Starting phenix.real_space_refine on Sat Nov 16 19:32:44 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ggh_40008/11_2024/8ggh_40008.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ggh_40008/11_2024/8ggh_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 { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ggh_40008/11_2024/8ggh_40008.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ggh_40008/11_2024/8ggh_40008.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ggh_40008/11_2024/8ggh_40008.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ggh_40008/11_2024/8ggh_40008.cif" } resolution = 3.29 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } 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): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5513/modules/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: 8.50, per 1000 atoms: 0.72 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: 3.08 Conformation dependent library (CDL) restraints added in 1.8 seconds 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: 1.39 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: 3.52 Time building geometry restraints manager: 3.52 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: 3.400 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: 0.500 Check model and map are aligned: 0.110 Set scattering table: 0.110 Process input model: 30.190 Find NCS groups from input model: 0.510 Set up NCS constraints: 0.060 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:2.930 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 37.820 ------------------------------------------------------------------------------- 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= 0.192 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 : 9.84 % Favored : 89.52 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. 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 TRP 0.012 0.001 TRP E 628 HIS 0.003 0.001 HIS A 172 PHE 0.010 0.001 PHE B 82 TYR 0.010 0.001 TYR E 568 ARG 0.005 0.000 ARG B 23 *********************** 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 : 1.550 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: 0.2216 time to fit residues: 49.9114 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 : 1.588 ------------------------------------------------------------------------------- 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 130 optimal weight: 6.9990 chunk 117 optimal weight: 1.9990 chunk 65 optimal weight: 2.9990 chunk 40 optimal weight: 5.9990 chunk 79 optimal weight: 3.9990 chunk 62 optimal weight: 2.9990 chunk 121 optimal weight: 4.9990 chunk 47 optimal weight: 4.9990 chunk 73 optimal weight: 9.9990 chunk 90 optimal weight: 6.9990 chunk 140 optimal weight: 10.0000 overall best weight: 3.3990 ------------------------------------------------------------------------------- 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 522 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8367 moved from start: 0.1488 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.047 12013 Z= 0.474 Angle : 0.741 9.321 16353 Z= 0.383 Chirality : 0.049 0.192 1955 Planarity : 0.006 0.110 2126 Dihedral : 5.081 62.345 1690 Min Nonbonded Distance : 2.458 Molprobity Statistics. All-atom Clashscore : 6.68 Ramachandran Plot: Outliers : 0.58 % Allowed : 10.03 % Favored : 89.39 % Rotamer: Outliers : 1.25 % Allowed : 10.11 % Favored : 88.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.89 % Cis-general : 0.00 % Twisted Proline : 0.94 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.15 (0.22), residues: 1565 helix: 0.58 (0.19), residues: 728 sheet: -1.29 (0.39), residues: 193 loop : -2.19 (0.24), residues: 644 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP E 628 HIS 0.009 0.002 HIS D 245 PHE 0.017 0.002 PHE B 27 TYR 0.015 0.002 TYR E 348 ARG 0.004 0.001 ARG B 23 *********************** 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 128 residues out of total 1276 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 112 time to evaluate : 1.569 Fit side-chains revert: symmetry clash REVERT: E 340 GLN cc_start: 0.8818 (mp10) cc_final: 0.8455 (mp10) REVERT: E 361 LYS cc_start: 0.8892 (pptt) cc_final: 0.8592 (pptt) REVERT: E 582 MET cc_start: 0.7507 (mtt) cc_final: 0.7277 (mtt) REVERT: E 585 MET cc_start: 0.8112 (ppp) cc_final: 0.7517 (ppp) outliers start: 16 outliers final: 11 residues processed: 121 average time/residue: 0.2375 time to fit residues: 43.3255 Evaluate side-chains 114 residues out of total 1276 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 103 time to evaluate : 1.438 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 VAL Chi-restraints excluded: chain A residue 216 VAL Chi-restraints excluded: chain C residue 50 ASP Chi-restraints excluded: chain B residue 128 ASN Chi-restraints excluded: chain B residue 178 TYR Chi-restraints excluded: chain D residue 99 LEU Chi-restraints excluded: chain D residue 128 ASN 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 78 optimal weight: 0.9980 chunk 43 optimal weight: 7.9990 chunk 117 optimal weight: 0.9980 chunk 95 optimal weight: 1.9990 chunk 38 optimal weight: 5.9990 chunk 141 optimal weight: 9.9990 chunk 152 optimal weight: 7.9990 chunk 125 optimal weight: 3.9990 chunk 139 optimal weight: 10.0000 chunk 48 optimal weight: 0.9990 chunk 113 optimal weight: 2.9990 overall best weight: 1.5986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 311 ASN E 546 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8325 moved from start: 0.1543 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.065 12013 Z= 0.245 Angle : 0.618 11.357 16353 Z= 0.317 Chirality : 0.045 0.198 1955 Planarity : 0.006 0.107 2126 Dihedral : 4.867 57.872 1689 Min Nonbonded Distance : 2.459 Molprobity Statistics. All-atom Clashscore : 5.63 Ramachandran Plot: Outliers : 0.58 % Allowed : 8.43 % Favored : 90.99 % Rotamer: Outliers : 1.57 % Allowed : 14.26 % Favored : 84.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.89 % Cis-general : 0.00 % Twisted Proline : 0.94 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.88 (0.22), residues: 1565 helix: 0.85 (0.20), residues: 727 sheet: -1.21 (0.38), residues: 193 loop : -2.09 (0.24), residues: 645 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP E 628 HIS 0.013 0.001 HIS E 601 PHE 0.014 0.001 PHE B 82 TYR 0.007 0.001 TYR E 583 ARG 0.003 0.000 ARG B 287 *********************** 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 134 residues out of total 1276 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 114 time to evaluate : 1.509 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 35 ASP cc_start: 0.7911 (t0) cc_final: 0.7678 (t0) REVERT: D 235 MET cc_start: 0.8111 (mmm) cc_final: 0.7874 (mtp) REVERT: E 361 LYS cc_start: 0.8965 (pptt) cc_final: 0.8713 (pptt) REVERT: E 582 MET cc_start: 0.7689 (mtt) cc_final: 0.7312 (mtt) outliers start: 20 outliers final: 11 residues processed: 128 average time/residue: 0.2184 time to fit residues: 42.1714 Evaluate side-chains 117 residues out of total 1276 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 106 time to evaluate : 1.459 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 VAL Chi-restraints excluded: chain A residue 216 VAL Chi-restraints excluded: chain C residue 50 ASP 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 D residue 83 VAL Chi-restraints excluded: chain D residue 99 LEU Chi-restraints excluded: chain D residue 128 ASN Chi-restraints excluded: chain E residue 427 ILE Chi-restraints excluded: chain E residue 546 HIS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 155 random chunks: chunk 139 optimal weight: 10.0000 chunk 106 optimal weight: 3.9990 chunk 73 optimal weight: 8.9990 chunk 15 optimal weight: 0.7980 chunk 67 optimal weight: 3.9990 chunk 94 optimal weight: 0.8980 chunk 141 optimal weight: 7.9990 chunk 149 optimal weight: 5.9990 chunk 134 optimal weight: 1.9990 chunk 40 optimal weight: 7.9990 chunk 124 optimal weight: 1.9990 overall best weight: 1.9386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8339 moved from start: 0.1684 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.060 12013 Z= 0.289 Angle : 0.634 12.793 16353 Z= 0.326 Chirality : 0.045 0.195 1955 Planarity : 0.006 0.108 2126 Dihedral : 4.850 55.357 1689 Min Nonbonded Distance : 2.461 Molprobity Statistics. All-atom Clashscore : 5.97 Ramachandran Plot: Outliers : 0.58 % Allowed : 9.58 % Favored : 89.84 % Rotamer: Outliers : 2.35 % Allowed : 15.36 % Favored : 82.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.89 % Cis-general : 0.00 % Twisted Proline : 0.94 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.87 (0.22), residues: 1565 helix: 0.89 (0.20), residues: 727 sheet: -1.21 (0.38), residues: 193 loop : -2.12 (0.24), residues: 645 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP E 628 HIS 0.008 0.001 HIS E 546 PHE 0.012 0.001 PHE B 82 TYR 0.010 0.001 TYR E 356 ARG 0.002 0.000 ARG B 23 *********************** 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 140 residues out of total 1276 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 110 time to evaluate : 1.550 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 316 GLU cc_start: 0.8507 (mm-30) cc_final: 0.7957 (mm-30) REVERT: E 361 LYS cc_start: 0.9006 (pptt) cc_final: 0.8800 (pptt) REVERT: E 582 MET cc_start: 0.7746 (mtt) cc_final: 0.7252 (mtt) REVERT: E 601 HIS cc_start: 0.6316 (t-170) cc_final: 0.5863 (t-170) outliers start: 30 outliers final: 20 residues processed: 134 average time/residue: 0.2392 time to fit residues: 48.5553 Evaluate side-chains 128 residues out of total 1276 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 108 time to evaluate : 1.438 ------------------------------------------------------------------------------- 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 C residue 6 VAL Chi-restraints excluded: chain C residue 50 ASP Chi-restraints excluded: chain C residue 85 VAL Chi-restraints excluded: chain C residue 88 VAL Chi-restraints excluded: chain C residue 146 VAL Chi-restraints excluded: chain C residue 293 ILE Chi-restraints excluded: chain B residue 81 VAL Chi-restraints excluded: chain D residue 83 VAL Chi-restraints excluded: chain D residue 111 VAL Chi-restraints excluded: chain D residue 128 ASN 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 427 ILE Chi-restraints excluded: chain E residue 546 HIS Chi-restraints excluded: chain E residue 587 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 155 random chunks: chunk 85 optimal weight: 1.9990 chunk 2 optimal weight: 0.9990 chunk 111 optimal weight: 3.9990 chunk 61 optimal weight: 5.9990 chunk 127 optimal weight: 6.9990 chunk 103 optimal weight: 4.9990 chunk 0 optimal weight: 4.9990 chunk 76 optimal weight: 2.9990 chunk 134 optimal weight: 1.9990 chunk 37 optimal weight: 0.7980 chunk 50 optimal weight: 0.0980 overall best weight: 1.1786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 101 ASN ** E 522 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 546 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8311 moved from start: 0.1745 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.068 12013 Z= 0.217 Angle : 0.611 13.433 16353 Z= 0.311 Chirality : 0.045 0.198 1955 Planarity : 0.005 0.107 2126 Dihedral : 4.740 53.520 1689 Min Nonbonded Distance : 2.400 Molprobity Statistics. All-atom Clashscore : 5.67 Ramachandran Plot: Outliers : 0.58 % Allowed : 8.31 % Favored : 91.12 % Rotamer: Outliers : 1.88 % Allowed : 17.08 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.72 (0.22), residues: 1565 helix: 1.06 (0.20), residues: 724 sheet: -1.15 (0.39), residues: 193 loop : -2.09 (0.25), residues: 648 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP E 628 HIS 0.007 0.001 HIS E 601 PHE 0.012 0.001 PHE B 82 TYR 0.013 0.001 TYR E 568 ARG 0.002 0.000 ARG B 23 *********************** 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 138 residues out of total 1276 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 114 time to evaluate : 1.411 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 35 ASP cc_start: 0.7858 (t0) cc_final: 0.7551 (t0) REVERT: E 361 LYS cc_start: 0.9007 (pptt) cc_final: 0.8784 (pptt) REVERT: E 582 MET cc_start: 0.7742 (mtt) cc_final: 0.6500 (mtt) REVERT: E 628 TRP cc_start: 0.8683 (t-100) cc_final: 0.8377 (t-100) outliers start: 24 outliers final: 19 residues processed: 133 average time/residue: 0.2110 time to fit residues: 42.7998 Evaluate side-chains 129 residues out of total 1276 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 110 time to evaluate : 1.414 ------------------------------------------------------------------------------- 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 85 VAL Chi-restraints excluded: chain C residue 88 VAL Chi-restraints excluded: chain C residue 146 VAL Chi-restraints excluded: chain C residue 167 ILE Chi-restraints excluded: chain C residue 277 VAL Chi-restraints excluded: chain C residue 293 ILE Chi-restraints excluded: chain B residue 13 ILE Chi-restraints excluded: chain B residue 81 VAL 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 427 ILE Chi-restraints excluded: chain E residue 546 HIS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 155 random chunks: chunk 134 optimal weight: 1.9990 chunk 29 optimal weight: 0.2980 chunk 87 optimal weight: 0.9980 chunk 36 optimal weight: 0.0470 chunk 149 optimal weight: 2.9990 chunk 124 optimal weight: 4.9990 chunk 69 optimal weight: 6.9990 chunk 12 optimal weight: 2.9990 chunk 49 optimal weight: 2.9990 chunk 78 optimal weight: 0.9990 chunk 144 optimal weight: 5.9990 overall best weight: 0.8682 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 522 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 546 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8290 moved from start: 0.1811 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.071 12013 Z= 0.194 Angle : 0.603 10.567 16353 Z= 0.307 Chirality : 0.044 0.220 1955 Planarity : 0.005 0.106 2126 Dihedral : 4.581 44.778 1689 Min Nonbonded Distance : 2.420 Molprobity Statistics. All-atom Clashscore : 5.51 Ramachandran Plot: Outliers : 0.51 % Allowed : 8.43 % Favored : 91.05 % Rotamer: Outliers : 2.04 % Allowed : 17.71 % Favored : 80.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.89 % Cis-general : 0.00 % Twisted Proline : 0.94 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.60 (0.22), residues: 1565 helix: 1.14 (0.20), residues: 725 sheet: -1.09 (0.39), residues: 193 loop : -2.01 (0.25), residues: 647 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP E 396 HIS 0.009 0.001 HIS E 546 PHE 0.012 0.001 PHE B 82 TYR 0.015 0.001 TYR E 568 ARG 0.002 0.000 ARG B 23 *********************** 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 152 residues out of total 1276 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 126 time to evaluate : 1.516 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 35 ASP cc_start: 0.7913 (t0) cc_final: 0.7530 (t0) REVERT: D 235 MET cc_start: 0.7998 (mmm) cc_final: 0.7780 (mtp) REVERT: E 353 ASN cc_start: 0.6070 (m-40) cc_final: 0.5457 (p0) REVERT: E 361 LYS cc_start: 0.9021 (pptt) cc_final: 0.8783 (pptt) REVERT: E 582 MET cc_start: 0.7253 (mtt) cc_final: 0.7050 (mtt) REVERT: E 628 TRP cc_start: 0.8689 (t-100) cc_final: 0.8476 (t-100) outliers start: 26 outliers final: 21 residues processed: 148 average time/residue: 0.2149 time to fit residues: 47.9403 Evaluate side-chains 136 residues out of total 1276 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 115 time to evaluate : 1.655 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 VAL Chi-restraints excluded: chain A residue 191 VAL Chi-restraints excluded: chain A residue 216 VAL 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 146 VAL Chi-restraints excluded: chain C residue 167 ILE Chi-restraints excluded: chain C residue 277 VAL Chi-restraints excluded: chain C residue 293 ILE Chi-restraints excluded: chain B residue 2 VAL Chi-restraints excluded: chain B residue 13 ILE Chi-restraints excluded: chain B residue 81 VAL Chi-restraints excluded: chain B residue 157 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 427 ILE Chi-restraints excluded: chain E residue 546 HIS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 155 random chunks: chunk 16 optimal weight: 3.9990 chunk 85 optimal weight: 2.9990 chunk 109 optimal weight: 0.7980 chunk 84 optimal weight: 0.8980 chunk 126 optimal weight: 0.7980 chunk 83 optimal weight: 2.9990 chunk 149 optimal weight: 1.9990 chunk 93 optimal weight: 2.9990 chunk 91 optimal weight: 2.9990 chunk 68 optimal weight: 1.9990 chunk 92 optimal weight: 5.9990 overall best weight: 1.2984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 311 ASN ** E 522 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 546 HIS ** E 609 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8301 moved from start: 0.1859 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.068 12013 Z= 0.224 Angle : 0.625 13.274 16353 Z= 0.315 Chirality : 0.044 0.210 1955 Planarity : 0.005 0.107 2126 Dihedral : 4.528 44.145 1689 Min Nonbonded Distance : 2.416 Molprobity Statistics. All-atom Clashscore : 5.84 Ramachandran Plot: Outliers : 0.51 % Allowed : 8.82 % Favored : 90.67 % Rotamer: Outliers : 2.51 % Allowed : 17.55 % Favored : 79.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.89 % Cis-general : 0.00 % Twisted Proline : 0.94 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.61 (0.22), residues: 1565 helix: 1.12 (0.20), residues: 725 sheet: -1.10 (0.39), residues: 193 loop : -2.01 (0.25), residues: 647 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP E 396 HIS 0.005 0.001 HIS E 601 PHE 0.024 0.001 PHE B 318 TYR 0.011 0.001 TYR E 568 ARG 0.002 0.000 ARG B 23 *********************** 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 149 residues out of total 1276 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 117 time to evaluate : 1.532 Fit side-chains revert: symmetry clash REVERT: C 35 ASP cc_start: 0.7986 (t0) cc_final: 0.7606 (t0) REVERT: B 157 LEU cc_start: 0.8508 (OUTLIER) cc_final: 0.8144 (tt) REVERT: D 235 MET cc_start: 0.7986 (mmm) cc_final: 0.7750 (mtp) REVERT: E 353 ASN cc_start: 0.6021 (m-40) cc_final: 0.5431 (p0) REVERT: E 361 LYS cc_start: 0.9020 (pptt) cc_final: 0.8798 (pptt) REVERT: E 582 MET cc_start: 0.7348 (mtt) cc_final: 0.6960 (mtt) REVERT: E 628 TRP cc_start: 0.8716 (t-100) cc_final: 0.8496 (t-100) outliers start: 32 outliers final: 25 residues processed: 144 average time/residue: 0.2110 time to fit residues: 46.9447 Evaluate side-chains 142 residues out of total 1276 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 116 time to evaluate : 1.423 ------------------------------------------------------------------------------- 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 146 VAL Chi-restraints excluded: chain C residue 167 ILE Chi-restraints excluded: chain C residue 277 VAL Chi-restraints excluded: chain C residue 293 ILE Chi-restraints excluded: chain B residue 2 VAL Chi-restraints excluded: chain B residue 13 ILE Chi-restraints excluded: chain B residue 81 VAL Chi-restraints excluded: chain B residue 157 LEU 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 179 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 D residue 295 THR Chi-restraints excluded: chain E residue 427 ILE Chi-restraints excluded: chain E residue 538 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 155 random chunks: chunk 59 optimal weight: 0.0980 chunk 89 optimal weight: 0.9980 chunk 45 optimal weight: 0.9980 chunk 29 optimal weight: 1.9990 chunk 28 optimal weight: 0.0970 chunk 94 optimal weight: 0.9990 chunk 101 optimal weight: 4.9990 chunk 73 optimal weight: 0.0980 chunk 13 optimal weight: 0.6980 chunk 117 optimal weight: 4.9990 chunk 135 optimal weight: 4.9990 overall best weight: 0.3978 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 340 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 609 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8253 moved from start: 0.1910 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.077 12013 Z= 0.173 Angle : 0.619 14.743 16353 Z= 0.306 Chirality : 0.044 0.204 1955 Planarity : 0.005 0.105 2126 Dihedral : 4.368 41.992 1689 Min Nonbonded Distance : 2.461 Molprobity Statistics. All-atom Clashscore : 5.76 Ramachandran Plot: Outliers : 0.51 % Allowed : 7.92 % Favored : 91.57 % Rotamer: Outliers : 2.43 % Allowed : 17.79 % Favored : 79.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.89 % Cis-general : 0.00 % Twisted Proline : 0.94 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.41 (0.23), residues: 1565 helix: 1.27 (0.20), residues: 722 sheet: -0.93 (0.39), residues: 191 loop : -1.89 (0.25), residues: 652 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP E 396 HIS 0.009 0.001 HIS E 601 PHE 0.023 0.001 PHE B 318 TYR 0.010 0.001 TYR E 568 ARG 0.002 0.000 ARG E 341 *********************** 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 159 residues out of total 1276 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 128 time to evaluate : 1.403 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 203 ASP cc_start: 0.8155 (t0) cc_final: 0.7857 (t0) REVERT: C 35 ASP cc_start: 0.7968 (t0) cc_final: 0.7557 (t0) REVERT: B 157 LEU cc_start: 0.8404 (OUTLIER) cc_final: 0.8014 (tt) REVERT: E 506 MET cc_start: 0.6609 (ppp) cc_final: 0.5014 (ppp) REVERT: E 628 TRP cc_start: 0.8688 (t-100) cc_final: 0.8443 (t-100) outliers start: 31 outliers final: 23 residues processed: 151 average time/residue: 0.2146 time to fit residues: 49.5444 Evaluate side-chains 143 residues out of total 1276 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 119 time to evaluate : 1.842 ------------------------------------------------------------------------------- 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 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 146 VAL Chi-restraints excluded: chain C residue 277 VAL Chi-restraints excluded: chain B residue 2 VAL Chi-restraints excluded: chain B residue 13 ILE Chi-restraints excluded: chain B residue 81 VAL Chi-restraints excluded: chain B residue 157 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 179 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 427 ILE Chi-restraints excluded: chain E residue 538 VAL 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 143 optimal weight: 10.0000 chunk 130 optimal weight: 8.9990 chunk 139 optimal weight: 0.9980 chunk 83 optimal weight: 0.8980 chunk 60 optimal weight: 0.0980 chunk 109 optimal weight: 0.8980 chunk 42 optimal weight: 1.9990 chunk 125 optimal weight: 0.5980 chunk 131 optimal weight: 20.0000 chunk 138 optimal weight: 8.9990 chunk 91 optimal weight: 0.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 340 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 609 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8256 moved from start: 0.1950 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= 0.189 Angle : 0.640 16.205 16353 Z= 0.315 Chirality : 0.044 0.212 1955 Planarity : 0.005 0.105 2126 Dihedral : 4.296 41.297 1689 Min Nonbonded Distance : 2.456 Molprobity Statistics. All-atom Clashscore : 5.76 Ramachandran Plot: Outliers : 0.51 % Allowed : 7.99 % Favored : 91.50 % Rotamer: Outliers : 2.19 % Allowed : 17.95 % Favored : 79.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.89 % Cis-general : 0.00 % Twisted Proline : 0.94 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.35 (0.23), residues: 1565 helix: 1.32 (0.20), residues: 724 sheet: -0.89 (0.39), residues: 191 loop : -1.87 (0.25), residues: 650 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP E 628 HIS 0.014 0.001 HIS E 601 PHE 0.022 0.001 PHE B 318 TYR 0.010 0.001 TYR E 568 ARG 0.002 0.000 ARG E 621 *********************** 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 148 residues out of total 1276 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 120 time to evaluate : 1.542 Fit side-chains revert: symmetry clash REVERT: A 203 ASP cc_start: 0.8200 (t0) cc_final: 0.7923 (t0) REVERT: C 35 ASP cc_start: 0.7985 (t0) cc_final: 0.7564 (t0) REVERT: B 94 MET cc_start: 0.7272 (tmm) cc_final: 0.6617 (tmm) REVERT: E 506 MET cc_start: 0.6532 (ppp) cc_final: 0.4915 (ppp) REVERT: E 628 TRP cc_start: 0.8671 (t-100) cc_final: 0.8465 (t-100) REVERT: E 633 MET cc_start: 0.7100 (OUTLIER) cc_final: 0.6717 (ttp) outliers start: 28 outliers final: 23 residues processed: 142 average time/residue: 0.2060 time to fit residues: 45.3681 Evaluate side-chains 143 residues out of total 1276 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 119 time to evaluate : 1.426 ------------------------------------------------------------------------------- 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 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 146 VAL Chi-restraints excluded: chain C residue 167 ILE Chi-restraints excluded: chain C residue 277 VAL Chi-restraints excluded: chain C residue 293 ILE Chi-restraints excluded: chain B residue 2 VAL Chi-restraints excluded: chain B residue 13 ILE 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 179 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 427 ILE 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 147 optimal weight: 10.0000 chunk 89 optimal weight: 0.3980 chunk 69 optimal weight: 5.9990 chunk 102 optimal weight: 5.9990 chunk 154 optimal weight: 0.7980 chunk 142 optimal weight: 6.9990 chunk 122 optimal weight: 5.9990 chunk 12 optimal weight: 0.9980 chunk 94 optimal weight: 5.9990 chunk 75 optimal weight: 3.9990 chunk 97 optimal weight: 1.9990 overall best weight: 1.6384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 340 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 609 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8303 moved from start: 0.1981 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.066 12013 Z= 0.259 Angle : 0.661 15.312 16353 Z= 0.329 Chirality : 0.045 0.224 1955 Planarity : 0.005 0.107 2126 Dihedral : 4.409 42.410 1689 Min Nonbonded Distance : 2.428 Molprobity Statistics. All-atom Clashscore : 6.01 Ramachandran Plot: Outliers : 0.51 % Allowed : 8.95 % Favored : 90.54 % Rotamer: Outliers : 2.04 % Allowed : 18.10 % Favored : 79.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.89 % Cis-general : 0.00 % Twisted Proline : 0.94 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.50 (0.22), residues: 1565 helix: 1.22 (0.20), residues: 729 sheet: -1.03 (0.39), residues: 193 loop : -2.00 (0.25), residues: 643 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP E 628 HIS 0.014 0.001 HIS E 601 PHE 0.022 0.001 PHE B 318 TYR 0.011 0.001 TYR E 568 ARG 0.002 0.000 ARG A 51 ********************** 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 140 residues out of total 1276 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 114 time to evaluate : 1.523 Fit side-chains revert: symmetry clash REVERT: A 203 ASP cc_start: 0.8249 (t0) cc_final: 0.8001 (t0) REVERT: C 35 ASP cc_start: 0.8045 (t0) cc_final: 0.7632 (t0) REVERT: B 94 MET cc_start: 0.7279 (tmm) cc_final: 0.6642 (tmm) REVERT: E 506 MET cc_start: 0.6650 (ppp) cc_final: 0.5063 (ppp) REVERT: E 633 MET cc_start: 0.7179 (OUTLIER) cc_final: 0.6705 (ttp) outliers start: 26 outliers final: 24 residues processed: 135 average time/residue: 0.2213 time to fit residues: 47.1984 Evaluate side-chains 137 residues out of total 1276 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 112 time to evaluate : 1.434 ------------------------------------------------------------------------------- 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 C residue 146 VAL Chi-restraints excluded: chain C residue 167 ILE Chi-restraints excluded: chain C residue 277 VAL Chi-restraints excluded: chain C residue 293 ILE Chi-restraints excluded: chain B residue 2 VAL Chi-restraints excluded: chain B residue 13 ILE Chi-restraints excluded: chain B residue 81 VAL Chi-restraints excluded: chain B residue 293 ILE Chi-restraints excluded: chain D residue 83 VAL Chi-restraints excluded: chain D residue 111 VAL Chi-restraints excluded: chain D residue 179 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 427 ILE 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 130 optimal weight: 6.9990 chunk 37 optimal weight: 0.0770 chunk 113 optimal weight: 0.0370 chunk 18 optimal weight: 0.9990 chunk 34 optimal weight: 0.0050 chunk 123 optimal weight: 0.9980 chunk 51 optimal weight: 3.9990 chunk 126 optimal weight: 0.8980 chunk 15 optimal weight: 2.9990 chunk 22 optimal weight: 0.8980 chunk 108 optimal weight: 1.9990 overall best weight: 0.3830 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 340 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 371 GLN ** E 609 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3617 r_free = 0.3617 target = 0.110477 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3155 r_free = 0.3155 target = 0.080950 restraints weight = 25241.365| |-----------------------------------------------------------------------------| r_work (start): 0.3135 rms_B_bonded: 3.24 r_work: 0.3021 rms_B_bonded: 3.65 restraints_weight: 0.5000 r_work (final): 0.3021 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8273 moved from start: 0.2019 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.077 12013 Z= 0.175 Angle : 0.636 16.858 16353 Z= 0.313 Chirality : 0.044 0.207 1955 Planarity : 0.005 0.104 2126 Dihedral : 4.288 40.480 1689 Min Nonbonded Distance : 2.427 Molprobity Statistics. All-atom Clashscore : 5.63 Ramachandran Plot: Outliers : 0.51 % Allowed : 8.31 % Favored : 91.18 % Rotamer: Outliers : 1.96 % Allowed : 18.42 % Favored : 79.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.89 % Cis-general : 0.00 % Twisted Proline : 0.94 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.34 (0.23), residues: 1565 helix: 1.31 (0.20), residues: 726 sheet: -0.91 (0.39), residues: 193 loop : -1.84 (0.25), residues: 646 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP E 628 HIS 0.013 0.001 HIS E 601 PHE 0.022 0.001 PHE B 318 TYR 0.009 0.001 TYR E 568 ARG 0.002 0.000 ARG B 23 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2471.57 seconds wall clock time: 52 minutes 45.94 seconds (3165.94 seconds total)