Starting phenix.real_space_refine on Sun Nov 17 05:00:21 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8w7a_37337/11_2024/8w7a_37337.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8w7a_37337/11_2024/8w7a_37337.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.77 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8w7a_37337/11_2024/8w7a_37337.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8w7a_37337/11_2024/8w7a_37337.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8w7a_37337/11_2024/8w7a_37337.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8w7a_37337/11_2024/8w7a_37337.cif" } resolution = 3.77 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= 0.003 sd= 0.056 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: 5 Type Number sf(0) Gaussians P 3 5.49 5 S 30 5.16 5 C 8419 2.51 5 N 2142 2.21 5 O 2423 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 54 residue(s): 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5513/modules/chem_data/mon_lib" Total number of atoms: 13017 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 6404 Number of conformers: 1 Conformer: "" Number of residues, atoms: 782, 6404 Classifications: {'peptide': 782} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 23, 'TRANS': 758} Chain breaks: 7 Chain: "B" Number of atoms: 6581 Number of conformers: 1 Conformer: "" Number of residues, atoms: 804, 6581 Classifications: {'peptide': 804} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 22, 'TRANS': 781} Chain breaks: 6 Chain: "B" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 32 Unusual residues: {'GTP': 1} Classifications: {'undetermined': 1} Time building chain proxies: 8.54, per 1000 atoms: 0.66 Number of scatterers: 13017 At special positions: 0 Unit cell: (102.102, 104.676, 135.564, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 30 16.00 P 3 15.00 O 2423 8.00 N 2142 7.00 C 8419 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: 3.09 Conformation dependent library (CDL) restraints added in 1.7 seconds 3112 Ramachandran restraints generated. 1556 Oldfield, 0 Emsley, 1556 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2960 Finding SS restraints... Secondary structure from input PDB file: 60 helices and 9 sheets defined 40.6% alpha, 3.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.30 Creating SS restraints... Processing helix chain 'A' and resid 71 through 78 removed outlier: 3.683A pdb=" N ASP A 75 " --> pdb=" O GLU A 71 " (cutoff:3.500A) Processing helix chain 'A' and resid 92 through 100 Processing helix chain 'A' and resid 126 through 133 removed outlier: 3.916A pdb=" N GLU A 130 " --> pdb=" O LEU A 126 " (cutoff:3.500A) Processing helix chain 'A' and resid 260 through 272 removed outlier: 3.779A pdb=" N ALA A 266 " --> pdb=" O SER A 262 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N SER A 267 " --> pdb=" O GLU A 263 " (cutoff:3.500A) Processing helix chain 'A' and resid 306 through 314 Processing helix chain 'A' and resid 326 through 342 removed outlier: 3.632A pdb=" N SER A 331 " --> pdb=" O LEU A 327 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N LYS A 332 " --> pdb=" O LEU A 328 " (cutoff:3.500A) removed outlier: 4.015A pdb=" N ILE A 333 " --> pdb=" O ARG A 329 " (cutoff:3.500A) removed outlier: 4.650A pdb=" N ILE A 338 " --> pdb=" O VAL A 334 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N ASN A 342 " --> pdb=" O ILE A 338 " (cutoff:3.500A) Processing helix chain 'A' and resid 401 through 413 removed outlier: 4.905A pdb=" N GLY A 407 " --> pdb=" O ILE A 403 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N ILE A 408 " --> pdb=" O ASP A 404 " (cutoff:3.500A) Processing helix chain 'A' and resid 420 through 425 removed outlier: 3.868A pdb=" N ASP A 424 " --> pdb=" O THR A 421 " (cutoff:3.500A) Processing helix chain 'A' and resid 431 through 445 removed outlier: 4.226A pdb=" N GLY A 437 " --> pdb=" O THR A 433 " (cutoff:3.500A) removed outlier: 4.027A pdb=" N LYS A 438 " --> pdb=" O ARG A 434 " (cutoff:3.500A) removed outlier: 3.939A pdb=" N LYS A 439 " --> pdb=" O ILE A 435 " (cutoff:3.500A) Processing helix chain 'A' and resid 447 through 452 Processing helix chain 'A' and resid 453 through 461 Processing helix chain 'A' and resid 488 through 509 removed outlier: 4.252A pdb=" N ILE A 492 " --> pdb=" O SER A 488 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N ILE A 497 " --> pdb=" O GLN A 493 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N ARG A 501 " --> pdb=" O ILE A 497 " (cutoff:3.500A) removed outlier: 4.671A pdb=" N GLY A 502 " --> pdb=" O LYS A 498 " (cutoff:3.500A) removed outlier: 3.980A pdb=" N PHE A 503 " --> pdb=" O LEU A 499 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N THR A 504 " --> pdb=" O LEU A 500 " (cutoff:3.500A) removed outlier: 4.119A pdb=" N THR A 506 " --> pdb=" O GLY A 502 " (cutoff:3.500A) Processing helix chain 'A' and resid 522 through 526 removed outlier: 3.651A pdb=" N LEU A 526 " --> pdb=" O TYR A 523 " (cutoff:3.500A) Processing helix chain 'A' and resid 537 through 550 removed outlier: 3.703A pdb=" N LEU A 546 " --> pdb=" O SER A 542 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N ALA A 547 " --> pdb=" O TYR A 543 " (cutoff:3.500A) Processing helix chain 'A' and resid 557 through 572 removed outlier: 3.884A pdb=" N ILE A 561 " --> pdb=" O ASP A 557 " (cutoff:3.500A) Processing helix chain 'A' and resid 584 through 595 removed outlier: 4.437A pdb=" N THR A 588 " --> pdb=" O GLY A 584 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N ILE A 589 " --> pdb=" O LYS A 585 " (cutoff:3.500A) Processing helix chain 'A' and resid 597 through 614 removed outlier: 5.748A pdb=" N ILE A 610 " --> pdb=" O THR A 606 " (cutoff:3.500A) removed outlier: 5.408A pdb=" N GLU A 611 " --> pdb=" O THR A 607 " (cutoff:3.500A) Processing helix chain 'A' and resid 624 through 639 removed outlier: 3.993A pdb=" N VAL A 631 " --> pdb=" O GLY A 627 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N GLY A 639 " --> pdb=" O PHE A 635 " (cutoff:3.500A) Processing helix chain 'A' and resid 642 through 661 removed outlier: 4.093A pdb=" N LEU A 650 " --> pdb=" O GLY A 646 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N ILE A 661 " --> pdb=" O THR A 657 " (cutoff:3.500A) Processing helix chain 'A' and resid 691 through 706 removed outlier: 3.566A pdb=" N ALA A 695 " --> pdb=" O HIS A 691 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N LEU A 697 " --> pdb=" O GLY A 693 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N TYR A 702 " --> pdb=" O PHE A 698 " (cutoff:3.500A) removed outlier: 4.341A pdb=" N LYS A 703 " --> pdb=" O GLY A 699 " (cutoff:3.500A) removed outlier: 5.121A pdb=" N LEU A 704 " --> pdb=" O GLU A 700 " (cutoff:3.500A) Processing helix chain 'A' and resid 707 through 720 removed outlier: 3.700A pdb=" N LYS A 711 " --> pdb=" O GLU A 707 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N LEU A 714 " --> pdb=" O TYR A 710 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N GLU A 715 " --> pdb=" O LYS A 711 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N LEU A 716 " --> pdb=" O ASN A 712 " (cutoff:3.500A) Processing helix chain 'A' and resid 721 through 723 No H-bonds generated for 'chain 'A' and resid 721 through 723' Processing helix chain 'A' and resid 748 through 759 removed outlier: 4.366A pdb=" N LEU A 752 " --> pdb=" O GLY A 748 " (cutoff:3.500A) Processing helix chain 'A' and resid 764 through 769 Processing helix chain 'A' and resid 770 through 778 Processing helix chain 'A' and resid 791 through 800 removed outlier: 3.568A pdb=" N ALA A 798 " --> pdb=" O GLY A 794 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N ASN A 799 " --> pdb=" O LEU A 795 " (cutoff:3.500A) Processing helix chain 'A' and resid 808 through 818 removed outlier: 4.188A pdb=" N LYS A 814 " --> pdb=" O SER A 810 " (cutoff:3.500A) removed outlier: 4.878A pdb=" N LEU A 815 " --> pdb=" O GLY A 811 " (cutoff:3.500A) Processing helix chain 'A' and resid 819 through 821 No H-bonds generated for 'chain 'A' and resid 819 through 821' Processing helix chain 'A' and resid 847 through 861 removed outlier: 3.937A pdb=" N VAL A 851 " --> pdb=" O GLY A 847 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N VAL A 856 " --> pdb=" O ALA A 852 " (cutoff:3.500A) removed outlier: 3.931A pdb=" N MET A 859 " --> pdb=" O LEU A 855 " (cutoff:3.500A) Processing helix chain 'B' and resid 69 through 74 Processing helix chain 'B' and resid 77 through 82 removed outlier: 4.249A pdb=" N GLU B 82 " --> pdb=" O LYS B 78 " (cutoff:3.500A) Processing helix chain 'B' and resid 92 through 100 Processing helix chain 'B' and resid 123 through 128 removed outlier: 3.630A pdb=" N GLN B 127 " --> pdb=" O GLU B 123 " (cutoff:3.500A) removed outlier: 4.466A pdb=" N ARG B 128 " --> pdb=" O SER B 124 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 123 through 128' Processing helix chain 'B' and resid 260 through 265 Processing helix chain 'B' and resid 270 through 275 removed outlier: 3.889A pdb=" N LEU B 275 " --> pdb=" O ALA B 271 " (cutoff:3.500A) Processing helix chain 'B' and resid 306 through 313 removed outlier: 3.765A pdb=" N THR B 311 " --> pdb=" O ASN B 307 " (cutoff:3.500A) Processing helix chain 'B' and resid 335 through 344 removed outlier: 3.819A pdb=" N ASN B 342 " --> pdb=" O ILE B 338 " (cutoff:3.500A) Processing helix chain 'B' and resid 407 through 412 removed outlier: 3.607A pdb=" N ILE B 411 " --> pdb=" O GLY B 407 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N ALA B 412 " --> pdb=" O ILE B 408 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 407 through 412' Processing helix chain 'B' and resid 420 through 425 removed outlier: 3.898A pdb=" N ASP B 424 " --> pdb=" O THR B 421 " (cutoff:3.500A) Processing helix chain 'B' and resid 431 through 445 removed outlier: 5.022A pdb=" N GLY B 437 " --> pdb=" O THR B 433 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N LYS B 438 " --> pdb=" O ARG B 434 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N LYS B 439 " --> pdb=" O ILE B 435 " (cutoff:3.500A) removed outlier: 4.781A pdb=" N LEU B 440 " --> pdb=" O GLU B 436 " (cutoff:3.500A) Processing helix chain 'B' and resid 448 through 465 removed outlier: 3.902A pdb=" N ASP B 452 " --> pdb=" O ARG B 448 " (cutoff:3.500A) removed outlier: 3.973A pdb=" N TYR B 453 " --> pdb=" O GLU B 449 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N LEU B 461 " --> pdb=" O LEU B 457 " (cutoff:3.500A) Processing helix chain 'B' and resid 488 through 498 removed outlier: 3.816A pdb=" N ILE B 492 " --> pdb=" O SER B 488 " (cutoff:3.500A) removed outlier: 4.166A pdb=" N PHE B 495 " --> pdb=" O ASP B 491 " (cutoff:3.500A) removed outlier: 3.958A pdb=" N ILE B 496 " --> pdb=" O ILE B 492 " (cutoff:3.500A) Processing helix chain 'B' and resid 500 through 505 Processing helix chain 'B' and resid 507 through 512 Processing helix chain 'B' and resid 536 through 550 removed outlier: 3.527A pdb=" N LEU B 540 " --> pdb=" O ASP B 536 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N GLN B 544 " --> pdb=" O LEU B 540 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N GLN B 545 " --> pdb=" O TRP B 541 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N LEU B 546 " --> pdb=" O SER B 542 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N LYS B 549 " --> pdb=" O GLN B 545 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N VAL B 550 " --> pdb=" O LEU B 546 " (cutoff:3.500A) Processing helix chain 'B' and resid 557 through 571 removed outlier: 3.953A pdb=" N ILE B 561 " --> pdb=" O ASP B 557 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N GLU B 568 " --> pdb=" O GLN B 564 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N VAL B 570 " --> pdb=" O ILE B 566 " (cutoff:3.500A) Processing helix chain 'B' and resid 584 through 596 removed outlier: 3.871A pdb=" N THR B 588 " --> pdb=" O GLY B 584 " (cutoff:3.500A) removed outlier: 3.900A pdb=" N ILE B 592 " --> pdb=" O THR B 588 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N TYR B 593 " --> pdb=" O ILE B 589 " (cutoff:3.500A) Processing helix chain 'B' and resid 598 through 616 removed outlier: 3.623A pdb=" N VAL B 602 " --> pdb=" O ILE B 598 " (cutoff:3.500A) removed outlier: 5.325A pdb=" N GLU B 611 " --> pdb=" O THR B 607 " (cutoff:3.500A) Processing helix chain 'B' and resid 625 through 639 Processing helix chain 'B' and resid 643 through 661 removed outlier: 3.556A pdb=" N LEU B 658 " --> pdb=" O ARG B 654 " (cutoff:3.500A) Processing helix chain 'B' and resid 663 through 667 removed outlier: 3.691A pdb=" N THR B 666 " --> pdb=" O ASN B 663 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N PHE B 667 " --> pdb=" O PRO B 664 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 663 through 667' Processing helix chain 'B' and resid 691 through 705 removed outlier: 3.686A pdb=" N LYS B 703 " --> pdb=" O GLY B 699 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N LEU B 704 " --> pdb=" O GLU B 700 " (cutoff:3.500A) removed outlier: 3.982A pdb=" N THR B 705 " --> pdb=" O ALA B 701 " (cutoff:3.500A) Processing helix chain 'B' and resid 708 through 710 No H-bonds generated for 'chain 'B' and resid 708 through 710' Processing helix chain 'B' and resid 711 through 722 removed outlier: 4.019A pdb=" N GLU B 715 " --> pdb=" O LYS B 711 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N LEU B 716 " --> pdb=" O ASN B 712 " (cutoff:3.500A) Processing helix chain 'B' and resid 748 through 757 removed outlier: 4.077A pdb=" N LEU B 752 " --> pdb=" O GLY B 748 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N LEU B 753 " --> pdb=" O SER B 749 " (cutoff:3.500A) removed outlier: 4.156A pdb=" N ASN B 757 " --> pdb=" O LEU B 753 " (cutoff:3.500A) Processing helix chain 'B' and resid 770 through 778 removed outlier: 3.582A pdb=" N LEU B 774 " --> pdb=" O TYR B 770 " (cutoff:3.500A) Processing helix chain 'B' and resid 792 through 799 removed outlier: 3.755A pdb=" N GLU B 796 " --> pdb=" O PHE B 792 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N ASN B 799 " --> pdb=" O LEU B 795 " (cutoff:3.500A) Processing helix chain 'B' and resid 808 through 813 Processing helix chain 'B' and resid 814 through 819 Processing helix chain 'B' and resid 847 through 860 removed outlier: 3.947A pdb=" N VAL B 851 " --> pdb=" O GLY B 847 " (cutoff:3.500A) removed outlier: 3.931A pdb=" N VAL B 856 " --> pdb=" O ALA B 852 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N ILE B 858 " --> pdb=" O GLY B 854 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N MET B 859 " --> pdb=" O LEU B 855 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 60 through 62 removed outlier: 3.718A pdb=" N ILE A 60 " --> pdb=" O CYS A 115 " (cutoff:3.500A) removed outlier: 4.307A pdb=" N CYS A 115 " --> pdb=" O ILE A 60 " (cutoff:3.500A) removed outlier: 4.060A pdb=" N ILE A 62 " --> pdb=" O ILE A 113 " (cutoff:3.500A) removed outlier: 3.984A pdb=" N ILE A 113 " --> pdb=" O ILE A 62 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N LYS A 88 " --> pdb=" O THR A 114 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 224 through 225 removed outlier: 4.191A pdb=" N ARG A 224 " --> pdb=" O ILE A 231 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N ILE A 231 " --> pdb=" O ARG A 224 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N GLY A 230 " --> pdb=" O GLU A 247 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 304 through 305 Processing sheet with id=AA4, first strand: chain 'A' and resid 725 through 727 removed outlier: 3.515A pdb=" N LYS A 726 " --> pdb=" O GLN A 734 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N GLN A 734 " --> pdb=" O LYS A 726 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N GLN A 737 " --> pdb=" O ARG A 740 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N ARG A 740 " --> pdb=" O GLN A 737 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 823 through 825 removed outlier: 3.648A pdb=" N CYS A 824 " --> pdb=" O VAL A 831 " (cutoff:3.500A) removed outlier: 3.970A pdb=" N VAL A 831 " --> pdb=" O CYS A 824 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA5 Processing sheet with id=AA6, first strand: chain 'B' and resid 35 through 37 removed outlier: 3.501A pdb=" N HIS B 35 " --> pdb=" O TYR B 47 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N TYR B 47 " --> pdb=" O HIS B 35 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N TYR B 45 " --> pdb=" O VAL B 37 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 233 through 234 removed outlier: 3.706A pdb=" N LEU B 296 " --> pdb=" O LYS B 246 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N PHE B 295 " --> pdb=" O GLY B 288 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N GLY B 288 " --> pdb=" O PHE B 295 " (cutoff:3.500A) removed outlier: 3.934A pdb=" N TRP B 286 " --> pdb=" O GLY B 297 " (cutoff:3.500A) removed outlier: 6.803A pdb=" N GLU B 299 " --> pdb=" O ILE B 284 " (cutoff:3.500A) removed outlier: 7.542A pdb=" N ILE B 284 " --> pdb=" O GLU B 299 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 304 through 305 Processing sheet with id=AA9, first strand: chain 'B' and resid 350 through 351 342 hydrogen bonds defined for protein. 981 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 3.45 Time building geometry restraints manager: 3.61 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.10 - 1.24: 1767 1.24 - 1.39: 3681 1.39 - 1.53: 7034 1.53 - 1.68: 805 1.68 - 1.82: 44 Bond restraints: 13331 Sorted by residual: bond pdb=" CG PRO A 139 " pdb=" CD PRO A 139 " ideal model delta sigma weight residual 1.503 1.101 0.402 3.40e-02 8.65e+02 1.40e+02 bond pdb=" C ARG B 249 " pdb=" N PRO B 250 " ideal model delta sigma weight residual 1.332 1.397 -0.065 1.12e-02 7.97e+03 3.37e+01 bond pdb=" CG PRO A 867 " pdb=" CD PRO A 867 " ideal model delta sigma weight residual 1.503 1.363 0.140 3.40e-02 8.65e+02 1.71e+01 bond pdb=" N PRO A 139 " pdb=" CA PRO A 139 " ideal model delta sigma weight residual 1.469 1.511 -0.042 1.28e-02 6.10e+03 1.09e+01 bond pdb=" CA LEU B 30 " pdb=" CB LEU B 30 " ideal model delta sigma weight residual 1.526 1.549 -0.022 9.30e-03 1.16e+04 5.72e+00 ... (remaining 13326 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.44: 17745 4.44 - 8.87: 255 8.87 - 13.31: 26 13.31 - 17.74: 5 17.74 - 22.18: 3 Bond angle restraints: 18034 Sorted by residual: angle pdb=" N PRO A 139 " pdb=" CD PRO A 139 " pdb=" CG PRO A 139 " ideal model delta sigma weight residual 103.20 81.02 22.18 1.50e+00 4.44e-01 2.19e+02 angle pdb=" CA PRO A 139 " pdb=" CB PRO A 139 " pdb=" CG PRO A 139 " ideal model delta sigma weight residual 104.50 85.03 19.47 1.90e+00 2.77e-01 1.05e+02 angle pdb=" N ILE A 844 " pdb=" CA ILE A 844 " pdb=" C ILE A 844 " ideal model delta sigma weight residual 112.29 104.61 7.68 9.40e-01 1.13e+00 6.68e+01 angle pdb=" CA GLN B 27 " pdb=" CB GLN B 27 " pdb=" CG GLN B 27 " ideal model delta sigma weight residual 114.10 129.00 -14.90 2.00e+00 2.50e-01 5.55e+01 angle pdb=" C PRO B 10 " pdb=" N PHE B 11 " pdb=" CA PHE B 11 " ideal model delta sigma weight residual 121.54 135.69 -14.15 1.91e+00 2.74e-01 5.49e+01 ... (remaining 18029 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.87: 6925 17.87 - 35.74: 754 35.74 - 53.62: 117 53.62 - 71.49: 17 71.49 - 89.36: 15 Dihedral angle restraints: 7828 sinusoidal: 3203 harmonic: 4625 Sorted by residual: dihedral pdb=" CA TYR B 429 " pdb=" C TYR B 429 " pdb=" N VAL B 430 " pdb=" CA VAL B 430 " ideal model delta harmonic sigma weight residual 180.00 139.02 40.98 0 5.00e+00 4.00e-02 6.72e+01 dihedral pdb=" CA PHE A 613 " pdb=" C PHE A 613 " pdb=" N GLU A 614 " pdb=" CA GLU A 614 " ideal model delta harmonic sigma weight residual -180.00 -145.11 -34.89 0 5.00e+00 4.00e-02 4.87e+01 dihedral pdb=" CA VAL B 76 " pdb=" C VAL B 76 " pdb=" N ALA B 77 " pdb=" CA ALA B 77 " ideal model delta harmonic sigma weight residual 180.00 146.77 33.23 0 5.00e+00 4.00e-02 4.42e+01 ... (remaining 7825 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.085: 1625 0.085 - 0.169: 262 0.169 - 0.254: 38 0.254 - 0.338: 9 0.338 - 0.423: 5 Chirality restraints: 1939 Sorted by residual: chirality pdb=" CB ILE A 561 " pdb=" CA ILE A 561 " pdb=" CG1 ILE A 561 " pdb=" CG2 ILE A 561 " both_signs ideal model delta sigma weight residual False 2.64 2.22 0.42 2.00e-01 2.50e+01 4.47e+00 chirality pdb=" CB ILE A 801 " pdb=" CA ILE A 801 " pdb=" CG1 ILE A 801 " pdb=" CG2 ILE A 801 " both_signs ideal model delta sigma weight residual False 2.64 2.25 0.40 2.00e-01 2.50e+01 3.91e+00 chirality pdb=" CB ILE A 661 " pdb=" CA ILE A 661 " pdb=" CG1 ILE A 661 " pdb=" CG2 ILE A 661 " both_signs ideal model delta sigma weight residual False 2.64 2.25 0.39 2.00e-01 2.50e+01 3.90e+00 ... (remaining 1936 not shown) Planarity restraints: 2281 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLY A 138 " -0.127 5.00e-02 4.00e+02 1.87e-01 5.61e+01 pdb=" N PRO A 139 " 0.323 5.00e-02 4.00e+02 pdb=" CA PRO A 139 " -0.114 5.00e-02 4.00e+02 pdb=" CD PRO A 139 " -0.082 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA TYR B 26 " 0.026 2.00e-02 2.50e+03 5.18e-02 2.69e+01 pdb=" C TYR B 26 " -0.090 2.00e-02 2.50e+03 pdb=" O TYR B 26 " 0.034 2.00e-02 2.50e+03 pdb=" N GLN B 27 " 0.030 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ALA A 150 " 0.068 5.00e-02 4.00e+02 1.01e-01 1.63e+01 pdb=" N PRO A 151 " -0.174 5.00e-02 4.00e+02 pdb=" CA PRO A 151 " 0.051 5.00e-02 4.00e+02 pdb=" CD PRO A 151 " 0.056 5.00e-02 4.00e+02 ... (remaining 2278 not shown) Histogram of nonbonded interaction distances: 2.26 - 2.79: 3044 2.79 - 3.32: 11334 3.32 - 3.84: 20718 3.84 - 4.37: 23039 4.37 - 4.90: 39665 Nonbonded interactions: 97800 Sorted by model distance: nonbonded pdb=" O CYS A 783 " pdb=" OH TYR A 822 " model vdw 2.261 3.040 nonbonded pdb=" O CYS B 783 " pdb=" OH TYR B 822 " model vdw 2.281 3.040 nonbonded pdb=" O ALA A 701 " pdb=" OG1 THR A 705 " model vdw 2.281 3.040 nonbonded pdb=" OD2 ASP B 583 " pdb=" OH TYR B 681 " model vdw 2.300 3.040 nonbonded pdb=" O LYS B 585 " pdb=" OG1 THR B 588 " model vdw 2.303 3.040 ... (remaining 97795 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' and (resid 4 through 154 or resid 222 through 869)) selection = (chain 'B' and (resid 4 through 117 or resid 121 through 142 or resid 146 throug \ h 153 or resid 201 or resid 222 through 233 or resid 241 through 670 or resid 67 \ 5 through 869)) } 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: 2.740 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.530 Check model and map are aligned: 0.110 Set scattering table: 0.140 Process input model: 32.180 Find NCS groups from input model: 0.810 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:2.630 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 39.210 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6519 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 : 0.007 0.402 13331 Z= 0.404 Angle : 1.373 22.175 18034 Z= 0.770 Chirality : 0.068 0.423 1939 Planarity : 0.009 0.187 2281 Dihedral : 15.090 89.362 4868 Min Nonbonded Distance : 2.261 Molprobity Statistics. All-atom Clashscore : 5.54 Ramachandran Plot: Outliers : 0.96 % Allowed : 10.67 % Favored : 88.37 % Rotamer: Outliers : 0.00 % Allowed : 0.50 % Favored : 99.50 % Cbeta Deviations : 0.07 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.39 % 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: -4.55 (0.17), residues: 1556 helix: -3.09 (0.15), residues: 606 sheet: -2.53 (0.65), residues: 63 loop : -3.11 (0.17), residues: 887 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.049 0.003 TRP B 204 HIS 0.020 0.002 HIS A 413 PHE 0.037 0.003 PHE A 5 TYR 0.034 0.003 TYR B 140 ARG 0.006 0.001 ARG A 128 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3112 Ramachandran restraints generated. 1556 Oldfield, 0 Emsley, 1556 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3112 Ramachandran restraints generated. 1556 Oldfield, 0 Emsley, 1556 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 252 residues out of total 1413 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 252 time to evaluate : 1.485 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 140 TYR cc_start: 0.7187 (p90) cc_final: 0.5859 (p90) REVERT: A 153 TYR cc_start: 0.5377 (m-80) cc_final: 0.5062 (m-80) REVERT: A 249 ARG cc_start: 0.7324 (ppt170) cc_final: 0.7123 (ppt170) REVERT: A 532 ILE cc_start: 0.7787 (mm) cc_final: 0.7443 (pt) REVERT: A 846 SER cc_start: 0.7997 (m) cc_final: 0.7793 (m) REVERT: B 557 ASP cc_start: 0.7595 (p0) cc_final: 0.7250 (p0) REVERT: B 615 ASN cc_start: 0.8194 (p0) cc_final: 0.7323 (p0) REVERT: B 656 TYR cc_start: 0.7066 (t80) cc_final: 0.6498 (t80) REVERT: B 660 TYR cc_start: 0.7740 (t80) cc_final: 0.7300 (t80) outliers start: 0 outliers final: 0 residues processed: 252 average time/residue: 0.2647 time to fit residues: 98.4754 Evaluate side-chains 177 residues out of total 1413 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 177 time to evaluate : 1.673 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 158 random chunks: chunk 133 optimal weight: 0.5980 chunk 119 optimal weight: 0.9980 chunk 66 optimal weight: 0.6980 chunk 40 optimal weight: 20.0000 chunk 80 optimal weight: 10.0000 chunk 63 optimal weight: 10.0000 chunk 123 optimal weight: 0.8980 chunk 47 optimal weight: 9.9990 chunk 75 optimal weight: 6.9990 chunk 92 optimal weight: 8.9990 chunk 143 optimal weight: 9.9990 overall best weight: 2.0382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 345 HIS A 608 HIS ** A 678 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 691 HIS A 868 GLN B 74 GLN ** B 81 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 522 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 544 GLN B 663 ASN B 712 ASN B 737 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6695 moved from start: 0.2017 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 13331 Z= 0.240 Angle : 0.814 10.106 18034 Z= 0.425 Chirality : 0.049 0.313 1939 Planarity : 0.006 0.130 2281 Dihedral : 7.487 77.712 1739 Min Nonbonded Distance : 2.430 Molprobity Statistics. All-atom Clashscore : 12.94 Ramachandran Plot: Outliers : 0.84 % Allowed : 10.73 % Favored : 88.43 % Rotamer: Outliers : 1.34 % Allowed : 10.76 % Favored : 87.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.13 % 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: -3.93 (0.18), residues: 1556 helix: -2.18 (0.18), residues: 642 sheet: -2.65 (0.63), residues: 63 loop : -3.05 (0.19), residues: 851 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP B 204 HIS 0.006 0.001 HIS B 345 PHE 0.024 0.002 PHE B 200 TYR 0.022 0.002 TYR A 416 ARG 0.006 0.001 ARG B 758 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3112 Ramachandran restraints generated. 1556 Oldfield, 0 Emsley, 1556 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3112 Ramachandran restraints generated. 1556 Oldfield, 0 Emsley, 1556 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 212 residues out of total 1413 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 193 time to evaluate : 1.424 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 140 TYR cc_start: 0.7251 (p90) cc_final: 0.5896 (p90) REVERT: A 153 TYR cc_start: 0.5254 (m-80) cc_final: 0.5049 (m-80) REVERT: A 249 ARG cc_start: 0.7063 (ppt170) cc_final: 0.6746 (ppt170) REVERT: A 417 MET cc_start: 0.4649 (mtt) cc_final: 0.4342 (mtt) REVERT: A 532 ILE cc_start: 0.8066 (mm) cc_final: 0.7707 (mm) REVERT: A 776 ARG cc_start: 0.7764 (mmp80) cc_final: 0.6577 (ttm-80) REVERT: B 557 ASP cc_start: 0.7634 (p0) cc_final: 0.7129 (p0) REVERT: B 656 TYR cc_start: 0.7060 (t80) cc_final: 0.6478 (t80) REVERT: B 770 TYR cc_start: 0.5229 (m-80) cc_final: 0.4811 (m-80) REVERT: B 863 LEU cc_start: 0.4336 (OUTLIER) cc_final: 0.3959 (mt) outliers start: 19 outliers final: 10 residues processed: 207 average time/residue: 0.2369 time to fit residues: 72.9215 Evaluate side-chains 179 residues out of total 1413 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 168 time to evaluate : 1.452 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 259 THR Chi-restraints excluded: chain A residue 426 THR Chi-restraints excluded: chain A residue 793 CYS Chi-restraints excluded: chain A residue 806 ASP Chi-restraints excluded: chain A residue 817 GLU Chi-restraints excluded: chain B residue 319 VAL Chi-restraints excluded: chain B residue 454 VAL Chi-restraints excluded: chain B residue 592 ILE Chi-restraints excluded: chain B residue 633 LEU Chi-restraints excluded: chain B residue 784 VAL Chi-restraints excluded: chain B residue 863 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 158 random chunks: chunk 79 optimal weight: 3.9990 chunk 44 optimal weight: 5.9990 chunk 119 optimal weight: 1.9990 chunk 97 optimal weight: 0.1980 chunk 39 optimal weight: 4.9990 chunk 143 optimal weight: 0.9990 chunk 155 optimal weight: 1.9990 chunk 128 optimal weight: 3.9990 chunk 142 optimal weight: 9.9990 chunk 49 optimal weight: 6.9990 chunk 115 optimal weight: 3.9990 overall best weight: 1.8388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 527 ASN B 81 HIS ** B 522 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6727 moved from start: 0.2567 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 13331 Z= 0.216 Angle : 0.750 9.370 18034 Z= 0.391 Chirality : 0.048 0.268 1939 Planarity : 0.005 0.094 2281 Dihedral : 7.159 79.903 1739 Min Nonbonded Distance : 2.506 Molprobity Statistics. All-atom Clashscore : 11.82 Ramachandran Plot: Outliers : 0.84 % Allowed : 11.50 % Favored : 87.66 % Rotamer: Outliers : 2.55 % Allowed : 14.72 % Favored : 82.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.13 % 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: -3.61 (0.19), residues: 1556 helix: -1.69 (0.19), residues: 637 sheet: -2.50 (0.63), residues: 58 loop : -3.05 (0.19), residues: 861 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP B 204 HIS 0.006 0.001 HIS B 345 PHE 0.031 0.002 PHE B 344 TYR 0.017 0.002 TYR A 47 ARG 0.003 0.000 ARG A 128 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3112 Ramachandran restraints generated. 1556 Oldfield, 0 Emsley, 1556 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3112 Ramachandran restraints generated. 1556 Oldfield, 0 Emsley, 1556 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 228 residues out of total 1413 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 192 time to evaluate : 1.398 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 140 TYR cc_start: 0.7296 (p90) cc_final: 0.5967 (p90) REVERT: A 153 TYR cc_start: 0.5397 (m-80) cc_final: 0.5195 (m-80) REVERT: A 249 ARG cc_start: 0.7179 (ppt170) cc_final: 0.6820 (ppt170) REVERT: A 648 GLU cc_start: 0.8307 (OUTLIER) cc_final: 0.7526 (pp20) REVERT: A 652 ARG cc_start: 0.7590 (mtp85) cc_final: 0.7328 (mtp85) REVERT: A 712 ASN cc_start: 0.6474 (m110) cc_final: 0.5878 (t0) REVERT: A 776 ARG cc_start: 0.7867 (mmp80) cc_final: 0.6595 (ttm-80) REVERT: A 795 LEU cc_start: 0.6857 (OUTLIER) cc_final: 0.6656 (mm) REVERT: B 557 ASP cc_start: 0.7668 (p0) cc_final: 0.6894 (p0) REVERT: B 656 TYR cc_start: 0.7011 (t80) cc_final: 0.6468 (t80) REVERT: B 770 TYR cc_start: 0.5343 (m-80) cc_final: 0.4803 (m-80) outliers start: 36 outliers final: 20 residues processed: 217 average time/residue: 0.2487 time to fit residues: 79.2889 Evaluate side-chains 189 residues out of total 1413 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 167 time to evaluate : 1.642 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 72 LEU Chi-restraints excluded: chain A residue 254 LEU Chi-restraints excluded: chain A residue 259 THR Chi-restraints excluded: chain A residue 426 THR Chi-restraints excluded: chain A residue 518 PHE Chi-restraints excluded: chain A residue 534 PHE Chi-restraints excluded: chain A residue 648 GLU Chi-restraints excluded: chain A residue 718 VAL Chi-restraints excluded: chain A residue 793 CYS Chi-restraints excluded: chain A residue 795 LEU Chi-restraints excluded: chain B residue 27 GLN Chi-restraints excluded: chain B residue 53 VAL Chi-restraints excluded: chain B residue 60 ILE Chi-restraints excluded: chain B residue 319 VAL Chi-restraints excluded: chain B residue 447 THR Chi-restraints excluded: chain B residue 454 VAL Chi-restraints excluded: chain B residue 504 THR Chi-restraints excluded: chain B residue 534 PHE Chi-restraints excluded: chain B residue 592 ILE Chi-restraints excluded: chain B residue 633 LEU Chi-restraints excluded: chain B residue 788 LEU Chi-restraints excluded: chain B residue 863 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 158 random chunks: chunk 142 optimal weight: 9.9990 chunk 108 optimal weight: 0.7980 chunk 74 optimal weight: 0.9990 chunk 15 optimal weight: 20.0000 chunk 68 optimal weight: 8.9990 chunk 96 optimal weight: 0.9980 chunk 144 optimal weight: 9.9990 chunk 152 optimal weight: 5.9990 chunk 75 optimal weight: 4.9990 chunk 136 optimal weight: 4.9990 chunk 41 optimal weight: 3.9990 overall best weight: 2.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 868 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 27 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6801 moved from start: 0.3055 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 13331 Z= 0.249 Angle : 0.756 9.762 18034 Z= 0.395 Chirality : 0.048 0.224 1939 Planarity : 0.005 0.054 2281 Dihedral : 7.088 79.087 1739 Min Nonbonded Distance : 2.477 Molprobity Statistics. All-atom Clashscore : 13.68 Ramachandran Plot: Outliers : 0.71 % Allowed : 11.70 % Favored : 87.60 % Rotamer: Outliers : 2.76 % Allowed : 17.27 % Favored : 79.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % 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: -3.57 (0.19), residues: 1556 helix: -1.57 (0.19), residues: 657 sheet: -2.64 (0.63), residues: 56 loop : -3.14 (0.19), residues: 843 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP B 204 HIS 0.007 0.001 HIS A 9 PHE 0.035 0.002 PHE B 200 TYR 0.016 0.002 TYR A 45 ARG 0.005 0.001 ARG B 821 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3112 Ramachandran restraints generated. 1556 Oldfield, 0 Emsley, 1556 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3112 Ramachandran restraints generated. 1556 Oldfield, 0 Emsley, 1556 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 224 residues out of total 1413 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 185 time to evaluate : 1.561 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 140 TYR cc_start: 0.7008 (p90) cc_final: 0.5790 (p90) REVERT: A 712 ASN cc_start: 0.6633 (m110) cc_final: 0.6141 (t0) REVERT: A 776 ARG cc_start: 0.7952 (mmp80) cc_final: 0.6661 (ttm110) REVERT: B 539 ILE cc_start: 0.8766 (mm) cc_final: 0.8501 (mm) REVERT: B 656 TYR cc_start: 0.7014 (t80) cc_final: 0.6425 (t80) REVERT: B 711 LYS cc_start: 0.8342 (pptt) cc_final: 0.8064 (pptt) REVERT: B 770 TYR cc_start: 0.5359 (m-80) cc_final: 0.4906 (m-80) REVERT: B 860 ASP cc_start: 0.6694 (m-30) cc_final: 0.6263 (m-30) REVERT: B 863 LEU cc_start: 0.4457 (OUTLIER) cc_final: 0.4064 (mt) outliers start: 39 outliers final: 24 residues processed: 213 average time/residue: 0.2484 time to fit residues: 78.2993 Evaluate side-chains 194 residues out of total 1413 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 169 time to evaluate : 1.444 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 VAL Chi-restraints excluded: chain A residue 72 LEU Chi-restraints excluded: chain A residue 254 LEU Chi-restraints excluded: chain A residue 259 THR Chi-restraints excluded: chain A residue 426 THR Chi-restraints excluded: chain A residue 518 PHE Chi-restraints excluded: chain A residue 670 VAL Chi-restraints excluded: chain A residue 773 SER Chi-restraints excluded: chain A residue 793 CYS Chi-restraints excluded: chain B residue 27 GLN Chi-restraints excluded: chain B residue 30 LEU Chi-restraints excluded: chain B residue 47 TYR Chi-restraints excluded: chain B residue 60 ILE Chi-restraints excluded: chain B residue 319 VAL Chi-restraints excluded: chain B residue 356 LEU Chi-restraints excluded: chain B residue 447 THR Chi-restraints excluded: chain B residue 454 VAL Chi-restraints excluded: chain B residue 504 THR Chi-restraints excluded: chain B residue 534 PHE Chi-restraints excluded: chain B residue 564 GLN Chi-restraints excluded: chain B residue 592 ILE Chi-restraints excluded: chain B residue 633 LEU Chi-restraints excluded: chain B residue 788 LEU Chi-restraints excluded: chain B residue 856 VAL Chi-restraints excluded: chain B residue 863 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 158 random chunks: chunk 127 optimal weight: 6.9990 chunk 86 optimal weight: 6.9990 chunk 2 optimal weight: 0.8980 chunk 113 optimal weight: 3.9990 chunk 63 optimal weight: 0.9980 chunk 130 optimal weight: 3.9990 chunk 105 optimal weight: 5.9990 chunk 0 optimal weight: 6.9990 chunk 77 optimal weight: 3.9990 chunk 137 optimal weight: 10.0000 chunk 38 optimal weight: 0.8980 overall best weight: 2.1584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 527 ASN ** B 27 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 545 GLN ** B 615 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6809 moved from start: 0.3343 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 13331 Z= 0.237 Angle : 0.744 9.924 18034 Z= 0.389 Chirality : 0.047 0.196 1939 Planarity : 0.005 0.052 2281 Dihedral : 6.984 79.366 1739 Min Nonbonded Distance : 2.464 Molprobity Statistics. All-atom Clashscore : 13.56 Ramachandran Plot: Outliers : 0.71 % Allowed : 12.02 % Favored : 87.28 % Rotamer: Outliers : 2.97 % Allowed : 18.83 % Favored : 78.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.13 % 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: -3.48 (0.19), residues: 1556 helix: -1.36 (0.19), residues: 648 sheet: -2.70 (0.61), residues: 56 loop : -3.19 (0.19), residues: 852 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP B 204 HIS 0.006 0.001 HIS A 9 PHE 0.020 0.002 PHE B 344 TYR 0.016 0.002 TYR A 45 ARG 0.005 0.000 ARG B 821 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3112 Ramachandran restraints generated. 1556 Oldfield, 0 Emsley, 1556 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3112 Ramachandran restraints generated. 1556 Oldfield, 0 Emsley, 1556 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 224 residues out of total 1413 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 182 time to evaluate : 1.448 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 140 TYR cc_start: 0.7027 (p90) cc_final: 0.5741 (p90) REVERT: A 505 LEU cc_start: 0.7340 (mt) cc_final: 0.7042 (mp) REVERT: A 712 ASN cc_start: 0.6541 (m110) cc_final: 0.6203 (t0) REVERT: A 776 ARG cc_start: 0.7954 (mmp80) cc_final: 0.6674 (ttm-80) REVERT: A 822 TYR cc_start: 0.7358 (m-80) cc_final: 0.7056 (m-80) REVERT: B 539 ILE cc_start: 0.8822 (mm) cc_final: 0.8575 (mm) REVERT: B 557 ASP cc_start: 0.7729 (p0) cc_final: 0.7359 (t0) REVERT: B 656 TYR cc_start: 0.7118 (t80) cc_final: 0.6462 (t80) REVERT: B 711 LYS cc_start: 0.8325 (pptt) cc_final: 0.8007 (pptt) REVERT: B 770 TYR cc_start: 0.5372 (m-80) cc_final: 0.4862 (m-80) REVERT: B 820 TYR cc_start: 0.7570 (OUTLIER) cc_final: 0.7197 (m-80) REVERT: B 860 ASP cc_start: 0.6554 (m-30) cc_final: 0.6177 (m-30) REVERT: B 863 LEU cc_start: 0.4420 (OUTLIER) cc_final: 0.4045 (mt) outliers start: 42 outliers final: 26 residues processed: 213 average time/residue: 0.2329 time to fit residues: 74.6163 Evaluate side-chains 186 residues out of total 1413 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 158 time to evaluate : 1.579 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 VAL Chi-restraints excluded: chain A residue 72 LEU Chi-restraints excluded: chain A residue 254 LEU Chi-restraints excluded: chain A residue 259 THR Chi-restraints excluded: chain A residue 426 THR Chi-restraints excluded: chain A residue 451 ILE Chi-restraints excluded: chain A residue 518 PHE Chi-restraints excluded: chain A residue 589 ILE Chi-restraints excluded: chain A residue 704 LEU Chi-restraints excluded: chain A residue 722 LEU Chi-restraints excluded: chain A residue 762 ILE Chi-restraints excluded: chain A residue 773 SER Chi-restraints excluded: chain A residue 797 VAL Chi-restraints excluded: chain B residue 27 GLN Chi-restraints excluded: chain B residue 30 LEU Chi-restraints excluded: chain B residue 47 TYR Chi-restraints excluded: chain B residue 60 ILE Chi-restraints excluded: chain B residue 319 VAL Chi-restraints excluded: chain B residue 356 LEU Chi-restraints excluded: chain B residue 454 VAL Chi-restraints excluded: chain B residue 504 THR Chi-restraints excluded: chain B residue 534 PHE Chi-restraints excluded: chain B residue 564 GLN Chi-restraints excluded: chain B residue 592 ILE Chi-restraints excluded: chain B residue 633 LEU Chi-restraints excluded: chain B residue 820 TYR Chi-restraints excluded: chain B residue 856 VAL Chi-restraints excluded: chain B residue 863 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 158 random chunks: chunk 51 optimal weight: 7.9990 chunk 137 optimal weight: 4.9990 chunk 30 optimal weight: 5.9990 chunk 89 optimal weight: 6.9990 chunk 37 optimal weight: 10.0000 chunk 152 optimal weight: 10.0000 chunk 126 optimal weight: 2.9990 chunk 70 optimal weight: 2.9990 chunk 12 optimal weight: 3.9990 chunk 50 optimal weight: 2.9990 chunk 80 optimal weight: 5.9990 overall best weight: 3.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 137 ASN ** A 868 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 27 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 385 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 481 HIS B 615 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6938 moved from start: 0.3910 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.057 13331 Z= 0.347 Angle : 0.835 11.170 18034 Z= 0.436 Chirality : 0.051 0.196 1939 Planarity : 0.005 0.053 2281 Dihedral : 7.391 78.864 1739 Min Nonbonded Distance : 2.423 Molprobity Statistics. All-atom Clashscore : 16.08 Ramachandran Plot: Outliers : 0.71 % Allowed : 13.05 % Favored : 86.25 % Rotamer: Outliers : 3.61 % Allowed : 19.39 % Favored : 77.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % 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: -3.64 (0.19), residues: 1556 helix: -1.48 (0.19), residues: 655 sheet: -2.93 (0.58), residues: 56 loop : -3.29 (0.19), residues: 845 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP A 590 HIS 0.010 0.002 HIS A 9 PHE 0.039 0.002 PHE A 13 TYR 0.019 0.002 TYR A 45 ARG 0.007 0.001 ARG B 821 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3112 Ramachandran restraints generated. 1556 Oldfield, 0 Emsley, 1556 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3112 Ramachandran restraints generated. 1556 Oldfield, 0 Emsley, 1556 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 219 residues out of total 1413 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 168 time to evaluate : 1.827 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 140 TYR cc_start: 0.7117 (p90) cc_final: 0.5836 (p90) REVERT: A 440 LEU cc_start: 0.5002 (OUTLIER) cc_final: 0.4573 (tp) REVERT: A 518 PHE cc_start: 0.6629 (OUTLIER) cc_final: 0.5862 (t80) REVERT: A 712 ASN cc_start: 0.6678 (m110) cc_final: 0.6313 (t0) REVERT: A 776 ARG cc_start: 0.7988 (mmp80) cc_final: 0.6672 (ttm-80) REVERT: B 475 LYS cc_start: 0.7452 (OUTLIER) cc_final: 0.7246 (pttm) REVERT: B 539 ILE cc_start: 0.8949 (mm) cc_final: 0.8706 (mm) REVERT: B 557 ASP cc_start: 0.7888 (p0) cc_final: 0.7313 (p0) REVERT: B 711 LYS cc_start: 0.8363 (pptt) cc_final: 0.7998 (pptt) REVERT: B 770 TYR cc_start: 0.5431 (m-80) cc_final: 0.5045 (m-80) REVERT: B 820 TYR cc_start: 0.7609 (OUTLIER) cc_final: 0.7258 (m-80) outliers start: 51 outliers final: 31 residues processed: 206 average time/residue: 0.2531 time to fit residues: 76.6126 Evaluate side-chains 189 residues out of total 1413 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 154 time to evaluate : 2.064 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 72 LEU Chi-restraints excluded: chain A residue 254 LEU Chi-restraints excluded: chain A residue 259 THR Chi-restraints excluded: chain A residue 426 THR Chi-restraints excluded: chain A residue 440 LEU Chi-restraints excluded: chain A residue 444 LEU Chi-restraints excluded: chain A residue 518 PHE Chi-restraints excluded: chain A residue 589 ILE Chi-restraints excluded: chain A residue 670 VAL Chi-restraints excluded: chain A residue 722 LEU Chi-restraints excluded: chain A residue 762 ILE Chi-restraints excluded: chain A residue 773 SER Chi-restraints excluded: chain A residue 797 VAL Chi-restraints excluded: chain A residue 843 ASP Chi-restraints excluded: chain B residue 27 GLN Chi-restraints excluded: chain B residue 30 LEU Chi-restraints excluded: chain B residue 47 TYR Chi-restraints excluded: chain B residue 60 ILE Chi-restraints excluded: chain B residue 158 VAL Chi-restraints excluded: chain B residue 319 VAL Chi-restraints excluded: chain B residue 345 HIS Chi-restraints excluded: chain B residue 356 LEU Chi-restraints excluded: chain B residue 416 TYR Chi-restraints excluded: chain B residue 454 VAL Chi-restraints excluded: chain B residue 475 LYS Chi-restraints excluded: chain B residue 504 THR Chi-restraints excluded: chain B residue 534 PHE Chi-restraints excluded: chain B residue 564 GLN Chi-restraints excluded: chain B residue 592 ILE Chi-restraints excluded: chain B residue 633 LEU Chi-restraints excluded: chain B residue 755 LEU Chi-restraints excluded: chain B residue 788 LEU Chi-restraints excluded: chain B residue 820 TYR Chi-restraints excluded: chain B residue 856 VAL Chi-restraints excluded: chain B residue 863 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 158 random chunks: chunk 147 optimal weight: 9.9990 chunk 17 optimal weight: 1.9990 chunk 87 optimal weight: 0.6980 chunk 111 optimal weight: 1.9990 chunk 86 optimal weight: 2.9990 chunk 128 optimal weight: 1.9990 chunk 85 optimal weight: 0.9980 chunk 152 optimal weight: 7.9990 chunk 95 optimal weight: 9.9990 chunk 92 optimal weight: 7.9990 chunk 70 optimal weight: 0.9980 overall best weight: 1.3384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 27 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 385 HIS ** B 615 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6795 moved from start: 0.3847 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 13331 Z= 0.199 Angle : 0.745 12.230 18034 Z= 0.384 Chirality : 0.047 0.201 1939 Planarity : 0.005 0.052 2281 Dihedral : 6.892 79.097 1739 Min Nonbonded Distance : 2.450 Molprobity Statistics. All-atom Clashscore : 13.45 Ramachandran Plot: Outliers : 0.58 % Allowed : 11.95 % Favored : 87.47 % Rotamer: Outliers : 3.18 % Allowed : 20.81 % Favored : 76.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % 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: -3.42 (0.20), residues: 1556 helix: -1.26 (0.19), residues: 667 sheet: -2.88 (0.56), residues: 66 loop : -3.20 (0.19), residues: 823 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.002 TRP A 590 HIS 0.005 0.001 HIS B 81 PHE 0.018 0.002 PHE A 13 TYR 0.016 0.001 TYR A 45 ARG 0.004 0.000 ARG B 99 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3112 Ramachandran restraints generated. 1556 Oldfield, 0 Emsley, 1556 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3112 Ramachandran restraints generated. 1556 Oldfield, 0 Emsley, 1556 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 235 residues out of total 1413 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 190 time to evaluate : 1.691 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 140 TYR cc_start: 0.7028 (p90) cc_final: 0.5749 (p90) REVERT: A 337 LEU cc_start: 0.6229 (OUTLIER) cc_final: 0.5991 (mm) REVERT: A 415 LEU cc_start: 0.6382 (mm) cc_final: 0.6074 (tp) REVERT: A 712 ASN cc_start: 0.6699 (m110) cc_final: 0.6360 (t0) REVERT: B 539 ILE cc_start: 0.8821 (mm) cc_final: 0.8571 (mm) REVERT: B 557 ASP cc_start: 0.7745 (p0) cc_final: 0.7221 (p0) REVERT: B 564 GLN cc_start: 0.9225 (OUTLIER) cc_final: 0.8919 (mp10) REVERT: B 656 TYR cc_start: 0.7132 (t80) cc_final: 0.6421 (t80) REVERT: B 711 LYS cc_start: 0.8333 (pptt) cc_final: 0.8006 (pptt) REVERT: B 770 TYR cc_start: 0.5421 (m-80) cc_final: 0.4940 (m-80) REVERT: B 820 TYR cc_start: 0.7521 (OUTLIER) cc_final: 0.7096 (m-80) REVERT: B 836 ASN cc_start: 0.7759 (t0) cc_final: 0.7427 (t0) REVERT: B 860 ASP cc_start: 0.6613 (m-30) cc_final: 0.6294 (m-30) outliers start: 45 outliers final: 27 residues processed: 219 average time/residue: 0.2485 time to fit residues: 81.0565 Evaluate side-chains 198 residues out of total 1413 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 168 time to evaluate : 1.513 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 72 LEU Chi-restraints excluded: chain A residue 87 PHE Chi-restraints excluded: chain A residue 254 LEU Chi-restraints excluded: chain A residue 259 THR Chi-restraints excluded: chain A residue 337 LEU Chi-restraints excluded: chain A residue 416 TYR Chi-restraints excluded: chain A residue 426 THR Chi-restraints excluded: chain A residue 518 PHE Chi-restraints excluded: chain A residue 704 LEU Chi-restraints excluded: chain A residue 722 LEU Chi-restraints excluded: chain A residue 762 ILE Chi-restraints excluded: chain A residue 773 SER Chi-restraints excluded: chain B residue 12 PHE Chi-restraints excluded: chain B residue 27 GLN Chi-restraints excluded: chain B residue 30 LEU Chi-restraints excluded: chain B residue 53 VAL Chi-restraints excluded: chain B residue 60 ILE Chi-restraints excluded: chain B residue 158 VAL Chi-restraints excluded: chain B residue 319 VAL Chi-restraints excluded: chain B residue 345 HIS Chi-restraints excluded: chain B residue 356 LEU Chi-restraints excluded: chain B residue 416 TYR Chi-restraints excluded: chain B residue 534 PHE Chi-restraints excluded: chain B residue 564 GLN Chi-restraints excluded: chain B residue 592 ILE Chi-restraints excluded: chain B residue 633 LEU Chi-restraints excluded: chain B residue 788 LEU Chi-restraints excluded: chain B residue 820 TYR Chi-restraints excluded: chain B residue 856 VAL Chi-restraints excluded: chain B residue 863 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 158 random chunks: chunk 94 optimal weight: 0.0770 chunk 60 optimal weight: 0.4980 chunk 90 optimal weight: 10.0000 chunk 45 optimal weight: 8.9990 chunk 29 optimal weight: 8.9990 chunk 96 optimal weight: 0.8980 chunk 103 optimal weight: 8.9990 chunk 75 optimal weight: 2.9990 chunk 14 optimal weight: 9.9990 chunk 119 optimal weight: 3.9990 chunk 138 optimal weight: 0.0000 overall best weight: 0.8944 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 413 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 227 ASN B 355 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6726 moved from start: 0.3892 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 13331 Z= 0.181 Angle : 0.732 11.603 18034 Z= 0.376 Chirality : 0.046 0.191 1939 Planarity : 0.005 0.060 2281 Dihedral : 6.628 77.768 1739 Min Nonbonded Distance : 2.430 Molprobity Statistics. All-atom Clashscore : 12.21 Ramachandran Plot: Outliers : 0.58 % Allowed : 12.28 % Favored : 87.15 % Rotamer: Outliers : 2.97 % Allowed : 21.59 % Favored : 75.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % 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: -3.31 (0.20), residues: 1556 helix: -1.12 (0.20), residues: 666 sheet: -2.73 (0.57), residues: 66 loop : -3.21 (0.19), residues: 824 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP A 590 HIS 0.006 0.001 HIS B 522 PHE 0.023 0.002 PHE B 344 TYR 0.029 0.001 TYR A 822 ARG 0.004 0.000 ARG A 821 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3112 Ramachandran restraints generated. 1556 Oldfield, 0 Emsley, 1556 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3112 Ramachandran restraints generated. 1556 Oldfield, 0 Emsley, 1556 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 227 residues out of total 1413 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 185 time to evaluate : 1.577 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 140 TYR cc_start: 0.7031 (p90) cc_final: 0.5763 (p90) REVERT: A 712 ASN cc_start: 0.6649 (m110) cc_final: 0.6336 (t0) REVERT: B 45 TYR cc_start: 0.7370 (t80) cc_final: 0.6855 (t80) REVERT: B 260 TYR cc_start: 0.7257 (m-80) cc_final: 0.6360 (t80) REVERT: B 539 ILE cc_start: 0.8725 (mm) cc_final: 0.8492 (mm) REVERT: B 557 ASP cc_start: 0.7833 (p0) cc_final: 0.7371 (p0) REVERT: B 711 LYS cc_start: 0.8424 (pptt) cc_final: 0.8044 (pptt) REVERT: B 770 TYR cc_start: 0.5294 (m-80) cc_final: 0.4775 (m-80) REVERT: B 820 TYR cc_start: 0.7465 (OUTLIER) cc_final: 0.7047 (m-80) REVERT: B 836 ASN cc_start: 0.7716 (t0) cc_final: 0.7459 (t0) REVERT: B 860 ASP cc_start: 0.6618 (m-30) cc_final: 0.6287 (m-30) outliers start: 42 outliers final: 29 residues processed: 211 average time/residue: 0.2458 time to fit residues: 77.4240 Evaluate side-chains 199 residues out of total 1413 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 169 time to evaluate : 1.509 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 VAL Chi-restraints excluded: chain A residue 72 LEU Chi-restraints excluded: chain A residue 254 LEU Chi-restraints excluded: chain A residue 259 THR Chi-restraints excluded: chain A residue 268 GLU Chi-restraints excluded: chain A residue 416 TYR Chi-restraints excluded: chain A residue 426 THR Chi-restraints excluded: chain A residue 518 PHE Chi-restraints excluded: chain A residue 534 PHE Chi-restraints excluded: chain A residue 704 LEU Chi-restraints excluded: chain A residue 722 LEU Chi-restraints excluded: chain A residue 762 ILE Chi-restraints excluded: chain A residue 773 SER Chi-restraints excluded: chain A residue 817 GLU Chi-restraints excluded: chain A residue 859 MET Chi-restraints excluded: chain B residue 27 GLN Chi-restraints excluded: chain B residue 53 VAL Chi-restraints excluded: chain B residue 158 VAL Chi-restraints excluded: chain B residue 319 VAL Chi-restraints excluded: chain B residue 345 HIS Chi-restraints excluded: chain B residue 356 LEU Chi-restraints excluded: chain B residue 416 TYR Chi-restraints excluded: chain B residue 534 PHE Chi-restraints excluded: chain B residue 564 GLN Chi-restraints excluded: chain B residue 592 ILE Chi-restraints excluded: chain B residue 633 LEU Chi-restraints excluded: chain B residue 788 LEU Chi-restraints excluded: chain B residue 820 TYR Chi-restraints excluded: chain B residue 856 VAL Chi-restraints excluded: chain B residue 863 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 158 random chunks: chunk 145 optimal weight: 0.9990 chunk 133 optimal weight: 10.0000 chunk 141 optimal weight: 5.9990 chunk 85 optimal weight: 8.9990 chunk 61 optimal weight: 9.9990 chunk 111 optimal weight: 3.9990 chunk 43 optimal weight: 1.9990 chunk 128 optimal weight: 0.8980 chunk 134 optimal weight: 0.9990 chunk 93 optimal weight: 5.9990 chunk 150 optimal weight: 0.7980 overall best weight: 1.1386 ------------------------------------------------------------------------------- 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: 0.6725 moved from start: 0.3999 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 13331 Z= 0.195 Angle : 0.735 11.260 18034 Z= 0.377 Chirality : 0.047 0.193 1939 Planarity : 0.005 0.052 2281 Dihedral : 6.537 76.423 1739 Min Nonbonded Distance : 2.429 Molprobity Statistics. All-atom Clashscore : 12.79 Ramachandran Plot: Outliers : 0.51 % Allowed : 12.02 % Favored : 87.47 % Rotamer: Outliers : 2.97 % Allowed : 22.08 % Favored : 74.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % 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: -3.24 (0.20), residues: 1556 helix: -1.04 (0.20), residues: 666 sheet: -2.63 (0.58), residues: 66 loop : -3.18 (0.19), residues: 824 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP A 590 HIS 0.005 0.001 HIS B 81 PHE 0.020 0.002 PHE B 344 TYR 0.025 0.001 TYR A 822 ARG 0.004 0.000 ARG A 821 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3112 Ramachandran restraints generated. 1556 Oldfield, 0 Emsley, 1556 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3112 Ramachandran restraints generated. 1556 Oldfield, 0 Emsley, 1556 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 227 residues out of total 1413 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 185 time to evaluate : 1.422 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 140 TYR cc_start: 0.7036 (p90) cc_final: 0.5766 (p90) REVERT: A 337 LEU cc_start: 0.6361 (OUTLIER) cc_final: 0.6101 (mm) REVERT: A 712 ASN cc_start: 0.6614 (m110) cc_final: 0.6399 (t0) REVERT: B 45 TYR cc_start: 0.7389 (t80) cc_final: 0.6880 (t80) REVERT: B 402 GLU cc_start: 0.7719 (mp0) cc_final: 0.7453 (mm-30) REVERT: B 539 ILE cc_start: 0.8721 (mm) cc_final: 0.8488 (mm) REVERT: B 557 ASP cc_start: 0.7913 (p0) cc_final: 0.7463 (p0) REVERT: B 590 TRP cc_start: 0.5414 (p-90) cc_final: 0.5098 (p-90) REVERT: B 711 LYS cc_start: 0.8405 (pptt) cc_final: 0.8015 (pptt) REVERT: B 755 LEU cc_start: 0.5044 (OUTLIER) cc_final: 0.4821 (tp) REVERT: B 770 TYR cc_start: 0.5326 (m-80) cc_final: 0.4769 (m-80) REVERT: B 820 TYR cc_start: 0.7434 (OUTLIER) cc_final: 0.7067 (m-80) REVERT: B 836 ASN cc_start: 0.7707 (t0) cc_final: 0.7387 (t0) REVERT: B 860 ASP cc_start: 0.6707 (m-30) cc_final: 0.6387 (m-30) outliers start: 42 outliers final: 35 residues processed: 209 average time/residue: 0.2445 time to fit residues: 75.8567 Evaluate side-chains 209 residues out of total 1413 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 171 time to evaluate : 1.496 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 VAL Chi-restraints excluded: chain A residue 72 LEU Chi-restraints excluded: chain A residue 87 PHE Chi-restraints excluded: chain A residue 254 LEU Chi-restraints excluded: chain A residue 259 THR Chi-restraints excluded: chain A residue 268 GLU Chi-restraints excluded: chain A residue 337 LEU Chi-restraints excluded: chain A residue 385 HIS Chi-restraints excluded: chain A residue 416 TYR Chi-restraints excluded: chain A residue 426 THR Chi-restraints excluded: chain A residue 444 LEU Chi-restraints excluded: chain A residue 518 PHE Chi-restraints excluded: chain A residue 534 PHE Chi-restraints excluded: chain A residue 581 LEU Chi-restraints excluded: chain A residue 589 ILE Chi-restraints excluded: chain A residue 704 LEU Chi-restraints excluded: chain A residue 722 LEU Chi-restraints excluded: chain A residue 762 ILE Chi-restraints excluded: chain A residue 774 LEU Chi-restraints excluded: chain A residue 817 GLU Chi-restraints excluded: chain A residue 859 MET Chi-restraints excluded: chain B residue 12 PHE Chi-restraints excluded: chain B residue 27 GLN Chi-restraints excluded: chain B residue 53 VAL Chi-restraints excluded: chain B residue 158 VAL Chi-restraints excluded: chain B residue 319 VAL Chi-restraints excluded: chain B residue 345 HIS Chi-restraints excluded: chain B residue 356 LEU Chi-restraints excluded: chain B residue 416 TYR Chi-restraints excluded: chain B residue 534 PHE Chi-restraints excluded: chain B residue 564 GLN Chi-restraints excluded: chain B residue 592 ILE Chi-restraints excluded: chain B residue 633 LEU Chi-restraints excluded: chain B residue 755 LEU Chi-restraints excluded: chain B residue 788 LEU Chi-restraints excluded: chain B residue 820 TYR Chi-restraints excluded: chain B residue 856 VAL Chi-restraints excluded: chain B residue 863 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 158 random chunks: chunk 91 optimal weight: 5.9990 chunk 71 optimal weight: 8.9990 chunk 104 optimal weight: 3.9990 chunk 157 optimal weight: 6.9990 chunk 144 optimal weight: 0.9980 chunk 125 optimal weight: 1.9990 chunk 13 optimal weight: 5.9990 chunk 96 optimal weight: 7.9990 chunk 76 optimal weight: 0.7980 chunk 99 optimal weight: 3.9990 chunk 133 optimal weight: 9.9990 overall best weight: 2.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 868 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 27 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 221 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6834 moved from start: 0.4187 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 13331 Z= 0.266 Angle : 0.787 10.789 18034 Z= 0.408 Chirality : 0.049 0.197 1939 Planarity : 0.005 0.052 2281 Dihedral : 6.815 75.227 1739 Min Nonbonded Distance : 2.418 Molprobity Statistics. All-atom Clashscore : 15.04 Ramachandran Plot: Outliers : 0.51 % Allowed : 12.72 % Favored : 86.76 % Rotamer: Outliers : 3.04 % Allowed : 22.22 % Favored : 74.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % 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: -3.28 (0.20), residues: 1556 helix: -1.10 (0.20), residues: 660 sheet: -2.13 (0.75), residues: 39 loop : -3.21 (0.19), residues: 857 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP A 590 HIS 0.007 0.001 HIS A 9 PHE 0.020 0.002 PHE B 344 TYR 0.025 0.002 TYR A 822 ARG 0.006 0.001 ARG B 821 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3112 Ramachandran restraints generated. 1556 Oldfield, 0 Emsley, 1556 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3112 Ramachandran restraints generated. 1556 Oldfield, 0 Emsley, 1556 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 215 residues out of total 1413 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 172 time to evaluate : 1.596 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 140 TYR cc_start: 0.7038 (p90) cc_final: 0.5769 (p90) REVERT: A 337 LEU cc_start: 0.6235 (OUTLIER) cc_final: 0.5951 (mm) REVERT: A 421 THR cc_start: 0.7365 (m) cc_final: 0.6459 (p) REVERT: A 712 ASN cc_start: 0.6711 (m110) cc_final: 0.6438 (t0) REVERT: B 260 TYR cc_start: 0.7299 (m-80) cc_final: 0.6209 (t80) REVERT: B 539 ILE cc_start: 0.8875 (mm) cc_final: 0.8645 (mm) REVERT: B 557 ASP cc_start: 0.7786 (p0) cc_final: 0.7350 (p0) REVERT: B 711 LYS cc_start: 0.8402 (pptt) cc_final: 0.8033 (pptt) REVERT: B 770 TYR cc_start: 0.5394 (m-80) cc_final: 0.4936 (m-80) REVERT: B 820 TYR cc_start: 0.7543 (OUTLIER) cc_final: 0.7170 (m-80) REVERT: B 836 ASN cc_start: 0.7767 (t0) cc_final: 0.7449 (t0) REVERT: B 860 ASP cc_start: 0.6832 (m-30) cc_final: 0.6496 (m-30) outliers start: 43 outliers final: 34 residues processed: 200 average time/residue: 0.2398 time to fit residues: 72.4717 Evaluate side-chains 201 residues out of total 1413 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 165 time to evaluate : 1.571 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 VAL Chi-restraints excluded: chain A residue 72 LEU Chi-restraints excluded: chain A residue 87 PHE Chi-restraints excluded: chain A residue 254 LEU Chi-restraints excluded: chain A residue 259 THR Chi-restraints excluded: chain A residue 268 GLU Chi-restraints excluded: chain A residue 337 LEU Chi-restraints excluded: chain A residue 385 HIS Chi-restraints excluded: chain A residue 416 TYR Chi-restraints excluded: chain A residue 426 THR Chi-restraints excluded: chain A residue 444 LEU Chi-restraints excluded: chain A residue 518 PHE Chi-restraints excluded: chain A residue 581 LEU Chi-restraints excluded: chain A residue 589 ILE Chi-restraints excluded: chain A residue 670 VAL Chi-restraints excluded: chain A residue 704 LEU Chi-restraints excluded: chain A residue 762 ILE Chi-restraints excluded: chain A residue 774 LEU Chi-restraints excluded: chain A residue 817 GLU Chi-restraints excluded: chain A residue 859 MET Chi-restraints excluded: chain B residue 12 PHE Chi-restraints excluded: chain B residue 27 GLN Chi-restraints excluded: chain B residue 53 VAL Chi-restraints excluded: chain B residue 158 VAL Chi-restraints excluded: chain B residue 319 VAL Chi-restraints excluded: chain B residue 345 HIS Chi-restraints excluded: chain B residue 356 LEU Chi-restraints excluded: chain B residue 416 TYR Chi-restraints excluded: chain B residue 534 PHE Chi-restraints excluded: chain B residue 589 ILE Chi-restraints excluded: chain B residue 633 LEU Chi-restraints excluded: chain B residue 755 LEU Chi-restraints excluded: chain B residue 788 LEU Chi-restraints excluded: chain B residue 820 TYR Chi-restraints excluded: chain B residue 856 VAL Chi-restraints excluded: chain B residue 863 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 158 random chunks: chunk 38 optimal weight: 5.9990 chunk 115 optimal weight: 0.0470 chunk 18 optimal weight: 9.9990 chunk 34 optimal weight: 0.1980 chunk 125 optimal weight: 0.7980 chunk 52 optimal weight: 2.9990 chunk 128 optimal weight: 0.0980 chunk 15 optimal weight: 20.0000 chunk 23 optimal weight: 0.3980 chunk 110 optimal weight: 5.9990 chunk 7 optimal weight: 9.9990 overall best weight: 0.3078 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 790 ASN A 800 ASN ** A 812 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 861 ASN B 33 ASN B 564 GLN B 572 ASN B 608 HIS ** B 818 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4488 r_free = 0.4488 target = 0.178820 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4195 r_free = 0.4195 target = 0.153644 restraints weight = 24426.202| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.4234 r_free = 0.4234 target = 0.157029 restraints weight = 15515.283| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.4262 r_free = 0.4262 target = 0.159338 restraints weight = 11298.156| |-----------------------------------------------------------------------------| r_work (final): 0.4274 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6635 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 0.043 13331 Z= 0.176 Angle : 0.743 11.134 18034 Z= 0.379 Chirality : 0.046 0.198 1939 Planarity : 0.005 0.057 2281 Dihedral : 6.277 72.791 1739 Min Nonbonded Distance : 2.427 Molprobity Statistics. All-atom Clashscore : 11.78 Ramachandran Plot: Outliers : 0.58 % Allowed : 10.93 % Favored : 88.50 % Rotamer: Outliers : 2.26 % Allowed : 23.07 % Favored : 74.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.05 (0.20), residues: 1556 helix: -0.91 (0.20), residues: 657 sheet: -2.32 (0.64), residues: 61 loop : -3.06 (0.19), residues: 838 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP A 291 HIS 0.006 0.001 HIS B 81 PHE 0.020 0.001 PHE B 344 TYR 0.022 0.001 TYR A 822 ARG 0.004 0.000 ARG B 99 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2479.18 seconds wall clock time: 46 minutes 34.75 seconds (2794.75 seconds total)