Starting phenix.real_space_refine on Fri Dec 8 22:46:40 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8eoj_28377/12_2023/8eoj_28377.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8eoj_28377/12_2023/8eoj_28377.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.07 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8eoj_28377/12_2023/8eoj_28377.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8eoj_28377/12_2023/8eoj_28377.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8eoj_28377/12_2023/8eoj_28377.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8eoj_28377/12_2023/8eoj_28377.pdb" } resolution = 3.07 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= 0.016 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 35 5.16 5 C 5936 2.51 5 N 1574 2.21 5 O 1782 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ASP 109": "OD1" <-> "OD2" Residue "A PHE 209": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 294": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/chem_data/mon_lib" Total number of atoms: 9327 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 3326 Number of conformers: 1 Conformer: "" Number of residues, atoms: 438, 3326 Classifications: {'peptide': 438} Incomplete info: {'truncation_to_alanine': 37} Link IDs: {'PTRANS': 18, 'TRANS': 419} Chain breaks: 7 Unresolved non-hydrogen bonds: 151 Unresolved non-hydrogen angles: 179 Unresolved non-hydrogen dihedrals: 129 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'GLN:plan1': 4, 'ASP:plan': 5, 'HIS:plan': 1, 'PHE:plan': 2, 'GLU:plan': 5, 'ARG:plan': 3} Unresolved non-hydrogen planarities: 83 Chain: "B" Number of atoms: 6001 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 781, 5996 Classifications: {'peptide': 781} Incomplete info: {'backbone_only': 1, 'truncation_to_alanine': 27} Link IDs: {'PTRANS': 19, 'TRANS': 761} Chain breaks: 9 Unresolved non-hydrogen bonds: 132 Unresolved non-hydrogen angles: 167 Unresolved non-hydrogen dihedrals: 111 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'GLN:plan1': 4, 'ASP:plan': 2, 'TYR:plan': 2, 'ASN:plan1': 3, 'HIS:plan': 1, 'PHE:plan': 3, 'GLU:plan': 4, 'ARG:plan': 4} Unresolved non-hydrogen planarities: 104 Conformer: "B" Number of residues, atoms: 781, 5996 Classifications: {'peptide': 781} Incomplete info: {'backbone_only': 1, 'truncation_to_alanine': 27} Link IDs: {'PTRANS': 19, 'TRANS': 761} Chain breaks: 9 Unresolved non-hydrogen bonds: 132 Unresolved non-hydrogen angles: 167 Unresolved non-hydrogen dihedrals: 111 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'GLN:plan1': 4, 'ASP:plan': 2, 'TYR:plan': 2, 'ASN:plan1': 3, 'HIS:plan': 1, 'PHE:plan': 3, 'GLU:plan': 4, 'ARG:plan': 4} Unresolved non-hydrogen planarities: 104 bond proxies already assigned to first conformer: 6064 Residues with excluded nonbonded symmetry interactions: 1 residue: pdb=" N APHE B 824 " occ=0.60 ... (8 atoms not shown) pdb=" CB BPHE B 824 " occ=0.40 Time building chain proxies: 8.17, per 1000 atoms: 0.88 Number of scatterers: 9327 At special positions: 0 Unit cell: (89.64, 100.44, 158.76, 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 35 16.00 O 1782 8.00 N 1574 7.00 C 5936 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=4, symmetry=0 Simple disulfide: pdb=" SG CYS B 174 " - pdb=" SG CYS B 194 " distance=2.03 Simple disulfide: pdb=" SG CYS B 298 " - pdb=" SG CYS B 301 " distance=2.03 Simple disulfide: pdb=" SG CYS B 440 " - pdb=" SG CYS B 445 " distance=2.03 Simple disulfide: pdb=" SG CYS B 827 " - pdb=" SG CYS B 878 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 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: 3.26 Conformation dependent library (CDL) restraints added in 2.7 seconds 2372 Ramachandran restraints generated. 1186 Oldfield, 0 Emsley, 1186 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2290 Finding SS restraints... Secondary structure from input PDB file: 40 helices and 10 sheets defined 37.7% alpha, 24.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.04 Creating SS restraints... Processing helix chain 'A' and resid 33 through 41 Processing helix chain 'A' and resid 53 through 73 Proline residue: A 61 - end of helix Processing helix chain 'A' and resid 87 through 95 removed outlier: 3.944A pdb=" N ALA A 91 " --> pdb=" O GLU A 87 " (cutoff:3.500A) Processing helix chain 'A' and resid 121 through 134 removed outlier: 3.957A pdb=" N LYS A 130 " --> pdb=" O VAL A 126 " (cutoff:3.500A) removed outlier: 4.023A pdb=" N LYS A 131 " --> pdb=" O ASN A 127 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N GLY A 134 " --> pdb=" O LYS A 130 " (cutoff:3.500A) Processing helix chain 'A' and resid 168 through 179 removed outlier: 3.913A pdb=" N ILE A 179 " --> pdb=" O ALA A 175 " (cutoff:3.500A) Processing helix chain 'A' and resid 189 through 196 removed outlier: 3.773A pdb=" N PHE A 193 " --> pdb=" O ASN A 189 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N SER A 194 " --> pdb=" O SER A 190 " (cutoff:3.500A) Processing helix chain 'A' and resid 223 through 234 removed outlier: 3.510A pdb=" N LEU A 234 " --> pdb=" O LYS A 230 " (cutoff:3.500A) Processing helix chain 'A' and resid 244 through 251 removed outlier: 3.548A pdb=" N GLY A 251 " --> pdb=" O LYS A 247 " (cutoff:3.500A) Processing helix chain 'A' and resid 267 through 282 removed outlier: 3.600A pdb=" N SER A 281 " --> pdb=" O THR A 277 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N PHE A 282 " --> pdb=" O ALA A 278 " (cutoff:3.500A) Processing helix chain 'A' and resid 295 through 297 No H-bonds generated for 'chain 'A' and resid 295 through 297' Processing helix chain 'A' and resid 298 through 305 removed outlier: 3.570A pdb=" N PHE A 305 " --> pdb=" O ILE A 301 " (cutoff:3.500A) Processing helix chain 'A' and resid 335 through 349 removed outlier: 4.167A pdb=" N CYS A 343 " --> pdb=" O ILE A 339 " (cutoff:3.500A) removed outlier: 4.519A pdb=" N HIS A 344 " --> pdb=" O THR A 340 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N GLY A 349 " --> pdb=" O ARG A 345 " (cutoff:3.500A) Processing helix chain 'A' and resid 397 through 414 Proline residue: A 405 - end of helix Processing helix chain 'A' and resid 464 through 472 removed outlier: 3.646A pdb=" N SER A 472 " --> pdb=" O LYS A 468 " (cutoff:3.500A) Processing helix chain 'B' and resid 106 through 112 Processing helix chain 'B' and resid 112 through 121 removed outlier: 3.673A pdb=" N LEU B 116 " --> pdb=" O GLY B 112 " (cutoff:3.500A) removed outlier: 4.126A pdb=" N GLU B 117 " --> pdb=" O LYS B 113 " (cutoff:3.500A) Processing helix chain 'B' and resid 142 through 154 removed outlier: 3.533A pdb=" N LYS B 149 " --> pdb=" O ILE B 145 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N SER B 154 " --> pdb=" O ARG B 150 " (cutoff:3.500A) Processing helix chain 'B' and resid 155 through 157 No H-bonds generated for 'chain 'B' and resid 155 through 157' Processing helix chain 'B' and resid 273 through 281 removed outlier: 4.209A pdb=" N ILE B 277 " --> pdb=" O ALA B 273 " (cutoff:3.500A) removed outlier: 4.516A pdb=" N LYS B 278 " --> pdb=" O ALA B 274 " (cutoff:3.500A) Processing helix chain 'B' and resid 306 through 313 removed outlier: 3.501A pdb=" N THR B 311 " --> pdb=" O LEU B 307 " (cutoff:3.500A) removed outlier: 4.043A pdb=" N LYS B 313 " --> pdb=" O ARG B 309 " (cutoff:3.500A) Processing helix chain 'B' and resid 316 through 320 removed outlier: 3.924A pdb=" N LEU B 320 " --> pdb=" O PRO B 317 " (cutoff:3.500A) Processing helix chain 'B' and resid 322 through 338 removed outlier: 3.507A pdb=" N VAL B 326 " --> pdb=" O LYS B 322 " (cutoff:3.500A) removed outlier: 3.885A pdb=" N ASN B 328 " --> pdb=" O GLU B 324 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N PHE B 329 " --> pdb=" O ALA B 325 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N LEU B 330 " --> pdb=" O VAL B 326 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N ALA B 331 " --> pdb=" O ARG B 327 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N PHE B 332 " --> pdb=" O ASN B 328 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N ILE B 333 " --> pdb=" O PHE B 329 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N GLN B 334 " --> pdb=" O LEU B 330 " (cutoff:3.500A) removed outlier: 3.941A pdb=" N THR B 338 " --> pdb=" O GLN B 334 " (cutoff:3.500A) Processing helix chain 'B' and resid 340 through 348 removed outlier: 3.668A pdb=" N ILE B 347 " --> pdb=" O GLU B 343 " (cutoff:3.500A) removed outlier: 3.880A pdb=" N LEU B 348 " --> pdb=" O ILE B 344 " (cutoff:3.500A) Processing helix chain 'B' and resid 355 through 365 removed outlier: 3.575A pdb=" N LEU B 359 " --> pdb=" O VAL B 355 " (cutoff:3.500A) Processing helix chain 'B' and resid 368 through 379 Processing helix chain 'B' and resid 386 through 399 removed outlier: 3.815A pdb=" N GLN B 390 " --> pdb=" O SER B 386 " (cutoff:3.500A) Processing helix chain 'B' and resid 404 through 417 Processing helix chain 'B' and resid 421 through 441 Processing helix chain 'B' and resid 447 through 463 removed outlier: 3.522A pdb=" N GLU B 452 " --> pdb=" O LYS B 448 " (cutoff:3.500A) Processing helix chain 'B' and resid 466 through 481 Processing helix chain 'B' and resid 482 through 484 No H-bonds generated for 'chain 'B' and resid 482 through 484' Processing helix chain 'B' and resid 485 through 494 Processing helix chain 'B' and resid 497 through 511 removed outlier: 3.549A pdb=" N TYR B 511 " --> pdb=" O ALA B 507 " (cutoff:3.500A) Processing helix chain 'B' and resid 517 through 529 removed outlier: 3.611A pdb=" N ARG B 526 " --> pdb=" O LYS B 522 " (cutoff:3.500A) removed outlier: 3.951A pdb=" N ILE B 527 " --> pdb=" O THR B 523 " (cutoff:3.500A) Processing helix chain 'B' and resid 536 through 550 Processing helix chain 'B' and resid 553 through 564 Processing helix chain 'B' and resid 568 through 585 removed outlier: 3.763A pdb=" N TYR B 574 " --> pdb=" O GLU B 570 " (cutoff:3.500A) Processing helix chain 'B' and resid 589 through 598 Processing helix chain 'B' and resid 604 through 609 removed outlier: 3.592A pdb=" N PHE B 608 " --> pdb=" O ASN B 604 " (cutoff:3.500A) Processing helix chain 'B' and resid 871 through 879 removed outlier: 4.119A pdb=" N MET B 877 " --> pdb=" O GLU B 873 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 21 through 23 removed outlier: 3.996A pdb=" N GLU A 21 " --> pdb=" O VAL A 28 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N LEU A 29 " --> pdb=" O LYS A 81 " (cutoff:3.500A) removed outlier: 4.540A pdb=" N ASP A 83 " --> pdb=" O LEU A 29 " (cutoff:3.500A) removed outlier: 5.944A pdb=" N LEU A 45 " --> pdb=" O ALA A 80 " (cutoff:3.500A) removed outlier: 7.224A pdb=" N VAL A 82 " --> pdb=" O LEU A 45 " (cutoff:3.500A) removed outlier: 5.896A pdb=" N GLU A 47 " --> pdb=" O VAL A 82 " (cutoff:3.500A) removed outlier: 4.262A pdb=" N LEU A 44 " --> pdb=" O PHE A 105 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N PHE A 105 " --> pdb=" O LEU A 44 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 186 through 187 removed outlier: 8.252A pdb=" N THR A 187 " --> pdb=" O VAL A 157 " (cutoff:3.500A) removed outlier: 6.931A pdb=" N GLY A 159 " --> pdb=" O THR A 187 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N PHE A 206 " --> pdb=" O ALA A 156 " (cutoff:3.500A) removed outlier: 4.083A pdb=" N ILE A 158 " --> pdb=" O VAL A 204 " (cutoff:3.500A) removed outlier: 4.547A pdb=" N VAL A 204 " --> pdb=" O ILE A 158 " (cutoff:3.500A) removed outlier: 4.180A pdb=" N PHE A 160 " --> pdb=" O GLY A 202 " (cutoff:3.500A) removed outlier: 4.222A pdb=" N GLY A 202 " --> pdb=" O PHE A 160 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 237 through 239 removed outlier: 5.777A pdb=" N ILE A 238 " --> pdb=" O PHE A 290 " (cutoff:3.500A) removed outlier: 5.981A pdb=" N ILE A 257 " --> pdb=" O ILE A 289 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N ILE A 318 " --> pdb=" O HIS A 256 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N ARG A 316 " --> pdb=" O LEU A 258 " (cutoff:3.500A) removed outlier: 3.970A pdb=" N LEU A 317 " --> pdb=" O TYR A 327 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N THR A 319 " --> pdb=" O THR A 325 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 370 through 371 removed outlier: 6.883A pdb=" N LYS A 370 " --> pdb=" O LYS A 424 " (cutoff:3.500A) removed outlier: 8.547A pdb=" N ASP A 426 " --> pdb=" O LYS A 370 " (cutoff:3.500A) removed outlier: 6.559A pdb=" N PHE A 389 " --> pdb=" O ALA A 423 " (cutoff:3.500A) removed outlier: 7.780A pdb=" N MET A 425 " --> pdb=" O PHE A 389 " (cutoff:3.500A) removed outlier: 6.651A pdb=" N GLU A 391 " --> pdb=" O MET A 425 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'B' and resid 236 through 238 removed outlier: 3.893A pdb=" N ILE B 250 " --> pdb=" O HIS B 236 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N PHE B 238 " --> pdb=" O GLY B 248 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N GLY B 248 " --> pdb=" O PHE B 238 " (cutoff:3.500A) removed outlier: 7.414A pdb=" N LYS B 35 " --> pdb=" O LYS B 259 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N VAL B 42 " --> pdb=" O TYR B 57 " (cutoff:3.500A) removed outlier: 4.356A pdb=" N TYR B 57 " --> pdb=" O VAL B 42 " (cutoff:3.500A) removed outlier: 6.604A pdb=" N ARG B 58 " --> pdb=" O VAL B 89 " (cutoff:3.500A) removed outlier: 4.662A pdb=" N VAL B 89 " --> pdb=" O ARG B 58 " (cutoff:3.500A) removed outlier: 6.859A pdb=" N SER B 60 " --> pdb=" O VAL B 87 " (cutoff:3.500A) removed outlier: 4.250A pdb=" N VAL B 87 " --> pdb=" O SER B 60 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N LEU B 125 " --> pdb=" O ILE B 80 " (cutoff:3.500A) removed outlier: 7.180A pdb=" N LEU B 124 " --> pdb=" O PHE B 135 " (cutoff:3.500A) removed outlier: 5.459A pdb=" N PHE B 135 " --> pdb=" O LEU B 124 " (cutoff:3.500A) removed outlier: 6.693A pdb=" N HIS B 126 " --> pdb=" O LYS B 133 " (cutoff:3.500A) removed outlier: 3.901A pdb=" N PHE B 135 " --> pdb=" O ILE B 287 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N SER B 137 " --> pdb=" O THR B 285 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 163 through 166 removed outlier: 9.491A pdb=" N ASN B 173 " --> pdb=" O ASP B 192 " (cutoff:3.500A) removed outlier: 8.225A pdb=" N ASP B 192 " --> pdb=" O ASN B 173 " (cutoff:3.500A) removed outlier: 4.297A pdb=" N LYS B 175 " --> pdb=" O ALA B 190 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N VAL B 185 " --> pdb=" O TYR B 220 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 617 through 623 removed outlier: 6.238A pdb=" N THR B 618 " --> pdb=" O LEU B 633 " (cutoff:3.500A) removed outlier: 7.553A pdb=" N LEU B 633 " --> pdb=" O THR B 618 " (cutoff:3.500A) removed outlier: 5.213A pdb=" N TYR B 620 " --> pdb=" O TYR B 631 " (cutoff:3.500A) removed outlier: 6.557A pdb=" N TYR B 631 " --> pdb=" O TYR B 620 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N GLU B 622 " --> pdb=" O SER B 629 " (cutoff:3.500A) removed outlier: 4.445A pdb=" N ARG B 644 " --> pdb=" O ALA B 668 " (cutoff:3.500A) removed outlier: 6.335A pdb=" N GLN B 652 " --> pdb=" O HIS B 660 " (cutoff:3.500A) removed outlier: 4.738A pdb=" N HIS B 660 " --> pdb=" O GLN B 652 " (cutoff:3.500A) removed outlier: 6.524A pdb=" N ILE B 654 " --> pdb=" O GLY B 658 " (cutoff:3.500A) removed outlier: 4.948A pdb=" N GLY B 658 " --> pdb=" O ILE B 654 " (cutoff:3.500A) removed outlier: 7.059A pdb=" N ALA B 690 " --> pdb=" O PHE B 706 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 728 through 737 removed outlier: 6.562A pdb=" N GLY B 755 " --> pdb=" O LEU B 734 " (cutoff:3.500A) removed outlier: 4.050A pdb=" N ASP B 736 " --> pdb=" O VAL B 753 " (cutoff:3.500A) removed outlier: 6.661A pdb=" N VAL B 753 " --> pdb=" O ASP B 736 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 728 through 737 removed outlier: 6.562A pdb=" N GLY B 755 " --> pdb=" O LEU B 734 " (cutoff:3.500A) removed outlier: 4.050A pdb=" N ASP B 736 " --> pdb=" O VAL B 753 " (cutoff:3.500A) removed outlier: 6.661A pdb=" N VAL B 753 " --> pdb=" O ASP B 736 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N LYS B 748 " --> pdb=" O ASP B 793 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N GLN B 754 " --> pdb=" O THR B 787 " (cutoff:3.500A) removed outlier: 4.274A pdb=" N ALA B 758 " --> pdb=" O THR B 783 " (cutoff:3.500A) removed outlier: 4.283A pdb=" N THR B 783 " --> pdb=" O ALA B 758 " (cutoff:3.500A) removed outlier: 4.303A pdb=" N ASP B 760 " --> pdb=" O ARG B 781 " (cutoff:3.500A) removed outlier: 4.718A pdb=" N ARG B 781 " --> pdb=" O ASP B 760 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N SER B 804 " --> pdb=" O PHE B 840 " (cutoff:3.500A) removed outlier: 3.958A pdb=" N PHE B 840 " --> pdb=" O SER B 804 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N GLU B 808 " --> pdb=" O PRO B 836 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N ALA B 835 " --> pdb=" O LEU B 863 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N SER B 855 " --> pdb=" O LYS B 843 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 763 through 764 removed outlier: 3.879A pdb=" N ALA B 764 " --> pdb=" O ARG B 777 " (cutoff:3.500A) removed outlier: 3.910A pdb=" N MET B 830 " --> pdb=" O PHE B 868 " (cutoff:3.500A) 409 hydrogen bonds defined for protein. 1167 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: 3.16 Time building geometry restraints manager: 3.59 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 3037 1.34 - 1.46: 1959 1.46 - 1.58: 4424 1.58 - 1.69: 0 1.69 - 1.81: 54 Bond restraints: 9474 Sorted by residual: bond pdb=" CA LYS B 299 " pdb=" C LYS B 299 " ideal model delta sigma weight residual 1.529 1.513 0.017 9.30e-03 1.16e+04 3.19e+00 bond pdb=" C LEU B 870 " pdb=" O LEU B 870 " ideal model delta sigma weight residual 1.243 1.230 0.013 9.50e-03 1.11e+04 1.98e+00 bond pdb=" N PRO A 441 " pdb=" CA PRO A 441 " ideal model delta sigma weight residual 1.469 1.478 -0.010 7.40e-03 1.83e+04 1.66e+00 bond pdb=" C LEU B 356 " pdb=" N PRO B 357 " ideal model delta sigma weight residual 1.335 1.351 -0.016 1.28e-02 6.10e+03 1.63e+00 bond pdb=" C ILE B 486 " pdb=" N PRO B 487 " ideal model delta sigma weight residual 1.335 1.350 -0.016 1.28e-02 6.10e+03 1.47e+00 ... (remaining 9469 not shown) Histogram of bond angle deviations from ideal: 99.46 - 106.36: 201 106.36 - 113.27: 5270 113.27 - 120.18: 3142 120.18 - 127.08: 4091 127.08 - 133.99: 76 Bond angle restraints: 12780 Sorted by residual: angle pdb=" C LEU B 870 " pdb=" CA LEU B 870 " pdb=" CB LEU B 870 " ideal model delta sigma weight residual 117.23 110.90 6.33 1.36e+00 5.41e-01 2.17e+01 angle pdb=" N THR A 110 " pdb=" CA THR A 110 " pdb=" C THR A 110 " ideal model delta sigma weight residual 110.80 119.53 -8.73 2.13e+00 2.20e-01 1.68e+01 angle pdb=" C ARG A 30 " pdb=" N LYS A 31 " pdb=" CA LYS A 31 " ideal model delta sigma weight residual 121.54 128.13 -6.59 1.91e+00 2.74e-01 1.19e+01 angle pdb=" CA LYS B 299 " pdb=" C LYS B 299 " pdb=" N GLY B 300 " ideal model delta sigma weight residual 119.52 116.81 2.71 7.90e-01 1.60e+00 1.18e+01 angle pdb=" C TYR B 138 " pdb=" N GLN B 139 " pdb=" CA GLN B 139 " ideal model delta sigma weight residual 121.54 127.75 -6.21 1.91e+00 2.74e-01 1.06e+01 ... (remaining 12775 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.39: 5407 17.39 - 34.79: 273 34.79 - 52.18: 75 52.18 - 69.58: 6 69.58 - 86.97: 2 Dihedral angle restraints: 5763 sinusoidal: 2234 harmonic: 3529 Sorted by residual: dihedral pdb=" CB CYS B 298 " pdb=" SG CYS B 298 " pdb=" SG CYS B 301 " pdb=" CB CYS B 301 " ideal model delta sinusoidal sigma weight residual -86.00 -166.60 80.60 1 1.00e+01 1.00e-02 8.03e+01 dihedral pdb=" CA ASP A 451 " pdb=" C ASP A 451 " pdb=" N ARG A 452 " pdb=" CA ARG A 452 " ideal model delta harmonic sigma weight residual 180.00 -161.66 -18.34 0 5.00e+00 4.00e-02 1.35e+01 dihedral pdb=" CA LEU B 741 " pdb=" C LEU B 741 " pdb=" N GLN B 742 " pdb=" CA GLN B 742 " ideal model delta harmonic sigma weight residual 180.00 164.25 15.75 0 5.00e+00 4.00e-02 9.92e+00 ... (remaining 5760 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.037: 1046 0.037 - 0.073: 294 0.073 - 0.110: 102 0.110 - 0.147: 39 0.147 - 0.184: 1 Chirality restraints: 1482 Sorted by residual: chirality pdb=" CA THR A 110 " pdb=" N THR A 110 " pdb=" C THR A 110 " pdb=" CB THR A 110 " both_signs ideal model delta sigma weight residual False 2.53 2.34 0.18 2.00e-01 2.50e+01 8.43e-01 chirality pdb=" CA ILE A 289 " pdb=" N ILE A 289 " pdb=" C ILE A 289 " pdb=" CB ILE A 289 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.80e-01 chirality pdb=" CA PHE A 440 " pdb=" N PHE A 440 " pdb=" C PHE A 440 " pdb=" CB PHE A 440 " both_signs ideal model delta sigma weight residual False 2.51 2.37 0.14 2.00e-01 2.50e+01 4.73e-01 ... (remaining 1479 not shown) Planarity restraints: 1629 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C TYR A 99 " -0.033 5.00e-02 4.00e+02 4.95e-02 3.91e+00 pdb=" N PRO A 100 " 0.086 5.00e-02 4.00e+02 pdb=" CA PRO A 100 " -0.024 5.00e-02 4.00e+02 pdb=" CD PRO A 100 " -0.028 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU B 567 " 0.028 5.00e-02 4.00e+02 4.24e-02 2.88e+00 pdb=" N PRO B 568 " -0.073 5.00e-02 4.00e+02 pdb=" CA PRO B 568 " 0.022 5.00e-02 4.00e+02 pdb=" CD PRO B 568 " 0.024 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PHE A 440 " -0.027 5.00e-02 4.00e+02 4.01e-02 2.58e+00 pdb=" N PRO A 441 " 0.069 5.00e-02 4.00e+02 pdb=" CA PRO A 441 " -0.020 5.00e-02 4.00e+02 pdb=" CD PRO A 441 " -0.023 5.00e-02 4.00e+02 ... (remaining 1626 not shown) Histogram of nonbonded interaction distances: 2.22 - 2.75: 918 2.75 - 3.29: 8798 3.29 - 3.83: 15426 3.83 - 4.36: 17538 4.36 - 4.90: 30571 Nonbonded interactions: 73251 Sorted by model distance: nonbonded pdb=" OH TYR A 116 " pdb=" O GLY A 119 " model vdw 2.216 2.440 nonbonded pdb=" OE1 GLU B 167 " pdb=" OH TYR B 178 " model vdw 2.261 2.440 nonbonded pdb=" O ILE B 560 " pdb=" OG SER B 563 " model vdw 2.277 2.440 nonbonded pdb=" O ALA A 336 " pdb=" OG1 THR A 340 " model vdw 2.299 2.440 nonbonded pdb=" OD1 ASP A 83 " pdb=" OG1 THR A 85 " model vdw 2.307 2.440 ... (remaining 73246 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. 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=0.40 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.670 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: 6.070 Check model and map are aligned: 0.150 Set scattering table: 0.090 Process input model: 31.330 Find NCS groups from input model: 0.250 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.720 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 42.340 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6042 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 : 0.002 0.034 9474 Z= 0.159 Angle : 0.555 8.731 12780 Z= 0.308 Chirality : 0.042 0.184 1482 Planarity : 0.004 0.049 1629 Dihedral : 11.261 86.970 3461 Min Nonbonded Distance : 2.216 Molprobity Statistics. All-atom Clashscore : 7.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.14 % Favored : 95.86 % Rotamer: Outliers : 3.76 % Allowed : 7.92 % Favored : 88.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % 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: -1.48 (0.22), residues: 1186 helix: -0.69 (0.22), residues: 411 sheet: -0.40 (0.33), residues: 274 loop : -1.44 (0.24), residues: 501 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 396 HIS 0.003 0.001 HIS B 529 PHE 0.014 0.001 PHE A 209 TYR 0.008 0.001 TYR B 620 ARG 0.001 0.000 ARG A 132 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2372 Ramachandran restraints generated. 1186 Oldfield, 0 Emsley, 1186 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2372 Ramachandran restraints generated. 1186 Oldfield, 0 Emsley, 1186 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 275 residues out of total 1049 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 238 time to evaluate : 1.007 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 37 outliers final: 11 residues processed: 265 average time/residue: 0.2579 time to fit residues: 90.8376 Evaluate side-chains 167 residues out of total 1049 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 156 time to evaluate : 0.995 Switching outliers to nearest non-outliers outliers start: 11 outliers final: 0 residues processed: 11 average time/residue: 0.0849 time to fit residues: 3.1967 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 102 optimal weight: 2.9990 chunk 91 optimal weight: 0.7980 chunk 50 optimal weight: 2.9990 chunk 31 optimal weight: 5.9990 chunk 61 optimal weight: 0.6980 chunk 48 optimal weight: 0.0980 chunk 94 optimal weight: 2.9990 chunk 36 optimal weight: 1.9990 chunk 57 optimal weight: 1.9990 chunk 70 optimal weight: 0.4980 chunk 109 optimal weight: 2.9990 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 256 HIS A 376 ASN A 430 ASN B 93 ASN ** B 292 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 502 HIS ** B 754 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6089 moved from start: 0.2489 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 9474 Z= 0.207 Angle : 0.655 15.032 12780 Z= 0.326 Chirality : 0.046 0.223 1482 Planarity : 0.005 0.105 1629 Dihedral : 4.508 17.042 1281 Min Nonbonded Distance : 2.078 Molprobity Statistics. All-atom Clashscore : 16.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.14 % Favored : 95.86 % Rotamer: Outliers : 3.25 % Allowed : 15.03 % Favored : 81.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % 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: -0.71 (0.24), residues: 1186 helix: 0.30 (0.24), residues: 422 sheet: -0.13 (0.33), residues: 270 loop : -1.29 (0.26), residues: 494 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP A 128 HIS 0.007 0.001 HIS B 502 PHE 0.019 0.002 PHE B 840 TYR 0.013 0.002 TYR A 268 ARG 0.006 0.001 ARG A 132 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2372 Ramachandran restraints generated. 1186 Oldfield, 0 Emsley, 1186 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2372 Ramachandran restraints generated. 1186 Oldfield, 0 Emsley, 1186 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 198 residues out of total 1049 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 166 time to evaluate : 1.088 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 32 outliers final: 12 residues processed: 189 average time/residue: 0.2457 time to fit residues: 62.9017 Evaluate side-chains 163 residues out of total 1049 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 151 time to evaluate : 1.135 Switching outliers to nearest non-outliers outliers start: 12 outliers final: 0 residues processed: 12 average time/residue: 0.0917 time to fit residues: 3.5259 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 61 optimal weight: 2.9990 chunk 34 optimal weight: 0.3980 chunk 91 optimal weight: 0.6980 chunk 74 optimal weight: 0.6980 chunk 30 optimal weight: 3.9990 chunk 110 optimal weight: 1.9990 chunk 118 optimal weight: 0.9980 chunk 98 optimal weight: 0.9990 chunk 109 optimal weight: 2.9990 chunk 37 optimal weight: 4.9990 chunk 88 optimal weight: 0.7980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 232 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 233 GLN A 256 HIS ** B 166 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 292 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 754 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6089 moved from start: 0.2982 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 9474 Z= 0.184 Angle : 0.594 12.508 12780 Z= 0.300 Chirality : 0.044 0.176 1482 Planarity : 0.004 0.067 1629 Dihedral : 4.389 17.792 1281 Min Nonbonded Distance : 2.027 Molprobity Statistics. All-atom Clashscore : 16.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.14 % Favored : 95.86 % Rotamer: Outliers : 2.23 % Allowed : 17.06 % Favored : 80.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % 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: -0.46 (0.24), residues: 1186 helix: 0.67 (0.25), residues: 418 sheet: -0.08 (0.33), residues: 269 loop : -1.23 (0.26), residues: 499 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP A 128 HIS 0.004 0.001 HIS B 335 PHE 0.021 0.002 PHE A 282 TYR 0.010 0.001 TYR A 414 ARG 0.008 0.000 ARG B 46 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2372 Ramachandran restraints generated. 1186 Oldfield, 0 Emsley, 1186 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2372 Ramachandran restraints generated. 1186 Oldfield, 0 Emsley, 1186 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 180 residues out of total 1049 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 158 time to evaluate : 1.029 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 22 outliers final: 10 residues processed: 176 average time/residue: 0.2375 time to fit residues: 57.3796 Evaluate side-chains 147 residues out of total 1049 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 137 time to evaluate : 1.022 Switching outliers to nearest non-outliers outliers start: 10 outliers final: 0 residues processed: 10 average time/residue: 0.0937 time to fit residues: 3.2132 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 108 optimal weight: 0.5980 chunk 82 optimal weight: 4.9990 chunk 57 optimal weight: 0.9980 chunk 12 optimal weight: 6.9990 chunk 52 optimal weight: 0.5980 chunk 73 optimal weight: 0.6980 chunk 110 optimal weight: 4.9990 chunk 116 optimal weight: 5.9990 chunk 104 optimal weight: 5.9990 chunk 31 optimal weight: 0.8980 chunk 97 optimal weight: 0.9980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 214 ASN A 232 ASN A 256 HIS ** B 166 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 292 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 358 GLN B 559 ASN ** B 754 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6101 moved from start: 0.3388 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 9474 Z= 0.184 Angle : 0.585 11.952 12780 Z= 0.297 Chirality : 0.044 0.156 1482 Planarity : 0.004 0.053 1629 Dihedral : 4.429 18.028 1281 Min Nonbonded Distance : 2.058 Molprobity Statistics. All-atom Clashscore : 16.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.14 % Favored : 95.86 % Rotamer: Outliers : 1.93 % Allowed : 18.07 % Favored : 80.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % 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: -0.42 (0.24), residues: 1186 helix: 0.83 (0.25), residues: 417 sheet: -0.14 (0.32), residues: 269 loop : -1.28 (0.26), residues: 500 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.002 TRP A 128 HIS 0.004 0.001 HIS B 335 PHE 0.030 0.002 PHE A 446 TYR 0.022 0.002 TYR A 393 ARG 0.003 0.000 ARG B 327 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2372 Ramachandran restraints generated. 1186 Oldfield, 0 Emsley, 1186 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2372 Ramachandran restraints generated. 1186 Oldfield, 0 Emsley, 1186 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 171 residues out of total 1049 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 152 time to evaluate : 1.012 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 19 outliers final: 13 residues processed: 165 average time/residue: 0.2369 time to fit residues: 53.7934 Evaluate side-chains 154 residues out of total 1049 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 141 time to evaluate : 0.962 Switching outliers to nearest non-outliers outliers start: 13 outliers final: 0 residues processed: 13 average time/residue: 0.0877 time to fit residues: 3.5869 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 66 optimal weight: 0.8980 chunk 1 optimal weight: 0.6980 chunk 87 optimal weight: 2.9990 chunk 48 optimal weight: 0.9980 chunk 99 optimal weight: 0.9990 chunk 80 optimal weight: 0.5980 chunk 0 optimal weight: 5.9990 chunk 59 optimal weight: 1.9990 chunk 104 optimal weight: 5.9990 chunk 29 optimal weight: 3.9990 chunk 39 optimal weight: 5.9990 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 214 ASN ** A 233 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 166 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 292 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 358 GLN ** B 754 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6108 moved from start: 0.3668 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 9474 Z= 0.189 Angle : 0.580 11.708 12780 Z= 0.293 Chirality : 0.044 0.167 1482 Planarity : 0.004 0.053 1629 Dihedral : 4.381 18.570 1281 Min Nonbonded Distance : 2.096 Molprobity Statistics. All-atom Clashscore : 16.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.48 % Favored : 95.52 % Rotamer: Outliers : 1.52 % Allowed : 18.88 % Favored : 79.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % 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: -0.48 (0.24), residues: 1186 helix: 0.90 (0.25), residues: 417 sheet: -0.24 (0.32), residues: 271 loop : -1.39 (0.26), residues: 498 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 396 HIS 0.004 0.001 HIS B 335 PHE 0.018 0.002 PHE A 282 TYR 0.017 0.002 TYR A 393 ARG 0.003 0.000 ARG B 623 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2372 Ramachandran restraints generated. 1186 Oldfield, 0 Emsley, 1186 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2372 Ramachandran restraints generated. 1186 Oldfield, 0 Emsley, 1186 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 164 residues out of total 1049 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 149 time to evaluate : 1.114 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 15 outliers final: 3 residues processed: 159 average time/residue: 0.2304 time to fit residues: 51.0529 Evaluate side-chains 147 residues out of total 1049 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 144 time to evaluate : 1.091 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.0863 time to fit residues: 1.9810 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 105 optimal weight: 0.8980 chunk 23 optimal weight: 2.9990 chunk 68 optimal weight: 1.9990 chunk 28 optimal weight: 1.9990 chunk 117 optimal weight: 0.9990 chunk 97 optimal weight: 0.0870 chunk 54 optimal weight: 2.9990 chunk 9 optimal weight: 1.9990 chunk 38 optimal weight: 8.9990 chunk 61 optimal weight: 0.0670 chunk 112 optimal weight: 3.9990 overall best weight: 0.8100 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 256 HIS A 430 ASN ** B 159 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 166 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 292 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 358 GLN ** B 754 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6107 moved from start: 0.3901 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 9474 Z= 0.186 Angle : 0.608 18.518 12780 Z= 0.298 Chirality : 0.044 0.177 1482 Planarity : 0.004 0.048 1629 Dihedral : 4.363 18.298 1281 Min Nonbonded Distance : 2.064 Molprobity Statistics. All-atom Clashscore : 16.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.56 % Favored : 95.44 % Rotamer: Outliers : 1.52 % Allowed : 20.10 % Favored : 78.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % 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: -0.39 (0.24), residues: 1186 helix: 0.97 (0.25), residues: 418 sheet: -0.21 (0.33), residues: 262 loop : -1.31 (0.26), residues: 506 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.002 TRP A 128 HIS 0.004 0.001 HIS B 335 PHE 0.021 0.002 PHE A 48 TYR 0.014 0.002 TYR A 393 ARG 0.002 0.000 ARG A 97 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2372 Ramachandran restraints generated. 1186 Oldfield, 0 Emsley, 1186 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2372 Ramachandran restraints generated. 1186 Oldfield, 0 Emsley, 1186 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 165 residues out of total 1049 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 150 time to evaluate : 1.100 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 15 outliers final: 8 residues processed: 158 average time/residue: 0.2295 time to fit residues: 50.2127 Evaluate side-chains 156 residues out of total 1049 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 148 time to evaluate : 1.029 Switching outliers to nearest non-outliers outliers start: 8 outliers final: 0 residues processed: 8 average time/residue: 0.0916 time to fit residues: 2.7694 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 13 optimal weight: 4.9990 chunk 66 optimal weight: 0.5980 chunk 85 optimal weight: 0.0270 chunk 98 optimal weight: 7.9990 chunk 65 optimal weight: 1.9990 chunk 116 optimal weight: 10.0000 chunk 72 optimal weight: 2.9990 chunk 71 optimal weight: 0.8980 chunk 53 optimal weight: 0.8980 chunk 46 optimal weight: 2.9990 chunk 69 optimal weight: 0.3980 overall best weight: 0.5638 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 256 HIS ** B 166 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 292 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6083 moved from start: 0.4038 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 9474 Z= 0.162 Angle : 0.565 11.536 12780 Z= 0.282 Chirality : 0.043 0.159 1482 Planarity : 0.003 0.044 1629 Dihedral : 4.287 17.723 1281 Min Nonbonded Distance : 2.106 Molprobity Statistics. All-atom Clashscore : 15.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.65 % Favored : 95.35 % Rotamer: Outliers : 0.91 % Allowed : 19.90 % Favored : 79.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % 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: -0.26 (0.24), residues: 1186 helix: 1.14 (0.26), residues: 416 sheet: -0.15 (0.33), residues: 262 loop : -1.28 (0.26), residues: 508 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 128 HIS 0.003 0.001 HIS B 335 PHE 0.018 0.001 PHE B 706 TYR 0.016 0.001 TYR B 511 ARG 0.002 0.000 ARG B 392 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2372 Ramachandran restraints generated. 1186 Oldfield, 0 Emsley, 1186 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2372 Ramachandran restraints generated. 1186 Oldfield, 0 Emsley, 1186 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 165 residues out of total 1049 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 156 time to evaluate : 1.156 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 9 outliers final: 2 residues processed: 162 average time/residue: 0.2341 time to fit residues: 52.3120 Evaluate side-chains 150 residues out of total 1049 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 148 time to evaluate : 0.979 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.0832 time to fit residues: 1.7242 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 35 optimal weight: 4.9990 chunk 22 optimal weight: 2.9990 chunk 74 optimal weight: 4.9990 chunk 79 optimal weight: 0.3980 chunk 57 optimal weight: 1.9990 chunk 10 optimal weight: 4.9990 chunk 91 optimal weight: 0.8980 chunk 106 optimal weight: 4.9990 chunk 111 optimal weight: 3.9990 chunk 101 optimal weight: 5.9990 chunk 108 optimal weight: 2.9990 overall best weight: 1.8586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 233 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 256 HIS ** B 159 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 292 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 390 GLN ** B 754 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6205 moved from start: 0.4317 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.055 9474 Z= 0.318 Angle : 0.712 11.619 12780 Z= 0.364 Chirality : 0.047 0.209 1482 Planarity : 0.004 0.039 1629 Dihedral : 4.995 20.951 1281 Min Nonbonded Distance : 2.036 Molprobity Statistics. All-atom Clashscore : 22.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.92 % Favored : 94.08 % Rotamer: Outliers : 1.32 % Allowed : 20.51 % Favored : 78.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % 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 (0.24), residues: 1186 helix: 0.57 (0.25), residues: 414 sheet: -0.21 (0.34), residues: 260 loop : -1.46 (0.26), residues: 512 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.051 0.003 TRP A 128 HIS 0.013 0.002 HIS B 126 PHE 0.024 0.002 PHE B 706 TYR 0.017 0.002 TYR B 284 ARG 0.006 0.001 ARG B 327 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2372 Ramachandran restraints generated. 1186 Oldfield, 0 Emsley, 1186 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2372 Ramachandran restraints generated. 1186 Oldfield, 0 Emsley, 1186 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 166 residues out of total 1049 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 153 time to evaluate : 1.051 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 13 outliers final: 3 residues processed: 158 average time/residue: 0.2358 time to fit residues: 51.6708 Evaluate side-chains 146 residues out of total 1049 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 143 time to evaluate : 1.082 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.0870 time to fit residues: 1.9536 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 111 optimal weight: 1.9990 chunk 65 optimal weight: 2.9990 chunk 47 optimal weight: 0.8980 chunk 85 optimal weight: 6.9990 chunk 33 optimal weight: 1.9990 chunk 98 optimal weight: 0.6980 chunk 102 optimal weight: 4.9990 chunk 108 optimal weight: 0.9990 chunk 71 optimal weight: 3.9990 chunk 114 optimal weight: 0.0770 chunk 70 optimal weight: 0.6980 overall best weight: 0.6740 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 256 HIS ** B 159 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 166 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 292 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 530 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6125 moved from start: 0.4409 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 9474 Z= 0.197 Angle : 0.646 16.994 12780 Z= 0.322 Chirality : 0.044 0.172 1482 Planarity : 0.004 0.042 1629 Dihedral : 4.667 19.288 1281 Min Nonbonded Distance : 2.073 Molprobity Statistics. All-atom Clashscore : 18.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.48 % Favored : 95.52 % Rotamer: Outliers : 0.61 % Allowed : 21.83 % Favored : 77.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % 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: -0.54 (0.24), residues: 1186 helix: 0.92 (0.26), residues: 412 sheet: -0.26 (0.34), residues: 257 loop : -1.44 (0.26), residues: 517 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.037 0.002 TRP A 128 HIS 0.005 0.001 HIS B 335 PHE 0.034 0.002 PHE B 706 TYR 0.018 0.002 TYR A 268 ARG 0.006 0.000 ARG B 327 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2372 Ramachandran restraints generated. 1186 Oldfield, 0 Emsley, 1186 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2372 Ramachandran restraints generated. 1186 Oldfield, 0 Emsley, 1186 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 155 residues out of total 1049 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 149 time to evaluate : 1.018 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 6 outliers final: 2 residues processed: 154 average time/residue: 0.2275 time to fit residues: 48.6016 Evaluate side-chains 144 residues out of total 1049 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 142 time to evaluate : 1.114 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.1033 time to fit residues: 1.8644 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 54 optimal weight: 0.7980 chunk 79 optimal weight: 0.5980 chunk 120 optimal weight: 0.0370 chunk 110 optimal weight: 4.9990 chunk 95 optimal weight: 0.6980 chunk 9 optimal weight: 0.8980 chunk 74 optimal weight: 0.6980 chunk 58 optimal weight: 0.0270 chunk 76 optimal weight: 0.8980 chunk 102 optimal weight: 0.6980 chunk 29 optimal weight: 1.9990 overall best weight: 0.4116 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 233 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 256 HIS ** B 159 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 166 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 292 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 530 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6082 moved from start: 0.4515 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 9474 Z= 0.170 Angle : 0.627 15.709 12780 Z= 0.307 Chirality : 0.043 0.159 1482 Planarity : 0.004 0.041 1629 Dihedral : 4.427 17.860 1281 Min Nonbonded Distance : 2.093 Molprobity Statistics. All-atom Clashscore : 16.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.31 % Favored : 95.69 % Rotamer: Outliers : 0.41 % Allowed : 22.44 % Favored : 77.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % 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: -0.45 (0.24), residues: 1186 helix: 1.04 (0.26), residues: 418 sheet: -0.24 (0.34), residues: 257 loop : -1.46 (0.26), residues: 511 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.002 TRP A 128 HIS 0.003 0.001 HIS B 335 PHE 0.026 0.001 PHE B 706 TYR 0.017 0.002 TYR B 284 ARG 0.005 0.000 ARG B 327 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2372 Ramachandran restraints generated. 1186 Oldfield, 0 Emsley, 1186 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2372 Ramachandran restraints generated. 1186 Oldfield, 0 Emsley, 1186 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 146 residues out of total 1049 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 142 time to evaluate : 1.032 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 4 outliers final: 2 residues processed: 145 average time/residue: 0.2420 time to fit residues: 48.5207 Evaluate side-chains 143 residues out of total 1049 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 141 time to evaluate : 1.049 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.0887 time to fit residues: 1.8518 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 88 optimal weight: 0.0370 chunk 14 optimal weight: 0.9980 chunk 26 optimal weight: 3.9990 chunk 96 optimal weight: 0.8980 chunk 40 optimal weight: 6.9990 chunk 98 optimal weight: 0.7980 chunk 12 optimal weight: 4.9990 chunk 17 optimal weight: 0.6980 chunk 84 optimal weight: 0.9990 chunk 5 optimal weight: 0.9990 chunk 69 optimal weight: 0.8980 overall best weight: 0.6658 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 233 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 256 HIS ** B 159 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 166 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 292 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 530 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 = 0.4736 r_free = 0.4736 target = 0.179778 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.4551 r_free = 0.4551 target = 0.164891 restraints weight = 25859.280| |-----------------------------------------------------------------------------| r_work (start): 0.4546 rms_B_bonded: 3.58 r_work: 0.4449 rms_B_bonded: 4.36 restraints_weight: 0.5000 r_work (final): 0.4449 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4451 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4451 r_free = 0.4451 target_work(ls_wunit_k1) = 0.158 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4451 r_free = 0.4451 target_work(ls_wunit_k1) = 0.158 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.4451 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6138 moved from start: 0.4610 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 9474 Z= 0.180 Angle : 0.623 13.155 12780 Z= 0.307 Chirality : 0.044 0.160 1482 Planarity : 0.004 0.040 1629 Dihedral : 4.424 18.104 1281 Min Nonbonded Distance : 2.099 Molprobity Statistics. All-atom Clashscore : 17.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.56 % Favored : 95.44 % Rotamer: Outliers : 0.91 % Allowed : 22.23 % Favored : 76.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % 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 (0.25), residues: 1186 helix: 1.14 (0.26), residues: 417 sheet: -0.21 (0.34), residues: 257 loop : -1.40 (0.27), residues: 512 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.035 0.002 TRP A 128 HIS 0.004 0.001 HIS B 335 PHE 0.024 0.001 PHE B 706 TYR 0.020 0.002 TYR B 284 ARG 0.008 0.000 ARG B 327 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2459.18 seconds wall clock time: 45 minutes 8.35 seconds (2708.35 seconds total)