Starting phenix.real_space_refine on Fri Sep 27 14:46:10 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6qti_4635/09_2024/6qti_4635_neut.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6qti_4635/09_2024/6qti_4635.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6qti_4635/09_2024/6qti_4635.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6qti_4635/09_2024/6qti_4635.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6qti_4635/09_2024/6qti_4635_neut.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6qti_4635/09_2024/6qti_4635_neut.cif" } resolution = 2.9 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.002 sd= 0.014 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 22 5.49 5 S 90 5.16 5 C 10296 2.51 5 N 2568 2.21 5 O 3020 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 7 residue(s): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/chem_data/mon_lib" Total number of atoms: 15996 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 7620 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1038, 7620 Classifications: {'peptide': 1038} Link IDs: {'PTRANS': 51, 'TRANS': 986} Chain: "B" Number of atoms: 7620 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1038, 7620 Classifications: {'peptide': 1038} Link IDs: {'PTRANS': 51, 'TRANS': 986} Chain: "A" Number of atoms: 362 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 362 Unusual residues: {'D12': 1, 'NAD': 1, 'NAP': 1, 'PC1': 6} Classifications: {'undetermined': 9} Link IDs: {None: 8} Unresolved non-hydrogen bonds: 66 Unresolved non-hydrogen angles: 66 Unresolved non-hydrogen dihedrals: 66 Chain: "B" Number of atoms: 394 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 394 Unusual residues: {'D12': 2, 'NAD': 1, 'NAP': 1, 'PC1': 6} Classifications: {'undetermined': 10} Link IDs: {None: 9} Unresolved non-hydrogen bonds: 46 Unresolved non-hydrogen angles: 46 Unresolved non-hydrogen dihedrals: 46 Time building chain proxies: 9.31, per 1000 atoms: 0.58 Number of scatterers: 15996 At special positions: 0 Unit cell: (138.45, 129.93, 126.735, 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 90 16.00 P 22 15.00 O 3020 8.00 N 2568 7.00 C 10296 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 4.09 Conformation dependent library (CDL) restraints added in 2.1 seconds 4144 Ramachandran restraints generated. 2072 Oldfield, 0 Emsley, 2072 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3696 Finding SS restraints... Secondary structure from input PDB file: 88 helices and 10 sheets defined 56.1% alpha, 5.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.14 Creating SS restraints... Processing helix chain 'A' and resid 33 through 37 removed outlier: 3.548A pdb=" N VAL A 36 " --> pdb=" O PRO A 33 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N GLN A 37 " --> pdb=" O ALA A 34 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 33 through 37' Processing helix chain 'A' and resid 59 through 67 removed outlier: 3.535A pdb=" N TYR A 63 " --> pdb=" O SER A 59 " (cutoff:3.500A) Processing helix chain 'A' and resid 117 through 127 removed outlier: 3.716A pdb=" N LEU A 121 " --> pdb=" O ASN A 117 " (cutoff:3.500A) removed outlier: 3.904A pdb=" N LYS A 126 " --> pdb=" O ASN A 122 " (cutoff:3.500A) removed outlier: 4.068A pdb=" N ARG A 127 " --> pdb=" O LYS A 123 " (cutoff:3.500A) Processing helix chain 'A' and resid 135 through 137 No H-bonds generated for 'chain 'A' and resid 135 through 137' Processing helix chain 'A' and resid 140 through 144 removed outlier: 3.507A pdb=" N ALA A 143 " --> pdb=" O VAL A 140 " (cutoff:3.500A) removed outlier: 4.037A pdb=" N GLN A 144 " --> pdb=" O THR A 141 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 140 through 144' Processing helix chain 'A' and resid 147 through 165 removed outlier: 3.634A pdb=" N VAL A 161 " --> pdb=" O GLY A 157 " (cutoff:3.500A) Processing helix chain 'A' and resid 194 through 205 Processing helix chain 'A' and resid 216 through 227 removed outlier: 3.534A pdb=" N LEU A 220 " --> pdb=" O ARG A 216 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N GLU A 221 " --> pdb=" O ALA A 217 " (cutoff:3.500A) Processing helix chain 'A' and resid 250 through 264 Processing helix chain 'A' and resid 337 through 356 Processing helix chain 'A' and resid 375 through 383 removed outlier: 3.747A pdb=" N VAL A 379 " --> pdb=" O THR A 375 " (cutoff:3.500A) Processing helix chain 'A' and resid 411 through 420 removed outlier: 3.668A pdb=" N LEU A 415 " --> pdb=" O THR A 411 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N GLU A 416 " --> pdb=" O VAL A 412 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N ALA A 417 " --> pdb=" O ALA A 413 " (cutoff:3.500A) Processing helix chain 'A' and resid 421 through 423 No H-bonds generated for 'chain 'A' and resid 421 through 423' Processing helix chain 'A' and resid 424 through 449 removed outlier: 3.799A pdb=" N VAL A 435 " --> pdb=" O THR A 431 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N TYR A 436 " --> pdb=" O SER A 432 " (cutoff:3.500A) Processing helix chain 'A' and resid 452 through 475 removed outlier: 3.834A pdb=" N SER A 456 " --> pdb=" O ASN A 452 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N VAL A 473 " --> pdb=" O GLY A 469 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N TRP A 474 " --> pdb=" O TYR A 470 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N GLY A 475 " --> pdb=" O HIS A 471 " (cutoff:3.500A) Processing helix chain 'A' and resid 477 through 479 No H-bonds generated for 'chain 'A' and resid 477 through 479' Processing helix chain 'A' and resid 480 through 492 Processing helix chain 'A' and resid 494 through 502 removed outlier: 4.099A pdb=" N GLY A 498 " --> pdb=" O LEU A 494 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N VAL A 501 " --> pdb=" O VAL A 497 " (cutoff:3.500A) removed outlier: 3.932A pdb=" N LEU A 502 " --> pdb=" O GLY A 498 " (cutoff:3.500A) Processing helix chain 'A' and resid 511 through 540 removed outlier: 3.607A pdb=" N ALA A 517 " --> pdb=" O SER A 513 " (cutoff:3.500A) removed outlier: 3.919A pdb=" N ALA A 518 " --> pdb=" O GLN A 514 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N LEU A 519 " --> pdb=" O GLY A 515 " (cutoff:3.500A) removed outlier: 4.795A pdb=" N THR A 521 " --> pdb=" O ALA A 517 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N VAL A 526 " --> pdb=" O PHE A 522 " (cutoff:3.500A) removed outlier: 4.399A pdb=" N ASN A 527 " --> pdb=" O ILE A 523 " (cutoff:3.500A) removed outlier: 4.029A pdb=" N ILE A 528 " --> pdb=" O SER A 524 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N ALA A 529 " --> pdb=" O SER A 525 " (cutoff:3.500A) Processing helix chain 'A' and resid 551 through 554 removed outlier: 3.526A pdb=" N LEU A 554 " --> pdb=" O TYR A 551 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 551 through 554' Processing helix chain 'A' and resid 555 through 572 removed outlier: 3.913A pdb=" N ALA A 559 " --> pdb=" O TYR A 555 " (cutoff:3.500A) Processing helix chain 'A' and resid 576 through 594 removed outlier: 3.976A pdb=" N LEU A 582 " --> pdb=" O GLN A 578 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N LEU A 592 " --> pdb=" O CYS A 588 " (cutoff:3.500A) Processing helix chain 'A' and resid 602 through 624 removed outlier: 3.531A pdb=" N ALA A 606 " --> pdb=" O ARG A 602 " (cutoff:3.500A) removed outlier: 4.581A pdb=" N GLY A 608 " --> pdb=" O GLY A 604 " (cutoff:3.500A) Processing helix chain 'A' and resid 626 through 648 removed outlier: 3.575A pdb=" N ALA A 631 " --> pdb=" O PRO A 627 " (cutoff:3.500A) Processing helix chain 'A' and resid 652 through 654 No H-bonds generated for 'chain 'A' and resid 652 through 654' Processing helix chain 'A' and resid 655 through 682 removed outlier: 3.757A pdb=" N LEU A 659 " --> pdb=" O ASP A 655 " (cutoff:3.500A) removed outlier: 4.020A pdb=" N SER A 665 " --> pdb=" O ALA A 661 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N LEU A 666 " --> pdb=" O ALA A 662 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N ALA A 670 " --> pdb=" O LEU A 666 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N VAL A 672 " --> pdb=" O GLY A 668 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N ALA A 677 " --> pdb=" O LEU A 673 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N ILE A 681 " --> pdb=" O ALA A 677 " (cutoff:3.500A) Processing helix chain 'A' and resid 683 through 686 Processing helix chain 'A' and resid 691 through 722 removed outlier: 3.935A pdb=" N ILE A 697 " --> pdb=" O ASN A 693 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N ALA A 699 " --> pdb=" O THR A 695 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N THR A 703 " --> pdb=" O ALA A 699 " (cutoff:3.500A) removed outlier: 3.922A pdb=" N SER A 711 " --> pdb=" O GLY A 707 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N GLY A 712 " --> pdb=" O VAL A 708 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N LEU A 720 " --> pdb=" O ALA A 716 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N GLY A 722 " --> pdb=" O GLY A 718 " (cutoff:3.500A) Processing helix chain 'A' and resid 735 through 748 Processing helix chain 'A' and resid 748 through 753 removed outlier: 3.527A pdb=" N PHE A 752 " --> pdb=" O GLY A 748 " (cutoff:3.500A) Processing helix chain 'A' and resid 758 through 781 removed outlier: 3.652A pdb=" N THR A 763 " --> pdb=" O THR A 759 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N CYS A 764 " --> pdb=" O THR A 760 " (cutoff:3.500A) Processing helix chain 'A' and resid 787 through 810 removed outlier: 4.043A pdb=" N VAL A 791 " --> pdb=" O ASP A 787 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N GLY A 800 " --> pdb=" O ASN A 796 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N LEU A 803 " --> pdb=" O SER A 799 " (cutoff:3.500A) Processing helix chain 'A' and resid 812 through 837 removed outlier: 3.931A pdb=" N THR A 816 " --> pdb=" O ASN A 812 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N ILE A 817 " --> pdb=" O ASN A 813 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N SER A 824 " --> pdb=" O ALA A 820 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N SER A 825 " --> pdb=" O LEU A 821 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N MET A 837 " --> pdb=" O MET A 833 " (cutoff:3.500A) Processing helix chain 'A' and resid 840 through 846 Processing helix chain 'A' and resid 870 through 881 removed outlier: 3.518A pdb=" N GLU A 880 " --> pdb=" O ASP A 876 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N ALA A 881 " --> pdb=" O MET A 877 " (cutoff:3.500A) Processing helix chain 'A' and resid 889 through 895 removed outlier: 4.284A pdb=" N CYS A 893 " --> pdb=" O GLY A 889 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N ALA A 895 " --> pdb=" O GLY A 891 " (cutoff:3.500A) Processing helix chain 'A' and resid 897 through 911 removed outlier: 3.704A pdb=" N ILE A 901 " --> pdb=" O ALA A 897 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N ASP A 903 " --> pdb=" O TYR A 899 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N GLU A 910 " --> pdb=" O LYS A 906 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N GLN A 911 " --> pdb=" O MET A 907 " (cutoff:3.500A) Processing helix chain 'A' and resid 928 through 938 removed outlier: 3.625A pdb=" N VAL A 932 " --> pdb=" O GLY A 928 " (cutoff:3.500A) Processing helix chain 'A' and resid 940 through 942 No H-bonds generated for 'chain 'A' and resid 940 through 942' Processing helix chain 'A' and resid 947 through 951 Processing helix chain 'A' and resid 971 through 976 Processing helix chain 'A' and resid 988 through 992 removed outlier: 3.557A pdb=" N LYS A 991 " --> pdb=" O GLU A 988 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N SER A 992 " --> pdb=" O VAL A 989 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 988 through 992' Processing helix chain 'A' and resid 1025 through 1042 Processing helix chain 'B' and resid 33 through 38 removed outlier: 3.548A pdb=" N ALA B 38 " --> pdb=" O ALA B 34 " (cutoff:3.500A) Processing helix chain 'B' and resid 59 through 66 removed outlier: 3.801A pdb=" N TYR B 63 " --> pdb=" O SER B 59 " (cutoff:3.500A) Processing helix chain 'B' and resid 73 through 78 removed outlier: 4.094A pdb=" N LEU B 77 " --> pdb=" O ALA B 73 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N ALA B 78 " --> pdb=" O LYS B 74 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 73 through 78' Processing helix chain 'B' and resid 99 through 101 No H-bonds generated for 'chain 'B' and resid 99 through 101' Processing helix chain 'B' and resid 117 through 126 removed outlier: 3.673A pdb=" N LEU B 121 " --> pdb=" O ASN B 117 " (cutoff:3.500A) Processing helix chain 'B' and resid 147 through 165 Processing helix chain 'B' and resid 194 through 207 removed outlier: 3.624A pdb=" N MET B 206 " --> pdb=" O ALA B 202 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N GLY B 207 " --> pdb=" O ALA B 203 " (cutoff:3.500A) Processing helix chain 'B' and resid 216 through 227 removed outlier: 3.987A pdb=" N LEU B 220 " --> pdb=" O ARG B 216 " (cutoff:3.500A) removed outlier: 3.952A pdb=" N GLU B 221 " --> pdb=" O ALA B 217 " (cutoff:3.500A) Processing helix chain 'B' and resid 250 through 265 removed outlier: 3.581A pdb=" N LYS B 259 " --> pdb=" O GLU B 255 " (cutoff:3.500A) Processing helix chain 'B' and resid 287 through 292 Processing helix chain 'B' and resid 333 through 336 Processing helix chain 'B' and resid 337 through 356 removed outlier: 3.549A pdb=" N ALA B 355 " --> pdb=" O LYS B 351 " (cutoff:3.500A) Processing helix chain 'B' and resid 375 through 383 removed outlier: 4.105A pdb=" N VAL B 379 " --> pdb=" O THR B 375 " (cutoff:3.500A) Processing helix chain 'B' and resid 411 through 421 removed outlier: 3.991A pdb=" N GLU B 418 " --> pdb=" O GLU B 414 " (cutoff:3.500A) removed outlier: 3.916A pdb=" N LYS B 419 " --> pdb=" O LEU B 415 " (cutoff:3.500A) Processing helix chain 'B' and resid 424 through 449 removed outlier: 3.547A pdb=" N LYS B 428 " --> pdb=" O THR B 424 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N THR B 429 " --> pdb=" O PRO B 425 " (cutoff:3.500A) Processing helix chain 'B' and resid 452 through 474 removed outlier: 3.888A pdb=" N SER B 456 " --> pdb=" O ASN B 452 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N VAL B 473 " --> pdb=" O GLY B 469 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N TRP B 474 " --> pdb=" O TYR B 470 " (cutoff:3.500A) Processing helix chain 'B' and resid 477 through 479 No H-bonds generated for 'chain 'B' and resid 477 through 479' Processing helix chain 'B' and resid 480 through 492 Processing helix chain 'B' and resid 494 through 501 removed outlier: 4.132A pdb=" N GLY B 498 " --> pdb=" O LEU B 494 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N VAL B 501 " --> pdb=" O VAL B 497 " (cutoff:3.500A) Processing helix chain 'B' and resid 511 through 540 Processing helix chain 'B' and resid 551 through 554 Processing helix chain 'B' and resid 555 through 571 removed outlier: 3.950A pdb=" N ALA B 559 " --> pdb=" O TYR B 555 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N GLY B 564 " --> pdb=" O GLY B 560 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N ALA B 568 " --> pdb=" O GLY B 564 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N SER B 569 " --> pdb=" O GLY B 565 " (cutoff:3.500A) Processing helix chain 'B' and resid 576 through 594 removed outlier: 3.757A pdb=" N LEU B 582 " --> pdb=" O GLN B 578 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N LEU B 592 " --> pdb=" O CYS B 588 " (cutoff:3.500A) Processing helix chain 'B' and resid 602 through 622 removed outlier: 4.468A pdb=" N GLY B 608 " --> pdb=" O GLY B 604 " (cutoff:3.500A) Processing helix chain 'B' and resid 626 through 651 removed outlier: 3.633A pdb=" N LYS B 649 " --> pdb=" O LEU B 645 " (cutoff:3.500A) removed outlier: 4.127A pdb=" N ARG B 650 " --> pdb=" O THR B 646 " (cutoff:3.500A) removed outlier: 3.899A pdb=" N ILE B 651 " --> pdb=" O ILE B 647 " (cutoff:3.500A) Processing helix chain 'B' and resid 655 through 682 removed outlier: 3.568A pdb=" N LEU B 659 " --> pdb=" O ASP B 655 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N HIS B 664 " --> pdb=" O VAL B 660 " (cutoff:3.500A) removed outlier: 4.243A pdb=" N SER B 665 " --> pdb=" O ALA B 661 " (cutoff:3.500A) removed outlier: 4.053A pdb=" N LEU B 666 " --> pdb=" O ALA B 662 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N ALA B 670 " --> pdb=" O LEU B 666 " (cutoff:3.500A) removed outlier: 3.982A pdb=" N ALA B 677 " --> pdb=" O LEU B 673 " (cutoff:3.500A) Processing helix chain 'B' and resid 683 through 686 Processing helix chain 'B' and resid 693 through 721 removed outlier: 3.867A pdb=" N ALA B 699 " --> pdb=" O THR B 695 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N SER B 711 " --> pdb=" O GLY B 707 " (cutoff:3.500A) Processing helix chain 'B' and resid 734 through 748 Processing helix chain 'B' and resid 748 through 753 Processing helix chain 'B' and resid 757 through 781 removed outlier: 3.666A pdb=" N GLY B 761 " --> pdb=" O SER B 757 " (cutoff:3.500A) Processing helix chain 'B' and resid 787 through 811 removed outlier: 4.174A pdb=" N VAL B 791 " --> pdb=" O ASP B 787 " (cutoff:3.500A) removed outlier: 4.073A pdb=" N LEU B 803 " --> pdb=" O SER B 799 " (cutoff:3.500A) removed outlier: 3.885A pdb=" N LEU B 809 " --> pdb=" O ALA B 805 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N LEU B 810 " --> pdb=" O GLU B 806 " (cutoff:3.500A) Processing helix chain 'B' and resid 812 through 837 removed outlier: 3.761A pdb=" N THR B 816 " --> pdb=" O ASN B 812 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N SER B 825 " --> pdb=" O LEU B 821 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N MET B 837 " --> pdb=" O MET B 833 " (cutoff:3.500A) Processing helix chain 'B' and resid 840 through 846 Processing helix chain 'B' and resid 870 through 881 removed outlier: 3.703A pdb=" N ALA B 881 " --> pdb=" O MET B 877 " (cutoff:3.500A) Processing helix chain 'B' and resid 889 through 895 removed outlier: 4.003A pdb=" N CYS B 893 " --> pdb=" O GLY B 889 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N ALA B 895 " --> pdb=" O GLY B 891 " (cutoff:3.500A) Processing helix chain 'B' and resid 897 through 910 Processing helix chain 'B' and resid 928 through 938 removed outlier: 3.726A pdb=" N VAL B 932 " --> pdb=" O GLY B 928 " (cutoff:3.500A) Processing helix chain 'B' and resid 940 through 942 No H-bonds generated for 'chain 'B' and resid 940 through 942' Processing helix chain 'B' and resid 946 through 951 Processing helix chain 'B' and resid 952 through 954 No H-bonds generated for 'chain 'B' and resid 952 through 954' Processing helix chain 'B' and resid 966 through 970 removed outlier: 3.594A pdb=" N VAL B 969 " --> pdb=" O ASN B 966 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N ASN B 970 " --> pdb=" O ASP B 967 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 966 through 970' Processing helix chain 'B' and resid 971 through 976 removed outlier: 3.521A pdb=" N ASP B 976 " --> pdb=" O ALA B 972 " (cutoff:3.500A) Processing helix chain 'B' and resid 988 through 992 removed outlier: 3.779A pdb=" N LYS B 991 " --> pdb=" O GLU B 988 " (cutoff:3.500A) Processing helix chain 'B' and resid 1025 through 1042 Processing sheet with id=AA1, first strand: chain 'A' and resid 69 through 71 removed outlier: 6.642A pdb=" N VAL A 46 " --> pdb=" O GLN A 69 " (cutoff:3.500A) removed outlier: 7.106A pdb=" N GLN A 71 " --> pdb=" O VAL A 46 " (cutoff:3.500A) removed outlier: 5.789A pdb=" N VAL A 48 " --> pdb=" O GLN A 71 " (cutoff:3.500A) removed outlier: 6.998A pdb=" N THR A 15 " --> pdb=" O LEU A 81 " (cutoff:3.500A) removed outlier: 7.833A pdb=" N VAL A 83 " --> pdb=" O THR A 15 " (cutoff:3.500A) removed outlier: 6.130A pdb=" N GLY A 17 " --> pdb=" O VAL A 83 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N MET A 386 " --> pdb=" O VAL A 131 " (cutoff:3.500A) removed outlier: 6.558A pdb=" N ALA A 133 " --> pdb=" O VAL A 384 " (cutoff:3.500A) removed outlier: 5.844A pdb=" N VAL A 384 " --> pdb=" O ALA A 133 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N GLN A 390 " --> pdb=" O LYS A 387 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 90 through 91 removed outlier: 3.771A pdb=" N ILE A 96 " --> pdb=" O ASN A 91 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 176 through 177 Processing sheet with id=AA4, first strand: chain 'A' and resid 209 through 210 removed outlier: 6.361A pdb=" N LEU A 271 " --> pdb=" O VAL A 301 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 867 through 868 removed outlier: 7.164A pdb=" N THR A 867 " --> pdb=" O MET A1021 " (cutoff:3.500A) removed outlier: 6.276A pdb=" N VAL A 995 " --> pdb=" O ALA A1020 " (cutoff:3.500A) removed outlier: 6.460A pdb=" N VAL A 960 " --> pdb=" O ILE A 996 " (cutoff:3.500A) removed outlier: 7.653A pdb=" N MET A 998 " --> pdb=" O VAL A 960 " (cutoff:3.500A) removed outlier: 6.856A pdb=" N VAL A 962 " --> pdb=" O MET A 998 " (cutoff:3.500A) removed outlier: 6.473A pdb=" N ILE A 884 " --> pdb=" O ARG A 916 " (cutoff:3.500A) removed outlier: 7.538A pdb=" N GLY A 918 " --> pdb=" O ILE A 884 " (cutoff:3.500A) removed outlier: 6.572A pdb=" N ILE A 886 " --> pdb=" O GLY A 918 " (cutoff:3.500A) removed outlier: 8.383A pdb=" N LEU A 945 " --> pdb=" O VAL A 915 " (cutoff:3.500A) removed outlier: 5.943A pdb=" N PHE A 917 " --> pdb=" O LEU A 945 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 69 through 71 removed outlier: 7.014A pdb=" N VAL B 46 " --> pdb=" O GLN B 69 " (cutoff:3.500A) removed outlier: 7.504A pdb=" N GLN B 71 " --> pdb=" O VAL B 46 " (cutoff:3.500A) removed outlier: 5.920A pdb=" N VAL B 48 " --> pdb=" O GLN B 71 " (cutoff:3.500A) removed outlier: 6.388A pdb=" N VAL B 16 " --> pdb=" O VAL B 47 " (cutoff:3.500A) removed outlier: 8.091A pdb=" N GLU B 49 " --> pdb=" O VAL B 16 " (cutoff:3.500A) removed outlier: 7.461A pdb=" N VAL B 18 " --> pdb=" O GLU B 49 " (cutoff:3.500A) removed outlier: 6.319A pdb=" N THR B 15 " --> pdb=" O LEU B 81 " (cutoff:3.500A) removed outlier: 7.599A pdb=" N VAL B 83 " --> pdb=" O THR B 15 " (cutoff:3.500A) removed outlier: 6.144A pdb=" N GLY B 17 " --> pdb=" O VAL B 83 " (cutoff:3.500A) removed outlier: 5.847A pdb=" N LEU B 108 " --> pdb=" O LEU B 132 " (cutoff:3.500A) removed outlier: 6.461A pdb=" N VAL B 131 " --> pdb=" O VAL B 385 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 90 through 91 removed outlier: 3.592A pdb=" N ILE B 96 " --> pdb=" O ASN B 91 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 176 through 177 removed outlier: 4.451A pdb=" N THR B 177 " --> pdb=" O GLY B 180 " (cutoff:3.500A) removed outlier: 3.951A pdb=" N GLY B 180 " --> pdb=" O THR B 177 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA8 Processing sheet with id=AA9, first strand: chain 'B' and resid 209 through 210 removed outlier: 6.427A pdb=" N VAL B 300 " --> pdb=" O ILE B 328 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 867 through 868 removed outlier: 6.938A pdb=" N THR B 867 " --> pdb=" O MET B1021 " (cutoff:3.500A) removed outlier: 7.795A pdb=" N LEU B1023 " --> pdb=" O THR B 867 " (cutoff:3.500A) removed outlier: 6.123A pdb=" N VAL B 995 " --> pdb=" O ALA B1020 " (cutoff:3.500A) removed outlier: 7.068A pdb=" N LEU B1022 " --> pdb=" O VAL B 995 " (cutoff:3.500A) removed outlier: 6.078A pdb=" N VAL B 997 " --> pdb=" O LEU B1022 " (cutoff:3.500A) removed outlier: 6.440A pdb=" N ILE B 884 " --> pdb=" O ARG B 916 " (cutoff:3.500A) removed outlier: 7.499A pdb=" N GLY B 918 " --> pdb=" O ILE B 884 " (cutoff:3.500A) removed outlier: 6.375A pdb=" N ILE B 886 " --> pdb=" O GLY B 918 " (cutoff:3.500A) removed outlier: 8.454A pdb=" N LEU B 945 " --> pdb=" O VAL B 915 " (cutoff:3.500A) removed outlier: 6.119A pdb=" N PHE B 917 " --> pdb=" O LEU B 945 " (cutoff:3.500A) 751 hydrogen bonds defined for protein. 2220 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: 6.27 Time building geometry restraints manager: 4.38 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 2662 1.32 - 1.44: 3779 1.44 - 1.57: 9631 1.57 - 1.69: 43 1.69 - 1.81: 160 Bond restraints: 16275 Sorted by residual: bond pdb=" O2B NAP B1102 " pdb=" P2B NAP B1102 " ideal model delta sigma weight residual 1.736 1.607 0.129 2.00e-02 2.50e+03 4.14e+01 bond pdb=" O2B NAP A1101 " pdb=" P2B NAP A1101 " ideal model delta sigma weight residual 1.736 1.610 0.126 2.00e-02 2.50e+03 4.00e+01 bond pdb=" C TYR A 683 " pdb=" N PRO A 684 " ideal model delta sigma weight residual 1.334 1.373 -0.039 8.40e-03 1.42e+04 2.19e+01 bond pdb=" O3 NAD B1103 " pdb=" PA NAD B1103 " ideal model delta sigma weight residual 1.653 1.589 0.064 2.00e-02 2.50e+03 1.03e+01 bond pdb=" O3 NAD A1102 " pdb=" PA NAD A1102 " ideal model delta sigma weight residual 1.653 1.591 0.062 2.00e-02 2.50e+03 9.72e+00 ... (remaining 16270 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.29: 21172 2.29 - 4.57: 686 4.57 - 6.86: 128 6.86 - 9.14: 38 9.14 - 11.43: 8 Bond angle restraints: 22032 Sorted by residual: angle pdb=" N VAL B 40 " pdb=" CA VAL B 40 " pdb=" C VAL B 40 " ideal model delta sigma weight residual 112.96 105.51 7.45 1.00e+00 1.00e+00 5.56e+01 angle pdb=" N VAL B 36 " pdb=" CA VAL B 36 " pdb=" C VAL B 36 " ideal model delta sigma weight residual 112.96 107.04 5.92 1.00e+00 1.00e+00 3.50e+01 angle pdb=" C GLN B 24 " pdb=" N ASN B 25 " pdb=" CA ASN B 25 " ideal model delta sigma weight residual 121.54 131.06 -9.52 1.91e+00 2.74e-01 2.49e+01 angle pdb=" N ILE A 579 " pdb=" CA ILE A 579 " pdb=" C ILE A 579 " ideal model delta sigma weight residual 112.96 108.17 4.79 1.00e+00 1.00e+00 2.29e+01 angle pdb=" C ALA B 38 " pdb=" N LEU B 39 " pdb=" CA LEU B 39 " ideal model delta sigma weight residual 121.54 130.22 -8.68 1.91e+00 2.74e-01 2.06e+01 ... (remaining 22027 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.00: 9270 17.00 - 34.01: 509 34.01 - 51.01: 143 51.01 - 68.01: 65 68.01 - 85.01: 28 Dihedral angle restraints: 10015 sinusoidal: 4177 harmonic: 5838 Sorted by residual: dihedral pdb=" CA GLY B 850 " pdb=" C GLY B 850 " pdb=" N THR B 851 " pdb=" CA THR B 851 " ideal model delta harmonic sigma weight residual -180.00 -152.67 -27.33 0 5.00e+00 4.00e-02 2.99e+01 dihedral pdb=" CA GLN A 37 " pdb=" C GLN A 37 " pdb=" N ALA A 38 " pdb=" CA ALA A 38 " ideal model delta harmonic sigma weight residual 180.00 153.52 26.48 0 5.00e+00 4.00e-02 2.81e+01 dihedral pdb=" CA ALA A 836 " pdb=" C ALA A 836 " pdb=" N MET A 837 " pdb=" CA MET A 837 " ideal model delta harmonic sigma weight residual 180.00 156.77 23.23 0 5.00e+00 4.00e-02 2.16e+01 ... (remaining 10012 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.083: 2180 0.083 - 0.166: 342 0.166 - 0.248: 26 0.248 - 0.331: 1 0.331 - 0.414: 1 Chirality restraints: 2550 Sorted by residual: chirality pdb=" CB ILE B 9 " pdb=" CA ILE B 9 " pdb=" CG1 ILE B 9 " pdb=" CG2 ILE B 9 " both_signs ideal model delta sigma weight residual False 2.64 2.23 0.41 2.00e-01 2.50e+01 4.28e+00 chirality pdb=" CA PHE B 365 " pdb=" N PHE B 365 " pdb=" C PHE B 365 " pdb=" CB PHE B 365 " both_signs ideal model delta sigma weight residual False 2.51 2.25 0.26 2.00e-01 2.50e+01 1.74e+00 chirality pdb=" CA ASP B 361 " pdb=" N ASP B 361 " pdb=" C ASP B 361 " pdb=" CB ASP B 361 " both_signs ideal model delta sigma weight residual False 2.51 2.28 0.23 2.00e-01 2.50e+01 1.36e+00 ... (remaining 2547 not shown) Planarity restraints: 2730 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB PHE B 365 " 0.014 2.00e-02 2.50e+03 2.10e-02 7.74e+00 pdb=" CG PHE B 365 " -0.048 2.00e-02 2.50e+03 pdb=" CD1 PHE B 365 " 0.019 2.00e-02 2.50e+03 pdb=" CD2 PHE B 365 " 0.016 2.00e-02 2.50e+03 pdb=" CE1 PHE B 365 " -0.002 2.00e-02 2.50e+03 pdb=" CE2 PHE B 365 " 0.000 2.00e-02 2.50e+03 pdb=" CZ PHE B 365 " 0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ALA A 805 " -0.013 2.00e-02 2.50e+03 2.62e-02 6.85e+00 pdb=" C ALA A 805 " 0.045 2.00e-02 2.50e+03 pdb=" O ALA A 805 " -0.017 2.00e-02 2.50e+03 pdb=" N GLU A 806 " -0.015 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C HIS A 920 " -0.040 5.00e-02 4.00e+02 6.05e-02 5.86e+00 pdb=" N PRO A 921 " 0.105 5.00e-02 4.00e+02 pdb=" CA PRO A 921 " -0.031 5.00e-02 4.00e+02 pdb=" CD PRO A 921 " -0.034 5.00e-02 4.00e+02 ... (remaining 2727 not shown) Histogram of nonbonded interaction distances: 2.29 - 2.81: 4331 2.81 - 3.33: 14305 3.33 - 3.86: 25774 3.86 - 4.38: 30345 4.38 - 4.90: 52582 Nonbonded interactions: 127337 Sorted by model distance: nonbonded pdb=" OE1 GLU B 306 " pdb=" OG1 THR B 331 " model vdw 2.289 3.040 nonbonded pdb=" OG1 THR B 495 " pdb=" OG SER B 524 " model vdw 2.292 3.040 nonbonded pdb=" O ASP B 953 " pdb=" OG1 THR B 957 " model vdw 2.298 3.040 nonbonded pdb=" OG1 THR B 411 " pdb=" O GLN B 974 " model vdw 2.300 3.040 nonbonded pdb=" OD2 ASP A 119 " pdb=" NZ LYS A 123 " model vdw 2.316 3.120 ... (remaining 127332 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 5 through 1042 or resid 1104 through 1105 or resid 1109)) selection = (chain 'B' and (resid 5 through 1042 or (resid 1104 and (name N or name C1 or na \ me C11 or name C12 or name C13 or name C14 or name C15 or name C2 or name C21 or \ name C22 or name C23 or name C24 or name C25 or name C26 or name C27 or name C2 \ 8 or name C29 or name C2A or name C2B or name C2C or name C2D or name C3 or name \ C31 or name C32 or name C33 or name C34 or name C35 or name C36 or name C37 or \ name C38 or name C39 or name C3A or name C3B or name C3C or name C3D or name C3E \ or name O11 or name O12 or name O13 or name O14 or name O21 or name O22 or name \ O31 or name O32 or name P )) or (resid 1105 and (name N or name C1 or name C11 \ or name C12 or name C13 or name C14 or name C15 or name C2 or name C21 or name C \ 22 or name C23 or name C24 or name C25 or name C26 or name C27 or name C28 or na \ me C29 or name C2A or name C2B or name C2C or name C2D or name C2E or name C3 or \ name C31 or name C32 or name C33 or name C34 or name C35 or name C36 or name C3 \ 7 or name C38 or name C39 or name C3A or name C3B or name C3C or name C3D or nam \ e C3E or name C3F or name C3G or name C3H or name C3I or name O11 or name O12 or \ name O13 or name O14 or name O21 or name O22 or name O31 or name O32 or name P \ )) or (resid 1109 and (name N or name C1 or name C11 or name C12 or name C13 or \ name C14 or name C15 or name C2 or name C21 or name C22 or name C23 or name C24 \ or name C25 or name C26 or name C27 or name C28 or name C29 or name C2A or name \ C2B or name C2C or name C3 or name C31 or name C32 or name C33 or name C34 or na \ me C35 or name C36 or name C37 or name O11 or name O12 or name O13 or name O14 o \ r name O21 or name O22 or name O31 or name O32 or name P )))) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.080 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: 0.010 Extract box with map and model: 0.690 Check model and map are aligned: 0.140 Set scattering table: 0.180 Process input model: 37.920 Find NCS groups from input model: 1.040 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:10.540 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 50.670 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8470 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 0.129 16275 Z= 0.456 Angle : 1.010 11.431 22032 Z= 0.509 Chirality : 0.058 0.414 2550 Planarity : 0.008 0.061 2730 Dihedral : 13.499 85.014 6319 Min Nonbonded Distance : 2.289 Molprobity Statistics. All-atom Clashscore : 3.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.56 % Favored : 93.44 % Rotamer: Outliers : 0.00 % Allowed : 3.68 % Favored : 96.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.74 (0.15), residues: 2072 helix: -2.29 (0.11), residues: 1080 sheet: -1.52 (0.37), residues: 186 loop : -2.80 (0.19), residues: 806 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.003 TRP B 801 HIS 0.019 0.003 HIS B 481 PHE 0.048 0.003 PHE B 365 TYR 0.025 0.003 TYR B 330 ARG 0.006 0.001 ARG B 537 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4144 Ramachandran restraints generated. 2072 Oldfield, 0 Emsley, 2072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4144 Ramachandran restraints generated. 2072 Oldfield, 0 Emsley, 2072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 301 residues out of total 1602 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 301 time to evaluate : 1.879 Fit side-chains REVERT: A 20 LYS cc_start: 0.8939 (tttp) cc_final: 0.8666 (ttpp) REVERT: A 74 LYS cc_start: 0.8766 (tmtp) cc_final: 0.8410 (tttm) REVERT: A 100 ASP cc_start: 0.8683 (m-30) cc_final: 0.8448 (m-30) REVERT: A 288 LYS cc_start: 0.8570 (ptmm) cc_final: 0.8228 (ptmm) REVERT: A 376 MET cc_start: 0.8797 (mmm) cc_final: 0.8524 (mmt) REVERT: A 427 ARG cc_start: 0.8088 (ttp-170) cc_final: 0.7670 (tpp-160) REVERT: A 476 VAL cc_start: 0.9136 (m) cc_final: 0.8874 (t) REVERT: A 501 VAL cc_start: 0.9178 (t) cc_final: 0.8784 (m) REVERT: A 503 MET cc_start: 0.8983 (ttt) cc_final: 0.8741 (ttt) REVERT: A 628 GLU cc_start: 0.8902 (mt-10) cc_final: 0.8500 (mp0) REVERT: A 754 MET cc_start: 0.6712 (mpt) cc_final: 0.6446 (ptt) REVERT: A 903 ASP cc_start: 0.8614 (t70) cc_final: 0.8233 (m-30) REVERT: A 906 LYS cc_start: 0.8790 (tttt) cc_final: 0.8575 (ttpp) REVERT: A 1038 ARG cc_start: 0.7366 (ttm110) cc_final: 0.7149 (ttp80) REVERT: B 74 LYS cc_start: 0.9155 (tmtt) cc_final: 0.8806 (mppt) REVERT: B 127 ARG cc_start: 0.7596 (tpm-80) cc_final: 0.7372 (mmt180) REVERT: B 414 GLU cc_start: 0.7284 (mm-30) cc_final: 0.6882 (mt-10) REVERT: B 681 ILE cc_start: 0.8976 (tt) cc_final: 0.8644 (pp) REVERT: B 858 LYS cc_start: 0.8219 (mmmt) cc_final: 0.7234 (pptt) outliers start: 0 outliers final: 0 residues processed: 301 average time/residue: 1.2157 time to fit residues: 406.2417 Evaluate side-chains 182 residues out of total 1602 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 182 time to evaluate : 1.701 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 206 random chunks: chunk 173 optimal weight: 0.7980 chunk 156 optimal weight: 0.9980 chunk 86 optimal weight: 8.9990 chunk 53 optimal weight: 6.9990 chunk 105 optimal weight: 7.9990 chunk 83 optimal weight: 1.9990 chunk 161 optimal weight: 5.9990 chunk 62 optimal weight: 5.9990 chunk 98 optimal weight: 4.9990 chunk 120 optimal weight: 0.0270 chunk 187 optimal weight: 3.9990 overall best weight: 1.5642 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 37 GLN A 128 ASN A 287 ASN A 310 ASN A 327 HIS A 348 ASN A 403 GLN A 552 ASN A 693 ASN A 811 ASN B 62 HIS B 166 ASN B 931 ASN B1034 GLN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8461 moved from start: 0.1581 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 16275 Z= 0.160 Angle : 0.563 5.992 22032 Z= 0.286 Chirality : 0.041 0.163 2550 Planarity : 0.005 0.049 2730 Dihedral : 12.437 86.797 2921 Min Nonbonded Distance : 2.446 Molprobity Statistics. All-atom Clashscore : 5.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.16 % Favored : 94.84 % Rotamer: Outliers : 2.62 % Allowed : 10.49 % Favored : 86.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.47 (0.18), residues: 2072 helix: 0.01 (0.15), residues: 1088 sheet: -1.29 (0.38), residues: 187 loop : -2.25 (0.20), residues: 797 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 801 HIS 0.007 0.001 HIS A 664 PHE 0.029 0.002 PHE B 365 TYR 0.012 0.001 TYR B 566 ARG 0.002 0.000 ARG B 139 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4144 Ramachandran restraints generated. 2072 Oldfield, 0 Emsley, 2072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4144 Ramachandran restraints generated. 2072 Oldfield, 0 Emsley, 2072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 276 residues out of total 1602 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 234 time to evaluate : 1.760 Fit side-chains REVERT: A 20 LYS cc_start: 0.8859 (tttp) cc_final: 0.8438 (ttpp) REVERT: A 74 LYS cc_start: 0.8777 (tmtp) cc_final: 0.8432 (tttm) REVERT: A 100 ASP cc_start: 0.8710 (m-30) cc_final: 0.8468 (m-30) REVERT: A 123 LYS cc_start: 0.8150 (OUTLIER) cc_final: 0.7931 (mtmm) REVERT: A 288 LYS cc_start: 0.8822 (ptmm) cc_final: 0.8421 (ptmm) REVERT: A 366 GLU cc_start: 0.8142 (pm20) cc_final: 0.7445 (pt0) REVERT: A 427 ARG cc_start: 0.8058 (ttp-170) cc_final: 0.7648 (tpt170) REVERT: A 428 LYS cc_start: 0.7903 (mttt) cc_final: 0.7642 (mttt) REVERT: A 476 VAL cc_start: 0.9127 (m) cc_final: 0.8894 (t) REVERT: A 541 MET cc_start: 0.8970 (mtt) cc_final: 0.8697 (mtt) REVERT: A 833 MET cc_start: 0.8791 (ttm) cc_final: 0.8561 (mtp) REVERT: A 877 MET cc_start: 0.8336 (ttp) cc_final: 0.8017 (ttp) REVERT: A 903 ASP cc_start: 0.8694 (t70) cc_final: 0.8230 (m-30) REVERT: B 74 LYS cc_start: 0.9033 (tmtt) cc_final: 0.8755 (mppt) REVERT: B 127 ARG cc_start: 0.7476 (tpm-80) cc_final: 0.7208 (mmm160) REVERT: B 337 MET cc_start: 0.8647 (OUTLIER) cc_final: 0.8376 (mtt) REVERT: B 414 GLU cc_start: 0.7241 (mm-30) cc_final: 0.6598 (mt-10) REVERT: B 503 MET cc_start: 0.8702 (OUTLIER) cc_final: 0.8498 (mtp) REVERT: B 833 MET cc_start: 0.8889 (ttm) cc_final: 0.7846 (tpp) REVERT: B 858 LYS cc_start: 0.8146 (mmmt) cc_final: 0.7260 (pptt) outliers start: 42 outliers final: 4 residues processed: 256 average time/residue: 1.1284 time to fit residues: 324.7116 Evaluate side-chains 192 residues out of total 1602 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 185 time to evaluate : 1.615 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 123 LYS Chi-restraints excluded: chain A residue 146 TYR Chi-restraints excluded: chain B residue 56 SER Chi-restraints excluded: chain B residue 326 THR Chi-restraints excluded: chain B residue 337 MET Chi-restraints excluded: chain B residue 503 MET Chi-restraints excluded: chain B residue 797 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 206 random chunks: chunk 103 optimal weight: 20.0000 chunk 58 optimal weight: 9.9990 chunk 155 optimal weight: 6.9990 chunk 127 optimal weight: 8.9990 chunk 51 optimal weight: 7.9990 chunk 187 optimal weight: 5.9990 chunk 202 optimal weight: 9.9990 chunk 166 optimal weight: 5.9990 chunk 185 optimal weight: 9.9990 chunk 63 optimal weight: 4.9990 chunk 150 optimal weight: 10.0000 overall best weight: 6.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 97 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 128 ASN A 144 GLN A 166 ASN A 327 HIS A 457 GLN ** A 552 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 811 ASN A1034 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8561 moved from start: 0.2059 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.054 16275 Z= 0.353 Angle : 0.649 6.331 22032 Z= 0.328 Chirality : 0.046 0.167 2550 Planarity : 0.005 0.049 2730 Dihedral : 12.725 87.796 2921 Min Nonbonded Distance : 2.127 Molprobity Statistics. All-atom Clashscore : 5.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.13 % Favored : 93.87 % Rotamer: Outliers : 3.31 % Allowed : 12.23 % Favored : 84.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.89 (0.18), residues: 2072 helix: 0.56 (0.16), residues: 1103 sheet: -1.20 (0.38), residues: 184 loop : -2.10 (0.21), residues: 785 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.002 TRP B 801 HIS 0.013 0.002 HIS B 481 PHE 0.054 0.002 PHE B 365 TYR 0.019 0.002 TYR B 941 ARG 0.006 0.001 ARG B 537 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4144 Ramachandran restraints generated. 2072 Oldfield, 0 Emsley, 2072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4144 Ramachandran restraints generated. 2072 Oldfield, 0 Emsley, 2072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 240 residues out of total 1602 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 187 time to evaluate : 1.876 Fit side-chains revert: symmetry clash REVERT: A 74 LYS cc_start: 0.8697 (tmtp) cc_final: 0.8383 (mttt) REVERT: A 100 ASP cc_start: 0.8757 (m-30) cc_final: 0.8513 (m-30) REVERT: A 197 LEU cc_start: 0.8861 (mt) cc_final: 0.8657 (mp) REVERT: A 221 GLU cc_start: 0.8376 (mp0) cc_final: 0.8015 (mp0) REVERT: A 288 LYS cc_start: 0.8809 (ptmm) cc_final: 0.8471 (ptmm) REVERT: A 403 GLN cc_start: 0.2912 (OUTLIER) cc_final: 0.1390 (tp40) REVERT: A 427 ARG cc_start: 0.8112 (ttp-170) cc_final: 0.7696 (tpt170) REVERT: A 428 LYS cc_start: 0.8001 (mttt) cc_final: 0.7734 (mttt) REVERT: A 476 VAL cc_start: 0.9291 (m) cc_final: 0.9087 (t) REVERT: A 877 MET cc_start: 0.8320 (ttp) cc_final: 0.7976 (ttp) REVERT: A 903 ASP cc_start: 0.8808 (t70) cc_final: 0.8193 (m-30) REVERT: B 74 LYS cc_start: 0.9160 (tmtt) cc_final: 0.8828 (mppt) REVERT: B 337 MET cc_start: 0.8825 (OUTLIER) cc_final: 0.8520 (mtt) REVERT: B 414 GLU cc_start: 0.7318 (mm-30) cc_final: 0.6617 (mt-10) REVERT: B 418 GLU cc_start: 0.7376 (OUTLIER) cc_final: 0.7098 (mp0) REVERT: B 503 MET cc_start: 0.9001 (OUTLIER) cc_final: 0.8759 (mtp) REVERT: B 600 THR cc_start: 0.8922 (p) cc_final: 0.8639 (p) REVERT: B 602 ARG cc_start: 0.8383 (OUTLIER) cc_final: 0.7277 (mpp-170) REVERT: B 858 LYS cc_start: 0.8229 (mmmt) cc_final: 0.7306 (pptt) outliers start: 53 outliers final: 18 residues processed: 226 average time/residue: 1.2037 time to fit residues: 303.6062 Evaluate side-chains 198 residues out of total 1602 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 175 time to evaluate : 1.760 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 162 VAL Chi-restraints excluded: chain A residue 333 LEU Chi-restraints excluded: chain A residue 403 GLN Chi-restraints excluded: chain A residue 569 SER Chi-restraints excluded: chain A residue 602 ARG Chi-restraints excluded: chain A residue 634 SER Chi-restraints excluded: chain A residue 811 ASN Chi-restraints excluded: chain A residue 818 VAL Chi-restraints excluded: chain B residue 101 LEU Chi-restraints excluded: chain B residue 141 THR Chi-restraints excluded: chain B residue 162 VAL Chi-restraints excluded: chain B residue 173 THR Chi-restraints excluded: chain B residue 326 THR Chi-restraints excluded: chain B residue 333 LEU Chi-restraints excluded: chain B residue 337 MET Chi-restraints excluded: chain B residue 418 GLU Chi-restraints excluded: chain B residue 503 MET Chi-restraints excluded: chain B residue 507 LEU Chi-restraints excluded: chain B residue 598 GLN Chi-restraints excluded: chain B residue 602 ARG Chi-restraints excluded: chain B residue 729 LEU Chi-restraints excluded: chain B residue 797 SER Chi-restraints excluded: chain B residue 851 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 206 random chunks: chunk 185 optimal weight: 9.9990 chunk 140 optimal weight: 6.9990 chunk 97 optimal weight: 9.9990 chunk 20 optimal weight: 9.9990 chunk 89 optimal weight: 0.9990 chunk 125 optimal weight: 8.9990 chunk 188 optimal weight: 30.0000 chunk 199 optimal weight: 9.9990 chunk 98 optimal weight: 9.9990 chunk 178 optimal weight: 9.9990 chunk 53 optimal weight: 4.9990 overall best weight: 6.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 128 ASN A 136 GLN ** A 552 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 811 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8567 moved from start: 0.2327 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.053 16275 Z= 0.344 Angle : 0.631 9.111 22032 Z= 0.319 Chirality : 0.046 0.175 2550 Planarity : 0.005 0.049 2730 Dihedral : 12.712 87.734 2921 Min Nonbonded Distance : 2.330 Molprobity Statistics. All-atom Clashscore : 5.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.13 % Favored : 93.87 % Rotamer: Outliers : 3.37 % Allowed : 13.36 % Favored : 83.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.59 (0.18), residues: 2072 helix: 0.85 (0.16), residues: 1107 sheet: -1.18 (0.38), residues: 184 loop : -2.03 (0.21), residues: 781 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.002 TRP B 801 HIS 0.011 0.002 HIS B 481 PHE 0.042 0.002 PHE B 365 TYR 0.016 0.002 TYR A 566 ARG 0.005 0.001 ARG B 537 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4144 Ramachandran restraints generated. 2072 Oldfield, 0 Emsley, 2072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4144 Ramachandran restraints generated. 2072 Oldfield, 0 Emsley, 2072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 231 residues out of total 1602 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 177 time to evaluate : 1.671 Fit side-chains revert: symmetry clash REVERT: A 74 LYS cc_start: 0.8777 (tmtp) cc_final: 0.8395 (mttt) REVERT: A 197 LEU cc_start: 0.8895 (mt) cc_final: 0.8683 (mp) REVERT: A 288 LYS cc_start: 0.8768 (ptmm) cc_final: 0.8485 (ptmm) REVERT: A 366 GLU cc_start: 0.8075 (pm20) cc_final: 0.7459 (pt0) REVERT: A 403 GLN cc_start: 0.2739 (OUTLIER) cc_final: 0.1273 (tp40) REVERT: A 416 GLU cc_start: 0.7188 (OUTLIER) cc_final: 0.6736 (mp0) REVERT: A 427 ARG cc_start: 0.8102 (ttp-170) cc_final: 0.7702 (tpt170) REVERT: A 428 LYS cc_start: 0.8009 (mttt) cc_final: 0.7744 (mttt) REVERT: A 538 MET cc_start: 0.9076 (OUTLIER) cc_final: 0.8782 (mtp) REVERT: A 877 MET cc_start: 0.8294 (ttp) cc_final: 0.8027 (ttp) REVERT: A 903 ASP cc_start: 0.8760 (t70) cc_final: 0.8208 (m-30) REVERT: B 74 LYS cc_start: 0.9182 (tmtt) cc_final: 0.8842 (mppt) REVERT: B 337 MET cc_start: 0.8835 (OUTLIER) cc_final: 0.8524 (mtt) REVERT: B 414 GLU cc_start: 0.7266 (mm-30) cc_final: 0.6722 (mt-10) REVERT: B 503 MET cc_start: 0.8989 (OUTLIER) cc_final: 0.8775 (mtp) REVERT: B 602 ARG cc_start: 0.8359 (OUTLIER) cc_final: 0.7257 (mpp-170) REVERT: B 858 LYS cc_start: 0.8239 (mmmt) cc_final: 0.7212 (pptt) REVERT: B 893 CYS cc_start: 0.8555 (m) cc_final: 0.8122 (t) outliers start: 54 outliers final: 26 residues processed: 217 average time/residue: 1.1461 time to fit residues: 278.2779 Evaluate side-chains 196 residues out of total 1602 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 164 time to evaluate : 1.733 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 146 TYR Chi-restraints excluded: chain A residue 162 VAL Chi-restraints excluded: chain A residue 226 LEU Chi-restraints excluded: chain A residue 333 LEU Chi-restraints excluded: chain A residue 403 GLN Chi-restraints excluded: chain A residue 416 GLU Chi-restraints excluded: chain A residue 533 LEU Chi-restraints excluded: chain A residue 538 MET Chi-restraints excluded: chain A residue 569 SER Chi-restraints excluded: chain A residue 602 ARG Chi-restraints excluded: chain A residue 634 SER Chi-restraints excluded: chain A residue 694 LEU Chi-restraints excluded: chain A residue 818 VAL Chi-restraints excluded: chain B residue 56 SER Chi-restraints excluded: chain B residue 101 LEU Chi-restraints excluded: chain B residue 105 SER Chi-restraints excluded: chain B residue 141 THR Chi-restraints excluded: chain B residue 142 ILE Chi-restraints excluded: chain B residue 173 THR Chi-restraints excluded: chain B residue 326 THR Chi-restraints excluded: chain B residue 333 LEU Chi-restraints excluded: chain B residue 337 MET Chi-restraints excluded: chain B residue 473 VAL Chi-restraints excluded: chain B residue 503 MET Chi-restraints excluded: chain B residue 507 LEU Chi-restraints excluded: chain B residue 533 LEU Chi-restraints excluded: chain B residue 598 GLN Chi-restraints excluded: chain B residue 602 ARG Chi-restraints excluded: chain B residue 729 LEU Chi-restraints excluded: chain B residue 797 SER Chi-restraints excluded: chain B residue 851 THR Chi-restraints excluded: chain B residue 956 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 206 random chunks: chunk 165 optimal weight: 4.9990 chunk 113 optimal weight: 10.0000 chunk 2 optimal weight: 10.0000 chunk 148 optimal weight: 3.9990 chunk 82 optimal weight: 1.9990 chunk 169 optimal weight: 10.0000 chunk 137 optimal weight: 6.9990 chunk 0 optimal weight: 20.0000 chunk 101 optimal weight: 5.9990 chunk 178 optimal weight: 7.9990 chunk 50 optimal weight: 0.0020 overall best weight: 3.3996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 128 ASN A 552 ASN A 811 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8539 moved from start: 0.2456 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.059 16275 Z= 0.221 Angle : 0.561 7.953 22032 Z= 0.284 Chirality : 0.043 0.161 2550 Planarity : 0.005 0.049 2730 Dihedral : 12.290 89.546 2921 Min Nonbonded Distance : 2.380 Molprobity Statistics. All-atom Clashscore : 5.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.55 % Favored : 94.45 % Rotamer: Outliers : 2.87 % Allowed : 15.04 % Favored : 82.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.11 (0.19), residues: 2072 helix: 1.30 (0.16), residues: 1103 sheet: -1.06 (0.38), residues: 184 loop : -1.85 (0.21), residues: 785 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP B 474 HIS 0.008 0.001 HIS B 866 PHE 0.035 0.001 PHE B 365 TYR 0.012 0.001 TYR B 566 ARG 0.003 0.000 ARG A1000 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4144 Ramachandran restraints generated. 2072 Oldfield, 0 Emsley, 2072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4144 Ramachandran restraints generated. 2072 Oldfield, 0 Emsley, 2072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 221 residues out of total 1602 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 175 time to evaluate : 1.756 Fit side-chains revert: symmetry clash REVERT: A 74 LYS cc_start: 0.8769 (tmtp) cc_final: 0.8391 (mttt) REVERT: A 144 GLN cc_start: 0.8865 (mm-40) cc_final: 0.8080 (mp10) REVERT: A 221 GLU cc_start: 0.8301 (mp0) cc_final: 0.7978 (mp0) REVERT: A 288 LYS cc_start: 0.8726 (ptmm) cc_final: 0.8449 (ptmm) REVERT: A 403 GLN cc_start: 0.2812 (OUTLIER) cc_final: 0.1385 (tp40) REVERT: A 427 ARG cc_start: 0.8015 (ttp-170) cc_final: 0.7628 (tpt170) REVERT: A 428 LYS cc_start: 0.7979 (mttt) cc_final: 0.7750 (mttt) REVERT: A 903 ASP cc_start: 0.8620 (t70) cc_final: 0.8216 (m-30) REVERT: B 74 LYS cc_start: 0.9227 (tmtt) cc_final: 0.8894 (mppt) REVERT: B 89 MET cc_start: 0.8205 (ptm) cc_final: 0.7995 (ptp) REVERT: B 337 MET cc_start: 0.8820 (OUTLIER) cc_final: 0.8519 (mtt) REVERT: B 390 GLN cc_start: 0.8050 (OUTLIER) cc_final: 0.7825 (tm-30) REVERT: B 414 GLU cc_start: 0.7216 (mm-30) cc_final: 0.6604 (mt-10) REVERT: B 600 THR cc_start: 0.8838 (p) cc_final: 0.8547 (p) REVERT: B 837 MET cc_start: 0.8715 (OUTLIER) cc_final: 0.8263 (mtp) REVERT: B 858 LYS cc_start: 0.8229 (mmmt) cc_final: 0.7203 (pptt) REVERT: B 866 HIS cc_start: 0.7958 (p-80) cc_final: 0.7750 (p-80) REVERT: B 893 CYS cc_start: 0.8717 (m) cc_final: 0.8385 (t) outliers start: 46 outliers final: 18 residues processed: 209 average time/residue: 1.2407 time to fit residues: 291.1560 Evaluate side-chains 190 residues out of total 1602 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 168 time to evaluate : 1.870 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 146 TYR Chi-restraints excluded: chain A residue 403 GLN Chi-restraints excluded: chain A residue 569 SER Chi-restraints excluded: chain A residue 602 ARG Chi-restraints excluded: chain A residue 634 SER Chi-restraints excluded: chain A residue 694 LEU Chi-restraints excluded: chain A residue 818 VAL Chi-restraints excluded: chain B residue 101 LEU Chi-restraints excluded: chain B residue 105 SER Chi-restraints excluded: chain B residue 173 THR Chi-restraints excluded: chain B residue 326 THR Chi-restraints excluded: chain B residue 337 MET Chi-restraints excluded: chain B residue 390 GLN Chi-restraints excluded: chain B residue 473 VAL Chi-restraints excluded: chain B residue 533 LEU Chi-restraints excluded: chain B residue 598 GLN Chi-restraints excluded: chain B residue 729 LEU Chi-restraints excluded: chain B residue 797 SER Chi-restraints excluded: chain B residue 837 MET Chi-restraints excluded: chain B residue 851 THR Chi-restraints excluded: chain B residue 930 LEU Chi-restraints excluded: chain B residue 956 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 206 random chunks: chunk 66 optimal weight: 9.9990 chunk 179 optimal weight: 9.9990 chunk 39 optimal weight: 1.9990 chunk 116 optimal weight: 20.0000 chunk 49 optimal weight: 4.9990 chunk 199 optimal weight: 20.0000 chunk 165 optimal weight: 9.9990 chunk 92 optimal weight: 6.9990 chunk 16 optimal weight: 9.9990 chunk 65 optimal weight: 8.9990 chunk 104 optimal weight: 10.0000 overall best weight: 6.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 128 ASN A 552 ASN A 811 ASN ** B 166 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 658 GLN B 866 HIS B 952 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8575 moved from start: 0.2590 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.062 16275 Z= 0.353 Angle : 0.627 8.356 22032 Z= 0.317 Chirality : 0.046 0.221 2550 Planarity : 0.005 0.051 2730 Dihedral : 12.613 86.239 2921 Min Nonbonded Distance : 2.330 Molprobity Statistics. All-atom Clashscore : 5.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.27 % Favored : 93.73 % Rotamer: Outliers : 3.56 % Allowed : 14.86 % Favored : 81.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.13 (0.19), residues: 2072 helix: 1.21 (0.16), residues: 1111 sheet: -0.94 (0.39), residues: 177 loop : -1.81 (0.21), residues: 784 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 801 HIS 0.008 0.002 HIS B 481 PHE 0.031 0.002 PHE B 365 TYR 0.017 0.002 TYR A 566 ARG 0.003 0.001 ARG A 537 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4144 Ramachandran restraints generated. 2072 Oldfield, 0 Emsley, 2072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4144 Ramachandran restraints generated. 2072 Oldfield, 0 Emsley, 2072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 231 residues out of total 1602 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 57 poor density : 174 time to evaluate : 1.673 Fit side-chains revert: symmetry clash REVERT: A 74 LYS cc_start: 0.8798 (tmtp) cc_final: 0.8333 (mttt) REVERT: A 144 GLN cc_start: 0.8894 (mm-40) cc_final: 0.8032 (mp10) REVERT: A 288 LYS cc_start: 0.8752 (ptmm) cc_final: 0.8521 (ptmm) REVERT: A 403 GLN cc_start: 0.2969 (OUTLIER) cc_final: 0.1476 (tp40) REVERT: A 416 GLU cc_start: 0.7169 (OUTLIER) cc_final: 0.6708 (mp0) REVERT: A 427 ARG cc_start: 0.8056 (ttp-170) cc_final: 0.7668 (tpt170) REVERT: A 428 LYS cc_start: 0.8040 (mttt) cc_final: 0.7780 (mttt) REVERT: A 628 GLU cc_start: 0.8785 (OUTLIER) cc_final: 0.8380 (mp0) REVERT: A 754 MET cc_start: 0.7010 (OUTLIER) cc_final: 0.6661 (ptt) REVERT: A 903 ASP cc_start: 0.8695 (t70) cc_final: 0.8236 (m-30) REVERT: A 956 ASP cc_start: 0.7496 (m-30) cc_final: 0.6937 (p0) REVERT: B 74 LYS cc_start: 0.9220 (tmtt) cc_final: 0.8898 (mppt) REVERT: B 89 MET cc_start: 0.8174 (ptm) cc_final: 0.7963 (ptp) REVERT: B 337 MET cc_start: 0.8826 (OUTLIER) cc_final: 0.8508 (mtt) REVERT: B 376 MET cc_start: 0.8571 (tpp) cc_final: 0.8231 (tpt) REVERT: B 390 GLN cc_start: 0.8159 (OUTLIER) cc_final: 0.7926 (tm-30) REVERT: B 414 GLU cc_start: 0.7181 (mm-30) cc_final: 0.6556 (mt-10) REVERT: B 427 ARG cc_start: 0.8140 (OUTLIER) cc_final: 0.7529 (tpm170) REVERT: B 858 LYS cc_start: 0.8314 (mmmt) cc_final: 0.7262 (pptt) REVERT: B 861 GLU cc_start: 0.7068 (pm20) cc_final: 0.6600 (mp0) REVERT: B 893 CYS cc_start: 0.8755 (m) cc_final: 0.8439 (t) outliers start: 57 outliers final: 29 residues processed: 216 average time/residue: 1.2128 time to fit residues: 292.8374 Evaluate side-chains 205 residues out of total 1602 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 169 time to evaluate : 2.352 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 94 LEU Chi-restraints excluded: chain A residue 146 TYR Chi-restraints excluded: chain A residue 162 VAL Chi-restraints excluded: chain A residue 333 LEU Chi-restraints excluded: chain A residue 403 GLN Chi-restraints excluded: chain A residue 416 GLU Chi-restraints excluded: chain A residue 487 VAL Chi-restraints excluded: chain A residue 569 SER Chi-restraints excluded: chain A residue 602 ARG Chi-restraints excluded: chain A residue 628 GLU Chi-restraints excluded: chain A residue 634 SER Chi-restraints excluded: chain A residue 652 GLN Chi-restraints excluded: chain A residue 694 LEU Chi-restraints excluded: chain A residue 754 MET Chi-restraints excluded: chain A residue 818 VAL Chi-restraints excluded: chain B residue 101 LEU Chi-restraints excluded: chain B residue 105 SER Chi-restraints excluded: chain B residue 141 THR Chi-restraints excluded: chain B residue 142 ILE Chi-restraints excluded: chain B residue 162 VAL Chi-restraints excluded: chain B residue 173 THR Chi-restraints excluded: chain B residue 209 ILE Chi-restraints excluded: chain B residue 321 VAL Chi-restraints excluded: chain B residue 326 THR Chi-restraints excluded: chain B residue 333 LEU Chi-restraints excluded: chain B residue 337 MET Chi-restraints excluded: chain B residue 390 GLN Chi-restraints excluded: chain B residue 427 ARG Chi-restraints excluded: chain B residue 473 VAL Chi-restraints excluded: chain B residue 533 LEU Chi-restraints excluded: chain B residue 598 GLN Chi-restraints excluded: chain B residue 729 LEU Chi-restraints excluded: chain B residue 797 SER Chi-restraints excluded: chain B residue 851 THR Chi-restraints excluded: chain B residue 930 LEU Chi-restraints excluded: chain B residue 956 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 206 random chunks: chunk 192 optimal weight: 7.9990 chunk 22 optimal weight: 6.9990 chunk 113 optimal weight: 10.0000 chunk 145 optimal weight: 3.9990 chunk 112 optimal weight: 20.0000 chunk 167 optimal weight: 6.9990 chunk 111 optimal weight: 10.0000 chunk 198 optimal weight: 8.9990 chunk 124 optimal weight: 9.9990 chunk 121 optimal weight: 2.9990 chunk 91 optimal weight: 2.9990 overall best weight: 4.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 128 ASN ** A 489 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 552 ASN A 811 ASN ** B 166 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 378 HIS B 658 GLN B 866 HIS B 952 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8558 moved from start: 0.2672 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 16275 Z= 0.272 Angle : 0.586 8.564 22032 Z= 0.297 Chirality : 0.044 0.205 2550 Planarity : 0.005 0.050 2730 Dihedral : 12.494 88.055 2921 Min Nonbonded Distance : 2.357 Molprobity Statistics. All-atom Clashscore : 5.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.84 % Favored : 94.16 % Rotamer: Outliers : 3.62 % Allowed : 15.29 % Favored : 81.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.11 (0.19), residues: 2072 helix: 1.42 (0.16), residues: 1109 sheet: -0.87 (0.40), residues: 177 loop : -1.71 (0.21), residues: 786 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 801 HIS 0.008 0.001 HIS B 866 PHE 0.030 0.002 PHE B 393 TYR 0.014 0.001 TYR B 566 ARG 0.003 0.000 ARG A 537 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4144 Ramachandran restraints generated. 2072 Oldfield, 0 Emsley, 2072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4144 Ramachandran restraints generated. 2072 Oldfield, 0 Emsley, 2072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 232 residues out of total 1602 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 58 poor density : 174 time to evaluate : 1.748 Fit side-chains revert: symmetry clash REVERT: A 74 LYS cc_start: 0.8823 (tmtp) cc_final: 0.8312 (mttt) REVERT: A 144 GLN cc_start: 0.8868 (mm-40) cc_final: 0.8061 (mp10) REVERT: A 221 GLU cc_start: 0.8297 (mp0) cc_final: 0.8022 (mp0) REVERT: A 288 LYS cc_start: 0.8745 (ptmm) cc_final: 0.8505 (ptmm) REVERT: A 403 GLN cc_start: 0.2977 (OUTLIER) cc_final: 0.1486 (tp40) REVERT: A 416 GLU cc_start: 0.7167 (OUTLIER) cc_final: 0.6700 (mp0) REVERT: A 427 ARG cc_start: 0.8026 (ttp-170) cc_final: 0.7668 (tpt170) REVERT: A 428 LYS cc_start: 0.8008 (mttt) cc_final: 0.7758 (mttt) REVERT: A 538 MET cc_start: 0.9103 (OUTLIER) cc_final: 0.8787 (mtp) REVERT: A 754 MET cc_start: 0.7016 (OUTLIER) cc_final: 0.6604 (ptt) REVERT: A 903 ASP cc_start: 0.8678 (t70) cc_final: 0.8233 (m-30) REVERT: A 956 ASP cc_start: 0.7437 (m-30) cc_final: 0.6938 (p0) REVERT: B 74 LYS cc_start: 0.9212 (tmtt) cc_final: 0.8892 (mppt) REVERT: B 89 MET cc_start: 0.8148 (ptm) cc_final: 0.7941 (ptp) REVERT: B 337 MET cc_start: 0.8819 (OUTLIER) cc_final: 0.8504 (mtt) REVERT: B 376 MET cc_start: 0.8579 (tpp) cc_final: 0.8231 (tpt) REVERT: B 390 GLN cc_start: 0.8144 (OUTLIER) cc_final: 0.7912 (tm-30) REVERT: B 403 GLN cc_start: 0.1782 (OUTLIER) cc_final: 0.1522 (tt0) REVERT: B 414 GLU cc_start: 0.7135 (mm-30) cc_final: 0.6517 (mt-10) REVERT: B 418 GLU cc_start: 0.7110 (OUTLIER) cc_final: 0.6853 (mp0) REVERT: B 427 ARG cc_start: 0.8122 (OUTLIER) cc_final: 0.7517 (tpm170) REVERT: B 837 MET cc_start: 0.8717 (OUTLIER) cc_final: 0.8194 (mtp) REVERT: B 858 LYS cc_start: 0.8310 (mmmt) cc_final: 0.7405 (pptt) outliers start: 58 outliers final: 31 residues processed: 216 average time/residue: 1.1794 time to fit residues: 284.2644 Evaluate side-chains 209 residues out of total 1602 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 168 time to evaluate : 1.739 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 94 LEU Chi-restraints excluded: chain A residue 146 TYR Chi-restraints excluded: chain A residue 226 LEU Chi-restraints excluded: chain A residue 333 LEU Chi-restraints excluded: chain A residue 403 GLN Chi-restraints excluded: chain A residue 416 GLU Chi-restraints excluded: chain A residue 487 VAL Chi-restraints excluded: chain A residue 507 LEU Chi-restraints excluded: chain A residue 533 LEU Chi-restraints excluded: chain A residue 538 MET Chi-restraints excluded: chain A residue 569 SER Chi-restraints excluded: chain A residue 602 ARG Chi-restraints excluded: chain A residue 634 SER Chi-restraints excluded: chain A residue 652 GLN Chi-restraints excluded: chain A residue 694 LEU Chi-restraints excluded: chain A residue 754 MET Chi-restraints excluded: chain A residue 806 GLU Chi-restraints excluded: chain A residue 818 VAL Chi-restraints excluded: chain B residue 101 LEU Chi-restraints excluded: chain B residue 105 SER Chi-restraints excluded: chain B residue 141 THR Chi-restraints excluded: chain B residue 142 ILE Chi-restraints excluded: chain B residue 162 VAL Chi-restraints excluded: chain B residue 173 THR Chi-restraints excluded: chain B residue 209 ILE Chi-restraints excluded: chain B residue 326 THR Chi-restraints excluded: chain B residue 333 LEU Chi-restraints excluded: chain B residue 337 MET Chi-restraints excluded: chain B residue 390 GLN Chi-restraints excluded: chain B residue 403 GLN Chi-restraints excluded: chain B residue 418 GLU Chi-restraints excluded: chain B residue 427 ARG Chi-restraints excluded: chain B residue 473 VAL Chi-restraints excluded: chain B residue 533 LEU Chi-restraints excluded: chain B residue 598 GLN Chi-restraints excluded: chain B residue 729 LEU Chi-restraints excluded: chain B residue 797 SER Chi-restraints excluded: chain B residue 837 MET Chi-restraints excluded: chain B residue 851 THR Chi-restraints excluded: chain B residue 930 LEU Chi-restraints excluded: chain B residue 956 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 206 random chunks: chunk 122 optimal weight: 10.0000 chunk 79 optimal weight: 5.9990 chunk 118 optimal weight: 6.9990 chunk 59 optimal weight: 5.9990 chunk 39 optimal weight: 20.0000 chunk 38 optimal weight: 0.6980 chunk 126 optimal weight: 10.0000 chunk 135 optimal weight: 10.0000 chunk 98 optimal weight: 6.9990 chunk 18 optimal weight: 9.9990 chunk 156 optimal weight: 5.9990 overall best weight: 5.1388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 128 ASN ** A 264 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 489 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 552 ASN A 811 ASN ** B 166 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 658 GLN B 866 HIS B 952 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8563 moved from start: 0.2750 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 16275 Z= 0.289 Angle : 0.601 11.407 22032 Z= 0.303 Chirality : 0.044 0.201 2550 Planarity : 0.005 0.050 2730 Dihedral : 12.512 88.144 2921 Min Nonbonded Distance : 2.353 Molprobity Statistics. All-atom Clashscore : 5.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.98 % Favored : 94.02 % Rotamer: Outliers : 3.31 % Allowed : 16.04 % Favored : 80.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.17 (0.19), residues: 2072 helix: 1.47 (0.16), residues: 1109 sheet: -0.83 (0.39), residues: 178 loop : -1.68 (0.22), residues: 785 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 474 HIS 0.009 0.001 HIS B 866 PHE 0.028 0.001 PHE B 365 TYR 0.015 0.002 TYR A 566 ARG 0.003 0.000 ARG A 537 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4144 Ramachandran restraints generated. 2072 Oldfield, 0 Emsley, 2072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4144 Ramachandran restraints generated. 2072 Oldfield, 0 Emsley, 2072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 230 residues out of total 1602 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 177 time to evaluate : 1.781 Fit side-chains revert: symmetry clash REVERT: A 74 LYS cc_start: 0.8850 (tmtp) cc_final: 0.8336 (mttt) REVERT: A 144 GLN cc_start: 0.8919 (mm-40) cc_final: 0.8141 (mp10) REVERT: A 221 GLU cc_start: 0.8312 (mp0) cc_final: 0.7997 (mp0) REVERT: A 288 LYS cc_start: 0.8738 (ptmm) cc_final: 0.8508 (ptmm) REVERT: A 403 GLN cc_start: 0.2998 (OUTLIER) cc_final: 0.1503 (tp40) REVERT: A 416 GLU cc_start: 0.7155 (OUTLIER) cc_final: 0.6689 (mp0) REVERT: A 419 LYS cc_start: 0.6950 (ttmt) cc_final: 0.6649 (tttp) REVERT: A 427 ARG cc_start: 0.8102 (ttp-170) cc_final: 0.7720 (tpt170) REVERT: A 428 LYS cc_start: 0.7998 (mttt) cc_final: 0.7744 (mttt) REVERT: A 754 MET cc_start: 0.7025 (OUTLIER) cc_final: 0.6618 (ptt) REVERT: A 903 ASP cc_start: 0.8692 (t70) cc_final: 0.8238 (m-30) REVERT: A 956 ASP cc_start: 0.7455 (m-30) cc_final: 0.6996 (p0) REVERT: B 74 LYS cc_start: 0.9285 (tmtt) cc_final: 0.9045 (tptt) REVERT: B 337 MET cc_start: 0.8817 (OUTLIER) cc_final: 0.8501 (mtt) REVERT: B 376 MET cc_start: 0.8554 (tpp) cc_final: 0.8183 (tpp) REVERT: B 390 GLN cc_start: 0.8158 (OUTLIER) cc_final: 0.7947 (tm-30) REVERT: B 414 GLU cc_start: 0.7117 (mm-30) cc_final: 0.6506 (mt-10) REVERT: B 418 GLU cc_start: 0.7130 (OUTLIER) cc_final: 0.6890 (mp0) REVERT: B 427 ARG cc_start: 0.8126 (OUTLIER) cc_final: 0.7519 (tpm170) REVERT: B 681 ILE cc_start: 0.8799 (tt) cc_final: 0.8580 (pt) REVERT: B 858 LYS cc_start: 0.8303 (mmmt) cc_final: 0.7255 (pptt) REVERT: B 861 GLU cc_start: 0.7120 (pm20) cc_final: 0.6622 (mp0) outliers start: 53 outliers final: 31 residues processed: 214 average time/residue: 1.2177 time to fit residues: 291.4242 Evaluate side-chains 210 residues out of total 1602 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 172 time to evaluate : 1.730 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 94 LEU Chi-restraints excluded: chain A residue 146 TYR Chi-restraints excluded: chain A residue 162 VAL Chi-restraints excluded: chain A residue 226 LEU Chi-restraints excluded: chain A residue 333 LEU Chi-restraints excluded: chain A residue 403 GLN Chi-restraints excluded: chain A residue 416 GLU Chi-restraints excluded: chain A residue 487 VAL Chi-restraints excluded: chain A residue 507 LEU Chi-restraints excluded: chain A residue 533 LEU Chi-restraints excluded: chain A residue 569 SER Chi-restraints excluded: chain A residue 602 ARG Chi-restraints excluded: chain A residue 634 SER Chi-restraints excluded: chain A residue 694 LEU Chi-restraints excluded: chain A residue 754 MET Chi-restraints excluded: chain A residue 806 GLU Chi-restraints excluded: chain A residue 818 VAL Chi-restraints excluded: chain B residue 105 SER Chi-restraints excluded: chain B residue 141 THR Chi-restraints excluded: chain B residue 142 ILE Chi-restraints excluded: chain B residue 162 VAL Chi-restraints excluded: chain B residue 173 THR Chi-restraints excluded: chain B residue 209 ILE Chi-restraints excluded: chain B residue 326 THR Chi-restraints excluded: chain B residue 333 LEU Chi-restraints excluded: chain B residue 337 MET Chi-restraints excluded: chain B residue 390 GLN Chi-restraints excluded: chain B residue 418 GLU Chi-restraints excluded: chain B residue 427 ARG Chi-restraints excluded: chain B residue 473 VAL Chi-restraints excluded: chain B residue 533 LEU Chi-restraints excluded: chain B residue 598 GLN Chi-restraints excluded: chain B residue 729 LEU Chi-restraints excluded: chain B residue 797 SER Chi-restraints excluded: chain B residue 851 THR Chi-restraints excluded: chain B residue 893 CYS Chi-restraints excluded: chain B residue 930 LEU Chi-restraints excluded: chain B residue 956 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 206 random chunks: chunk 180 optimal weight: 5.9990 chunk 190 optimal weight: 8.9990 chunk 173 optimal weight: 8.9990 chunk 185 optimal weight: 4.9990 chunk 111 optimal weight: 5.9990 chunk 80 optimal weight: 0.7980 chunk 145 optimal weight: 0.0470 chunk 56 optimal weight: 2.9990 chunk 167 optimal weight: 8.9990 chunk 174 optimal weight: 2.9990 chunk 184 optimal weight: 6.9990 overall best weight: 2.3684 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 128 ASN ** A 264 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 489 ASN A 552 ASN ** B 166 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 658 GLN B 866 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8526 moved from start: 0.2806 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 16275 Z= 0.183 Angle : 0.551 11.249 22032 Z= 0.280 Chirality : 0.042 0.192 2550 Planarity : 0.004 0.049 2730 Dihedral : 12.113 88.190 2921 Min Nonbonded Distance : 2.361 Molprobity Statistics. All-atom Clashscore : 5.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.41 % Favored : 94.59 % Rotamer: Outliers : 2.56 % Allowed : 16.60 % Favored : 80.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.47 (0.19), residues: 2072 helix: 1.73 (0.16), residues: 1114 sheet: -0.78 (0.40), residues: 178 loop : -1.58 (0.22), residues: 780 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP B 474 HIS 0.010 0.001 HIS B 866 PHE 0.038 0.001 PHE B 393 TYR 0.010 0.001 TYR A 11 ARG 0.002 0.000 ARG A1038 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4144 Ramachandran restraints generated. 2072 Oldfield, 0 Emsley, 2072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4144 Ramachandran restraints generated. 2072 Oldfield, 0 Emsley, 2072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 220 residues out of total 1602 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 179 time to evaluate : 1.809 Fit side-chains revert: symmetry clash REVERT: A 74 LYS cc_start: 0.8876 (tmtp) cc_final: 0.8328 (mttt) REVERT: A 144 GLN cc_start: 0.8878 (mm-40) cc_final: 0.8160 (mp10) REVERT: A 221 GLU cc_start: 0.8290 (mp0) cc_final: 0.7998 (mp0) REVERT: A 288 LYS cc_start: 0.8711 (ptmm) cc_final: 0.8498 (ptmm) REVERT: A 403 GLN cc_start: 0.2993 (OUTLIER) cc_final: 0.1606 (tp40) REVERT: A 416 GLU cc_start: 0.7041 (OUTLIER) cc_final: 0.6600 (mp0) REVERT: A 427 ARG cc_start: 0.8049 (ttp-170) cc_final: 0.7690 (tpt170) REVERT: A 501 VAL cc_start: 0.9159 (t) cc_final: 0.8798 (m) REVERT: A 754 MET cc_start: 0.6849 (OUTLIER) cc_final: 0.6611 (ptt) REVERT: A 903 ASP cc_start: 0.8665 (t70) cc_final: 0.8224 (m-30) REVERT: A 956 ASP cc_start: 0.7464 (m-30) cc_final: 0.6784 (p0) REVERT: B 74 LYS cc_start: 0.9277 (tmtt) cc_final: 0.9047 (tptt) REVERT: B 337 MET cc_start: 0.8798 (OUTLIER) cc_final: 0.8499 (mtt) REVERT: B 376 MET cc_start: 0.8463 (tpp) cc_final: 0.8082 (tpp) REVERT: B 414 GLU cc_start: 0.7136 (mm-30) cc_final: 0.6547 (mt-10) REVERT: B 427 ARG cc_start: 0.8095 (OUTLIER) cc_final: 0.7491 (tpm170) REVERT: B 858 LYS cc_start: 0.8308 (mmmt) cc_final: 0.7413 (pptt) outliers start: 41 outliers final: 18 residues processed: 206 average time/residue: 1.2049 time to fit residues: 276.8034 Evaluate side-chains 194 residues out of total 1602 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 171 time to evaluate : 1.749 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 146 TYR Chi-restraints excluded: chain A residue 226 LEU Chi-restraints excluded: chain A residue 333 LEU Chi-restraints excluded: chain A residue 403 GLN Chi-restraints excluded: chain A residue 416 GLU Chi-restraints excluded: chain A residue 487 VAL Chi-restraints excluded: chain A residue 507 LEU Chi-restraints excluded: chain A residue 602 ARG Chi-restraints excluded: chain A residue 634 SER Chi-restraints excluded: chain A residue 694 LEU Chi-restraints excluded: chain A residue 754 MET Chi-restraints excluded: chain A residue 806 GLU Chi-restraints excluded: chain B residue 105 SER Chi-restraints excluded: chain B residue 141 THR Chi-restraints excluded: chain B residue 173 THR Chi-restraints excluded: chain B residue 176 ILE Chi-restraints excluded: chain B residue 326 THR Chi-restraints excluded: chain B residue 337 MET Chi-restraints excluded: chain B residue 427 ARG Chi-restraints excluded: chain B residue 749 ILE Chi-restraints excluded: chain B residue 797 SER Chi-restraints excluded: chain B residue 851 THR Chi-restraints excluded: chain B residue 930 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 206 random chunks: chunk 121 optimal weight: 8.9990 chunk 195 optimal weight: 0.5980 chunk 119 optimal weight: 0.9990 chunk 92 optimal weight: 7.9990 chunk 136 optimal weight: 8.9990 chunk 205 optimal weight: 8.9990 chunk 188 optimal weight: 0.8980 chunk 163 optimal weight: 10.0000 chunk 16 optimal weight: 0.9980 chunk 126 optimal weight: 40.0000 chunk 100 optimal weight: 10.0000 overall best weight: 2.2984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 128 ASN ** A 264 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 552 ASN B 122 ASN B 403 GLN B 658 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8520 moved from start: 0.2874 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 16275 Z= 0.179 Angle : 0.548 11.685 22032 Z= 0.276 Chirality : 0.042 0.192 2550 Planarity : 0.004 0.050 2730 Dihedral : 11.940 87.410 2921 Min Nonbonded Distance : 2.405 Molprobity Statistics. All-atom Clashscore : 5.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.41 % Favored : 94.59 % Rotamer: Outliers : 1.56 % Allowed : 17.98 % Favored : 80.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.65 (0.19), residues: 2072 helix: 1.88 (0.16), residues: 1111 sheet: -0.61 (0.40), residues: 174 loop : -1.51 (0.22), residues: 787 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP B 474 HIS 0.003 0.001 HIS A 664 PHE 0.027 0.001 PHE B 365 TYR 0.020 0.001 TYR A 364 ARG 0.002 0.000 ARG A1038 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4144 Ramachandran restraints generated. 2072 Oldfield, 0 Emsley, 2072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4144 Ramachandran restraints generated. 2072 Oldfield, 0 Emsley, 2072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 206 residues out of total 1602 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 181 time to evaluate : 1.699 Fit side-chains revert: symmetry clash REVERT: A 74 LYS cc_start: 0.8829 (tmtp) cc_final: 0.8325 (mttt) REVERT: A 144 GLN cc_start: 0.8889 (mm-40) cc_final: 0.8187 (mp10) REVERT: A 221 GLU cc_start: 0.8289 (mp0) cc_final: 0.7995 (mp0) REVERT: A 288 LYS cc_start: 0.8770 (ptmm) cc_final: 0.8509 (ptmm) REVERT: A 403 GLN cc_start: 0.3140 (OUTLIER) cc_final: 0.1770 (tp40) REVERT: A 416 GLU cc_start: 0.7050 (OUTLIER) cc_final: 0.6574 (mp0) REVERT: A 427 ARG cc_start: 0.8046 (ttp-170) cc_final: 0.7635 (mmt180) REVERT: A 501 VAL cc_start: 0.9130 (t) cc_final: 0.8760 (m) REVERT: A 754 MET cc_start: 0.6824 (OUTLIER) cc_final: 0.6607 (ptt) REVERT: A 903 ASP cc_start: 0.8674 (t70) cc_final: 0.8227 (m-30) REVERT: A 956 ASP cc_start: 0.7467 (m-30) cc_final: 0.6782 (p0) REVERT: B 74 LYS cc_start: 0.9287 (tmtt) cc_final: 0.9059 (tptt) REVERT: B 337 MET cc_start: 0.8791 (OUTLIER) cc_final: 0.8498 (mtt) REVERT: B 376 MET cc_start: 0.8469 (tpp) cc_final: 0.8158 (tpp) REVERT: B 414 GLU cc_start: 0.7100 (mm-30) cc_final: 0.6635 (mt-10) REVERT: B 427 ARG cc_start: 0.8084 (OUTLIER) cc_final: 0.7483 (tpm170) REVERT: B 858 LYS cc_start: 0.8299 (mmmt) cc_final: 0.7413 (pptt) outliers start: 25 outliers final: 15 residues processed: 198 average time/residue: 1.2170 time to fit residues: 269.4338 Evaluate side-chains 192 residues out of total 1602 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 172 time to evaluate : 1.772 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 146 TYR Chi-restraints excluded: chain A residue 226 LEU Chi-restraints excluded: chain A residue 333 LEU Chi-restraints excluded: chain A residue 403 GLN Chi-restraints excluded: chain A residue 416 GLU Chi-restraints excluded: chain A residue 507 LEU Chi-restraints excluded: chain A residue 602 ARG Chi-restraints excluded: chain A residue 634 SER Chi-restraints excluded: chain A residue 694 LEU Chi-restraints excluded: chain A residue 754 MET Chi-restraints excluded: chain A residue 806 GLU Chi-restraints excluded: chain B residue 105 SER Chi-restraints excluded: chain B residue 326 THR Chi-restraints excluded: chain B residue 337 MET Chi-restraints excluded: chain B residue 427 ARG Chi-restraints excluded: chain B residue 749 ILE Chi-restraints excluded: chain B residue 797 SER Chi-restraints excluded: chain B residue 851 THR Chi-restraints excluded: chain B residue 893 CYS Chi-restraints excluded: chain B residue 930 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 206 random chunks: chunk 129 optimal weight: 9.9990 chunk 174 optimal weight: 10.0000 chunk 50 optimal weight: 9.9990 chunk 150 optimal weight: 8.9990 chunk 24 optimal weight: 2.9990 chunk 45 optimal weight: 8.9990 chunk 163 optimal weight: 9.9990 chunk 68 optimal weight: 0.2980 chunk 168 optimal weight: 0.9980 chunk 20 optimal weight: 10.0000 chunk 30 optimal weight: 9.9990 overall best weight: 4.4586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 128 ASN ** A 264 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 552 ASN B 658 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3517 r_free = 0.3517 target = 0.126931 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3066 r_free = 0.3066 target = 0.093402 restraints weight = 21162.977| |-----------------------------------------------------------------------------| r_work (start): 0.3040 rms_B_bonded: 1.83 r_work: 0.2929 rms_B_bonded: 2.46 restraints_weight: 0.5000 r_work: 0.2808 rms_B_bonded: 4.02 restraints_weight: 0.2500 r_work (final): 0.2808 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8435 moved from start: 0.2882 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 16275 Z= 0.260 Angle : 0.587 11.358 22032 Z= 0.295 Chirality : 0.044 0.186 2550 Planarity : 0.004 0.051 2730 Dihedral : 12.146 89.250 2921 Min Nonbonded Distance : 2.382 Molprobity Statistics. All-atom Clashscore : 5.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.74 % Favored : 94.26 % Rotamer: Outliers : 2.06 % Allowed : 17.67 % Favored : 80.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.52 (0.19), residues: 2072 helix: 1.75 (0.16), residues: 1115 sheet: -0.82 (0.38), residues: 184 loop : -1.50 (0.22), residues: 773 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 474 HIS 0.005 0.001 HIS B 481 PHE 0.035 0.001 PHE B 393 TYR 0.014 0.001 TYR A 566 ARG 0.002 0.000 ARG A 537 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5301.64 seconds wall clock time: 93 minutes 43.79 seconds (5623.79 seconds total)