Starting phenix.real_space_refine on Mon Mar 18 01:52:19 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5hi9_6580/03_2024/5hi9_6580.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5hi9_6580/03_2024/5hi9_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_6580/03_2024/5hi9_6580.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5hi9_6580/03_2024/5hi9_6580.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5hi9_6580/03_2024/5hi9_6580.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5hi9_6580/03_2024/5hi9_6580.pdb" } resolution = 4.4 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.004 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-dev-5265/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: 10.39, per 1000 atoms: 0.53 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: 7.49 Conformation dependent library (CDL) restraints added in 3.6 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: 1.94 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: 6.28 Time building geometry restraints manager: 8.16 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: 0.940 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.030 Extract box with map and model: 2.860 Check model and map are aligned: 0.320 Set scattering table: 0.190 Process input model: 49.900 Find NCS groups from input model: 1.470 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: 0.010 Load rotamer database and sin/cos tables:3.270 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 59.090 ------------------------------------------------------------------------------- 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 % Allowed : 7.48 % Favored : 91.59 % 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 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP C 677 HIS 0.005 0.001 HIS A 251 PHE 0.014 0.002 PHE C 81 TYR 0.018 0.002 TYR D 323 ARG 0.005 0.001 ARG B 77 *********************** 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 : 2.239 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: A 154 ASN cc_start: 0.8806 (m-40) cc_final: 0.8454 (m-40) REVERT: A 170 ILE cc_start: 0.8173 (mt) cc_final: 0.7922 (tp) REVERT: A 216 LEU cc_start: 0.9022 (pp) cc_final: 0.8683 (pp) REVERT: A 251 HIS cc_start: 0.8276 (m90) cc_final: 0.7974 (m170) REVERT: A 271 TYR cc_start: 0.8640 (t80) cc_final: 0.8154 (t80) REVERT: A 394 PHE cc_start: 0.7138 (t80) cc_final: 0.6811 (t80) REVERT: A 433 MET cc_start: 0.4715 (mtp) cc_final: 0.4427 (mtm) REVERT: A 481 LEU cc_start: 0.8426 (tp) cc_final: 0.8008 (pp) REVERT: A 482 LEU cc_start: 0.8553 (tp) cc_final: 0.8337 (tp) REVERT: A 629 TYR cc_start: 0.8455 (m-10) cc_final: 0.8249 (m-80) REVERT: A 641 LEU cc_start: 0.9084 (mp) cc_final: 0.8824 (tt) REVERT: A 645 MET cc_start: 0.9142 (mmp) cc_final: 0.8870 (mmm) REVERT: A 661 LYS cc_start: 0.7931 (mppt) cc_final: 0.7174 (mttt) REVERT: A 664 LYS cc_start: 0.8575 (mtmt) cc_final: 0.7993 (mtmt) REVERT: A 666 ILE cc_start: 0.9691 (mt) cc_final: 0.9412 (tp) REVERT: A 694 ARG cc_start: 0.6952 (OUTLIER) cc_final: 0.5959 (ttt-90) REVERT: B 154 ASN cc_start: 0.8815 (m-40) cc_final: 0.8503 (m-40) REVERT: B 170 ILE cc_start: 0.8260 (mt) cc_final: 0.8047 (tp) REVERT: B 216 LEU cc_start: 0.9023 (pp) cc_final: 0.8657 (pp) REVERT: B 251 HIS cc_start: 0.8284 (m90) cc_final: 0.7976 (m170) REVERT: B 299 LEU cc_start: 0.9181 (mm) cc_final: 0.8714 (tp) REVERT: B 319 PHE cc_start: 0.7171 (p90) cc_final: 0.6791 (p90) REVERT: B 345 LEU cc_start: 0.7331 (tm) cc_final: 0.7004 (mp) REVERT: B 347 SER cc_start: 0.7203 (t) cc_final: 0.6453 (p) REVERT: B 394 PHE cc_start: 0.7319 (t80) cc_final: 0.7063 (t80) REVERT: B 433 MET cc_start: 0.5001 (mtp) cc_final: 0.4722 (mtm) REVERT: B 481 LEU cc_start: 0.8437 (tp) cc_final: 0.8042 (pp) REVERT: B 482 LEU cc_start: 0.8514 (tp) cc_final: 0.8205 (tp) REVERT: B 530 GLN cc_start: 0.9234 (tp40) cc_final: 0.8980 (tm-30) REVERT: B 629 TYR cc_start: 0.8405 (m-10) cc_final: 0.8045 (m-80) REVERT: B 641 LEU cc_start: 0.9070 (mp) cc_final: 0.8559 (tt) REVERT: B 645 MET cc_start: 0.9089 (mmp) cc_final: 0.8824 (mmm) REVERT: B 666 ILE cc_start: 0.9670 (mt) cc_final: 0.9394 (tp) REVERT: B 694 ARG cc_start: 0.7068 (OUTLIER) cc_final: 0.5840 (ttt-90) REVERT: C 154 ASN cc_start: 0.8817 (m-40) cc_final: 0.8466 (m-40) REVERT: C 170 ILE cc_start: 0.8164 (mt) cc_final: 0.7871 (tp) REVERT: C 216 LEU cc_start: 0.9009 (pp) cc_final: 0.8497 (pp) REVERT: C 251 HIS cc_start: 0.8278 (m90) cc_final: 0.7981 (m170) REVERT: C 271 TYR cc_start: 0.8653 (t80) cc_final: 0.8168 (t80) REVERT: C 345 LEU cc_start: 0.7444 (tm) cc_final: 0.7062 (mp) REVERT: C 394 PHE cc_start: 0.7342 (t80) cc_final: 0.7102 (t80) REVERT: C 433 MET cc_start: 0.4773 (mtp) cc_final: 0.4442 (mtm) REVERT: C 481 LEU cc_start: 0.8365 (tp) cc_final: 0.7970 (pp) REVERT: C 544 TYR cc_start: 0.8268 (t80) cc_final: 0.7980 (t80) REVERT: C 633 THR cc_start: 0.8808 (m) cc_final: 0.8563 (p) REVERT: C 637 LEU cc_start: 0.8510 (mt) cc_final: 0.8266 (mt) REVERT: C 641 LEU cc_start: 0.9060 (mp) cc_final: 0.8793 (tt) REVERT: C 645 MET cc_start: 0.9058 (mmp) cc_final: 0.8819 (mmm) REVERT: C 661 LYS cc_start: 0.7850 (mppt) cc_final: 0.7075 (mttt) REVERT: C 664 LYS cc_start: 0.8564 (mtmt) cc_final: 0.8028 (mtmt) REVERT: C 666 ILE cc_start: 0.9665 (mt) cc_final: 0.9390 (tp) REVERT: C 694 ARG cc_start: 0.7044 (OUTLIER) cc_final: 0.5880 (ttt-90) REVERT: D 154 ASN cc_start: 0.8807 (m-40) cc_final: 0.8463 (m-40) REVERT: D 170 ILE cc_start: 0.8173 (mt) cc_final: 0.7920 (tp) REVERT: D 216 LEU cc_start: 0.9023 (pp) cc_final: 0.8673 (pp) REVERT: D 251 HIS cc_start: 0.8268 (m90) cc_final: 0.7976 (m170) REVERT: D 271 TYR cc_start: 0.8636 (t80) cc_final: 0.8154 (t80) REVERT: D 345 LEU cc_start: 0.7428 (tm) cc_final: 0.7007 (mp) REVERT: D 394 PHE cc_start: 0.7108 (t80) cc_final: 0.6813 (t80) REVERT: D 433 MET cc_start: 0.4900 (mtp) cc_final: 0.4645 (mtm) REVERT: D 481 LEU cc_start: 0.8447 (tp) cc_final: 0.8047 (pp) REVERT: D 482 LEU cc_start: 0.8541 (tp) cc_final: 0.8331 (tp) REVERT: D 633 THR cc_start: 0.8869 (m) cc_final: 0.8644 (p) REVERT: D 637 LEU cc_start: 0.8512 (mt) cc_final: 0.8264 (mt) REVERT: D 641 LEU cc_start: 0.9070 (mp) cc_final: 0.8791 (tt) REVERT: D 645 MET cc_start: 0.9105 (mmp) cc_final: 0.8864 (mmm) REVERT: D 666 ILE cc_start: 0.9666 (mt) cc_final: 0.9389 (tp) REVERT: D 694 ARG cc_start: 0.7034 (OUTLIER) cc_final: 0.5887 (ttt-90) outliers start: 20 outliers final: 4 residues processed: 694 average time/residue: 0.3457 time to fit residues: 347.3813 Evaluate side-chains 391 residues out of total 2140 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 383 time to evaluate : 2.114 ------------------------------------------------------------------------------- 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: 0.9990 chunk 181 optimal weight: 5.9990 chunk 100 optimal weight: 3.9990 chunk 62 optimal weight: 8.9990 chunk 122 optimal weight: 7.9990 chunk 97 optimal weight: 4.9990 chunk 188 optimal weight: 0.7980 chunk 72 optimal weight: 9.9990 chunk 114 optimal weight: 1.9990 chunk 140 optimal weight: 4.9990 chunk 217 optimal weight: 6.9990 overall best weight: 2.5588 ------------------------------------------------------------------------------- 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 259 ASN ** A 354 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 370 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 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 ** B 129 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 133 ASN ** 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 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 259 ASN ** C 370 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 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 259 ASN ** D 370 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 396 ASN ** D 452 GLN ** 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: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7700 moved from start: 0.4690 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 20124 Z= 0.237 Angle : 0.836 10.808 27288 Z= 0.417 Chirality : 0.046 0.286 3064 Planarity : 0.006 0.069 3380 Dihedral : 7.634 29.097 2632 Min Nonbonded Distance : 2.104 Molprobity Statistics. All-atom Clashscore : 17.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.38 % Favored : 93.62 % Rotamer: Outliers : 0.00 % Allowed : 5.65 % Favored : 94.35 % 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: -3.04 (0.15), residues: 2384 helix: -1.88 (0.13), residues: 1160 sheet: -3.83 (0.44), residues: 72 loop : -1.94 (0.18), residues: 1152 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP D 660 HIS 0.006 0.001 HIS B 363 PHE 0.017 0.002 PHE C 207 TYR 0.015 0.001 TYR B 228 ARG 0.006 0.001 ARG B 539 *********************** 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 445 residues out of total 2140 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 445 time to evaluate : 2.255 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: A 122 MET cc_start: 0.8296 (mtt) cc_final: 0.8083 (mtp) REVERT: A 141 GLN cc_start: 0.9230 (tp40) cc_final: 0.9003 (tp-100) REVERT: A 144 LYS cc_start: 0.9700 (tptp) cc_final: 0.9372 (ptpt) REVERT: A 170 ILE cc_start: 0.8672 (mt) cc_final: 0.8423 (tp) REVERT: A 208 TYR cc_start: 0.7316 (t80) cc_final: 0.7090 (t80) REVERT: A 221 LYS cc_start: 0.6516 (pttt) cc_final: 0.6278 (pttm) REVERT: A 251 HIS cc_start: 0.8583 (m90) cc_final: 0.8364 (m90) REVERT: A 270 MET cc_start: 0.8961 (mmm) cc_final: 0.8730 (mmm) REVERT: A 271 TYR cc_start: 0.8414 (t80) cc_final: 0.8065 (t80) REVERT: A 388 ARG cc_start: 0.8720 (mtp180) cc_final: 0.8505 (ptp-170) REVERT: A 394 PHE cc_start: 0.7200 (t80) cc_final: 0.6972 (t80) REVERT: A 433 MET cc_start: 0.5720 (mtp) cc_final: 0.5509 (mtm) REVERT: A 481 LEU cc_start: 0.8674 (tp) cc_final: 0.8423 (pp) REVERT: A 482 LEU cc_start: 0.8653 (tp) cc_final: 0.8417 (tp) REVERT: A 633 THR cc_start: 0.8639 (p) cc_final: 0.8436 (t) REVERT: A 637 LEU cc_start: 0.8566 (tt) cc_final: 0.8323 (pp) REVERT: A 645 MET cc_start: 0.9042 (mmp) cc_final: 0.8830 (mmm) REVERT: A 646 SER cc_start: 0.9105 (t) cc_final: 0.8814 (p) REVERT: A 663 GLN cc_start: 0.9211 (tp-100) cc_final: 0.8612 (tt0) REVERT: B 97 GLU cc_start: 0.9194 (mp0) cc_final: 0.8935 (tp30) REVERT: B 170 ILE cc_start: 0.8671 (mt) cc_final: 0.8417 (tp) REVERT: B 221 LYS cc_start: 0.6479 (pttt) cc_final: 0.6253 (pttm) REVERT: B 270 MET cc_start: 0.8891 (mmm) cc_final: 0.8625 (mmm) REVERT: B 308 ILE cc_start: 0.8353 (tp) cc_final: 0.7885 (mm) REVERT: B 372 MET cc_start: 0.8775 (mmp) cc_final: 0.8391 (mpp) REVERT: B 481 LEU cc_start: 0.8616 (tp) cc_final: 0.8414 (pp) REVERT: B 488 VAL cc_start: 0.8141 (t) cc_final: 0.7932 (m) REVERT: B 527 VAL cc_start: 0.9211 (t) cc_final: 0.8661 (m) REVERT: B 530 GLN cc_start: 0.9278 (tp40) cc_final: 0.9069 (pp30) REVERT: B 544 TYR cc_start: 0.8357 (t80) cc_final: 0.7945 (t80) REVERT: B 645 MET cc_start: 0.9151 (mmp) cc_final: 0.8889 (mmm) REVERT: C 170 ILE cc_start: 0.8657 (mt) cc_final: 0.8386 (tp) REVERT: C 270 MET cc_start: 0.8955 (mmm) cc_final: 0.8739 (mmm) REVERT: C 271 TYR cc_start: 0.8407 (t80) cc_final: 0.8061 (t80) REVERT: C 394 PHE cc_start: 0.7103 (t80) cc_final: 0.6868 (t80) REVERT: C 433 MET cc_start: 0.5528 (mtp) cc_final: 0.5283 (mtm) REVERT: C 468 MET cc_start: 0.9111 (mpp) cc_final: 0.8781 (mpp) REVERT: C 481 LEU cc_start: 0.8659 (tp) cc_final: 0.8395 (pp) REVERT: C 482 LEU cc_start: 0.8625 (tp) cc_final: 0.8359 (tp) REVERT: C 544 TYR cc_start: 0.8281 (t80) cc_final: 0.7984 (t80) REVERT: C 645 MET cc_start: 0.9123 (mmp) cc_final: 0.8873 (mmm) REVERT: D 122 MET cc_start: 0.8256 (mtt) cc_final: 0.8049 (mtp) REVERT: D 170 ILE cc_start: 0.8667 (mt) cc_final: 0.8411 (tp) REVERT: D 208 TYR cc_start: 0.7405 (t80) cc_final: 0.7201 (t80) REVERT: D 221 LYS cc_start: 0.6467 (pttt) cc_final: 0.6145 (pttm) REVERT: D 270 MET cc_start: 0.8956 (mmm) cc_final: 0.8737 (mmm) REVERT: D 271 TYR cc_start: 0.8417 (t80) cc_final: 0.8064 (t80) REVERT: D 433 MET cc_start: 0.5698 (mtp) cc_final: 0.5496 (mtm) REVERT: D 481 LEU cc_start: 0.8665 (tp) cc_final: 0.8418 (pp) REVERT: D 482 LEU cc_start: 0.8628 (tp) cc_final: 0.8393 (tp) REVERT: D 645 MET cc_start: 0.9111 (mmp) cc_final: 0.8831 (mmm) REVERT: D 646 SER cc_start: 0.9064 (t) cc_final: 0.8774 (p) REVERT: D 663 GLN cc_start: 0.9291 (tp-100) cc_final: 0.8714 (tt0) REVERT: D 664 LYS cc_start: 0.9030 (mtmt) cc_final: 0.8688 (mtpt) outliers start: 0 outliers final: 0 residues processed: 445 average time/residue: 0.3264 time to fit residues: 216.4778 Evaluate side-chains 313 residues out of total 2140 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 313 time to evaluate : 2.358 ------------------------------------------------------------------------------- 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: 9.9990 chunk 181 optimal weight: 0.4980 chunk 148 optimal weight: 0.5980 chunk 60 optimal weight: 10.0000 chunk 218 optimal weight: 7.9990 chunk 235 optimal weight: 20.0000 chunk 194 optimal weight: 0.7980 chunk 216 optimal weight: 10.0000 chunk 74 optimal weight: 0.9990 chunk 175 optimal weight: 9.9990 overall best weight: 0.7182 ------------------------------------------------------------------------------- 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 396 ASN A 413 HIS ** A 452 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 511 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 655 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 ** B 655 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 673 ASN ** C 129 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 133 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 396 ASN C 413 HIS ** C 452 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 655 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 673 ASN ** D 129 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 133 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 396 ASN D 413 HIS ** D 452 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 673 ASN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7677 moved from start: 0.5614 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 20124 Z= 0.178 Angle : 0.754 11.446 27288 Z= 0.372 Chirality : 0.043 0.262 3064 Planarity : 0.005 0.051 3380 Dihedral : 6.881 28.188 2632 Min Nonbonded Distance : 2.070 Molprobity Statistics. All-atom Clashscore : 16.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.51 % Favored : 92.49 % Rotamer: Outliers : 0.05 % Allowed : 4.95 % Favored : 95.00 % 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: -2.77 (0.15), residues: 2384 helix: -1.48 (0.13), residues: 1204 sheet: -3.34 (0.45), residues: 72 loop : -2.06 (0.17), residues: 1108 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP A 386 HIS 0.004 0.001 HIS C 169 PHE 0.017 0.001 PHE A 540 TYR 0.022 0.001 TYR C 323 ARG 0.008 0.001 ARG D 539 *********************** 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 416 residues out of total 2140 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 415 time to evaluate : 2.242 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: A 221 LYS cc_start: 0.6172 (pttt) cc_final: 0.5790 (pttm) REVERT: A 231 GLU cc_start: 0.8679 (mt-10) cc_final: 0.8215 (pt0) REVERT: A 255 MET cc_start: 0.8947 (mmm) cc_final: 0.8675 (tmm) REVERT: A 301 LEU cc_start: 0.9271 (mt) cc_final: 0.9055 (tt) REVERT: A 319 PHE cc_start: 0.8056 (p90) cc_final: 0.7799 (p90) REVERT: A 376 GLU cc_start: 0.9007 (pm20) cc_final: 0.8486 (pm20) REVERT: A 394 PHE cc_start: 0.7304 (t80) cc_final: 0.7063 (t80) REVERT: A 433 MET cc_start: 0.5630 (mtp) cc_final: 0.5423 (mtm) REVERT: A 468 MET cc_start: 0.9151 (mpp) cc_final: 0.8600 (mpp) REVERT: A 481 LEU cc_start: 0.8660 (tp) cc_final: 0.8416 (pp) REVERT: A 601 PHE cc_start: 0.8916 (m-10) cc_final: 0.8165 (t80) REVERT: A 646 SER cc_start: 0.9108 (t) cc_final: 0.8788 (p) REVERT: A 663 GLN cc_start: 0.9277 (tp-100) cc_final: 0.8515 (tp40) REVERT: B 221 LYS cc_start: 0.6284 (pttt) cc_final: 0.6052 (pttm) REVERT: B 251 HIS cc_start: 0.8528 (m90) cc_final: 0.8154 (m90) REVERT: B 255 MET cc_start: 0.8873 (mmm) cc_final: 0.8612 (tmm) REVERT: B 277 MET cc_start: 0.9239 (mmm) cc_final: 0.8989 (mmm) REVERT: B 288 GLU cc_start: 0.7253 (mt-10) cc_final: 0.6976 (tt0) REVERT: B 308 ILE cc_start: 0.8475 (tp) cc_final: 0.8249 (mp) REVERT: B 319 PHE cc_start: 0.7882 (p90) cc_final: 0.7304 (p90) REVERT: B 372 MET cc_start: 0.8895 (mmp) cc_final: 0.8391 (mpp) REVERT: B 468 MET cc_start: 0.9197 (mpp) cc_final: 0.8957 (mpp) REVERT: B 481 LEU cc_start: 0.8769 (tp) cc_final: 0.8489 (pp) REVERT: B 629 TYR cc_start: 0.8620 (m-80) cc_final: 0.8252 (m-80) REVERT: B 641 LEU cc_start: 0.9076 (mp) cc_final: 0.8686 (tt) REVERT: C 319 PHE cc_start: 0.8037 (p90) cc_final: 0.7806 (p90) REVERT: C 376 GLU cc_start: 0.9162 (pm20) cc_final: 0.8617 (pm20) REVERT: C 433 MET cc_start: 0.5651 (mtp) cc_final: 0.5247 (mpp) REVERT: C 481 LEU cc_start: 0.8703 (tp) cc_final: 0.8436 (pp) REVERT: C 544 TYR cc_start: 0.8214 (t80) cc_final: 0.7914 (t80) REVERT: C 601 PHE cc_start: 0.8878 (m-10) cc_final: 0.8159 (t80) REVERT: C 641 LEU cc_start: 0.8938 (mp) cc_final: 0.8684 (tt) REVERT: C 645 MET cc_start: 0.9091 (mmp) cc_final: 0.8780 (mmm) REVERT: C 670 GLU cc_start: 0.8989 (pm20) cc_final: 0.8626 (pm20) REVERT: D 208 TYR cc_start: 0.7235 (t80) cc_final: 0.7009 (t80) REVERT: D 221 LYS cc_start: 0.6157 (pttt) cc_final: 0.5823 (pttm) REVERT: D 231 GLU cc_start: 0.8686 (mt-10) cc_final: 0.8228 (pt0) REVERT: D 255 MET cc_start: 0.8961 (mmm) cc_final: 0.8718 (tmm) REVERT: D 319 PHE cc_start: 0.8009 (p90) cc_final: 0.7801 (p90) REVERT: D 376 GLU cc_start: 0.9004 (pm20) cc_final: 0.8491 (pm20) REVERT: D 433 MET cc_start: 0.5692 (mtp) cc_final: 0.5452 (mtm) REVERT: D 468 MET cc_start: 0.9123 (mpp) cc_final: 0.8613 (mpp) REVERT: D 481 LEU cc_start: 0.8635 (tp) cc_final: 0.8405 (pp) REVERT: D 601 PHE cc_start: 0.8883 (m-10) cc_final: 0.8180 (t80) REVERT: D 641 LEU cc_start: 0.9021 (mp) cc_final: 0.8688 (tt) REVERT: D 645 MET cc_start: 0.9066 (mmp) cc_final: 0.8703 (mmm) REVERT: D 646 SER cc_start: 0.9116 (t) cc_final: 0.8842 (p) REVERT: D 663 GLN cc_start: 0.9230 (tp-100) cc_final: 0.8728 (tt0) REVERT: D 664 LYS cc_start: 0.8819 (mtmt) cc_final: 0.8554 (mttt) outliers start: 1 outliers final: 0 residues processed: 416 average time/residue: 0.3023 time to fit residues: 190.9645 Evaluate side-chains 274 residues out of total 2140 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 274 time to evaluate : 2.191 ------------------------------------------------------------------------------- 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: 7.9990 chunk 113 optimal weight: 9.9990 chunk 24 optimal weight: 20.0000 chunk 104 optimal weight: 6.9990 chunk 146 optimal weight: 0.9980 chunk 219 optimal weight: 20.0000 chunk 231 optimal weight: 0.0000 chunk 114 optimal weight: 7.9990 chunk 207 optimal weight: 0.8980 chunk 62 optimal weight: 6.9990 overall best weight: 3.1788 ------------------------------------------------------------------------------- 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 438 HIS ** A 452 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 673 ASN ** B 129 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 396 ASN B 438 HIS ** B 452 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 673 ASN ** C 129 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 396 ASN C 438 HIS ** C 452 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 673 ASN ** D 129 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 396 ASN D 438 HIS ** D 452 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 673 ASN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7854 moved from start: 0.6730 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 20124 Z= 0.237 Angle : 0.756 10.105 27288 Z= 0.377 Chirality : 0.043 0.247 3064 Planarity : 0.005 0.045 3380 Dihedral : 6.784 30.039 2632 Min Nonbonded Distance : 2.043 Molprobity Statistics. All-atom Clashscore : 21.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.59 % Favored : 92.41 % Rotamer: Outliers : 0.00 % Allowed : 4.44 % Favored : 95.56 % 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: -2.46 (0.16), residues: 2384 helix: -1.11 (0.14), residues: 1200 sheet: -3.21 (0.48), residues: 72 loop : -2.07 (0.17), residues: 1112 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP C 454 HIS 0.008 0.002 HIS C 370 PHE 0.021 0.002 PHE B 207 TYR 0.019 0.002 TYR C 323 ARG 0.007 0.001 ARG A 193 *********************** 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 339 residues out of total 2140 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 339 time to evaluate : 2.431 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: A 270 MET cc_start: 0.9042 (mmm) cc_final: 0.8822 (mmm) REVERT: A 277 MET cc_start: 0.9262 (mmm) cc_final: 0.8760 (mmm) REVERT: A 319 PHE cc_start: 0.7738 (p90) cc_final: 0.7433 (p90) REVERT: A 345 LEU cc_start: 0.8060 (mp) cc_final: 0.7793 (mp) REVERT: A 394 PHE cc_start: 0.7486 (t80) cc_final: 0.7269 (t80) REVERT: A 529 ILE cc_start: 0.8826 (tt) cc_final: 0.8267 (tt) REVERT: A 645 MET cc_start: 0.9018 (mmp) cc_final: 0.8700 (mmp) REVERT: A 670 GLU cc_start: 0.9123 (pm20) cc_final: 0.8719 (pm20) REVERT: B 255 MET cc_start: 0.9112 (mmm) cc_final: 0.8884 (mmm) REVERT: B 277 MET cc_start: 0.9297 (mmm) cc_final: 0.8921 (mmm) REVERT: B 358 GLU cc_start: 0.8530 (tp30) cc_final: 0.8163 (tt0) REVERT: B 529 ILE cc_start: 0.9164 (mm) cc_final: 0.8836 (mm) REVERT: B 636 LEU cc_start: 0.8973 (mm) cc_final: 0.8622 (tt) REVERT: B 645 MET cc_start: 0.9110 (mmp) cc_final: 0.8884 (mmm) REVERT: B 670 GLU cc_start: 0.9169 (pm20) cc_final: 0.8796 (pm20) REVERT: C 277 MET cc_start: 0.9267 (mmm) cc_final: 0.8741 (mmm) REVERT: C 301 LEU cc_start: 0.9352 (mt) cc_final: 0.9028 (tt) REVERT: C 319 PHE cc_start: 0.7740 (p90) cc_final: 0.7436 (p90) REVERT: C 645 MET cc_start: 0.9087 (mmp) cc_final: 0.8794 (mmm) REVERT: C 670 GLU cc_start: 0.9157 (pm20) cc_final: 0.8805 (pm20) REVERT: D 277 MET cc_start: 0.9270 (mmm) cc_final: 0.8755 (mmm) REVERT: D 301 LEU cc_start: 0.9353 (mt) cc_final: 0.9052 (tt) REVERT: D 319 PHE cc_start: 0.7745 (p90) cc_final: 0.7449 (p90) REVERT: D 345 LEU cc_start: 0.8145 (mp) cc_final: 0.7914 (mp) REVERT: D 641 LEU cc_start: 0.9018 (mp) cc_final: 0.8721 (tt) REVERT: D 645 MET cc_start: 0.9072 (mmp) cc_final: 0.8763 (mmm) REVERT: D 670 GLU cc_start: 0.9165 (pm20) cc_final: 0.8765 (pm20) outliers start: 0 outliers final: 0 residues processed: 339 average time/residue: 0.3063 time to fit residues: 164.0450 Evaluate side-chains 246 residues out of total 2140 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 246 time to evaluate : 2.305 ------------------------------------------------------------------------------- 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: 9.9990 chunk 131 optimal weight: 5.9990 chunk 3 optimal weight: 0.0010 chunk 172 optimal weight: 2.9990 chunk 95 optimal weight: 9.9990 chunk 197 optimal weight: 6.9990 chunk 160 optimal weight: 0.6980 chunk 0 optimal weight: 9.9990 chunk 118 optimal weight: 30.0000 chunk 208 optimal weight: 0.9990 chunk 58 optimal weight: 20.0000 overall best weight: 2.1392 ------------------------------------------------------------------------------- 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 ** A 452 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** ** B 452 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 129 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 396 ASN ** 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 452 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7838 moved from start: 0.7153 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 20124 Z= 0.187 Angle : 0.717 11.213 27288 Z= 0.352 Chirality : 0.042 0.246 3064 Planarity : 0.004 0.044 3380 Dihedral : 6.371 28.217 2632 Min Nonbonded Distance : 2.040 Molprobity Statistics. All-atom Clashscore : 18.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.17 % Favored : 92.83 % Rotamer: Outliers : 0.00 % Allowed : 3.83 % Favored : 96.17 % 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: -2.27 (0.16), residues: 2384 helix: -0.89 (0.14), residues: 1248 sheet: -3.12 (0.44), residues: 72 loop : -2.10 (0.18), residues: 1064 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP B 333 HIS 0.006 0.001 HIS A 169 PHE 0.017 0.001 PHE C 540 TYR 0.030 0.002 TYR A 400 ARG 0.006 0.000 ARG D 369 *********************** 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 319 residues out of total 2140 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 319 time to evaluate : 2.474 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: A 270 MET cc_start: 0.8990 (mmm) cc_final: 0.8642 (mmm) REVERT: A 345 LEU cc_start: 0.7962 (mp) cc_final: 0.7693 (mp) REVERT: A 368 ASN cc_start: 0.7089 (t0) cc_final: 0.6525 (t0) REVERT: A 370 HIS cc_start: 0.7687 (p-80) cc_final: 0.7438 (p-80) REVERT: A 511 ASN cc_start: 0.9311 (t0) cc_final: 0.8674 (p0) REVERT: A 645 MET cc_start: 0.8985 (mmp) cc_final: 0.8686 (mmp) REVERT: A 670 GLU cc_start: 0.9130 (pm20) cc_final: 0.8819 (pm20) REVERT: B 277 MET cc_start: 0.9279 (mmm) cc_final: 0.8905 (mmm) REVERT: B 358 GLU cc_start: 0.8568 (tp30) cc_final: 0.8206 (tt0) REVERT: B 511 ASN cc_start: 0.9247 (t0) cc_final: 0.8673 (p0) REVERT: B 546 VAL cc_start: 0.9319 (m) cc_final: 0.9110 (p) REVERT: B 636 LEU cc_start: 0.8847 (mm) cc_final: 0.8463 (tp) REVERT: B 644 LEU cc_start: 0.9172 (pp) cc_final: 0.8912 (pp) REVERT: B 645 MET cc_start: 0.9137 (mmp) cc_final: 0.8906 (mmm) REVERT: B 670 GLU cc_start: 0.9120 (pm20) cc_final: 0.8839 (pm20) REVERT: C 301 LEU cc_start: 0.9346 (mt) cc_final: 0.9022 (tt) REVERT: C 641 LEU cc_start: 0.9125 (mp) cc_final: 0.8785 (tt) REVERT: C 645 MET cc_start: 0.9006 (mmp) cc_final: 0.8700 (mmm) REVERT: C 670 GLU cc_start: 0.9203 (pm20) cc_final: 0.8884 (pm20) REVERT: D 255 MET cc_start: 0.9242 (mmm) cc_final: 0.9024 (mmm) REVERT: D 301 LEU cc_start: 0.9326 (mt) cc_final: 0.8985 (tt) REVERT: D 345 LEU cc_start: 0.8054 (mp) cc_final: 0.7800 (mp) REVERT: D 645 MET cc_start: 0.8996 (mmp) cc_final: 0.8782 (mmm) REVERT: D 670 GLU cc_start: 0.9148 (pm20) cc_final: 0.8839 (pm20) outliers start: 0 outliers final: 0 residues processed: 319 average time/residue: 0.2867 time to fit residues: 144.0736 Evaluate side-chains 247 residues out of total 2140 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 247 time to evaluate : 2.219 ------------------------------------------------------------------------------- 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: 0.7980 chunk 208 optimal weight: 2.9990 chunk 45 optimal weight: 5.9990 chunk 136 optimal weight: 9.9990 chunk 57 optimal weight: 0.8980 chunk 232 optimal weight: 4.9990 chunk 192 optimal weight: 8.9990 chunk 107 optimal weight: 7.9990 chunk 19 optimal weight: 0.2980 chunk 76 optimal weight: 10.0000 chunk 121 optimal weight: 0.3980 overall best weight: 1.0782 ------------------------------------------------------------------------------- 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 452 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 655 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 129 GLN ** 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 370 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 396 ASN ** C 452 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 129 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 370 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 452 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7807 moved from start: 0.7431 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 20124 Z= 0.160 Angle : 0.714 10.943 27288 Z= 0.344 Chirality : 0.041 0.238 3064 Planarity : 0.004 0.043 3380 Dihedral : 6.116 28.793 2632 Min Nonbonded Distance : 2.043 Molprobity Statistics. All-atom Clashscore : 17.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.59 % Favored : 93.41 % Rotamer: Outliers : 0.00 % Allowed : 3.04 % Favored : 96.96 % 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: -2.16 (0.16), residues: 2384 helix: -0.80 (0.14), residues: 1288 sheet: -3.10 (0.42), residues: 72 loop : -2.07 (0.18), residues: 1024 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP C 333 HIS 0.005 0.001 HIS A 169 PHE 0.021 0.001 PHE D 540 TYR 0.025 0.001 TYR C 400 ARG 0.010 0.000 ARG D 369 *********************** 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 329 residues out of total 2140 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 329 time to evaluate : 2.393 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: A 270 MET cc_start: 0.8983 (mmm) cc_final: 0.8710 (mmm) REVERT: A 315 LEU cc_start: 0.9156 (tp) cc_final: 0.8701 (tp) REVERT: A 345 LEU cc_start: 0.8021 (mp) cc_final: 0.7762 (mp) REVERT: A 376 GLU cc_start: 0.9249 (pm20) cc_final: 0.8847 (pm20) REVERT: A 641 LEU cc_start: 0.9039 (mp) cc_final: 0.8672 (tt) REVERT: A 645 MET cc_start: 0.9000 (mmp) cc_final: 0.8682 (mmp) REVERT: A 670 GLU cc_start: 0.9154 (pm20) cc_final: 0.8826 (pm20) REVERT: B 277 MET cc_start: 0.9120 (mmm) cc_final: 0.8817 (mmm) REVERT: B 345 LEU cc_start: 0.8243 (mp) cc_final: 0.7991 (mp) REVERT: B 347 SER cc_start: 0.9246 (p) cc_final: 0.8902 (t) REVERT: B 358 GLU cc_start: 0.8627 (tp30) cc_final: 0.8151 (mt-10) REVERT: B 511 ASN cc_start: 0.9270 (t0) cc_final: 0.8692 (p0) REVERT: B 547 PHE cc_start: 0.8180 (m-80) cc_final: 0.7866 (m-80) REVERT: B 644 LEU cc_start: 0.9192 (pp) cc_final: 0.8935 (pp) REVERT: B 670 GLU cc_start: 0.9090 (pm20) cc_final: 0.8828 (pm20) REVERT: C 301 LEU cc_start: 0.9428 (mt) cc_final: 0.8954 (tt) REVERT: C 315 LEU cc_start: 0.9173 (tp) cc_final: 0.8717 (tp) REVERT: C 345 LEU cc_start: 0.8025 (mp) cc_final: 0.7819 (mp) REVERT: C 376 GLU cc_start: 0.9170 (pm20) cc_final: 0.8416 (pm20) REVERT: C 670 GLU cc_start: 0.9153 (pm20) cc_final: 0.8839 (pm20) REVERT: D 231 GLU cc_start: 0.8756 (mt-10) cc_final: 0.8269 (pt0) REVERT: D 255 MET cc_start: 0.9248 (mmm) cc_final: 0.9035 (mmm) REVERT: D 301 LEU cc_start: 0.9415 (mt) cc_final: 0.9103 (tt) REVERT: D 315 LEU cc_start: 0.9162 (tp) cc_final: 0.8689 (tp) REVERT: D 345 LEU cc_start: 0.7964 (mp) cc_final: 0.7730 (mp) REVERT: D 358 GLU cc_start: 0.8521 (tp30) cc_final: 0.8303 (tt0) REVERT: D 372 MET cc_start: 0.9148 (mmt) cc_final: 0.8876 (mmt) REVERT: D 376 GLU cc_start: 0.9250 (pm20) cc_final: 0.8871 (pm20) REVERT: D 478 LEU cc_start: 0.9065 (mm) cc_final: 0.8820 (mt) REVERT: D 645 MET cc_start: 0.9006 (mmp) cc_final: 0.8695 (mmm) REVERT: D 670 GLU cc_start: 0.9132 (pm20) cc_final: 0.8816 (pm20) outliers start: 0 outliers final: 0 residues processed: 329 average time/residue: 0.2856 time to fit residues: 147.3939 Evaluate side-chains 263 residues out of total 2140 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 263 time to evaluate : 2.337 ------------------------------------------------------------------------------- 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: 10.0000 chunk 26 optimal weight: 0.0770 chunk 132 optimal weight: 8.9990 chunk 169 optimal weight: 0.7980 chunk 131 optimal weight: 5.9990 chunk 195 optimal weight: 0.7980 chunk 129 optimal weight: 4.9990 chunk 231 optimal weight: 3.9990 chunk 144 optimal weight: 0.9980 chunk 141 optimal weight: 5.9990 chunk 106 optimal weight: 9.9990 overall best weight: 1.3340 ------------------------------------------------------------------------------- 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 452 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 129 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 247 ASN ** B 251 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 452 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 530 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 129 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** ** D 129 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 452 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7816 moved from start: 0.7744 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 20124 Z= 0.174 Angle : 0.710 11.000 27288 Z= 0.341 Chirality : 0.042 0.233 3064 Planarity : 0.004 0.043 3380 Dihedral : 5.937 28.610 2632 Min Nonbonded Distance : 2.064 Molprobity Statistics. All-atom Clashscore : 17.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.96 % Favored : 93.04 % Rotamer: Outliers : 0.00 % Allowed : 2.10 % Favored : 97.90 % 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: -2.17 (0.16), residues: 2384 helix: -0.75 (0.14), residues: 1288 sheet: -2.77 (0.44), residues: 72 loop : -2.19 (0.18), residues: 1024 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP B 333 HIS 0.005 0.001 HIS D 169 PHE 0.018 0.001 PHE D 540 TYR 0.017 0.001 TYR B 271 ARG 0.008 0.000 ARG D 369 *********************** 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 323 residues out of total 2140 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 323 time to evaluate : 2.270 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: A 231 GLU cc_start: 0.8868 (mt-10) cc_final: 0.8289 (pt0) REVERT: A 315 LEU cc_start: 0.9041 (tp) cc_final: 0.8800 (tp) REVERT: A 345 LEU cc_start: 0.8005 (mp) cc_final: 0.7717 (mp) REVERT: A 507 LEU cc_start: 0.8524 (tt) cc_final: 0.8322 (tt) REVERT: A 645 MET cc_start: 0.8959 (mmp) cc_final: 0.8742 (mmp) REVERT: A 670 GLU cc_start: 0.9101 (pm20) cc_final: 0.8818 (pm20) REVERT: B 231 GLU cc_start: 0.8925 (mt-10) cc_final: 0.8366 (pt0) REVERT: B 277 MET cc_start: 0.9141 (mmm) cc_final: 0.8892 (mmm) REVERT: B 347 SER cc_start: 0.9275 (p) cc_final: 0.8976 (t) REVERT: B 358 GLU cc_start: 0.8674 (tp30) cc_final: 0.8209 (mt-10) REVERT: B 468 MET cc_start: 0.9223 (mpp) cc_final: 0.9010 (mpp) REVERT: B 547 PHE cc_start: 0.8227 (m-80) cc_final: 0.7867 (m-80) REVERT: B 636 LEU cc_start: 0.8733 (mm) cc_final: 0.8358 (tp) REVERT: B 644 LEU cc_start: 0.9192 (pp) cc_final: 0.8895 (pp) REVERT: B 645 MET cc_start: 0.9078 (mmp) cc_final: 0.8757 (mmm) REVERT: C 231 GLU cc_start: 0.8801 (mt-10) cc_final: 0.8504 (mt-10) REVERT: C 301 LEU cc_start: 0.9461 (mt) cc_final: 0.9081 (tt) REVERT: C 312 ARG cc_start: 0.9275 (ptm-80) cc_final: 0.8993 (ttp80) REVERT: C 315 LEU cc_start: 0.9085 (tp) cc_final: 0.8841 (tp) REVERT: C 372 MET cc_start: 0.9100 (mmt) cc_final: 0.8859 (mmt) REVERT: C 478 LEU cc_start: 0.9188 (mm) cc_final: 0.8925 (mt) REVERT: C 670 GLU cc_start: 0.9150 (pm20) cc_final: 0.8868 (pm20) REVERT: D 231 GLU cc_start: 0.8805 (mt-10) cc_final: 0.8294 (pt0) REVERT: D 301 LEU cc_start: 0.9440 (mt) cc_final: 0.9096 (tt) REVERT: D 312 ARG cc_start: 0.9282 (ptm-80) cc_final: 0.9000 (ttp80) REVERT: D 315 LEU cc_start: 0.9042 (tp) cc_final: 0.8807 (tp) REVERT: D 345 LEU cc_start: 0.7990 (mp) cc_final: 0.7741 (mp) REVERT: D 358 GLU cc_start: 0.8551 (tp30) cc_final: 0.8335 (tt0) REVERT: D 478 LEU cc_start: 0.9121 (mm) cc_final: 0.8864 (mt) REVERT: D 519 PHE cc_start: 0.3861 (t80) cc_final: 0.3647 (t80) REVERT: D 670 GLU cc_start: 0.9166 (pm20) cc_final: 0.8862 (pm20) outliers start: 0 outliers final: 0 residues processed: 323 average time/residue: 0.2806 time to fit residues: 143.4325 Evaluate side-chains 245 residues out of total 2140 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 245 time to evaluate : 2.397 ------------------------------------------------------------------------------- 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: 0.0270 chunk 92 optimal weight: 9.9990 chunk 138 optimal weight: 0.5980 chunk 69 optimal weight: 5.9990 chunk 45 optimal weight: 5.9990 chunk 44 optimal weight: 5.9990 chunk 147 optimal weight: 2.9990 chunk 157 optimal weight: 10.0000 chunk 114 optimal weight: 0.9990 chunk 21 optimal weight: 0.5980 chunk 181 optimal weight: 0.9990 overall best weight: 0.6442 ------------------------------------------------------------------------------- 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 452 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 129 GLN ** 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 370 HIS ** 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 452 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7781 moved from start: 0.7993 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 20124 Z= 0.157 Angle : 0.711 11.018 27288 Z= 0.337 Chirality : 0.042 0.212 3064 Planarity : 0.004 0.045 3380 Dihedral : 5.762 27.770 2632 Min Nonbonded Distance : 2.082 Molprobity Statistics. All-atom Clashscore : 16.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.67 % Favored : 93.33 % Rotamer: Outliers : 0.00 % Allowed : 1.07 % Favored : 98.93 % 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: -1.89 (0.16), residues: 2384 helix: -0.61 (0.14), residues: 1236 sheet: -2.35 (0.49), residues: 72 loop : -1.90 (0.18), residues: 1076 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP B 333 HIS 0.007 0.001 HIS B 169 PHE 0.013 0.001 PHE B 547 TYR 0.022 0.001 TYR C 228 ARG 0.006 0.000 ARG D 369 *********************** 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 335 residues out of total 2140 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 335 time to evaluate : 2.378 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: A 221 LYS cc_start: 0.5714 (pttt) cc_final: 0.5483 (pttm) REVERT: A 231 GLU cc_start: 0.8849 (mt-10) cc_final: 0.8335 (pt0) REVERT: A 270 MET cc_start: 0.9006 (mmp) cc_final: 0.8580 (mmm) REVERT: A 345 LEU cc_start: 0.7988 (mp) cc_final: 0.7688 (mp) REVERT: A 365 LYS cc_start: 0.9266 (mptt) cc_final: 0.8898 (mmtm) REVERT: A 640 MET cc_start: 0.7654 (mmm) cc_final: 0.7260 (mmp) REVERT: A 663 GLN cc_start: 0.9287 (tp-100) cc_final: 0.8421 (tp40) REVERT: B 184 VAL cc_start: 0.9149 (t) cc_final: 0.8933 (m) REVERT: B 228 TYR cc_start: 0.8330 (t80) cc_final: 0.8063 (t80) REVERT: B 231 GLU cc_start: 0.8910 (mt-10) cc_final: 0.8601 (mt-10) REVERT: B 277 MET cc_start: 0.9114 (mmm) cc_final: 0.8851 (mmm) REVERT: B 345 LEU cc_start: 0.8192 (mp) cc_final: 0.7954 (mp) REVERT: B 347 SER cc_start: 0.9244 (p) cc_final: 0.8935 (t) REVERT: B 468 MET cc_start: 0.9214 (mpp) cc_final: 0.8976 (mpp) REVERT: B 529 ILE cc_start: 0.8939 (mm) cc_final: 0.8660 (tp) REVERT: B 547 PHE cc_start: 0.8110 (m-80) cc_final: 0.7605 (m-80) REVERT: B 636 LEU cc_start: 0.8707 (mm) cc_final: 0.8339 (tp) REVERT: B 644 LEU cc_start: 0.8990 (pp) cc_final: 0.8636 (pp) REVERT: B 645 MET cc_start: 0.9004 (mmp) cc_final: 0.8794 (mmm) REVERT: C 231 GLU cc_start: 0.8800 (mt-10) cc_final: 0.8495 (mt-10) REVERT: C 253 LEU cc_start: 0.9662 (mm) cc_final: 0.9419 (mt) REVERT: C 270 MET cc_start: 0.8778 (mmt) cc_final: 0.8323 (mmp) REVERT: C 301 LEU cc_start: 0.9498 (mt) cc_final: 0.9034 (tt) REVERT: C 305 GLU cc_start: 0.8893 (pm20) cc_final: 0.8570 (mp0) REVERT: C 312 ARG cc_start: 0.9253 (ptm-80) cc_final: 0.8985 (ttp80) REVERT: C 315 LEU cc_start: 0.8995 (tp) cc_final: 0.8792 (tp) REVERT: C 372 MET cc_start: 0.9045 (mmt) cc_final: 0.8805 (mmt) REVERT: D 231 GLU cc_start: 0.8833 (mt-10) cc_final: 0.8349 (pt0) REVERT: D 253 LEU cc_start: 0.9680 (mm) cc_final: 0.9405 (mt) REVERT: D 270 MET cc_start: 0.8826 (mmt) cc_final: 0.8443 (mmp) REVERT: D 301 LEU cc_start: 0.9459 (mt) cc_final: 0.9104 (tt) REVERT: D 312 ARG cc_start: 0.9244 (ptm-80) cc_final: 0.8983 (ttp80) REVERT: D 315 LEU cc_start: 0.9061 (tp) cc_final: 0.8859 (tp) REVERT: D 358 GLU cc_start: 0.8559 (tp30) cc_final: 0.8309 (tt0) REVERT: D 645 MET cc_start: 0.9007 (mmp) cc_final: 0.8761 (mmm) outliers start: 0 outliers final: 0 residues processed: 335 average time/residue: 0.2930 time to fit residues: 153.1136 Evaluate side-chains 259 residues out of total 2140 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 259 time to evaluate : 2.505 ------------------------------------------------------------------------------- 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: 5.9990 chunk 221 optimal weight: 20.0000 chunk 202 optimal weight: 3.9990 chunk 215 optimal weight: 9.9990 chunk 129 optimal weight: 0.9990 chunk 93 optimal weight: 7.9990 chunk 169 optimal weight: 20.0000 chunk 66 optimal weight: 0.0870 chunk 194 optimal weight: 7.9990 chunk 203 optimal weight: 6.9990 chunk 214 optimal weight: 8.9990 overall best weight: 3.6166 ------------------------------------------------------------------------------- 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 452 GLN ** B 129 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 141 GLN ** B 251 HIS ** 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 247 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 370 HIS ** 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 247 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 452 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7935 moved from start: 0.8520 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 20124 Z= 0.248 Angle : 0.761 9.666 27288 Z= 0.375 Chirality : 0.045 0.261 3064 Planarity : 0.005 0.069 3380 Dihedral : 6.246 28.785 2632 Min Nonbonded Distance : 2.122 Molprobity Statistics. All-atom Clashscore : 21.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.05 % Favored : 91.95 % Rotamer: Outliers : 0.00 % Allowed : 0.84 % Favored : 99.16 % 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: -2.09 (0.16), residues: 2384 helix: -0.95 (0.14), residues: 1308 sheet: -0.93 (0.58), residues: 88 loop : -1.93 (0.19), residues: 988 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP D 333 HIS 0.007 0.001 HIS A 169 PHE 0.026 0.002 PHE D 319 TYR 0.023 0.002 TYR D 228 ARG 0.010 0.001 ARG D 369 *********************** 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 314 residues out of total 2140 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 314 time to evaluate : 2.109 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: A 140 LEU cc_start: 0.9298 (mt) cc_final: 0.8965 (mt) REVERT: A 231 GLU cc_start: 0.8913 (mt-10) cc_final: 0.8362 (pt0) REVERT: A 270 MET cc_start: 0.9093 (mmp) cc_final: 0.8848 (mmt) REVERT: A 345 LEU cc_start: 0.8291 (mp) cc_final: 0.8086 (mp) REVERT: A 347 SER cc_start: 0.9405 (p) cc_final: 0.9110 (t) REVERT: A 376 GLU cc_start: 0.9115 (pm20) cc_final: 0.8901 (pm20) REVERT: A 404 MET cc_start: 0.7102 (tpt) cc_final: 0.6812 (tpp) REVERT: A 471 TYR cc_start: 0.7859 (p90) cc_final: 0.7229 (p90) REVERT: A 472 PHE cc_start: 0.8464 (m-10) cc_final: 0.7868 (m-80) REVERT: A 640 MET cc_start: 0.7674 (mmm) cc_final: 0.7152 (mmp) REVERT: A 670 GLU cc_start: 0.9234 (pm20) cc_final: 0.9014 (pm20) REVERT: B 277 MET cc_start: 0.9153 (mmm) cc_final: 0.8860 (mmm) REVERT: B 347 SER cc_start: 0.9382 (p) cc_final: 0.9144 (t) REVERT: B 358 GLU cc_start: 0.8900 (tp30) cc_final: 0.8431 (mt-10) REVERT: B 468 MET cc_start: 0.9300 (mpp) cc_final: 0.9075 (mpp) REVERT: B 547 PHE cc_start: 0.8193 (m-80) cc_final: 0.7893 (m-80) REVERT: B 636 LEU cc_start: 0.8682 (mm) cc_final: 0.8261 (tt) REVERT: B 644 LEU cc_start: 0.9043 (pp) cc_final: 0.8741 (pp) REVERT: B 645 MET cc_start: 0.9081 (mmp) cc_final: 0.8867 (mmm) REVERT: B 663 GLN cc_start: 0.9452 (tp-100) cc_final: 0.8834 (tp40) REVERT: B 670 GLU cc_start: 0.9244 (pm20) cc_final: 0.9027 (pm20) REVERT: C 253 LEU cc_start: 0.9667 (mm) cc_final: 0.9466 (mt) REVERT: C 301 LEU cc_start: 0.9492 (mt) cc_final: 0.9070 (tt) REVERT: C 315 LEU cc_start: 0.9092 (tp) cc_final: 0.8798 (tp) REVERT: C 345 LEU cc_start: 0.8390 (mp) cc_final: 0.8124 (mp) REVERT: C 387 ASP cc_start: 0.9244 (m-30) cc_final: 0.9039 (p0) REVERT: C 471 TYR cc_start: 0.7807 (p90) cc_final: 0.7463 (p90) REVERT: C 472 PHE cc_start: 0.8497 (m-10) cc_final: 0.8295 (m-10) REVERT: C 645 MET cc_start: 0.9011 (mmp) cc_final: 0.8712 (mmm) REVERT: C 670 GLU cc_start: 0.9266 (pm20) cc_final: 0.9039 (pm20) REVERT: D 231 GLU cc_start: 0.8987 (mt-10) cc_final: 0.8458 (pt0) REVERT: D 270 MET cc_start: 0.9011 (mmt) cc_final: 0.8747 (mmp) REVERT: D 301 LEU cc_start: 0.9493 (mt) cc_final: 0.9126 (tt) REVERT: D 312 ARG cc_start: 0.9265 (ptm-80) cc_final: 0.8955 (ttp80) REVERT: D 358 GLU cc_start: 0.8686 (tp30) cc_final: 0.8301 (tt0) REVERT: D 376 GLU cc_start: 0.9095 (pm20) cc_final: 0.8894 (pm20) REVERT: D 471 TYR cc_start: 0.7826 (p90) cc_final: 0.7489 (p90) REVERT: D 640 MET cc_start: 0.7907 (mmm) cc_final: 0.7476 (mmp) REVERT: D 670 GLU cc_start: 0.9248 (pm20) cc_final: 0.9029 (pm20) outliers start: 0 outliers final: 0 residues processed: 314 average time/residue: 0.2856 time to fit residues: 141.1869 Evaluate side-chains 238 residues out of total 2140 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 238 time to evaluate : 1.784 ------------------------------------------------------------------------------- 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: 20.0000 chunk 227 optimal weight: 3.9990 chunk 139 optimal weight: 0.7980 chunk 108 optimal weight: 20.0000 chunk 158 optimal weight: 8.9990 chunk 239 optimal weight: 6.9990 chunk 220 optimal weight: 5.9990 chunk 190 optimal weight: 5.9990 chunk 19 optimal weight: 3.9990 chunk 147 optimal weight: 2.9990 chunk 116 optimal weight: 6.9990 overall best weight: 3.5588 ------------------------------------------------------------------------------- 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 354 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 129 GLN ** 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 247 ASN ** 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** ** D 129 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 247 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 251 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7942 moved from start: 0.8846 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 20124 Z= 0.231 Angle : 0.744 10.437 27288 Z= 0.365 Chirality : 0.044 0.236 3064 Planarity : 0.005 0.045 3380 Dihedral : 6.219 28.609 2632 Min Nonbonded Distance : 2.095 Molprobity Statistics. All-atom Clashscore : 20.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.72 % Favored : 92.28 % Rotamer: Outliers : 0.00 % Allowed : 0.47 % Favored : 99.53 % 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: -1.90 (0.16), residues: 2384 helix: -0.82 (0.14), residues: 1244 sheet: -0.90 (0.56), residues: 88 loop : -1.75 (0.18), residues: 1052 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP B 333 HIS 0.006 0.001 HIS A 169 PHE 0.027 0.002 PHE D 547 TYR 0.021 0.002 TYR C 228 ARG 0.008 0.001 ARG D 369 ********************** 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 303 residues out of total 2140 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 303 time to evaluate : 2.301 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: A 231 GLU cc_start: 0.8902 (mt-10) cc_final: 0.8371 (pt0) REVERT: A 347 SER cc_start: 0.9416 (p) cc_final: 0.9167 (t) REVERT: A 376 GLU cc_start: 0.9106 (pm20) cc_final: 0.8882 (pm20) REVERT: A 404 MET cc_start: 0.7512 (tpt) cc_final: 0.7186 (tpp) REVERT: A 547 PHE cc_start: 0.8122 (m-80) cc_final: 0.7390 (m-10) REVERT: A 645 MET cc_start: 0.8979 (mmp) cc_final: 0.8760 (mmm) REVERT: A 670 GLU cc_start: 0.9298 (pm20) cc_final: 0.9076 (pm20) REVERT: B 140 LEU cc_start: 0.9120 (mt) cc_final: 0.8739 (mt) REVERT: B 277 MET cc_start: 0.9225 (mmm) cc_final: 0.8949 (mmm) REVERT: B 468 MET cc_start: 0.9291 (mpp) cc_final: 0.9063 (mpp) REVERT: B 547 PHE cc_start: 0.8217 (m-80) cc_final: 0.7887 (m-80) REVERT: B 645 MET cc_start: 0.9113 (mmp) cc_final: 0.8855 (mmm) REVERT: B 670 GLU cc_start: 0.9250 (pm20) cc_final: 0.8219 (tt0) REVERT: C 140 LEU cc_start: 0.9250 (mt) cc_final: 0.9014 (mt) REVERT: C 255 MET cc_start: 0.9327 (mmm) cc_final: 0.8990 (mmm) REVERT: C 301 LEU cc_start: 0.9499 (mt) cc_final: 0.9005 (tt) REVERT: C 345 LEU cc_start: 0.8472 (mp) cc_final: 0.8158 (mp) REVERT: C 347 SER cc_start: 0.9512 (p) cc_final: 0.9259 (t) REVERT: C 381 LEU cc_start: 0.9418 (tt) cc_final: 0.9193 (mm) REVERT: C 645 MET cc_start: 0.9026 (mmp) cc_final: 0.8815 (mmm) REVERT: C 670 GLU cc_start: 0.9287 (pm20) cc_final: 0.8277 (tt0) REVERT: D 231 GLU cc_start: 0.8908 (mt-10) cc_final: 0.8356 (pt0) REVERT: D 270 MET cc_start: 0.9029 (mmt) cc_final: 0.8670 (mmp) REVERT: D 301 LEU cc_start: 0.9407 (mt) cc_final: 0.9098 (tp) REVERT: D 345 LEU cc_start: 0.8435 (mp) cc_final: 0.8163 (mp) REVERT: D 347 SER cc_start: 0.9504 (p) cc_final: 0.9238 (t) REVERT: D 358 GLU cc_start: 0.8838 (tp30) cc_final: 0.8452 (tt0) REVERT: D 376 GLU cc_start: 0.9112 (pm20) cc_final: 0.8893 (pm20) REVERT: D 471 TYR cc_start: 0.7698 (p90) cc_final: 0.7322 (p90) REVERT: D 472 PHE cc_start: 0.8094 (m-80) cc_final: 0.7793 (m-80) REVERT: D 547 PHE cc_start: 0.8197 (m-80) cc_final: 0.7463 (m-10) REVERT: D 640 MET cc_start: 0.7773 (mmm) cc_final: 0.7323 (mmp) REVERT: D 645 MET cc_start: 0.9012 (mmp) cc_final: 0.8709 (mmm) outliers start: 0 outliers final: 0 residues processed: 303 average time/residue: 0.2593 time to fit residues: 127.6525 Evaluate side-chains 233 residues out of total 2140 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 233 time to evaluate : 2.153 ------------------------------------------------------------------------------- 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: 2.9990 chunk 202 optimal weight: 0.4980 chunk 58 optimal weight: 10.0000 chunk 175 optimal weight: 0.8980 chunk 28 optimal weight: 1.9990 chunk 52 optimal weight: 4.9990 chunk 190 optimal weight: 0.5980 chunk 79 optimal weight: 3.9990 chunk 195 optimal weight: 0.9990 chunk 24 optimal weight: 2.9990 chunk 35 optimal weight: 20.0000 overall best weight: 0.9984 ------------------------------------------------------------------------------- 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 186 ASN B 247 ASN B 251 HIS B 452 GLN B 487 GLN ** C 129 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 186 ASN ** C 370 HIS ** 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 247 ASN ** D 251 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3693 r_free = 0.3693 target = 0.083819 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3366 r_free = 0.3366 target = 0.067418 restraints weight = 93305.974| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3399 r_free = 0.3399 target = 0.068943 restraints weight = 61504.887| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3421 r_free = 0.3421 target = 0.069981 restraints weight = 44995.367| |-----------------------------------------------------------------------------| r_work (final): 0.3402 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7889 moved from start: 0.9000 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= 0.168 Angle : 0.725 10.919 27288 Z= 0.346 Chirality : 0.043 0.222 3064 Planarity : 0.004 0.044 3380 Dihedral : 5.864 27.621 2632 Min Nonbonded Distance : 2.088 Molprobity Statistics. All-atom Clashscore : 17.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.59 % Favored : 92.41 % Rotamer: Outliers : 0.00 % Allowed : 0.42 % Favored : 99.58 % 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: -1.89 (0.17), residues: 2384 helix: -0.70 (0.14), residues: 1260 sheet: -0.73 (0.56), residues: 88 loop : -1.94 (0.19), residues: 1036 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP B 333 HIS 0.004 0.001 HIS C 169 PHE 0.022 0.001 PHE A 547 TYR 0.021 0.001 TYR C 228 ARG 0.006 0.000 ARG D 369 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3882.19 seconds wall clock time: 73 minutes 26.82 seconds (4406.82 seconds total)