Starting phenix.real_space_refine on Sat Aug 23 11:39:43 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8ggh_40008/08_2025/8ggh_40008.cif Found real_map, /net/cci-nas-00/data/ceres_data/8ggh_40008/08_2025/8ggh_40008.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.29 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8ggh_40008/08_2025/8ggh_40008.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8ggh_40008/08_2025/8ggh_40008.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8ggh_40008/08_2025/8ggh_40008.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8ggh_40008/08_2025/8ggh_40008.map" } resolution = 3.29 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= 0.020 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: 4 Type Number sf(0) Gaussians S 68 5.16 5 C 7476 2.51 5 N 2071 2.21 5 O 2183 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 8 residue(s): 0.01s 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: 11798 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 2390 Number of conformers: 1 Conformer: "" Number of residues, atoms: 323, 2390 Classifications: {'peptide': 323} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 23, 'TRANS': 299} Chain: "C" Number of atoms: 2390 Number of conformers: 1 Conformer: "" Number of residues, atoms: 323, 2390 Classifications: {'peptide': 323} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 23, 'TRANS': 299} Chain: "B" Number of atoms: 2390 Number of conformers: 1 Conformer: "" Number of residues, atoms: 323, 2390 Classifications: {'peptide': 323} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 22, 'TRANS': 299} Chain: "D" Number of atoms: 2355 Number of conformers: 1 Conformer: "" Number of residues, atoms: 319, 2355 Classifications: {'peptide': 319} Link IDs: {'PCIS': 1, 'PTRANS': 22, 'TRANS': 295} Chain: "E" Number of atoms: 2273 Number of conformers: 1 Conformer: "" Number of residues, atoms: 289, 2273 Classifications: {'peptide': 289} Link IDs: {'PTRANS': 15, 'TRANS': 273} Chain breaks: 1 Time building chain proxies: 3.17, per 1000 atoms: 0.27 Number of scatterers: 11798 At special positions: 0 Unit cell: (102.34, 102.34, 137.6, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 68 16.00 O 2183 8.00 N 2071 7.00 C 7476 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: 1.01 Conformation dependent library (CDL) restraints added in 590.3 milliseconds Enol-peptide restraints added in 953.7 nanoseconds 3130 Ramachandran restraints generated. 1565 Oldfield, 0 Emsley, 1565 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2890 Finding SS restraints... Secondary structure from input PDB file: 60 helices and 12 sheets defined 50.0% alpha, 9.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.43 Creating SS restraints... Processing helix chain 'A' and resid 12 through 25 removed outlier: 3.894A pdb=" N SER A 16 " --> pdb=" O GLY A 12 " (cutoff:3.500A) removed outlier: 3.948A pdb=" N ARG A 23 " --> pdb=" O LEU A 19 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N GLU A 24 " --> pdb=" O LEU A 20 " (cutoff:3.500A) Processing helix chain 'A' and resid 38 through 47 removed outlier: 3.517A pdb=" N SER A 47 " --> pdb=" O ALA A 43 " (cutoff:3.500A) Processing helix chain 'A' and resid 69 through 76 Processing helix chain 'A' and resid 97 through 116 removed outlier: 4.735A pdb=" N GLY A 105 " --> pdb=" O ASN A 101 " (cutoff:3.500A) removed outlier: 4.209A pdb=" N ILE A 106 " --> pdb=" O VAL A 102 " (cutoff:3.500A) Processing helix chain 'A' and resid 129 through 145 removed outlier: 3.734A pdb=" N THR A 134 " --> pdb=" O VAL A 130 " (cutoff:3.500A) Proline residue: A 135 - end of helix Processing helix chain 'A' and resid 156 through 168 removed outlier: 4.285A pdb=" N GLY A 160 " --> pdb=" O SER A 156 " (cutoff:3.500A) Processing helix chain 'A' and resid 206 through 225 removed outlier: 3.623A pdb=" N GLN A 215 " --> pdb=" O ARG A 211 " (cutoff:3.500A) removed outlier: 5.069A pdb=" N GLY A 218 " --> pdb=" O VAL A 214 " (cutoff:3.500A) removed outlier: 5.218A pdb=" N THR A 219 " --> pdb=" O GLN A 215 " (cutoff:3.500A) Processing helix chain 'A' and resid 232 through 252 removed outlier: 3.535A pdb=" N GLY A 239 " --> pdb=" O MET A 235 " (cutoff:3.500A) removed outlier: 4.140A pdb=" N PHE A 242 " --> pdb=" O ALA A 238 " (cutoff:3.500A) Processing helix chain 'A' and resid 297 through 317 removed outlier: 3.552A pdb=" N LEU A 301 " --> pdb=" O GLU A 297 " (cutoff:3.500A) removed outlier: 3.988A pdb=" N GLU A 302 " --> pdb=" O LYS A 298 " (cutoff:3.500A) removed outlier: 4.836A pdb=" N GLU A 303 " --> pdb=" O GLU A 299 " (cutoff:3.500A) Processing helix chain 'C' and resid 13 through 23 removed outlier: 3.872A pdb=" N ARG C 23 " --> pdb=" O LEU C 19 " (cutoff:3.500A) Processing helix chain 'C' and resid 38 through 44 removed outlier: 3.603A pdb=" N VAL C 42 " --> pdb=" O GLY C 38 " (cutoff:3.500A) Processing helix chain 'C' and resid 69 through 76 removed outlier: 3.666A pdb=" N THR C 73 " --> pdb=" O ASP C 69 " (cutoff:3.500A) Processing helix chain 'C' and resid 98 through 118 removed outlier: 3.796A pdb=" N GLY C 105 " --> pdb=" O ASN C 101 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N ILE C 106 " --> pdb=" O VAL C 102 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N VAL C 107 " --> pdb=" O ASN C 103 " (cutoff:3.500A) removed outlier: 3.873A pdb=" N MET C 108 " --> pdb=" O ALA C 104 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N SER C 116 " --> pdb=" O LEU C 112 " (cutoff:3.500A) removed outlier: 4.546A pdb=" N VAL C 117 " --> pdb=" O THR C 113 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N SER C 118 " --> pdb=" O CYS C 114 " (cutoff:3.500A) Processing helix chain 'C' and resid 129 through 145 Proline residue: C 135 - end of helix removed outlier: 4.289A pdb=" N ILE C 144 " --> pdb=" O THR C 140 " (cutoff:3.500A) Processing helix chain 'C' and resid 157 through 171 removed outlier: 3.502A pdb=" N PHE C 166 " --> pdb=" O ARG C 162 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N ALA C 170 " --> pdb=" O PHE C 166 " (cutoff:3.500A) Processing helix chain 'C' and resid 194 through 197 removed outlier: 4.073A pdb=" N ILE C 197 " --> pdb=" O TYR C 194 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 194 through 197' Processing helix chain 'C' and resid 203 through 216 removed outlier: 3.615A pdb=" N GLN C 215 " --> pdb=" O ARG C 211 " (cutoff:3.500A) Processing helix chain 'C' and resid 217 through 225 removed outlier: 3.804A pdb=" N VAL C 221 " --> pdb=" O ALA C 217 " (cutoff:3.500A) Processing helix chain 'C' and resid 234 through 252 Processing helix chain 'C' and resid 294 through 319 removed outlier: 4.137A pdb=" N LYS C 310 " --> pdb=" O GLY C 306 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N ALA C 313 " --> pdb=" O LYS C 309 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N GLY C 315 " --> pdb=" O ASN C 311 " (cutoff:3.500A) Processing helix chain 'B' and resid 12 through 23 removed outlier: 3.733A pdb=" N SER B 16 " --> pdb=" O GLY B 12 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N ARG B 23 " --> pdb=" O LEU B 19 " (cutoff:3.500A) Processing helix chain 'B' and resid 38 through 47 Processing helix chain 'B' and resid 69 through 74 Processing helix chain 'B' and resid 99 through 116 removed outlier: 3.834A pdb=" N ASN B 103 " --> pdb=" O LEU B 99 " (cutoff:3.500A) Processing helix chain 'B' and resid 129 through 145 Proline residue: B 135 - end of helix removed outlier: 3.830A pdb=" N ILE B 144 " --> pdb=" O THR B 140 " (cutoff:3.500A) Processing helix chain 'B' and resid 156 through 168 removed outlier: 4.312A pdb=" N GLY B 160 " --> pdb=" O SER B 156 " (cutoff:3.500A) Processing helix chain 'B' and resid 186 through 190 removed outlier: 4.050A pdb=" N ILE B 190 " --> pdb=" O ASP B 187 " (cutoff:3.500A) Processing helix chain 'B' and resid 203 through 225 removed outlier: 3.601A pdb=" N GLU B 209 " --> pdb=" O SER B 205 " (cutoff:3.500A) removed outlier: 5.309A pdb=" N GLY B 218 " --> pdb=" O VAL B 214 " (cutoff:3.500A) removed outlier: 6.335A pdb=" N THR B 219 " --> pdb=" O GLN B 215 " (cutoff:3.500A) removed outlier: 4.052A pdb=" N GLU B 220 " --> pdb=" O VAL B 216 " (cutoff:3.500A) removed outlier: 4.056A pdb=" N VAL B 221 " --> pdb=" O ALA B 217 " (cutoff:3.500A) removed outlier: 4.064A pdb=" N VAL B 222 " --> pdb=" O GLY B 218 " (cutoff:3.500A) Processing helix chain 'B' and resid 233 through 251 Processing helix chain 'B' and resid 296 through 322 removed outlier: 3.649A pdb=" N LYS B 310 " --> pdb=" O GLY B 306 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N ARG B 320 " --> pdb=" O GLU B 316 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N SER B 321 " --> pdb=" O THR B 317 " (cutoff:3.500A) Processing helix chain 'D' and resid 11 through 22 removed outlier: 3.971A pdb=" N SER D 16 " --> pdb=" O GLY D 12 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N LEU D 19 " --> pdb=" O GLN D 15 " (cutoff:3.500A) removed outlier: 4.138A pdb=" N LEU D 20 " --> pdb=" O SER D 16 " (cutoff:3.500A) Processing helix chain 'D' and resid 38 through 47 Processing helix chain 'D' and resid 71 through 76 Processing helix chain 'D' and resid 95 through 114 removed outlier: 3.536A pdb=" N LEU D 99 " --> pdb=" O THR D 95 " (cutoff:3.500A) removed outlier: 4.852A pdb=" N GLY D 105 " --> pdb=" O ASN D 101 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N ILE D 106 " --> pdb=" O VAL D 102 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N MET D 108 " --> pdb=" O ALA D 104 " (cutoff:3.500A) removed outlier: 3.826A pdb=" N CYS D 114 " --> pdb=" O LEU D 110 " (cutoff:3.500A) Processing helix chain 'D' and resid 132 through 145 removed outlier: 3.532A pdb=" N ILE D 136 " --> pdb=" O SER D 132 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N ILE D 144 " --> pdb=" O THR D 140 " (cutoff:3.500A) Processing helix chain 'D' and resid 156 through 170 removed outlier: 4.247A pdb=" N GLY D 160 " --> pdb=" O SER D 156 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N ALA D 170 " --> pdb=" O PHE D 166 " (cutoff:3.500A) Processing helix chain 'D' and resid 186 through 190 Processing helix chain 'D' and resid 203 through 215 removed outlier: 3.816A pdb=" N GLN D 215 " --> pdb=" O ARG D 211 " (cutoff:3.500A) Processing helix chain 'D' and resid 216 through 225 Processing helix chain 'D' and resid 231 through 250 removed outlier: 3.832A pdb=" N ALA D 240 " --> pdb=" O ALA D 236 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N THR D 243 " --> pdb=" O GLY D 239 " (cutoff:3.500A) Processing helix chain 'D' and resid 294 through 316 removed outlier: 3.608A pdb=" N GLU D 299 " --> pdb=" O THR D 295 " (cutoff:3.500A) Processing helix chain 'E' and resid 334 through 343 Processing helix chain 'E' and resid 361 through 370 removed outlier: 3.549A pdb=" N GLU E 365 " --> pdb=" O LYS E 361 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N LEU E 370 " --> pdb=" O GLY E 366 " (cutoff:3.500A) Processing helix chain 'E' and resid 374 through 387 removed outlier: 3.517A pdb=" N ALA E 378 " --> pdb=" O ASN E 374 " (cutoff:3.500A) Processing helix chain 'E' and resid 392 through 406 removed outlier: 4.174A pdb=" N TRP E 396 " --> pdb=" O ASN E 392 " (cutoff:3.500A) removed outlier: 4.015A pdb=" N ARG E 397 " --> pdb=" O VAL E 393 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N ARG E 398 " --> pdb=" O GLU E 394 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N LEU E 399 " --> pdb=" O ALA E 395 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N THR E 401 " --> pdb=" O ARG E 397 " (cutoff:3.500A) Processing helix chain 'E' and resid 410 through 423 removed outlier: 3.770A pdb=" N ILE E 414 " --> pdb=" O CYS E 410 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N LEU E 422 " --> pdb=" O HIS E 418 " (cutoff:3.500A) Processing helix chain 'E' and resid 427 through 436 removed outlier: 4.489A pdb=" N LEU E 433 " --> pdb=" O VAL E 429 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N SER E 436 " --> pdb=" O ALA E 432 " (cutoff:3.500A) Processing helix chain 'E' and resid 437 through 441 removed outlier: 3.562A pdb=" N GLU E 440 " --> pdb=" O HIS E 437 " (cutoff:3.500A) Processing helix chain 'E' and resid 442 through 456 removed outlier: 3.808A pdb=" N ALA E 446 " --> pdb=" O ASN E 442 " (cutoff:3.500A) removed outlier: 3.859A pdb=" N LEU E 447 " --> pdb=" O VAL E 443 " (cutoff:3.500A) removed outlier: 4.133A pdb=" N GLN E 448 " --> pdb=" O GLY E 444 " (cutoff:3.500A) removed outlier: 4.259A pdb=" N SER E 456 " --> pdb=" O SER E 452 " (cutoff:3.500A) Processing helix chain 'E' and resid 493 through 501 Processing helix chain 'E' and resid 510 through 515 Processing helix chain 'E' and resid 517 through 524 removed outlier: 3.682A pdb=" N HIS E 521 " --> pdb=" O LEU E 517 " (cutoff:3.500A) Processing helix chain 'E' and resid 528 through 536 removed outlier: 3.919A pdb=" N LYS E 532 " --> pdb=" O ASP E 528 " (cutoff:3.500A) Processing helix chain 'E' and resid 544 through 554 removed outlier: 4.091A pdb=" N THR E 554 " --> pdb=" O LYS E 550 " (cutoff:3.500A) Processing helix chain 'E' and resid 555 through 559 Processing helix chain 'E' and resid 564 through 575 removed outlier: 4.206A pdb=" N TYR E 568 " --> pdb=" O ALA E 564 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N ASN E 569 " --> pdb=" O LEU E 565 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N LEU E 572 " --> pdb=" O TYR E 568 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N ILE E 574 " --> pdb=" O ARG E 570 " (cutoff:3.500A) Processing helix chain 'E' and resid 579 through 592 Processing helix chain 'E' and resid 594 through 610 removed outlier: 3.542A pdb=" N ALA E 598 " --> pdb=" O GLN E 594 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N ALA E 610 " --> pdb=" O ILE E 606 " (cutoff:3.500A) Processing helix chain 'E' and resid 626 through 631 removed outlier: 3.793A pdb=" N LEU E 631 " --> pdb=" O LEU E 627 " (cutoff:3.500A) Processing helix chain 'E' and resid 643 through 647 removed outlier: 3.518A pdb=" N SER E 647 " --> pdb=" O VAL E 644 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 55 through 59 removed outlier: 3.547A pdb=" N ALA A 59 " --> pdb=" O LEU A 33 " (cutoff:3.500A) removed outlier: 6.456A pdb=" N VAL A 4 " --> pdb=" O SER A 32 " (cutoff:3.500A) removed outlier: 8.092A pdb=" N TYR A 34 " --> pdb=" O VAL A 4 " (cutoff:3.500A) removed outlier: 5.818A pdb=" N PHE A 123 " --> pdb=" O LEU A 153 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 181 through 183 Processing sheet with id=AA3, first strand: chain 'A' and resid 257 through 263 removed outlier: 4.048A pdb=" N ALA A 260 " --> pdb=" O MET A 275 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N MET A 275 " --> pdb=" O ALA A 260 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N ARG A 286 " --> pdb=" O VAL A 278 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'C' and resid 55 through 60 removed outlier: 3.945A pdb=" N ASP C 35 " --> pdb=" O ALA C 59 " (cutoff:3.500A) removed outlier: 5.830A pdb=" N PHE C 123 " --> pdb=" O LEU C 153 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 181 through 183 Processing sheet with id=AA6, first strand: chain 'C' and resid 257 through 263 removed outlier: 3.978A pdb=" N ALA C 260 " --> pdb=" O MET C 275 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N MET C 275 " --> pdb=" O ALA C 260 " (cutoff:3.500A) removed outlier: 5.609A pdb=" N ARG C 287 " --> pdb=" O PRO C 276 " (cutoff:3.500A) removed outlier: 7.253A pdb=" N VAL C 278 " --> pdb=" O GLU C 285 " (cutoff:3.500A) removed outlier: 4.045A pdb=" N GLY C 283 " --> pdb=" O GLY C 280 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 55 through 58 removed outlier: 3.542A pdb=" N TYR B 34 " --> pdb=" O VAL B 6 " (cutoff:3.500A) removed outlier: 4.507A pdb=" N ALA B 5 " --> pdb=" O VAL B 81 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N VAL B 83 " --> pdb=" O ALA B 5 " (cutoff:3.500A) removed outlier: 7.087A pdb=" N PHE B 82 " --> pdb=" O CYS B 124 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 181 through 182 Processing sheet with id=AA9, first strand: chain 'B' and resid 257 through 263 removed outlier: 4.002A pdb=" N ALA B 260 " --> pdb=" O MET B 275 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N MET B 275 " --> pdb=" O ALA B 260 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N LEU B 273 " --> pdb=" O VAL B 262 " (cutoff:3.500A) removed outlier: 5.395A pdb=" N ARG B 287 " --> pdb=" O PRO B 276 " (cutoff:3.500A) removed outlier: 7.166A pdb=" N VAL B 278 " --> pdb=" O GLU B 285 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'D' and resid 56 through 60 removed outlier: 6.200A pdb=" N LEU D 31 " --> pdb=" O LYS D 57 " (cutoff:3.500A) removed outlier: 8.165A pdb=" N ALA D 59 " --> pdb=" O LEU D 31 " (cutoff:3.500A) removed outlier: 6.661A pdb=" N LEU D 33 " --> pdb=" O ALA D 59 " (cutoff:3.500A) removed outlier: 3.882A pdb=" N VAL D 4 " --> pdb=" O THR D 30 " (cutoff:3.500A) removed outlier: 3.872A pdb=" N ILE D 84 " --> pdb=" O CYS D 124 " (cutoff:3.500A) removed outlier: 6.042A pdb=" N PHE D 123 " --> pdb=" O LEU D 153 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'D' and resid 181 through 182 Processing sheet with id=AB3, first strand: chain 'D' and resid 257 through 263 removed outlier: 3.769A pdb=" N ALA D 260 " --> pdb=" O MET D 275 " (cutoff:3.500A) 519 hydrogen bonds defined for protein. 1515 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.28 Time building geometry restraints manager: 1.36 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 3912 1.34 - 1.46: 1140 1.46 - 1.57: 6845 1.57 - 1.69: 0 1.69 - 1.81: 116 Bond restraints: 12013 Sorted by residual: bond pdb=" CA LYS E 361 " pdb=" CB LYS E 361 " ideal model delta sigma weight residual 1.525 1.545 -0.020 8.30e-03 1.45e+04 5.79e+00 bond pdb=" CA THR D 127 " pdb=" C THR D 127 " ideal model delta sigma weight residual 1.523 1.500 0.023 1.34e-02 5.57e+03 2.90e+00 bond pdb=" C HIS C 172 " pdb=" N PRO C 173 " ideal model delta sigma weight residual 1.335 1.355 -0.020 1.28e-02 6.10e+03 2.48e+00 bond pdb=" C ASN C 128 " pdb=" N PRO C 129 " ideal model delta sigma weight residual 1.334 1.369 -0.036 2.34e-02 1.83e+03 2.31e+00 bond pdb=" CB PRO C 129 " pdb=" CG PRO C 129 " ideal model delta sigma weight residual 1.492 1.566 -0.074 5.00e-02 4.00e+02 2.17e+00 ... (remaining 12008 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.09: 16058 2.09 - 4.17: 248 4.17 - 6.26: 39 6.26 - 8.34: 5 8.34 - 10.43: 3 Bond angle restraints: 16353 Sorted by residual: angle pdb=" C LEU B 63 " pdb=" N PRO B 64 " pdb=" CA PRO B 64 " ideal model delta sigma weight residual 120.38 111.49 8.89 1.03e+00 9.43e-01 7.46e+01 angle pdb=" C SER E 641 " pdb=" CA SER E 641 " pdb=" CB SER E 641 " ideal model delta sigma weight residual 116.54 110.42 6.12 1.15e+00 7.56e-01 2.83e+01 angle pdb=" N VAL B 130 " pdb=" CA VAL B 130 " pdb=" C VAL B 130 " ideal model delta sigma weight residual 110.42 115.26 -4.84 9.60e-01 1.09e+00 2.54e+01 angle pdb=" C LYS E 361 " pdb=" CA LYS E 361 " pdb=" CB LYS E 361 " ideal model delta sigma weight residual 111.20 114.43 -3.23 7.10e-01 1.98e+00 2.07e+01 angle pdb=" N HIS A 172 " pdb=" CA HIS A 172 " pdb=" C HIS A 172 " ideal model delta sigma weight residual 109.81 119.79 -9.98 2.21e+00 2.05e-01 2.04e+01 ... (remaining 16348 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 19.50: 6729 19.50 - 38.99: 528 38.99 - 58.49: 71 58.49 - 77.98: 14 77.98 - 97.48: 7 Dihedral angle restraints: 7349 sinusoidal: 2854 harmonic: 4495 Sorted by residual: dihedral pdb=" CA ASN D 128 " pdb=" C ASN D 128 " pdb=" N PRO D 129 " pdb=" CA PRO D 129 " ideal model delta harmonic sigma weight residual 180.00 82.52 97.48 0 5.00e+00 4.00e-02 3.80e+02 dihedral pdb=" CA ASN C 128 " pdb=" C ASN C 128 " pdb=" N PRO C 129 " pdb=" CA PRO C 129 " ideal model delta harmonic sigma weight residual -180.00 -158.96 -21.04 0 5.00e+00 4.00e-02 1.77e+01 dihedral pdb=" CA TYR E 348 " pdb=" C TYR E 348 " pdb=" N PRO E 349 " pdb=" CA PRO E 349 " ideal model delta harmonic sigma weight residual -180.00 -160.44 -19.56 0 5.00e+00 4.00e-02 1.53e+01 ... (remaining 7346 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.057: 1603 0.057 - 0.114: 319 0.114 - 0.171: 29 0.171 - 0.228: 3 0.228 - 0.285: 1 Chirality restraints: 1955 Sorted by residual: chirality pdb=" CA HIS A 172 " pdb=" N HIS A 172 " pdb=" C HIS A 172 " pdb=" CB HIS A 172 " both_signs ideal model delta sigma weight residual False 2.51 2.23 0.28 2.00e-01 2.50e+01 2.03e+00 chirality pdb=" CA PRO C 129 " pdb=" N PRO C 129 " pdb=" C PRO C 129 " pdb=" CB PRO C 129 " both_signs ideal model delta sigma weight residual False 2.72 2.52 0.20 2.00e-01 2.50e+01 1.01e+00 chirality pdb=" CA ASN B 128 " pdb=" N ASN B 128 " pdb=" C ASN B 128 " pdb=" CB ASN B 128 " both_signs ideal model delta sigma weight residual False 2.51 2.32 0.19 2.00e-01 2.50e+01 9.42e-01 ... (remaining 1952 not shown) Planarity restraints: 2126 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASN C 128 " -0.069 5.00e-02 4.00e+02 1.04e-01 1.74e+01 pdb=" N PRO C 129 " 0.180 5.00e-02 4.00e+02 pdb=" CA PRO C 129 " -0.055 5.00e-02 4.00e+02 pdb=" CD PRO C 129 " -0.056 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PRO C 64 " -0.065 5.00e-02 4.00e+02 9.91e-02 1.57e+01 pdb=" N PRO C 65 " 0.171 5.00e-02 4.00e+02 pdb=" CA PRO C 65 " -0.053 5.00e-02 4.00e+02 pdb=" CD PRO C 65 " -0.054 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C TYR E 348 " 0.053 5.00e-02 4.00e+02 8.08e-02 1.05e+01 pdb=" N PRO E 349 " -0.140 5.00e-02 4.00e+02 pdb=" CA PRO E 349 " 0.043 5.00e-02 4.00e+02 pdb=" CD PRO E 349 " 0.044 5.00e-02 4.00e+02 ... (remaining 2123 not shown) Histogram of nonbonded interaction distances: 2.08 - 2.64: 101 2.64 - 3.21: 10783 3.21 - 3.77: 17029 3.77 - 4.34: 22174 4.34 - 4.90: 37399 Nonbonded interactions: 87486 Sorted by model distance: nonbonded pdb=" OD1 ASP A 203 " pdb=" N GLU A 204 " model vdw 2.075 3.120 nonbonded pdb=" O GLU E 492 " pdb=" N ARG E 494 " model vdw 2.213 3.120 nonbonded pdb=" O PRO C 129 " pdb=" OG1 THR C 133 " model vdw 2.217 3.040 nonbonded pdb=" OG1 THR C 264 " pdb=" O CYS C 270 " model vdw 2.224 3.040 nonbonded pdb=" O SER B 156 " pdb=" OG SER B 156 " model vdw 2.292 3.040 ... (remaining 87481 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and resid 1 through 319) selection = (chain 'B' and resid 1 through 319) selection = (chain 'C' and resid 1 through 319) selection = chain 'D' } 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: 6.330 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: 0.210 Check model and map are aligned: 0.040 Set scattering table: 0.030 Process input model: 12.960 Find NCS groups from input model: 0.230 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.460 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 21.300 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8257 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 : 0.003 0.074 12013 Z= 0.142 Angle : 0.638 10.431 16353 Z= 0.352 Chirality : 0.045 0.285 1955 Planarity : 0.006 0.104 2126 Dihedral : 13.949 97.478 4459 Min Nonbonded Distance : 2.075 Molprobity Statistics. All-atom Clashscore : 7.18 Ramachandran Plot: Outliers : 0.64 % Allowed : 9.78 % Favored : 89.58 % Rotamer: Outliers : 0.24 % Allowed : 0.55 % Favored : 99.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.89 % Cis-general : 0.00 % Twisted Proline : 0.94 % 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: -1.03 (0.22), residues: 1565 helix: 0.65 (0.20), residues: 714 sheet: -1.25 (0.43), residues: 159 loop : -2.00 (0.24), residues: 692 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 23 TYR 0.010 0.001 TYR E 568 PHE 0.010 0.001 PHE B 82 TRP 0.012 0.001 TRP E 628 HIS 0.003 0.001 HIS A 172 Details of bonding type rmsd covalent geometry : bond 0.00283 (12013) covalent geometry : angle 0.63761 (16353) hydrogen bonds : bond 0.20536 ( 519) hydrogen bonds : angle 6.30905 ( 1515) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3130 Ramachandran restraints generated. 1565 Oldfield, 0 Emsley, 1565 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3130 Ramachandran restraints generated. 1565 Oldfield, 0 Emsley, 1565 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 148 residues out of total 1276 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 145 time to evaluate : 0.521 Fit side-chains REVERT: E 356 TYR cc_start: 0.8091 (m-80) cc_final: 0.7872 (m-80) REVERT: E 361 LYS cc_start: 0.8786 (pptt) cc_final: 0.8506 (pptt) REVERT: E 547 MET cc_start: 0.8059 (ttp) cc_final: 0.7610 (tmm) REVERT: E 582 MET cc_start: 0.7064 (mtt) cc_final: 0.6221 (mtt) REVERT: E 628 TRP cc_start: 0.8606 (t-100) cc_final: 0.8334 (t-100) outliers start: 3 outliers final: 1 residues processed: 148 average time/residue: 0.1028 time to fit residues: 23.0336 Evaluate side-chains 115 residues out of total 1276 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 114 time to evaluate : 0.468 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 66 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 155 random chunks: chunk 98 optimal weight: 0.8980 chunk 107 optimal weight: 7.9990 chunk 10 optimal weight: 3.9990 chunk 66 optimal weight: 3.9990 chunk 130 optimal weight: 6.9990 chunk 124 optimal weight: 5.9990 chunk 103 optimal weight: 5.9990 chunk 77 optimal weight: 0.8980 chunk 122 optimal weight: 0.0570 chunk 91 optimal weight: 3.9990 chunk 149 optimal weight: 0.9990 overall best weight: 1.3702 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 387 GLN E 430 HIS E 609 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3609 r_free = 0.3609 target = 0.110248 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3159 r_free = 0.3159 target = 0.081565 restraints weight = 25629.102| |-----------------------------------------------------------------------------| r_work (start): 0.3141 rms_B_bonded: 3.10 r_work: 0.3027 rms_B_bonded: 3.49 restraints_weight: 0.5000 r_work (final): 0.3027 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8215 moved from start: 0.1157 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.070 12013 Z= 0.155 Angle : 0.641 10.520 16353 Z= 0.326 Chirality : 0.046 0.204 1955 Planarity : 0.006 0.103 2126 Dihedral : 4.711 62.173 1690 Min Nonbonded Distance : 2.475 Molprobity Statistics. All-atom Clashscore : 5.76 Ramachandran Plot: Outliers : 0.58 % Allowed : 8.24 % Favored : 91.18 % Rotamer: Outliers : 1.02 % Allowed : 9.09 % Favored : 89.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.89 % Cis-general : 0.00 % Twisted Proline : 0.94 % 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: -0.72 (0.22), residues: 1565 helix: 0.98 (0.20), residues: 715 sheet: -0.99 (0.39), residues: 191 loop : -2.01 (0.24), residues: 659 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 23 TYR 0.016 0.001 TYR E 348 PHE 0.014 0.001 PHE B 82 TRP 0.009 0.001 TRP E 628 HIS 0.010 0.001 HIS E 359 Details of bonding type rmsd covalent geometry : bond 0.00359 (12013) covalent geometry : angle 0.64145 (16353) hydrogen bonds : bond 0.05197 ( 519) hydrogen bonds : angle 4.64075 ( 1515) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3130 Ramachandran restraints generated. 1565 Oldfield, 0 Emsley, 1565 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3130 Ramachandran restraints generated. 1565 Oldfield, 0 Emsley, 1565 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 137 residues out of total 1276 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 124 time to evaluate : 0.527 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 35 ASP cc_start: 0.8228 (t0) cc_final: 0.7747 (t0) REVERT: B 244 MET cc_start: 0.8440 (tpt) cc_final: 0.8218 (tpp) REVERT: D 108 MET cc_start: 0.8367 (mtm) cc_final: 0.8165 (mtm) REVERT: E 361 LYS cc_start: 0.8854 (pptt) cc_final: 0.8555 (pptt) REVERT: E 582 MET cc_start: 0.7410 (mtt) cc_final: 0.6988 (mtt) outliers start: 13 outliers final: 8 residues processed: 131 average time/residue: 0.0965 time to fit residues: 19.3943 Evaluate side-chains 119 residues out of total 1276 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 111 time to evaluate : 0.503 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 216 VAL Chi-restraints excluded: chain C residue 88 VAL Chi-restraints excluded: chain B residue 293 ILE Chi-restraints excluded: chain D residue 99 LEU Chi-restraints excluded: chain E residue 414 ILE Chi-restraints excluded: chain E residue 427 ILE Chi-restraints excluded: chain E residue 587 VAL Chi-restraints excluded: chain E residue 639 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 155 random chunks: chunk 45 optimal weight: 0.9980 chunk 112 optimal weight: 2.9990 chunk 52 optimal weight: 0.0980 chunk 127 optimal weight: 10.0000 chunk 33 optimal weight: 0.9990 chunk 109 optimal weight: 3.9990 chunk 76 optimal weight: 2.9990 chunk 129 optimal weight: 0.5980 chunk 15 optimal weight: 3.9990 chunk 119 optimal weight: 0.9990 chunk 42 optimal weight: 0.9980 overall best weight: 0.7382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 101 ASN E 609 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3586 r_free = 0.3586 target = 0.109578 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3113 r_free = 0.3113 target = 0.079579 restraints weight = 25440.488| |-----------------------------------------------------------------------------| r_work (start): 0.3164 rms_B_bonded: 3.29 r_work: 0.3047 rms_B_bonded: 3.69 restraints_weight: 0.5000 r_work (final): 0.3047 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8201 moved from start: 0.1328 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.074 12013 Z= 0.117 Angle : 0.576 7.786 16353 Z= 0.293 Chirality : 0.044 0.208 1955 Planarity : 0.005 0.103 2126 Dihedral : 4.507 54.742 1689 Min Nonbonded Distance : 2.464 Molprobity Statistics. All-atom Clashscore : 5.38 Ramachandran Plot: Outliers : 0.58 % Allowed : 7.99 % Favored : 91.44 % Rotamer: Outliers : 1.18 % Allowed : 12.07 % Favored : 86.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.89 % Cis-general : 0.00 % Twisted Proline : 0.94 % 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: -0.45 (0.22), residues: 1565 helix: 1.20 (0.20), residues: 716 sheet: -0.77 (0.40), residues: 191 loop : -1.88 (0.25), residues: 658 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG E 621 TYR 0.008 0.001 TYR E 568 PHE 0.013 0.001 PHE B 82 TRP 0.008 0.001 TRP E 628 HIS 0.009 0.001 HIS E 601 Details of bonding type rmsd covalent geometry : bond 0.00261 (12013) covalent geometry : angle 0.57621 (16353) hydrogen bonds : bond 0.04100 ( 519) hydrogen bonds : angle 4.27525 ( 1515) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3130 Ramachandran restraints generated. 1565 Oldfield, 0 Emsley, 1565 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3130 Ramachandran restraints generated. 1565 Oldfield, 0 Emsley, 1565 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 145 residues out of total 1276 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 130 time to evaluate : 0.517 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 24 GLU cc_start: 0.8054 (mp0) cc_final: 0.7846 (mp0) REVERT: A 203 ASP cc_start: 0.8554 (t0) cc_final: 0.8293 (t0) REVERT: C 35 ASP cc_start: 0.8288 (t0) cc_final: 0.7914 (t0) REVERT: B 244 MET cc_start: 0.8371 (tpt) cc_final: 0.8146 (tpp) REVERT: D 108 MET cc_start: 0.8332 (mtm) cc_final: 0.8068 (mtp) REVERT: D 235 MET cc_start: 0.8336 (mmm) cc_final: 0.7932 (mtp) REVERT: E 350 PHE cc_start: 0.8190 (t80) cc_final: 0.7976 (t80) REVERT: E 361 LYS cc_start: 0.8938 (pptt) cc_final: 0.8705 (pptt) REVERT: E 363 MET cc_start: 0.8930 (tpp) cc_final: 0.8674 (tpp) REVERT: E 582 MET cc_start: 0.7380 (mtt) cc_final: 0.7021 (mtt) outliers start: 15 outliers final: 7 residues processed: 140 average time/residue: 0.1014 time to fit residues: 21.2692 Evaluate side-chains 123 residues out of total 1276 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 116 time to evaluate : 0.504 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 85 VAL Chi-restraints excluded: chain C residue 88 VAL Chi-restraints excluded: chain B residue 81 VAL Chi-restraints excluded: chain B residue 293 ILE Chi-restraints excluded: chain D residue 262 VAL Chi-restraints excluded: chain D residue 268 HIS Chi-restraints excluded: chain E residue 639 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 155 random chunks: chunk 65 optimal weight: 0.6980 chunk 139 optimal weight: 5.9990 chunk 110 optimal weight: 0.8980 chunk 31 optimal weight: 0.8980 chunk 125 optimal weight: 0.0980 chunk 18 optimal weight: 1.9990 chunk 25 optimal weight: 2.9990 chunk 105 optimal weight: 7.9990 chunk 0 optimal weight: 5.9990 chunk 95 optimal weight: 6.9990 chunk 119 optimal weight: 0.9980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 311 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3590 r_free = 0.3590 target = 0.109846 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3116 r_free = 0.3116 target = 0.079768 restraints weight = 25522.852| |-----------------------------------------------------------------------------| r_work (start): 0.3162 rms_B_bonded: 3.29 r_work: 0.3047 rms_B_bonded: 3.68 restraints_weight: 0.5000 r_work (final): 0.3047 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8152 moved from start: 0.1505 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.074 12013 Z= 0.115 Angle : 0.577 9.722 16353 Z= 0.293 Chirality : 0.044 0.205 1955 Planarity : 0.005 0.103 2126 Dihedral : 4.395 51.726 1689 Min Nonbonded Distance : 2.478 Molprobity Statistics. All-atom Clashscore : 5.59 Ramachandran Plot: Outliers : 0.58 % Allowed : 7.86 % Favored : 91.57 % Rotamer: Outliers : 1.57 % Allowed : 14.03 % Favored : 84.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.89 % Cis-general : 0.00 % Twisted Proline : 0.94 % 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: -0.37 (0.22), residues: 1565 helix: 1.29 (0.20), residues: 715 sheet: -0.71 (0.40), residues: 191 loop : -1.88 (0.25), residues: 659 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG E 580 TYR 0.015 0.001 TYR E 348 PHE 0.012 0.001 PHE B 82 TRP 0.006 0.001 TRP E 628 HIS 0.016 0.001 HIS E 601 Details of bonding type rmsd covalent geometry : bond 0.00260 (12013) covalent geometry : angle 0.57691 (16353) hydrogen bonds : bond 0.03690 ( 519) hydrogen bonds : angle 4.10662 ( 1515) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3130 Ramachandran restraints generated. 1565 Oldfield, 0 Emsley, 1565 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3130 Ramachandran restraints generated. 1565 Oldfield, 0 Emsley, 1565 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 143 residues out of total 1276 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 123 time to evaluate : 0.511 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 203 ASP cc_start: 0.8534 (t0) cc_final: 0.8246 (t0) REVERT: C 35 ASP cc_start: 0.8300 (t0) cc_final: 0.7835 (t0) REVERT: B 244 MET cc_start: 0.8344 (tpt) cc_final: 0.8029 (tpp) REVERT: D 108 MET cc_start: 0.8309 (mtm) cc_final: 0.8030 (mtp) REVERT: D 235 MET cc_start: 0.8297 (mmm) cc_final: 0.7920 (mtp) REVERT: E 350 PHE cc_start: 0.8251 (t80) cc_final: 0.8012 (t80) REVERT: E 361 LYS cc_start: 0.8967 (pptt) cc_final: 0.8739 (pptt) REVERT: E 363 MET cc_start: 0.8934 (tpp) cc_final: 0.8692 (tpp) REVERT: E 582 MET cc_start: 0.7413 (mtt) cc_final: 0.7148 (mtt) outliers start: 20 outliers final: 12 residues processed: 135 average time/residue: 0.0950 time to fit residues: 19.7953 Evaluate side-chains 126 residues out of total 1276 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 114 time to evaluate : 0.491 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 191 VAL Chi-restraints excluded: chain A residue 216 VAL Chi-restraints excluded: chain C residue 85 VAL Chi-restraints excluded: chain C residue 88 VAL Chi-restraints excluded: chain B residue 81 VAL Chi-restraints excluded: chain B residue 293 ILE Chi-restraints excluded: chain D residue 33 LEU Chi-restraints excluded: chain D residue 83 VAL Chi-restraints excluded: chain D residue 262 VAL Chi-restraints excluded: chain D residue 268 HIS Chi-restraints excluded: chain E residue 414 ILE Chi-restraints excluded: chain E residue 639 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 155 random chunks: chunk 104 optimal weight: 0.9980 chunk 1 optimal weight: 0.9980 chunk 3 optimal weight: 2.9990 chunk 121 optimal weight: 3.9990 chunk 95 optimal weight: 5.9990 chunk 148 optimal weight: 4.9990 chunk 28 optimal weight: 7.9990 chunk 107 optimal weight: 5.9990 chunk 100 optimal weight: 0.7980 chunk 86 optimal weight: 0.0870 chunk 153 optimal weight: 0.0870 overall best weight: 0.5936 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 311 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3627 r_free = 0.3627 target = 0.110572 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3175 r_free = 0.3175 target = 0.081289 restraints weight = 25836.850| |-----------------------------------------------------------------------------| r_work (start): 0.3147 rms_B_bonded: 3.23 r_work: 0.3033 rms_B_bonded: 3.65 restraints_weight: 0.5000 r_work (final): 0.3033 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8314 moved from start: 0.1627 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.076 12013 Z= 0.109 Angle : 0.565 7.890 16353 Z= 0.287 Chirality : 0.043 0.208 1955 Planarity : 0.005 0.102 2126 Dihedral : 4.309 49.764 1689 Min Nonbonded Distance : 2.483 Molprobity Statistics. All-atom Clashscore : 5.09 Ramachandran Plot: Outliers : 0.58 % Allowed : 7.80 % Favored : 91.63 % Rotamer: Outliers : 1.49 % Allowed : 14.81 % Favored : 83.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.89 % Cis-general : 0.00 % Twisted Proline : 0.94 % 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: -0.27 (0.23), residues: 1565 helix: 1.39 (0.20), residues: 715 sheet: -0.64 (0.40), residues: 191 loop : -1.86 (0.25), residues: 659 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 23 TYR 0.009 0.001 TYR E 568 PHE 0.023 0.001 PHE B 318 TRP 0.005 0.001 TRP E 628 HIS 0.010 0.001 HIS E 601 Details of bonding type rmsd covalent geometry : bond 0.00245 (12013) covalent geometry : angle 0.56542 (16353) hydrogen bonds : bond 0.03374 ( 519) hydrogen bonds : angle 3.94719 ( 1515) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3130 Ramachandran restraints generated. 1565 Oldfield, 0 Emsley, 1565 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3130 Ramachandran restraints generated. 1565 Oldfield, 0 Emsley, 1565 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 150 residues out of total 1276 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 131 time to evaluate : 0.479 Fit side-chains revert: symmetry clash REVERT: A 139 GLN cc_start: 0.8603 (tp-100) cc_final: 0.8402 (tp-100) REVERT: A 203 ASP cc_start: 0.8551 (t0) cc_final: 0.8324 (t0) REVERT: C 35 ASP cc_start: 0.8263 (t0) cc_final: 0.7795 (t0) REVERT: B 244 MET cc_start: 0.8444 (tpt) cc_final: 0.8058 (tpp) REVERT: D 235 MET cc_start: 0.8341 (mmm) cc_final: 0.7982 (mtp) REVERT: E 350 PHE cc_start: 0.8357 (t80) cc_final: 0.8150 (t80) REVERT: E 361 LYS cc_start: 0.8990 (pptt) cc_final: 0.8716 (pptt) REVERT: E 582 MET cc_start: 0.7389 (mtt) cc_final: 0.7114 (mtt) REVERT: E 628 TRP cc_start: 0.8703 (t-100) cc_final: 0.8423 (t-100) outliers start: 19 outliers final: 13 residues processed: 143 average time/residue: 0.0998 time to fit residues: 21.7209 Evaluate side-chains 133 residues out of total 1276 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 120 time to evaluate : 0.459 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 191 VAL Chi-restraints excluded: chain A residue 216 VAL Chi-restraints excluded: chain A residue 235 MET Chi-restraints excluded: chain C residue 85 VAL Chi-restraints excluded: chain C residue 88 VAL Chi-restraints excluded: chain B residue 81 VAL Chi-restraints excluded: chain B residue 293 ILE Chi-restraints excluded: chain D residue 33 LEU Chi-restraints excluded: chain D residue 83 VAL Chi-restraints excluded: chain D residue 111 VAL Chi-restraints excluded: chain D residue 262 VAL Chi-restraints excluded: chain D residue 268 HIS Chi-restraints excluded: chain E residue 639 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 155 random chunks: chunk 31 optimal weight: 0.7980 chunk 44 optimal weight: 6.9990 chunk 130 optimal weight: 3.9990 chunk 37 optimal weight: 6.9990 chunk 40 optimal weight: 0.9990 chunk 22 optimal weight: 3.9990 chunk 120 optimal weight: 3.9990 chunk 153 optimal weight: 5.9990 chunk 117 optimal weight: 0.2980 chunk 86 optimal weight: 2.9990 chunk 27 optimal weight: 1.9990 overall best weight: 1.4186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 311 ASN ** E 371 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 584 ASN ** E 609 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3556 r_free = 0.3556 target = 0.107304 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3076 r_free = 0.3076 target = 0.077291 restraints weight = 25457.395| |-----------------------------------------------------------------------------| r_work (start): 0.3100 rms_B_bonded: 3.26 r_work: 0.2984 rms_B_bonded: 3.66 restraints_weight: 0.5000 r_work (final): 0.2984 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8335 moved from start: 0.1728 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.067 12013 Z= 0.144 Angle : 0.610 11.060 16353 Z= 0.307 Chirality : 0.044 0.203 1955 Planarity : 0.005 0.105 2126 Dihedral : 4.334 41.446 1689 Min Nonbonded Distance : 2.482 Molprobity Statistics. All-atom Clashscore : 5.47 Ramachandran Plot: Outliers : 0.58 % Allowed : 8.37 % Favored : 91.05 % Rotamer: Outliers : 1.33 % Allowed : 15.91 % Favored : 82.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.89 % Cis-general : 0.00 % Twisted Proline : 0.94 % 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: -0.32 (0.23), residues: 1565 helix: 1.38 (0.20), residues: 716 sheet: -0.78 (0.40), residues: 193 loop : -1.89 (0.25), residues: 656 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG E 535 TYR 0.009 0.001 TYR E 568 PHE 0.019 0.001 PHE B 318 TRP 0.008 0.001 TRP E 628 HIS 0.006 0.001 HIS E 601 Details of bonding type rmsd covalent geometry : bond 0.00346 (12013) covalent geometry : angle 0.61045 (16353) hydrogen bonds : bond 0.04214 ( 519) hydrogen bonds : angle 4.06473 ( 1515) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3130 Ramachandran restraints generated. 1565 Oldfield, 0 Emsley, 1565 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3130 Ramachandran restraints generated. 1565 Oldfield, 0 Emsley, 1565 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 131 residues out of total 1276 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 114 time to evaluate : 0.482 Fit side-chains revert: symmetry clash REVERT: C 35 ASP cc_start: 0.8432 (t0) cc_final: 0.7960 (t0) REVERT: B 244 MET cc_start: 0.8509 (tpt) cc_final: 0.8285 (tpp) REVERT: E 350 PHE cc_start: 0.8334 (t80) cc_final: 0.8036 (t80) REVERT: E 361 LYS cc_start: 0.9033 (pptt) cc_final: 0.8776 (pptt) REVERT: E 582 MET cc_start: 0.7295 (mtt) cc_final: 0.6829 (mtt) REVERT: E 585 MET cc_start: 0.8291 (ppp) cc_final: 0.8026 (ppp) REVERT: E 628 TRP cc_start: 0.8740 (t-100) cc_final: 0.8430 (t-100) outliers start: 17 outliers final: 15 residues processed: 126 average time/residue: 0.0927 time to fit residues: 17.9175 Evaluate side-chains 124 residues out of total 1276 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 109 time to evaluate : 0.458 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 73 THR Chi-restraints excluded: chain A residue 191 VAL Chi-restraints excluded: chain A residue 216 VAL Chi-restraints excluded: chain A residue 235 MET Chi-restraints excluded: chain C residue 85 VAL Chi-restraints excluded: chain C residue 88 VAL Chi-restraints excluded: chain B residue 81 VAL Chi-restraints excluded: chain B residue 293 ILE Chi-restraints excluded: chain D residue 33 LEU Chi-restraints excluded: chain D residue 83 VAL Chi-restraints excluded: chain D residue 111 VAL Chi-restraints excluded: chain D residue 250 LEU Chi-restraints excluded: chain D residue 262 VAL Chi-restraints excluded: chain D residue 268 HIS Chi-restraints excluded: chain E residue 633 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 155 random chunks: chunk 18 optimal weight: 0.7980 chunk 97 optimal weight: 0.7980 chunk 142 optimal weight: 10.0000 chunk 1 optimal weight: 0.7980 chunk 53 optimal weight: 4.9990 chunk 82 optimal weight: 3.9990 chunk 108 optimal weight: 0.8980 chunk 99 optimal weight: 3.9990 chunk 139 optimal weight: 4.9990 chunk 22 optimal weight: 2.9990 chunk 109 optimal weight: 0.9990 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 609 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3573 r_free = 0.3573 target = 0.108397 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3099 r_free = 0.3099 target = 0.078554 restraints weight = 25251.821| |-----------------------------------------------------------------------------| r_work (start): 0.3120 rms_B_bonded: 3.25 r_work: 0.3000 rms_B_bonded: 3.68 restraints_weight: 0.5000 r_work (final): 0.3000 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8351 moved from start: 0.1797 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.073 12013 Z= 0.117 Angle : 0.594 13.090 16353 Z= 0.297 Chirality : 0.044 0.212 1955 Planarity : 0.005 0.104 2126 Dihedral : 4.296 40.972 1689 Min Nonbonded Distance : 2.443 Molprobity Statistics. All-atom Clashscore : 5.51 Ramachandran Plot: Outliers : 0.51 % Allowed : 8.18 % Favored : 91.31 % Rotamer: Outliers : 1.65 % Allowed : 16.30 % Favored : 82.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.89 % Cis-general : 0.00 % Twisted Proline : 0.94 % 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: -0.23 (0.23), residues: 1565 helix: 1.43 (0.20), residues: 715 sheet: -0.65 (0.40), residues: 191 loop : -1.85 (0.25), residues: 659 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 23 TYR 0.007 0.001 TYR E 568 PHE 0.018 0.001 PHE B 318 TRP 0.004 0.001 TRP E 628 HIS 0.006 0.001 HIS E 601 Details of bonding type rmsd covalent geometry : bond 0.00271 (12013) covalent geometry : angle 0.59385 (16353) hydrogen bonds : bond 0.03661 ( 519) hydrogen bonds : angle 3.95912 ( 1515) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3130 Ramachandran restraints generated. 1565 Oldfield, 0 Emsley, 1565 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3130 Ramachandran restraints generated. 1565 Oldfield, 0 Emsley, 1565 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 137 residues out of total 1276 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 116 time to evaluate : 0.485 Fit side-chains revert: symmetry clash REVERT: C 35 ASP cc_start: 0.8415 (t0) cc_final: 0.7936 (t0) REVERT: B 244 MET cc_start: 0.8515 (tpt) cc_final: 0.8199 (tpp) REVERT: D 235 MET cc_start: 0.8300 (mmm) cc_final: 0.7919 (mtp) REVERT: E 350 PHE cc_start: 0.8351 (t80) cc_final: 0.8122 (t80) REVERT: E 361 LYS cc_start: 0.9058 (pptt) cc_final: 0.8822 (pptt) REVERT: E 506 MET cc_start: 0.6884 (ppp) cc_final: 0.5298 (ppp) REVERT: E 582 MET cc_start: 0.7266 (mtt) cc_final: 0.6833 (mtt) REVERT: E 585 MET cc_start: 0.8276 (ppp) cc_final: 0.8075 (ppp) REVERT: E 628 TRP cc_start: 0.8673 (t-100) cc_final: 0.8426 (t-100) outliers start: 21 outliers final: 16 residues processed: 132 average time/residue: 0.0945 time to fit residues: 19.3620 Evaluate side-chains 129 residues out of total 1276 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 113 time to evaluate : 0.438 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 73 THR Chi-restraints excluded: chain A residue 191 VAL Chi-restraints excluded: chain A residue 216 VAL Chi-restraints excluded: chain A residue 235 MET Chi-restraints excluded: chain C residue 6 VAL Chi-restraints excluded: chain C residue 85 VAL Chi-restraints excluded: chain C residue 88 VAL Chi-restraints excluded: chain C residue 99 LEU Chi-restraints excluded: chain B residue 81 VAL Chi-restraints excluded: chain B residue 293 ILE Chi-restraints excluded: chain D residue 33 LEU Chi-restraints excluded: chain D residue 83 VAL Chi-restraints excluded: chain D residue 111 VAL Chi-restraints excluded: chain D residue 262 VAL Chi-restraints excluded: chain D residue 268 HIS Chi-restraints excluded: chain E residue 633 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 155 random chunks: chunk 138 optimal weight: 5.9990 chunk 88 optimal weight: 2.9990 chunk 99 optimal weight: 5.9990 chunk 45 optimal weight: 2.9990 chunk 49 optimal weight: 0.6980 chunk 39 optimal weight: 0.3980 chunk 48 optimal weight: 0.7980 chunk 21 optimal weight: 0.9990 chunk 4 optimal weight: 0.9990 chunk 63 optimal weight: 1.9990 chunk 107 optimal weight: 0.0980 overall best weight: 0.5982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 609 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3622 r_free = 0.3622 target = 0.110170 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3165 r_free = 0.3165 target = 0.080903 restraints weight = 25697.412| |-----------------------------------------------------------------------------| r_work (start): 0.3140 rms_B_bonded: 3.20 r_work: 0.3026 rms_B_bonded: 3.62 restraints_weight: 0.5000 r_work (final): 0.3026 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8327 moved from start: 0.1876 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.075 12013 Z= 0.111 Angle : 0.601 15.500 16353 Z= 0.298 Chirality : 0.044 0.206 1955 Planarity : 0.005 0.102 2126 Dihedral : 4.223 40.152 1689 Min Nonbonded Distance : 2.376 Molprobity Statistics. All-atom Clashscore : 5.22 Ramachandran Plot: Outliers : 0.51 % Allowed : 7.28 % Favored : 92.20 % Rotamer: Outliers : 1.57 % Allowed : 17.16 % Favored : 81.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.89 % Cis-general : 0.00 % Twisted Proline : 0.94 % 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: -0.15 (0.23), residues: 1565 helix: 1.48 (0.20), residues: 717 sheet: -0.61 (0.40), residues: 191 loop : -1.79 (0.25), residues: 657 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 23 TYR 0.007 0.001 TYR E 568 PHE 0.017 0.001 PHE B 318 TRP 0.004 0.001 TRP E 628 HIS 0.007 0.001 HIS E 601 Details of bonding type rmsd covalent geometry : bond 0.00250 (12013) covalent geometry : angle 0.60086 (16353) hydrogen bonds : bond 0.03319 ( 519) hydrogen bonds : angle 3.87188 ( 1515) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3130 Ramachandran restraints generated. 1565 Oldfield, 0 Emsley, 1565 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3130 Ramachandran restraints generated. 1565 Oldfield, 0 Emsley, 1565 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 139 residues out of total 1276 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 119 time to evaluate : 0.483 Fit side-chains revert: symmetry clash REVERT: C 35 ASP cc_start: 0.8364 (t0) cc_final: 0.7897 (t0) REVERT: B 244 MET cc_start: 0.8468 (tpt) cc_final: 0.8040 (tpp) REVERT: D 235 MET cc_start: 0.8258 (mmm) cc_final: 0.7934 (mtp) REVERT: E 350 PHE cc_start: 0.8391 (t80) cc_final: 0.8172 (t80) REVERT: E 361 LYS cc_start: 0.9095 (pptt) cc_final: 0.8879 (pptt) REVERT: E 506 MET cc_start: 0.6881 (ppp) cc_final: 0.5294 (ppp) REVERT: E 582 MET cc_start: 0.7280 (mtt) cc_final: 0.6792 (mtt) REVERT: E 628 TRP cc_start: 0.8686 (t-100) cc_final: 0.8453 (t-100) outliers start: 20 outliers final: 18 residues processed: 132 average time/residue: 0.1053 time to fit residues: 21.3823 Evaluate side-chains 133 residues out of total 1276 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 115 time to evaluate : 0.498 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 VAL Chi-restraints excluded: chain A residue 73 THR Chi-restraints excluded: chain A residue 191 VAL Chi-restraints excluded: chain A residue 216 VAL Chi-restraints excluded: chain A residue 235 MET Chi-restraints excluded: chain C residue 6 VAL Chi-restraints excluded: chain C residue 85 VAL Chi-restraints excluded: chain C residue 88 VAL Chi-restraints excluded: chain C residue 99 LEU Chi-restraints excluded: chain B residue 293 ILE Chi-restraints excluded: chain D residue 33 LEU Chi-restraints excluded: chain D residue 83 VAL Chi-restraints excluded: chain D residue 111 VAL Chi-restraints excluded: chain D residue 139 GLN Chi-restraints excluded: chain D residue 250 LEU Chi-restraints excluded: chain D residue 262 VAL Chi-restraints excluded: chain D residue 268 HIS Chi-restraints excluded: chain E residue 633 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 155 random chunks: chunk 27 optimal weight: 0.7980 chunk 141 optimal weight: 0.6980 chunk 104 optimal weight: 0.5980 chunk 4 optimal weight: 0.8980 chunk 149 optimal weight: 3.9990 chunk 73 optimal weight: 10.0000 chunk 151 optimal weight: 0.9980 chunk 44 optimal weight: 4.9990 chunk 113 optimal weight: 1.9990 chunk 111 optimal weight: 1.9990 chunk 97 optimal weight: 1.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 522 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3619 r_free = 0.3619 target = 0.109885 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3161 r_free = 0.3161 target = 0.080637 restraints weight = 25395.668| |-----------------------------------------------------------------------------| r_work (start): 0.3135 rms_B_bonded: 3.18 r_work: 0.3022 rms_B_bonded: 3.59 restraints_weight: 0.5000 r_work (final): 0.3022 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8331 moved from start: 0.1922 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.073 12013 Z= 0.114 Angle : 0.593 15.561 16353 Z= 0.295 Chirality : 0.044 0.205 1955 Planarity : 0.005 0.103 2126 Dihedral : 4.186 39.970 1689 Min Nonbonded Distance : 2.446 Molprobity Statistics. All-atom Clashscore : 4.97 Ramachandran Plot: Outliers : 0.51 % Allowed : 7.92 % Favored : 91.57 % Rotamer: Outliers : 1.49 % Allowed : 17.40 % Favored : 81.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.89 % Cis-general : 0.00 % Twisted Proline : 0.94 % 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 (0.23), residues: 1565 helix: 1.49 (0.20), residues: 717 sheet: -0.61 (0.41), residues: 181 loop : -1.77 (0.25), residues: 667 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B 23 TYR 0.011 0.001 TYR E 568 PHE 0.011 0.001 PHE B 82 TRP 0.005 0.001 TRP E 628 HIS 0.004 0.001 HIS E 418 Details of bonding type rmsd covalent geometry : bond 0.00263 (12013) covalent geometry : angle 0.59320 (16353) hydrogen bonds : bond 0.03424 ( 519) hydrogen bonds : angle 3.87809 ( 1515) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3130 Ramachandran restraints generated. 1565 Oldfield, 0 Emsley, 1565 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3130 Ramachandran restraints generated. 1565 Oldfield, 0 Emsley, 1565 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 134 residues out of total 1276 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 115 time to evaluate : 0.499 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 35 ASP cc_start: 0.8361 (t0) cc_final: 0.7893 (t0) REVERT: B 94 MET cc_start: 0.7198 (tmm) cc_final: 0.6622 (tmm) REVERT: D 235 MET cc_start: 0.8267 (mmm) cc_final: 0.7952 (mtp) REVERT: E 361 LYS cc_start: 0.9089 (pptt) cc_final: 0.8888 (pptt) REVERT: E 506 MET cc_start: 0.6852 (ppp) cc_final: 0.5257 (ppp) REVERT: E 582 MET cc_start: 0.7225 (mtt) cc_final: 0.7008 (mtt) REVERT: E 628 TRP cc_start: 0.8668 (t-100) cc_final: 0.8447 (t-100) REVERT: E 633 MET cc_start: 0.7111 (OUTLIER) cc_final: 0.6732 (ttp) outliers start: 19 outliers final: 16 residues processed: 129 average time/residue: 0.0977 time to fit residues: 19.5170 Evaluate side-chains 131 residues out of total 1276 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 114 time to evaluate : 0.667 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 VAL Chi-restraints excluded: chain A residue 73 THR Chi-restraints excluded: chain A residue 191 VAL Chi-restraints excluded: chain A residue 216 VAL Chi-restraints excluded: chain A residue 235 MET Chi-restraints excluded: chain C residue 6 VAL Chi-restraints excluded: chain C residue 85 VAL Chi-restraints excluded: chain C residue 88 VAL Chi-restraints excluded: chain C residue 99 LEU Chi-restraints excluded: chain B residue 293 ILE Chi-restraints excluded: chain D residue 33 LEU Chi-restraints excluded: chain D residue 83 VAL Chi-restraints excluded: chain D residue 111 VAL Chi-restraints excluded: chain D residue 250 LEU Chi-restraints excluded: chain D residue 262 VAL Chi-restraints excluded: chain D residue 268 HIS Chi-restraints excluded: chain E residue 633 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 155 random chunks: chunk 98 optimal weight: 0.0770 chunk 1 optimal weight: 0.9980 chunk 83 optimal weight: 0.5980 chunk 122 optimal weight: 1.9990 chunk 145 optimal weight: 1.9990 chunk 105 optimal weight: 2.9990 chunk 13 optimal weight: 0.5980 chunk 59 optimal weight: 4.9990 chunk 112 optimal weight: 2.9990 chunk 110 optimal weight: 2.9990 chunk 146 optimal weight: 10.0000 overall best weight: 0.8540 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 359 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 522 ASN E 546 HIS E 549 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3582 r_free = 0.3582 target = 0.109004 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3106 r_free = 0.3106 target = 0.078976 restraints weight = 25452.491| |-----------------------------------------------------------------------------| r_work (start): 0.3123 rms_B_bonded: 3.27 r_work: 0.3006 rms_B_bonded: 3.68 restraints_weight: 0.5000 r_work (final): 0.3006 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8294 moved from start: 0.1959 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.073 12013 Z= 0.118 Angle : 0.602 15.632 16353 Z= 0.299 Chirality : 0.044 0.214 1955 Planarity : 0.005 0.103 2126 Dihedral : 4.167 39.821 1689 Min Nonbonded Distance : 2.434 Molprobity Statistics. All-atom Clashscore : 5.13 Ramachandran Plot: Outliers : 0.51 % Allowed : 7.60 % Favored : 91.88 % Rotamer: Outliers : 1.65 % Allowed : 17.16 % Favored : 81.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.89 % Cis-general : 0.00 % Twisted Proline : 0.94 % 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: -0.12 (0.23), residues: 1565 helix: 1.53 (0.20), residues: 717 sheet: -0.58 (0.40), residues: 191 loop : -1.81 (0.25), residues: 657 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 23 TYR 0.012 0.001 TYR E 568 PHE 0.014 0.001 PHE E 350 TRP 0.006 0.001 TRP E 628 HIS 0.012 0.001 HIS E 546 Details of bonding type rmsd covalent geometry : bond 0.00274 (12013) covalent geometry : angle 0.60225 (16353) hydrogen bonds : bond 0.03486 ( 519) hydrogen bonds : angle 3.87523 ( 1515) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3130 Ramachandran restraints generated. 1565 Oldfield, 0 Emsley, 1565 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3130 Ramachandran restraints generated. 1565 Oldfield, 0 Emsley, 1565 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 135 residues out of total 1276 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 114 time to evaluate : 0.471 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 35 ASP cc_start: 0.8413 (t0) cc_final: 0.7939 (t0) REVERT: B 94 MET cc_start: 0.7064 (tmm) cc_final: 0.6467 (tmm) REVERT: D 235 MET cc_start: 0.8250 (mmm) cc_final: 0.7932 (mtp) REVERT: E 506 MET cc_start: 0.6864 (ppp) cc_final: 0.5270 (ppp) REVERT: E 628 TRP cc_start: 0.8718 (t-100) cc_final: 0.8482 (t-100) REVERT: E 633 MET cc_start: 0.7107 (OUTLIER) cc_final: 0.6685 (ttp) outliers start: 21 outliers final: 17 residues processed: 129 average time/residue: 0.0938 time to fit residues: 18.9137 Evaluate side-chains 131 residues out of total 1276 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 113 time to evaluate : 0.493 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 VAL Chi-restraints excluded: chain A residue 73 THR Chi-restraints excluded: chain A residue 191 VAL Chi-restraints excluded: chain A residue 216 VAL Chi-restraints excluded: chain A residue 235 MET Chi-restraints excluded: chain C residue 6 VAL Chi-restraints excluded: chain C residue 85 VAL Chi-restraints excluded: chain C residue 88 VAL Chi-restraints excluded: chain C residue 99 LEU Chi-restraints excluded: chain B residue 293 ILE Chi-restraints excluded: chain D residue 33 LEU Chi-restraints excluded: chain D residue 83 VAL Chi-restraints excluded: chain D residue 111 VAL Chi-restraints excluded: chain D residue 250 LEU Chi-restraints excluded: chain D residue 262 VAL Chi-restraints excluded: chain D residue 268 HIS Chi-restraints excluded: chain E residue 546 HIS Chi-restraints excluded: chain E residue 633 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 155 random chunks: chunk 49 optimal weight: 0.0870 chunk 129 optimal weight: 7.9990 chunk 151 optimal weight: 0.9980 chunk 47 optimal weight: 2.9990 chunk 3 optimal weight: 5.9990 chunk 108 optimal weight: 0.0980 chunk 140 optimal weight: 2.9990 chunk 0 optimal weight: 3.9990 chunk 97 optimal weight: 0.4980 chunk 35 optimal weight: 4.9990 chunk 21 optimal weight: 0.8980 overall best weight: 0.5158 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 359 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 546 HIS E 549 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3628 r_free = 0.3628 target = 0.110461 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3170 r_free = 0.3170 target = 0.081131 restraints weight = 25794.995| |-----------------------------------------------------------------------------| r_work (start): 0.3145 rms_B_bonded: 3.21 r_work: 0.3032 rms_B_bonded: 3.63 restraints_weight: 0.5000 r_work (final): 0.3032 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8286 moved from start: 0.1989 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.076 12013 Z= 0.111 Angle : 0.605 14.211 16353 Z= 0.301 Chirality : 0.044 0.206 1955 Planarity : 0.005 0.102 2126 Dihedral : 4.141 39.350 1689 Min Nonbonded Distance : 2.431 Molprobity Statistics. All-atom Clashscore : 5.42 Ramachandran Plot: Outliers : 0.51 % Allowed : 7.67 % Favored : 91.82 % Rotamer: Outliers : 1.57 % Allowed : 17.40 % Favored : 81.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.89 % Cis-general : 0.00 % Twisted Proline : 0.94 % 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 (0.23), residues: 1565 helix: 1.54 (0.20), residues: 717 sheet: -0.55 (0.40), residues: 191 loop : -1.78 (0.25), residues: 657 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B 23 TYR 0.011 0.001 TYR E 568 PHE 0.016 0.001 PHE E 350 TRP 0.004 0.001 TRP E 628 HIS 0.019 0.001 HIS E 546 Details of bonding type rmsd covalent geometry : bond 0.00253 (12013) covalent geometry : angle 0.60537 (16353) hydrogen bonds : bond 0.03270 ( 519) hydrogen bonds : angle 3.83347 ( 1515) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2620.88 seconds wall clock time: 45 minutes 45.40 seconds (2745.40 seconds total)