Starting phenix.real_space_refine on Sun Aug 24 05:43:38 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7uic_26543/08_2025/7uic_26543.cif Found real_map, /net/cci-nas-00/data/ceres_data/7uic_26543/08_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_26543/08_2025/7uic_26543.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7uic_26543/08_2025/7uic_26543.map" model { file = "/net/cci-nas-00/data/ceres_data/7uic_26543/08_2025/7uic_26543.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7uic_26543/08_2025/7uic_26543.cif" } resolution = 3.7 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 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): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/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: 4.23, per 1000 atoms: 0.24 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: 1.56 Conformation dependent library (CDL) restraints added in 664.4 milliseconds Enol-peptide restraints added in 238.4 nanoseconds 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: 0.76 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: 3.30 Time building geometry restraints manager: 2.03 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: 1.520 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.290 Check model and map are aligned: 0.050 Set scattering table: 0.060 Process input model: 17.070 Find NCS groups from input model: 0.080 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.330 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 20.450 ------------------------------------------------------------------------------- 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 : 9.79 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 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 ARG 0.008 0.000 ARG e 869 TYR 0.017 0.001 TYR p 556 PHE 0.022 0.001 PHE e 724 TRP 0.013 0.001 TRP e 373 HIS 0.003 0.001 HIS p 231 Details of bonding type rmsd covalent geometry : bond 0.00211 (17650) covalent geometry : angle 0.50899 (23870) hydrogen bonds : bond 0.25872 ( 788) hydrogen bonds : angle 7.49059 ( 2265) *********************** 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 : 0.675 Fit side-chains 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: 0.7533 (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: 0.7794 (tpp) outliers start: 0 outliers final: 0 residues processed: 158 average time/residue: 0.1216 time to fit residues: 30.4771 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 : 0.650 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 212 random chunks: chunk 98 optimal weight: 7.9990 chunk 194 optimal weight: 1.9990 chunk 107 optimal weight: 0.9990 chunk 10 optimal weight: 8.9990 chunk 66 optimal weight: 0.8980 chunk 130 optimal weight: 20.0000 chunk 124 optimal weight: 6.9990 chunk 103 optimal weight: 3.9990 chunk 200 optimal weight: 6.9990 chunk 77 optimal weight: 5.9990 chunk 122 optimal weight: 20.0000 overall best weight: 2.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: c 32 GLN 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 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: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3808 r_free = 0.3808 target = 0.046687 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3643 r_free = 0.3643 target = 0.039384 restraints weight = 214056.090| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3654 r_free = 0.3654 target = 0.039827 restraints weight = 173160.923| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 22)----------------| | r_work = 0.3662 r_free = 0.3662 target = 0.040152 restraints weight = 147115.873| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3667 r_free = 0.3667 target = 0.040375 restraints weight = 131043.145| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.3671 r_free = 0.3671 target = 0.040542 restraints weight = 120569.015| |-----------------------------------------------------------------------------| r_work (final): 0.3617 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7288 moved from start: 0.1741 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= 0.165 Angle : 0.633 10.734 23870 Z= 0.326 Chirality : 0.044 0.220 2739 Planarity : 0.004 0.060 3020 Dihedral : 3.848 16.794 2269 Min Nonbonded Distance : 2.478 Molprobity Statistics. All-atom Clashscore : 13.04 Ramachandran Plot: Outliers : 0.05 % Allowed : 1.94 % Favored : 98.01 % Rotamer: Outliers : 0.71 % Allowed : 6.80 % Favored : 92.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.51 (0.18), residues: 2108 helix: 1.02 (0.16), residues: 984 sheet: -0.38 (0.35), residues: 224 loop : -0.11 (0.20), residues: 900 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG e 869 TYR 0.023 0.001 TYR p 556 PHE 0.026 0.002 PHE p 794 TRP 0.017 0.002 TRP p 280 HIS 0.005 0.001 HIS n1070 Details of bonding type rmsd covalent geometry : bond 0.00333 (17650) covalent geometry : angle 0.63344 (23870) hydrogen bonds : bond 0.05783 ( 788) hydrogen bonds : angle 5.56743 ( 2265) *********************** 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 111 residues out of total 1985 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 97 time to evaluate : 0.754 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: c 38 ASP cc_start: 0.8460 (m-30) cc_final: 0.8150 (m-30) REVERT: e 449 MET cc_start: 0.6941 (mpp) cc_final: 0.6736 (mpp) REVERT: n 1019 MET cc_start: 0.8809 (mpp) cc_final: 0.8481 (mpp) REVERT: n 1067 MET cc_start: 0.7974 (mmm) cc_final: 0.7659 (mmm) REVERT: o 899 MET cc_start: 0.8162 (ppp) cc_final: 0.7524 (tpt) REVERT: p 240 LEU cc_start: 0.9617 (tp) cc_final: 0.9343 (pp) REVERT: p 295 MET cc_start: 0.8902 (mmt) cc_final: 0.8632 (mmp) REVERT: p 645 MET cc_start: 0.8902 (tpt) cc_final: 0.8319 (tpp) outliers start: 14 outliers final: 8 residues processed: 105 average time/residue: 0.1209 time to fit residues: 20.8316 Evaluate side-chains 93 residues out of total 1985 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 85 time to evaluate : 0.659 ------------------------------------------------------------------------------- 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 n residue 972 TYR Chi-restraints excluded: chain p residue 296 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 139 optimal weight: 0.0040 chunk 197 optimal weight: 9.9990 chunk 47 optimal weight: 5.9990 chunk 64 optimal weight: 0.8980 chunk 48 optimal weight: 2.9990 chunk 1 optimal weight: 6.9990 chunk 0 optimal weight: 6.9990 chunk 109 optimal weight: 3.9990 chunk 27 optimal weight: 1.9990 chunk 145 optimal weight: 4.9990 chunk 137 optimal weight: 10.0000 overall best weight: 1.9798 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** e 360 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** e 453 GLN ** e 916 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** e1093 HIS ** e1113 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** n1024 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** p 161 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** p 253 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** p 319 ASN p 327 ASN p 480 GLN ** p 536 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** p 630 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 = 0.3796 r_free = 0.3796 target = 0.046187 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3633 r_free = 0.3633 target = 0.038895 restraints weight = 217808.972| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3644 r_free = 0.3644 target = 0.039358 restraints weight = 175164.956| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3651 r_free = 0.3651 target = 0.039639 restraints weight = 148282.051| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3656 r_free = 0.3656 target = 0.039869 restraints weight = 133372.275| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.3659 r_free = 0.3659 target = 0.040050 restraints weight = 122181.607| |-----------------------------------------------------------------------------| r_work (final): 0.3614 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7337 moved from start: 0.2292 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 17650 Z= 0.123 Angle : 0.569 13.771 23870 Z= 0.284 Chirality : 0.042 0.146 2739 Planarity : 0.004 0.057 3020 Dihedral : 3.818 16.519 2269 Min Nonbonded Distance : 2.545 Molprobity Statistics. All-atom Clashscore : 11.34 Ramachandran Plot: Outliers : 0.05 % Allowed : 1.57 % Favored : 98.39 % Rotamer: Outliers : 0.96 % Allowed : 9.02 % Favored : 90.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.67 (0.18), residues: 2108 helix: 1.20 (0.16), residues: 982 sheet: -0.25 (0.35), residues: 222 loop : -0.10 (0.20), residues: 904 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG e 869 TYR 0.020 0.001 TYR c 71 PHE 0.021 0.001 PHE c 47 TRP 0.013 0.001 TRP p 280 HIS 0.005 0.001 HIS n 962 Details of bonding type rmsd covalent geometry : bond 0.00253 (17650) covalent geometry : angle 0.56937 (23870) hydrogen bonds : bond 0.04347 ( 788) hydrogen bonds : angle 5.09324 ( 2265) *********************** 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 112 residues out of total 1985 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 93 time to evaluate : 0.777 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: 0.8398 (m-30) cc_final: 0.8108 (m-30) REVERT: e 684 MET cc_start: 0.8081 (pmm) cc_final: 0.7766 (pmm) REVERT: n 1067 MET cc_start: 0.8273 (mmm) cc_final: 0.7805 (mmm) REVERT: o 945 MET cc_start: 0.4168 (mmm) cc_final: 0.2812 (ptt) REVERT: p 130 MET cc_start: 0.8999 (tmm) cc_final: 0.8276 (tmm) REVERT: p 240 LEU cc_start: 0.9588 (tp) cc_final: 0.9220 (pp) outliers start: 19 outliers final: 8 residues processed: 106 average time/residue: 0.1216 time to fit residues: 21.3324 Evaluate side-chains 92 residues out of total 1985 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 84 time to evaluate : 0.720 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain b residue 99 GLU Chi-restraints excluded: chain e residue 715 THR Chi-restraints excluded: chain o residue 858 LEU Chi-restraints excluded: chain p residue 296 LEU Chi-restraints excluded: chain p residue 571 ILE Chi-restraints excluded: chain p residue 656 LEU Chi-restraints excluded: chain p residue 702 VAL Chi-restraints excluded: chain p residue 794 PHE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 212 random chunks: chunk 137 optimal weight: 6.9990 chunk 152 optimal weight: 0.0570 chunk 173 optimal weight: 6.9990 chunk 82 optimal weight: 0.0980 chunk 56 optimal weight: 2.9990 chunk 209 optimal weight: 4.9990 chunk 118 optimal weight: 0.8980 chunk 175 optimal weight: 7.9990 chunk 207 optimal weight: 10.0000 chunk 186 optimal weight: 0.8980 chunk 193 optimal weight: 0.0770 overall best weight: 0.4056 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** c 46 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** c 80 GLN ** e 360 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** e 453 GLN e 776 ASN ** e 916 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** e1093 HIS ** e1113 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** n1024 ASN ** 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 536 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3820 r_free = 0.3820 target = 0.046807 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3650 r_free = 0.3650 target = 0.039589 restraints weight = 217726.957| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3660 r_free = 0.3660 target = 0.040021 restraints weight = 177007.496| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3667 r_free = 0.3667 target = 0.040333 restraints weight = 152163.247| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3672 r_free = 0.3672 target = 0.040552 restraints weight = 136176.589| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3676 r_free = 0.3676 target = 0.040694 restraints weight = 125542.624| |-----------------------------------------------------------------------------| r_work (final): 0.3637 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7171 moved from start: 0.2467 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.045 17650 Z= 0.100 Angle : 0.556 10.493 23870 Z= 0.271 Chirality : 0.042 0.313 2739 Planarity : 0.004 0.057 3020 Dihedral : 3.692 16.085 2269 Min Nonbonded Distance : 2.466 Molprobity Statistics. All-atom Clashscore : 8.78 Ramachandran Plot: Outliers : 0.05 % Allowed : 1.85 % Favored : 98.10 % Rotamer: Outliers : 0.71 % Allowed : 10.73 % Favored : 88.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.76 (0.18), residues: 2108 helix: 1.27 (0.16), residues: 986 sheet: -0.11 (0.36), residues: 225 loop : -0.07 (0.20), residues: 897 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG c 67 TYR 0.009 0.001 TYR c 71 PHE 0.015 0.001 PHE c 47 TRP 0.010 0.001 TRP e 907 HIS 0.005 0.001 HIS n 962 Details of bonding type rmsd covalent geometry : bond 0.00205 (17650) covalent geometry : angle 0.55566 (23870) hydrogen bonds : bond 0.03762 ( 788) hydrogen bonds : angle 4.82620 ( 2265) *********************** 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 107 residues out of total 1985 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 93 time to evaluate : 0.857 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: c 38 ASP cc_start: 0.8171 (m-30) cc_final: 0.7881 (m-30) REVERT: e 791 LEU cc_start: 0.9056 (tp) cc_final: 0.8619 (tp) REVERT: e 820 LEU cc_start: 0.9019 (tt) cc_final: 0.8465 (pp) REVERT: n 1067 MET cc_start: 0.7741 (mmm) cc_final: 0.7273 (mmm) REVERT: o 899 MET cc_start: 0.8000 (ppp) cc_final: 0.6839 (tpt) REVERT: o 945 MET cc_start: 0.3729 (mmm) cc_final: 0.2635 (ptt) REVERT: p 130 MET cc_start: 0.8785 (tmm) cc_final: 0.8394 (tmm) REVERT: p 164 MET cc_start: 0.7160 (ptt) cc_final: 0.6847 (ptp) REVERT: p 240 LEU cc_start: 0.9564 (tp) cc_final: 0.9249 (pp) REVERT: p 295 MET cc_start: 0.8612 (mmt) cc_final: 0.8389 (mmp) REVERT: p 510 MET cc_start: 0.8037 (mpp) cc_final: 0.7834 (mpp) REVERT: p 645 MET cc_start: 0.9112 (tpp) cc_final: 0.8344 (tpp) outliers start: 14 outliers final: 9 residues processed: 104 average time/residue: 0.1245 time to fit residues: 21.5147 Evaluate side-chains 93 residues out of total 1985 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 84 time to evaluate : 0.717 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain b residue 99 GLU Chi-restraints excluded: chain e residue 449 MET 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 483 LYS Chi-restraints excluded: chain p residue 571 ILE 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 185 optimal weight: 5.9990 chunk 38 optimal weight: 1.9990 chunk 202 optimal weight: 4.9990 chunk 116 optimal weight: 0.5980 chunk 47 optimal weight: 0.0170 chunk 49 optimal weight: 10.0000 chunk 111 optimal weight: 20.0000 chunk 5 optimal weight: 3.9990 chunk 130 optimal weight: 8.9990 chunk 30 optimal weight: 30.0000 chunk 109 optimal weight: 0.0980 overall best weight: 1.3422 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: c 46 GLN ** e 360 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 916 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** e1093 HIS ** e1113 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** p 161 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** p 253 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** p 480 GLN ** p 536 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3808 r_free = 0.3808 target = 0.046297 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3637 r_free = 0.3637 target = 0.039344 restraints weight = 216162.037| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3650 r_free = 0.3650 target = 0.039742 restraints weight = 178996.829| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3657 r_free = 0.3657 target = 0.040014 restraints weight = 153822.475| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 19)----------------| | r_work = 0.3661 r_free = 0.3661 target = 0.040178 restraints weight = 137223.624| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.3665 r_free = 0.3665 target = 0.040316 restraints weight = 128255.071| |-----------------------------------------------------------------------------| r_work (final): 0.3625 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7223 moved from start: 0.2720 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 17650 Z= 0.103 Angle : 0.539 9.784 23870 Z= 0.266 Chirality : 0.041 0.184 2739 Planarity : 0.004 0.055 3020 Dihedral : 3.654 16.465 2269 Min Nonbonded Distance : 2.475 Molprobity Statistics. All-atom Clashscore : 9.87 Ramachandran Plot: Outliers : 0.05 % Allowed : 1.94 % Favored : 98.01 % Rotamer: Outliers : 1.01 % Allowed : 11.69 % Favored : 87.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.82 (0.18), residues: 2108 helix: 1.33 (0.16), residues: 995 sheet: -0.27 (0.34), residues: 234 loop : -0.01 (0.21), residues: 879 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG e 869 TYR 0.015 0.001 TYR c 71 PHE 0.016 0.001 PHE e 795 TRP 0.009 0.001 TRP e 907 HIS 0.006 0.001 HIS n 962 Details of bonding type rmsd covalent geometry : bond 0.00215 (17650) covalent geometry : angle 0.53912 (23870) hydrogen bonds : bond 0.03547 ( 788) hydrogen bonds : angle 4.70709 ( 2265) *********************** 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 109 residues out of total 1985 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 89 time to evaluate : 0.737 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: c 38 ASP cc_start: 0.8206 (m-30) cc_final: 0.7918 (m-30) REVERT: e 467 MET cc_start: 0.8158 (OUTLIER) cc_final: 0.7229 (tpp) REVERT: e 820 LEU cc_start: 0.9025 (tt) cc_final: 0.8642 (pp) REVERT: n 1067 MET cc_start: 0.7988 (mmm) cc_final: 0.7430 (mmm) REVERT: o 899 MET cc_start: 0.8009 (ppp) cc_final: 0.6944 (tpt) REVERT: o 945 MET cc_start: 0.3505 (mmm) cc_final: 0.2325 (ptt) REVERT: p 240 LEU cc_start: 0.9583 (tp) cc_final: 0.9248 (pp) REVERT: p 295 MET cc_start: 0.8662 (mmt) cc_final: 0.8440 (mmp) REVERT: p 645 MET cc_start: 0.9214 (tpp) cc_final: 0.8394 (tpp) REVERT: p 972 MET cc_start: 0.7119 (tpt) cc_final: 0.6788 (tpt) outliers start: 20 outliers final: 11 residues processed: 105 average time/residue: 0.1232 time to fit residues: 21.6240 Evaluate side-chains 94 residues out of total 1985 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 82 time to evaluate : 0.727 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain b residue 99 GLU Chi-restraints excluded: chain e residue 449 MET Chi-restraints excluded: chain e residue 467 MET Chi-restraints excluded: chain e residue 715 THR Chi-restraints excluded: chain n residue 886 THR Chi-restraints excluded: chain n residue 970 VAL Chi-restraints excluded: chain o residue 858 LEU Chi-restraints excluded: chain p residue 296 LEU Chi-restraints excluded: chain p residue 356 LEU Chi-restraints excluded: chain p residue 483 LYS Chi-restraints excluded: chain p residue 571 ILE Chi-restraints excluded: chain p residue 794 PHE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 212 random chunks: chunk 178 optimal weight: 1.9990 chunk 40 optimal weight: 0.9990 chunk 206 optimal weight: 4.9990 chunk 24 optimal weight: 6.9990 chunk 37 optimal weight: 5.9990 chunk 168 optimal weight: 8.9990 chunk 52 optimal weight: 4.9990 chunk 18 optimal weight: 9.9990 chunk 72 optimal weight: 9.9990 chunk 188 optimal weight: 7.9990 chunk 150 optimal weight: 10.0000 overall best weight: 3.7990 ------------------------------------------------------------------------------- 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 46 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 360 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** e 398 ASN ** e 453 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** e 901 ASN ** e 916 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e1113 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** p 161 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** p 253 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** p 319 ASN p 327 ASN p 480 GLN ** p 536 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** p 538 ASN p 687 GLN p 812 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3746 r_free = 0.3746 target = 0.044157 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3590 r_free = 0.3590 target = 0.037474 restraints weight = 225665.719| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.3599 r_free = 0.3599 target = 0.037844 restraints weight = 183569.532| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 23)----------------| | r_work = 0.3605 r_free = 0.3605 target = 0.038121 restraints weight = 158368.673| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3610 r_free = 0.3610 target = 0.038320 restraints weight = 141834.558| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.3612 r_free = 0.3612 target = 0.038455 restraints weight = 130914.117| |-----------------------------------------------------------------------------| r_work (final): 0.3567 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7337 moved from start: 0.3316 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 17650 Z= 0.183 Angle : 0.632 8.964 23870 Z= 0.319 Chirality : 0.043 0.224 2739 Planarity : 0.004 0.050 3020 Dihedral : 4.005 17.920 2269 Min Nonbonded Distance : 2.462 Molprobity Statistics. All-atom Clashscore : 15.54 Ramachandran Plot: Outliers : 0.05 % Allowed : 2.75 % Favored : 97.20 % Rotamer: Outliers : 1.41 % Allowed : 12.34 % Favored : 86.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.59 (0.18), residues: 2108 helix: 1.15 (0.16), residues: 1000 sheet: -0.42 (0.33), residues: 234 loop : -0.12 (0.21), residues: 874 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG o 868 TYR 0.017 0.002 TYR c 71 PHE 0.019 0.002 PHE c 47 TRP 0.015 0.002 TRP e 298 HIS 0.006 0.001 HIS n 962 Details of bonding type rmsd covalent geometry : bond 0.00377 (17650) covalent geometry : angle 0.63179 (23870) hydrogen bonds : bond 0.03947 ( 788) hydrogen bonds : angle 4.93637 ( 2265) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4216 Ramachandran restraints generated. 2108 Oldfield, 0 Emsley, 2108 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4216 Ramachandran restraints generated. 2108 Oldfield, 0 Emsley, 2108 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 109 residues out of total 1985 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 81 time to evaluate : 0.795 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: 0.8276 (m-30) cc_final: 0.7977 (m-30) REVERT: n 1067 MET cc_start: 0.8260 (mmm) cc_final: 0.7520 (mmm) REVERT: p 132 MET cc_start: 0.8017 (pmm) cc_final: 0.7813 (pmm) REVERT: p 295 MET cc_start: 0.8751 (mmt) cc_final: 0.8542 (mmt) REVERT: p 645 MET cc_start: 0.9273 (tpp) cc_final: 0.8448 (tpp) outliers start: 28 outliers final: 19 residues processed: 99 average time/residue: 0.1303 time to fit residues: 21.1577 Evaluate side-chains 96 residues out of total 1985 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 77 time to evaluate : 0.747 ------------------------------------------------------------------------------- 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 75 ARG 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 o residue 876 PHE 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 578 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 794 PHE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 212 random chunks: chunk 164 optimal weight: 5.9990 chunk 65 optimal weight: 0.8980 chunk 34 optimal weight: 0.0470 chunk 5 optimal weight: 8.9990 chunk 109 optimal weight: 5.9990 chunk 180 optimal weight: 6.9990 chunk 24 optimal weight: 2.9990 chunk 87 optimal weight: 1.9990 chunk 206 optimal weight: 0.8980 chunk 35 optimal weight: 8.9990 chunk 177 optimal weight: 7.9990 overall best weight: 1.3682 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: b 51 GLN ** c 46 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** e 398 ASN e 453 GLN ** e 916 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e1113 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** p 161 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** p 253 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** p 480 GLN p 812 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3774 r_free = 0.3774 target = 0.045019 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3610 r_free = 0.3610 target = 0.038100 restraints weight = 221029.701| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3619 r_free = 0.3619 target = 0.038484 restraints weight = 182997.248| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3626 r_free = 0.3626 target = 0.038756 restraints weight = 158370.899| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3630 r_free = 0.3630 target = 0.038943 restraints weight = 142192.711| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3633 r_free = 0.3633 target = 0.039077 restraints weight = 132214.120| |-----------------------------------------------------------------------------| r_work (final): 0.3595 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7318 moved from start: 0.3357 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= 0.106 Angle : 0.569 10.886 23870 Z= 0.277 Chirality : 0.041 0.181 2739 Planarity : 0.003 0.054 3020 Dihedral : 3.840 17.771 2269 Min Nonbonded Distance : 2.426 Molprobity Statistics. All-atom Clashscore : 11.31 Ramachandran Plot: Outliers : 0.05 % Allowed : 1.99 % Favored : 97.96 % Rotamer: Outliers : 1.11 % Allowed : 13.00 % Favored : 85.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.71 (0.18), residues: 2108 helix: 1.17 (0.16), residues: 1014 sheet: -0.21 (0.33), residues: 233 loop : -0.03 (0.21), residues: 861 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG c 75 TYR 0.013 0.001 TYR c 71 PHE 0.018 0.001 PHE o 876 TRP 0.009 0.001 TRP e 907 HIS 0.006 0.001 HIS n 962 Details of bonding type rmsd covalent geometry : bond 0.00227 (17650) covalent geometry : angle 0.56949 (23870) hydrogen bonds : bond 0.03440 ( 788) hydrogen bonds : angle 4.68581 ( 2265) *********************** 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 103 residues out of total 1985 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 81 time to evaluate : 0.782 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: c 38 ASP cc_start: 0.8282 (m-30) cc_final: 0.7987 (m-30) REVERT: e 449 MET cc_start: 0.7266 (mtt) cc_final: 0.6843 (mpp) REVERT: e 820 LEU cc_start: 0.9085 (tt) cc_final: 0.8602 (pp) REVERT: n 1067 MET cc_start: 0.8005 (mmm) cc_final: 0.7349 (mmm) REVERT: o 899 MET cc_start: 0.7953 (ppp) cc_final: 0.7006 (tpt) REVERT: o 945 MET cc_start: 0.3508 (mmm) cc_final: 0.1774 (ptt) REVERT: p 164 MET cc_start: 0.8278 (pmm) cc_final: 0.8076 (pmm) REVERT: p 295 MET cc_start: 0.8842 (mmt) cc_final: 0.8487 (mmp) REVERT: p 645 MET cc_start: 0.9228 (tpp) cc_final: 0.8282 (tpp) REVERT: p 972 MET cc_start: 0.7294 (tpt) cc_final: 0.6894 (tpt) outliers start: 22 outliers final: 19 residues processed: 98 average time/residue: 0.1311 time to fit residues: 20.9109 Evaluate side-chains 98 residues out of total 1985 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 79 time to evaluate : 0.708 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 407 VAL Chi-restraints excluded: chain e residue 467 MET Chi-restraints excluded: chain e residue 715 THR Chi-restraints excluded: chain n residue 886 THR Chi-restraints excluded: chain n residue 970 VAL Chi-restraints excluded: chain o residue 858 LEU Chi-restraints excluded: chain p residue 296 LEU Chi-restraints excluded: chain p residue 356 LEU Chi-restraints excluded: chain p residue 483 LYS Chi-restraints excluded: chain p residue 571 ILE Chi-restraints excluded: chain p residue 578 LEU 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 Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 212 random chunks: chunk 97 optimal weight: 6.9990 chunk 195 optimal weight: 6.9990 chunk 95 optimal weight: 20.0000 chunk 154 optimal weight: 10.0000 chunk 59 optimal weight: 4.9990 chunk 129 optimal weight: 20.0000 chunk 99 optimal weight: 6.9990 chunk 135 optimal weight: 0.8980 chunk 182 optimal weight: 4.9990 chunk 209 optimal weight: 10.0000 chunk 101 optimal weight: 6.9990 overall best weight: 4.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** c 46 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 82 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 360 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** e 398 ASN ** e 753 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** e 769 GLN ** e 916 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e1093 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** e1113 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** p 253 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** p 465 GLN p 480 GLN ** p 536 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** p 812 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3723 r_free = 0.3723 target = 0.043093 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3567 r_free = 0.3567 target = 0.036597 restraints weight = 227772.717| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3576 r_free = 0.3576 target = 0.036929 restraints weight = 189119.775| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3582 r_free = 0.3582 target = 0.037172 restraints weight = 164516.223| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3586 r_free = 0.3586 target = 0.037352 restraints weight = 149034.171| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3589 r_free = 0.3589 target = 0.037465 restraints weight = 138538.929| |-----------------------------------------------------------------------------| r_work (final): 0.3541 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7441 moved from start: 0.3858 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.067 17650 Z= 0.223 Angle : 0.677 10.787 23870 Z= 0.344 Chirality : 0.043 0.208 2739 Planarity : 0.004 0.049 3020 Dihedral : 4.229 19.496 2269 Min Nonbonded Distance : 2.431 Molprobity Statistics. All-atom Clashscore : 18.94 Ramachandran Plot: Outliers : 0.05 % Allowed : 3.32 % Favored : 96.63 % Rotamer: Outliers : 1.31 % Allowed : 13.55 % Favored : 85.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.40 (0.18), residues: 2108 helix: 0.93 (0.16), residues: 1009 sheet: -0.50 (0.32), residues: 232 loop : -0.17 (0.21), residues: 867 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG c 75 TYR 0.028 0.002 TYR c 71 PHE 0.019 0.002 PHE c 47 TRP 0.015 0.002 TRP p 468 HIS 0.008 0.001 HIS n 962 Details of bonding type rmsd covalent geometry : bond 0.00454 (17650) covalent geometry : angle 0.67714 (23870) hydrogen bonds : bond 0.04061 ( 788) hydrogen bonds : angle 5.00171 ( 2265) *********************** 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 103 residues out of total 1985 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 77 time to evaluate : 0.751 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: c 38 ASP cc_start: 0.8450 (m-30) cc_final: 0.8182 (m-30) REVERT: e 449 MET cc_start: 0.7221 (mtt) cc_final: 0.6892 (mpp) REVERT: n 1067 MET cc_start: 0.8323 (mmm) cc_final: 0.7609 (mmm) REVERT: o 899 MET cc_start: 0.7833 (ppp) cc_final: 0.5847 (tpp) REVERT: o 945 MET cc_start: 0.3791 (mmm) cc_final: 0.2262 (ptt) REVERT: p 295 MET cc_start: 0.8844 (mmt) cc_final: 0.8581 (mmt) REVERT: p 645 MET cc_start: 0.9361 (tpp) cc_final: 0.8528 (tpp) outliers start: 26 outliers final: 17 residues processed: 97 average time/residue: 0.1302 time to fit residues: 20.6915 Evaluate side-chains 93 residues out of total 1985 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 76 time to evaluate : 0.707 ------------------------------------------------------------------------------- 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 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 o residue 876 PHE Chi-restraints excluded: chain p residue 483 LYS Chi-restraints excluded: chain p residue 571 ILE Chi-restraints excluded: chain p residue 578 LEU 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 Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 212 random chunks: chunk 40 optimal weight: 0.4980 chunk 126 optimal weight: 9.9990 chunk 106 optimal weight: 0.0370 chunk 3 optimal weight: 2.9990 chunk 14 optimal weight: 4.9990 chunk 145 optimal weight: 10.0000 chunk 157 optimal weight: 5.9990 chunk 78 optimal weight: 5.9990 chunk 205 optimal weight: 0.7980 chunk 93 optimal weight: 8.9990 chunk 119 optimal weight: 0.9990 overall best weight: 1.0662 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** c 46 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** e 753 GLN e 902 GLN ** e 916 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e1113 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** p 161 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** p 253 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** p 480 GLN p 812 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3757 r_free = 0.3757 target = 0.044390 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3597 r_free = 0.3597 target = 0.037645 restraints weight = 225730.726| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.3610 r_free = 0.3610 target = 0.038087 restraints weight = 182389.160| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3617 r_free = 0.3617 target = 0.038387 restraints weight = 152475.267| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3622 r_free = 0.3622 target = 0.038578 restraints weight = 135148.827| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.3626 r_free = 0.3626 target = 0.038737 restraints weight = 124865.518| |-----------------------------------------------------------------------------| r_work (final): 0.3578 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7334 moved from start: 0.3812 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.049 17650 Z= 0.111 Angle : 0.635 18.188 23870 Z= 0.305 Chirality : 0.043 0.327 2739 Planarity : 0.004 0.055 3020 Dihedral : 3.996 20.801 2269 Min Nonbonded Distance : 2.462 Molprobity Statistics. All-atom Clashscore : 11.60 Ramachandran Plot: Outliers : 0.05 % Allowed : 2.09 % Favored : 97.87 % Rotamer: Outliers : 1.01 % Allowed : 14.11 % Favored : 84.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.61 (0.18), residues: 2108 helix: 1.08 (0.16), residues: 1016 sheet: -0.42 (0.32), residues: 248 loop : -0.01 (0.22), residues: 844 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG c 84 TYR 0.022 0.001 TYR c 71 PHE 0.020 0.001 PHE e 350 TRP 0.016 0.001 TRP e 298 HIS 0.007 0.001 HIS n 962 Details of bonding type rmsd covalent geometry : bond 0.00239 (17650) covalent geometry : angle 0.63453 (23870) hydrogen bonds : bond 0.03591 ( 788) hydrogen bonds : angle 4.75445 ( 2265) *********************** 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 99 residues out of total 1985 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 79 time to evaluate : 0.747 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: c 38 ASP cc_start: 0.8358 (m-30) cc_final: 0.8104 (m-30) REVERT: e 1126 MET cc_start: 0.6705 (ttp) cc_final: 0.6213 (tmm) REVERT: n 1067 MET cc_start: 0.8239 (mmm) cc_final: 0.7689 (mmm) REVERT: o 899 MET cc_start: 0.7870 (ppp) cc_final: 0.6807 (tpt) REVERT: o 945 MET cc_start: 0.3782 (mmm) cc_final: 0.2813 (ptt) REVERT: p 295 MET cc_start: 0.8876 (mmt) cc_final: 0.8510 (mmp) REVERT: p 510 MET cc_start: 0.8019 (mpp) cc_final: 0.7778 (mpp) REVERT: p 645 MET cc_start: 0.9191 (tpp) cc_final: 0.8318 (tpt) outliers start: 20 outliers final: 14 residues processed: 95 average time/residue: 0.1230 time to fit residues: 19.3794 Evaluate side-chains 89 residues out of total 1985 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 75 time to evaluate : 0.761 ------------------------------------------------------------------------------- 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 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 483 LYS Chi-restraints excluded: chain p residue 656 LEU Chi-restraints excluded: chain p residue 690 PHE Chi-restraints excluded: chain p residue 702 VAL Chi-restraints excluded: chain p residue 786 VAL Chi-restraints excluded: chain p residue 794 PHE Chi-restraints excluded: chain p residue 903 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 212 random chunks: chunk 24 optimal weight: 10.0000 chunk 63 optimal weight: 5.9990 chunk 139 optimal weight: 0.0470 chunk 11 optimal weight: 0.0370 chunk 171 optimal weight: 9.9990 chunk 81 optimal weight: 6.9990 chunk 113 optimal weight: 0.9990 chunk 88 optimal weight: 6.9990 chunk 72 optimal weight: 7.9990 chunk 91 optimal weight: 8.9990 chunk 115 optimal weight: 2.9990 overall best weight: 2.0162 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: b 51 GLN ** c 46 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** e 398 ASN ** e 916 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e1113 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** p 253 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** p 480 GLN ** p 812 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3746 r_free = 0.3746 target = 0.043976 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3589 r_free = 0.3589 target = 0.037248 restraints weight = 224681.345| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3601 r_free = 0.3601 target = 0.037657 restraints weight = 181902.238| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3609 r_free = 0.3609 target = 0.037938 restraints weight = 154040.152| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3613 r_free = 0.3613 target = 0.038126 restraints weight = 137430.506| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3617 r_free = 0.3617 target = 0.038268 restraints weight = 127445.798| |-----------------------------------------------------------------------------| r_work (final): 0.3574 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7351 moved from start: 0.3930 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= 0.125 Angle : 0.640 16.136 23870 Z= 0.311 Chirality : 0.042 0.203 2739 Planarity : 0.004 0.053 3020 Dihedral : 3.987 20.091 2269 Min Nonbonded Distance : 2.451 Molprobity Statistics. All-atom Clashscore : 13.44 Ramachandran Plot: Outliers : 0.05 % Allowed : 2.61 % Favored : 97.34 % Rotamer: Outliers : 0.91 % Allowed : 14.11 % Favored : 84.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.63 (0.18), residues: 2108 helix: 1.09 (0.16), residues: 1017 sheet: -0.28 (0.32), residues: 237 loop : -0.06 (0.21), residues: 854 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG c 84 TYR 0.024 0.001 TYR c 71 PHE 0.021 0.001 PHE o 876 TRP 0.010 0.001 TRP e 298 HIS 0.008 0.001 HIS n 962 Details of bonding type rmsd covalent geometry : bond 0.00269 (17650) covalent geometry : angle 0.64019 (23870) hydrogen bonds : bond 0.03613 ( 788) hydrogen bonds : angle 4.75686 ( 2265) ********************** 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 93 residues out of total 1985 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 75 time to evaluate : 0.729 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: b 48 MET cc_start: 0.9223 (mmm) cc_final: 0.8770 (tpt) REVERT: c 38 ASP cc_start: 0.8366 (m-30) cc_final: 0.8114 (m-30) REVERT: e 1126 MET cc_start: 0.6725 (ttp) cc_final: 0.6209 (tmm) REVERT: n 1067 MET cc_start: 0.8076 (mmm) cc_final: 0.7500 (mmm) REVERT: o 899 MET cc_start: 0.7960 (ppp) cc_final: 0.6687 (tpt) REVERT: o 945 MET cc_start: 0.3973 (mmm) cc_final: 0.2918 (ptt) REVERT: p 150 MET cc_start: 0.7030 (ppp) cc_final: 0.6768 (ppp) REVERT: p 175 MET cc_start: 0.7672 (OUTLIER) cc_final: 0.7285 (mmt) REVERT: p 295 MET cc_start: 0.8845 (mmt) cc_final: 0.8492 (mmp) REVERT: p 645 MET cc_start: 0.9281 (tpp) cc_final: 0.8384 (tpt) outliers start: 18 outliers final: 16 residues processed: 89 average time/residue: 0.1270 time to fit residues: 18.6243 Evaluate side-chains 92 residues out of total 1985 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 75 time to evaluate : 0.747 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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 175 MET Chi-restraints excluded: chain p residue 296 LEU Chi-restraints excluded: chain p residue 483 LYS Chi-restraints excluded: chain p residue 656 LEU Chi-restraints excluded: chain p residue 690 PHE Chi-restraints excluded: chain p residue 702 VAL Chi-restraints excluded: chain p residue 786 VAL Chi-restraints excluded: chain p residue 794 PHE Chi-restraints excluded: chain p residue 903 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 212 random chunks: chunk 123 optimal weight: 9.9990 chunk 175 optimal weight: 0.9990 chunk 64 optimal weight: 2.9990 chunk 119 optimal weight: 0.5980 chunk 198 optimal weight: 4.9990 chunk 209 optimal weight: 1.9990 chunk 26 optimal weight: 1.9990 chunk 172 optimal weight: 0.6980 chunk 8 optimal weight: 0.9980 chunk 125 optimal weight: 3.9990 chunk 206 optimal weight: 9.9990 overall best weight: 1.0584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** c 46 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 916 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e1113 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** p 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 = 0.3760 r_free = 0.3760 target = 0.044396 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3603 r_free = 0.3603 target = 0.037548 restraints weight = 224283.206| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3614 r_free = 0.3614 target = 0.037997 restraints weight = 181180.497| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3621 r_free = 0.3621 target = 0.038284 restraints weight = 153356.793| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 18)----------------| | r_work = 0.3626 r_free = 0.3626 target = 0.038477 restraints weight = 136660.015| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3629 r_free = 0.3629 target = 0.038636 restraints weight = 126855.380| |-----------------------------------------------------------------------------| r_work (final): 0.3583 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7328 moved from start: 0.3957 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.051 17650 Z= 0.108 Angle : 0.640 17.472 23870 Z= 0.307 Chirality : 0.042 0.210 2739 Planarity : 0.004 0.056 3020 Dihedral : 3.918 22.027 2269 Min Nonbonded Distance : 2.453 Molprobity Statistics. All-atom Clashscore : 10.85 Ramachandran Plot: Outliers : 0.05 % Allowed : 2.04 % Favored : 97.91 % Rotamer: Outliers : 0.86 % Allowed : 14.16 % Favored : 84.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.69 (0.18), residues: 2108 helix: 1.12 (0.16), residues: 1016 sheet: -0.22 (0.33), residues: 238 loop : 0.00 (0.22), residues: 854 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG e 869 TYR 0.022 0.001 TYR c 71 PHE 0.023 0.001 PHE e 350 TRP 0.010 0.001 TRP e 373 HIS 0.008 0.001 HIS n 962 Details of bonding type rmsd covalent geometry : bond 0.00236 (17650) covalent geometry : angle 0.64001 (23870) hydrogen bonds : bond 0.03457 ( 788) hydrogen bonds : angle 4.66902 ( 2265) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3515.34 seconds wall clock time: 61 minutes 50.43 seconds (3710.43 seconds total)