Starting phenix.real_space_refine (version: 1.21rc1) on Tue Apr 25 07:24:17 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5hi9_6580/04_2023/5hi9_6580.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5hi9_6580/04_2023/5hi9_6580.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5hi9_6580/04_2023/5hi9_6580.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5hi9_6580/04_2023/5hi9_6580.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5hi9_6580/04_2023/5hi9_6580.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5hi9_6580/04_2023/5hi9_6580.pdb" } resolution = 4.4 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 ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.004 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 112 5.16 5 C 12828 2.51 5 N 3300 2.21 5 O 3396 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 75": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 311": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 317": "NH1" <-> "NH2" Residue "A ARG 328": "NH1" <-> "NH2" Residue "A PHE 330": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 339": "NH1" <-> "NH2" Residue "A ARG 369": "NH1" <-> "NH2" Residue "A ARG 371": "NH1" <-> "NH2" Residue "A ARG 388": "NH1" <-> "NH2" Residue "A ARG 392": "NH1" <-> "NH2" Residue "A ARG 458": "NH1" <-> "NH2" Residue "A ARG 459": "NH1" <-> "NH2" Residue "A ARG 460": "NH1" <-> "NH2" Residue "A ARG 490": "NH1" <-> "NH2" Residue "A PHE 491": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 493": "OE1" <-> "OE2" Residue "A TYR 497": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 517": "NH1" <-> "NH2" Residue "A ARG 535": "NH1" <-> "NH2" Residue "A ARG 539": "NH1" <-> "NH2" Residue "A ARG 560": "NH1" <-> "NH2" Residue "A ARG 617": "NH1" <-> "NH2" Residue "A ARG 619": "NH1" <-> "NH2" Residue "A ARG 679": "NH1" <-> "NH2" Residue "A ARG 687": "NH1" <-> "NH2" Residue "A ARG 706": "NH1" <-> "NH2" Residue "B PHE 75": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 311": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 317": "NH1" <-> "NH2" Residue "B ARG 328": "NH1" <-> "NH2" Residue "B PHE 330": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 339": "NH1" <-> "NH2" Residue "B ARG 369": "NH1" <-> "NH2" Residue "B ARG 371": "NH1" <-> "NH2" Residue "B ARG 388": "NH1" <-> "NH2" Residue "B ARG 392": "NH1" <-> "NH2" Residue "B ARG 458": "NH1" <-> "NH2" Residue "B ARG 459": "NH1" <-> "NH2" Residue "B ARG 460": "NH1" <-> "NH2" Residue "B ARG 490": "NH1" <-> "NH2" Residue "B PHE 491": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 493": "OE1" <-> "OE2" Residue "B TYR 497": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 517": "NH1" <-> "NH2" Residue "B ARG 535": "NH1" <-> "NH2" Residue "B ARG 539": "NH1" <-> "NH2" Residue "B ARG 560": "NH1" <-> "NH2" Residue "B ARG 617": "NH1" <-> "NH2" Residue "B ARG 619": "NH1" <-> "NH2" Residue "B ARG 679": "NH1" <-> "NH2" Residue "B ARG 687": "NH1" <-> "NH2" Residue "B PHE 705": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 706": "NH1" <-> "NH2" Residue "C PHE 75": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 311": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 317": "NH1" <-> "NH2" Residue "C ARG 328": "NH1" <-> "NH2" Residue "C PHE 330": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 339": "NH1" <-> "NH2" Residue "C ARG 369": "NH1" <-> "NH2" Residue "C ARG 371": "NH1" <-> "NH2" Residue "C ARG 388": "NH1" <-> "NH2" Residue "C ARG 392": "NH1" <-> "NH2" Residue "C ARG 458": "NH1" <-> "NH2" Residue "C ARG 459": "NH1" <-> "NH2" Residue "C ARG 460": "NH1" <-> "NH2" Residue "C ARG 490": "NH1" <-> "NH2" Residue "C PHE 491": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 493": "OE1" <-> "OE2" Residue "C TYR 497": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 517": "NH1" <-> "NH2" Residue "C ARG 535": "NH1" <-> "NH2" Residue "C ARG 539": "NH1" <-> "NH2" Residue "C ARG 560": "NH1" <-> "NH2" Residue "C ARG 617": "NH1" <-> "NH2" Residue "C ARG 619": "NH1" <-> "NH2" Residue "C ARG 679": "NH1" <-> "NH2" Residue "C ARG 687": "NH1" <-> "NH2" Residue "C ARG 706": "NH1" <-> "NH2" Residue "D PHE 75": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 311": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 317": "NH1" <-> "NH2" Residue "D ARG 328": "NH1" <-> "NH2" Residue "D PHE 330": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 339": "NH1" <-> "NH2" Residue "D ARG 369": "NH1" <-> "NH2" Residue "D ARG 371": "NH1" <-> "NH2" Residue "D ARG 388": "NH1" <-> "NH2" Residue "D ARG 392": "NH1" <-> "NH2" Residue "D ARG 458": "NH1" <-> "NH2" Residue "D ARG 459": "NH1" <-> "NH2" Residue "D ARG 460": "NH1" <-> "NH2" Residue "D ARG 490": "NH1" <-> "NH2" Residue "D PHE 491": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 493": "OE1" <-> "OE2" Residue "D TYR 497": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 517": "NH1" <-> "NH2" Residue "D ARG 535": "NH1" <-> "NH2" Residue "D ARG 539": "NH1" <-> "NH2" Residue "D ARG 560": "NH1" <-> "NH2" Residue "D ARG 617": "NH1" <-> "NH2" Residue "D ARG 619": "NH1" <-> "NH2" Residue "D ARG 679": "NH1" <-> "NH2" Residue "D ARG 687": "NH1" <-> "NH2" Residue "D ARG 706": "NH1" <-> "NH2" Time to flip residues: 0.08s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4938/modules/chem_data/mon_lib" Total number of atoms: 19636 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 4909 Number of conformers: 1 Conformer: "" Number of residues, atoms: 602, 4909 Classifications: {'peptide': 602} Link IDs: {'CIS': 2, 'PCIS': 1, 'PTRANS': 17, 'TRANS': 581} Chain breaks: 2 Chain: "B" Number of atoms: 4909 Number of conformers: 1 Conformer: "" Number of residues, atoms: 602, 4909 Classifications: {'peptide': 602} Link IDs: {'CIS': 2, 'PCIS': 1, 'PTRANS': 17, 'TRANS': 581} Chain breaks: 2 Chain: "C" Number of atoms: 4909 Number of conformers: 1 Conformer: "" Number of residues, atoms: 602, 4909 Classifications: {'peptide': 602} Link IDs: {'CIS': 2, 'PCIS': 1, 'PTRANS': 17, 'TRANS': 581} Chain breaks: 2 Chain: "D" Number of atoms: 4909 Number of conformers: 1 Conformer: "" Number of residues, atoms: 602, 4909 Classifications: {'peptide': 602} Link IDs: {'CIS': 2, 'PCIS': 1, 'PTRANS': 17, 'TRANS': 581} Chain breaks: 2 Time building chain proxies: 10.20, per 1000 atoms: 0.52 Number of scatterers: 19636 At special positions: 0 Unit cell: (143.19, 143.19, 116.1, 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 112 16.00 O 3396 8.00 N 3300 7.00 C 12828 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 - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 8.40 Conformation dependent library (CDL) restraints added in 2.9 seconds 4768 Ramachandran restraints generated. 2384 Oldfield, 0 Emsley, 2384 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4536 Finding SS restraints... Secondary structure from input PDB file: 136 helices and 4 sheets defined 60.8% alpha, 1.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.92 Creating SS restraints... Processing helix chain 'A' and resid 76 through 87 Processing helix chain 'A' and resid 94 through 103 Processing helix chain 'A' and resid 119 through 128 removed outlier: 3.612A pdb=" N LEU A 126 " --> pdb=" O MET A 122 " (cutoff:3.500A) removed outlier: 4.214A pdb=" N LEU A 128 " --> pdb=" O ALA A 124 " (cutoff:3.500A) Processing helix chain 'A' and resid 135 through 147 removed outlier: 3.747A pdb=" N GLY A 147 " --> pdb=" O ASP A 143 " (cutoff:3.500A) Processing helix chain 'A' and resid 151 through 155 Processing helix chain 'A' and resid 159 through 163 removed outlier: 3.839A pdb=" N TYR A 162 " --> pdb=" O ASP A 159 " (cutoff:3.500A) Processing helix chain 'A' and resid 167 through 172 Processing helix chain 'A' and resid 177 through 187 removed outlier: 4.197A pdb=" N LYS A 181 " --> pdb=" O LEU A 177 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N LEU A 182 " --> pdb=" O GLN A 178 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N ASN A 186 " --> pdb=" O LEU A 182 " (cutoff:3.500A) Processing helix chain 'A' and resid 212 through 220 removed outlier: 3.779A pdb=" N CYS A 219 " --> pdb=" O SER A 215 " (cutoff:3.500A) Processing helix chain 'A' and resid 224 through 232 removed outlier: 3.544A pdb=" N TYR A 228 " --> pdb=" O ASP A 224 " (cutoff:3.500A) removed outlier: 3.860A pdb=" N LEU A 230 " --> pdb=" O VAL A 226 " (cutoff:3.500A) Processing helix chain 'A' and resid 248 through 257 removed outlier: 3.987A pdb=" N ALA A 252 " --> pdb=" O THR A 248 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N VAL A 254 " --> pdb=" O LEU A 250 " (cutoff:3.500A) Processing helix chain 'A' and resid 260 through 282 removed outlier: 3.527A pdb=" N GLY A 273 " --> pdb=" O HIS A 269 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N LEU A 275 " --> pdb=" O TYR A 271 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N ARG A 280 " --> pdb=" O GLN A 276 " (cutoff:3.500A) Processing helix chain 'A' and resid 297 through 305 removed outlier: 4.111A pdb=" N ALA A 303 " --> pdb=" O LEU A 299 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N LYS A 304 " --> pdb=" O LYS A 300 " (cutoff:3.500A) removed outlier: 3.874A pdb=" N GLU A 305 " --> pdb=" O LEU A 301 " (cutoff:3.500A) Processing helix chain 'A' and resid 310 through 316 Processing helix chain 'A' and resid 356 through 361 removed outlier: 3.691A pdb=" N ALA A 361 " --> pdb=" O LEU A 357 " (cutoff:3.500A) Processing helix chain 'A' and resid 370 through 375 removed outlier: 3.707A pdb=" N LEU A 375 " --> pdb=" O ARG A 371 " (cutoff:3.500A) Processing helix chain 'A' and resid 375 through 407 removed outlier: 3.528A pdb=" N LEU A 381 " --> pdb=" O PRO A 377 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N LEU A 382 " --> pdb=" O LEU A 378 " (cutoff:3.500A) removed outlier: 4.892A pdb=" N GLN A 383 " --> pdb=" O ASN A 379 " (cutoff:3.500A) removed outlier: 3.942A pdb=" N GLU A 384 " --> pdb=" O LYS A 380 " (cutoff:3.500A) removed outlier: 4.077A pdb=" N LYS A 385 " --> pdb=" O LEU A 381 " (cutoff:3.500A) removed outlier: 4.879A pdb=" N ARG A 388 " --> pdb=" O GLU A 384 " (cutoff:3.500A) removed outlier: 4.272A pdb=" N SER A 391 " --> pdb=" O ASP A 387 " (cutoff:3.500A) removed outlier: 4.182A pdb=" N ARG A 392 " --> pdb=" O ARG A 388 " (cutoff:3.500A) removed outlier: 4.559A pdb=" N TYR A 403 " --> pdb=" O CYS A 399 " (cutoff:3.500A) removed outlier: 4.099A pdb=" N MET A 404 " --> pdb=" O TYR A 400 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N ILE A 406 " --> pdb=" O VAL A 402 " (cutoff:3.500A) Processing helix chain 'A' and resid 408 through 414 Processing helix chain 'A' and resid 431 through 459 removed outlier: 3.761A pdb=" N LEU A 435 " --> pdb=" O GLU A 431 " (cutoff:3.500A) removed outlier: 4.549A pdb=" N HIS A 438 " --> pdb=" O LEU A 434 " (cutoff:3.500A) removed outlier: 4.564A pdb=" N ILE A 439 " --> pdb=" O LEU A 435 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N LEU A 440 " --> pdb=" O LEU A 436 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N LEU A 443 " --> pdb=" O ILE A 439 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N GLY A 445 " --> pdb=" O ILE A 441 " (cutoff:3.500A) removed outlier: 4.425A pdb=" N LEU A 448 " --> pdb=" O GLY A 444 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N GLN A 452 " --> pdb=" O LEU A 448 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N TYR A 455 " --> pdb=" O GLY A 451 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N PHE A 456 " --> pdb=" O GLN A 452 " (cutoff:3.500A) Processing helix chain 'A' and resid 463 through 465 No H-bonds generated for 'chain 'A' and resid 463 through 465' Processing helix chain 'A' and resid 466 through 483 removed outlier: 4.143A pdb=" N TYR A 471 " --> pdb=" O PHE A 467 " (cutoff:3.500A) removed outlier: 6.581A pdb=" N PHE A 472 " --> pdb=" O MET A 468 " (cutoff:3.500A) removed outlier: 4.312A pdb=" N GLU A 473 " --> pdb=" O ASP A 469 " (cutoff:3.500A) removed outlier: 3.820A pdb=" N PHE A 476 " --> pdb=" O PHE A 472 " (cutoff:3.500A) removed outlier: 3.926A pdb=" N LEU A 477 " --> pdb=" O GLU A 473 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N GLN A 479 " --> pdb=" O LEU A 475 " (cutoff:3.500A) Processing helix chain 'A' and resid 483 through 491 removed outlier: 4.116A pdb=" N GLN A 487 " --> pdb=" O THR A 483 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N VAL A 488 " --> pdb=" O VAL A 484 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N LEU A 489 " --> pdb=" O LEU A 485 " (cutoff:3.500A) removed outlier: 4.349A pdb=" N PHE A 491 " --> pdb=" O GLN A 487 " (cutoff:3.500A) Processing helix chain 'A' and resid 500 through 511 removed outlier: 3.834A pdb=" N SER A 504 " --> pdb=" O LEU A 500 " (cutoff:3.500A) Processing helix chain 'A' and resid 512 through 514 No H-bonds generated for 'chain 'A' and resid 512 through 514' Processing helix chain 'A' and resid 522 through 545 removed outlier: 3.547A pdb=" N SER A 526 " --> pdb=" O THR A 522 " (cutoff:3.500A) removed outlier: 4.046A pdb=" N MET A 528 " --> pdb=" O ILE A 524 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N VAL A 532 " --> pdb=" O MET A 528 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N ARG A 535 " --> pdb=" O LYS A 531 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N VAL A 543 " --> pdb=" O ARG A 539 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N LEU A 545 " --> pdb=" O LEU A 541 " (cutoff:3.500A) Processing helix chain 'A' and resid 548 through 559 Processing helix chain 'A' and resid 560 through 561 No H-bonds generated for 'chain 'A' and resid 560 through 561' Processing helix chain 'A' and resid 591 through 591 No H-bonds generated for 'chain 'A' and resid 591 through 591' Processing helix chain 'A' and resid 592 through 597 Processing helix chain 'A' and resid 597 through 602 Processing helix chain 'A' and resid 619 through 627 removed outlier: 3.538A pdb=" N LEU A 623 " --> pdb=" O ARG A 619 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N LEU A 627 " --> pdb=" O LEU A 623 " (cutoff:3.500A) Processing helix chain 'A' and resid 628 through 650 removed outlier: 4.002A pdb=" N LEU A 632 " --> pdb=" O ALA A 628 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N TYR A 634 " --> pdb=" O VAL A 630 " (cutoff:3.500A) removed outlier: 4.137A pdb=" N MET A 640 " --> pdb=" O LEU A 636 " (cutoff:3.500A) Processing helix chain 'A' and resid 654 through 668 removed outlier: 4.256A pdb=" N LYS A 661 " --> pdb=" O TRP A 657 " (cutoff:3.500A) Processing helix chain 'A' and resid 669 through 671 No H-bonds generated for 'chain 'A' and resid 669 through 671' Processing helix chain 'B' and resid 76 through 87 Processing helix chain 'B' and resid 94 through 103 Processing helix chain 'B' and resid 119 through 128 removed outlier: 3.612A pdb=" N LEU B 126 " --> pdb=" O MET B 122 " (cutoff:3.500A) removed outlier: 4.214A pdb=" N LEU B 128 " --> pdb=" O ALA B 124 " (cutoff:3.500A) Processing helix chain 'B' and resid 135 through 147 removed outlier: 3.746A pdb=" N GLY B 147 " --> pdb=" O ASP B 143 " (cutoff:3.500A) Processing helix chain 'B' and resid 151 through 155 Processing helix chain 'B' and resid 159 through 163 removed outlier: 3.839A pdb=" N TYR B 162 " --> pdb=" O ASP B 159 " (cutoff:3.500A) Processing helix chain 'B' and resid 167 through 172 Processing helix chain 'B' and resid 177 through 187 removed outlier: 4.197A pdb=" N LYS B 181 " --> pdb=" O LEU B 177 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N LEU B 182 " --> pdb=" O GLN B 178 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N ASN B 186 " --> pdb=" O LEU B 182 " (cutoff:3.500A) Processing helix chain 'B' and resid 212 through 220 removed outlier: 3.778A pdb=" N CYS B 219 " --> pdb=" O SER B 215 " (cutoff:3.500A) Processing helix chain 'B' and resid 224 through 232 removed outlier: 3.544A pdb=" N TYR B 228 " --> pdb=" O ASP B 224 " (cutoff:3.500A) removed outlier: 3.860A pdb=" N LEU B 230 " --> pdb=" O VAL B 226 " (cutoff:3.500A) Processing helix chain 'B' and resid 248 through 257 removed outlier: 3.986A pdb=" N ALA B 252 " --> pdb=" O THR B 248 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N VAL B 254 " --> pdb=" O LEU B 250 " (cutoff:3.500A) Processing helix chain 'B' and resid 260 through 282 removed outlier: 3.527A pdb=" N GLY B 273 " --> pdb=" O HIS B 269 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N LEU B 275 " --> pdb=" O TYR B 271 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N ARG B 280 " --> pdb=" O GLN B 276 " (cutoff:3.500A) Processing helix chain 'B' and resid 297 through 305 removed outlier: 4.112A pdb=" N ALA B 303 " --> pdb=" O LEU B 299 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N LYS B 304 " --> pdb=" O LYS B 300 " (cutoff:3.500A) removed outlier: 3.874A pdb=" N GLU B 305 " --> pdb=" O LEU B 301 " (cutoff:3.500A) Processing helix chain 'B' and resid 310 through 316 Processing helix chain 'B' and resid 356 through 361 removed outlier: 3.691A pdb=" N ALA B 361 " --> pdb=" O LEU B 357 " (cutoff:3.500A) Processing helix chain 'B' and resid 370 through 375 removed outlier: 3.707A pdb=" N LEU B 375 " --> pdb=" O ARG B 371 " (cutoff:3.500A) Processing helix chain 'B' and resid 375 through 407 removed outlier: 3.529A pdb=" N LEU B 381 " --> pdb=" O PRO B 377 " (cutoff:3.500A) removed outlier: 3.826A pdb=" N LEU B 382 " --> pdb=" O LEU B 378 " (cutoff:3.500A) removed outlier: 4.893A pdb=" N GLN B 383 " --> pdb=" O ASN B 379 " (cutoff:3.500A) removed outlier: 3.942A pdb=" N GLU B 384 " --> pdb=" O LYS B 380 " (cutoff:3.500A) removed outlier: 4.076A pdb=" N LYS B 385 " --> pdb=" O LEU B 381 " (cutoff:3.500A) removed outlier: 4.878A pdb=" N ARG B 388 " --> pdb=" O GLU B 384 " (cutoff:3.500A) removed outlier: 4.271A pdb=" N SER B 391 " --> pdb=" O ASP B 387 " (cutoff:3.500A) removed outlier: 4.182A pdb=" N ARG B 392 " --> pdb=" O ARG B 388 " (cutoff:3.500A) removed outlier: 4.558A pdb=" N TYR B 403 " --> pdb=" O CYS B 399 " (cutoff:3.500A) removed outlier: 4.099A pdb=" N MET B 404 " --> pdb=" O TYR B 400 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N ILE B 406 " --> pdb=" O VAL B 402 " (cutoff:3.500A) Processing helix chain 'B' and resid 408 through 414 Processing helix chain 'B' and resid 431 through 459 removed outlier: 3.760A pdb=" N LEU B 435 " --> pdb=" O GLU B 431 " (cutoff:3.500A) removed outlier: 4.549A pdb=" N HIS B 438 " --> pdb=" O LEU B 434 " (cutoff:3.500A) removed outlier: 4.564A pdb=" N ILE B 439 " --> pdb=" O LEU B 435 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N LEU B 440 " --> pdb=" O LEU B 436 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N LEU B 443 " --> pdb=" O ILE B 439 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N GLY B 445 " --> pdb=" O ILE B 441 " (cutoff:3.500A) removed outlier: 4.425A pdb=" N LEU B 448 " --> pdb=" O GLY B 444 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N GLN B 452 " --> pdb=" O LEU B 448 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N TYR B 455 " --> pdb=" O GLY B 451 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N PHE B 456 " --> pdb=" O GLN B 452 " (cutoff:3.500A) Processing helix chain 'B' and resid 463 through 465 No H-bonds generated for 'chain 'B' and resid 463 through 465' Processing helix chain 'B' and resid 466 through 483 removed outlier: 4.143A pdb=" N TYR B 471 " --> pdb=" O PHE B 467 " (cutoff:3.500A) removed outlier: 6.581A pdb=" N PHE B 472 " --> pdb=" O MET B 468 " (cutoff:3.500A) removed outlier: 4.311A pdb=" N GLU B 473 " --> pdb=" O ASP B 469 " (cutoff:3.500A) removed outlier: 3.820A pdb=" N PHE B 476 " --> pdb=" O PHE B 472 " (cutoff:3.500A) removed outlier: 3.926A pdb=" N LEU B 477 " --> pdb=" O GLU B 473 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N GLN B 479 " --> pdb=" O LEU B 475 " (cutoff:3.500A) Processing helix chain 'B' and resid 483 through 491 removed outlier: 4.116A pdb=" N GLN B 487 " --> pdb=" O THR B 483 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N VAL B 488 " --> pdb=" O VAL B 484 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N LEU B 489 " --> pdb=" O LEU B 485 " (cutoff:3.500A) removed outlier: 4.349A pdb=" N PHE B 491 " --> pdb=" O GLN B 487 " (cutoff:3.500A) Processing helix chain 'B' and resid 500 through 511 removed outlier: 3.834A pdb=" N SER B 504 " --> pdb=" O LEU B 500 " (cutoff:3.500A) Processing helix chain 'B' and resid 512 through 514 No H-bonds generated for 'chain 'B' and resid 512 through 514' Processing helix chain 'B' and resid 522 through 545 removed outlier: 3.547A pdb=" N SER B 526 " --> pdb=" O THR B 522 " (cutoff:3.500A) removed outlier: 4.046A pdb=" N MET B 528 " --> pdb=" O ILE B 524 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N VAL B 532 " --> pdb=" O MET B 528 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N ARG B 535 " --> pdb=" O LYS B 531 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N VAL B 543 " --> pdb=" O ARG B 539 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N LEU B 545 " --> pdb=" O LEU B 541 " (cutoff:3.500A) Processing helix chain 'B' and resid 548 through 559 Processing helix chain 'B' and resid 560 through 561 No H-bonds generated for 'chain 'B' and resid 560 through 561' Processing helix chain 'B' and resid 591 through 591 No H-bonds generated for 'chain 'B' and resid 591 through 591' Processing helix chain 'B' and resid 592 through 597 Processing helix chain 'B' and resid 597 through 602 Processing helix chain 'B' and resid 619 through 627 removed outlier: 3.538A pdb=" N LEU B 623 " --> pdb=" O ARG B 619 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N LEU B 627 " --> pdb=" O LEU B 623 " (cutoff:3.500A) Processing helix chain 'B' and resid 628 through 650 removed outlier: 4.002A pdb=" N LEU B 632 " --> pdb=" O ALA B 628 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N TYR B 634 " --> pdb=" O VAL B 630 " (cutoff:3.500A) removed outlier: 4.137A pdb=" N MET B 640 " --> pdb=" O LEU B 636 " (cutoff:3.500A) Processing helix chain 'B' and resid 654 through 668 removed outlier: 4.256A pdb=" N LYS B 661 " --> pdb=" O TRP B 657 " (cutoff:3.500A) Processing helix chain 'B' and resid 669 through 671 No H-bonds generated for 'chain 'B' and resid 669 through 671' Processing helix chain 'C' and resid 76 through 87 Processing helix chain 'C' and resid 94 through 103 Processing helix chain 'C' and resid 119 through 128 removed outlier: 3.612A pdb=" N LEU C 126 " --> pdb=" O MET C 122 " (cutoff:3.500A) removed outlier: 4.213A pdb=" N LEU C 128 " --> pdb=" O ALA C 124 " (cutoff:3.500A) Processing helix chain 'C' and resid 135 through 147 removed outlier: 3.747A pdb=" N GLY C 147 " --> pdb=" O ASP C 143 " (cutoff:3.500A) Processing helix chain 'C' and resid 151 through 155 Processing helix chain 'C' and resid 159 through 163 removed outlier: 3.839A pdb=" N TYR C 162 " --> pdb=" O ASP C 159 " (cutoff:3.500A) Processing helix chain 'C' and resid 167 through 172 Processing helix chain 'C' and resid 177 through 187 removed outlier: 4.197A pdb=" N LYS C 181 " --> pdb=" O LEU C 177 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N LEU C 182 " --> pdb=" O GLN C 178 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N ASN C 186 " --> pdb=" O LEU C 182 " (cutoff:3.500A) Processing helix chain 'C' and resid 212 through 220 removed outlier: 3.778A pdb=" N CYS C 219 " --> pdb=" O SER C 215 " (cutoff:3.500A) Processing helix chain 'C' and resid 224 through 232 removed outlier: 3.544A pdb=" N TYR C 228 " --> pdb=" O ASP C 224 " (cutoff:3.500A) removed outlier: 3.860A pdb=" N LEU C 230 " --> pdb=" O VAL C 226 " (cutoff:3.500A) Processing helix chain 'C' and resid 248 through 257 removed outlier: 3.987A pdb=" N ALA C 252 " --> pdb=" O THR C 248 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N VAL C 254 " --> pdb=" O LEU C 250 " (cutoff:3.500A) Processing helix chain 'C' and resid 260 through 282 removed outlier: 3.528A pdb=" N GLY C 273 " --> pdb=" O HIS C 269 " (cutoff:3.500A) removed outlier: 3.835A pdb=" N LEU C 275 " --> pdb=" O TYR C 271 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N ARG C 280 " --> pdb=" O GLN C 276 " (cutoff:3.500A) Processing helix chain 'C' and resid 297 through 305 removed outlier: 4.111A pdb=" N ALA C 303 " --> pdb=" O LEU C 299 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N LYS C 304 " --> pdb=" O LYS C 300 " (cutoff:3.500A) removed outlier: 3.874A pdb=" N GLU C 305 " --> pdb=" O LEU C 301 " (cutoff:3.500A) Processing helix chain 'C' and resid 310 through 316 Processing helix chain 'C' and resid 356 through 361 removed outlier: 3.691A pdb=" N ALA C 361 " --> pdb=" O LEU C 357 " (cutoff:3.500A) Processing helix chain 'C' and resid 370 through 375 removed outlier: 3.707A pdb=" N LEU C 375 " --> pdb=" O ARG C 371 " (cutoff:3.500A) Processing helix chain 'C' and resid 375 through 407 removed outlier: 3.528A pdb=" N LEU C 381 " --> pdb=" O PRO C 377 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N LEU C 382 " --> pdb=" O LEU C 378 " (cutoff:3.500A) removed outlier: 4.893A pdb=" N GLN C 383 " --> pdb=" O ASN C 379 " (cutoff:3.500A) removed outlier: 3.941A pdb=" N GLU C 384 " --> pdb=" O LYS C 380 " (cutoff:3.500A) removed outlier: 4.077A pdb=" N LYS C 385 " --> pdb=" O LEU C 381 " (cutoff:3.500A) removed outlier: 4.878A pdb=" N ARG C 388 " --> pdb=" O GLU C 384 " (cutoff:3.500A) removed outlier: 4.272A pdb=" N SER C 391 " --> pdb=" O ASP C 387 " (cutoff:3.500A) removed outlier: 4.182A pdb=" N ARG C 392 " --> pdb=" O ARG C 388 " (cutoff:3.500A) removed outlier: 4.559A pdb=" N TYR C 403 " --> pdb=" O CYS C 399 " (cutoff:3.500A) removed outlier: 4.100A pdb=" N MET C 404 " --> pdb=" O TYR C 400 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N ILE C 406 " --> pdb=" O VAL C 402 " (cutoff:3.500A) Processing helix chain 'C' and resid 408 through 414 Processing helix chain 'C' and resid 431 through 459 removed outlier: 3.761A pdb=" N LEU C 435 " --> pdb=" O GLU C 431 " (cutoff:3.500A) removed outlier: 4.549A pdb=" N HIS C 438 " --> pdb=" O LEU C 434 " (cutoff:3.500A) removed outlier: 4.564A pdb=" N ILE C 439 " --> pdb=" O LEU C 435 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N LEU C 440 " --> pdb=" O LEU C 436 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N LEU C 443 " --> pdb=" O ILE C 439 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N GLY C 445 " --> pdb=" O ILE C 441 " (cutoff:3.500A) removed outlier: 4.425A pdb=" N LEU C 448 " --> pdb=" O GLY C 444 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N GLN C 452 " --> pdb=" O LEU C 448 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N TYR C 455 " --> pdb=" O GLY C 451 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N PHE C 456 " --> pdb=" O GLN C 452 " (cutoff:3.500A) Processing helix chain 'C' and resid 463 through 465 No H-bonds generated for 'chain 'C' and resid 463 through 465' Processing helix chain 'C' and resid 466 through 483 removed outlier: 4.143A pdb=" N TYR C 471 " --> pdb=" O PHE C 467 " (cutoff:3.500A) removed outlier: 6.582A pdb=" N PHE C 472 " --> pdb=" O MET C 468 " (cutoff:3.500A) removed outlier: 4.312A pdb=" N GLU C 473 " --> pdb=" O ASP C 469 " (cutoff:3.500A) removed outlier: 3.820A pdb=" N PHE C 476 " --> pdb=" O PHE C 472 " (cutoff:3.500A) removed outlier: 3.926A pdb=" N LEU C 477 " --> pdb=" O GLU C 473 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N GLN C 479 " --> pdb=" O LEU C 475 " (cutoff:3.500A) Processing helix chain 'C' and resid 483 through 491 removed outlier: 4.116A pdb=" N GLN C 487 " --> pdb=" O THR C 483 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N VAL C 488 " --> pdb=" O VAL C 484 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N LEU C 489 " --> pdb=" O LEU C 485 " (cutoff:3.500A) removed outlier: 4.349A pdb=" N PHE C 491 " --> pdb=" O GLN C 487 " (cutoff:3.500A) Processing helix chain 'C' and resid 500 through 511 removed outlier: 3.834A pdb=" N SER C 504 " --> pdb=" O LEU C 500 " (cutoff:3.500A) Processing helix chain 'C' and resid 512 through 514 No H-bonds generated for 'chain 'C' and resid 512 through 514' Processing helix chain 'C' and resid 522 through 545 removed outlier: 3.546A pdb=" N SER C 526 " --> pdb=" O THR C 522 " (cutoff:3.500A) removed outlier: 4.046A pdb=" N MET C 528 " --> pdb=" O ILE C 524 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N VAL C 532 " --> pdb=" O MET C 528 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N ARG C 535 " --> pdb=" O LYS C 531 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N VAL C 543 " --> pdb=" O ARG C 539 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N LEU C 545 " --> pdb=" O LEU C 541 " (cutoff:3.500A) Processing helix chain 'C' and resid 548 through 559 Processing helix chain 'C' and resid 560 through 561 No H-bonds generated for 'chain 'C' and resid 560 through 561' Processing helix chain 'C' and resid 591 through 591 No H-bonds generated for 'chain 'C' and resid 591 through 591' Processing helix chain 'C' and resid 592 through 597 Processing helix chain 'C' and resid 597 through 602 Processing helix chain 'C' and resid 619 through 627 removed outlier: 3.538A pdb=" N LEU C 623 " --> pdb=" O ARG C 619 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N LEU C 627 " --> pdb=" O LEU C 623 " (cutoff:3.500A) Processing helix chain 'C' and resid 628 through 650 removed outlier: 4.002A pdb=" N LEU C 632 " --> pdb=" O ALA C 628 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N TYR C 634 " --> pdb=" O VAL C 630 " (cutoff:3.500A) removed outlier: 4.137A pdb=" N MET C 640 " --> pdb=" O LEU C 636 " (cutoff:3.500A) Processing helix chain 'C' and resid 654 through 668 removed outlier: 4.256A pdb=" N LYS C 661 " --> pdb=" O TRP C 657 " (cutoff:3.500A) Processing helix chain 'C' and resid 669 through 671 No H-bonds generated for 'chain 'C' and resid 669 through 671' Processing helix chain 'D' and resid 76 through 87 Processing helix chain 'D' and resid 94 through 103 Processing helix chain 'D' and resid 119 through 128 removed outlier: 3.612A pdb=" N LEU D 126 " --> pdb=" O MET D 122 " (cutoff:3.500A) removed outlier: 4.213A pdb=" N LEU D 128 " --> pdb=" O ALA D 124 " (cutoff:3.500A) Processing helix chain 'D' and resid 135 through 147 removed outlier: 3.746A pdb=" N GLY D 147 " --> pdb=" O ASP D 143 " (cutoff:3.500A) Processing helix chain 'D' and resid 151 through 155 Processing helix chain 'D' and resid 159 through 163 removed outlier: 3.839A pdb=" N TYR D 162 " --> pdb=" O ASP D 159 " (cutoff:3.500A) Processing helix chain 'D' and resid 167 through 172 Processing helix chain 'D' and resid 177 through 187 removed outlier: 4.197A pdb=" N LYS D 181 " --> pdb=" O LEU D 177 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N LEU D 182 " --> pdb=" O GLN D 178 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N ASN D 186 " --> pdb=" O LEU D 182 " (cutoff:3.500A) Processing helix chain 'D' and resid 212 through 220 removed outlier: 3.779A pdb=" N CYS D 219 " --> pdb=" O SER D 215 " (cutoff:3.500A) Processing helix chain 'D' and resid 224 through 232 removed outlier: 3.543A pdb=" N TYR D 228 " --> pdb=" O ASP D 224 " (cutoff:3.500A) removed outlier: 3.859A pdb=" N LEU D 230 " --> pdb=" O VAL D 226 " (cutoff:3.500A) Processing helix chain 'D' and resid 248 through 257 removed outlier: 3.986A pdb=" N ALA D 252 " --> pdb=" O THR D 248 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N VAL D 254 " --> pdb=" O LEU D 250 " (cutoff:3.500A) Processing helix chain 'D' and resid 260 through 282 removed outlier: 3.527A pdb=" N GLY D 273 " --> pdb=" O HIS D 269 " (cutoff:3.500A) removed outlier: 3.835A pdb=" N LEU D 275 " --> pdb=" O TYR D 271 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N ARG D 280 " --> pdb=" O GLN D 276 " (cutoff:3.500A) Processing helix chain 'D' and resid 297 through 305 removed outlier: 4.112A pdb=" N ALA D 303 " --> pdb=" O LEU D 299 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N LYS D 304 " --> pdb=" O LYS D 300 " (cutoff:3.500A) removed outlier: 3.875A pdb=" N GLU D 305 " --> pdb=" O LEU D 301 " (cutoff:3.500A) Processing helix chain 'D' and resid 310 through 316 Processing helix chain 'D' and resid 356 through 361 removed outlier: 3.691A pdb=" N ALA D 361 " --> pdb=" O LEU D 357 " (cutoff:3.500A) Processing helix chain 'D' and resid 370 through 375 removed outlier: 3.708A pdb=" N LEU D 375 " --> pdb=" O ARG D 371 " (cutoff:3.500A) Processing helix chain 'D' and resid 375 through 407 removed outlier: 3.528A pdb=" N LEU D 381 " --> pdb=" O PRO D 377 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N LEU D 382 " --> pdb=" O LEU D 378 " (cutoff:3.500A) removed outlier: 4.892A pdb=" N GLN D 383 " --> pdb=" O ASN D 379 " (cutoff:3.500A) removed outlier: 3.941A pdb=" N GLU D 384 " --> pdb=" O LYS D 380 " (cutoff:3.500A) removed outlier: 4.077A pdb=" N LYS D 385 " --> pdb=" O LEU D 381 " (cutoff:3.500A) removed outlier: 4.879A pdb=" N ARG D 388 " --> pdb=" O GLU D 384 " (cutoff:3.500A) removed outlier: 4.271A pdb=" N SER D 391 " --> pdb=" O ASP D 387 " (cutoff:3.500A) removed outlier: 4.182A pdb=" N ARG D 392 " --> pdb=" O ARG D 388 " (cutoff:3.500A) removed outlier: 4.558A pdb=" N TYR D 403 " --> pdb=" O CYS D 399 " (cutoff:3.500A) removed outlier: 4.100A pdb=" N MET D 404 " --> pdb=" O TYR D 400 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N ILE D 406 " --> pdb=" O VAL D 402 " (cutoff:3.500A) Processing helix chain 'D' and resid 408 through 414 Processing helix chain 'D' and resid 431 through 459 removed outlier: 3.761A pdb=" N LEU D 435 " --> pdb=" O GLU D 431 " (cutoff:3.500A) removed outlier: 4.549A pdb=" N HIS D 438 " --> pdb=" O LEU D 434 " (cutoff:3.500A) removed outlier: 4.565A pdb=" N ILE D 439 " --> pdb=" O LEU D 435 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N LEU D 440 " --> pdb=" O LEU D 436 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N LEU D 443 " --> pdb=" O ILE D 439 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N GLY D 445 " --> pdb=" O ILE D 441 " (cutoff:3.500A) removed outlier: 4.425A pdb=" N LEU D 448 " --> pdb=" O GLY D 444 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N GLN D 452 " --> pdb=" O LEU D 448 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N TYR D 455 " --> pdb=" O GLY D 451 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N PHE D 456 " --> pdb=" O GLN D 452 " (cutoff:3.500A) Processing helix chain 'D' and resid 463 through 465 No H-bonds generated for 'chain 'D' and resid 463 through 465' Processing helix chain 'D' and resid 466 through 483 removed outlier: 4.143A pdb=" N TYR D 471 " --> pdb=" O PHE D 467 " (cutoff:3.500A) removed outlier: 6.581A pdb=" N PHE D 472 " --> pdb=" O MET D 468 " (cutoff:3.500A) removed outlier: 4.311A pdb=" N GLU D 473 " --> pdb=" O ASP D 469 " (cutoff:3.500A) removed outlier: 3.820A pdb=" N PHE D 476 " --> pdb=" O PHE D 472 " (cutoff:3.500A) removed outlier: 3.925A pdb=" N LEU D 477 " --> pdb=" O GLU D 473 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N GLN D 479 " --> pdb=" O LEU D 475 " (cutoff:3.500A) Processing helix chain 'D' and resid 483 through 491 removed outlier: 4.116A pdb=" N GLN D 487 " --> pdb=" O THR D 483 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N VAL D 488 " --> pdb=" O VAL D 484 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N LEU D 489 " --> pdb=" O LEU D 485 " (cutoff:3.500A) removed outlier: 4.350A pdb=" N PHE D 491 " --> pdb=" O GLN D 487 " (cutoff:3.500A) Processing helix chain 'D' and resid 500 through 511 removed outlier: 3.833A pdb=" N SER D 504 " --> pdb=" O LEU D 500 " (cutoff:3.500A) Processing helix chain 'D' and resid 512 through 514 No H-bonds generated for 'chain 'D' and resid 512 through 514' Processing helix chain 'D' and resid 522 through 545 removed outlier: 3.547A pdb=" N SER D 526 " --> pdb=" O THR D 522 " (cutoff:3.500A) removed outlier: 4.046A pdb=" N MET D 528 " --> pdb=" O ILE D 524 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N VAL D 532 " --> pdb=" O MET D 528 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N ARG D 535 " --> pdb=" O LYS D 531 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N VAL D 543 " --> pdb=" O ARG D 539 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N LEU D 545 " --> pdb=" O LEU D 541 " (cutoff:3.500A) Processing helix chain 'D' and resid 548 through 559 Processing helix chain 'D' and resid 560 through 561 No H-bonds generated for 'chain 'D' and resid 560 through 561' Processing helix chain 'D' and resid 591 through 591 No H-bonds generated for 'chain 'D' and resid 591 through 591' Processing helix chain 'D' and resid 592 through 597 Processing helix chain 'D' and resid 597 through 602 Processing helix chain 'D' and resid 619 through 627 removed outlier: 3.537A pdb=" N LEU D 623 " --> pdb=" O ARG D 619 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N LEU D 627 " --> pdb=" O LEU D 623 " (cutoff:3.500A) Processing helix chain 'D' and resid 628 through 650 removed outlier: 4.003A pdb=" N LEU D 632 " --> pdb=" O ALA D 628 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N TYR D 634 " --> pdb=" O VAL D 630 " (cutoff:3.500A) removed outlier: 4.136A pdb=" N MET D 640 " --> pdb=" O LEU D 636 " (cutoff:3.500A) Processing helix chain 'D' and resid 654 through 668 removed outlier: 4.256A pdb=" N LYS D 661 " --> pdb=" O TRP D 657 " (cutoff:3.500A) Processing helix chain 'D' and resid 669 through 671 No H-bonds generated for 'chain 'D' and resid 669 through 671' Processing sheet with id=AA1, first strand: chain 'A' and resid 332 through 334 removed outlier: 3.526A pdb=" N CYS A 334 " --> pdb=" O VAL A 340 " (cutoff:3.500A) removed outlier: 4.117A pdb=" N VAL A 340 " --> pdb=" O CYS A 334 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 332 through 334 removed outlier: 3.526A pdb=" N CYS B 334 " --> pdb=" O VAL B 340 " (cutoff:3.500A) removed outlier: 4.117A pdb=" N VAL B 340 " --> pdb=" O CYS B 334 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 332 through 334 removed outlier: 3.527A pdb=" N CYS C 334 " --> pdb=" O VAL C 340 " (cutoff:3.500A) removed outlier: 4.117A pdb=" N VAL C 340 " --> pdb=" O CYS C 334 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'D' and resid 332 through 334 removed outlier: 3.526A pdb=" N CYS D 334 " --> pdb=" O VAL D 340 " (cutoff:3.500A) removed outlier: 4.117A pdb=" N VAL D 340 " --> pdb=" O CYS D 334 " (cutoff:3.500A) 728 hydrogen bonds defined for protein. 2136 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: 4.77 Time building geometry restraints manager: 8.99 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: 6009 1.34 - 1.46: 2845 1.46 - 1.57: 11096 1.57 - 1.69: 2 1.69 - 1.81: 172 Bond restraints: 20124 Sorted by residual: bond pdb=" C SER B 366 " pdb=" N PRO B 367 " ideal model delta sigma weight residual 1.336 1.393 -0.057 1.20e-02 6.94e+03 2.24e+01 bond pdb=" C SER D 366 " pdb=" N PRO D 367 " ideal model delta sigma weight residual 1.336 1.392 -0.056 1.20e-02 6.94e+03 2.22e+01 bond pdb=" C SER A 366 " pdb=" N PRO A 367 " ideal model delta sigma weight residual 1.336 1.392 -0.056 1.20e-02 6.94e+03 2.19e+01 bond pdb=" C SER C 366 " pdb=" N PRO C 367 " ideal model delta sigma weight residual 1.336 1.392 -0.056 1.20e-02 6.94e+03 2.17e+01 bond pdb=" CA ILE C 308 " pdb=" C ILE C 308 " ideal model delta sigma weight residual 1.524 1.563 -0.040 1.30e-02 5.92e+03 9.28e+00 ... (remaining 20119 not shown) Histogram of bond angle deviations from ideal: 94.21 - 102.59: 88 102.59 - 110.96: 6124 110.96 - 119.34: 10264 119.34 - 127.71: 10568 127.71 - 136.09: 244 Bond angle restraints: 27288 Sorted by residual: angle pdb=" N ILE D 308 " pdb=" CA ILE D 308 " pdb=" C ILE D 308 " ideal model delta sigma weight residual 110.72 125.67 -14.95 1.01e+00 9.80e-01 2.19e+02 angle pdb=" N ILE A 308 " pdb=" CA ILE A 308 " pdb=" C ILE A 308 " ideal model delta sigma weight residual 110.72 125.67 -14.95 1.01e+00 9.80e-01 2.19e+02 angle pdb=" N ILE C 308 " pdb=" CA ILE C 308 " pdb=" C ILE C 308 " ideal model delta sigma weight residual 110.72 125.66 -14.94 1.01e+00 9.80e-01 2.19e+02 angle pdb=" N ILE B 308 " pdb=" CA ILE B 308 " pdb=" C ILE B 308 " ideal model delta sigma weight residual 110.72 125.65 -14.93 1.01e+00 9.80e-01 2.19e+02 angle pdb=" C LYS B 307 " pdb=" CA LYS B 307 " pdb=" CB LYS B 307 " ideal model delta sigma weight residual 109.89 130.32 -20.43 1.60e+00 3.91e-01 1.63e+02 ... (remaining 27283 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.92: 10642 15.92 - 31.85: 902 31.85 - 47.77: 214 47.77 - 63.69: 37 63.69 - 79.61: 17 Dihedral angle restraints: 11812 sinusoidal: 4784 harmonic: 7028 Sorted by residual: dihedral pdb=" CA GLU C 493 " pdb=" C GLU C 493 " pdb=" N THR C 494 " pdb=" CA THR C 494 " ideal model delta harmonic sigma weight residual 180.00 100.39 79.61 0 5.00e+00 4.00e-02 2.54e+02 dihedral pdb=" CA GLU A 493 " pdb=" C GLU A 493 " pdb=" N THR A 494 " pdb=" CA THR A 494 " ideal model delta harmonic sigma weight residual 180.00 100.42 79.58 0 5.00e+00 4.00e-02 2.53e+02 dihedral pdb=" CA GLU D 493 " pdb=" C GLU D 493 " pdb=" N THR D 494 " pdb=" CA THR D 494 " ideal model delta harmonic sigma weight residual 180.00 100.44 79.56 0 5.00e+00 4.00e-02 2.53e+02 ... (remaining 11809 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.150: 2880 0.150 - 0.299: 144 0.299 - 0.449: 32 0.449 - 0.599: 4 0.599 - 0.749: 4 Chirality restraints: 3064 Sorted by residual: chirality pdb=" CA THR C 494 " pdb=" N THR C 494 " pdb=" C THR C 494 " pdb=" CB THR C 494 " both_signs ideal model delta sigma weight residual False 2.53 1.78 0.75 2.00e-01 2.50e+01 1.40e+01 chirality pdb=" CA THR A 494 " pdb=" N THR A 494 " pdb=" C THR A 494 " pdb=" CB THR A 494 " both_signs ideal model delta sigma weight residual False 2.53 1.78 0.75 2.00e-01 2.50e+01 1.39e+01 chirality pdb=" CA THR B 494 " pdb=" N THR B 494 " pdb=" C THR B 494 " pdb=" CB THR B 494 " both_signs ideal model delta sigma weight residual False 2.53 1.78 0.75 2.00e-01 2.50e+01 1.39e+01 ... (remaining 3061 not shown) Planarity restraints: 3380 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA GLU B 318 " -0.019 2.00e-02 2.50e+03 3.86e-02 1.49e+01 pdb=" C GLU B 318 " 0.067 2.00e-02 2.50e+03 pdb=" O GLU B 318 " -0.026 2.00e-02 2.50e+03 pdb=" N PHE B 319 " -0.022 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLU C 318 " -0.019 2.00e-02 2.50e+03 3.85e-02 1.48e+01 pdb=" C GLU C 318 " 0.067 2.00e-02 2.50e+03 pdb=" O GLU C 318 " -0.026 2.00e-02 2.50e+03 pdb=" N PHE C 319 " -0.022 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLU A 318 " 0.019 2.00e-02 2.50e+03 3.84e-02 1.47e+01 pdb=" C GLU A 318 " -0.066 2.00e-02 2.50e+03 pdb=" O GLU A 318 " 0.025 2.00e-02 2.50e+03 pdb=" N PHE A 319 " 0.022 2.00e-02 2.50e+03 ... (remaining 3377 not shown) Histogram of nonbonded interaction distances: 2.03 - 2.61: 169 2.61 - 3.18: 17044 3.18 - 3.75: 31035 3.75 - 4.33: 42687 4.33 - 4.90: 63617 Nonbonded interactions: 154552 Sorted by model distance: nonbonded pdb=" NH1 ARG B 694 " pdb=" N GLY B 695 " model vdw 2.033 3.200 nonbonded pdb=" NH1 ARG C 694 " pdb=" N GLY C 695 " model vdw 2.033 3.200 nonbonded pdb=" NH1 ARG D 694 " pdb=" N GLY D 695 " model vdw 2.033 3.200 nonbonded pdb=" NH1 ARG A 694 " pdb=" N GLY A 695 " model vdw 2.033 3.200 nonbonded pdb=" NH1 ARG B 694 " pdb=" CA GLY B 695 " model vdw 2.229 3.520 ... (remaining 154547 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue 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: 0.680 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.010 Extract box with map and model: 3.690 Check model and map are aligned: 0.320 Set scattering table: 0.180 Process input model: 48.080 Find NCS groups from input model: 1.030 Set up NCS constraints: 0.100 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.380 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 56.480 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7408 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 : 0.009 0.057 20124 Z= 0.558 Angle : 1.464 20.435 27288 Z= 0.955 Chirality : 0.086 0.749 3064 Planarity : 0.006 0.069 3380 Dihedral : 13.125 79.612 7276 Min Nonbonded Distance : 2.033 Molprobity Statistics. All-atom Clashscore : 23.50 Ramachandran Plot: Outliers : 0.84 % Allowed : 7.72 % Favored : 91.44 % Rotamer Outliers : 0.93 % Cbeta Deviations : 0.88 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 0.34 % Twisted Proline : 5.56 % Twisted General : 2.58 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.25 (0.14), residues: 2384 helix: -3.02 (0.11), residues: 1180 sheet: -2.94 (0.50), residues: 40 loop : -2.53 (0.16), residues: 1164 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4768 Ramachandran restraints generated. 2384 Oldfield, 0 Emsley, 2384 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4768 Ramachandran restraints generated. 2384 Oldfield, 0 Emsley, 2384 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 694 residues out of total 2140 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 674 time to evaluate : 2.437 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 20 outliers final: 4 residues processed: 694 average time/residue: 0.3558 time to fit residues: 359.8140 Evaluate side-chains 355 residues out of total 2140 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 351 time to evaluate : 2.568 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.1668 time to fit residues: 4.6120 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 202 optimal weight: 3.9990 chunk 181 optimal weight: 5.9990 chunk 100 optimal weight: 9.9990 chunk 62 optimal weight: 8.9990 chunk 122 optimal weight: 7.9990 chunk 97 optimal weight: 4.9990 chunk 188 optimal weight: 0.8980 chunk 72 optimal weight: 10.0000 chunk 114 optimal weight: 0.9980 chunk 140 optimal weight: 2.9990 chunk 217 optimal weight: 6.9990 overall best weight: 2.7786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 129 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 133 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 251 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 259 ASN A 396 ASN ** A 452 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 511 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 521 HIS A 651 HIS ** A 673 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 129 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 133 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 251 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 396 ASN ** B 452 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 511 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 521 HIS B 651 HIS ** B 655 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 673 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 129 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 133 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 251 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 259 ASN C 396 ASN ** C 452 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 511 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 521 HIS ** C 673 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 129 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 133 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 251 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 259 ASN D 396 ASN ** D 452 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 511 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 521 HIS ** D 673 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7709 moved from start: 0.4913 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.031 20124 Z= 0.244 Angle : 0.842 10.925 27288 Z= 0.422 Chirality : 0.045 0.269 3064 Planarity : 0.006 0.070 3380 Dihedral : 7.650 29.457 2632 Min Nonbonded Distance : 2.103 Molprobity Statistics. All-atom Clashscore : 17.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.96 % Favored : 93.04 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 0.34 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.01 (0.15), residues: 2384 helix: -1.79 (0.13), residues: 1168 sheet: -3.62 (0.47), residues: 72 loop : -2.04 (0.18), residues: 1144 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4768 Ramachandran restraints generated. 2384 Oldfield, 0 Emsley, 2384 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4768 Ramachandran restraints generated. 2384 Oldfield, 0 Emsley, 2384 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 435 residues out of total 2140 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 435 time to evaluate : 2.472 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 435 average time/residue: 0.3294 time to fit residues: 218.3539 Evaluate side-chains 287 residues out of total 2140 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 287 time to evaluate : 2.429 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 3.2471 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 121 optimal weight: 0.6980 chunk 67 optimal weight: 7.9990 chunk 181 optimal weight: 0.5980 chunk 148 optimal weight: 6.9990 chunk 60 optimal weight: 10.0000 chunk 218 optimal weight: 4.9990 chunk 235 optimal weight: 0.0070 chunk 194 optimal weight: 2.9990 chunk 216 optimal weight: 9.9990 chunk 74 optimal weight: 9.9990 chunk 175 optimal weight: 0.7980 overall best weight: 1.0200 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 129 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 396 ASN A 413 HIS ** A 452 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 511 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 129 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 396 ASN B 413 HIS ** B 452 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 511 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 639 ASN ** C 129 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 396 ASN C 413 HIS ** C 452 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 129 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 396 ASN D 413 HIS ** D 452 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 511 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7702 moved from start: 0.5786 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.036 20124 Z= 0.180 Angle : 0.763 11.300 27288 Z= 0.376 Chirality : 0.043 0.267 3064 Planarity : 0.005 0.050 3380 Dihedral : 6.932 28.365 2632 Min Nonbonded Distance : 2.071 Molprobity Statistics. All-atom Clashscore : 16.96 Ramachandran Plot: Outliers : 0.17 % Allowed : 7.51 % Favored : 92.32 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 0.34 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.70 (0.15), residues: 2384 helix: -1.43 (0.13), residues: 1208 sheet: -3.12 (0.48), residues: 72 loop : -2.04 (0.17), residues: 1104 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4768 Ramachandran restraints generated. 2384 Oldfield, 0 Emsley, 2384 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4768 Ramachandran restraints generated. 2384 Oldfield, 0 Emsley, 2384 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 397 residues out of total 2140 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 397 time to evaluate : 2.426 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 397 average time/residue: 0.3143 time to fit residues: 190.6323 Evaluate side-chains 260 residues out of total 2140 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 260 time to evaluate : 2.445 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 3.2629 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 215 optimal weight: 8.9990 chunk 164 optimal weight: 4.9990 chunk 113 optimal weight: 5.9990 chunk 24 optimal weight: 9.9990 chunk 104 optimal weight: 20.0000 chunk 146 optimal weight: 5.9990 chunk 219 optimal weight: 20.0000 chunk 231 optimal weight: 5.9990 chunk 114 optimal weight: 0.9990 chunk 207 optimal weight: 10.0000 chunk 62 optimal weight: 8.9990 overall best weight: 4.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 129 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 141 GLN ** A 247 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 259 ASN A 396 ASN A 438 HIS ** A 452 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 129 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 133 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 141 GLN ** B 247 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 396 ASN B 438 HIS ** B 452 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 663 GLN ** C 129 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 247 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 324 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 396 ASN C 438 HIS ** C 452 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 129 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 247 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 396 ASN D 438 HIS ** D 452 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7947 moved from start: 0.7268 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.040 20124 Z= 0.299 Angle : 0.830 9.471 27288 Z= 0.419 Chirality : 0.046 0.248 3064 Planarity : 0.006 0.059 3380 Dihedral : 7.165 30.084 2632 Min Nonbonded Distance : 2.049 Molprobity Statistics. All-atom Clashscore : 26.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.52 % Favored : 91.48 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 0.34 % Twisted Proline : 1.39 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.62 (0.16), residues: 2384 helix: -1.36 (0.13), residues: 1272 sheet: -2.75 (0.54), residues: 72 loop : -2.03 (0.18), residues: 1040 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4768 Ramachandran restraints generated. 2384 Oldfield, 0 Emsley, 2384 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4768 Ramachandran restraints generated. 2384 Oldfield, 0 Emsley, 2384 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 335 residues out of total 2140 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 335 time to evaluate : 2.542 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 335 average time/residue: 0.3157 time to fit residues: 162.0504 Evaluate side-chains 208 residues out of total 2140 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 208 time to evaluate : 2.320 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 3.2114 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 193 optimal weight: 4.9990 chunk 131 optimal weight: 8.9990 chunk 3 optimal weight: 20.0000 chunk 172 optimal weight: 2.9990 chunk 95 optimal weight: 10.0000 chunk 197 optimal weight: 4.9990 chunk 160 optimal weight: 20.0000 chunk 0 optimal weight: 10.0000 chunk 118 optimal weight: 40.0000 chunk 208 optimal weight: 3.9990 chunk 58 optimal weight: 30.0000 overall best weight: 5.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 129 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 235 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 247 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 324 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 452 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 511 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 129 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 247 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 316 GLN ** B 324 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 396 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 452 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 511 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 129 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 141 GLN ** C 247 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 324 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 396 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 452 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 129 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 133 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 141 GLN ** D 247 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 269 HIS ** D 324 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 452 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7989 moved from start: 0.8107 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.051 20124 Z= 0.301 Angle : 0.813 10.824 27288 Z= 0.410 Chirality : 0.045 0.258 3064 Planarity : 0.006 0.063 3380 Dihedral : 6.945 30.543 2632 Min Nonbonded Distance : 2.029 Molprobity Statistics. All-atom Clashscore : 25.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.56 % Favored : 91.44 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 0.34 % Twisted Proline : 0.00 % Twisted General : 0.09 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.48 (0.16), residues: 2384 helix: -1.22 (0.14), residues: 1260 sheet: -2.44 (0.52), residues: 72 loop : -2.03 (0.18), residues: 1052 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4768 Ramachandran restraints generated. 2384 Oldfield, 0 Emsley, 2384 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4768 Ramachandran restraints generated. 2384 Oldfield, 0 Emsley, 2384 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 293 residues out of total 2140 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 293 time to evaluate : 2.399 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 293 average time/residue: 0.2933 time to fit residues: 136.0794 Evaluate side-chains 213 residues out of total 2140 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 213 time to evaluate : 2.306 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 3.3047 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 78 optimal weight: 0.9990 chunk 208 optimal weight: 7.9990 chunk 45 optimal weight: 6.9990 chunk 136 optimal weight: 6.9990 chunk 57 optimal weight: 20.0000 chunk 232 optimal weight: 4.9990 chunk 192 optimal weight: 9.9990 chunk 107 optimal weight: 10.0000 chunk 19 optimal weight: 4.9990 chunk 76 optimal weight: 10.0000 chunk 121 optimal weight: 2.9990 overall best weight: 4.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 129 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 235 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 247 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 324 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 452 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 511 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 129 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 186 ASN B 235 GLN ** B 247 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 316 GLN B 324 GLN ** B 452 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 511 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 663 GLN ** C 129 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 186 ASN ** C 247 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 316 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 324 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 370 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 452 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 511 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 129 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 133 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 186 ASN ** D 247 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 324 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 452 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 511 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7989 moved from start: 0.8525 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.048 20124 Z= 0.267 Angle : 0.797 11.255 27288 Z= 0.394 Chirality : 0.044 0.234 3064 Planarity : 0.005 0.040 3380 Dihedral : 6.792 33.153 2632 Min Nonbonded Distance : 2.062 Molprobity Statistics. All-atom Clashscore : 25.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.81 % Favored : 91.19 % Rotamer Outliers : 0.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 0.34 % Twisted Proline : 2.78 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.47 (0.16), residues: 2384 helix: -1.24 (0.13), residues: 1320 sheet: -2.06 (0.56), residues: 72 loop : -2.04 (0.19), residues: 992 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4768 Ramachandran restraints generated. 2384 Oldfield, 0 Emsley, 2384 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4768 Ramachandran restraints generated. 2384 Oldfield, 0 Emsley, 2384 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 309 residues out of total 2140 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 308 time to evaluate : 2.456 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 1 outliers final: 0 residues processed: 309 average time/residue: 0.2806 time to fit residues: 139.1463 Evaluate side-chains 224 residues out of total 2140 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 224 time to evaluate : 2.348 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 3.2393 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 223 optimal weight: 3.9990 chunk 26 optimal weight: 0.0470 chunk 132 optimal weight: 8.9990 chunk 169 optimal weight: 0.7980 chunk 131 optimal weight: 5.9990 chunk 195 optimal weight: 2.9990 chunk 129 optimal weight: 6.9990 chunk 231 optimal weight: 20.0000 chunk 144 optimal weight: 2.9990 chunk 141 optimal weight: 0.0170 chunk 106 optimal weight: 6.9990 overall best weight: 1.3720 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 129 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 186 ASN ** A 247 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 324 GLN A 452 GLN ** B 129 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 247 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 354 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 452 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 129 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 133 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 247 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 324 GLN ** C 370 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 452 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 655 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 129 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 247 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 324 GLN D 452 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7911 moved from start: 0.8697 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.046 20124 Z= 0.184 Angle : 0.758 12.538 27288 Z= 0.366 Chirality : 0.043 0.224 3064 Planarity : 0.004 0.045 3380 Dihedral : 6.306 30.173 2632 Min Nonbonded Distance : 2.055 Molprobity Statistics. All-atom Clashscore : 20.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.21 % Favored : 92.79 % Rotamer Outliers : 0.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 0.34 % Twisted Proline : 1.39 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.22 (0.16), residues: 2384 helix: -1.04 (0.13), residues: 1316 sheet: -1.98 (0.53), residues: 72 loop : -1.90 (0.19), residues: 996 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4768 Ramachandran restraints generated. 2384 Oldfield, 0 Emsley, 2384 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4768 Ramachandran restraints generated. 2384 Oldfield, 0 Emsley, 2384 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 334 residues out of total 2140 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 331 time to evaluate : 2.472 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 3 outliers final: 3 residues processed: 334 average time/residue: 0.2742 time to fit residues: 147.8896 Evaluate side-chains 244 residues out of total 2140 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 241 time to evaluate : 2.376 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.2049 time to fit residues: 4.1989 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 143 optimal weight: 10.0000 chunk 92 optimal weight: 10.0000 chunk 138 optimal weight: 0.7980 chunk 69 optimal weight: 0.9980 chunk 45 optimal weight: 1.9990 chunk 44 optimal weight: 4.9990 chunk 147 optimal weight: 9.9990 chunk 157 optimal weight: 3.9990 chunk 114 optimal weight: 7.9990 chunk 21 optimal weight: 0.7980 chunk 181 optimal weight: 0.0970 overall best weight: 0.9380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 129 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 247 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 129 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 247 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 313 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 452 GLN ** C 129 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 133 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 247 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 370 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 452 GLN ** D 129 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 247 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7880 moved from start: 0.8883 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.040 20124 Z= 0.178 Angle : 0.746 12.300 27288 Z= 0.357 Chirality : 0.042 0.221 3064 Planarity : 0.004 0.043 3380 Dihedral : 6.031 28.616 2632 Min Nonbonded Distance : 2.093 Molprobity Statistics. All-atom Clashscore : 18.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.38 % Favored : 92.62 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 0.34 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.98 (0.16), residues: 2384 helix: -0.83 (0.14), residues: 1284 sheet: -1.93 (0.53), residues: 72 loop : -1.80 (0.19), residues: 1028 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4768 Ramachandran restraints generated. 2384 Oldfield, 0 Emsley, 2384 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4768 Ramachandran restraints generated. 2384 Oldfield, 0 Emsley, 2384 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 338 residues out of total 2140 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 338 time to evaluate : 2.357 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 338 average time/residue: 0.2962 time to fit residues: 158.0666 Evaluate side-chains 234 residues out of total 2140 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 234 time to evaluate : 2.453 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 3.2852 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 210 optimal weight: 3.9990 chunk 221 optimal weight: 2.9990 chunk 202 optimal weight: 0.0050 chunk 215 optimal weight: 9.9990 chunk 129 optimal weight: 2.9990 chunk 93 optimal weight: 6.9990 chunk 169 optimal weight: 20.0000 chunk 66 optimal weight: 6.9990 chunk 194 optimal weight: 4.9990 chunk 203 optimal weight: 9.9990 chunk 214 optimal weight: 8.9990 overall best weight: 3.0002 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 129 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 247 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 259 ASN ** A 673 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 129 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 247 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 313 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 129 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 247 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 370 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 129 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 247 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 316 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7937 moved from start: 0.9173 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.051 20124 Z= 0.218 Angle : 0.750 12.363 27288 Z= 0.370 Chirality : 0.043 0.230 3064 Planarity : 0.005 0.064 3380 Dihedral : 6.208 29.232 2632 Min Nonbonded Distance : 2.097 Molprobity Statistics. All-atom Clashscore : 21.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.06 % Favored : 90.94 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 0.34 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.91 (0.17), residues: 2384 helix: -0.83 (0.14), residues: 1256 sheet: -0.91 (0.54), residues: 88 loop : -1.76 (0.19), residues: 1040 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4768 Ramachandran restraints generated. 2384 Oldfield, 0 Emsley, 2384 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4768 Ramachandran restraints generated. 2384 Oldfield, 0 Emsley, 2384 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 298 residues out of total 2140 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 298 time to evaluate : 2.250 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 298 average time/residue: 0.2905 time to fit residues: 139.2366 Evaluate side-chains 222 residues out of total 2140 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 222 time to evaluate : 2.779 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 3.4746 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 141 optimal weight: 0.8980 chunk 227 optimal weight: 0.8980 chunk 139 optimal weight: 0.0770 chunk 108 optimal weight: 20.0000 chunk 158 optimal weight: 7.9990 chunk 239 optimal weight: 5.9990 chunk 220 optimal weight: 20.0000 chunk 190 optimal weight: 0.9980 chunk 19 optimal weight: 5.9990 chunk 147 optimal weight: 0.0000 chunk 116 optimal weight: 9.9990 overall best weight: 0.5742 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 102 ASN ** A 129 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 247 ASN ** B 129 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 247 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 313 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 102 ASN ** C 129 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 247 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 313 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 370 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 102 ASN ** D 129 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 247 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 316 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7854 moved from start: 0.9296 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.043 20124 Z= 0.173 Angle : 0.753 12.311 27288 Z= 0.359 Chirality : 0.042 0.205 3064 Planarity : 0.004 0.044 3380 Dihedral : 5.879 27.868 2632 Min Nonbonded Distance : 2.093 Molprobity Statistics. All-atom Clashscore : 17.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.54 % Favored : 93.46 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 0.34 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.88 (0.17), residues: 2384 helix: -0.66 (0.14), residues: 1260 sheet: -0.80 (0.54), residues: 88 loop : -1.97 (0.19), residues: 1036 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4768 Ramachandran restraints generated. 2384 Oldfield, 0 Emsley, 2384 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4768 Ramachandran restraints generated. 2384 Oldfield, 0 Emsley, 2384 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 321 residues out of total 2140 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 321 time to evaluate : 2.542 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 321 average time/residue: 0.2876 time to fit residues: 146.5736 Evaluate side-chains 244 residues out of total 2140 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 244 time to evaluate : 2.364 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 3.1899 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 151 optimal weight: 0.4980 chunk 202 optimal weight: 0.0010 chunk 58 optimal weight: 3.9990 chunk 175 optimal weight: 0.9990 chunk 28 optimal weight: 0.6980 chunk 52 optimal weight: 7.9990 chunk 190 optimal weight: 2.9990 chunk 79 optimal weight: 0.9980 chunk 195 optimal weight: 0.0770 chunk 24 optimal weight: 8.9990 chunk 35 optimal weight: 7.9990 overall best weight: 0.4544 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 129 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 129 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 247 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 129 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 247 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 313 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 370 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 129 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 247 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 = 0.3715 r_free = 0.3715 target = 0.085742 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3409 r_free = 0.3409 target = 0.069776 restraints weight = 95597.868| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3441 r_free = 0.3441 target = 0.071263 restraints weight = 64822.229| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3462 r_free = 0.3462 target = 0.072272 restraints weight = 48361.237| |-----------------------------------------------------------------------------| r_work (final): 0.3442 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7848 moved from start: 0.9429 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.034 20124 Z= 0.165 Angle : 0.732 11.422 27288 Z= 0.350 Chirality : 0.042 0.219 3064 Planarity : 0.004 0.046 3380 Dihedral : 5.736 28.087 2632 Min Nonbonded Distance : 2.102 Molprobity Statistics. All-atom Clashscore : 17.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.01 % Favored : 92.99 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 0.34 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.69 (0.17), residues: 2384 helix: -0.59 (0.14), residues: 1252 sheet: -0.54 (0.54), residues: 88 loop : -1.78 (0.19), residues: 1044 =============================================================================== Job complete usr+sys time: 3780.49 seconds wall clock time: 70 minutes 12.69 seconds (4212.69 seconds total)