Starting phenix.real_space_refine on Sun Jun 15 13:22:26 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7uic_26543/06_2025/7uic_26543.cif Found real_map, /net/cci-nas-00/data/ceres_data/7uic_26543/06_2025/7uic_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/cci-nas-00/data/ceres_data/7uic_26543/06_2025/7uic_26543.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7uic_26543/06_2025/7uic_26543.map" model { file = "/net/cci-nas-00/data/ceres_data/7uic_26543/06_2025/7uic_26543.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7uic_26543/06_2025/7uic_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-5710/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: 11.40, per 1000 atoms: 0.66 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: 4.26 Conformation dependent library (CDL) restraints added in 2.1 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: 2.47 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: 6.94 Time building geometry restraints manager: 5.03 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: 13.800 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.760 Check model and map are aligned: 0.140 Set scattering table: 0.180 Process input model: 44.680 Find NCS groups from input model: 0.280 Set up NCS constraints: 0.110 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:4.790 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 64.760 ------------------------------------------------------------------------------- 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= 0.110 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 Details of bonding type rmsd hydrogen bonds : bond 0.25872 ( 788) hydrogen bonds : angle 7.49059 ( 2265) covalent geometry : bond 0.00211 (17650) covalent geometry : angle 0.50899 (23870) *********************** 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 to be fit. rotamer outliers: 0 poor density : 158 time to evaluate : 1.972 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: 0.2706 time to fit residues: 67.9867 Evaluate side-chains 91 residues out of total 1985 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 91 time to evaluate : 2.284 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3793 r_free = 0.3793 target = 0.046178 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3628 r_free = 0.3628 target = 0.038964 restraints weight = 216191.740| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3640 r_free = 0.3640 target = 0.039420 restraints weight = 174670.917| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3647 r_free = 0.3647 target = 0.039726 restraints weight = 147819.801| |-----------------------------------------------------------------------------| r_work (final): 0.3591 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7337 moved from start: 0.1977 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= 0.181 Angle : 0.650 9.226 23870 Z= 0.333 Chirality : 0.044 0.208 2739 Planarity : 0.004 0.061 3020 Dihedral : 3.977 17.047 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 Details of bonding type rmsd hydrogen bonds : bond 0.05368 ( 788) hydrogen bonds : angle 5.52855 ( 2265) covalent geometry : bond 0.00359 (17650) covalent geometry : angle 0.64985 (23870) *********************** 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 to be fit. rotamer outliers: 17 poor density : 96 time to evaluate : 2.202 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: 0.8478 (m-30) cc_final: 0.8177 (m-30) REVERT: e 449 MET cc_start: 0.7099 (mpp) cc_final: 0.6823 (mpp) REVERT: n 1019 MET cc_start: 0.8837 (mpp) cc_final: 0.8585 (mpp) REVERT: n 1067 MET cc_start: 0.8178 (mmm) cc_final: 0.7858 (mmm) REVERT: p 240 LEU cc_start: 0.9589 (tp) cc_final: 0.9270 (pp) REVERT: p 295 MET cc_start: 0.8912 (mmt) cc_final: 0.8647 (mmp) REVERT: p 645 MET cc_start: 0.8983 (tpt) cc_final: 0.8392 (tpp) outliers start: 17 outliers final: 11 residues processed: 106 average time/residue: 0.2708 time to fit residues: 47.2728 Evaluate side-chains 94 residues out of total 1985 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 83 time to evaluate : 2.301 ------------------------------------------------------------------------------- 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 191 optimal weight: 9.9990 chunk 99 optimal weight: 0.7980 chunk 178 optimal weight: 10.0000 chunk 129 optimal weight: 9.9990 chunk 7 optimal weight: 9.9990 chunk 93 optimal weight: 10.0000 chunk 182 optimal weight: 20.0000 chunk 166 optimal weight: 7.9990 chunk 69 optimal weight: 8.9990 chunk 192 optimal weight: 3.9990 chunk 53 optimal weight: 4.9990 overall best weight: 5.3588 ------------------------------------------------------------------------------- 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 398 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 453 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** e 573 HIS e 901 ASN ** e 916 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 319 ASN p 327 ASN ** p 465 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** p 538 ASN p 687 GLN p 771 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3731 r_free = 0.3731 target = 0.043611 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.3576 r_free = 0.3576 target = 0.036840 restraints weight = 225053.030| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3586 r_free = 0.3586 target = 0.037233 restraints weight = 181817.701| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3592 r_free = 0.3592 target = 0.037530 restraints weight = 156142.705| |-----------------------------------------------------------------------------| r_work (final): 0.3538 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7481 moved from start: 0.2969 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.064 17650 Z= 0.248 Angle : 0.693 11.358 23870 Z= 0.357 Chirality : 0.044 0.303 2739 Planarity : 0.004 0.059 3020 Dihedral : 4.305 18.396 2269 Min Nonbonded Distance : 2.484 Molprobity Statistics. All-atom Clashscore : 18.62 Ramachandran Plot: Outliers : 0.05 % Allowed : 2.75 % Favored : 97.20 % Rotamer: Outliers : 1.46 % Allowed : 10.43 % Favored : 88.11 % 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: 0.20 (0.18), residues: 2108 helix: 0.72 (0.16), residues: 996 sheet: -0.43 (0.35), residues: 217 loop : -0.26 (0.20), residues: 895 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP p 468 HIS 0.006 0.001 HIS e1086 PHE 0.027 0.002 PHE c 47 TYR 0.015 0.002 TYR p 853 ARG 0.005 0.001 ARG o 868 Details of bonding type rmsd hydrogen bonds : bond 0.05068 ( 788) hydrogen bonds : angle 5.56025 ( 2265) covalent geometry : bond 0.00496 (17650) covalent geometry : angle 0.69280 (23870) *********************** 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 108 residues out of total 1985 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 79 time to evaluate : 2.142 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: c 38 ASP cc_start: 0.8489 (m-30) cc_final: 0.8201 (m-30) REVERT: e 858 LEU cc_start: 0.9128 (OUTLIER) cc_final: 0.8854 (mm) REVERT: n 1067 MET cc_start: 0.8445 (mmm) cc_final: 0.7968 (mmm) REVERT: o 945 MET cc_start: 0.4189 (mmm) cc_final: 0.1918 (ptt) REVERT: p 295 MET cc_start: 0.8775 (mmt) cc_final: 0.8542 (mmp) outliers start: 29 outliers final: 18 residues processed: 100 average time/residue: 0.2627 time to fit residues: 43.2425 Evaluate side-chains 95 residues out of total 1985 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 76 time to evaluate : 1.988 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 c residue 76 ASP 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 858 LEU Chi-restraints excluded: chain o residue 858 LEU Chi-restraints excluded: chain p residue 242 ILE 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 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 779 LEU 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 133 optimal weight: 4.9990 chunk 63 optimal weight: 5.9990 chunk 4 optimal weight: 4.9990 chunk 131 optimal weight: 10.0000 chunk 70 optimal weight: 4.9990 chunk 206 optimal weight: 10.0000 chunk 172 optimal weight: 0.9990 chunk 73 optimal weight: 9.9990 chunk 5 optimal weight: 5.9990 chunk 8 optimal weight: 4.9990 chunk 17 optimal weight: 6.9990 overall best weight: 4.1990 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** e 776 ASN ** e 916 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** e1105 ASN ** 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 465 GLN p 480 GLN ** p 812 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3727 r_free = 0.3727 target = 0.043299 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3567 r_free = 0.3567 target = 0.036614 restraints weight = 226825.674| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3577 r_free = 0.3577 target = 0.037002 restraints weight = 186145.514| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3583 r_free = 0.3583 target = 0.037277 restraints weight = 158899.156| |-----------------------------------------------------------------------------| r_work (final): 0.3531 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7433 moved from start: 0.3447 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 17650 Z= 0.187 Angle : 0.613 9.022 23870 Z= 0.316 Chirality : 0.043 0.247 2739 Planarity : 0.004 0.060 3020 Dihedral : 4.319 19.076 2269 Min Nonbonded Distance : 2.513 Molprobity Statistics. All-atom Clashscore : 17.10 Ramachandran Plot: Outliers : 0.05 % Allowed : 2.99 % Favored : 96.96 % Rotamer: Outliers : 1.91 % Allowed : 12.24 % 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: 0.17 (0.18), residues: 2108 helix: 0.68 (0.16), residues: 1011 sheet: -0.68 (0.33), residues: 236 loop : -0.15 (0.21), residues: 861 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP e 907 HIS 0.006 0.001 HIS n1070 PHE 0.025 0.002 PHE c 47 TYR 0.014 0.001 TYR c 71 ARG 0.005 0.000 ARG c 75 Details of bonding type rmsd hydrogen bonds : bond 0.04291 ( 788) hydrogen bonds : angle 5.32633 ( 2265) covalent geometry : bond 0.00378 (17650) covalent geometry : angle 0.61276 (23870) *********************** 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 119 residues out of total 1985 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 81 time to evaluate : 2.294 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: 0.8734 (OUTLIER) cc_final: 0.8431 (tmm) REVERT: c 38 ASP cc_start: 0.8404 (m-30) cc_final: 0.8145 (m-30) REVERT: e 299 LEU cc_start: 0.8784 (OUTLIER) cc_final: 0.8550 (mm) REVERT: n 1067 MET cc_start: 0.8183 (mmm) cc_final: 0.7630 (mmm) REVERT: o 899 MET cc_start: 0.8070 (ppp) cc_final: 0.6379 (tpt) REVERT: p 295 MET cc_start: 0.8827 (mmt) cc_final: 0.8506 (mmp) REVERT: p 645 MET cc_start: 0.9125 (tpp) cc_final: 0.8347 (tpp) outliers start: 38 outliers final: 20 residues processed: 110 average time/residue: 0.2654 time to fit residues: 48.6985 Evaluate side-chains 96 residues out of total 1985 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 74 time to evaluate : 2.046 ------------------------------------------------------------------------------- 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 299 LEU Chi-restraints excluded: chain e residue 344 GLU Chi-restraints excluded: chain e residue 408 VAL Chi-restraints excluded: chain e residue 467 MET 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 o residue 922 THR 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 599 LEU 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 Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 212 random chunks: chunk 13 optimal weight: 4.9990 chunk 173 optimal weight: 10.0000 chunk 38 optimal weight: 0.0030 chunk 156 optimal weight: 7.9990 chunk 69 optimal weight: 8.9990 chunk 120 optimal weight: 0.5980 chunk 49 optimal weight: 9.9990 chunk 41 optimal weight: 8.9990 chunk 57 optimal weight: 10.0000 chunk 46 optimal weight: 1.9990 chunk 79 optimal weight: 3.9990 overall best weight: 2.3196 ------------------------------------------------------------------------------- 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 453 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 771 ASN p 812 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3736 r_free = 0.3736 target = 0.043607 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.3569 r_free = 0.3569 target = 0.036893 restraints weight = 230250.218| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3579 r_free = 0.3579 target = 0.037253 restraints weight = 188423.353| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3584 r_free = 0.3584 target = 0.037526 restraints weight = 164193.062| |-----------------------------------------------------------------------------| r_work (final): 0.3539 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7439 moved from start: 0.3610 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.065 17650 Z= 0.128 Angle : 0.566 10.855 23870 Z= 0.286 Chirality : 0.042 0.171 2739 Planarity : 0.004 0.055 3020 Dihedral : 4.135 19.375 2269 Min Nonbonded Distance : 2.478 Molprobity Statistics. All-atom Clashscore : 13.64 Ramachandran Plot: Outliers : 0.05 % Allowed : 2.51 % Favored : 97.44 % Rotamer: Outliers : 1.36 % Allowed : 13.40 % Favored : 85.24 % 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: 0.40 (0.18), residues: 2108 helix: 0.92 (0.16), residues: 1010 sheet: -0.51 (0.34), residues: 236 loop : -0.14 (0.21), residues: 862 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP e 907 HIS 0.006 0.001 HIS n 962 PHE 0.017 0.001 PHE c 47 TYR 0.011 0.001 TYR p 376 ARG 0.003 0.000 ARG e 869 Details of bonding type rmsd hydrogen bonds : bond 0.03823 ( 788) hydrogen bonds : angle 5.01409 ( 2265) covalent geometry : bond 0.00269 (17650) covalent geometry : angle 0.56582 (23870) *********************** 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 106 residues out of total 1985 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 79 time to evaluate : 1.988 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: 0.8754 (OUTLIER) cc_final: 0.8467 (tmm) REVERT: c 38 ASP cc_start: 0.8450 (m-30) cc_final: 0.8205 (m-30) REVERT: e 449 MET cc_start: 0.7286 (mtt) cc_final: 0.6829 (mpp) REVERT: n 1067 MET cc_start: 0.8363 (mmm) cc_final: 0.7792 (mmm) REVERT: o 899 MET cc_start: 0.8222 (ppp) cc_final: 0.6792 (tpt) REVERT: o 945 MET cc_start: 0.4298 (mmm) cc_final: 0.2917 (ptt) REVERT: p 150 MET cc_start: 0.5808 (tmm) cc_final: 0.5600 (ppp) REVERT: p 295 MET cc_start: 0.8845 (mmt) cc_final: 0.8506 (mmp) REVERT: p 645 MET cc_start: 0.9265 (tpp) cc_final: 0.8414 (tpp) REVERT: p 740 MET cc_start: 0.8857 (pmm) cc_final: 0.8503 (pmm) outliers start: 27 outliers final: 15 residues processed: 100 average time/residue: 0.2564 time to fit residues: 42.1925 Evaluate side-chains 91 residues out of total 1985 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 75 time to evaluate : 1.990 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain b residue 46 MET 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 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 794 PHE Chi-restraints excluded: chain p residue 903 LEU Chi-restraints excluded: chain p residue 914 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 212 random chunks: chunk 28 optimal weight: 10.0000 chunk 176 optimal weight: 0.5980 chunk 126 optimal weight: 8.9990 chunk 189 optimal weight: 4.9990 chunk 138 optimal weight: 7.9990 chunk 56 optimal weight: 2.9990 chunk 102 optimal weight: 3.9990 chunk 144 optimal weight: 10.0000 chunk 185 optimal weight: 0.9990 chunk 125 optimal weight: 6.9990 chunk 83 optimal weight: 5.9990 overall best weight: 2.7188 ------------------------------------------------------------------------------- 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** ** 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** ** e1086 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** e1113 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 926 GLN ** 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 = 0.3722 r_free = 0.3722 target = 0.043221 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3562 r_free = 0.3562 target = 0.036599 restraints weight = 229174.024| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3575 r_free = 0.3575 target = 0.037003 restraints weight = 186815.525| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3581 r_free = 0.3581 target = 0.037265 restraints weight = 155692.762| |-----------------------------------------------------------------------------| r_work (final): 0.3528 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7450 moved from start: 0.3872 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 17650 Z= 0.140 Angle : 0.585 16.584 23870 Z= 0.293 Chirality : 0.042 0.231 2739 Planarity : 0.004 0.052 3020 Dihedral : 4.106 18.048 2269 Min Nonbonded Distance : 2.536 Molprobity Statistics. All-atom Clashscore : 14.36 Ramachandran Plot: Outliers : 0.05 % Allowed : 2.99 % Favored : 96.96 % Rotamer: Outliers : 1.56 % Allowed : 14.06 % Favored : 84.38 % 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: 0.45 (0.18), residues: 2108 helix: 0.97 (0.16), residues: 1018 sheet: -0.56 (0.33), residues: 241 loop : -0.11 (0.22), residues: 849 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 0.016 0.001 PHE e 350 TYR 0.010 0.001 TYR c 71 ARG 0.005 0.000 ARG p 138 Details of bonding type rmsd hydrogen bonds : bond 0.03791 ( 788) hydrogen bonds : angle 4.94689 ( 2265) covalent geometry : bond 0.00292 (17650) covalent geometry : angle 0.58535 (23870) *********************** 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 107 residues out of total 1985 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 76 time to evaluate : 2.051 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: 0.8868 (OUTLIER) cc_final: 0.8593 (tmm) REVERT: c 38 ASP cc_start: 0.8484 (m-30) cc_final: 0.8248 (m-30) REVERT: e 449 MET cc_start: 0.7184 (mtt) cc_final: 0.6818 (mpp) REVERT: n 1067 MET cc_start: 0.8321 (mmm) cc_final: 0.7750 (mmm) REVERT: o 899 MET cc_start: 0.8271 (ppp) cc_final: 0.6221 (tpp) REVERT: o 945 MET cc_start: 0.4279 (mmm) cc_final: 0.2782 (ptt) REVERT: p 132 MET cc_start: 0.7691 (ttp) cc_final: 0.7166 (ttp) REVERT: p 295 MET cc_start: 0.8834 (mmt) cc_final: 0.8506 (mmp) outliers start: 31 outliers final: 19 residues processed: 101 average time/residue: 0.2616 time to fit residues: 43.8942 Evaluate side-chains 93 residues out of total 1985 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 73 time to evaluate : 2.036 ------------------------------------------------------------------------------- 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 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 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 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 212 random chunks: chunk 72 optimal weight: 0.8980 chunk 118 optimal weight: 0.9990 chunk 140 optimal weight: 0.0770 chunk 130 optimal weight: 0.0040 chunk 171 optimal weight: 2.9990 chunk 52 optimal weight: 10.0000 chunk 205 optimal weight: 0.0970 chunk 105 optimal weight: 7.9990 chunk 64 optimal weight: 4.9990 chunk 78 optimal weight: 10.0000 chunk 110 optimal weight: 3.9990 overall best weight: 0.4150 ------------------------------------------------------------------------------- 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 e 453 GLN ** e 916 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** e1093 HIS ** 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: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3755 r_free = 0.3755 target = 0.044344 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3596 r_free = 0.3596 target = 0.037565 restraints weight = 223727.216| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3610 r_free = 0.3610 target = 0.037999 restraints weight = 180554.996| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3617 r_free = 0.3617 target = 0.038286 restraints weight = 149348.178| |-----------------------------------------------------------------------------| r_work (final): 0.3567 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7340 moved from start: 0.3826 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.042 17650 Z= 0.104 Angle : 0.579 12.662 23870 Z= 0.283 Chirality : 0.042 0.243 2739 Planarity : 0.004 0.055 3020 Dihedral : 3.907 17.997 2269 Min Nonbonded Distance : 2.435 Molprobity Statistics. All-atom Clashscore : 10.68 Ramachandran Plot: Outliers : 0.05 % Allowed : 1.99 % Favored : 97.96 % Rotamer: Outliers : 1.71 % Allowed : 14.26 % Favored : 84.03 % 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: 0.67 (0.18), residues: 2108 helix: 1.17 (0.16), residues: 1014 sheet: -0.44 (0.32), residues: 254 loop : -0.00 (0.22), residues: 840 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP e 373 HIS 0.006 0.001 HIS n 962 PHE 0.016 0.001 PHE o 876 TYR 0.011 0.001 TYR e 461 ARG 0.002 0.000 ARG e 869 Details of bonding type rmsd hydrogen bonds : bond 0.03472 ( 788) hydrogen bonds : angle 4.70440 ( 2265) covalent geometry : bond 0.00217 (17650) covalent geometry : angle 0.57930 (23870) *********************** 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 116 residues out of total 1985 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 82 time to evaluate : 2.043 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: b 46 MET cc_start: 0.8851 (OUTLIER) cc_final: 0.8550 (tmm) REVERT: c 38 ASP cc_start: 0.8345 (m-30) cc_final: 0.8105 (m-30) REVERT: e 449 MET cc_start: 0.6947 (mtt) cc_final: 0.6728 (mpp) REVERT: n 1067 MET cc_start: 0.8206 (mmm) cc_final: 0.7691 (mmm) REVERT: o 883 LEU cc_start: 0.8850 (mt) cc_final: 0.8588 (mt) REVERT: o 899 MET cc_start: 0.8162 (ppp) cc_final: 0.6384 (tpp) REVERT: o 945 MET cc_start: 0.4059 (mmm) cc_final: 0.2925 (ptt) REVERT: p 295 MET cc_start: 0.8873 (mmt) cc_final: 0.8518 (mmp) REVERT: p 645 MET cc_start: 0.9127 (tpp) cc_final: 0.8329 (tpp) REVERT: p 972 MET cc_start: 0.7603 (tpt) cc_final: 0.7281 (tpt) outliers start: 34 outliers final: 18 residues processed: 110 average time/residue: 0.2803 time to fit residues: 49.6582 Evaluate side-chains 97 residues out of total 1985 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 78 time to evaluate : 2.047 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain b residue 46 MET Chi-restraints excluded: chain b residue 51 GLN Chi-restraints excluded: chain b residue 73 LEU Chi-restraints excluded: chain b residue 99 GLU Chi-restraints excluded: chain e residue 387 GLU Chi-restraints excluded: chain e residue 407 VAL Chi-restraints excluded: chain e residue 467 MET 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 340 THR 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 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 208 optimal weight: 7.9990 chunk 71 optimal weight: 0.0970 chunk 126 optimal weight: 5.9990 chunk 198 optimal weight: 6.9990 chunk 92 optimal weight: 8.9990 chunk 192 optimal weight: 6.9990 chunk 94 optimal weight: 20.0000 chunk 98 optimal weight: 0.7980 chunk 0 optimal weight: 10.0000 chunk 146 optimal weight: 7.9990 chunk 107 optimal weight: 0.5980 overall best weight: 2.8982 ------------------------------------------------------------------------------- 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** ** 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** ** o 926 GLN ** 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 430 HIS ** 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 = 0.3728 r_free = 0.3728 target = 0.043161 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3563 r_free = 0.3563 target = 0.036550 restraints weight = 228621.582| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3573 r_free = 0.3573 target = 0.036906 restraints weight = 189754.914| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3579 r_free = 0.3579 target = 0.037159 restraints weight = 164032.390| |-----------------------------------------------------------------------------| r_work (final): 0.3533 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7450 moved from start: 0.4091 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 17650 Z= 0.146 Angle : 0.612 10.926 23870 Z= 0.304 Chirality : 0.042 0.203 2739 Planarity : 0.004 0.055 3020 Dihedral : 3.988 18.841 2269 Min Nonbonded Distance : 2.426 Molprobity Statistics. All-atom Clashscore : 14.62 Ramachandran Plot: Outliers : 0.05 % Allowed : 2.89 % Favored : 97.06 % Rotamer: Outliers : 1.26 % Allowed : 14.91 % Favored : 83.83 % 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: 0.64 (0.18), residues: 2108 helix: 1.14 (0.16), residues: 1022 sheet: -0.56 (0.32), residues: 239 loop : 0.00 (0.22), residues: 847 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP e 298 HIS 0.006 0.001 HIS n 962 PHE 0.017 0.001 PHE e 350 TYR 0.015 0.001 TYR p 905 ARG 0.016 0.000 ARG c 75 Details of bonding type rmsd hydrogen bonds : bond 0.03643 ( 788) hydrogen bonds : angle 4.76543 ( 2265) covalent geometry : bond 0.00307 (17650) covalent geometry : angle 0.61197 (23870) *********************** 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 101 residues out of total 1985 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 76 time to evaluate : 2.008 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: b 46 MET cc_start: 0.8958 (OUTLIER) cc_final: 0.8678 (tmm) REVERT: c 38 ASP cc_start: 0.8411 (m-30) cc_final: 0.8164 (m-30) REVERT: e 449 MET cc_start: 0.7255 (mtt) cc_final: 0.6906 (mpp) REVERT: n 1008 HIS cc_start: -0.2226 (OUTLIER) cc_final: -0.2542 (t-170) REVERT: n 1067 MET cc_start: 0.8274 (mmm) cc_final: 0.7705 (mmm) REVERT: o 899 MET cc_start: 0.8392 (ppp) cc_final: 0.6523 (tpp) REVERT: o 945 MET cc_start: 0.4141 (mmm) cc_final: 0.2796 (ptt) REVERT: p 645 MET cc_start: 0.9297 (tpp) cc_final: 0.8425 (tpt) REVERT: p 972 MET cc_start: 0.7705 (tpt) cc_final: 0.7460 (tpt) outliers start: 25 outliers final: 20 residues processed: 95 average time/residue: 0.2643 time to fit residues: 41.4172 Evaluate side-chains 97 residues out of total 1985 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 75 time to evaluate : 1.999 ------------------------------------------------------------------------------- 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 467 MET Chi-restraints excluded: chain n residue 970 VAL Chi-restraints excluded: chain n residue 1008 HIS Chi-restraints excluded: chain o residue 858 LEU Chi-restraints excluded: chain p residue 296 LEU Chi-restraints excluded: chain p residue 299 THR Chi-restraints excluded: chain p residue 340 THR Chi-restraints excluded: chain p residue 356 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 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 106 optimal weight: 6.9990 chunk 121 optimal weight: 2.9990 chunk 79 optimal weight: 5.9990 chunk 100 optimal weight: 9.9990 chunk 55 optimal weight: 9.9990 chunk 133 optimal weight: 3.9990 chunk 114 optimal weight: 0.9990 chunk 17 optimal weight: 4.9990 chunk 99 optimal weight: 0.9990 chunk 129 optimal weight: 1.9990 chunk 78 optimal weight: 5.9990 overall best weight: 2.1990 ------------------------------------------------------------------------------- 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** ** 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** ** o 926 GLN ** 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 430 HIS ** 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 = 0.3731 r_free = 0.3731 target = 0.043400 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3566 r_free = 0.3566 target = 0.036777 restraints weight = 231012.483| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3577 r_free = 0.3577 target = 0.037158 restraints weight = 190638.075| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3584 r_free = 0.3584 target = 0.037422 restraints weight = 163333.619| |-----------------------------------------------------------------------------| r_work (final): 0.3536 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7438 moved from start: 0.4204 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= 0.123 Angle : 0.602 11.650 23870 Z= 0.296 Chirality : 0.042 0.199 2739 Planarity : 0.004 0.062 3020 Dihedral : 3.995 19.293 2269 Min Nonbonded Distance : 2.448 Molprobity Statistics. All-atom Clashscore : 13.41 Ramachandran Plot: Outliers : 0.05 % Allowed : 2.75 % Favored : 97.20 % Rotamer: Outliers : 1.21 % Allowed : 15.31 % Favored : 83.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.65 (0.18), residues: 2108 helix: 1.16 (0.16), residues: 1020 sheet: -0.70 (0.32), residues: 249 loop : 0.04 (0.22), residues: 839 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP e 373 HIS 0.006 0.001 HIS n 962 PHE 0.015 0.001 PHE o 876 TYR 0.012 0.001 TYR p 905 ARG 0.011 0.000 ARG c 75 Details of bonding type rmsd hydrogen bonds : bond 0.03530 ( 788) hydrogen bonds : angle 4.70992 ( 2265) covalent geometry : bond 0.00262 (17650) covalent geometry : angle 0.60164 (23870) *********************** 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 to be fit. rotamer outliers: 24 poor density : 78 time to evaluate : 2.042 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: b 46 MET cc_start: 0.8260 (OUTLIER) cc_final: 0.7874 (tmm) REVERT: c 38 ASP cc_start: 0.8394 (m-30) cc_final: 0.8151 (m-30) REVERT: e 449 MET cc_start: 0.7186 (mtt) cc_final: 0.6912 (mpp) REVERT: n 1008 HIS cc_start: -0.2129 (OUTLIER) cc_final: -0.2481 (t-170) REVERT: n 1067 MET cc_start: 0.8362 (mmm) cc_final: 0.7830 (mmm) REVERT: o 899 MET cc_start: 0.8381 (ppp) cc_final: 0.6482 (tpp) REVERT: o 945 MET cc_start: 0.4277 (mmm) cc_final: 0.3005 (ptt) REVERT: p 295 MET cc_start: 0.8914 (mmt) cc_final: 0.8565 (mmp) REVERT: p 645 MET cc_start: 0.9282 (tpp) cc_final: 0.8402 (tpt) REVERT: p 972 MET cc_start: 0.7773 (tpt) cc_final: 0.7512 (tpt) outliers start: 24 outliers final: 19 residues processed: 96 average time/residue: 0.2846 time to fit residues: 45.4450 Evaluate side-chains 95 residues out of total 1985 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 74 time to evaluate : 2.014 ------------------------------------------------------------------------------- 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 467 MET Chi-restraints excluded: chain n residue 970 VAL Chi-restraints excluded: chain n residue 1008 HIS Chi-restraints excluded: chain o residue 858 LEU Chi-restraints excluded: chain p residue 296 LEU Chi-restraints excluded: chain p residue 299 THR Chi-restraints excluded: chain p residue 340 THR Chi-restraints excluded: chain p residue 356 LEU 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 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 17 optimal weight: 2.9990 chunk 96 optimal weight: 9.9990 chunk 47 optimal weight: 30.0000 chunk 175 optimal weight: 0.0170 chunk 207 optimal weight: 9.9990 chunk 138 optimal weight: 3.9990 chunk 124 optimal weight: 1.9990 chunk 208 optimal weight: 8.9990 chunk 132 optimal weight: 6.9990 chunk 110 optimal weight: 0.0170 chunk 93 optimal weight: 5.9990 overall best weight: 1.8062 ------------------------------------------------------------------------------- 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** ** 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** ** o 926 GLN ** 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 430 HIS ** 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 = 0.3735 r_free = 0.3735 target = 0.043442 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3574 r_free = 0.3574 target = 0.036848 restraints weight = 226556.892| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3588 r_free = 0.3588 target = 0.037235 restraints weight = 188324.488| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3594 r_free = 0.3594 target = 0.037479 restraints weight = 158763.414| |-----------------------------------------------------------------------------| r_work (final): 0.3541 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7469 moved from start: 0.4291 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.048 17650 Z= 0.116 Angle : 0.628 18.261 23870 Z= 0.303 Chirality : 0.043 0.253 2739 Planarity : 0.004 0.056 3020 Dihedral : 3.989 21.034 2269 Min Nonbonded Distance : 2.461 Molprobity Statistics. All-atom Clashscore : 12.95 Ramachandran Plot: Outliers : 0.05 % Allowed : 2.66 % Favored : 97.30 % Rotamer: Outliers : 1.11 % Allowed : 15.52 % Favored : 83.38 % 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: 0.67 (0.18), residues: 2108 helix: 1.17 (0.16), residues: 1022 sheet: -0.63 (0.32), residues: 254 loop : 0.04 (0.22), residues: 832 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 0.022 0.001 PHE e 350 TYR 0.012 0.001 TYR p 905 ARG 0.010 0.000 ARG c 75 Details of bonding type rmsd hydrogen bonds : bond 0.03504 ( 788) hydrogen bonds : angle 4.69593 ( 2265) covalent geometry : bond 0.00250 (17650) covalent geometry : angle 0.62841 (23870) ********************** 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 98 residues out of total 1985 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 76 time to evaluate : 2.269 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: 0.8488 (OUTLIER) cc_final: 0.8111 (tmm) REVERT: b 48 MET cc_start: 0.8694 (tpt) cc_final: 0.8474 (mmm) REVERT: c 38 ASP cc_start: 0.8449 (m-30) cc_final: 0.8209 (m-30) REVERT: e 414 TYR cc_start: 0.7802 (OUTLIER) cc_final: 0.6316 (t80) REVERT: e 449 MET cc_start: 0.7193 (mtt) cc_final: 0.6925 (mpp) REVERT: n 1008 HIS cc_start: -0.2248 (OUTLIER) cc_final: -0.2580 (t-170) REVERT: n 1067 MET cc_start: 0.8470 (mmm) cc_final: 0.7959 (mmm) REVERT: o 899 MET cc_start: 0.8477 (ppp) cc_final: 0.6808 (tpp) REVERT: o 945 MET cc_start: 0.4233 (mmm) cc_final: 0.3024 (ptt) REVERT: p 295 MET cc_start: 0.8964 (mmt) cc_final: 0.8598 (mmp) REVERT: p 645 MET cc_start: 0.9283 (tpp) cc_final: 0.8400 (tpt) REVERT: p 972 MET cc_start: 0.7887 (tpt) cc_final: 0.7638 (tpt) outliers start: 22 outliers final: 19 residues processed: 94 average time/residue: 0.3142 time to fit residues: 48.7626 Evaluate side-chains 96 residues out of total 1985 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 74 time to evaluate : 2.349 ------------------------------------------------------------------------------- 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 387 GLU Chi-restraints excluded: chain e residue 407 VAL Chi-restraints excluded: chain e residue 414 TYR Chi-restraints excluded: chain e residue 467 MET Chi-restraints excluded: chain n residue 970 VAL Chi-restraints excluded: chain n residue 1008 HIS Chi-restraints excluded: chain o residue 858 LEU Chi-restraints excluded: chain p residue 296 LEU Chi-restraints excluded: chain p residue 299 THR Chi-restraints excluded: chain p residue 340 THR 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 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 40 optimal weight: 0.9980 chunk 52 optimal weight: 0.9990 chunk 48 optimal weight: 10.0000 chunk 116 optimal weight: 0.8980 chunk 68 optimal weight: 0.8980 chunk 27 optimal weight: 9.9990 chunk 190 optimal weight: 4.9990 chunk 178 optimal weight: 5.9990 chunk 105 optimal weight: 6.9990 chunk 60 optimal weight: 4.9990 chunk 78 optimal weight: 0.7980 overall best weight: 0.9182 ------------------------------------------------------------------------------- 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** ** e 916 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** e1086 HIS ** 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 430 HIS ** 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 = 0.3747 r_free = 0.3747 target = 0.043875 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3589 r_free = 0.3589 target = 0.037272 restraints weight = 224463.395| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3603 r_free = 0.3603 target = 0.037673 restraints weight = 181682.684| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 22)----------------| | r_work = 0.3609 r_free = 0.3609 target = 0.037915 restraints weight = 153571.735| |-----------------------------------------------------------------------------| r_work (final): 0.3560 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7373 moved from start: 0.4334 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= 0.102 Angle : 0.613 18.083 23870 Z= 0.294 Chirality : 0.042 0.267 2739 Planarity : 0.004 0.057 3020 Dihedral : 3.880 21.922 2269 Min Nonbonded Distance : 2.484 Molprobity Statistics. All-atom Clashscore : 11.14 Ramachandran Plot: Outliers : 0.05 % Allowed : 2.04 % Favored : 97.91 % Rotamer: Outliers : 1.21 % Allowed : 15.31 % Favored : 83.48 % 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: 0.76 (0.18), residues: 2108 helix: 1.24 (0.16), residues: 1023 sheet: -0.47 (0.32), residues: 249 loop : 0.05 (0.22), residues: 836 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP e 373 HIS 0.007 0.001 HIS n 962 PHE 0.018 0.001 PHE o 876 TYR 0.032 0.001 TYR c 71 ARG 0.010 0.000 ARG c 75 Details of bonding type rmsd hydrogen bonds : bond 0.03296 ( 788) hydrogen bonds : angle 4.53904 ( 2265) covalent geometry : bond 0.00221 (17650) covalent geometry : angle 0.61295 (23870) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5915.07 seconds wall clock time: 105 minutes 24.60 seconds (6324.60 seconds total)