Starting phenix.real_space_refine on Sat Dec 28 12:37:42 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8k0z_36781/12_2024/8k0z_36781.cif Found real_map, /net/cci-nas-00/data/ceres_data/8k0z_36781/12_2024/8k0z_36781.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8k0z_36781/12_2024/8k0z_36781.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8k0z_36781/12_2024/8k0z_36781.map" model { file = "/net/cci-nas-00/data/ceres_data/8k0z_36781/12_2024/8k0z_36781.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8k0z_36781/12_2024/8k0z_36781.cif" } resolution = 3.7 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.006 sd= 0.101 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 52 5.16 5 C 5524 2.51 5 N 1416 2.21 5 O 1492 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 8 residue(s): 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5532/modules/chem_data/mon_lib" Total number of atoms: 8484 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" Number of atoms: 4242 Number of conformers: 1 Conformer: "" Number of residues, atoms: 546, 4242 Classifications: {'peptide': 546} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 18, 'TRANS': 527} Chain breaks: 4 Restraints were copied for chains: B Time building chain proxies: 7.82, per 1000 atoms: 0.92 Number of scatterers: 8484 At special positions: 0 Unit cell: (108.9, 73.7, 122.1, 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 52 16.00 O 1492 8.00 N 1416 7.00 C 5524 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: 1.96 Conformation dependent library (CDL) restraints added in 1.3 seconds 2144 Ramachandran restraints generated. 1072 Oldfield, 0 Emsley, 1072 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2004 Finding SS restraints... Secondary structure from input PDB file: 50 helices and 6 sheets defined 57.5% alpha, 5.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.01 Creating SS restraints... Processing helix chain 'A' and resid 106 through 116 removed outlier: 3.579A pdb=" N LEU A 110 " --> pdb=" O GLY A 106 " (cutoff:3.500A) removed outlier: 4.004A pdb=" N LEU A 111 " --> pdb=" O LYS A 107 " (cutoff:3.500A) Processing helix chain 'A' and resid 135 through 140 removed outlier: 3.763A pdb=" N LYS A 140 " --> pdb=" O LYS A 136 " (cutoff:3.500A) Processing helix chain 'A' and resid 156 through 169 Processing helix chain 'A' and resid 175 through 180 removed outlier: 3.679A pdb=" N LEU A 179 " --> pdb=" O ARG A 175 " (cutoff:3.500A) Processing helix chain 'A' and resid 212 through 219 removed outlier: 3.732A pdb=" N SER A 216 " --> pdb=" O ARG A 212 " (cutoff:3.500A) Processing helix chain 'A' and resid 240 through 255 removed outlier: 3.813A pdb=" N VAL A 246 " --> pdb=" O ALA A 242 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N ALA A 253 " --> pdb=" O LEU A 249 " (cutoff:3.500A) Processing helix chain 'A' and resid 270 through 275 removed outlier: 3.644A pdb=" N MET A 274 " --> pdb=" O ARG A 270 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N PHE A 275 " --> pdb=" O VAL A 271 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 270 through 275' Processing helix chain 'A' and resid 295 through 303 removed outlier: 3.614A pdb=" N PHE A 299 " --> pdb=" O ALA A 295 " (cutoff:3.500A) removed outlier: 3.943A pdb=" N GLU A 300 " --> pdb=" O MET A 296 " (cutoff:3.500A) removed outlier: 4.116A pdb=" N SER A 301 " --> pdb=" O ALA A 297 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N VAL A 302 " --> pdb=" O TYR A 298 " (cutoff:3.500A) Processing helix chain 'A' and resid 311 through 320 removed outlier: 3.652A pdb=" N LEU A 316 " --> pdb=" O PRO A 312 " (cutoff:3.500A) Processing helix chain 'A' and resid 338 through 349 removed outlier: 3.722A pdb=" N VAL A 342 " --> pdb=" O ARG A 338 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N THR A 347 " --> pdb=" O THR A 343 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N LEU A 348 " --> pdb=" O ALA A 344 " (cutoff:3.500A) Processing helix chain 'A' and resid 349 through 356 removed outlier: 3.516A pdb=" N LYS A 354 " --> pdb=" O ALA A 350 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N THR A 355 " --> pdb=" O PRO A 351 " (cutoff:3.500A) removed outlier: 4.231A pdb=" N CYS A 356 " --> pdb=" O GLN A 352 " (cutoff:3.500A) Processing helix chain 'A' and resid 379 through 397 removed outlier: 4.210A pdb=" N TRP A 386 " --> pdb=" O CYS A 382 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N HIS A 395 " --> pdb=" O CYS A 391 " (cutoff:3.500A) Processing helix chain 'A' and resid 397 through 406 removed outlier: 3.515A pdb=" N ARG A 402 " --> pdb=" O LEU A 398 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N HIS A 403 " --> pdb=" O LYS A 399 " (cutoff:3.500A) Processing helix chain 'A' and resid 407 through 425 removed outlier: 3.512A pdb=" N PHE A 412 " --> pdb=" O LEU A 408 " (cutoff:3.500A) removed outlier: 3.964A pdb=" N GLN A 413 " --> pdb=" O LEU A 409 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N VAL A 414 " --> pdb=" O ARG A 410 " (cutoff:3.500A) Processing helix chain 'A' and resid 432 through 454 removed outlier: 3.615A pdb=" N ARG A 436 " --> pdb=" O ASP A 432 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N GLY A 438 " --> pdb=" O HIS A 434 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N SER A 444 " --> pdb=" O LEU A 440 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N GLY A 448 " --> pdb=" O SER A 444 " (cutoff:3.500A) Proline residue: A 451 - end of helix removed outlier: 3.764A pdb=" N ASN A 454 " --> pdb=" O LEU A 450 " (cutoff:3.500A) Processing helix chain 'A' and resid 457 through 462 removed outlier: 3.683A pdb=" N GLN A 461 " --> pdb=" O PHE A 457 " (cutoff:3.500A) removed outlier: 3.859A pdb=" N GLU A 462 " --> pdb=" O THR A 458 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 457 through 462' Processing helix chain 'A' and resid 463 through 472 removed outlier: 3.552A pdb=" N ALA A 471 " --> pdb=" O THR A 467 " (cutoff:3.500A) Processing helix chain 'A' and resid 476 through 492 removed outlier: 3.617A pdb=" N MET A 482 " --> pdb=" O SER A 478 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N ALA A 483 " --> pdb=" O SER A 479 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N HIS A 484 " --> pdb=" O TYR A 480 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N GLY A 487 " --> pdb=" O ALA A 483 " (cutoff:3.500A) removed outlier: 4.056A pdb=" N SER A 490 " --> pdb=" O LEU A 486 " (cutoff:3.500A) removed outlier: 3.966A pdb=" N MET A 491 " --> pdb=" O GLY A 487 " (cutoff:3.500A) Processing helix chain 'A' and resid 494 through 504 removed outlier: 3.505A pdb=" N LEU A 500 " --> pdb=" O PRO A 496 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N THR A 501 " --> pdb=" O ALA A 497 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N PHE A 502 " --> pdb=" O SER A 498 " (cutoff:3.500A) Processing helix chain 'A' and resid 512 through 542 removed outlier: 3.549A pdb=" N PHE A 516 " --> pdb=" O GLY A 512 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N SER A 521 " --> pdb=" O LEU A 517 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N GLY A 532 " --> pdb=" O LEU A 528 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N LEU A 533 " --> pdb=" O ALA A 529 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N GLY A 534 " --> pdb=" O SER A 530 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N ILE A 541 " --> pdb=" O LEU A 537 " (cutoff:3.500A) Processing helix chain 'A' and resid 549 through 561 Processing helix chain 'A' and resid 575 through 579 removed outlier: 3.687A pdb=" N VAL A 579 " --> pdb=" O MET A 576 " (cutoff:3.500A) Processing helix chain 'A' and resid 580 through 594 removed outlier: 3.879A pdb=" N TYR A 584 " --> pdb=" O SER A 580 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N LEU A 588 " --> pdb=" O TYR A 584 " (cutoff:3.500A) Processing helix chain 'A' and resid 627 through 631 removed outlier: 3.943A pdb=" N GLY A 631 " --> pdb=" O GLU A 628 " (cutoff:3.500A) Processing helix chain 'A' and resid 635 through 658 removed outlier: 3.723A pdb=" N VAL A 639 " --> pdb=" O MET A 635 " (cutoff:3.500A) removed outlier: 4.115A pdb=" N VAL A 641 " --> pdb=" O THR A 637 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N TYR A 649 " --> pdb=" O MET A 645 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N ARG A 650 " --> pdb=" O PHE A 646 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N ALA A 656 " --> pdb=" O LEU A 652 " (cutoff:3.500A) Processing helix chain 'B' and resid 106 through 116 removed outlier: 3.578A pdb=" N LEU B 110 " --> pdb=" O GLY B 106 " (cutoff:3.500A) removed outlier: 4.004A pdb=" N LEU B 111 " --> pdb=" O LYS B 107 " (cutoff:3.500A) Processing helix chain 'B' and resid 135 through 140 removed outlier: 3.763A pdb=" N LYS B 140 " --> pdb=" O LYS B 136 " (cutoff:3.500A) Processing helix chain 'B' and resid 156 through 169 Processing helix chain 'B' and resid 175 through 180 removed outlier: 3.679A pdb=" N LEU B 179 " --> pdb=" O ARG B 175 " (cutoff:3.500A) Processing helix chain 'B' and resid 212 through 219 removed outlier: 3.732A pdb=" N SER B 216 " --> pdb=" O ARG B 212 " (cutoff:3.500A) Processing helix chain 'B' and resid 240 through 255 removed outlier: 3.813A pdb=" N VAL B 246 " --> pdb=" O ALA B 242 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N ALA B 253 " --> pdb=" O LEU B 249 " (cutoff:3.500A) Processing helix chain 'B' and resid 270 through 275 removed outlier: 3.643A pdb=" N MET B 274 " --> pdb=" O ARG B 270 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N PHE B 275 " --> pdb=" O VAL B 271 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 270 through 275' Processing helix chain 'B' and resid 295 through 303 removed outlier: 3.615A pdb=" N PHE B 299 " --> pdb=" O ALA B 295 " (cutoff:3.500A) removed outlier: 3.943A pdb=" N GLU B 300 " --> pdb=" O MET B 296 " (cutoff:3.500A) removed outlier: 4.117A pdb=" N SER B 301 " --> pdb=" O ALA B 297 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N VAL B 302 " --> pdb=" O TYR B 298 " (cutoff:3.500A) Processing helix chain 'B' and resid 311 through 320 removed outlier: 3.652A pdb=" N LEU B 316 " --> pdb=" O PRO B 312 " (cutoff:3.500A) Processing helix chain 'B' and resid 338 through 349 removed outlier: 3.722A pdb=" N VAL B 342 " --> pdb=" O ARG B 338 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N THR B 347 " --> pdb=" O THR B 343 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N LEU B 348 " --> pdb=" O ALA B 344 " (cutoff:3.500A) Processing helix chain 'B' and resid 349 through 356 removed outlier: 3.517A pdb=" N LYS B 354 " --> pdb=" O ALA B 350 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N THR B 355 " --> pdb=" O PRO B 351 " (cutoff:3.500A) removed outlier: 4.231A pdb=" N CYS B 356 " --> pdb=" O GLN B 352 " (cutoff:3.500A) Processing helix chain 'B' and resid 379 through 397 removed outlier: 4.210A pdb=" N TRP B 386 " --> pdb=" O CYS B 382 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N HIS B 395 " --> pdb=" O CYS B 391 " (cutoff:3.500A) Processing helix chain 'B' and resid 397 through 406 removed outlier: 3.516A pdb=" N ARG B 402 " --> pdb=" O LEU B 398 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N HIS B 403 " --> pdb=" O LYS B 399 " (cutoff:3.500A) Processing helix chain 'B' and resid 407 through 425 removed outlier: 3.513A pdb=" N PHE B 412 " --> pdb=" O LEU B 408 " (cutoff:3.500A) removed outlier: 3.965A pdb=" N GLN B 413 " --> pdb=" O LEU B 409 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N VAL B 414 " --> pdb=" O ARG B 410 " (cutoff:3.500A) Processing helix chain 'B' and resid 432 through 454 removed outlier: 3.615A pdb=" N ARG B 436 " --> pdb=" O ASP B 432 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N GLY B 438 " --> pdb=" O HIS B 434 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N SER B 444 " --> pdb=" O LEU B 440 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N GLY B 448 " --> pdb=" O SER B 444 " (cutoff:3.500A) Proline residue: B 451 - end of helix removed outlier: 3.765A pdb=" N ASN B 454 " --> pdb=" O LEU B 450 " (cutoff:3.500A) Processing helix chain 'B' and resid 457 through 462 removed outlier: 3.682A pdb=" N GLN B 461 " --> pdb=" O PHE B 457 " (cutoff:3.500A) removed outlier: 3.859A pdb=" N GLU B 462 " --> pdb=" O THR B 458 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 457 through 462' Processing helix chain 'B' and resid 463 through 472 removed outlier: 3.553A pdb=" N ALA B 471 " --> pdb=" O THR B 467 " (cutoff:3.500A) Processing helix chain 'B' and resid 476 through 492 removed outlier: 3.618A pdb=" N MET B 482 " --> pdb=" O SER B 478 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N ALA B 483 " --> pdb=" O SER B 479 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N HIS B 484 " --> pdb=" O TYR B 480 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N GLY B 487 " --> pdb=" O ALA B 483 " (cutoff:3.500A) removed outlier: 4.056A pdb=" N SER B 490 " --> pdb=" O LEU B 486 " (cutoff:3.500A) removed outlier: 3.968A pdb=" N MET B 491 " --> pdb=" O GLY B 487 " (cutoff:3.500A) Processing helix chain 'B' and resid 494 through 504 removed outlier: 3.505A pdb=" N LEU B 500 " --> pdb=" O PRO B 496 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N THR B 501 " --> pdb=" O ALA B 497 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N PHE B 502 " --> pdb=" O SER B 498 " (cutoff:3.500A) Processing helix chain 'B' and resid 512 through 542 removed outlier: 3.548A pdb=" N PHE B 516 " --> pdb=" O GLY B 512 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N SER B 521 " --> pdb=" O LEU B 517 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N GLY B 532 " --> pdb=" O LEU B 528 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N LEU B 533 " --> pdb=" O ALA B 529 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N GLY B 534 " --> pdb=" O SER B 530 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N ILE B 541 " --> pdb=" O LEU B 537 " (cutoff:3.500A) Processing helix chain 'B' and resid 549 through 561 Processing helix chain 'B' and resid 575 through 579 removed outlier: 3.687A pdb=" N VAL B 579 " --> pdb=" O MET B 576 " (cutoff:3.500A) Processing helix chain 'B' and resid 580 through 594 removed outlier: 3.878A pdb=" N TYR B 584 " --> pdb=" O SER B 580 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N LEU B 588 " --> pdb=" O TYR B 584 " (cutoff:3.500A) Processing helix chain 'B' and resid 627 through 631 removed outlier: 3.943A pdb=" N GLY B 631 " --> pdb=" O GLU B 628 " (cutoff:3.500A) Processing helix chain 'B' and resid 635 through 658 removed outlier: 3.722A pdb=" N VAL B 639 " --> pdb=" O MET B 635 " (cutoff:3.500A) removed outlier: 4.114A pdb=" N VAL B 641 " --> pdb=" O THR B 637 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N TYR B 649 " --> pdb=" O MET B 645 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N ARG B 650 " --> pdb=" O PHE B 646 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N ALA B 656 " --> pdb=" O LEU B 652 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 90 through 91 Processing sheet with id=AA2, first strand: chain 'A' and resid 45 through 47 removed outlier: 5.443A pdb=" N VAL A 45 " --> pdb=" O GLY A 86 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N LEU A 84 " --> pdb=" O TYR A 47 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 142 through 145 removed outlier: 6.416A pdb=" N GLY A 143 " --> pdb=" O VAL A 229 " (cutoff:3.500A) removed outlier: 6.662A pdb=" N LEU A 228 " --> pdb=" O VAL A 261 " (cutoff:3.500A) removed outlier: 6.204A pdb=" N MET A 97 " --> pdb=" O THR A 262 " (cutoff:3.500A) removed outlier: 6.828A pdb=" N VAL A 278 " --> pdb=" O VAL A 289 " (cutoff:3.500A) removed outlier: 4.260A pdb=" N VAL A 289 " --> pdb=" O VAL A 278 " (cutoff:3.500A) removed outlier: 6.751A pdb=" N LEU A 280 " --> pdb=" O LEU A 287 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 90 through 91 Processing sheet with id=AA5, first strand: chain 'B' and resid 45 through 47 removed outlier: 5.444A pdb=" N VAL B 45 " --> pdb=" O GLY B 86 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N LEU B 84 " --> pdb=" O TYR B 47 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 142 through 145 removed outlier: 6.414A pdb=" N GLY B 143 " --> pdb=" O VAL B 229 " (cutoff:3.500A) removed outlier: 6.663A pdb=" N LEU B 228 " --> pdb=" O VAL B 261 " (cutoff:3.500A) removed outlier: 6.204A pdb=" N MET B 97 " --> pdb=" O THR B 262 " (cutoff:3.500A) removed outlier: 6.828A pdb=" N VAL B 278 " --> pdb=" O VAL B 289 " (cutoff:3.500A) removed outlier: 4.260A pdb=" N VAL B 289 " --> pdb=" O VAL B 278 " (cutoff:3.500A) removed outlier: 6.752A pdb=" N LEU B 280 " --> pdb=" O LEU B 287 " (cutoff:3.500A) 336 hydrogen bonds defined for protein. 978 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: 2.66 Time building geometry restraints manager: 2.29 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: 2604 1.34 - 1.46: 1753 1.46 - 1.58: 4219 1.58 - 1.70: 0 1.70 - 1.81: 84 Bond restraints: 8660 Sorted by residual: bond pdb=" CB PRO A 451 " pdb=" CG PRO A 451 " ideal model delta sigma weight residual 1.492 1.401 0.091 5.00e-02 4.00e+02 3.28e+00 bond pdb=" CB PRO B 451 " pdb=" CG PRO B 451 " ideal model delta sigma weight residual 1.492 1.402 0.090 5.00e-02 4.00e+02 3.24e+00 bond pdb=" CG LEU B 509 " pdb=" CD2 LEU B 509 " ideal model delta sigma weight residual 1.521 1.462 0.059 3.30e-02 9.18e+02 3.18e+00 bond pdb=" CG LEU A 509 " pdb=" CD2 LEU A 509 " ideal model delta sigma weight residual 1.521 1.463 0.058 3.30e-02 9.18e+02 3.13e+00 bond pdb=" CB VAL A 185 " pdb=" CG1 VAL A 185 " ideal model delta sigma weight residual 1.521 1.463 0.058 3.30e-02 9.18e+02 3.07e+00 ... (remaining 8655 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.64: 11362 2.64 - 5.27: 328 5.27 - 7.91: 38 7.91 - 10.54: 10 10.54 - 13.18: 2 Bond angle restraints: 11740 Sorted by residual: angle pdb=" N VAL B 185 " pdb=" CA VAL B 185 " pdb=" C VAL B 185 " ideal model delta sigma weight residual 112.96 107.28 5.68 1.00e+00 1.00e+00 3.23e+01 angle pdb=" N VAL A 185 " pdb=" CA VAL A 185 " pdb=" C VAL A 185 " ideal model delta sigma weight residual 112.96 107.31 5.65 1.00e+00 1.00e+00 3.20e+01 angle pdb=" N SER B 571 " pdb=" CA SER B 571 " pdb=" C SER B 571 " ideal model delta sigma weight residual 110.80 119.37 -8.57 2.13e+00 2.20e-01 1.62e+01 angle pdb=" N SER A 571 " pdb=" CA SER A 571 " pdb=" C SER A 571 " ideal model delta sigma weight residual 110.80 119.35 -8.55 2.13e+00 2.20e-01 1.61e+01 angle pdb=" CB ARG B 436 " pdb=" CG ARG B 436 " pdb=" CD ARG B 436 " ideal model delta sigma weight residual 111.30 120.21 -8.91 2.30e+00 1.89e-01 1.50e+01 ... (remaining 11735 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.02: 4828 15.02 - 30.04: 211 30.04 - 45.06: 39 45.06 - 60.07: 6 60.07 - 75.09: 6 Dihedral angle restraints: 5090 sinusoidal: 1968 harmonic: 3122 Sorted by residual: dihedral pdb=" CA VAL B 177 " pdb=" C VAL B 177 " pdb=" N LYS B 178 " pdb=" CA LYS B 178 " ideal model delta harmonic sigma weight residual 180.00 155.40 24.60 0 5.00e+00 4.00e-02 2.42e+01 dihedral pdb=" CA VAL A 177 " pdb=" C VAL A 177 " pdb=" N LYS A 178 " pdb=" CA LYS A 178 " ideal model delta harmonic sigma weight residual 180.00 155.42 24.58 0 5.00e+00 4.00e-02 2.42e+01 dihedral pdb=" CA PRO A 570 " pdb=" C PRO A 570 " pdb=" N SER A 571 " pdb=" CA SER A 571 " ideal model delta harmonic sigma weight residual 180.00 155.76 24.24 0 5.00e+00 4.00e-02 2.35e+01 ... (remaining 5087 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.058: 928 0.058 - 0.115: 393 0.115 - 0.172: 63 0.172 - 0.230: 12 0.230 - 0.287: 4 Chirality restraints: 1400 Sorted by residual: chirality pdb=" CB VAL A 177 " pdb=" CA VAL A 177 " pdb=" CG1 VAL A 177 " pdb=" CG2 VAL A 177 " both_signs ideal model delta sigma weight residual False -2.63 -2.34 -0.29 2.00e-01 2.50e+01 2.07e+00 chirality pdb=" CB VAL B 177 " pdb=" CA VAL B 177 " pdb=" CG1 VAL B 177 " pdb=" CG2 VAL B 177 " both_signs ideal model delta sigma weight residual False -2.63 -2.35 -0.28 2.00e-01 2.50e+01 2.02e+00 chirality pdb=" CB ILE B 630 " pdb=" CA ILE B 630 " pdb=" CG1 ILE B 630 " pdb=" CG2 ILE B 630 " both_signs ideal model delta sigma weight residual False 2.64 2.90 -0.26 2.00e-01 2.50e+01 1.68e+00 ... (remaining 1397 not shown) Planarity restraints: 1440 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LEU A 450 " 0.040 5.00e-02 4.00e+02 6.01e-02 5.78e+00 pdb=" N PRO A 451 " -0.104 5.00e-02 4.00e+02 pdb=" CA PRO A 451 " 0.029 5.00e-02 4.00e+02 pdb=" CD PRO A 451 " 0.034 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU B 450 " -0.040 5.00e-02 4.00e+02 5.97e-02 5.70e+00 pdb=" N PRO B 451 " 0.103 5.00e-02 4.00e+02 pdb=" CA PRO B 451 " -0.029 5.00e-02 4.00e+02 pdb=" CD PRO B 451 " -0.034 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ALA A 350 " -0.035 5.00e-02 4.00e+02 5.28e-02 4.46e+00 pdb=" N PRO A 351 " 0.091 5.00e-02 4.00e+02 pdb=" CA PRO A 351 " -0.026 5.00e-02 4.00e+02 pdb=" CD PRO A 351 " -0.030 5.00e-02 4.00e+02 ... (remaining 1437 not shown) Histogram of nonbonded interaction distances: 2.36 - 2.87: 2935 2.87 - 3.38: 7214 3.38 - 3.89: 12545 3.89 - 4.39: 15057 4.39 - 4.90: 26518 Nonbonded interactions: 64269 Sorted by model distance: nonbonded pdb=" O TYR B 298 " pdb=" OG SER B 301 " model vdw 2.364 3.040 nonbonded pdb=" O TYR A 298 " pdb=" OG SER A 301 " model vdw 2.364 3.040 nonbonded pdb=" N GLY A 572 " pdb=" N MET A 573 " model vdw 2.423 2.560 nonbonded pdb=" OG SER B 452 " pdb=" O SER B 530 " model vdw 2.423 3.040 nonbonded pdb=" OG SER A 452 " pdb=" O SER A 530 " model vdw 2.424 3.040 ... (remaining 64264 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' } 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: 0.650 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.360 Check model and map are aligned: 0.070 Set scattering table: 0.090 Process input model: 24.910 Find NCS groups from input model: 0.230 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.990 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 29.320 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8074 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 : 0.010 0.091 8660 Z= 0.660 Angle : 1.063 13.178 11740 Z= 0.561 Chirality : 0.062 0.287 1400 Planarity : 0.007 0.060 1440 Dihedral : 9.688 75.092 3086 Min Nonbonded Distance : 2.364 Molprobity Statistics. All-atom Clashscore : 1.80 Ramachandran Plot: Outliers : 0.19 % Allowed : 7.84 % Favored : 91.98 % Rotamer: Outliers : 0.00 % Allowed : 0.65 % Favored : 99.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -6.16 (0.16), residues: 1072 helix: -4.85 (0.06), residues: 588 sheet: -1.12 (0.62), residues: 62 loop : -3.10 (0.25), residues: 422 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.004 TRP B 447 HIS 0.013 0.003 HIS A 219 PHE 0.027 0.004 PHE B 163 TYR 0.023 0.003 TYR A 526 ARG 0.017 0.001 ARG B 436 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2144 Ramachandran restraints generated. 1072 Oldfield, 0 Emsley, 1072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2144 Ramachandran restraints generated. 1072 Oldfield, 0 Emsley, 1072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 217 residues out of total 926 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 217 time to evaluate : 0.950 Fit side-chains REVERT: A 87 VAL cc_start: 0.8387 (t) cc_final: 0.8124 (t) REVERT: A 105 SER cc_start: 0.9055 (p) cc_final: 0.8675 (t) REVERT: B 87 VAL cc_start: 0.8350 (t) cc_final: 0.8096 (t) REVERT: B 105 SER cc_start: 0.9063 (p) cc_final: 0.8659 (t) REVERT: B 294 ASP cc_start: 0.8217 (p0) cc_final: 0.7994 (p0) REVERT: B 454 ASN cc_start: 0.8619 (m110) cc_final: 0.8114 (m110) outliers start: 0 outliers final: 0 residues processed: 217 average time/residue: 0.2950 time to fit residues: 81.4114 Evaluate side-chains 125 residues out of total 926 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 125 time to evaluate : 0.970 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 91 optimal weight: 0.9990 chunk 81 optimal weight: 0.9980 chunk 45 optimal weight: 0.9980 chunk 27 optimal weight: 10.0000 chunk 55 optimal weight: 7.9990 chunk 43 optimal weight: 0.6980 chunk 84 optimal weight: 0.5980 chunk 32 optimal weight: 0.9990 chunk 51 optimal weight: 3.9990 chunk 63 optimal weight: 0.6980 chunk 98 optimal weight: 0.8980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 219 HIS A 427 HIS A 531 GLN B 219 HIS B 531 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8156 moved from start: 0.2927 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.021 8660 Z= 0.187 Angle : 0.634 7.253 11740 Z= 0.328 Chirality : 0.042 0.153 1400 Planarity : 0.005 0.038 1440 Dihedral : 5.398 47.593 1180 Min Nonbonded Distance : 2.593 Molprobity Statistics. All-atom Clashscore : 3.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.25 % Favored : 93.75 % Rotamer: Outliers : 1.51 % Allowed : 6.70 % Favored : 91.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.19 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.11 (0.21), residues: 1072 helix: -2.74 (0.16), residues: 590 sheet: -0.67 (0.64), residues: 62 loop : -2.83 (0.26), residues: 420 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 447 HIS 0.005 0.001 HIS A 219 PHE 0.018 0.002 PHE B 42 TYR 0.010 0.001 TYR A 508 ARG 0.004 0.000 ARG A 180 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2144 Ramachandran restraints generated. 1072 Oldfield, 0 Emsley, 1072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2144 Ramachandran restraints generated. 1072 Oldfield, 0 Emsley, 1072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 164 residues out of total 926 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 150 time to evaluate : 1.038 Fit side-chains REVERT: A 454 ASN cc_start: 0.8869 (m110) cc_final: 0.8537 (m-40) REVERT: A 482 MET cc_start: 0.7832 (tpp) cc_final: 0.7615 (mmm) REVERT: A 576 MET cc_start: 0.7223 (ttm) cc_final: 0.6985 (ttp) REVERT: B 319 LEU cc_start: 0.8894 (mp) cc_final: 0.8679 (mp) REVERT: B 454 ASN cc_start: 0.8780 (m110) cc_final: 0.8419 (m110) REVERT: B 482 MET cc_start: 0.7844 (tpp) cc_final: 0.7625 (mmm) REVERT: B 514 VAL cc_start: 0.8282 (OUTLIER) cc_final: 0.8080 (p) REVERT: B 576 MET cc_start: 0.7244 (ttm) cc_final: 0.7032 (ttp) outliers start: 14 outliers final: 3 residues processed: 164 average time/residue: 0.2092 time to fit residues: 47.2240 Evaluate side-chains 121 residues out of total 926 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 117 time to evaluate : 1.013 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 514 VAL Chi-restraints excluded: chain B residue 173 LEU Chi-restraints excluded: chain B residue 184 SER Chi-restraints excluded: chain B residue 514 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 54 optimal weight: 9.9990 chunk 30 optimal weight: 2.9990 chunk 81 optimal weight: 20.0000 chunk 66 optimal weight: 3.9990 chunk 27 optimal weight: 6.9990 chunk 98 optimal weight: 2.9990 chunk 106 optimal weight: 2.9990 chunk 87 optimal weight: 4.9990 chunk 97 optimal weight: 0.7980 chunk 33 optimal weight: 3.9990 chunk 78 optimal weight: 8.9990 overall best weight: 2.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 247 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8361 moved from start: 0.4110 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.042 8660 Z= 0.481 Angle : 0.797 9.861 11740 Z= 0.401 Chirality : 0.049 0.161 1400 Planarity : 0.005 0.044 1440 Dihedral : 5.541 48.094 1180 Min Nonbonded Distance : 2.546 Molprobity Statistics. All-atom Clashscore : 4.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.62 % Favored : 93.38 % Rotamer: Outliers : 2.70 % Allowed : 9.50 % Favored : 87.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.96 (0.24), residues: 1072 helix: -1.65 (0.20), residues: 596 sheet: -1.16 (0.61), residues: 62 loop : -2.39 (0.28), residues: 414 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP B 426 HIS 0.007 0.002 HIS A 434 PHE 0.018 0.002 PHE A 646 TYR 0.016 0.002 TYR A 475 ARG 0.004 0.001 ARG A 470 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2144 Ramachandran restraints generated. 1072 Oldfield, 0 Emsley, 1072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2144 Ramachandran restraints generated. 1072 Oldfield, 0 Emsley, 1072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 146 residues out of total 926 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 121 time to evaluate : 1.025 Fit side-chains REVERT: A 247 GLN cc_start: 0.8099 (mm-40) cc_final: 0.7750 (mm-40) REVERT: A 274 MET cc_start: 0.7683 (mmt) cc_final: 0.7219 (mmt) REVERT: A 569 VAL cc_start: 0.9180 (t) cc_final: 0.8766 (m) REVERT: B 274 MET cc_start: 0.7671 (mmt) cc_final: 0.7403 (mmt) REVERT: B 514 VAL cc_start: 0.8781 (OUTLIER) cc_final: 0.8569 (p) REVERT: B 569 VAL cc_start: 0.9051 (t) cc_final: 0.8740 (m) outliers start: 25 outliers final: 12 residues processed: 139 average time/residue: 0.2277 time to fit residues: 42.9074 Evaluate side-chains 115 residues out of total 926 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 102 time to evaluate : 1.067 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 184 SER Chi-restraints excluded: chain A residue 198 VAL Chi-restraints excluded: chain A residue 202 THR Chi-restraints excluded: chain A residue 337 VAL Chi-restraints excluded: chain A residue 340 THR Chi-restraints excluded: chain A residue 479 SER Chi-restraints excluded: chain A residue 514 VAL Chi-restraints excluded: chain B residue 184 SER Chi-restraints excluded: chain B residue 198 VAL Chi-restraints excluded: chain B residue 202 THR Chi-restraints excluded: chain B residue 340 THR Chi-restraints excluded: chain B residue 479 SER Chi-restraints excluded: chain B residue 514 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 97 optimal weight: 0.6980 chunk 73 optimal weight: 0.9980 chunk 50 optimal weight: 0.6980 chunk 10 optimal weight: 2.9990 chunk 46 optimal weight: 1.9990 chunk 65 optimal weight: 1.9990 chunk 98 optimal weight: 0.9980 chunk 104 optimal weight: 0.9990 chunk 51 optimal weight: 3.9990 chunk 93 optimal weight: 0.9990 chunk 28 optimal weight: 5.9990 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 454 ASN B 461 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8274 moved from start: 0.4521 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 8660 Z= 0.183 Angle : 0.593 8.341 11740 Z= 0.300 Chirality : 0.041 0.128 1400 Planarity : 0.003 0.040 1440 Dihedral : 4.977 43.702 1180 Min Nonbonded Distance : 2.557 Molprobity Statistics. All-atom Clashscore : 3.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.04 % Favored : 94.96 % Rotamer: Outliers : 1.84 % Allowed : 12.53 % Favored : 85.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.19 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.27 (0.25), residues: 1072 helix: -1.06 (0.21), residues: 596 sheet: -0.86 (0.61), residues: 62 loop : -2.13 (0.29), residues: 414 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 447 HIS 0.003 0.001 HIS A 484 PHE 0.016 0.001 PHE B 502 TYR 0.008 0.001 TYR A 508 ARG 0.003 0.000 ARG B 180 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2144 Ramachandran restraints generated. 1072 Oldfield, 0 Emsley, 1072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2144 Ramachandran restraints generated. 1072 Oldfield, 0 Emsley, 1072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 132 residues out of total 926 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 115 time to evaluate : 1.016 Fit side-chains REVERT: A 247 GLN cc_start: 0.8117 (mm-40) cc_final: 0.7740 (mm-40) REVERT: A 274 MET cc_start: 0.7650 (mmt) cc_final: 0.7191 (mmt) REVERT: A 420 LEU cc_start: 0.8870 (OUTLIER) cc_final: 0.8609 (mm) REVERT: A 569 VAL cc_start: 0.8838 (t) cc_final: 0.8489 (m) REVERT: B 274 MET cc_start: 0.7615 (mmt) cc_final: 0.7352 (mmt) REVERT: B 514 VAL cc_start: 0.8481 (OUTLIER) cc_final: 0.8231 (p) REVERT: B 569 VAL cc_start: 0.8700 (t) cc_final: 0.8390 (m) outliers start: 17 outliers final: 10 residues processed: 129 average time/residue: 0.2335 time to fit residues: 41.0399 Evaluate side-chains 112 residues out of total 926 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 100 time to evaluate : 1.001 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 184 SER Chi-restraints excluded: chain A residue 337 VAL Chi-restraints excluded: chain A residue 418 SER Chi-restraints excluded: chain A residue 420 LEU Chi-restraints excluded: chain A residue 465 ILE Chi-restraints excluded: chain A residue 484 HIS Chi-restraints excluded: chain A residue 514 VAL Chi-restraints excluded: chain B residue 184 SER Chi-restraints excluded: chain B residue 337 VAL Chi-restraints excluded: chain B residue 418 SER Chi-restraints excluded: chain B residue 465 ILE Chi-restraints excluded: chain B residue 514 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 86 optimal weight: 0.7980 chunk 59 optimal weight: 4.9990 chunk 1 optimal weight: 8.9990 chunk 77 optimal weight: 3.9990 chunk 43 optimal weight: 2.9990 chunk 89 optimal weight: 0.8980 chunk 72 optimal weight: 0.6980 chunk 0 optimal weight: 9.9990 chunk 53 optimal weight: 0.9980 chunk 93 optimal weight: 2.9990 chunk 26 optimal weight: 9.9990 overall best weight: 1.2782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8312 moved from start: 0.4765 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.028 8660 Z= 0.240 Angle : 0.614 8.331 11740 Z= 0.308 Chirality : 0.042 0.132 1400 Planarity : 0.003 0.040 1440 Dihedral : 4.818 42.647 1180 Min Nonbonded Distance : 2.580 Molprobity Statistics. All-atom Clashscore : 3.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.32 % Favored : 94.68 % Rotamer: Outliers : 3.35 % Allowed : 12.31 % Favored : 84.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.77 (0.26), residues: 1072 helix: -0.66 (0.22), residues: 594 sheet: -0.56 (0.66), residues: 62 loop : -1.91 (0.30), residues: 416 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 447 HIS 0.004 0.001 HIS A 484 PHE 0.013 0.001 PHE B 499 TYR 0.009 0.001 TYR A 508 ARG 0.003 0.000 ARG A 410 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2144 Ramachandran restraints generated. 1072 Oldfield, 0 Emsley, 1072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2144 Ramachandran restraints generated. 1072 Oldfield, 0 Emsley, 1072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 146 residues out of total 926 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 115 time to evaluate : 1.040 Fit side-chains revert: symmetry clash REVERT: A 48 ARG cc_start: 0.6049 (tpm170) cc_final: 0.5667 (tpm170) REVERT: A 274 MET cc_start: 0.7683 (mmt) cc_final: 0.7363 (mmt) REVERT: A 490 SER cc_start: 0.8639 (m) cc_final: 0.8384 (p) REVERT: A 493 LEU cc_start: 0.8601 (OUTLIER) cc_final: 0.8204 (mp) REVERT: A 569 VAL cc_start: 0.8814 (t) cc_final: 0.8588 (m) REVERT: B 180 ARG cc_start: 0.7624 (ttm110) cc_final: 0.7418 (ttm110) REVERT: B 232 GLU cc_start: 0.7876 (tp30) cc_final: 0.7667 (tp30) REVERT: B 274 MET cc_start: 0.7638 (mmt) cc_final: 0.7334 (mmt) REVERT: B 490 SER cc_start: 0.8646 (m) cc_final: 0.8372 (p) REVERT: B 493 LEU cc_start: 0.8594 (OUTLIER) cc_final: 0.8214 (mp) REVERT: B 514 VAL cc_start: 0.8570 (OUTLIER) cc_final: 0.8325 (p) outliers start: 31 outliers final: 20 residues processed: 142 average time/residue: 0.2104 time to fit residues: 41.2597 Evaluate side-chains 127 residues out of total 926 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 104 time to evaluate : 0.994 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 148 ASP Chi-restraints excluded: chain A residue 184 SER Chi-restraints excluded: chain A residue 202 THR Chi-restraints excluded: chain A residue 337 VAL Chi-restraints excluded: chain A residue 340 THR Chi-restraints excluded: chain A residue 418 SER Chi-restraints excluded: chain A residue 465 ILE Chi-restraints excluded: chain A residue 479 SER Chi-restraints excluded: chain A residue 484 HIS Chi-restraints excluded: chain A residue 493 LEU Chi-restraints excluded: chain A residue 503 THR Chi-restraints excluded: chain A residue 514 VAL Chi-restraints excluded: chain B residue 184 SER Chi-restraints excluded: chain B residue 202 THR Chi-restraints excluded: chain B residue 281 LEU Chi-restraints excluded: chain B residue 337 VAL Chi-restraints excluded: chain B residue 340 THR Chi-restraints excluded: chain B residue 418 SER Chi-restraints excluded: chain B residue 465 ILE Chi-restraints excluded: chain B residue 479 SER Chi-restraints excluded: chain B residue 493 LEU Chi-restraints excluded: chain B residue 503 THR Chi-restraints excluded: chain B residue 514 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 35 optimal weight: 0.7980 chunk 94 optimal weight: 0.9990 chunk 20 optimal weight: 2.9990 chunk 61 optimal weight: 0.0000 chunk 25 optimal weight: 2.9990 chunk 104 optimal weight: 0.9980 chunk 86 optimal weight: 1.9990 chunk 48 optimal weight: 0.5980 chunk 8 optimal weight: 5.9990 chunk 34 optimal weight: 1.9990 chunk 54 optimal weight: 9.9990 overall best weight: 0.6786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 247 GLN B 454 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8271 moved from start: 0.4918 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 8660 Z= 0.165 Angle : 0.608 12.899 11740 Z= 0.293 Chirality : 0.041 0.176 1400 Planarity : 0.003 0.038 1440 Dihedral : 4.647 40.678 1180 Min Nonbonded Distance : 2.589 Molprobity Statistics. All-atom Clashscore : 3.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.97 % Favored : 94.03 % Rotamer: Outliers : 2.59 % Allowed : 13.82 % Favored : 83.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.19 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.28 (0.26), residues: 1072 helix: -0.30 (0.22), residues: 584 sheet: -0.20 (0.68), residues: 62 loop : -1.62 (0.30), residues: 426 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 447 HIS 0.002 0.001 HIS A 484 PHE 0.020 0.001 PHE A 502 TYR 0.009 0.001 TYR B 508 ARG 0.004 0.000 ARG A 602 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2144 Ramachandran restraints generated. 1072 Oldfield, 0 Emsley, 1072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2144 Ramachandran restraints generated. 1072 Oldfield, 0 Emsley, 1072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 134 residues out of total 926 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 110 time to evaluate : 1.094 Fit side-chains revert: symmetry clash REVERT: A 274 MET cc_start: 0.7601 (mmt) cc_final: 0.7310 (mmt) REVERT: A 293 ARG cc_start: 0.7599 (ptp-170) cc_final: 0.7352 (ptp-170) REVERT: A 490 SER cc_start: 0.8603 (m) cc_final: 0.8324 (p) REVERT: A 502 PHE cc_start: 0.7978 (t80) cc_final: 0.7722 (t80) REVERT: B 274 MET cc_start: 0.7521 (mmt) cc_final: 0.7232 (mmt) REVERT: B 293 ARG cc_start: 0.7594 (ptp-170) cc_final: 0.7350 (ptp-170) REVERT: B 490 SER cc_start: 0.8568 (m) cc_final: 0.8311 (p) REVERT: B 514 VAL cc_start: 0.8428 (OUTLIER) cc_final: 0.8182 (p) outliers start: 24 outliers final: 17 residues processed: 132 average time/residue: 0.1930 time to fit residues: 36.0645 Evaluate side-chains 125 residues out of total 926 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 107 time to evaluate : 1.014 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 148 ASP Chi-restraints excluded: chain A residue 184 SER Chi-restraints excluded: chain A residue 337 VAL Chi-restraints excluded: chain A residue 340 THR Chi-restraints excluded: chain A residue 418 SER Chi-restraints excluded: chain A residue 432 ASP Chi-restraints excluded: chain A residue 465 ILE Chi-restraints excluded: chain A residue 479 SER Chi-restraints excluded: chain A residue 484 HIS Chi-restraints excluded: chain A residue 514 VAL Chi-restraints excluded: chain B residue 184 SER Chi-restraints excluded: chain B residue 202 THR Chi-restraints excluded: chain B residue 281 LEU Chi-restraints excluded: chain B residue 337 VAL Chi-restraints excluded: chain B residue 340 THR Chi-restraints excluded: chain B residue 418 SER Chi-restraints excluded: chain B residue 465 ILE Chi-restraints excluded: chain B residue 514 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 100 optimal weight: 2.9990 chunk 11 optimal weight: 1.9990 chunk 59 optimal weight: 9.9990 chunk 76 optimal weight: 4.9990 chunk 87 optimal weight: 2.9990 chunk 58 optimal weight: 0.9990 chunk 104 optimal weight: 0.9980 chunk 65 optimal weight: 3.9990 chunk 63 optimal weight: 0.9980 chunk 48 optimal weight: 1.9990 chunk 64 optimal weight: 0.1980 overall best weight: 1.0384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 454 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8297 moved from start: 0.5034 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 8660 Z= 0.205 Angle : 0.602 9.525 11740 Z= 0.295 Chirality : 0.042 0.168 1400 Planarity : 0.003 0.037 1440 Dihedral : 4.588 41.006 1180 Min Nonbonded Distance : 2.579 Molprobity Statistics. All-atom Clashscore : 3.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.60 % Favored : 94.40 % Rotamer: Outliers : 2.48 % Allowed : 13.61 % Favored : 83.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.02 (0.26), residues: 1072 helix: -0.15 (0.22), residues: 586 sheet: 0.01 (0.70), residues: 62 loop : -1.43 (0.31), residues: 424 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 447 HIS 0.003 0.001 HIS A 484 PHE 0.015 0.001 PHE A 502 TYR 0.009 0.001 TYR A 508 ARG 0.002 0.000 ARG B 602 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2144 Ramachandran restraints generated. 1072 Oldfield, 0 Emsley, 1072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2144 Ramachandran restraints generated. 1072 Oldfield, 0 Emsley, 1072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 132 residues out of total 926 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 109 time to evaluate : 0.964 Fit side-chains REVERT: A 274 MET cc_start: 0.7519 (mmt) cc_final: 0.7213 (mmt) REVERT: A 490 SER cc_start: 0.8646 (m) cc_final: 0.8334 (p) REVERT: B 490 SER cc_start: 0.8633 (m) cc_final: 0.8301 (p) REVERT: B 514 VAL cc_start: 0.8467 (OUTLIER) cc_final: 0.8225 (p) outliers start: 23 outliers final: 18 residues processed: 129 average time/residue: 0.1942 time to fit residues: 35.4100 Evaluate side-chains 123 residues out of total 926 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 104 time to evaluate : 0.978 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 148 ASP Chi-restraints excluded: chain A residue 184 SER Chi-restraints excluded: chain A residue 337 VAL Chi-restraints excluded: chain A residue 340 THR Chi-restraints excluded: chain A residue 418 SER Chi-restraints excluded: chain A residue 432 ASP Chi-restraints excluded: chain A residue 465 ILE Chi-restraints excluded: chain A residue 479 SER Chi-restraints excluded: chain A residue 484 HIS Chi-restraints excluded: chain A residue 514 VAL Chi-restraints excluded: chain B residue 184 SER Chi-restraints excluded: chain B residue 202 THR Chi-restraints excluded: chain B residue 281 LEU Chi-restraints excluded: chain B residue 337 VAL Chi-restraints excluded: chain B residue 418 SER Chi-restraints excluded: chain B residue 465 ILE Chi-restraints excluded: chain B residue 479 SER Chi-restraints excluded: chain B residue 514 VAL Chi-restraints excluded: chain B residue 569 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 41 optimal weight: 0.0570 chunk 62 optimal weight: 5.9990 chunk 31 optimal weight: 1.9990 chunk 20 optimal weight: 2.9990 chunk 66 optimal weight: 2.9990 chunk 70 optimal weight: 2.9990 chunk 51 optimal weight: 0.9990 chunk 9 optimal weight: 0.8980 chunk 81 optimal weight: 5.9990 chunk 94 optimal weight: 0.5980 chunk 99 optimal weight: 0.7980 overall best weight: 0.6700 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8264 moved from start: 0.5162 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 8660 Z= 0.155 Angle : 0.597 10.648 11740 Z= 0.290 Chirality : 0.040 0.140 1400 Planarity : 0.003 0.037 1440 Dihedral : 4.498 39.484 1180 Min Nonbonded Distance : 2.562 Molprobity Statistics. All-atom Clashscore : 3.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.06 % Favored : 93.94 % Rotamer: Outliers : 2.16 % Allowed : 14.69 % Favored : 83.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.19 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.84 (0.27), residues: 1072 helix: 0.02 (0.22), residues: 596 sheet: 0.32 (0.71), residues: 62 loop : -1.45 (0.31), residues: 414 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 447 HIS 0.002 0.001 HIS A 484 PHE 0.018 0.001 PHE B 502 TYR 0.007 0.001 TYR B 508 ARG 0.010 0.000 ARG B 602 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2144 Ramachandran restraints generated. 1072 Oldfield, 0 Emsley, 1072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2144 Ramachandran restraints generated. 1072 Oldfield, 0 Emsley, 1072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 129 residues out of total 926 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 109 time to evaluate : 0.885 Fit side-chains REVERT: A 274 MET cc_start: 0.7512 (mmt) cc_final: 0.7210 (mmt) REVERT: A 293 ARG cc_start: 0.7666 (ptp-170) cc_final: 0.7307 (ptp-170) REVERT: A 490 SER cc_start: 0.8631 (m) cc_final: 0.8311 (p) REVERT: A 502 PHE cc_start: 0.8000 (t80) cc_final: 0.7791 (t80) REVERT: B 293 ARG cc_start: 0.7540 (ptp-170) cc_final: 0.7311 (ptp-170) REVERT: B 490 SER cc_start: 0.8620 (m) cc_final: 0.8315 (p) REVERT: B 514 VAL cc_start: 0.8408 (OUTLIER) cc_final: 0.8182 (p) outliers start: 20 outliers final: 18 residues processed: 127 average time/residue: 0.1974 time to fit residues: 35.7393 Evaluate side-chains 127 residues out of total 926 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 108 time to evaluate : 0.946 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 148 ASP Chi-restraints excluded: chain A residue 184 SER Chi-restraints excluded: chain A residue 337 VAL Chi-restraints excluded: chain A residue 340 THR Chi-restraints excluded: chain A residue 418 SER Chi-restraints excluded: chain A residue 432 ASP Chi-restraints excluded: chain A residue 465 ILE Chi-restraints excluded: chain A residue 479 SER Chi-restraints excluded: chain A residue 484 HIS Chi-restraints excluded: chain A residue 514 VAL Chi-restraints excluded: chain B residue 184 SER Chi-restraints excluded: chain B residue 202 THR Chi-restraints excluded: chain B residue 281 LEU Chi-restraints excluded: chain B residue 337 VAL Chi-restraints excluded: chain B residue 418 SER Chi-restraints excluded: chain B residue 465 ILE Chi-restraints excluded: chain B residue 479 SER Chi-restraints excluded: chain B residue 514 VAL Chi-restraints excluded: chain B residue 569 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 90 optimal weight: 2.9990 chunk 97 optimal weight: 0.9990 chunk 99 optimal weight: 0.6980 chunk 58 optimal weight: 3.9990 chunk 42 optimal weight: 2.9990 chunk 76 optimal weight: 0.9990 chunk 29 optimal weight: 2.9990 chunk 87 optimal weight: 4.9990 chunk 91 optimal weight: 0.9990 chunk 96 optimal weight: 1.9990 chunk 63 optimal weight: 0.4980 overall best weight: 0.8386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 454 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8277 moved from start: 0.5242 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 8660 Z= 0.178 Angle : 0.618 11.021 11740 Z= 0.297 Chirality : 0.041 0.143 1400 Planarity : 0.003 0.037 1440 Dihedral : 4.471 40.127 1180 Min Nonbonded Distance : 2.550 Molprobity Statistics. All-atom Clashscore : 3.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.41 % Favored : 94.59 % Rotamer: Outliers : 2.05 % Allowed : 14.15 % Favored : 83.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.71 (0.27), residues: 1072 helix: 0.12 (0.22), residues: 596 sheet: 0.49 (0.71), residues: 62 loop : -1.41 (0.32), residues: 414 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 447 HIS 0.002 0.001 HIS A 484 PHE 0.010 0.001 PHE B 499 TYR 0.010 0.001 TYR B 475 ARG 0.004 0.000 ARG A 602 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2144 Ramachandran restraints generated. 1072 Oldfield, 0 Emsley, 1072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2144 Ramachandran restraints generated. 1072 Oldfield, 0 Emsley, 1072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 128 residues out of total 926 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 109 time to evaluate : 0.951 Fit side-chains REVERT: A 274 MET cc_start: 0.7449 (mmt) cc_final: 0.7144 (mmt) REVERT: A 490 SER cc_start: 0.8646 (m) cc_final: 0.8335 (p) REVERT: A 502 PHE cc_start: 0.7992 (t80) cc_final: 0.7784 (t80) REVERT: B 293 ARG cc_start: 0.7580 (ptp-170) cc_final: 0.7357 (ptp-170) REVERT: B 490 SER cc_start: 0.8645 (m) cc_final: 0.8309 (p) REVERT: B 514 VAL cc_start: 0.8436 (OUTLIER) cc_final: 0.8220 (p) outliers start: 19 outliers final: 17 residues processed: 126 average time/residue: 0.2044 time to fit residues: 36.4297 Evaluate side-chains 123 residues out of total 926 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 105 time to evaluate : 1.096 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 162 VAL Chi-restraints excluded: chain A residue 184 SER Chi-restraints excluded: chain A residue 337 VAL Chi-restraints excluded: chain A residue 340 THR Chi-restraints excluded: chain A residue 418 SER Chi-restraints excluded: chain A residue 432 ASP Chi-restraints excluded: chain A residue 479 SER Chi-restraints excluded: chain A residue 484 HIS Chi-restraints excluded: chain A residue 514 VAL Chi-restraints excluded: chain B residue 162 VAL Chi-restraints excluded: chain B residue 184 SER Chi-restraints excluded: chain B residue 202 THR Chi-restraints excluded: chain B residue 281 LEU Chi-restraints excluded: chain B residue 337 VAL Chi-restraints excluded: chain B residue 418 SER Chi-restraints excluded: chain B residue 479 SER Chi-restraints excluded: chain B residue 514 VAL Chi-restraints excluded: chain B residue 569 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 102 optimal weight: 0.9980 chunk 62 optimal weight: 4.9990 chunk 48 optimal weight: 0.9980 chunk 71 optimal weight: 3.9990 chunk 107 optimal weight: 1.9990 chunk 99 optimal weight: 0.8980 chunk 85 optimal weight: 2.9990 chunk 8 optimal weight: 4.9990 chunk 66 optimal weight: 2.9990 chunk 52 optimal weight: 0.5980 chunk 68 optimal weight: 0.0980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8263 moved from start: 0.5342 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 8660 Z= 0.161 Angle : 0.615 11.620 11740 Z= 0.295 Chirality : 0.041 0.142 1400 Planarity : 0.003 0.037 1440 Dihedral : 4.431 39.543 1180 Min Nonbonded Distance : 2.548 Molprobity Statistics. All-atom Clashscore : 3.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.34 % Favored : 93.66 % Rotamer: Outliers : 2.05 % Allowed : 14.25 % Favored : 83.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.19 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.53 (0.27), residues: 1072 helix: 0.29 (0.22), residues: 594 sheet: 0.71 (0.70), residues: 62 loop : -1.39 (0.31), residues: 416 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 447 HIS 0.002 0.001 HIS B 434 PHE 0.020 0.001 PHE B 502 TYR 0.008 0.001 TYR B 475 ARG 0.005 0.000 ARG B 602 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2144 Ramachandran restraints generated. 1072 Oldfield, 0 Emsley, 1072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2144 Ramachandran restraints generated. 1072 Oldfield, 0 Emsley, 1072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 129 residues out of total 926 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 110 time to evaluate : 0.908 Fit side-chains REVERT: A 274 MET cc_start: 0.7445 (mmt) cc_final: 0.7212 (mmt) REVERT: A 490 SER cc_start: 0.8635 (m) cc_final: 0.8292 (p) REVERT: B 490 SER cc_start: 0.8679 (m) cc_final: 0.8357 (p) REVERT: B 514 VAL cc_start: 0.8392 (OUTLIER) cc_final: 0.8176 (p) outliers start: 19 outliers final: 16 residues processed: 127 average time/residue: 0.2061 time to fit residues: 36.6101 Evaluate side-chains 124 residues out of total 926 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 107 time to evaluate : 0.939 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 162 VAL Chi-restraints excluded: chain A residue 337 VAL Chi-restraints excluded: chain A residue 340 THR Chi-restraints excluded: chain A residue 418 SER Chi-restraints excluded: chain A residue 432 ASP Chi-restraints excluded: chain A residue 479 SER Chi-restraints excluded: chain A residue 484 HIS Chi-restraints excluded: chain A residue 514 VAL Chi-restraints excluded: chain B residue 162 VAL Chi-restraints excluded: chain B residue 184 SER Chi-restraints excluded: chain B residue 202 THR Chi-restraints excluded: chain B residue 281 LEU Chi-restraints excluded: chain B residue 337 VAL Chi-restraints excluded: chain B residue 418 SER Chi-restraints excluded: chain B residue 479 SER Chi-restraints excluded: chain B residue 514 VAL Chi-restraints excluded: chain B residue 569 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 91 optimal weight: 3.9990 chunk 26 optimal weight: 10.0000 chunk 79 optimal weight: 6.9990 chunk 12 optimal weight: 0.6980 chunk 23 optimal weight: 7.9990 chunk 85 optimal weight: 2.9990 chunk 35 optimal weight: 0.0970 chunk 88 optimal weight: 1.9990 chunk 10 optimal weight: 2.9990 chunk 15 optimal weight: 2.9990 chunk 75 optimal weight: 0.9980 overall best weight: 1.3582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 454 ASN B 112 ASN B 454 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3430 r_free = 0.3430 target = 0.133516 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.2965 r_free = 0.2965 target = 0.096233 restraints weight = 11251.020| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.2989 r_free = 0.2989 target = 0.097969 restraints weight = 8630.680| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3002 r_free = 0.3002 target = 0.098989 restraints weight = 7305.604| |-----------------------------------------------------------------------------| r_work (final): 0.2993 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8238 moved from start: 0.5367 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 8660 Z= 0.254 Angle : 0.667 11.728 11740 Z= 0.322 Chirality : 0.043 0.140 1400 Planarity : 0.003 0.039 1440 Dihedral : 4.618 42.146 1180 Min Nonbonded Distance : 2.542 Molprobity Statistics. All-atom Clashscore : 3.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.78 % Favored : 94.22 % Rotamer: Outliers : 1.94 % Allowed : 14.69 % Favored : 83.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.55 (0.27), residues: 1072 helix: 0.29 (0.22), residues: 592 sheet: 0.65 (0.70), residues: 62 loop : -1.42 (0.32), residues: 418 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 447 HIS 0.004 0.001 HIS A 484 PHE 0.012 0.001 PHE B 499 TYR 0.015 0.001 TYR B 475 ARG 0.006 0.000 ARG B 602 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1743.38 seconds wall clock time: 32 minutes 49.95 seconds (1969.95 seconds total)