Starting phenix.real_space_refine on Thu Sep 18 19:41:39 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/5hi9_6580/09_2025/5hi9_6580.cif Found real_map, /net/cci-nas-00/data/ceres_data/5hi9_6580/09_2025/5hi9_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 { model { file = "/net/cci-nas-00/data/ceres_data/5hi9_6580/09_2025/5hi9_6580.cif" } default_model = "/net/cci-nas-00/data/ceres_data/5hi9_6580/09_2025/5hi9_6580.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/5hi9_6580/09_2025/5hi9_6580.map" default_real_map = "/net/cci-nas-00/data/ceres_data/5hi9_6580/09_2025/5hi9_6580.map" } resolution = 4.4 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs 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. Time to flip 105 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/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: 4.54, per 1000 atoms: 0.23 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 - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.77 Conformation dependent library (CDL) restraints added in 732.3 milliseconds Enol-peptide restraints added in 238.4 nanoseconds 4768 Ramachandran restraints generated. 2384 Oldfield, 0 Emsley, 2384 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4536 Finding SS restraints... Secondary structure from input PDB file: 136 helices and 4 sheets defined 60.8% alpha, 1.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.66 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: 3.03 Time building geometry restraints manager: 2.34 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: 0.00 - 4.09: 26818 4.09 - 8.17: 410 8.17 - 12.26: 28 12.26 - 16.35: 20 16.35 - 20.43: 12 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 Time spend for trying shortcut: 0.06 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: 0.640 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.010 Extract box with map and model: 0.260 Check model and map are aligned: 0.050 Set scattering table: 0.050 Process input model: 17.470 Find NCS groups from input model: 0.160 Set up NCS constraints: 0.040 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:1.320 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 20.020 ------------------------------------------------------------------------------- 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= 0.614 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 : 23.45 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. 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 ARG 0.005 0.001 ARG B 77 TYR 0.018 0.002 TYR D 323 PHE 0.014 0.002 PHE C 81 TRP 0.016 0.002 TRP C 677 HIS 0.005 0.001 HIS A 251 Details of bonding type rmsd covalent geometry : bond 0.00865 (20124) covalent geometry : angle 1.46450 (27288) hydrogen bonds : bond 0.25244 ( 728) hydrogen bonds : angle 9.96884 ( 2136) *********************** 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 to be fit. rotamer outliers: 20 poor density : 674 time to evaluate : 0.771 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: A 154 ASN cc_start: 0.8806 (m-40) cc_final: 0.8452 (m-40) REVERT: A 170 ILE cc_start: 0.8173 (mt) cc_final: 0.7920 (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: 0.7975 (m170) REVERT: A 271 TYR cc_start: 0.8640 (t80) cc_final: 0.8187 (t80) REVERT: A 394 PHE cc_start: 0.7138 (t80) cc_final: 0.6810 (t80) REVERT: A 433 MET cc_start: 0.4715 (mtp) cc_final: 0.4428 (mtm) REVERT: A 481 LEU cc_start: 0.8426 (tp) cc_final: 0.8007 (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: 0.8245 (m-80) REVERT: A 645 MET cc_start: 0.9142 (mmp) cc_final: 0.8871 (mmm) REVERT: A 661 LYS cc_start: 0.7931 (mppt) cc_final: 0.7172 (mttt) REVERT: A 664 LYS cc_start: 0.8575 (mtmt) cc_final: 0.7998 (mtmt) REVERT: A 666 ILE cc_start: 0.9691 (mt) cc_final: 0.9409 (tp) REVERT: A 694 ARG cc_start: 0.6952 (OUTLIER) cc_final: 0.5955 (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: 0.8656 (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: 0.8713 (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: 0.7003 (mp) REVERT: B 347 SER cc_start: 0.7203 (t) cc_final: 0.6452 (p) REVERT: B 394 PHE cc_start: 0.7319 (t80) cc_final: 0.7060 (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: 0.8043 (pp) REVERT: B 482 LEU cc_start: 0.8514 (tp) cc_final: 0.8205 (tp) REVERT: B 529 ILE cc_start: 0.8864 (mp) cc_final: 0.8490 (tt) REVERT: B 530 GLN cc_start: 0.9234 (tp40) cc_final: 0.8935 (tm-30) REVERT: B 629 TYR cc_start: 0.8405 (m-10) cc_final: 0.8028 (m-80) REVERT: B 641 LEU cc_start: 0.9070 (mp) cc_final: 0.8547 (tt) REVERT: B 645 MET cc_start: 0.9089 (mmp) cc_final: 0.8822 (mmm) REVERT: B 666 ILE cc_start: 0.9670 (mt) cc_final: 0.9393 (tp) REVERT: B 694 ARG cc_start: 0.7068 (OUTLIER) cc_final: 0.5838 (ttt-90) REVERT: C 154 ASN cc_start: 0.8817 (m-40) cc_final: 0.8465 (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: 0.7982 (m170) REVERT: C 271 TYR cc_start: 0.8653 (t80) cc_final: 0.8201 (t80) REVERT: C 345 LEU cc_start: 0.7444 (tm) cc_final: 0.7063 (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: 0.7969 (pp) REVERT: C 544 TYR cc_start: 0.8268 (t80) cc_final: 0.7981 (t80) REVERT: C 633 THR cc_start: 0.8808 (m) cc_final: 0.8560 (p) REVERT: C 637 LEU cc_start: 0.8510 (mt) cc_final: 0.8270 (mt) REVERT: C 641 LEU cc_start: 0.9060 (mp) cc_final: 0.8792 (tt) REVERT: C 645 MET cc_start: 0.9058 (mmp) cc_final: 0.8822 (mmm) REVERT: C 661 LYS cc_start: 0.7850 (mppt) cc_final: 0.7072 (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: 0.9388 (tp) REVERT: C 694 ARG cc_start: 0.7044 (OUTLIER) cc_final: 0.5875 (ttt-90) REVERT: D 154 ASN cc_start: 0.8807 (m-40) cc_final: 0.8461 (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: 0.8674 (pp) REVERT: D 251 HIS cc_start: 0.8268 (m90) cc_final: 0.7977 (m170) REVERT: D 271 TYR cc_start: 0.8636 (t80) cc_final: 0.8188 (t80) REVERT: D 345 LEU cc_start: 0.7428 (tm) cc_final: 0.7006 (mp) REVERT: D 394 PHE cc_start: 0.7108 (t80) cc_final: 0.6794 (t80) REVERT: D 433 MET cc_start: 0.4900 (mtp) cc_final: 0.4644 (mtm) REVERT: D 481 LEU cc_start: 0.8447 (tp) cc_final: 0.8046 (pp) REVERT: D 482 LEU cc_start: 0.8541 (tp) cc_final: 0.8330 (tp) REVERT: D 633 THR cc_start: 0.8869 (m) cc_final: 0.8641 (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: 0.8792 (tt) REVERT: D 645 MET cc_start: 0.9105 (mmp) cc_final: 0.8863 (mmm) REVERT: D 661 LYS cc_start: 0.7841 (mppt) cc_final: 0.7095 (mttt) REVERT: D 664 LYS cc_start: 0.8591 (mtmt) cc_final: 0.8049 (mtmt) REVERT: D 666 ILE cc_start: 0.9666 (mt) cc_final: 0.9386 (tp) REVERT: D 694 ARG cc_start: 0.7034 (OUTLIER) cc_final: 0.5883 (ttt-90) outliers start: 20 outliers final: 4 residues processed: 694 average time/residue: 0.1627 time to fit residues: 165.4420 Evaluate side-chains 405 residues out of total 2140 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 397 time to evaluate : 0.740 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 216 optimal weight: 3.9990 chunk 98 optimal weight: 9.9990 chunk 194 optimal weight: 5.9990 chunk 227 optimal weight: 4.9990 chunk 107 optimal weight: 8.9990 chunk 10 optimal weight: 6.9990 chunk 66 optimal weight: 7.9990 chunk 130 optimal weight: 5.9990 chunk 124 optimal weight: 2.9990 chunk 103 optimal weight: 3.9990 chunk 235 optimal weight: 6.9990 overall best weight: 4.3990 ------------------------------------------------------------------------------- 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 259 ASN ** A 354 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 396 ASN A 413 HIS A 452 GLN ** A 511 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 521 HIS A 651 HIS ** A 655 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 129 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 370 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 396 ASN B 413 HIS B 521 HIS B 651 HIS B 655 ASN ** C 129 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 259 ASN ** C 370 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 413 HIS C 452 GLN C 521 HIS C 655 ASN ** D 129 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 259 ASN D 396 ASN D 413 HIS D 452 GLN D 521 HIS ** D 655 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 21 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3716 r_free = 0.3716 target = 0.083478 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3395 r_free = 0.3395 target = 0.067531 restraints weight = 96683.863| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3426 r_free = 0.3426 target = 0.068854 restraints weight = 65366.236| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 46)----------------| | r_work = 0.3448 r_free = 0.3448 target = 0.069809 restraints weight = 49224.600| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3461 r_free = 0.3461 target = 0.070432 restraints weight = 39756.001| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 43)----------------| | r_work = 0.3471 r_free = 0.3471 target = 0.070869 restraints weight = 34294.047| |-----------------------------------------------------------------------------| r_work (final): 0.3457 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7763 moved from start: 0.5086 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.044 20124 Z= 0.231 Angle : 0.890 11.789 27288 Z= 0.452 Chirality : 0.048 0.289 3064 Planarity : 0.007 0.096 3380 Dihedral : 7.851 31.564 2632 Min Nonbonded Distance : 2.531 Molprobity Statistics. All-atom Clashscore : 16.86 Ramachandran Plot: Outliers : 0.17 % Allowed : 6.80 % Favored : 93.04 % 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 : 5.56 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -3.03 (0.15), residues: 2384 helix: -1.91 (0.13), residues: 1136 sheet: -4.03 (0.47), residues: 72 loop : -1.90 (0.18), residues: 1176 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG D 539 TYR 0.021 0.002 TYR B 228 PHE 0.022 0.002 PHE C 207 TRP 0.025 0.003 TRP B 223 HIS 0.008 0.002 HIS B 313 Details of bonding type rmsd covalent geometry : bond 0.00480 (20124) covalent geometry : angle 0.88959 (27288) hydrogen bonds : bond 0.05246 ( 728) hydrogen bonds : angle 5.99104 ( 2136) *********************** 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 422 residues out of total 2140 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 422 time to evaluate : 0.970 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: A 271 TYR cc_start: 0.8306 (t80) cc_final: 0.8042 (t80) REVERT: A 301 LEU cc_start: 0.9155 (mt) cc_final: 0.8935 (tt) REVERT: A 394 PHE cc_start: 0.6259 (t80) cc_final: 0.6054 (t80) REVERT: A 433 MET cc_start: 0.6029 (mtp) cc_final: 0.5709 (mtm) REVERT: A 481 LEU cc_start: 0.8494 (tp) cc_final: 0.8234 (pp) REVERT: A 482 LEU cc_start: 0.8881 (tp) cc_final: 0.8574 (tp) REVERT: A 529 ILE cc_start: 0.8992 (mp) cc_final: 0.8650 (tt) REVERT: A 633 THR cc_start: 0.8798 (p) cc_final: 0.8590 (t) REVERT: A 637 LEU cc_start: 0.8526 (tt) cc_final: 0.8302 (pp) REVERT: A 641 LEU cc_start: 0.9407 (tt) cc_final: 0.8806 (tt) REVERT: A 645 MET cc_start: 0.9293 (mmp) cc_final: 0.8928 (mmm) REVERT: A 646 SER cc_start: 0.9235 (t) cc_final: 0.8865 (p) REVERT: A 663 GLN cc_start: 0.9111 (tp-100) cc_final: 0.8218 (tp40) REVERT: A 670 GLU cc_start: 0.8784 (pm20) cc_final: 0.8467 (pm20) REVERT: B 271 TYR cc_start: 0.8400 (t80) cc_final: 0.8155 (t80) REVERT: B 301 LEU cc_start: 0.9148 (mt) cc_final: 0.8920 (tt) REVERT: B 394 PHE cc_start: 0.6448 (t80) cc_final: 0.6200 (t80) REVERT: B 404 MET cc_start: 0.7011 (tpt) cc_final: 0.6809 (tpp) REVERT: B 433 MET cc_start: 0.5861 (mtp) cc_final: 0.5583 (mtm) REVERT: B 488 VAL cc_start: 0.7507 (t) cc_final: 0.7250 (m) REVERT: B 529 ILE cc_start: 0.9078 (mp) cc_final: 0.8704 (tt) REVERT: B 544 TYR cc_start: 0.8699 (t80) cc_final: 0.8282 (t80) REVERT: B 607 MET cc_start: 0.5091 (tpt) cc_final: 0.4801 (tpt) REVERT: B 645 MET cc_start: 0.9279 (mmp) cc_final: 0.8979 (mmm) REVERT: B 663 GLN cc_start: 0.8997 (tp-100) cc_final: 0.8179 (tp40) REVERT: B 670 GLU cc_start: 0.8830 (pm20) cc_final: 0.8483 (pm20) REVERT: C 271 TYR cc_start: 0.8289 (t80) cc_final: 0.8004 (t80) REVERT: C 394 PHE cc_start: 0.6234 (t80) cc_final: 0.6004 (t80) REVERT: C 433 MET cc_start: 0.5789 (mtp) cc_final: 0.5507 (mtm) REVERT: C 468 MET cc_start: 0.9196 (mpp) cc_final: 0.8879 (mpp) REVERT: C 481 LEU cc_start: 0.8479 (tp) cc_final: 0.8249 (pp) REVERT: C 482 LEU cc_start: 0.8889 (tp) cc_final: 0.8563 (tp) REVERT: C 529 ILE cc_start: 0.9095 (mp) cc_final: 0.8637 (tt) REVERT: C 544 TYR cc_start: 0.8544 (t80) cc_final: 0.8245 (t80) REVERT: C 645 MET cc_start: 0.9237 (mmp) cc_final: 0.8875 (mmm) REVERT: C 663 GLN cc_start: 0.9053 (tp-100) cc_final: 0.8223 (tp40) REVERT: C 670 GLU cc_start: 0.8834 (pm20) cc_final: 0.8509 (pm20) REVERT: D 271 TYR cc_start: 0.8308 (t80) cc_final: 0.8005 (t80) REVERT: D 311 PHE cc_start: 0.8296 (t80) cc_final: 0.8016 (t80) REVERT: D 394 PHE cc_start: 0.6170 (t80) cc_final: 0.5963 (t80) REVERT: D 433 MET cc_start: 0.5832 (mtp) cc_final: 0.5543 (mtm) REVERT: D 481 LEU cc_start: 0.8480 (tp) cc_final: 0.8243 (pp) REVERT: D 482 LEU cc_start: 0.8905 (tp) cc_final: 0.8578 (tp) REVERT: D 529 ILE cc_start: 0.9111 (mp) cc_final: 0.8663 (tt) REVERT: D 544 TYR cc_start: 0.8586 (t80) cc_final: 0.8291 (t80) REVERT: D 645 MET cc_start: 0.9274 (mmp) cc_final: 0.9038 (mmm) REVERT: D 670 GLU cc_start: 0.8856 (pm20) cc_final: 0.8511 (pm20) outliers start: 0 outliers final: 0 residues processed: 422 average time/residue: 0.1426 time to fit residues: 92.8927 Evaluate side-chains 287 residues out of total 2140 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 287 time to evaluate : 0.543 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 15 optimal weight: 1.9990 chunk 183 optimal weight: 9.9990 chunk 4 optimal weight: 4.9990 chunk 67 optimal weight: 7.9990 chunk 130 optimal weight: 10.0000 chunk 85 optimal weight: 0.9990 chunk 45 optimal weight: 9.9990 chunk 168 optimal weight: 20.0000 chunk 79 optimal weight: 0.9990 chunk 148 optimal weight: 2.9990 chunk 226 optimal weight: 6.9990 overall best weight: 2.3990 ------------------------------------------------------------------------------- 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 324 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 511 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 129 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 324 GLN B 452 GLN ** B 511 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 129 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 324 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 511 ASN ** D 129 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 324 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 511 ASN ** D 655 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3719 r_free = 0.3719 target = 0.084351 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3397 r_free = 0.3397 target = 0.068155 restraints weight = 96893.100| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3427 r_free = 0.3427 target = 0.069536 restraints weight = 66348.862| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3447 r_free = 0.3447 target = 0.070469 restraints weight = 50206.761| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3460 r_free = 0.3460 target = 0.071089 restraints weight = 41076.566| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.3469 r_free = 0.3469 target = 0.071504 restraints weight = 35721.160| |-----------------------------------------------------------------------------| r_work (final): 0.3448 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7799 moved from start: 0.5965 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 20124 Z= 0.164 Angle : 0.768 10.659 27288 Z= 0.387 Chirality : 0.044 0.244 3064 Planarity : 0.005 0.048 3380 Dihedral : 7.115 28.805 2632 Min Nonbonded Distance : 2.541 Molprobity Statistics. All-atom Clashscore : 16.15 Ramachandran Plot: Outliers : 0.04 % Allowed : 7.84 % Favored : 92.11 % Rotamer: Outliers : 0.05 % Allowed : 6.12 % Favored : 93.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 0.34 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.78 (0.15), residues: 2384 helix: -1.43 (0.13), residues: 1204 sheet: -3.71 (0.45), residues: 72 loop : -2.13 (0.18), residues: 1108 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG C 197 TYR 0.021 0.002 TYR A 228 PHE 0.022 0.001 PHE B 540 TRP 0.024 0.002 TRP D 386 HIS 0.004 0.001 HIS B 370 Details of bonding type rmsd covalent geometry : bond 0.00335 (20124) covalent geometry : angle 0.76805 (27288) hydrogen bonds : bond 0.04260 ( 728) hydrogen bonds : angle 5.38784 ( 2136) *********************** 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 361 residues out of total 2140 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 360 time to evaluate : 0.769 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: A 231 GLU cc_start: 0.8352 (mt-10) cc_final: 0.7962 (pt0) REVERT: A 301 LEU cc_start: 0.9261 (mt) cc_final: 0.8968 (tt) REVERT: A 433 MET cc_start: 0.5866 (mtp) cc_final: 0.5599 (mtm) REVERT: A 481 LEU cc_start: 0.8559 (tp) cc_final: 0.8321 (pp) REVERT: A 529 ILE cc_start: 0.8959 (mp) cc_final: 0.8553 (tt) REVERT: A 547 PHE cc_start: 0.8006 (m-10) cc_final: 0.7650 (m-10) REVERT: A 641 LEU cc_start: 0.9466 (tt) cc_final: 0.8762 (tt) REVERT: A 645 MET cc_start: 0.9247 (mmp) cc_final: 0.8808 (mmm) REVERT: A 663 GLN cc_start: 0.9219 (tp-100) cc_final: 0.8277 (tp40) REVERT: A 670 GLU cc_start: 0.8814 (pm20) cc_final: 0.8504 (pm20) REVERT: B 271 TYR cc_start: 0.8408 (t80) cc_final: 0.7640 (t80) REVERT: B 301 LEU cc_start: 0.9269 (mt) cc_final: 0.8958 (tt) REVERT: B 311 PHE cc_start: 0.8333 (t80) cc_final: 0.8073 (t80) REVERT: B 319 PHE cc_start: 0.7550 (p90) cc_final: 0.6991 (p90) REVERT: B 324 GLN cc_start: 0.7716 (OUTLIER) cc_final: 0.6047 (mp-120) REVERT: B 433 MET cc_start: 0.5784 (mtp) cc_final: 0.5492 (mtm) REVERT: B 636 LEU cc_start: 0.9136 (mm) cc_final: 0.8787 (tt) REVERT: B 641 LEU cc_start: 0.9308 (mp) cc_final: 0.8876 (mp) REVERT: B 645 MET cc_start: 0.9209 (mmp) cc_final: 0.8986 (mmm) REVERT: B 670 GLU cc_start: 0.8863 (pm20) cc_final: 0.8488 (pm20) REVERT: C 319 PHE cc_start: 0.7275 (p90) cc_final: 0.6632 (p90) REVERT: C 433 MET cc_start: 0.5831 (mtp) cc_final: 0.5539 (mtm) REVERT: C 481 LEU cc_start: 0.8620 (tp) cc_final: 0.8358 (pp) REVERT: C 529 ILE cc_start: 0.9079 (mp) cc_final: 0.8678 (tt) REVERT: C 601 PHE cc_start: 0.8810 (m-10) cc_final: 0.7939 (t80) REVERT: C 637 LEU cc_start: 0.8500 (tt) cc_final: 0.8193 (pp) REVERT: C 641 LEU cc_start: 0.9132 (mp) cc_final: 0.8842 (tt) REVERT: C 645 MET cc_start: 0.9231 (mmp) cc_final: 0.8914 (mmm) REVERT: C 663 GLN cc_start: 0.9159 (tp-100) cc_final: 0.8144 (tp40) REVERT: C 666 ILE cc_start: 0.9672 (mt) cc_final: 0.9449 (tp) REVERT: C 670 GLU cc_start: 0.8908 (pm20) cc_final: 0.8538 (pm20) REVERT: D 433 MET cc_start: 0.5824 (mtp) cc_final: 0.5535 (mtm) REVERT: D 481 LEU cc_start: 0.8558 (tp) cc_final: 0.8319 (pp) REVERT: D 547 PHE cc_start: 0.7926 (m-10) cc_final: 0.7573 (m-10) REVERT: D 641 LEU cc_start: 0.9320 (mp) cc_final: 0.8897 (mt) REVERT: D 645 MET cc_start: 0.9264 (mmp) cc_final: 0.8905 (mmm) REVERT: D 663 GLN cc_start: 0.9152 (tp-100) cc_final: 0.8115 (tp40) REVERT: D 670 GLU cc_start: 0.8843 (pm20) cc_final: 0.8493 (pm20) outliers start: 1 outliers final: 0 residues processed: 361 average time/residue: 0.1354 time to fit residues: 77.1750 Evaluate side-chains 248 residues out of total 2140 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 247 time to evaluate : 0.720 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 43 optimal weight: 1.9990 chunk 20 optimal weight: 5.9990 chunk 192 optimal weight: 0.0170 chunk 225 optimal weight: 7.9990 chunk 84 optimal weight: 4.9990 chunk 67 optimal weight: 0.0980 chunk 92 optimal weight: 7.9990 chunk 190 optimal weight: 6.9990 chunk 128 optimal weight: 20.0000 chunk 148 optimal weight: 0.9990 chunk 5 optimal weight: 10.0000 overall best weight: 1.6224 ------------------------------------------------------------------------------- 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 324 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 370 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 438 HIS ** B 129 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 438 HIS ** B 487 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 129 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 269 HIS ** C 324 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 438 HIS ** C 487 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 129 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 269 HIS ** D 324 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 370 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 438 HIS ** D 655 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3719 r_free = 0.3719 target = 0.084994 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3404 r_free = 0.3404 target = 0.068641 restraints weight = 92004.056| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3436 r_free = 0.3436 target = 0.070084 restraints weight = 61487.836| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3457 r_free = 0.3457 target = 0.071057 restraints weight = 45767.577| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 41)----------------| | r_work = 0.3471 r_free = 0.3471 target = 0.071714 restraints weight = 37049.161| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3479 r_free = 0.3479 target = 0.072155 restraints weight = 31878.906| |-----------------------------------------------------------------------------| r_work (final): 0.3467 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7792 moved from start: 0.6591 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 20124 Z= 0.138 Angle : 0.733 11.223 27288 Z= 0.366 Chirality : 0.044 0.244 3064 Planarity : 0.004 0.047 3380 Dihedral : 6.726 29.096 2632 Min Nonbonded Distance : 2.580 Molprobity Statistics. All-atom Clashscore : 16.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.63 % Favored : 93.37 % 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 : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.58 (0.15), residues: 2384 helix: -1.15 (0.13), residues: 1236 sheet: -3.52 (0.45), residues: 72 loop : -2.20 (0.17), residues: 1076 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 193 TYR 0.027 0.001 TYR A 400 PHE 0.013 0.001 PHE C 207 TRP 0.018 0.002 TRP B 386 HIS 0.004 0.001 HIS C 370 Details of bonding type rmsd covalent geometry : bond 0.00289 (20124) covalent geometry : angle 0.73274 (27288) hydrogen bonds : bond 0.03864 ( 728) hydrogen bonds : angle 5.24347 ( 2136) *********************** 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 356 residues out of total 2140 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 356 time to evaluate : 0.826 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: A 231 GLU cc_start: 0.8387 (mt-10) cc_final: 0.7983 (pt0) REVERT: A 301 LEU cc_start: 0.9200 (mt) cc_final: 0.8989 (tt) REVERT: A 319 PHE cc_start: 0.7003 (p90) cc_final: 0.6720 (p90) REVERT: A 368 ASN cc_start: 0.5611 (t0) cc_final: 0.5221 (t0) REVERT: A 370 HIS cc_start: 0.7391 (p-80) cc_final: 0.7071 (p-80) REVERT: A 433 MET cc_start: 0.5853 (mtp) cc_final: 0.5585 (mtm) REVERT: A 529 ILE cc_start: 0.8982 (mp) cc_final: 0.8607 (tt) REVERT: A 547 PHE cc_start: 0.8058 (m-10) cc_final: 0.7710 (m-10) REVERT: A 641 LEU cc_start: 0.9453 (tt) cc_final: 0.8809 (tt) REVERT: A 645 MET cc_start: 0.9240 (mmp) cc_final: 0.8838 (mmm) REVERT: A 663 GLN cc_start: 0.9167 (tp-100) cc_final: 0.8183 (tp-100) REVERT: A 670 GLU cc_start: 0.8764 (pm20) cc_final: 0.8558 (pm20) REVERT: B 271 TYR cc_start: 0.8613 (t80) cc_final: 0.8285 (t80) REVERT: B 301 LEU cc_start: 0.9189 (mt) cc_final: 0.8920 (tt) REVERT: B 319 PHE cc_start: 0.7089 (p90) cc_final: 0.6694 (p90) REVERT: B 433 MET cc_start: 0.5819 (mtp) cc_final: 0.5548 (mtm) REVERT: B 547 PHE cc_start: 0.8124 (m-80) cc_final: 0.7899 (m-80) REVERT: B 636 LEU cc_start: 0.9084 (mm) cc_final: 0.8697 (tp) REVERT: B 641 LEU cc_start: 0.9339 (mp) cc_final: 0.8932 (mt) REVERT: B 645 MET cc_start: 0.9224 (mmp) cc_final: 0.9003 (mmm) REVERT: B 666 ILE cc_start: 0.9672 (mt) cc_final: 0.9429 (tp) REVERT: B 670 GLU cc_start: 0.8863 (pm20) cc_final: 0.8561 (pm20) REVERT: C 231 GLU cc_start: 0.8393 (mt-10) cc_final: 0.7983 (pt0) REVERT: C 433 MET cc_start: 0.5876 (mtp) cc_final: 0.5600 (mtm) REVERT: C 529 ILE cc_start: 0.9087 (mp) cc_final: 0.8755 (tt) REVERT: C 547 PHE cc_start: 0.8005 (m-10) cc_final: 0.7690 (m-10) REVERT: C 645 MET cc_start: 0.9227 (mmp) cc_final: 0.8956 (mmm) REVERT: C 663 GLN cc_start: 0.9222 (tp-100) cc_final: 0.8361 (tp40) REVERT: C 666 ILE cc_start: 0.9679 (mt) cc_final: 0.9478 (tp) REVERT: C 670 GLU cc_start: 0.8874 (pm20) cc_final: 0.8548 (pm20) REVERT: D 231 GLU cc_start: 0.8404 (mt-10) cc_final: 0.7997 (pt0) REVERT: D 319 PHE cc_start: 0.7023 (p90) cc_final: 0.6737 (p90) REVERT: D 433 MET cc_start: 0.5895 (mtp) cc_final: 0.5606 (mtm) REVERT: D 481 LEU cc_start: 0.8674 (tp) cc_final: 0.8341 (pp) REVERT: D 482 LEU cc_start: 0.9142 (mt) cc_final: 0.8895 (mt) REVERT: D 547 PHE cc_start: 0.8054 (m-10) cc_final: 0.7716 (m-10) REVERT: D 641 LEU cc_start: 0.9260 (mp) cc_final: 0.8770 (tt) REVERT: D 645 MET cc_start: 0.9246 (mmp) cc_final: 0.8788 (mmm) REVERT: D 663 GLN cc_start: 0.9153 (tp-100) cc_final: 0.8367 (tp40) REVERT: D 670 GLU cc_start: 0.8893 (pm20) cc_final: 0.8523 (pm20) outliers start: 0 outliers final: 0 residues processed: 356 average time/residue: 0.1251 time to fit residues: 72.4356 Evaluate side-chains 251 residues out of total 2140 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 251 time to evaluate : 0.762 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 184 optimal weight: 0.8980 chunk 56 optimal weight: 9.9990 chunk 235 optimal weight: 0.7980 chunk 146 optimal weight: 3.9990 chunk 212 optimal weight: 3.9990 chunk 10 optimal weight: 0.0020 chunk 239 optimal weight: 10.0000 chunk 11 optimal weight: 1.9990 chunk 233 optimal weight: 0.9990 chunk 106 optimal weight: 6.9990 chunk 120 optimal weight: 10.0000 overall best weight: 0.9392 ------------------------------------------------------------------------------- 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 324 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 370 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 129 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 487 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 129 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 324 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 129 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 324 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 370 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3750 r_free = 0.3750 target = 0.086838 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3425 r_free = 0.3425 target = 0.070188 restraints weight = 94403.835| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3459 r_free = 0.3459 target = 0.071744 restraints weight = 62482.008| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3481 r_free = 0.3481 target = 0.072795 restraints weight = 46170.325| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3495 r_free = 0.3495 target = 0.073466 restraints weight = 36870.268| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.3506 r_free = 0.3506 target = 0.074012 restraints weight = 31624.969| |-----------------------------------------------------------------------------| r_work (final): 0.3485 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7769 moved from start: 0.6994 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 20124 Z= 0.123 Angle : 0.726 10.983 27288 Z= 0.353 Chirality : 0.043 0.293 3064 Planarity : 0.004 0.052 3380 Dihedral : 6.327 29.059 2632 Min Nonbonded Distance : 2.578 Molprobity Statistics. All-atom Clashscore : 15.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.54 % Favored : 93.46 % Rotamer: Outliers : 0.00 % Allowed : 4.25 % Favored : 95.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 0.34 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.37 (0.16), residues: 2384 helix: -1.04 (0.13), residues: 1248 sheet: -3.08 (0.47), residues: 60 loop : -2.08 (0.18), residues: 1076 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D 371 TYR 0.026 0.001 TYR B 400 PHE 0.014 0.001 PHE B 540 TRP 0.020 0.001 TRP D 660 HIS 0.004 0.001 HIS B 169 Details of bonding type rmsd covalent geometry : bond 0.00256 (20124) covalent geometry : angle 0.72568 (27288) hydrogen bonds : bond 0.03501 ( 728) hydrogen bonds : angle 4.98574 ( 2136) *********************** 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 344 residues out of total 2140 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 344 time to evaluate : 0.790 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 301 LEU cc_start: 0.9121 (mt) cc_final: 0.8813 (tt) REVERT: A 433 MET cc_start: 0.5824 (mtp) cc_final: 0.5577 (mtm) REVERT: A 522 THR cc_start: 0.8415 (t) cc_final: 0.8196 (p) REVERT: A 529 ILE cc_start: 0.9043 (mp) cc_final: 0.8688 (tt) REVERT: A 547 PHE cc_start: 0.8083 (m-10) cc_final: 0.7757 (m-80) REVERT: A 641 LEU cc_start: 0.9513 (tt) cc_final: 0.8593 (tt) REVERT: A 645 MET cc_start: 0.9105 (mmp) cc_final: 0.8780 (mmm) REVERT: A 663 GLN cc_start: 0.9191 (tp-100) cc_final: 0.8174 (tp-100) REVERT: A 670 GLU cc_start: 0.8907 (pm20) cc_final: 0.8613 (pm20) REVERT: B 271 TYR cc_start: 0.8233 (t80) cc_final: 0.7965 (t80) REVERT: B 288 GLU cc_start: 0.7270 (mt-10) cc_final: 0.6910 (tt0) REVERT: B 301 LEU cc_start: 0.9045 (mt) cc_final: 0.8757 (tt) REVERT: B 433 MET cc_start: 0.5806 (mtp) cc_final: 0.5550 (mtm) REVERT: B 547 PHE cc_start: 0.8140 (m-80) cc_final: 0.7936 (m-80) REVERT: B 640 MET cc_start: 0.8373 (mmt) cc_final: 0.8044 (mmm) REVERT: B 641 LEU cc_start: 0.9418 (mp) cc_final: 0.8792 (tt) REVERT: C 433 MET cc_start: 0.5839 (mtp) cc_final: 0.5572 (mtm) REVERT: C 529 ILE cc_start: 0.9078 (mp) cc_final: 0.8771 (tt) REVERT: C 547 PHE cc_start: 0.8191 (m-10) cc_final: 0.7869 (m-80) REVERT: C 641 LEU cc_start: 0.9298 (mp) cc_final: 0.9048 (tt) REVERT: C 645 MET cc_start: 0.9222 (mmp) cc_final: 0.9001 (mmm) REVERT: C 663 GLN cc_start: 0.9272 (tp-100) cc_final: 0.8400 (tp40) REVERT: C 670 GLU cc_start: 0.8910 (pm20) cc_final: 0.8647 (pm20) REVERT: D 433 MET cc_start: 0.5856 (mtp) cc_final: 0.5580 (mtm) REVERT: D 547 PHE cc_start: 0.8261 (m-10) cc_final: 0.7950 (m-10) REVERT: D 645 MET cc_start: 0.9171 (mmp) cc_final: 0.8910 (mmm) REVERT: D 663 GLN cc_start: 0.9231 (tp-100) cc_final: 0.8280 (tp-100) outliers start: 0 outliers final: 0 residues processed: 344 average time/residue: 0.1358 time to fit residues: 73.9262 Evaluate side-chains 270 residues out of total 2140 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 270 time to evaluate : 0.801 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 162 optimal weight: 2.9990 chunk 122 optimal weight: 0.1980 chunk 211 optimal weight: 2.9990 chunk 184 optimal weight: 0.0870 chunk 187 optimal weight: 7.9990 chunk 139 optimal weight: 7.9990 chunk 84 optimal weight: 0.9980 chunk 101 optimal weight: 0.0770 chunk 11 optimal weight: 6.9990 chunk 96 optimal weight: 20.0000 chunk 77 optimal weight: 3.9990 overall best weight: 0.8718 ------------------------------------------------------------------------------- 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 324 GLN ** A 370 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 487 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 129 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 487 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 129 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 324 GLN ** C 370 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 487 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 129 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 324 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 370 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3762 r_free = 0.3762 target = 0.087423 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3444 r_free = 0.3444 target = 0.071142 restraints weight = 94510.462| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3476 r_free = 0.3476 target = 0.072549 restraints weight = 65195.119| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3495 r_free = 0.3495 target = 0.073468 restraints weight = 49223.714| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3509 r_free = 0.3509 target = 0.074154 restraints weight = 40199.604| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 49)----------------| | r_work = 0.3518 r_free = 0.3518 target = 0.074646 restraints weight = 34828.319| |-----------------------------------------------------------------------------| r_work (final): 0.3499 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7757 moved from start: 0.7354 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 20124 Z= 0.124 Angle : 0.738 11.167 27288 Z= 0.357 Chirality : 0.042 0.220 3064 Planarity : 0.004 0.058 3380 Dihedral : 6.186 29.239 2632 Min Nonbonded Distance : 2.575 Molprobity Statistics. All-atom Clashscore : 13.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.87 % Favored : 94.13 % Rotamer: Outliers : 0.09 % Allowed : 3.69 % Favored : 96.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 0.34 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.08 (0.16), residues: 2384 helix: -0.85 (0.14), residues: 1240 sheet: -2.67 (0.49), residues: 60 loop : -1.88 (0.18), residues: 1084 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 369 TYR 0.017 0.001 TYR A 271 PHE 0.023 0.001 PHE C 540 TRP 0.019 0.001 TRP D 333 HIS 0.003 0.001 HIS B 169 Details of bonding type rmsd covalent geometry : bond 0.00262 (20124) covalent geometry : angle 0.73842 (27288) hydrogen bonds : bond 0.03381 ( 728) hydrogen bonds : angle 4.87860 ( 2136) *********************** 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 357 residues out of total 2140 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 355 time to evaluate : 0.856 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: A 243 ASP cc_start: 0.8923 (p0) cc_final: 0.8407 (p0) REVERT: A 301 LEU cc_start: 0.9151 (mt) cc_final: 0.8754 (tt) REVERT: A 345 LEU cc_start: 0.7911 (mp) cc_final: 0.7688 (mp) REVERT: A 433 MET cc_start: 0.5765 (mtp) cc_final: 0.5524 (mtm) REVERT: A 522 THR cc_start: 0.8435 (t) cc_final: 0.8157 (p) REVERT: A 529 ILE cc_start: 0.9041 (mp) cc_final: 0.8693 (tt) REVERT: A 547 PHE cc_start: 0.8268 (m-10) cc_final: 0.7972 (m-80) REVERT: A 641 LEU cc_start: 0.9384 (tt) cc_final: 0.8923 (tt) REVERT: A 663 GLN cc_start: 0.9185 (tp-100) cc_final: 0.8154 (tp-100) REVERT: B 221 LYS cc_start: 0.5334 (pttt) cc_final: 0.5027 (pttm) REVERT: B 231 GLU cc_start: 0.8490 (mt-10) cc_final: 0.8225 (mt-10) REVERT: B 270 MET cc_start: 0.8356 (mmm) cc_final: 0.7932 (mmp) REVERT: B 271 TYR cc_start: 0.8174 (t80) cc_final: 0.7817 (t80) REVERT: B 301 LEU cc_start: 0.9286 (mt) cc_final: 0.8772 (tt) REVERT: B 365 LYS cc_start: 0.9139 (mptt) cc_final: 0.8845 (mmtm) REVERT: B 433 MET cc_start: 0.5832 (mtp) cc_final: 0.5573 (mtm) REVERT: B 547 PHE cc_start: 0.8092 (m-80) cc_final: 0.7858 (m-80) REVERT: B 636 LEU cc_start: 0.8925 (mm) cc_final: 0.8449 (tp) REVERT: B 640 MET cc_start: 0.8277 (mmt) cc_final: 0.8010 (mmm) REVERT: C 231 GLU cc_start: 0.8454 (mt-10) cc_final: 0.8219 (mt-10) REVERT: C 372 MET cc_start: 0.8576 (mmt) cc_final: 0.8275 (mmt) REVERT: C 433 MET cc_start: 0.5853 (mtp) cc_final: 0.5591 (mtm) REVERT: C 478 LEU cc_start: 0.9179 (mm) cc_final: 0.8960 (mt) REVERT: C 529 ILE cc_start: 0.9103 (mp) cc_final: 0.8800 (tt) REVERT: C 547 PHE cc_start: 0.8178 (m-10) cc_final: 0.7929 (m-80) REVERT: C 641 LEU cc_start: 0.9362 (mp) cc_final: 0.8847 (tt) REVERT: C 663 GLN cc_start: 0.9139 (tp-100) cc_final: 0.8184 (tp40) REVERT: D 433 MET cc_start: 0.5877 (mtp) cc_final: 0.5601 (mtm) REVERT: D 547 PHE cc_start: 0.8212 (m-10) cc_final: 0.7961 (m-80) REVERT: D 646 SER cc_start: 0.9437 (t) cc_final: 0.9078 (p) REVERT: D 663 GLN cc_start: 0.9204 (tp-100) cc_final: 0.8224 (tp-100) outliers start: 2 outliers final: 0 residues processed: 357 average time/residue: 0.1473 time to fit residues: 80.7355 Evaluate side-chains 265 residues out of total 2140 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 265 time to evaluate : 0.803 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 103 optimal weight: 7.9990 chunk 144 optimal weight: 0.8980 chunk 205 optimal weight: 6.9990 chunk 148 optimal weight: 0.9990 chunk 66 optimal weight: 9.9990 chunk 51 optimal weight: 8.9990 chunk 138 optimal weight: 4.9990 chunk 4 optimal weight: 9.9990 chunk 100 optimal weight: 5.9990 chunk 86 optimal weight: 0.0570 chunk 221 optimal weight: 0.3980 overall best weight: 1.4702 ------------------------------------------------------------------------------- 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 324 GLN ** A 370 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 487 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 129 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 487 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 129 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 324 GLN ** C 370 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 487 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 129 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 324 GLN ** D 370 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 487 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3747 r_free = 0.3747 target = 0.086721 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3420 r_free = 0.3420 target = 0.070235 restraints weight = 95512.625| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3452 r_free = 0.3452 target = 0.071696 restraints weight = 64738.788| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3472 r_free = 0.3472 target = 0.072671 restraints weight = 48371.796| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3485 r_free = 0.3485 target = 0.073317 restraints weight = 39240.972| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 43)----------------| | r_work = 0.3495 r_free = 0.3495 target = 0.073801 restraints weight = 33914.255| |-----------------------------------------------------------------------------| r_work (final): 0.3470 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7791 moved from start: 0.7688 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 20124 Z= 0.126 Angle : 0.732 11.002 27288 Z= 0.354 Chirality : 0.042 0.197 3064 Planarity : 0.004 0.059 3380 Dihedral : 6.097 30.959 2632 Min Nonbonded Distance : 2.574 Molprobity Statistics. All-atom Clashscore : 14.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.29 % Favored : 93.71 % Rotamer: Outliers : 0.14 % Allowed : 1.45 % Favored : 98.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 0.34 % Twisted Proline : 5.56 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.87 (0.16), residues: 2384 helix: -0.63 (0.14), residues: 1220 sheet: -2.28 (0.51), residues: 60 loop : -1.84 (0.18), residues: 1104 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 312 TYR 0.012 0.001 TYR B 228 PHE 0.015 0.001 PHE B 540 TRP 0.019 0.001 TRP B 333 HIS 0.004 0.001 HIS B 169 Details of bonding type rmsd covalent geometry : bond 0.00270 (20124) covalent geometry : angle 0.73163 (27288) hydrogen bonds : bond 0.03333 ( 728) hydrogen bonds : angle 4.82410 ( 2136) *********************** 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 332 residues out of total 2140 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 329 time to evaluate : 0.786 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 231 GLU cc_start: 0.8359 (mt-10) cc_final: 0.8086 (mt-10) REVERT: A 301 LEU cc_start: 0.9099 (mt) cc_final: 0.8790 (tt) REVERT: A 345 LEU cc_start: 0.7916 (mp) cc_final: 0.7680 (mp) REVERT: A 365 LYS cc_start: 0.8998 (mptt) cc_final: 0.8751 (mmtm) REVERT: A 374 VAL cc_start: 0.9502 (m) cc_final: 0.9278 (p) REVERT: A 433 MET cc_start: 0.5824 (mtp) cc_final: 0.5587 (mtm) REVERT: A 522 THR cc_start: 0.8461 (t) cc_final: 0.8220 (p) REVERT: A 529 ILE cc_start: 0.9054 (mp) cc_final: 0.8765 (tt) REVERT: A 641 LEU cc_start: 0.9372 (tt) cc_final: 0.8852 (tt) REVERT: A 645 MET cc_start: 0.9153 (mmp) cc_final: 0.8761 (mmm) REVERT: A 663 GLN cc_start: 0.9159 (tp-100) cc_final: 0.8214 (tp40) REVERT: B 231 GLU cc_start: 0.8500 (mt-10) cc_final: 0.8221 (mt-10) REVERT: B 270 MET cc_start: 0.8389 (mmm) cc_final: 0.7971 (mmp) REVERT: B 301 LEU cc_start: 0.9206 (mt) cc_final: 0.8745 (tt) REVERT: B 365 LYS cc_start: 0.9085 (mptt) cc_final: 0.8835 (mmtm) REVERT: B 372 MET cc_start: 0.8572 (mmt) cc_final: 0.8226 (mmt) REVERT: B 433 MET cc_start: 0.5821 (mtp) cc_final: 0.5586 (mtm) REVERT: B 478 LEU cc_start: 0.9133 (mm) cc_final: 0.8909 (mt) REVERT: B 547 PHE cc_start: 0.8118 (m-80) cc_final: 0.7869 (m-80) REVERT: B 640 MET cc_start: 0.8297 (mmt) cc_final: 0.8075 (mmm) REVERT: B 663 GLN cc_start: 0.9258 (tp-100) cc_final: 0.8529 (tp40) REVERT: C 231 GLU cc_start: 0.8494 (mt-10) cc_final: 0.8230 (mt-10) REVERT: C 270 MET cc_start: 0.8223 (mmp) cc_final: 0.7923 (mmp) REVERT: C 365 LYS cc_start: 0.8950 (mmpt) cc_final: 0.8702 (mmtm) REVERT: C 372 MET cc_start: 0.8637 (mmt) cc_final: 0.8350 (mmt) REVERT: C 433 MET cc_start: 0.5862 (mtp) cc_final: 0.5598 (mtm) REVERT: C 663 GLN cc_start: 0.9178 (tp-100) cc_final: 0.8223 (tp40) REVERT: D 270 MET cc_start: 0.8199 (mmp) cc_final: 0.7929 (mmp) REVERT: D 345 LEU cc_start: 0.7959 (mp) cc_final: 0.7745 (mp) REVERT: D 433 MET cc_start: 0.5862 (mtp) cc_final: 0.5599 (mtm) REVERT: D 663 GLN cc_start: 0.9215 (tp-100) cc_final: 0.8224 (tp-100) outliers start: 3 outliers final: 0 residues processed: 332 average time/residue: 0.1312 time to fit residues: 69.3800 Evaluate side-chains 252 residues out of total 2140 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 252 time to evaluate : 0.797 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 104 optimal weight: 5.9990 chunk 43 optimal weight: 4.9990 chunk 147 optimal weight: 9.9990 chunk 112 optimal weight: 3.9990 chunk 105 optimal weight: 8.9990 chunk 200 optimal weight: 1.9990 chunk 191 optimal weight: 7.9990 chunk 82 optimal weight: 3.9990 chunk 157 optimal weight: 3.9990 chunk 208 optimal weight: 0.8980 chunk 189 optimal weight: 3.9990 overall best weight: 2.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 129 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 247 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 324 GLN ** A 370 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 487 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 129 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 487 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 129 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 316 GLN ** C 370 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 487 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 129 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 316 GLN D 324 GLN ** D 370 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 487 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3691 r_free = 0.3691 target = 0.083767 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3355 r_free = 0.3355 target = 0.067277 restraints weight = 96468.896| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3387 r_free = 0.3387 target = 0.068726 restraints weight = 64760.954| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.3408 r_free = 0.3408 target = 0.069716 restraints weight = 48012.431| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3422 r_free = 0.3422 target = 0.070369 restraints weight = 38790.364| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.3432 r_free = 0.3432 target = 0.070821 restraints weight = 33446.317| |-----------------------------------------------------------------------------| r_work (final): 0.3408 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7879 moved from start: 0.8114 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= 0.157 Angle : 0.743 9.718 27288 Z= 0.366 Chirality : 0.044 0.210 3064 Planarity : 0.005 0.061 3380 Dihedral : 6.184 31.091 2632 Min Nonbonded Distance : 2.552 Molprobity Statistics. All-atom Clashscore : 15.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.13 % Favored : 92.87 % Rotamer: Outliers : 0.05 % Allowed : 1.54 % Favored : 98.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 0.34 % Twisted Proline : 4.17 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.85 (0.16), residues: 2384 helix: -0.69 (0.14), residues: 1232 sheet: -1.94 (0.53), residues: 60 loop : -1.77 (0.18), residues: 1092 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.001 ARG B 317 TYR 0.023 0.002 TYR D 228 PHE 0.037 0.002 PHE D 330 TRP 0.023 0.002 TRP B 333 HIS 0.005 0.001 HIS D 169 Details of bonding type rmsd covalent geometry : bond 0.00334 (20124) covalent geometry : angle 0.74296 (27288) hydrogen bonds : bond 0.03447 ( 728) hydrogen bonds : angle 4.89278 ( 2136) *********************** 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 324 residues out of total 2140 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 323 time to evaluate : 0.781 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 270 MET cc_start: 0.8162 (mmt) cc_final: 0.7955 (mmp) REVERT: A 271 TYR cc_start: 0.8414 (t80) cc_final: 0.8135 (t80) REVERT: A 301 LEU cc_start: 0.9209 (mt) cc_final: 0.8945 (tt) REVERT: A 345 LEU cc_start: 0.7900 (mp) cc_final: 0.7679 (mp) REVERT: A 365 LYS cc_start: 0.9120 (mptt) cc_final: 0.8823 (mmtm) REVERT: A 404 MET cc_start: 0.7526 (tpt) cc_final: 0.7262 (tpp) REVERT: A 529 ILE cc_start: 0.9073 (mp) cc_final: 0.8766 (tt) REVERT: A 663 GLN cc_start: 0.9246 (tp-100) cc_final: 0.8307 (tp40) REVERT: A 670 GLU cc_start: 0.9142 (pm20) cc_final: 0.8836 (pm20) REVERT: B 208 TYR cc_start: 0.7623 (t80) cc_final: 0.7372 (t80) REVERT: B 270 MET cc_start: 0.8387 (mmm) cc_final: 0.7856 (mmp) REVERT: B 300 LYS cc_start: 0.9227 (ptpt) cc_final: 0.8826 (ptpt) REVERT: B 301 LEU cc_start: 0.9217 (mt) cc_final: 0.8709 (tt) REVERT: B 372 MET cc_start: 0.8594 (mmt) cc_final: 0.8218 (mmt) REVERT: B 547 PHE cc_start: 0.8023 (m-80) cc_final: 0.7783 (m-80) REVERT: B 640 MET cc_start: 0.8265 (mmt) cc_final: 0.8038 (mmm) REVERT: C 208 TYR cc_start: 0.7613 (t80) cc_final: 0.7229 (t80) REVERT: C 231 GLU cc_start: 0.8493 (mt-10) cc_final: 0.8229 (mt-10) REVERT: C 253 LEU cc_start: 0.9542 (mm) cc_final: 0.9320 (tp) REVERT: C 270 MET cc_start: 0.8393 (mmp) cc_final: 0.8142 (mmp) REVERT: C 271 TYR cc_start: 0.8254 (t80) cc_final: 0.7977 (t80) REVERT: C 365 LYS cc_start: 0.9088 (mmpt) cc_final: 0.8838 (mmtm) REVERT: C 404 MET cc_start: 0.7182 (tpt) cc_final: 0.6941 (tpp) REVERT: C 645 MET cc_start: 0.9159 (mmp) cc_final: 0.8908 (mmm) REVERT: C 663 GLN cc_start: 0.9218 (tp-100) cc_final: 0.8290 (tp40) REVERT: C 670 GLU cc_start: 0.9139 (pm20) cc_final: 0.8831 (pm20) REVERT: D 208 TYR cc_start: 0.7726 (t80) cc_final: 0.7427 (t80) REVERT: D 270 MET cc_start: 0.8378 (mmp) cc_final: 0.8164 (mmp) REVERT: D 271 TYR cc_start: 0.8326 (t80) cc_final: 0.8065 (t80) REVERT: D 319 PHE cc_start: 0.7173 (p90) cc_final: 0.6913 (p90) REVERT: D 345 LEU cc_start: 0.8018 (mp) cc_final: 0.7773 (mp) REVERT: D 372 MET cc_start: 0.8725 (mmt) cc_final: 0.8391 (mmt) REVERT: D 404 MET cc_start: 0.7194 (tpt) cc_final: 0.6940 (tpp) REVERT: D 645 MET cc_start: 0.9217 (mmp) cc_final: 0.9014 (mmm) outliers start: 1 outliers final: 0 residues processed: 324 average time/residue: 0.1306 time to fit residues: 67.2191 Evaluate side-chains 249 residues out of total 2140 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 249 time to evaluate : 0.692 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 226 optimal weight: 8.9990 chunk 167 optimal weight: 5.9990 chunk 66 optimal weight: 2.9990 chunk 211 optimal weight: 9.9990 chunk 203 optimal weight: 0.3980 chunk 223 optimal weight: 8.9990 chunk 239 optimal weight: 3.9990 chunk 9 optimal weight: 5.9990 chunk 62 optimal weight: 20.0000 chunk 95 optimal weight: 10.0000 chunk 178 optimal weight: 20.0000 overall best weight: 3.8788 ------------------------------------------------------------------------------- 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 156 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 251 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 316 GLN A 324 GLN ** A 370 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 487 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 129 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 316 GLN ** B 487 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 487 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 129 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 251 HIS D 259 ASN ** D 370 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 487 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3641 r_free = 0.3641 target = 0.081177 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3311 r_free = 0.3311 target = 0.064945 restraints weight = 94377.483| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3343 r_free = 0.3343 target = 0.066300 restraints weight = 63049.030| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3363 r_free = 0.3363 target = 0.067216 restraints weight = 46960.699| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 46)----------------| | r_work = 0.3377 r_free = 0.3377 target = 0.067852 restraints weight = 38183.968| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3385 r_free = 0.3385 target = 0.068259 restraints weight = 33027.127| |-----------------------------------------------------------------------------| r_work (final): 0.3371 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7947 moved from start: 0.8640 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= 0.181 Angle : 0.776 10.055 27288 Z= 0.385 Chirality : 0.045 0.239 3064 Planarity : 0.005 0.075 3380 Dihedral : 6.391 30.381 2632 Min Nonbonded Distance : 2.552 Molprobity Statistics. All-atom Clashscore : 17.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.55 % Favored : 92.45 % Rotamer: Outliers : 0.05 % Allowed : 1.12 % Favored : 98.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 0.34 % Twisted Proline : 4.17 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.97 (0.16), residues: 2384 helix: -0.72 (0.14), residues: 1248 sheet: -1.94 (0.54), residues: 72 loop : -1.92 (0.18), residues: 1064 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG C 317 TYR 0.026 0.002 TYR B 228 PHE 0.045 0.002 PHE D 330 TRP 0.022 0.002 TRP C 333 HIS 0.006 0.001 HIS B 169 Details of bonding type rmsd covalent geometry : bond 0.00388 (20124) covalent geometry : angle 0.77574 (27288) hydrogen bonds : bond 0.03601 ( 728) hydrogen bonds : angle 5.05862 ( 2136) *********************** 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 308 residues out of total 2140 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 307 time to evaluate : 0.521 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: A 208 TYR cc_start: 0.7893 (t80) cc_final: 0.7664 (t80) REVERT: A 251 HIS cc_start: 0.8455 (m-70) cc_final: 0.8150 (m-70) REVERT: A 255 MET cc_start: 0.8867 (mmm) cc_final: 0.8440 (mmm) REVERT: A 301 LEU cc_start: 0.9343 (mt) cc_final: 0.9088 (tt) REVERT: A 404 MET cc_start: 0.7831 (tpt) cc_final: 0.7466 (tpp) REVERT: A 529 ILE cc_start: 0.9098 (mp) cc_final: 0.8811 (tt) REVERT: A 663 GLN cc_start: 0.9243 (tp-100) cc_final: 0.8348 (tp40) REVERT: A 670 GLU cc_start: 0.9264 (pm20) cc_final: 0.9047 (pm20) REVERT: B 208 TYR cc_start: 0.7738 (t80) cc_final: 0.7426 (t80) REVERT: B 243 ASP cc_start: 0.9139 (p0) cc_final: 0.8919 (p0) REVERT: B 270 MET cc_start: 0.8455 (mmm) cc_final: 0.7954 (mmp) REVERT: B 301 LEU cc_start: 0.9257 (mt) cc_final: 0.8785 (tt) REVERT: B 372 MET cc_start: 0.8642 (mmt) cc_final: 0.8272 (mmt) REVERT: B 374 VAL cc_start: 0.9510 (m) cc_final: 0.9294 (p) REVERT: B 381 LEU cc_start: 0.9432 (tt) cc_final: 0.9228 (mm) REVERT: B 404 MET cc_start: 0.7568 (tpt) cc_final: 0.7242 (tpp) REVERT: B 547 PHE cc_start: 0.8090 (m-80) cc_final: 0.7861 (m-80) REVERT: B 640 MET cc_start: 0.8314 (mmt) cc_final: 0.8091 (mmm) REVERT: B 644 LEU cc_start: 0.9148 (pp) cc_final: 0.8936 (pp) REVERT: B 670 GLU cc_start: 0.9230 (pm20) cc_final: 0.8986 (pm20) REVERT: C 231 GLU cc_start: 0.8442 (mt-10) cc_final: 0.8172 (mt-10) REVERT: C 243 ASP cc_start: 0.9183 (p0) cc_final: 0.8977 (p0) REVERT: C 270 MET cc_start: 0.8548 (mmp) cc_final: 0.8341 (mmp) REVERT: C 271 TYR cc_start: 0.8323 (t80) cc_final: 0.8060 (t80) REVERT: C 365 LYS cc_start: 0.9072 (mmpt) cc_final: 0.8859 (mmtm) REVERT: C 404 MET cc_start: 0.7631 (tpt) cc_final: 0.7313 (tpp) REVERT: C 663 GLN cc_start: 0.9233 (tp-100) cc_final: 0.8329 (tp40) REVERT: C 670 GLU cc_start: 0.9263 (pm20) cc_final: 0.8976 (pm20) REVERT: D 208 TYR cc_start: 0.7811 (t80) cc_final: 0.7499 (t80) REVERT: D 270 MET cc_start: 0.8549 (mmp) cc_final: 0.8334 (mmp) REVERT: D 271 TYR cc_start: 0.8523 (t80) cc_final: 0.8279 (t80) REVERT: D 372 MET cc_start: 0.8801 (mmt) cc_final: 0.8551 (mmt) REVERT: D 404 MET cc_start: 0.7659 (tpt) cc_final: 0.7340 (tpp) REVERT: D 640 MET cc_start: 0.7715 (mmm) cc_final: 0.7006 (mmp) REVERT: D 670 GLU cc_start: 0.9253 (pm20) cc_final: 0.9028 (pm20) outliers start: 1 outliers final: 0 residues processed: 308 average time/residue: 0.1170 time to fit residues: 57.6251 Evaluate side-chains 239 residues out of total 2140 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 239 time to evaluate : 0.782 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 89 optimal weight: 0.0470 chunk 107 optimal weight: 20.0000 chunk 182 optimal weight: 0.9980 chunk 79 optimal weight: 0.9990 chunk 193 optimal weight: 2.9990 chunk 106 optimal weight: 6.9990 chunk 131 optimal weight: 8.9990 chunk 103 optimal weight: 9.9990 chunk 97 optimal weight: 0.4980 chunk 57 optimal weight: 6.9990 chunk 178 optimal weight: 6.9990 overall best weight: 1.1082 ------------------------------------------------------------------------------- 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 156 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 186 ASN A 247 ASN ** A 251 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 370 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 487 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 129 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 186 ASN ** B 251 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 487 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 129 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 251 HIS C 316 GLN ** C 370 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 487 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 129 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 186 ASN D 247 ASN ** D 251 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 370 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 487 GLN ** 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 = 0.3698 r_free = 0.3698 target = 0.084465 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3385 r_free = 0.3385 target = 0.068141 restraints weight = 92910.930| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3417 r_free = 0.3417 target = 0.069618 restraints weight = 61101.771| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3437 r_free = 0.3437 target = 0.070624 restraints weight = 45017.483| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3451 r_free = 0.3451 target = 0.071306 restraints weight = 36179.056| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 43)----------------| | r_work = 0.3461 r_free = 0.3461 target = 0.071801 restraints weight = 31030.161| |-----------------------------------------------------------------------------| r_work (final): 0.3447 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7878 moved from start: 0.8746 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 20124 Z= 0.128 Angle : 0.759 11.364 27288 Z= 0.365 Chirality : 0.044 0.248 3064 Planarity : 0.005 0.063 3380 Dihedral : 6.033 28.594 2632 Min Nonbonded Distance : 2.478 Molprobity Statistics. All-atom Clashscore : 15.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.54 % Favored : 93.46 % Rotamer: Outliers : 0.00 % Allowed : 0.33 % Favored : 99.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 0.34 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.85 (0.16), residues: 2384 helix: -0.61 (0.14), residues: 1216 sheet: -1.72 (0.57), residues: 60 loop : -1.87 (0.18), residues: 1108 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 312 TYR 0.020 0.001 TYR D 228 PHE 0.032 0.001 PHE A 330 TRP 0.023 0.001 TRP A 333 HIS 0.004 0.001 HIS A 169 Details of bonding type rmsd covalent geometry : bond 0.00277 (20124) covalent geometry : angle 0.75878 (27288) hydrogen bonds : bond 0.03269 ( 728) hydrogen bonds : angle 4.90679 ( 2136) ********************** 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 325 residues out of total 2140 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 325 time to evaluate : 0.719 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 208 TYR cc_start: 0.7805 (t80) cc_final: 0.7507 (t80) REVERT: A 251 HIS cc_start: 0.8784 (m-70) cc_final: 0.8555 (m-70) REVERT: A 270 MET cc_start: 0.8493 (mmp) cc_final: 0.8111 (mmt) REVERT: A 301 LEU cc_start: 0.9426 (mt) cc_final: 0.9029 (tp) REVERT: A 345 LEU cc_start: 0.8028 (mp) cc_final: 0.7745 (mp) REVERT: A 404 MET cc_start: 0.7546 (tpt) cc_final: 0.7336 (tpp) REVERT: A 529 ILE cc_start: 0.8996 (mp) cc_final: 0.8768 (tt) REVERT: A 663 GLN cc_start: 0.9316 (tp-100) cc_final: 0.8418 (tp40) REVERT: B 208 TYR cc_start: 0.7634 (t80) cc_final: 0.7363 (t80) REVERT: B 231 GLU cc_start: 0.8554 (mt-10) cc_final: 0.8300 (mt-10) REVERT: B 243 ASP cc_start: 0.9139 (p0) cc_final: 0.8884 (p0) REVERT: B 253 LEU cc_start: 0.9620 (mm) cc_final: 0.9326 (tp) REVERT: B 255 MET cc_start: 0.9028 (mmm) cc_final: 0.8602 (mmm) REVERT: B 270 MET cc_start: 0.8752 (mmm) cc_final: 0.8239 (mmp) REVERT: B 301 LEU cc_start: 0.9327 (mt) cc_final: 0.8846 (tt) REVERT: B 315 LEU cc_start: 0.9221 (tp) cc_final: 0.8744 (tp) REVERT: B 319 PHE cc_start: 0.7146 (p90) cc_final: 0.6436 (p90) REVERT: B 372 MET cc_start: 0.8712 (mmt) cc_final: 0.8478 (mmt) REVERT: B 404 MET cc_start: 0.7443 (tpt) cc_final: 0.7229 (tpp) REVERT: B 547 PHE cc_start: 0.8053 (m-80) cc_final: 0.7791 (m-80) REVERT: B 640 MET cc_start: 0.8308 (mmt) cc_final: 0.8063 (mmm) REVERT: B 645 MET cc_start: 0.9247 (mmp) cc_final: 0.9037 (mmm) REVERT: C 208 TYR cc_start: 0.7564 (t80) cc_final: 0.7345 (t80) REVERT: C 231 GLU cc_start: 0.8555 (mt-10) cc_final: 0.8325 (mt-10) REVERT: C 243 ASP cc_start: 0.9143 (p0) cc_final: 0.8856 (p0) REVERT: C 251 HIS cc_start: 0.8519 (m90) cc_final: 0.8181 (m-70) REVERT: C 270 MET cc_start: 0.8562 (mmp) cc_final: 0.8288 (mmp) REVERT: C 299 LEU cc_start: 0.9407 (tp) cc_final: 0.9164 (tt) REVERT: C 345 LEU cc_start: 0.8366 (mp) cc_final: 0.8124 (mp) REVERT: C 365 LYS cc_start: 0.9124 (mmpt) cc_final: 0.8780 (mmtm) REVERT: C 404 MET cc_start: 0.7473 (tpt) cc_final: 0.7263 (tpp) REVERT: C 600 LEU cc_start: 0.8860 (mp) cc_final: 0.8623 (tp) REVERT: C 663 GLN cc_start: 0.9243 (tp-100) cc_final: 0.8331 (tp40) REVERT: D 208 TYR cc_start: 0.7807 (t80) cc_final: 0.7468 (t80) REVERT: D 231 GLU cc_start: 0.8610 (mt-10) cc_final: 0.8318 (mt-10) REVERT: D 243 ASP cc_start: 0.9061 (p0) cc_final: 0.8850 (p0) REVERT: D 253 LEU cc_start: 0.9666 (mm) cc_final: 0.9348 (tp) REVERT: D 270 MET cc_start: 0.8578 (mmp) cc_final: 0.8368 (mmp) REVERT: D 271 TYR cc_start: 0.8601 (t80) cc_final: 0.8381 (t80) REVERT: D 315 LEU cc_start: 0.9089 (tp) cc_final: 0.8658 (tp) REVERT: D 372 MET cc_start: 0.8816 (mmt) cc_final: 0.8583 (mmt) REVERT: D 404 MET cc_start: 0.7480 (tpt) cc_final: 0.7255 (tpp) REVERT: D 640 MET cc_start: 0.7536 (mmm) cc_final: 0.6827 (mmp) REVERT: D 663 GLN cc_start: 0.9256 (tp-100) cc_final: 0.8510 (tp40) outliers start: 0 outliers final: 0 residues processed: 325 average time/residue: 0.1260 time to fit residues: 66.2973 Evaluate side-chains 248 residues out of total 2140 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 248 time to evaluate : 0.675 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 112 optimal weight: 6.9990 chunk 10 optimal weight: 0.0770 chunk 40 optimal weight: 0.1980 chunk 142 optimal weight: 0.8980 chunk 234 optimal weight: 5.9990 chunk 226 optimal weight: 10.0000 chunk 223 optimal weight: 10.0000 chunk 191 optimal weight: 0.9990 chunk 9 optimal weight: 9.9990 chunk 5 optimal weight: 4.9990 chunk 77 optimal weight: 0.9990 overall best weight: 0.6342 ------------------------------------------------------------------------------- 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 251 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 316 GLN ** A 370 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 487 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 129 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 251 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 313 HIS ** B 370 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 487 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 129 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 186 ASN C 259 ASN ** C 370 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 487 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 487 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3725 r_free = 0.3725 target = 0.085921 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3415 r_free = 0.3415 target = 0.069585 restraints weight = 92095.784| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3446 r_free = 0.3446 target = 0.071039 restraints weight = 61885.143| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3466 r_free = 0.3466 target = 0.072049 restraints weight = 46004.319| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.3481 r_free = 0.3481 target = 0.072764 restraints weight = 37055.532| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3490 r_free = 0.3490 target = 0.073251 restraints weight = 31691.216| |-----------------------------------------------------------------------------| r_work (final): 0.3478 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7823 moved from start: 0.8910 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 20124 Z= 0.124 Angle : 0.747 11.598 27288 Z= 0.357 Chirality : 0.043 0.273 3064 Planarity : 0.004 0.061 3380 Dihedral : 5.862 27.713 2632 Min Nonbonded Distance : 2.570 Molprobity Statistics. All-atom Clashscore : 14.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.54 % Favored : 93.46 % Rotamer: Outliers : 0.00 % Allowed : 0.56 % Favored : 99.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 0.34 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.82 (0.16), residues: 2384 helix: -0.60 (0.14), residues: 1224 sheet: -0.92 (0.56), residues: 88 loop : -1.91 (0.18), residues: 1072 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 312 TYR 0.017 0.001 TYR D 228 PHE 0.021 0.001 PHE A 330 TRP 0.020 0.001 TRP A 333 HIS 0.005 0.001 HIS B 251 Details of bonding type rmsd covalent geometry : bond 0.00263 (20124) covalent geometry : angle 0.74744 (27288) hydrogen bonds : bond 0.03204 ( 728) hydrogen bonds : angle 4.76725 ( 2136) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3076.59 seconds wall clock time: 54 minutes 10.10 seconds (3250.10 seconds total)