLU cc_start: 0.8213 (mm-30) cc_final: 0.7900 (mm-30) REVERT: I 145 GLU cc_start: 0.8202 (tp30) cc_final: 0.7777 (tp30) REVERT: J 58 GLN cc_start: 0.8767 (OUTLIER) cc_final: 0.8554 (mt0) REVERT: K 265 ARG cc_start: 0.8686 (ttt180) cc_final: 0.7938 (ttp80) REVERT: K 321 LYS cc_start: 0.7551 (pttt) cc_final: 0.6838 (mttt) REVERT: K 381 ARG cc_start: 0.7966 (ttp-170) cc_final: 0.7655 (ptm160) REVERT: K 391 GLU cc_start: 0.8066 (pt0) cc_final: 0.7821 (pt0) REVERT: K 427 PHE cc_start: 0.7910 (m-10) cc_final: 0.7451 (m-10) outliers start: 35 outliers final: 29 residues processed: 225 average time/residue: 0.1511 time to fit residues: 48.1209 Evaluate side-chains 217 residues out of total 1478 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 187 time to evaluate : 0.566 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 27 VAL Chi-restraints excluded: chain C residue 215 ILE Chi-restraints excluded: chain C residue 261 VAL Chi-restraints excluded: chain C residue 281 TYR Chi-restraints excluded: chain C residue 351 THR Chi-restraints excluded: chain D residue 71 VAL Chi-restraints excluded: chain D residue 73 LEU Chi-restraints excluded: chain D residue 84 ILE Chi-restraints excluded: chain D residue 110 ILE Chi-restraints excluded: chain E residue 40 SER Chi-restraints excluded: chain E residue 78 ILE Chi-restraints excluded: chain E residue 91 TYR Chi-restraints excluded: chain E residue 110 SER Chi-restraints excluded: chain E residue 149 LEU Chi-restraints excluded: chain F residue 54 VAL Chi-restraints excluded: chain G residue 44 VAL Chi-restraints excluded: chain G residue 66 THR Chi-restraints excluded: chain G residue 67 THR Chi-restraints excluded: chain G residue 118 THR Chi-restraints excluded: chain G residue 167 THR Chi-restraints excluded: chain H residue 71 VAL Chi-restraints excluded: chain I residue 40 SER Chi-restraints excluded: chain I residue 80 VAL Chi-restraints excluded: chain I residue 91 TYR Chi-restraints excluded: chain I residue 134 GLU Chi-restraints excluded: chain J residue 58 GLN Chi-restraints excluded: chain K residue 182 SER Chi-restraints excluded: chain K residue 218 LEU Chi-restraints excluded: chain K residue 241 ASP Chi-restraints excluded: chain K residue 347 ARG Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 172 random chunks: chunk 20 optimal weight: 0.7980 chunk 138 optimal weight: 3.9990 chunk 148 optimal weight: 2.9990 chunk 95 optimal weight: 2.9990 chunk 117 optimal weight: 5.9990 chunk 115 optimal weight: 3.9990 chunk 137 optimal weight: 0.9990 chunk 38 optimal weight: 0.9990 chunk 147 optimal weight: 1.9990 chunk 30 optimal weight: 0.8980 chunk 64 optimal weight: 2.9990 overall best weight: 1.1386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 99 ASN C 161 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3742 r_free = 0.3742 target = 0.136473 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3324 r_free = 0.3324 target = 0.104592 restraints weight = 21484.823| |-----------------------------------------------------------------------------| r_work (start): 0.3317 rms_B_bonded: 1.72 r_work: 0.3123 rms_B_bonded: 2.69 restraints_weight: 0.5000 r_work: 0.2997 rms_B_bonded: 4.30 restraints_weight: 0.2500 r_work (final): 0.2997 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8413 moved from start: 0.3179 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 15740 Z= 0.140 Angle : 0.693 11.058 21697 Z= 0.324 Chirality : 0.057 0.608 2472 Planarity : 0.004 0.047 2448 Dihedral : 18.714 179.463 3206 Min Nonbonded Distance : 2.344 Molprobity Statistics. All-atom Clashscore : 5.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.70 % Favored : 98.30 % Rotamer: Outliers : 2.30 % Allowed : 13.33 % Favored : 84.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.08 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.00 (0.21), residues: 1648 helix: 1.05 (0.27), residues: 391 sheet: -1.26 (0.25), residues: 363 loop : 0.23 (0.21), residues: 894 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG C 183 TYR 0.019 0.001 TYR F 41 PHE 0.012 0.001 PHE K 382 TRP 0.014 0.001 TRP G 380 HIS 0.004 0.001 HIS C 259 Details of bonding type rmsd/Z covalent geometry : bond 0.00329 / 0.14 (15740) covalent geometry : angle 0.69289 / 0.32 (21697) hydrogen bonds : bond 0.03600 / 1.85 ( 515) hydrogen bonds : angle 4.80054 / 1.96 ( 1293) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3296 Ramachandran restraints generated. 1648 Oldfield, 0 Emsley, 1648 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3296 Ramachandran restraints generated. 1648 Oldfield, 0 Emsley, 1648 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 227 residues out of total 1478 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 193 time to evaluate : 0.555 Fit side-chains REVERT: C 60 ASP cc_start: 0.8733 (OUTLIER) cc_final: 0.8524 (p0) REVERT: C 164 GLU cc_start: 0.7648 (tt0) cc_final: 0.7312 (mm-30) REVERT: C 203 LYS cc_start: 0.7972 (mtmt) cc_final: 0.7356 (mttp) REVERT: C 284 ARG cc_start: 0.8088 (mmt-90) cc_final: 0.7758 (mmt180) REVERT: C 421 GLU cc_start: 0.5035 (mm-30) cc_final: 0.3893 (pt0) REVERT: D 133 MET cc_start: 0.7442 (tpp) cc_final: 0.7115 (tpt) REVERT: F 8 ASN cc_start: 0.6792 (p0) cc_final: 0.6586 (p0) REVERT: F 21 ASP cc_start: 0.6378 (p0) cc_final: 0.6071 (p0) REVERT: F 25 GLN cc_start: 0.7793 (pt0) cc_final: 0.7461 (pm20) REVERT: F 59 GLN cc_start: 0.5635 (mt0) cc_final: 0.5284 (mm-40) REVERT: G 66 THR cc_start: 0.8244 (OUTLIER) cc_final: 0.7920 (t) REVERT: G 243 MET cc_start: 0.8702 (ttp) cc_final: 0.8128 (ttp) REVERT: H 115 GLU cc_start: 0.8188 (mm-30) cc_final: 0.7980 (mm-30) REVERT: I 141 GLU cc_start: 0.7218 (pt0) cc_final: 0.6942 (pt0) REVERT: I 145 GLU cc_start: 0.8202 (tp30) cc_final: 0.7801 (tp30) REVERT: J 58 GLN cc_start: 0.8788 (OUTLIER) cc_final: 0.8579 (mt0) REVERT: K 265 ARG cc_start: 0.8677 (ttt180) cc_final: 0.7975 (ttp80) REVERT: K 321 LYS cc_start: 0.7510 (pttt) cc_final: 0.6808 (mttt) REVERT: K 381 ARG cc_start: 0.7940 (ttp-170) cc_final: 0.7634 (ptm160) REVERT: K 391 GLU cc_start: 0.8037 (pt0) cc_final: 0.7797 (pt0) REVERT: K 427 PHE cc_start: 0.7902 (m-10) cc_final: 0.7181 (m-10) outliers start: 34 outliers final: 31 residues processed: 222 average time/residue: 0.1471 time to fit residues: 46.8140 Evaluate side-chains 223 residues out of total 1478 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 189 time to evaluate : 0.553 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 27 VAL Chi-restraints excluded: chain C residue 60 ASP Chi-restraints excluded: chain C residue 215 ILE Chi-restraints excluded: chain C residue 261 VAL Chi-restraints excluded: chain C residue 281 TYR Chi-restraints excluded: chain C residue 351 THR Chi-restraints excluded: chain C residue 363 VAL Chi-restraints excluded: chain D residue 71 VAL Chi-restraints excluded: chain D residue 73 LEU Chi-restraints excluded: chain D residue 84 ILE Chi-restraints excluded: chain D residue 110 ILE Chi-restraints excluded: chain E residue 40 SER Chi-restraints excluded: chain E residue 78 ILE Chi-restraints excluded: chain E residue 91 TYR Chi-restraints excluded: chain E residue 110 SER Chi-restraints excluded: chain E residue 129 VAL Chi-restraints excluded: chain E residue 149 LEU Chi-restraints excluded: chain F residue 54 VAL Chi-restraints excluded: chain G residue 44 VAL Chi-restraints excluded: chain G residue 66 THR Chi-restraints excluded: chain G residue 67 THR Chi-restraints excluded: chain G residue 118 THR Chi-restraints excluded: chain G residue 167 THR Chi-restraints excluded: chain H residue 71 VAL Chi-restraints excluded: chain I residue 40 SER Chi-restraints excluded: chain I residue 80 VAL Chi-restraints excluded: chain I residue 91 TYR Chi-restraints excluded: chain I residue 134 GLU Chi-restraints excluded: chain J residue 58 GLN Chi-restraints excluded: chain K residue 182 SER Chi-restraints excluded: chain K residue 218 LEU Chi-restraints excluded: chain K residue 241 ASP Chi-restraints excluded: chain K residue 347 ARG Chi-restraints excluded: chain K residue 461 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 172 random chunks: chunk 70 optimal weight: 2.9990 chunk 143 optimal weight: 1.9990 chunk 16 optimal weight: 0.2980 chunk 36 optimal weight: 3.9990 chunk 26 optimal weight: 2.9990 chunk 67 optimal weight: 0.6980 chunk 165 optimal weight: 5.9990 chunk 90 optimal weight: 2.9990 chunk 135 optimal weight: 2.9990 chunk 31 optimal weight: 4.9990 chunk 15 optimal weight: 0.9990 overall best weight: 1.3986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 99 ASN C 161 ASN H 106 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3734 r_free = 0.3734 target = 0.135823 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3315 r_free = 0.3315 target = 0.104052 restraints weight = 21591.242| |-----------------------------------------------------------------------------| r_work (start): 0.3299 rms_B_bonded: 1.73 r_work: 0.3108 rms_B_bonded: 2.66 restraints_weight: 0.5000 r_work: 0.2983 rms_B_bonded: 4.25 restraints_weight: 0.2500 r_work (final): 0.2983 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8419 moved from start: 0.3247 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.065 15740 Z= 0.156 Angle : 0.702 11.033 21697 Z= 0.329 Chirality : 0.057 0.623 2472 Planarity : 0.005 0.048 2448 Dihedral : 18.685 179.117 3206 Min Nonbonded Distance : 2.340 Molprobity Statistics. All-atom Clashscore : 5.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.88 % Favored : 98.12 % Rotamer: Outliers : 2.30 % Allowed : 13.33 % Favored : 84.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.08 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.04 (0.21), residues: 1648 helix: 1.03 (0.27), residues: 391 sheet: -1.30 (0.25), residues: 369 loop : 0.24 (0.21), residues: 888 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG I 41 TYR 0.021 0.001 TYR F 41 PHE 0.012 0.002 PHE K 382 TRP 0.017 0.001 TRP K 405 HIS 0.004 0.001 HIS C 259 Details of bonding type rmsd/Z covalent geometry : bond 0.00369 / 0.16 (15740) covalent geometry : angle 0.70221 / 0.33 (21697) hydrogen bonds : bond 0.03702 / 1.91 ( 515) hydrogen bonds : angle 4.81243 / 1.96 ( 1293) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3296 Ramachandran restraints generated. 1648 Oldfield, 0 Emsley, 1648 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3296 Ramachandran restraints generated. 1648 Oldfield, 0 Emsley, 1648 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 220 residues out of total 1478 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 186 time to evaluate : 0.566 Fit side-chains REVERT: C 116 GLU cc_start: 0.7701 (mt-10) cc_final: 0.7340 (pt0) REVERT: C 164 GLU cc_start: 0.7572 (tt0) cc_final: 0.7271 (mm-30) REVERT: C 203 LYS cc_start: 0.7966 (mtmt) cc_final: 0.7350 (mttp) REVERT: C 284 ARG cc_start: 0.8145 (mmt-90) cc_final: 0.7806 (mmt180) REVERT: C 421 GLU cc_start: 0.5028 (mm-30) cc_final: 0.3998 (mt-10) REVERT: D 97 TYR cc_start: 0.6940 (m-80) cc_final: 0.6635 (m-80) REVERT: D 133 MET cc_start: 0.7446 (tpp) cc_final: 0.7117 (tpt) REVERT: F 25 GLN cc_start: 0.7937 (pt0) cc_final: 0.7301 (pm20) REVERT: F 59 GLN cc_start: 0.5645 (mt0) cc_final: 0.5303 (mm-40) REVERT: G 66 THR cc_start: 0.8220 (OUTLIER) cc_final: 0.7891 (t) REVERT: G 243 MET cc_start: 0.8752 (ttp) cc_final: 0.8158 (ttp) REVERT: H 115 GLU cc_start: 0.8209 (mm-30) cc_final: 0.7942 (mm-30) REVERT: I 141 GLU cc_start: 0.7193 (pt0) cc_final: 0.6927 (pt0) REVERT: I 145 GLU cc_start: 0.8213 (tp30) cc_final: 0.7788 (tp30) REVERT: J 58 GLN cc_start: 0.8741 (OUTLIER) cc_final: 0.8531 (mt0) REVERT: K 265 ARG cc_start: 0.8690 (ttt180) cc_final: 0.7985 (ttp80) REVERT: K 321 LYS cc_start: 0.7591 (pttt) cc_final: 0.6910 (mttt) REVERT: K 381 ARG cc_start: 0.7975 (ttp-170) cc_final: 0.7679 (ptm160) REVERT: K 391 GLU cc_start: 0.8030 (pt0) cc_final: 0.7785 (pt0) REVERT: K 427 PHE cc_start: 0.7908 (m-10) cc_final: 0.7100 (m-10) outliers start: 34 outliers final: 32 residues processed: 216 average time/residue: 0.1461 time to fit residues: 44.9109 Evaluate side-chains 219 residues out of total 1478 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 185 time to evaluate : 0.691 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 27 VAL Chi-restraints excluded: chain C residue 215 ILE Chi-restraints excluded: chain C residue 261 VAL Chi-restraints excluded: chain C residue 281 TYR Chi-restraints excluded: chain C residue 351 THR Chi-restraints excluded: chain C residue 363 VAL Chi-restraints excluded: chain D residue 71 VAL Chi-restraints excluded: chain D residue 73 LEU Chi-restraints excluded: chain D residue 84 ILE Chi-restraints excluded: chain D residue 110 ILE Chi-restraints excluded: chain E residue 40 SER Chi-restraints excluded: chain E residue 78 ILE Chi-restraints excluded: chain E residue 91 TYR Chi-restraints excluded: chain E residue 110 SER Chi-restraints excluded: chain E residue 129 VAL Chi-restraints excluded: chain E residue 149 LEU Chi-restraints excluded: chain F residue 54 VAL Chi-restraints excluded: chain G residue 44 VAL Chi-restraints excluded: chain G residue 66 THR Chi-restraints excluded: chain G residue 67 THR Chi-restraints excluded: chain G residue 118 THR Chi-restraints excluded: chain G residue 167 THR Chi-restraints excluded: chain H residue 71 VAL Chi-restraints excluded: chain I residue 40 SER Chi-restraints excluded: chain I residue 80 VAL Chi-restraints excluded: chain I residue 91 TYR Chi-restraints excluded: chain I residue 134 GLU Chi-restraints excluded: chain J residue 42 SER Chi-restraints excluded: chain J residue 58 GLN Chi-restraints excluded: chain K residue 182 SER Chi-restraints excluded: chain K residue 218 LEU Chi-restraints excluded: chain K residue 241 ASP Chi-restraints excluded: chain K residue 347 ARG Chi-restraints excluded: chain K residue 461 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 172 random chunks: chunk 145 optimal weight: 5.9990 chunk 49 optimal weight: 0.6980 chunk 11 optimal weight: 0.6980 chunk 118 optimal weight: 1.9990 chunk 20 optimal weight: 0.9990 chunk 68 optimal weight: 4.9990 chunk 15 optimal weight: 5.9990 chunk 9 optimal weight: 0.7980 chunk 73 optimal weight: 0.9980 chunk 69 optimal weight: 5.9990 chunk 88 optimal weight: 3.9990 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 99 ASN C 161 ASN C 276 HIS H 106 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3764 r_free = 0.3764 target = 0.138337 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3351 r_free = 0.3351 target = 0.106567 restraints weight = 21564.849| |-----------------------------------------------------------------------------| r_work (start): 0.3337 rms_B_bonded: 1.72 r_work: 0.3150 rms_B_bonded: 2.66 restraints_weight: 0.5000 r_work: 0.3024 rms_B_bonded: 4.27 restraints_weight: 0.2500 r_work (final): 0.3024 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8387 moved from start: 0.3389 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 15740 Z= 0.122 Angle : 0.669 9.170 21697 Z= 0.313 Chirality : 0.054 0.546 2472 Planarity : 0.004 0.046 2448 Dihedral : 18.638 179.611 3206 Min Nonbonded Distance : 2.181 Molprobity Statistics. All-atom Clashscore : 6.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.64 % Favored : 98.36 % Rotamer: Outliers : 2.23 % Allowed : 13.40 % Favored : 84.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.08 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.10 (0.21), residues: 1648 helix: 1.13 (0.27), residues: 391 sheet: -1.18 (0.26), residues: 362 loop : 0.29 (0.21), residues: 895 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG I 41 TYR 0.021 0.001 TYR F 41 PHE 0.013 0.001 PHE E 70 TRP 0.015 0.001 TRP K 405 HIS 0.004 0.001 HIS J 44 Details of bonding type rmsd/Z covalent geometry : bond 0.00281 / 0.12 (15740) covalent geometry : angle 0.66901 / 0.31 (21697) hydrogen bonds : bond 0.03394 / 1.75 ( 515) hydrogen bonds : angle 4.69237 / 1.91 ( 1293) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4204.75 seconds wall clock time: 72 minutes 38.86 seconds (4358.86 seconds total)