Starting phenix.real_space_refine on Sat Oct 11 07:49:28 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8w7a_37337/10_2025/8w7a_37337.cif Found real_map, /net/cci-nas-00/data/ceres_data/8w7a_37337/10_2025/8w7a_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/cci-nas-00/data/ceres_data/8w7a_37337/10_2025/8w7a_37337.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8w7a_37337/10_2025/8w7a_37337.map" model { file = "/net/cci-nas-00/data/ceres_data/8w7a_37337/10_2025/8w7a_37337.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8w7a_37337/10_2025/8w7a_37337.cif" } resolution = 3.77 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.003 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): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5842/lib/python3.9/site-packages/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: 3.15, per 1000 atoms: 0.24 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: 0.88 Conformation dependent library (CDL) restraints added in 618.9 milliseconds Enol-peptide restraints added in 1.2 microseconds 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: 0.38 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: 2.22 Time building geometry restraints manager: 1.26 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: 1.410 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: 0.270 Check model and map are aligned: 0.060 Set scattering table: 0.030 Process input model: 12.440 Find NCS groups from input model: 0.220 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.440 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 15.890 ------------------------------------------------------------------------------- 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= 0.305 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -4.55 (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 ARG 0.006 0.001 ARG A 128 TYR 0.034 0.003 TYR B 140 PHE 0.037 0.003 PHE A 5 TRP 0.049 0.003 TRP B 204 HIS 0.020 0.002 HIS A 413 Details of bonding type rmsd covalent geometry : bond 0.00662 (13331) covalent geometry : angle 1.37255 (18034) hydrogen bonds : bond 0.22672 ( 342) hydrogen bonds : angle 8.30379 ( 981) *********************** 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 : 0.513 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: 0.5063 (m-80) REVERT: A 249 ARG cc_start: 0.7324 (ppt170) cc_final: 0.7121 (ppt170) REVERT: A 532 ILE cc_start: 0.7787 (mm) cc_final: 0.7426 (pt) REVERT: A 846 SER cc_start: 0.7997 (m) cc_final: 0.7796 (m) REVERT: B 557 ASP cc_start: 0.7595 (p0) cc_final: 0.7253 (p0) REVERT: B 615 ASN cc_start: 0.8194 (p0) cc_final: 0.7324 (p0) REVERT: B 656 TYR cc_start: 0.7066 (t80) cc_final: 0.6499 (t80) REVERT: B 660 TYR cc_start: 0.7740 (t80) cc_final: 0.7301 (t80) outliers start: 0 outliers final: 0 residues processed: 252 average time/residue: 0.1007 time to fit residues: 37.6646 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 : 0.544 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 158 random chunks: chunk 98 optimal weight: 2.9990 chunk 107 optimal weight: 0.5980 chunk 10 optimal weight: 3.9990 chunk 66 optimal weight: 0.6980 chunk 130 optimal weight: 2.9990 chunk 124 optimal weight: 6.9990 chunk 103 optimal weight: 0.8980 chunk 77 optimal weight: 2.9990 chunk 122 optimal weight: 3.9990 chunk 91 optimal weight: 3.9990 chunk 149 optimal weight: 0.9990 overall best weight: 1.2384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4427 r_free = 0.4427 target = 0.174554 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.4112 r_free = 0.4112 target = 0.147225 restraints weight = 24048.716| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.4158 r_free = 0.4158 target = 0.151111 restraints weight = 14219.302| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.4189 r_free = 0.4189 target = 0.153732 restraints weight = 9874.661| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 43)----------------| | r_work = 0.4210 r_free = 0.4210 target = 0.155531 restraints weight = 7674.058| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.4223 r_free = 0.4223 target = 0.156753 restraints weight = 6426.827| |-----------------------------------------------------------------------------| r_work (final): 0.4249 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6561 moved from start: 0.1928 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= 0.141 Angle : 0.777 9.650 18034 Z= 0.404 Chirality : 0.048 0.301 1939 Planarity : 0.006 0.129 2281 Dihedral : 7.303 77.628 1739 Min Nonbonded Distance : 2.444 Molprobity Statistics. All-atom Clashscore : 11.05 Ramachandran Plot: Outliers : 0.84 % Allowed : 10.41 % Favored : 88.75 % Rotamer: Outliers : 1.20 % Allowed : 10.47 % Favored : 88.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.13 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -3.89 (0.18), residues: 1556 helix: -2.13 (0.18), residues: 636 sheet: -2.59 (0.63), residues: 63 loop : -3.03 (0.18), residues: 857 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 654 TYR 0.019 0.002 TYR A 416 PHE 0.024 0.002 PHE B 200 TRP 0.018 0.002 TRP B 204 HIS 0.005 0.001 HIS B 522 Details of bonding type rmsd covalent geometry : bond 0.00300 (13331) covalent geometry : angle 0.77664 (18034) hydrogen bonds : bond 0.04594 ( 342) hydrogen bonds : angle 5.57726 ( 981) *********************** 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 207 residues out of total 1413 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 190 time to evaluate : 0.462 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 140 TYR cc_start: 0.7144 (p90) cc_final: 0.5870 (p90) REVERT: A 153 TYR cc_start: 0.5304 (m-80) cc_final: 0.5099 (m-80) REVERT: A 249 ARG cc_start: 0.7024 (ppt170) cc_final: 0.6726 (ppt170) REVERT: A 417 MET cc_start: 0.4475 (mtt) cc_final: 0.4151 (mtt) REVERT: A 532 ILE cc_start: 0.7996 (mm) cc_final: 0.7484 (pt) REVERT: A 559 TYR cc_start: 0.7858 (m-80) cc_final: 0.7634 (m-80) REVERT: A 776 ARG cc_start: 0.7732 (mmp80) cc_final: 0.6576 (ttm-80) REVERT: B 557 ASP cc_start: 0.7578 (p0) cc_final: 0.7071 (p0) REVERT: B 656 TYR cc_start: 0.7003 (t80) cc_final: 0.6484 (t80) REVERT: B 863 LEU cc_start: 0.4277 (OUTLIER) cc_final: 0.3941 (mt) outliers start: 17 outliers final: 9 residues processed: 201 average time/residue: 0.0952 time to fit residues: 29.1819 Evaluate side-chains 177 residues out of total 1413 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 167 time to evaluate : 0.385 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 426 THR Chi-restraints excluded: chain A residue 718 VAL 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 863 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 158 random chunks: chunk 121 optimal weight: 7.9990 chunk 2 optimal weight: 5.9990 chunk 111 optimal weight: 0.5980 chunk 26 optimal weight: 7.9990 chunk 42 optimal weight: 4.9990 chunk 58 optimal weight: 2.9990 chunk 5 optimal weight: 8.9990 chunk 127 optimal weight: 7.9990 chunk 137 optimal weight: 7.9990 chunk 94 optimal weight: 10.0000 chunk 89 optimal weight: 9.9990 overall best weight: 4.5188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 39 ASN A 137 ASN A 345 HIS ** A 678 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 868 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 522 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4333 r_free = 0.4333 target = 0.164633 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3982 r_free = 0.3982 target = 0.136342 restraints weight = 25088.337| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.4025 r_free = 0.4025 target = 0.139609 restraints weight = 15894.380| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.4054 r_free = 0.4054 target = 0.141855 restraints weight = 11798.393| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.4067 r_free = 0.4067 target = 0.143093 restraints weight = 9651.299| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 39)----------------| | r_work = 0.4084 r_free = 0.4084 target = 0.144251 restraints weight = 8491.886| |-----------------------------------------------------------------------------| r_work (final): 0.4097 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6974 moved from start: 0.3265 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.057 13331 Z= 0.293 Angle : 0.919 10.597 18034 Z= 0.486 Chirality : 0.054 0.290 1939 Planarity : 0.006 0.094 2281 Dihedral : 7.936 81.884 1739 Min Nonbonded Distance : 2.430 Molprobity Statistics. All-atom Clashscore : 17.71 Ramachandran Plot: Outliers : 0.90 % Allowed : 12.98 % Favored : 86.12 % Rotamer: Outliers : 3.54 % Allowed : 14.58 % Favored : 81.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.20 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -4.03 (0.18), residues: 1556 helix: -2.12 (0.17), residues: 655 sheet: -2.79 (0.58), residues: 70 loop : -3.23 (0.19), residues: 831 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 128 TYR 0.023 0.003 TYR A 416 PHE 0.037 0.003 PHE B 13 TRP 0.017 0.002 TRP B 696 HIS 0.012 0.002 HIS A 9 Details of bonding type rmsd covalent geometry : bond 0.00668 (13331) covalent geometry : angle 0.91930 (18034) hydrogen bonds : bond 0.05504 ( 342) hydrogen bonds : angle 5.90873 ( 981) *********************** 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 227 residues out of total 1413 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 177 time to evaluate : 0.492 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 140 TYR cc_start: 0.7301 (p90) cc_final: 0.5958 (p90) REVERT: A 249 ARG cc_start: 0.7214 (ppt170) cc_final: 0.6800 (ppt170) REVERT: A 532 ILE cc_start: 0.7773 (mm) cc_final: 0.7165 (mp) REVERT: A 776 ARG cc_start: 0.7880 (mmp80) cc_final: 0.6638 (ttm-80) REVERT: B 564 GLN cc_start: 0.9173 (OUTLIER) cc_final: 0.8936 (mt0) REVERT: B 595 PHE cc_start: 0.7885 (t80) cc_final: 0.7672 (t80) REVERT: B 711 LYS cc_start: 0.8449 (pptt) cc_final: 0.7916 (pptt) REVERT: B 770 TYR cc_start: 0.5621 (m-80) cc_final: 0.5134 (m-80) REVERT: B 835 ASP cc_start: 0.6657 (m-30) cc_final: 0.6393 (t70) REVERT: B 863 LEU cc_start: 0.4400 (OUTLIER) cc_final: 0.4064 (mp) outliers start: 50 outliers final: 26 residues processed: 215 average time/residue: 0.1007 time to fit residues: 32.0328 Evaluate side-chains 182 residues out of total 1413 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 154 time to evaluate : 0.374 ------------------------------------------------------------------------------- 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 670 VAL Chi-restraints excluded: chain A residue 752 LEU Chi-restraints excluded: chain A residue 773 SER Chi-restraints excluded: chain A residue 793 CYS 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 259 THR Chi-restraints excluded: chain B residue 319 VAL Chi-restraints excluded: chain B residue 356 LEU Chi-restraints excluded: chain B residue 367 ILE 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 602 VAL Chi-restraints excluded: chain B residue 633 LEU Chi-restraints excluded: chain B residue 653 LEU Chi-restraints excluded: chain B residue 723 VAL Chi-restraints excluded: chain B residue 784 VAL 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 72 optimal weight: 8.9990 chunk 101 optimal weight: 6.9990 chunk 157 optimal weight: 2.9990 chunk 151 optimal weight: 6.9990 chunk 78 optimal weight: 4.9990 chunk 142 optimal weight: 10.0000 chunk 103 optimal weight: 6.9990 chunk 44 optimal weight: 2.9990 chunk 88 optimal weight: 1.9990 chunk 35 optimal weight: 4.9990 chunk 156 optimal weight: 0.9980 overall best weight: 2.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 678 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 27 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 81 HIS B 385 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4363 r_free = 0.4363 target = 0.166715 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.4019 r_free = 0.4019 target = 0.138788 restraints weight = 24104.655| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.4061 r_free = 0.4061 target = 0.142118 restraints weight = 15255.336| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.4091 r_free = 0.4091 target = 0.144402 restraints weight = 11249.447| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.4108 r_free = 0.4108 target = 0.145882 restraints weight = 9162.457| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.4119 r_free = 0.4119 target = 0.146859 restraints weight = 7961.086| |-----------------------------------------------------------------------------| r_work (final): 0.4134 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6912 moved from start: 0.3453 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= 0.196 Angle : 0.802 9.899 18034 Z= 0.420 Chirality : 0.049 0.234 1939 Planarity : 0.005 0.053 2281 Dihedral : 7.517 80.889 1739 Min Nonbonded Distance : 2.454 Molprobity Statistics. All-atom Clashscore : 15.04 Ramachandran Plot: Outliers : 0.77 % Allowed : 12.66 % Favored : 86.57 % Rotamer: Outliers : 3.18 % Allowed : 18.61 % Favored : 78.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -3.88 (0.18), residues: 1556 helix: -1.84 (0.18), residues: 654 sheet: -2.84 (0.63), residues: 56 loop : -3.28 (0.18), residues: 846 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 128 TYR 0.021 0.002 TYR A 45 PHE 0.034 0.002 PHE B 200 TRP 0.021 0.002 TRP B 590 HIS 0.008 0.001 HIS A 9 Details of bonding type rmsd covalent geometry : bond 0.00443 (13331) covalent geometry : angle 0.80161 (18034) hydrogen bonds : bond 0.04672 ( 342) hydrogen bonds : angle 5.63180 ( 981) *********************** 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 216 residues out of total 1413 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 171 time to evaluate : 0.334 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 102 LYS cc_start: 0.6566 (mmtp) cc_final: 0.6359 (mmtp) REVERT: A 140 TYR cc_start: 0.7074 (p90) cc_final: 0.5819 (p90) REVERT: A 712 ASN cc_start: 0.6645 (m110) cc_final: 0.6137 (t0) REVERT: A 776 ARG cc_start: 0.7927 (mmp80) cc_final: 0.6634 (ttm110) REVERT: B 260 TYR cc_start: 0.7542 (m-80) cc_final: 0.7337 (m-80) REVERT: B 539 ILE cc_start: 0.8800 (mm) cc_final: 0.8548 (mm) REVERT: B 557 ASP cc_start: 0.7762 (p0) cc_final: 0.7391 (t0) REVERT: B 595 PHE cc_start: 0.7729 (t80) cc_final: 0.7523 (t80) REVERT: B 711 LYS cc_start: 0.8442 (pptt) cc_final: 0.8043 (pptt) REVERT: B 770 TYR cc_start: 0.5534 (m-80) cc_final: 0.5085 (m-80) REVERT: B 788 LEU cc_start: 0.5544 (OUTLIER) cc_final: 0.5149 (tt) REVERT: B 863 LEU cc_start: 0.4318 (OUTLIER) cc_final: 0.3992 (mt) outliers start: 45 outliers final: 25 residues processed: 205 average time/residue: 0.0965 time to fit residues: 29.6099 Evaluate side-chains 184 residues out of total 1413 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 157 time to evaluate : 0.477 ------------------------------------------------------------------------------- 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 451 ILE Chi-restraints excluded: chain A residue 589 ILE Chi-restraints excluded: chain A residue 633 LEU Chi-restraints excluded: chain A residue 752 LEU Chi-restraints excluded: chain A residue 762 ILE Chi-restraints excluded: chain A residue 793 CYS 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 225 PHE Chi-restraints excluded: chain B residue 319 VAL Chi-restraints excluded: chain B residue 356 LEU Chi-restraints excluded: chain B residue 416 TYR 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 809 PHE 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 57 optimal weight: 8.9990 chunk 31 optimal weight: 4.9990 chunk 114 optimal weight: 1.9990 chunk 40 optimal weight: 20.0000 chunk 24 optimal weight: 9.9990 chunk 20 optimal weight: 5.9990 chunk 43 optimal weight: 0.9980 chunk 9 optimal weight: 2.9990 chunk 126 optimal weight: 3.9990 chunk 109 optimal weight: 4.9990 chunk 152 optimal weight: 0.0050 overall best weight: 2.0000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 678 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 27 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 545 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4381 r_free = 0.4381 target = 0.168599 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4047 r_free = 0.4047 target = 0.141163 restraints weight = 25142.393| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.4087 r_free = 0.4087 target = 0.144411 restraints weight = 15938.235| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.4117 r_free = 0.4117 target = 0.146768 restraints weight = 11795.830| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.4136 r_free = 0.4136 target = 0.148321 restraints weight = 9559.100| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 41)----------------| | r_work = 0.4149 r_free = 0.4149 target = 0.149348 restraints weight = 8289.484| |-----------------------------------------------------------------------------| r_work (final): 0.4159 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6868 moved from start: 0.3576 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 13331 Z= 0.161 Angle : 0.751 8.852 18034 Z= 0.392 Chirality : 0.048 0.199 1939 Planarity : 0.005 0.053 2281 Dihedral : 7.194 79.527 1739 Min Nonbonded Distance : 2.459 Molprobity Statistics. All-atom Clashscore : 13.29 Ramachandran Plot: Outliers : 0.71 % Allowed : 12.53 % Favored : 86.76 % Rotamer: Outliers : 3.26 % Allowed : 19.60 % Favored : 77.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.13 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -3.73 (0.19), residues: 1556 helix: -1.58 (0.19), residues: 662 sheet: -3.03 (0.56), residues: 66 loop : -3.31 (0.19), residues: 828 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 511 TYR 0.017 0.002 TYR A 260 PHE 0.017 0.002 PHE A 503 TRP 0.026 0.002 TRP A 590 HIS 0.006 0.001 HIS A 9 Details of bonding type rmsd covalent geometry : bond 0.00360 (13331) covalent geometry : angle 0.75140 (18034) hydrogen bonds : bond 0.04319 ( 342) hydrogen bonds : angle 5.40313 ( 981) *********************** 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 232 residues out of total 1413 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 186 time to evaluate : 0.508 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 140 TYR cc_start: 0.6919 (p90) cc_final: 0.5668 (p90) REVERT: A 518 PHE cc_start: 0.6702 (OUTLIER) cc_final: 0.6306 (t80) REVERT: A 712 ASN cc_start: 0.6624 (m110) cc_final: 0.6211 (t0) REVERT: A 776 ARG cc_start: 0.7991 (mmp80) cc_final: 0.6710 (ttm-80) REVERT: B 539 ILE cc_start: 0.8805 (mm) cc_final: 0.8560 (mm) REVERT: B 557 ASP cc_start: 0.7717 (p0) cc_final: 0.7085 (p0) REVERT: B 564 GLN cc_start: 0.9109 (OUTLIER) cc_final: 0.8812 (mp10) REVERT: B 590 TRP cc_start: 0.5420 (p-90) cc_final: 0.4928 (p-90) REVERT: B 595 PHE cc_start: 0.7740 (t80) cc_final: 0.7539 (t80) REVERT: B 711 LYS cc_start: 0.8432 (pptt) cc_final: 0.7999 (pptt) REVERT: B 770 TYR cc_start: 0.5667 (m-80) cc_final: 0.5248 (m-80) REVERT: B 788 LEU cc_start: 0.5654 (OUTLIER) cc_final: 0.5375 (tt) REVERT: B 820 TYR cc_start: 0.7621 (OUTLIER) cc_final: 0.7314 (m-80) REVERT: B 863 LEU cc_start: 0.4233 (OUTLIER) cc_final: 0.3943 (mp) outliers start: 46 outliers final: 25 residues processed: 221 average time/residue: 0.1006 time to fit residues: 33.0542 Evaluate side-chains 195 residues out of total 1413 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 165 time to evaluate : 0.490 ------------------------------------------------------------------------------- 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 581 LEU Chi-restraints excluded: chain A residue 589 ILE Chi-restraints excluded: chain A residue 614 GLU Chi-restraints excluded: chain A residue 704 LEU Chi-restraints excluded: chain A residue 752 LEU Chi-restraints excluded: chain A residue 762 ILE 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 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 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 809 PHE Chi-restraints excluded: chain B residue 820 TYR 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 154 optimal weight: 0.8980 chunk 41 optimal weight: 0.9980 chunk 42 optimal weight: 0.9980 chunk 124 optimal weight: 3.9990 chunk 56 optimal weight: 7.9990 chunk 157 optimal weight: 2.9990 chunk 28 optimal weight: 0.4980 chunk 24 optimal weight: 9.9990 chunk 142 optimal weight: 9.9990 chunk 29 optimal weight: 9.9990 chunk 47 optimal weight: 6.9990 overall best weight: 1.2782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 678 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 790 ASN ** B 27 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 355 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4408 r_free = 0.4408 target = 0.171206 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.4088 r_free = 0.4088 target = 0.144683 restraints weight = 24673.586| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.4128 r_free = 0.4128 target = 0.147884 restraints weight = 16116.419| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.4155 r_free = 0.4155 target = 0.150090 restraints weight = 12057.965| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.4173 r_free = 0.4173 target = 0.151596 restraints weight = 9855.229| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.4181 r_free = 0.4181 target = 0.152335 restraints weight = 8570.799| |-----------------------------------------------------------------------------| r_work (final): 0.4193 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6809 moved from start: 0.3699 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 13331 Z= 0.137 Angle : 0.733 10.195 18034 Z= 0.380 Chirality : 0.047 0.290 1939 Planarity : 0.005 0.052 2281 Dihedral : 6.883 78.824 1739 Min Nonbonded Distance : 2.474 Molprobity Statistics. All-atom Clashscore : 12.29 Ramachandran Plot: Outliers : 0.71 % Allowed : 11.31 % Favored : 87.98 % Rotamer: Outliers : 3.47 % Allowed : 20.31 % Favored : 76.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -3.53 (0.19), residues: 1556 helix: -1.36 (0.19), residues: 663 sheet: -2.92 (0.56), residues: 66 loop : -3.25 (0.19), residues: 827 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 146 TYR 0.026 0.001 TYR A 822 PHE 0.027 0.001 PHE B 200 TRP 0.024 0.002 TRP A 590 HIS 0.005 0.001 HIS B 81 Details of bonding type rmsd covalent geometry : bond 0.00301 (13331) covalent geometry : angle 0.73339 (18034) hydrogen bonds : bond 0.04036 ( 342) hydrogen bonds : angle 5.25546 ( 981) *********************** 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 223 residues out of total 1413 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 174 time to evaluate : 0.451 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 140 TYR cc_start: 0.6844 (p90) cc_final: 0.5602 (p90) REVERT: A 518 PHE cc_start: 0.6568 (OUTLIER) cc_final: 0.6277 (t80) REVERT: A 712 ASN cc_start: 0.6535 (m110) cc_final: 0.6194 (t0) REVERT: A 776 ARG cc_start: 0.7923 (mmp80) cc_final: 0.6665 (ttm-80) REVERT: B 539 ILE cc_start: 0.8702 (mm) cc_final: 0.8456 (mm) REVERT: B 557 ASP cc_start: 0.7738 (p0) cc_final: 0.7451 (t0) REVERT: B 564 GLN cc_start: 0.8920 (OUTLIER) cc_final: 0.8719 (mp10) REVERT: B 590 TRP cc_start: 0.5151 (p-90) cc_final: 0.4757 (p-90) REVERT: B 711 LYS cc_start: 0.8436 (pptt) cc_final: 0.7992 (pptt) REVERT: B 755 LEU cc_start: 0.5389 (OUTLIER) cc_final: 0.5017 (tp) REVERT: B 770 TYR cc_start: 0.5751 (m-80) cc_final: 0.5272 (m-80) REVERT: B 788 LEU cc_start: 0.5538 (OUTLIER) cc_final: 0.5283 (tt) REVERT: B 820 TYR cc_start: 0.7453 (OUTLIER) cc_final: 0.7136 (m-80) REVERT: B 863 LEU cc_start: 0.4059 (OUTLIER) cc_final: 0.3792 (mt) outliers start: 49 outliers final: 27 residues processed: 208 average time/residue: 0.1036 time to fit residues: 32.1803 Evaluate side-chains 194 residues out of total 1413 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 161 time to evaluate : 0.666 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 24 ILE 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 330 VAL 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 614 GLU Chi-restraints excluded: chain A residue 653 LEU Chi-restraints excluded: chain A residue 754 LEU Chi-restraints excluded: chain A residue 762 ILE Chi-restraints excluded: chain A residue 773 SER Chi-restraints excluded: chain A residue 806 ASP 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 319 VAL Chi-restraints excluded: chain B residue 345 HIS Chi-restraints excluded: chain B residue 356 LEU 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 809 PHE Chi-restraints excluded: chain B residue 820 TYR 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 65 optimal weight: 2.9990 chunk 40 optimal weight: 20.0000 chunk 58 optimal weight: 10.0000 chunk 79 optimal weight: 3.9990 chunk 78 optimal weight: 5.9990 chunk 1 optimal weight: 0.2980 chunk 80 optimal weight: 3.9990 chunk 61 optimal weight: 6.9990 chunk 147 optimal weight: 4.9990 chunk 136 optimal weight: 10.0000 chunk 36 optimal weight: 1.9990 overall best weight: 2.6588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 678 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 27 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 481 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4358 r_free = 0.4358 target = 0.166848 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4025 r_free = 0.4025 target = 0.139487 restraints weight = 25005.409| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.4066 r_free = 0.4066 target = 0.142767 restraints weight = 15870.916| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.4094 r_free = 0.4094 target = 0.145029 restraints weight = 11748.573| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.4109 r_free = 0.4109 target = 0.146367 restraints weight = 9593.670| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.4123 r_free = 0.4123 target = 0.147448 restraints weight = 8404.715| |-----------------------------------------------------------------------------| r_work (final): 0.4135 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6916 moved from start: 0.3967 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 13331 Z= 0.189 Angle : 0.778 12.000 18034 Z= 0.406 Chirality : 0.049 0.254 1939 Planarity : 0.005 0.052 2281 Dihedral : 7.085 78.849 1739 Min Nonbonded Distance : 2.436 Molprobity Statistics. All-atom Clashscore : 14.57 Ramachandran Plot: Outliers : 0.64 % Allowed : 12.98 % Favored : 86.38 % Rotamer: Outliers : 3.82 % Allowed : 20.24 % Favored : 75.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -3.51 (0.19), residues: 1556 helix: -1.33 (0.19), residues: 662 sheet: -2.70 (0.60), residues: 56 loop : -3.28 (0.19), residues: 838 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 99 TYR 0.019 0.002 TYR B 45 PHE 0.028 0.002 PHE A 13 TRP 0.024 0.002 TRP A 590 HIS 0.007 0.001 HIS A 9 Details of bonding type rmsd covalent geometry : bond 0.00429 (13331) covalent geometry : angle 0.77799 (18034) hydrogen bonds : bond 0.04444 ( 342) hydrogen bonds : angle 5.50917 ( 981) *********************** 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 225 residues out of total 1413 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 171 time to evaluate : 0.513 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 140 TYR cc_start: 0.6983 (p90) cc_final: 0.5746 (p90) REVERT: A 337 LEU cc_start: 0.6182 (OUTLIER) cc_final: 0.5931 (mm) REVERT: A 440 LEU cc_start: 0.5265 (OUTLIER) cc_final: 0.4812 (tp) REVERT: A 518 PHE cc_start: 0.6739 (OUTLIER) cc_final: 0.6399 (t80) REVERT: A 524 TYR cc_start: 0.7125 (OUTLIER) cc_final: 0.6724 (t80) REVERT: A 712 ASN cc_start: 0.6739 (m110) cc_final: 0.6406 (t0) REVERT: A 776 ARG cc_start: 0.7975 (mmp80) cc_final: 0.6679 (ttm-80) REVERT: B 140 TYR cc_start: 0.7048 (t80) cc_final: 0.6793 (t80) REVERT: B 539 ILE cc_start: 0.8861 (mm) cc_final: 0.8634 (mm) REVERT: B 557 ASP cc_start: 0.7740 (p0) cc_final: 0.7276 (p0) REVERT: B 564 GLN cc_start: 0.9137 (OUTLIER) cc_final: 0.8819 (mp10) REVERT: B 590 TRP cc_start: 0.5465 (p-90) cc_final: 0.4990 (p-90) REVERT: B 711 LYS cc_start: 0.8449 (pptt) cc_final: 0.7968 (pptt) REVERT: B 770 TYR cc_start: 0.5667 (m-80) cc_final: 0.5225 (m-80) REVERT: B 820 TYR cc_start: 0.7502 (OUTLIER) cc_final: 0.7179 (m-80) REVERT: B 863 LEU cc_start: 0.4305 (OUTLIER) cc_final: 0.3985 (mt) outliers start: 54 outliers final: 37 residues processed: 212 average time/residue: 0.1062 time to fit residues: 33.4233 Evaluate side-chains 202 residues out of total 1413 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 158 time to evaluate : 0.419 ------------------------------------------------------------------------------- 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 286 TRP 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 440 LEU Chi-restraints excluded: chain A residue 444 LEU Chi-restraints excluded: chain A residue 518 PHE Chi-restraints excluded: chain A residue 524 TYR Chi-restraints excluded: chain A residue 581 LEU Chi-restraints excluded: chain A residue 589 ILE Chi-restraints excluded: chain A residue 614 GLU Chi-restraints excluded: chain A residue 653 LEU Chi-restraints excluded: chain A residue 704 LEU Chi-restraints excluded: chain A residue 754 LEU Chi-restraints excluded: chain A residue 762 ILE Chi-restraints excluded: chain A residue 774 LEU Chi-restraints excluded: chain A residue 797 VAL Chi-restraints excluded: chain A residue 806 ASP Chi-restraints excluded: chain A residue 817 GLU Chi-restraints excluded: chain B residue 12 PHE Chi-restraints excluded: chain B residue 27 GLN Chi-restraints excluded: chain B residue 80 CYS 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 476 VAL 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 645 LEU Chi-restraints excluded: chain B residue 755 LEU Chi-restraints excluded: chain B residue 788 LEU Chi-restraints excluded: chain B residue 809 PHE Chi-restraints excluded: chain B residue 820 TYR 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 153 optimal weight: 0.9990 chunk 39 optimal weight: 0.9990 chunk 75 optimal weight: 4.9990 chunk 33 optimal weight: 4.9990 chunk 5 optimal weight: 8.9990 chunk 151 optimal weight: 7.9990 chunk 67 optimal weight: 3.9990 chunk 134 optimal weight: 0.9980 chunk 148 optimal weight: 8.9990 chunk 57 optimal weight: 1.9990 chunk 124 optimal weight: 4.9990 overall best weight: 1.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 678 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 27 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 413 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4386 r_free = 0.4386 target = 0.169358 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4064 r_free = 0.4064 target = 0.142602 restraints weight = 24683.163| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.4103 r_free = 0.4103 target = 0.145764 restraints weight = 16159.695| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.4130 r_free = 0.4130 target = 0.147915 restraints weight = 12106.482| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.4143 r_free = 0.4143 target = 0.149173 restraints weight = 9938.492| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 42)----------------| | r_work = 0.4159 r_free = 0.4159 target = 0.150305 restraints weight = 8756.662| |-----------------------------------------------------------------------------| r_work (final): 0.4170 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6860 moved from start: 0.4062 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= 0.153 Angle : 0.751 12.314 18034 Z= 0.389 Chirality : 0.048 0.258 1939 Planarity : 0.005 0.052 2281 Dihedral : 6.860 79.175 1739 Min Nonbonded Distance : 2.428 Molprobity Statistics. All-atom Clashscore : 13.33 Ramachandran Plot: Outliers : 0.58 % Allowed : 12.08 % Favored : 87.34 % Rotamer: Outliers : 3.96 % Allowed : 20.74 % Favored : 75.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -3.43 (0.20), residues: 1556 helix: -1.22 (0.20), residues: 668 sheet: -2.81 (0.57), residues: 66 loop : -3.27 (0.19), residues: 822 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 99 TYR 0.018 0.002 TYR B 45 PHE 0.022 0.002 PHE A 13 TRP 0.024 0.002 TRP A 590 HIS 0.006 0.001 HIS A 9 Details of bonding type rmsd covalent geometry : bond 0.00344 (13331) covalent geometry : angle 0.75055 (18034) hydrogen bonds : bond 0.04160 ( 342) hydrogen bonds : angle 5.39019 ( 981) *********************** 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 232 residues out of total 1413 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 176 time to evaluate : 0.466 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 140 TYR cc_start: 0.6814 (p90) cc_final: 0.5649 (p90) REVERT: A 153 TYR cc_start: 0.5121 (m-80) cc_final: 0.4896 (m-80) REVERT: A 268 GLU cc_start: 0.5986 (OUTLIER) cc_final: 0.5681 (tt0) REVERT: A 337 LEU cc_start: 0.6264 (OUTLIER) cc_final: 0.6042 (mm) REVERT: A 440 LEU cc_start: 0.5291 (OUTLIER) cc_final: 0.4913 (tp) REVERT: A 518 PHE cc_start: 0.6560 (OUTLIER) cc_final: 0.6260 (t80) REVERT: A 524 TYR cc_start: 0.6873 (OUTLIER) cc_final: 0.6474 (t80) REVERT: A 712 ASN cc_start: 0.6526 (m110) cc_final: 0.6248 (t0) REVERT: B 140 TYR cc_start: 0.6991 (t80) cc_final: 0.6770 (t80) REVERT: B 539 ILE cc_start: 0.8741 (mm) cc_final: 0.8509 (mm) REVERT: B 557 ASP cc_start: 0.7693 (p0) cc_final: 0.7361 (p0) REVERT: B 564 GLN cc_start: 0.8941 (OUTLIER) cc_final: 0.8731 (mp10) REVERT: B 590 TRP cc_start: 0.5329 (p-90) cc_final: 0.5020 (p-90) REVERT: B 711 LYS cc_start: 0.8445 (pptt) cc_final: 0.7979 (pptt) REVERT: B 755 LEU cc_start: 0.5502 (OUTLIER) cc_final: 0.5206 (tp) REVERT: B 770 TYR cc_start: 0.5767 (m-80) cc_final: 0.5305 (m-80) REVERT: B 820 TYR cc_start: 0.7308 (OUTLIER) cc_final: 0.7006 (m-80) REVERT: B 860 ASP cc_start: 0.6582 (m-30) cc_final: 0.6298 (m-30) REVERT: B 863 LEU cc_start: 0.4279 (OUTLIER) cc_final: 0.3922 (mt) outliers start: 56 outliers final: 40 residues processed: 218 average time/residue: 0.1021 time to fit residues: 33.5978 Evaluate side-chains 216 residues out of total 1413 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 167 time to evaluate : 0.548 ------------------------------------------------------------------------------- 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 286 TRP 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 440 LEU Chi-restraints excluded: chain A residue 444 LEU Chi-restraints excluded: chain A residue 518 PHE Chi-restraints excluded: chain A residue 524 TYR Chi-restraints excluded: chain A residue 581 LEU Chi-restraints excluded: chain A residue 589 ILE Chi-restraints excluded: chain A residue 614 GLU Chi-restraints excluded: chain A residue 653 LEU Chi-restraints excluded: chain A residue 670 VAL Chi-restraints excluded: chain A residue 704 LEU Chi-restraints excluded: chain A residue 722 LEU Chi-restraints excluded: chain A residue 752 LEU Chi-restraints excluded: chain A residue 754 LEU Chi-restraints excluded: chain A residue 762 ILE Chi-restraints excluded: chain A residue 774 LEU Chi-restraints excluded: chain A residue 793 CYS Chi-restraints excluded: chain A residue 797 VAL Chi-restraints excluded: chain A residue 806 ASP Chi-restraints excluded: chain A residue 817 GLU Chi-restraints excluded: chain A residue 853 ILE Chi-restraints excluded: chain B residue 12 PHE Chi-restraints excluded: chain B residue 27 GLN Chi-restraints excluded: chain B residue 47 TYR Chi-restraints excluded: chain B residue 53 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 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 645 LEU Chi-restraints excluded: chain B residue 755 LEU Chi-restraints excluded: chain B residue 809 PHE Chi-restraints excluded: chain B residue 820 TYR 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 2 optimal weight: 0.9980 chunk 114 optimal weight: 0.7980 chunk 62 optimal weight: 7.9990 chunk 45 optimal weight: 0.4980 chunk 91 optimal weight: 8.9990 chunk 123 optimal weight: 7.9990 chunk 70 optimal weight: 8.9990 chunk 132 optimal weight: 2.9990 chunk 90 optimal weight: 2.9990 chunk 26 optimal weight: 2.9990 chunk 3 optimal weight: 1.9990 overall best weight: 1.4584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 678 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 227 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 413 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 432 GLN B 572 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4403 r_free = 0.4403 target = 0.170780 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.4082 r_free = 0.4082 target = 0.144107 restraints weight = 24846.694| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 47)----------------| | r_work = 0.4123 r_free = 0.4123 target = 0.147353 restraints weight = 16067.574| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.4150 r_free = 0.4150 target = 0.149550 restraints weight = 11942.464| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.4164 r_free = 0.4164 target = 0.150846 restraints weight = 9754.637| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.4180 r_free = 0.4180 target = 0.151998 restraints weight = 8561.148| |-----------------------------------------------------------------------------| r_work (final): 0.4194 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6817 moved from start: 0.4104 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 13331 Z= 0.142 Angle : 0.750 12.253 18034 Z= 0.385 Chirality : 0.048 0.242 1939 Planarity : 0.005 0.061 2281 Dihedral : 6.738 78.520 1739 Min Nonbonded Distance : 2.442 Molprobity Statistics. All-atom Clashscore : 12.29 Ramachandran Plot: Outliers : 0.58 % Allowed : 12.28 % Favored : 87.15 % Rotamer: Outliers : 3.75 % Allowed : 21.23 % Favored : 75.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -3.35 (0.20), residues: 1556 helix: -1.15 (0.20), residues: 667 sheet: -2.76 (0.56), residues: 66 loop : -3.23 (0.19), residues: 823 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 99 TYR 0.023 0.002 TYR A 822 PHE 0.022 0.002 PHE A 13 TRP 0.024 0.002 TRP A 590 HIS 0.005 0.001 HIS B 522 Details of bonding type rmsd covalent geometry : bond 0.00316 (13331) covalent geometry : angle 0.74985 (18034) hydrogen bonds : bond 0.04083 ( 342) hydrogen bonds : angle 5.29518 ( 981) *********************** 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 234 residues out of total 1413 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 181 time to evaluate : 0.500 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 140 TYR cc_start: 0.6825 (p90) cc_final: 0.5660 (p90) REVERT: A 153 TYR cc_start: 0.5172 (m-80) cc_final: 0.4951 (m-80) REVERT: A 268 GLU cc_start: 0.5899 (OUTLIER) cc_final: 0.5601 (tt0) REVERT: A 337 LEU cc_start: 0.6247 (OUTLIER) cc_final: 0.6030 (mm) REVERT: A 440 LEU cc_start: 0.5203 (OUTLIER) cc_final: 0.4927 (tp) REVERT: A 513 GLU cc_start: 0.6856 (mm-30) cc_final: 0.6370 (mt-10) REVERT: A 524 TYR cc_start: 0.6846 (OUTLIER) cc_final: 0.6484 (t80) REVERT: A 712 ASN cc_start: 0.6513 (m110) cc_final: 0.6226 (t0) REVERT: B 539 ILE cc_start: 0.8690 (mm) cc_final: 0.8450 (mm) REVERT: B 557 ASP cc_start: 0.7634 (p0) cc_final: 0.7275 (p0) REVERT: B 564 GLN cc_start: 0.8945 (OUTLIER) cc_final: 0.8675 (mp10) REVERT: B 590 TRP cc_start: 0.5321 (p-90) cc_final: 0.5048 (p-90) REVERT: B 711 LYS cc_start: 0.8530 (pptt) cc_final: 0.8059 (pptt) REVERT: B 755 LEU cc_start: 0.5528 (OUTLIER) cc_final: 0.5215 (tp) REVERT: B 770 TYR cc_start: 0.5755 (m-80) cc_final: 0.5295 (m-80) REVERT: B 820 TYR cc_start: 0.7331 (OUTLIER) cc_final: 0.7126 (m-80) REVERT: B 860 ASP cc_start: 0.6363 (m-30) cc_final: 0.6036 (m-30) REVERT: B 863 LEU cc_start: 0.4328 (OUTLIER) cc_final: 0.3998 (mt) outliers start: 53 outliers final: 39 residues processed: 219 average time/residue: 0.0973 time to fit residues: 32.4574 Evaluate side-chains 216 residues out of total 1413 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 169 time to evaluate : 0.487 ------------------------------------------------------------------------------- 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 286 TRP 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 440 LEU Chi-restraints excluded: chain A residue 444 LEU Chi-restraints excluded: chain A residue 524 TYR Chi-restraints excluded: chain A residue 581 LEU Chi-restraints excluded: chain A residue 588 THR Chi-restraints excluded: chain A residue 589 ILE Chi-restraints excluded: chain A residue 648 GLU Chi-restraints excluded: chain A residue 653 LEU Chi-restraints excluded: chain A residue 670 VAL Chi-restraints excluded: chain A residue 704 LEU Chi-restraints excluded: chain A residue 722 LEU Chi-restraints excluded: chain A residue 752 LEU Chi-restraints excluded: chain A residue 754 LEU Chi-restraints excluded: chain A residue 762 ILE Chi-restraints excluded: chain A residue 774 LEU Chi-restraints excluded: chain A residue 806 ASP Chi-restraints excluded: chain A residue 817 GLU Chi-restraints excluded: chain A residue 853 ILE Chi-restraints excluded: chain B residue 12 PHE Chi-restraints excluded: chain B residue 27 GLN Chi-restraints excluded: chain B residue 47 TYR Chi-restraints excluded: chain B residue 53 VAL Chi-restraints excluded: chain B residue 80 CYS 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 534 PHE Chi-restraints excluded: chain B residue 564 GLN Chi-restraints excluded: chain B residue 633 LEU Chi-restraints excluded: chain B residue 645 LEU Chi-restraints excluded: chain B residue 755 LEU Chi-restraints excluded: chain B residue 809 PHE Chi-restraints excluded: chain B residue 820 TYR 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 5 optimal weight: 0.8980 chunk 21 optimal weight: 7.9990 chunk 36 optimal weight: 0.0270 chunk 48 optimal weight: 3.9990 chunk 142 optimal weight: 0.9980 chunk 107 optimal weight: 5.9990 chunk 75 optimal weight: 3.9990 chunk 85 optimal weight: 5.9990 chunk 138 optimal weight: 20.0000 chunk 99 optimal weight: 0.7980 chunk 30 optimal weight: 10.0000 overall best weight: 1.3440 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 678 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 868 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 221 ASN B 227 ASN ** B 413 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4414 r_free = 0.4414 target = 0.171815 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.4096 r_free = 0.4096 target = 0.145277 restraints weight = 24901.452| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 47)----------------| | r_work = 0.4137 r_free = 0.4137 target = 0.148556 restraints weight = 16032.096| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.4165 r_free = 0.4165 target = 0.150783 restraints weight = 11910.669| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.4179 r_free = 0.4179 target = 0.152137 restraints weight = 9707.659| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 43)----------------| | r_work = 0.4195 r_free = 0.4195 target = 0.153252 restraints weight = 8497.808| |-----------------------------------------------------------------------------| r_work (final): 0.4206 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6789 moved from start: 0.4197 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 13331 Z= 0.139 Angle : 0.749 12.193 18034 Z= 0.384 Chirality : 0.048 0.234 1939 Planarity : 0.005 0.058 2281 Dihedral : 6.650 77.107 1739 Min Nonbonded Distance : 2.425 Molprobity Statistics. All-atom Clashscore : 12.25 Ramachandran Plot: Outliers : 0.58 % Allowed : 11.95 % Favored : 87.47 % Rotamer: Outliers : 3.75 % Allowed : 21.51 % Favored : 74.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -3.27 (0.20), residues: 1556 helix: -1.08 (0.20), residues: 665 sheet: -2.66 (0.57), residues: 66 loop : -3.20 (0.19), residues: 825 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 99 TYR 0.022 0.001 TYR A 822 PHE 0.025 0.002 PHE B 698 TRP 0.024 0.002 TRP A 590 HIS 0.004 0.001 HIS A 522 Details of bonding type rmsd covalent geometry : bond 0.00308 (13331) covalent geometry : angle 0.74929 (18034) hydrogen bonds : bond 0.04060 ( 342) hydrogen bonds : angle 5.29751 ( 981) ********************** 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 228 residues out of total 1413 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 175 time to evaluate : 0.475 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 140 TYR cc_start: 0.6825 (p90) cc_final: 0.5659 (p90) REVERT: A 153 TYR cc_start: 0.5137 (m-80) cc_final: 0.4914 (m-80) REVERT: A 268 GLU cc_start: 0.5909 (OUTLIER) cc_final: 0.5625 (tt0) REVERT: A 337 LEU cc_start: 0.6321 (OUTLIER) cc_final: 0.6109 (mm) REVERT: A 513 GLU cc_start: 0.6879 (mm-30) cc_final: 0.6394 (mt-10) REVERT: A 524 TYR cc_start: 0.6792 (OUTLIER) cc_final: 0.6325 (t80) REVERT: A 712 ASN cc_start: 0.6507 (m110) cc_final: 0.6210 (t0) REVERT: B 539 ILE cc_start: 0.8669 (mm) cc_final: 0.8442 (mm) REVERT: B 557 ASP cc_start: 0.7642 (p0) cc_final: 0.7305 (t0) REVERT: B 564 GLN cc_start: 0.8887 (OUTLIER) cc_final: 0.8601 (mp10) REVERT: B 590 TRP cc_start: 0.5260 (p-90) cc_final: 0.5032 (p-90) REVERT: B 654 ARG cc_start: 0.8503 (mmm-85) cc_final: 0.8210 (tpp-160) REVERT: B 711 LYS cc_start: 0.8527 (pptt) cc_final: 0.8087 (pptt) REVERT: B 755 LEU cc_start: 0.5464 (OUTLIER) cc_final: 0.5177 (tp) REVERT: B 770 TYR cc_start: 0.5694 (m-80) cc_final: 0.5255 (m-80) REVERT: B 860 ASP cc_start: 0.6387 (m-30) cc_final: 0.6089 (m-30) REVERT: B 863 LEU cc_start: 0.4384 (OUTLIER) cc_final: 0.4064 (mt) outliers start: 53 outliers final: 39 residues processed: 214 average time/residue: 0.1041 time to fit residues: 33.3562 Evaluate side-chains 213 residues out of total 1413 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 168 time to evaluate : 0.487 ------------------------------------------------------------------------------- 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 286 TRP 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 524 TYR Chi-restraints excluded: chain A residue 581 LEU Chi-restraints excluded: chain A residue 588 THR Chi-restraints excluded: chain A residue 589 ILE Chi-restraints excluded: chain A residue 648 GLU Chi-restraints excluded: chain A residue 704 LEU Chi-restraints excluded: chain A residue 722 LEU Chi-restraints excluded: chain A residue 754 LEU Chi-restraints excluded: chain A residue 762 ILE Chi-restraints excluded: chain A residue 774 LEU 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 A residue 853 ILE Chi-restraints excluded: chain B residue 12 PHE Chi-restraints excluded: chain B residue 27 GLN Chi-restraints excluded: chain B residue 47 TYR Chi-restraints excluded: chain B residue 53 VAL Chi-restraints excluded: chain B residue 80 CYS 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 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 645 LEU Chi-restraints excluded: chain B residue 755 LEU Chi-restraints excluded: chain B residue 809 PHE 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 68 optimal weight: 8.9990 chunk 114 optimal weight: 0.7980 chunk 86 optimal weight: 1.9990 chunk 132 optimal weight: 1.9990 chunk 119 optimal weight: 0.8980 chunk 50 optimal weight: 5.9990 chunk 52 optimal weight: 5.9990 chunk 74 optimal weight: 0.9990 chunk 1 optimal weight: 4.9990 chunk 0 optimal weight: 4.9990 chunk 55 optimal weight: 5.9990 overall best weight: 1.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 678 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 861 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 868 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 413 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 572 ASN B 608 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4418 r_free = 0.4418 target = 0.172303 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.4102 r_free = 0.4102 target = 0.145834 restraints weight = 24650.724| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.4142 r_free = 0.4142 target = 0.149062 restraints weight = 15891.219| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.4169 r_free = 0.4169 target = 0.151266 restraints weight = 11815.013| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.4187 r_free = 0.4187 target = 0.152764 restraints weight = 9633.480| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 21)----------------| | r_work = 0.4195 r_free = 0.4195 target = 0.153479 restraints weight = 8378.290| |-----------------------------------------------------------------------------| r_work (final): 0.4207 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6787 moved from start: 0.4258 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= 0.140 Angle : 0.751 12.026 18034 Z= 0.385 Chirality : 0.048 0.224 1939 Planarity : 0.005 0.059 2281 Dihedral : 6.584 75.143 1739 Min Nonbonded Distance : 2.396 Molprobity Statistics. All-atom Clashscore : 12.40 Ramachandran Plot: Outliers : 0.58 % Allowed : 12.28 % Favored : 87.15 % Rotamer: Outliers : 3.47 % Allowed : 22.43 % Favored : 74.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -3.18 (0.20), residues: 1556 helix: -1.01 (0.20), residues: 665 sheet: -2.31 (0.70), residues: 49 loop : -3.17 (0.19), residues: 842 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 99 TYR 0.022 0.001 TYR A 822 PHE 0.028 0.002 PHE B 595 TRP 0.024 0.002 TRP A 590 HIS 0.004 0.001 HIS B 522 Details of bonding type rmsd covalent geometry : bond 0.00311 (13331) covalent geometry : angle 0.75124 (18034) hydrogen bonds : bond 0.03992 ( 342) hydrogen bonds : angle 5.27381 ( 981) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1918.41 seconds wall clock time: 34 minutes 9.06 seconds (2049.06 seconds total)