Starting phenix.real_space_refine on Thu Mar 5 04:46:23 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7zpm_14858/03_2026/7zpm_14858.cif Found real_map, /net/cci-nas-00/data/ceres_data/7zpm_14858/03_2026/7zpm_14858.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.81 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7zpm_14858/03_2026/7zpm_14858.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7zpm_14858/03_2026/7zpm_14858.map" model { file = "/net/cci-nas-00/data/ceres_data/7zpm_14858/03_2026/7zpm_14858.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7zpm_14858/03_2026/7zpm_14858.cif" } resolution = 2.81 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.014 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 148 5.16 5 C 12231 2.51 5 N 3309 2.21 5 O 3642 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 7 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 19330 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 4142 Number of conformers: 1 Conformer: "" Number of residues, atoms: 515, 4142 Classifications: {'peptide': 515} Link IDs: {'PTRANS': 28, 'TRANS': 486} Chain: "B" Number of atoms: 4853 Number of conformers: 1 Conformer: "" Number of residues, atoms: 610, 4853 Classifications: {'peptide': 610} Link IDs: {'PCIS': 1, 'PTRANS': 27, 'TRANS': 581} Chain breaks: 3 Chain: "C" Number of atoms: 659 Number of conformers: 1 Conformer: "" Number of residues, atoms: 80, 659 Classifications: {'peptide': 80} Link IDs: {'PTRANS': 6, 'TRANS': 73} Chain: "D" Number of atoms: 4133 Number of conformers: 1 Conformer: "" Number of residues, atoms: 514, 4133 Classifications: {'peptide': 514} Link IDs: {'PTRANS': 28, 'TRANS': 485} Chain: "E" Number of atoms: 4884 Number of conformers: 1 Conformer: "" Number of residues, atoms: 613, 4884 Classifications: {'peptide': 613} Link IDs: {'PCIS': 1, 'PTRANS': 27, 'TRANS': 584} Chain breaks: 3 Chain: "F" Number of atoms: 659 Number of conformers: 1 Conformer: "" Number of residues, atoms: 80, 659 Classifications: {'peptide': 80} Link IDs: {'PTRANS': 6, 'TRANS': 73} Time building chain proxies: 4.18, per 1000 atoms: 0.22 Number of scatterers: 19330 At special positions: 0 Unit cell: (115.523, 187.829, 95.5765, 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 148 16.00 O 3642 8.00 N 3309 7.00 C 12231 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.77 Conformation dependent library (CDL) restraints added in 802.9 milliseconds 4776 Ramachandran restraints generated. 2388 Oldfield, 0 Emsley, 2388 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4548 Finding SS restraints... Secondary structure from input PDB file: 104 helices and 23 sheets defined 49.6% alpha, 13.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.48 Creating SS restraints... Processing helix chain 'A' and resid 209 through 215 removed outlier: 3.634A pdb=" N ARG A 213 " --> pdb=" O GLY A 209 " (cutoff:3.500A) Processing helix chain 'A' and resid 216 through 218 No H-bonds generated for 'chain 'A' and resid 216 through 218' Processing helix chain 'A' and resid 225 through 235 Processing helix chain 'A' and resid 240 through 249 removed outlier: 3.744A pdb=" N GLY A 244 " --> pdb=" O GLY A 240 " (cutoff:3.500A) Processing helix chain 'A' and resid 302 through 312 Processing helix chain 'A' and resid 330 through 345 removed outlier: 3.547A pdb=" N TYR A 334 " --> pdb=" O ILE A 330 " (cutoff:3.500A) Processing helix chain 'A' and resid 346 through 351 removed outlier: 3.718A pdb=" N GLU A 349 " --> pdb=" O GLN A 346 " (cutoff:3.500A) Processing helix chain 'A' and resid 363 through 370 Processing helix chain 'A' and resid 380 through 385 removed outlier: 4.052A pdb=" N LYS A 385 " --> pdb=" O GLU A 382 " (cutoff:3.500A) Processing helix chain 'A' and resid 405 through 415 Processing helix chain 'A' and resid 433 through 451 Processing helix chain 'A' and resid 453 through 476 removed outlier: 3.597A pdb=" N GLU A 457 " --> pdb=" O CYS A 453 " (cutoff:3.500A) Processing helix chain 'A' and resid 533 through 538 removed outlier: 3.776A pdb=" N GLU A 538 " --> pdb=" O HIS A 535 " (cutoff:3.500A) Processing helix chain 'A' and resid 572 through 580 Processing helix chain 'A' and resid 582 through 604 removed outlier: 3.576A pdb=" N LEU A 586 " --> pdb=" O ARG A 582 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N GLU A 599 " --> pdb=" O MET A 595 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N VAL A 602 " --> pdb=" O ALA A 598 " (cutoff:3.500A) Processing helix chain 'A' and resid 607 through 613 Processing helix chain 'A' and resid 632 through 650 Processing helix chain 'A' and resid 652 through 674 removed outlier: 4.106A pdb=" N LYS A 664 " --> pdb=" O ALA A 660 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N LEU A 665 " --> pdb=" O GLU A 661 " (cutoff:3.500A) Processing helix chain 'A' and resid 682 through 692 Processing helix chain 'A' and resid 697 through 715 removed outlier: 3.596A pdb=" N LEU A 715 " --> pdb=" O LEU A 711 " (cutoff:3.500A) Processing helix chain 'B' and resid 5 through 11 Processing helix chain 'B' and resid 17 through 22 Processing helix chain 'B' and resid 35 through 49 Processing helix chain 'B' and resid 84 through 99 Processing helix chain 'B' and resid 101 through 114 removed outlier: 3.800A pdb=" N GLU B 112 " --> pdb=" O LEU B 108 " (cutoff:3.500A) removed outlier: 4.065A pdb=" N ILE B 113 " --> pdb=" O GLU B 109 " (cutoff:3.500A) Processing helix chain 'B' and resid 119 through 124 Processing helix chain 'B' and resid 138 through 153 removed outlier: 3.594A pdb=" N LEU B 143 " --> pdb=" O ALA B 139 " (cutoff:3.500A) removed outlier: 4.095A pdb=" N ALA B 144 " --> pdb=" O ALA B 140 " (cutoff:3.500A) Processing helix chain 'B' and resid 156 through 161 removed outlier: 3.657A pdb=" N SER B 160 " --> pdb=" O ALA B 157 " (cutoff:3.500A) Processing helix chain 'B' and resid 162 through 174 removed outlier: 3.848A pdb=" N MET B 174 " --> pdb=" O VAL B 170 " (cutoff:3.500A) Processing helix chain 'B' and resid 214 through 222 Processing helix chain 'B' and resid 245 through 247 No H-bonds generated for 'chain 'B' and resid 245 through 247' Processing helix chain 'B' and resid 248 through 264 Processing helix chain 'B' and resid 275 through 292 removed outlier: 4.033A pdb=" N LYS B 281 " --> pdb=" O GLU B 277 " (cutoff:3.500A) removed outlier: 3.844A pdb=" N LEU B 282 " --> pdb=" O LYS B 278 " (cutoff:3.500A) removed outlier: 4.042A pdb=" N ALA B 283 " --> pdb=" O LYS B 279 " (cutoff:3.500A) removed outlier: 4.452A pdb=" N ASN B 292 " --> pdb=" O LYS B 288 " (cutoff:3.500A) Processing helix chain 'B' and resid 314 through 326 Processing helix chain 'B' and resid 330 through 338 removed outlier: 3.622A pdb=" N VAL B 336 " --> pdb=" O TRP B 332 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N LEU B 337 " --> pdb=" O PHE B 333 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N SER B 338 " --> pdb=" O ARG B 334 " (cutoff:3.500A) Processing helix chain 'B' and resid 338 through 345 removed outlier: 3.637A pdb=" N ILE B 342 " --> pdb=" O SER B 338 " (cutoff:3.500A) Processing helix chain 'B' and resid 370 through 375 removed outlier: 3.506A pdb=" N ALA B 374 " --> pdb=" O GLU B 371 " (cutoff:3.500A) Processing helix chain 'B' and resid 382 through 393 Processing helix chain 'B' and resid 412 through 426 Processing helix chain 'B' and resid 428 through 433 Processing helix chain 'B' and resid 455 through 473 removed outlier: 3.519A pdb=" N VAL B 473 " --> pdb=" O THR B 469 " (cutoff:3.500A) Processing helix chain 'B' and resid 518 through 538 removed outlier: 3.779A pdb=" N MET B 523 " --> pdb=" O GLU B 519 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N SER B 524 " --> pdb=" O SER B 520 " (cutoff:3.500A) Processing helix chain 'B' and resid 540 through 560 Processing helix chain 'B' and resid 572 through 583 Processing helix chain 'B' and resid 590 through 594 Processing helix chain 'B' and resid 607 through 612 Processing helix chain 'B' and resid 617 through 625 Processing helix chain 'C' and resid 42 through 53 removed outlier: 3.572A pdb=" N ALA C 52 " --> pdb=" O LYS C 48 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N MET C 53 " --> pdb=" O TRP C 49 " (cutoff:3.500A) Processing helix chain 'C' and resid 60 through 66 Processing helix chain 'C' and resid 93 through 103 removed outlier: 3.729A pdb=" N THR C 97 " --> pdb=" O PRO C 93 " (cutoff:3.500A) Processing helix chain 'C' and resid 110 through 115 removed outlier: 3.869A pdb=" N TYR C 115 " --> pdb=" O TYR C 111 " (cutoff:3.500A) Processing helix chain 'C' and resid 115 through 120 Processing helix chain 'D' and resid 209 through 216 removed outlier: 3.894A pdb=" N ASP D 216 " --> pdb=" O ARG D 212 " (cutoff:3.500A) Processing helix chain 'D' and resid 225 through 235 removed outlier: 3.633A pdb=" N GLY D 235 " --> pdb=" O ALA D 231 " (cutoff:3.500A) Processing helix chain 'D' and resid 240 through 249 removed outlier: 3.822A pdb=" N GLY D 244 " --> pdb=" O GLY D 240 " (cutoff:3.500A) Processing helix chain 'D' and resid 302 through 312 Processing helix chain 'D' and resid 330 through 345 removed outlier: 3.548A pdb=" N TYR D 334 " --> pdb=" O ILE D 330 " (cutoff:3.500A) Processing helix chain 'D' and resid 346 through 351 removed outlier: 3.666A pdb=" N GLU D 349 " --> pdb=" O GLN D 346 " (cutoff:3.500A) Processing helix chain 'D' and resid 363 through 370 Processing helix chain 'D' and resid 380 through 385 removed outlier: 4.043A pdb=" N LYS D 385 " --> pdb=" O GLU D 382 " (cutoff:3.500A) Processing helix chain 'D' and resid 405 through 415 Processing helix chain 'D' and resid 433 through 451 removed outlier: 3.680A pdb=" N GLU D 449 " --> pdb=" O TYR D 445 " (cutoff:3.500A) Processing helix chain 'D' and resid 453 through 476 Processing helix chain 'D' and resid 533 through 538 removed outlier: 3.738A pdb=" N GLU D 538 " --> pdb=" O HIS D 535 " (cutoff:3.500A) Processing helix chain 'D' and resid 572 through 580 Processing helix chain 'D' and resid 582 through 603 removed outlier: 3.586A pdb=" N LEU D 586 " --> pdb=" O ARG D 582 " (cutoff:3.500A) removed outlier: 4.252A pdb=" N VAL D 602 " --> pdb=" O ALA D 598 " (cutoff:3.500A) removed outlier: 4.146A pdb=" N LYS D 603 " --> pdb=" O GLU D 599 " (cutoff:3.500A) Processing helix chain 'D' and resid 607 through 613 Processing helix chain 'D' and resid 632 through 650 Processing helix chain 'D' and resid 652 through 674 removed outlier: 4.013A pdb=" N LYS D 664 " --> pdb=" O ALA D 660 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N LEU D 665 " --> pdb=" O GLU D 661 " (cutoff:3.500A) Processing helix chain 'D' and resid 682 through 692 Processing helix chain 'D' and resid 697 through 715 removed outlier: 3.631A pdb=" N LEU D 715 " --> pdb=" O LEU D 711 " (cutoff:3.500A) Processing helix chain 'E' and resid 5 through 11 Processing helix chain 'E' and resid 17 through 22 Processing helix chain 'E' and resid 35 through 49 Processing helix chain 'E' and resid 84 through 99 Processing helix chain 'E' and resid 101 through 116 removed outlier: 4.275A pdb=" N GLN E 116 " --> pdb=" O GLU E 112 " (cutoff:3.500A) Processing helix chain 'E' and resid 119 through 124 Processing helix chain 'E' and resid 138 through 153 removed outlier: 3.945A pdb=" N ALA E 144 " --> pdb=" O ALA E 140 " (cutoff:3.500A) Processing helix chain 'E' and resid 157 through 161 removed outlier: 3.884A pdb=" N GLY E 161 " --> pdb=" O ASN E 158 " (cutoff:3.500A) Processing helix chain 'E' and resid 162 through 173 removed outlier: 3.599A pdb=" N PHE E 166 " --> pdb=" O ARG E 162 " (cutoff:3.500A) Processing helix chain 'E' and resid 174 through 176 No H-bonds generated for 'chain 'E' and resid 174 through 176' Processing helix chain 'E' and resid 213 through 221 Processing helix chain 'E' and resid 248 through 265 removed outlier: 3.557A pdb=" N PHE E 254 " --> pdb=" O GLY E 250 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N VAL E 255 " --> pdb=" O PHE E 251 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N LYS E 265 " --> pdb=" O SER E 261 " (cutoff:3.500A) Processing helix chain 'E' and resid 275 through 289 removed outlier: 3.811A pdb=" N ALA E 280 " --> pdb=" O ASN E 276 " (cutoff:3.500A) removed outlier: 4.350A pdb=" N LYS E 281 " --> pdb=" O GLU E 277 " (cutoff:3.500A) removed outlier: 3.937A pdb=" N LEU E 282 " --> pdb=" O LYS E 278 " (cutoff:3.500A) removed outlier: 4.047A pdb=" N ALA E 283 " --> pdb=" O LYS E 279 " (cutoff:3.500A) Processing helix chain 'E' and resid 314 through 326 Processing helix chain 'E' and resid 330 through 338 Processing helix chain 'E' and resid 339 through 346 Processing helix chain 'E' and resid 369 through 373 removed outlier: 3.528A pdb=" N MET E 372 " --> pdb=" O PRO E 369 " (cutoff:3.500A) Processing helix chain 'E' and resid 377 through 381 removed outlier: 3.665A pdb=" N TYR E 380 " --> pdb=" O ASP E 377 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N PHE E 381 " --> pdb=" O LEU E 378 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 377 through 381' Processing helix chain 'E' and resid 382 through 393 removed outlier: 3.774A pdb=" N GLU E 387 " --> pdb=" O LYS E 383 " (cutoff:3.500A) removed outlier: 3.857A pdb=" N LYS E 388 " --> pdb=" O SER E 384 " (cutoff:3.500A) Processing helix chain 'E' and resid 412 through 426 removed outlier: 3.598A pdb=" N LEU E 426 " --> pdb=" O SER E 422 " (cutoff:3.500A) Processing helix chain 'E' and resid 428 through 433 Processing helix chain 'E' and resid 455 through 473 removed outlier: 3.530A pdb=" N VAL E 473 " --> pdb=" O THR E 469 " (cutoff:3.500A) Processing helix chain 'E' and resid 518 through 538 removed outlier: 3.757A pdb=" N MET E 523 " --> pdb=" O GLU E 519 " (cutoff:3.500A) removed outlier: 3.832A pdb=" N SER E 524 " --> pdb=" O SER E 520 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N ASP E 538 " --> pdb=" O MET E 534 " (cutoff:3.500A) Processing helix chain 'E' and resid 540 through 560 Processing helix chain 'E' and resid 572 through 583 Processing helix chain 'E' and resid 590 through 594 Processing helix chain 'E' and resid 607 through 612 Processing helix chain 'E' and resid 617 through 625 Processing helix chain 'F' and resid 42 through 52 removed outlier: 3.585A pdb=" N ALA F 52 " --> pdb=" O LYS F 48 " (cutoff:3.500A) Processing helix chain 'F' and resid 60 through 66 Processing helix chain 'F' and resid 93 through 103 removed outlier: 3.739A pdb=" N THR F 97 " --> pdb=" O PRO F 93 " (cutoff:3.500A) Processing helix chain 'F' and resid 110 through 115 removed outlier: 3.793A pdb=" N TYR F 115 " --> pdb=" O TYR F 111 " (cutoff:3.500A) Processing helix chain 'F' and resid 115 through 120 Processing sheet with id=AA1, first strand: chain 'A' and resid 258 through 259 Processing sheet with id=AA2, first strand: chain 'A' and resid 290 through 294 removed outlier: 4.044A pdb=" N ARG A 496 " --> pdb=" O ASP A 294 " (cutoff:3.500A) removed outlier: 7.405A pdb=" N TYR A 501 " --> pdb=" O PHE A 525 " (cutoff:3.500A) removed outlier: 6.475A pdb=" N LEU A 563 " --> pdb=" O GLU A 544 " (cutoff:3.500A) removed outlier: 5.596A pdb=" N GLU A 544 " --> pdb=" O LEU A 563 " (cutoff:3.500A) removed outlier: 7.105A pdb=" N VAL A 565 " --> pdb=" O VAL A 542 " (cutoff:3.500A) removed outlier: 5.255A pdb=" N VAL A 542 " --> pdb=" O VAL A 565 " (cutoff:3.500A) removed outlier: 6.675A pdb=" N VAL A 542 " --> pdb=" O ILE A 323 " (cutoff:3.500A) removed outlier: 6.366A pdb=" N GLY A 546 " --> pdb=" O GLU A 319 " (cutoff:3.500A) removed outlier: 7.808A pdb=" N GLU A 319 " --> pdb=" O GLY A 546 " (cutoff:3.500A) removed outlier: 8.721A pdb=" N MET A 548 " --> pdb=" O TRP A 317 " (cutoff:3.500A) removed outlier: 9.595A pdb=" N TRP A 317 " --> pdb=" O MET A 548 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 290 through 294 removed outlier: 4.044A pdb=" N ARG A 496 " --> pdb=" O ASP A 294 " (cutoff:3.500A) removed outlier: 6.636A pdb=" N MET A 485 " --> pdb=" O TYR A 501 " (cutoff:3.500A) removed outlier: 4.704A pdb=" N PHE A 503 " --> pdb=" O ILE A 483 " (cutoff:3.500A) removed outlier: 6.613A pdb=" N ILE A 483 " --> pdb=" O PHE A 503 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 353 through 355 Processing sheet with id=AA5, first strand: chain 'A' and resid 391 through 392 Processing sheet with id=AA6, first strand: chain 'A' and resid 627 through 631 removed outlier: 3.912A pdb=" N GLY A 622 " --> pdb=" O GLU A 629 " (cutoff:3.500A) removed outlier: 6.167A pdb=" N GLY A 631 " --> pdb=" O PRO A 620 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 54 through 57 Processing sheet with id=AA8, first strand: chain 'B' and resid 128 through 130 removed outlier: 3.502A pdb=" N ARG B 135 " --> pdb=" O ASP B 130 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 178 through 181 Processing sheet with id=AB1, first strand: chain 'B' and resid 223 through 224 Processing sheet with id=AB2, first strand: chain 'B' and resid 489 through 491 Processing sheet with id=AB3, first strand: chain 'B' and resid 667 through 668 removed outlier: 4.752A pdb=" N ILE B 667 " --> pdb=" O THR C 58 " (cutoff:3.500A) removed outlier: 3.940A pdb=" N MET C 90 " --> pdb=" O SER C 79 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'D' and resid 258 through 259 removed outlier: 4.763A pdb=" N ASP E 305 " --> pdb=" O SER E 478 " (cutoff:3.500A) removed outlier: 8.945A pdb=" N LYS E 480 " --> pdb=" O THR E 303 " (cutoff:3.500A) removed outlier: 10.519A pdb=" N THR E 303 " --> pdb=" O LYS E 480 " (cutoff:3.500A) removed outlier: 10.263A pdb=" N SER E 482 " --> pdb=" O THR E 301 " (cutoff:3.500A) removed outlier: 11.498A pdb=" N THR E 301 " --> pdb=" O SER E 482 " (cutoff:3.500A) removed outlier: 10.359A pdb=" N ILE E 484 " --> pdb=" O SER E 299 " (cutoff:3.500A) removed outlier: 11.334A pdb=" N SER E 299 " --> pdb=" O ILE E 484 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'D' and resid 290 through 294 removed outlier: 7.444A pdb=" N TYR D 501 " --> pdb=" O PHE D 525 " (cutoff:3.500A) removed outlier: 6.280A pdb=" N GLY D 555 " --> pdb=" O ARG D 551 " (cutoff:3.500A) removed outlier: 4.555A pdb=" N ARG D 551 " --> pdb=" O GLY D 555 " (cutoff:3.500A) removed outlier: 5.949A pdb=" N VAL D 557 " --> pdb=" O LEU D 549 " (cutoff:3.500A) removed outlier: 4.414A pdb=" N LEU D 549 " --> pdb=" O VAL D 557 " (cutoff:3.500A) removed outlier: 5.663A pdb=" N ARG D 559 " --> pdb=" O ASP D 547 " (cutoff:3.500A) removed outlier: 4.531A pdb=" N ASP D 547 " --> pdb=" O ARG D 559 " (cutoff:3.500A) removed outlier: 6.627A pdb=" N MET D 561 " --> pdb=" O ILE D 545 " (cutoff:3.500A) removed outlier: 6.673A pdb=" N VAL D 542 " --> pdb=" O ILE D 323 " (cutoff:3.500A) removed outlier: 6.489A pdb=" N GLY D 546 " --> pdb=" O GLU D 319 " (cutoff:3.500A) removed outlier: 8.021A pdb=" N GLU D 319 " --> pdb=" O GLY D 546 " (cutoff:3.500A) removed outlier: 8.786A pdb=" N MET D 548 " --> pdb=" O TRP D 317 " (cutoff:3.500A) removed outlier: 9.471A pdb=" N TRP D 317 " --> pdb=" O MET D 548 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'D' and resid 290 through 294 removed outlier: 6.578A pdb=" N MET D 485 " --> pdb=" O TYR D 501 " (cutoff:3.500A) removed outlier: 4.685A pdb=" N PHE D 503 " --> pdb=" O ILE D 483 " (cutoff:3.500A) removed outlier: 6.563A pdb=" N ILE D 483 " --> pdb=" O PHE D 503 " (cutoff:3.500A) removed outlier: 4.552A pdb=" N ILE D 505 " --> pdb=" O GLN D 481 " (cutoff:3.500A) removed outlier: 6.615A pdb=" N GLN D 481 " --> pdb=" O ILE D 505 " (cutoff:3.500A) removed outlier: 4.676A pdb=" N PHE D 480 " --> pdb=" O MET D 360 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'D' and resid 391 through 392 Processing sheet with id=AB8, first strand: chain 'D' and resid 628 through 631 removed outlier: 6.806A pdb=" N GLU D 629 " --> pdb=" O ILE D 621 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'E' and resid 54 through 57 Processing sheet with id=AC1, first strand: chain 'E' and resid 128 through 130 removed outlier: 3.558A pdb=" N ARG E 135 " --> pdb=" O ASP E 130 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'E' and resid 179 through 182 Processing sheet with id=AC3, first strand: chain 'E' and resid 223 through 224 removed outlier: 6.642A pdb=" N LEU E 224 " --> pdb=" O ARG E 350 " (cutoff:3.500A) removed outlier: 4.268A pdb=" N LYS E 347 " --> pdb=" O LEU E 403 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'E' and resid 489 through 491 Processing sheet with id=AC5, first strand: chain 'E' and resid 667 through 668 removed outlier: 4.631A pdb=" N ILE E 667 " --> pdb=" O THR F 58 " (cutoff:3.500A) removed outlier: 5.580A pdb=" N THR F 81 " --> pdb=" O MET F 90 " (cutoff:3.500A) 927 hydrogen bonds defined for protein. 2514 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: 3.91 Time building geometry restraints manager: 2.40 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: 6319 1.34 - 1.46: 3423 1.46 - 1.57: 9749 1.57 - 1.69: 0 1.69 - 1.81: 256 Bond restraints: 19747 Sorted by residual: bond pdb=" CG1 ILE B 389 " pdb=" CD1 ILE B 389 " ideal model delta sigma weight residual 1.513 1.472 0.041 3.90e-02 6.57e+02 1.13e+00 bond pdb=" CG GLU E 109 " pdb=" CD GLU E 109 " ideal model delta sigma weight residual 1.516 1.496 0.020 2.50e-02 1.60e+03 6.67e-01 bond pdb=" CB PRO B 272 " pdb=" CG PRO B 272 " ideal model delta sigma weight residual 1.506 1.536 -0.030 3.90e-02 6.57e+02 5.93e-01 bond pdb=" CB PRO A 376 " pdb=" CG PRO A 376 " ideal model delta sigma weight residual 1.492 1.455 0.037 5.00e-02 4.00e+02 5.44e-01 bond pdb=" CB GLU A 449 " pdb=" CG GLU A 449 " ideal model delta sigma weight residual 1.520 1.500 0.020 3.00e-02 1.11e+03 4.64e-01 ... (remaining 19742 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.73: 26309 1.73 - 3.47: 320 3.47 - 5.20: 41 5.20 - 6.93: 10 6.93 - 8.67: 1 Bond angle restraints: 26681 Sorted by residual: angle pdb=" N GLU E 109 " pdb=" CA GLU E 109 " pdb=" CB GLU E 109 " ideal model delta sigma weight residual 110.28 114.78 -4.50 1.55e+00 4.16e-01 8.43e+00 angle pdb=" C GLU D 298 " pdb=" N GLY D 299 " pdb=" CA GLY D 299 " ideal model delta sigma weight residual 121.41 126.79 -5.38 1.96e+00 2.60e-01 7.52e+00 angle pdb=" N GLY D 299 " pdb=" CA GLY D 299 " pdb=" C GLY D 299 " ideal model delta sigma weight residual 113.18 119.56 -6.38 2.37e+00 1.78e-01 7.24e+00 angle pdb=" C ARG B 386 " pdb=" N GLU B 387 " pdb=" CA GLU B 387 " ideal model delta sigma weight residual 120.72 116.27 4.45 1.67e+00 3.59e-01 7.09e+00 angle pdb=" N GLU B 387 " pdb=" CA GLU B 387 " pdb=" CB GLU B 387 " ideal model delta sigma weight residual 110.39 114.55 -4.16 1.66e+00 3.63e-01 6.27e+00 ... (remaining 26676 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.43: 10971 17.43 - 34.87: 885 34.87 - 52.30: 140 52.30 - 69.73: 36 69.73 - 87.17: 16 Dihedral angle restraints: 12048 sinusoidal: 5022 harmonic: 7026 Sorted by residual: dihedral pdb=" CA MET A 523 " pdb=" C MET A 523 " pdb=" N GLU A 524 " pdb=" CA GLU A 524 " ideal model delta harmonic sigma weight residual 180.00 -162.56 -17.44 0 5.00e+00 4.00e-02 1.22e+01 dihedral pdb=" CA TYR D 540 " pdb=" C TYR D 540 " pdb=" N CYS D 541 " pdb=" CA CYS D 541 " ideal model delta harmonic sigma weight residual 180.00 163.13 16.87 0 5.00e+00 4.00e-02 1.14e+01 dihedral pdb=" CA TRP E 613 " pdb=" C TRP E 613 " pdb=" N GLU E 614 " pdb=" CA GLU E 614 " ideal model delta harmonic sigma weight residual 180.00 163.40 16.60 0 5.00e+00 4.00e-02 1.10e+01 ... (remaining 12045 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.035: 1904 0.035 - 0.069: 762 0.069 - 0.104: 174 0.104 - 0.138: 62 0.138 - 0.173: 4 Chirality restraints: 2906 Sorted by residual: chirality pdb=" CB VAL D 450 " pdb=" CA VAL D 450 " pdb=" CG1 VAL D 450 " pdb=" CG2 VAL D 450 " both_signs ideal model delta sigma weight residual False -2.63 -2.46 -0.17 2.00e-01 2.50e+01 7.47e-01 chirality pdb=" CB VAL A 450 " pdb=" CA VAL A 450 " pdb=" CG1 VAL A 450 " pdb=" CG2 VAL A 450 " both_signs ideal model delta sigma weight residual False -2.63 -2.46 -0.17 2.00e-01 2.50e+01 7.43e-01 chirality pdb=" CG LEU D 641 " pdb=" CB LEU D 641 " pdb=" CD1 LEU D 641 " pdb=" CD2 LEU D 641 " both_signs ideal model delta sigma weight residual False -2.59 -2.44 -0.15 2.00e-01 2.50e+01 5.70e-01 ... (remaining 2903 not shown) Planarity restraints: 3441 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C TYR C 111 " 0.037 5.00e-02 4.00e+02 5.60e-02 5.01e+00 pdb=" N PRO C 112 " -0.097 5.00e-02 4.00e+02 pdb=" CA PRO C 112 " 0.029 5.00e-02 4.00e+02 pdb=" CD PRO C 112 " 0.031 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA ALA A 598 " -0.011 2.00e-02 2.50e+03 2.22e-02 4.92e+00 pdb=" C ALA A 598 " 0.038 2.00e-02 2.50e+03 pdb=" O ALA A 598 " -0.014 2.00e-02 2.50e+03 pdb=" N GLU A 599 " -0.013 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG A 583 " -0.179 9.50e-02 1.11e+02 8.05e-02 3.99e+00 pdb=" NE ARG A 583 " 0.011 2.00e-02 2.50e+03 pdb=" CZ ARG A 583 " 0.000 2.00e-02 2.50e+03 pdb=" NH1 ARG A 583 " 0.002 2.00e-02 2.50e+03 pdb=" NH2 ARG A 583 " -0.006 2.00e-02 2.50e+03 ... (remaining 3438 not shown) Histogram of nonbonded interaction distances: 1.82 - 2.44: 54 2.44 - 3.05: 12041 3.05 - 3.67: 28880 3.67 - 4.28: 44741 4.28 - 4.90: 74460 Nonbonded interactions: 160176 Sorted by model distance: nonbonded pdb=" NE2 GLN A 217 " pdb=" OD1 ASN B 58 " model vdw 1.820 3.120 nonbonded pdb=" O THR E 323 " pdb=" NH2 ARG E 334 " model vdw 2.171 3.120 nonbonded pdb=" OH TYR E 129 " pdb=" OD1 ASN E 134 " model vdw 2.194 3.040 nonbonded pdb=" OE1 GLU E 267 " pdb=" NZ LYS E 288 " model vdw 2.209 3.120 nonbonded pdb=" O ILE B 18 " pdb=" OG1 THR B 21 " model vdw 2.231 3.040 ... (remaining 160171 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 203 through 716) selection = chain 'D' } ncs_group { reference = (chain 'B' and (resid 1 through 633 or resid 657 through 670)) selection = (chain 'E' and (resid 1 through 183 or resid 209 through 633 or resid 657 throug \ h 670)) } ncs_group { reference = chain 'C' selection = chain 'F' } 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: 8.040 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: 0.290 Check model and map are aligned: 0.060 Set scattering table: 0.050 Process input model: 18.100 Find NCS groups from input model: 0.260 Set up NCS constraints: 0.020 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: 0.010 Load rotamer database and sin/cos tables:9.480 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 36.320 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8655 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 0.041 19747 Z= 0.102 Angle : 0.494 8.666 26681 Z= 0.255 Chirality : 0.040 0.173 2906 Planarity : 0.004 0.080 3441 Dihedral : 13.141 87.166 7500 Min Nonbonded Distance : 1.820 Molprobity Statistics. All-atom Clashscore : 6.91 Ramachandran Plot: Outliers : 0.08 % Allowed : 3.52 % Favored : 96.40 % Rotamer: Outliers : 0.14 % Allowed : 0.47 % Favored : 99.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.61 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.23 (0.17), residues: 2388 helix: 0.60 (0.16), residues: 1074 sheet: -0.20 (0.32), residues: 243 loop : -0.86 (0.19), residues: 1071 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG E 334 TYR 0.018 0.001 TYR E 253 PHE 0.012 0.001 PHE E 357 TRP 0.032 0.001 TRP E 131 HIS 0.005 0.001 HIS D 713 Details of bonding type rmsd covalent geometry : bond 0.00232 (19747) covalent geometry : angle 0.49364 (26681) hydrogen bonds : bond 0.16657 ( 916) hydrogen bonds : angle 6.43783 ( 2514) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4776 Ramachandran restraints generated. 2388 Oldfield, 0 Emsley, 2388 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4776 Ramachandran restraints generated. 2388 Oldfield, 0 Emsley, 2388 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 257 residues out of total 2142 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 254 time to evaluate : 0.656 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: D 206 GLU cc_start: 0.7562 (mm-30) cc_final: 0.6996 (mm-30) outliers start: 3 outliers final: 1 residues processed: 257 average time/residue: 0.8197 time to fit residues: 229.6284 Evaluate side-chains 176 residues out of total 2142 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 175 time to evaluate : 0.702 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 90 MET Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 216 optimal weight: 1.9990 chunk 98 optimal weight: 0.0270 chunk 194 optimal weight: 2.9990 chunk 227 optimal weight: 3.9990 chunk 107 optimal weight: 4.9990 chunk 10 optimal weight: 2.9990 chunk 66 optimal weight: 8.9990 chunk 130 optimal weight: 2.9990 chunk 124 optimal weight: 1.9990 chunk 103 optimal weight: 3.9990 chunk 235 optimal weight: 0.4980 overall best weight: 1.5044 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 217 GLN B 367 GLN ** B 425 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 460 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 350 ASN E 367 GLN ** E 425 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 428 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 460 GLN F 82 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3428 r_free = 0.3428 target = 0.062215 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2835 r_free = 0.2835 target = 0.041754 restraints weight = 66536.492| |-----------------------------------------------------------------------------| r_work (start): 0.2788 rms_B_bonded: 3.18 r_work: 0.2644 rms_B_bonded: 3.42 restraints_weight: 0.5000 r_work (final): 0.2644 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8923 moved from start: 0.1620 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 19747 Z= 0.181 Angle : 0.590 8.815 26681 Z= 0.303 Chirality : 0.042 0.241 2906 Planarity : 0.005 0.083 3441 Dihedral : 4.050 47.938 2613 Min Nonbonded Distance : 2.548 Molprobity Statistics. All-atom Clashscore : 6.31 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.14 % Favored : 96.82 % Rotamer: Outliers : 1.35 % Allowed : 6.96 % Favored : 91.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.61 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.30 (0.17), residues: 2388 helix: 1.07 (0.16), residues: 1090 sheet: 0.08 (0.32), residues: 240 loop : -0.64 (0.19), residues: 1058 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG A 269 TYR 0.013 0.001 TYR E 253 PHE 0.023 0.001 PHE B 166 TRP 0.017 0.001 TRP E 580 HIS 0.003 0.001 HIS D 713 Details of bonding type rmsd covalent geometry : bond 0.00418 (19747) covalent geometry : angle 0.59029 (26681) hydrogen bonds : bond 0.04382 ( 916) hydrogen bonds : angle 4.84909 ( 2514) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4776 Ramachandran restraints generated. 2388 Oldfield, 0 Emsley, 2388 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4776 Ramachandran restraints generated. 2388 Oldfield, 0 Emsley, 2388 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 205 residues out of total 2142 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 176 time to evaluate : 0.690 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: A 328 LYS cc_start: 0.9300 (OUTLIER) cc_final: 0.8995 (mtpp) REVERT: B 40 MET cc_start: 0.9122 (mtp) cc_final: 0.8919 (ttm) REVERT: B 116 GLN cc_start: 0.8870 (tp40) cc_final: 0.8598 (tm-30) REVERT: B 215 ARG cc_start: 0.8627 (mtp85) cc_final: 0.8288 (ttt180) REVERT: B 356 MET cc_start: 0.9167 (ttt) cc_final: 0.8815 (tpt) REVERT: B 430 LYS cc_start: 0.9159 (OUTLIER) cc_final: 0.8687 (ptpt) REVERT: B 507 MET cc_start: 0.8543 (OUTLIER) cc_final: 0.8034 (mpp) REVERT: C 69 GLU cc_start: 0.8876 (OUTLIER) cc_final: 0.8535 (tp30) REVERT: C 116 LYS cc_start: 0.8639 (ttmt) cc_final: 0.8151 (pptt) REVERT: E 111 MET cc_start: 0.9370 (mtm) cc_final: 0.9099 (mtt) REVERT: E 113 ILE cc_start: 0.9367 (tp) cc_final: 0.9051 (pp) REVERT: E 348 MET cc_start: 0.8642 (mmm) cc_final: 0.8247 (mmm) REVERT: E 353 LYS cc_start: 0.8990 (OUTLIER) cc_final: 0.8642 (pptt) REVERT: E 372 MET cc_start: 0.8965 (mmm) cc_final: 0.8542 (tpt) outliers start: 29 outliers final: 8 residues processed: 186 average time/residue: 0.6978 time to fit residues: 142.6744 Evaluate side-chains 184 residues out of total 2142 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 171 time to evaluate : 0.757 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 328 LYS Chi-restraints excluded: chain A residue 393 TYR Chi-restraints excluded: chain B residue 1 MET Chi-restraints excluded: chain B residue 219 ILE Chi-restraints excluded: chain B residue 373 LEU Chi-restraints excluded: chain B residue 387 GLU Chi-restraints excluded: chain B residue 430 LYS Chi-restraints excluded: chain B residue 507 MET Chi-restraints excluded: chain B residue 534 MET Chi-restraints excluded: chain C residue 69 GLU Chi-restraints excluded: chain C residue 90 MET Chi-restraints excluded: chain E residue 120 ASP Chi-restraints excluded: chain E residue 353 LYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 109 optimal weight: 0.4980 chunk 181 optimal weight: 5.9990 chunk 203 optimal weight: 4.9990 chunk 233 optimal weight: 0.8980 chunk 60 optimal weight: 6.9990 chunk 45 optimal weight: 0.8980 chunk 185 optimal weight: 1.9990 chunk 88 optimal weight: 3.9990 chunk 65 optimal weight: 1.9990 chunk 194 optimal weight: 3.9990 chunk 140 optimal weight: 3.9990 overall best weight: 1.2584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 47 HIS ** B 425 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 460 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 42 ASN E 116 GLN ** E 425 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 42 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3427 r_free = 0.3427 target = 0.062009 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2833 r_free = 0.2833 target = 0.041569 restraints weight = 67100.416| |-----------------------------------------------------------------------------| r_work (start): 0.2775 rms_B_bonded: 3.19 r_work: 0.2630 rms_B_bonded: 3.43 restraints_weight: 0.5000 r_work (final): 0.2630 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8929 moved from start: 0.1874 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 19747 Z= 0.153 Angle : 0.549 9.286 26681 Z= 0.278 Chirality : 0.041 0.233 2906 Planarity : 0.004 0.076 3441 Dihedral : 3.994 45.560 2613 Min Nonbonded Distance : 2.518 Molprobity Statistics. All-atom Clashscore : 6.13 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.18 % Favored : 96.78 % Rotamer: Outliers : 1.73 % Allowed : 8.26 % Favored : 90.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.61 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.42 (0.18), residues: 2388 helix: 1.20 (0.16), residues: 1091 sheet: 0.15 (0.32), residues: 249 loop : -0.63 (0.20), residues: 1048 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 269 TYR 0.010 0.001 TYR A 305 PHE 0.011 0.001 PHE E 333 TRP 0.014 0.001 TRP E 580 HIS 0.003 0.000 HIS D 713 Details of bonding type rmsd covalent geometry : bond 0.00354 (19747) covalent geometry : angle 0.54887 (26681) hydrogen bonds : bond 0.03913 ( 916) hydrogen bonds : angle 4.62705 ( 2514) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4776 Ramachandran restraints generated. 2388 Oldfield, 0 Emsley, 2388 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4776 Ramachandran restraints generated. 2388 Oldfield, 0 Emsley, 2388 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 211 residues out of total 2142 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 174 time to evaluate : 0.810 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 328 LYS cc_start: 0.9306 (OUTLIER) cc_final: 0.9012 (mtpp) REVERT: B 40 MET cc_start: 0.9169 (mtp) cc_final: 0.8911 (ptm) REVERT: B 116 GLN cc_start: 0.8899 (tp40) cc_final: 0.8634 (tm-30) REVERT: B 356 MET cc_start: 0.9200 (ttt) cc_final: 0.8856 (tpt) REVERT: B 409 MET cc_start: 0.7018 (OUTLIER) cc_final: 0.6710 (ptt) REVERT: C 69 GLU cc_start: 0.8930 (OUTLIER) cc_final: 0.8432 (tp30) REVERT: C 116 LYS cc_start: 0.8633 (ttmt) cc_final: 0.8129 (pptt) REVERT: D 378 LYS cc_start: 0.9488 (mmmm) cc_final: 0.9047 (tppt) REVERT: D 424 GLU cc_start: 0.7943 (OUTLIER) cc_final: 0.7675 (mp0) REVERT: E 113 ILE cc_start: 0.9372 (tp) cc_final: 0.9097 (pp) REVERT: E 348 MET cc_start: 0.8818 (OUTLIER) cc_final: 0.8397 (mmm) REVERT: E 353 LYS cc_start: 0.9100 (OUTLIER) cc_final: 0.8679 (pptt) REVERT: E 372 MET cc_start: 0.8966 (mmm) cc_final: 0.8559 (tpt) REVERT: F 69 GLU cc_start: 0.8709 (tt0) cc_final: 0.8105 (tp30) outliers start: 37 outliers final: 6 residues processed: 192 average time/residue: 0.6863 time to fit residues: 145.9525 Evaluate side-chains 175 residues out of total 2142 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 163 time to evaluate : 0.720 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 328 LYS Chi-restraints excluded: chain A residue 360 MET Chi-restraints excluded: chain A residue 450 VAL Chi-restraints excluded: chain B residue 387 GLU Chi-restraints excluded: chain B residue 409 MET Chi-restraints excluded: chain C residue 69 GLU Chi-restraints excluded: chain D residue 379 VAL Chi-restraints excluded: chain D residue 424 GLU Chi-restraints excluded: chain D residue 450 VAL Chi-restraints excluded: chain D residue 549 LEU Chi-restraints excluded: chain E residue 348 MET Chi-restraints excluded: chain E residue 353 LYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 169 optimal weight: 4.9990 chunk 203 optimal weight: 5.9990 chunk 44 optimal weight: 2.9990 chunk 74 optimal weight: 7.9990 chunk 119 optimal weight: 1.9990 chunk 21 optimal weight: 4.9990 chunk 36 optimal weight: 3.9990 chunk 145 optimal weight: 1.9990 chunk 48 optimal weight: 0.9980 chunk 89 optimal weight: 0.7980 chunk 214 optimal weight: 0.7980 overall best weight: 1.3184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 312 ASN ** B 425 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 460 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 425 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 42 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3419 r_free = 0.3419 target = 0.061525 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.2828 r_free = 0.2828 target = 0.041331 restraints weight = 66795.890| |-----------------------------------------------------------------------------| r_work (start): 0.2769 rms_B_bonded: 3.16 r_work: 0.2622 rms_B_bonded: 3.43 restraints_weight: 0.5000 r_work (final): 0.2622 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8941 moved from start: 0.2115 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 19747 Z= 0.154 Angle : 0.556 9.229 26681 Z= 0.278 Chirality : 0.041 0.227 2906 Planarity : 0.004 0.074 3441 Dihedral : 3.879 18.046 2610 Min Nonbonded Distance : 2.541 Molprobity Statistics. All-atom Clashscore : 6.23 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.14 % Favored : 96.82 % Rotamer: Outliers : 1.45 % Allowed : 9.80 % Favored : 88.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.61 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.51 (0.18), residues: 2388 helix: 1.28 (0.16), residues: 1099 sheet: 0.23 (0.33), residues: 251 loop : -0.62 (0.20), residues: 1038 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 215 TYR 0.012 0.001 TYR A 305 PHE 0.028 0.001 PHE B 166 TRP 0.013 0.001 TRP E 580 HIS 0.004 0.001 HIS A 510 Details of bonding type rmsd covalent geometry : bond 0.00357 (19747) covalent geometry : angle 0.55595 (26681) hydrogen bonds : bond 0.03729 ( 916) hydrogen bonds : angle 4.50527 ( 2514) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4776 Ramachandran restraints generated. 2388 Oldfield, 0 Emsley, 2388 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4776 Ramachandran restraints generated. 2388 Oldfield, 0 Emsley, 2388 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 200 residues out of total 2142 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 169 time to evaluate : 0.738 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 328 LYS cc_start: 0.9326 (OUTLIER) cc_final: 0.9029 (mtpp) REVERT: A 374 MET cc_start: 0.9158 (tpp) cc_final: 0.8725 (mpp) REVERT: B 40 MET cc_start: 0.9156 (mtp) cc_final: 0.8901 (ptm) REVERT: B 116 GLN cc_start: 0.8895 (tp40) cc_final: 0.8635 (tm-30) REVERT: B 356 MET cc_start: 0.9218 (ttt) cc_final: 0.8826 (tpt) REVERT: B 372 MET cc_start: 0.9218 (tpp) cc_final: 0.8946 (tmm) REVERT: B 409 MET cc_start: 0.7044 (ptt) cc_final: 0.6597 (ptt) REVERT: B 430 LYS cc_start: 0.9159 (OUTLIER) cc_final: 0.8752 (ptpt) REVERT: C 61 LYS cc_start: 0.8961 (mmtm) cc_final: 0.8688 (mmtp) REVERT: C 69 GLU cc_start: 0.8963 (OUTLIER) cc_final: 0.8465 (tp30) REVERT: C 116 LYS cc_start: 0.8628 (ttmt) cc_final: 0.8126 (pptt) REVERT: C 120 GLU cc_start: 0.7391 (tt0) cc_final: 0.7019 (tt0) REVERT: D 378 LYS cc_start: 0.9487 (mmmm) cc_final: 0.9168 (tppt) REVERT: E 290 MET cc_start: 0.8931 (mmm) cc_final: 0.8674 (mmm) REVERT: E 348 MET cc_start: 0.8924 (OUTLIER) cc_final: 0.8500 (mmm) REVERT: E 353 LYS cc_start: 0.9113 (OUTLIER) cc_final: 0.8733 (pptt) REVERT: E 372 MET cc_start: 0.9022 (mmm) cc_final: 0.8535 (tpp) REVERT: F 69 GLU cc_start: 0.8736 (tt0) cc_final: 0.8225 (tp30) outliers start: 31 outliers final: 9 residues processed: 188 average time/residue: 0.7026 time to fit residues: 146.1019 Evaluate side-chains 178 residues out of total 2142 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 164 time to evaluate : 0.708 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 328 LYS Chi-restraints excluded: chain A residue 450 VAL Chi-restraints excluded: chain B residue 302 ILE Chi-restraints excluded: chain B residue 387 GLU Chi-restraints excluded: chain B residue 430 LYS Chi-restraints excluded: chain C residue 69 GLU Chi-restraints excluded: chain D residue 450 VAL Chi-restraints excluded: chain D residue 548 MET Chi-restraints excluded: chain D residue 549 LEU Chi-restraints excluded: chain E residue 119 VAL Chi-restraints excluded: chain E residue 120 ASP Chi-restraints excluded: chain E residue 348 MET Chi-restraints excluded: chain E residue 353 LYS Chi-restraints excluded: chain F residue 91 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 74 optimal weight: 7.9990 chunk 181 optimal weight: 0.9990 chunk 126 optimal weight: 0.9980 chunk 23 optimal weight: 0.7980 chunk 173 optimal weight: 0.7980 chunk 56 optimal weight: 7.9990 chunk 202 optimal weight: 5.9990 chunk 80 optimal weight: 1.9990 chunk 25 optimal weight: 4.9990 chunk 22 optimal weight: 5.9990 chunk 195 optimal weight: 0.1980 overall best weight: 0.7582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 136 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 425 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 460 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 42 ASN ** E 425 ASN ** 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 = 0.3430 r_free = 0.3430 target = 0.061994 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2844 r_free = 0.2844 target = 0.041750 restraints weight = 66636.938| |-----------------------------------------------------------------------------| r_work (start): 0.2796 rms_B_bonded: 3.18 r_work: 0.2652 rms_B_bonded: 3.43 restraints_weight: 0.5000 r_work (final): 0.2652 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8920 moved from start: 0.2255 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 19747 Z= 0.116 Angle : 0.553 11.659 26681 Z= 0.272 Chirality : 0.040 0.318 2906 Planarity : 0.004 0.073 3441 Dihedral : 3.823 19.025 2610 Min Nonbonded Distance : 2.510 Molprobity Statistics. All-atom Clashscore : 6.26 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.06 % Favored : 96.90 % Rotamer: Outliers : 1.35 % Allowed : 11.11 % Favored : 87.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.61 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.55 (0.18), residues: 2388 helix: 1.31 (0.16), residues: 1101 sheet: 0.26 (0.33), residues: 241 loop : -0.58 (0.20), residues: 1046 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 215 TYR 0.011 0.001 TYR D 305 PHE 0.022 0.001 PHE B 357 TRP 0.012 0.001 TRP A 577 HIS 0.003 0.000 HIS D 713 Details of bonding type rmsd covalent geometry : bond 0.00267 (19747) covalent geometry : angle 0.55264 (26681) hydrogen bonds : bond 0.03487 ( 916) hydrogen bonds : angle 4.42073 ( 2514) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4776 Ramachandran restraints generated. 2388 Oldfield, 0 Emsley, 2388 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4776 Ramachandran restraints generated. 2388 Oldfield, 0 Emsley, 2388 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 196 residues out of total 2142 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 167 time to evaluate : 0.806 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 328 LYS cc_start: 0.9310 (OUTLIER) cc_final: 0.9013 (mtpp) REVERT: A 374 MET cc_start: 0.9161 (tpp) cc_final: 0.8663 (mpp) REVERT: B 40 MET cc_start: 0.9145 (mtp) cc_final: 0.8872 (ptm) REVERT: B 116 GLN cc_start: 0.8858 (tp40) cc_final: 0.8637 (tm-30) REVERT: B 126 ARG cc_start: 0.8297 (mtt180) cc_final: 0.7641 (mmm160) REVERT: B 356 MET cc_start: 0.9218 (ttt) cc_final: 0.8424 (tpt) REVERT: B 408 MET cc_start: 0.7738 (ppp) cc_final: 0.7534 (ppp) REVERT: B 409 MET cc_start: 0.7226 (OUTLIER) cc_final: 0.6498 (ptt) REVERT: B 411 MET cc_start: 0.9084 (mmm) cc_final: 0.8769 (mmm) REVERT: B 430 LYS cc_start: 0.9162 (OUTLIER) cc_final: 0.8748 (ptpt) REVERT: C 60 ASP cc_start: 0.8415 (t0) cc_final: 0.8200 (p0) REVERT: C 62 ARG cc_start: 0.8578 (ptt-90) cc_final: 0.8190 (ptt-90) REVERT: C 69 GLU cc_start: 0.8953 (OUTLIER) cc_final: 0.8455 (tp30) REVERT: D 211 MET cc_start: 0.9130 (OUTLIER) cc_final: 0.8901 (mtt) REVERT: D 378 LYS cc_start: 0.9501 (mmmm) cc_final: 0.9203 (tppt) REVERT: E 348 MET cc_start: 0.8943 (OUTLIER) cc_final: 0.8525 (mmm) REVERT: E 372 MET cc_start: 0.9016 (mmm) cc_final: 0.8539 (tpp) REVERT: E 407 MET cc_start: 0.8163 (mtp) cc_final: 0.7955 (mmt) REVERT: F 69 GLU cc_start: 0.8757 (tt0) cc_final: 0.8243 (tp30) REVERT: F 116 LYS cc_start: 0.7757 (tppt) cc_final: 0.7120 (pptt) outliers start: 29 outliers final: 9 residues processed: 182 average time/residue: 0.6945 time to fit residues: 140.2761 Evaluate side-chains 178 residues out of total 2142 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 163 time to evaluate : 0.534 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 311 MET Chi-restraints excluded: chain A residue 328 LYS Chi-restraints excluded: chain A residue 450 VAL Chi-restraints excluded: chain B residue 1 MET Chi-restraints excluded: chain B residue 387 GLU Chi-restraints excluded: chain B residue 409 MET Chi-restraints excluded: chain B residue 430 LYS Chi-restraints excluded: chain C residue 69 GLU Chi-restraints excluded: chain C residue 80 LYS Chi-restraints excluded: chain D residue 211 MET Chi-restraints excluded: chain D residue 379 VAL Chi-restraints excluded: chain D residue 549 LEU Chi-restraints excluded: chain E residue 119 VAL Chi-restraints excluded: chain E residue 348 MET Chi-restraints excluded: chain F residue 91 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 40 optimal weight: 0.0070 chunk 2 optimal weight: 3.9990 chunk 73 optimal weight: 3.9990 chunk 19 optimal weight: 5.9990 chunk 127 optimal weight: 2.9990 chunk 111 optimal weight: 0.0570 chunk 41 optimal weight: 0.8980 chunk 131 optimal weight: 3.9990 chunk 86 optimal weight: 1.9990 chunk 4 optimal weight: 0.8980 chunk 151 optimal weight: 0.8980 overall best weight: 0.5516 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 425 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 460 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 310 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 425 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 42 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3442 r_free = 0.3442 target = 0.062484 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2860 r_free = 0.2860 target = 0.042212 restraints weight = 66247.441| |-----------------------------------------------------------------------------| r_work (start): 0.2814 rms_B_bonded: 3.19 r_work: 0.2670 rms_B_bonded: 3.45 restraints_weight: 0.5000 r_work (final): 0.2670 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8911 moved from start: 0.2377 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 19747 Z= 0.102 Angle : 0.544 12.014 26681 Z= 0.266 Chirality : 0.039 0.266 2906 Planarity : 0.004 0.073 3441 Dihedral : 3.727 19.987 2610 Min Nonbonded Distance : 2.526 Molprobity Statistics. All-atom Clashscore : 6.05 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.22 % Favored : 96.73 % Rotamer: Outliers : 1.21 % Allowed : 11.86 % Favored : 86.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.61 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.69 (0.18), residues: 2388 helix: 1.42 (0.16), residues: 1097 sheet: 0.31 (0.33), residues: 243 loop : -0.49 (0.20), residues: 1048 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG E 126 TYR 0.011 0.001 TYR A 305 PHE 0.031 0.001 PHE B 166 TRP 0.013 0.001 TRP A 577 HIS 0.003 0.000 HIS B 47 Details of bonding type rmsd covalent geometry : bond 0.00234 (19747) covalent geometry : angle 0.54387 (26681) hydrogen bonds : bond 0.03264 ( 916) hydrogen bonds : angle 4.30688 ( 2514) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4776 Ramachandran restraints generated. 2388 Oldfield, 0 Emsley, 2388 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4776 Ramachandran restraints generated. 2388 Oldfield, 0 Emsley, 2388 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 193 residues out of total 2142 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 167 time to evaluate : 0.819 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 328 LYS cc_start: 0.9288 (OUTLIER) cc_final: 0.8985 (mtpp) REVERT: A 374 MET cc_start: 0.9226 (tpp) cc_final: 0.8615 (mpp) REVERT: B 40 MET cc_start: 0.9119 (mtp) cc_final: 0.8831 (ptm) REVERT: B 116 GLN cc_start: 0.8850 (tp40) cc_final: 0.8632 (tm-30) REVERT: B 356 MET cc_start: 0.9171 (ttt) cc_final: 0.8857 (tpt) REVERT: B 409 MET cc_start: 0.7172 (OUTLIER) cc_final: 0.6671 (ptt) REVERT: B 411 MET cc_start: 0.9084 (mmm) cc_final: 0.8792 (mmm) REVERT: C 69 GLU cc_start: 0.9001 (OUTLIER) cc_final: 0.8531 (tp30) REVERT: D 211 MET cc_start: 0.9145 (OUTLIER) cc_final: 0.8943 (mtt) REVERT: D 378 LYS cc_start: 0.9490 (mmmm) cc_final: 0.9223 (tppt) REVERT: E 290 MET cc_start: 0.8884 (mmm) cc_final: 0.8558 (mmm) REVERT: E 348 MET cc_start: 0.8908 (OUTLIER) cc_final: 0.8500 (mmm) REVERT: E 353 LYS cc_start: 0.9162 (OUTLIER) cc_final: 0.8786 (pptt) REVERT: E 372 MET cc_start: 0.9027 (mmm) cc_final: 0.8595 (tpp) REVERT: E 409 MET cc_start: 0.7105 (ppp) cc_final: 0.6794 (ppp) REVERT: F 69 GLU cc_start: 0.8759 (tt0) cc_final: 0.8284 (tp30) REVERT: F 116 LYS cc_start: 0.7817 (tppt) cc_final: 0.7199 (pptt) outliers start: 26 outliers final: 12 residues processed: 183 average time/residue: 0.7132 time to fit residues: 144.7273 Evaluate side-chains 180 residues out of total 2142 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 162 time to evaluate : 0.740 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 328 LYS Chi-restraints excluded: chain A residue 450 VAL Chi-restraints excluded: chain B residue 219 ILE Chi-restraints excluded: chain B residue 302 ILE Chi-restraints excluded: chain B residue 387 GLU Chi-restraints excluded: chain B residue 409 MET Chi-restraints excluded: chain C residue 69 GLU Chi-restraints excluded: chain C residue 80 LYS Chi-restraints excluded: chain D residue 211 MET Chi-restraints excluded: chain D residue 450 VAL Chi-restraints excluded: chain D residue 548 MET Chi-restraints excluded: chain D residue 549 LEU Chi-restraints excluded: chain E residue 120 ASP Chi-restraints excluded: chain E residue 156 THR Chi-restraints excluded: chain E residue 302 ILE Chi-restraints excluded: chain E residue 348 MET Chi-restraints excluded: chain E residue 353 LYS Chi-restraints excluded: chain F residue 91 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 140 optimal weight: 1.9990 chunk 199 optimal weight: 0.6980 chunk 116 optimal weight: 2.9990 chunk 108 optimal weight: 0.2980 chunk 54 optimal weight: 0.2980 chunk 223 optimal weight: 0.9980 chunk 81 optimal weight: 0.3980 chunk 152 optimal weight: 1.9990 chunk 110 optimal weight: 6.9990 chunk 203 optimal weight: 0.9980 chunk 172 optimal weight: 1.9990 overall best weight: 0.5380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 425 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 460 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 425 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3444 r_free = 0.3444 target = 0.062564 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2863 r_free = 0.2863 target = 0.042277 restraints weight = 66584.498| |-----------------------------------------------------------------------------| r_work (start): 0.2812 rms_B_bonded: 3.20 r_work: 0.2669 rms_B_bonded: 3.44 restraints_weight: 0.5000 r_work (final): 0.2669 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8907 moved from start: 0.2445 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.048 19747 Z= 0.103 Angle : 0.547 10.537 26681 Z= 0.267 Chirality : 0.039 0.228 2906 Planarity : 0.004 0.071 3441 Dihedral : 3.705 20.792 2610 Min Nonbonded Distance : 2.455 Molprobity Statistics. All-atom Clashscore : 5.92 Ramachandran Plot: Outliers : 0.04 % Allowed : 2.89 % Favored : 97.07 % Rotamer: Outliers : 1.49 % Allowed : 11.90 % Favored : 86.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.61 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.69 (0.18), residues: 2388 helix: 1.43 (0.16), residues: 1098 sheet: 0.27 (0.34), residues: 234 loop : -0.49 (0.20), residues: 1056 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.000 ARG E 126 TYR 0.010 0.001 TYR A 305 PHE 0.015 0.001 PHE B 357 TRP 0.012 0.001 TRP A 577 HIS 0.003 0.000 HIS B 47 Details of bonding type rmsd covalent geometry : bond 0.00237 (19747) covalent geometry : angle 0.54692 (26681) hydrogen bonds : bond 0.03213 ( 916) hydrogen bonds : angle 4.26584 ( 2514) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4776 Ramachandran restraints generated. 2388 Oldfield, 0 Emsley, 2388 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4776 Ramachandran restraints generated. 2388 Oldfield, 0 Emsley, 2388 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 196 residues out of total 2142 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 164 time to evaluate : 0.738 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: A 328 LYS cc_start: 0.9277 (OUTLIER) cc_final: 0.8971 (mtpp) REVERT: A 374 MET cc_start: 0.9217 (tpp) cc_final: 0.8578 (mpp) REVERT: B 40 MET cc_start: 0.9147 (mtp) cc_final: 0.8828 (ptm) REVERT: B 116 GLN cc_start: 0.8857 (tp40) cc_final: 0.8637 (tm-30) REVERT: B 126 ARG cc_start: 0.8323 (mtt180) cc_final: 0.7727 (mmm160) REVERT: B 356 MET cc_start: 0.9161 (ttt) cc_final: 0.8893 (tpt) REVERT: B 408 MET cc_start: 0.7815 (ppp) cc_final: 0.7604 (ppp) REVERT: B 409 MET cc_start: 0.7398 (OUTLIER) cc_final: 0.6601 (ptt) REVERT: B 411 MET cc_start: 0.9048 (mmm) cc_final: 0.8695 (mmm) REVERT: B 430 LYS cc_start: 0.9176 (OUTLIER) cc_final: 0.8830 (ptpt) REVERT: C 61 LYS cc_start: 0.8884 (mmtm) cc_final: 0.8487 (mptm) REVERT: C 66 MET cc_start: 0.9059 (mtm) cc_final: 0.8609 (mtm) REVERT: C 69 GLU cc_start: 0.9015 (OUTLIER) cc_final: 0.8537 (tp30) REVERT: D 378 LYS cc_start: 0.9472 (mmmm) cc_final: 0.9240 (tppt) REVERT: E 290 MET cc_start: 0.8946 (mmm) cc_final: 0.8634 (mmm) REVERT: E 353 LYS cc_start: 0.9172 (OUTLIER) cc_final: 0.8810 (pptt) REVERT: E 372 MET cc_start: 0.9024 (mmm) cc_final: 0.8605 (tpp) REVERT: F 69 GLU cc_start: 0.8765 (tt0) cc_final: 0.8288 (tp30) outliers start: 32 outliers final: 13 residues processed: 183 average time/residue: 0.6724 time to fit residues: 137.1591 Evaluate side-chains 181 residues out of total 2142 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 163 time to evaluate : 0.748 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 328 LYS Chi-restraints excluded: chain A residue 354 ILE Chi-restraints excluded: chain A residue 450 VAL Chi-restraints excluded: chain B residue 219 ILE Chi-restraints excluded: chain B residue 302 ILE Chi-restraints excluded: chain B residue 387 GLU Chi-restraints excluded: chain B residue 409 MET Chi-restraints excluded: chain B residue 430 LYS Chi-restraints excluded: chain B residue 628 MET Chi-restraints excluded: chain C residue 69 GLU Chi-restraints excluded: chain D residue 450 VAL Chi-restraints excluded: chain D residue 549 LEU Chi-restraints excluded: chain E residue 156 THR Chi-restraints excluded: chain E residue 302 ILE Chi-restraints excluded: chain E residue 348 MET Chi-restraints excluded: chain E residue 353 LYS Chi-restraints excluded: chain E residue 592 SER Chi-restraints excluded: chain F residue 91 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 48 optimal weight: 0.9990 chunk 190 optimal weight: 3.9990 chunk 72 optimal weight: 0.9980 chunk 133 optimal weight: 0.8980 chunk 89 optimal weight: 4.9990 chunk 215 optimal weight: 0.4980 chunk 146 optimal weight: 2.9990 chunk 220 optimal weight: 1.9990 chunk 173 optimal weight: 0.8980 chunk 37 optimal weight: 1.9990 chunk 153 optimal weight: 0.9980 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 425 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 460 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 425 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 42 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3436 r_free = 0.3436 target = 0.062175 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.2858 r_free = 0.2858 target = 0.042007 restraints weight = 66771.705| |-----------------------------------------------------------------------------| r_work (start): 0.2807 rms_B_bonded: 3.17 r_work: 0.2662 rms_B_bonded: 3.44 restraints_weight: 0.5000 r_work (final): 0.2662 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8919 moved from start: 0.2494 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 19747 Z= 0.121 Angle : 0.568 12.962 26681 Z= 0.276 Chirality : 0.040 0.182 2906 Planarity : 0.004 0.069 3441 Dihedral : 3.724 20.768 2610 Min Nonbonded Distance : 2.417 Molprobity Statistics. All-atom Clashscore : 6.00 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.06 % Favored : 96.90 % Rotamer: Outliers : 1.21 % Allowed : 12.51 % Favored : 86.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.61 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.72 (0.18), residues: 2388 helix: 1.45 (0.16), residues: 1098 sheet: 0.26 (0.33), residues: 243 loop : -0.47 (0.20), residues: 1047 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG E 126 TYR 0.013 0.001 TYR D 305 PHE 0.043 0.001 PHE B 166 TRP 0.011 0.001 TRP E 580 HIS 0.002 0.000 HIS B 47 Details of bonding type rmsd covalent geometry : bond 0.00282 (19747) covalent geometry : angle 0.56828 (26681) hydrogen bonds : bond 0.03298 ( 916) hydrogen bonds : angle 4.25956 ( 2514) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4776 Ramachandran restraints generated. 2388 Oldfield, 0 Emsley, 2388 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4776 Ramachandran restraints generated. 2388 Oldfield, 0 Emsley, 2388 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 191 residues out of total 2142 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 165 time to evaluate : 0.755 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 211 MET cc_start: 0.8873 (pmm) cc_final: 0.8656 (pmm) REVERT: A 328 LYS cc_start: 0.9279 (OUTLIER) cc_final: 0.8973 (mtpp) REVERT: B 40 MET cc_start: 0.9166 (mtp) cc_final: 0.8828 (ptm) REVERT: B 116 GLN cc_start: 0.8859 (tp40) cc_final: 0.8644 (tm-30) REVERT: B 126 ARG cc_start: 0.8355 (mtt180) cc_final: 0.7715 (mmm160) REVERT: B 246 MET cc_start: 0.7708 (tpp) cc_final: 0.7507 (mmm) REVERT: B 356 MET cc_start: 0.9123 (ttt) cc_final: 0.8792 (tpt) REVERT: B 409 MET cc_start: 0.7278 (OUTLIER) cc_final: 0.6572 (ptt) REVERT: B 411 MET cc_start: 0.9039 (mmm) cc_final: 0.8747 (mmm) REVERT: B 430 LYS cc_start: 0.9173 (OUTLIER) cc_final: 0.8838 (ptpt) REVERT: C 69 GLU cc_start: 0.9020 (OUTLIER) cc_final: 0.8537 (tp30) REVERT: D 378 LYS cc_start: 0.9467 (mmmm) cc_final: 0.9256 (tppt) REVERT: E 353 LYS cc_start: 0.9174 (OUTLIER) cc_final: 0.8836 (pptt) REVERT: E 372 MET cc_start: 0.9041 (mmm) cc_final: 0.8616 (tpp) REVERT: F 69 GLU cc_start: 0.8756 (tt0) cc_final: 0.8292 (tp30) REVERT: F 116 LYS cc_start: 0.7582 (tppt) cc_final: 0.6916 (pptt) outliers start: 26 outliers final: 14 residues processed: 181 average time/residue: 0.7054 time to fit residues: 142.3366 Evaluate side-chains 179 residues out of total 2142 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 160 time to evaluate : 0.817 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 328 LYS Chi-restraints excluded: chain A residue 450 VAL Chi-restraints excluded: chain B residue 219 ILE Chi-restraints excluded: chain B residue 302 ILE Chi-restraints excluded: chain B residue 387 GLU Chi-restraints excluded: chain B residue 409 MET Chi-restraints excluded: chain B residue 430 LYS Chi-restraints excluded: chain B residue 628 MET Chi-restraints excluded: chain C residue 69 GLU Chi-restraints excluded: chain D residue 450 VAL Chi-restraints excluded: chain D residue 549 LEU Chi-restraints excluded: chain E residue 119 VAL Chi-restraints excluded: chain E residue 120 ASP Chi-restraints excluded: chain E residue 156 THR Chi-restraints excluded: chain E residue 302 ILE Chi-restraints excluded: chain E residue 348 MET Chi-restraints excluded: chain E residue 353 LYS Chi-restraints excluded: chain E residue 592 SER Chi-restraints excluded: chain F residue 91 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 110 optimal weight: 4.9990 chunk 6 optimal weight: 0.9990 chunk 90 optimal weight: 0.7980 chunk 200 optimal weight: 6.9990 chunk 134 optimal weight: 3.9990 chunk 161 optimal weight: 0.7980 chunk 197 optimal weight: 4.9990 chunk 182 optimal weight: 3.9990 chunk 234 optimal weight: 0.7980 chunk 41 optimal weight: 0.5980 chunk 27 optimal weight: 3.9990 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 425 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 460 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 42 ASN ** E 425 ASN ** 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 = 0.3436 r_free = 0.3436 target = 0.062184 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2861 r_free = 0.2861 target = 0.042087 restraints weight = 66454.835| |-----------------------------------------------------------------------------| r_work (start): 0.2809 rms_B_bonded: 3.16 r_work: 0.2664 rms_B_bonded: 3.44 restraints_weight: 0.5000 r_work (final): 0.2664 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8917 moved from start: 0.2542 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 19747 Z= 0.119 Angle : 0.588 12.563 26681 Z= 0.283 Chirality : 0.040 0.283 2906 Planarity : 0.004 0.069 3441 Dihedral : 3.769 24.157 2610 Min Nonbonded Distance : 2.412 Molprobity Statistics. All-atom Clashscore : 6.44 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.02 % Favored : 96.94 % Rotamer: Outliers : 1.17 % Allowed : 13.03 % Favored : 85.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.61 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.65 (0.18), residues: 2388 helix: 1.41 (0.16), residues: 1105 sheet: 0.15 (0.33), residues: 236 loop : -0.51 (0.20), residues: 1047 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG E 126 TYR 0.012 0.001 TYR D 305 PHE 0.037 0.001 PHE B 166 TRP 0.011 0.001 TRP A 577 HIS 0.002 0.000 HIS A 713 Details of bonding type rmsd covalent geometry : bond 0.00275 (19747) covalent geometry : angle 0.58774 (26681) hydrogen bonds : bond 0.03286 ( 916) hydrogen bonds : angle 4.25098 ( 2514) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4776 Ramachandran restraints generated. 2388 Oldfield, 0 Emsley, 2388 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4776 Ramachandran restraints generated. 2388 Oldfield, 0 Emsley, 2388 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 189 residues out of total 2142 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 164 time to evaluate : 0.654 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: A 211 MET cc_start: 0.8639 (pmm) cc_final: 0.8288 (pmm) REVERT: A 328 LYS cc_start: 0.9283 (OUTLIER) cc_final: 0.8975 (mtpp) REVERT: A 374 MET cc_start: 0.9115 (tpp) cc_final: 0.8875 (mpp) REVERT: A 543 LEU cc_start: 0.9481 (OUTLIER) cc_final: 0.9178 (mt) REVERT: B 40 MET cc_start: 0.9164 (mtp) cc_final: 0.8820 (ptm) REVERT: B 116 GLN cc_start: 0.8880 (tp40) cc_final: 0.8661 (tm-30) REVERT: B 126 ARG cc_start: 0.8323 (mtt180) cc_final: 0.7775 (mmm160) REVERT: B 356 MET cc_start: 0.9135 (ttt) cc_final: 0.8818 (tpt) REVERT: B 409 MET cc_start: 0.7181 (OUTLIER) cc_final: 0.6582 (pmt) REVERT: B 411 MET cc_start: 0.8969 (mmm) cc_final: 0.8719 (mmm) REVERT: B 430 LYS cc_start: 0.9167 (OUTLIER) cc_final: 0.8835 (ptpt) REVERT: C 69 GLU cc_start: 0.9021 (OUTLIER) cc_final: 0.8549 (tp30) REVERT: E 353 LYS cc_start: 0.9179 (OUTLIER) cc_final: 0.8839 (pptt) REVERT: E 372 MET cc_start: 0.9001 (mmm) cc_final: 0.8601 (tpp) REVERT: E 379 LYS cc_start: 0.9248 (mppt) cc_final: 0.8790 (tptp) REVERT: E 409 MET cc_start: 0.6889 (ppp) cc_final: 0.6449 (ppp) REVERT: F 69 GLU cc_start: 0.8757 (tt0) cc_final: 0.8285 (tp30) outliers start: 25 outliers final: 14 residues processed: 181 average time/residue: 0.6522 time to fit residues: 131.5805 Evaluate side-chains 180 residues out of total 2142 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 160 time to evaluate : 0.763 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 328 LYS Chi-restraints excluded: chain A residue 354 ILE Chi-restraints excluded: chain A residue 450 VAL Chi-restraints excluded: chain A residue 543 LEU Chi-restraints excluded: chain B residue 219 ILE Chi-restraints excluded: chain B residue 302 ILE Chi-restraints excluded: chain B residue 387 GLU Chi-restraints excluded: chain B residue 409 MET Chi-restraints excluded: chain B residue 430 LYS Chi-restraints excluded: chain C residue 69 GLU Chi-restraints excluded: chain D residue 450 VAL Chi-restraints excluded: chain D residue 549 LEU Chi-restraints excluded: chain E residue 119 VAL Chi-restraints excluded: chain E residue 124 GLN Chi-restraints excluded: chain E residue 156 THR Chi-restraints excluded: chain E residue 302 ILE Chi-restraints excluded: chain E residue 348 MET Chi-restraints excluded: chain E residue 353 LYS Chi-restraints excluded: chain E residue 592 SER Chi-restraints excluded: chain F residue 91 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 111 optimal weight: 3.9990 chunk 66 optimal weight: 6.9990 chunk 184 optimal weight: 6.9990 chunk 87 optimal weight: 1.9990 chunk 41 optimal weight: 0.0470 chunk 210 optimal weight: 0.0770 chunk 63 optimal weight: 6.9990 chunk 43 optimal weight: 0.6980 chunk 61 optimal weight: 4.9990 chunk 208 optimal weight: 0.7980 chunk 123 optimal weight: 0.0770 overall best weight: 0.3394 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 425 ASN ** B 460 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 533 ASN B 537 ASN ** E 310 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 425 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 42 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3455 r_free = 0.3455 target = 0.062954 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.2882 r_free = 0.2882 target = 0.042768 restraints weight = 66657.620| |-----------------------------------------------------------------------------| r_work (start): 0.2833 rms_B_bonded: 3.21 r_work: 0.2690 rms_B_bonded: 3.47 restraints_weight: 0.5000 r_work (final): 0.2690 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8898 moved from start: 0.2673 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.046 19747 Z= 0.101 Angle : 0.610 13.016 26681 Z= 0.289 Chirality : 0.040 0.269 2906 Planarity : 0.004 0.074 3441 Dihedral : 3.751 29.118 2610 Min Nonbonded Distance : 2.466 Molprobity Statistics. All-atom Clashscore : 6.26 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.14 % Favored : 96.82 % Rotamer: Outliers : 1.21 % Allowed : 13.21 % Favored : 85.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.61 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.70 (0.18), residues: 2388 helix: 1.46 (0.16), residues: 1094 sheet: 0.16 (0.33), residues: 236 loop : -0.48 (0.20), residues: 1058 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.000 ARG E 126 TYR 0.011 0.001 TYR D 305 PHE 0.013 0.001 PHE E 357 TRP 0.013 0.001 TRP A 577 HIS 0.003 0.000 HIS B 47 Details of bonding type rmsd covalent geometry : bond 0.00231 (19747) covalent geometry : angle 0.61011 (26681) hydrogen bonds : bond 0.03113 ( 916) hydrogen bonds : angle 4.19676 ( 2514) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4776 Ramachandran restraints generated. 2388 Oldfield, 0 Emsley, 2388 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4776 Ramachandran restraints generated. 2388 Oldfield, 0 Emsley, 2388 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 200 residues out of total 2142 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 174 time to evaluate : 0.686 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: A 211 MET cc_start: 0.8386 (pmm) cc_final: 0.8075 (pmm) REVERT: A 328 LYS cc_start: 0.9257 (OUTLIER) cc_final: 0.8951 (mtpp) REVERT: A 374 MET cc_start: 0.9132 (tpp) cc_final: 0.8832 (mpp) REVERT: B 40 MET cc_start: 0.9150 (mtp) cc_final: 0.8838 (ptm) REVERT: B 126 ARG cc_start: 0.8275 (mtt180) cc_final: 0.7701 (mmm160) REVERT: B 409 MET cc_start: 0.6787 (OUTLIER) cc_final: 0.6339 (pmt) REVERT: B 411 MET cc_start: 0.8946 (mmm) cc_final: 0.8684 (mmm) REVERT: C 69 GLU cc_start: 0.9031 (tt0) cc_final: 0.8645 (tp30) REVERT: D 397 GLU cc_start: 0.8509 (tp30) cc_final: 0.8244 (tm-30) REVERT: E 353 LYS cc_start: 0.9198 (OUTLIER) cc_final: 0.8861 (pptt) REVERT: E 372 MET cc_start: 0.9003 (mmm) cc_final: 0.8633 (tpp) REVERT: E 379 LYS cc_start: 0.9254 (mppt) cc_final: 0.8777 (tptp) REVERT: E 409 MET cc_start: 0.6836 (ppp) cc_final: 0.6412 (ppp) REVERT: F 69 GLU cc_start: 0.8751 (tt0) cc_final: 0.8346 (tp30) outliers start: 26 outliers final: 14 residues processed: 191 average time/residue: 0.6642 time to fit residues: 141.1621 Evaluate side-chains 182 residues out of total 2142 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 165 time to evaluate : 0.731 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 328 LYS Chi-restraints excluded: chain A residue 450 VAL Chi-restraints excluded: chain B residue 219 ILE Chi-restraints excluded: chain B residue 302 ILE Chi-restraints excluded: chain B residue 387 GLU Chi-restraints excluded: chain B residue 409 MET Chi-restraints excluded: chain D residue 450 VAL Chi-restraints excluded: chain D residue 549 LEU Chi-restraints excluded: chain E residue 119 VAL Chi-restraints excluded: chain E residue 120 ASP Chi-restraints excluded: chain E residue 124 GLN Chi-restraints excluded: chain E residue 156 THR Chi-restraints excluded: chain E residue 302 ILE Chi-restraints excluded: chain E residue 348 MET Chi-restraints excluded: chain E residue 353 LYS Chi-restraints excluded: chain E residue 592 SER Chi-restraints excluded: chain F residue 91 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 194 optimal weight: 5.9990 chunk 95 optimal weight: 5.9990 chunk 64 optimal weight: 0.2980 chunk 159 optimal weight: 5.9990 chunk 128 optimal weight: 1.9990 chunk 211 optimal weight: 4.9990 chunk 193 optimal weight: 0.9980 chunk 56 optimal weight: 0.4980 chunk 230 optimal weight: 2.9990 chunk 150 optimal weight: 0.0970 chunk 221 optimal weight: 0.3980 overall best weight: 0.4578 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 145 ASN B 367 GLN ** B 460 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 42 ASN ** E 425 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3454 r_free = 0.3454 target = 0.062898 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2880 r_free = 0.2880 target = 0.042715 restraints weight = 66699.107| |-----------------------------------------------------------------------------| r_work (start): 0.2832 rms_B_bonded: 3.20 r_work: 0.2690 rms_B_bonded: 3.46 restraints_weight: 0.5000 r_work (final): 0.2690 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8899 moved from start: 0.2734 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.041 19747 Z= 0.107 Angle : 0.626 12.902 26681 Z= 0.299 Chirality : 0.040 0.256 2906 Planarity : 0.004 0.092 3441 Dihedral : 3.755 27.768 2610 Min Nonbonded Distance : 2.370 Molprobity Statistics. All-atom Clashscore : 6.23 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.10 % Favored : 96.86 % Rotamer: Outliers : 1.03 % Allowed : 13.77 % Favored : 85.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.61 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.70 (0.18), residues: 2388 helix: 1.44 (0.16), residues: 1101 sheet: 0.14 (0.33), residues: 236 loop : -0.46 (0.20), residues: 1051 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.022 0.000 ARG E 126 TYR 0.011 0.001 TYR A 305 PHE 0.042 0.001 PHE B 166 TRP 0.014 0.001 TRP F 98 HIS 0.002 0.000 HIS B 47 Details of bonding type rmsd covalent geometry : bond 0.00246 (19747) covalent geometry : angle 0.62620 (26681) hydrogen bonds : bond 0.03163 ( 916) hydrogen bonds : angle 4.20173 ( 2514) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5446.53 seconds wall clock time: 95 minutes 7.15 seconds (5707.15 seconds total)