Starting phenix.real_space_refine on Sat Aug 23 23:53:38 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8ouf_17191/08_2025/8ouf_17191.cif Found real_map, /net/cci-nas-00/data/ceres_data/8ouf_17191/08_2025/8ouf_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_2025/8ouf_17191.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8ouf_17191/08_2025/8ouf_17191.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8ouf_17191/08_2025/8ouf_17191.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8ouf_17191/08_2025/8ouf_17191.map" } 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): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/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: {'RNA': 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: 4.21, per 1000 atoms: 0.28 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: 1.18 Conformation dependent library (CDL) restraints added in 793.0 milliseconds Enol-peptide restraints added in 715.3 nanoseconds 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: 1.79 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: 2.52 Time building geometry restraints manager: 1.67 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: 19831 1.64 - 3.27: 1546 3.27 - 4.91: 281 4.91 - 6.55: 28 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=" C3' U B 416 " pdb=" C2' U B 416 " pdb=" O2' U B 416 " ideal model delta sigma weight residual 110.70 117.54 -6.84 1.50e+00 4.44e-01 2.08e+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 ... (remaining 21692 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.69: 8619 17.69 - 35.38: 742 35.38 - 53.07: 150 53.07 - 70.76: 146 70.76 - 88.45: 55 Dihedral angle restraints: 9712 sinusoidal: 4841 harmonic: 4871 Sorted by residual: dihedral pdb=" CA GLY K 365 " pdb=" C GLY K 365 " pdb=" N HIS K 366 " pdb=" CA HIS K 366 " ideal model delta harmonic sigma weight residual 180.00 151.49 28.51 0 5.00e+00 4.00e-02 3.25e+01 dihedral pdb=" CA CYS C 220 " pdb=" C CYS C 220 " pdb=" N GLU C 221 " pdb=" CA GLU C 221 " ideal model delta harmonic sigma weight residual 180.00 152.23 27.77 0 5.00e+00 4.00e-02 3.09e+01 dihedral pdb=" CA GLN D 119 " pdb=" C GLN D 119 " pdb=" N LEU D 120 " pdb=" CA LEU D 120 " ideal model delta harmonic sigma weight residual -180.00 -152.60 -27.40 0 5.00e+00 4.00e-02 3.00e+01 ... (remaining 9709 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.059: 1590 0.059 - 0.117: 592 0.117 - 0.176: 203 0.176 - 0.235: 79 0.235 - 0.293: 8 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 -2.75 -2.46 -0.29 2.00e-01 2.50e+01 2.15e+00 chirality pdb=" CA ASN G 99 " pdb=" N ASN G 99 " pdb=" C ASN G 99 " pdb=" CB ASN G 99 " both_signs ideal model delta sigma weight residual False 2.51 2.23 0.28 2.00e-01 2.50e+01 1.97e+00 chirality pdb=" CA LYS K 321 " pdb=" N LYS K 321 " pdb=" C LYS K 321 " pdb=" CB LYS K 321 " both_signs ideal model delta sigma weight residual False 2.51 2.24 0.27 2.00e-01 2.50e+01 1.82e+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: 1.960 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.240 Check model and map are aligned: 0.040 Set scattering table: 0.040 Process input model: 16.820 Find NCS groups from input model: 0.190 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.260 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 20.600 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7358 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= 0.416 Angle : 0.993 8.185 21697 Z= 0.613 Chirality : 0.074 0.293 2472 Planarity : 0.006 0.074 2448 Dihedral : 17.150 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 aren 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 covalent geometry : bond 0.00617 (15740) covalent geometry : angle 0.99309 (21697) hydrogen bonds : bond 0.17897 ( 515) hydrogen bonds : angle 7.46710 ( 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 : 0.540 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: 0.1403 time to fit residues: 57.2671 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 : 0.552 ------------------------------------------------------------------------------- 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... Flipped N/Q/H residues before XYZ refinement: 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 = 0.3708 r_free = 0.3708 target = 0.133867 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3270 r_free = 0.3270 target = 0.101302 restraints weight = 21552.389| |-----------------------------------------------------------------------------| r_work (start): 0.3248 rms_B_bonded: 1.62 r_work: 0.3069 rms_B_bonded: 2.51 restraints_weight: 0.5000 r_work: 0.2949 rms_B_bonded: 3.96 restraints_weight: 0.2500 r_work (final): 0.2949 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8287 moved from start: 0.1553 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.073 15740 Z= 0.197 Angle : 0.696 8.972 21697 Z= 0.362 Chirality : 0.046 0.243 2472 Planarity : 0.005 0.046 2448 Dihedral : 16.889 88.690 3206 Min Nonbonded Distance : 2.487 Molprobity Statistics. All-atom Clashscore : 3.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.46 % Favored : 98.54 % Rotamer: Outliers : 1.08 % Allowed : 6.50 % Favored : 92.42 % 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 aren not related in a simple way. whole: -0.33 (0.20), residues: 1648 helix: 0.46 (0.26), residues: 389 sheet: -1.42 (0.24), residues: 375 loop : 0.21 (0.21), residues: 884 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG G 111 TYR 0.029 0.002 TYR C 281 PHE 0.016 0.002 PHE K 382 TRP 0.020 0.002 TRP G 380 HIS 0.009 0.001 HIS E 132 Details of bonding type rmsd covalent geometry : bond 0.00467 (15740) covalent geometry : angle 0.69629 (21697) hydrogen bonds : bond 0.04917 ( 515) hydrogen bonds : angle 5.62119 ( 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: 16 poor density : 231 time to evaluate : 0.332 Fit side-chains REVERT: C 164 GLU cc_start: 0.7663 (tt0) cc_final: 0.7368 (mm-30) REVERT: C 203 LYS cc_start: 0.7859 (mtmt) cc_final: 0.7361 (mttp) REVERT: C 284 ARG cc_start: 0.8054 (mmt-90) cc_final: 0.7823 (mmt180) REVERT: E 44 THR cc_start: 0.8367 (m) cc_final: 0.8138 (p) REVERT: E 57 GLN cc_start: 0.7738 (mm-40) cc_final: 0.7488 (mm-40) REVERT: F 25 GLN cc_start: 0.8050 (pt0) cc_final: 0.7567 (pm20) REVERT: F 36 SER cc_start: 0.8911 (p) cc_final: 0.8659 (t) REVERT: G 243 MET cc_start: 0.8662 (ttp) cc_final: 0.8395 (ttp) REVERT: H 130 SER cc_start: 0.8276 (m) cc_final: 0.8050 (m) REVERT: I 113 ASP cc_start: 0.9013 (m-30) cc_final: 0.8719 (m-30) REVERT: K 265 ARG cc_start: 0.8499 (ttt180) cc_final: 0.7691 (ttp80) REVERT: K 274 LEU cc_start: 0.9204 (mt) cc_final: 0.8923 (mt) outliers start: 16 outliers final: 10 residues processed: 240 average time/residue: 0.1337 time to fit residues: 44.2555 Evaluate side-chains 211 residues out of total 1478 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 201 time to evaluate : 0.523 ------------------------------------------------------------------------------- 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 Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 172 random chunks: chunk 142 optimal weight: 4.9990 chunk 154 optimal weight: 2.9990 chunk 164 optimal weight: 5.9990 chunk 7 optimal weight: 10.0000 chunk 47 optimal weight: 8.9990 chunk 28 optimal weight: 8.9990 chunk 52 optimal weight: 6.9990 chunk 117 optimal weight: 0.9980 chunk 49 optimal weight: 5.9990 chunk 32 optimal weight: 3.9990 chunk 79 optimal weight: 2.9990 overall best weight: 3.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 99 ASN C 168 GLN ** I 57 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 273 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3665 r_free = 0.3665 target = 0.130681 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3225 r_free = 0.3225 target = 0.098288 restraints weight = 21811.174| |-----------------------------------------------------------------------------| r_work (start): 0.3204 rms_B_bonded: 1.61 r_work: 0.3030 rms_B_bonded: 2.42 restraints_weight: 0.5000 r_work: 0.2910 rms_B_bonded: 3.82 restraints_weight: 0.2500 r_work (final): 0.2910 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8327 moved from start: 0.2094 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.119 15740 Z= 0.282 Angle : 0.724 9.004 21697 Z= 0.375 Chirality : 0.048 0.246 2472 Planarity : 0.005 0.047 2448 Dihedral : 16.881 88.775 3206 Min Nonbonded Distance : 2.474 Molprobity Statistics. All-atom Clashscore : 4.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.70 % Favored : 98.30 % Rotamer: Outliers : 2.30 % Allowed : 9.54 % Favored : 88.16 % 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 aren not related in a simple way. whole: -0.63 (0.20), residues: 1648 helix: 0.32 (0.26), residues: 386 sheet: -1.61 (0.24), residues: 399 loop : 0.01 (0.21), residues: 863 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG I 41 TYR 0.020 0.002 TYR G 281 PHE 0.017 0.002 PHE C 59 TRP 0.022 0.002 TRP G 380 HIS 0.006 0.002 HIS E 132 Details of bonding type rmsd covalent geometry : bond 0.00675 (15740) covalent geometry : angle 0.72413 (21697) hydrogen bonds : bond 0.05127 ( 515) hydrogen bonds : angle 5.53425 ( 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 233 residues out of total 1478 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 199 time to evaluate : 0.538 Fit side-chains revert: symmetry clash REVERT: C 164 GLU cc_start: 0.7653 (tt0) cc_final: 0.7386 (mm-30) REVERT: C 203 LYS cc_start: 0.7981 (mtmt) cc_final: 0.7383 (mttp) REVERT: C 284 ARG cc_start: 0.8226 (mmt-90) cc_final: 0.7902 (mmt180) REVERT: D 143 LYS cc_start: 0.7633 (mtmt) cc_final: 0.6899 (mmmm) REVERT: E 57 GLN cc_start: 0.7719 (mm-40) cc_final: 0.7442 (mm-40) REVERT: F 21 ASP cc_start: 0.6647 (p0) cc_final: 0.6126 (p0) REVERT: F 25 GLN cc_start: 0.8143 (pt0) cc_final: 0.7570 (pm20) REVERT: F 36 SER cc_start: 0.9009 (p) cc_final: 0.8765 (t) REVERT: F 59 GLN cc_start: 0.5777 (mt0) cc_final: 0.5362 (mt0) REVERT: G 243 MET cc_start: 0.8712 (ttp) cc_final: 0.8368 (ttp) REVERT: H 130 SER cc_start: 0.8385 (m) cc_final: 0.8162 (m) REVERT: I 113 ASP cc_start: 0.9015 (m-30) cc_final: 0.8718 (m-30) REVERT: I 122 ARG cc_start: 0.7923 (mmm160) cc_final: 0.7441 (mtm110) REVERT: J 58 GLN cc_start: 0.8795 (OUTLIER) cc_final: 0.8577 (mt0) REVERT: K 211 TYR cc_start: 0.7234 (m-80) cc_final: 0.6659 (m-80) REVERT: K 265 ARG cc_start: 0.8587 (ttt180) cc_final: 0.7764 (ttp80) REVERT: K 321 LYS cc_start: 0.7724 (pttt) cc_final: 0.6931 (mttt) outliers start: 34 outliers final: 22 residues processed: 223 average time/residue: 0.1348 time to fit residues: 42.3630 Evaluate side-chains 211 residues out of total 1478 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 188 time to evaluate : 0.393 ------------------------------------------------------------------------------- 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 230 CYS Chi-restraints excluded: chain C residue 261 VAL Chi-restraints excluded: chain C residue 329 VAL 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 G residue 167 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 I residue 148 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 273 HIS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 172 random chunks: chunk 43 optimal weight: 4.9990 chunk 83 optimal weight: 0.0980 chunk 108 optimal weight: 0.4980 chunk 11 optimal weight: 0.8980 chunk 122 optimal weight: 4.9990 chunk 127 optimal weight: 0.0470 chunk 155 optimal weight: 5.9990 chunk 40 optimal weight: 6.9990 chunk 170 optimal weight: 1.9990 chunk 152 optimal weight: 0.7980 chunk 87 optimal weight: 2.9990 overall best weight: 0.4678 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 99 ASN I 30 ASN I 57 GLN K 273 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3731 r_free = 0.3731 target = 0.135840 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3307 r_free = 0.3307 target = 0.103787 restraints weight = 21647.370| |-----------------------------------------------------------------------------| r_work (start): 0.3283 rms_B_bonded: 1.60 r_work: 0.3109 rms_B_bonded: 2.45 restraints_weight: 0.5000 r_work: 0.2989 rms_B_bonded: 3.89 restraints_weight: 0.2500 r_work (final): 0.2989 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8248 moved from start: 0.2376 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 15740 Z= 0.112 Angle : 0.577 8.713 21697 Z= 0.295 Chirality : 0.041 0.193 2472 Planarity : 0.004 0.045 2448 Dihedral : 16.704 83.831 3206 Min Nonbonded Distance : 2.517 Molprobity Statistics. All-atom Clashscore : 5.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.70 % Favored : 98.30 % Rotamer: Outliers : 1.49 % Allowed : 10.76 % Favored : 87.75 % 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 aren not related in a simple way. whole: -0.21 (0.21), residues: 1648 helix: 0.81 (0.27), residues: 392 sheet: -1.44 (0.24), residues: 379 loop : 0.21 (0.21), residues: 877 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG I 41 TYR 0.014 0.001 TYR G 281 PHE 0.011 0.001 PHE K 382 TRP 0.012 0.001 TRP C 380 HIS 0.020 0.001 HIS K 273 Details of bonding type rmsd covalent geometry : bond 0.00254 (15740) covalent geometry : angle 0.57712 (21697) hydrogen bonds : bond 0.03863 ( 515) hydrogen bonds : angle 5.06528 ( 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 235 residues out of total 1478 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 213 time to evaluate : 0.401 Fit side-chains REVERT: C 164 GLU cc_start: 0.7808 (tt0) cc_final: 0.7446 (mm-30) REVERT: C 203 LYS cc_start: 0.7924 (mtmt) cc_final: 0.7364 (mttp) REVERT: C 284 ARG cc_start: 0.8025 (mmt-90) cc_final: 0.7808 (mmm-85) REVERT: C 421 GLU cc_start: 0.4308 (mm-30) cc_final: 0.3495 (pt0) REVERT: E 57 GLN cc_start: 0.7545 (mm-40) cc_final: 0.7267 (mm-40) REVERT: F 21 ASP cc_start: 0.6642 (p0) cc_final: 0.6313 (p0) REVERT: F 25 GLN cc_start: 0.7868 (pt0) cc_final: 0.7432 (pm20) REVERT: G 66 THR cc_start: 0.8169 (p) cc_final: 0.7924 (t) REVERT: G 243 MET cc_start: 0.8527 (ttp) cc_final: 0.8077 (ttp) REVERT: H 115 GLU cc_start: 0.8041 (mm-30) cc_final: 0.7775 (mm-30) REVERT: I 113 ASP cc_start: 0.8908 (m-30) cc_final: 0.8690 (m-30) REVERT: K 265 ARG cc_start: 0.8530 (ttt180) cc_final: 0.7823 (ttp80) REVERT: K 321 LYS cc_start: 0.7673 (pttt) cc_final: 0.6975 (mttt) REVERT: K 337 GLN cc_start: 0.7133 (mt0) cc_final: 0.6925 (mt0) REVERT: K 391 GLU cc_start: 0.8087 (pt0) cc_final: 0.7818 (pt0) outliers start: 22 outliers final: 12 residues processed: 230 average time/residue: 0.1298 time to fit residues: 41.9972 Evaluate side-chains 205 residues out of total 1478 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 193 time to evaluate : 0.466 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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 118 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 K residue 218 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 172 random chunks: chunk 123 optimal weight: 0.9990 chunk 170 optimal weight: 6.9990 chunk 51 optimal weight: 0.1980 chunk 136 optimal weight: 3.9990 chunk 38 optimal weight: 0.9990 chunk 3 optimal weight: 9.9990 chunk 85 optimal weight: 0.6980 chunk 80 optimal weight: 1.9990 chunk 10 optimal weight: 6.9990 chunk 117 optimal weight: 0.7980 chunk 144 optimal weight: 8.9990 overall best weight: 0.7384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 99 ASN C 360 HIS G 270 GLN I 147 GLN J 25 GLN J 26 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3720 r_free = 0.3720 target = 0.135200 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3301 r_free = 0.3301 target = 0.103412 restraints weight = 21686.675| |-----------------------------------------------------------------------------| r_work (start): 0.3289 rms_B_bonded: 1.54 r_work: 0.3118 rms_B_bonded: 2.37 restraints_weight: 0.5000 r_work: 0.2997 rms_B_bonded: 3.76 restraints_weight: 0.2500 r_work (final): 0.2997 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8223 moved from start: 0.2607 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 15740 Z= 0.114 Angle : 0.552 8.328 21697 Z= 0.281 Chirality : 0.040 0.177 2472 Planarity : 0.004 0.044 2448 Dihedral : 16.563 80.818 3206 Min Nonbonded Distance : 2.517 Molprobity Statistics. All-atom Clashscore : 4.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.58 % Favored : 98.42 % Rotamer: Outliers : 2.17 % Allowed : 11.71 % Favored : 86.13 % 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 aren not related in a simple way. whole: -0.13 (0.21), residues: 1648 helix: 0.97 (0.27), residues: 392 sheet: -1.49 (0.25), residues: 380 loop : 0.27 (0.21), residues: 876 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG I 41 TYR 0.014 0.001 TYR F 41 PHE 0.011 0.001 PHE K 382 TRP 0.011 0.001 TRP C 380 HIS 0.005 0.001 HIS K 273 Details of bonding type rmsd covalent geometry : bond 0.00265 (15740) covalent geometry : angle 0.55191 (21697) hydrogen bonds : bond 0.03574 ( 515) hydrogen bonds : angle 4.88945 ( 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 239 residues out of total 1478 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 207 time to evaluate : 0.570 Fit side-chains REVERT: C 164 GLU cc_start: 0.7685 (tt0) cc_final: 0.7409 (mm-30) REVERT: C 203 LYS cc_start: 0.7982 (mtmt) cc_final: 0.7380 (mttp) REVERT: C 284 ARG cc_start: 0.8022 (mmt-90) cc_final: 0.7753 (mmt180) REVERT: C 421 GLU cc_start: 0.4536 (mm-30) cc_final: 0.3688 (pt0) REVERT: E 57 GLN cc_start: 0.7544 (mm-40) cc_final: 0.7248 (mm-40) REVERT: F 21 ASP cc_start: 0.6524 (p0) cc_final: 0.6252 (p0) REVERT: F 25 GLN cc_start: 0.7763 (pt0) cc_final: 0.7433 (pm20) REVERT: G 66 THR cc_start: 0.8180 (OUTLIER) cc_final: 0.7910 (t) REVERT: G 243 MET cc_start: 0.8575 (ttp) cc_final: 0.8113 (ttp) REVERT: H 108 GLU cc_start: 0.7630 (tt0) cc_final: 0.7320 (mt-10) REVERT: H 115 GLU cc_start: 0.8034 (mm-30) cc_final: 0.7761 (mm-30) REVERT: I 113 ASP cc_start: 0.8935 (m-30) cc_final: 0.8730 (m-30) REVERT: J 58 GLN cc_start: 0.8710 (OUTLIER) cc_final: 0.8469 (mt0) REVERT: K 265 ARG cc_start: 0.8448 (ttt180) cc_final: 0.7823 (ttp80) REVERT: K 321 LYS cc_start: 0.7625 (pttt) cc_final: 0.6943 (mttt) REVERT: K 337 GLN cc_start: 0.7100 (mt0) cc_final: 0.6850 (tt0) REVERT: K 391 GLU cc_start: 0.8007 (pt0) cc_final: 0.7774 (pt0) outliers start: 32 outliers final: 20 residues processed: 229 average time/residue: 0.1356 time to fit residues: 43.5022 Evaluate side-chains 220 residues out of total 1478 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 198 time to evaluate : 0.437 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 129 VAL 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 210 GLU Chi-restraints excluded: chain H residue 71 VAL Chi-restraints excluded: chain I residue 78 ILE Chi-restraints excluded: chain I residue 80 VAL 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=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: 0.8980 chunk 50 optimal weight: 5.9990 chunk 20 optimal weight: 1.9990 chunk 18 optimal weight: 3.9990 chunk 16 optimal weight: 1.9990 chunk 65 optimal weight: 3.9990 chunk 105 optimal weight: 3.9990 overall best weight: 1.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 99 ASN H 106 ASN J 25 GLN J 26 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3710 r_free = 0.3710 target = 0.134288 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3285 r_free = 0.3285 target = 0.102307 restraints weight = 21677.279| |-----------------------------------------------------------------------------| r_work (start): 0.3274 rms_B_bonded: 1.55 r_work: 0.3102 rms_B_bonded: 2.36 restraints_weight: 0.5000 r_work: 0.2983 rms_B_bonded: 3.73 restraints_weight: 0.2500 r_work (final): 0.2983 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8242 moved from start: 0.2707 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.062 15740 Z= 0.144 Angle : 0.566 8.285 21697 Z= 0.288 Chirality : 0.041 0.177 2472 Planarity : 0.004 0.050 2448 Dihedral : 16.524 79.802 3206 Min Nonbonded Distance : 2.333 Molprobity Statistics. All-atom Clashscore : 4.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.58 % Favored : 98.42 % Rotamer: Outliers : 2.30 % Allowed : 12.38 % Favored : 85.32 % 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 aren not related in a simple way. whole: -0.14 (0.21), residues: 1648 helix: 0.95 (0.27), residues: 392 sheet: -1.46 (0.24), residues: 388 loop : 0.26 (0.21), residues: 868 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG I 41 TYR 0.014 0.001 TYR F 41 PHE 0.012 0.001 PHE K 382 TRP 0.012 0.001 TRP G 380 HIS 0.004 0.001 HIS C 259 Details of bonding type rmsd covalent geometry : bond 0.00340 (15740) covalent geometry : angle 0.56556 (21697) hydrogen bonds : bond 0.03686 ( 515) hydrogen bonds : angle 4.87772 ( 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 238 residues out of total 1478 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 204 time to evaluate : 0.455 Fit side-chains revert: symmetry clash REVERT: C 164 GLU cc_start: 0.7688 (tt0) cc_final: 0.7390 (mm-30) REVERT: C 203 LYS cc_start: 0.7987 (mtmt) cc_final: 0.7379 (mttp) REVERT: C 284 ARG cc_start: 0.8056 (mmt-90) cc_final: 0.7763 (mmt180) REVERT: C 421 GLU cc_start: 0.4608 (mm-30) cc_final: 0.3735 (pt0) REVERT: E 57 GLN cc_start: 0.7567 (mm-40) cc_final: 0.7275 (mm-40) REVERT: F 2 PHE cc_start: 0.8144 (m-80) cc_final: 0.7899 (m-80) REVERT: G 66 THR cc_start: 0.8220 (OUTLIER) cc_final: 0.7916 (t) REVERT: G 243 MET cc_start: 0.8596 (ttp) cc_final: 0.8125 (ttp) REVERT: H 115 GLU cc_start: 0.8036 (mm-30) cc_final: 0.7768 (mm-30) REVERT: I 113 ASP cc_start: 0.8932 (m-30) cc_final: 0.8671 (m-30) REVERT: J 58 GLN cc_start: 0.8712 (OUTLIER) cc_final: 0.8478 (mt0) REVERT: K 265 ARG cc_start: 0.8613 (ttt180) cc_final: 0.7894 (ttp80) REVERT: K 321 LYS cc_start: 0.7641 (pttt) cc_final: 0.6904 (mttt) REVERT: K 337 GLN cc_start: 0.7069 (mt0) cc_final: 0.6843 (tt0) REVERT: K 360 LEU cc_start: 0.8510 (mt) cc_final: 0.8284 (mt) REVERT: K 391 GLU cc_start: 0.8006 (pt0) cc_final: 0.7748 (pt0) outliers start: 34 outliers final: 25 residues processed: 230 average time/residue: 0.1206 time to fit residues: 39.5002 Evaluate side-chains 218 residues out of total 1478 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 191 time to evaluate : 0.534 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 329 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 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 210 GLU Chi-restraints excluded: chain H residue 71 VAL Chi-restraints excluded: chain H residue 139 LYS 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 347 ARG Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 172 random chunks: chunk 137 optimal weight: 2.9990 chunk 13 optimal weight: 0.0570 chunk 71 optimal weight: 5.9990 chunk 1 optimal weight: 9.9990 chunk 8 optimal weight: 4.9990 chunk 102 optimal weight: 1.9990 chunk 132 optimal weight: 4.9990 chunk 2 optimal weight: 6.9990 chunk 25 optimal weight: 8.9990 chunk 144 optimal weight: 0.4980 chunk 42 optimal weight: 1.9990 overall best weight: 1.5104 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 99 ASN H 106 ASN J 25 GLN J 26 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3706 r_free = 0.3706 target = 0.133959 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3279 r_free = 0.3279 target = 0.101925 restraints weight = 21535.481| |-----------------------------------------------------------------------------| r_work (start): 0.3263 rms_B_bonded: 1.55 r_work: 0.3096 rms_B_bonded: 2.33 restraints_weight: 0.5000 r_work: 0.2979 rms_B_bonded: 3.67 restraints_weight: 0.2500 r_work (final): 0.2979 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8246 moved from start: 0.2771 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.067 15740 Z= 0.155 Angle : 0.575 7.988 21697 Z= 0.293 Chirality : 0.041 0.177 2472 Planarity : 0.004 0.052 2448 Dihedral : 16.519 80.050 3206 Min Nonbonded Distance : 2.464 Molprobity Statistics. All-atom Clashscore : 4.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.64 % Favored : 98.36 % Rotamer: Outliers : 2.30 % Allowed : 13.13 % Favored : 84.57 % 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 aren not related in a simple way. whole: -0.16 (0.21), residues: 1648 helix: 0.95 (0.27), residues: 391 sheet: -1.42 (0.25), residues: 376 loop : 0.18 (0.21), residues: 881 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG I 41 TYR 0.015 0.001 TYR F 41 PHE 0.013 0.002 PHE K 382 TRP 0.013 0.001 TRP G 380 HIS 0.006 0.001 HIS E 132 Details of bonding type rmsd covalent geometry : bond 0.00370 (15740) covalent geometry : angle 0.57457 (21697) hydrogen bonds : bond 0.03719 ( 515) hydrogen bonds : angle 4.88071 ( 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 232 residues out of total 1478 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 198 time to evaluate : 0.550 Fit side-chains revert: symmetry clash REVERT: C 164 GLU cc_start: 0.7603 (tt0) cc_final: 0.7379 (mm-30) REVERT: C 203 LYS cc_start: 0.7979 (mtmt) cc_final: 0.7400 (mttp) REVERT: C 284 ARG cc_start: 0.8085 (mmt-90) cc_final: 0.7757 (mmt180) REVERT: C 421 GLU cc_start: 0.4871 (mm-30) cc_final: 0.3848 (pt0) REVERT: D 133 MET cc_start: 0.7444 (tpp) cc_final: 0.7090 (tpt) REVERT: F 25 GLN cc_start: 0.7813 (pt0) cc_final: 0.7328 (pm20) REVERT: G 66 THR cc_start: 0.8233 (OUTLIER) cc_final: 0.7931 (t) REVERT: G 243 MET cc_start: 0.8578 (ttp) cc_final: 0.8098 (ttp) REVERT: H 115 GLU cc_start: 0.8064 (mm-30) cc_final: 0.7812 (mm-30) REVERT: I 113 ASP cc_start: 0.8921 (m-30) cc_final: 0.8672 (m-30) REVERT: J 58 GLN cc_start: 0.8714 (OUTLIER) cc_final: 0.8484 (mt0) REVERT: K 265 ARG cc_start: 0.8625 (ttt180) cc_final: 0.7904 (ttp80) REVERT: K 321 LYS cc_start: 0.7537 (pttt) cc_final: 0.6644 (mttt) REVERT: K 337 GLN cc_start: 0.7081 (mt0) cc_final: 0.6860 (tt0) REVERT: K 360 LEU cc_start: 0.8482 (mt) cc_final: 0.8273 (mt) REVERT: K 391 GLU cc_start: 0.8000 (pt0) cc_final: 0.7756 (pt0) outliers start: 34 outliers final: 30 residues processed: 224 average time/residue: 0.1266 time to fit residues: 40.4444 Evaluate side-chains 226 residues out of total 1478 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 194 time to evaluate : 0.343 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 152 LEU 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 102 ASN 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 210 GLU Chi-restraints excluded: chain H residue 71 VAL Chi-restraints excluded: chain H residue 139 LYS 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 26 GLN 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 172 random chunks: chunk 132 optimal weight: 2.9990 chunk 7 optimal weight: 10.0000 chunk 125 optimal weight: 0.9990 chunk 77 optimal weight: 0.9980 chunk 144 optimal weight: 2.9990 chunk 3 optimal weight: 8.9990 chunk 17 optimal weight: 8.9990 chunk 117 optimal weight: 0.1980 chunk 114 optimal weight: 0.6980 chunk 121 optimal weight: 1.9990 chunk 29 optimal weight: 0.9980 overall best weight: 0.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 106 ASN J 25 GLN J 26 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3717 r_free = 0.3717 target = 0.134769 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3297 r_free = 0.3297 target = 0.103061 restraints weight = 21577.882| |-----------------------------------------------------------------------------| r_work (start): 0.3289 rms_B_bonded: 1.54 r_work: 0.3118 rms_B_bonded: 2.41 restraints_weight: 0.5000 r_work: 0.3000 rms_B_bonded: 3.82 restraints_weight: 0.2500 r_work (final): 0.3000 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8238 moved from start: 0.2907 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 15740 Z= 0.113 Angle : 0.547 8.321 21697 Z= 0.278 Chirality : 0.040 0.163 2472 Planarity : 0.004 0.052 2448 Dihedral : 16.477 79.988 3206 Min Nonbonded Distance : 2.208 Molprobity Statistics. All-atom Clashscore : 4.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.40 % Favored : 98.60 % Rotamer: Outliers : 2.37 % Allowed : 13.46 % Favored : 84.17 % 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 aren not related in a simple way. whole: -0.07 (0.21), residues: 1648 helix: 1.05 (0.27), residues: 392 sheet: -1.34 (0.25), residues: 369 loop : 0.20 (0.21), residues: 887 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG I 41 TYR 0.014 0.001 TYR F 41 PHE 0.011 0.001 PHE K 382 TRP 0.010 0.001 TRP C 380 HIS 0.004 0.001 HIS C 259 Details of bonding type rmsd covalent geometry : bond 0.00265 (15740) covalent geometry : angle 0.54661 (21697) hydrogen bonds : bond 0.03430 ( 515) hydrogen bonds : angle 4.79775 ( 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 241 residues out of total 1478 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 206 time to evaluate : 0.575 Fit side-chains revert: symmetry clash REVERT: C 164 GLU cc_start: 0.7656 (tt0) cc_final: 0.7400 (mm-30) REVERT: C 203 LYS cc_start: 0.7964 (mtmt) cc_final: 0.7402 (mttp) REVERT: C 284 ARG cc_start: 0.8035 (mmt-90) cc_final: 0.7749 (mmt180) REVERT: C 421 GLU cc_start: 0.4987 (mm-30) cc_final: 0.3975 (pt0) REVERT: D 97 TYR cc_start: 0.7127 (m-80) cc_final: 0.6869 (m-80) REVERT: D 133 MET cc_start: 0.7515 (tpp) cc_final: 0.7185 (tpt) REVERT: F 2 PHE cc_start: 0.8183 (m-80) cc_final: 0.7916 (m-80) REVERT: F 25 GLN cc_start: 0.7757 (pt0) cc_final: 0.7291 (pm20) REVERT: G 66 THR cc_start: 0.8251 (OUTLIER) cc_final: 0.7987 (t) REVERT: G 243 MET cc_start: 0.8501 (ttp) cc_final: 0.8022 (ttp) REVERT: H 115 GLU cc_start: 0.8064 (mm-30) cc_final: 0.7827 (mm-30) REVERT: I 113 ASP cc_start: 0.8859 (m-30) cc_final: 0.8613 (m-30) REVERT: J 58 GLN cc_start: 0.8744 (OUTLIER) cc_final: 0.8528 (mt0) REVERT: K 265 ARG cc_start: 0.8518 (ttt180) cc_final: 0.7915 (ttp80) REVERT: K 321 LYS cc_start: 0.7402 (pttt) cc_final: 0.6761 (mttt) REVERT: K 391 GLU cc_start: 0.7954 (pt0) cc_final: 0.7727 (pt0) outliers start: 35 outliers final: 31 residues processed: 232 average time/residue: 0.1277 time to fit residues: 41.8360 Evaluate side-chains 230 residues out of total 1478 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 197 time to evaluate : 0.394 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 27 VAL Chi-restraints excluded: chain C residue 261 VAL Chi-restraints excluded: chain C residue 281 TYR Chi-restraints excluded: chain C residue 329 VAL 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 D residue 122 ASP Chi-restraints excluded: chain D residue 152 LEU 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 118 THR Chi-restraints excluded: chain G residue 210 GLU Chi-restraints excluded: chain H residue 71 VAL Chi-restraints excluded: chain H residue 139 LYS 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 J residue 26 GLN 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: 0.6980 chunk 138 optimal weight: 4.9990 chunk 148 optimal weight: 3.9990 chunk 95 optimal weight: 2.9990 chunk 117 optimal weight: 0.6980 chunk 115 optimal weight: 0.8980 chunk 137 optimal weight: 0.8980 chunk 38 optimal weight: 1.9990 chunk 147 optimal weight: 5.9990 chunk 30 optimal weight: 0.5980 chunk 64 optimal weight: 3.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 161 ASN J 25 GLN J 26 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3732 r_free = 0.3732 target = 0.135948 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3313 r_free = 0.3313 target = 0.104163 restraints weight = 21529.613| |-----------------------------------------------------------------------------| r_work (start): 0.3301 rms_B_bonded: 1.54 r_work: 0.3134 rms_B_bonded: 2.33 restraints_weight: 0.5000 r_work: 0.3016 rms_B_bonded: 3.70 restraints_weight: 0.2500 r_work (final): 0.3016 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8211 moved from start: 0.3036 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= 0.111 Angle : 0.543 8.650 21697 Z= 0.276 Chirality : 0.040 0.163 2472 Planarity : 0.004 0.051 2448 Dihedral : 16.443 79.717 3206 Min Nonbonded Distance : 2.469 Molprobity Statistics. All-atom Clashscore : 5.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.58 % Favored : 98.42 % Rotamer: Outliers : 2.77 % Allowed : 13.53 % Favored : 83.69 % 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 aren not related in a simple way. whole: -0.02 (0.21), residues: 1648 helix: 1.12 (0.27), residues: 394 sheet: -1.27 (0.25), residues: 376 loop : 0.21 (0.21), residues: 878 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG I 41 TYR 0.017 0.001 TYR E 135 PHE 0.010 0.001 PHE K 382 TRP 0.013 0.001 TRP K 405 HIS 0.004 0.001 HIS C 259 Details of bonding type rmsd covalent geometry : bond 0.00258 (15740) covalent geometry : angle 0.54329 (21697) hydrogen bonds : bond 0.03333 ( 515) hydrogen bonds : angle 4.73263 ( 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 246 residues out of total 1478 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 205 time to evaluate : 0.492 Fit side-chains REVERT: C 164 GLU cc_start: 0.7665 (tt0) cc_final: 0.7443 (mm-30) REVERT: C 203 LYS cc_start: 0.7969 (mtmt) cc_final: 0.7408 (mttp) REVERT: C 284 ARG cc_start: 0.8030 (mmt-90) cc_final: 0.7745 (mmt180) REVERT: D 97 TYR cc_start: 0.6992 (m-80) cc_final: 0.6734 (m-80) REVERT: D 133 MET cc_start: 0.7468 (tpp) cc_final: 0.7161 (tpt) REVERT: F 2 PHE cc_start: 0.8183 (m-80) cc_final: 0.7920 (m-80) REVERT: F 8 ASN cc_start: 0.6653 (p0) cc_final: 0.6313 (p0) REVERT: F 25 GLN cc_start: 0.7700 (pt0) cc_final: 0.7245 (pm20) REVERT: G 66 THR cc_start: 0.8234 (OUTLIER) cc_final: 0.7971 (t) REVERT: G 243 MET cc_start: 0.8480 (ttp) cc_final: 0.7998 (ttp) REVERT: H 115 GLU cc_start: 0.8071 (mm-30) cc_final: 0.7840 (mm-30) REVERT: I 113 ASP cc_start: 0.8861 (m-30) cc_final: 0.8614 (m-30) REVERT: I 141 GLU cc_start: 0.7108 (pt0) cc_final: 0.6852 (pt0) REVERT: J 58 GLN cc_start: 0.8746 (OUTLIER) cc_final: 0.8527 (mt0) REVERT: K 265 ARG cc_start: 0.8483 (ttt180) cc_final: 0.7893 (ttp80) REVERT: K 321 LYS cc_start: 0.7430 (pttt) cc_final: 0.6758 (mttt) REVERT: K 381 ARG cc_start: 0.7893 (ttp-170) cc_final: 0.7453 (ptm160) REVERT: K 391 GLU cc_start: 0.7935 (pt0) cc_final: 0.7694 (pt0) outliers start: 41 outliers final: 31 residues processed: 236 average time/residue: 0.1236 time to fit residues: 41.7656 Evaluate side-chains 232 residues out of total 1478 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 199 time to evaluate : 0.405 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 27 VAL 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 D residue 152 LEU Chi-restraints excluded: chain E residue 28 LEU 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 210 GLU 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 172 random chunks: chunk 70 optimal weight: 8.9990 chunk 143 optimal weight: 0.9990 chunk 16 optimal weight: 2.9990 chunk 36 optimal weight: 4.9990 chunk 26 optimal weight: 1.9990 chunk 67 optimal weight: 6.9990 chunk 165 optimal weight: 5.9990 chunk 90 optimal weight: 0.0050 chunk 135 optimal weight: 0.9980 chunk 31 optimal weight: 5.9990 chunk 15 optimal weight: 2.9990 overall best weight: 1.4000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 99 ASN C 161 ASN E 68 GLN F 10 GLN G 68 HIS J 25 GLN J 26 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3719 r_free = 0.3719 target = 0.134894 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3294 r_free = 0.3294 target = 0.102694 restraints weight = 21634.970| |-----------------------------------------------------------------------------| r_work (start): 0.3274 rms_B_bonded: 1.76 r_work: 0.3081 rms_B_bonded: 2.65 restraints_weight: 0.5000 r_work: 0.2956 rms_B_bonded: 4.22 restraints_weight: 0.2500 r_work (final): 0.2956 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8271 moved from start: 0.3041 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.063 15740 Z= 0.148 Angle : 0.569 7.876 21697 Z= 0.289 Chirality : 0.041 0.187 2472 Planarity : 0.004 0.051 2448 Dihedral : 16.447 79.547 3206 Min Nonbonded Distance : 2.441 Molprobity Statistics. All-atom Clashscore : 5.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.70 % Favored : 98.30 % Rotamer: Outliers : 2.23 % Allowed : 13.73 % 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 aren not related in a simple way. whole: -0.03 (0.21), residues: 1648 helix: 1.11 (0.27), residues: 393 sheet: -1.26 (0.25), residues: 376 loop : 0.19 (0.21), residues: 879 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG I 41 TYR 0.017 0.001 TYR F 41 PHE 0.012 0.002 PHE K 382 TRP 0.013 0.001 TRP G 380 HIS 0.004 0.001 HIS C 259 Details of bonding type rmsd covalent geometry : bond 0.00352 (15740) covalent geometry : angle 0.56876 (21697) hydrogen bonds : bond 0.03541 ( 515) hydrogen bonds : angle 4.76798 ( 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 227 residues out of total 1478 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 194 time to evaluate : 0.359 Fit side-chains REVERT: C 164 GLU cc_start: 0.7601 (tt0) cc_final: 0.7266 (mm-30) REVERT: C 203 LYS cc_start: 0.7959 (mtmt) cc_final: 0.7396 (mttp) REVERT: C 284 ARG cc_start: 0.8113 (mmt-90) cc_final: 0.7790 (mmt180) REVERT: D 97 TYR cc_start: 0.7019 (m-80) cc_final: 0.6756 (m-80) REVERT: D 133 MET cc_start: 0.7502 (tpp) cc_final: 0.7186 (tpt) REVERT: F 2 PHE cc_start: 0.8208 (m-80) cc_final: 0.7934 (m-80) REVERT: F 8 ASN cc_start: 0.6684 (p0) cc_final: 0.6357 (p0) REVERT: F 25 GLN cc_start: 0.7766 (pt0) cc_final: 0.7282 (pm20) REVERT: G 66 THR cc_start: 0.8289 (OUTLIER) cc_final: 0.7976 (t) REVERT: G 243 MET cc_start: 0.8598 (ttp) cc_final: 0.8128 (ttp) REVERT: H 115 GLU cc_start: 0.8154 (mm-30) cc_final: 0.7854 (mm-30) REVERT: I 113 ASP cc_start: 0.8907 (m-30) cc_final: 0.8661 (m-30) REVERT: I 141 GLU cc_start: 0.7171 (pt0) cc_final: 0.6914 (pt0) REVERT: J 58 GLN cc_start: 0.8750 (OUTLIER) cc_final: 0.8527 (mt0) REVERT: K 265 ARG cc_start: 0.8567 (ttt180) cc_final: 0.7957 (ttp80) REVERT: K 321 LYS cc_start: 0.7513 (pttt) cc_final: 0.6820 (mttt) REVERT: K 381 ARG cc_start: 0.7969 (ttp-170) cc_final: 0.7541 (ptm160) REVERT: K 391 GLU cc_start: 0.8022 (pt0) cc_final: 0.7783 (pt0) outliers start: 33 outliers final: 31 residues processed: 220 average time/residue: 0.1189 time to fit residues: 36.9878 Evaluate side-chains 225 residues out of total 1478 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 192 time to evaluate : 0.403 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 27 VAL 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 D residue 152 LEU Chi-restraints excluded: chain E residue 28 LEU 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 210 GLU 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 172 random chunks: chunk 145 optimal weight: 3.9990 chunk 49 optimal weight: 0.4980 chunk 11 optimal weight: 0.9990 chunk 118 optimal weight: 0.7980 chunk 20 optimal weight: 0.8980 chunk 68 optimal weight: 8.9990 chunk 15 optimal weight: 4.9990 chunk 9 optimal weight: 0.0070 chunk 73 optimal weight: 0.0670 chunk 69 optimal weight: 5.9990 chunk 88 optimal weight: 2.9990 overall best weight: 0.4536 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 161 ASN C 276 HIS F 10 GLN J 25 GLN J 26 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3758 r_free = 0.3758 target = 0.137875 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3347 r_free = 0.3347 target = 0.106593 restraints weight = 21569.276| |-----------------------------------------------------------------------------| r_work (start): 0.3337 rms_B_bonded: 1.68 r_work: 0.3149 rms_B_bonded: 2.57 restraints_weight: 0.5000 r_work: 0.3028 rms_B_bonded: 4.08 restraints_weight: 0.2500 r_work (final): 0.3028 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8214 moved from start: 0.3271 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 15740 Z= 0.097 Angle : 0.529 9.634 21697 Z= 0.267 Chirality : 0.039 0.156 2472 Planarity : 0.004 0.050 2448 Dihedral : 16.357 79.569 3206 Min Nonbonded Distance : 2.428 Molprobity Statistics. All-atom Clashscore : 5.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.88 % Favored : 98.12 % Rotamer: Outliers : 1.96 % Allowed : 14.14 % Favored : 83.90 % 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 aren not related in a simple way. whole: 0.09 (0.21), residues: 1648 helix: 1.20 (0.27), residues: 394 sheet: -1.15 (0.25), residues: 370 loop : 0.24 (0.21), residues: 884 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG I 41 TYR 0.015 0.001 TYR E 135 PHE 0.010 0.001 PHE K 382 TRP 0.018 0.001 TRP K 405 HIS 0.004 0.001 HIS J 44 Details of bonding type rmsd covalent geometry : bond 0.00221 (15740) covalent geometry : angle 0.52917 (21697) hydrogen bonds : bond 0.03114 ( 515) hydrogen bonds : angle 4.61839 ( 1293) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4024.30 seconds wall clock time: 69 minutes 30.38 seconds (4170.38 seconds total)