Starting phenix.real_space_refine on Tue Dec 31 20:33:35 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7yum_34108/12_2024/7yum_34108.cif Found real_map, /net/cci-nas-00/data/ceres_data/7yum_34108/12_2024/7yum_34108.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7yum_34108/12_2024/7yum_34108.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7yum_34108/12_2024/7yum_34108.map" model { file = "/net/cci-nas-00/data/ceres_data/7yum_34108/12_2024/7yum_34108.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7yum_34108/12_2024/7yum_34108.cif" } resolution = 3.8 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.055 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 60 5.16 5 C 10480 2.51 5 N 2904 2.21 5 O 3132 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 74 residue(s): 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5532/modules/chem_data/mon_lib" Total number of atoms: 16576 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 4144 Number of conformers: 1 Conformer: "" Number of residues, atoms: 532, 4144 Classifications: {'peptide': 532} Link IDs: {'PTRANS': 32, 'TRANS': 499} Chain: "B" Number of atoms: 4144 Number of conformers: 1 Conformer: "" Number of residues, atoms: 532, 4144 Classifications: {'peptide': 532} Link IDs: {'PTRANS': 32, 'TRANS': 499} Chain: "C" Number of atoms: 4144 Number of conformers: 1 Conformer: "" Number of residues, atoms: 532, 4144 Classifications: {'peptide': 532} Link IDs: {'PTRANS': 32, 'TRANS': 499} Chain: "D" Number of atoms: 4144 Number of conformers: 1 Conformer: "" Number of residues, atoms: 532, 4144 Classifications: {'peptide': 532} Link IDs: {'PTRANS': 32, 'TRANS': 499} Time building chain proxies: 10.12, per 1000 atoms: 0.61 Number of scatterers: 16576 At special positions: 0 Unit cell: (118.08, 109.88, 143.5, 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 60 16.00 O 3132 8.00 N 2904 7.00 C 10480 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: 4.15 Conformation dependent library (CDL) restraints added in 2.1 seconds 4240 Ramachandran restraints generated. 2120 Oldfield, 0 Emsley, 2120 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3904 Finding SS restraints... Secondary structure from input PDB file: 87 helices and 18 sheets defined 44.6% alpha, 9.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.57 Creating SS restraints... Processing helix chain 'A' and resid 245 through 255 removed outlier: 4.145A pdb=" N LYS A 251 " --> pdb=" O GLU A 247 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N ILE A 253 " --> pdb=" O LEU A 249 " (cutoff:3.500A) removed outlier: 3.893A pdb=" N GLU A 254 " --> pdb=" O ARG A 250 " (cutoff:3.500A) Processing helix chain 'A' and resid 259 through 273 removed outlier: 4.254A pdb=" N ARG A 272 " --> pdb=" O LYS A 268 " (cutoff:3.500A) Processing helix chain 'A' and resid 280 through 296 removed outlier: 3.770A pdb=" N VAL A 296 " --> pdb=" O TRP A 292 " (cutoff:3.500A) Processing helix chain 'A' and resid 307 through 315 Processing helix chain 'A' and resid 316 through 318 No H-bonds generated for 'chain 'A' and resid 316 through 318' Processing helix chain 'A' and resid 324 through 336 Processing helix chain 'A' and resid 360 through 373 Processing helix chain 'A' and resid 403 through 411 removed outlier: 3.756A pdb=" N HIS A 407 " --> pdb=" O GLY A 403 " (cutoff:3.500A) Processing helix chain 'A' and resid 434 through 444 removed outlier: 3.529A pdb=" N ALA A 438 " --> pdb=" O ASP A 434 " (cutoff:3.500A) removed outlier: 4.195A pdb=" N ASP A 444 " --> pdb=" O LEU A 440 " (cutoff:3.500A) Processing helix chain 'A' and resid 447 through 451 removed outlier: 3.566A pdb=" N THR A 450 " --> pdb=" O GLN A 447 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N PHE A 451 " --> pdb=" O ASN A 448 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 447 through 451' Processing helix chain 'A' and resid 478 through 482 Processing helix chain 'A' and resid 494 through 505 Processing helix chain 'A' and resid 505 through 514 removed outlier: 3.672A pdb=" N LYS A 509 " --> pdb=" O TYR A 505 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N SER A 514 " --> pdb=" O GLN A 510 " (cutoff:3.500A) Processing helix chain 'A' and resid 523 through 534 Processing helix chain 'A' and resid 540 through 560 removed outlier: 3.670A pdb=" N GLU A 560 " --> pdb=" O LYS A 556 " (cutoff:3.500A) Processing helix chain 'A' and resid 573 through 578 removed outlier: 3.733A pdb=" N TYR A 577 " --> pdb=" O ASP A 573 " (cutoff:3.500A) Processing helix chain 'A' and resid 631 through 647 Processing helix chain 'A' and resid 679 through 693 Processing helix chain 'A' and resid 717 through 728 removed outlier: 3.980A pdb=" N LYS A 721 " --> pdb=" O GLY A 717 " (cutoff:3.500A) Processing helix chain 'A' and resid 738 through 740 No H-bonds generated for 'chain 'A' and resid 738 through 740' Processing helix chain 'A' and resid 761 through 770 removed outlier: 3.792A pdb=" N VAL A 765 " --> pdb=" O ASP A 761 " (cutoff:3.500A) removed outlier: 4.374A pdb=" N LEU A 770 " --> pdb=" O LEU A 766 " (cutoff:3.500A) Processing helix chain 'B' and resid 244 through 256 Processing helix chain 'B' and resid 259 through 271 Processing helix chain 'B' and resid 283 through 296 removed outlier: 3.847A pdb=" N VAL B 296 " --> pdb=" O TRP B 292 " (cutoff:3.500A) Processing helix chain 'B' and resid 308 through 316 Processing helix chain 'B' and resid 325 through 339 removed outlier: 4.034A pdb=" N ILE B 329 " --> pdb=" O VAL B 325 " (cutoff:3.500A) Processing helix chain 'B' and resid 361 through 373 removed outlier: 3.660A pdb=" N ASN B 373 " --> pdb=" O ALA B 369 " (cutoff:3.500A) Processing helix chain 'B' and resid 386 through 390 Processing helix chain 'B' and resid 403 through 412 removed outlier: 3.678A pdb=" N VAL B 412 " --> pdb=" O ALA B 408 " (cutoff:3.500A) Processing helix chain 'B' and resid 434 through 444 removed outlier: 4.122A pdb=" N ALA B 438 " --> pdb=" O ASP B 434 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N ASP B 444 " --> pdb=" O LEU B 440 " (cutoff:3.500A) Processing helix chain 'B' and resid 447 through 451 removed outlier: 3.721A pdb=" N THR B 450 " --> pdb=" O GLN B 447 " (cutoff:3.500A) Processing helix chain 'B' and resid 494 through 506 Processing helix chain 'B' and resid 506 through 514 Processing helix chain 'B' and resid 523 through 535 removed outlier: 3.636A pdb=" N ILE B 527 " --> pdb=" O THR B 523 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N THR B 535 " --> pdb=" O ILE B 531 " (cutoff:3.500A) Processing helix chain 'B' and resid 541 through 560 Processing helix chain 'B' and resid 573 through 579 removed outlier: 3.651A pdb=" N TYR B 577 " --> pdb=" O ASP B 573 " (cutoff:3.500A) Processing helix chain 'B' and resid 630 through 647 removed outlier: 3.771A pdb=" N LYS B 634 " --> pdb=" O GLY B 630 " (cutoff:3.500A) Processing helix chain 'B' and resid 648 through 652 removed outlier: 3.749A pdb=" N GLY B 652 " --> pdb=" O GLN B 649 " (cutoff:3.500A) Processing helix chain 'B' and resid 679 through 693 Processing helix chain 'B' and resid 717 through 728 removed outlier: 4.100A pdb=" N LYS B 721 " --> pdb=" O GLY B 717 " (cutoff:3.500A) Processing helix chain 'B' and resid 738 through 740 No H-bonds generated for 'chain 'B' and resid 738 through 740' Processing helix chain 'B' and resid 742 through 746 Processing helix chain 'B' and resid 747 through 752 removed outlier: 3.715A pdb=" N LEU B 751 " --> pdb=" O PRO B 747 " (cutoff:3.500A) Processing helix chain 'B' and resid 761 through 769 removed outlier: 3.714A pdb=" N VAL B 765 " --> pdb=" O ASP B 761 " (cutoff:3.500A) Processing helix chain 'C' and resid 244 through 256 Processing helix chain 'C' and resid 259 through 269 Processing helix chain 'C' and resid 281 through 295 Processing helix chain 'C' and resid 308 through 315 Processing helix chain 'C' and resid 316 through 318 No H-bonds generated for 'chain 'C' and resid 316 through 318' Processing helix chain 'C' and resid 324 through 338 removed outlier: 3.558A pdb=" N ARG C 328 " --> pdb=" O ASP C 324 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N LEU C 338 " --> pdb=" O ALA C 334 " (cutoff:3.500A) Processing helix chain 'C' and resid 361 through 372 Processing helix chain 'C' and resid 403 through 412 Processing helix chain 'C' and resid 423 through 427 removed outlier: 4.073A pdb=" N MET C 427 " --> pdb=" O ILE C 424 " (cutoff:3.500A) Processing helix chain 'C' and resid 435 through 444 removed outlier: 3.958A pdb=" N VAL C 442 " --> pdb=" O ALA C 438 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N ASP C 444 " --> pdb=" O LEU C 440 " (cutoff:3.500A) Processing helix chain 'C' and resid 478 through 482 removed outlier: 3.548A pdb=" N LEU C 482 " --> pdb=" O ARG C 479 " (cutoff:3.500A) Processing helix chain 'C' and resid 494 through 515 removed outlier: 3.549A pdb=" N TYR C 505 " --> pdb=" O ILE C 501 " (cutoff:3.500A) removed outlier: 5.734A pdb=" N TRP C 507 " --> pdb=" O ARG C 503 " (cutoff:3.500A) Proline residue: C 508 - end of helix Processing helix chain 'C' and resid 523 through 534 removed outlier: 3.662A pdb=" N ILE C 527 " --> pdb=" O THR C 523 " (cutoff:3.500A) Processing helix chain 'C' and resid 540 through 560 removed outlier: 3.514A pdb=" N GLU C 560 " --> pdb=" O LYS C 556 " (cutoff:3.500A) Processing helix chain 'C' and resid 573 through 579 removed outlier: 3.662A pdb=" N TYR C 577 " --> pdb=" O ASP C 573 " (cutoff:3.500A) Processing helix chain 'C' and resid 630 through 647 removed outlier: 3.652A pdb=" N LYS C 634 " --> pdb=" O GLY C 630 " (cutoff:3.500A) Processing helix chain 'C' and resid 679 through 693 Processing helix chain 'C' and resid 717 through 728 Processing helix chain 'C' and resid 747 through 752 Processing helix chain 'C' and resid 761 through 770 removed outlier: 3.526A pdb=" N VAL C 765 " --> pdb=" O ASP C 761 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N LEU C 770 " --> pdb=" O LEU C 766 " (cutoff:3.500A) Processing helix chain 'D' and resid 244 through 255 removed outlier: 3.832A pdb=" N LYS D 252 " --> pdb=" O ALA D 248 " (cutoff:3.500A) removed outlier: 4.237A pdb=" N ILE D 253 " --> pdb=" O LEU D 249 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N GLU D 254 " --> pdb=" O ARG D 250 " (cutoff:3.500A) Processing helix chain 'D' and resid 259 through 273 Processing helix chain 'D' and resid 283 through 296 Processing helix chain 'D' and resid 307 through 316 Processing helix chain 'D' and resid 324 through 337 removed outlier: 4.206A pdb=" N ARG D 328 " --> pdb=" O ASP D 324 " (cutoff:3.500A) Processing helix chain 'D' and resid 360 through 372 Processing helix chain 'D' and resid 386 through 390 removed outlier: 3.639A pdb=" N ILE D 390 " --> pdb=" O GLU D 387 " (cutoff:3.500A) Processing helix chain 'D' and resid 404 through 411 Processing helix chain 'D' and resid 435 through 444 removed outlier: 3.822A pdb=" N MET D 439 " --> pdb=" O PRO D 435 " (cutoff:3.500A) Processing helix chain 'D' and resid 473 through 477 removed outlier: 3.711A pdb=" N THR D 476 " --> pdb=" O THR D 473 " (cutoff:3.500A) Processing helix chain 'D' and resid 478 through 482 Processing helix chain 'D' and resid 494 through 505 Processing helix chain 'D' and resid 505 through 514 removed outlier: 3.740A pdb=" N LYS D 509 " --> pdb=" O TYR D 505 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N ARG D 512 " --> pdb=" O PRO D 508 " (cutoff:3.500A) Processing helix chain 'D' and resid 523 through 535 removed outlier: 3.914A pdb=" N ILE D 527 " --> pdb=" O THR D 523 " (cutoff:3.500A) removed outlier: 4.240A pdb=" N THR D 535 " --> pdb=" O ILE D 531 " (cutoff:3.500A) Processing helix chain 'D' and resid 540 through 560 removed outlier: 3.527A pdb=" N GLU D 560 " --> pdb=" O LYS D 556 " (cutoff:3.500A) Processing helix chain 'D' and resid 573 through 578 Processing helix chain 'D' and resid 630 through 647 removed outlier: 3.965A pdb=" N LYS D 634 " --> pdb=" O GLY D 630 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N SER D 636 " --> pdb=" O VAL D 632 " (cutoff:3.500A) Processing helix chain 'D' and resid 648 through 652 Processing helix chain 'D' and resid 679 through 691 Processing helix chain 'D' and resid 717 through 729 Processing helix chain 'D' and resid 738 through 745 removed outlier: 4.216A pdb=" N ALA D 741 " --> pdb=" O ASP D 738 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N GLU D 744 " --> pdb=" O ALA D 741 " (cutoff:3.500A) Processing helix chain 'D' and resid 747 through 754 removed outlier: 3.912A pdb=" N LEU D 751 " --> pdb=" O PRO D 747 " (cutoff:3.500A) Processing helix chain 'D' and resid 762 through 769 Processing sheet with id=AA1, first strand: chain 'A' and resid 352 through 354 removed outlier: 6.014A pdb=" N VAL A 352 " --> pdb=" O ILE A 488 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'A' and resid 418 through 422 removed outlier: 3.504A pdb=" N ILE A 468 " --> pdb=" O ILE A 419 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 520 through 522 removed outlier: 6.405A pdb=" N GLU A 521 " --> pdb=" O ILE A 569 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA3 Processing sheet with id=AA4, first strand: chain 'A' and resid 596 through 603 removed outlier: 6.736A pdb=" N SER A 624 " --> pdb=" O VAL A 665 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 700 through 702 removed outlier: 6.751A pdb=" N ILE A 733 " --> pdb=" O LYS A 757 " (cutoff:3.500A) removed outlier: 7.102A pdb=" N VAL A 759 " --> pdb=" O ILE A 733 " (cutoff:3.500A) removed outlier: 6.199A pdb=" N LEU A 735 " --> pdb=" O VAL A 759 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 378 through 380 removed outlier: 6.384A pdb=" N ILE B 379 " --> pdb=" O ASP B 422 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 596 through 603 removed outlier: 3.703A pdb=" N THR B 603 " --> pdb=" O GLY B 606 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 732 through 736 removed outlier: 6.744A pdb=" N ILE B 733 " --> pdb=" O LYS B 757 " (cutoff:3.500A) removed outlier: 7.217A pdb=" N VAL B 759 " --> pdb=" O ILE B 733 " (cutoff:3.500A) removed outlier: 5.821A pdb=" N LEU B 735 " --> pdb=" O VAL B 759 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA8 Processing sheet with id=AA9, first strand: chain 'C' and resid 353 through 354 Processing sheet with id=AB1, first strand: chain 'C' and resid 418 through 421 removed outlier: 3.604A pdb=" N ILE C 468 " --> pdb=" O ILE C 419 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 521 through 522 removed outlier: 6.302A pdb=" N GLU C 521 " --> pdb=" O ILE C 569 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB2 Processing sheet with id=AB3, first strand: chain 'C' and resid 596 through 601 removed outlier: 6.186A pdb=" N SER C 624 " --> pdb=" O VAL C 665 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 701 through 702 removed outlier: 6.986A pdb=" N ALA C 701 " --> pdb=" O VAL C 734 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB4 Processing sheet with id=AB5, first strand: chain 'D' and resid 353 through 354 Processing sheet with id=AB6, first strand: chain 'D' and resid 376 through 380 removed outlier: 6.227A pdb=" N HIS D 377 " --> pdb=" O LEU D 420 " (cutoff:3.500A) removed outlier: 7.221A pdb=" N ASP D 422 " --> pdb=" O HIS D 377 " (cutoff:3.500A) removed outlier: 6.407A pdb=" N ILE D 379 " --> pdb=" O ASP D 422 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'D' and resid 596 through 603 removed outlier: 5.537A pdb=" N LYS D 622 " --> pdb=" O LEU D 663 " (cutoff:3.500A) removed outlier: 7.261A pdb=" N VAL D 665 " --> pdb=" O LYS D 622 " (cutoff:3.500A) removed outlier: 6.723A pdb=" N SER D 624 " --> pdb=" O VAL D 665 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'D' and resid 700 through 702 removed outlier: 6.426A pdb=" N ALA D 701 " --> pdb=" O VAL D 734 " (cutoff:3.500A) removed outlier: 6.191A pdb=" N ILE D 733 " --> pdb=" O LYS D 757 " (cutoff:3.500A) removed outlier: 6.996A pdb=" N VAL D 759 " --> pdb=" O ILE D 733 " (cutoff:3.500A) removed outlier: 6.082A pdb=" N LEU D 735 " --> pdb=" O VAL D 759 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB8 Processing sheet with id=AB9, first strand: chain 'D' and resid 705 through 707 removed outlier: 3.759A pdb=" N GLU D 705 " --> pdb=" O MET D 713 " (cutoff:3.500A) 630 hydrogen bonds defined for protein. 1818 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 4.75 Time building geometry restraints manager: 4.65 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: 5284 1.34 - 1.45: 2577 1.45 - 1.57: 8903 1.57 - 1.69: 0 1.69 - 1.81: 120 Bond restraints: 16884 Sorted by residual: bond pdb=" C ILE B 419 " pdb=" N LEU B 420 " ideal model delta sigma weight residual 1.331 1.295 0.036 1.40e-02 5.10e+03 6.73e+00 bond pdb=" CG LEU B 769 " pdb=" CD1 LEU B 769 " ideal model delta sigma weight residual 1.521 1.437 0.084 3.30e-02 9.18e+02 6.52e+00 bond pdb=" CG LEU B 723 " pdb=" CD1 LEU B 723 " ideal model delta sigma weight residual 1.521 1.437 0.084 3.30e-02 9.18e+02 6.43e+00 bond pdb=" CB GLN C 499 " pdb=" CG GLN C 499 " ideal model delta sigma weight residual 1.520 1.445 0.075 3.00e-02 1.11e+03 6.20e+00 bond pdb=" CG1 ILE B 468 " pdb=" CD1 ILE B 468 " ideal model delta sigma weight residual 1.513 1.420 0.093 3.90e-02 6.57e+02 5.69e+00 ... (remaining 16879 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.51: 22365 3.51 - 7.02: 461 7.02 - 10.52: 51 10.52 - 14.03: 5 14.03 - 17.54: 2 Bond angle restraints: 22884 Sorted by residual: angle pdb=" N GLY B 539 " pdb=" CA GLY B 539 " pdb=" C GLY B 539 " ideal model delta sigma weight residual 111.21 118.38 -7.17 1.04e+00 9.25e-01 4.76e+01 angle pdb=" C ALA D 400 " pdb=" N MET D 401 " pdb=" CA MET D 401 " ideal model delta sigma weight residual 120.97 138.51 -17.54 2.84e+00 1.24e-01 3.81e+01 angle pdb=" C GLY B 321 " pdb=" N LEU B 322 " pdb=" CA LEU B 322 " ideal model delta sigma weight residual 121.54 131.70 -10.16 1.91e+00 2.74e-01 2.83e+01 angle pdb=" C MET A 698 " pdb=" N ASP A 699 " pdb=" CA ASP A 699 " ideal model delta sigma weight residual 122.08 129.85 -7.77 1.47e+00 4.63e-01 2.80e+01 angle pdb=" N ILE B 468 " pdb=" CA ILE B 468 " pdb=" C ILE B 468 " ideal model delta sigma weight residual 109.34 99.73 9.61 2.08e+00 2.31e-01 2.13e+01 ... (remaining 22879 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.15: 9612 15.15 - 30.31: 627 30.31 - 45.46: 120 45.46 - 60.62: 9 60.62 - 75.77: 20 Dihedral angle restraints: 10388 sinusoidal: 4300 harmonic: 6088 Sorted by residual: dihedral pdb=" CA GLU D 591 " pdb=" C GLU D 591 " pdb=" N PRO D 592 " pdb=" CA PRO D 592 " ideal model delta harmonic sigma weight residual 180.00 -132.24 -47.76 0 5.00e+00 4.00e-02 9.12e+01 dihedral pdb=" CA PRO B 673 " pdb=" C PRO B 673 " pdb=" N LYS B 674 " pdb=" CA LYS B 674 " ideal model delta harmonic sigma weight residual -180.00 -138.02 -41.98 0 5.00e+00 4.00e-02 7.05e+01 dihedral pdb=" CA LYS B 347 " pdb=" C LYS B 347 " pdb=" N ALA B 348 " pdb=" CA ALA B 348 " ideal model delta harmonic sigma weight residual 180.00 140.73 39.27 0 5.00e+00 4.00e-02 6.17e+01 ... (remaining 10385 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.080: 2058 0.080 - 0.160: 485 0.160 - 0.240: 52 0.240 - 0.320: 6 0.320 - 0.400: 3 Chirality restraints: 2604 Sorted by residual: chirality pdb=" CB ILE C 379 " pdb=" CA ILE C 379 " pdb=" CG1 ILE C 379 " pdb=" CG2 ILE C 379 " both_signs ideal model delta sigma weight residual False 2.64 2.24 0.40 2.00e-01 2.50e+01 4.00e+00 chirality pdb=" CB ILE C 468 " pdb=" CA ILE C 468 " pdb=" CG1 ILE C 468 " pdb=" CG2 ILE C 468 " both_signs ideal model delta sigma weight residual False 2.64 2.28 0.37 2.00e-01 2.50e+01 3.41e+00 chirality pdb=" CG LEU C 462 " pdb=" CB LEU C 462 " pdb=" CD1 LEU C 462 " pdb=" CD2 LEU C 462 " both_signs ideal model delta sigma weight residual False -2.59 -2.27 -0.32 2.00e-01 2.50e+01 2.57e+00 ... (remaining 2601 not shown) Planarity restraints: 2972 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASP D 434 " -0.051 5.00e-02 4.00e+02 7.72e-02 9.53e+00 pdb=" N PRO D 435 " 0.134 5.00e-02 4.00e+02 pdb=" CA PRO D 435 " -0.041 5.00e-02 4.00e+02 pdb=" CD PRO D 435 " -0.042 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLU A 773 " 0.049 5.00e-02 4.00e+02 7.38e-02 8.70e+00 pdb=" N PRO A 774 " -0.127 5.00e-02 4.00e+02 pdb=" CA PRO A 774 " 0.034 5.00e-02 4.00e+02 pdb=" CD PRO A 774 " 0.044 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PRO C 356 " -0.044 5.00e-02 4.00e+02 6.61e-02 6.99e+00 pdb=" N PRO C 357 " 0.114 5.00e-02 4.00e+02 pdb=" CA PRO C 357 " -0.033 5.00e-02 4.00e+02 pdb=" CD PRO C 357 " -0.037 5.00e-02 4.00e+02 ... (remaining 2969 not shown) Histogram of nonbonded interaction distances: 2.21 - 2.75: 2181 2.75 - 3.29: 16004 3.29 - 3.82: 27292 3.82 - 4.36: 31640 4.36 - 4.90: 53127 Nonbonded interactions: 130244 Sorted by model distance: nonbonded pdb=" O LYS C 587 " pdb=" OG1 THR C 590 " model vdw 2.209 3.040 nonbonded pdb=" OG1 THR D 603 " pdb=" O GLY D 606 " model vdw 2.257 3.040 nonbonded pdb=" OG1 THR A 603 " pdb=" O GLY A 606 " model vdw 2.257 3.040 nonbonded pdb=" OD2 ASP A 425 " pdb=" OG1 THR A 473 " model vdw 2.259 3.040 nonbonded pdb=" O ARG C 336 " pdb=" OG1 THR C 339 " model vdw 2.260 3.040 ... (remaining 130239 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' 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=0.00 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: 3.250 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: 0.020 Extract box with map and model: 0.670 Check model and map are aligned: 0.100 Set scattering table: 0.130 Process input model: 36.350 Find NCS groups from input model: 0.480 Set up NCS constraints: 0.060 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:2.730 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 43.800 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7254 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 0.110 16884 Z= 0.660 Angle : 1.257 17.540 22884 Z= 0.676 Chirality : 0.067 0.400 2604 Planarity : 0.009 0.077 2972 Dihedral : 11.165 75.772 6484 Min Nonbonded Distance : 2.209 Molprobity Statistics. All-atom Clashscore : 8.96 Ramachandran Plot: Outliers : 0.09 % Allowed : 12.31 % Favored : 87.59 % Rotamer: Outliers : 0.34 % Allowed : 3.61 % Favored : 96.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.34 % Twisted General : 0.45 % 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: -4.61 (0.15), residues: 2120 helix: -2.79 (0.13), residues: 855 sheet: -2.52 (0.30), residues: 229 loop : -3.45 (0.16), residues: 1036 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.037 0.005 TRP D 563 HIS 0.020 0.003 HIS B 319 PHE 0.025 0.004 PHE A 467 TYR 0.039 0.004 TYR D 289 ARG 0.020 0.001 ARG D 374 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4240 Ramachandran restraints generated. 2120 Oldfield, 0 Emsley, 2120 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4240 Ramachandran restraints generated. 2120 Oldfield, 0 Emsley, 2120 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 411 residues out of total 1772 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 405 time to evaluate : 1.925 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 258 MET cc_start: 0.6708 (mtt) cc_final: 0.6261 (mtt) REVERT: A 353 LEU cc_start: 0.7996 (mt) cc_final: 0.7777 (mt) REVERT: A 366 ARG cc_start: 0.8425 (mpt-90) cc_final: 0.8173 (mtt90) REVERT: A 425 ASP cc_start: 0.8147 (p0) cc_final: 0.7810 (p0) REVERT: A 745 GLU cc_start: 0.8168 (mt-10) cc_final: 0.6994 (tm-30) REVERT: B 378 ARG cc_start: 0.7734 (mtp180) cc_final: 0.7462 (mtm180) REVERT: B 380 SER cc_start: 0.8767 (t) cc_final: 0.8554 (t) REVERT: B 387 GLU cc_start: 0.8148 (mt-10) cc_final: 0.7275 (pp20) REVERT: B 422 ASP cc_start: 0.8193 (m-30) cc_final: 0.7571 (m-30) REVERT: B 484 ARG cc_start: 0.6506 (mmt180) cc_final: 0.6301 (mtp85) REVERT: B 698 MET cc_start: 0.7082 (mmt) cc_final: 0.6754 (tpp) REVERT: B 733 ILE cc_start: 0.8943 (mp) cc_final: 0.8731 (mm) REVERT: B 748 LYS cc_start: 0.8055 (ptmm) cc_final: 0.7712 (ptmm) REVERT: C 258 MET cc_start: 0.3766 (mmt) cc_final: 0.2426 (mmt) REVERT: C 405 LEU cc_start: 0.8972 (mt) cc_final: 0.8746 (mm) REVERT: D 276 MET cc_start: 0.5103 (mmt) cc_final: 0.4815 (ptt) REVERT: D 328 ARG cc_start: 0.8262 (mpt180) cc_final: 0.7930 (mmt-90) REVERT: D 331 GLU cc_start: 0.7953 (mt-10) cc_final: 0.7720 (mt-10) REVERT: D 385 ARG cc_start: 0.7032 (ppt-90) cc_final: 0.6224 (mmt-90) REVERT: D 439 MET cc_start: 0.8007 (tpt) cc_final: 0.7726 (tmm) REVERT: D 584 ARG cc_start: 0.7936 (mtp-110) cc_final: 0.7536 (mtm110) REVERT: D 659 ASN cc_start: 0.8421 (m-40) cc_final: 0.7805 (p0) REVERT: D 698 MET cc_start: 0.5322 (mmm) cc_final: 0.4716 (mmm) REVERT: D 705 GLU cc_start: 0.6497 (mt-10) cc_final: 0.6220 (mt-10) REVERT: D 719 LYS cc_start: 0.6900 (tttt) cc_final: 0.6482 (ttpt) outliers start: 6 outliers final: 3 residues processed: 410 average time/residue: 0.3843 time to fit residues: 215.8681 Evaluate side-chains 239 residues out of total 1772 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 236 time to evaluate : 1.874 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 333 LEU Chi-restraints excluded: chain B residue 501 ILE Chi-restraints excluded: chain D residue 765 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 212 random chunks: chunk 179 optimal weight: 3.9990 chunk 160 optimal weight: 2.9990 chunk 89 optimal weight: 0.8980 chunk 54 optimal weight: 8.9990 chunk 108 optimal weight: 7.9990 chunk 85 optimal weight: 0.9990 chunk 166 optimal weight: 9.9990 chunk 64 optimal weight: 3.9990 chunk 101 optimal weight: 0.9980 chunk 123 optimal weight: 1.9990 chunk 192 optimal weight: 6.9990 overall best weight: 1.5786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 449 ASN A 472 ASN A 475 GLN A 495 ASN A 598 GLN A 664 HIS B 377 HIS B 449 ASN B 475 GLN B 510 GLN B 726 HIS C 277 GLN C 472 ASN C 726 HIS D 346 ASN ** D 377 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 593 GLN D 628 GLN D 726 HIS Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7215 moved from start: 0.2790 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 16884 Z= 0.241 Angle : 0.804 13.184 22884 Z= 0.408 Chirality : 0.048 0.374 2604 Planarity : 0.007 0.062 2972 Dihedral : 7.256 46.891 2329 Min Nonbonded Distance : 2.501 Molprobity Statistics. All-atom Clashscore : 13.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.01 % Favored : 90.99 % Rotamer: Outliers : 2.14 % Allowed : 10.89 % Favored : 86.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.78 % Twisted General : 0.10 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.33 (0.16), residues: 2120 helix: -1.35 (0.16), residues: 862 sheet: -1.97 (0.31), residues: 213 loop : -3.07 (0.17), residues: 1045 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.002 TRP A 563 HIS 0.006 0.001 HIS B 319 PHE 0.015 0.002 PHE A 466 TYR 0.021 0.002 TYR B 768 ARG 0.009 0.001 ARG B 503 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4240 Ramachandran restraints generated. 2120 Oldfield, 0 Emsley, 2120 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4240 Ramachandran restraints generated. 2120 Oldfield, 0 Emsley, 2120 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 320 residues out of total 1772 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 282 time to evaluate : 2.008 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 258 MET cc_start: 0.6427 (mtt) cc_final: 0.6188 (mtt) REVERT: A 378 ARG cc_start: 0.8094 (ttp80) cc_final: 0.7695 (mtp180) REVERT: A 407 HIS cc_start: 0.8719 (m-70) cc_final: 0.7954 (m-70) REVERT: A 422 ASP cc_start: 0.7621 (m-30) cc_final: 0.5714 (m-30) REVERT: A 702 MET cc_start: 0.6906 (ptt) cc_final: 0.6053 (ptt) REVERT: A 703 THR cc_start: 0.6183 (t) cc_final: 0.5786 (m) REVERT: B 378 ARG cc_start: 0.7671 (mtp180) cc_final: 0.7412 (mtp180) REVERT: B 422 ASP cc_start: 0.7873 (m-30) cc_final: 0.7083 (m-30) REVERT: B 673 PRO cc_start: 0.7648 (Cg_exo) cc_final: 0.7423 (Cg_endo) REVERT: B 733 ILE cc_start: 0.8979 (mp) cc_final: 0.8565 (mm) REVERT: C 258 MET cc_start: 0.4422 (mmt) cc_final: 0.3171 (mmt) REVERT: C 401 MET cc_start: 0.7780 (tpp) cc_final: 0.6629 (pmm) REVERT: C 409 MET cc_start: 0.5837 (mmm) cc_final: 0.5566 (mmm) REVERT: C 425 ASP cc_start: 0.7643 (p0) cc_final: 0.6831 (p0) REVERT: C 726 HIS cc_start: 0.8013 (OUTLIER) cc_final: 0.7506 (t70) REVERT: D 258 MET cc_start: 0.2375 (mtt) cc_final: 0.1708 (mtt) REVERT: D 328 ARG cc_start: 0.8130 (mpt180) cc_final: 0.7859 (mmt-90) REVERT: D 331 GLU cc_start: 0.7916 (mt-10) cc_final: 0.7573 (mt-10) REVERT: D 385 ARG cc_start: 0.7096 (ppt-90) cc_final: 0.6263 (mmt-90) REVERT: D 553 LYS cc_start: 0.6758 (mttt) cc_final: 0.6469 (mtmt) REVERT: D 557 PHE cc_start: 0.8553 (m-80) cc_final: 0.8112 (m-80) REVERT: D 578 LEU cc_start: 0.7757 (tt) cc_final: 0.7445 (tt) REVERT: D 705 GLU cc_start: 0.6850 (mt-10) cc_final: 0.6093 (pt0) REVERT: D 713 MET cc_start: 0.7895 (mmm) cc_final: 0.7210 (mmm) outliers start: 38 outliers final: 19 residues processed: 305 average time/residue: 0.3501 time to fit residues: 151.6398 Evaluate side-chains 226 residues out of total 1772 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 206 time to evaluate : 1.912 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 290 LEU Chi-restraints excluded: chain A residue 310 HIS Chi-restraints excluded: chain A residue 389 GLU Chi-restraints excluded: chain A residue 678 SER Chi-restraints excluded: chain B residue 333 LEU Chi-restraints excluded: chain B residue 364 LEU Chi-restraints excluded: chain B residue 393 HIS Chi-restraints excluded: chain B residue 528 LEU Chi-restraints excluded: chain B residue 611 THR Chi-restraints excluded: chain B residue 658 TYR Chi-restraints excluded: chain C residue 305 VAL Chi-restraints excluded: chain C residue 342 LEU Chi-restraints excluded: chain C residue 344 VAL Chi-restraints excluded: chain C residue 572 SER Chi-restraints excluded: chain C residue 580 ILE Chi-restraints excluded: chain C residue 699 ASP Chi-restraints excluded: chain C residue 726 HIS Chi-restraints excluded: chain D residue 354 VAL Chi-restraints excluded: chain D residue 735 LEU Chi-restraints excluded: chain D residue 765 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 212 random chunks: chunk 106 optimal weight: 30.0000 chunk 59 optimal weight: 3.9990 chunk 160 optimal weight: 0.6980 chunk 131 optimal weight: 0.9980 chunk 53 optimal weight: 20.0000 chunk 192 optimal weight: 0.0770 chunk 208 optimal weight: 10.0000 chunk 171 optimal weight: 7.9990 chunk 191 optimal weight: 5.9990 chunk 65 optimal weight: 0.9990 chunk 154 optimal weight: 1.9990 overall best weight: 0.9542 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 726 HIS D 319 HIS D 377 HIS ** D 727 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7179 moved from start: 0.3466 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 16884 Z= 0.189 Angle : 0.718 10.705 22884 Z= 0.363 Chirality : 0.046 0.181 2604 Planarity : 0.006 0.067 2972 Dihedral : 6.467 44.742 2327 Min Nonbonded Distance : 2.420 Molprobity Statistics. All-atom Clashscore : 12.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.68 % Favored : 91.32 % Rotamer: Outliers : 2.31 % Allowed : 13.43 % Favored : 84.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.78 % Twisted General : 0.05 % 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: -2.58 (0.17), residues: 2120 helix: -0.58 (0.17), residues: 857 sheet: -1.82 (0.29), residues: 249 loop : -2.74 (0.18), residues: 1014 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP C 298 HIS 0.010 0.001 HIS C 726 PHE 0.016 0.001 PHE D 466 TYR 0.015 0.001 TYR D 534 ARG 0.007 0.000 ARG B 391 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4240 Ramachandran restraints generated. 2120 Oldfield, 0 Emsley, 2120 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4240 Ramachandran restraints generated. 2120 Oldfield, 0 Emsley, 2120 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 286 residues out of total 1772 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 245 time to evaluate : 1.802 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 258 MET cc_start: 0.6216 (mtt) cc_final: 0.5999 (mtt) REVERT: A 401 MET cc_start: 0.7618 (tmm) cc_final: 0.7395 (tmm) REVERT: A 407 HIS cc_start: 0.8883 (m-70) cc_final: 0.8355 (m-70) REVERT: A 422 ASP cc_start: 0.7328 (m-30) cc_final: 0.5766 (m-30) REVERT: A 427 MET cc_start: 0.2529 (mpp) cc_final: 0.2325 (mpp) REVERT: A 702 MET cc_start: 0.6902 (ptt) cc_final: 0.6228 (ptt) REVERT: A 703 THR cc_start: 0.5898 (t) cc_final: 0.5608 (m) REVERT: B 673 PRO cc_start: 0.7618 (Cg_exo) cc_final: 0.7367 (Cg_endo) REVERT: B 698 MET cc_start: 0.6720 (tpp) cc_final: 0.6507 (mmt) REVERT: B 733 ILE cc_start: 0.8923 (mp) cc_final: 0.8666 (mm) REVERT: C 258 MET cc_start: 0.4215 (mmt) cc_final: 0.3009 (mmt) REVERT: C 401 MET cc_start: 0.7009 (tpp) cc_final: 0.6479 (pmm) REVERT: C 409 MET cc_start: 0.5577 (mmm) cc_final: 0.5245 (mmm) REVERT: C 425 ASP cc_start: 0.7518 (p0) cc_final: 0.6764 (p0) REVERT: D 368 ILE cc_start: 0.9426 (mt) cc_final: 0.9090 (mt) REVERT: D 385 ARG cc_start: 0.7218 (ppt-90) cc_final: 0.6379 (mmt-90) REVERT: D 557 PHE cc_start: 0.8603 (m-80) cc_final: 0.8135 (m-80) REVERT: D 578 LEU cc_start: 0.7677 (tt) cc_final: 0.7458 (tt) REVERT: D 705 GLU cc_start: 0.6679 (mt-10) cc_final: 0.6104 (pt0) REVERT: D 713 MET cc_start: 0.7900 (mmm) cc_final: 0.7033 (mmm) REVERT: D 719 LYS cc_start: 0.6909 (ttpt) cc_final: 0.6646 (tttt) outliers start: 41 outliers final: 24 residues processed: 268 average time/residue: 0.3249 time to fit residues: 127.7457 Evaluate side-chains 234 residues out of total 1772 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 210 time to evaluate : 1.842 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 290 LEU Chi-restraints excluded: chain A residue 310 HIS Chi-restraints excluded: chain A residue 389 GLU Chi-restraints excluded: chain A residue 617 VAL Chi-restraints excluded: chain B residue 333 LEU Chi-restraints excluded: chain B residue 364 LEU Chi-restraints excluded: chain B residue 393 HIS Chi-restraints excluded: chain B residue 528 LEU Chi-restraints excluded: chain B residue 611 THR Chi-restraints excluded: chain B residue 658 TYR Chi-restraints excluded: chain B residue 771 LEU Chi-restraints excluded: chain C residue 305 VAL Chi-restraints excluded: chain C residue 342 LEU Chi-restraints excluded: chain C residue 468 ILE Chi-restraints excluded: chain C residue 580 ILE Chi-restraints excluded: chain C residue 681 ILE Chi-restraints excluded: chain D residue 262 VAL Chi-restraints excluded: chain D residue 353 LEU Chi-restraints excluded: chain D residue 354 VAL Chi-restraints excluded: chain D residue 401 MET Chi-restraints excluded: chain D residue 682 THR Chi-restraints excluded: chain D residue 702 MET Chi-restraints excluded: chain D residue 735 LEU Chi-restraints excluded: chain D residue 765 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 212 random chunks: chunk 190 optimal weight: 1.9990 chunk 145 optimal weight: 0.9990 chunk 100 optimal weight: 5.9990 chunk 21 optimal weight: 6.9990 chunk 92 optimal weight: 2.9990 chunk 129 optimal weight: 0.9990 chunk 193 optimal weight: 0.2980 chunk 204 optimal weight: 6.9990 chunk 101 optimal weight: 0.9980 chunk 183 optimal weight: 8.9990 chunk 55 optimal weight: 8.9990 overall best weight: 1.0586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 664 HIS D 340 GLN ** D 598 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 664 HIS D 727 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7170 moved from start: 0.3883 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 16884 Z= 0.183 Angle : 0.686 9.537 22884 Z= 0.346 Chirality : 0.045 0.198 2604 Planarity : 0.005 0.060 2972 Dihedral : 6.056 45.377 2327 Min Nonbonded Distance : 2.442 Molprobity Statistics. All-atom Clashscore : 12.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.25 % Favored : 91.75 % Rotamer: Outliers : 3.10 % Allowed : 14.45 % Favored : 82.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.78 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.10 (0.18), residues: 2120 helix: -0.12 (0.18), residues: 855 sheet: -1.57 (0.31), residues: 243 loop : -2.52 (0.19), residues: 1022 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP B 298 HIS 0.004 0.001 HIS B 319 PHE 0.019 0.001 PHE D 466 TYR 0.013 0.001 TYR C 505 ARG 0.005 0.000 ARG B 391 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4240 Ramachandran restraints generated. 2120 Oldfield, 0 Emsley, 2120 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4240 Ramachandran restraints generated. 2120 Oldfield, 0 Emsley, 2120 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 293 residues out of total 1772 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 238 time to evaluate : 1.869 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 258 MET cc_start: 0.6289 (mtt) cc_final: 0.6059 (mtt) REVERT: A 378 ARG cc_start: 0.8064 (mtp180) cc_final: 0.7734 (mmm-85) REVERT: A 420 LEU cc_start: 0.8600 (tp) cc_final: 0.8348 (tp) REVERT: A 422 ASP cc_start: 0.6721 (m-30) cc_final: 0.6436 (m-30) REVERT: A 427 MET cc_start: 0.2583 (mpp) cc_final: 0.2300 (mpp) REVERT: A 702 MET cc_start: 0.6836 (ptt) cc_final: 0.5991 (ptt) REVERT: A 703 THR cc_start: 0.5981 (t) cc_final: 0.5737 (m) REVERT: B 401 MET cc_start: 0.5879 (mmp) cc_final: 0.5117 (mmm) REVERT: B 504 GLN cc_start: 0.7705 (OUTLIER) cc_final: 0.7172 (mp10) REVERT: C 258 MET cc_start: 0.4132 (mmt) cc_final: 0.2833 (mmt) REVERT: C 401 MET cc_start: 0.6835 (tpp) cc_final: 0.6437 (pmm) REVERT: C 409 MET cc_start: 0.5484 (mmm) cc_final: 0.5187 (mmm) REVERT: C 425 ASP cc_start: 0.7368 (p0) cc_final: 0.6635 (p0) REVERT: C 531 ILE cc_start: 0.8533 (OUTLIER) cc_final: 0.8192 (pt) REVERT: D 385 ARG cc_start: 0.7268 (ppt-90) cc_final: 0.6425 (mmt90) REVERT: D 557 PHE cc_start: 0.8518 (m-80) cc_final: 0.8197 (m-80) REVERT: D 657 PHE cc_start: 0.7488 (p90) cc_final: 0.7169 (p90) REVERT: D 698 MET cc_start: 0.3643 (tpt) cc_final: 0.3293 (tpp) REVERT: D 705 GLU cc_start: 0.6643 (mt-10) cc_final: 0.6047 (pt0) outliers start: 55 outliers final: 34 residues processed: 273 average time/residue: 0.3247 time to fit residues: 130.5842 Evaluate side-chains 245 residues out of total 1772 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 209 time to evaluate : 1.998 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 290 LEU Chi-restraints excluded: chain A residue 310 HIS Chi-restraints excluded: chain A residue 380 SER Chi-restraints excluded: chain A residue 389 GLU Chi-restraints excluded: chain A residue 453 ASP Chi-restraints excluded: chain A residue 470 THR Chi-restraints excluded: chain A residue 678 SER Chi-restraints excluded: chain B residue 333 LEU Chi-restraints excluded: chain B residue 364 LEU Chi-restraints excluded: chain B residue 393 HIS Chi-restraints excluded: chain B residue 504 GLN Chi-restraints excluded: chain B residue 528 LEU Chi-restraints excluded: chain B residue 580 ILE Chi-restraints excluded: chain B residue 590 THR Chi-restraints excluded: chain B residue 611 THR Chi-restraints excluded: chain B residue 624 SER Chi-restraints excluded: chain B residue 658 TYR Chi-restraints excluded: chain B residue 691 LEU Chi-restraints excluded: chain B residue 771 LEU Chi-restraints excluded: chain C residue 305 VAL Chi-restraints excluded: chain C residue 342 LEU Chi-restraints excluded: chain C residue 468 ILE Chi-restraints excluded: chain C residue 520 ILE Chi-restraints excluded: chain C residue 531 ILE Chi-restraints excluded: chain C residue 572 SER Chi-restraints excluded: chain C residue 580 ILE Chi-restraints excluded: chain C residue 632 VAL Chi-restraints excluded: chain C residue 681 ILE Chi-restraints excluded: chain D residue 353 LEU Chi-restraints excluded: chain D residue 354 VAL Chi-restraints excluded: chain D residue 401 MET Chi-restraints excluded: chain D residue 663 LEU Chi-restraints excluded: chain D residue 681 ILE Chi-restraints excluded: chain D residue 702 MET Chi-restraints excluded: chain D residue 735 LEU Chi-restraints excluded: chain D residue 765 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 212 random chunks: chunk 170 optimal weight: 0.7980 chunk 116 optimal weight: 0.8980 chunk 2 optimal weight: 0.5980 chunk 152 optimal weight: 0.9990 chunk 84 optimal weight: 3.9990 chunk 174 optimal weight: 0.6980 chunk 141 optimal weight: 5.9990 chunk 0 optimal weight: 20.0000 chunk 104 optimal weight: 7.9990 chunk 183 optimal weight: 4.9990 chunk 51 optimal weight: 0.7980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 337 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 499 GLN ** D 598 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7142 moved from start: 0.4216 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 16884 Z= 0.169 Angle : 0.677 9.700 22884 Z= 0.336 Chirality : 0.044 0.215 2604 Planarity : 0.005 0.058 2972 Dihedral : 5.708 47.120 2327 Min Nonbonded Distance : 2.436 Molprobity Statistics. All-atom Clashscore : 11.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.31 % Favored : 92.69 % Rotamer: Outliers : 2.99 % Allowed : 16.08 % Favored : 80.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.78 % Twisted General : 0.05 % 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: -1.74 (0.18), residues: 2120 helix: 0.17 (0.18), residues: 864 sheet: -1.19 (0.32), residues: 235 loop : -2.39 (0.19), residues: 1021 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP C 298 HIS 0.007 0.001 HIS D 647 PHE 0.010 0.001 PHE D 466 TYR 0.023 0.001 TYR C 768 ARG 0.006 0.000 ARG C 484 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4240 Ramachandran restraints generated. 2120 Oldfield, 0 Emsley, 2120 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4240 Ramachandran restraints generated. 2120 Oldfield, 0 Emsley, 2120 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 285 residues out of total 1772 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 232 time to evaluate : 1.993 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 258 MET cc_start: 0.6169 (mtt) cc_final: 0.5592 (mmm) REVERT: A 353 LEU cc_start: 0.7602 (OUTLIER) cc_final: 0.7360 (mm) REVERT: A 366 ARG cc_start: 0.8400 (mpt90) cc_final: 0.8138 (mtt90) REVERT: A 372 MET cc_start: 0.7065 (tpp) cc_final: 0.6471 (ttm) REVERT: A 378 ARG cc_start: 0.8157 (mtp180) cc_final: 0.7739 (mmm-85) REVERT: A 401 MET cc_start: 0.7519 (tpp) cc_final: 0.6349 (pmm) REVERT: A 420 LEU cc_start: 0.8582 (tp) cc_final: 0.8318 (tp) REVERT: A 635 GLU cc_start: 0.9453 (OUTLIER) cc_final: 0.9094 (mp0) REVERT: A 657 PHE cc_start: 0.6955 (p90) cc_final: 0.6740 (p90) REVERT: A 702 MET cc_start: 0.6717 (ptt) cc_final: 0.6071 (ptp) REVERT: A 703 THR cc_start: 0.6004 (t) cc_final: 0.5789 (m) REVERT: B 401 MET cc_start: 0.5742 (mmp) cc_final: 0.5384 (mmm) REVERT: B 504 GLN cc_start: 0.7688 (OUTLIER) cc_final: 0.7187 (mp10) REVERT: C 258 MET cc_start: 0.4201 (mmt) cc_final: 0.2933 (mmt) REVERT: C 401 MET cc_start: 0.6750 (tpp) cc_final: 0.6462 (pmm) REVERT: C 409 MET cc_start: 0.5419 (mmm) cc_final: 0.5168 (mmm) REVERT: C 425 ASP cc_start: 0.7468 (p0) cc_final: 0.6774 (p0) REVERT: D 385 ARG cc_start: 0.7251 (ppt-90) cc_final: 0.6425 (mmt90) REVERT: D 427 MET cc_start: 0.7383 (ptm) cc_final: 0.7164 (ptp) REVERT: D 485 MET cc_start: 0.7584 (mmp) cc_final: 0.7211 (mmm) REVERT: D 557 PHE cc_start: 0.8545 (m-80) cc_final: 0.8226 (m-80) REVERT: D 657 PHE cc_start: 0.7352 (p90) cc_final: 0.7032 (p90) REVERT: D 698 MET cc_start: 0.3433 (tpt) cc_final: 0.3033 (tpp) REVERT: D 705 GLU cc_start: 0.6617 (mt-10) cc_final: 0.6055 (pt0) outliers start: 53 outliers final: 32 residues processed: 267 average time/residue: 0.3108 time to fit residues: 123.4119 Evaluate side-chains 244 residues out of total 1772 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 209 time to evaluate : 1.829 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 310 HIS Chi-restraints excluded: chain A residue 353 LEU Chi-restraints excluded: chain A residue 380 SER Chi-restraints excluded: chain A residue 389 GLU Chi-restraints excluded: chain A residue 453 ASP Chi-restraints excluded: chain A residue 617 VAL Chi-restraints excluded: chain A residue 635 GLU Chi-restraints excluded: chain A residue 769 LEU Chi-restraints excluded: chain B residue 333 LEU Chi-restraints excluded: chain B residue 393 HIS Chi-restraints excluded: chain B residue 504 GLN Chi-restraints excluded: chain B residue 580 ILE Chi-restraints excluded: chain B residue 590 THR Chi-restraints excluded: chain B residue 611 THR Chi-restraints excluded: chain B residue 624 SER Chi-restraints excluded: chain B residue 658 TYR Chi-restraints excluded: chain B residue 678 SER Chi-restraints excluded: chain C residue 285 VAL Chi-restraints excluded: chain C residue 305 VAL Chi-restraints excluded: chain C residue 468 ILE Chi-restraints excluded: chain C residue 572 SER Chi-restraints excluded: chain C residue 580 ILE Chi-restraints excluded: chain C residue 624 SER Chi-restraints excluded: chain C residue 632 VAL Chi-restraints excluded: chain C residue 642 THR Chi-restraints excluded: chain C residue 681 ILE Chi-restraints excluded: chain C residue 702 MET Chi-restraints excluded: chain D residue 353 LEU Chi-restraints excluded: chain D residue 354 VAL Chi-restraints excluded: chain D residue 378 ARG Chi-restraints excluded: chain D residue 401 MET Chi-restraints excluded: chain D residue 682 THR Chi-restraints excluded: chain D residue 735 LEU Chi-restraints excluded: chain D residue 759 VAL Chi-restraints excluded: chain D residue 765 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 212 random chunks: chunk 68 optimal weight: 1.9990 chunk 184 optimal weight: 3.9990 chunk 40 optimal weight: 0.7980 chunk 120 optimal weight: 10.0000 chunk 50 optimal weight: 10.0000 chunk 205 optimal weight: 2.9990 chunk 170 optimal weight: 5.9990 chunk 94 optimal weight: 0.9990 chunk 17 optimal weight: 9.9990 chunk 67 optimal weight: 6.9990 chunk 107 optimal weight: 9.9990 overall best weight: 2.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 337 GLN C 407 HIS D 499 GLN D 593 GLN D 598 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7229 moved from start: 0.4277 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 16884 Z= 0.244 Angle : 0.710 9.149 22884 Z= 0.353 Chirality : 0.045 0.223 2604 Planarity : 0.005 0.058 2972 Dihedral : 5.750 48.910 2327 Min Nonbonded Distance : 2.429 Molprobity Statistics. All-atom Clashscore : 13.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.68 % Favored : 91.32 % Rotamer: Outliers : 3.16 % Allowed : 16.08 % Favored : 80.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.78 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.78 (0.18), residues: 2120 helix: 0.17 (0.18), residues: 867 sheet: -1.51 (0.32), residues: 240 loop : -2.37 (0.19), residues: 1013 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP D 563 HIS 0.007 0.001 HIS B 319 PHE 0.012 0.002 PHE A 466 TYR 0.017 0.002 TYR D 643 ARG 0.006 0.000 ARG D 584 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4240 Ramachandran restraints generated. 2120 Oldfield, 0 Emsley, 2120 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4240 Ramachandran restraints generated. 2120 Oldfield, 0 Emsley, 2120 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 269 residues out of total 1772 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 213 time to evaluate : 1.969 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: A 353 LEU cc_start: 0.7590 (OUTLIER) cc_final: 0.7350 (mm) REVERT: A 366 ARG cc_start: 0.8367 (mpt90) cc_final: 0.8162 (mpt90) REVERT: A 372 MET cc_start: 0.7314 (tpp) cc_final: 0.6483 (ttm) REVERT: A 378 ARG cc_start: 0.8198 (mtp180) cc_final: 0.7836 (mmm-85) REVERT: A 420 LEU cc_start: 0.8556 (tp) cc_final: 0.8304 (tp) REVERT: A 422 ASP cc_start: 0.7460 (m-30) cc_final: 0.6864 (m-30) REVERT: A 485 MET cc_start: 0.7868 (mmm) cc_final: 0.7561 (mmt) REVERT: A 513 GLU cc_start: 0.7757 (pt0) cc_final: 0.7507 (pt0) REVERT: A 632 VAL cc_start: 0.6301 (OUTLIER) cc_final: 0.6090 (p) REVERT: A 635 GLU cc_start: 0.9522 (OUTLIER) cc_final: 0.9193 (mp0) REVERT: A 702 MET cc_start: 0.6864 (ptt) cc_final: 0.5921 (ptt) REVERT: A 703 THR cc_start: 0.6107 (t) cc_final: 0.5782 (m) REVERT: B 401 MET cc_start: 0.5843 (mmp) cc_final: 0.5401 (mmm) REVERT: B 504 GLN cc_start: 0.7743 (OUTLIER) cc_final: 0.7171 (mp10) REVERT: B 691 LEU cc_start: 0.9191 (OUTLIER) cc_final: 0.8881 (tt) REVERT: C 258 MET cc_start: 0.4283 (mmt) cc_final: 0.3015 (mmt) REVERT: C 401 MET cc_start: 0.6731 (tpp) cc_final: 0.6429 (pmm) REVERT: C 405 LEU cc_start: 0.9077 (mm) cc_final: 0.8725 (mm) REVERT: C 409 MET cc_start: 0.5587 (mmm) cc_final: 0.5367 (mmm) REVERT: C 425 ASP cc_start: 0.7520 (p0) cc_final: 0.6893 (p0) REVERT: D 385 ARG cc_start: 0.7208 (ppt-90) cc_final: 0.6377 (mmt90) REVERT: D 427 MET cc_start: 0.7350 (ptm) cc_final: 0.7085 (ptp) REVERT: D 557 PHE cc_start: 0.8571 (m-80) cc_final: 0.8244 (m-80) REVERT: D 705 GLU cc_start: 0.6669 (mt-10) cc_final: 0.6107 (pt0) outliers start: 56 outliers final: 38 residues processed: 253 average time/residue: 0.2901 time to fit residues: 110.7184 Evaluate side-chains 241 residues out of total 1772 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 198 time to evaluate : 2.029 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 310 HIS Chi-restraints excluded: chain A residue 353 LEU Chi-restraints excluded: chain A residue 380 SER Chi-restraints excluded: chain A residue 389 GLU Chi-restraints excluded: chain A residue 453 ASP Chi-restraints excluded: chain A residue 470 THR Chi-restraints excluded: chain A residue 617 VAL Chi-restraints excluded: chain A residue 632 VAL Chi-restraints excluded: chain A residue 635 GLU Chi-restraints excluded: chain A residue 762 VAL Chi-restraints excluded: chain A residue 769 LEU Chi-restraints excluded: chain B residue 325 VAL Chi-restraints excluded: chain B residue 333 LEU Chi-restraints excluded: chain B residue 364 LEU Chi-restraints excluded: chain B residue 393 HIS Chi-restraints excluded: chain B residue 504 GLN Chi-restraints excluded: chain B residue 514 SER Chi-restraints excluded: chain B residue 528 LEU Chi-restraints excluded: chain B residue 580 ILE Chi-restraints excluded: chain B residue 590 THR Chi-restraints excluded: chain B residue 611 THR Chi-restraints excluded: chain B residue 624 SER Chi-restraints excluded: chain B residue 658 TYR Chi-restraints excluded: chain B residue 691 LEU Chi-restraints excluded: chain C residue 305 VAL Chi-restraints excluded: chain C residue 469 THR Chi-restraints excluded: chain C residue 520 ILE Chi-restraints excluded: chain C residue 572 SER Chi-restraints excluded: chain C residue 574 ILE Chi-restraints excluded: chain C residue 580 ILE Chi-restraints excluded: chain C residue 623 LEU Chi-restraints excluded: chain C residue 624 SER Chi-restraints excluded: chain C residue 632 VAL Chi-restraints excluded: chain C residue 681 ILE Chi-restraints excluded: chain C residue 702 MET Chi-restraints excluded: chain C residue 759 VAL Chi-restraints excluded: chain D residue 353 LEU Chi-restraints excluded: chain D residue 354 VAL Chi-restraints excluded: chain D residue 378 ARG Chi-restraints excluded: chain D residue 401 MET Chi-restraints excluded: chain D residue 682 THR Chi-restraints excluded: chain D residue 735 LEU Chi-restraints excluded: chain D residue 765 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 212 random chunks: chunk 197 optimal weight: 0.0870 chunk 23 optimal weight: 3.9990 chunk 116 optimal weight: 0.0030 chunk 149 optimal weight: 5.9990 chunk 172 optimal weight: 0.8980 chunk 114 optimal weight: 0.9990 chunk 204 optimal weight: 0.9990 chunk 127 optimal weight: 0.9990 chunk 124 optimal weight: 3.9990 chunk 94 optimal weight: 4.9990 chunk 126 optimal weight: 0.7980 overall best weight: 0.5570 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 337 GLN D 499 GLN ** D 727 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7134 moved from start: 0.4603 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 16884 Z= 0.170 Angle : 0.677 10.114 22884 Z= 0.333 Chirality : 0.044 0.229 2604 Planarity : 0.005 0.055 2972 Dihedral : 5.465 49.735 2327 Min Nonbonded Distance : 2.422 Molprobity Statistics. All-atom Clashscore : 11.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.70 % Favored : 93.30 % Rotamer: Outliers : 2.60 % Allowed : 16.70 % Favored : 80.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.78 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.38 (0.19), residues: 2120 helix: 0.51 (0.18), residues: 864 sheet: -1.15 (0.31), residues: 272 loop : -2.21 (0.20), residues: 984 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP B 298 HIS 0.003 0.001 HIS C 726 PHE 0.013 0.001 PHE D 466 TYR 0.014 0.001 TYR D 643 ARG 0.009 0.000 ARG D 584 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4240 Ramachandran restraints generated. 2120 Oldfield, 0 Emsley, 2120 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4240 Ramachandran restraints generated. 2120 Oldfield, 0 Emsley, 2120 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 274 residues out of total 1772 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 228 time to evaluate : 1.877 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 353 LEU cc_start: 0.7541 (OUTLIER) cc_final: 0.7297 (mm) REVERT: A 372 MET cc_start: 0.7306 (tpp) cc_final: 0.6565 (ttm) REVERT: A 378 ARG cc_start: 0.8173 (mtp180) cc_final: 0.7892 (mmm-85) REVERT: A 401 MET cc_start: 0.7524 (tpp) cc_final: 0.6180 (pmm) REVERT: A 420 LEU cc_start: 0.8582 (tp) cc_final: 0.8293 (tp) REVERT: A 422 ASP cc_start: 0.7473 (m-30) cc_final: 0.6658 (m-30) REVERT: A 427 MET cc_start: 0.2090 (mpp) cc_final: 0.1877 (mmm) REVERT: A 482 LEU cc_start: 0.8219 (OUTLIER) cc_final: 0.7722 (mm) REVERT: A 485 MET cc_start: 0.7981 (mmm) cc_final: 0.7732 (mmt) REVERT: A 635 GLU cc_start: 0.9501 (OUTLIER) cc_final: 0.9178 (mp0) REVERT: A 702 MET cc_start: 0.6681 (ptt) cc_final: 0.6363 (ptp) REVERT: A 703 THR cc_start: 0.5963 (t) cc_final: 0.5753 (m) REVERT: A 713 MET cc_start: 0.8801 (mmm) cc_final: 0.7963 (mpp) REVERT: B 504 GLN cc_start: 0.7652 (OUTLIER) cc_final: 0.7122 (mp10) REVERT: C 258 MET cc_start: 0.4382 (mmt) cc_final: 0.3054 (mmt) REVERT: C 401 MET cc_start: 0.6822 (tpp) cc_final: 0.6522 (pmm) REVERT: C 405 LEU cc_start: 0.9083 (mm) cc_final: 0.8726 (mm) REVERT: C 425 ASP cc_start: 0.7433 (p0) cc_final: 0.6801 (p0) REVERT: D 557 PHE cc_start: 0.8585 (m-80) cc_final: 0.8263 (m-80) REVERT: D 657 PHE cc_start: 0.7276 (p90) cc_final: 0.6956 (p90) REVERT: D 698 MET cc_start: 0.3449 (tpt) cc_final: 0.2990 (tpp) REVERT: D 705 GLU cc_start: 0.6551 (mt-10) cc_final: 0.6033 (pt0) REVERT: D 713 MET cc_start: 0.8071 (mmm) cc_final: 0.7226 (mmm) outliers start: 46 outliers final: 29 residues processed: 260 average time/residue: 0.3073 time to fit residues: 118.7625 Evaluate side-chains 244 residues out of total 1772 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 211 time to evaluate : 1.948 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 310 HIS Chi-restraints excluded: chain A residue 353 LEU Chi-restraints excluded: chain A residue 453 ASP Chi-restraints excluded: chain A residue 470 THR Chi-restraints excluded: chain A residue 482 LEU Chi-restraints excluded: chain A residue 635 GLU Chi-restraints excluded: chain B residue 333 LEU Chi-restraints excluded: chain B residue 393 HIS Chi-restraints excluded: chain B residue 504 GLN Chi-restraints excluded: chain B residue 580 ILE Chi-restraints excluded: chain B residue 590 THR Chi-restraints excluded: chain B residue 624 SER Chi-restraints excluded: chain B residue 658 TYR Chi-restraints excluded: chain B residue 678 SER Chi-restraints excluded: chain C residue 285 VAL Chi-restraints excluded: chain C residue 412 VAL Chi-restraints excluded: chain C residue 414 VAL Chi-restraints excluded: chain C residue 520 ILE Chi-restraints excluded: chain C residue 572 SER Chi-restraints excluded: chain C residue 580 ILE Chi-restraints excluded: chain C residue 624 SER Chi-restraints excluded: chain C residue 632 VAL Chi-restraints excluded: chain C residue 665 VAL Chi-restraints excluded: chain C residue 681 ILE Chi-restraints excluded: chain C residue 702 MET Chi-restraints excluded: chain D residue 353 LEU Chi-restraints excluded: chain D residue 354 VAL Chi-restraints excluded: chain D residue 378 ARG Chi-restraints excluded: chain D residue 401 MET Chi-restraints excluded: chain D residue 682 THR Chi-restraints excluded: chain D residue 735 LEU Chi-restraints excluded: chain D residue 762 VAL Chi-restraints excluded: chain D residue 765 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 212 random chunks: chunk 81 optimal weight: 2.9990 chunk 122 optimal weight: 1.9990 chunk 61 optimal weight: 3.9990 chunk 40 optimal weight: 0.8980 chunk 39 optimal weight: 0.9990 chunk 129 optimal weight: 0.1980 chunk 139 optimal weight: 2.9990 chunk 101 optimal weight: 8.9990 chunk 19 optimal weight: 9.9990 chunk 160 optimal weight: 0.0770 chunk 185 optimal weight: 9.9990 overall best weight: 0.8342 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 447 GLN ** D 727 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7140 moved from start: 0.4810 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 16884 Z= 0.181 Angle : 0.695 10.919 22884 Z= 0.341 Chirality : 0.045 0.316 2604 Planarity : 0.005 0.055 2972 Dihedral : 5.345 50.802 2327 Min Nonbonded Distance : 2.442 Molprobity Statistics. All-atom Clashscore : 12.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.93 % Favored : 93.07 % Rotamer: Outliers : 2.60 % Allowed : 17.44 % Favored : 79.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.78 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.21 (0.19), residues: 2120 helix: 0.69 (0.18), residues: 864 sheet: -0.84 (0.33), residues: 241 loop : -2.19 (0.20), residues: 1015 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP C 298 HIS 0.003 0.001 HIS B 319 PHE 0.013 0.001 PHE D 466 TYR 0.011 0.001 TYR D 289 ARG 0.010 0.000 ARG C 512 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4240 Ramachandran restraints generated. 2120 Oldfield, 0 Emsley, 2120 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4240 Ramachandran restraints generated. 2120 Oldfield, 0 Emsley, 2120 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 270 residues out of total 1772 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 224 time to evaluate : 2.186 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 295 GLU cc_start: 0.8982 (mp0) cc_final: 0.8591 (mp0) REVERT: A 353 LEU cc_start: 0.7502 (OUTLIER) cc_final: 0.7231 (mm) REVERT: A 372 MET cc_start: 0.7361 (tpp) cc_final: 0.6561 (ttm) REVERT: A 378 ARG cc_start: 0.8157 (mtp180) cc_final: 0.7920 (mmm-85) REVERT: A 401 MET cc_start: 0.7631 (tpp) cc_final: 0.6311 (pmm) REVERT: A 420 LEU cc_start: 0.8538 (tp) cc_final: 0.8212 (tp) REVERT: A 422 ASP cc_start: 0.7577 (m-30) cc_final: 0.6721 (m-30) REVERT: A 482 LEU cc_start: 0.8224 (OUTLIER) cc_final: 0.7714 (mm) REVERT: A 485 MET cc_start: 0.7966 (mmm) cc_final: 0.7724 (mmt) REVERT: A 513 GLU cc_start: 0.7562 (pt0) cc_final: 0.7308 (pt0) REVERT: A 635 GLU cc_start: 0.9463 (OUTLIER) cc_final: 0.9245 (mp0) REVERT: A 657 PHE cc_start: 0.6941 (p90) cc_final: 0.6727 (p90) REVERT: A 702 MET cc_start: 0.6897 (ptt) cc_final: 0.6690 (ptm) REVERT: A 703 THR cc_start: 0.5912 (t) cc_final: 0.5698 (m) REVERT: A 713 MET cc_start: 0.8795 (mmm) cc_final: 0.8016 (mpp) REVERT: B 504 GLN cc_start: 0.7666 (OUTLIER) cc_final: 0.7083 (mp10) REVERT: C 258 MET cc_start: 0.4467 (mmt) cc_final: 0.3193 (mmt) REVERT: C 401 MET cc_start: 0.6803 (tpp) cc_final: 0.6536 (pmm) REVERT: C 425 ASP cc_start: 0.7439 (p0) cc_final: 0.6888 (p0) REVERT: D 557 PHE cc_start: 0.8584 (m-80) cc_final: 0.8279 (m-80) REVERT: D 657 PHE cc_start: 0.7249 (p90) cc_final: 0.6971 (p90) REVERT: D 698 MET cc_start: 0.3332 (tpt) cc_final: 0.2882 (tpp) REVERT: D 705 GLU cc_start: 0.6647 (mt-10) cc_final: 0.6063 (pt0) REVERT: D 709 ARG cc_start: 0.8468 (mmm160) cc_final: 0.7783 (tpt170) REVERT: D 713 MET cc_start: 0.8038 (mmm) cc_final: 0.7231 (mmm) outliers start: 46 outliers final: 34 residues processed: 257 average time/residue: 0.3019 time to fit residues: 117.6561 Evaluate side-chains 249 residues out of total 1772 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 211 time to evaluate : 2.079 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 310 HIS Chi-restraints excluded: chain A residue 353 LEU Chi-restraints excluded: chain A residue 380 SER Chi-restraints excluded: chain A residue 453 ASP Chi-restraints excluded: chain A residue 470 THR Chi-restraints excluded: chain A residue 482 LEU Chi-restraints excluded: chain A residue 632 VAL Chi-restraints excluded: chain A residue 635 GLU Chi-restraints excluded: chain B residue 333 LEU Chi-restraints excluded: chain B residue 364 LEU Chi-restraints excluded: chain B residue 482 LEU Chi-restraints excluded: chain B residue 504 GLN Chi-restraints excluded: chain B residue 514 SER Chi-restraints excluded: chain B residue 580 ILE Chi-restraints excluded: chain B residue 590 THR Chi-restraints excluded: chain B residue 658 TYR Chi-restraints excluded: chain B residue 678 SER Chi-restraints excluded: chain B residue 771 LEU Chi-restraints excluded: chain C residue 285 VAL Chi-restraints excluded: chain C residue 308 ILE Chi-restraints excluded: chain C residue 412 VAL Chi-restraints excluded: chain C residue 414 VAL Chi-restraints excluded: chain C residue 520 ILE Chi-restraints excluded: chain C residue 580 ILE Chi-restraints excluded: chain C residue 624 SER Chi-restraints excluded: chain C residue 632 VAL Chi-restraints excluded: chain C residue 642 THR Chi-restraints excluded: chain C residue 665 VAL Chi-restraints excluded: chain C residue 681 ILE Chi-restraints excluded: chain C residue 702 MET Chi-restraints excluded: chain D residue 353 LEU Chi-restraints excluded: chain D residue 354 VAL Chi-restraints excluded: chain D residue 378 ARG Chi-restraints excluded: chain D residue 401 MET Chi-restraints excluded: chain D residue 682 THR Chi-restraints excluded: chain D residue 735 LEU Chi-restraints excluded: chain D residue 762 VAL Chi-restraints excluded: chain D residue 765 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 212 random chunks: chunk 195 optimal weight: 7.9990 chunk 178 optimal weight: 6.9990 chunk 190 optimal weight: 0.0470 chunk 114 optimal weight: 0.9980 chunk 82 optimal weight: 10.0000 chunk 149 optimal weight: 1.9990 chunk 58 optimal weight: 3.9990 chunk 172 optimal weight: 9.9990 chunk 180 optimal weight: 0.0870 chunk 189 optimal weight: 0.9990 chunk 125 optimal weight: 5.9990 overall best weight: 0.8260 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 727 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7127 moved from start: 0.4976 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 16884 Z= 0.178 Angle : 0.703 12.874 22884 Z= 0.344 Chirality : 0.044 0.248 2604 Planarity : 0.005 0.055 2972 Dihedral : 5.273 51.497 2327 Min Nonbonded Distance : 2.468 Molprobity Statistics. All-atom Clashscore : 11.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.79 % Favored : 93.21 % Rotamer: Outliers : 2.43 % Allowed : 17.78 % Favored : 79.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.78 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.17 (0.19), residues: 2120 helix: 0.71 (0.18), residues: 866 sheet: -0.83 (0.34), residues: 240 loop : -2.17 (0.20), residues: 1014 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.058 0.002 TRP D 507 HIS 0.003 0.001 HIS B 454 PHE 0.012 0.001 PHE D 466 TYR 0.011 0.001 TYR C 505 ARG 0.007 0.000 ARG A 366 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4240 Ramachandran restraints generated. 2120 Oldfield, 0 Emsley, 2120 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4240 Ramachandran restraints generated. 2120 Oldfield, 0 Emsley, 2120 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 263 residues out of total 1772 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 220 time to evaluate : 1.962 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 353 LEU cc_start: 0.7488 (OUTLIER) cc_final: 0.7230 (mm) REVERT: A 372 MET cc_start: 0.7374 (tpp) cc_final: 0.6490 (ttm) REVERT: A 420 LEU cc_start: 0.8564 (tp) cc_final: 0.8145 (tp) REVERT: A 422 ASP cc_start: 0.7646 (m-30) cc_final: 0.6579 (m-30) REVERT: A 485 MET cc_start: 0.7954 (mmm) cc_final: 0.7718 (mmt) REVERT: A 635 GLU cc_start: 0.9398 (OUTLIER) cc_final: 0.9086 (mp0) REVERT: A 657 PHE cc_start: 0.6920 (p90) cc_final: 0.6706 (p90) REVERT: A 702 MET cc_start: 0.6902 (ptt) cc_final: 0.6646 (ptm) REVERT: A 703 THR cc_start: 0.5981 (t) cc_final: 0.5780 (m) REVERT: A 713 MET cc_start: 0.8836 (mmm) cc_final: 0.8059 (mpp) REVERT: B 422 ASP cc_start: 0.7814 (m-30) cc_final: 0.7565 (p0) REVERT: B 504 GLN cc_start: 0.7638 (OUTLIER) cc_final: 0.7103 (mp10) REVERT: C 258 MET cc_start: 0.4360 (mmt) cc_final: 0.3010 (mmt) REVERT: C 401 MET cc_start: 0.6815 (tpp) cc_final: 0.6547 (pmm) REVERT: C 425 ASP cc_start: 0.7462 (p0) cc_final: 0.6940 (p0) REVERT: D 509 LYS cc_start: 0.8976 (tppt) cc_final: 0.8767 (mttm) REVERT: D 557 PHE cc_start: 0.8605 (m-80) cc_final: 0.8311 (m-80) REVERT: D 657 PHE cc_start: 0.7213 (p90) cc_final: 0.6934 (p90) REVERT: D 705 GLU cc_start: 0.6623 (mt-10) cc_final: 0.6053 (pt0) REVERT: D 709 ARG cc_start: 0.8561 (mmm160) cc_final: 0.7571 (tpt90) REVERT: D 713 MET cc_start: 0.8044 (mmm) cc_final: 0.7277 (mmm) outliers start: 43 outliers final: 33 residues processed: 249 average time/residue: 0.2930 time to fit residues: 110.4280 Evaluate side-chains 243 residues out of total 1772 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 207 time to evaluate : 1.892 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 310 HIS Chi-restraints excluded: chain A residue 353 LEU Chi-restraints excluded: chain A residue 364 LEU Chi-restraints excluded: chain A residue 380 SER Chi-restraints excluded: chain A residue 453 ASP Chi-restraints excluded: chain A residue 482 LEU Chi-restraints excluded: chain A residue 632 VAL Chi-restraints excluded: chain A residue 635 GLU Chi-restraints excluded: chain B residue 333 LEU Chi-restraints excluded: chain B residue 364 LEU Chi-restraints excluded: chain B residue 504 GLN Chi-restraints excluded: chain B residue 514 SER Chi-restraints excluded: chain B residue 580 ILE Chi-restraints excluded: chain B residue 590 THR Chi-restraints excluded: chain B residue 658 TYR Chi-restraints excluded: chain C residue 285 VAL Chi-restraints excluded: chain C residue 305 VAL Chi-restraints excluded: chain C residue 308 ILE Chi-restraints excluded: chain C residue 412 VAL Chi-restraints excluded: chain C residue 414 VAL Chi-restraints excluded: chain C residue 520 ILE Chi-restraints excluded: chain C residue 580 ILE Chi-restraints excluded: chain C residue 624 SER Chi-restraints excluded: chain C residue 632 VAL Chi-restraints excluded: chain C residue 665 VAL Chi-restraints excluded: chain C residue 681 ILE Chi-restraints excluded: chain C residue 702 MET Chi-restraints excluded: chain D residue 353 LEU Chi-restraints excluded: chain D residue 354 VAL Chi-restraints excluded: chain D residue 378 ARG Chi-restraints excluded: chain D residue 401 MET Chi-restraints excluded: chain D residue 524 ASP Chi-restraints excluded: chain D residue 682 THR Chi-restraints excluded: chain D residue 735 LEU Chi-restraints excluded: chain D residue 762 VAL Chi-restraints excluded: chain D residue 765 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 212 random chunks: chunk 201 optimal weight: 2.9990 chunk 122 optimal weight: 6.9990 chunk 95 optimal weight: 3.9990 chunk 139 optimal weight: 0.4980 chunk 211 optimal weight: 0.8980 chunk 194 optimal weight: 1.9990 chunk 168 optimal weight: 0.7980 chunk 17 optimal weight: 4.9990 chunk 129 optimal weight: 0.0050 chunk 103 optimal weight: 0.8980 chunk 133 optimal weight: 3.9990 overall best weight: 0.6194 ------------------------------------------------------------------------------- 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: 0.7108 moved from start: 0.5143 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 16884 Z= 0.178 Angle : 0.708 12.085 22884 Z= 0.346 Chirality : 0.044 0.257 2604 Planarity : 0.005 0.054 2972 Dihedral : 5.148 52.106 2327 Min Nonbonded Distance : 2.452 Molprobity Statistics. All-atom Clashscore : 11.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.70 % Favored : 93.30 % Rotamer: Outliers : 1.92 % Allowed : 18.40 % Favored : 79.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.78 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.06 (0.19), residues: 2120 helix: 0.81 (0.18), residues: 860 sheet: -0.79 (0.32), residues: 258 loop : -2.10 (0.20), residues: 1002 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.042 0.001 TRP D 507 HIS 0.002 0.001 HIS C 726 PHE 0.011 0.001 PHE D 466 TYR 0.011 0.001 TYR C 505 ARG 0.009 0.000 ARG A 378 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4240 Ramachandran restraints generated. 2120 Oldfield, 0 Emsley, 2120 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4240 Ramachandran restraints generated. 2120 Oldfield, 0 Emsley, 2120 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 254 residues out of total 1772 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 220 time to evaluate : 2.405 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 309 ASN cc_start: 0.8236 (m-40) cc_final: 0.7314 (p0) REVERT: A 353 LEU cc_start: 0.7444 (OUTLIER) cc_final: 0.7185 (mm) REVERT: A 372 MET cc_start: 0.7319 (tpp) cc_final: 0.6460 (ttm) REVERT: A 401 MET cc_start: 0.7403 (tpp) cc_final: 0.6065 (pmm) REVERT: A 427 MET cc_start: 0.1459 (mpp) cc_final: 0.1219 (mmt) REVERT: A 482 LEU cc_start: 0.8175 (OUTLIER) cc_final: 0.7713 (mm) REVERT: A 485 MET cc_start: 0.7965 (mmm) cc_final: 0.7716 (mmt) REVERT: A 513 GLU cc_start: 0.7502 (pt0) cc_final: 0.7238 (pt0) REVERT: A 657 PHE cc_start: 0.6905 (p90) cc_final: 0.6699 (p90) REVERT: A 698 MET cc_start: 0.6636 (mmm) cc_final: 0.5315 (mmm) REVERT: A 702 MET cc_start: 0.6912 (ptt) cc_final: 0.6710 (ptm) REVERT: A 713 MET cc_start: 0.8791 (mmm) cc_final: 0.8036 (mpp) REVERT: B 422 ASP cc_start: 0.7831 (m-30) cc_final: 0.7624 (p0) REVERT: B 504 GLN cc_start: 0.7688 (OUTLIER) cc_final: 0.7185 (mp10) REVERT: C 258 MET cc_start: 0.4614 (mmt) cc_final: 0.3201 (mmt) REVERT: C 347 LYS cc_start: 0.8375 (mmtm) cc_final: 0.7605 (mmtm) REVERT: C 401 MET cc_start: 0.6786 (tpp) cc_final: 0.6552 (pmm) REVERT: C 425 ASP cc_start: 0.7433 (p0) cc_final: 0.6886 (p0) REVERT: D 385 ARG cc_start: 0.7111 (ppt-90) cc_final: 0.6447 (mmt90) REVERT: D 557 PHE cc_start: 0.8640 (m-80) cc_final: 0.8336 (m-80) REVERT: D 657 PHE cc_start: 0.7166 (p90) cc_final: 0.6920 (p90) REVERT: D 705 GLU cc_start: 0.6633 (mt-10) cc_final: 0.6065 (pt0) REVERT: D 709 ARG cc_start: 0.8525 (mmm160) cc_final: 0.7508 (tpt90) REVERT: D 713 MET cc_start: 0.8064 (mmm) cc_final: 0.7314 (mmm) outliers start: 34 outliers final: 28 residues processed: 243 average time/residue: 0.3434 time to fit residues: 124.7486 Evaluate side-chains 238 residues out of total 1772 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 207 time to evaluate : 2.043 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 310 HIS Chi-restraints excluded: chain A residue 353 LEU Chi-restraints excluded: chain A residue 364 LEU Chi-restraints excluded: chain A residue 453 ASP Chi-restraints excluded: chain A residue 482 LEU Chi-restraints excluded: chain A residue 632 VAL Chi-restraints excluded: chain B residue 393 HIS Chi-restraints excluded: chain B residue 482 LEU Chi-restraints excluded: chain B residue 504 GLN Chi-restraints excluded: chain B residue 514 SER Chi-restraints excluded: chain B residue 580 ILE Chi-restraints excluded: chain B residue 590 THR Chi-restraints excluded: chain B residue 658 TYR Chi-restraints excluded: chain B residue 678 SER Chi-restraints excluded: chain C residue 285 VAL Chi-restraints excluded: chain C residue 308 ILE Chi-restraints excluded: chain C residue 412 VAL Chi-restraints excluded: chain C residue 414 VAL Chi-restraints excluded: chain C residue 520 ILE Chi-restraints excluded: chain C residue 580 ILE Chi-restraints excluded: chain C residue 632 VAL Chi-restraints excluded: chain C residue 665 VAL Chi-restraints excluded: chain C residue 681 ILE Chi-restraints excluded: chain C residue 702 MET Chi-restraints excluded: chain D residue 353 LEU Chi-restraints excluded: chain D residue 378 ARG Chi-restraints excluded: chain D residue 401 MET Chi-restraints excluded: chain D residue 682 THR Chi-restraints excluded: chain D residue 735 LEU Chi-restraints excluded: chain D residue 762 VAL Chi-restraints excluded: chain D residue 765 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 212 random chunks: chunk 179 optimal weight: 5.9990 chunk 51 optimal weight: 9.9990 chunk 155 optimal weight: 0.9980 chunk 24 optimal weight: 1.9990 chunk 46 optimal weight: 3.9990 chunk 168 optimal weight: 2.9990 chunk 70 optimal weight: 0.9980 chunk 172 optimal weight: 10.0000 chunk 21 optimal weight: 0.3980 chunk 31 optimal weight: 8.9990 chunk 147 optimal weight: 0.7980 overall best weight: 1.0382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 278 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4292 r_free = 0.4292 target = 0.135625 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3856 r_free = 0.3856 target = 0.109251 restraints weight = 53216.025| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3872 r_free = 0.3872 target = 0.110397 restraints weight = 39790.048| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3889 r_free = 0.3889 target = 0.111477 restraints weight = 26617.663| |-----------------------------------------------------------------------------| r_work (final): 0.3883 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7097 moved from start: 0.5234 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 16884 Z= 0.187 Angle : 0.710 12.367 22884 Z= 0.346 Chirality : 0.044 0.250 2604 Planarity : 0.005 0.058 2972 Dihedral : 5.024 34.239 2325 Min Nonbonded Distance : 2.464 Molprobity Statistics. All-atom Clashscore : 12.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.26 % Favored : 92.74 % Rotamer: Outliers : 2.03 % Allowed : 18.57 % Favored : 79.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.78 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.05 (0.19), residues: 2120 helix: 0.75 (0.18), residues: 873 sheet: -0.65 (0.33), residues: 254 loop : -2.11 (0.20), residues: 993 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.002 TRP D 507 HIS 0.003 0.001 HIS B 319 PHE 0.012 0.001 PHE D 466 TYR 0.011 0.001 TYR C 505 ARG 0.006 0.000 ARG D 584 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3450.36 seconds wall clock time: 64 minutes 30.93 seconds (3870.93 seconds total)