Starting phenix.real_space_refine on Fri Sep 27 22:53:12 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7uic_26543/09_2024/7uic_26543.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7uic_26543/09_2024/7uic_26543.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7uic_26543/09_2024/7uic_26543.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7uic_26543/09_2024/7uic_26543.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7uic_26543/09_2024/7uic_26543.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7uic_26543/09_2024/7uic_26543.cif" } resolution = 3.7 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.002 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 72 5.16 5 C 11113 2.51 5 N 2869 2.21 5 O 3249 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 17 residue(s): 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/chem_data/mon_lib" Total number of atoms: 17303 Number of models: 1 Model: "" Number of chains: 6 Chain: "b" Number of atoms: 516 Number of conformers: 1 Conformer: "" Number of residues, atoms: 65, 516 Classifications: {'peptide': 65} Link IDs: {'TRANS': 64} Chain breaks: 1 Chain: "c" Number of atoms: 891 Number of conformers: 1 Conformer: "" Number of residues, atoms: 110, 891 Classifications: {'peptide': 110} Link IDs: {'PTRANS': 4, 'TRANS': 105} Chain: "e" Number of atoms: 5916 Number of conformers: 1 Conformer: "" Number of residues, atoms: 729, 5916 Classifications: {'peptide': 729} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 20, 'TRANS': 708} Chain breaks: 4 Chain: "n" Number of atoms: 1780 Number of conformers: 1 Conformer: "" Number of residues, atoms: 220, 1780 Classifications: {'peptide': 220} Link IDs: {'PTRANS': 9, 'TRANS': 210} Chain breaks: 1 Chain: "o" Number of atoms: 894 Number of conformers: 1 Conformer: "" Number of residues, atoms: 111, 894 Classifications: {'peptide': 111} Link IDs: {'PTRANS': 3, 'TRANS': 107} Chain: "p" Number of atoms: 7306 Number of conformers: 1 Conformer: "" Number of residues, atoms: 903, 7306 Classifications: {'peptide': 903} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 42, 'TRANS': 860} Chain breaks: 3 Time building chain proxies: 10.03, per 1000 atoms: 0.58 Number of scatterers: 17303 At special positions: 0 Unit cell: (149.04, 184.92, 129.72, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 72 16.00 O 3249 8.00 N 2869 7.00 C 11113 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: 4.25 Conformation dependent library (CDL) restraints added in 2.2 seconds 4216 Ramachandran restraints generated. 2108 Oldfield, 0 Emsley, 2108 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4150 Finding SS restraints... Secondary structure from input PDB file: 89 helices and 15 sheets defined 55.8% alpha, 11.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.03 Creating SS restraints... Processing helix chain 'b' and resid 28 through 51 removed outlier: 3.646A pdb=" N THR b 33 " --> pdb=" O LYS b 29 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N PHE b 36 " --> pdb=" O LEU b 32 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N LEU b 40 " --> pdb=" O PHE b 36 " (cutoff:3.500A) removed outlier: 3.912A pdb=" N GLU b 45 " --> pdb=" O LYS b 41 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N MET b 46 " --> pdb=" O VAL b 42 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N GLN b 50 " --> pdb=" O MET b 46 " (cutoff:3.500A) Processing helix chain 'b' and resid 66 through 104 Processing helix chain 'c' and resid 10 through 19 Processing helix chain 'c' and resid 20 through 22 No H-bonds generated for 'chain 'c' and resid 20 through 22' Processing helix chain 'c' and resid 23 through 56 removed outlier: 4.112A pdb=" N LEU c 41 " --> pdb=" O ARG c 37 " (cutoff:3.500A) Proline residue: c 42 - end of helix Processing helix chain 'c' and resid 63 through 95 Processing helix chain 'c' and resid 95 through 100 Processing helix chain 'c' and resid 100 through 110 removed outlier: 4.078A pdb=" N GLU c 104 " --> pdb=" O SER c 100 " (cutoff:3.500A) Processing helix chain 'e' and resid 288 through 305 Processing helix chain 'e' and resid 312 through 325 removed outlier: 4.494A pdb=" N THR e 321 " --> pdb=" O TYR e 317 " (cutoff:3.500A) removed outlier: 4.403A pdb=" N SER e 322 " --> pdb=" O SER e 318 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N PHE e 325 " --> pdb=" O THR e 321 " (cutoff:3.500A) Processing helix chain 'e' and resid 334 through 356 Processing helix chain 'e' and resid 367 through 387 removed outlier: 4.555A pdb=" N LEU e 381 " --> pdb=" O ILE e 377 " (cutoff:3.500A) Proline residue: e 382 - end of helix Processing helix chain 'e' and resid 392 through 402 removed outlier: 3.847A pdb=" N VAL e 396 " --> pdb=" O SER e 392 " (cutoff:3.500A) Processing helix chain 'e' and resid 404 through 419 removed outlier: 4.448A pdb=" N VAL e 408 " --> pdb=" O ASP e 404 " (cutoff:3.500A) Processing helix chain 'e' and resid 438 through 450 removed outlier: 3.821A pdb=" N ASP e 442 " --> pdb=" O ASP e 438 " (cutoff:3.500A) Processing helix chain 'e' and resid 457 through 462 removed outlier: 3.846A pdb=" N TYR e 461 " --> pdb=" O VAL e 457 " (cutoff:3.500A) Processing helix chain 'e' and resid 493 through 505 removed outlier: 3.636A pdb=" N PHE e 497 " --> pdb=" O ASN e 493 " (cutoff:3.500A) Processing helix chain 'e' and resid 506 through 510 removed outlier: 3.679A pdb=" N ILE e 510 " --> pdb=" O LEU e 507 " (cutoff:3.500A) Processing helix chain 'e' and resid 520 through 528 removed outlier: 3.503A pdb=" N GLN e 524 " --> pdb=" O ASN e 520 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N HIS e 527 " --> pdb=" O PHE e 523 " (cutoff:3.500A) Processing helix chain 'e' and resid 529 through 532 removed outlier: 3.711A pdb=" N VAL e 532 " --> pdb=" O PHE e 529 " (cutoff:3.500A) No H-bonds generated for 'chain 'e' and resid 529 through 532' Processing helix chain 'e' and resid 533 through 555 removed outlier: 3.525A pdb=" N GLN e 537 " --> pdb=" O ALA e 533 " (cutoff:3.500A) removed outlier: 4.242A pdb=" N ARG e 538 " --> pdb=" O PRO e 534 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N GLU e 539 " --> pdb=" O THR e 535 " (cutoff:3.500A) Processing helix chain 'e' and resid 556 through 570 removed outlier: 3.554A pdb=" N ILE e 560 " --> pdb=" O ASN e 556 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N ALA e 561 " --> pdb=" O TYR e 557 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N LYS e 562 " --> pdb=" O ASN e 558 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N PHE e 569 " --> pdb=" O ALA e 565 " (cutoff:3.500A) removed outlier: 4.008A pdb=" N ASN e 570 " --> pdb=" O LEU e 566 " (cutoff:3.500A) Processing helix chain 'e' and resid 573 through 580 removed outlier: 3.764A pdb=" N THR e 577 " --> pdb=" O HIS e 573 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N ILE e 578 " --> pdb=" O SER e 574 " (cutoff:3.500A) Processing helix chain 'e' and resid 583 through 598 Processing helix chain 'e' and resid 599 through 604 removed outlier: 3.592A pdb=" N ARG e 602 " --> pdb=" O ARG e 599 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N ASN e 603 " --> pdb=" O ASN e 600 " (cutoff:3.500A) removed outlier: 4.059A pdb=" N GLY e 604 " --> pdb=" O GLY e 601 " (cutoff:3.500A) No H-bonds generated for 'chain 'e' and resid 599 through 604' Processing helix chain 'e' and resid 611 through 637 removed outlier: 3.515A pdb=" N LEU e 628 " --> pdb=" O SER e 624 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N ILE e 630 " --> pdb=" O ALA e 626 " (cutoff:3.500A) Processing helix chain 'e' and resid 640 through 648 removed outlier: 3.973A pdb=" N VAL e 644 " --> pdb=" O SER e 640 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N ALA e 645 " --> pdb=" O VAL e 641 " (cutoff:3.500A) Processing helix chain 'e' and resid 656 through 664 removed outlier: 4.023A pdb=" N ASN e 660 " --> pdb=" O SER e 656 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N SER e 663 " --> pdb=" O ILE e 659 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N ASN e 664 " --> pdb=" O ASN e 660 " (cutoff:3.500A) Processing helix chain 'e' and resid 682 through 701 removed outlier: 3.853A pdb=" N LYS e 687 " --> pdb=" O ASP e 683 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N HIS e 689 " --> pdb=" O LEU e 685 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N ASN e 690 " --> pdb=" O THR e 686 " (cutoff:3.500A) Processing helix chain 'e' and resid 706 through 713 removed outlier: 3.777A pdb=" N ILE e 710 " --> pdb=" O THR e 706 " (cutoff:3.500A) Processing helix chain 'e' and resid 714 through 736 removed outlier: 3.720A pdb=" N ASN e 720 " --> pdb=" O ARG e 716 " (cutoff:3.500A) Proline residue: e 723 - end of helix Processing helix chain 'e' and resid 741 through 750 removed outlier: 3.882A pdb=" N TYR e 750 " --> pdb=" O GLY e 746 " (cutoff:3.500A) Processing helix chain 'e' and resid 751 through 753 No H-bonds generated for 'chain 'e' and resid 751 through 753' Processing helix chain 'e' and resid 756 through 759 removed outlier: 3.533A pdb=" N GLY e 759 " --> pdb=" O LEU e 756 " (cutoff:3.500A) No H-bonds generated for 'chain 'e' and resid 756 through 759' Processing helix chain 'e' and resid 760 through 777 removed outlier: 3.670A pdb=" N PHE e 764 " --> pdb=" O LEU e 760 " (cutoff:3.500A) removed outlier: 4.284A pdb=" N TYR e 765 " --> pdb=" O ILE e 761 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N TRP e 766 " --> pdb=" O LYS e 762 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N LEU e 767 " --> pdb=" O THR e 763 " (cutoff:3.500A) removed outlier: 4.191A pdb=" N GLU e 768 " --> pdb=" O PHE e 764 " (cutoff:3.500A) removed outlier: 4.354A pdb=" N GLN e 769 " --> pdb=" O TYR e 765 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N CYS e 773 " --> pdb=" O GLN e 769 " (cutoff:3.500A) Processing helix chain 'e' and resid 780 through 796 removed outlier: 3.957A pdb=" N LEU e 794 " --> pdb=" O LEU e 790 " (cutoff:3.500A) Processing helix chain 'e' and resid 804 through 815 removed outlier: 3.564A pdb=" N LEU e 814 " --> pdb=" O ALA e 810 " (cutoff:3.500A) removed outlier: 4.208A pdb=" N ASN e 815 " --> pdb=" O VAL e 811 " (cutoff:3.500A) Processing helix chain 'e' and resid 815 through 825 removed outlier: 4.020A pdb=" N LEU e 819 " --> pdb=" O ASN e 815 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N LYS e 825 " --> pdb=" O LYS e 821 " (cutoff:3.500A) Processing helix chain 'e' and resid 847 through 859 removed outlier: 3.565A pdb=" N ILE e 851 " --> pdb=" O LEU e 847 " (cutoff:3.500A) Processing helix chain 'e' and resid 867 through 872 removed outlier: 3.877A pdb=" N ILE e 871 " --> pdb=" O ASP e 867 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N ASN e 872 " --> pdb=" O PRO e 868 " (cutoff:3.500A) No H-bonds generated for 'chain 'e' and resid 867 through 872' Processing helix chain 'e' and resid 894 through 909 removed outlier: 3.509A pdb=" N ILE e 898 " --> pdb=" O PRO e 894 " (cutoff:3.500A) Processing helix chain 'e' and resid 916 through 928 removed outlier: 3.859A pdb=" N GLU e 922 " --> pdb=" O ASP e 918 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N LEU e 923 " --> pdb=" O TYR e 919 " (cutoff:3.500A) Processing helix chain 'e' and resid 928 through 947 removed outlier: 3.702A pdb=" N VAL e 936 " --> pdb=" O PHE e 932 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N LYS e 938 " --> pdb=" O PHE e 934 " (cutoff:3.500A) removed outlier: 4.241A pdb=" N THR e 939 " --> pdb=" O ASP e 935 " (cutoff:3.500A) removed outlier: 4.222A pdb=" N GLU e 941 " --> pdb=" O LEU e 937 " (cutoff:3.500A) removed outlier: 4.334A pdb=" N TYR e 942 " --> pdb=" O LYS e 938 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N LYS e 943 " --> pdb=" O THR e 939 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N THR e 946 " --> pdb=" O TYR e 942 " (cutoff:3.500A) Processing helix chain 'e' and resid 958 through 975 removed outlier: 3.786A pdb=" N VAL e 964 " --> pdb=" O ASP e 960 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N PHE e 968 " --> pdb=" O VAL e 964 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N LEU e 974 " --> pdb=" O TYR e 970 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N TYR e 975 " --> pdb=" O PHE e 971 " (cutoff:3.500A) Processing helix chain 'e' and resid 980 through 992 removed outlier: 4.431A pdb=" N SER e 984 " --> pdb=" O ALA e 980 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N GLN e 985 " --> pdb=" O GLU e 981 " (cutoff:3.500A) removed outlier: 4.431A pdb=" N GLU e 988 " --> pdb=" O SER e 984 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N ASN e 992 " --> pdb=" O GLU e 988 " (cutoff:3.500A) Processing helix chain 'e' and resid 1079 through 1083 removed outlier: 4.231A pdb=" N LEU e1083 " --> pdb=" O LYS e1079 " (cutoff:3.500A) No H-bonds generated for 'chain 'e' and resid 1079 through 1083' Processing helix chain 'e' and resid 1087 through 1106 removed outlier: 3.669A pdb=" N LEU e1091 " --> pdb=" O SER e1087 " (cutoff:3.500A) Processing helix chain 'e' and resid 1109 through 1130 removed outlier: 3.734A pdb=" N TYR e1119 " --> pdb=" O LYS e1115 " (cutoff:3.500A) Processing helix chain 'n' and resid 835 through 850 Processing helix chain 'n' and resid 902 through 906 removed outlier: 4.124A pdb=" N ILE n 906 " --> pdb=" O PRO n 903 " (cutoff:3.500A) Processing helix chain 'n' and resid 907 through 914 Processing helix chain 'n' and resid 917 through 943 removed outlier: 5.146A pdb=" N SER n 930 " --> pdb=" O GLN n 926 " (cutoff:3.500A) removed outlier: 5.358A pdb=" N LEU n 931 " --> pdb=" O PHE n 927 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N ARG n 942 " --> pdb=" O ILE n 938 " (cutoff:3.500A) Processing helix chain 'n' and resid 1015 through 1026 removed outlier: 4.042A pdb=" N MET n1019 " --> pdb=" O ALA n1015 " (cutoff:3.500A) Processing helix chain 'n' and resid 1058 through 1074 removed outlier: 4.578A pdb=" N GLU n1063 " --> pdb=" O PRO n1059 " (cutoff:3.500A) Proline residue: n1064 - end of helix removed outlier: 3.509A pdb=" N MET n1067 " --> pdb=" O GLU n1063 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N ILE n1072 " --> pdb=" O GLU n1068 " (cutoff:3.500A) Processing helix chain 'o' and resid 849 through 876 removed outlier: 4.012A pdb=" N GLU o 874 " --> pdb=" O LYS o 870 " (cutoff:3.500A) Processing helix chain 'o' and resid 879 through 893 Processing helix chain 'o' and resid 906 through 915 removed outlier: 4.176A pdb=" N VAL o 910 " --> pdb=" O PRO o 906 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N ASN o 914 " --> pdb=" O VAL o 910 " (cutoff:3.500A) Processing helix chain 'o' and resid 922 through 932 Processing helix chain 'p' and resid 272 through 277 removed outlier: 3.538A pdb=" N ASP p 277 " --> pdb=" O GLN p 273 " (cutoff:3.500A) Processing helix chain 'p' and resid 473 through 478 Processing helix chain 'p' and resid 490 through 494 Processing helix chain 'p' and resid 503 through 505 No H-bonds generated for 'chain 'p' and resid 503 through 505' Processing helix chain 'p' and resid 541 through 543 No H-bonds generated for 'chain 'p' and resid 541 through 543' Processing helix chain 'p' and resid 544 through 562 removed outlier: 3.529A pdb=" N THR p 550 " --> pdb=" O SER p 546 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N TYR p 556 " --> pdb=" O LEU p 552 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N VAL p 557 " --> pdb=" O ALA p 553 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N SER p 559 " --> pdb=" O GLY p 555 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N HIS p 561 " --> pdb=" O VAL p 557 " (cutoff:3.500A) Processing helix chain 'p' and resid 566 through 584 removed outlier: 3.551A pdb=" N THR p 570 " --> pdb=" O ALA p 566 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N ILE p 571 " --> pdb=" O GLU p 567 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N HIS p 576 " --> pdb=" O ALA p 572 " (cutoff:3.500A) removed outlier: 3.964A pdb=" N LEU p 583 " --> pdb=" O ARG p 579 " (cutoff:3.500A) Processing helix chain 'p' and resid 584 through 603 removed outlier: 3.705A pdb=" N ALA p 588 " --> pdb=" O ASP p 584 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N LYS p 589 " --> pdb=" O ARG p 585 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N GLU p 590 " --> pdb=" O LYS p 586 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N THR p 593 " --> pdb=" O LYS p 589 " (cutoff:3.500A) removed outlier: 3.847A pdb=" N LEU p 599 " --> pdb=" O LEU p 595 " (cutoff:3.500A) removed outlier: 3.834A pdb=" N TYR p 600 " --> pdb=" O LEU p 596 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N SER p 601 " --> pdb=" O LYS p 597 " (cutoff:3.500A) Processing helix chain 'p' and resid 610 through 619 removed outlier: 3.841A pdb=" N MET p 614 " --> pdb=" O PRO p 610 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N ASP p 615 " --> pdb=" O LYS p 611 " (cutoff:3.500A) removed outlier: 4.058A pdb=" N LYS p 616 " --> pdb=" O GLU p 612 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N THR p 619 " --> pdb=" O ASP p 615 " (cutoff:3.500A) Processing helix chain 'p' and resid 622 through 634 removed outlier: 4.340A pdb=" N LEU p 628 " --> pdb=" O GLN p 624 " (cutoff:3.500A) removed outlier: 3.894A pdb=" N GLN p 630 " --> pdb=" O ILE p 626 " (cutoff:3.500A) Processing helix chain 'p' and resid 640 through 676 removed outlier: 4.356A pdb=" N GLU p 644 " --> pdb=" O GLU p 640 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N ALA p 646 " --> pdb=" O ILE p 642 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N PHE p 659 " --> pdb=" O VAL p 655 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N ARG p 664 " --> pdb=" O ASN p 660 " (cutoff:3.500A) removed outlier: 4.146A pdb=" N ASN p 665 " --> pdb=" O GLY p 661 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N ALA p 669 " --> pdb=" O ASN p 665 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N ILE p 670 " --> pdb=" O PHE p 666 " (cutoff:3.500A) removed outlier: 4.075A pdb=" N GLU p 671 " --> pdb=" O HIS p 667 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N ILE p 673 " --> pdb=" O ALA p 669 " (cutoff:3.500A) removed outlier: 3.915A pdb=" N SER p 674 " --> pdb=" O ILE p 670 " (cutoff:3.500A) Processing helix chain 'p' and resid 682 through 723 removed outlier: 3.951A pdb=" N PHE p 686 " --> pdb=" O ASN p 682 " (cutoff:3.500A) removed outlier: 4.305A pdb=" N GLN p 687 " --> pdb=" O PRO p 683 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N GLN p 693 " --> pdb=" O ILE p 689 " (cutoff:3.500A) removed outlier: 4.210A pdb=" N ILE p 696 " --> pdb=" O LYS p 692 " (cutoff:3.500A) removed outlier: 3.945A pdb=" N HIS p 697 " --> pdb=" O GLN p 693 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N SER p 698 " --> pdb=" O ASP p 694 " (cutoff:3.500A) removed outlier: 3.861A pdb=" N LEU p 699 " --> pdb=" O LEU p 695 " (cutoff:3.500A) removed outlier: 4.019A pdb=" N ILE p 700 " --> pdb=" O ILE p 696 " (cutoff:3.500A) Proline residue: p 701 - end of helix removed outlier: 3.715A pdb=" N TRP p 705 " --> pdb=" O PRO p 701 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N ILE p 710 " --> pdb=" O PHE p 706 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N TYR p 712 " --> pdb=" O LYS p 708 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N LEU p 713 " --> pdb=" O PHE p 709 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N LEU p 718 " --> pdb=" O THR p 714 " (cutoff:3.500A) removed outlier: 4.030A pdb=" N ASN p 722 " --> pdb=" O LEU p 718 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N ASP p 723 " --> pdb=" O ILE p 719 " (cutoff:3.500A) Processing helix chain 'p' and resid 726 through 729 removed outlier: 3.669A pdb=" N TYR p 729 " --> pdb=" O ASN p 726 " (cutoff:3.500A) No H-bonds generated for 'chain 'p' and resid 726 through 729' Processing helix chain 'p' and resid 730 through 738 removed outlier: 3.992A pdb=" N GLY p 734 " --> pdb=" O THR p 730 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N PHE p 736 " --> pdb=" O VAL p 732 " (cutoff:3.500A) Processing helix chain 'p' and resid 738 through 762 removed outlier: 3.702A pdb=" N ARG p 742 " --> pdb=" O ALA p 738 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N THR p 743 " --> pdb=" O LYS p 739 " (cutoff:3.500A) Processing helix chain 'p' and resid 767 through 769 No H-bonds generated for 'chain 'p' and resid 767 through 769' Processing helix chain 'p' and resid 770 through 783 removed outlier: 4.483A pdb=" N SER p 774 " --> pdb=" O LEU p 770 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N LEU p 781 " --> pdb=" O LEU p 777 " (cutoff:3.500A) Processing helix chain 'p' and resid 787 through 809 removed outlier: 3.607A pdb=" N LEU p 795 " --> pdb=" O PHE p 791 " (cutoff:3.500A) removed outlier: 3.985A pdb=" N CYS p 806 " --> pdb=" O PHE p 802 " (cutoff:3.500A) Processing helix chain 'p' and resid 812 through 820 removed outlier: 3.745A pdb=" N PHE p 816 " --> pdb=" O GLN p 812 " (cutoff:3.500A) Processing helix chain 'p' and resid 825 through 827 No H-bonds generated for 'chain 'p' and resid 825 through 827' Processing helix chain 'p' and resid 828 through 843 removed outlier: 3.596A pdb=" N GLY p 832 " --> pdb=" O TYR p 828 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N ASP p 833 " --> pdb=" O ALA p 829 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N PHE p 834 " --> pdb=" O LYS p 830 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N LEU p 835 " --> pdb=" O VAL p 831 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N LEU p 836 " --> pdb=" O GLY p 832 " (cutoff:3.500A) removed outlier: 4.104A pdb=" N ASN p 840 " --> pdb=" O LEU p 836 " (cutoff:3.500A) removed outlier: 4.288A pdb=" N ASN p 841 " --> pdb=" O GLN p 837 " (cutoff:3.500A) removed outlier: 3.994A pdb=" N VAL p 843 " --> pdb=" O ALA p 839 " (cutoff:3.500A) Processing helix chain 'p' and resid 844 through 847 Processing helix chain 'p' and resid 848 through 855 removed outlier: 3.557A pdb=" N PHE p 854 " --> pdb=" O ALA p 850 " (cutoff:3.500A) Processing helix chain 'p' and resid 863 through 867 Processing helix chain 'p' and resid 878 through 882 Processing helix chain 'p' and resid 886 through 890 Processing helix chain 'p' and resid 891 through 895 removed outlier: 3.666A pdb=" N ARG p 895 " --> pdb=" O ILE p 892 " (cutoff:3.500A) Processing helix chain 'p' and resid 896 through 900 Processing helix chain 'p' and resid 914 through 920 Processing helix chain 'p' and resid 940 through 944 Processing helix chain 'p' and resid 954 through 960 removed outlier: 3.725A pdb=" N THR p 960 " --> pdb=" O THR p 957 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'e' and resid 479 through 482 removed outlier: 4.471A pdb=" N LEU e 479 " --> pdb=" O VAL e 491 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'n' and resid 856 through 860 removed outlier: 7.168A pdb=" N SER n 866 " --> pdb=" O ILE n 858 " (cutoff:3.500A) removed outlier: 5.660A pdb=" N LEU n 860 " --> pdb=" O GLU n 864 " (cutoff:3.500A) removed outlier: 7.200A pdb=" N GLU n 864 " --> pdb=" O LEU n 860 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N PHE n 867 " --> pdb=" O CYS n 880 " (cutoff:3.500A) removed outlier: 3.970A pdb=" N THR n 895 " --> pdb=" O LYS n 883 " (cutoff:3.500A) removed outlier: 3.926A pdb=" N SER n 885 " --> pdb=" O ASN n 893 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N ASN n 893 " --> pdb=" O SER n 885 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'n' and resid 956 through 963 removed outlier: 3.545A pdb=" N ASN n 958 " --> pdb=" O VAL n 970 " (cutoff:3.500A) removed outlier: 4.343A pdb=" N HIS n 962 " --> pdb=" O GLU n 966 " (cutoff:3.500A) removed outlier: 7.115A pdb=" N GLU n 966 " --> pdb=" O HIS n 962 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N GLU n 985 " --> pdb=" O HIS n1000 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N LYS n 987 " --> pdb=" O GLN n 998 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N PHE n 999 " --> pdb=" O CYS n1057 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'o' and resid 938 through 939 Processing sheet with id=AA5, first strand: chain 'p' and resid 8 through 10 Processing sheet with id=AA6, first strand: chain 'p' and resid 33 through 35 Processing sheet with id=AA7, first strand: chain 'p' and resid 101 through 102 removed outlier: 3.538A pdb=" N PHE p 102 " --> pdb=" O GLU p 178 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA7 Processing sheet with id=AA8, first strand: chain 'p' and resid 105 through 110 removed outlier: 7.145A pdb=" N CYS p 124 " --> pdb=" O SER p 106 " (cutoff:3.500A) removed outlier: 5.579A pdb=" N ILE p 108 " --> pdb=" O ALA p 122 " (cutoff:3.500A) removed outlier: 7.633A pdb=" N ALA p 122 " --> pdb=" O ILE p 108 " (cutoff:3.500A) removed outlier: 5.732A pdb=" N TRP p 110 " --> pdb=" O MET p 120 " (cutoff:3.500A) removed outlier: 7.561A pdb=" N MET p 120 " --> pdb=" O TRP p 110 " (cutoff:3.500A) removed outlier: 7.334A pdb=" N MET p 130 " --> pdb=" O GLN p 153 " (cutoff:3.500A) removed outlier: 5.470A pdb=" N GLN p 153 " --> pdb=" O MET p 130 " (cutoff:3.500A) removed outlier: 7.699A pdb=" N MET p 132 " --> pdb=" O VAL p 151 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N GLN p 153 " --> pdb=" O TYR p 160 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N TYR p 160 " --> pdb=" O GLN p 153 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'p' and resid 190 through 195 removed outlier: 6.906A pdb=" N ILE p 242 " --> pdb=" O LEU p 191 " (cutoff:3.500A) removed outlier: 4.939A pdb=" N PHE p 193 " --> pdb=" O LEU p 240 " (cutoff:3.500A) removed outlier: 7.164A pdb=" N LEU p 240 " --> pdb=" O PHE p 193 " (cutoff:3.500A) removed outlier: 5.708A pdb=" N TRP p 195 " --> pdb=" O ALA p 238 " (cutoff:3.500A) removed outlier: 7.767A pdb=" N ALA p 238 " --> pdb=" O TRP p 195 " (cutoff:3.500A) removed outlier: 6.742A pdb=" N GLN p 253 " --> pdb=" O LYS p 236 " (cutoff:3.500A) removed outlier: 4.424A pdb=" N ALA p 238 " --> pdb=" O TRP p 251 " (cutoff:3.500A) removed outlier: 6.922A pdb=" N TRP p 251 " --> pdb=" O ALA p 238 " (cutoff:3.500A) removed outlier: 4.726A pdb=" N LEU p 240 " --> pdb=" O ASP p 249 " (cutoff:3.500A) removed outlier: 6.918A pdb=" N ASP p 249 " --> pdb=" O LEU p 240 " (cutoff:3.500A) removed outlier: 5.106A pdb=" N ILE p 242 " --> pdb=" O GLN p 247 " (cutoff:3.500A) removed outlier: 7.027A pdb=" N GLN p 247 " --> pdb=" O ILE p 242 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'p' and resid 216 through 224 removed outlier: 3.765A pdb=" N ARG p 220 " --> pdb=" O PHE p 207 " (cutoff:3.500A) removed outlier: 4.590A pdb=" N PHE p 207 " --> pdb=" O ARG p 220 " (cutoff:3.500A) removed outlier: 6.262A pdb=" N GLN p 222 " --> pdb=" O SER p 205 " (cutoff:3.500A) removed outlier: 4.894A pdb=" N SER p 205 " --> pdb=" O GLN p 222 " (cutoff:3.500A) removed outlier: 6.507A pdb=" N VAL p 224 " --> pdb=" O ILE p 203 " (cutoff:3.500A) removed outlier: 5.326A pdb=" N ILE p 203 " --> pdb=" O VAL p 224 " (cutoff:3.500A) removed outlier: 6.736A pdb=" N CYS p 208 " --> pdb=" O ILE p 487 " (cutoff:3.500A) removed outlier: 4.451A pdb=" N ILE p 487 " --> pdb=" O CYS p 208 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N LYS p 485 " --> pdb=" O PHE p 210 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'p' and resid 281 through 288 removed outlier: 3.966A pdb=" N PHE p 283 " --> pdb=" O TYR p 300 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N SER p 301 " --> pdb=" O ASN p 306 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N ASN p 306 " --> pdb=" O SER p 301 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N THR p 339 " --> pdb=" O ILE p 307 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N LEU p 337 " --> pdb=" O PHE p 309 " (cutoff:3.500A) removed outlier: 6.119A pdb=" N LYS p 311 " --> pdb=" O PHE p 335 " (cutoff:3.500A) removed outlier: 5.293A pdb=" N PHE p 335 " --> pdb=" O LYS p 311 " (cutoff:3.500A) removed outlier: 6.782A pdb=" N HIS p 313 " --> pdb=" O ILE p 333 " (cutoff:3.500A) removed outlier: 5.148A pdb=" N ILE p 333 " --> pdb=" O HIS p 313 " (cutoff:3.500A) removed outlier: 7.194A pdb=" N ASN p 315 " --> pdb=" O LEU p 331 " (cutoff:3.500A) removed outlier: 6.062A pdb=" N LEU p 331 " --> pdb=" O ASN p 315 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'p' and resid 353 through 358 removed outlier: 6.660A pdb=" N LEU p 353 " --> pdb=" O ASN p 377 " (cutoff:3.500A) removed outlier: 7.153A pdb=" N ASN p 377 " --> pdb=" O LEU p 353 " (cutoff:3.500A) removed outlier: 4.160A pdb=" N ASN p 355 " --> pdb=" O LEU p 375 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N ILE p 433 " --> pdb=" O VAL p 386 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N ARG p 388 " --> pdb=" O SER p 431 " (cutoff:3.500A) removed outlier: 4.615A pdb=" N SER p 431 " --> pdb=" O ARG p 388 " (cutoff:3.500A) removed outlier: 7.229A pdb=" N ARG p 390 " --> pdb=" O ARG p 429 " (cutoff:3.500A) removed outlier: 5.722A pdb=" N ARG p 429 " --> pdb=" O ARG p 390 " (cutoff:3.500A) removed outlier: 6.960A pdb=" N ALA p 392 " --> pdb=" O LEU p 427 " (cutoff:3.500A) removed outlier: 5.113A pdb=" N LEU p 427 " --> pdb=" O ALA p 392 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'p' and resid 439 through 444 removed outlier: 6.908A pdb=" N TYR p 454 " --> pdb=" O THR p 440 " (cutoff:3.500A) removed outlier: 4.362A pdb=" N ILE p 442 " --> pdb=" O SER p 452 " (cutoff:3.500A) removed outlier: 6.707A pdb=" N SER p 452 " --> pdb=" O ILE p 442 " (cutoff:3.500A) removed outlier: 4.715A pdb=" N SER p 444 " --> pdb=" O PHE p 450 " (cutoff:3.500A) removed outlier: 6.767A pdb=" N PHE p 450 " --> pdb=" O SER p 444 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N PHE p 453 " --> pdb=" O GLU p 461 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N GLU p 461 " --> pdb=" O PHE p 453 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'p' and resid 497 through 498 removed outlier: 4.021A pdb=" N TRP p 509 " --> pdb=" O LYS p 522 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'p' and resid 932 through 933 788 hydrogen bonds defined for protein. 2265 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: 5.31 Time building geometry restraints manager: 4.97 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 5031 1.34 - 1.46: 2775 1.46 - 1.58: 9727 1.58 - 1.70: 0 1.70 - 1.82: 117 Bond restraints: 17650 Sorted by residual: bond pdb=" C PRO p 504 " pdb=" N PRO p 505 " ideal model delta sigma weight residual 1.334 1.348 -0.014 1.51e-02 4.39e+03 8.51e-01 bond pdb=" C TRP p 955 " pdb=" N PRO p 956 " ideal model delta sigma weight residual 1.334 1.354 -0.020 2.34e-02 1.83e+03 7.61e-01 bond pdb=" CA PRO p 504 " pdb=" C PRO p 504 " ideal model delta sigma weight residual 1.517 1.525 -0.008 9.30e-03 1.16e+04 7.49e-01 bond pdb=" CD GLU b 99 " pdb=" OE1 GLU b 99 " ideal model delta sigma weight residual 1.249 1.233 0.016 1.90e-02 2.77e+03 7.27e-01 bond pdb=" CA GLU b 99 " pdb=" CB GLU b 99 " ideal model delta sigma weight residual 1.528 1.542 -0.013 1.59e-02 3.96e+03 7.08e-01 ... (remaining 17645 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.56: 23491 1.56 - 3.12: 268 3.12 - 4.67: 79 4.67 - 6.23: 23 6.23 - 7.79: 9 Bond angle restraints: 23870 Sorted by residual: angle pdb=" N GLN c 80 " pdb=" CA GLN c 80 " pdb=" CB GLN c 80 " ideal model delta sigma weight residual 110.39 116.35 -5.96 1.66e+00 3.63e-01 1.29e+01 angle pdb=" N GLU b 99 " pdb=" CA GLU b 99 " pdb=" CB GLU b 99 " ideal model delta sigma weight residual 110.16 115.21 -5.05 1.48e+00 4.57e-01 1.16e+01 angle pdb=" C LEU c 79 " pdb=" N GLN c 80 " pdb=" CA GLN c 80 " ideal model delta sigma weight residual 120.72 115.44 5.28 1.67e+00 3.59e-01 1.00e+01 angle pdb=" N GLU e 344 " pdb=" CA GLU e 344 " pdb=" CB GLU e 344 " ideal model delta sigma weight residual 110.28 114.05 -3.77 1.55e+00 4.16e-01 5.92e+00 angle pdb=" CA GLN c 80 " pdb=" CB GLN c 80 " pdb=" CG GLN c 80 " ideal model delta sigma weight residual 114.10 118.87 -4.77 2.00e+00 2.50e-01 5.70e+00 ... (remaining 23865 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.23: 9639 17.23 - 34.46: 905 34.46 - 51.68: 161 51.68 - 68.91: 24 68.91 - 86.14: 13 Dihedral angle restraints: 10742 sinusoidal: 4395 harmonic: 6347 Sorted by residual: dihedral pdb=" CA GLU c 22 " pdb=" C GLU c 22 " pdb=" N ASN c 23 " pdb=" CA ASN c 23 " ideal model delta harmonic sigma weight residual 180.00 161.61 18.39 0 5.00e+00 4.00e-02 1.35e+01 dihedral pdb=" CG ARG p 388 " pdb=" CD ARG p 388 " pdb=" NE ARG p 388 " pdb=" CZ ARG p 388 " ideal model delta sinusoidal sigma weight residual 180.00 136.18 43.82 2 1.50e+01 4.44e-03 1.02e+01 dihedral pdb=" CG ARG e 440 " pdb=" CD ARG e 440 " pdb=" NE ARG e 440 " pdb=" CZ ARG e 440 " ideal model delta sinusoidal sigma weight residual 180.00 136.89 43.11 2 1.50e+01 4.44e-03 9.96e+00 ... (remaining 10739 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.034: 1815 0.034 - 0.068: 669 0.068 - 0.101: 199 0.101 - 0.135: 54 0.135 - 0.169: 2 Chirality restraints: 2739 Sorted by residual: chirality pdb=" CA GLU e 387 " pdb=" N GLU e 387 " pdb=" C GLU e 387 " pdb=" CB GLU e 387 " both_signs ideal model delta sigma weight residual False 2.51 2.34 0.17 2.00e-01 2.50e+01 7.15e-01 chirality pdb=" CA PRO n1017 " pdb=" N PRO n1017 " pdb=" C PRO n1017 " pdb=" CB PRO n1017 " both_signs ideal model delta sigma weight residual False 2.72 2.58 0.14 2.00e-01 2.50e+01 4.63e-01 chirality pdb=" CA GLU b 99 " pdb=" N GLU b 99 " pdb=" C GLU b 99 " pdb=" CB GLU b 99 " both_signs ideal model delta sigma weight residual False 2.51 2.38 0.13 2.00e-01 2.50e+01 4.35e-01 ... (remaining 2736 not shown) Planarity restraints: 3020 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C TRP p 955 " -0.049 5.00e-02 4.00e+02 7.40e-02 8.76e+00 pdb=" N PRO p 956 " 0.128 5.00e-02 4.00e+02 pdb=" CA PRO p 956 " -0.038 5.00e-02 4.00e+02 pdb=" CD PRO p 956 " -0.041 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C TYR n1016 " 0.039 5.00e-02 4.00e+02 5.83e-02 5.43e+00 pdb=" N PRO n1017 " -0.101 5.00e-02 4.00e+02 pdb=" CA PRO n1017 " 0.029 5.00e-02 4.00e+02 pdb=" CD PRO n1017 " 0.033 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PRO p 504 " 0.032 5.00e-02 4.00e+02 4.87e-02 3.79e+00 pdb=" N PRO p 505 " -0.084 5.00e-02 4.00e+02 pdb=" CA PRO p 505 " 0.024 5.00e-02 4.00e+02 pdb=" CD PRO p 505 " 0.028 5.00e-02 4.00e+02 ... (remaining 3017 not shown) Histogram of nonbonded interaction distances: 2.21 - 2.75: 1800 2.75 - 3.29: 17872 3.29 - 3.82: 27737 3.82 - 4.36: 32345 4.36 - 4.90: 53924 Nonbonded interactions: 133678 Sorted by model distance: nonbonded pdb=" OE1 GLN e 902 " pdb=" OG1 THR e 913 " model vdw 2.212 3.040 nonbonded pdb=" OG SER p 817 " pdb=" O GLU p 823 " model vdw 2.214 3.040 nonbonded pdb=" OE2 GLU e 768 " pdb=" ND2 ASN e 815 " model vdw 2.236 3.120 nonbonded pdb=" OE1 GLU n 941 " pdb=" NE2 HIS n1070 " model vdw 2.239 3.120 nonbonded pdb=" OG SER p 914 " pdb=" OE1 GLU p 917 " model vdw 2.239 3.040 ... (remaining 133673 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 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.190 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.700 Check model and map are aligned: 0.120 Set scattering table: 0.190 Process input model: 38.380 Find NCS groups from input model: 0.160 Set up NCS constraints: 0.070 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.730 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 43.560 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6151 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 : 0.002 0.033 17650 Z= 0.136 Angle : 0.509 7.789 23870 Z= 0.254 Chirality : 0.040 0.169 2739 Planarity : 0.004 0.074 3020 Dihedral : 13.617 86.139 6592 Min Nonbonded Distance : 2.212 Molprobity Statistics. All-atom Clashscore : 9.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.04 % Favored : 98.96 % Rotamer: Outliers : 0.00 % Allowed : 0.35 % Favored : 99.65 % 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: 0.41 (0.18), residues: 2108 helix: 0.77 (0.17), residues: 961 sheet: -0.35 (0.36), residues: 216 loop : 0.06 (0.20), residues: 931 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP e 373 HIS 0.003 0.001 HIS p 231 PHE 0.022 0.001 PHE e 724 TYR 0.017 0.001 TYR p 556 ARG 0.008 0.000 ARG e 869 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4216 Ramachandran restraints generated. 2108 Oldfield, 0 Emsley, 2108 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4216 Ramachandran restraints generated. 2108 Oldfield, 0 Emsley, 2108 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 158 residues out of total 1985 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 158 time to evaluate : 2.045 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: b 47 MET cc_start: 0.7823 (ptp) cc_final: 0.7527 (ptp) REVERT: c 38 ASP cc_start: 0.7862 (m-30) cc_final: 0.7600 (m-30) REVERT: o 899 MET cc_start: 0.7539 (ppp) cc_final: 0.7225 (mmp) REVERT: p 645 MET cc_start: 0.8078 (tpt) cc_final: 0.7795 (tpp) outliers start: 0 outliers final: 0 residues processed: 158 average time/residue: 0.2693 time to fit residues: 67.7089 Evaluate side-chains 91 residues out of total 1985 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 91 time to evaluate : 2.018 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 212 random chunks: chunk 179 optimal weight: 5.9990 chunk 160 optimal weight: 0.8980 chunk 89 optimal weight: 3.9990 chunk 54 optimal weight: 7.9990 chunk 108 optimal weight: 9.9990 chunk 85 optimal weight: 10.0000 chunk 166 optimal weight: 8.9990 chunk 64 optimal weight: 0.9990 chunk 101 optimal weight: 4.9990 chunk 123 optimal weight: 6.9990 chunk 192 optimal weight: 6.9990 overall best weight: 3.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** c 32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** c 59 GLN ** c 80 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 360 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** e 453 GLN e 488 GLN e 815 ASN ** e 916 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** e1093 HIS ** e1113 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** n1020 HIS n1024 ASN p 6 HIS p 40 ASN ** p 161 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** p 253 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** p 313 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** p 319 ASN p 327 ASN p 349 HIS ** p 536 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** p 630 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** p 771 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6372 moved from start: 0.1978 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 17650 Z= 0.232 Angle : 0.650 9.224 23870 Z= 0.333 Chirality : 0.044 0.208 2739 Planarity : 0.004 0.061 3020 Dihedral : 3.977 17.048 2269 Min Nonbonded Distance : 2.509 Molprobity Statistics. All-atom Clashscore : 14.36 Ramachandran Plot: Outliers : 0.05 % Allowed : 2.23 % Favored : 97.72 % Rotamer: Outliers : 0.86 % Allowed : 7.30 % Favored : 91.84 % 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 (0.18), residues: 2108 helix: 0.98 (0.16), residues: 982 sheet: -0.38 (0.36), residues: 213 loop : -0.12 (0.20), residues: 913 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP p 280 HIS 0.006 0.001 HIS n1070 PHE 0.027 0.002 PHE p 794 TYR 0.025 0.001 TYR p 556 ARG 0.005 0.001 ARG p 194 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4216 Ramachandran restraints generated. 2108 Oldfield, 0 Emsley, 2108 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4216 Ramachandran restraints generated. 2108 Oldfield, 0 Emsley, 2108 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 113 residues out of total 1985 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 96 time to evaluate : 1.909 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: c 38 ASP cc_start: 0.8009 (m-30) cc_final: 0.7718 (m-30) REVERT: n 1067 MET cc_start: 0.7688 (mmm) cc_final: 0.7371 (mmm) REVERT: o 922 THR cc_start: 0.7279 (m) cc_final: 0.7070 (p) REVERT: p 645 MET cc_start: 0.8574 (tpt) cc_final: 0.8014 (tpp) outliers start: 17 outliers final: 11 residues processed: 106 average time/residue: 0.2514 time to fit residues: 43.8937 Evaluate side-chains 93 residues out of total 1985 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 82 time to evaluate : 1.865 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain b residue 73 LEU Chi-restraints excluded: chain b residue 99 GLU Chi-restraints excluded: chain e residue 344 GLU Chi-restraints excluded: chain e residue 467 MET Chi-restraints excluded: chain e residue 715 THR Chi-restraints excluded: chain e residue 794 LEU Chi-restraints excluded: chain n residue 972 TYR Chi-restraints excluded: chain p residue 296 LEU Chi-restraints excluded: chain p residue 356 LEU Chi-restraints excluded: chain p residue 571 ILE Chi-restraints excluded: chain p residue 702 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 212 random chunks: chunk 106 optimal weight: 8.9990 chunk 59 optimal weight: 1.9990 chunk 160 optimal weight: 5.9990 chunk 131 optimal weight: 10.0000 chunk 53 optimal weight: 7.9990 chunk 192 optimal weight: 10.0000 chunk 208 optimal weight: 30.0000 chunk 171 optimal weight: 7.9990 chunk 191 optimal weight: 5.9990 chunk 65 optimal weight: 0.0970 chunk 154 optimal weight: 0.5980 overall best weight: 2.9384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** c 32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 360 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 453 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 916 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** e1093 HIS ** e1113 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** n1024 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** p 161 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** p 253 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** p 538 ASN ** p 630 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** p 771 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6420 moved from start: 0.2462 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 17650 Z= 0.204 Angle : 0.594 12.580 23870 Z= 0.299 Chirality : 0.043 0.314 2739 Planarity : 0.004 0.057 3020 Dihedral : 3.936 17.117 2269 Min Nonbonded Distance : 2.541 Molprobity Statistics. All-atom Clashscore : 12.78 Ramachandran Plot: Outliers : 0.05 % Allowed : 2.18 % Favored : 97.77 % Rotamer: Outliers : 1.06 % Allowed : 9.87 % Favored : 89.07 % 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: 0.58 (0.18), residues: 2108 helix: 1.08 (0.16), residues: 991 sheet: -0.25 (0.36), residues: 216 loop : -0.10 (0.20), residues: 901 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP e 907 HIS 0.004 0.001 HIS n1070 PHE 0.023 0.002 PHE c 47 TYR 0.010 0.001 TYR p 600 ARG 0.004 0.000 ARG o 868 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4216 Ramachandran restraints generated. 2108 Oldfield, 0 Emsley, 2108 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4216 Ramachandran restraints generated. 2108 Oldfield, 0 Emsley, 2108 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 109 residues out of total 1985 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 88 time to evaluate : 2.190 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: c 38 ASP cc_start: 0.7941 (m-30) cc_final: 0.7680 (m-30) REVERT: n 1067 MET cc_start: 0.7825 (mmm) cc_final: 0.7347 (mmm) REVERT: o 899 MET cc_start: 0.7722 (ppp) cc_final: 0.6383 (tpt) REVERT: o 945 MET cc_start: 0.4359 (mmm) cc_final: 0.2553 (ptt) outliers start: 21 outliers final: 11 residues processed: 102 average time/residue: 0.2736 time to fit residues: 46.4688 Evaluate side-chains 94 residues out of total 1985 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 83 time to evaluate : 2.007 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain b residue 99 GLU Chi-restraints excluded: chain e residue 344 GLU Chi-restraints excluded: chain e residue 467 MET Chi-restraints excluded: chain e residue 715 THR Chi-restraints excluded: chain o residue 858 LEU Chi-restraints excluded: chain p residue 571 ILE Chi-restraints excluded: chain p residue 636 CYS Chi-restraints excluded: chain p residue 656 LEU Chi-restraints excluded: chain p residue 690 PHE Chi-restraints excluded: chain p residue 702 VAL Chi-restraints excluded: chain p residue 794 PHE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 212 random chunks: chunk 190 optimal weight: 5.9990 chunk 145 optimal weight: 0.0070 chunk 100 optimal weight: 4.9990 chunk 21 optimal weight: 10.0000 chunk 92 optimal weight: 9.9990 chunk 129 optimal weight: 0.5980 chunk 193 optimal weight: 2.9990 chunk 204 optimal weight: 4.9990 chunk 101 optimal weight: 20.0000 chunk 183 optimal weight: 9.9990 chunk 55 optimal weight: 6.9990 overall best weight: 2.7204 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** c 32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 46 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** c 80 GLN ** e 360 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** e 453 GLN e 776 ASN ** e 916 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e1113 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** n1024 ASN ** p 161 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** p 253 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** p 480 GLN ** p 812 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6459 moved from start: 0.2886 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 17650 Z= 0.187 Angle : 0.574 9.385 23870 Z= 0.290 Chirality : 0.042 0.232 2739 Planarity : 0.004 0.054 3020 Dihedral : 3.952 17.598 2269 Min Nonbonded Distance : 2.544 Molprobity Statistics. All-atom Clashscore : 12.66 Ramachandran Plot: Outliers : 0.05 % Allowed : 2.70 % Favored : 97.25 % Rotamer: Outliers : 1.21 % Allowed : 11.49 % Favored : 87.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 0.63 (0.18), residues: 2108 helix: 1.16 (0.16), residues: 991 sheet: -0.37 (0.35), residues: 219 loop : -0.09 (0.21), residues: 898 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP e 907 HIS 0.006 0.001 HIS p 162 PHE 0.021 0.001 PHE c 47 TYR 0.010 0.001 TYR p 853 ARG 0.004 0.000 ARG o 868 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4216 Ramachandran restraints generated. 2108 Oldfield, 0 Emsley, 2108 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4216 Ramachandran restraints generated. 2108 Oldfield, 0 Emsley, 2108 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 111 residues out of total 1985 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 87 time to evaluate : 2.124 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: b 46 MET cc_start: 0.7870 (OUTLIER) cc_final: 0.7586 (tmm) REVERT: c 38 ASP cc_start: 0.7937 (m-30) cc_final: 0.7668 (m-30) REVERT: e 791 LEU cc_start: 0.7018 (tp) cc_final: 0.6518 (tp) REVERT: n 1067 MET cc_start: 0.7876 (mmm) cc_final: 0.7275 (mmm) REVERT: o 899 MET cc_start: 0.7734 (ppp) cc_final: 0.6513 (tpt) REVERT: o 945 MET cc_start: 0.4478 (mmm) cc_final: 0.2584 (ptt) REVERT: p 645 MET cc_start: 0.8575 (tpp) cc_final: 0.8161 (tpp) outliers start: 24 outliers final: 16 residues processed: 105 average time/residue: 0.2604 time to fit residues: 45.3909 Evaluate side-chains 98 residues out of total 1985 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 81 time to evaluate : 1.995 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain b residue 46 MET Chi-restraints excluded: chain b residue 73 LEU Chi-restraints excluded: chain b residue 99 GLU Chi-restraints excluded: chain e residue 344 GLU Chi-restraints excluded: chain e residue 467 MET Chi-restraints excluded: chain e residue 715 THR Chi-restraints excluded: chain n residue 886 THR Chi-restraints excluded: chain n residue 970 VAL Chi-restraints excluded: chain o residue 858 LEU Chi-restraints excluded: chain p residue 296 LEU Chi-restraints excluded: chain p residue 483 LYS Chi-restraints excluded: chain p residue 571 ILE Chi-restraints excluded: chain p residue 636 CYS Chi-restraints excluded: chain p residue 656 LEU Chi-restraints excluded: chain p residue 690 PHE Chi-restraints excluded: chain p residue 702 VAL Chi-restraints excluded: chain p residue 794 PHE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 212 random chunks: chunk 170 optimal weight: 4.9990 chunk 116 optimal weight: 0.0770 chunk 2 optimal weight: 20.0000 chunk 152 optimal weight: 9.9990 chunk 84 optimal weight: 3.9990 chunk 174 optimal weight: 2.9990 chunk 141 optimal weight: 10.0000 chunk 0 optimal weight: 20.0000 chunk 104 optimal weight: 5.9990 chunk 183 optimal weight: 7.9990 chunk 51 optimal weight: 0.9980 overall best weight: 2.6144 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** b 51 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 46 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 360 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** e 901 ASN ** e 916 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e1113 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** p 161 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** p 253 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** p 465 GLN p 480 GLN p 687 GLN p 771 ASN p 812 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6483 moved from start: 0.3204 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 17650 Z= 0.181 Angle : 0.569 9.233 23870 Z= 0.286 Chirality : 0.042 0.174 2739 Planarity : 0.004 0.052 3020 Dihedral : 3.967 18.134 2269 Min Nonbonded Distance : 2.532 Molprobity Statistics. All-atom Clashscore : 13.21 Ramachandran Plot: Outliers : 0.05 % Allowed : 2.51 % Favored : 97.44 % Rotamer: Outliers : 1.26 % Allowed : 12.75 % Favored : 85.99 % 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: 0.62 (0.18), residues: 2108 helix: 1.12 (0.16), residues: 1004 sheet: -0.29 (0.35), residues: 220 loop : -0.11 (0.21), residues: 884 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP e 907 HIS 0.006 0.001 HIS n 962 PHE 0.019 0.001 PHE c 47 TYR 0.010 0.001 TYR p 600 ARG 0.004 0.000 ARG p 138 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4216 Ramachandran restraints generated. 2108 Oldfield, 0 Emsley, 2108 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4216 Ramachandran restraints generated. 2108 Oldfield, 0 Emsley, 2108 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 107 residues out of total 1985 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 82 time to evaluate : 2.062 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: b 46 MET cc_start: 0.7881 (OUTLIER) cc_final: 0.7625 (tmm) REVERT: c 38 ASP cc_start: 0.7953 (m-30) cc_final: 0.7684 (m-30) REVERT: n 1067 MET cc_start: 0.7811 (mmm) cc_final: 0.7205 (mmm) REVERT: o 899 MET cc_start: 0.7905 (ppp) cc_final: 0.6799 (tpt) REVERT: o 945 MET cc_start: 0.4274 (mmm) cc_final: 0.2429 (ptt) REVERT: p 645 MET cc_start: 0.8872 (tpp) cc_final: 0.8234 (tpt) outliers start: 25 outliers final: 17 residues processed: 100 average time/residue: 0.2586 time to fit residues: 42.4579 Evaluate side-chains 94 residues out of total 1985 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 76 time to evaluate : 2.020 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain b residue 46 MET Chi-restraints excluded: chain b residue 73 LEU Chi-restraints excluded: chain b residue 99 GLU Chi-restraints excluded: chain e residue 344 GLU Chi-restraints excluded: chain e residue 407 VAL Chi-restraints excluded: chain e residue 467 MET Chi-restraints excluded: chain e residue 715 THR Chi-restraints excluded: chain n residue 886 THR Chi-restraints excluded: chain n residue 970 VAL Chi-restraints excluded: chain o residue 858 LEU Chi-restraints excluded: chain p residue 296 LEU Chi-restraints excluded: chain p residue 483 LYS Chi-restraints excluded: chain p residue 571 ILE Chi-restraints excluded: chain p residue 636 CYS Chi-restraints excluded: chain p residue 656 LEU Chi-restraints excluded: chain p residue 690 PHE Chi-restraints excluded: chain p residue 702 VAL Chi-restraints excluded: chain p residue 794 PHE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 212 random chunks: chunk 68 optimal weight: 4.9990 chunk 184 optimal weight: 9.9990 chunk 40 optimal weight: 20.0000 chunk 120 optimal weight: 8.9990 chunk 50 optimal weight: 1.9990 chunk 205 optimal weight: 1.9990 chunk 170 optimal weight: 7.9990 chunk 94 optimal weight: 8.9990 chunk 17 optimal weight: 5.9990 chunk 67 optimal weight: 0.8980 chunk 107 optimal weight: 0.0370 overall best weight: 1.9864 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** b 51 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 46 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 916 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e1113 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** p 161 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** p 253 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** p 480 GLN ** p 812 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6470 moved from start: 0.3408 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.046 17650 Z= 0.158 Angle : 0.555 10.146 23870 Z= 0.276 Chirality : 0.041 0.184 2739 Planarity : 0.004 0.054 3020 Dihedral : 3.898 17.895 2269 Min Nonbonded Distance : 2.562 Molprobity Statistics. All-atom Clashscore : 11.40 Ramachandran Plot: Outliers : 0.05 % Allowed : 2.47 % Favored : 97.49 % Rotamer: Outliers : 1.31 % Allowed : 12.85 % Favored : 85.84 % 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: 0.69 (0.18), residues: 2108 helix: 1.13 (0.16), residues: 1015 sheet: -0.19 (0.35), residues: 222 loop : -0.03 (0.21), residues: 871 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP e 907 HIS 0.006 0.001 HIS n 962 PHE 0.017 0.001 PHE e 350 TYR 0.008 0.001 TYR c 71 ARG 0.003 0.000 ARG c 75 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4216 Ramachandran restraints generated. 2108 Oldfield, 0 Emsley, 2108 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4216 Ramachandran restraints generated. 2108 Oldfield, 0 Emsley, 2108 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 109 residues out of total 1985 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 83 time to evaluate : 1.958 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: b 46 MET cc_start: 0.7989 (OUTLIER) cc_final: 0.7734 (tmm) REVERT: c 38 ASP cc_start: 0.7986 (m-30) cc_final: 0.7747 (m-30) REVERT: n 1067 MET cc_start: 0.7778 (mmm) cc_final: 0.7176 (mmm) REVERT: o 899 MET cc_start: 0.7873 (ppp) cc_final: 0.6805 (tpt) REVERT: p 645 MET cc_start: 0.8788 (tpp) cc_final: 0.8202 (tpp) REVERT: p 972 MET cc_start: 0.5648 (tpt) cc_final: 0.5276 (tpt) outliers start: 26 outliers final: 16 residues processed: 102 average time/residue: 0.2666 time to fit residues: 44.0232 Evaluate side-chains 95 residues out of total 1985 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 78 time to evaluate : 1.935 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain b residue 46 MET Chi-restraints excluded: chain b residue 73 LEU Chi-restraints excluded: chain b residue 99 GLU Chi-restraints excluded: chain e residue 344 GLU Chi-restraints excluded: chain e residue 407 VAL Chi-restraints excluded: chain e residue 715 THR Chi-restraints excluded: chain n residue 970 VAL Chi-restraints excluded: chain o residue 858 LEU Chi-restraints excluded: chain p residue 296 LEU Chi-restraints excluded: chain p residue 356 LEU Chi-restraints excluded: chain p residue 483 LYS Chi-restraints excluded: chain p residue 571 ILE Chi-restraints excluded: chain p residue 656 LEU Chi-restraints excluded: chain p residue 690 PHE Chi-restraints excluded: chain p residue 786 VAL Chi-restraints excluded: chain p residue 794 PHE Chi-restraints excluded: chain p residue 903 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 212 random chunks: chunk 197 optimal weight: 0.3980 chunk 23 optimal weight: 2.9990 chunk 116 optimal weight: 5.9990 chunk 149 optimal weight: 8.9990 chunk 172 optimal weight: 0.9990 chunk 114 optimal weight: 5.9990 chunk 204 optimal weight: 0.7980 chunk 127 optimal weight: 6.9990 chunk 124 optimal weight: 8.9990 chunk 94 optimal weight: 40.0000 chunk 126 optimal weight: 6.9990 overall best weight: 2.2386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** b 51 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 46 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 916 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e1113 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** p 161 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** p 253 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** p 480 GLN ** p 812 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6494 moved from start: 0.3596 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 17650 Z= 0.177 Angle : 0.589 11.244 23870 Z= 0.292 Chirality : 0.042 0.187 2739 Planarity : 0.004 0.052 3020 Dihedral : 3.917 18.326 2269 Min Nonbonded Distance : 2.433 Molprobity Statistics. All-atom Clashscore : 12.46 Ramachandran Plot: Outliers : 0.05 % Allowed : 2.56 % Favored : 97.39 % Rotamer: Outliers : 1.41 % Allowed : 13.25 % Favored : 85.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.71 (0.18), residues: 2108 helix: 1.13 (0.16), residues: 1020 sheet: -0.20 (0.35), residues: 227 loop : -0.00 (0.21), residues: 861 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP e 298 HIS 0.006 0.001 HIS n 962 PHE 0.015 0.001 PHE c 47 TYR 0.011 0.001 TYR p 556 ARG 0.002 0.000 ARG c 75 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4216 Ramachandran restraints generated. 2108 Oldfield, 0 Emsley, 2108 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4216 Ramachandran restraints generated. 2108 Oldfield, 0 Emsley, 2108 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 109 residues out of total 1985 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 81 time to evaluate : 2.029 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: b 46 MET cc_start: 0.8092 (OUTLIER) cc_final: 0.7778 (tmm) REVERT: b 48 MET cc_start: 0.8868 (mmm) cc_final: 0.8289 (tpt) REVERT: c 38 ASP cc_start: 0.8000 (m-30) cc_final: 0.7763 (m-30) REVERT: n 1067 MET cc_start: 0.7865 (mmm) cc_final: 0.7229 (mmm) REVERT: o 899 MET cc_start: 0.7931 (ppp) cc_final: 0.6358 (tpp) REVERT: o 945 MET cc_start: 0.4149 (mmm) cc_final: 0.2295 (ptt) REVERT: p 645 MET cc_start: 0.8858 (tpp) cc_final: 0.8192 (tpp) outliers start: 28 outliers final: 17 residues processed: 104 average time/residue: 0.2744 time to fit residues: 46.8939 Evaluate side-chains 96 residues out of total 1985 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 78 time to evaluate : 2.061 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain b residue 46 MET Chi-restraints excluded: chain b residue 73 LEU Chi-restraints excluded: chain b residue 99 GLU Chi-restraints excluded: chain e residue 344 GLU Chi-restraints excluded: chain e residue 407 VAL Chi-restraints excluded: chain e residue 715 THR Chi-restraints excluded: chain n residue 970 VAL Chi-restraints excluded: chain o residue 858 LEU Chi-restraints excluded: chain p residue 483 LYS Chi-restraints excluded: chain p residue 571 ILE Chi-restraints excluded: chain p residue 636 CYS Chi-restraints excluded: chain p residue 656 LEU Chi-restraints excluded: chain p residue 690 PHE Chi-restraints excluded: chain p residue 702 VAL Chi-restraints excluded: chain p residue 786 VAL Chi-restraints excluded: chain p residue 794 PHE Chi-restraints excluded: chain p residue 903 LEU Chi-restraints excluded: chain p residue 914 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 212 random chunks: chunk 81 optimal weight: 6.9990 chunk 122 optimal weight: 0.0370 chunk 61 optimal weight: 7.9990 chunk 40 optimal weight: 2.9990 chunk 39 optimal weight: 1.9990 chunk 129 optimal weight: 7.9990 chunk 139 optimal weight: 20.0000 chunk 101 optimal weight: 20.0000 chunk 19 optimal weight: 0.9990 chunk 160 optimal weight: 0.7980 chunk 185 optimal weight: 7.9990 overall best weight: 1.3664 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** b 51 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 46 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 753 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** e 902 GLN ** e 916 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e1113 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** p 161 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** p 187 ASN ** p 253 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** p 480 GLN ** p 812 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6462 moved from start: 0.3695 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.045 17650 Z= 0.151 Angle : 0.585 11.438 23870 Z= 0.286 Chirality : 0.042 0.297 2739 Planarity : 0.004 0.054 3020 Dihedral : 3.855 19.775 2269 Min Nonbonded Distance : 2.441 Molprobity Statistics. All-atom Clashscore : 11.43 Ramachandran Plot: Outliers : 0.05 % Allowed : 2.28 % Favored : 97.68 % Rotamer: Outliers : 1.26 % Allowed : 13.45 % Favored : 85.29 % 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: 0.74 (0.18), residues: 2108 helix: 1.17 (0.16), residues: 1014 sheet: -0.31 (0.34), residues: 237 loop : 0.06 (0.22), residues: 857 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP e 298 HIS 0.006 0.001 HIS n 962 PHE 0.018 0.001 PHE e 350 TYR 0.009 0.001 TYR p 556 ARG 0.003 0.000 ARG c 84 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4216 Ramachandran restraints generated. 2108 Oldfield, 0 Emsley, 2108 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4216 Ramachandran restraints generated. 2108 Oldfield, 0 Emsley, 2108 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 106 residues out of total 1985 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 81 time to evaluate : 1.903 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: b 46 MET cc_start: 0.8131 (OUTLIER) cc_final: 0.7837 (tmm) REVERT: b 48 MET cc_start: 0.8816 (mmm) cc_final: 0.8237 (tpt) REVERT: c 38 ASP cc_start: 0.7957 (m-30) cc_final: 0.7725 (m-30) REVERT: n 1067 MET cc_start: 0.8008 (mmm) cc_final: 0.7474 (mmm) REVERT: o 899 MET cc_start: 0.7860 (ppp) cc_final: 0.6285 (tpp) REVERT: o 945 MET cc_start: 0.4463 (mmm) cc_final: 0.3243 (ptt) REVERT: p 645 MET cc_start: 0.8700 (tpp) cc_final: 0.8170 (tpt) REVERT: p 972 MET cc_start: 0.5942 (tpt) cc_final: 0.5555 (tpt) outliers start: 25 outliers final: 14 residues processed: 100 average time/residue: 0.2530 time to fit residues: 41.4038 Evaluate side-chains 96 residues out of total 1985 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 81 time to evaluate : 2.008 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain b residue 46 MET Chi-restraints excluded: chain b residue 73 LEU Chi-restraints excluded: chain b residue 99 GLU Chi-restraints excluded: chain e residue 407 VAL Chi-restraints excluded: chain n residue 970 VAL Chi-restraints excluded: chain o residue 858 LEU Chi-restraints excluded: chain p residue 483 LYS Chi-restraints excluded: chain p residue 571 ILE Chi-restraints excluded: chain p residue 656 LEU Chi-restraints excluded: chain p residue 690 PHE Chi-restraints excluded: chain p residue 702 VAL Chi-restraints excluded: chain p residue 786 VAL Chi-restraints excluded: chain p residue 794 PHE Chi-restraints excluded: chain p residue 903 LEU Chi-restraints excluded: chain p residue 914 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 212 random chunks: chunk 195 optimal weight: 7.9990 chunk 178 optimal weight: 1.9990 chunk 190 optimal weight: 5.9990 chunk 114 optimal weight: 10.0000 chunk 82 optimal weight: 9.9990 chunk 149 optimal weight: 3.9990 chunk 58 optimal weight: 0.9980 chunk 172 optimal weight: 6.9990 chunk 180 optimal weight: 1.9990 chunk 189 optimal weight: 5.9990 chunk 125 optimal weight: 6.9990 overall best weight: 2.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** b 51 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 459 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 753 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** e 902 GLN ** e 916 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e1086 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** e1113 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** p 253 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** p 480 GLN ** p 812 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6538 moved from start: 0.3961 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 17650 Z= 0.207 Angle : 0.636 14.870 23870 Z= 0.314 Chirality : 0.043 0.265 2739 Planarity : 0.004 0.052 3020 Dihedral : 4.011 22.462 2269 Min Nonbonded Distance : 2.455 Molprobity Statistics. All-atom Clashscore : 14.88 Ramachandran Plot: Outliers : 0.05 % Allowed : 3.08 % Favored : 96.87 % Rotamer: Outliers : 1.16 % Allowed : 13.65 % Favored : 85.19 % 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: 0.61 (0.18), residues: 2108 helix: 1.09 (0.16), residues: 1018 sheet: -0.46 (0.33), residues: 232 loop : -0.03 (0.22), residues: 858 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP e 298 HIS 0.007 0.001 HIS n 962 PHE 0.015 0.001 PHE o 876 TYR 0.012 0.001 TYR p 556 ARG 0.003 0.000 ARG c 84 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4216 Ramachandran restraints generated. 2108 Oldfield, 0 Emsley, 2108 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4216 Ramachandran restraints generated. 2108 Oldfield, 0 Emsley, 2108 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 102 residues out of total 1985 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 79 time to evaluate : 2.147 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: b 46 MET cc_start: 0.8235 (OUTLIER) cc_final: 0.7952 (tmm) REVERT: b 48 MET cc_start: 0.8922 (mmm) cc_final: 0.8432 (tpt) REVERT: c 38 ASP cc_start: 0.8025 (m-30) cc_final: 0.7813 (m-30) REVERT: e 467 MET cc_start: 0.7425 (tpp) cc_final: 0.6541 (tpp) REVERT: n 1067 MET cc_start: 0.7955 (mmm) cc_final: 0.7399 (mmm) REVERT: o 899 MET cc_start: 0.7875 (ppp) cc_final: 0.6470 (tpp) REVERT: o 945 MET cc_start: 0.4395 (mmm) cc_final: 0.3156 (ptt) REVERT: p 645 MET cc_start: 0.8874 (tpp) cc_final: 0.8300 (tpp) outliers start: 23 outliers final: 18 residues processed: 96 average time/residue: 0.2814 time to fit residues: 44.4870 Evaluate side-chains 95 residues out of total 1985 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 76 time to evaluate : 1.899 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain b residue 46 MET Chi-restraints excluded: chain b residue 73 LEU Chi-restraints excluded: chain b residue 80 PHE Chi-restraints excluded: chain b residue 99 GLU Chi-restraints excluded: chain e residue 407 VAL Chi-restraints excluded: chain e residue 715 THR Chi-restraints excluded: chain n residue 970 VAL Chi-restraints excluded: chain n residue 1019 MET Chi-restraints excluded: chain o residue 858 LEU Chi-restraints excluded: chain p residue 451 VAL Chi-restraints excluded: chain p residue 483 LYS Chi-restraints excluded: chain p residue 571 ILE Chi-restraints excluded: chain p residue 656 LEU Chi-restraints excluded: chain p residue 690 PHE Chi-restraints excluded: chain p residue 702 VAL Chi-restraints excluded: chain p residue 786 VAL Chi-restraints excluded: chain p residue 794 PHE Chi-restraints excluded: chain p residue 903 LEU Chi-restraints excluded: chain p residue 914 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 212 random chunks: chunk 201 optimal weight: 0.9980 chunk 122 optimal weight: 7.9990 chunk 95 optimal weight: 0.8980 chunk 139 optimal weight: 0.0570 chunk 211 optimal weight: 5.9990 chunk 194 optimal weight: 0.9980 chunk 168 optimal weight: 9.9990 chunk 17 optimal weight: 0.9980 chunk 129 optimal weight: 3.9990 chunk 103 optimal weight: 5.9990 chunk 133 optimal weight: 3.9990 overall best weight: 0.7898 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: b 51 GLN ** c 32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 360 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 459 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** e 753 GLN ** e 916 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e1113 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** p 161 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** p 253 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** p 480 GLN ** p 812 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6449 moved from start: 0.3971 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.043 17650 Z= 0.150 Angle : 0.628 18.387 23870 Z= 0.302 Chirality : 0.043 0.258 2739 Planarity : 0.004 0.056 3020 Dihedral : 3.898 21.855 2269 Min Nonbonded Distance : 2.463 Molprobity Statistics. All-atom Clashscore : 11.28 Ramachandran Plot: Outliers : 0.05 % Allowed : 2.28 % Favored : 97.68 % Rotamer: Outliers : 0.96 % Allowed : 14.01 % Favored : 85.04 % 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: 0.62 (0.18), residues: 2108 helix: 1.11 (0.16), residues: 1019 sheet: -0.56 (0.32), residues: 249 loop : 0.01 (0.22), residues: 840 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP e 373 HIS 0.007 0.001 HIS n 962 PHE 0.029 0.001 PHE e 887 TYR 0.014 0.001 TYR p 905 ARG 0.002 0.000 ARG c 84 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4216 Ramachandran restraints generated. 2108 Oldfield, 0 Emsley, 2108 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4216 Ramachandran restraints generated. 2108 Oldfield, 0 Emsley, 2108 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 103 residues out of total 1985 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 84 time to evaluate : 1.913 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: b 46 MET cc_start: 0.8184 (OUTLIER) cc_final: 0.7884 (tmm) REVERT: c 38 ASP cc_start: 0.7950 (m-30) cc_final: 0.7739 (m-30) REVERT: e 467 MET cc_start: 0.7089 (tpp) cc_final: 0.5985 (tpp) REVERT: n 1067 MET cc_start: 0.7911 (mmm) cc_final: 0.7415 (mmm) REVERT: o 869 PHE cc_start: 0.8970 (OUTLIER) cc_final: 0.8245 (p90) REVERT: o 883 LEU cc_start: 0.8542 (mt) cc_final: 0.8172 (mt) REVERT: o 899 MET cc_start: 0.7821 (ppp) cc_final: 0.6274 (tpp) REVERT: o 945 MET cc_start: 0.4437 (mmm) cc_final: 0.3165 (ptt) REVERT: p 645 MET cc_start: 0.8689 (tpp) cc_final: 0.8153 (tpt) REVERT: p 972 MET cc_start: 0.5942 (tpt) cc_final: 0.5545 (tpt) outliers start: 19 outliers final: 13 residues processed: 97 average time/residue: 0.2681 time to fit residues: 43.1428 Evaluate side-chains 94 residues out of total 1985 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 79 time to evaluate : 2.097 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain b residue 46 MET Chi-restraints excluded: chain b residue 73 LEU Chi-restraints excluded: chain b residue 99 GLU Chi-restraints excluded: chain e residue 407 VAL Chi-restraints excluded: chain n residue 970 VAL Chi-restraints excluded: chain o residue 858 LEU Chi-restraints excluded: chain o residue 869 PHE Chi-restraints excluded: chain p residue 451 VAL Chi-restraints excluded: chain p residue 483 LYS Chi-restraints excluded: chain p residue 656 LEU Chi-restraints excluded: chain p residue 690 PHE Chi-restraints excluded: chain p residue 702 VAL Chi-restraints excluded: chain p residue 786 VAL Chi-restraints excluded: chain p residue 794 PHE Chi-restraints excluded: chain p residue 903 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 212 random chunks: chunk 179 optimal weight: 2.9990 chunk 51 optimal weight: 0.6980 chunk 155 optimal weight: 0.1980 chunk 24 optimal weight: 7.9990 chunk 46 optimal weight: 1.9990 chunk 168 optimal weight: 3.9990 chunk 70 optimal weight: 6.9990 chunk 172 optimal weight: 3.9990 chunk 21 optimal weight: 0.5980 chunk 31 optimal weight: 2.9990 chunk 147 optimal weight: 0.1980 overall best weight: 0.7382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** c 32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 360 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 916 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e1113 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** p 161 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** p 253 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** p 480 GLN ** p 812 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3764 r_free = 0.3764 target = 0.044489 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3606 r_free = 0.3606 target = 0.037717 restraints weight = 225559.585| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3617 r_free = 0.3617 target = 0.038142 restraints weight = 183662.441| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3625 r_free = 0.3625 target = 0.038423 restraints weight = 156085.874| |-----------------------------------------------------------------------------| r_work (final): 0.3580 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7344 moved from start: 0.4017 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.044 17650 Z= 0.149 Angle : 0.636 17.606 23870 Z= 0.305 Chirality : 0.043 0.266 2739 Planarity : 0.004 0.061 3020 Dihedral : 3.837 20.665 2269 Min Nonbonded Distance : 2.464 Molprobity Statistics. All-atom Clashscore : 10.59 Ramachandran Plot: Outliers : 0.05 % Allowed : 2.32 % Favored : 97.63 % Rotamer: Outliers : 1.01 % Allowed : 14.11 % Favored : 84.89 % 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: 0.69 (0.18), residues: 2108 helix: 1.15 (0.16), residues: 1018 sheet: -0.44 (0.32), residues: 237 loop : 0.02 (0.22), residues: 853 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP e 373 HIS 0.007 0.001 HIS n 962 PHE 0.019 0.001 PHE o 876 TYR 0.012 0.001 TYR p 905 ARG 0.002 0.000 ARG c 67 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2655.64 seconds wall clock time: 49 minutes 40.57 seconds (2980.57 seconds total)